Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008472.1 Hibiscus syriacus cultivar Beakdansim tig00111298_pilon, whole genome shotgun sequence
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: 548252
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:317376 original size:103 final size:103
Alignment explanation
Indices: 317186--317444 Score: 308
Period size: 103 Copynumber: 2.5 Consensus size: 103
317176 AAAACATATT
*
317186 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAATATTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATATTTT
* *
317251 CAATGTTTATGTTTCAATAGAAACTATCTCAAGGGAGA
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGA
* * * *
317289 CAAA-ATTTTGTTTCAAGGGAACCTATCTCAAGAGAGACAAAACTTCATTTCAAGGGAATTTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TTCATTTCAAGGGAAATATTT
* * *
317353 TTAATGTTTATGTTTCAAGAGAAATTGTCTCAAGAGAGA
65 TCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGA
* * * * * * * * *
317392 CGAA-ACTTAG-TTCTAAAAGAAAATGTCTCAAGGGAGACGAAATTTATTTCAAG
1 CAAAGATTTTGTTTC-AAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAG
317445 AGAGACGAGA
Statistics
Matches: 133, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
102 49 0.37
103 84 0.63
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (103 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATATTTT
CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGA
Found at i:317447 original size:19 final size:21
Alignment explanation
Indices: 317419--317468 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
317409 AGAAAATGTC
*
317419 TCAAGGGAGACGAAATTTATT
1 TCAAGAGAGACGAAATTTATT
* *
317440 TCAAGAGAGACGAGATTTGTT
1 TCAAGAGAGACGAAATTTATT
317461 TCAAGAGA
1 TCAAGAGA
317469 AACTATCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGACGAAATTTATT
Found at i:317676 original size:52 final size:52
Alignment explanation
Indices: 317593--317695 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
317583 ATCTTGAGTA
* *
317593 AAATAAATCTTCTTCTGAGTAAAACAGTCTCAAGTGAGACAAAGTCTGTTTG
1 AAATAAATCTTCTTCTGAGTAAAACAATCTCAAGTGAGACAAAGTATGTTTG
317645 AAATAAATCTTCTT-TCGAGTAAAACAATCTCAAGTGAGACAAAGTATGTTT
1 AAATAAATCTTCTTCT-GAGTAAAACAATCTCAAGTGAGACAAAGTATGTTT
317696 TAAGAAAAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 1 0.02
52 47 0.98
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (52 bp):
AAATAAATCTTCTTCTGAGTAAAACAATCTCAAGTGAGACAAAGTATGTTTG
Found at i:319175 original size:183 final size:183
Alignment explanation
Indices: 318867--319220 Score: 611
Period size: 183 Copynumber: 1.9 Consensus size: 183
318857 ATCAGGTTTA
* *
318867 ACTGAAGGGTTCGTCTCATCACAAAGTCTTCAGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCGTCTCATCACAAAGTCTTCAGACTGAAAAAAGCAGTGGAGCAAACACCGAATT
* *
318932 GCCAAGTTTTCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTT
318997 TCCTCTATAACCAATTGCCTTAGTGAAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGAAATAGCTCAGCTTTAGAGGGACAAATC
*
319050 ACTGAAGGGTTCGTCTCATCACAAAGTCTT-TGAACTGAAAAAAGCAGTGGAGCAAACACCGAAT
1 ACTGAAGGGTTCGTCTCATCACAAAGTCTTCAG-ACTGAAAAAAGCAGTGGAGCAAACACCGAAT
*
319114 TGCCAAGTGTCCGAGCAGTGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
65 TGCCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
* * *
319179 TTTCTCTATAACCAATTGCTTTAGTGGAATAGCTCAGCTTTA
130 TTCCTCTATAACCAATTGCCTTAGTGAAATAGCTCAGCTTTA
319221 CGGATTTAAT
Statistics
Matches: 161, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
182 1 0.01
183 160 0.99
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCGTCTCATCACAAAGTCTTCAGACTGAAAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGAAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:324415 original size:21 final size:21
Alignment explanation
Indices: 324380--324419 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
324370 AATTTCAATT
324380 ATTAAATTAATTAATATTTTA
1 ATTAAATTAATTAATATTTTA
324401 ATTATAATTAA-TAATATTT
1 ATTA-AATTAATTAATATTT
324420 CAACCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTAAATTAATTAATATTTTA
Found at i:324708 original size:78 final size:79
Alignment explanation
Indices: 324620--324775 Score: 201
Period size: 79 Copynumber: 2.0 Consensus size: 79
324610 GTTAATATGT
** *
324620 TTTAACATTTTCGGTAAAGTATTACCTAAAACATT-TTTTTTCTACC-GCAAATATTAATAT-TG
1 TTTAACATTTTCGGTAAAACACTACCTAAAACATTATTTTTTCTACCAG-AAATATTAATATATG
*
324682 AGCGCTACCTAAAATA
65 -GCGATACCTAAAATA
* * *
324698 TTTAACATTTTTGGTAAAACACTACCTAAAATATTATTTTTTCTACCAGAAATGTTAATATATGG
1 TTTAACATTTTCGGTAAAACACTACCTAAAACATTATTTTTTCTACCAGAAATATTAATATATGG
*
324763 TGATACCTAAAAT
66 CGATACCTAAAAT
324776 GTTATTTATT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
78 30 0.45
79 34 0.51
80 3 0.04
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (79 bp):
TTTAACATTTTCGGTAAAACACTACCTAAAACATTATTTTTTCTACCAGAAATATTAATATATGG
CGATACCTAAAATA
Found at i:325670 original size:36 final size:36
Alignment explanation
Indices: 325613--325964 Score: 560
Period size: 36 Copynumber: 9.8 Consensus size: 36
325603 ATGCACTACA
* *
325613 TCCTTCCGTTCGACTTAAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* * *
325649 TTCTTCTGTTCGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
325685 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* **
325721 TCATTCCGTTCCTCTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
**
325757 TCCTTCCGTTCCTCTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
325793 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* **
325829 TCATTCCGTTCCTCTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
*
325865 TCTTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
*
325901 TCCTTCCGTTCGACTTGAATTGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
*
325937 TCCTTCCGTTCGACTTGAATTGGAAGTG
1 TCCTTCCGTTCGACTTGAATCGGAAGTG
325965 TAGATGAAAT
Statistics
Matches: 296, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 296 1.00
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.31
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
Found at i:327552 original size:15 final size:15
Alignment explanation
Indices: 327532--327560 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
327522 TGATAAAAAA
327532 GAGAAAACAACTCTC
1 GAGAAAACAACTCTC
327547 GAGAAAACAACTCT
1 GAGAAAACAACTCT
327561 TAAGAAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.24, G:0.14, T:0.14
Consensus pattern (15 bp):
GAGAAAACAACTCTC
Found at i:327566 original size:15 final size:15
Alignment explanation
Indices: 327533--327569 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
327523 GATAAAAAAG
*
327533 AGAAAACAACTCTCG
1 AGAAAACAACTCTCA
*
327548 AGAAAACAACTCTTA
1 AGAAAACAACTCTCA
327563 AGAAAAC
1 AGAAAAC
327570 TCTCTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.22, G:0.11, T:0.14
Consensus pattern (15 bp):
AGAAAACAACTCTCA
Found at i:335158 original size:392 final size:393
Alignment explanation
Indices: 334397--335181 Score: 1506
Period size: 393 Copynumber: 2.0 Consensus size: 393
334387 ATGAACAAGC
334397 TCTTCCACCGTACTTGGACCAGTTCATGGTGGTGTATTTGGACGATATCGTGGTATATAGTAACT
1 TCTTCCACCGTACTTGGACCAGTTCATGGTGGTGTATTTGGACGATATCGTGGTATATAGTAACT
334462 CCATGGAGGAGCATATAGACCACTTGAGGATTGTGTTCAATACACTTTAAGAGAACGAGCTATAC
66 CCATGGAGGAGCATATAGACCACTTGAGGATTGTGTTCAATACACTTTAAGAGAACGAGCTATAC
334527 GTCAAGAAGGAAAAGTGCACGTTTGCCACTGAGGAAGTACACTTCCTTGGACATGTAATCGGCCC
131 GTCAAGAAGGAAAAGTGCACGTTTGCCACTGAGGAAGTACACTTCCTTGGACATGTAATCGGCCC
334592 ACGAGAAGTTATTAATGGACGGAAACAAAATCAAGGCCATAACCGACTGGGAGCCGCCAACCAAG
196 ACGAGAAGTTATTAATGGACGGAAACAAAATCAAGGCCATAACCGACTGGGAGCCGCCAACCAAG
334657 GTAAGTGAGTGAGGTTATTCCTTGGTCTAGTAAATTATTATCACGGTTTATACAGGGTTATTCGG
261 GTAAGTGAGTGAGGTTATTCCTTGGTCTAGTAAATTATTATCACGGTTTATACAGGGTTATTCGG
*
334722 CACGAGCATCACCATTGACGGACCTACTCAAGAAGGGGAGACATGGGA-TGGTCCGAACAATGTC
326 CACGAGCATCACCATTGACGGACCTACTCAAGAAGGGAAGACATGGGAGTGGTCCGAACAATGTC
334786 AGA
391 AGA
334789 TCTTCCAACCGTACTTGGACCAGTTCATGGTGGTGTATTTGGACGATATCGTGGTATATAGTAAC
1 TCTTCC-ACCGTACTTGGACCAGTTCATGGTGGTGTATTTGGACGATATCGTGGTATATAGTAAC
334854 TCCATGGAGGAGCATATAGACCACTTGAGGATTGTGTTCAATACACTTTAAGAGAACGAGCTATA
65 TCCATGGAGGAGCATATAGACCACTTGAGGATTGTGTTCAATACACTTTAAGAGAACGAGCTATA
334919 CGTCAAGAAGGAAAAGTGCACGTTTGCCACTG-GGAAGTACACTTCCTTGGACATGTAATCGG-C
130 CGTCAAGAAGGAAAAGTGCACGTTTGCCACTGAGGAAGTACACTTCCTTGGACATGTAATCGGCC
334982 CACGAGAAGTTATTAATGGACGGAAACAAAATCAAGGCCATAACCGACTGGGAGCCGCCAACCAA
195 CACGAGAAGTTATTAATGGACGGAAACAAAATCAAGGCCATAACCGACTGGGAGCCGCCAACCAA
335047 GGTAAGTGAGATGAGGTTATTCCTTGGTCTAGTAAATTATTATCATCGG-TTATACAGGGTTATT
260 GGTAAGTGAG-TGAGGTTATTCCTTGGTCTAGTAAATTATTATCA-CGGTTTATACAGGGTTATT
335111 CGGCACGAGCATCACCATTGACGGACCTACTCAAGAAGGGAAGACATGGGAGTGGTCCGAACAAT
323 CGGCACGAGCATCACCATTGACGGACCTACTCAAGAAGGGAAGACATGGGAGTGGTCCGAACAAT
335176 GTCAGA
388 GTCAGA
335182 AGGCCTTTAA
Statistics
Matches: 388, Mismatches: 1, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
391 76 0.20
392 135 0.35
393 177 0.46
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.24
Consensus pattern (393 bp):
TCTTCCACCGTACTTGGACCAGTTCATGGTGGTGTATTTGGACGATATCGTGGTATATAGTAACT
CCATGGAGGAGCATATAGACCACTTGAGGATTGTGTTCAATACACTTTAAGAGAACGAGCTATAC
GTCAAGAAGGAAAAGTGCACGTTTGCCACTGAGGAAGTACACTTCCTTGGACATGTAATCGGCCC
ACGAGAAGTTATTAATGGACGGAAACAAAATCAAGGCCATAACCGACTGGGAGCCGCCAACCAAG
GTAAGTGAGTGAGGTTATTCCTTGGTCTAGTAAATTATTATCACGGTTTATACAGGGTTATTCGG
CACGAGCATCACCATTGACGGACCTACTCAAGAAGGGAAGACATGGGAGTGGTCCGAACAATGTC
AGA
Found at i:340662 original size:20 final size:20
Alignment explanation
Indices: 340637--340676 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
340627 AGTACATAGA
340637 TTATTGTCTAAAATAAGGAG
1 TTATTGTCTAAAATAAGGAG
340657 TTATTGTCTAAAATAAGGAG
1 TTATTGTCTAAAATAAGGAG
340677 GACCATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (20 bp):
TTATTGTCTAAAATAAGGAG
Found at i:342896 original size:14 final size:14
Alignment explanation
Indices: 342850--342960 Score: 59
Period size: 14 Copynumber: 8.6 Consensus size: 14
342840 TAGATATTAA
342850 TTTTAATATTAATTT
1 TTTTAATATTAA-TT
342865 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* *
342875 ATTAAATATTAATT
1 TTTTAATATTAATT
*
342889 TTTTAATATT-ATA
1 TTTTAATATTAATT
*
342902 TTATAGATATT-A--
1 TTTTA-ATATTAATT
342914 TTTTAATATTAATTT
1 TTTTAATATTAA-TT
342929 TTTTAA-A-TAA--
1 TTTTAATATTAATT
*
342939 -ATTAATATTAATT
1 TTTTAATATTAATT
342952 TTTTAATAT
1 TTTTAATAT
342961 ATATTATATA
Statistics
Matches: 73, Mismatches: 9, Indels: 29
0.66 0.08 0.26
Matches are distributed among these distances:
9 4 0.05
10 5 0.07
11 9 0.12
12 8 0.11
13 12 0.16
14 23 0.32
15 12 0.16
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (14 bp):
TTTTAATATTAATT
Found at i:342941 original size:64 final size:64
Alignment explanation
Indices: 342825--342978 Score: 258
Period size: 64 Copynumber: 2.4 Consensus size: 64
342815 AGGTTTTATA
*
342825 TTTAATTTTATATTATAGATATTAATTTTAATATTAATTTTTTTAAATAAATTAAATATTAATTT
1 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTTAAATAAATT-AATATTAATTT
342890 TTTAATATTATATTATAGATATT-ATTTTAATATTAATTTTTTTAAATAAATTAATATTAATTT
1 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTTAAATAAATTAATATTAATTT
* *
342953 TTTAATA-TATATTATATATTTTAATT
1 TTTAATATTATATTATAGATATTAATT
342979 ATATCATATA
Statistics
Matches: 85, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
62 13 0.15
63 21 0.25
64 29 0.34
65 22 0.26
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (64 bp):
TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTTAAATAAATTAATATTAATTT
Found at i:342948 original size:24 final size:24
Alignment explanation
Indices: 342916--342972 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 24
342906 AGATATTATT
342916 TTAATATTAATTTTTTTAA-ATAAA
1 TTAATATTAA-TTTTTTAATATAAA
*
342940 TTAATATTAATTTTTTAATATATA
1 TTAATATTAATTTTTTAATATAAA
342964 TTATATATT
1 TTA-ATATT
342973 TTAATTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 8 0.27
24 17 0.57
25 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTAATATTAATTTTTTAATATAAA
Found at i:342966 original size:18 final size:18
Alignment explanation
Indices: 342938--343031 Score: 61
Period size: 18 Copynumber: 5.3 Consensus size: 18
342928 TTTTTAAATA
*
342938 AATTAATATTA-ATTTTTT
1 AATT-ATATTATATATTTT
342956 AATATATATTATATATTTT
1 AAT-TATATTATATATTTT
* **
342975 AATTATATCATATAAATT
1 AATTATATTATATATTTT
* **
342993 ATTTATA-TAT-TATTAA
1 AATTATATTATATATTTT
* *
343009 AATTTTA-TATTTATTTT
1 AATTATATTATATATTTT
343026 AATTAT
1 AATTAT
343032 TTTGATTTAA
Statistics
Matches: 58, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
16 10 0.17
17 11 0.19
18 27 0.47
19 10 0.17
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTATATTATATATTTT
Found at i:342981 original size:20 final size:19
Alignment explanation
Indices: 342938--343034 Score: 60
Period size: 20 Copynumber: 5.0 Consensus size: 19
342928 TTTTTAAATA
*
342938 AATTA-ATATTAATTTTTT
1 AATTATATATTAATATTTT
342956 AA-TATATATTATATATTTT
1 AATTATATATTA-ATATTTT
342975 AATTATATCATATAA-ATTATT
1 AATTATAT-AT-TAATATT-TT
* *
342996 TA-TATATTATTAAAATTTT
1 AATTATA-TATTAATATTTT
*
343015 ATATT-TATTTTAATTATTTT
1 A-ATTATATATTAA-TATTTT
343035 GATTTAAGTT
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
17 2 0.03
18 8 0.13
19 18 0.29
20 25 0.40
21 8 0.13
22 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTATATATTAATATTTT
Found at i:343378 original size:62 final size:57
Alignment explanation
Indices: 343312--343433 Score: 147
Period size: 58 Copynumber: 2.0 Consensus size: 57
343302 TGAATATATA
*
343312 TTTAAAAAAATTAAAAGTATTACATAATTGCA-TATTTAATAATAGTTTAATGATAATTAATG
1 TTTAAAAAAA-TAAAAGT-GT--ATAATT-CATTA-TTAATAATAGTTTAATGATAATTAATG
* *
343374 TTTAAAAAAATAGAAGTGTATGATTCATTGATTAATAATAGTTTAATGATAATTAATG
1 TTTAAAAAAATAAAAGTGTATAATTCATT-ATTAATAATAGTTTAATGATAATTAATG
343432 TT
1 TT
343434 GTTGTGCCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
57 2 0.04
58 35 0.64
59 1 0.02
60 1 0.02
61 6 0.11
62 10 0.18
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (57 bp):
TTTAAAAAAATAAAAGTGTATAATTCATTATTAATAATAGTTTAATGATAATTAATG
Found at i:343699 original size:31 final size:31
Alignment explanation
Indices: 343641--343700 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
343631 TAGTTGTATG
* **
343641 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTACAAAACTAA
343672 AATTATTTAAATCTCAGTATTACAAAACT
1 AATTATTTAAATCTCAGTATTACAAAACT
343701 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTACAAAACTAA
Found at i:346075 original size:17 final size:17
Alignment explanation
Indices: 346053--346096 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
346043 AAGATGGTCC
346053 GTTTCATCAACCTATGA
1 GTTTCATCAACCTATGA
346070 GTTTCATCAACCTATGA
1 GTTTCATCAACCTATGA
*
346087 GTTGCATCAA
1 GTTTCATCAA
346097 TCGTATTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (17 bp):
GTTTCATCAACCTATGA
Found at i:358324 original size:676 final size:679
Alignment explanation
Indices: 357033--358387 Score: 2664
Period size: 676 Copynumber: 2.0 Consensus size: 679
357023 ATACACATAC
357033 GGAGGTTATACACATCCTCTCACTTCTATCAGGAAGGTTTATTACTACCCAGAATGCAATGAATG
1 GGAGGTTATACACATCCTCTCACTTCTATCAGGAAGGTTTATTACTACCCAGAATGCAATGAATG
357098 TGATGATCCCTGCCAAGTTCTAGCCCTTAAATGTGAAGAGGAATGATGTAAATATATTGTTCATT
66 TGATGATCCCTGCCAAGTTCTAGCCCTTAAATGTGAAGAGGAATGATGTAAATATATTGTTCATT
357163 GGAGCTGCATACAACCTAGTCAACGATAGTGGTAGTGAAATAATTTGGTTTTTTTTTTGTTTCAC
131 GGAGCTGCATACAACCTAGTCAACGATAGTGGTAGTGAAATAATTTGGTTTTTTTTTTGTTTCAC
357228 CGTCTTTGTAGTGCATTTTATGGTATTAGTAGTGATTTTGCAACTTGAATTGTTTTGTCTTACAA
196 CGTCTTTGTAGTGCATTTTATGGTATTAGTAGTGATTTTGCAACTTGAATTGTTTTGTCTTACAA
357293 TATATTTGTTGTAATAACATTTTTTATGAAAACATTTACGAAATATTAAAAAAATGAGTTGTTTT
261 TATATTTGTTGTAATAACATTTTTTATGAAAACATTTACGAAATATTAAAAAAATGAGTTGTTTT
357358 TATTATAAAGAGTTAAATTTTATTTACGATACAAATTCAATAAGAAAATAATAAGAAAAAGTAAA
326 TATTATAAAGAGTTAAATTTTATTTACGATACAAATTCAATAAGAAAATAATAAGAAAAAGTAAA
357423 TCAAAAGAACACAAAAATAAAATGAACATACATTTTAGATAAAAAAAAAACTATAGATTAGAGAA
391 TCAAAAGAACACAAAAATAAAATGAACATACATTTTAGATAAAAAAAAAACTATAGATTAGAGAA
357488 AATCATAAACATAAGAGAAAAAATTAACTATAATTGAAATTGTACAAGAGATTACGAAAAAATAA
456 AATCATAAACATAAGAGAAAAAATTAACTATAATTGAAATTGTACAAGAGATTACGAAAAAATAA
357553 TCAATTCTCTCATAATCTTAAAGACTAAATCTAATAATCTATTTATATGAACTATAACAAGGAGT
521 TCAATTCTCTCATAATCTTAAAGACTAAATCTAATAATCTATTTATATGAACTATAACAAGGAGT
*
357618 CTCTTTTTACTAGGATTTATTACTTTTAATTCAATCTA-TACATTAGGTATTGACGTGTATGAAC
586 CTCTTTTTACTAGGATTTATTACTTTTAATTAAATCTATTACATTAGGTATTGACGTGTATGAAC
357682 ATAAAACATGTTAGG-TACATGA-TCTTA
651 ATAAAACATGTTAGGCTACATGATTCTTA
357709 GGAGGTTATACACATCCTCTCACTTCTATCAGGAAGGTTTATTACTACCCAGAATGCAATGAATG
1 GGAGGTTATACACATCCTCTCACTTCTATCAGGAAGGTTTATTACTACCCAGAATGCAATGAATG
357774 TGATGATCCCTGCCAAGTTCTAGCCCTTAAATGTGAAGAGGAATGATGTAAATATATTGTTCATT
66 TGATGATCCCTGCCAAGTTCTAGCCCTTAAATGTGAAGAGGAATGATGTAAATATATTGTTCATT
357839 GGAGCTGCATACAACCTAGTCAACGATAGTGGTAGTGAAATAATTTGGTTTTTTTTTTTGTTTCA
131 GGAGCTGCATACAACCTAGTCAACGATAGTGGTAGTGAAATAATTTGG-TTTTTTTTTTGTTTCA
357904 CCGTCTTTGTAGTGCATTTTATGGTATTAGTAGTGATTTTGCAACTTGAATTGTTTTGTCTTACA
195 CCGTCTTTGTAGTGCATTTTATGGTATTAGTAGTGATTTTGCAACTTGAATTGTTTTGTCTTACA
357969 ATATATTTGTTGTAATAACATTTTTTATGAAAACATTTACGAAATATTAAAAAAATGAGTTGTTT
260 ATATATTTGTTGTAATAACATTTTTTATGAAAACATTTACGAAATATTAAAAAAATGAGTTGTTT
358034 TTATTATAAAGAGTTAAATTTTATTTACGATACAAATTCAATAAGAAAATAATAAGAAAAAGTAA
325 TTATTATAAAGAGTTAAATTTTATTTACGATACAAATTCAATAAGAAAATAATAAGAAAAAGTAA
358099 ATCAAAAGAACACAAAAATAAAATGAACATACATTTTAGAT-AAAAAAAAACTATAGATTAGAGA
390 ATCAAAAGAACACAAAAATAAAATGAACATACATTTTAGATAAAAAAAAAACTATAGATTAGAGA
358163 AAATCATAAACATAAGAGAAAAAATTAACTATAATTGAAATTGTACAAGAGATTACGAAAAAATA
455 AAATCATAAACATAAGAGAAAAAATTAACTATAATTGAAATTGTACAAGAGATTACGAAAAAATA
358228 ATCAATTCTCTCATAATCTTAAAGACTAAATCTAATAATCTATTTATATGAACTATAACAAGGAG
520 ATCAATTCTCTCATAATCTTAAAGACTAAATCTAATAATCTATTTATATGAACTATAACAAGGAG
358293 TCTCTTTTTACTAGGATTTATTACTTTTAATTAAATCTATTACATTAGGTATTGACGTGTATGAA
585 TCTCTTTTTACTAGGATTTATTACTTTTAATTAAATCTATTACATTAGGTATTGACGTGTATGAA
358358 CATAAAACATGTTAGGCTACATGATTCTTA
650 CATAAAACATGTTAGGCTACATGATTCTTA
358388 TTGATCGAAA
Statistics
Matches: 674, Mismatches: 1, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
676 369 0.55
677 293 0.43
678 7 0.01
679 5 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (679 bp):
GGAGGTTATACACATCCTCTCACTTCTATCAGGAAGGTTTATTACTACCCAGAATGCAATGAATG
TGATGATCCCTGCCAAGTTCTAGCCCTTAAATGTGAAGAGGAATGATGTAAATATATTGTTCATT
GGAGCTGCATACAACCTAGTCAACGATAGTGGTAGTGAAATAATTTGGTTTTTTTTTTGTTTCAC
CGTCTTTGTAGTGCATTTTATGGTATTAGTAGTGATTTTGCAACTTGAATTGTTTTGTCTTACAA
TATATTTGTTGTAATAACATTTTTTATGAAAACATTTACGAAATATTAAAAAAATGAGTTGTTTT
TATTATAAAGAGTTAAATTTTATTTACGATACAAATTCAATAAGAAAATAATAAGAAAAAGTAAA
TCAAAAGAACACAAAAATAAAATGAACATACATTTTAGATAAAAAAAAAACTATAGATTAGAGAA
AATCATAAACATAAGAGAAAAAATTAACTATAATTGAAATTGTACAAGAGATTACGAAAAAATAA
TCAATTCTCTCATAATCTTAAAGACTAAATCTAATAATCTATTTATATGAACTATAACAAGGAGT
CTCTTTTTACTAGGATTTATTACTTTTAATTAAATCTATTACATTAGGTATTGACGTGTATGAAC
ATAAAACATGTTAGGCTACATGATTCTTA
Found at i:365965 original size:27 final size:26
Alignment explanation
Indices: 365924--365976 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
365914 ACGATCAACA
*
365924 GTCAACGGTCCGGTCGGGTCGGGTCGG
1 GTCAACGGTCAGGTCGGGTC-GGTCGG
365951 GTCAACGGTCAGGTCGGGTCGGTCGG
1 GTCAACGGTCAGGTCGGGTCGGTCGG
365977 TCGGGTCAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.09, C:0.25, G:0.47, T:0.19
Consensus pattern (26 bp):
GTCAACGGTCAGGTCGGGTCGGTCGG
Found at i:365992 original size:9 final size:10
Alignment explanation
Indices: 365980--366020 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
365970 CGGTCGGTCG
365980 GGTCAG-ACC
1 GGTCAGAACC
365989 GGTCA-AACC
1 GGTCAGAACC
365998 GGTTC-GAACC
1 GG-TCAGAACC
366008 GGTCAGAACC
1 GGTCAGAACC
366018 GGT
1 GGT
366021 TGAAAACTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
9 12 0.43
10 16 0.57
ACGTcount: A:0.24, C:0.29, G:0.32, T:0.15
Consensus pattern (10 bp):
GGTCAGAACC
Found at i:373224 original size:7 final size:7
Alignment explanation
Indices: 373212--373242 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
373202 GTCAAAGAAA
373212 GTCAACG
1 GTCAACG
373219 GTCAACG
1 GTCAACG
373226 GTCAACG
1 GTCAACG
373233 GTCAACG
1 GTCAACG
373240 GTC
1 GTC
373243 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:373249 original size:5 final size:5
Alignment explanation
Indices: 373239--373305 Score: 73
Period size: 5 Copynumber: 12.8 Consensus size: 5
373229 AACGGTCAAC
* *
373239 GGTCG GGTCG GGTCG GGTCAAT GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
373288 GGTCG GGTC- GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC
373306 AGACCAGTCA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
4 4 0.08
5 41 0.77
7 8 0.15
ACGTcount: A:0.06, C:0.21, G:0.52, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:373264 original size:22 final size:22
Alignment explanation
Indices: 373232--373298 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
373222 AACGGTCAAC
373232 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
373254 GGTCAATGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
373276 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
373298 G
1 G
373299 TCGGGTCAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.21, G:0.51, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:373328 original size:19 final size:19
Alignment explanation
Indices: 373304--373342 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
373294 GTCGGTCGGG
373304 TCAGACCAGTCAAACCGGT
1 TCAGACCAGTCAAACCGGT
*
373323 TCAGACCGGTCAAACCGGT
1 TCAGACCAGTCAAACCGGT
373342 T
1 T
373343 AAACCGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (19 bp):
TCAGACCAGTCAAACCGGT
Found at i:375022 original size:23 final size:23
Alignment explanation
Indices: 375004--375064 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
374994 CTCGTATAAA
375004 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
375027 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
375050 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
375065 TATAAGATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:375416 original size:25 final size:25
Alignment explanation
Indices: 375388--375444 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
375378 CTTAATGCAT
*
375388 ATAATATGAAATCATG-TCATGTATC
1 ATAATATGAAAT-ACGATCATGTATC
375413 ATAATATGAAATACGATCATGTATC
1 ATAATATGAAATACGATCATGTATC
*
375438 AAAATAT
1 ATAATAT
375445 TGAATATAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 2 0.07
25 27 0.93
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (25 bp):
ATAATATGAAATACGATCATGTATC
Found at i:376378 original size:3 final size:3
Alignment explanation
Indices: 376370--376399 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
376360 TCTTCACGGG
376370 GAA GAA GAA GAAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA G-AA GAA GAA GAA GAA GAA GA
376400 GAAATCTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:376391 original size:16 final size:17
Alignment explanation
Indices: 376370--376402 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
376360 TCTTCACGGG
376370 GAAGAAGAAGAA-AGAA
1 GAAGAAGAAGAAGAGAA
376386 GAAGAAGAAGAAGAGAA
1 GAAGAAGAAGAAGAGAA
376403 ATCTGGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GAAGAAGAAGAAGAGAA
Found at i:381995 original size:23 final size:23
Alignment explanation
Indices: 381934--381995 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
381924 CTCGTATAAA
*
381934 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
381957 TGCACCGAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
*
381980 TGCACCGTAGTGCCAT
1 TGCACCGAAGTGCCAT
381996 ATAAGATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCATGTAGAAT
Found at i:394424 original size:29 final size:28
Alignment explanation
Indices: 394392--394456 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
394382 AATCAAGAAC
*
394392 AAAAAAGAAA-AGAAGCAAAAAAACAAAGA
1 AAAAAAGAAACAAAAG--AAAAAACAAAGA
*
394421 AAAAAGAGAAACAAAAGAAAAAAGAAAGA
1 AAAAA-AGAAACAAAAGAAAAAACAAAGA
394450 ACAAAAA
1 A-AAAAA
394457 TCAAAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
29 18 0.58
30 9 0.29
31 4 0.13
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (28 bp):
AAAAAAGAAACAAAAGAAAAAACAAAGA
Found at i:394435 original size:25 final size:26
Alignment explanation
Indices: 394389--394473 Score: 83
Period size: 25 Copynumber: 3.3 Consensus size: 26
394379 TCTAATCAAG
*
394389 AACAAA-AAAGAAAAGAAGCAAAA-A
1 AACAAAGAAAGAAAAGAAACAAAAGA
394413 AACAAAGAAA-AAAGAGAAACAAAAGA
1 AACAAAGAAAGAAA-AGAAACAAAAGA
394439 AA-AAAGAAAGAACAA-AAATCAAAAAGA
1 AACAAAGAAAGAA-AAGAAA-C-AAAAGA
394466 AA-AAAGAA
1 AACAAAGAA
394474 CAAAAAGCAC
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
24 9 0.17
25 22 0.42
26 7 0.13
27 15 0.28
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.01
Consensus pattern (26 bp):
AACAAAGAAAGAAAAGAAACAAAAGA
Found at i:394439 original size:18 final size:18
Alignment explanation
Indices: 394394--394469 Score: 73
Period size: 18 Copynumber: 3.9 Consensus size: 18
394384 TCAAGAACAA
*
394394 AAAAGAAAAGAAGCAAAAAA
1 AAAAGAAAA-AAG-AAAAAC
*
394414 ACAAAGAAAAAAGAGAAAC
1 A-AAAGAAAAAAGAAAAAC
394433 AAAAGAAAAAAGAAAGAAC
1 AAAAGAAAAAAGAAA-AAC
394452 AAAA-ATCAAAAAGAAAAA
1 AAAAGA--AAAAAGAAAAA
394470 AGAACAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
18 14 0.29
19 14 0.29
20 13 0.27
21 8 0.16
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.01
Consensus pattern (18 bp):
AAAAGAAAAAAGAAAAAC
Found at i:394442 original size:30 final size:31
Alignment explanation
Indices: 394386--394456 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
394376 AGATCTAATC
*
394386 AAGAACAAAAAAGAAAAGAAGCAAAAAAACA
1 AAGAACAAAAAAGAAAAAAAGCAAAAAAACA
* *
394417 AAGAA-AAAAGAGAAACAAAAG--AAAAAAGA
1 AAGAACAAAAAAGAAA-AAAAGCAAAAAAACA
394446 AAGAACAAAAA
1 AAGAACAAAAA
394457 TCAAAAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 12 0.35
30 13 0.38
31 9 0.26
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (31 bp):
AAGAACAAAAAAGAAAAAAAGCAAAAAAACA
Found at i:394443 original size:7 final size:7
Alignment explanation
Indices: 394392--394478 Score: 52
Period size: 7 Copynumber: 11.9 Consensus size: 7
394382 AATCAAGAAC
394392 AAAAAAG
1 AAAAAAG
394399 AAAAGAAG
1 AAAA-AAG
*
394407 CAAAAA-
1 AAAAAAG
*
394413 AACAAAG
1 AAAAAAG
394420 AAAAAAGAG
1 -AAAAA-AG
394429 AAACAAAAG
1 -AA-AAAAG
394438 AAAAAAG
1 AAAAAAG
*
394445 AAAGAA-
1 AAAAAAG
* *
394451 CAAAAAT
1 AAAAAAG
*
394458 CAAAAAG
1 AAAAAAG
394465 AAAAAAG
1 AAAAAAG
394472 AACAAAA
1 AA-AAAA
394479 AGCACATGCA
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
6 8 0.12
7 30 0.47
8 16 0.25
9 7 0.11
10 3 0.05
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:394456 original size:20 final size:19
Alignment explanation
Indices: 394393--394469 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 19
394383 ATCAAGAACA
394393 AAAAAGAAAAGAAGCAAAAA-
1 AAAAAGAAAA-AAG-AAAAAC
*
394413 AACAAAGAAAAAAGAGAAAC
1 AA-AAAGAAAAAAGAAAAAC
394433 -AAAAGAAAAAAGAAAGAAC
1 AAAAAGAAAAAAGAAA-AAC
**
394452 AAAAATCAAAAAGAAAAA
1 AAAAAGAAAAAAGAAAAA
394470 AGAACAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
18 13 0.27
19 10 0.20
20 18 0.37
21 8 0.16
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.01
Consensus pattern (19 bp):
AAAAAGAAAAAAGAAAAAC
Found at i:394464 original size:16 final size:16
Alignment explanation
Indices: 394386--394480 Score: 63
Period size: 16 Copynumber: 5.8 Consensus size: 16
394376 AGATCTAATC
*
394386 AAGAACAAAAA-AGAA
1 AAGAACAAAAAGAAAA
*
394401 AAGAAGCAAAAA-AACA
1 AAGAA-CAAAAAGAAAA
394417 AAGAA-AAAAGAGAAACAA
1 AAGAACAAAA-AG-AA-AA
*
394435 AAGAAAAAAGAAAGAACAA
1 AAG-AACAA-AAAGAA-AA
*
394454 AA-ATCAAAAAGAAAA
1 AAGAACAAAAAGAAAA
394469 AAGAACAAAAAG
1 AAGAACAAAAAG
394481 CACATGCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
14 4 0.06
15 10 0.15
16 27 0.42
17 5 0.08
18 4 0.06
19 9 0.14
20 4 0.06
21 2 0.03
ACGTcount: A:0.78, C:0.07, G:0.14, T:0.01
Consensus pattern (16 bp):
AAGAACAAAAAGAAAA
Found at i:396195 original size:106 final size:106
Alignment explanation
Indices: 396068--396813 Score: 1186
Period size: 106 Copynumber: 7.0 Consensus size: 106
396058 ATATCTTGCC
* * * * * *
396068 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
396133 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
396174 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* **
396239 AATTTTAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
396280 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
396345 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATTTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
396386 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
396451 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATGTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
396492 ACTCCAGACAATGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
396557 AATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* ** ** *
396598 ACTCAAGACAACAAAAGTTCAACTTCACGACGAAGGGACTACTGGTTGTCAATAAAAAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* ** *
396663 AATTTCAGAGTCAATTTTGACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
396704 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
396769 AATTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
396810 ACTC
1 ACTC
396814 GGAACAATGC
Statistics
Matches: 591, Mismatches: 49, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 591 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:397600 original size:37 final size:37
Alignment explanation
Indices: 397543--397647 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
397533 CCTTTTCGTC
*
397543 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
397580 TTGCTATGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
* *
397617 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTATGATTCAAACTCCTAAAAATAGGAT
397648 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:398201 original size:19 final size:19
Alignment explanation
Indices: 398112--398202 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 19
398102 TTTTTTACAC
*
398112 TATATAT-TA-TTATTATA
1 TATATATATATTTATTATT
* *
398129 TATACATATATTTTTTATT
1 TATATATATATTTATTATT
* *
398148 TATTTATATTCATTTGGTTATTT
1 TATATATA-T-ATTT-ATTA-TT
*
398171 TTTAATACTATATTTATTATT
1 TAT-ATA-TATATTTATTATT
398192 TATATATATAT
1 TATATATATAT
398203 ATATATACTT
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
17 6 0.11
18 2 0.04
19 17 0.30
20 4 0.07
21 8 0.14
22 6 0.11
23 8 0.14
24 3 0.05
25 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (19 bp):
TATATATATATTTATTATT
Found at i:398423 original size:18 final size:19
Alignment explanation
Indices: 398402--398452 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
398392 TATTTGGGTT
398402 TTTTTATATTATATTA-TA
1 TTTTTATATTATATTATTA
*
398420 TTTTCATATTACTATTATTA
1 TTTTTATATTA-TATTATTA
*
398440 TTGTTATGATTAT
1 TTTTTAT-ATTAT
398453 TATTTTTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 5 0.19
20 8 0.30
21 4 0.15
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTTATATTATATTATTA
Found at i:398551 original size:29 final size:30
Alignment explanation
Indices: 398510--398590 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 30
398500 TCATTCATTC
*
398510 ATTTATTT-ATTTATTTATTTTTTATTCTT
1 ATTTTTTTCATTTATTTATTTTTTATTCTT
** *
398539 -TTTTTTTTTTTTACTTA-TTTTTATTCTT
1 ATTTTTTTCATTTATTTATTTTTTATTCTT
*
398567 CATTTTTTTCATTTATTCATTTTT
1 -ATTTTTTTCATTTATTTATTTTT
398591 CCCTCTAACA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
28 17 0.41
29 7 0.17
30 13 0.32
31 4 0.10
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (30 bp):
ATTTTTTTCATTTATTTATTTTTTATTCTT
Found at i:398559 original size:19 final size:18
Alignment explanation
Indices: 398511--398560 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
398501 CATTCATTCA
*
398511 TTTATTTATTTATTTATTT
1 TTTA-TTATTTTTTTATTT
* *
398530 TTTATTCTTTTTTTTTTT
1 TTTATTATTTTTTTATTT
398548 TTTACTTATTTTT
1 TTTA-TTATTTTT
398561 ATTCTTCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.14, C:0.04, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTATTATTTTTTTATTT
Found at i:398572 original size:28 final size:29
Alignment explanation
Indices: 398502--398575 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
398492 TTAATATTTC
* *
398502 ATTCATTCATTTATTTATTTATTTATTTTTT
1 ATTC-TTCATTT-TTTTTTTACTTATTTTTT
**
398533 ATTCTTTTTTTTTTTTTTACTTA-TTTTT
1 ATTCTTCATTTTTTTTTTACTTATTTTTT
398561 ATTCTTCATTTTTTT
1 ATTCTTCATTTTTTT
398576 CATTTATTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 18 0.49
29 10 0.27
30 5 0.14
31 4 0.11
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (29 bp):
ATTCTTCATTTTTTTTTTACTTATTTTTT
Found at i:398575 original size:16 final size:15
Alignment explanation
Indices: 398527--398575 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
398517 TATTTATTTA
398527 TTTTTTATTCTT-TT
1 TTTTTTATTCTTATT
398541 TTTTTT-TT-TTACTT
1 TTTTTTATTCTTA-TT
*
398555 ATTTTTATTCTTCATT
1 TTTTTTATTCTT-ATT
398571 TTTTT
1 TTTTT
398576 CATTTATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 2 0.07
13 2 0.07
14 13 0.46
15 2 0.07
16 8 0.29
17 1 0.04
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTATTCTTATT
Found at i:400090 original size:18 final size:19
Alignment explanation
Indices: 400038--400091 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
400028 TTCTCTTATT
*
400038 TTTACTTAAATTAT-TTTTA
1 TTTATTTAAA-TATCTTTTA
*
400057 TTTATTTAATTA-CTTTTA
1 TTTATTTAAATATCTTTTA
400075 -TTATTTAAATATCTTTT
1 TTTATTTAAATATCTTTT
400092 TACCAAACCC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 10 0.33
18 12 0.40
19 8 0.27
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATTTAAATATCTTTTA
Found at i:403892 original size:3 final size:3
Alignment explanation
Indices: 403849--403875 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
403839 GATCATCACC
403849 GTG GTG GTG GTG GTG GTG GTG GTG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG
403876 ACGGTGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GTG
Found at i:416529 original size:176 final size:173
Alignment explanation
Indices: 416245--416605 Score: 605
Period size: 176 Copynumber: 2.1 Consensus size: 173
416235 ATAAAAATTA
* *
416245 AATATTTTATAATTCAAAAAAACAGTTTATAATTCATTTAAATAATATAATTATAAAATAAAATT
1 AATATTTT-TAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATAATTATAAAATAAAATT
* *
416310 TTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTGGATCTTAAATTATT
65 TTATATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATTGGATCTTAAATTATT
*
416375 AATTGGGTTTTAAATGATTTGGGCTGAGCCCATATGTTATATAT
130 AATTGGGTTTTAAATAATTTGGGCTGAGCCCATATGTTATATAT
*
416419 AATATTTTTAATTCAGAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
1 AATATTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAAT-A-ATATAATTATAAAAT-AAAA
*
416484 TTTTATATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTA
63 TTTTATATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATTGGATCTTAAATTA
*
416549 TTAATTGGGTTTTAAATAATTTGGGCTGAGCCGATATGTTATATAT
128 TTAATTGGGTTTTAAATAATTTGGGCTGAGCCCATATGTTATATAT
*
416595 AATATATTTAA
1 AATATTTTTAA
416606 AATTTAAAAT
Statistics
Matches: 175, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
173 31 0.18
174 9 0.05
175 15 0.09
176 120 0.69
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.44
Consensus pattern (173 bp):
AATATTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATAATTATAAAATAAAATTT
TATATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATTGGATCTTAAATTATTA
ATTGGGTTTTAAATAATTTGGGCTGAGCCCATATGTTATATAT
Found at i:425229 original size:13 final size:12
Alignment explanation
Indices: 425206--425234 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
425196 AATAAAACCC
425206 TTTTGTTTTTTT
1 TTTTGTTTTTTT
425218 TTTTGTTTTTTT
1 TTTTGTTTTTTT
425230 TTTTG
1 TTTTG
425235 GCAGGAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:442769 original size:15 final size:16
Alignment explanation
Indices: 442744--442774 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
442734 ACCGGTTTTG
442744 ACCCGACCCGTTGACC
1 ACCCGACCCGTTGACC
442760 ACCCGA-CCGTTGACC
1 ACCCGACCCGTTGACC
442775 GGGTGCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.13
Consensus pattern (16 bp):
ACCCGACCCGTTGACC
Found at i:442845 original size:28 final size:29
Alignment explanation
Indices: 442775--442859 Score: 163
Period size: 29 Copynumber: 3.0 Consensus size: 29
442765 ACCGTTGACC
442775 GGGTGCTATTTTGGGAATTAATTCGAAAT
1 GGGTGCTATTTTGGGAATTAATTCGAAAT
442804 GGGTGCTATTTTGGGAATTAATTCGAAAT
1 GGGTGCTATTTTGGGAATTAATTCGAAAT
442833 -GGTGCTATTTTGGGAATTAATTCGAAA
1 GGGTGCTATTTTGGGAATTAATTCGAAA
442860 AAGGTTATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 27 0.48
29 29 0.52
ACGTcount: A:0.28, C:0.07, G:0.27, T:0.38
Consensus pattern (29 bp):
GGGTGCTATTTTGGGAATTAATTCGAAAT
Found at i:442880 original size:29 final size:29
Alignment explanation
Indices: 442776--442880 Score: 149
Period size: 29 Copynumber: 3.7 Consensus size: 29
442766 CCGTTGACCG
**
442776 GGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAAAA
*
442805 GGTGCTATTTTGGGAATTAATTCG-AAAT
1 GGTGCTATTTTGGGAATTAATTCGAAAAA
442833 GGTGCTATTTTGGGAATTAATTCGAAAAA
1 GGTGCTATTTTGGGAATTAATTCGAAAAA
** *
442862 GGTTATATTTTGGTAATTA
1 GGTGCTATTTTGGGAATTA
442881 TTTAAAAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
28 26 0.38
29 43 0.62
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.40
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAAAA
Found at i:443877 original size:42 final size:41
Alignment explanation
Indices: 443818--444022 Score: 268
Period size: 42 Copynumber: 4.8 Consensus size: 41
443808 GAAGTATTAT
*
443818 CAGGTCCCTTCGCTGTGTGCGAAGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
*
443860 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
*
443902 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCT
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCC
*
443944 CAGGTCCCTTTGCTGTGTGCAAGGATAAACCTTACAGTTTTCC
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAG-TTTCC
* * *
443987 TAGG-CTCCTCTGCTTTGTGCACAGGTTAAGCCTTAC
1 CAGGTC-CCTTTGCTGTGTGCA-AGG-TAAGCCTTAC
444023 TAGTGTATAG
Statistics
Matches: 147, Mismatches: 11, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
41 4 0.03
42 111 0.76
43 20 0.14
44 12 0.08
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTCC
Found at i:462337 original size:11 final size:11
Alignment explanation
Indices: 462321--462345 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
462311 AGTAGCGTTC
462321 TAAAAAAATAT
1 TAAAAAAATAT
462332 TAAAAAAATAT
1 TAAAAAAATAT
462343 TAA
1 TAA
462346 TATTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAAAAAATAT
Found at i:474048 original size:22 final size:24
Alignment explanation
Indices: 474023--474076 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
474013 AACAATTTAT
*
474023 TTAACTAAAC-AATATTAAT-TAA
1 TTAACTAAACTAATATAAATATAA
474045 TTAATCT-AACTAATATAAATATAA
1 TTAA-CTAAACTAATATAAATATAA
474069 TT-ACTAAA
1 TTAACTAAA
474077 ATATAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 9 0.33
23 13 0.48
24 5 0.19
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (24 bp):
TTAACTAAACTAATATAAATATAA
Found at i:474053 original size:23 final size:23
Alignment explanation
Indices: 474023--474083 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
474013 AACAATTTAT
*
474023 TTAACTAAAC-AATATTAAT-TAA
1 TTAACT-AACTAATATAAATATAA
474045 TTAATCTAACTAATATAAATATAA
1 TTAA-CTAACTAATATAAATATAA
474069 TT-ACTAA--AATATAAA
1 TTAACTAACTAATATAAA
474084 AAACCAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 8 0.23
22 11 0.31
23 11 0.31
24 5 0.14
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (23 bp):
TTAACTAACTAATATAAATATAA
Found at i:474404 original size:55 final size:55
Alignment explanation
Indices: 474345--474486 Score: 148
Period size: 55 Copynumber: 2.6 Consensus size: 55
474335 TGTCTGCTCC
* *
474345 CTATTCATTCAGGGAGTATA-ATATTCTAACAATTTTCA-ATAAACGGGCCCCCTCT
1 CTATTC-TTCAGAGAGTATAGATATTCTAACAATCTTCATA-AAACGGGCCCCCTCT
* * * * *
474400 CTATTCTATCAAAGAGTATAGA-ACTCTAACAATCTTCATAAAATGGGTCCTCTCT
1 CTATTCT-TCAGAGAGTATAGATATTCTAACAATCTTCATAAAACGGGCCCCCTCT
*
474455 ATATTCCTTCAGAGAGTATAGATATTC-AACAA
1 CTATT-CTTCAGAGAGTATAGATATTCTAACAA
474487 ACGGGTCCAC
Statistics
Matches: 72, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
54 1 0.01
55 64 0.89
56 7 0.10
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (55 bp):
CTATTCTTCAGAGAGTATAGATATTCTAACAATCTTCATAAAACGGGCCCCCTCT
Found at i:474569 original size:55 final size:54
Alignment explanation
Indices: 474479--474692 Score: 252
Period size: 55 Copynumber: 3.9 Consensus size: 54
474469 AGTATAGATA
* * * * *
474479 TTCAACAAACGGGTCCACTCCCTATTCCATGAGAGAGTATAGGACTCGAATAGTT
1 TTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAA-AGTT
* * *
474534 TTCAACAAACG-GATCCGCTCTCTATTCCTTTAGAGAGTATAGAACTCGAACAATCT
1 TTCAACAAACGTG-TCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAA-AGT-T
* * * *
474590 TT-AACAAACGTGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACGATC
1 TTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAAG-TT
*
474644 TTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGA
1 TTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGA
474693 CCTTCATAAA
Statistics
Matches: 139, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.02
55 132 0.95
56 4 0.03
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (54 bp):
TTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAAGTT
Found at i:474648 original size:110 final size:110
Alignment explanation
Indices: 474482--474692 Score: 282
Period size: 110 Copynumber: 1.9 Consensus size: 110
474472 ATAGATATTC
* * * *
474482 AACAAACGGGTCCACTCCCTATTCCATGAGAGAGTATAGGACTCGAATAGTTTTCAACAAACG-G
1 AACAAACGGGTCCACTCCCTATTCCATCAGAGAGTATAGAACTCGAAGAGTCTTCAACAAACGTG
* *
474546 ATCCGCTCTCTATTCCTTTAGAGAGTATAGAACTCGAACAATCTTT
66 -TCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTT
* ** * *
474592 AACAAACGTGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACGA-TCTTCAACAAACGT
1 AACAAACGGGTCCACTCCCTATTCCATCAGAGAGTATAGAACTCGAA-GAGTCTTCAACAAACGT
*
474656 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGA
65 GTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGA
474693 CCTTCATAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
110 85 0.98
111 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (110 bp):
AACAAACGGGTCCACTCCCTATTCCATCAGAGAGTATAGAACTCGAAGAGTCTTCAACAAACGTG
TCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTT
Found at i:474750 original size:37 final size:37
Alignment explanation
Indices: 474709--474781 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
474699 TAAAATATGT
* *
474709 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
1 TTGCTTCACTACTCTTCCATGAAGACTTAAGATTGAC
474746 TTGCTTCACTACTCTTCCATGAAGACTTAAGATTGA
1 TTGCTTCACTACTCTTCCATGAAGACTTAAGATTGA
474782 ACTATTTCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCATGAAGACTTAAGATTGAC
Found at i:476089 original size:26 final size:26
Alignment explanation
Indices: 476058--476113 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
476048 TGAACCCTCC
*
476058 TTTTA-TTTCTTTTTTTTTTCATCATT
1 TTTTATTTTCTTTTTTCTTTC-TCATT
476084 TTTTATTTTCTTTTTTCTTTCTCATT
1 TTTTATTTTCTTTTTTCTTTCTCATT
476110 TTTT
1 TTTT
476114 CTTCCATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTTATTTTCTTTTTTCTTTCTCATT
Found at i:476123 original size:26 final size:27
Alignment explanation
Indices: 476058--476123 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 27
476048 TGAACCCTCC
* *
476058 TTTTA-TTTCTTTTTTTTTTCATCATT
1 TTTTACTTCCTTTTTTCTTTCATCATT
* *
476084 TTTTATTTTCTTTTTTCTTTC-TCATT
1 TTTTACTTCCTTTTTTCTTTCATCATT
*
476110 TTTT-CTTCCATTTT
1 TTTTACTTCCTTTTT
476124 CCATTTTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.20
26 14 0.40
27 14 0.40
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTTACTTCCTTTTTTCTTTCATCATT
Found at i:476130 original size:45 final size:44
Alignment explanation
Indices: 476080--476196 Score: 128
Period size: 45 Copynumber: 2.5 Consensus size: 44
476070 TTTTTTTCAT
*
476080 CATTTTTTATTTTCTTTTTTCTTTCTCATTTTTT-CTTCCATTTTC
1 CATTTTTTATTTTCTTTTTTCTTT-TCATTTTTTCCAT-CATTTTC
* * *
476125 CATTTTTTCTGTTCTTTTTTTCTTTTCATTTTTTCCATCATTTTT
1 CATTTTTTATTTTC-TTTTTTCTTTTCATTTTTTCCATCATTTTC
*
476170 CATTTTTTCCATTTTTCTTTCTTCTTT
1 CATTTTTT--A-TTTTCTTTTTTCTTT
476197 AAGCGAAATA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
45 35 0.58
46 12 0.20
47 9 0.15
48 4 0.07
ACGTcount: A:0.09, C:0.20, G:0.01, T:0.71
Consensus pattern (44 bp):
CATTTTTTATTTTCTTTTTTCTTTTCATTTTTTCCATCATTTTC
Found at i:476145 original size:13 final size:13
Alignment explanation
Indices: 476125--476159 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
476115 TTCCATTTTC
476125 CATTTTTTCTGTT
1 CATTTTTTCTGTT
* *
476138 CTTTTTTTCTTTT
1 CATTTTTTCTGTT
476151 CATTTTTTC
1 CATTTTTTC
476160 CATCATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.74
Consensus pattern (13 bp):
CATTTTTTCTGTT
Found at i:476167 original size:38 final size:38
Alignment explanation
Indices: 476057--476169 Score: 99
Period size: 45 Copynumber: 2.8 Consensus size: 38
476047 TTGAACCCTC
*
476057 CTTTTATTTCTTTT--TTTTTT-CATCATTTTTTATTTT
1 CTTTT-TTTCTTTTCATTTTTTCCATCATTTTTTATGTT
*
476093 C-TTTTTTCTTTCTCATTTTTTCTTCCATTTTCCATTTTTTCTGTT
1 CTTTTTTTCTTT-TCA--TTTT-TTCCA---T-CATTTTTTATGTT
476138 CTTTTTTTCTTTTCATTTTTTCCATCATTTTT
1 CTTTTTTTCTTTTCATTTTTTCCATCATTTTT
476170 CATTTTTTCC
Statistics
Matches: 63, Mismatches: 2, Indels: 22
0.72 0.02 0.25
Matches are distributed among these distances:
34 7 0.11
35 4 0.06
36 1 0.02
38 7 0.11
39 5 0.08
40 2 0.03
41 2 0.03
42 5 0.08
43 4 0.06
44 1 0.02
45 15 0.24
46 10 0.16
ACGTcount: A:0.09, C:0.18, G:0.01, T:0.73
Consensus pattern (38 bp):
CTTTTTTTCTTTTCATTTTTTCCATCATTTTTTATGTT
Found at i:481205 original size:15 final size:15
Alignment explanation
Indices: 481185--481218 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
481175 GGTTACTGGT
481185 TCATTGATAACAGGC
1 TCATTGATAACAGGC
481200 TCATTGATAACAGGC
1 TCATTGATAACAGGC
481215 TCAT
1 TCAT
481219 CTTCTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (15 bp):
TCATTGATAACAGGC
Found at i:485789 original size:15 final size:15
Alignment explanation
Indices: 485769--485805 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
485759 TTAAAGAATC
485769 CTACCCACATGTTGG
1 CTACCCACATGTTGG
485784 CTACCCACATGTTGG
1 CTACCCACATGTTGG
485799 CTACCCA
1 CTACCCA
485806 ATCATGCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (15 bp):
CTACCCACATGTTGG
Found at i:490921 original size:2 final size:2
Alignment explanation
Indices: 490916--490949 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
490906 TATATATATA
490916 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
490950 GGTGGGTGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:494843 original size:13 final size:13
Alignment explanation
Indices: 494809--494837 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
494799 TAATGCCCCC
494809 TTTATATTATTAT
1 TTTATATTATTAT
494822 TTTATATTATTAT
1 TTTATATTATTAT
494835 TTT
1 TTT
494838 CAATTAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATATTATTAT
Found at i:503408 original size:65 final size:65
Alignment explanation
Indices: 503181--503638 Score: 526
Period size: 65 Copynumber: 7.0 Consensus size: 65
503171 CTTGGTCGGT
* * **
503181 GGGTGATCACCGAAGAGGTAAACGACTGAACAATAAAAGGTGCTTCACATTCATAGGTGAAAATC
1 GGGTGATCGCCGAAGAGGTAAACGACTGAAC-ATGAAAGGTGCTTCATGTTCATAGGTGAAAATC
503246 C
65 C
* * *
503247 GGGTGATCACCAAAGAGGTAAACGACTGAACATGAAAGGTACTTCATGTTCATAGGTGTGAAAAT
1 GGGTGATCGCCGAAGAGGTAAACGACTGAACATGAAAGGTGCTTCATGTTCATA-G-GTGAAAAT
503312 CC
64 CC
* *
503314 GGGTGATCAG-CAAAGAGGTAAACAACTGAACATGAAAGGTGCTTTC-TGTTCATAGGTGAAAAT
1 GGGTGATC-GCCGAAGAGGTAAACGACTGAACATGAAAGGTGC-TTCATGTTCATAGGTGAAAAT
*
503377 TC
64 CC
* * * ** *
503379 TGGTGGTCGCCGAAGAGATAAACGACTGAACATGAAAGGTATTTCATGTTCATAAGTGAAAATCC
1 GGGTGATCGCCGAAGAGGTAAACGACTGAACATGAAAGGTGCTTCATGTTCATAGGTGAAAATCC
* * *
503444 GGGTGAT-GTCCGAAGAGGTAAACGGCTGAACATGAAAGGTGCTTCATGTTCAAAGGTGAAAACC
1 GGGTGATCG-CCGAAGAGGTAAACGACTGAACATGAAAGGTGCTTCATGTTCATAGGTGAAAATC
503508 C
65 C
* * * * * * * *
503509 GAGTGATCGCTGAAGAGATAAACGGCTGAACATGAAAAGTGTTTCGTGTTCATAGGTGGAAATCC
1 GGGTGATCGCCGAAGAGGTAAACGACTGAACATGAAAGGTGCTTCATGTTCATAGGTGAAAATCC
* * * * * * *
503574 AGATGTTTGCTGAAGAGGTAAAATGACTGAACATGAAAGGTGCTTCATGTTCATGGGTGAAAATC
1 GGGTGATCGCCGAAGAGGT-AAACGACTGAACATGAAAGGTGCTTCATGTTCATAGGTGAAAATC
503639 AAACCCCCAT
Statistics
Matches: 334, Mismatches: 49, Indels: 18
0.83 0.12 0.04
Matches are distributed among these distances:
64 5 0.01
65 199 0.60
66 71 0.21
67 56 0.17
68 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (65 bp):
GGGTGATCGCCGAAGAGGTAAACGACTGAACATGAAAGGTGCTTCATGTTCATAGGTGAAAATCC
Found at i:506848 original size:94 final size:94
Alignment explanation
Indices: 506673--506857 Score: 252
Period size: 94 Copynumber: 2.0 Consensus size: 94
506663 AACGGTGTCG
* * *
506673 GTATATGGAATGTACAAGTACTTGATATGCTTATTCTCAGATAACATCTTCCTACAAGCAAAGAG
1 GTATATGGAATGTACAAGTACTTCAGATGCTTATTCTCAGACAACATCTTCCTACAAGCAAAGAG
* *
506738 GTAAAATGCTTTCAATGTTTGAGAATACA
66 ATAAAATGCTTACAATGTTTGAGAATACA
*
506767 GTATATGGAATGTACAAGTACTTCACGA-GCTTACATT-T-GGACAACATCTTCCTACAAGCAAA
1 GTATATGGAATGTACAAGTACTTCA-GATGCTT--ATTCTCAGACAACATCTTCCTACAAGCAAA
506829 GAGATATAAA-GCTTACAATGTTTGAGAAT
63 GAGATA-AAATGCTTACAATGTTTGAGAAT
506858 CAAATTCTTC
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
94 73 0.90
95 5 0.06
96 3 0.04
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (94 bp):
GTATATGGAATGTACAAGTACTTCAGATGCTTATTCTCAGACAACATCTTCCTACAAGCAAAGAG
ATAAAATGCTTACAATGTTTGAGAATACA
Found at i:515728 original size:17 final size:18
Alignment explanation
Indices: 515706--515740 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
515696 TATACGACTA
515706 ATATATAT-TTATATATT
1 ATATATATATTATATATT
515723 ATATATATAATTATATAT
1 ATATATAT-ATTATATAT
515741 ATACAGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATATATATTATATATT
Found at i:515750 original size:19 final size:19
Alignment explanation
Indices: 515708--515761 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
515698 TACGACTAAT
* *
515708 ATATATTTATATATTATAT
1 ATATAATTATATATTATAC
515727 ATATAATTATATA-TATAC
1 ATATAATTATATATTATAC
*
515745 AGTATAAATAT-TATTAT
1 A-TATAATTATATATTAT
515762 TATTATTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 7 0.23
19 23 0.77
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATAATTATATATTATAC
Found at i:516935 original size:2 final size:2
Alignment explanation
Indices: 516928--516960 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
516918 ATTATTTTGT
*
516928 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
516961 TTACGTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:516961 original size:12 final size:12
Alignment explanation
Indices: 516928--516963 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
516918 ATTATTTTGT
*
516928 TATATATATATA
1 TATATATATTTA
516940 TATATATATTTA
1 TATATATATTTA
516952 TATATATATTTA
1 TATATATATTTA
516964 CGTTTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TATATATATTTA
Found at i:517118 original size:18 final size:17
Alignment explanation
Indices: 517084--517127 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
517074 TTACTTTCGG
517084 TTTTTCTATTTCATATTA
1 TTTTT-TATTTCATATTA
*
517102 TTTTTTATTTTATTATTA
1 TTTTTTATTTCA-TATTA
517120 TTATTTTA
1 TT-TTTTA
517128 CTTGTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 12 0.52
19 5 0.22
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTATTTCATATTA
Found at i:517345 original size:19 final size:18
Alignment explanation
Indices: 517318--517356 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
517308 TTATATTCAC
*
517318 TTTTTTTATCTTCTTTAT
1 TTTTTTTATCTTCCTTAT
*
517336 TTTTTATTATTTTCCTTAT
1 TTTTT-TTATCTTCCTTAT
517355 TT
1 TT
517357 CATTAGTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTTATCTTCCTTAT
Found at i:529236 original size:106 final size:106
Alignment explanation
Indices: 529067--529262 Score: 295
Period size: 106 Copynumber: 1.8 Consensus size: 106
529057 GCACAAGCTC
* * * *
529067 AACTTCACGGCGAAGGGGCGGCTGACTGTCAATAAACGATTCCCCAATTTCAGATCCAATTTCAA
1 AACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATTCCCCAATTCCAGAACCAATTTCAA
529132 CTTCACAG-CGAAGGACATTGGACTCAAGACACCACAAATTT
66 CTTCA-AGACGAAGGACATTGGACTCAAGACACCACAAATTT
* * *
529173 AACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAATAATTTCCCAGTTCCAGAACCAATTTCAA
1 AACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATTCCCCAATTCCAGAACCAATTTCAA
* *
529238 CTTCATGACGAAGGATATTGGACTC
66 CTTCAAGACGAAGGACATTGGACTC
529263 GGAGCAACGC
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
105 1 0.01
106 79 0.99
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (106 bp):
AACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATTCCCCAATTCCAGAACCAATTTCAA
CTTCAAGACGAAGGACATTGGACTCAAGACACCACAAATTT
Found at i:529746 original size:17 final size:16
Alignment explanation
Indices: 529724--529765 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
529714 TATACGACTA
*
529724 ATATATATTTATATATT
1 ATATATAATTATATA-T
529741 ATATATAATTATATAT
1 ATATATAATTATATAT
529757 ATATTATAA
1 ATA-TATAA
529766 ATATTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATATAATTATATAT
Found at i:529755 original size:12 final size:11
Alignment explanation
Indices: 529724--529781 Score: 65
Period size: 10 Copynumber: 5.8 Consensus size: 11
529714 TATACGACTA
*
529724 ATATA-TATTT
1 ATATATTATAT
529734 ATATATTATAT
1 ATATATTATAT
529745 ATA-ATTATAT
1 ATATATTATAT
529755 ATATATTATA-
1 ATATATTATAT
529765 A-ATATTAT-T
1 ATATATTATAT
529774 AT-TATTAT
1 ATATATTAT
529782 TTTAAAAACT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
9 14 0.33
10 16 0.37
11 13 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATATTATAT
Found at i:529757 original size:21 final size:19
Alignment explanation
Indices: 529732--529781 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 19
529722 TAATATATAT
*
529732 TTATATATTATATATAATTA
1 TTATATATTATAAAT-ATTA
529752 TATATATATTATAAATATTA
1 T-TATATATTATAAATATTA
529772 TTAT-TATTAT
1 TTATATATTAT
529782 TTTAAAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 6 0.21
19 3 0.11
20 6 0.21
21 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATATATTATAAATATTA
Found at i:529774 original size:23 final size:22
Alignment explanation
Indices: 529732--529787 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
529722 TAATATATAT
529732 TTATATATTAT--ATATAATTA
1 TTATATATTATAAATATAATTA
*
529752 TATATATATTATAAATATTATTA
1 T-TATATATTATAAATATAATTA
*
529775 TTAT-TATTTTAAA
1 TTATATATTATAAA
529788 AACTAACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 1 0.03
21 18 0.58
22 3 0.10
23 9 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATATATTATAAATATAATTA
Found at i:530989 original size:2 final size:2
Alignment explanation
Indices: 530978--531009 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
530968 CATTTTTTCT
*
530978 TA TA TG 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
531010 CTTTCGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:531051 original size:18 final size:17
Alignment explanation
Indices: 531017--531060 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
531007 ATACTTTCGG
531017 TTTTTCTATTTCATATTA
1 TTTTT-TATTTCATATTA
*
531035 TTTTTTATTTTATTATTA
1 TTTTTTATTTCA-TATTA
531053 TTATTTTA
1 TT-TTTTA
531061 CTTGTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 12 0.52
19 5 0.22
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTATTTCATATTA
Found at i:531220 original size:19 final size:18
Alignment explanation
Indices: 531196--531241 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
531186 GTTAGTGTTA
531196 TTATTTTTCTTCATTCTAT
1 TTATTTTT-TTCATTCTAT
*
531215 TTATTTCTTTTTATTCTAT
1 TTATTT-TTTTCATTCTAT
*
531234 TCATTTTT
1 TTATTTTT
531242 ATATTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 20 0.83
20 2 0.08
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATTTTTTTCATTCTAT
Found at i:541323 original size:2 final size:2
Alignment explanation
Indices: 541316--541340 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
541306 TGAAGGTTGG
541316 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
541341 GTATGTAAAG
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.