Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 2 of 103
Found at i:490768 original size:93 final size:93
Alignment explanation
Indices: 490642--490943 Score: 370
Period size: 93 Copynumber: 3.0 Consensus size: 93
490632 TGTCATGTCA
* * * *
490642 GCTTGGAAATTTTAATATAATCAGTCTAAGTCTTTAATATGTATGTTCAAAGCAGTTGCTTCGCT
1 GCTTGGAAATTTTGATATAATCAGTCCAAGTCTTTGATATGCATGTTCAAAGCAGTTGCTTCGCT
*
490707 TCTTCTTCTTTTGTAAATTCGATTGTTG
66 TCTTCTTCTTTTGTACATTCGATTGTTG
*
490735 GCTTGGAAATTTTGATATAATCAGTCCAAGTCTTTGATATGCATGTTCAAAGCAGTTGCTTTGCT
1 GCTTGGAAATTTTGATATAATCAGTCCAAGTCTTTGATATGCATGTTCAAAGCAGTTGCTTCGCT
490800 TCTTCTTCTTTTGTACATTCGATTGTTCAAAGTGTCTTG
66 TCTTCTTCTTTTGTACATTCGA----T-----TG--TTG
*
490839 TTAGCTTGGAAATTTTGATATAATCAGTCCAAGTCTTTGATATGCACGTTCAAAGCAATTGCTTT
1 ---GCTTGGAAATTTTGATATAATCAGTCCAAGTCTTTGATATGCATGTTCAAAGC-A--G--TT
490904 GCTTCGCTTCTTCTTCTTTTGTACATTCGATTGTTG
58 GCTTCGCTTCTTCTTCTTTTGTACATTCGATTGTTG
490940 GCTT
1 GCTT
490944 CAAAGTGTCT
Statistics
Matches: 182, Mismatches: 8, Indels: 33
0.82 0.04 0.15
Matches are distributed among these distances:
93 81 0.45
97 1 0.01
98 4 0.02
101 3 0.02
102 2 0.01
103 2 0.01
104 3 0.02
107 52 0.29
108 2 0.01
110 1 0.01
112 31 0.17
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.44
Consensus pattern (93 bp):
GCTTGGAAATTTTGATATAATCAGTCCAAGTCTTTGATATGCATGTTCAAAGCAGTTGCTTCGCT
TCTTCTTCTTTTGTACATTCGATTGTTG
Found at i:490991 original size:117 final size:112
Alignment explanation
Indices: 490729--491017 Score: 421
Period size: 107 Copynumber: 2.6 Consensus size: 112
490719 GTAAATTCGA
*
490729 TTGTTGGCTTGGAAATTTTGATATAATCAGTCCAAGTCTTTGATATGCATGTTCAAAGC-A--G-
1 TTGTTAGCTTGGAAATTTTGATATAATCAGTCCAAGTCTTTGATATGCATGTTCAAAGCAATTGC
*
490790 -TTGCTTTGCTTCTTCTTCTTTTGTACATTCGATTGTTCAAAGTGTC
66 TTTGCTTCGCTTCTTCTTCTTTTGTACATTCGATTGTTCAAAGTGTC
*
490836 TTGTTAGCTTGGAAATTTTGATATAATCAGTCCAAGTCTTTGATATGCACGTTCAAAGCAATTGC
1 TTGTTAGCTTGGAAATTTTGATATAATCAGTCCAAGTCTTTGATATGCATGTTCAAAGCAATTGC
490901 TTTGCTTCGCTTCTTCTTCTTTTGTACATTCGATTGTTGGCTTCAAAGTGTC
66 TTTGCTTCGCTTCTTCTTCTTTTGTACATTCGA---TT-G-TTCAAAGTGTC
* * * *
490953 TTGTTAGTTTGGAAATTTTGATATAATCAGTCTAAGTC-TT-AAATGCATGTTCAAAGCAGTTGC
1 TTGTTAGCTTGGAAATTTTGATATAATCAGTCCAAGTCTTTGATATGCATGTTCAAAGCAATTGC
491016 TT
66 TT
491018 CTCTTCTTCC
Statistics
Matches: 164, Mismatches: 8, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
107 57 0.35
108 1 0.01
110 1 0.01
112 31 0.19
115 24 0.15
116 3 0.02
117 47 0.29
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (112 bp):
TTGTTAGCTTGGAAATTTTGATATAATCAGTCCAAGTCTTTGATATGCATGTTCAAAGCAATTGC
TTTGCTTCGCTTCTTCTTCTTTTGTACATTCGATTGTTCAAAGTGTC
Found at i:492105 original size:36 final size:36
Alignment explanation
Indices: 492058--492142 Score: 170
Period size: 36 Copynumber: 2.4 Consensus size: 36
492048 TATCTTTTAC
492058 AAGTTTGGTTGAACGTTTGCCTTCATTTGAATAATG
1 AAGTTTGGTTGAACGTTTGCCTTCATTTGAATAATG
492094 AAGTTTGGTTGAACGTTTGCCTTCATTTGAATAATG
1 AAGTTTGGTTGAACGTTTGCCTTCATTTGAATAATG
492130 AAGTTTGGTTGAA
1 AAGTTTGGTTGAA
492143 TGTCCATATC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (36 bp):
AAGTTTGGTTGAACGTTTGCCTTCATTTGAATAATG
Found at i:495524 original size:30 final size:31
Alignment explanation
Indices: 495488--495550 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
495478 TAAGATGGAG
495488 AATTTTTAGTTTAGCTCTTCCAAA-ATTTAT
1 AATTTTTAGTTTAGCTCTTCCAAAGATTTAT
*
495518 AATTTTTATTTTAGCTCTTCCAAAGATTTAT
1 AATTTTTAGTTTAGCTCTTCCAAAGATTTAT
495549 AA
1 AA
495551 CATGACCTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (31 bp):
AATTTTTAGTTTAGCTCTTCCAAAGATTTAT
Found at i:500314 original size:2 final size:2
Alignment explanation
Indices: 500307--500333 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
500297 GGTAAAATTC
500307 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
500334 AATAATTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:508401 original size:52 final size:52
Alignment explanation
Indices: 508325--508428 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 52
508315 CAGAAATGCT
* * * *
508325 GTAAAAGTCAAGGTCTAAGGACACCATTTCCATTTTTCCTTCTTTGAGAAAA
1 GTAAAAGTCAAGGTCTAAGAACACCATTTCCATTTCTCCTCCTTCGAGAAAA
*
508377 GTAAAAGTCAAGGTCTTAGAACACCATTTCCATTTCTCCTCCTTCGAGAAAA
1 GTAAAAGTCAAGGTCTAAGAACACCATTTCCATTTCTCCTCCTTCGAGAAAA
508429 CTTGGTATAG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (52 bp):
GTAAAAGTCAAGGTCTAAGAACACCATTTCCATTTCTCCTCCTTCGAGAAAA
Found at i:514128 original size:117 final size:117
Alignment explanation
Indices: 513922--514148 Score: 409
Period size: 117 Copynumber: 1.9 Consensus size: 117
513912 AGATTAATGA
*
513922 ATTTGATATAAACGAAAAATAGAACAACCATTCTGGCATTTGAGAAAGGAAATCTGGCCTGGCAT
1 ATTTGATATAAACCAAAAATAGAACAACCATTCTGGCATTTGAGAAAGGAAATCTGGCCTGGCAT
*
513987 GGCACGTAAAGCGTGGCAGCACATTTGCCGCGGATCAAGCATGGAGTGAGCC
66 GGCACGTAAAGCGTGGCAGCACATTTGCCGCGGATCAAGAATGGAGTGAGCC
* **
514039 ATTTGATATAAACCAGAAATAGAACAACCATTCTGGCATTTGAGAAAGGAAATCTGTTCTGGCAT
1 ATTTGATATAAACCAAAAATAGAACAACCATTCTGGCATTTGAGAAAGGAAATCTGGCCTGGCAT
514104 GGCACGTAAAGCGTGGCAGCACATTTGCCGCGGATCAAGAATGGA
66 GGCACGTAAAGCGTGGCAGCACATTTGCCGCGGATCAAGAATGGA
514149 AGAAGCCACT
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
117 105 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.22
Consensus pattern (117 bp):
ATTTGATATAAACCAAAAATAGAACAACCATTCTGGCATTTGAGAAAGGAAATCTGGCCTGGCAT
GGCACGTAAAGCGTGGCAGCACATTTGCCGCGGATCAAGAATGGAGTGAGCC
Found at i:515936 original size:3 final size:3
Alignment explanation
Indices: 515928--515956 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
515918 ATTCAAAGCT
515928 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
515957 TGAAAGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:516470 original size:39 final size:39
Alignment explanation
Indices: 516426--516516 Score: 159
Period size: 39 Copynumber: 2.4 Consensus size: 39
516416 AATGAATCAG
516426 AAATTATTAATAAATGTCTCTTAAATGAAAAAGTATAA-A
1 AAATTATTAATAAATGTCTCTTAAATGAAAAAGT-TAATA
516465 AAATTATTAATAAATGTCTCTTAAATGAAAAAGTTAATA
1 AAATTATTAATAAATGTCTCTTAAATGAAAAAGTTAATA
516504 AAATT-TTAATAAA
1 AAATTATTAATAAA
516517 AAAAGCCTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
38 11 0.22
39 40 0.78
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (39 bp):
AAATTATTAATAAATGTCTCTTAAATGAAAAAGTTAATA
Found at i:520983 original size:63 final size:64
Alignment explanation
Indices: 520864--521004 Score: 230
Period size: 63 Copynumber: 2.2 Consensus size: 64
520854 TGAAGAAAAA
* **
520864 AATTGTTTGATTGATTCATGAAAAAGAAAATAGGATAAAGGGCTTTTCTAATTTGATGAATAAT
1 AATTGTTTGATTGACTCACAAAAAAGAAAATAGGATAAAGGGCTTTTCTAATTTGATGAATAAT
* *
520928 AATTGTTTGATTGACTCACAAAAAAGAAAATAGGA-AAAGGGTTTTTCTAATTTGATGAATTAT
1 AATTGTTTGATTGACTCACAAAAAAGAAAATAGGATAAAGGGCTTTTCTAATTTGATGAATAAT
520991 AATTGTTTGATTGA
1 AATTGTTTGATTGA
521005 TTTGAAAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
63 40 0.56
64 32 0.44
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (64 bp):
AATTGTTTGATTGACTCACAAAAAAGAAAATAGGATAAAGGGCTTTTCTAATTTGATGAATAAT
Found at i:525973 original size:153 final size:153
Alignment explanation
Indices: 525691--526084 Score: 614
Period size: 154 Copynumber: 2.6 Consensus size: 153
525681 TGTTAAACCT
* *
525691 AAATCCTCCAATACATATTAATAGCTATTTGGTTTG-GAGAAAAAAATAAAAAAATTTGTTTGAT
1 AAATTCTCCAATACATATTAATAGTTATTTGGTTTGAGAGAAAAAAATAAAAAAA-TTGTTTGAT
* *
525755 TGATTAACGAAAAAAGAAAATAAGGCAAAGGGTTTTTCTAAAATAATAATTGTTTGATTGATT-A
65 TGATTTACAAAAAAAGAAAATAAGGCAAAGGGTTTTTCTAAAATAATAATTGTTTGATTGATTAA
525819 AAAAAGAGAATAAGACAAAATATC
130 AAAAAGAGAATAAGACAAAATATC
*
525843 AAATTCTCCAATACATATTAATAGTTATTTGGTTTGGAGAGAAAAAAATAAAAAAAATGTTTGAT
1 AAATTCTCCAATACATATTAATAGTTATTTGGTTT-GAGAGAAAAAAATAAAAAAATTGTTTGAT
525908 TGATTTACAAAAAAAGAAAATAAGGCAAAGGGTTTTTCTAAAATAATAATTGTTTGATTGATTAA
65 TGATTTACAAAAAAAGAAAATAAGGCAAAGGGTTTTTCTAAAATAATAATTGTTTGATTGATTAA
*
525973 AAAAAGAGAATAAGACAAAATGTC
130 AAAAAGAGAATAAGACAAAATATC
* * * * *
525997 AAATTCTCCCATACATATTAATAGTTATTTGATTTTGAGAGAGAGAAGAGAAAAAAATTG-TTGA
1 AAATTCTCCAATACATATTAATAGTTATTTG-GTTTGAGAGA-AAAAAATAAAAAAATTGTTTG-
*
526061 ATTGATTTACAAAATAAGAAAATA
63 ATTGATTTACAAAAAAAGAAAATA
526085 GGACTAAGGG
Statistics
Matches: 223, Mismatches: 13, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
152 33 0.15
153 70 0.31
154 81 0.36
155 39 0.17
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.31
Consensus pattern (153 bp):
AAATTCTCCAATACATATTAATAGTTATTTGGTTTGAGAGAAAAAAATAAAAAAATTGTTTGATT
GATTTACAAAAAAAGAAAATAAGGCAAAGGGTTTTTCTAAAATAATAATTGTTTGATTGATTAAA
AAAAGAGAATAAGACAAAATATC
Found at i:526147 original size:154 final size:151
Alignment explanation
Indices: 525691--526084 Score: 551
Period size: 153 Copynumber: 2.6 Consensus size: 151
525681 TGTTAAACCT
* * * **
525691 AAATCCTCCAATACATATTAATAGCTATTTGGTTTGGAGA-AAAAAATA-AAAAAATTTGTTTGA
1 AAATTCTCCAATACATATTAATAGTTATTTGATTTGGAGAGAAAAAA-AGAAAAAAAATGTTTGA
* *
525754 TTGATTAACGAAAAAAGAAAATAAGGCAAAGGGTTTTTCTAAAATAATAATTGTTTGATTGATTA
65 TTGATTTACAAAAAAAGAAAATAAGGCAAAGGGTTTTTCTAAAATAATAATTGTTTGATTGATT-
525819 AAAAAGAGAATAAGACAAAATATC
129 AAAAAGAGAATAAGA-AAAATATC
* *
525843 AAATTCTCCAATACATATTAATAGTTATTTGGTTTGGAGAGAAAAAAATAAAAAAAATGTTTGAT
1 AAATTCTCCAATACATATTAATAGTTATTTGATTTGGAGAGAAAAAAAGAAAAAAAATGTTTGAT
525908 TGATTTACAAAAAAAGAAAATAAGGCAAAGGGTTTTTCTAAAATAATAATTGTTTGATTGATTAA
66 TGATTTACAAAAAAAGAAAATAAGGCAAAGGGTTTTTCTAAAATAATAATTGTTTGATTGATT--
*
525973 AAAAAGAGAATAAGACAAAATGTC
129 AAAAAGAGAATAAGA-AAAATATC
* * * * *
525997 AAATTCTCCCATACATATTAATAGTTATTTGATTTTGAGAGAGAGAAGAGAAAAAAATTG-TTGA
1 AAATTCTCCAATACATATTAATAGTTATTTGATTTGGAGAGA-AAAAAAGAAAAAAAATGTTTG-
*
526061 ATTGATTTACAAAATAAGAAAATA
64 ATTGATTTACAAAAAAAGAAAATA
526085 GGACTAAGGG
Statistics
Matches: 222, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
152 39 0.18
153 81 0.36
154 66 0.30
155 36 0.16
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.31
Consensus pattern (151 bp):
AAATTCTCCAATACATATTAATAGTTATTTGATTTGGAGAGAAAAAAAGAAAAAAAATGTTTGAT
TGATTTACAAAAAAAGAAAATAAGGCAAAGGGTTTTTCTAAAATAATAATTGTTTGATTGATTAA
AAAGAGAATAAGAAAAATATC
Found at i:530223 original size:15 final size:15
Alignment explanation
Indices: 530189--530232 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
530179 ATACTAATAT
*
530189 TTTTATGATGATTAAA
1 TTTTATTAT-ATTAAA
*
530205 ATTTATTAATATTAAA
1 TTTTATT-ATATTAAA
530221 TTTTATTATATT
1 TTTTATTATATT
530233 TGGTATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 5 0.21
16 17 0.71
17 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (15 bp):
TTTTATTATATTAAA
Found at i:530705 original size:28 final size:28
Alignment explanation
Indices: 530656--530711 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
530646 ATTGTCGGTT
***
530656 TAGCATGAGCATATATGGTGATTCGAAA
1 TAGCATGAGCATATACAATGATTCGAAA
*
530684 TAGCATGAGCATATACAATGATTGGAAA
1 TAGCATGAGCATATACAATGATTCGAAA
530712 CACGAGGCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (28 bp):
TAGCATGAGCATATACAATGATTCGAAA
Found at i:531133 original size:32 final size:32
Alignment explanation
Indices: 531090--531171 Score: 110
Period size: 32 Copynumber: 2.6 Consensus size: 32
531080 TTAAAACCAT
* ** *
531090 GACAACCTCCCTTGGCTCTCTTCTAGAATCAC
1 GACATCCTCCCTTAACTCCCTTCTAGAATCAC
*
531122 GACATCTTCCCTTAACTCCCTTCTAGAATCAC
1 GACATCCTCCCTTAACTCCCTTCTAGAATCAC
*
531154 GACATCCTCCCTAAACTC
1 GACATCCTCCCTTAACTC
531172 TATGACACCA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.24, C:0.39, G:0.09, T:0.28
Consensus pattern (32 bp):
GACATCCTCCCTTAACTCCCTTCTAGAATCAC
Found at i:531554 original size:19 final size:19
Alignment explanation
Indices: 531532--531571 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
531522 ATTCATGGCT
531532 TCTATCTAGGATCATGACA
1 TCTATCTAGGATCATGACA
531551 TCTATCTAGGATCATGACA
1 TCTATCTAGGATCATGACA
531570 TC
1 TC
531572 CTCCTTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (19 bp):
TCTATCTAGGATCATGACA
Found at i:544332 original size:35 final size:35
Alignment explanation
Indices: 544287--544358 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
544277 GGTAATTTTG
544287 TTTGAGTTTAGTAGTCTTTAATAAATTTCTATCTT
1 TTTGAGTTTAGTAGTCTTTAATAAATTTCTATCTT
544322 TTTGAGTTTAGTAGTCTTTAATAAATTTCTATCTT
1 TTTGAGTTTAGTAGTCTTTAATAAATTTCTATCTT
544357 TT
1 TT
544359 GCATTTTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56
Consensus pattern (35 bp):
TTTGAGTTTAGTAGTCTTTAATAAATTTCTATCTT
Found at i:546279 original size:20 final size:19
Alignment explanation
Indices: 546245--546283 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
546235 ATTCCTGATT
546245 AAGTGTATGGTAATGGTAAA
1 AAGTGTATGGTAAT-GTAAA
546265 AAGTGTATTGG-AATGTAAA
1 AAGTGTA-TGGTAATGTAAA
546284 GAATATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 10 0.56
21 3 0.17
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (19 bp):
AAGTGTATGGTAATGTAAA
Found at i:553054 original size:23 final size:20
Alignment explanation
Indices: 553026--553066 Score: 55
Period size: 23 Copynumber: 1.9 Consensus size: 20
553016 ATCATTTAAT
553026 TATAAAATATTATTTTATAAATG
1 TATAAAA-A-TATTTT-TAAATG
553049 TATAAAAATATTTTTAAA
1 TATAAAAATATTTTTAAA
553067 AATTATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 1 0.06
23 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TATAAAAATATTTTTAAATG
Found at i:556186 original size:2 final size:2
Alignment explanation
Indices: 556174--556209 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
556164 CGAAAGCATA
*
556174 AT AT TT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
556210 AAAGAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:559266 original size:233 final size:233
Alignment explanation
Indices: 558826--559273 Score: 645
Period size: 233 Copynumber: 1.9 Consensus size: 233
558816 TTTAGCGATA
* * * *
558826 AAGAAAATGTTGGTCCGCCTTGGCAATTTGTATAAACCAATAAAAGATGCATCACCTTAAAGCAG
1 AAGAAAATGTTGGTCCACCTAGACAATTTGTATAAACCAATAAAAGATGCACCACCTTAAAGCAG
*
558891 CCCAGCATGACCAAACATAATATAGGCAACAGGGAAAAGAGGAGATCGACAAGAAATTGACCACC
66 CCCAGCATGACCAAACAGAATATAGGCAACAGGGAAAAGAGGAGATCGACAAGAAATTGACCACC
*
558956 TCGGCAAAGTTGCCTAGCCTTCAAATTTCTATTCTACAATTTACAATCACTTCCAAAATTTAAAT
131 TCGGCAAAGTTGCCCAGCCTTCAAATTTCTATTCTACAATTTACAATCACTTCCAAAATTTAAAT
559021 CAAAACGGTATTGAG-AAACCCACGTTGTTTGGTGATG
196 CAAAACGGTATTGAGCAAACCCACGTTGTTTGGTGATG
* **
559058 AAGAATATGTTGGTCCACCTAGAC-ATTTGGTATTAAACCAATGGAAGAT-CTACCACCTTAAAG
1 AAGAAAATGTTGGTCCACCTAGACAATTT-GTA-TAAACCAATAAAAGATGC-ACCACCTTAAAG
* ** * * * *
559121 CAGCCTAGCATGACCACTCAGAATATTGGCAACAGGGAAAAGAGGAGATTGACAAGAATTTGATC
63 CAGCCCAGCATGACCAAACAGAATATAGGCAACAGGGAAAAGAGGAGATCGACAAGAAATTGACC
* *
559186 ACCTCGGCAAAGTTGCCCAGCCTTTAAATTTCTATTCTTC-ATCTTACAATCACTTCCAAGAA-T
128 ACCTCGGCAAAGTTGCCCAGCCTTCAAATTTCTATTCTACAAT-TTACAATCACTTCCAA-AATT
*
559249 TAAATCAAAAGGGTATTGAGCAAAC
191 TAAATCAAAACGGTATTGAGCAAAC
559274 ATGAGAAATG
Statistics
Matches: 191, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
231 4 0.02
232 26 0.14
233 155 0.81
234 6 0.03
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (233 bp):
AAGAAAATGTTGGTCCACCTAGACAATTTGTATAAACCAATAAAAGATGCACCACCTTAAAGCAG
CCCAGCATGACCAAACAGAATATAGGCAACAGGGAAAAGAGGAGATCGACAAGAAATTGACCACC
TCGGCAAAGTTGCCCAGCCTTCAAATTTCTATTCTACAATTTACAATCACTTCCAAAATTTAAAT
CAAAACGGTATTGAGCAAACCCACGTTGTTTGGTGATG
Found at i:560850 original size:19 final size:20
Alignment explanation
Indices: 560826--560872 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
560816 CTTTTTTTTT
* *
560826 AAATATTTATATTATTA-AA
1 AAATATTAATATTAATATAA
560845 AAATATTAATATTAATATAA
1 AAATATTAATATTAATATAA
560865 AAATATTA
1 AAATATTA
560873 TTAATTATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATATTAATATTAATATAA
Found at i:561884 original size:242 final size:239
Alignment explanation
Indices: 561337--561900 Score: 689
Period size: 242 Copynumber: 2.3 Consensus size: 239
561327 GAAATCCCTA
* ** * * ** *
561337 ATTACTTACTTAATCTGATTGAACAATAAAACATATTACTTAATCGGATGGACGTTAAAGATCTC
1 ATTATTTACTTAATCAAATTGAACAATAAAAAATATTACTTATTCAAATGGACATTAAAGATCTC
* *
561402 CATATTACTTAATCAATCGAACATTGGATAAAAGAAATTATTTAATGAGAGTAAACAATAGAGAC
66 CATATTACTTAATCGATCGAACATTGGATAAAAGAAATTATTTAATGAGAGTAAACAATAGAAAC
* * * * * *
561467 CTCATATTTTTTGGTCGAATTAGACGCTGAGATAAAAGATATTATTTAATCAAACTGCATAATGG
131 CTCATATTTTTTGATCGAATTAAACACTGAGATAAAAAATATTATTTAATCAAACTGAATAATAG
*
561532 AGCTCCCCACATGACTTAATCAGATCATACATTAAAAATTCTTG
196 AGCTCCCCACATGACTTAATCAGATCATACATTAAAAATTATTG
* * ** * *
561576 ATTCTTTACTTAATCATATCCAACAATAAAAAATATTACTTATTCAAATAGAAGATTTAAAGATC
1 ATTATTTACTTAATCAAATTGAACAATAAAAAATATTACTTATTCAAAT-GGACA-TTAAAGATC
* * * * * *
561641 TCTATATTACTTACTCGATTGGACATTGGATAAAAGAAATTATTTAATTAGA-TCAGACAATAGA
64 TCCATATTACTTAATCGATCGAACATTGGATAAAAGAAATTATTTAATGAGAGT-AAACAATAGA
* * **
561705 AACCTCATATTTTTTGATCGAATTAAACATTGAGATAAAAAAATATTATTTAATTAATTTGAATA
128 AACCTCATATTTTTTGATCGAATTAAACACTGAGAT-AAAAAATATTATTTAATCAAACTGAATA
* *** * * *
561770 ATAGAGTTTTTCATATTACTTAATTAGATCATACATTAAAAATTATTG
192 ATAGAGCTCCCCACATGACTTAATCAGATCATACATTAAAAATTATTG
* *
561818 ATTATTTACTTAATCAAATTGAACAACAAAAAATATTACTTATTTAAATCGGACATGTAAAGATC
1 ATTATTTACTTAATCAAATTGAACAATAAAAAATATTACTTATTCAAAT-GGACAT-TAAAGATC
561883 TCCATATTACTTAATCGA
64 TCCATATTACTTAATCGA
561901 ATGGGACACT
Statistics
Matches: 270, Mismatches: 50, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
239 39 0.14
240 3 0.01
241 96 0.36
242 132 0.49
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (239 bp):
ATTATTTACTTAATCAAATTGAACAATAAAAAATATTACTTATTCAAATGGACATTAAAGATCTC
CATATTACTTAATCGATCGAACATTGGATAAAAGAAATTATTTAATGAGAGTAAACAATAGAAAC
CTCATATTTTTTGATCGAATTAAACACTGAGATAAAAAATATTATTTAATCAAACTGAATAATAG
AGCTCCCCACATGACTTAATCAGATCATACATTAAAAATTATTG
Found at i:563068 original size:60 final size:60
Alignment explanation
Indices: 562947--563068 Score: 138
Period size: 60 Copynumber: 2.0 Consensus size: 60
562937 GAGGAGCCGT
* * * * ** *
562947 GGAGGTCAGACAAGGAAGGAGCAACTGGGGAGAGAAGGGTACCAGGAGCTGGGAAGCAAA
1 GGAGGCCAGACAAGGAAGGAGCAACTAGGAACAGAAGGGTACCAGGAAATGGGAAGAAAA
* **
563007 GGAGGCCAGACAAGGAAGGAGCAGA-TAGGAACTGAAGGGTACCAGGAAATGGGCCGAAAA
1 GGAGGCCAGACAAGGAAGGAGCA-ACTAGGAACAGAAGGGTACCAGGAAATGGGAAGAAAA
563067 GG
1 GG
563069 TGGACTCAGC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 50 0.98
61 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.42, T:0.07
Consensus pattern (60 bp):
GGAGGCCAGACAAGGAAGGAGCAACTAGGAACAGAAGGGTACCAGGAAATGGGAAGAAAA
Found at i:569539 original size:48 final size:48
Alignment explanation
Indices: 569483--569574 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
569473 AACACTCTCA
569483 ATATCTGAATTT-AAAGAAAT-TTTAACAATCTCTAAAAATTTCTTTTTC
1 ATATCTGAATTTGAAA-AAATCTTT-ACAATCTCTAAAAATTTCTTTTTC
* *
569531 ATATCTGAATTTGGAAAAATCTTTACAATCTCTAAAGATTTCTT
1 ATATCTGAATTTGAAAAAATCTTTACAATCTCTAAAAATTTCTT
569575 CTCATAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
48 35 0.88
49 5 0.12
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (48 bp):
ATATCTGAATTTGAAAAAATCTTTACAATCTCTAAAAATTTCTTTTTC
Found at i:572292 original size:48 final size:48
Alignment explanation
Indices: 572215--572326 Score: 145
Period size: 48 Copynumber: 2.3 Consensus size: 48
572205 AAAGATTTAT
* * * *
572215 TCTCAAAAGATTTTTTCTCTGTATCTGAATTTGGAGAAATCTTTAG-AA
1 TCTCTAAAGATTTCTTCTCAGTATCTGAATTTGAAGAAATCTTT-GTAA
* *
572263 TCTCTAAAGATTTCTTCTCAGTGTTTGAATTTGAAGAAATCTTTGTAA
1 TCTCTAAAGATTTCTTCTCAGTATCTGAATTTGAAGAAATCTTTGTAA
*
572311 TTTCTAAAGATTTCTT
1 TCTCTAAAGATTTCTT
572327 TTCGAAGGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 55 0.98
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.45
Consensus pattern (48 bp):
TCTCTAAAGATTTCTTCTCAGTATCTGAATTTGAAGAAATCTTTGTAA
Found at i:573969 original size:64 final size:63
Alignment explanation
Indices: 573895--574929 Score: 1014
Period size: 64 Copynumber: 16.1 Consensus size: 63
573885 TATATATTCG
* * * *
573895 AATTAAACATATGTGATATTTTATATTAATTCTTTTACATTTATGTTAATAATATATAAATTTG
1 AATT-AACATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTA
* * * * * **
573959 AATTACACATATGTGATATTTTATGTTAATTTTTATTCATTTAAGTTAATAATTTATAAATCCA
1 AATTA-ACATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTA
* * * * * *
574023 ATTTAAACATATGTGATATTTAACGTTAATTCTTATATATTTAAGTTAGTAATATATAAATTTG
1 AATT-AACATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTA
* * * ** * **
574087 AATTAAGGATATGTGATAGTTAAGGTTAATTCTTATACATTTACATTAATAATATGTAAATTCG
1 AATTAA-CATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTA
* * *
574151 AATTAAGTATATGTGATATTTTATATTAATTCTTATACATTTATGTTAATAATATATAAATTTA
1 AATTAA-CATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTA
* * *
574215 AATTACACATATGTGATATTTTATGTTAATTCTTATACATTTAAGTTAATAATTTATAAATTTA
1 AATTA-ACATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTA
* * * * * * *
574279 AATTAAGCGTATGTGACATTTAACGTTAATTCTTATATATTTACGTTAATAATATATAAATCTG
1 AATTAA-CATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTA
* * *** * * * * *
574343 AAGTAAGAATATACAAAATTTAATGGTAATTCTTATACATTTATGCTAATAATTTATAAATTTG
1 AATTAA-CATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTA
** * * * * * *
574407 AATTAAGTGTATGTGGTTTTTTATATTAATTCTTATGCATATATGTTAATAATATATAAATTTA
1 AATTAA-CATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTA
* * * * * *
574471 AATTATGCAGATGTGATAGTTT-ATGTTCATTCTTATACATTTAGGTTAGTGATATATAAATTTA
1 AATTA-ACATATGTGATA-TTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTA
* * * *
574535 AATTAAGCATATGTGTTTTTTAATGTTAATTATTTTACATTTATGATAATAATAATATATAAATT
1 AATTAA-CATATGTGATATTTAATGTTAATTCTTATACATTTATG-T--TAATAATATATAAATT
*
574600 CA
62 TA
* *
574602 AATTAAACATATGTGATATTTAATGTTAATTCTTATACATTTATATTGATAATATTATATAGATT
1 AATT-AACATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATA-TATA-A-ATT
*
574667 CA
62 TA
* * *
574669 AATTAAGGATATGTGAT-TTTAATGTTAATTCTTATACATTTATGTTAATAATGTATAAATTTG
1 AATTAA-CATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTA
* * * *
574732 AATTAAACATATATGATATTTAACGTTAATTATTATATATTTATGTTAATAATATATAAATTTA
1 AATT-AACATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTA
* * * * *
574796 AATTACACATATGTGGTATTTTATGTTAATTTTTATACATTTA-GATTAATAATTTATAAATTCA
1 AATTA-ACATATGTGATATTTAATGTTAATTCTTATACATTTATG-TTAATAATATATAAATTTA
** ** * * * * *
574860 AATTAAGGGTATGTGATATTTAACATTAATTTTTTTACATTTACGTTAATAATTTATAAATTTG
1 AATTAA-CATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTA
574924 AATTAA
1 AATTAA
574930 ACATTAATTG
Statistics
Matches: 804, Mismatches: 144, Indels: 46
0.81 0.14 0.05
Matches are distributed among these distances:
63 25 0.03
64 655 0.81
65 15 0.02
66 37 0.05
67 70 0.09
68 2 0.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (63 bp):
AATTAACATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTA
Found at i:574119 original size:192 final size:191
Alignment explanation
Indices: 573895--575932 Score: 1331
Period size: 192 Copynumber: 10.8 Consensus size: 191
573885 TATATATTCG
* * * *
573895 AATTAAACATATGTGATATTTTATATTAATTCTTTTACATTTATGTTAATAATATATAAATTTGA
1 AATTAAGCATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTGA
* * * * * *
573960 ATTACACATATGTGATATTTTATGTTAATTTTTATTCATTTAAGTTAATAATTTATAAATCCAAT
66 ATTA-ACATATGTGATATTTTATGTTAATTCTTATACATTTATGTTAATAATATATAAATTCAAA
* * * * *
574025 TTAAACATATGTGATATTTAACGTTAATTCTTATATATTTAAGTTAGTAATATATAAATTTG
130 TTAAGCATATGTGATATTTAATGTTAATTCTTATACATTTAAGTTAATAATATATAAATTTA
* * * ** * *
574087 AATTAAGGATATGTGATAGTTAAGGTTAATTCTTATACATTTACATTAATAATATGTAAATTCGA
1 AATTAAGCATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTGA
* * *
574152 ATTAAGTATATGTGATATTTTATATTAATTCTTATACATTTATGTTAATAATATATAAATTTAAA
66 ATTAA-CATATGTGATATTTTATGTTAATTCTTATACATTTATGTTAATAATATATAAATTCAAA
* *
574217 TTACA-CATATGTGATATTTTATGTTAATTCTTATACATTTAAGTTAATAATTTATAAATTTA
130 TTA-AGCATATGTGATATTTAATGTTAATTCTTATACATTTAAGTTAATAATATATAAATTTA
* * * * * *
574279 AATTAAGCGTATGTGACATTTAACGTTAATTCTTATATATTTACGTTAATAATATATAAATCTGA
1 AATTAAGCATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTGA
* * *** * * * * * **
574344 AGTAAGAATATACAAAATTTAATGGTAATTCTTATACATTTATGCTAATAATTTATAAATTTGAA
66 ATTAA-CATATGTGATATTTTATGTTAATTCTTATACATTTATGTTAATAATATATAAATTCAAA
** * * * * * * *
574409 TTAAGTGTATGTGGTTTTTTATATTAATTCTTATGCATATATGTTAATAATATATAAATTTA
130 TTAAGCATATGTGATATTTAATGTTAATTCTTATACATTTAAGTTAATAATATATAAATTTA
* * * * * * *
574471 AATTATGCAGATGTGATAGTTT-ATGTTCATTCTTATACATTTAGGTTAGTGATATATAAATTTA
1 AATTAAGCATATGTGATA-TTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTG
* * *
574535 AATTAAGCATATGTG-TTTTTTAATGTTAATTATTTTACATTTATGATAATAATAATATATAAAT
65 AATTAA-CATATGTGATATTTT-ATGTTAATTCTTATACATTTATG-T--TAATAATATATAAAT
* *
574599 TCAAATTAAACATATGTGATATTTAATGTTAATTCTTATACATTTATA-TTGATAATATTATATA
125 TCAAATTAAGCATATGTGATATTTAATGTTAATTCTTATACATTTA-AGTTAATAATA-TATA-A
*
574663 GATTCA
187 -ATTTA
* *
574669 AATTAAGGATATGTGAT-TTTAATGTTAATTCTTATACATTTATGTTAATAATGTATAAATTTGA
1 AATTAAGCATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTGA
* * * * * *
574733 ATTAAACATATATGATATTTAACGTTAATTATTATATATTTATGTTAATAATATATAAATTTAAA
66 ATT-AACATATGTGATATTTTATGTTAATTCTTATACATTTATGTTAATAATATATAAATTCAAA
* * * * *
574798 TTACA-CATATGTGGTATTTTATGTTAATTTTTATACATTT-AGATTAATAATTTATAAATTCA
130 TTA-AGCATATGTGATATTTAATGTTAATTCTTATACATTTAAG-TTAATAATATATAAATTTA
** ** * * * *
574860 AATTAAGGGTATGTGATATTTAACATTAATTTTTTTACATTTACGTTAATAATTTATAAATTTGA
1 AATTAAGCATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTGA
* * * * ** * *
574925 ATTAA-ACAT-T-A-A---T-TG-CAATACATT-TACATTAATAATATATAA-ATTTAAATTACG
66 ATTAACATATGTGATATTTTATGTTAATTC-TTATACATTTATGTTA-ATAATATATAAATT-CA
* * * * * * ** *
574979 CA-TATGTGATA-GT-TTATGTTAAT-TCTTATACATT-TA-GGTT-A---A-TAATATATAAAC
128 AATTAAG-CATATGTGATAT-TTAATGT-TAATTC-TTATACATTTAAGTTAATAATATATAAAT
*
575033 TCA
189 TTA
** * * * ** ** * * *
575036 ATCTAAACATAGATGTTATTTACTGTTAAT-TT--TGCACATTTATGTTA--A---CAATATGTA
1 AATTAAGCAT--ATGTGA--TA-T-TTAATGTTAATTCTTATACAT-TTATGTTAATAATATATA
** * * * * * *
575093 AATTCAAAATAAATATATGTGATATTTAATGTTAATTCTTAAACATTTTTGTTAGTAATATATAA
59 AATT-TGAATTAACATATGTGATATTTTATGTTAATTCTTATACATTTATGTTAATAATATATAA
* * ** *
575158 ATTCAAATTAAGGATATGCGATATTTAATGTTAATTCTTATACATTTACCTTAACAATATATAAA
123 ATTCAAATTAAGCATATGTGATATTTAATGTTAATTCTTATACATTTAAGTTAATAATATATAAA
**
575223 TTCG
188 TTTA
* * * * * *
575227 AATTAAGTATATGTGATATTTTATATTAATTCTTA-ATATTTATGTTAATAATATATAAACTTAA
1 AATTAAGCATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTGA
* * * * *
575291 ATTACACATATGTGGTATTTTATTTTAATTTTTATATATTTA-GATTAATAATTTATAAATTCAA
66 ATTA-ACATATGTGATATTTTATGTTAATTCTTATACATTTATG-TTAATAATATATAAATTCAA
* ** * * * * *
575355 ATTAAGCGTATGTGATATTTAACATTAATTTTTTTACATTTACGTTAATAATTTAT-AATTTG
129 ATTAAGCATATGTGATATTTAATGTTAATTCTTATACATTTAAGTTAATAATATATAAATTTA
* * * * *
575417 AATTAA-C-TAT-T-A-A--T--TG-TGATACATT-TACA-TTA--ATAAT-ATATA-AATTCGT
1 AATTAAGCATATGTGATATTTAATGTTAATTC-TTATACATTTATGTTAATAATATATAAAT-TT
* ** * * * * * * * *
575466 -ATTGCATATATGCGATATTTAACGTTAATTCTTATAAATTTGTGTTAGTAACT-TATAAATTTA
64 GAATTAACATATGTGATATTTTATGTTAATTCTTATACATTTATGTTAATAA-TATATAAATTCA
* * * * *
575529 AATTACGCATATGTGATAGTTT-ATGTTAATTCTTATACATTTAGGTTAGTAATATGTAAATTCA
128 AATTAAGCATATGTGATA-TTTAATGTTAATTCTTATACATTTAAGTTAATAATATATAAATTTA
* * * **
575593 AATTAAGCATATGTGATGTTTTACGTTAATTCTTATACA-TTATGTTAATAATATATAAATTCAA
1 AATTAAGCATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTGA
* * * * * ** *
575657 ATTAAGTATATGTGACATTTTACGCTAATTCTTATACATTTAGGTTAATAATATATAAAGCCCAA
66 ATTAA-CATATGTGATATTTTATGTTAATTCTTATACATTTATGTTAATAATATATAAATTCAAA
* * * * * * *
575722 TTAAGTAGATGTAATATTTTA-GCTTAATTCTTATACATTTATGTTAATAATTTATAAATTTG
130 TTAAGCATATGTGATATTTAATG-TTAATTCTTATACATTTAAGTTAATAATATATAAATTTA
* * * * * * * * **
575784 AATTAATCATATATGATAATTT-ATCTTAATTTTTATACATCTAAGTTAATAATATACAAAGTCA
1 AATTAAGCATATGTGAT-ATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTG
* * ** * *
575848 AATTAAGCGTATGTAATATTTTACCTTAAATT-TTTTACATTTATGTTAATGATATATAAATTCA
65 AATTAA-CATATGTGATATTTTATGTT-AATTCTTATACATTTATGTTAATAATATATAAATTCA
* ** *
575912 AAATAAGTTTATATGATATTT
128 AATTAAGCATATGTGATATTT
575933 TGTTTATACG
Statistics
Matches: 1423, Mismatches: 326, Indels: 194
0.73 0.17 0.10
Matches are distributed among these distances:
175 96 0.07
176 42 0.03
177 11 0.01
178 13 0.01
179 6 0.00
180 14 0.01
181 15 0.01
182 37 0.03
183 15 0.01
184 15 0.01
185 43 0.03
186 24 0.02
187 7 0.00
188 11 0.01
189 11 0.01
190 32 0.02
191 269 0.19
192 531 0.37
193 12 0.01
194 61 0.04
195 58 0.04
196 8 0.01
197 68 0.05
198 24 0.02
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (191 bp):
AATTAAGCATATGTGATATTTAATGTTAATTCTTATACATTTATGTTAATAATATATAAATTTGA
ATTAACATATGTGATATTTTATGTTAATTCTTATACATTTATGTTAATAATATATAAATTCAAAT
TAAGCATATGTGATATTTAATGTTAATTCTTATACATTTAAGTTAATAATATATAAATTTA
Found at i:574725 original size:21 final size:21
Alignment explanation
Indices: 574701--574795 Score: 70
Period size: 21 Copynumber: 4.5 Consensus size: 21
574691 TGTTAATTCT
* *
574701 TATACATTTATGTTAATAATG
1 TATAAATTTATGTTAATAATA
*
574722 TATAAATTTGA-ATTAA-ACATA
1 TATAAATTT-ATGTTAATA-ATA
* * *
574743 TATGATATTTAACGTTAATTAT-
1 TAT-AAATTT-ATGTTAATAATA
*
574765 TATATATTTATGTTAATAATA
1 TATAAATTTATGTTAATAATA
574786 TATAAATTTA
1 TATAAATTTA
574796 AATTACACAT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
20 10 0.17
21 32 0.55
22 10 0.17
23 6 0.10
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.47
Consensus pattern (21 bp):
TATAAATTTATGTTAATAATA
Found at i:574787 original size:19 final size:21
Alignment explanation
Indices: 574742--574789 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
574732 AATTAAACAT
574742 ATATGATATTTAACGTTAATTA
1 ATAT-ATATTTAACGTTAATTA
* *
574764 TTATATATTT-ATGTTAA-TA
1 ATATATATTTAACGTTAATTA
574783 ATATATA
1 ATATATA
574790 AATTTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 8 0.35
20 6 0.26
21 6 0.26
22 3 0.13
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (21 bp):
ATATATATTTAACGTTAATTA
Found at i:574966 original size:112 final size:112
Alignment explanation
Indices: 574830--575031 Score: 280
Period size: 112 Copynumber: 1.8 Consensus size: 112
574820 GTTAATTTTT
* * ** *
574830 ATACATTTAGATTAATAATTTATAAATTCAAATTAAGGGTATGTGATA-TTTAACATTAATTTTT
1 ATACATTTACATTAATAATATATAAATTCAAATTAAGCATATGTGATAGTTT-ACATTAATTCTT
* *
574894 TTACATTTACGTTAATAATTTATAAATTTGAATTAAACATTAATTGCA
65 ATACATTTACGTTAATAATATATAAATTTGAATTAAACATTAATTGCA
* * **
574942 ATACATTTACATTAATAATATATAAATTTAAATTACGCATATGTGATAGTTTATGTTAATTCTTA
1 ATACATTTACATTAATAATATATAAATTCAAATTAAGCATATGTGATAGTTTACATTAATTCTTA
*
575007 TACATTTAGGTTAATAATATATAAA
66 TACATTTACGTTAATAATATATAAA
575032 CTCAATCTAA
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
112 74 0.96
113 3 0.04
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (112 bp):
ATACATTTACATTAATAATATATAAATTCAAATTAAGCATATGTGATAGTTTACATTAATTCTTA
TACATTTACGTTAATAATATATAAATTTGAATTAAACATTAATTGCA
Found at i:575010 original size:64 final size:63
Alignment explanation
Indices: 574942--575412 Score: 434
Period size: 64 Copynumber: 7.4 Consensus size: 63
574932 ATTAATTGCA
* * *
574942 ATACATTTACATTAATAATATATAAATTTAAATTACGCATATGTGATAGTTTATGTTAATTCTT
1 ATACATTTACGTTAATAATATATAAATTCAAATTAAGCATATGTGATA-TTTATGTTAATTCTT
* * * *
575006 ATACATTTAGGTTAATAATATATAAACTC-AATCTAAACATA-GATGTTATTTACTGTTAATT-T
1 ATACATTTACGTTAATAATATATAAATTCAAAT-TAAGCATATG-TGATATTTA-TGTTAATTCT
575068 T
63 T
** * * * * **
575069 GCACATTTATGTTAACAATATGTAAATTCAAAATAAATATATGTGATATTTAATGTTAATTCTT
1 ATACATTTACGTTAATAATATATAAATTCAAATTAAGCATATGTGATATTT-ATGTTAATTCTT
* ** * * *
575133 AAACATTTTTGTTAGTAATATATAAATTCAAATTAAGGATATGCGATATTTAATGTTAATTCTT
1 ATACATTTACGTTAATAATATATAAATTCAAATTAAGCATATGTGATATTT-ATGTTAATTCTT
* * * * *
575197 ATACATTTACCTTAACAATATATAAATTCGAATTAAGTATATGTGATATTTTATATTAATTCTT
1 ATACATTTACGTTAATAATATATAAATTCAAATTAAGCATATGTGATA-TTTATGTTAATTCTT
* * * * *
575261 A-ATATTTATGTTAATAATATATAAACTT-AAATTACA-CATATGTGGTATTTTATTTTAATTTT
1 ATACATTTACGTTAATAATATATAAA-TTCAAATTA-AGCATATGTGATA-TTTATGTTAATTCT
575323 T
63 T
* * * ** *
575324 ATATATTTA-GATTAATAATTTATAAATTCAAATTAAGCGTATGTGATATTTAACATTAATTTTT
1 ATACATTTACG-TTAATAATATATAAATTCAAATTAAGCATATGTGATATTT-ATGTTAATTCTT
* *
575388 TTACATTTACGTTAATAATTTATAA
1 ATACATTTACGTTAATAATATATAA
575413 TTTGAATTAA
Statistics
Matches: 339, Mismatches: 52, Indels: 32
0.80 0.12 0.08
Matches are distributed among these distances:
63 111 0.33
64 224 0.66
65 4 0.01
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (63 bp):
ATACATTTACGTTAATAATATATAAATTCAAATTAAGCATATGTGATATTTATGTTAATTCTT
Found at i:575421 original size:127 final size:127
Alignment explanation
Indices: 574942--575412 Score: 432
Period size: 127 Copynumber: 3.7 Consensus size: 127
574932 ATTAATTGCA
* * * **
574942 ATACATTTACATTAATAATATATAAATTTAAATTACGCATATGTGATAGTTT-ATGTTAATTCTT
1 ATACATTTACATTAACAATATATAAATTCAAATTAAGCATATGTGATA-TTTAACATTAATTCTT
* * * * *
575006 ATACATTTAGGTTAATAATATATAAAC-TCAATCTAAACATA-GATGTTATTTACTGTTAATT-T
65 A-ACATTTACGTTAATAATATATAAACTTAAAT-TACACATATG-TGGTATTTAATGTTAATTCT
575068 T
127 T
** ** * * ** **
575069 GCACATTTATGTTAACAATATGTAAATTCAAAATAAATATATGTGATATTTAATGTTAATTCTTA
1 ATACATTTACATTAACAATATATAAATTCAAATTAAGCATATGTGATATTTAACATTAATTCTT-
** * * * *
575134 AACATTTTTGTTAGTAATATATAAA-TTCAAATTA-AGGATATGCGATATTTAATGTTAATTCTT
65 AACATTTACGTTAATAATATATAAACTT-AAATTACA-CATATGTGGTATTTAATGTTAATTCTT
* * * * *
575197 ATACATTTACCTTAACAATATATAAATTCGAATTAAGTATATGTGATATTTTATATTAATTCTTA
1 ATACATTTACATTAACAATATATAAATTCAAATTAAGCATATGTGATATTTAACATTAATTCTTA
* * * * *
575262 ATATTTATGTTAATAATATATAAACTTAAATTACACATATGTGGTATTTTATTTTAATTTTT
66 ACATTTACGTTAATAATATATAAACTTAAATTACACATATGTGGTATTTAATGTTAATTCTT
* * * * * *
575324 ATATATTTAGATTAATAATTTATAAATTCAAATTAAGCGTATGTGATATTTAACATTAATTTTTT
1 ATACATTTACATTAACAATATATAAATTCAAATTAAGCATATGTGATATTTAACATTAA-TTCTT
* *
575389 TACATTTACGTTAATAATTTATAA
65 AACATTTACGTTAATAATATATAA
575413 TTTGAATTAA
Statistics
Matches: 281, Mismatches: 53, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
126 4 0.01
127 189 0.67
128 88 0.31
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (127 bp):
ATACATTTACATTAACAATATATAAATTCAAATTAAGCATATGTGATATTTAACATTAATTCTTA
ACATTTACGTTAATAATATATAAACTTAAATTACACATATGTGGTATTTAATGTTAATTCTT
Found at i:575541 original size:64 final size:64
Alignment explanation
Indices: 575473--575933 Score: 396
Period size: 64 Copynumber: 7.2 Consensus size: 64
575463 CGTATTGCAT
* * * * *
575473 ATATGCGATATTTAACGTTAATTCTTATAAATTTGTGTTAGTAACT-TATAAATTTAAATTACGC
1 ATATGTGATATTTTACGTTAATTCTTATACATTTGTGTTAGTAA-TATATAAATTCAAATTAAGC
* * *
575537 ATATGTGATAGTTTATGTTAATTCTTATACATTTAG-GTTAGTAATATGTAAATTCAAATTAAGC
1 ATATGTGATATTTTACGTTAATTCTTATACATTT-GTGTTAGTAATATATAAATTCAAATTAAGC
* * * *
575601 ATATGTGATGTTTTACGTTAATTCTTATACA-TTATGTTAATAATATATAAATTCAAATTAAGT
1 ATATGTGATATTTTACGTTAATTCTTATACATTTGTGTTAGTAATATATAAATTCAAATTAAGC
* * * ** * *
575664 ATATGTGACATTTTACGCTAATTCTTATACATTTAG-GTTAATAATATATAAAGCCCAATTAAGT
1 ATATGTGATATTTTACGTTAATTCTTATACATTT-GTGTTAGTAATATATAAATTCAAATTAAGC
* * * * * ** *
575728 AGATGTAATATTTTA-GCTTAATTCTTATACATTTATGTTAATAATTTATAAATTTGAATTAATC
1 ATATGTGATATTTTACG-TTAATTCTTATACATTTGTGTTAGTAATATATAAATTCAAATTAAGC
* * * * ** * * *
575792 ATATATGATAATTTATC-TTAATTTTTATACATCTAAGTTAATAATATACAAAGTCAAATTAAGC
1 ATATGTGATATTTTA-CGTTAATTCTTATACATTTGTGTTAGTAATATATAAATTCAAATTAAGC
* * * * * * * * *
575856 GTATGTAATATTTTACCTTAAATT-TTTTACATTTATGTTAATGATATATAAATTCAAAATAAGT
1 ATATGTGATATTTTACGTT-AATTCTTATACATTTGTGTTAGTAATATATAAATTCAAATTAAGC
* *
575920 TTATATGATATTTT
1 ATATGTGATATTTT
575934 GTTTATACGA
Statistics
Matches: 324, Mismatches: 62, Indels: 22
0.79 0.15 0.05
Matches are distributed among these distances:
63 58 0.18
64 261 0.81
65 5 0.02
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.45
Consensus pattern (64 bp):
ATATGTGATATTTTACGTTAATTCTTATACATTTGTGTTAGTAATATATAAATTCAAATTAAGC
Found at i:575925 original size:128 final size:128
Alignment explanation
Indices: 575480--575929 Score: 480
Period size: 128 Copynumber: 3.5 Consensus size: 128
575470 CATATATGCG
* * * * * * * * *
575480 ATATTTAACGTTAATTCTTATAAATTTGTGTTAGTAACT-TATAAATTTAAATTACGCATATGTG
1 ATATTTTACCTTAATTCTTATACATTTATGTTAATAA-TATATAAATTCAAATTAAGTATATATG
* * * * * * *
575544 ATAGTTTATGTTAATTCTTATACATTTAGGTTAGTAATATGTAAATTCAAATTAAGCATATGTG
65 ATAATTTATCTTAATTCTTATACATTTAGGTTAATAATATATAAAGTCAAATTAAGCGTATGTA
* * *
575608 ATGTTTTACGTTAATTCTTATACA-TTATGTTAATAATATATAAATTCAAATTAAGTATATGTGA
1 ATATTTTACCTTAATTCTTATACATTTATGTTAATAATATATAAATTCAAATTAAGTATATATGA
* * * * * *
575672 CATTTTA-CGCTAATTCTTATACATTTAGGTTAATAATATATAAAGCCCAATTAAGTAG-ATGTA
66 TAATTTATC-TTAATTCTTATACATTTAGGTTAATAATATATAAAGTCAAATTAAG-CGTATGTA
* * **
575735 ATATTTTAGCTTAATTCTTATACATTTATGTTAATAATTTATAAATTTGAATTAA-TCATATATG
1 ATATTTTACCTTAATTCTTATACATTTATGTTAATAATATATAAATTCAAATTAAGT-ATATATG
* * * *
575799 ATAATTTATCTTAATTTTTATACATCTAAGTTAATAATATACAAAGTCAAATTAAGCGTATGTA
65 ATAATTTATCTTAATTCTTATACATTTAGGTTAATAATATATAAAGTCAAATTAAGCGTATGTA
* * * *
575863 ATATTTTACCTTAAATT-TTTTACATTTATGTTAATGATATATAAATTCAAAATAAGTTTATATG
1 ATATTTTACCTT-AATTCTTATACATTTATGTTAATAATATATAAATTCAAATTAAGTATATATG
575927 ATA
65 ATA
575930 TTTTGTTTAT
Statistics
Matches: 268, Mismatches: 45, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
126 1 0.00
127 105 0.39
128 156 0.58
129 6 0.02
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.44
Consensus pattern (128 bp):
ATATTTTACCTTAATTCTTATACATTTATGTTAATAATATATAAATTCAAATTAAGTATATATGA
TAATTTATCTTAATTCTTATACATTTAGGTTAATAATATATAAAGTCAAATTAAGCGTATGTA
Found at i:576795 original size:2 final size:2
Alignment explanation
Indices: 576732--576777 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
576722 ACATATGTGA
576732 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
576771 AT AT AT A
1 AT AT AT A
576778 AATTTAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:576836 original size:61 final size:63
Alignment explanation
Indices: 576765--576901 Score: 206
Period size: 61 Copynumber: 2.2 Consensus size: 63
576755 TATATATATA
* * * *
576765 TTAATAATATATAAATTTAAATTACATATATGTGAT-TTT-TTTTAATTTTTATACATTTAGG
1 TTAATAATATATAAAGTTAAATTAAACATATGTGATATTTATGTTAATTTTTATACATTTAGG
*
576826 TTAATAATATATAAAGTTAAATTAAACATATGTGATATTTAATGTTAATTTTTATACATTTATG
1 TTAATAATATATAAAGTTAAATTAAACATATGTGATATTT-ATGTTAATTTTTATACATTTAGG
576890 TTAATAATATAT
1 TTAATAATATAT
576902 GCGTATTTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
61 33 0.49
62 3 0.04
64 32 0.47
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.50
Consensus pattern (63 bp):
TTAATAATATATAAAGTTAAATTAAACATATGTGATATTTATGTTAATTTTTATACATTTAGG
Found at i:576885 original size:64 final size:61
Alignment explanation
Indices: 576765--577226 Score: 271
Period size: 64 Copynumber: 7.6 Consensus size: 61
576755 TATATATATA
* * * *
576765 TTAATAATATATAAATTTAAATTACATATATGTGATTTTTTTTAATTTTTATACATTTAGG
1 TTAATAATATATAAAGTTAAATTAAACATATGTGATTTTTGTTAATTTTTATACATTTAGG
*
576826 TTAATAATATATAAAGTTAAATTAAACATATGTGATATTTAATGTTAATTTTTATACATTTATG
1 TTAATAATATATAAAGTTAAATTAAACATATGTGAT-TTT--TGTTAATTTTTATACATTTAGG
** * ** *
576890 TTAATAATATAT-GCG-T--ATTTAAC---TGT--TAATT-TT--TT---AT--ATTTATG
1 TTAATAATATATAAAGTTAAATTAAACATATGTGATTTTTGTTAATTTTTATACATTTAGG
* * * * * **
576934 TTAATAATATATAAACTCAAATTAAGCATATATGATTTTAAAGTTAATTTTTATACATTTACA
1 TTAATAATATATAAAGTTAAATTAAACATATGTGATTTT--TGTTAATTTTTATACATTTAGG
* * * *
576997 TTAATAATATATAAA-TTCAAAATTACACATTTGAT-ATTTTATGTTAATTTTTATAAATTTACG
1 TTAATAATATATAAAGTT--AAATTAAACATATG-TGATTTT-TGTTAATTTTTATACATTTAGG
* * * **
577060 TTAATATTATATAAA-TTCAAATTAAGCATATGTGATATTTTATTTTAATTTTTATACATTTATA
1 TTAATAATATATAAAGTT-AAATTAAACATATGTG--ATTTT-TGTTAATTTTTATACATTTAGG
* * * * ** * * *
577124 TTAATAATATATAAAATTCAATTAAGCTTACATGATATTTTACATTAATTTTTATACATTAAAG
1 TTAATAATATATAAAGTTAAATTAAACATATGTGAT-TTTT--GTTAATTTTTATACATTTAGG
* *
577188 TTAATATTGTTATATAAATTTAAATTAAACATATGTGAT
1 TTAATA---ATATATAAAGTTAAATTAAACATATGTGAT
577227 AGGAAAACTT
Statistics
Matches: 311, Mismatches: 55, Indels: 64
0.72 0.13 0.15
Matches are distributed among these distances:
44 19 0.06
46 2 0.01
48 5 0.02
49 2 0.01
51 4 0.01
52 1 0.00
53 2 0.01
54 1 0.00
55 1 0.00
56 2 0.01
57 3 0.01
58 2 0.01
60 6 0.02
61 36 0.12
62 19 0.06
63 60 0.19
64 120 0.39
65 3 0.01
67 23 0.07
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (61 bp):
TTAATAATATATAAAGTTAAATTAAACATATGTGATTTTTGTTAATTTTTATACATTTAGG
Found at i:576909 original size:44 final size:44
Alignment explanation
Indices: 576861--576945 Score: 145
Period size: 44 Copynumber: 1.9 Consensus size: 44
576851 ACATATGTGA
576861 TATTTAA-TGTTAATTTTTATACATTTATGTTAATAATATATGCG
1 TATTTAACTGTTAATTTTT-TACATTTATGTTAATAATATATGCG
*
576905 TATTTAACTGTTAATTTTTTATATTTATGTTAATAATATAT
1 TATTTAACTGTTAATTTTTTACATTTATGTTAATAATATAT
576946 AAACTCAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 28 0.72
45 11 0.28
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (44 bp):
TATTTAACTGTTAATTTTTTACATTTATGTTAATAATATATGCG
Found at i:576983 original size:171 final size:166
Alignment explanation
Indices: 576755--577071 Score: 422
Period size: 170 Copynumber: 1.9 Consensus size: 166
576745 TATATATATA
* * **
576755 TATATATATATTAATAATATATAAATTTAAATTACATATATGTGATTTTTTTTAATTTTTATACA
1 TATATATATATTAATAATATATAAACTCAAATTACATATA-GTGATTTTAGTTAATTTTTATACA
** *
576820 TTTAGGTTAATAATATATAAAGTT-AAATTAAACATATGTGATATTTAATGTTAATTTTTATACA
65 TTTACATTAATAATATATAAA-TTAAAATTAAACAT-T-TGATATTTAATGTTAATTTTTATAAA
*
576884 TTTATGTTAATAATATATGCGTATTTAACTGTTAATTTTT
127 TTTACGTTAATAATATATGCGTATTTAACTGTTAATTTTT
* *
576924 TATATTTATGTTAATAATATATAAACTCAAATTAAGCATATA-TGATTTTAAAGTTAATTTTTAT
1 TATATATATATTAATAATATATAAACTCAAATT-A-CATATAGTGATTTT--AGTTAATTTTTAT
* *
576988 ACATTTACATTAATAATATATAAATTCAAAATTACACATTTGATATTTTATGTTAATTTTTATAA
62 ACATTTACATTAATAATATATAAATT-AAAATTAAACATTTGATATTTAATGTTAATTTTTATAA
*
577053 ATTTACGTTAATATTATAT
126 ATTTACGTTAATAATATAT
577072 AAATTCAAAT
Statistics
Matches: 129, Mismatches: 13, Indels: 11
0.84 0.08 0.07
Matches are distributed among these distances:
169 36 0.28
170 43 0.33
171 40 0.31
172 10 0.08
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (166 bp):
TATATATATATTAATAATATATAAACTCAAATTACATATAGTGATTTTAGTTAATTTTTATACAT
TTACATTAATAATATATAAATTAAAATTAAACATTTGATATTTAATGTTAATTTTTATAAATTTA
CGTTAATAATATATGCGTATTTAACTGTTAATTTTT
Found at i:577001 original size:63 final size:64
Alignment explanation
Indices: 576896--577227 Score: 302
Period size: 64 Copynumber: 5.2 Consensus size: 64
576886 TATGTTAATA
* * * ** *
576896 ATATATGCGTATTTAACTGTTAATTTTT-TATATTTATGTTAATAATATATAAACTCAAATTAAG
1 ATATATG-ATATTTAA-AGTTAATTTTTATACATTTACATTAATAATATATAAATTCAAATTAAG
576960 C
64 C
576961 ATATATGAT-TTTAAAGTTAATTTTTATACATTTACATTAATAATATATAAATTCAAAATTACA-
1 ATATATGATATTTAAAGTTAATTTTTATACATTTACATTAATAATATATAAATTC-AAATTA-AG
577024 C
64 C
* * * * *
577025 AT-T-TGATATTTTATGTTAATTTTTATAAATTTACGTTAATATTATATAAATTCAAATTAAGC
1 ATATATGATATTTAAAGTTAATTTTTATACATTTACATTAATAATATATAAATTCAAATTAAGC
* * ** *
577087 ATATGTGATATTTTATTTTAATTTTTATACATTTATATTAATAATATATAAAATTC-AATTAAGC
1 ATATATGATATTTAAAGTTAATTTTTATACATTTACATTAATAATATAT-AAATTCAAATTAAGC
* * * * * *
577151 TTACATGATATTTTACA-TTAATTTTTATACA-TTAAAGTTAATATTGTTATATAAATTTAAATT
1 ATATATGATA-TTTAAAGTTAATTTTTATACATTTACA-TTAATA---ATATATAAATTCAAATT
*
577214 AAAC
61 AAGC
*
577218 ATATGTGATA
1 ATATATGATA
577228 GGAAAACTTG
Statistics
Matches: 224, Mismatches: 29, Indels: 26
0.80 0.10 0.09
Matches are distributed among these distances:
61 1 0.00
62 23 0.10
63 75 0.33
64 84 0.38
65 17 0.08
66 5 0.02
67 19 0.08
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (64 bp):
ATATATGATATTTAAAGTTAATTTTTATACATTTACATTAATAATATATAAATTCAAATTAAGC
Found at i:577005 original size:107 final size:109
Alignment explanation
Indices: 576806--577008 Score: 311
Period size: 108 Copynumber: 1.9 Consensus size: 109
576796 GTGATTTTTT
* * * *
576806 TTAATTTTTATACATTTAGGTTAATAATATATAAAGTTAAATTAAACATATGTGATATTTAATGT
1 TTAATTTTTATACATTTAGGTTAATAATATATAAACTCAAATTAAACATATATGATATTTAAAGT
**
576871 TAATTTTTATACATTTATGTTAATAATATATGCGTATTTAACTG
66 TAATTTTTATACATTTACATTAATAATATATGCGTATTTAACTG
* * *
576915 TTAATTTTT-TATATTTATGTTAATAATATATAAACTCAAATTAAGCATATATGAT-TTTAAAGT
1 TTAATTTTTATACATTTAGGTTAATAATATATAAACTCAAATTAAACATATATGATATTTAAAGT
576978 TAATTTTTATACATTTACATTAATAATATAT
66 TAATTTTTATACATTTACATTAATAATATAT
577009 AAATTCAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 36 0.42
108 40 0.47
109 9 0.11
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (109 bp):
TTAATTTTTATACATTTAGGTTAATAATATATAAACTCAAATTAAACATATATGATATTTAAAGT
TAATTTTTATACATTTACATTAATAATATATGCGTATTTAACTG
Found at i:577062 original size:20 final size:21
Alignment explanation
Indices: 577034--577076 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
577024 CATTTGATAT
* *
577034 TTTATGTTAAT-TTTTATAAA
1 TTTACGTTAATATTATATAAA
577054 TTTACGTTAATATTATATAAA
1 TTTACGTTAATATTATATAAA
577075 TT
1 TT
577077 CAAATTAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTACGTTAATATTATATAAA
Found at i:577147 original size:126 final size:126
Alignment explanation
Indices: 576913--577227 Score: 370
Period size: 126 Copynumber: 2.5 Consensus size: 126
576903 CGTATTTAAC
* * * * *
576913 TGTTAATTTTT-TATATTTATGTTAATAATATATAAACTCAAATTAAGCATATATGAT-TTTAAA
1 TGTTAATTTTTATAAATTTAAGTTAATATTATATAAATTCAAATTAAGCATATGTGATATTTAAA
576976 GTTAATTTTTATACATTTACATTAATAATATATAAATTCAAAATTACA-CATT-TGATATTTTA
66 GTTAATTTTTATACATTTACATTAATAATATATAAATTC-AAATTA-AGC-TTATGATATTTTA
* * *
577038 TGTTAATTTTTATAAATTTACGTTAATATTATATAAATTCAAATTAAGCATATGTGATATTTTAT
1 TGTTAATTTTTATAAATTTAAGTTAATATTATATAAATTCAAATTAAGCATATGTGATATTTAAA
* *
577103 TTTAATTTTTATACATTTATATTAATAATATATAAAATTC-AATTAAGCTTACATGATATTTTA
66 GTTAATTTTTATACATTTACATTAATAATATAT-AAATTCAAATTAAGCTT--ATGATATTTTA
** * * * *
577166 CATTAATTTTTATACATTAAAGTTAATATTGTTATATAAATTTAAATTAAACATATGTGATA
1 TGTTAATTTTTATAAATTTAAGTTAATA---TTATATAAATTCAAATTAAGCATATGTGATA
577228 GGAAAACTTG
Statistics
Matches: 164, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
125 14 0.09
126 47 0.29
127 35 0.21
128 39 0.24
131 29 0.18
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (126 bp):
TGTTAATTTTTATAAATTTAAGTTAATATTATATAAATTCAAATTAAGCATATGTGATATTTAAA
GTTAATTTTTATACATTTACATTAATAATATATAAATTCAAATTAAGCTTATGATATTTTA
Found at i:578278 original size:36 final size:36
Alignment explanation
Indices: 578230--578299 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
578220 TTTAGTCCAT
* *
578230 TTTATTCTGAGTTTTAGTTAGTTTAGTTTTCAGGAG
1 TTTATTCGGAGTTTTAGTTAGTTTAGCTTTCAGGAG
578266 TTTATTCGGAGTTTTAGTTAGTTTAGCTTTCAGG
1 TTTATTCGGAGTTTTAGTTAGTTTAGCTTTCAGG
578300 GAAGTTAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.19, C:0.07, G:0.23, T:0.51
Consensus pattern (36 bp):
TTTATTCGGAGTTTTAGTTAGTTTAGCTTTCAGGAG
Found at i:580644 original size:21 final size:20
Alignment explanation
Indices: 580627--580890 Score: 82
Period size: 21 Copynumber: 12.3 Consensus size: 20
580617 AATATTTATG
580627 TTAATAATATATAAATTTAAA
1 TTAAT-ATATATAAATTTAAA
*
580648 TTACATATATATGATATTTAAA
1 TTA-ATATATAT-AAATTTAAA
* * * *
580670 GTTAATTTTTATACATTTACA
1 -TTAATATATATAAATTTAAA
580691 TTAATAATATATAAATTTTAAA
1 TTAAT-ATATATAAA-TTTAAA
* * * * **
580713 TTACACACATTTGATATTTTATG
1 TTA-ATATATAT-A-AATTTAAA
* * *
580736 TTAAT-TCTTATACATTTAAG
1 TTAATAT-ATATAAATTTAAA
*
580756 TTAATAATATATAAATTCAAA
1 TTAAT-ATATATAAATTTAAA
* * *
580777 TTAAACATATATGATATTTTACA
1 TT-AATATATAT-A-AATTTAAA
* * *
580800 TTAAT-TCTTATACATTTATA
1 TTAATAT-ATATAAATTTAAA
* *
580820 TTAATAATATATAAAATTCAA
1 TTAAT-ATATATAAATTTAAA
** *
580841 TTGAGCATATATAATATTTTATA
1 TT-AATATATATAA-A-TTTAAA
* * *
580864 TTAATTTATATACATTAAAA
1 TTAATATATATAAATTTAAA
580884 TTAATAT
1 TTAATAT
580891 TATTATATAA
Statistics
Matches: 171, Mismatches: 52, Indels: 41
0.65 0.20 0.16
Matches are distributed among these distances:
20 35 0.20
21 61 0.36
22 50 0.29
23 24 0.14
24 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (20 bp):
TTAATATATATAAATTTAAA
Found at i:580811 original size:64 final size:63
Alignment explanation
Indices: 580627--580923 Score: 314
Period size: 64 Copynumber: 4.6 Consensus size: 63
580617 AATATTTATG
* * * * *
580627 TTAATAATATATAAATTTAAATTACATATATATGATA-TTTAAAGTTAATTTTTATACATTTACA
1 TTAATAATATATAAATTCAAATTAAACATATATGATATTTTATA-TTAATTCTTATACATTTA-A
* * * * *
580691 TTAATAATATATAAATTTTAAATTACACACATTTGATATTTTATGTTAATTCTTATACATTTAA
1 TTAATAATATATAAA-TTCAAATTAAACATATATGATATTTTATATTAATTCTTATACATTTAA
*
580755 GTTAATAATATATAAATTCAAATTAAACATATATGATATTTTACATTAATTCTTATACATTTATA
1 -TTAATAATATATAAATTCAAATTAAACATATATGATATTTTATATTAATTCTTATACATTTA-A
* * * *
580820 TTAATAATATATAAAATTC-AATTGAGCATATATAATATTTTATATTAATT-TATATACATTAAA
1 TTAATAATATAT-AAATTCAAATTAAACATATATGATATTTTATATTAATTCT-TATACATT-TA
580883 A
63 A
*
580884 TTAATATTATTATATAAATT-AACATTAAACATATGTGATA
1 TTAATA--A-TATATAAATTCAA-ATTAAACATATATGATA
580924 GGAAATCTTG
Statistics
Matches: 200, Mismatches: 21, Indels: 21
0.83 0.09 0.09
Matches are distributed among these distances:
63 1 0.00
64 111 0.56
65 59 0.29
66 11 0.05
67 18 0.09
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (63 bp):
TTAATAATATATAAATTCAAATTAAACATATATGATATTTTATATTAATTCTTATACATTTAA
Found at i:580918 original size:129 final size:126
Alignment explanation
Indices: 580627--580918 Score: 322
Period size: 129 Copynumber: 2.2 Consensus size: 126
580617 AATATTTATG
* *
580627 TTAATAATATATAAATTTAAATTACATATATATGATATTTAAAGTTAATTTTTATACATTTACAT
1 TTAATAATATATAAA-TTAAATTA-A-ACATATGATATTTAAAGTTAATTCTTATACATTTACAT
* * * * * *
580692 TAATAATATATAAATTTTAAATTACACACATTTGATATTTTATGTTAATTCTTATACATTTAAG
63 TAATAATATATAAATATTAAATTACACACATATAATATTTTATATTAATTCTTATACATTAAAA
* *
580756 TTAATAATATATAAATTCAAATTAAACATATATGATATTTTACA-TTAATTCTTATACATTTATA
1 TTAATAATATATAAATT-AAATTAAAC--ATATGATA-TTTAAAGTTAATTCTTATACATTTACA
* * *
580820 TTAATAATATATAAA-ATTCAATTGA-GCATATATAATATTTTATATTAATT-TATATACATTAA
62 TTAATAATATATAAATATTAAATT-ACACACATATAATATTTTATATTAATTCT-TATACATTAA
580882 AA
125 AA
580884 TTAATATTATTATATAAATTAACATTAAACATATG
1 TTAATA--A-TATATAAATTAA-ATTAAACATATG
580919 TGATAGGAAA
Statistics
Matches: 140, Mismatches: 13, Indels: 20
0.81 0.08 0.12
Matches are distributed among these distances:
127 2 0.01
128 45 0.32
129 68 0.49
130 8 0.06
131 17 0.12
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (126 bp):
TTAATAATATATAAATTAAATTAAACATATGATATTTAAAGTTAATTCTTATACATTTACATTAA
TAATATATAAATATTAAATTACACACATATAATATTTTATATTAATTCTTATACATTAAAA
Found at i:581664 original size:48 final size:48
Alignment explanation
Indices: 581592--581698 Score: 144
Period size: 48 Copynumber: 2.2 Consensus size: 48
581582 TTTATTCTCA
* *
581592 AAAGAGTTT-TTCTCTGTATCTGAATTTGGAGAAATCTTTACAATCCCT
1 AAAGA-TTTCTTCTCAGTATCTGAATTTGAAGAAATCTTTACAATCCCT
* * **
581640 AAAGATTTCTTCTCAGTATTTGAATTTGAAGAAATCTTTATAATTTCT
1 AAAGATTTCTTCTCAGTATCTGAATTTGAAGAAATCTTTACAATCCCT
581688 AAAGATTTCTT
1 AAAGATTTCTT
581699 TTCTAAGGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 3 0.06
48 49 0.94
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (48 bp):
AAAGATTTCTTCTCAGTATCTGAATTTGAAGAAATCTTTACAATCCCT
Found at i:581703 original size:15 final size:15
Alignment explanation
Indices: 581683--581713 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
581673 ATCTTTATAA
581683 TTTCTAAAGATTTCT
1 TTTCTAAAGATTTCT
*
581698 TTTCTAAGGATTTCT
1 TTTCTAAAGATTTCT
581713 T
1 T
581714 CTCAATTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.55
Consensus pattern (15 bp):
TTTCTAAAGATTTCT
Found at i:583527 original size:252 final size:252
Alignment explanation
Indices: 583019--584041 Score: 1124
Period size: 252 Copynumber: 4.1 Consensus size: 252
583009 TTGACAATGT
* * * *
583019 TTATTTCAATTTTATGAC-TTTTTAC-TTGTATTTTTATAAATTTACATCAAGATTTTTAAAAGG
1 TTATTTCAACTTTATGACTTTTTTACATT-CATTCTTATAAATTTACATCAAGATTTTTAAATGG
* *
583082 TTAATTTTCATTACAAGTGTTTTTATTTTTATGTTTACACATTTATAAATTAAAATTTTAAATGA
65 TTAATTTTCATTACAAGTGTTTTTATTTTTATGCTTATACATTTATAAATTAAAATTTTAAATGA
* * *
583147 TTAAA-ATTTTTA-CTTCAAAAATATAAATATAATTTATTAATTTTCACTTAAAGTATATTTACT
130 TTAAATTTTTTTAGC-TCAAAAATATAAATATAAATGATTAATTTTCACTTAAAGTATATTTACT
* * * *
583210 TTATTTGAA-TGACTTGTTGCAATAACTATTATACATTTACATCAATATTTTTATAATAT
194 TTATTT-AATTGACTTGTTACAATAACTATTATACATTTACGTCAATATTTTAATAATAC
* * * *
583269 TTATTTCAACTTTATGA-TTGTTTACATACATTCTTGTAAATTTACATCAAAATTTTTAAATGGT
1 TTATTTCAACTTTATGACTTTTTTACATTCATTCTTATAAATTTACATCAAGATTTTTAAATGGT
* * *
583333 TAATTTTCATTACAAGTGTTTTTATTTTTATGCTTATACAATTATAACTTTAAACTTTTAAATGA
66 TAATTTTCATTACAAGTGTTTTTATTTTTATGCTTATACATTTATAA-ATTAAAATTTTAAATGA
*
583398 TTAAATTTTTTTAGCTCAAAAATATAAATATAAATTATTAATTTTCACTTAAAGTATATTTACTT
130 TTAAATTTTTTTAGCTCAAAAATATAAATATAAATGATTAATTTTCACTTAAAGTATATTTACTT
*** * * * **
583463 TATTTAATTGACTTGTTATGGTAACTTTTATAGATTTACGTTAATATTTTAACCATAC
195 TATTTAATTGACTTGTTACAATAACTATTATACATTTACGTCAATATTTTAATAATAC
* *
583521 TTATTTCAACTTTATGA-TTTTTTA-AGTTTATTCTTATAAACTTA-AGTCAAGATTTTTAAATG
1 TTATTTCAACTTTATGACTTTTTTACA-TTCATTCTTATAAATTTACA-TCAAGATTTTTAAATG
* ** ** * *
583583 G-TAATTTTTATTGTAAGTGTTTTTATTTTTATTATCATGCATTTATAAATTAAAATTTTTAAAT
64 GTTAATTTTCATTACAAGTGTTTTTATTTTTATGCTTATACATTTATAAATTAAAA-TTTTAAAT
* ** * * *
583647 GGTTAAATATTTTTT-GCTTGACAATATAAATATAAATGATCAATATTCAC-TAAAGGTAT-TTT
128 GATTAAAT-TTTTTTAGCTCAAAAATATAAATATAAATGATTAATTTTCACTTAAA-GTATATTT
* * * * * * *
583709 ATTTTGTCTAAATTGACTTGTTACAATAACTCTTACACATTTAAGTCAATATTTTAGTAATAC
191 ACTTTAT-TTAATTGACTTGTTACAATAACTATTATACATTTACGTCAATATTTTAATAATAC
* * * * * * *
583772 TTATTTCAACTTTATTATTTTTTTACATTCATTCTGATAAATTTATATCAATATTTTTAACTAGT
1 TTATTTCAACTTTATGACTTTTTTACATTCATTCTTATAAATTTACATCAAGATTTTTAAATGGT
* *
583837 TAATTTT-ATTTACAAGTGTTTTTATTTTTATTCTTATACATTTATAAATTAAAATTTATAATTG
66 TAATTTTCA-TTACAAGTGTTTTTATTTTTATGCTTATACATTTATAAATTAAAATTT-TAAATG
* * * *
583901 ATTAAATTTTTTTAACTCAAAAATATAAATAGAAATGATTAATTCTT-ACTTAAAATATGTTTAT
129 ATTAAATTTTTTTAGCTCAAAAATATAAATATAAATGATTAATT-TTCACTTAAAGTATATTTA-
** * * * * * *
583965 TCTTGCTTCAATTAACTTGTTACCAA-AATTCTTACACACTTACGTCAATATTTTAATAATAC
192 -CTTTATTTAATTGACTTGTTA-CAATAACTATTATACATTTACGTCAATATTTTAATAATAC
* *
584027 TTATTTTAACCTTAT
1 TTATTTCAACTTTAT
584042 AATTGTTTGC
Statistics
Matches: 651, Mismatches: 97, Indels: 45
0.82 0.12 0.06
Matches are distributed among these distances:
250 114 0.18
251 171 0.26
252 203 0.31
253 89 0.14
254 10 0.02
255 58 0.09
256 6 0.01
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.49
Consensus pattern (252 bp):
TTATTTCAACTTTATGACTTTTTTACATTCATTCTTATAAATTTACATCAAGATTTTTAAATGGT
TAATTTTCATTACAAGTGTTTTTATTTTTATGCTTATACATTTATAAATTAAAATTTTAAATGAT
TAAATTTTTTTAGCTCAAAAATATAAATATAAATGATTAATTTTCACTTAAAGTATATTTACTTT
ATTTAATTGACTTGTTACAATAACTATTATACATTTACGTCAATATTTTAATAATAC
Found at i:583906 original size:504 final size:502
Alignment explanation
Indices: 583019--583963 Score: 1261
Period size: 504 Copynumber: 1.9 Consensus size: 502
583009 TTGACAATGT
* * *
583019 TTATTTCAATTTTATGACTTTTTACTTGTATTTTTATAAATTTACATCAAGATTTTTAAAAGGTT
1 TTATTTCAACTTTATGACTTTTTACTTGTATTCTTATAAACTTACATCAAGATTTTTAAAAGGTT
*
583084 AATTTTCATTACAAGTGTTTTTATTTTTATGTTTACACATTTATAAATTAAAATTTTAAATGATT
66 AATTTTCATTACAAGTGTTTTTATTTTTATGTATACACATTTATAAATTAAAATTTTAAATGATT
* * * *
583149 AAAATTTTTACTTCAAAAATATAAATATAATTTATTAATTTTCACTTAAAGTATATTTACTTTAT
131 AAAATTTTTACTTCAAAAATATAAATATAAATGATCAATATTCACTTAAAGTATATTTACTTTAT
* * * * *
583214 TTGAATGACTTGTTGCAATAACTATTATACATTTACATCAATATTTTTATAATATTTATTTCAAC
196 CTAAATGACTTGTTACAATAACTATTACACATTTACATCAATATTTTTATAATACTTATTTCAAC
*
583279 TTTATGATTGTTTACATACATTCTTGTAAATTTACATCAAAATTTTTAAATGGTTAATTTTCATT
261 TTTATGATTGTTTACATACATTCTTGTAAATTTACATCAAAATTTTTAAATAGTTAATTTTCATT
* *
583344 ACAAGTGTTTTTATTTTTATGCTTATACAATTATAACTTTAAACTTTTAAATGATTAAATTTTTT
326 ACAAGTGTTTTTATTTTTATGCTTATACAATTATAACATTAAAATTTTAAATGATTAAATTTTTT
* * * *
583409 TAGCTCAAAAATATAAATATAAATTATTAATT-TTCACTTAAAGTATATTTACTTTATTTAATTG
391 TAACTCAAAAATATAAATAGAAATGATTAATTCTT-ACTTAAAATATATTTACTTTATTTAATTG
583473 ACTTGTTATGGTAACTTTTATAGATTTACGTTAATATTTTAACCATAC
455 ACTTGTTATGGTAACTTTTATAGATTTACGTTAATATTTTAACCATAC
* * *
583521 TTATTTCAACTTTATGATTTTTTAAGTT-TATTCTTATAAACTTA-AGTCAAGATTTTTAAATGG
1 TTATTTCAACTTTATGACTTTTT-ACTTGTATTCTTATAAACTTACA-TCAAGATTTTTAAAAGG
* **
583584 -TAATTTTTATTGTAAGTGTTTTTATTTTTAT-TAT-CATGCATTTATAAATTAAAATTTTTAAA
64 TTAATTTTCATTACAAGTGTTTTTATTTTTATGTATACA--CATTTATAAATTAAAA-TTTTAAA
* * * *
583646 TGGTTAAATATTTTTTGCTT-GACAATATAAATATAAATGATCAATATTCAC-TAAAGGTAT-TT
126 TGATTAAA-A-TTTTTACTTCAAAAATATAAATATAAATGATCAATATTCACTTAAA-GTATATT
* * *
583708 TATTTTGTCTAAATTGACTTGTTACAATAACTCTTACACATTTA-AGTCAATA-TTTTAGTAATA
188 TACTTTATCTAAA-TGACTTGTTACAATAACTATTACACATTTACA-TCAATATTTTTA-TAATA
* * * * * *
583771 CTTATTTCAACTTTATTATTTTTTTACATTCATTC-TGATAAATTTATATCAATATTTTTAACTA
250 CTTATTTCAACTTTATGA-TTGTTTACATACATTCTTG-TAAATTTACATCAAAATTTTTAAATA
* *
583835 GTTAATTTT-ATTTACAAGTGTTTTTATTTTTATTCTTATACATTTATAA-ATTAAAATTTATAA
313 GTTAATTTTCA-TTACAAGTGTTTTTATTTTTATGCTTATACAATTATAACATTAAAATTT-TAA
* *
583898 TTGATTAAATTTTTTTAACTCAAAAATATAAATAGAAATGATTAATTCTTACTTAAAATATGTTT
376 ATGATTAAATTTTTTTAACTCAAAAATATAAATAGAAATGATTAATTCTTACTTAAAATATATTT
583963 A
441 A
583964 TTCTTGCTTC
Statistics
Matches: 384, Mismatches: 43, Indels: 30
0.84 0.09 0.07
Matches are distributed among these distances:
499 2 0.01
500 2 0.01
501 45 0.12
502 86 0.22
503 98 0.26
504 149 0.39
505 2 0.01
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (502 bp):
TTATTTCAACTTTATGACTTTTTACTTGTATTCTTATAAACTTACATCAAGATTTTTAAAAGGTT
AATTTTCATTACAAGTGTTTTTATTTTTATGTATACACATTTATAAATTAAAATTTTAAATGATT
AAAATTTTTACTTCAAAAATATAAATATAAATGATCAATATTCACTTAAAGTATATTTACTTTAT
CTAAATGACTTGTTACAATAACTATTACACATTTACATCAATATTTTTATAATACTTATTTCAAC
TTTATGATTGTTTACATACATTCTTGTAAATTTACATCAAAATTTTTAAATAGTTAATTTTCATT
ACAAGTGTTTTTATTTTTATGCTTATACAATTATAACATTAAAATTTTAAATGATTAAATTTTTT
TAACTCAAAAATATAAATAGAAATGATTAATTCTTACTTAAAATATATTTACTTTATTTAATTGA
CTTGTTATGGTAACTTTTATAGATTTACGTTAATATTTTAACCATAC
Found at i:584195 original size:43 final size:43
Alignment explanation
Indices: 584113--584195 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
584103 TACATTTACA
* * * *
584113 TTAATAATACATAAATTCATATTAAGTATATGTGGTATTTAGG
1 TTAATAATACATAAATTCAAATTAAGCATATATGATATTTAGG
*
584156 TTAATAATATATAAATTCAAATTACA-CATATATGATATTT
1 TTAATAATACATAAATTCAAATTA-AGCATATATGATATTT
584196 TATATTAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 33 0.97
44 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.42
Consensus pattern (43 bp):
TTAATAATACATAAATTCAAATTAAGCATATATGATATTTAGG
Found at i:584224 original size:64 final size:63
Alignment explanation
Indices: 584149--585476 Score: 938
Period size: 64 Copynumber: 20.5 Consensus size: 63
584139 TATATGTGGT
* *
584149 ATTTAGGTTAATAATATATAAATTCAAATTACACATATATGATATTTTATATTAATTCTTATAC
1 ATTTACGTTAATAATATATAAATTCAAATTA-ACATATGTGATATTTTATATTAATTCTTATAC
* * * * * * *
584213 ATTTACATTAATATTATATAAATTCAAATTAAACTTATCTGATACTTTATCTTAATTTTTATAC
1 ATTTACGTTAATAATATATAAATTCAAATT-AACATATGTGATATTTTATATTAATTCTTATAC
* * *
584277 ATTTACGTTAATAATATATAAATTCAAATTAAGTATATGTGATATTTTATGTTAAATCTTATAC
1 ATTTACGTTAATAATATATAAATTCAAATTAA-CATATGTGATATTTTATATTAATTCTTATAC
* * * * *
584341 ATTTACAG-TAATAATTTATAAATTCAAATGAAACATATATGATATTTTACATTAATTCTTTTAC
1 ATTTAC-GTTAATAATATATAAATTCAAAT-TAACATATGTGATATTTTATATTAATTCTTATAC
** * * * * * *
584405 ATTTATTTTAATAATATAAAAATTTAAATTAAATATATGTTATATTTTACATTAATTTTTATAC
1 ATTTACGTTAATAATATATAAATTCAAATT-AACATATGTGATATTTTATATTAATTCTTATAC
* * * *
584469 AGTTATGTTAATAATATATAAATTCAAATTACACATATGTGATATTTTATGTTAATTCTTATAT
1 ATTTACGTTAATAATATATAAATTCAAATTA-ACATATGTGATATTTTATATTAATTCTTATAC
* * * *
584533 ATTTACGTTAATAGTATATAAATTCAAAGTAAGCATATGTGATGTTTTACT-TTAATCCTTATAC
1 ATTTACGTTAATAATATATAAATTCAAATTAA-CATATGTGATATTTTA-TATTAATTCTTATAC
* * * *
584597 ATTTACGTTAATAATATATAAAATT-AAATTAAGAATATGTGATCTTTTACATTAATTCTTTTAC
1 ATTTACGTTAATAATATAT-AAATTCAAATTAA-CATATGTGATATTTTATATTAATTCTTATAC
* * * * ** *
584661 ATTTAGGTTAATAATATATAAATTGAAGTTAAGTATATGTGATATTTTACGTTAATTCTTATAT
1 ATTTACGTTAATAATATATAAATTCAAATTAA-CATATGTGATATTTTATATTAATTCTTATAC
* * * * * * *
584725 ATTTAGGTTGATAATATCTAAATTAAAATTACACATATGTAATATTTTATGTTAATTTTTATAC
1 ATTTACGTTAATAATATATAAATTCAAATTA-ACATATGTGATATTTTATATTAATTCTTATAC
* * * * **
584789 ATTTATGGTAATAGTATATAAATTCAAATGAAGCATATGTGATATTTTATGCTAATTCTTATAC
1 ATTTACGTTAATAATATATAAATTCAAATTAA-CATATGTGATATTTTATATTAATTCTTATAC
* * * * ** *
584853 ATTTAAGTTAATAATAT-TAAATGCAAATTAAGCATATGTGATATGTTACATTCGTTTTTATAC
1 ATTTACGTTAATAATATATAAATTCAAATTAA-CATATGTGATATTTTATATTAATTCTTATAC
* ** * * *
584916 ATTTATGTTAATAATATATAAATTCGTATTAAGCATATGTAATATTTAACATTAATTGC-TATAC
1 ATTTACGTTAATAATATATAAATTCAAATTAA-CATATGTGATATTTTATATTAATT-CTTATAC
* * * * ** * **
584980 ATTTACGTTATGTGATATTAATAATATAT-AAATT--CATACTTTTA-ATAATATATAAATTCAA
1 ATTTACGTTA-ATAATA-T-ATAA-AT-TCAAATTAACATA-TGTGATATTTTATATTAATTCTT
585041 ATTAC
60 A-TAC
* * * *
585046 ATATATGCGATATTTAATGTTAATTTTTAATAATTTATAATTAA-ATTATGCAT-ATGTGATAAT
1 AT-T-TACG----TTAA---TAATATAT-A-AATTCA-AATTAACA-TATG--TGA--T-AT--T
* *
585109 TTATGTCAATTCTTATAC
46 TTATATTAATTCTTATAC
* * * * * *
585127 ATTTAGGTTAATAATATATAAATTCAAATGGAGCATAAT-TGATATTTTATGTTAATTCCTATAT
1 ATTTACGTTAATAATATATAAATTCAAAT-TAACAT-ATGTGATATTTTATATTAATTCTTATAC
* * ** *
585191 ATTTACTTTAATAATATATAAATTCATATTAAGTGTATGTAATATTTT-TACGTTAATTCTTATA
1 ATTTACGTTAATAATATATAAATTCAAATTAA-CATATGTGATATTTTATA--TTAATTCTTATA
585255 C
63 C
* * ** * * ** *
585256 ATTTATGTTAGTAATATATAAATTTGAGTTAAGTATATGTGATATTTTACCTTAATTTTTATAC
1 ATTTACGTTAATAATATATAAATTCAAATTAA-CATATGTGATATTTTATATTAATTCTTATAC
* * *** *** * *
585320 ATTTATGTTAATAAAATATAAATTTGGATTAAACATATGTGATATTTTGCCTTAATTTTTACAC
1 ATTTACGTTAATAATATATAAATTCAAATT-AACATATGTGATATTTTATATTAATTCTTATAC
* * * ** ** ** * *
585384 ATTTACATTAATAATATATAAATGCAAATTGAGCATATGCAATATTGAACGTTAATTTTTATAT
1 ATTTACGTTAATAATATATAAATTCAAATT-AACATATGTGATATTTTATATTAATTCTTATAC
**
585448 ATTTATATTAATAATATATAAATT-AAATT
1 ATTTACGTTAATAATATATAAATTCAAATT
585477 TAGTATATAT
Statistics
Matches: 1014, Mismatches: 192, Indels: 117
0.77 0.15 0.09
Matches are distributed among these distances:
63 72 0.07
64 765 0.75
65 81 0.08
66 11 0.01
67 6 0.01
68 9 0.01
69 5 0.00
70 7 0.01
71 4 0.00
72 11 0.01
73 5 0.00
74 8 0.01
75 6 0.01
76 3 0.00
77 1 0.00
79 2 0.00
80 3 0.00
81 5 0.00
82 10 0.01
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.46
Consensus pattern (63 bp):
ATTTACGTTAATAATATATAAATTCAAATTAACATATGTGATATTTTATATTAATTCTTATAC
Found at i:584232 original size:21 final size:21
Alignment explanation
Indices: 584208--584296 Score: 51
Period size: 21 Copynumber: 4.2 Consensus size: 21
584198 TATTAATTCT
584208 TATACATTTACATTAATATTA
1 TATACATTTACATTAATATTA
* * *
584229 TATAAATTCAAATTAA-ACTTA
1 TATACATTTACATTAATA-TTA
*
584250 TCTGATAC-TTTATC-TTAAT-TTT
1 --T-ATACATTTA-CATTAATATTA
* *
584272 TATACATTTACGTTAATAATA
1 TATACATTTACATTAATATTA
584293 TATA
1 TATA
584297 AATTCAAATT
Statistics
Matches: 50, Mismatches: 9, Indels: 18
0.65 0.12 0.23
Matches are distributed among these distances:
19 5 0.10
20 11 0.22
21 21 0.42
22 2 0.04
23 8 0.16
24 3 0.06
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.47
Consensus pattern (21 bp):
TATACATTTACATTAATATTA
Found at i:584294 original size:128 final size:128
Alignment explanation
Indices: 584149--585476 Score: 1051
Period size: 128 Copynumber: 10.2 Consensus size: 128
584139 TATATGTGGT
* *
584149 ATTTAGGTTAATAATATATAAATTCAAATTACA-CATATATGATATTTTATATTAATTCTTATAC
1 ATTTATGTTAATAATATATAAATTCAAATTA-AGCATATGTGATATTTTATATTAATTCTTATAC
* * * *
584213 ATTTACATTAATATTATATAAATTCAAATTAAACTTATCTGATACTTTATCTTAATTTTTATAC
65 ATTTACATTAATAATATATAAATTCAAATTAAACATATGTGATATTTTATCTTAATTTTTATAC
* * * *
584277 ATTTACGTTAATAATATATAAATTCAAATTAAGTATATGTGATATTTTATGTTAAATCTTATACA
1 ATTTATGTTAATAATATATAAATTCAAATTAAGCATATGTGATATTTTATATTAATTCTTATACA
* * * *
584342 TTTACAGTAATAATTTATAAATTCAAATGAAACATATATGATATTTTA-CATTAATTCTTT-TAC
66 TTTACATTAATAATATATAAATTCAAATTAAACATATGTGATATTTTATC-TTAATT-TTTATAC
* * * ** * * *
584405 ATTTATTTTAATAATATAAAAATTTAAATTAAATATATGTTATATTTTACATTAATTTTTATACA
1 ATTTATGTTAATAATATATAAATTCAAATTAAGCATATGTGATATTTTATATTAATTCTTATACA
* ** * * * *
584470 GTTATGTTAATAATATATAAATTCAAATTACACATATGTGATATTTTATGTTAATTCTTATAT
66 TTTACATTAATAATATATAAATTCAAATTAAACATATGTGATATTTTATCTTAATTTTTATAC
* * * * *
584533 ATTTACGTTAATAGTATATAAATTCAAAGTAAGCATATGTGATGTTTTACT-TTAATCCTTATAC
1 ATTTATGTTAATAATATATAAATTCAAATTAAGCATATGTGATATTTTA-TATTAATTCTTATAC
* *
584597 ATTTACGTTAATAATATATAAAATT-AAATTAAGA-ATATGTGATCTTTTA-CATTAATTCTTT-
65 ATTTACATTAATAATATAT-AAATTCAAATTAA-ACATATGTGATATTTTATC-TTAATT-TTTA
584658 TAC
126 TAC
* * * * ** *
584661 ATTTAGGTTAATAATATATAAATTGAAGTTAAGTATATGTGATATTTTACGTTAATTCTTATATA
1 ATTTATGTTAATAATATATAAATTCAAATTAAGCATATGTGATATTTTATATTAATTCTTATACA
** * * * * * *
584726 TTTAGGTTGATAATATCTAAATTAAAATTACACATATGTAATATTTTATGTTAATTTTTATAC
66 TTTACATTAATAATATATAAATTCAAATTAAACATATGTGATATTTTATCTTAATTTTTATAC
* * * **
584789 ATTTATGGTAATAGTATATAAATTCAAATGAAGCATATGTGATATTTTATGCTAATTCTTATACA
1 ATTTATGTTAATAATATATAAATTCAAATTAAGCATATGTGATATTTTATATTAATTCTTATACA
* * * **
584854 TTTA-AGTTAATAATAT-TAAATGCAAATTAAGCATATGTGATATGTTA-CATTCGTTTTTATAC
66 TTTACA-TTAATAATATATAAATTCAAATTAAACATATGTGATATTTTATC-TTAATTTTTATAC
** * * *
584916 ATTTATGTTAATAATATATAAATTCGTATTAAGCATATGTAATATTTAACATTAATTGC-TATAC
1 ATTTATGTTAATAATATATAAATTCAAATTAAGCATATGTGATATTTTATATTAATT-CTTATAC
* * * * **
584980 ATTTACGTTATGTGATATTAATAATATATAAATTCATACTTTTAATA-ATATAT-A-AATTCAAA
65 ATTTAC----------ATTAATAATATATAAATTCA-A--ATTAA-ACATATGTGATATTTTATC
* *** *
585042 TTACATATATGCGAT
116 TTA-AT-TTTTATAC
* * * * *
585057 ATTTAATGTTAATTTTTAATAATTTATAATT-AAATTATGCATATGTGATAATTTATGTCAATTC
1 ATTT-ATGTTAA----TAAT-ATATA-AATTCAAATTAAGCATATGTGATATTTTATATTAATTC
** ** * * *
585121 TTATACATTTAGGTTAATAATATATAAATTCAAATGGAGCATAAT-TGATATTTTATGTTAATTC
59 TTATACATTTACATTAATAATATATAAATTCAAATTAAACAT-ATGTGATATTTTATCTTAATTT
* *
585185 CTATAT
123 TTATAC
* ** *
585191 ATTTACT-TTAATAATATATAAATTCATATTAAGTGTATGTAATATTTT-TACGTTAATTCTTAT
1 ATTTA-TGTTAATAATATATAAATTCAAATTAAGCATATGTGATATTTTATA--TTAATTCTTAT
** * ** * ** *
585254 ACATTTATGTTAGTAATATATAAATTTGAGTTAAGTATATGTGATATTTTACCTTAATTTTTATA
63 ACATTTACATTAATAATATATAAATTCAAATTAAACATATGTGATATTTTATCTTAATTTTTATA
585319 C
128 C
* *** * *** * *
585320 ATTTATGTTAATAAAATATAAATTTGGATTAAACATATGTGATATTTTGCCTTAATTTTTACACA
1 ATTTATGTTAATAATATATAAATTCAAATTAAGCATATGTGATATTTTATATTAATTCTTATACA
* * * ** * * *
585385 TTTACATTAATAATATATAAATGCAAATTGAGCATATGCAATA-TTGAACGTTAATTTTTATAT
66 TTTACATTAATAATATATAAATTCAAATTAAACATATGTGATATTTTATC-TTAATTTTTATAC
*
585448 ATTTATATTAATAATATATAAATT-AAATT
1 ATTTATGTTAATAATATATAAATTCAAATT
585477 TAGTATATAT
Statistics
Matches: 950, Mismatches: 193, Indels: 115
0.76 0.15 0.09
Matches are distributed among these distances:
127 118 0.12
128 574 0.60
129 113 0.12
133 5 0.01
134 13 0.01
135 5 0.01
136 8 0.01
137 29 0.03
138 8 0.01
139 6 0.01
140 2 0.00
141 16 0.02
142 7 0.01
146 5 0.01
147 37 0.04
148 4 0.00
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.46
Consensus pattern (128 bp):
ATTTATGTTAATAATATATAAATTCAAATTAAGCATATGTGATATTTTATATTAATTCTTATACA
TTTACATTAATAATATATAAATTCAAATTAAACATATGTGATATTTTATCTTAATTTTTATAC
Found at i:584484 original size:192 final size:192
Alignment explanation
Indices: 584149--585484 Score: 1147
Period size: 192 Copynumber: 6.9 Consensus size: 192
584139 TATATGTGGT
* * *
584149 ATTTAGGTTAATAATATATAAATTCAAATTACACATATATGATATTTTATATTAATTCTTATACA
1 ATTTAGGTTAATAATATATAAATTCAAATTAAACATATGTGATATTTTACATTAATTCTTATACA
* * * *
584214 TTTACATTAATATTATATAAATTCAAATTAAACT-TATCTGATACTTTATC-TTAATTTTTATAC
66 TTTACTTTAATAATATATAAATTCAAATTAAA-TATATGTGATATTTTA-CATTAATTTTTATAC
* * *
584277 ATTTACGTTAATAATATATAAATTCAAATTAAGTATATGTGATATTTTATGTTAAATCTTATAC
129 ATTTATGTTAATAATATATAAATTCAAATTAAGTATATGTGATATTTTACGTTAATTCTTATAC
* * * * *
584341 ATTTACAG-TAATAATTTATAAATTCAAATGAAACATATATGATATTTTACATTAATTCTTTTAC
1 ATTTA-GGTTAATAATATATAAATTCAAATTAAACATATGTGATATTTTACATTAATTCTTATAC
* * * *
584405 ATTTATTTTAATAATATAAAAATTTAAATTAAATATATGTTATATTTTACATTAATTTTTATACA
65 ATTTACTTTAATAATATATAAATTCAAATTAAATATATGTGATATTTTACATTAATTTTTATACA
* * * *
584470 GTTATGTTAATAATATATAAATTCAAATTACA-CATATGTGATATTTTATGTTAATTCTTATAT
130 TTTATGTTAATAATATATAAATTCAAATTA-AGTATATGTGATATTTTACGTTAATTCTTATAC
* * * * * * *
584533 ATTTACGTTAATAGTATATAAATTCAAAGTAAGCATATGTGATGTTTTACTTTAATCCTTATACA
1 ATTTAGGTTAATAATATATAAATTCAAATTAAACATATGTGATATTTTACATTAATTCTTATACA
* *
584598 TTTACGTTAATAATATATAAAATT-AAATTAAGA-ATATGTGATCTTTTACATTAATTCTTT-TA
66 TTTACTTTAATAATATAT-AAATTCAAATTAA-ATATATGTGATATTTTACATTAATT-TTTATA
* * * *
584660 CATTTAGGTTAATAATATATAAATTGAAGTTAAGTATATGTGATATTTTACGTTAATTCTTATAT
128 CATTTATGTTAATAATATATAAATTCAAATTAAGTATATGTGATATTTTACGTTAATTCTTATAC
* * * * * ** *
584725 ATTTAGGTTGATAATATCTAAATTAAAATTACACATATGTAATATTTTATGTTAATTTTTATACA
1 ATTTAGGTTAATAATATATAAATTCAAATTAAACATATGTGATATTTTACATTAATTCTTATACA
* * * ** *** *
584790 TTTA-TGGTAATAGTATATAAATTCAAATGAAGCATATGTGATATTTTATGCTAATTCTTATACA
66 TTTACT-TTAATAATATATAAATTCAAATTAAATATATGTGATATTTTACATTAATTTTTATACA
* * * * * ** *
584854 TTTAAGTTAATAATAT-TAAATGCAAATTAAGCATATGTGATATGTTACATTCGTTTTTATAC
130 TTTATGTTAATAATATATAAATTCAAATTAAGTATATGTGATATTTTACGTTAATTCTTATAC
* ** * * *
584916 ATTTATGTTAATAATATATAAATTCGTATTAAGCATATGTAATATTTAACATTAATTGC-TATAC
1 ATTTAGGTTAATAATATATAAATTCAAATTAAACATATGTGATATTTTACATTAATT-CTTATAC
* * * *
584980 ATTTACGTTATGTGATATTAATAATATATAAATTCATACTTTTAATAATATAT-AAATTCAAATT
65 ATTTAC---------T-TTAATAATATATAAATTCA-A-ATTAAAT-ATATGTGATATT----TT
* ** * * * * *
585044 ACATATATGCGATATTTA-ATGTTAATTTTTAATAATTTAT-AATT-AAATTATGCATATGTGAT
113 ACAT-TA----ATTTTTATACATTTA-TGTTAATAATATATAAATTCAAATTAAGTATATGTGAT
* * *
585106 AATTTATGTCAATTCTTATAC
172 ATTTTACGTTAATTCTTATAC
** * ** * *
585127 ATTTAGGTTAATAATATATAAATTCAAATGGAGCATAAT-TGATATTTTATGTTAATTCCTATAT
1 ATTTAGGTTAATAATATATAAATTCAAATTAAACAT-ATGTGATATTTTACATTAATTCTTATAC
* * * * * *
585191 ATTTACTTTAATAATATATAAATTCATATTAAGTGTATGTAATATTTTTACGTTAATTCTTATAC
65 ATTTACTTTAATAATATATAAATTCAAATTAAATATATGTGATA-TTTTACATTAATTTTTATAC
* ** * * *
585256 ATTTATGTTAGTAATATATAAATTTGAGTTAAGTATATGTGATATTTTACCTTAATTTTTATAC
129 ATTTATGTTAATAATATATAAATTCAAATTAAGTATATGTGATATTTTACGTTAATTCTTATAC
* * *** * * * *
585320 ATTTATGTTAATAAAATATAAATTTGGATTAAACATATGTGATATTTTGCCTTAATTTTTACACA
1 ATTTAGGTTAATAATATATAAATTCAAATTAAACATATGTGATATTTTACATTAATTCTTATACA
* * * ** ** ** * *
585385 TTTACATTAATAATATATAAATGCAAATTGAGCATATGCAATATTGAACGTTAATTTTTATATAT
66 TTTACTTTAATAATATATAAATTCAAATTAAATATATGTGATATTTTACATTAATTTTTATACAT
* *
585450 TTATATTAATAATATATAAATT-AAATTTAGTATAT
131 TTATGTTAATAATATATAAATTCAAATTAAGTATAT
585485 ATATGTGACA
Statistics
Matches: 913, Mismatches: 185, Indels: 93
0.77 0.16 0.08
Matches are distributed among these distances:
191 129 0.14
192 476 0.52
193 124 0.14
195 2 0.00
196 5 0.01
198 4 0.00
199 6 0.01
200 2 0.00
201 37 0.04
202 2 0.00
203 6 0.01
204 5 0.01
207 3 0.00
208 2 0.00
210 1 0.00
211 89 0.10
212 19 0.02
213 1 0.00
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.46
Consensus pattern (192 bp):
ATTTAGGTTAATAATATATAAATTCAAATTAAACATATGTGATATTTTACATTAATTCTTATACA
TTTACTTTAATAATATATAAATTCAAATTAAATATATGTGATATTTTACATTAATTTTTATACAT
TTATGTTAATAATATATAAATTCAAATTAAGTATATGTGATATTTTACGTTAATTCTTATAC
Found at i:585271 original size:129 final size:127
Alignment explanation
Indices: 585116--585471 Score: 365
Period size: 129 Copynumber: 2.8 Consensus size: 127
585106 AATTTATGTC
* * *
585116 AATTCTTATACATTTAGGTTAATAATATATAAATTCAAATGGAGCATAATTGATATTTTATGTTA
1 AATTCTTATACATTTACGTTAATAATATATAAATTCAAATTGAGCAT-ATTGATATTTTACGTTA
** * *** *
585181 ATTCCTATATATTTACT-TTAATAATATATAAATTCATATTAAGTGTATGTAATATTTTTACGTT
65 ATTTTTATATATTTA-TATTAATAATATATAAATTCAGATTAAACATATGTAATA-TTTTACCTT
* * ** * * * *
585245 AATTCTTATACATTTATGTTAGTAATATATAAATTTGAGTTAAGTATATGTGATATTTTACCTTA
1 AATTCTTATACATTTACGTTAATAATATATAAATTCAAATTGAGCATAT-TGATATTTTACGTTA
* * * ** * *
585310 ATTTTTATACATTTATGTTAATAAAATATAAATTTGGATTAAACATATGTGATATTTTGCCTT
65 ATTTTTATATATTTATATTAATAATATATAAATTCAGATTAAACATATGTAATATTTTACCTT
* * * * **
585373 AATTTTTACACATTTACATTAATAATATATAAATGCAAATTGAGCATA-TGCAATATTGAACGTT
1 AATTCTTATACATTTACGTTAATAATATATAAATTCAAATTGAGCATATTG--ATATTTTACGTT
585437 AATTTTTATATATTTATATTAATAATATATAAATT
64 AATTTTTATATATTTATATTAATAATATATAAATT
585472 AAATTTAGTA
Statistics
Matches: 183, Mismatches: 40, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
126 2 0.01
128 88 0.48
129 93 0.51
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (127 bp):
AATTCTTATACATTTACGTTAATAATATATAAATTCAAATTGAGCATATTGATATTTTACGTTAA
TTTTTATATATTTATATTAATAATATATAAATTCAGATTAAACATATGTAATATTTTACCTT
Found at i:586110 original size:64 final size:64
Alignment explanation
Indices: 586009--586133 Score: 155
Period size: 64 Copynumber: 2.0 Consensus size: 64
585999 TATATATATA
* * *
586009 TAAATTTAAATTACGTATATGGAAAATTTAAGTTTAATTTTTATATATTGATGTTAATAATTTG
1 TAAATTTAAATTACATATATGGAAAATTTAAGTTTAATTCTTATATATTGAAGTTAATAATTTG
* * * *
586073 TAAATTTAAATTGCACATATAT-GATAATTTATG-TTAATTCTTGTATATTTAAGTTAATAAT
1 TAAATTTAAATT--ACATATATGGAAAATTTAAGTTTAATTCTTATATATTGAAGTTAATAAT
586134 ATATATATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 36 0.69
65 9 0.17
66 7 0.13
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (64 bp):
TAAATTTAAATTACATATATGGAAAATTTAAGTTTAATTCTTATATATTGAAGTTAATAATTTG
Found at i:586167 original size:138 final size:140
Alignment explanation
Indices: 585999--586278 Score: 313
Period size: 138 Copynumber: 2.0 Consensus size: 140
585989 ACATAATTTT
* * * * * * **
585999 TATATATATATAAATTTAAATTACGTATATG-GAAAATTTAAGT-TTAATTTTTATATATTGATG
1 TATATATATATAAACTCAAATAAAGCATATGTG-AAATTTAA-TATTAATTTTTATACATTGACA
* * * * *
586062 TTAATAAT-T-TGTAAATTTAAATT-GCACATATATGATAATTT-ATGTTAATTCTTGTATATTT
64 TTAATAATATATATAAATTCAAATTAAC-CATATATGAT-ATTTAATGTTAATTCTTATACATTT
586123 A-AGTTAATAATATA
127 ACA-TTAATAATATA
* *
586137 TATATATATATAAACTCAAATAAAGCATATGTGATATTTAATATTAATTTTTATACATTTACATT
1 TATATATATATAAACTCAAATAAAGCATATGTGAAATTTAATATTAATTTTTATACATTGACATT
* *
586202 AATAATATATATATATTCAAATTAACCATATGTGATATTTAATGTTAATTCTTATACATTTACAT
66 AATAATATATATAAATTCAAATTAACCATATATGATATTTAATGTTAATTCTTATACATTTACAT
586267 TAATAATATA
131 TAATAATATA
586277 TA
1 TA
586279 AATTTGAATT
Statistics
Matches: 118, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
137 1 0.01
138 57 0.48
139 6 0.05
140 52 0.44
141 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (140 bp):
TATATATATATAAACTCAAATAAAGCATATGTGAAATTTAATATTAATTTTTATACATTGACATT
AATAATATATATAAATTCAAATTAACCATATATGATATTTAATGTTAATTCTTATACATTTACAT
TAATAATATA
Found at i:586185 original size:74 final size:70
Alignment explanation
Indices: 586088--586278 Score: 223
Period size: 66 Copynumber: 2.7 Consensus size: 70
586078 TTAAATTGCA
* * *
586088 CATATATGATAATTT-ATGTTAATTCTTGTATATTTA-AGTTAATAATATATATATATATATAAA
1 CATATGTGAT-ATTTAATGTTAATTCTTATACATTTACA-TTAATAATATATATATATATAT---
*
586151 CTCAAATAAAG
61 -TCAAATAAAC
* *
586162 CATATGTGATATTTAATATTAATTTTTATACATTTACA-T--TAATA-ATATATATATATTCAAA
1 CATATGTGATATTTAATGTTAATTCTTATACATTTACATTAATAATATATATATATATATTCAAA
*
586223 TTAAC
66 TAAAC
586228 CATATGTGATATTTAATGTTAATTCTTATACATTTACATTAATAATATATA
1 CATATGTGATATTTAATGTTAATTCTTATACATTTACATTAATAATATATA
586279 AATTTGAATT
Statistics
Matches: 102, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
66 44 0.43
67 1 0.01
69 5 0.05
70 15 0.15
71 5 0.05
73 5 0.05
74 26 0.25
75 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (70 bp):
CATATGTGATATTTAATGTTAATTCTTATACATTTACATTAATAATATATATATATATATTCAAA
TAAAC
Found at i:586311 original size:64 final size:66
Alignment explanation
Indices: 586140--586341 Score: 210
Period size: 66 Copynumber: 3.1 Consensus size: 66
586130 TAATATATAT
* * * * ** *
586140 ATATATATAAACTCAAATAAAGCATATGTGATATTTAATATTAATTTTTATACATTTACATTAAT
1 ATATATATATATTCAAATTAACCATATGCCATATTTAATGTTAATTTTTATACATTTACATTAAT
586205 A
66 A
** *
586206 ATATATATATATTCAAATTAACCATATGTGATATTTAATGTTAATTCTTATACATTTACATTAAT
1 ATATATATATATTCAAATTAACCATATGCCATATTTAATGTTAATTTTTATACATTTACATTAAT
586271 A
66 A
** ** * * * * *
586272 ATATATA-A-ATTTGAATTAAGGATGTGCCATATTTTATGTTAATTTTTATATATTTTCGTTAAT
1 ATATATATATATTCAAATTAACCATATGCCATATTTAATGTTAATTTTTATACATTTACATTAAT
586335 A
66 A
*
586336 AAATAT
1 ATATAT
586342 TTAATGTTAA
Statistics
Matches: 117, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
64 49 0.42
65 1 0.01
66 67 0.57
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (66 bp):
ATATATATATATTCAAATTAACCATATGCCATATTTAATGTTAATTTTTATACATTTACATTAAT
A
Found at i:586362 original size:79 final size:78
Alignment explanation
Indices: 586274--586420 Score: 208
Period size: 79 Copynumber: 1.9 Consensus size: 78
586264 CATTAATAAT
** *
586274 ATATAAATTTGAATTAAGGAT-GTGCCATATTTTATGTTAATTTTTATATATTT-TCGTTAATAA
1 ATATAAATTTGAATTAAACATAGTG--ATATTTTATATTAATTTTTATATATTTAT-GTTAATAA
586337 AATATTTAATGTTAAC
63 AATATTTAATGTTAAC
*
586353 ATATAAATTTGAATTAAACATACGTGATATTTTATATTAATTTTTATATATTTATGTTAATAATA
1 ATATAAATTTGAATTAAACATA-GTGATATTTTATATTAATTTTTATATATTTATGTTAATAAAA
586418 TAT
65 TAT
586421 AAATTTAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
79 57 0.93
80 1 0.02
81 3 0.05
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (78 bp):
ATATAAATTTGAATTAAACATAGTGATATTTTATATTAATTTTTATATATTTATGTTAATAAAAT
ATTTAATGTTAAC
Found at i:586432 original size:64 final size:64
Alignment explanation
Indices: 586353--586707 Score: 363
Period size: 64 Copynumber: 5.5 Consensus size: 64
586343 TAATGTTAAC
* ** * * **
586353 ATATAAATTTGAATTAAACATACGTGATATTTTATATTAATTTTTATATATTTATGTTAATAAT
1 ATATAAATTTAAATTAAACATATATGATATTTTACATTAATTTTTATACATTTAAATTAATAAT
**
586417 ATATAAATTTAAATTAAACATATATGATATTTTACATTAATTCTTT-TACATTTATTTTAATAAT
1 ATATAAATTTAAATTAAACATATATGATATTTTACATTAATT-TTTATACATTTAAATTAATAAT
* * * *
586481 ATAAAAATTTAAATTAAATATATGTTATATTTTACATTAATTTTTATACA-TTAAAGTTAATATT
1 ATATAAATTTAAATTAAACATATATGATATTTTACATTAATTTTTATACATTTAAA-TTAATA--
*
586545 GTT
63 -AT
* * * *
586548 ATATAAATTTAAATTAAACATATATGATATTTTACATTAATTCTGATATATTTACATTAATAAT
1 ATATAAATTTAAATTAAACATATATGATATTTTACATTAATTTTTATACATTTAAATTAATAAT
* * * * * * * * *
586612 ATATAAAATTCAGTTGAGCATATATAATATTTTATATTAATTTATATACATTAAAATTAATATTA
1 ATATAAATTTAAATTAAACATATATGATATTTTACATTAATTTTTATACATTTAAATTAATA--A
586677 TT
64 -T
* *
586679 ATATAAATTAAAATTAAACATATGTGATA
1 ATATAAATTTAAATTAAACATATATGATA
586708 GGAAATCTTG
Statistics
Matches: 238, Mismatches: 43, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
63 6 0.03
64 152 0.64
65 3 0.01
66 1 0.00
67 72 0.30
68 4 0.02
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (64 bp):
ATATAAATTTAAATTAAACATATATGATATTTTACATTAATTTTTATACATTTAAATTAATAAT
Found at i:586476 original size:131 final size:129
Alignment explanation
Indices: 586349--586707 Score: 398
Period size: 131 Copynumber: 2.8 Consensus size: 129
586339 TATTTAATGT
* * * * * *
586349 TAACATATAAATTTGAATTAAACATACGTGATATTTTATATTAATTTTTATATATTTATGTTAAT
1 TAACATAAAAATTTAAATTAAACATACGTGATATTTTACATTAATTTTTATACATTAAAGTTAAT
586414 A-ATATATAAATTTAAATTAAACATATATGATATTTTACATTAATTCTTTTACATTTATTTTAA
66 ATATATATAAATTTAAATTAAACATATATGATATTTTACATTAATTCTTTTACATTTATTTTAA
* * * *
586477 TAATATAAAAATTTAAATTAAATATATGTTATATTTTACATTAATTTTTATACATTAAAGTTAAT
1 TAACATAAAAATTTAAATTAAACATACGTGATATTTTACATTAATTTTTATACATTAAAGTTAAT
* ** * **
586542 ATTGTTATATAAATTTAAATTAAACATATATGATATTTTACATTAATTCTGATATATTTACATTA
66 A-T-ATATATAAATTTAAATTAAACATATATGATATTTTACATTAATTCTTTTACATTTATTTTA
586607 A
129 A
* * * * * ** * * * *
586608 TAATATATAAAA-TTCAGTTGAGCATATATAATATTTTATATTAATTTATATACATTAAAATTAA
1 TAACATA-AAAATTTAAATTAAACATACGTGATATTTTACATTAATTTTTATACATTAAAGTTAA
* *
586672 TATTATTATATAAATTAAAATTAAACATATGTGATA
65 TA-TA-TATATAAATTTAAATTAAACATATATGATA
586708 GGAAATCTTG
Statistics
Matches: 197, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
128 56 0.28
131 137 0.70
132 4 0.02
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (129 bp):
TAACATAAAAATTTAAATTAAACATACGTGATATTTTACATTAATTTTTATACATTAAAGTTAAT
ATATATATAAATTTAAATTAAACATATATGATATTTTACATTAATTCTTTTACATTTATTTTAA
Found at i:586542 original size:207 final size:195
Alignment explanation
Indices: 586143--586702 Score: 530
Period size: 195 Copynumber: 2.8 Consensus size: 195
586133 TATATATATA
* * * *
586143 TATATAAACTCAAA-TAAAGCATATGTGATATTTAATATTAATTTTTATACATTTACATTAATAA
1 TATATAAATTTAAATTAAA-CATATGTGATATTTTATATTAATTTTTATATATTTACATTAATAA
* * * * *
586207 TATATATATATTCAAATTAACCATATGTGATATTTAATGTTAATTCTTATACATTTACATTAATA
65 TATATA-A-ATTTAAATTAAACATATATGATATTTTATATTAATTCTTATACATTTACATTAATA
* * * * ** * ***
586272 ATATATAAATTTGAATTAAGGATGTGCCATATTTTATGTTAATTTTTATATATTTTCGTTAATAA
128 ATATAAAAATTTAAATTAAAGATATGCCATATTTTACATTAATTTTTATACATTAAAG-T--T--
586337 AATATTTAATGT
188 AATA--T--TGT
* * **
586349 TAACATATAAATTTGAATTAAACATACGTGATATTTTATATTAATTTTTATATATTTATGTTAAT
1 T---ATATAAATTTAAATTAAACATATGTGATATTTTATATTAATTTTTATATATTTACATTAAT
* * **
586414 AATATATAAATTTAAATTAAACATATATGATATTTTACATTAATTCTTTTACATTTATTTTAATA
63 AATATATAAATTTAAATTAAACATATATGATATTTTATATTAATTCTTATACATTTACATTAATA
* **
586479 ATATAAAAATTTAAATTAAATATATGTTATATTTTACATTAATTTTTATACATTAAAGTTAATAT
128 ATATAAAAATTTAAATTAAAGATATGCCATATTTTACATTAATTTTTATACATTAAAGTTAATAT
586544 TGT
193 TGT
* * * *
586547 TATATAAATTTAAATTAAACATATATGATATTTTACATTAATTCTGATATATTTACATTAATAAT
1 TATATAAATTTAAATTAAACATATGTGATATTTTATATTAATTTTTATATATTTACATTAATAAT
* * * * * * * *
586612 ATATAAAATTCAGTTGAGCATATATAATATTTTATATTAATT-TATATACATTAAAATTAATATT
66 ATATAAATTTAAATTAAACATATATGATATTTTATATTAATTCT-TATACATTTACATTAATA--
* * *
586676 ATTATATAAATTAAAATTAAACATATG
128 A-TATAAAAATTTAAATTAAAGATATG
586703 TGATAGGAAA
Statistics
Matches: 294, Mismatches: 52, Indels: 24
0.79 0.14 0.06
Matches are distributed among these distances:
194 1 0.00
195 105 0.36
197 1 0.00
198 26 0.09
200 1 0.00
202 4 0.01
204 1 0.00
206 2 0.01
207 92 0.31
208 1 0.00
209 56 0.19
210 4 0.01
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.47
Consensus pattern (195 bp):
TATATAAATTTAAATTAAACATATGTGATATTTTATATTAATTTTTATATATTTACATTAATAAT
ATATAAATTTAAATTAAACATATATGATATTTTATATTAATTCTTATACATTTACATTAATAATA
TAAAAATTTAAATTAAAGATATGCCATATTTTACATTAATTTTTATACATTAAAGTTAATATTGT
Found at i:586615 original size:19 final size:20
Alignment explanation
Indices: 586571--586616 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
586561 TTAAACATAT
*
586571 ATGATAT-TTTACATTAATT
1 ATGATATATTTACATTAATA
*
586590 CTGATATATTTACATTAATA
1 ATGATATATTTACATTAATA
586610 AT-ATATA
1 ATGATATA
586617 AAATTCAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (20 bp):
ATGATATATTTACATTAATA
Found at i:587241 original size:65 final size:65
Alignment explanation
Indices: 587160--587303 Score: 261
Period size: 65 Copynumber: 2.2 Consensus size: 65
587150 AAATGCAGTA
* *
587160 AAAATCTTCTCCACAGAACTAAAGCAGGTCTCAACAGAGGTAAAATTAAAAGAGAATCCTCACCC
1 AAAATCTTCTCCACAGAACTAAAGCAGGTCTCAACAGAGCTAAAATTAAAAGAGAATCCTCAACC
*
587225 AAAATCTTCTCCACAGAGCTAAAGCAGGTCTCAACAGAGCTAAAATTAAAAGAGAATCCTCAACC
1 AAAATCTTCTCCACAGAACTAAAGCAGGTCTCAACAGAGCTAAAATTAAAAGAGAATCCTCAACC
587290 AAAATCTTCTCCAC
1 AAAATCTTCTCCAC
587304 TCCATTACAA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 76 1.00
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.19
Consensus pattern (65 bp):
AAAATCTTCTCCACAGAACTAAAGCAGGTCTCAACAGAGCTAAAATTAAAAGAGAATCCTCAACC
Found at i:589221 original size:16 final size:15
Alignment explanation
Indices: 589202--589244 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
589192 TTATTTAAAT
*
589202 TTAAAATTTAACAAAA
1 TTAAAATATAA-AAAA
*
589218 TTAACAATATAATAAA
1 TTAA-AATATAAAAAA
589234 TTAAAATATAA
1 TTAAAATATAA
589245 TACAATAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAAATATAAAAAA
Found at i:589243 original size:15 final size:16
Alignment explanation
Indices: 589215--589246 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
589205 AAATTTAACA
589215 AAATTAACAATATAAT
1 AAATTAACAATATAAT
589231 AAATTAA-AATATAAT
1 AAATTAACAATATAAT
589246 A
1 A
589247 CAATAGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTAACAATATAAT
Found at i:591824 original size:44 final size:44
Alignment explanation
Indices: 591774--591858 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 44
591764 CAATTATGTA
591774 CGAGTCCATTCTCATT-TAAGTTTCTCAATAACTTAATTTCTTCT
1 CGAGTCCATTCTC-TTATAAGTTTCTCAATAACTTAATTTCTTCT
* * *
591818 CGAGTCCATTCTCTTATAGGTTTCTTAATAATTTAATTTCT
1 CGAGTCCATTCTCTTATAAGTTTCTCAATAACTTAATTTCT
591859 CCCAGGATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 2 0.05
44 35 0.95
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (44 bp):
CGAGTCCATTCTCTTATAAGTTTCTCAATAACTTAATTTCTTCT
Found at i:596750 original size:23 final size:24
Alignment explanation
Indices: 596724--596769 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
596714 AGATATTTTA
596724 AAATGA-TTTTTTTATTTTTTATG
1 AAATGATTTTTTTTATTTTTTATG
*
596747 AAATTATTTTTTTTATTTTTTAT
1 AAATGATTTTTTTTATTTTTTAT
596770 TTTAAAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (24 bp):
AAATGATTTTTTTTATTTTTTATG
Found at i:601813 original size:99 final size:99
Alignment explanation
Indices: 601642--601840 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
601632 ATCTTATCCA
601642 AGGTATATCCTTAATATTTCCTTGATCATAAGGACACGGGAGTATTATGCTAAAATCAACTTGAA
1 AGGTATATCCTTAATATTTCCTTGATCATAAGGACACGGGAGTATTATGCTAAAATCAACTTGAA
601707 AATAAGCAATTTATTTCTATTAATTTGTTATGAG
66 AATAAGCAATTTATTTCTATTAATTTGTTATGAG
601741 AGGTATATCCTTAATATTTCCTTGATCATAAGGACACGGGAGTATTATGCTAAAATCAACTTGAA
1 AGGTATATCCTTAATATTTCCTTGATCATAAGGACACGGGAGTATTATGCTAAAATCAACTTGAA
601806 AATAAGCAATTTATTTCTATTAATTTGTTATGAG
66 AATAAGCAATTTATTTCTATTAATTTGTTATGAG
601840 A
1 A
601841 TGTGTTTGTT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (99 bp):
AGGTATATCCTTAATATTTCCTTGATCATAAGGACACGGGAGTATTATGCTAAAATCAACTTGAA
AATAAGCAATTTATTTCTATTAATTTGTTATGAG
Found at i:610352 original size:12 final size:12
Alignment explanation
Indices: 610336--610446 Score: 99
Period size: 12 Copynumber: 9.6 Consensus size: 12
610326 ATTGCAATAC
610336 ATATATGTATAT
1 ATATATGTATAT
*
610348 GTATATG--TAT
1 ATATATGTATAT
*
610358 ATATGTGTATAT
1 ATATATGTATAT
610370 ATATATGTATAT
1 ATATATGTATAT
* *
610382 ATATGTGTGTAT
1 ATATATGTATAT
*
610394 A-A-ATGTGTAT
1 ATATATGTATAT
*
610404 ATGTA--TATAT
1 ATATATGTATAT
610414 ATATATGTATAT
1 ATATATGTATAT
*
610426 GCATATATATATAT
1 --ATATATGTATAT
610440 ATATATG
1 ATATATG
610447 AAGATTTGAG
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
10 24 0.30
11 1 0.01
12 43 0.54
14 11 0.14
ACGTcount: A:0.38, C:0.01, G:0.14, T:0.48
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:610353 original size:14 final size:14
Alignment explanation
Indices: 610336--610445 Score: 112
Period size: 14 Copynumber: 7.6 Consensus size: 14
610326 ATTGCAATAC
*
610336 ATATATGTATATGT
1 ATATATATATATGT
*
610350 ATATGTATATATGT
1 ATATATATATATGT
*
610364 GTATATATATATGT
1 ATATATATATATGT
* *
610378 ATATATATGTGTGT
1 ATATATATATATGT
* *
610392 ATAAATGTGTATATGT
1 AT--ATATATATATGT
610408 ATATATATATATGT
1 ATATATATATATGT
*
610422 ATATGCATATATATAT
1 ATAT--ATATATATGT
610438 ATATATAT
1 ATATATAT
610446 GAAGATTTGA
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
14 55 0.71
16 23 0.29
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (14 bp):
ATATATATATATGT
Found at i:610360 original size:2 final size:2
Alignment explanation
Indices: 610336--610445 Score: 76
Period size: 2 Copynumber: 55.0 Consensus size: 2
610326 ATTGCAATAC
* * * * * *
610336 AT AT AT GT AT AT GT AT AT GT AT AT AT GT GT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
610378 AT AT AT AT GT GT GT AT AA AT GT GT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* **
610420 GT AT AT GC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
610446 GAAGATTTGA
Statistics
Matches: 84, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (2 bp):
AT
Found at i:611061 original size:16 final size:17
Alignment explanation
Indices: 611032--611064 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
611022 AAATACGATT
611032 TAAAAAAATGAAAAATAC
1 TAAAAAAA-GAAAAATAC
611050 TAAAAAAA-AAAAATA
1 TAAAAAAAGAAAAATA
611065 AACAGAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (17 bp):
TAAAAAAAGAAAAATAC
Found at i:620169 original size:28 final size:28
Alignment explanation
Indices: 620129--620191 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
620119 GGGATCCCTT
*
620129 TACTTCATTCCTTGTATTAATTAATCAC
1 TACTGCATTCCTTGTATTAATTAATCAC
*
620157 TACTGCATTCCTTGTGTTAATTAATCAC
1 TACTGCATTCCTTGTATTAATTAATCAC
*
620185 TATTGCA
1 TACTGCA
620192 ACTATAAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.44
Consensus pattern (28 bp):
TACTGCATTCCTTGTATTAATTAATCAC
Found at i:626702 original size:21 final size:23
Alignment explanation
Indices: 626660--626702 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
626650 ATTTTTTACT
**
626660 TGGATTGTATAATTATGTTTTTA
1 TGGATTGTATAATTATCATTTTA
626683 TGGATT-TAT-ATTATCATTTT
1 TGGATTGTATAATTATCATTTT
626703 CGGGTTTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 3 0.17
23 6 0.33
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (23 bp):
TGGATTGTATAATTATCATTTTA
Found at i:633853 original size:26 final size:26
Alignment explanation
Indices: 633807--633904 Score: 126
Period size: 26 Copynumber: 3.7 Consensus size: 26
633797 TGTATATGGA
*
633807 AGAAGTGGAT-AATAATTTTACCATT
1 AGAAGTGGATGGATAATTTTACCATT
633832 AGAAGTGGATGGATAATTTTACCATT
1 AGAAGTGGATGGATAATTTTACCATT
* * **
633858 AGAAGTAGATGGATAATTTCAACCCACC
1 AGAAGTGGATGGATAATTT-TA-CCATT
633886 AGAAGTGGATGGATAATTT
1 AGAAGTGGATGGATAATTT
633905 CAACCCACTA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.16
26 32 0.50
27 1 0.02
28 21 0.33
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (26 bp):
AGAAGTGGATGGATAATTTTACCATT
Found at i:633898 original size:28 final size:28
Alignment explanation
Indices: 633807--633958 Score: 161
Period size: 28 Copynumber: 5.6 Consensus size: 28
633797 TGTATATGGA
* * *
633807 AGAAGTGGAT-AATAATTT-TA-CCATT
1 AGAAGTGGATGGATAATTTCAACCCACT
* *
633832 AGAAGTGGATGGATAATTT-TA-CCATT
1 AGAAGTGGATGGATAATTTCAACCCACT
* *
633858 AGAAGTAGATGGATAATTTCAACCCACC
1 AGAAGTGGATGGATAATTTCAACCCACT
633886 AGAAGTGGATGGATAATTTCAACCCACT
1 AGAAGTGGATGGATAATTTCAACCCACT
* ** *
633914 AGATGTGGATAAATACTTTCAACCCACT
1 AGAAGTGGATGGATAATTTCAACCCACT
*
633942 AGAAGTGGATGAATAAT
1 AGAAGTGGATGGATAAT
633959 GAAAATACAA
Statistics
Matches: 110, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
25 10 0.09
26 32 0.29
27 1 0.01
28 67 0.61
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (28 bp):
AGAAGTGGATGGATAATTTCAACCCACT
Found at i:637671 original size:44 final size:43
Alignment explanation
Indices: 637620--637706 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 43
637610 TATGAGAATA
*
637620 ATACTGCTTGCATAGCACAGTTAAAGGAAAGATATATTAAAAG
1 ATACTGCTTGCATAGCACAGCTAAAGGAAAGATATATTAAAAG
* *
637663 NATACTGCTTGCATAGCACAGCTAAAGGCATGATATATTAAAAG
1 -ATACTGCTTGCATAGCACAGCTAAAGGAAAGATATATTAAAAG
637707 CGATCGAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.25
Consensus pattern (43 bp):
ATACTGCTTGCATAGCACAGCTAAAGGAAAGATATATTAAAAG
Found at i:643398 original size:23 final size:22
Alignment explanation
Indices: 643366--643408 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
643356 GTTAGCCCAA
643366 GTTCTCTGTTTTAAATCAGCTT
1 GTTCTCTGTTTTAAATCAGCTT
643388 GTTCTGCTGTTTTAAATCAGC
1 GTTCT-CTGTTTTAAATCAGC
643409 CGCTTGTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.47
Consensus pattern (22 bp):
GTTCTCTGTTTTAAATCAGCTT
Found at i:662202 original size:11 final size:11
Alignment explanation
Indices: 662169--662202 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
662159 AAGAAACAAC
662169 TTTGCACAAAT
1 TTTGCACAAAT
* *
662180 TTTGTACGAAT
1 TTTGCACAAAT
662191 TTTGCACAAAT
1 TTTGCACAAAT
662202 T
1 T
662203 CTATTTATCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (11 bp):
TTTGCACAAAT
Found at i:664368 original size:13 final size:13
Alignment explanation
Indices: 664350--664375 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
664340 TGAGAAAAAA
664350 AGAAGTCAATTCT
1 AGAAGTCAATTCT
664363 AGAAGTCAATTCT
1 AGAAGTCAATTCT
664376 TGATCTTCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
AGAAGTCAATTCT
Found at i:671042 original size:2 final size:2
Alignment explanation
Indices: 671035--671085 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
671025 ATATAACTAT
671035 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
671077 TA TA TA TA T
1 TA TA TA TA T
671086 TGCAAAGTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:672695 original size:86 final size:86
Alignment explanation
Indices: 672545--672716 Score: 299
Period size: 86 Copynumber: 2.0 Consensus size: 86
672535 TGCCTCACAG
* *
672545 CCACTATTGCATGAGCAACAAGTGATTCCTGAATTCGTTGATGCGATCAGGACTCGGCCCAAGGA
1 CCACCATTGCACGAGCAACAAGTGATTCCTGAATTCGTTGATGCGATCAGGACTCGGCCCAAGGA
672610 TAAAAAAAATTAAAGAGACCT
66 TAAAAAAAATTAAAGAGACCT
* *
672631 CCACCATTGCACGAGTAACAAGTGATTGCTGAATTCGTTGATGCGATCAGGACTCGGCCCAAGGA
1 CCACCATTGCACGAGCAACAAGTGATTCCTGAATTCGTTGATGCGATCAGGACTCGGCCCAAGGA
*
672696 TAAAAAACATTAAAGAGACCT
66 TAAAAAAAATTAAAGAGACCT
672717 TTGAATGCTT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (86 bp):
CCACCATTGCACGAGCAACAAGTGATTCCTGAATTCGTTGATGCGATCAGGACTCGGCCCAAGGA
TAAAAAAAATTAAAGAGACCT
Found at i:674824 original size:79 final size:75
Alignment explanation
Indices: 674584--674840 Score: 266
Period size: 75 Copynumber: 3.4 Consensus size: 75
674574 AAAAGAAAAC
* * * * * * *
674584 ATCATCATAGAAACGTATTAATTAGATTTGGAATATAAAAACGTA-CTTGATTTTTTATTCATAA
1 ATCATCATAAAAACATACTAACTAGATTTAGAATATAAAAACGTATC-TAATTCTTTATTCATAA
* *
674648 TTTAACACAAA
65 TTTGATACAAA
* * * *
674659 ATCATTATAAAAATATACAAACTAGATTTAGAATATAAAAACGTATCTGATTCTTTATTCATAAT
1 ATCATCATAAAAACATACTAACTAGATTTAGAATATAAAAACGTATCTAATTCTTTATTCATAAT
674724 TTGATACAAA
66 TTGATACAAA
* * * * * *
674734 ATCATCTTAAAAACATTCTAACTAGATTTAGAATATAAAAACACTTATCTAATTTTTTTTTTTCG
1 ATCATCATAAAAACATACTAACTAGATTTAGAATAT-AAAA-ACGTATCTAA--TTCTTTATTCA
*
674799 TAATTTGATATAAA
62 TAATTTGATACAAA
*
674813 ATCATCATAAAAACGTACTAACTA-ATTT
1 ATCATCATAAAAACATACTAACTAGATTT
674841 TTTATTCGTA
Statistics
Matches: 152, Mismatches: 25, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
75 93 0.61
76 5 0.03
77 8 0.05
78 4 0.03
79 42 0.28
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.38
Consensus pattern (75 bp):
ATCATCATAAAAACATACTAACTAGATTTAGAATATAAAAACGTATCTAATTCTTTATTCATAAT
TTGATACAAA
Found at i:674852 original size:50 final size:50
Alignment explanation
Indices: 674788--674887 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
674778 TTATCTAATT
* *
674788 TTTTTTTTTCGTAATTTGATATAAAATCATCATAAAAACGTACTAACTAA
1 TTTTTTATTCGTAATTTGATACAAAATCATCATAAAAACGTACTAACTAA
** *
674838 TTTTTTATTCGTAATTTGATACAGTATCATCATAAAAATGTACTAACTAA
1 TTTTTTATTCGTAATTTGATACAAAATCATCATAAAAACGTACTAACTAA
674888 ATTTAAAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (50 bp):
TTTTTTATTCGTAATTTGATACAAAATCATCATAAAAACGTACTAACTAA
Found at i:677891 original size:164 final size:165
Alignment explanation
Indices: 677706--678026 Score: 484
Period size: 164 Copynumber: 2.0 Consensus size: 165
677696 TTTTACGCCA
* * * *
677706 TGGCCTTCTTTATTAGAATCACCGGCAGAATCAGCTCCTTCCTCATTGAGAATCTCCTTGTTCTT
1 TGGCCTTCTTCATTAGAATCACCGACAGAATCAGCCCCTTCCTCATTGAGAATCTCCTTGTTCAT
*
677771 GTTGCTCATCCTT-AACTTGGTGTTCAAGACGCACTTTCTTTCTGCCATATCTGAGATCAGCACA
66 GTTGCTCAT-CTTCAACTTGGTGATCAAGACGCACTTTCTTTCTGCCATATCTGAGATCAGCACA
*
677835 CAG-AAAGGAATTACGATAAACACAACCGTACGTCG
130 CAGAAAAGGAATTACGAAAAACACAACCGTACGTCG
* **
677870 TGGCCTTCTTCATTAGAATCACCGACAGGATTTGCCCCTTCCTCATTGAGAATCTCCTTGTTCAT
1 TGGCCTTCTTCATTAGAATCACCGACAGAATCAGCCCCTTCCTCATTGAGAATCTCCTTGTTCAT
* * * * * *
677935 GTTGCTTATCTTCAATTTGGTGATCAAGACGCATTTTCTTTCTGCCATATCTGAGCTTAGCATAC
66 GTTGCTCATCTTCAACTTGGTGATCAAGACGCACTTTCTTTCTGCCATATCTGAGATCAGCACAC
678000 AGAAAAGGAATTACGAAAAACACAACC
131 AGAAAAGGAATTACGAAAAACACAACC
678027 ATAGAAGCAA
Statistics
Matches: 140, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
163 3 0.02
164 114 0.81
165 23 0.16
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (165 bp):
TGGCCTTCTTCATTAGAATCACCGACAGAATCAGCCCCTTCCTCATTGAGAATCTCCTTGTTCAT
GTTGCTCATCTTCAACTTGGTGATCAAGACGCACTTTCTTTCTGCCATATCTGAGATCAGCACAC
AGAAAAGGAATTACGAAAAACACAACCGTACGTCG
Found at i:678549 original size:16 final size:16
Alignment explanation
Indices: 678528--678559 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
678518 AATTGTGTAT
*
678528 TTTTTTTAAAATATTA
1 TTTTTTTAAAAAATTA
678544 TTTTTTTAAAAAATTA
1 TTTTTTTAAAAAATTA
678560 ACAATGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTTTAAAAAATTA
Found at i:678727 original size:13 final size:13
Alignment explanation
Indices: 678709--678733 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
678699 GGTAAATTTC
678709 TTTTTATAAGTTT
1 TTTTTATAAGTTT
678722 TTTTTATAAGTT
1 TTTTTATAAGTT
678734 ATAATTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (13 bp):
TTTTTATAAGTTT
Found at i:678753 original size:18 final size:20
Alignment explanation
Indices: 678712--678753 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
678702 AAATTTCTTT
* *
678712 TTATAAGTTTTTTTTATAAG
1 TTATAAGTTTTTGTTATAAA
678732 TTATAA-TTTTTGTTA-AAA
1 TTATAAGTTTTTGTTATAAA
678750 TTAT
1 TTAT
678754 CATAGAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 8 0.40
20 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (20 bp):
TTATAAGTTTTTGTTATAAA
Found at i:678901 original size:13 final size:13
Alignment explanation
Indices: 678885--678909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
678875 TCCTATTTGT
678885 AGCTTTTTTTTTA
1 AGCTTTTTTTTTA
678898 AGCTTTTTTTTT
1 AGCTTTTTTTTT
678910 TAAAAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.72
Consensus pattern (13 bp):
AGCTTTTTTTTTA
Found at i:679958 original size:2 final size:2
Alignment explanation
Indices: 679951--679986 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
679941 ATAATACTAC
679951 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
679987 GGTGTGAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:686999 original size:4 final size:4
Alignment explanation
Indices: 686990--687014 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
686980 TTCCTTTCTC
686990 CTTT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT C
687015 ACTTGACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
CTTT
Found at i:692450 original size:10 final size:10
Alignment explanation
Indices: 692393--692456 Score: 53
Period size: 10 Copynumber: 6.7 Consensus size: 10
692383 ACGTAACAGT
*
692393 TATATGAATA
1 TATATAAATA
*
692403 AATATAAATA
1 TATATAAATA
* *
692413 AATATAATTA
1 TATATAAATA
692423 -AT-TAAAT-
1 TATATAAATA
*
692430 TATATATATA
1 TATATAAATA
692440 TATATAAATA
1 TATATAAATA
*
692450 TACATAA
1 TATATAA
692457 TATTTAACTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
8 6 0.14
9 6 0.14
10 32 0.73
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (10 bp):
TATATAAATA
Found at i:703020 original size:19 final size:20
Alignment explanation
Indices: 702996--703033 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
702986 ATTCAAAAAT
*
702996 ATTATTTTTTAT-AATTTTA
1 ATTATTTTTAATCAATTTTA
703015 ATTATTTTTAATCAATTTT
1 ATTATTTTTAATCAATTTT
703034 TGACATGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTATTTTTAATCAATTTTA
Found at i:703885 original size:21 final size:21
Alignment explanation
Indices: 703840--703885 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
703830 CGTGATTGAT
* *
703840 TTTTAGGTATTACGTAATTAG
1 TTTTAGGTATTACGTAACTAA
* *
703861 TTTTAGGTATTGCGTGACTAA
1 TTTTAGGTATTACGTAACTAA
703882 TTTT
1 TTTT
703886 TAAATAATGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.50
Consensus pattern (21 bp):
TTTTAGGTATTACGTAACTAA
Found at i:704061 original size:21 final size:21
Alignment explanation
Indices: 704002--704062 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
703992 TATCAAAAAC
*
704002 TAGTCACGCAATACCCAAAGT
1 TAGTCACGCAATACCTAAAGT
* * *
704023 CAGTTACGCAATATCTAAAGT
1 TAGTCACGCAATACCTAAAGT
704044 TAGTCACGCAATACCTAAA
1 TAGTCACGCAATACCTAAA
704063 AACTAATCAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (21 bp):
TAGTCACGCAATACCTAAAGT
Found at i:705413 original size:18 final size:18
Alignment explanation
Indices: 705390--705425 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
705380 CCATAGAGAT
705390 CATTGCAATCAAAATCAA
1 CATTGCAATCAAAATCAA
705408 CATTGCAATCAAAATCAA
1 CATTGCAATCAAAATCAA
705426 ACTCAAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (18 bp):
CATTGCAATCAAAATCAA
Found at i:708481 original size:18 final size:21
Alignment explanation
Indices: 708458--708499 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 21
708448 GTAGTCACTA
708458 AAAAAAT-AATA-ATAAA-AT
1 AAAAAATAAATATATAAATAT
708476 AAAAAATAAATATATAAATAT
1 AAAAAATAAATATATAAATAT
708497 AAA
1 AAA
708500 CTATATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 4 0.19
20 5 0.24
21 5 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATAAATATATAAATAT
Found at i:708797 original size:10 final size:10
Alignment explanation
Indices: 708782--708824 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
708772 CCACAATAAA
708782 AAAAAAATAC
1 AAAAAAATAC
*
708792 AAAAAAAAAC
1 AAAAAAATAC
708802 AAAAAAATATAC
1 -AAAAAA-ATAC
708814 AAAAAAATAC
1 AAAAAAATAC
708824 A
1 A
708825 CAATGGGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 14 0.48
11 12 0.41
12 3 0.10
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:708797 original size:12 final size:12
Alignment explanation
Indices: 708776--708820 Score: 60
Period size: 11 Copynumber: 4.0 Consensus size: 12
708766 ACCCATCCAC
708776 AATA-AAAAAAA
1 AATACAAAAAAA
708787 AATAC-AAAAAA
1 AATACAAAAAAA
708798 AA-ACAAAAAAA
1 AATACAAAAAAA
*
708809 TATACAAAAAAA
1 AATACAAAAAAA
708821 TACACAATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 2 0.07
11 19 0.63
12 9 0.30
ACGTcount: A:0.84, C:0.07, G:0.00, T:0.09
Consensus pattern (12 bp):
AATACAAAAAAA
Found at i:708821 original size:12 final size:12
Alignment explanation
Indices: 708780--708827 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
708770 ATCCACAATA
*
708780 AAAAAAAAATAC
1 AAAAAAATATAC
708792 AAAAAAA-A-AC
1 AAAAAAATATAC
708802 AAAAAAATATAC
1 AAAAAAATATAC
*
708814 AAAAAAATACAC
1 AAAAAAATATAC
708826 AA
1 AA
708828 TGGGTGAGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
10 9 0.27
11 2 0.06
12 22 0.67
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAATATAC
Found at i:710150 original size:15 final size:14
Alignment explanation
Indices: 710118--710178 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
710108 AATATATAAT
710118 ATAAATAAAAAATA
1 ATAAATAAAAAATA
* *
710132 ATAAATAGACAAATC
1 ATAAATA-AAAAATA
*
710147 ATAAATAATATCAAAGA
1 ATAAATAA-A--AAATA
710164 ATAAATAAAAAATA
1 ATAAATAAAAAATA
710178 A
1 A
710179 AATGATAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
14 13 0.35
15 12 0.32
16 1 0.03
17 11 0.30
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.21
Consensus pattern (14 bp):
ATAAATAAAAAATA
Found at i:710209 original size:42 final size:44
Alignment explanation
Indices: 710104--710211 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 44
710094 ACAAAATCTT
*
710104 AAAAAATATATAAT-ATAAATAAAAAATAATAAATAGACAAATC
1 AAAAAATATATAATAATAAATAAAAAATAATAAATAGACAAAAC
* *
710147 ATAAATAATATCA-AAGAATAAATAAAAAAT-A-AAAT-GATAATAAC
1 A-AAA-AATAT-ATAATAATAAATAAAAAATAATAAATAGACAA-AAC
710191 AAAAAATATATAATAATAAAT
1 AAAAAATATATAATAATAAAT
710212 GTATGGAAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
41 1 0.02
42 14 0.25
43 8 0.15
44 10 0.18
45 8 0.15
46 14 0.25
ACGTcount: A:0.69, C:0.04, G:0.03, T:0.24
Consensus pattern (44 bp):
AAAAAATATATAATAATAAATAAAAAATAATAAATAGACAAAAC
Found at i:719340 original size:4 final size:4
Alignment explanation
Indices: 719331--719355 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
719321 CAGCTAAACG
719331 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
719356 TTCAGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:726006 original size:12 final size:12
Alignment explanation
Indices: 725991--726021 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
725981 GCAAAAATAG
725991 AAATAAAATTAA
1 AAATAAAATTAA
726003 AAATAAAATTAA
1 AAATAAAATTAA
726015 AAA-AAAA
1 AAATAAAA
726022 AAAGGAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
AAATAAAATTAA
Found at i:742204 original size:88 final size:87
Alignment explanation
Indices: 742105--742280 Score: 318
Period size: 88 Copynumber: 2.0 Consensus size: 87
742095 ACAAAGAAAA
742105 CTAGAAAAAAAAAAAAACCGTAACAATTCACCGTTTTATTTCATGAAGGCTGTTTTTTGTTTGTT
1 CTAGAAAAAAAAAAAAACCGTAACAATTCACCGTTTTATTTCATGAAGGCTGTTTTTTGTTTGTT
*
742170 TGTTTG-TTTATTTTGTTGATTT
66 TGTTTGTTTTA-GTTGTTGATTT
742192 NCTAGAAAAAAAAAAAAACCGTAACAATTCACCGTTTTATTTCATGAAGGCTGTTTTTTGTTTGT
1 -CTAGAAAAAAAAAAAAACCGTAACAATTCACCGTTTTATTTCATGAAGGCTGTTTTTTGTTTGT
742257 TTGTTTGTTTTAGTTGTTGATTT
65 TTGTTTGTTTTAGTTGTTGATTT
742280 C
1 C
742281 AATTGGAAGA
Statistics
Matches: 86, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
87 1 0.01
88 81 0.94
89 4 0.05
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (87 bp):
CTAGAAAAAAAAAAAAACCGTAACAATTCACCGTTTTATTTCATGAAGGCTGTTTTTTGTTTGTT
TGTTTGTTTTAGTTGTTGATTT
Found at i:742521 original size:3 final size:3
Alignment explanation
Indices: 742513--742537 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
742503 TACATCATTC
742513 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
742538 ATAAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:764731 original size:22 final size:22
Alignment explanation
Indices: 764703--764748 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
764693 GAGATTGTGG
764703 TTGGGGGATCTTATATCTTTCT
1 TTGGGGGATCTTATATCTTTCT
764725 TTGGGGGATCTTATATCTTTCT
1 TTGGGGGATCTTATATCTTTCT
764747 TT
1 TT
764749 TTGTCCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.13, C:0.13, G:0.22, T:0.52
Consensus pattern (22 bp):
TTGGGGGATCTTATATCTTTCT
Found at i:805479 original size:10 final size:11
Alignment explanation
Indices: 805459--805490 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
805449 TCTGATTAAG
805459 AAAAACAAAAA
1 AAAAACAAAAA
805470 AAAAACAAAAA
1 AAAAACAAAAA
805481 AAAGAACAAA
1 AAA-AACAAA
805491 GAAGGAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:806283 original size:29 final size:29
Alignment explanation
Indices: 806251--806331 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
806241 TTGAAAATCT
806251 TTTAAATAAATTTTTATTATTTTATTAT-A
1 TTTAAATAAATTTTTA-TATTTTATTATAA
* *
806280 TTTAATTAAATTTTTATATTTTTATTTTAA
1 TTTAAATAAATTTTTATA-TTTTATTATAA
*
806310 ATTAAATAAATTTTTATATTTT
1 TTTAAATAAATTTTTATATTTT
806332 TTTTATGCGA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
28 2 0.04
29 27 0.59
30 17 0.37
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTAAATAAATTTTTATATTTTATTATAA
Found at i:806322 original size:30 final size:29
Alignment explanation
Indices: 806252--806337 Score: 111
Period size: 30 Copynumber: 2.9 Consensus size: 29
806242 TGAAAATCTT
*
806252 TTAAATAAATTTTTAT-TATTTTATTATAT
1 TTAAATAAATTTTTATAT-TTTTATTATAA
* *
806281 TTAATTAAATTTTTATATTTTTATTTTAAA
1 TTAAATAAATTTTTATATTTTTATTAT-AA
*
806311 TTAAATAAATTTTTATATTTTTTTTAT
1 TTAAATAAATTTTTATATTTTTATTAT
806338 GCGACATGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
29 23 0.47
30 26 0.53
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
TTAAATAAATTTTTATATTTTTATTATAA
Found at i:816626 original size:14 final size:14
Alignment explanation
Indices: 816608--816645 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
816598 GTATTTTATA
816608 AAAAATATTAAATAT
1 AAAAATATTAAA-AT
*
816623 AAAAA-GTTAAAAT
1 AAAAATATTAAAAT
816636 AAAAATATTA
1 AAAAATATTA
816646 CGTAATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 7 0.35
14 8 0.40
15 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
AAAAATATTAAAAT
Found at i:820377 original size:30 final size:30
Alignment explanation
Indices: 820343--820410 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
820333 TGGTCGATCG
820343 TCTTCAGTAACGAGATCAGCTCCCAC-AACT
1 TCTTCAGTAACGAGATCAGCTCCC-CTAACT
* *
820373 TCTTCAGTACCGAGATCAGCTCCCCTTACT
1 TCTTCAGTAACGAGATCAGCTCCCCTAACT
820403 TCTTCAGT
1 TCTTCAGT
820411 TATGAAATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 1 0.03
30 34 0.97
ACGTcount: A:0.24, C:0.34, G:0.13, T:0.29
Consensus pattern (30 bp):
TCTTCAGTAACGAGATCAGCTCCCCTAACT
Found at i:822236 original size:117 final size:117
Alignment explanation
Indices: 822019--822236 Score: 289
Period size: 117 Copynumber: 1.9 Consensus size: 117
822009 ATATTAATTG
* * *
822019 AAATTGAATTGAAAGGTTATTAATTTTTTATAAAAATATCAGGCTTTCAGTATGACAATAAAGTA
1 AAATTGAACTGAAAGGTTATTAATTTTTTATAAAAATATCAGGCTTTCAGTATAACAATAAAATA
* **
822084 TGAATTTTTTCACATAAAATAAAATAATTTTAAAAAATTAGTATTTAAGTCA
66 TAAATTTTTTCACATAAAATAAAATAATTAAAAAAAATTAGTATTTAAGTCA
* * * * *
822136 AAATTGAACTGAACGGTTATTAATTTTTTATAAAAATTAT-GGGTTTTGAGTATAATAA-AAAAT
1 AAATTGAACTGAAAGGTTATTAATTTTTTATAAAAA-TATCAGGCTTTCAGTATAACAATAAAAT
822199 ATAAATTTTTTTCACATAAAAT-AAATGAATTAAAAAAA
65 ATAAA-TTTTTTCACATAAAATAAAAT-AATTAAAAAAA
822237 TAAAAAATTA
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
116 12 0.14
117 72 0.83
118 3 0.03
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (117 bp):
AAATTGAACTGAAAGGTTATTAATTTTTTATAAAAATATCAGGCTTTCAGTATAACAATAAAATA
TAAATTTTTTCACATAAAATAAAATAATTAAAAAAAATTAGTATTTAAGTCA
Found at i:825412 original size:2 final size:2
Alignment explanation
Indices: 825407--825431 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
825397 GTGTGTGTGT
825407 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
825432 CAGATTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:829266 original size:36 final size:36
Alignment explanation
Indices: 829218--829292 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
829208 AAACGCATGA
* *
829218 TAAATTCGTGTCAACTTTAAGGTAACATACACACAC
1 TAAATTCATGTCAACTTTAAGGTAACATACAAACAC
829254 TAAATTCATGTCAACTTTAAGGTAACATACAAACAC
1 TAAATTCATGTCAACTTTAAGGTAACATACAAACAC
829290 TAA
1 TAA
829293 TCACACTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (36 bp):
TAAATTCATGTCAACTTTAAGGTAACATACAAACAC
Done.