Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 7 of 113
Found at i:1813286 original size:11 final size:12
Alignment explanation
Indices: 1813248--1813288 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1813238 ATATTATTTT
1813248 TAATATAAATATAA
1 TAAT-TAAATA-AA
1813262 -AATTAAATAAA
1 TAATTAAATAAA
1813273 TAATTAAA-AAA
1 TAATTAAATAAA
1813284 TAATT
1 TAATT
1813289 TTATTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.38
12 13 0.50
13 3 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TAATTAAATAAA
Found at i:1815686 original size:34 final size:34
Alignment explanation
Indices: 1815648--1815722 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
1815638 CAAGAGACTA
* * *
1815648 GGTTTTTGGCTTATGCCCTCTGTGCAAGATCTAG
1 GGTTTTTGCCTTATGACCTCTGTGCAAGACCTAG
1815682 GGTTTTTGCCTTATGACCTCTGTGCAAGACCTAG
1 GGTTTTTGCCTTATGACCTCTGTGCAAGACCTAG
1815716 GGTTTTT
1 GGTTTTT
1815723 ACTTTTCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.40
Consensus pattern (34 bp):
GGTTTTTGCCTTATGACCTCTGTGCAAGACCTAG
Found at i:1819165 original size:2 final size:2
Alignment explanation
Indices: 1819147--1819179 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1819137 AAATAAAAAC
*
1819147 AT AT AA AT AT A- 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
1819180 TGTGATTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1819315 original size:2 final size:2
Alignment explanation
Indices: 1819308--1819334 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1819298 TCCTGGGACA
1819308 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1819335 ATATATATAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1820875 original size:106 final size:106
Alignment explanation
Indices: 1820688--1820879 Score: 255
Period size: 106 Copynumber: 1.8 Consensus size: 106
1820678 ATCTTTTAGG
* *
1820688 AAATTATAAGGCTTTTCAATATGTTGGTAAAACCTTATTTTGGAAAAATATTGACATTCAAATAT
1 AAATTATAAAGCTTTTCAATATGTTGGTAAAACCTTATTTTGAAAAAATATTGACATTCAAATAT
*
1820753 GTTAGTAAAGCTTTTTATTTATATATTTATTGAAATAAATA
66 ATTAGTAAAGCTTTTTATTTATATATTTATTGAAATAAATA
* * * *
1820794 AAATTATAAAGTTTTTCAATATGTTGGTAAAAACC-TATTTTTTAAAAAATAATTG-CCTTCCAA
1 AAATTATAAAGCTTTTCAATATGTTGGT-AAAACCTTA-TTTTGAAAAAAT-ATTGACATTCAAA
* *
1820857 TCTATTAGTAAGGC-TTTTATTTA
63 TATATTAGTAAAGCTTTTTATTTA
1820880 AAATTTTATT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
106 37 0.50
107 33 0.45
108 4 0.05
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (106 bp):
AAATTATAAAGCTTTTCAATATGTTGGTAAAACCTTATTTTGAAAAAATATTGACATTCAAATAT
ATTAGTAAAGCTTTTTATTTATATATTTATTGAAATAAATA
Found at i:1822625 original size:82 final size:83
Alignment explanation
Indices: 1822498--1822720 Score: 245
Period size: 82 Copynumber: 2.7 Consensus size: 83
1822488 ATTACATCCA
* * * * *
1822498 AAGGTCTTACAAATTTTGATTCTAAAACAGATTTAACTCGA-AAGACTTACGAATCTTACTCGA-
1 AAGGTCTTACAAATTTTGATT-TAAAATAGATTCAGCTC-ATAAGACTTACAAATATTACT-GAG
1822561 AGGACTTAGAGATTATGC-CC
63 AGGACTTAGAGATTATGCTCC
* * * * *
1822581 AGGGTCTTACAAATCTCGATTTAAAATAGATTCAGCTCATAAGACTTACAAATATTTCTTAGAGG
1 AAGGTCTTACAAATTTTGATTTAAAATAGATTCAGCTCATAAGACTTACAAATATTACTGAGAGG
* *
1822646 ATTTAGAGATTATGCTCG
66 ACTTAGAGATTATGCTCC
* * * *
1822664 AAAGTTTTATAAATTTTGACTTTAAAATAGATTCAGCTCGTAAGACTTACAAATATT
1 AAGGTCTTACAAATTTTGA-TTTAAAATAGATTCAGCTCATAAGACTTACAAATATT
1822721 GTTTGAAAGA
Statistics
Matches: 117, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
81 2 0.02
82 47 0.40
83 32 0.27
84 36 0.31
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (83 bp):
AAGGTCTTACAAATTTTGATTTAAAATAGATTCAGCTCATAAGACTTACAAATATTACTGAGAGG
ACTTAGAGATTATGCTCC
Found at i:1827992 original size:18 final size:21
Alignment explanation
Indices: 1827940--1827998 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1827930 CTATTATGCA
*
1827940 ATGACATGATGAATGAATGATG
1 ATGACAT-ATAAATGAATGATG
*
1827962 ATGATATATAAATGAATGA-G
1 ATGACATATAAATGAATGATG
1827982 ATG-CATA-AAATGAATGA
1 ATGACATATAAATGAATGA
1827999 AAATAAACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.29
19 3 0.09
20 4 0.12
21 11 0.32
22 6 0.18
ACGTcount: A:0.47, C:0.03, G:0.22, T:0.27
Consensus pattern (21 bp):
ATGACATATAAATGAATGATG
Found at i:1828476 original size:21 final size:20
Alignment explanation
Indices: 1828435--1828485 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1828425 CTCATGTTAT
* *
1828435 ATATATACAAATGAATGACAA
1 ATATATA-AAATAAATAACAA
1828456 ATATATAAAATAAATAAACAA
1 ATATATAAAATAAAT-AACAA
*
1828477 ATAAATAAA
1 ATATATAAA
1828486 TACAAGCAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.24
Consensus pattern (20 bp):
ATATATAAAATAAATAACAA
Found at i:1830399 original size:20 final size:22
Alignment explanation
Indices: 1830359--1830401 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1830349 TTTTCATCCT
1830359 TGTTTTAATATTTAAAATTATCA
1 TGTTTTAATATTT-AAATTATCA
1830382 TGTTTTAAT-TTT-AATTATCA
1 TGTTTTAATATTTAAATTATCA
1830402 AAATCATCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
22 3 0.15
23 9 0.45
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (22 bp):
TGTTTTAATATTTAAATTATCA
Found at i:1830488 original size:16 final size:16
Alignment explanation
Indices: 1830469--1830515 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1830459 ATAAAAATTT
*
1830469 AAAATCAAATAAATAA
1 AAAATAAAATAAATAA
*
1830485 AAAACTAAAAT-ATTAA
1 AAAA-TAAAATAAATAA
*
1830501 AAAATTAAATAAATA
1 AAAATAAAATAAATA
1830516 TACAAGACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 5 0.20
16 15 0.60
17 5 0.20
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAAAATAAATAA
Found at i:1831441 original size:2 final size:2
Alignment explanation
Indices: 1831420--1831462 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
1831410 TAAGATACTA
* * * *
1831420 AT AT AT AC AC AT AT AA AT AT AT AT AT AT GT 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
1831462 A
1 A
1831463 CACACACACA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1834429 original size:2 final size:2
Alignment explanation
Indices: 1834422--1834449 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1834412 TGTTCATCTC
1834422 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
1834450 CATAAACAGG
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:1837340 original size:3 final size:3
Alignment explanation
Indices: 1837332--1837359 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1837322 TTGGCAAGGA
1837332 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1837360 TCAGACGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1841688 original size:6 final size:6
Alignment explanation
Indices: 1841677--1841704 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1841667 TAAGAGATAA
1841677 GTGTTC GTGTTC GTGTTC GTGTTC GTGT
1 GTGTTC GTGTTC GTGTTC GTGTTC GTGT
1841705 GAGCATTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.36, T:0.50
Consensus pattern (6 bp):
GTGTTC
Found at i:1845442 original size:20 final size:19
Alignment explanation
Indices: 1845417--1845456 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1845407 AAGTGCATGG
1845417 AGAAAATAAAAAGAACAAAA
1 AGAAAA-AAAAAGAACAAAA
* *
1845437 AGAAAAGAAAAGACCAAAA
1 AGAAAAAAAAAGAACAAAA
1845456 A
1 A
1845457 AATTAAGTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.78, C:0.07, G:0.12, T:0.03
Consensus pattern (19 bp):
AGAAAAAAAAAGAACAAAA
Found at i:1852547 original size:50 final size:48
Alignment explanation
Indices: 1852493--1852588 Score: 122
Period size: 49 Copynumber: 2.0 Consensus size: 48
1852483 CATTGGAAAA
1852493 TAAATTTTTAAAAAA-TTATAAACCTTTTCAAAAATAAATTTCTAGAAAGT
1 TAAATTTTTAAAAAATTTAT-AA-CTTTTCAAAAATAAATTTC-AGAAAGT
* * * *
1852543 TAAATTTTTAAAAGATTTATGATTTTTCAAAAATTAATTTCAGAAA
1 TAAATTTTTAAAAAATTTATAACTTTTCAAAAATAAATTTCAGAAA
1852589 AATCATTTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
48 5 0.12
49 17 0.41
50 15 0.37
51 4 0.10
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (48 bp):
TAAATTTTTAAAAAATTTATAACTTTTCAAAAATAAATTTCAGAAAGT
Found at i:1852650 original size:34 final size:35
Alignment explanation
Indices: 1852611--1852681 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
1852601 ATGGAAAAAC
1852611 TATGATTTTTT-AAAAATTTACTTT-ATAAAAATTA
1 TATGATTTTTTAAAAAATTTACTTTCA-AAAAATTA
*
1852645 TATGATTTTTTAAAAAATTTATTTTCAAAAAATTA
1 TATGATTTTTTAAAAAATTTACTTTCAAAAAATTA
1852680 TA
1 TA
1852682 AAACTCTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 11 0.32
35 22 0.65
36 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (35 bp):
TATGATTTTTTAAAAAATTTACTTTCAAAAAATTA
Found at i:1853325 original size:2 final size:2
Alignment explanation
Indices: 1853318--1853343 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1853308 AATATAAAGC
1853318 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
1853344 CTAGAGCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1857953 original size:16 final size:16
Alignment explanation
Indices: 1857934--1857966 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1857924 TATATAAAAT
1857934 AAAACTTACAATTATA
1 AAAACTTACAATTATA
*
1857950 AAAACTTGCAATTATA
1 AAAACTTACAATTATA
1857966 A
1 A
1857967 GTATGTTAAT
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:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAACTTACAATTATA
Found at i:1859585 original size:33 final size:33
Alignment explanation
Indices: 1859517--1859585 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
1859507 ATAAAAAAAT
* *
1859517 AATTTTATATTAAAAATTACTTAAATAATTTAA
1 AATTTTATATTAAAAAATACTTAAATAATTAAA
1859550 AATTTTATATTAAAATAATA-TATAAA-AATTAAA
1 AATTTTATATTAAAA-AATACT-TAAATAATTAAA
1859583 AAT
1 AAT
1859586 CAGTAAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (33 bp):
AATTTTATATTAAAAAATACTTAAATAATTAAA
Found at i:1860146 original size:16 final size:17
Alignment explanation
Indices: 1860125--1860157 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1860115 TCTAATCGAA
1860125 TTTTTA-TATTTAAATT
1 TTTTTATTATTTAAATT
*
1860141 TTTTTATTATTTTAATT
1 TTTTTATTATTTAAATT
1860158 AATAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTATTATTTAAATT
Found at i:1861079 original size:25 final size:25
Alignment explanation
Indices: 1861033--1861080 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1861023 TTTAAATATA
* *
1861033 ATAAATAAATTTTATTAGTTAATGC
1 ATAAATAAATTTTATAAATTAATGC
1861058 ATAAATAAATATTT-TAAATTAAT
1 ATAAATAAAT-TTTATAAATTAAT
1861081 TTTATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (25 bp):
ATAAATAAATTTTATAAATTAATGC
Found at i:1861114 original size:38 final size:38
Alignment explanation
Indices: 1861025--1861123 Score: 110
Period size: 38 Copynumber: 2.6 Consensus size: 38
1861015 TTTGATAATT
*
1861025 TAAATATAATAAATAAATTTTATTAGTTAATGCATAAA
1 TAAATATAATAAATAAATTTTATTAGTTAATGAATAAA
** * * *
1861063 TAAATATTTTAAATTAATTTTATTA-TTTATTAATAAA
1 TAAATATAATAAATAAATTTTATTAGTTAATGAATAAA
**
1861100 TTTTATATAATAAATAAATTTTAT
1 -TAAATATAATAAATAAATTTTAT
1861124 AAATATTAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
37 9 0.18
38 40 0.82
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (38 bp):
TAAATATAATAAATAAATTTTATTAGTTAATGAATAAA
Found at i:1861117 original size:18 final size:17
Alignment explanation
Indices: 1861094--1861128 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
1861084 ATTATTTATT
1861094 AATAAATTTTATATAATA
1 AATAAATTTTATA-AATA
1861112 AATAAATTTTATAAATA
1 AATAAATTTTATAAATA
1861129 TTAAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAAATTTTATAAATA
Found at i:1861135 original size:20 final size:19
Alignment explanation
Indices: 1861071--1861136 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
1861061 AATAAATATT
* *
1861071 TTAAATTAATTTTATTAT-
1 TTAAATAAATTTTATAATA
1861089 TTATTAATAAATTTTAT-ATA
1 TTA--AATAAATTTTATAATA
*
1861109 ATAAATAAATTTTATAAATA
1 TTAAATAAATTTTAT-AATA
1861129 TTAAATAA
1 TTAAATAA
1861137 TTTAAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 15 0.38
19 2 0.05
20 23 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAATAAATTTTATAATA
Found at i:1865810 original size:28 final size:27
Alignment explanation
Indices: 1865771--1865825 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
1865761 TAAATAATTG
1865771 AAATTTATTTATTTATTA-TATAGTGAT
1 AAATTTATTTATTTATTATTATA-TGAT
1865798 AAATTTGATTTATTTATTATTATATGAT
1 AAATTT-ATTTATTTATTATTATATGAT
1865826 TGTTAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 6 0.23
28 16 0.62
29 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (27 bp):
AAATTTATTTATTTATTATTATATGAT
Found at i:1868436 original size:13 final size:13
Alignment explanation
Indices: 1868399--1868437 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1868389 AGTAACGATA
1868399 TATTTTAATTTATT
1 TATTTTAATTT-TT
* *
1868413 AATTTTGATTTTT
1 TATTTTAATTTTT
1868426 TATTTTAATTTT
1 TATTTTAATTTT
1868438 ATTTAATCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
TATTTTAATTTTT
Found at i:1868790 original size:101 final size:101
Alignment explanation
Indices: 1868615--1868817 Score: 379
Period size: 101 Copynumber: 2.0 Consensus size: 101
1868605 CTCCCCTATG
*
1868615 GTCCTCAATAACATCTCACCTTTCCCGTTTGTGTTCTAACTCTTCTTGTTCTTAAGCTTTGAGGC
1 GTCCTCAATAACATCTCACCTTTCCCATTTGTGTTCTAACTCTTCTTGTTCTTAAGCTTTGAGGC
1868680 CATGAAGACTGGTAATAATTAATTACACTTTTCTTT
66 CATGAAGACTGGTAATAATTAATTACACTTTTCTTT
*
1868716 GTCCTCAATAACATCTCACCTTTCCCATTTGTGTTCTCACTCTTCTTGTTCTTAAGCTTTGAGGC
1 GTCCTCAATAACATCTCACCTTTCCCATTTGTGTTCTAACTCTTCTTGTTCTTAAGCTTTGAGGC
*
1868781 CATGAAGACTGGTAATAATTAATTGCACTTTTCTTT
66 CATGAAGACTGGTAATAATTAATTACACTTTTCTTT
1868817 G
1 G
1868818 CTTCCATGCT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.41
Consensus pattern (101 bp):
GTCCTCAATAACATCTCACCTTTCCCATTTGTGTTCTAACTCTTCTTGTTCTTAAGCTTTGAGGC
CATGAAGACTGGTAATAATTAATTACACTTTTCTTT
Found at i:1872927 original size:10 final size:11
Alignment explanation
Indices: 1872896--1872924 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1872886 CCAGATGGTG
1872896 AATTCTTTAAA
1 AATTCTTTAAA
1872907 AATTCTTTAAA
1 AATTCTTTAAA
1872918 AATTCTT
1 AATTCTT
1872925 AAACAGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (11 bp):
AATTCTTTAAA
Found at i:1878277 original size:57 final size:57
Alignment explanation
Indices: 1878189--1878315 Score: 218
Period size: 57 Copynumber: 2.2 Consensus size: 57
1878179 CATTACCCAA
*
1878189 CTCCTGAAAGTAATCCACAAGTATCTTCCCCTTACCATCAACCTGCCCAATATCCTC
1 CTCCTGAAAGTAATCCACAAGTATCTTCCCCTTACCAACAACCTGCCCAATATCCTC
* * *
1878246 CTCCTGAAAGTAATTCACAAGTATCTTCCCCTTATCAACAACCTGCTCAATATCCTC
1 CTCCTGAAAGTAATCCACAAGTATCTTCCCCTTACCAACAACCTGCCCAATATCCTC
1878303 CTCCTGAAAGTAA
1 CTCCTGAAAGTAA
1878316 CTCTGAGCTA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 66 1.00
ACGTcount: A:0.30, C:0.35, G:0.08, T:0.28
Consensus pattern (57 bp):
CTCCTGAAAGTAATCCACAAGTATCTTCCCCTTACCAACAACCTGCCCAATATCCTC
Found at i:1880942 original size:33 final size:33
Alignment explanation
Indices: 1880900--1880965 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1880890 AATATGTAAA
*
1880900 TATATGCATAATGTGTTTAGAATCTTTAGATAT
1 TATATGCATAATATGTTTAGAATCTTTAGATAT
1880933 TATATGCATAATATGTTTAGAATCTTTAGATAT
1 TATATGCATAATATGTTTAGAATCTTTAGATAT
1880966 GAGTTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (33 bp):
TATATGCATAATATGTTTAGAATCTTTAGATAT
Found at i:1887216 original size:102 final size:102
Alignment explanation
Indices: 1887040--1887243 Score: 399
Period size: 102 Copynumber: 2.0 Consensus size: 102
1887030 TTTGAAAATC
*
1887040 GATTCGCCATCTTAGATTAAGCCGGTTTCATTTGCAATAAACCCAATTCTAGAGCTAAAGTCATC
1 GATTCGCCATCTTAGATTAAGCCGGTTTCATTTGCAACAAACCCAATTCTAGAGCTAAAGTCATC
1887105 AAAATCTAAATACCACATTCTTCAAATATAAACACTT
66 AAAATCTAAATACCACATTCTTCAAATATAAACACTT
1887142 GATTCGCCATCTTAGATTAAGCCGGTTTCATTTGCAACAAACCCAATTCTAGAGCTAAAGTCATC
1 GATTCGCCATCTTAGATTAAGCCGGTTTCATTTGCAACAAACCCAATTCTAGAGCTAAAGTCATC
1887207 AAAATCTAAATACCACATTCTTCAAATATAAACACTT
66 AAAATCTAAATACCACATTCTTCAAATATAAACACTT
1887244 CCTATTATCT
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (102 bp):
GATTCGCCATCTTAGATTAAGCCGGTTTCATTTGCAACAAACCCAATTCTAGAGCTAAAGTCATC
AAAATCTAAATACCACATTCTTCAAATATAAACACTT
Found at i:1891278 original size:12 final size:12
Alignment explanation
Indices: 1891261--1891316 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
1891251 TATTTTTAAT
1891261 TTAAATATAAAA
1 TTAAATATAAAA
*
1891273 TTAAATAT-ATA
1 TTAAATATAAAA
1891284 -TAAATATAAAA
1 TTAAATATAAAA
1891295 TTAAATA-AATAA
1 TTAAATATAA-AA
*
1891307 TTAAAAATAA
1 TTAAATATAA
1891317 TTTTATATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 7 0.19
11 6 0.16
12 22 0.59
13 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TTAAATATAAAA
Found at i:1891302 original size:16 final size:17
Alignment explanation
Indices: 1891256--1891311 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
1891246 AATATTATTT
*
1891256 TTAATTTAAATATAAAA
1 TTAAATTAAATATAAAA
*
1891273 TTAAA-TATATATAAATA
1 TTAAATTAAATATAAA-A
*
1891290 TAAAATTAAATA-AATAA
1 TTAAATTAAATATAA-AA
1891307 TTAAA
1 TTAAA
1891312 AATAATTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 9 0.29
17 16 0.52
18 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAATTAAATATAAAA
Found at i:1896638 original size:21 final size:20
Alignment explanation
Indices: 1896598--1896638 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1896588 TAATATATAA
*
1896598 TTTATTTTTAATTAATTTTT
1 TTTATTTTTAAATAATTTTT
1896618 TTTATTTTTCAAATATATTTT
1 TTTATTTTT-AAATA-ATTTT
1896639 AAAAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 4 0.22
22 5 0.28
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTTTTAAATAATTTTT
Found at i:1897148 original size:2 final size:2
Alignment explanation
Indices: 1897141--1897167 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1897131 AACAAATTCG
1897141 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1897168 TAATTGAAAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1904087 original size:2 final size:2
Alignment explanation
Indices: 1904080--1904116 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1904070 ATAGGATGGC
1904080 AT AT AT AT AT AT AT AT A- 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
1904117 CAGTTTTGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1904102 original size:17 final size:17
Alignment explanation
Indices: 1904080--1904113 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1904070 ATAGGATGGC
1904080 ATATATATATATATATA
1 ATATATATATATATATA
1904097 ATATATATATATATATA
1 ATATATATATATATATA
1904114 TATCAGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:1918957 original size:32 final size:33
Alignment explanation
Indices: 1918909--1918993 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 33
1918899 TTATTTAAAT
* * *
1918909 TTAACTTAAATAAAATTTTAATTTAATTTAA-TTA
1 TTAA-TTAAATCAAATTTTAA-ATAATATAATTTA
1918943 TT-ATTAAATCAAA-TTTAAATAATATAATTTA
1 TTAATTAAATCAAATTTTAAATAATATAATTTA
*
1918974 TTAATTAAATCGAATTTTAA
1 TTAATTAAATCAAATTTTAA
1918994 CATGTTTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
30 7 0.16
31 10 0.23
32 19 0.43
33 6 0.14
34 2 0.05
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (33 bp):
TTAATTAAATCAAATTTTAAATAATATAATTTA
Found at i:1919149 original size:6 final size:6
Alignment explanation
Indices: 1919140--1919230 Score: 66
Period size: 6 Copynumber: 15.5 Consensus size: 6
1919130 TTAATAAAAA
* * *
1919140 TAAATT TAAA-- T-AATT TAAATT TTATTT TAAA-T TAATTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* * *
1919184 AAAAAAT AAAATTT TAAATTT TAAA-T TAAATT TAAATT TAAATT TAA
1 -TAAATT TAAA-TT TAAA-TT TAAATT TAAATT TAAATT TAAATT TAA
1919231 TATTGTATGA
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
3 2 0.03
4 1 0.01
5 10 0.15
6 40 0.59
7 15 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:1919177 original size:11 final size:11
Alignment explanation
Indices: 1919144--1919185 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1919134 TAAAAATAAA
1919144 TTTAAA-TAA-
1 TTTAAATTAAT
*
1919153 TTTAAATTTTAT
1 TTTAAA-TTAAT
1919165 TTTAAATTAAT
1 TTTAAATTAAT
1919176 TTTAAATTAA
1 TTTAAATTAA
1919186 AAAATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 6 0.21
11 16 0.57
12 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTAAATTAAT
Found at i:1919182 original size:38 final size:39
Alignment explanation
Indices: 1919140--1919226 Score: 117
Period size: 38 Copynumber: 2.3 Consensus size: 39
1919130 TTAATAAAAA
* * *
1919140 TAAATTTAAATAATTTAAATTTT-ATTTTAAATTAATTT
1 TAAATTTAAATAAATAAAATTTTAATTTTAAATTAAATT
1919178 TAAA-TTAAA-AAATAAAATTTTAAATTTTAAATTAAATT
1 TAAATTTAAATAAATAAAATTTT-AATTTTAAATTAAATT
1919216 TAAATTTAAAT
1 TAAATTTAAAT
1919227 TTAATATTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 10 0.24
37 5 0.12
38 22 0.52
39 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (39 bp):
TAAATTTAAATAAATAAAATTTTAATTTTAAATTAAATT
Found at i:1920160 original size:20 final size:21
Alignment explanation
Indices: 1920125--1920164 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1920115 TGGCTGCGTT
1920125 TATTTGATGTTTTAAAGATTA
1 TATTTGATGTTTTAAAGATTA
*
1920146 TATTTGTTG-TTTAAAGATT
1 TATTTGATGTTTTAAAGATT
1920165 GTTGTTACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (21 bp):
TATTTGATGTTTTAAAGATTA
Found at i:1921261 original size:2 final size:2
Alignment explanation
Indices: 1921254--1921295 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1921244 TTGCAACGGT
1921254 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1921295 T
1 T
1921296 TTGCCTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1929950 original size:2 final size:2
Alignment explanation
Indices: 1929943--1929979 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1929933 GGTTTGCATT
1929943 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 T
1929980 TTTTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1930016 original size:1 final size:1
Alignment explanation
Indices: 1929979--1930009 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
1929969 TATATATATA
*
1929979 TTTTTTTTTTTTTTTTTTTTTATTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1930010 CCTTTTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:1930406 original size:195 final size:195
Alignment explanation
Indices: 1930074--1930465 Score: 748
Period size: 195 Copynumber: 2.0 Consensus size: 195
1930064 AGTGTCAGGC
1930074 CCATTCTGTGTTGCTAAGGAAGTGCTGATATCTGTGTAATTGCATCCTGTCATAGACTGAAGGCA
1 CCATTCTGTGTTGCTAAGGAAGTGCTGATATCTGTGTAATTGCATCCTGTCATAGACTGAAGGCA
**
1930139 GGTTATTGTCAGATCAAGATGAATTTCATGTCACCGTAAGAATTAGTCTTTCCCTAGATCGGGCC
66 GGTTAGAGTCAGATCAAGATGAATTTCATGTCACCGTAAGAATTAGTCTTTCCCTAGATCGGGCC
1930204 TATCTTCTTTCAGATCTTATACCATTGTGGTATCCTTTCTTTCTAGGTTCAGCCAACGATTCATT
131 TATCTTCTTTCAGATCTTATACCATTGTGGTATCCTTTCTTTCTAGGTTCAGCCAACGATTCATT
*
1930269 CCATTCTGTGTTGCTAAGGAAGTGCTGATATCTGTGTAATTGCATCCTGTCATTGACTGAAGGCA
1 CCATTCTGTGTTGCTAAGGAAGTGCTGATATCTGTGTAATTGCATCCTGTCATAGACTGAAGGCA
*
1930334 GGTTAGAGTCAGATCAAGATGAATTTCATGTCACCGTAAGAATTAGTCTTTCCTTAGATCGGGCC
66 GGTTAGAGTCAGATCAAGATGAATTTCATGTCACCGTAAGAATTAGTCTTTCCCTAGATCGGGCC
1930399 TATCTTCTTTCAGATCTTATACCATTGTGGTATCCTTTCTTTCTAGGTTCAGCCAACGATTCATT
131 TATCTTCTTTCAGATCTTATACCATTGTGGTATCCTTTCTTTCTAGGTTCAGCCAACGATTCATT
1930464 CC
1 CC
1930466 CACAGTATGA
Statistics
Matches: 193, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
195 193 1.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (195 bp):
CCATTCTGTGTTGCTAAGGAAGTGCTGATATCTGTGTAATTGCATCCTGTCATAGACTGAAGGCA
GGTTAGAGTCAGATCAAGATGAATTTCATGTCACCGTAAGAATTAGTCTTTCCCTAGATCGGGCC
TATCTTCTTTCAGATCTTATACCATTGTGGTATCCTTTCTTTCTAGGTTCAGCCAACGATTCATT
Found at i:1937284 original size:21 final size:21
Alignment explanation
Indices: 1937258--1937302 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1937248 TTAATATAAT
* * *
1937258 ATTAAATTTTTAATTTTGATA
1 ATTAAAATTTAAAGTTTGATA
1937279 ATTAAAATTTAAAGTTTGATA
1 ATTAAAATTTAAAGTTTGATA
1937300 ATT
1 ATT
1937303 TTAATAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
ATTAAAATTTAAAGTTTGATA
Found at i:1940285 original size:2 final size:2
Alignment explanation
Indices: 1940273--1940302 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1940263 ACGATTTTAG
1940273 AT AT A- 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
1940303 CACGTATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1959388 original size:10 final size:9
Alignment explanation
Indices: 1959373--1959397 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1959363 ACTATCCAAC
1959373 AAAAAAAAT
1 AAAAAAAAT
1959382 AAAAAAAAT
1 AAAAAAAAT
1959391 AAAAAAA
1 AAAAAAA
1959398 CTGAATGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:1969542 original size:12 final size:12
Alignment explanation
Indices: 1969527--1969551 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1969517 ACAACAGCTG
1969527 TCAACAACACCA
1 TCAACAACACCA
1969539 TCAACAACACCA
1 TCAACAACACCA
1969551 T
1 T
1969552 GCCTCAACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.40, G:0.00, T:0.12
Consensus pattern (12 bp):
TCAACAACACCA
Found at i:1971146 original size:233 final size:233
Alignment explanation
Indices: 1970739--1971205 Score: 925
Period size: 233 Copynumber: 2.0 Consensus size: 233
1970729 GTTTACCGTA
1970739 ATAAGACACTGTACCCTTGATACTTTGTAGCTAGTCCATAAACCAATCATAAGCGACTGATCCCT
1 ATAAGACACTGTACCCTTGATACTTTGTAGCTAGTCCATAAACCAATCATAAGCGACTGATCCCT
1970804 TGTAATAAATCAATTTTGCGCTGAAACTTCTCTATGCATGTTTTTACAGAGTATGGCTAATAATG
66 TGTAATAAATCAATTTTGCGCTGAAACTTCTCTATGCATGTTTTTACAGAGTATGGCTAATAATG
1970869 GTCATGTGATTATATTCAAAATGATAAAGTACACATGTTGAATATGGGTCTTTGTTTGCAGGAAC
131 GTCATGTGATTATATTCAAAATGATAAAGTACACATGTTGAATATGGGTCTTTGTTTGCAGGAAC
*
1970934 AAACAGAAAGATTTGGTTTATGCTGTATCTGAAGTCAC
196 AAACAGAAAGATTTGGTTCATGCTGTATCTGAAGTCAC
1970972 ATAAGACACTGTACCCTTGATACTTTGTAGCTAGTCCATAAACCAATCATAAGCGACTGATCCCT
1 ATAAGACACTGTACCCTTGATACTTTGTAGCTAGTCCATAAACCAATCATAAGCGACTGATCCCT
1971037 TGTAATAAATCAATTTTGCGCTGAAACTTCTCTATGCATGTTTTTACAGAGTATGGCTAATAATG
66 TGTAATAAATCAATTTTGCGCTGAAACTTCTCTATGCATGTTTTTACAGAGTATGGCTAATAATG
1971102 GTCATGTGATTATATTCAAAATGATAAAGTACACATGTTGAATATGGGTCTTTGTTTGCAGGAAC
131 GTCATGTGATTATATTCAAAATGATAAAGTACACATGTTGAATATGGGTCTTTGTTTGCAGGAAC
1971167 AAACAGAAAGATTTGGTTCATGCTGTATCTGAAGTCAC
196 AAACAGAAAGATTTGGTTCATGCTGTATCTGAAGTCAC
1971205 A
1 A
1971206 CACATATATA
Statistics
Matches: 233, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
233 233 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (233 bp):
ATAAGACACTGTACCCTTGATACTTTGTAGCTAGTCCATAAACCAATCATAAGCGACTGATCCCT
TGTAATAAATCAATTTTGCGCTGAAACTTCTCTATGCATGTTTTTACAGAGTATGGCTAATAATG
GTCATGTGATTATATTCAAAATGATAAAGTACACATGTTGAATATGGGTCTTTGTTTGCAGGAAC
AAACAGAAAGATTTGGTTCATGCTGTATCTGAAGTCAC
Found at i:1972601 original size:36 final size:36
Alignment explanation
Indices: 1972551--1972620 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
1972541 AATAAATTAA
1972551 ATTGAATTTAAATATTTTAA-TATTTAAATTTTATCG
1 ATTGAATTTAAATATTTTAATTATTT-AATTTTATCG
* * *
1972587 ATTGATTTTTAATATTTTAATTATTTCATTTTAT
1 ATTGAATTTAAATATTTTAATTATTTAATTTTAT
1972621 GACGATTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 25 0.83
37 5 0.17
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (36 bp):
ATTGAATTTAAATATTTTAATTATTTAATTTTATCG
Found at i:1973396 original size:2 final size:2
Alignment explanation
Indices: 1973389--1973431 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1973379 CGAAAACAGC
1973389 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
1973431 A
1 A
1973432 GACACACACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1974051 original size:21 final size:23
Alignment explanation
Indices: 1974027--1974070 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1974017 TATAATATAA
1974027 TAATT-TA-AATATTAAATTTAT
1 TAATTATATAATATTAAATTTAT
*
1974048 TAATTACTATAATATTAATTTTA
1 TAATTA-TATAATATTAAATTTA
1974071 AATAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
23 2 0.11
24 12 0.63
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATTATATAATATTAAATTTAT
Found at i:1974141 original size:32 final size:31
Alignment explanation
Indices: 1974099--1974168 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 31
1974089 ATCATTATTT
* *
1974099 TTTATATATTATATT-AATTTATTTATTTATAA
1 TTTAAATATTATATTAAATAT-TTTA-TTATAA
1974131 TTTAAATATTATATTAAATATTTTATTATAA
1 TTTAAATATTATATTAAATATTTTATTATAA
1974162 TTTAAAT
1 TTTAAAT
1974169 GTCATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 13 0.37
32 18 0.51
33 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTAAATATTATATTAAATATTTTATTATAA
Found at i:1974620 original size:16 final size:17
Alignment explanation
Indices: 1974601--1974636 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1974591 TATAAAAATA
1974601 TAAAAA-TAATATAATT
1 TAAAAATTAATATAATT
1974617 TAAAAATTTAATATAATT
1 TAAAAA-TTAATATAATT
1974635 TA
1 TA
1974637 TATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
18 12 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAAATTAATATAATT
Found at i:1975386 original size:29 final size:29
Alignment explanation
Indices: 1975302--1975383 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 29
1975292 TAATGAAATA
*
1975302 TTTAATATAATATTTAAATTTTAAAATTT
1 TTTAATATAATATATAAATTTTAAAATTT
1975331 TTTAATATAATATATAAATTTTAAAATTT
1 TTTAATATAATATATAAATTTTAAAATTT
*
1975360 TTTAAT-TAATATA-ATATTTTAAAA
1 TTTAATATAATATATAAATTTTAAAA
1975384 AATATTTATT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
27 10 0.20
28 7 0.14
29 34 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTAATATAATATATAAATTTTAAAATTT
Found at i:1975391 original size:28 final size:27
Alignment explanation
Indices: 1975297--1975391 Score: 93
Period size: 29 Copynumber: 3.3 Consensus size: 27
1975287 AAATATAATG
1975297 AAATATTTAATATAATATTTAAATTTTAA
1 AAATATTTAATATAATA--TAAATTTTAA
* *
1975326 AATTTTTTAATATAATATATAAATTTTAA
1 AAATATTTAATAT-A-ATATAAATTTTAA
* *
1975355 AATTTTTTAAT-TAATATAATATTTTAAA
1 AAATATTTAATATAATATAA-ATTTT-AA
1975383 AAATATTTA
1 AAATATTTA
1975392 TTCATCACGT
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
26 6 0.10
27 6 0.10
28 10 0.17
29 32 0.55
30 1 0.02
31 3 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AAATATTTAATATAATATAAATTTTAA
Found at i:1979550 original size:22 final size:22
Alignment explanation
Indices: 1979522--1979568 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1979512 CTCCTAGCGC
1979522 TATCAATCAATGTTTTAAAATT
1 TATCAATCAATGTTTTAAAATT
1979544 TATCAATCAATGTTTTAAAATT
1 TATCAATCAATGTTTTAAAATT
1979566 TAT
1 TAT
1979569 TCCAAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (22 bp):
TATCAATCAATGTTTTAAAATT
Found at i:1980874 original size:10 final size:10
Alignment explanation
Indices: 1980856--1980894 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1980846 TAAAAATTAC
*
1980856 AAATATTTTA
1 AAATTTTTTA
*
1980866 AAATTTTTTG
1 AAATTTTTTA
1980876 AAATTTTTTA
1 AAATTTTTTA
1980886 AAATATTTT
1 AAAT-TTTT
1980895 CTTTATCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 21 0.84
11 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
AAATTTTTTA
Found at i:1980879 original size:20 final size:21
Alignment explanation
Indices: 1980856--1980894 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1980846 TAAAAATTAC
1980856 AAATATTTTAAAAT-TTTTTG
1 AAATATTTTAAAATATTTTTG
*
1980876 AAATTTTTTAAAATATTTT
1 AAATATTTTAAAATATTTT
1980895 CTTTATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
AAATATTTTAAAATATTTTTG
Found at i:1985592 original size:2 final size:2
Alignment explanation
Indices: 1985585--1985616 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1985575 AATAATACTA
1985585 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
1985617 TGCTGTCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1986794 original size:15 final size:15
Alignment explanation
Indices: 1986774--1986803 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1986764 TTAGTTTCTA
*
1986774 TATAAATTTTATTTT
1 TATAAATATTATTTT
1986789 TATAAATATTATTTT
1 TATAAATATTATTTT
1986804 CAAAATCTAA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATAAATATTATTTT
Found at i:1986838 original size:2 final size:2
Alignment explanation
Indices: 1986831--1986859 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1986821 CCACCCAACA
1986831 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
1986860 GAGAGAGAGA
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:1986864 original size:2 final size:2
Alignment explanation
Indices: 1986859--1986883 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1986849 ATATATATAT
1986859 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1986884 AGAATTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1987043 original size:2 final size:2
Alignment explanation
Indices: 1987036--1987070 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1987026 ACATACATAC
1987036 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
1987071 GTAAAGATTC
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:1992649 original size:18 final size:19
Alignment explanation
Indices: 1992628--1992680 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
1992618 ATAAAAGTGT
*
1992628 TAAATTATTTAA-AATTTA
1 TAAATTATTAAATAATTTA
*
1992646 TAAA-TAATAAATAATTTA
1 TAAATTATTAAATAATTTA
*
1992664 -AAATTATTAAATTATTT
1 TAAATTATTAAATAATTT
1992681 TATATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAATTATTAAATAATTTA
Found at i:1995187 original size:23 final size:23
Alignment explanation
Indices: 1995138--1995190 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1995128 AAACAGTAAT
* * *
1995138 AAAAATTATTATAGTTATAATTA
1 AAAAAATATTATAATTACAATTA
*
1995161 AAAAAATATTATAATTACGATTGA
1 AAAAAATATTATAATTACAATT-A
1995185 AAAAAA
1 AAAAAA
1995191 ATTTTAACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (23 bp):
AAAAAATATTATAATTACAATTA
Found at i:1997124 original size:20 final size:18
Alignment explanation
Indices: 1997082--1997129 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1997072 ATTTAAATTT
*
1997082 AAATAAAAAAATTAAAAC
1 AAATAAAAAAATAAAAAC
*
1997100 AAATAAAAAGATAAGAAATC
1 AAATAAAAAAATAA-AAA-C
1997120 AAATAAAAAA
1 AAATAAAAAA
1997130 CCTTGCAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 12 0.48
19 3 0.12
20 10 0.40
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (18 bp):
AAATAAAAAAATAAAAAC
Found at i:1997585 original size:11 final size:11
Alignment explanation
Indices: 1997571--1997621 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
1997561 TTTAAATTCG
1997571 ATTTAAATAAA
1 ATTTAAATAAA
**
1997582 ATTTAAATTTA
1 ATTTAAATAAA
* **
1997593 ATTTAATTATT
1 ATTTAAATAAA
1997604 A-TTAAATAAA
1 ATTTAAATAAA
1997614 ATTTAAAT
1 ATTTAAAT
1997622 TTGAATAATT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
10 7 0.23
11 24 0.77
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTTAAATAAA
Found at i:2007075 original size:20 final size:21
Alignment explanation
Indices: 2007047--2007108 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 21
2007037 TAAAATAATT
2007047 TTTTA-AATTATTTATTTA-A
1 TTTTATAATTATTTATTTATA
*
2007066 TTTTATAATTATTTATATATA
1 TTTTATAATTATTTATTTATA
* *
2007087 TATT-TAATTTTTTATTTATA
1 TTTTATAATTATTTATTTATA
2007107 TT
1 TT
2007109 AAAATAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 5 0.14
20 27 0.75
21 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTATAATTATTTATTTATA
Found at i:2007096 original size:28 final size:29
Alignment explanation
Indices: 2007041--2007111 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
2007031 TATATATAAA
* *
2007041 ATAATTTTTTAAATTATTTATTTAATTTT
1 ATAATTATTTAAATTATATATTTAATTTT
*
2007070 ATAATTATTTATA-TATATATTTAATTTT
1 ATAATTATTTAAATTATATATTTAATTTT
* *
2007098 TTATTTATATTAAA
1 ATAATTAT-TTAAA
2007112 ATAATTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 20 0.57
29 15 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
ATAATTATTTAAATTATATATTTAATTTT
Found at i:2007630 original size:13 final size:13
Alignment explanation
Indices: 2007612--2007641 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2007602 GACTTAAGTC
*
2007612 TTAAATTTCATGT
1 TTAAATTTCATAT
2007625 TTAAATTTCATAT
1 TTAAATTTCATAT
2007638 TTAA
1 TTAA
2007642 GACTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (13 bp):
TTAAATTTCATAT
Found at i:2010017 original size:25 final size:25
Alignment explanation
Indices: 2009976--2010042 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
2009966 TATATTTTTA
*
2009976 TTAATA-AAATATTTTAAACTCAAAT
1 TTAATATAAATA-ATTAAACTCAAAT
* ***
2010001 TTAATATAAATAATTAAATTTTTAT
1 TTAATATAAATAATTAAACTCAAAT
2010026 TTAATATAAA-AATTAAA
1 TTAATATAAATAATTAAA
2010043 TTTATTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.19
25 24 0.67
26 5 0.14
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (25 bp):
TTAATATAAATAATTAAACTCAAAT
Found at i:2010044 original size:24 final size:25
Alignment explanation
Indices: 2009999--2010045 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2009989 TTAAACTCAA
2009999 ATTTAATATAAATAATTAAATTTTT
1 ATTTAATATAAATAATTAAATTTTT
2010024 ATTTAATATAAA-AATTAAATTT
1 ATTTAATATAAATAATTAAATTT
2010046 ATTTTAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTTAATATAAATAATTAAATTTTT
Found at i:2010770 original size:173 final size:173
Alignment explanation
Indices: 2010591--2010902 Score: 450
Period size: 173 Copynumber: 1.8 Consensus size: 173
2010581 TCTGAGATCG
* * * * *
2010591 GACCGGCAGCGGGATCGGCAGCAGCACGC-GGGGGGACCGAGTCGGTCTCCGGCTTGCGCATTAT
1 GACCGGCAGCGAGATCGGCAGCAGCACGCAGGAGGGACCGAGCCGATCTCCGGCTTGCGCATCAT
* * **
2010655 GCCTCC-CCGGACCGACTGAACGCCCGCACGCTCGTTTCGTGGGTTGACTTAGGCACACGGAA-T
66 ACC-CCTCC-GACCGACTAAACGCCCGCACGCTCGTTTCGTGGGTTGACTTAAACACAC-GAAGT
2010718 TCATTCCATGTCTAAGCTCCAACCGGACCGAGGGTTGCGGCAGCTA
128 TCATTCCATGTCTAAGCTCCAACCGGACCGAGGGTTGCGGCAGCTA
* *
2010764 GACCGGCAGCGAGATCGGCAGCAGCACGCAGGAGGGATCGGGCCGATCTCCGGCTTGCGCATCAT
1 GACCGGCAGCGAGATCGGCAGCAGCACGCAGGAGGGACCGAGCCGATCTCCGGCTTGCGCATCAT
* **
2010829 ACCCCTCCGACTGACTAAACGTTCGCACGCTCGTTTCGTGGGTTGACTTAAACACACGAAGTTCA
66 ACCCCTCCGACCGACTAAACGCCCGCACGCTCGTTTCGTGGGTTGACTTAAACACACGAAGTTCA
2010894 TTCCATGTC
131 TTCCATGTC
2010903 ATGTTTTCGT
Statistics
Matches: 122, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
172 3 0.02
173 86 0.70
174 33 0.27
ACGTcount: A:0.20, C:0.31, G:0.30, T:0.19
Consensus pattern (173 bp):
GACCGGCAGCGAGATCGGCAGCAGCACGCAGGAGGGACCGAGCCGATCTCCGGCTTGCGCATCAT
ACCCCTCCGACCGACTAAACGCCCGCACGCTCGTTTCGTGGGTTGACTTAAACACACGAAGTTCA
TTCCATGTCTAAGCTCCAACCGGACCGAGGGTTGCGGCAGCTA
Found at i:2011530 original size:17 final size:18
Alignment explanation
Indices: 2011494--2011535 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2011484 TTTAATTGAA
2011494 TTATATATTTTTATTAAT
1 TTATATATTTTTATTAAT
2011512 TTATATATTTTT-TTAAT
1 TTATATATTTTTATTAAT
*
2011529 TTTTATA
1 TTATATA
2011536 AAATAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATATATTTTTATTAAT
Found at i:2011685 original size:32 final size:33
Alignment explanation
Indices: 2011641--2011707 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
2011631 CCAAATCAAT
*
2011641 AAAATTCTATTTAAA-TTAAAT-TAATTTTACAA
1 AAAATTCTATTTAAATTTAAATCAAATTTTA-AA
2011673 AAAATT-TAATTTAAATTTAAATCAAATTTTAAA
1 AAAATTCT-ATTTAAATTTAAATCAAATTTTAAA
2011706 AA
1 AA
2011708 TTTATAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 1 0.03
32 13 0.42
33 10 0.32
34 7 0.23
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (33 bp):
AAAATTCTATTTAAATTTAAATCAAATTTTAAA
Found at i:2022961 original size:16 final size:18
Alignment explanation
Indices: 2022932--2022965 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2022922 GACTTTTTTT
2022932 TTTTTTAGATTTTAAAAA
1 TTTTTTAGATTTTAAAAA
2022950 TTTTTT-GA-TTTAAAAA
1 TTTTTTAGATTTTAAAAA
2022966 AGTAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTTTTAGATTTTAAAAA
Found at i:2022966 original size:17 final size:18
Alignment explanation
Indices: 2022932--2022966 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2022922 GACTTTTTTT
*
2022932 TTTTTTAGATTTTAAAAA
1 TTTTTTAGATTTAAAAAA
2022950 TTTTTT-GATTTAAAAAA
1 TTTTTTAGATTTAAAAAA
2022967 GTAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
TTTTTTAGATTTAAAAAA
Found at i:2023152 original size:19 final size:19
Alignment explanation
Indices: 2023125--2023161 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2023115 TACACTATAT
* *
2023125 TTATTTATAAAATATACAA
1 TTATATATAAAAAATACAA
2023144 TTATATATAAAAAATACA
1 TTATATATAAAAAATACA
2023162 TAAACCGAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TTATATATAAAAAATACAA
Found at i:2032434 original size:2 final size:2
Alignment explanation
Indices: 2032427--2032454 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2032417 GCGTATATGC
2032427 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
2032455 TATCGTGAGA
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:2032973 original size:12 final size:12
Alignment explanation
Indices: 2032956--2032980 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2032946 ACCTCCAGTT
2032956 GAGATGTTTTCA
1 GAGATGTTTTCA
2032968 GAGATGTTTTCA
1 GAGATGTTTTCA
2032980 G
1 G
2032981 GGTGAGTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (12 bp):
GAGATGTTTTCA
Found at i:2043664 original size:2 final size:2
Alignment explanation
Indices: 2043657--2043682 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2043647 TAAGTAAACA
2043657 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
2043683 ATGTTTTTTC
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2047067 original size:29 final size:28
Alignment explanation
Indices: 2047034--2047088 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
2047024 ATTTAGATAA
*
2047034 TTTTTT-ATAAATATATATTAATATTTAT
1 TTTTTTAATAAAAATATATTAAT-TTTAT
2047062 TTTTTTAATAAAAATATATTAATTTTA
1 TTTTTTAATAAAAATATATTAATTTTA
2047089 ATTAATCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTTTTAATAAAAATATATTAATTTTAT
Found at i:2047078 original size:21 final size:21
Alignment explanation
Indices: 2047053--2047134 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
2047043 AATATATATT
2047053 AATATTTATTTTTTTAATAAA
1 AATATTTATTTTTTTAATAAA
*
2047074 AATATATTAATTTTAATTAATCTAAAA
1 AATAT-TT-ATTTT-TTTAA--T-AAA
*
2047101 TAATAATTTATATTGTTTAATAAA
1 -AAT-ATTTAT-TTTTTTAATAAA
2047125 AA-ATTTATTT
1 AATATTTATTT
2047135 ACTAAATATA
Statistics
Matches: 49, Mismatches: 3, Indels: 19
0.69 0.04 0.27
Matches are distributed among these distances:
20 2 0.04
21 11 0.22
22 2 0.04
23 7 0.14
24 7 0.14
25 1 0.02
26 1 0.02
27 9 0.18
28 7 0.14
29 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
AATATTTATTTTTTTAATAAA
Found at i:2047080 original size:23 final size:24
Alignment explanation
Indices: 2047054--2047135 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 24
2047044 ATATATATTA
2047054 ATATTTATTTTTTTAAT-AAAAAT
1 ATATTTATTTTTTTAATAAAAAAT
* *
2047077 ATATTAATTTTAATTAATCTAAAATAAT
1 ATATTTATTTT-TTTAA--TAAAA-AAT
*
2047105 A-ATTTATATTGTTTAATAAAAAAT
1 ATATTTAT-TTTTTTAATAAAAAAT
*
2047129 TTATTTA
1 ATATTTA
2047136 CTAAATATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
23 10 0.22
24 7 0.15
25 10 0.22
26 1 0.02
27 12 0.26
28 6 0.13
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (24 bp):
ATATTTATTTTTTTAATAAAAAAT
Found at i:2047148 original size:51 final size:49
Alignment explanation
Indices: 2047052--2047150 Score: 114
Period size: 51 Copynumber: 2.0 Consensus size: 49
2047042 AAATATATAT
* *
2047052 TAATATTTATTTTTTTAATAAAAATATATTAATTTTAATTAATCTAAAA
1 TAATATTTATTTGTTTAATAAAAATATATTAATTTTAAATAATCTAAAA
2047101 TAATAATTTATATTGTTTAATAAAAA-AT-TT-ATTTACTAAATATATCTAAA
1 TAAT-ATTTAT-TTGTTTAATAAAAATATATTAATTT--TAAATA-ATCTAAA
2047151 TATATAAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
48 4 0.09
49 6 0.14
50 13 0.30
51 20 0.47
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.48
Consensus pattern (49 bp):
TAATATTTATTTGTTTAATAAAAATATATTAATTTTAAATAATCTAAAA
Found at i:2051426 original size:1 final size:1
Alignment explanation
Indices: 2051420--2051446 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2051410 GCATGTCCTT
2051420 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
2051447 CTCCCTGTGC
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2058034 original size:13 final size:12
Alignment explanation
Indices: 2058018--2058047 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
2058008 AGTTTTGGGA
2058018 TTTTCTTTTTCTT
1 TTTTCTTTTT-TT
2058031 TTTTCTTTTTTT
1 TTTTCTTTTTTT
2058043 TTTTC
1 TTTTC
2058048 ATTTACAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:2062039 original size:18 final size:19
Alignment explanation
Indices: 2062006--2062043 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2061996 ACCCATTCCA
2062006 TAGCCGGTCACCTCCTCCG
1 TAGCCGGTCACCTCCTCCG
*
2062025 TAGCCGG-CGCCTCCTCCG
1 TAGCCGGTCACCTCCTCCG
2062043 T
1 T
2062044 CGTCCACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.08, C:0.47, G:0.24, T:0.21
Consensus pattern (19 bp):
TAGCCGGTCACCTCCTCCG
Found at i:2069348 original size:22 final size:22
Alignment explanation
Indices: 2069308--2069355 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2069298 AATTTAAAAT
*
2069308 TTTAATAAAAATTATAAATAAA
1 TTTAATAAAAATTAAAAATAAA
*
2069330 TTTAAT-AAAATTAAAAAATATA
1 TTTAATAAAAATT-AAAAATAAA
2069352 TTTA
1 TTTA
2069356 TATTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAATAAAAATTAAAAATAAA
Found at i:2070969 original size:16 final size:18
Alignment explanation
Indices: 2070950--2070984 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
2070940 AAATTATATT
2070950 TTTAAATT-TT-ATATAA
1 TTTAAATTATTAATATAA
2070966 TTTAAATTATTAATATAA
1 TTTAAATTATTAATATAA
2070984 T
1 T
2070985 ATTTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 2 0.12
18 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAAATTATTAATATAA
Found at i:2071004 original size:19 final size:20
Alignment explanation
Indices: 2070965--2071005 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
2070955 ATTTTATATA
* *
2070965 ATTTAAATTATTAATATAAT
1 ATTTAAAATATTAATAAAAT
2070985 ATTTAAAATA-TAATAAAAT
1 ATTTAAAATATTAATAAAAT
2071004 AT
1 AT
2071006 ATAAGTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTAAAATATTAATAAAAT
Found at i:2113777 original size:13 final size:14
Alignment explanation
Indices: 2113761--2113790 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2113751 TTTTTATTCA
2113761 AAATAATT-TTAAT
1 AAATAATTATTAAT
2113774 AAATAATTATTAAT
1 AAATAATTATTAAT
2113788 AAA
1 AAA
2113791 ATTCAAACTT
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:2122779 original size:16 final size:16
Alignment explanation
Indices: 2122758--2122798 Score: 73
Period size: 16 Copynumber: 2.5 Consensus size: 16
2122748 AATGCAACAA
2122758 AACATGGAGTTCAGAG
1 AACATGGAGTTCAGAG
2122774 AACATGGAGTTCAGAG
1 AACATGGAGTTCAGAG
2122790 AACCATGGA
1 AA-CATGGA
2122799 AAGGCCTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.39, C:0.15, G:0.29, T:0.17
Consensus pattern (16 bp):
AACATGGAGTTCAGAG
Found at i:2130892 original size:16 final size:16
Alignment explanation
Indices: 2130838--2130900 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
2130828 AATAAATATG
*
2130838 AATAATTTTAATATTTT
1 AATAATTTT-ATTTTTT
*
2130855 --TAATTTT-TTTTTA
1 AATAATTTTATTTTTT
2130868 AATAAAATTTTATTTTTT
1 AAT--AATTTTATTTTTT
2130886 AATAATTTTATTTTT
1 AATAATTTTATTTTT
2130901 ATTTTTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
13 4 0.11
15 8 0.21
16 12 0.32
17 6 0.16
18 8 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AATAATTTTATTTTTT
Found at i:2130962 original size:19 final size:17
Alignment explanation
Indices: 2130919--2130953 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2130909 ATTTAAATAA
* *
2130919 TTTTTACTAACATATAT
1 TTTTTAATAAAATATAT
2130936 TTTTTAATAAAATATAT
1 TTTTTAATAAAATATAT
2130953 T
1 T
2130954 AATTTTAATT
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:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTTAATAAAATATAT
Found at i:2130995 original size:25 final size:25
Alignment explanation
Indices: 2130931--2131008 Score: 72
Period size: 25 Copynumber: 3.1 Consensus size: 25
2130921 TTTACTAACA
*
2130931 TATATTTTTTAATAAAATATATTAATT
1 TATATTATTTAATAAAATA-A-TAATT
*
2130958 T-TA--ATTAATATAAAATAATAATT
1 TATATTATTTA-ATAAAATAATAATT
* *
2130981 TATATTATTTAATAAAAAAATTATT
1 TATATTATTTAATAAAATAATAATT
2131006 TAT
1 TAT
2131009 TAAATATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
23 6 0.14
24 6 0.14
25 23 0.55
26 6 0.14
27 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TATATTATTTAATAAAATAATAATT
Found at i:2131009 original size:23 final size:23
Alignment explanation
Indices: 2130933--2131010 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
2130923 TACTAACATA
* * *
2130933 TATTTTTTAATAAAATATATTAAT
1 TATTATTTAATAAAA-AAATTATT
* *
2130957 T-TTAATTAATATAAAATAATAATTT
1 TATTATTTAATA-AAAA-AATTA-TT
2130982 ATATTATTTAATAAAAAAATTATT
1 -TATTATTTAATAAAAAAATTATT
2131006 TATTA
1 TATTA
2131011 AATATATATA
Statistics
Matches: 42, Mismatches: 7, Indels: 11
0.70 0.12 0.18
Matches are distributed among these distances:
23 14 0.33
24 9 0.21
25 5 0.12
26 5 0.12
27 9 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTATTTAATAAAAAAATTATT
Found at i:2131635 original size:24 final size:24
Alignment explanation
Indices: 2131598--2131643 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
2131588 ATTTATTTTT
2131598 AAAATTATTATTAA-ATTATTAAAA
1 AAAATTATTATTAATATT-TTAAAA
2131622 AAAATTA-TATTTAATATTTTAA
1 AAAATTATTA-TTAATATTTTAA
2131644 TTATTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 2 0.10
24 15 0.75
25 3 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AAAATTATTATTAATATTTTAAAA
Found at i:2139850 original size:29 final size:29
Alignment explanation
Indices: 2139798--2139864 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
2139788 AAATTATTAA
* **
2139798 AATAATTATTT-ATAATTTAAATTTAATT
1 AATATTTATTTAATAATAAAAATTTAATT
*
2139826 AATATTTATTTAATAATAAAAATTTTATT
1 AATATTTATTTAATAATAAAAATTTAATT
2139855 AAT-TTT-TTTA
1 AATATTTATTTA
2139865 CAAAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 4 0.12
28 13 0.38
29 17 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
AATATTTATTTAATAATAAAAATTTAATT
Found at i:2139906 original size:10 final size:10
Alignment explanation
Indices: 2139891--2139917 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2139881 AATATACATC
2139891 AAAATTTATT
1 AAAATTTATT
2139901 AAAATTTATT
1 AAAATTTATT
2139911 AAAATTT
1 AAAATTT
2139918 TACCTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
AAAATTTATT
Found at i:2145812 original size:30 final size:29
Alignment explanation
Indices: 2145778--2145881 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 29
2145768 TAATTAAGAG
** *
2145778 TTTATTTAGCTATAAGTTAAA-AGTTAAAAA
1 TTTATTTAAATATAAATTAAAGA-TT-AAAA
2145808 TTTATTTAAATATAAATTAAAGATTAAAA
1 TTTATTTAAATATAAATTAAAGATTAAAA
* * *
2145837 TTTATTTAAATACAAATTAAAAATAAAAA
1 TTTATTTAAATATAAATTAAAGATTAAAA
*
2145866 ATTATTTAAATATAAA
1 TTTATTTAAATATAAA
2145882 AAAAATTATC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
29 44 0.68
30 20 0.31
31 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (29 bp):
TTTATTTAAATATAAATTAAAGATTAAAA
Found at i:2145839 original size:29 final size:28
Alignment explanation
Indices: 2145769--2145889 Score: 118
Period size: 29 Copynumber: 4.2 Consensus size: 28
2145759 AAAATTGATT
* ** *
2145769 AATTAAGAGTTTATTTAGCTATAAGTTAA
1 AATTAA-AATTTATTTAAATATAAATTAA
2145798 AAGTTAAAAATTTATTTAAATATAAATTAA
1 AA-TT-AAAATTTATTTAAATATAAATTAA
*
2145828 AGATTAAAATTTATTTAAATACAAATTAAA
1 A-ATTAAAATTTATTTAAATATAAATT-AA
* * *
2145858 AATAAAAAATTATTTAAATATAAA-AAA
1 AATTAAAATTTATTTAAATATAAATTAA
2145885 AATTA
1 AATTA
2145890 TCTAACTAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
27 6 0.08
29 43 0.55
30 26 0.33
31 3 0.04
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (28 bp):
AATTAAAATTTATTTAAATATAAATTAA
Found at i:2152981 original size:21 final size:24
Alignment explanation
Indices: 2152946--2152989 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
2152936 TTCATTGATT
2152946 TTTTTATAAATTATTT-AATATAA
1 TTTTTATAAATTATTTAAATATAA
2152969 TTTTTA-AAA-TATTTAAATATA
1 TTTTTATAAATTATTTAAATATA
2152990 TTTAGATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 9 0.45
23 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTTATAAATTATTTAAATATAA
Found at i:2158764 original size:2 final size:2
Alignment explanation
Indices: 2158757--2158790 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2158747 ATCAAGATAA
* *
2158757 AT AT AT AT AT GT GT 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
2158791 CACCCTGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2161407 original size:17 final size:17
Alignment explanation
Indices: 2161367--2161409 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2161357 TTTATTTCAA
*
2161367 ATAAAAAATTAATTTAT
1 ATAAAAATTTAATTTAT
* *
2161384 ATTAAAATTTTATTTAT
1 ATAAAAATTTAATTTAT
*
2161401 GTAAAAATT
1 ATAAAAATT
2161410 AAAGATTAAG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
ATAAAAATTTAATTTAT
Found at i:2161456 original size:29 final size:30
Alignment explanation
Indices: 2161384--2161487 Score: 106
Period size: 29 Copynumber: 3.5 Consensus size: 30
2161374 ATTAATTTAT
* * * *
2161384 ATTAAAATTTTATTTATGTAAAAATTAAAG
1 ATTAAAAGTTTATTTGTATATAAATTAAAG
**
2161414 ATTAAGGGTTTATTTGTATATAAATTAAA-
1 ATTAAAAGTTTATTTGTATATAAATTAAAG
*
2161443 ATTAAAAGTTTATTT-AAT-TCAAATTAAAG
1 ATTAAAAGTTTATTTGTATAT-AAATTAAAG
*
2161472 ATTAAAAATTTATTTG
1 ATTAAAAGTTTATTTG
2161488 AATGTAATAA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
27 1 0.02
28 10 0.16
29 27 0.44
30 23 0.38
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.44
Consensus pattern (30 bp):
ATTAAAAGTTTATTTGTATATAAATTAAAG
Found at i:2166234 original size:15 final size:17
Alignment explanation
Indices: 2166214--2166263 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
2166204 TTGAATATAA
*
2166214 ATAAAAAT-ATTATT-T
1 ATAAAAATCATAATTAT
2166229 ATAAAAATCATAATTAT
1 ATAAAAATCATAATTAT
*
2166246 ATAAACGATCATAATTAT
1 ATAAA-AATCATAATTAT
2166264 TTGAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 8 0.27
16 5 0.17
17 6 0.20
18 11 0.37
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (17 bp):
ATAAAAATCATAATTAT
Found at i:2176842 original size:2 final size:2
Alignment explanation
Indices: 2176835--2176859 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2176825 AAAGAGTTAC
2176835 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2176860 CTTCGAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2177421 original size:26 final size:27
Alignment explanation
Indices: 2177376--2177429 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
2177366 GGGAGGAGAT
2177376 TAAAATTATTTTTTTTATTTTTAATTA
1 TAAAATTATTTTTTTTATTTTTAATTA
2177403 TAAAATTA-TTTTTTTATTTTTAATTA
1 TAAAATTATTTTTTTTATTTTTAATTA
2177429 T
1 T
2177430 CTCTCTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TAAAATTATTTTTTTTATTTTTAATTA
Found at i:2177841 original size:8 final size:8
Alignment explanation
Indices: 2177828--2177864 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
2177818 TTTTTATTTA
2177828 TATATATT
1 TATATATT
*
2177836 TATATAAT
1 TATATATT
2177844 TATATATT
1 TATATATT
*
2177852 TAAATATT
1 TATATATT
2177860 TATAT
1 TATAT
2177865 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATATATT
Found at i:2177868 original size:14 final size:16
Alignment explanation
Indices: 2177828--2177883 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
2177818 TTTTTATTTA
*
2177828 TATATATTTATATAAT
1 TATATATTTAAATAAT
2177844 TATATATTTAAAT-AT
1 TATATATTTAAATAAT
*
2177859 T-TATATTTAAAAAAT
1 TATATATTTAAATAAT
* *
2177874 AATATTTTTA
1 TATATATTTA
2177884 TTAATTCGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
14 10 0.29
15 5 0.15
16 19 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATATTTAAATAAT
Found at i:2178212 original size:18 final size:18
Alignment explanation
Indices: 2178186--2178222 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2178176 ATATCATGAA
*
2178186 AAAAAATTTAATTATAAT
1 AAAAAATTTAATAATAAT
*
2178204 AAAATATTTAATAATAAT
1 AAAAAATTTAATAATAAT
2178222 A
1 A
2178223 TTTAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAAATTTAATAATAAT
Found at i:2198716 original size:26 final size:23
Alignment explanation
Indices: 2198653--2198730 Score: 138
Period size: 23 Copynumber: 3.4 Consensus size: 23
2198643 GATTGTTGTC
2198653 TATTGCTTCTGTATTGTTGTGAT
1 TATTGCTTCTGTATTGTTGTGAT
2198676 TATTGCTTCTGTATTGTTGTGAT
1 TATTGCTTCTGTATTGTTGTGAT
* *
2198699 TATTGTTTCTGTATTATTGTGAT
1 TATTGCTTCTGTATTGTTGTGAT
2198722 TATTGCTTC
1 TATTGCTTC
2198731 AGGCGCAACA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.14, C:0.09, G:0.19, T:0.58
Consensus pattern (23 bp):
TATTGCTTCTGTATTGTTGTGAT
Found at i:2200056 original size:13 final size:15
Alignment explanation
Indices: 2200038--2200071 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
2200028 AATTAGACTA
2200038 AAAAGAT-CAAAA-T
1 AAAAGATCCAAAACT
2200051 AAAAGATCCAAAACT
1 AAAAGATCCAAAACT
2200066 AAAAGA
1 AAAAGA
2200072 GAAAAATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 5 0.26
15 7 0.37
ACGTcount: A:0.68, C:0.12, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAGATCCAAAACT
Found at i:2208467 original size:13 final size:13
Alignment explanation
Indices: 2208449--2208473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2208439 AATTAGACTA
2208449 AAAAGATCAAAAT
1 AAAAGATCAAAAT
2208462 AAAAGATCAAAA
1 AAAAGATCAAAA
2208474 ACTAAAAAAA
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:0.72, C:0.08, G:0.08, T:0.12
Consensus pattern (13 bp):
AAAAGATCAAAAT
Found at i:2230905 original size:21 final size:21
Alignment explanation
Indices: 2230873--2230931 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
2230863 TATAACATAA
*
2230873 AAAATCAT-AAAAAATAATTTT
1 AAAAT-ATAAAAAAAAAATTTT
2230894 AAAATATAAAAATAAAAATTTT
1 AAAATATAAAAA-AAAAATTTT
*
2230916 -AGATATAAAAAAAAAA
1 AAAATATAAAAAAAAAA
2230932 ATGGATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 7 0.21
21 19 0.56
22 8 0.24
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAATATAAAAAAAAAATTTT
Done.