Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 356 of 410
Found at i:109839844 original size:15 final size:15
Alignment explanation
Indices: 109839824--109839854 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
109839814 TTACTTCTAA
109839824 GAAACAACATCATGG
1 GAAACAACATCATGG
109839839 GAAACAACATCATGG
1 GAAACAACATCATGG
109839854 G
1 G
109839855 TGTACGGGTC
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:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (15 bp):
GAAACAACATCATGG
Found at i:109842338 original size:3 final size:3
Alignment explanation
Indices: 109842324--109842379 Score: 103
Period size: 3 Copynumber: 18.3 Consensus size: 3
109842314 AAAAATATAC
109842324 AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
109842370 AAT AAT AAT A
1 AAT AAT AAT A
109842380 TGGAAATACA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:109842874 original size:18 final size:17
Alignment explanation
Indices: 109842853--109842888 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
109842843 AGAAAAAAAA
109842853 AAGAAAAGAGAGAGAGGG
1 AAGAAAAGAGAGAG-GGG
*
109842871 AAGAAAGGAGAGAGGGG
1 AAGAAAAGAGAGAGGGG
109842888 A
1 A
109842889 GAGGGGAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAGAGAGGGG
Found at i:109843510 original size:7 final size:7
Alignment explanation
Indices: 109843490--109843556 Score: 62
Period size: 7 Copynumber: 8.9 Consensus size: 7
109843480 CGGCTGATTA
109843490 GGGTTTT
1 GGGTTTT
109843497 GGGGTTTT
1 -GGGTTTT
109843505 GGGTTTT
1 GGGTTTT
109843512 GGGTTTGT
1 GGGTTT-T
*
109843520 AAGGGGTTT
1 --GGGTTTT
109843529 GGGCTTTT
1 GGG-TTTT
* *
109843537 GTGTATT
1 GGGTTTT
109843544 GGGTTTT
1 GGGTTTT
109843551 GGGTTT
1 GGGTTT
109843557 GTAAGGGTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
7 30 0.61
8 13 0.27
9 1 0.02
10 5 0.10
ACGTcount: A:0.04, C:0.01, G:0.43, T:0.51
Consensus pattern (7 bp):
GGGTTTT
Found at i:109843531 original size:32 final size:32
Alignment explanation
Indices: 109843489--109843549 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
109843479 TCGGCTGATT
* * *
109843489 AGGGTTTTGGGGTTTTGGGTTTTGGGTTTGTA
1 AGGGGTTTGGGCTTTTGGGTATTGGGTTTGTA
*
109843521 AGGGGTTTGGGCTTTTGTGTATTGGGTTT
1 AGGGGTTTGGGCTTTTGGGTATTGGGTTT
109843550 TGGGTTTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.07, C:0.02, G:0.43, T:0.49
Consensus pattern (32 bp):
AGGGGTTTGGGCTTTTGGGTATTGGGTTTGTA
Found at i:109844414 original size:54 final size:54
Alignment explanation
Indices: 109844323--109844476 Score: 256
Period size: 54 Copynumber: 2.9 Consensus size: 54
109844313 CATATGACCT
* *
109844323 AAGGCTCAACTCACTTCTCGCAATATGGGTTGATTTTTGAAAAACAAAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAA
*
109844377 AAGG-TACAACTCACCTCTCGCAATATGAGTTGTTTTTTGAAAAACAAAAATTAA
1 AAGGCT-CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAA
*
109844431 AAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
109844477 GGAATTGGAA
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
53 1 0.01
54 91 0.98
55 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (54 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAA
Found at i:109857538 original size:3 final size:3
Alignment explanation
Indices: 109857524--109857606 Score: 157
Period size: 3 Copynumber: 27.3 Consensus size: 3
109857514 AAAAATATAC
109857524 AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
109857570 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
109857607 TGGAAATACA
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 76 0.96
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:109858104 original size:18 final size:17
Alignment explanation
Indices: 109858081--109858116 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
109858071 GAAAAAAAAA
109858081 AAGAAAAGAGAGAGAGGG
1 AAGAAAAGAGAGAG-GGG
*
109858099 AAGAAAGGAGAGAGGGG
1 AAGAAAAGAGAGAGGGG
109858116 A
1 A
109858117 GAGGGGAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAGAGAGGGG
Found at i:109867226 original size:12 final size:12
Alignment explanation
Indices: 109867211--109867240 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
109867201 GTGAATAAAG
*
109867211 AAGATAAATGGA
1 AAGATAAATAGA
109867223 AAGATAAATAGA
1 AAGATAAATAGA
109867235 AAGATA
1 AAGATA
109867241 GAACGTGGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (12 bp):
AAGATAAATAGA
Found at i:109877852 original size:40 final size:40
Alignment explanation
Indices: 109877733--109877870 Score: 138
Period size: 40 Copynumber: 3.5 Consensus size: 40
109877723 CTTCCAGTTA
* * *
109877733 ATGAGACACTGGGTGTCAATTTACTACTTCAGATTTATTCG
1 ATGAGACACTGGGTGTCAAATTATTACTTC-GATTTATCCG
* * * * *
109877774 ATGAGGCATTCGGTGTC-AA-T-TTACTTCGGTTTAGCCG
1 ATGAGACACTGGGTGTCAAATTATTACTTCGATTTATCCG
* *
109877811 ATGAGACATTGGGTGTCAAATTATTACTTCGAATTATCCG
1 ATGAGACACTGGGTGTCAAATTATTACTTCGATTTATCCG
* *
109877851 ATGAGGCACTGGGTGCCAAA
1 ATGAGACACTGGGTGTCAAA
109877871 CTGGTGTGTT
Statistics
Matches: 78, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
37 22 0.28
38 8 0.10
39 2 0.03
40 32 0.41
41 14 0.18
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAAATTATTACTTCGATTTATCCG
Found at i:109880015 original size:17 final size:18
Alignment explanation
Indices: 109879983--109880023 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
109879973 CATATGGCAC
109879983 TTTTATTATATTTACCAA
1 TTTTATTATATTTACCAA
*
109880001 TTTTATT-TCTTTACCAA
1 TTTTATTATATTTACCAA
109880018 TATTTA
1 T-TTTA
109880024 AAATTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTATTATATTTACCAA
Found at i:109891112 original size:14 final size:14
Alignment explanation
Indices: 109891093--109891122 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
109891083 ATCTAAACAA
109891093 TAGCAACAAAATAG
1 TAGCAACAAAATAG
*
109891107 TAGCAACATAATAG
1 TAGCAACAAAATAG
109891121 TA
1 TA
109891123 AAATGGTAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (14 bp):
TAGCAACAAAATAG
Found at i:109901783 original size:48 final size:48
Alignment explanation
Indices: 109901580--109901896 Score: 255
Period size: 48 Copynumber: 6.6 Consensus size: 48
109901570 GGGTAAATTA
* * * **
109901580 CCGATGCCATGTTCCAGACATGGTCTTACATTGGCTCACATGTCGAG-G
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAC-AGTG
* * * * ** *
109901628 CTGATGCCATGTCCCAGAAATGATCTTACACTAGCTCTCATTTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAACAGTG
* * * * *
109901676 CTGATGCCATGTCCCAGACATAGTTTTACATTGGCTCTCATAA-TGTGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAACAGT-G
* * * * * *
109901724 CC-ATTGTCATGTCCCAGACATGGTCTTACACTAGCACACCTAACAGCG
1 CCGA-TGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAACAGTG
** * * *
109901772 CCGATGCCATGTCCTGGAGATGGTCTTACAGTGGCTCTCATAACATTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAACAGTG
* * * * * * *
109901820 TCGATGCCATGTTCCAAACATGGTCTTATACTGGCTTTTATATC-GTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAACAGTG
*
109901867 GCGATGCCATGTCCCAGACATGGTCTTACA
1 CCGATGCCATGTCCCAGACATGGTCTTACA
109901897 TCAGGACACA
Statistics
Matches: 207, Mismatches: 57, Indels: 11
0.75 0.21 0.04
Matches are distributed among these distances:
47 31 0.15
48 174 0.84
49 2 0.01
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAACAGTG
Found at i:109902281 original size:31 final size:31
Alignment explanation
Indices: 109902229--109902288 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
109902219 ATAATTCATA
*
109902229 TTTTGAAAAAATGATCGTTTTGCCTTTAGAC
1 TTTTGAAAAAATGATCGTTTTGCCCTTAGAC
109902260 TTTT-AAAAAAT-ATACGATTTTGCCCTTAG
1 TTTTGAAAAAATGAT-CG-TTTTGCCCTTAG
109902289 GCTCGTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 2 0.08
30 9 0.35
31 15 0.58
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (31 bp):
TTTTGAAAAAATGATCGTTTTGCCCTTAGAC
Found at i:109905279 original size:14 final size:14
Alignment explanation
Indices: 109905244--109905276 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
109905234 AAGAGAAAGG
109905244 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
109905258 AAAAAAT-AAAAAT
1 AAAAAATAAAAAAT
109905271 AAAAAA
1 AAAAAA
109905277 ATACTCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAATAAAAAAT
Found at i:109905299 original size:6 final size:7
Alignment explanation
Indices: 109905244--109905276 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
109905234 AAGAGAAAGG
109905244 AAAAAAT
1 AAAAAAT
109905251 AAAAAAT
1 AAAAAAT
109905258 AAAAAAT
1 AAAAAAT
109905265 -AAAAAT
1 AAAAAAT
109905271 AAAAAA
1 AAAAAA
109905277 ATACTCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:109906064 original size:8 final size:8
Alignment explanation
Indices: 109906051--109906099 Score: 55
Period size: 8 Copynumber: 5.9 Consensus size: 8
109906041 AAATAGATTT
109906051 ATAAAAAA
1 ATAAAAAA
109906059 AT-AAAAA
1 ATAAAAAA
109906066 ATAAAAAA
1 ATAAAAAA
109906074 ATAAAATAA
1 ATAAAA-AA
*
109906083 AAAACAAAA
1 ATAA-AAAA
109906092 ATGAAAAA
1 AT-AAAAA
109906100 TGAACAAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
7 7 0.20
8 13 0.37
9 11 0.31
10 4 0.11
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.12
Consensus pattern (8 bp):
ATAAAAAA
Found at i:109906066 original size:7 final size:7
Alignment explanation
Indices: 109906054--109906092 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
109906044 TAGATTTATA
109906054 AAAAAAT
1 AAAAAAT
109906061 AAAAAAT
1 AAAAAAT
109906068 AAAAAA-
1 AAAAAAT
*
109906074 ATAAAAT
1 AAAAAAT
*
109906081 AAAAAAC
1 AAAAAAT
109906088 AAAAA
1 AAAAA
109906093 TGAAAAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (7 bp):
AAAAAAT
Found at i:109906079 original size:13 final size:13
Alignment explanation
Indices: 109906051--109906099 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
109906041 AAATAGATTT
109906051 ATAAAAAAATAAAAA
1 ATAAAAAAAT--AAA
109906066 ATAAAAAAATAAA
1 ATAAAAAAATAAA
109906079 ATAAAAAACA-AAA
1 ATAAAAAA-ATAAA
109906092 ATGAAAAA
1 AT-AAAAA
109906100 TGAACAAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 16 0.50
14 6 0.19
15 10 0.31
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.12
Consensus pattern (13 bp):
ATAAAAAAATAAA
Found at i:109906086 original size:15 final size:15
Alignment explanation
Indices: 109906051--109906079 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
109906041 AAATAGATTT
109906051 ATAAAAAAATAAAAA
1 ATAAAAAAATAAAAA
109906066 ATAAAAAAATAAAA
1 ATAAAAAAATAAAA
109906080 TAAAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
ATAAAAAAATAAAAA
Found at i:109906100 original size:20 final size:19
Alignment explanation
Indices: 109906053--109906092 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
109906043 ATAGATTTAT
*
109906053 AAAAAAATAAAAAATAAAA
1 AAAAAAATAAAAAACAAAA
109906072 AAATAAAATAAAAAACAAAA
1 AAA-AAAATAAAAAACAAAA
109906092 A
1 A
109906093 TGAAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.10
Consensus pattern (19 bp):
AAAAAAATAAAAAACAAAA
Found at i:109908822 original size:6 final size:7
Alignment explanation
Indices: 109908805--109908829 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
109908795 AGTCATTTTA
109908805 AAAAAAG
1 AAAAAAG
109908812 AAAAAAG
1 AAAAAAG
109908819 AAAAAAG
1 AAAAAAG
109908826 AAAA
1 AAAA
109908830 TCACTCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:109909153 original size:48 final size:48
Alignment explanation
Indices: 109909082--109909177 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
109909072 TCTTTAAGGT
109909082 GCAATTTTTACACGGGAAGAAAAAGAAAAATGTTCATAGGTTTGCTTA
1 GCAATTTTTACACGGGAAGAAAAAGAAAAATGTTCATAGGTTTGCTTA
* *
109909130 GCAATTTTTATACGGGAAGAAAAAGAAAACTGTTCATAGGTTTGCTTA
1 GCAATTTTTACACGGGAAGAAAAAGAAAAATGTTCATAGGTTTGCTTA
109909178 ATAAAATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (48 bp):
GCAATTTTTACACGGGAAGAAAAAGAAAAATGTTCATAGGTTTGCTTA
Found at i:109912710 original size:21 final size:21
Alignment explanation
Indices: 109912685--109912724 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
109912675 CATTCTTGAT
* *
109912685 AATAATTAATAATATTGATTA
1 AATAATAAATAATAATGATTA
109912706 AATAATAAATAATAATGAT
1 AATAATAAATAATAATGAT
109912725 ATTTCAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
AATAATAAATAATAATGATTA
Found at i:109913521 original size:14 final size:15
Alignment explanation
Indices: 109913497--109913525 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
109913487 TGTGATTATT
109913497 ATGATGATTGATATG
1 ATGATGATTGATATG
109913512 ATGA-GATTGATATG
1 ATGATGATTGATATG
109913526 TTAATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (15 bp):
ATGATGATTGATATG
Found at i:109914620 original size:340 final size:340
Alignment explanation
Indices: 109914000--109914682 Score: 1287
Period size: 340 Copynumber: 2.0 Consensus size: 340
109913990 TAGATATGCA
109914000 AATTATCCATTGCAATGTTTTAATTGAAGTATGACACTTTCTGAAGAAAAAAATATCAAAACTTG
1 AATTATCCATTGCAATGTTTTAATTGAAGTATGACACTTTCTGAAGAAAAAAATATCAAAACTTG
*
109914065 AGTTTTCTAAAGATAAACAATTTCAAACAAAATTCGGTTTTCTCAACAAAGATGGTTTAAGCAAT
66 AGTTTTCTAAAGATAAACAATTTCAAACAAAATTCAGTTTTCTCAACAAAGATGGTTTAAGCAAT
*
109914130 GACGATTTTTAAGAGAAAATAGCTAAATGATTTTTTTTGCGCCATCAATATGGAAAATGTGATCT
131 GACGATTTTTAAGAGAAAATAGCTAAATGATTTTTTTTGCGCCATCAATATGGAAAATGTAATCT
109914195 TCGAGATTCGGCCATAACGTTTAGGCCAGGTTTAATGGGTTACACTTCTGGCGGATTAGAGTTTG
196 TCGAGATTCGGCCATAACGTTTAGGCCAGGTTTAATGGGTTACACTTCTGGCGGATTAGAGTTTG
*
109914260 GCATAAAGTATCTGTTGTAGACGTGATTAAAGGTTTTATATTAGGTTATTCTATTATTTAAGAAA
261 GCATAAAGTATCTGTTGTAGAAGTGATTAAAGGTTTTATATTAGGTTATTCTATTATTTAAGAAA
*
109914325 AGAATATGATAAGTG
326 AGAATATGATAAGCG
*
109914340 AATTATCCATTGCAATGTTTTAATTGAAGTATGACACTTTCTGAAG-GAAAAATATCAAAACTTG
1 AATTATCCATTGCAATGTTTTAATTGAAGTATGACACTTTCTGAAGAAAAAAATATCAAAACTTG
109914404 AGTTTTCTAAAGATAAACAATTTCAAACAAAATTCAGTTTTCTCAACAAAGATGGTTTAAGCAAT
66 AGTTTTCTAAAGATAAACAATTTCAAACAAAATTCAGTTTTCTCAACAAAGATGGTTTAAGCAAT
*
109914469 GACGATTTTTAAGAGAAAATAGCTAAATGATTTTCTTTTGTGCCATCAATATGGAAAATGTAATC
131 GACGATTTTTAAGAGAAAATAGCTAAATGATTTT-TTTTGCGCCATCAATATGGAAAATGTAATC
*
109914534 TTCGAGATTCGGCCATAACGTTTAGGCCAGGTTTAATGGGTTACACTTCTGGTGGATTAGAGTTT
195 TTCGAGATTCGGCCATAACGTTTAGGCCAGGTTTAATGGGTTACACTTCTGGCGGATTAGAGTTT
109914599 GGCATAAAGTATCTGTTGTAGAAGTGATTAAAGGTTTTATATTAGGTTATTCTATTATTTAAGAA
260 GGCATAAAGTATCTGTTGTAGAAGTGATTAAAGGTTTTATATTAGGTTATTCTATTATTTAAGAA
109914664 AAGAATATGATAAGCG
325 AAGAATATGATAAGCG
109914680 AAT
1 AAT
109914683 AAGTAAGCCT
Statistics
Matches: 335, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
339 115 0.34
340 220 0.66
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (340 bp):
AATTATCCATTGCAATGTTTTAATTGAAGTATGACACTTTCTGAAGAAAAAAATATCAAAACTTG
AGTTTTCTAAAGATAAACAATTTCAAACAAAATTCAGTTTTCTCAACAAAGATGGTTTAAGCAAT
GACGATTTTTAAGAGAAAATAGCTAAATGATTTTTTTTGCGCCATCAATATGGAAAATGTAATCT
TCGAGATTCGGCCATAACGTTTAGGCCAGGTTTAATGGGTTACACTTCTGGCGGATTAGAGTTTG
GCATAAAGTATCTGTTGTAGAAGTGATTAAAGGTTTTATATTAGGTTATTCTATTATTTAAGAAA
AGAATATGATAAGCG
Found at i:109919227 original size:24 final size:25
Alignment explanation
Indices: 109919181--109919233 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
109919171 TCTCCGGAGT
* *
109919181 TTCTCGATATTGGCTCGTTTG-AAC
1 TTCTCGATATTGGCTCATCTGAAAC
109919205 TTCTCGATATATGGCT-ATCTGAAAC
1 TTCTCGATAT-TGGCTCATCTGAAAC
109919230 TTCT
1 TTCT
109919234 TGTTTAATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (25 bp):
TTCTCGATATTGGCTCATCTGAAAC
Found at i:109919304 original size:24 final size:24
Alignment explanation
Indices: 109919251--109919306 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
109919241 TGGCTTTTCG
*
109919251 GAGCTACCTGTTATTGGCTCACAT
1 GAGCTTCCTGTTATTGGCTCACAT
**
109919275 GAGCTTCCTGATTA-TGGCTCTTAT
1 GAGCTTCCTG-TTATTGGCTCACAT
109919299 GAGCTTCC
1 GAGCTTCC
109919307 CATTATATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (24 bp):
GAGCTTCCTGTTATTGGCTCACAT
Found at i:109923931 original size:31 final size:30
Alignment explanation
Indices: 109923876--109923934 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
109923866 GTAAATACTC
***
109923876 AAAATTTGAAGGGTTAAAGTGTAAATATGA
1 AAAATTTGAAGGACCAAAGTGTAAATATGA
109923906 AAAATTTGAAGGACCAATAGTGTAAATAT
1 AAAATTTGAAGGACCAA-AGTGTAAATAT
109923935 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.29
Consensus pattern (30 bp):
AAAATTTGAAGGACCAAAGTGTAAATATGA
Found at i:109924201 original size:24 final size:22
Alignment explanation
Indices: 109924174--109924229 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 22
109924164 AGATAAATAT
109924174 TATTTTATTAATATTTTAATAAG
1 TATTTTATTAATATTTT-ATAAG
* *
109924197 ATATTTTATTATTATTTTATTAG
1 -TATTTTATTAATATTTTATAAG
109924220 TATTTTATTA
1 TATTTTATTA
109924230 GTATATCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 10 0.33
23 4 0.13
24 16 0.53
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
TATTTTATTAATATTTTATAAG
Found at i:109924230 original size:11 final size:11
Alignment explanation
Indices: 109924174--109924233 Score: 75
Period size: 11 Copynumber: 5.3 Consensus size: 11
109924164 AGATAAATAT
*
109924174 TATTTTATTAA
1 TATTTTATTAG
*
109924185 TATTTTAATAAG
1 TATTTT-ATTAG
*
109924197 ATATTTTATTAT
1 -TATTTTATTAG
109924209 TATTTTATTAG
1 TATTTTATTAG
109924220 TATTTTATTAG
1 TATTTTATTAG
109924231 TAT
1 TAT
109924234 ATCAAGAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
11 30 0.71
12 6 0.14
13 6 0.14
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (11 bp):
TATTTTATTAG
Found at i:109927838 original size:40 final size:40
Alignment explanation
Indices: 109927759--109927916 Score: 151
Period size: 40 Copynumber: 4.0 Consensus size: 40
109927749 TTCGAATGAT
* * * *
109927759 ATCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGC-GAGTTACTAA
* *
109927799 ATCCGGACTAAGATCCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
109927839 ATCCGGACTAAGATCCGAAGGCTTTCGAGCAAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
** *
109927879 ATCCGGGTTGAG-TCCCGAAGGCATTCGTGCGAGTTACT
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACT
109927917 GTAACCGGGC
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 89 0.93
41 6 0.06
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:109927937 original size:80 final size:80
Alignment explanation
Indices: 109927759--109927946 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 80
109927749 TTCGAATGAT
* *
109927759 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
109927824 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* ** *
109927839 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGC-AAGCT-ACTAAATCCGGGTTGAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGACTAAGAT-CCGAAGG
* *
109927900 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
109927920 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
109927947 ATGTGTAGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 2 0.02
80 79 0.87
81 10 0.11
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:109935920 original size:40 final size:40
Alignment explanation
Indices: 109935841--109935998 Score: 151
Period size: 40 Copynumber: 4.0 Consensus size: 40
109935831 TTCGAATGAT
* * * *
109935841 ATCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGC-GAGTTACTAA
* *
109935881 ATCCGGACTAAGATCCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
109935921 ATCCGGACTAAGATCCGAAGGCTTTCGAGCAAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
** *
109935961 ATCCGGGTTGAG-TCCCGAAGGCATTCGTGCGAGTTACT
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACT
109935999 GTAACCGGGC
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 89 0.93
41 6 0.06
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:109936019 original size:80 final size:80
Alignment explanation
Indices: 109935841--109936028 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 80
109935831 TTCGAATGAT
* *
109935841 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
109935906 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* ** *
109935921 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGC-AAGCT-ACTAAATCCGGGTTGAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGACTAAGAT-CCGAAGG
* *
109935982 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
109936002 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
109936029 ATGTGTAGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 2 0.02
80 79 0.87
81 10 0.11
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:109937476 original size:46 final size:46
Alignment explanation
Indices: 109937421--109937742 Score: 414
Period size: 46 Copynumber: 7.0 Consensus size: 46
109937411 ACGGGGTGTT
**
109937421 ACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
1 ACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
* ** *
109937467 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTG
1 ACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
* * *
109937513 ACGTGAAAAGAATAAGACCATGGTTGAGAGATACCATGGCAACATG
1 ACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
** * * *
109937559 ACGGGAAATGAATAGGACCATGGTTGAAAGATACCATGGCAGCGTG
1 ACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
* *
109937605 ACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGAAACGTG
1 ACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
*
109937651 ACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
1 ACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
* * * * *
109937697 ATA-GAAAATGAGTAAGACCATAGTTTAAAGAT-CCTATGGCATCATG
1 ACATG-AAATGAATAAGACCATGGTTGAAAGATACC-ATGGCAACATG
109937743 TCAAAGATAA
Statistics
Matches: 245, Mismatches: 29, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
45 3 0.01
46 242 0.99
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.20
Consensus pattern (46 bp):
ACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
Found at i:109937673 original size:138 final size:138
Alignment explanation
Indices: 109937433--109937742 Score: 460
Period size: 138 Copynumber: 2.2 Consensus size: 138
109937423 ATGAAATGTG
* **
109937433 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
* * * *
109937498 TACCATGGCAACGTGACGTGAAAAGAATAAGACCATGGTTGAGAGATACCATGGCAACATGACGG
66 TACCATGGAAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
*
109937563 GAAATGAA
131 AAAATGAA
* * *
109937571 TAGGACCATGGTTGAAAGATACCATGGCAGCGTGACATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
*
109937636 TACCATGGAAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGATAG
66 TACCATGGAAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
*
109937701 AAAATGAG
131 AAAATGAA
* * *
109937709 TAAGACCATAGTTTAAAGAT-CCTATGGCATCATG
1 TAAGACCATGGTTGAAAGATACC-ATGGCAACATG
109937743 TCAAAGATAA
Statistics
Matches: 153, Mismatches: 18, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
137 2 0.01
138 151 0.99
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (138 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
TACCATGGAAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
AAAATGAA
Found at i:109938484 original size:42 final size:42
Alignment explanation
Indices: 109938423--109938560 Score: 141
Period size: 42 Copynumber: 3.3 Consensus size: 42
109938413 ACAATAACTA
* * *
109938423 GGATATGACATCAAGATAAGACTACGTGTAAGACCATATTTG
1 GGATATGGCATCGATATAAGACTACGTGTAAGACCATATTTG
* *
109938465 GGATATGGCATCGATATAAGACTTCGTGTAAGACCATAGTTG
1 GGATATGGCATCGATATAAGACTACGTGTAAGACCATATTTG
* * * ** * * * *
109938507 AGCTATTCGCATCGATACGAGATTACATGTAAGACCATATCTA
1 GGATA-TGGCATCGATATAAGACTACGTGTAAGACCATATTTG
109938550 GGATATGGCAT
1 GGATATGGCAT
109938561 TGGTACGATA
Statistics
Matches: 76, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
42 45 0.59
43 31 0.41
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (42 bp):
GGATATGGCATCGATATAAGACTACGTGTAAGACCATATTTG
Found at i:109939611 original size:51 final size:51
Alignment explanation
Indices: 109939529--109939648 Score: 168
Period size: 51 Copynumber: 2.4 Consensus size: 51
109939519 CTCAAACTTA
* *
109939529 CTTCATACTTCATCCGGAATTATTACCTTGTTGCTCTAACTTCAACAAGAG
1 CTTCATATTTCATCCGGAATAATTACCTTGTTGCTCTAACTTCAACAAGAG
* ** * *
109939580 CTTCATATTTCATCTGGAATAATTAGTTTGTTGCTCTAGCTTTAACAAGAG
1 CTTCATATTTCATCCGGAATAATTACCTTGTTGCTCTAACTTCAACAAGAG
*
109939631 CTTCATATTTTATCCGGA
1 CTTCATATTTCATCCGGA
109939649 TAACTTAGGT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (51 bp):
CTTCATATTTCATCCGGAATAATTACCTTGTTGCTCTAACTTCAACAAGAG
Found at i:109948138 original size:15 final size:16
Alignment explanation
Indices: 109948112--109948141 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
109948102 CATTTGCTTC
109948112 AGTGATTATGGGTGTA
1 AGTGATTATGGGTGTA
109948128 AGTGA-TATGGGTGT
1 AGTGATTATGGGTGT
109948142 GTGTTTGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37
Consensus pattern (16 bp):
AGTGATTATGGGTGTA
Found at i:109954577 original size:5 final size:5
Alignment explanation
Indices: 109954556--109954595 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
109954546 CGATCTATCC
109954556 TTCTT TCTCTGT TTCTT TTCTT TTCTT TTC-T TTCTT TTCT
1 TTCTT T-TCT-T TTCTT TTCTT TTCTT TTCTT TTCTT TTCT
109954596 AATTTGTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 4 0.12
5 20 0.62
6 6 0.19
7 2 0.06
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.75
Consensus pattern (5 bp):
TTCTT
Found at i:109954591 original size:14 final size:16
Alignment explanation
Indices: 109954556--109954595 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
109954546 CGATCTATCC
109954556 TTCTTTCTCTGTTTCTT
1 TTCTTT-TCTGTTTCTT
109954573 TTCTTTTCT-TTTC-T
1 TTCTTTTCTGTTTCTT
109954587 TTCTTTTCT
1 TTCTTTTCT
109954596 AATTTGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.43
15 4 0.17
16 3 0.13
17 6 0.26
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.75
Consensus pattern (16 bp):
TTCTTTTCTGTTTCTT
Found at i:109955006 original size:25 final size:25
Alignment explanation
Indices: 109954991--109955045 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
109954981 CTATTGGGTC
109954991 GTCACAACACTGTAACGACTCGATA
1 GTCACAACACTGTAACGACTCGATA
109955016 GTCACAACACTGTAACGACTCGATA
1 GTCACAACACTGTAACGACTCGATA
109955041 GTCAC
1 GTCAC
109955046 GAGTAATTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.20
Consensus pattern (25 bp):
GTCACAACACTGTAACGACTCGATA
Found at i:109966700 original size:17 final size:16
Alignment explanation
Indices: 109966674--109966707 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
109966664 TTCTCTGCTA
109966674 TAATTATAAAAACACC
1 TAATTATAAAAACACC
*
109966690 TAATATATAAACACACC
1 TAAT-TATAAAAACACC
109966707 T
1 T
109966708 TTCTTCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (16 bp):
TAATTATAAAAACACC
Found at i:109967612 original size:29 final size:29
Alignment explanation
Indices: 109967580--109967656 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
109967570 TTAAGTTTTA
109967580 ATAAAAAATATTAAAAAATTA-TAAAAGTC
1 ATAAAAAATATTAAAAAATTATTAAAA-TC
**
109967609 ATAAAAGAATA-TAAAATTTTATTAAAATC
1 ATAAAA-AATATTAAAAAATTATTAAAATC
109967638 ATAAAAAA-ATTAATAAAAT
1 ATAAAAAATATTAA-AAAAT
109967657 ACATAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.03
28 5 0.12
29 25 0.62
30 9 0.22
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (29 bp):
ATAAAAAATATTAAAAAATTATTAAAATC
Found at i:109967635 original size:50 final size:48
Alignment explanation
Indices: 109967535--109967666 Score: 121
Period size: 49 Copynumber: 2.7 Consensus size: 48
109967525 AACCATGGAC
* * *
109967535 AAAAAAT-TTATAAAAA-TA-AAAATCAATAAAAATTATTAAGTTTTAAT
1 AAAAAATATTA-AAAAATTATAAAATC-ATAAAAAATATAAAATTTTAAT
109967582 AAAAAATATTAAAAAATTATAAAAGTCATAAAAGAATATAAAATTTT-AT
1 AAAAAATATTAAAAAATTATAAAA-TCATAAAA-AATATAAAATTTTAAT
* *
109967631 -TAAAATCATAAAAAAATTAATAAAATACATAAAAAA
1 AAAAAAT-ATTAAAAAATT-ATAAAAT-CATAAAAAA
109967667 GACCTTTTAA
Statistics
Matches: 72, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
47 12 0.17
48 10 0.14
49 25 0.35
50 25 0.35
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (48 bp):
AAAAAATATTAAAAAATTATAAAATCATAAAAAATATAAAATTTTAAT
Found at i:109967881 original size:19 final size:20
Alignment explanation
Indices: 109967845--109967902 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
109967835 ATACGATAAT
109967845 TTTTATAATTCTTTTACAAA
1 TTTTATAATTCTTTTACAAA
**
109967865 TTTTATAATTC-TTTACATC
1 TTTTATAATTCTTTTACAAA
109967884 TTTTATAATT-TTCTTACAA
1 TTTTATAATTCTT-TTACAA
109967903 CTTTATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTATAATTCTTTTACAAA
Found at i:109967906 original size:20 final size:19
Alignment explanation
Indices: 109967845--109967916 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
109967835 ATACGATAAT
*
109967845 TTTTATAATTCTTTTACAAA
1 TTTTATAATT-TTTTACAAC
* *
109967865 TTTTATAATTCTTTACATC
1 TTTTATAATTTTTTACAAC
109967884 TTTTATAATTTTCTTACAAC
1 TTTTATAATTTT-TTACAAC
*
109967904 TTTATAAAATTTT
1 TTT-TATAATTTT
109967917 ATAAATTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 17 0.39
20 19 0.43
21 8 0.18
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAC
Found at i:109967907 original size:19 final size:18
Alignment explanation
Indices: 109967846--109967910 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 18
109967836 TACGATAATT
*
109967846 TTTATAATTCTTTTACAAAT
1 TTTATAATT-TTTTAC-AAC
* *
109967866 TTTATAATTCTTTACATC
1 TTTATAATTTTTTACAAC
109967884 TTTTATAATTTTCTTACAAC
1 -TTTATAATTTT-TTACAAC
109967904 TTTATAA
1 TTTATAA
109967911 AATTTTATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 22 0.58
20 15 0.39
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTATAATTTTTTACAAC
Found at i:109974094 original size:5 final size:5
Alignment explanation
Indices: 109974084--109974155 Score: 51
Period size: 5 Copynumber: 14.2 Consensus size: 5
109974074 ATACTTAAGT
109974084 ATATA ATATA ATA-A TATAATA ATATA ATA-A TATAATA ATATA ATATA
1 ATATA ATATA ATATA -AT-ATA ATATA ATATA -AT-ATA ATATA ATATA
* * * *
109974131 ATAAA ACATA AAATA A-ATA AAATA A
1 ATATA ATATA ATATA ATATA ATATA A
109974156 AACAAAAGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
4 6 0.11
5 42 0.75
6 6 0.11
7 2 0.04
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (5 bp):
ATATA
Found at i:109974134 original size:8 final size:8
Alignment explanation
Indices: 109974086--109974128 Score: 86
Period size: 8 Copynumber: 5.4 Consensus size: 8
109974076 ACTTAAGTAT
109974086 ATAATATA
1 ATAATATA
109974094 ATAATATA
1 ATAATATA
109974102 ATAATATA
1 ATAATATA
109974110 ATAATATA
1 ATAATATA
109974118 ATAATATA
1 ATAATATA
109974126 ATA
1 ATA
109974129 TAATAAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATAATATA
Found at i:109974149 original size:21 final size:22
Alignment explanation
Indices: 109974091--109974168 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 22
109974081 AGTATATAAT
* * *
109974091 ATAATAATATAATAATATAATAAT
1 ATAAGAATA-AATAAAATAA-AAC
* *
109974115 ATAATAATATAATATAATAAAAC
1 ATAAGAATA-AATAAAATAAAAC
109974138 ATAA-AATAAATAAAATAAAAC
1 ATAAGAATAAATAAAATAAAAC
*
109974159 AAAAGAATAA
1 ATAAGAATAA
109974169 GAATAGAGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 15 0.31
22 9 0.19
23 6 0.12
24 18 0.38
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (22 bp):
ATAAGAATAAATAAAATAAAAC
Found at i:109974191 original size:11 final size:11
Alignment explanation
Indices: 109974154--109974222 Score: 57
Period size: 11 Copynumber: 5.9 Consensus size: 11
109974144 TAAATAAAAT
*
109974154 AAAACAAAAGA
1 AAAAGAAAAGA
* *
109974165 ATAAGAATAGA
1 AAAAGAAAAGA
* *
109974176 GAAAGAAATGAA
1 AAAAGAAAAG-A
109974188 AAAGAGAGAAAGA
1 AAA-AGA-AAAGA
109974201 AAGAAGAAAAGA
1 AA-AAGAAAAGA
109974213 AAAAGAAAAG
1 AAAAGAAAAG
109974223 GGAAATTTAG
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
11 22 0.49
12 10 0.22
13 9 0.20
14 4 0.09
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.04
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:109978494 original size:25 final size:25
Alignment explanation
Indices: 109978466--109978533 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
109978456 GAAGCTCATA
*
109978466 CGAGCCAATGTC-GAGAAGGTTCAAG
1 CGAGCCAATATCGGA-AAGGTTCAAG
109978491 CGAGCCAATATCGGAAAGGTTCAAG
1 CGAGCCAATATCGGAAAGGTTCAAG
*
109978516 CGAGCTAATATCGGAAAG
1 CGAGCCAATATCGGAAAG
109978534 CTCACAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 38 0.95
26 2 0.05
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.16
Consensus pattern (25 bp):
CGAGCCAATATCGGAAAGGTTCAAG
Found at i:109978669 original size:24 final size:24
Alignment explanation
Indices: 109978642--109978718 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
109978632 AAATTAGGAT
109978642 GCTCCAAAGAACTATTAACGGGAA
1 GCTCCAAAGAACTATTAACGGGAA
* *
109978666 GCTCGC-AAGAACCATATAATGGGAA
1 GCTC-CAAAGAACTAT-TAACGGGAA
* * *
109978691 GCT-CATAAGAGCTAATAACGGGAC
1 GCTCCA-AAGAACTATTAACGGGAA
109978715 GCTC
1 GCTC
109978719 TTCGAGCTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
23 1 0.02
24 22 0.54
25 18 0.44
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (24 bp):
GCTCCAAAGAACTATTAACGGGAA
Found at i:109978693 original size:25 final size:24
Alignment explanation
Indices: 109978648--109978694 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
109978638 GGATGCTCCA
*
109978648 AAGAACTATTAACGGGAAGCTCGC
1 AAGAACCATTAACGGGAAGCTCGC
*
109978672 AAGAACCATATAATGGGAAGCTC
1 AAGAACCAT-TAACGGGAAGCTC
109978695 ATAAGAGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (24 bp):
AAGAACCATTAACGGGAAGCTCGC
Found at i:109988383 original size:24 final size:25
Alignment explanation
Indices: 109988358--109988434 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 25
109988348 TATAACAAAA
109988358 TTTATATTACAAAGTTTGTTCCAATT
1 TTTATATTACAAAGTTTGTTCCAA-T
** * *
109988384 TTTAATATTGTAATGTAT-TT--AA-
1 TTT-ATATTACAAAGTTTGTTCCAAT
*
109988406 TTTATATTACAAAGTTTGTTCCAAG
1 TTTATATTACAAAGTTTGTTCCAAT
109988431 TTTA
1 TTTA
109988435 GTGTTGTAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 11
0.67 0.14 0.19
Matches are distributed among these distances:
21 10 0.26
22 5 0.13
24 4 0.11
25 4 0.11
26 5 0.13
27 10 0.26
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (25 bp):
TTTATATTACAAAGTTTGTTCCAAT
Found at i:109988418 original size:62 final size:62
Alignment explanation
Indices: 109988236--109988418 Score: 303
Period size: 62 Copynumber: 3.0 Consensus size: 62
109988226 GTACCTAATC
* * *
109988236 TATATTACAAAGTTTGTTTCAATTTTTAATGTTGTAATGTATTTAATTTATATAAAAAAATT
1 TATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATAACAAAATT
* * *
109988298 TATATTATAAAGTTTGTTCTAATTTTTATTATTGTAATGTATTTAATTTATATAACAAAATT
1 TATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATAACAAAATT
*
109988360 TATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATTACAAA
1 TATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATAACAAA
109988419 GTTTGTTCCA
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 111 1.00
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (62 bp):
TATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATAACAAAATT
Found at i:109989246 original size:12 final size:13
Alignment explanation
Indices: 109989210--109989247 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
109989200 AAATATTTGA
109989210 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
109989223 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
109989237 CTTG-TCTTAAT
1 CTTGTTCTTAAT
109989248 ATTCTATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:109993866 original size:14 final size:14
Alignment explanation
Indices: 109993847--109993881 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
109993837 CAAATTACAT
109993847 GTTAGAATAGTATC
1 GTTAGAATAGTATC
109993861 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
109993875 ATTAGAA
1 GTTAGAA
109993882 AAAAAAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:109996290 original size:46 final size:46
Alignment explanation
Indices: 109996223--109996397 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
109996213 TGTAACCCGC
109996223 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* *
109996269 CCATAAGTGAACTCGGACTCAACTCAACGAGCACGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
109996319 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
109996362 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
109996398 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 62 0.58
47 25 0.23
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:109996338 original size:93 final size:93
Alignment explanation
Indices: 109996231--109996401 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
109996221 GCCCATAAGT
** *
109996231 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
109996296 CGAGCACGGATGCCTAGTTACATCTCAC
66 CGAGCACGGATGCCTAGTTACATCTCAC
*
109996324 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
**
109996389 CGAGTTCGGATGC
66 CGAGCACGGATGC
109996402 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCACGGATGCCTAGTTACATCTCAC
Found at i:109999880 original size:44 final size:44
Alignment explanation
Indices: 109999778--109999938 Score: 184
Period size: 46 Copynumber: 3.6 Consensus size: 44
109999768 GTCGATGCCG
* * *
109999778 TGTCCCAGACAGGTCTTACACT-GACACATGTAACCGT-GCTGACGCA
1 TGTCCCAGACATGTCTTACACTAG-CACATCT---CGTAGCCGACGCA
109999824 TGTCCCAGACATGTCTTACACTAGCACATCTCGTAGCCGACGCA
1 TGTCCCAGACATGTCTTACACTAGCACATCTCGTAGCCGACGCA
* * *
109999868 TGTCCCAGACATGTCTGACACTGGCTATCATCTCG-AGGCCGATGCA
1 TGTCCCAGACATGTCTTACACTAGC-A-CATCTCGTA-GCCGACGCA
109999914 TGTCCCAGACATGTCTTACACTAGC
1 TGTCCCAGACATGTCTTACACTAGC
109999939 CCTCGTCTCA
Statistics
Matches: 102, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
43 3 0.03
44 31 0.30
45 2 0.02
46 65 0.64
47 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (44 bp):
TGTCCCAGACATGTCTTACACTAGCACATCTCGTAGCCGACGCA
Found at i:109999955 original size:46 final size:43
Alignment explanation
Indices: 109999821--109999983 Score: 166
Period size: 46 Copynumber: 3.6 Consensus size: 43
109999811 CCGTGCTGAC
*
109999821 GCATGTCCCAGACATGTCTTACACTAGCACATCTCGT-AGCCGAC
1 GCATGTCCCAGACATGTCTTACACTAGC-CATCTC-TCAGCCGAT
* * *
109999865 GCATGTCCCAGACATGTCTGACACTGGCTATCATCTCGAGGCCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCCATC-TCTC-A-GCCGAT
*
109999911 GCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAATGCCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCCATC-TCTC-A-GCCGAT
* *
109999957 GCCATGTCTCATACATGGTCTTACACT
1 G-CATGTCCCAGACAT-GTCTTACACT
109999984 GGCACACAAA
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
43 4 0.04
44 28 0.28
45 1 0.01
46 45 0.45
47 12 0.12
48 10 0.10
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.26
Consensus pattern (43 bp):
GCATGTCCCAGACATGTCTTACACTAGCCATCTCTCAGCCGAT
Found at i:110002502 original size:46 final size:46
Alignment explanation
Indices: 110002435--110002609 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
110002425 TGTAACCCGC
110002435 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* *
110002481 CCATAAGTGAACTCGGACTCAACTCAACGAGCACGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
110002531 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
110002574 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
110002610 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 62 0.58
47 25 0.23
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:110002550 original size:93 final size:93
Alignment explanation
Indices: 110002443--110002613 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
110002433 GCCCATAAGT
** *
110002443 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
110002508 CGAGCACGGATGCCTAGTTACATCTCAC
66 CGAGCACGGATGCCTAGTTACATCTCAC
*
110002536 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
**
110002601 CGAGTTCGGATGC
66 CGAGCACGGATGC
110002614 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCACGGATGCCTAGTTACATCTCAC
Found at i:110006558 original size:50 final size:49
Alignment explanation
Indices: 110006441--110006678 Score: 271
Period size: 49 Copynumber: 4.8 Consensus size: 49
110006431 TGAGGTCGCA
* * * * *
110006441 TGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCA-AAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCAGATAA-T-TGGTCACG
* * **
110006492 TGTGTAGTACTAAGTGCAGACTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACG
*
110006542 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
** * *
110006591 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* * * *
110006640 TGTGTAGTACTATGTGCAAGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
110006679 GCTTTGGCTA
Statistics
Matches: 162, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
49 87 0.54
50 46 0.28
51 29 0.18
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
Found at i:110006621 original size:99 final size:100
Alignment explanation
Indices: 110006434--110006673 Score: 288
Period size: 99 Copynumber: 2.4 Consensus size: 100
110006424 TCTATTGTGA
* * *
110006434 GGTCGCATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCAAAAACTGTGATCACGTGTGTAG
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCAAAAACTGTGATCACGTGTGTAG
**
110006499 TACTAAGTGCAGACTACTACGTGTA-TCAGATGGTT
66 TACTAAGTGCAGACTACTACGTGTACT-AGATAATT
* * ** * *
110006534 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-TGGTCACGTGTGTA
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCAAAAACTGTGATCACGTGTGTA
* *
110006597 GTACTAAGTGCAGGCTACTACGTGTACTGGATAATT
65 GTACTAAGTGCAGACTACTACGTGTACTAGATAATT
* * * *
110006633 GGTCGCATGTGTAGTACTATGTGCAAGCTACTATGCGTACC
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACC
110006674 AGATAGCTTT
Statistics
Matches: 119, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
98 35 0.29
99 43 0.36
100 2 0.02
101 39 0.33
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (100 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCAAAAACTGTGATCACGTGTGTAG
TACTAAGTGCAGACTACTACGTGTACTAGATAATT
Found at i:110015161 original size:35 final size:35
Alignment explanation
Indices: 110015074--110015482 Score: 338
Period size: 35 Copynumber: 11.6 Consensus size: 35
110015064 CATGGCAAAG
* *
110015074 TGTGAAATGTAGGTATGGTGTGATCAAATCCATACTGTGT
1 TGTGAAACGTAGGTAT-G-GT-ATC--ATCCATACTGAGT
** *
110015114 TAAGAAACGTAGGTATGGTATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * *
110015149 TGTGAAATGTAGGTATGGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
*
110015184 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * * *
110015219 TGTGAGACGTAGGTATGGTATTAACCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * * *
110015254 TGTGAAACATAGGTATGGTATTAACCATACTGAGC
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * *
110015289 TGTGAAACGTAGGTATGGTAT-TTCCATACCGAGC
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* ** * * *
110015323 TATGAAACGTAGGTATGGCGTCGTCCATATTGAGC
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * * *
110015358 TATGATACGTAGGTATGGCATCGTCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* ** **
110015393 TATGAAATATAGGTATGGTATTTTCCATA-TCGAG-
1 TGTGAAACGTAGGTATGGTATCATCCATACT-GAGT
** * * * ** * * *
110015427 CATGAAAAGTAGGTGTGGTGTTTTTCATGCCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
110015462 TGTGAAACGTAGGTATGGTAT
1 TGTGAAACGTAGGTATGGTAT
110015483 TTCAATGAGG
Statistics
Matches: 310, Mismatches: 55, Indels: 13
0.82 0.15 0.03
Matches are distributed among these distances:
34 54 0.17
35 237 0.76
37 3 0.01
38 2 0.01
39 1 0.00
40 13 0.04
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
Found at i:110015267 original size:105 final size:105
Alignment explanation
Indices: 110015074--110015483 Score: 367
Period size: 104 Copynumber: 3.9 Consensus size: 105
110015064 CATGGCAAAG
* * *
110015074 TGTGAAATGTAGGTATGGTGTGATCAAATCCATACTGTGTTAAGAAACGTAGGTATGGTATCATC
1 TGTGAAATGTAGGTAT-G-GT-ATC--ATCCATACTGAGTTATGAAACGTAGGTATGGTATCAAC
** *
110015139 CATACCGAGTTGTGAAATGTAGGTATGGTATTAACCATACTGAGT
61 CATACCGAGTTGTGAAACATAGGTATGGTATTAACCATACTGAGC
* * *
110015184 TGTGAAATGTAGGTATGGTATCATCCATACTGAGTTGTGAGACGTAGGTATGGTATTAACCATAC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGTTATGAAACGTAGGTATGGTATCAACCATAC
110015249 CGAGTTGTGAAACATAGGTATGGTATTAACCATACTGAGC
66 CGAGTTGTGAAACATAGGTATGGTATTAACCATACTGAGC
* * * * ** ** *
110015289 TGTGAAACGTAGGTATGGTAT-TTCCATACCGAGCTATGAAACGTAGGTATGGCGTCGTCCATAT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGTTATGAAACGTAGGTATGGTATCAACCATAC
* * * * * * *** *
110015353 TGAGCTATGATACGTAGGTATGGCATCGTCCATACTGAGT
66 CGAGTTGTGAAACATAGGTATGGTATTAACCATACTGAGC
* * ** * * * * **** *
110015393 TATGAAATATAGGTATGGTATTTTCCATA-TCGAG-CATGAAAAGTAGGTGTGGTGTTTTTCATG
1 TGTGAAATGTAGGTATGGTATCATCCATACT-GAGTTATGAAACGTAGGTATGGTATCAACCATA
*
110015456 CCGAGTTGTGAAACGTAGGTATGGTATT
65 CCGAGTTGTGAAACATAGGTATGGTATT
110015484 TCAATGAGGA
Statistics
Matches: 248, Mismatches: 50, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
104 122 0.49
105 104 0.42
107 3 0.01
108 2 0.01
109 1 0.00
110 16 0.06
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (105 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGTTATGAAACGTAGGTATGGTATCAACCATAC
CGAGTTGTGAAACATAGGTATGGTATTAACCATACTGAGC
Found at i:110015393 original size:139 final size:139
Alignment explanation
Indices: 110015101--110015479 Score: 411
Period size: 139 Copynumber: 2.7 Consensus size: 139
110015091 GTGTGATCAA
* * * * * * *
110015101 ATCCATACTGTGTTAAGAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAATGTAGGTATG
1 ATCCATACTGAGTTATGAAACATAGGTATGGTATTATCCATACTGAGCTGTGAAAAGTAGGTATG
* * * * * *
110015166 GTATTAACCATACTGAGTTGTGAAATGTAGGTATGGTATCATCCATACTGAGTTGTGAGACGTAG
66 GTATT-TCCATACCGAGTTGTGAAACGTAGGTATGGCATCATCCATACTGAGCTATGAGACGTAG
* *
110015231 GTATGGTATT
130 GTATGGCATC
* * * * *
110015241 AACCATACCGAGTTGTGAAACATAGGTATGGTATTAACCATACTGAGCTGTGAAACGTAGGTATG
1 ATCCATACTGAGTTATGAAACATAGGTATGGTATTATCCATACTGAGCTGTGAAAAGTAGGTATG
* * * * * *
110015306 GTATTTCCATACCGAGCTATGAAACGTAGGTATGGCGTCGTCCATATTGAGCTATGATACGTAGG
66 GTATTTCCATACCGAGTTGTGAAACGTAGGTATGGCATCATCCATACTGAGCTATGAGACGTAGG
110015371 TATGGCATC
131 TATGGCATC
* * * * *
110015380 GTCCATACTGAGTTATGAAATATAGGTATGGTATTTTCCATA-TCGAGC-ATGAAAAGTAGGTGT
1 ATCCATACTGAGTTATGAAACATAGGTATGGTATTATCCATACT-GAGCTGTGAAAAGTAGGTAT
* * *
110015443 GGTGTTTTTCATGCCGAGTTGTGAAACGTAGGTATGG
65 GGT-ATTTCCATACCGAGTTGTGAAACGTAGGTATGG
110015480 TATTTCAATG
Statistics
Matches: 197, Mismatches: 40, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
138 16 0.08
139 122 0.62
140 59 0.30
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (139 bp):
ATCCATACTGAGTTATGAAACATAGGTATGGTATTATCCATACTGAGCTGTGAAAAGTAGGTATG
GTATTTCCATACCGAGTTGTGAAACGTAGGTATGGCATCATCCATACTGAGCTATGAGACGTAGG
TATGGCATC
Found at i:110015617 original size:31 final size:31
Alignment explanation
Indices: 110015579--110015639 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
110015569 ATAAGTAATT
110015579 TGATCAGTGAAAAATGGTAGCCCCGGCTACC
1 TGATCAGTGAAAAATGGTAGCCCCGGCTACC
* * **
110015610 TGATCAGTGAATATTGGTAGCTTCGGCTAC
1 TGATCAGTGAAAAATGGTAGCCCCGGCTAC
110015640 AAGTGACAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (31 bp):
TGATCAGTGAAAAATGGTAGCCCCGGCTACC
Found at i:110019781 original size:16 final size:17
Alignment explanation
Indices: 110019754--110019786 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
110019744 TAATAGTTAC
*
110019754 AATTATATAAAATAATT
1 AATTATATAAAAAAATT
110019771 AATTA-ATAAAAAAATT
1 AATTATATAAAAAAATT
110019787 TCTCCACCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTATATAAAAAAATT
Found at i:110020333 original size:20 final size:19
Alignment explanation
Indices: 110020263--110020341 Score: 81
Period size: 19 Copynumber: 4.2 Consensus size: 19
110020253 TACTTTTGTA
* * *
110020263 AAAATTAAAAAAAACTTAT
1 AAAATTAATAAAAATTTTT
*
110020282 AAAA-T-ATAAAAAATTTT
1 AAAATTAATAAAAATTTTT
110020299 AAAATTAATAAAAATTTTT
1 AAAATTAATAAAAATTTTT
* *
110020318 AAAAGTTATTAAAAATTTCT
1 AAAA-TTAATAAAAATTTTT
110020338 AAAA
1 AAAA
110020342 AATATTAAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
17 13 0.25
18 2 0.04
19 19 0.37
20 17 0.33
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (19 bp):
AAAATTAATAAAAATTTTT
Found at i:110020341 original size:30 final size:29
Alignment explanation
Indices: 110020307--110020443 Score: 75
Period size: 30 Copynumber: 4.6 Consensus size: 29
110020297 TTAAAATTAA
110020307 TAAAAATTTTTAAAAGTTATTAAAAATTT
1 TAAAAATTTTTAAAAGTTATTAAAAATTT
* * * * *
110020336 CTAAAAAATATT-AAAGCATATTAAAAAGCTG
1 -TAAAAATTTTTAAAAG-TTATTAAAAA-TTT
* *
110020367 T-AAAATTATTTAAAAATT-CTAAAAACTATT
1 TAAAAATT-TTTAAAAGTTATTAAAAA-T-TT
* *
110020397 TAAAAATTTGTGAAAA-TTATTAAAAATGAT
1 TAAAAATTT-TTAAAAGTTATTAAAAAT-TT
* *
110020427 TAAAAATTGTAAAAAGT
1 TAAAAATTTTTAAAAGT
110020444 ATAAGAATTT
Statistics
Matches: 79, Mismatches: 19, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
29 20 0.25
30 38 0.48
31 21 0.27
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.36
Consensus pattern (29 bp):
TAAAAATTTTTAAAAGTTATTAAAAATTT
Found at i:110020432 original size:20 final size:19
Alignment explanation
Indices: 110020282--110020434 Score: 82
Period size: 20 Copynumber: 7.8 Consensus size: 19
110020272 AAAAACTTAT
*
110020282 AAAATATAAAAAATT-TTA
1 AAAATATTAAAAATTATTA
* * *
110020300 AAATTAATAAAAATTTTTA
1 AAAATATTAAAAATTATTA
*
110020319 AAAGTTATTAAAAATT-TCTAA
1 AAA-ATATTAAAAATTAT-T-A
*
110020340 AAAATATTAAAGCA-TATTA
1 AAAATATTAAA-AATTATTA
**
110020359 AAAAGCTGT-AAAATTATTTA
1 AAAATAT-TAAAAATTA-TTA
*
110020379 AAAAT-TCTAAAAACTATTTA
1 AAAATAT-TAAAAATTA-TTA
* *
110020399 AAAATTTGTGAAAATTATTA
1 AAAATAT-TAAAAATTATTA
110020419 AAAATGATTAAAAATT
1 AAAAT-ATTAAAAATT
110020435 GTAAAAAGTA
Statistics
Matches: 106, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
18 13 0.12
19 19 0.18
20 59 0.56
21 15 0.14
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (19 bp):
AAAATATTAAAAATTATTA
Found at i:110020874 original size:10 final size:10
Alignment explanation
Indices: 110020855--110020884 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
110020845 GTGGCAATAG
*
110020855 GTTTGAAGTA
1 GTTTGGAGTA
110020865 GTTTGGAGTA
1 GTTTGGAGTA
110020875 GTTTGGAGTA
1 GTTTGGAGTA
110020885 CAATCAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (10 bp):
GTTTGGAGTA
Found at i:110041021 original size:23 final size:23
Alignment explanation
Indices: 110040994--110041039 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
110040984 TTATTTATCT
110040994 CTATCTTAAAAGTGTTATCCTGA
1 CTATCTTAAAAGTGTTATCCTGA
110041017 CTATCTTAAAAGTGTTATCCTGA
1 CTATCTTAAAAGTGTTATCCTGA
110041040 TACCATCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (23 bp):
CTATCTTAAAAGTGTTATCCTGA
Found at i:110047767 original size:22 final size:24
Alignment explanation
Indices: 110047739--110047794 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
110047729 GCTGTTAAAA
110047739 TTAGTACAATGT-AA-TCATTCAT
1 TTAGTACAATGTAAATTCATTCAT
*
110047761 TTAGTAC-ATGTGAAATTCATTCTT
1 TTAGTACAATGT-AAATTCATTCAT
110047785 TGTAGTACAA
1 T-TAGTACAA
110047795 CTTCCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.14
22 7 0.25
23 2 0.07
24 8 0.29
25 6 0.21
26 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (24 bp):
TTAGTACAATGTAAATTCATTCAT
Found at i:110048582 original size:11 final size:11
Alignment explanation
Indices: 110048566--110048590 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
110048556 GGTGTGTAAA
110048566 CAAGTTTCAAG
1 CAAGTTTCAAG
110048577 CAAGTTTCAAG
1 CAAGTTTCAAG
110048588 CAA
1 CAA
110048591 ATTAATCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (11 bp):
CAAGTTTCAAG
Found at i:110051428 original size:3 final size:3
Alignment explanation
Indices: 110051420--110051448 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
110051410 GCCACTCACT
110051420 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
110051449 CCTGACACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:110066490 original size:64 final size:63
Alignment explanation
Indices: 110066389--110066518 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 63
110066379 TCTTTTACTC
* *
110066389 CATTGATTATAGATAAGATAATAATCATTGTTTTTTATATACTAAAAAAAGTTAATATATATTA
1 CATTGATTATAGATAAGACAATAATCATTGTTTTTTATATAC-AAAAAAAGTTAATATATATCA
* *
110066453 CATTGATTATAGATAAGGCAATAATCATTGTTTTTTATATACAAAAAAAGTTAATATGTATCA
1 CATTGATTATAGATAAGACAATAATCATTGTTTTTTATATACAAAAAAAGTTAATATATATCA
110066516 CAT
1 CAT
110066519 CATGCCATGC
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
63 22 0.35
64 40 0.65
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (63 bp):
CATTGATTATAGATAAGACAATAATCATTGTTTTTTATATACAAAAAAAGTTAATATATATCA
Found at i:110069788 original size:301 final size:294
Alignment explanation
Indices: 110069214--110069797 Score: 681
Period size: 301 Copynumber: 2.0 Consensus size: 294
110069204 TTAATATATA
* * **
110069214 CAATTGATAAAGATAATAAATTGTGCATATTAAAATAAAAATGTATAAAAATATCAAAATGAAGT
1 CAATTGATAAAGATAATAAATTGTACATATTAAAATAAAAATATATAAAAATATCAAAATGAAAC
* * *
110069279 TTTGCTTGAGTGGTAAAATTGAGGTTTTATTAATCTAATTTGTGTAGGTTCAAATCTCACTATAT
66 TTTGCTTGAGTGGTAAAATTAAGGTTTTATTAATCTAATTGGTGTAGATTCAAATCTCACTATAT
* * *
110069344 ATATCTTTATTGGTTTTTAAATAAAAAGACTAAAATACCCTCGAATAATGTAACTTATTTTAATT
131 ATATCTTTATTGGTTTTTAAATAAAAAGAC-AAAATAACCTCGAATAATATAACTTATATTAATT
*** * ** * *
110069409 ATGGAAGGATATTTTTGTAATTTTTCTAACTGAGTTGGTTCCCGATTGACTTGTGACACCAACTA
195 ACAAAAAGATATTTTCATAATTTTCCTAACTGAGTTGGTGCCCGATTGACTTGTGACACCAACTA
110069474 AATCAGGAGCTTAAATAATAGTAAGTATAGAGATG
260 AATCAGGAGCTTAAATAATAGTAAGTATAGAGATG
** * * *
110069509 CAATTGATGGAGATAATAATTTGTACATATTAATATAAAAATATATAAAATATATTAAAATGAAA
1 CAATTGATAAAGATAATAAATTGTACATATTAAAATAAAAATATATAAAA-ATATCAAAATGAAA
* * *
110069574 CTTTGGTTGAGTGGTAAAATTAAGGTTTTATTAATCTAATTGGTGTAGATTTAAATC-CTGCTAT
65 CTTTGCTTGAGTGGTAAAATTAAGGTTTTATTAATCTAATTGGTGTAGATTCAAATCTC-ACTAT
* * * *
110069638 TTGCGTAT-TTCTATTGGTTTTTTGTTAAAATGAAAAGAC-AAATAACCTTGAATAATATAACTT
129 AT--ATATCTT-TATTGG---TTT-TT-AAATAAAAAGACAAAATAACCTCGAATAATATAACTT
* * * *
110069701 ATATTAATTACAAAAATATATTTTCATAATTTTCCTAATTGAGTTGGTGCTCGGTTGA-TTCGTG
186 ATATTAATTACAAAAAGATATTTTCATAATTTTCCTAACTGAGTTGGTGCCCGATTGACTT-GTG
* * * * *
110069765 ATACTAACTCAGTCAGTAGCTTAAATAATAGTA
250 ACACCAACTAAATCAGGAGCTTAAATAATAGTA
110069798 TAGATATACG
Statistics
Matches: 239, Mismatches: 39, Indels: 16
0.81 0.13 0.05
Matches are distributed among these distances:
295 45 0.19
296 68 0.28
297 2 0.01
298 9 0.04
300 2 0.01
301 100 0.42
302 2 0.01
303 11 0.05
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (294 bp):
CAATTGATAAAGATAATAAATTGTACATATTAAAATAAAAATATATAAAAATATCAAAATGAAAC
TTTGCTTGAGTGGTAAAATTAAGGTTTTATTAATCTAATTGGTGTAGATTCAAATCTCACTATAT
ATATCTTTATTGGTTTTTAAATAAAAAGACAAAATAACCTCGAATAATATAACTTATATTAATTA
CAAAAAGATATTTTCATAATTTTCCTAACTGAGTTGGTGCCCGATTGACTTGTGACACCAACTAA
ATCAGGAGCTTAAATAATAGTAAGTATAGAGATG
Found at i:110074516 original size:46 final size:44
Alignment explanation
Indices: 110074463--110074583 Score: 163
Period size: 46 Copynumber: 2.7 Consensus size: 44
110074453 GACGAGAGCT
110074463 AGTGTAAGACATGTCTGGGACATGCATCAGCCT-CGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GCCTACGAG-T-TAAGCC
* * *
110074509 AGTGTAAGACATGTCTAGGACATGCATCGGCTACGAGTTAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGCCTACGAGTTAAGCC
110074553 AGTGTAAGACCATGTCTGGGACATGGCATCG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCG
110074584 ACATCTTATC
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
44 14 0.21
45 17 0.25
46 37 0.54
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGCCTACGAGTTAAGCC
Found at i:110083546 original size:21 final size:21
Alignment explanation
Indices: 110083503--110083546 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
110083493 TTTCTAGTTG
* *
110083503 CTCTAGAACAATTAGGAGATT
1 CTCTAGAACAAATACGAGATT
* *
110083524 CTCTAGAAGAAATACGAGGTT
1 CTCTAGAACAAATACGAGATT
110083545 CT
1 CT
110083547 GCTTTTGGCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (21 bp):
CTCTAGAACAAATACGAGATT
Found at i:110084724 original size:14 final size:14
Alignment explanation
Indices: 110084705--110084732 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
110084695 TATATTAGTA
110084705 TTTTCTATTCTATT
1 TTTTCTATTCTATT
110084719 TTTTCTATTCTATT
1 TTTTCTATTCTATT
110084733 AGTATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:110084740 original size:6 final size:6
Alignment explanation
Indices: 110084729--110084772 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
110084719 TTTTCTATTC
110084729 TATTAG TATTAG -ATTAG TATTAG --TTAG -ATTAG -ATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
110084772 T
1 T
110084773 TAGTGATCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 4 0.11
5 14 0.40
6 17 0.49
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (6 bp):
TATTAG
Found at i:110084744 original size:11 final size:11
Alignment explanation
Indices: 110084730--110084776 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
110084720 TTTCTATTCT
110084730 ATTAGTATTAG
1 ATTAGTATTAG
110084741 ATTAGTATTAG
1 ATTAGTATTAG
110084752 -TTAG-ATTAG
1 ATTAGTATTAG
110084761 ATTAGTATTAG
1 ATTAGTATTAG
110084772 -TTAGT
1 ATTAGT
110084777 GATCCCGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 5 0.15
10 13 0.38
11 16 0.47
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (11 bp):
ATTAGTATTAG
Found at i:110084761 original size:20 final size:21
Alignment explanation
Indices: 110084731--110084776 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
110084721 TTCTATTCTA
110084731 TTAGTATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
110084752 TTAG-ATTAGATTAGTATTAG
1 TTAGTATTAGATTAGTATTAG
110084772 TTAGT
1 TTAGT
110084777 GATCCCGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.48
Consensus pattern (21 bp):
TTAGTATTAGATTAGTATTAG
Found at i:110084775 original size:15 final size:14
Alignment explanation
Indices: 110084737--110084766 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
110084727 TCTATTAGTA
110084737 TTAGATTAGTATTAG
1 TTAGATTAG-ATTAG
110084752 TTAGATTAGATTAG
1 TTAGATTAGATTAG
110084766 T
1 T
110084767 ATTAGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (14 bp):
TTAGATTAGATTAG
Found at i:110087453 original size:73 final size:73
Alignment explanation
Indices: 110087334--110087509 Score: 307
Period size: 73 Copynumber: 2.4 Consensus size: 73
110087324 CAAGGCATAT
110087334 CAAGCCACACGCCCGTGTGCTAGGCCGTGTGAGCATACTGACTTGCAATATTAAGGTGCAGGGGT
1 CAAGCCACACGCCCGTGTGCTAGGCCGTGTGAGCATACTGACTTGCAATATTAAGGTGCAGGGGT
* *
110087399 CCCATGGC
66 CACACGGC
* *
110087407 CAAGCCACACTCCCGTGTGCTAGGTCGTGTGAGCATACTGACTTGCAATATTAAGGTGCAGGGGT
1 CAAGCCACACGCCCGTGTGCTAGGCCGTGTGAGCATACTGACTTGCAATATTAAGGTGCAGGGGT
110087472 CACACGGC
66 CACACGGC
*
110087480 CAAGCCACACGCTCGTGTGCTAGGCCGTGT
1 CAAGCCACACGCCCGTGTGCTAGGCCGTGT
110087510 AAAAATTTTT
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 96 1.00
ACGTcount: A:0.22, C:0.28, G:0.30, T:0.21
Consensus pattern (73 bp):
CAAGCCACACGCCCGTGTGCTAGGCCGTGTGAGCATACTGACTTGCAATATTAAGGTGCAGGGGT
CACACGGC
Found at i:110087845 original size:14 final size:15
Alignment explanation
Indices: 110087826--110087858 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
110087816 AACCTATATG
*
110087826 CATATT-TCTCAAAT
1 CATATTATCTCAAAC
110087840 CATATTATCTCAAAC
1 CATATTATCTCAAAC
110087855 CATA
1 CATA
110087859 CATTATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.36
Consensus pattern (15 bp):
CATATTATCTCAAAC
Found at i:110088584 original size:25 final size:26
Alignment explanation
Indices: 110088514--110088604 Score: 118
Period size: 26 Copynumber: 3.6 Consensus size: 26
110088504 CTCATGCAAA
*
110088514 CATGTAA-ATGGGAAGCTCTTTCGAGC
1 CATGTAACA-GGGAAGCTCATTCGAGC
110088540 CATGTAACAGGGAAGCTCATGT-GAGC
1 CATGTAACAGGGAAGCTCAT-TCGAGC
110088566 CATGTAACA-GGAAGCTCATTCGAGC
1 CATGTAACAGGGAAGCTCATTCGAGC
*
110088591 CAT-TAATAGGGAAG
1 CATGTAACAGGGAAG
110088605 TTCAAGCTAG
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
24 5 0.08
25 22 0.37
26 30 0.51
27 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (26 bp):
CATGTAACAGGGAAGCTCATTCGAGC
Found at i:110108529 original size:14 final size:14
Alignment explanation
Indices: 110108510--110108540 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
110108500 TATGAGTAAG
*
110108510 AATTTTCGTTGAGT
1 AATTTTCGTTGAAT
110108524 AATTTTCGTTGAAT
1 AATTTTCGTTGAAT
110108538 AAT
1 AAT
110108541 GATTCCAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.48
Consensus pattern (14 bp):
AATTTTCGTTGAAT
Found at i:110113317 original size:36 final size:37
Alignment explanation
Indices: 110113243--110113338 Score: 167
Period size: 36 Copynumber: 2.6 Consensus size: 37
110113233 TGTGAAAATG
110113243 TGGCATATAATTGATGGTTTTAGAGTAAAAAAAAAAA
1 TGGCATATAATTGATGGTTTTAGAGTAAAAAAAAAAA
110113280 TGGCATATAATTGATGGTTTTAGAGT-AAAAAAAAAA
1 TGGCATATAATTGATGGTTTTAGAGTAAAAAAAAAAA
* *
110113316 TGCCATATAATTGATGGTGTTAG
1 TGGCATATAATTGATGGTTTTAG
110113339 TGAGTAATAT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
36 31 0.54
37 26 0.46
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (37 bp):
TGGCATATAATTGATGGTTTTAGAGTAAAAAAAAAAA
Found at i:110120235 original size:3 final size:3
Alignment explanation
Indices: 110120229--110120255 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
110120219 ATAAAATCTC
110120229 CTG CTG CTG CTG CTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG
110120256 GGAAGCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:110122930 original size:77 final size:77
Alignment explanation
Indices: 110122803--110122956 Score: 281
Period size: 77 Copynumber: 2.0 Consensus size: 77
110122793 TTGAGACTTG
* *
110122803 GATAATACTAAAATACAAAAGGAAAAAAGAAAATCATATTCATATTCAACTGCAACTAATTTTAA
1 GATAATACTAAAATACAAAAGGAAAAAAGAAAACCATACTCATATTCAACTGCAACTAATTTTAA
110122868 AAGCTAACCACA
66 AAGCTAACCACA
*
110122880 GATAATACTAAAATACAAAAGGAAAAAGGAAAACCATACTCATATTCAACTGCAACTAATTTTAA
1 GATAATACTAAAATACAAAAGGAAAAAAGAAAACCATACTCATATTCAACTGCAACTAATTTTAA
110122945 AAGCTAACCACA
66 AAGCTAACCACA
110122957 CATGAATTAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.53, C:0.17, G:0.08, T:0.22
Consensus pattern (77 bp):
GATAATACTAAAATACAAAAGGAAAAAAGAAAACCATACTCATATTCAACTGCAACTAATTTTAA
AAGCTAACCACA
Found at i:110126326 original size:31 final size:30
Alignment explanation
Indices: 110126271--110126364 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 30
110126261 AATTATACCA
* * *
110126271 TTAGTTACTAAATTATAAGTAAATTTTCGTT
1 TTAGTTATTAAATTAT-TGAAAATTTTCGTT
*
110126302 TTAGTTATTAAATTATTCGAAAATTTTCATT
1 TTAGTTATTAAATTATT-GAAAATTTTCGTT
* * * *
110126333 TAAGTCATTAAACTATTGAAAAGTTTTTGTT
1 TTAGTTATTAAATTATTGAAAA-TTTTCGTT
110126364 T
1 T
110126365 AAGTCATTGA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
30 5 0.10
31 47 0.90
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (30 bp):
TTAGTTATTAAATTATTGAAAATTTTCGTT
Found at i:110126366 original size:31 final size:31
Alignment explanation
Indices: 110126291--110126372 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
110126281 AATTATAAGT
* * *
110126291 AAATTTTCGTTTTAGTTATTAAATTATTCGA
1 AAATTTTCGTTTAAGTCATTAAACTATTCGA
*
110126322 AAATTTTCATTTAAGTCATTAAACTATT-GA
1 AAATTTTCGTTTAAGTCATTAAACTATTCGA
*
110126352 AAAGTTTTTGTTTAAGTCATT
1 AAA-TTTTCGTTTAAGTCATT
110126373 GATCTTTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
30 5 0.11
31 39 0.89
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (31 bp):
AAATTTTCGTTTAAGTCATTAAACTATTCGA
Found at i:110128533 original size:2 final size:2
Alignment explanation
Indices: 110128528--110128554 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
110128518 CGTGAAAATC
110128528 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
110128555 GGAAAAAGAT
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:110128656 original size:20 final size:20
Alignment explanation
Indices: 110128631--110128673 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
110128621 ATCAATATTC
*
110128631 TTATCCTGAATTTTAGGATT
1 TTATCCTGAATTTAAGGATT
*
110128651 TTATCCTGAATTTAAGTATT
1 TTATCCTGAATTTAAGGATT
110128671 TTA
1 TTA
110128674 ATTTGGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (20 bp):
TTATCCTGAATTTAAGGATT
Found at i:110129268 original size:26 final size:25
Alignment explanation
Indices: 110129222--110129281 Score: 59
Period size: 28 Copynumber: 2.3 Consensus size: 25
110129212 AAATGGATGG
110129222 AAGATAAAAAAATTAACAAACAAGTAT
1 AAGATAAAAAAATT-A-AAACAAGTAT
**
110129249 AAAGATAAAAAAATCT-AAACTCGTAT
1 -AAGATAAAAAAAT-TAAAACAAGTAT
110129275 AAGATAA
1 AAGATAA
110129282 GCTCTGATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 7 0.24
26 8 0.28
28 13 0.45
29 1 0.03
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.20
Consensus pattern (25 bp):
AAGATAAAAAAATTAAAACAAGTAT
Found at i:110129984 original size:23 final size:22
Alignment explanation
Indices: 110129924--110129985 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
110129914 TTTCACATAA
* *
110129924 TATTATTTTAATAACTTAATTATT
1 TATTATTTT-TTAA-TTCATTATT
110129948 TATTATTTTTTAATTCATTATT
1 TATTATTTTTTAATTCATTATT
110129970 T-TTATTGTTTTTAATT
1 TATTA-T-TTTTTAATT
110129986 AGTTGGTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 3 0.09
22 10 0.29
23 12 0.35
24 9 0.26
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (22 bp):
TATTATTTTTTAATTCATTATT
Found at i:110132078 original size:60 final size:63
Alignment explanation
Indices: 110132014--110132164 Score: 184
Period size: 60 Copynumber: 2.4 Consensus size: 63
110132004 TTTTAATAAG
* *
110132014 ATTATTATTAAATATATTTTAATAAAAATAAAAT-AAATAT-TTTAATAATATT-TTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAAAATAAAATATATTTAATAACATTCTTAACATA
* ** * *
110132074 ATTATTATTAAATAAAATAAAAT-AAAATAAAATAAAATATAATTTAATACCATTCTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAAAATAAAATAT-ATTTAATAACATTCTTAACATA
*
110132137 ATTATTATTAAAATATAAATTAATAAAA
1 ATTATTATT-AAATATAATTTAATAAAA
110132165 CTCATAATAT
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
59 10 0.14
60 25 0.34
62 10 0.14
63 16 0.22
64 10 0.14
65 3 0.04
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (63 bp):
ATTATTATTAAATATAATTTAATAAAAATAAAATAAAATATATTTAATAACATTCTTAACATA
Found at i:110132093 original size:5 final size:5
Alignment explanation
Indices: 110132083--110132112 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
110132073 AATTATTATT
110132083 AAATA AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA
110132113 TAATTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:110132188 original size:39 final size:38
Alignment explanation
Indices: 110132105--110132192 Score: 90
Period size: 39 Copynumber: 2.3 Consensus size: 38
110132095 ATAAAATAAA
* ** * *
110132105 ATAAAATATAATTTAATACCATTCTTAATATAATTATT
1 ATAAAATATAAATTAATAAAACTCATAATATAATTATT
110132143 ATTAAAATATAAATTAATAAAACTCATAATAT-ATGATATT
1 A-TAAAATATAAATTAATAAAACTCATAATATAAT--TATT
110132183 ATAAAA-ATAA
1 ATAAAATATAA
110132193 TATATAACCT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
38 7 0.17
39 30 0.71
40 5 0.12
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.39
Consensus pattern (38 bp):
ATAAAATATAAATTAATAAAACTCATAATATAATTATT
Found at i:110139149 original size:15 final size:15
Alignment explanation
Indices: 110139126--110139157 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
110139116 CATTTCACTG
*
110139126 TTATGTCTTTTGTAT
1 TTATATCTTTTGTAT
110139141 TTATATCTTTTGTAT
1 TTATATCTTTTGTAT
110139156 TT
1 TT
110139158 TGAATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATATCTTTTGTAT
Found at i:110149570 original size:11 final size:11
Alignment explanation
Indices: 110149550--110149582 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
110149540 GGAGGCTGAA
*
110149550 GGCTGCTGCGG
1 GGCTGTTGCGG
110149561 GGCTGTTGCGG
1 GGCTGTTGCGG
110149572 GGCTGTTGCGG
1 GGCTGTTGCGG
110149583 CGCAAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.21, G:0.55, T:0.24
Consensus pattern (11 bp):
GGCTGTTGCGG
Found at i:110151070 original size:16 final size:17
Alignment explanation
Indices: 110151049--110151080 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
110151039 TAACATATAT
110151049 ATTATTAT-ATTATTAA
1 ATTATTATAATTATTAA
110151065 ATTATTATAATTATTA
1 ATTATTATAATTATTA
110151081 TTTCTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTATTATAATTATTAA
Found at i:110156020 original size:26 final size:27
Alignment explanation
Indices: 110155991--110156050 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
110155981 CCACATATAT
*
110155991 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
110156017 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
110156044 ATATCTG
1 ATATCTG
110156051 GCAGCTTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:110158465 original size:20 final size:20
Alignment explanation
Indices: 110158442--110158513 Score: 117
Period size: 20 Copynumber: 3.5 Consensus size: 20
110158432 AAATCCAAAT
110158442 TAAAATACTGAAATTCAGGA
1 TAAAATACTGAAATTCAGGA
*
110158462 TAAAATCCTGAAATTCAGGA
1 TAAAATACTGAAATTCAGGA
*
110158482 TAAAATCCTGAAATTCAGGA
1 TAAAATACTGAAATTCAGGA
110158502 TAAGAATACTGA
1 TAA-AATACTGA
110158514 TGTGGTATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 42 0.86
21 7 0.14
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.25
Consensus pattern (20 bp):
TAAAATACTGAAATTCAGGA
Found at i:110159606 original size:17 final size:18
Alignment explanation
Indices: 110159586--110159619 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
110159576 AAGTGAATTG
110159586 AAATTGC-GAAATTAAAT
1 AAATTGCAGAAATTAAAT
110159603 AAATTGCAGAAATTAAA
1 AAATTGCAGAAATTAAA
110159620 ATGAGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATTGCAGAAATTAAAT
Found at i:110160355 original size:10 final size:10
Alignment explanation
Indices: 110160336--110160394 Score: 86
Period size: 10 Copynumber: 6.0 Consensus size: 10
110160326 TGAAATTCTA
110160336 AAAGATAAAT
1 AAAGATAAAT
110160346 ACAA-ATAAAT
1 A-AAGATAAAT
*
110160356 AAAGATAATT
1 AAAGATAAAT
110160366 AAAGATAAAT
1 AAAGATAAAT
110160376 AAAGATAAAT
1 AAAGATAAAT
110160386 AAA-ATAAAT
1 AAAGATAAAT
110160395 CCTAAAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
9 8 0.18
10 35 0.78
11 2 0.04
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:110161039 original size:11 final size:11
Alignment explanation
Indices: 110161011--110161056 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
110161001 TATTAATATG
110161011 TCTTTT-TTTT
1 TCTTTTCTTTT
110161021 TCTTTTTTCTTTT
1 TC--TTTTCTTTT
110161034 TCTTTTCTTTT
1 TCTTTTCTTTT
110161045 T-TTTCTCTTTT
1 TCTTT-TCTTTT
110161056 T
1 T
110161057 AATAGAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.16
11 17 0.53
12 4 0.12
13 6 0.19
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:110161039 original size:18 final size:17
Alignment explanation
Indices: 110161011--110161046 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
110161001 TATTAATATG
110161011 TCTTTTTTTTTCTTTTT
1 TCTTTTTTTTTCTTTTT
110161028 TCTTTTTCTTTTCTTTTT
1 TCTTTTT-TTTTCTTTTT
110161046 T
1 T
110161047 TTCTCTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (17 bp):
TCTTTTTTTTTCTTTTT
Found at i:110162019 original size:11 final size:10
Alignment explanation
Indices: 110161998--110162060 Score: 51
Period size: 10 Copynumber: 6.2 Consensus size: 10
110161988 TGAAAATAAT
*
110161998 AAATAATAAA
1 AAATAAGAAA
110162008 ATAATAAGAAA
1 A-AATAAGAAA
110162019 AAATAA-ATAA
1 AAATAAGA-AA
110162029 AAATAA-AAA
1 AAATAAGAAA
110162038 AGAA-AAGAAA
1 A-AATAAGAAA
*
110162048 AGAAAAAGAAA
1 A-AATAAGAAA
110162059 AA
1 AA
110162061 TTGAGTTGCC
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
9 6 0.13
10 25 0.53
11 16 0.34
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (10 bp):
AAATAAGAAA
Found at i:110162023 original size:18 final size:18
Alignment explanation
Indices: 110161992--110162054 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 18
110161982 AATATCTGAA
* *
110161992 AATAATAAATAATAAAAT
1 AATAAGAAAAAATAAAAT
110162010 AATAAGAAAAAAT-AAAT
1 AATAAGAAAAAATAAAAT
* * * *
110162027 AAAAATAAAAAAGAAAAG
1 AATAAGAAAAAATAAAAT
110162045 AA-AAGAAAAA
1 AATAAGAAAAA
110162055 GAAAAATTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
17 21 0.57
18 16 0.43
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.14
Consensus pattern (18 bp):
AATAAGAAAAAATAAAAT
Found at i:110162045 original size:29 final size:31
Alignment explanation
Indices: 110161990--110162061 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
110161980 TTAATATCTG
*
110161990 AAAATAATAAATAATAAAATAATAAGAAAA-A
1 AAAATAA-AAATAATAAAAGAATAAGAAAAGA
110162021 ATAAATAAAAATAA-AAAAGAA-AAGAAAAGA
1 A-AAATAAAAATAATAAAAGAATAAGAAAAGA
*
110162051 AAAAGAAAAAT
1 AAAATAAAAAT
110162062 TGAGTTGCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 16 0.43
30 8 0.22
31 7 0.19
32 6 0.16
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (31 bp):
AAAATAAAAATAATAAAAGAATAAGAAAAGA
Found at i:110167704 original size:17 final size:19
Alignment explanation
Indices: 110167679--110167722 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
110167669 ATTTAAAGTG
*
110167679 AAATGAAATTG-CGAAATT
1 AAATGAAATTGTAGAAATT
110167697 AAAT-AAATTGTAGAAATT
1 AAATGAAATTGTAGAAATT
110167715 AAAATGAA
1 -AAATGAA
110167723 GAAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.27
18 10 0.45
19 4 0.18
20 2 0.09
ACGTcount: A:0.57, C:0.02, G:0.14, T:0.27
Consensus pattern (19 bp):
AAATGAAATTGTAGAAATT
Found at i:110168454 original size:10 final size:10
Alignment explanation
Indices: 110168435--110168494 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
110168425 TGAAATTCTA
110168435 AAAGATAAAT
1 AAAGATAAAT
110168445 ACAA-ATAAAT
1 A-AAGATAAAT
*
110168455 AAAGATAATT
1 AAAGATAAAT
110168465 AAAGATAAAT
1 AAAGATAAAT
110168475 AAAGATAAAT
1 AAAGATAAAT
110168485 GAAA-ATAAAT
1 -AAAGATAAAT
110168495 CCTAAAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Done.