Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 27 of 147
Found at i:5605147 original size:11 final size:11
Alignment explanation
Indices: 5605117--5605168 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
5605107 CTTTCATATA
*
5605117 TTTTTTATTTTC
1 TTTTTT-TTTCC
*
5605129 TCTTTTTTTCC
1 TTTTTTTTTCC
5605140 TTTTTTTTTCAC
1 TTTTTTTTTC-C
*
5605152 TTTTTTTCTTTC
1 TTTTTTT-TTCC
5605164 TTTTT
1 TTTTT
5605169 CATCCATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
11 13 0.38
12 19 0.56
13 2 0.06
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTTTTCC
Found at i:5605155 original size:20 final size:21
Alignment explanation
Indices: 5605118--5605170 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
5605108 TTTCATATAT
*
5605118 TTTTTATTTTCTCTTTTTTTCC
1 TTTTT-TTTTCACTTTTTTTCC
5605140 TTTTTTTTTCACTTTTTTT-C
1 TTTTTTTTTCACTTTTTTTCC
*
5605160 TTTCTTTTTCA
1 TTTTTTTTTCA
5605171 TCCATTTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 11 0.38
21 13 0.45
22 5 0.17
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTTTTTCACTTTTTTTCC
Found at i:5605209 original size:31 final size:32
Alignment explanation
Indices: 5605151--5605210 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
5605141 TTTTTTTTCA
* *
5605151 CTTTTTTTCTTTCTTTTTCATCCATTTTCCCC
1 CTTTTTTTCTTTCTCTTTCATCAATTTTCCCC
5605183 CTTTTTTT-TTTCATCTTTCAT-AATTTTC
1 CTTTTTTTCTTTC-TCTTTCATCAATTTTC
5605211 TTTTCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.10, C:0.25, G:0.00, T:0.65
Consensus pattern (32 bp):
CTTTTTTTCTTTCTCTTTCATCAATTTTCCCC
Found at i:5609339 original size:5 final size:5
Alignment explanation
Indices: 5609331--5609395 Score: 80
Period size: 5 Copynumber: 12.8 Consensus size: 5
5609321 TTATTTAAAG
*
5609331 AAAAT AAAAT --AAT AAAAT GAAAAT AAAAT GAAAT GAAAAT AAAAAT
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT -AAAAT -AAAAT
5609377 AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
5609396 AATATTAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
3 3 0.06
5 36 0.68
6 14 0.26
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:5609396 original size:11 final size:11
Alignment explanation
Indices: 5609331--5609396 Score: 73
Period size: 11 Copynumber: 5.9 Consensus size: 11
5609321 TTATTTAAAG
5609331 AAAATAAAATAAT
1 AAAAT-AAA-AAT
*
5609344 AAAATGAAAAT
1 AAAATAAAAAT
*
5609355 AAAAT-GAAAT
1 AAAATAAAAAT
5609365 GAAAATAAAAAT
1 -AAAATAAAAAT
5609377 AAAAT-AAAAT
1 AAAATAAAAAT
5609387 AAAATAAAAA
1 AAAATAAAAA
5609397 ATATTAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
10 14 0.30
11 22 0.47
12 6 0.13
13 5 0.11
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:5609396 original size:16 final size:16
Alignment explanation
Indices: 5609341--5609395 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
5609331 AAAATAAAAT
5609341 AATAAAATGAAAATAA
1 AATAAAATGAAAATAA
*
5609357 AATGAAATGAAAATAAA
1 AATAAAATGAAAAT-AA
5609374 AATAAAAT-AAAATAA
1 AATAAAATGAAAATAA
5609389 AATAAAA
1 AATAAAA
5609396 AATATTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 9 0.25
16 18 0.50
17 9 0.25
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (16 bp):
AATAAAATGAAAATAA
Found at i:5609407 original size:14 final size:15
Alignment explanation
Indices: 5609331--5609395 Score: 80
Period size: 16 Copynumber: 4.3 Consensus size: 15
5609321 TTATTTAAAG
5609331 AAAATAAAAT--AAT
1 AAAATAAAATAAAAT
5609344 AAAATGAAAATAAAAT
1 AAAAT-AAAATAAAAT
*
5609360 GAAATGAAAATAAAAAT
1 AAAAT-AAAAT-AAAAT
5609377 AAAATAAAATAAAAT
1 AAAATAAAATAAAAT
5609392 AAAA
1 AAAA
5609396 AATATTAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
13 5 0.11
14 5 0.11
15 9 0.20
16 18 0.39
17 9 0.20
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:5609426 original size:4 final size:4
Alignment explanation
Indices: 5609373--5609449 Score: 54
Period size: 4 Copynumber: 19.0 Consensus size: 4
5609363 ATGAAAATAA
* * *
5609373 AAAT AAAAT AAAAT AAAAT AAA- AAAT -ATT AAAT AATT CTAAT ATAAT
1 AAAT -AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A-AAT
5609420 AAAT AAAT AAAT AAAT AAAT -AAT AAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
5609450 GAAAAAAAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
3 11 0.18
4 29 0.48
5 20 0.33
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:5610330 original size:17 final size:17
Alignment explanation
Indices: 5610281--5610344 Score: 85
Period size: 17 Copynumber: 3.7 Consensus size: 17
5610271 AACAATAAAA
*
5610281 AAATAATAATAA-GGAT
1 AAATAATAATAATAGAT
*
5610297 AATATATTAATTAATAGAT
1 AA-ATAATAA-TAATAGAT
5610316 AAATAATAATAATAGAT
1 AAATAATAATAATAGAT
5610333 AAATAATAATAA
1 AAATAATAATAA
5610345 AGTATATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
16 2 0.05
17 26 0.62
18 9 0.21
19 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
AAATAATAATAATAGAT
Found at i:5610337 original size:11 final size:10
Alignment explanation
Indices: 5610261--5610345 Score: 52
Period size: 11 Copynumber: 8.3 Consensus size: 10
5610251 AAGAAAAGAA
5610261 AAATAA-AAT
1 AAATAATAAT
* *
5610270 AAACAATAAAA
1 AAATAAT-AAT
5610281 AAATAATAAT
1 AAATAATAAT
5610291 AAGGATAATATATT
1 AA--ATAATA-A-T
*
5610305 AATTAATAGAT
1 AAATAATA-AT
5610316 AAATAATAAT
1 AAATAATAAT
*
5610326 -AAT-A-GAT
1 AAATAATAAT
5610333 AAATAATAAT
1 AAATAATAAT
5610343 AAA
1 AAA
5610346 GTATATATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
7 2 0.03
8 4 0.07
9 9 0.16
10 11 0.19
11 16 0.28
12 12 0.21
13 1 0.02
14 3 0.05
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (10 bp):
AAATAATAAT
Found at i:5610396 original size:25 final size:25
Alignment explanation
Indices: 5610368--5610424 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
5610358 ATATTAACAG
* * *
5610368 ATAAATACTAAAAATATATATATTA
1 ATAAATACTAAAAATAAATAAATAA
* *
5610393 ATAAATAGTAACAATAAATAAATAA
1 ATAAATACTAAAAATAAATAAATAA
5610418 ATAAATA
1 ATAAATA
5610425 AGATACAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (25 bp):
ATAAATACTAAAAATAAATAAATAA
Found at i:5610440 original size:22 final size:21
Alignment explanation
Indices: 5610412--5610461 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5610402 AACAATAAAT
5610412 AAATAAATAA-ATAAGATACAAA
1 AAATAAA-AATATAAGA-ACAAA
* *
5610434 AAATAAAAATATCAGAATAAA
1 AAATAAAAATATAAGAACAAA
5610455 AAATAAA
1 AAATAAA
5610462 CGGGTCTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (21 bp):
AAATAAAAATATAAGAACAAA
Found at i:5610784 original size:18 final size:18
Alignment explanation
Indices: 5610757--5610801 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
5610747 TTTTTGTTAT
5610757 ATTT-ATTTAC-TTTTAA
1 ATTTAATTTACATTTTAA
*
5610773 ATTTAAATTTACATTTTCA
1 ATTT-AATTTACATTTTAA
5610792 ATTTAATTTA
1 ATTTAATTTA
5610802 GTATTACGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 4 0.16
18 12 0.48
19 9 0.36
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTAATTTACATTTTAA
Found at i:5614106 original size:16 final size:17
Alignment explanation
Indices: 5614085--5614126 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
5614075 ATGTTAACTC
5614085 TTATTTTTTATTT-AAA
1 TTATTTTTTATTTGAAA
*
5614101 TTA-TTTTTATTTGTAA
1 TTATTTTTTATTTGAAA
5614117 TTAATTTTTT
1 TT-ATTTTTT
5614127 TTACATTGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 1 0.05
18 5 0.23
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATTTTTTATTTGAAA
Found at i:5614375 original size:20 final size:20
Alignment explanation
Indices: 5614310--5614381 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
5614300 GGTTTAGAAT
*
5614310 TATTATTTAT-TTGTAATAA
1 TATTATTTATGTTATAATAA
* * *
5614329 TAATTCTTTTATGTTACCAAAAA
1 T-ATT-ATTTATGTTA-TAATAA
5614352 TATTATTTATGTTATAATAA
1 TATTATTTATGTTATAATAA
*
5614372 TATTTTTTAT
1 TATTATTTAT
5614382 ACTTGTTCAT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
19 1 0.02
20 16 0.39
21 14 0.34
22 5 0.12
23 5 0.12
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTATTTATGTTATAATAA
Found at i:5614584 original size:19 final size:18
Alignment explanation
Indices: 5614562--5614631 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 18
5614552 TATTCTCACT
5614562 TTTTTTATGTTAAAATGTA
1 TTTTTTATGTTAAAAT-TA
* *
5614581 TTTTTTTTGTTTAGAATTA
1 TTTTTTATG-TTAAAATTA
* *
5614600 TTTTTTATTTATAAAAATAAA
1 TTTTTTATGT-T-AAAAT-TA
5614621 TTTTTTATGTT
1 TTTTTTATGTT
5614632 GTCAATTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.03
19 18 0.45
20 11 0.28
21 10 0.25
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (18 bp):
TTTTTTATGTTAAAATTA
Found at i:5614584 original size:20 final size:19
Alignment explanation
Indices: 5614561--5614605 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
5614551 CTATTCTCAC
5614561 TTTTTTTATG-TTAAAATGTA
1 TTTTTTT-TGTTTAAAAT-TA
*
5614581 TTTTTTTTGTTTAGAATTA
1 TTTTTTTTGTTTAAAATTA
5614600 TTTTTT
1 TTTTTT
5614606 ATTTATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (19 bp):
TTTTTTTTGTTTAAAATTA
Found at i:5614920 original size:925 final size:932
Alignment explanation
Indices: 5613665--5615452 Score: 2195
Period size: 925 Copynumber: 1.9 Consensus size: 932
5613655 TATTTTTAGT
* * *
5613665 TTTAAAATTATTTTTTATTTATAATAATACATTTTTTACGTTGTCACTTTAATCATTTACATTAC
1 TTTAAAATTATTTTTTATTTATAAAAATAAATTTTTTACGTTGTCAATTTAATCATTTACATTAC
*** ** *
5613730 AATAAAATTTGTTATGTTTGTTCTTGCATTTTATTATATTTAAAATTATCACAAAATTTTCTTAC
66 AATAAAATCCCTTATGCGTGTTCTTACATTTTATTATATTTAAAATTATCACAAAATTTTCTTAC
** * * * *
5613795 GTATTATGACACTTCAAACATATTTTACGCTAAATTATATCAATTTTACGATTATTCTCACCTAT
131 GTATTACAACACTTCAAACATATTTTACGCTAAATGATACCAAATTTACAATTATTCTCACCTAT
* * * *
5613860 TTACTTTAACACTTATTTTTAATTTAAAATTATTTTTATTTATAATACTAATTTTTTTACTTTAC
196 TTACTTTAACACTTATTTTTAAGTGAAAATTATTTTTATGTATAATACTAATTTTTTTACGTTAC
* * *
5613925 AAATTTATTATGTTTCAATAATATCTTTTTATATTTATTATTACTTTTCATTACTTTTAAAATTA
261 AAATTTATTACGTTTCAATAATATCTTTTTACATTTATTATTACTTTTCATTACATTTAAAATTA
* * * *
5613990 TTACAATTTTTTTGTTAAGGTGTAATGATACTTCTAACTATTTTAT-TTAAAATAATACCAGTTT
326 TTACAAATTTTTTCTTAAGGTGTAATAATACTTCTAACTATTTTATATT-AAATAATACCAATTT
* * ** **
5614054 TAGGATTATTCTCATCGTTTTATGTTAACTCTT-ATTTTTTATTT-AAATTA-TTTTTATTTGTA
390 TAGAATTATTCTCACCGTTTTACATTAACTCTTAACATTTTATTTAAAATTATTTTTTATTTGTA
* * * *
5614116 ATTAAT-TTTTTTTACATTGCCAACTTAATTATTTATGTTATAATAATATCTTTTTA-A-GCTTG
455 A-AAATATTGTTTTACATTGCCAACTTAATTATTTATATTATAATAAT-TCTTTTTACATGATTG
* * * *
5614178 TTATCTTTCATTACGTTTAGGATTATCATAACTTTTT-CTTAAAGG-T-AC-TTCTAACCATTTT
518 TTATATTTCATTACGTTTAGAAGTATCACAACTTTTTCCTTAAAGGTTGACATTCTAACCATTTT
* * * *
5614239 ACACCAAATGATA-TCAATTTTATAATTACTCTCACCTTTTAT-ATATTAGCACTTATTTTTT-G
583 ACACCAAATAATACT-AATTTTATAATTACTCTCACATTTTATAATACTAACACTTATTTTTTAG
* * *
5614301 GTTTAGAATTATTATTTATTTGTAATAATAATTCTTTTATGTTACCAAAAATATTATTTATGTTA
647 G-TTAGAATTATTAATTATTTGTAATAATAATTATTTTACGTTACCAAAAATATTATTTATGTTA
* * *
5614366 TAATAATATTTTTTATACTTGTTCATATTTTTTATTACGTTTAGAA-TTATCACAACT-TTTAAT
711 CAATAAT-TTTTTTACACTTGTTCATACTTTTTATTACGTTTA-AATTTATCACAACTCTTT-AT
* * *
5614429 TA-AGGTGATATGACACTTATAATCAAATTTACAACAAATAACACCAATTTTTACAATTATTTTT
773 TAGA-GTGATATAACAATTATAATCAAATTTACAACAAATAACACCAA-TTTTACAATTATTCTT
*
5614493 ATCTTTTTACATTACGACATTGTAAAATATTTTACACCAATTGATTCCAATTTTTCAACTATTCT
836 ATATTTTTACATTACGACATTGTAAAATATTTTACACCAATTGATTCCAATTTTTCAACTATTCT
5614558 CACTTTTTTTATGTTAAAATGTATTTTTTTTG
901 CACTTTTTTTATGTTAAAATGTATTTTTTTTG
* * *
5614590 TTTAGAATTATTTTTTATTTATAAAAATAAATTTTTTATGTTGTCAATTT-AT-ATTTACGTTAC
1 TTTAAAATTATTTTTTATTTATAAAAATAAATTTTTTACGTTGTCAATTTAATCATTTACATTAC
* * * *
5614653 AATAAAATCCCTTATGCGTGTTCTTACCTTTTATTATGTTTAGAATTATCACAAATTTTTCTTAA
66 AATAAAATCCCTTATGCGTGTTCTTACATTTTATTATATTTAAAATTATCACAAAATTTTCTT-A
* ** * * * *
5614718 GGTATTACAACACCTT-TGATATATTTTACG-TCATATGATACCAAATTTACAATTATTCTTATC
130 CGTATTACAACA-CTTCAAACATATTTTACGCT-AAATGATACCAAATTTACAATTATTCTCACC
* * *
5614781 T-TATTA-TGTTAATATTTATTTTTTAAGTGAATTATT-TTTTTATGTATAATACTAATTTTTTT
193 TAT-TTACT-TTAACACTTA-TTTTTAAGTGAA-AATTATTTTTATGTATAATACTAATTTTTTT
* * * * *
5614843 ACGTTATC-AATTTATTACGTTTCAGTAGTATCTTTTTACATTTGTTGTTACTTTTTATTACATT
254 ACGTTA-CAAATTTATTACGTTTCAATAATATCTTTTTACATTTATTATTACTTTTCATTACATT
* *
5614907 TAGAATTATTACAAATTTTTTCTTATGGTGTAATAATACTTCTAACTATTTTATATTAAATAATA
318 TAAAATTATTACAAATTTTTTCTTAAGGTGTAATAATACTTCTAACTATTTTATATTAAATAATA
* * *
5614972 TCAATTTTATAATTATTCTCACCGTTTTGCATTAACTCTTAACATTTTATTTAAAATTATTTTTT
383 CCAATTTTAGAATTATTCTCACCGTTTTACATTAACTCTTAACATTTTATTTAAAATTA--TTTT
* * *
5615037 TTGTTTGTAAAAATAGTTGTTTTATATTGCCAACTTAATTATTTATATTATAATAATTTTTTTTA
446 TTATTTGTAAAAATA-TTGTTTTACATTGCCAACTTAATTATTTATATTATAATAATTCTTTTTA
* * *
5615102 CATTTATTGTTATATTTCATTACGTTTAGAAGTATTACAACTTTTTCCTTTAAGGTATTATGACA
510 CA-TGATTGTTATATTTCATTACGTTTAGAAGTATCACAACTTTTTCCTTAAAGG---T-TGAC-
* ** * *
5615167 ATTCTTACCATTTTATGCCAAATAATACTAATTTTATGATTACTCTCACATTTTTTAATACTAAC
569 ATTCTAACCATTTTACACCAAATAATACTAATTTTATAATTACTCTCACATTTTATAATACTAAC
*
5615232 ACTTATTTTTTAGGTTAGAATTATTAATTATTTGTAATAATAATTATTTTACGTTGCCAAAAATA
634 ACTTATTTTTTAGGTTAGAATTATTAATTATTTGTAATAATAATTATTTTACGTTACCAAAAATA
* * *
5615297 TTATTTATGTTACAATAATTTTTTTCCACTTGTTCTTACTTTTTATTACGTTTAAATTTATTACA
699 TTATTTATGTTACAATAATTTTTTTACACTTGTTCATACTTTTTATTACGTTTAAATTTATCACA
* * * * * *** * * *
5615362 ACTCTTTGTTAGAGTGTTATAATAATTCTAATCCAATTTATGCCAAGTGACACCAATTTTATAAT
764 ACTCTTTATTAGAGTGATATAACAATTATAATCAAATTTACAACAAATAACACCAATTTTACAAT
5615427 TATTCTTATATTTTTACATTACGACA
829 TATTCTTATATTTTTACATTACGACA
5615453 ATTTTAACAT
Statistics
Matches: 722, Mismatches: 107, Indels: 52
0.82 0.12 0.06
Matches are distributed among these distances:
923 66 0.09
924 59 0.08
925 225 0.31
926 15 0.02
927 6 0.01
929 3 0.00
930 19 0.03
931 39 0.05
933 35 0.05
934 7 0.01
939 1 0.00
940 2 0.00
941 34 0.05
942 122 0.17
943 87 0.12
944 2 0.00
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (932 bp):
TTTAAAATTATTTTTTATTTATAAAAATAAATTTTTTACGTTGTCAATTTAATCATTTACATTAC
AATAAAATCCCTTATGCGTGTTCTTACATTTTATTATATTTAAAATTATCACAAAATTTTCTTAC
GTATTACAACACTTCAAACATATTTTACGCTAAATGATACCAAATTTACAATTATTCTCACCTAT
TTACTTTAACACTTATTTTTAAGTGAAAATTATTTTTATGTATAATACTAATTTTTTTACGTTAC
AAATTTATTACGTTTCAATAATATCTTTTTACATTTATTATTACTTTTCATTACATTTAAAATTA
TTACAAATTTTTTCTTAAGGTGTAATAATACTTCTAACTATTTTATATTAAATAATACCAATTTT
AGAATTATTCTCACCGTTTTACATTAACTCTTAACATTTTATTTAAAATTATTTTTTATTTGTAA
AAATATTGTTTTACATTGCCAACTTAATTATTTATATTATAATAATTCTTTTTACATGATTGTTA
TATTTCATTACGTTTAGAAGTATCACAACTTTTTCCTTAAAGGTTGACATTCTAACCATTTTACA
CCAAATAATACTAATTTTATAATTACTCTCACATTTTATAATACTAACACTTATTTTTTAGGTTA
GAATTATTAATTATTTGTAATAATAATTATTTTACGTTACCAAAAATATTATTTATGTTACAATA
ATTTTTTTACACTTGTTCATACTTTTTATTACGTTTAAATTTATCACAACTCTTTATTAGAGTGA
TATAACAATTATAATCAAATTTACAACAAATAACACCAATTTTACAATTATTCTTATATTTTTAC
ATTACGACATTGTAAAATATTTTACACCAATTGATTCCAATTTTTCAACTATTCTCACTTTTTTT
ATGTTAAAATGTATTTTTTTTG
Found at i:5615963 original size:223 final size:221
Alignment explanation
Indices: 5615532--5615973 Score: 473
Period size: 223 Copynumber: 2.0 Consensus size: 221
5615522 TTTTTATATT
* *
5615532 TATTGTTACTTTTCATTACGTTTAGAATTATCACAATGTTTTGTTAAAGTGTAACGATACTTATA
1 TATTATTACTTTTCATTACGTTTAGAACTATCACAATGTTTTGTTAAAGTGTAACGATACTTATA
* ** *
5615597 ACTATTTTATATTAAATAATTCTAATTTTATAATTATTCTCCCTTTTTTACATTAACTTTTATTT
66 ACTATTTTATATTAAATAATTCTAATTTTATAATTATTCTCACTTTTTTACATTAACACTTAGTT
* * * * * * * *
5615662 TTTTGGTTAAAATTATTTTTTTTATTTGTAATAATATTTCTTTTATATTACCAGCTTACTTATTT
131 TATTGGTTAAAATTATTTCTTTGAGTTGTAATAATAATTCTTTTACATTACCAACTTAATTATTT
*** * *
5615727 TTGTTATAATAATATCTTTTTATGCC
196 ACATTACAATAATAACTTTTTATGCC
* * * ** * *
5615753 TATTATTACTTTTCATTATC-TTTATAACTATTACAATTTTTTGTTAGTGTGTTACGATACTTCT
1 TATTATTACTTTTCATTA-CGTTTAGAACTATCACAATGTTTTGTTAAAGTGTAACGATACTTAT
* * **
5615817 AACTCATTTTATATTAAATGACA-TC-AATTTTTTTTATTATTCTCACTTTTTTATGTTAACACT
65 AACT-ATTTTATATTAAAT-A-ATTCTAA-TTTTATAATTATTCTCACTTTTTTACATTAACACT
* * *
5615880 T-GTTTATTGGTTTATAATTA-TTCTTTGGGTT-TAAGGTAATAATTCTTTTACATTATCAACTT
126 TAGTTTATTGG-TTAAAATTATTTCTTTGAGTTGTAA--TAATAATTCTTTTACATTACCAACTT
5615942 AATTATTTACATTACAATAATAACTTTTTATG
188 AATTATTTACATTACAATAATAACTTTTTATG
5615974 TTTGTCCTTA
Statistics
Matches: 180, Mismatches: 33, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
221 60 0.33
222 31 0.17
223 88 0.49
224 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.53
Consensus pattern (221 bp):
TATTATTACTTTTCATTACGTTTAGAACTATCACAATGTTTTGTTAAAGTGTAACGATACTTATA
ACTATTTTATATTAAATAATTCTAATTTTATAATTATTCTCACTTTTTTACATTAACACTTAGTT
TATTGGTTAAAATTATTTCTTTGAGTTGTAATAATAATTCTTTTACATTACCAACTTAATTATTT
ACATTACAATAATAACTTTTTATGCC
Found at i:5621428 original size:18 final size:17
Alignment explanation
Indices: 5621405--5621449 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
5621395 ATCATAATAC
5621405 TAAATTAAATTGAAAATG
1 TAAATTAAATTGAAAA-G
*
5621423 TAAATTTAAATTTAAAAG
1 TAAA-TTAAATTGAAAAG
5621441 TAAA-TAAAT
1 TAAATTAAAT
5621450 ATAACAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 5 0.20
18 9 0.36
19 11 0.44
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (17 bp):
TAAATTAAATTGAAAAG
Found at i:5621825 original size:3 final size:3
Alignment explanation
Indices: 5621819--5621848 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5621809 ATTTTTTTTC
5621819 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5621849 TGATTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5622134 original size:20 final size:19
Alignment explanation
Indices: 5622096--5622138 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
5622086 ATGATTTACA
* *
5622096 ATTAAGTTGTCAATAATTTT
1 ATTAAGTTATAAATAA-TTT
*
5622116 ATTAAGTTATAAATGATTT
1 ATTAAGTTATAAATAATTT
5622135 ATTA
1 ATTA
5622139 CAAAGTTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (19 bp):
ATTAAGTTATAAATAATTT
Found at i:5622209 original size:22 final size:22
Alignment explanation
Indices: 5622151--5622209 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
5622141 AAGTTATCGA
*
5622151 TAATTTACTATTAAATTAATAC
1 TAATTTACTATTATATTAATAC
* * *
5622173 TAATTTACTACTATATTATTAT
1 TAATTTACTATTATATTAATAC
*
5622195 TAATTTATTATTATA
1 TAATTTACTATTATA
5622210 ACTGATTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATTTACTATTATATTAATAC
Found at i:5622281 original size:22 final size:22
Alignment explanation
Indices: 5622256--5622325 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
5622246 AAGTTAACAC
*
5622256 TTATAATTGAATTACTATTAAG
1 TTATAATTGATTTACTATTAAG
*
5622278 TTATAAATT-ATTTACTATTAAT
1 TTAT-AATTGATTTACTATTAAG
***
5622300 TTATCCCTGATTTACTATTAAG
1 TTATAATTGATTTACTATTAAG
5622322 TTAT
1 TTAT
5622326 CGATAATTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 1 0.03
22 35 0.88
23 4 0.10
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.50
Consensus pattern (22 bp):
TTATAATTGATTTACTATTAAG
Found at i:5622326 original size:22 final size:22
Alignment explanation
Indices: 5622267--5622357 Score: 83
Period size: 22 Copynumber: 4.1 Consensus size: 22
5622257 TATAATTGAA
* *
5622267 TTACTATTAAGTTATAAATTAT
1 TTACTATTAAGTTATCAATGAT
* **
5622289 TTACTATTAATTTATCCCTGAT
1 TTACTATTAAGTTATCAATGAT
* *
5622311 TTACTATTAAGTTATCGATAAT
1 TTACTATTAAGTTATCAATGAT
* * * *
5622333 TTGCTATTAAATTAACAATAAT
1 TTACTATTAAGTTATCAATGAT
5622355 TTA
1 TTA
5622358 TTACTAAGCT
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.47
Consensus pattern (22 bp):
TTACTATTAAGTTATCAATGAT
Found at i:5622357 original size:44 final size:44
Alignment explanation
Indices: 5622267--5622357 Score: 101
Period size: 44 Copynumber: 2.1 Consensus size: 44
5622257 TATAATTGAA
* * * ** *
5622267 TTACTATTAAGTTATAAATTATTTACTATTAATTTATCCCTGAT
1 TTACTATTAAGTTATAAATAATTTACTATTAAATTAACAATAAT
** *
5622311 TTACTATTAAGTTATCGATAATTTGCTATTAAATTAACAATAAT
1 TTACTATTAAGTTATAAATAATTTACTATTAAATTAACAATAAT
5622355 TTA
1 TTA
5622358 TTACTAAGCT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.47
Consensus pattern (44 bp):
TTACTATTAAGTTATAAATAATTTACTATTAAATTAACAATAAT
Found at i:5623159 original size:21 final size:21
Alignment explanation
Indices: 5623135--5623211 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
5623125 TCATCTGTTA
*
5623135 CCAAAATAATATCAAAGGTTG
1 CCAAAATCATATCAAAGGTTG
*
5623156 CCAAAATTGCAT-TC-AAGATTG
1 CCAAAA-T-CATATCAAAGGTTG
** *
5623177 CCAAAATTTTATCAAA-GTTA
1 CCAAAATCATATCAAAGGTTG
5623197 CCAAAATCATATCAA
1 CCAAAATCATATCAA
5623212 CAATTACTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
19 1 0.02
20 18 0.41
21 20 0.45
22 3 0.07
23 2 0.05
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.27
Consensus pattern (21 bp):
CCAAAATCATATCAAAGGTTG
Found at i:5623166 original size:63 final size:62
Alignment explanation
Indices: 5623093--5623211 Score: 150
Period size: 63 Copynumber: 1.9 Consensus size: 62
5623083 TTGAAGGCTA
** **
5623093 CCAAAATTGCA-TCAATGATTACCAATGTTATATCATCTGTTACCAAAATAATATCAAAGGTTG
1 CCAAAATTGCATTCAA-GATTACCAAAATTATATCA-AAGTTACCAAAATAATATCAAAGGTTG
* * *
5623156 CCAAAATTGCATTCAAGATTGCCAAAATTTTATCAAAGTTACCAAAATCATATCAA
1 CCAAAATTGCATTCAAGATTACCAAAATTATATCAAAGTTACCAAAATAATATCAA
5623212 CAATTACTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
62 18 0.38
63 26 0.54
64 4 0.08
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (62 bp):
CCAAAATTGCATTCAAGATTACCAAAATTATATCAAAGTTACCAAAATAATATCAAAGGTTG
Found at i:5623223 original size:21 final size:20
Alignment explanation
Indices: 5623132--5623224 Score: 62
Period size: 21 Copynumber: 4.5 Consensus size: 20
5623122 ATATCATCTG
* *
5623132 TTACCAAAATAATATCAAAGG
1 TTACCAAAATCATATCAAA-A
* *
5623153 TTGCCAAAATTGCAT-TCAAGA
1 TTACCAAAA-T-CATATCAAAA
* ** *
5623174 TTGCCAAAATTTTATCAAAG
1 TTACCAAAATCATATCAAAA
5623194 TTACCAAAATCATATCAACAA
1 TTACCAAAATCATATCAA-AA
*
5623215 TTACTAAAAT
1 TTACCAAAAT
5623225 TATAACATAA
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.02
20 20 0.36
21 27 0.49
22 5 0.09
23 2 0.04
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (20 bp):
TTACCAAAATCATATCAAAA
Found at i:5623424 original size:21 final size:21
Alignment explanation
Indices: 5623398--5623469 Score: 101
Period size: 21 Copynumber: 3.4 Consensus size: 21
5623388 GTTTATCAAA
*
5623398 ATCAAAATTATATCAAAGATT
1 ATCAAAATTATATCAAAGGTT
*
5623419 ATCAAATTATATATCAAAGGTT
1 ATCAAAAT-TATATCAAAGGTT
5623441 A-CTAAAATTATATCAAAGGTT
1 ATC-AAAATTATATCAAAGGTT
5623462 ATCAAAAT
1 ATCAAAAT
5623470 GGTTTCTTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 27 0.60
22 18 0.40
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (21 bp):
ATCAAAATTATATCAAAGGTT
Found at i:5623543 original size:21 final size:21
Alignment explanation
Indices: 5623519--5623559 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5623509 ATAAAAACTA
*
5623519 TATCAAAGTTTATCAAAATTG
1 TATCAAAGGTTATCAAAATTG
*
5623540 TATCAAAGGTTCTCAAAATT
1 TATCAAAGGTTATCAAAATT
5623560 AGACCCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (21 bp):
TATCAAAGGTTATCAAAATTG
Found at i:5623612 original size:21 final size:21
Alignment explanation
Indices: 5623588--5623765 Score: 71
Period size: 21 Copynumber: 8.6 Consensus size: 21
5623578 ATGCTATCAA
5623588 AAAATTATATCAATAATTACC
1 AAAATTATATCAATAATTACC
* **
5623609 AAAAGTATATC-ATAAATTATT
1 AAAATTATATCAAT-AATTACC
* * **
5623630 TAAATTATA-CGAA-AGGTTATG
1 AAAATTATATC-AATA-ATTACC
* * * *
5623651 AAATTTACATCAATAGGTTATC
1 AAAATTATATCAATA-ATTACC
* * * *
5623673 AACATTTTATTAAAAATTACC
1 AAAATTATATCAATAATTACC
* * *
5623694 AAAATTATATTAATAGTTACT
1 AAAATTATATCAATAATTACC
*
5623715 AAAACTATA--AA-AATTACC
1 AAAATTATATCAATAATTACC
* * *
5623733 AAAATTATATTAATAGTTACT
1 AAAATTATATCAATAATTACC
*
5623754 AAAACTATATCA
1 AAAATTATATCA
5623766 TGTTACCAAA
Statistics
Matches: 116, Mismatches: 32, Indels: 18
0.70 0.19 0.11
Matches are distributed among these distances:
18 13 0.11
19 2 0.02
20 6 0.05
21 77 0.66
22 18 0.16
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAATTATATCAATAATTACC
Found at i:5623620 original size:34 final size:32
Alignment explanation
Indices: 5623565--5623628 Score: 76
Period size: 34 Copynumber: 1.9 Consensus size: 32
5623555 AAATTAGACC
*
5623565 CAATATTACCAAAATGCTATCAAAAAATTATAT
1 CAATATTACCAAAATGATATC-AAAAATTATAT
*
5623598 CAATAATTACCAAAA-GTATATCATAAATTAT
1 CAAT-ATTACCAAAATG-ATATCAAAAATTAT
5623629 TTAAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 13 0.48
34 14 0.52
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.31
Consensus pattern (32 bp):
CAATATTACCAAAATGATATCAAAAATTATAT
Found at i:5623726 original size:39 final size:39
Alignment explanation
Indices: 5623683--5623762 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
5623673 AACATTTTAT
5623683 TAAAAATTACCAAAATTATATTAATAGTTACTAAAACTA
1 TAAAAATTACCAAAATTATATTAATAGTTACTAAAACTA
5623722 TAAAAATTACCAAAATTATATTAATAGTTACTAAAACTA
1 TAAAAATTACCAAAATTATATTAATAGTTACTAAAACTA
5623761 TA
1 TA
5623763 TCATGTTACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.34
Consensus pattern (39 bp):
TAAAAATTACCAAAATTATATTAATAGTTACTAAAACTA
Found at i:5623736 original size:18 final size:18
Alignment explanation
Indices: 5623683--5623741 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
5623673 AACATTTTAT
5623683 TAAAAATTACCAAAATTA
1 TAAAAATTACCAAAATTA
* * *
5623701 TATTAATAGTTACTAAAACTA
1 TA--AA-AATTACCAAAATTA
5623722 TAAAAATTACCAAAATTA
1 TAAAAATTACCAAAATTA
5623740 TA
1 TA
5623742 TTAATAGTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
18 15 0.47
19 2 0.06
20 2 0.06
21 13 0.41
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (18 bp):
TAAAAATTACCAAAATTA
Found at i:5623892 original size:21 final size:22
Alignment explanation
Indices: 5623868--5623924 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
5623858 AGTTATCAAA
5623868 ATCAAAATTATATCATAA-ATT
1 ATCAAAATTATATCATAAGATT
* *
5623889 ATCAAAATTGTA-CCTAAGATT
1 ATCAAAATTATATCATAAGATT
*
5623910 ACCAAAATTATATCA
1 ATCAAAATTATATCA
5623925 AACTTACTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 4 0.14
21 24 0.83
22 1 0.03
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (22 bp):
ATCAAAATTATATCATAAGATT
Found at i:5623936 original size:20 final size:21
Alignment explanation
Indices: 5623908--5623963 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
5623898 GTACCTAAGA
*
5623908 TTACCAAAATTATATCAAAC-
1 TTACTAAAATTATATCAAACG
5623928 TTACTAAAATT-TCATCAAACG
1 TTACTAAAATTAT-ATCAAACG
*
5623949 TTACTGAAATTATAT
1 TTACTAAAATTATAT
5623964 AAATAGTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 17 0.55
21 12 0.39
22 1 0.03
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.36
Consensus pattern (21 bp):
TTACTAAAATTATATCAAACG
Found at i:5624046 original size:21 final size:21
Alignment explanation
Indices: 5623992--5624046 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
5623982 TATCTCAATT
* *
5623992 AGTTATCAAAATAGTAATAAA
1 AGTTACCAAAATTGTAATAAA
*
5624013 AGTTACCAAAATTGTATTAAA
1 AGTTACCAAAATTGTAATAAA
* *
5624034 GGTTACTAAAATT
1 AGTTACCAAAATT
5624047 TTATGAATTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (21 bp):
AGTTACCAAAATTGTAATAAA
Found at i:5624118 original size:27 final size:26
Alignment explanation
Indices: 5624082--5624132 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
5624072 TAAAGGTTAC
*
5624082 CAAAATATATCAAA-GGTTATCAAAAT
1 CAAAATATAT-AAATAGTTATCAAAAT
5624108 CAAAACTATATAAATAGTTATCAAA
1 CAAAA-TATATAAATAGTTATCAAA
5624133 TTATATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (26 bp):
CAAAATATATAAATAGTTATCAAAAT
Found at i:5624146 original size:20 final size:20
Alignment explanation
Indices: 5624114--5624348 Score: 68
Period size: 21 Copynumber: 11.4 Consensus size: 20
5624104 AAATCAAAAC
5624114 TATAT-AAATAGTTATCAAAT
1 TATATCAAA-AGTTATCAAAT
*
5624134 TATATCAAAAGTTA-CTAAAA
1 TATATCAAAAGTTATC-AAAT
* *
5624154 TAGTATTAAACGTTATCAAAT
1 TA-TATCAAAAGTTATCAAAT
* * **
5624175 TTTATTAACTGTTATCAAATT
1 TATATCAAAAGTTATCAAA-T
* * * *
5624196 TCTAACAAAGGTCATTGC-AA-
1 TATATCAAAAGTTA-T-CAAAT
* *
5624216 TATAT-AAAAGATTATCGAGT
1 TATATCAAAAG-TTATCAAAT
* *
5624236 TATATCAAAATTTACTAAAAT
1 TATATCAAAAGTTA-TCAAAT
* *
5624257 TATATCCAAGGTTA-CAAAAAT
1 TATATCAAAAGTTATC--AAAT
* * **
5624278 TGTATTAATGGTTATCAAAAT
1 TATATCAAAAGTTATC-AAAT
* *
5624299 TATATCATAAGTTACCAAAT
1 TATATCAAAAGTTATCAAAT
** * * *
5624319 CGTATTAAAGGCTATCAAAAT
1 TATATCAAAAGTTATC-AAAT
5624340 TATATCAAA
1 TATATCAAA
5624349 CTTACTAAAA
Statistics
Matches: 153, Mismatches: 46, Indels: 31
0.67 0.20 0.13
Matches are distributed among these distances:
18 1 0.01
19 7 0.05
20 56 0.37
21 83 0.54
22 5 0.03
23 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (20 bp):
TATATCAAAAGTTATCAAAT
Found at i:5624336 original size:41 final size:41
Alignment explanation
Indices: 5624252--5624359 Score: 128
Period size: 41 Copynumber: 2.6 Consensus size: 41
5624242 AAAATTTACT
* * * *
5624252 AAAATTATATCCAAGGTTACAAAAATTGTATTAATGGTTATC
1 AAAATTATAT-CAAAGTTACAAAAATCGTATTAAAGGCTATC
*
5624294 AAAATTATATCATAAGTTAC-CAAATCGTATTAAAGGCTATC
1 AAAATTATATCA-AAGTTACAAAAATCGTATTAAAGGCTATC
*
5624335 AAAATTATATCAAACTTACTAAAAA
1 AAAATTATATCAAAGTTAC-AAAAA
5624360 ATTTATTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
40 6 0.11
41 31 0.55
42 19 0.34
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.32
Consensus pattern (41 bp):
AAAATTATATCAAAGTTACAAAAATCGTATTAAAGGCTATC
Found at i:5625134 original size:53 final size:52
Alignment explanation
Indices: 5625038--5625142 Score: 124
Period size: 53 Copynumber: 2.0 Consensus size: 52
5625028 ATCATCTAAG
* * *
5625038 TACCAAAATTATATTAAAGGTTATAAAAATTGCATCAAAAGTTATCTAAATT
1 TACCAAAATTATATAAAAGGTTACAAAAATTGCATCAAAAGTTATCAAAATT
* *
5625090 TACCAAAATTCTATCAAAAGGTTACAAAAATT--ATGACAATAGTTATCAAAATT
1 TACCAAAATTATAT-AAAAGGTTACAAAAATTGCAT--CAAAAGTTATCAAAATT
5625143 ATATCATAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
51 2 0.04
52 13 0.29
53 30 0.67
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (52 bp):
TACCAAAATTATATAAAAGGTTACAAAAATTGCATCAAAAGTTATCAAAATT
Found at i:5625196 original size:20 final size:20
Alignment explanation
Indices: 5625093--5625197 Score: 88
Period size: 21 Copynumber: 5.0 Consensus size: 20
5625083 CTAAATTTAC
*
5625093 CAAAATTCTATCAAAAGGTTA
1 CAAAATTATATCAAAA-GTTA
*
5625114 CAAAAATTATGA-CAATAGTTA
1 C-AAAATTAT-ATCAAAAGTTA
* *
5625135 TCAAAATTATATCATAAGCTA
1 -CAAAATTATATCAAAAGTTA
*
5625156 TCAAAA-TATTATCAAATGTTA
1 -CAAAATTA-TATCAAAAGTTA
*
5625177 CAAAATTATATTAAAAGTTA
1 CAAAATTATATCAAAAGTTA
5625197 C
1 C
5625198 CAAACTTTCT
Statistics
Matches: 68, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
20 19 0.28
21 36 0.53
22 12 0.18
23 1 0.01
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (20 bp):
CAAAATTATATCAAAAGTTA
Found at i:5625867 original size:33 final size:29
Alignment explanation
Indices: 5625829--5625911 Score: 78
Period size: 33 Copynumber: 2.7 Consensus size: 29
5625819 TGACTGTCAC
5625829 TTAAAAAATTACTTTTAATAATAAATAAATTT
1 TTAAAAAATTA-TTTTAAT--TAAATAAATTT
* *
5625861 TGTAAAAATATAAATTGTTAATTTAATAAATTT
1 T-TAAAAA-AT-TATT-TTAATTAAATAAATTT
5625894 TTAAAAAA-TATTTTAATT
1 TTAAAAAATTATTTTAATT
5625912 GATCATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
28 6 0.14
29 3 0.07
31 1 0.02
32 7 0.16
33 17 0.39
34 4 0.09
35 6 0.14
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (29 bp):
TTAAAAAATTATTTTAATTAAATAAATTT
Found at i:5625943 original size:24 final size:24
Alignment explanation
Indices: 5625916--5625982 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 24
5625906 TTAATTGATC
5625916 ATTTTTAATATTTTTTAAATTA-AT
1 ATTTTT-ATATTTTTTAAATTATAT
**
5625940 ATTTTTATAATGCTTT-AATTATAT
1 ATTTTTAT-ATTTTTTAAATTATAT
5625964 ATTTTTTATATTATTTTAA
1 A-TTTTTATATT-TTTTAA
5625983 TTAGTTTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
23 7 0.21
24 16 0.47
25 10 0.29
26 1 0.03
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (24 bp):
ATTTTTATATTTTTTAAATTATAT
Found at i:5625981 original size:25 final size:25
Alignment explanation
Indices: 5625902--5625985 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 25
5625892 TTTTAAAAAA
* *
5625902 TATTTTAATTGAT-CATTTTTAATAT
1 TATTTTAATT-ATATATTTTTTATAT
*
5625927 T-TTTTAAATTA-ATA-TTTTTATAA
1 TATTTT-AATTATATATTTTTTATAT
**
5625950 TGCTTTAATTATATATTTTTTATAT
1 TATTTTAATTATATATTTTTTATAT
5625975 TATTTTAATTA
1 TATTTTAATTA
5625986 GTTTCTTTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
23 13 0.28
24 12 0.26
25 22 0.47
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
TATTTTAATTATATATTTTTTATAT
Found at i:5627139 original size:21 final size:20
Alignment explanation
Indices: 5627106--5627146 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
5627096 AAAAATATCT
*
5627106 TTTATAATTATTTAATATTTA
1 TTTATAATCATTTAA-ATTTA
*
5627127 TTTATCATCATTTAAATTTA
1 TTTATAATCATTTAAATTTA
5627147 AATTTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATAATCATTTAAATTTA
Found at i:5635039 original size:16 final size:17
Alignment explanation
Indices: 5635012--5635044 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
5635002 AATCTAATTG
5635012 AATTTTTATATTTTAAT
1 AATTTTTATATTTTAAT
5635029 AATTTTT-TATTTTAAT
1 AATTTTTATATTTTAAT
5635045 TAAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
AATTTTTATATTTTAAT
Found at i:5635053 original size:18 final size:17
Alignment explanation
Indices: 5635015--5635062 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 17
5635005 CTAATTGAAT
5635015 TTTTATATTTTAAT-AA
1 TTTTATATTTTAATAAA
*
5635031 TTTTTTATTTTAATTAAAA
1 TTTTATATTTTAA-T-AAA
5635050 TTTTATTATTTTA
1 TTTTA-TATTTTA
5635063 CCTTTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
19 6 0.23
20 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATATTTTAATAAA
Found at i:5635058 original size:20 final size:20
Alignment explanation
Indices: 5635024--5635062 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
5635014 TTTTTATATT
5635024 TTAATAATTTTTTATTTTAA
1 TTAATAATTTTTTATTTTAA
5635044 TTAA-AATTTTATTATTTTA
1 TTAATAATTTT-TTATTTTA
5635063 CCTTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTAATAATTTTTTATTTTAA
Found at i:5635829 original size:12 final size:12
Alignment explanation
Indices: 5635807--5635846 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
5635797 ATTTTTATAT
5635807 AAATT-AATTTA
1 AAATTAAATTTA
*
5635818 AACTTAAATTTA
1 AAATTAAATTTA
5635830 AAATTAAATTTA
1 AAATTAAATTTA
5635842 AAATT
1 AAATT
5635847 TTTTTGTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 4 0.15
12 22 0.85
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (12 bp):
AAATTAAATTTA
Found at i:5638322 original size:14 final size:15
Alignment explanation
Indices: 5638291--5638322 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5638281 GTTGGTTTTG
5638291 GTTTGTTTAAAGTTT
1 GTTTGTTTAAAGTTT
5638306 GTTTGTTTAAA-TTT
1 GTTTGTTTAAAGTTT
5638320 GTT
1 GTT
5638323 AGATTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (15 bp):
GTTTGTTTAAAGTTT
Found at i:5640512 original size:30 final size:30
Alignment explanation
Indices: 5640454--5640583 Score: 122
Period size: 30 Copynumber: 4.4 Consensus size: 30
5640444 TCATTTTATT
*
5640454 TAAACTTTTATATTTTT-A-TTACATTCAAA
1 TAAACTCTTA-ATTTTTAATTTACATTCAAA
* * *
5640483 TAAACACTTAATTTTTATTTTACAATCAAA
1 TAAACTCTTAATTTTTAATTTACATTCAAA
* * **
5640513 TAAACTTTTAAATTTTAATTTACACCCAAA
1 TAAACTCTTAATTTTTAATTTACATTCAAA
* * *
5640543 TAAAC-CTTTAGTTTTTAATTTATATTTAAA
1 TAAACTC-TTAATTTTTAATTTACATTCAAA
5640573 TAAACTCTTAA
1 TAAACTCTTAA
5640584 CATAAATAGA
Statistics
Matches: 79, Mismatches: 18, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
28 6 0.08
29 8 0.10
30 64 0.81
31 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.01, T:0.46
Consensus pattern (30 bp):
TAAACTCTTAATTTTTAATTTACATTCAAA
Found at i:5640519 original size:59 final size:60
Alignment explanation
Indices: 5640454--5640583 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 60
5640444 TCATTTTATT
* * ** *
5640454 TAAACTTTTATATTTTTA-TTACATTCAAATAAACAC-TTAATTTTTATTTTACAATCAAA
1 TAAACTTTTAAATTTTAATTTACACCCAAATAAAC-CTTTAATTTTTAATTTACAATCAAA
* * * *
5640513 TAAACTTTTAAATTTTAATTTACACCCAAATAAACCTTTAGTTTTTAATTTATATTTAAA
1 TAAACTTTTAAATTTTAATTTACACCCAAATAAACCTTTAATTTTTAATTTACAATCAAA
*
5640573 TAAACTCTTAA
1 TAAACTTTTAA
5640584 CATAAATAGA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 17 0.29
60 42 0.71
ACGTcount: A:0.41, C:0.12, G:0.01, T:0.46
Consensus pattern (60 bp):
TAAACTTTTAAATTTTAATTTACACCCAAATAAACCTTTAATTTTTAATTTACAATCAAA
Found at i:5641380 original size:24 final size:26
Alignment explanation
Indices: 5641353--5641413 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
5641343 AATAAATTCG
*
5641353 ATTATTATATTC-AGTTCAAACTC-A
1 ATTATTATATTCAAATTCAAACTCGA
*
5641377 ATTATTTATATTCAAATTCGAACTCGA
1 ATTA-TTATATTCAAATTCAAACTCGA
*
5641404 ATTAATATAT
1 ATTATTATAT
5641414 ATAGGTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 4 0.13
25 8 0.26
26 14 0.45
27 5 0.16
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.43
Consensus pattern (26 bp):
ATTATTATATTCAAATTCAAACTCGA
Found at i:5646688 original size:14 final size:14
Alignment explanation
Indices: 5646657--5646705 Score: 71
Period size: 15 Copynumber: 3.4 Consensus size: 14
5646647 CATAAATAAT
*
5646657 AAATAAATTATAACC
1 AAATAAATT-TAAAC
5646672 AAATAAATTTAAAC
1 AAATAAATTTAAAC
5646686 AAATAAATCTTAAAC
1 AAATAAAT-TTAAAC
5646701 AAATA
1 AAATA
5646706 TAAATGAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (14 bp):
AAATAAATTTAAAC
Found at i:5646722 original size:20 final size:20
Alignment explanation
Indices: 5646686--5646735 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
5646676 AAATTTAAAC
*
5646686 AAATAAATCTTAAACAAATAT
1 AAATAAAT-TCAAACAAATAT
*
5646707 AAATGAATTCAAACAAATAT
1 AAATAAATTCAAACAAATAT
5646727 AAATAAATT
1 AAATAAATT
5646736 TTAAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (20 bp):
AAATAAATTCAAACAAATAT
Found at i:5648937 original size:10 final size:10
Alignment explanation
Indices: 5648922--5648946 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5648912 TCGCAACTTT
5648922 ATAATTAAAA
1 ATAATTAAAA
5648932 ATAATTAAAA
1 ATAATTAAAA
5648942 ATAAT
1 ATAAT
5648947 AATTTATAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATAATTAAAA
Found at i:5651821 original size:21 final size:22
Alignment explanation
Indices: 5651796--5651838 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
5651786 AATATGTTCG
*
5651796 TTTATACATG-TTCGTTTAATA
1 TTTATAAATGATTCGTTTAATA
5651817 TTTATAAATGAATTCGTTTAAT
1 TTTATAAATG-ATTCGTTTAAT
5651839 TTAATTGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
23 10 0.53
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (22 bp):
TTTATAAATGATTCGTTTAATA
Found at i:5652085 original size:22 final size:22
Alignment explanation
Indices: 5652060--5652103 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5652050 AAGTTCAGTC
5652060 GCTGGAATAGAATTTGAAACTG
1 GCTGGAATAGAATTTGAAACTG
5652082 GCTGGAATAGAATTTGAAACTG
1 GCTGGAATAGAATTTGAAACTG
5652104 AGCAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.27
Consensus pattern (22 bp):
GCTGGAATAGAATTTGAAACTG
Found at i:5660702 original size:2 final size:2
Alignment explanation
Indices: 5660682--5660725 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
5660672 TATCTAATGT
* * * *
5660682 TA TA TA CA TA CA TA CA TA TA TA TA TA TA TA TA TG 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
5660724 TA
1 TA
5660726 AACCGGGCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:5661668 original size:2 final size:2
Alignment explanation
Indices: 5661663--5661700 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5661653 TCTCTCTCTC
* *
5661663 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5661701 ATAGAGCTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5663279 original size:359 final size:358
Alignment explanation
Indices: 5662598--5663560 Score: 1176
Period size: 359 Copynumber: 2.7 Consensus size: 358
5662588 TTAGCCTTCT
* *
5662598 TTTTCTTCAGCTCTTTTCTACAATGATAAATA-AGCAAAACTTGCAGTCAATTTAAAAGACTAGC
1 TTTTCTTCAGCTCTTTTCTAAAATGATAAATATA-CAAAACTTGCAGTCAATTTAAAAGATTAGC
* * *
5662662 TTCACATTTTCTATTGTATTTCCATGTTTTACATTTACATCACAATCCCTTGGAAAAAATTTAGA
65 TTCACATTTACTATTGTATTTCCATATTTTACATTTACATCACAATCCCTTGGAAAAAACTTAGA
*
5662727 AAATTGGACATTCAATAGACCAAAGTTAAATTAAAAAATTATTGGAGTTAAGACTAAAAGAATTT
130 AAATTGGACATTCAATAGACCAAAGTTAAATT-AAAAATTATTGGAGTTAAGATTAAAAGAATTT
* * * * * * * * * ** * *
5662792 TGAACACGAAATTTAATTTAATTTATTCATCTAGTCATTCTTAAAAAATGAGGTTTAACGTATTT
194 TGAATATGAAATTTAATTCAATTAATTTATATAATAATTTTTAAAAAAT-ACATTAAACATATTT
* * * * *
5662857 AAGGTTCAACTCTAATAATTTATAACTTTTTTCTTTGAATTATGATCTCTTTGTGAAAAAAAAAT
258 AAGATTCAAATCTAATAACTTATAACTTTTTTCTTTGAATTACGATATCTTTGTGAAAAAAAAAT
* * * *
5662922 -TTCTAATGAATTTT-TGAGAATTGAAGATTTTGTAA
323 AGT-TAATGAATTTTCTAAGAATTAAAGAATTTGTAA
* * * *
5662957 TTTTCTTTAGCTCTTTTCTAGAATGATAAATATACAAAACTTGCAGTTAATTTAAAAAATTAGCT
1 TTTTCTTCAGCTCTTTTCTAAAATGATAAATATACAAAACTTGCAGTCAATTTAAAAGATTAGCT
* *
5663022 TCACATTTACTGA-TGCATTTCCATATTTTACATTTACATCACAATCCCTTGGCAAAAACTTAGA
66 TCACATTTACT-ATTGTATTTCCATATTTTACATTTACATCACAATCCCTTGGAAAAAACTTAGA
* * * *
5663086 AAATAT-GACACTCAATACACCAAAGTTAAATTAAAAATTTCTTAGAGTTAAGATTAAAAGAATT
130 AAAT-TGGACATTCAATAGACCAAAGTTAAATTAAAAA-TTATTGGAGTTAAGATTAAAAGAATT
* * * * *
5663150 TTAAATATGAAATTTAATTCGATTGATTTATATAATAATTTTTTACAAAATACCATTAAATATAT
193 TTGAATATGAAATTTAATTCAATTAATTTATATAATAA-TTTTTAAAAAATA-CATTAAACATAT
* ** * * *
5663215 TTACGATTCAAATCTCAA-AACTTATATTTTTTTATTTTTGAATTACGATAT-TTTTTG-TAAAA
256 TTAAGATTCAAATCT-AATAACTTATAACTTTTT-TCTTTGAATTACGATATCTTTGTGAAAAAA
*
5663277 AAATAAGTTAATGACTTTTCTAAGAATTAAAGAATTTGTAA
319 AAAT-AGTTAATGAATTTTCTAAGAATTAAAGAATTTGTAA
5663318 TTTTCTTCAGC-CTTTT-TAAAATGATAAATATACAAAACTTGCAGTCAATTTAAAAGATTAGCT
1 TTTTCTTCAGCTCTTTTCTAAAATGATAAATATACAAAACTTGCAGTCAATTTAAAAGATTAGCT
*
5663381 TCAAATTTA-TATTGTATTTCCATATTTTACATTTACATCACAATCCCTTTGGAAAAAAAACTTA
66 TCACATTTACTATTGTATTTCCATATTTTACATTTACATCACAATCCC-TTGG--AAAAAACTTA
* * * *
5663445 GAAAATTGGAC-TTCAATAGACCAAAGTTTAATTAAAAGATTGTTGGAGTTAAAATTAAAAAAAT
128 GAAAATTGGACATTCAATAGACCAAAGTTAAATTAAAA-ATTATTGGAGTTAAGATTAAAAGAAT
* * *
5663509 TTTGAGTATGAAATTTAATTCAATTAATTTATACAATTATTTTTAAAAAATA
192 TTTGAATATGAAATTTAATTCAATTAATTTATATAATAATTTTTAAAAAATA
5663561 AAATTTAAAT
Statistics
Matches: 518, Mismatches: 69, Indels: 34
0.83 0.11 0.05
Matches are distributed among these distances:
357 1 0.00
358 40 0.08
359 271 0.52
360 142 0.27
361 64 0.12
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (358 bp):
TTTTCTTCAGCTCTTTTCTAAAATGATAAATATACAAAACTTGCAGTCAATTTAAAAGATTAGCT
TCACATTTACTATTGTATTTCCATATTTTACATTTACATCACAATCCCTTGGAAAAAACTTAGAA
AATTGGACATTCAATAGACCAAAGTTAAATTAAAAATTATTGGAGTTAAGATTAAAAGAATTTTG
AATATGAAATTTAATTCAATTAATTTATATAATAATTTTTAAAAAATACATTAAACATATTTAAG
ATTCAAATCTAATAACTTATAACTTTTTTCTTTGAATTACGATATCTTTGTGAAAAAAAAATAGT
TAATGAATTTTCTAAGAATTAAAGAATTTGTAA
Found at i:5664973 original size:20 final size:19
Alignment explanation
Indices: 5664948--5664994 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 19
5664938 AATAATTTTT
5664948 TAATTAAAATATTAAAATA
1 TAATTAAAATATTAAAATA
5664967 TATATTAAAATATTAAAATA
1 TA-ATTAAAATATTAAAATA
5664987 TAATTAAA
1 TAATTAAA
5664995 TTTATGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAATTAAAATATTAAAATA
Found at i:5670310 original size:24 final size:24
Alignment explanation
Indices: 5670278--5670324 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
5670268 TCTTATGTCG
5670278 AGCTCCTTTGTGTAAGAAAAAAAA
1 AGCTCCTTTGTGTAAGAAAAAAAA
5670302 AGCTCCTTTGTGTAAGAAAAAAA
1 AGCTCCTTTGTGTAAGAAAAAAA
5670325 CAGTGATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.26
Consensus pattern (24 bp):
AGCTCCTTTGTGTAAGAAAAAAAA
Found at i:5673540 original size:18 final size:18
Alignment explanation
Indices: 5673517--5673670 Score: 109
Period size: 18 Copynumber: 8.3 Consensus size: 18
5673507 TTTATTAATG
5673517 TAATATAATATTAGTTT-T
1 TAATATAATATTA-TTTAT
*
5673535 TAATATTATATTATTTAT
1 TAATATAATATTATTTAT
*
5673553 TAATATATTATAATATTATAT
1 TAATATA--ATATTATT-TAT
**
5673574 TAATAGCATATTATTTAT
1 TAATATAATATTATTTAT
* *
5673592 TAATATATTATTATAATAT
1 TAATATAATATTAT-TTAT
* *
5673611 TAAT-TAATTAATATAATAT
1 TAATATAA-TATTAT-TTAT
*
5673630 TCAT-TAATACATTA-TTAT
1 TAATATAAT--ATTATTTAT
5673648 TAATATAATATTATTTAT
1 TAATATAATATTATTTAT
*
5673666 AAATA
1 TAATA
5673671 AAATTATATT
Statistics
Matches: 109, Mismatches: 17, Indels: 20
0.75 0.12 0.14
Matches are distributed among these distances:
17 7 0.06
18 50 0.46
19 34 0.31
20 10 0.09
21 8 0.07
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (18 bp):
TAATATAATATTATTTAT
Found at i:5673588 original size:39 final size:39
Alignment explanation
Indices: 5673507--5673614 Score: 130
Period size: 39 Copynumber: 2.8 Consensus size: 39
5673497 TTTTTGTTAT
* * * **
5673507 TTTATTAATGTAATATAATATTAGTTTTTAATATTATATTA
1 TTTATTAATATATTATAATATTA--TATTAATAGCATATTA
5673548 TTTATTAATATATTATAATATTATATTAATAGCATATTA
1 TTTATTAATATATTATAATATTATATTAATAGCATATTA
*
5673587 TTTATTAATATATTAT--TATAATATTAAT
1 TTTATTAATATATTATAATATTATATTAAT
5673615 TAATTAATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
37 11 0.18
39 29 0.48
41 21 0.34
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.55
Consensus pattern (39 bp):
TTTATTAATATATTATAATATTATATTAATAGCATATTA
Found at i:5673598 original size:26 final size:27
Alignment explanation
Indices: 5673569--5673625 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
5673559 ATTATAATAT
* *
5673569 TATATTAATAGCATATT-ATTTATTAA
1 TATATTAATAGAATATTAATTAATTAA
* *
5673595 TATATTATTATAATATTAATTAATTAA
1 TATATTAATAGAATATTAATTAATTAA
5673622 TATA
1 TATA
5673626 ATATTCATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TATATTAATAGAATATTAATTAATTAA
Found at i:5673636 original size:42 final size:41
Alignment explanation
Indices: 5673520--5673653 Score: 123
Period size: 42 Copynumber: 3.2 Consensus size: 41
5673510 ATTAATGTAA
* * * *
5673520 TATAATATTAGTT-TTTAATATTATATTATTTAT-TAATATAT
1 TATAATATTAATTAATTAATATAATATTATTAATAT-AT-TAT
*
5673561 TATAATATTATATTAA-TAGCATATTAT-TTATTAATATATTAT
1 TATAATATTA-ATTAATTA--ATATAATATTATTAATATATTAT
*
5673603 TATAATATTAATTAATTAATATAATATTCATTAATACATTAT
1 TATAATATTAATTAATTAATATAATATT-ATTAATATATTAT
5673645 TATTAATAT
1 TA-TAATAT
5673654 AATATTATTT
Statistics
Matches: 79, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
40 6 0.08
41 17 0.22
42 33 0.42
43 15 0.19
44 8 0.10
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (41 bp):
TATAATATTAATTAATTAATATAATATTATTAATATATTAT
Found at i:5673646 original size:45 final size:42
Alignment explanation
Indices: 5673558--5673660 Score: 127
Period size: 42 Copynumber: 2.4 Consensus size: 42
5673548 TTTATTAATA
* * *
5673558 TATTATAATATTATATTAATAGCATATTATTTATTAATATAT
1 TATTATAATATTATATTAATAACATAATATTCATTAATATAT
* *
5673600 TATTATAATATTA-ATTAATTAATATAATATTCATTAATACAT
1 TATTATAATATTATATTAA-TAACATAATATTCATTAATATAT
*
5673642 TATTATTAATATAATATTA
1 TATTA-TAATATTATATTA
5673661 TTTATAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 5 0.10
42 36 0.69
43 7 0.13
44 4 0.08
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (42 bp):
TATTATAATATTATATTAATAACATAATATTCATTAATATAT
Found at i:5674669 original size:136 final size:134
Alignment explanation
Indices: 5674438--5674687 Score: 347
Period size: 136 Copynumber: 1.9 Consensus size: 134
5674428 AGATTGTTTG
* * *
5674438 TGTTAGATTTTCTCCAGATTCATTAGATCTGACTCTAGTTTATGTGTTTTTGACTTTGGATCTTG
1 TGTTAGATTTTCTCCAGATTCATCAGATCTGACTATAGTTTATGTGTTTTTGACTTTGGATCTTC
* * * *
5674503 ATGATTTGTGTTTAAAGATGTGATTTTTAGTGTTTTGTTGAGATTTTAGTTTTTCTCTGTTTGAC
66 AAGATTTCTGTTTAAAGATGTGACTTTTAGTGTTTCGTTGAGATTTTAGTTTTTCTCTGTTTGAC
5674568 TTTA
131 TTTA
* * ** * * * *
5674572 TGTTTGATTTTCTCTAGATTTGTCAGATCTGGCTATAGTTTATGTGTTTTTTTTACTTTTGATGT
1 TGTTAGATTTTCTCCAGATTCATCAGATCTGACTATAGTTTATGTG--TTTTTGACTTTGGATCT
5674637 TCAAGATTTCTGTTTAAAGATGTGACTTTTAGTGTTTCGTTGAGATTTTAG
64 TCAAGATTTCTGTTTAAAGATGTGACTTTTAGTGTTTCGTTGAGATTTTAG
5674688 GTTTAGAACG
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
134 39 0.39
136 60 0.61
ACGTcount: A:0.19, C:0.09, G:0.20, T:0.53
Consensus pattern (134 bp):
TGTTAGATTTTCTCCAGATTCATCAGATCTGACTATAGTTTATGTGTTTTTGACTTTGGATCTTC
AAGATTTCTGTTTAAAGATGTGACTTTTAGTGTTTCGTTGAGATTTTAGTTTTTCTCTGTTTGAC
TTTA
Found at i:5678661 original size:29 final size:30
Alignment explanation
Indices: 5678629--5678699 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
5678619 TATATTTTGA
5678629 AAATAAATTTTTATATTTT-TATTGTATTT
1 AAATAAATTTTTATATTTTGTATTGTATTT
* * * *
5678658 AAATTAATTTTGATCTTTTGTTTTGTATTT
1 AAATAAATTTTTATATTTTGTATTGTATTT
5678688 AAATAAATTTTT
1 AAATAAATTTTT
5678700 GTTTCAAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 16 0.46
30 19 0.54
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (30 bp):
AAATAAATTTTTATATTTTGTATTGTATTT
Found at i:5678758 original size:30 final size:30
Alignment explanation
Indices: 5678724--5678790 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
5678714 ATTGATTTAT
*
5678724 ATTAAGAATTTATTT-ATATATAAATTAAAA
1 ATTAAAAATTTATTTGA-ATATAAATTAAAA
5678754 ATTAAAAATTTATTTGAATATAAATTAAAA
1 ATTAAAAATTTATTTGAATATAAATTAAAA
*
5678784 GTTAAAA
1 ATTAAAA
5678791 GCTTATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (30 bp):
ATTAAAAATTTATTTGAATATAAATTAAAA
Found at i:5678797 original size:30 final size:30
Alignment explanation
Indices: 5678724--5678799 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
5678714 ATTGATTTAT
* *
5678724 ATTAAGAATTTATTTATATATAAATTAAAA
1 ATTAAAAACTTATTTATATATAAATTAAAA
*
5678754 ATTAAAAATTTATTTGA-ATATAAATTAAAA
1 ATTAAAAACTTATTT-ATATATAAATTAAAA
* *
5678784 GTTAAAAGCTTATTTA
1 ATTAAAAACTTATTTA
5678800 AATGTAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 1 0.02
30 39 0.95
31 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.42
Consensus pattern (30 bp):
ATTAAAAACTTATTTATATATAAATTAAAA
Found at i:5679346 original size:38 final size:38
Alignment explanation
Indices: 5679304--5679376 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
5679294 TTATTTTTTC
5679304 ATATAAATATAAAT-TATAACAAATAAT-TTTTATATAAA
1 ATAT-AATATAAATATATAA-AAATAATATTTTATATAAA
*
5679342 ATATAATATAAATATATAAATATAATATTTTATAT
1 ATATAATATAAATATATAAAAATAATATTTTATAT
5679377 TACATAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 15 0.47
38 17 0.53
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (38 bp):
ATATAATATAAATATATAAAAATAATATTTTATATAAA
Found at i:5679347 original size:18 final size:19
Alignment explanation
Indices: 5679326--5679376 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
5679316 ATTATAACAA
5679326 ATAATTTTTATATA-AAAT
1 ATAATTTTTATATATAAAT
* **
5679344 ATAATATAAATATATAAAT
1 ATAATTTTTATATATAAAT
5679363 ATAATATTTTATAT
1 ATAAT-TTTTATAT
5679377 TACATAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 11 0.44
19 9 0.36
20 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATTTTTATATATAAAT
Found at i:5679387 original size:37 final size:36
Alignment explanation
Indices: 5679306--5679388 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 36
5679296 ATTTTTTCAT
5679306 ATAAATATAAATTATAACAAATAATTTTTATATAAA
1 ATAAATATAAATTATAACAAATAATTTTTATATAAA
* * *
5679342 ATATAATATAAATATATAA-ATATAATATTTTATATTAC
1 ATA-AATATAAAT-TATAACAAATAAT-TTTTATATAAA
5679380 ATAAATATA
1 ATAAATATA
5679389 CTAATAACCA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
36 3 0.07
37 21 0.51
38 17 0.41
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (36 bp):
ATAAATATAAATTATAACAAATAATTTTTATATAAA
Found at i:5680162 original size:21 final size:21
Alignment explanation
Indices: 5680114--5680155 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5680104 AAAGATAATA
* *
5680114 ATAATGATGAAATTAATTATT
1 ATAATAATAAAATTAATTATT
5680135 ATAATAATAAAATTAA-TATT
1 ATAATAATAAAATTAATTATT
5680155 A
1 A
5680156 ATGATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
ATAATAATAAAATTAATTATT
Found at i:5680197 original size:18 final size:18
Alignment explanation
Indices: 5680135--5680197 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 18
5680125 ATTAATTATT
5680135 ATAA-TAATA-AAAT-TA
1 ATAATTAATATAAATATA
*
5680150 AT-ATTAATGATAAAAATA
1 ATAATTAAT-ATAAATATA
*
5680168 TATATTTAAATATAAATATA
1 -ATAATT-AATATAAATATA
5680188 ATAATTAATA
1 ATAATTAATA
5680198 AATACATTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
14 1 0.03
15 6 0.16
16 1 0.03
17 3 0.08
18 6 0.16
19 7 0.19
20 10 0.27
21 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
ATAATTAATATAAATATA
Found at i:5680535 original size:22 final size:21
Alignment explanation
Indices: 5680484--5680560 Score: 57
Period size: 22 Copynumber: 3.4 Consensus size: 21
5680474 AAATATATTT
5680484 TTATTTTATTAAATTTATATA
1 TTATTTTATTAAATTTATATA
* *
5680505 TAATTTTTATTAAAATTT-TTTA
1 TTA-TTTTATT-AAATTTATATA
*
5680527 TTATATTTATATCATATTATTATATA
1 TTAT-TTTAT-T-A-AAT-TTATATA
5680553 TTATTTTA
1 TTATTTTA
5680561 GATTGATATG
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
21 3 0.07
22 17 0.40
23 8 0.19
24 2 0.05
25 6 0.14
26 7 0.16
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTTTATTAAATTTATATA
Found at i:5687003 original size:33 final size:35
Alignment explanation
Indices: 5686966--5687037 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 35
5686956 AAATAAAAAT
* *
5686966 ATTTTGATTTAATT-AAATTATATATTTT-TA-TTA
1 ATTTTGATTAAATTAAAATAAT-TATTTTATATTTA
*
5686999 ATTTTTATTAAATTAAAATAATTATTTTATATTTA
1 ATTTTGATTAAATTAAAATAATTATTTTATATTTA
5687034 ATTT
1 ATTT
5687038 ATTTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 18 0.55
34 8 0.24
35 7 0.21
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (35 bp):
ATTTTGATTAAATTAAAATAATTATTTTATATTTA
Found at i:5688584 original size:16 final size:16
Alignment explanation
Indices: 5688532--5688584 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
5688522 TTAATACAGG
5688532 ATTA-AAATATT-AGA
1 ATTATAAATATTAAGA
*
5688546 ATTTATTAAT-TTAAG-
1 A-TTATAAATATTAAGA
*
5688561 ATTTTAAATATTAAGA
1 ATTATAAATATTAAGA
5688577 ATTATAAA
1 ATTATAAA
5688585 AATACTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 7 0.23
15 11 0.37
16 12 0.40
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (16 bp):
ATTATAAATATTAAGA
Found at i:5691882 original size:16 final size:16
Alignment explanation
Indices: 5691863--5691893 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5691853 AAAATCTAAA
5691863 ATATTAAATTTTATAT
1 ATATTAAATTTTATAT
*
5691879 ATATTATATTTTATA
1 ATATTAAATTTTATA
5691894 AAAATTTATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTAAATTTTATAT
Found at i:5691957 original size:21 final size:21
Alignment explanation
Indices: 5691931--5691977 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
5691921 ATATAAAAAT
* *
5691931 TTAAATATATATTTAATTTTA
1 TTAAATATATATATAATATTA
*
5691952 TTAAATCTATATATAATATTA
1 TTAAATATATATATAATATTA
5691973 TTAAA
1 TTAAA
5691978 ATTTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAATATATATATAATATTA
Found at i:5693513 original size:21 final size:21
Alignment explanation
Indices: 5693487--5693528 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5693477 ATGCTATCTA
5693487 AGAGAGAAACATTGAGAGTTT
1 AGAGAGAAACATTGAGAGTTT
5693508 AGAGAGAAACATTGAGAGTTT
1 AGAGAGAAACATTGAGAGTTT
5693529 TTTAGTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24
Consensus pattern (21 bp):
AGAGAGAAACATTGAGAGTTT
Found at i:5694433 original size:52 final size:51
Alignment explanation
Indices: 5694365--5694507 Score: 173
Period size: 52 Copynumber: 2.8 Consensus size: 51
5694355 CTTGTAAAAA
* *
5694365 AAGAATTCTAAGAGAAAGATGATTCTTAATAGGTAAGTTTGACTTGCAAGAG
1 AAGAATTCTAAGAGAAAGA-GATTCTTAATAGGTAAGTTTAACTTACAAGAG
* * *
5694417 AAGAATTCTAAAAGAAAAGAGATTCTTAATAGGCAAGTTTAACTTACAGGAG
1 AAGAATTCTAAGAG-AAAGAGATTCTTAATAGGTAAGTTTAACTTACAAGAG
* * *
5694469 AAG--TTCTAAGAGGAGAGGGATTCTTAATGGGTAAGTTTA
1 AAGAATTCTAAGA-GAAAGAGATTCTTAATAGGTAAGTTTA
5694508 TATGGTTATA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
50 29 0.37
51 1 0.01
52 44 0.56
53 5 0.06
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.28
Consensus pattern (51 bp):
AAGAATTCTAAGAGAAAGAGATTCTTAATAGGTAAGTTTAACTTACAAGAG
Found at i:5695032 original size:31 final size:31
Alignment explanation
Indices: 5694994--5695072 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
5694984 CTTTTAGTCA
*
5694994 AACAAATGGTATAAGAGCTGTGGTGATCCCC
1 AACAAATGGTATCAGAGCTGTGGTGATCCCC
* *
5695025 AACAAATGGTATCAGAGCTGTGGTGTTTCCC
1 AACAAATGGTATCAGAGCTGTGGTGATCCCC
*
5695056 AACAAGTGGTATCAGAG
1 AACAAATGGTATCAGAG
5695073 TTGAAGGTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.24
Consensus pattern (31 bp):
AACAAATGGTATCAGAGCTGTGGTGATCCCC
Found at i:5695103 original size:25 final size:25
Alignment explanation
Indices: 5695069--5695123 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
5695059 AAGTGGTATC
* *
5695069 AGAGTTGAAGGTTCAAAACGTGACA
1 AGAGTTGAAGATTCAAAACGTGAAA
* *
5695094 AGAGTTGAAGATTCAACATGTGAAA
1 AGAGTTGAAGATTCAAAACGTGAAA
5695119 AGAGT
1 AGAGT
5695124 CAAAGGCTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.42, C:0.09, G:0.27, T:0.22
Consensus pattern (25 bp):
AGAGTTGAAGATTCAAAACGTGAAA
Found at i:5695186 original size:25 final size:25
Alignment explanation
Indices: 5695140--5695189 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5695130 CTCGAGACGT
*
5695140 GAAAGAGCTAAAAGTTCGAGATGTG
1 GAAAGAGCTAAAAGTTCAAGATGTG
* *
5695165 GAAAGAGCTAAAGGTTTAAGATGTG
1 GAAAGAGCTAAAAGTTCAAGATGTG
5695190 AGAAGTGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.06, G:0.32, T:0.22
Consensus pattern (25 bp):
GAAAGAGCTAAAAGTTCAAGATGTG
Found at i:5695632 original size:52 final size:52
Alignment explanation
Indices: 5695483--5695633 Score: 196
Period size: 53 Copynumber: 2.9 Consensus size: 52
5695473 GAAGACTTGT
* * *
5695483 AAAAGAAGAATTCTAAGA-GAAAGATGATTCTTAATAGGTAAGTTTGACTTGC
1 AAAAGAAGAATTCTAAGAGGAAAGA-GATTCTTAATAGGCAAGTTTAACTTAC
*
5695535 AAAAGAAGAATTCTAAAAGGAAAAGAGATTCTTAATAGGCAAGTTTAACTTAC
1 AAAAGAAGAATTCTAAGAGG-AAAGAGATTCTTAATAGGCAAGTTTAACTTAC
** * * *
5695588 AGGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGCAAGTTTA
1 AAAAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTTA
5695634 TATGGTTATA
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
52 40 0.46
53 42 0.48
54 5 0.06
ACGTcount: A:0.43, C:0.08, G:0.23, T:0.26
Consensus pattern (52 bp):
AAAAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTTAACTTAC
Found at i:5696157 original size:31 final size:31
Alignment explanation
Indices: 5696119--5696183 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
5696109 GCTTTTAGCT
*
5696119 CAAAAAATGGTATCAGAGTTGTGGTGATCCC
1 CAAAAAATGGTATCAGAGCTGTGGTGATCCC
*
5696150 CAAAAAATGGTATCAGAGCTGTGGTGTTCCC
1 CAAAAAATGGTATCAGAGCTGTGGTGATCCC
5696181 CAA
1 CAA
5696184 CATAATTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (31 bp):
CAAAAAATGGTATCAGAGCTGTGGTGATCCC
Found at i:5700743 original size:49 final size:50
Alignment explanation
Indices: 5700683--5700803 Score: 129
Period size: 50 Copynumber: 2.4 Consensus size: 50
5700673 AAATGCAATG
* *
5700683 TATTATATT-A-ATTGTTTATTTGTTTTGGTTTACAACTTTTTTCAAGATA
1 TATTATATTAATATTG-TAATTTGTTTTAGTTTACAACTTTTTTCAAGATA
* * * *
5700732 TATTCTATTAATATTGTAATTTTTTTTAGTTTACATCTTTTTTCAATATA
1 TATTATATTAATATTGTAATTTGTTTTAGTTTACAACTTTTTTCAAGATA
* * * *
5700782 TATTTTATCACTATTGCAATTT
1 TATTATATTAATATTGTAATTT
5700804 CATTTTTATG
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 8 0.13
50 48 0.80
51 4 0.07
ACGTcount: A:0.27, C:0.08, G:0.07, T:0.58
Consensus pattern (50 bp):
TATTATATTAATATTGTAATTTGTTTTAGTTTACAACTTTTTTCAAGATA
Found at i:5700766 original size:50 final size:50
Alignment explanation
Indices: 5700700--5700803 Score: 136
Period size: 50 Copynumber: 2.1 Consensus size: 50
5700690 TTAATTGTTT
* * *
5700700 ATTTGTTTTGGTTTACAACTTTTTTCAAGATATATTCTATTAATATTGTA
1 ATTTGTTTTAGTTTACAACTTTTTTCAAGATATATTCTATCAATATTGCA
* * * * *
5700750 ATTTTTTTTAGTTTACATCTTTTTTCAATATATATTTTATCACTATTGCA
1 ATTTGTTTTAGTTTACAACTTTTTTCAAGATATATTCTATCAATATTGCA
5700800 ATTT
1 ATTT
5700804 CATTTTTATG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.57
Consensus pattern (50 bp):
ATTTGTTTTAGTTTACAACTTTTTTCAAGATATATTCTATCAATATTGCA
Found at i:5700838 original size:13 final size:13
Alignment explanation
Indices: 5700820--5700845 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5700810 TATGGAAAAT
5700820 AATATATTTTTTC
1 AATATATTTTTTC
5700833 AATATATTTTTTC
1 AATATATTTTTTC
5700846 TTTTTCACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
AATATATTTTTTC
Found at i:5703470 original size:24 final size:25
Alignment explanation
Indices: 5703421--5703473 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
5703411 TTACTTAAGG
*
5703421 AAAATAAATAAATAAGAAAACCAAT
1 AAAATAAATAAATAAGAAAACAAAT
*
5703446 AAAATAAA-AAAT-TGAAAACAAAAT
1 AAAATAAATAAATAAGAAAAC-AAAT
5703470 AAAA
1 AAAA
5703474 ATATAAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 11 0.44
25 8 0.32
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (25 bp):
AAAATAAATAAATAAGAAAACAAAT
Found at i:5703474 original size:25 final size:26
Alignment explanation
Indices: 5703421--5703476 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
5703411 TTACTTAAGG
*
5703421 AAAATAAATAAATAAGAAAACCAAT-
1 AAAATAAATAAATAAGAAAACAAATA
*
5703446 AAAATAAA-AAAT-TGAAAACAAAATA
1 AAAATAAATAAATAAGAAAAC-AAATA
5703471 AAAATA
1 AAAATA
5703477 TAAACATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 6 0.22
24 7 0.26
25 14 0.52
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (26 bp):
AAAATAAATAAATAAGAAAACAAATA
Found at i:5704372 original size:3 final size:3
Alignment explanation
Indices: 5704361--5704418 Score: 56
Period size: 3 Copynumber: 21.3 Consensus size: 3
5704351 GAATAAAAAA
* *
5704361 AAT AA- AAT AAT AAT AAT AAT AAT AAT -AT AAT -AT GAT AGT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5704405 AAT -AT AAT -AT AAT A
1 AAT AAT AAT AAT AAT A
5704419 TACTATAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
2 12 0.26
3 34 0.74
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:5704445 original size:5 final size:5
Alignment explanation
Indices: 5704370--5704433 Score: 74
Period size: 5 Copynumber: 12.2 Consensus size: 5
5704360 AAATAAAATA
*
5704370 ATAAT AATAAT AATAAT ATAAT ATGAT AGTAAT ATAAT ATAAT ATAAT
1 ATAAT -ATAAT -ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT
* *
5704418 ATACT ATAAT ACAAT A
1 ATAAT ATAAT ATAAT A
5704434 ATGTACTATA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
5 37 0.71
6 15 0.29
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:5704887 original size:14 final size:14
Alignment explanation
Indices: 5704870--5704918 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
5704860 TTATTTTTTG
5704870 TAATAAATTTTAAT
1 TAATAAATTTTAAT
*
5704884 TAAT-AATTTTTAT
1 TAATAAATTTTAAT
5704897 TAA-AATATTTTAAT
1 TAATAA-ATTTTAAT
5704911 TAATAAAT
1 TAATAAAT
5704919 AAAATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 12 0.40
14 16 0.53
15 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TAATAAATTTTAAT
Found at i:5705942 original size:21 final size:21
Alignment explanation
Indices: 5705879--5705942 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
5705869 TTTGTTATAT
*
5705879 ATATTAT-TATTTA-TAAAAA
1 ATATTATATTTTTATTAAAAA
* *
5705898 AT-TTAACATGTTTTATTTTAAAA
1 ATATT-ATAT-TTTTA-TTAAAAA
5705921 ATATTATATTTTTATTAAAAA
1 ATATTATATTTTTATTAAAAA
5705942 A
1 A
5705943 ACCTATATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
18 2 0.06
19 3 0.09
20 1 0.03
21 11 0.32
22 5 0.15
23 10 0.29
24 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
ATATTATATTTTTATTAAAAA
Found at i:5706513 original size:30 final size:31
Alignment explanation
Indices: 5706477--5706536 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
5706467 TTTGCCATCT
*
5706477 AATAGCTAAAC-AAAAATCAAGATAATAATC
1 AATAGCTAAACAAAAAATAAAGATAATAATC
*
5706507 AATAGCTAAACAAAAAATAAAGATAGTAAT
1 AATAGCTAAACAAAAAATAAAGATAATAAT
5706537 TAGAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.20
Consensus pattern (31 bp):
AATAGCTAAACAAAAAATAAAGATAATAATC
Found at i:5708385 original size:2 final size:2
Alignment explanation
Indices: 5708373--5708403 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5708363 AAAGTTCAAC
*
5708373 TA TA TA GA 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 T
5708404 TAATAACACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5708934 original size:21 final size:20
Alignment explanation
Indices: 5708910--5709002 Score: 66
Period size: 22 Copynumber: 4.5 Consensus size: 20
5708900 AAATTATATA
5708910 TATTTTATTAAACTTAATTTT
1 TATTTTA-TAAACTTAATTTT
* *
5708931 TATTTTATATAATTTGTATTTT
1 TATTTTATA-AACTT-AATTTT
* *
5708953 TAATTTATATA-TTAA-TTT
1 TATTTTATAAACTTAATTTT
*
5708971 TATTTTAAATAATCTTAATTTT
1 TATTTT--ATAAACTTAATTTT
*
5708993 AATTTT-TAAA
1 TATTTTATAAA
5709003 TATATAAATT
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
18 8 0.14
19 4 0.07
20 7 0.12
21 16 0.29
22 21 0.38
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (20 bp):
TATTTTATAAACTTAATTTT
Found at i:5708954 original size:22 final size:24
Alignment explanation
Indices: 5708926--5709001 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 24
5708916 ATTAAACTTA
*
5708926 ATTTTT-ATTT-TATATA-ATTTGT
1 ATTTTTAATTTATATATTAATTT-T
5708948 ATTTTTAATTTATATATTAATTTT
1 ATTTTTAATTTATATATTAATTTT
* *
5708972 A-TTTTAA-ATA-ATCTTAATTTT
1 ATTTTTAATTTATATATTAATTTT
5708993 AATTTTTAA
1 -ATTTTTAA
5709002 ATATATAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
21 10 0.22
22 9 0.20
23 16 0.35
24 7 0.15
25 4 0.09
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (24 bp):
ATTTTTAATTTATATATTAATTTT
Found at i:5709519 original size:18 final size:18
Alignment explanation
Indices: 5709496--5709533 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5709486 TTATTTTTTT
5709496 ATTAAA-ATAATATAAAAA
1 ATTAAAGATAAT-TAAAAA
*
5709514 ATTAAAGTTAATTAAAAA
1 ATTAAAGATAATTAAAAA
5709532 AT
1 AT
5709534 AAATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
ATTAAAGATAATTAAAAA
Found at i:5711487 original size:3 final size:3
Alignment explanation
Indices: 5711479--5711504 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5711469 TTAGTGATAT
5711479 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
5711505 TTGCAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:5713095 original size:31 final size:30
Alignment explanation
Indices: 5713054--5713143 Score: 128
Period size: 30 Copynumber: 2.9 Consensus size: 30
5713044 ATGATTTATG
*
5713054 TTAAGAGCTTATTTAGGTACAAATTAAAAGT
1 TTAAGGGCTTATTT-GGTACAAATTAAAAGT
5713085 TTAAGGGCTTATTTGGATACAAATT-AAAGT
1 TTAAGGGCTTATTTGG-TACAAATTAAAAGT
*
5713115 TTAAGGGCTTATTTGAGTTCAAATTAAAA
1 TTAAGGGCTTATTTG-GTACAAATTAAAA
5713144 ATTAAGGTTG
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
30 29 0.54
31 25 0.46
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.37
Consensus pattern (30 bp):
TTAAGGGCTTATTTGGTACAAATTAAAAGT
Found at i:5713509 original size:32 final size:33
Alignment explanation
Indices: 5713451--5713514 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
5713441 GATGATTGTG
5713451 TATTGTGCTATTATTCTATCTCCATAAACATTT
1 TATTGTGCTATTATTCTATCTCCATAAACATTT
5713484 TATTGTGCTATTATTC-ATCTCCATAAACATT
1 TATTGTGCTATTATTCTATCTCCATAAACATT
5713515 CATTTATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (33 bp):
TATTGTGCTATTATTCTATCTCCATAAACATTT
Found at i:5715154 original size:38 final size:39
Alignment explanation
Indices: 5715101--5715174 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 39
5715091 CGAATTTTCA
*
5715101 TTGAGGAAAAGTGTAC-ATTGAGGAAAAAATGAGAGAATGT
1 TTGAGGAAAAGTGTACTATTGA-AAAAAAATGA-AGAATGT
5715141 TTGA-GAAAA-TGTACTATTGAAAAAAAATGAAGAA
1 TTGAGGAAAAGTGTACTATTGAAAAAAAATGAAGAA
5715175 AAAAATCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
37 4 0.12
38 14 0.44
39 10 0.31
40 4 0.12
ACGTcount: A:0.50, C:0.03, G:0.24, T:0.23
Consensus pattern (39 bp):
TTGAGGAAAAGTGTACTATTGAAAAAAAATGAAGAATGT
Found at i:5720517 original size:2 final size:2
Alignment explanation
Indices: 5720510--5720552 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5720500 TGAACAGGTA
5720510 TC TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC TC
5720552 T
1 T
5720553 ATCTGCACCA
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5725952 original size:12 final size:12
Alignment explanation
Indices: 5725935--5725959 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5725925 CCTCTCTCTC
5725935 TCTCTTCTTCTT
1 TCTCTTCTTCTT
5725947 TCTCTTCTTCTT
1 TCTCTTCTTCTT
5725959 T
1 T
5725960 TGGGTACAGA
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TCTCTTCTTCTT
Found at i:5726473 original size:3 final size:3
Alignment explanation
Indices: 5726465--5726535 Score: 97
Period size: 3 Copynumber: 23.7 Consensus size: 3
5726455 AGACGCTATT
* * * *
5726465 TGC TGC TGC TGC TGC TTC TGC TGC CGC TGC TGC TGC TGC TGC TGT TGT
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
*
5726513 TGC TGG TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TG
5726536 AGGGGTCGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.00, C:0.30, G:0.34, T:0.37
Consensus pattern (3 bp):
TGC
Found at i:5735937 original size:333 final size:333
Alignment explanation
Indices: 5735315--5736597 Score: 1693
Period size: 333 Copynumber: 3.9 Consensus size: 333
5735305 CTTAGTAATT
* * *
5735315 AATTACAT-AAGGCATTTGTTAGA-AACAGACGACTTTAAAATTTTCTCACTAAATATTTTAAAA
1 AATTAC-TGAAGGCATTTGTTA-ATAACAGACGCCTTCAAAATTTTCTCACTAAATATTTTAAGA
* *
5735378 ATTATTAAAGGCGTCTTCTACTGTAAAATATCTTCGAT-TATACCACTACACATATTGTAATACT
64 ATTATTAAAGGCGTCTTCTACTGTAAAATACCTT--ATATATACCACTACACATATTGTAACACT
* *
5735442 GTTATTGAATGCGTATATTTAAGATAGATGCCTTTAATAATTTCTATCACAGTTTGTATATAATT
127 GTTATTAAAGGCGTATATTTAAGATAGATGCCTTTAATAATTTCTATCACAGTTTGTATATAATT
* * * * * *
5735507 ACTGAAGGTGATTTTAGATAACAATGCCTTTAATAATTTTTCTAATAAAAGTTTTCAGAATTATT
192 ACTGAAGGCGATTTCAGATAACAACGCCTTCAATAATTTTCCTAATAAAAGTTTTCAGGATTATT
* * * *
5735572 AAAGGCATCTTTTATTATAAGCCACCTTCGATATACTACGATGGTAATCGAATGTGAGTATTAGA
257 AAAGGCGTATTTTATTATAAGCCACCTTCGATATACCACGATGGTAATCGAATGCGAGTATTAGA
** *
5735637 AAAGGCGTCATC
322 AAAGGCACCTTC
* *
5735649 AATTACTGAAGGCATTTGTTAATAACATACGCCTTCAAAATTTT-TCCACTAAATATTTTGAGAA
1 AATTACTGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTCT-CACTAAATATTTTAAGAA
* ** *
5735713 TTATTAAAGGCGTCTTCTATTGTAAAATACCTTATATATACGGCTACACATATTGTAATACTGTT
65 TTATTAAAGGCGTCTTCTACTGTAAAATACCTTATATATACCACTACACATATTGTAACACTGTT
* * *
5735778 ATTAAAGGTGTATATTTAAGATAGACGCCTTTAATAATTTTTATCACAGTTTGTATATAATTACT
130 ATTAAAGGCGTATATTTAAGATAGATGCCTTTAATAATTTCTATCACAGTTTGTATATAATTACT
*
5735843 GAAGGCGATTTCAGATAACAACGCCTTCAATAATTTTCCAAATAAAAGTTTTCAGGATTATTAAA
195 GAAGGCGATTTCAGATAACAACGCCTTCAATAATTTTCCTAATAAAAGTTTTCAGGATTATTAAA
* * **
5735908 GAG-GTTTTTTATTATAAGTCATTTTCGATATACCACGATGGTAATCGAATGCGAGTATTAGAAA
260 G-GCGTATTTTATTATAAGCCACCTTCGATATACCACGATGGTAATCGAATGCGAGTATTAGAAA
5735972 AGGCACCTTC
324 AGGCACCTTC
*
5735982 AATTACTGAAGGCATTTGTTAATAACAAACGCCTTCAAAATTTT-TCTACTAAATATTTTAAGAA
1 AATTACTGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTCTC-ACTAAATATTTTAAGAA
* * * * **
5736046 TTATTAAAGGCTTCTTCTACTATAAAATACTTTCTATATACCGTTACACATATTGTAACACTGTT
65 TTATTAAAGGCGTCTTCTACTGTAAAATACCTTATATATACCACTACACATATTGTAACACTGTT
* * * * * *
5736111 ATTGAATGCGTATATTTAAGATAGATGCCTTTAATAATTTTTATTATAGTTTGTATATAATTAAT
130 ATTAAAGGCGTATATTTAAGATAGATGCCTTTAATAATTTCTATCACAGTTTGTATATAATTACT
** * * * *
5736176 GAAGGTTATTTCAGATAACAACACCTTTAATAA-TTTCTCTAATAAAAGTTTTTAAGATTATTAA
195 GAAGGCGATTTCAGATAACAACGCCTTCAATAATTTTC-CTAATAAAAGTTTTCAGGATTATTAA
* * **
5736240 AGGCGTATTTTATTATAAGCCACCTTCGATATACCACGATGGTAATCAAAGGCGTTTATTAGAAA
259 AGGCGTATTTTATTATAAGCCACCTTCGATATACCACGATGGTAATCGAATGCGAGTATTAGAAA
*
5736305 AAGCACCTTC
324 AGGCACCTTC
*
5736315 AATTACTGAAGGCATTTGTTAATAACAGACGCCTTCATAATTTTCTCACTAAATATTTTAAGAAT
1 AATTACTGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTCTCACTAAATATTTTAAGAAT
* * * * * * *
5736380 TATTAAATGCATCTTCTACTGTAAAATGCCTTTTATATATCACTATATATATTGTAACACTGTTA
66 TATTAAAGGCGTCTTCTACTGTAAAATACCTTATATATACCACTACACATATTGTAACACTGTTA
* * ** *
5736445 TTAAAGGCTTATATTTAAGATAAAAACCTTTAATAATTTCTATCATAGTTTGTATATAATTACTG
131 TTAAAGGCGTATATTTAAGATAGATGCCTTTAATAATTTCTATCACAGTTTGTATATAATTACTG
* * * * * *
5736510 AAGGCGATTTCAGATAACAACGCCTTCAATATTTTTTC-AACAAAATTTTTTTA-GATTGTTAAA
196 AAGGCGATTTCAGATAACAACGCCTTCAATAATTTTCCTAATAAAA-GTTTTCAGGATTATTAAA
** * *
5736573 TACGTCTTTTATTATAAGCCGCCTT
260 GGCGTATTTTATTATAAGCCACCTT
5736598 TAATAATTTG
Statistics
Matches: 839, Mismatches: 99, Indels: 24
0.87 0.10 0.02
Matches are distributed among these distances:
332 44 0.05
333 705 0.84
334 90 0.11
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (333 bp):
AATTACTGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTCTCACTAAATATTTTAAGAAT
TATTAAAGGCGTCTTCTACTGTAAAATACCTTATATATACCACTACACATATTGTAACACTGTTA
TTAAAGGCGTATATTTAAGATAGATGCCTTTAATAATTTCTATCACAGTTTGTATATAATTACTG
AAGGCGATTTCAGATAACAACGCCTTCAATAATTTTCCTAATAAAAGTTTTCAGGATTATTAAAG
GCGTATTTTATTATAAGCCACCTTCGATATACCACGATGGTAATCGAATGCGAGTATTAGAAAAG
GCACCTTC
Found at i:5736460 original size:666 final size:667
Alignment explanation
Indices: 5735315--5736545 Score: 1877
Period size: 666 Copynumber: 1.8 Consensus size: 667
5735305 CTTAGTAATT
* *
5735315 AATTACATAAGGCATTTGTTAGAAACAGACGACTTTAAAATTTTCTCACTAAATATTTTAAAAAT
1 AATTACATAAGGCATTTGTTAGAAACAAACGACTTCAAAATTTTCTCACTAAATATTTTAAAAAT
* *
5735380 TATTAAAGGCGTCTTCTACTGTAAAATATCTTCGATTATACCACTACACATATTGTAATACTGTT
66 TATTAAAGGCGTCTTCTACTATAAAATATCTTCGATTATACCACTACACATATTGTAACACTGTT
*
5735445 ATTGAATGCGTATATTTAAGATAGATGCCTTTAATAATTTCTATCACAGTTTGTATATAATTACT
131 ATTGAATGCGTATATTTAAGATAGATGCCTTTAATAATTTCTATCACAGTTTGTATATAATTAAT
* ** * *
5735510 GAAGGTGATTTTAGATAACAATGCCTTTAATAATTTTTCTAATAAAAGTTTTCAGAATTATTAAA
196 GAAGGTGATTTCAGATAACAACACCTTTAATAATTTCTCTAATAAAAGTTTTAAGAATTATTAAA
* * * * *
5735575 GGCATCTTTTATTATAAGCCACCTTCGATATACTACGATGGTAATCGAATGTGAGTATTAGAAAA
261 GGCATATTTTATTATAAGCCACCTTCGATATACCACGATGGTAATCAAAGGCGAGTATTAGAAAA
* ** *
5735640 GGCGTCATCAATTACTGAAGGCATTTGTTAATAACATACGCCTTCAAAATTTTTCCACTAAATAT
326 AGCACCATCAATTACTGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTTCCACTAAATAT
* * * *
5735705 TTTGAGAATTATTAAAGGCGTCTTCTATTGTAAAATACCTTATATATACGGCTACACATATTGTA
391 TTTAAGAATTATTAAAGGCATCTTCTACTGTAAAATACCTTATATATACGACTACACATATTGTA
* * ** *
5735770 ATACTGTTATTAAAGGTGTATATTTAAGATAGACGCCTTTAATAATTTTTATCACAGTTTGTATA
456 ACACTGTTATTAAAGGTGTATATTTAAGATAAAAACCTTTAATAATTTCTATCACAGTTTGTATA
5735835 TAATTACTGAAGGCGATTTCAGATAACAACGCCTTCAATAATTTTCCAAATAAAAGTTTTCAGGA
521 TAATTACTGAAGGCGATTTCAGATAACAACGCCTTCAATAATTTTCCAAATAAAAGTTTTCAGGA
5735900 TTATTAAAGAGGTTTTTTATTATAAGTCATTTTCGATATACCACGATGGTAATCGAATGCGAGTA
586 TTATTAAAGAGGTTTTTTATTATAAGTCATTTTCGATATACCACGATGGTAATCGAATGCGAGTA
5735965 TTAGAAAAGGCACCTTC
651 TTAGAAAAGGCACCTTC
* *
5735982 AATTAC-TGAAGGCATTTGTTA-ATAACAAACGCCTTCAAAATTTT-TCTACTAAATATTTTAAG
1 AATTACAT-AAGGCATTTGTTAGA-AACAAACGACTTCAAAATTTTCTC-ACTAAATATTTTAAA
* * **
5736044 AATTATTAAAGGCTTCTTCTACTATAAAATA-CTTTCTA-TATACCGTTACACATATTGTAACAC
63 AATTATTAAAGGCGTCTTCTACTATAAAATATC-TTCGATTATACCACTACACATATTGTAACAC
* * *
5736107 TGTTATTGAATGCGTATATTTAAGATAGATGCCTTTAATAATTTTTATTATAGTTTGTATATAAT
127 TGTTATTGAATGCGTATATTTAAGATAGATGCCTTTAATAATTTCTATCACAGTTTGTATATAAT
*
5736172 TAATGAAGGTTATTTCAGATAACAACACCTTTAATAATTTCTCTAATAAAAGTTTTTAAG-ATTA
192 TAATGAAGGTGATTTCAGATAACAACACCTTTAATAATTTCTCTAATAAAAG-TTTTAAGAATTA
* **
5736236 TTAAAGGCGTATTTTATTATAAGCCACCTTCGATATACCACGATGGTAATCAAAGGCGTTTATTA
256 TTAAAGGCATATTTTATTATAAGCCACCTTCGATATACCACGATGGTAATCAAAGGCGAGTATTA
* *
5736301 GAAAAAGCACCTTCAATTACTGAAGGCATTTGTTAATAACAGACGCCTTCATAA-TTTTCTCACT
321 GAAAAAGCACCATCAATTACTGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTTC-CACT
* * * * *
5736365 AAATATTTTAAGAATTATTAAATGCATCTTCTACTGTAAAATGCCTTTTATATATC-ACTATATA
385 AAATATTTTAAGAATTATTAAAGGCATCTTCTACTGTAAAATACCTTATATATA-CGACTACACA
*
5736429 TATTGTAACACTGTTATTAAAGGCT-TATATTTAAGATAAAAACCTTTAATAATTTCTATCATAG
449 TATTGTAACACTGTTATTAAAGG-TGTATATTTAAGATAAAAACCTTTAATAATTTCTATCACAG
*
5736493 TTTGTATATAATTACTGAAGGCGATTTCAGATAACAACGCCTTCAATATTTTT
513 TTTGTATATAATTACTGAAGGCGATTTCAGATAACAACGCCTTCAATAATTTT
5736546 TCAACAAAAT
Statistics
Matches: 506, Mismatches: 50, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
665 5 0.01
666 409 0.81
667 92 0.18
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (667 bp):
AATTACATAAGGCATTTGTTAGAAACAAACGACTTCAAAATTTTCTCACTAAATATTTTAAAAAT
TATTAAAGGCGTCTTCTACTATAAAATATCTTCGATTATACCACTACACATATTGTAACACTGTT
ATTGAATGCGTATATTTAAGATAGATGCCTTTAATAATTTCTATCACAGTTTGTATATAATTAAT
GAAGGTGATTTCAGATAACAACACCTTTAATAATTTCTCTAATAAAAGTTTTAAGAATTATTAAA
GGCATATTTTATTATAAGCCACCTTCGATATACCACGATGGTAATCAAAGGCGAGTATTAGAAAA
AGCACCATCAATTACTGAAGGCATTTGTTAATAACAGACGCCTTCAAAATTTTTCCACTAAATAT
TTTAAGAATTATTAAAGGCATCTTCTACTGTAAAATACCTTATATATACGACTACACATATTGTA
ACACTGTTATTAAAGGTGTATATTTAAGATAAAAACCTTTAATAATTTCTATCACAGTTTGTATA
TAATTACTGAAGGCGATTTCAGATAACAACGCCTTCAATAATTTTCCAAATAAAAGTTTTCAGGA
TTATTAAAGAGGTTTTTTATTATAAGTCATTTTCGATATACCACGATGGTAATCGAATGCGAGTA
TTAGAAAAGGCACCTTC
Found at i:5737244 original size:18 final size:18
Alignment explanation
Indices: 5737216--5737261 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
5737206 CCTTATTGAC
*
5737216 TGATA-TGTATTGCTGAA
1 TGATATTGTATTACTGAA
5737233 TGATATTGTATTACTGAA
1 TGATATTGTATTACTGAA
5737251 TGATATTGTAT
1 TGATATTGTAT
5737262 GATATTAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (18 bp):
TGATATTGTATTACTGAA
Found at i:5745217 original size:115 final size:115
Alignment explanation
Indices: 5745101--5745318 Score: 354
Period size: 115 Copynumber: 1.9 Consensus size: 115
5745091 TTTATTAAAT
* *
5745101 TTTTTA-AAAATAAAAAT-ATAATTTTATATCAAAATTTATTTAAATATATTAAAATTTTATATT
1 TTTTTATAAAA-AAAAATAATAATTTTATATCAAAATCTATTTAAATATATTAAAATTTTAGATT
5745164 AAAATAATATA-AAAA-AACAAAATGTTTAAATTTTAAAACCAAGAAACTGAA
65 AAAATAATATATAAAACAA-AAAAT-TTTAAATTTTAAAACCAAGAAACTGAA
5745215 TTTTTATAAAAAAAAATAATAATTTTATATCAAAATCTATTTAAATATATTAAAATTTTAGATTA
1 TTTTTATAAAAAAAAATAATAATTTTATATCAAAATCTATTTAAATATATTAAAATTTTAGATTA
5745280 AAATAATATATTAAAACAAAAAATTTTAAATTTTAAAAC
66 AAATAATATA-TAAAACAAAAAATTTTAAATTTTAAAAC
5745319 TGATAAACCG
Statistics
Matches: 97, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
114 12 0.12
115 59 0.61
116 15 0.15
117 9 0.09
118 2 0.02
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (115 bp):
TTTTTATAAAAAAAAATAATAATTTTATATCAAAATCTATTTAAATATATTAAAATTTTAGATTA
AAATAATATATAAAACAAAAAATTTTAAATTTTAAAACCAAGAAACTGAA
Found at i:5749048 original size:19 final size:20
Alignment explanation
Indices: 5749019--5749059 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
5749009 TTAGGCACGT
5749019 GGAGAGATTGGATGGGGTGG
1 GGAGAGATTGGATGGGGTGG
* *
5749039 GGAG-GATTGGGTGTGGTGG
1 GGAGAGATTGGATGGGGTGG
5749058 GG
1 GG
5749060 CGTTGGGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.15, C:0.00, G:0.63, T:0.22
Consensus pattern (20 bp):
GGAGAGATTGGATGGGGTGG
Found at i:5749120 original size:44 final size:39
Alignment explanation
Indices: 5749034--5749109 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 39
5749024 GATTGGATGG
5749034 GGTGGGGA-GGATTGGGTGTGGTGGGGCGTTGGGGGGAA
1 GGTGGGGAGGGATTGGGTGTGGTGGGGCGTTGGGGGGAA
*
5749072 GGTGGGGAGGGATTGGGTGTGGTGGGGATGTTGGGGGG
1 GGTGGGGAGGGATTGGGTGTGGTGGGG-CGTTGGGGGG
5749110 GGGGAAGGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 8 0.23
39 18 0.51
40 9 0.26
ACGTcount: A:0.09, C:0.01, G:0.67, T:0.22
Consensus pattern (39 bp):
GGTGGGGAGGGATTGGGTGTGGTGGGGCGTTGGGGGGAA
Found at i:5749127 original size:44 final size:39
Alignment explanation
Indices: 5749042--5749130 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 39
5749032 GGGGTGGGGA
**
5749042 GGATTGGGTGTGGTGGGGCGTTGGGGGGAAGGTGGGGAG
1 GGATTGGGTGTGGTGGGGCGTTGGGGGGAAGGTGGAAAG
*
5749081 GGATTGGGTGTGGTGGGGATGTTGGGGGGGGGGAAGGTGGAAAG
1 GGATTGGGTGTGGTGGGG-CGTT----GGGGGGAAGGTGGAAAG
5749125 GGATTG
1 GGATTG
5749131 ATGGGGGTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 18 0.43
40 3 0.07
44 21 0.50
ACGTcount: A:0.13, C:0.01, G:0.64, T:0.21
Consensus pattern (39 bp):
GGATTGGGTGTGGTGGGGCGTTGGGGGGAAGGTGGAAAG
Found at i:5749402 original size:20 final size:20
Alignment explanation
Indices: 5749364--5749401 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5749354 GATTGTGTTA
*
5749364 TATATTAATTTATAATTTTG
1 TATATGAATTTATAATTTTG
5749384 TATATGAATTT-TAATTTT
1 TATATGAATTTATAATTTT
5749402 TTTGTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TATATGAATTTATAATTTTG
Done.