Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 148 of 297
Found at i:51026129 original size:30 final size:30
Alignment explanation
Indices: 51026093--51026174 Score: 121
Period size: 30 Copynumber: 2.7 Consensus size: 30
51026083 ACTTTTCTCA
*
51026093 ACTAGCCACACCTTTTCCACCACTAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
51026123 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
51026153 ACTAGCCACA-CTTTCTCCACCA
1 ACTAGCCACACCTTT-TCCACCA
51026175 TCACTTGTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 3 0.07
30 43 0.93
ACGTcount: A:0.26, C:0.46, G:0.04, T:0.24
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:51038717 original size:3 final size:3
Alignment explanation
Indices: 51038711--51038736 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
51038701 ACTTTGTTGT
51038711 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
51038737 CAAGTGTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:51045326 original size:16 final size:16
Alignment explanation
Indices: 51045302--51045332 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51045292 ATTAATTTAT
*
51045302 TATTTTTCTTCTGTTA
1 TATTCTTCTTCTGTTA
51045318 TATTCTTCTTCTGTT
1 TATTCTTCTTCTGTT
51045333 GTACTCTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.16, G:0.06, T:0.68
Consensus pattern (16 bp):
TATTCTTCTTCTGTTA
Found at i:51045340 original size:16 final size:16
Alignment explanation
Indices: 51045307--51045340 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
51045297 TTTATTATTT
*
51045307 TTCTTCTGTTATATTC
1 TTCTTCTGTTATACTC
*
51045323 TTCTTCTGTTGTACTC
1 TTCTTCTGTTATACTC
51045339 TT
1 TT
51045341 TGGAACTGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.21, G:0.09, T:0.62
Consensus pattern (16 bp):
TTCTTCTGTTATACTC
Found at i:51055187 original size:64 final size:65
Alignment explanation
Indices: 51055119--51055247 Score: 217
Period size: 64 Copynumber: 2.0 Consensus size: 65
51055109 TTTTTTGGGG
51055119 GAGAAATAAAAAAAAGAAGAGATAGAAG-AAAAAAAGTGTAATCTCTCTGAA-ATTTTTCTTTAA
1 GAGAAATAAAAAAAA-AAGAGATAGAAGAAAAAAAAGTGTAATCTCTCTGAAGATTTTTCTTTAA
51055182 A
65 A
* *
51055183 GAGAAATAAAAAAAAAATAGATTGAAGAAAAAAAAGTGTAATCTCTCTGAAGATTTTTCTTTAAA
1 GAGAAATAAAAAAAAAAGAGATAGAAGAAAAAAAAGTGTAATCTCTCTGAAGATTTTTCTTTAAA
51055248 AAAAACATCA
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
63 10 0.16
64 38 0.62
65 13 0.21
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (65 bp):
GAGAAATAAAAAAAAAAGAGATAGAAGAAAAAAAAGTGTAATCTCTCTGAAGATTTTTCTTTAAA
Found at i:51055343 original size:11 final size:12
Alignment explanation
Indices: 51055322--51055355 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
51055312 CGGCTTAAGG
51055322 TTTTTTCTTTTC
1 TTTTTTCTTTTC
51055334 TTTTTT-TTTTC
1 TTTTTTCTTTTC
51055345 TTTTTTCTTTT
1 TTTTTTCTTTT
51055356 ATTATTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:51067018 original size:17 final size:17
Alignment explanation
Indices: 51066996--51067033 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
51066986 TATTTATATA
* *
51066996 TTAATATATTTTTTATC
1 TTAATAGATTTCTTATC
51067013 TTAATAGATTTCTTATC
1 TTAATAGATTTCTTATC
51067030 TTAA
1 TTAA
51067034 AATACTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (17 bp):
TTAATAGATTTCTTATC
Found at i:51067554 original size:130 final size:130
Alignment explanation
Indices: 51067388--51067759 Score: 458
Period size: 130 Copynumber: 2.9 Consensus size: 130
51067378 AAAATTCTTC
*
51067388 AAAACGAAGACGAAATTTGATGTTTTGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * *
51067453 TTTCGCATTTGCTCAAAATAATTGAATTTCCCTTCGAAATTCCATTCATATCTTTTAAAATCCCT
66 TTTCGCATTTGCTCAAAATAATCGAATATCACTTCAAAATTCCACTCATATCTTTTAAAATCCCT
* * * *
51067518 TAAACGAAGATGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCGA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * *
51067583 TTTCGCATTTGCTCAAAATAATCGAATATCACTTTAAAATTTCGCTCGTGTCTTTTAAAATCCCT
66 TTTCGCATTTGCTCAAAATAATCGAATATCACTTCAAAATTCCACTCATATCTTTTAAAATCCCT
* * * * * * * *
51067648 AAAACGAAGGCGATATCTGGTATTTGGCAATTCGTGGGATCGTGCCCTAACGTGTTGGGTAGCAA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * * * *
51067713 TTTCTCGA-TTGTTTAAAATAATCAAATACCCCTTCAAAATTTCACTC
66 TTTCGC-ATTTGCTCAAAATAATCGAATATCACTTCAAAATTCCACTC
51067760 GGCTCTTCTA
Statistics
Matches: 207, Mismatches: 34, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
130 206 1.00
131 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (130 bp):
AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
TTTCGCATTTGCTCAAAATAATCGAATATCACTTCAAAATTCCACTCATATCTTTTAAAATCCCT
Found at i:51067856 original size:131 final size:130
Alignment explanation
Indices: 51067415--51067866 Score: 381
Period size: 130 Copynumber: 3.5 Consensus size: 130
51067405 TGATGTTTTG
* * * * * *
51067415 CAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGCTCAAAATAATTGAAT
1 CAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCGATTTCTCGTTTGTTCAAAATAA-TCAAA
* * * * * * * * *** * * * * *
51067480 TTCC-CTTCGAAATTCCATTCATATCTTTTAAAATCCCTTAAACGAAGATGAGATTTGATGTTTG
65 TACCACTTCAAAATTTCACTCGTGTCTTTAAAAATCCCTAAAACGAAGGCAATATCTGGTATTCG
*
51067544 G
130 A
* * * *
51067545 CAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCGATTTCGCATTTGCTCAAAATAATCGAAT
1 CAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCGATTTCTCGTTTGTTCAAAATAATCAAAT
* * * * * * *
51067610 ATCACTTTAAAATTTCGCTCGTGTCTTTTAAAATCCCTAAAACGAAGGCGATATCTGGTATTTGG
66 ACCACTTCAAAATTTCACTCGTGTCTTTAAAAATCCCTAAAACGAAGGCAATATCTGGTATTCGA
* * * * * *
51067675 CAATTCGTGGGATCGTGCCCTAACGTGTTGGGTAGCAATTTCTCGATTGTTTAAAATAATCAAAT
1 CAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCGATTTCTCGTTTGTTCAAAATAATCAAAT
* * * *
51067740 ACCCCTTCAAAATTTCACTCG-GCTCTTCTAAAAATCCTTTAAAACGAGGGCAATA-CTCGGTGT
66 ACCACTTCAAAATTTCACTCGTG-TCTT-TAAAAATCC-CTAAAACGAAGGCAATATCT-GGTAT
51067803 TCGA
127 TCGA
* * * * * *
51067807 CAATTCG-GGAATCATGCCTTATCGTGCTGGGTTGTGATTTCTCGTTTGTTCAAAACAATC
1 CAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCGATTTCTCGTTTGTTCAAAATAATC
51067867 GAGTATTCCT
Statistics
Matches: 265, Mismatches: 52, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
129 5 0.02
130 181 0.68
131 52 0.20
132 27 0.10
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (130 bp):
CAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCGATTTCTCGTTTGTTCAAAATAATCAAAT
ACCACTTCAAAATTTCACTCGTGTCTTTAAAAATCCCTAAAACGAAGGCAATATCTGGTATTCGA
Found at i:51076314 original size:108 final size:108
Alignment explanation
Indices: 51076125--51076341 Score: 398
Period size: 108 Copynumber: 2.0 Consensus size: 108
51076115 AGGTATCTCT
* *
51076125 TTAATTAGACTTGATAGACAACATAATATTCCCTTGAATCGATTTGCTTATTTTGCTTAATTCGT
1 TTAATTAGACTTGATAGACAACATAATAGTCCCTTGAATCAATTTGCTTATTTTGCTTAATTCGT
51076190 CCACTTTATGCAACTTAATATTAGTTAAATGTTAGATAATAGG
66 CCACTTTATGCAACTTAATATTAGTTAAATGTTAGATAATAGG
*
51076233 TTAATTAGACTTGATAGACGACATAATAGTCCCTTGAATCAATTTGCTTATTTTGCTTAATTCGT
1 TTAATTAGACTTGATAGACAACATAATAGTCCCTTGAATCAATTTGCTTATTTTGCTTAATTCGT
*
51076298 CCATTTTATGCAACTTAATATTAGTTAAATGTTAGATAATAGG
66 CCACTTTATGCAACTTAATATTAGTTAAATGTTAGATAATAGG
51076341 T
1 T
51076342 GAATCAATAT
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 105 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (108 bp):
TTAATTAGACTTGATAGACAACATAATAGTCCCTTGAATCAATTTGCTTATTTTGCTTAATTCGT
CCACTTTATGCAACTTAATATTAGTTAAATGTTAGATAATAGG
Found at i:51078743 original size:14 final size:12
Alignment explanation
Indices: 51078731--51078776 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
51078721 CACGTATATG
51078731 TATATAAAAATA
1 TATATAAAAATA
51078743 TATATAAAAATTA
1 TATATAAAAA-TA
*
51078756 TAAAATATAAAATA
1 T-ATATA-AAAATA
51078770 TATATAA
1 TATATAA
51078777 GTATGTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 11 0.38
13 7 0.24
14 7 0.24
15 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TATATAAAAATA
Found at i:51078790 original size:27 final size:26
Alignment explanation
Indices: 51078731--51078793 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
51078721 CACGTATATG
51078731 TATATA-AAAATATATATAAAAATTA
1 TATATATAAAATATATATAAAAATTA
* **
51078756 TAAAATATAAAATATATATAAGTATGTA
1 T-ATATATAAAATATATATAAAAAT-TA
51078784 TATATATAAA
1 TATATATAAA
51078794 TGAGGAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 4 0.13
27 23 0.74
28 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (26 bp):
TATATATAAAATATATATAAAAATTA
Found at i:51079293 original size:2 final size:2
Alignment explanation
Indices: 51079286--51079365 Score: 60
Period size: 2 Copynumber: 41.5 Consensus size: 2
51079276 GTGTATGTAT
* * *
51079286 TA TA TA TA TT TT TA -A TA CTA TA T- TA TG TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
51079326 TA TA TT TA TA TA TA TA TA TA T- TA TA TT TT TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51079366 TTTTAATATC
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
1 4 0.06
2 57 0.90
3 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (2 bp):
TA
Found at i:51079309 original size:23 final size:23
Alignment explanation
Indices: 51079283--51079352 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 23
51079273 AATGTGTATG
*
51079283 TATTATATATATTTTTA-ATACTA
1 TATTATATATATTATTATATA-TA
*
51079306 TATTATGTATA-TATTATATATA
1 TATTATATATATTATTATATATA
51079328 TATT-TATATA-TA-TATATATTA
1 TATTATATATATTATTATATA-TA
51079349 TATT
1 TATT
51079353 TTTATGTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 6 0.14
21 13 0.31
22 10 0.24
23 13 0.31
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (23 bp):
TATTATATATATTATTATATATA
Found at i:51079339 original size:14 final size:14
Alignment explanation
Indices: 51079320--51079401 Score: 68
Period size: 14 Copynumber: 6.1 Consensus size: 14
51079310 ATGTATATAT
51079320 TATATATATATTTA
1 TATATATATATTTA
51079334 TATATATATA--TA
1 TATATATATATTTA
51079346 T-TATAT-T-TTTA
1 TATATATATATTTA
* *
51079357 TGTATATATTTTTA
1 TATATATATATTTA
*
51079371 -ATATCACATTATTTA
1 TATAT-ATA-TATTTA
*
51079386 TATATATATTTTTA
1 TATATATATATTTA
51079400 TA
1 TA
51079402 CATTATCCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
10 1 0.02
11 8 0.15
12 8 0.15
13 4 0.07
14 23 0.42
15 7 0.13
16 4 0.07
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (14 bp):
TATATATATATTTA
Found at i:51079404 original size:25 final size:25
Alignment explanation
Indices: 51079286--51079407 Score: 87
Period size: 23 Copynumber: 4.9 Consensus size: 25
51079276 GTGTATGTAT
51079286 TATATATATTTTTAATAC--TATATTA
1 TATATATATTTTT-ATACATTAT-TTA
* * *
51079311 TGTATATA-TTATATATA-TATTTA
1 TATATATATTTTTATACATTATTTA
*
51079334 TATATATATATATTAT--ATT-TTTA
1 TATATATAT-TTTTATACATTATTTA
*
51079357 TGTATATATTTTTAATATCACATTATTTA
1 TATATATA-TTTT--TAT-ACATTATTTA
51079386 TATATATATTTTTATACATTAT
1 TATATATATTTTTATACATTAT
51079408 CCCATGTAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 22
0.71 0.08 0.20
Matches are distributed among these distances:
23 27 0.35
24 8 0.10
25 21 0.27
26 3 0.04
28 7 0.09
29 11 0.14
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (25 bp):
TATATATATTTTTATACATTATTTA
Found at i:51079557 original size:3 final size:3
Alignment explanation
Indices: 51079549--51079604 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
51079539 TAAATTCATA
* *
51079549 TAT TAT TAT CAT TAT T-T T-T TA- TGT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
51079593 TAT TAT TAT TAT
1 TAT TAT TAT TAT
51079605 CATTGTCATT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 7 0.15
3 39 0.85
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:51079564 original size:29 final size:29
Alignment explanation
Indices: 51079532--51079593 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
51079522 CATATATATA
51079532 TATTTTTTAAATTCATA-TATTATTATCAT
1 TATTTTTTAAATT-ATATTATTATTATCAT
** *
51079561 TATTTTTTATGTTATATTATTATTATTAT
1 TATTTTTTAAATTATATTATTATTATCAT
51079590 TATT
1 TATT
51079594 ATTATTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 3 0.10
29 26 0.90
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (29 bp):
TATTTTTTAAATTATATTATTATTATCAT
Found at i:51081881 original size:84 final size:84
Alignment explanation
Indices: 51081704--51081882 Score: 304
Period size: 84 Copynumber: 2.1 Consensus size: 84
51081694 AATTCAATAG
* *
51081704 AATCGATTATTACAAGCATCAAACTAAACAATTATTCAATAATGAATTTAAACTAACGAAACAGA
1 AATCGATTATTACAAGCATCAAACTAAACAATTATTCAATAACGAATTTAAACTAACCAAACAGA
51081769 GATCTCCTCGAGTTCTTAT
66 GATCTCCTCGAGTTCTTAT
* *
51081788 AATCAATTATTACAAGCATCAAACTAAACAATTATTCAATAACGAATTTATACTAACCAAACAGA
1 AATCGATTATTACAAGCATCAAACTAAACAATTATTCAATAACGAATTTAAACTAACCAAACAGA
*
51081853 GATCTCCTCGCGTTCTTAT
66 GATCTCCTCGAGTTCTTAT
*
51081872 AATTGATTATT
1 AATCGATTATT
51081883 GCATTTTGTC
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.31
Consensus pattern (84 bp):
AATCGATTATTACAAGCATCAAACTAAACAATTATTCAATAACGAATTTAAACTAACCAAACAGA
GATCTCCTCGAGTTCTTAT
Found at i:51093989 original size:10 final size:11
Alignment explanation
Indices: 51093961--51093986 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
51093951 TGTTTTTATT
51093961 AAAAATTAGAA
1 AAAAATTAGAA
51093972 AAAAATTAGAA
1 AAAAATTAGAA
51093983 AAAA
1 AAAA
51093987 TTAAAATCAA
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAATTAGAA
Found at i:51094070 original size:10 final size:9
Alignment explanation
Indices: 51094017--51094121 Score: 56
Period size: 9 Copynumber: 11.2 Consensus size: 9
51094007 AATTTTTTTT
*
51094017 AAAATTTAA
1 AAAATATAA
*
51094026 TAAAATATTA
1 -AAAATATAA
51094036 AAAAT-T-A
1 AAAATATAA
51094043 AAAAT-TAA
1 AAAATATAA
51094051 AAAATATAA
1 AAAATATAA
*
51094060 AAAATCGTAAA
1 AAAAT-AT-AA
51094071 AATATATATAA
1 AA-A-ATATAA
*
51094082 AAAATTTGTAA
1 AAAA--TATAA
*
51094093 AAAAT-TAT
1 AAAATATAA
51094101 AAAATATATA
1 AAAATATA-A
*
51094111 GAAATATAA
1 AAAATATAA
51094120 AA
1 AA
51094122 TTTTATAAAG
Statistics
Matches: 76, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
7 7 0.09
8 14 0.18
9 19 0.25
10 16 0.21
11 16 0.21
12 2 0.03
13 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAATATAA
Found at i:51094070 original size:26 final size:25
Alignment explanation
Indices: 51094015--51094083 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 25
51094005 ATAATTTTTT
* *
51094015 TTAAAATTTAATAAAATATTAAAAA
1 TTAAAAATTAATAAAATATAAAAAA
51094040 TTAAAAATTAA-AAAATATAAAAAA
1 TTAAAAATTAATAAAATATAAAAAA
51094064 TCGTAAAAATATATATAAAA
1 T--TAAAAAT-TA-ATAAAA
51094084 AATTTGTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
24 13 0.35
25 10 0.27
26 7 0.19
27 2 0.05
28 1 0.03
29 4 0.11
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (25 bp):
TTAAAAATTAATAAAATATAAAAAA
Found at i:51094079 original size:22 final size:22
Alignment explanation
Indices: 51094049--51094104 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
51094039 ATTAAAAATT
51094049 AAAAA-ATATAAAAAA-TCGTA
1 AAAAATATATAAAAAATTCGTA
*
51094069 AAAATATATATAAAAAATTTGTA
1 AAAA-ATATATAAAAAATTCGTA
51094092 AAAAAT-TATAAAA
1 AAAAATATATAAAA
51094105 TATATAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.12
21 8 0.25
22 12 0.38
23 8 0.25
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATATATAAAAAATTCGTA
Found at i:51094190 original size:48 final size:46
Alignment explanation
Indices: 51094035--51094194 Score: 130
Period size: 48 Copynumber: 3.4 Consensus size: 46
51094025 ATAAAATATT
* * *
51094035 AAAAATT-AAAAATTAAAAAATATAAA-AAATCGTAAAAATATATATAA
1 AAAAATTAAAAAATTATAAAATATAAAGAAAT-AT-AAAAT-TTTATAA
* *
51094082 AAAATTTGTAAAAAATTATAAAATATATAGAAATATAAAATTTTATAA
1 AAAA-AT-TAAAAAATTATAAAATATAAAGAAATATAAAATTTTATAA
****
51094130 AGTCGTTAAAAAATTATACAAAATATAAAGAAATAT-AAATTTCT-TAA
1 AAAAATTAAAAAATTAT--AAAATATAAAGAAATATAAAATTT-TATAA
51094177 AAAAATTATAAAAATTAT
1 AAAAATTA-AAAAATTAT
51094195 CGTACCAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
46 11 0.12
47 18 0.20
48 34 0.37
49 6 0.07
50 18 0.20
51 4 0.04
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (46 bp):
AAAAATTAAAAAATTATAAAATATAAAGAAATATAAAATTTTATAA
Found at i:51094252 original size:18 final size:19
Alignment explanation
Indices: 51094211--51094253 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
51094201 AAAAGAAACA
51094211 TTTTATATTTTTTCTATAC
1 TTTTATATTTTTTCTATAC
*
51094230 TTTTAT-TTATTTT-TATTC
1 TTTTATATT-TTTTCTATAC
51094248 TTTTAT
1 TTTTAT
51094254 CAATTTCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTATATTTTTTCTATAC
Found at i:51094413 original size:38 final size:37
Alignment explanation
Indices: 51094344--51094421 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 37
51094334 TGATTTTTAT
* *
51094344 AAAATTTTAATTTTTTTATTTTTTACGATTTTTATAAA
1 AAAATTTTAATTTTTATAATTTTTAC-ATTTTTATAAA
*
51094382 AAAATTTCTAATTTTTAATAATTTTTA-ATTTTTATTAA
1 AAAATTT-TAATTTTT-ATAATTTTTACATTTTTATAAA
51094420 AA
1 AA
51094422 TTTAATAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 19 0.54
39 8 0.23
40 8 0.23
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (37 bp):
AAAATTTTAATTTTTATAATTTTTACATTTTTATAAA
Found at i:51095342 original size:34 final size:34
Alignment explanation
Indices: 51095304--51095369 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
51095294 TTTGGGCGGC
51095304 AAAGATTGGGCATACTTCAGTGTTAGGGTTTGGT
1 AAAGATTGGGCATACTTCAGTGTTAGGGTTTGGT
*
51095338 AAAGATTGGGCATATTTCAGTGTTAGGGTTTG
1 AAAGATTGGGCATACTTCAGTGTTAGGGTTTG
51095370 ATATAAGTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (34 bp):
AAAGATTGGGCATACTTCAGTGTTAGGGTTTGGT
Found at i:51097782 original size:47 final size:47
Alignment explanation
Indices: 51097674--51097783 Score: 143
Period size: 47 Copynumber: 2.3 Consensus size: 47
51097664 CGGGATAACT
* *
51097674 ACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTAC
1 ACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTAC
* * *
51097721 ACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-AC
1 ACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTAC
51097768 ACATAGTG-TCTCATCG
1 ACATAGTGCT-TCATCG
51097784 ACTCAATGTC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 51 0.94
48 2 0.04
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (47 bp):
ACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTAC
Found at i:51115052 original size:90 final size:92
Alignment explanation
Indices: 51114940--51115524 Score: 370
Period size: 104 Copynumber: 5.8 Consensus size: 92
51114930 AGCTAAAACA
* * ** *
51114940 ACCAGTTTTAAGCTATAAACCCATAAATTTCCTCCATAATTTAATCAACAATTACCCCATTTCAT
1 ACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTTAATCAACAATAACCCCATTTCAT
51115005 T-ATCCACTAGCAAAAACTAAAAG-CC
66 TAATCCACTAGCAAAAACTAAAAGACC
* * *
51115030 GCCAATTTTAAGCTGTAAACCCATAAATTTCTTCCATTGTTTAACAATCAACAATCACCCCATTT
1 ACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTT---AATCAACAATAACCCCATTT
51115095 CATTAATCCACTAG-AAAATACTAAAATCCAGCTAAAACC
63 CATTAATCCACTAGCAAAA-ACT-AAA---AG-----ACC
51115134 ACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTTAA-CAATTACCAATAACCCCATT
1 ACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTTAATC-A--A-CAATAACCCCATT
**
51115198 TCATTAATCCACTAGCAATTACTAAAATCCAGCTGAAACC
62 TCATTAATCCACTAGCAAAAACT-AAA---A---G--ACC
* * * *
51115238 AACAATTTTTAAGCTGTAAACCCACAAATTTCCTACATAGTTTAACCATCAACAATAACCCCATT
1 ACCAA-TTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTT-A--ATCAACAATAACCCCATT
* * * **
51115303 TCATTAACCCATTATCAATTACTAAAATCCAGCTAAAACC
62 TCATTAATCCACTAGCAAAAACT-AAA---AG-----ACC
* * * *
51115343 ACCGATTTTAAGCTGTAAACTCATAAAATTCCTCCATGGTTTAA-CAATCAATGATCACCCCATT
1 ACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTTAATCAA-CAAT-A--ACCCCATT
* **
51115407 TCATTGATCCACTAGCAATTACTAAAATCCAGCAAAACTC
62 TCATTAATCCACTAGCAAAAACT-AAA---AG----AC-C
* * *
51115447 ACCAATTTTAAGCTGTAAACCCATAAAATTCCTACATAGTTTAACAATCAACAATAACCCCATTT
1 ACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTT---AATCAACAATAACCCCATTT
*
51115512 CACTAATCCACTA
63 CATTAATCCACTA
51115525 TCAATTACCA
Statistics
Matches: 418, Mismatches: 37, Indels: 66
0.80 0.07 0.13
Matches are distributed among these distances:
90 36 0.09
93 27 0.06
94 12 0.03
95 3 0.01
98 2 0.00
100 4 0.01
101 8 0.02
102 2 0.00
103 7 0.02
104 216 0.52
105 85 0.20
106 3 0.01
107 7 0.02
108 5 0.01
109 1 0.00
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.29
Consensus pattern (92 bp):
ACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTTAATCAACAATAACCCCATTTCAT
TAATCCACTAGCAAAAACTAAAAGACC
Found at i:51115211 original size:104 final size:104
Alignment explanation
Indices: 51115021--51115583 Score: 770
Period size: 104 Copynumber: 5.4 Consensus size: 104
51115011 CTAGCAAAAA
* * * *
51115021 CTAAAAGCCGCCAATTTTAAGCTGTAAACCCATAAATTTCTTCCATTGTTTAACAATCAACAATC
1 CTAAAA-CCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATAGTTTAACAATCAACAATA
* *
51115086 ACCCCATTTCATTAATCCACTAGAAAATACTAAAATCCAG
65 ACCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
* * *
51115126 CTAAAACCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTTAACAATTACCAATAA
1 CTAAAACCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATAGTTTAACAATCAACAATAA
51115191 CCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
66 CCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
* * * * *
51115230 CTGAAACCAACAATTTTTAAGCTGTAAACCCACAAATTTCCTACATAGTTTAACCATCAACAATA
1 CTAAAACCACCAA-TTTTAAGCTGTAAACCCATAAATTTCCTCCATAGTTTAACAATCAACAATA
* * *
51115295 ACCCCATTTCATTAACCCATTATCAATTACTAAAATCCAG
65 ACCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
* * * * ** *
51115335 CTAAAACCACCGATTTTAAGCTGTAAACTCATAAAATTCCTCCATGGTTTAACAATCAATGATCA
1 CTAAAACCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATAGTTTAACAATCAACAATAA
*
51115400 CCCCATTTCATTGATCCACTAGCAATTACTAAAATCCAG
66 CCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
* *
51115439 C-AAAACTCACCAATTTTAAGCTGTAAACCCATAAAATTCCTACATAGTTTAACAATCAACAATA
1 CTAAAAC-CACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATAGTTTAACAATCAACAATA
* * *
51115503 ACCCCATTTCACTAATCCACTATCAATTACCAAAATCCAG
65 ACCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
* ** *
51115543 CTTAAGTCATCAATTTTAAGCTGTAAACCCA-AAATTATCCT
1 CTAAAACCACCAATTTTAAGCTGTAAACCCATAAATT-TCCT
51115584 AAAAAAAAGG
Statistics
Matches: 404, Mismatches: 50, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
103 9 0.02
104 295 0.73
105 100 0.25
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (104 bp):
CTAAAACCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATAGTTTAACAATCAACAATAA
CCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
Found at i:51115405 original size:209 final size:208
Alignment explanation
Indices: 51115032--51115573 Score: 789
Period size: 209 Copynumber: 2.6 Consensus size: 208
51115022 TAAAAGCCGC
* * * *
51115032 CAATTTTAAGCTGTAAACCCATAAATTTCTTCCATTGTTTAACAATCAACAATCACCCCATTTCA
1 CAATTTTAAGCTGTAAACCCATAAATTTCCTACATAGTTTAACAATCAACAATAACCCCATTTCA
** * *
51115097 TTAATCCACTAGAAAATACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAACCCATAAAT
66 TTAATCCACTATCAATTACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAACCCATAAAA
* * *
51115162 TTCCTCCATTGTTTAACAATTACCAATAACCCCATTTCATTAATCCACTAGCAATTACTAAAATC
131 TTCCTCCATGGTTTAACAATCAACAATAACCCCATTTCATTAATCCACTAGCAATTACTAAAATC
*
51115227 CAGCTGAAAC-CAA
196 CAGC-AAAACTCAA
* *
51115240 CAATTTTTAAGCTGTAAACCCACAAATTTCCTACATAGTTTAACCATCAACAATAACCCCATTTC
1 CAA-TTTTAAGCTGTAAACCCATAAATTTCCTACATAGTTTAACAATCAACAATAACCCCATTTC
* * * *
51115305 ATTAACCCATTATCAATTACTAAAATCCAGCTAAAACCACCGATTTTAAGCTGTAAACTCATAAA
65 ATTAATCCACTATCAATTACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAACCCATAAA
** * *
51115370 ATTCCTCCATGGTTTAACAATCAATGATCACCCCATTTCATTGATCCACTAGCAATTACTAAAAT
130 ATTCCTCCATGGTTTAACAATCAACAATAACCCCATTTCATTAATCCACTAGCAATTACTAAAAT
*
51115435 CCAGCAAAACTCAC
195 CCAGCAAAACTCAA
*
51115449 CAATTTTAAGCTGTAAACCCATAAAATTCCTACATAGTTTAACAATCAACAATAACCCCATTTCA
1 CAATTTTAAGCTGTAAACCCATAAATTTCCTACATAGTTTAACAATCAACAATAACCCCATTTCA
* * * ** *
51115514 CTAATCCACTATCAATTACCAAAATCCAGCTTAAGTCATCAATTTTAAGCTGTAAACCCA
66 TTAATCCACTATCAATTACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAACCCA
51115574 AAATTATCCT
Statistics
Matches: 296, Mismatches: 36, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
208 116 0.39
209 180 0.61
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (208 bp):
CAATTTTAAGCTGTAAACCCATAAATTTCCTACATAGTTTAACAATCAACAATAACCCCATTTCA
TTAATCCACTATCAATTACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAACCCATAAAA
TTCCTCCATGGTTTAACAATCAACAATAACCCCATTTCATTAATCCACTAGCAATTACTAAAATC
CAGCAAAACTCAA
Found at i:51119556 original size:15 final size:15
Alignment explanation
Indices: 51119521--51119572 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
51119511 TTAAGAATTT
*
51119521 TATTAAATTAT-ATA
1 TATTTAATTATAATA
51119535 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
51119549 TATTTAATAATAAT-
1 TATTTAATTATAATA
51119563 TATGTTAATT
1 TAT-TTAATT
51119573 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:51119600 original size:120 final size:120
Alignment explanation
Indices: 51119459--51119688 Score: 460
Period size: 120 Copynumber: 1.9 Consensus size: 120
51119449 TTTGAGTAAA
51119459 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
51119524 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
66 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
51119579 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
51119644 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
66 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
51119689 TAAATATGAT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 110 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (120 bp):
TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
Found at i:51119654 original size:61 final size:61
Alignment explanation
Indices: 51119469--51119656 Score: 208
Period size: 61 Copynumber: 3.1 Consensus size: 61
51119459 TTATAGTATC
51119469 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * * * * *
51119530 ATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAATTTA-TATTTTA-TAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATT-ATTAAGAATTTTATTA-AATT
51119589 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
51119650 ATATATT
1 ATATATT
51119657 TTAATTATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 29 0.30
60 26 0.27
61 36 0.37
62 3 0.03
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
Found at i:51119671 original size:16 final size:16
Alignment explanation
Indices: 51119650--51119691 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
51119640 TTATTAAATT
*
51119650 ATATATTTTAATTATA
1 ATATATTTTAATAATA
51119666 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
51119681 AT-TATGTTTAA
1 ATATAT-TTTAA
51119692 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:51119676 original size:15 final size:15
Alignment explanation
Indices: 51119641--51119682 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
51119631 TTAAGAATTT
*
51119641 TATTAAATTAT-ATA
1 TATTTAATTATAATA
51119655 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
51119669 TATTTAATAATAAT
1 TATTTAATTATAAT
51119683 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:51119917 original size:45 final size:43
Alignment explanation
Indices: 51119817--51119926 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
51119807 TTTTCCATTA
51119817 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* * ***
51119856 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
51119901 TGCTATTACACCTCTATTCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
51119927 CCTCTAATCC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 23 0.40
46 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:51119928 original size:16 final size:16
Alignment explanation
Indices: 51119907--51119974 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
51119897 GATTTGCTAT
*
51119907 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
51119923 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
51119939 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
51119955 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
51119971 TACA
1 TACA
51119975 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:51121080 original size:19 final size:18
Alignment explanation
Indices: 51121032--51121080 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
51121022 TTTTATATAA
*
51121032 TTTATAATTT-TTTTATAT
1 TTTA-AATTTATTTAATAT
*
51121050 TTTAACTTTATTTAATAT
1 TTTAAATTTATTTAATAT
51121068 TTGTAAATTTATT
1 TT-TAAATTTATT
51121081 ATATTAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 13 0.50
19 9 0.35
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTAAATTTATTTAATAT
Found at i:51125686 original size:20 final size:20
Alignment explanation
Indices: 51125661--51125710 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
51125651 TGGCTTAAAA
51125661 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
51125681 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
51125698 GTGGTAGTGGATT
1 TTGGTAGTGGATT
51125711 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:51130325 original size:20 final size:20
Alignment explanation
Indices: 51130300--51130349 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
51130290 TGGCTTAAAA
51130300 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
51130320 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
51130337 GTGGTAGTGGATT
1 TTGGTAGTGGATT
51130350 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:51131664 original size:14 final size:15
Alignment explanation
Indices: 51131645--51131673 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
51131635 GAGCTTACAG
51131645 GTTTTTTT-TTCTTT
1 GTTTTTTTATTCTTT
51131659 GTTTTTTTATTCTTT
1 GTTTTTTTATTCTTT
51131674 CTTATGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.03, C:0.07, G:0.07, T:0.83
Consensus pattern (15 bp):
GTTTTTTTATTCTTT
Found at i:51148211 original size:18 final size:18
Alignment explanation
Indices: 51148190--51148229 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
51148180 ATTTATGTTT
51148190 GTATATATACATATGTAG
1 GTATATATACATATGTAG
51148208 GTATATATACATATGTAG
1 GTATATATACATATGTAG
51148226 GTAT
1 GTAT
51148230 GCATGCGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (18 bp):
GTATATATACATATGTAG
Found at i:51148270 original size:18 final size:18
Alignment explanation
Indices: 51148183--51148271 Score: 70
Period size: 18 Copynumber: 4.6 Consensus size: 18
51148173 TGTATGTATT
*
51148183 TATGTTTGTATATATACA
1 TATGTATGTATATATACA
*
51148201 TATGTAGGTATATATACA
1 TATGTATGTATATATACA
* * *
51148219 TATGTAGGTATGCATGCGTGCA
1 TATGTATGTAT--AT--ATACA
*
51148241 TTTATGTTTGTATATATACA
1 --TATGTATGTATATATACA
51148261 TATGTATGTAT
1 TATGTATGTAT
51148272 GCATATATGT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
18 37 0.66
20 5 0.09
22 5 0.09
24 9 0.16
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (18 bp):
TATGTATGTATATATACA
Found at i:51148289 original size:42 final size:42
Alignment explanation
Indices: 51148208--51148295 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
51148198 ACATATGTAG
* * *
51148208 GTATATATACATATGTAGGTATGCATGCGTGCATTTATGTTT
1 GTATATATACATATGTAGGTATGCATACATGCATTTATGTGT
* * *
51148250 GTATATATACATATGTATGTATGCATATATG-TTTGTATGTGT
1 GTATATATACATATGTAGGTATGCATACATGCATT-TATGTGT
51148292 GTAT
1 GTAT
51148296 TGGTATATGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.05
42 37 0.95
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.45
Consensus pattern (42 bp):
GTATATATACATATGTAGGTATGCATACATGCATTTATGTGT
Found at i:51149351 original size:21 final size:21
Alignment explanation
Indices: 51149316--51149402 Score: 56
Period size: 21 Copynumber: 4.2 Consensus size: 21
51149306 GGTTTAAAAT
*
51149316 TTTGA-GTTTAGGATTTGAGG
1 TTTGAGGTTTAAGATTTGAGG
*
51149336 TTTGAGGTTTAAGATTCGA-G
1 TTTGAGGTTTAAGATTTGAGG
* * * *
51149356 TTTG-GGATATAAGGTTTAAAG
1 TTTGAGG-TTTAAGATTTGAGG
* *
51149377 TTT-AGGGTTCAAGATTTGAGA
1 TTTGA-GGTTTAAGATTTGAGG
51149398 TTTGA
1 TTTGA
51149403 AATTTGGGAT
Statistics
Matches: 49, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
19 2 0.04
20 18 0.37
21 26 0.53
22 3 0.06
ACGTcount: A:0.26, C:0.02, G:0.30, T:0.41
Consensus pattern (21 bp):
TTTGAGGTTTAAGATTTGAGG
Found at i:51150208 original size:64 final size:64
Alignment explanation
Indices: 51150090--51150230 Score: 194
Period size: 64 Copynumber: 2.2 Consensus size: 64
51150080 ATTTAACACA
* * ** * * **
51150090 TATT-GACATATATCTCAACATTTGTGTAGAATTACAACTTTCACGTATTTAAAAAAATACTTG
1 TATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCCAAAAAAATACTTG
*
51150153 TATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCCAAAAAAATATTTG
1 TATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCCAAAAAAATACTTG
51150217 TATTCGACACATAT
1 TATTCGACACATAT
51150231 TAACATATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
63 4 0.06
64 64 0.94
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (64 bp):
TATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCCAAAAAAATACTTG
Found at i:51150250 original size:138 final size:137
Alignment explanation
Indices: 51150003--51150452 Score: 465
Period size: 149 Copynumber: 3.2 Consensus size: 137
51149993 CGCATATCCA
* * * *
51150003 AAAAATAATACTTGTATTTGACACATAT-CTAACATTTATGTACAATTACAACTTCCACATAT-A
1 AAAAA-AATACTTGTATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCA
** ** * ** *
51150066 TGGAAAATCGTTATATTTAACACATATTGACATATATCTCAACATTTGTGTAGAATTACAACTTT
65 -AAAAAATATTTGTATTCGACACATATTGACATATATCTCAACATTTGTGTAGAATTACAACTTC
51150131 CACGTATTT
129 CACGTATTT
51150140 AAAAAAATACTTGTATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCCA
1 AAAAAAATACTTGTATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATAT-CA
* * *
51150205 AAAAAATATTTGTATTCGACACATATTAACATATATCTCAACATTTGTGTGGAATTACAACATCC
65 AAAAAATATTTGTATTCGACACATATTGACATATATCTCAACATTTGTGTAGAATTACAACTTCC
*
51150270 ACATATTT
130 ACGTATTT
* * * *
51150278 AAAAAAAAATACTTGTATTCGATACATATTAACACACATTCCATCATTCGTGTAGAATTATAAAT
1 --AAAAAAATACTTGTATTCGACACATA-T--C-C-CA----A-CATTCATGTAGAATTACAACT
* * * * * * *
51150343 TACACATATCTAAAAAATATTTGTATTCGACATATATCGACACATATCCCAACATTCGTGTAGAA
54 TCCACATATCAAAAAAATATTTGTATTCGACACATATTGACATATATCTCAACATTTGTGTAGAA
51150408 TTACAACTTCCACGTATTT
119 TTACAACTTCCACGTATTT
* ** *
51150427 -GAAAAATACTTCCATTCGCCACATAT
1 AAAAAAATACTTGTATTCGACACATAT
51150453 GAATAATGTA
Statistics
Matches: 262, Mismatches: 36, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
136 21 0.08
137 36 0.14
138 61 0.23
139 1 0.00
140 25 0.10
141 1 0.00
143 1 0.00
144 1 0.00
145 3 0.01
146 20 0.08
149 66 0.25
150 26 0.10
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (137 bp):
AAAAAAATACTTGTATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCAA
AAAAATATTTGTATTCGACACATATTGACATATATCTCAACATTTGTGTAGAATTACAACTTCCA
CGTATTT
Found at i:51150432 original size:73 final size:73
Alignment explanation
Indices: 51150159--51150452 Score: 309
Period size: 73 Copynumber: 4.0 Consensus size: 73
51150149 CTTGTATTCG
* *
51150159 ACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCCAAAAAAATATTTGTATTCGA
1 ACACATATCCCAACATTCGTGTAGAATTACAACTTCCACATAT-CTAAAAAATATTTGTATTCGA
*
51150224 CACATATTA
65 CACATATCA
* * * * * * *
51150233 ACATATATCTCAACATTTGTGTGGAATTACAACATCCACATATTTAAAAAAAAATACTTGTATTC
1 ACACATATCCCAACATTCGTGTAGAATTACAACTTCCACATATCT---AAAAAATATTTGTATTC
* *
51150298 GATACATATTA
63 GACACATATCA
* * * * * *
51150309 ACACACATTCCATCATTCGTGTAGAATTATAAATTACACATATCTAAAAAATATTTGTATTCGAC
1 ACACATATCCCAACATTCGTGTAGAATTACAACTTCCACATATCTAAAAAATATTTGTATTCGAC
* *
51150374 ATATATCG
66 ACATATCA
* * * * ** *
51150382 ACACATATCCCAACATTCGTGTAGAATTACAACTTCCACGTATTTGAAAAATACTTCCATTCGCC
1 ACACATATCCCAACATTCGTGTAGAATTACAACTTCCACATATCTAAAAAATATTTGTATTCGAC
51150447 ACATAT
66 ACATAT
51150453 GAATAATGTA
Statistics
Matches: 176, Mismatches: 41, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
73 80 0.45
74 37 0.21
76 59 0.34
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.32
Consensus pattern (73 bp):
ACACATATCCCAACATTCGTGTAGAATTACAACTTCCACATATCTAAAAAATATTTGTATTCGAC
ACATATCA
Found at i:51153620 original size:18 final size:19
Alignment explanation
Indices: 51153581--51153622 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
51153571 TAAACTATGA
51153581 TTTAAATTTTAAATTGATT
1 TTTAAATTTTAAATTGATT
51153600 TTTAAATTTTTAAA-T-ATT
1 TTTAAA-TTTTAAATTGATT
51153618 TTTAA
1 TTTAA
51153623 TTAAGTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.36
19 7 0.32
20 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTAAATTTTAAATTGATT
Found at i:51158350 original size:18 final size:18
Alignment explanation
Indices: 51158321--51158387 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
51158311 TCCTCCTCCT
* *
51158321 CCTCCTCCTCTTCTTCTT
1 CCTCCTCTTCTTCTTCTA
*
51158339 CTTCCTCTTCTTCTTCTA
1 CCTCCTCTTCTTCTTCTA
* *
51158357 CCTCCACTTCTTCATACT-
1 CCTCCTCTTCTTC-TTCTA
*
51158375 CCACCTCTTCTTC
1 CCTCCTCTTCTTC
51158388 CATAGTCTCC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 37 0.93
19 3 0.08
ACGTcount: A:0.07, C:0.46, G:0.00, T:0.46
Consensus pattern (18 bp):
CCTCCTCTTCTTCTTCTA
Found at i:51158366 original size:15 final size:15
Alignment explanation
Indices: 51158333--51158385 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
51158323 TCCTCCTCTT
* **
51158333 CTTCTTCTTCCTCTT
1 CTTCTTCTACCTCCA
51158348 CTTCTTCTACCTCCA
1 CTTCTTCTACCTCCA
51158363 CTTCTTCATA-CTCCA
1 CTTCTTC-TACCTCCA
*
51158378 CCTCTTCT
1 CTTCTTCT
51158386 TCCATAGTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 1 0.03
15 30 0.91
16 2 0.06
ACGTcount: A:0.09, C:0.43, G:0.00, T:0.47
Consensus pattern (15 bp):
CTTCTTCTACCTCCA
Found at i:51160672 original size:18 final size:18
Alignment explanation
Indices: 51160644--51160678 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
51160634 AATTTTTTTT
51160644 ATTTTTAA-TTTTAAATA
1 ATTTTTAATTTTTAAATA
51160661 ATTTTATAATTTTTAAAT
1 ATTTT-TAATTTTTAAAT
51160679 TATTATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTAATTTTTAAATA
Found at i:51160874 original size:24 final size:23
Alignment explanation
Indices: 51160820--51160875 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
51160810 AAAGATTAAT
51160820 AATTAAATTTAACTAAAAAATAAA
1 AATTAAA-TTAACTAAAAAATAAA
*
51160844 AACTAAATTAAC-AAAATATATAAA
1 AATTAAATTAACTAAAA-A-ATAAA
*
51160868 TATTAAAT
1 AATTAAAT
51160876 ACATTTGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 6 0.22
24 17 0.63
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (23 bp):
AATTAAATTAACTAAAAAATAAA
Found at i:51176250 original size:100 final size:100
Alignment explanation
Indices: 51176077--51176527 Score: 503
Period size: 100 Copynumber: 4.5 Consensus size: 100
51176067 AAATATATGG
* * * * * * * *
51176077 AAGTAATTATCCCGTATCACCGCCGTCACACGATATCTCTTGAGGCAAGGATCAAATGATCAAAT
1 AAGTAATAATCCCATATCAACGCCATCACACAATTTCTCTCGAGGCAAGGATCAAATGAGCAAAT
* *
51176142 TAAGACTACGTATTACATAACCATGATTCATACAC
66 TAAGACTACATATTACATAACCATGATTCATATAC
* * * ** ** *
51176177 AAGTAATAAGCCCTTATCAAGGCTGTCACACAATTTCTCTCGAGGCAAGGATTGAGTGAGCAAAT
1 AAGTAATAATCCCATATCAACGCCATCACACAATTTCTCTCGAGGCAAGGATCAAATGAGCAAAT
*
51176242 TAAGACTACATATTACATAACCGTGATTCATATAC
66 TAAGACTACATATTACATAACCATGATTCATATAC
* * ** * *
51176277 AAGTAA-ATATCCCATATCATCGCCATCACACAATTGCTCTTAAGGCGAGGATCAAATGATCAAA
1 AAGTAATA-ATCCCATATCAACGCCATCACACAATTTCTCTCGAGGCAAGGATCAAATGAGCAAA
* *
51176341 TCAAGACTACATAGTACATAACCATGATTCATATAC
65 TTAAGACTACATATTACATAACCATGATTCATATAC
* * *
51176377 AAGTAATAATCCCATATC-ACTGCCATCACACGATTTCTCTCGTGGCAAGTATCAAATGAGCAAA
1 AAGTAATAATCCCATATCAAC-GCCATCACACAATTTCTCTCGAGGCAAGGATCAAATGAGCAAA
* *
51176441 TTAAGACTACATATTACATAACCATTATTCATATGC
65 TTAAGACTACATATTACATAACCATGATTCATATAC
* * * * * * *
51176477 AAGTAA-ATATCCCGTATCATCGCCACCACGCGATTTCTCTCAAAGCAAGGA
1 AAGTAATA-ATCCCATATCAACGCCATCACACAATTTCTCTCGAGGCAAGGA
51176528 CCGATACAGT
Statistics
Matches: 292, Mismatches: 54, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
99 3 0.01
100 287 0.98
101 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (100 bp):
AAGTAATAATCCCATATCAACGCCATCACACAATTTCTCTCGAGGCAAGGATCAAATGAGCAAAT
TAAGACTACATATTACATAACCATGATTCATATAC
Found at i:51176473 original size:200 final size:200
Alignment explanation
Indices: 51176077--51176501 Score: 600
Period size: 200 Copynumber: 2.1 Consensus size: 200
51176067 AAATATATGG
* * * * *
51176077 AAGTAATTATCCCGTATCACCGCCGTCACACGATATCTCTTGAGGCAAGGATCAAATGATCAAAT
1 AAGTAAATATCCCGTATCATCGCCATCACACAATATCTCTTAAGGCAAGGATCAAATGATCAAAT
* * * * **
51176142 TAAGACTACGTATTACATAACCATGATTCATACACAAGTAATAAGCCCTTATCAAGGCTGTCACA
66 CAAGACTACATAGTACATAACCATGATTCATACACAAGTAATAAGCCCATATCAAGGCCATCACA
** * *
51176207 CAATTTCTCTCGAGGCAAGGATTGAGTGAGCAAATTAAGACTACATATTACATAACCGTGATTCA
131 CAATTTCTCTCGAGGCAAGGATCAAATGAGCAAATTAAGACTACATATTACATAACCATGATTCA
51176272 TATAC
196 TATAC
* *
51176277 AAGTAAATATCCCATATCATCGCCATCACACAAT-TGCTCTTAAGGCGAGGATCAAATGATCAAA
1 AAGTAAATATCCCGTATCATCGCCATCACACAATAT-CTCTTAAGGCAAGGATCAAATGATCAAA
* * **
51176341 TCAAGACTACATAGTACATAACCATGATTCATATACAAGTAATAATCCCATATCACTGCCATCAC
65 TCAAGACTACATAGTACATAACCATGATTCATACACAAGTAATAAGCCCATATCAAGGCCATCAC
* * * *
51176406 ACGATTTCTCTCGTGGCAAGTATCAAATGAGCAAATTAAGACTACATATTACATAACCATTATTC
130 ACAATTTCTCTCGAGGCAAGGATCAAATGAGCAAATTAAGACTACATATTACATAACCATGATTC
*
51176471 ATATGC
195 ATATAC
51176477 AAGTAAATATCCCGTATCATCGCCA
1 AAGTAAATATCCCGTATCATCGCCA
51176502 CCACGCGATT
Statistics
Matches: 197, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
199 1 0.01
200 196 0.99
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (200 bp):
AAGTAAATATCCCGTATCATCGCCATCACACAATATCTCTTAAGGCAAGGATCAAATGATCAAAT
CAAGACTACATAGTACATAACCATGATTCATACACAAGTAATAAGCCCATATCAAGGCCATCACA
CAATTTCTCTCGAGGCAAGGATCAAATGAGCAAATTAAGACTACATATTACATAACCATGATTCA
TATAC
Found at i:51177187 original size:24 final size:24
Alignment explanation
Indices: 51177138--51177195 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
51177128 AAAATAACTC
* *
51177138 TTAA-TATTTATATTTTATGTAAT
1 TTAACTATTTTTATTTTATATAAT
51177161 TTAACTATTTTTATTTT-TATAAT
1 TTAACTATTTTTATTTTATATAAT
* *
51177184 TTTACTTTTTTT
1 TTAACTATTTTT
51177196 TGACATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (24 bp):
TTAACTATTTTTATTTTATATAAT
Found at i:51177410 original size:25 final size:25
Alignment explanation
Indices: 51177376--51177423 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
51177366 TACGAGTTAG
51177376 ATTTTTAGAATCAAAGCTAATTTAA
1 ATTTTTAGAATCAAAGCTAATTTAA
51177401 ATTTTTAGAATCAAAGCTAATTT
1 ATTTTTAGAATCAAAGCTAATTT
51177424 GAGACAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTTTTAGAATCAAAGCTAATTTAA
Found at i:51180352 original size:15 final size:16
Alignment explanation
Indices: 51180323--51180367 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
51180313 AATGCGCTTC
*
51180323 ATTTATTAT-TTATAT
1 ATTTATTATATAATAT
51180338 AATTT-TTATA-AATAT
1 -ATTTATTATATAATAT
51180353 ATTTATTATATAATA
1 ATTTATTATATAATA
51180368 ATTATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 4 0.16
15 13 0.52
16 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTATTATATAATAT
Found at i:51181521 original size:44 final size:44
Alignment explanation
Indices: 51181469--51181558 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
51181459 AAAACTAAAA
51181469 TTGTAAGGATAATTATTTAGTCCACTAACAATGGAGTAAAATTC
1 TTGTAAGGATAATTATTTAGTCCACTAACAATGGAGTAAAATTC
51181513 TTGTAAGGATAATTATTTAGTCCACTAACAATGGAGTAAAATTC
1 TTGTAAGGATAATTATTTAGTCCACTAACAATGGAGTAAAATTC
51181557 TT
1 TT
51181559 CCTGAGCAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (44 bp):
TTGTAAGGATAATTATTTAGTCCACTAACAATGGAGTAAAATTC
Found at i:51185073 original size:43 final size:43
Alignment explanation
Indices: 51185019--51185109 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
51185009 TTAAGCTAAC
* * *
51185019 TTCTATGATTATAAAAATGGGTAATTAAAAG-ACAAATTTCAGA
1 TTCTTTGATTATAAAAATGGATAATTAAAAGCA-AAAATTCAGA
*
51185062 TTCTTTGATTATTAAAATGGATAATTAAAAGCAAAAATTCAGA
1 TTCTTTGATTATAAAAATGGATAATTAAAAGCAAAAATTCAGA
51185105 TTCTT
1 TTCTT
51185110 GTAAATTGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (43 bp):
TTCTTTGATTATAAAAATGGATAATTAAAAGCAAAAATTCAGA
Found at i:51185204 original size:16 final size:15
Alignment explanation
Indices: 51185183--51185229 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
51185173 TTATGGAGAT
51185183 TTTTAAAATATTAATA
1 TTTTAAAAT-TTAATA
51185199 TTTTAAAATTT-ATCA
1 TTTTAAAATTTAAT-A
*
51185214 ATTTAAAATGTTAATA
1 TTTTAAAAT-TTAATA
51185230 AGTATAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 2 0.07
15 11 0.41
16 12 0.44
17 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
TTTTAAAATTTAATA
Found at i:51185915 original size:43 final size:43
Alignment explanation
Indices: 51185849--51185934 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
51185839 TACAAATATG
*
51185849 TAAGGCAACCAATTTGATGTCTTTTCCAACTTAATACCCAACC
1 TAAGACAACCAATTTGATGTCTTTTCCAACTTAATACCCAACC
**
51185892 TAAGACAACCAATTTGATGTCTTTTCCAACTTTCTACCCAACC
1 TAAGACAACCAATTTGATGTCTTTTCCAACTTAATACCCAACC
51185935 CATTCCTGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.31
Consensus pattern (43 bp):
TAAGACAACCAATTTGATGTCTTTTCCAACTTAATACCCAACC
Found at i:51185993 original size:32 final size:34
Alignment explanation
Indices: 51185952--51186094 Score: 132
Period size: 32 Copynumber: 4.0 Consensus size: 34
51185942 GATTAAACCA
*
51185952 ACCAATTTGATCAA-ATCCAAACATCCAT-ATGG
1 ACCAATTTGATCAAGATCAAAACATCCATGATGG
*
51185984 ACCAATTTGATCAAGTTCAAAACATCCATGATGG
1 ACCAATTTGATCAAGATCAAAACATCCATGATGG
*
51186018 AAACAAGAGTTTCAATTTGATCAA-ATCCAAACATCCATG-TGG
1 --AC--------CAATTTGATCAAGATCAAAACATCCATGATGG
*
51186060 ACCAATTTGATCAAGTTCAAAACATCCATGATGG
1 ACCAATTTGATCAAGATCAAAACATCCATGATGG
51186094 A
1 A
51186095 AACAAGAGTT
Statistics
Matches: 91, Mismatches: 6, Indels: 26
0.74 0.05 0.21
Matches are distributed among these distances:
32 26 0.29
33 25 0.27
34 8 0.09
36 2 0.02
40 2 0.02
42 3 0.03
43 13 0.14
44 12 0.13
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (34 bp):
ACCAATTTGATCAAGATCAAAACATCCATGATGG
Found at i:51186036 original size:44 final size:44
Alignment explanation
Indices: 51185986--51186105 Score: 138
Period size: 33 Copynumber: 3.0 Consensus size: 44
51185976 CCATATGGAC
51185986 CAATTTGATCAAGTTCAAAACATCCATGATGGAAACAAGAGTTT
1 CAATTTGATCAAGTTCAAAACATCCATGATGGAAACAAGAGTTT
* *
51186030 CAATTTGATCAA-ATCCAAACATCCATG-TGG--AC--------
1 CAATTTGATCAAGTTCAAAACATCCATGATGGAAACAAGAGTTT
51186062 CAATTTGATCAAGTTCAAAACATCCATGATGGAAACAAGAGTTT
1 CAATTTGATCAAGTTCAAAACATCCATGATGGAAACAAGAGTTT
51186106 TGCAAGAATC
Statistics
Matches: 60, Mismatches: 4, Indels: 24
0.68 0.05 0.27
Matches are distributed among these distances:
32 12 0.20
33 13 0.22
34 3 0.05
36 2 0.03
40 2 0.03
42 3 0.05
43 13 0.22
44 12 0.20
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (44 bp):
CAATTTGATCAAGTTCAAAACATCCATGATGGAAACAAGAGTTT
Found at i:51186080 original size:76 final size:76
Alignment explanation
Indices: 51185954--51186105 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
51185944 TTAAACCAAC
51185954 CAATTTGATCAAATCCAAACATCCATATGGACCAATTTGATCAAGTTCAAAACATCCATGATGGA
1 CAATTTGATCAAATCCAAACATCCATATGGACCAATTTGATCAAGTTCAAAACATCCATGATGGA
51186019 AACAAGAGTTT
66 AACAAGAGTTT
*
51186030 CAATTTGATCAAATCCAAACATCCATGTGGACCAATTTGATCAAGTTCAAAACATCCATGATGGA
1 CAATTTGATCAAATCCAAACATCCATATGGACCAATTTGATCAAGTTCAAAACATCCATGATGGA
51186095 AACAAGAGTTT
66 AACAAGAGTTT
51186106 TGCAAGAATC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (76 bp):
CAATTTGATCAAATCCAAACATCCATATGGACCAATTTGATCAAGTTCAAAACATCCATGATGGA
AACAAGAGTTT
Found at i:51196616 original size:21 final size:21
Alignment explanation
Indices: 51196592--51196631 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
51196582 TTTAATAGAT
*
51196592 TAAAATTAAA-AAATGTTAAAA
1 TAAAATAAAATAAAT-TTAAAA
51196613 TAAAATAAAATAAATTTAA
1 TAAAATAAAATAAATTTAA
51196632 TTCTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (21 bp):
TAAAATAAAATAAATTTAAAA
Found at i:51206050 original size:19 final size:18
Alignment explanation
Indices: 51206000--51206050 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
51205990 TTTATGAATT
51206000 TTTTATAATTATTTTTAAA
1 TTTTA-AATTATTTTTAAA
* *
51206019 -TTTGATTTAATTTTATAAA
1 TTTTAAATT-ATTTT-TAAA
51206038 TTTTAAATTATTT
1 TTTTAAATTATTT
51206051 ATTGATGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
17 3 0.12
18 8 0.32
19 8 0.32
20 6 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTAAATTATTTTTAAA
Found at i:51207431 original size:6 final size:6
Alignment explanation
Indices: 51207420--51207449 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
51207410 CCAAAATTTA
51207420 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
51207450 CTTTTGTTGT
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:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:51210854 original size:24 final size:24
Alignment explanation
Indices: 51210827--51210872 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
51210817 ATAACCTCTT
51210827 TATAAAATT-TTAACAAATGAAAAA
1 TATAAAATTATTAA-AAATGAAAAA
* *
51210851 TATATAATTATTAAATATGAAA
1 TATAAAATTATTAAAAATGAAA
51210873 TTAAAATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (24 bp):
TATAAAATTATTAAAAATGAAAAA
Found at i:51213803 original size:22 final size:22
Alignment explanation
Indices: 51213775--51213839 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
51213765 AATTTAAATT
51213775 TTATATTTATCAAATAATTTAA
1 TTATATTTATCAAATAATTTAA
*
51213797 TTATATTTCAT-AATTAATTTTAA
1 TTATATTT-ATCAAATAA-TTTAA
* *
51213820 GTA-ATATATCAAATATATTT
1 TTATATTTATCAAATA-ATTT
51213840 TTAACTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 2 0.06
22 23 0.66
23 10 0.29
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (22 bp):
TTATATTTATCAAATAATTTAA
Found at i:51218186 original size:29 final size:30
Alignment explanation
Indices: 51218121--51218188 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
51218111 AATTTTAAAA
*
51218121 TTATACATGAATTTTAGTTTAATGTATAATT
1 TTATACATGAATTTGAGTTT-ATGTATAATT
* *
51218152 GTATACATGAACTTTGA-TTT-TGTGTAATT
1 TTATACATGAA-TTTGAGTTTATGTATAATT
51218181 TTATACAT
1 TTATACAT
51218189 AAAATTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 15 0.47
31 13 0.41
32 4 0.12
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (30 bp):
TTATACATGAATTTGAGTTTATGTATAATT
Found at i:51221021 original size:3 final size:3
Alignment explanation
Indices: 51221013--51221041 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
51221003 ATCCCTTGCT
51221013 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
51221042 TATAACTATG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:51222681 original size:31 final size:27
Alignment explanation
Indices: 51222637--51222702 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
51222627 AAAACAACTT
51222637 TTAGTTCTTGAACTTAGCAATTTTTCCCAAC
1 TTAG-TCTTGAACTT--C-ATTTTTCCCAAC
* *
51222668 TTAGTCTTAGAACTTCTTTTTTTCCAAC
1 TTAGTCTT-GAACTTCATTTTTCCCAAC
51222696 TTAGTCT
1 TTAGTCT
51222703 AAGTTCACAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 17 0.53
29 1 0.03
30 4 0.12
31 10 0.31
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (27 bp):
TTAGTCTTGAACTTCATTTTTCCCAAC
Found at i:51224858 original size:21 final size:23
Alignment explanation
Indices: 51224832--51224875 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
51224822 AATTTCAAAA
51224832 TAAATAT-AAA-TAAAAAAAATT
1 TAAATATCAAATTAAAAAAAATT
*
51224853 TAAATATCAAATTAAGAAAAATT
1 TAAATATCAAATTAAAAAAAATT
51224876 GACAAGTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 3 0.15
23 10 0.50
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
TAAATATCAAATTAAAAAAAATT
Found at i:51225101 original size:15 final size:13
Alignment explanation
Indices: 51225071--51225100 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
51225061 TTAACATTAA
51225071 TTTTATTATAGAT
1 TTTTATTATAGAT
*
51225084 TTTTATTATATAT
1 TTTTATTATAGAT
51225097 TTTT
1 TTTT
51225101 TATATAGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
TTTTATTATAGAT
Found at i:51230512 original size:7 final size:7
Alignment explanation
Indices: 51230502--51230528 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
51230492 TTTATTGTTT
51230502 ATAAATA
1 ATAAATA
51230509 ATAAATA
1 ATAAATA
51230516 ATAAATA
1 ATAAATA
51230523 ATAAAT
1 ATAAAT
51230529 TATATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
ATAAATA
Found at i:51230578 original size:15 final size:16
Alignment explanation
Indices: 51230558--51230589 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
51230548 TTTTATAATT
51230558 AATTTTAAA-AATAAA
1 AATTTTAAATAATAAA
51230573 AATTTTAAATAATAAA
1 AATTTTAAATAATAAA
51230589 A
1 A
51230590 TGCGGATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATTTTAAATAATAAA
Found at i:51235960 original size:13 final size:13
Alignment explanation
Indices: 51235942--51235966 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51235932 ATGAAATGTG
51235942 ATTTCAATTTTAA
1 ATTTCAATTTTAA
51235955 ATTTCAATTTTA
1 ATTTCAATTTTA
51235967 TAGGGATTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTCAATTTTAA
Found at i:51236091 original size:19 final size:19
Alignment explanation
Indices: 51236054--51236091 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
51236044 AGGACTCACT
51236054 AAGCTCACTGTAAGTTTTTA
1 AAGCTCACTGT-AGTTTTTA
51236074 AAGCTCACTTGT-GTTTTT
1 AAGCTCAC-TGTAGTTTTT
51236092 TTTTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 8 0.47
21 3 0.18
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.45
Consensus pattern (19 bp):
AAGCTCACTGTAGTTTTTA
Found at i:51236657 original size:150 final size:149
Alignment explanation
Indices: 51236384--51236894 Score: 543
Period size: 150 Copynumber: 3.5 Consensus size: 149
51236374 AACACTCTTG
*
51236384 GTATGAATTCGTAATCTTAAATGATCGTGTTTCAAAAGTTAACTTAGTTTGCATTTTGTGTTT-G
1 GTATGAATTCGTAATCTTAAATGATCGTGTTTCGAAAGTTAACTTAGTTTGCA--TTGTGTTTCG
* * *
51236448 AAATTGAAGTTTGAGATCAAAGTTGTTAAGAATATGGTCTGTATATTTGGGAGCCGAGTGTTGGG
64 AAATCGAAGTTTGATATCAAAGTTGTTAAGAATAAGGTCTGTATATTTGGGAGCCGAGTGTTGGG
*
51236513 ATGGTAAGTACTTCCCGATTA
129 ATGGGAAGTACTTCCCGATTA
** ** *
51236534 GTATGAATTCGTAATCTTAAACCATCACGATTCGAAAGTTAACTTAGTTTGCATTGTGTTTCGAA
1 GTATGAATTCGTAATCTTAAATGATCGTGTTTCGAAAGTTAACTTAGTTTGCATTGTGTTTCGAA
* * * **
51236599 ATCGAATTTTGATATCAAAGTTGTTAAGAATACAGTTCTGTTTATTTGGGAGTGGAGTGTTGGGA
66 ATCGAAGTTTGATATCAAAGTTGTTAAGAATA-AGGTCTGTATATTTGGGAGCCGAGTGTTGGGA
* * *
51236664 TGGGAATTACTTCCTGATTG
130 TGGGAAGTACTTCCCGATTA
* * * *
51236684 GTATGAATTTGTAATCATAAATGATCGTGTTTCGAATGTTAAC-TAGGTTTGCATTTTGTGTTCG
1 GTATGAATTCGTAATCTTAAATGATCGTGTTTCGAAAGTTAACTTA-GTTTGCATTGTGT-TTCG
** **
51236748 AAATCGAAGTTTGAGT-TTGAAGTTGTTAAG----A-------ATA-TTGGGAGTGGAGTGTTGG
64 AAATCGAAGTTTGA-TATCAAAGTTGTTAAGAATAAGGTCTGTATATTTGGGAGCCGAGTGTTGG
* *
51236800 AATGGGAAGTACTTCCCGATTG
128 GATGGGAAGTACTTCCCGATTA
* * *
51236822 GTATGAATTCGTAATCATAAATGATCGTGTTTC-AGATGTTAACTTGGTTTGCATTTTGTGTTT-
1 GTATGAATTCGTAATCTTAAATGATCGTGTTTCGA-AAGTTAACTTAGTTTGCA--TTGTGTTTC
51236885 GAAATCGAAG
63 GAAATCGAAG
51236895 ATAGAATCTG
Statistics
Matches: 315, Mismatches: 37, Indels: 30
0.82 0.10 0.08
Matches are distributed among these distances:
137 1 0.00
138 94 0.30
139 5 0.02
140 5 0.02
146 1 0.00
148 8 0.03
149 34 0.11
150 137 0.43
151 29 0.09
152 1 0.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.39
Consensus pattern (149 bp):
GTATGAATTCGTAATCTTAAATGATCGTGTTTCGAAAGTTAACTTAGTTTGCATTGTGTTTCGAA
ATCGAAGTTTGATATCAAAGTTGTTAAGAATAAGGTCTGTATATTTGGGAGCCGAGTGTTGGGAT
GGGAAGTACTTCCCGATTA
Found at i:51236864 original size:138 final size:138
Alignment explanation
Indices: 51236644--51236894 Score: 432
Period size: 138 Copynumber: 1.8 Consensus size: 138
51236634 TTCTGTTTAT
* * * *
51236644 TTGGGAGTGGAGTGTTGGGATGGGAATTACTTCCTGATTGGTATGAATTTGTAATCATAAATGAT
1 TTGGGAGTGGAGTGTTGGAATGGGAAGTACTTCCCGATTGGTATGAATTCGTAATCATAAATGAT
51236709 CGTGTTTCGAATGTTAACTAGGTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGTTTGAAGTTGT
66 CGTGTTTCGAATGTTAACTAGGTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGTTTGAAGTTGT
51236774 TAAGAATA
131 TAAGAATA
51236782 TTGGGAGTGGAGTGTTGGAATGGGAAGTACTTCCCGATTGGTATGAATTCGTAATCATAAATGAT
1 TTGGGAGTGGAGTGTTGGAATGGGAAGTACTTCCCGATTGGTATGAATTCGTAATCATAAATGAT
* *
51236847 CGTGTTTC-AGATGTTAACTTGGTTTGCATTTTGTGTTTGAAATCGAAG
66 CGTGTTTCGA-ATGTTAACTAGGTTTGCATTTTGTGTTCGAAATCGAAG
51236895 ATAGAATCTG
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
137 1 0.01
138 105 0.99
ACGTcount: A:0.25, C:0.08, G:0.28, T:0.38
Consensus pattern (138 bp):
TTGGGAGTGGAGTGTTGGAATGGGAAGTACTTCCCGATTGGTATGAATTCGTAATCATAAATGAT
CGTGTTTCGAATGTTAACTAGGTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGTTTGAAGTTGT
TAAGAATA
Found at i:51241467 original size:26 final size:26
Alignment explanation
Indices: 51241431--51241514 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
51241421 TGATACAAAT
*
51241431 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
51241457 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
51241483 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
51241509 TGATAA
1 TGATAA
51241515 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:51244514 original size:14 final size:14
Alignment explanation
Indices: 51244463--51244517 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
51244453 ATGTATAGGG
*
51244463 GGTTTGCATGCATCAA
1 GGTTTGCA--CATAAA
*
51244479 GGTTCGCACATAAA
1 GGTTTGCACATAAA
*
51244493 GAGTTTGCACTTAAA
1 G-GTTTGCACATAAA
51244508 GGTTTGCACA
1 GGTTTGCACA
51244518 AGTAAGCATG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
14 14 0.42
15 12 0.36
16 7 0.21
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (14 bp):
GGTTTGCACATAAA
Found at i:51244613 original size:22 final size:22
Alignment explanation
Indices: 51244531--51244617 Score: 66
Period size: 22 Copynumber: 3.9 Consensus size: 22
51244521 AAGCATGCGA
51244531 GGTTCACATGGTAAACTAGGTAG
1 GGTTCACATGGTAAA-TAGGTAG
* * * * * *
51244554 GGTTTACATGTTTAGACATGTAA
1 GGTTCACATG-GTAAATAGGTAG
** **
51244577 GGTTTGCATATTAAATAGGTAG
1 GGTTCACATGGTAAATAGGTAG
51244599 GGTTCACATGGTAAATAGG
1 GGTTCACATGGTAAATAGG
51244618 GTTCGCATGT
Statistics
Matches: 47, Mismatches: 16, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
22 23 0.49
23 21 0.45
24 3 0.06
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.32
Consensus pattern (22 bp):
GGTTCACATGGTAAATAGGTAG
Found at i:51244619 original size:18 final size:18
Alignment explanation
Indices: 51244596--51244631 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
51244586 ATTAAATAGG
51244596 TAGGGTTCACATGGTAAA
1 TAGGGTTCACATGGTAAA
* *
51244614 TAGGGTTCGCATGTTAAA
1 TAGGGTTCACATGGTAAA
51244632 CATGTAAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.31
Consensus pattern (18 bp):
TAGGGTTCACATGGTAAA
Found at i:51244754 original size:15 final size:15
Alignment explanation
Indices: 51244734--51244786 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
51244724 ATCAACTACA
51244734 GTTCGCCTAATAGGG
1 GTTCGCCTAATAGGG
*
51244749 GTTCGCCT-ATAGGA
1 GTTCGCCTAATAGGG
* *
51244763 GTTCACATAA-AGGGG
1 GTTCGCCTAATA-GGG
51244778 GTTCGCCTA
1 GTTCGCCTA
51244787 TTAATTTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (15 bp):
GTTCGCCTAATAGGG
Found at i:51244766 original size:14 final size:15
Alignment explanation
Indices: 51244733--51244766 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
51244723 TATCAACTAC
51244733 AGTTCGCCTAATAGG
1 AGTTCGCCTAATAGG
*
51244748 GGTTCGCCT-ATAGG
1 AGTTCGCCTAATAGG
51244762 AGTTC
1 AGTTC
51244767 ACATAAAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (15 bp):
AGTTCGCCTAATAGG
Found at i:51247931 original size:41 final size:40
Alignment explanation
Indices: 51247882--51248000 Score: 127
Period size: 37 Copynumber: 3.0 Consensus size: 40
51247872 TTTGACTTTG
*
51247882 AGTTGATGAGACACTGGGTATCAATTTATTACTTCGGATTA
1 AGTTGATGAGACACTGGGTGTCAA-TTATTACTTCGGATTA
* * * *
51247923 ATTTGATGAGGCACTGGGTGCCAA-T-TTACTTC-GATTT
1 AGTTGATGAGACACTGGGTGTCAATTATTACTTCGGATTA
* * *
51247960 AGCTGATGAGACACTGGGTGTCAACTTATTGCTTCGAATTA
1 AGTTGATGAGACACTGGGTGTCAA-TTATTACTTCGGATTA
51248001 TCCGATGAGG
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
37 24 0.39
38 7 0.11
39 2 0.03
40 6 0.10
41 23 0.37
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (40 bp):
AGTTGATGAGACACTGGGTGTCAATTATTACTTCGGATTA
Found at i:51250544 original size:18 final size:17
Alignment explanation
Indices: 51250523--51250581 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 17
51250513 TTATTACTTA
51250523 TATTATCATTATTATCAT
1 TATTAT-ATTATTATCAT
*
51250541 TATTATTATTA-TATCAC
1 TATTA-TATTATTATCAT
*
51250558 TATT-TATTATTGT-AT
1 TATTATATTATTATCAT
51250573 TATTATATT
1 TATTATATT
51250582 CATTTTCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 10 0.29
16 6 0.17
17 9 0.26
18 9 0.26
19 1 0.03
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (17 bp):
TATTATATTATTATCAT
Found at i:51253273 original size:12 final size:12
Alignment explanation
Indices: 51253249--51253289 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
51253239 AGTATAACAA
*
51253249 TAAATTTAA-AT
1 TAAAATTAATAT
51253260 TAAAATTAATAT
1 TAAAATTAATAT
*
51253272 TAATATTAATA-
1 TAAAATTAATAT
51253283 TAAAATT
1 TAAAATT
51253290 GTAAACTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 14 0.54
12 12 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAATTAATAT
Found at i:51255143 original size:50 final size:50
Alignment explanation
Indices: 51255068--51255167 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
51255058 TGTCAACATG
* *
51255068 CCATAATGTTCTATTAATACTGAGACTGGAGCATTTGTGTTGAAGGAGTT
1 CCATAATATTCTATTAATACTGAGACTGAAGCATTTGTGTTGAAGGAGTT
** *
51255118 CCATAATATTCTATTAATGTTGAGACTGAAGCATTTGTGTTGATGGAGTT
1 CCATAATATTCTATTAATACTGAGACTGAAGCATTTGTGTTGAAGGAGTT
51255168 TATCCTTCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (50 bp):
CCATAATATTCTATTAATACTGAGACTGAAGCATTTGTGTTGAAGGAGTT
Found at i:51258932 original size:17 final size:17
Alignment explanation
Indices: 51258907--51258940 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
51258897 ATTAACAAAT
*
51258907 AATTCAAAATTTCATAA
1 AATTCAAAAATTCATAA
*
51258924 AATTTAAAAATTCATAA
1 AATTCAAAAATTCATAA
51258941 TTTTTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTCAAAAATTCATAA
Found at i:51260055 original size:19 final size:19
Alignment explanation
Indices: 51260013--51260055 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
51260003 CTATATAATT
* *
51260013 GATACTATTTAATAATTAA
1 GATAATATTTAATAATAAA
*
51260032 GATAATATTTAATTATAAA
1 GATAATATTTAATAATAAA
*
51260051 TATAA
1 GATAA
51260056 ATAACATTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (19 bp):
GATAATATTTAATAATAAA
Found at i:51261072 original size:75 final size:75
Alignment explanation
Indices: 51260972--51261233 Score: 395
Period size: 75 Copynumber: 3.5 Consensus size: 75
51260962 TTTTCGAGGT
* *
51260972 TTGGGTCATTGTCTCGAGGGTTAGAAATCTAGTTACCATAACTATGCAATAGGCAACTTGTTAAC
1 TTGGGTCATTGTCTCGAGGGATAGAAATCTAGTTACCATACCTATGCAATAGGCAACTTGTTAAC
51261037 CAATTGGAGA
66 CAATTGGAGA
* *
51261047 TTGGGTCATTGTCTCGAGGGATAGAAATCTAGTTACCTTACCTATGCCATAGGCAACTTGTTAAC
1 TTGGGTCATTGTCTCGAGGGATAGAAATCTAGTTACCATACCTATGCAATAGGCAACTTGTTAAC
* * *
51261112 CAATCGAAGC
66 CAATTGGAGA
* * *
51261122 TT-GGTCCATTG--TCGAGGGTTAGAAATCTAGTTTCCATACCAATGCAATAGGCAACTTGTTAA
1 TTGGGT-CATTGTCTCGAGGGATAGAAATCTAGTTACCATACCTATGCAATAGGCAACTTGTTAA
51261184 CCAATTGGAGA
65 CCAATTGGAGA
*
51261195 TTGGGTCATTGTCTCGAGGGATAGAAATCTGGTTACCAT
1 TTGGGTCATTGTCTCGAGGGATAGAAATCTAGTTACCAT
51261234 CGATTTTGAT
Statistics
Matches: 165, Mismatches: 18, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
73 61 0.37
74 6 0.04
75 98 0.59
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (75 bp):
TTGGGTCATTGTCTCGAGGGATAGAAATCTAGTTACCATACCTATGCAATAGGCAACTTGTTAAC
CAATTGGAGA
Found at i:51270178 original size:45 final size:45
Alignment explanation
Indices: 51270129--51270288 Score: 241
Period size: 45 Copynumber: 3.6 Consensus size: 45
51270119 GGTATTATGA
* * *
51270129 CCTGCTAGGCTCGAAA-GCCTGAATAGTATCTCACCGGCATTATAG
1 CCTGCTAGGCTC-AAAGGCCCGAATAGTGTCTCACCGGCATAATAG
51270174 CCTGCTAGGCTCAAAGGCCCGAATAGTGTCTCACCGGCATAATAG
1 CCTGCTAGGCTCAAAGGCCCGAATAGTGTCTCACCGGCATAATAG
** *
51270219 CCTGCTAGGCTCAAAGGCTTGAATAGTGTCTCACCAGCATAATAG
1 CCTGCTAGGCTCAAAGGCCCGAATAGTGTCTCACCGGCATAATAG
*
51270264 CTTGCTAGGCTCAAAGGCCCGAATA
1 CCTGCTAGGCTCAAAGGCCCGAATA
51270289 TAATACCAGC
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
44 3 0.03
45 102 0.97
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (45 bp):
CCTGCTAGGCTCAAAGGCCCGAATAGTGTCTCACCGGCATAATAG
Found at i:51270330 original size:38 final size:38
Alignment explanation
Indices: 51270281--51270383 Score: 134
Period size: 38 Copynumber: 2.7 Consensus size: 38
51270271 GGCTCAAAGG
* * * * *
51270281 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGAGATTTAA
51270319 CCCGGATATAATACCAGCACGAAGCCTGCGAGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGAGATTTAA
* **
51270357 CCCGGATATATTTTCAGCACGAAGCCT
1 CCCGGATATAATACCAGCACGAAGCCT
51270384 ACAGGTCTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGAGATTTAA
Found at i:51272148 original size:20 final size:21
Alignment explanation
Indices: 51272117--51272157 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
51272107 GTAGGAATGT
51272117 TTTCTAAAAATTATGCATTGA
1 TTTCTAAAAATTATGCATTGA
*
51272138 TTTCT-AAAATTTTGCATTGA
1 TTTCTAAAAATTATGCATTGA
51272158 CATTATCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (21 bp):
TTTCTAAAAATTATGCATTGA
Found at i:51274823 original size:20 final size:21
Alignment explanation
Indices: 51274775--51274826 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
51274765 AAACCTTGGT
*
51274775 AGGTATCGATA-CTTTTCTTA
1 AGGTATCGATATATTTTCTTA
*
51274795 AGGTGTCGATATATTTTC-TA
1 AGGTATCGATATATTTTCTTA
*
51274815 ATGTATCGATAT
1 AGGTATCGATAT
51274827 TTCTGCTCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (21 bp):
AGGTATCGATATATTTTCTTA
Found at i:51275366 original size:2 final size:2
Alignment explanation
Indices: 51275359--51275391 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
51275349 GAGTAAAAAT
51275359 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
51275392 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:51278836 original size:21 final size:21
Alignment explanation
Indices: 51278809--51278857 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
51278799 ATTGAAATAA
*
51278809 AAAAAAATATTGGCT-TCTATT
1 AAAAAAATATTAGCTCT-TATT
*
51278830 TAAAAAATATTAGCTCTTATT
1 AAAAAAATATTAGCTCTTATT
51278851 AAAAAAA
1 AAAAAAA
51278858 ATATAGCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (21 bp):
AAAAAAATATTAGCTCTTATT
Found at i:51279190 original size:22 final size:22
Alignment explanation
Indices: 51279165--51279207 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
51279155 TCTCCCTATT
51279165 TTGCTACCATTTCATTATTATG
1 TTGCTACCATTTCATTATTATG
* **
51279187 TTGCTACTATTTTGTTATTAT
1 TTGCTACCATTTCATTATTAT
51279208 TGTTTAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.56
Consensus pattern (22 bp):
TTGCTACCATTTCATTATTATG
Found at i:51288619 original size:15 final size:15
Alignment explanation
Indices: 51288599--51288628 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
51288589 AAAGCAAATG
51288599 AACTAGGAAGATCAT
1 AACTAGGAAGATCAT
51288614 AACTAGGAAGATCAT
1 AACTAGGAAGATCAT
51288629 TTTATAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (15 bp):
AACTAGGAAGATCAT
Found at i:51299685 original size:22 final size:23
Alignment explanation
Indices: 51299659--51299701 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
51299649 TAAAATAAAA
**
51299659 TTAGGGATTTAGGTT-ATTTTTG
1 TTAGGGAAATAGGTTGATTTTTG
51299681 TTAGGGAAATAGGTTGATTTT
1 TTAGGGAAATAGGTTGATTTT
51299702 GGAGAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (23 bp):
TTAGGGAAATAGGTTGATTTTTG
Found at i:51312852 original size:77 final size:77
Alignment explanation
Indices: 51312771--51312934 Score: 256
Period size: 77 Copynumber: 2.1 Consensus size: 77
51312761 TCTGCTTGGA
* *
51312771 GAGGTAAAGTAAATTCTGGGTATTTCTTTGATTTAATTTTCTGGGTTTCTTTTTGGTGTTTGTTT
1 GAGGTAAAGTAAATTCTGGGTATTTCTTTGATTTAACTTTCTGGATTTCTTTTTGGTGTTTGTTT
*
51312836 GGTGAAAAAATG
66 GATGAAAAAATG
* **
51312848 GAGGTAAAGTAAATTCTGGGTGTTTCTTTGATTTTGCTTTCTGGATTTCTTTTTGGTGTTTGTTT
1 GAGGTAAAGTAAATTCTGGGTATTTCTTTGATTTAACTTTCTGGATTTCTTTTTGGTGTTTGTTT
*
51312913 GATGAGAAAATG
66 GATGAAAAAATG
*
51312925 AAGGTAAAGT
1 GAGGTAAAGT
51312935 TTAACAATTT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.46
Consensus pattern (77 bp):
GAGGTAAAGTAAATTCTGGGTATTTCTTTGATTTAACTTTCTGGATTTCTTTTTGGTGTTTGTTT
GATGAAAAAATG
Found at i:51324359 original size:15 final size:14
Alignment explanation
Indices: 51324339--51324371 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
51324329 GATTAAATCA
51324339 ATTTTTAATAATATT
1 ATTTTTAATAAT-TT
51324354 ATTTTTAATAATTT
1 ATTTTTAATAATTT
51324368 ATTT
1 ATTT
51324372 AATTAAACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTTTAATAATTT
Found at i:51325706 original size:31 final size:29
Alignment explanation
Indices: 51325645--51325712 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
51325635 ACAGTAATAG
* *
51325645 ATTTTAGTTTATATACTTTGATTTGATCA
1 ATTTTAGTTTATAGACTTTGATTAGATCA
51325674 ATTTTAGTTTATAGACTTTTTGAATTAG-TCA
1 ATTTTAGTTTATAGAC--TTTG-ATTAGATCA
51325705 ATTTTAGT
1 ATTTTAGT
51325713 ATTTGTCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 15 0.44
31 15 0.44
32 4 0.12
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.54
Consensus pattern (29 bp):
ATTTTAGTTTATAGACTTTGATTAGATCA
Found at i:51328969 original size:70 final size:70
Alignment explanation
Indices: 51328851--51328986 Score: 254
Period size: 70 Copynumber: 1.9 Consensus size: 70
51328841 AAATGTTCAG
51328851 ATTGGTATATAAGAACGGTTAGATCCAATCTCTTGATCCCCATGGAAAGGAAAAAGAATTACACA
1 ATTGGTATATAAGAACGGTTAGATCCAATCTCTTGATCCCCATGGAAAGGAAAAAGAATTACACA
51328916 TGAAC
66 TGAAC
* *
51328921 ATTGGTATATAAGTACGGTTAGATCCAATCTCTTGATCCCCATTGAAAGGAAAAAGAATTACACA
1 ATTGGTATATAAGAACGGTTAGATCCAATCTCTTGATCCCCATGGAAAGGAAAAAGAATTACACA
51328986 T
66 T
51328987 TCTTCTTTCT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (70 bp):
ATTGGTATATAAGAACGGTTAGATCCAATCTCTTGATCCCCATGGAAAGGAAAAAGAATTACACA
TGAAC
Found at i:51332093 original size:20 final size:20
Alignment explanation
Indices: 51332068--51332106 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
51332058 ACAAAGAAAC
*
51332068 TAAGTTTAAGTACTTAATTG
1 TAAGTTCAAGTACTTAATTG
51332088 TAAGTTCAAGTACTTAATT
1 TAAGTTCAAGTACTTAATT
51332107 AGATAAAATT
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:0.36, C:0.08, G:0.13, T:0.44
Consensus pattern (20 bp):
TAAGTTCAAGTACTTAATTG
Found at i:51337412 original size:195 final size:195
Alignment explanation
Indices: 51337097--51337487 Score: 660
Period size: 195 Copynumber: 2.0 Consensus size: 195
51337087 AGTAAAGTTC
* * *
51337097 AATACATTTGGATGCATAATTTAGATTTTTTTTGATAATTAAGTTGATCTCAATGCTTATGTTAT
1 AATACATTTGGATACAGAATTTAGATTTTTTTTGATAATTAAGTTGATCTCAATGCTTATATTAT
* * *
51337162 TGTTTCGCAACGAATTAAATGGTTTGAAAAGAGTAAGGTTAATGATTAGGAGGATTTAGTGTTTT
66 TGTTTCGCAAAGAATTAAATGGTTCGAAAAGAGTAAGGTTAATGATTAAGAGGATTTAGTGTTTT
*
51337227 ATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTTGTTTTGTTTTGTTCGAATT
131 ATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTGGTTTTGTTTTGTTCGAATT
51337292 AATACATTTGGATACAGAATTTAGATTTTTTTT-ATAAATTAAGTTGATCTCAATGCTTATATTA
1 AATACATTTGGATACAGAATTTAGATTTTTTTTGAT-AATTAAGTTGATCTCAATGCTTATATTA
* * *
51337356 TTGTTTCGTAAAGAGTTAAATGGTTCG-AAGGAGTAAGGTTAATCGATTAAGAGGATTTAGTGTT
65 TTGTTTCGCAAAGAATTAAATGGTTCGAAAAGAGTAAGGTTAAT-GATTAAGAGGATTTAGTGTT
51337420 TTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTGGTTTTGTTTTGTTCGAA
129 TTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTGGTTTTGTTTTGTTCGAA
51337485 TT
194 TT
51337487 A
1 A
51337488 GATGCTTGAA
Statistics
Matches: 184, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
194 17 0.09
195 167 0.91
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (195 bp):
AATACATTTGGATACAGAATTTAGATTTTTTTTGATAATTAAGTTGATCTCAATGCTTATATTAT
TGTTTCGCAAAGAATTAAATGGTTCGAAAAGAGTAAGGTTAATGATTAAGAGGATTTAGTGTTTT
ATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTGGTTTTGTTTTGTTCGAATT
Found at i:51337668 original size:217 final size:218
Alignment explanation
Indices: 51337292--51337683 Score: 671
Period size: 217 Copynumber: 1.8 Consensus size: 218
51337282 TGTTCGAATT
* *
51337292 AATACATTTGGATACAGAATTTAGATTTTTTTTATAAATTAAGTTGATCTCAATGCTTATATTAT
1 AATACATTGGGATACAGAAATTAGATTTTTTTTATAAATTAAGTTGATCTCAATGCTTATATTAT
51337357 TGTTTCGTAAAGAGTTAAATGGTTCGAAGGAGTAAGGTTAATCGATTAAGAGGATTTAGTGTTTT
66 TGTTTCGTAAAGAGTTAAATGGTTCGAAGGAGTAAGGTTAATCGATTAAGAGGATTTAGTGTTTT
*
51337422 ATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTGGTTTTGTTTTGTTCGAATT
131 ATGGTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTGGTTTTGTTTTGTTCGAATT
51337487 AGATGCTTGAATTAGTAAAGTTC
196 AGATGCTTGAATTAGTAAAGTTC
* *
51337510 AATACATTGGGATACAGAAATTGGATTTTTTTT-TTAATTAAGTTGATCTCAATGCTTATATTAT
1 AATACATTGGGATACAGAAATTAGATTTTTTTTATAAATTAAGTTGATCTCAATGCTTATATTAT
* * * * *
51337574 TGTTTCGTAACGAGTTAGATGGTTTGAAGGAGTAAGGTTAATTGATTAGGAGGATTTAGTGTTTT
66 TGTTTCGTAAAGAGTTAAATGGTTCGAAGGAGTAAGGTTAATCGATTAAGAGGATTTAGTGTTTT
51337639 ATGGTTGATAT-TAGATTTTGATTTTCAGGGAAAATTTGAATTTTT
131 ATGGTTGAT-TCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTT
51337684 TTTTTGGTTG
Statistics
Matches: 163, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
217 132 0.81
218 31 0.19
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (218 bp):
AATACATTGGGATACAGAAATTAGATTTTTTTTATAAATTAAGTTGATCTCAATGCTTATATTAT
TGTTTCGTAAAGAGTTAAATGGTTCGAAGGAGTAAGGTTAATCGATTAAGAGGATTTAGTGTTTT
ATGGTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTGGTTTTGTTTTGTTCGAATT
AGATGCTTGAATTAGTAAAGTTC
Found at i:51348838 original size:163 final size:165
Alignment explanation
Indices: 51348529--51349279 Score: 554
Period size: 163 Copynumber: 4.5 Consensus size: 165
51348519 GGTATTAGAT
* * * * ** * * * *
51348529 ACTTACTCGAGTTCGGCTAATGTAAGAAGTGTATAATGAATTCTCAAAATTATACTTACCTTATT
1 ACTTACTCGAGTTTGGCTAAAGTAAGAA-TGTGTCATGAATTCTCCGAACTATGCTTACTTTACT
* * * * * * * *
51348594 CGAACTCTT-TTTTTACTCTAAAATACCAATGTTTGAAACTTGTTTTTGACACT-TATTC-AATC
65 -AAACTCTTCATTTT-CTCTAAAATACCCATGCTTGATATTTGTTTTTGACA-TGCATGCAAAT-
* * * *
51348656 AT-AGATTTTAATTGTTTTTAGACATACATA-T-TA-AAC
126 GTGAGTTTTTGATTGTTTTTAGACATATATACTATATAAC
* * *
51348692 ACTTACTCGAGTTTGGCTAATGCAA-AAAGTGTCATGAATTCTCCGAACTATGCTTACTTTACTT
1 ACTTACTCGAGTTTGGCTAAAGTAAGAATGTGTCATGAATTCTCCGAACTATGCTTACTTTAC-T
* * * * *
51348756 AAACTTTTCATTTTCTCTAAAACACCCGTGCTCGATATTTGTTTTTGATATGCATGCCAACATG-
65 AAACTCTTCATTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCATG-CAA-ATGT
* * *
51348820 G-GTTTTTGGTTAGTTTTTAGACATGTATACTTGTATAAC
128 GAGTTTTTGATT-GTTTTTAGACATATATAC-TATATAAC
* * ** *
51348859 ACATTTATTTGAGTTCAGCTAAAGTAAGAGATGTGTCATGAATTCTCCGAATTATG------TT-
1 AC--TTACTCGAGTTTGGCTAAAGTAAGA-ATGTGTCATGAATTCTCCGAACTATGCTTACTTTA
*
51348917 C-AAACTCTTCATTTTCTCTAAAATACGCATGCTTGATATTTGTTTTTGACATGCATGCAAATGT
63 CTAAACTCTTCATTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCATGCAAATGT
51348981 GAGTTTTTGATTGTTTTTAGACATATGTATACTCATATCACAC
128 GAGTTTTTGATTGTTTTTAGACATA--TATACT-ATAT-A-AC
* * * *
51349024 ATTTACTCGAGTTTGGCTAAAGTAAGAAGTGTGTCATGAATTATACAAACTATGCTTACTTTACT
1 ACTTACTCGAGTTTGGCTAAAGTAAGAA-TGTGTCATGAATTCTCCGAACTATGCTTACTTTACT
* *** * ***
51349089 CAAACTCTTCATTTTCTCTAAAATACCAATGCTTGATATTTGTTTTTGACACATATACAAACACG
65 -AAACTCTTCATTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCATGCAAATGTG
* ** * * * * *
51349154 AG-TTTTGATTATCATTAAACATGTACACT-TGTATC
129 AGTTTTTGATTGTTTTTAGACATATATACTATATAAC
** * * *
51349189 ACGAACTCAAGTTTGGCTAAAGTAAGAAGTGTGTCATGAATTCTTCGAA-TCATGCTTATTTTAC
1 ACTTACTCGAGTTTGGCTAAAGTAAGAA-TGTGTCATGAATTCTCCGAACT-ATGCTTACTTTA-
* *
51349253 CCAAACCCTTCATTTTCTCTAAAATAC
63 CTAAACTCTTCATTTTCTCTAAAATAC
51349280 TCATATTTGA
Statistics
Matches: 470, Mismatches: 83, Indels: 68
0.76 0.13 0.11
Matches are distributed among these distances:
160 4 0.01
161 78 0.17
162 76 0.16
163 89 0.19
164 5 0.01
165 84 0.18
166 4 0.01
167 7 0.01
169 24 0.05
170 2 0.00
171 40 0.09
172 57 0.12
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (165 bp):
ACTTACTCGAGTTTGGCTAAAGTAAGAATGTGTCATGAATTCTCCGAACTATGCTTACTTTACTA
AACTCTTCATTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCATGCAAATGTGAG
TTTTTGATTGTTTTTAGACATATATACTATATAAC
Found at i:51348957 original size:162 final size:166
Alignment explanation
Indices: 51348756--51349139 Score: 444
Period size: 162 Copynumber: 2.3 Consensus size: 166
51348746 TACTTTACTT
* * * * *
51348756 AAACTTTTCATTTTCTCTAAAACACCCGTGCTCGATATTTGTTTTTGATATGCATGCCAACATG-
1 AAACTCTTCATTTTCTCTAAAATA-CCATGCTTGATATTTGTTTTTGACATGCATG-CAA-ATGT
* ** * *
51348820 G-GTTTTTGGTTAGTTTTTAGAC-ATGTATACTTGTATAACACATTTATTTGAGTTCAGCTAAAG
63 GAGTTTTTGATT-GTTTTTAGACAATGTATACTCATATAACACATTTACTCGAGTTCAGCTAAAG
*
51348883 TAAG-AGATGTGTCATGAATTCT-C-CGA-ATTA-TGT-TC
127 TAAGAAG-TGTGTCATGAATTATACACGAGATTACTGTATC
51348918 AAACTCTTCATTTTCTCTAAAATACGCATGCTTGATATTTGTTTTTGACATGCATGCAAATGTGA
1 AAACTCTTCATTTTCTCTAAAATAC-CATGCTTGATATTTGTTTTTGACATGCATGCAAATGTGA
* **
51348983 GTTTTTGATTGTTTTTAGACATATGTATACTCATATCACACATTTACTCGAGTTTGGCTAAAGTA
65 GTTTTTGATTGTTTTTAGACA-ATGTATACTCATATAACACATTTACTCGAGTTCAGCTAAAGTA
* * *
51349048 AGAAGTGTGTCATGAATTATACAAACTATGCTTACTTTACTC
129 AGAAGTGTGTCATGAATTATAC--ACGA-GATTACTGTA-TC
51349090 AAACTCTTCATTTTCTCTAAAATACCAATGCTTGATATTTGTTTTTGACA
1 AAACTCTTCATTTTCTCTAAAATACC-ATGCTTGATATTTGTTTTTGACA
51349140 CATATACAAA
Statistics
Matches: 189, Mismatches: 17, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
160 3 0.02
161 15 0.08
162 58 0.31
163 52 0.28
164 3 0.02
167 2 0.01
169 3 0.02
170 2 0.01
171 1 0.01
172 50 0.26
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.41
Consensus pattern (166 bp):
AAACTCTTCATTTTCTCTAAAATACCATGCTTGATATTTGTTTTTGACATGCATGCAAATGTGAG
TTTTTGATTGTTTTTAGACAATGTATACTCATATAACACATTTACTCGAGTTCAGCTAAAGTAAG
AAGTGTGTCATGAATTATACACGAGATTACTGTATC
Found at i:51353145 original size:22 final size:23
Alignment explanation
Indices: 51353119--51353163 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
51353109 TTATGTATTT
*
51353119 TATATTATATTAAAAT-TAAATA
1 TATATAATATTAAAATGTAAATA
*
51353141 TATATAATATTATAATGTAAATA
1 TATATAATATTAAAATGTAAATA
51353164 AAACTCTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TATATAATATTAAAATGTAAATA
Found at i:51358964 original size:37 final size:38
Alignment explanation
Indices: 51358908--51358980 Score: 121
Period size: 37 Copynumber: 1.9 Consensus size: 38
51358898 GCTTAACTAT
*
51358908 TTTAATATAGTTTACATTATGAAATTAT-TTTTTTATA
1 TTTAATATAGTTTAAATTATGAAATTATATTTTTTATA
*
51358945 TTTAATATATTTTAAATTATGAAATTATATTTTTTA
1 TTTAATATAGTTTAAATTATGAAATTATATTTTTTA
51358981 CTCAACTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (38 bp):
TTTAATATAGTTTAAATTATGAAATTATATTTTTTATA
Found at i:51359047 original size:41 final size:41
Alignment explanation
Indices: 51358998--51359082 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
51358988 TAATTACCAA
51358998 TAAACTTAATCGAATTCTAATGTCAACTTAAATACAAAAAT
1 TAAACTTAATCGAATTCTAATGTCAACTTAAATACAAAAAT
51359039 TAAACTTAATCGAATTCTAATGTCAACTTAAATACAAAAAT
1 TAAACTTAATCGAATTCTAATGTCAACTTAAATACAAAAAT
51359080 TAA
1 TAA
51359083 TTAAGCTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (41 bp):
TAAACTTAATCGAATTCTAATGTCAACTTAAATACAAAAAT
Found at i:51369606 original size:18 final size:18
Alignment explanation
Indices: 51369585--51369622 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
51369575 TTTAAAAAAA
51369585 TATAAA-TTTTGAAATTTT
1 TATAAAGTTTTG-AATTTT
51369603 TATAAATGTTTTGAATTTT
1 TATAAA-GTTTTGAATTTT
51369622 T
1 T
51369623 TTGTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (18 bp):
TATAAAGTTTTGAATTTT
Found at i:51370387 original size:11 final size:11
Alignment explanation
Indices: 51370358--51370394 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
51370348 TCATGTTAAC
*
51370358 AAATAATT-TT
1 AAATAATTATA
51370368 AAA-AATTATA
1 AAATAATTATA
51370378 AAATAATTATA
1 AAATAATTATA
51370389 AAATAA
1 AAATAA
51370395 AAAATTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
9 4 0.17
10 7 0.29
11 13 0.54
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATAATTATA
Found at i:51377482 original size:59 final size:59
Alignment explanation
Indices: 51377385--51377513 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
51377375 ACCAAAAAAA
* *
51377385 TATAAATTTACTAATAGTTTAGCGACTTTGAATGTAGTTTACCCATAATTAAAACAATC
1 TATAAAATTACTAATAGTTTAGCGACTTTGAATCTAGTTTACCCATAATTAAAACAATC
* * * * * *
51377444 TATAAAATTACTACTAGTTTAGTGATTTTGAATCTAGTTTACCGATAATTAGAACGATC
1 TATAAAATTACTAATAGTTTAGCGACTTTGAATCTAGTTTACCCATAATTAAAACAATC
51377503 TATAAATATTA
1 TATAAA-ATTA
51377514 GATTATGTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
59 57 0.93
60 4 0.07
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (59 bp):
TATAAAATTACTAATAGTTTAGCGACTTTGAATCTAGTTTACCCATAATTAAAACAATC
Found at i:51382631 original size:50 final size:50
Alignment explanation
Indices: 51382556--51382705 Score: 248
Period size: 50 Copynumber: 3.0 Consensus size: 50
51382546 CCATGGAAAC
51382556 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * *
51382606 AAGTGATAAGTAATAACTTCGGCTACACTTATCTGATTAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
51382656 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGG-CAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAA-GGACAAATGA
51382706 CAACNTTCCA
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
50 89 0.98
51 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Done.