Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008439.1 Hibiscus syriacus cultivar Beakdansim tig00111238_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2703160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:2020358 original size:64 final size:63
Alignment explanation
Indices: 2020273--2020433 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
2020263 TTGTTTAAGG
* * * *
2020273 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTTA
* *
2020337 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTTA
* *
2020401 TGCATCGATACAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
2020434 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTA
Found at i:2021981 original size:149 final size:150
Alignment explanation
Indices: 2021808--2022124 Score: 575
Period size: 151 Copynumber: 2.1 Consensus size: 150
2021798 GAGTCGAGGG
*
2021808 TCTACGCGGTCCTTCGGG-ATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACA
1 TCTACGCGGTCCTTCGGGAATATATATATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACA
2021872 TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
66 TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
2021937 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
2021957 TCTACGCGGTCCTTCGGGATATATATATATATTATGTGGAACATGTGTGAAGTCTTGAACGACAC
1 TCTACGCGGTCCTTCGGGA-ATATATATATATTATGTGGAACATGTGTGAAGTCTTGAAAGACAC
*
2022022 ATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTAT
65 ATACTTGATCCCTAATATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTAT
2022087 TATATGGCACTACGGTGCAAT
130 TATATGGCACTACGGTGCAAT
2022108 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
2022125 TGCAATTATA
Statistics
Matches: 162, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
149 18 0.11
150 1 0.01
151 143 0.88
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGAATATATATATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACA
TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
ATATGGCACTACGGTGCAAT
Found at i:2022125 original size:23 final size:23
Alignment explanation
Indices: 2022092--2022136 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2022082 ATTATTATAT
*
2022092 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
2022115 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
2022137 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:2024128 original size:28 final size:28
Alignment explanation
Indices: 2024063--2024129 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
2024053 TTATTTCGGG
* *
2024063 TTGGGTCGGATTTTTTTAAGTATGCTAT
1 TTGGGTCGGGTTTTTTTAAGTATGATAT
* *
2024091 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TTGGGTCGGGTTTTTTTAAGTATGATAT
2024119 TTGGGTCGGGT
1 TTGGGTCGGGT
2024130 CGGGTTTAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.13, C:0.07, G:0.33, T:0.46
Consensus pattern (28 bp):
TTGGGTCGGGTTTTTTTAAGTATGATAT
Found at i:2025635 original size:43 final size:43
Alignment explanation
Indices: 2025574--2025664 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
2025564 CGAAGGCTGT
2025574 CAAATTAAACCATTCAAAGTTTAGACTCTTAAACTCTTCTTTA
1 CAAATTAAACCATTCAAAGTTTAGACTCTTAAACTCTTCTTTA
*
2025617 CAAATTAAACCATTCAAAGTTTAGACTCTTTAACTCTTCTTTA
1 CAAATTAAACCATTCAAAGTTTAGACTCTTAAACTCTTCTTTA
2025660 CAAAT
1 CAAAT
2025665 AGCGATAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.37
Consensus pattern (43 bp):
CAAATTAAACCATTCAAAGTTTAGACTCTTAAACTCTTCTTTA
Found at i:2035126 original size:2 final size:2
Alignment explanation
Indices: 2035119--2035162 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2035109 CCGACAAAAT
2035119 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2035160 AG A
1 AG A
2035163 TTGTCATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2037348 original size:22 final size:22
Alignment explanation
Indices: 2037305--2037350 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2037295 ATTGAACCAA
* * *
2037305 AAATTAAAATAATTTAATATTT
1 AAATTAAAATAAATGAAAATTT
2037327 AAATTAAAATAAATGAAAATTT
1 AAATTAAAATAAATGAAAATTT
2037349 AA
1 AA
2037351 TGATAAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
AAATTAAAATAAATGAAAATTT
Found at i:2053116 original size:23 final size:23
Alignment explanation
Indices: 2053055--2053119 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
2053045 AATAATTATA
* *
2053055 TCTTTTTGACACGTTTATCTCTG
1 TCTTTATGACACGTTTTTCTCTG
2053078 TCTTTATGACACGTTTTTCTCTG
1 TCTTTATGACACGTTTTTCTCTG
* * *
2053101 TCTTTGTGGCATGTTTTTC
1 TCTTTATGACACGTTTTTC
2053120 GGTCATTTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.11, C:0.20, G:0.15, T:0.54
Consensus pattern (23 bp):
TCTTTATGACACGTTTTTCTCTG
Found at i:2062331 original size:13 final size:13
Alignment explanation
Indices: 2062313--2062337 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2062303 AATGAAAATG
2062313 AGAAAAAAGAAAA
1 AGAAAAAAGAAAA
2062326 AGAAAAAAGAAA
1 AGAAAAAAGAAA
2062338 TGGTTGAAAA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AGAAAAAAGAAAA
Found at i:2065570 original size:18 final size:18
Alignment explanation
Indices: 2065547--2065584 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2065537 AATGTAAACG
2065547 TTGACATTCCCCATCATT
1 TTGACATTCCCCATCATT
2065565 TTGACATTCCCCATCATT
1 TTGACATTCCCCATCATT
2065583 TT
1 TT
2065585 TGGTTAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.32, G:0.05, T:0.42
Consensus pattern (18 bp):
TTGACATTCCCCATCATT
Found at i:2069813 original size:6 final size:6
Alignment explanation
Indices: 2069802--2069869 Score: 136
Period size: 6 Copynumber: 11.3 Consensus size: 6
2069792 GACACGTATT
2069802 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2069850 ACCACG ACCACG ACCACG AC
1 ACCACG ACCACG ACCACG AC
2069870 GGCGGCGGCG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2070114 original size:19 final size:20
Alignment explanation
Indices: 2070089--2070179 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 20
2070079 CTTATTTTGG
2070089 ATTTTTCACTATCACAACAC
1 ATTTTTCACTATCACAACAC
2070109 -TTTTTCACTATCGCAACAACAC
1 ATTTTTCACTAT--C-ACAACAC
* * *
2070131 GTTTTTCAAACTCTCGCAACAC
1 ATTTTTC--ACTATCACAACAC
* *
2070153 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCACAACAC
2070172 ATTTTTCA
1 ATTTTTCA
2070180 AAATCGCGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
19 24 0.41
20 5 0.09
21 5 0.09
22 13 0.22
23 7 0.12
25 4 0.07
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (20 bp):
ATTTTTCACTATCACAACAC
Found at i:2070554 original size:107 final size:107
Alignment explanation
Indices: 2070368--2070582 Score: 385
Period size: 107 Copynumber: 2.0 Consensus size: 107
2070358 AACTTAACTT
* * * *
2070368 GTTTACTGTAAAGACTTTCCCTGCTTGTTCTTGGGCAAAGCACGCTCTGGTTGTGTGTCTGATGG
1 GTTTACTGTAAAGACTTTCCCTGCCTGTTCTTGAGCAAAGCACGCTCTGGCTGTGTGCCTGATGG
2070433 CTTCGTTTGCGGTTCATGGACGGCACATCATCACATATAGGG
66 CTTCGTTTGCGGTTCATGGACGGCACATCATCACATATAGGG
2070475 GTTTACTGTAAAGACTTTCCCTGCCTGTTCTTGAGCAAAGCACGCTCTGGCTGTGTGCCTGATGG
1 GTTTACTGTAAAGACTTTCCCTGCCTGTTCTTGAGCAAAGCACGCTCTGGCTGTGTGCCTGATGG
*
2070540 CTTCGTTTGGGGTTCATGGACGGCACATCATCACATATAGGG
66 CTTCGTTTGCGGTTCATGGACGGCACATCATCACATATAGGG
2070582 G
1 G
2070583 CTGCTGCAAT
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 103 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.32
Consensus pattern (107 bp):
GTTTACTGTAAAGACTTTCCCTGCCTGTTCTTGAGCAAAGCACGCTCTGGCTGTGTGCCTGATGG
CTTCGTTTGCGGTTCATGGACGGCACATCATCACATATAGGG
Found at i:2071470 original size:31 final size:30
Alignment explanation
Indices: 2071435--2071509 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 30
2071425 ATTTTAGGTG
*
2071435 TTAAATTAATATTTTATCTAAAGTTTAAATA
1 TTAAATTAATATTTTATCTAAA-TTTAAAGA
* * *
2071466 TTAAAGTAATATTTTATTTAAATTTAGAGA
1 TTAAATTAATATTTTATCTAAATTTAAAGA
*
2071496 TTAAATTAAAATTT
1 TTAAATTAATATTT
2071510 AAATATTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
30 18 0.47
31 20 0.53
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.48
Consensus pattern (30 bp):
TTAAATTAATATTTTATCTAAATTTAAAGA
Found at i:2080396 original size:2 final size:2
Alignment explanation
Indices: 2080385--2080429 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
2080375 ATAAGAAGCA
2080385 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2080426 AT AT
1 AT AT
2080430 CCCTTTCACA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2105482 original size:9 final size:9
Alignment explanation
Indices: 2105468--2105492 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2105458 AATGTCCAAG
2105468 ACCAATCAA
1 ACCAATCAA
2105477 ACCAATCAA
1 ACCAATCAA
2105486 ACCAATC
1 ACCAATC
2105493 CTTTTGGAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.36, G:0.00, T:0.12
Consensus pattern (9 bp):
ACCAATCAA
Found at i:2106196 original size:242 final size:242
Alignment explanation
Indices: 2105755--2106240 Score: 787
Period size: 242 Copynumber: 2.0 Consensus size: 242
2105745 AAATAAAGAC
* *
2105755 AACAGACATTTTAGTATCATTGCCGGGTATTTCACAAAATAAACACACACAAATGAACCGACTAT
1 AACAGACATTTTAGTATCATTGCCGGGTATTTCACAAAATAAACACACACAAACGAACCAACTAT
* *
2105820 AACATTTTAAGTGCAAAAGCGAATCCAGGGATATAACAAAGATGATCTGGTAACATACATATTAA
66 AACATTTTAAGAGCAAAAGCGAATCCAGGGATATAACAAAGATGATCTGATAACATACATATTAA
* * * * *
2105885 AAGCTGACAATATGCTTAGCTAATCCTTACTCCATTTATTTCAGAAATGAGCTTATCCTTGTCAT
131 AAGCTGACAAAATGCTTAGCTAATCCTTACTCCATTTATTTCAGAAATGAGCCTATACTCGTAAT
2105950 CCGATGCCATGAACATAAAAACATCAACTTTTAGAAGCCATTTAGAG
196 CCGATGCCATGAACATAAAAACATCAACTTTTAGAAGCCATTTAGAG
* *
2105997 AACATACATTTTAGTATCATTGCCTGGTATTTCACCAAAATAAACACACAC-AACGAACCAACGT
1 AACAGACATTTTAGTATCATTGCCGGGTATTTCA-CAAAATAAACACACACAAACGAACCAAC-T
* * * *
2106061 -TTACATTTTAAGAGCAAAAGTGAATCCAGGGATTTAACAAAGATGATCTTATAACATACATATT
64 ATAACATTTTAAGAGCAAAAGCGAATCCAGGGATATAACAAAGATGATCTGATAACATACATATT
* *
2106125 AAAAGCTGACAAAATTCTTAGTTAATCCTTACTCCATTTATTTCAGAAATGAGCCTATACTCGTA
129 AAAAGCTGACAAAATGCTTAGCTAATCCTTACTCCATTTATTTCAGAAATGAGCCTATACTCGTA
2106190 ATCCGATGCCATGAACATAAAAACATCAACTTTTAGAAGCCATTTAGAG
194 ATCCGATGCCATGAACATAAAAACATCAACTTTTAGAAGCCATTTAGAG
2106239 AA
1 AA
2106241 TCAATCCGCG
Statistics
Matches: 225, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
242 208 0.92
243 17 0.08
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (242 bp):
AACAGACATTTTAGTATCATTGCCGGGTATTTCACAAAATAAACACACACAAACGAACCAACTAT
AACATTTTAAGAGCAAAAGCGAATCCAGGGATATAACAAAGATGATCTGATAACATACATATTAA
AAGCTGACAAAATGCTTAGCTAATCCTTACTCCATTTATTTCAGAAATGAGCCTATACTCGTAAT
CCGATGCCATGAACATAAAAACATCAACTTTTAGAAGCCATTTAGAG
Found at i:2107287 original size:112 final size:112
Alignment explanation
Indices: 2107157--2107619 Score: 721
Period size: 112 Copynumber: 4.1 Consensus size: 112
2107147 TTGTCGGTTT
* * * *
2107157 GTGTCGATACTTTATAAAAATATATTGATCCATAATAATATAACAGGTAAAAAAATGATAAAATC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
2107222 GGTCTATAAATGACAAAACATGTAAAGCGCTACCGGATATATTGAAA
66 GATCTATAAATAACAAAACATGTAAAGCGCTACCGGATATATTGAAA
2107269 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * **
2107334 GGTCTATAAATGACAAAACAGGTAAAGCGCTACATGATATATTGAAA
66 GATCTATAAATAACAAAACATGTAAAGCGCTACCGGATATATTGAAA
* *
2107381 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
**
2107446 GATCTATAAATAACAAAACA-GATAAAGCGCTACTAGATATATTGAAA
66 GATCTATAAATAACAAAACATG-TAAAGCGCTACCGGATATATTGAAA
* *
2107493 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
2107558 GATCTATAAATAACAAAACATGTAAAGCACTACCGGATATGTTGATA
66 GATCTATAAATAACAAAACATGTAAAGCGCTACCGGATATATTGAAA
*
2107605 GTATCGATACTTTAT
1 GTGTCGATACTTTAT
2107620 TATAAGTATC
Statistics
Matches: 326, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
111 1 0.00
112 324 0.99
113 1 0.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GATCTATAAATAACAAAACATGTAAAGCGCTACCGGATATATTGAAA
Found at i:2107629 original size:20 final size:20
Alignment explanation
Indices: 2107604--2107677 Score: 139
Period size: 20 Copynumber: 3.7 Consensus size: 20
2107594 ATATGTTGAT
2107604 AGTATCGATACTTTATTATA
1 AGTATCGATACTTTATTATA
2107624 AGTATCGATACTTTATTATA
1 AGTATCGATACTTTATTATA
2107644 AGTATCGATACTTTATTATA
1 AGTATCGATACTTTATTATA
*
2107664 AGTATCGACACTTT
1 AGTATCGATACTTT
2107678 TGGAATTTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (20 bp):
AGTATCGATACTTTATTATA
Found at i:2107863 original size:180 final size:182
Alignment explanation
Indices: 2107643--2107983 Score: 578
Period size: 180 Copynumber: 1.9 Consensus size: 182
2107633 ACTTTATTAT
* *
2107643 AAGTATCGATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGCAGTTATAGCAC
1 AAGTATCGATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCAC
*
2107708 TAATAAAGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAAAAGTTAAAAATATGA
66 TAATAAAGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAAAAGGTAAAAATATGA
** *
2107773 CAAAATCGGTCTCGAAATGA-AAAATCGGTAAAGAGCTACCGGATATGTTGA
131 CAAAATCAATCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGA
* *
2107824 AAGTGTCGATACTTTATTAT-AGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGC
1 AAGTATCGATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCAC
* *
2107888 TAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA
66 TAATAAAGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAAAAGGTAAAAATATGA
2107953 CAAAATCAATCTCGAAATGACAAAACCGGTA
131 CAAAATCAATCTCGAAATGACAAAACCGGTA
2107984 GTAAAAAAGT
Statistics
Matches: 149, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
180 121 0.81
181 28 0.19
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
AAGTATCGATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCAC
TAATAAAGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAAAAGGTAAAAATATGA
CAAAATCAATCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGA
Found at i:2108443 original size:23 final size:23
Alignment explanation
Indices: 2108417--2108464 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2108407 AAATATGTCA
* * *
2108417 ATATAAGCGTTATCTATTATATT
1 ATATAAGCGCTACCTAATATATT
2108440 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATATATT
2108463 AT
1 AT
2108465 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATATATT
Found at i:2110773 original size:15 final size:15
Alignment explanation
Indices: 2110753--2110782 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2110743 TCTCGTGGAA
*
2110753 GTTCCAGAGTTGTGG
1 GTTCCAGAGTCGTGG
2110768 GTTCCAGAGTCGTGG
1 GTTCCAGAGTCGTGG
2110783 CTGATATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.17, G:0.40, T:0.30
Consensus pattern (15 bp):
GTTCCAGAGTCGTGG
Found at i:2117814 original size:82 final size:82
Alignment explanation
Indices: 2117713--2118067 Score: 577
Period size: 82 Copynumber: 4.3 Consensus size: 82
2117703 TTATGGACTA
* *
2117713 ATGTCATGCCAAACCTTGCTGACATGTACGAATCAGTAAGCAAGCTACTGATCTCAAGATAATCC
1 ATGTCATGCCAAACCTTGCTAACATGTACGAATCAGTAAGCAAGCTACTGATTTCAAGATAATCC
*
2117778 AATTAGAATGGTAGACC
66 AATTAGTATGGTAGACC
* *
2117795 ATGTCATGCCAAACCTTGCTGACATGTACGAATCAGTAAGCAAGCTACTGATTTCAGGATAATCC
1 ATGTCATGCCAAACCTTGCTAACATGTACGAATCAGTAAGCAAGCTACTGATTTCAAGATAATCC
2117860 AATTAGTATGGTAGACC
66 AATTAGTATGGTAGACC
* * * * *
2117877 ATTTCAAGCCAAACCTTGCTAACATATACGAGTCAGTAAGCAAGCTATTGATTTCAAGATAATCC
1 ATGTCATGCCAAACCTTGCTAACATGTACGAATCAGTAAGCAAGCTACTGATTTCAAGATAATCC
2117942 AATTAGTATGGTAGACC
66 AATTAGTATGGTAGACC
* *
2117959 ATGTCATGCCAAACCATGCTAACATGTACGAATCAGTAAGCAAGCTACTGATTTCAAGTTAATCC
1 ATGTCATGCCAAACCTTGCTAACATGTACGAATCAGTAAGCAAGCTACTGATTTCAAGATAATCC
2118024 AATTAGTAT-GTAGACC
66 AATTAGTATGGTAGACC
* *
2118040 ATGTCAAGCAAAACCTTGCTAACATGTA
1 ATGTCATGCCAAACCTTGCTAACATGTA
2118068 ATCAGCAAGC
Statistics
Matches: 253, Mismatches: 20, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
81 32 0.13
82 221 0.87
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (82 bp):
ATGTCATGCCAAACCTTGCTAACATGTACGAATCAGTAAGCAAGCTACTGATTTCAAGATAATCC
AATTAGTATGGTAGACC
Found at i:2124175 original size:22 final size:22
Alignment explanation
Indices: 2124148--2124192 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2124138 AAATTTATTA
2124148 ATTTATATTTATATTAAGTTCT
1 ATTTATATTTATATTAAGTTCT
*
2124170 ATTTATGTTTATATTAAGTTCT
1 ATTTATATTTATATTAAGTTCT
2124192 A
1 A
2124193 CGTAATTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (22 bp):
ATTTATATTTATATTAAGTTCT
Found at i:2124296 original size:16 final size:16
Alignment explanation
Indices: 2124277--2124321 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2124267 GAGCAACGCG
*
2124277 CTTAATGAACAACGAA
1 CTTAATAAACAACGAA
* * *
2124293 CTTAACAAGCAACGAG
1 CTTAATAAACAACGAA
2124309 CTTAATAAACAAC
1 CTTAATAAACAAC
2124322 AAATCAAGTC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (16 bp):
CTTAATAAACAACGAA
Found at i:2148119 original size:6 final size:6
Alignment explanation
Indices: 2148101--2148139 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
2148091 GTTTATTTCG
*
2148101 ATTTTT ATGTTTT ATTTTT CATTTTC ATTTTT ATTTTT A
1 ATTTTT AT-TTTT ATTTTT -ATTTTT ATTTTT ATTTTT A
2148140 CTTAGATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 18 0.62
7 11 0.38
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (6 bp):
ATTTTT
Found at i:2148119 original size:13 final size:12
Alignment explanation
Indices: 2148101--2148139 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
2148091 GTTTATTTCG
2148101 ATTTTTATGTTTT
1 ATTTTTAT-TTTT
*
2148114 ATTTTTCATTTTC
1 ATTTTT-ATTTTT
2148127 ATTTTTATTTTT
1 ATTTTTATTTTT
2148139 A
1 A
2148140 CTTAGATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 6 0.26
13 15 0.65
14 2 0.09
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:2158295 original size:18 final size:19
Alignment explanation
Indices: 2158263--2158298 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2158253 GTTATTAAAA
*
2158263 ATTATAAAATAATTTTATG
1 ATTAAAAAATAATTTTATG
2158282 ATTAAAAAAT-ATTTTAT
1 ATTAAAAAATAATTTTAT
2158299 TAAATCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTAAAAAATAATTTTATG
Found at i:2158476 original size:31 final size:31
Alignment explanation
Indices: 2158409--2158477 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
2158399 CGTAATCTTT
* * * * *
2158409 AATAGTCGATAAACTCAATAAAACAATGTCT
1 AATAATCGAAAAACTCAACAAAACAACGTCA
* *
2158440 TATAATCGAAAAACTCAACAAAATAACGTCA
1 AATAATCGAAAAACTCAACAAAACAACGTCA
2158471 AATAATC
1 AATAATC
2158478 ATAATACCAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.23
Consensus pattern (31 bp):
AATAATCGAAAAACTCAACAAAACAACGTCA
Found at i:2163591 original size:22 final size:21
Alignment explanation
Indices: 2163566--2163617 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
2163556 TTTGATTATT
*
2163566 AATTATTTTATTTTATTAGTTA
1 AATTATTTTA-ATTATTAGTTA
*
2163588 AATTAATTTTAATTGTTAGTTA
1 AATT-ATTTTAATTATTAGTTA
2163610 AATTATTT
1 AATTATTT
2163618 AAATGATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 4 0.15
22 17 0.63
23 6 0.22
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (21 bp):
AATTATTTTAATTATTAGTTA
Found at i:2173146 original size:16 final size:16
Alignment explanation
Indices: 2173125--2173155 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2173115 AAAAATAAAT
2173125 GAACATAAACGAACAC
1 GAACATAAACGAACAC
2173141 GAACATAAACGAACA
1 GAACATAAACGAACA
2173156 AATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:2173249 original size:16 final size:16
Alignment explanation
Indices: 2173228--2173294 Score: 71
Period size: 16 Copynumber: 4.2 Consensus size: 16
2173218 TAAATAAACG
**
2173228 AACATAAACGCGCACA
1 AACATAAACGAACACA
*
2173244 AACATAAACGAACACG
1 AACATAAACGAACACA
* *
2173260 AACATAAATGAACACG
1 AACATAAACGAACACA
* *
2173276 AACATAAACAAACATA
1 AACATAAACGAACACA
2173292 AAC
1 AAC
2173295 GTTGAAGACC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.58, C:0.24, G:0.09, T:0.09
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:2173280 original size:32 final size:32
Alignment explanation
Indices: 2173225--2173289 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
2173215 TAATAAATAA
** *
2173225 ACGAACATAAACGCGCACAAACATAAACGAAC
1 ACGAACATAAACGAACACAAACATAAACAAAC
* *
2173257 ACGAACATAAATGAACACGAACATAAACAAAC
1 ACGAACATAAACGAACACAAACATAAACAAAC
2173289 A
1 A
2173290 TAAACGTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.57, C:0.25, G:0.11, T:0.08
Consensus pattern (32 bp):
ACGAACATAAACGAACACAAACATAAACAAAC
Found at i:2173542 original size:11 final size:11
Alignment explanation
Indices: 2173526--2173597 Score: 126
Period size: 11 Copynumber: 6.5 Consensus size: 11
2173516 GAGACTTGAA
2173526 CTCGATTCAAG
1 CTCGATTCAAG
2173537 CTCGATTCAAG
1 CTCGATTCAAG
2173548 CTCGATTCAAG
1 CTCGATTCAAG
2173559 CTCGATTCAAG
1 CTCGATTCAAG
*
2173570 CTCAATTCTAAG
1 CTCGATTC-AAG
2173582 CTCGATTCAAG
1 CTCGATTCAAG
2173593 CTCGA
1 CTCGA
2173598 CATTGCCCCA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
11 48 0.83
12 10 0.17
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (11 bp):
CTCGATTCAAG
Found at i:2174437 original size:14 final size:14
Alignment explanation
Indices: 2174420--2174466 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
2174410 AATGAACATA
2174420 AACGAACATAACCG
1 AACGAACATAACCG
*
2174434 AACGAACATAAACG
1 AACGAACATAACCG
*
2174448 AACATAACATAACCG
1 AAC-GAACATAACCG
2174463 AACG
1 AACG
2174467 TTCACGAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.53, C:0.26, G:0.13, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:2178309 original size:20 final size:19
Alignment explanation
Indices: 2178270--2178310 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
2178260 GTGAATCTTA
2178270 ATTTTTTAAATTTCTTTTT
1 ATTTTTTAAATTTCTTTTT
2178289 ATTTTATTATAATTT-TTTTT
1 ATTTT-TTA-AATTTCTTTTT
2178309 AT
1 AT
2178311 GAATTCTCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 10 0.50
21 5 0.25
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTTTTTAAATTTCTTTTT
Found at i:2182949 original size:45 final size:45
Alignment explanation
Indices: 2182883--2182968 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
2182873 TGGAGCGTCA
*
2182883 TTTTAGTTTATCGTTTCTATTTATTTAAGTTATGCACCTTGTAAT
1 TTTTAGTTTATCGTTTATATTTATTTAAGTTATGCACCTTGTAAT
* * *
2182928 TTTTTGTTTATCGTTTATATTTTTTTAAGTTATGGACCTTG
1 TTTTAGTTTATCGTTTATATTTATTTAAGTTATGCACCTTG
2182969 CCGCCCATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.20, C:0.09, G:0.13, T:0.58
Consensus pattern (45 bp):
TTTTAGTTTATCGTTTATATTTATTTAAGTTATGCACCTTGTAAT
Found at i:2185831 original size:2 final size:2
Alignment explanation
Indices: 2185824--2185849 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2185814 CCTTGTCCTG
2185824 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
2185850 AAAGAAGACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2193623 original size:39 final size:39
Alignment explanation
Indices: 2193548--2193624 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
2193538 CTCCAAACCC
* *
2193548 TTTTTATATTTGATGATGGGGACAATACCAGCCTTAGGA
1 TTTTTATATTTGATGATAGGGACAACACCAGCCTTAGGA
* * * *
2193587 TTTTTATATTTGCTGATAGGTACAACACTAGTCTTAGG
1 TTTTTATATTTGATGATAGGGACAACACCAGCCTTAGG
2193625 TTGGTCGTCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (39 bp):
TTTTTATATTTGATGATAGGGACAACACCAGCCTTAGGA
Found at i:2197413 original size:21 final size:20
Alignment explanation
Indices: 2197384--2197423 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2197374 TAAAGAAAAA
* *
2197384 AATATAAAAATAAAGGATAT
1 AATATAAAAAAAAAAGATAT
2197404 AATATGAAAAAAAAAAGATA
1 AATAT-AAAAAAAAAAGATA
2197424 ATTAATAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (20 bp):
AATATAAAAAAAAAAGATAT
Found at i:2202918 original size:22 final size:20
Alignment explanation
Indices: 2202869--2202918 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
2202859 ATATTTGAAT
2202869 AGATT-AGTTTTAATGTCAA
1 AGATTGAGTTTTAATGTCAA
*
2202888 AGGTATGAGTGTTTAATGTCAA
1 AGAT-TGAGT-TTTAATGTCAA
2202910 ATGATTGAG
1 A-GATTGAG
2202919 AGTTATCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 1 0.04
21 3 0.12
22 16 0.64
23 2 0.08
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (20 bp):
AGATTGAGTTTTAATGTCAA
Found at i:2212424 original size:73 final size:73
Alignment explanation
Indices: 2212305--2212452 Score: 260
Period size: 73 Copynumber: 2.0 Consensus size: 73
2212295 TACTCACCTG
*
2212305 AAATGCAAGAGTACATGTCCTTAAGGCTATACTGAAAACTGCAAGAGTACCGGAGAGAATTGAGC
1 AAATGCAAGAGTACATGTCCGTAAGGCTATACTGAAAACTGCAAGAGTACCGGAGAGAATTGAGC
2212370 TTGGGTCT
66 TTGGGTCT
* * *
2212378 AAATGCAAGAGTACATGTGCGTAAGGCTATACTGAAAACTGCAAGAGTACTGGAGAGAATTGAGG
1 AAATGCAAGAGTACATGTCCGTAAGGCTATACTGAAAACTGCAAGAGTACCGGAGAGAATTGAGC
2212443 TTGGGTCT
66 TTGGGTCT
2212451 AA
1 AA
2212453 GATGAAATGC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (73 bp):
AAATGCAAGAGTACATGTCCGTAAGGCTATACTGAAAACTGCAAGAGTACCGGAGAGAATTGAGC
TTGGGTCT
Found at i:2216189 original size:15 final size:15
Alignment explanation
Indices: 2216169--2216244 Score: 77
Period size: 15 Copynumber: 5.3 Consensus size: 15
2216159 ATTATCGATG
**
2216169 AATTTTTATAAAAAT
1 AATTTTTATTTAAAT
2216184 AATTTTTATTTAAAT
1 AATTTTTATTTAAAT
* * *
2216199 -A-TATTATTGATA-
1 AATTTTTATTTAAAT
*
2216211 AATTTTTATATAAAT
1 AATTTTTATTTAAAT
2216226 AATTTTTATTTAAAT
1 AATTTTTATTTAAAT
2216241 AATT
1 AATT
2216245 AGAATTTCAC
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
13 9 0.19
14 8 0.17
15 31 0.65
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (15 bp):
AATTTTTATTTAAAT
Found at i:2216200 original size:42 final size:42
Alignment explanation
Indices: 2216154--2216245 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
2216144 ATAATAAAAT
*
2216154 AATATATTATCGATGAATTTTTATAAAAATAATTTTTATTTA
1 AATATATTATCGATAAATTTTTATAAAAATAATTTTTATTTA
* *
2216196 AATATATTATTGATAAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATAAATTTTTATAAAAATAATTTTTATTTA
2216238 AATA-ATTA
1 AATATATTA
2216246 GAATTTCACT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (42 bp):
AATATATTATCGATAAATTTTTATAAAAATAATTTTTATTTA
Found at i:2216240 original size:27 final size:26
Alignment explanation
Indices: 2216184--2216234 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
2216174 TTATAAAAAT
*
2216184 AATTTTTATTTAAATATATTATTGATA
1 AATTTTTATATAAATATATTATT-ATA
*
2216211 AATTTTTATATAAATA-ATTTTTAT
1 AATTTTTATATAAATATATTATTAT
2216235 TTAAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 5 0.23
27 15 0.68
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
AATTTTTATATAAATATATTATTATA
Found at i:2216564 original size:30 final size:30
Alignment explanation
Indices: 2216530--2216586 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
2216520 ATGACACATA
*
2216530 ACTTAATTGTTACAATCAATTAATTGAGCG
1 ACTTAATTATTACAATCAATTAATTGAGCG
**
2216560 ACTTAATTATTACAATTGATTAATTGA
1 ACTTAATTATTACAATCAATTAATTGA
2216587 CTGACTGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.40
Consensus pattern (30 bp):
ACTTAATTATTACAATCAATTAATTGAGCG
Found at i:2220157 original size:14 final size:14
Alignment explanation
Indices: 2220138--2220171 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2220128 AATCAACATA
*
2220138 AAAAATTTAAAACT
1 AAAAATATAAAACT
*
2220152 AAAAATATATAACT
1 AAAAATATAAAACT
2220166 AAAAAT
1 AAAAAT
2220172 GATCATTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATATAAAACT
Found at i:2220620 original size:6 final size:6
Alignment explanation
Indices: 2220609--2220635 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2220599 GAGCTCCATT
2220609 GGTATG GGTATG GGTATG GGTATG GGT
1 GGTATG GGTATG GGTATG GGTATG GGT
2220636 GGAAGGCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTATG
Found at i:2232028 original size:4 final size:4
Alignment explanation
Indices: 2232021--2232047 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2232011 TCATGCATGT
2232021 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
2232048 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:2234202 original size:34 final size:33
Alignment explanation
Indices: 2234126--2234232 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
2234116 GTGGTAAGAA
* *
2234126 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
2234160 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
2234195 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
2234229 ATTT
1 ATTT
2234233 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:2234214 original size:36 final size:34
Alignment explanation
Indices: 2234159--2234237 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
2234149 TTTAAATAGT
*
2234159 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
2234191 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
2234225 TATTATTTATTTA
1 TATTATTTTTTTA
2234238 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:2234460 original size:21 final size:21
Alignment explanation
Indices: 2234430--2234477 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2234420 GCAGGGGTAC
* *
2234430 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
2234451 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
2234472 ATGCCA
1 ATGCCA
2234478 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:2234507 original size:21 final size:21
Alignment explanation
Indices: 2234481--2234574 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
2234471 TATGCCATCT
* *
2234481 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
2234502 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
2234523 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
2234544 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
2234565 CCGCAGGGTT
1 CCGCAGGGTT
2234575 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:2235136 original size:33 final size:34
Alignment explanation
Indices: 2235077--2235173 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
2235067 AAATGTTTTT
*
2235077 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
2235111 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
2235144 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
2235174 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:2235180 original size:34 final size:33
Alignment explanation
Indices: 2235075--2235180 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
2235065 ATAAATGTTT
*
2235075 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
2235109 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
2235141 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
2235176 TTAAA
1 TTAAA
2235181 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:2235785 original size:126 final size:126
Alignment explanation
Indices: 2235560--2235912 Score: 697
Period size: 126 Copynumber: 2.8 Consensus size: 126
2235550 TTTAAGTTAT
2235560 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
2235625 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
2235686 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
2235751 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
2235812 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
2235877 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
2235913 CCGATTATAG
Statistics
Matches: 226, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 226 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (126 bp):
TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:2235992 original size:8 final size:8
Alignment explanation
Indices: 2235979--2236019 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2235969 TCACAATCTT
2235979 TCAAATTC
1 TCAAATTC
2235987 TCAAATTC
1 TCAAATTC
* *
2235995 CCAAACTC
1 TCAAATTC
2236003 T-AAATTC
1 TCAAATTC
2236010 TCAAATTC
1 TCAAATTC
2236018 TC
1 TC
2236020 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:2240248 original size:43 final size:43
Alignment explanation
Indices: 2240187--2240273 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
2240177 AAACTTACTC
* *
2240187 AAACATAAGTGACCATTTGTATAATTTATCCATTTTTGATGCA
1 AAACATAAGTGACCATTTGTATAATTTACCCAGTTTTGATGCA
2240230 AAACATAAGTGACCATTTGTATAATTTACCCAGTTTTGATGCA
1 AAACATAAGTGACCATTTGTATAATTTACCCAGTTTTGATGCA
2240273 A
1 A
2240274 TAGACAATTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (43 bp):
AAACATAAGTGACCATTTGTATAATTTACCCAGTTTTGATGCA
Found at i:2249786 original size:16 final size:17
Alignment explanation
Indices: 2249765--2249798 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2249755 TTAGTGAATA
2249765 TATCAA-ATAATATATT
1 TATCAAGATAATATATT
*
2249781 TATCAAGATTATATATT
1 TATCAAGATAATATATT
2249798 T
1 T
2249799 TTAGTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
TATCAAGATAATATATT
Found at i:2251982 original size:32 final size:32
Alignment explanation
Indices: 2251938--2251998 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
2251928 GAAATCTTAT
*
2251938 TAGGAAGTGCCTCTAAAAGTACTCCAGATTGC
1 TAGGAAGAGCCTCTAAAAGTACTCCAGATTGC
*
2251970 TAGGAAGAGCCTCTAAAAGTCCTCCAGAT
1 TAGGAAGAGCCTCTAAAAGTACTCCAGAT
2251999 GGGGTAGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (32 bp):
TAGGAAGAGCCTCTAAAAGTACTCCAGATTGC
Found at i:2268126 original size:54 final size:55
Alignment explanation
Indices: 2268068--2268313 Score: 230
Period size: 54 Copynumber: 4.5 Consensus size: 55
2268058 CTAGATTTTA
* * * * * *
2268068 GATTGAAACACAAAGGTGCTCAGTCA-TTTTGGCTGCATAGAGGTGTCAGTCCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTC
* * * *
2268122 GATTGAAGCATAGAGGTGCTCAATC-GTCTTAGCTACACAGAGGTGTTAGCTCC-C
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAG-TCCTC
** * * * **
2268176 GGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTATC
1 GATTGAAGCACAGAGGTGCTCAATCA---TTTTTAGCTACACAGAGGTGTCAGTCCTC
* * *
2268234 GATTGAAGCAAAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAG-CTCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTC-CTC
*
2268289 AATTGAAGCACAGAGGTGCTCAATC
1 GATTGAAGCACAGAGGTGCTCAATC
2268314 GTTAATTCTA
Statistics
Matches: 152, Mismatches: 32, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
54 61 0.40
55 48 0.32
57 1 0.01
58 42 0.28
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTC
Found at i:2268241 original size:58 final size:55
Alignment explanation
Indices: 2268019--2268313 Score: 197
Period size: 54 Copynumber: 5.4 Consensus size: 55
2268009 TCATTTGTAA
* * * * *
2268019 AAGCACAGAGGTGCTCAATC-CTTCTAA-TGCACAGAGGTG-CTAGATTTTAGATTG
1 AAGCACAGAGGTGCTCAATCACTTTTAACTACACAGAGGTGTC-AGCTATCA-ATTG
* * * ** * * * *
2268073 AAACACAAAGGTGCTCAGTCA-TTTTGGCTGCATAGAGGTGTCAG-TCCTCGATTG
1 AAGCACAGAGGTGCTCAATCACTTTTAACTACACAGAGGTGTCAGCT-ATCAATTG
* * * * * ** ***
2268127 AAGCATAGAGGTGCTCAATC-GTCTTAGCTACACAGAGGTGTTAGCTCCCGGCTG
1 AAGCACAGAGGTGCTCAATCACTTTTAACTACACAGAGGTGTCAGCTATCAATTG
* * * * *
2268181 AAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTATCGATTG
1 AAGCACAGAGGTGCTCAATCA---CTTTTAACTACACAGAGGTGTCAGCTATCAATTG
* ** *
2268239 AAGCAAAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAGCTCTCAATTG
1 AAGCACAGAGGTGCTCAATCACTTTTAACTACACAGAGGTGTCAGCTATCAATTG
2268294 AAGCACAGAGGTGCTCAATC
1 AAGCACAGAGGTGCTCAATC
2268314 GTTAATTCTA
Statistics
Matches: 187, Mismatches: 44, Indels: 19
0.75 0.18 0.08
Matches are distributed among these distances:
54 82 0.44
55 61 0.33
56 1 0.01
58 43 0.23
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (55 bp):
AAGCACAGAGGTGCTCAATCACTTTTAACTACACAGAGGTGTCAGCTATCAATTG
Found at i:2268249 original size:112 final size:113
Alignment explanation
Indices: 2268100--2268310 Score: 307
Period size: 112 Copynumber: 1.9 Consensus size: 113
2268090 GTCATTTTGG
* * * *
2268100 CTGCATAGAGGTGTCAGTCCTCGATTGAAGCATAGAGGTGCTCAATC-GTCTTAGCTACACAGAG
1 CTGCACAGAGGTGTCAGTCATCGATTGAAGCAAAGAGGTGCTCAATCACTCTTAGCTACACAGAG
* **
2268164 GTGTTAGCTCCCGGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAA
66 GTGTCAGCTCCCAACTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAA
* * *
2268212 CTGCACAGAGGTGTCAGTTATCGATTGAAGCAAAGAGGTGCTCAATCACTTTTGGCTACACAGAG
1 CTGCACAGAGGTGTCAGTCATCGATTGAAGCAAAGAGGTGCTCAATCACTCTTAGCTACACAGAG
* *
2268277 GTGTCAGCTCTCAATTGAAGCACAGAGGTGCTCA
66 GTGTCAGCTCCCAACTGAAGCACAGAGGTGCTCA
2268311 ATCGTTAATT
Statistics
Matches: 86, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
112 43 0.50
113 43 0.50
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (113 bp):
CTGCACAGAGGTGTCAGTCATCGATTGAAGCAAAGAGGTGCTCAATCACTCTTAGCTACACAGAG
GTGTCAGCTCCCAACTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAA
Found at i:2268329 original size:55 final size:54
Alignment explanation
Indices: 2268106--2268335 Score: 196
Period size: 55 Copynumber: 4.1 Consensus size: 54
2268096 TTGGCTGCAT
* *
2268106 AGAGGTGTCAG-TCCTCGATTGAAGCATAGAGGTGCTCAATCGTCTTA-GCTACAC
1 AGAGGTGTCAGCT-CTCGATTGAAGCACAGAGGTGCTCAATCGT-TTATTCTACAC
* * ** * * * *
2268160 AGAGGTGTTAGCTCCCGGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCAC
1 AGAGGTGTCAGCTCTCGATTGAAGCACAGAGGTGCTCAATC--GTTTATT--CTACAC
* * * * *
2268218 AGAGGTGTCAGTTATCGATTGAAGCAAAGAGGTGCTCAATCACTTT-TGGCTACAC
1 AGAGGTGTCAGCTCTCGATTGAAGCACAGAGGTGCTCAATC-GTTTAT-TCTACAC
* *
2268273 AGAGGTGTCAGCTCTCAATTGAAGCACAGAGGTGCTCAATCGTTAATTCTAGCAC
1 AGAGGTGTCAGCTCTCGATTGAAGCACAGAGGTGCTCAATCGTTTATTCTA-CAC
*
2268328 AGTGGTGT
1 AGAGGTGT
2268336 TATGGATTCA
Statistics
Matches: 137, Mismatches: 30, Indels: 17
0.74 0.16 0.09
Matches are distributed among these distances:
54 38 0.28
55 56 0.41
56 2 0.01
57 3 0.02
58 38 0.28
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (54 bp):
AGAGGTGTCAGCTCTCGATTGAAGCACAGAGGTGCTCAATCGTTTATTCTACAC
Found at i:2268564 original size:81 final size:81
Alignment explanation
Indices: 2268429--2268587 Score: 237
Period size: 81 Copynumber: 2.0 Consensus size: 81
2268419 GCGAGTTACA
* *
2268429 GAGAATGGTTCACACACGAAATGGCAGAGCAACAAGCTCGCACATAGGTGTAGAGCAGGAAGTTA
1 GAGAATGGTTCACACACGAAATGGCAGAGCAACAAGCTCGCACAGAGGTGTAGAGCAGGAAGCTA
* *
2268494 CTGAGCCGGTTGTACC
66 CCGAGCCAGTTGTACC
* * * * *
2268510 GAGAATGGTTCGCACACGAAATGGCGGATCGACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
1 GAGAATGGTTCACACACGAAATGGCAGAGCAACAAGCTCGCACAGAGGTGTAGAGCAGGAAGCTA
2268575 CCGAGCCAGTTGT
66 CCGAGCCAGTTGT
2268588 GCAAGAGACT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 69 1.00
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.17
Consensus pattern (81 bp):
GAGAATGGTTCACACACGAAATGGCAGAGCAACAAGCTCGCACAGAGGTGTAGAGCAGGAAGCTA
CCGAGCCAGTTGTACC
Found at i:2272011 original size:6 final size:6
Alignment explanation
Indices: 2272002--2272026 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2271992 CTCTTCTTCT
2272002 TCCTCG TCCTCG TCCTCG TCCTCG T
1 TCCTCG TCCTCG TCCTCG TCCTCG T
2272027 ACTCCTTCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.48, G:0.16, T:0.36
Consensus pattern (6 bp):
TCCTCG
Found at i:2275121 original size:31 final size:30
Alignment explanation
Indices: 2275086--2275175 Score: 117
Period size: 31 Copynumber: 2.9 Consensus size: 30
2275076 ATTAAGAAAA
* *
2275086 TTTTCTGTATTAGAGAACAGCATGCAATATT
1 TTTTCTATATT-GAGAACAACATGCAATATT
2275117 TTTTCTATATTGAAGAACAACATGCAATATT
1 TTTTCTATATTG-AGAACAACATGCAATATT
* *
2275148 TTTTTTATATTGGAGAACATCATGCAAT
1 TTTTCTATATT-GAGAACAACATGCAAT
2275176 GTCATGTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.02
31 51 0.96
32 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (30 bp):
TTTTCTATATTGAGAACAACATGCAATATT
Found at i:2275768 original size:23 final size:23
Alignment explanation
Indices: 2275721--2275778 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 23
2275711 AAAAAATATG
*
2275721 TTTTTTTCTTAAAAAGAATTCAAA
1 TTTTTTT-TTAAAAAAAATTCAAA
2275745 TTTTTTTTTAAAAAAAAGTT-AAA
1 TTTTTTTTTAAAAAAAA-TTCAAA
2275768 TCTGTTTTTTT
1 T-T-TTTTTTT
2275779 TCTTTTTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 13 0.43
24 10 0.33
25 7 0.23
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (23 bp):
TTTTTTTTTAAAAAAAATTCAAA
Found at i:2283209 original size:2 final size:2
Alignment explanation
Indices: 2283202--2283245 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2283192 TTGATTAATG
2283202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2283244 AT
1 AT
2283246 GTATGTATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2296643 original size:40 final size:41
Alignment explanation
Indices: 2296599--2296682 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 41
2296589 TTTAATAAAT
* * * *
2296599 ATAATGTTTCGATTCTATCATAATTCTTAATAAACTAA-GA
1 ATAATGTTTCAACTCAATCATAATTCTTAATAAAATAATGA
* *
2296639 ATAATGTTTTAACTCAATCTTAATTCTTAATAAAATAATGA
1 ATAATGTTTCAACTCAATCATAATTCTTAATAAAATAATGA
2296680 ATA
1 ATA
2296683 TAATCCTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 32 0.86
41 5 0.14
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (41 bp):
ATAATGTTTCAACTCAATCATAATTCTTAATAAAATAATGA
Found at i:2309588 original size:35 final size:33
Alignment explanation
Indices: 2309549--2309637 Score: 106
Period size: 36 Copynumber: 2.5 Consensus size: 33
2309539 TCTCACTTTA
2309549 GTAAATGCTTCTTTGAAAATGGTTTTCAAAGTTTG
1 GTAAATG-TT-TTTGAAAATGGTTTTCAAAGTTTG
* *
2309584 GTAAATATTTATTTGAAAAATGTTTTTCAAAGTTTG
1 GTAAAT-GTT-TTTG-AAAATGGTTTTCAAAGTTTG
*
2309620 GTAGATGTTTTTGAAAAT
1 GTAAATGTTTTTGAAAAT
2309638 AGGAATGGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
33 5 0.11
34 4 0.09
35 14 0.30
36 24 0.51
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (33 bp):
GTAAATGTTTTTGAAAATGGTTTTCAAAGTTTG
Found at i:2314195 original size:36 final size:35
Alignment explanation
Indices: 2314108--2314212 Score: 167
Period size: 35 Copynumber: 3.0 Consensus size: 35
2314098 TGGCAACCAA
*
2314108 CTTTGAAAATGGTTTTCAAAGTTGGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
2314143 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
2314178 TTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
2314213 GGTAGGTGTT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 42 0.64
36 24 0.36
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.46
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2316397 original size:31 final size:31
Alignment explanation
Indices: 2316353--2316412 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
2316343 AATACTTCAC
*
2316353 ATATATTTCTAAAAATCTACAAAAATTTATA
1 ATATATTTCTAAAAATCTAAAAAAATTTATA
* *
2316384 ATATACTTT-TAAAATTGTAAAAAAATTTA
1 ATATA-TTTCTAAAAATCTAAAAAAATTTA
2316413 AATTATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.40
Consensus pattern (31 bp):
ATATATTTCTAAAAATCTAAAAAAATTTATA
Found at i:2319166 original size:17 final size:17
Alignment explanation
Indices: 2319141--2319181 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2319131 AACTACAATA
* *
2319141 TGCTTGAAAGGGCTCCT
1 TGCTCGAAAGGGATCCT
2319158 TGCTCGAAAGGGATCCT
1 TGCTCGAAAGGGATCCT
2319175 TG-TCGAA
1 TGCTCGAA
2319182 GGTCGGCGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (17 bp):
TGCTCGAAAGGGATCCT
Found at i:2320968 original size:15 final size:15
Alignment explanation
Indices: 2320943--2320977 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
2320933 ATTTCTATGT
2320943 AAATATTTTTTT-AA
1 AAATATTTTTTTAAA
2320957 AAATATTTTTTTAAA
1 AAATATTTTTTTAAA
2320972 AAATAT
1 AAATAT
2320978 AAAAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATATTTTTTTAAA
Found at i:2321015 original size:28 final size:29
Alignment explanation
Indices: 2320964--2321020 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2320954 TAAAAATATT
2320964 TTTTTAAAAAATATAAAAATTATTTGTTTA
1 TTTTTAAAAAATATAAAAATTATTT-TTTA
*
2320994 TTTTT-AAAATTATAAAAA-TATTTTTTA
1 TTTTTAAAAAATATAAAAATTATTTTTTA
2321021 ATTATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 4 0.15
28 5 0.19
29 12 0.46
30 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (29 bp):
TTTTTAAAAAATATAAAAATTATTTTTTA
Found at i:2321382 original size:12 final size:13
Alignment explanation
Indices: 2321352--2321388 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2321342 TTAACATTGA
2321352 AAAAATAAAATAT
1 AAAAATAAAATAT
2321365 AAAAATAAAATAT
1 AAAAATAAAATAT
*
2321378 -TAAATAAAATA
1 AAAAATAAAATA
2321389 ATACAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATAAAATAT
Found at i:2329921 original size:22 final size:23
Alignment explanation
Indices: 2329896--2329949 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
2329886 ATATTATGTA
2329896 TATAAATGTTATGAATTTAAT-T
1 TATAAATGTTATGAATTTAATAT
* * **
2329918 TATAATTCTTATTTATTTAATAT
1 TATAAATGTTATGAATTTAATAT
*
2329941 TATACATGT
1 TATAAATGT
2329950 AATTAGGGAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (23 bp):
TATAAATGTTATGAATTTAATAT
Found at i:2331106 original size:25 final size:25
Alignment explanation
Indices: 2331078--2331126 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2331068 ATAATCATAT
2331078 TTAATATAAAAATAAGAATTTATAA
1 TTAATATAAAAATAAGAATTTATAA
* * * *
2331103 TTAATTTAAACATTATAATTTATA
1 TTAATATAAAAATAAGAATTTATA
2331127 TAAATTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
TTAATATAAAAATAAGAATTTATAA
Found at i:2332080 original size:2 final size:2
Alignment explanation
Indices: 2332073--2332111 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2332063 ATATAGTTCC
2332073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2332112 CATGTGGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2342069 original size:11 final size:11
Alignment explanation
Indices: 2342053--2342078 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2342043 ATATTAACTC
2342053 TTTAATATGTA
1 TTTAATATGTA
2342064 TTTAATATGTA
1 TTTAATATGTA
2342075 TTTA
1 TTTA
2342079 TGCGAATCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (11 bp):
TTTAATATGTA
Found at i:2355255 original size:17 final size:17
Alignment explanation
Indices: 2355233--2355272 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2355223 GAGGTACTCT
2355233 GGTGCAATATGCCCAAC
1 GGTGCAATATGCCCAAC
2355250 GGTGCAATATGCCCAAC
1 GGTGCAATATGCCCAAC
*
2355267 AGTGCA
1 GGTGCA
2355273 GTGGTCACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (17 bp):
GGTGCAATATGCCCAAC
Found at i:2360813 original size:102 final size:102
Alignment explanation
Indices: 2360637--2360840 Score: 390
Period size: 102 Copynumber: 2.0 Consensus size: 102
2360627 ATTTCCCCAG
*
2360637 GAGCTGCACAATAAATTACAACCAAAATTGAGCTTTCAAATTGAAGTTCTCATTGTTGACTGGTA
1 GAGCTGCACAATAAATTACAACCAAAATTGAGCTTTCAAATTGAAGTTCTCATTGTTGAATGGTA
2360702 CCTCCAAAAAATTACCTCATAATTATCTTCCTACTTA
66 CCTCCAAAAAATTACCTCATAATTATCTTCCTACTTA
*
2360739 GAGCTGCACGATAAATTACAACCAAAATTGAGCTTTCAAATTGAAGTTCTCATTGTTGAATGGTA
1 GAGCTGCACAATAAATTACAACCAAAATTGAGCTTTCAAATTGAAGTTCTCATTGTTGAATGGTA
2360804 CCTCCAAAAAATTACCTCATAATTATCTTCCTACTTA
66 CCTCCAAAAAATTACCTCATAATTATCTTCCTACTTA
2360841 TTTACTGCTC
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.32
Consensus pattern (102 bp):
GAGCTGCACAATAAATTACAACCAAAATTGAGCTTTCAAATTGAAGTTCTCATTGTTGAATGGTA
CCTCCAAAAAATTACCTCATAATTATCTTCCTACTTA
Found at i:2397104 original size:23 final size:22
Alignment explanation
Indices: 2397078--2397121 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
2397068 GTTTAATATA
2397078 AATTA-AATAAAAATATATGTTTG
1 AATTATAA-AAAAAT-TATGTTTG
2397101 AATTATTAAAAAAATTATGTT
1 AATTA-TAAAAAAATTATGTT
2397122 GGTCTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
24 6 0.32
25 2 0.11
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (22 bp):
AATTATAAAAAAATTATGTTTG
Found at i:2397164 original size:2 final size:2
Alignment explanation
Indices: 2397157--2397185 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2397147 TTTAATCTAA
2397157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2397186 ATTATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2397552 original size:24 final size:24
Alignment explanation
Indices: 2397506--2397553 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2397496 TTATATAAAA
* *
2397506 TTAAAAAAGAAAATTATATATTTT
1 TTAAAAAAGAAAATCATAAATTTT
2397530 TTAAAAAAGAAACA-CATAAATTTT
1 TTAAAAAAGAAA-ATCATAAATTTT
2397554 GAAATAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (24 bp):
TTAAAAAAGAAAATCATAAATTTT
Found at i:2422865 original size:36 final size:35
Alignment explanation
Indices: 2422824--2422942 Score: 141
Period size: 36 Copynumber: 3.3 Consensus size: 35
2422814 CTCCTACTTT
* *
2422824 TGCTTCTATGAAAGGATCTTAAAGGACTTCTGCTGA
1 TGCTTCTCTGAAA-GATCTTACAGGACTTCTGCTGA
* *
2422860 TGCTTCGCCTCAAAGATCTTACAGGACTTCTGCTGA
1 TGCTTC-TCTGAAAGATCTTACAGGACTTCTGCTGA
*
2422896 TGGTTCTCCTCG-AAGATCTTACAGGACTTCTGCTGA
1 TGCTTCT-CT-GAAAGATCTTACAGGACTTCTGCTGA
*
2422932 CGCTTCTCTGA
1 TGCTTCTCTGA
2422943 GAGCGTGCTC
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
34 1 0.01
35 2 0.03
36 63 0.90
37 4 0.06
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (35 bp):
TGCTTCTCTGAAAGATCTTACAGGACTTCTGCTGA
Found at i:2424633 original size:24 final size:21
Alignment explanation
Indices: 2424584--2424634 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
2424574 CAGAATCACT
*
2424584 ATCAGAATCTGATGATTCTGA
1 ATCAGAATCTGAAGATTCTGA
*
2424605 CTCAGAATCTGAAGAACTCTCTGA
1 ATCAGAATCTGAAG-A-T-TCTGA
2424629 ATCAGA
1 ATCAGA
2424635 TGAATAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 12 0.50
22 1 0.04
23 1 0.04
24 10 0.42
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (21 bp):
ATCAGAATCTGAAGATTCTGA
Found at i:2429131 original size:21 final size:21
Alignment explanation
Indices: 2429106--2429164 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
2429096 TAAGAGCTTT
* *
2429106 AATTATAAAAGTAAAAA-GTG
1 AATTATAAAAGTAAAAATCTC
*
2429126 ATATTA-AAGAATTAAAAATCTC
1 A-ATTATAA-AAGTAAAAATCTC
2429148 AATTATAAAAGTAAAAA
1 AATTATAAAAGTAAAAA
2429165 AATACGATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
20 3 0.10
21 24 0.77
22 4 0.13
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.27
Consensus pattern (21 bp):
AATTATAAAAGTAAAAATCTC
Found at i:2429140 original size:42 final size:43
Alignment explanation
Indices: 2429059--2429165 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 43
2429049 AATTTAGGAG
* * *
2429059 TCTCAATTACAAAAGTAAAAAATGGGATTAAAAAAATT-AAGA
1 TCTCAATTATAAAAGTAAAAAATGAGATTAAAAAAATTAAAAA
* * * * *
2429101 GCTTTAATTATAAAAGTAAAAAGTGATATT-AAAGAATTAAAAA
1 TC-TCAATTATAAAAGTAAAAAATGAGATTAAAAAAATTAAAAA
2429144 TCTCAATTATAAAAGTAAAAAA
1 TCTCAATTATAAAAGTAAAAAA
2429166 ATACGATTGA
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
42 26 0.50
43 26 0.50
ACGTcount: A:0.57, C:0.06, G:0.10, T:0.27
Consensus pattern (43 bp):
TCTCAATTATAAAAGTAAAAAATGAGATTAAAAAAATTAAAAA
Found at i:2440515 original size:5 final size:5
Alignment explanation
Indices: 2440500--2440544 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
2440490 CAATTTAGTC
*
2440500 TTAATT TTAAT TTAAT TTAA- TTAAT TTAAT TTAA- TAAAT TTAAT T
1 TTAA-T TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
2440545 ATTTAATCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
4 7 0.20
5 24 0.69
6 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTAAT
Found at i:2440525 original size:9 final size:9
Alignment explanation
Indices: 2440506--2440551 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
2440496 AGTCTTAATT
2440506 TTAATTTAA
1 TTAATTTAA
2440515 TTTAA-TTAA
1 -TTAATTTAA
2440524 TTTAATTTAA
1 -TTAATTTAA
*
2440534 TAAATTTAA
1 TTAATTTAA
2440543 TT-ATTTAA
1 TTAATTTAA
2440551 T
1 T
2440552 CGACATGTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 7 0.21
9 18 0.55
10 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TTAATTTAA
Found at i:2440525 original size:14 final size:14
Alignment explanation
Indices: 2440506--2440544 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
2440496 AGTCTTAATT
2440506 TTAATTTAATTTAA
1 TTAATTTAATTTAA
2440520 TTAATTTAATTTAA
1 TTAATTTAATTTAA
*
2440534 TAAATTTAATT
1 TTAATTTAATT
2440545 ATTTAATCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAATTTAATTTAA
Found at i:2445989 original size:51 final size:52
Alignment explanation
Indices: 2445908--2446011 Score: 174
Period size: 51 Copynumber: 2.0 Consensus size: 52
2445898 CCGTTTGTCA
* * *
2445908 ATAAATCATTATTATTTGTATGTCTTATTTAATTGTAACAATATCATTCTTC
1 ATAAATCATAATTATTTGTATGTATTATTTAATGGTAACAATATCATTCTTC
2445960 ATAAATCATAATTA-TTGTATGTATTATTTAATGGTAACAATATCATTCTTC
1 ATAAATCATAATTATTTGTATGTATTATTTAATGGTAACAATATCATTCTTC
2446011 A
1 A
2446012 CTGCTAGTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 36 0.73
52 13 0.27
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.47
Consensus pattern (52 bp):
ATAAATCATAATTATTTGTATGTATTATTTAATGGTAACAATATCATTCTTC
Found at i:2446246 original size:15 final size:15
Alignment explanation
Indices: 2446203--2446248 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
2446193 TCTTTATATA
2446203 AATTTAAATATT-TTT
1 AATTTAAA-ATTATTT
2446218 AA--TAAAATTA-TT
1 AATTTAAAATTATTT
2446230 AATTTAAAATTATTT
1 AATTTAAAATTATTT
2446245 AATT
1 AATT
2446249 ATGTTTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 7 0.26
13 4 0.15
14 8 0.30
15 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTTAAAATTATTT
Found at i:2446356 original size:2 final size:2
Alignment explanation
Indices: 2446345--2446376 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2446335 AAATCTAACA
*
2446345 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2446377 TATTGTCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2447621 original size:145 final size:146
Alignment explanation
Indices: 2447495--2447784 Score: 363
Period size: 146 Copynumber: 2.0 Consensus size: 146
2447485 ATCTAATATC
* *** *
2447495 TTTTAT-ATTTAAAAAATTAAAGATA-AAAAATATTACATTTATTTTAATTTTATTTCTTCCACT
1 TTTTATAATTAAAAAAATTAAAGATATAAAAATATTA-ATTT-TTTTAATTTTAAAACTTACACT
* *
2447558 AAATACGGTTTAAAATATAAAT-ATCTATTTAATTATAAAATATTATTATA-TTTTTAACTATTT
64 AAACACGGTTTAAAATATAAATGATCTATTTAATTATAAAATAATATTATACTTTTTAACTATTT
* *
2447621 TAAGTTCTCTTATATTTAT
129 TAAATTATCTTATA-TTAT
* * *
2447640 TTTTATAATTAAAAAAATTAAAGGTATAAAAATATTAATTTTTTTTATTTTAAAACTTACATTAA
1 TTTTATAATTAAAAAAATTAAAGATATAAAAATATTAATTTTTTTAATTTTAAAACTTACACTAA
* * *
2447705 ACACGGTTTAAAATATATATGATTTATTTAATTATAAAATAATATTATACTTGTTTAACTAATTT
66 ACACGGTTTAAAATATAAATGATCTATTTAATTATAAAATAATATTATACTT-TTTAACTATTTT
* *
2447770 AGATTTTCTTATATT
130 AAATTATCTTATATT
2447785 TTATAATTGA
Statistics
Matches: 124, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
145 42 0.34
146 47 0.38
147 14 0.11
148 21 0.17
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (146 bp):
TTTTATAATTAAAAAAATTAAAGATATAAAAATATTAATTTTTTTAATTTTAAAACTTACACTAA
ACACGGTTTAAAATATAAATGATCTATTTAATTATAAAATAATATTATACTTTTTAACTATTTTA
AATTATCTTATATTAT
Found at i:2451285 original size:26 final size:26
Alignment explanation
Indices: 2451248--2451297 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2451238 TGAATTATAC
2451248 TTTACAAATGTTAAATTATTTTTAGT
1 TTTACAAATGTTAAATTATTTTTAGT
* *
2451274 TTTA-AAATTGTTTATTTATTTTTA
1 TTTACAAA-TGTTAAATTATTTTTA
2451298 ATTAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (26 bp):
TTTACAAATGTTAAATTATTTTTAGT
Found at i:2451991 original size:22 final size:22
Alignment explanation
Indices: 2451963--2452016 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
2451953 ATTATATATA
2451963 TTTTTTTTATTTAAGTGTCTAT
1 TTTTTTTTATTTAAGTGTCTAT
2451985 TTTTTTTTATTTAAGTGTCTAT
1 TTTTTTTTATTTAAGTGTCTAT
2452007 TTTTTTTTAT
1 TTTTTTTTAT
2452017 AAATGTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.17, C:0.04, G:0.07, T:0.72
Consensus pattern (22 bp):
TTTTTTTTATTTAAGTGTCTAT
Found at i:2455506 original size:14 final size:14
Alignment explanation
Indices: 2455489--2455516 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2455479 ATCATAACAA
2455489 AATTATATAACTAT
1 AATTATATAACTAT
2455503 AATTATATAACTAT
1 AATTATATAACTAT
2455517 TCTTTCACTT
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:2455791 original size:9 final size:10
Alignment explanation
Indices: 2455764--2455802 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
2455754 AACAAAAATC
*
2455764 CCGGTTTTTC
1 CCGGTTTTTT
2455774 CCGGTTTTTT
1 CCGGTTTTTT
*
2455784 CTGGTTTTTT
1 CCGGTTTTTT
2455794 CCGGTTTTT
1 CCGGTTTTT
2455803 GGACGGTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.00, C:0.21, G:0.21, T:0.59
Consensus pattern (10 bp):
CCGGTTTTTT
Found at i:2455966 original size:2 final size:2
Alignment explanation
Indices: 2455959--2456012 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
2455949 TCACATGTAC
2455959 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2456000 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
2456013 ATTTCATCAG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2456109 original size:16 final size:17
Alignment explanation
Indices: 2456077--2456128 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2456067 CACATAAGTA
2456077 AATATGTTTAATAAAAT
1 AATATGTTTAATAAAAT
*
2456094 AATATGTTT-TTAAAAT
1 AATATGTTTAATAAAAT
* *
2456110 -ATATATTTATATAACAT
1 AATATGTTTA-ATAAAAT
2456127 AA
1 AA
2456129 AAGGTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 7 0.25
16 6 0.21
17 14 0.50
18 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
AATATGTTTAATAAAAT
Found at i:2458631 original size:2 final size:2
Alignment explanation
Indices: 2458624--2458651 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2458614 AAGAGATGTT
2458624 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2458652 GAAATAGACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2470549 original size:34 final size:35
Alignment explanation
Indices: 2470479--2470550 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
2470469 TTTTCCATAG
*
2470479 TTAAACTTATATGTATATCCAGTCATCTTTTCTTT
1 TTAAACTTATATGTATATCCAGCCATCTTTTCTTT
* *
2470514 TTAAA-TTATATGTATATGCAGCCTTCTATTT-TTT
1 TTAAACTTATATGTATATCCAGCCATCT-TTTCTTT
2470548 TTA
1 TTA
2470551 TATATAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 25 0.76
35 8 0.24
ACGTcount: A:0.26, C:0.14, G:0.07, T:0.53
Consensus pattern (35 bp):
TTAAACTTATATGTATATCCAGCCATCTTTTCTTT
Found at i:2471083 original size:51 final size:51
Alignment explanation
Indices: 2471007--2471415 Score: 563
Period size: 51 Copynumber: 8.0 Consensus size: 51
2470997 GGCGCAGACA
** * *
2471007 CAGCAAGGTGGAAAC-TCAGAGTCCCAAACATATACTCAACTACCTCAACAG
1 CAGCAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAG
* * ***
2471058 CAGCAAGGTGGAAACTTTGGATCCCAAACATATAGTCAGCTATGGCAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* * * * *
2471109 CAGCAAGGTGGAAACTTTGGATCCCAGACGTATAGTCAGCTACCGCAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
*
2471160 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCATCTACCACAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* *
2471211 CAGCAAGGTGGAAACATT-GATACCCAAACATATACTCTGCTACCACATCAG
1 CAGCAAGGTGGAAACATTGGAT-CCCAAACATATACTCAGCTACCACAACAG
*
2471262 CAGCAAGGTGGAAACAATGGATCCCAAACATATACTCAGCTACCACAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* * *
2471313 CAGCAAGGTGGAAACATT-GATTCCCAAACATTTACTCTGTTACCACAACAG
1 CAGCAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAG
* *
2471364 CAGCAAGGTGGAAACATTGGTTCCCAAACATATACTCAGCTACCACAGCAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
2471415 C
1 C
2471416 TCTTAATGTC
Statistics
Matches: 321, Mismatches: 32, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
50 5 0.02
51 309 0.96
52 7 0.02
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.18
Consensus pattern (51 bp):
CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
Found at i:2478274 original size:2 final size:2
Alignment explanation
Indices: 2478267--2478301 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2478257 GTTTCTTTTA
2478267 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2478302 GATTAATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2486920 original size:59 final size:57
Alignment explanation
Indices: 2486771--2486920 Score: 142
Period size: 59 Copynumber: 2.5 Consensus size: 57
2486761 AATTAATTCT
* * * * * *
2486771 TAAACTTTTAAATATTTCAATTTCATCTTCAAACTATGATTCTCATTTTAAATTAGTCT
1 TAAACTTTT-AATATTTCAATTTCATCCT-AAACTATGAATCTCATTCTAAATGAATCC
* *
2486830 TCAAACTTTTAAAATTTTAA-TTCTATCCCTAAA-TAATGAATCTCATTCTAAATGAATCCC
1 T-AAACTTTTAATATTTCAATTTC-AT-CCTAAACT-ATGAATCTCATTCTAAATGAAT-CC
2486890 TAAACTTTTGAATATTTCAATTTCATCCTAA
1 TAAACTTTT-AATATTTCAATTTCATCCTAA
2486921 TATTCGTCCA
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
58 4 0.05
59 45 0.61
60 22 0.30
61 3 0.04
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.43
Consensus pattern (57 bp):
TAAACTTTTAATATTTCAATTTCATCCTAAACTATGAATCTCATTCTAAATGAATCC
Found at i:2487150 original size:29 final size:29
Alignment explanation
Indices: 2487111--2487222 Score: 86
Period size: 29 Copynumber: 3.8 Consensus size: 29
2487101 TGAATGTCAT
*
2487111 AGTTTAGGAATACAATTAAAATATTCAAA
1 AGTTTAAGAATACAATTAAAATATTCAAA
* *
2487140 AGTTTAAGAATTA-ATTTAAAATGATAATCATA
1 AGTTTAAGAA-TACAATTAAAAT-AT--TCAAA
* * *
2487172 A-TTTGAGAATAAAATTAAAATATTTAAA
1 AGTTTAAGAATACAATTAAAATATTCAAA
* *
2487200 AGTTCAAGGAT-CAATCTAAAATA
1 AGTTTAAGAATACAAT-TAAAATA
2487223 AAGACCATAA
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
28 7 0.11
29 30 0.46
30 8 0.12
31 15 0.23
32 5 0.08
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (29 bp):
AGTTTAAGAATACAATTAAAATATTCAAA
Found at i:2487156 original size:60 final size:60
Alignment explanation
Indices: 2487090--2487221 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
2487080 ATTTTTGGGG
* * * *
2487090 TCAATTTAAAATGA-ATGTCATAGTTT-AGGAATACAATTAAAATATTCAAAAGTTTAAGAA
1 TCAATTTAAAATGATA-ATCATAATTTGA-GAATAAAATTAAAATATTCAAAAGTTCAAGAA
* * *
2487150 TTAATTTAAAATGATAATCATAATTTGAGAATAAAATTAAAATATTTAAAAGTTCAAGGA
1 TCAATTTAAAATGATAATCATAATTTGAGAATAAAATTAAAATATTCAAAAGTTCAAGAA
*
2487210 TCAATCTAAAAT
1 TCAATTTAAAAT
2487222 AAAGACCATA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
60 59 0.97
61 2 0.03
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (60 bp):
TCAATTTAAAATGATAATCATAATTTGAGAATAAAATTAAAATATTCAAAAGTTCAAGAA
Found at i:2487232 original size:60 final size:60
Alignment explanation
Indices: 2487118--2487233 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
2487108 CATAGTTTAG
* * * * * *
2487118 GAATACAATTAAAATATTCAAAAGTTTAAGAATTAATTTAAAATGATAATCATAATTTGA
1 GAATAAAATTAAAATATTCAAAAGTTCAAGAATCAATCTAAAATGAAAACCATAATTTGA
* *
2487178 GAATAAAATTAAAATATTTAAAAGTTCAAGGATCAATCTAAAAT-AAAGACCATAAT
1 GAATAAAATTAAAATATTCAAAAGTTCAAGAATCAATCTAAAATGAAA-ACCATAAT
2487234 GCAATAACAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (60 bp):
GAATAAAATTAAAATATTCAAAAGTTCAAGAATCAATCTAAAATGAAAACCATAATTTGA
Found at i:2487558 original size:13 final size:13
Alignment explanation
Indices: 2487540--2487574 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
2487530 TATTGTTGAC
2487540 TATAAATTTAAAT
1 TATAAATTTAAAT
2487553 TATAAATTTAAAT
1 TATAAATTTAAAT
*
2487566 TTTAAATTT
1 TATAAATTT
2487575 GATACAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TATAAATTTAAAT
Found at i:2496210 original size:31 final size:31
Alignment explanation
Indices: 2496149--2496211 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
2496139 GACTCTCAAC
* * **
2496149 TTTAGATAAAATATTAATTTAATCTTTAAAT
1 TTTAAATAAAATATCAATTTAATCCGTAAAT
2496180 TTTAAATAAAATATCAATTT-ATCACGTAAAT
1 TTTAAATAAAATATCAATTTAATC-CGTAAAT
2496211 T
1 T
2496212 CAATCAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (31 bp):
TTTAAATAAAATATCAATTTAATCCGTAAAT
Found at i:2496538 original size:12 final size:12
Alignment explanation
Indices: 2496521--2496546 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2496511 ATCAAATGTA
2496521 TTTGTTTAGTTT
1 TTTGTTTAGTTT
2496533 TTTGTTTAGTTT
1 TTTGTTTAGTTT
2496545 TT
1 TT
2496547 AATCTCTCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (12 bp):
TTTGTTTAGTTT
Found at i:2505687 original size:15 final size:15
Alignment explanation
Indices: 2505667--2505696 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2505657 AACTTCATAC
2505667 CATCTTCTAGACGCA
1 CATCTTCTAGACGCA
*
2505682 CATCTTCTGGACGCA
1 CATCTTCTAGACGCA
2505697 GACTTTGACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.27
Consensus pattern (15 bp):
CATCTTCTAGACGCA
Found at i:2515348 original size:53 final size:53
Alignment explanation
Indices: 2515291--2515395 Score: 165
Period size: 53 Copynumber: 2.0 Consensus size: 53
2515281 GGTGGTCCTC
* *
2515291 CATTTCTGCACTTTTTTTATTCTTATTTGTACACTTATATTAAATTATGTCCA
1 CATTTCTGCACATTTTTTATGCTTATTTGTACACTTATATTAAATTATGTCCA
* * *
2515344 CATTTCTGCTCATTTTTTATGCTTATTTGTACACTTTTATTAAATTCTGTCC
1 CATTTCTGCACATTTTTTATGCTTATTTGTACACTTATATTAAATTATGTCC
2515396 GGATCCCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.22, C:0.18, G:0.07, T:0.53
Consensus pattern (53 bp):
CATTTCTGCACATTTTTTATGCTTATTTGTACACTTATATTAAATTATGTCCA
Found at i:2516437 original size:27 final size:26
Alignment explanation
Indices: 2516388--2516438 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2516378 TTTTATCCCA
*
2516388 TAAAATTTAATAAGTTATTTCCTACT
1 TAAAATTTAATAAGTTATCTCCTACT
* *
2516414 TAAAATTTTATAAGGTTGTCTCCTA
1 TAAAATTTAATAA-GTTATCTCCTA
2516439 ACATGAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (26 bp):
TAAAATTTAATAAGTTATCTCCTACT
Found at i:2519758 original size:6 final size:6
Alignment explanation
Indices: 2519740--2519780 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
2519730 AAATTCCTGT
*
2519740 AATTTA AATTTTA AATTTA AATTTA AA-TTA TATTT- AATTTA
1 AATTTA AA-TTTA AATTTA AATTTA AATTTA AATTTA AATTTA
2519781 GTTATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 8 0.27
6 16 0.53
7 6 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
AATTTA
Found at i:2519776 original size:11 final size:12
Alignment explanation
Indices: 2519740--2519780 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
2519730 AAATTCCTGT
2519740 AATTTAAATTTTA
1 AATTTAAA-TTTA
2519753 AATTTAAATTTA
1 AATTTAAATTTA
*
2519765 AA-TTATATTT-
1 AATTTAAATTTA
2519775 AATTTA
1 AATTTA
2519781 GTTATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 2 0.08
11 10 0.38
12 6 0.23
13 8 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AATTTAAATTTA
Found at i:2521071 original size:57 final size:59
Alignment explanation
Indices: 2520998--2521158 Score: 175
Period size: 57 Copynumber: 2.7 Consensus size: 59
2520988 ATATGACCTC
* * * * *
2520998 CATTCTAAATTGATCCTTAAGCTTTTGAATATTTCAATTTCATCACAAACTATGA-T-T
1 CATTATAAATTAATCCTTAAACTTTTGAATATTCCAATTTCATCACAAACTAGGACTCT
* * * *
2521055 CATTATAAATTAATCCTCAAAATTTTGAAAATTCCAATTTCATCCATAAACTAGGACTCT
1 CATTATAAATTAATCCTTAAACTTTTGAATATTCCAATTTCAT-CACAAACTAGGACTCT
* * *
2521115 TATTATAAATTAAT-CTTCAAACTTTTTAATCTTCCAATTTCATC
1 CATTATAAATTAATCCTT-AAACTTTTGAATATTCCAATTTCATC
2521159 CCCAAATTCA
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
57 36 0.42
58 10 0.12
59 4 0.05
60 35 0.41
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.41
Consensus pattern (59 bp):
CATTATAAATTAATCCTTAAACTTTTGAATATTCCAATTTCATCACAAACTAGGACTCT
Done.