Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009460.1 Hibiscus syriacus cultivar Beakdansim tig00113722_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: 2853300
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 4 of 14
Found at i:563023 original size:19 final size:18
Alignment explanation
Indices: 562994--563077 Score: 66
Period size: 17 Copynumber: 4.6 Consensus size: 18
562984 TATTATTTCC
*
562994 TTTATTTT-TTATTCTTT
1 TTTATTTTCTTTTTCTTT
*
563011 TTTATTTTCTTTATC-TT
1 TTTATTTTCTTTTTCTTT
*
563028 TTTATCTTT-ATTTTCTTT
1 TTTAT-TTTCTTTTTCTTT
* *
563046 GTTTCTTTTGTTTTTCTTTAT
1 -TTTATTTTCTTTTTC-TT-T
563067 TTTATTTTCTT
1 TTTATTTTCTT
563078 CCTTTAATAC
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
17 19 0.37
18 12 0.23
19 9 0.17
20 11 0.21
21 1 0.02
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTATTTTCTTTTTCTTT
Found at i:573701 original size:13 final size:13
Alignment explanation
Indices: 573683--573717 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
573673 AATAGTCATT
573683 TCAGATTTTGGAA
1 TCAGATTTTGGAA
573696 TCAGATTTTGGAA
1 TCAGATTTTGGAA
573709 TCAGATTTT
1 TCAGATTTT
573718 ATCATATCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.43
Consensus pattern (13 bp):
TCAGATTTTGGAA
Found at i:574147 original size:25 final size:27
Alignment explanation
Indices: 574118--574169 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 27
574108 GAATTTTATA
574118 TTAAGATGAGA-AAATTTA-AATATTT
1 TTAAGATGAGATAAATTTATAATATTT
*
574143 TTAAGGTGAGATAAATTTATAATATTT
1 TTAAGATGAGATAAATTTATAATATTT
574170 AAATATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 10 0.42
26 7 0.29
27 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (27 bp):
TTAAGATGAGATAAATTTATAATATTT
Found at i:574177 original size:35 final size:35
Alignment explanation
Indices: 574131--574204 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
574121 AGATGAGAAA
*
574131 ATTTAAATATTTTTAAGGTGAGATAAATTTATAAT
1 ATTTAAATATTTTTAAGGTGAGACAAATTTATAAT
574166 ATTTAAATATTTTTAAGGTGAGACAAATTTATAAT
1 ATTTAAATATTTTTAAGGTGAGACAAATTTATAAT
574201 ATTT
1 ATTT
574205 CGAGGGAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.46
Consensus pattern (35 bp):
ATTTAAATATTTTTAAGGTGAGACAAATTTATAAT
Found at i:576391 original size:2 final size:2
Alignment explanation
Indices: 576341--576373 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
576331 CTAAAAAACA
576341 AT AT AT 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 AT AT AT A
576374 CACACACATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:578472 original size:31 final size:31
Alignment explanation
Indices: 578407--578472 Score: 73
Period size: 31 Copynumber: 2.1 Consensus size: 31
578397 ATATATTTCG
* *
578407 TATTTTAGTGTATATATACTTAAATTAATAA
1 TATTTTAGTATATATATACTTAAATAAATAA
*
578438 TATTTTA-TATATATATTAACTTAAA-AAATTA
1 TATTTTAGTATATATA-T-ACTTAAATAAATAA
578469 TATT
1 TATT
578473 AACTTATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 7 0.23
31 16 0.53
32 7 0.23
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (31 bp):
TATTTTAGTATATATATACTTAAATAAATAA
Found at i:578484 original size:18 final size:17
Alignment explanation
Indices: 578448--578489 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
578438 TATTTTATAT
578448 ATATATTAACTTAAAAA
1 ATATATTAACTTAAAAA
**
578465 ATTATATTAACTTATTAA
1 A-TATATTAACTTAAAAA
578483 ATATATT
1 ATATATT
578490 TTATTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATATTAACTTAAAAA
Found at i:578516 original size:22 final size:21
Alignment explanation
Indices: 578491--578536 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
578481 AAATATATTT
578491 TATTATCAATTTAATTTAAAAA
1 TATT-TCAATTTAATTTAAAAA
* * *
578513 TATTTTATTTTTATTTAAAAA
1 TATTTCAATTTAATTTAAAAA
578534 TAT
1 TAT
578537 ATCTTTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTTCAATTTAATTTAAAAA
Found at i:578548 original size:21 final size:21
Alignment explanation
Indices: 578499--578554 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
578489 TTTATTATCA
*
578499 ATTTA-ATTTAAAAATATTTT
1 ATTTATATTTAAAAATATTCT
*
578519 ATTTTTATTTAAAAATATATCT
1 ATTTATATTTAAAAATAT-TCT
578541 -TTTATA-TTAAAAAT
1 ATTTATATTTAAAAAT
578555 TATGACTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 12 0.39
21 17 0.55
22 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTATATTTAAAAATATTCT
Found at i:578960 original size:42 final size:42
Alignment explanation
Indices: 578898--579066 Score: 151
Period size: 42 Copynumber: 4.0 Consensus size: 42
578888 CATAAATTAA
* * *
578898 AACGAAATGAAACATGACACTTTCGATTCTCGTCTAAAGTAG
1 AACGAAATAAAACATAACACTTTCAATTCTCGTCTAAAGTAG
** * * * *
578940 AACGAAAGGAAGCATAACACTTTTAATTATCGTCTAAAGTAT
1 AACGAAATAAAACATAACACTTTCAATTCTCGTCTAAAGTAG
* ** * * *
578982 AACAAAATAAAACATTGCACTTTCAATTTTCGTCCAAAGTAA
1 AACGAAATAAAACATAACACTTTCAATTCTCGTCTAAAGTAG
* * ** *
579024 AAC-AAAAAAAACATAACATTTTTTATTCTCGTCTAATGTAG
1 AACGAAATAAAACATAACACTTTCAATTCTCGTCTAAAGTAG
579065 AA
1 AA
579067 TAGAAGAAAA
Statistics
Matches: 100, Mismatches: 27, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
41 30 0.30
42 70 0.70
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (42 bp):
AACGAAATAAAACATAACACTTTCAATTCTCGTCTAAAGTAG
Found at i:579048 original size:84 final size:83
Alignment explanation
Indices: 578902--579059 Score: 185
Period size: 84 Copynumber: 1.9 Consensus size: 83
578892 AATTAAAACG
* * * * ** *
578902 AAATGAAACATGACACTTTCGATTCTCGTCTAAAGTAGAACGAAAGGAAGCATAACACTTTTAAT
1 AAATAAAACATGACACTTTCAATTCTCGTCCAAAGTAAAACGAAAAAAAACATAACACTTTT-AT
578967 TATCGTCTAAAGTATAACA
65 TATCGTCTAAAGTATAACA
* *
578986 AAATAAAACATTG-CACTTTCAATTTTCGTCCAAAGTAAAAC-AAAAAAAACATAACATTTTTTA
1 AAATAAAACA-TGACACTTTCAATTCTCGTCCAAAGTAAAACGAAAAAAAACATAACA-CTTTTA
*
579049 TTCTCGTCTAA
64 TTATCGTCTAA
579060 TGTAGAATAG
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
83 23 0.37
84 37 0.60
85 2 0.03
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (83 bp):
AAATAAAACATGACACTTTCAATTCTCGTCCAAAGTAAAACGAAAAAAAACATAACACTTTTATT
ATCGTCTAAAGTATAACA
Found at i:579669 original size:17 final size:17
Alignment explanation
Indices: 579647--579685 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
579637 TGAATCAAAT
*
579647 TAATTATATATTATTTA
1 TAATTAGATATTATTTA
579664 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
579681 -AATTA
1 TAATTA
579686 ATTATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:581279 original size:21 final size:20
Alignment explanation
Indices: 581255--581298 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
581245 TCATTTTTTA
*
581255 AATTTTAAAAATTATTAATTG
1 AATTTT-AAAATTATTAATAG
* *
581276 AATTTTCAAATTGTTAATAG
1 AATTTTAAAATTATTAATAG
581296 AAT
1 AAT
581299 AATGTCATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (20 bp):
AATTTTAAAATTATTAATAG
Found at i:581604 original size:10 final size:10
Alignment explanation
Indices: 581589--581613 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
581579 ATTATATGTT
581589 TGTTCATTTA
1 TGTTCATTTA
581599 TGTTCATTTA
1 TGTTCATTTA
581609 TGTTC
1 TGTTC
581614 GAACTGAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.60
Consensus pattern (10 bp):
TGTTCATTTA
Found at i:605201 original size:17 final size:17
Alignment explanation
Indices: 605170--605217 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
605160 TGTTAATATA
605170 AAACCTAAG-TAAAACTT
1 AAACCTAAGCT-AAACTT
605187 AAACCTAAGCTAAAC-T
1 AAACCTAAGCTAAACTT
*
605203 AAA-CTAAACTAAACT
1 AAACCTAAGCTAAACT
605218 CTGCCGCTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.36
16 4 0.14
17 13 0.46
18 1 0.04
ACGTcount: A:0.54, C:0.21, G:0.04, T:0.21
Consensus pattern (17 bp):
AAACCTAAGCTAAACTT
Found at i:606587 original size:55 final size:53
Alignment explanation
Indices: 606519--607010 Score: 375
Period size: 55 Copynumber: 9.1 Consensus size: 53
606509 AGGATAAGCG
* * * *
606519 AGACTTGAA-AATCTTCAAATAACGGGTCTGCTCCCTATTCTTTTAAGGAGTATA
1 AGACTCGAACAATCTTCAAA-AACGTGTCCGCTCCCTATTC-TTCAAGGAGTATA
* *** * * *
606573 AGATTCGAACAATCTTTGGCAAACGTGTCTGCTGCCTATTCATTCAGGGAGTATA
1 AGACTCGAACAATC-TTCAAAAACGTGTCCGCTCCCTATTC-TTCAAGGAGTATA
* * * *
606628 AGACTCAAACAATCTTCAACAAACGTGTCTGCTCCCTGTTCATTCAGGGAGTATA
1 AGACTCGAACAATCTTCAA-AAACGTGTCCGCTCCCTATTC-TTCAAGGAGTATA
* * *
606683 AGACTCGAATAATCTTTAACAAACGGGTCCGCTCCCTATTCCTTC-AGAGAGTATA
1 AGACTCGAACAATCTTCAA-AAACGTGTCCGCTCCCTATT-CTTCAAG-GAGTATA
*
606738 AGACTCG----ATCTTCAATAAACGTGTCCACTCCCTATTCCTTC-AGAGAGTATA
1 AGACTCGAACAATCTTCAA-AAACGTGTCCGCTCCCTATT-CTTCAAG-GAGTATA
* * *
606789 GGACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCGTTCAGGGAGTATA
1 AGACTCGAACAATCTTCAA-AAACGTGTCCGCTCCCTATTC-TTCAAGGAGTATA
* *
606844 TA-ACTCGAACAATCTTCATAAAACGTGTCCGCTCTCTATTCCTTCAAAGAGTAT-
1 -AGACTCGAACAATCTTCA-AAAACGTGTCCGCTCCCTATT-CTTCAAGGAGTATA
* * *
606898 AGAACTCAAACAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTC-AGAGAGTATA
1 AG-ACTCGAACAATCTTCAA-AAACGTGTCCGCTCCCTATT-CTTCAAG-GAGTATA
* ** *
606954 GGACT----CAATCTTCATCGAACTTGTCCGCTCCCTATTCCTTC-AGAGAGTATA
1 AGACTCGAACAATCTTCA-AAAACGTGTCCGCTCCCTATT-CTTCAAG-GAGTATA
*
607005 GGACTC
1 AGACTC
607011 AATCTTCAAC
Statistics
Matches: 372, Mismatches: 45, Indels: 44
0.81 0.10 0.10
Matches are distributed among these distances:
51 95 0.26
53 1 0.00
54 13 0.03
55 255 0.69
56 8 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (53 bp):
AGACTCGAACAATCTTCAAAAACGTGTCCGCTCCCTATTCTTCAAGGAGTATA
Found at i:606721 original size:110 final size:109
Alignment explanation
Indices: 606528--607010 Score: 482
Period size: 110 Copynumber: 4.5 Consensus size: 109
606518 GAGACTTGAA
* * * * * * ***
606528 AATCTTCAAATAACGGGTCTGCTCCCTATTCTTTTAAGGAGTATAAGATTCGAACAATCTTTGGC
1 AATCTTCAAA-AACGTGTCCGCTCCCTATTCCTTCAAAGAGTATAAGACTCGAACAATCTTCAAC
* * * * *
606593 AAACGTGTCTGCTGCCTATTCATTCAGGGAGTATAAGACTCAAAC
65 AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAAC
* * * ** * *
606638 AATCTTCAACAAACGTGTCTGCTCCCTGTTCATTCAGGGAGTATAAGACTCGAATAATCTTTAAC
1 AATCTTCAA-AAACGTGTCCGCTCCCTATTCCTTCAAAGAGTATAAGACTCGAACAATCTTCAAC
606703 AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACT----C
65 AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAAC
* * * *
606744 GATCTTCAATAAACGTGTCCACTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAAC
1 AATCTTCAA-AAACGTGTCCGCTCCCTATTCCTTCAAAGAGTATAAGACTCGAACAATCTTCAAC
* * *
606809 AAACGGGTCCGCTCCCTATTCGTTCAGGGAGTATATA-ACTCGAAC
65 AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA-AGACTCAAAC
* *
606854 AATCTTCATAAAACGTGTCCGCTCTCTATTCCTTCAAAGAGTAT-AGAACTCAAACAATCTTCAA
1 AATCTTCA-AAAACGTGTCCGCTCCCTATTCCTTCAAAGAGTATAAG-ACTCGAACAATCTTCAA
* ** *
606918 CGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----C
64 CAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAAC
** * * *
606960 AATCTTCATCGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 AATCTTCA-AAAACGTGTCCGCTCCCTATTCCTTCAAAGAGTATAAGACTC
607011 AATCTTCAAC
Statistics
Matches: 319, Mismatches: 44, Indels: 24
0.82 0.11 0.06
Matches are distributed among these distances:
106 136 0.43
107 2 0.01
109 1 0.00
110 178 0.56
111 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (109 bp):
AATCTTCAAAAACGTGTCCGCTCCCTATTCCTTCAAAGAGTATAAGACTCGAACAATCTTCAACA
AACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAAC
Found at i:606808 original size:161 final size:161
Alignment explanation
Indices: 606519--607010 Score: 498
Period size: 161 Copynumber: 3.0 Consensus size: 161
606509 AGGATAAGCG
* * * * * * *
606519 AGACTTGAA-AATCTTCA-AATAACGGGTCTGCTCCCTATTCTTTTAAGGAGTATAAGATTCGAA
1 AGACTCGAACAATCTTCATAA-AACGGGTCCGCTCCCTATTCCTTCAAAGAGTAT-AGA-AC-TA
*** * * * * *
606582 CAATCTTTGGCAAACGTGTCTGCTGCCTATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAA
62 CAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC-AACAATCTTCAA
* *
606647 CAAACGTGTCTGCTCCCTGTTCATTCAGGGAGTATA
126 CAAACGTGTCCGCTCCCTATTCATTCAGGGAGTATA
* * * *
606683 AGACTCGAATAATCTTTA-ACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA-AGACT-CG
1 AGACTCGAACAATCTTCATA-AAACGGGTCCGCTCCCTATTCCTTCAAAGAGTATAGA-ACTACA
* *
606745 ATCTTCAATAAACGTGTCCACTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACA
64 ATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC-AACAATCTTCAACA
* *
606810 AACGGGTCCGCTCCCTATTCGTTCAGGGAGTATA
128 AACGTGTCCGCTCCCTATTCATTCAGGGAGTATA
* *
606844 TA-ACTCGAACAATCTTCATAAAACGTGTCCGCTCTCTATTCCTTCAAAGAGTATAGAACTCAAA
1 -AGACTCGAACAATCTTCATAAAACGGGTCCGCTCCCTATTCCTTCAAAGAGTATAGAACT---A
* * *
606908 CAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT---CAATCTTCATC
62 CAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAACAATCTTCAAC
* * * *
606970 GAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATA
127 AAACGTGTCCGCTCCCTATTCATTCAGGGAGTATA
*
607005 GGACTC
1 AGACTC
607011 AATCTTCAAC
Statistics
Matches: 275, Mismatches: 43, Indels: 23
0.81 0.13 0.07
Matches are distributed among these distances:
161 178 0.65
162 3 0.01
163 2 0.01
164 9 0.03
165 82 0.30
166 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (161 bp):
AGACTCGAACAATCTTCATAAAACGGGTCCGCTCCCTATTCCTTCAAAGAGTATAGAACTACAAT
CTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAACAATCTTCAACAAAC
GTGTCCGCTCCCTATTCATTCAGGGAGTATA
Found at i:606931 original size:216 final size:216
Alignment explanation
Indices: 606549--607010 Score: 583
Period size: 216 Copynumber: 2.1 Consensus size: 216
606539 AACGGGTCTG
* * * * *** * * *
606549 CTCCCTATTCTTTTA-AGGAGTATAAGATTCGAACAATCTTTGGCAAACGTGTCTGCTGCCTATT
1 CTCCCTATTCCTTCAGA-GAGTATAGGACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATT
* * **
606613 CATTCAGGGAGTATAAGACTCAAACAATCTTCAACAAACGTGTCTGCTCCCTGTTCATTCAGGGA
65 CATTCAGGGAGTATAAGACTCAAACAATCTTCAACAAACGTGTCCGCTCCCTATTCATTCAAAGA
* * *
606678 GTATAAGACTCGAATAATCTTTAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACT
130 GTATAAGACTCAAACAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACT
*
606743 CGATCTTCAAT-AAACGTGTCCA
195 CAATCTTC-ATCAAACGTGTCCA
606765 CTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTC
1 CTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTC
* * * *
606830 GTTCAGGGAGTATATA-ACTCGAACAATCTTCATA-AAACGTGTCCGCTCTCTATTCCTTCAAAG
66 ATTCAGGGAGTATA-AGACTCAAACAATCTTCA-ACAAACGTGTCCGCTCCCTATTCATTCAAAG
* ** *
606893 AGTAT-AGAACTCAAACAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGA
129 AGTATAAG-ACTCAAACAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGA
* * *
606957 CTCAATCTTCATCGAACTTGTCCG
193 CTCAATCTTCATCAAACGTGTCCA
606981 CTCCCTATTCCTTCAGAGAGTATAGGACTC
1 CTCCCTATTCCTTCAGAGAGTATAGGACTC
607011 AATCTTCAAC
Statistics
Matches: 212, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
215 4 0.02
216 205 0.97
217 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (216 bp):
CTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTC
ATTCAGGGAGTATAAGACTCAAACAATCTTCAACAAACGTGTCCGCTCCCTATTCATTCAAAGAG
TATAAGACTCAAACAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTC
AATCTTCATCAAACGTGTCCA
Found at i:608476 original size:43 final size:44
Alignment explanation
Indices: 608386--608487 Score: 122
Period size: 43 Copynumber: 2.3 Consensus size: 44
608376 TATTTCTCTT
*
608386 TTTTTCATTTTTCTCTTTTTGTTTTTCTCTTTCATTTTTCTTCCA
1 TTTTTCATTTTT-TCTTTTTGTTTTTCTCTTTCATTTTTCATCCA
* *
608431 TTTTCCATTTTTTCTTTTT-TTTTTCT-TTTCGTTTTTTCCAT-CA
1 TTTTTCATTTTTTCTTTTTGTTTTTCTCTTTC-ATTTTT-CATCCA
608474 TTTTTC-TTTTTTCT
1 TTTTTCATTTTTTCT
608488 CATTCATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
42 12 0.24
43 19 0.37
44 9 0.18
45 11 0.22
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.74
Consensus pattern (44 bp):
TTTTTCATTTTTTCTTTTTGTTTTTCTCTTTCATTTTTCATCCA
Found at i:608478 original size:19 final size:20
Alignment explanation
Indices: 608456--608498 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
608446 TTTTTTTTTC
608456 TTTTCGTTTTTTC-CA-TCAT
1 TTTTC-TTTTTTCTCATTCAT
608475 TTTTCTTTTTTCTCATTCAT
1 TTTTCTTTTTTCTCATTCAT
608495 TTTT
1 TTTT
608499 TTCTTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTCTTTTTTCTCATTCAT
Found at i:608490 original size:16 final size:16
Alignment explanation
Indices: 608386--608651 Score: 96
Period size: 16 Copynumber: 16.2 Consensus size: 16
608376 TATTTCTCTT
*
608386 TTTTTCATTTTTCTC-
1 TTTTTCTTTTTTCTCA
*
608401 TTTTTGTTTTTCTCTTTCA
1 TTTTTCTTTTT-TC--TCA
608420 TTTTTCTTCCATTTTC-CA
1 TTTTTCTT---TTTTCTCA
**
608438 TTTTTTCTTTTTT-TTT
1 -TTTTTCTTTTTTCTCA
608454 TCTTTTCGTTTTTTCCATCA
1 T-TTTTC-TTTTTT-C-TCA
608474 TTTTTCTTTTTTCTCA
1 TTTTTCTTTTTTCTCA
**
608490 TTCAT-TTTTTTCTTC-
1 TTTTTCTTTTTTC-TCA
*
608505 TTTTTC-TTCTTCTCA
1 TTTTTCTTTTTTCTCA
*
608520 TTTTTATTATTATT-T--
1 TTTTTCTT-TT-TTCTCA
*
608535 TTTTTCATTTTT-TCA
1 TTTTTCTTTTTTCTCA
*
608550 TTTTT-TTCATTTTTTCA
1 TTTTTCTT--TTTTCTCA
*
608567 TTTTTTCATTTTT-TCA
1 -TTTTTCTTTTTTCTCA
*
608583 TTTTTTCATTTTT-TCA
1 -TTTTTCTTTTTTCTCA
*
608599 TTTTTTCATTTTT-TCA
1 -TTTTTCTTTTTTCTCA
*
608615 TTTTTTCATTTTT-TCA
1 -TTTTTCTTTTTTCTCA
608631 TTTTTTCATTTTTTCTC-
1 -TTTTTC-TTTTTTCTCA
608648 TTTT
1 TTTT
608652 ATTTATTCTT
Statistics
Matches: 203, Mismatches: 19, Indels: 57
0.73 0.07 0.20
Matches are distributed among these distances:
13 3 0.01
14 5 0.02
15 41 0.20
16 86 0.42
17 21 0.10
18 19 0.09
19 21 0.10
20 2 0.01
21 2 0.01
22 3 0.01
ACGTcount: A:0.09, C:0.16, G:0.01, T:0.74
Consensus pattern (16 bp):
TTTTTCTTTTTTCTCA
Found at i:608547 original size:8 final size:8
Alignment explanation
Indices: 608534--608645 Score: 215
Period size: 8 Copynumber: 13.9 Consensus size: 8
608524 TATTATTATT
608534 TTTTTTCA
1 TTTTTTCA
608542 TTTTTTCA
1 TTTTTTCA
608550 TTTTTTTCA
1 -TTTTTTCA
608559 TTTTTTCA
1 TTTTTTCA
608567 TTTTTTCA
1 TTTTTTCA
608575 TTTTTTCA
1 TTTTTTCA
608583 TTTTTTCA
1 TTTTTTCA
608591 TTTTTTCA
1 TTTTTTCA
608599 TTTTTTCA
1 TTTTTTCA
608607 TTTTTTCA
1 TTTTTTCA
608615 TTTTTTCA
1 TTTTTTCA
608623 TTTTTTCA
1 TTTTTTCA
608631 TTTTTTCA
1 TTTTTTCA
608639 TTTTTTC
1 TTTTTTC
608646 TCTTTTATTT
Statistics
Matches: 103, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
8 95 0.92
9 8 0.08
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTCA
Found at i:616585 original size:25 final size:23
Alignment explanation
Indices: 616539--616585 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
616529 GAAGTTGCTT
*
616539 CTCTACTTTTTCAATTCGATCTG
1 CTCTACTTTTTCAATTCAATCTG
*
616562 CTCTACTCTTTTGAATGTCAATCT
1 CTCTACT-TTTTCAAT-TCAATCT
616586 CCAATCCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 7 0.35
25 6 0.30
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.47
Consensus pattern (23 bp):
CTCTACTTTTTCAATTCAATCTG
Found at i:618288 original size:45 final size:47
Alignment explanation
Indices: 618221--618327 Score: 155
Period size: 45 Copynumber: 2.3 Consensus size: 47
618211 CCATGCTTTG
*
618221 TTATTCATAAAAATAAATCCTAATCGCATGATATCTAATTCGCATGC-
1 TTATTCA-AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
*
618268 TTATTCAAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCA
1 TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
618314 TTTATTCGAAAAAA
1 -TTATTC-AAAAAA
618328 CGAAAATAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
45 27 0.49
46 9 0.16
47 13 0.24
48 6 0.11
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (47 bp):
TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
Found at i:618866 original size:2 final size:2
Alignment explanation
Indices: 618859--618885 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
618849 ATTAAATTAA
618859 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
618886 AACAAAACTT
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:632715 original size:31 final size:31
Alignment explanation
Indices: 632680--632820 Score: 237
Period size: 31 Copynumber: 4.5 Consensus size: 31
632670 CATAGATCCT
*
632680 GAAGAACCTAGGTAAACAATCCATATGTCCC
1 GAAGAACATAGGTAAACAATCCATATGTCCC
*
632711 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAATCCATATGTCCC
* *
632742 GAAGAACATAGGTAAACAGTCCATATGCCCC
1 GAAGAACATAGGTAAACAATCCATATGTCCC
*
632773 GAAGAACATAGGTAAACAATCCATATGTGCC
1 GAAGAACATAGGTAAACAATCCATATGTCCC
632804 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
632821 CCTCGACCCT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAATCCATATGTCCC
Found at i:637621 original size:31 final size:31
Alignment explanation
Indices: 637583--637705 Score: 194
Period size: 31 Copynumber: 4.0 Consensus size: 31
637573 CCCGAAGGAC
*
637583 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
637614 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
637645 CAGTCTATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
637676 CAGTCCATATGTCCCGAAGAGCATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
637706 TGTAGATGCT
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
31 84 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:647820 original size:20 final size:20
Alignment explanation
Indices: 647761--647823 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
647751 TGAAACAAAC
*
647761 CCATCAGTAAGTCTTTCGAG
1 CCATCAGTAAGTCTTTCGGG
* *
647781 -CATGATGATGAAGTCCTTCGGG
1 CCATCA-G-T-AAGTCTTTCGGG
647803 CCATCAGTAAGTCTTTCGGG
1 CCATCAGTAAGTCTTTCGGG
647823 C
1 C
647824 ATGATGATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
19 4 0.12
20 13 0.38
21 2 0.06
22 11 0.32
23 4 0.12
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (20 bp):
CCATCAGTAAGTCTTTCGGG
Found at i:647820 original size:42 final size:42
Alignment explanation
Indices: 647761--648169 Score: 187
Period size: 42 Copynumber: 9.6 Consensus size: 42
647751 TGAAACAAAC
*
647761 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* * *
647803 CCATCAGTAAGTCTTTCGGGCATGATGATTAAATCATTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
** ** * * * * *
647845 TAATTTGTAAGCCTTCACCGAAGAAT-AGTGAAGCAAATCCATCAGTAAGTG
1 CCATCAGTAAGTCTT--TCG-AGCATGA-TGATG-AAATCCTTC-G---G-G
*
647896 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
** ** * * *
647938 TAATTTGTAAG-CCTTC-ACCGAATAGTAGTGAAGCAAA----T----
1 CCATCAGTAAGTCTTTCGA--GCAT-G-A-TGATG-AAATCCTTCGGG
*
647976 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* * * *
648018 TCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* * * * *
648060 CCATAAGTAAGTCTTTCGAGGATGATGATTAAATCATTCAGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* *** * * * *
648102 TCATTTTTGAGTCTTTCGAGTAAGATAAT-AAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
** * *
648143 TTATCCA-TAAGTCTTTCGGGTATGATG
1 CCAT-CAGTAAGTCTTTCGAGCATGATG
648170 TTTTCACACC
Statistics
Matches: 272, Mismatches: 67, Indels: 57
0.69 0.17 0.14
Matches are distributed among these distances:
34 2 0.01
35 4 0.01
36 1 0.00
37 1 0.00
38 11 0.04
39 4 0.01
40 2 0.01
41 33 0.12
42 157 0.58
43 2 0.01
44 4 0.01
45 9 0.03
46 11 0.04
47 9 0.03
48 7 0.03
49 3 0.01
50 1 0.00
51 11 0.04
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (42 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
Found at i:647887 original size:122 final size:122
Alignment explanation
Indices: 647669--647894 Score: 353
Period size: 122 Copynumber: 1.9 Consensus size: 122
647659 TAAACAATCT
* * *
647669 AAGTCCTTTGGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAGTCTTTCAGGTAATTTATAAG
1 AAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAATCATTCAGGTAATTTATAAG
* *
647734 CCTTCATCGAAGAGTAGTGAAACAAACCCATCAGTAAGTCTTTCGAGCATGATGATG
66 CCTTCACCGAAGAATAGTGAAACAAACCCATCAGTAAGTCTTTCGAGCATGATGATG
* * * *
647791 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGGGCATGATGATTAAATCATTCGGGTAATTTGTAAG
1 AAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAATCATTCAGGTAATTTATAAG
* *
647856 CCTTCACCGAAGAATAGTGAAGCAAATCCATCAGTAAGT
66 CCTTCACCGAAGAATAGTGAAACAAACCCATCAGTAAGT
647895 GCCATCAGTA
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
122 93 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (122 bp):
AAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAATCATTCAGGTAATTTATAAG
CCTTCACCGAAGAATAGTGAAACAAACCCATCAGTAAGTCTTTCGAGCATGATGATG
Found at i:647901 original size:13 final size:13
Alignment explanation
Indices: 647883--647907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
647873 TGAAGCAAAT
647883 CCATCAGTAAGTG
1 CCATCAGTAAGTG
647896 CCATCAGTAAGT
1 CCATCAGTAAGT
647908 CTTTCGAGCA
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:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:647967 original size:93 final size:93
Alignment explanation
Indices: 647802--647987 Score: 336
Period size: 93 Copynumber: 2.0 Consensus size: 93
647792 AGTCCTTCGG
*
647802 GCCATCAGTAAGTCTTTCGGGCATGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAA
647867 GAATAGTGAAGCAAATCCATCAGTAAGT
66 GAATAGTGAAGCAAATCCATCAGTAAGT
*
647895 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAA
* *
647960 TAGTAGTGAAGCAAATCCATCAGTAAGT
66 GAATAGTGAAGCAAATCCATCAGTAAGT
647988 CTTTCGAGCA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (93 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAA
GAATAGTGAAGCAAATCCATCAGTAAGT
Found at i:648009 original size:22 final size:21
Alignment explanation
Indices: 647983--648088 Score: 69
Period size: 20 Copynumber: 5.0 Consensus size: 21
647973 AATCCATCAG
647983 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCATGATGA
* * *
648004 TGAAGTCCTTCGGGTCATCA-G-
1 T-AAGTCTTTCGAG-CATGATGA
648025 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCATGATGA
* * *
648046 TTAAATCATTC-AGGCCAT-AAG-
1 -TAAGTCTTTCGA-G-CATGATGA
*
648067 TAAGTCTTTCGAGGATGATGA
1 TAAGTCTTTCGAGCATGATGA
648088 T
1 T
648089 TAAATCATTC
Statistics
Matches: 62, Mismatches: 13, Indels: 20
0.65 0.14 0.21
Matches are distributed among these distances:
19 6 0.10
20 22 0.35
21 5 0.08
22 22 0.35
23 7 0.11
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (21 bp):
TAAGTCTTTCGAGCATGATGA
Found at i:648642 original size:53 final size:53
Alignment explanation
Indices: 648584--648787 Score: 311
Period size: 53 Copynumber: 3.8 Consensus size: 53
648574 ATCACACCAT
*
648584 AAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAG
* * *
648637 AAGATTATTCGAGTTCTACTCCCTGAAGTAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAG
* * *
648690 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTTGGTC-G
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGACAG
* *
648743 AAGATTGTTCGAGTTCTACTCCCTGAAGCAATAGGGAGCAAACCC
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC
648788 TTTTTTTTAG
Statistics
Matches: 138, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
53 135 0.98
54 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAG
Found at i:652223 original size:64 final size:64
Alignment explanation
Indices: 652084--652240 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 64
652074 TAATGAAGGT
* * * ** *
652084 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTTGTATTATTAAAGAG
* * * *
652148 ATACATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGT-TGTATTATTAAAGAG
* * *
652211 AGTGCATTGATGCACTTCTTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
652241 AGACCTTCAA
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
63 2 0.03
64 70 0.91
65 5 0.06
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTTGTATTATTAAAGAG
Found at i:652785 original size:3 final size:3
Alignment explanation
Indices: 652777--652808 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
652767 TCTCGTACAT
652777 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
652809 TGATGAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:657130 original size:12 final size:12
Alignment explanation
Indices: 657113--657155 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
657103 TATCTAATAA
657113 ATAATTATTTTT
1 ATAATTATTTTT
**
657125 ATAATTATAATT
1 ATAATTATTTTT
*
657137 ATAATAATTTTTT
1 ATAATTA-TTTTT
657150 ATAATT
1 ATAATT
657156 GAAATATAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATAATTATTTTT
Found at i:662188 original size:45 final size:46
Alignment explanation
Indices: 662121--662216 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 46
662111 TTATTTTCGT
*
662121 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGTTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCACGCGGTTAGG-TTA
* * *
662168 TTTTTCGAA-CAA-GCATGCGAATTAGATATCACGCGGTTCGGTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCACGCGGTTAGGTTA
662212 TTTTT
1 TTTTT
662217 GTGAATAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
44 8 0.18
45 26 0.58
46 2 0.04
47 9 0.20
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.38
Consensus pattern (46 bp):
TTTTTCGAATAAATGCATGCGAACTAGATATCACGCGGTTAGGTTA
Found at i:671854 original size:9 final size:8
Alignment explanation
Indices: 671835--672037 Score: 65
Period size: 9 Copynumber: 23.2 Consensus size: 8
671825 TCGCTTGAAG
671835 AAGAAATAA
1 AAGAAA-AA
671844 AAGAGAAAA
1 AAGA-AAAA
671853 AATGAAAAA
1 AA-GAAAAA
*
671862 ATGAAAAA
1 AAGAAAAA
671870 AATGAAAAA
1 AA-GAAAAA
*
671879 TAATAAAAATGA
1 -AA-GAAAA--A
671891 GAAGAAGAAA
1 -AAGAA-AAA
*
671901 AAGAAGAA
1 AAGAAAAA
671909 AAG-AAAA
1 AAGAAAAA
*
671916 ATGAGAAAA
1 AAGA-AAAA
671925 AAGAAAAA
1 AAGAAAAA
* *
671933 TGATGGAAAA
1 --AAGAAAAA
671943 AAGAAAAGA
1 AAGAAAA-A
671952 AA-AAAAGA
1 AAGAAAA-A
671960 GAAGAAAAAA
1 -AAG-AAAAA
671970 AATGGAAAATA
1 AA--GAAAA-A
671981 GAAGAAAAA
1 -AAGAAAAA
*
671990 ATG-AAAA
1 AAGAAAAA
*
671997 ATG-AAAA
1 AAGAAAAA
*
672004 AAGAGAAAT
1 AAGA-AAAA
* **
672013 GAGAAATG
1 AAGAAAAA
672021 AA-AAAAA
1 AAGAAAAA
672028 AAGAAAAA
1 AAGAAAAA
672036 AA
1 AA
672038 AGGAGAGTTC
Statistics
Matches: 150, Mismatches: 22, Indels: 45
0.69 0.10 0.21
Matches are distributed among these distances:
7 23 0.15
8 39 0.26
9 45 0.30
10 28 0.19
11 8 0.05
12 7 0.05
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (8 bp):
AAGAAAAA
Found at i:671855 original size:14 final size:15
Alignment explanation
Indices: 671832--672026 Score: 80
Period size: 14 Copynumber: 12.1 Consensus size: 15
671822 ATTTCGCTTG
*
671832 AAGAAGAAAT-AAAA
1 AAGAAAAAATGAAAA
*
671846 GAGAAAAAATGAAAA
1 AAGAAAAAATGAAAA
671861 AATGAAAAAAATGAAAA
1 AA-G-AAAAAATGAAAA
*
671878 ATA-ATAAAAATGAGAAG
1 A-AGA-AAAAATGA-AAA
671895 AAG-AAAAA-GAAGAA
1 AAGAAAAAATGAA-AA
671909 AAG-AAAAATGAGAAAA
1 AAGAAAAAAT--GAAAA
671925 AAGAAAAATGATGGAAAA
1 AAGAAAAA--AT-GAAAA
**
671943 AAGAAAAGAAAAAAAGA
1 AAGAAAA-AATGAAA-A
671960 GAAGAAAAAAAATGGAAAATA
1 -AAG--AAAAAAT-G-AAA-A
671981 GAAGAAAAAATGAAAA
1 -AAGAAAAAATGAAAA
* *
671997 ATGAAAAAA-GAGAA
1 AAGAAAAAATGAAAA
* *
672011 ATG-AGAAATGAAAA
1 AAGAAAAAATGAAAA
672025 AA
1 AA
672027 AAAGAAAAAA
Statistics
Matches: 143, Mismatches: 16, Indels: 44
0.70 0.08 0.22
Matches are distributed among these distances:
13 5 0.03
14 31 0.22
15 19 0.13
16 19 0.13
17 28 0.20
18 17 0.12
19 12 0.08
20 4 0.03
21 8 0.06
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.08
Consensus pattern (15 bp):
AAGAAAAAATGAAAA
Found at i:671925 original size:54 final size:53
Alignment explanation
Indices: 671858--672025 Score: 155
Period size: 54 Copynumber: 3.1 Consensus size: 53
671848 GAAAAAATGA
*
671858 AAAAATGAAAAAAATGAAAAATAAT-AAAAATGAGAAGAAGAAAAAGAAGAAAAG
1 AAAAATGAGAAAAATGAAAAATAATGAAAAATGA-AAGAAGAAAAAG-AGAAAAG
* * * *
671912 AAAAATGAGAAAAAAGAAAAATGATGGAAAAAAGAAAAGAA-AAAAAGAGAAGAAA
1 AAAAATGAGAAAAATGAAAAATAAT-GAAAAATG-AAAGAAGAAAAAGAGAA-AAG
* * * *
671967 AAAAATG-G-AAAATAGAAGAAAAAATGAAAAATGAAAAAAGAGAAATGAGAAATG
1 AAAAATGAGAAAAAT-GAA-AAATAATGAAAAATGAAAGAAGA-AAAAGAGAAAAG
672021 AAAAA
1 AAAAA
672026 AAAAGAAAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
53 9 0.10
54 44 0.47
55 28 0.30
56 11 0.12
57 1 0.01
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.08
Consensus pattern (53 bp):
AAAAATGAGAAAAATGAAAAATAATGAAAAATGAAAGAAGAAAAAGAGAAAAG
Found at i:671943 original size:18 final size:16
Alignment explanation
Indices: 671867--672018 Score: 101
Period size: 16 Copynumber: 9.8 Consensus size: 16
671857 AAAAAATGAA
*
671867 AAAAATGA-AAAATAAT
1 AAAAATGAGAAAA-AAG
*
671883 AAAAATGAG-AAGAAG
1 AAAAATGAGAAAAAAG
*
671898 AAAAA-GA-AGAAAAG
1 AAAAATGAGAAAAAAG
671912 AAAAATGAGAAAAAAG
1 AAAAATGAGAAAAAAG
671928 AAAAATGATGGAAAAAAG
1 AAAAATGA--GAAAAAAG
671946 -AAAA-GA-AAAAAAG
1 AAAAATGAGAAAAAAG
* *
671959 -AGAA-GAAAAAAAATG
1 AAAAATGAGAAAAAA-G
*
671974 GAAAATAGAAGAAAAAATG
1 AAAAAT-G-AGAAAAAA-G
671993 AAAAAT--GAAAAAAG
1 AAAAATGAGAAAAAAG
*
672007 AGAAATGAGAAA
1 AAAAATGAGAAA
672019 TGAAAAAAAA
Statistics
Matches: 112, Mismatches: 10, Indels: 28
0.75 0.07 0.19
Matches are distributed among these distances:
13 12 0.11
14 23 0.21
15 17 0.15
16 33 0.29
17 4 0.04
18 9 0.08
19 14 0.12
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (16 bp):
AAAAATGAGAAAAAAG
Found at i:671948 original size:7 final size:7
Alignment explanation
Indices: 671832--672036 Score: 69
Period size: 7 Copynumber: 26.3 Consensus size: 7
671822 ATTTCGCTTG
*
671832 AAGAAGA
1 AAGAAAA
*
671839 AATAAAA
1 AAGAAAA
*
671846 GAGAAAA
1 AAGAAAA
671853 AATGAAAA
1 AA-GAAAA
671861 AATGAAAAA
1 AA-G-AAAA
671870 AATGAAAA
1 AA-GAAAA
671878 ATA-ATAAA
1 A-AGA-AAA
*
671886 AATGAGAAG
1 AA-GA-AAA
671895 AAG-AAA
1 AAGAAAA
671901 AAGAAGAA
1 AAGAA-AA
671909 AAGAAAA
1 AAGAAAA
671916 ATGAGAAAA
1 A--AGAAAA
671925 AAGAAAA
1 AAGAAAA
671932 ATGATGGAAAA
1 A--A--GAAAA
671943 AAGAAAA
1 AAGAAAA
671950 GAA-AAAA
1 -AAGAAAA
671957 AGAGAAGAA
1 A-AGAA-AA
671966 AA-AAAA
1 AAGAAAA
**
671972 TGGAAAATA
1 AAG-AAA-A
671981 GAAGAAAA
1 -AAGAAAA
671989 AATGAAAA
1 AA-GAAAA
*
671997 ATGAAAA
1 AAGAAAA
672004 AAGAGAAA
1 AAGA-AAA
*
672012 TGAGAAATGA
1 -AAGAAA--A
672022 AA-AAAA
1 AAGAAAA
672028 AAGAAAA
1 AAGAAAA
672035 AA
1 AA
672037 AAGGAGAGTT
Statistics
Matches: 154, Mismatches: 16, Indels: 56
0.68 0.07 0.25
Matches are distributed among these distances:
6 11 0.07
7 52 0.34
8 49 0.32
9 34 0.22
10 2 0.01
11 6 0.04
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (7 bp):
AAGAAAA
Found at i:671950 original size:47 final size:45
Alignment explanation
Indices: 671867--672018 Score: 125
Period size: 45 Copynumber: 3.3 Consensus size: 45
671857 AAAAAATGAA
* *
671867 AAAAATGA-AAAATAATAAAAATGAG-AAGAAGAAAAAGAAGAAAAG
1 AAAAATGAGAAAA-AAGAAAAATGAGAAAAAAGAAAAAGAA-AAAAG
671912 AAAAATGAGAAAAAAGAAAAATGATGGAAAAAAG-AAAAGAAAAAA-
1 AAAAATGAGAAAAAAGAAAAATGA--GAAAAAAGAAAAAGAAAAAAG
* * *
671957 AGAGAA-GAAAAAAAATGGAAAATAGAAGAAAAAATGAAAAATGAAAAAAG
1 A-AAAATGAGAAAAAA-GAAAAAT-G-AGAAAAAA-GAAAAA-GAAAAAAG
*
672007 AGAAATGAGAAA
1 AAAAATGAGAAA
672019 TGAAAAAAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 21
0.75 0.07 0.18
Matches are distributed among these distances:
45 27 0.31
46 24 0.28
47 10 0.12
48 10 0.12
49 9 0.10
50 6 0.07
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (45 bp):
AAAAATGAGAAAAAAGAAAAATGAGAAAAAAGAAAAAGAAAAAAG
Found at i:671986 original size:39 final size:39
Alignment explanation
Indices: 671896--672036 Score: 123
Period size: 39 Copynumber: 3.6 Consensus size: 39
671886 AATGAGAAGA
*
671896 AGAAAAAGAAGAAAAGAAAAATGAGAAAAAAGAAAAATG
1 AGAAAAAGAAGAAAAGAAAAAAGAGAAAAAAGAAAAATG
* *
671935 ATGGAAAA-AAGAAAAGAAAAAAAGAGAAGAAA-AAAAATG
1 A-GAAAAAGAAGAAAAG-AAAAAAGAGAAAAAAGAAAAATG
*
671974 -GAAAATAGAAGAAAA-AATGAAAA-ATGAAAAAAGAGAAATG
1 AGAAAA-AGAAGAAAAGAA--AAAAGA-GAAAAAAGAAAAATG
*
672014 AGAAATGAA-AAAAAAAGAAAAAA
1 AGAAA--AAGAAGAAAAGAAAAAA
672037 AAGGAGAGTT
Statistics
Matches: 83, Mismatches: 7, Indels: 23
0.73 0.06 0.20
Matches are distributed among these distances:
37 6 0.07
38 2 0.02
39 33 0.40
40 28 0.34
41 10 0.12
42 3 0.04
43 1 0.01
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (39 bp):
AGAAAAAGAAGAAAAGAAAAAAGAGAAAAAAGAAAAATG
Found at i:672003 original size:36 final size:36
Alignment explanation
Indices: 671899--672005 Score: 92
Period size: 36 Copynumber: 2.9 Consensus size: 36
671889 GAGAAGAAGA
* **
671899 AAAAGAAGAAAAGAAAAATGAGAAAAAAGAAAAATGATGG
1 AAAA-AAG-AAAGAAAAA-AAG-AAAAAGAAAAAAAATGG
*
671939 AAAAAAGAAAAGAAAAAAAG-AGAAGAAAAAAAATGG
1 AAAAAAG-AAAGAAAAAAAGAAAAAGAAAAAAAATGG
* *
671975 AAAATAG-AAGAAAAAATGAAAAATGAAAAAA
1 AAAAAAGAAAGAAAAAAAGAAAAA-GAAAAAA
672006 GAGAAATGAG
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
34 10 0.17
35 3 0.05
36 26 0.45
38 2 0.03
39 13 0.22
40 4 0.07
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.07
Consensus pattern (36 bp):
AAAAAAGAAAGAAAAAAAGAAAAAGAAAAAAAATGG
Found at i:672025 original size:55 final size:53
Alignment explanation
Indices: 671852--672026 Score: 160
Period size: 55 Copynumber: 3.2 Consensus size: 53
671842 AAAAGAGAAA
* *
671852 AAATGAAAAAATGAAAAAAATGAAAAATAAT-AAAAATGAGAAGAAGAAAAAGAAG
1 AAATGAAAAAATGGAAAAAA-GAAAAATAATGAAAAATGA-AAAAAGAAAAAG-AG
* * *
671907 AAAAG-AAAAATGAGAAAAAAGAAAAATGATGGAAAAAAGAAAAGAA-AAAAAGAG
1 AAATGAAAAAATG-GAAAAAAGAAAAATAAT-GAAAAATGAAAA-AAGAAAAAGAG
* * * *
671961 AAGA-AAAAAAATGGAAAATAGAAGAAAAAATGAAAAATGAAAAAAGAGAAATGAG
1 AA-ATGAAAAAATGGAAAAAAGAA-AAATAATGAAAAATGAAAAAAGA-AAAAGAG
672016 AAATGAAAAAA
1 AAATGAAAAAA
672027 AAAGAAAAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 20
0.75 0.09 0.15
Matches are distributed among these distances:
53 2 0.02
54 42 0.43
55 45 0.46
56 9 0.09
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (53 bp):
AAATGAAAAAATGGAAAAAAGAAAAATAATGAAAAATGAAAAAAGAAAAAGAG
Found at i:673152 original size:21 final size:21
Alignment explanation
Indices: 673126--673170 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
673116 GATTTCTGGG
* *
673126 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
673147 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
673168 CAA
1 CAA
673171 ACGAACATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:673243 original size:23 final size:22
Alignment explanation
Indices: 673199--673243 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
673189 AATGCCAGAG
*
673199 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
673221 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
673244 AAAATGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:674580 original size:32 final size:31
Alignment explanation
Indices: 674538--674665 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
674528 AGAGTCGAGG
674538 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
674569 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
674601 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
674632 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
674663 GTT
1 GTT
674666 ACCGAGGATC
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
31 54 0.66
32 28 0.34
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:674685 original size:30 final size:30
Alignment explanation
Indices: 674624--674720 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
674614 CTAAGGAACA
* * ***
674624 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
674655 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
674685 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
674715 TCTGGA
1 TATGGA
674721 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:674721 original size:30 final size:30
Alignment explanation
Indices: 674651--674723 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
674641 GGTTCTTCGG
* *
674651 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
674681 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
674711 GACCTCTGGATAG
1 GACCTCTGGATAG
674724 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:676378 original size:37 final size:36
Alignment explanation
Indices: 676324--676395 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 36
676314 AAACAGGCCA
*
676324 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGAAAACC
1 ATCTTAAGCCTTCACGGAAAAGTAGTGAAGAAAACC
* *
676360 ATCTGTAAGCCTTCACGGAAAATTAGTGAAGCAAAC
1 ATCT-TAAGCCTTCACGGAAAAGTAGTGAAGAAAAC
676396 TCATTTTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 4 0.12
37 28 0.88
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGGAAAAGTAGTGAAGAAAACC
Found at i:676461 original size:51 final size:51
Alignment explanation
Indices: 676397--676764 Score: 235
Period size: 51 Copynumber: 6.9 Consensus size: 51
676387 GAAGCAAACT
* *
676397 CATTTTATGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGATCGGACA
1 CATTTTATAAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
676448 CATTTTATAAAGATCAAGTCATATACTCTCTGAAAGAATAGGGAGCGGACT
1 CATTTTATAAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
** * * *
676499 TGTTTGT-TAAAGATTGAGTCCTACACTCTCTGAAGGAATAGGGAGCGGA-T
1 CATTT-TATAAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
676549 C-TGTTTATTGAAGATTTCCGAGTTCAATACTCTCTGAAGGAATAGGGAGCGGAC-
1 CAT-TTTA-TAAAGA--T-CGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * * *
676603 C-TGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAACAGAGAGCTGACC
1 CAT-TTTA-TAAAGA----TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * * * *
676659 CGTTTTATTGAAGATTATTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 CATTTTA-T-AA-A-GA-TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
676715 CATTTTATGAAGATTGTTCGAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 CATTTTAT-AA-A--GATCGAGTCCTATACTCT-CTGAAGGAATAGGGAGC
676765 AGGCTCGTCA
Statistics
Matches: 262, Mismatches: 38, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
49 2 0.01
50 3 0.01
51 90 0.34
52 1 0.00
53 1 0.00
54 46 0.18
55 66 0.25
56 49 0.19
57 2 0.01
58 1 0.00
59 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (51 bp):
CATTTTATAAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:676598 original size:54 final size:54
Alignment explanation
Indices: 676410--676764 Score: 315
Period size: 55 Copynumber: 6.6 Consensus size: 54
676400 TTTATGAAGA
* * *
676410 TCGAGTCCTATACTCTCTGAAGGAATAGGGATCGGACACAT-TTTA-TAAAGA---
1 TCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGAC-C-TGTTTATTGAAGATTT
* * * * *
676461 TCAAG-TCATATACTCTCTGAAAGAATAGGGAGCGGACTTGTTTGTTAAAGA--T
1 TCGAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGATTT
* * *
676513 T-GAGTCCTACACTCTCTGAAGGAATAGGGAGCGGATCTGTTTATTGAAGATTT
1 TCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGATTT
* *
676566 CCGAGTTCAATACTCTCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGATTTT
1 TCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGA-TTT
* * * *
676621 TCGAGTTCTATACTCTCTGAAGGAACAGAGAGCTGACCCGTTTTATTGAAGATTAT
1 TCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCTG-TTTATTGAAGATT-T
* * * *
676677 TCAAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACACAT-TTTA-TGAAGATTGT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGAC-C-TGTTTATTGAAGATT-T
676732 TCGAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
1 TCGAGTTC-TATACTCT-CTGAAGGAATAGGGAGC
676765 AGGCTCGTCA
Statistics
Matches: 255, Mismatches: 34, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
49 1 0.00
50 4 0.02
51 76 0.30
52 2 0.01
53 1 0.00
54 46 0.18
55 78 0.31
56 46 0.18
57 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (54 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGATTT
Found at i:676726 original size:111 final size:109
Alignment explanation
Indices: 676410--676756 Score: 272
Period size: 111 Copynumber: 3.2 Consensus size: 109
676400 TTTATGAAGA
* * * * * * *
676410 TCGAGTCCTATACTCTCTGAAGGAATAGGGATCGGACACATTT-TATAAAGA--T-CAAG-TCAT
1 TCGAGTTCTATACTCTCTGAAGGAACAGAGAGCGGACCCGTTTAT-TGAAGATTTCCAAGTTCA-
* * * * * *
676470 ATACTCTCTGAAAGAATAGGGAGCGGACTTGTTTGTTAAAGA---T
64 ATACTCTCTGAAGGAATAGAGAGCAGACCTGTTTATTGAAGATTGT
* * * * * * *
676513 T-GAGTCCTACACTCTCTGAAGGAATAGGGAGCGGATCTGTTTATTGAAGATTTCCGAGTTCAAT
1 TCGAGTTCTATACTCTCTGAAGGAACAGAGAGCGGACCCGTTTATTGAAGATTTCCAAGTTCAAT
* * *
676577 ACTCTCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGATTTT
66 ACTCTCTGAAGGAATAGAGAGCAGACCTGTTTATTGAAGATTGT
* *
676621 TCGAGTTCTATACTCTCTGAAGGAACAGAGAGCTGACCCGTTTTATTGAAGATTATTCAAG-TCT
1 TCGAGTTCTATACTCTCTGAAGGAACAGAGAGCGGACCCG-TTTATTGAAGATT-TCCAAGTTC-
* *
676685 TATACTCTCTGAATGAATAGAGAGCAGACACAT-TTTA-TGAAGATTGT
63 AATACTCTCTGAAGGAATAGAGAGCAGAC-C-TGTTTATTGAAGATTGT
676732 TCGAG-TCTTATACT-TCCTGAAGGAA
1 TCGAGTTC-TATACTCT-CTGAAGGAA
676757 TAGGGAGCAG
Statistics
Matches: 202, Mismatches: 26, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
102 40 0.20
103 2 0.01
104 1 0.00
105 41 0.20
106 3 0.01
108 2 0.01
109 31 0.15
110 18 0.09
111 58 0.29
112 5 0.02
113 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (109 bp):
TCGAGTTCTATACTCTCTGAAGGAACAGAGAGCGGACCCGTTTATTGAAGATTTCCAAGTTCAAT
ACTCTCTGAAGGAATAGAGAGCAGACCTGTTTATTGAAGATTGT
Found at i:676781 original size:55 final size:54
Alignment explanation
Indices: 676575--676794 Score: 167
Period size: 55 Copynumber: 4.0 Consensus size: 54
676565 TCCGAGTTCA
* * * * * *
676575 ATACTCTCTGAAGGAATAGGGAGCGGAC-CTGTTTATTGAAGATTTTTCGAGT-TCT
1 ATACTCTCTGAAGGAATAGAGAGCAGACAC-ATAT-TTGAAGATTATTCAAGTCT-T
* * * * *
676630 ATACTCTCTGAAGGAACAGAGAGCTGACCCGTTTTATTGAAGATTATTCAAGTCTT
1 ATACTCTCTGAAGGAATAGAGAGCAGACAC-ATAT-TTGAAGATTATTCAAGTCTT
* * * *
676686 ATACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGTTCGAGTCTT
1 ATACTCTCTGAAGGAATAGAGAGCAGACACATATT-TGAAGATTATTCAAGTCTT
* * * * *
676741 ATACT-TCCTGAAGGAATAGGGAGCAGGCTCGTCATTTGAAGATTTTTCAAGTCT
1 ATACTCT-CTGAAGGAATAGAGAGCAGACACAT-ATTTGAAGATTATTCAAGTCT
676795 CACTTATCCC
Statistics
Matches: 138, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
54 2 0.01
55 86 0.62
56 49 0.36
57 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (54 bp):
ATACTCTCTGAAGGAATAGAGAGCAGACACATATTTGAAGATTATTCAAGTCTT
Found at i:687497 original size:62 final size:62
Alignment explanation
Indices: 687400--687523 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
687390 CTACTATTCC
687400 TATAAAAAAATAATGCCATAACAACATTTCATCAGCGGAATCAAAAATGGGATGTGGGATAG
1 TATAAAAAAATAATGCCATAACAACATTTCATCAGCGGAATCAAAAATGGGATGTGGGATAG
687462 TATAAAAAAATAATGCCATAACAACATTTCATCAGCGGAATCAAAAATGGGATGTGGGATAG
1 TATAAAAAAATAATGCCATAACAACATTTCATCAGCGGAATCAAAAATGGGATGTGGGATAG
687524 AGGCAAACCG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (62 bp):
TATAAAAAAATAATGCCATAACAACATTTCATCAGCGGAATCAAAAATGGGATGTGGGATAG
Found at i:714023 original size:21 final size:21
Alignment explanation
Indices: 713994--714046 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
713984 ATTCTGACTA
713994 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
714015 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
714036 TCGCAATGCGA
1 TCGCATTGCGA
714047 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:714099 original size:21 final size:20
Alignment explanation
Indices: 714036--714258 Score: 169
Period size: 20 Copynumber: 10.7 Consensus size: 20
714026 TTTTCCTAAT
714036 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
714056 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
714076 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
714097 TCGCAATGCGAATACGTAAATCCTAA
1 TCGCAATGCGAATACGT--A----AA
* * *
714123 TTCGCATTGCGATTTACGT-AT
1 -TCGCAATGCGA-ATACGTAAA
** * * * *
714144 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGA-ATACGTAAA
714165 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
714185 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
714205 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
714226 TTGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
714246 TCGCAATGCGAAT
1 TCGCAATGCGAAT
714259 CTGACTATCG
Statistics
Matches: 162, Mismatches: 30, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
20 97 0.60
21 47 0.29
22 1 0.01
26 2 0.01
27 10 0.06
28 5 0.03
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:714108 original size:41 final size:41
Alignment explanation
Indices: 714036--714258 Score: 166
Period size: 41 Copynumber: 5.3 Consensus size: 41
714026 TTTTCCTAAT
* * *
714036 TCGCAATGCGAA-TACGTAAATCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
714076 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
* * * ** * * * *
714117 TC-CTAATTCGCATT-GCGATTTACGTATTCGCGTTGCGATTTTCATAAT
1 TCGC-AATGCGAATTAG-GA---A---AATCGCAATGCGA-ATACGTAAA
* * * * *
714165 TCGCAATGCGAA-TACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
* *
714205 TCGCAATGCGAATTAGGAAAATTGCAATGCGAATACATAAA
1 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
714246 TCGCAATGCGAAT
1 TCGCAATGCGAAT
714259 CTGACTATCG
Statistics
Matches: 139, Mismatches: 31, Indels: 25
0.71 0.16 0.13
Matches are distributed among these distances:
40 31 0.22
41 80 0.58
44 2 0.01
47 12 0.09
48 13 0.09
49 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (41 bp):
TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
Found at i:714159 original size:129 final size:130
Alignment explanation
Indices: 713994--714247 Score: 429
Period size: 129 Copynumber: 2.0 Consensus size: 130
713984 ATTCTGACTA
* *
713994 TCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCG
1 TCGCATTGCGATTTCACAAATTCGCGTTGCGATTTTCATAATTCGCAATGCGAATACGTAAATCG
* *
714059 CAACGCGAATACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAATCCTAAT
66 CAACGCGAATAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATACATAAATCCTAAT
**
714124 TCGCATTGCGATTT-ACGTATTCGCGTTGCGATTTTCATAATTCGCAATGCGAATACGTAAATCG
1 TCGCATTGCGATTTCACAAATTCGCGTTGCGATTTTCATAATTCGCAATGCGAATACGTAAATCG
* *
714188 CAACGCGATTAAGTAAATCGCAATGCGAATTAGGAAAATTGCAATGCGAATACATAAATC
66 CAACGCGAATAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATACATAAATC
714248 GCAATGCGAA
Statistics
Matches: 116, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
129 102 0.88
130 14 0.12
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (130 bp):
TCGCATTGCGATTTCACAAATTCGCGTTGCGATTTTCATAATTCGCAATGCGAATACGTAAATCG
CAACGCGAATAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATACATAAATCCTAAT
Found at i:714283 original size:41 final size:39
Alignment explanation
Indices: 714150--714284 Score: 114
Period size: 41 Copynumber: 3.3 Consensus size: 39
714140 GTATTCGCGT
* *
714150 TGCGATTTTCATAATTCGCAATGCGAATAC-GTAAATCGCAA
1 TGCGA-TTACATAAATCGCAATGCGAAT-CTG-AAATCGCAA
* *
714191 CGCGATTA-AGTAAATCGCAATGCGAAT-TAGGAAAATTGCAA
1 TGCGATTACA-TAAATCGCAATGCGAATCT--G-AAATCGCAA
* *
714232 TGCGAATACATAAATCGCAATGCGAATCTGACTATCGCAA
1 TGCGATTACATAAATCGCAATGCGAATCTGA-AATCGCAA
714272 TGCGATTTACATA
1 TGCGA-TTACATA
714285 GCGTCATTCG
Statistics
Matches: 76, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
39 2 0.03
40 30 0.39
41 42 0.55
42 2 0.03
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (39 bp):
TGCGATTACATAAATCGCAATGCGAATCTGAAATCGCAA
Found at i:714543 original size:27 final size:27
Alignment explanation
Indices: 714486--714538 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
714476 CATCGCCGGC
* *
714486 GAAATCCCTCACAAACATTCACAGTCA
1 GAAATCCCTCACAAACATTCAAAATCA
*
714513 GAAATCCCTCACAATCATTCAGAAAT
1 GAAATCCCTCACAAACATTCA-AAAT
714539 GGAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.42, C:0.30, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCCCTCACAAACATTCAAAATCA
Found at i:714844 original size:19 final size:20
Alignment explanation
Indices: 714802--714856 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
714792 TAGTTTCGAG
714802 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGCGGA
**
714822 AATGACTATCGCAACGC-GA
1 AATGAAAATCGCAACGCGGA
714841 AATGAAAATCGCAACG
1 AATGAAAATCGCAACG
714857 AGATAATCGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGGA
Found at i:714924 original size:14 final size:14
Alignment explanation
Indices: 714905--714959 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
714895 TTCATTTCGT
714905 GTTGCGATTCTCTC
1 GTTGCGATTCTCTC
*
714919 GTTGCGATTTTCATTTCGC
1 GTTGCGA--TTC---TCTC
714938 GTTGCGATTCTCTC
1 GTTGCGATTCTCTC
714952 GTTGCGAT
1 GTTGCGAT
714960 AGTCATTTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.24, G:0.24, T:0.44
Consensus pattern (14 bp):
GTTGCGATTCTCTC
Found at i:714934 original size:33 final size:33
Alignment explanation
Indices: 714887--715008 Score: 145
Period size: 33 Copynumber: 3.5 Consensus size: 33
714877 CAAAATCGCA
* *
714887 TTGCAATTTTCATTTCGTGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
714920 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
714953 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGCG------ATTCTCTCG
714993 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
715009 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
33 44 0.58
34 9 0.12
39 1 0.01
40 22 0.29
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:714985 original size:20 final size:20
Alignment explanation
Indices: 714918--715008 Score: 81
Period size: 20 Copynumber: 4.9 Consensus size: 20
714908 GCGATTCTCT
714918 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATTTTCATTTCCG
*
714937 CGTTGCGA--TTC---T-CT
1 CGTTGCGATTTTCATTTCCG
**
714951 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
*
714971 CGTTGCGATTTTCA-TTCTCT
1 CGTTGCGATTTTCATTTC-CG
714991 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
715009 AACCAAAAGA
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.17
16 2 0.03
17 3 0.05
19 12 0.21
20 28 0.48
21 3 0.05
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:716886 original size:94 final size:93
Alignment explanation
Indices: 716695--717070 Score: 598
Period size: 94 Copynumber: 4.1 Consensus size: 93
716685 TAGATTGCTT
* *
716695 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
716756 ATTTGTCTTTTTTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
716785 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
**
716850 ATTTGTCTTTGTTTTACCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
716879 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTCAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
716944 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
716973 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
717038 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
717066 AGTAA
1 AGTAA
717071 TGCAATCCAT
Statistics
Matches: 268, Mismatches: 13, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
90 35 0.13
92 3 0.01
93 25 0.09
94 205 0.76
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:717208 original size:19 final size:19
Alignment explanation
Indices: 717159--717274 Score: 125
Period size: 20 Copynumber: 6.3 Consensus size: 19
717149 TCTTTTGGTT
* * *
717159 GAAATGAAAATTGCAACGA
1 GAAACGAAAATCGCAACGC
*
717178 GAGAATGAAAATCGCAACGC
1 GA-AACGAAAATCGCAACGC
717198 GAAACGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
717217 GAAATGAAAATCGCAA--C
1 GAAACGAAAATCGCAACGC
717234 G--AC-AAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
717250 GAAACGAAAAATCGCTACGC
1 GAAACG-AAAATCGCAACGC
717270 GAAAC
1 GAAAC
717275 TATAATCGCG
Statistics
Matches: 84, Mismatches: 6, Indels: 13
0.82 0.06 0.13
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 33 0.39
20 34 0.40
ACGTcount: A:0.48, C:0.22, G:0.21, T:0.09
Consensus pattern (19 bp):
GAAACGAAAATCGCAACGC
Found at i:717241 original size:33 final size:36
Alignment explanation
Indices: 717164--717264 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 36
717154 TGGTTGAAAT
* *
717164 GAAAATTGCAACGAGAGAATGAAAATCGCAACGCGAAAC
1 GAAAATCGCAACGCGA-AATGAAAATCGCAAC-CG-AAC
717203 GAAAATCGCAACGCGAAATGAAAATCGCAA-CG-AC
1 GAAAATCGCAACGCGAAATGAAAATCGCAACCGAAC
*
717237 -AAAATCGCAACGCGAAACGAAAAATCGC
1 GAAAATCGCAACGCGAAATG-AAAATCGC
717265 TACGCGAAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
33 18 0.31
34 10 0.17
36 2 0.03
38 14 0.24
39 14 0.24
ACGTcount: A:0.49, C:0.22, G:0.21, T:0.09
Consensus pattern (36 bp):
GAAAATCGCAACGCGAAATGAAAATCGCAACCGAAC
Found at i:717320 original size:19 final size:19
Alignment explanation
Indices: 717280--717387 Score: 91
Period size: 19 Copynumber: 5.8 Consensus size: 19
717270 GAAACTATAA
**
717280 TCGCGTTGCGATTTTTGGTT
1 TCGCGTTGCGA-TTTTCATT
717300 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
717319 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
717333 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
717352 TCGCGATGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
717373 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
717388 AAGTTCCATT
Statistics
Matches: 70, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 30 0.43
20 11 0.16
21 13 0.19
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:717857 original size:21 final size:21
Alignment explanation
Indices: 717833--717899 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
717823 TCATTCCTCG
717833 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
717854 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
717875 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
717896 AGAG
1 AGAG
717900 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:717857 original size:42 final size:42
Alignment explanation
Indices: 717781--717899 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
717771 GACTCGCCTG
* * * * * * *
717781 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
717823 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
717865 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
717900 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:719270 original size:14 final size:14
Alignment explanation
Indices: 719251--719286 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
719241 ATTGTTTAAT
719251 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
719265 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
719279 TGATTTGT
1 TGATTTGT
719287 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:719409 original size:19 final size:19
Alignment explanation
Indices: 719393--719439 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
719383 AAAAATGACT
*
719393 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
719412 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
719431 ATCGCAACG
1 ATCGCAACG
719440 ACAAAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:719496 original size:19 final size:19
Alignment explanation
Indices: 719464--719610 Score: 99
Period size: 19 Copynumber: 8.5 Consensus size: 19
719454 CGAAACTAAA
*
719464 TTCGCATTGTGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
719483 TTCGCTTTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
719499 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
719516 TTCACATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
719532 AT--CATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
719549 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
719565 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
719582 TTCGCATTGCGATAGTCAT
1 TTCGCATTGCGATTTTCAT
719601 TTCCGCATTG
1 TT-CGCATTG
719611 AGATAGACAT
Statistics
Matches: 99, Mismatches: 13, Indels: 31
0.69 0.09 0.22
Matches are distributed among these distances:
14 20 0.20
16 18 0.18
17 17 0.17
19 37 0.37
20 7 0.07
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:719516 original size:33 final size:33
Alignment explanation
Indices: 719474--719594 Score: 197
Period size: 33 Copynumber: 3.7 Consensus size: 33
719464 TTCGCATTGT
* *
719474 GATTTTCATTTCGCTTTGCGATTCCCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
* * *
719507 GATTTTCATTTCACATTGCGATTCTATCATTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
719540 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
719573 GATTTTCATTTCGCATTGCGAT
1 GATTTTCATTTCGCATTGCGAT
719595 AGTCATTTCC
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
Found at i:719574 original size:66 final size:66
Alignment explanation
Indices: 719468--719594 Score: 218
Period size: 66 Copynumber: 1.9 Consensus size: 66
719458 ACTAAATTCG
* *
719468 CATTGTGATTTTCATTTCGCTTTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGCGATTCTA
1 CATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGCGATTCTA
719533 T
66 T
* *
719534 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 CATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGCGAT
719595 AGTCATTTCC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.46
Consensus pattern (66 bp):
CATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGCGATTCTA
T
Found at i:719609 original size:20 final size:19
Alignment explanation
Indices: 719578--719621 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
719568 GTTGCGATTT
*
719578 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGAGATAG
719597 TCATTTCCGCATTGAGATAG
1 TCATTT-CGCATTGAGATAG
*
719617 ACATT
1 TCATT
719622 AAGATGATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (19 bp):
TCATTTCGCATTGAGATAG
Found at i:719660 original size:20 final size:20
Alignment explanation
Indices: 719588--719660 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 20
719578 TCATTTCGCA
**
719588 TTGCGATAGTCATTTCCGCA
1 TTGCGATAGTCATTTCCGTG
* * **
719608 TTGAGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCG-TG
719628 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
719649 TTGCGATAGTCA
1 TTGCGATAGTCA
719661 AATGAATGCC
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
19 3 0.08
20 21 0.55
21 11 0.29
22 3 0.08
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:722165 original size:24 final size:24
Alignment explanation
Indices: 722131--722184 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
722121 CTGAAAAATC
722131 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
722155 ATCAAAGTCCGGGTATTGATCAAG
1 ATCAAAATCCGAGTATTGACCAAG
722179 ATCAAA
1 ATCAAA
722185 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:723070 original size:20 final size:19
Alignment explanation
Indices: 723047--723280 Score: 180
Period size: 20 Copynumber: 11.5 Consensus size: 19
723037 AGAATCTCGT
723047 TGCGATTTACTAAATCGCAA
1 TGCGA-TTACTAAATCGCAA
*
723067 TGCGATTACGTAAATCGAAA
1 TGCGATTAC-TAAATCGCAA
* ** *
723087 TACGAATTAGAAAAATCACAA
1 TGCG-ATTA-CTAAATCGCAA
*
723108 TGCGAATACGTAAATCGCAA
1 TGCGATTAC-TAAATCGCAA
723128 TGCGATTACGTAAATCGCAA
1 TGCGATTAC-TAAATCGCAA
**
723148 TGCGAATTAAGAAAATCGCAA
1 TGCG-ATT-ACTAAATCGCAA
723169 TGCGATTACGTAAATCGCAA
1 TGCGATTAC-TAAATCGCAA
* **
723189 AGCGAATTAGAAAAATCGCAA
1 TGCG-ATTA-CTAAATCGCAA
**
723210 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTA-CTAAATCGCAA
*
723231 TGCGATTGCGTAAATCGCAA
1 TGCGATTAC-TAAATCGCAA
**
723251 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTA-CTAAATCGCAA
723272 TGCGATTAC
1 TGCGATTAC
723281 GTATTCGCAT
Statistics
Matches: 174, Mismatches: 28, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
19 5 0.03
20 86 0.49
21 82 0.47
22 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (19 bp):
TGCGATTACTAAATCGCAA
Found at i:723102 original size:21 final size:20
Alignment explanation
Indices: 723058--723357 Score: 238
Period size: 21 Copynumber: 14.7 Consensus size: 20
723048 GCGATTTACT
*
723058 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTA-GA
* *
723078 AAATCGAAATACGAATTAGAA
1 AAATCGCAATGCGAATTAG-A
* *
723099 AAATCACAATGCGAA-TACGT
1 AAATCGCAATGCGAATTA-GA
*
723119 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTA-GA
723139 AAATCGCAATGCGAATTAAGA
1 AAATCGCAATGCGAATT-AGA
*
723160 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTA-GA
*
723180 AAATCGCAAAGCGAATTAGAA
1 AAATCGCAATGCGAATTAG-A
723201 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTA-GA
* *
723222 AAATCGCAATGCG-ATTGCGT
1 AAATCGCAATGCGAATT-AGA
723242 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTA-GA
723263 AAATCGCAATGCG-ATTACG-
1 AAATCGCAATGCGAATTA-GA
* * * *
723282 TATTCGCATTGCGATTTACG-
1 AAATCGCAATGCGAATTA-GA
* * *
723302 TATTCGCATTGCGAATTAGGA
1 AAATCGCAATGCGAATTA-GA
* * *
723323 AAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCGAA-TTAGA
723344 AAATCGCAATGCGA
1 AAATCGCAATGCGA
723358 TAGTCAGAAT
Statistics
Matches: 233, Mismatches: 31, Indels: 31
0.79 0.11 0.11
Matches are distributed among these distances:
19 12 0.05
20 106 0.45
21 111 0.48
22 4 0.02
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
AAATCGCAATGCGAATTAGA
Found at i:723109 original size:41 final size:40
Alignment explanation
Indices: 723058--723358 Score: 270
Period size: 41 Copynumber: 7.4 Consensus size: 40
723048 GCGATTTACT
* *
723058 AAATCGCAATGCGATTACGTAAATCGAAATACGAATTAGAA
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAG-A
* * *
723099 AAATCACAATGCGAATACGTAAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTA-GA
* * *
723139 AAATCGCAATGCGAATTAAGAAAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCG-ATTACGTAAATCGCAATGCGAATTA-GA
* *
723180 AAATCGCAAAGCGAATTA-GAAAAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCG-ATTACG-TAAATCGCAATGCGAATTA-GA
*
723222 AAATCGCAATGCGATTGCGTAAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTA-GA
* * *
723263 AAATCGCAATGCGATTACGT-ATTCGCATTGCGATTTACG-
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTA-GA
* * * * * * * *
723302 TATTCGCATTGCGAATTAGGAAAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCG-ATTACGTAAATCGCAATGCGAA-TTAGA
723344 AAATCGCAATGCGAT
1 AAATCGCAATGCGAT
723359 AGTCAGAATC
Statistics
Matches: 218, Mismatches: 33, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
39 10 0.05
40 37 0.17
41 141 0.65
42 30 0.14
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (40 bp):
AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGA
Found at i:723122 original size:61 final size:61
Alignment explanation
Indices: 723047--723358 Score: 314
Period size: 61 Copynumber: 5.1 Consensus size: 61
723037 AGAATCTCGT
* * *
723047 TGCGATTTAC-TAAATCGCAATGCGATTACGTAAATCGAAATACGAATTAGAAAAATCACAA
1 TGCGA-TTACGTAAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGAAAAATCGCAA
*
723108 TGCGAATACGTAAATCGCAATGCGATTACGTAAATCGCAATGCGAATTA-AGAAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGA-AAAATCGCAA
* * *
723169 TGCGATTACGTAAATCGCAAAGCGAATTA-GAAAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCG-ATTACG-TAAATCGCAATGCGAATTAGAAAAATCGCAA
* * * * * *
723231 TGCGATTGCGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCG-ATTACG--TATTCGCAT
1 TGCGATTACGTAAATCGCAATGCG-ATTACGTAAATCGCAATGCGAATTA-GAAAAATCGCAA
* * * * * * **
723291 TGCGATTTACGT-ATTCGCATTGCGAATTAGGAAAATCGCAACGCGAATTTGGGAAATCGCAA
1 TGCGA-TTACGTAAATCGCAATGCG-ATTACGTAAATCGCAATGCGAATTAGAAAAATCGCAA
723353 TGCGAT
1 TGCGAT
723359 AGTCAGAATC
Statistics
Matches: 219, Mismatches: 21, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
60 46 0.21
61 87 0.40
62 85 0.39
63 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (61 bp):
TGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGAAAAATCGCAA
Found at i:723294 original size:19 final size:20
Alignment explanation
Indices: 723266--723315 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
723256 ATTAGGAAAA
*
723266 TCGCAATGCGA-TTACGTAT
1 TCGCATTGCGATTTACGTAT
723285 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
723305 TCGCATTGCGA
1 TCGCATTGCGA
723316 ATTAGGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:724216 original size:77 final size:75
Alignment explanation
Indices: 724105--724473 Score: 337
Period size: 77 Copynumber: 4.8 Consensus size: 75
724095 TGCGTCTAAA
* * * *
724105 AATGTCATAGTTCACTAAGAAATAGGTTGTGATATGGAATGTTAATATTTTTACTAATAAAATAA
1 AATGTCATGGTTCACTAAGAAATA-GAT-TGATATAGAATGTTAATATTTTTATTAATAAAATAA
724170 GTTGCGCCCAAG
64 GTTGCGCCCAAG
* * * *
724182 AATATCATGGTTTACTAAGAAATAAATTACGATATAGAATGTTAATATTTTTATTAATAAAATGA
1 AATGTCATGGTTCACTAAGAAATAGATT--GATATAGAATGTTAATATTTTTATTAATAAAATAA
* **
724247 GTTACTTCCAAG
64 GTTGCGCCCAAG
* * * * *
724259 AATGTCATGGTTCACTAAGAAGTAGGTTGTTATATGAAATGTTAATATTTTTATTAACAAAATAG
1 AATGTCATGGTTCACTAAGAAATAGATTGATATA-G-AATGTTAATATTTTTATTAATAAAATAA
*** *
724324 GTTGCATTCAAA
64 GTTGCGCCCAAG
* * **
724336 AATGTC-TGGTTCACTAAGAAATTTGATGTGATCTAGAATGTTAATATTTTTATTAATAAAATGG
1 AATGTCATGGTTCACTAAGAAA-TAGAT-TGATATAGAATGTTAATATTTTTATTAATAAAATAA
* *
724400 GTTGCGCACAGG
64 GTTGCGCCCAAG
* * * * * *
724412 AATGTTATGGTTCACTAAGAAAGCAAGTTGTGATTTAGAATTTTAATATTTCTATT-ATAAAA
1 AATGTCATGGTTCACTAAGAAA--TAGAT-TGATATAGAATGTTAATATTTTTATTAATAAAA
724474 AATTGAAAGT
Statistics
Matches: 240, Mismatches: 44, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
75 6 0.03
76 54 0.22
77 149 0.62
78 31 0.13
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (75 bp):
AATGTCATGGTTCACTAAGAAATAGATTGATATAGAATGTTAATATTTTTATTAATAAAATAAGT
TGCGCCCAAG
Found at i:724422 original size:153 final size:153
Alignment explanation
Indices: 724105--724433 Score: 412
Period size: 153 Copynumber: 2.1 Consensus size: 153
724095 TGCGTCTAAA
* * *
724105 AATGTCATAGTTCACTAAGAAATAGGTTGTGATATGGAATGTTAATATTTTTACTAATAAAATAA
1 AATGTCATGGTTCACTAAGAAATAGGTTGTGATATGAAATGTTAATATTTTTACTAACAAAATAA
* * *
724170 GTTGCGCCCAAGAATATCATGGTTTACTAAGAAATAAATTACGATATAGAATGTTAATATTTTTA
66 GTTGCACCCAAAAATATCATGGTTCACTAAGAAATAAATTA-GATATAGAATGTTAATATTTTTA
*
724235 TTAATAAAATGAGTTACTTCCAAG
130 TTAATAAAATGAGTTACTGCCAAG
* * * *
724259 AATGTCATGGTTCACTAAGAAGTAGGTTGTTATATGAAATGTTAATATTTTTATTAACAAAATAG
1 AATGTCATGGTTCACTAAGAAATAGGTTGTGATATGAAATGTTAATATTTTTACTAACAAAATAA
** * ** *
724324 GTTGCATTCAAAAATGTC-TGGTTCACTAAGAAATTTGATGT-GATCTAGAATGTTAATATTTTT
66 GTTGCACCCAAAAATATCATGGTTCACTAAGAAA-TAAAT-TAGATATAGAATGTTAATATTTTT
* * *
724387 ATTAATAAAATGGGTTGC-GCACAGG
129 ATTAATAAAATGAGTTACTGC-CAAG
*
724412 AATGTTATGGTTCACTAAGAAA
1 AATGTCATGGTTCACTAAGAAA
724434 GCAAGTTGTG
Statistics
Matches: 150, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
152 1 0.01
153 74 0.49
154 74 0.49
155 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (153 bp):
AATGTCATGGTTCACTAAGAAATAGGTTGTGATATGAAATGTTAATATTTTTACTAACAAAATAA
GTTGCACCCAAAAATATCATGGTTCACTAAGAAATAAATTAGATATAGAATGTTAATATTTTTAT
TAATAAAATGAGTTACTGCCAAG
Found at i:724659 original size:81 final size:80
Alignment explanation
Indices: 724558--724908 Score: 246
Period size: 81 Copynumber: 4.5 Consensus size: 80
724548 GAGAAGACTT
* * * *
724558 AAAGTATCTATATTTTTTCAAAAGTATCGGTACTTTTAAATTTGAAAGTTAAAATATAATTTTTC
1 AAAGTATCGATACTTTTTCAAAAGTATCGATACTTTTAAATTCGAAAGTTAAAATATAA-TTTTC
724623 ATGTTTTTTTAATTCG
65 ATGTTTTTTTAATTCG
* * * * * * *
724639 AAAGTATCCATACTTTTTCAAAAGTATCAATACTTTCT-AATT-TAAAG-AAAAACATGGAAATG
1 AAAGTATCGATACTTTTTCAAAAGTATCGATACTTT-TAAATTCGAAAGTTAAAATAT--AATTT
** * * *
724701 AGAAG--GTTGT-A----
63 TCATGTTTTTTTAATTCG
* * *
724712 AAA-TATCGATATTTTTTTCAAAAGTATCGATA-TTTTAAATTCAAAAGTTAAAATATCATTTTC
1 AAAGTATCGATA-CTTTTTCAAAAGTATCGATACTTTTAAATTCGAAAGTTAAAATATAATTTT-
* *
724775 CATATTTTTTTTAATTTG
64 CAT-GTTTTTTTAATTCG
* * * *
724793 AAAGTATCAATA--TTTTCTAAAAGTA-CTAATATTTTTAAATTCGAAAGTTAAAATATTATTTT
1 AAAGTATCGATACTTTTTC-AAAAGTATC-GATACTTTTAAATTCGAAAGTTAAAATATAATTTT
*
724855 CTATGTTTTTTAAATTCG
64 C-ATGTTTTTTTAATTCG
* * *
724873 AAAGTATGGATACCTTTCCAAAAGTATCGATACTTT
1 AAAGTATCGATACTTTTTCAAAAGTATCGATACTTT
724909 CGAATTTAAA
Statistics
Matches: 205, Mismatches: 41, Indels: 48
0.70 0.14 0.16
Matches are distributed among these distances:
71 1 0.00
72 16 0.08
73 26 0.13
74 6 0.03
76 3 0.01
77 2 0.01
78 3 0.01
79 12 0.06
80 39 0.19
81 84 0.41
82 13 0.06
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (80 bp):
AAAGTATCGATACTTTTTCAAAAGTATCGATACTTTTAAATTCGAAAGTTAAAATATAATTTTCA
TGTTTTTTTAATTCG
Found at i:724748 original size:153 final size:153
Alignment explanation
Indices: 724515--724817 Score: 407
Period size: 153 Copynumber: 2.0 Consensus size: 153
724505 TCGATACTCC
* * * *
724515 ATACTTTCGAATTTATAGGAAAACATGGAAAATGAGAAGACTTAAAGTATCTATATTTTTTCAAA
1 ATACTTTCGAATTTAAAGAAAAACATGGAAAATGAGAAGACTTAAAATATCGATATTTTTTCAAA
* ** *
724580 AGTATCGGTACTTTTAAATTTGAAAGTTAAAATATAATTTTTCAT-GTTTTTTTAATTCGAAAGT
66 AGTATCGATACTTTTAAATTCAAAAGTTAAAATATAATTTTCCATAGTTTTTTTAATTCGAAAGT
*
724644 ATCCATACTTTT-TCAAAAGTATCA
131 ATCAATA-TTTTCT-AAAAGTATCA
* **
724668 ATACTTTCTAATTTAAAGAAAAACATGG-AAATGAGAAGGTTGTAAAATATCGATATTTTTTTCA
1 ATACTTTCGAATTTAAAGAAAAACATGGAAAATGAGAAGACT-TAAAATATCGATA-TTTTTTCA
* * *
724732 AAAGTATCGATA-TTTTAAATTCAAAAGTTAAAATATCATTTTCCATATTTTTTTTAATTTGAAA
64 AAAGTATCGATACTTTTAAATTCAAAAGTTAAAATATAATTTTCCATAGTTTTTTTAATTCGAAA
724796 GTATCAATATTTTCTAAAAGTA
129 GTATCAATATTTTCTAAAAGTA
724818 CTAATATTTT
Statistics
Matches: 131, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
152 11 0.08
153 77 0.59
154 43 0.33
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (153 bp):
ATACTTTCGAATTTAAAGAAAAACATGGAAAATGAGAAGACTTAAAATATCGATATTTTTTCAAA
AGTATCGATACTTTTAAATTCAAAAGTTAAAATATAATTTTCCATAGTTTTTTTAATTCGAAAGT
ATCAATATTTTCTAAAAGTATCA
Found at i:724758 original size:23 final size:21
Alignment explanation
Indices: 724711--724759 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
724701 AGAAGGTTGT
*
724711 AAAA-TATCGATATTTTTTTC
1 AAAAGTATCGATATTTTATTC
724731 AAAAGTATCGATATTTTAAATTC
1 AAAAGTATCGATATTTT--ATTC
724754 AAAAGT
1 AAAAGT
724760 TAAAATATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 12 0.48
23 9 0.36
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (21 bp):
AAAAGTATCGATATTTTATTC
Found at i:725213 original size:100 final size:99
Alignment explanation
Indices: 725039--725565 Score: 508
Period size: 99 Copynumber: 5.3 Consensus size: 99
725029 GTTATGCTCG
* * * ** * *
725039 TGATAACGTAATAGGTAGCTCATTTTTTAATGTCAATTGTTTAAATTATAAGTATCAAATCGCTT
1 TGATAACATAATAAGTAG-TCATTTTTTTATGTCAACCGTTTAAATTATAAGTATGAAATCGTTT
* *
725104 ATATGATGCAAAAGTAAGATAAAACATGTTTCTCA
65 ATATTATGCAAAAGTAAGACAAAACATGTTTCTCA
* * * * * * *
725139 TGATAACGTAGTATGTAGTACATTTTTTTATATCAACCGTTTAATTTATATGTATGAAATTGTTT
1 TGATAACATAATAAGTAGT-CATTTTTTTATGTCAACCGTTTAAATTATAAGTATGAAATCGTTT
*
725204 ATATTATGCAAAAGTAAGACAAAGCATGTTAT-TCA
65 ATATTATGCAAAAGTAAGACAAAACATGTT-TCTCA
* ** * * * *
725239 TGATAACGTCGTACGCA-TCACCTTTTTTATGTCAACCGTTTAAGTTATAAGTATGAAATCGTTT
1 TGATAACATAATAAGTAGTCA-TTTTTTTATGTCAACCGTTTAAATTATAAGTATGAAATCGTTT
* * * * *
725303 ATAATATGGAAAAATAAGACAAAACATATTGCTCA
65 ATATTATGCAAAAGTAAGACAAAACATGTTTCTCA
* * * * *
725338 TGATAACATACTAAATAG-CGA-TTTTTTATTGTCAACTGTTTAAATTATAAGTATAAAATTGTT
1 TGATAACATAATAAGTAGTC-ATTTTTTTA-TGTCAACCGTTTAAATTATAAGTATGAAATCGTT
*
725401 TATATTATGCAAAAGTAAGACAAAACATGTTGCTCA
64 TATATTATGCAAAAGTAAGACAAAACATGTTTCTCA
* * * * * * *
725437 AGATAACATACTAGGTAGCGTC-TTTTTTTAATATTAACCGTTTAAGTTATAAGTATGAAACCGT
1 TGATAACATAATAAGTA--GTCATTTTTTT-ATGTCAACCGTTTAAATTATAAGTATGAAATCGT
* * *
725501 TTATATTATGTAAAAGTAAGACAAAATA-GATTTTTCA
63 TTATATTATGCAAAAGTAAGACAAAACATG-TTTCTCA
725538 TGATAACATAATAAGTAGTGCATTTTTT
1 TGATAACATAATAAGTAGT-CATTTTTT
725566 ATGCAAAAGT
Statistics
Matches: 353, Mismatches: 59, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
98 9 0.03
99 158 0.45
100 99 0.28
101 85 0.24
102 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (99 bp):
TGATAACATAATAAGTAGTCATTTTTTTATGTCAACCGTTTAAATTATAAGTATGAAATCGTTTA
TATTATGCAAAAGTAAGACAAAACATGTTTCTCA
Found at i:725541 original size:200 final size:200
Alignment explanation
Indices: 725040--725567 Score: 591
Period size: 200 Copynumber: 2.6 Consensus size: 200
725030 TTATGCTCGT
* ** * * *
725040 GATAACGTAATAGGTAGCTCATTTTTTAATGTCAATTGTTTAAATTATAAGTATCAAATCGCTTA
1 GATAACGTACTAGGTAGCTCATTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAAATCGTTTA
* * * * *
725105 TATGATGCAAAAGTAAGATAAAACATG-TTTCTCATGATAACGTAGTATGTAGTAC-ATTTTTT-
66 TATTATGCAAAAGTAAGACAAAACA-GATTTCTCATGATAACATAATAAGTAG--CGATTTTTTA
* * * *
725167 TATATCAACCGTTTAATTTATATGTATGAAATTGTTTATATTATGCAAAAGTAAGACAAAGCATG
128 TATATCAACCGTTTAAATTATAAGTATAAAATTGTTTATATTATGCAAAAGTAAGACAAAACATG
* *
725232 TTATTCAT
193 TTACTCAA
* * * * *
725240 GATAACGT-CGTACGCATCACCTTTTTT-ATGTCAACCGTTTAAGTTATAAGTATGAAATCGTTT
1 GATAACGTAC-TAGGTAGCTCATTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAAATCGTTT
* * * * * * *
725303 ATAATATGGAAAAATAAGACAAAACATATTGCTCATGATAACATACTAAATAGCGATTTTTTAT-
65 ATATTATGCAAAAGTAAGACAAAACAGATTTCTCATGATAACATAATAAGTAGCGATTTTTTATA
* *
725367 TGTCAACTGTTTAAATTATAAGTATAAAATTGTTTATATTATGCAAAAGTAAGACAAAACATGTT
130 TATCAACCGTTTAAATTATAAGTATAAAATTGTTTATATTATGCAAAAGTAAGACAAAACATGTT
*
725432 GCTCAA
195 ACTCAA
* * * * *
725438 GATAACATACTAGGTAGCGTCTTTTTTTAATATTAACCGTTTAAGTTATAAGTATGAAACCGTTT
1 GATAACGTACTAGGTAGC-TCATTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAAATCGTTT
* * * *
725503 ATATTATGTAAAAGTAAGACAAAATAGATTTTTCATGATAACATAATAAGTAGTGCATTTTTTAT
65 ATATTATGCAAAAGTAAGACAAAACAGATTTCTCATGATAACATAATAAGTAGCG-ATTTTTTAT
725568 GCAAAAGTAT
Statistics
Matches: 270, Mismatches: 50, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
197 1 0.00
198 81 0.30
199 81 0.30
200 98 0.36
201 9 0.03
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (200 bp):
GATAACGTACTAGGTAGCTCATTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAAATCGTTTA
TATTATGCAAAAGTAAGACAAAACAGATTTCTCATGATAACATAATAAGTAGCGATTTTTTATAT
ATCAACCGTTTAAATTATAAGTATAAAATTGTTTATATTATGCAAAAGTAAGACAAAACATGTTA
CTCAA
Found at i:725991 original size:74 final size:72
Alignment explanation
Indices: 725819--726030 Score: 198
Period size: 73 Copynumber: 2.9 Consensus size: 72
725809 GATCATATTC
* * ** * * * *
725819 ATCAACTTGTTCAATATCTAAAAGTATCTCTATTCATCGCATAAGTTTCAATATTTT-AAGTTTT
1 ATCAACTT-TTTAATATTTAAAAGTATCGATAATAAT-GCATAAGTATCAATATTTTAAAATTTT
725883 GATCTTTTT
64 GATCTTTTT
* * * *
725892 ATCAACTTTTTAATTTTTAAAAGTATTGATCATTACTGCATAAGTATCAATATTTTAAAATTTTG
1 ATCAACTTTTTAATATTTAAAAGTATCGAT-AATAATGCATAAGTATCAATATTTTAAAATTTTG
725957 ATCTTATCTT
65 ATCTT-T-TT
** *
725967 -T-AACCTTTTTAATATTTAAAAGTATCGATAATAATATATTAAGTATTAATA-TTTAAAATTTT
1 ATCAA-CTTTTTAATATTTAAAAGTATCGATAATAATGCA-TAAGTATCAATATTTTAAAATTTT
726029 GA
64 GA
726031 ACCTTTTTTT
Statistics
Matches: 116, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
72 34 0.29
73 44 0.38
74 36 0.31
75 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (72 bp):
ATCAACTTTTTAATATTTAAAAGTATCGATAATAATGCATAAGTATCAATATTTTAAAATTTTGA
TCTTTTT
Found at i:726043 original size:74 final size:74
Alignment explanation
Indices: 725858--726035 Score: 179
Period size: 74 Copynumber: 2.4 Consensus size: 74
725848 CTATTCATCG
* * * * *
725858 CATAAGTTTCAATATTTT-AAGTTTTGATCTT-T-TTATCAA-CTTTTTAATTTTTAAAAGTATT
1 CATAAGTATCAATATTTTAAAATTTTGACCTTATCTT-T-AACCTTTTTAATATTTAAAAGTATC
* * *
725919 GATCATTACTG
64 GATCAATAATA
*
725930 CATAAGTATCAATATTTTAAAATTTTGATCTTATCTTTAACCTTTTTAATATTTAAAAGTATCGA
1 CATAAGTATCAATATTTTAAAATTTTGACCTTATCTTTAACCTTTTTAATATTTAAAAGTATCGA
725995 T-AATAATA
66 TCAATAATA
* *
726003 TATTAAGTATTAATA-TTTAAAATTTTGAACCTT
1 CA-TAAGTATCAATATTTTAAAATTTTG-ACCTT
726036 TTTTTTAAAT
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
72 17 0.19
73 31 0.34
74 40 0.44
75 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (74 bp):
CATAAGTATCAATATTTTAAAATTTTGACCTTATCTTTAACCTTTTTAATATTTAAAAGTATCGA
TCAATAATA
Found at i:726527 original size:77 final size:78
Alignment explanation
Indices: 726380--726527 Score: 199
Period size: 78 Copynumber: 1.9 Consensus size: 78
726370 AGCGCAACTC
* * * * * * * * *
726380 ATTTTATTATTAAAAATAGTAAGATTCCATATTGCAACATTCTTTCTTAGTGAATCATGACATTC
1 ATTTTATTAATAAAAATAGTAACATTACAGATCGCAACACTATTTCTTAGTGAACCATGACATTA
726445 TTGAGCGCGACCT
66 TTGAGCGCGACCT
*
726458 ATTTTATTAATAAAAATATTAACATTACAGATCGCAAC-CTATTTCTTAGTGAACCATGACATTA
1 ATTTTATTAATAAAAATAGTAACATTACAGATCGCAACACTATTTCTTAGTGAACCATGACATTA
726522 TTGAGC
66 TTGAGC
726528 ACAACCACGT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
77 28 0.47
78 32 0.53
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (78 bp):
ATTTTATTAATAAAAATAGTAACATTACAGATCGCAACACTATTTCTTAGTGAACCATGACATTA
TTGAGCGCGACCT
Found at i:727527 original size:54 final size:54
Alignment explanation
Indices: 727457--727809 Score: 521
Period size: 54 Copynumber: 6.5 Consensus size: 54
727447 TAAAAATATT
* * * * * *
727457 ATGAATTCCATAGGTTGCATACATAGAGCCTAAATGGTTGTTCATCAA-TATATG
1 ATGAATTCCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACT-TATG
727511 ATGAATTCCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACTTATG
1 ATGAATTCCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACTTATG
* *
727565 ATGAATTCTGTGGGTTGCACACATAGTGCCAAAGCGGTTGTTCATCAACTTATG
1 ATGAATTCCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACTTATG
* *
727619 ATGAATTCCGTAGATTGCACACATAGTGCCAAAACGGTTGTTCATCAACTTATG
1 ATGAATTCCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACTTATG
** *
727673 ATGAATTTTGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATTAACTTATG
1 ATGAATTCCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACTTATG
* * *
727727 ATGAATTTCC-TGGGTTGCATACATATTGCCAAAATGGTTGTTCATCAACTTATG
1 ATGAA-TTCCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACTTATG
*
727781 ATGAATTTCGTGGGTTGCACACATAGTGC
1 ATGAATTCCGTGGGTTGCACACATAGTGC
727810 ATAAAGTACA
Statistics
Matches: 270, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
53 3 0.01
54 264 0.98
55 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33
Consensus pattern (54 bp):
ATGAATTCCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACTTATG
Found at i:731762 original size:23 final size:24
Alignment explanation
Indices: 731705--731763 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
731695 TTTTTGATCA
731705 AAGTCAAAGTCAAAGTCAATGGTC
1 AAGTCAAAGTCAAAGTCAATGGTC
* **
731729 AACTC-TGGTCAAAGTCAATGGTC
1 AAGTCAAAGTCAAAGTCAATGGTC
731752 -AGTCAAAGTCAA
1 AAGTCAAAGTCAA
731764 TGGGTTGACT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 3 0.11
23 21 0.75
24 4 0.14
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (24 bp):
AAGTCAAAGTCAAAGTCAATGGTC
Found at i:732803 original size:31 final size:31
Alignment explanation
Indices: 732730--732805 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
732720 TCAAAATGCA
*
732730 TAAGATATGATCACTTACATTTTTATTTAAT
1 TAAGATATGGTCACTTACATTTTTATTTAAT
*
732761 TAAGATATGGTCACTTTCATTTTTATTTAAT
1 TAAGATATGGTCACTTACATTTTTATTTAAT
*
732792 TAAGATGTGGTCAC
1 TAAGATATGGTCAC
732806 CCCGAGTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.46
Consensus pattern (31 bp):
TAAGATATGGTCACTTACATTTTTATTTAAT
Found at i:733140 original size:31 final size:31
Alignment explanation
Indices: 733067--733142 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
733057 TCAAAATACA
*
733067 TAAGATATGATCACTTATATTTTTATTTAAT
1 TAAGATATGGTCACTTATATTTTTATTTAAT
733098 TAAGATATGGTCACTT-TCATTTTTATTTAAT
1 TAAGATATGGTCACTTAT-ATTTTTATTTAAT
*
733129 TAAGATGTGGTCAC
1 TAAGATATGGTCAC
733143 CCCAAGTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 1 0.02
31 41 0.98
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (31 bp):
TAAGATATGGTCACTTATATTTTTATTTAAT
Found at i:733887 original size:24 final size:22
Alignment explanation
Indices: 733865--733924 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 22
733855 TATAATTTTA
733865 TATATATTAACTTAAAATATTT
1 TATATATTAACTTAAAATATTT
733887 T-TATATTAACTTATTAAATAATTT
1 TATATATTAACTTA--AAAT-ATTT
*
733911 TA-CTATTAACTTAA
1 TATATATTAACTTAA
733925 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 12 0.36
22 2 0.06
23 4 0.12
24 15 0.45
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (22 bp):
TATATATTAACTTAAAATATTT
Found at i:733891 original size:21 final size:21
Alignment explanation
Indices: 733867--733924 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 21
733857 TAATTTTATA
*
733867 TATATTAACTTAAAATATTTT
1 TATATTAACTTAAAATAATTT
733888 TATATTAACTTATTAAATAATTT
1 TATATTAACTTA--AAATAATTT
733911 TACTATTAACTTAA
1 TA-TATTAACTTAA
733925 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 12 0.36
22 1 0.03
23 10 0.30
24 10 0.30
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATTAACTTAAAATAATTT
Found at i:734375 original size:2 final size:2
Alignment explanation
Indices: 734370--734408 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
734360 TCAGAAAGAT
734370 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
734409 GTGGACAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:747523 original size:19 final size:19
Alignment explanation
Indices: 747488--747529 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
747478 TTGTGTTTTC
*
747488 AGGTTTGGGTGATTATGTT
1 AGGTTTGGGTGACTATGTT
747507 AGGTTATGGGTG-CTATGTT
1 AGGTT-TGGGTGACTATGTT
747526 -GGTT
1 AGGTT
747530 GTTTAAGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 11 0.52
20 6 0.29
ACGTcount: A:0.14, C:0.02, G:0.38, T:0.45
Consensus pattern (19 bp):
AGGTTTGGGTGACTATGTT
Found at i:752071 original size:19 final size:19
Alignment explanation
Indices: 752043--752084 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
752033 AATTTACATA
*
752043 TTAA-ATTAAATTA-ATAT
1 TTAATATTAAAATATATAT
752060 CTTAATATTAAAATATATAT
1 -TTAATATTAAAATATATAT
752080 TTAAT
1 TTAAT
752085 TTTTATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 13 0.62
20 4 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAATATTAAAATATATAT
Found at i:752118 original size:28 final size:30
Alignment explanation
Indices: 752051--752179 Score: 124
Period size: 29 Copynumber: 4.4 Consensus size: 30
752041 TATTAAATTA
* *
752051 AATTAATATCTTAA-TATTAAAATATATATTT
1 AATTATTATCTTAACT-TAAAAATATAT-TTT
*
752082 AATTTTTATCTTAACTT-AAAATATATTTT
1 AATTATTATCTTAACTTAAAAATATATTTT
*
752111 -ATTATTATTTTAACTTAAAAATATATTTT
1 AATTATTATCTTAACTTAAAAATATATTTT
* * *
752140 AATT-TTTTATTAACTTCAAAAATATAATTT
1 AATTATTATCTTAACTT-AAAAATATATTTT
*
752170 -ATTCTTATCT
1 AATTATTATCT
752180 AATATAAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
28 14 0.17
29 28 0.33
30 28 0.33
31 13 0.15
32 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (30 bp):
AATTATTATCTTAACTTAAAAATATATTTT
Found at i:752188 original size:28 final size:29
Alignment explanation
Indices: 752069--752195 Score: 111
Period size: 28 Copynumber: 4.3 Consensus size: 29
752059 TCTTAATATT
752069 AAAATATATATTTAATTTTTATCTTAACTT-
1 AAAATATA-ATTTAATTTTTATC-TAACTTA
* * *
752099 AAAATAT-ATTTTATTATTATTTTAACTTA
1 AAAATATAATTTAATTTTTA-TCTAACTTA
*
752128 AAAATATATTTTAATTTTTTAT-TAACTTCA
1 AAAATATAATTTAA-TTTTTATCTAACTT-A
*
752158 AAAATATAATTT-ATTCTTATCTAA-TATA
1 AAAATATAATTTAATTTTTATCTAACT-TA
*
752186 AAAATTTAAT
1 AAAATATAAT
752196 AACAACTAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 16
0.76 0.08 0.15
Matches are distributed among these distances:
28 33 0.41
29 19 0.23
30 24 0.30
31 5 0.06
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (29 bp):
AAAATATAATTTAATTTTTATCTAACTTA
Found at i:764231 original size:46 final size:46
Alignment explanation
Indices: 764181--764275 Score: 145
Period size: 46 Copynumber: 2.1 Consensus size: 46
764171 ATCTTTTAAT
* *
764181 TGTAATTATTTTATTTAATTAAAATATTATTATAAATAAATCATTG
1 TGTAATTATGTTATTTAATTAAAATATTAATATAAATAAATCATTG
* * *
764227 TGTAATTATGTTATTTAATTACAATATTAATATAAGTGAATCATTG
1 TGTAATTATGTTATTTAATTAAAATATTAATATAAATAAATCATTG
764273 TGT
1 TGT
764276 TGCCAAATCT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48
Consensus pattern (46 bp):
TGTAATTATGTTATTTAATTAAAATATTAATATAAATAAATCATTG
Found at i:768154 original size:21 final size:21
Alignment explanation
Indices: 768128--768170 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
768118 GCTAAATGGG
768128 TAAGATT-TTCAAATTGATTTT
1 TAAGATTATTC-AATTGATTTT
*
768149 TAAGATTATTCGATTGATTTT
1 TAAGATTATTCAATTGATTTT
768170 T
1 T
768171 GGGTTAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (21 bp):
TAAGATTATTCAATTGATTTT
Found at i:770612 original size:53 final size:53
Alignment explanation
Indices: 770550--770657 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
770540 ACCCACAACC
770550 TTTTCCTAATCCAAATCCCAATAAACTTTCAGCACCAAATTCTGGTTTTCGTA
1 TTTTCCTAATCCAAATCCCAATAAACTTTCAGCACCAAATTCTGGTTTTCGTA
*
770603 TTTTCCTAATCCAAATCCCAATCAACTTTCAGCACCAAATTCTGGTTTTCGTA
1 TTTTCCTAATCCAAATCCCAATAAACTTTCAGCACCAAATTCTGGTTTTCGTA
770656 TT
1 TT
770658 GACCAGTTAG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.37
Consensus pattern (53 bp):
TTTTCCTAATCCAAATCCCAATAAACTTTCAGCACCAAATTCTGGTTTTCGTA
Found at i:773260 original size:20 final size:20
Alignment explanation
Indices: 773235--773278 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
773225 GAGATTGTTA
*
773235 CGAAAGTCAAATTCGCAACG
1 CGAAAGTCAAATTCGAAACG
*
773255 CGAAAGTTAAATTCGAAACG
1 CGAAAGTCAAATTCGAAACG
773275 CGAA
1 CGAA
773279 TTTGACTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.16
Consensus pattern (20 bp):
CGAAAGTCAAATTCGAAACG
Found at i:773419 original size:37 final size:37
Alignment explanation
Indices: 773369--773503 Score: 110
Period size: 37 Copynumber: 3.5 Consensus size: 37
773359 CAAATCAACT
773369 TTTACAAATCAATTAAACAAGCAAAAAATAAGAATTA
1 TTTACAAATCAATTAAACAAGCAAAAAATAAGAATTA
* * *** * *
773406 TTTACACATCAATTAAACAAATC-AACTTTTAGAAATCAA
1 TTTACAAATCAATTAAAC-AAGCAAAAAATAAG-AAT-TA
**
773445 CTTTTACAAATCAATTAAACAAGCAAAAAATAATTATTA
1 --TTTACAAATCAATTAAACAAGCAAAAAATAAGAATTA
* **
773484 TTTCCTCATCAATTAAACAA
1 TTTACAAATCAATTAAACAA
773504 ATCAACTTTT
Statistics
Matches: 73, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
37 39 0.53
38 6 0.08
39 2 0.03
40 5 0.07
41 21 0.29
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.30
Consensus pattern (37 bp):
TTTACAAATCAATTAAACAAGCAAAAAATAAGAATTA
Found at i:773443 original size:14 final size:14
Alignment explanation
Indices: 773422--773458 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
773412 CATCAATTAA
773422 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
773436 AGAAATCAACTTTT
1 ACAAATCAACTTTT
773450 ACAAATCAA
1 ACAAATCAA
773459 TTAAACAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.19, G:0.03, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:773494 original size:78 final size:78
Alignment explanation
Indices: 773358--773533 Score: 307
Period size: 78 Copynumber: 2.3 Consensus size: 78
773348 ATTTAAAACA
773358 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
773423 CAAATCAACTTTT
66 CAAATCAACTTTT
* ** * *
773436 AGAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTATTATTTCCTCATCAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
773501 CAAATCAACTTTT
66 CAAATCAACTTTT
773514 ACAAATCAACTTTTACAAAT
1 ACAAATCAACTTTTACAAAT
773534 ACATCAATTT
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 92 1.00
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (78 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
CAAATCAACTTTT
Found at i:773519 original size:14 final size:14
Alignment explanation
Indices: 773500--773533 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
773490 CATCAATTAA
773500 ACAAATCAACTTTT
1 ACAAATCAACTTTT
773514 ACAAATCAACTTTT
1 ACAAATCAACTTTT
773528 ACAAAT
1 ACAAAT
773534 ACATCAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:777815 original size:23 final size:21
Alignment explanation
Indices: 777784--777843 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
777774 TCCCCTGTGG
*
777784 GGGGAGAATCGGTTCCCCTTCAAA
1 GGGG-GAATCGATTCCCC-TC-AA
777808 GGGGGAATCGATT-CCCTCAA
1 GGGGGAATCGATTCCCCTCAA
*
777828 GGGGGGATCGATTCCC
1 GGGGGAATCGATTCCC
777844 TCTGCACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 14 0.42
21 4 0.12
22 3 0.09
23 8 0.24
24 4 0.12
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTCAA
Found at i:777831 original size:20 final size:20
Alignment explanation
Indices: 777806--777845 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
777796 TTCCCCTTCA
777806 AAGGGGGAATCGATTCCCTC
1 AAGGGGGAATCGATTCCCTC
*
777826 AAGGGGGGATCGATTCCCTC
1 AAGGGGGAATCGATTCCCTC
777846 TGCACCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.20
Consensus pattern (20 bp):
AAGGGGGAATCGATTCCCTC
Found at i:784264 original size:21 final size:21
Alignment explanation
Indices: 784238--784352 Score: 124
Period size: 21 Copynumber: 5.5 Consensus size: 21
784228 ATGAATCGGG
*
784238 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* **
784259 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
784280 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
* **
784301 CTCTT-AAAGGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
* * *
784322 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
784343 CTCTTGAACG
1 CTCTTGAACG
784353 ATGACAGGTG
Statistics
Matches: 76, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
20 4 0.05
21 69 0.91
22 3 0.04
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Done.