Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 78 of 259
Found at i:25333880 original size:21 final size:19
Alignment explanation
Indices: 25333837--25333880 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
25333827 GAGCTCAAAT
* *
25333837 GAGCTGAAATGAGTTCATG
1 GAGCTGAAATGAGCTAATG
25333856 GAGCTGGAAATGAGCTAATTG
1 GAGCT-GAAATGAGCTAA-TG
25333877 GAGC
1 GAGC
25333881 CCAATGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 10 0.48
21 6 0.29
ACGTcount: A:0.32, C:0.11, G:0.34, T:0.23
Consensus pattern (19 bp):
GAGCTGAAATGAGCTAATG
Found at i:25351846 original size:24 final size:23
Alignment explanation
Indices: 25351793--25351869 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 23
25351783 ATTAATTAGA
**
25351793 AAATGGTATTTGGTTTTGGTACG
1 AAATGGTATTTGGAATTGGTACG
** *
25351816 ATTTGGTATTTGGGAATTGGTACT
1 AAATGGTATTT-GGAATTGGTACG
** *
25351840 AAATGGTA-AAGGATTTGGTACG
1 AAATGGTATTTGGAATTGGTACG
25351862 AAATGGTA
1 AAATGGTA
25351870 ATGGTTCAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
22 18 0.43
23 9 0.21
24 15 0.36
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.38
Consensus pattern (23 bp):
AAATGGTATTTGGAATTGGTACG
Found at i:25354992 original size:13 final size:12
Alignment explanation
Indices: 25354973--25355007 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
25354963 ATAGGTGCGT
25354973 AAAAAAAAAGTTTG
1 AAAAAAAAA--TTG
25354987 AAAAAAAAATTG
1 AAAAAAAAATTG
25354999 AAAAAAAAA
1 AAAAAAAAA
25355008 ATTGCATACG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
14 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:25355008 original size:13 final size:13
Alignment explanation
Indices: 25354973--25355011 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
25354963 ATAGGTGCGT
*
25354973 AAAAAAAAAGTTTG
1 AAAAAAAAA-ATTG
25354987 -AAAAAAAAATTG
1 AAAAAAAAAATTG
25354999 AAAAAAAAAATTG
1 AAAAAAAAAATTG
25355012 CATACGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 3 0.13
13 20 0.87
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (13 bp):
AAAAAAAAAATTG
Found at i:25356006 original size:18 final size:18
Alignment explanation
Indices: 25355985--25356019 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25355975 AGAAAAGAAA
25355985 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
25356003 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
25356020 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:25358994 original size:12 final size:12
Alignment explanation
Indices: 25358967--25359003 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
25358957 ATAGGTGCGT
*
25358967 AAAAAAAAGTTCG
1 AAAAAAAAATT-G
25358980 AAAAAAAAATTG
1 AAAAAAAAATTG
25358992 AAAAAAAAATTG
1 AAAAAAAAATTG
25359004 CATACGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.70, C:0.03, G:0.11, T:0.16
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:25359996 original size:18 final size:18
Alignment explanation
Indices: 25359975--25360009 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25359965 AGAAAAGAAA
25359975 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
25359993 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
25360010 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:25366619 original size:10 final size:10
Alignment explanation
Indices: 25366604--25366636 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
25366594 TTTGAGAATT
25366604 TGATTAACGG
1 TGATTAACGG
25366614 TGATTAACGG
1 TGATTAACGG
25366624 TGATTAACGG
1 TGATTAACGG
25366634 TGA
1 TGA
25366637 GGTTTGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (10 bp):
TGATTAACGG
Found at i:25369976 original size:12 final size:12
Alignment explanation
Indices: 25369961--25370054 Score: 50
Period size: 11 Copynumber: 7.6 Consensus size: 12
25369951 TCAAAACGTG
25369961 AAAAAAAATCG-
1 AAAAAAAATCGA
* *
25369972 AAAAAAATTTGA
1 AAAAAAAATCGA
*
25369984 AAAAAAAATTGA
1 AAAAAAAATCGA
*
25369996 TTGAAAAAAATTC-A
1 ---AAAAAAAATCGA
*
25370010 AAAAAAAGT-GA
1 AAAAAAAATCGA
25370021 AAAAAAAATCAAGCA
1 AAAAAAAATC--G-A
**
25370036 AAAAAAAAAAGA
1 AAAAAAAATCGA
25370048 AAAAAAA
1 AAAAAAA
25370055 GGTGAGCAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
11 26 0.40
12 19 0.29
13 1 0.02
14 2 0.03
15 17 0.26
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:25370989 original size:17 final size:18
Alignment explanation
Indices: 25370957--25370990 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25370947 AGAAAAGAAA
25370957 ATTGAAAAAGAAATTGAG
1 ATTGAAAAAGAAATTGAG
*
25370975 ATTGAGAAA-AAATTGA
1 ATTGAAAAAGAAATTGA
25370991 AAAAGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (18 bp):
ATTGAAAAAGAAATTGAG
Found at i:25376499 original size:20 final size:20
Alignment explanation
Indices: 25376476--25376522 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
25376466 GGGTTAAGAT
*
25376476 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
25376496 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
25376516 TGAGCTG
1 TGAGCTG
25376523 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:25378015 original size:10 final size:10
Alignment explanation
Indices: 25377959--25378015 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
25377949 ATAAAATAAA
*
25377959 TGAGCTGAAT
1 TGAGCTCAAT
*
25377969 TGTAGCTAAAT
1 TG-AGCTCAAT
*
25377980 TGAGCTCGAT
1 TGAGCTCAAT
* *
25377990 TGAGCTGAAA
1 TGAGCTCAAT
25378000 TGAGCTCAAT
1 TGAGCTCAAT
*
25378010 TTAGCT
1 TGAGCT
25378016 GGTCGGAGTT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
10 28 0.76
11 9 0.24
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (10 bp):
TGAGCTCAAT
Found at i:25378016 original size:20 final size:20
Alignment explanation
Indices: 25377956--25378016 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
25377946 CCAATAAAAT
*
25377956 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATT-TAGCTG
* *
25377976 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTTAGCTG
25377997 AAATGAGCTCAATTTAGCTG
1 AAATGAGCTCAATTTAGCTG
25378017 GTCGGAGTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (20 bp):
AAATGAGCTCAATTTAGCTG
Found at i:25379744 original size:48 final size:48
Alignment explanation
Indices: 25379692--25379797 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
25379682 TTGTCTTTTC
*
25379692 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
25379740 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
25379788 TTTCTTTTTC
1 TTTCTTTTTC
25379798 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:25380998 original size:10 final size:11
Alignment explanation
Indices: 25380983--25381011 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
25380973 CAACTCAAAT
25380983 TTTTTTTTGA-
1 TTTTTTTTGAC
25380993 TTTTTTTTGAC
1 TTTTTTTTGAC
25381004 TTTTTTTT
1 TTTTTTTT
25381012 TACATTACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:25385349 original size:22 final size:22
Alignment explanation
Indices: 25385319--25385362 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
25385309 TTTGGTATTT
25385319 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
25385341 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
25385363 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:25388222 original size:20 final size:19
Alignment explanation
Indices: 25388199--25388263 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
25388189 AAGCTCAAAC
25388199 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
25388219 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
25388239 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
25388259 GAGCT
1 GAGCT
25388264 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:25388727 original size:20 final size:20
Alignment explanation
Indices: 25388704--25388750 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
25388694 GGGTTAAGAT
*
25388704 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
25388724 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
25388744 TGAGCTG
1 TGAGCTG
25388751 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:25389279 original size:20 final size:20
Alignment explanation
Indices: 25389256--25389302 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
25389246 GGGTTAAGAT
*
25389256 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
25389276 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
25389296 TGAGCTG
1 TGAGCTG
25389303 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:25389728 original size:27 final size:25
Alignment explanation
Indices: 25389681--25389745 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 25
25389671 ACAGCTTTTA
* * *
25389681 AATATGTCTTAATTAATTTAAGTGTTT
1 AATATGTCTTGATTAAGTTAA--ATTT
*
25389708 AATATGTCTTGATTTAGTTAAATTT
1 AATATGTCTTGATTAAGTTAAATTT
*
25389733 AAGATGTCTTGAT
1 AATATGTCTTGAT
25389746 GTCATTTAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
25 15 0.45
27 18 0.55
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (25 bp):
AATATGTCTTGATTAAGTTAAATTT
Found at i:25390957 original size:11 final size:10
Alignment explanation
Indices: 25390941--25390980 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
25390931 TGTAGTTTTC
25390941 AAAAAAAATT
1 AAAAAAAATT
*
25390951 AAAAAAAATC
1 AAAAAAAATT
*
25390961 GAAAAAAATT
1 AAAAAAAATT
25390971 GAAAAAAAAT
1 -AAAAAAAAT
25390981 ATATTGCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (10 bp):
AAAAAAAATT
Found at i:25393444 original size:45 final size:45
Alignment explanation
Indices: 25393395--25393658 Score: 420
Period size: 45 Copynumber: 5.9 Consensus size: 45
25393385 TCGGCCATGG
* * * * *
25393395 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
25393440 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
25393485 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
25393530 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
25393575 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * **
25393620 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
25393659 TCCACCTCTT
Statistics
Matches: 205, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 205 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:25396532 original size:22 final size:20
Alignment explanation
Indices: 25396500--25396548 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
25396490 GCCGAATTTA
25396500 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
25396523 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
25396543 TGAACA
1 TGAACA
25396549 CCTAAATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:25397356 original size:14 final size:13
Alignment explanation
Indices: 25397337--25397376 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
25397327 AAAGGTGAAG
25397337 AAATTCAGAAAAAA
1 AAATTC-GAAAAAA
25397351 AAATTC-AAAAAA
1 AAATTCGAAAAAA
25397363 AAA-TCGAAAAAA
1 AAATTCGAAAAAA
25397375 AA
1 AA
25397377 GGGAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 17 0.68
14 6 0.24
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (13 bp):
AAATTCGAAAAAA
Found at i:25398364 original size:37 final size:37
Alignment explanation
Indices: 25398313--25398383 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
25398303 CATTCTTGTA
25398313 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
25398350 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
25398384 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:25398383 original size:6 final size:6
Alignment explanation
Indices: 25398323--25398372 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
25398313 AAGAGAAAAC
*
25398323 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
25398372 A
1 A
25398373 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:25398465 original size:11 final size:12
Alignment explanation
Indices: 25398433--25398463 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
25398423 TTGAGAGAAC
25398433 TTGAAAAAGCCT
1 TTGAAAAAGCCT
25398445 TTGAAAAAGCCT
1 TTGAAAAAGCCT
25398457 TTGAAAA
1 TTGAAAA
25398464 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:25406673 original size:45 final size:45
Alignment explanation
Indices: 25406624--25406885 Score: 411
Period size: 45 Copynumber: 5.9 Consensus size: 45
25406614 TCGGCCATGG
* * * * *
25406624 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
25406669 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
25406714 TGCTTCCTC-AATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
25406758 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
25406803 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * *
25406848 TGCTTCCTTAATTTGTTCCA-CAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
25406886 TCCACCTCTT
Statistics
Matches: 203, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
44 60 0.30
45 143 0.70
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:25406776 original size:89 final size:89
Alignment explanation
Indices: 25406624--25406885 Score: 427
Period size: 89 Copynumber: 2.9 Consensus size: 89
25406614 TCGGCCATGG
* * *
25406624 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAATGCTTCCTTAAATTCTTCCA
1 TGCTTCCTCAA-TTCTTCCATGAATTATGCATGATGTTGGCCAAATGCTTCCTTAAATTCTTCCA
25406689 TGAATTATGCATGATGTTGGTCAAA
65 TGAATTATGCATGATGTTGGTCAAA
*
25406714 TGCTTCCTCAATTCTTCCATGAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCAT
1 TGCTTCCTCAATTCTTCCATGAATTATGCATGATGTTGGCCAAATGCTTCCTTAAATTCTTCCAT
25406779 GAATTATGCATGATGTTGGTCAAA
66 GAATTATGCATGATGTTGGTCAAA
* * *
25406803 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTTCCTTAATTTGTTCCA
1 TGCTTCCTC-AATTCTTCCATGAATTATGCATGATGTTGGCCAAATGCTTCCTTAAATTCTTCCA
*
25406868 -CAATTATGCATGATGTTG
65 TGAATTATGCATGATGTTG
25406886 TCCACCTCTT
Statistics
Matches: 162, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
89 100 0.62
90 62 0.38
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (89 bp):
TGCTTCCTCAATTCTTCCATGAATTATGCATGATGTTGGCCAAATGCTTCCTTAAATTCTTCCAT
GAATTATGCATGATGTTGGTCAAA
Found at i:25406873 original size:134 final size:134
Alignment explanation
Indices: 25406624--25406885 Score: 427
Period size: 134 Copynumber: 2.0 Consensus size: 134
25406614 TCGGCCATGG
* * * *
25406624 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAATGCTTCCTTAAATTCTTCCA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
*
25406689 TGAATTATGCATGATGTTGGTCAAATGCTTCCTCAATTCTTCCATGAATTATGCATGATGTTGGC
66 TGAATTATGCATGATGTTGGTCAAATGCTTCCTCAATTCTTCCATCAATTATGCATGATGTTGGC
25406754 CAAA
131 CAAA
* *
25406758 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
* *
25406823 TGAATTATGCATGATGTTGGTCAAATGCTTCCTTAATTTGTTCCA-CAATTATGCATGATGTTG
66 TGAATTATGCATGATGTTGGTCAAATGCTTCCTCAA-TTCTTCCATCAATTATGCATGATGTTG
25406886 TCCACCTCTT
Statistics
Matches: 118, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
134 111 0.94
135 7 0.06
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (134 bp):
TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
TGAATTATGCATGATGTTGGTCAAATGCTTCCTCAATTCTTCCATCAATTATGCATGATGTTGGC
CAAA
Found at i:25410313 original size:23 final size:22
Alignment explanation
Indices: 25410262--25410313 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
25410252 CCTCGTCTTT
*
25410262 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
25410284 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
25410307 TTCTTTT
1 TTCTTTT
25410314 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:25417890 original size:13 final size:13
Alignment explanation
Indices: 25417872--25417896 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25417862 TGGTCATCAT
25417872 GGTGTGAACACAA
1 GGTGTGAACACAA
25417885 GGTGTGAACACA
1 GGTGTGAACACA
25417897 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:25418930 original size:18 final size:18
Alignment explanation
Indices: 25418909--25418943 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25418899 TTTTTCTTTT
25418909 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
25418927 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
25418944 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:25419856 original size:23 final size:23
Alignment explanation
Indices: 25419811--25419854 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
25419801 ACTCACAATA
25419811 CTTTTCACTTTTTTTGTTCTTTT
1 CTTTTCACTTTTTTTGTTCTTTT
25419834 CTTTT-ACTTTTTTT-TTCTTTT
1 CTTTTCACTTTTTTTGTTCTTTT
25419855 TTTAACTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (23 bp):
CTTTTCACTTTTTTTGTTCTTTT
Found at i:25419886 original size:37 final size:33
Alignment explanation
Indices: 25419830--25419921 Score: 105
Period size: 37 Copynumber: 2.7 Consensus size: 33
25419820 TTTTTTGTTC
*
25419830 TTTTCTTTT-ACTTTTTTTTTCTTTTTTTAACTCGA
1 TTTTTTTTTCACTTTTTTTTTCTTTTTTT---TCGA
*
25419865 TTTTTTTTGTCACTTTTTTTTTCCTTTTTTTCGA
1 TTTTTTTT-TCACTTTTTTTTTCTTTTTTTTCGA
* *
25419899 TTTTTTTTTTAATTTTTTTTTCT
1 TTTTTTTTTCACTTTTTTTTTCT
25419922 GAATCAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
33 12 0.24
34 12 0.24
35 7 0.14
36 1 0.02
37 18 0.36
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (33 bp):
TTTTTTTTTCACTTTTTTTTTCTTTTTTTTCGA
Found at i:25419891 original size:11 final size:11
Alignment explanation
Indices: 25419812--25419895 Score: 55
Period size: 11 Copynumber: 7.2 Consensus size: 11
25419802 CTCACAATAC
25419812 TTTTCACTTTTT
1 TTTTC-CTTTTT
*
25419824 TTGTT-CTTTTC
1 TT-TTCCTTTTT
*
25419835 TTTTACTTTTT
1 TTTTCCTTTTT
25419846 TTTT-CTTTTT
1 TTTTCCTTTTT
* *
25419856 TTAACTCGATTTTT
1 TT--TTC-CTTTTT
25419870 TTTGTCACTTTTT
1 TTT-TC-CTTTTT
25419883 TTTTCCTTTTT
1 TTTTCCTTTTT
25419894 TT
1 TT
25419896 CGATTTTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
10 10 0.17
11 24 0.41
12 5 0.09
13 12 0.21
14 7 0.12
ACGTcount: A:0.07, C:0.14, G:0.04, T:0.75
Consensus pattern (11 bp):
TTTTCCTTTTT
Found at i:25419892 original size:22 final size:22
Alignment explanation
Indices: 25419867--25419917 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
25419857 TAACTCGATT
25419867 TTTTTTGTC-ACTTTTTTTTTCC
1 TTTTTT-TCGACTTTTTTTTTCC
* **
25419889 TTTTTTTCGATTTTTTTTTTAA
1 TTTTTTTCGACTTTTTTTTTCC
25419911 TTTTTTT
1 TTTTTTT
25419918 TTCTGAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.78
Consensus pattern (22 bp):
TTTTTTTCGACTTTTTTTTTCC
Found at i:25419904 original size:12 final size:12
Alignment explanation
Indices: 25419861--25419958 Score: 62
Period size: 12 Copynumber: 7.9 Consensus size: 12
25419851 TTTTTTTAAC
25419861 TCGATTTTTTTT
1 TCGATTTTTTTT
25419873 GTC-ACTTTTTTTT
1 -TCGA-TTTTTTTT
*
25419886 TC---CTTTTTT
1 TCGATTTTTTTT
25419895 TCGATTTTTTTT
1 TCGATTTTTTTT
**
25419907 TTAATTTTTTTT
1 TCGATTTTTTTT
25419919 TCTGAATCAATTTTTTT
1 TC-G-AT---TTTTTTT
25419936 TCGAATTTTTTTT
1 TCG-ATTTTTTTT
25419949 T-GATTTTTTT
1 TCGATTTTTTT
25419959 GTTACTCCAA
Statistics
Matches: 70, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
9 8 0.11
11 8 0.11
12 21 0.30
13 18 0.26
14 2 0.03
16 4 0.06
17 9 0.13
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.72
Consensus pattern (12 bp):
TCGATTTTTTTT
Found at i:25421656 original size:15 final size:14
Alignment explanation
Indices: 25421633--25421663 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
25421623 TCGCAATTTC
25421633 AAAAAAAAAAACAA
1 AAAAAAAAAAACAA
25421647 AAAAACAAAAAACAA
1 AAAAA-AAAAAACAA
25421662 AA
1 AA
25421664 GAGAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAACAA
Found at i:25425129 original size:20 final size:20
Alignment explanation
Indices: 25425104--25425158 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
25425094 TGTGGTTCAA
*
25425104 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
25425124 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
25425144 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
25425159 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:25432945 original size:4 final size:4
Alignment explanation
Indices: 25432936--25432963 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
25432926 TTAAACTAAG
25432936 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
25432964 AATAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:25434374 original size:23 final size:22
Alignment explanation
Indices: 25434322--25434374 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
25434312 TCCACGTCTT
25434322 TTTCTTTTATTTCTTTTTCTAA
1 TTTCTTTTATTTCTTTTTCTAA
*
25434344 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTAT-TTCTTT-TTCTAA
25434367 TTTCTTTT
1 TTTCTTTT
25434375 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTCTTTTATTTCTTTTTCTAA
Found at i:25434419 original size:18 final size:17
Alignment explanation
Indices: 25434318--25434421 Score: 52
Period size: 18 Copynumber: 5.8 Consensus size: 17
25434308 CCTTTCCACG
25434318 TCTTTTTC-TTTT-ATT
1 TCTTTTTCTTTTTCATT
**
25434333 TCTTTTTCTAATTCATT
1 TCTTTTTCTTTTTCATT
*
25434350 T-TCTCTTCTTTCTTCAATT
1 TCT-TTTTCTTT-TTC-ATT
** * *
25434369 TCTTTTTCACTCTCAATC
1 TCTTTTTCTTTTTC-ATT
25434387 TCTTTTTGCTCTTTTTCATT
1 TC-TTTT--TCTTTTTCATT
25434407 CTCTTTTTCTTTTTC
1 -TCTTTTTCTTTTTC
25434422 CTCACTTGTT
Statistics
Matches: 65, Mismatches: 14, Indels: 17
0.68 0.15 0.18
Matches are distributed among these distances:
15 8 0.12
16 3 0.05
17 9 0.14
18 18 0.28
19 13 0.20
20 7 0.11
21 7 0.11
ACGTcount: A:0.10, C:0.23, G:0.01, T:0.66
Consensus pattern (17 bp):
TCTTTTTCTTTTTCATT
Found at i:25436759 original size:4 final size:4
Alignment explanation
Indices: 25436750--25436781 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
25436740 TTAAACTAAG
25436750 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
25436782 AATAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:25440085 original size:10 final size:10
Alignment explanation
Indices: 25440072--25440109 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
25440062 TTGTAGCTAA
25440072 ATTGAGCTCG
1 ATTGAGCTCG
25440082 ATTGAGCT-G
1 ATTGAGCTCG
25440091 ACTTGAGCTCG
1 A-TTGAGCTCG
*
25440102 AGTGAGCT
1 ATTGAGCT
25440110 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:25440089 original size:20 final size:20
Alignment explanation
Indices: 25440049--25440109 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
25440039 ACCAATAAAA
25440049 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
25440069 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
25440089 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
25440109 T
1 T
25440110 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:25440110 original size:20 final size:20
Alignment explanation
Indices: 25440073--25440110 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
25440063 TGTAGCTAAA
*
25440073 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
25440093 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
25440111 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:25444264 original size:10 final size:10
Alignment explanation
Indices: 25444251--25444288 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
25444241 TTGTAGCTAA
25444251 ATTGAGCTCG
1 ATTGAGCTCG
25444261 ATTGAGCT-G
1 ATTGAGCTCG
25444270 ACTTGAGCTCG
1 A-TTGAGCTCG
*
25444281 AGTGAGCT
1 ATTGAGCT
25444289 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:25444268 original size:20 final size:20
Alignment explanation
Indices: 25444228--25444288 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
25444218 ACCAATAAAA
25444228 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
25444248 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
25444268 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
25444288 T
1 T
25444289 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:25444289 original size:20 final size:20
Alignment explanation
Indices: 25444252--25444289 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
25444242 TGTAGCTAAA
*
25444252 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
25444272 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
25444290 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:25447778 original size:33 final size:33
Alignment explanation
Indices: 25447740--25447802 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
25447730 GATTACTCAC
25447740 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
25447773 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
25447803 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:25447829 original size:14 final size:15
Alignment explanation
Indices: 25447805--25447884 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 15
25447795 TCTCTTTCAA
*
25447805 TTTCTTTTTTCACTT
1 TTTCTTTTTTCAATT
25447820 TTTC-TTTTTCAATT
1 TTTCTTTTTTCAATT
25447834 TTT-TTTCATTCTCAA--
1 TTTCTTT--TT-TCAATT
25447849 TTTC-TTTTTCAA-T
1 TTTCTTTTTTCAATT
25447862 TTTCTTTTCTTC-A-T
1 TTTCTTTT-TTCAATT
25447876 TTTCTTTTT
1 TTTCTTTTT
25447885 CTCTCACCTT
Statistics
Matches: 56, Mismatches: 1, Indels: 18
0.75 0.01 0.24
Matches are distributed among these distances:
12 4 0.07
13 7 0.12
14 27 0.48
15 12 0.21
16 2 0.04
17 4 0.07
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTCTTTTTTCAATT
Found at i:25447829 original size:27 final size:27
Alignment explanation
Indices: 25447799--25447885 Score: 97
Period size: 27 Copynumber: 3.1 Consensus size: 27
25447789 TCAAGCTCTC
25447799 TTTCAATTTCTTTT-TTCACTTTTTCTT
1 TTTCAATTTCTTTTCTTCAC-TTTTCTT
* * *
25447826 TTTCAATTTTTTTTCATTCTCAATTTCTT
1 TTTCAATTTCTTTTC-TTCAC-TTTTCTT
25447855 TTTCAATTTTCTTTTCTTCA-TTTTCTT
1 TTTCAA-TTTCTTTTCTTCACTTTTCTT
25447882 TTTC
1 TTTC
25447886 TCTCACCTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
27 23 0.46
29 19 0.38
30 8 0.16
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTCAATTTCTTTTCTTCACTTTTCTT
Found at i:25447869 original size:12 final size:12
Alignment explanation
Indices: 25447781--25447974 Score: 58
Period size: 12 Copynumber: 16.7 Consensus size: 12
25447771 TTTTCACTTG
25447781 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
25447792 AGCTCTCTTTCA
1 ATTTCTTTTTCA
25447804 ATTTCTTTTTTCA
1 ATTTC-TTTTTCA
*
25447817 CTTTTTCTTTTTCA
1 --ATTTCTTTTTCA
25447831 ATTT-TTTTTC-
1 ATTTCTTTTTCA
25447841 A-TTC----TCA
1 ATTTCTTTTTCA
25447848 ATTTCTTTTTCA
1 ATTTCTTTTTCA
25447860 ATTTTCTTTTCTTCA
1 A-TTTC-TTT-TTCA
* *
25447875 TTTTCTTTTTCT
1 ATTTCTTTTTCA
* ** * *
25447887 CTCACCTTTTCG
1 ATTTCTTTTTCA
25447899 ATTTCTTTTTC-
1 ATTTCTTTTTCA
*
25447910 TTTTGCAATTTTT--
1 ATTT-C--TTTTTCA
25447923 -TTTCTTTTTCA
1 ATTTCTTTTTCA
*
25447934 TTTTCTTTTT--
1 ATTTCTTTTTCA
* *
25447944 GTTT-TCTTTCA
1 ATTTCTTTTTCA
25447955 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
25447967 ATCTCTTT
1 ATTTCTTT
25447975 CTCCTTTTCT
Statistics
Matches: 135, Mismatches: 25, Indels: 45
0.66 0.12 0.22
Matches are distributed among these distances:
6 2 0.01
7 1 0.01
8 3 0.02
9 11 0.08
10 4 0.03
11 16 0.12
12 58 0.43
13 13 0.10
14 19 0.14
15 8 0.06
ACGTcount: A:0.12, C:0.20, G:0.02, T:0.66
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:25447870 original size:18 final size:17
Alignment explanation
Indices: 25447817--25447942 Score: 60
Period size: 17 Copynumber: 7.0 Consensus size: 17
25447807 TCTTTTTTCA
* *
25447817 CTTTTTCTTTTTCAATTT
1 CTTTTTCATTTTC-TTTT
* *
25447835 -TTTTTCATTCTCAATTT
1 CTTTTTCATTTTC-TTTT
25447852 CTTTTTCAATTTTCTTTT
1 CTTTTTC-ATTTTCTTTT
* **
25447870 CTTCATTTTCTTTTTCTCTCA
1 C-T--TTTTCATTTTCT-TTT
*
25447891 CCTTTTCGA-TTTCTTTTT
1 CTTTTTC-ATTTTC-TTTT
*
25447909 CTTTTGCAATTTT-TTTT
1 CTTTTTC-ATTTTCTTTT
25447926 CTTTTTCATTTTCTTTT
1 CTTTTTCATTTTCTTTT
25447943 TGTTTTCTTT
Statistics
Matches: 83, Mismatches: 15, Indels: 21
0.70 0.13 0.18
Matches are distributed among these distances:
16 5 0.06
17 29 0.35
18 26 0.31
19 10 0.12
20 6 0.07
21 7 0.08
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (17 bp):
CTTTTTCATTTTCTTTT
Found at i:25447948 original size:23 final size:22
Alignment explanation
Indices: 25447900--25447964 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
25447890 ACCTTTTCGA
*
25447900 TTTCTTTTTC-TTTTGCAATTTTT
1 TTTCTTTTTCATTTT-C-TTTTTT
25447923 TTTCTTTTTCATTTTCTTTTTGT
1 TTTCTTTTTCATTTTCTTTTT-T
*
25447946 TTTC--TTTCAATTTCTTTTT
1 TTTCTTTTTCATTTTCTTTTT
25447965 CAATCTCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 14 0.37
22 4 0.11
23 16 0.42
24 4 0.11
ACGTcount: A:0.08, C:0.14, G:0.03, T:0.75
Consensus pattern (22 bp):
TTTCTTTTTCATTTTCTTTTTT
Found at i:25447949 original size:17 final size:17
Alignment explanation
Indices: 25447900--25447949 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 17
25447890 ACCTTTTCGA
25447900 TTTCTTTTTCTTTTGCAAT
1 TTTCTTTTT-TTTT-CAAT
25447919 TTT-TTTTCTTTTTC-AT
1 TTTCTTTT-TTTTTCAAT
25447935 TTTCTTTTTGTTTTC
1 TTTCTTTTT-TTTTC
25447950 TTTCAATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 6 0.21
17 10 0.36
18 8 0.29
19 4 0.14
ACGTcount: A:0.06, C:0.14, G:0.04, T:0.76
Consensus pattern (17 bp):
TTTCTTTTTTTTTCAAT
Found at i:25447965 original size:6 final size:6
Alignment explanation
Indices: 25447817--25447952 Score: 53
Period size: 6 Copynumber: 22.7 Consensus size: 6
25447807 TCTTTTTTCA
** * * ** *
25447817 CTTTTT CTTTTT CAATTT -TTTTT CATTCT CAATTT CTTTTT CAATTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C-TTTTT
* * ** * ** *
25447865 CTTTTCTT CATTTT CTTTTT CTCTCA CCTTTT CGATTT CTTTTT CTTTTG
1 C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
** * *
25447915 CAATTT -TTTTT CTTTTT CATTTT CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
25447953 CAATTTCTTT
Statistics
Matches: 89, Mismatches: 36, Indels: 10
0.66 0.27 0.07
Matches are distributed among these distances:
5 10 0.11
6 67 0.75
7 9 0.10
8 3 0.03
ACGTcount: A:0.10, C:0.18, G:0.02, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:25447981 original size:86 final size:85
Alignment explanation
Indices: 25447817--25447983 Score: 185
Period size: 86 Copynumber: 1.9 Consensus size: 85
25447807 TCTTTTTTCA
* **
25447817 CTTTTTCTTTTTCAATTTTTTTTCATTCTCAATTTCTTTTTCAATTTTCTTTTCTTCATTTTCTT
1 CTTTTTCTTTTGCAATTTTTTTTCATTCTCAATTTCTTTTT-AATTTTCTTTTCTTCATTTTCAA
*
25447882 TTTCTCTCACCTTTTCGATTT
65 TCTCTCTCACCTTTTCGATTT
* * * * *
25447903 CTTTTTCTTTTGCAATTTTTTTTCTTTTTCATTTTCTTTTT-GTTTTC-TTTCAATTTCTTTTTC
1 CTTTTTCTTTTGCAATTTTTTTTCATTCTCAATTTCTTTTTAATTTTCTTTTC---TTCATTTTC
* *
25447966 AATCTCTTTCTCCTTTTC
63 AATCTCTCTCACCTTTTC
25447984 TCGCTCAATG
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
83 4 0.06
84 5 0.07
86 58 0.87
ACGTcount: A:0.10, C:0.20, G:0.02, T:0.68
Consensus pattern (85 bp):
CTTTTTCTTTTGCAATTTTTTTTCATTCTCAATTTCTTTTTAATTTTCTTTTCTTCATTTTCAAT
CTCTCTCACCTTTTCGATTT
Found at i:25449663 original size:12 final size:12
Alignment explanation
Indices: 25449633--25449690 Score: 62
Period size: 12 Copynumber: 4.6 Consensus size: 12
25449623 TAGTTTCTCG
* *
25449633 AAAAAAACTCGA
1 AAAAAAATTCAA
25449645 AAAAAAATTCAA
1 AAAAAAATTCAA
*
25449657 AAAAAAATTTTTGAA
1 AAAAAAA---TTCAA
25449672 AAAAAAATTCAA
1 AAAAAAATTCAA
25449684 AAAAAAA
1 AAAAAAA
25449691 AATTGGTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 28 0.72
15 11 0.28
ACGTcount: A:0.72, C:0.07, G:0.03, T:0.17
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:25449694 original size:14 final size:13
Alignment explanation
Indices: 25449644--25449691 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
25449634 AAAAAACTCG
25449644 AAAAAAAATTCAA
1 AAAAAAAATTCAA
* **
25449657 AAAAAAATTTTTGA
1 AAAAAAA-ATTCAA
25449671 AAAAAAAATTCAA
1 AAAAAAAATTCAA
25449684 AAAAAAAA
1 AAAAAAAA
25449692 ATTGGTTTCC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
13 18 0.64
14 10 0.36
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:25449755 original size:15 final size:16
Alignment explanation
Indices: 25449735--25449770 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
25449725 TCAAGTTGAC
25449735 AAAAAAA-TTCGTGAA
1 AAAAAAATTTCGTGAA
25449750 AAAAAAATTTCGTGAA
1 AAAAAAATTTCGTGAA
25449766 AAAAA
1 AAAAA
25449771 GAAGAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.64, C:0.06, G:0.11, T:0.19
Consensus pattern (16 bp):
AAAAAAATTTCGTGAA
Found at i:25455701 original size:11 final size:11
Alignment explanation
Indices: 25455684--25455734 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 11
25455674 GTGCAAGATG
25455684 AAGCTCAATCT
1 AAGCTCAATCT
*
25455695 CAGCTCAA-C-
1 AAGCTCAATCT
25455704 AAGCTCAATCT
1 AAGCTCAATCT
*
25455715 CAGCTCAA-C-
1 AAGCTCAATCT
25455724 AAGCTCAATCT
1 AAGCTCAATCT
25455735 TAGTTTTTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 14 0.44
10 4 0.12
11 14 0.44
ACGTcount: A:0.35, C:0.33, G:0.10, T:0.22
Consensus pattern (11 bp):
AAGCTCAATCT
Found at i:25455709 original size:20 final size:20
Alignment explanation
Indices: 25455684--25455734 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
25455674 GTGCAAGATG
25455684 AAGCTCAATCTCAGCTCAAC
1 AAGCTCAATCTCAGCTCAAC
25455704 AAGCTCAATCTCAGCTCAAC
1 AAGCTCAATCTCAGCTCAAC
25455724 AAGCTCAATCT
1 AAGCTCAATCT
25455735 TAGTTTTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.33, G:0.10, T:0.22
Consensus pattern (20 bp):
AAGCTCAATCTCAGCTCAAC
Found at i:25457329 original size:22 final size:22
Alignment explanation
Indices: 25457304--25457352 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
25457294 AAATTGATTG
*
25457304 AAAAAAAAAAAGAAAAAAAAGT
1 AAAAAAAAAAACAAAAAAAAGT
*
25457326 AAAAAAAAGAACAAAAAAAAGT
1 AAAAAAAAAAACAAAAAAAAGT
*
25457348 GAAAA
1 AAAAA
25457353 GTCTTGTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.84, C:0.02, G:0.10, T:0.04
Consensus pattern (22 bp):
AAAAAAAAAAACAAAAAAAAGT
Found at i:25457352 original size:10 final size:9
Alignment explanation
Indices: 25457307--25457343 Score: 56
Period size: 10 Copynumber: 3.9 Consensus size: 9
25457297 TTGATTGAAA
25457307 AAAAAAAAG
1 AAAAAAAAG
25457316 AAAAAAAAG
1 AAAAAAAAG
25457325 TAAAAAAAAG
1 -AAAAAAAAG
25457335 AACAAAAAA
1 AA-AAAAAA
25457344 AAGTGAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 11 0.42
10 15 0.58
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:25458233 original size:18 final size:18
Alignment explanation
Indices: 25458212--25458246 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25458202 AGAAAAGAAA
25458212 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
25458230 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
25458247 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:25463165 original size:13 final size:13
Alignment explanation
Indices: 25463147--25463171 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25463137 TGGTCATCAT
25463147 GGTGTGAACACAA
1 GGTGTGAACACAA
25463160 GGTGTGAACACA
1 GGTGTGAACACA
25463172 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:25463738 original size:30 final size:30
Alignment explanation
Indices: 25463653--25463749 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
25463643 TAAACTAAAA
* *
25463653 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * * *
25463683 TGAGTTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
25463713 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
25463742 ATGAGCTA
1 -TGAGCTA
25463750 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:25465167 original size:14 final size:14
Alignment explanation
Indices: 25465120--25465167 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
25465110 GTACGAATGG
*
25465120 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
25465134 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
25465148 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
25465162 ATTGGT
1 AATGGT
25465168 CAGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:25472549 original size:17 final size:17
Alignment explanation
Indices: 25472490--25472549 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
25472480 GAGACAGCCA
* * *
25472490 CCATACATGCACTTGAG
1 CCATTCATGCATTTGAT
25472507 CCATTCATGCATTCT-AT
1 CCATTCATGCATT-TGAT
*
25472524 -CATCCCATGCATTTGAT
1 CCAT-TCATGCATTTGAT
25472541 CCATTCATG
1 CCATTCATG
25472550 GACTAGCCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.12
17 26 0.76
18 4 0.12
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.33
Consensus pattern (17 bp):
CCATTCATGCATTTGAT
Found at i:25473031 original size:30 final size:30
Alignment explanation
Indices: 25472946--25473042 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
25472936 TAAACTAAAA
* *
25472946 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
* * * * * *
25472976 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
*
25473006 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
25473035 ATGAGCTA
1 -TGAGCTA
25473043 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
Found at i:25475324 original size:30 final size:30
Alignment explanation
Indices: 25475254--25475335 Score: 78
Period size: 30 Copynumber: 2.7 Consensus size: 30
25475244 TTTTGTTTCA
* *
25475254 ATTTCTTTTTCATCTTCTTTTTCACTCTCAG
1 ATTTCTTTTTCTTC-TCTTTTTCAATCTCAG
*
25475285 ATTTC-TTTTCGTTCTCTTTTTCAATCTTA-
1 ATTTCTTTTTC-TTCTCTTTTTCAATCTCAG
* *
25475314 TTTTCTTTTTCATTTTCTTTTT
1 ATTTCTTTTTC-TTCTCTTTTT
25475336 GCTTTTCAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 4 0.09
30 32 0.74
31 7 0.16
ACGTcount: A:0.11, C:0.21, G:0.02, T:0.66
Consensus pattern (30 bp):
ATTTCTTTTTCTTCTCTTTTTCAATCTCAG
Found at i:25475353 original size:12 final size:12
Alignment explanation
Indices: 25475338--25475368 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
25475328 TTCTTTTTGC
25475338 TTTTCAAAGGCT
1 TTTTCAAAGGCT
25475350 TTTTCAAAGGCT
1 TTTTCAAAGGCT
25475362 TTTTCAA
1 TTTTCAA
25475369 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:25475426 original size:5 final size:5
Alignment explanation
Indices: 25475416--25475472 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
25475406 CTCTTGCCTC
*
25475416 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TACTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
25475463 TCTTT TCTTT
1 TCTTT TCTTT
25475473 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:25475456 original size:15 final size:14
Alignment explanation
Indices: 25475416--25475472 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
25475406 CTCTTGCCTC
*
25475416 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
25475431 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
25475446 TCTTTTACTTTTTCTTT
1 TCTTTT-CTTTTTC--T
25475463 TCTTTTCTTT
1 TCTTTTCTTT
25475473 ATTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:25475473 original size:21 final size:21
Alignment explanation
Indices: 25475416--25475483 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
25475406 CTCTTGCCTC
* *
25475416 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTACTTTT
*
25475437 TCTTTT-TCTTCTTTTACTTTT
1 TCTTTTCTTTTC-TTTACTTTT
25475458 TCTTTTCTTTTCTTTA-TTTT
1 TCTTTTCTTTTCTTTACTTTT
25475478 CTCTTT
1 -TCTTT
25475484 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTACTTTT
Found at i:25476421 original size:12 final size:12
Alignment explanation
Indices: 25476401--25476446 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
25476391 TCATATTTTT
25476401 TTTTCTTTTCGAA
1 TTTT-TTTTCGAA
*
25476414 TTTTTTTTTGAA
1 TTTTTTTTCGAA
25476426 TTTTTTTTTCGAA
1 -TTTTTTTTCGAA
25476439 TTTTTTTT
1 TTTTTTTT
25476447 TGACTTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 15 0.50
13 15 0.50
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:25476435 original size:25 final size:26
Alignment explanation
Indices: 25476400--25476449 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
25476390 TTCATATTTT
25476400 TTTTTCTTTTCGAATTTTTTTTTGAA
1 TTTTTCTTTTCGAATTTTTTTTTGAA
25476426 TTTTT-TTTTCGAATTTTTTTTTGA
1 TTTTTCTTTTCGAATTTTTTTTTGA
25476450 CTTGTATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (26 bp):
TTTTTCTTTTCGAATTTTTTTTTGAA
Found at i:25476447 original size:13 final size:13
Alignment explanation
Indices: 25476400--25476447 Score: 80
Period size: 13 Copynumber: 3.7 Consensus size: 13
25476390 TTCATATTTT
25476400 TTTTTCTTTTCGAA
1 TTTTT-TTTTCGAA
25476414 TTTTTTTTT-GAA
1 TTTTTTTTTCGAA
25476426 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
25476439 TTTTTTTTT
1 TTTTTTTTT
25476448 GACTTGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.36
13 16 0.48
14 5 0.15
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.75
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:25479740 original size:30 final size:30
Alignment explanation
Indices: 25479655--25479751 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
25479645 TAAACTAAAA
* *
25479655 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
25479685 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
25479715 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
25479744 ATGAGCTA
1 -TGAGCTA
25479752 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:25481944 original size:12 final size:12
Alignment explanation
Indices: 25481929--25481959 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
25481919 TTTCTTTTGC
25481929 TTTTCAAAGGCT
1 TTTTCAAAGGCT
25481941 TTTTCAAAGGCT
1 TTTTCAAAGGCT
25481953 TTTTCAA
1 TTTTCAA
25481960 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:25487883 original size:15 final size:14
Alignment explanation
Indices: 25487863--25487910 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
25487853 CTCATTTTCA
25487863 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
25487878 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
*
25487892 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTT
25487907 TCTT
1 TCTT
25487911 CTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:25487915 original size:22 final size:21
Alignment explanation
Indices: 25487863--25487921 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
25487853 CTCATTTTCA
* *
25487863 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
25487884 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
25487905 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
25487922 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:25488945 original size:22 final size:20
Alignment explanation
Indices: 25488920--25488961 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
25488910 TTTTTTTCGG
25488920 ATTTTTTTTCAATATTTTTTTA
1 ATTTTTTTTC-AT-TTTTTTTA
25488942 ATTTTTTTTCATTTTTTTTA
1 ATTTTTTTTCATTTTTTTTA
25488962 CAATACCGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.40
21 2 0.10
22 10 0.50
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (20 bp):
ATTTTTTTTCATTTTTTTTA
Found at i:25490968 original size:30 final size:30
Alignment explanation
Indices: 25490934--25491030 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
25490924 TAAACTAAAA
25490934 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
25490964 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
25490994 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
25491023 ATGAGCTA
1 -TGAGCTA
25491031 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:25491370 original size:228 final size:228
Alignment explanation
Indices: 25490970--25491425 Score: 833
Period size: 228 Copynumber: 2.0 Consensus size: 228
25490960 AAGTTGAGCT
*
25490970 GAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCGTGAGCTAAATATGAGCTAGGAG
1 GAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCATGAGCTAAATATGAGCTAGGAG
25491035 TGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTGAATAAGCTGGATTTGAGCTAGACGGAG
66 TGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTGAATAAGCTGGATTTGAGCTAGACGGAG
*
25491100 CTCGTGGAGCTGGAAACGAGCTGGGATCAGCTTGCCAACATGTCAATG-TCCGGCTTGACAGACT
131 CTCGTGGAGCTGGAAACGAGCTGGGATCAGCTTGCCAACATGTCAATGCT-CAGCTTGACAGACT
25491164 TGTTCGATGAAATTCGCGGGGCGTGCTCGTATCA
195 TGTTCGATGAAATTCGCGGGGCGTGCTCGTATCA
*
25491198 GAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCATGAGCTGAATATGAGCTAGGAG
1 GAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCATGAGCTAAATATGAGCTAGGAG
*
25491263 TGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTGAATAAGCTGGATTTGAGCTGGACGGAG
66 TGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTGAATAAGCTGGATTTGAGCTAGACGGAG
* *
25491328 CTCGTGGAGCTGGAAACGAGCTGGGATTAGCTTGCTAACATGTCAATGCTCAGCTTGACAGACTT
131 CTCGTGGAGCTGGAAACGAGCTGGGATCAGCTTGCCAACATGTCAATGCTCAGCTTGACAGACTT
*
25491393 GTTCGATGAAGTTCGCGGGGCGTGCTCGTATCA
196 GTTCGATGAAATTCGCGGGGCGTGCTCGTATCA
25491426 CCTCTTGTGT
Statistics
Matches: 220, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
228 219 1.00
229 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (228 bp):
GAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCATGAGCTAAATATGAGCTAGGAG
TGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTGAATAAGCTGGATTTGAGCTAGACGGAG
CTCGTGGAGCTGGAAACGAGCTGGGATCAGCTTGCCAACATGTCAATGCTCAGCTTGACAGACTT
GTTCGATGAAATTCGCGGGGCGTGCTCGTATCA
Found at i:25497733 original size:14 final size:15
Alignment explanation
Indices: 25497681--25497735 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
25497671 ACTCTCCTCA
*
25497681 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
25497696 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
* *
25497711 TTGTCTT-TCTCTTT
1 TTCTTTTCTCTCTTT
25497725 TTCTTTT-TCTC
1 TTCTTTTCTCTC
25497736 GATCAATAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
14 15 0.45
15 18 0.55
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.73
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:25501722 original size:30 final size:30
Alignment explanation
Indices: 25501688--25501784 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
25501678 TAAACTAAAA
*
25501688 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
25501718 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
25501748 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
25501777 ATGAGCTA
1 -TGAGCTA
25501785 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:25505636 original size:12 final size:12
Alignment explanation
Indices: 25505598--25505629 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
25505588 CACTCTCAAA
25505598 TTTC-TTTTCAT
1 TTTCTTTTTCAT
25505609 TTTCTTTTTCAT
1 TTTCTTTTTCAT
25505621 TTTCTTTTT
1 TTTCTTTTT
25505630 GCTTTTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTCTTTTTCAT
Found at i:25505727 original size:6 final size:6
Alignment explanation
Indices: 25505711--25505760 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
25505701 TTTCTTTTTA
*
25505711 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
25505760 T
1 T
25505761 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:25505743 original size:37 final size:37
Alignment explanation
Indices: 25505700--25505770 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
25505690 CTTGCCTCTC
25505700 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
25505737 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
25505771 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:25505771 original size:16 final size:16
Alignment explanation
Indices: 25505696--25505756 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
25505686 GCCTCTTGCC
*
25505696 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
25505712 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
25505728 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
25505744 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
25505757 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:25508498 original size:30 final size:30
Alignment explanation
Indices: 25508464--25508560 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
25508454 TAAACTAAAA
*
25508464 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
25508494 TGAGCTGAGGCTGAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
25508524 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
25508553 ATGAGCTA
1 -TGAGCTA
25508561 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:25509435 original size:16 final size:15
Alignment explanation
Indices: 25509394--25509437 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
25509384 CTTTTCACTC
25509394 TCTTTTGTTTTCTTTT
1 TCTTTTGTTTT-TTTT
* *
25509410 TCTTAT-TTTTTTCT
1 TCTTTTGTTTTTTTT
25509424 TCTTTTGTTTTTTT
1 TCTTTTGTTTTTTT
25509438 ACAATATTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 8 0.35
15 10 0.43
16 5 0.22
ACGTcount: A:0.02, C:0.11, G:0.05, T:0.82
Consensus pattern (15 bp):
TCTTTTGTTTTTTTT
Found at i:25511486 original size:22 final size:21
Alignment explanation
Indices: 25511455--25511505 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
25511445 ACCTCTTTGA
25511455 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCAATTCGTACC-AAT
*
25511478 ACCATACCATTTCGTACCAAT
1 ACCATACCAATTCGTACCAAT
*
25511499 TCCATAC
1 ACCATAC
25511506 TATTTCAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 13 0.50
23 4 0.15
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.27
Consensus pattern (21 bp):
ACCATACCAATTCGTACCAAT
Found at i:25511505 original size:21 final size:21
Alignment explanation
Indices: 25511460--25511522 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
25511450 TTTGAACCAT
* *
25511460 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
25511482 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* **
25511503 TACTATTTCAAACCAATTCC
1 TACCATTTCGTACCAATTCC
25511523 CAAATACCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 23 0.64
22 13 0.36
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:25518271 original size:30 final size:30
Alignment explanation
Indices: 25518235--25518331 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
25518225 AGCTCACTCC
25518235 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
25518265 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
25518295 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
25518325 TAGCTCA
1 TAGCTCA
25518332 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:25520879 original size:9 final size:10
Alignment explanation
Indices: 25520872--25520933 Score: 65
Period size: 11 Copynumber: 6.0 Consensus size: 10
25520862 AAGAGAAAAC
25520872 AAAGAAAAGA
1 AAAGAAAAGA
25520882 AAAGAAAAGAA
1 AAAGAAAAG-A
25520893 AAAGCAAAAGA
1 AAAG-AAAAGA
*
25520904 AGA-AAAAGA
1 AAAGAAAAGA
25520913 AAATGAAATA-A
1 AAA-GAAA-AGA
25520924 AAAGAAAAGA
1 AAAGAAAAGA
25520934 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
9 9 0.20
10 14 0.32
11 15 0.34
12 6 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:25520892 original size:15 final size:14
Alignment explanation
Indices: 25520865--25520933 Score: 66
Period size: 16 Copynumber: 4.6 Consensus size: 14
25520855 TCTTGTAAAG
* *
25520865 AGAAAACAAAGAAA
1 AGAAAAGAAAAAAA
25520879 AGAAAAGAAAAGAAAA
1 AGAAAAG-AAA-AAAA
*
25520895 AGCAAAAGAAGAAAA
1 AG-AAAAGAAAAAAA
25520910 AGAAAATGAAATAAAA
1 AGAAAA-GAAA-AAAA
25520926 AGAAAAGA
1 AGAAAAGA
25520934 GAGGCAAGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.22
15 14 0.30
16 17 0.37
17 5 0.11
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (14 bp):
AGAAAAGAAAAAAA
Found at i:25520901 original size:6 final size:5
Alignment explanation
Indices: 25520872--25520933 Score: 65
Period size: 5 Copynumber: 12.0 Consensus size: 5
25520862 AAGAGAAAAC
*
25520872 AAAGA AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA
1 AAAGA AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA
25520919 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
25520934 GAGGCAAGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.08
5 30 0.61
6 14 0.29
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:25520913 original size:31 final size:30
Alignment explanation
Indices: 25520876--25520933 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
25520866 GAAAACAAAG
25520876 AAAAGAAAA-GAAAAGAAAAAGCAAAAGAAGA
1 AAAAGAAAATG-AAAGAAAAAG-AAAAGAAGA
*
25520907 AAAAGAAAATGAAATAAAAAGAAAAGA
1 AAAAGAAAATGAAAGAAAAAGAAAAGA
25520934 GAGGCAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 6 0.24
31 18 0.72
32 1 0.04
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (30 bp):
AAAAGAAAATGAAAGAAAAAGAAAAGAAGA
Found at i:25521041 original size:30 final size:30
Alignment explanation
Indices: 25520993--25521077 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
25520983 GAAAAAGCCT
*
25520993 TTGAAAAACAAAAAGAAAATGAAA-ATGAGA
1 TTGAAAAAGAAAAAGAAAA-GAAATATGAGA
* * *
25521023 TTGAAAAAGAGAACGAAAAGAAATTTGAGA
1 TTGAAAAAGAAAAAGAAAAGAAATATGAGA
* * *
25521053 GTGAAAAAGAAGATGAAAAAGAAAT
1 TTGAAAAAGAAAAAG-AAAAGAAAT
25521078 TGAAACAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
29 4 0.09
30 32 0.71
31 9 0.20
ACGTcount: A:0.62, C:0.02, G:0.21, T:0.14
Consensus pattern (30 bp):
TTGAAAAAGAAAAAGAAAAGAAATATGAGA
Found at i:25525579 original size:30 final size:30
Alignment explanation
Indices: 25525545--25525642 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
25525535 AGCTCACTCC
25525545 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
25525575 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
25525605 CAAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 -TAGCTCAACTTCAGCTCACGAGCTAAACCT
25525636 TAGCTCA
1 TAGCTCA
25525643 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
29 1 0.02
30 29 0.55
31 23 0.43
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:25526233 original size:29 final size:29
Alignment explanation
Indices: 25526199--25526255 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
25526189 AGCTCGAATT
25526199 AGCTCACA-TGAGCTTAATTTAGCTCGTTA
1 AGCTCA-ATTGAGCTTAATTTAGCTCGTTA
* *
25526228 AGCTCAATTTAGCTTACTTTAGCTCGTT
1 AGCTCAATTGAGCTTAATTTAGCTCGTT
25526256 TGAGCTTGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.39
Consensus pattern (29 bp):
AGCTCAATTGAGCTTAATTTAGCTCGTTA
Found at i:25527872 original size:13 final size:13
Alignment explanation
Indices: 25527856--25527905 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
25527846 CAAAAAAATC
25527856 AAAAAAAAATTTG
1 AAAAAAAAATTTG
25527869 AAAAAAAAATTTG
1 AAAAAAAAATTTG
* *
25527882 ATTGAAAAAAAAATTC
1 A---AAAAAAAATTTG
25527898 AAAAAAAA
1 AAAAAAAA
25527906 GTGAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 21 0.66
16 11 0.34
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (13 bp):
AAAAAAAAATTTG
Found at i:25529012 original size:11 final size:12
Alignment explanation
Indices: 25528998--25529112 Score: 58
Period size: 12 Copynumber: 9.2 Consensus size: 12
25528988 GAAATTGAAA
25528998 AAAAC-AAAAAG
1 AAAACGAAAAAG
*
25529009 AAAACGAAGAAG
1 AAAACGAAAAAG
* **
25529021 AAAAAGAAATTG
1 AAAACGAAAAAG
25529033 CAAAA-GAAAAAG
1 -AAAACGAAAAAG
*
25529045 AAATCGAAAAATTG
1 AAAACGAAAAA--G
*
25529059 -AGA-GAAAAAG
1 AAAACGAAAAAG
*
25529069 AAAATGAAGAAAAG
1 AAAACG-A-AAAAG
*
25529083 AAAATTGAAAAAG
1 AAAA-CGAAAAAG
25529096 AAAAGCGAAAAAAG
1 AAAA-CG-AAAAAG
25529110 AAA
1 AAA
25529113 TTGAAAGAGA
Statistics
Matches: 80, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
10 1 0.01
11 10 0.12
12 31 0.39
13 16 0.20
14 20 0.25
15 2 0.03
ACGTcount: A:0.70, C:0.04, G:0.18, T:0.07
Consensus pattern (12 bp):
AAAACGAAAAAG
Found at i:25529055 original size:18 final size:18
Alignment explanation
Indices: 25528982--25529055 Score: 76
Period size: 18 Copynumber: 4.0 Consensus size: 18
25528972 GAAAGAGATT
*
25528982 GAAAAAGAAATTGAAAAAAA
1 GAAAAAGAAATCG--AAAAA
* * *
25529002 CAAAAAGAAAACGAAGAA
1 GAAAAAGAAATCGAAAAA
* *
25529020 GAAAAAGAAATTGCAAAA
1 GAAAAAGAAATCGAAAAA
25529038 GAAAAAGAAATCGAAAAA
1 GAAAAAGAAATCGAAAAA
25529056 TTGAGAGAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
18 33 0.77
20 10 0.23
ACGTcount: A:0.72, C:0.05, G:0.16, T:0.07
Consensus pattern (18 bp):
GAAAAAGAAATCGAAAAA
Found at i:25529083 original size:14 final size:14
Alignment explanation
Indices: 25529063--25529112 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
25529053 AAATTGAGAG
25529063 AAAAAGAAAA-TGA
1 AAAAAGAAAAGTGA
*
25529076 AGAAAAGAAAATTG-
1 A-AAAAGAAAAGTGA
*
25529090 AAAAAGAAAAGCGA
1 AAAAAGAAAAGTGA
25529104 AAAAAGAAA
1 AAAAAGAAA
25529113 TTGAAAGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 11 0.34
14 19 0.59
15 2 0.06
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (14 bp):
AAAAAGAAAAGTGA
Found at i:25529092 original size:27 final size:26
Alignment explanation
Indices: 25529062--25529118 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
25529052 AAAATTGAGA
*
25529062 GAAAAAGAAAA-TGAAGAAAAGAAAATT
1 GAAAAAGAAAAGCGAA-AAAAG-AAATT
25529089 GAAAAAGAAAAGCGAAAAAAGAAATT
1 GAAAAAGAAAAGCGAAAAAAGAAATT
25529115 GAAA
1 GAAA
25529119 GAGAGCTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 9 0.32
27 16 0.57
28 3 0.11
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (26 bp):
GAAAAAGAAAAGCGAAAAAAGAAATT
Found at i:25529096 original size:13 final size:13
Alignment explanation
Indices: 25529062--25529118 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
25529052 AAAATTGAGA
25529062 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
25529074 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
**
25529089 GAAAAAGAAAAGC
1 GAAAAAGAAAATT
25529102 GAAAAA-AGAAATT
1 GAAAAAGA-AAATT
25529115 GAAA
1 GAAA
25529119 GAGAGCTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
12 2 0.05
13 23 0.62
14 10 0.27
15 2 0.05
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:25529176 original size:33 final size:33
Alignment explanation
Indices: 25529115--25529177 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
25529105 AAAAGAAATT
25529115 GAAAGAGAGCTTGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGCTTGAAAAGAAATCAAGTGAAAAA
*
25529148 GAAAGAGAG-TCTGTAAAAGAAA-CGAGTGAA
1 GAAAGAGAGCT-TG-AAAAGAAATCAAGTGAA
25529178 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 1 0.04
33 18 0.67
34 8 0.30
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGCTTGAAAAGAAATCAAGTGAAAAA
Found at i:25530984 original size:20 final size:20
Alignment explanation
Indices: 25530961--25531006 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
25530951 CCAGCTCGAA
*
25530961 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
25530981 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
25531001 TTAGCT
1 TTAGCT
25531007 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:25530988 original size:30 final size:30
Alignment explanation
Indices: 25530953--25531026 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
25530943 AGTTTTTCCC
25530953 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
25530983 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
25531013 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
25531027 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:25531926 original size:20 final size:20
Alignment explanation
Indices: 25531901--25531940 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
25531891 ACATTAGTAG
25531901 CTGAATTTTAATAGGCATTA
1 CTGAATTTTAATAGGCATTA
25531921 CTGAATTTTAATAGGCATTA
1 CTGAATTTTAATAGGCATTA
25531941 GAGAGCCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (20 bp):
CTGAATTTTAATAGGCATTA
Found at i:25534647 original size:9 final size:10
Alignment explanation
Indices: 25534640--25534696 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
25534630 AAGAGAAAAT
25534640 AAAGAAAAGA
1 AAAGAAAAGA
25534650 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
25534662 AAAGAAGA-A
1 AAAGAAAAGA
25534671 AAAGAAAATGA
1 AAAGAAAA-GA
25534682 AATA-AAAAGA
1 AA-AGAAAAGA
25534692 AAAGA
1 AAAGA
25534697 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:25534664 original size:6 final size:5
Alignment explanation
Indices: 25534640--25534696 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
25534630 AAGAGAAAAT
*
25534640 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
25534687 AAAGA AAAGA
1 AAAGA AAAGA
25534697 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:25534671 original size:15 final size:14
Alignment explanation
Indices: 25534640--25534696 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
25534630 AAGAGAAAAT
25534640 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
25534656 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
25534671 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
25534687 AAAGAAAAGA
1 AAAGAAAAGA
25534697 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:25534773 original size:12 final size:12
Alignment explanation
Indices: 25534765--25534845 Score: 56
Period size: 12 Copynumber: 6.8 Consensus size: 12
25534755 TTTGAAAAGC
25534765 AAAAAGAAAATG
1 AAAAAGAAAATG
25534777 AAAAAGAAAATG
1 AAAAAGAAAATG
** *
25534789 AAATTGAAAAAG
1 AAAAAGAAAATG
**
25534801 AAAGCGAAAA-G
1 AAAAAGAAAATG
** * *
25534812 AAATTTGAGAGTG
1 AAA-AAGAAAATG
*
25534825 AAAAAGAAGATG
1 AAAAAGAAAATG
25534837 AAAAAGAAA
1 AAAAAGAAA
25534846 TTGGAACAAA
Statistics
Matches: 52, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
11 4 0.08
12 44 0.85
13 4 0.08
ACGTcount: A:0.67, C:0.01, G:0.21, T:0.11
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:25534799 original size:30 final size:31
Alignment explanation
Indices: 25534765--25534846 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
25534755 TTTGAAAAGC
*
25534765 AAAAAGAAAATGAAAAAGAAA-ATGAAATTG
1 AAAAAGAAAATGAAAAAGAAATATGAAAGTG
** * *
25534795 AAAAAGAAAGCG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAAAGTG
*
25534825 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
25534847 TGGAACAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.19
30 25 0.60
31 9 0.21
ACGTcount: A:0.66, C:0.01, G:0.21, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAAAGTG
Done.