Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, 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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 98 of 100
Found at i:17314556 original size:29 final size:29
Alignment explanation
Indices: 17314505--17314562 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
17314495 TTTTTTATAC
17314505 ATAAGCTTAAAACCTTAAAAATC-ACAAA
1 ATAAGCTTAAAACCTTAAAAATCAACAAA
*
17314533 ATAAGCATTAAAACAC-TAACAATCAACAAA
1 ATAAGC-TTAAAAC-CTTAAAAATCAACAAA
17314563 CTTTTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 6 0.23
29 14 0.54
30 6 0.23
ACGTcount: A:0.59, C:0.19, G:0.03, T:0.19
Consensus pattern (29 bp):
ATAAGCTTAAAACCTTAAAAATCAACAAA
Found at i:17316877 original size:22 final size:21
Alignment explanation
Indices: 17316850--17316890 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
17316840 AGAGAAATCT
* *
17316850 GTGAAACAAGAGATGTAAGGTG
1 GTGAAAAAAAAGATG-AAGGTG
17316872 GTGAAAAAAAAGATGAAGG
1 GTGAAAAAAAAGATGAAGG
17316891 GTACTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.49, C:0.02, G:0.34, T:0.15
Consensus pattern (21 bp):
GTGAAAAAAAAGATGAAGGTG
Found at i:17318711 original size:77 final size:77
Alignment explanation
Indices: 17318630--17318777 Score: 233
Period size: 77 Copynumber: 1.9 Consensus size: 77
17318620 TTACTTCAAT
* * * **
17318630 TTTTTTCTTTATTTCAAGTTTTAATCATTGATTCTTTAGATCTAGTTTTATTCGGCCTTAATTAA
1 TTTTTTCTTTATTTCAAGTTTCAATCACTGATTATTTAGATCTAGTTTTATTCAACCTTAATTAA
17318695 AGATTTCTACAA
66 AGATTTCTACAA
* *
17318707 TTTTTTCTTTATTTGAAGTTTCAATCACTGATTATTTAGATCTAGTTTTATTCAACCTTAATTCA
1 TTTTTTCTTTATTTCAAGTTTCAATCACTGATTATTTAGATCTAGTTTTATTCAACCTTAATTAA
17318772 AGATTT
66 AGATTT
17318778 TTAGTGACAG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 64 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (77 bp):
TTTTTTCTTTATTTCAAGTTTCAATCACTGATTATTTAGATCTAGTTTTATTCAACCTTAATTAA
AGATTTCTACAA
Found at i:17322480 original size:23 final size:23
Alignment explanation
Indices: 17322448--17322491 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
17322438 TTCCCCACTT
*
17322448 TTCTTTTTTCTTTTAGTTCTTAG
1 TTCTTATTTCTTTTAGTTCTTAG
*
17322471 TTCTTATTTCTTTTTGTTCTT
1 TTCTTATTTCTTTTAGTTCTT
17322492 TAGTAGAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.07, C:0.14, G:0.07, T:0.73
Consensus pattern (23 bp):
TTCTTATTTCTTTTAGTTCTTAG
Found at i:17323510 original size:18 final size:18
Alignment explanation
Indices: 17323475--17323513 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17323465 CTTAGGATAG
17323475 GTATACTTTGAGTATTTT
1 GTATACTTTGAGTATTTT
*
17323493 GTATA-TTTGAAGTGTTTT
1 GTATACTTTG-AGTATTTT
17323511 GTA
1 GTA
17323514 GGAATAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.23, C:0.03, G:0.21, T:0.54
Consensus pattern (18 bp):
GTATACTTTGAGTATTTT
Found at i:17325691 original size:10 final size:10
Alignment explanation
Indices: 17325662--17325693 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
17325652 ATCTTATCTC
17325662 TTTTCTTTAG
1 TTTTCTTTAG
17325672 -TTTC-TTAG
1 TTTTCTTTAG
17325680 TTTTCTTTAG
1 TTTTCTTTAG
17325690 TTTT
1 TTTT
17325694 TTTGTATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 4 0.20
9 8 0.40
10 8 0.40
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.72
Consensus pattern (10 bp):
TTTTCTTTAG
Found at i:17329223 original size:39 final size:37
Alignment explanation
Indices: 17329178--17329266 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 37
17329168 CTTCCTGATC
* * * * * *
17329178 TTAAACCCTAAACCAATAGGTTAAAGCCTAAACTTGGAG
1 TTAAACCCTAAACCAA-AAGTGAAACCCCAAACCTAG-G
17329217 TTAAACCCTAAACCAAAAGTGAAACCCCAAACCTAGG
1 TTAAACCCTAAACCAAAAGTGAAACCCCAAACCTAGG
17329254 TTAAACCCTAAAC
1 TTAAACCCTAAAC
17329267 TCTAAGTCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
37 14 0.32
38 14 0.32
39 16 0.36
ACGTcount: A:0.44, C:0.26, G:0.11, T:0.19
Consensus pattern (37 bp):
TTAAACCCTAAACCAAAAGTGAAACCCCAAACCTAGG
Found at i:17329497 original size:45 final size:46
Alignment explanation
Indices: 17329407--17329507 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 46
17329397 TAATCCATAC
* * * * *
17329407 TACATTCATGTGTATTTGTGATTGGCATTTACATTATTTAATTTGT
1 TACATTCATGTGCATTTGTCATTAGCATTTACATAATCTAATTTGT
* *
17329453 TACATTCATGTGCATTT-TCTTTAGCATTTACATAATCTAGTTTGT
1 TACATTCATGTGCATTTGTCATTAGCATTTACATAATCTAATTTGT
*
17329498 TGCATTCATG
1 TACATTCATG
17329508 CATTTTAGCT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 31 0.66
46 16 0.34
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.50
Consensus pattern (46 bp):
TACATTCATGTGCATTTGTCATTAGCATTTACATAATCTAATTTGT
Found at i:17344267 original size:121 final size:121
Alignment explanation
Indices: 17344053--17344295 Score: 414
Period size: 121 Copynumber: 2.0 Consensus size: 121
17344043 ATGGACCCAG
*
17344053 TAGCCATGATTATCCCCTAATCAAACTTCTTTTTGGCTGACGCCCAGGTCCCACCAGTTATTACA
1 TAGCCATGATTATCCCCTAATCAAACTTCTTTTTGGCTAACGCCCAGGTCCCACCAGTTATTACA
17344118 TTAATAATTCATACAATGGGCTTGTTATTTACATCATTTCATTAGTCATCCCTTTA
66 TTAATAATTCATACAATGGGCTTGTTATTTACATCATTTCATTAGTCATCCCTTTA
* * * **
17344174 TAGCCATGATTGTCCCTTAATCAAACTTCTTTTTGGCTAATGCTTAGGTCCCACCAGTTATTACA
1 TAGCCATGATTATCCCCTAATCAAACTTCTTTTTGGCTAACGCCCAGGTCCCACCAGTTATTACA
* *
17344239 TTAATAATTCCTACAATGGGCTTGTTATTTACATCATTTCGTTAGTCATCCCTTTA
66 TTAATAATTCATACAATGGGCTTGTTATTTACATCATTTCATTAGTCATCCCTTTA
17344295 T
1 T
17344296 TTGAACCTCT
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
121 114 1.00
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (121 bp):
TAGCCATGATTATCCCCTAATCAAACTTCTTTTTGGCTAACGCCCAGGTCCCACCAGTTATTACA
TTAATAATTCATACAATGGGCTTGTTATTTACATCATTTCATTAGTCATCCCTTTA
Found at i:17350112 original size:22 final size:22
Alignment explanation
Indices: 17350086--17350133 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
17350076 AGAAGTTCGA
*
17350086 TTTCTCTTAAATAAGATTTTAT
1 TTTCTCTTAAATAAGATTTCAT
17350108 TTTCTCTTAAATAAGATTTCAT
1 TTTCTCTTAAATAAGATTTCAT
17350130 TTTC
1 TTTC
17350134 AAAATTTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTCTCTTAAATAAGATTTCAT
Found at i:17354257 original size:2 final size:2
Alignment explanation
Indices: 17354252--17354308 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
17354242 GTAGACATAA
17354252 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17354294 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
17354309 AACTTTTGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17354712 original size:16 final size:16
Alignment explanation
Indices: 17354654--17354714 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
17354644 CTTCTATCAT
17354654 TAACTAGATTCATATAGAGA
1 TAACTAGATTC--AT-GA-A
* *
17354674 TAACTAGATTCTTGTA
1 TAACTAGATTCATGAA
* *
17354690 TAGCTAGTTTCATGAA
1 TAACTAGATTCATGAA
17354706 TAACTAGAT
1 TAACTAGAT
17354715 GAATGAATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
16 20 0.61
17 1 0.03
18 1 0.03
20 11 0.33
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (16 bp):
TAACTAGATTCATGAA
Found at i:17364036 original size:202 final size:198
Alignment explanation
Indices: 17363496--17364048 Score: 524
Period size: 202 Copynumber: 2.7 Consensus size: 198
17363486 TAATGTGACA
* * * * * * *
17363496 ATTTACC-TTGTCATTAATATATCAGATTTTATCATTCATTTTGTGATGATTATAACCTTCAATG
1 ATTTACCTTTATCACTAACATATCAGATTTTATCATT-TTTTTGTGACGATTATAGCTTTCAATG
* * * * *
17363560 ACATTATTC-TTTATAAATAGCTGACGAAAATTAATGTTATATAAAAAAAACATAA-TGAGATAT
65 AC-TT-TTCTTTTATAAATAGCTGACGAAAACTAATGTAAAAAAAAAAAAACATAAGTGACAT-T
* * * *
17363623 TTGATTTTATTGTCA-CGTTTGATATTATCTTATAATCATTCGTGACTATAATTGTGTCACCAAT
127 TT-ATTTTATTGTCATAG-TAGACATTATCTTACAATCATTCGTGACTATAATTGTGTCACCAAT
* **
17363687 ATTATGACG
190 ACTACAACG
* * *
17363696 ATTTACCTTTGTCACTAATATATAAGATTTTATCATTTATTTTGTGACGATTATAGCCTTT-AAT
1 ATTTACCTTTATCACTAACATATCAGATTTTATCATTT-TTTTGTGACGATTATAG-CTTTCAAT
* * * * ** ** **
17363760 GATTTTTTTGTTTATAAATAGTTGACGAAAACTAATGTCACAAAAATTAATGCATAAGGTGATGT
64 GACTTTTCT-TTTATAAATAGCTGACGAAAACTAATGT-AAAAAAAAAAAAACATAA-GTGACAT
* * * * *
17363825 TTGATTTTATTATCATAGTAGACATTATCTTACAATCATTGGTGA-TGATAATTTTGTCACTAAT
126 TTTATTTTATTGTCATAGTAGACATTATCTTACAATCATTCGTGACT-ATAATTGTGTCACCAAT
17363889 ACTACAACG
190 ACTACAACG
* * * *
17363898 ATTTACTTTCTATCACTAACATATCAGATTTTCTCCTTTTTTTGTGACGAATATAGCTTTCAATG
1 ATTTACCTT-TATCACTAACATATCAGATTTTATCATTTTTTTGTGACGATTATAGCTTTCAATG
* *
17363963 ACTTTTCTTTTCATAAATAACTAACGAAAACTAATGTAAAAAAAAAAAAAACATAGAGTGACATT
65 ACTTTTCTTTT-ATAAATAGCTGACGAAAACTAATGT-AAAAAAAAAAAAACATA-AGTGACATT
*
17364028 TTATTTTATTGTCATGGTAGA
127 TTATTTTATTGTCATAGTAGA
17364049 TTTACAATAG
Statistics
Matches: 284, Mismatches: 55, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
199 2 0.01
200 9 0.03
201 81 0.29
202 160 0.56
203 28 0.10
204 4 0.01
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.41
Consensus pattern (198 bp):
ATTTACCTTTATCACTAACATATCAGATTTTATCATTTTTTTGTGACGATTATAGCTTTCAATGA
CTTTTCTTTTATAAATAGCTGACGAAAACTAATGTAAAAAAAAAAAAACATAAGTGACATTTTAT
TTTATTGTCATAGTAGACATTATCTTACAATCATTCGTGACTATAATTGTGTCACCAATACTACA
ACG
Found at i:17369202 original size:37 final size:37
Alignment explanation
Indices: 17369108--17369230 Score: 149
Period size: 37 Copynumber: 3.3 Consensus size: 37
17369098 AAACCTTTGT
* * *
17369108 CCTTATTTTTAAAGTTGTGTGCCTTAGTGTTAAGGAG
1 CCTTATTTTTAAAGTTGTGTGCCTTTGTGTGAAAGAG
* *
17369145 CCCTTTATTTTTAAAATTGTGTGCCTTTTTGTGAAAGAG
1 -CC-TTATTTTTAAAGTTGTGTGCCTTTGTGTGAAAGAG
* *
17369184 CCTTATTTTTAAAGTTGTGTACCTTTGTGTGAAATAG
1 CCTTATTTTTAAAGTTGTGTGCCTTTGTGTGAAAGAG
*
17369221 CCCT-TTTTTA
1 CCTTATTTTTA
17369231 TTTTTTTAAG
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 6 0.08
37 34 0.46
38 4 0.05
39 30 0.41
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (37 bp):
CCTTATTTTTAAAGTTGTGTGCCTTTGTGTGAAAGAG
Found at i:17369625 original size:3 final size:3
Alignment explanation
Indices: 17369617--17369659 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
17369607 TTATGTTTTG
17369617 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
17369660 GTATATATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17377055 original size:21 final size:21
Alignment explanation
Indices: 17377030--17377090 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
17377020 AATAGGCAAT
* *
17377030 TACATCATATAAAATAAAAAA
1 TACATCAAATAAAAGAAAAAA
* *
17377051 TACATCAAATAATAGAAGAAA
1 TACATCAAATAAAAGAAAAAA
*
17377072 TACATCAAATAATAGAAAA
1 TACATCAAATAAAAGAAAA
17377091 TTAAAACAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (21 bp):
TACATCAAATAAAAGAAAAAA
Found at i:17378687 original size:55 final size:55
Alignment explanation
Indices: 17378615--17378729 Score: 151
Period size: 55 Copynumber: 2.1 Consensus size: 55
17378605 ATTGATAGAC
* * * * *
17378615 CAAGATCTAAGCCACATCCAA-TAATAGCTAATGGTAAAAACACATTTGAATATAT
1 CAAGATCTAAGCCACATCAAACAAATAGCAAATAGTAAAAACACATATG-ATATAT
* *
17378670 CAAGATTTAAGTCACATCAAACAAATAGCAAATAGTAAAAACACATATGATATAT
1 CAAGATCTAAGCCACATCAAACAAATAGCAAATAGTAAAAACACATATGATATAT
17378725 CAAGA
1 CAAGA
17378730 ACATTTAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
55 29 0.56
56 23 0.44
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.23
Consensus pattern (55 bp):
CAAGATCTAAGCCACATCAAACAAATAGCAAATAGTAAAAACACATATGATATAT
Found at i:17379289 original size:17 final size:17
Alignment explanation
Indices: 17379267--17379308 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
17379257 ATTATAAAAT
17379267 ATGACTACGTTTTTAAG
1 ATGACTACGTTTTTAAG
*
17379284 ATGACTACTTTTTTAAG
1 ATGACTACGTTTTTAAG
*
17379301 ATAACTAC
1 ATGACTAC
17379309 ATTATGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (17 bp):
ATGACTACGTTTTTAAG
Found at i:17382031 original size:23 final size:24
Alignment explanation
Indices: 17382005--17382062 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
17381995 AATACATATA
*
17382005 TAAAATTTTAAAATCTC-AAACTT
1 TAAAAATTTAAAATCTCAAAACTT
17382028 TAAAAATTTAAAATCTCAAAACTT
1 TAAAAATTTAAAATCTCAAAACTT
17382052 TAAAAATTTAA
1 TAAAAATTTAA
17382063 TAAGTTTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 16 0.48
24 17 0.52
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.36
Consensus pattern (24 bp):
TAAAAATTTAAAATCTCAAAACTT
Found at i:17382839 original size:15 final size:15
Alignment explanation
Indices: 17382819--17382847 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17382809 TATCATATTT
17382819 GATTACTATCTTTAA
1 GATTACTATCTTTAA
17382834 GATTACTATCTTTA
1 GATTACTATCTTTA
17382848 TAAATTGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (15 bp):
GATTACTATCTTTAA
Found at i:17383395 original size:14 final size:15
Alignment explanation
Indices: 17383376--17383405 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
17383366 TAATATGTTC
17383376 AAAATAAAT-ATATA
1 AAAATAAATAATATA
17383390 AAAATAAATAATATA
1 AAAATAAATAATATA
17383405 A
1 A
17383406 TTAAAATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAATAATATA
Found at i:17383880 original size:20 final size:20
Alignment explanation
Indices: 17383855--17383893 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17383845 ACTAAAATGA
* *
17383855 AATAGTTTTAAATTTTAAAT
1 AATAGTATTAAATTATAAAT
17383875 AATAGTATTAAATTATAAA
1 AATAGTATTAAATTATAAA
17383894 CAATTATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AATAGTATTAAATTATAAAT
Found at i:17391641 original size:145 final size:144
Alignment explanation
Indices: 17391346--17391742 Score: 463
Period size: 145 Copynumber: 2.7 Consensus size: 144
17391336 TGGAAGTGTG
* * * * * *
17391346 AAATTATCAAAATACCCCTATGAGAGATATTTTTGTAATTTCACCTTTTCGAGCTCAAATTTTTA
1 AAATTATCAAAATACCCTTATAAG-GGTA-TTTTGTAATTTGACCTTTTCAAGCTCAGATTTTTA
* * * * * * *
17391411 TGATACCTTCCATATCTCAATTTCATAATATTTCATGATTTCTGGTGCATTTGAAATCACAGCAG
64 TGAAACTTTCCAAATCTCAATTTTATAATATTTCATGATTTTTGGTGCATTTGAAACCACAACAG
** * *
17391476 TACCTTGAAAATTATG
129 TACCTCAAAAAATATA
* * * *
17391492 AAATTATCAAAATACCCTTAAAAGGGTACTTTTATAATTTGACCTTTTCAAGCTCGGATTTTCAT
1 AAATTATCAAAATACCCTTATAAGGGTA-TTTTGTAATTTGACCTTTTCAAGCTCAGATTTTTAT
* * *
17391557 GAAACTTTCCAAATTTTAATTTTATAATACTTCATGATTTTTGGTGCATTTGAAACCACAACAGT
65 GAAACTTTCCAAATCTCAATTTTATAATATTTCATGATTTTTGGTGCATTTGAAACCACAACAGT
*
17391622 ACCTCAAAAAATGTA
130 ACCTCAAAAAATATA
* * * *
17391637 AAATTATC-AAATACCTTTATAAGGGTATTTTCGTAATTTGAGCTTTCCAAGCTTAGATTTTTAT
1 AAATTATCAAAATACCCTTATAAGGGTATTTT-GTAATTTGACCTTTTCAAGCTCAGATTTTTAT
* * *
17391701 GAAACTTTTCAGATCTCAATTTTATAATATTTCATAATTTTT
65 GAAACTTTCCAAATCTCAATTTTATAATATTTCATGATTTTT
17391743 AATATTTTAA
Statistics
Matches: 210, Mismatches: 40, Indels: 4
0.83 0.16 0.02
Matches are distributed among these distances:
143 4 0.02
144 79 0.38
145 106 0.50
146 21 0.10
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (144 bp):
AAATTATCAAAATACCCTTATAAGGGTATTTTGTAATTTGACCTTTTCAAGCTCAGATTTTTATG
AAACTTTCCAAATCTCAATTTTATAATATTTCATGATTTTTGGTGCATTTGAAACCACAACAGTA
CCTCAAAAAATATA
Found at i:17392666 original size:41 final size:41
Alignment explanation
Indices: 17392616--17392693 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
17392606 ATAAATTTTA
17392616 GGTTAAAGAAACACCTTAAATAATGATCATTTAAGGCATTG
1 GGTTAAAGAAACACCTTAAATAATGATCATTTAAGGCATTG
* ** * * *
17392657 GGTTGAAGAAATGCCTTAAATGATTATTATTTAAGGC
1 GGTTAAAGAAACACCTTAAATAATGATCATTTAAGGC
17392694 GTTTCTTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.32
Consensus pattern (41 bp):
GGTTAAAGAAACACCTTAAATAATGATCATTTAAGGCATTG
Found at i:17392720 original size:42 final size:40
Alignment explanation
Indices: 17392629--17392773 Score: 139
Period size: 41 Copynumber: 3.5 Consensus size: 40
17392619 TAAAGAAACA
* * * *** *
17392629 CCTTAAATAATGATCATTTAAGGCATTGGGTTGAAGAAATG
1 CCTTAAATGATTATCATTTAAGGCGTTTTCTTTAA-AAATG
* * *
17392670 CCTTAAATGATTATTATTTAAGGCGTTTCTTTTTAAAAAATA
1 CCTTAAATGATTATCATTTAAGGCGTTT-TCTTT-AAAAATG
17392712 CCTTAAATG-TTGATCATTTAAGGCGTTTTCTTTAAAAATG
1 CCTTAAATGATT-ATCATTTAAGGCGTTTTCTTTAAAAATG
* *
17392752 CCTTCAATGATGATCATTTAAG
1 CCTTAAATGATTATCATTTAAG
17392774 ATTTTTTTCC
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
40 24 0.28
41 30 0.35
42 30 0.35
43 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (40 bp):
CCTTAAATGATTATCATTTAAGGCGTTTTCTTTAAAAATG
Found at i:17396092 original size:48 final size:48
Alignment explanation
Indices: 17396020--17396206 Score: 213
Period size: 48 Copynumber: 3.9 Consensus size: 48
17396010 CTTAGTAAAG
* *
17396020 GCTCGACAACTTTAAAAAT-CATCTTGAAAAAGCTCCTCTCAATAGAA
1 GCTCAACAACTTTAAAAATCCATCTTGAAAAAGCTCCTCTCAACAGAA
*
17396067 GCTCAACAACTTTAAAAATCCATCTTG-AAAA-CTCCTCTCAGCAG-A
1 GCTCAACAACTTTAAAAATCCATCTTGAAAAAGCTCCTCTCAACAGAA
* * *
17396112 GACTCAACAACTTT-AAAATCTCATCTTGGAAAAGCTCCTCTCAGCAGAG
1 G-CTCAACAACTTTAAAAATC-CATCTTGAAAAAGCTCCTCTCAACAGAA
** * **
17396161 GCTCAACAACTTTTGAATTTTATCTTGAAAAAAGCTCCTCTCAACA
1 GCTCAACAACTTTAAAAATCCATCTTG-AAAAAGCTCCTCTCAACA
17396207 AATGCTTGAT
Statistics
Matches: 122, Mismatches: 10, Indels: 14
0.84 0.07 0.10
Matches are distributed among these distances:
45 8 0.07
46 30 0.25
47 26 0.21
48 38 0.31
49 20 0.16
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.27
Consensus pattern (48 bp):
GCTCAACAACTTTAAAAATCCATCTTGAAAAAGCTCCTCTCAACAGAA
Found at i:17396308 original size:49 final size:49
Alignment explanation
Indices: 17396252--17396745 Score: 445
Period size: 48 Copynumber: 10.3 Consensus size: 49
17396242 AAATGCTCCT
** * * *
17396252 CTCAACAACTTTTGAATTTTATCTTTGAAAAAACTTCTCTCAGTAGAGG
1 CTCAACAACTTTAAAATTTCATCTTTGAAAAAGCTTCTCTCAGCAGAGG
*
17396301 CTCAACAAC-TTAGAA----A--TTTG-AAAAGCTTCTCTCAGCA-AGG
1 CTCAACAACTTTAAAATTTCATCTTTGAAAAAGCTTCTCTCAGCAGAGG
** *
17396341 CTCAGTAACTTTAAAATTTCATCTTGGAAAAAGC-TCATCTCAGCAGAGG
1 CTCAACAACTTTAAAATTTCATCTTTGAAAAAGCTTC-TCTCAGCAGAGG
* * *
17396390 CTCAACAACTTTAAAATTTTCAT-ATTGAAAAAGCTCCTCAT-AGTAGAGG
1 CTCAACAACTTTAAAA-TTTCATCTTTGAAAAAGCTTCTC-TCAGCAGAGG
* * * *
17396439 CTCAACAAC-TTATAATTTCATCTTGGAAAAAGC-TCATTTTCAGCAGAGA
1 CTCAACAACTTTAAAATTTCATCTTTGAAAAAGCTTC--TCTCAGCAGAGG
* * *
17396488 CTCAACAACTTTTAAATTTTATC-TTGACAAAAGCTCCTCTCAGCAGAGG
1 CTCAACAACTTTAAAATTTCATCTTTGA-AAAAGCTTCTCTCAGCAGAGG
* * *
17396537 CTCAACAACTTTAAAATCTCATC-TTAAAAAAGCTTCTCTCAGTAGA-G
1 CTCAACAACTTTAAAATTTCATCTTTGAAAAAGCTTCTCTCAGCAGAGG
* * * *
17396584 CTTCAACAACTTTAAAATCTCAT-TTTGAAAAAGCTCCTTTCAGGAGAGG
1 C-TCAACAACTTTAAAATTTCATCTTTGAAAAAGCTTCTCTCAGCAGAGG
* * * *
17396633 ATCAATAACTTTAAAATTTCATC-TTGAAAAAACTCCTCTCAGCAGAGG
1 CTCAACAACTTTAAAATTTCATCTTTGAAAAAGCTTCTCTCAGCAGAGG
* * * *
17396681 CTCAACAATTTTAAAAATCTCAT-TTT-AAGAAAGCTCCTCTCAACAGAGG
1 CTCAACAACTTT-AAAATTTCATCTTTGAA-AAAGCTTCTCTCAGCAGAGG
*
17396730 CTCAATAACTTTAAAA
1 CTCAACAACTTTAAAA
17396746 ATCTCATATG
Statistics
Matches: 367, Mismatches: 51, Indels: 55
0.78 0.11 0.12
Matches are distributed among these distances:
40 10 0.03
41 20 0.05
42 4 0.01
44 1 0.00
45 1 0.00
47 14 0.04
48 147 0.40
49 145 0.40
50 24 0.07
51 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (49 bp):
CTCAACAACTTTAAAATTTCATCTTTGAAAAAGCTTCTCTCAGCAGAGG
Found at i:17396735 original size:97 final size:97
Alignment explanation
Indices: 17396252--17396745 Score: 496
Period size: 97 Copynumber: 5.2 Consensus size: 97
17396242 AAATGCTCCT
* ** * * * * *
17396252 CTCAACAACTTTTGAATTTTATCTTTGAAAAAACTTCTCTCAGTAGAGGCTCAACAAC-TTAGAA
1 CTCAATAACTTTAAAATTTCATCTTGGAAAAAACTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
*
17396316 ----AT-TTG-AAAAGCTTCTCTCAGCA-AGG
66 TCTCATATTGAAAAAGCTCCTCTCAGCAGAGG
* * *
17396341 CTCAGTAACTTTAAAATTTCATCTTGGAAAAAGCTCATCTCAGCAGAGGCTCAACAACTTTAAAA
1 CTCAATAACTTTAAAATTTCATCTTGGAAAAAACTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
* *
17396406 TTTTCATATTGAAAAAGCTCCTCAT-AGTAGAGG
66 -TCTCATATTGAAAAAGCTCCTC-TCAGCAGAGG
* * * * * * *
17396439 CTCAACAAC-TTATAATTTCATCTTGGAAAAAGCTCATTTTCAGCAGAGACTCAACAACTTTTAA
1 CTCAATAACTTTAAAATTTCATCTTGGAAAAAACTC-CTCTCAGCAGAGGCTCAACAACTTTAAA
* * *
17396503 ATTTTATCTTGACAAAAGCTCCTCTCAGCAGAGG
65 ATCTCATATTGA-AAAAGCTCCTCTCAGCAGAGG
* * * *
17396537 CTCAACAACTTTAAAATCTCATCTT--AAAAAAGCTTCTCTCAGTAGA-GCTTCAACAACTTTAA
1 CTCAATAACTTTAAAATTTCATCTTGGAAAAAA-CTCCTCTCAGCAGAGGC-TCAACAACTTTAA
* * *
17396599 AATCTCATTTTGAAAAAGCTCCTTTCAGGAGAGG
64 AATCTCATATTGAAAAAGCTCCTCTCAGCAGAGG
* *
17396633 ATCAATAACTTTAAAATTTCATCTT-GAAAAAACTCCTCTCAGCAGAGGCTCAACAATTTTAAAA
1 CTCAATAACTTTAAAATTTCATCTTGGAAAAAACTCCTCTCAGCAGAGGCTCAACAACTTT-AAA
* *
17396697 ATCTCAT-TTTAAGAAAGCTCCTCTCAACAGAGG
65 ATCTCATATTGAA-AAAGCTCCTCTCAGCAGAGG
17396730 CTCAATAACTTTAAAA
1 CTCAATAACTTTAAAA
17396746 ATCTCATATG
Statistics
Matches: 337, Mismatches: 48, Indels: 32
0.81 0.12 0.08
Matches are distributed among these distances:
89 48 0.14
90 5 0.01
95 2 0.01
96 71 0.21
97 133 0.39
98 65 0.19
99 13 0.04
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (97 bp):
CTCAATAACTTTAAAATTTCATCTTGGAAAAAACTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
TCTCATATTGAAAAAGCTCCTCTCAGCAGAGG
Found at i:17396752 original size:49 final size:48
Alignment explanation
Indices: 17396321--17396745 Score: 482
Period size: 48 Copynumber: 8.8 Consensus size: 48
17396311 TAGAAATTTG
* **
17396321 AAAAGCTTCTCTCAGCA-AGGCTCAGTAACTTTAAAATTTCATCTTGGA
1 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTT-GA
* *
17396369 AAAAGCTCATCTCAGCAGAGGCTCAACAACTTTAAAATTTTCATATTGA
1 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TTTCATCTTGA
* *
17396418 AAAAGCTCCTCAT-AGTAGAGGCTCAACAAC-TTATAATTTCATCTTGGA
1 AAAAGCTCCTC-TCAGCAGAGGCTCAACAACTTTAAAATTTCATCTT-GA
* * * * *
17396466 AAAAGCTCATTTTCAGCAGAGACTCAACAACTTTTAAATTTTATCTTGA
1 AAAAGCTC-CTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGA
* *
17396515 CAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTAA
1 -AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGA
* * * *
17396564 AAAAGCTTCTCTCAGTAGA-GCTTCAACAACTTTAAAATCTCATTTTGA
1 AAAAGCTCCTCTCAGCAGAGGC-TCAACAACTTTAAAATTTCATCTTGA
* * * *
17396612 AAAAGCTCCTTTCAGGAGAGGATCAATAACTTTAAAATTTCATCTTGA
1 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGA
* * * *
17396660 AAAAACTCCTCTCAGCAGAGGCTCAACAATTTTAAAAATCTCAT-TTTA
1 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATTTCATCTTGA
* *
17396708 AGAAAGCTCCTCTCAACAGAGGCTCAATAACTTTAAAA
1 A-AAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
17396746 ATCTCATATG
Statistics
Matches: 319, Mismatches: 46, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
47 10 0.03
48 146 0.46
49 134 0.42
50 29 0.09
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.29
Consensus pattern (48 bp):
AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGA
Found at i:17397014 original size:19 final size:19
Alignment explanation
Indices: 17396984--17397027 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
17396974 GACCATTGTA
17396984 TTCTTC-CTACCGATACTT
1 TTCTTCACTACCGATACTT
17397002 TTCTTCACTACCGATACTT
1 TTCTTCACTACCGATACTT
17397021 TTCTTCA
1 TTCTTCA
17397028 AAAGTCTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.18, C:0.32, G:0.05, T:0.45
Consensus pattern (19 bp):
TTCTTCACTACCGATACTT
Found at i:17400484 original size:15 final size:16
Alignment explanation
Indices: 17400456--17400486 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
17400446 ATTTTATTAA
17400456 TTATTTTATTTAATTT
1 TTATTTTATTTAATTT
17400472 TTATTTT-TTTAATTT
1 TTATTTTATTTAATTT
17400487 AAATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTTTATTTAATTT
Found at i:17400679 original size:18 final size:18
Alignment explanation
Indices: 17400656--17400698 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
17400646 TCTCTCATTT
*
17400656 TTTATTACTTA-TTCTTAA
1 TTTATTAATTAGTT-TTAA
*
17400674 TTTATTAATTAGTTTTTA
1 TTTATTAATTAGTTTTAA
17400692 TTTATTA
1 TTTATTA
17400699 TTTTATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTAATTAGTTTTAA
Found at i:17400736 original size:19 final size:20
Alignment explanation
Indices: 17400691--17400738 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
17400681 ATTAGTTTTT
* *
17400691 ATTTATTATTTTATATAAAA
1 ATTTTTTATTGTATATAAAA
**
17400711 AAATTTTATTGTAT-TAAAA
1 ATTTTTTATTGTATATAAAA
17400730 ATTTTTTAT
1 ATTTTTTAT
17400739 AAATACTCCA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTTTTATTGTATATAAAA
Found at i:17400863 original size:10 final size:10
Alignment explanation
Indices: 17400843--17400877 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
17400833 GGATAAAAAT
17400843 TTTTTTAATTA
1 TTTTTT-ATTA
17400854 TTTTTTATTA
1 TTTTTTATTA
*
17400864 TTCTTTATTA
1 TTTTTTATTA
17400874 TTTT
1 TTTT
17400878 AAAAGATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:17404186 original size:16 final size:17
Alignment explanation
Indices: 17404156--17404190 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
17404146 ATATCTACCA
17404156 TTTTGAAAAGTTATATTT
1 TTTTGAAAAG-TATATTT
17404174 TTTTGAAAA-TATATTT
1 TTTTGAAAAGTATATTT
17404190 T
1 T
17404191 CAAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (17 bp):
TTTTGAAAAGTATATTT
Found at i:17404241 original size:20 final size:21
Alignment explanation
Indices: 17404212--17404250 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
17404202 AACACTTTTC
17404212 AAAAATAAATTGTAAAAAATG
1 AAAAATAAATTGTAAAAAATG
*
17404233 AAAAA-AAATTTTAAAAAA
1 AAAAATAAATTGTAAAAAA
17404251 AATTACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (21 bp):
AAAAATAAATTGTAAAAAATG
Found at i:17404350 original size:23 final size:24
Alignment explanation
Indices: 17404305--17404351 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
17404295 TAAAAAAGTT
*
17404305 ATTATTAAAAAATTATAAATTTTAAA
1 ATTAATAAAAAATTAT--ATTTTAAA
17404331 ATTAATAAAAAATTAT-TTTTA
1 ATTAATAAAAAATTATATTTTA
17404352 TTATTTTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
26 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTAATAAAAAATTATATTTTAAA
Found at i:17404973 original size:22 final size:22
Alignment explanation
Indices: 17404948--17404991 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17404938 TGTACATAAA
* *
17404948 ATTACAATTATATGTATATTTT
1 ATTACAAATATATGTACATTTT
*
17404970 ATTATAAATATATGTACATTTT
1 ATTACAAATATATGTACATTTT
17404992 TTGAGACCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (22 bp):
ATTACAAATATATGTACATTTT
Found at i:17415686 original size:15 final size:16
Alignment explanation
Indices: 17415658--17415688 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
17415648 ATTTTATTAA
17415658 TTATTTTATTTAATTT
1 TTATTTTATTTAATTT
17415674 TTATTTT-TTTAATTT
1 TTATTTTATTTAATTT
17415689 AAATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTTTATTTAATTT
Found at i:17416064 original size:10 final size:10
Alignment explanation
Indices: 17416049--17416082 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
17416039 GATAAAAATT
*
17416049 TTTTTTTTTA
1 TTTTTTATTA
17416059 TTTTTTATTA
1 TTTTTTATTA
*
17416069 TTCTTTATTA
1 TTTTTTATTA
17416079 TTTT
1 TTTT
17416083 AAAAGATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:17431215 original size:18 final size:17
Alignment explanation
Indices: 17431192--17431226 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
17431182 ATGTGTGTGA
17431192 ATTTTTCTTTTGTTTTTG
1 ATTTTT-TTTTGTTTTTG
*
17431210 ATTTTTTTTTTTTTTTG
1 ATTTTTTTTTGTTTTTG
17431227 GAATCAAAAT
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:0.06, C:0.03, G:0.09, T:0.83
Consensus pattern (17 bp):
ATTTTTTTTTGTTTTTG
Found at i:17432001 original size:16 final size:16
Alignment explanation
Indices: 17431982--17432013 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17431972 ATTTTATTAA
17431982 TTATTTTATTTAATTT
1 TTATTTTATTTAATTT
*
17431998 TTATTTTTTTTAATTT
1 TTATTTTATTTAATTT
17432014 AAATTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TTATTTTATTTAATTT
Found at i:17432210 original size:18 final size:18
Alignment explanation
Indices: 17432187--17432229 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
17432177 TCTCTCATTT
*
17432187 TTTATTACTTA-TTCTTAA
1 TTTATTAATTAGTT-TTAA
*
17432205 TTTATTAATTAGTTTTTA
1 TTTATTAATTAGTTTTAA
17432223 TTTATTA
1 TTTATTA
17432230 TTTTATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTAATTAGTTTTAA
Found at i:17432251 original size:21 final size:21
Alignment explanation
Indices: 17432222--17432261 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17432212 ATTAGTTTTT
*
17432222 ATTTATTATTTTATATAAAAAA
1 ATTTATTATTGTAT-TAAAAAA
17432244 ATTT-TTATTGTATTAAAA
1 ATTTATTATTGTATTAAAA
17432262 TTTTTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
ATTTATTATTGTATTAAAAAA
Found at i:17432399 original size:10 final size:9
Alignment explanation
Indices: 17432375--17432406 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
17432365 GATAAAAATT
17432375 TTTTTATTA
1 TTTTTATTA
17432384 TTTTTATTA
1 TTTTTATTA
17432393 TTCTTTATTA
1 TT-TTTATTA
17432403 TTTT
1 TTTT
17432407 AAAAGATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTATTA
Found at i:17436041 original size:14 final size:15
Alignment explanation
Indices: 17436017--17436047 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
17436007 AAATATTATG
17436017 ATTTCTCAAAAATAA
1 ATTTCTCAAAAATAA
17436032 ATTT-TCAAAAATAA
1 ATTTCTCAAAAATAA
17436046 AT
1 AT
17436048 GTTATTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTTCTCAAAAATAA
Found at i:17443197 original size:13 final size:13
Alignment explanation
Indices: 17443175--17443227 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 13
17443165 TACTGCCCTA
*
17443175 AATAACAAAGAAC
1 AATAAAAAAGAAC
17443188 AATAAAAAAGAAC
1 AATAAAAAAGAAC
17443201 TAAATAAGAACAAAGAAC
1 --AAT-A-AA-AAAGAAC
17443219 AATAAAAAA
1 AATAAAAAA
17443228 TAAAAAATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
13 15 0.44
14 2 0.06
15 4 0.12
16 4 0.12
17 2 0.06
18 7 0.21
ACGTcount: A:0.74, C:0.09, G:0.08, T:0.09
Consensus pattern (13 bp):
AATAAAAAAGAAC
Found at i:17455897 original size:16 final size:16
Alignment explanation
Indices: 17455878--17455925 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
17455868 TTTATTAAAA
17455878 TATAAATTTAAAATTT
1 TATAAATTTAAAATTT
*
17455894 TATAATTTTTAAAATTT
1 TATAA-ATTTAAAATTT
* *
17455911 TTTAAA-ATAAAATTT
1 TATAAATTTAAAATTT
17455926 AGTTAGAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 8 0.30
16 5 0.19
17 14 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATAAATTTAAAATTT
Found at i:17456185 original size:14 final size:15
Alignment explanation
Indices: 17456161--17456193 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
17456151 ATTCTTTTGC
17456161 TATTAAATTAATTTT
1 TATTAAATTAATTTT
17456176 TATT-AATTAATTTT
1 TATTAAATTAATTTT
17456190 TATT
1 TATT
17456194 TTTATGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTAAATTAATTTT
Found at i:17461291 original size:6 final size:7
Alignment explanation
Indices: 17461276--17461305 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
17461266 ATTGGATTAA
17461276 TTTTATT
1 TTTTATT
17461283 TTTTATT
1 TTTTATT
17461290 TTTTATT
1 TTTTATT
*
17461297 TTTCATT
1 TTTTATT
17461304 TT
1 TT
17461306 CTTACTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTATT
Found at i:17461295 original size:14 final size:14
Alignment explanation
Indices: 17461276--17461315 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
17461266 ATTGGATTAA
*
17461276 TTTTATTTTTTATT
1 TTTTATTTTTCATT
17461290 TTTTATTTTTCATT
1 TTTTATTTTTCATT
*
17461304 TTCTTACTTTTC
1 TT-TTATTTTTC
17461316 TTGTCTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTTTTCATT
Found at i:17462940 original size:28 final size:28
Alignment explanation
Indices: 17462909--17462981 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
17462899 TCTAAATTGA
*
17462909 TTTGATTTTTAATTACGATTT-AAATAAT
1 TTTGATTTTTAATTA-AATTTAAAATAAT
* * *
17462937 TTTGATATTTGATTAAATTTAAAATTAT
1 TTTGATTTTTAATTAAATTTAAAATAAT
* *
17462965 TTTAATTTGTAATTAAA
1 TTTGATTTTTAATTAAA
17462982 AGGAATTATC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
27 4 0.11
28 32 0.89
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.53
Consensus pattern (28 bp):
TTTGATTTTTAATTAAATTTAAAATAAT
Found at i:17463649 original size:9 final size:9
Alignment explanation
Indices: 17463635--17463700 Score: 60
Period size: 9 Copynumber: 7.3 Consensus size: 9
17463625 AATACATATA
17463635 TAAAAATTT
1 TAAAAATTT
*
17463644 TAAAAATCT
1 TAAAAATTT
* *
17463653 CAAAACTTT
1 TAAAAATTT
*
17463662 AAAAAATTT
1 TAAAAATTT
*
17463671 TAAAAATCT
1 TAAAAATTT
* *
17463680 CAAAACTTT
1 TAAAAATTT
*
17463689 AAAAAATTT
1 TAAAAATTT
17463698 TAA
1 TAA
17463701 TAAGTTTTTG
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAAATTT
Found at i:17463668 original size:27 final size:27
Alignment explanation
Indices: 17463636--17463700 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
17463626 ATACATATAT
17463636 AAAAATTTTAAAAATCTCAAAACTTTA
1 AAAAATTTTAAAAATCTCAAAACTTTA
17463663 AAAAATTTTAAAAATCTCAAAACTTTA
1 AAAAATTTTAAAAATCTCAAAACTTTA
17463690 AAAAATTTTAA
1 AAAAATTTTAA
17463701 TAAGTTTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (27 bp):
AAAAATTTTAAAAATCTCAAAACTTTA
Found at i:17465308 original size:14 final size:15
Alignment explanation
Indices: 17465289--17465318 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
17465279 TAATATGTTC
17465289 AAAATAAAT-ATATA
1 AAAATAAATAATATA
17465303 AAAATAAATAATATA
1 AAAATAAATAATATA
17465318 A
1 A
17465319 TTAAAATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAATAATATA
Found at i:17465794 original size:20 final size:20
Alignment explanation
Indices: 17465769--17465807 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17465759 ACTGAAATGA
* *
17465769 AATAGTTTTAAATTTTAAAT
1 AATAGTATTAAATTATAAAT
17465789 AATAGTATTAAATTATAAA
1 AATAGTATTAAATTATAAA
17465808 CAATTATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AATAGTATTAAATTATAAAT
Found at i:17469061 original size:15 final size:15
Alignment explanation
Indices: 17469041--17469080 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
17469031 ACAATGTTCT
*
17469041 CAAATTTTAGATCTA
1 CAAATTATAGATCTA
17469056 CAAATTATAGATCTA
1 CAAATTATAGATCTA
17469071 CAAATTATAG
1 CAAATTATAG
17469081 TAACTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.35
Consensus pattern (15 bp):
CAAATTATAGATCTA
Found at i:17473567 original size:145 final size:145
Alignment explanation
Indices: 17473264--17473662 Score: 519
Period size: 145 Copynumber: 2.7 Consensus size: 145
17473254 GTTGTATTTG
* * * *
17473264 AAAGTGTGAAATTATCAAAATACCCCTATGAGAGATATTTTTGTAATTTGACCTTTTCGAGCTCA
1 AAAGTGTGAAATTATCAAAATACCCTTATAAG-GGTATTTTTGTAATTTGACCTTTTCAAGCTCA
* * * * *
17473329 AATTTTTATGATACCTTCAATATCTCAATTTCATAATATTTCATGATTTCTGGTGCATTTGAAAT
65 GATTTTTATGAAACTTTCCATATCTCAATTTCATAATATTTCATGATTTCTGGTGCATTTGAAAC
** *
17473394 CACAGCAATACCTTAA
130 CACAAAAATACCTCAA
* * * * *
17473410 AAATTATGAAATTATCAAAATACCCTTAAAAGGGTATTTTTATAATTTGACCTTTTCAAGCTCGG
1 AAAGTGTGAAATTATCAAAATACCCTTATAAGGGTATTTTTGTAATTTGACCTTTTCAAGCTCAG
* * * * *
17473475 ATTTTCATGAAACTTTCCATATTTTAATTTCATAATACTTCATGATTTTTGGTGCATTTGAAACC
66 ATTTTTATGAAACTTTCCATATCTCAATTTCATAATATTTCATGATTTCTGGTGCATTTGAAACC
17473540 ACAAAAATACCTCAA
131 ACAAAAATACCTCAA
* * * * *
17473555 AAAGTGTAAAATTATCAAAATACCTTTATAAGGGTATTTTCGTAATTTGACCTTCTCAAGCTTAG
1 AAAGTGTGAAATTATCAAAATACCCTTATAAGGGTATTTTTGTAATTTGACCTTTTCAAGCTCAG
* * *
17473620 ATTTTTATGAAACTTTTCAGATCTCAATTTTATAATATTTCAT
66 ATTTTTATGAAACTTTCCATATCTCAATTTCATAATATTTCAT
17473663 AATTGTTAAT
Statistics
Matches: 214, Mismatches: 39, Indels: 1
0.84 0.15 0.00
Matches are distributed among these distances:
145 187 0.87
146 27 0.13
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (145 bp):
AAAGTGTGAAATTATCAAAATACCCTTATAAGGGTATTTTTGTAATTTGACCTTTTCAAGCTCAG
ATTTTTATGAAACTTTCCATATCTCAATTTCATAATATTTCATGATTTCTGGTGCATTTGAAACC
ACAAAAATACCTCAA
Found at i:17474300 original size:62 final size:61
Alignment explanation
Indices: 17474106--17474305 Score: 167
Period size: 62 Copynumber: 3.3 Consensus size: 61
17474096 TACAAAAAAT
* * * ** * *
17474106 TGAATGGAGTTATTTAAGGCATTTCTGGCCAAAAATGCCTTTAATAATCCCCTTCAATTTTTA
1 TGAAGGGA-TTATTCAAGGCATTTTTGGTAAAAAAT-CCTTGAATAATCCCCTTTAATTTTTA
* ** ** *
17474169 TGAGGGGATTATT---GGTGTTTTTGGTAAAAAATGCCTTGAATAATCCTATCTAATTTTT-
1 TGAAGGGATTATTCAAGGCATTTTTGGTAAAAAAT-CCTTGAATAATCCCCTTTAATTTTTA
*
17474227 TGAAAGGGATTATTCAAGGCATTTTTGGCTAGAAACAT-CTTGAATAATCCCCTTTAATTTTTA
1 TG-AAGGGATTATTCAAGGCATTTTTGG-TA-AAAAATCCTTGAATAATCCCCTTTAATTTTTA
* *
17474290 TGAAGAGATTACTCAA
1 TGAAGGGATTATTCAA
17474306 TGCGTTACAT
Statistics
Matches: 109, Mismatches: 21, Indels: 15
0.75 0.14 0.10
Matches are distributed among these distances:
58 2 0.02
59 45 0.41
62 47 0.43
63 10 0.09
64 5 0.05
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (61 bp):
TGAAGGGATTATTCAAGGCATTTTTGGTAAAAAATCCTTGAATAATCCCCTTTAATTTTTA
Found at i:17474641 original size:42 final size:41
Alignment explanation
Indices: 17474553--17474706 Score: 157
Period size: 42 Copynumber: 3.7 Consensus size: 41
17474543 TAAAGAAACA
* ** *** *
17474553 CCTTAAATAATGATCATTTAAGGTATTTGGGTTGAAGAAATG
1 CCTTAAATGATGATCATTTAAGGCGTTTTTCTT-AAAAAATG
* * *
17474595 CCTTAAATGATCATTATTTAAGGCGTTTCTTCTTAAAAAATA
1 CCTTAAATGATGATCATTTAAGGCGTTT-TTCTTAAAAAATG
* *
17474637 CCTTAAATGTTGATCATTTAAGGCG-TTTTCTTTAAAAATG
1 CCTTAAATGATGATCATTTAAGGCGTTTTTCTTAAAAAATG
* *
17474677 CCTTCAATGATGATCATTTAAGACGTTTTT
1 CCTTAAATGATGATCATTTAAGGCGTTTTT
17474707 TTCCCAAAAA
Statistics
Matches: 92, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
40 33 0.36
41 6 0.07
42 51 0.55
43 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (41 bp):
CCTTAAATGATGATCATTTAAGGCGTTTTTCTTAAAAAATG
Found at i:17478019 original size:48 final size:48
Alignment explanation
Indices: 17477943--17478641 Score: 704
Period size: 49 Copynumber: 14.6 Consensus size: 48
17477933 ATCTTAGTAA
* * * **
17477943 AGGCTCGATAACTTTAAAA-ATCATCTTGAAAAAGCTCCTCTCAATAG
1 AGGCTCAACAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTCAGCAG
* *
17477990 AGGCTCAACAACTTTAAAAATCCATCTTG-AAAA-CTCCTCTCAGCAG
1 AGGCTCAACAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTCAGCAG
* * * *
17478036 A-GATCAACAACTTTAAAATCTCATCTTGGAAAATCTCCTCTCAGCAG
1 AGGCTCAACAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTCAGCAG
** * * **
17478083 AGGCTCAACAACTTTTGAATTTTATCTTGAAAAAAGCTCCTTTCAATAG
1 AGGCTCAACAACTTTAAAATTTCATCTTG-AAAAAGCTCCTCTCAGCAG
* * * * * **
17478132 AGGCTCGATAATTTTTGAAAATTTAAAATC-TAAAAAATGCTCCTCTCAATAG
1 AGGCTCAACAA-CTTT-AAAATTT--CATCTTGAAAAA-GCTCCTCTCAGCAG
* * ** * * *
17478184 AAGCTCAATAACTTTTGAATTTTATCTTGAAAAAAAG-TTCTCTCA-TAG
1 AGGCTCAACAACTTTAAAATTTCATCTTG--AAAAAGCTCCTCTCAGCAG
*
17478232 AGGCTCAACAACTTTAGAA----AT-TTGAAAAAGCTCCTCTCAGCAG
1 AGGCTCAACAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTCAGCAG
* *
17478275 AGGCTCAACAACTTTAAAATTTCATATTGGAAAAAGCTCATCTCAGCAG
1 AGGCTCAACAACTTTAAAATTTCATCTT-GAAAAAGCTCCTCTCAGCAG
* *
17478324 AGGCTCAACAACTTTAAAATTTTCATATTGAAAAAGCTCCTCTTAGCAG
1 AGGCTCAACAACTTTAAAA-TTTCATCTTGAAAAAGCTCCTCTCAGCAG
* *
17478373 AGGCTCAACAACTTTAAAATTTCATCTCGAAAAAAGCTCCTTTCAGCAG
1 AGGCTCAACAACTTTAAAATTTCATCTTG-AAAAAGCTCCTCTCAGCAG
* ** *
17478422 AGACTCAACAACTTTTGAATTTTATCTTGACAAAAGCTCCTCTCAGCAG
1 AGGCTCAACAACTTTAAAATTTCATCTTGA-AAAAGCTCCTCTCAGCAG
* * **
17478471 AGGCTCAACAACTTTAAAATCTCATCTTGGAAAAGCTCCTCTCAATAG
1 AGGCTCAACAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTCAGCAG
* * *
17478519 AGGCTCAACAACTTTAAAATCTCAT-TTGAAAAAGCTCCTTTCAGGAG
1 AGGCTCAACAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTCAGCAG
* * *
17478566 AAGATCAATAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTCAGCAG
1 AGGCTCAACAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTCAGCAG
* *
17478614 AGGCTCAACAATTTTAAAAATCTCATCT
1 AGGCTCAACAACTTT-AAAATTTCATCT
17478642 GTTCTCAAAA
Statistics
Matches: 548, Mismatches: 78, Indels: 50
0.81 0.12 0.07
Matches are distributed among these distances:
41 6 0.01
42 7 0.01
43 23 0.04
44 2 0.00
45 23 0.04
46 16 0.03
47 76 0.14
48 134 0.24
49 199 0.36
50 18 0.03
51 18 0.03
52 23 0.04
53 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (48 bp):
AGGCTCAACAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTCAGCAG
Found at i:17482241 original size:17 final size:18
Alignment explanation
Indices: 17482218--17482262 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
17482208 TAGAGGTTCT
*
17482218 AGATTCATAAAG-GTTTC
1 AGATTCATAAAGACTTTC
* *
17482235 AGGTTCACAAAGACTTTC
1 AGATTCATAAAGACTTTC
17482253 AGATTCATAA
1 AGATTCATAA
17482263 GAATAGAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (18 bp):
AGATTCATAAAGACTTTC
Found at i:17482343 original size:86 final size:86
Alignment explanation
Indices: 17482181--17482417 Score: 307
Period size: 86 Copynumber: 2.8 Consensus size: 86
17482171 NNNNNNNNNN
* * *
17482181 GAAAATTTCACAAGATTTCAAGTTTCGTAGAGGTTCTAGATTCATAAAGGTTTCAGGTTCACAAA
1 GAAAAATTCACAAGATTTCAAGTTTCGTAGAGGTTCTAGATTTACAAAGGTTTCAGGTTCACAAA
17482246 GACTTTCAGATTCATAAGAAT
66 GACTTTCAGATTCATAAGAAT
* ** * * *
17482267 -AGAATATTCACAAGATTTCAAGTTTCGTAGAAATTCTAGATTTGCAAAGGTTTTAGGTTCGCAA
1 GA-AAAATTCACAAGATTTCAAGTTTCGTAGAGGTTCTAGATTTACAAAGGTTTCAGGTTCACAA
* * *
17482331 GGATTTTTAGATTCATAAGAAT
65 AGACTTTCAGATTCATAAGAAT
* * *
17482353 GAAAAATTCACAAGA-TTCTAAGTTTTGCAGAGGTTCTGGATTTACAAAGGTTTCAGGTTCACAA
1 GAAAAATTCACAAGATTTC-AAGTTTCGTAGAGGTTCTAGATTTACAAAGGTTTCAGGTTCACAA
17482417 A
65 A
17482418 AAATTTAAAG
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
85 4 0.03
86 121 0.96
87 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (86 bp):
GAAAAATTCACAAGATTTCAAGTTTCGTAGAGGTTCTAGATTTACAAAGGTTTCAGGTTCACAAA
GACTTTCAGATTCATAAGAAT
Found at i:17482434 original size:19 final size:19
Alignment explanation
Indices: 17482410--17482450 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
17482400 AGGTTTCAGG
*
17482410 TTCACAAAAAATTTAAAGA
1 TTCACAAAAAATTCAAAGA
**
17482429 TTCACAATCAATTCAAAGA
1 TTCACAAAAAATTCAAAGA
17482448 TTC
1 TTC
17482451 GTAAGAGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (19 bp):
TTCACAAAAAATTCAAAGA
Found at i:17482509 original size:19 final size:19
Alignment explanation
Indices: 17482482--17482526 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
17482472 GAAATTCAGG
*
17482482 TTCGCAAGAACTTCAAAAA
1 TTCGCAAGAAATTCAAAAA
* *
17482501 TTCGTAAGAAATTCAAAGA
1 TTCGCAAGAAATTCAAAAA
17482520 TTCGCAA
1 TTCGCAA
17482527 AGCTTTAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24
Consensus pattern (19 bp):
TTCGCAAGAAATTCAAAAA
Found at i:17482568 original size:71 final size:71
Alignment explanation
Indices: 17482438--17482650 Score: 225
Period size: 71 Copynumber: 3.0 Consensus size: 71
17482428 ATTCACAATC
* * *
17482438 AATTCAAAGATTCGTAAGAGTTTCAGTTTCACAAGAAATTCAGGTTCGCAAGAACTTCAAAAATT
1 AATTCAAAGATTCGCAAGAGTTT-AGTTTCACAAGAAATTCAAGTTTGCAAGAACTTCAAAAATT
17482503 CGTAAGA
65 CGTAAGA
* * *
17482510 AATTCAAAGATTCGCAA-AGCTTTAGTTTCACAAGAAATTCAAGTTTGCAATAAATTCAAAGATT
1 AATTCAAAGATTCGCAAGAG-TTTAGTTTCACAAGAAATTCAAGTTTGCAAGAACTTCAAAAATT
**
17482574 CACAAGA
65 CGTAAGA
** * * * * *
17482581 GCTTC--AGTTTCGCAAGAAATTTAGGTTCGCAAGAAATTCAAAGATTTGCAAGAACTTAAAAAA
1 AATTCAAAGATTCGCAAG-AGTTTAGTTTCACAAGAAATTC-AAG-TTTGCAAGAACTTCAAAAA
17482644 TTCGTAA
63 TTCGTAA
17482651 AAGATTTAGG
Statistics
Matches: 116, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
69 9 0.08
70 18 0.16
71 50 0.43
72 39 0.34
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (71 bp):
AATTCAAAGATTCGCAAGAGTTTAGTTTCACAAGAAATTCAAGTTTGCAAGAACTTCAAAAATTC
GTAAGA
Found at i:17482632 original size:36 final size:34
Alignment explanation
Indices: 17482530--17482634 Score: 95
Period size: 36 Copynumber: 3.0 Consensus size: 34
17482520 TTCGCAAAGC
* *
17482530 TTTAGTTTCACAAGAAATTCAAGTTTGCAATAAA
1 TTTAGATTCACAAGAAATTCAAGTTTGCAAGAAA
* **
17482564 TTCAAAGATTCACAAGAGCTTC-AGTTTCGCAAGAAA
1 TT--TAGATTCACAAGAAATTCAAGTTT-GCAAGAAA
* *
17482600 TTTAGGTTCGCAAGAAATTCAAAGATTTGCAAGAA
1 TTTAGATTCACAAGAAATTC-AAG-TTTGCAAGAA
17482635 CTTAAAAAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
34 15 0.27
35 5 0.09
36 32 0.58
37 3 0.05
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (34 bp):
TTTAGATTCACAAGAAATTCAAGTTTGCAAGAAA
Found at i:17482633 original size:53 final size:53
Alignment explanation
Indices: 17482501--17482633 Score: 178
Period size: 53 Copynumber: 2.5 Consensus size: 53
17482491 ACTTCAAAAA
* *
17482501 TTCGTAAGAAATTCAAAGATTCGCAA-AGCTTTAGTTTCACAAGAAATTCAAG
1 TTCGCAAGAAATTCAAAGATTCGCAAGAGCTTCAGTTTCACAAGAAATTCAAG
* * * * * *
17482553 TTTGCAATAAATTCAAAGATTCACAAGAGCTTCAGTTTCGCAAGAAATTTAGG
1 TTCGCAAGAAATTCAAAGATTCGCAAGAGCTTCAGTTTCACAAGAAATTCAAG
*
17482606 TTCGCAAGAAATTCAAAGATTTGCAAGA
1 TTCGCAAGAAATTCAAAGATTCGCAAGA
17482634 ACTTAAAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
52 22 0.32
53 46 0.68
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (53 bp):
TTCGCAAGAAATTCAAAGATTCGCAAGAGCTTCAGTTTCACAAGAAATTCAAG
Found at i:17482766 original size:24 final size:24
Alignment explanation
Indices: 17482739--17482810 Score: 60
Period size: 22 Copynumber: 3.1 Consensus size: 24
17482729 AGGGGTTCAC
17482739 TTCAAAGATTCTTATTCAAAAAAT
1 TTCAAAGATTCTTATTCAAAAAAT
* * *
17482763 TTC-AAG-GTCTTACATC-CAAAAT
1 TTCAAAGATTCTTA-TTCAAAAAAT
** *
17482785 TTCAAAGATTCACATTTAAAAAAT
1 TTCAAAGATTCTTATTCAAAAAAT
17482809 TT
1 TT
17482811 TTGGGTTTCA
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
22 13 0.37
23 9 0.26
24 13 0.37
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (24 bp):
TTCAAAGATTCTTATTCAAAAAAT
Found at i:17499009 original size:30 final size:31
Alignment explanation
Indices: 17498970--17499029 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
17498960 TTTTTATTCT
* * *
17498970 ATAAGAATGAGTTTGTTATACTTAAATGCAA
1 ATAAGAATGAGCTTATTATACTCAAATGCAA
17499001 ATAA-AATGAGCTTATTATACTCAAATGCA
1 ATAAGAATGAGCTTATTATACTCAAATGCA
17499030 TGTTATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (31 bp):
ATAAGAATGAGCTTATTATACTCAAATGCAA
Found at i:17501598 original size:41 final size:41
Alignment explanation
Indices: 17501486--17501922 Score: 217
Period size: 41 Copynumber: 10.4 Consensus size: 41
17501476 AGGCAATGTA
* * * * *
17501486 ACTTTAAAATTTGAAAAAAAATCCTCTAACTAAAGGTCAT-AA
1 ACTTTAAAATTTG--AAAAACTCCTCTAACCAGAGGTAATGAC
** * * *
17501528 AC-TTATAAATTCTAGAAAAGTTCCTCTAACTAGATGTGATGAC
1 ACTTTA-AAATT-T-GAAAAACTCCTCTAACCAGAGGTAATGAC
* *
17501571 ACTTTAAAATTTGAAAAACTCATCTAACCAGAGGTAATGAA
1 ACTTTAAAATTTGAAAAACTCCTCTAACCAGAGGTAATGAC
** * *
17501612 AC-TTAAAATTTGGAAATGCTCCTCTAACCAAAGGTAACG-C
1 ACTTTAAAATTT-GAAAAACTCCTCTAACCAGAGGTAATGAC
* *
17501652 AACTTTAAAATTTGAAAAAGCTCCTCTAACTAAAGGTAATGTA-
1 -ACTTTAAAATTTGAAAAA-CTCCTCTAACCAGAGGTAATG-AC
* * * * * *
17501695 ACTTTTAAATTAGGAAAAACTCCT-TAACCATAGGCATTGAA
1 ACTTTAAAATT-TGAAAAACTCCTCTAACCAGAGGTAATGAC
* * * * * *
17501736 ACTTTAAAATGTGAAAAAGCTCTTTTAATCAGAGGTTATGAA
1 ACTTTAAAATTTGAAAAA-CTCCTCTAACCAGAGGTAATGAC
* * * * *
17501778 ACTTTTAAATTTTAGGAAAAGCTCCTCTAACTAGAGGCAATGAA
1 AC-TTTAAAATTT--GAAAAACTCCTCTAACCAGAGGTAATGAC
* ** * * *
17501822 AC-TTAACATTTGAAATAGTTCATCTAACTAGAGGTAAT-ATA
1 ACTTTAAAATTTGAAA-AACTCCTCTAACCAGAGGTAATGA-C
* * ** * *
17501863 ACTTTAAAAATTAGAAAAGCTTTTCTAACCAAAGG-AATGAA
1 ACTTT-AAAATTTGAAAAACTCCTCTAACCAGAGGTAATGAC
*
17501904 ACTTTTAAAATTTAAAAAA
1 AC-TTTAAAATTTGAAAAA
17501923 TTTTGCTTGA
Statistics
Matches: 309, Mismatches: 62, Indels: 49
0.74 0.15 0.12
Matches are distributed among these distances:
40 21 0.07
41 117 0.38
42 111 0.36
43 32 0.10
44 23 0.07
45 5 0.02
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (41 bp):
ACTTTAAAATTTGAAAAACTCCTCTAACCAGAGGTAATGAC
Found at i:17501675 original size:42 final size:42
Alignment explanation
Indices: 17501474--17501922 Score: 326
Period size: 42 Copynumber: 10.7 Consensus size: 42
17501464 TTATCTAAAT
* * ** *
17501474 AGAGGCAATGTAACTTTAAAATTTGAAAAAAAATCCTCTAACT
1 AGAGGTAATGAAACTTTAAAATTTG-AAAAAGCTCCTCTAACC
* * * *
17501517 AAAGGTCAT-AAAC-TTATAAATTCT-AGAAAAGTTCCTCTAACT
1 AGAGGTAATGAAACTTTA-AAATT-TGA-AAAAGCTCCTCTAACC
* * * *
17501559 AGATGTGATGACACTTTAAAATTTGAAAAA-CTCATCTAACC
1 AGAGGTAATGAAACTTTAAAATTTGAAAAAGCTCCTCTAACC
* *
17501600 AGAGGTAATGAAAC-TTAAAATTTGGAAATGCTCCTCTAACC
1 AGAGGTAATGAAACTTTAAAATTTGAAAAAGCTCCTCTAACC
* * * *
17501641 AAAGGTAACGCAACTTTAAAATTTGAAAAAGCTCCTCTAACT
1 AGAGGTAATGAAACTTTAAAATTTGAAAAAGCTCCTCTAACC
* * * *
17501683 AAAGGTAATGTAACTTTTAAATTAGGAAAAA-CTCCT-TAACC
1 AGAGGTAATGAAACTTTAAAATT-TGAAAAAGCTCCTCTAACC
* * * * * * *
17501724 ATAGGCATTGAAACTTTAAAATGTGAAAAAGCTCTTTTAATC
1 AGAGGTAATGAAACTTTAAAATTTGAAAAAGCTCCTCTAACC
* * * *
17501766 AGAGGTTATGAAACTTTTAAATTTTAGGAAAAGCTCCTCTAACT
1 AGAGGTAATGAAAC-TTTAAAATTT-GAAAAAGCTCCTCTAACC
* * * * * *
17501810 AGAGGCAATGAAAC-TTAACATTTGAAATAGTTCATCTAACT
1 AGAGGTAATGAAACTTTAAAATTTGAAAAAGCTCCTCTAACC
* **
17501851 AGAGGTAAT-ATAACTTTAAAAATT-AGAAAAGCTTTTCTAACC
1 AGAGGTAATGA-AACTTTAAAATTTGA-AAAAGCTCCTCTAACC
* *
17501893 AAAGG-AATGAAACTTTTAAAATTTAAAAAA
1 AGAGGTAATGAAAC-TTTAAAATTTGAAAAA
17501923 TTTTGCTTGA
Statistics
Matches: 319, Mismatches: 68, Indels: 39
0.75 0.16 0.09
Matches are distributed among these distances:
40 20 0.06
41 101 0.32
42 139 0.44
43 31 0.10
44 28 0.09
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (42 bp):
AGAGGTAATGAAACTTTAAAATTTGAAAAAGCTCCTCTAACC
Found at i:17501723 original size:83 final size:84
Alignment explanation
Indices: 17501476--17501922 Score: 383
Period size: 83 Copynumber: 5.3 Consensus size: 84
17501466 ATCTAAATAG
* ** * * * *
17501476 AGGCAATGTAACTTTAAAATTTGAAAAAAAATCCTCTAACTAAAGGTCAT-AAACTTATAAATTC
1 AGGCAATGAAACTTTAAAATTTG-AAAAAGCTCATCTAACTAGAGGTAATGAAACTT-TAAAAT-
* * *
17501540 TA-GAAAAGTTCCTCTAACTAG
63 TAGGAAAAGCTCCTCTAACCAA
* ** * * *
17501561 ATGTGATGACACTTTAAAATTTGAAAAA-CTCATCTAACCAGAGGTAATGAAAC-TTAAAATTTG
1 AGGCAATGAAACTTTAAAATTTGAAAAAGCTCATCTAACTAGAGGTAATGAAACTTTAAAATTAG
*
17501624 GAAATGCTCCTCTAACCAA
66 GAAAAGCTCCTCTAACCAA
* * * * * * *
17501643 AGGTAACGCAACTTTAAAATTTGAAAAAGCTCCTCTAACTAAAGGTAATGTAACTTTTAAATTAG
1 AGGCAATGAAACTTTAAAATTTGAAAAAGCTCATCTAACTAGAGGTAATGAAACTTTAAAATTAG
* *
17501708 GAAAAACTCCT-TAACCAT
66 GAAAAGCTCCTCTAACCAA
* * * * * *
17501726 AGGCATTGAAACTTTAAAATGTGAAAAAGCTCTTTTAA-TCAGAGGTTATGAAACTTTTAAATTT
1 AGGCAATGAAACTTTAAAATTTGAAAAAGCTCATCTAACT-AGAGGTAATGAAAC-TTTAAA-AT
* *
17501790 TAGGAAAAGCTCCTCTAACTAG
63 TAGGAAAAGCTCCTCTAACCAA
* * *
17501812 AGGCAATGAAAC-TTAACATTTGAAATAGTTCATCTAACTAGAGGTAAT-ATAACTTTAAAAATT
1 AGGCAATGAAACTTTAAAATTTGAAAAAGCTCATCTAACTAGAGGTAATGA-AACTTT-AAAATT
**
17501875 A-GAAAAGCTTTTCTAACCAA
64 AGGAAAAGCTCCTCTAACCAA
*
17501895 AGG-AATGAAACTTTTAAAATTTAAAAAA
1 AGGCAATGAAAC-TTTAAAATTTGAAAAA
17501923 TTTTGCTTGA
Statistics
Matches: 288, Mismatches: 61, Indels: 27
0.77 0.16 0.07
Matches are distributed among these distances:
81 1 0.00
82 52 0.18
83 103 0.36
84 50 0.17
85 65 0.23
86 17 0.06
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (84 bp):
AGGCAATGAAACTTTAAAATTTGAAAAAGCTCATCTAACTAGAGGTAATGAAACTTTAAAATTAG
GAAAAGCTCCTCTAACCAA
Found at i:17503727 original size:17 final size:17
Alignment explanation
Indices: 17503690--17503728 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
17503680 AAAAGAGTGA
17503690 AAAAG-GAAATGAAAAG
1 AAAAGAGAAATGAAAAG
17503706 AAAAGAGAAA-GAGAAAG
1 AAAAGAGAAATGA-AAAG
17503723 AAAAGA
1 AAAAGA
17503729 TGAACAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03
Consensus pattern (17 bp):
AAAAGAGAAATGAAAAG
Found at i:17504957 original size:12 final size:13
Alignment explanation
Indices: 17504938--17504976 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
17504928 TTTTGAATAT
17504938 TGCATTTGCATCA
1 TGCATTTGCATCA
*
17504951 T-CATTTGAATCA
1 TGCATTTGCATCA
*
17504963 TGTATTTGCATCA
1 TGCATTTGCATCA
17504976 T
1 T
17504977 TTTGTGAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.44
Consensus pattern (13 bp):
TGCATTTGCATCA
Found at i:17505734 original size:33 final size:34
Alignment explanation
Indices: 17505691--17505795 Score: 119
Period size: 33 Copynumber: 3.2 Consensus size: 34
17505681 TATTTGATTC
*
17505691 CATTTTTTGACTTCACCTT-AGTCTAAGTCATTT
1 CATTTTTTGACTTCACCTTCAGTCTAAGTCATTA
*
17505724 CTTTTTTTGAC-T-ACCATTCAGTCTAAGTCATTA
1 CATTTTTTGACTTCACC-TTCAGTCTAAGTCATTA
* * * *
17505757 CATTTTTAGACTTC-CATTCAGTCCAAGTCATTG
1 CATTTTTTGACTTCACCTTCAGTCTAAGTCATTA
17505790 CATTTT
1 CATTTT
17505796 AAGACTTTGG
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
31 3 0.05
32 3 0.05
33 53 0.87
34 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.46
Consensus pattern (34 bp):
CATTTTTTGACTTCACCTTCAGTCTAAGTCATTA
Found at i:17505811 original size:33 final size:33
Alignment explanation
Indices: 17505741--17505895 Score: 107
Period size: 33 Copynumber: 4.7 Consensus size: 33
17505731 TGACTACCAT
* * * ****
17505741 TCAGTCTAAGTCATTACATTTTTAGACTTCCAT
1 TCAGTCCAAGTCATTGCATTTTAAGACTTTGGC
17505774 TCAGTCCAAGTCATTGCATTTTAAGACTTTGGC
1 TCAGTCCAAGTCATTGCATTTTAAGACTTTGGC
* * * * * *
17505807 TCAGTCTAGGCCATTTCATTTTTAGACTTTGGT
1 TCAGTCCAAGTCATTGCATTTTAAGACTTTGGC
* *
17505840 TTAGT-CTAGATCATTGCATTTTCAA-ACTTTGGC
1 TCAGTCCAAG-TCATTGCATTTT-AAGACTTTGGC
* * *
17505873 TTAGTCCAAATGATTGCAATTTT
1 TCAGTCCAAGTCATTGC-ATTTT
17505896 TTACTTCAGT
Statistics
Matches: 94, Mismatches: 24, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
32 1 0.01
33 85 0.90
34 8 0.09
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (33 bp):
TCAGTCCAAGTCATTGCATTTTAAGACTTTGGC
Found at i:17505811 original size:66 final size:66
Alignment explanation
Indices: 17505741--17505878 Score: 163
Period size: 66 Copynumber: 2.1 Consensus size: 66
17505731 TGACTACCAT
*
17505741 TCAGTCTAAGTCATTACATTTTTAGACTTCCATTCAGTCCAAG-TCATTGCATTTT-AAGACTTT
1 TCAGTCTAAGCCATTACATTTTTAGACTTCCATTCAGT-CAAGATCATTGCATTTTCAA-ACTTT
17505804 GGC
64 GGC
* * *** * *
17505807 TCAGTCTAGGCCATTTCATTTTTAGACTTTGGTTTAGTCTAGATCATTGCATTTTCAAACTTTGG
1 TCAGTCTAAGCCATTACATTTTTAGACTTCCATTCAGTCAAGATCATTGCATTTTCAAACTTTGG
17505872 C
66 C
*
17505873 TTAGTC
1 TCAGTC
17505879 CAAATGATTG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
65 3 0.05
66 56 0.92
67 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (66 bp):
TCAGTCTAAGCCATTACATTTTTAGACTTCCATTCAGTCAAGATCATTGCATTTTCAAACTTTGG
C
Found at i:17506557 original size:23 final size:23
Alignment explanation
Indices: 17506515--17506558 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
17506505 AACTAATCCT
*
17506515 AAAGAAAATAATTAATAGATTTC
1 AAAGAAAAGAATTAATAGATTTC
17506538 AAAGTAAAAGAATTAA-AGATT
1 AAAG-AAAAGAATTAATAGATT
17506559 GTAAACAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.27
Consensus pattern (23 bp):
AAAGAAAAGAATTAATAGATTTC
Found at i:17506869 original size:18 final size:18
Alignment explanation
Indices: 17506848--17506894 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
17506838 GCAATAACTT
17506848 AACTAAAAGAAA-TAAAAA
1 AACTAAAAGAAACT-AAAA
* *
17506866 AACTAAAA-AAACTTAGA
1 AACTAAAAGAAACTAAAA
17506883 AACTAAAAGAAA
1 AACTAAAAGAAA
17506895 GAAATGAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.72, C:0.09, G:0.06, T:0.13
Consensus pattern (18 bp):
AACTAAAAGAAACTAAAA
Found at i:17510524 original size:110 final size:110
Alignment explanation
Indices: 17510331--17510554 Score: 355
Period size: 110 Copynumber: 2.0 Consensus size: 110
17510321 CTTCGGGTTG
* *
17510331 TCTTACAAAGCTAGGTAGGTTGACTATTATGGGTTCATCATCTTTTGTATCAGAATCATCCATCC
1 TCTTACAAAGCTAGGTAGGTTAACTATTATGGGTTCATCATCTTCTGTATCAGAATCATCCATCC
*
17510396 TAACATCCCTAAAGAATATATTGCACTGCATCAT-TTTTTGCCTTA
66 TAACATCCCTAAAGAATATATTGCACTGCATC-TCTTCTTGCCTTA
17510441 TCTTACAAAGCTAGGTAGGTTAACTATTATGGGTTCATCATCTTCCT-TATC-GAAATCATCCAT
1 TCTTACAAAGCTAGGTAGGTTAACTATTATGGGTTCATCATCTT-CTGTATCAG-AATCATCCAT
* *
17510504 CCTAACATCCCTAAAGAATATATTGCATTGCATCTCTTCTTGCCTTG
64 CCTAACATCCCTAAAGAATATATTGCACTGCATCTCTTCTTGCCTTA
17510551 TCTT
1 TCTT
17510555 TTTGGGTTAG
Statistics
Matches: 106, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
109 2 0.02
110 103 0.97
111 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (110 bp):
TCTTACAAAGCTAGGTAGGTTAACTATTATGGGTTCATCATCTTCTGTATCAGAATCATCCATCC
TAACATCCCTAAAGAATATATTGCACTGCATCTCTTCTTGCCTTA
Found at i:17513558 original size:22 final size:22
Alignment explanation
Indices: 17513526--17513576 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
17513516 TATTCTTAAT
* *
17513526 TTTTTTTAAAAACTATTTTTGA
1 TTTTTTAAAAAAATATTTTTGA
17513548 TTTTTTAAAAAAATATTTTTGA
1 TTTTTTAAAAAAATATTTTTGA
17513570 TTTTTTA
1 TTTTTTA
17513577 GTAAGCTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (22 bp):
TTTTTTAAAAAAATATTTTTGA
Found at i:17515356 original size:22 final size:23
Alignment explanation
Indices: 17515326--17515379 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
17515316 TTTTTAAATT
17515326 TTTTGTTTTCA-GCT-TTTCTTTCA
1 TTTT-TTTTCATGCTCTTT-TTTCA
*
17515349 TTTTTTTTCATGCTCTTTTTTCT
1 TTTTTTTTCATGCTCTTTTTTCA
17515372 TTTTTTTT
1 TTTTTTTT
17515380 TTAGATGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 6 0.21
23 19 0.68
24 3 0.11
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.74
Consensus pattern (23 bp):
TTTTTTTTCATGCTCTTTTTTCA
Found at i:17519039 original size:21 final size:21
Alignment explanation
Indices: 17519013--17519052 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17519003 NAAGATGAAA
17519013 AAGAAAAAAAAAGAAAAAAAG
1 AAGAAAAAAAAAGAAAAAAAG
*
17519034 AAGAAAAAAAATGAAAAAA
1 AAGAAAAAAAAAGAAAAAA
17519053 TGGAAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (21 bp):
AAGAAAAAAAAAGAAAAAAAG
Found at i:17519050 original size:8 final size:8
Alignment explanation
Indices: 17519039--17519082 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
17519029 AAAAGAAGAA
17519039 AAAAAATG
1 AAAAAATG
17519047 AAAAAATGG
1 AAAAAAT-G
17519056 AAAAAGATG
1 AAAAA-ATG
*
17519065 AAAAAAAG
1 AAAAAATG
*
17519073 AGAAAATG
1 AAAAAATG
17519081 AA
1 AA
17519083 GACTCAGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
8 16 0.53
9 12 0.40
10 2 0.07
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (8 bp):
AAAAAATG
Found at i:17519051 original size:11 final size:10
Alignment explanation
Indices: 17519010--17519052 Score: 68
Period size: 10 Copynumber: 4.2 Consensus size: 10
17519000 NNNNAAGATG
17519010 AAAAAGAAAA
1 AAAAAGAAAA
17519020 AAAAAGAAAA
1 AAAAAGAAAA
17519030 AAAGAAGAAAA
1 AAA-AAGAAAA
*
17519041 AAAATGAAAA
1 AAAAAGAAAA
17519051 AA
1 AA
17519053 TGGAAAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 21 0.68
11 10 0.32
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:17519077 original size:10 final size:10
Alignment explanation
Indices: 17519010--17519078 Score: 60
Period size: 11 Copynumber: 7.2 Consensus size: 10
17519000 NNNNAAGATG
17519010 AAAAAGA-AA
1 AAAAAGAGAA
17519019 AAAAA-AGAA
1 AAAAAGAGAA
17519028 AAAAAGAAGAA
1 AAAAAG-AGAA
17519039 AAAAA-ATGAA
1 AAAAAGA-GAA
*
17519049 AAAATG-G--
1 AAAAAGAGAA
17519056 AAAAAGATGAA
1 AAAAAGA-GAA
17519067 AAAAAGAGAA
1 AAAAAGAGAA
17519077 AA
1 AA
17519079 TGAAGACTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
7 5 0.10
8 1 0.02
9 15 0.31
10 12 0.24
11 16 0.33
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (10 bp):
AAAAAGAGAA
Found at i:17519077 original size:28 final size:29
Alignment explanation
Indices: 17519010--17519078 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
17519000 NNNNAAGATG
*
17519010 AAAAAGAAAAAAAAAGAAAAAAAGAAGAA
1 AAAAAGAGAAAAAAAGAAAAAAAGAAGAA
* * *
17519039 AAAAA-ATGAAAAAATG-GAAAAAGATGAA
1 AAAAAGA-GAAAAAAAGAAAAAAAGAAGAA
17519067 AAAAAGAGAAAA
1 AAAAAGAGAAAA
17519079 TGAAGACTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (29 bp):
AAAAAGAGAAAAAAAGAAAAAAAGAAGAA
Found at i:17520336 original size:21 final size:21
Alignment explanation
Indices: 17520263--17520375 Score: 140
Period size: 21 Copynumber: 5.3 Consensus size: 21
17520253 CTAAATTTTC
17520263 AAATGAGAATC--TGAGTCTT
1 AAATGAGAATCTTTGAGTCTT
*
17520282 AAATGAGAATCTTTGAGACATTTT
1 AAATGAGAATCTTTGAG---TCTT
17520306 CAAATGAGAATCTTTGAGTCTT
1 -AAATGAGAATCTTTGAGTCTT
* * *
17520328 AAATAAGAATCTTTGAGCCTC
1 AAATGAGAATCTTTGAGTCTT
17520349 AAATGAGAATCTTTGAGTCTT
1 AAATGAGAATCTTTGAGTCTT
17520370 AAATGA
1 AAATGA
17520376 TAATTTTTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
19 11 0.14
21 46 0.57
22 3 0.04
24 3 0.04
25 17 0.21
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.34
Consensus pattern (21 bp):
AAATGAGAATCTTTGAGTCTT
Found at i:17520338 original size:46 final size:45
Alignment explanation
Indices: 17520257--17520373 Score: 172
Period size: 42 Copynumber: 2.7 Consensus size: 45
17520247 GAAATCCTAA
*
17520257 ATTTTCAAATGAGAATC--TGAGTCTTAAATGAGAATCTTTGAGAC
1 ATTTTCAAATGAGAATCTTTGAGTCTTAAATAAGAATCTTTGAG-C
17520301 ATTTTCAAATGAGAATCTTTGAGTCTTAAATAAGAATCTTTGAGC
1 ATTTTCAAATGAGAATCTTTGAGTCTTAAATAAGAATCTTTGAGC
*
17520346 ---CTCAAATGAGAATCTTTGAGTCTTAAAT
1 ATTTTCAAATGAGAATCTTTGAGTCTTAAAT
17520374 GATAATTTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
42 27 0.39
44 17 0.25
45 1 0.01
46 24 0.35
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (45 bp):
ATTTTCAAATGAGAATCTTTGAGTCTTAAATAAGAATCTTTGAGC
Found at i:17520397 original size:88 final size:86
Alignment explanation
Indices: 17520261--17520429 Score: 205
Period size: 88 Copynumber: 1.9 Consensus size: 86
17520251 TCCTAAATTT
* * * ** * * *
17520261 TCAAATGAGAATCTGAGTCTTAAATGAGAATCTTTGAGACATTTTCAAATGAGAATCTTTGAGTC
1 TCAAATGAGAATCTGAGTCTTAAATGAGAATCTTTAAAAAATCCTCAAATAAAAATCTTTGAAT-
17520326 TT-AAATAAGAATCTTTGAGCC
65 TTCAAATAAGAATCTTTGAGCC
* *
17520347 TCAAATGAGAATCTTTGAGTCTTAAATGATAATTTTTAAAAAATCCTCAAATAAAAATCTTTGAA
1 TCAAATGAGAATC--TGAGTCTTAAATGAGAATCTTTAAAAAATCCTCAAATAAAAATCTTTGAA
*
17520412 TTTCAAATGAGAATCTTT
64 TTTCAAATAAGAATCTTT
17520430 AAAGTGTGAA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
86 13 0.19
87 2 0.03
88 54 0.78
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (86 bp):
TCAAATGAGAATCTGAGTCTTAAATGAGAATCTTTAAAAAATCCTCAAATAAAAATCTTTGAATT
TCAAATAAGAATCTTTGAGCC
Found at i:17520420 original size:46 final size:46
Alignment explanation
Indices: 17520278--17520432 Score: 122
Period size: 46 Copynumber: 3.5 Consensus size: 46
17520268 AGAATCTGAG
* * * ** * * *
17520278 TCTTAAATGAGAATCTTTGAGACATTTTCAAATGAGAATCTTTGAG
1 TCTTAAATGAGAATCTTTAAAAAATCCTCAAATAAAAATCTTTGAA
* * * * * *
17520324 TCTTAAATAAGAATCTTT----GAGCCTCAAATGAGAATCTTTGAG
1 TCTTAAATGAGAATCTTTAAAAAATCCTCAAATAAAAATCTTTGAA
* *
17520366 TCTTAAATGATAATTTTTAAAAAATCCTCAAATAAAAATCTTTGAA
1 TCTTAAATGAGAATCTTTAAAAAATCCTCAAATAAAAATCTTTGAA
17520412 T-TTCAAATGAGAATCTTTAAA
1 TCTT-AAATGAGAATCTTTAAA
17520433 GTGTGAAACC
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
42 35 0.39
45 2 0.02
46 52 0.58
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (46 bp):
TCTTAAATGAGAATCTTTAAAAAATCCTCAAATAAAAATCTTTGAA
Found at i:17520484 original size:19 final size:20
Alignment explanation
Indices: 17520460--17520505 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
17520450 TTTTGAATAT
17520460 GAATCTTCAAAC-AAAATGA
1 GAATCTTCAAACTAAAATGA
** *
17520479 GAATCTTTGAACTCAAATGA
1 GAATCTTCAAACTAAAATGA
17520499 GAATCTT
1 GAATCTT
17520506 TGAGCTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
GAATCTTCAAACTAAAATGA
Found at i:17520498 original size:20 final size:20
Alignment explanation
Indices: 17520473--17520548 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
17520463 TCTTCAAACA
17520473 AAATGAGAATCTTTGAACTC
1 AAATGAGAATCTTTGAACTC
* *
17520493 AAATGAGAATCTTTGAGCTT
1 AAATGAGAATCTTTGAACTC
* * *
17520513 AAATGAGATTATTTGAATTC
1 AAATGAGAATCTTTGAACTC
17520533 AAATGAGAATCTTTGA
1 AAATGAGAATCTTTGA
17520549 GGTGTAAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.34
Consensus pattern (20 bp):
AAATGAGAATCTTTGAACTC
Found at i:17520519 original size:40 final size:40
Alignment explanation
Indices: 17520473--17520549 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
17520463 TCTTCAAACA
*
17520473 AAATGAGAATCTTTGAACTCAAATGAGAATCTTTGAGCTT
1 AAATGAGAATATTTGAACTCAAATGAGAATCTTTGAGCTT
* *
17520513 AAATGAGATTATTTGAATTCAAATGAGAATCTTTGAG
1 AAATGAGAATATTTGAACTCAAATGAGAATCTTTGAG
17520550 GTGTAAAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (40 bp):
AAATGAGAATATTTGAACTCAAATGAGAATCTTTGAGCTT
Found at i:17520565 original size:117 final size:121
Alignment explanation
Indices: 17520406--17520629 Score: 312
Period size: 117 Copynumber: 1.9 Consensus size: 121
17520396 AATAAAAATC
* * * *
17520406 TTTGAATTTCAAATGAGAATCTTTAAAGTGTGAAACCTAAAATTTTTTGAATATGAATCTTCAAA
1 TTTGAATTTCAAATGAGAATCTTTAAAGTGTAAAACCCAAAATTTATCGAATATGAATCTTCAAA
* *
17520471 C-AAAATGAGAATC-TTTGA-ACTCAAATGAGAATCTTTGAGCTTAAATGAGATTA
66 CTAAAATGAGAACCTTTTGAGACTCAAATGAGAATATTTGAGCTTAAATGAGATTA
* * *
17520524 TTTGAA-TTCAAATGAGAATCTTTGAGGTGTAAAACCCAAAATTTATCGAATGTGAATCTTCAAA
1 TTTGAATTTCAAATGAGAATCTTTAAAGTGTAAAACCCAAAATTTATCGAATATGAATCTTCAAA
* **
17520588 CTCAAATGAGAACCTTTTGAGTTTCAAATGAGAATATTTGAG
66 CTAAAATGAGAACCTTTTGAGACTCAAATGAGAATATTTGAG
17520630 GTGTGAAACC
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
117 52 0.57
118 16 0.18
119 5 0.05
120 18 0.20
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (121 bp):
TTTGAATTTCAAATGAGAATCTTTAAAGTGTAAAACCCAAAATTTATCGAATATGAATCTTCAAA
CTAAAATGAGAACCTTTTGAGACTCAAATGAGAATATTTGAGCTTAAATGAGATTA
Found at i:17520629 original size:21 final size:21
Alignment explanation
Indices: 17520589--17520629 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
17520579 ATCTTCAAAC
17520589 TCAAATGAGAACCTTTTGAGTT
1 TCAAATGAGAA-CTTTTGAGTT
17520611 TCAAATGAGAA-TATTTGAG
1 TCAAATGAGAACT-TTTGAG
17520630 GTGTGAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 6 0.33
22 11 0.61
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.34
Consensus pattern (21 bp):
TCAAATGAGAACTTTTGAGTT
Found at i:17520687 original size:80 final size:80
Alignment explanation
Indices: 17520530--17520685 Score: 188
Period size: 81 Copynumber: 1.9 Consensus size: 80
17520520 ATTATTTGAA
* * *
17520530 TTCAAATGAGAATCTTTGAGGTGTAAAACCCAAAATTTATCGAATGTGAATCTTCAAACTCAAAT
1 TTCAAATGAGAATATTTGAGGTGTAAAACCCAAAATTCATCGAATGTGAATCTTCAAACTCAAAC
*
17520595 GAGAACCTTTTGAGT
66 GAAAACCTTTTGAGT
* * * * * *
17520610 TTCAAATGAGAATATTTGAGGTGTGAAACCTTAAAGTTCATTGAATGTGAATGTTTAAACT-AGA
1 TTCAAATGAGAATATTTGAGGTGTAAAACC-CAAAATTCATCGAATGTGAATCTTCAAACTCA-A
*
17520674 ACGAAAAGCTTT
64 ACGAAAACCTTT
17520686 GAACTCAACT
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
80 29 0.46
81 34 0.54
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (80 bp):
TTCAAATGAGAATATTTGAGGTGTAAAACCCAAAATTCATCGAATGTGAATCTTCAAACTCAAAC
GAAAACCTTTTGAGT
Found at i:17520755 original size:42 final size:44
Alignment explanation
Indices: 17520700--17520783 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
17520690 TCAACTTTTG
* * *
17520700 GATGTGAATCTCTAA-ATTT-TTTAGTGAGAACCTTTGAACTTA
1 GATGTGAAACTCTAAGATTTCTTGAATGAGAACCTTTGAACTTA
*
17520742 GATGTGAAACTCTAAGATTTCTTGAATGTGAACCTTTGAACT
1 GATGTGAAACTCTAAGATTTCTTGAATGAGAACCTTTGAACT
17520784 CGAATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 14 0.39
43 4 0.11
44 18 0.50
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (44 bp):
GATGTGAAACTCTAAGATTTCTTGAATGAGAACCTTTGAACTTA
Found at i:17521055 original size:28 final size:27
Alignment explanation
Indices: 17521001--17521055 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
17520991 GGTTCTTGTG
*
17521001 AATTTGAACCTTTGAATTTTGAATTCA
1 AATTTGAACCTTTGAATTTTCAATTCA
* * *
17521028 AATTGTGAATCTTTGAGTTTTCATTTCA
1 AATT-TGAACCTTTGAATTTTCAATTCA
17521056 TCAAACCTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (27 bp):
AATTTGAACCTTTGAATTTTCAATTCA
Found at i:17521176 original size:41 final size:41
Alignment explanation
Indices: 17521094--17521243 Score: 162
Period size: 42 Copynumber: 3.6 Consensus size: 41
17521084 ATGATTGTCA
* *
17521094 ATGAGCATTTTAATTTTTCAAAGTTATGGTGTCTCTGTTTAG
1 ATGAGCATTTT-ATTTTTCAAAGTTGTGGTGCCTCTGTTTAG
*
17521136 ATGAGCATTTTACTTTTT-AAAGTTGTGGTGCCTCTATTTAG
1 ATGAGCATTTTA-TTTTTCAAAGTTGTGGTGCCTCTGTTTAG
* * *
17521177 A-GAAGCCTTTTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAG
1 ATG-AG-CATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAG
* * *
17521219 AGGAAC-TTTTATTTTTTAAAGTTGT
1 ATGAGCATTTTATTTTTCAAAGTTGT
17521244 TGAGCTTTTA
Statistics
Matches: 94, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
40 19 0.20
41 30 0.32
42 44 0.47
43 1 0.01
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (41 bp):
ATGAGCATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAG
Found at i:17521240 original size:40 final size:41
Alignment explanation
Indices: 17521099--17521263 Score: 145
Period size: 40 Copynumber: 4.0 Consensus size: 41
17521089 TGTCAATGAG
* * * * * * * *
17521099 CATTTTAATTTTTCAAAGTTATGGTGTCTCTGTTTAGATGAG
1 CATTTT-ATTTTTTAAAGTTGTTGAGCCTCTATTTAGAGGAA
* * *
17521141 CATTTTACTTTTTAAAGTTGTGGTGCCTCTATTTAGA-GAA
1 CATTTTATTTTTTAAAGTTGTTGAGCCTCTATTTAGAGGAA
* * *
17521181 GCCTTTTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAGGAA
1 --CATTTTATTTTTTAAAGTTGTTGAGCCTCTATTTAGAGGAA
* *
17521224 C-TTTTATTTTTTAAAGTTGTTGAGCTTTTATTTAGAGGAA
1 CATTTTATTTTTTAAAGTTGTTGAGCCTCTATTTAGAGGAA
17521264 GTCTAAGTAT
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
40 37 0.36
41 27 0.26
42 37 0.36
43 3 0.03
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (41 bp):
CATTTTATTTTTTAAAGTTGTTGAGCCTCTATTTAGAGGAA
Found at i:17521860 original size:21 final size:21
Alignment explanation
Indices: 17521802--17521874 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
17521792 CAGCCGAGTA
*
17521802 ATTTTGTTT-TTTTTTTTTGT
1 ATTTTGTTTATTTTTTTTAGT
*
17521822 ATGTTT-TTTAGATCTTTTTTAGT
1 AT-TTTGTTT--ATTTTTTTTAGT
17521845 ATTTTGTTTA-TTTTTTTATGT
1 ATTTTGTTTATTTTTTTTA-GT
*
17521866 GTTTTGTTT
1 ATTTTGTTT
17521875 TAGCATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
20 12 0.28
21 14 0.33
22 3 0.07
23 14 0.33
ACGTcount: A:0.11, C:0.01, G:0.12, T:0.75
Consensus pattern (21 bp):
ATTTTGTTTATTTTTTTTAGT
Found at i:17521884 original size:43 final size:42
Alignment explanation
Indices: 17521802--17521884 Score: 96
Period size: 43 Copynumber: 1.9 Consensus size: 42
17521792 CAGCCGAGTA
* *
17521802 ATTTTGTTTTTTTTTTTTGTATGTTTTTTAGATCTTTTTTAGT
1 ATTTTGTTTTTTTTTTATGTATGTTTTTTAGA-CATTTTTAGT
* *
17521845 ATTTTGTTTATTTTTTTATGTGTTTTGTTTTAG-CATTTTT
1 ATTTTGTTT-TTTTTTTATGTATGTT-TTTTAGACATTTTT
17521885 TATTAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
43 15 0.44
44 13 0.38
45 6 0.18
ACGTcount: A:0.12, C:0.02, G:0.12, T:0.73
Consensus pattern (42 bp):
ATTTTGTTTTTTTTTTATGTATGTTTTTTAGACATTTTTAGT
Found at i:17524004 original size:17 final size:20
Alignment explanation
Indices: 17523982--17524021 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
17523972 TTAATTTTGT
17523982 AAAACAA-AG-TGTAA-AAA
1 AAAACAAGAGTTGTAATAAA
17523999 AAAACAAGAGTTGTAATAAA
1 AAAACAAGAGTTGTAATAAA
17524019 AAA
1 AAA
17524022 TTGAGGAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 2 0.10
19 5 0.25
20 6 0.30
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.15
Consensus pattern (20 bp):
AAAACAAGAGTTGTAATAAA
Found at i:17530353 original size:16 final size:16
Alignment explanation
Indices: 17530332--17530367 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
17530322 TTTTATTAAG
*
17530332 TGAATATATGAATGAA
1 TGAATAAATGAATGAA
*
17530348 TGAATAAATGAATGAT
1 TGAATAAATGAATGAA
17530364 TGAA
1 TGAA
17530368 GGACAAAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (16 bp):
TGAATAAATGAATGAA
Found at i:17532098 original size:21 final size:21
Alignment explanation
Indices: 17532074--17532120 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
17532064 TCCAAATATG
*
17532074 AAAAATGATAAAAATG-AATGT
1 AAAAATGAT-AAAATGAAATGC
*
17532095 AAAAATGATCAAATGAAATGC
1 AAAAATGATAAAATGAAATGC
17532116 AAAAA
1 AAAAA
17532121 GTACAATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.64, C:0.04, G:0.13, T:0.19
Consensus pattern (21 bp):
AAAAATGATAAAATGAAATGC
Found at i:17533036 original size:16 final size:16
Alignment explanation
Indices: 17533015--17533048 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
17533005 AACAGTTTTT
17533015 AAAAAAATCAAAATTA
1 AAAAAAATCAAAATTA
*
17533031 AAAAAAATTAAAATTA
1 AAAAAAATCAAAATTA
17533047 AA
1 AA
17533049 TATTAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAAAATCAAAATTA
Found at i:17533831 original size:15 final size:16
Alignment explanation
Indices: 17533811--17533840 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17533801 TCCATTTAAC
17533811 TTTATCTTTT-TTTTT
1 TTTATCTTTTGTTTTT
17533826 TTTATCTTTTGTTTT
1 TTTATCTTTTGTTTT
17533841 AAAAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.83
Consensus pattern (16 bp):
TTTATCTTTTGTTTTT
Found at i:17535027 original size:21 final size:21
Alignment explanation
Indices: 17535001--17535044 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
17534991 TTTCTTCTTG
17535001 TTTCCTT-TCTTCTCTCTTTCT
1 TTTCCTTCTCTTCTCT-TTTCT
17535022 TTTCCTTCTCTTCTCTTTTCT
1 TTTCCTTCTCTTCTCTTTTCT
17535043 TT
1 TT
17535045 ATTCTCTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTCCTTCTCTTCTCTTTTCT
Found at i:17535132 original size:10 final size:10
Alignment explanation
Indices: 17535114--17535157 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
17535104 TTTTTCATTC
*
17535114 TTCTTTTTTT
1 TTCTCTTTTT
17535124 TTCTCTTTTT
1 TTCTCTTTTT
17535134 TTC-CTTTTT
1 TTCTCTTTTT
*
17535143 TTTTCTTTTCT
1 TTCTCTTTT-T
17535154 TTCT
1 TTCT
17535158 TCCAGTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 8 0.28
10 17 0.59
11 4 0.14
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTCTCTTTTT
Found at i:17536248 original size:19 final size:18
Alignment explanation
Indices: 17536206--17536248 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
17536196 CTCAAAATTT
*
17536206 AATTAG-ATTGGGCTTTG
1 AATTAGAATTGGGCTTAG
*
17536223 AAATAGAATATGGGCTTAG
1 AATTAGAAT-TGGGCTTAG
17536242 AATTAGA
1 AATTAGA
17536249 CTCACATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 2 0.10
19 14 0.67
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.33
Consensus pattern (18 bp):
AATTAGAATTGGGCTTAG
Found at i:17536438 original size:13 final size:13
Alignment explanation
Indices: 17536412--17536450 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
17536402 TTAAGCTGGC
17536412 TTAAATCGAAACAT
1 TTAAATC-AAACAT
17536426 TTAAATCAAACAT
1 TTAAATCAAACAT
**
17536439 AAAAATCAAACA
1 TTAAATCAAACA
17536451 AATTCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.23
Consensus pattern (13 bp):
TTAAATCAAACAT
Found at i:17543315 original size:40 final size:40
Alignment explanation
Indices: 17543265--17543353 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
17543255 TGAATATAAC
* * * ** *
17543265 TTATTTATATTAACGAATTTTTATATATTATTAAAAAATT
1 TTATCTATATTAACGAATATTCATATACCATTAAAAAAAT
* * *
17543305 TTATCTATATTGATGGATATTCATATACCATTAAAAAAAT
1 TTATCTATATTAACGAATATTCATATACCATTAAAAAAAT
17543345 TTATCTATA
1 TTATCTATA
17543354 CCGGTGACTA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (40 bp):
TTATCTATATTAACGAATATTCATATACCATTAAAAAAAT
Found at i:17544726 original size:3 final size:3
Alignment explanation
Indices: 17544718--17544743 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17544708 TATAATCTAT
17544718 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
17544744 TAATAATAAT
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:17544748 original size:3 final size:3
Alignment explanation
Indices: 17544742--17544815 Score: 103
Period size: 3 Copynumber: 24.7 Consensus size: 3
17544732 CAACAACAAC
17544742 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
17544790 GAT GAT GAT GAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
17544816 CATAATCTAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17545314 original size:75 final size:75
Alignment explanation
Indices: 17545235--17545408 Score: 213
Period size: 75 Copynumber: 2.3 Consensus size: 75
17545225 AAAAAGCCAA
* * * *
17545235 AGAAAGAGATAGGGAAAGGAAAAGGAAAAAAAGGGGAGATAGTTTGATGTCTAACAAGAAGGGGA
1 AGAAAGAGAAAAGAAAAGGAAAAGGAAAAAAAGGGGAGATAGTTTGATGTCTAACAAGAAGAGGA
17545300 AGCATGGTGG
66 AGCATGGTGG
* ** * * * ** *
17545310 AGAAAGAGAAAAGAAAAGGGAAATTAGAAGAGGGGGAGATAGTTTGATGTCTAATGAGAAGATGA
1 AGAAAGAGAAAAGAAAAGGAAAAGGAAAAAAAGGGGAGATAGTTTGATGTCTAACAAGAAGAGGA
*
17545375 GGCATGGTGG
66 AGCATGGTGG
17545385 AGAAAGAGAAAAGAAAAGGGAAAA
1 AGAAAGAGAAAAGAAAA-GGAAAA
17545409 TAGAGCATGG
Statistics
Matches: 83, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
75 78 0.94
76 5 0.06
ACGTcount: A:0.48, C:0.03, G:0.36, T:0.13
Consensus pattern (75 bp):
AGAAAGAGAAAAGAAAAGGAAAAGGAAAAAAAGGGGAGATAGTTTGATGTCTAACAAGAAGAGGA
AGCATGGTGG
Found at i:17562047 original size:24 final size:24
Alignment explanation
Indices: 17562010--17562056 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
17562000 AAGATTTCTT
* *
17562010 GAAGTTCAGTTATCATCATCAAAGG
1 GAAGTTCAGATATCACCA-CAAAGG
17562035 GAAG-TCAGATATCACCACAAAG
1 GAAGTTCAGATATCACCACAAAG
17562057 AAAAATATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (24 bp):
GAAGTTCAGATATCACCACAAAGG
Found at i:17562259 original size:29 final size:29
Alignment explanation
Indices: 17562197--17562475 Score: 219
Period size: 29 Copynumber: 9.8 Consensus size: 29
17562187 CTTATTGATA
* * *
17562197 CCAGCTAAACTGGGCTT-AAATTTGAGTA
1 CCAGCTAAACTAGGCTTAAAATTTGTGTG
* *
17562225 CAAGCTAAACTAGGTTTAAAATTTGTGTG
1 CCAGCTAAACTAGGCTTAAAATTTGTGTG
* * * ** *
17562254 CTAGCTAAACTAGGTTTAAAATATGAATA
1 CCAGCTAAACTAGGCTTAAAATTTGTGTG
* *
17562283 CCAGCTAAATTAGGCTT-AAATTTGTGTA
1 CCAGCTAAACTAGGCTTAAAATTTGTGTG
*
17562311 CCAGCTAAACTAGACTT-AAATTTGTGTG
1 CCAGCTAAACTAGGCTTAAAATTTGTGTG
* * *
17562339 CTAGCTAAACT-GAGTTTAAAATTTGGGTG
1 CCAGCTAAACTAG-GCTTAAAATTTGTGTG
* * *
17562368 CCAACTAAACTAGGCTTAAAATATGAGTG
1 CCAGCTAAACTAGGCTTAAAATTTGTGTG
* * * * *
17562397 CTAACTAAATTAGGCTT-AAATATGTGTA
1 CCAGCTAAACTAGGCTTAAAATTTGTGTG
* * * *
17562425 CCAACTAAACT-GCGTTTAAAATCTGTGCG
1 CCAGCTAAACTAG-GCTTAAAATTTGTGTG
* *
17562454 CCAGCTAAACTGGGTTTAAAAT
1 CCAGCTAAACTAGGCTTAAAAT
17562476 ATGAGTTGTA
Statistics
Matches: 205, Mismatches: 39, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
27 2 0.01
28 80 0.39
29 121 0.59
30 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (29 bp):
CCAGCTAAACTAGGCTTAAAATTTGTGTG
Found at i:17562262 original size:57 final size:57
Alignment explanation
Indices: 17562197--17562435 Score: 216
Period size: 57 Copynumber: 4.2 Consensus size: 57
17562187 CTTATTGATA
*
17562197 CCAGCTAAACTGGGCTTAAATTTGAGTACAAGCTAAACTAGGTTTAAAATTTGTGTG
1 CCAGCTAAACTAGGCTTAAATTTGAGTACAAGCTAAACTAGGTTTAAAATTTGTGTG
* * * * * * * *
17562254 CTAGCTAAACTAGGTTTAAAATATGAATACCAGCTAAATTAGGCTT-AAATTTGTGTA
1 CCAGCTAAACTAGGCTT-AAATTTGAGTACAAGCTAAACTAGGTTTAAAATTTGTGTG
* * * * *
17562311 CCAGCTAAACTAGACTTAAATTTGTGTGCTAGCTAAACT-GAGTTTAAAATTTGGGTG
1 CCAGCTAAACTAGGCTTAAATTTGAGTACAAGCTAAACTAG-GTTTAAAATTTGTGTG
* * * * * * *
17562368 CCAACTAAACTAGGCTTAAAATATGAGTGCTAA-CTAAATTAGGCTT-AAATATGTGTA
1 CCAGCTAAACTAGGCTT-AAATTTGAGTAC-AAGCTAAACTAGGTTTAAAATTTGTGTG
*
17562425 CCAACTAAACT
1 CCAGCTAAACT
17562436 GCGTTTAAAA
Statistics
Matches: 145, Mismatches: 31, Indels: 12
0.77 0.16 0.06
Matches are distributed among these distances:
55 1 0.01
56 19 0.13
57 81 0.56
58 42 0.29
59 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (57 bp):
CCAGCTAAACTAGGCTTAAATTTGAGTACAAGCTAAACTAGGTTTAAAATTTGTGTG
Done.