Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, 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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 85 of 117
Found at i:15376582 original size:35 final size:35
Alignment explanation
Indices: 15376509--15376588 Score: 90
Period size: 36 Copynumber: 2.3 Consensus size: 35
15376499 GTGAATTTCA
* * * * *
15376509 TTAAAACTTTCTCGATGGCAAATTCCAACCTTTGT
1 TTAAAACTTTCTCAACGGCAAAATCCAACCTATCT
*
15376544 TTAAAAACTTTCTCAACGGCAAAATCTAACC-ATCT
1 TT-AAAACTTTCTCAACGGCAAAATCCAACCTATCT
15376579 TTAAAACTTT
1 TTAAAACTTT
15376589 TTGGGTGGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 8 0.21
35 6 0.16
36 24 0.63
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (35 bp):
TTAAAACTTTCTCAACGGCAAAATCCAACCTATCT
Found at i:15377284 original size:12 final size:11
Alignment explanation
Indices: 15377264--15377293 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
15377254 TCTCTTAAAG
15377264 AAAAAAAAAAC
1 AAAAAAAAAAC
15377275 AAAAACAAAAAC
1 AAAAA-AAAAAC
15377287 AAAAAAA
1 AAAAAAA
15377294 CCAAGTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:15377466 original size:21 final size:20
Alignment explanation
Indices: 15377440--15377481 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
15377430 AGAAGAAACC
15377440 AAAGAAAAGAAAAAATCCTTT
1 AAAGAAAA-AAAAAATCCTTT
*
15377461 AAAGAAGAAAAAAATCCTTT
1 AAAGAAAAAAAAAATCCTTT
15377481 A
1 A
15377482 CCAAGCCCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.19
Consensus pattern (20 bp):
AAAGAAAAAAAAAATCCTTT
Found at i:15377768 original size:49 final size:49
Alignment explanation
Indices: 15377657--15377785 Score: 143
Period size: 49 Copynumber: 2.6 Consensus size: 49
15377647 ATGAAATCCG
* * * * *
15377657 TTGCCTATCTTTACAAGAGCACTTTTCAAATAATGATTTTTAAAGTTAC
1 TTGCCTATCTCTATAAGAGCACTTTTCAAAAAAAGATTTTTAAAGTCAC
** * * *
15377706 TTGTGTATGTCTATAGGAGTACTTTTCAAAAAAAGATTTTTAAAGTCAC
1 TTGCCTATCTCTATAAGAGCACTTTTCAAAAAAAGATTTTTAAAGTCAC
*
15377755 TTGCCTATCTCTATATA-AGCCCTTTTCAAAA
1 TTGCCTATCTCTATA-AGAGCACTTTTCAAAA
15377786 GGAAATTTTT
Statistics
Matches: 63, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
49 63 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (49 bp):
TTGCCTATCTCTATAAGAGCACTTTTCAAAAAAAGATTTTTAAAGTCAC
Found at i:15378058 original size:50 final size:49
Alignment explanation
Indices: 15377978--15378097 Score: 127
Period size: 50 Copynumber: 2.4 Consensus size: 49
15377968 AGAGCCATTT
* *** **
15377978 AAAAAAAAAAATTTAAAATTTGTTGGCTATCTTCATATG-AGTCATTTTC
1 AAAAAAAAAAATTTAAAGTTTGCCCGCTATCTTCATA-GAAACCATTTTC
*
15378027 AAAAAAATAAAATTTAAAGTTTGCCCTCTATCTTCATAGAAACCATTTTC
1 AAAAAAA-AAAATTTAAAGTTTGCCCGCTATCTTCATAGAAACCATTTTC
* *
15378077 -AAAAAGAAATTTTAAAGTTTG
1 AAAAAAAAAAATTTAAAGTTTG
15378098 TTACATATTT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
48 14 0.23
49 13 0.22
50 33 0.55
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (49 bp):
AAAAAAAAAAATTTAAAGTTTGCCCGCTATCTTCATAGAAACCATTTTC
Found at i:15378129 original size:48 final size:48
Alignment explanation
Indices: 15377945--15378134 Score: 183
Period size: 48 Copynumber: 3.9 Consensus size: 48
15377935 GATTTTTTAA
* *
15377945 AAAGTTTGTTGCTTATCTTTATAAGAGCCA-TTT-AAAAAAAAAAATTT
1 AAAGTTTGTTGC-TATCTTCATAGGAGCCATTTTCAAAAAAAAAAATTT
* * *
15377992 AAAATTTGTTGGCTATCTTCATATGAGTCATTTTCAAAAAAATAAAATTT
1 AAAGTTTGTT-GCTATCTTCATAGGAGCCATTTTCAAAAAAA-AAAATTT
* * * * *
15378042 AAAGTTTGCCCT-CTATCTTCATAGAAACCATTTTC-AAAAAGAAATTTT
1 AAAGTTTG--TTGCTATCTTCATAGGAGCCATTTTCAAAAAAAAAAATTT
* *
15378090 AAAGTTTGTTACATATTTTCATAGGAGCCA-TTTCAAAAAAAAAAA
1 AAAGTTTGTTGC-TATCTTCATAGGAGCCATTTTCAAAAAAAAAAA
15378135 AAATCTCTAA
Statistics
Matches: 116, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
46 1 0.01
47 28 0.24
48 41 0.35
49 12 0.10
50 33 0.28
52 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (48 bp):
AAAGTTTGTTGCTATCTTCATAGGAGCCATTTTCAAAAAAAAAAATTT
Found at i:15381056 original size:2 final size:2
Alignment explanation
Indices: 15381049--15381087 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
15381039 AAATCACAGA
15381049 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15381088 AACTAGCTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15381592 original size:42 final size:42
Alignment explanation
Indices: 15381511--15381595 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
15381501 TCACTCTATC
*
15381511 TTTTACATTTAACGAAGACTTTTATTAACCTACCCTTAAAAT
1 TTTTACATTTAACGAAGACTTTTATTAACCTACACTTAAAAT
* * *
15381553 TTTTACTTTTAATGAAAGA-TTTTATTAATCCT-CATTTAAAAT
1 TTTTACATTTAACG-AAGACTTTTATTAA-CCTACACTTAAAAT
15381595 T
1 T
15381596 ACTTTTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 30 0.81
43 7 0.19
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (42 bp):
TTTTACATTTAACGAAGACTTTTATTAACCTACACTTAAAAT
Found at i:15387698 original size:11 final size:11
Alignment explanation
Indices: 15387682--15387717 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
15387672 CTTGACTTTT
15387682 TTTTTCTATTC
1 TTTTTCTATTC
*
15387693 TTTTTCTATTA
1 TTTTTCTATTC
15387704 TTTTT-TATTC
1 TTTTTCTATTC
15387714 TTTT
1 TTTT
15387718 CCAAGCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTCTATTC
Found at i:15393127 original size:17 final size:17
Alignment explanation
Indices: 15393074--15393127 Score: 81
Period size: 17 Copynumber: 3.2 Consensus size: 17
15393064 TCACATACAT
*
15393074 AATTCCATGAAACCCCA
1 AATTCCATGAAACCTCA
* *
15393091 AAGTCTATGAAACCTCA
1 AATTCCATGAAACCTCA
15393108 AATTCCATGAAACCTCA
1 AATTCCATGAAACCTCA
15393125 AAT
1 AAT
15393128 CTTAAATCGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.22
Consensus pattern (17 bp):
AATTCCATGAAACCTCA
Found at i:15394081 original size:5 final size:5
Alignment explanation
Indices: 15394071--15394145 Score: 61
Period size: 5 Copynumber: 15.4 Consensus size: 5
15394061 TAAGTATTGA
**
15394071 TATTT TATTT TATGA TATTT TATTT ATATTT TGA--T TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT -TATTT T-ATTT TATTT TATTT TATTT
*
15394121 T-TATT TA-TT TA-TT TATTG TATTT TA
1 TAT-TT TATTT TATTT TATTT TATTT TA
15394146 AAAAAGAGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
3 1 0.02
4 11 0.19
5 39 0.68
6 6 0.11
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:15394867 original size:25 final size:25
Alignment explanation
Indices: 15394820--15394867 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
15394810 AAGTTTTTAA
* *
15394820 AGAGAAAATAGAGAGAATCAAGTAG
1 AGAGAAAAAAGAGAAAATCAAGTAG
* *
15394845 AGAGAAAAAAGGGAAAATTAAGT
1 AGAGAAAAAAGAGAAAATCAAGT
15394868 GAAAATTTGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.58, C:0.02, G:0.27, T:0.12
Consensus pattern (25 bp):
AGAGAAAAAAGAGAAAATCAAGTAG
Found at i:15395009 original size:8 final size:8
Alignment explanation
Indices: 15394996--15395046 Score: 68
Period size: 8 Copynumber: 6.2 Consensus size: 8
15394986 CCTATTTCAT
15394996 TTTTTTTA
1 TTTTTTTA
15395004 TTTTTTTA
1 TTTTTTTA
15395012 TTTTTTTA
1 TTTTTTTA
15395020 TCTTTTTTA
1 T-TTTTTTA
15395029 TTTGTTTT-
1 TTT-TTTTA
*
15395037 TTATTTTA
1 TTTTTTTA
15395045 TT
1 TT
15395047 GTTTGTTTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
7 4 0.10
8 23 0.59
9 12 0.31
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.84
Consensus pattern (8 bp):
TTTTTTTA
Found at i:15395026 original size:25 final size:25
Alignment explanation
Indices: 15394988--15395045 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
15394978 AAGTCCAACC
* *
15394988 TATTTCATTTTTTTTATTT-TTTTAT
1 TATTTTATCTTTTTTATTTGTTTT-T
*
15395013 TTTTTTATCTTTTTTATTTGTTTTT
1 TATTTTATCTTTTTTATTTGTTTTT
15395038 TATTTTAT
1 TATTTTAT
15395046 TGTTTGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.14, C:0.03, G:0.02, T:0.81
Consensus pattern (25 bp):
TATTTTATCTTTTTTATTTGTTTTT
Found at i:15395059 original size:16 final size:15
Alignment explanation
Indices: 15395024--15395067 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
15395014 TTTTTATCTT
15395024 TTTTATTTGTTTTTTA
1 TTTTA-TTGTTTTTTA
*
15395040 TTTTATTGTTTGTTTC
1 TTTTATTGTTT-TTTA
15395056 TTTTATTGTTTT
1 TTTTATTGTTTT
15395068 GATTATTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.09, C:0.02, G:0.09, T:0.80
Consensus pattern (15 bp):
TTTTATTGTTTTTTA
Found at i:15395500 original size:23 final size:25
Alignment explanation
Indices: 15395460--15395506 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
15395450 AATTTGACAA
*
15395460 TATATATTATCATGAA-TTTGTATG
1 TATATATTATCATAAATTTTGTATG
15395484 TATATA-TATCATAAATTTTGTAT
1 TATATATTATCATAAATTTTGTAT
15395507 TTGATTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (25 bp):
TATATATTATCATAAATTTTGTATG
Found at i:15397052 original size:19 final size:19
Alignment explanation
Indices: 15397016--15397055 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
15397006 TAAGATTTTA
15397016 TTTTTATTTTATTTTTTGAT
1 TTTTTATTTTA-TTTTTGAT
15397036 TTTTTATTTGTA-TTTTGAT
1 TTTTTATTT-TATTTTTGAT
15397055 T
1 T
15397056 GATTGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 9 0.47
21 2 0.11
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (19 bp):
TTTTTATTTTATTTTTGAT
Found at i:15397065 original size:26 final size:26
Alignment explanation
Indices: 15397011--15397070 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
15397001 GGTTTTAAGA
* **
15397011 TTTTATTTTTATTTTATTTTTTGATT
1 TTTTATTTGTATTTTATTGATTGATT
15397037 TTTTATTTGTATTTTGATTGATTGA-T
1 TTTTATTTGTATTTT-ATTGATTGATT
15397063 TTTTATTT
1 TTTTATTT
15397071 ATTGTATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 23 0.77
27 7 0.23
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (26 bp):
TTTTATTTGTATTTTATTGATTGATT
Found at i:15398165 original size:15 final size:15
Alignment explanation
Indices: 15398145--15398178 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
15398135 TATAAATTGG
*
15398145 TTTATTTATATTAAT
1 TTTATTTATATTAAA
*
15398160 TTTATTTATTTTAAA
1 TTTATTTATATTAAA
15398175 TTTA
1 TTTA
15398179 AGAAAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATTTATATTAAA
Found at i:15402734 original size:2 final size:2
Alignment explanation
Indices: 15402727--15402751 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15402717 GCACAGCTGT
15402727 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
15402752 TTGGGAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:15404453 original size:18 final size:18
Alignment explanation
Indices: 15404417--15404460 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
15404407 TCCTGACTTC
15404417 TCTTTCTCTTTCGTCTCTT
1 TCTTTC-CTTTCGTCTCTT
15404436 TCTTTCCTTGTC-TCTCTT
1 TCTTTCCTT-TCGTCTCTT
*
15404454 TTTTTCC
1 TCTTTCC
15404461 AAAGAATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.00, C:0.32, G:0.05, T:0.64
Consensus pattern (18 bp):
TCTTTCCTTTCGTCTCTT
Found at i:15406766 original size:13 final size:13
Alignment explanation
Indices: 15406750--15406774 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15406740 AATAATGAAA
15406750 TAAAAACATAAAT
1 TAAAAACATAAAT
15406763 TAAAAACATAAA
1 TAAAAACATAAA
15406775 AAATGCATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAAACATAAAT
Found at i:15407453 original size:24 final size:25
Alignment explanation
Indices: 15407425--15407481 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 25
15407415 TCTTTTTAGA
*
15407425 AAATTTTCATATTTTAAGAATA-TT
1 AAATTTTCATATTTTAAAAATATTT
*
15407449 AAA-TTTAATATTTTAAAAATATTT
1 AAATTTTCATATTTTAAAAATATTT
*
15407473 TAATTTTCA
1 AAATTTTCA
15407482 AAAAAATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 16 0.59
24 7 0.26
25 4 0.15
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (25 bp):
AAATTTTCATATTTTAAAAATATTT
Found at i:15409232 original size:17 final size:19
Alignment explanation
Indices: 15409210--15409247 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
15409200 ATATTATTTT
15409210 AATTTTGA-TGCA-TTAAA
1 AATTTTGATTGCATTTAAA
15409227 AATTTTGATTGCATTTAAA
1 AATTTTGATTGCATTTAAA
15409246 AA
1 AA
15409248 GGAGTAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (19 bp):
AATTTTGATTGCATTTAAA
Found at i:15411919 original size:4 final size:4
Alignment explanation
Indices: 15411905--15411949 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
15411895 TGGATACATA
* * *
15411905 AATG GATG AATG AATG AATA AATG AATG AATG AATG TATG AATG A
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG A
15411950 CAAAGCTCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.24, T:0.27
Consensus pattern (4 bp):
AATG
Found at i:15413225 original size:2 final size:2
Alignment explanation
Indices: 15413218--15413242 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15413208 AATGATACTA
15413218 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
15413243 CAAAAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15415258 original size:13 final size:13
Alignment explanation
Indices: 15415244--15415287 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
15415234 TTCAGTTGAG
*
15415244 GGTTTTATTTTAG
1 GGTTTTATTTTAA
15415257 GGTTTTATTTTAA
1 GGTTTTATTTTAA
*
15415270 GGTTTTACTTTAA
1 GGTTTTATTTTAA
15415283 GGTTT
1 GGTTT
15415288 CAAGGTTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.18, C:0.02, G:0.20, T:0.59
Consensus pattern (13 bp):
GGTTTTATTTTAA
Found at i:15415432 original size:21 final size:19
Alignment explanation
Indices: 15415408--15415453 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
15415398 ATATTTTCAC
15415408 TTTATTAAAATTTTATTACT
1 TTTATTAAAATTTTATTA-T
**
15415428 ATTTATTAATCTTTTATTAT
1 -TTTATTAAAATTTTATTAT
15415448 TTTATT
1 TTTATT
15415454 TTTATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 1 0.04
21 16 0.70
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATTAAAATTTTATTAT
Found at i:15420356 original size:145 final size:145
Alignment explanation
Indices: 15420152--15420661 Score: 471
Period size: 146 Copynumber: 3.5 Consensus size: 145
15420142 GATATTTTCA
* * * * **
15420152 TAATTTGACCTTCCCAAGCTTGAATTTTTC-TAAAAC-ATTCTAGACCTTAATCCTATAATATTT
1 TAATTTGACCTTTCCAAGCTTGAA-ATTTCATAAAACTTTTC-AGATCTTAATTTTATAATATTT
** * *
15420215 CATGATTTTTTATGCATTTAAAATCATAACAGTACCCTTAAAAGTGTGAAATTACTAAAATACTC
64 CATGATTTTTTATGCATTTAAAATCATAGTAGTACCCTCAAAAGTGTGAAATTACCAAAATACTC
15420280 TTATAGGGGTATTTTTG
129 TTATAGGGGTATTTTTG
* *
15420297 TAATTTGACCTTTCCAAGCTTGAAATTTCATAAAACTTTTCAGATCTTATTTTTGTAATATTTCA
1 TAATTTGACCTTTCCAAGCTTGAAATTTCATAAAACTTTTCAGATCTTAATTTTATAATATTTCA
** * * *
15420362 TTGATTTTTGGTG-AGTTCAAAATCATAGTAGTA-TCTCAAGAAATGTGAAATTACCAAAATA-T
66 -TGATTTTTTATGCA-TTTAAAATCATAGTAGTACCCTCAA-AAGTGTGAAATTACCAAAATACT
*
15420424 CCTT-TAAGGAGTATTTTTG
128 -CTTAT-AGGGGTATTTTTG
* * * * * * *
15420443 TAATTTGGCCTTTTCGAGCTTGGAATTTCATGAAACTTTAT-AGATTTTAGTTTTTATAATATTT
1 TAATTTGACCTTTCCAAGCTTGAAATTTCATAAAACTTT-TCAGATCTTA-ATTTTATAATATTT
* * * * *
15420507 CATAATTTTTTATGCATTTGAAATCATAGTAGT-CCTCTGAAAAGTGTGAAACTACCAAAATACC
64 CATGATTTTTTATGCATTTAAAATCATAGTAGTACC-CTCAAAAGTGTGAAATTACCAAAATACT
* *
15420571 CTTATATGGGTATTTATG
128 CTTATAGGGGTATTTTTG
*** ** ** * * * *
15420589 TAATTT-AGCCTTTTTGAGCTCAAAATTTCACGAAACTTTTCGGATCATAATATTATAATTTTTC
1 TAATTTGA-CCTTTCCAAGCTTGAAATTTCATAAAACTTTTCAGATCTTAATTTTATAATATTTC
15420653 ATGATTTTT
65 ATGATTTTT
15420662 AGTGTTTTAA
Statistics
Matches: 298, Mismatches: 51, Indels: 32
0.78 0.13 0.08
Matches are distributed among these distances:
144 4 0.01
145 76 0.26
146 196 0.66
147 22 0.07
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (145 bp):
TAATTTGACCTTTCCAAGCTTGAAATTTCATAAAACTTTTCAGATCTTAATTTTATAATATTTCA
TGATTTTTTATGCATTTAAAATCATAGTAGTACCCTCAAAAGTGTGAAATTACCAAAATACTCTT
ATAGGGGTATTTTTG
Found at i:15420600 original size:146 final size:144
Alignment explanation
Indices: 15420205--15420661 Score: 492
Period size: 146 Copynumber: 3.1 Consensus size: 144
15420195 ACCTTAATCC
** *
15420205 TATAATATTTCATGATTTTTTATGCATTTAAAATCATAACAGTACC-CTTAAAAGTGTGAAATTA
1 TATAATATTTCATGATTTTTTATGCATTTAAAATCATAGTAGT-CCTCTCAAAAGTGTGAAATTA
* * * * * *
15420269 CTAAAATACTCTTATAGGGGTATTTTTGTAATTTGACCTTTCCAAGCTTGAAATTTCATAAAACT
65 CCAAAATACCCTTATAAGGGTATTTTTGTAATTTG-CCTTTTCGAGCTTGAAATTTCATGAAACT
15420334 TTTCAGATCTTATTTT
129 TTTCAGATCTTATTTT
* ** * * *
15420350 TGTAATATTTCATTGATTTTTGGTG-AGTTCAAAATCATAGTAGT-ATCTCAAGAAATGTGAAAT
1 TATAATATTTCA-TGATTTTTTATGCA-TTTAAAATCATAGTAGTCCTCTCAA-AAGTGTGAAAT
* *
15420413 TACCAAAATATCCTT-TAAGGAGTATTTTTGTAATTTGGCCTTTTCGAGCTTGGAATTTCATGAA
63 TACCAAAATACCCTTATAAGG-GTATTTTTGTAATTT-GCCTTTTCGAGCTTGAAATTTCATGAA
*
15420477 ACTTTAT-AGATTTTAGTTTT
126 ACTTT-TCAGATCTTA-TTTT
* * * *
15420497 TATAATATTTCATAATTTTTTATGCATTTGAAATCATAGTAGTCCTCTGAAAAGTGTGAAACTAC
1 TATAATATTTCATGATTTTTTATGCATTTAAAATCATAGTAGTCCTCTCAAAAGTGTGAAATTAC
* * * ** *
15420562 CAAAATACCCTTATATGGGTATTTATGTAATTTAGCCTTTTTGAGCTCAAAATTTCACGAAACTT
66 CAAAATACCCTTATAAGGGTATTTTTGTAATTT-GCCTTTTCGAGCTTGAAATTTCATGAAACTT
* * * *
15420627 TTCGGATCATAATAT
130 TTCAGATCTTATTTT
*
15420642 TATAATTTTTCATGATTTTT
1 TATAATATTTCATGATTTTT
15420662 AGTGTTTTAA
Statistics
Matches: 256, Mismatches: 44, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
145 41 0.16
146 188 0.73
147 27 0.11
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (144 bp):
TATAATATTTCATGATTTTTTATGCATTTAAAATCATAGTAGTCCTCTCAAAAGTGTGAAATTAC
CAAAATACCCTTATAAGGGTATTTTTGTAATTTGCCTTTTCGAGCTTGAAATTTCATGAAACTTT
TCAGATCTTATTTT
Found at i:15427040 original size:2 final size:2
Alignment explanation
Indices: 15427033--15427059 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15427023 TGAACATACC
15427033 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
15427060 CAAGATAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15427135 original size:2 final size:2
Alignment explanation
Indices: 15427124--15427157 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
15427114 ATAAAACACC
15427124 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15427158 TTGCTAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15427213 original size:136 final size:136
Alignment explanation
Indices: 15427044--15427293 Score: 500
Period size: 136 Copynumber: 1.8 Consensus size: 136
15427034 ATATATATAT
15427044 ATATATATATATATATCAAGATAGACTTTTGTCGCTAATGATGAGACAACGTATAAAACACTTGT
1 ATATATATATATATATCAAGATAGACTTTTGTCGCTAATGATGAGACAACGTATAAAACACTTGT
15427109 AATGCATAAAACACCTATAATATATATATATATATATATATATATATATTTGCTAGAAAAGGAAG
66 AATGCATAAAACACCTATAATATATATATATATATATATATATATATATTTGCTAGAAAAGGAAG
15427174 ACTTTC
131 ACTTTC
15427180 ATATATATATATATATCAAGATAGACTTTTGTCGCTAATGATGAGACAACGTATAAAACACTTGT
1 ATATATATATATATATCAAGATAGACTTTTGTCGCTAATGATGAGACAACGTATAAAACACTTGT
15427245 AATGCATAAAACACCTATAATATATATATATATATATATATATATATAT
66 AATGCATAAAACACCTATAATATATATATATATATATATATATATATAT
15427294 GTGTGTGTGT
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 114 1.00
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (136 bp):
ATATATATATATATATCAAGATAGACTTTTGTCGCTAATGATGAGACAACGTATAAAACACTTGT
AATGCATAAAACACCTATAATATATATATATATATATATATATATATATTTGCTAGAAAAGGAAG
ACTTTC
Found at i:15427271 original size:2 final size:2
Alignment explanation
Indices: 15427260--15427293 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
15427250 ATAAAACACC
15427260 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15427294 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15435397 original size:12 final size:12
Alignment explanation
Indices: 15435380--15435405 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15435370 AAATCACCAT
15435380 CCAAACCCTAAA
1 CCAAACCCTAAA
15435392 CCAAACCCTAAA
1 CCAAACCCTAAA
15435404 CC
1 CC
15435406 CTAAATCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.46, G:0.00, T:0.08
Consensus pattern (12 bp):
CCAAACCCTAAA
Found at i:15435404 original size:7 final size:7
Alignment explanation
Indices: 15435382--15435507 Score: 76
Period size: 7 Copynumber: 19.3 Consensus size: 7
15435372 ATCACCATCC
15435382 AAACCCT
1 AAACCCT
15435389 AAA-CC-
1 AAACCCT
15435394 AAACCCT
1 AAACCCT
15435401 AAACCCT
1 AAACCCT
*
15435408 AAA-TC-
1 AAACCCT
15435413 AAACCCT
1 AAACCCT
15435420 AAACCCT
1 AAACCCT
*
15435427 AAACCTT
1 AAACCCT
**
15435434 AAATTCT
1 AAACCCT
15435441 AAACCCT
1 AAACCCT
15435448 AATA---T
1 AA-ACCCT
**
15435453 AAGGCCT
1 AAACCCT
15435460 ACAA-CCT
1 A-AACCCT
*
15435467 AAAACCT
1 AAACCCT
15435474 AAACCCT
1 AAACCCT
*
15435481 -AGCCCT
1 AAACCCT
15435487 AAA--CT
1 AAACCCT
*
15435492 GAACCCT
1 AAACCCT
15435499 AAACCCT
1 AAACCCT
15435506 AA
1 AA
15435508 CTTAGACCCT
Statistics
Matches: 91, Mismatches: 15, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
5 13 0.14
6 13 0.14
7 63 0.69
8 2 0.02
ACGTcount: A:0.44, C:0.35, G:0.03, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:15435405 original size:38 final size:39
Alignment explanation
Indices: 15435363--15435507 Score: 122
Period size: 38 Copynumber: 3.7 Consensus size: 39
15435353 ATCACCTTTC
* *
15435363 AAACCCTAAATCACCATCC-AAACCCTAAACC-AAACCCT
1 AAACCCTAAATCA-AACCCTAAACCCTAAACCTAAACCCT
**
15435401 AAACCCTAAATCAAACCCTAAACCCTAAACCTTAAATTCT
1 AAACCCTAAATCAAACCCTAAACCCTAAACC-TAAACCCT
**
15435441 AAACCCTAATAT-AAGGCCTACAA-CCTAAAACCTAAACCCT
1 AAACCCTAA-ATCAAACCCTA-AACCCT-AAACCTAAACCCT
* *
15435481 -AGCCCTAAA-CTGAACCCTAAACCCTAA
1 AAACCCTAAATC-AAACCCTAAACCCTAA
15435508 CTTAGACCCT
Statistics
Matches: 86, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
37 3 0.03
38 30 0.35
39 15 0.17
40 29 0.34
41 9 0.10
ACGTcount: A:0.44, C:0.36, G:0.03, T:0.17
Consensus pattern (39 bp):
AAACCCTAAATCAAACCCTAAACCCTAAACCTAAACCCT
Found at i:15435415 original size:19 final size:19
Alignment explanation
Indices: 15435324--15435429 Score: 94
Period size: 19 Copynumber: 5.6 Consensus size: 19
15435314 CATTTCTTAT
*
15435324 TAAACCCTAAATC-AACCA
1 TAAACCCTAAATCAAACCC
* *
15435342 TGAAACCTTAAATC--ACCTT
1 T-AAACCCTAAATCAAACC-C
* *
15435361 TCAAACCCTAAATCACCATCC
1 T-AAACCCTAAATCA-AACCC
*
15435382 -AAACCCTAAACCAAACCC
1 TAAACCCTAAATCAAACCC
15435400 TAAACCCTAAATCAAACCC
1 TAAACCCTAAATCAAACCC
15435419 TAAACCCTAAA
1 TAAACCCTAAA
15435430 CCTTAAATTC
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
18 7 0.10
19 63 0.88
22 2 0.03
ACGTcount: A:0.45, C:0.36, G:0.01, T:0.18
Consensus pattern (19 bp):
TAAACCCTAAATCAAACCC
Found at i:15435505 original size:19 final size:19
Alignment explanation
Indices: 15435382--15435507 Score: 98
Period size: 19 Copynumber: 6.5 Consensus size: 19
15435372 ATCACCATCC
*
15435382 AAACCCTAAACCAAACCCT
1 AAACCCTAAACTAAACCCT
15435401 AAACCCTAAA-TCAAACCCT
1 AAACCCTAAACT-AAACCCT
**
15435420 AAACCCTAAACCTTAAATTCT
1 AAACCCTAAA-C-TAAACCCT
**
15435441 AAACCCTAATA-TAAGGCCT
1 AAACCCTAA-ACTAAACCCT
15435460 ACAA-CCTAAAACCTAAACCCT
1 A-AACCCT-AAA-CTAAACCCT
* *
15435481 -AGCCCTAAACTGAACCCT
1 AAACCCTAAACTAAACCCT
15435499 AAACCCTAA
1 AAACCCTAA
15435508 CTTAGACCCT
Statistics
Matches: 85, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
18 8 0.09
19 48 0.56
20 7 0.08
21 20 0.24
22 2 0.02
ACGTcount: A:0.44, C:0.35, G:0.03, T:0.17
Consensus pattern (19 bp):
AAACCCTAAACTAAACCCT
Found at i:15445357 original size:21 final size:20
Alignment explanation
Indices: 15445333--15445371 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
15445323 GGTTATTGTT
15445333 AGAAAAAATAAATAAGATAAG
1 AGAAAAAATAAA-AAGATAAG
* *
15445354 AGAAATAATAGAAAGATA
1 AGAAAAAATAAAAAGATA
15445372 TTTTGGCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (20 bp):
AGAAAAAATAAAAAGATAAG
Found at i:15446211 original size:27 final size:27
Alignment explanation
Indices: 15446173--15446224 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
15446163 AATTTGAATG
15446173 GATTTTATTGGTGCTTAACAAACACAT
1 GATTTTATTGGTGCTTAACAAACACAT
15446200 GATTTTATTGGTGCTTAACAAACAC
1 GATTTTATTGGTGCTTAACAAACAC
15446225 TTAACAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (27 bp):
GATTTTATTGGTGCTTAACAAACACAT
Found at i:15452138 original size:33 final size:33
Alignment explanation
Indices: 15452065--15452369 Score: 257
Period size: 33 Copynumber: 9.5 Consensus size: 33
15452055 ACATCTTAGC
* *
15452065 TAAACTAGGCTTAAA--TT--TTGGGTGCCAGC
1 TAAACTAGGCTTAAATTTTCATTGGGTGCTAGT
* * *
15452094 TAAATTTGGCTTAAATTTTCATTGGGTGCTAGG
1 TAAACTAGGCTTAAATTTTCATTGGGTGCTAGT
* *
15452127 TAGACTAGGCTTAAATTTTTC-TT-GGTGCTAGA
1 TAAACTAGGCTTAAA-TTTTCATTGGGTGCTAGT
*
15452159 TAATCTAGGCTTAAGATTTTCATT-GGTGCTAGT
1 TAAACTAGGCTTAA-ATTTTCATTGGGTGCTAGT
15452192 TAAACT-GAGCTTAAATTTTCATTGGGTGCTAG-
1 TAAACTAG-GCTTAAATTTTCATTGGGTGCTAGT
* * *
15452224 CAAACTTGGCTTAAGATTTTCATTGGGTGCTAGA
1 TAAACTAGGCTTAA-ATTTTCATTGGGTGCTAGT
* * * *
15452258 TAATCT-GAGTTTAAGATTTTCATTGGTTG-TCAGC
1 TAAACTAG-GCTTAA-ATTTTCATTGGGTGCT-AGT
*
15452292 TAAACT-GGACTTAAATTTTCATTGGGTGCCAGT
1 TAAACTAGG-CTTAAATTTTCATTGGGTGCTAGT
*
15452325 TAAA-TAAGGCTTAAA---TC-TTGGGTGCCAGT
1 TAAACT-AGGCTTAAATTTTCATTGGGTGCTAGT
15452354 TAAACTAGGCTTAAAT
1 TAAACTAGGCTTAAAT
15452370 CCTTGGTAAC
Statistics
Matches: 233, Mismatches: 23, Indels: 39
0.79 0.08 0.13
Matches are distributed among these distances:
29 38 0.16
30 3 0.01
31 2 0.01
32 47 0.20
33 101 0.43
34 42 0.18
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (33 bp):
TAAACTAGGCTTAAATTTTCATTGGGTGCTAGT
Found at i:15452187 original size:65 final size:66
Alignment explanation
Indices: 15452082--15452320 Score: 244
Period size: 65 Copynumber: 3.6 Consensus size: 66
15452072 GGCTTAAATT
* * * *
15452082 TTGGGTGCCAGCTAAATTTGGCTTAA-ATTTTCATTGGGTGCTAGGTAGACT-AGGCTTAAATTT
1 TTGGGTGCTAGC-AAACTAGGCTTAAGATTTTCATTGGGTGCTAGGTAAACTGA-GCTTAAA-TT
15452145 TTC-
63 TTCA
*
15452148 TT-GGTGCTAG-ATAATCTAGGCTTAAGATTTTCATT-GGTGCTAGTTAAACTGAGCTTAAATTT
1 TTGGGTGCTAGCA-AA-CTAGGCTTAAGATTTTCATTGGGTGCTAGGTAAACTGAGCTTAAATTT
15452210 TCA
64 TCA
* * * *
15452213 TTGGGTGCTAGCAAACTTGGCTTAAGATTTTCATTGGGTGCTAGATAATCTGAGTTTAAGATTTT
1 TTGGGTGCTAGCAAACTAGGCTTAAGATTTTCATTGGGTGCTAGGTAAACTGAGCTTAA-ATTTT
15452278 CA
65 CA
*
15452280 TTGGTTG-TCAGCTAAACT-GGACTTAA-ATTTTCATTGGGTGC
1 TTGGGTGCT-AGC-AAACTAGG-CTTAAGATTTTCATTGGGTGC
15452321 CAGTTAAATA
Statistics
Matches: 151, Mismatches: 10, Indels: 23
0.82 0.05 0.12
Matches are distributed among these distances:
63 1 0.01
64 7 0.05
65 56 0.37
66 43 0.28
67 34 0.23
68 10 0.07
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (66 bp):
TTGGGTGCTAGCAAACTAGGCTTAAGATTTTCATTGGGTGCTAGGTAAACTGAGCTTAAATTTTC
A
Found at i:15452355 original size:29 final size:30
Alignment explanation
Indices: 15452313--15452375 Score: 103
Period size: 29 Copynumber: 2.1 Consensus size: 30
15452303 TAAATTTTCA
15452313 TTGGGTGCCAGTTAAA-TAAGGCTTAAAT-C
1 TTGGGTGCCAGTTAAACT-AGGCTTAAATCC
15452342 TTGGGTGCCAGTTAAACTAGGCTTAAATCC
1 TTGGGTGCCAGTTAAACTAGGCTTAAATCC
15452372 TTGG
1 TTGG
15452376 TAACAGTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 26 0.81
30 6 0.19
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (30 bp):
TTGGGTGCCAGTTAAACTAGGCTTAAATCC
Found at i:15452382 original size:29 final size:29
Alignment explanation
Indices: 15452321--15452398 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
15452311 CATTGGGTGC
**
15452321 CAGTTAAA-TAAGGCTTAAATCTTGGGTGC
1 CAGTTAAACT-AGGCTTAAATCTTGGGTAA
15452350 CAGTTAAACTAGGCTTAAATCCTT-GGTAA
1 CAGTTAAACTAGGCTTAAAT-CTTGGGTAA
* * *
15452379 CAGTTAGACTGGGTTTAAAT
1 CAGTTAAACTAGGCTTAAAT
15452399 TTTCCTTGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 38 0.90
30 4 0.10
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (29 bp):
CAGTTAAACTAGGCTTAAATCTTGGGTAA
Found at i:15452442 original size:32 final size:29
Alignment explanation
Indices: 15452406--15452479 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 29
15452396 AATTTTCCTT
*
15452406 GGTGCCAACTAATCTGGGCTTAAAATTCATTA
1 GGTGCCAGCTAATCTGGGCTTAAAA-TC--TA
* *
15452438 GGTGCTAGCTAGA-CTGTGCTTAAAATCTA
1 GGTGCCAGCTA-ATCTGGGCTTAAAATCTA
15452467 GGTGCCAGCTAAT
1 GGTGCCAGCTAAT
15452480 ATTAGGCTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
28 1 0.03
29 12 0.33
31 2 0.06
32 20 0.56
33 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (29 bp):
GGTGCCAGCTAATCTGGGCTTAAAATCTA
Found at i:15452522 original size:94 final size:95
Alignment explanation
Indices: 15452393--15452581 Score: 206
Period size: 96 Copynumber: 2.0 Consensus size: 95
15452383 TAGACTGGGT
* * * * * * * *
15452393 TTAAATTTTCCTTGGTGCCAACTAATCTGGGCTTAAAAT-TCATTA-G-GTGCTAGCTAGACTGT
1 TTAAATTTTCATTGATGCCAAATAATCTAGACTT-AAATCTCATTATGAATGCTAGCTAAACTGG
*
15452455 GCTTAAAATCTAGGTGCCAGCTAATATTAGGC
65 GCTTAAAACCTAGGTGCCAGCTAA-ATTAGGC
**
15452487 TTAAATTTTCATTGATGCCAAATAAAT-TAGACTTAAATCTTTTTATGAATGCTAGCTAAACTGG
1 TTAAATTTTCATTGATGCCAAAT-AATCTAGACTTAAATCTCATTATGAATGCTAGCTAAACTGG
* *
15452551 GTTTAAAACCTAGGTGCTAGCTAAATTAGGC
65 GCTTAAAACCTAGGTGCCAGCTAAATTAGGC
15452582 CAAATCTTAG
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
93 4 0.05
94 29 0.37
95 11 0.14
96 34 0.44
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (95 bp):
TTAAATTTTCATTGATGCCAAATAATCTAGACTTAAATCTCATTATGAATGCTAGCTAAACTGGG
CTTAAAACCTAGGTGCCAGCTAAATTAGGC
Found at i:15452802 original size:22 final size:22
Alignment explanation
Indices: 15452777--15452857 Score: 81
Period size: 22 Copynumber: 3.7 Consensus size: 22
15452767 TACATGCTAG
*
15452777 CTAAACTGGGCTTATGTGCCAA
1 CTAAACTAGGCTTATGTGCCAA
* * *
15452799 CTAAACTAAGCTTGTGTGCGAA
1 CTAAACTAGGCTTATGTGCCAA
* * * *
15452821 CTAATCTAGGCTAATCTGTCAA
1 CTAAACTAGGCTTATGTGCCAA
*
15452843 CTAAACTAAGCTTAT
1 CTAAACTAGGCTTAT
15452858 ATACCAGCTA
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (22 bp):
CTAAACTAGGCTTATGTGCCAA
Found at i:15453861 original size:26 final size:26
Alignment explanation
Indices: 15453832--15453882 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
15453822 TTTCATTTCA
15453832 TTTTTTCTTTTCCTTATTTTCCTTTG
1 TTTTTTCTTTTCCTTATTTTCCTTTG
* * *
15453858 TTTTTTTTTTTCTTTCTTTTCCTTT
1 TTTTTTCTTTTCCTTATTTTCCTTT
15453883 TCCTCATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (26 bp):
TTTTTTCTTTTCCTTATTTTCCTTTG
Found at i:15456864 original size:4 final size:4
Alignment explanation
Indices: 15456850--15456894 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
15456840 TGGATACATA
* * *
15456850 AATG GATG AATG AATG AATA AATG AATG AATG AATG CATG AATG A
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG A
15456895 CAAAGCTCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.49, C:0.02, G:0.24, T:0.24
Consensus pattern (4 bp):
AATG
Found at i:15460204 original size:13 final size:12
Alignment explanation
Indices: 15460187--15460230 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
15460177 TTCAGTTGAG
15460187 GGTTTTATTTTA
1 GGTTTTATTTTA
15460199 GCGTTTTATTTTAA
1 G-GTTTTATTTT-A
*
15460213 GGTTTTACTTTAA
1 GGTTTTA-TTTTA
15460226 GGTTT
1 GGTTT
15460231 CAAGGTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 1 0.04
13 22 0.79
14 5 0.18
ACGTcount: A:0.18, C:0.05, G:0.18, T:0.59
Consensus pattern (12 bp):
GGTTTTATTTTA
Found at i:15460507 original size:9 final size:9
Alignment explanation
Indices: 15460495--15460578 Score: 51
Period size: 9 Copynumber: 9.2 Consensus size: 9
15460485 TTTTAAGATT
*
15460495 TTTTTATTG
1 TTTTTATTA
15460504 TTTTTATTA
1 TTTTTATTA
*
15460513 TTTTTGTATA
1 TTTTTAT-TA
*** *
15460523 AACTTAATA
1 TTTTTATTA
* *
15460532 TTGTTCTTA
1 TTTTTATTA
*
15460541 TTATTATTA
1 TTTTTATTA
*
15460550 TTGTTATTA
1 TTTTTATTA
*
15460559 TTATTATTA
1 TTTTTATTA
*
15460568 TTATTATTA
1 TTTTTATTA
15460577 TT
1 TT
15460579 AATAAAAAAA
Statistics
Matches: 58, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
9 54 0.93
10 4 0.07
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (9 bp):
TTTTTATTA
Found at i:15460546 original size:3 final size:3
Alignment explanation
Indices: 15460538--15460579 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
15460528 AATATTGTTC
*
15460538 TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15460580 ATAAAAAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:15465668 original size:145 final size:143
Alignment explanation
Indices: 15465517--15465973 Score: 526
Period size: 146 Copynumber: 3.1 Consensus size: 143
15465507 ACCTTAATCC
** *
15465517 TATAATATTTCATGATTTTTGATGCATTTAAAATCATAACAGTACCTATAAAAGTGTGAAATTAC
1 TATAATATTTCATGATTTTTGATGCATTTAAAATCATAGTAGTACCTCTAAAAGTGTGAAATTAC
* * * *
15465582 CAAAATACTCTTATAAGGGTTTTTTTGTAATTTGACCTTTCCAAGCTTGAAATTTCATAAAACTT
66 CAAAATAC-CTTATAAGGGTATTTTTGTAATTTGACCTTTTCGAGCTTGAAATTTCATGAAACTT
15465647 TTCAGATCTCATTTT
130 TTCAGATCT-ATTTT
* * * * * * *
15465662 TGTAATATTTCATTGATTTTTGGTG-AGTTCAGAATCATAGTAGTATCTCGAGAAGTGTGAAATT
1 TATAATATTTCA-TGATTTTTGATGCA-TTTAAAATCATAGTAGTACCTCTAAAAGTGTGAAATT
* *
15465726 ACCAAAATACCTTTTAAGGGGTATTTTTGTAATTTTG-CCTTTTCGAGCTTGGAATTTCATGAAA
64 ACCAAAATACCTTATAA-GGGTATTTTTGTAA-TTTGACCTTTTCGAGCTTGAAATTTCATGAAA
*
15465790 CTTTTTAGATCTTAGTTTT
127 CTTTTCAGATC-TA-TTTT
* * *
15465809 TATAATATTTCATGATTTTTTATGCATTTGAAATCATAGTAGT-CCTCTGAAAAGTGTGAAACTA
1 TATAATATTTCATGATTTTTGATGCATTTAAAATCATAGTAGTACCTCT-AAAAGTGTGAAATTA
* * * ** *
15465873 CCAAAATACCTTTATATGGGTATTTATGTAATTT-AGCCTTTTTGAGCTCAAAATTTCACGAAAC
65 CCAAAATACC-TTATAAGGGTATTTTTGTAATTTGA-CCTTTTCGAGCTTGAAATTTCATGAAAC
* *
15465937 TTTTCAGATCATAATAT
128 TTTTCAGATC-TATTTT
15465954 TATAATATTTCATGATTTTT
1 TATAATATTTCATGATTTTT
15465974 AGTGTTTTAA
Statistics
Matches: 262, Mismatches: 39, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
145 46 0.18
146 191 0.73
147 25 0.10
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.42
Consensus pattern (143 bp):
TATAATATTTCATGATTTTTGATGCATTTAAAATCATAGTAGTACCTCTAAAAGTGTGAAATTAC
CAAAATACCTTATAAGGGTATTTTTGTAATTTGACCTTTTCGAGCTTGAAATTTCATGAAACTTT
TCAGATCTATTTT
Found at i:15467089 original size:21 final size:22
Alignment explanation
Indices: 15467064--15467127 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 22
15467054 ACTATGAGTT
*
15467064 ATTGTGA-TATATTGCTTTTAC
1 ATTGTGAGTATATTGCTTCTAC
* *
15467085 ATTGTTATGTTTATTGCTTCTAC
1 ATTGTGA-GTATATTGCTTCTAC
* *
15467108 ATTGTTATGTTTATTGCTTC
1 ATTGTGA-GTATATTGCTTC
15467128 ATGCCTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 6 0.16
23 32 0.84
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.56
Consensus pattern (22 bp):
ATTGTGAGTATATTGCTTCTAC
Found at i:15467100 original size:23 final size:23
Alignment explanation
Indices: 15467073--15467127 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
15467063 TATTGTGATA
*
15467073 TATTGCTTTTACATTGTTATGTT
1 TATTGCTTCTACATTGTTATGTT
15467096 TATTGCTTCTACATTGTTATGTT
1 TATTGCTTCTACATTGTTATGTT
15467119 TATTGCTTC
1 TATTGCTTC
15467128 ATGCCTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.16, C:0.13, G:0.13, T:0.58
Consensus pattern (23 bp):
TATTGCTTCTACATTGTTATGTT
Found at i:15474292 original size:13 final size:13
Alignment explanation
Indices: 15474274--15474316 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
15474264 TTCGCTTGAA
15474274 AAAAAAAAGAAAG
1 AAAAAAAAGAAAG
*
15474287 AAAAAAAAGATAG
1 AAAAAAAAGAAAG
15474300 AAAAAAAAGAAAAG
1 AAAAAAAAG-AAAG
15474314 AAA
1 AAA
15474317 GGAAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 21 0.78
14 6 0.22
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Found at i:15474312 original size:18 final size:17
Alignment explanation
Indices: 15474272--15474336 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
15474262 ATTTCGCTTG
*
15474272 AAAAAAA-AAAGAAAGA
1 AAAAAAAGAAAGAAAAA
*
15474288 AAAAAAAGATAGAAAAA
1 AAAAAAAGAAAGAAAAA
15474305 AAAGAAAAGAAAGGAAAAA
1 AAA-AAAAGAAA-GAAAAA
15474324 ATAAAAAA-AAAGA
1 A-AAAAAAGAAAGA
15474337 TTCGAACTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
16 7 0.17
17 12 0.29
18 10 0.24
19 11 0.26
20 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAAAGAAAAA
Found at i:15474313 original size:27 final size:26
Alignment explanation
Indices: 15474273--15474336 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 26
15474263 TTTCGCTTGA
15474273 AAAAAAAAAG-AAAGAAA-AAAAAGAT
1 AAAAAAAAAGAAAAGAAAGAAAAA-AT
15474298 AGAAAAAAAAGAAAAGAAAGGAAAAAAT
1 A-AAAAAAAAGAAAAGAAA-GAAAAAAT
15474326 AAAAAAAAAGA
1 AAAAAAAAAGA
15474337 TTCGAACTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
25 1 0.03
26 9 0.26
27 17 0.49
28 3 0.09
29 5 0.14
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (26 bp):
AAAAAAAAAGAAAAGAAAGAAAAAAT
Found at i:15474321 original size:10 final size:9
Alignment explanation
Indices: 15474274--15474336 Score: 58
Period size: 9 Copynumber: 7.1 Consensus size: 9
15474264 TTCGCTTGAA
15474274 AAAAAAAAG
1 AAAAAAAAG
*
15474283 AAAGAAAA-
1 AAAAAAAAG
* *
15474291 AAAAGATAG
1 AAAAAAAAG
15474300 AAAAAAAAG
1 AAAAAAAAG
*
15474309 AAAAGAAAGG
1 AAAA-AAAAG
*
15474319 AAAAAATA-
1 AAAAAAAAG
15474327 AAAAAAAAG
1 AAAAAAAAG
15474336 A
1 A
15474337 TTCGAACTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
8 12 0.29
9 21 0.51
10 8 0.20
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:15475326 original size:36 final size:35
Alignment explanation
Indices: 15475263--15475331 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
15475253 CTGGTTGTTC
* *
15475263 TTATTTTTTGACTTGCGATTTAGTCCCAATCATAT
1 TTATTTTTTGACTTACAATTTAGTCCCAATCATAT
* * *
15475298 TTATTTTCTTGGCTTACAATTTATTCCCAGTCAT
1 TTATTTT-TTGACTTACAATTTAGTCCCAATCAT
15475332 TTTTTTCGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 7 0.25
36 21 0.75
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.49
Consensus pattern (35 bp):
TTATTTTTTGACTTACAATTTAGTCCCAATCATAT
Found at i:15475713 original size:142 final size:142
Alignment explanation
Indices: 15475564--15475819 Score: 320
Period size: 142 Copynumber: 1.8 Consensus size: 142
15475554 TCAACTTGTA
* * * *
15475564 GTTTAGTCCCAATTATATTTATTTTCTTGGCTTACGGTTTAATCTCGCTCATCTTT-TTTCTCAA
1 GTTTAGTCCCAATCATATTTATTTTCTTGGCTTACGATTTAATCCCGATCATCTTTGTTTC-CAA
* * *
15475628 CTTCAT-GTTCAATCTAAGTCATATTTATTTTT-TCTACTTGCAGTTTAGTCCCAATCATCTTTA
65 CTT-ATGGTTCAATCTAAGTCAAATTTATTTTTAT-GACTTGCAATTTAGTCCCAATCATCTTTA
15475691 TTTTCTTAACCTGAG
128 TTTTCTTAACCTGAG
** * ** *
15475706 GTTTAGTCTTAGTCATATTTATTTTCTTGGCTTGTGATTTAATCCCGATCATTTTTGTTTCCAAC
1 GTTTAGTCCCAATCATATTTATTTTCTTGGCTTACGATTTAATCCCGATCATCTTTGTTTCCAAC
* **
15475771 TTGTGGTTCAATCTTGGTCAAATTTATTTTTATGACTTGCAATTTAGTC
66 TTATGGTTCAATCTAAGTCAAATTTATTTTTATGACTTGCAATTTAGTC
15475820 TTGATTATCT
Statistics
Matches: 95, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
141 1 0.01
142 89 0.94
143 5 0.05
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49
Consensus pattern (142 bp):
GTTTAGTCCCAATCATATTTATTTTCTTGGCTTACGATTTAATCCCGATCATCTTTGTTTCCAAC
TTATGGTTCAATCTAAGTCAAATTTATTTTTATGACTTGCAATTTAGTCCCAATCATCTTTATTT
TCTTAACCTGAG
Found at i:15475757 original size:72 final size:69
Alignment explanation
Indices: 15475578--15475800 Score: 164
Period size: 70 Copynumber: 3.2 Consensus size: 69
15475568 AGTCCCAATT
* * * *
15475578 ATATTTATTTTCTTGGCTTACGG-TTTAATCTCGCTCATCTTTTTTCTCAACTTCATGTTCAATC
1 ATATTTATTTTCTTGGCTT--GGATTTAATCCCGATCATCTTTTTTCTCAACCTCAGGTTCAATC
15475642 TAAGTC
64 TAAGTC
** * * * * * * *
15475648 ATATTTATTTT-TTCTACTTGCAGTTTAGTCCCAATCATCTTTATTTTCTTAACCTGAGGTTTAG
1 ATATTTATTTTCTT-GGCTTGGA-TTTAATCCCGATCATC-TT-TTTTCTCAACCTCAGGTTCAA
*
15475712 TCTTAGTC
62 TCTAAGTC
* * **
15475720 ATATTTATTTTCTTGGCTTGTGATTTAATCCCGATCATTTTTGTTTC-CAACTTGTGGTTCAATC
1 ATATTTATTTTCTTGGCTTG-GATTTAATCCCGATCATCTTT-TTTCTCAACCTCAGGTTCAATC
**
15475784 TTGGTC
64 TAAGTC
*
15475790 AAATTTATTTT
1 ATATTTATTTT
15475801 TATGACTTGC
Statistics
Matches: 118, Mismatches: 27, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
68 1 0.01
69 2 0.02
70 54 0.46
71 8 0.07
72 50 0.42
73 3 0.03
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.50
Consensus pattern (69 bp):
ATATTTATTTTCTTGGCTTGGATTTAATCCCGATCATCTTTTTTCTCAACCTCAGGTTCAATCTA
AGTC
Found at i:15475899 original size:36 final size:35
Alignment explanation
Indices: 15475859--15475931 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
15475849 TTTAATCCTA
* *
15475859 ATTATCTTTCTTTTCACATCTTGTGATTCAATCTCG
1 ATTATCTTTATTTTCACAT-TTGTGATTCAATATCG
***
15475895 ATTATCTTTATTTTTTTATTTGTGATTCAATATCG
1 ATTATCTTTATTTTCACATTTGTGATTCAATATCG
15475930 AT
1 AT
15475932 CACTTTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
35 17 0.53
36 15 0.47
ACGTcount: A:0.22, C:0.15, G:0.08, T:0.55
Consensus pattern (35 bp):
ATTATCTTTATTTTCACATTTGTGATTCAATATCG
Found at i:15482615 original size:2 final size:2
Alignment explanation
Indices: 15482608--15482638 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15482598 TGAACATACC
15482608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15482639 CAAGATAGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15482707 original size:2 final size:2
Alignment explanation
Indices: 15482696--15482735 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
15482686 ATAAAACACC
*
15482696 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15482736 TTGCTAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:15492540 original size:2 final size:2
Alignment explanation
Indices: 15492531--15492562 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
15492521 ATAATAAAAA
15492531 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15492563 GAAGAAAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15493108 original size:28 final size:28
Alignment explanation
Indices: 15493077--15493130 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
15493067 ATGTTAAAAG
*
15493077 AAAAAGAAAAAG-AAAAAAATTAAAAACT
1 AAAAA-AAAAAGCAAAAAAATGAAAAACT
*
15493105 AAAAAAAAAAGCAATAAAATGAAAAA
1 AAAAAAAAAAGCAAAAAAATGAAAAA
15493131 AACTGAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.80, C:0.04, G:0.07, T:0.09
Consensus pattern (28 bp):
AAAAAAAAAAGCAAAAAAATGAAAAACT
Found at i:15493342 original size:21 final size:21
Alignment explanation
Indices: 15493325--15493366 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
15493315 TATAAAATTT
*
15493325 ATTAATAAAAACTAAAAATAG
1 ATTAATAAAAAATAAAAATAG
*
15493346 CTTAATAAAAAAT-AAAATAG
1 ATTAATAAAAAATAAAAATAG
15493366 A
1 A
15493367 AAAAACAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (21 bp):
ATTAATAAAAAATAAAAATAG
Found at i:15494511 original size:12 final size:12
Alignment explanation
Indices: 15494496--15494564 Score: 75
Period size: 12 Copynumber: 5.8 Consensus size: 12
15494486 GAAAATATTA
*
15494496 ATGAAGATAGTG
1 ATGAAGATACTG
*
15494508 ATGAAGATATTG
1 ATGAAGATACTG
* *
15494520 ATGAGGGTACTG
1 ATGAAGATACTG
*
15494532 ATGAAGATATTG
1 ATGAAGATACTG
* *
15494544 ATAAAGATACTA
1 ATGAAGATACTG
15494556 ATGAAGATA
1 ATGAAGATA
15494565 GTGCTAAACA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.28
Consensus pattern (12 bp):
ATGAAGATACTG
Found at i:15494554 original size:24 final size:24
Alignment explanation
Indices: 15494474--15494564 Score: 92
Period size: 24 Copynumber: 3.8 Consensus size: 24
15494464 TAATAGTAAA
** * *
15494474 AAAGATAAGGATGAAAATATTAAT
1 AAAGATACTGATGAAGATATTGAT
* *
15494498 GAAGATAGTGATGAAGATATTGAT
1 AAAGATACTGATGAAGATATTGAT
* * *
15494522 GAGGGTACTGATGAAGATATTGAT
1 AAAGATACTGATGAAGATATTGAT
*
15494546 AAAGATACTAATGAAGATA
1 AAAGATACTGATGAAGATA
15494565 GTGCTAAACA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.47, C:0.02, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAGATACTGATGAAGATATTGAT
Found at i:15494572 original size:24 final size:24
Alignment explanation
Indices: 15494499--15494572 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 24
15494489 AATATTAATG
* * * *
15494499 AAGATAGTGATGAAGATATTGATG
1 AAGATACTAATGAAGATAGTGATA
* * * *
15494523 AGGGTACTGATGAAGATATTGATA
1 AAGATACTAATGAAGATAGTGATA
*
15494547 AAGATACTAATGAAGATAGTGCTA
1 AAGATACTAATGAAGATAGTGATA
15494571 AA
1 AA
15494573 CATGGGACTG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.27
Consensus pattern (24 bp):
AAGATACTAATGAAGATAGTGATA
Found at i:15495900 original size:24 final size:24
Alignment explanation
Indices: 15495873--15495951 Score: 92
Period size: 24 Copynumber: 3.3 Consensus size: 24
15495863 AAATATAAGA
*
15495873 TAAATAAATAAATAATTTACATGG
1 TAAATAAATAAATAATTTACATGC
15495897 TAAATAAATAAATAAAATTTA-A--C
1 TAAATAAATAAAT--AATTTACATGC
* *
15495920 TAAATAAATAAACAATTTACATGT
1 TAAATAAATAAATAATTTACATGC
15495944 TAAATAAA
1 TAAATAAA
15495952 CAATTATTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
21 6 0.13
22 1 0.02
23 12 0.26
24 21 0.45
25 1 0.02
26 6 0.13
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (24 bp):
TAAATAAATAAATAATTTACATGC
Found at i:15495937 original size:47 final size:48
Alignment explanation
Indices: 15495850--15495951 Score: 145
Period size: 47 Copynumber: 2.1 Consensus size: 48
15495840 TTAATTTAAA
*
15495850 AAATAAATAATAAAAATATAAGATAAATAAATAAATAATTTACATGGT
1 AAATAAATAATAAAAATATAAGATAAATAAATAAACAATTTACATGGT
* * *
15495898 AAATAAATAA-ATAAAATTTAA-CTAAATAAATAAACAATTTACATGTT
1 AAATAAATAATA-AAAATATAAGATAAATAAATAAACAATTTACATGGT
15495945 AAATAAA
1 AAATAAA
15495952 CAATTATTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
47 31 0.63
48 18 0.37
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (48 bp):
AAATAAATAATAAAAATATAAGATAAATAAATAAACAATTTACATGGT
Found at i:15497723 original size:25 final size:25
Alignment explanation
Indices: 15497689--15497747 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
15497679 TACTTTCTAA
15497689 CATTGCCTAGGGATCTTGGTCTTAG
1 CATTGCCTAGGGATCTTGGTCTTAG
15497714 CATTGCCTAGGGATCTTGGTCTTAG
1 CATTGCCTAGGGATCTTGGTCTTAG
15497739 CATTGCCTA
1 CATTGCCTA
15497748 TTGCCCATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (25 bp):
CATTGCCTAGGGATCTTGGTCTTAG
Found at i:15498111 original size:25 final size:25
Alignment explanation
Indices: 15498044--15498112 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 25
15498034 ACTCAAACCT
*
15498044 AACCTAACCTAAATCCAAACCCTAA
1 AACCTAACCTAAATTCAAACCCTAA
* *
15498069 AACCTAACCTAAAATCAAACCCTGA
1 AACCTAACCTAAATTCAAACCCTAA
* *
15498094 AACCTATCCTTAATTCAAA
1 AACCTAACCTAAATTCAAA
15498113 AATCTAATCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.20
Consensus pattern (25 bp):
AACCTAACCTAAATTCAAACCCTAA
Found at i:15498277 original size:18 final size:18
Alignment explanation
Indices: 15498219--15498308 Score: 65
Period size: 18 Copynumber: 4.7 Consensus size: 18
15498209 ACCCTAAAAC
* *
15498219 CAACCCCTAAACTAAAGT
1 CAACCTCTAAACCAAAGT
* *
15498237 TAACC-CTTAAACCCCAAATT
1 CAACCTC-TAAA--CCAAAGT
15498257 CAACCTCTAAACCAAAGT
1 CAACCTCTAAACCAAAGT
* *
15498275 CAACCTCGAAACCTTAAGAT
1 CAACCTCTAAACC-AAAG-T
15498295 CCAACCTCTAAACC
1 -CAACCTCTAAACC
15498309 CAAAATCAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
17 1 0.02
18 26 0.46
19 3 0.05
20 14 0.25
21 13 0.23
ACGTcount: A:0.41, C:0.36, G:0.04, T:0.19
Consensus pattern (18 bp):
CAACCTCTAAACCAAAGT
Found at i:15498287 original size:38 final size:39
Alignment explanation
Indices: 15498218--15498317 Score: 96
Period size: 38 Copynumber: 2.6 Consensus size: 39
15498208 AACCCTAAAA
* * * *
15498218 CCAACCCCTAAACTAAAGTTAACCCTTAAACCCCAA-AT
1 CCAACCTCTAAACCAAAGTCAACCCTGAAACCCCAAGAT
* **
15498256 TCAACCTCTAAACCAAAGTCAA-CCTCGAAACCTTAAGAT
1 CCAACCTCTAAACCAAAGTCAACCCT-GAAACCCCAAGAT
*
15498295 CCAACCTCTAAACCCAAAATCAA
1 CCAACCTCTAAA-CCAAAGTCAA
15498318 ACCCAAACCT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
37 3 0.06
38 25 0.50
39 13 0.26
40 9 0.18
ACGTcount: A:0.43, C:0.35, G:0.04, T:0.18
Consensus pattern (39 bp):
CCAACCTCTAAACCAAAGTCAACCCTGAAACCCCAAGAT
Found at i:15498306 original size:39 final size:36
Alignment explanation
Indices: 15498257--15498345 Score: 101
Period size: 39 Copynumber: 2.4 Consensus size: 36
15498247 ACCCCAAATT
*
15498257 CAACCTCTAAACCAAAGTC-AACCTCGAAACCTTAAGATC
1 CAACCTCTAAACCAAAATCAAACC-C-AAACCTTAA-A-C
15498296 CAACCTCTAAACCCAAAATCAAACCCAAACCTTAAAC
1 CAACCTCTAAA-CCAAAATCAAACCCAAACCTTAAAC
15498333 CTAACC-CTAAACC
1 C-AACCTCTAAACC
15498346 CTAACCTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
36 2 0.04
37 7 0.15
38 5 0.11
39 20 0.43
40 8 0.17
41 4 0.09
ACGTcount: A:0.44, C:0.37, G:0.03, T:0.16
Consensus pattern (36 bp):
CAACCTCTAAACCAAAATCAAACCCAAACCTTAAAC
Found at i:15498311 original size:13 final size:13
Alignment explanation
Indices: 15498295--15498352 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
15498285 ACCTTAAGAT
15498295 CCAACCTCTAAAC
1 CCAACCTCTAAAC
**
15498308 CCAAAATC-AAAC
1 CCAACCTCTAAAC
15498320 CCAAACCT-TAAAC
1 CC-AACCTCTAAAC
*
15498333 CTAACC-CTAAAC
1 CCAACCTCTAAAC
15498345 CCTAACCT
1 CC-AACCT
15498353 AAATCCTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
12 16 0.47
13 18 0.53
ACGTcount: A:0.43, C:0.41, G:0.00, T:0.16
Consensus pattern (13 bp):
CCAACCTCTAAAC
Found at i:15505656 original size:11 final size:10
Alignment explanation
Indices: 15505631--15505655 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15505621 GAAAAAAATG
15505631 AAAAATTTAA
1 AAAAATTTAA
15505641 AAAAATTTAA
1 AAAAATTTAA
15505651 AAAAA
1 AAAAA
15505656 AGAAAAAAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATTTAA
Found at i:15505719 original size:5 final size:6
Alignment explanation
Indices: 15505703--15505751 Score: 64
Period size: 6 Copynumber: 7.8 Consensus size: 6
15505693 AAAAAGTTGT
15505703 GAAAAA GAAAAA GAAAAA GAATAAA -ACCAAAA GAAAAA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAA-AAA GA--AAAA GAAAAA GAAAAA GAAAA
15505752 CAAAAACAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 31 0.79
7 6 0.15
8 2 0.05
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:15506165 original size:9 final size:10
Alignment explanation
Indices: 15506145--15506178 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
15506135 AAAAAATGGG
15506145 AAATTAAAAA
1 AAATTAAAAA
15506155 AAATTAAAAA
1 AAATTAAAAA
**
15506165 AAAAGAAAAA
1 AAATTAAAAA
15506175 AAAT
1 AAAT
15506179 CAAGCTAGCT
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:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (10 bp):
AAATTAAAAA
Found at i:15506253 original size:6 final size:6
Alignment explanation
Indices: 15506213--15506241 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
15506203 AAAAAGTTGT
15506213 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
15506242 CAAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:15514209 original size:37 final size:37
Alignment explanation
Indices: 15514149--15514226 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
15514139 AAATTCTTCA
* * * *
15514149 ATTTCATTATTTAAAACTGCACATGAGATTAATGTGT
1 ATTTCATTATTTAAAACTACACATGAAATTAACGTAT
** *
15514186 ATTTCATTATTTTTACCTACACATGAAATTAACGTAT
1 ATTTCATTATTTAAAACTACACATGAAATTAACGTAT
15514223 ATTT
1 ATTT
15514227 AGGAGTAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.44
Consensus pattern (37 bp):
ATTTCATTATTTAAAACTACACATGAAATTAACGTAT
Found at i:15517743 original size:27 final size:29
Alignment explanation
Indices: 15517690--15517748 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 29
15517680 AATCTTTTTT
* *
15517690 TTTTTTAATTTTCTTTTGAAAGCAAATAA
1 TTTTTTAATTTTCTTTTAAAAGAAAATAA
* *
15517719 TTTTTTAA-TTT-TTTTAAAATAAAATTA
1 TTTTTTAATTTTCTTTTAAAAGAAAATAA
15517746 TTT
1 TTT
15517749 ATTTTTGGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 15 0.58
28 3 0.12
29 8 0.31
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (29 bp):
TTTTTTAATTTTCTTTTAAAAGAAAATAA
Found at i:15518256 original size:13 final size:13
Alignment explanation
Indices: 15518238--15518551 Score: 135
Period size: 13 Copynumber: 24.2 Consensus size: 13
15518228 TCTCAATTAG
15518238 GGTTTAGGGTTTA
1 GGTTTAGGGTTTA
**
15518251 GGTTTAGAATTTA
1 GGTTTAGGGTTTA
*
15518264 GG-TTA-GGTTTG
1 GGTTTAGGGTTTA
* *
15518275 GGATTT-TGGATTA
1 GG-TTTAGGGTTTA
15518288 GGGTTTAGGG-TTA
1 -GGTTTAGGGTTTA
* * ** *
15518301 AGTATAGATTTTT
1 GGTTTAGGGTTTA
15518314 GGTTTAGGG-TTA
1 GGTTTAGGGTTTA
* *
15518326 GGGTTTA-AGTATTG
1 -GGTTTAGGGT-TTA
15518340 GGTTTAGGGTTTA
1 GGTTTAGGGTTTA
15518353 GGTTTAAGGG-TTA
1 GGTTT-AGGGTTTA
* * *
15518366 TGG-CTAGGTTTTG
1 -GGTTTAGGGTTTA
* *
15518379 GGTTTAAGGTTTT
1 GGTTTAGGGTTTA
*
15518392 GGTTTAGGGTTAA
1 GGTTTAGGGTTTA
*
15518405 GTTTTAGGGTTTAA
1 GGTTTAGGGTTT-A
*
15518419 GGTTTCA--ATTTA
1 GGTTT-AGGGTTTA
* *
15518431 GGGTTAAGGTTTA
1 GGTTTAGGGTTTA
*
15518444 GGATTTTGGGTTTA
1 GG-TTTAGGGTTTA
*
15518458 GTGTTTAGGATTTA
1 G-GTTTAGGGTTTA
*
15518472 GGTTCAGGGTTTA
1 GGTTTAGGGTTTA
* *
15518485 GGGTTAAGGTTTA
1 GGTTTAGGGTTTA
** *
15518498 TATTTAAGGTTTA
1 GGTTTAGGGTTTA
* * * *
15518511 GATCTAGAGTTTT
1 GGTTTAGGGTTTA
* *
15518524 GATTTATGGTTTA
1 GGTTTAGGGTTTA
*
15518537 GGTTTAGTGTTTA
1 GGTTTAGGGTTTA
15518550 GG
1 GG
15518552 GTTTTAGTTT
Statistics
Matches: 218, Mismatches: 63, Indels: 40
0.68 0.20 0.12
Matches are distributed among these distances:
11 6 0.03
12 21 0.10
13 151 0.69
14 38 0.17
15 2 0.01
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (13 bp):
GGTTTAGGGTTTA
Found at i:15518465 original size:21 final size:20
Alignment explanation
Indices: 15518212--15518486 Score: 78
Period size: 20 Copynumber: 14.4 Consensus size: 20
15518202 ATTTTAGGTC
15518212 GGTTTAGGATTTAGGGTCTCAA
1 GGTTTAGGATTTAGGGT-T-AA
* *
15518234 ---TTAGGGTTTAGGGTTTA
1 GGTTTAGGATTTAGGGTTAA
*
15518251 GGTTTAGAATTTA-GGTT-A
1 GGTTTAGGATTTAGGGTTAA
* * * *
15518269 GGTTTGGGATTTTGGATTAG
1 GGTTTAGGATTTAGGGTTAA
* *
15518289 GGTTTAGG-GTTA-AG-TATA
1 GGTTTAGGATTTAGGGTTA-A
* * *
15518307 GATTTTTGG-TTTAGGGTTAG
1 G-GTTTAGGATTTAGGGTTAA
* *
15518327 GGTTTAAG-TATT-GGGTTTAG
1 GGTTTAGGAT-TTAGGG-TTAA
*
15518347 GGTTTAGG-TTTAAGGGTTAT
1 GGTTTAGGATTT-AGGGTTAA
* *
15518367 GG-CTAGG-TTTTGGGTTTAA
1 GGTTTAGGATTTAGGG-TTAA
*
15518386 GGTTTTGG-TTTAGGGTTAA
1 GGTTTAGGATTTAGGGTTAA
15518405 -G--T----TTTAGGGTTTAA
1 GGTTTAGGATTTAGGG-TTAA
15518419 GGTTTCA--ATTTAGGGTTAA
1 GGTTT-AGGATTTAGGGTTAA
* *
15518438 GGTTTAGGATTTTGGGTTTA
1 GGTTTAGGATTTAGGGTTAA
*
15518458 GTGTTTAGGATTTA-GGTTCAG
1 G-GTTTAGGATTTAGGGTT-AA
15518479 GGTTTAGG
1 GGTTTAGG
15518487 GTTAAGGTTT
Statistics
Matches: 191, Mismatches: 36, Indels: 54
0.68 0.13 0.19
Matches are distributed among these distances:
13 7 0.04
14 4 0.02
15 1 0.01
16 1 0.01
17 4 0.02
18 18 0.09
19 65 0.34
20 74 0.39
21 17 0.09
ACGTcount: A:0.20, C:0.02, G:0.34, T:0.44
Consensus pattern (20 bp):
GGTTTAGGATTTAGGGTTAA
Found at i:15518548 original size:7 final size:6
Alignment explanation
Indices: 15518238--15518551 Score: 103
Period size: 7 Copynumber: 48.3 Consensus size: 6
15518228 TCTCAATTAG
* * * *
15518238 GGTTTA GGGTTTA GGTTTA GAATTTA GG-TTA GGTTTG GGATTTT GGATTA
1 GGTTTA -GGTTTA GGTTTA G-GTTTA GGTTTA GGTTTA GG-TTTA GGTTTA
* * * * * * * *
15518288 GGGTTTA GGGTTA AGTATA GATTTTT GGTTTA GGGTTA GGGTTTA AGTATTG
1 -GGTTTA GGTTTA GGTTTA G-GTTTA GGTTTA GGTTTA -GGTTTA GGT-TTA
* * * *
15518340 GGTTTA GGGTTTA GGTTTAA GGGTTA TGG-CTA GGTTTTG GGTTTAA GGTTTT
1 GGTTTA -GGTTTA GGTTT-A GGTTTA -GGTTTA GG-TTTA GGTTT-A GGTTTA
* * * *
15518392 GGTTTA GGGTTAA GTTTTA GGGTTTAA GGTTTCA -ATTTA GGGTTAA GGTTTA
1 GGTTTA -GGTTTA GGTTTA -GGTTT-A GGTTT-A GGTTTA -GGTTTA GGTTTA
* * *
15518444 GGATTTTG GGTTTA GTGTTTA GGATTTA GGTTCA GGGTTTA GGGTTAA
1 GG--TTTA GGTTTA G-GTTTA GG-TTTA GGTTTA -GGTTTA -GGTTTA
** * * * *
15518492 GGTTTA TATTTAA GGTTTA GATCTA GAGTTTT GATTTA TGGTTTA GGTTTA
1 GGTTTA GGTTT-A GGTTTA GGTTTA G-GTTTA GGTTTA -GGTTTA GGTTTA
15518543 GTGTTTA GG
1 G-GTTTA GG
15518552 GTTTTAGTTT
Statistics
Matches: 223, Mismatches: 57, Indels: 55
0.67 0.17 0.16
Matches are distributed among these distances:
5 8 0.04
6 96 0.43
7 113 0.51
8 6 0.03
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (6 bp):
GGTTTA
Found at i:15518563 original size:33 final size:33
Alignment explanation
Indices: 15518340--15518574 Score: 126
Period size: 33 Copynumber: 7.2 Consensus size: 33
15518330 TTAAGTATTG
* * *
15518340 GGTTTAGGGTTTA-GGTTTAAGGGTTATGG-CTA
1 GGTTTAGGGTTTAGGGTTTTA-GTTTATGGTTTA
* * * * *
15518372 GGTTTTGGGTTTAAGGTTTTGGTTTAGGGTTAA
1 GGTTTAGGGTTTAGGGTTTTAGTTTATGGTTTA
* * * * * *
15518405 GTTTTAGGGTTTAAGGTTTCAATTTAGGGTTAA
1 GGTTTAGGGTTTAGGGTTTTAGTTTATGGTTTA
* *
15518438 GGTTTAGGATTTTGGG-TTTAGTGTT-TAGGATTTA
1 GGTTTAGGGTTTAGGGTTTTAGT-TTAT-GG-TTTA
* * *
15518472 GGTTCAGGGTTTAGGG-TTAAGGTTTAT-ATTTAA
1 GGTTTAGGGTTTAGGGTTTTA-GTTTATGGTTT-A
* * *
15518505 GGTTTA-GATCTAGAGTTTT-GATTTATGGTTTA
1 GGTTTAGGGTTTAGGGTTTTAG-TTTATGGTTTA
* **
15518537 GGTTTAGTGTTTAGGGTTTTAGTTTATAATTTA
1 GGTTTAGGGTTTAGGGTTTTAGTTTATGGTTTA
15518570 GGTTT
1 GGTTT
15518575 TGCATGGTGC
Statistics
Matches: 153, Mismatches: 37, Indels: 25
0.71 0.17 0.12
Matches are distributed among these distances:
31 1 0.01
32 43 0.28
33 84 0.55
34 22 0.14
35 3 0.02
ACGTcount: A:0.20, C:0.02, G:0.31, T:0.48
Consensus pattern (33 bp):
GGTTTAGGGTTTAGGGTTTTAGTTTATGGTTTA
Found at i:15518623 original size:26 final size:26
Alignment explanation
Indices: 15518573--15518628 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
15518563 TAATTTAGGT
*
15518573 TTTGCATGGTGCTTTAAGGTTTAAGG
1 TTTGCATGGTGCTTTAAGGTCTAAGG
* **
15518599 TTTGCATGGTGGTTTGGGGTCTAAGG
1 TTTGCATGGTGCTTTAAGGTCTAAGG
15518625 TTTG
1 TTTG
15518629 TGTGGTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.14, C:0.07, G:0.36, T:0.43
Consensus pattern (26 bp):
TTTGCATGGTGCTTTAAGGTCTAAGG
Found at i:15519625 original size:13 final size:13
Alignment explanation
Indices: 15519607--15519632 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15519597 AGCTCTCCAA
15519607 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
15519620 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
15519633 CCTCCTCTAT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:15520330 original size:129 final size:123
Alignment explanation
Indices: 15520067--15520340 Score: 336
Period size: 129 Copynumber: 2.2 Consensus size: 123
15520057 CTTAAAAGGT
* * *
15520067 ATTTTGGTAATTTTACACCTTTCGAGGTGCAATTGAGGTTTTCAAGGCATTATAAAATATTTTAG
1 ATTTTAGTAATTTCACACCTTTCGAGGTGCAATTGAGGTTTTCAAGGCATTATAAAATATTTAAG
15520132 AACATGATTTGGAAAGTTTCACAAAAAACAGACCTCGAAAATACCCCAAAATGAGGGC
66 AACATGATTTGGAAAGTTTCACAAAAAACAGACCTCGAAAATACCCCAAAATGAGGGC
* * **
15520190 ATTTTAATAATTTCACACTTTTCGAGGTGGGATTGAGGTTTTCAAGGCATTAAAAATTATAAAAT
1 ATTTTAGTAATTTCACACCTTTCGAGGTGCAATTGAGGTTTTCAAGGC-------ATTATAAAAT
* ** * *
15520255 ATTTAAGAACATGATTTGGAATGTTTTGCAAAAGAA-A-ATCTCGAAAATACCCTAAAATGAGGG
59 ATTTAAGAACATGATTTGGAAAGTTTCACAAAA-AACAGACCTCGAAAATACCCCAAAATGAGGG
15520318 C
123 C
* *
15520319 ATTTTAGTAATTTTAAACCTTT
1 ATTTTAGTAATTTCACACCTTT
15520341 TGAAGTGTGA
Statistics
Matches: 127, Mismatches: 16, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
123 42 0.33
129 43 0.34
130 40 0.31
131 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (123 bp):
ATTTTAGTAATTTCACACCTTTCGAGGTGCAATTGAGGTTTTCAAGGCATTATAAAATATTTAAG
AACATGATTTGGAAAGTTTCACAAAAAACAGACCTCGAAAATACCCCAAAATGAGGGC
Found at i:15520341 original size:130 final size:124
Alignment explanation
Indices: 15520067--15520341 Score: 342
Period size: 130 Copynumber: 2.2 Consensus size: 124
15520057 CTTAAAAGGT
* *
15520067 ATTTTGGTAATTTTACACC-TTTCGAGGTGCAATTGAGGTTTTCAAGGCATTATAAAATATTTTA
1 ATTTTAGTAATTTTACACCTTTTCGAGGTGCAATTGAGGTTTTCAAGGCATTATAAAATATTTAA
15520131 GAACATGATTTGGAAAGTTTCACAAAAAACAGACCTCGAAAATACCCCAAAATGAGGGC
66 GAACATGATTTGGAAAGTTTCACAAAAAACAGACCTCGAAAATACCCCAAAATGAGGGC
* * **
15520190 ATTTTAATAATTTCACA-CTTTTCGAGGTGGGATTGAGGTTTTCAAGGCATTAAAAATTATAAAA
1 ATTTTAGTAATTTTACACCTTTTCGAGGTGCAATTGAGGTTTTCAAGGC-------ATTATAAAA
* ** * *
15520254 TATTTAAGAACATGATTTGGAATGTTTTGCAAAAGAA-A-ATCTCGAAAATACCCTAAAATGAGG
59 TATTTAAGAACATGATTTGGAAAGTTTCACAAAA-AACAGACCTCGAAAATACCCCAAAATGAGG
15520317 GC
123 GC
*
15520319 ATTTTAGTAATTTTAAACCTTTT
1 ATTTTAGTAATTTTACACCTTTT
15520342 GAAGTGTGAT
Statistics
Matches: 128, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
122 1 0.01
123 41 0.32
129 39 0.30
130 45 0.35
131 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (124 bp):
ATTTTAGTAATTTTACACCTTTTCGAGGTGCAATTGAGGTTTTCAAGGCATTATAAAATATTTAA
GAACATGATTTGGAAAGTTTCACAAAAAACAGACCTCGAAAATACCCCAAAATGAGGGC
Found at i:15520374 original size:129 final size:130
Alignment explanation
Indices: 15520115--15520384 Score: 330
Period size: 129 Copynumber: 2.1 Consensus size: 130
15520105 TTTTCAAGGC
*
15520115 ATTATAAAATATTTTAGAACATGATTTGGAAAGTTTCACAAAAAACAGACCTCGAAAATACCCCA
1 ATTATAAAATATTTAAGAACATGATTTGGAAAGTTTCACAAAAAACAGACCTCGAAAATACCCCA
* * ** * **
15520180 AAATGAGGGCATTTTAATAATTTCACACTTTTCGAGGTGGGATTGAGGTTTTCAAGGCATTAAAA
66 AAATGAGGGCATTTTAATAATTTCAAACTTTTCGAAGTGGGATAAAGGTTTTCAAGACACCAAAA
* ** * *
15520245 ATTATAAAATATTTAAGAACATGATTTGGAATGTTTTGCAAAAGAA-A-ATCTCGAAAATACCCT
1 ATTATAAAATATTTAAGAACATGATTTGGAAAGTTTCACAAAA-AACAGACCTCGAAAATACCCC
* * * * *
15520308 AAAATGAGGGCATTTTAGTAATTTTAAACCTTTT-GAAGTGTGATAAAGGTTTTTAATACACCAA
65 AAAATGAGGGCATTTTAATAATTTCAAA-CTTTTCGAAGTGGGATAAAGGTTTTCAAGACACCAA
15520372 AA
129 AA
*
15520374 ATTATCAAATA
1 ATTATAAAATA
15520385 ATATCAGACA
Statistics
Matches: 119, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
129 72 0.61
130 45 0.38
131 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (130 bp):
ATTATAAAATATTTAAGAACATGATTTGGAAAGTTTCACAAAAAACAGACCTCGAAAATACCCCA
AAATGAGGGCATTTTAATAATTTCAAACTTTTCGAAGTGGGATAAAGGTTTTCAAGACACCAAAA
Found at i:15521252 original size:50 final size:49
Alignment explanation
Indices: 15521197--15521403 Score: 152
Period size: 50 Copynumber: 4.1 Consensus size: 49
15521187 CTTAACTTTA
*
15521197 AAAAGCTCATCCTAAATAAAGGCTTTTAAACTTTTAAAAACTCCATTTTG
1 AAAAGCTCATCCTAAACAAAGGCTTTTAAAC-TTTAAAAACTCCATTTTG
* ** * ** * *
15521247 GAAAGCTTC-TTATAAATAAAGG-TTTTGAAACTTTAAAAATCTTAACTTTA
1 AAAAGC-TCATCCTAAACAAAGGCTTTT-AAACTTTAAAAA-CTCCATTTTG
* ** * * **
15521297 AAAAACTTTTCCTAAACAAAAGC-TTTAAAGCTTTCAAAATCTCTTTTTTG
1 AAAAGCTCATCCTAAACAAAGGCTTTTAAA-CTTT-AAAAACTCCATTTTG
* *
15521347 AAAAGCTTATCCTAAACAAAGGCTTTGAAACTTTAAAAA-TCTCATCTTTG
1 AAAAGCTCATCCTAAACAAAGGCTTTTAAACTTTAAAAACTC-CAT-TTTG
15521397 AAAAGCT
1 AAAAGCT
15521404 ACTCATATGT
Statistics
Matches: 120, Mismatches: 27, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
48 2 0.02
49 21 0.17
50 86 0.72
51 11 0.09
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.35
Consensus pattern (49 bp):
AAAAGCTCATCCTAAACAAAGGCTTTTAAACTTTAAAAACTCCATTTTG
Found at i:15521286 original size:100 final size:100
Alignment explanation
Indices: 15521142--15521403 Score: 287
Period size: 100 Copynumber: 2.6 Consensus size: 100
15521132 AAATCTTAAC
* *
15521142 TTTGAAAAGTCTCTTTCA-AAACAGAGGCTTTGAAA-TTTCAAAAATCTTAACTTTAAAAAGCTC
1 TTTGAAAAG-CT-TATCATAAACAAAGGCTTTGAAACTTT-AAAAATCTTAACTTTAAAAAGCTC
* * *
15521205 ATCCTAAATAAAGGCTTTTAAA-CTTTTAAAAACTCCAT
63 ATCCTAAACAAAAGC-TTTAAAGCTTTCAAAAACTCCAT
* * * * * * **
15521243 TTTGGAAAGCTTCTTATAAATAAAGGTTTTGAAACTTTAAAAATCTTAACTTTAAAAAACTTTTC
1 TTTGAAAAGCTTATCATAAACAAAGGCTTTGAAACTTTAAAAATCTTAACTTTAAAAAGCTCATC
* **
15521308 CTAAACAAAAGCTTTAAAGCTTTCAAAATCTCTTT
66 CTAAACAAAAGCTTTAAAGCTTTCAAAAACTCCAT
* * * *
15521343 TTTGAAAAGCTTATCCTAAACAAAGGCTTTGAAACTTTAAAAATCTCATCTTTGAAAAGCT
1 TTTGAAAAGCTTATCATAAACAAAGGCTTTGAAACTTTAAAAATCTTAACTTTAAAAAGCT
15521404 ACTCATATGT
Statistics
Matches: 133, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
99 9 0.07
100 113 0.85
101 11 0.08
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (100 bp):
TTTGAAAAGCTTATCATAAACAAAGGCTTTGAAACTTTAAAAATCTTAACTTTAAAAAGCTCATC
CTAAACAAAAGCTTTAAAGCTTTCAAAAACTCCAT
Found at i:15521371 original size:150 final size:151
Alignment explanation
Indices: 15521109--15521431 Score: 372
Period size: 150 Copynumber: 2.1 Consensus size: 151
15521099 GGCACGTCTA
* ** * *
15521109 AAATAGAGATTTTGAAACTTTAAAAATCTTAACTTTGAAAAGTCTCTTTCAAAACAGAGGCTTTG
1 AAATAGAGGTTTTGAAACTTTAAAAATCTTAACTTTGAAAAAACTCTTTCAAAACAAAAGCTTTG
* *
15521174 AAATTTCAAAAATCTTAACTTTAAAAAGCTCATCCTAAATAAAGGCTTTTAAACTTTTAAAAA-C
66 AAATTTCAAAAATCTTAACTTTAAAAAGCTCATCCTAAACAAAGGCTTTGAAAC-TTTAAAAATC
* * *
15521238 TCCAT-TTTGGAAAGCTTCTTAT
130 T-CATCTTTGAAAAGCTACTCAT
* *
15521260 AAATAAAGGTTTTGAAACTTTAAAAATCTTAACTTT-AAAAAACT-TTTCCTAAACAAAAGCTTT
1 AAATAGAGGTTTTGAAACTTTAAAAATCTTAACTTTGAAAAAACTCTTT-CAAAACAAAAGCTTT
** * *
15521323 -AAAGCTTTC-AAAATCTCT-TTTTTGAAAAGCTTATCCTAAACAAAGGCTTTGAAACTTTAAAA
65 GAAA--TTTCAAAAATCT-TAACTTTAAAAAGCTCATCCTAAACAAAGGCTTTGAAACTTTAAAA
15521385 ATCTCATCTTTGAAAAGCTACTCAT
127 ATCTCATCTTTGAAAAGCTACTCAT
** *
15521410 ATGTAGAGGCTTTGAAACTTTA
1 AAATAGAGGTTTTGAAACTTTA
15521432 TAAAGTCTCA
Statistics
Matches: 146, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
149 17 0.12
150 90 0.62
151 39 0.27
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (151 bp):
AAATAGAGGTTTTGAAACTTTAAAAATCTTAACTTTGAAAAAACTCTTTCAAAACAAAAGCTTTG
AAATTTCAAAAATCTTAACTTTAAAAAGCTCATCCTAAACAAAGGCTTTGAAACTTTAAAAATCT
CATCTTTGAAAAGCTACTCAT
Found at i:15521420 original size:50 final size:48
Alignment explanation
Indices: 15521366--15521552 Score: 151
Period size: 50 Copynumber: 3.8 Consensus size: 48
15521356 TCCTAAACAA
15521366 AGGCTTTGAAACTTTAAAAATCTCATCTTTGAAAAGCTACTCATATGTAG
1 AGGCTTTGAAACTTTAAAAATCTCATCTTTGAAAAGCTACTC-TA-GTAG
* * * * * *
15521416 AGGCTTTGAAACTTTATAAAGTCTCATTTTTTAAAAGATCCTCTAGAATGG
1 AGGCTTTGAAACTTTA-AAAATCTCATCTTTGAAAAGCTACTCTAG--TAG
* * * * *
15521467 AGTCTTTGAAACTTTAAAAAACTCATTTTTAAAAAGCTTA-TCCTAAATAG
1 AGGCTTTGAAACTTTAAAAATCTCATCTTTGAAAAGC-TACT-CT-AGTAG
* ** * *
15521517 ATGCTTCAAAACTTTAAAAATATTATCTTTGAAAAG
1 AGGCTTTGAAACTTTAAAAATCTCATCTTTGAAAAG
15521553 TTTGATTGTA
Statistics
Matches: 108, Mismatches: 23, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
49 1 0.01
50 65 0.60
51 41 0.38
52 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.36
Consensus pattern (48 bp):
AGGCTTTGAAACTTTAAAAATCTCATCTTTGAAAAGCTACTCTAGTAG
Found at i:15535046 original size:113 final size:113
Alignment explanation
Indices: 15534846--15535172 Score: 503
Period size: 113 Copynumber: 2.9 Consensus size: 113
15534836 AAACTCATAA
* * * * * **
15534846 AAACAAAAATT-CCTCACTTGACATTTCAACTTTAGCATTATTGACCTTTGATTCCAATGCTATC
1 AAACAAAAGTTCCCT-ACTTGACACTTCAGCTTTAGCATCATTGACCCTCAATTCCAATGCTATC
*
15534910 AATCATCAAAACTACTAATCAGTTCTTGAAACTTCATAGAATTTGATAG
65 AATCATCAAAACTACTAACCAGTTCTTGAAACTTCATAGAATTTGATAG
*
15534959 AAACAAAAGTTCCCTACTTGACACTTCAGCTTTAGCATCATTGACCCTCAATTCTAATGCTATCA
1 AAACAAAAGTTCCCTACTTGACACTTCAGCTTTAGCATCATTGACCCTCAATTCCAATGCTATCA
15535024 ATCATCAAAACTACTAACCAGTTCTTGAAACTTCATAGAATTTGATAG
66 ATCATCAAAACTACTAACCAGTTCTTGAAACTTCATAGAATTTGATAG
* *
15535072 AAACAAAAGTTCCCTACTTGACACTTCAGCTTTAGCACCATTGACCCTCAATTCCAATGTTATCA
1 AAACAAAAGTTCCCTACTTGACACTTCAGCTTTAGCATCATTGACCCTCAATTCCAATGCTATCA
* ** *
15535137 ATCATTAAAACTACTAAGTAGTTCTTTAAACTTCAT
66 ATCATCAAAACTACTAACCAGTTCTTGAAACTTCAT
15535173 GCAATTTACG
Statistics
Matches: 197, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
113 194 0.98
114 3 0.02
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (113 bp):
AAACAAAAGTTCCCTACTTGACACTTCAGCTTTAGCATCATTGACCCTCAATTCCAATGCTATCA
ATCATCAAAACTACTAACCAGTTCTTGAAACTTCATAGAATTTGATAG
Found at i:15539802 original size:14 final size:14
Alignment explanation
Indices: 15539759--15539817 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
15539749 TTAGGATTTT
*
15539759 AATTTTAGAGTATC
1 AATTTTAGAGTTTC
*
15539773 -A-TTTAGGGCTTT-
1 AATTTTAGAG-TTTC
15539785 AATTTTATG-GTTTC
1 AATTTTA-GAGTTTC
15539799 AATTTTAGAGTTTC
1 AATTTTAGAGTTTC
15539813 AATTT
1 AATTT
15539818 CATTAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
12 6 0.16
13 8 0.22
14 22 0.59
15 1 0.03
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (14 bp):
AATTTTAGAGTTTC
Found at i:15540665 original size:55 final size:55
Alignment explanation
Indices: 15540575--15540686 Score: 163
Period size: 55 Copynumber: 2.0 Consensus size: 55
15540565 AAAAAAAAAC
* * *
15540575 CTTAGTTCACGCCAGTGCCTCTTTTCCCTCTTTTTCTTTTCG-TTTTTCTGGTCTT
1 CTTAGGTCACGCCACTGCCTCTTTTCCCTCCTTTTCTTTTCGCTTTTT-TGGTCTT
* *
15540630 CTTAGGTCATGCCACTGCCTCTTTTCCTTCCTTTTCTTTTCGCTTTTTTGGTCTT
1 CTTAGGTCACGCCACTGCCTCTTTTCCCTCCTTTTCTTTTCGCTTTTTTGGTCTT
15540685 CT
1 CT
15540687 CCTCCTCTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 46 0.90
56 5 0.10
ACGTcount: A:0.05, C:0.29, G:0.12, T:0.53
Consensus pattern (55 bp):
CTTAGGTCACGCCACTGCCTCTTTTCCCTCCTTTTCTTTTCGCTTTTTTGGTCTT
Found at i:15540733 original size:19 final size:19
Alignment explanation
Indices: 15540705--15540757 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
15540695 ATGGTGCAGA
15540705 TTTTTT-TTTTGTTCT-TCG
1 TTTTTTGTTTTGTTCTCT-G
*
15540723 TTTTTTGTTTTTTTCTCTG
1 TTTTTTGTTTTGTTCTCTG
*
15540742 TGTTTTGTTTCTGTTC
1 TTTTTTGTTT-TGTTC
15540758 ACGTTCCTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 6 0.21
19 18 0.62
20 5 0.17
ACGTcount: A:0.00, C:0.11, G:0.13, T:0.75
Consensus pattern (19 bp):
TTTTTTGTTTTGTTCTCTG
Found at i:15541571 original size:13 final size:12
Alignment explanation
Indices: 15541545--15541584 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
15541535 TTGAGCCAAA
15541545 TTATATTATTAT
1 TTATATTATTAT
*
15541557 TTATATGTTTTAT
1 TTATAT-TATTAT
*
15541570 TTTTATTATTAT
1 TTATATTATTAT
15541582 TTA
1 TTA
15541585 CTTTTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (12 bp):
TTATATTATTAT
Found at i:15541615 original size:20 final size:21
Alignment explanation
Indices: 15541572--15541617 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
15541562 TGTTTTATTT
* **
15541572 TTATTATTATTTACTTTTTTA
1 TTATTATTATTTACTATTAGA
15541593 TTATTA-TATTTACTATTAGA
1 TTATTATTATTTACTATTAGA
15541613 TTATT
1 TTATT
15541618 TTTAATCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (21 bp):
TTATTATTATTTACTATTAGA
Found at i:15541813 original size:14 final size:14
Alignment explanation
Indices: 15541780--15541819 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
15541770 TCGAACAAAA
*
15541780 TTAAGAATGGGCTA
1 TTAAGAATGGGCTT
15541794 TT---AATGGGCTT
1 TTAAGAATGGGCTT
15541805 TTAAGAATGGGCTT
1 TTAAGAATGGGCTT
15541819 T
1 T
15541820 CATCAGGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
11 10 0.45
14 12 0.55
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.38
Consensus pattern (14 bp):
TTAAGAATGGGCTT
Found at i:15543050 original size:25 final size:25
Alignment explanation
Indices: 15543016--15543063 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
15543006 TCGATTATTT
15543016 TAGAAAAAACATTTTTAGCCACCGA
1 TAGAAAAAACATTTTTAGCCACCGA
15543041 TAGAAAAAACATTTTTAGCCACC
1 TAGAAAAAACATTTTTAGCCACC
15543064 AAGAGGGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (25 bp):
TAGAAAAAACATTTTTAGCCACCGA
Found at i:15546513 original size:15 final size:15
Alignment explanation
Indices: 15546472--15546502 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
15546462 ATCCATATAT
15546472 TTGTTCATTTGCTTA
1 TTGTTCATTTGCTTA
15546487 TTGTTCATTTGCTTA
1 TTGTTCATTTGCTTA
15546502 T
1 T
15546503 GTTTTCTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (15 bp):
TTGTTCATTTGCTTA
Found at i:15555637 original size:154 final size:155
Alignment explanation
Indices: 15555342--15555656 Score: 391
Period size: 154 Copynumber: 2.0 Consensus size: 155
15555332 ACTGAGATAT
* * * * *
15555342 CATGATCCACATAGGCCTAATTTAGTACTTTTAACAGTTCGTTCCTATGATGCTCAAAGTTTGGC
1 CATGCTCCACATAGGCCTAATTTAGTACTTTCAACAATTCGTTCCTATAATGCTCAAAGTTTAGC
* ***
15555407 AATAAAGACAATAGTGAAATCTGTGTTGGCATCTTGTTAAGTCAATCTACTACACTATATTCGCT
66 AATAAAGACAATAGTGAAATCTATGCCAGCATCTTGTTAAGTCAATCTACTACACTATATTCGCT
* *
15555472 ATGCCTAATGATTTT-CAAAATTCA
131 AAGCCTAATGATTTTAAAAAATTCA
* * * * **
15555496 TATGCTCCACATAGGCCTAGTTTAGTACTTTCAGCAATAT-GTTCTTATAATGCTTTAAGTTTAG
1 CATGCTCCACATAGGCCTAATTTAGTACTTTCAACAAT-TCGTTCCTATAATGCTCAAAGTTTAG
* * ** *
15555560 CAATAGAGACAATAGTGAAATCTATGCCAGCATTTTGTTAAGTTGATCTACTATACTATATTCGC
65 CAATAAAGACAATAGTGAAATCTATGCCAGCATCTTGTTAAGTCAATCTACTACACTATATTCGC
* *
15555625 TAAGCTTGATGATTTTAAAAAATTCA
130 TAAGCCTAATGATTTTAAAAAATTCA
15555651 CATGCT
1 CATGCT
15555657 TCCCTTTCTA
Statistics
Matches: 134, Mismatches: 25, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
154 120 0.90
155 14 0.10
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (155 bp):
CATGCTCCACATAGGCCTAATTTAGTACTTTCAACAATTCGTTCCTATAATGCTCAAAGTTTAGC
AATAAAGACAATAGTGAAATCTATGCCAGCATCTTGTTAAGTCAATCTACTACACTATATTCGCT
AAGCCTAATGATTTTAAAAAATTCA
Found at i:15561585 original size:17 final size:17
Alignment explanation
Indices: 15561565--15561599 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
15561555 TTTTCTTATG
*
15561565 TTTTT-ATTTTTCACTT
1 TTTTTAATTTTCCACTT
15561581 TTTTTAATTTTCCACTT
1 TTTTTAATTTTCCACTT
15561598 TT
1 TT
15561600 AAGAAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTAATTTTCCACTT
Found at i:15562661 original size:14 final size:14
Alignment explanation
Indices: 15562625--15562666 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
15562615 AAGGTCTAAG
*
15562625 TTAGGTTTTAGGGT
1 TTAGGATTTAGGGT
*
15562639 TCA-GATTTAGGGT
1 TTAGGATTTAGGGT
*
15562652 TTAGGATTTATGGT
1 TTAGGATTTAGGGT
15562666 T
1 T
15562667 AGGGTTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (14 bp):
TTAGGATTTAGGGT
Found at i:15562699 original size:25 final size:24
Alignment explanation
Indices: 15562671--15562750 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 24
15562661 ATGGTTAGGG
15562671 TTAAATTTAGTATTAGGATTTTGGT
1 TTAAATTTAGTATTAGG-TTTTGGT
** *
15562696 TTAAGGTTAGGTATAAGGTTTTGGT
1 TTAAATTTA-GTATTAGGTTTTGGT
* * *
15562721 TTAGCATTTAGTGTTAGGGTTTCGGT
1 TTA-AATTTAGTATTA-GGTTTTGGT
15562747 TTAA
1 TTAA
15562751 GGTTTAAGTT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
25 21 0.50
26 21 0.50
ACGTcount: A:0.24, C:0.03, G:0.26, T:0.47
Consensus pattern (24 bp):
TTAAATTTAGTATTAGGTTTTGGT
Found at i:15562754 original size:13 final size:13
Alignment explanation
Indices: 15562693--15563036 Score: 117
Period size: 13 Copynumber: 26.4 Consensus size: 13
15562683 TTAGGATTTT
15562693 GGTTTAAGG-TTA
1 GGTTTAAGGTTTA
* *
15562705 GGTATAAGGTTTT
1 GGTTTAAGGTTTA
*
15562718 GGTTT-AGCATTTA
1 GGTTTAAG-GTTTA
* *
15562731 -GTGTTAGGGTTTC
1 GGT-TTAAGGTTTA
15562744 GGTTTAAGGTTTA
1 GGTTTAAGGTTTA
* ***
15562757 AGTTTTTTGTTTA
1 GGTTTAAGGTTTA
15562770 GGTTT-AGAGTTTA
1 GGTTTAAG-GTTTA
* *
15562783 GGGTTTAGGGTTAA
1 -GGTTTAAGGTTTA
*
15562797 GGTTTAAGGTTTTG
1 GGTTTAAGG-TTTA
15562811 GGTTTAAGGTTTTA
1 GGTTTAAGG-TTTA
15562825 -GTTTAAGG-TTA
1 GGTTTAAGGTTTA
**
15562836 GTGTTTGGGGTTTGA
1 G-GTTTAAGGTTT-A
*
15562851 GGTTT--GGCTTA
1 GGTTTAAGGTTTA
15562862 GGGTTTCAA--TTTA
1 -GGTTT-AAGGTTTA
* *
15562875 GGGTT-AGCATTTA
1 GGTTTAAG-GTTTA
*
15562888 GGATTAAGGTTTA
1 GGTTTAAGGTTTA
**
15562901 GTGTTTAAAATTTA
1 G-GTTTAAGGTTTA
**
15562915 GGTTTGGGGTTT-
1 GGTTTAAGGTTTA
* *
15562927 GGTTTAGGGTTTT
1 GGTTTAAGGTTTA
* *
15562940 GATTT-AGGGTTA
1 GGTTTAAGGTTTA
15562952 GGGTTT-AGGTTT-
1 -GGTTTAAGGTTTA
* * *
15562964 GCAATTTAGGGTTAAA
1 G--GTTTAAGGTT-TA
*
15562980 GG-TTAAAGTTTA
1 GGTTTAAGGTTTA
* *
15562992 GATTTAAGGTTTT
1 GGTTTAAGGTTTA
15563005 GGTTTAAGGTTTA
1 GGTTTAAGGTTTA
* *
15563018 AGTTTAAGATTTAA
1 GGTTTAAGGTTT-A
15563032 GGTTT
1 GGTTT
15563037 GGGATTTATG
Statistics
Matches: 242, Mismatches: 59, Indels: 60
0.67 0.16 0.17
Matches are distributed among these distances:
10 1 0.00
11 5 0.02
12 42 0.17
13 136 0.56
14 54 0.22
15 3 0.01
16 1 0.00
ACGTcount: A:0.21, C:0.02, G:0.31, T:0.46
Consensus pattern (13 bp):
GGTTTAAGGTTTA
Found at i:15562761 original size:6 final size:7
Alignment explanation
Indices: 15562744--15562834 Score: 66
Period size: 7 Copynumber: 13.6 Consensus size: 7
15562734 TTAGGGTTTC
15562744 GGTTTAA
1 GGTTTAA
15562751 GGTTTAA
1 GGTTTAA
**
15562758 -GTTTTT
1 GGTTTAA
*
15562764 TGTTT-A
1 GGTTTAA
15562770 GGTTT-A
1 GGTTTAA
*
15562776 GAGTTTAG
1 G-GTTTAA
15562784 GGTTT-A
1 GGTTTAA
*
15562790 GGGTTAA
1 GGTTTAA
15562797 GGTTTAA
1 GGTTTAA
**
15562804 GGTTTTG
1 GGTTTAA
15562811 GGTTTAA
1 GGTTTAA
*
15562818 GGTTTTA
1 GGTTTAA
15562825 -GTTTAA
1 GGTTTAA
15562831 GGTT
1 GGTT
15562835 AGTGTTTGGG
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
6 19 0.29
7 45 0.69
8 1 0.02
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (7 bp):
GGTTTAA
Found at i:15562799 original size:27 final size:27
Alignment explanation
Indices: 15562769--15562834 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
15562759 TTTTTTGTTT
*
15562769 AGGTTT-AGAGTTTAGGGTTTAGGGTTA
1 AGGTTTAAG-GTTTAGGGTTTAAGGTTA
* *
15562796 AGGTTTAAGGTTTTGGGTTTAAGGTTTT
1 AGGTTTAAGGTTTAGGGTTTAAGG-TTA
15562824 A-GTTTAAGGTT
1 AGGTTTAAGGTT
15562835 AGTGTTTGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (27 bp):
AGGTTTAAGGTTTAGGGTTTAAGGTTA
Found at i:15562855 original size:27 final size:26
Alignment explanation
Indices: 15562610--15562867 Score: 88
Period size: 26 Copynumber: 9.9 Consensus size: 26
15562600 GTTTTGGGTT
* *
15562610 GGTTTAAGGTCTAA-GTTAGGTTTTAG
1 GGTTT-AGGTTTAAGGTTAGGGTTTAG
* * * * *
15562636 GGTTCAGATTTAGGGTTTAGGATTTAT
1 GGTTTAGGTTTAAGG-TTAGGGTTTAG
* **
15562663 GG-TTAGGGTTAAATTTA--GTATTAG
1 GGTTTAGGTTTAAGGTTAGGGT-TTAG
* * * *
15562687 GATTTTGGTTTAAGGTTA-GGTATAA
1 GGTTTAGGTTTAAGGTTAGGGTTTAG
* * *
15562712 GGTTTTGGTTT-AGCATTTAGTG-TTAG
1 GGTTTAGGTTTAAG--GTTAGGGTTTAG
* * **
15562738 GGTTTCGGTTTAAGGTTTA-AGTTTTT
1 GGTTTAGGTTTAAGG-TTAGGGTTTAG
* *
15562764 TGTTTAGGTTTAGAGTTTAGGGTTTAG
1 GGTTTAGGTTTA-AGGTTAGGGTTTAG
* *
15562791 GGTTAAGGTTTAAGGTTTTGGGTTTAAG
1 GGTTTAGGTTTAAGG-TTAGGGTTT-AG
* * *
15562819 GTTTTA-GTTTAAGGTTAGTGTTTGG
1 GGTTTAGGTTTAAGGTTAGGGTTTAG
15562844 GGTTTGAGGTTT--GGCTTAGGGTTT
1 GGTTT-AGGTTTAAGG-TTAGGGTTT
15562868 CAATTTAGGG
Statistics
Matches: 166, Mismatches: 48, Indels: 36
0.66 0.19 0.14
Matches are distributed among these distances:
23 1 0.01
24 6 0.04
25 39 0.23
26 64 0.39
27 50 0.30
28 6 0.04
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.47
Consensus pattern (26 bp):
GGTTTAGGTTTAAGGTTAGGGTTTAG
Found at i:15563017 original size:7 final size:7
Alignment explanation
Indices: 15562968--15563036 Score: 56
Period size: 7 Copynumber: 10.4 Consensus size: 7
15562958 AGGTTTGCAA
*
15562968 TTTAGGG
1 TTTAAGG
*
15562975 TTAAAGG
1 TTTAAGG
*
15562982 -TTAAAG
1 TTTAAGG
*
15562988 TTT-AGA
1 TTTAAGG
15562994 TTTAAGG
1 TTTAAGG
*
15563001 TTT-TGG
1 TTTAAGG
15563007 TTTAAGG
1 TTTAAGG
15563014 TTTAA-G
1 TTTAAGG
*
15563020 TTTAAGA
1 TTTAAGG
15563027 TTTAAGG
1 TTTAAGG
15563034 TTT
1 TTT
15563037 GGGATTTATG
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
6 19 0.40
7 28 0.60
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (7 bp):
TTTAAGG
Found at i:15563033 original size:33 final size:32
Alignment explanation
Indices: 15562972--15563050 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
15562962 TTGCAATTTA
* *
15562972 GGGTTAAAGGTTAAAGTTTAGATTTAAGGTTT
1 GGGTTTAAGGTTTAAGTTTAGATTTAAGGTTT
*
15563004 TGGTTTAAGGTTTAAGTTTAAGATTTAAGGTTT
1 GGGTTTAAGGTTTAAGTTT-AGATTTAAGGTTT
*
15563037 GGGATTTATGGTTT
1 GGG-TTTAAGGTTT
15563051 GCATGGTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 16 0.40
33 15 0.38
34 9 0.22
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.46
Consensus pattern (32 bp):
GGGTTTAAGGTTTAAGTTTAGATTTAAGGTTT
Found at i:15566561 original size:6 final size:6
Alignment explanation
Indices: 15566550--15566618 Score: 52
Period size: 6 Copynumber: 11.0 Consensus size: 6
15566540 TCACTTGGTA
* * *
15566550 AAAAAG AAAAAG AGAACA- AAAAAG AATGAAGG AAAAAT AAGAGAAG -AAAAG
1 AAAAAG AAAAAG A-AAAAG AAAAAG AA--AAAG AAAAAG AA-A-AAG AAAAAG
15566601 AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG
15566619 GAAGAATGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
5 6 0.12
6 32 0.64
7 5 0.10
8 7 0.14
ACGTcount: A:0.75, C:0.01, G:0.20, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:15567656 original size:33 final size:33
Alignment explanation
Indices: 15567578--15567661 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
15567568 ATATTTCAGT
* * *
15567578 AATATTGTAGATTGATTTGATATTGATTTAAAG
1 AATATTATATATTAATTTGATATTGATTTAAAG
* *
15567611 AATATTAGATATTAATTTGATATTGATTTAGAG
1 AATATTATATATTAATTTGATATTGATTTAAAG
*
15567644 AATATTTTATATTAATTT
1 AATATTATATATTAATTT
15567662 AGTTCATTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (33 bp):
AATATTATATATTAATTTGATATTGATTTAAAG
Done.