Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008302.1 Hibiscus syriacus cultivar Beakdansim tig00110988_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: 3402722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 17
Found at i:1833509 original size:24 final size:24
Alignment explanation
Indices: 1833482--1833535 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1833472 GTATTCGAAA
* *
1833482 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1833506 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1833530 TTTGAT
1 TTTGAT
1833536 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1836510 original size:20 final size:20
Alignment explanation
Indices: 1836480--1836539 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
1836470 CTTTTGGTTG
1836480 AAATGAAAATCGCAACGAGA
1 AAATGAAAATCGCAACGAGA
* * *
1836500 TAATGAGAATCGCAACGCGA
1 AAATGAAAATCGCAACGAGA
**
1836520 AAATGACTATCGCAACGAGA
1 AAATGAAAATCGCAACGAGA
1836540 GAATCGCAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (20 bp):
AAATGAAAATCGCAACGAGA
Found at i:1836547 original size:14 final size:14
Alignment explanation
Indices: 1836528--1836564 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1836518 GAAAATGACT
1836528 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1836542 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1836556 ATCGCAACG
1 ATCGCAACG
1836565 CGAAATGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.41, C:0.24, G:0.27, T:0.08
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1836589 original size:47 final size:48
Alignment explanation
Indices: 1836504--1836597 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 48
1836494 ACGAGATAAT
*
1836504 GAGAATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAACGA
1 GAGAATCGCAACGCGAAAATGACTATCCCAACGAGAGAATCGCAACGA
* *
1836552 GAGAATCGCAACGCG-AAATGACTATCCCGACTAGAGAATCGCAACG
1 GAGAATCGCAACGCGAAAATGACTATCCCAACGAGAGAATCGCAACG
1836598 CGAAATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
47 28 0.65
48 15 0.35
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.12
Consensus pattern (48 bp):
GAGAATCGCAACGCGAAAATGACTATCCCAACGAGAGAATCGCAACGA
Found at i:1836612 original size:19 final size:19
Alignment explanation
Indices: 1836588--1836657 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
1836578 CCGACTAGAG
*
1836588 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
1836607 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1836626 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1836645 AATCGCAATGCGA
1 AATCGCAACGCGA
1836658 TTTTTGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1836689 original size:19 final size:19
Alignment explanation
Indices: 1836653--1836697 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1836643 AAAATCGCAA
*
1836653 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1836672 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1836691 TACGATT
1 TGCGATT
1836698 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.09, C:0.16, G:0.22, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1837275 original size:20 final size:19
Alignment explanation
Indices: 1837249--1837302 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
1837239 GACGCTATGT
1837249 AAATCGCGTTGCGAAAGTC
1 AAATCGCGTTGCGAAAGTC
1837268 AGAATCGCGTTGCGAAAGTC
1 A-AATCGCGTTGCGAAAGTC
*
1837288 AATATCTCGTTGCGA
1 AA-ATCGCGTTGCGA
1837303 TTTTGTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (19 bp):
AAATCGCGTTGCGAAAGTC
Found at i:1837336 original size:20 final size:20
Alignment explanation
Indices: 1837311--1837364 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1837301 GATTTTGTAT
*
1837311 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGCAAG
*
1837331 TATCGCATTGCGATAGCCAG
1 TATCGCATTGCGATAGCAAG
1837351 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1837365 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (20 bp):
TATCGCATTGCGATAGCAAG
Found at i:1837362 original size:61 final size:61
Alignment explanation
Indices: 1837251--1837367 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 61
1837241 CGCTATGTAA
* * * * * *
1837251 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAATATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGCCAATATCGCATTGCGATTTTGTATT
* * * *
1837312 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGCCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGCCAATATCGCATTGCGATTTT
1837368 CCCAATTCGC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGCCAATATCGCATTGCGATTTTGTATT
Found at i:1837475 original size:21 final size:21
Alignment explanation
Indices: 1837435--1837475 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1837425 ACTGTATACC
**
1837435 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1837456 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1837476 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1839067 original size:18 final size:18
Alignment explanation
Indices: 1839027--1839071 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1839017 GCTTGAGATA
*
1839027 ACCTAAAGAAAATAAAAT
1 ACCTAAAGAAAATAAAAC
* *
1839045 GCCTAAAGAAAATAGAAC
1 ACCTAAAGAAAATAAAAC
1839063 ACCTAAAGA
1 ACCTAAAGA
1839072 TAATCCTAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.60, C:0.16, G:0.11, T:0.13
Consensus pattern (18 bp):
ACCTAAAGAAAATAAAAC
Found at i:1840387 original size:14 final size:15
Alignment explanation
Indices: 1840368--1840401 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1840358 TGCAATGGGC
1840368 TATGAAAAG-TGAAA
1 TATGAAAAGATGAAA
1840382 TATGAAAAGAATGAAA
1 TATGAAAAG-ATGAAA
1840398 TATG
1 TATG
1840402 TCAAATTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
16 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (15 bp):
TATGAAAAGATGAAA
Found at i:1848620 original size:19 final size:19
Alignment explanation
Indices: 1848578--1848631 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
1848568 ATCGGTCGGG
*
1848578 TCGGGTCAGACCGGTCAAA
1 TCGGTTCAGACCGGTCAAA
*
1848597 TCGGTTCAGACCGGTCAGA
1 TCGGTTCAGACCGGTCAAA
1848616 TCGGTTC-GAACCGGTC
1 TCGGTTCAG-ACCGGTC
1848632 GAAACTGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 1 0.03
19 31 0.97
ACGTcount: A:0.20, C:0.28, G:0.31, T:0.20
Consensus pattern (19 bp):
TCGGTTCAGACCGGTCAAA
Found at i:1848668 original size:9 final size:9
Alignment explanation
Indices: 1848581--1848670 Score: 54
Period size: 10 Copynumber: 9.3 Consensus size: 9
1848571 GGTCGGGTCG
*
1848581 GGTCAGACC
1 GGTCAAACC
*
1848590 GGTCAAATC
1 GGTCAAACC
*
1848599 GGTTCAGACC
1 GG-TCAAACC
* *
1848609 GGTCAGATC
1 GGTCAAACC
*
1848618 GGTTCGAACC
1 GG-TCAAACC
*
1848628 GGTCGAAACT
1 GGTC-AAACC
*
1848638 GGTCAAAACA
1 GGTC-AAACC
1848648 GGTTCAAAACC
1 GG-TC-AAACC
1848659 GGTCAAACC
1 GGTCAAACC
1848668 GGT
1 GGT
1848671 TTTCCAGCTG
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
9 27 0.42
10 28 0.44
11 9 0.14
ACGTcount: A:0.29, C:0.26, G:0.28, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1855850 original size:17 final size:17
Alignment explanation
Indices: 1855828--1855860 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1855818 CGGTCAACGG
1855828 TCAACGGTCGGGTCGGA
1 TCAACGGTCGGGTCGGA
1855845 TCAACGGTCGGGTCGG
1 TCAACGGTCGGGTCGG
1855861 TCGGGTCGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.24, G:0.42, T:0.18
Consensus pattern (17 bp):
TCAACGGTCGGGTCGGA
Found at i:1857373 original size:84 final size:84
Alignment explanation
Indices: 1857242--1857440 Score: 310
Period size: 84 Copynumber: 2.4 Consensus size: 84
1857232 CTTTTACTGG
* * * *
1857242 GAGTATCGGTACTTCTCTCAATATTGATACTAATTTTAGGTTCGATGTTTAAGAAATTAAGGTGA
1 GAGTATCGATATTTCTCTCAGTATCGATACTAATTTTAGGTTCGATGTTTAAGAAATTAAGGTGA
1857307 GTATCGATACCCTTAACTA
66 GTATCGATACCCTTAACTA
* * *
1857326 GAGTATCGATATTTCCCTCAGTATCGATACTAATTTTAGGTTTGATGTTTAAGAAATTAAGGTTA
1 GAGTATCGATATTTCTCTCAGTATCGATACTAATTTTAGGTTCGATGTTTAAGAAATTAAGGTGA
1857391 GTATCGATACCCTTAACTA
66 GTATCGATACCCTTAACTA
*
1857410 GAGTATCGATATTCTCTCTC-GTATCAATACT
1 GAGTATCGATATT-TCTCTCAGTATCGATACT
1857441 CCCTTAGTAT
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
84 100 0.95
85 5 0.05
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (84 bp):
GAGTATCGATATTTCTCTCAGTATCGATACTAATTTTAGGTTCGATGTTTAAGAAATTAAGGTGA
GTATCGATACCCTTAACTA
Found at i:1861432 original size:22 final size:18
Alignment explanation
Indices: 1861389--1861458 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
1861379 TTCAGTATTC
*
1861389 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
1861407 GTCCCGAAGGACCACTGTATAT
1 GTCCCGAAGGACCAC----TAT
*
1861429 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
1861447 GTCCCGAAGGAC
1 GTCCCGAAGGAC
1861459 TACTCCTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 28 0.62
22 17 0.38
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.20
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:1866586 original size:22 final size:18
Alignment explanation
Indices: 1866543--1866612 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
1866533 TTTAGTATTC
*
1866543 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
1866561 GTCCCGAAGGACCACTGTATAT
1 GTCCCGAAGGACCAC----TAT
*
1866583 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
1866601 GTCCCGAAGGAC
1 GTCCCGAAGGAC
1866613 TACTCCTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 28 0.62
22 17 0.38
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.20
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:1871709 original size:18 final size:18
Alignment explanation
Indices: 1871686--1871755 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
1871676 TTCAGTATTC
*
1871686 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
*
1871704 GTCCCGAAAGACCACTATATAT
1 GTCCCGAAGGACCAC----TAT
* *
1871726 GTCCCGTATGACCACTAT
1 GTCCCGAAGGACCACTAT
1871744 GTCCCGAAGGAC
1 GTCCCGAAGGAC
1871756 TACTCCTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 26 0.62
22 16 0.38
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.21
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:1871729 original size:22 final size:22
Alignment explanation
Indices: 1871701--1871743 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1871691 GTAGGACCAC
1871701 TATGTCCCGAAAGACCACTATA
1 TATGTCCCGAAAGACCACTATA
* *
1871723 TATGTCCCGTATGACCACTAT
1 TATGTCCCGAAAGACCACTAT
1871744 GTCCCGAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (22 bp):
TATGTCCCGAAAGACCACTATA
Found at i:1876675 original size:29 final size:29
Alignment explanation
Indices: 1876639--1876706 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1876629 CATTTTACAC
* *
1876639 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
* * *
1876668 AAATAGCACTCATTTCGAATTAATTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
*
1876697 GAATAGCACC
1 AAATAGCACC
1876707 ACAACTGAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (29 bp):
AAATAGCACCCATTTCAAAATAATTACCA
Found at i:1876716 original size:29 final size:29
Alignment explanation
Indices: 1876683--1876793 Score: 177
Period size: 29 Copynumber: 3.8 Consensus size: 29
1876673 GCACTCATTT
* *
1876683 CGAATTAATTACCAGAATAGCACCACAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
* *
1876712 TGAATTATTTACCAGAATAGCACTAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
1876741 CGAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
*
1876770 CGAATTATTTACCTGAATAGCACC
1 CGAATTATTTACCAGAATAGCACC
1876794 GGTCAACGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 75 1.00
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.23
Consensus pattern (29 bp):
CGAATTATTTACCAGAATAGCACCAAAAC
Found at i:1876836 original size:13 final size:13
Alignment explanation
Indices: 1876820--1876844 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1876810 CCGGGTAGGG
1876820 TCAACGGGTCGGT
1 TCAACGGGTCGGT
1876833 TCAACGGGTCGG
1 TCAACGGGTCGG
1876845 GTCGGGTCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
TCAACGGGTCGGT
Found at i:1884150 original size:29 final size:29
Alignment explanation
Indices: 1884116--1884221 Score: 149
Period size: 29 Copynumber: 3.7 Consensus size: 29
1884106 GCATCCATTT
* * *
1884116 CGAATTAATTACCATAATAGCACTAAAAT
1 CGAATTATTTACCAGAATAGCACTAAAAC
* *
1884145 CAAATTATTTACCATAATAGCACTAAAAC
1 CGAATTATTTACCAGAATAGCACTAAAAC
* *
1884174 CGAATTATTTACCAGAATAGTACCAAAAC
1 CGAATTATTTACCAGAATAGCACTAAAAC
1884203 CGAATTATTTACCAGAATA
1 CGAATTATTTACCAGAATA
1884222 ACACCGGTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (29 bp):
CGAATTATTTACCAGAATAGCACTAAAAC
Found at i:1884250 original size:17 final size:18
Alignment explanation
Indices: 1884228--1884261 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1884218 AATAACACCG
1884228 GTCAAC-GGTCGGGTCGA
1 GTCAACGGGTCGGGTCGA
1884245 GTCAACGGGTCGGGTCG
1 GTCAACGGGTCGGGTCG
1884262 TGACCGGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.18
Consensus pattern (18 bp):
GTCAACGGGTCGGGTCGA
Found at i:1884387 original size:20 final size:20
Alignment explanation
Indices: 1884362--1884411 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1884352 CTCCGGGGCT
1884362 CTAAAAATTACAGAAAATTC
1 CTAAAAATTACAGAAAATTC
*
1884382 CTAAAAATTACGGAAAATTC
1 CTAAAAATTACAGAAAATTC
1884402 CTAAAAATTA
1 CTAAAAATTA
1884412 TTTTGAGCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (20 bp):
CTAAAAATTACAGAAAATTC
Found at i:1885393 original size:19 final size:20
Alignment explanation
Indices: 1885371--1885408 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1885361 ATATTAATCC
1885371 AAAATAAAAT-AAAATAATG
1 AAAATAAAATGAAAATAATG
1885390 AAAATAAAATGAAAATAAT
1 AAAATAAAATGAAAATAAT
1885409 ACAATGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAATAAAATGAAAATAATG
Found at i:1885402 original size:11 final size:11
Alignment explanation
Indices: 1885371--1885407 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1885361 ATATTAATCC
1885371 AAAATAAAAT-
1 AAAATAAAATG
1885381 AAAAT--AATG
1 AAAATAAAATG
1885390 AAAATAAAATG
1 AAAATAAAATG
1885401 AAAATAA
1 AAAATAA
1885408 TACAATGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 3 0.12
9 5 0.21
10 5 0.21
11 11 0.46
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (11 bp):
AAAATAAAATG
Found at i:1885534 original size:19 final size:19
Alignment explanation
Indices: 1885510--1885603 Score: 76
Period size: 19 Copynumber: 5.3 Consensus size: 19
1885500 ATATGTATAA
1885510 TATATACTATTTTCAAAAC
1 TATATACTATTTTCAAAAC
* *
1885529 TATATA--A-TAT-ATAA-
1 TATATACTATTTTCAAAAC
*
1885543 TATATATTATTTTCAAAAC
1 TATATACTATTTTCAAAAC
* *
1885562 TATATAATATTTTTAAAA-
1 TATATACTATTTTCAAAAC
* *
1885580 T-CATACTATTTTTAAAAC
1 TATATACTATTTTCAAAAC
1885598 TATATA
1 TATATA
1885604 TAATATATGA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
14 6 0.10
15 3 0.05
16 3 0.05
17 17 0.29
18 5 0.08
19 25 0.42
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATACTATTTTCAAAAC
Found at i:1885542 original size:33 final size:34
Alignment explanation
Indices: 1885499--1885603 Score: 140
Period size: 33 Copynumber: 3.0 Consensus size: 34
1885489 CTTTCTAAAA
1885499 AATATGTATAATATATACTATTTTCAAAACTATAT
1 AATAT-TATAATATATACTATTTTCAAAACTATAT
*
1885534 AATA-TATAATATATATTATTTTCAAAACTATAT
1 AATATTATAATATATACTATTTTCAAAACTATAT
* * *
1885567 AATATTTTTAAAATCATACTATTTTTAAAACTATAT
1 AATA-TTATAATAT-ATACTATTTTCAAAACTATAT
1885603 A
1 A
1885604 TAATATATGA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
33 32 0.52
35 10 0.16
36 20 0.32
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.45
Consensus pattern (34 bp):
AATATTATAATATATACTATTTTCAAAACTATAT
Found at i:1886100 original size:37 final size:39
Alignment explanation
Indices: 1886074--1886276 Score: 127
Period size: 38 Copynumber: 5.5 Consensus size: 39
1886064 TTGGAAATTT
*
1886074 TATAATATATGATTTTTAAAAACATTTTTAGAAAACTTA
1 TATAATATATGATTTTGAAAAACATTTTTAGAAAACTTA
* * *
1886113 TATAATATATGGTTTTG-AAAATA-TTTT-GAAAAATATA
1 TATAATATATGATTTTGAAAAACATTTTTAGAAAACT-TA
** *
1886150 TATCCTATATAGATTTTGAAAAAC--GTTT-GAAAA--TA
1 TATAATATAT-GATTTTGAAAAACATTTTTAGAAAACTTA
* *
1886185 T-T-ATATA-GTTTTTAAAAAACA-TTTTA-AAAA-TGTA
1 TATAATATATGATTTTGAAAAACATTTTTAGAAAACT-TA
* *
1886219 TATATTATATGATTTTTGAAAAACA-TTTT-GAAAA-TACA
1 TATAATATATGA-TTTTGAAAAACATTTTTAGAAAACT-TA
1886257 TATAATATAT-AGTTTTGAAA
1 TATAATATATGA-TTTTGAAA
1886277 TCATTTTGAA
Statistics
Matches: 132, Mismatches: 20, Indels: 26
0.74 0.11 0.15
Matches are distributed among these distances:
31 11 0.08
32 7 0.05
33 4 0.03
34 4 0.03
35 4 0.03
36 10 0.08
37 24 0.18
38 49 0.37
39 19 0.14
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (39 bp):
TATAATATATGATTTTGAAAAACATTTTTAGAAAACTTA
Found at i:1886179 original size:38 final size:36
Alignment explanation
Indices: 1886074--1886276 Score: 115
Period size: 37 Copynumber: 5.6 Consensus size: 36
1886064 TTGGAAATTT
*
1886074 TATA-ATATAT-GATTTTTAAAAACATTTTTAGAAAACT-
1 TATATATATATAGATTTTGAAAAACA--TTT-GAAAA-TA
* *
1886111 TATATA-ATATATGGTTTTGAAAATA-TTTTGAAAAATA
1 TATATATATATA-GATTTTGAAAA-ACATTTG-AAAATA
* *
1886148 TATATCCTATATAGATTTTGAAAAACGTTTG--AA-A
1 TATAT-ATATATAGATTTTGAAAAACATTTGAAAATA
* * *
1886182 -ATAT-TATATAGTTTTTAAAAAACATTTTAAAA-A
1 TATATATATATAGATTTTGAAAAACATTTGAAAATA
*
1886215 TGTATATATTATATGATTTTTGAAAAACATTTTGAAAATA
1 TATATATA-TATA-GA-TTTTGAAAAACA-TTTGAAAATA
*
1886255 CATATAATATATAG-TTTTGAAA
1 TATAT-ATATATAGATTTTGAAA
1886277 TCATTTTGAA
Statistics
Matches: 131, Mismatches: 16, Indels: 38
0.71 0.09 0.21
Matches are distributed among these distances:
31 20 0.15
33 7 0.05
34 4 0.03
35 4 0.03
36 6 0.05
37 30 0.23
38 26 0.20
39 22 0.17
40 9 0.07
41 3 0.02
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (36 bp):
TATATATATATAGATTTTGAAAAACATTTGAAAATA
Found at i:1886203 original size:31 final size:31
Alignment explanation
Indices: 1886155--1886222 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1886145 ATATATATCC
* *
1886155 TATATAGATTTTGAAAAACGTTTGAAAATAT-
1 TATATAGATTTTAAAAAACATTTGAAAA-ATG
* *
1886186 TATATAGTTTTTAAAAAACATTTTAAAAATG
1 TATATAGATTTTAAAAAACATTTGAAAAATG
1886217 TATATA
1 TATATA
1886223 TTATATGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (31 bp):
TATATAGATTTTAAAAAACATTTGAAAAATG
Found at i:1886260 original size:69 final size:70
Alignment explanation
Indices: 1886130--1886260 Score: 169
Period size: 69 Copynumber: 1.9 Consensus size: 70
1886120 TATGGTTTTG
* * *
1886130 AAAATATTTTGAAAAATATATATCCTATATAGATTTTGAAAAACGTTTGAAAATATTATATAGTT
1 AAAACATTTTGAAAAATATATATACTATATAGATTTTGAAAAACGTTTGAAAATATCATATAGTT
1886195 TTTAA
66 TTTAA
* * *
1886200 AAAACATTTT-AAAAATGTATATATTATAT-GATTTTTGAAAAACATTTTGAAAATA-CATATA
1 AAAACATTTTGAAAAATATATATACTATATAGA-TTTTGAAAAAC-GTTTGAAAATATCATATA
1886261 ATATATAGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
68 2 0.04
69 32 0.60
70 19 0.36
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (70 bp):
AAAACATTTTGAAAAATATATATACTATATAGATTTTGAAAAACGTTTGAAAATATCATATAGTT
TTTAA
Found at i:1886293 original size:25 final size:25
Alignment explanation
Indices: 1886265--1886314 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1886255 CATATAATAT
*
1886265 ATAGTTTTGAAATCA-TTTTGAAAAC
1 ATAGTTTT-AAAACATTTTTGAAAAC
1886290 ATAGTTTTAAAACATTTTTGAAAAC
1 ATAGTTTTAAAACATTTTTGAAAAC
1886315 TATATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (25 bp):
ATAGTTTTAAAACATTTTTGAAAAC
Found at i:1886349 original size:30 final size:28
Alignment explanation
Indices: 1886294--1886350 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
1886284 GAAAACATAG
*
1886294 TTTTAAAACATTTTTGAAAACTATATAA
1 TTTTAAAACATTTTTGAAAAATATATAA
*
1886322 TTTTAAAAACAATTTTTTAAAAATATATA
1 TTTT-AAAAC-ATTTTTGAAAAATATATA
1886351 TAATATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 5 0.20
30 16 0.64
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (28 bp):
TTTTAAAACATTTTTGAAAAATATATAA
Found at i:1886385 original size:38 final size:39
Alignment explanation
Indices: 1886315--1886438 Score: 128
Period size: 38 Copynumber: 3.2 Consensus size: 39
1886305 TTTTGAAAAC
* *
1886315 TATATAATTTTAAAAACAATTTTTTAAAAATATATATAA
1 TATATAATTTTGAAAATAATTTTTTAAAAATATATATAA
* *
1886354 TATATAATTTT-AAAATATTTTTTTAAAAATATATATTA
1 TATATAATTTTGAAAATAATTTTTTAAAAATATATATAA
** * * *
1886392 TATAGGATTTTGGAAAATAGTTTTATAATAATA-ATAATAA
1 TATATAATTTT-GAAAATAATTTTTTAAAAATATAT-ATAA
1886432 TA-ATAAT
1 TATATAAT
1886439 ATTGTTATTT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
38 33 0.46
39 16 0.23
40 22 0.31
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (39 bp):
TATATAATTTTGAAAATAATTTTTTAAAAATATATATAA
Found at i:1886452 original size:4 final size:4
Alignment explanation
Indices: 1886443--1886472 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1886433 AATAATATTG
1886443 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1886473 TTATTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:1890805 original size:2 final size:2
Alignment explanation
Indices: 1890794--1890826 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1890784 AAAATATTAA
1890794 AT AT -T 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
1890827 TAAATACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1891393 original size:14 final size:14
Alignment explanation
Indices: 1891371--1891421 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
1891361 TCGGTAATTT
*
1891371 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
1891385 GTTCATTTATGTTC
1 GTTCATTTATGTTC
*
1891399 G----TTTATGTGC
1 GTTCATTTATGTTC
1891409 GTTCATTTATGTT
1 GTTCATTTATGTT
1891422 TAGCCCAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
10 9 0.30
14 21 0.70
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:1891402 original size:24 final size:24
Alignment explanation
Indices: 1891370--1891421 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1891360 TTCGGTAATT
*
1891370 TGTTCGTTTATGTTCGTTCATTTA
1 TGTTCGTTTATGTGCGTTCATTTA
1891394 TGTTCGTTTATGTGCGTTCATTTA
1 TGTTCGTTTATGTGCGTTCATTTA
1891418 TGTT
1 TGTT
1891422 TAGCCCAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.58
Consensus pattern (24 bp):
TGTTCGTTTATGTGCGTTCATTTA
Found at i:1891626 original size:23 final size:23
Alignment explanation
Indices: 1891600--1891654 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
1891590 CATTTATGCC
*
1891600 CGTTTACGTTCATTTATTATGTT
1 CGTTTACATTCATTTATTATGTT
* * *
1891623 CGTTTGCATTCGTTTATTGTGTT
1 CGTTTACATTCATTTATTATGTT
*
1891646 CATTTACAT
1 CGTTTACAT
1891655 CCTTTCGTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.15, G:0.15, T:0.55
Consensus pattern (23 bp):
CGTTTACATTCATTTATTATGTT
Found at i:1894053 original size:11 final size:12
Alignment explanation
Indices: 1894024--1894056 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1894014 TTATTATATT
1894024 TTTATAAAAAAA
1 TTTATAAAAAAA
1894036 TTGTATAAAAAAA
1 TT-TATAAAAAAA
1894049 -TTATAAAA
1 TTTATAAAA
1894057 CATTATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 7 0.35
12 3 0.15
13 10 0.50
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
TTTATAAAAAAA
Found at i:1894168 original size:11 final size:11
Alignment explanation
Indices: 1894149--1894195 Score: 78
Period size: 11 Copynumber: 4.4 Consensus size: 11
1894139 ATTATCTATT
1894149 TAATTTTAAAA
1 TAATTTTAAAA
1894160 TAATTTTAAAA
1 TAATTTTAAAA
1894171 TAA-TTTAAAA
1 TAATTTTAAAA
*
1894181 TAGTTTTAAAA
1 TAATTTTAAAA
1894192 TAAT
1 TAAT
1894196 ATCCAACTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:1894179 original size:21 final size:21
Alignment explanation
Indices: 1894153--1894195 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1894143 TCTATTTAAT
1894153 TTTAAAATAATTTTAAAATAA
1 TTTAAAATAATTTTAAAATAA
*
1894174 TTTAAAATAGTTTTAAAATAA
1 TTTAAAATAATTTTAAAATAA
1894195 T
1 T
1894196 ATCCAACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTTAAAATAATTTTAAAATAA
Found at i:1894270 original size:15 final size:15
Alignment explanation
Indices: 1894222--1894273 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 15
1894212 GGTTCCATAC
1894222 AATATTATTTAAAATT
1 AATATTATTTAAAA-T
*
1894238 AAATAGATAATTTAAAAAT
1 -AAT--ATTATTT-AAAAT
1894257 AATATTATTTAAAAT
1 AATATTATTTAAAAT
1894272 AA
1 AA
1894274 ATAATTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 7 0.23
16 6 0.20
17 3 0.10
18 3 0.10
19 7 0.23
20 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AATATTATTTAAAAT
Found at i:1894277 original size:19 final size:19
Alignment explanation
Indices: 1894222--1894278 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
1894212 GGTTCCATAC
1894222 AATATTATTTAAAATTAAAT
1 AATATTATTTAAAA-TAAAT
1894242 AGATA--ATTT--AA-AAAT
1 A-ATATTATTTAAAATAAAT
1894257 AATATTATTTAAAATAAAT
1 AATATTATTTAAAATAAAT
1894276 AAT
1 AAT
1894279 TAATATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
14 3 0.10
15 5 0.16
16 4 0.13
17 2 0.06
18 2 0.06
19 11 0.35
20 1 0.03
21 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AATATTATTTAAAATAAAT
Found at i:1894282 original size:23 final size:23
Alignment explanation
Indices: 1894253--1894329 Score: 91
Period size: 23 Copynumber: 3.2 Consensus size: 23
1894243 GATAATTTAA
1894253 AAATAATATTATTTAAAATAAAT
1 AAATAATATTATTTAAAATAAAT
* * *
1894276 AATTAATATTATTTGAAACAAAT
1 AAATAATATTATTTAAAATAAAT
*
1894299 AAATAATATGATTTTAAAAATTAAAT
1 AAATAATATTA-TTT-AAAA-TAAAT
1894325 AAATA
1 AAATA
1894330 TTTTAAAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
23 29 0.66
24 3 0.07
25 3 0.07
26 9 0.20
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (23 bp):
AAATAATATTATTTAAAATAAAT
Found at i:1903736 original size:21 final size:21
Alignment explanation
Indices: 1903710--1903792 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 21
1903700 CAGATCCCCA
*
1903710 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1903731 GGGGGGAATCGGTTCCCCT-T
1 GGGGGGAATCGATTCCCCTGT
* * *
1903751 CAAAGGGGGAATCGGTTCCCTCAG-
1 ---GGGGGGAATCGATTCCC-CTGT
1903775 GGGGAGGAATCGATTCCC
1 GGGG-GGAATCGATTCCC
1903793 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
20 1 0.02
21 20 0.40
22 12 0.24
23 16 0.32
24 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.37, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1903771 original size:22 final size:22
Alignment explanation
Indices: 1903732--1903793 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
1903722 TTCCCCTGTG
1903732 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCCTTCAAA
**
1903755 GGGGGAATCGGTTCCC-TCAGG
1 GGGGGAATCGGTTCCCTTCAAA
*
1903776 GGGAGGAATCGATTCCCT
1 GGG-GGAATCGGTTCCCT
1903794 CTGCACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.18
22 15 0.44
23 13 0.38
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.21
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTTCAAA
Found at i:1910032 original size:28 final size:26
Alignment explanation
Indices: 1909999--1910050 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
1909989 TTTAATAAAT
* *
1909999 AATTTATTTTCTTCTTAAGAATTTTATA
1 AATTTATCTTATT-TTAA-AATTTTATA
1910027 AATTTATCTTATTTTAAAATTTTA
1 AATTTATCTTATTTTAAAATTTTA
1910051 AAGATCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 4 0.18
28 11 0.50
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (26 bp):
AATTTATCTTATTTTAAAATTTTATA
Found at i:1919063 original size:15 final size:15
Alignment explanation
Indices: 1919043--1919078 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1919033 TATTTGGGTG
*
1919043 TTATATTAATATCGT
1 TTATATTAATACCGT
1919058 TTATATTAATACCGT
1 TTATATTAATACCGT
1919073 TTATAT
1 TTATAT
1919079 GGTATAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (15 bp):
TTATATTAATACCGT
Found at i:1919540 original size:496 final size:479
Alignment explanation
Indices: 1918600--1919559 Score: 1203
Period size: 496 Copynumber: 2.0 Consensus size: 479
1918590 TTATTTTTTT
* * * * *
1918600 GTATAACCTGATTTTAATTTTAGTTACATAATGGGCTCGTTGTATTAAAAAAGGAAGTATCTTCT
1 GTATAACATAATTTTAATTTTAGTTACATAATGGGCTCATGGTATTAAAAAAGGAAGTATCATCT
* * * * *
1918665 GTATCATGTAATAATACGTGGACAATTCCAGCATTGTTGTCTCTGGGAATACATGCAATATATCA
66 GTATCATATAATAACACGTGGACAATTCCAGCATTGCTGCCTCTGGGAATACACGCAATATATCA
* ** *
1918730 CTCAAGCTTTTTGTCGTATTGGCTATCGCTCGTACGAGTGAGAGAGAGAGAATTATTCATCTTCA
131 CTCAAGCTCTTTGTCGTATTGGAAATCGCTCGTACAAGT-AGAGAGAGAGAATTATTCATCTTCA
* * * * *
1918795 TTAGCTTAAAAACTTGGGTCATTATCGACTTGAATCTGCGAACGCTCAAACCTTGAGGTGAAAAT
195 TTAGCTTAAAAACTTAGGTAATTATCGACTTGAATCTACAAACGCTCAAACCTTGAGGAGAAAAT
* * * *
1918860 TGATTTTTCCACTCAATGGATAACGAGCCTCTTCCTCGTTTAGTAAGACGTTTTTTTTCTCAACT
260 TGATTTTTCCACTCAATGGATAACAAGCATCTTCCTCATTTAGTAAGACGTTTTTTGTCTCAACT
*
1918925 CTAACAGTTTCAGGTGTAGTGGGGCCCATCTTCCTTCTCCGTTAAAAGATTTAAAAAAAAAAGTT
325 CTAACAGTTTCAGGTGTAGTGGGGCCCATCTTCCTTCACCGTTAAAAGATTTAAAAAAAAAAGTT
* *
1918990 TCCTTCACTCTCACATTCAATCTTGATTGAGGTGATAACAAATTATTTGGGTGTTATATTAATAT
390 TCCTTCACTCTCAAATTCAATCTTGATTGAGGCGATAACAAATTATTTGGGTGTTATATTAATAT
*
1919055 CGTTTATATTAATACCGTTTATATG
455 CATTTATATTAATACCGTTTATATG
*
1919080 GTATAACATAATTTTAATTTTAGTTACATCATGGG-TCCATGGTA-TAAAAAAGGAAGTATCATC
1 GTATAACATAATTTTAATTTTAGTTACATAATGGGCT-CATGGTATTAAAAAAGGAAGTATCATC
* ** *
1919143 TGTATCTTATAATAACACGTGGACAATTTTAGTATTGCTGCCTCTGGGAATACACGCAAATATAT
65 TGTATCATATAATAACACGTGGACAATTCCAGCATTGCTGCCTCTGGGAATACACGC-AATATAT
* *
1919208 CA-TCCAGCCTCTTTGTCGTATTGGAAATCGCTCGTACAAGT-GAGAGAGAGAATTGTTCATCTT
129 CACTCAAG-CTCTTTGTCGTATTGGAAATCGCTCGTACAAGTAGAGAGAGAGAATTATTCATCTT
* *
1919271 CATTAGCTTAAAAACTTAGGTAATTATCGTCTTGAATCTACAAAAACCTTGAATTTGCAAACACT
193 CATTAGCTTAAAAACTTAGGTAATTATCGACTTGAATCTAC--AAA-C--G---CT-C-AA-A--
*
1919336 CGATCATTGAGGAGAAAATTGATTTTTCCACTCAATGGATAACAAGCATCTTCCTCATTTCGTAA
245 C---C-TTGAGGAGAAAATTGATTTTTCCACTCAATGGATAACAAGCATCTTCCTCATTTAGTAA
** * * *
1919401 GACGTTTGTTTGTCTCAGTTAC-AACAGTTTCAGGTGTAGTGGGGCTCATCTTCCTTCACTGTTC
306 GACGTTT-TTTGTCTCAACT-CTAACAGTTTCAGGTGTAGTGGGGCCCATCTTCCTTCACCGTTA
* ** * * * * **
1919465 AAAGCTCTT-AAAGCAGAAGTTTCCTTCACTTTCAAATTCAATCTTGGTTGAGGCGATAATAGTT
369 AAAGAT-TTAAAAAAAAAAGTTTCCTTCACTCTCAAATTCAATCTTGATTGAGGCGATAACAAAT
1919529 TATTTGGGTGTTATATTAATATCATTTATAT
433 TATTTGGGTGTTATATTAATATCATTTATAT
1919560 GGTCGTAATC
Statistics
Matches: 406, Mismatches: 51, Indels: 30
0.83 0.10 0.06
Matches are distributed among these distances:
478 58 0.14
479 71 0.17
480 77 0.19
481 1 0.00
483 1 0.00
486 1 0.00
487 1 0.00
488 2 0.00
489 1 0.00
491 1 0.00
494 1 0.00
495 61 0.15
496 127 0.31
497 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (479 bp):
GTATAACATAATTTTAATTTTAGTTACATAATGGGCTCATGGTATTAAAAAAGGAAGTATCATCT
GTATCATATAATAACACGTGGACAATTCCAGCATTGCTGCCTCTGGGAATACACGCAATATATCA
CTCAAGCTCTTTGTCGTATTGGAAATCGCTCGTACAAGTAGAGAGAGAGAATTATTCATCTTCAT
TAGCTTAAAAACTTAGGTAATTATCGACTTGAATCTACAAACGCTCAAACCTTGAGGAGAAAATT
GATTTTTCCACTCAATGGATAACAAGCATCTTCCTCATTTAGTAAGACGTTTTTTGTCTCAACTC
TAACAGTTTCAGGTGTAGTGGGGCCCATCTTCCTTCACCGTTAAAAGATTTAAAAAAAAAAGTTT
CCTTCACTCTCAAATTCAATCTTGATTGAGGCGATAACAAATTATTTGGGTGTTATATTAATATC
ATTTATATTAATACCGTTTATATG
Found at i:1920790 original size:2 final size:2
Alignment explanation
Indices: 1920783--1920809 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1920773 TCTTTATCTT
1920783 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1920810 TACATAGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1921966 original size:401 final size:401
Alignment explanation
Indices: 1921223--1922027 Score: 1574
Period size: 401 Copynumber: 2.0 Consensus size: 401
1921213 CATTCACCCT
1921223 AGAACTAGCTCAAACATGAAAGGCTACCTTCTAACAATTGTGACCTTTCATGAATGATGTTGCCC
1 AGAACTAGCTCAAACATGAAAGGCTACCTTCTAACAATTGTGACCTTTCATGAATGATGTTGCCC
1921288 ATGAAGGTGCCCTTTCATCAAGGTACACGTTGGTGAATAGTTTACATCCATTGGAGGCCTAAATC
66 ATGAAGGTGCCCTTTCATCAAGGTACACGTTGGTGAATAGTTTACATCCATTGGAGGCCTAAATC
1921353 ATGAAGGGACATGAGACAAAGCACCATGCCTATTCGGCCAACATCCACATGCTTTGCACATGAGA
131 ATGAAGGGACATGAGACAAAGCACCATGCCTATTCGGCCAACATCCACATGCTTTGCACATGAGA
*
1921418 GCTTTGGGCGCCAAAATAAACCAGCACATCATCATTCGGCCAAGAAGGATGACTTTGGCATCAAG
196 GCTTTGGGCGCCAAAATAAACCAGCACATCACCATTCGGCCAAGAAGGATGACTTTGGCATCAAG
*
1921483 ATGAACAAGCATTTACCATTCGGCCAAGGGAAATATATCTTCATCATTGCCGAAACATCATGATC
261 ATGAACAAGCATTTACCATTCGACCAAGGGAAATATATCTTCATCATTGCCGAAACATCATGATC
1921548 CCTTTGAAGAGGTAGCCGAACCCTTACCAAGCCAAGGGACTTCTCCTTTCATTTTAAAGCATTAT
326 CCTTTGAAGAGGTAGCCGAACCCTTACCAAGCCAAGGGACTTCTCCTTTCATTTTAAAGCATTAT
1921613 GTACTTTCATA
391 GTACTTTCATA
1921624 AGAACTAGCTCAAACATGAAAGGCTACCTTCTAACAATTGTGACCTTTCATGAATGATGTTGCCC
1 AGAACTAGCTCAAACATGAAAGGCTACCTTCTAACAATTGTGACCTTTCATGAATGATGTTGCCC
1921689 ATGAAGGTGCCCTTTCATCAAGGTACACGTTGGTGAATAGTTTACATCCATTGGAGGCCTAAATC
66 ATGAAGGTGCCCTTTCATCAAGGTACACGTTGGTGAATAGTTTACATCCATTGGAGGCCTAAATC
* *
1921754 ATGAAGGGACATGAGACAAAGCACCATGCCTATTCGTCCACCATCCACATGCTTTGCACATGAGA
131 ATGAAGGGACATGAGACAAAGCACCATGCCTATTCGGCCAACATCCACATGCTTTGCACATGAGA
1921819 GCTTTGGGCGCCAAAATAAACCAGCACATCACCATTCGGCCAAGAAGGATGACTTTGGCATCAAG
196 GCTTTGGGCGCCAAAATAAACCAGCACATCACCATTCGGCCAAGAAGGATGACTTTGGCATCAAG
1921884 ATGAACAAGCATTTACCATTCGACCAAGGGAAATATATCTTCATCATTGCCGAAACATCATGATC
261 ATGAACAAGCATTTACCATTCGACCAAGGGAAATATATCTTCATCATTGCCGAAACATCATGATC
1921949 CCTTTGAAGAGGTAGCCGAACCCTTACCAAGCCAAGGGACTTCTCCTTTCATTTTAAAGCATTAT
326 CCTTTGAAGAGGTAGCCGAACCCTTACCAAGCCAAGGGACTTCTCCTTTCATTTTAAAGCATTAT
1922014 GTACTTTCATA
391 GTACTTTCATA
1922025 AGA
1 AGA
1922028 GTCATGTATC
Statistics
Matches: 400, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
401 400 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (401 bp):
AGAACTAGCTCAAACATGAAAGGCTACCTTCTAACAATTGTGACCTTTCATGAATGATGTTGCCC
ATGAAGGTGCCCTTTCATCAAGGTACACGTTGGTGAATAGTTTACATCCATTGGAGGCCTAAATC
ATGAAGGGACATGAGACAAAGCACCATGCCTATTCGGCCAACATCCACATGCTTTGCACATGAGA
GCTTTGGGCGCCAAAATAAACCAGCACATCACCATTCGGCCAAGAAGGATGACTTTGGCATCAAG
ATGAACAAGCATTTACCATTCGACCAAGGGAAATATATCTTCATCATTGCCGAAACATCATGATC
CCTTTGAAGAGGTAGCCGAACCCTTACCAAGCCAAGGGACTTCTCCTTTCATTTTAAAGCATTAT
GTACTTTCATA
Found at i:1922507 original size:12 final size:13
Alignment explanation
Indices: 1922486--1922519 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1922476 TATTTACTTA
*
1922486 TCCATATCT-ATT
1 TCCATTTCTAATT
1922498 TCCATTTCTAATT
1 TCCATTTCTAATT
1922511 TCCATTTCT
1 TCCATTTCT
1922520 TTCTTATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (13 bp):
TCCATTTCTAATT
Found at i:1924556 original size:195 final size:195
Alignment explanation
Indices: 1924224--1924613 Score: 647
Period size: 195 Copynumber: 2.0 Consensus size: 195
1924214 AACTCAACAA
* * * * *
1924224 GGATAACTGAGGAAAAGAAACCCTTGAATGGTCAATAGACATTCGGTGTTTTAAATGTCTTGGGA
1 GGATAACCGAGGAAAAGAAACCCCTGAACGATCAAGAGACATTCGGTGTTTTAAATGTCTTGGGA
1924289 GGGGGCATGTTTCTACACAATGTCCCAACCGAAACACTATGTTACTACTTGGAAATGGTGATAAT
66 GGGGGCATGTTTCTACACAATGTCCCAACCGAAACACTATGTTACTACTTGGAAATGGTGATAAT
* *
1924354 GAATCTGACCACGAAGAAGAAGAAGCAACACCAACCGAAGTCGAGGAAGAAG-TGAAAATTGGGG
131 GAATCTGACCACGAAGAAGAAAAAGCAACACCAACCGAAGTCGAGGAAGAAGCAG-AAATTGGGG
1924418 C
195 C
*
1924419 GGATAACCGAGGAAAAGAAACCCCTGAACGATCAAGAGATATTCGGTGTTTTAAATGTCTTGGGA
1 GGATAACCGAGGAAAAGAAACCCCTGAACGATCAAGAGACATTCGGTGTTTTAAATGTCTTGGGA
* * *
1924484 GGGGGTATGTTTCTACACAATGTTCCAACCGAAACACTATGTTACTACTTGGAAATGGTGATATT
66 GGGGGCATGTTTCTACACAATGTCCCAACCGAAACACTATGTTACTACTTGGAAATGGTGATAAT
* *
1924549 GAATCTGACCATGAAGAAGAAAAAGCAGCACCAACCGAAGTCGAGGAAGAAGCAGAAATTGGGGC
131 GAATCTGACCACGAAGAAGAAAAAGCAACACCAACCGAAGTCGAGGAAGAAGCAGAAATTGGGGC
1924614 TCCCATGGAA
Statistics
Matches: 181, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
195 180 0.99
196 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.22
Consensus pattern (195 bp):
GGATAACCGAGGAAAAGAAACCCCTGAACGATCAAGAGACATTCGGTGTTTTAAATGTCTTGGGA
GGGGGCATGTTTCTACACAATGTCCCAACCGAAACACTATGTTACTACTTGGAAATGGTGATAAT
GAATCTGACCACGAAGAAGAAAAAGCAACACCAACCGAAGTCGAGGAAGAAGCAGAAATTGGGGC
Found at i:1928014 original size:17 final size:17
Alignment explanation
Indices: 1927992--1928025 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1927982 TCATTATCAA
1927992 CTTGAATCTGCAAACAC
1 CTTGAATCTGCAAACAC
*
1928009 CTTGAATCTTCAAACAC
1 CTTGAATCTGCAAACAC
1928026 TCAAACCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.26
Consensus pattern (17 bp):
CTTGAATCTGCAAACAC
Found at i:1942092 original size:20 final size:20
Alignment explanation
Indices: 1942067--1942104 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1942057 TTTTGATGCA
*
1942067 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
1942087 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
1942105 TTTGAAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:1943799 original size:12 final size:12
Alignment explanation
Indices: 1943782--1943807 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1943772 TGAGCCTGAA
1943782 CAGCCCGAGGAG
1 CAGCCCGAGGAG
1943794 CAGCCCGAGGAG
1 CAGCCCGAGGAG
1943806 CA
1 CA
1943808 AGCACAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.35, G:0.38, T:0.00
Consensus pattern (12 bp):
CAGCCCGAGGAG
Found at i:1944931 original size:20 final size:20
Alignment explanation
Indices: 1944898--1944935 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1944888 ATTTTATACT
*
1944898 TAGGGAACCGATTCCCCCTA
1 TAGGGAACCAATTCCCCCTA
*
1944918 TAGGGTACCAATTCCCCC
1 TAGGGAACCAATTCCCCC
1944936 CACGCTCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (20 bp):
TAGGGAACCAATTCCCCCTA
Found at i:1947824 original size:2 final size:2
Alignment explanation
Indices: 1947759--1947808 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1947749 AATAAAAATG
1947759 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
1947801 AT AT AT AT
1 AT AT AT AT
1947809 GAGTTAAATC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1956589 original size:2 final size:2
Alignment explanation
Indices: 1956582--1956611 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1956572 AGGAGAAAAC
1956582 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
1956612 GTGTGTGTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1964801 original size:27 final size:27
Alignment explanation
Indices: 1964770--1964822 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1964760 TCGGTCAGAG
1964770 ACCATATTTAAAATTTTAAATCATAAT
1 ACCATATTTAAAATTTTAAATCATAAT
**
1964797 ACCATATTTAAGTTTTTAAATCATAA
1 ACCATATTTAAAATTTTAAATCATAA
1964823 CACGAATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (27 bp):
ACCATATTTAAAATTTTAAATCATAAT
Found at i:1973926 original size:24 final size:23
Alignment explanation
Indices: 1973897--1973943 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
1973887 AAAAAATCAG
*
1973897 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTCAAGCTCGA-ACTC
1973921 GAGCTCGATTCAAGCTCGAACTC
1 GAGCTCGATTCAAGCTCGAACTC
1973944 AAACTCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.21
Consensus pattern (23 bp):
GAGCTCGATTCAAGCTCGAACTC
Found at i:1976041 original size:23 final size:23
Alignment explanation
Indices: 1976014--1976078 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
1976004 CAGCTCGTAT
1976014 AATTGCACCAAAGTGCCATGTAG
1 AATTGCACCAAAGTGCCATGTAG
* * **
1976037 AATTGTACCAGAGTGCCGCGTAG
1 AATTGCACCAAAGTGCCATGTAG
**
1976060 AATTGCACCGTAGTGCCAT
1 AATTGCACCAAAGTGCCAT
1976079 ATAATAATGT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (23 bp):
AATTGCACCAAAGTGCCATGTAG
Found at i:1979719 original size:14 final size:14
Alignment explanation
Indices: 1979700--1979754 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
1979690 CATATAATCT
*
1979700 GGTTTAGGGGTTAG
1 GGTTTAGGGTTTAG
* *
1979714 GGTTTAAGGTTTAT
1 GGTTTAGGGTTTAG
* *
1979728 AGTTTAGGATTTAG
1 GGTTTAGGGTTTAG
*
1979742 GGTTTAGGATTTA
1 GGTTTAGGGTTTA
1979755 TAGAATAAGG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.44
Consensus pattern (14 bp):
GGTTTAGGGTTTAG
Found at i:1979726 original size:21 final size:21
Alignment explanation
Indices: 1979700--1979749 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1979690 CATATAATCT
*
1979700 GGTTTAGGGGTTAGGGTTTAA
1 GGTTTAGGGGTTAGGATTTAA
** * *
1979721 GGTTTATAGTTTAGGATTTAG
1 GGTTTAGGGGTTAGGATTTAA
1979742 GGTTTAGG
1 GGTTTAGG
1979750 ATTTATAGAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (21 bp):
GGTTTAGGGGTTAGGATTTAA
Found at i:1979741 original size:28 final size:28
Alignment explanation
Indices: 1979701--1979757 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1979691 ATATAATCTG
*
1979701 GTTTAGGGGTTAGGGTTTAAGG-TTTATA
1 GTTTAGGAGTTAGGGTTT-AGGATTTATA
*
1979729 GTTTAGGATTTAGGGTTTAGGATTTATA
1 GTTTAGGAGTTAGGGTTTAGGATTTATA
1979757 G
1 G
1979758 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (28 bp):
GTTTAGGAGTTAGGGTTTAGGATTTATA
Found at i:1979768 original size:28 final size:28
Alignment explanation
Indices: 1979710--1979773 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
1979700 GGTTTAGGGG
* *
1979710 TTAGGGTTTAAGGTTTATAGTTTAGGAT
1 TTAGGGTTTAAGGTTTATAGATAAGGAT
1979738 TTAGGGTTT-AGGATTTATAGAATAAGG-T
1 TTAGGGTTTAAGG-TTTATAG-ATAAGGAT
*
1979766 TTAAGGTT
1 TTAGGGTT
1979774 CATTACAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 3 0.10
28 24 0.77
29 4 0.13
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (28 bp):
TTAGGGTTTAAGGTTTATAGATAAGGAT
Found at i:1979880 original size:7 final size:7
Alignment explanation
Indices: 1979870--1979904 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
1979860 TGGTTTATAT
1979870 TTTAGGG
1 TTTAGGG
1979877 TTTAGGG
1 TTTAGGG
1979884 -TTAGGG
1 TTTAGGG
1979890 -TTAGGG
1 TTTAGGG
1979896 TTTAGGG
1 TTTAGGG
1979903 TT
1 TT
1979905 CATTATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
TTTAGGG
Found at i:1979889 original size:6 final size:6
Alignment explanation
Indices: 1979871--1979904 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
1979861 GGTTTATATT
1979871 TTAGGG TTTAGGG TTAGGG TTAGGG TTTAGGG TT
1 TTAGGG -TTAGGG TTAGGG TTAGGG -TTAGGG TT
1979905 CATTATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 14 0.54
7 12 0.46
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.41
Consensus pattern (6 bp):
TTAGGG
Found at i:1979889 original size:13 final size:13
Alignment explanation
Indices: 1979870--1979904 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
1979860 TGGTTTATAT
1979870 TTTAGGGTTTAGGG
1 TTTAGGG-TTAGGG
1979884 -TTAGGGTTAGGG
1 TTTAGGGTTAGGG
1979896 TTTAGGGTT
1 TTTAGGGTT
1979905 CATTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (13 bp):
TTTAGGGTTAGGG
Found at i:1980054 original size:41 final size:42
Alignment explanation
Indices: 1979953--1980054 Score: 197
Period size: 42 Copynumber: 2.5 Consensus size: 42
1979943 GTATTATAGA
1979953 ATTTTTAATATATTTTTAAAAAGTTATAATTATCAATAGTGT
1 ATTTTTAATATATTTTTAAAAAGTTATAATTATCAATAGTGT
1979995 ATTTTTAATATATTTTTAAAAAGTTATAATTATCAATAGTGT
1 ATTTTTAATATATTTTTAAAAAGTTATAATTATCAATAGTGT
1980037 A-TTTTAATATATTTTTAA
1 ATTTTTAATATATTTTTAA
1980055 TAATGTAATT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 17 0.28
42 43 0.72
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (42 bp):
ATTTTTAATATATTTTTAAAAAGTTATAATTATCAATAGTGT
Found at i:1981988 original size:36 final size:36
Alignment explanation
Indices: 1981948--1982028 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
1981938 GATAACTTGG
1981948 TTTGAGCATATTTGCAACACTAGTGGGATAACCTAA
1 TTTGAGCATATTTGCAACACTAGTGGGATAACCTAA
* **
1981984 TTTGAGTATATTTTTAACACTAGTGGGATAACCTAA
1 TTTGAGCATATTTGCAACACTAGTGGGATAACCTAA
1982020 TTTGAGCAT
1 TTTGAGCAT
1982029 TATCAACATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36
Consensus pattern (36 bp):
TTTGAGCATATTTGCAACACTAGTGGGATAACCTAA
Found at i:1989018 original size:64 final size:63
Alignment explanation
Indices: 1988888--1989009 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 63
1988878 CCCTTTTGAT
* * * * *
1988888 AAAATGTGAATCGAATATAAATAAAATTGACGTTTGCATACAACAAAATAAATTGATTAACTA
1 AAAATGTGAATCGAATACAAATAAAATTGACATTTACATAAAACAAAATAAATTGACTAACTA
* * *
1988951 AAAATGTGAATTGAATACAAATGCAAATTGACATTTACATAAAATAAAATAAATT-ACTA
1 AAAATGTGAATCGAATACAAAT-AAAATTGACATTTACATAAAACAAAATAAATTGACTA
1989010 TTTAAAAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
63 23 0.46
64 27 0.54
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.29
Consensus pattern (63 bp):
AAAATGTGAATCGAATACAAATAAAATTGACATTTACATAAAACAAAATAAATTGACTAACTA
Found at i:1990965 original size:25 final size:25
Alignment explanation
Indices: 1990924--1991047 Score: 223
Period size: 25 Copynumber: 5.0 Consensus size: 25
1990914 CATTAGGGGA
* *
1990924 TTAGGG-TTAAAACCCTAATTTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
1990948 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
1990973 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
1990998 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
1991023 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
1991048 GGGTTGATTG
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
24 6 0.06
25 91 0.94
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:1991124 original size:3 final size:3
Alignment explanation
Indices: 1991111--1991157 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
1991101 AATATGTAAT
1991111 TAA TAA T-A TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1991155 TAA
1 TAA
1991158 CGATAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1991375 original size:43 final size:44
Alignment explanation
Indices: 1991314--1991421 Score: 128
Period size: 43 Copynumber: 2.4 Consensus size: 44
1991304 TGTTGGGGAC
* * * *
1991314 GACACTGCTCATACGTGATGAAGAGTT-TGGGTCGTCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAGTTCTGGGCCATCTAAAGGT
*
1991357 GACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAGTTCTGGGCCATCTAAAGGT
*
1991401 GATAACACGGTTCCTACGTGA
1 G---ACACGGCTCCTACGTGA
1991422 CGAGGACGGC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
43 25 0.45
44 14 0.25
47 16 0.29
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (44 bp):
GACACGGCTCCTACGTGATGAAGAGTTCTGGGCCATCTAAAGGT
Found at i:1991502 original size:40 final size:40
Alignment explanation
Indices: 1991446--1991679 Score: 416
Period size: 40 Copynumber: 5.9 Consensus size: 40
1991436 TATCTATGGT
* * *
1991446 TGACACGGTTCCTACGTGATGAGGAGATCTGGTCGGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA
1991486 TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA
1991526 TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA
*
1991566 TGACACGGCTCATACGTGATGAAGAGATCTGATCGGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA
*
1991606 TGAAACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA
1991646 TGACAC-GCTCATACGTGATGAAGAGATCTGGTCG
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCG
1991680 TCTAAAGGTG
Statistics
Matches: 187, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
39 28 0.15
40 159 0.85
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.21
Consensus pattern (40 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA
Found at i:1991781 original size:28 final size:28
Alignment explanation
Indices: 1991740--1991793 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1991730 TAGGATAATG
*
1991740 GTTTCAAAGAAAACCAACTCAAAGATGT
1 GTTTCAAAGAAAACAAACTCAAAGATGT
1991768 GTTTCAATAG-AAACAAACTCAAAGAT
1 GTTTCAA-AGAAAACAAACTCAAAGAT
1991794 TGGATTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (28 bp):
GTTTCAAAGAAAACAAACTCAAAGATGT
Found at i:1992409 original size:66 final size:66
Alignment explanation
Indices: 1992252--1992399 Score: 289
Period size: 66 Copynumber: 2.3 Consensus size: 66
1992242 TGTCTCATGC
1992252 GAGACAAAA-TTTGTTTTAATAGAAACGATATCAAATGTGGGTATCTTCAAAAGAAGTTGTCTCG
1 GAGACAAAATTTTGTTTTAATAGAAACGATATCAAATGTGGGTATCTTCAAAAGAAGTTGTCTCG
1992316 A
66 A
1992317 GAGACAAAATTTTGTTTTAATAGAAACGATATCAAATGTGGGTATCTTCAAAAGAAGTTGTCTCG
1 GAGACAAAATTTTGTTTTAATAGAAACGATATCAAATGTGGGTATCTTCAAAAGAAGTTGTCTCG
1992382 A
66 A
1992383 GAGACAAAATTTTGTTT
1 GAGACAAAATTTTGTTT
1992400 CAAAGGAAAC
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
65 9 0.11
66 73 0.89
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (66 bp):
GAGACAAAATTTTGTTTTAATAGAAACGATATCAAATGTGGGTATCTTCAAAAGAAGTTGTCTCG
A
Found at i:1992544 original size:27 final size:27
Alignment explanation
Indices: 1992509--1992570 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
1992499 GTGAGACCAA
1992509 ATTTGTTTCAAAAGAAACAAACTCAAAG
1 ATTT-TTTCAAAAGAAACAAACTCAAAG
*
1992537 ATTTTTTCAAAAGAAACAATCTCAAAG
1 ATTTTTTCAAAAGAAACAAACTCAAAG
1992564 ATTTTTT
1 ATTTTTT
1992571 TTTTTCTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 29 0.88
28 4 0.12
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (27 bp):
ATTTTTTCAAAAGAAACAAACTCAAAG
Found at i:1992698 original size:26 final size:25
Alignment explanation
Indices: 1992669--1992792 Score: 88
Period size: 29 Copynumber: 4.5 Consensus size: 25
1992659 CAAAACTTTG
* *
1992669 TTTCAAAATAAATAGACTCAAAGATT
1 TTTCAAAAGAAACA-ACTCAAAGATT
1992695 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAG--ATT
* *
1992722 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAAC-AACTCAAAGA--TT
1992751 TATTCAAAATG-AACAAACTCAAAGATATT
1 T-TTCAAAA-GAAAC-AACTCAAAG--ATT
*
1992780 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
1992793 TGTCTCAAGA
Statistics
Matches: 82, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
25 8 0.10
26 12 0.15
27 6 0.07
28 20 0.24
29 34 0.41
30 1 0.01
31 1 0.01
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (25 bp):
TTTCAAAAGAAACAACTCAAAGATT
Found at i:1992752 original size:29 final size:29
Alignment explanation
Indices: 1992684--1992785 Score: 133
Period size: 29 Copynumber: 3.7 Consensus size: 29
1992674 AAATAAATAG
*
1992684 ACTCAAAG--ATTT-TTCAAAAGAAAC-A
1 ACTCAAAGATATTTATTCAAAAGGAACAA
1992709 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATATTTATTCAAAAGGAACAA
* * *
1992738 ACTCCAAGATTTTTATTCAAAATGAACAA
1 ACTCAAAGATATTTATTCAAAAGGAACAA
1992767 ACTCAAAGATATTT-TTCAA
1 ACTCAAAGATATTTATTCAA
1992786 GAGAAACTGT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
25 8 0.12
27 4 0.06
28 16 0.24
29 39 0.58
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (29 bp):
ACTCAAAGATATTTATTCAAAAGGAACAA
Found at i:1993119 original size:36 final size:35
Alignment explanation
Indices: 1993035--1993138 Score: 129
Period size: 36 Copynumber: 3.0 Consensus size: 35
1993025 GAGAAAATGA
* * *
1993035 TGTCTCAAGCGAGACGAAATTTGCTTTT-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTGAGAAAT
* **
1993069 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT-GAGAAAT
*
1993105 TGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTGAGAAA
1993139 CGATCTCAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 23 0.40
35 6 0.10
36 29 0.50
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.34
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTGAGAAAT
Found at i:1993146 original size:35 final size:32
Alignment explanation
Indices: 1993036--1993165 Score: 109
Period size: 35 Copynumber: 3.8 Consensus size: 32
1993026 AGAAAATGAT
*
1993036 GTCTCAAGCGAGACGAAATTTGCTTTT-AGATATA
1 GTCTCAAGCGAGAC-AAATTTGTTTTTGAGA-A-A
**
1993070 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAA
1 GTCTCAAGCGAGAC-AAATTTGTTTTT-GAGAAA
1993104 TTGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAA
1 --GTCTCAAGCGAGACAAA-TTTGTTTTTGAGAAA
* *
1993139 CGATCTCAAGTGAGATCAACTTTGTTT
1 -G-TCTCAAGCGAGA-CAAATTTGTTT
1993166 AATGTGAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
34 25 0.31
35 28 0.35
36 27 0.34
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (32 bp):
GTCTCAAGCGAGACAAATTTGTTTTTGAGAAA
Found at i:1993292 original size:105 final size:100
Alignment explanation
Indices: 1993106--1993337 Score: 252
Period size: 105 Copynumber: 2.3 Consensus size: 100
1993096 TAGAGAAATT
* *
1993106 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAACGATCTCAAGTGAGATCAACTTTGTTTAATGT
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
* *
1993171 GAAACAAATCCGAAATTTGGATCCCAAAGGGAAAAG
65 GAAACAAATCCAAAATTTGGATCCCAAAGGAAAAAG
* *
1993207 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAA-CAATCTAAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AGAAACAATC--TC-AA-GTGAGATCAACTTTGTTT
* * * * * *
1993271 -TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 AAT-GTGAAACAAATCCAAAATTTGGATCCCAAAGGAAAAAG
* *
1993312 GTCTCAAGCGAAACACAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
1993338 AAAATTCTCA
Statistics
Matches: 110, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
100 5 0.05
101 22 0.20
102 7 0.06
103 2 0.02
104 3 0.03
105 71 0.65
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (100 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTG
AAACAAATCCAAAATTTGGATCCCAAAGGAAAAAG
Found at i:1993810 original size:4 final size:4
Alignment explanation
Indices: 1993801--1993840 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
1993791 TGTATCATGG
1993801 ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1993841 ACTTTTCTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 32 0.94
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:1995049 original size:12 final size:11
Alignment explanation
Indices: 1995021--1995058 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
1995011 TCCTCTTTTG
*
1995021 TTCTTTGCTTT
1 TTCTTTGATTT
1995032 TTCTTTGATTT
1 TTCTTTGATTT
1995043 TTGCTTTGATTT
1 TT-CTTTGATTT
1995055 TTCT
1 TTCT
1995059 CTTGCTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:1995718 original size:20 final size:20
Alignment explanation
Indices: 1995650--1995724 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
1995640 TAAATACGTG
*
1995650 TTTCAAGGT-GGAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
* *
1995669 TTTCAAGGTCTCAAAGAGAGGGAATG
1 TTTCAAGG--TCGAA-A-A--GAATA
1995695 TTTCAAGGTCGAAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
1995715 TTTCAAGGTC
1 TTTCAAGGTC
1995725 TCAAAGAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 8 0.18
20 14 0.32
21 1 0.02
22 2 0.05
23 2 0.05
24 5 0.11
26 12 0.27
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (20 bp):
TTTCAAGGTCGAAAAGAATA
Found at i:1995738 original size:26 final size:26
Alignment explanation
Indices: 1995660--1995739 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
1995650 TTTCAAGGTG
1995660 GAAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
** *
1995686 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATATTTCAAGGTCTCAAAGA
1995707 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
*
1995732 GATAGAAT
1 GAAAGAAT
1995740 GTCAAAATTG
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 20 0.49
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (26 bp):
GAAAGAATATTTCAAGGTCTCAAAGA
Found at i:1995740 original size:46 final size:45
Alignment explanation
Indices: 1995648--1995741 Score: 152
Period size: 46 Copynumber: 2.1 Consensus size: 45
1995638 AATAAATACG
* *
1995648 TGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
*
1995693 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
1995739 TGT
1 TGT
1995742 CAAAATTGGT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 11 0.24
46 34 0.76
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:2001853 original size:25 final size:25
Alignment explanation
Indices: 2001812--2001910 Score: 173
Period size: 25 Copynumber: 4.0 Consensus size: 25
2001802 CATTAGGGGA
* *
2001812 TTAGGG-TTAAAACCCTAATTTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2001836 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2001861 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2001886 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2001911 GGGTTGATTG
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
24 6 0.08
25 66 0.92
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:2001988 original size:3 final size:3
Alignment explanation
Indices: 2001975--2002021 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
2001965 AATATGTAAT
2001975 TAA TAA T-A TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2002019 TAA
1 TAA
2002022 CGATAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2004294 original size:2 final size:2
Alignment explanation
Indices: 2004287--2004314 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2004277 ATAATTAACA
2004287 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
2004315 TTTAATTTTC
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:2009383 original size:16 final size:15
Alignment explanation
Indices: 2009362--2009393 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
2009352 TGACTAATGG
2009362 GCTTAACGAGCAGCGA
1 GCTTAACGAGCA-CGA
2009378 GCTTAACGAGCACGA
1 GCTTAACGAGCACGA
2009393 G
1 G
2009394 TCGAGCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.31, C:0.25, G:0.31, T:0.12
Consensus pattern (15 bp):
GCTTAACGAGCACGA
Found at i:2010503 original size:4 final size:4
Alignment explanation
Indices: 2010494--2010827 Score: 668
Period size: 4 Copynumber: 83.5 Consensus size: 4
2010484 AATCATTTGC
2010494 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
2010542 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
2010590 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
2010638 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
2010686 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
2010734 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
2010782 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
2010828 CATGCATGCA
Statistics
Matches: 330, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 330 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:2012070 original size:18 final size:18
Alignment explanation
Indices: 2012049--2012091 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2012039 GTTGTTTTTA
*
2012049 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
2012067 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
2012085 AAATAAA
1 AAATAAA
2012092 CAAATTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:2012781 original size:76 final size:75
Alignment explanation
Indices: 2012678--2012884 Score: 290
Period size: 76 Copynumber: 2.7 Consensus size: 75
2012668 TCTTAAATCC
* *
2012678 TAATTAAAACACTTAAAA-CTATGTAAACTAAAATATATAAAACAAAGATAAAATACAAAAATAA
1 TAATTAAAATA-TTAAAACCTATTTAAACTAAAATAT-TAAAACAAAGATAAAATACAAAAATAA
2012742 TATCCTAAAACT
64 TATCCTAAAACT
* * *
2012754 TAATTAACATATTAAAACCTATTTAAACTAAAATACTTAAAACAAAGATAAAACATAAAAATAAT
1 TAATTAAAATATTAAAACCTATTTAAACTAAAATA-TTAAAACAAAGATAAAATACAAAAATAAT
2012819 ATCCTAAAACT
65 ATCCTAAAACT
* * * *
2012830 TAATTAAAATACTAAAACCAATTTAAACTAAAATACCTAAAACCAAGATAAAATA
1 TAATTAAAATATTAAAACCTATTTAAACTAAAATA-TTAAAACAAAGATAAAATA
2012885 TAATATTTAA
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
75 6 0.05
76 111 0.94
77 1 0.01
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.26
Consensus pattern (75 bp):
TAATTAAAATATTAAAACCTATTTAAACTAAAATATTAAAACAAAGATAAAATACAAAAATAATA
TCCTAAAACT
Found at i:2012881 original size:25 final size:24
Alignment explanation
Indices: 2012777--2012881 Score: 70
Period size: 25 Copynumber: 4.2 Consensus size: 24
2012767 AAAACCTATT
*
2012777 TAAACTAAAATACTTAAAACAAAGA
1 TAAACTAAAATAC-TAAAACCAAGA
* *
2012802 TAAAACATAAAA-A-TAATATCCTAAAA
1 T-AAAC-TAAAATACTAA-AACC-AAGA
* * **
2012828 CTTAATTAAAATACTAAAACCAATT
1 -TAAACTAAAATACTAAAACCAAGA
2012853 TAAACTAAAATACCTAAAACCAAGA
1 TAAACTAAAATA-CTAAAACCAAGA
2012878 TAAA
1 TAAA
2012882 ATATAATATT
Statistics
Matches: 60, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
24 13 0.22
25 24 0.40
26 14 0.23
27 9 0.15
ACGTcount: A:0.61, C:0.14, G:0.02, T:0.23
Consensus pattern (24 bp):
TAAACTAAAATACTAAAACCAAGA
Found at i:2012889 original size:25 final size:24
Alignment explanation
Indices: 2012834--2012889 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
2012824 AAAACTTAAT
** *
2012834 TAAAATACTAAAACCAATTTAAAC
1 TAAAATACTAAAACCAAGATAAAA
2012858 TAAAATACCTAAAACCAAGATAAAA
1 TAAAATA-CTAAAACCAAGATAAAA
*
2012883 TATAATA
1 TAAAATA
2012890 TTTAAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.61, C:0.14, G:0.02, T:0.23
Consensus pattern (24 bp):
TAAAATACTAAAACCAAGATAAAA
Found at i:2014964 original size:16 final size:16
Alignment explanation
Indices: 2014945--2014977 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2014935 TAAAGTTTGC
2014945 TAAAAATAAAACAAAA
1 TAAAAATAAAACAAAA
*
2014961 TAAAAATAAAACGAAA
1 TAAAAATAAAACAAAA
2014977 T
1 T
2014978 GGGTTGTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (16 bp):
TAAAAATAAAACAAAA
Found at i:2017435 original size:32 final size:31
Alignment explanation
Indices: 2017348--2017440 Score: 87
Period size: 32 Copynumber: 2.9 Consensus size: 31
2017338 CTTGGTAAAT
* * *
2017348 TGTCCATGTGTTCCTTAGAACATAGGCAATCC
1 TGTCCATATGTTTC-TAGAACATAGGTAATCC
* * * * *
2017380 TGTTCATATGTCTCAAAAGACATAGGTAATTC
1 TGTCCATATGTTTCTAGA-ACATAGGTAATCC
2017412 TGTCCATATGTTTCGTAGAACATAGGTAA
1 TGTCCATATGTTTC-TAGAACATAGGTAA
2017441 ACCCTTGACT
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
31 2 0.04
32 43 0.91
33 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (31 bp):
TGTCCATATGTTTCTAGAACATAGGTAATCC
Found at i:2018197 original size:18 final size:18
Alignment explanation
Indices: 2018171--2018223 Score: 81
Period size: 18 Copynumber: 2.9 Consensus size: 18
2018161 TTCAGTATTC
*
2018171 GTCCCGAAGGACCACTAT
1 GTCCTGAAGGACCACTAT
2018189 GTCCTGAAGGACCACTAT
1 GTCCTGAAGGACCACTAT
2018207 GT-CTCGAAGGACCACTA
1 GTCCT-GAAGGACCACTA
2018224 GATACGTCCC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 2 0.06
18 31 0.94
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (18 bp):
GTCCTGAAGGACCACTAT
Found at i:2018239 original size:22 final size:22
Alignment explanation
Indices: 2018170--2018306 Score: 139
Period size: 22 Copynumber: 6.6 Consensus size: 22
2018160 GTTCAGTATT
2018170 CGTCCCGAAGGACCACT--AT-
1 CGTCCCGAAGGACCACTGGATA
*
2018189 -GTCCTGAAGGACCACT--AT-
1 CGTCCCGAAGGACCACTGGATA
* *
2018207 -GTCTCGAAGGACCACTAGATA
1 CGTCCCGAAGGACCACTGGATA
*
2018228 CGTCCCGAAGGACAACTGGATA
1 CGTCCCGAAGGACCACTGGATA
*
2018250 CG-CCCTGAAAGACCACTGGATA
1 CGTCCC-GAAGGACCACTGGATA
*
2018272 CGTCCCGAAGGGCCACTGGATA
1 CGTCCCGAAGGACCACTGGATA
*
2018294 CGTCCTGAAGGAC
1 CGTCCCGAAGGAC
2018307 TAATATACCC
Statistics
Matches: 100, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
18 31 0.31
20 2 0.02
21 3 0.03
22 61 0.61
23 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (22 bp):
CGTCCCGAAGGACCACTGGATA
Found at i:2018711 original size:22 final size:20
Alignment explanation
Indices: 2018684--2018736 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
2018674 CTAATCACTT
2018684 ATTTCACATTACTTATATTCTA
1 ATTTCACATTACTTA-ATTC-A
* *
2018706 GTTTCATATATTACTTAATTCA
1 ATTTC--ACATTACTTAATTCA
2018728 ATTTCACAT
1 ATTTCACAT
2018737 AGCTTGTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
20 3 0.12
22 9 0.36
23 4 0.16
24 9 0.36
ACGTcount: A:0.32, C:0.17, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTTCACATTACTTAATTCA
Found at i:2019022 original size:2 final size:2
Alignment explanation
Indices: 2019015--2019055 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2019005 TACAAATTCC
2019015 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2019056 CTAACTCATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2019828 original size:66 final size:64
Alignment explanation
Indices: 2019676--2019836 Score: 209
Period size: 64 Copynumber: 2.5 Consensus size: 64
2019666 CCTTGACGGA
* * * *
2019676 TGCATCGATGCACTACC-CATGCATCGGTGCATAAATCCTATTCGATGTTTGTATTTTAAGTAGG
1 TGCATCGATGCACT-CCTTATGCATCGATGCATAAATCCTATTCGATGTTTGTAATTTAAATAGG
** *
2019740 TGCATCGATGCACTCCTTATGCATCGATGCATAAATGGTATTCGATGTTTAATTAATTTAAAT-G
1 TGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTT--GTAATTTAAATAG
2019804 AG
64 -G
2019806 TGCATCGATGCACTCCTTATGCATCGATGCA
1 TGCATCGATGCACTCCTTATGCATCGATGCA
2019837 CCTTCAACAA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
63 2 0.02
64 43 0.50
65 1 0.01
66 40 0.47
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (64 bp):
TGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTGTAATTTAAATAGG
Found at i:2023168 original size:22 final size:22
Alignment explanation
Indices: 2023107--2023181 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
2023097 GTTCAGTATT
*
2023107 CGTCCCGAAGGACCACTAGATA
1 CGTCCCGAAGGACCACTGGATA
*
2023129 CATCCCGAAGGACCACTGGATA
1 CGTCCCGAAGGACCACTGGATA
* *
2023151 CGTCCCGAAGGGCCACTGAATA
1 CGTCCCGAAGGACCACTGGATA
*
2023173 CGTACCGAA
1 CGTCCCGAA
2023182 TGACTAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.32, G:0.24, T:0.13
Consensus pattern (22 bp):
CGTCCCGAAGGACCACTGGATA
Found at i:2023901 original size:2 final size:2
Alignment explanation
Indices: 2023894--2023926 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2023884 TACAAATTCC
2023894 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 T
2023927 CTAACTCGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2028482 original size:18 final size:17
Alignment explanation
Indices: 2028433--2028489 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
2028423 TAGAAAAAGT
*
2028433 ATAATAAAATAAATAATT
1 ATAA-AAAATAAATAATA
*
2028451 ATAAAAAAGGAAATAATA
1 ATAAAAAA-TAAATAATA
*
2028469 ATAAAATAATAAATATTA
1 ATAAAA-AATAAATAATA
2028487 ATA
1 ATA
2028490 GTAATAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 4 0.12
18 27 0.82
19 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (17 bp):
ATAAAAAATAAATAATA
Found at i:2028551 original size:18 final size:18
Alignment explanation
Indices: 2028530--2028572 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2028520 GTTGTTTTTA
* *
2028530 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAACAATT
2028548 AAATAAAAGAAAACAATT
1 AAATAAAAGAAAACAATT
2028566 AAATAAA
1 AAATAAA
2028573 CAAATTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (18 bp):
AAATAAAAGAAAACAATT
Found at i:2032742 original size:33 final size:35
Alignment explanation
Indices: 2032684--2032758 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 35
2032674 GAAGACTGAT
* * *
2032684 ATAAAATATTTTAAAATTTATAAA-TTGATTTAGA
1 ATAAAATATTTAAAAAATTATAAATTTGATTTAAA
2032718 ATAAAATATTTAAAAAATTA-AAATTTGATTTAAA
1 ATAAAATATTTAAAAAATTATAAATTTGATTTAAA
2032752 ATGAAAA
1 AT-AAAA
2032759 ATCATAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 3 0.08
34 29 0.81
35 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (35 bp):
ATAAAATATTTAAAAAATTATAAATTTGATTTAAA
Found at i:2039702 original size:3 final size:3
Alignment explanation
Indices: 2039696--2039720 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2039686 AACAAACAAG
2039696 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
2039721 TTATTGTTGG
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:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2041655 original size:14 final size:14
Alignment explanation
Indices: 2041626--2041657 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2041616 ACATTGAACC
2041626 TTTATATGAATCTT
1 TTTATATGAATCTT
2041640 TTTAT-TGAATCTT
1 TTTATATGAATCTT
2041653 TTTAT
1 TTTAT
2041658 CGATTTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (14 bp):
TTTATATGAATCTT
Found at i:2043728 original size:22 final size:22
Alignment explanation
Indices: 2043702--2043751 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
2043692 AGGGCTCAGA
2043702 TCGGGTGGAGGGTATATATTTT
1 TCGGGTGGAGGGTATATATTTT
*
2043724 TCGGGTGGGGGGTATATATTTT
1 TCGGGTGGAGGGTATATATTTT
2043746 TCGGGT
1 TCGGGT
2043752 TGAGTTGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.14, C:0.06, G:0.40, T:0.40
Consensus pattern (22 bp):
TCGGGTGGAGGGTATATATTTT
Found at i:2046003 original size:32 final size:31
Alignment explanation
Indices: 2045932--2046024 Score: 98
Period size: 32 Copynumber: 3.0 Consensus size: 31
2045922 CCTATTCTTC
*
2045932 TAACAATTAGATAAATTTAATGATCATTTTG
1 TAACAATTTGATAAATTTAATGATCATTTTG
* * * *
2045963 -CACTAATTTTATAAATTTTACTGATCTTTTTG
1 TAAC-AATTTGATAAA-TTTAATGATCATTTTG
* *
2045995 TAACAATTTGATAAGTTTAATGATTATTTT
1 TAACAATTTGATAAATTTAATGATCATTTT
2046025 ATAATTTTTA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
30 2 0.04
31 21 0.44
32 23 0.48
33 2 0.04
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (31 bp):
TAACAATTTGATAAATTTAATGATCATTTTG
Found at i:2051521 original size:28 final size:27
Alignment explanation
Indices: 2051464--2051524 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
2051454 AATATGATTT
* * *
2051464 ATGCACCGATGCATGGATAGTGCATTG
1 ATGCATCGATACATGGATAGTGCATCG
*
2051491 ATGCATCGATACATGGTGTAGTGCATCG
1 ATGCATCGATACATGG-ATAGTGCATCG
2051519 ATGCAT
1 ATGCAT
2051525 GCCTTCATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (27 bp):
ATGCATCGATACATGGATAGTGCATCG
Found at i:2052312 original size:30 final size:30
Alignment explanation
Indices: 2052242--2052314 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
2052232 GGTTCTTCGG
* *
2052242 GACCTATGGACAGTTACCGAGGATATTTAT
1 GACCTCTGGATAGTTACCGAGGATATTTAT
*
2052272 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATATTTAT
2052302 GACCTCTGGATAG
1 GACCTCTGGATAG
2052315 GTCCTTCGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATATTTAT
Done.