Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004507.1 Hibiscus syriacus cultivar Beakdansim tig00009942_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: 1776135
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1370305 original size:21 final size:23
Alignment explanation
Indices: 1370259--1370306 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
1370249 ATTTTTTAAT
*
1370259 AATAAAAAAATTATTTTTAATTAA
1 AATAAAAAAATTA-TTTTAATAAA
1370283 AATAAAAAAATTATTTATAA-AAA
1 AATAAAAAAATTATTT-TAATAAA
1370306 A
1 A
1370307 CTATTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AATAAAAAAATTATTTTAATAAA
Found at i:1380002 original size:2 final size:2
Alignment explanation
Indices: 1379995--1380026 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1379985 GTGCCATAGC
1379995 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
1380027 GTTTTCACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1386536 original size:21 final size:21
Alignment explanation
Indices: 1386512--1386657 Score: 100
Period size: 21 Copynumber: 7.1 Consensus size: 21
1386502 GCAAATTTGT
*
1386512 GTTGCATTTCGCGTTGCGATA
1 GTTGAATTTCGCGTTGCGATA
**
1386533 GTTGAAAATCGCGTTGCGAT-
1 GTTGAATTTCGCGTTGCGATA
* ** *
1386553 TTTCCATTTCACGTTGCGATA
1 GTTGAATTTCGCGTTGCGATA
** *
1386574 GTTGAAAATCGCGTTGAGAT-
1 GTTGAATTTCGCGTTGCGATA
* ** *
1386594 TTTCCATTTTGCGTTGCGATA
1 GTTGAATTTCGCGTTGCGATA
**
1386615 GTTGAAAATCGCGTTGCGAT-
1 GTTGAATTTCGCGTTGCGATA
* **
1386635 TTTTTATTTCGCGTTGCGATA
1 GTTGAATTTCGCGTTGCGATA
1386656 GT
1 GT
1386658 CTACAGTTGT
Statistics
Matches: 87, Mismatches: 35, Indels: 6
0.68 0.27 0.05
Matches are distributed among these distances:
20 42 0.48
21 45 0.52
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (21 bp):
GTTGAATTTCGCGTTGCGATA
Found at i:1386561 original size:41 final size:41
Alignment explanation
Indices: 1386516--1386657 Score: 239
Period size: 41 Copynumber: 3.5 Consensus size: 41
1386506 ATTTGTGTTG
1386516 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
1386557 CATTTCACGTTGCGATAGTTGAAAATCGCGTTGAGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
1386598 CATTTTGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
1386639 TATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
1386658 CTACAGTTGT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:1386698 original size:82 final size:82
Alignment explanation
Indices: 1386530--1386704 Score: 210
Period size: 82 Copynumber: 2.1 Consensus size: 82
1386520 TCGCGTTGCG
1386530 ATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACGTTGCGATAGTTGAAAATCGCGTTGAGATT
1 ATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACGTTGCGATAGTTGAAAATCGCGTTGAGATT
** * *
1386595 TTCCATTTTGCGTTGCG
66 TTCCAAATTGCGGTGCA
** * * * * *
1386612 ATAGTTGAAAATCGCGTTGCGATTTTTTATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGA
1 ATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACGTTGCGATAGT-TGAAAATCG-CGTTGAGA
1386676 TTTTCCAAATT-CGGTGCA
64 TTTTCCAAATTGCGGTGCA
*
1386694 ATAGTTAAAAA
1 ATAGTTGAAAA
1386705 AAAGATTTGT
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
82 62 0.78
83 17 0.22
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (82 bp):
ATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACGTTGCGATAGTTGAAAATCGCGTTGAGATT
TTCCAAATTGCGGTGCA
Found at i:1389135 original size:2 final size:2
Alignment explanation
Indices: 1389128--1389171 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1389118 TGCATGATAC
1389128 AT AT AT 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 AT AT AT
1389170 AT
1 AT
1389172 GCTTGGAGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1393669 original size:10 final size:10
Alignment explanation
Indices: 1393654--1393728 Score: 50
Period size: 10 Copynumber: 7.5 Consensus size: 10
1393644 CTGTTTAAGG
1393654 TATATTTTAT
1 TATATTTTAT
*
1393664 TATATTTTAA
1 TATATTTTAT
*
1393674 TATTTTTGTAT
1 TATATTT-TAT
1393685 T-TAATTTTAT
1 TAT-ATTTTAT
* *
1393695 TAAATATT-T
1 TATATTTTAT
1393704 TA-A-TTTATT
1 TATATTTTA-T
1393713 TATATTTTACT
1 TATATTTTA-T
1393724 TATAT
1 TATAT
1393729 AATTTTTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
7 2 0.04
8 1 0.02
9 6 0.12
10 25 0.50
11 16 0.32
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (10 bp):
TATATTTTAT
Found at i:1393695 original size:26 final size:25
Alignment explanation
Indices: 1393656--1393704 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1393646 GTTTAAGGTA
* *
1393656 TATTTTATTATATTTTAATATTTTTG
1 TATTTAATTATA-TTAAATATTTTTG
*
1393682 TATTTAATTTTATTAAATATTTT
1 TATTTAATTATATTAAATATTTT
1393705 AATTTATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
TATTTAATTATATTAAATATTTTTG
Found at i:1393705 original size:18 final size:16
Alignment explanation
Indices: 1393659--1393721 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 16
1393649 TAAGGTATAT
1393659 TTTATT-ATATTTTAA
1 TTTATTAATATTTTAA
**
1393674 TATT-TTTGTA-TTTAA
1 T-TTATTAATATTTTAA
1393689 TTTTATTAAATATTTTAA
1 -TTTATT-AATATTTTAA
*
1393707 TTTATTTATATTTTA
1 TTTATTAATATTTTA
1393722 CTTATATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
15 10 0.26
16 15 0.39
17 8 0.21
18 5 0.13
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTATTAATATTTTAA
Found at i:1393719 original size:33 final size:31
Alignment explanation
Indices: 1393657--1393719 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
1393647 TTTAAGGTAT
*
1393657 ATTTTATTATATTTTAATATTTTTGTATTTA
1 ATTTTATTATATTTTAATATTTTTATATTTA
1393688 ATTTTATTAAATATTTTAAT-TTATTTATATTT
1 ATTTTATT--ATATTTTAATATT-TTTATATTT
1393720 TACTTATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 8 0.29
32 2 0.07
33 18 0.64
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (31 bp):
ATTTTATTATATTTTAATATTTTTATATTTA
Found at i:1399528 original size:16 final size:16
Alignment explanation
Indices: 1399504--1399545 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1399494 TTGCAAGTAG
1399504 AATTAAAATTTATAAT
1 AATTAAAATTTATAAT
* * *
1399520 AATTCAAATATGTAAT
1 AATTAAAATTTATAAT
1399536 AATTAAAATT
1 AATTAAAATT
1399546 AATTACTATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
AATTAAAATTTATAAT
Found at i:1407091 original size:21 final size:21
Alignment explanation
Indices: 1407050--1407088 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1407040 ACCAACAAAG
*
1407050 AACAAAAACCAGTACGAGGAC
1 AACAAAAACCACTACGAGGAC
*
1407071 AACAAAAAGCACTA-GAGG
1 AACAAAAACCACTACGAGG
1407089 GACGGTAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.54, C:0.21, G:0.21, T:0.05
Consensus pattern (21 bp):
AACAAAAACCACTACGAGGAC
Found at i:1412786 original size:2 final size:2
Alignment explanation
Indices: 1412779--1412812 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1412769 TGTTATTTAA
1412779 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
1412813 CGTTAAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1413333 original size:10 final size:10
Alignment explanation
Indices: 1413292--1413327 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1413282 TCTTTCAAAT
1413292 TTTTTATTAC
1 TTTTTATTAC
1413302 TTTTTATTAC
1 TTTTTATTAC
1413312 TTTTTATT--
1 TTTTTATTAC
1413320 TTTTTATT
1 TTTTTATT
1413328 TATTTTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
10 18 0.69
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTATTAC
Found at i:1420058 original size:114 final size:114
Alignment explanation
Indices: 1419870--1420089 Score: 352
Period size: 114 Copynumber: 1.9 Consensus size: 114
1419860 CACATTCTCG
*
1419870 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
* * *
1419935 GGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTGCTCA
66 GATAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
* *
1419984 TAGTAGAAATAA-AGAGGCCCAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATCTGATCTGGTT
1 TAGTAGAAATAAGA-AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
* *
1420048 CGATAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
65 CGATAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
1420090 CTGCATGATC
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
113 1 0.01
114 96 0.99
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
GATAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
Found at i:1422217 original size:54 final size:54
Alignment explanation
Indices: 1422130--1422285 Score: 276
Period size: 54 Copynumber: 2.9 Consensus size: 54
1422120 AGAAATCTTG
* * * *
1422130 GCAGAAGCCATAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGAACATCTGA
1422184 GCAGAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGAACATCTGA
1422238 GCAGAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGAAC
1 GCAGAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGAAC
1422286 CTGCTATTCT
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 98 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.22
Consensus pattern (54 bp):
GCAGAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGAACATCTGA
Found at i:1423553 original size:182 final size:184
Alignment explanation
Indices: 1423210--1423577 Score: 614
Period size: 182 Copynumber: 2.0 Consensus size: 184
1423200 CCAATCAAAA
*
1423210 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCCTAGTTTCTCATTCAATCTTTTCTAAAAATG
1 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
* * *
1423275 AAATTGTTGAAAAGTAAGAAAACGATTTTCTTAGTTTTTTTACTTGGTAAACTATTTCCCACATC
66 AAATTATTGAAAAGTAAGAAAACGATTTCCTTAG-TTTTTTACTTAGTAAACTATTTCCCACATC
*
1423340 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGTCTTCGGGAACTTTTTGATGT
130 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGT
* **
1423395 TGTTATTTTGAAAAATAATGAGAAAACGATTTCTATAGTTTCTCATTTTATCTTTTCT-AAAATG
1 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
* *
1423459 AAATTATTGAAAAGTAAGAAAACGATTTCCTTAG-TTTTTACTTATTAAACTATTTCCTACATCT
66 AAATTATTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTACTTAGTAAACTATTTCCCACATCT
*
1423523 GTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
131 GTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGT
1423577 T
1 T
1423578 TTCAAAGCCT
Statistics
Matches: 172, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
182 80 0.47
184 38 0.22
185 54 0.31
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (184 bp):
TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
AAATTATTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTACTTAGTAAACTATTTCCCACATCT
GTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGT
Found at i:1423713 original size:75 final size:75
Alignment explanation
Indices: 1423518--1423932 Score: 704
Period size: 76 Copynumber: 5.5 Consensus size: 75
1423508 CTATTTCCTA
1423518 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1423583 AGCCTTAGGGT
66 A-CCTTCGGGT
*
1423594 CATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1423659 ACCTTCGGGT
66 ACCTTCGGGT
1423669 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1423734 AGCCTTAGGGT
66 A-CCTTCGGGT
* *
1423745 CATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1423810 ACCTTCGGGT
66 ACCTTCGGGT
*
1423820 CATTTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-
1423885 AAAACCTTCGGGT
64 -AAACCTTCGGGT
* * *
1423898 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAA
1423933 TATTTTCATC
Statistics
Matches: 321, Mismatches: 14, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
75 110 0.34
76 168 0.52
77 3 0.01
78 40 0.12
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (75 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ACCTTCGGGT
Found at i:1423792 original size:151 final size:151
Alignment explanation
Indices: 1423518--1423932 Score: 731
Period size: 151 Copynumber: 2.7 Consensus size: 151
1423508 CTATTTCCTA
1423518 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1423583 AGCCTTAGGGTCATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
1423648 GATGTTTTCAAACCTTCGGGT
131 GATGTTTTCAAACCTTCGGGT
1423669 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1423734 AGCCTTAGGGTCATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
1423799 GATGTTTTCAAACCTTCGGGT
131 GATGTTTTCAAACCTTCGGGT
*
1423820 CATTTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-
* * * * *
1423885 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
64 AAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAA
1423933 TATTTTCATC
Statistics
Matches: 252, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
151 179 0.71
152 31 0.12
153 42 0.17
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (151 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAACCTTCGGGT
Found at i:1424070 original size:3 final size:3
Alignment explanation
Indices: 1424064--1424114 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
1424054 AATAATAATA
* * *
1424064 ATT ATT ATA ATT ATT ATT AAT ATA ATAT ATT ATT ATT ATT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT A-TT ATT
1424111 ATT A
1 ATT A
1424115 AATATATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 35 0.88
4 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1424084 original size:25 final size:25
Alignment explanation
Indices: 1424056--1424106 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
1424046 TTTTTCATAA
1424056 TAATAATAAT-TATTATAATTATTAT
1 TAAT-ATAATATATTATAATTATTAT
*
1424081 TAATATAATATATTATTATTATTAT
1 TAATATAATATATTATAATTATTAT
1424106 T
1 T
1424107 TATTATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TAATATAATATATTATAATTATTAT
Found at i:1424118 original size:28 final size:28
Alignment explanation
Indices: 1424053--1424139 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 28
1424043 AATTTTTTCA
1424053 TAATAATAATA-ATTATTATAATTATTAT
1 TAAT-ATAATATATTATTATAATTATTAT
*
1424081 TAATATAATATATTATTATTATTATTTAT
1 TAATATAATATATTATTATAATTA-TTAT
*
1424110 TATTA-AATATATATATATATATATATATTA
1 TAATATAATATAT-TAT-TATA-AT-TATTA
1424140 CAAATTACAT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
27 6 0.12
28 23 0.46
29 11 0.22
30 3 0.06
31 5 0.10
32 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TAATATAATATATTATTATAATTATTAT
Found at i:1425802 original size:2 final size:2
Alignment explanation
Indices: 1425795--1425830 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1425785 TGTTATTTAA
1425795 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
1425831 TCTTTAAATT
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:1427783 original size:18 final size:17
Alignment explanation
Indices: 1427760--1427793 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1427750 TAACGAATGT
*
1427760 TATTATAGTCATTATAAA
1 TATTATAATCA-TATAAA
1427778 TATTATAATCATATAA
1 TATTATAATCATATAA
1427794 TAATAATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (17 bp):
TATTATAATCATATAAA
Found at i:1434159 original size:37 final size:36
Alignment explanation
Indices: 1434117--1434256 Score: 210
Period size: 36 Copynumber: 3.9 Consensus size: 36
1434107 CGATACATCT
* *
1434117 TTCCGTTCGATTAGAATCGGAAGTGCCGATGCTTCCC
1 TTCCGTTCGATTTGAATCGGAAGTGCCGATGCCT-CC
*
1434154 TTCCGTTCGATTTGAATCGGAAGTGCCGATGCCTAC
1 TTCCGTTCGATTTGAATCGGAAGTGCCGATGCCTCC
* *
1434190 TTCCATTCAATTTGAATCGGAAGTGCCGATGCCTCC
1 TTCCGTTCGATTTGAATCGGAAGTGCCGATGCCTCC
*
1434226 TTCCGTTCTATTTGAATCGGAAGTG-CGATGC
1 TTCCGTTCGATTTGAATCGGAAGTGCCGATGC
1434257 TTTCTTTCGT
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
35 6 0.06
36 57 0.60
37 32 0.34
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (36 bp):
TTCCGTTCGATTTGAATCGGAAGTGCCGATGCCTCC
Found at i:1437313 original size:20 final size:20
Alignment explanation
Indices: 1437288--1437325 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1437278 GACAGAGATT
1437288 AAAATAT-TAGATTATTTAAA
1 AAAATATATA-ATTATTTAAA
1437308 AAAATATATAATTATTTA
1 AAAATATATAATTATTTA
1437326 TTAGCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAATATATAATTATTTAAA
Found at i:1442175 original size:13 final size:14
Alignment explanation
Indices: 1442157--1442185 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1442147 TACTAAATCA
1442157 TTTTT-AAAATATT
1 TTTTTAAAAATATT
1442170 TTTTTAAAAATATT
1 TTTTTAAAAATATT
1442184 TT
1 TT
1442186 ATGTGTGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTAAAAATATT
Found at i:1451559 original size:20 final size:20
Alignment explanation
Indices: 1451534--1451574 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1451524 ATTTATTAAT
1451534 ATTATTATAAGTT-AAATAAA
1 ATTATTATAA-TTAAAATAAA
*
1451554 ATTATTTTAATTAAAATAAA
1 ATTATTATAATTAAAATAAA
1451574 A
1 A
1451575 AAATAAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTATTATAATTAAAATAAA
Found at i:1453870 original size:2 final size:2
Alignment explanation
Indices: 1453863--1453890 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1453853 TATTGTTAAC
1453863 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
1453891 TAAAAAATAT
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):
AT
Found at i:1460484 original size:24 final size:25
Alignment explanation
Indices: 1460435--1460498 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
1460425 ACACTCTATA
* *
1460435 TAATAAAAATATAAATTAAATTAAT
1 TAATAAAAATATAAAGTAAATAAAT
*
1460460 TAATAAAAATATGAAGT-AATAAAT
1 TAATAAAAATATAAAGTAAATAAAT
1460484 TAATAAAAATCATAA
1 TAATAAAAAT-ATAA
1460499 TATTTAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 16 0.47
25 18 0.53
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (25 bp):
TAATAAAAATATAAAGTAAATAAAT
Found at i:1460507 original size:24 final size:24
Alignment explanation
Indices: 1460435--1460493 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
1460425 ACACTCTATA
* * *
1460435 TAATAAAAATATAAATTAAATTAAT
1 TAATAAAAATATGAAGT-AATAAAT
1460460 TAATAAAAATATGAAGTAATAAAT
1 TAATAAAAATATGAAGTAATAAAT
1460484 TAATAAAAAT
1 TAATAAAAAT
1460494 CATAATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
24 16 0.52
25 15 0.48
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (24 bp):
TAATAAAAATATGAAGTAATAAAT
Found at i:1466658 original size:2 final size:2
Alignment explanation
Indices: 1466651--1466694 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1466641 CGTGTTAATC
1466651 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1466693 TA
1 TA
1466695 AAGTGTGTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1469242 original size:21 final size:21
Alignment explanation
Indices: 1469218--1469289 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
1469208 CATACATAAA
1469218 AACCACAAAATACCTTAGTTT
1 AACCACAAAATACCTTAGTTT
* *
1469239 AACCACACAAA-AACATA-TTGT
1 AACCACA-AAATACCTTAGTT-T
*
1469260 AATTCCATAAAATACCTTAGTTT
1 AA--CCACAAAATACCTTAGTTT
*
1469283 CACCACA
1 AACCACA
1469290 TGAAATACAT
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
20 2 0.05
21 18 0.47
22 6 0.16
23 10 0.26
24 2 0.05
ACGTcount: A:0.44, C:0.25, G:0.04, T:0.26
Consensus pattern (21 bp):
AACCACAAAATACCTTAGTTT
Found at i:1469607 original size:21 final size:21
Alignment explanation
Indices: 1469581--1469620 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1469571 TGTTACTGGA
*
1469581 TGAGATGAAGTTACTGCAAAC
1 TGAGATGAAGCTACTGCAAAC
*
1469602 TGAGATGAAGCTGCTGCAA
1 TGAGATGAAGCTACTGCAA
1469621 GTTGTTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.23
Consensus pattern (21 bp):
TGAGATGAAGCTACTGCAAAC
Found at i:1472071 original size:39 final size:38
Alignment explanation
Indices: 1471982--1472095 Score: 138
Period size: 39 Copynumber: 2.9 Consensus size: 38
1471972 TCAGCAATCG
* * *
1471982 ACCCACCTTCAATTGGTCCACCGTCATCACCATCAACC
1 ACCCACCTTCAACTGGACCACCATCATCACCATCAACC
**
1472020 ACCTCACCTTCAACTGGACCACCATCATCACCATCAAGTG
1 ACC-CACCTTCAACTGGACCACCATCATCACCATCAA-CC
* * *
1472060 GCCCACTTTCAACTGGCCCACCATCATCACCATCAA
1 ACCCACCTTCAACTGGACCACCATCATCACCATCAA
1472096 TTGCCCTACT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
38 3 0.05
39 61 0.92
40 2 0.03
ACGTcount: A:0.28, C:0.43, G:0.09, T:0.20
Consensus pattern (38 bp):
ACCCACCTTCAACTGGACCACCATCATCACCATCAACC
Found at i:1484081 original size:58 final size:59
Alignment explanation
Indices: 1483983--1484124 Score: 148
Period size: 58 Copynumber: 2.4 Consensus size: 59
1483973 AGATCGAATG
** * * * *
1483983 TTTAAAAGTTTGGGGATTAATTTAGAATGAAGATCGTAGTT-TGGA-GATAAAATGAAATA
1 TTTAAAAGTTTAAGGACTGATTTAGAACGAAGATCATAGTTATGGATG--AAAATGAAATA
* *
1484042 -TTAAAAGTTTAAGTACTGATTTAGAACGATAG-TCATAGTTCATGGATGAAATTGAAATA
1 TTTAAAAGTTTAAGGACTGATTTAGAACGA-AGATCATAGTT-ATGGATGAAAATGAAATA
1484101 TTTAAAAGTTTAAGGACTGATTTA
1 TTTAAAAGTTTAAGGACTGATTTA
1484125 AAATGATTCA
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
58 30 0.43
59 12 0.17
60 26 0.38
61 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.35
Consensus pattern (59 bp):
TTTAAAAGTTTAAGGACTGATTTAGAACGAAGATCATAGTTATGGATGAAAATGAAATA
Found at i:1493710 original size:15 final size:15
Alignment explanation
Indices: 1493686--1493715 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1493676 ATCATTTTAA
*
1493686 TAAAATTTAAAATAT
1 TAAAAATTAAAATAT
1493701 TAAAAATTAAAATAT
1 TAAAAATTAAAATAT
1493716 ATATATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAAATTAAAATAT
Found at i:1494723 original size:171 final size:172
Alignment explanation
Indices: 1494437--1494781 Score: 683
Period size: 171 Copynumber: 2.0 Consensus size: 172
1494427 TTAAAAAAAT
1494437 AATAAATGCGAACCAATTTAAACTCCACGACTCCACCAATCTTCAACATTTTTCTCTCACTTCAT
1 AATAAATGCGAACCAATTTAAACTCCACGACTCCACCAATCTTCAACATTTTTCTCTCACTTCAT
1494502 TTAGTTATGAATTTCTTCTCCTTAAATTAACTCTAAAACTTCTTCAAATCTTCAGTAACGTTAAC
66 TTAGTTATGAATTTCTTCTCCTTAAATTAACTCTAAAACTTCTTCAAATCTTCAGTAACGTTAAC
1494567 TTTTTTTTTTATTTAATCTTACTAATTAAACCCCAAAGATCC
131 TTTTTTTTTTATTTAATCTTACTAATTAAACCCCAAAGATCC
1494609 AATAAATGCGAACCAATTT-AACTCCACGACTCCACCAATCTTCAACATTTTTCTCTCACTTCAT
1 AATAAATGCGAACCAATTTAAACTCCACGACTCCACCAATCTTCAACATTTTTCTCTCACTTCAT
1494673 TTAGTTATGAATTTCTTCTCCTTAAATTAACTCTAAAACTTCTTCAAATCTTCAGTAACGTTAAC
66 TTAGTTATGAATTTCTTCTCCTTAAATTAACTCTAAAACTTCTTCAAATCTTCAGTAACGTTAAC
1494738 TTTTTTTTTTATTTAATCTTACTAATTAAACCCCAAAGATCC
131 TTTTTTTTTTATTTAATCTTACTAATTAAACCCCAAAGATCC
1494780 AA
1 AA
1494782 ATATGATAGC
Statistics
Matches: 173, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
171 154 0.89
172 19 0.11
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.39
Consensus pattern (172 bp):
AATAAATGCGAACCAATTTAAACTCCACGACTCCACCAATCTTCAACATTTTTCTCTCACTTCAT
TTAGTTATGAATTTCTTCTCCTTAAATTAACTCTAAAACTTCTTCAAATCTTCAGTAACGTTAAC
TTTTTTTTTTATTTAATCTTACTAATTAAACCCCAAAGATCC
Found at i:1495615 original size:96 final size:95
Alignment explanation
Indices: 1495497--1495687 Score: 373
Period size: 96 Copynumber: 2.0 Consensus size: 95
1495487 TAAGTTCAAG
1495497 GGCTGTTCATATCTTCAAGGGAGCATGCAATGAAGGGTGATTTAATTCACTTATCAAGACAATTT
1 GGCTGTTCATATCTTCAAGGGAGCATGCAATGAAGGGTGATTTAATTCACTTATCAAGACAATTT
1495562 TCAGCATGGAATAGCAAGAGTCTTCCACCC
66 TCAGCATGGAATAGCAAGAGTCTTCCACCC
1495592 GGCTGTTCATATTCTTCAAGGGAGCATGCAATGAAGGGTGATTTAATTCACTTATCAAGACAATT
1 GGCTGTTCATA-TCTTCAAGGGAGCATGCAATGAAGGGTGATTTAATTCACTTATCAAGACAATT
1495657 TTCAGCATGGAATAGCAAGAGTCTTCCACCC
65 TTCAGCATGGAATAGCAAGAGTCTTCCACCC
1495688 CTTGGACGAA
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 11 0.12
96 84 0.88
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (95 bp):
GGCTGTTCATATCTTCAAGGGAGCATGCAATGAAGGGTGATTTAATTCACTTATCAAGACAATTT
TCAGCATGGAATAGCAAGAGTCTTCCACCC
Found at i:1496516 original size:16 final size:15
Alignment explanation
Indices: 1496491--1496525 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
1496481 GGGTCAGTAC
1496491 AAAATCAAAAAGAAA
1 AAAATCAAAAAGAAA
1496506 AAAAGTCAAAAAGAAA
1 AAAA-TCAAAAAGAAA
1496522 AAAA
1 AAAA
1496526 AAGTTTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.80, C:0.06, G:0.09, T:0.06
Consensus pattern (15 bp):
AAAATCAAAAAGAAA
Found at i:1498326 original size:58 final size:57
Alignment explanation
Indices: 1498238--1498354 Score: 209
Period size: 58 Copynumber: 2.0 Consensus size: 57
1498228 TAACTGTAAT
1498238 GGCTCACGAGGAGGAGAACTAAAGGTGACCAAAC-AGTTCGAATTGCTTTCTCCATA
1 GGCTCACGAGGAGGAGAACTAAAGGTGACCAAACAAGTTCGAATTGCTTTCTCCATA
1498294 GGCTCAACGATGGAGGAGAACTAAAGGTGACCAAACAAGTTCGAATTGCTTTCTCCATA
1 GGCTC-ACGA-GGAGGAGAACTAAAGGTGACCAAACAAGTTCGAATTGCTTTCTCCATA
1498353 GG
1 GG
1498355 GAAGTACAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
56 5 0.09
57 4 0.07
58 25 0.43
59 24 0.41
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (57 bp):
GGCTCACGAGGAGGAGAACTAAAGGTGACCAAACAAGTTCGAATTGCTTTCTCCATA
Found at i:1504636 original size:34 final size:34
Alignment explanation
Indices: 1504598--1504666 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
1504588 CAATTGTACA
*
1504598 AAATATAGTCATATCTCGAATAATTTGAAGGACT
1 AAATATAATCATATCTCGAATAATTTGAAGGACT
*
1504632 AAATATAATCATATCTTGAATAATTTGAAGGACT
1 AAATATAATCATATCTCGAATAATTTGAAGGACT
1504666 A
1 A
1504667 TTCACAAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (34 bp):
AAATATAATCATATCTCGAATAATTTGAAGGACT
Found at i:1504832 original size:25 final size:25
Alignment explanation
Indices: 1504786--1504833 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1504776 AATATTTAAA
* * *
1504786 AAAAATATATATTATATTTTAAATT
1 AAAAATATATAATACATATTAAATT
*
1504811 AAAAATATTTAATACATATTAAA
1 AAAAATATATAATACATATTAAA
1504834 AGACTCGTAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
AAAAATATATAATACATATTAAATT
Found at i:1505619 original size:22 final size:22
Alignment explanation
Indices: 1505578--1505619 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1505568 TAAAAATTAA
*
1505578 AAATTAAATAGAAAATTAAATT
1 AAATTAAATAGAAAAATAAATT
1505600 AAATTAAATA-AATAAATAAA
1 AAATTAAATAGAA-AAATAAA
1505620 AAAATAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AAATTAAATAGAAAAATAAATT
Found at i:1505694 original size:2 final size:2
Alignment explanation
Indices: 1505687--1505712 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1505677 AAATAGAATA
1505687 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
1505713 CAAATAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1506949 original size:17 final size:18
Alignment explanation
Indices: 1506922--1506962 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1506912 AAAAAAAGAG
1506922 TAAATAATAAATAA-ATAA
1 TAAA-AATAAATAACATAA
1506940 TAAAAATAAATAACATAA
1 TAAAAATAAATAACATAA
1506958 TAAAA
1 TAAAA
1506963 CGAAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAAAATAAATAACATAA
Found at i:1506968 original size:18 final size:17
Alignment explanation
Indices: 1506930--1506969 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1506920 AGTAAATAAT
*
1506930 AAATAAATAATAAAAAT
1 AAATAAATAATAAAAAG
*
1506947 AAATAACATAATAAAACG
1 AAATAA-ATAATAAAAAG
1506965 AAATA
1 AAATA
1506970 TATATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (17 bp):
AAATAAATAATAAAAAG
Found at i:1506974 original size:2 final size:2
Alignment explanation
Indices: 1506967--1507024 Score: 84
Period size: 2 Copynumber: 29.0 Consensus size: 2
1506957 ATAAAACGAA
1506967 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A-T
1507010 AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1507025 TTTTAAAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.04
2 46 0.88
3 4 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1507006 original size:27 final size:27
Alignment explanation
Indices: 1506967--1507024 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
1506957 ATAAAACGAA
*
1506967 ATATATATTATATA-TATATATATATAT
1 ATATATATGATATACTATATA-ATATAT
1506994 ATATATATGATATACTATATAATATAT
1 ATATATATGATATACTATATAATATAT
1507021 ATAT
1 ATAT
1507025 TTTTAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 23 0.79
28 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
ATATATATGATATACTATATAATATAT
Found at i:1507124 original size:38 final size:36
Alignment explanation
Indices: 1507102--1507479 Score: 281
Period size: 38 Copynumber: 9.6 Consensus size: 36
1507092 ATTTTAATTT
*
1507102 TTTTTCAAAACTATATATTATATATAAGTTTTCAAAAAATG
1 TTTTT-AAAACTATATA-T-TATATAA-TTTT-TAAAAATG
*
1507143 TTTTTAAAACTATATTTTATATAATTTTTCAAAAATG
1 TTTTTAAAACTATATATTATATAATTTTT-AAAAATG
1507180 TTTTTTAAAAACTATATATTATATAATTTTTCCAAAAATG
1 -TTTTT-AAAACTATATATTATATAATTTTT--AAAAATG
* *
1507220 TTTTTAAAAGTATATATTATATAATTTTTCAAAAATA
1 TTTTTAAAACTATATATTATATAATTTTT-AAAAATG
*
1507257 TTTTTAAAAACTATATATTATATAATTTTCCCAAAAATG
1 TTTTT-AAAACTATATATTATATAATTTT--TAAAAATG
** *
1507296 TTTTTAAATGTATATATTATATAACTTTTCAAAAATG
1 TTTTTAAAACTATATATTATATAA-TTTTTAAAAATG
* * *
1507333 TTATTAAAACGTTTTAAAAGCTATATAATATATAAATATTTTCAAAACG
1 ----T------TTTTAAAA-CTATATATTATAT-AAT-TTTTAAAAATG
* *
1507382 TTTTCAAAACTATATATTATAT-ATATTTTAAAAATA
1 TTTTTAAAACTATATATTATATAAT-TTTTAAAAATG
* * * **
1507418 TTTTCAAAACTATACAATATATAAATTTTCGAAAATCG
1 TTTTTAAAACTATATATTATAT-AATTTTTAAAAAT-G
*
1507456 TTTTCTGAAAATTATATATTATAT
1 TTTT-T-AAAACTATATATTATAT
1507480 TTTGTCAAAA
Statistics
Matches: 281, Mismatches: 30, Indels: 53
0.77 0.08 0.15
Matches are distributed among these distances:
36 31 0.11
37 39 0.14
38 92 0.33
39 51 0.18
40 32 0.11
41 6 0.02
45 1 0.00
47 7 0.02
48 12 0.04
49 10 0.04
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (36 bp):
TTTTTAAAACTATATATTATATAATTTTTAAAAATG
Found at i:1507219 original size:77 final size:77
Alignment explanation
Indices: 1507101--1507334 Score: 362
Period size: 76 Copynumber: 3.0 Consensus size: 77
1507091 TATTTTAATT
* * * * *
1507101 TTTTTTCAAAACTATATATTATATATAAGTTTTCAAAAAATGTTTTTAAAACTATATTTTATATA
1 TTTTTTAAAAACTATATA-T-TATATAATTTTTCCAAAAATGTTTTTAAAAGTATATATTATATA
1507166 ATTTTTCAAAAATG
64 ATTTTTCAAAAATG
1507180 TTTTTTAAAAACTATATATTATATAATTTTTCCAAAAATGTTTTTAAAAGTATATATTATATAAT
1 TTTTTTAAAAACTATATATTATATAATTTTTCCAAAAATGTTTTTAAAAGTATATATTATATAAT
1507245 TTTTCAAAAAT-
66 TTTTCAAAAATG
* * * *
1507256 ATTTTTAAAAACTATATATTATATAATTTTCCCAAAAATGTTTTTAAATGTATATATTATATAAC
1 TTTTTTAAAAACTATATATTATATAATTTTTCCAAAAATGTTTTTAAAAGTATATATTATATAAT
1507321 TTTTCAAAAATG
66 TTTTCAAAAATG
1507333 TT
1 TT
1507335 ATTAAAACGT
Statistics
Matches: 144, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
76 72 0.50
77 54 0.38
78 1 0.01
79 17 0.12
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (77 bp):
TTTTTTAAAAACTATATATTATATAATTTTTCCAAAAATGTTTTTAAAAGTATATATTATATAAT
TTTTCAAAAATG
Found at i:1507303 original size:76 final size:75
Alignment explanation
Indices: 1507102--1507496 Score: 354
Period size: 76 Copynumber: 5.1 Consensus size: 75
1507092 ATTTTAATTT
* * * *
1507102 TTTTTCAAAACTATATATTATATATAAGTTTTCAAAAAATGTTTTTAAAACTATATTTTATATAA
1 TTTTTAAAAACTATATA-T-TATATAA-TTTTCCAAAAATGTTTTTAAAAGTATATATTATATAA
*
1507167 TTTTTCAAAAATGT
63 TTTTTCAAAAAT-A
1507181 TTTTTAAAAACTATATATTATATAATTTTTCCAAAAATGTTTTTAAAAGTATATATTATATAATT
1 TTTTTAAAAACTATATATTATATAA-TTTTCCAAAAATGTTTTTAAAAGTATATATTATATAATT
1507246 TTTCAAAAATA
65 TTTCAAAAATA
* *
1507257 TTTTTAAAAACTATATATTATATAATTTTCCCAAAAATGTTTTTAAATGTATATATTATATAACT
1 TTTTTAAAAACTATATATTATATAATTTT-CCAAAAATGTTTTTAAAAGTATATATTATATAATT
1507322 TTTCAAAAATGTTA
65 TTTCAAAAA---TA
* * * * * *
1507336 TTAAAACGTTTTAAAAGCTATATAATATATAAATATTTTC-AAAACGTTTTCAAAACTATATATT
1 -T------TTTTAAAAACTATATATTATAT-AAT-TTTCCAAAAATGTTTTTAAAAGTATATATT
1507400 ATAT-ATATTTT-AAAAATA
57 ATATAAT-TTTTCAAAAATA
* * * * *
1507418 -TTTTCAAAACTATACAATATATAAATTTT-CGAAAATCGTTTTCTGAAAATTATATATTATAT-
1 TTTTTAAAAACTATATATTATAT-AATTTTCCAAAAAT-GTTTT-T-AAAAGTATATATTATATA
* *
1507480 -TTTGTCAAAAACA
62 ATTTTTCAAAAATA
1507493 TTTT
1 TTTT
1507497 CACAAGCTAT
Statistics
Matches: 272, Mismatches: 24, Indels: 43
0.80 0.07 0.13
Matches are distributed among these distances:
72 1 0.00
73 7 0.03
74 31 0.11
75 11 0.04
76 86 0.32
77 53 0.19
78 1 0.00
79 18 0.07
80 1 0.00
82 2 0.01
85 6 0.02
86 48 0.18
87 4 0.01
88 3 0.01
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (75 bp):
TTTTTAAAAACTATATATTATATAATTTTCCAAAAATGTTTTTAAAAGTATATATTATATAATTT
TTCAAAAATA
Found at i:1507422 original size:36 final size:36
Alignment explanation
Indices: 1507338--1507479 Score: 124
Period size: 36 Copynumber: 3.8 Consensus size: 36
1507328 AAATGTTATT
* * *
1507338 AAAACGTTTT-AAAAGCTATATAATATATAAATATTTTC
1 AAAATGTTTTCAAAA-CTATAT-AT-TATATATATTTTA
*
1507376 AAAACGTTTTCAAAACTATATATTATATATATTTTA
1 AAAATGTTTTCAAAACTATATATTATATATATTTTA
* * * * *
1507412 AAAATATTTTCAAAACTATACAATATATAAATTTTCG
1 AAAATGTTTTCAAAACTATATATTATATATATTTT-A
*
1507449 AAAATCGTTTTCTGAAAATTATATATTATAT
1 AAAAT-GTTTTC--AAAACTATATATTATAT
1507480 TTTGTCAAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
36 41 0.47
37 7 0.08
38 21 0.24
39 4 0.05
40 14 0.16
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (36 bp):
AAAATGTTTTCAAAACTATATATTATATATATTTTA
Found at i:1507561 original size:14 final size:16
Alignment explanation
Indices: 1507529--1507559 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1507519 ATATATATAC
1507529 ATATAATAAAACAAAA
1 ATATAATAAAACAAAA
1507545 ATAT-ATAAAACAAAA
1 ATATAATAAAACAAAA
1507560 TAACTCCGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (16 bp):
ATATAATAAAACAAAA
Found at i:1507734 original size:32 final size:31
Alignment explanation
Indices: 1507705--1507764 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1507695 GGCCACTTTC
*
1507705 ATTTTTATTTAATTAAAGATGTGGTCACTTAT
1 ATTTTTATTTAATT-AAGATGTGATCACTTAT
*
1507737 GTTTTTATTTAATTAAGATGTGATCACT
1 ATTTTTATTTAATTAAGATGTGATCACT
1507765 GAGGGGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (31 bp):
ATTTTTATTTAATTAAGATGTGATCACTTAT
Found at i:1509593 original size:19 final size:20
Alignment explanation
Indices: 1509569--1509617 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1509559 ATATGATTTT
* * *
1509569 ATTTTGAAAGCTAAAATG-G
1 ATTTTGAAAACCAAAATGAA
1509588 ATTTTGAAAACCAAAATGAA
1 ATTTTGAAAACCAAAATGAA
1509608 ATTTTGAAAA
1 ATTTTGAAAA
1509618 AGGATTTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (20 bp):
ATTTTGAAAACCAAAATGAA
Found at i:1511581 original size:20 final size:20
Alignment explanation
Indices: 1511556--1511593 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1511546 GAAGGGTTAG
1511556 AAACACCTATCCAAGCAATC
1 AAACACCTATCCAAGCAATC
1511576 AAACACCTATCCAAGCAA
1 AAACACCTATCCAAGCAA
1511594 GCAATCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.34, G:0.05, T:0.13
Consensus pattern (20 bp):
AAACACCTATCCAAGCAATC
Found at i:1512747 original size:40 final size:40
Alignment explanation
Indices: 1512693--1512889 Score: 263
Period size: 40 Copynumber: 4.9 Consensus size: 40
1512683 CGATTAGGAA
* *
1512693 AATCGCAATGCGA-TTACGTATTCGCATTGCGATTTTCCT
1 AATCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCT
* * *
1512732 AATTCGCATTGCGATTTACGTAACCGCATTGCGATTTACGT
1 AA-TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCT
* *
1512773 AACCGCATTGCGATTTACGTAACCGCATTGCGATTTTCCT
1 AATCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCT
*
1512813 AATCGCATTGCGATTTACGTAATCGCATTGCAATTTTCCT
1 AATCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCT
* *
1512853 AATTCGTACTT-CGATTTACGTAATCGTATTGCGATTT
1 AA-TCGCA-TTGCGATTTACGTAATCGCATTGCGATTT
1512890 AGTAAATCGC
Statistics
Matches: 140, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
39 2 0.01
40 84 0.60
41 52 0.37
42 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (40 bp):
AATCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCT
Found at i:1512761 original size:20 final size:20
Alignment explanation
Indices: 1512631--1512900 Score: 235
Period size: 20 Copynumber: 13.3 Consensus size: 20
1512621 GATTCTGACT
1512631 ATCGCATTACGCGA-TTACGTAA
1 ATCGCATT--GCGATTTACGT-A
* * * *
1512653 ATCGCAATGCGAATTAGGAAA
1 ATCGCATTGCGATTTACG-TA
* * *
1512674 ATCGCAATGCGA-TTAGGAAA
1 ATCGCATTGCGATTTACG-TA
*
1512694 ATCGCAATGCGA-TTACGTA
1 ATCGCATTGCGATTTACGTA
* * *
1512713 TTCGCATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTA
1512733 ATTCGCATTGCGATTTACGTA
1 A-TCGCATTGCGATTTACGTA
*
1512754 ACCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
*
1512774 ACCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
* * *
1512794 ACCGCATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTA
1512814 ATCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
* * *
1512834 ATCGCATTGCAATTTTCCTA
1 ATCGCATTGCGATTTACGTA
*
1512854 ATTCGTACTT-CGATTTACGTA
1 A-TCGCA-TTGCGATTTACGTA
*
1512875 ATCGTATTGCGATTTA-GTAA
1 ATCGCATTGCGATTTACGT-A
1512895 ATCGCA
1 ATCGCA
1512901 ACGAGATTCT
Statistics
Matches: 214, Mismatches: 26, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
19 15 0.07
20 142 0.66
21 48 0.22
22 9 0.04
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATTTACGTA
Found at i:1513790 original size:24 final size:24
Alignment explanation
Indices: 1513763--1513816 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1513753 ATATTCGAAA
1513763 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1513787 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1513811 TTTGAT
1 TTTGAT
1513817 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1516348 original size:20 final size:20
Alignment explanation
Indices: 1516281--1516353 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
1516271 GGCAATCATT
1516281 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACACGGAAA
**
1516301 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-CA-CGGAAA
*
1516322 TGTCTATCGCAACACGGAAA
1 TGACTATCGCAACACGGAAA
1516342 TGACTATCGCAA
1 TGACTATCGCAA
1516354 TGCGTAATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
19 1 0.02
20 26 0.62
21 14 0.33
22 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
TGACTATCGCAACACGGAAA
Found at i:1516369 original size:19 final size:18
Alignment explanation
Indices: 1516347--1516445 Score: 70
Period size: 19 Copynumber: 5.8 Consensus size: 18
1516337 GGAAATGACT
1516347 ATCGCAATGCGTAATGAAA
1 ATCGCAATGCG-AATGAAA
*
1516366 ATCGCAA--CG-A-GAGA
1 ATCGCAATGCGAATGAAA
1516380 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCG-AATGAAA
**
1516399 ATCGCAA--CG-A-GGGA
1 ATCGCAATGCGAATGAAA
**
1516413 ATCGCAAAACGAAATGAAA
1 ATCGCAATGCG-AATGAAA
1516432 ATCGCAATGCGAAT
1 ATCGCAATGCGAAT
1516446 TTAGTTTCGC
Statistics
Matches: 62, Mismatches: 8, Indels: 21
0.68 0.09 0.23
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 5 0.08
19 28 0.45
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAATGAAA
Found at i:1516389 original size:33 final size:33
Alignment explanation
Indices: 1516347--1516438 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
1516337 GGAAATGACT
*
1516347 ATCGCAATGCGTAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1516380 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1516413 ATCGCAAAACGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1516439 TGCGAATTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1516492 original size:33 final size:33
Alignment explanation
Indices: 1516450--1516529 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
1516440 GCGAATTTAG
* * *
1516450 TTTCGCGTTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1516483 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
1516516 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1516530 AGTCATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:1516497 original size:19 final size:19
Alignment explanation
Indices: 1516469--1516529 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
1516459 GCGATTTTGT
*
1516469 CGTTGTGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1516488 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
1516502 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1516521 CATTGCGAT
1 CGTTGCGAT
1516530 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 10 0.30
16 3 0.09
17 3 0.09
19 17 0.52
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1516655 original size:14 final size:14
Alignment explanation
Indices: 1516636--1516672 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1516626 CATCAATTAA
1516636 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1516650 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1516664 ACAAATCAA
1 ACAAATCAA
1516673 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1518438 original size:18 final size:18
Alignment explanation
Indices: 1518417--1518480 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
1518407 AAATTCGCAA
*
1518417 TGCGATTACAGTTCGCGT
1 TGCGATTTCAGTTCGCGT
**
1518435 TGCGATTTTGGTTTCGCGT
1 TGCGATTTCAG-TTCGCGT
* *
1518454 TGCAATTTTCATTTCGCGT
1 TGCGA-TTTCAGTTCGCGT
1518473 TGCGATTT
1 TGCGATTT
1518481 TCATTCTCTC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 11 0.31
19 22 0.61
20 3 0.08
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (18 bp):
TGCGATTTCAGTTCGCGT
Found at i:1518452 original size:19 final size:19
Alignment explanation
Indices: 1518428--1518495 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
1518418 GCGATTACAG
**
1518428 TTCGCGTTGCGATTTTGGT
1 TTCGCGTTGCGATTTTCAT
*
1518447 TTCGCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
1518466 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1518485 TCTCTCGTTGC
1 T-TCGCGTTGC
1518496 TGGAACTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 35 0.81
20 8 0.19
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1518590 original size:20 final size:20
Alignment explanation
Indices: 1518565--1518621 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
1518555 TGCGATTACA
*
1518565 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTC
*
1518585 GTTTCGCGTTGC-AATTTTC
1 GTTTCGCGTTGCGATTTTTC
*
1518604 ATTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
1518622 CATTCTCTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.09, C:0.18, G:0.25, T:0.49
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTC
Found at i:1518634 original size:39 final size:39
Alignment explanation
Indices: 1518566--1518647 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
1518556 GCGATTACAG
**
1518566 TTTCGCGTTGCGATTTTTGGTTTCGCGTTGCAATTTTCA
1 TTTCGCGTTGCGATTTTTCATTTCGCGTTGCAATTTTCA
* **
1518605 TTTCGCGTTGCGA-TTTTCATTCTCTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTTTTCATT-TCGCGTTGCAATTTTCA
1518644 TTTC
1 TTTC
1518648 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 6 0.16
39 31 0.84
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.51
Consensus pattern (39 bp):
TTTCGCGTTGCGATTTTTCATTTCGCGTTGCAATTTTCA
Found at i:1518639 original size:20 final size:19
Alignment explanation
Indices: 1518566--1518647 Score: 101
Period size: 20 Copynumber: 4.2 Consensus size: 19
1518556 GCGATTACAG
**
1518566 TTTCGCGTTGCGATTTTTGG
1 TTTCGCGTTGCGA-TTTTCA
*
1518586 TTTCGCGTTGCAATTTTCA
1 TTTCGCGTTGCGATTTTCA
1518605 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* *
1518624 TTCTCTCGTTGTGATTTTCA
1 TT-TCGCGTTGCGATTTTCA
1518644 TTTC
1 TTTC
1518648 AACCAAAAGA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 26 0.47
20 29 0.53
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.51
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:1518848 original size:94 final size:94
Alignment explanation
Indices: 1518736--1519111 Score: 629
Period size: 94 Copynumber: 4.1 Consensus size: 94
1518726 ATGGATTGCA
* *
1518736 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1518800 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1518829 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1518894 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1518923 TTACTTTCAACCAAAAGACAAAACAAAGATAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1518988 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1519017 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT-AATAA-ACA-A-
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
1519077 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
1519107 TTACT
1 TTACT
1519112 AAGCAATCTA
Statistics
Matches: 272, Mismatches: 8, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
90 33 0.12
91 1 0.00
92 3 0.01
93 27 0.10
94 208 0.76
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1520811 original size:20 final size:19
Alignment explanation
Indices: 1520784--1520952 Score: 108
Period size: 14 Copynumber: 9.8 Consensus size: 19
1520774 TCTTTTGGTT
1520784 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1520803 GATAATGAAAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1520824 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1520843 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1520857 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1520876 G--A-G--AATCACAACGC
1 GAAATGAAAATCGCAACGA
*
1520890 GAAATGAAAATCGCAA--T
1 GAAATGAAAATCGCAACGA
1520907 G--A-GAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1520923 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1520937 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1520953 TGCGATTTTG
Statistics
Matches: 118, Mismatches: 13, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
14 42 0.36
15 1 0.01
16 8 0.07
17 6 0.05
19 29 0.25
20 30 0.25
21 2 0.02
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1520870 original size:33 final size:33
Alignment explanation
Indices: 1520784--1520921 Score: 168
Period size: 33 Copynumber: 4.0 Consensus size: 33
1520774 TCTTTTGGTT
1520784 GAAATGAAAATCGCAACGAGATAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAG---A-G--AATCGCAACGC
**
1520823 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1520857 GAAATGAAAATCGCAACGAGAGAATCACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1520890 GAAATGAAAATCGCAATGAGAAAATCGCAACG
1 GAAATGAAAATCGCAACGAGAGAATCGCAACG
1520922 AGAGAATCGC
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
33 59 0.66
34 11 0.12
36 1 0.01
37 1 0.01
40 18 0.20
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1520913 original size:47 final size:47
Alignment explanation
Indices: 1520862--1520954 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
1520852 AACGCGAAAT
1520862 GAAAATCGCAACGAGAGAATCACAACGCGAAATGAAAATCGCAATGA
1 GAAAATCGCAACGAGAGAATCACAACGCGAAATGAAAATCGCAATGA
*
1520909 GAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATG
1 GAAAATCGCAACGAGAGAATCACAACGCGAAATGAAAATCGCAATG
1520955 CGATTTTGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (47 bp):
GAAAATCGCAACGAGAGAATCACAACGCGAAATGAAAATCGCAATGA
Found at i:1521001 original size:33 final size:33
Alignment explanation
Indices: 1520953--1521045 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
1520943 AAAATCGCAA
**
1520953 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
1520986 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
* ** *
1521019 TACGATAGTCATTTCCACGTTGCGATT
1 TGCGATTTTCATTT-CGCGTTGCGATT
1521046 TCATTCTCGA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 41 0.79
34 11 0.21
ACGTcount: A:0.13, C:0.22, G:0.23, T:0.43
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:1521610 original size:20 final size:20
Alignment explanation
Indices: 1521587--1521829 Score: 130
Period size: 20 Copynumber: 11.7 Consensus size: 20
1521577 CGATAGTCAG
1521587 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
1521607 ATTCGCATTACGATTTTCCT
1 ATTCGCATTGCGATTTACGT
* *
1521627 AATTCGTATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
*
1521648 AATT-GCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* * *
1521668 ATTCGCATTGCGAATTATGAA
1 ATTCGCATTGCGATTTACG-T
* ** * *
1521689 AATCGCAACGCGAATACGTAAATCGCA
1 ATTCGCATTGCG-AT---T-TA-CG-T
* * * *
1521716 ATTCGCAATGCGAATTAGGAA
1 ATTCGCATTGCGATTTACG-T
* * *
1521737 AATCGCAATGCGA-ATACGT
1 ATTCGCATTGCGATTTACGT
* * *
1521756 AATCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
1521776 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* *
1521797 AATCGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
1521817 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1521830 ATTAGGAAAA
Statistics
Matches: 170, Mismatches: 42, Indels: 22
0.73 0.18 0.09
Matches are distributed among these distances:
19 15 0.09
20 77 0.45
21 60 0.35
22 2 0.01
23 1 0.01
25 1 0.01
26 2 0.01
27 12 0.07
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1521662 original size:41 final size:40
Alignment explanation
Indices: 1521587--1521680 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 40
1521577 CGATAGTCAG
*
1521587 ATTCGCATTGCGATTTACGTATTCGCATTACGATTTTCCT
1 ATTCGCATTGCGATTTACGTATTCGCATTACGATTTACCT
* * * * *
1521627 AATTCGTATTGCGATTTACTTAATT-GCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT-ATTCGCATTACGATTTACCT
1521668 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1521681 ATTATGAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 12 0.27
41 30 0.67
42 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.41
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTATTCGCATTACGATTTACCT
Found at i:1521729 original size:27 final size:28
Alignment explanation
Indices: 1521691--1521745 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1521681 ATTATGAAAA
*
1521691 TCGCAACGCGAA-TACGTAAATCGCAAT
1 TCGCAACGCGAATTACGAAAATCGCAAT
* *
1521718 TCGCAATGCGAATTAGGAAAATCGCAAT
1 TCGCAACGCGAATTACGAAAATCGCAAT
1521746 GCGAATACGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (28 bp):
TCGCAACGCGAATTACGAAAATCGCAAT
Found at i:1521739 original size:48 final size:47
Alignment explanation
Indices: 1521668--1521762 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 47
1521658 CGATTTACGT
* *
1521668 ATTCGCATTGCGAATTATGAAAATCGCAACGCGAATACGTAAATCGCA
1 ATTCGCAATGCGAATTAGGAAAATCGCAACGCGAATACGT-AATCGCA
*
1521716 ATTCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAATCGCA
1 ATTCGCAATGCGAATTAGGAAAATCGCAACGCGAATACGTAATCGCA
1521763 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 7 0.16
48 37 0.84
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (47 bp):
ATTCGCAATGCGAATTAGGAAAATCGCAACGCGAATACGTAATCGCA
Found at i:1521744 original size:21 final size:20
Alignment explanation
Indices: 1521718--1521871 Score: 85
Period size: 21 Copynumber: 7.5 Consensus size: 20
1521708 AAATCGCAAT
*
1521718 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACG-AAA
*
1521739 TCGCAATGCGAA-TACGTAA
1 TCGCAATGCGAATTACGAAA
* * * * *
1521758 TCGCATTGCGATTTTCCTAAT
1 TCGCAATGCGA-ATTACGAAA
* * *
1521779 TCGCATTGCGATTTACGTAA
1 TCGCAATGCGAATTACGAAA
* * * * *
1521799 TCGCATTGTGATTTACGTAT
1 TCGCAATGCGAATTACGAAA
* *
1521819 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTACG-AAA
* **
1521840 TCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAA-TTACGAAA
1521861 TCGCAATGCGA
1 TCGCAATGCGA
1521872 TAGTCAGAAT
Statistics
Matches: 106, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
19 12 0.11
20 40 0.38
21 50 0.47
22 4 0.04
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (20 bp):
TCGCAATGCGAATTACGAAA
Found at i:1521806 original size:41 final size:40
Alignment explanation
Indices: 1521751--1521829 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 40
1521741 GCAATGCGAA
*
1521751 TACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATT
1 TACGTAATCGCATTGCGATTTACCT-ATTCGCATTGCGATT
* *
1521792 TACGTAATCGCATTGTGATTTACGTATTCGCATTGCGA
1 TACGTAATCGCATTGCGATTTACCTATTCGCATTGCGA
1521830 ATTAGGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 13 0.37
41 22 0.63
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (40 bp):
TACGTAATCGCATTGCGATTTACCTATTCGCATTGCGATT
Found at i:1521842 original size:41 final size:41
Alignment explanation
Indices: 1521739--1521844 Score: 117
Period size: 41 Copynumber: 2.6 Consensus size: 41
1521729 ATTAGGAAAA
* * *
1521739 TCGCAATGCGAA-TACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGAATTACGAAATCGCATTGCGATTTACCTAAT
* * * *
1521779 TCGCATTGCGATTTACGTAATCGCATTGTGATTTACGT-AT
1 TCGCATTGCGAATTACGAAATCGCATTGCGATTTACCTAAT
*
1521819 TCGCATTGCGAATTAGGAAAATCGCA
1 TCGCATTGCGAATTACG-AAATCGCA
1521845 ACGCGAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
40 27 0.48
41 29 0.52
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (41 bp):
TCGCATTGCGAATTACGAAATCGCATTGCGATTTACCTAAT
Found at i:1529997 original size:47 final size:47
Alignment explanation
Indices: 1529928--1530021 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
1529918 GTATTTGGGA
1529928 ATAAGCTTGATGAGAGTGGTAATATAGTGAGAAAAAAGGCTAGACTT
1 ATAAGCTTGATGAGAGTGGTAATATAGTGAGAAAAAAGGCTAGACTT
1529975 ATAAGCTTGATGAGAGTGGTAATATAGTGAGAAAAAAGGCTAGACTT
1 ATAAGCTTGATGAGAGTGGTAATATAGTGAGAAAAAAGGCTAGACTT
1530022 GTTGCTCAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.40, C:0.06, G:0.28, T:0.26
Consensus pattern (47 bp):
ATAAGCTTGATGAGAGTGGTAATATAGTGAGAAAAAAGGCTAGACTT
Found at i:1531578 original size:21 final size:21
Alignment explanation
Indices: 1531549--1531619 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
1531539 CCTTTGAATG
*
1531549 TGCATCGATTCATCTTGCTGA
1 TGCACCGATTCATCTTGCTGA
* * *
1531570 TGCACCGATGCACGCCTTGAATG-
1 TGCACCGATTCA--TCTTG-CTGA
*
1531593 TGCATCGATTCATCTTGCTGA
1 TGCACCGATTCATCTTGCTGA
1531614 TGCACC
1 TGCACC
1531620 AATGCACGCC
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
20 2 0.05
21 19 0.51
23 14 0.38
24 2 0.05
ACGTcount: A:0.20, C:0.28, G:0.21, T:0.31
Consensus pattern (21 bp):
TGCACCGATTCATCTTGCTGA
Found at i:1531590 original size:44 final size:44
Alignment explanation
Indices: 1531525--1531645 Score: 190
Period size: 44 Copynumber: 2.7 Consensus size: 44
1531515 CACTTAACAG
*
1531525 TGCATCGATGCATC-CCTTTGAATGTGCATCGATTCATCTTGCTGA
1 TGCACCGATGCA-CGCC-TTGAATGTGCATCGATTCATCTTGCTGA
1531570 TGCACCGATGCACGCCTTGAATGTGCATCGATTCATCTTGCTGA
1 TGCACCGATGCACGCCTTGAATGTGCATCGATTCATCTTGCTGA
* *
1531614 TGCACCAATGCACGCCTTGAATGTACATCGAT
1 TGCACCGATGCACGCCTTGAATGTGCATCGAT
1531646 GCACAGGGTC
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
44 59 0.82
45 13 0.18
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (44 bp):
TGCACCGATGCACGCCTTGAATGTGCATCGATTCATCTTGCTGA
Found at i:1531596 original size:23 final size:23
Alignment explanation
Indices: 1531570--1531649 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 23
1531560 ATCTTGCTGA
1531570 TGCACCGATGCACGCCTTGAATG
1 TGCACCGATGCACGCCTTGAATG
* * * *
1531593 TGCATCGATTCA--TCTTG-CTG
1 TGCACCGATGCACGCCTTGAATG
*
1531613 ATGCACCAATGCACGCCTTGAATG
1 -TGCACCGATGCACGCCTTGAATG
* *
1531637 TACATCGATGCAC
1 TGCACCGATGCAC
1531650 AGGGTCATGC
Statistics
Matches: 41, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
20 2 0.05
21 13 0.32
23 24 0.59
24 2 0.05
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (23 bp):
TGCACCGATGCACGCCTTGAATG
Found at i:1532072 original size:2 final size:2
Alignment explanation
Indices: 1532065--1532101 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1532055 TTTGAACTTA
1532065 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1532102 ATTTTGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1534404 original size:65 final size:63
Alignment explanation
Indices: 1534335--1534494 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 63
1534325 AAATAAATTG
* *
1534335 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCATCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TG-
1534399 A
63 A
* * * *
1534400 AACATCGAATGCATTTGATGCATCGATGAACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGA
*
1534464 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
1534495 TCTTAATGCA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 1 0.01
64 29 0.34
65 50 0.59
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGA
Found at i:1536183 original size:84 final size:83
Alignment explanation
Indices: 1535842--1536459 Score: 556
Period size: 84 Copynumber: 7.4 Consensus size: 83
1535832 ATAGTGTGAT
* * * * * * * * **
1535842 TGATGTGTCATTGAGCTGAATGGAATCGAACTCGATA-AT-TTTGTTGACAGATAGCCCTTTTTT
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGA-AGGTCTTTGTTGGCAGATAACCCTTCTCG
*
1535905 CCTTGAGCTATGCTGTAAA
65 CCTTGAGCTATGCTGCAAA
** * * * * * * *
1535924 TTTTTCATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTCGGCAGATAGCCCTTCTC
1 -TGAT-GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTC
* *
1535989 GCCTTGAGCTATGTTGTAAA
64 GCCTTGAGCTATGCTGCAAA
* * * * *
1536009 TGATGTGCATTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGT
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGC
* * *
1536074 CTTGAGTTATGTTGTAAA
66 CTTGAGCTATGCTGCAAA
* * *
1536092 TGATGTGCCTTTGAGTTGAGTGTAATCGAACTCAAAGGTCCTTGATTGGCAGATAACCCTTCTCG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG-TTGGCAGATAACCCTTCTCG
* * *
1536157 ACTTAAGCTATACTGCAAA
65 CCTTGAGCTATGCTGCAAA
* * * * *
1536176 TGTTGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCAAATAACCTTTCTAG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTCG
* *
1536241 CCTTAAGTTATGCTGCAAA
65 CCTTGAGCTATGCTGCAAA
* * * ** * * * * *
1536260 TGATGTGTCTTGGAGTTGAGCATAGTCGAACTCGAAGGTCTTTTGTTGGTAAATATCCCTTCTTG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTCG
* * *
1536325 CCTTGAGATATGTTGCAAT
65 CCTTGAGCTATGCTGCAAA
* * * * * *
1536344 TGATGTTCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCTTTCTCG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTCG
* *
1536409 ACTTGAGCTATGCTGTAAA
65 CCTTGAGCTATGCTGCAAA
* * *
1536428 TGTTGTGCCTTTGAGCTGAGTATAATCAAACT
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACT
1536460 TGTAGAAAAC
Statistics
Matches: 442, Mismatches: 88, Indels: 9
0.82 0.16 0.02
Matches are distributed among these distances:
83 107 0.24
84 296 0.67
85 39 0.09
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (83 bp):
TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGC
CTTGAGCTATGCTGCAAA
Found at i:1536395 original size:252 final size:250
Alignment explanation
Indices: 1535931--1536459 Score: 639
Period size: 252 Copynumber: 2.1 Consensus size: 250
1535921 AAATTTTTCA
* * * * * * * *
1535931 TGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTCGGCAGATAGCCCTTCTCGCCTTGA
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTTTTTATCGGCAAATAACCCTTCTAGCCTTAA
* * ** *
1535996 GCTATGTTGTAAATGATGTGCATTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGA
66 GCTATGCTGCAAATGATGTGCATTGGAGCTGAGCATAATCGAACTCGAAGGTCTTGGTTGACAAA
* * * * * *
1536061 TAACCCTTCTCGTCTTGAGTTATGTTGTAAATGATGTGCCTTTGAGTTGAGTGTAATCGAACTCA
131 TAACCCTTCTCGCCTTGAGATATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCA
1536126 AAGGTCCTTGATTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGTTG
196 AAGGTCCTTGATTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGTTG
* *
1536181 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCAAATAACCTTTCTAGCCTTA
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT-TTTTATCGGCAAATAACCCTTCTAGCCTTA
* * * * **
1536246 AGTTATGCTGCAAATGATGTGTC-TTGGAGTTGAGCATAGTCGAACTCGAAGGTCTTTTGTTGGT
65 AGCTATGCTGCAAATGATGTG-CATTGGAGCTGAGCATAATCGAACTCGAAGGTC-TTGGTTGAC
* * * * *
1536310 AAATATCCCTTCTTGCCTTGAGATATGTTGCAATTGATGTTCCTTGGAGCTGAGCGTAGTCGAAC
128 AAATAACCCTTCTCGCCTTGAGATATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAAC
* * * * * * *
1536375 TCGAAGGTCTTTTG-TTGGCAGATAGCCTTTCTCGACTTGAGCTATGCTGTAAATGTTG
193 TCAAAGGTC-CTTGATTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGTTG
* *
1536433 TGCCTTTGAGCTGAGTATAATCAAACT
1 TGCCTTTGAGCTGAGTGTAATCGAACT
1536460 TGTAGAAAAC
Statistics
Matches: 234, Mismatches: 41, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
250 31 0.13
251 68 0.29
252 132 0.56
253 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (250 bp):
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTTTTTATCGGCAAATAACCCTTCTAGCCTTAA
GCTATGCTGCAAATGATGTGCATTGGAGCTGAGCATAATCGAACTCGAAGGTCTTGGTTGACAAA
TAACCCTTCTCGCCTTGAGATATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCA
AAGGTCCTTGATTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGTTG
Found at i:1536846 original size:66 final size:66
Alignment explanation
Indices: 1536756--1536916 Score: 193
Period size: 66 Copynumber: 2.5 Consensus size: 66
1536746 GAATAAATTT
* * * *
1536756 AACATCAAATGCATTTTATACATCGATGCACATACCATGCATCAATGCACTCAGGGTT-TTATGA
1 AACATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCAATGCACTCAGGCTTGTT-TGA
1536820 AA
65 AA
* * * *
1536822 AACATCGAATACATTTTATGCATCGATGCACAGGCCATGCATCGATGCACTCTGGCTTGTTTGAA
1 AACATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCAATGCACTCAGGCTTGTTTGAA
1536887 A
66 A
* * *
1536888 TAC--CGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
1536917 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 23 0.28
66 57 0.70
67 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCAATGCACTCAGGCTTGTTTGAA
A
Found at i:1537174 original size:11 final size:10
Alignment explanation
Indices: 1537158--1537201 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 10
1537148 ACAAGAATCA
1537158 AGAATCAAGAG
1 AGAATCAA-AG
1537169 AGAATC-AA-
1 AGAATCAAAG
1537177 AGAATCAAGAG
1 AGAATCAA-AG
1537188 AGAATCAAAG
1 AGAATCAAAG
1537198 AGAA
1 AGAA
1537202 AGCATCAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 6 0.20
9 2 0.07
10 8 0.27
11 14 0.47
ACGTcount: A:0.59, C:0.09, G:0.23, T:0.09
Consensus pattern (10 bp):
AGAATCAAAG
Found at i:1537181 original size:19 final size:19
Alignment explanation
Indices: 1537151--1537198 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1537141 AGAAATAACA
1537151 AGAATC-AAGAATCAAGAG
1 AGAATCAAAGAATCAAGAG
1537169 AGAATCAAAGAATCAAGAG
1 AGAATCAAAGAATCAAGAG
1537188 AGAATCAAAGA
1 AGAATCAAAGA
1537199 GAAAGCATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 6 0.21
19 23 0.79
ACGTcount: A:0.58, C:0.10, G:0.21, T:0.10
Consensus pattern (19 bp):
AGAATCAAAGAATCAAGAG
Found at i:1544744 original size:84 final size:84
Alignment explanation
Indices: 1544603--1545155 Score: 621
Period size: 84 Copynumber: 6.6 Consensus size: 84
1544593 AACTCAACAT
* * * * * * * *
1544603 AACTCGAAGGTATTTTATTAGCAGACATCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCA
1 AACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCC
*
1544668 TTGGAGCTGAGCGTAGTCA
66 TTGGAGCTGAGCGTAGTCG
* * * *
1544687 AACTCGAAGGTCTTTTGTTGGGAAATAGCCCTTCTTGCCTTGAGTTATGTTACAAATGATGTGTC
1 AACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCC
* * *
1544752 TTAGAGCTGATCGTAGTTG
66 TTGGAGCTGAGCGTAGTCG
* * * * * *
1544771 AACTCGAAGGTCTTTTGTTGGTAGATATCCCTTCTCGCCTTGAGTTATACTGCAAATGATATGCC
1 AACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCC
*
1544836 TTGGAGCTGAGTGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * * *
1544855 AACTCGAAGGTCATTTGTTGGCGAATAGCCTTTCTTGCCTTGTA-CTATGTTGCAAATGATGTGC
1 AACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTG-AGTTATGCTGCAAATGATGTGC
1544919 CTTGGAGCTGAGCGTAGT-G
65 CTTGGAGCTGAGCGTAGTCG
* * * *
1544938 AACTCGAAGGTTTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGC-AATG-TGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCC
*
1545001 TTGGAGCAGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * ** *
1545020 AACTCGAAAGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATATTGCAAATTATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCC
* * * *
1545085 TTTGAGCTAAGTGTAATCG
66 TTGGAGCTGAGCGTAGTCG
* ** * * * *
1545104 AACTCGAAGGTC-TTGGCCGACAGATAACCCTTCTCGCCTTGAGTTATGCTGC
1 AACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGCTGC
1545156 CAATAGTTTC
Statistics
Matches: 388, Mismatches: 76, Indels: 11
0.82 0.16 0.02
Matches are distributed among these distances:
81 22 0.06
82 51 0.13
83 76 0.20
84 238 0.61
85 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (84 bp):
AACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCC
TTGGAGCTGAGCGTAGTCG
Found at i:1545049 original size:165 final size:167
Alignment explanation
Indices: 1544603--1545155 Score: 718
Period size: 168 Copynumber: 3.3 Consensus size: 167
1544593 AACTCAACAT
* * * * * *
1544603 AACTCGAAGGTATTTTATTAGCAGACATCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCA
1 AACTCGAAGGTTTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCC
* * *
1544668 TTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGGAAATAGCCCTTCTTGCCTTGAGTT
66 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCT
* * *
1544733 ATGTTACAAATGATGTGTCTTAGAGCTGATCGTAGTTG
131 ATGTTGCAAATGATGTGCCTTAGAGCTGAGCGTAG-TG
* * * * * *
1544771 AACTCGAAGGTCTTTTGTTGGTAGATATCCCTTCTCGCCTTGAGTTATACTGCAAATGATATGCC
1 AACTCGAAGGTTTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCC
* * * *
1544836 TTGGAGCTGAGTGTAGTCGAACTCGAAGGTCATTTGTTGGCGAATAGCCTTTCTTGCCTTGTA-C
66 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTG-AGC
*
1544900 TATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTG
130 TATGTTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTG
1544938 AACTCGAAGGTTTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGC-AATG-TGTGCC
1 AACTCGAAGGTTTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCC
* *
1545001 TTGGAGCAGAGCGTAGTCGAACTCGAAAGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCT
66 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCT
* * * * * *
1545066 ATATTGCAAATTATGTGCCTTTGAGCTAAGTGTAATCG
131 ATGTTGCAAATGATGTGCCTTAGAGCTGAGCGTAGT-G
* * ** * *
1545104 AACTCGAAGG-TCTTGGCCGACAGATAACCCTTCTCGCCTTGAGTTATGCTGC
1 AACTCGAAGGTTTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGC
1545156 CAATAGTTTC
Statistics
Matches: 338, Mismatches: 44, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
164 1 0.00
165 128 0.38
166 15 0.04
167 50 0.15
168 143 0.42
169 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (167 bp):
AACTCGAAGGTTTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCC
TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCT
ATGTTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTG
Found at i:1545682 original size:18 final size:18
Alignment explanation
Indices: 1545661--1545695 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1545651 TGTTAGTTAG
*
1545661 AAAAAAATGAAAGTAAAT
1 AAAAAAATGAAAATAAAT
*
1545679 AAAATAATGAAAATAAA
1 AAAAAAATGAAAATAAA
1545696 ATAGAGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (18 bp):
AAAAAAATGAAAATAAAT
Found at i:1545720 original size:14 final size:14
Alignment explanation
Indices: 1545664--1545953 Score: 89
Period size: 14 Copynumber: 20.4 Consensus size: 14
1545654 TAGTTAGAAA
*
1545664 AAAATGAAAGTAAAT
1 AAAAT-AAAGAAAAT
*
1545679 AAAATAATGAAAAT
1 AAAATAAAGAAAAT
*
1545693 AAAATAGAGAAAAT
1 AAAATAAAGAAAAT
* *
1545707 AAAACAAAGCAAAT
1 AAAATAAAGAAAAT
* *
1545721 GAGATAAAGAGGAAA-
1 AAAATAAAGA--AAAT
1545736 AAAATAAAGAAAAT
1 AAAATAAAGAAAAT
* *
1545750 AAATAAAAATAAAAT
1 AAA-ATAAAGAAAAT
1545765 AAAA-AATAGATAAAGT
1 AAAATAA-AGA-AAA-T
**
1545781 AAAGATAAA-AAGGT
1 AAA-ATAAAGAAAAT
1545795 -AAATAAA-ATAAAT
1 AAAATAAAGA-AAAT
* * * *
1545808 GGAACTAAGGAAAAC
1 -AAAATAAAGAAAAT
* *
1545823 AAAAGAAATAAAGGAT
1 AAAATAAAGAAA--AT
* *
1545839 -AGATAAA-TAAAT
1 AAAATAAAGAAAAT
* *
1545851 ACAATAAACAAAAT
1 AAAATAAAGAAAAT
*
1545865 AAAGATAAA-AATAAA
1 AAA-ATAAAGAA-AAT
*
1545880 AAAATAAAAATAAAT
1 AAAATAAAGA-AAAT
* *
1545895 AACATAAATAAAA-
1 AAAATAAAGAAAAT
* *
1545908 AACATAAATAAAA-
1 AAAATAAAGAAAAT
* *
1545921 AACATAAATAAAA-
1 AAAATAAAGAAAAT
*
1545934 AAACATAAATAAAAT
1 AAA-ATAAAGAAAAT
1545949 AAAAT
1 AAAAT
1545954 TATTATAATA
Statistics
Matches: 211, Mismatches: 41, Indels: 47
0.71 0.14 0.16
Matches are distributed among these distances:
12 8 0.04
13 42 0.20
14 80 0.38
15 66 0.31
16 11 0.05
17 2 0.01
18 2 0.01
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.16
Consensus pattern (14 bp):
AAAATAAAGAAAAT
Found at i:1545764 original size:11 final size:10
Alignment explanation
Indices: 1545735--1545951 Score: 58
Period size: 10 Copynumber: 20.9 Consensus size: 10
1545725 TAAAGAGGAA
1545735 AAAAATAAA-
1 AAAAATAAAT
*
1545744 GAAAATAAAT
1 AAAAATAAAT
1545754 AAAAATAAAAT
1 AAAAAT-AAAT
*
1545765 AAAAAATAGAT
1 -AAAAATAAAT
*
1545776 AAAGTAA-AGAT
1 AAA--AATAAAT
1545787 AAAAAGGTAAAT
1 AAAAA--TAAAT
1545799 -AAAATAAAT
1 AAAAATAAAT
**
1545808 GGAACTAAGGAAA-
1 --AA--AAATAAAT
*
1545821 ACAAAAGAAAT
1 A-AAAATAAAT
* *
1545832 AAAGGATAGAT
1 AAA-AATAAAT
1545843 AAATAAATACAAT
1 AAA-A-ATA-AAT
*
1545856 AAACA-AAAT
1 AAAAATAAAT
*
1545865 AAAGATAAA-
1 AAAAATAAAT
*
1545874 AATAAAAAAAT
1 AA-AAATAAAT
1545885 AAAAATAAAT
1 AAAAATAAAT
*
1545895 -AACATAAAT
1 AAAAATAAAT
*
1545904 AAAAA-ACAT
1 AAAAATAAAT
* *
1545913 AAATAAAAAAC
1 AAA-AATAAAT
*
1545924 ATAAATAAA-
1 AAAAATAAAT
1545933 AAAACATAAAT
1 AAAA-ATAAAT
1545944 -AAAATAAA
1 AAAAATAAA
1545952 ATTATTATAA
Statistics
Matches: 156, Mismatches: 26, Indels: 52
0.67 0.11 0.22
Matches are distributed among these distances:
9 46 0.29
10 50 0.32
11 34 0.22
12 16 0.10
13 5 0.03
14 5 0.03
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:1545885 original size:20 final size:21
Alignment explanation
Indices: 1545853--1545952 Score: 77
Period size: 23 Copynumber: 4.8 Consensus size: 21
1545843 AAATAAATAC
*
1545853 AATAAACAAAATAAAGATAAA
1 AATAAACAAAATAAAAATAAA
1545874 AATAAA-AAAATAAAAAT--A
1 AATAAACAAAATAAAAATAAA
1545892 AAT-AACATAAATAAAAA-ACATA
1 AATAAACA-AAATAAAAATA-A-A
*
1545914 AATAAA-AAACATAAATAAAAAA
1 AATAAACAAA-ATAAA-AATAAA
*
1545936 ACATAAATAAAATAAAA
1 A-ATAAACAAAATAAAA
1545953 TTATTATAAT
Statistics
Matches: 66, Mismatches: 1, Indels: 23
0.73 0.01 0.26
Matches are distributed among these distances:
17 2 0.03
18 5 0.08
19 9 0.14
20 10 0.15
21 8 0.12
22 13 0.20
23 15 0.23
24 4 0.06
ACGTcount: A:0.78, C:0.05, G:0.01, T:0.16
Consensus pattern (21 bp):
AATAAACAAAATAAAAATAAA
Found at i:1545889 original size:26 final size:25
Alignment explanation
Indices: 1545860--1545952 Score: 82
Period size: 26 Copynumber: 3.6 Consensus size: 25
1545850 TACAATAAAC
1545860 AAAATAAAGATAAAAATAAAAAAATA
1 AAAATAAA-ATAAAAATAAAAAAATA
1545886 AAAAT-AAATAACATAAATAAAAAACATA
1 AAAATAAAAT-A-A-AAATAAAAAA-ATA
* * *
1545914 AATAA-AAAACATAAATAAAAAAACA
1 AA-AATAAAATAAAAATAAAAAAATA
*
1545939 TAAATAAAATAAAA
1 AAAATAAAATAAAA
1545953 TTATTATAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
24 4 0.07
25 13 0.24
26 16 0.30
27 10 0.19
28 6 0.11
29 5 0.09
ACGTcount: A:0.78, C:0.04, G:0.01, T:0.16
Consensus pattern (25 bp):
AAAATAAAATAAAAATAAAAAAATA
Found at i:1545902 original size:53 final size:51
Alignment explanation
Indices: 1545818--1545951 Score: 128
Period size: 53 Copynumber: 2.5 Consensus size: 51
1545808 GGAACTAAGG
* * * *
1545818 AAAACAAAAGAAATAAAGGATAGATAAATAAATACAATAAACA-AAATAAAGATA-
1 AAAATAAAA-AAATAAA-AATAAATAAATAAATA-AA-AAACATAAATAAA-AAAC
1545872 AAAATAAAAAAATAAAAATAAATAACATAAATAAAAAACATAAATAAAAAAC
1 AAAATAAAAAAATAAAAATAAATAA-ATAAATAAAAAACATAAATAAAAAAC
* *
1545924 ATAAATAAAAAAACATAAATAAAATAAA
1 A-AAATAAAAAAATAAAAAT-AAATAAA
1545952 ATTATTATAA
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
51 7 0.10
52 17 0.25
53 31 0.45
54 14 0.20
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (51 bp):
AAAATAAAAAAATAAAAATAAATAAATAAATAAAAAACATAAATAAAAAAC
Found at i:1545947 original size:13 final size:13
Alignment explanation
Indices: 1545873--1545947 Score: 107
Period size: 13 Copynumber: 5.6 Consensus size: 13
1545863 ATAAAGATAA
1545873 AAATAAAAAA-AT
1 AAATAAAAAACAT
*
1545885 AAAAATAAATAACAT
1 --AAATAAAAAACAT
1545900 AAATAAAAAACAT
1 AAATAAAAAACAT
1545913 AAATAAAAAACAT
1 AAATAAAAAACAT
1545926 AAATAAAAAAACAT
1 AAAT-AAAAAACAT
1545940 AAATAAAA
1 AAATAAAA
1545948 TAAAATTATT
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
13 33 0.58
14 22 0.39
15 2 0.04
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAAAAAACAT
Found at i:1546038 original size:23 final size:21
Alignment explanation
Indices: 1546012--1546067 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 21
1546002 AATACAAATA
* *
1546012 AAAAAAATAAATATAAAGGGGAT
1 AAAAAAATAAAAATAAA--GAAT
*
1546035 AAAAAGATAAAAATAAAGAAT
1 AAAAAAATAAAAATAAAGAAT
1546056 AAAAAAATAAAA
1 AAAAAAATAAAA
1546068 GGGAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 14 0.48
23 15 0.52
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (21 bp):
AAAAAAATAAAAATAAAGAAT
Found at i:1546083 original size:38 final size:38
Alignment explanation
Indices: 1545995--1546100 Score: 101
Period size: 38 Copynumber: 2.7 Consensus size: 38
1545985 ACTAAAAAGA
* * *
1545995 ATAAGAAAATACAAATAAAAA-AAATAAATATAAAGGGG
1 ATAAAAAAATAAAAATAAAAATAAA-AAATATAAAAGGG
*
1546033 ATAAAAAGATAAAAATAAAGAATAAAAAA-ATAAAAGGG
1 ATAAAAAAATAAAAATAAA-AATAAAAAATATAAAAGGG
1546071 A-AAAATAAATAAACAAATAAAATATAAAAA
1 ATAAAA-AAAT-AA-AAATAAAA-ATAAAAA
1546101 GTAAAAATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
37 4 0.07
38 28 0.49
39 8 0.14
40 17 0.30
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (38 bp):
ATAAAAAAATAAAAATAAAAATAAAAAATATAAAAGGG
Found at i:1546099 original size:25 final size:26
Alignment explanation
Indices: 1546053--1546105 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
1546043 AAAAATAAAG
*
1546053 AATAAAAAAATAAAAGGGAAAAA-TA
1 AATAAAAAAATAAAAGAGAAAAAGTA
* * *
1546078 AATAAACAAATAAAATATAAAAAGTA
1 AATAAAAAAATAAAAGAGAAAAAGTA
1546104 AA
1 AA
1546106 AATATATAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (26 bp):
AATAAAAAAATAAAAGAGAAAAAGTA
Found at i:1546107 original size:15 final size:15
Alignment explanation
Indices: 1546033--1546111 Score: 56
Period size: 15 Copynumber: 5.2 Consensus size: 15
1546023 TATAAAGGGG
1546033 ATAAAAAGATAAAAAT
1 ATAAAAAG-TAAAAAT
* *
1546049 A-AAGAA-TAAAAAA
1 ATAAAAAGTAAAAAT
* *
1546062 ATAAAAGGGAAAAAT
1 ATAAAAAGTAAAAAT
*
1546077 AAATAAACAAAT-AAAAT
1 --ATAAA-AAGTAAAAAT
1546094 ATAAAAAGTAAAAAT
1 ATAAAAAGTAAAAAT
1546109 ATA
1 ATA
1546112 TAAGAATGAT
Statistics
Matches: 47, Mismatches: 10, Indels: 13
0.67 0.14 0.19
Matches are distributed among these distances:
13 7 0.15
14 6 0.13
15 22 0.47
16 1 0.02
17 10 0.21
18 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.16
Consensus pattern (15 bp):
ATAAAAAGTAAAAAT
Found at i:1550599 original size:64 final size:64
Alignment explanation
Indices: 1550506--1550693 Score: 238
Period size: 64 Copynumber: 3.0 Consensus size: 64
1550496 GCACTCATTG
* * * * * *
1550506 ATGCATCGTTGCATTC-GGGTTTTAAGAAAACATCGAATGCATTATATGAAACGATGCACTACC
1 ATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTTTATGCATCGATGCACTACC
* * *
1550569 ATGCATCGATGCACTCAGGGTTTTATGAAAATATTGAATGCATTTTATGCATCGATGCACAGACC
1 ATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTTTATGCATCGATGCAC-TACC
* *
1550634 ATACATCGATGCACTCAGGCTTGTT-TG-AAACATCGAATGCATTTTATGCATCGATGCACT
1 ATGCATCGATGCACTCAGGGTT-TTATGAAAACATCGAATGCATTTTATGCATCGATGCACT
1550694 CTTAGTGCAC
Statistics
Matches: 108, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
63 14 0.13
64 67 0.62
65 25 0.23
66 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (64 bp):
ATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTTTATGCATCGATGCACTACC
Found at i:1556524 original size:21 final size:23
Alignment explanation
Indices: 1556493--1556552 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
1556483 ATGCATCCCT
1556493 TTGAATGTGCATCGATACA-T-C
1 TTGAATGTGCATCGATACACTCC
* *
1556514 TTGAA-GATGCACCGATGCACTCC
1 TTGAATG-TGCATCGATACACTCC
1556537 TTGAATGTGCATCGAT
1 TTGAATGTGCATCGAT
1556553 GCACACTGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
20 1 0.03
21 15 0.47
22 1 0.03
23 14 0.44
24 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (23 bp):
TTGAATGTGCATCGATACACTCC
Found at i:1556547 original size:23 final size:22
Alignment explanation
Indices: 1556493--1556556 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
1556483 ATGCATCCCT
*
1556493 TTGAATGTGCATCGATACA-TC
1 TTGAATGTGCATCGATGCACTC
*
1556514 TTGAA-GATGCACCGATGCACTCC
1 TTGAATG-TGCATCGATGCACT-C
1556537 TTGAATGTGCATCGATGCAC
1 TTGAATGTGCATCGATGCAC
1556557 ACTGCCATGC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.03
21 15 0.42
22 1 0.03
23 18 0.50
24 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (22 bp):
TTGAATGTGCATCGATGCACTC
Found at i:1559299 original size:64 final size:64
Alignment explanation
Indices: 1559206--1559393 Score: 256
Period size: 64 Copynumber: 3.0 Consensus size: 64
1559196 GCACTCATTG
* * * *
1559206 ATGCATCGATGCACT-TGGGTTTTAAGAAAACATCGAATGCATTATATGCATCAATGCACTACC
1 ATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTTTATGCATCGATGCACTACC
* * *
1559269 ATGCATCGATGCAGTCAGGGTTTTATGAAAACATTGAATGTATTTTATGCATCGATGCACATACC
1 ATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTTTATGCATCGATGCAC-TACC
* *
1559334 ATGCATCGATGCACTCAAGCTTGTT-TG-AAACATCGAATGCATTTTATGCATCGATGCACT
1 ATGCATCGATGCACTCAGGGTT-TTATGAAAACATCGAATGCATTTTATGCATCGATGCACT
1559394 CTTAGTGCAC
Statistics
Matches: 110, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
63 15 0.14
64 68 0.62
65 25 0.23
66 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (64 bp):
ATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTTTATGCATCGATGCACTACC
Found at i:1565177 original size:27 final size:27
Alignment explanation
Indices: 1565135--1565202 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
1565125 CTGTAGGAAT
1565135 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1565160 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1565187 TATAGAGATATGATTT
1 TATAGAGATATGATTT
1565203 TGCAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:1577779 original size:130 final size:132
Alignment explanation
Indices: 1577444--1577847 Score: 665
Period size: 130 Copynumber: 3.0 Consensus size: 132
1577434 TTGGGTTCTG
1577444 ATCTCCAGAAGATTGGTGCTTCTCCCATTGGATCTTGTGAATCAAGCTTAGAATGTTACATTATC
1 ATCTCCAGAAGATTGGTGCTTCTCCCATTGGATCTTGTGAATCAAGCTTAGAATGTTACATTATC
1577509 AATCGGTCTTGTGACA-CC-CAACTA-ATTTAAATAGAAATTAAATCGAAGGTGTTTTCATATTT
66 AATCGGTCTTGTGACACCCTCAACTAGATTTAAATAGAAATTAAATCGAAGGTGTTTTC--A--T
*
1577571 AATTTGGGTTCTG
127 AA------TT-TA
1577584 ATCTCCAGAAGATTGGTGCTTCTCCCATTGGATCTTGTGAATCAAGCTTAGAATGTTACATTATC
1 ATCTCCAGAAGATTGGTGCTTCTCCCATTGGATCTTGTGAATCAAGCTTAGAATGTTACATTATC
1577649 AATCGGTCTTGTGACACCCTC-ACTA-ATTTAAATAGAAATTAAATCGAAGGTGTTTTCATAATT
66 AATCGGTCTTGTGACACCCTCAACTAGATTTAAATAGAAATTAAATCGAAGGTGTTTTCATAATT
1577712 TA
131 TA
1577714 ATCTCCAGAAGATTGGTGCTTCTCCCATTGGATCTTGTGAATCAAGCTTAGAATGTTACATTATC
1 ATCTCCAGAAGATTGGTGCTTCTCCCATTGGATCTTGTGAATCAAGCTTAGAATGTTACATTATC
1577779 AATCGGTCTTGTGACACCCTCAACTAGATTTAAATAGAAATTAAATCGAAGGTGTTTTCATAATT
66 AATCGGTCTTGTGACACCCTCAACTAGATTTAAATAGAAATTAAATCGAAGGTGTTTTCATAATT
1577844 TA
131 TA
1577846 AT
1 AT
1577848 TGGAATCAAA
Statistics
Matches: 259, Mismatches: 1, Indels: 16
0.94 0.00 0.06
Matches are distributed among these distances:
130 87 0.34
131 6 0.02
132 42 0.16
137 3 0.01
139 1 0.00
140 81 0.31
141 38 0.15
142 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (132 bp):
ATCTCCAGAAGATTGGTGCTTCTCCCATTGGATCTTGTGAATCAAGCTTAGAATGTTACATTATC
AATCGGTCTTGTGACACCCTCAACTAGATTTAAATAGAAATTAAATCGAAGGTGTTTTCATAATT
TA
Found at i:1578192 original size:3 final size:3
Alignment explanation
Indices: 1578184--1578224 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1578174 ATTTTATCAT
1578184 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1578225 TTCTTATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1579571 original size:2 final size:2
Alignment explanation
Indices: 1579564--1579598 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1579554 TATTCAACCT
1579564 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 T
1579599 CAAAACGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1581091 original size:2 final size:2
Alignment explanation
Indices: 1581084--1581125 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1581074 AAATTCAAGA
1581084 AT AT AT 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 AT AT AT
1581126 TTTAAATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1586675 original size:30 final size:30
Alignment explanation
Indices: 1586641--1586700 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1586631 TAAAAAACTT
1586641 TATGATATTAATGGTTAAGGTCTTAGATAG
1 TATGATATTAATGGTTAAGGTCTTAGATAG
*
1586671 TATGATATTATTGGTTAAGGTCTTAGATAG
1 TATGATATTAATGGTTAAGGTCTTAGATAG
1586701 GCTTTCACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.23, T:0.42
Consensus pattern (30 bp):
TATGATATTAATGGTTAAGGTCTTAGATAG
Found at i:1587137 original size:2 final size:2
Alignment explanation
Indices: 1587132--1587157 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1587122 AAATATGAAG
1587132 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
1587158 CGTTATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1589081 original size:15 final size:16
Alignment explanation
Indices: 1589042--1589082 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1589032 CAATAGCCTC
* *
1589042 TGAATCATTCAGCATT
1 TGAATCATTCAACACT
1589058 TGAATCATTCAACACT
1 TGAATCATTCAACACT
1589074 TG-ATCATTC
1 TGAATCATTC
1589083 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAACACT
Found at i:1589807 original size:30 final size:29
Alignment explanation
Indices: 1589741--1589883 Score: 103
Period size: 30 Copynumber: 4.8 Consensus size: 29
1589731 TAAAAATATT
* * * *
1589741 TTTAAATTAAGAATATATATATATATATTAA
1 TTTAAA-TAATAATA-AAATATATTTAATAA
*
1589772 GTTAAATCAATAATAAAATATATTTAATAA
1 TTTAAAT-AATAATAAAATATATTTAATAA
* *
1589802 TTTAAAATAATAATATAATATAATTAATAA
1 TTT-AAATAATAATAAAATATATTTAATAA
* * * *
1589832 ATTAAGATAA-AAT-ATATAAATTCAA-AA
1 TTTAA-ATAATAATAAAATATATTTAATAA
*
1589859 TTGAAAATAATAATAAAATATATTT
1 TT-TAAATAATAATAAAATATATTT
1589884 TAGATTTAAA
Statistics
Matches: 87, Mismatches: 19, Indels: 14
0.73 0.16 0.12
Matches are distributed among these distances:
27 7 0.08
28 12 0.14
29 12 0.14
30 41 0.47
31 15 0.17
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (29 bp):
TTTAAATAATAATAAAATATATTTAATAA
Done.