Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 183 of 189
Found at i:54443264 original size:41 final size:41
Alignment explanation
Indices: 54443216--54443301 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
54443206 TGACATGGGG
54443216 TTATATTTTACACAAATATAATAATCTTCTTGTTTTGCTCA
1 TTATATTTTACACAAATATAATAATCTTCTTGTTTTGCTCA
* *
54443257 TTATATTTTACACAAATATAATATTCTTCTTGTTTTGTTCA
1 TTATATTTTACACAAATATAATAATCTTCTTGTTTTGCTCA
54443298 TTAT
1 TTAT
54443302 TATATTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.30, C:0.13, G:0.05, T:0.52
Consensus pattern (41 bp):
TTATATTTTACACAAATATAATAATCTTCTTGTTTTGCTCA
Found at i:54448464 original size:18 final size:17
Alignment explanation
Indices: 54448420--54448464 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
54448410 CATAACTCTT
*
54448420 AACATAA-CAGATACAA
1 AACATAATCACATACAA
54448436 AACATATATCACATACAGA
1 AACATA-ATCACATACA-A
54448455 AACATAATCA
1 AACATAATCA
54448465 AATGCAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 6 0.24
17 1 0.04
18 11 0.44
19 7 0.28
ACGTcount: A:0.58, C:0.20, G:0.04, T:0.18
Consensus pattern (17 bp):
AACATAATCACATACAA
Found at i:54450212 original size:77 final size:77
Alignment explanation
Indices: 54450085--54450241 Score: 314
Period size: 77 Copynumber: 2.0 Consensus size: 77
54450075 CACAAACATA
54450085 TATCACATGTCACATTATCCCATATTAATTCTCAATCCACAACACACAATTGCATATTTTGCAAA
1 TATCACATGTCACATTATCCCATATTAATTCTCAATCCACAACACACAATTGCATATTTTGCAAA
54450150 TTAAACGAGGGG
66 TTAAACGAGGGG
54450162 TATCACATGTCACATTATCCCATATTAATTCTCAATCCACAACACACAATTGCATATTTTGCAAA
1 TATCACATGTCACATTATCCCATATTAATTCTCAATCCACAACACACAATTGCATATTTTGCAAA
54450227 TTAAACGAGGGG
66 TTAAACGAGGGG
54450239 TAT
1 TAT
54450242 AAGAATGCTT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 80 1.00
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (77 bp):
TATCACATGTCACATTATCCCATATTAATTCTCAATCCACAACACACAATTGCATATTTTGCAAA
TTAAACGAGGGG
Found at i:54451430 original size:2 final size:2
Alignment explanation
Indices: 54451423--54451455 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54451413 GAAGATTGGA
54451423 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 A
54451456 ATACGAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54453774 original size:30 final size:30
Alignment explanation
Indices: 54453728--54453792 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
54453718 TATCGGTTAT
* *
54453728 AAATACATATCATAATAAACAATTACTAAA
1 AAATGCATACCATAATAAACAATTACTAAA
*
54453758 AAATGCATACCATAATAAACAATTACTAGA
1 AAATGCATACCATAATAAACAATTACTAAA
54453788 AAATG
1 AAATG
54453793 TTTAACTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.25
Consensus pattern (30 bp):
AAATGCATACCATAATAAACAATTACTAAA
Found at i:54457044 original size:33 final size:32
Alignment explanation
Indices: 54457003--54457070 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
54456993 AATAAAAGAA
*
54457003 GAAAGCCTCCAATAATCCACTTAGATTGCTCT
1 GAAAGCCTCCAATAATCCACTTAAATTGCTCT
*
54457035 GAAAGGCCTCCAATAATCCACTTAAATTGCTTT
1 GAAA-GCCTCCAATAATCCACTTAAATTGCTCT
54457068 GAA
1 GAA
54457071 TCAAAAGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (32 bp):
GAAAGCCTCCAATAATCCACTTAAATTGCTCT
Found at i:54468259 original size:22 final size:25
Alignment explanation
Indices: 54468234--54468280 Score: 73
Period size: 22 Copynumber: 2.0 Consensus size: 25
54468224 TATAAACATA
54468234 AACATATA-AA-TAAT-TATTATTT
1 AACATATATAATTAATATATTATTT
54468256 AACATATATAATTAATATATTATTT
1 AACATATATAATTAATATATTATTT
54468281 TCTATAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.36
23 2 0.09
24 4 0.18
25 8 0.36
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (25 bp):
AACATATATAATTAATATATTATTT
Found at i:54475897 original size:45 final size:45
Alignment explanation
Indices: 54475847--54475943 Score: 185
Period size: 45 Copynumber: 2.2 Consensus size: 45
54475837 AATTAAAAGG
54475847 TCAATAAAGAAATATATAAAAATAAGCTGTCATGAAAGGACTAAA
1 TCAATAAAGAAATATATAAAAATAAGCTGTCATGAAAGGACTAAA
54475892 TCAATAAAGAAATATATAAAAATAAGCTGTCATGAAAGGACTAAA
1 TCAATAAAGAAATATATAAAAATAAGCTGTCATGAAAGGACTAAA
*
54475937 TTAATAA
1 TCAATAA
54475944 GATCAGGTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (45 bp):
TCAATAAAGAAATATATAAAAATAAGCTGTCATGAAAGGACTAAA
Found at i:54505267 original size:9 final size:9
Alignment explanation
Indices: 54505244--54505287 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
54505234 ATTCGATTTA
*
54505244 AAATTAAGT
1 AAATTAATT
54505253 -AATTAATT
1 AAATTAATT
54505261 AAATTAATT
1 AAATTAATT
54505270 AAATTAATT
1 AAATTAATT
54505279 GAAATTAAT
1 -AAATTAAT
54505288 AATTAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
8 7 0.22
9 17 0.53
10 8 0.25
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (9 bp):
AAATTAATT
Found at i:54509899 original size:40 final size:40
Alignment explanation
Indices: 54509841--54509926 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
54509831 ATACTCTCTA
54509841 TCTGGTGTGTTTCAATTGGATTAGCCCTTATGAGCTTCTG
1 TCTGGTGTGTTTCAATTGGATTAGCCCTTATGAGCTTCTG
* **
54509881 TCTGGTGTGTTTCGATTGGATTAGCTTTTATGAGCTTCTG
1 TCTGGTGTGTTTCAATTGGATTAGCCCTTATGAGCTTCTG
54509921 TCTGGT
1 TCTGGT
54509927 AGGTTCGGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.13, C:0.15, G:0.27, T:0.45
Consensus pattern (40 bp):
TCTGGTGTGTTTCAATTGGATTAGCCCTTATGAGCTTCTG
Found at i:54514166 original size:15 final size:15
Alignment explanation
Indices: 54514143--54514206 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
54514133 TAACTTAAAA
*
54514143 TTCAATACTTAATTT
1 TTCAACACTTAATTT
** *
54514158 TTCAGTACTTATTTT
1 TTCAACACTTAATTT
*
54514173 TTCAACACTTATTTTTT
1 TTCAACACTTA--ATTT
*
54514190 TTCAGCACTTAATTT
1 TTCAACACTTAATTT
54514205 TT
1 TT
54514207 TTAGTTTATC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
15 27 0.66
17 14 0.34
ACGTcount: A:0.25, C:0.16, G:0.03, T:0.56
Consensus pattern (15 bp):
TTCAACACTTAATTT
Found at i:54514191 original size:17 final size:18
Alignment explanation
Indices: 54514169--54514208 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
54514159 TCAGTACTTA
54514169 TTTTTTCAACACTT-ATT
1 TTTTTTCAACACTTAATT
*
54514186 TTTTTTCAGCACTTAATT
1 TTTTTTCAACACTTAATT
54514204 TTTTT
1 TTTTT
54514209 AGTTTATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.20, C:0.15, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTTTCAACACTTAATT
Found at i:54526720 original size:14 final size:14
Alignment explanation
Indices: 54526701--54526740 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
54526691 TTGATTGGCA
54526701 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
54526715 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
54526729 GAAAAATGTTTT
1 GTAAAATGTTTT
54526741 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:54526749 original size:20 final size:20
Alignment explanation
Indices: 54526724--54526763 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54526714 CGTAAAATGA
*
54526724 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
54526744 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
54526764 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:54526753 original size:34 final size:35
Alignment explanation
Indices: 54526709--54526775 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
54526699 CAGTAAAATG
*
54526709 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
54526743 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
54526776 CTAGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:54526887 original size:20 final size:20
Alignment explanation
Indices: 54526862--54526900 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54526852 GTTTTTACAT
54526862 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
54526882 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
54526901 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:54526960 original size:15 final size:15
Alignment explanation
Indices: 54526931--54526983 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 15
54526921 TATTGCAATG
*
54526931 ATTTATTTATAAATAA
1 ATTT-TTTATTAATAA
54526947 ATTTTTTATTAATAAA
1 ATTTTTTATTAAT-AA
54526963 AGTTTTTTATCTAATTAA
1 A-TTTTTTAT-TAA-TAA
54526981 ATT
1 ATT
54526984 CCAAATGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 8 0.25
16 7 0.22
17 10 0.31
18 6 0.19
19 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
ATTTTTTATTAATAA
Found at i:54527174 original size:14 final size:14
Alignment explanation
Indices: 54527155--54527194 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
54527145 TTGATTGCCA
54527155 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
54527169 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
54527183 GGAAAATGTTTT
1 GTAAAATGTTTT
54527195 ACTTTTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:54530033 original size:18 final size:18
Alignment explanation
Indices: 54530012--54530062 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
54530002 AGGAATGAAG
54530012 GAAGGGAGAAGAATGGAT
1 GAAGGGAGAAGAATGGAT
*** *
54530030 GAAGGGAGCTTATTGGAT
1 GAAGGGAGAAGAATGGAT
54530048 GAAGGGAGAAGAATG
1 GAAGGGAGAAGAATG
54530063 CCTGAGAGCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.43, T:0.16
Consensus pattern (18 bp):
GAAGGGAGAAGAATGGAT
Found at i:54530331 original size:14 final size:14
Alignment explanation
Indices: 54530300--54530337 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
54530290 CTATCCACCG
54530300 GAAGAGAG-AAAGA
1 GAAGAGAGAAAAGA
*
54530313 AAAGAGAGAAAAGA
1 GAAGAGAGAAAAGA
*
54530327 GAAGAAAGAAA
1 GAAGAGAGAAA
54530338 GAAAAAATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (14 bp):
GAAGAGAGAAAAGA
Found at i:54530580 original size:60 final size:60
Alignment explanation
Indices: 54530505--54530619 Score: 194
Period size: 60 Copynumber: 1.9 Consensus size: 60
54530495 TTTTTACAAA
* * *
54530505 TATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTACAAATTTTTGTGTTTGTAAT
1 TATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTACAAATTGTTGTGTTTGTAAT
*
54530565 TATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTT
1 TATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTACAAATTGTTGTGTTT
54530620 AGTTTAGTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (60 bp):
TATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTACAAATTGTTGTGTTTGTAAT
Found at i:54531210 original size:21 final size:22
Alignment explanation
Indices: 54531170--54531210 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54531160 TTGACAAATG
*
54531170 TTTTAATTAAAATTATTTAAAA
1 TTTTAATTAAAATAATTTAAAA
54531192 TTTTAATTAAAA-AATTTAA
1 TTTTAATTAAAATAATTTAA
54531211 CACTCACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTAATTAAAATAATTTAAAA
Found at i:54534923 original size:23 final size:23
Alignment explanation
Indices: 54534897--54534995 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
54534887 ATAGGTGCCA
54534897 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54534920 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
54534943 CACTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54534966 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54534989 CACTGAT
1 CACTGAT
54534996 CAATAACACT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:54535247 original size:18 final size:17
Alignment explanation
Indices: 54535221--54535259 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
54535211 ATTTTCCTTC
54535221 CACATTCAA-TAATAATT
1 CACATTCAAGT-ATAATT
54535238 CACATATCAAGTATAATT
1 CACAT-TCAAGTATAATT
54535256 CACA
1 CACA
54535260 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 14 0.70
19 1 0.05
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.31
Consensus pattern (17 bp):
CACATTCAAGTATAATT
Found at i:54537165 original size:33 final size:33
Alignment explanation
Indices: 54537128--54537199 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
54537118 TCCTAACTCA
* *
54537128 TATCCACCTCAGTACTCCGCTCCTTCCGGCTCG
1 TATCCACCTCAGTACTCCGCTCCTTCCGACCCG
* *
54537161 TATCCACCTCAGTACTTCGCTCCTTTCGACCCG
1 TATCCACCTCAGTACTCCGCTCCTTCCGACCCG
54537194 TATCCA
1 TATCCA
54537200 TCGCCGTACT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.15, C:0.43, G:0.12, T:0.29
Consensus pattern (33 bp):
TATCCACCTCAGTACTCCGCTCCTTCCGACCCG
Found at i:54537209 original size:33 final size:33
Alignment explanation
Indices: 54537128--54537211 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
54537118 TCCTAACTCA
* * *
54537128 TATCCACCTCAGTACTCCGCTCCTTCCGGCTCG
1 TATCCACCGCAGTACTCCGCTCCTTCCGACCCG
* * *
54537161 TATCCACCTCAGTACTTCGCTCCTTTCGACCCG
1 TATCCACCGCAGTACTCCGCTCCTTCCGACCCG
* *
54537194 TATCCATCGCCGTACTCC
1 TATCCACCGCAGTACTCC
54537212 ACTACTCCCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.14, C:0.44, G:0.13, T:0.29
Consensus pattern (33 bp):
TATCCACCGCAGTACTCCGCTCCTTCCGACCCG
Found at i:54551912 original size:79 final size:79
Alignment explanation
Indices: 54551781--54551938 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
54551771 CCCTTATGAG
54551781 AACTTCCTAGGATTTTCAAGCCTAGGATTTAGAAACGCATAATCTATACCAACTAATCCTATTAT
1 AACTTCCTAGGATTTTCAAGCCTAGGATTTAGAAACGCATAATCTATACCAACTAATCCTATTAT
*
54551846 GACCTCGTATTCTT
66 GAACTCGTATTCTT
54551860 AACTTCCTAGGATTTTCAAGCCTAGGATTTAGAAACGCATAATCTATACCAACTAATCCTATTAT
1 AACTTCCTAGGATTTTCAAGCCTAGGATTTAGAAACGCATAATCTATACCAACTAATCCTATTAT
54551925 GAACTCGTATTCTT
66 GAACTCGTATTCTT
54551939 TTGTTAATTA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.34
Consensus pattern (79 bp):
AACTTCCTAGGATTTTCAAGCCTAGGATTTAGAAACGCATAATCTATACCAACTAATCCTATTAT
GAACTCGTATTCTT
Found at i:54562634 original size:2 final size:2
Alignment explanation
Indices: 54562627--54562657 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54562617 TTGTGATTTC
54562627 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 A
54562658 ACTTTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54562866 original size:25 final size:26
Alignment explanation
Indices: 54562848--54562897 Score: 84
Period size: 25 Copynumber: 1.9 Consensus size: 26
54562838 ATCTAGAATC
54562848 TAAACCCTAAAC-TAAATCTAAACAT
1 TAAACCCTAAACATAAATCTAAACAT
54562873 TAAACCCTAAACATAAACTCTAAAC
1 TAAACCCTAAACATAAA-TCTAAAC
54562898 CCAAACCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 12 0.52
26 4 0.17
27 7 0.30
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (26 bp):
TAAACCCTAAACATAAATCTAAACAT
Found at i:54562889 original size:13 final size:13
Alignment explanation
Indices: 54562848--54562897 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
54562838 ATCTAGAATC
54562848 TAAACCCTAAAC-
1 TAAACCCTAAACA
*
54562860 TAAA-TCTAAACA
1 TAAACCCTAAACA
54562872 TTAAACCCTAAACA
1 -TAAACCCTAAACA
*
54562886 TAAACTCTAAAC
1 TAAACCCTAAAC
54562898 CCAAACCTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
11 6 0.19
12 4 0.12
13 15 0.47
14 7 0.22
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (13 bp):
TAAACCCTAAACA
Found at i:54565543 original size:20 final size:20
Alignment explanation
Indices: 54565509--54565550 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
54565499 AATTATTTAA
** *
54565509 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
54565529 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
54565549 AT
1 AT
54565551 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:54568918 original size:41 final size:41
Alignment explanation
Indices: 54568873--54569017 Score: 236
Period size: 41 Copynumber: 3.5 Consensus size: 41
54568863 GACTTTAAGT
*
54568873 CTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
54568914 CTAGCAGGCTAAGTGGCGATGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
54568955 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
54568996 CTAGCAGGCTAATTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
54569018 ATATGTTAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:54571907 original size:21 final size:21
Alignment explanation
Indices: 54571877--54571924 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
54571867 AACAAATAGA
*
54571877 AAACACAAAGAAATTCTTGCC
1 AAACAAAAAGAAATTCTTGCC
*
54571898 AAACAAAAAGAAATTCTTGTC
1 AAACAAAAAGAAATTCTTGCC
54571919 AAACAA
1 AAACAA
54571925 CTTTGCTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.54, C:0.19, G:0.08, T:0.19
Consensus pattern (21 bp):
AAACAAAAAGAAATTCTTGCC
Found at i:54573423 original size:20 final size:20
Alignment explanation
Indices: 54573389--54573430 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
54573379 AACTATTTAA
** *
54573389 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
54573409 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
54573429 AT
1 AT
54573431 GTATTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:54583700 original size:20 final size:20
Alignment explanation
Indices: 54583648--54583701 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
54583638 GTATAAACTT
54583648 ATAAAA-ATTATAAAATTTA
1 ATAAAATATTATAAAATTTA
54583667 ATAAAATATT-TAAAACTTTCA
1 ATAAAATATTATAAAA-TTT-A
54583688 AT-AAAT-TTATAAAA
1 ATAAAATATTATAAAA
54583702 AAATATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 13 0.42
20 15 0.48
21 3 0.10
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAAAATATTATAAAATTTA
Found at i:54583723 original size:10 final size:9
Alignment explanation
Indices: 54583542--54583773 Score: 67
Period size: 9 Copynumber: 24.0 Consensus size: 9
54583532 TATTTTTCTC
*
54583542 ATAAAAATC
1 ATAAAAATT
*
54583551 ATAAAAAATA
1 AT-AAAAATT
54583561 ATAAAAAGATT
1 AT-AAAA-ATT
* *
54583572 ATAATAATC
1 ATAAAAATT
*
54583581 AT-AAAATG
1 ATAAAAATT
*
54583589 ATAAAAAAT
1 ATAAAAATT
*
54583598 ATTAAATATT
1 A-TAAAAATT
*
54583608 ACATATTAAAAAT
1 --ATA--AAAATT
*
54583621 ATAAAAAGT
1 ATAAAAATT
*
54583630 A-AAAATTT
1 ATAAAAATT
* *
54583638 GTATAAACTT
1 ATA-AAAATT
54583648 ATAAAAATT
1 ATAAAAATT
*
54583657 ATAAAATTT
1 ATAAAAATT
54583666 AATAAAATATT
1 -ATAAAA-ATT
*
54583677 -TAAAACTT
1 ATAAAAATT
54583685 -TCAATAAATTT
1 AT-AA-AAA-TT
54583696 ATAAAAAAATAT
1 AT--AAAAAT-T
*
54583708 AAAAAAATT
1 ATAAAAATT
54583717 CATAAAAACTT
1 -ATAAAAA-TT
*
54583728 ATAAATATT
1 ATAAAAATT
**
54583737 ATAAAGCTT
1 ATAAAAATT
*
54583746 ATGAATAATT
1 AT-AAAAATT
**
54583756 ATAAAGCTT
1 ATAAAAATT
54583765 ATAAAAATT
1 ATAAAAATT
54583774 TTAATAAGAG
Statistics
Matches: 165, Mismatches: 37, Indels: 42
0.68 0.15 0.17
Matches are distributed among these distances:
8 14 0.08
9 61 0.37
10 61 0.37
11 16 0.10
12 7 0.04
13 6 0.04
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:54583740 original size:19 final size:18
Alignment explanation
Indices: 54583642--54583769 Score: 71
Period size: 19 Copynumber: 6.6 Consensus size: 18
54583632 AAATTTGTAT
*
54583642 AAACTTATAAAAATTATA
1 AAACTTATAAATATTATA
*
54583660 AAATTTAATAAAATATT-TA
1 AAACTT-AT-AAATATTATA
54583679 AAACTTTCAATAAAT-TTATAAA
1 AAAC-TT--ATAAATATTAT--A
* * *
54583701 AAAATATAAAAAAATTCATAA
1 AAACT-TATAAATATT-AT-A
54583722 AAACTTATAAATATTATA
1 AAACTTATAAATATTATA
* *
54583740 AAGCTTATGAATAATTATA
1 AAACTTATAAAT-ATTATA
*
54583759 AAGCTTATAAA
1 AAACTTATAAA
54583770 AATTTTAATA
Statistics
Matches: 87, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
18 16 0.18
19 27 0.31
20 25 0.29
21 12 0.14
22 7 0.08
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.34
Consensus pattern (18 bp):
AAACTTATAAATATTATA
Found at i:54590830 original size:7 final size:7
Alignment explanation
Indices: 54590818--54590843 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54590808 GTATAGAAAA
54590818 TAAAATT
1 TAAAATT
54590825 TAAAATT
1 TAAAATT
54590832 TAAAATT
1 TAAAATT
54590839 TAAAA
1 TAAAA
54590844 CATATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
TAAAATT
Found at i:54594117 original size:24 final size:24
Alignment explanation
Indices: 54594082--54594130 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
54594072 GAGGATGACC
* *
54594082 CAGAATTGGCAA-TTGCTTTGATAG
1 CAGAATTAGCAACTTG-TTTCATAG
54594106 CAGAATTAGCAACTTGTTTCATAG
1 CAGAATTAGCAACTTGTTTCATAG
54594130 C
1 C
54594131 CATATCTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (24 bp):
CAGAATTAGCAACTTGTTTCATAG
Found at i:54597944 original size:23 final size:23
Alignment explanation
Indices: 54597918--54597993 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
54597908 ATAAGTGCCA
54597918 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54597941 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54597964 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54597987 CACTGAT
1 CACTGAT
54597994 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:54598093 original size:8 final size:8
Alignment explanation
Indices: 54598080--54598108 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
54598070 ACCCGGGACT
54598080 CACTGTAA
1 CACTGTAA
54598088 CACTGTAA
1 CACTGTAA
54598096 CACTGTAA
1 CACTGTAA
54598104 CACTG
1 CACTG
54598109 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:54598239 original size:18 final size:17
Alignment explanation
Indices: 54598213--54598251 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
54598203 ATTTTCCTTC
54598213 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
54598230 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
54598248 CACA
1 CACA
54598252 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:54605280 original size:23 final size:23
Alignment explanation
Indices: 54605254--54605329 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
54605244 ATAAGTGCCA
54605254 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54605277 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54605300 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54605323 CACTGAT
1 CACTGAT
54605330 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:54605429 original size:8 final size:8
Alignment explanation
Indices: 54605416--54605444 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
54605406 ACCCGGGACT
54605416 CACTGTAA
1 CACTGTAA
54605424 CACTGTAA
1 CACTGTAA
54605432 CACTGTAA
1 CACTGTAA
54605440 CACTG
1 CACTG
54605445 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:54605575 original size:18 final size:17
Alignment explanation
Indices: 54605549--54605587 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
54605539 ATTTTCCTTC
54605549 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
54605566 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
54605584 CACA
1 CACA
54605588 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:54606912 original size:18 final size:18
Alignment explanation
Indices: 54606870--54606912 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
54606860 GCCGGTGCGG
* *
54606870 TGGCCGATGATCGGGCCC
1 TGGCCGGTGAACGGGCCC
54606888 TGGCCGGTGAACGGGCCC
1 TGGCCGGTGAACGGGCCC
54606906 TGGCCGG
1 TGGCCGG
54606913 ACTAATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.09, C:0.33, G:0.44, T:0.14
Consensus pattern (18 bp):
TGGCCGGTGAACGGGCCC
Found at i:54609452 original size:15 final size:15
Alignment explanation
Indices: 54609432--54609472 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
54609422 TTTATTGATT
54609432 TTTTTATATTATTTA
1 TTTTTATATTATTTA
54609447 TTTTTA-ATGTA-TTA
1 TTTTTATAT-TATTTA
*
54609461 TTTTTCTATTAT
1 TTTTTATATTAT
54609473 AATTATTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTTTATATTATTTA
Found at i:54613165 original size:33 final size:33
Alignment explanation
Indices: 54613083--54613165 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
54613073 TGGTCCAACC
* ** *
54613083 ATGGTCTTACGTTTAAGGTGTCATAACCCAGTT
1 ATGGTCTTACATTTAAAATGTCATAACCCAGCT
* **
54613116 ATGGTCTTTTCA-TTAAAATGTCATGGCCCAGCT
1 ATGGTC-TTACATTTAAAATGTCATAACCCAGCT
54613149 ATGGTCTTACATTTAAA
1 ATGGTCTTACATTTAAA
54613166 CATTGCCATA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
32 4 0.10
33 33 0.82
34 3 0.08
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (33 bp):
ATGGTCTTACATTTAAAATGTCATAACCCAGCT
Found at i:54617637 original size:40 final size:40
Alignment explanation
Indices: 54617575--54617669 Score: 127
Period size: 40 Copynumber: 2.3 Consensus size: 40
54617565 CTTTTCTTTC
* *
54617575 TTTCTTTCCTTCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
1 TTTCTTT-CTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
* * *
54617616 TTTCTTTCTTTCTCCCTTCTCTGTTTTGTTTTGCTCTTTT
1 TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
54617656 TTTCTTTTCTTTCT
1 TTTC-TTTCTTTCT
54617670 TTCTTTGTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 32 0.67
41 16 0.33
ACGTcount: A:0.00, C:0.27, G:0.07, T:0.65
Consensus pattern (40 bp):
TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
Found at i:54620096 original size:13 final size:14
Alignment explanation
Indices: 54620080--54620112 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54620070 AATAAATATA
54620080 TATTTTTT-ATTTT
1 TATTTTTTAATTTT
54620093 TATTTTTTAATTTT
1 TATTTTTTAATTTT
*
54620107 AATTTT
1 TATTTT
54620113 AAAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:54622030 original size:9 final size:8
Alignment explanation
Indices: 54622010--54622034 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54622000 TTTCTTAAAC
54622010 TTTTTTAA
1 TTTTTTAA
54622018 TTTTTTAA
1 TTTTTTAA
54622026 TTTTTTAA
1 TTTTTTAA
54622034 T
1 T
54622035 CGGATTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTAA
Found at i:54635047 original size:15 final size:15
Alignment explanation
Indices: 54635027--54635059 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
54635017 AATCCTTTAA
54635027 AAACTA-TAAAAATAT
1 AAACTATTAAAAAT-T
54635042 AAACTATTAAAAATT
1 AAACTATTAAAAATT
54635057 AAA
1 AAA
54635060 AATTCATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (15 bp):
AAACTATTAAAAATT
Found at i:54652308 original size:21 final size:21
Alignment explanation
Indices: 54652284--54652323 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
54652274 TAACTCTAAC
54652284 ATTTATAAAA-TTTATAATTAA
1 ATTT-TAAAACTTTATAATTAA
*
54652305 ATTTTAAAACTTTTTAATT
1 ATTTTAAAACTTTATAATT
54652324 CTTAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTTAAAACTTTATAATTAA
Found at i:54652558 original size:26 final size:24
Alignment explanation
Indices: 54652510--54652558 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
54652500 GCTGAATCGG
* *
54652510 TTTTATAAATTTCTTATTTTTAAC
1 TTTTATAAATTTATTATTGTTAAC
54652534 TTTTATAAACTTTAATTATTGTTAA
1 TTTTATAAA-TTT-ATTATTGTTAA
54652559 TCTCGCAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 3 0.14
26 9 0.43
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTTATAAATTTATTATTGTTAAC
Found at i:54653233 original size:19 final size:19
Alignment explanation
Indices: 54653209--54653263 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
54653199 AATACCCTTT
54653209 TTTTTATAAATAA-TATATA
1 TTTTTATAAATAATTAT-TA
*
54653228 TTTTTATCAATAATTATTA
1 TTTTTATAAATAATTATTA
* *
54653247 TTTTAAAAAAT-ATTATT
1 TTTTTATAAATAATTATT
54653264 TCAATATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 6 0.19
19 22 0.71
20 3 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTTATAAATAATTATTA
Found at i:54661491 original size:24 final size:24
Alignment explanation
Indices: 54661438--54661507 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
54661428 TAAAATCATT
**
54661438 TAATTTATTATTTATTATTATCTTA
1 TAATTTATTATACATTATTAT-TTA
* *
54661463 -GATTTATTATGCATTATTATTTA
1 TAATTTATTATACATTATTATTTA
*
54661486 TAATTTATCA-ACATTATTATTT
1 TAATTTATTATACATTATTATTT
54661508 TAAATTCATC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
23 14 0.37
24 24 0.63
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.59
Consensus pattern (24 bp):
TAATTTATTATACATTATTATTTA
Found at i:54661513 original size:23 final size:24
Alignment explanation
Indices: 54661451--54661586 Score: 77
Period size: 24 Copynumber: 5.8 Consensus size: 24
54661441 TTTATTATTT
* * * *
54661451 ATTATTATCTTAGATTTATTATGC
1 ATTATTATTTTAAATTTATCATAC
54661475 ATTATTA-TTTATAATTTATCA-AC
1 ATTATTATTTTA-AATTTATCATAC
*
54661498 ATTATTATTTTAAATTCATCATTAAC
1 ATTATTATTTTAAATTTATCA-T-AC
* * **
54661524 ATTAATA-TTT---TTAATCATGT
1 ATTATTATTTTAAATTTATCATAC
** * *
54661544 ATTATTATTTTAAACGTATCACAT
1 ATTATTATTTTAAATTTATCATAC
*
54661568 ATTATTATTTTAAAATTAT
1 ATTATTATTTTAAATTTAT
54661587 TATCAAAATT
Statistics
Matches: 86, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
20 6 0.07
21 4 0.05
22 6 0.07
23 19 0.22
24 40 0.47
25 3 0.03
26 8 0.09
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (24 bp):
ATTATTATTTTAAATTTATCATAC
Found at i:54674397 original size:12 final size:12
Alignment explanation
Indices: 54674380--54674409 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
54674370 TGCATAGTGA
54674380 GGGAGTATGTGC
1 GGGAGTATGTGC
54674392 GGGAGTATGTGC
1 GGGAGTATGTGC
54674404 GGGAGT
1 GGGAGT
54674410 TTAGTGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.07, G:0.53, T:0.23
Consensus pattern (12 bp):
GGGAGTATGTGC
Found at i:54675801 original size:11 final size:11
Alignment explanation
Indices: 54675785--54675825 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
54675775 TACTACAACA
54675785 AAAAGAAAAAG
1 AAAAGAAAAAG
54675796 AAAAGAAAAAG
1 AAAAGAAAAAG
54675807 -AAAG-AAAAG
1 AAAAGAAAAAG
*
54675816 AAGAGAAAAA
1 AAAAGAAAAA
54675826 AATGAAAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 5 0.19
10 7 0.26
11 15 0.56
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:54678009 original size:50 final size:50
Alignment explanation
Indices: 54677894--54678128 Score: 371
Period size: 50 Copynumber: 4.7 Consensus size: 50
54677884 GATAATAACA
* ** * *
54677894 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * *
54677945 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
54677995 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
54678045 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
54678095 TGCCAACGCCATGTCCCAGACATGGTCTTACATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATG
54678129 TCCCAGACAT
Statistics
Matches: 170, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
50 137 0.81
51 33 0.19
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:54678130 original size:21 final size:21
Alignment explanation
Indices: 54678104--54678149 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
54678094 GTGCCAACGC
54678104 CATGTCCCAGACATGGTCTTA
1 CATGTCCCAGACATGGTCTTA
54678125 CATGTCCCAGACATGGTCTTA
1 CATGTCCCAGACATGGTCTTA
54678146 CATG
1 CATG
54678150 GGACCTCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (21 bp):
CATGTCCCAGACATGGTCTTA
Found at i:54678170 original size:71 final size:71
Alignment explanation
Indices: 54678054--54678199 Score: 283
Period size: 71 Copynumber: 2.1 Consensus size: 71
54678044 GTGCCAATGC
54678054 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATG
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATG
54678119 GTCTTA
66 GTCTTA
*
54678125 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAGACATG
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATG
54678190 GTCTTA
66 GTCTTA
54678196 CATG
1 CATG
54678200 GGACCTCTTT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26
Consensus pattern (71 bp):
CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATG
GTCTTA
Found at i:54678323 original size:13 final size:13
Alignment explanation
Indices: 54678302--54678332 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
54678292 GCTTAGATCA
*
54678302 TCATCAAATAAAT
1 TCATAAAATAAAT
54678315 TCATAAAATAAAT
1 TCATAAAATAAAT
54678328 TCATA
1 TCATA
54678333 GTTGCTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:54688084 original size:29 final size:30
Alignment explanation
Indices: 54688025--54688082 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
54688015 TCCGAGCCTT
*
54688025 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
54688055 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
54688083 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:54688312 original size:13 final size:13
Alignment explanation
Indices: 54688294--54688325 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
54688284 TTTCCAGCAA
54688294 TTATGAATTTATT
1 TTATGAATTTATT
54688307 TTATGAATTTATT
1 TTATGAATTTATT
*
54688320 TGATGA
1 TTATGA
54688326 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:54688533 original size:50 final size:50
Alignment explanation
Indices: 54688420--54688661 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
54688410 ATTTGGGTAA
* * *
54688420 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
54688476 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
54688526 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
54688576 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
54688626 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
54688662 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:54688609 original size:100 final size:103
Alignment explanation
Indices: 54688420--54688669 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
54688410 ATTTGGGTAA
54688420 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
54688485 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
54688526 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
54688588 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
54688626 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
54688670 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:54692874 original size:13 final size:13
Alignment explanation
Indices: 54692856--54692886 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
54692846 TTTCCAGCAA
54692856 TATGAATTTATTT
1 TATGAATTTATTT
54692869 TATGAATTTATTT
1 TATGAATTTATTT
*
54692882 GATGA
1 TATGA
54692887 TGATCCAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:54693055 original size:50 final size:50
Alignment explanation
Indices: 54692980--54693172 Score: 296
Period size: 50 Copynumber: 3.8 Consensus size: 50
54692970 ATTTGGGTAA
54692980 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
54693030 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
54693080 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
54693130 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
54693173 TGTTATTATC
Statistics
Matches: 129, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 95 0.74
51 34 0.26
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:54700852 original size:50 final size:50
Alignment explanation
Indices: 54700737--54701022 Score: 459
Period size: 49 Copynumber: 5.7 Consensus size: 50
54700727 GATAATAACA
* ** * *
54700737 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
54700788 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
54700838 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
54700888 TGCC-ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCTG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
54700937 TGCCAA-GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
54700986 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
54701023 TCTTTTACCC
Statistics
Matches: 218, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
49 95 0.44
50 90 0.41
51 33 0.15
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:54700928 original size:99 final size:98
Alignment explanation
Indices: 54700737--54701022 Score: 464
Period size: 99 Copynumber: 2.9 Consensus size: 98
54700727 GATAATAACA
** * *
54700737 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATGT
1 TGCC-AAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTG-CCATGCCATGT
* *
54700802 CCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
63 CCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
54700838 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCATGCCATGTCC
1 TGCCAA-GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCATGCCATGTCC
*
54700903 CAGACATGGTCTTACATGGGACCTCTCATCTCTG
65 CAGACATGGTCTTACATGGGACCTCTCATCTCGG
54700937 TGCCAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCC
1 TGCCAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCC-ATGCCATGTCC
54701002 CAGACATGGTCTTACATGGGA
65 CAGACATGGTCTTACATGGGA
54701023 TCTTTTACCC
Statistics
Matches: 176, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
98 47 0.27
99 82 0.47
100 13 0.07
101 34 0.19
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.26
Consensus pattern (98 bp):
TGCCAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCATGCCATGTCCC
AGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:54701141 original size:13 final size:13
Alignment explanation
Indices: 54701120--54701151 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
54701110 GCTTGGATCA
*
54701120 TCATCAAATAAAT
1 TCATAAAATAAAT
54701133 TCATAAAATAAAT
1 TCATAAAATAAAT
54701146 TCATAA
1 TCATAA
54701152 TTGCTGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:54702494 original size:21 final size:21
Alignment explanation
Indices: 54702454--54702587 Score: 85
Period size: 21 Copynumber: 6.4 Consensus size: 21
54702444 CAGATACGTC
*
54702454 AACAGAAGCTCA-AA-AGCTG
1 AACAAAAGCTCATAAGAGCTG
54702473 AACAAAAGCTCATAAGAGCTG
1 AACAAAAGCTCATAAGAGCTG
* * *
54702494 AATAGAAA-CTCATAAAAGTTG
1 AACA-AAAGCTCATAAGAGCTG
* * * *
54702515 AATAGAAGCTCGTAAGGGCTG
1 AACAAAAGCTCATAAGAGCTG
* * * *
54702536 AACAGAAACCCCAAAAGAGCTA
1 AACA-AAAGCTCATAAGAGCTG
* * *
54702558 AACAGAAGCTCAAAAGAGCTA
1 AACAAAAGCTCATAAGAGCTG
54702579 AACAGAAAG
1 AACA-AAAG
54702588 TAAAACACGA
Statistics
Matches: 88, Mismatches: 21, Indels: 9
0.75 0.18 0.08
Matches are distributed among these distances:
19 11 0.12
20 4 0.05
21 53 0.60
22 20 0.23
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (21 bp):
AACAAAAGCTCATAAGAGCTG
Found at i:54706157 original size:21 final size:20
Alignment explanation
Indices: 54706105--54706159 Score: 87
Period size: 19 Copynumber: 2.8 Consensus size: 20
54706095 TGCATTGCTT
54706105 TCTTGTTG-TTTTTCAACTC
1 TCTTGTTGCTTTTTCAACTC
54706124 TCTTGTTGC-TTTTCAACTC
1 TCTTGTTGCTTTTTCAACTC
54706143 TCTTGTTGCTATTTTCA
1 TCTTGTTGCT-TTTTCA
54706160 TTTCTAGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 27 0.82
21 6 0.18
ACGTcount: A:0.11, C:0.22, G:0.11, T:0.56
Consensus pattern (20 bp):
TCTTGTTGCTTTTTCAACTC
Found at i:54707370 original size:21 final size:22
Alignment explanation
Indices: 54707341--54707401 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
54707331 ATTGGAAACC
54707341 TAAT-TTTAAATATATTATTTA
1 TAATATTTAAATATATTATTTA
*
54707362 -AATATTTAAATATGTT-TTTA
1 TAATATTTAAATATATTATTTA
* *
54707382 TCATATTATAAACATATTAT
1 TAATATT-TAAATATATTAT
54707402 AATCAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 7 0.22
21 16 0.50
22 8 0.25
23 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (22 bp):
TAATATTTAAATATATTATTTA
Found at i:54707515 original size:6 final size:6
Alignment explanation
Indices: 54707504--54707540 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
54707494 TTTAATCAGT
*
54707504 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TCTTAA T
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA T
54707541 AGTTATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTTAA
Found at i:54707852 original size:13 final size:13
Alignment explanation
Indices: 54707834--54707875 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
54707824 TTTTAAATAA
*
54707834 TTACTATTTATTT
1 TTACTAATTATTT
54707847 TTACTAATTATTAT
1 TTACTAATTATT-T
*
54707861 TT-TTAATTATTT
1 TTACTAATTATTT
54707873 TTA
1 TTA
54707876 AACAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 3 0.12
13 19 0.76
14 3 0.12
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (13 bp):
TTACTAATTATTT
Found at i:54709240 original size:36 final size:36
Alignment explanation
Indices: 54709193--54709262 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
54709183 AAATGAATGA
54709193 AATTTTTAACATAAGAGTCGGTTTGATCTTTGAAGG
1 AATTTTTAACATAAGAGTCGGTTTGATCTTTGAAGG
*
54709229 AATTTTTAACATAAGGGTCGGTTTGATCTTTGAA
1 AATTTTTAACATAAGAGTCGGTTTGATCTTTGAA
54709263 CTAACGTACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (36 bp):
AATTTTTAACATAAGAGTCGGTTTGATCTTTGAAGG
Found at i:54722297 original size:26 final size:26
Alignment explanation
Indices: 54722261--54722315 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
54722251 TAATAAAAGA
54722261 TGTGTAAGTTGTTTGCGTTTTGTTTT
1 TGTGTAAGTTGTTTGCGTTTTGTTTT
54722287 TGTGTAAGTTGTTTGCGTTTTGTTTT
1 TGTGTAAGTTGTTTGCGTTTTGTTTT
54722313 TGT
1 TGT
54722316 ATATTTGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.07, C:0.04, G:0.27, T:0.62
Consensus pattern (26 bp):
TGTGTAAGTTGTTTGCGTTTTGTTTT
Found at i:54726721 original size:47 final size:47
Alignment explanation
Indices: 54726670--54726795 Score: 119
Period size: 47 Copynumber: 2.7 Consensus size: 47
54726660 AAAATTGTAG
* * * *
54726670 CCCTTGAA-CAATTATTGTGAAAGTCAATTTGTTTGGCTTAATAGTAT
1 CCCTTGAAGCAATT-TTATGAAAGCCAATTTGTTTGACGTAATAGTAT
* * * *
54726717 CCCTTAAAGGAGTTTTATGGAAGCCAATTTGTTTGACGTAATAGTAT
1 CCCTTGAAGCAATTTTATGAAAGCCAATTTGTTTGACGTAATAGTAT
* * * * *
54726764 CCCTTGAGGGAATTTTGTGAAATCCAAGTTGT
1 CCCTTGAAGCAATTTTATGAAAGCCAATTTGT
54726796 ATAATGTGAT
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
47 60 0.95
48 3 0.05
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (47 bp):
CCCTTGAAGCAATTTTATGAAAGCCAATTTGTTTGACGTAATAGTAT
Found at i:54734135 original size:15 final size:16
Alignment explanation
Indices: 54734109--54734139 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
54734099 AAATGTAAGT
54734109 TTTAATAATATATAAA
1 TTTAATAATATATAAA
54734125 TTTAA-AATATATAAA
1 TTTAATAATATATAAA
54734140 AATATTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAATAATATATAAA
Found at i:54739976 original size:18 final size:17
Alignment explanation
Indices: 54739948--54739995 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
54739938 TTAGGTCAAC
54739948 AAATAATTTAAAATTATA
1 AAAT-ATTTAAAATTATA
*
54739966 ATAATATTTAAAATTTTA
1 A-AATATTTAAAATTATA
*
54739984 AAATATATAAAA
1 AAATATTTAAAA
54739996 AAAATCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 10 0.37
18 14 0.52
19 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATTTAAAATTATA
Found at i:54739994 original size:17 final size:18
Alignment explanation
Indices: 54739956--54739995 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
54739946 ACAAATAATT
*
54739956 TAAAATTATAATAATATT
1 TAAAATTATAATAATATA
*
54739974 TAAAATTTTAA-AATATA
1 TAAAATTATAATAATATA
54739991 TAAAA
1 TAAAA
54739996 AAAATCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATTATAATAATATA
Found at i:54771886 original size:13 final size:13
Alignment explanation
Indices: 54771868--54771892 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54771858 TATTTTAATA
54771868 TTATTTTGTGTGT
1 TTATTTTGTGTGT
54771881 TTATTTTGTGTG
1 TTATTTTGTGTG
54771893 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:54773512 original size:41 final size:40
Alignment explanation
Indices: 54773467--54773820 Score: 457
Period size: 41 Copynumber: 8.7 Consensus size: 40
54773457 CGGACGTTAC
54773467 GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAA
1 GTCTAGCAGGCTTAATGCCGGTGAA-TAATTCAGACTTTAA
54773508 GTCTAGCAGGCTTAATGCCGGTG-ATACATTTCAGACTTTAA
1 GTCTAGCAGGCTTAATGCCGGTGAATA-A-TTCAGACTTTAA
*
54773549 GTCTAGCAGGCTTAATGCCGGTGATATATTTCAGACTTTAA
1 GTCTAGCAGGCTTAATGCCGGTGA-ATAATTCAGACTTTAA
*
54773590 GTCTAGCAGGCTTAATGCCGGTGATATATTTCAGACTTTAA
1 GTCTAGCAGGCTTAATGCCGGTGA-ATAATTCAGACTTTAA
54773631 GTCTAGCAGGCTTAATGCCGGTG-ATACATTTCAGACTTTAA
1 GTCTAGCAGGCTTAATGCCGGTGAATA-A-TTCAGACTTTAA
* *
54773672 GTCTAACAGGCTTAATGCCGGTGATATATTTCAGACTTTAA
1 GTCTAGCAGGCTTAATGCCGGTGA-ATAATTCAGACTTTAA
* *
54773713 GTCTAGCAGGCTTAATGCCGGTG-ATACATTTCAGACTATAT
1 GTCTAGCAGGCTTAATGCCGGTGAATA-A-TTCAGACTTTAA
* *
54773754 GTCTAGCAGGC-TAAGTGCCGGTGTACTGAA-TCAGGCTTTAA
1 GTCTAGCAGGCTTAA-TGCCGGTG-AAT-AATTCAGACTTTAA
* **
54773795 GCCTAGCAGGCAAAATGCCGGTGAAT
1 GTCTAGCAGGCTTAATGCCGGTGAAT
54773821 CTGTTTAAAT
Statistics
Matches: 283, Mismatches: 15, Indels: 31
0.86 0.05 0.09
Matches are distributed among these distances:
39 8 0.03
40 7 0.02
41 257 0.91
42 2 0.01
43 8 0.03
44 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (40 bp):
GTCTAGCAGGCTTAATGCCGGTGAATAATTCAGACTTTAA
Found at i:54773567 original size:82 final size:83
Alignment explanation
Indices: 54773467--54773820 Score: 517
Period size: 82 Copynumber: 4.3 Consensus size: 83
54773457 CGGACGTTAC
54773467 GTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGT
1 GTCTAGCAGGCTTAATGCCGGTGAA-TACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGT
54773530 GATACATTTCAGACTTTAA
65 GATACATTTCAGACTTTAA
*
54773549 GTCTAGCAGGCTTAATGCCGGTG-ATATATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
1 GTCTAGCAGGCTTAATGCCGGTGAATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
*
54773613 ATATATTTCAGACTTTAA
66 ATACATTTCAGACTTTAA
*
54773631 GTCTAGCAGGCTTAATGCCGGTG-ATACATTTCAGACTTTAAGTCTAACAGGCTTAATGCCGGTG
1 GTCTAGCAGGCTTAATGCCGGTGAATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
*
54773695 ATATATTTCAGACTTTAA
66 ATACATTTCAGACTTTAA
* *
54773713 GTCTAGCAGGCTTAATGCCGGTG-ATACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCGGT
1 GTCTAGCAGGCTTAATGCCGGTGAATACATTTCAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGT
* *
54773776 G-TAC-TGAATCAGGCTTTAA
65 GATACAT--TTCAGACTTTAA
* **
54773795 GCCTAGCAGGCAAAATGCCGGTGAAT
1 GTCTAGCAGGCTTAATGCCGGTGAAT
54773821 CTGTTTAAAT
Statistics
Matches: 254, Mismatches: 12, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
80 3 0.01
81 7 0.03
82 242 0.95
83 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (83 bp):
GTCTAGCAGGCTTAATGCCGGTGAATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
ATACATTTCAGACTTTAA
Found at i:54773686 original size:123 final size:123
Alignment explanation
Indices: 54773467--54773776 Score: 543
Period size: 123 Copynumber: 2.5 Consensus size: 123
54773457 CGGACGTTAC
*
54773467 GTCTAGCAGGCTTAATGCCGGTGA-AGTAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
1 GTCTAGCAGGCTTAATGCCGGTGATA-TATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
*
54773531 ATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATATATTTCAGACTTTAA
65 ATACATTTCAGACTTTAAGTCTAACAGGCTTAATGCCGGTGATATATTTCAGACTTTAA
54773590 GTCTAGCAGGCTTAATGCCGGTGATATATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
1 GTCTAGCAGGCTTAATGCCGGTGATATATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
54773655 TACATTTCAGACTTTAAGTCTAACAGGCTTAATGCCGGTGATATATTTCAGACTTTAA
66 TACATTTCAGACTTTAAGTCTAACAGGCTTAATGCCGGTGATATATTTCAGACTTTAA
* * *
54773713 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 GTCTAGCAGGCTTAATGCCGGTGATATATTTCAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTG
54773777 TACTGAATCA
Statistics
Matches: 180, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
122 3 0.02
123 176 0.98
124 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (123 bp):
GTCTAGCAGGCTTAATGCCGGTGATATATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
TACATTTCAGACTTTAAGTCTAACAGGCTTAATGCCGGTGATATATTTCAGACTTTAA
Found at i:54773793 original size:123 final size:122
Alignment explanation
Indices: 54773467--54773818 Score: 541
Period size: 123 Copynumber: 2.9 Consensus size: 122
54773457 CGGACGTTAC
54773467 GTCTAGCAGGCTTAATGCCGGTGAAGTAA-TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
1 GTCTAGCAGGCTTAATGCCGGTG-A-TAATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
54773531 ATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATATATTTCAGACTTTAA
64 ATACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATATATTTCAGACTTTAA
54773590 GTCTAGCAGGCTTAATGCCGGTGATATATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
1 GTCTAGCAGGCTTAATGCCGGTGATA-ATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
*
54773655 TACATTTCAGACTTTAAGTCTAACAGGCTTAATGCCGGTGATATATTTCAGACTTTAA
65 TACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATATATTTCAGACTTTAA
* *
54773713 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 GTCTAGCAGGCTTAATGCCGGTGATA-ATTTCAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTG
* * * **
54773777 -TAC-TGAATCAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
64 ATACAT--TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
54773819 ATCTGTTTAA
Statistics
Matches: 214, Mismatches: 10, Indels: 10
0.91 0.04 0.04
Matches are distributed among these distances:
121 3 0.01
122 8 0.04
123 203 0.95
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (122 bp):
GTCTAGCAGGCTTAATGCCGGTGATAATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGAT
ACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATATATTTCAGACTTTAA
Found at i:54775194 original size:12 final size:11
Alignment explanation
Indices: 54775179--54775208 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
54775169 AAAAAATAAA
54775179 AAAAAGTATTTT
1 AAAAA-TATTTT
54775191 AAAAATATTTT
1 AAAAATATTTT
54775202 AAAAATA
1 AAAAATA
54775209 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:54776494 original size:16 final size:17
Alignment explanation
Indices: 54776464--54776496 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54776454 GACTATACAT
*
54776464 AAAATTTTAATAAATAA
1 AAAATATTAATAAATAA
54776481 AAAATATTAA-AAATAA
1 AAAATATTAATAAATAA
54776497 TATAAGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATATTAATAAATAA
Found at i:54779073 original size:50 final size:50
Alignment explanation
Indices: 54778962--54779151 Score: 200
Period size: 50 Copynumber: 3.7 Consensus size: 50
54778952 AATGAGATCT
* * * * *
54778962 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAAATGTCC
1 CATGTAAGACCATATCTGGGACATGGCATTGGCACCA---ATA-TAAG-AA-CTCC
* *
54779018 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCAATATAAGAACTCT
1 CATGTAAGACCATATCTGGGACATGGCATTGGCACCAATATAAGAACTCC
* * * * *
54779068 TATGTAAGACCATATCTGGGACATGACATGGGCACCGATATGAGAACTCC
1 CATGTAAGACCATATCTGGGACATGGCATTGGCACCAATATAAGAACTCC
* *
54779118 CATGTAATACCATATCTGGGATATGGCATTGGCA
1 CATGTAAGACCATATCTGGGACATGGCATTGGCA
54779152 GTACAGAAAA
Statistics
Matches: 117, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
50 74 0.63
51 2 0.02
52 3 0.03
53 2 0.02
56 36 0.31
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (50 bp):
CATGTAAGACCATATCTGGGACATGGCATTGGCACCAATATAAGAACTCC
Found at i:54779417 original size:12 final size:12
Alignment explanation
Indices: 54779400--54779431 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
54779390 ACGAGTTATT
*
54779400 TAAGTAAGCAAG
1 TAAGTAAACAAG
54779412 TAAGTAAACAAG
1 TAAGTAAACAAG
54779424 TAAGTAAA
1 TAAGTAAA
54779432 GAAGCGAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (12 bp):
TAAGTAAACAAG
Found at i:54781031 original size:16 final size:15
Alignment explanation
Indices: 54780992--54781034 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
54780982 CCTTAAAATA
54780992 ATAAATTTTTAATTT
1 ATAAATTTTTAATTT
* **
54781007 AGATCTTTTATAATTT
1 ATAAATTTT-TAATTT
54781023 ATAAATTTTTAA
1 ATAAATTTTTAA
54781035 ATTAATAATA
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
ATAAATTTTTAATTT
Found at i:54783078 original size:31 final size:31
Alignment explanation
Indices: 54783043--54783102 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
54783033 ATCATAAAAT
** *
54783043 TATTTGAAAGTTTTTATTTAAATCACTAAAC
1 TATTTGAAAACTTTTATTCAAATCACTAAAC
*
54783074 TATTTGAAAACTTTTATTCAAGTCACTAA
1 TATTTGAAAACTTTTATTCAAATCACTAA
54783103 TTACTTGGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (31 bp):
TATTTGAAAACTTTTATTCAAATCACTAAAC
Found at i:54783780 original size:17 final size:18
Alignment explanation
Indices: 54783749--54783785 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
54783739 TGATTGGCCC
*
54783749 AATTATAAAATTATTAAA
1 AATTATAAAAATATTAAA
54783767 AATTA-AAAAATATTAAA
1 AATTATAAAAATATTAAA
54783784 AA
1 AA
54783786 AGTTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTATAAAAATATTAAA
Found at i:54788227 original size:13 final size:13
Alignment explanation
Indices: 54788209--54788233 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54788199 TTCGAGAGTT
54788209 ATTAATATTTATA
1 ATTAATATTTATA
54788222 ATTAATATTTAT
1 ATTAATATTTAT
54788234 TTACATGTCC
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTAATATTTATA
Found at i:54808058 original size:23 final size:22
Alignment explanation
Indices: 54808006--54808058 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
54807996 TCCACGTCTT
*
54808006 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
54808028 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
54808051 TTTCTTTT
1 TTTCTTTT
54808059 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:54810216 original size:18 final size:17
Alignment explanation
Indices: 54810185--54810218 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54810175 TAAAAATAAA
54810185 ACTTTACAACTTGGCCC
1 ACTTTACAACTTGGCCC
*
54810202 ACTTTGACAATTTGGCC
1 ACTTT-ACAACTTGGCC
54810219 TGATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (17 bp):
ACTTTACAACTTGGCCC
Found at i:54810897 original size:26 final size:27
Alignment explanation
Indices: 54810868--54810926 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
54810858 CCTAAAAATC
54810868 AACTTTTTG-AAACCTTAAAGGAAGTT
1 AACTTTTTGTAAACCTTAAAGGAAGTT
* **
54810894 AAC-TTTTGTCATTCTTAAAGGAAGTT
1 AACTTTTTGTAAACCTTAAAGGAAGTT
*
54810920 GACTTTT
1 AACTTTT
54810927 GTTCATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 5 0.19
26 19 0.70
27 3 0.11
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (27 bp):
AACTTTTTGTAAACCTTAAAGGAAGTT
Found at i:54811554 original size:2 final size:2
Alignment explanation
Indices: 54811547--54811587 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
54811537 GAAAATTCTC
*
54811547 AT AT AT AT GT AT AT A- AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54811587 A
1 A
54811588 GTACTACAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54811573 original size:21 final size:21
Alignment explanation
Indices: 54811547--54811587 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54811537 GAAAATTCTC
*
54811547 ATATATATGTATATAATATAT
1 ATATATATATATATAATATAT
*
54811568 ATATATATATATATATTATA
1 ATATATATATATATAATATA
54811588 GTACTACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATATATATATATATAATATAT
Found at i:54812898 original size:5 final size:6
Alignment explanation
Indices: 54812883--54812907 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
54812873 TGATTAACAA
54812883 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
54812908 GAGAATATAA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:54816444 original size:26 final size:26
Alignment explanation
Indices: 54816407--54816478 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
54816397 TATTTGGACT
54816407 TTTATTTTAAAATTTTTAAATAATTA
1 TTTATTTTAAAATTTTTAAATAATTA
* *
54816433 TTT-TTTTGAAAA-TTTT-ATTAATTT
1 TTTATTTT-AAAATTTTTAAATAATTA
*
54816457 TTTATTTTTAGAATTTTTAAAT
1 TTTA-TTTTAAAATTTTTAAAT
54816479 TTGATATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
24 9 0.24
25 11 0.30
26 15 0.41
27 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (26 bp):
TTTATTTTAAAATTTTTAAATAATTA
Found at i:54817449 original size:7 final size:7
Alignment explanation
Indices: 54817437--54817461 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54817427 AATTCAGTAC
54817437 TTTTATA
1 TTTTATA
54817444 TTTTATA
1 TTTTATA
54817451 TTTTATA
1 TTTTATA
54817458 TTTT
1 TTTT
54817462 TTAATATTAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTATA
Found at i:54819090 original size:24 final size:25
Alignment explanation
Indices: 54819058--54819104 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
54819048 CTTTCGAGTT
*
54819058 AAATTAAAT-AAATATTTTGAATTC
1 AAATTAAATCAAATAATTTGAATTC
*
54819082 AAATTAAATCATATAATTTGAAT
1 AAATTAAATCAAATAATTTGAAT
54819105 AATTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (25 bp):
AAATTAAATCAAATAATTTGAATTC
Found at i:54838914 original size:61 final size:59
Alignment explanation
Indices: 54838844--54839021 Score: 150
Period size: 61 Copynumber: 2.9 Consensus size: 59
54838834 TTGTTAAATT
*
54838844 ATATTTAATAATAATTATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGA
1 ATATTTAATAATAA-TATTTTATA-TATTATATATTATGATTTTAATAAATTCATATAAGA
* * * * * *
54838905 ATATTTAATACTAAGAATTTTATTAAATTATATATT-T--TTGTTAAATTATATTTA-ATAATA
1 ATATTTAATAATAA-TATTTTA-TATATTATATATTATGATT-TT-AA-TAAATTCATATAAGA
* * *
54838965 ATTATTTTA-AATTATATTTTATAATATTATATATTATAATTTTAATAAATTCATATA
1 A-TATTTAATAATAATATTTTAT-ATATTATATATTATGATTTTAATAAATTCATATA
54839022 TTTTATCAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
58 3 0.03
59 25 0.27
60 17 0.18
61 43 0.47
62 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (59 bp):
ATATTTAATAATAATATTTTATATATTATATATTATGATTTTAATAAATTCATATAAGA
Found at i:54838974 original size:26 final size:25
Alignment explanation
Indices: 54838936--54838994 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
54838926 ATTAAATTAT
*
54838936 ATATTTTTGTTAAATTATATTTAATA
1 ATATTATT-TTAAATTATATTTAATA
*
54838962 ATAATTATTTTAAATTATATTTTATA
1 AT-ATTATTTTAAATTATATTTAATA
54838988 ATATTAT
1 ATATTAT
54838995 ATATTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 20 0.67
27 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATATTATTTTAAATTATATTTAATA
Found at i:54838993 original size:15 final size:15
Alignment explanation
Indices: 54838949--54839004 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
54838939 TTTTTGTTAA
*
54838949 ATTATATTTAATAAT
1 ATTATATTTTATAAT
*
54838964 AAT-TA-TTT-TAA-
1 ATTATATTTTATAAT
54838975 ATTATATTTTATAAT
1 ATTATATTTTATAAT
*
54838990 ATTATATATTATAAT
1 ATTATATTTTATAAT
54839005 TTTAATAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.06
12 5 0.15
13 5 0.15
14 5 0.15
15 16 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATATTTTATAAT
Found at i:54839020 original size:24 final size:22
Alignment explanation
Indices: 54838975--54839043 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
54838965 ATTATTTTAA
54838975 ATTATATTTTATAATATTATAT
1 ATTATATTTTATAATATTATAT
* *
54838997 ATTATAATTT-TAATA-AAT-T
1 ATTATATTTTATAATATTATAT
54839016 CA-TATATTTTATCAA-ATTATAT
1 -ATTATATTTTAT-AATATTATAT
54839038 ATTATA
1 ATTATA
54839044 AAAAATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
19 8 0.22
20 5 0.14
21 10 0.27
22 14 0.38
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTATATTTTATAATATTATAT
Found at i:54839039 original size:17 final size:17
Alignment explanation
Indices: 54838921--54839060 Score: 61
Period size: 17 Copynumber: 8.6 Consensus size: 17
54838911 AATACTAAGA
*
54838921 ATTTTATTAAATTATAT
1 ATTTTAATAAATTATAT
**
54838938 ATTTTTGTTAAA-T-TAT
1 A-TTTTAATAAATTATAT
*
54838954 A-TTTAAT-AATAAT-T
1 ATTTTAATAAATTATAT
* *
54838968 ATTTTAAATTATATTTTAT
1 ATTTT-AA-TAAATTATAT
* *
54838987 AATATT-ATATATTATA-
1 -ATTTTAATAAATTATAT
54839003 ATTTTAATAAATTCATAT
1 ATTTTAATAAATT-ATAT
54839021 ATTTT-ATCAAATTATAT
1 ATTTTAAT-AAATTATAT
*
54839038 ATTATAA-AAA--ATAT
1 ATTTTAATAAATTATAT
54839052 A-TTTAATAA
1 ATTTTAATAA
54839061 TAATTATGTT
Statistics
Matches: 95, Mismatches: 13, Indels: 33
0.67 0.09 0.23
Matches are distributed among these distances:
13 6 0.06
14 13 0.14
15 8 0.08
16 15 0.16
17 24 0.25
18 24 0.25
19 1 0.01
20 4 0.04
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
ATTTTAATAAATTATAT
Found at i:54839309 original size:16 final size:16
Alignment explanation
Indices: 54839288--54839355 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
54839278 GATTTGCTAT
54839288 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
* *
54839304 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
54839320 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
54839336 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
54839352 TACA
1 TACA
54839356 GCGAACCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:54848140 original size:15 final size:14
Alignment explanation
Indices: 54848115--54848147 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
54848105 AATCAGCAGC
54848115 AAGAAAAG-A-AAA
1 AAGAAAAGAAGAAA
54848127 AAGAAAAGAAGAAA
1 AAGAAAAGAAGAAA
54848141 AAGAAAA
1 AAGAAAA
54848148 ATACATCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 1 0.05
14 10 0.53
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAGAAA
Found at i:54848826 original size:28 final size:29
Alignment explanation
Indices: 54848768--54848826 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
54848758 AATCCAATCC
*
54848768 TTTTATCTTTTTTTAAATTTAATCTCTCA
1 TTTTATCTTTTTTTAAATTTAATCTCACA
* *
54848797 TTTTAT-TTTTGTTTCATTTTAATC-CACA
1 TTTTATCTTTT-TTTAAATTTAATCTCACA
54848825 TT
1 TT
54848827 AAAGAGCTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.22, C:0.14, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTATCTTTTTTTAAATTTAATCTCACA
Found at i:54849038 original size:18 final size:18
Alignment explanation
Indices: 54849015--54849051 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54849005 TCATCATTAT
54849015 TATTAGTATTAT-TATTTA
1 TATTAGT-TTATATATTTA
54849033 TATTAGTTTATATATTTA
1 TATTAGTTTATATATTTA
54849051 T
1 T
54849052 CTACATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TATTAGTTTATATATTTA
Found at i:54852637 original size:45 final size:45
Alignment explanation
Indices: 54852564--54852739 Score: 239
Period size: 45 Copynumber: 4.0 Consensus size: 45
54852554 GTGTATTGAG
* **
54852564 TATCATTGGTTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGG
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
* * *
54852609 TACCTTTGATTATAAAGGTGGTTGCTATGTGCTGACTCCACCGAA
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
* **
54852654 AATCATTGAAAATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
* *
54852699 TATAATTGATTATAAGGGTGG-TGCTATGTGCTGA-TCCACCG
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCG
54852740 TGTAACGGTT
Statistics
Matches: 114, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
43 7 0.06
44 13 0.11
45 94 0.82
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (45 bp):
TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
Found at i:54870630 original size:3 final size:3
Alignment explanation
Indices: 54870624--54870652 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
54870614 TCAAGACAGG
54870624 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
54870653 GAAGAAGAAC
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:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:54876870 original size:43 final size:43
Alignment explanation
Indices: 54876823--54877008 Score: 189
Period size: 43 Copynumber: 4.3 Consensus size: 43
54876813 AGAACATGAC
* *
54876823 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGTTAAATGTCATGTT
1 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTAAAGGTCATGTT
* * * *
54876866 CTTTAGCTGCATTTGTGAG-AAAAGAGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCGTTT-TTAGTAAAAGCGCCGCTAAAGGTCATGTT
* * *
54876909 CTATT-GCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGTT
1 CT-TTAGCGGCGTTTTTAGTAAAAGCGCCGCTAAAGGTCATGTT
** * * * *
54876952 CTTTAGCAACATTTTTAATAAAAGCACTGCTAAA-GTCCATGTT
1 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTAAAGGT-CATGTT
54876995 CTTTAGCGGCGTTT
1 CTTTAGCGGCGTTT
54877009 GTGGGAAAAT
Statistics
Matches: 114, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
42 5 0.04
43 104 0.91
44 5 0.04
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTAAAGGTCATGTT
Found at i:54876965 original size:86 final size:86
Alignment explanation
Indices: 54876823--54877017 Score: 243
Period size: 86 Copynumber: 2.3 Consensus size: 86
54876813 AGAACATGAC
* * * * * ** *
54876823 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGTTAAATGTCATGTTCTTTAGCTGCATTTGTGAGAAA
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCAACATTTGTAAGAAA
54876888 AG-AGCCGCTAAAGGT-CATGTT
66 AGCA-CCGCTAAA-GTCCATGTT
* *
54876909 CTATT-GCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCAACATTTTTAATAA
1 CT-TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCAACATTTGTAAGAA
*
54876973 AAGCACTGCTAAAGTCCATGTT
65 AAGCACCGCTAAAGTCCATGTT
54876995 CTTTAGCGGCGTTTGTGGGAAAA
1 CTTTAGCGGCGTTTGTGGGAAAA
54877018 TACCACTAAC
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
85 4 0.04
86 87 0.93
87 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (86 bp):
CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCAACATTTGTAAGAAA
AGCACCGCTAAAGTCCATGTT
Found at i:54879055 original size:6 final size:6
Alignment explanation
Indices: 54879044--54879073 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
54879034 TAATACACTA
54879044 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
54879074 TAATCCGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ACTAAT
Found at i:54889425 original size:29 final size:29
Alignment explanation
Indices: 54889383--54889438 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
54889373 GGCAAAATAT
54889383 TTATAAAATTAAAAATA-TGTTATAAAAGC
1 TTATAAAATTAAAAATATTGTT-TAAAAGC
* *
54889412 TTATCAAATTAAAATTATTGTTTAAAA
1 TTATAAAATTAAAAATATTGTTTAAAA
54889439 ATATGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (29 bp):
TTATAAAATTAAAAATATTGTTTAAAAGC
Done.