Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, 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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 7 of 100
Found at i:1615582 original size:9 final size:10
Alignment explanation
Indices: 1615553--1615577 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1615543 ATTAAAAATT
1615553 ATTTTTTTAA
1 ATTTTTTTAA
1615563 ATTTTTTTAA
1 ATTTTTTTAA
1615573 ATTTT
1 ATTTT
1615578 ATAAACGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
ATTTTTTTAA
Found at i:1619285 original size:35 final size:35
Alignment explanation
Indices: 1619236--1619304 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
1619226 TTTAAGCATT
* *
1619236 TCTACCTGCTTGATTA-CTTATGGACTGCCGGTATC
1 TCTACCTGCATGATTATC-TATGGACTGCAGGTATC
1619271 TCTACCTGCATGATTATCTATGGACTGCAGGTAT
1 TCTACCTGCATGATTATCTATGGACTGCAGGTAT
1619305 TCGTGTTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (35 bp):
TCTACCTGCATGATTATCTATGGACTGCAGGTATC
Found at i:1620355 original size:34 final size:34
Alignment explanation
Indices: 1620317--1620386 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
1620307 GTTTTTGAAT
*
1620317 TGGTTTCAGTTTAAATGTCTAGAATTT-TCTGGTA
1 TGGTTTCAGTTTAAATGTCAAGAATTTCT-TGGTA
*
1620351 TGGTTTCAGTTTGAATGTCAAGAATTTCTTGGTA
1 TGGTTTCAGTTTAAATGTCAAGAATTTCTTGGTA
1620385 TG
1 TG
1620387 TTGGATGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 32 0.97
35 1 0.03
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.46
Consensus pattern (34 bp):
TGGTTTCAGTTTAAATGTCAAGAATTTCTTGGTA
Found at i:1621520 original size:33 final size:33
Alignment explanation
Indices: 1621483--1621545 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
1621473 TGTTGGTATG
*
1621483 GTGGGTACCGGTA-TTGGTGCTGGAGTTGGGCTT
1 GTGGGAACCGG-AGTTGGTGCTGGAGTTGGGCTT
**
1621516 GTGGGAAGTGGAGTTGGTGCTGGAGTTGGG
1 GTGGGAACCGGAGTTGGTGCTGGAGTTGGG
1621546 ATCGTCGGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 1 0.04
33 25 0.96
ACGTcount: A:0.11, C:0.08, G:0.51, T:0.30
Consensus pattern (33 bp):
GTGGGAACCGGAGTTGGTGCTGGAGTTGGGCTT
Found at i:1621559 original size:33 final size:33
Alignment explanation
Indices: 1621496--1621559 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
1621486 GGTACCGGTA
* *
1621496 TTGGTGCTGGAGTTGGGCTTGTGGGAAGTGGAG
1 TTGGTGCTGGAGTTGGGATCGTGGGAAGTGGAG
1621529 TTGGTGCTGGAGTTGGGATCGTCGGG-AGTGG
1 TTGGTGCTGGAGTTGGGATCGT-GGGAAGTGG
1621560 CCTTGGAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.89
34 3 0.11
ACGTcount: A:0.11, C:0.08, G:0.52, T:0.30
Consensus pattern (33 bp):
TTGGTGCTGGAGTTGGGATCGTGGGAAGTGGAG
Found at i:1628051 original size:8 final size:8
Alignment explanation
Indices: 1628040--1628065 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1628030 TACACAATTT
1628040 ATTTTTAA
1 ATTTTTAA
1628048 ATTTTTAA
1 ATTTTTAA
1628056 ATTTTTAA
1 ATTTTTAA
1628064 AT
1 AT
1628066 GGATATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTTTAA
Found at i:1628370 original size:31 final size:30
Alignment explanation
Indices: 1628327--1628388 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
1628317 AAATTAAATG
* *
1628327 AATTCTTAAATATTTATTTTTTATTTAATTA
1 AATTCTTAAATATATA-TTTTTATCTAATTA
*
1628358 AATTTTTAAATATATATTTTTATCTAATTA
1 AATTCTTAAATATATATTTTTATCTAATTA
1628388 A
1 A
1628389 TCCGGATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (30 bp):
AATTCTTAAATATATATTTTTATCTAATTA
Found at i:1628380 original size:30 final size:30
Alignment explanation
Indices: 1628309--1628388 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
1628299 TTCTGAATTT
* * * *
1628309 TATATTTTAAATTAAATGAATTCTTAAATA
1 TATATTTTTATTTAATTAAATTCTTAAATA
* *
1628339 TTTATTTTTTATTTAATTAAATTTTTAAATA
1 TATA-TTTTTATTTAATTAAATTCTTAAATA
*
1628370 TATATTTTTATCTAATTAA
1 TATATTTTTATTTAATTAA
1628389 TCCGGATGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 17 0.41
31 24 0.59
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (30 bp):
TATATTTTTATTTAATTAAATTCTTAAATA
Found at i:1628647 original size:17 final size:18
Alignment explanation
Indices: 1628624--1628658 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1628614 TTTTATTCTT
* *
1628624 TTTTTTTATTTTCAAAAG
1 TTTTTTAATTATCAAAAG
1628642 TTTTTTAATTATCAAAA
1 TTTTTTAATTATCAAAA
1628659 CTACCTCCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTTTTAATTATCAAAAG
Found at i:1632994 original size:1 final size:1
Alignment explanation
Indices: 1632988--1633014 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1632978 ACTATGGTGG
1632988 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1633015 GACTTCTACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1633534 original size:24 final size:25
Alignment explanation
Indices: 1633505--1633556 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1633495 AAAAAAATTC
*
1633505 ATATATACTA-TATTTTATTTACGT
1 ATATATACTATTATTTTATTTACAT
*
1633529 ATATATACTATTTTTTTATTTACAT
1 ATATATACTATTATTTTATTTACAT
1633554 ATA
1 ATA
1633557 AATATTGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.56
Consensus pattern (25 bp):
ATATATACTATTATTTTATTTACAT
Found at i:1633637 original size:37 final size:37
Alignment explanation
Indices: 1633596--1633670 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
1633586 ATATATCTGT
* *
1633596 ATATATATATACATTATTAAATTTATTAGAAAATAAA
1 ATATAGATATACATTATTAAATTTATTAAAAAATAAA
*
1633633 ATATAGATATATATTATTAAATTTATTAAAAAATAAA
1 ATATAGATATACATTATTAAATTTATTAAAAAATAAA
1633670 A
1 A
1633671 ATTTACTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (37 bp):
ATATAGATATACATTATTAAATTTATTAAAAAATAAA
Found at i:1634817 original size:2 final size:2
Alignment explanation
Indices: 1634810--1634835 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1634800 ATGAAGGTGG
1634810 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
1634836 ATGTATGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:1645923 original size:2 final size:2
Alignment explanation
Indices: 1645916--1645945 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1645906 CATACAAACA
*
1645916 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1645946 TGAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1645950 original size:12 final size:12
Alignment explanation
Indices: 1645916--1645950 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1645906 CATACAAACA
*
1645916 AGAGAGAGAGAG
1 AGAGAGAGAAAG
1645928 AGAGAGAGAAAG
1 AGAGAGAGAAAG
*
1645940 AGAGAGTGAAA
1 AGAGAGAGAAA
1645951 AAAAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.43, T:0.03
Consensus pattern (12 bp):
AGAGAGAGAAAG
Found at i:1655895 original size:22 final size:22
Alignment explanation
Indices: 1655870--1655919 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
1655860 ATTTTTTGTA
1655870 TTATTGTCTAGGTGA-T-AATTTT
1 TTATTGTCT--GTGATTGAATTTT
1655892 TTATTG-CTGTGATTGAATTTT
1 TTATTGTCTGTGATTGAATTTT
1655913 TTATTGT
1 TTATTGT
1655920 GGATTTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.16
20 1 0.04
21 14 0.56
22 6 0.24
ACGTcount: A:0.20, C:0.04, G:0.18, T:0.58
Consensus pattern (22 bp):
TTATTGTCTGTGATTGAATTTT
Found at i:1655991 original size:19 final size:19
Alignment explanation
Indices: 1655967--1656008 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1655957 TTGTTTTTGA
*
1655967 GTTGTTCTGTTGAGGCTTT
1 GTTGTTCTGTTAAGGCTTT
1655986 GTTGTTCTGTTAAGGCTTT
1 GTTGTTCTGTTAAGGCTTT
1656005 GTTG
1 GTTG
1656009 GTGAATTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.10, G:0.31, T:0.52
Consensus pattern (19 bp):
GTTGTTCTGTTAAGGCTTT
Found at i:1661301 original size:2 final size:2
Alignment explanation
Indices: 1661294--1661322 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1661284 TCTAACTGGG
1661294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1661323 GCTTGTTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1661405 original size:2 final size:2
Alignment explanation
Indices: 1661393--1661431 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1661383 CTAACTGTAA
1661393 CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1661432 ATATATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1661436 original size:2 final size:2
Alignment explanation
Indices: 1661431--1661456 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1661421 TCTCTCTCTC
1661431 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1661457 GGTTATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1665806 original size:12 final size:12
Alignment explanation
Indices: 1665770--1665807 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1665760 TATTGATTTG
1665770 AATATTTTATTA
1 AATATTTTATTA
*
1665782 AATTTTTTATTA
1 AATATTTTATTA
1665794 AATCATTTT-TTA
1 AAT-ATTTTATTA
1665806 AA
1 AA
1665808 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
AATATTTTATTA
Found at i:1666389 original size:21 final size:21
Alignment explanation
Indices: 1666363--1666407 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1666353 CCTTTCTTCT
1666363 TCCTTTAGAATTTCTTAAGTC
1 TCCTTTAGAATTTCTTAAGTC
1666384 TCCTTTAGAATTTCTTAAGTC
1 TCCTTTAGAATTTCTTAAGTC
1666405 TCC
1 TCC
1666408 AGTACAAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.47
Consensus pattern (21 bp):
TCCTTTAGAATTTCTTAAGTC
Found at i:1675480 original size:4 final size:4
Alignment explanation
Indices: 1675471--1675500 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1675461 AATAAGTTAA
1675471 AAAT AAAT AAAT AAAT AAAT AAA- AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1675501 AAGGTGTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:1675488 original size:12 final size:11
Alignment explanation
Indices: 1675459--1675500 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1675449 GGTTCCGACT
* *
1675459 AAAATAAGTTA
1 AAAATAAATAA
1675470 AAAATAAATAA
1 AAAATAAATAA
1675481 ATAAATAAATAA
1 A-AAATAAATAA
1675493 AAAATAAA
1 AAAATAAA
1675501 AAGGTGTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:1675693 original size:52 final size:52
Alignment explanation
Indices: 1675615--1675719 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
1675605 CGAGAAGAGT
*
1675615 GGAGAGAATTGTTAAGGCTAACCCTTTTTTTCGAGACAAGGAGTAAAGTCAA
1 GGAGAGAATTGTTAAGGCTAACCCTTTTTTTCAAGACAAGGAGTAAAGTCAA
* *
1675667 GGAGAGTATTGTTAAGGCTAACCCTTTTTTTCAAGACAAGGAGTAAATTCAA
1 GGAGAGAATTGTTAAGGCTAACCCTTTTTTTCAAGACAAGGAGTAAAGTCAA
1675719 G
1 G
1675720 AACAGAACAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (52 bp):
GGAGAGAATTGTTAAGGCTAACCCTTTTTTTCAAGACAAGGAGTAAAGTCAA
Found at i:1691580 original size:10 final size:10
Alignment explanation
Indices: 1691565--1691595 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1691555 TAGTCCTCTT
1691565 TATGTGTGTG
1 TATGTGTGTG
1691575 TATGTGTGTG
1 TATGTGTGTG
*
1691585 TGTGTGTGTG
1 TATGTGTGTG
1691595 T
1 T
1691596 TTTGTCACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.06, C:0.00, G:0.42, T:0.52
Consensus pattern (10 bp):
TATGTGTGTG
Found at i:1693965 original size:2 final size:2
Alignment explanation
Indices: 1693958--1693998 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1693948 TTCTGGTTAT
1693958 AC AC AC AC AC AC AC 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 AC AC AC AC AC AC AC A
1693999 TACATATATA
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:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1696452 original size:22 final size:22
Alignment explanation
Indices: 1696418--1696470 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
1696408 AAAAAATCAT
* * *
1696418 AAAAATAAGTTTTAA-ATATTA
1 AAAAATAAATTTTAAGACATAA
1696439 AAAAATATAATTTTAAGACATAA
1 AAAAATA-AATTTTAAGACATAA
1696462 AAAAATAAA
1 AAAAATAAA
1696471 AAAATGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.26
22 9 0.33
23 11 0.41
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAAATAAATTTTAAGACATAA
Found at i:1700179 original size:21 final size:21
Alignment explanation
Indices: 1700154--1700198 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1700144 GATACTTGAG
*
1700154 ATAA-TTAACATTTAAATTATA
1 ATAATTTAA-ATTAAAATTATA
*
1700175 ATAATTTAAATTAAAATTTTA
1 ATAATTTAAATTAAAATTATA
1700196 ATA
1 ATA
1700199 TTTTTAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATTTAAATTAAAATTATA
Found at i:1705849 original size:17 final size:15
Alignment explanation
Indices: 1705828--1705872 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 15
1705818 GTTAATTATA
1705828 AAAAGGCCAAAAAATT
1 AAAAGGCCAAAAAA-T
*
1705844 ATAAAGGCCTAAAAAT
1 A-AAAGGCCAAAAAAT
1705860 AAAAGGACCAAAA
1 AAAAGG-CCAAAA
1705873 TAGGTTCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 5 0.20
16 8 0.32
17 12 0.48
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.11
Consensus pattern (15 bp):
AAAAGGCCAAAAAAT
Found at i:1716822 original size:13 final size:14
Alignment explanation
Indices: 1716804--1716833 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1716794 AGTATGTTTA
1716804 AAATAATT-TTAAT
1 AAATAATTATTAAT
1716817 AAATAATTATTAAT
1 AAATAATTATTAAT
1716831 AAA
1 AAA
1716834 ATTTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATAATTATTAAT
Found at i:1722378 original size:9 final size:9
Alignment explanation
Indices: 1722364--1722389 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1722354 CGAAGGGAAT
1722364 AAGCAGCAA
1 AAGCAGCAA
1722373 AAGCAGCAA
1 AAGCAGCAA
1722382 AAGCAGCA
1 AAGCAGCA
1722390 TTTAACATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.23, G:0.23, T:0.00
Consensus pattern (9 bp):
AAGCAGCAA
Found at i:1725131 original size:15 final size:15
Alignment explanation
Indices: 1725097--1725127 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1725087 TGGTCAGAGT
1725097 TATAGGAGATCGAGC
1 TATAGGAGATCGAGC
1725112 TATAGGAGATC-AGC
1 TATAGGAGATCGAGC
1725126 TA
1 TA
1725128 ATAGTTCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.35, C:0.13, G:0.29, T:0.23
Consensus pattern (15 bp):
TATAGGAGATCGAGC
Found at i:1735699 original size:299 final size:299
Alignment explanation
Indices: 1735161--1735762 Score: 1204
Period size: 299 Copynumber: 2.0 Consensus size: 299
1735151 GTAATGCCTT
1735161 TGTTGTCTGGCTCACTTTGTTTTAGCTTTGTTTTAAGTCCCTTTAATGGAACCCTAGGGTAGCGT
1 TGTTGTCTGGCTCACTTTGTTTTAGCTTTGTTTTAAGTCCCTTTAATGGAACCCTAGGGTAGCGT
1735226 AGTCTTTCTCCAAATCCACTTAAGGTCTAGTTATGTGTGGGAAGAGCCAGGTGGGGAAGGGAGCG
66 AGTCTTTCTCCAAATCCACTTAAGGTCTAGTTATGTGTGGGAAGAGCCAGGTGGGGAAGGGAGCG
1735291 GATTGGATTTACAAATATGTTCCAATTTACTGAAAGTAAACAATCTGAAGTTTGATCATTCAATT
131 GATTGGATTTACAAATATGTTCCAATTTACTGAAAGTAAACAATCTGAAGTTTGATCATTCAATT
1735356 ACGTTAAACTATGATCCAGGAATCATATTCTTTCTTATAGTGACTCGACACAAAATTTAATTTAA
196 ACGTTAAACTATGATCCAGGAATCATATTCTTTCTTATAGTGACTCGACACAAAATTTAATTTAA
1735421 ATCTGCAGAATGAACTGGATATAGAAATATTAGGTGATG
261 ATCTGCAGAATGAACTGGATATAGAAATATTAGGTGATG
1735460 TGTTGTCTGGCTCACTTTGTTTTAGCTTTGTTTTAAGTCCCTTTAATGGAACCCTAGGGTAGCGT
1 TGTTGTCTGGCTCACTTTGTTTTAGCTTTGTTTTAAGTCCCTTTAATGGAACCCTAGGGTAGCGT
1735525 AGTCTTTCTCCAAATCCACTTAAGGTCTAGTTATGTGTGGGAAGAGCCAGGTGGGGAAGGGAGCG
66 AGTCTTTCTCCAAATCCACTTAAGGTCTAGTTATGTGTGGGAAGAGCCAGGTGGGGAAGGGAGCG
1735590 GATTGGATTTACAAATATGTTCCAATTTACTGAAAGTAAACAATCTGAAGTTTGATCATTCAATT
131 GATTGGATTTACAAATATGTTCCAATTTACTGAAAGTAAACAATCTGAAGTTTGATCATTCAATT
1735655 ACGTTAAACTATGATCCAGGAATCATATTCTTTCTTATAGTGACTCGACACAAAATTTAATTTAA
196 ACGTTAAACTATGATCCAGGAATCATATTCTTTCTTATAGTGACTCGACACAAAATTTAATTTAA
1735720 ATCTGCAGAATGAACTGGATATAGAAATATTAGGTGATG
261 ATCTGCAGAATGAACTGGATATAGAAATATTAGGTGATG
1735759 TGTT
1 TGTT
1735763 ACCCTATTTT
Statistics
Matches: 303, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
299 303 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (299 bp):
TGTTGTCTGGCTCACTTTGTTTTAGCTTTGTTTTAAGTCCCTTTAATGGAACCCTAGGGTAGCGT
AGTCTTTCTCCAAATCCACTTAAGGTCTAGTTATGTGTGGGAAGAGCCAGGTGGGGAAGGGAGCG
GATTGGATTTACAAATATGTTCCAATTTACTGAAAGTAAACAATCTGAAGTTTGATCATTCAATT
ACGTTAAACTATGATCCAGGAATCATATTCTTTCTTATAGTGACTCGACACAAAATTTAATTTAA
ATCTGCAGAATGAACTGGATATAGAAATATTAGGTGATG
Found at i:1738656 original size:32 final size:30
Alignment explanation
Indices: 1738603--1738661 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 30
1738593 ATATTAAAAA
* * *
1738603 TTTTTAAAATTTAATTTGAATTTAATTAAT
1 TTTTTAAAATTTAAATCGAATTAAATTAAT
1738633 TTTTTATATAATTTAAATCGAATTAAATT
1 TTTTTA-A-AATTTAAATCGAATTAAATT
1738662 TTACGAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.25
31 1 0.04
32 17 0.71
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (30 bp):
TTTTTAAAATTTAAATCGAATTAAATTAAT
Found at i:1739434 original size:31 final size:31
Alignment explanation
Indices: 1739396--1739454 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1739386 CTTGCCGAGA
*
1739396 GAGTTTGAAAGAAAGGTAAAAAAAAAATTAC
1 GAGTTTGAAAAAAAGGTAAAAAAAAAATTAC
* *
1739427 GAGTTTGAAAAAAAGTTAAAAAAGAAAT
1 GAGTTTGAAAAAAAGGTAAAAAAAAAAT
1739455 GGTTGCCCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.59, C:0.02, G:0.19, T:0.20
Consensus pattern (31 bp):
GAGTTTGAAAAAAAGGTAAAAAAAAAATTAC
Found at i:1741843 original size:20 final size:21
Alignment explanation
Indices: 1741818--1741858 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
1741808 TGTTCTTCTA
1741818 ATTCGGTGCCTG-TGCCACTG
1 ATTCGGTGCCTGTTGCCACTG
1741838 ATTCGGTGCCTGTTGCCACTG
1 ATTCGGTGCCTGTTGCCACTG
1741859 CTGTGGATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.10, C:0.29, G:0.29, T:0.32
Consensus pattern (21 bp):
ATTCGGTGCCTGTTGCCACTG
Found at i:1743275 original size:10 final size:10
Alignment explanation
Indices: 1743260--1743287 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1743250 AATAGGGTGT
1743260 AATCGAGTCG
1 AATCGAGTCG
1743270 AATCGAGTCG
1 AATCGAGTCG
1743280 AATCGAGT
1 AATCGAGT
1743288 GAAACAGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (10 bp):
AATCGAGTCG
Found at i:1746680 original size:3 final size:3
Alignment explanation
Indices: 1746664--1746726 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
1746654 ACGTTTGAAG
* * *
1746664 TAA TAA TCA CAA TAA T-A TAA AAA TAA TAGA TAA TAA TTAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA -TAA TAA TAA
1746710 TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1746727 AACACACCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 4 0.08
3 40 0.80
4 6 0.12
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1746726 original size:14 final size:14
Alignment explanation
Indices: 1746674--1746728 Score: 69
Period size: 14 Copynumber: 3.9 Consensus size: 14
1746664 TAATAATCAC
1746674 AATAAT-ATAAAAAT
1 AATAATAAT-AAAAT
*
1746688 AATAGATAAT-AATT
1 AATA-ATAATAAAAT
1746702 AATAATAATAAAAT
1 AATAATAATAAAAT
1746716 AATAATAATAAAA
1 AATAATAATAAAA
1746729 CACACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
13 5 0.14
14 27 0.75
15 2 0.06
16 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:1754091 original size:23 final size:25
Alignment explanation
Indices: 1754066--1754113 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1754056 AAAAAATTTT
*
1754066 AAAATT-TATATCATATTTTATATA
1 AAAATTATATATCATAATTTATATA
*
1754090 AAAATTATATATTATAATTTATAT
1 AAAATTATATATCATAATTTATAT
1754114 TAATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
AAAATTATATATCATAATTTATATA
Found at i:1754175 original size:19 final size:18
Alignment explanation
Indices: 1754143--1754190 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
1754133 ATATATTTTT
*
1754143 AATTTTATTAAAAAATATA
1 AATTATATT-AAAAATATA
* *
1754162 AATTATCATTAAAATTTTA
1 AATTAT-ATTAAAAATATA
1754181 AATTATATTA
1 AATTATATTA
1754191 TTTTTATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 18 0.72
20 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTATATTAAAAATATA
Found at i:1754199 original size:11 final size:11
Alignment explanation
Indices: 1754183--1754223 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
1754173 AAATTTTAAA
1754183 TTATATTATTT
1 TTATATTATTT
1754194 TTATATTTATTTT
1 TTATA-TTA-TTT
*
1754207 TTATATTATAT
1 TTATATTATTT
1754218 TTATAT
1 TTATAT
1754224 CGTATTATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 13 0.48
12 6 0.22
13 8 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATATTATTT
Found at i:1754209 original size:13 final size:13
Alignment explanation
Indices: 1754183--1754219 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1754173 AAATTTTAAA
1754183 TTATA-TTA-TTT
1 TTATATTTATTTT
1754194 TTATATTTATTTT
1 TTATATTTATTTT
1754207 TTATATTATATTT
1 TTATATT-TATTT
1754220 ATATCGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.22
12 3 0.13
13 10 0.43
14 5 0.22
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATATTTATTTT
Found at i:1754343 original size:88 final size:90
Alignment explanation
Indices: 1754240--1754416 Score: 261
Period size: 88 Copynumber: 2.0 Consensus size: 90
1754230 ATCGTACTAT
* * *
1754240 ATTTAAAATTATCAAA-TCATCACAATTTCATATGAGGTTTTT-GAAAAGAAAAA-AACTTAAAT
1 ATTTAAAATTATCAAACT-ATCACAATTTCATACGAGGTTTTTAGAAAAAAAAAAGAACTCAAAT
*
1754302 TATTGTTTTTTTCTCAATCAAAATGG
65 TATTATTTTTTTCTCAATCAAAATGG
* *
1754328 ATTTAAAGTTATCAAACTATCACAATTTCATGCGAGGTTTTTGAGAAAAAAAAAAGAACTCAAAT
1 ATTTAAAATTATCAAACTATCACAATTTCATACGAGGTTTTT-AGAAAAAAAAAAGAACTCAAAT
1754393 TATTATTTTTTTCTCAATCAAAAT
65 TATTATTTTTTTCTCAATCAAAAT
1754417 AGGTTTTGAT
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
88 37 0.47
89 1 0.01
90 10 0.13
91 31 0.39
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.37
Consensus pattern (90 bp):
ATTTAAAATTATCAAACTATCACAATTTCATACGAGGTTTTTAGAAAAAAAAAAGAACTCAAATT
ATTATTTTTTTCTCAATCAAAATGG
Found at i:1756497 original size:3 final size:3
Alignment explanation
Indices: 1756489--1756525 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1756479 TACTTACATT
1756489 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1756526 AGCTTGATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1761300 original size:19 final size:20
Alignment explanation
Indices: 1761273--1761311 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1761263 ACAGAGGATC
* *
1761273 AAATGACAA-AGCTAAACTG
1 AAATCACAATAGCCAAACTG
1761292 AAATCACAATAGCCAAACTG
1 AAATCACAATAGCCAAACTG
1761312 CACAGTGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (20 bp):
AAATCACAATAGCCAAACTG
Found at i:1768078 original size:22 final size:22
Alignment explanation
Indices: 1768017--1768064 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1768007 TTGCATGAGA
1768017 TAATAAATAATAACATTTTGAT
1 TAATAAATAATAACATTTTGAT
1768039 TAATAAATAATAACATTTTGAT
1 TAATAAATAATAACATTTTGAT
1768061 TAAT
1 TAAT
1768065 TAAAAATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (22 bp):
TAATAAATAATAACATTTTGAT
Found at i:1768506 original size:22 final size:20
Alignment explanation
Indices: 1768462--1768516 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
1768452 AATTTGTGTA
*
1768462 TATTTATTTTAATGATTTATATT
1 TATTTA-TTT-ATGAATTATA-T
1768485 TATTTATTTATGAATTATTAT
1 TATTTATTTATGAATTA-TAT
1768506 TATTTGATTTA
1 TATTT-ATTTA
1768517 CTGATAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 13 0.45
22 10 0.34
23 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (20 bp):
TATTTATTTATGAATTATAT
Found at i:1779718 original size:16 final size:16
Alignment explanation
Indices: 1779688--1779720 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1779678 AACGGCCAAA
1779688 GAAGATGGAAGGGGGG
1 GAAGATGGAAGGGGGG
1779704 GAAGA-GGAAGAGGGGG
1 GAAGATGGAAG-GGGGG
1779720 G
1 G
1779721 GGGGGGGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.64, T:0.03
Consensus pattern (16 bp):
GAAGATGGAAGGGGGG
Found at i:1781310 original size:30 final size:30
Alignment explanation
Indices: 1781274--1781330 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1781264 ATTAATTAGA
1781274 ATTAATATATAT-TTTATTAAAAAATTATAT
1 ATTAATATATATATTTA-TAAAAAATTATAT
1781304 ATTAATATATATATTTATAAAAAATTA
1 ATTAATATATATATTTATAAAAAATTA
1781331 CTTAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
ATTAATATATATATTTATAAAAAATTATAT
Found at i:1781761 original size:8 final size:8
Alignment explanation
Indices: 1781750--1781831 Score: 50
Period size: 8 Copynumber: 10.8 Consensus size: 8
1781740 ATCAAAATAT
1781750 ATATATTA
1 ATATATTA
*
1781758 ATATTTTA
1 ATATATTA
1781766 A-AT-TT-
1 ATATATTA
*
1781771 ATATATAA
1 ATATATTA
*
1781779 ATAT-TTT
1 ATATATTA
*
1781786 ATATATAA
1 ATATATTA
*
1781794 ATATATAA
1 ATATATTA
1781802 ATATATATA
1 ATATAT-TA
*
1781811 ATATTTTA
1 ATATATTA
1781819 A-AT-TTAA
1 ATATATT-A
1781826 ATATAT
1 ATATAT
1781832 ATAAAATTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
5 1 0.02
6 6 0.10
7 12 0.21
8 32 0.55
9 7 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATATTA
Found at i:1781773 original size:23 final size:22
Alignment explanation
Indices: 1781744--1781801 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
1781734 TTTTATATCA
1781744 AAATATATATAT-TAATATTTT
1 AAATATATATATATAATATTTT
*
1781765 AAATTTATATATA-AATATTTT
1 AAATATATATATATAATATTTT
* *
1781786 ATATATAAATATATAA
1 AAATATATATATATAA
1781802 ATATATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATATATATATATAATATTTT
Found at i:1781775 original size:48 final size:53
Alignment explanation
Indices: 1781723--1781832 Score: 151
Period size: 53 Copynumber: 2.2 Consensus size: 53
1781713 AAAATTTAAA
1781723 ATATATATAA-ATTTTATAT-CAAA-ATAT-ATATAT-TAATATTTTAAATTT
1 ATATATATAATATTTTATATACAAATATATAATATATATAATATTTTAAATTT
*
1781771 ATATATA-AATATTTTATATATAAATATATAAATATATATAATATTTTAAATTT
1 ATATATATAATATTTTATATACAAATATAT-AATATATATAATATTTTAAATTT
*
1781824 AAATATATA
1 ATATATATA
1781833 TAAAATTATA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
47 2 0.04
48 16 0.30
49 3 0.06
50 4 0.08
52 6 0.11
53 21 0.40
54 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (53 bp):
ATATATATAATATTTTATATACAAATATATAATATATATAATATTTTAAATTT
Found at i:1781786 original size:15 final size:15
Alignment explanation
Indices: 1781768--1781829 Score: 70
Period size: 15 Copynumber: 4.0 Consensus size: 15
1781758 ATATTTTAAA
1781768 TTTATATATAAATAT
1 TTTATATATAAATAT
1781783 TTTATATATAAATAT
1 TTTATATATAAATAT
**
1781798 ATAAATATATATAATAT
1 -TTTATATATA-AATAT
* *
1781815 TTTAAATTTAAATAT
1 TTTATATATAAATAT
1781830 ATATAAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
15 20 0.51
16 14 0.36
17 5 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTATATATAAATAT
Found at i:1781797 original size:36 final size:34
Alignment explanation
Indices: 1781721--1781845 Score: 112
Period size: 35 Copynumber: 3.6 Consensus size: 34
1781711 AAAAAATTTA
* * *
1781721 AAATATATATAAATTTTATATCAA-AATATATATAT
1 AAATAT-TATAAATTATATAT-AATATTTTATATAT
* *
1781756 TAATATTTTAAATTTATATATAAATATTTTATATAT
1 AAATATTATAAA-TTATATAT-AATATTTTATATAT
* *
1781792 AAATA-TATAAA-TATATATAATATTTTAAATTT
1 AAATATTATAAATTATATATAATATTTTATATAT
1781824 AAATATATATAAAATTATATAT
1 AAATAT-TAT-AAATTATATAT
1781846 TTTTAAAATT
Statistics
Matches: 74, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
32 17 0.23
33 7 0.09
34 8 0.11
35 22 0.30
36 20 0.27
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (34 bp):
AAATATTATAAATTATATATAATATTTTATATAT
Found at i:1781802 original size:23 final size:24
Alignment explanation
Indices: 1781721--1781805 Score: 81
Period size: 23 Copynumber: 3.6 Consensus size: 24
1781711 AAAAAATTTA
*
1781721 AAATATATATAA-ATTTTATATCAA
1 AAATATATATAATATTTTATAT-AT
1781745 AATATATATATTAATATTTTA-A-AT
1 AA-ATATATA-TAATATTTTATATAT
**
1781769 TTATATATA-AATATTTTATATAT
1 AAATATATATAATATTTTATATAT
1781792 AAATATATA-AATAT
1 AAATATATATAATAT
1781806 ATATAATATT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
21 9 0.18
22 1 0.02
23 21 0.41
24 3 0.06
25 7 0.14
26 4 0.08
27 6 0.12
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATATATATAATATTTTATATAT
Found at i:1781842 original size:10 final size:11
Alignment explanation
Indices: 1781719--1781844 Score: 62
Period size: 12 Copynumber: 11.2 Consensus size: 11
1781709 TTAAAAAATT
1781719 TAAAATATATA
1 TAAAATATATA
* *
1781730 TAAATTTTATA
1 TAAAATATATA
1781741 TCAAAATATATA
1 T-AAAATATATA
* *
1781753 TATTAATAT-TT
1 TA-AAATATATA
*
1781764 TAAATTTATATA
1 TAAA-ATATATA
*
1781776 TAAATATTTTATA
1 TAAA-A-TATATA
*
1781789 TATAA-ATATA
1 TAAAATATATA
1781799 T-AAATATATA
1 TAAAATATATA
* * *
1781809 TAATATTTTAAA
1 TAA-AATATATA
*
1781821 TTTAAATATATA
1 -TAAAATATATA
1781833 TAAAAT-TATA
1 TAAAATATATA
1781843 TA
1 TA
1781845 TTTTTAAAAT
Statistics
Matches: 84, Mismatches: 22, Indels: 19
0.67 0.18 0.15
Matches are distributed among these distances:
9 2 0.02
10 18 0.21
11 23 0.27
12 31 0.37
13 10 0.12
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (11 bp):
TAAAATATATA
Found at i:1781847 original size:24 final size:24
Alignment explanation
Indices: 1781794--1781847 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1781784 TTATATATAA
* * *
1781794 ATATATAAATATATATAATATTTT
1 ATATTTAAATATATATAAAATTAT
*
1781818 AAATTTAAATATATATAAAATTAT
1 ATATTTAAATATATATAAAATTAT
1781842 ATATTT
1 ATATTT
1781848 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATTTAAATATATATAAAATTAT
Found at i:1781852 original size:26 final size:24
Alignment explanation
Indices: 1781714--1781839 Score: 83
Period size: 27 Copynumber: 4.9 Consensus size: 24
1781704 ATTTTTTAAA
1781714 AAATTTAAA-ATATATATAAATTTT
1 AAATTTAAATATATATA-AAATTTT
* **
1781738 ATATCAAAATATATATATTAATATTTT
1 AAATTTAAATATATATA--AA-ATTTT
* *** *
1781765 AAATTTATATATAAATATTTTATATAT
1 AAATTTA-A-ATATATATAAAAT-TTT
*
1781792 AAATATATAAATATATATAATATTTT
1 AAAT-T-TAAATATATATAAAATTTT
1781818 AAATTTAAATATATATAAAATT
1 AAATTTAAATATATATAAAATT
1781840 ATATATTTTT
Statistics
Matches: 78, Mismatches: 16, Indels: 16
0.71 0.15 0.15
Matches are distributed among these distances:
24 22 0.28
25 8 0.10
26 11 0.14
27 25 0.32
28 3 0.04
29 9 0.12
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATTTAAATATATATAAAATTTT
Found at i:1781912 original size:32 final size:30
Alignment explanation
Indices: 1781771--1781927 Score: 106
Period size: 32 Copynumber: 5.0 Consensus size: 30
1781761 TTTTAAATTT
*
1781771 ATATATAAATATTTTATATATAAATATATAA
1 ATATATTAATATTTTATATA-AAATATATAA
* *
1781802 ATATATATAATATTTTAAATTTAAATATATATA
1 ATATAT-TAATATTTTATA-TAAAATATATA-A
* * *
1781835 A-A-ATTATATATTTT-TA-AAATTTTTGTAAA
1 ATATATTA-ATATTTTATATAAA-ATATAT-AA
*
1781864 ATAAAATTAATAATTTTATATCAAAATATACTAA
1 AT-ATATTAAT-ATTTTATAT-AAAATATA-TAA
*
1781898 ATATATTAATATTTTATATTAAATAATATA
1 ATATATTAATATTTTATATAAAAT-ATATA
1781928 TACAAATTTA
Statistics
Matches: 98, Mismatches: 13, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
28 2 0.02
29 5 0.05
30 4 0.04
31 24 0.24
32 41 0.42
33 12 0.12
34 6 0.06
35 4 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (30 bp):
ATATATTAATATTTTATATAAAATATATAA
Found at i:1785966 original size:1 final size:1
Alignment explanation
Indices: 1785960--1785984 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1785950 TTGTAAACAA
1785960 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1785985 CAGATGCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1787406 original size:14 final size:14
Alignment explanation
Indices: 1787383--1787412 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1787373 AATTTAGTTG
*
1787383 ATTTGATTTTGTTT
1 ATTTGATTTTGATT
1787397 ATTTGATTTTGATT
1 ATTTGATTTTGATT
1787411 AT
1 AT
1787413 AATTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (14 bp):
ATTTGATTTTGATT
Found at i:1790696 original size:26 final size:27
Alignment explanation
Indices: 1790646--1790705 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
1790636 AAAATTGGAT
*
1790646 TTTAATTTAGTTAAATAATCTAATTTA
1 TTTAATTTAGTTAAATAATCTAATTAA
1790673 TTTAATTTAGTT-AATAAT-TGAATTAA
1 TTTAATTTAGTTAAATAATCT-AATTAA
1790699 TTTAATT
1 TTTAATT
1790706 GTTCATCGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 1 0.03
26 18 0.58
27 12 0.39
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (27 bp):
TTTAATTTAGTTAAATAATCTAATTAA
Found at i:1795844 original size:9 final size:9
Alignment explanation
Indices: 1795830--1795857 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1795820 AATAATATTT
1795830 AAATAATAA
1 AAATAATAA
1795839 AAATAATAA
1 AAATAATAA
1795848 AAATAATAA
1 AAATAATAA
1795857 A
1 A
1795858 TTGAATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAATAA
Found at i:1808107 original size:2 final size:2
Alignment explanation
Indices: 1808100--1808134 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1808090 GAAACATGGA
1808100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1808135 ATGTTTGCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1808487 original size:11 final size:11
Alignment explanation
Indices: 1808471--1808506 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
1808461 CAGTTTCCTT
1808471 TCACATTTCCA
1 TCACATTTCCA
1808482 TCACATTTCCA
1 TCACATTTCCA
*
1808493 TCCCATTTCCA
1 TCACATTTCCA
1808504 TCA
1 TCA
1808507 TTCCACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.25, C:0.39, G:0.00, T:0.36
Consensus pattern (11 bp):
TCACATTTCCA
Found at i:1808612 original size:15 final size:14
Alignment explanation
Indices: 1808570--1808620 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
1808560 TTGATTTAAA
1808570 AAATTTAATAATTT
1 AAATTTAATAATTT
1808584 -AATCTTAAAATAATTT
1 AAAT-TT--AATAATTT
*
1808600 AAATTTGAATAATTC
1 AAATTT-AATAATTT
1808615 AAATTT
1 AAATTT
1808621 CAAATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 3 0.10
14 2 0.06
15 13 0.42
16 10 0.32
17 3 0.10
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (14 bp):
AAATTTAATAATTT
Found at i:1811764 original size:27 final size:27
Alignment explanation
Indices: 1811734--1811792 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
1811724 GTGTGAACAA
1811734 AGAATTAGATCGATGCATAACCGCTCC
1 AGAATTAGATCGATGCATAACCGCTCC
1811761 AGAATTAGATCGATGCATAACCGCTCC
1 AGAATTAGATCGATGCATAACCGCTCC
1811788 A-AATT
1 AGAATT
1811793 GGAATCCCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.12
27 28 0.88
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (27 bp):
AGAATTAGATCGATGCATAACCGCTCC
Found at i:1812834 original size:30 final size:30
Alignment explanation
Indices: 1812795--1812863 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
1812785 TCCAATCAAT
*
1812795 AATTCAATTAAATAAAAATAAAAATTTAAA
1 AATTTAATTAAATAAAAATAAAAATTTAAA
** * *
1812825 GTTTTAATTAGATAAAAATAAATATTTAAA
1 AATTTAATTAAATAAAAATAAAAATTTAAA
1812855 AATTTAATT
1 AATTTAATT
1812864 GATTGTAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (30 bp):
AATTTAATTAAATAAAAATAAAAATTTAAA
Found at i:1814614 original size:18 final size:18
Alignment explanation
Indices: 1814580--1814631 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
1814570 AACTACCTTG
*
1814580 AAACAGAGAAA-ACAAAC
1 AAACAGACAAATACAAAC
1814597 AAACAGACAAATACAAAC
1 AAACAGACAAATACAAAC
* *
1814615 AAACATACAAATTCAAA
1 AAACAGACAAATACAAA
1814632 AACCTGAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
17 10 0.32
18 21 0.68
ACGTcount: A:0.67, C:0.19, G:0.06, T:0.08
Consensus pattern (18 bp):
AAACAGACAAATACAAAC
Found at i:1816551 original size:2 final size:2
Alignment explanation
Indices: 1816544--1816572 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1816534 CACAATACCA
1816544 AC 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 AC A
1816573 AAACCAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1818139 original size:38 final size:38
Alignment explanation
Indices: 1818092--1818170 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
1818082 TTCTATTTAC
*
1818092 AATTTGTTTGTATGATCTATAGGTCAAGAGTCAATACA
1 AATTTGTTTGTATGATCTAAAGGTCAAGAGTCAATACA
1818130 AATTTGTTTGTATGATCTAAAGGTCAAGAGTCAATACA
1 AATTTGTTTGTATGATCTAAAGGTCAAGAGTCAATACA
1818168 AAT
1 AAT
1818171 GTCGTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (38 bp):
AATTTGTTTGTATGATCTAAAGGTCAAGAGTCAATACA
Found at i:1818335 original size:29 final size:30
Alignment explanation
Indices: 1818301--1818374 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
1818291 TTTACATTTC
*
1818301 TAAATAAATCTTTATATTTTTA-TTATATT
1 TAAATAAATTTTTATATTTTTATTTATATT
*
1818330 TAAATAAATTTTTATCTTTTTATTTATATT
1 TAAATAAATTTTTATATTTTTATTTATATT
*
1818360 CAAATAAATTTTTAT
1 TAAATAAATTTTTAT
1818375 TTCAAATGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 20 0.49
30 21 0.51
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (30 bp):
TAAATAAATTTTTATATTTTTATTTATATT
Found at i:1818380 original size:17 final size:19
Alignment explanation
Indices: 1818352--1818386 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1818342 TATCTTTTTA
1818352 TTTATATTCAAAT-AAATT
1 TTTATATTCAAATGAAATT
1818370 TTTAT-TTCAAATGAAAT
1 TTTATATTCAAATGAAAT
1818387 AATGATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (19 bp):
TTTATATTCAAATGAAATT
Found at i:1818486 original size:31 final size:30
Alignment explanation
Indices: 1818404--1818500 Score: 101
Period size: 30 Copynumber: 3.3 Consensus size: 30
1818394 TATATTAAAA
* *
1818404 ATTTATTTAAGTATAAATTAAAAATTATTT
1 ATTTATTTAAATATAAATTAAAAATTAATT
* * *
1818434 ATTTATTTTAATATAACTTAAAGATTAAATT
1 ATTTATTTAAATATAAATTAAAAATT-AATT
*
1818465 ATTTATTTAAA-ATTAAATT--AAATTAATA
1 ATTTATTTAAATA-TAAATTAAAAATTAATT
1818493 ATTTATTT
1 ATTTATTT
1818501 GAATGCAATA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
28 11 0.20
29 4 0.07
30 23 0.41
31 18 0.32
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (30 bp):
ATTTATTTAAATATAAATTAAAAATTAATT
Found at i:1818596 original size:24 final size:21
Alignment explanation
Indices: 1818545--1818603 Score: 55
Period size: 24 Copynumber: 2.6 Consensus size: 21
1818535 AATGGATAAA
1818545 ATTTAAGATTTTATTTTTTGTT
1 ATTT-AGATTTTATTTTTTGTT
*
1818567 ATTTTAGATTTTATAATTTTTATTT
1 A-TTTAGATTTTAT--TTTTT-GTT
*
1818592 ATTTACATTTTA
1 ATTTAGATTTTA
1818604 AGAGCACAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 10 0.32
23 3 0.10
24 15 0.48
25 3 0.10
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (21 bp):
ATTTAGATTTTATTTTTTGTT
Found at i:1825390 original size:16 final size:17
Alignment explanation
Indices: 1825369--1825403 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1825359 AAAAAGTTAA
1825369 AAATATAATT-TTATTT
1 AAATATAATTATTATTT
*
1825385 AAATATATTTATTATTT
1 AAATATAATTATTATTT
1825402 AA
1 AA
1825404 TTAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATATAATTATTATTT
Found at i:1843009 original size:22 final size:22
Alignment explanation
Indices: 1842978--1843020 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1842968 TGTATATTTA
1842978 TATTTATATCTCTAAAATTAAG
1 TATTTATATCTCTAAAATTAAG
* *
1843000 TATTTGTATCTCTAGAATTAA
1 TATTTATATCTCTAAAATTAA
1843021 AAATAAAAAA
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:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (22 bp):
TATTTATATCTCTAAAATTAAG
Found at i:1843354 original size:158 final size:159
Alignment explanation
Indices: 1843059--1843370 Score: 443
Period size: 158 Copynumber: 2.0 Consensus size: 159
1843049 CAATTATAGG
1843059 ATCAATTTTTAAGAAGACTTAATTTTCTAGTTTAACCTCTAGTTAGTTGTATATAAACCTAAGAT
1 ATCAATTTTTAAGAAGACTTAATTTTCTAGTTTAACCTCTAGTTAGTTGTATATAAACCTAAGAT
* *
1843124 GCTTGTATAATTTTTAATGAGCAGTTTTTCAATATACATTCAGTTTTTTCTCTTATTTTTTCACA
66 ACTTGTATAATTTTTAATGAGCAGTTTTTCAATATACATTCAGTTTTTTCTCTTAGTTTTTCACA
* *
1843189 TAGTTTTA-TTTCTTAGTTTTTTCATAAAT
131 CAATTTTATTTTCTTA-TTTTTTCATAAAT
* * * *
1843218 ATCAATTTTTAGGAAGATTTAGTTTAT-TAGTTTAACC-CTTAGTTAG-TGTATATAAACTTAAG
1 ATCAATTTTTAAGAAGACTTAATTT-TCTAGTTTAACCTC-TAGTTAGTTGTATATAAACCTAAG
* * * * *
1843280 CTACTTGTATAATTTTTAATGAGTAGTTTTTTAATATACATTTAGTTTTTTCTTTTAGTTTTTCA
64 ATACTTGTATAATTTTTAATGAGCAGTTTTTCAATATACATTCAGTTTTTTCTCTTAGTTTTTCA
*
1843345 CACAATTTTATTTTTTTATTTTTTCA
129 CACAATTTTATTTTCTTATTTTTTCA
1843371 CATGATATTA
Statistics
Matches: 136, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
158 90 0.66
159 45 0.33
160 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (159 bp):
ATCAATTTTTAAGAAGACTTAATTTTCTAGTTTAACCTCTAGTTAGTTGTATATAAACCTAAGAT
ACTTGTATAATTTTTAATGAGCAGTTTTTCAATATACATTCAGTTTTTTCTCTTAGTTTTTCACA
CAATTTTATTTTCTTATTTTTTCATAAAT
Found at i:1851661 original size:24 final size:26
Alignment explanation
Indices: 1851607--1851661 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
1851597 GGGAAGCAAA
* *
1851607 ATTTTCGGCCTTCATTGTTGACTTCT
1 ATTTTAGGCCTTCATAGTTGACTTCT
1851633 ATTTTAGGCCTTCATAGTT-A-TTCT
1 ATTTTAGGCCTTCATAGTTGACTTCT
1851657 ATTTT
1 ATTTT
1851662 TCCCTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 9 0.33
25 1 0.04
26 17 0.63
ACGTcount: A:0.16, C:0.18, G:0.13, T:0.53
Consensus pattern (26 bp):
ATTTTAGGCCTTCATAGTTGACTTCT
Found at i:1855380 original size:22 final size:22
Alignment explanation
Indices: 1855354--1855396 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1855344 TATGTAATTC
* *
1855354 TATTTGTATATCTAGAATTAAA
1 TATTTATATACCTAGAATTAAA
*
1855376 TATTTATATCCCTAGAATTAA
1 TATTTATATACCTAGAATTAA
1855397 GGATAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (22 bp):
TATTTATATACCTAGAATTAAA
Found at i:1886061 original size:25 final size:25
Alignment explanation
Indices: 1886032--1886082 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
1886022 TGAAAAATTT
*
1886032 AAATTTAA-ATTCGATTCTTAATTCG
1 AAATTTAATATTCGATTC-AAATTCG
1886057 AAATTTAATATTCGATTCAAATTCG
1 AAATTTAATATTCGATTCAAATTCG
1886082 A
1 A
1886083 TTAAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (25 bp):
AAATTTAATATTCGATTCAAATTCG
Found at i:1886179 original size:23 final size:25
Alignment explanation
Indices: 1886153--1886206 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
1886143 GTTCGATTAA
* *
1886153 TATATTAAA-ATAAATTTAATT-TT
1 TATATTAAATAAAAAATTAATTATT
1886176 TATATTAAATAAAAAATTAATTATT
1 TATATTAAATAAAAAATTAATTATT
1886201 TATATT
1 TATATT
1886207 CATATTCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 9 0.33
24 10 0.37
25 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TATATTAAATAAAAAATTAATTATT
Found at i:1886264 original size:14 final size:14
Alignment explanation
Indices: 1886242--1886275 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1886232 TAATTAAAAT
1886242 AATAAAAAAATTTA
1 AATAAAAAAATTTA
*
1886256 AATATAAAAATTTA
1 AATAAAAAAATTTA
*
1886270 ATTAAA
1 AATAAA
1886276 CTCACAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATAAAAAAATTTA
Found at i:1886264 original size:16 final size:17
Alignment explanation
Indices: 1886233--1886265 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1886223 ATATTTTATT
1886233 AATTAAAATAATAAAAA
1 AATTAAAATAATAAAAA
*
1886250 AATTTAAAT-ATAAAAA
1 AATTAAAATAATAAAAA
1886266 TTTAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATTAAAATAATAAAAA
Found at i:1886679 original size:10 final size:10
Alignment explanation
Indices: 1886650--1886681 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
1886640 TATTAATATT
1886650 AATA-ATTTA
1 AATATATTTA
1886659 AATAT-TTTA
1 AATATATTTA
1886668 AATATATTTA
1 AATATATTTA
1886678 AATA
1 AATA
1886682 AAAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AATATATTTA
Found at i:1889524 original size:14 final size:15
Alignment explanation
Indices: 1889497--1889529 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1889487 TTTTTAATAT
*
1889497 TTAAATCTTAATTTA
1 TTAAATATTAATTTA
1889512 TTAAATATT-ATTTA
1 TTAAATATTAATTTA
1889526 TTAA
1 TTAA
1889530 TAATAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAAATATTAATTTA
Found at i:1890752 original size:30 final size:30
Alignment explanation
Indices: 1890718--1890816 Score: 91
Period size: 30 Copynumber: 3.3 Consensus size: 30
1890708 AAAAATAAAA
1890718 AAATTATATTTTATAATTTTATATTAATAT
1 AAATTATATTTTATAATTTTATATTAATAT
* *
1890748 AAATTATAATATATAATTTT-TATGTGAA-AT
1 AAATTATATTTTATAATTTTATAT-T-AATAT
*
1890778 ATAATATAAATTTTA-ATATTTTAT-TTAATAT
1 A-AAT-TATATTTTATA-ATTTTATATTAATAT
1890809 AAA-TATAT
1 AAATTATAT
1890817 GATTCATCAT
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
28 4 0.07
29 3 0.05
30 26 0.46
31 10 0.18
32 12 0.21
33 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
AAATTATATTTTATAATTTTATATTAATAT
Found at i:1891568 original size:6 final size:6
Alignment explanation
Indices: 1891559--1891606 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
1891549 ATCATCAGTT
* * * * *
1891559 TCAACA TCAACA ACAACA ACAACA TCAACA TCAGCA ACAACA GCAACA
1 TCAACA TCAACA TCAACA TCAACA TCAACA TCAACA TCAACA TCAACA
1891607 GCAGTGGCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.54, C:0.33, G:0.04, T:0.08
Consensus pattern (6 bp):
TCAACA
Found at i:1891578 original size:9 final size:9
Alignment explanation
Indices: 1891560--1891606 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
1891550 TCATCAGTTT
*
1891560 CAACATCAA
1 CAACAGCAA
*
1891569 CAACAACAA
1 CAACAGCAA
*
1891578 CAACATCAA
1 CAACAGCAA
*
1891587 CATCAGCAA
1 CAACAGCAA
1891596 CAACAGCAA
1 CAACAGCAA
1891605 CA
1 CA
1891607 GCAGTGGCTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.55, C:0.34, G:0.04, T:0.06
Consensus pattern (9 bp):
CAACAGCAA
Found at i:1892379 original size:100 final size:100
Alignment explanation
Indices: 1892206--1892408 Score: 406
Period size: 100 Copynumber: 2.0 Consensus size: 100
1892196 TATTAATTGT
1892206 GCAGTTATTGAATTTGATACTTCCTTCTTAATGATATTGTATAGCAGAACTATAATTTTAAAATT
1 GCAGTTATTGAATTTGATACTTCCTTCTTAATGATATTGTATAGCAGAACTATAATTTTAAAATT
1892271 TCTTGAAGTTTTTGCTTTTATCAGCTAGGTTTAGA
66 TCTTGAAGTTTTTGCTTTTATCAGCTAGGTTTAGA
1892306 GCAGTTATTGAATTTGATACTTCCTTCTTAATGATATTGTATAGCAGAACTATAATTTTAAAATT
1 GCAGTTATTGAATTTGATACTTCCTTCTTAATGATATTGTATAGCAGAACTATAATTTTAAAATT
1892371 TCTTGAAGTTTTTGCTTTTATCAGCTAGGTTTAGA
66 TCTTGAAGTTTTTGCTTTTATCAGCTAGGTTTAGA
1892406 GCA
1 GCA
1892409 ATTGCAGCAT
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 103 1.00
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.44
Consensus pattern (100 bp):
GCAGTTATTGAATTTGATACTTCCTTCTTAATGATATTGTATAGCAGAACTATAATTTTAAAATT
TCTTGAAGTTTTTGCTTTTATCAGCTAGGTTTAGA
Found at i:1897445 original size:13 final size:14
Alignment explanation
Indices: 1897417--1897449 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1897407 TCTATTTAAT
1897417 ATTTGTAAACTTTTA
1 ATTT-TAAACTTTTA
1897432 ATTTTAAA-TTTTA
1 ATTTTAAACTTTTA
1897445 ATTTT
1 ATTTT
1897450 TTTTCGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 4 0.22
15 4 0.22
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (14 bp):
ATTTTAAACTTTTA
Found at i:1897740 original size:6 final size:6
Alignment explanation
Indices: 1897718--1897779 Score: 56
Period size: 6 Copynumber: 9.8 Consensus size: 6
1897708 AGTTATAAAT
*
1897718 ATTTAAA ATTT-A ATTTAA ATTTAA ATTAAA TATTTATA TGATTT-A ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA -ATTTA-A --ATTTAA ATTTAA
1897769 ATTTAA ATTTA
1 ATTTAA ATTTA
1897780 TTAGTTTAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
5 9 0.19
6 24 0.51
7 9 0.19
8 1 0.02
9 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:1897767 original size:33 final size:31
Alignment explanation
Indices: 1897713--1897777 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 31
1897703 AATAAAGTTA
1897713 TAAATATTTAAAATTTAATTTAAATTTAAAT
1 TAAATATTTAAAATTTAATTTAAATTTAAAT
*
1897744 TAAATATTTATATGATTTAATTTAAATTTAAAT
1 TAAATATTTA-A-AATTTAATTTAAATTTAAAT
1897777 T
1 T
1897778 TATTAGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 10 0.32
32 1 0.03
33 20 0.65
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (31 bp):
TAAATATTTAAAATTTAATTTAAATTTAAAT
Found at i:1897851 original size:22 final size:22
Alignment explanation
Indices: 1897826--1897879 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
1897816 AACTTTTTTT
*
1897826 ATTTATATAT-TATTTTAATATA
1 ATTTATATATATATTTAAATA-A
*
1897848 ATTTTTA-ATATATTTAAATAA
1 ATTTATATATATATTTAAATAA
*
1897869 ATTTAAATATA
1 ATTTATATATA
1897880 AAATAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTATATATATATTTAAATAA
Found at i:1897877 original size:20 final size:21
Alignment explanation
Indices: 1897839--1897879 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1897829 TATATATTAT
* *
1897839 TTTAATATAATTTTTAATATA
1 TTTAATATAAATTTAAATATA
1897860 TTTAA-ATAAATTTAAATATA
1 TTTAATATAAATTTAAATATA
1897880 AAATAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATATAAATTTAAATATA
Found at i:1899057 original size:7 final size:7
Alignment explanation
Indices: 1899045--1899069 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1899035 CAAAGATGAT
1899045 TTTCAAC
1 TTTCAAC
1899052 TTTCAAC
1 TTTCAAC
1899059 TTTCAAC
1 TTTCAAC
1899066 TTTC
1 TTTC
1899070 TTTAATGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (7 bp):
TTTCAAC
Found at i:1905052 original size:2 final size:2
Alignment explanation
Indices: 1905045--1905075 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1905035 ACATACATAC
1905045 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1905076 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1905080 original size:2 final size:2
Alignment explanation
Indices: 1905075--1905104 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1905065 ATATATATAT
1905075 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1905105 GAATTAATTA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1906595 original size:20 final size:21
Alignment explanation
Indices: 1906553--1906595 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1906543 AAAAATAATA
*
1906553 TAAAAAATTATATTTGTGTTT
1 TAAAAAATTATATTTGTATTT
1906574 TAAAAAA-TATATTT-TATATT
1 TAAAAAATTATATTTGTAT-TT
1906594 TA
1 TA
1906596 TTCATATCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 11 0.55
21 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TAAAAAATTATATTTGTATTT
Found at i:1906882 original size:17 final size:17
Alignment explanation
Indices: 1906856--1906890 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1906846 AAATTATTTT
1906856 TAATAATAATAATAATA
1 TAATAATAATAATAATA
* *
1906873 TAATATTAATATTAATA
1 TAATAATAATAATAATA
1906890 T
1 T
1906891 TAGTCATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATAATAATAATAATA
Found at i:1906890 original size:6 final size:6
Alignment explanation
Indices: 1906855--1906892 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1906845 AAAATTATTT
* *
1906855 TTAATA ATAATA ATAATA -TAATA TTAATA TTAATA TTA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTA
1906893 GTCATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TTAATA
Found at i:1911320 original size:11 final size:11
Alignment explanation
Indices: 1911304--1911345 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
1911294 AATCTCATGA
1911304 GAGATTTGTTT
1 GAGATTTGTTT
*
1911315 GAGATTTGTTA
1 GAGATTTGTTT
*
1911326 GAAATTTGTTT
1 GAGATTTGTTT
1911337 GAGATTTGT
1 GAGATTTGT
1911346 CAAATATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:1911357 original size:21 final size:22
Alignment explanation
Indices: 1911307--1911359 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1911297 CTCATGAGAG
*
1911307 ATTTGTTTGAGATTTGTTAGAA
1 ATTTGTTTGAGATTTGTCAGAA
1911329 ATTTGTTTGAGATTTGTC--AA
1 ATTTGTTTGAGATTTGTCAGAA
1911349 ATATTGTTTGA
1 AT-TTGTTTGA
1911360 TGGATAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 4 0.14
21 8 0.28
22 17 0.59
ACGTcount: A:0.26, C:0.02, G:0.21, T:0.51
Consensus pattern (22 bp):
ATTTGTTTGAGATTTGTCAGAA
Found at i:1911428 original size:52 final size:52
Alignment explanation
Indices: 1911371--1911526 Score: 167
Period size: 52 Copynumber: 3.0 Consensus size: 52
1911361 GGATAAGAAA
* * *
1911371 ACTTGCAAAAGAAAAATT-TCAAGAGAAAGAAGATTCTTAATGAGTAAGTTTG
1 ACTTGCAAGAGAAGAATTCT-AAGAGAAAGAGGATTCTTAATGAGTAAGTTTG
* *
1911423 ACTTGCAAGAGAAGAATTCTAAAAGGAAAG-GGATTTTTAAT-AGGTAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGA-GAAAGAGGATTCTTAATGA-GTAAGTTTG
* * * *
1911475 ACTTACAGGAGAAGAATTCTAAGAG-AAGAGGGATTCTTAATGGGCAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGAAAGA-GGATTCTTAATGAGTAAGTTTG
1911527 TATGGTTATA
Statistics
Matches: 87, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
50 3 0.03
51 2 0.02
52 76 0.87
53 6 0.07
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (52 bp):
ACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGATTCTTAATGAGTAAGTTTG
Found at i:1921139 original size:9 final size:10
Alignment explanation
Indices: 1921113--1921138 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1921103 TTTTGCTAAT
1921113 AAAAAAATAA
1 AAAAAAATAA
1921123 AAAAAAATAA
1 AAAAAAATAA
1921133 AAAAAA
1 AAAAAA
1921139 TGGTTGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:1921746 original size:15 final size:15
Alignment explanation
Indices: 1921726--1921755 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1921716 ATTTATTTTC
1921726 AATAAAAAAACAAAA
1 AATAAAAAAACAAAA
*
1921741 AATAAAAAAATAAAA
1 AATAAAAAAACAAAA
1921756 TTTTGATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (15 bp):
AATAAAAAAACAAAA
Found at i:1921916 original size:192 final size:191
Alignment explanation
Indices: 1921584--1921940 Score: 426
Period size: 192 Copynumber: 1.9 Consensus size: 191
1921574 AATAAGTATT
*
1921584 AATTATCCAATGATGAAATTTATAAAAATTTCAAATGGTAAATTTTTATAAAATTCTTAGGTGAG
1 AATTATCCAATGATGAAATTTATAAAAATTTCAAATGGTAAATTTTTATAAAATTCTTAGGTGAA
* * * * * * *
1921649 AAATTTTATCTAAATTTATTCTAAATGGTGGAATAATTTAGATAAAGTTTTAATAACAATAATTA
66 AAATTCTATCTAAATTTATCCCAAATAGTGGAAGAATTAAAATAAAGTTTTAATAACAATAATTA
1921714 ATATTTATTTTCAATAAAAAAACAAAAAATAAAAAAATAAAATTTTGATTTAAAATATGTGAC
131 ATATTTATTTTC-ATAAAAAAA-AAAAAATAAAAAAATAAAATTTTGATTTAAAATATGTGAC
*
1921777 AATTATCCAATGAT-AAATTCT-TAAAAATTTTAAATGGTAAATTTTT-TGAGAAA-TCTTTAGG
1 AATTATCCAATGATGAAATT-TATAAAAATTTCAAATGGTAAATTTTTAT-A-AAATTC-TTAGG
* **
1921838 TGAAAAATCTCT-T-TAAATTTGTCCCAAATAGTGGAAGAATTAAAATGAATTTTTTAA-AA-AA
62 TGAAAAAT-TCTATCTAAATTTATCCCAAATAGTGGAAGAATTAAAAT-AAAGTTTTAATAACAA
* * *
1921899 TAATTTTAATA-TTATTTTCTTTAAAAAAAAGAAATAAAAAAA
125 TAA--TTAATATTTATTTTCATAAAAAAAAAAAAATAAAAAAA
1921941 ATTTCTAAAT
Statistics
Matches: 141, Mismatches: 15, Indels: 19
0.81 0.09 0.11
Matches are distributed among these distances:
190 13 0.09
191 13 0.09
192 68 0.48
193 45 0.32
194 2 0.01
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.38
Consensus pattern (191 bp):
AATTATCCAATGATGAAATTTATAAAAATTTCAAATGGTAAATTTTTATAAAATTCTTAGGTGAA
AAATTCTATCTAAATTTATCCCAAATAGTGGAAGAATTAAAATAAAGTTTTAATAACAATAATTA
ATATTTATTTTCATAAAAAAAAAAAAATAAAAAAATAAAATTTTGATTTAAAATATGTGAC
Found at i:1925499 original size:10 final size:10
Alignment explanation
Indices: 1925467--1925499 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1925457 GATAGAAAGC
1925467 AAAA-AAAAA
1 AAAACAAAAA
*
1925476 AAAACAAAAC
1 AAAACAAAAA
1925486 AAAACAAAAA
1 AAAACAAAAA
1925496 AAAA
1 AAAA
1925500 GAGAAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAACAAAAA
Found at i:1925884 original size:8 final size:7
Alignment explanation
Indices: 1925870--1925913 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
1925860 ACTAATGGAT
1925870 AGAAAAA
1 AGAAAAA
1925877 ATGAAAAA
1 A-GAAAAA
*
1925885 GGAAAAA
1 AGAAAAA
1925892 A-AAAAA
1 AGAAAAA
1925898 AGAAAAA
1 AGAAAAA
1925905 GAGAAAAA
1 -AGAAAAA
1925913 A
1 A
1925914 ATGAAAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 6 0.19
7 13 0.41
8 13 0.41
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (7 bp):
AGAAAAA
Found at i:1925898 original size:21 final size:21
Alignment explanation
Indices: 1925872--1925914 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
1925862 TAATGGATAG
*
1925872 AAAAAATGAAAAAG-GAAAAA
1 AAAAAAAGAAAAAGAGAAAAA
1925892 AAAAAAAGAAAAAGAGAAAAA
1 AAAAAAAGAAAAAGAGAAAAA
1925913 AA
1 AA
1925915 TGAAAGAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAAAAAGAGAAAAA
Found at i:1927116 original size:22 final size:21
Alignment explanation
Indices: 1927088--1927282 Score: 129
Period size: 21 Copynumber: 8.7 Consensus size: 21
1927078 ATGAATTCTT
1927088 AAATGAGAATCTTTGAGCTTTC
1 AAATGAGAATCTTTGAG-TTTC
1927110 AAATGAGAATCTTTGAGCTTTC
1 AAATGAGAATCTTTGAG-TTTC
* *
1927132 AAATGAGAATCTTTAAAAAATTTTC
1 AAATGAGAATCTTT----GAGTTTC
* * *
1927157 AAATGAGAATCTTTAAAAAATCCTC
1 AAATGAGAATCTTT---GAGT-TTC
* * * *
1927182 AAATAAAAATCTTTAAGTCTC
1 AAATGAGAATCTTTGAGTTTC
* * *
1927203 GAATAAGAATCTTTAAGAAATTTC
1 AAATGAGAATCTTT--G-AGTTTC
*
1927227 AAATGAGAATATTTGAGTTTC
1 AAATGAGAATCTTTGAGTTTC
* *
1927248 AAATTAGAATATTTGAGTTTC
1 AAATGAGAATCTTTGAGTTTC
*
1927269 AAATGAAAATCTTT
1 AAATGAGAATCTTT
1927283 AAGAAAAACT
Statistics
Matches: 145, Mismatches: 20, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
21 51 0.35
22 40 0.28
24 21 0.14
25 32 0.22
26 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (21 bp):
AAATGAGAATCTTTGAGTTTC
Found at i:1927162 original size:25 final size:25
Alignment explanation
Indices: 1927128--1927197 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
1927118 ATCTTTGAGC
1927128 TTTCAAATGAGAATCTTTAAAAAAT
1 TTTCAAATGAGAATCTTTAAAAAAT
1927153 TTTCAAATGAGAATCTTTAAAAAAT
1 TTTCAAATGAGAATCTTTAAAAAAT
** * *
1927178 CCTCAAATAAAAATCTTTAA
1 TTTCAAATGAGAATCTTTAA
1927198 GTCTCGAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (25 bp):
TTTCAAATGAGAATCTTTAAAAAAT
Found at i:1927838 original size:41 final size:41
Alignment explanation
Indices: 1927764--1927940 Score: 187
Period size: 40 Copynumber: 4.4 Consensus size: 41
1927754 GAAACCTTAC
* ** ** * *
1927764 TTATGTTTCAAAAGTCGTTGAGTCTCTGCTTAGAGGAGCCT
1 TTATTTTTCAAAAGTCGTTGAACCTCTATTTAAAGGAGCTT
* * *
1927805 TTATTTTTCAAAAGTCGTTAAACCTCTATTTAGATGAGCTT
1 TTATTTTTCAAAAGTCGTTGAACCTCTATTTAAAGGAGCTT
** * * *
1927846 TTATTTTTCAAAA-TTATTGAGCCTCTGTTTAAAGAAGCTT
1 TTATTTTTCAAAAGTCGTTGAACCTCTATTTAAAGGAGCTT
* *
1927886 TTATTTTTC-AAAGTTGTTGAACCTCTATTTAAAGGAGCAT
1 TTATTTTTCAAAAGTCGTTGAACCTCTATTTAAAGGAGCTT
1927926 TTATTTTTCAAAAGT
1 TTATTTTTCAAAAGT
1927941 TGTAGAGCTT
Statistics
Matches: 113, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 3 0.03
40 59 0.52
41 51 0.45
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (41 bp):
TTATTTTTCAAAAGTCGTTGAACCTCTATTTAAAGGAGCTT
Found at i:1927930 original size:80 final size:81
Alignment explanation
Indices: 1927781--1927938 Score: 219
Period size: 80 Copynumber: 2.0 Consensus size: 81
1927771 TCAAAAGTCG
* * * * * *
1927781 TTGAGTCTCTGCTTAGAGGAGCCTTTATTTTTCAAAAGTCGTTAAACCTCTATTTAGATGAGCTT
1 TTGAGCCTCTGCTTAAAGAAGCCTTTATTTTTCAAAAGTCGTTAAACCTCTATTTAAAGGAGCAT
1927846 TTATTTTTCAAAATTA
66 TTATTTTTCAAAATTA
* * * *
1927862 TTGAGCCTCTGTTTAAAGAAGCTTTTATTTTTC-AAAGTTGTTGAACCTCTATTTAAAGGAGCAT
1 TTGAGCCTCTGCTTAAAGAAGCCTTTATTTTTCAAAAGTCGTTAAACCTCTATTTAAAGGAGCAT
1927926 TTATTTTTCAAAA
66 TTATTTTTCAAAA
1927939 GTTGTAGAGC
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
80 39 0.58
81 28 0.42
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (81 bp):
TTGAGCCTCTGCTTAAAGAAGCCTTTATTTTTCAAAAGTCGTTAAACCTCTATTTAAAGGAGCAT
TTATTTTTCAAAATTA
Found at i:1927958 original size:41 final size:41
Alignment explanation
Indices: 1927764--1927962 Score: 204
Period size: 41 Copynumber: 4.9 Consensus size: 41
1927754 GAAACCTTAC
* * * * * *
1927764 TTATGTTTCAAAAGTCGTTGAGTCTCTGCTTAGAGGAGCCT
1 TTATTTTTCAAAAGTTGTTGAGCCTCTGTTTAAAGGAGCTT
* * * * * *
1927805 TTATTTTTCAAAAGTCGTTAAACCTCTATTTAGATGAGCTT
1 TTATTTTTCAAAAGTTGTTGAGCCTCTGTTTAAAGGAGCTT
* *
1927846 TTATTTTTCAAAA-TTATTGAGCCTCTGTTTAAAGAAGCTT
1 TTATTTTTCAAAAGTTGTTGAGCCTCTGTTTAAAGGAGCTT
* * *
1927886 TTATTTTTC-AAAGTTGTTGAACCTCTATTTAAAGGAGCAT
1 TTATTTTTCAAAAGTTGTTGAGCCTCTGTTTAAAGGAGCTT
* * *
1927926 TTATTTTTCAAAAGTTGTAGAGCTTTTGTTTAAAGGA
1 TTATTTTTCAAAAGTTGTTGAGCCTCTGTTTAAAGGA
1927963 ATTTTTAGGA
Statistics
Matches: 130, Mismatches: 26, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
39 3 0.02
40 59 0.45
41 68 0.52
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.43
Consensus pattern (41 bp):
TTATTTTTCAAAAGTTGTTGAGCCTCTGTTTAAAGGAGCTT
Found at i:1928562 original size:19 final size:18
Alignment explanation
Indices: 1928537--1928578 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1928527 AGCCGTTTCA
*
1928537 TTTTTTTATATTTTTATT
1 TTTTTTTATATGTTTATT
*
1928555 TATTTTTTATGTGTTTATT
1 T-TTTTTTATATGTTTATT
1928574 TTTTT
1 TTTTT
1928579 AGTAGTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (18 bp):
TTTTTTTATATGTTTATT
Found at i:1932034 original size:2 final size:2
Alignment explanation
Indices: 1932016--1932059 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1932006 ACCAATTCAC
* *
1932016 AT AT AA AT AT AT CT 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
1932058 AT
1 AT
1932060 CTGCAGACGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1935528 original size:22 final size:24
Alignment explanation
Indices: 1935503--1935556 Score: 85
Period size: 22 Copynumber: 2.3 Consensus size: 24
1935493 TTCGAAATTA
1935503 ATAAAATATTATTTTT-TA-AAAT
1 ATAAAATATTATTTTTATATAAAT
1935525 ATAAAATATTATTTTTAATATAAAT
1 ATAAAATATTATTTTT-ATATAAAT
1935550 ATAAAAT
1 ATAAAAT
1935557 TATATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.55
24 2 0.07
25 11 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAAATATTATTTTTATATAAAT
Done.