Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004920.1 Hibiscus syriacus cultivar Beakdansim tig00011079_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: 1590857
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 3 of 7
Found at i:405425 original size:39 final size:38
Alignment explanation
Indices: 405332--405439 Score: 112
Period size: 39 Copynumber: 2.8 Consensus size: 38
405322 AAATGATTTC
*
405332 AAAAATATATGTTATATAATTTTC-AAAATGTTTTTAAA
1 AAAAATATAT-TTATATAATTTTCAAAAACGTTTTTAAA
***
405370 ACTTATATATTGTATATAAGTTTTCAAAAACGTTTTTAAA
1 AAAAATATATT-TATATAA-TTTTCAAAAACGTTTTTAAA
*
405410 AAAAACTATA-TTATATATATTTTCAGAAAC
1 AAAAA-TATATTTATATA-ATTTTCAAAAAC
405440 CATTTTTTGT
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
37 1 0.02
38 14 0.25
39 21 0.37
40 17 0.30
41 4 0.07
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (38 bp):
AAAAATATATTTATATAATTTTCAAAAACGTTTTTAAA
Found at i:405455 original size:149 final size:141
Alignment explanation
Indices: 405153--405497 Score: 329
Period size: 149 Copynumber: 2.4 Consensus size: 141
405143 TCAAAAAATA
* * * *
405153 TTTTTTAAACTATATATTATA-TTTAAAAATGTTTTCAAAACTATATACCATATAGTTTTCAAAA
1 TTTTTTAAACTATATATTATATTTTCAAAATGATTTCAAAAATATATACCATATAATTTTCAAAA
* * * **
405217 ATGATTTTAAAAATATTATATGAGTTTTCCAAAATATTTTTAAAACTATATATTATATAAAATTT
66 ATGATTTTAAAAATATTATATAAGTTTTCAAAAACATTTTTAAAAAAATATATTATATAAAATTT
***
405282 TCAAAAATGTTT
131 TCAAAAA-CCAT
* ***
405294 TTATTTTAAACTATACATTATATTTTCAAAATGATTTCAAAAATATATGTTATATAATTTTC-AA
1 TT-TTTTAAACTATATATTATATTTTCAAAATGATTTCAAAAATATATACCATATAATTTTCAAA
* *
405358 AATGTTTTTAAAACTTATATATTGTATATAAGTTTTCAAAAACGTTTTTAAAAAAAACTATATTA
65 AATGATTTT-AAA---A-ATA-T-TATATAAGTTTTCAAAAACATTTTT-AAAAAAA-TATATTA
* *
405423 TAT-ATATTTTCAGAAACCAT
121 TATAAAATTTTCAAAAACCAT
* ** *
405443 TTTTTGTAAACTATATGTTATATTTTCAAAAACACTTTCAAAAAT-TATACTATAT
1 TTTTT-TAAACTATATATTATATTTTCAAAATGA-TTTCAAAAATATATACCATAT
405498 TATCGTATAT
Statistics
Matches: 165, Mismatches: 26, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
141 2 0.01
142 28 0.17
143 35 0.21
146 1 0.01
147 3 0.02
148 4 0.02
149 56 0.34
150 26 0.16
151 10 0.06
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (141 bp):
TTTTTTAAACTATATATTATATTTTCAAAATGATTTCAAAAATATATACCATATAATTTTCAAAA
ATGATTTTAAAAATATTATATAAGTTTTCAAAAACATTTTTAAAAAAATATATTATATAAAATTT
TCAAAAACCAT
Found at i:406739 original size:106 final size:106
Alignment explanation
Indices: 406426--407546 Score: 1870
Period size: 106 Copynumber: 10.6 Consensus size: 106
406416 TATTGTTCCC
* * * * * *
406426 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTTTGGAACTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
* *
406491 CAGTC-GTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
66 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
406532 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
406596 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
406637 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
*
406702 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
406743 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
406807 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
406848 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
* *
406913 AAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
406954 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
*
407019 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
407060 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGCGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
*
407125 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
407166 AGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
407231 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
407272 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
*
407337 CAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
407378 AGTCCAATATCTTTCGATGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
407443 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
407484 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
407547 GACAACTTTT
Statistics
Matches: 971, Mismatches: 41, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
104 1 0.00
105 200 0.21
106 770 0.79
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:411570 original size:10 final size:9
Alignment explanation
Indices: 411544--411569 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
411534 TAGGGGGACC
411544 AAAAAAAAT
1 AAAAAAAAT
411553 AAAAAAAAT
1 AAAAAAAAT
411562 AAAAAAAA
1 AAAAAAAA
411570 AATGGAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:412737 original size:33 final size:31
Alignment explanation
Indices: 412694--412761 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 31
412684 ACTATATACC
412694 ATATAGTTTTCAAAAATGA-TTTTAAAAATATT
1 ATATAGTTTTCAAAAAT-ATTTTTAAAAATA-T
* *
412726 ATATGAGTTTTCCAAAATATTTTTAAAACTAT
1 ATAT-AGTTTTCAAAAATATTTTTAAAAATAT
412758 ATAT
1 ATAT
412762 TATATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATAGTTTTCAAAAATATTTTTAAAAATAT
Found at i:412851 original size:35 final size:36
Alignment explanation
Indices: 412807--412890 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 36
412797 TATACATTAT
412807 ATTTTCAAAATGATTTCAAAA-ATATA-TGTTATATA
1 ATTTTCAAAATGATTTCAAAATATATATTG-TATATA
* *
412842 ATTTTCAAAATGTTTTTAAAACTTATATATTGTATATA
1 ATTTTCAAAATGATTTCAAAA--TATATATTGTATATA
412880 AGTTTTCAAAA
1 A-TTTTCAAAA
412891 ACGTTTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 19 0.45
38 12 0.29
39 11 0.26
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (36 bp):
ATTTTCAAAATGATTTCAAAATATATATTGTATATA
Found at i:412956 original size:149 final size:141
Alignment explanation
Indices: 412645--412990 Score: 324
Period size: 150 Copynumber: 2.4 Consensus size: 141
412635 CAAAAAAATA
* * * *
412645 TTTTTTAAACTATATATTATA-TTTAAAAATGTTTTCAAAACTATATACCATATAGTTTTCAAAA
1 TTTTTTAAACTATATATTATATTTTCAAAATGATTTCAAAAATATATACCATATAATTTTCAAAA
* * **
412709 ATGATTTTAAAAATATTATATGAGTTTTCCAAAATATTTTTAAAACTATATATTATATAAAATTT
66 ATGATTTTAAAAATATTATATAAGTTTTCAAAAATATTTTTAAAAAAATATATTATATAAAATTT
***
412774 TCAAAAATGTTT
131 TCAAAAA-CCAT
* ***
412786 TTATTTTAAACTATACATTATATTTTCAAAATGATTTCAAAAATATATGTTATATAATTTTC-AA
1 TT-TTTTAAACTATATATTATATTTTCAAAATGATTTCAAAAATATATACCATATAATTTTCAAA
*
412850 AATGTTTTTAAAACTTATATATTGTATATAAGTTTTCAAAAACGT-TTTTTAAAAAAACTATATT
65 AATGATTTT-AAA---A-ATA-T-TATATAAGTTTTCAAAAA--TATTTTTAAAAAAA-TATATT
* *
412914 ATAT-ATATTTTCAGAAACCAT
120 ATATAAAATTTTCAAAAACCAT
* ** *
412935 TTTTTGTAAACTATATGTTATATTTTTCAAAAACACTTTCAAAAAT-TATACTATAT
1 TTTTT-TAAACTATATATTATA-TTTTCAAAATGA-TTTCAAAAATATATACCATAT
412991 TATCGTATAT
Statistics
Matches: 166, Mismatches: 24, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
141 2 0.01
142 28 0.17
143 35 0.21
146 1 0.01
147 3 0.02
148 4 0.02
149 33 0.20
150 39 0.23
151 21 0.13
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.45
Consensus pattern (141 bp):
TTTTTTAAACTATATATTATATTTTCAAAATGATTTCAAAAATATATACCATATAATTTTCAAAA
ATGATTTTAAAAATATTATATAAGTTTTCAAAAATATTTTTAAAAAAATATATTATATAAAATTT
TCAAAAACCAT
Found at i:415156 original size:3 final size:3
Alignment explanation
Indices: 415150--415236 Score: 142
Period size: 3 Copynumber: 29.0 Consensus size: 3
415140 TTTACCCATT
415150 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
415198 TTA TTA TTA TTA -TA TTTA TTA -TA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA T-TA TTA TTA TTA TTA
415237 AAAAAATAAT
Statistics
Matches: 80, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.05
3 71 0.89
4 5 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:416794 original size:23 final size:26
Alignment explanation
Indices: 416768--416822 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
416758 CCTTTTCTGA
416768 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTCTAAATATATATAAATTATTT
*
416791 TATTTATAAATATATATAAATTATTT
1 TATTTCTAAATATATATAAATTATTT
416817 T-TTTCT
1 TATTTCT
416823 TTTTTTCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 9 0.33
26 6 0.22
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTTCTAAATATATATAAATTATTT
Found at i:417354 original size:22 final size:21
Alignment explanation
Indices: 417321--417362 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
417311 CTTTTCAAAT
* *
417321 TTTTTATATATTTATTTATTA
1 TTTTCATATATTTATATATTA
417342 TTTTCATAGTATTTATATATT
1 TTTTCATA-TATTTATATATT
417363 TTCTTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTCATATATTTATATATTA
Found at i:420698 original size:15 final size:15
Alignment explanation
Indices: 420678--420709 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
420668 ATCAATACCT
420678 TTTTGCATACATACA
1 TTTTGCATACATACA
*
420693 TTTTGCATACATTCA
1 TTTTGCATACATACA
420708 TT
1 TT
420710 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:428022 original size:8 final size:8
Alignment explanation
Indices: 428009--428045 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
427999 CTTGAAGAAA
428009 AAAAAAAG
1 AAAAAAAG
428017 AAAAAAAG
1 AAAAAAAG
428025 AAAAAAA-
1 AAAAAAAG
428032 AGAAAAAAG
1 A-AAAAAAG
428041 AAAAA
1 AAAAA
428046 GGGGGTCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.04
8 25 0.93
9 1 0.04
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:428022 original size:9 final size:9
Alignment explanation
Indices: 428008--428039 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
427998 GCTTGAAGAA
428008 AAAAAAAAG
1 AAAAAAAAG
428017 -AAAAAAAG
1 AAAAAAAAG
428025 AAAAAAAAG
1 AAAAAAAAG
428034 AAAAAA
1 AAAAAA
428040 GAAAAAGGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:428030 original size:17 final size:16
Alignment explanation
Indices: 428008--428045 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
427998 GCTTGAAGAA
428008 AAAAAAAAGAAAAAAAG
1 AAAAAAAAG-AAAAAAG
428025 AAAAAAAAGAAAAAAG
1 AAAAAAAAGAAAAAAG
428041 AAAAA
1 AAAAA
428046 GGGGGTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:429195 original size:94 final size:94
Alignment explanation
Indices: 429032--429322 Score: 464
Period size: 94 Copynumber: 3.1 Consensus size: 94
429022 ACAAGTGTTG
429032 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
*
429097 AAAACCAATCATTGAATTTGAAAAATAAA
66 AAAACCAATCATTGGATTTGAAAAATAAA
* *
429126 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTTGGTATGAACCCCGG
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
429191 AAAACCAATCATTGGATTTG--AAATAAA
66 AAAACCAATCATTGGATTTGAAAAATAAA
** *
429218 -GAAACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
1 TG-TGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCC
* *
429282 -AAAAACCAATCATTGGATTTGAAAGATGAA
64 GAAAAACCAATCATTGGATTTGAAAAATAAA
429312 TGTGCTCATAG
1 TGTGCTCATAG
429323 TAGAAATAAG
Statistics
Matches: 180, Mismatches: 12, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
91 1 0.01
92 30 0.17
93 58 0.32
94 90 0.50
95 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (94 bp):
TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
AAAACCAATCATTGGATTTGAAAAATAAA
Found at i:429450 original size:115 final size:115
Alignment explanation
Indices: 429210--429425 Score: 355
Period size: 115 Copynumber: 1.9 Consensus size: 115
429200 CATTGGATTT
*
429210 GAAATAAAGAA-ACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAT-AAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* * * *
429274 TGAACCACAAAAACCAATCATTGGATTTGAAAGATGAATGTGCTCATAGTA
65 GGAACCACAAAAACCAATCATTGGAATTAAAAGATGAATGTGATCATAGTA
429325 GAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAG
1 GAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAG
*
429390 GAACCAC-AGAACCAATCATTGGAATTAAAAGATGAA
66 GAACCACAAAAACCAATCATTGGAATTAAAAGATGAA
429426 CTGTATGATC
Statistics
Matches: 95, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
114 31 0.33
115 64 0.67
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (115 bp):
GAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAG
GAACCACAAAAACCAATCATTGGAATTAAAAGATGAATGTGATCATAGTA
Found at i:430270 original size:113 final size:112
Alignment explanation
Indices: 430113--431012 Score: 1252
Period size: 113 Copynumber: 8.0 Consensus size: 112
430103 AGCAAAGTTC
*
430113 AAATCCATCATTCGATAGATCAGCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCGATGGATCAGCATTACCAG-GAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
430178 AAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACTTTTCGCTT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTT
* * **
430226 GAATTCATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCGATGGATCAGCATTACCAGG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
430291 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTT
* ** * **
430339 GAATTAATCATTCGATGGATTAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCGATGGATCAGCATTACCAGG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
430404 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTCCGCTT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTT
* * ** *
430452 GAATTCATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTAAAG
1 AAATCCATCATTCGATGGATCAGCATTACCAGG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
*
430517 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTC
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTT
* * *
430565 AAATCCATCACTT-GATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAA
1 AAATCCATCA-TTCGATGGATCAGCATTACCAG-GAAAGTTCATAATGAGAAGAACTCATCTGAA
*
430629 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG-TT
64 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTT
* * *
430677 CAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 -AAATCCATCATTCGATGGATCAGCATTACCAG-GAAAGTTCATAATGAGAAGAACTCATCTGAA
*
430742 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG-TT
64 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTT
* * * *
430790 CAAATCCATCATTTGATGGATCAACATTTCCAGGTAAAGTTCATAATGAGAAGAATTCATCTGAA
1 -AAATCCATCATTCGATGGATCAGCATTACCAGG-AAAGTTCATAATGAGAAGAACTCATCTGAA
* * *
430855 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTC
64 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTT
* * * *
430904 AAATCCATCACTT-GATGGATCAACCTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCA-TTCGATGGATCAGCATTACC-AGGAAAGTTCATAATGAGAAGAACTCATCTGAA
* * * *
430968 AAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTT
64 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
431013 GAATGACTCT
Statistics
Matches: 738, Mismatches: 37, Indels: 23
0.92 0.05 0.03
Matches are distributed among these distances:
112 10 0.01
113 711 0.96
114 17 0.02
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (112 bp):
AAATCCATCATTCGATGGATCAGCATTACCAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTT
Found at i:430881 original size:24 final size:23
Alignment explanation
Indices: 430838--430882 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
430828 GTTCATAATG
*
430838 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
430861 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
430883 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:431233 original size:3 final size:3
Alignment explanation
Indices: 431227--431290 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
431217 TTTACCCATT
* *
431227 TTA TTA TTA TTAA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
431273 -TA TATA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA
431291 AAAAAAATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 2 0.04
3 46 0.85
4 6 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:432836 original size:23 final size:26
Alignment explanation
Indices: 432804--432853 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
432794 CATTTTCTGA
*
432804 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
432827 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
432853 T
1 T
432854 TTCTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:435091 original size:23 final size:23
Alignment explanation
Indices: 435065--435133 Score: 120
Period size: 23 Copynumber: 3.0 Consensus size: 23
435055 CACCACAGCT
* *
435065 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
435088 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
435111 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
435134 TATAAAAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.19
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:435876 original size:64 final size:64
Alignment explanation
Indices: 435723--435878 Score: 163
Period size: 64 Copynumber: 2.4 Consensus size: 64
435713 TAATGGAGGT
* ** *
435723 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAAAAGAG
* * * * * *
435788 ATGCATCAATGTACTCCTTATGCATCGATGCATTAATTGC-ATTCGATGTTTGTATTTTAAAAGA
1 ATGCATCGATGCACTACATATGCATCGATGCA-TAAATCCTATTCGATGTTTGTA-TTTAAAAGA
435852 G
64 G
* *
435853 -TGCATCGATGCACTTCATGTGCATCG
1 ATGCATCGATGCACTACATATGCATCG
435879 GTACACCTTG
Statistics
Matches: 74, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
64 48 0.65
65 26 0.35
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAAAAGAG
Found at i:450690 original size:31 final size:31
Alignment explanation
Indices: 450648--450707 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
450638 CAGTTATGTC
*
450648 AGGGACTATATTGAAAAAGGACTAAATGTTG
1 AGGGACCATATTGAAAAAGGACTAAATGTTG
* *
450679 AGGGACCATATTGCAAACGGACTAAATGT
1 AGGGACCATATTGAAAAAGGACTAAATGT
450708 GGGAGATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (31 bp):
AGGGACCATATTGAAAAAGGACTAAATGTTG
Found at i:456037 original size:50 final size:50
Alignment explanation
Indices: 455952--456049 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 50
455942 TAATTAAAGT
*
455952 CTTTAAAAATCCATATCCTCCAACTAGATACAATCCTTTAATAAAAATGC
1 CTTTAAAAATCCATATCCTCCAACTAAATACAATCCTTTAATAAAAATGC
* * * *
456002 CTTTGAAAATCCGTATCCTCCAACTAAATATAATCCTTTAGTAAAAAT
1 CTTTAAAAATCCATATCCTCCAACTAAATACAATCCTTTAATAAAAAT
456050 ACTGACAGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (50 bp):
CTTTAAAAATCCATATCCTCCAACTAAATACAATCCTTTAATAAAAATGC
Found at i:459192 original size:45 final size:47
Alignment explanation
Indices: 459119--459224 Score: 126
Period size: 45 Copynumber: 2.3 Consensus size: 47
459109 TTTATTTTCG
* * * *
459119 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTT-AGGTTTA
1 TTTTTTGAAT-AATGCATGCGAACTAGATACCATGCAGTTAAGATTTA
* *
459166 TTTTTTGAATAA-GCATGCGAATTAGATACCATGCAGTTAAGATTTC
1 TTTTTTGAATAATGCATGCGAACTAGATACCATGCAGTTAAGATTTA
459212 TTTTTGTGAATAA
1 TTTTT-TGAATAA
459225 CAAAGCATGG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
45 23 0.45
46 12 0.24
47 16 0.31
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (47 bp):
TTTTTTGAATAATGCATGCGAACTAGATACCATGCAGTTAAGATTTA
Found at i:468942 original size:19 final size:18
Alignment explanation
Indices: 468920--468961 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
468910 AAAAAACGAA
468920 AAAAAAGAAGAAAAAATGG
1 AAAAAAGAAGAAAAAAT-G
**
468939 AAAAGGGAAGAAAAAATG
1 AAAAAAGAAGAAAAAATG
468957 AAAAA
1 AAAAA
468962 TAAAAAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (18 bp):
AAAAAAGAAGAAAAAATG
Found at i:468959 original size:8 final size:8
Alignment explanation
Indices: 468948--468984 Score: 51
Period size: 7 Copynumber: 4.9 Consensus size: 8
468938 GAAAAGGGAA
468948 GAAAAAAT
1 GAAAAAAT
468956 G-AAAAAT
1 GAAAAAAT
*
468963 AAAAAAAT
1 GAAAAAAT
468971 G-AAAAAT
1 GAAAAAAT
468978 GAAAAAA
1 GAAAAAA
468985 GAGAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
7 13 0.52
8 12 0.48
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
GAAAAAAT
Found at i:468969 original size:15 final size:15
Alignment explanation
Indices: 468949--468995 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
468939 AAAAGGGAAG
468949 AAAAAATGAAAAATA
1 AAAAAATGAAAAATA
*
468964 AAAAAATGAAAAATG
1 AAAAAATGAAAAATA
*
468979 AAAAAA-GAGAAATA
1 AAAAAATGAAAAATA
468993 AAA
1 AAA
468996 GGAGGGTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 9 0.31
15 20 0.69
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (15 bp):
AAAAAATGAAAAATA
Found at i:470410 original size:51 final size:51
Alignment explanation
Indices: 470349--470703 Score: 532
Period size: 51 Copynumber: 6.9 Consensus size: 51
470339 AAATTCGTTT
470349 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
470400 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
470451 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
470502 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * *
470553 GTTGAAGATTGAGTCCT-TACTCTCTGAAGGAATAGAGAGCGGACACGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * * ** *
470603 ATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGGGAACGGACCCGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * * *
470654 TTTGAAGATTGTTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACA
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
470704 CGTTTACTAA
Statistics
Matches: 283, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
50 44 0.16
51 207 0.73
54 1 0.00
55 31 0.11
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:470692 original size:55 final size:52
Alignment explanation
Indices: 470344--470827 Score: 529
Period size: 51 Copynumber: 9.3 Consensus size: 52
470334 GAAGCAAATT
470344 CGTTTGTTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
470395 AGTTCGTTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
470446 AGTTCGTTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
470497 AGTTCGTTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
470548 AGTTCGTTGAAGATT-GAGTCCT-TACTCTCTGAAGGAATAGAGAGCGGACA
1 CGTTTGTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
470598 CGTTTATTGAAGA-TCGAGTCTTATACTCTCTGAAGGAATAGGGAACGGACC
1 CGTTTGTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * *
470649 CGTTTTTTGAAGATTGTTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACA
1 CGTTTGTTGAAGA---TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
** * * * * *
470704 CGTTTACTAAAGATTATTCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
1 CGTTTGTTGAAG---ATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
** * * *
470759 CGTTTACTGAAGATTGTTCGAGTCTTATACTC-CATGAA-TAATAGGGAGCAGACA
1 CGTTTGTTGAAGA---TTCGAGTCCTATACTCTC-TGAAGGAATAGGGAGCGGACA
470813 CGTTT-TCTGAAGATT
1 CGTTTGT-TGAAGATT
470828 TTTCAAGTCT
Statistics
Matches: 396, Mismatches: 23, Indels: 28
0.89 0.05 0.06
Matches are distributed among these distances:
49 1 0.00
50 43 0.11
51 212 0.54
52 1 0.00
54 27 0.07
55 111 0.28
58 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (52 bp):
CGTTTGTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:470850 original size:54 final size:55
Alignment explanation
Indices: 470577--470837 Score: 300
Period size: 55 Copynumber: 4.8 Consensus size: 55
470567 CCTTACTCTC
* * * *
470577 TGAAGGAATAGAGAGCGGACACGTTTATTGAAG---A-TCGAGTCTTATACTCTC-
1 TGAATGAATAGGGAGCAGACACGTTTACTGAAGATTATTCGAGTCTTATACTC-CA
* * * * ** * *
470628 TGAAGGAATAGGGAACGGACCCGTTTTTTGAAGATTGTTCGAGTCTTATACTCCC
1 TGAATGAATAGGGAGCAGACACGTTTACTGAAGATTATTCGAGTCTTATACTCCA
* * *
470683 TGAACGAATAGGGAGCAGACACGTTTACTAAAGATTATTCGAGTCTTATACTCCC
1 TGAATGAATAGGGAGCAGACACGTTTACTGAAGATTATTCGAGTCTTATACTCCA
*
470738 TGAATGAATAGGGAGCAGACACGTTTACTGAAGATTGTTCGAGTCTTATACTCCA
1 TGAATGAATAGGGAGCAGACACGTTTACTGAAGATTATTCGAGTCTTATACTCCA
* * *
470793 TGAAT-AATAGGGAGCAGACACGTTTTCTGAAGATTTTTCAAGTCT
1 TGAATGAATAGGGAGCAGACACGTTTACTGAAGATTATTCGAGTCT
470838 CACTTATCAT
Statistics
Matches: 185, Mismatches: 20, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
51 29 0.16
54 38 0.21
55 118 0.64
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (55 bp):
TGAATGAATAGGGAGCAGACACGTTTACTGAAGATTATTCGAGTCTTATACTCCA
Found at i:478601 original size:20 final size:20
Alignment explanation
Indices: 478558--478608 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
478548 TTATCATTAT
*
478558 AAATAATTTTAAATCTTCTT
1 AAATAATTTTAAATCTTCTC
* * *
478578 AAATAATTTTTATTTTTCTC
1 AAATAATTTTAAATCTTCTC
*
478598 AAATAAATTTA
1 AAATAATTTTA
478609 TATAACTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATAATTTTAAATCTTCTC
Found at i:479309 original size:12 final size:12
Alignment explanation
Indices: 479272--479312 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
479262 ACTATATGGT
*
479272 ATGAACAGTACC
1 ATGAACAATACC
*
479284 GTGAACAATA--
1 ATGAACAATACC
479294 ATGAACAATACC
1 ATGAACAATACC
479306 ATGAACA
1 ATGAACA
479313 GTGCTACAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.49, C:0.20, G:0.15, T:0.17
Consensus pattern (12 bp):
ATGAACAATACC
Found at i:480046 original size:31 final size:31
Alignment explanation
Indices: 480008--480163 Score: 144
Period size: 31 Copynumber: 5.0 Consensus size: 31
479998 CCGGAAGGAC
* *
480008 CAGTCCATAGATTCCGAAGAACCTAGGTAAT
1 CAGTCCATAGATTCCGAAGAACATAGGTAAA
480039 CAGTCCAT--ATGTCACGAAGAACATAGGTAAA
1 CAGTCCATAGAT-TC-CGAAGAACATAGGTAAA
* *
480070 CATTCCATATG-TCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATTCCGAAGAACATAGGTAAA
*
480101 CAGTCCAT--ATGTCTCGAATAACATAGGTAAA
1 CAGTCCATAGAT-TC-CGAAGAACATAGGTAAA
* * *
480132 CAGTCTATATG-TCCCTAAGAACATAGGTAAA
1 CAGTCCATA-GATTCCGAAGAACATAGGTAAA
480163 C
1 C
480164 CCTCGACCCT
Statistics
Matches: 103, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
29 3 0.03
30 3 0.03
31 93 0.90
32 2 0.02
33 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (31 bp):
CAGTCCATAGATTCCGAAGAACATAGGTAAA
Found at i:480108 original size:62 final size:62
Alignment explanation
Indices: 480008--480163 Score: 224
Period size: 62 Copynumber: 2.5 Consensus size: 62
479998 CCGGAAGGAC
* * *
480008 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCACGAAGAACATAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAACAGTCCATATGTCACGAAGAACATAGGTAAA
* * *
480070 CATTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCTCGAATAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCACGAAGAACATAGGTAAA
* *
480132 CAGTCTATATGTCCCTAAGAACATAGGTAAAC
1 CAGTCCATATGTCCCGAAGAACATAGGTAAAC
480164 CCTCGACCCT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
62 83 0.99
63 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (62 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCACGAAGAACATAGGTAAA
Found at i:483634 original size:4 final size:4
Alignment explanation
Indices: 483625--483657 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
483615 TATGATGTTG
483625 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
483658 ATACACACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:485475 original size:23 final size:23
Alignment explanation
Indices: 485449--485512 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
485439 AGCTCATATA
*
485449 AATTGCACCGAAGTGCTACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
485472 AATTGCACCGTAGTGCCATGTAG
1 AATTGCACCGAAGTGCCACGTAG
***
485495 AAAAACACCGAAGTGCCA
1 AATTGCACCGAAGTGCCA
485513 TATAAGGTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:486541 original size:65 final size:67
Alignment explanation
Indices: 486422--486571 Score: 250
Period size: 65 Copynumber: 2.3 Consensus size: 67
486412 ACCCATTCAA
486422 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATACTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATACTAGAGGGGAATCGATACCCCCA
486487 -G
66 GG
* *
486488 GGGGAACCGATACCCCCTCAACGAATATGAA-TTCCAGAATGCTAGTGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATACTAGAGGGGAATCGATACCCCCA
486552 GGG
66 -GG
*
486555 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
486572 ATGAGAAAAA
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
65 31 0.39
66 31 0.39
67 17 0.22
ACGTcount: A:0.30, C:0.29, G:0.25, T:0.16
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATACTAGAGGGGAATCGATACCCCCA
GG
Found at i:487243 original size:149 final size:149
Alignment explanation
Indices: 487050--487353 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
487040 GGGTAGAGGG
*
487050 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAATATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
487115 ACTTGATCCCTAGTATATGTATATGATTCTTAAAGAATTCTATGTAGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAAGAATTCTATGTAGTCCTTATGGACATCATTA
487180 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
487199 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
487264 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAAGAATTCTATGTAGTCCTTATGGACATCATTA
*
487329 TATGGCACTACGGTGTAAT
131 TATGGCACTACGGTGCAAT
487348 TCTACG
1 TCTACG
487354 GGGTACTTCG
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAAGAATTCTATGTAGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:493474 original size:21 final size:21
Alignment explanation
Indices: 493432--493474 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
493422 TTTCTGGGTT
* * *
493432 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
493453 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
493474 A
1 A
493475 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:493534 original size:66 final size:65
Alignment explanation
Indices: 493454--493602 Score: 237
Period size: 66 Copynumber: 2.3 Consensus size: 65
493444 ACCCATTCAA
493454 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATACTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAA-TTCCAGAATACTAG-GGGGAATCGATACCCCCA
493519 -G
64 GG
* *
493520 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGTGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATACTAGGGGGAATCGATACCCCCA-G
493585 G
65 G
*
493586 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
493603 ATGAGAAAAA
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
64 17 0.22
65 13 0.17
66 48 0.62
ACGTcount: A:0.30, C:0.29, G:0.25, T:0.16
Consensus pattern (65 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATACTAGGGGGAATCGATACCCCCAGG
Found at i:494277 original size:149 final size:149
Alignment explanation
Indices: 494081--494384 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
494071 GGGTAGAGGG
494081 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* * *
494146 ATTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACACCATTA
*
494211 TATGGCACTACGGTGCAAT
131 TATGACACTACGGTGCAAT
*
494230 TCTATGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
494295 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACACCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACACCATTA
494360 TATGACACTACGGTGCAAT
131 TATGACACTACGGTGCAAT
494379 TCTACG
1 TCTACG
494385 GGGCACTTCG
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACACCATTA
TATGACACTACGGTGCAAT
Found at i:496557 original size:21 final size:21
Alignment explanation
Indices: 496531--496592 Score: 115
Period size: 21 Copynumber: 3.0 Consensus size: 21
496521 TCTGGTTCGG
496531 TTGAATGGGTACCGATTCCCA
1 TTGAATGGGTACCGATTCCCA
*
496552 TTGAATGGGTATCGATTCCCA
1 TTGAATGGGTACCGATTCCCA
496573 TTGAATGGGTACCGATTCCC
1 TTGAATGGGTACCGATTCCC
496593 CTAGCCCAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (21 bp):
TTGAATGGGTACCGATTCCCA
Found at i:503248 original size:22 final size:23
Alignment explanation
Indices: 503195--503248 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
503185 ACAAGTTTTG
*
503195 AATGAGCTTTAAATGATTTATCA
1 AATGAGCTTTAAATGATTCATCA
* *
503218 AATGTGCTTTGAACT-ATTCAT-A
1 AATGAGCTTT-AAATGATTCATCA
503240 AATGAGCTT
1 AATGAGCTT
503249 GTTGTGAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 9 0.35
23 14 0.54
24 3 0.12
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (23 bp):
AATGAGCTTTAAATGATTCATCA
Found at i:511010 original size:23 final size:23
Alignment explanation
Indices: 510984--511036 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
510974 ATCGCACCTA
*
510984 AGTGCCACTTAGAATTGCACCGG
1 AGTGCCACGTAGAATTGCACCGG
* *
511007 AGTGCCGCGTAGAATTGCACCGT
1 AGTGCCACGTAGAATTGCACCGG
511030 AGTGCCA
1 AGTGCCA
511037 TATAATAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (23 bp):
AGTGCCACGTAGAATTGCACCGG
Found at i:511223 original size:103 final size:103
Alignment explanation
Indices: 511055--511269 Score: 394
Period size: 103 Copynumber: 2.1 Consensus size: 103
511045 TGTCCATAAG
*
511055 GACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTAGGTGTCTCACCAGAC
511120 CTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 CTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
*
511158 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTAGGTGTCTCACCAGAC
* *
511223 CTCACACATGTTCCAAAGAATACATATATGTCTCGAAG
66 CTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
511261 GACCACATA
1 GACCACATA
511270 GACCCTCTAC
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTAGGTGTCTCACCAGAC
CTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:520045 original size:50 final size:50
Alignment explanation
Indices: 519981--520080 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
519971 AGGGATAATA
*
519981 TTACGTGTGGAGTCGAGGAAGGAGAGGAACATTAATTGTGTC-TGTTATTT
1 TTACGTGTGAAGTCGAGGAAGGAGAGGAACATTAATTGTGTCAT-TTATTT
520031 TTACGTGTGAAGTCGAGGAAGGAGAGGAACATTAATTGTGTCATTTATTT
1 TTACGTGTGAAGTCGAGGAAGGAGAGGAACATTAATTGTGTCATTTATTT
520081 AATTATTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 47 0.98
51 1 0.02
ACGTcount: A:0.28, C:0.08, G:0.30, T:0.34
Consensus pattern (50 bp):
TTACGTGTGAAGTCGAGGAAGGAGAGGAACATTAATTGTGTCATTTATTT
Found at i:535702 original size:155 final size:157
Alignment explanation
Indices: 535413--535730 Score: 532
Period size: 155 Copynumber: 2.0 Consensus size: 157
535403 TTTCTTGTTC
* *
535413 CCATTCTATGTTTTCTCCATGGAAGGCTTTCACTTGTTTGGGCTTTCTCTCTGTTAAAGTGTAGA
1 CCATTCTATGGTTTCTCCATGGAAGGCGTTCACTTGTTTGGGC-TTCTCTCTGTTAAAGTGTAGA
*
535478 TTTTATGGCTGCAGAGACATGTTTTTGTTTGTAAAACAAAAACAATATTTAAATGGTATTTAACT
65 TTTTATGGCTGCAGAGACATGTTTTTGTTTGTAAAACAAAAACAATATTTAAATGGTATTTAACC
* *
535543 AGACTGATTATAGCCTGTTTTGACTATG
130 AGACTGATTATAGCATGTCTTGACTATG
* *
535571 GCATTCTATGGTTTCTCCATGGAAGGCGTTCGCTTGTTTGGGC-TCTCTCTGTTAAAGTGTAGAT
1 CCATTCTATGGTTTCTCCATGGAAGGCGTTCACTTGTTTGGGCTTCTCTCTGTTAAAGTGTAGAT
* *
535635 TTTATGGTTGCAGAGACATG-TTTTGTTTGTAAAACAGAAACAATATTTAAATGGTATTTAACCA
66 TTTATGGCTGCAGAGACATGTTTTTGTTTGTAAAACAAAAACAATATTTAAATGGTATTTAACCA
535699 GACTGATTATAGCATGTCTTGACTATG
131 GACTGATTATAGCATGTCTTGACTATG
535726 CCATT
1 CCATT
535731 TCCTTCTCCT
Statistics
Matches: 150, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
155 71 0.47
156 40 0.27
158 39 0.26
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.40
Consensus pattern (157 bp):
CCATTCTATGGTTTCTCCATGGAAGGCGTTCACTTGTTTGGGCTTCTCTCTGTTAAAGTGTAGAT
TTTATGGCTGCAGAGACATGTTTTTGTTTGTAAAACAAAAACAATATTTAAATGGTATTTAACCA
GACTGATTATAGCATGTCTTGACTATG
Found at i:543164 original size:133 final size:133
Alignment explanation
Indices: 542924--543191 Score: 457
Period size: 133 Copynumber: 2.0 Consensus size: 133
542914 TACCTGTTAT
* *
542924 ATATGTAAACAAAACACAATAAGTAGGTTCTTCTGTAGACAATTGAGTGTCTCTTTTCACAAATC
1 ATATGTAAACAAAACAAAATAAGTAGGGTCTTCTGTAGACAATTGAGTGTCTCTTTTCACAAATC
* *
542989 CTATGTTGTATTCGTTTGTTGTTTTAGCAGCATTTGTGCTTTTCAGATATGTCCAATCTCAATTT
66 CTACGTTGTATTCGTTTGTTGTTTTAGCAGCATTTGTACTTTTCAGATATGTCCAATCTCAATTT
543054 TTA
131 TTA
* *
543057 ATATGTAAACAAAACAAAATAAGT-GGCGTCTTCTGTAGACAATTGAGTGTCTGTTTTCACAACT
1 ATATGTAAACAAAACAAAATAAGTAGG-GTCTTCTGTAGACAATTGAGTGTCTCTTTTCACAAAT
*
543121 CCTACGTTGTATTCGTTTGTTGTTTTAGCAGCATTTGTACTTTTCAGATATGTCCAATCTCATTT
65 CCTACGTTGTATTCGTTTGTTGTTTTAGCAGCATTTGTACTTTTCAGATATGTCCAATCTCAATT
543186 TTTA
130 TTTA
543190 AT
1 AT
543192 TTTTTGCCCT
Statistics
Matches: 127, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
132 2 0.02
133 125 0.98
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (133 bp):
ATATGTAAACAAAACAAAATAAGTAGGGTCTTCTGTAGACAATTGAGTGTCTCTTTTCACAAATC
CTACGTTGTATTCGTTTGTTGTTTTAGCAGCATTTGTACTTTTCAGATATGTCCAATCTCAATTT
TTA
Found at i:551010 original size:9 final size:9
Alignment explanation
Indices: 550996--551025 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
550986 GGTGTCTTTG
550996 GGTTTTTTT
1 GGTTTTTTT
551005 GG-TTTTTT
1 GGTTTTTTT
551013 GGTTTTTTT
1 GGTTTTTTT
551022 GGTT
1 GGTT
551026 ATGTTGGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.00, C:0.00, G:0.27, T:0.73
Consensus pattern (9 bp):
GGTTTTTTT
Found at i:558633 original size:55 final size:55
Alignment explanation
Indices: 558568--558671 Score: 190
Period size: 55 Copynumber: 1.9 Consensus size: 55
558558 ACCTCCCGAG
* *
558568 TTGCATATTGTGTTGACCCAAATACAATATGGAGGACTACTTGATTAGTAAGCCT
1 TTGCATATTGTGTTGACCCAAATACAAGATGGAGAACTACTTGATTAGTAAGCCT
558623 TTGCATATTGTGTTGACCCAAATACAAGATGGAGAACTACTTGATTAGT
1 TTGCATATTGTGTTGACCCAAATACAAGATGGAGAACTACTTGATTAGT
558672 GAGCGATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (55 bp):
TTGCATATTGTGTTGACCCAAATACAAGATGGAGAACTACTTGATTAGTAAGCCT
Found at i:569789 original size:11 final size:11
Alignment explanation
Indices: 569773--569811 Score: 78
Period size: 11 Copynumber: 3.5 Consensus size: 11
569763 AAAATTCAAC
569773 AGTTTGAATTA
1 AGTTTGAATTA
569784 AGTTTGAATTA
1 AGTTTGAATTA
569795 AGTTTGAATTA
1 AGTTTGAATTA
569806 AGTTTG
1 AGTTTG
569812 CAGCAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (11 bp):
AGTTTGAATTA
Found at i:592751 original size:40 final size:40
Alignment explanation
Indices: 592690--592766 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
592680 GGATTTCAAA
* *
592690 TTCGCAACTCAATTTCTGAATTTGCAACGCAAATTTTGTT
1 TTCGCAACTCAATTTCTGAATTCGCAACACAAATTTTGTT
* *
592730 TTCGCAACTCGATTT-TCGAATTCGCAACACGAATTTT
1 TTCGCAACTCAATTTCT-GAATTCGCAACACAAATTTT
592767 AATTTCGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.03
40 31 0.97
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (40 bp):
TTCGCAACTCAATTTCTGAATTCGCAACACAAATTTTGTT
Found at i:592773 original size:20 final size:20
Alignment explanation
Indices: 592690--592797 Score: 57
Period size: 20 Copynumber: 5.5 Consensus size: 20
592680 GGATTTCAAA
*
592690 TTCGCAACTC-AATTTCTGAAT
1 TTCGCAACACGAATTT-T-AAT
* * **
592711 TT-GCAACGCAAATTTTGTT
1 TTCGCAACACGAATTTTAAT
*
592730 TTCGCAACTCG-ATTTTCGAA-
1 TTCGCAACACGAATTTT--AAT
592750 TTCGCAACACGAATTTTAAT
1 TTCGCAACACGAATTTTAAT
* * *
592770 TTCGTAACA-G-GTTTTAGT
1 TTCGCAACACGAATTTTAAT
592788 TTCGCAACAC
1 TTCGCAACAC
592798 AAATGTTTTG
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
18 14 0.21
19 11 0.16
20 31 0.46
21 12 0.18
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (20 bp):
TTCGCAACACGAATTTTAAT
Found at i:592773 original size:40 final size:39
Alignment explanation
Indices: 592661--592773 Score: 100
Period size: 40 Copynumber: 2.8 Consensus size: 39
592651 CGTGTTGCGG
* * * * *
592661 TTTTCAAATTCGCAATACTGGATTTCAAATTCGCAACTCA
1 TTTTCGAATTCGCAACAC-GAATTTTAATTTCGCAACTCA
* * * * **
592701 ATTTCTGAATTTGCAACGCAAATTTTGTTTTCGCAACTCGA
1 TTTTC-GAATTCGCAACACGAATTTTAATTTCGCAACTC-A
592742 TTTTCGAATTCGCAACACGAATTTTAATTTCG
1 TTTTCGAATTCGCAACACGAATTTTAATTTCG
592774 TAACAGGTTT
Statistics
Matches: 54, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
40 40 0.74
41 14 0.26
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.38
Consensus pattern (39 bp):
TTTTCGAATTCGCAACACGAATTTTAATTTCGCAACTCA
Found at i:593751 original size:24 final size:24
Alignment explanation
Indices: 593724--593770 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
593714 GTATTCAAAA
593724 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
593748 TTTGATTTTGGTCAATACTCGGA
1 TTTGATCTTGGTCAATACCCGGA
593771 TTTTATGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:594351 original size:2 final size:2
Alignment explanation
Indices: 594344--594370 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
594334 CTTTTAAAAC
594344 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
594371 CTCACATCCT
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:595859 original size:17 final size:18
Alignment explanation
Indices: 595827--595860 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
595817 AACTAACATT
595827 TTTTATGCACATCAATAG
1 TTTTATGCACATCAATAG
*
595845 TTTTAT-CAGATCAATA
1 TTTTATGCACATCAATA
595861 ATTCTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (18 bp):
TTTTATGCACATCAATAG
Found at i:596043 original size:36 final size:36
Alignment explanation
Indices: 595996--596068 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
595986 GATAAATTAT
595996 AATCTACATATCCATGGTTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGTTGATTCTTTTATCACTTA
596032 AATCTACATATCCATGGTTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGTTGATTCTTTTATCACTTA
596068 A
1 A
596069 TTCGAGAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (36 bp):
AATCTACATATCCATGGTTGATTCTTTTATCACTTA
Found at i:596757 original size:9 final size:9
Alignment explanation
Indices: 596743--596790 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
596733 GTCGGGTTGG
596743 AACCGGTCA
1 AACCGGTCA
596752 AACCGGTCAA
1 AACCGGTC-A
* *
596762 AACAGCTCCAA
1 AACCGGT-C-A
596773 AACCGGTCA
1 AACCGGTCA
596782 AACCGGTCA
1 AACCGGTCA
596791 TTTTTCCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 18 0.55
10 7 0.21
11 8 0.24
ACGTcount: A:0.38, C:0.33, G:0.19, T:0.10
Consensus pattern (9 bp):
AACCGGTCA
Found at i:600720 original size:36 final size:36
Alignment explanation
Indices: 600673--600750 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
600663 GATAAATTAT
*
600673 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCAATGGCTGATTCTTTTATCACTTA
*
600709 AATCTACATATCAATGGCTTATTCTTTTATCACTTA
1 AATCTACATATCAATGGCTGATTCTTTTATCACTTA
*
600745 ATTCTA
1 AATCTA
600751 GAACTTGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (36 bp):
AATCTACATATCAATGGCTGATTCTTTTATCACTTA
Found at i:601602 original size:21 final size:21
Alignment explanation
Indices: 601558--601603 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
601548 GATTTCTGGG
* * **
601558 CAAGGGGAATCGGTACCCGTT
1 CAAGGGGAACCGATACCCCCT
601579 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCCCT
601600 CAAG
1 CAAG
601604 CGAACCAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCCCT
Found at i:601676 original size:24 final size:22
Alignment explanation
Indices: 601627--601668 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
601617 ACAGAATGTC
601627 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
601648 CAGGAGGGAACCGATTCCCCC
1 AAGGAGGGAACCGATACCCCC
601669 CTAAAGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.29, C:0.36, G:0.29, T:0.07
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:602011 original size:18 final size:19
Alignment explanation
Indices: 601974--602012 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
601964 TGTTGTTATA
*
601974 ATTATATGTGATTATCTGT
1 ATTATATGTGATTATATGT
*
601993 ATTATAT-TGATTGTATGT
1 ATTATATGTGATTATATGT
602011 AT
1 AT
602013 GCATGACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (19 bp):
ATTATATGTGATTATATGT
Found at i:602624 original size:31 final size:31
Alignment explanation
Indices: 602586--602677 Score: 132
Period size: 31 Copynumber: 3.0 Consensus size: 31
602576 GGGTCGAGGG
*
602586 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGA
*
602617 TTACCTATGTTCTTCGGGATATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGA
* *
602648 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
602678 GTCCTTCGGG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGA
Found at i:605852 original size:21 final size:21
Alignment explanation
Indices: 605808--605853 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
605798 GATTTCTGGG
* * *
605808 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
605829 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
605850 CAAG
1 CAAG
605854 CGAACCAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:605925 original size:23 final size:22
Alignment explanation
Indices: 605877--605925 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
605867 ACAGAATGTC
605877 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
605898 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
605921 AAGGA
1 AAGGA
605926 AAAATGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:606871 original size:31 final size:31
Alignment explanation
Indices: 606833--606955 Score: 194
Period size: 31 Copynumber: 4.0 Consensus size: 31
606823 GGGTCGAGGG
*
606833 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
606864 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
606895 TTACCTATGTTCTTCGGAACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
606926 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
606956 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:609823 original size:11 final size:10
Alignment explanation
Indices: 609793--609833 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
609783 GGGCTTTGTA
609793 ATTTAATATT
1 ATTTAATATT
609803 ATTTATATATGT
1 ATTTA-ATAT-T
609815 ATTTAATATAT
1 ATTTAATAT-T
609826 ATTTAATA
1 ATTTAATA
609834 ATAATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:609837 original size:3 final size:3
Alignment explanation
Indices: 609829--609920 Score: 148
Period size: 3 Copynumber: 30.7 Consensus size: 3
609819 AATATATATT
* *
609829 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
609877 TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA CAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
609921 TTTATAATAT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:610641 original size:114 final size:114
Alignment explanation
Indices: 610246--611025 Score: 1181
Period size: 114 Copynumber: 6.8 Consensus size: 114
610236 GATAGAATTA
* * *
610246 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTTTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* * * * * * * * * *
610311 GAACTCTAC-CTGGCAATGTTGATACATCAA-ATGATGAATTCAAGCAAAAGA
63 GAAC-CTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
* *
610362 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTTTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* * * * * * * * * *
610427 GAACTCTAC-CTGGCAATGTTGATACATCAA-ATGATGAATTCAAGCAAAAGA
63 GAAC-CTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
*
610478 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
610543 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
610592 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
610657 CCTTCTCTGGAAAATATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
610706 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
610771 CCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
610820 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
610885 CATTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
610934 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
610999 CCTTCTCTGGAAAAGCTAATCTATCAA
66 CCTTCTCTGGAAAAGATAATCCATCAA
611026 ATGATAGATT
Statistics
Matches: 641, Mismatches: 21, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
112 2 0.00
113 35 0.05
114 443 0.69
116 161 0.25
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (114 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
Found at i:611903 original size:83 final size:83
Alignment explanation
Indices: 611764--612218 Score: 829
Period size: 83 Copynumber: 5.5 Consensus size: 83
611754 CCTACCGAAT
*
611764 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCATCTTCTAAATTCAA
611829 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
611847 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCATCTTCTAAATTCAA
611912 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
611930 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCATCTTCTAAATTCAA
611995 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
* * *
612013 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCATCTTCTAAATTCAA
*
612078 TGATTGGTTCTGCTAAAC
66 TGATTGGTTCTGCCAAAC
* * *
612096 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCATCTTCTAAATTCAA
*
612161 TGATTGGTTCTGCTAAAC
66 TGATTGGTTCTGCCAAAC
612179 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
612219 GAGCCCATTG
Statistics
Matches: 367, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 367 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCATCTTCTAAATTCAA
TGATTGGTTCTGCCAAAC
Found at i:613387 original size:9 final size:9
Alignment explanation
Indices: 613373--613412 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
613363 TTGACCCCCC
613373 TTTTTTCTT
1 TTTTTTCTT
613382 TTTTTTCTT
1 TTTTTTCTT
*
613391 TTTTCT-TT
1 TTTTTTCTT
613399 TTTTTTCATT
1 TTTTTTC-TT
613409 TTTT
1 TTTT
613413 CTTCAAGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 7 0.26
9 14 0.52
10 6 0.22
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:613413 original size:18 final size:17
Alignment explanation
Indices: 613372--613415 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
613362 CTTGACCCCC
613372 CTTTTTTC-TTTTTTTT
1 CTTTTTTCTTTTTTTTT
613388 CTTTTTTCTTTTTTTTT
1 CTTTTTTCTTTTTTTTT
613405 CATTTTTTCTT
1 C-TTTTTTCTT
613416 CAAGCATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 8 0.31
17 9 0.35
18 9 0.35
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (17 bp):
CTTTTTTCTTTTTTTTT
Found at i:626224 original size:11 final size:10
Alignment explanation
Indices: 626194--626234 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
626184 GGGCTTTGTA
626194 ATTTAATATT
1 ATTTAATATT
626204 ATTTATATATGT
1 ATTTA-ATAT-T
626216 ATTTAATATAT
1 ATTTAATAT-T
626227 ATTTAATA
1 ATTTAATA
626235 ATAATAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:626238 original size:3 final size:3
Alignment explanation
Indices: 626230--626315 Score: 136
Period size: 3 Copynumber: 28.7 Consensus size: 3
626220 AATATATATT
* *
626230 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
626278 TAA TAA TAA TAA TAA TTA TAA TAA CAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
626316 TTTATAAACA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:627622 original size:3 final size:3
Alignment explanation
Indices: 627608--627640 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
627598 AACTCTGAAA
*
627608 AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
627641 TCCTCGAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:629719 original size:12 final size:12
Alignment explanation
Indices: 629702--629742 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
629692 AGCAAAAGGA
*
629702 AATCAAAATCGC
1 AATCAAAATCAC
*
629714 AATCAAAATCAA
1 AATCAAAATCAC
*
629726 AATCAAAATCCC
1 AATCAAAATCAC
629738 AATCA
1 AATCA
629743 CAACCGGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (12 bp):
AATCAAAATCAC
Found at i:629723 original size:6 final size:6
Alignment explanation
Indices: 629701--629735 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
629691 AAGCAAAAGG
* *
629701 AAATCA AAATCG CAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
629736 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:629966 original size:20 final size:20
Alignment explanation
Indices: 629920--629967 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
629910 TTGTTGCGAT
*
629920 TGTTGCGAAAGTCAAATTTG
1 TGTTGCGAAAGTCAAATTCG
***
629940 CAATGCGAAAGTCAAATTCG
1 TGTTGCGAAAGTCAAATTCG
629960 TGTTGCGA
1 TGTTGCGA
629968 TTATTACGAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (20 bp):
TGTTGCGAAAGTCAAATTCG
Found at i:630152 original size:37 final size:36
Alignment explanation
Indices: 630102--630209 Score: 99
Period size: 37 Copynumber: 2.9 Consensus size: 36
630092 CAAATCAACT
630102 TTTACAAATCAATTAAACAAGCAAAAAATAAGAATTA
1 TTTACAAATCAATTAAACAAGCAAAAAATAA-AATTA
* * * **** *
630139 TTTACACATCAATTAAAAAATCAACTTTTACAAATCAA
1 TTTACAAATCAATTAAACAAGCAAAAAATA-AAAT-TA
630177 CTTTTACAAATCAATTAAACAAGCAAAAAATAA
1 --TTTACAAATCAATTAAACAAGCAAAAAATAA
630210 TTCTTATTTC
Statistics
Matches: 52, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
37 26 0.50
38 2 0.04
39 1 0.02
40 23 0.44
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.27
Consensus pattern (36 bp):
TTTACAAATCAATTAAACAAGCAAAAAATAAAATTA
Found at i:630175 original size:14 final size:14
Alignment explanation
Indices: 630156--630190 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
630146 ATCAATTAAA
630156 AAATCAACTTTTAC
1 AAATCAACTTTTAC
630170 AAATCAACTTTTAC
1 AAATCAACTTTTAC
630184 AAATCAA
1 AAATCAA
630191 TTAAACAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:630218 original size:77 final size:78
Alignment explanation
Indices: 630091--630265 Score: 298
Period size: 77 Copynumber: 2.3 Consensus size: 78
630081 ATTTAAAACA
630091 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
630156 -AAATCAACTTTT
66 CAAATCAACTTTT
*** * *
630168 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
630233 CAAATCAACTTTT
66 CAAATCAACTTTT
630246 ACAAATCAACTTTTACAAAT
1 ACAAATCAACTTTTACAAAT
630266 ACATCAATTT
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
77 60 0.65
78 32 0.35
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (78 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
CAAATCAACTTTT
Found at i:630251 original size:14 final size:14
Alignment explanation
Indices: 630232--630265 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
630222 CATCAATTAA
630232 ACAAATCAACTTTT
1 ACAAATCAACTTTT
630246 ACAAATCAACTTTT
1 ACAAATCAACTTTT
630260 ACAAAT
1 ACAAAT
630266 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:631219 original size:2 final size:2
Alignment explanation
Indices: 631208--631247 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
631198 TATGCTGTTT
631208 TA TA -A 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 TA T
631248 TAGTGAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:631681 original size:21 final size:21
Alignment explanation
Indices: 631657--631756 Score: 98
Period size: 21 Copynumber: 4.8 Consensus size: 21
631647 GGGAGGGACT
631657 TCTTGAACGATGACAGAGGCC
1 TCTTGAACGATGACAGAGGCC
* *
631678 TCTTGAATGGTGGGA-AG-GGCC
1 TCTTGAACGAT--GACAGAGGCC
* *
631699 TCTTGAAGGATGACAGGGGCC
1 TCTTGAACGATGACAGAGGCC
* *
631720 TCTTGAATGAT-AGGAGAGGCC
1 TCTTGAACGATGA-CAGAGGCC
631741 TCTTGAACGATGACAG
1 TCTTGAACGATGACAG
631757 GTGAATCAGG
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.03
20 3 0.05
21 54 0.84
22 3 0.05
23 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.34, T:0.22
Consensus pattern (21 bp):
TCTTGAACGATGACAGAGGCC
Found at i:631703 original size:42 final size:41
Alignment explanation
Indices: 631644--631756 Score: 154
Period size: 42 Copynumber: 2.7 Consensus size: 41
631634 GCTTTCGAAC
*
631644 GGTGGGAGGGACTTCTTGAACGATGACAGAGGCCTCTTGAAT
1 GGTGGGAGGG-CCTCTTGAACGATGACAGAGGCCTCTTGAAT
* *
631686 GGTGGGAAGGGCCTCTTGAAGGATGACAGGGGCCTCTTGAAT
1 GGTGGG-AGGGCCTCTTGAACGATGACAGAGGCCTCTTGAAT
* *
631728 GATAGGAGAGGCCTCTTGAACGATGACAG
1 GGTGGGAG-GGCCTCTTGAACGATGACAG
631757 GTGAATCAGG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
41 2 0.03
42 57 0.90
43 4 0.06
ACGTcount: A:0.25, C:0.17, G:0.37, T:0.21
Consensus pattern (41 bp):
GGTGGGAGGGCCTCTTGAACGATGACAGAGGCCTCTTGAAT
Found at i:632150 original size:21 final size:21
Alignment explanation
Indices: 632060--632175 Score: 56
Period size: 21 Copynumber: 5.5 Consensus size: 21
632050 AACACCATTT
* * * *
632060 TCATCGCGTAAAACATCTACC
1 TCATCACGTAAAGCACCGACC
* *
632081 TCACCACGTAAAG-ATCGAACC
1 TCATCACGTAAAGCACCG-ACC
* * **
632102 TCATCACGTCATGCACC-ATTG
1 TCATCACGTAAAGCACCGA-CC
* *
632123 TCTTCACGTAAAGTACCGACC
1 TCATCACGTAAAGCACCGACC
* * **
632144 TCCTCACGCAAAGCATTGACC
1 TCATCACGTAAAGCACCGACC
632165 TCATCACGTAA
1 TCATCACGTAA
632176 CTCCCCTAAC
Statistics
Matches: 68, Mismatches: 23, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
20 4 0.06
21 61 0.90
22 3 0.04
ACGTcount: A:0.31, C:0.34, G:0.13, T:0.22
Consensus pattern (21 bp):
TCATCACGTAAAGCACCGACC
Found at i:633843 original size:20 final size:20
Alignment explanation
Indices: 633820--633860 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
633810 TCGCAACGCT
633820 ATTTTCATTTTCGCGTTGCG
1 ATTTTCATTTTCGCGTTGCG
* *
633840 ATTTTCATTTTTGTGTTGCG
1 ATTTTCATTTTCGCGTTGCG
633860 A
1 A
633861 ATTTAAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.20, T:0.54
Consensus pattern (20 bp):
ATTTTCATTTTCGCGTTGCG
Found at i:634234 original size:22 final size:22
Alignment explanation
Indices: 634203--634254 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
634193 GATAGATGGA
634203 TTTCGCCGGAGATAGGGACGGG
1 TTTCGCCGGAGATAGGGACGGG
* * *
634225 TTTCGTCGGAGATGGGGACGGA
1 TTTCGCCGGAGATAGGGACGGG
*
634247 TGTCGCCG
1 TTTCGCCG
634255 TAGAGAGTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.15, C:0.19, G:0.44, T:0.21
Consensus pattern (22 bp):
TTTCGCCGGAGATAGGGACGGG
Found at i:634444 original size:20 final size:20
Alignment explanation
Indices: 634421--634507 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
634411 TGACTTATGT
*
634421 GTTGCGAATTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* *
634441 GTTGCGATTTACAGATTCGT
1 GTTGCGATTTACAAATTCGC
*
634461 ATTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
634481 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
634501 GTTGCGA
1 GTTGCGA
634508 ATTTGGAAAC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:634466 original size:40 final size:40
Alignment explanation
Indices: 634422--634510 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 40
634412 GACTTATGTG
*
634422 TTGCGAATTACAAATTCGCGTTGCGATTTACAGATTCGTA
1 TTGCGAATTACAAATTCGCGTTGCGATTTACAGATTCGCA
* * *
634462 TTGCGATTTACAAATTCGCGTTGCGATTTACATATTCGCG
1 TTGCGAATTACAAATTCGCGTTGCGATTTACAGATTCGCA
634502 TTGCGAATT
1 TTGCGAATT
634511 TGGAAACTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (40 bp):
TTGCGAATTACAAATTCGCGTTGCGATTTACAGATTCGCA
Found at i:634525 original size:40 final size:40
Alignment explanation
Indices: 634422--634527 Score: 106
Period size: 40 Copynumber: 2.6 Consensus size: 40
634412 GACTTATGTG
* * * *
634422 TTGCGAATTACAAATTCGCGTTGCGATTTACAGATTCGTA
1 TTGCGATTTACAAACTCGAGTTGCGATTTACAGATTCGCA
* * * *
634462 TTGCGATTTACAAATTCGCGTTGCGATTTACATATTCGCG
1 TTGCGATTTACAAACTCGAGTTGCGATTTACAGATTCGCA
**
634502 TTGCGAATTTGGAAACT-GAGTTGCGA
1 TTGCG-ATTTACAAACTCGAGTTGCGA
634528 AATTGGAGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 49 0.86
41 8 0.14
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (40 bp):
TTGCGATTTACAAACTCGAGTTGCGATTTACAGATTCGCA
Found at i:653160 original size:21 final size:22
Alignment explanation
Indices: 653130--653171 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
653120 ATGTTATTAT
* *
653130 TTTAAGGATT-TTTTTTCTCTC
1 TTTAAAGATTGTTTATTCTCTC
653151 TTTAAAGATTGTTTATTCTCT
1 TTTAAAGATTGTTTATTCTCT
653172 GAACTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (22 bp):
TTTAAAGATTGTTTATTCTCTC
Found at i:660271 original size:34 final size:33
Alignment explanation
Indices: 660233--660337 Score: 115
Period size: 34 Copynumber: 3.1 Consensus size: 33
660223 TTAATCAAGG
660233 AGGGTTATAGTGTAATTCGTATCTTATGTATTTC
1 AGGGTTATAGTGTAATT-GTATCTTATGTATTTC
*
660267 AGGGTTAGAGTGTAATGTGTATCTTATGTAATTT-
1 AGGGTTATAGTGTAAT-TGTATCTTATGT-ATTTC
* * *
660301 AGGGTT-TGAGTGCATTTTGTATCTTATGTAATTC
1 AGGGTTAT-AGTGTA-ATTGTATCTTATGTATTTC
660335 AGG
1 AGG
660338 TTAATTAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
33 3 0.05
34 52 0.85
35 6 0.10
ACGTcount: A:0.24, C:0.07, G:0.25, T:0.45
Consensus pattern (33 bp):
AGGGTTATAGTGTAATTGTATCTTATGTATTTC
Found at i:668993 original size:34 final size:34
Alignment explanation
Indices: 668941--669010 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
668931 TTCAAAGCAT
* *
668941 ATATTTATTTAGTGTCAAAATATAAGGCTTATAC
1 ATATTTATTGAGTATCAAAATATAAGGCTTATAC
668975 ATATTTATTGAGTATCAAAATATAAGGCTTATAC
1 ATATTTATTGAGTATCAAAATATAAGGCTTATAC
669009 AT
1 AT
669011 GAACCACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (34 bp):
ATATTTATTGAGTATCAAAATATAAGGCTTATAC
Found at i:673700 original size:21 final size:21
Alignment explanation
Indices: 673642--673701 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
673632 TTGGGGTTTT
673642 TTTATT-AAAAT-A-ATATTA
1 TTTATTAAAAATAATATATTA
* * * *
673660 TTAATTAATAATATTTTATTA
1 TTTATTAAAAATAATATATTA
673681 TTTATTAAAAATAATATATTA
1 TTTATTAAAAATAATATATTA
673702 GTTAACTTAT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
18 5 0.16
19 4 0.13
21 22 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTATTAAAAATAATATATTA
Found at i:673764 original size:38 final size:37
Alignment explanation
Indices: 673674--673777 Score: 137
Period size: 38 Copynumber: 2.8 Consensus size: 37
673664 TTAATAATAT
673674 TTTATTATTTATTAA-AAA-TAATATATTAGTTAACTTA
1 TTTATTATTTATTAATAAATTAATA-ATTA-TTAACTTA
673711 TTT-TT-TTTATTAATAAATTAATAATTATT-ACTTAGA
1 TTTATTATTTATTAATAAATTAATAATTATTAACTT--A
673747 TTTATTATTTATTAATAAATTAATAATTATT
1 TTTATTATTTATTAATAAATTAATAATTATT
673778 TATTAAAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
34 4 0.07
35 10 0.16
36 13 0.21
37 10 0.16
38 24 0.39
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (37 bp):
TTTATTATTTATTAATAAATTAATAATTATTAACTTA
Found at i:673990 original size:2 final size:2
Alignment explanation
Indices: 673983--674010 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
673973 TAGTGGTAAC
673983 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
674011 AAGAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:676393 original size:21 final size:21
Alignment explanation
Indices: 676354--676392 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
676344 AAACAATTGG
676354 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
676375 TAACAATTGATAT-ATTTT
1 TAACAATTGATATCATTTT
676393 TCATTAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:676667 original size:23 final size:21
Alignment explanation
Indices: 676617--676695 Score: 76
Period size: 21 Copynumber: 3.7 Consensus size: 21
676607 AGGGTGTCAA
676617 AGTGCATCCATGCACC--CCTGT
1 AGTGCATCCATGCACCTGCC--T
676638 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACCTG-C-CT
*
676661 AGTGCATCGATGCACCATG--T
1 AGTGCATCCATGCACC-TGCCT
676681 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
676696 TCCATTTCGA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
20 15 0.29
21 16 0.31
23 16 0.31
24 3 0.06
25 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCTGCCT
Found at i:678028 original size:47 final size:48
Alignment explanation
Indices: 677914--678061 Score: 183
Period size: 49 Copynumber: 3.1 Consensus size: 48
677904 TATAGATGTA
* * * *
677914 GATGATTTAGCACGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAAT
1 GATGACTTAGCACATCTGACGTCTTTGTGACGATGGT-CTACTATTAAT
* *
677963 GATGATTTAGCACGTCTGACGTCTTTGTGACGATGGT-TACTATTAAT
1 GATGACTTAGCACATCTGACGTCTTTGTGACGATGGTCTACTATTAAT
* *
678010 GATGACTTAGGATATCTGACGTCTTTGTGAC-AGTGGTGCTACTATTAAT
1 GATGACTTAGCACATCTGACGTCTTTGTGACGA-TGGT-CTACTATTAAT
678059 GAT
1 GAT
678062 AAATAGCACG
Statistics
Matches: 90, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
46 1 0.01
47 41 0.46
49 48 0.53
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (48 bp):
GATGACTTAGCACATCTGACGTCTTTGTGACGATGGTCTACTATTAAT
Found at i:678094 original size:48 final size:49
Alignment explanation
Indices: 677914--678150 Score: 248
Period size: 48 Copynumber: 4.9 Consensus size: 49
677904 TATAGATGTA
*
677914 GATGATTTAGCACGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAAT
1 GATGACTTAGCACGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAAT
* * *
677963 GATGATTTAGCACGTCTGACGTCTTTGTGACGATGGT--TACTATTAAT
1 GATGACTTAGCACGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAAT
* ** **
678010 GATGACTTAGGATATCTGACGTCTTTGTGACAGTGGTGCTACTATTAAT
1 GATGACTTAGCACGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAAT
** * * * * * *
678059 GAT-AAATAGCACGCCTGGCGTCTGTGTGATGGTGGTGCTATTATGAAC
1 GATGACTTAGCACGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAAT
* * * * *
678107 GGT-ACCTAGCACGTCTGACTTCTGTGTGATGGTGGTGTTACTAT
1 GATGACTTAGCACGTCTGACGTCTTTGTGATGGTGGTGCTACTAT
678151 CGATGGTACC
Statistics
Matches: 157, Mismatches: 29, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
47 41 0.26
48 68 0.43
49 48 0.31
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.36
Consensus pattern (49 bp):
GATGACTTAGCACGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAAT
Found at i:678374 original size:30 final size:30
Alignment explanation
Indices: 678295--678376 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 30
678285 TATGAATGAA
* * *
678295 AAGTGAATGATACATGCTACGAAATGAATT
1 AAGTGAATGATACATGCTATGAAATAAATG
*
678325 AAATGAATGATACATGCTATGAAATAAATG
1 AAGTGAATGATACATGCTATGAAATAAATG
678355 AAGTGAATG-TAACATGCTATGA
1 AAGTGAATGAT-ACATGCTATGA
678377 TATGATATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 1 0.02
30 45 0.98
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.27
Consensus pattern (30 bp):
AAGTGAATGATACATGCTATGAAATAAATG
Found at i:678380 original size:5 final size:5
Alignment explanation
Indices: 678372--678400 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
678362 TGTAACATGC
678372 TATGA TATGA TATGA TATGA TATGA -ATGA
1 TATGA TATGA TATGA TATGA TATGA TATGA
678401 AAAGCTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
TATGA
Found at i:685658 original size:21 final size:21
Alignment explanation
Indices: 685634--685674 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
685624 CAATAAAGAA
*
685634 CCAAGACAA-TTTATTGCAAAG
1 CCAAGA-AACTTTATTACAAAG
685655 CCAAGAAACTTTATTACAAA
1 CCAAGAAACTTTATTACAAA
685675 ACCATAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (21 bp):
CCAAGAAACTTTATTACAAAG
Found at i:693346 original size:13 final size:13
Alignment explanation
Indices: 693328--693367 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
693318 ACCGAGTCGA
*
693328 ACTGAGTCAATTC
1 ACTGAGTCAACTC
*
693341 ACTGAGTTAACTC
1 ACTGAGTCAACTC
*
693354 ACTAAGTCAACTC
1 ACTGAGTCAACTC
693367 A
1 A
693368 TTTCAGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (13 bp):
ACTGAGTCAACTC
Found at i:693453 original size:22 final size:22
Alignment explanation
Indices: 693423--693464 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
693413 GACATGATCG
*
693423 TTGATTTTGACCATAGTTGACT
1 TTGACTTTGACCATAGTTGACT
*
693445 TTGACTTTGACCATATTTGA
1 TTGACTTTGACCATAGTTGA
693465 ATTTAACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (22 bp):
TTGACTTTGACCATAGTTGACT
Found at i:694950 original size:18 final size:19
Alignment explanation
Indices: 694927--694963 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
694917 CCAATAATCC
694927 TATTCCC-TGGTAATCTTT
1 TATTCCCTTGGTAATCTTT
694945 TATTCCCTTTGGTAATCTT
1 TATTCCC-TTGGTAATCTT
694964 ACATTCCGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.16, C:0.22, G:0.11, T:0.51
Consensus pattern (19 bp):
TATTCCCTTGGTAATCTTT
Found at i:707669 original size:16 final size:17
Alignment explanation
Indices: 707650--707684 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
707640 TTATGCTTTA
707650 AAAAAATAA-AAAAAAT
1 AAAAAATAATAAAAAAT
*
707666 AAAAAATAATGAAAAAT
1 AAAAAATAATAAAAAAT
707683 AA
1 AA
707685 TGGTATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAAAATAATAAAAAAT
Found at i:710112 original size:21 final size:21
Alignment explanation
Indices: 710086--710249 Score: 139
Period size: 21 Copynumber: 7.7 Consensus size: 21
710076 GGGTTCTATT
710086 TGGTCCTTCGGGATATATATG
1 TGGTCCTTCGGGATATATATG
* *
710107 TGGTCCTTTGGAATATATATG
1 TGGTCCTTCGGGATATATATG
* * * *
710128 AGGTCCTTCGAGACATATATT
1 TGGTCCTTCGGGATATATATG
* * *
710149 TGGTCCTTTGGAACATATATG
1 TGGTCCTTCGGGATATATATG
* * * *
710170 TGGTCCTTAGGCACAATTATATA
1 TGGTCCTTCGGGA-TA-TATATG
*
710193 TGGTTCTTCGGGATATATATG
1 TGGTCCTTCGGGATATATATG
** *
710214 TGGTTTTTCAGGATATATATG
1 TGGTCCTTCGGGATATATATG
* *
710235 AGGTCATTCGGGATA
1 TGGTCCTTCGGGATA
710250 ATTTTATATG
Statistics
Matches: 113, Mismatches: 28, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
21 96 0.85
22 2 0.02
23 15 0.13
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.38
Consensus pattern (21 bp):
TGGTCCTTCGGGATATATATG
Found at i:713984 original size:35 final size:35
Alignment explanation
Indices: 713945--714016 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
713935 TAGCACAAAC
713945 TAAGAGAAAACTATACTATACGTACTAAAAATATG
1 TAAGAGAAAACTATACTATACGTACTAAAAATATG
713980 TAAGAGAAAACTATACTATACGTACTAAAAATATG
1 TAAGAGAAAACTATACTATACGTACTAAAAATATG
714015 TA
1 TA
714017 TTTTTTTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.26
Consensus pattern (35 bp):
TAAGAGAAAACTATACTATACGTACTAAAAATATG
Found at i:725875 original size:2 final size:2
Alignment explanation
Indices: 725862--725983 Score: 183
Period size: 2 Copynumber: 61.5 Consensus size: 2
725852 AAATACATAC
* * *
725862 AT AT AT AC AT AT AT AC AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
725904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
725946 AT AT AT AT AT AT A- AT AT AT AT AC 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 AT AT AT A
725984 GGGCATGATC
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
1 1 0.01
2 106 0.99
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:732392 original size:83 final size:83
Alignment explanation
Indices: 732194--732409 Score: 326
Period size: 83 Copynumber: 2.6 Consensus size: 83
732184 CTTCCGCAAC
**
732194 ACCTTGTTCCAATAGTTAGAGTAAATTTCTTGCTATATAAGAGTCCTTTCCGTTACACATAGCAT
1 ACCTTGTTCCAATAGTTAGAGTAAATTTCTTGCTATATAAGTTTCCTTTCCGTTA-ACATAGCAT
*
732259 CTTGGGCTCTTACTCCCCT
65 CTTGGGCTCTTACTCCCAT
* * * *
732278 ACCTTGTTCTAATAGTTAGAGTAAATATCTTGCTATATAAGTTTCCTTTTCGTT-ACATAGCATT
1 ACCTTGTTCCAATAGTTAGAGTAAATTTCTTGCTATATAAGTTTCCTTTCCGTTAACATAGCATC
732342 TTGGGGCTCTTACTCCCAT
66 TT-GGGCTCTTACTCCCAT
* *
732361 ACCTTGTTCCAATAGTTACAGTAAATTTCTTGTTATATAAGTTTCCTTT
1 ACCTTGTTCCAATAGTTAGAGTAAATTTCTTGCTATATAAGTTTCCTTT
732410 GTAATCAAGT
Statistics
Matches: 120, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
82 11 0.09
83 60 0.50
84 49 0.41
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (83 bp):
ACCTTGTTCCAATAGTTAGAGTAAATTTCTTGCTATATAAGTTTCCTTTCCGTTAACATAGCATC
TTGGGCTCTTACTCCCAT
Found at i:735438 original size:21 final size:21
Alignment explanation
Indices: 735324--735437 Score: 174
Period size: 21 Copynumber: 5.4 Consensus size: 21
735314 CACTTGTTTT
735324 CAATGCGAACTTCGACTATCG
1 CAATGCGAACTTCGACTATCG
735345 CAATGCGAACTTCGACTATCG
1 CAATGCGAACTTCGACTATCG
* *
735366 TAATGCAAACTTCGACTATCG
1 CAATGCGAACTTCGACTATCG
*
735387 CAATGCGAACTTGGACTATCG
1 CAATGCGAACTTCGACTATCG
* * *
735408 CAATACGAATTTGGACTATCG
1 CAATGCGAACTTCGACTATCG
735429 CAATGCGAA
1 CAATGCGAA
735438 TATGTAAATC
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 85 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
CAATGCGAACTTCGACTATCG
Found at i:735476 original size:21 final size:21
Alignment explanation
Indices: 735446--735610 Score: 99
Period size: 21 Copynumber: 7.8 Consensus size: 21
735436 AATATGTAAA
* *
735446 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
735467 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* * * *
735488 TCGCGTTGCGATTTTCCAAATTCAACT
1 TCGCATTGCGA---T---AGTCCAAGT
* *
735515 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
735536 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* ** *
735557 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATAGTCCAAGT
*
735578 TCG--TTGCGATAGTCCAAAT
1 TCGCATTGCGATAGTCCAAGT
735597 TCG--TTGCGATAGTC
1 TCGCATTGCGATAGTC
735611 TAAAATCGCA
Statistics
Matches: 117, Mismatches: 17, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
19 28 0.24
20 13 0.11
21 57 0.49
22 1 0.01
24 1 0.01
25 1 0.01
27 6 0.05
28 10 0.09
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:735584 original size:19 final size:19
Alignment explanation
Indices: 735541--735610 Score: 95
Period size: 19 Copynumber: 3.6 Consensus size: 19
735531 CATATTCGCA
*
735541 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAATT--CG
**
735562 TTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAATTCG
735581 TTGCGATAGTCCAAATTCG
1 TTGCGATAGTCCAAATTCG
735600 TTGCGATAGTC
1 TTGCGATAGTC
735611 TAAAATCGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 30 0.68
21 14 0.32
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (19 bp):
TTGCGATAGTCCAAATTCG
Found at i:736325 original size:21 final size:21
Alignment explanation
Indices: 736280--736433 Score: 149
Period size: 21 Copynumber: 7.4 Consensus size: 21
736270 ATTTTGGATT
*
736280 ATCGCAACGAACTTGGACT--
1 ATCGCAACGAACTTGGAATAA
* *
736299 ATCGCAACAAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
736320 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
736341 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
736362 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
736383 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
736404 ATTGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
736425 ATCGCAACG
1 ATCGCAACG
736434 CGAACTTCGA
Statistics
Matches: 111, Mismatches: 14, Indels: 18
0.78 0.10 0.13
Matches are distributed among these distances:
19 36 0.32
21 56 0.50
23 19 0.17
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:736341 original size:42 final size:42
Alignment explanation
Indices: 736280--736473 Score: 229
Period size: 42 Copynumber: 4.7 Consensus size: 42
736270 ATTTTGGATT
*
736280 ATCGCAA--CGAACTTGGACTATCGCAACAAATTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
* *
736320 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
736362 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
* * * * * *
736404 ATTGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACT--
1 ATCGCAACGCGAACTTGGACT--ATCGCAA--CGAATTTGGAATAA
736446 ATCGCAACGCGAACTTGGACTATCGCAA
1 ATCGCAACGCGAACTTGGACTATCGCAA
736474 TGCGAATATG
Statistics
Matches: 132, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
40 17 0.13
42 96 0.73
44 19 0.14
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
Found at i:736449 original size:21 final size:21
Alignment explanation
Indices: 736425--736479 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
736415 TTTGGAATAA
736425 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
736446 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
736467 ATCGCAATGCGAA
1 ATCGCAACGCGAA
736480 TATGTAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Done.