Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008798.1 Hibiscus syriacus cultivar Beakdansim tig00111947_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: 1825372
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1518739 original size:30 final size:30
Alignment explanation
Indices: 1518596--1518722 Score: 206
Period size: 30 Copynumber: 4.3 Consensus size: 30
1518586 GAAGGACCTA
1518596 TCCAGAGGTCACAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGATCCTCGGTAACTG
1518626 TCCAGAGGTCACAAAGATCCTC-GTAACTG
1 TCCAGAGGTCACAAAGATCCTCGGTAACTG
*
1518655 TCC--AGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGATCCTCGGTAACTG
*
1518683 TCAAGAGGTCACAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGATCCTCGGTAACTG
*
1518713 TCCATAGGTC
1 TCCAGAGGTC
1518723 CCGAAGAACC
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
27 16 0.18
28 9 0.10
29 10 0.11
30 54 0.61
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGATCCTCGGTAACTG
Found at i:1519761 original size:21 final size:20
Alignment explanation
Indices: 1519731--1519774 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
1519721 ATTCTGTCGT
*
1519731 TTGAAGGGTATCGATTCCCC
1 TTGAAGGGTACCGATTCCCC
1519751 TTGAATGGGTACCGATTCCCC
1 TTGAA-GGGTACCGATTCCCC
1519772 TTG
1 TTG
1519775 CCCAAAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (20 bp):
TTGAAGGGTACCGATTCCCC
Found at i:1522413 original size:30 final size:30
Alignment explanation
Indices: 1522267--1522396 Score: 242
Period size: 30 Copynumber: 4.3 Consensus size: 30
1522257 GAAGGACCTA
1522267 TCCAGAGGTCACAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGATCCTCGGTAACTG
1522297 TCCAGAGGTCACAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGATCCTCGGTAACTG
*
1522327 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGATCCTCGGTAACTG
1522357 TCCAGAGGTCACAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGATCCTCGGTAACTG
*
1522387 TCCATAGGTC
1 TCCAGAGGTC
1522397 CCGAAGAACC
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 97 1.00
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGATCCTCGGTAACTG
Found at i:1523444 original size:21 final size:21
Alignment explanation
Indices: 1523420--1523464 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1523410 ATTCTGTCGT
*
1523420 TTGAAGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1523441 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1523462 TTG
1 TTG
1523465 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1524677 original size:47 final size:48
Alignment explanation
Indices: 1524592--1524688 Score: 119
Period size: 47 Copynumber: 2.0 Consensus size: 48
1524582 AGAAGACTCA
* *
1524592 AAATTTATTCACTTTAAAATCTTATTCGAACATGTTAAGAAAATATTT
1 AAATTCATTCACTTTAAAATCTTATTCGAACATATTAAGAAAATATTT
* *
1524640 AAATTCATTCTCTTT-AAATCTTA-TCGGAATC-TATTAAGAAAATCTTT
1 AAATTCATTCACTTTAAAATCTTATTC-GAA-CATATTAAGAAAATATTT
1524687 AA
1 AA
1524689 GTTTGAATCC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
46 2 0.05
47 27 0.63
48 14 0.33
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.41
Consensus pattern (48 bp):
AAATTCATTCACTTTAAAATCTTATTCGAACATATTAAGAAAATATTT
Found at i:1530156 original size:16 final size:16
Alignment explanation
Indices: 1530135--1530177 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
1530125 CATTTAATAA
1530135 ATAAACGAACATGAAC
1 ATAAACGAACATGAAC
1530151 ATAAACGAACATGAAC
1 ATAAACGAACATGAAC
1530167 ATAAACGAACA
1 ATAAACGAACA
1530178 AATTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.12
Consensus pattern (16 bp):
ATAAACGAACATGAAC
Found at i:1536634 original size:39 final size:40
Alignment explanation
Indices: 1536558--1536639 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 40
1536548 AAATAAACAA
*
1536558 AAATTGGGACACTGTTGTGAAGCATATTCGACCTGATC-G
1 AAATTGGGACACTATTGTGAAGCATATTCGACCTGATCAG
* * *
1536597 AAATTGGGACATTATTGTGAAGCGT-TTCGGACGTGATCAG
1 AAATTGGGACACTATTGTGAAGCATATTC-GACCTGATCAG
1536637 AAA
1 AAA
1536640 GTCTTTGCTG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 3 0.08
39 30 0.81
40 4 0.11
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (40 bp):
AAATTGGGACACTATTGTGAAGCATATTCGACCTGATCAG
Found at i:1537493 original size:14 final size:15
Alignment explanation
Indices: 1537451--1537483 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1537441 TTAATTCAAG
*
1537451 AATAAATAATAAAAA
1 AATATATAATAAAAA
1537466 AATATATAATAAAAA
1 AATATATAATAAAAA
1537481 AAT
1 AAT
1537484 CATTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AATATATAATAAAAA
Found at i:1537508 original size:28 final size:28
Alignment explanation
Indices: 1537476--1537537 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
1537466 AATATATAAT
1537476 AAAAAAATCA-TTATA-AAATTAAAGATA
1 AAAAAAAT-ATTTATATAAATTAAAGATA
*
1537503 GAAAAAAATATTTTTATAAATTAAAGATA
1 -AAAAAAATATTTATATAAATTAAAGATA
1537532 AAAAAA
1 AAAAAA
1537538 TAAGTTTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 1 0.03
28 18 0.58
29 12 0.39
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (28 bp):
AAAAAAATATTTATATAAATTAAAGATA
Found at i:1537508 original size:29 final size:28
Alignment explanation
Indices: 1537471--1537537 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
1537461 AAAAAAATAT
1537471 ATAATAAAAAA-ATCATTATAAAATTAAAG
1 ATAA-AAAAAATATCATTAT-AAATTAAAG
**
1537500 ATAGAAAAAAATATTTTTATAAATTAAAG
1 ATA-AAAAAAATATCATTATAAATTAAAG
1537529 ATAAAAAAA
1 ATAAAAAAA
1537538 TAAGTTTACT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 6 0.18
29 21 0.62
30 7 0.21
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (28 bp):
ATAAAAAAAATATCATTATAAATTAAAG
Found at i:1538089 original size:38 final size:37
Alignment explanation
Indices: 1538021--1538157 Score: 159
Period size: 38 Copynumber: 3.7 Consensus size: 37
1538011 ATTCTATTCG
* * **
1538021 AATATAAATTAAT-AATAATATACTTATATTTTAATTG
1 AATATAAATTTATAAATAATATATTTATA-TTTAATAA
* * *
1538058 AATATAAATTCATCAATAATATATTTTTATTTAATAA
1 AATATAAATTTATAAATAATATATTTATATTTAATAA
* * *
1538095 AATATAAATTTATAAATAATATATTCATAATTCAATCA
1 AATATAAATTTATAAATAATATATTTAT-ATTTAATAA
1538133 AATATAAATTTATAAATAATATATT
1 AATATAAATTTATAAATAATATATT
1538158 CCAATTTGAA
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
37 42 0.48
38 45 0.52
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
AATATAAATTTATAAATAATATATTTATATTTAATAA
Found at i:1538158 original size:38 final size:37
Alignment explanation
Indices: 1538021--1538157 Score: 159
Period size: 37 Copynumber: 3.7 Consensus size: 37
1538011 ATTCTATTCG
* * **
1538021 AATATAAATTAAT-AATAATATACTTATATTTTAATTG
1 AATATAAATTTATAAATAATATA-TTATAATTTAATAA
* * * *
1538058 AATATAAATTCATCAATAATATATTTTTATTTAATAA
1 AATATAAATTTATAAATAATATATTATAATTTAATAA
* *
1538095 AATATAAATTTATAAATAATATATTCATAATTCAATCA
1 AATATAAATTTATAAATAATATATT-ATAATTTAATAA
1538133 AATATAAATTTATAAATAATATATT
1 AATATAAATTTATAAATAATATATT
1538158 CCAATTTGAA
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
37 44 0.51
38 42 0.49
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
AATATAAATTTATAAATAATATATTATAATTTAATAA
Found at i:1541427 original size:37 final size:37
Alignment explanation
Indices: 1541386--1541570 Score: 194
Period size: 38 Copynumber: 4.9 Consensus size: 37
1541376 CTACAATATC
* *
1541386 GTATTCTAATCGAATATAAATTCCT-AATAATATATTT
1 GTATT-TAATTGAATATAAATTCATAAATAATATATTT
* *
1541423 GTATTTTAATTAAATATGAATTCATAAATAATATATTT
1 GTA-TTTAATTGAATATAAATTCATAAATAATATATTT
* ** *
1541461 GTACTTAATCAAATATAAATTTATAAATAATATATTT
1 GTATTTAATTGAATATAAATTCATAAATAATATATTT
* *
1541498 CTATTTCAATTGAATATAAATTCGTAAATAATATATTT
1 GTATTT-AATTGAATATAAATTCATAAATAATATATTT
* * *
1541536 -TAATTTAAATTGAATATAAATCCTTGAATAATATA
1 GT-ATTT-AATTGAATATAAATTCATAAATAATATA
1541571 ATATTATCCT
Statistics
Matches: 126, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
37 53 0.42
38 73 0.58
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (37 bp):
GTATTTAATTGAATATAAATTCATAAATAATATATTT
Found at i:1541503 original size:75 final size:74
Alignment explanation
Indices: 1541392--1541535 Score: 207
Period size: 75 Copynumber: 1.9 Consensus size: 74
1541382 TATCGTATTC
* * * * *
1541392 TAATCGAATATAAATTCCTAATAATATATTTGTATTTTAATTAAATATGAATTCATAAATAATAT
1 TAATCAAATATAAATTCATAATAATATATTTCTATTTCAATTAAATATAAATTCATAAATAATAT
1541457 ATTTGTACT
66 ATTTGTACT
* * *
1541466 TAATCAAATATAAATTTATAAATAATATATTTCTATTTCAATTGAATATAAATTCGTAAATAATA
1 TAATCAAATATAAATTCAT-AATAATATATTTCTATTTCAATTAAATATAAATTCATAAATAATA
1541531 TATTT
65 TATTT
1541536 TAATTTAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
74 16 0.26
75 45 0.74
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (74 bp):
TAATCAAATATAAATTCATAATAATATATTTCTATTTCAATTAAATATAAATTCATAAATAATAT
ATTTGTACT
Found at i:1541960 original size:21 final size:21
Alignment explanation
Indices: 1541934--1541973 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1541924 GACTATCGCA
1541934 TTGCGATTTCCCAAATTCGTG
1 TTGCGATTTCCCAAATTCGTG
* *
1541955 TTGCGATTTTCCTAATTCG
1 TTGCGATTTCCCAAATTCG
1541974 CAATGCGAAT
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:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGTG
Found at i:1541980 original size:21 final size:21
Alignment explanation
Indices: 1541929--1541981 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1541919 ATTCTGACTA
1541929 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
** * *
1541950 TCGTGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1541971 TCGCAATGCGA
1 TCGCATTGCGA
1541982 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1541996 original size:20 final size:20
Alignment explanation
Indices: 1541971--1542137 Score: 248
Period size: 20 Copynumber: 8.3 Consensus size: 20
1541961 TTTTCCTAAT
1541971 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * **
1541991 TCGCAACGTGAATTTGGTAAA
1 TCGCAATGCGAA-TACGTAAA
*
1542012 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
1542032 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1542052 TCGCAATGCG-ATCACGTAAA
1 TCGCAATGCGAAT-ACGTAAA
1542072 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1542092 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1542112 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
1542132 TCGCAA
1 TCGCAA
1542138 CCAGAATCTG
Statistics
Matches: 133, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
19 3 0.02
20 113 0.85
21 17 0.13
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1542155 original size:60 final size:60
Alignment explanation
Indices: 1541971--1542158 Score: 201
Period size: 60 Copynumber: 3.1 Consensus size: 60
1541961 TTTTCCTAAT
* * *
1541971 TCGCAATGCGAATACGTAAATCGCAACGTGAATTTGGTAAATCGCAATGCG-AT-T-ACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATCT-GTAAATCGCAATGCGAATCTGAC-T--A
* *
1542032 TCGCAATGCGAATACGTAAATCGCAATGCG-ATCACGTAAATCGCAATGCGAATAC-GTA-AA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATC-TGTAAATCGCAATGCGAAT-CTG-ACTA
*
1542092 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTAAATCGCAA-CCAGAATCTGACTA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTAAATCGCAATGC-GAATCTGACTA
1542152 TCGCAAT
1 TCGCAAT
1542159 ACTGAATTTC
Statistics
Matches: 109, Mismatches: 8, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
59 3 0.03
60 72 0.66
61 33 0.30
64 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTAAATCGCAATGCGAATCTGACTA
Found at i:1543026 original size:24 final size:24
Alignment explanation
Indices: 1542999--1543052 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1542989 GTATTCGAAA
1542999 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1543023 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1543047 TTTGAT
1 TTTGAT
1543053 GATTTTTTAG
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:1545526 original size:20 final size:20
Alignment explanation
Indices: 1545484--1545568 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
1545474 CAACGCGGAA
1545484 ATCGCAACGC-GAATATG-CT
1 ATCGCAACGCGGAA-ATGACT
*
1545503 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
1545523 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
*
1545543 ATCGCAACGCAGAAATGACT
1 ATCGCAACGCGGAAATGACT
1545563 ATCGCA
1 ATCGCA
1545569 TTGCGATTCA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
19 12 0.21
20 45 0.79
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:1545606 original size:33 final size:33
Alignment explanation
Indices: 1545564--1545631 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
1545554 GAAATGACTA
**
1545564 TCGCATTGCGATTCACTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCACTCGTTGCGATAGTCATT
**
1545597 TCGCATTGCGATTTTCTCGTTGCGATAGTCATT
1 TCGCATTGCGATTCACTCGTTGCGATAGTCATT
1545630 TC
1 TC
1545632 CGCGTTGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.43
Consensus pattern (33 bp):
TCGCATTGCGATTCACTCGTTGCGATAGTCATT
Found at i:1545763 original size:14 final size:14
Alignment explanation
Indices: 1545744--1545780 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1545734 CATCAATTAA
1545744 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1545758 ACAAATCATCTTTT
1 ACAAATCAACATTT
1545772 ACAAATCAA
1 ACAAATCAA
1545781 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1547746 original size:20 final size:20
Alignment explanation
Indices: 1547732--1547776 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1547722 AAATCACAAC
1547732 GCGAAAATGACAATCGCAAT
1 GCGAAAATGACAATCGCAAT
*
1547752 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACAATCGCAAT
1547772 GCGAA
1 GCGAA
1547777 TTTAACTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (20 bp):
GCGAAAATGACAATCGCAAT
Found at i:1547784 original size:20 final size:20
Alignment explanation
Indices: 1547732--1547790 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1547722 AAATCACAAC
* *
1547732 GCGAAAATGACAATCGCAAT
1 GCGAAAATAACTATCGCAAT
*
1547752 GCGAAAATGACTATCGCAAT
1 GCGAAAATAACTATCGCAAT
**
1547772 GCGAATTTAACTATCGCAA
1 GCGAAAATAACTATCGCAA
1547791 CGAGAGAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (20 bp):
GCGAAAATAACTATCGCAAT
Found at i:1547856 original size:20 final size:20
Alignment explanation
Indices: 1547831--1547879 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1547821 CAACAACAAA
1547831 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1547851 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1547871 ATCGCAACG
1 ATCGCAACG
1547880 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1547947 original size:20 final size:20
Alignment explanation
Indices: 1547922--1548067 Score: 187
Period size: 20 Copynumber: 7.6 Consensus size: 20
1547912 GCAATTCTTT
**
1547922 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
* *
1547942 CATTGCGATAGTCAGTTTCT
1 CATTGCGATAGTCATTTTCG
1547962 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
1547982 CATTGCGATAGTCATTTTTG
1 CATTGCGATAGTCATTTTCG
*
1548002 CATTGCGAT--TC--TCTCG
1 CATTGCGATAGTCATTTTCG
1548018 --TTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
1548036 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
1548056 CATTGCGATAGT
1 CATTGCGATAGT
1548068 AAACTATTAT
Statistics
Matches: 110, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
14 7 0.06
16 5 0.05
18 6 0.05
20 92 0.84
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:1548022 original size:94 final size:93
Alignment explanation
Indices: 1547886--1548067 Score: 256
Period size: 94 Copynumber: 1.9 Consensus size: 93
1547876 AACGAGAGAA
** *
1547886 TCGCAATGCGATTTTCATTTTGCATTGCAATTCTTTCATTGCGATAGTCAAATTCGCATTGCGAT
1 TCGCAATGCGATAGTCATTTTGCATTGCAATTCTCTCATTGCGATAGTCAAATTCGCATTGCGAT
*
1547951 AGTCAGTTTCTCATTGCGATAGTCATTT
66 AGTCAGTTTCGCATTGCGATAGTCATTT
* * * ** *
1547979 TCGCATTGCGATAGTCATTTTTGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGA
1 TCGCAATGCGATAGTCA-TTTTGCATTGCAATTCTCTCATTGCGATAGTCAAATTCGCATTGCGA
*
1548044 TAGTCATTTTCGCATTGCGATAGT
65 TAGTCAGTTTCGCATTGCGATAGT
1548068 AAACTATTAT
Statistics
Matches: 77, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
93 14 0.18
94 63 0.82
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (93 bp):
TCGCAATGCGATAGTCATTTTGCATTGCAATTCTCTCATTGCGATAGTCAAATTCGCATTGCGAT
AGTCAGTTTCGCATTGCGATAGTCATTT
Found at i:1548027 original size:54 final size:54
Alignment explanation
Indices: 1547922--1548064 Score: 187
Period size: 54 Copynumber: 2.5 Consensus size: 54
1547912 GCAATTCTTT
**
1547922 CATTGCGATAGTCAAATTCGCATTGCGATAGTCAGTTTCTCATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCGCATTGCGAT--TC----TCTCATTGCGATAGTCATTTTCG
* *
1547982 CATTGCGATAGTCATTTTTGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCGCATTGCGATTCTCTCATTGCGATAGTCATTTTCG
*
1548036 CGTTGCGATAGTCATTTTCGCATTGCGAT
1 CATTGCGATAGTCATTTTCGCATTGCGAT
1548065 AGTAAACTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
54 49 0.64
58 2 0.03
60 26 0.34
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (54 bp):
CATTGCGATAGTCATTTTCGCATTGCGATTCTCTCATTGCGATAGTCATTTTCG
Found at i:1549972 original size:20 final size:20
Alignment explanation
Indices: 1549949--1550012 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
1549939 CTGAAACTTT
1549949 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
1549969 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
1549989 CTATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGA
1550008 AAATC
1 AAATC
1550013 ACATTGCTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 9 0.23
20 30 0.77
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:1550055 original size:20 final size:20
Alignment explanation
Indices: 1550030--1550076 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1550020 TATTCTCTCG
1550030 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
1550050 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
1550070 TTGCGAT
1 TTGCGAT
1550077 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:1550726 original size:20 final size:20
Alignment explanation
Indices: 1550650--1550722 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
1550640 TGTAAATCGC
1550650 ACGTAATCGCATTACGATTT
1 ACGTAATCGCATTACGATTT
1550670 ACGTAATCGCATTACGATTT
1 ACGTAATCGCATTACGATTT
* *
1550690 ACGTAATCGCGTTGCGATTT
1 ACGTAATCGCATTACGATTT
*
1550710 ACGTATTCGCATT
1 ACGTAATCGCATT
1550723 GCGAATTAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (20 bp):
ACGTAATCGCATTACGATTT
Found at i:1550747 original size:21 final size:21
Alignment explanation
Indices: 1550723--1550768 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1550713 TATTCGCATT
1550723 GCGAATTAGGAAAACCGCAAC
1 GCGAATTAGGAAAACCGCAAC
* * * *
1550744 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAACCGCAAC
1550765 GCGA
1 GCGA
1550769 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.28, T:0.15
Consensus pattern (21 bp):
GCGAATTAGGAAAACCGCAAC
Found at i:1553358 original size:12 final size:12
Alignment explanation
Indices: 1553341--1553365 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1553331 ATATAAGTGA
1553341 TATTTTTTAAAT
1 TATTTTTTAAAT
1553353 TATTTTTTAAAT
1 TATTTTTTAAAT
1553365 T
1 T
1553366 TTTGCCTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTTTTAAAT
Found at i:1553747 original size:17 final size:17
Alignment explanation
Indices: 1553725--1553758 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1553715 TCTAGAAAGA
*
1553725 TTTTTTT-TTTAAGATT
1 TTTTTTTATTTAAAATT
1553741 TTTTTTTATTTAAAATT
1 TTTTTTTATTTAAAATT
1553758 T
1 T
1553759 ATTTAAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTTTATTTAAAATT
Found at i:1553748 original size:13 final size:14
Alignment explanation
Indices: 1553721--1553747 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1553711 TTAATCTAGA
1553721 AAGATTTTTTTTTT
1 AAGATTTTTTTTTT
1553735 AAGATTTTTTTTT
1 AAGATTTTTTTTT
1553748 ATTTAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (14 bp):
AAGATTTTTTTTTT
Found at i:1555525 original size:119 final size:119
Alignment explanation
Indices: 1555310--1555545 Score: 404
Period size: 119 Copynumber: 2.0 Consensus size: 119
1555300 GTTTCACTTA
1555310 TACAATGTACCTCTTGAACTCTATTTAGGAACTGGTTTAGGATACATTGTTAGTGCAATAGGTGA
1 TACAATGTACCTCTTGAACTCTATTTAGGAACTGGTTTAGGATACATTGTTAGTGCAATAGGTGA
* *
1555375 CCATCTTTACATGGATTTTGTCACAGATTCTAGGAAAAGATT-GAAGTATGCTTT
66 CCATATTTACATAGATTTTGTCACAGATTCTAGGAAAAGATTAG-AGTATGCTTT
*
1555429 TACAATGTACCTCTTGAACTCTATTTAGGAACTGGTTTAGGCTACATTGTTAGTGCAATAGGTGA
1 TACAATGTACCTCTTGAACTCTATTTAGGAACTGGTTTAGGATACATTGTTAGTGCAATAGGTGA
*
1555494 CCCTATTTACATAGATTTTGTCACA-ACTTCTAGGAAAAGATTAGAGTATGCT
66 CCATATTTACATAGATTTTGTCACAGA-TTCTAGGAAAAGATTAGAGTATGCT
1555546 AAAATTTGTG
Statistics
Matches: 111, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
118 1 0.01
119 109 0.98
120 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (119 bp):
TACAATGTACCTCTTGAACTCTATTTAGGAACTGGTTTAGGATACATTGTTAGTGCAATAGGTGA
CCATATTTACATAGATTTTGTCACAGATTCTAGGAAAAGATTAGAGTATGCTTT
Found at i:1562309 original size:20 final size:20
Alignment explanation
Indices: 1562284--1562324 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1562274 TTATTTATTA
*
1562284 ACTCATATATAAGCTTGTTT
1 ACTCATATATAAGCTCGTTT
1562304 ACTCATATATAAGCTCGTTT
1 ACTCATATATAAGCTCGTTT
1562324 A
1 A
1562325 TCAACTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (20 bp):
ACTCATATATAAGCTCGTTT
Found at i:1565987 original size:2 final size:2
Alignment explanation
Indices: 1565980--1566017 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1565970 ACAACTTTTA
1565980 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
1566018 TTCAAATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1566381 original size:20 final size:20
Alignment explanation
Indices: 1566353--1566395 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1566343 ACCACCGATA
* * *
1566353 TTCTTTATTGTATTTTTATT
1 TTCTATATTATATCTTTATT
1566373 TTCTATATTATATCTTTATT
1 TTCTATATTATATCTTTATT
1566393 TTC
1 TTC
1566396 CTTTACTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (20 bp):
TTCTATATTATATCTTTATT
Found at i:1566462 original size:23 final size:23
Alignment explanation
Indices: 1566436--1566485 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
1566426 GTGTTGCACG
*
1566436 TTTTCATT-TGCTTTTATGATATA
1 TTTTCATTATGCTTTT-TGACATA
*
1566459 TTTT-TTTATGCTTTTTGACATA
1 TTTTCATTATGCTTTTTGACATA
1566481 TTTTC
1 TTTTC
1566486 GATTCTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.18, C:0.10, G:0.08, T:0.64
Consensus pattern (23 bp):
TTTTCATTATGCTTTTTGACATA
Found at i:1568663 original size:3 final size:3
Alignment explanation
Indices: 1568651--1568686 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
1568641 TTAATCCGAT
1568651 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
1568687 TTATTATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1571589 original size:3 final size:3
Alignment explanation
Indices: 1571581--1571605 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1571571 TTAATCCAAG
1571581 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1571606 ATATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1580486 original size:23 final size:23
Alignment explanation
Indices: 1580458--1580503 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1580448 AATATGTTCG
* *
1580458 CGAATGTTAAATTAACATTTTCA
1 CGAATGTTAAAATAACATATTCA
1580481 CGAATGTTAAAATAACATATTCA
1 CGAATGTTAAAATAACATATTCA
1580504 TGAACGCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (23 bp):
CGAATGTTAAAATAACATATTCA
Found at i:1580514 original size:23 final size:23
Alignment explanation
Indices: 1580465--1580514 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
1580455 TCGCGAATGT
* * * *
1580465 TAAATTAACATTTTCACGAATGT
1 TAAAATAACATATTCACGAACGC
*
1580488 TAAAATAACATATTCATGAACGC
1 TAAAATAACATATTCACGAACGC
1580511 TAAA
1 TAAA
1580515 TGAATAAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (23 bp):
TAAAATAACATATTCACGAACGC
Found at i:1581462 original size:17 final size:18
Alignment explanation
Indices: 1581426--1581466 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1581416 ATATTATGTA
*
1581426 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
1581444 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
1581461 TTTACT
1 TTTACT
1581467 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:1583769 original size:26 final size:24
Alignment explanation
Indices: 1583679--1583770 Score: 66
Period size: 25 Copynumber: 3.8 Consensus size: 24
1583669 CATCGATATA
* * *
1583679 TTTATTTTATTATATTTGTATTTAC
1 TTTATTTTGTTAAATTT-AATTTAC
1583704 TTTATTTTGTTAAATTGTAATTT--
1 TTTATTTTGTTAAATT-TAATTTAC
*
1583727 TTTATTATT-TCT-CATTTAATACTTAC
1 TTTATT-TTGT-TAAATTTAAT--TTAC
1583753 TTTATTTTGTTAAATTTA
1 TTTATTTTGTTAAATTTA
1583771 TTGGGCTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 17
0.71 0.07 0.23
Matches are distributed among these distances:
22 4 0.08
23 10 0.19
24 5 0.09
25 21 0.40
26 13 0.25
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.64
Consensus pattern (24 bp):
TTTATTTTGTTAAATTTAATTTAC
Found at i:1584296 original size:17 final size:17
Alignment explanation
Indices: 1584274--1584308 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1584264 TAGTCTTGAC
1584274 GTGTATGCGAGCAAGTT
1 GTGTATGCGAGCAAGTT
*
1584291 GTGTATGTGAGCAAGTT
1 GTGTATGCGAGCAAGTT
1584308 G
1 G
1584309 CTATCACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.09, G:0.37, T:0.31
Consensus pattern (17 bp):
GTGTATGCGAGCAAGTT
Found at i:1587165 original size:14 final size:12
Alignment explanation
Indices: 1587130--1587157 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1587120 AATAAGTATA
1587130 ATAAAAAAATTT
1 ATAAAAAAATTT
1587142 ATAAAAAAATTT
1 ATAAAAAAATTT
1587154 ATAA
1 ATAA
1587158 CGAAAAATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAAAAAATTT
Found at i:1587404 original size:51 final size:51
Alignment explanation
Indices: 1587312--1587421 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 51
1587302 AGGCGCGAAT
* **
1587312 CAGGGAGCGCGTTATACCCACGTGTAAGCCATGTCAACATATAGCGCGGTA
1 CAGGGAGCGCGCTATACCCACGTGTAAGCCAAATCAACATATAGCGCGGTA
* * * *
1587363 CAGGGGGCGCGCTATACCCCACGTG-ACGCCAAATCAGCATATAGCG-GG-G
1 CAGGGAGCGCGCTATA-CCCACGTGTAAGCCAAATCAACATATAGCGCGGTA
1587412 CAGGGAGCGC
1 CAGGGAGCGC
1587422 ATTTTACTAC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 9 0.18
50 2 0.04
51 31 0.62
52 8 0.16
ACGTcount: A:0.25, C:0.28, G:0.32, T:0.15
Consensus pattern (51 bp):
CAGGGAGCGCGCTATACCCACGTGTAAGCCAAATCAACATATAGCGCGGTA
Found at i:1589739 original size:19 final size:19
Alignment explanation
Indices: 1589715--1589756 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1589705 AGTTTCCAAT
1589715 TTCGCAACTGAAAGTCAAA
1 TTCGCAACTGAAAGTCAAA
**
1589734 TTCGCAACTGAATTTCAAA
1 TTCGCAACTGAAAGTCAAA
1589753 TTCG
1 TTCG
1589757 TAACATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (19 bp):
TTCGCAACTGAAAGTCAAA
Found at i:1592988 original size:18 final size:18
Alignment explanation
Indices: 1592965--1593000 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1592955 AAGCAAAAGG
*
1592965 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1592983 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1593001 CAACCGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1593403 original size:20 final size:20
Alignment explanation
Indices: 1593360--1593404 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1593350 TCGCAAACTG
*
1593360 AATTTGACTATCGCGTAGCG
1 AATTTGACTATCGCGTAGCA
*
1593380 AATTTGACTTTCGCGTTA-CA
1 AATTTGACTATCGCG-TAGCA
1593400 AATTT
1 AATTT
1593405 ACCTTCAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (20 bp):
AATTTGACTATCGCGTAGCA
Found at i:1593508 original size:25 final size:25
Alignment explanation
Indices: 1593470--1593521 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1593460 AAATCAATTA
*
1593470 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
*
1593495 AACATTGTTATGGGTATATTATTTG
1 AACATTGTTATGGGTACATTATTTG
1593520 AA
1 AA
1593522 AAAATAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:1593927 original size:18 final size:18
Alignment explanation
Indices: 1593906--1593942 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1593896 GTAATTGGAG
1593906 TTTGAATTTCAATTTCAA
1 TTTGAATTTCAATTTCAA
* *
1593924 TTTGAGTTTGAATTTCAA
1 TTTGAATTTCAATTTCAA
1593942 T
1 T
1593943 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTCAATTTCAA
Found at i:1593949 original size:24 final size:24
Alignment explanation
Indices: 1593898--1593950 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1593888 TTTCATATGT
* * *
1593898 AATTGGAGTTTGAATTTCAATTTC
1 AATTTGAGTTTGAATTTCAATATA
1593922 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTCAATATA
1593946 AATTT
1 AATTT
1593951 CGGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTCAATATA
Found at i:1594297 original size:39 final size:39
Alignment explanation
Indices: 1594254--1594340 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
1594244 TCCGATGCTC
1594254 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
1594293 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1594332 ATCAAAATC
1 ATCAAAATC
1594341 TACAACTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:1594541 original size:20 final size:20
Alignment explanation
Indices: 1594516--1594558 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1594506 ATGTTGCGAT
* *
1594516 CAACGCGAAATTTAAATTCG
1 CAACGCGAAAGTCAAATTCG
1594536 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
1594556 CAA
1 CAA
1594559 ACCGAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:1594731 original size:66 final size:65
Alignment explanation
Indices: 1594661--1594826 Score: 186
Period size: 66 Copynumber: 2.6 Consensus size: 65
1594651 TTTTAGAAAC
*
1594661 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAAATCTTATTTACAAATC-AATT
1594726 A
65 A
* * **
1594727 AACAAATCAACTTTTACAAATCAATT----AATC-AAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAAATCTTATTTACAAATCAATTA
* *
1594787 AACAAATCAAC--ATA-AAATTCAATTAAACAAAGAAAAAAAA
1 AACAAATCAACTTTTACAAA-TCAATTAAAC-AAGCAAAAAAA
1594827 GTGTACCCCA
Statistics
Matches: 85, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
57 3 0.04
58 8 0.09
60 16 0.19
61 21 0.25
62 3 0.04
63 2 0.02
64 6 0.07
66 26 0.31
ACGTcount: A:0.56, C:0.16, G:0.01, T:0.27
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAAATCTTATTTACAAATCAATTA
Found at i:1596192 original size:21 final size:21
Alignment explanation
Indices: 1596168--1596263 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
1596158 GGCGGGACCA
*
1596168 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * *
1596189 CTTGAACGGTGGGAGGGGCTT
1 CTTGAACGATGAGAGGGGCCT
*
1596210 CTTCG-ATGATGAGAGGGGCCT
1 CTT-GAACGATGAGAGGGGCCT
*
1596231 CTTGAACGAT-AGGAGGCGCCT
1 CTTGAACGATGA-GAGGGGCCT
*
1596252 CTTGAATGATGA
1 CTTGAACGATGA
1596264 TAGGTGCATC
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 56 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:1596246 original size:42 final size:42
Alignment explanation
Indices: 1596168--1596263 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
1596158 GGCGGGACCA
* * * * *
1596168 CTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCT
*
1596210 CTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGCGCCT
1 CTT-GAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCT
1596252 CTTGAATGATGA
1 CTTGAATGATGA
1596264 TAGGTGCATC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.02
42 44 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (42 bp):
CTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCT
Found at i:1598916 original size:20 final size:20
Alignment explanation
Indices: 1598891--1598935 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1598881 GCGTAAAAAC
*
1598891 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
1598911 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
1598931 ATTTG
1 ATTTG
1598936 GAAAATCGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:1599394 original size:64 final size:64
Alignment explanation
Indices: 1599289--1599415 Score: 218
Period size: 64 Copynumber: 2.0 Consensus size: 64
1599279 AATATTGAGA
* * *
1599289 GCCCTCCCACCCACATTCCACGTTGTATCAAATATCATGCAAATTGTTGGGAAGAAACCAAACT
1 GCCCTCCCACCCACATTCCACGTTGCAACAAATATCATGCAAATTGTTGGAAAGAAACCAAACT
*
1599353 GCCCTCCCACCCACATTCCACGTTGCAACAAATATCCTGCAAATTGTTGGAAAGAAACCAAAC
1 GCCCTCCCACCCACATTCCACGTTGCAACAAATATCATGCAAATTGTTGGAAAGAAACCAAAC
1599416 AACAGAACAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.34, C:0.31, G:0.13, T:0.21
Consensus pattern (64 bp):
GCCCTCCCACCCACATTCCACGTTGCAACAAATATCATGCAAATTGTTGGAAAGAAACCAAACT
Found at i:1600657 original size:40 final size:39
Alignment explanation
Indices: 1600613--1601045 Score: 234
Period size: 42 Copynumber: 10.6 Consensus size: 39
1600603 TACATATAGC
1600613 GGCGTTTTTGA-ACAAACGCCGCAAAATACTATACTTTAGT
1 GGCGTTTTT-ATACAAACGCCGCAAAA-ACTATACTTTAGT
* * *
1600653 GGCGTTTTTATAAAAACGCCGC-TAAACGTA-A-TGTAGT
1 GGCGTTTTTATACAAACGCCGCAAAAAC-TATACTTTAGT
* *
1600690 GGC-TTTTTATACAAACGCCGCTATAAACTAGTATTTTAGT
1 GGCGTTTTTATACAAACGCCGC-AAAAACTA-TACTTTAGT
* * * * *
1600730 GGCGTTTTTATACAAACGCTGCTATAGACATGTACTTTTGT
1 GGCGTTTTTATACAAACGCCGC-AAAAAC-TATACTTTAGT
* * * *
1600771 GGCGTTTTAATACCAAACGACGCTATAGACTCATACTTTAGT
1 GGCGTTTTTATA-CAAACGCCGC-AAAAACT-ATACTTTAGT
* * * * *
1600813 GGCATTTTTACACAAACGCCGCTATAGACAC-GTACTTTTGT
1 GGCGTTTTTATACAAACGCCGC-A-A-AAACTATACTTTAGT
* * * *
1600854 GGCGTTTTAATACCAAACGCCGCTATAGACAC-GTACTTTTGT
1 GGCGTTTTTATA-CAAACGCCGC-A-A-AAACTATACTTTAGT
* * * * *
1600896 GGCGTTTTAATACCAAACGCCGCTATAGATTCGTACTTTAGT
1 GGCGTTTTTATA-CAAACGCCGC-AAAAACT-ATACTTTAGT
* * * *
1600938 GGCGTTTTTACACAAACGCCGCTATAGACAC-GTACTTTTGT
1 GGCGTTTTTATACAAACGCCGC-A-A-AAACTATACTTTAGT
* * * *
1600979 GGCGTTTTAATAACAAACGCCGCTATAGACTCGTACTTTAGT
1 GGCGTTTTTAT-ACAAACGCCGC-AAAAACT-ATACTTTAGT
*
1601021 GGCGTTTTAATACCAAACGCCGCAA
1 GGCGTTTTTATA-CAAACGCCGCAA
1601046 TTGTCATATA
Statistics
Matches: 329, Mismatches: 42, Indels: 43
0.79 0.10 0.10
Matches are distributed among these distances:
36 17 0.05
37 10 0.03
38 8 0.02
39 6 0.02
40 32 0.10
41 102 0.31
42 149 0.45
43 5 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (39 bp):
GGCGTTTTTATACAAACGCCGCAAAAACTATACTTTAGT
Found at i:1600796 original size:42 final size:43
Alignment explanation
Indices: 1600688--1601043 Score: 456
Period size: 42 Copynumber: 8.6 Consensus size: 43
1600678 ACGTAATGTA
* * *
1600688 GTGGC-TTTTTATA-CAAACGCCGCTATAAAC-TAGTA-TTTT
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACATCGTACTTTT
* *
1600727 AGTGGCGTTTTTATA-CAAACGCTGCTATAGACAT-GTACTTTT
1 -GTGGCGTTTTAATACCAAACGCCGCTATAGACATCGTACTTTT
* * *
1600769 GTGGCGTTTTAATACCAAACGACGCTATAGAC-TCATACTTTA
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACATCGTACTTTT
*
1600811 GTGGCATTTT--TACACAAACGCCGCTATAGACA-CGTACTTTT
1 GTGGCGTTTTAATAC-CAAACGCCGCTATAGACATCGTACTTTT
1600852 GTGGCGTTTTAATACCAAACGCCGCTATAGACA-CGTACTTTT
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACATCGTACTTTT
* *
1600894 GTGGCGTTTTAATACCAAACGCCGCTATAGA-TTCGTACTTTA
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACATCGTACTTTT
1600936 GTGGCGTTTT--TACACAAACGCCGCTATAGACA-CGTACTTTT
1 GTGGCGTTTTAATAC-CAAACGCCGCTATAGACATCGTACTTTT
* *
1600977 GTGGCGTTTTAATAACAAACGCCGCTATAGAC-TCGTACTTTA
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACATCGTACTTTT
1601019 GTGGCGTTTTAATACCAAACGCCGC
1 GTGGCGTTTTAATACCAAACGCCGC
1601044 AATTGTCATA
Statistics
Matches: 282, Mismatches: 19, Indels: 28
0.86 0.06 0.09
Matches are distributed among these distances:
40 11 0.04
41 106 0.38
42 160 0.57
43 5 0.02
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (43 bp):
GTGGCGTTTTAATACCAAACGCCGCTATAGACATCGTACTTTT
Found at i:1600828 original size:83 final size:85
Alignment explanation
Indices: 1600643--1601043 Score: 457
Period size: 83 Copynumber: 4.9 Consensus size: 85
1600633 GCAAAATACT
* * *
1600643 ATACTTTAGTGGCGTTTTTATA-A-AAACGCCGC--TA-A-A-CGTAATGTAGTGGC-TTTTTAT
1 ATACTTTAGTGGCG-TTTTATACACAAACGCCGCTATAGACATCGTACTTTAGTGGCGTTTTAAT
1600700 A-CAAACGCCGCTATA-A-AC
65 ACCAAACGCCGCTATAGACAC
* * * *
1600718 TAGTATTTTAGTGGCGTTTT-TATACAAACGCTGCTATAGACAT-GTACTTTTGTGGCGTTTTAA
1 -A-TACTTTAGTGGCGTTTTATACACAAACGCCGCTATAGACATCGTACTTTAGTGGCGTTTTAA
* *
1600781 TACCAAACGACGCTATAGACTC
64 TACCAAACGCCGCTATAGACAC
* *
1600803 ATACTTTAGTGGCATTTT-TACACAAACGCCGCTATAGACA-CGTACTTTTGTGGCGTTTTAATA
1 ATACTTTAGTGGCGTTTTATACACAAACGCCGCTATAGACATCGTACTTTAGTGGCGTTTTAATA
1600866 CCAAACGCCGCTATAGACAC
66 CCAAACGCCGCTATAGACAC
* * *
1600886 GTACTTTTGTGGCGTTTTAATAC-CAAACGCCGCTATAGA-TTCGTACTTTAGTGGCGTTTT--T
1 ATACTTTAGTGGCGTTTT-ATACACAAACGCCGCTATAGACATCGTACTTTAGTGGCGTTTTAAT
1600947 ACACAAACGCCGCTATAGACAC
65 AC-CAAACGCCGCTATAGACAC
* *
1600969 GTACTTTTGTGGCGTTTTAATA-ACAAACGCCGCTATAGAC-TCGTACTTTAGTGGCGTTTTAAT
1 ATACTTTAGTGGCGTTTT-ATACACAAACGCCGCTATAGACATCGTACTTTAGTGGCGTTTTAAT
1601032 ACCAAACGCCGC
65 ACCAAACGCCGC
1601044 AATTGTCATA
Statistics
Matches: 285, Mismatches: 19, Indels: 34
0.84 0.06 0.10
Matches are distributed among these distances:
75 2 0.01
76 6 0.02
77 20 0.07
79 2 0.01
80 1 0.00
81 11 0.04
82 10 0.04
83 180 0.63
84 46 0.16
85 7 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (85 bp):
ATACTTTAGTGGCGTTTTATACACAAACGCCGCTATAGACATCGTACTTTAGTGGCGTTTTAATA
CCAAACGCCGCTATAGACAC
Found at i:1601040 original size:125 final size:123
Alignment explanation
Indices: 1600644--1601043 Score: 555
Period size: 125 Copynumber: 3.3 Consensus size: 123
1600634 CAAAATACTA
* * * * *
1600644 TACTTTAGTGGCGTTTTTATA-AAAACGCCGCTA-A-A-CGTAATGTAGTGGCTTTTTATACAAA
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGATCGTACTTTAGTGGCTTTTTACACAAA
* * *
1600705 CGCCGCTATAAACTA-GTA-TTTTAGTGGCGTTTTTAT-ACAAACGCTGCTATAGACAT-G
66 CGCCGCTATAGAC-ACGTACTTTT-GTGGCGTTTTAATAACAAACGCCGCTATAGAC-TCG
* * *
1600762 TACTTTTGTGGCGTTTTAATACCAAACGACGCTATAGACTCATACTTTAGTGGCATTTTTACACA
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGA-TCGTACTTTAGTGGC-TTTTTACACA
* *
1600827 AACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACG
64 AACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATAACAAACGCCGCTATAGACTCG
*
1600887 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGATTCGTACTTTAGTGGCGTTTTTACACA
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGA-TCGTACTTTAGTGGC-TTTTTACACA
1600952 AACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATAACAAACGCCGCTATAGACTCG
64 AACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATAACAAACGCCGCTATAGACTCG
1601012 TACTTTAGTGGCGTTTTAATACCAAACGCCGC
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGC
1601044 AATTGTCATA
Statistics
Matches: 252, Mismatches: 20, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
118 19 0.08
119 10 0.04
120 1 0.00
121 1 0.00
123 12 0.05
124 38 0.15
125 171 0.68
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (123 bp):
TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGATCGTACTTTAGTGGCTTTTTACACAAA
CGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATAACAAACGCCGCTATAGACTCG
Found at i:1604731 original size:21 final size:21
Alignment explanation
Indices: 1604689--1604747 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1604679 TGATTTATTA
**
1604689 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
1604710 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
* *
1604731 TTATCGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
1604748 ATTGGAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:1604978 original size:43 final size:43
Alignment explanation
Indices: 1604907--1605167 Score: 321
Period size: 43 Copynumber: 6.1 Consensus size: 43
1604897 CTTTTACGGT
* *
1604907 GTTTGTGGGAAAAACGCCGCTAAATATCAAGACCTATTGCGGC
1 GTTTGTTGGAAAAACGCCGCTAAATATCAACACCTATTGCGGC
* * *
1604950 GTTT-ATGGACAAAACGCCGCTAAATATCAACACCTATTGAGGT
1 GTTTGTTGGA-AAAACGCCGCTAAATATCAACACCTATTGCGGC
* * *
1604993 GTTTG-TGGAAAAAATGCCGCTAAATCTCAACACATATTGCGGC
1 GTTTGTTGG-AAAAACGCCGCTAAATATCAACACCTATTGCGGC
* *
1605036 GTTTGTTGGAAAAACACCGCTAAATCTCAACACCTATTGCGGC
1 GTTTGTTGGAAAAACGCCGCTAAATATCAACACCTATTGCGGC
* *
1605079 GTTTGTTGGAAAAA-GCCACCAAATATCAACACCTATTGCGGC
1 GTTTGTTGGAAAAACGCCGCTAAATATCAACACCTATTGCGGC
* * *** *
1605121 GTTTGTTGGACAAACGCCGCTATATATCGTTACCTATTGCGGT
1 GTTTGTTGGAAAAACGCCGCTAAATATCAACACCTATTGCGGC
1605164 GTTT
1 GTTT
1605168 TTTGTTACCA
Statistics
Matches: 188, Mismatches: 25, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
42 40 0.21
43 144 0.77
44 4 0.02
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (43 bp):
GTTTGTTGGAAAAACGCCGCTAAATATCAACACCTATTGCGGC
Found at i:1606926 original size:29 final size:29
Alignment explanation
Indices: 1606884--1606972 Score: 160
Period size: 29 Copynumber: 3.1 Consensus size: 29
1606874 GTGTTGCCGT
1606884 AGGTCGCCATGGCATCCAGGCAAGCTTGG
1 AGGTCGCCATGGCATCCAGGCAAGCTTGG
1606913 AGGTCGCCATGGCATCCAGGCAAGCTTGG
1 AGGTCGCCATGGCATCCAGGCAAGCTTGG
* *
1606942 AGGTCGCCATGGCATCCGGGCGAGCTTGG
1 AGGTCGCCATGGCATCCAGGCAAGCTTGG
1606971 AG
1 AG
1606973 TCTCTGCATG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.19, C:0.27, G:0.37, T:0.17
Consensus pattern (29 bp):
AGGTCGCCATGGCATCCAGGCAAGCTTGG
Found at i:1607027 original size:60 final size:60
Alignment explanation
Indices: 1606959--1607080 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
1606949 CATGGCATCC
1606959 GGGCGAGCTTGGAGTCTCTGCATGGCTGTGCATGGCGGCATGGCAACGTGGCATGGGTCT
1 GGGCGAGCTTGGAGTCTCTGCATGGCTGTGCATGGCGGCATGGCAACGTGGCATGGGTCT
1607019 GGGCGAGCTTGGAGTCTCTGCATGGCTGTGCATGGCGGCATGGCAACGTGGCATGGGTCT
1 GGGCGAGCTTGGAGTCTCTGCATGGCTGTGCATGGCGGCATGGCAACGTGGCATGGGTCT
1607079 GG
1 GG
1607081 TGACAGCATG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.13, C:0.21, G:0.43, T:0.23
Consensus pattern (60 bp):
GGGCGAGCTTGGAGTCTCTGCATGGCTGTGCATGGCGGCATGGCAACGTGGCATGGGTCT
Found at i:1607133 original size:29 final size:28
Alignment explanation
Indices: 1607100--1607183 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 28
1607090 GGCAACGTGG
1607100 GTAGGTCGCCAGGGAATCCCAGCGACATT
1 GTAGGTCGCCAGGG-ATCCCAGCGACATT
1607129 GTAGGTCGCCAGGGCATCCCAGCGACATT
1 GTAGGTCGCCAGGG-ATCCCAGCGACATT
*
1607158 GTAGGTCGCCAAGGGATCCCAACGAC
1 GTAGGTCGCC-AGGGATCCCAGCGAC
1607184 CTATGCCTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 48 0.92
30 4 0.08
ACGTcount: A:0.24, C:0.30, G:0.31, T:0.15
Consensus pattern (28 bp):
GTAGGTCGCCAGGGATCCCAGCGACATT
Found at i:1607278 original size:12 final size:11
Alignment explanation
Indices: 1607258--1607293 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1607248 GAAATCAGCT
1607258 GCATTATTGCA
1 GCATTATTGCA
*
1607269 GCACTTATTGCT
1 GCA-TTATTGCA
1607281 GCATTATTGCA
1 GCATTATTGCA
1607292 GC
1 GC
1607294 CCGTGAACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (11 bp):
GCATTATTGCA
Found at i:1607517 original size:8 final size:9
Alignment explanation
Indices: 1607487--1607524 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1607477 GTAAGTTTTT
1607487 TTTTAATTA
1 TTTTAATTA
1607496 TTTTAATTA
1 TTTTAATTA
*
1607505 GTTT-ATTA
1 TTTTAATTA
1607513 TTTTAAATTA
1 TTTT-AATTA
1607523 TT
1 TT
1607525 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:1607646 original size:28 final size:27
Alignment explanation
Indices: 1607607--1607659 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
1607597 ATATTAAAAA
1607607 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
1607635 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
1607660 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:1607665 original size:27 final size:29
Alignment explanation
Indices: 1607606--1607670 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
1607596 TATATTAAAA
1607606 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
1607635 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
1607661 AAATAGTTAA
1 AAATAATTAA
1607671 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:1607806 original size:26 final size:28
Alignment explanation
Indices: 1607779--1607840 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
1607769 ATAAAAGAAT
*
1607779 AATTATT-TAAATTAGTTTATTGTTATA
1 AATTATTATAAATTAGTTTATTATTATA
*
1607806 AATTATTAGTTAATTAGTTTATTATTATA
1 AATTATTA-TAAATTAGTTTATTATTATA
1607835 AATTAT
1 AATTAT
1607841 GGTAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 7 0.23
29 24 0.77
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (28 bp):
AATTATTATAAATTAGTTTATTATTATA
Found at i:1607890 original size:21 final size:21
Alignment explanation
Indices: 1607865--1607904 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1607855 GTTAATTAGT
1607865 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
*
1607886 TTGTTAGTTTACGTTATAT
1 TTGTTAGTTTAAGTTATAT
1607905 CATATAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:1608151 original size:30 final size:30
Alignment explanation
Indices: 1608083--1608208 Score: 94
Period size: 30 Copynumber: 4.4 Consensus size: 30
1608073 AGTAGTTAAT
* * *
1608083 TAGTTTTTTAGTAGTAAATTATAATTAAA-AA
1 TAGTTTATTAGT-TTAAGTTAT-ATTAAAGAA
*
1608114 TCA-TTTATTAGTTTAATTTATATTAAAGAA
1 T-AGTTTATTAGTTTAAGTTATATTAAAGAA
*
1608144 TAGTTTATTA-ATTAACGTTATATTAAAGAA
1 TAGTTTATTAGTTTAA-GTTATATTAAAGAA
1608174 TA---T-TTA----AAGTTATATTAAAGAA
1 TAGTTTATTAGTTTAAGTTATATTAAAGAA
1608196 TAGTTTATTAGTT
1 TAGTTTATTAGTT
1608209 GTTTAAGGGA
Statistics
Matches: 79, Mismatches: 5, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
22 16 0.20
23 2 0.03
25 1 0.01
26 6 0.08
27 1 0.01
29 11 0.14
30 32 0.41
31 9 0.11
32 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.47
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAGTTATATTAAAGAA
Found at i:1608185 original size:22 final size:23
Alignment explanation
Indices: 1608155--1608202 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
1608145 AGTTTATTAA
*
1608155 TTAACGTTATATTAAAGAATA-T
1 TTAAAGTTATATTAAAGAATAGT
1608177 TTAAAGTTATATTAAAGAATAGT
1 TTAAAGTTATATTAAAGAATAGT
1608200 TTA
1 TTA
1608203 TTAGTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (23 bp):
TTAAAGTTATATTAAAGAATAGT
Found at i:1609502 original size:18 final size:18
Alignment explanation
Indices: 1609479--1609514 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1609469 TATTTTTAAT
1609479 TATTATTTAAATTAAATA
1 TATTATTTAAATTAAATA
* *
1609497 TATTATTTGATTTAAATA
1 TATTATTTAAATTAAATA
1609515 AATTTTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TATTATTTAAATTAAATA
Found at i:1609511 original size:23 final size:23
Alignment explanation
Indices: 1609483--1609528 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1609473 TTTAATTATT
1609483 ATTTAAATTAAA-TATATTATTTG
1 ATTTAAA-TAAATTATATTATTTG
*
1609506 ATTTAAATAAATTTTATTATTTG
1 ATTTAAATAAATTATATTATTTG
1609529 TAATTTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
ATTTAAATAAATTATATTATTTG
Found at i:1609527 original size:18 final size:21
Alignment explanation
Indices: 1609477--1609527 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
1609467 GTTATTTTTA
1609477 ATTATTATTTAAATTAAATAT
1 ATTATTATTTAAATTAAATAT
1609498 ATTATTTGATTTAAA-TAAAT-T
1 ATTA-TT-ATTTAAATTAAATAT
1609519 -TTATTATTT
1 ATTATTATTT
1609528 GTAATTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 3 0.11
21 5 0.18
22 7 0.25
23 7 0.25
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTATTATTTAAATTAAATAT
Found at i:1610520 original size:14 final size:14
Alignment explanation
Indices: 1610501--1610545 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1610491 AAGTCGTAAC
1610501 TCATTACTATCAAA
1 TCATTACTATCAAA
1610515 TCATTAC--T-AAA
1 TCATTACTATCAAA
*
1610526 TCATTAATATCAAA
1 TCATTACTATCAAA
1610540 TCATTA
1 TCATTA
1610546 AATATTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 9 0.33
12 1 0.04
13 1 0.04
14 16 0.59
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (14 bp):
TCATTACTATCAAA
Found at i:1610561 original size:21 final size:22
Alignment explanation
Indices: 1610501--1610555 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 22
1610491 AAGTCGTAAC
*
1610501 TCATTACTATCAAATCATTACTAAA
1 TCATTAATATCAAATCA-T--TAAA
1610526 TCATTAATATCAAATCATTAAA
1 TCATTAATATCAAATCATTAAA
1610548 T-ATTAATA
1 TCATTAATA
1610556 ATAAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 7 0.24
22 5 0.17
24 1 0.03
25 16 0.55
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (22 bp):
TCATTAATATCAAATCATTAAA
Found at i:1610566 original size:21 final size:22
Alignment explanation
Indices: 1610517--1610566 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1610507 CTATCAAATC
*
1610517 ATTACTAAATCATTAATATCAA
1 ATTATTAAATCATTAATATCAA
*
1610539 ATCATTAAAT-ATTAATAAT-AA
1 ATTATTAAATCATTAAT-ATCAA
1610560 ATTATTA
1 ATTATTA
1610567 TTACTAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTATTAAATCATTAATATCAA
Found at i:1610581 original size:10 final size:10
Alignment explanation
Indices: 1610566--1610592 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1610556 ATAAATTATT
1610566 ATTACTAATC
1 ATTACTAATC
1610576 ATTACTAATC
1 ATTACTAATC
1610586 ATTACTA
1 ATTACTA
1610593 TCAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:1610636 original size:49 final size:49
Alignment explanation
Indices: 1610576--1611283 Score: 709
Period size: 49 Copynumber: 13.3 Consensus size: 49
1610566 ATTACTAATC
* *
1610576 ATTACTAATCATTACTATCAAATTATTAAAAATTAATAATAATTTCATT
1 ATTATTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* * * *
1610625 ATCATTAATCATTACTAAATCATTAAT-ATCAAATCATTAAATATTAATAATAATTTTATT
1 ATTATTAATCATTACT--ATCA--AATCATTAAA-AATT--A-A-TAA---TAATTTCATT
*
1610685 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTATTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
1610734 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATT
1 ATTATTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC---ATT
* *
1610786 ACTAATCATTACTAAATCATTACTATCAAATCTTTAAAAATTAATAATAATTTTATT
1 A-T--T-A-T--T-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1610843 ATTATTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATT
1 ATTATTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC---ATT
1610895 ACTAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 A-T--T-A-T--T-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* *
1610952 GTTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTATTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* * *
1611001 ATTATTAATCATTACTAAATCATTAAT-ATCAAATCATTAAATATTAATAATAATTTCATA
1 ATTATTAATCATTACT--ATCA--AATCATTAAA-AATT--A-A-TAA---TAATTTCATT
*
1611061 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTATTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
1611110 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATT
1 ATTATTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC---ATT
*
1611162 AATAATCATTACTAATCATTACTATCAAATCATTAAAAAATAATAATAATTTCATT
1 -AT--T-A-T--TAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* *
1611218 ATTACTAATTATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTATTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
1611267 ATTACTAATCATTACTA
1 ATTATTAATCATTACTA
1611284 AATCATTAAT
Statistics
Matches: 569, Mismatches: 32, Indels: 116
0.79 0.04 0.16
Matches are distributed among these distances:
49 277 0.49
50 2 0.00
51 8 0.01
52 29 0.05
53 21 0.04
54 4 0.01
55 7 0.01
56 22 0.04
57 24 0.04
58 8 0.01
59 42 0.07
60 125 0.22
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTATTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:1610664 original size:60 final size:59
Alignment explanation
Indices: 1610513--1610701 Score: 299
Period size: 60 Copynumber: 3.2 Consensus size: 59
1610503 ATTACTATCA
*
1610513 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTATTATTACT
* * * * *
1610572 AATCATTACT-AATCATTACTATCAAATTATTAAAAATTAATAATAATTTCATTATCATT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTT-ATTATTACT
1610631 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTTATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA-TTTATTATTACT
1610691 AATCATTACTA
1 AATCATTACTA
1610702 TCAAATCATT
Statistics
Matches: 116, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
58 35 0.30
59 27 0.23
60 51 0.44
61 3 0.03
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (59 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTATTATTACT
Found at i:1610702 original size:109 final size:108
Alignment explanation
Indices: 1610576--1611404 Score: 848
Period size: 109 Copynumber: 7.6 Consensus size: 108
1610566 ATTACTAATC
* * *
1610576 ATTACTAATCATTACTATCAAATTATTAAAAATTAATAATAATTTCATTATCATTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1610641 AAATCATTAATATCAAATCATTAAATATTAATAATAATTTTATT
66 -AATCATTAATATCAAATCATTAAATATTAATAATAATTTTATT
1610685 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
* * * * *
1610750 -ATCA--AATCATTAAA-AATT-AATAATAAT-TTCATTATTACTAAT
66 AATCATTAAT-ATCAAATCATTAAATATTAATAATAATT-TTA-T--T
* * *
1610792 CATTACTAAATCATTACTATCAAATCTTTAAAAATTAATAATAATTTTATTATTATTAATCATTA
1 -ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA
* * * * *
1610857 CT-ATCA--AATCATTAAA-AATT-AATAATAAT-TTCATTATTACTAAT
64 CTAATCATTAAT-ATCAAATCATTAAATATTAATAATAATT-TTA-T--T
*
1610901 CATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTGTTACTAATCATTA
1 -ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA
* * * * * *
1610966 CT-ATCA--AATCATTAAA-AATT-AATAATAATTTCATTATTATTAATC
64 CTAATCATTAAT-ATCAAATCATTAAATATTAA--TAATAATT-TT-ATT
* *
1611011 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTC------A-T-A--ATTAC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
* * *
1611066 TAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
65 TAATCATTAATATCAAATCATTAAATATTAATAATAATTTTATT
*
1611110 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTAATAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
* * * *
1611175 AATCATTACTATCAAATCATTAAAAAATAATAATAATTTCATT
66 AATCATTAATATCAAATCATTAAATATTAATAATAATTTTATT
*
1611218 ATTACTAATTATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1611283 AAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATTAAT
66 -AATCATTAATATCAAATCATTAAATATTAATAAT-A----ATT-TTA-T--T
* *
1611336 CATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTA
1 -ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA
1611401 CTAA
64 CTAA
1611405 ATTTTATAAA
Statistics
Matches: 641, Mismatches: 41, Indels: 66
0.86 0.05 0.09
Matches are distributed among these distances:
98 38 0.06
99 14 0.02
100 5 0.01
101 12 0.02
102 6 0.01
103 11 0.02
104 12 0.02
105 8 0.01
106 6 0.01
107 5 0.01
108 117 0.18
109 325 0.51
110 1 0.00
111 1 0.00
112 8 0.01
113 1 0.00
114 3 0.00
115 2 0.00
116 1 0.00
118 1 0.00
119 8 0.01
120 56 0.09
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (108 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
AATCATTAATATCAAATCATTAAATATTAATAATAATTTTATT
Found at i:1610809 original size:60 final size:60
Alignment explanation
Indices: 1610734--1610859 Score: 218
Period size: 60 Copynumber: 2.1 Consensus size: 60
1610724 TAATTTCATT
1610734 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * *
1610793 ATTACTAAATCATTACTATCAAATCTTTAAAAATTAATAATAATTTTATTATTATTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1610853 ATTACTA
1 ATTACTA
1610860 TCAAATCATT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
59 6 0.10
60 57 0.90
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:1610823 original size:158 final size:158
Alignment explanation
Indices: 1610517--1611403 Score: 1009
Period size: 158 Copynumber: 5.4 Consensus size: 158
1610507 CTATCAAATC
* * *
1610517 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACT
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAAT--A--A-T-TT-C--ATTATTACT
* * *
1610582 AATCATTACTATCAAATTATTAAAAATTAATAATAATTTCATTATCATTAATCATTACTAAATCA
57 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
1610647 TTAATATCAAATCATTAAATATTAATAATAATT-TTATT
122 TT-ATATCAAATC-TTAAATATTAATAATAATTATTATT
1610685 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1610749 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCA
66 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA-TATCA
*
1610814 AATCTTTAAAAATTAATAATAATT-TTATT
130 AATC-TTAAATATTAATAATAATTATTATT
*
1610843 ATTA-TTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC------A-T--T-ATTAC
*
1610907 TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTGTTACTAATCATTACTATCA
56 T-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC--T-A
* * * *
1610972 AATCATTA-A--AAA--TT-AATAATAATTTCATTATTATTAATC
117 AATCATTATATCAAATCTTAAATATTAA--TAATAATTATT-ATT
* * *
1611011 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATAATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1611076 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTA-A-
66 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC--T-AAATCATTATAT
* * *
1611139 -AAA--TT-AATAATAAT-TTCATTATTAATAAT
128 CAAATCTTAAATATTAATAATAATTATT-AT--T
* *
1611168 CATTACT-AATCATTACTATCAAATCATTAAAAAATAATAATAATTTCATTATTACTAATTATTA
1 -ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA
1611232 CTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
65 CTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATT-ATATC
1611297 AAATCATTAAATATTAATAATAATTTCATTATTATTAAT
129 AAATC-TTAAATATTAATAAT-A----ATTATTA-T--T
* *
1611336 CATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTA
1 -ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA
1611401 CTA
65 CTA
1611404 AATTTTATAA
Statistics
Matches: 645, Mismatches: 34, Indels: 79
0.85 0.04 0.10
Matches are distributed among these distances:
154 8 0.01
155 12 0.02
156 2 0.00
157 104 0.16
158 241 0.37
159 6 0.01
160 1 0.00
161 4 0.01
162 10 0.02
163 3 0.00
164 7 0.01
165 4 0.01
166 6 0.01
167 36 0.06
168 38 0.06
169 152 0.24
170 1 0.00
171 1 0.00
172 9 0.01
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (158 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
TATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTATATCAA
ATCTTAAATATTAATAATAATTATTATT
Found at i:1610913 original size:60 final size:60
Alignment explanation
Indices: 1610849--1610968 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
1610839 TATTATTATT
1610849 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTA
*
1610909 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTGTTACTAATCATTACTA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTA
1610969 TCAAATCATT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (60 bp):
AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTA
Found at i:1611022 original size:60 final size:60
Alignment explanation
Indices: 1610953--1611077 Score: 207
Period size: 60 Copynumber: 2.1 Consensus size: 60
1610943 AATTTCATTG
* * *
1610953 TTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTATTAATCA
1 TTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATAATTACTAATCA
*
1611012 TTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATAATTACTAATCA
1 TTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATAATTACTAATCA
1611072 TTACTA
1 TTACTA
1611078 TCAAATCATT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
59 5 0.08
60 56 0.92
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (60 bp):
TTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATAATTACTAATCA
Found at i:1611251 original size:24 final size:24
Alignment explanation
Indices: 1611165--1611252 Score: 59
Period size: 24 Copynumber: 3.6 Consensus size: 24
1611155 CATTATTAAT
** *
1611165 AATCATTACTAATCATTACTATCA
1 AATCATTAAAAATTATTACTATCA
* * * **
1611189 AATCATTAAAAAATAATAATAATTT
1 AATCATTAAAAATTATTACT-ATCA
* * **
1611214 CATTATTACTAATTATTACTATCA
1 AATCATTAAAAATTATTACTATCA
1611238 AATCATTAAAAATTA
1 AATCATTAAAAATTA
1611253 ATAATAATTT
Statistics
Matches: 42, Mismatches: 21, Indels: 2
0.65 0.32 0.03
Matches are distributed among these distances:
24 27 0.64
25 15 0.36
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (24 bp):
AATCATTAAAAATTATTACTATCA
Found at i:1611291 original size:21 final size:21
Alignment explanation
Indices: 1611267--1611406 Score: 57
Period size: 21 Copynumber: 7.0 Consensus size: 21
1611257 TAATTTCATT
*
1611267 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
* *
1611288 ATTAAT-ATCAAATCATTAAAT-
1 ATTAATAATC--ATTACTAAATC
* * *
1611309 ATTAATAATAATT--T-CATT
1 ATTAATAATCATTACTAAATC
*
1611327 ATTATTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
* * *
1611348 ATTACT-ATCAAATCATTAAAT-
1 ATTAATAATC--ATTACTAAATC
* *
1611369 ATTAATAATAATT--T-CATC
1 ATTAATAATCATTACTAAATC
*
1611387 ATTACTAATCATTACTAAAT
1 ATTAATAATCATTACTAAAT
1611407 TTTATAAATA
Statistics
Matches: 85, Mismatches: 20, Indels: 28
0.64 0.15 0.21
Matches are distributed among these distances:
17 4 0.05
18 24 0.28
20 12 0.14
21 25 0.29
22 20 0.24
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAATAATCATTACTAAATC
Found at i:1611300 original size:60 final size:60
Alignment explanation
Indices: 1611218--1611406 Score: 326
Period size: 60 Copynumber: 3.2 Consensus size: 60
1611208 TAATTTCATT
* *
1611218 ATTACT-AATTATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
1611277 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
1611337 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1611397 ATTACTAAAT
1 ATTACTAAAT
1611407 TTTATAAATA
Statistics
Matches: 122, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
59 6 0.05
60 116 0.95
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:1614495 original size:28 final size:28
Alignment explanation
Indices: 1614464--1614517 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
1614454 ATAATCTAAT
* *
1614464 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTCAAACTAACAAACTAATATA
1614492 ATATAACTCAAACTAACAAACTAATA
1 ATATAACTCAAACTAACAAACTAATA
1614518 ATTTATACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (28 bp):
ATATAACTCAAACTAACAAACTAATATA
Found at i:1614524 original size:28 final size:28
Alignment explanation
Indices: 1614460--1614524 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
1614450 TTATATAATC
* *
1614460 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTCAAACTAACAAACTAA
1614488 T-ATAATATAACTCAAACTAACAAACTAA
1 TAAT-ATATAACTCAAACTAACAAACTAA
*
1614516 TAATTTATA
1 TAATATATA
1614525 CTAACAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 28 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
TAATATATAACTCAAACTAACAAACTAA
Found at i:1615250 original size:29 final size:30
Alignment explanation
Indices: 1615172--1615256 Score: 120
Period size: 29 Copynumber: 2.9 Consensus size: 30
1615162 GTTGGACGTC
** *
1615172 GGGCGTGCATGGCGACCTATAAGGTC-ACT
1 GGGCGTGCATGGCGACCTACCATGTCGACT
*
1615201 GGGCGTGCATGGCGACCTACCATGTCGCCT
1 GGGCGTGCATGGCGACCTACCATGTCGACT
1615231 -GGCGTGCATGGCGACCTACCATGTCG
1 GGGCGTGCATGGCGACCTACCATGTCG
1615257 GTGAAGCTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 49 0.96
30 2 0.04
ACGTcount: A:0.16, C:0.29, G:0.34, T:0.20
Consensus pattern (30 bp):
GGGCGTGCATGGCGACCTACCATGTCGACT
Found at i:1615343 original size:29 final size:29
Alignment explanation
Indices: 1615301--1615356 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1615291 ACAAGGTCGC
1615301 TAGGTCGCTGGGAGTGCATGGCGACCTTG
1 TAGGTCGCTGGGAGTGCATGGCGACCTTG
* *
1615330 TAGGTCGCTGGGAGTGCTTGGTGACCT
1 TAGGTCGCTGGGAGTGCATGGCGACCT
1615357 ATGGTTGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.12, C:0.20, G:0.41, T:0.27
Consensus pattern (29 bp):
TAGGTCGCTGGGAGTGCATGGCGACCTTG
Found at i:1615900 original size:20 final size:20
Alignment explanation
Indices: 1615870--1615919 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1615860 CTATTTTGTA
* *
1615870 AATTGATTTTATAAATCTTT
1 AATTTATTTTATAAATCTAT
* *
1615890 GATTTATTTTATACATCTAT
1 AATTTATTTTATAAATCTAT
1615910 AATTTATTTT
1 AATTTATTTT
1615920 TTGTTATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (20 bp):
AATTTATTTTATAAATCTAT
Found at i:1617844 original size:23 final size:22
Alignment explanation
Indices: 1617818--1617879 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 22
1617808 ATATAACTTA
*
1617818 ATAATAATAAAATAATCATGAAG
1 ATAATAATAAAATAATCA-AAAG
1617841 ATAATAATTTAAACAT-ATCAAAAG
1 ATAATAA--TAAA-ATAATCAAAAG
1617865 -TAATAATAAAATAAT
1 ATAATAATAAAATAAT
1617880 AATTAAAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
20 2 0.06
21 6 0.18
23 13 0.38
24 3 0.09
25 8 0.24
26 2 0.06
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (22 bp):
ATAATAATAAAATAATCAAAAG
Found at i:1619275 original size:3 final size:3
Alignment explanation
Indices: 1619267--1619323 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
1619257 ATATATATAT
* * *
1619267 TAA TAA TAA TAA TAA TAA TAA TAA TATT TAG TAA TAA TAA -AT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
1619312 TAA TAA TAA TAA
1 TAA TAA TAA TAA
1619324 AATTTAAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
2 1 0.02
3 44 0.94
4 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1619317 original size:33 final size:31
Alignment explanation
Indices: 1619267--1619329 Score: 99
Period size: 33 Copynumber: 2.0 Consensus size: 31
1619257 ATATATATAT
*
1619267 TAATAATAATAATAATAATAATAATATTTAG
1 TAATAATAATAATAATAATAATAAAATTTAG
1619298 TAATAATAAATTAATAATAATAATAAAATTTA
1 TAATAAT-AA-TAATAATAATAATAAAATTTA
1619330 AATGAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 7 0.24
32 2 0.07
33 20 0.69
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (31 bp):
TAATAATAATAATAATAATAATAAAATTTAG
Found at i:1620196 original size:76 final size:76
Alignment explanation
Indices: 1619451--1620169 Score: 1357
Period size: 76 Copynumber: 9.5 Consensus size: 76
1619441 GATGGAAATG
* *
1619451 TTTGAAAACATCATGAACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1619516 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1619527 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1619592 CCCGAAGGCTT
66 CCCGAAGGCTT
1619603 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1619668 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1619679 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1619744 CCCGAAGGCTT
66 CCCGAAGGCTT
1619755 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1619820 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
1619831 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATTAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1619896 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1619907 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
1619972 CCCAAAGGCTT
66 CCCGAAGGCTT
1619983 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1620048 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1620059 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1620124 CCCGAAGGCTT
66 CCCGAAGGCTT
1620135 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1620170 TGGGAAATAG
Statistics
Matches: 628, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 628 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:1621320 original size:54 final size:53
Alignment explanation
Indices: 1621238--1621393 Score: 231
Period size: 54 Copynumber: 2.9 Consensus size: 53
1621228 AGAATAGCAG
***
1621238 GTTCGTAAAACATTTGACAGTGCATTCATCCTTTCTTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTC-TGTGGTTTCTGCTCAGAT
*
1621292 GTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTC-TGTGGTTTCTGCTCAGAT
* *
1621346 GGTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTT-CTGTGGTTTCTGC
1621394 CAAGATTTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 92 0.99
55 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCTGTGGTTTCTGCTCAGAT
Found at i:1622356 original size:75 final size:74
Alignment explanation
Indices: 1622268--1622437 Score: 207
Period size: 74 Copynumber: 2.3 Consensus size: 74
1622258 ATTGTGGGCC
* * *
1622268 TTCAGCATGCCCCAACA-TTGGCTAATACAAGTGTTCAAAATGCATCAATAGTTCTGATTCTGAT
1 TTCAGCATGCCCCAACATTTGGCTAATA-AA-TATTCAAAATACATCAACAGTTCTGATTCTGAT
*
1622332 TGAAATGGGTT
64 TGAAAAGGGTT
* * * ** * *
1622343 TTCAGCATGCCCCAACATTTTGCTGATAAATATTCAGAATATTTCAACATTTCTGATTCTGTTTG
1 TTCAGCATGCCCCAACATTTGGCTAATAAATATTCAAAATACATCAACAGTTCTGATTCTGATTG
1622408 AAAAGGGTT
66 AAAAGGGTT
*
1622417 TTCAGCATGCCCCAATATTTG
1 TTCAGCATGCCCCAACATTTG
1622438 CTTCTTGTTA
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
74 54 0.67
75 19 0.23
76 8 0.10
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (74 bp):
TTCAGCATGCCCCAACATTTGGCTAATAAATATTCAAAATACATCAACAGTTCTGATTCTGATTG
AAAAGGGTT
Found at i:1623854 original size:83 final size:83
Alignment explanation
Indices: 1623684--1624078 Score: 565
Period size: 83 Copynumber: 4.7 Consensus size: 83
1623674 TTGGTTTTTG
* * *
1623684 GGTTCATACTAAACCAGATCAGATAACTCAAAGAACACTTCCATAAGATGTTATGAGCACATTCA
1 GGTTC-TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCA
* ** * *
1623749 TTTTTAAAATTTAATAACT
65 TCTTCCAAATTCAATAATT
* * *
1623768 GGTTCTGCCAAACCAGATCAGATAAATCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCAT
1 GGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
* *
1623833 CTTCCGAATTCAATGATT
66 CTTCCAAATTCAATAATT
* *
1623851 GGTTTTACCAAACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTATGAGCACATTCAT
1 GGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
*
1623916 CTTTCAAATTCAATAATT
66 CTTCCAAATTCAATAATT
* * *
1623934 GGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCT
1 GGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
* *
1623999 CTTCCAATTTCAATGATT
66 CTTCCAAATTCAATAATT
* * *
1624017 GGTTCTGCCAAACCTGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACATT
1 GGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1624079 GCATTTGTTC
Statistics
Matches: 279, Mismatches: 32, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
83 274 0.98
84 5 0.02
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (83 bp):
GGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
CTTCCAAATTCAATAATT
Found at i:1626656 original size:2 final size:2
Alignment explanation
Indices: 1626649--1626688 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1626639 ACAACAAATG
1626649 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
1626689 TAAAGGATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1631884 original size:11 final size:11
Alignment explanation
Indices: 1631870--1631939 Score: 54
Period size: 11 Copynumber: 6.0 Consensus size: 11
1631860 ATAACTTAAT
1631870 AATAATAATAA
1 AATAATAATAA
*
1631881 AATAATCATGAA
1 AATAATAAT-AA
*
1631893 GATAATAATTTAA
1 AATAATAA--TAA
1631906 ACAT-AT-ATCAA
1 A-ATAATAAT-AA
1631917 AAGTAATAATAA
1 AA-TAATAATAA
1631929 AATAATAATAA
1 AATAATAATAA
1631940 TTAAAATGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
10 2 0.04
11 21 0.45
12 15 0.32
13 6 0.13
14 3 0.06
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (11 bp):
AATAATAATAA
Found at i:1633327 original size:3 final size:3
Alignment explanation
Indices: 1633319--1633370 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
1633309 ATATATATAT
* * *
1633319 TAA TAA TAA TAA TAA TAA TATT TAG TAA TAA TAA -ATT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA
1633365 TAA TAA
1 TAA TAA
1633371 AATTTAAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
2 1 0.02
3 37 0.90
4 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1633332 original size:31 final size:36
Alignment explanation
Indices: 1633297--1633369 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
1633287 TTTGGGCTTG
*
1633297 TAATATATA-T-ATATATATATATTAATAATAATAATAA
1 TAATATATAGTAATA-ATAAAT-TTAATAATAATAAT-A
*
1633334 TAATATTTAGTAATAATAAATTTAATAATAATAATA
1 TAATATATAGTAATAATAAATTTAATAATAATAATA
1633370 AAATTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 1 0.03
37 22 0.69
38 6 0.19
39 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (36 bp):
TAATATATAGTAATAATAAATTTAATAATAATAATA
Found at i:1633339 original size:25 final size:25
Alignment explanation
Indices: 1633297--1633366 Score: 68
Period size: 28 Copynumber: 2.6 Consensus size: 25
1633287 TTTGGGCTTG
*
1633297 TAATATATATATATATATATATTAATAA
1 TAATA-ATA-ATA-ATATATAGTAATAA
*
1633325 TAATAATAATAATATTTAGTAATAA
1 TAATAATAATAATATATAGTAATAA
1633350 TAAATTTAATAATAATA
1 T-AA--TAATAATAATA
1633367 ATAAAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
25 13 0.35
26 5 0.14
27 3 0.08
28 16 0.43
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (25 bp):
TAATAATAATAATATATAGTAATAA
Found at i:1635458 original size:20 final size:20
Alignment explanation
Indices: 1635433--1635498 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
1635423 TTTTCCGACT
1635433 ATCGCAACGCGAATATGTAA
1 ATCGCAACGCGAATATGTAA
* * *
1635453 ATCGCAATGCGAGTATG-ACT
1 ATCGCAACGCGAATATGTA-A
1635473 ATCGCAACGCGAATATGTAA
1 ATCGCAACGCGAATATGTAA
1635493 ATCGCA
1 ATCGCA
1635499 TTGCGATATG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 1 0.03
20 36 0.95
21 1 0.03
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATATGTAA
Found at i:1635478 original size:40 final size:39
Alignment explanation
Indices: 1635429--1635508 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 39
1635419 GCGATTTTCC
1635429 GACTATCGCAACGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATGCGA-TAT
*
1635469 GACTATCGCAACGCGAATATGTAAATCGCATTGCGATAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATGCGATAT
1635508 G
1 G
1635509 CGATTATGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 4 0.10
40 35 0.90
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.24
Consensus pattern (39 bp):
GACTATCGCAACGCGAATATGTAAATCGCAATGCGATAT
Found at i:1635531 original size:20 final size:20
Alignment explanation
Indices: 1635429--1635569 Score: 86
Period size: 20 Copynumber: 6.7 Consensus size: 20
1635419 GCGATTTTCC
* *
1635429 GACTATCGCAACGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
1635449 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGATTAT
* *
1635469 GACTATCGCAACGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
1635489 GTAAATCGCATTGCGATATGCGATTAT
1 G---A-C-TATCGC-A-ATGCGATTAT
*
1635516 GACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGATTAT
* * *
1635536 GACTATCACAACGCGATTCT
1 GACTATCGCAATGCGATTAT
*
1635556 GACTGTCGCAATGC
1 GACTATCGCAATGC
1635570 TGAATTTCAA
Statistics
Matches: 94, Mismatches: 18, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
19 1 0.01
20 69 0.73
21 2 0.02
22 4 0.04
23 2 0.02
24 2 0.02
25 4 0.04
26 1 0.01
27 9 0.10
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:1636425 original size:24 final size:24
Alignment explanation
Indices: 1636393--1636446 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1636383 GTATTCGAAA
1636393 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1636417 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1636441 TTTGAT
1 TTTGAT
1636447 GATGTTTCAG
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:1638731 original size:18 final size:18
Alignment explanation
Indices: 1638708--1638747 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1638698 AGCAAAAGGC
*
1638708 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
1638726 AATCAAAATCCCAATCAA
1 AATCAAAATCCCAATCAA
1638744 AATC
1 AATC
1638748 CAAAGCTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.55, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1638889 original size:20 final size:20
Alignment explanation
Indices: 1638864--1639137 Score: 167
Period size: 20 Copynumber: 14.7 Consensus size: 20
1638854 CACATTCATT
* *
1638864 TGACTATCGCAATGTGAATA
1 TGACTATCGCAACGCGAATA
* *
1638884 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
*
1638904 TGAATATCGCAACAG-G---A
1 TGACTATCGCAAC-GCGAATA
* *
1638921 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
1638938 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
*
1638958 TGACTATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
1638975 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
1638992 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
1639012 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
1639032 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* * * *
1639052 TAACTAT-ACAA--TG-AGA
1 TGACTATCGCAACGCGAATA
*
1639068 T-A--ATCACAACGCGAA-A
1 TGACTATCGCAACGCGAATA
* *
1639084 TGACTATAGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * * *
1639104 TGATTATCGCAATGGGAATT
1 TGACTATCGCAACGCGAATA
1639124 TGACTATCGCAACG
1 TGACTATCGCAACG
1639138 AGAAAATCGC
Statistics
Matches: 201, Mismatches: 31, Indels: 44
0.73 0.11 0.16
Matches are distributed among these distances:
13 3 0.01
14 20 0.10
15 2 0.01
16 7 0.03
17 10 0.05
18 2 0.01
19 15 0.07
20 141 0.70
21 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:1639025 original size:54 final size:54
Alignment explanation
Indices: 1638869--1639025 Score: 260
Period size: 54 Copynumber: 2.9 Consensus size: 54
1638859 TCATTTGACT
* * * *
1638869 ATCGCAATGTGAATATGACTATCGCAACGTGAATTTGAATATCGCAACAGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGTGAATTTGACTATCGCAACGGGATA
1638923 ATCGCAATGCGAAAATGACTATCGCAACGTGAATTTGACTATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGTGAATTTGACTATCGCAACGGGATA
* *
1638977 ATCGCAATGCGAAAATGACTATCGCAACGCGAATATGACTATCGCAACG
1 ATCGCAATGCGAAAATGACTATCGCAACGTGAATTTGACTATCGCAACG
1639026 CGAATATGAC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 97 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.22
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGACTATCGCAACGTGAATTTGACTATCGCAACGGGATA
Done.