Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007725.1 Hibiscus syriacus cultivar Beakdansim tig00109972_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: 3026330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:1304726 original size:20 final size:20
Alignment explanation
Indices: 1304684--1304733 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1304674 TTATTTATTA
*
1304684 TTTATT-TTATATATTATAT
1 TTTATTATTATATAATATAT
1304703 TTTATTATTACTATAATA-AT
1 TTTATTATTA-TATAATATAT
1304723 TTTATTATTAT
1 TTTATTATTAT
1304734 TATTATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 7 0.25
20 15 0.54
21 6 0.21
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATTATTATATAATATAT
Found at i:1304736 original size:29 final size:28
Alignment explanation
Indices: 1304700--1304761 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
1304690 TTATATATTA
1304700 TATTTTATTATTACTATAAT-AATTTTAT
1 TATTTTATTATTACTA-AATAAATTTTAT
*
1304728 TATTATTATTATTATTAAATAAATTTTAT
1 TATT-TTATTATTACTAAATAAATTTTAT
1304757 TATTT
1 TATTT
1304762 CAGATCCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (28 bp):
TATTTTATTATTACTAAATAAATTTTAT
Found at i:1304760 original size:3 final size:3
Alignment explanation
Indices: 1304673--1304744 Score: 62
Period size: 3 Copynumber: 24.3 Consensus size: 3
1304663 TCCATTACTC
* *
1304673 ATT ATTT ATT ATTT ATT -TT ATAT ATT A-T ATT -TT ATT ATT ACT ATA
1 ATT A-TT ATT A-TT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
*
1304718 ATA ATT -TT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1304745 AATAAATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
2 8 0.14
3 41 0.71
4 9 0.16
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1306179 original size:27 final size:27
Alignment explanation
Indices: 1306113--1306165 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1306103 TTTATTACTA
* *
1306113 ATTATTTTTTATTATAGTTTTAATTTC
1 ATTAATTTTTGTTATAGTTTTAATTTC
*
1306140 ATTAATTTTTGTTATTGTTTTAATTT
1 ATTAATTTTTGTTATAGTTTTAATTT
1306166 TATATGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.68
Consensus pattern (27 bp):
ATTAATTTTTGTTATAGTTTTAATTTC
Found at i:1306227 original size:2 final size:2
Alignment explanation
Indices: 1306211--1306253 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1306201 TTATTTAGTC
*
1306211 AT AT AA AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1306252 AT
1 AT
1306254 GTAATAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1306474 original size:20 final size:22
Alignment explanation
Indices: 1306446--1306495 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
1306436 ATCTTATATA
1306446 TATATATATATATTT-ATAAAAT
1 TATA-ATATATATTTCATAAAAT
* *
1306468 T-TAATATATTTTTCTTAAAAT
1 TATAATATATATTTCATAAAAT
1306489 TATAATA
1 TATAATA
1306496 ATAAATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 9 0.38
21 9 0.38
22 6 0.25
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TATAATATATATTTCATAAAAT
Found at i:1307511 original size:5 final size:5
Alignment explanation
Indices: 1307501--1307529 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1307491 AAGCTCTAGC
1307501 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1307530 TCCTGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:1308707 original size:26 final size:25
Alignment explanation
Indices: 1308646--1308707 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
1308636 TACATTTGCA
**
1308646 TTTGCATTTTGTATTTTTTTTTCATT
1 TTTGCA-TTTGTATTTAATTTTCATT
* *
1308672 TTTACGTTTGTATTTAAATTTTCATT
1 TTTGCATTTGTATTT-AATTTTCATT
1308698 TTTGCATTTG
1 TTTGCATTTG
1308708 CATCTTTGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
25 9 0.31
26 20 0.69
ACGTcount: A:0.16, C:0.08, G:0.10, T:0.66
Consensus pattern (25 bp):
TTTGCATTTGTATTTAATTTTCATT
Found at i:1310198 original size:15 final size:15
Alignment explanation
Indices: 1310178--1310218 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
1310168 ATACCAGTGA
*
1310178 AAAGAGTCTGGATAC
1 AAAGAGTATGGATAC
1310193 AAAGAGTATGGATAC
1 AAAGAGTATGGATAC
1310208 AAAGAGTATGG
1 AAAGAGTATGG
1310219 TGAATATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.29, T:0.20
Consensus pattern (15 bp):
AAAGAGTATGGATAC
Found at i:1314402 original size:75 final size:75
Alignment explanation
Indices: 1314277--1314513 Score: 305
Period size: 75 Copynumber: 3.2 Consensus size: 75
1314267 GCAAATGTTA
* * * * *
1314277 GGGCATGCTGAAAGTCCATTTCAATTAGAATCAGGAATGTTGATGTATTTTGAACGTTCATATCA
1 GGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGACGCATTTTGAACGTTCGTATCA
1314342 GTAAATGCTG
66 GTAAATGCTG
* * * * *
1314352 GGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAAATATGGACGCATTTTGAACCTTTGTATCA
1 GGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGACGCATTTTGAACGTTCGTATCA
* *
1314417 ATAAATGTTG
66 GTAAATGCTG
*
1314427 GGGCATGCTGAAAGCCCATTTCAATCAGAAAT-AGGAATGTTGACGCATTTTGAATGTTCGTATC
1 GGGCATGCTGAAAGCCCATTTCAATCAG-AATCAGGAATGTTGACGCATTTTGAACGTTCGTATC
* * *
1314491 AGCAATTACTG
65 AGTAAATGCTG
*
1314502 GAGCATGCTGAA
1 GGGCATGCTGAA
1314514 GGCCAACGTC
Statistics
Matches: 137, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
75 134 0.98
76 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (75 bp):
GGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGACGCATTTTGAACGTTCGTATCA
GTAAATGCTG
Found at i:1316474 original size:113 final size:113
Alignment explanation
Indices: 1316274--1316608 Score: 537
Period size: 113 Copynumber: 3.0 Consensus size: 113
1316264 CAAAGATTCA
* * * *
1316274 AATTCATCATTCAATGGATCAACATTTCCGGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
1316338 AGTAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCG
66 AGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCG
* *
1316386 AATTCATCACTCGATTGATCAACTTTTCCAGAGAGAGTTCATAAAGAGAAGAACTCATCTGAAGA
1 AATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
1316451 AGGAAGAATAAGTTCATAGTGAGAAGAACTTGTTCAACTTTTTGCTCG
66 AGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCG
*
1316499 AATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTTATCTGAAGA
1 AATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
1316564 AGGAAGAAAAAGCTCATAATGAGAAGAACTTATTCAACCTTTTGC
66 AGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
1316609 ATGATTCTAT
Statistics
Matches: 205, Mismatches: 17, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
112 27 0.13
113 178 0.87
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (113 bp):
AATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCG
Found at i:1317016 original size:26 final size:26
Alignment explanation
Indices: 1316981--1317039 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
1316971 TTATTTATTA
*
1316981 TATTTTTATTATTACTATAAT-AATTT
1 TATTATTATTATTACTA-AATAAATTT
*
1317007 TATTATTATTATTATTAAATAAATTT
1 TATTATTATTATTACTAAATAAATTT
1317033 TATTATT
1 TATTATT
1317040 TCAGATCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TATTATTATTATTACTAAATAAATTT
Found at i:1317927 original size:15 final size:15
Alignment explanation
Indices: 1317907--1317935 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1317897 CTCAGTTAGA
1317907 GAGAGAATGAGAAAG
1 GAGAGAATGAGAAAG
1317922 GAGAGAATGAGAAA
1 GAGAGAATGAGAAA
1317936 TAATGGCCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (15 bp):
GAGAGAATGAGAAAG
Found at i:1318451 original size:27 final size:25
Alignment explanation
Indices: 1318412--1318462 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
1318402 ATTACTAATT
1318412 ATTTTTTTATTATAGTTTTAATTTC
1 ATTTTTTTATTATAGTTTTAATTTC
*
1318437 ATTTATTTTAGTTATTGTTTTAATTT
1 ATTT-TTTTA-TTATAGTTTTAATTT
1318463 TATATGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
26 5 0.22
27 14 0.61
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.69
Consensus pattern (25 bp):
ATTTTTTTATTATAGTTTTAATTTC
Found at i:1318521 original size:2 final size:2
Alignment explanation
Indices: 1318508--1318545 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1318498 TTATTTAGTC
*
1318508 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1318546 TTGTAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1318768 original size:20 final size:22
Alignment explanation
Indices: 1318740--1318789 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
1318730 ATCTTATATA
1318740 TATATATATATATTT-ATAAAAT
1 TATA-ATATATATTTCATAAAAT
* *
1318762 T-TAATATATTTTTCTTAAAAT
1 TATAATATATATTTCATAAAAT
1318783 TATAATA
1 TATAATA
1318790 ATAAATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 9 0.38
21 9 0.38
22 6 0.25
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TATAATATATATTTCATAAAAT
Found at i:1320671 original size:29 final size:27
Alignment explanation
Indices: 1320638--1320691 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
1320628 TCATATATAC
*
1320638 AAATAATTATATTTATTTAATATAAAAAT
1 AAATAAATATATTTATTT--TATAAAAAT
1320667 AAATAAATATATTTATTTTATAAAA
1 AAATAAATATATTTATTTTATAAAA
1320692 TGTGTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.29
29 17 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AAATAAATATATTTATTTTATAAAAAT
Found at i:1320679 original size:25 final size:25
Alignment explanation
Indices: 1320632--1320681 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1320622 CGATGATCAT
* * * *
1320632 ATATACAAATAATTATATTTATTTA
1 ATATAAAAATAAATAAATATATTTA
1320657 ATATAAAAATAAATAAATATATTTA
1 ATATAAAAATAAATAAATATATTTA
1320682 TTTTATAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATAAAAATAAATAAATATATTTA
Found at i:1320734 original size:31 final size:32
Alignment explanation
Indices: 1320699--1320769 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 32
1320689 AAATGTGTAT
1320699 AATTGAATCTAAATTAAAT-TTTTATAAATAC
1 AATTGAATCTAAATTAAATATTTTATAAATAC
* * **
1320730 AATTGAAT-TGAATTCAATATTTTATTTATAC
1 AATTGAATCTAAATTAAATATTTTATAAATAC
*
1320761 AATTAAATC
1 AATTGAATC
1320770 GGAATCAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 8 0.24
31 25 0.76
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (32 bp):
AATTGAATCTAAATTAAATATTTTATAAATAC
Found at i:1322002 original size:60 final size:59
Alignment explanation
Indices: 1321870--1322053 Score: 160
Period size: 60 Copynumber: 3.1 Consensus size: 59
1321860 GCGTTGTATG
* * *
1321870 TCCCCAATATATGACCCTCATT-TCAAATTAGTCCAT-AAAC-TTTGAAACATTTCAATTTCA
1 TCCCCAATCTATGA-CTTCATTCT-AAATTAGTCC-TCAAACTTTTG-AACATTTCATTTTCA
* ** * *
1321930 TTCTTAAACTATGACTATCATTCTAAAGTAGTCCTCAAACTTTTGAACATTTCATTTTCA
1 TCCCCAATCTATGACT-TCATTCTAAATTAGTCCTCAAACTTTTGAACATTTCATTTTCA
* * * *
1321990 TCCCCAATCTATGATCTTCATCCTAAATTGGTCCCCAAACTTTTTGAATATTTCAATTTT-A
1 TCCCCAATCTATGA-CTTCATTCTAAATTAGTCCTCAAAC-TTTTGAACATTTC-ATTTTCA
1322051 TCC
1 TCC
1322054 TAAAATATTC
Statistics
Matches: 100, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
59 2 0.02
60 70 0.70
61 23 0.23
62 5 0.05
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (59 bp):
TCCCCAATCTATGACTTCATTCTAAATTAGTCCTCAAACTTTTGAACATTTCATTTTCA
Found at i:1322900 original size:16 final size:17
Alignment explanation
Indices: 1322879--1322937 Score: 77
Period size: 16 Copynumber: 3.6 Consensus size: 17
1322869 TTATAATTCC
1322879 TAAATGATAATTGAA-T
1 TAAATGATAATTGAACT
1322895 TAAATGATAATTGAACT
1 TAAATGATAATTGAACT
* *
1322912 TGAATGA-AATTGAACA
1 TAAATGATAATTGAACT
*
1322928 CAAATGATAA
1 TAAATGATAA
1322938 GATTAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 28 0.76
17 9 0.24
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGATAATTGAACT
Found at i:1324523 original size:17 final size:15
Alignment explanation
Indices: 1324490--1324530 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1324480 ATCTTAGTCA
1324490 TTTTA-AATAAATAT
1 TTTTATAATAAATAT
1324504 TTTTATAATAAA-AT
1 TTTTATAATAAATAT
1324518 TATTT-TAATAAAT
1 T-TTTATAATAAAT
1324531 GTAAATACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTTATAATAAATAT
Found at i:1324526 original size:14 final size:15
Alignment explanation
Indices: 1324489--1324530 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
1324479 TATCTTAGTC
1324489 ATTTTAAATAAATATT
1 ATTTT-AATAAATATT
1324505 -TTTATAATAAA-ATT
1 ATTT-TAATAAATATT
1324519 ATTTTAATAAAT
1 ATTTTAATAAAT
1324531 GTAAATACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 10 0.43
15 12 0.52
16 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTAATAAATATT
Found at i:1340799 original size:276 final size:269
Alignment explanation
Indices: 1340265--1340810 Score: 1029
Period size: 276 Copynumber: 2.0 Consensus size: 269
1340255 CTGTCACAAT
1340265 CTGATAATTTAATTTTTTTTAAATTATATATTTAAAAAACATAAAAAATTGAATAACCTCAAACT
1 CTGATAATTTAATTTTTTTTAAATTATATATTTAAAAAACATAAAAAATTGAATAACCTCAAACT
1340330 TTAAAAATCATCATTCAACTCTTAAACCTACGTTGGTCGTTGCCCTTTGCCGTTGAAGAAACTCC
66 TTAAAAATCATCATTCAACTCTTAAACCTACGTTGGTCGTTGCCCTTTGCCGTTGAAGAAACTCC
1340395 ACCAACCTCACCTCCCCCGCAACCAAATCCCTATGAAATTATGACCAATCGACGGCGAATCGACG
131 ACCAACCTCACCTCCCCCGCAACCAAATCCCTATGAAATTATGACCAATCGACGGCGAATCGACG
1340460 TTTTATATCCGTAAAACTTAGGATGAAAATTGTGATCCCAAGCGATTCTAACGACCAATCGACGA
196 TTTTATATCCGTAAAACTTAGGATGAAAATTGTGATCCCAAGCGATTCTAACGACCAATCGACGA
1340525 CAGCTATAG
261 CAGCTATAG
1340534 CTGATAATTTTAATTTTTTTTAAATTATATATTTAAAAAACATAAAAAAATTGAATAACCTCAAA
1 CTGATAA-TTTAATTTTTTTTAAATTATATATTTAAAAAACAT-AAAAAATTGAATAACCTC-AA
1340599 ACTTTAAAAATCATCATTTCAACTCTTAAACCTACGTTGGTCGTTGCCCTTTGCCGTTGAAGAAA
63 ACTTTAAAAATCATCA-TTCAACTCTTAAACCTACGTTGGTCGTTGCCCTTTGCCGTTGAAGAAA
1340664 CTCCACCCAACCTCACCTCCCCCGACAACCAAATCCCTATGAAATTATGACCAATCGACGGCGAA
127 CTCCA-CCAACCTCACCTCCCCCG-CAACCAAATCCCTATGAAATTATGACCAATCGACGGCGAA
1340729 TCGACGTTTTATATCCCGTAAAACTTAGGATGAAAATTGTGATCCCAAGCGATTCTAACGACCAA
190 TCGACGTTTTATAT-CCGTAAAACTTAGGATGAAAATTGTGATCCCAAGCGATTCTAACGACCAA
1340794 TCGACGACAGCTATAG
254 TCGACGACAGCTATAG
1340810 C
1 C
1340811 AGCGTATGAC
Statistics
Matches: 270, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
269 7 0.03
270 35 0.13
271 18 0.07
272 18 0.07
273 53 0.20
274 18 0.07
275 54 0.20
276 67 0.25
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.29
Consensus pattern (269 bp):
CTGATAATTTAATTTTTTTTAAATTATATATTTAAAAAACATAAAAAATTGAATAACCTCAAACT
TTAAAAATCATCATTCAACTCTTAAACCTACGTTGGTCGTTGCCCTTTGCCGTTGAAGAAACTCC
ACCAACCTCACCTCCCCCGCAACCAAATCCCTATGAAATTATGACCAATCGACGGCGAATCGACG
TTTTATATCCGTAAAACTTAGGATGAAAATTGTGATCCCAAGCGATTCTAACGACCAATCGACGA
CAGCTATAG
Found at i:1343904 original size:6 final size:6
Alignment explanation
Indices: 1343893--1343966 Score: 148
Period size: 6 Copynumber: 12.3 Consensus size: 6
1343883 GACACGTATT
1343893 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1343941 ACCACG ACCACG ACCACG ACCACG AC
1 ACCACG ACCACG ACCACG ACCACG AC
1343967 GGACGGCGGC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1351180 original size:16 final size:16
Alignment explanation
Indices: 1351138--1351169 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1351128 CAATATACGA
*
1351138 ATAAAAATATATTTAT
1 ATAAATATATATTTAT
1351154 ATAAATATATATTTAT
1 ATAAATATATATTTAT
1351170 TTAGATGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAATATATATTTAT
Found at i:1351246 original size:14 final size:16
Alignment explanation
Indices: 1351210--1351246 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1351200 TATTAATGTA
1351210 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
1351227 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
1351242 T-AATA
1 TGAATA
1351247 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:1351919 original size:128 final size:126
Alignment explanation
Indices: 1351710--1351967 Score: 408
Period size: 128 Copynumber: 2.0 Consensus size: 126
1351700 AATTTTCTTC
* *
1351710 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
1351775 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT--CATATAAA
* * *
1351838 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* *
1351903 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTATGACCAAATTGATTATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATCATATAAA
1351964 TAAT
1 TAAT
1351968 AAAGACTGAA
Statistics
Matches: 120, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
126 11 0.09
128 109 0.91
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.37
Consensus pattern (126 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATCATATAAA
Found at i:1352393 original size:35 final size:35
Alignment explanation
Indices: 1352343--1352418 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
1352333 AATTGAATTT
* *
1352343 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
1352378 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
1352413 AATTGA
1 AATTGA
1352419 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:1353908 original size:6 final size:6
Alignment explanation
Indices: 1353891--1353920 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1353881 ATCACCACTC
*
1353891 AATAAA AGTAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA
1353921 GGGATAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:1357694 original size:2 final size:2
Alignment explanation
Indices: 1357687--1357711 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1357677 TTTGATTTAA
1357687 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 A
1357712 ATACTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1358573 original size:60 final size:60
Alignment explanation
Indices: 1358467--1358579 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
1358457 CGCCTTCTCA
* * * * * *
1358467 GGGTTTTGTCCGAGCTGGCGCCACAGTGGAAAAGTGCGGATTATGAAGTGCACCTTCGTG
1 GGGTTCTGTCCGAGCTGGAGCCACAGTGCAAAAGTGCAGATCATGAAGCGCACCTTCGTG
* *
1358527 GGGTTCTGTCCGAGCTGGAGGCAC-GTAGCAAAGGTGCAGATCATGAAGCGCAC
1 GGGTTCTGTCCGAGCTGGAGCCACAGT-GCAAAAGTGCAGATCATGAAGCGCAC
1358580 ATTTGCTGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
59 2 0.05
60 42 0.95
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.21
Consensus pattern (60 bp):
GGGTTCTGTCCGAGCTGGAGCCACAGTGCAAAAGTGCAGATCATGAAGCGCACCTTCGTG
Found at i:1362145 original size:20 final size:20
Alignment explanation
Indices: 1362115--1362176 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
1362105 TACTCAAGTG
*
1362115 AAAATTAAATAAAAACATTA
1 AAAACTAAATAAAAACATTA
* *
1362135 CAAACTAAATATAAAA-ATAA
1 AAAACTAAATA-AAAACATTA
* *
1362155 AAAATTAAATAGAAACATTA
1 AAAACTAAATAAAAACATTA
1362175 AA
1 AA
1362177 TACAAACGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.09
20 26 0.79
21 4 0.12
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAACTAAATAAAAACATTA
Found at i:1362198 original size:53 final size:56
Alignment explanation
Indices: 1362114--1362238 Score: 136
Period size: 53 Copynumber: 2.3 Consensus size: 56
1362104 CTACTCAAGT
1362114 GAAAATTAAATAAAAACATTACAAACTAAAT-A-TAAA-AATAAAAA-ATTAAATA
1 GAAAATTAAATAAAAACATTACAAACTAAATAATTAAATAATAAAAACATTAAATA
* * * *
1362166 GAAACATTAAATACAAACGTTAC-AATTCAAATAATTAAATAATAAAAACATTAAGAAA
1 GAAA-ATTAAATAAAAACATTACAAACT-AAATAATTAAATAATAAAAACATTAA-ATA
*
1362224 CAAAA-TAAATAAAAA
1 GAAAATTAAATAAAAA
1362239 GTCCATAAGT
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
52 7 0.12
53 20 0.33
54 1 0.02
55 4 0.07
56 17 0.28
57 6 0.10
58 5 0.08
ACGTcount: A:0.66, C:0.08, G:0.03, T:0.22
Consensus pattern (56 bp):
GAAAATTAAATAAAAACATTACAAACTAAATAATTAAATAATAAAAACATTAAATA
Found at i:1362317 original size:45 final size:45
Alignment explanation
Indices: 1362206--1362375 Score: 261
Period size: 45 Copynumber: 3.7 Consensus size: 45
1362196 ATAATTAAAT
*
1362206 AATAAAAACATTAAGAAACAAAATAAAT-AAAAAGTCCATAAGTAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAAGTCCATAA-T-TA
* *
1362252 TAATAAAAACATTAAGAAATAAAATAAATAAAAAATTCCATAATTA
1 -AATAAAAACATTAAGAAACAAAATAAATAAAAAAGTCCATAATTA
* *
1362298 AATAAAAACATTAAGAAATAAAATAAATAAAAAAGTCAATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAAGTCCATAATTA
1362343 AATAAAAACATTAAGAAACAAAATAAATAAAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAA
1362376 CAAGTTTATC
Statistics
Matches: 116, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
45 75 0.65
46 1 0.01
47 28 0.24
48 12 0.10
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.21
Consensus pattern (45 bp):
AATAAAAACATTAAGAAACAAAATAAATAAAAAAGTCCATAATTA
Found at i:1362801 original size:21 final size:21
Alignment explanation
Indices: 1362777--1362829 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1362767 CCTTACGGTG
1362777 GCATCTGAAATGGTTGTGGTT
1 GCATCTGAAATGGTTGTGGTT
1362798 GCATCTGAAATGGTTGTGGTT
1 GCATCTGAAATGGTTGTGGTT
*
1362819 GCATCAGAAAT
1 GCATCTGAAAT
1362830 AACCGCGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.11, G:0.30, T:0.34
Consensus pattern (21 bp):
GCATCTGAAATGGTTGTGGTT
Found at i:1363405 original size:2 final size:2
Alignment explanation
Indices: 1363398--1363433 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1363388 ATTGAAACTA
1363398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1363434 TCTTATCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1371954 original size:4 final size:4
Alignment explanation
Indices: 1371945--1371987 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
1371935 ATCATGTCAT
* * *
1371945 CATA CATA CATG CATG CATG CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
1371988 TTGTTTATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:1379992 original size:9 final size:9
Alignment explanation
Indices: 1379978--1380052 Score: 75
Period size: 9 Copynumber: 8.7 Consensus size: 9
1379968 ATCAATATCT
*
1379978 TCATCAGCA
1 TCATCACCA
*
1379987 TCATCATCA
1 TCATCACCA
1379996 TCATCA-C-
1 TCATCACCA
1380003 -CATCACCA
1 TCATCACCA
*
1380011 TCATCAACA
1 TCATCACCA
1380020 TCATCACCA
1 TCATCACCA
*
1380029 TCACCACCA
1 TCATCACCA
* *
1380038 CCATTACCA
1 TCATCACCA
1380047 TCATCA
1 TCATCA
1380053 TTGTCATCTA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
6 5 0.09
7 1 0.02
8 1 0.02
9 47 0.87
ACGTcount: A:0.35, C:0.41, G:0.01, T:0.23
Consensus pattern (9 bp):
TCATCACCA
Found at i:1380032 original size:6 final size:6
Alignment explanation
Indices: 1379979--1380049 Score: 70
Period size: 6 Copynumber: 11.8 Consensus size: 6
1379969 TCAATATCTT
* * * * * *
1379979 CATCAG CATCAT CATCAT CATCAC CATCAC CATCAT CAACAT CATCAC
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC
* *
1380027 CATCAC CACCAC CATTAC CATCA
1 CATCAC CATCAC CATCAC CATCA
1380050 TCATTGTCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.35, C:0.42, G:0.01, T:0.21
Consensus pattern (6 bp):
CATCAC
Found at i:1380032 original size:24 final size:24
Alignment explanation
Indices: 1379979--1380034 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
1379969 TCAATATCTT
* *
1379979 CATCAGCATCATCATCATCATCAC
1 CATCACCATCATCAACATCATCAC
1380003 CATCACCATCATCAACATCATCAC
1 CATCACCATCATCAACATCATCAC
1380027 CATCACCA
1 CATCACCA
1380035 CCACCATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.36, C:0.41, G:0.02, T:0.21
Consensus pattern (24 bp):
CATCACCATCATCAACATCATCAC
Found at i:1380051 original size:3 final size:3
Alignment explanation
Indices: 1379978--1380031 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
1379968 ATCAATATCT
* * * *
1379978 TCA TCA GCA TCA TCA TCA TCA TCA CCA TCA CCA TCA TCA ACA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
*
1380026 CCA TCA
1 TCA TCA
1380032 CCACCACCAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.35, C:0.39, G:0.02, T:0.24
Consensus pattern (3 bp):
TCA
Found at i:1382020 original size:20 final size:20
Alignment explanation
Indices: 1381995--1382033 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1381985 TAAATAAATA
*
1381995 AATAAATTATTCAACATAAT
1 AATAAATTATTCAAAATAAT
1382015 AATAAATTATTCAAAATAA
1 AATAAATTATTCAAAATAA
1382034 ATATATGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAAATTATTCAAAATAAT
Found at i:1382032 original size:17 final size:18
Alignment explanation
Indices: 1381988--1382089 Score: 72
Period size: 17 Copynumber: 5.7 Consensus size: 18
1381978 CTTCAAATAA
1381988 ATAAATAAATAAATTATTC
1 ATAAAT-AATAAATTATTC
*
1382007 AACATAATAATAAATTATTC
1 -ATA-AATAATAAATTATTC
* *
1382027 A-AAATAA-ATA-TATGC
1 ATAAATAATAAATTATTC
**
1382042 ATAAATAA-AAATT-TGAA
1 ATAAATAATAAATTAT-TC
1382059 ATAAATAATAAATTATTC
1 ATAAATAATAAATTATTC
1382077 A-AAATATATAAAT
1 ATAAATA-ATAAAT
1382090 AAATAAAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
15 5 0.07
16 11 0.16
17 19 0.28
18 13 0.19
19 2 0.03
20 14 0.21
21 3 0.04
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (18 bp):
ATAAATAATAAATTATTC
Found at i:1382096 original size:50 final size:50
Alignment explanation
Indices: 1381982--1382096 Score: 144
Period size: 50 Copynumber: 2.3 Consensus size: 50
1381972 ATATCCCTTC
*
1381982 AAATAAATAAATAAATAAATTATTCAACATAATAATAAATTATTCAAAAT
1 AAATAAATAAATAAATAAAATATTCAACATAATAATAAATTATTCAAAAT
* ** *
1382032 AAATATATGCATAAATAAAA-ATTTGAA-ATAAATAATAAATTATTCAAAAT
1 AAATAAATAAATAAATAAAATA-TTCAACAT-AATAATAAATTATTCAAAAT
*
1382082 ATATAAATAAATAAA
1 AAATAAATAAATAAA
1382097 AATTACCTCC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 3 0.06
50 51 0.94
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (50 bp):
AAATAAATAAATAAATAAAATATTCAACATAATAATAAATTATTCAAAAT
Found at i:1385651 original size:9 final size:9
Alignment explanation
Indices: 1385637--1385662 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1385627 ACCTTCATTT
1385637 AAATAAGAA
1 AAATAAGAA
1385646 AAATAAGAA
1 AAATAAGAA
1385655 AAATAAGA
1 AAATAAGA
1385663 CTTACTTCCA
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:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (9 bp):
AAATAAGAA
Found at i:1399015 original size:40 final size:40
Alignment explanation
Indices: 1398960--1399039 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1398950 ACATAATATA
1398960 GTGAGCCTGCAAGAGATGGAACTGGAGATGGTCCCCATAC
1 GTGAGCCTGCAAGAGATGGAACTGGAGATGGTCCCCATAC
1399000 GTGAGCCTGCAAGAGATGGAACTGGAGATGGTCCCCATAC
1 GTGAGCCTGCAAGAGATGGAACTGGAGATGGTCCCCATAC
1399040 ATCAGTATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.23, G:0.33, T:0.17
Consensus pattern (40 bp):
GTGAGCCTGCAAGAGATGGAACTGGAGATGGTCCCCATAC
Found at i:1400576 original size:16 final size:17
Alignment explanation
Indices: 1400545--1400577 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1400535 CGTATCACTG
1400545 ACAAAATTTCACTATTC
1 ACAAAATTTCACTATTC
1400562 ACAAAATTT-ACTATTC
1 ACAAAATTTCACTATTC
1400578 GAGTGAACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.36
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:1410323 original size:2 final size:2
Alignment explanation
Indices: 1410316--1410354 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1410306 GCCAATTTAT
1410316 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T- 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
1410355 TTTATTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1410371 original size:21 final size:21
Alignment explanation
Indices: 1410345--1410386 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1410335 ATATATTATA
1410345 TATTATATATTTT-ATTATTTT
1 TATTATA-ATTTTAATTATTTT
1410366 TATTATAATTTTCAATTATTT
1 TATTATAATTTT-AATTATTT
1410387 CACTCTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 7 0.37
22 7 0.37
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTATAATTTTAATTATTTT
Found at i:1410458 original size:39 final size:39
Alignment explanation
Indices: 1410379--1410483 Score: 121
Period size: 39 Copynumber: 2.7 Consensus size: 39
1410369 TATAATTTTC
*
1410379 AATTATTTCAC-TCTAACATTCTAAATTTCTGATTTCTTA
1 AATTATTTCACAT-TAACATTCTAAATTTCTAATTTCTTA
1410418 AATT-TTGTCACCA-TAACATTCTAAA-TTCTTAATATT-TTA
1 AATTATT-TCA-CATTAACATTCTAAATTTC-TAAT-TTCTTA
1410457 AATTATTTCACATTAACATTCTAAATT
1 AATTATTTCACATTAACATTCTAAATT
1410484 ACTTTTTAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 15
0.78 0.01 0.21
Matches are distributed among these distances:
38 7 0.12
39 44 0.77
40 6 0.11
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.47
Consensus pattern (39 bp):
AATTATTTCACATTAACATTCTAAATTTCTAATTTCTTA
Found at i:1412497 original size:54 final size:52
Alignment explanation
Indices: 1412424--1412589 Score: 207
Period size: 54 Copynumber: 3.2 Consensus size: 52
1412414 ATAAGGTTAT
** *
1412424 TTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAA
1 TTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAAT-ATGGA-TTGAA
* * *
1412478 TTATTTTAAAATAAATTATTTTAAAATAAATTATTATAAAATATGGATTGAT
1 TTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGATTGAA
* *
1412530 TTATTTTAAAATAATTTATTTT-AAATAATTTA-T-T--AGTATGGATTGAT
1 TTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGATTGAA
1412577 TTATTTTAAAATA
1 TTATTTTAAAATA
1412590 TGGATTGATT
Statistics
Matches: 103, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
47 25 0.24
49 1 0.01
50 1 0.01
51 9 0.09
52 24 0.23
53 3 0.03
54 40 0.39
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (52 bp):
TTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGATTGAA
Found at i:1412534 original size:22 final size:22
Alignment explanation
Indices: 1412508--1412608 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
1412498 TTAAAATAAA
*
1412508 TTATTATAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
** * *
1412530 TTATTTTAAAATAATTTATTTTAA
1 TTATTTTAAAAT-ATGGA-TTGAT
* * * *
1412554 ATAATTTATTAGTATGGATTGAT
1 TTATTTTA-AAATATGGATTGAT
1412577 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
1412599 TTATTTTAAA
1 TTATTTTAAA
1412609 TAATTTATTA
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
22 33 0.56
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:1412557 original size:14 final size:15
Alignment explanation
Indices: 1412422--1412563 Score: 136
Period size: 15 Copynumber: 9.5 Consensus size: 15
1412412 TAATAAGGTT
1412422 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1412437 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1412452 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1412467 ATTTA-TTT----TA
1 ATTTATTTTAAAATA
1412477 A-TTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1412491 AATTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
1412506 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
1412525 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
1412543 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
1412557 ATTTATT
1 ATTTATT
1412564 AGTATGGATT
Statistics
Matches: 109, Mismatches: 5, Indels: 27
0.77 0.04 0.19
Matches are distributed among these distances:
9 3 0.03
10 6 0.06
14 17 0.16
15 63 0.58
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1412581 original size:32 final size:32
Alignment explanation
Indices: 1412543--1412726 Score: 192
Period size: 32 Copynumber: 6.4 Consensus size: 32
1412533 TTTTAAAATA
1412543 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1412575 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1412597 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1412629 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
1412651 ATTTATTTTAAATAATTTATTAGTATAGACTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
1412683 ATTTATTTTAAATAATTTATTTGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1412715 ATTTATTTTAAA
1 ATTTATTTTAAA
1412727 ATATGGATTG
Statistics
Matches: 128, Mismatches: 4, Indels: 40
0.74 0.02 0.23
Matches are distributed among these distances:
22 28 0.22
23 8 0.06
25 2 0.02
26 6 0.05
28 6 0.05
29 2 0.02
31 8 0.06
32 68 0.53
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:1412608 original size:54 final size:54
Alignment explanation
Indices: 1412543--1412838 Score: 377
Period size: 54 Copynumber: 5.4 Consensus size: 54
1412533 TTTTAAAATA
1412543 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1412597 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * *
1412651 ATTTATTTTAAATAATTTATTAGTATAGACTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * ***
1412701 ATTT-GTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTTTATGGATTG
1 ATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
1412763 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1412817 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
1412839 TTGTAGTTGT
Statistics
Matches: 206, Mismatches: 22, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
49 3 0.01
50 14 0.07
52 2 0.01
53 5 0.02
54 137 0.67
55 3 0.01
56 4 0.02
57 2 0.01
58 15 0.07
59 2 0.01
60 2 0.01
62 14 0.07
63 3 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:1412645 original size:22 final size:22
Alignment explanation
Indices: 1412620--1412662 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1412610 AATTTATTAG
1412620 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1412642 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1412663 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1412670 original size:14 final size:14
Alignment explanation
Indices: 1412651--1412704 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1412641 ATATGGATTG
1412651 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1412665 ATTTATTAGTATAGACTG
1 ATTTATT--T-TA-AATA
1412683 ATTTATTTTAAATA
1 ATTTATTTTAAATA
1412697 ATTTATTT
1 ATTTATTT
1412705 GTATAGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1412811 original size:22 final size:22
Alignment explanation
Indices: 1412786--1412828 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1412776 AATTTATTAG
1412786 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1412808 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1412829 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1412888 original size:31 final size:31
Alignment explanation
Indices: 1412853--1412911 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1412843 AGTTGTATAG
* *
1412853 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
1412884 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
1412912 CTTTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:1420140 original size:29 final size:29
Alignment explanation
Indices: 1420106--1420161 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
1420096 CCTAAATTAA
1420106 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1420135 TTTGATGTCATTGCTTACATCAATTTA
1 TTTGATGTCATTGCTTACATCAATTTA
1420162 ATTAGGTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.48
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1424634 original size:29 final size:29
Alignment explanation
Indices: 1424600--1424658 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1424590 CCTAAATTAA
1424600 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1424629 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1424658 T
1 T
1424659 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1434734 original size:24 final size:24
Alignment explanation
Indices: 1434699--1434793 Score: 75
Period size: 24 Copynumber: 3.8 Consensus size: 24
1434689 ACAACATAAA
1434699 AATATAATATTTAATAATATAATAT
1 AATAT-ATATTTAATAATATAATAT
* * *
1434724 AATATATATTTATTATTTTAATAT
1 AATATATATTTAATAATATAATAT
* * * *
1434748 ACTCAATTTATATAAGAATATAATACT
1 AAT--ATATATTTAATAATATAATA-T
*
1434775 ATTATAT-TTTAATAATATA
1 AATATATATTTAATAATATA
1434794 TAATAAATTA
Statistics
Matches: 53, Mismatches: 14, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
24 28 0.53
25 8 0.15
26 14 0.26
27 3 0.06
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (24 bp):
AATATATATTTAATAATATAATAT
Found at i:1434930 original size:24 final size:23
Alignment explanation
Indices: 1434902--1434957 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1434892 TAGTCTAATA
1434902 ATATTATAAAAAAATTCTTAAAAT
1 ATATTATAAAAAAATT-TTAAAAT
* *
1434926 ATATT-TATTAATAATTTTAAAAT
1 ATATTATA-AAAAAATTTTAAAAT
*
1434949 ATAATATAA
1 ATATTATAA
1434958 TATTTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATTATAAAAAAATTTTAAAAT
Found at i:1434958 original size:21 final size:23
Alignment explanation
Indices: 1434914--1434964 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1434904 ATTATAAAAA
*
1434914 AATTCTTAAAATATATTTATTAAT
1 AATT-TTAAAATATATATATTAAT
1434938 AATTTTAAAATATA-ATA-TAAT
1 AATTTTAAAATATATATATTAAT
*
1434959 ATTTTT
1 AATTTT
1434965 TTATTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.36
22 2 0.08
23 10 0.40
24 4 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AATTTTAAAATATATATATTAAT
Found at i:1435137 original size:22 final size:23
Alignment explanation
Indices: 1435109--1435154 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1435099 AATTATTCTA
*
1435109 AAATTTTTAAAAT-ACTAATATT
1 AAATTTTTAAAATAAATAATATT
*
1435131 AAATTTTTATAATAAATAATATT
1 AAATTTTTAAAATAAATAATATT
1435154 A
1 A
1435155 TTTATTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATTTTTAAAATAAATAATATT
Found at i:1435907 original size:33 final size:33
Alignment explanation
Indices: 1435870--1435992 Score: 132
Period size: 33 Copynumber: 3.8 Consensus size: 33
1435860 TTCGTCCTAC
1435870 TAGGATTCAAACTCCTAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAATAGGATAGAATTT
* *
1435903 TAGGATTCAAACTCCTAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAATAGGATAGAA-TTT
1435937 GCTAGGATTC-AA-----AAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAATAGGATAGAATTT
* *
1435966 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAA-ATAGGAT
1435993 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
27 6 0.08
28 2 0.03
29 3 0.04
30 12 0.16
33 31 0.42
34 10 0.14
35 2 0.03
36 8 0.11
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (33 bp):
TAGGATTCAAACTCCTAAAATAGGATAGAATTT
Found at i:1440050 original size:23 final size:23
Alignment explanation
Indices: 1440007--1440050 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1439997 CAATCAAGAA
* *
1440007 CAAAAAAGAAAAGAAGCAAAAAG
1 CAAAAAAAAAAAAAAGCAAAAAG
1440030 CAAAAAAAAAAATAAAG-AAAA
1 CAAAAAAAAAAA-AAAGCAAAA
1440051 GAGAAACAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (23 bp):
CAAAAAAAAAAAAAAGCAAAAAG
Found at i:1440235 original size:11 final size:12
Alignment explanation
Indices: 1440214--1440242 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1440204 CGAAGATCAT
1440214 GAAACATCCAGA
1 GAAACATCCAGA
1440226 GAAA-ATCCAGA
1 GAAACATCCAGA
1440237 GAAACA
1 GAAACA
1440243 CATATGAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.55, C:0.21, G:0.17, T:0.07
Consensus pattern (12 bp):
GAAACATCCAGA
Found at i:1440754 original size:21 final size:22
Alignment explanation
Indices: 1440728--1440777 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
1440718 CCCCATCAAT
1440728 CCTTTGAGCATCAAATACC-AA
1 CCTTTGAGCATCAAATACCAAA
*
1440749 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
1440771 CCTTTGA
1 CCTTTGA
1440778 CCAAACACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:1441674 original size:36 final size:35
Alignment explanation
Indices: 1441625--1441728 Score: 145
Period size: 36 Copynumber: 2.9 Consensus size: 35
1441615 GTGCTCACCA
1441625 TTGTCTCTCTTGAGACAGTTTACCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTT-CCTTGAAACAAACT
* *
1441661 TTGTCTCTGTTGAGACAGTTTCCCTTGAAACAAATT
1 TTGTCTCTCTTGAGACAGTTT-CCTTGAAACAAACT
* *
1441697 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTC-CTTGAAACA
1441729 TAAACATTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 1 0.02
36 60 0.98
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.38
Consensus pattern (35 bp):
TTGTCTCTCTTGAGACAGTTTCCTTGAAACAAACT
Found at i:1441822 original size:101 final size:101
Alignment explanation
Indices: 1441660--1441993 Score: 548
Period size: 101 Copynumber: 3.3 Consensus size: 101
1441650 TGAAACAAAC
* * *
1441660 TTTGTCTCTGTTGAGACAGTTTCCCTTGAAACAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGA
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
*
1441725 AACATAAACATTGAAAACATTTCCCTTGAAATGAGT
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAAT
** *
1441761 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTCCGTCTCCATTGAGACAGTTTCTCTTGA
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1441826 AACATAAACATTGAAAACATTTCCCTTGAAATGAAT
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAAT
1441862 TTTG--TCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1441925 -AACATAAACATTGAAAACATTTCCCTTGAAATGAAT
65 AAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
** *
1441961 TCCGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1441994 TAAACATTGA
Statistics
Matches: 217, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
99 64 0.29
100 30 0.14
101 123 0.57
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (101 bp):
TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
AACATAAACATTGAAAACATTTCCCTTGAAATGAAT
Found at i:1441888 original size:34 final size:36
Alignment explanation
Indices: 1441845--1441926 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 36
1441835 ATTGAAAACA
** *
1441845 TTTCCCTTGAAA-TGAATTTTGTCT-CTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCTTGAGACAG
1441879 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCT-CCTTGAGACAG
*
1441916 TTTCTCTTGAA
1 TTTCCCTTGAA
1441927 CATAAACATT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
34 12 0.29
35 10 0.24
37 19 0.46
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCTTGAGACAG
Found at i:1441918 original size:37 final size:34
Alignment explanation
Indices: 1441630--1441926 Score: 131
Period size: 36 Copynumber: 8.7 Consensus size: 34
1441620 CACCATTGTC
* * *
1441630 TCTCTTGAGACAGTTTACCTTGAAACAAACTTTG
1 TCTCTTGAGACAGTTTCCCTTGAAAAAAATTTTG
* *
1441664 TCTCTGTTGAGACAGTTTCCCTTGAAACAAATTTTT
1 TCTC--TTGAGACAGTTTCCCTTGAAAAAAATTTTG
*
1441700 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAA-----
1 TCT--CTTGAGACAGTTTCCCTTGAAA-A-AAATTTTG
* * ** *
1441733 -C-ATTGAAAACA-TTTCCCTTGAAATGAGTTTTG
1 TCTCTTG-AGACAGTTTCCCTTGAAAAAAATTTTG
* * **
1441765 TCTCTCTTGAGATAGTTTCCCTTGAAACAAATTCCG
1 --TCTCTTGAGACAGTTTCCCTTGAAAAAAATTTTG
*
1441801 TCTCCATTGAGACAGTTTCTCTTGAAACATAAA-----
1 TCT-C-TTGAGACAGTTTCCCTTGAAA-A-AAATTTTG
* * **
1441834 -C-ATTGAAAACA-TTTCCCTTGAAATGAATTTTG
1 TCTCTTG-AGACAGTTTCCCTTGAAAAAAATTTTG
*
1441866 TCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTG
1 TCTCTTGAGACAGTTTCCCTTGAAA-AAAATTTTG
*
1441901 TCTCCCTTGAGACAGTTTCTCTTGAA
1 TCT--CTTGAGACAGTTTCCCTTGAA
1441927 CATAAACATT
Statistics
Matches: 196, Mismatches: 34, Indels: 63
0.67 0.12 0.22
Matches are distributed among these distances:
27 3 0.02
29 28 0.14
30 8 0.04
32 2 0.01
33 4 0.02
34 22 0.11
35 15 0.08
36 88 0.45
37 19 0.10
38 7 0.04
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (34 bp):
TCTCTTGAGACAGTTTCCCTTGAAAAAAATTTTG
Found at i:1441950 original size:164 final size:164
Alignment explanation
Indices: 1441780--1442091 Score: 513
Period size: 164 Copynumber: 1.9 Consensus size: 164
1441770 CTTGAGATAG
1441780 TTTCCCTTGAAACAAATTCCGTCTC-CATTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAATTCCGTCTCTC-TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
1441844 ATTTCCCTTGAAATGAATTT-TGTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
65 ATTTCCCTTGAAATGAATTTCTCTCTCTTGAGACAGTTTCCC-TGAAACAAAA-TTTGTCTCCCT
1441908 TGAGACAG-TTTCTCTTGAACATAAACATTGAAAACA
128 TGAGACAGTTTTCTCTTGAACATAAACATTGAAAACA
** *
1441944 TTTCCCTTGAAATGAATTCCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACA
1 TTTCCCTTGAAACAAATTCCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
1442009 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTGAAACAAAATTTGTCTCCCTTG
66 TTTCCCTTGAAATGAATTTC-TCTCTCTTGAGACAGTTTCCCTGAAACAAAATTTGTCTCCCTTG
1442074 AGACAGTTTTCTCTTGAA
130 AGACAGTTTTCTCTTGAA
1442092 GCATCATCTT
Statistics
Matches: 138, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
164 98 0.71
165 22 0.16
166 18 0.13
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (164 bp):
TTTCCCTTGAAACAAATTCCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
TTTCCCTTGAAATGAATTTCTCTCTCTTGAGACAGTTTCCCTGAAACAAAATTTGTCTCCCTTGA
GACAGTTTTCTCTTGAACATAAACATTGAAAACA
Found at i:1441999 original size:65 final size:65
Alignment explanation
Indices: 1441900--1442057 Score: 275
Period size: 65 Copynumber: 2.5 Consensus size: 65
1441890 ACAAAATTTT
*
1441900 GTCTCCCTTGAGACAGTTTCTCTTG-AACATAAACATTGAAAACATTTCCCTTGAAATGAATTCC
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTCC
* *
1441964 GTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTC
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTCC
1442029 GTCTCTCTTGAGACAGTTTCTC-TGAAACA
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACA
1442058 AAATTTGTCT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
64 30 0.34
65 59 0.66
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (65 bp):
GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTCC
Found at i:1443172 original size:105 final size:105
Alignment explanation
Indices: 1442831--1443597 Score: 1026
Period size: 105 Copynumber: 7.3 Consensus size: 105
1442821 GCCATATGCG
* * * * * *
1442831 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
1442896 GGGA-CGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* *
1442940 ATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGCGCGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG-ACGAAGG
*
1443005 GACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCA
65 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
1443046 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1443111 ACCGCTGCTTGTCAACAACAACTTCTTAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * *
1443151 ATTTCAACTTCACAACAAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACAAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
1443216 ACCGTTGTTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * *
1443256 ATTTCAACTTCACAACGAAGGATATTGGACTTCATACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
1443321 ACCACTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
1443361 ATTTCAATTTCACAACGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
1443426 ACCACTGCTTGTCAACAA-AA-TT-TC-A-TTCATATTCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * * *
1443461 ATTTTAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** *
1443526 A-CGACTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* * *
1443567 ATTTCAACTTCACGACGGAGGATATTAGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
1443598 TGGAACAATG
Statistics
Matches: 592, Mismatches: 57, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
99 1 0.00
100 77 0.13
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 318 0.54
106 139 0.23
107 21 0.04
108 2 0.00
109 21 0.04
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
Found at i:1444201 original size:33 final size:34
Alignment explanation
Indices: 1444135--1444257 Score: 111
Period size: 33 Copynumber: 3.8 Consensus size: 34
1444125 TTCGTCCTAC
1444135 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
1444169 TAGGATTCAAACTCCT-AAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1444203 GCTAGGATTC--A-----AAAAATAGGATAG-ATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
1444231 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
1444258 CCACAAGCAC
Statistics
Matches: 71, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
26 6 0.08
28 4 0.06
29 1 0.01
30 10 0.14
33 22 0.31
34 20 0.28
36 8 0.11
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:1444794 original size:16 final size:15
Alignment explanation
Indices: 1444775--1444836 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 15
1444765 GCTTTTACTT
1444775 TTTATATATTTTATCA
1 TTTATATATTTTAT-A
*
1444791 TTTATTTATTTTTATA
1 TTTATATA-TTTTATA
*
1444807 TTTATCATATTTTATG
1 TTTAT-ATATTTTATA
*
1444823 TTTTTATATCTTTA
1 TTTATATAT-TTTA
1444837 CTTGTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 4 0.10
16 27 0.69
17 8 0.21
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTATATATTTTATA
Found at i:1444794 original size:23 final size:23
Alignment explanation
Indices: 1444740--1444814 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 23
1444730 TTATTATTAT
*
1444740 TTTACTTATATATATATATATATATGCT
1 TTTACTTAT-T-TATATAT-T-TAT-CA
1444768 TTTACTT-TTTATATATTTTATCA
1 TTTACTTATTTATATA-TTTATCA
* *
1444791 TTTATTTATTTTTATATTTATCA
1 TTTACTTATTTATATATTTATCA
1444814 T
1 T
1444815 ATTTTATGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
23 15 0.36
24 10 0.24
25 7 0.17
26 2 0.05
27 1 0.02
28 7 0.17
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (23 bp):
TTTACTTATTTATATATTTATCA
Found at i:1444836 original size:26 final size:24
Alignment explanation
Indices: 1444774--1444836 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 24
1444764 TGCTTTTACT
1444774 TTTTATATATTTTATCATTTATTTA
1 TTTT-TATATTTTATCATTTATTTA
*
1444799 TTTTTATA-TTTATCATATT-TTATG
1 TTTTTATATTTTATCAT-TTATT-TA
1444823 TTTTTATATCTTTA
1 TTTTTATAT-TTTA
1444837 CTTGTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
23 10 0.30
24 15 0.45
25 4 0.12
26 4 0.12
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTTTATATTTTATCATTTATTTA
Found at i:1449498 original size:297 final size:297
Alignment explanation
Indices: 1448964--1449558 Score: 1181
Period size: 297 Copynumber: 2.0 Consensus size: 297
1448954 TTCCCACTGC
1448964 ACAATAAAACTAACGAAATTTAATGGACTATGGTAAAATATATAAATAGTCCATCGACTATAAGA
1 ACAATAAAACTAACGAAATTTAATGGACTATGGTAAAATATATAAATAGTCCATCGACTATAAGA
1449029 TATTAATTTATTAAATCGTTTGACTATTAAAAGTTATAAAATGATCTTTTGACTATAGATTATTG
66 TATTAATTTATTAAATCGTTTGACTATTAAAAGTTATAAAATGATCTTTTGACTATAGATTATTG
1449094 ATTCGTTAACTCCCTCAACTATTAAAAGTTACAAAATGGTCATCCGACTATTTATTATGTTCTAA
131 ATTCGTTAACTCCCTCAACTATTAAAAGTTACAAAATGGTCATCCGACTATTTATTATGTTCTAA
*
1449159 ACTCGTCATTTTTCGTAAAAAAATTGACAATTATCTAAGTCGAATGTTAACATGATGATTGAGAT
196 ACTCGTCATTTTTCCTAAAAAAATTGACAATTATCTAAGTCGAATGTTAACATGATGATTGAGAT
1449224 ATGAATCATTTGAGACTCTGTGATTAGATTTAATTAT
261 ATGAATCATTTGAGACTCTGTGATTAGATTTAATTAT
1449261 ACAATAAAACTAACGAAATTTAATGGACTATGGTAAAATATATAAATAGTCCATCGACTATAAGA
1 ACAATAAAACTAACGAAATTTAATGGACTATGGTAAAATATATAAATAGTCCATCGACTATAAGA
1449326 TATTAATTTATTAAATCGTTTGACTATTAAAAGTTATAAAATGATCTTTTGACTATAGATTATTG
66 TATTAATTTATTAAATCGTTTGACTATTAAAAGTTATAAAATGATCTTTTGACTATAGATTATTG
1449391 ATTCGTTAACTCCCTCAACTATTAAAAGTTACAAAATGGTCATCCGACTATTTATTATGTTCTAA
131 ATTCGTTAACTCCCTCAACTATTAAAAGTTACAAAATGGTCATCCGACTATTTATTATGTTCTAA
1449456 ACTCGTCATTTTTCCTAAAAAAATTGACAATTATCTAAGTCGAATGTTAACATGATGATTGAGAT
196 ACTCGTCATTTTTCCTAAAAAAATTGACAATTATCTAAGTCGAATGTTAACATGATGATTGAGAT
1449521 ATGAATCATTTGAGACTCTGTGATTAGATTTAATTAT
261 ATGAATCATTTGAGACTCTGTGATTAGATTTAATTAT
1449558 A
1 A
1449559 TCACATCCAA
Statistics
Matches: 297, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
297 297 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (297 bp):
ACAATAAAACTAACGAAATTTAATGGACTATGGTAAAATATATAAATAGTCCATCGACTATAAGA
TATTAATTTATTAAATCGTTTGACTATTAAAAGTTATAAAATGATCTTTTGACTATAGATTATTG
ATTCGTTAACTCCCTCAACTATTAAAAGTTACAAAATGGTCATCCGACTATTTATTATGTTCTAA
ACTCGTCATTTTTCCTAAAAAAATTGACAATTATCTAAGTCGAATGTTAACATGATGATTGAGAT
ATGAATCATTTGAGACTCTGTGATTAGATTTAATTAT
Found at i:1454315 original size:37 final size:37
Alignment explanation
Indices: 1454273--1454345 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
1454263 AGCCATGAGG
1454273 GATTCCAATTCATTTGGAAAACTTGAACCAAACATGA
1 GATTCCAATTCATTTGGAAAACTTGAACCAAACATGA
*
1454310 GATTCCAATTCCTTTGGAAAACTTGAACCAAACATG
1 GATTCCAATTCATTTGGAAAACTTGAACCAAACATG
1454346 GAAAAGTGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (37 bp):
GATTCCAATTCATTTGGAAAACTTGAACCAAACATGA
Found at i:1454748 original size:60 final size:60
Alignment explanation
Indices: 1454572--1454749 Score: 227
Period size: 60 Copynumber: 3.0 Consensus size: 60
1454562 GTATCACATG
* *
1454572 TCCCTAAACTATGACTCTCATTTTAAATTGATCCCTAAACTTTTAAATATTCCAATTTCT
1 TCCCTAAACTATGACTCTCATTTTAAATTGGTCCCTAAACTTTTGAATATTCCAATTTCT
* * * * * *
1454632 TCCCCAAACTATGAATCTCATTTTAAATTAGT-TCTAAACTTTTGAACATTCTAATTT-T
1 TCCCTAAACTATGACTCTCATTTTAAATTGGTCCCTAAACTTTTGAATATTCCAATTTCT
* *
1454690 ATCCCTAAACTATGACCCTC-TTTCTAAATTGGTCCCCAAACTTTTGAATATTCCAATTTC
1 -TCCCTAAACTATGACTCTCATTT-TAAATTGGTCCCTAAACTTTTGAATATTCCAATTTC
1454750 AATCCCAAAT
Statistics
Matches: 98, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
58 4 0.04
59 45 0.46
60 49 0.50
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (60 bp):
TCCCTAAACTATGACTCTCATTTTAAATTGGTCCCTAAACTTTTGAATATTCCAATTTCT
Found at i:1454984 original size:30 final size:28
Alignment explanation
Indices: 1454888--1454985 Score: 74
Period size: 30 Copynumber: 3.3 Consensus size: 28
1454878 ATATACATGT
1454888 AGTTTGGGATAAAATTGGAATGTTCAAGA
1 AGTTTGGGAT-AAATTGGAATGTTCAAGA
* * *
1454917 AGTTTGGGGACTAATTTTGAATGAATGTC-A-T
1 AGTTT-GGGA-TAAATTGGAATG--T-TCAAGA
*
1454948 AGTTTGGTGATGAAATTGGAATGTTCAAGG
1 AGTTTGG-GAT-AAATTGGAATGTTCAAGA
1454978 AGTTTGGG
1 AGTTTGGG
1454986 GACTAATGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
28 2 0.04
29 8 0.15
30 23 0.43
31 17 0.31
32 2 0.04
33 2 0.04
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35
Consensus pattern (28 bp):
AGTTTGGGATAAATTGGAATGTTCAAGA
Found at i:1455024 original size:27 final size:26
Alignment explanation
Indices: 1454938--1455021 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 26
1454928 TAATTTTGAA
* *
1454938 TGAATGTCATAGTTTGGTGATGAAAT
1 TGAATGTCATAATTTGGGGATGAAAT
1454964 TGGAATGTTCA-AGGAGTTTGGGGACT--AA-
1 T-GAATG-TCATA--A-TTTGGGGA-TGAAAT
1454992 TGAATGTCATAATTTGGGGATGAAAT
1 TGAATGTCATAATTTGGGGATGAAAT
1455018 TGAA
1 TGAA
1455022 ATGTTTAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 20
0.68 0.03 0.29
Matches are distributed among these distances:
23 1 0.02
24 8 0.17
25 3 0.07
26 8 0.17
27 12 0.26
28 4 0.09
29 2 0.04
30 7 0.15
31 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (26 bp):
TGAATGTCATAATTTGGGGATGAAAT
Found at i:1455121 original size:59 final size:60
Alignment explanation
Indices: 1454997--1455126 Score: 145
Period size: 59 Copynumber: 2.2 Consensus size: 60
1454987 ACTAATGAAT
* * * * * * *
1454997 GTCATAATTTGGGGATGAAATTGAAATGTTTAAAAGTTTGAGGATTAATTTAGAATGATA
1 GTCATAATTTAGGGATGAAATTGAAATATTTAAAAGTTTAAGGATCAATTTAAAATAACA
* * * *
1455057 ATCATAGTTTAGGGATTAAATTGAAA-ATTTAAAAGTTTAAGGATCAATTTAAAATAACG
1 GTCATAATTTAGGGATGAAATTGAAATATTTAAAAGTTTAAGGATCAATTTAAAATAACA
*
1455116 GTCATACTTTA
1 GTCATAATTTA
1455127 AGGACATGTG
Statistics
Matches: 57, Mismatches: 13, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
59 35 0.61
60 22 0.39
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (60 bp):
GTCATAATTTAGGGATGAAATTGAAATATTTAAAAGTTTAAGGATCAATTTAAAATAACA
Found at i:1456922 original size:103 final size:103
Alignment explanation
Indices: 1456594--1456914 Score: 633
Period size: 103 Copynumber: 3.1 Consensus size: 103
1456584 GTAGAGGGTC
1456594 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1456659 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1456697 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1456762 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1456800 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1456865 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1456903 TATGTGGTCCTT
1 TATGTGGTCCTT
1456915 ATGGACATTA
Statistics
Matches: 216, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 216 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1456964 original size:23 final size:23
Alignment explanation
Indices: 1456931--1456993 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
1456921 ATTATTATAT
1456931 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1456954 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
1456977 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
1456994 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1463803 original size:22 final size:22
Alignment explanation
Indices: 1463778--1463832 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1463768 TACTCTTCTT
1463778 ATCTTCTTCTCCTAAAACTCAC
1 ATCTTCTTCTCCTAAAACTCAC
* * * *
1463800 ATCTTCTTATCTTAAAGCTTAC
1 ATCTTCTTCTCCTAAAACTCAC
1463822 ATCTTCTTCTC
1 ATCTTCTTCTC
1463833 TAGCAAACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.44
Consensus pattern (22 bp):
ATCTTCTTCTCCTAAAACTCAC
Found at i:1466668 original size:21 final size:21
Alignment explanation
Indices: 1466639--1466683 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1466629 TTACGAAAGT
*
1466639 CACTGTAGCAGTGCATCGATG
1 CACTATAGCAGTGCATCGATG
*
1466660 CACTATAGCAGTTCATCGATG
1 CACTATAGCAGTGCATCGATG
1466681 CAC
1 CAC
1466684 AATTTTGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (21 bp):
CACTATAGCAGTGCATCGATG
Found at i:1467434 original size:20 final size:20
Alignment explanation
Indices: 1467386--1467436 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1467376 ATCGATACCC
*
1467386 AGTATTCAGTATCGATACTCA
1 AGTATT-AGTACCGATACTCA
** *
1467407 AGGGTTAGTACCGATACTGA
1 AGTATTAGTACCGATACTCA
1467427 AGTATTAGTA
1 AGTATTAGTA
1467437 TTGGCACCCA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (20 bp):
AGTATTAGTACCGATACTCA
Found at i:1471171 original size:18 final size:19
Alignment explanation
Indices: 1471129--1471171 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
1471119 ATATTGAGAT
1471129 TGATCAACATAATGCAGCTGG
1 TGATCAACATAATGCA-C-GG
1471150 TGATCAACATAATGCA-GG
1 TGATCAACATAATGCACGG
1471168 TGAT
1 TGAT
1471172 GGTGGTAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.27
21 16 0.73
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (19 bp):
TGATCAACATAATGCACGG
Found at i:1473954 original size:13 final size:13
Alignment explanation
Indices: 1473936--1473960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1473926 TGTTAATGAC
1473936 TAAAAAAATATTT
1 TAAAAAAATATTT
1473949 TAAAAAAATATT
1 TAAAAAAATATT
1473961 ATTTTTTTAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAAAAATATTT
Found at i:1484499 original size:18 final size:18
Alignment explanation
Indices: 1484476--1484531 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
1484466 CCTATTCTTT
1484476 GGCGAGCAAGGAATCATC
1 GGCGAGCAAGGAATCATC
* *
1484494 GGCGAGCAAGGATTCATA
1 GGCGAGCAAGGAATCATC
*
1484512 GGCGATG-AAGGAGTCATC
1 GGCGA-GCAAGGAATCATC
1484530 GG
1 GG
1484532 GGACGAGGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 32 0.97
19 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.38, T:0.14
Consensus pattern (18 bp):
GGCGAGCAAGGAATCATC
Found at i:1485664 original size:23 final size:23
Alignment explanation
Indices: 1485638--1485693 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
1485628 TCTGTGTTTG
*
1485638 GCTCATTTAGCATTCTTGAACAT
1 GCTCATTTAACATTCTTGAACAT
**
1485661 GCTCATTTAATGTTCTTGAACAT
1 GCTCATTTAACATTCTTGAACAT
1485684 GCTCATTTAA
1 GCTCATTTAA
1485694 TGTTCATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (23 bp):
GCTCATTTAACATTCTTGAACAT
Found at i:1485694 original size:23 final size:23
Alignment explanation
Indices: 1485650--1485703 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
1485640 TCATTTAGCA
1485650 TTCTTGAACATGCTCATTTAATG
1 TTCTTGAACATGCTCATTTAATG
1485673 TTCTTGAACATGCTCATTTAATG
1 TTCTTGAACATGCTCATTTAATG
*
1485696 TTCATGAA
1 TTCTTGAA
1485704 TATATTCGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (23 bp):
TTCTTGAACATGCTCATTTAATG
Found at i:1485715 original size:23 final size:23
Alignment explanation
Indices: 1485654--1485720 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
1485644 TTAGCATTCT
* *
1485654 TGAACATGCTCATTTAATGTTCT
1 TGAACATACTCATTTAATGTTCA
*
1485677 TGAACATGCTCATTTAATGTTCA
1 TGAACATACTCATTTAATGTTCA
* * *
1485700 TGAATATATTCGTTT-ATGTTC
1 TGAACATACTCATTTAATGTTC
1485721 GTCAACATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 6 0.15
23 33 0.85
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (23 bp):
TGAACATACTCATTTAATGTTCA
Found at i:1486746 original size:48 final size:51
Alignment explanation
Indices: 1486692--1486803 Score: 142
Period size: 48 Copynumber: 2.3 Consensus size: 51
1486682 TAGATTAGAT
*
1486692 TTATTATTTTATTA-AGAATTAAGATATAGT-AAAA-A-TATATTTAATTGA
1 TTATTATTTTATTAGA-AATTAAGATATAATCAAAATATTATATTTAATTGA
* * * *
1486740 TTATTATTTTATTAGAAATTAGGATATAATCAAAATATTATCTTTATTTTA
1 TTATTATTTTATTAGAAATTAAGATATAATCAAAATATTATATTTAATTGA
1486791 TTATTATTTTATT
1 TTATTATTTTATT
1486804 GAGTAGTTAC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
48 26 0.47
49 5 0.09
50 1 0.02
51 23 0.42
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (51 bp):
TTATTATTTTATTAGAAATTAAGATATAATCAAAATATTATATTTAATTGA
Found at i:1487608 original size:16 final size:16
Alignment explanation
Indices: 1487587--1487622 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1487577 TATTTTTAAT
1487587 AAAAAATCAAACAAGA
1 AAAAAATCAAACAAGA
1487603 AAAAAATCAAACAAGA
1 AAAAAATCAAACAAGA
1487619 AAAA
1 AAAA
1487623 GGCAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.78, C:0.11, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAAAATCAAACAAGA
Found at i:1487628 original size:15 final size:16
Alignment explanation
Indices: 1487587--1487644 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
1487577 TATTTTTAAT
*
1487587 AAAAAATCAAACAAGA
1 AAAAAAGCAAACAAGA
*
1487603 AAAAAATCAAACAAG-
1 AAAAAAGCAAACAAGA
* *
1487618 AAAAAGGCAAA-AAAA
1 AAAAAAGCAAACAAGA
1487633 AAGAAAAGCAAA
1 AA-AAAAGCAAA
1487645 AAAATCTCAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 2 0.06
15 11 0.31
16 23 0.64
ACGTcount: A:0.76, C:0.10, G:0.10, T:0.03
Consensus pattern (16 bp):
AAAAAAGCAAACAAGA
Found at i:1491196 original size:31 final size:31
Alignment explanation
Indices: 1491161--1491222 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1491151 TCTTTTTTCC
* *
1491161 AATTTTTTTTATCTTT-TTATCTTTTCTTTTT
1 AATTTTTTTAAT-TTTATTATATTTTCTTTTT
*
1491192 AATTTTTTTAATTTTATTTTATTTTCTTTTT
1 AATTTTTTTAATTTTATTATATTTTCTTTTT
1491223 GATGAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (31 bp):
AATTTTTTTAATTTTATTATATTTTCTTTTT
Found at i:1493133 original size:18 final size:17
Alignment explanation
Indices: 1493079--1493127 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1493069 TTGGACCCTT
* *
1493079 AGTGCATCGGTGCATTAA
1 AGTGCATCGATGCA-TCA
1493097 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1493115 AGTGCATTCGATG
1 AGTGCA-TCGATG
1493128 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1493213 original size:46 final size:46
Alignment explanation
Indices: 1493163--1493262 Score: 146
Period size: 46 Copynumber: 2.2 Consensus size: 46
1493153 TGCATGGCTG
1493163 GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAAATCCTCA
1 GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAAATCCTCA
* * *** *
1493209 GTGCATCGGTGCATGGTATGTATTCGATGTTTTCATAAAATCCTCA
1 GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAAATCCTCA
1493255 GTGCATCG
1 GTGCATCG
1493263 GTGCATGGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (46 bp):
GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAAATCCTCA
Found at i:1493236 original size:64 final size:64
Alignment explanation
Indices: 1493100--1493224 Score: 162
Period size: 64 Copynumber: 1.9 Consensus size: 64
1493090 GCATTAAGAG
* * * *
1493100 TGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCGATACATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGA
* * *
1493164 TGCATCGATACATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG
1 TGCATCGATACATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGG
1493225 TATGTATTCG
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 26 0.49
65 24 0.45
66 3 0.06
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (64 bp):
TGCATCGATACATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGA
Found at i:1493263 original size:46 final size:46
Alignment explanation
Indices: 1493184--1493275 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
1493174 CATCAAATGC
1493184 ATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTATGT
1 ATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTATGT
1493230 ATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTATGT
1 ATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTATGT
1493276 GCATCGATGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (46 bp):
ATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTATGT
Found at i:1494725 original size:347 final size:348
Alignment explanation
Indices: 1494092--1494765 Score: 835
Period size: 347 Copynumber: 1.9 Consensus size: 348
1494082 AAATTACGCA
* * * *
1494092 TTTAGTATCTAAATTATTAGTTTTGATCTATTTTAGCACCTAGACTTTTAATTTTTTTCAAAATC
1 TTTAGTATCTAAACTATTAGTTTTGATCCATTTTAGCACCTAAACTTTCAA-TTTTTTCAAAATC
* * *
1494157 ATACTTAAAGTTTAGTTTTTATTTCATTTTAGTATCCGTTCAAAATTGAACGTTATGTTTTGAAA
65 ATACCTAAAGTTTAGTTTTTATTTCATTTTAGTATCCGTTCAAAATTGAACATTAAGTTTTGAAA
* * * * * *
1494222 ATATTTAAAGTTTATGTATTAAAACATGCCAAAACTAATACTTTAGGTACTAAATGCGTTAAGGT
130 ATATTTAAAATTTATGTACTAAAACATACAAAAACTAATACTTTAGGCACTAAACGCGTTAAGGT
* *
1494287 TTTAACGACGGTAGCTAAAATGAAACAAAAACTAAACTTTATGTATGATTTTGAAAAAATTGAAA
195 TTTAACGACGGTAGCTAAAATGAAACAAAAACTAAACTTTAGGTATGATTTTGAAAAAATAGAAA
* * **
1494352 GTTTAGGTTCTAAAACAAACCAAAATTGATAGTTTAGGTACTAAATTTATAATTTACCCTTTTTA
260 GTTTAGGTACTAAAACAAACCAAAATTGATAGTTTAGATACTAAATGCATAATTTACCCTTTTTA
1494417 TAATTATTTTGGGTAAATTACATG
325 TAATTATTTTGGGTAAATTACATG
* * *
1494441 TTTAGTA-CTTAAACTATTAGTTTTGGTCCGTTTTAGTACCTAAACTTTCAA-TTTTT-AAAATC
1 TTTAGTATC-TAAACTATTAGTTTTGATCCATTTTAGCACCTAAACTTTCAATTTTTTCAAAATC
* * * *
1494503 ATACCTAAA-TTTAGTTTTTGTTTTATTTTAGTA-CTGTATTCAAAATTTAACATTAAGTTTTGG
65 ATACCTAAAGTTTAGTTTTTATTTCATTTTAGTATCCG--TTCAAAATTGAACATTAAGTTTT-G
* * * * * * *
1494566 AAATTTTTTAAAATTTA-GATACTAAAACATATAAAAATTGATAGTTTAGGCACTAAACGTGTTA
127 AAAATATTTAAAATTTATG-TACTAAAACATACAAAAACTAATACTTTAGGCACTAAACGCGTTA
* **
1494630 AGTTTTTAACAGTGGGTA-CTAAAATGAAACAAAAACTAAA-TATTAGGTATGATTTTGAAATAA
191 AGGTTTTAAC-GACGGTAGCTAAAATGAAACAAAAACTAAACT-TTAGGTATGATTTTGAAA-AA
* * * *
1494693 ATAGAAA-TTTAGGTACTAAAATATATCAAAATTGATAGTTTAGATACTAAATGCGTAATTTACC
253 ATAGAAAGTTTAGGTACTAAAACAAACCAAAATTGATAGTTTAGATACTAAATGCATAATTTACC
*
1494757 TTTTTTATA
318 CTTTTTATA
1494766 TATAATTATT
Statistics
Matches: 276, Mismatches: 41, Indels: 18
0.82 0.12 0.05
Matches are distributed among these distances:
344 2 0.01
345 22 0.08
346 36 0.13
347 160 0.58
348 14 0.05
349 42 0.15
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.41
Consensus pattern (348 bp):
TTTAGTATCTAAACTATTAGTTTTGATCCATTTTAGCACCTAAACTTTCAATTTTTTCAAAATCA
TACCTAAAGTTTAGTTTTTATTTCATTTTAGTATCCGTTCAAAATTGAACATTAAGTTTTGAAAA
TATTTAAAATTTATGTACTAAAACATACAAAAACTAATACTTTAGGCACTAAACGCGTTAAGGTT
TTAACGACGGTAGCTAAAATGAAACAAAAACTAAACTTTAGGTATGATTTTGAAAAAATAGAAAG
TTTAGGTACTAAAACAAACCAAAATTGATAGTTTAGATACTAAATGCATAATTTACCCTTTTTAT
AATTATTTTGGGTAAATTACATG
Found at i:1495342 original size:4 final size:4
Alignment explanation
Indices: 1495333--1495493 Score: 214
Period size: 4 Copynumber: 40.2 Consensus size: 4
1495323 TATGATGGGG
*
1495333 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * *
1495381 GCAT GCAT GCAT GCAT ACAT ACAT GCAT ACAT ACAT GCAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
1495429 ACAT ACAT ACAT ACAT ACAT GCAT GCAT ACAT ACAT ACAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
1495477 GCAT ACAT ACAT GCAT A
1 ACAT ACAT ACAT ACAT A
1495494 TACATATAGT
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 145 1.00
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:1504059 original size:64 final size:65
Alignment explanation
Indices: 1503989--1504144 Score: 176
Period size: 64 Copynumber: 2.4 Consensus size: 65
1503979 ATGCACATGA
* **
1503989 AGTGCATCGATGCA-CTCTTTTAAAATACAAACATCGAAT-GCAATTAATGCATCGATGCATAAG
1 AGTGCATCGATGCATCCCCATT-AAATACAAACATCGAATAG-AATTAATGCATCGATGCAT-AG
1504052 -G-
63 TGT
* * * *
1504053 AGTGCATCGATGTATCCCCATTAAATACAAACATCGAATAGGATTTATGCATCGATGCATGGTGT
1 AGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGAATTAATGCATCGATGCATAGTGT
1504118 AGTGCATCGATGCATACCTCCATTAAA
1 AGTGCATCGATGCAT-CC-CCATTAAA
1504145 AGATGAAAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 48 0.62
65 19 0.24
66 2 0.03
67 8 0.10
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (65 bp):
AGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGAATTAATGCATCGATGCATAGTGT
Found at i:1504424 original size:25 final size:25
Alignment explanation
Indices: 1504369--1504426 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
1504359 ATAAGTCTAG
* *
1504369 ATTCAATATTTTGATACATGATCGTA
1 ATTC-ATATTATGATACATGATCATA
*
1504395 TTTCATATTATGATACATGA-CATGA
1 ATTCATATTATGATACATGATCAT-A
1504420 ATTCATA
1 ATTCATA
1504427 CCATATGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 2 0.07
25 22 0.81
26 3 0.11
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Consensus pattern (25 bp):
ATTCATATTATGATACATGATCATA
Found at i:1504749 original size:23 final size:23
Alignment explanation
Indices: 1504723--1504785 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
1504713 ATTATTATAT
1504723 GGCACTCTGGTGCAATTCTATGA
1 GGCACTCTGGTGCAATTCTATGA
* * *
1504746 GGCACTCCGGTGTAATTCTATGT
1 GGCACTCTGGTGCAATTCTATGA
1504769 GGCACT-TCGGTGCAATT
1 GGCACTCT-GGTGCAATT
1504786 ATACGAGCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (23 bp):
GGCACTCTGGTGCAATTCTATGA
Found at i:1505779 original size:31 final size:31
Alignment explanation
Indices: 1505741--1505894 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
1505731 CCCGAAGGAC
* *
1505741 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
1505772 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1505803 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1505834 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1505865 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
1505895 CCCTCGACCC
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:1506791 original size:21 final size:21
Alignment explanation
Indices: 1506761--1506805 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1506751 ATTCTGTCGT
* *
1506761 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1506782 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1506803 TTG
1 TTG
1506806 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1509804 original size:31 final size:31
Alignment explanation
Indices: 1509766--1509919 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
1509756 TCCCGAAGAC
* *
1509766 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
1509797 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1509828 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1509859 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1509890 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
1509920 CCCTCGACCC
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:1510814 original size:21 final size:21
Alignment explanation
Indices: 1510784--1510828 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1510774 ATTCTGTCGT
* *
1510784 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1510805 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1510826 TTG
1 TTG
1510829 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1517444 original size:64 final size:65
Alignment explanation
Indices: 1517374--1517529 Score: 185
Period size: 64 Copynumber: 2.4 Consensus size: 65
1517364 ATGCACATGA
* **
1517374 AGTGCATCGATGCA-CTCTTTTAAAATACAAACATCGAAT-GTAATTAATGCATCGATGCATAAG
1 AGTGCATCGATGCATCCCCATT-AAATACAAACATCGAATAG-AATTAATGCATCGATGCAT-AG
1517437 -G-
63 TGT
* * *
1517438 AGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTATGCATCGATGCATGGTGT
1 AGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGAATTAATGCATCGATGCATAGTGT
1517503 AGTGCATCGATGCATACCTCCATTAAA
1 AGTGCATCGATGCAT-CC-CCATTAAA
1517530 AGATGAAAAT
Statistics
Matches: 80, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 49 0.61
65 20 0.25
66 2 0.03
67 8 0.10
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (65 bp):
AGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGAATTAATGCATCGATGCATAGTGT
Found at i:1517809 original size:25 final size:25
Alignment explanation
Indices: 1517754--1517811 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
1517744 ATAAGTCTAG
* *
1517754 ATTCAATATTTTGATACATGATCGTA
1 ATTC-ATATTATGATACATGATCATA
*
1517780 TTTCATATTATGATACATGA-CATGA
1 ATTCATATTATGATACATGATCAT-A
1517805 ATTCATA
1 ATTCATA
1517812 CCATATGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 2 0.07
25 22 0.81
26 3 0.11
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Consensus pattern (25 bp):
ATTCATATTATGATACATGATCATA
Found at i:1518165 original size:23 final size:23
Alignment explanation
Indices: 1518107--1518175 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
1518097 CATTATTATA
* *
1518107 TGGCACTCTGGTGAAATTCTATG
1 TGGCACTCTGGTGCAATTCTACG
*
1518130 CGGCACTCTGGTGCAATTCTACG
1 TGGCACTCTGGTGCAATTCTACG
*
1518153 TGGCACT-TCGGTGCAATTATACG
1 TGGCACTCT-GGTGCAATTCTACG
1518176 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTCTGGTGCAATTCTACG
Found at i:1520672 original size:19 final size:20
Alignment explanation
Indices: 1520636--1520673 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1520626 TTTTAAATGG
*
1520636 ACTTTGAATTATTTTTGAAA
1 ACTTTGAATTACTTTTGAAA
1520656 ACTTTGAA-TACTTTTGAA
1 ACTTTGAATTACTTTTGAA
1520674 TAAATTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (20 bp):
ACTTTGAATTACTTTTGAAA
Found at i:1528825 original size:2 final size:2
Alignment explanation
Indices: 1528814--1528852 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1528804 TATACACAAT
1528814 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1528853 AACTTGGGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.