Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 118 of 210
Found at i:39559933 original size:6 final size:6
Alignment explanation
Indices: 39559917--39559952 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
39559907 ATCAATTATA
* *
39559917 AGAAAC AGAAAG TGAAAG AGAAAG AGAAAG AGAAAG
1 AGAAAG AGAAAG AGAAAG AGAAAG AGAAAG AGAAAG
39559953 GGAGAATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.64, C:0.03, G:0.31, T:0.03
Consensus pattern (6 bp):
AGAAAG
Found at i:39570195 original size:13 final size:13
Alignment explanation
Indices: 39570177--39570201 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39570167 ATATATATTC
39570177 ATGGAATTGAAAA
1 ATGGAATTGAAAA
39570190 ATGGAATTGAAA
1 ATGGAATTGAAA
39570202 TGAATTGTAT
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:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (13 bp):
ATGGAATTGAAAA
Found at i:39570357 original size:40 final size:40
Alignment explanation
Indices: 39570273--39570348 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
39570263 TGCACCCCAA
* *
39570273 TGCCCCTATAAACACTTCAATGTCCCTGTTTGCACAACTG
1 TGCCCCTATAAACACTTCAATGCCCCTGTTAGCACAACTG
**
39570313 TGCCCCTATAAACACTTCGGTGCCCCTGTTAGCACA
1 TGCCCCTATAAACACTTCAATGCCCCTGTTAGCACA
39570349 TTCGTGCCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (40 bp):
TGCCCCTATAAACACTTCAATGCCCCTGTTAGCACAACTG
Found at i:39570368 original size:40 final size:40
Alignment explanation
Indices: 39570324--39570425 Score: 118
Period size: 40 Copynumber: 2.5 Consensus size: 40
39570314 GCCCCTATAA
* *
39570324 ACACTTCGGTGCCCCTG-TTAGCACATTCGTGCCCTTGACT
1 ACACTTCGGTGCCCCTGATT-GCACACTCGTGCCCTTAACT
* *
39570364 ACAC-TCGGGTGCCCCTGATTGCACACTCGTGCTCTTAATT
1 ACACTTC-GGTGCCCCTGATTGCACACTCGTGCCCTTAACT
* *
39570404 GCACTTCGATGCCCCTGATTGC
1 ACACTTCGGTGCCCCTGATTGC
39570426 CCTTTGGTGC
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
39 2 0.04
40 47 0.89
41 4 0.08
ACGTcount: A:0.16, C:0.34, G:0.21, T:0.29
Consensus pattern (40 bp):
ACACTTCGGTGCCCCTGATTGCACACTCGTGCCCTTAACT
Found at i:39570395 original size:20 final size:20
Alignment explanation
Indices: 39570332--39570425 Score: 61
Period size: 20 Copynumber: 4.7 Consensus size: 20
39570322 AAACACTTCG
*
39570332 GTGCCCCTG-TTAGCACATTC
1 GTGCCCCTGATT-GCACACTC
* *
39570352 GTGCCCTTGACT--ACACTC
1 GTGCCCCTGATTGCACACTC
39570370 GGGTGCCCCTGATTGCACACTC
1 --GTGCCCCTGATTGCACACTC
* * * *
39570392 GTGCTCTTAATTGCAC-TTC
1 GTGCCCCTGATTGCACACTC
39570411 GATGCCCCTGATTGC
1 G-TGCCCCTGATTGC
39570426 CCTTTGGTGC
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
18 5 0.09
19 3 0.05
20 41 0.73
21 1 0.02
22 6 0.11
ACGTcount: A:0.15, C:0.34, G:0.21, T:0.30
Consensus pattern (20 bp):
GTGCCCCTGATTGCACACTC
Found at i:39584461 original size:36 final size:36
Alignment explanation
Indices: 39584411--39584484 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
39584401 TATAGTTGCT
39584411 TTCTTTCAACGTGAAACCTTTCTCTAGATGCATCTG
1 TTCTTTCAACGTGAAACCTTTCTCTAGATGCATCTG
*
39584447 TTCTTTCAATGTGAAACCTTTCTCTAGATGCATCTG
1 TTCTTTCAACGTGAAACCTTTCTCTAGATGCATCTG
39584483 TT
1 TT
39584485 GGTTCTTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (36 bp):
TTCTTTCAACGTGAAACCTTTCTCTAGATGCATCTG
Found at i:39585406 original size:30 final size:30
Alignment explanation
Indices: 39585349--39585408 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
39585339 GCTTTTTGAA
* * * *
39585349 AATATTTACAAAACGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGAAACCAAATTTTT
39585379 AATATTTACAAAAAGAGAAACCAAATTTTT
1 AATATTTACAAAAAGAGAAACCAAATTTTT
39585409 TAAAATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (30 bp):
AATATTTACAAAAAGAGAAACCAAATTTTT
Found at i:39590133 original size:2 final size:2
Alignment explanation
Indices: 39590091--39590115 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39590081 NNNNNNNNNT
39590091 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39590116 GTGTGTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39590794 original size:75 final size:75
Alignment explanation
Indices: 39590671--39591349 Score: 1256
Period size: 75 Copynumber: 9.2 Consensus size: 75
39590661 CGGGTCACCG
39590671 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
1 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
39590736 AACATGAAGA
66 AACATGAAGA
39590746 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
1 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
39590811 AACATGAAGA
66 AACATGAAGA
39590821 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
1 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
39590886 AACATGAAGA
66 AACATGAAGA
39590896 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
1 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
39590961 AACATGAAGA
66 AACATGAAGA
39590971 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
1 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
39591036 AACATGAAGA
66 AACATGAAGA
39591046 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
1 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
39591111 AACATGAAGA
66 AACATGAAGA
39591121 ATAATGTAAAATATGTACGTGTATG-TT-TATATATATA--TATGTATAAATATATTTGTAAGAA
1 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
39591182 AACATGAAGA
66 AACATGAAGA
*
39591192 ATAATGTAAAATATGTACGTGTATG-TT-TATATATATA--TATGTATAAATATATTTCTAAGAA
1 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
39591253 AACATGAAGA
66 AACATGAAGA
39591263 ATAATGTAAAATATGTACGTGTATGTTTATATATATATA--TATG--TAAATATATTTGTAAGAA
1 ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
39591324 AACATGAAGA
66 AACATGAAGA
*
39591334 ATAATATAAAATATGT
1 ATAATGTAAAATATGT
39591350 GGAAACATAC
Statistics
Matches: 599, Mismatches: 3, Indels: 8
0.98 0.00 0.01
Matches are distributed among these distances:
71 171 0.29
72 2 0.00
73 24 0.04
74 2 0.00
75 400 0.67
ACGTcount: A:0.45, C:0.03, G:0.14, T:0.38
Consensus pattern (75 bp):
ATAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTAAGAA
AACATGAAGA
Found at i:39593258 original size:16 final size:16
Alignment explanation
Indices: 39593229--39593279 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
39593219 ACAACTAAAT
*
39593229 TATTA-ATTATAGTTC
1 TATTACATTACAGTTC
*
39593244 TATTTCATTACAGTTC
1 TATTACATTACAGTTC
*
39593260 TATTACATTACAGTTT
1 TATTACATTACAGTTC
39593276 TATT
1 TATT
39593280 CTATTCCCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 4 0.13
16 27 0.87
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (16 bp):
TATTACATTACAGTTC
Found at i:39596403 original size:16 final size:17
Alignment explanation
Indices: 39596379--39596425 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
39596369 TGCCAAGTTC
39596379 ATGCATATCATAACAAA
1 ATGCATATCATAACAAA
* **
39596396 AT-CATATC-TAAGATT
1 ATGCATATCATAACAAA
39596411 ATGCATATCATAACA
1 ATGCATATCATAACA
39596426 CATGCATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
15 6 0.25
16 12 0.50
17 6 0.25
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (17 bp):
ATGCATATCATAACAAA
Found at i:39596430 original size:16 final size:16
Alignment explanation
Indices: 39596378--39596432 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
39596368 TTGCCAAGTT
39596378 CATGCATATCATAACAA
1 CATGCATATCATAAC-A
* *
39596395 AAT-CATATC-TAAGA
1 CATGCATATCATAACA
*
39596409 TTATGCATATCATAACA
1 -CATGCATATCATAACA
39596426 CATGCAT
1 CATGCAT
39596433 TGATTAGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
14 1 0.03
15 5 0.17
16 18 0.60
17 6 0.20
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (16 bp):
CATGCATATCATAACA
Found at i:39603134 original size:4 final size:4
Alignment explanation
Indices: 39603127--39603164 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
39603117 ACTTGCTTGA
39603127 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
39603165 GCATGATGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:39612212 original size:2 final size:2
Alignment explanation
Indices: 39612207--39612235 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39612197 ATATATGAGT
39612207 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
39612236 GGGTTAGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39614047 original size:9 final size:9
Alignment explanation
Indices: 39614033--39614065 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
39614023 CTTAAAGAAC
39614033 AAAAAAAA-
1 AAAAAAAAG
39614041 AAAAAAAAG
1 AAAAAAAAG
*
39614050 AAAAAGAAG
1 AAAAAAAAG
39614059 AAAAAAA
1 AAAAAAA
39614066 GGTAAAGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:39620308 original size:13 final size:13
Alignment explanation
Indices: 39620290--39620314 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39620280 TAAACTCTAT
39620290 TTTCAAGTTATGG
1 TTTCAAGTTATGG
39620303 TTTCAAGTTATG
1 TTTCAAGTTATG
39620315 TTCTATACGT
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:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
TTTCAAGTTATGG
Found at i:39626605 original size:20 final size:20
Alignment explanation
Indices: 39626580--39626617 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39626570 GCAGAAAAGT
39626580 AGCTTGTCTACAATACTGAC
1 AGCTTGTCTACAATACTGAC
* *
39626600 AGCTTGTTTGCAATACTG
1 AGCTTGTCTACAATACTG
39626618 GTGGCTTGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (20 bp):
AGCTTGTCTACAATACTGAC
Found at i:39626671 original size:21 final size:20
Alignment explanation
Indices: 39626610--39626673 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
39626600 AGCTTGTTTG
* *
39626610 CAATACTGGTGGCTTGTCCA
1 CAATACTGGTGGTTTGACCA
* **
39626630 TAATACTGGCAGTTT-ATCCA
1 CAATACTGGTGGTTTGA-CCA
39626650 CAATTACTGGTGGTTTGACCA
1 CAA-TACTGGTGGTTTGACCA
39626671 CAA
1 CAA
39626674 ACTAGTGTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
20 16 0.48
21 16 0.48
22 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (20 bp):
CAATACTGGTGGTTTGACCA
Found at i:39630512 original size:22 final size:22
Alignment explanation
Indices: 39630487--39630535 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
39630477 ACAAAACAAA
* *
39630487 AAGAAAGAAA-AAAATGAAACT
1 AAGAAAGAAATAAAAAGAAAAT
39630508 CAAG-AAGAAATAAAAAGAAAAT
1 -AAGAAAGAAATAAAAAGAAAAT
39630530 AAGAAA
1 AAGAAA
39630536 AGAAGTGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.73, C:0.04, G:0.14, T:0.08
Consensus pattern (22 bp):
AAGAAAGAAATAAAAAGAAAAT
Found at i:39630533 original size:21 final size:21
Alignment explanation
Indices: 39630491--39630534 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
39630481 AACAAAAAGA
* *
39630491 AAGAAAAAAATGAAACTCAAG
1 AAGAAAAAAAAGAAAATCAAG
39630512 AAGAAATAAAAAGAAAAT-AAG
1 AAGAAA-AAAAAGAAAATCAAG
39630533 AA
1 AA
39630535 AAGAAGTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.09
Consensus pattern (21 bp):
AAGAAAAAAAAGAAAATCAAG
Found at i:39635713 original size:30 final size:30
Alignment explanation
Indices: 39635679--39635735 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
39635669 GTAGGCCTAT
**
39635679 CAACAGCGTCCATACAATCACCAGGCCCAG
1 CAACAGCACCCATACAATCACCAGGCCCAG
* *
39635709 CAACAGTACCCATACAATCACCGGGCC
1 CAACAGCACCCATACAATCACCAGGCC
39635736 GAACACTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.33, C:0.40, G:0.16, T:0.11
Consensus pattern (30 bp):
CAACAGCACCCATACAATCACCAGGCCCAG
Found at i:39639461 original size:126 final size:126
Alignment explanation
Indices: 39639232--39639516 Score: 437
Period size: 126 Copynumber: 2.3 Consensus size: 126
39639222 CAAATGGAAG
* * *
39639232 TACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTCTTTCAGTACTTTTGCTGACATTGCATTCTGC
1 TACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTCTTTCAGTACTTTTGCTAACAATGCATCCTGC
* *
39639297 TTGAAGCATTTTGGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAGAAAC
66 TTAAAGCATTTTGGACACTATTTGCTCAAAAACATCTTCTCAAAATTATTTTTTCAGAAAC
* *
39639358 TACTGTAGCAAAAGGGCGTCTACGTGAGAGCTTCTTTCAGTACTTTTGCTAACAATGCATCCTGC
1 TACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTCTTTCAGTACTTTTGCTAACAATGCATCCTGC
* * * *
39639423 TTAAAGCGTGTTT-GACACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAGGAAC
66 TTAAAGCAT-TTTGGACACTATTTGCTCAAAAACATCTTCTCAAAATTATTTTTTCAGAAAC
* *
39639484 TACAGTAGCAAAAGAACGTCCACGTGAGAGCTT
1 TACTGTAGCAAAAGAGCGTCCACGTGAGAGCTT
39639517 TTTTAAATTA
Statistics
Matches: 143, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
126 140 0.98
127 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (126 bp):
TACTGTAGCAAAAGAGCGTCCACGTGAGAGCTTCTTTCAGTACTTTTGCTAACAATGCATCCTGC
TTAAAGCATTTTGGACACTATTTGCTCAAAAACATCTTCTCAAAATTATTTTTTCAGAAAC
Found at i:39639588 original size:7 final size:7
Alignment explanation
Indices: 39639576--39639605 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
39639566 TTTTCCTTAA
39639576 AAACCCT
1 AAACCCT
39639583 AAACCCT
1 AAACCCT
39639590 AAACCCT
1 AAACCCT
39639597 AAACCCT
1 AAACCCT
39639604 AA
1 AA
39639606 TCTAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.13
Consensus pattern (7 bp):
AAACCCT
Found at i:39639750 original size:94 final size:95
Alignment explanation
Indices: 39639541--39639971 Score: 543
Period size: 95 Copynumber: 4.5 Consensus size: 95
39639531 ATAATTAAAT
*
39639541 TAACCCTAAACCTTAATTTATTTGA--TTTTCCTTAAAAACCCTAAACCCTAAACCCTAAACCCT
1 TAACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAA-CCTAAA--C---A--CTAAACCCT
*
39639604 AATCTAATTTTTTTAAAATTTATAGTTAATTTACTCAAG
58 AATCTAA-TTTTTTAAAATTTATAATTAATTTACTCAAG
* *
39639643 TAACCCCAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCTAAACACTAAACCTTAATCT-AT
1 TAACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCTAAACACTAAACCCTAATCTAAT
**
39639707 TTTTTTTAATTTATAATTAATTTACTCAAG
66 TTTTTAAAATTTATAATTAATTTACTCAAG
39639737 TAACCCTAAACCCTAATTTATTTGATTTTTT-CTTAAAAACCTTAAACACTAAACCCTAATCT-A
1 TAACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACC-TAAACACTAAACCCTAATCTAA
39639800 TTTTTTAAAAATTTATAATTAATTTACTCAAG
65 TTTTTT-AAAATTTATAATTAATTTACTCAAG
* * * *
39639832 TAACCCTAAACCTTAATTTATTTAATTTTTT-CTTAAAAGCCATAAACACTAAACTCTAATCTAA
1 TAACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACC-TAAACACTAAACCCTAATCTAA
* * *
39639896 TTTTTTAAAACTTATAATTAATTTAATTAAG
65 TTTTTTAAAATTTATAATTAATTTACTCAAG
* * * * *
39639927 AAACCCTAAACTCTTATTTATTT-AATTTTTCCTTAAAACCCTAAA
1 TAACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCTAAA
39639972 TCTAAAAACC
Statistics
Matches: 299, Mismatches: 24, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
93 10 0.03
94 94 0.31
95 131 0.44
96 20 0.07
98 1 0.00
101 1 0.00
102 23 0.08
103 6 0.02
104 13 0.04
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.41
Consensus pattern (95 bp):
TAACCCTAAACCCTAATTTATTTGATTTTTTCCTTAAAAACCTAAACACTAAACCCTAATCTAAT
TTTTTAAAATTTATAATTAATTTACTCAAG
Found at i:39639829 original size:189 final size:193
Alignment explanation
Indices: 39639541--39639969 Score: 577
Period size: 189 Copynumber: 2.2 Consensus size: 193
39639531 ATAATTAAAT
* *
39639541 TAACCCTAAACCTTAATTTATTTGA-TTTTCCTTAAAAACCCTAAACCCTAAACCCTAAACCCTA
1 TAACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCT--A---TAAACACTAAACCCTA
* * *
39639605 ATCTAATTTTTTTAAAATTTATAGTTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTGATT
61 ATCTAATTTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTAATT
** * *
39639670 TTTTCCTTAAAAACC-TAAACACTAAAC-CTTAATCT-ATTTTTTTTAATTTATAATTAATTTAC
126 TTTT-CTTAAAAACCATAAACACTAAACTC-TAATCTAATTTTTTAAAACTTATAATTAATTTAA
39639732 TCAAG
189 TCAAG
*
39639737 TAACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAA-CCT-TAAACACTAAACCCTAATCT-
1 TAACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTATAAACACTAAACCCTAATCTA
* *
39639799 ATTTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCTTAATTTATTTAATTTTTTC
66 ATTTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTAATTTTTTC
* *
39639864 TTAAAAGCCATAAACACTAAACTCTAATCTAATTTTTTAAAACTTATAATTAATTTAATTAAG
131 TTAAAAACCATAAACACTAAACTCTAATCTAATTTTTTAAAACTTATAATTAATTTAATCAAG
* * * *
39639927 AAACCCTAAACTCTTATTTATTTAATTTTTCCTT-AAAACCCTA
1 TAACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTA
39639970 AATCTAAAAA
Statistics
Matches: 208, Mismatches: 19, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
188 9 0.04
189 81 0.39
190 79 0.38
196 27 0.13
197 12 0.06
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.41
Consensus pattern (193 bp):
TAACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTATAAACACTAAACCCTAATCTA
ATTTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTAATTTTTTC
TTAAAAACCATAAACACTAAACTCTAATCTAATTTTTTAAAACTTATAATTAATTTAATCAAG
Found at i:39649165 original size:13 final size:13
Alignment explanation
Indices: 39649149--39649188 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
39649139 GGTAATATCA
*
39649149 TAAAGTAAAAAAC
1 TAAAATAAAAAAC
39649162 TAAAATAAATAAAC
1 TAAAATAAA-AAAC
*
39649176 AAAAATAAAAAAC
1 TAAAATAAAAAAC
39649189 AAACAACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.15
Consensus pattern (13 bp):
TAAAATAAAAAAC
Found at i:39649189 original size:13 final size:13
Alignment explanation
Indices: 39649154--39649191 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
39649144 TATCATAAAG
*
39649154 TAAAAAACTAAAA
1 TAAAAAACAAAAA
39649167 TAAATAAACAAAAA
1 TAAA-AAACAAAAA
39649181 TAAAAAACAAA
1 TAAAAAACAAA
39649192 CAACTAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (13 bp):
TAAAAAACAAAAA
Found at i:39657172 original size:50 final size:50
Alignment explanation
Indices: 39657094--39657206 Score: 154
Period size: 50 Copynumber: 2.2 Consensus size: 50
39657084 TGATGGATTA
* * **
39657094 TATGGGATAGAAATGCATCAAATGGATTTGCGGAGGAAAGTTTGGTTAAGC
1 TATGGGA-AGAAATGAATCAAATAGATTTGCGGAGGAAAGGCTGGTTAAGC
* *
39657145 TATGGGAATAAATGAATCAAATAGATTTGCGGAGGAAAGGCTGGTTAAGT
1 TATGGGAAGAAATGAATCAAATAGATTTGCGGAGGAAAGGCTGGTTAAGC
*
39657195 TATAGGAAGAAA
1 TATGGGAAGAAA
39657207 GGAGTTTCGC
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
50 47 0.87
51 7 0.13
ACGTcount: A:0.38, C:0.06, G:0.30, T:0.26
Consensus pattern (50 bp):
TATGGGAAGAAATGAATCAAATAGATTTGCGGAGGAAAGGCTGGTTAAGC
Found at i:39668514 original size:19 final size:21
Alignment explanation
Indices: 39668473--39668517 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
39668463 TATAAATACC
39668473 CCCCTTTTTATGTGTAATTTG
1 CCCCTTTTTATGTGTAATTTG
*
39668494 CCCCTTTTT-TG-GTATTTTG
1 CCCCTTTTTATGTGTAATTTG
39668513 CCCCT
1 CCCCT
39668518 AATAATACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 2 0.09
21 9 0.39
ACGTcount: A:0.09, C:0.27, G:0.13, T:0.51
Consensus pattern (21 bp):
CCCCTTTTTATGTGTAATTTG
Found at i:39669100 original size:24 final size:26
Alignment explanation
Indices: 39669061--39669108 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
39669051 AAAGTTTTCC
*
39669061 AAGCTTAAAAACATAAATTGTTCAAG
1 AAGCTTAAAAACATAAACTGTTCAAG
39669087 AAGC-TAAAAA-ATAAACTGTTCA
1 AAGCTTAAAAACATAAACTGTTCA
39669109 TGAATTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 6 0.29
26 4 0.19
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.25
Consensus pattern (26 bp):
AAGCTTAAAAACATAAACTGTTCAAG
Found at i:39669860 original size:21 final size:20
Alignment explanation
Indices: 39669831--39669871 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
39669821 AAGAATTAGT
*
39669831 AAAAATTATAAAAATTGTAA
1 AAAAATTATAAAAAATGTAA
39669851 AAAAATTTATAAAAAATGTAA
1 AAAAA-TTATAAAAAATGTAA
39669872 CATTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAAAAATGTAA
Found at i:39669961 original size:11 final size:11
Alignment explanation
Indices: 39669945--39669979 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
39669935 TTTTATAAAG
39669945 TTGTAAGAAAA
1 TTGTAAGAAAA
39669956 TTGTAAGAAAA
1 TTGTAAGAAAA
*
39669967 TTGTAAAAAAA
1 TTGTAAGAAAA
39669978 TT
1 TT
39669980 TAAAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (11 bp):
TTGTAAGAAAA
Found at i:39669983 original size:10 final size:11
Alignment explanation
Indices: 39669945--39669985 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
39669935 TTTTATAAAG
*
39669945 TTGTAAGAAAA
1 TTGTAAAAAAA
*
39669956 TTGTAAGAAAA
1 TTGTAAAAAAA
39669967 TTGTAAAAAAA
1 TTGTAAAAAAA
39669978 TT-TAAAAA
1 TTGTAAAAA
39669986 TATAAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 6 0.21
11 23 0.79
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (11 bp):
TTGTAAAAAAA
Found at i:39669992 original size:26 final size:28
Alignment explanation
Indices: 39669963--39670014 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
39669953 AAATTGTAAG
39669963 AAAA-TTGTAAAAAAATT-TAAAAATAT
1 AAAATTTGTAAAAAAATTATAAAAATAT
39669989 AAAATTTGTAAAAAAATTATAAAAAT
1 AAAATTTGTAAAAAAATTATAAAAAT
39670015 TATCATGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 4 0.17
27 13 0.54
28 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (28 bp):
AAAATTTGTAAAAAAATTATAAAAATAT
Found at i:39672230 original size:19 final size:20
Alignment explanation
Indices: 39672192--39672232 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
39672182 TAGAAAAATC
39672192 TTATTATGTATAAATTATAA
1 TTATTATGTATAAATTATAA
39672212 TTATTA-GT-TAAATTTATAA
1 TTATTATGTATAAA-TTATAA
39672231 TT
1 TT
39672233 TCCAGATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 10 0.50
20 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TTATTATGTATAAATTATAA
Found at i:39672321 original size:21 final size:24
Alignment explanation
Indices: 39672297--39672341 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 24
39672287 TCAAGTGTAA
*
39672297 TTTGAACAA-AAA-AAA-TTATTT
1 TTTGAAAAATAAATAAATTTATTT
39672318 TTTGAAAAATAAATAAATTTATTT
1 TTTGAAAAATAAATAAATTTATTT
39672342 CCAGTTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 3 0.15
23 3 0.15
24 6 0.30
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
TTTGAAAAATAAATAAATTTATTT
Found at i:39674813 original size:26 final size:26
Alignment explanation
Indices: 39674784--39674835 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
39674774 GCTTCAAGAT
*
39674784 CCAAAATGTATAACTTGTGTCAAATA
1 CCAAAATGCATAACTTGTGTCAAATA
*
39674810 CCAAAATGCATAACTTTTGTCAAATA
1 CCAAAATGCATAACTTGTGTCAAATA
39674836 TAAGTACCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (26 bp):
CCAAAATGCATAACTTGTGTCAAATA
Found at i:39675333 original size:83 final size:84
Alignment explanation
Indices: 39675232--39675402 Score: 335
Period size: 83 Copynumber: 2.0 Consensus size: 84
39675222 AATAAAAAAA
39675232 ATTAGATTAAATTGTGAGTAAAACAAAAATCTAAACACAAAAATACATCATATTAATAATACTAA
1 ATTAGATTAAATTGTGAGTAAAACAAAAATCTAAACACAAAAATACATCATATTAATAATACTAA
39675297 ATGAATATAATTGTTTATC
66 ATGAATATAATTGTTTATC
39675316 ATTAGATT-AATTGTGAGTAAAACAAAAATCTAAACACAAAAATACATCATATTAATAATACTAA
1 ATTAGATTAAATTGTGAGTAAAACAAAAATCTAAACACAAAAATACATCATATTAATAATACTAA
39675380 ATGAATATAATTGTTTATC
66 ATGAATATAATTGTTTATC
39675399 ATTA
1 ATTA
39675403 TTAAAGTTTC
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 79 0.91
84 8 0.09
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (84 bp):
ATTAGATTAAATTGTGAGTAAAACAAAAATCTAAACACAAAAATACATCATATTAATAATACTAA
ATGAATATAATTGTTTATC
Found at i:39678105 original size:16 final size:17
Alignment explanation
Indices: 39678079--39678112 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
39678069 ATTAGTTTTA
39678079 AAAATATAAATATACAT
1 AAAATATAAATATACAT
39678096 AAAA-ATAAATATACAT
1 AAAATATAAATATACAT
39678112 A
1 A
39678113 TTAACTGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATATAAATATACAT
Found at i:39678290 original size:3 final size:3
Alignment explanation
Indices: 39678282--39678331 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
39678272 GAAAATTCTC
* *
39678282 ATA ATA ATA GTA ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
39678328 ATA A
1 ATA A
39678332 CAATTTGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39679952 original size:44 final size:44
Alignment explanation
Indices: 39679901--39680010 Score: 132
Period size: 44 Copynumber: 2.5 Consensus size: 44
39679891 TTCTGCTCTT
* * *
39679901 TGCAACTTCAGAGAGATAAGATCCA-AGGTTTTAATCCGCTTCAC
1 TGCAACTTCAGGGAGATAAGAT-CATAGGCTTTAATCCGCTCCAC
* * * *
39679945 TGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATCATAGGCTTTAATCCGCTCCAC
*
39679989 TGCAACTTTAGGGAGATAAGAT
1 TGCAACTTCAGGGAGATAAGAT
39680011 TTGCCATATT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 1 0.02
44 55 0.98
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
TGCAACTTCAGGGAGATAAGATCATAGGCTTTAATCCGCTCCAC
Found at i:39680394 original size:45 final size:45
Alignment explanation
Indices: 39680335--39680524 Score: 206
Period size: 45 Copynumber: 4.2 Consensus size: 45
39680325 GCCAATACAT
39680335 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGA
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGA
* * * * *
39680380 GAAGACAAGATCTGCTTTATTTGATTTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGA
* * * * * *
39680425 GAAGGCAAGATCTGGTATC-TCTGATCTACTTC-ACGCCAGTA-CA
1 GAAGACAAGATCTGCTTTCTTC-GATCTACTTCGCCACCAGTATGA
** * *
39680468 TGAAGACAAGATCTGCTTTCTTCGATCTGTTTCTCCACCAGTATGG
1 -GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGA
39680514 GAAGACAAGAT
1 GAAGACAAGAT
39680525 GTATTCTTTA
Statistics
Matches: 115, Mismatches: 25, Indels: 10
0.77 0.17 0.07
Matches are distributed among these distances:
44 32 0.28
45 83 0.72
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (45 bp):
GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGA
Found at i:39680599 original size:44 final size:44
Alignment explanation
Indices: 39680536--39680913 Score: 405
Period size: 44 Copynumber: 8.7 Consensus size: 44
39680526 TATTCTTTAT
* * * *
39680536 CTATTCCACGGCTGCCCAGGGAGATAGAATTCTCAATCTTCAGC
1 CTATTCCACTGCTGACCAGGGAGATAGGATTCTCAATCTTCAAC
* *
39680580 CTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAAC
1 CTATTCCACTGCTGACCAGGGAGATAGGATTCTCAATCTTCAAC
** * *
39680624 CTATTCCACTGCTGTTCAGGGAGATAGG--GCTC--T-TT-AAT
1 CTATTCCACTGCTGACCAGGGAGATAGGATTCTCAATCTTCAAC
* *
39680662 CTATTCCACTGCTG-CTCAGGGAGATAGAATTCTCAATCTTCAAT
1 CTATTCCACTGCTGAC-CAGGGAGATAGGATTCTCAATCTTCAAC
* * *
39680706 CTATTCCACTGCTGATCAGGGAGATAGGA-CCTACAATCTTCAAT
1 CTATTCCACTGCTGACCAGGGAGATAGGATTCT-CAATCTTCAAC
*
39680750 CTATTCCACTGCTG-CCTAGGGAGATAGAATTCTCAATCTTCAAC
1 CTATTCCACTGCTGACC-AGGGAGATAGGATTCTCAATCTTCAAC
* ** *
39680794 CTATTCCATTGCTGACCAGGGAGATAGGATTCAGAATCTTTAAC
1 CTATTCCACTGCTGACCAGGGAGATAGGATTCTCAATCTTCAAC
* ** * * * *
39680838 CTATTCGACTATTGTCCAGGGAGATAGGATTCTTTAATCTTTAGC
1 CTATTCCACTGCTGACCAGGGAGATAGGATTC-TCAATCTTCAAC
39680883 CTATTCCACTGCTGACCAGGGAGATAAGGAT
1 CTATTCCACTGCTGACCAGGGAGAT-AGGAT
39680914 GGGGACATCA
Statistics
Matches: 282, Mismatches: 38, Indels: 26
0.82 0.11 0.08
Matches are distributed among these distances:
38 27 0.10
39 2 0.01
40 4 0.01
42 3 0.01
43 5 0.02
44 202 0.72
45 34 0.12
46 5 0.02
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (44 bp):
CTATTCCACTGCTGACCAGGGAGATAGGATTCTCAATCTTCAAC
Found at i:39680759 original size:126 final size:125
Alignment explanation
Indices: 39680529--39680908 Score: 379
Period size: 126 Copynumber: 3.0 Consensus size: 125
39680519 CAAGATGTAT
*
39680529 TCTTTATCTATTCCACGGCTGCCCAGGGAGATAGAATTCTCAATCTTCAGCCTATTCCACTGCTG
1 TCTTTATCTATTCCACGGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTG
* * *
39680594 ACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTG-TTCAGGGAGATAGGGC
66 ACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGCCT-AGGGAGATAGGGC
* * *
39680654 TCTTTAATCTATTCCACTGCTGCTCAGGGAGATAGAATTCTCAATCTTCAATCTATTCCACTGCT
1 TCTTT-ATCTATTCCACGGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCT
* * **
39680719 GATCAGGGAGATAGGAC-CTACAATCTTCAATCTATTCCACTGCTGCCTAGGGAGATAGAATTC
65 GACCAGGGAGATAGGACTC-ACAATCTTCAACCTATTCCACTGCTGCCTAGGGAGATAG--GGC
* ** * * ** * *
39680782 TCAATCTTCAACCTATTCCATTGCTGACCAGGGAGATAGGATTCAGAATCTTTAACCTATTCGAC
1 TC--T-TT--ATCTATTCCACGGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCAC
** * * ** * *
39680847 TATTGTCCAGGGAGATAGGATTCTTTAATCTTTAGCCTATTCCACTGCTGACC-AGGGAGATA
61 TGCTGACCAGGGAGATAGGACTC-ACAATCTTCAACCTATTCCACTGCTG-CCTAGGGAGATA
39680909 AGGATGGGGA
Statistics
Matches: 213, Mismatches: 31, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
125 6 0.03
126 104 0.49
127 1 0.00
128 3 0.01
130 1 0.00
131 2 0.01
132 62 0.29
133 32 0.15
134 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (125 bp):
TCTTTATCTATTCCACGGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTG
ACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGCCTAGGGAGATAGGGC
Found at i:39681052 original size:88 final size:88
Alignment explanation
Indices: 39680924--39681320 Score: 641
Period size: 88 Copynumber: 4.5 Consensus size: 88
39680914 GGGGACATCA
* * * *
39680924 ATCTGTTTCGCTGTCGGTGTAGGAAGGCAAGATCTACTATTTTTAACCTACTCCGCTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
39680989 GGGAGGCAAGGCTGGTGTCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
* * *
39681012 ATCTGCTTCTCTGTCGGTGCAGGAGGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
*
39681077 GGGAGGCAAGGCTGGTGTCTTTG
66 GGGAGGCAAGGCTGGTGTCTTCG
* *
39681100 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTTCTCCGCTGTAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
* * *
39681165 GGGAGGCAAGGTTGTTATCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
* * *
39681188 ATCTGCTTCACTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGTTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
*
39681253 GGGAGGCAAGGCTGGTGTCTTTG
66 GGGAGGCAAGGCTGGTGTCTTCG
39681276 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
39681321 CTGATCTGCT
Statistics
Matches: 281, Mismatches: 28, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 281 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (88 bp):
ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
GGGAGGCAAGGCTGGTGTCTTCG
Found at i:39681304 original size:44 final size:44
Alignment explanation
Indices: 39680987--39681315 Score: 162
Period size: 44 Copynumber: 7.5 Consensus size: 44
39680977 CGCTGCAACC
* * * * *
39680987 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCTCTGTCGGTG
1 CAGGAAGGCAAGGCTGCTATCTTTGATCTGCTTCGCTGTCGGTG
* * * * * ****
39681031 CAGGAGGGCAAGATCTGCTAT-TTTTAGCCTGCTCCGCTG-CAACC
1 CAGGAAGGCAAG-GCTGCTATCTTTGA-TCTGCTTCGCTGTCGGTG
* * *
39681075 CAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGGCTGCTATCTTTGATCTGCTTCGCTGTCGGTG
* * * * * * ****
39681119 CAGGAAGGCAAGATCTGCTATTTTTAACCTTCTCCGCTGT-AACC
1 CAGGAAGGCAAG-GCTGCTATCTTTGATCTGCTTCGCTGTCGGTG
* * * * *
39681163 CAGGGAGGCAAGGTTGTTATCTTCGATCTGCTTCACTGTCGGTG
1 CAGGAAGGCAAGGCTGCTATCTTTGATCTGCTTCGCTGTCGGTG
* * * * * * * ****
39681207 TAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGTTG-CAACC
1 CAGGAAGGCAAG-GCTGCTATCTTTGATCTGCTTCGCTGTCGGTG
* * *
39681251 CAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGGCTGCTATCTTTGATCTGCTTCGCTGTCGGTG
*
39681295 CAGGAAGGCAAGATCTGCTAT
1 CAGGAAGGCAAG-GCTGCTAT
39681316 TTTTACTGAT
Statistics
Matches: 188, Mismatches: 88, Indels: 17
0.64 0.30 0.06
Matches are distributed among these distances:
43 50 0.27
44 84 0.45
45 54 0.29
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.29
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGCTATCTTTGATCTGCTTCGCTGTCGGTG
Found at i:39682442 original size:42 final size:42
Alignment explanation
Indices: 39682395--39682497 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 42
39682385 TAGATTACCA
* * *
39682395 CATGCCCCAATCTGATCAAGATTCGAGTTGCTCTAATCACTT
1 CATGCCCCATTCTGATCAAGATTCGAGTCGCTCTAATCACCT
** * ** * *
39682437 CATGCCTTATTTTGATCACTATTTGAGTCGCTCTGATCACCT
1 CATGCCCCATTCTGATCAAGATTCGAGTCGCTCTAATCACCT
*
39682479 CATGTCCCATTCTGATCAA
1 CATGCCCCATTCTGATCAA
39682498 AATTTGAGCC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (42 bp):
CATGCCCCATTCTGATCAAGATTCGAGTCGCTCTAATCACCT
Found at i:39687087 original size:17 final size:17
Alignment explanation
Indices: 39687065--39687101 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 17
39687055 ATATTAGTTT
39687065 TAAAAATATAAATATACA
1 TAAAAA-ATAAATATACA
39687083 TAAAAAATAAATATACA
1 TAAAAAATAAATATACA
39687100 TA
1 TA
39687102 TATATATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAAAATAAATATACA
Found at i:39687147 original size:3 final size:3
Alignment explanation
Indices: 39687139--39687181 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
39687129 GCATATGAAT
* * *
39687139 ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATT ATA ATG ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
39687182 CAATTTATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:39687175 original size:15 final size:15
Alignment explanation
Indices: 39687142--39687186 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
39687132 TATGAATATA
* *
39687142 ATAATAATAATAGTA
1 ATAATAATAATAATT
39687157 ATAATAATAATAATT
1 ATAATAATAATAATT
* *
39687172 ATAATGATAACAATT
1 ATAATAATAATAATT
39687187 TATTTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (15 bp):
ATAATAATAATAATT
Found at i:39687214 original size:3 final size:3
Alignment explanation
Indices: 39687208--39687272 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
39687198 ATGAATTACA
39687208 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
39687256 AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AA
39687273 ATGCAATTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39691857 original size:13 final size:14
Alignment explanation
Indices: 39691839--39691867 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
39691829 TTGTTGCTGA
39691839 TTTTTCCC-CTTCT
1 TTTTTCCCTCTTCT
39691852 TTTTTCCCTCTTCT
1 TTTTTCCCTCTTCT
39691866 TT
1 TT
39691868 ACTTTGTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTTCCCTCTTCT
Found at i:39692772 original size:205 final size:206
Alignment explanation
Indices: 39692406--39692819 Score: 821
Period size: 205 Copynumber: 2.0 Consensus size: 206
39692396 TTTAATGAGA
39692406 TTGTTGTATTGCAGATGTCTGTCAACAAGTTTGAAGTCAATCTTCATCGGTTGTAAAAGTGACCT
1 TTGTTGTATTGCAGATGTCTGTCAACAAGTTTGAAGTCAATCTTCATCGGTTGTAAAAGTGACCT
39692471 AAGCCATTTTTGTTAGTCGAGGCAAGTATTAGTTTAATTTTGATCATGGATGTATAAGAAGGAGA
66 AAGCCATTTTTGTTAGTCGAGGCAAGTATTAGTTTAATTTTGATCATGGATGTATAAGAAGGAGA
39692536 TTAGTCCTATTGTTAGCTATTAATGGAAAATGTGTTTGAATGCAGATTTTGGGTGTTTGTAGATC
131 TTAGTCCTATTGTTAGCTATTAATGGAAAATGTGTTTGAATGCAGATTTTGGGTGTTTGTAGATC
39692601 TAGGTGCGCCT
196 TAGGTGCGCCT
39692612 TTGTTGTATTGCA-ATGTCTGTCAACAAGTTTGAAGTCAATCTTCATCGGTTGTAAAAGTGACCT
1 TTGTTGTATTGCAGATGTCTGTCAACAAGTTTGAAGTCAATCTTCATCGGTTGTAAAAGTGACCT
39692676 AAGCCATTTTTGTTAGTCGAGGCAAGTATTAGTTTAATTTTGATCATGGATGTATAAGAAGGAGA
66 AAGCCATTTTTGTTAGTCGAGGCAAGTATTAGTTTAATTTTGATCATGGATGTATAAGAAGGAGA
39692741 TTAGTCCTATTGTTAGCTATTAATGGAAAATGTGTTTGAATGCAGATTTTGGGTGTTTGTAGATC
131 TTAGTCCTATTGTTAGCTATTAATGGAAAATGTGTTTGAATGCAGATTTTGGGTGTTTGTAGATC
39692806 TAGGTGCGCCT
196 TAGGTGCGCCT
39692817 TTG
1 TTG
39692820 CAATCAGGTG
Statistics
Matches: 208, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
205 195 0.94
206 13 0.06
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (206 bp):
TTGTTGTATTGCAGATGTCTGTCAACAAGTTTGAAGTCAATCTTCATCGGTTGTAAAAGTGACCT
AAGCCATTTTTGTTAGTCGAGGCAAGTATTAGTTTAATTTTGATCATGGATGTATAAGAAGGAGA
TTAGTCCTATTGTTAGCTATTAATGGAAAATGTGTTTGAATGCAGATTTTGGGTGTTTGTAGATC
TAGGTGCGCCT
Found at i:39692987 original size:27 final size:27
Alignment explanation
Indices: 39692946--39693169 Score: 200
Period size: 27 Copynumber: 8.3 Consensus size: 27
39692936 AGGAATCATG
* * * *
39692946 GGTAAAATGATCGAATTACCCCCGAAA
1 GGTAAAATTACCGAAATACCCTCGAAA
*
39692973 GGTAAAATTACCGAAACACCCTC-AAA
1 GGTAAAATTACCGAAATACCCTCGAAA
* * *
39692999 GGGTAAAATTATCGAAATACCTTCGAAG
1 -GGTAAAATTACCGAAATACCCTCGAAA
**
39693027 GGTAAAATTACTAAAATACCCTCGAAA
1 GGTAAAATTACCGAAATACCCTCGAAA
* *
39693054 GGTAAAATTACCAAAATACCCTCGAAG
1 GGTAAAATTACCGAAATACCCTCGAAA
*** * *
39693081 GGTAAAATTTTTGAAATACCTTCAAAA
1 GGTAAAATTACCGAAATACCCTCGAAA
* * *
39693108 GATAAAATTACCAAAATACCC-CTGAAG
1 GGTAAAATTACCGAAATACCCTC-GAAA
* * * *
39693135 GGTAAAATTATCGAGATACCCCCGAAG
1 GGTAAAATTACCGAAATACCCTCGAAA
39693162 GGTAAAAT
1 GGTAAAAT
39693170 GATTGTTATT
Statistics
Matches: 158, Mismatches: 35, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
26 4 0.03
27 151 0.96
28 3 0.02
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (27 bp):
GGTAAAATTACCGAAATACCCTCGAAA
Found at i:39693053 original size:81 final size:80
Alignment explanation
Indices: 39692965--39693169 Score: 275
Period size: 81 Copynumber: 2.5 Consensus size: 80
39692955 ATCGAATTAC
* * * * *
39692965 CCCCGAAAGGTAAAATTACCGAAACACCCTCAAAGGGTAAAATTATCGAAATACCTTCGAAGGGT
1 CCCCGAAAGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTATCGAAATACCTTCAAAAGAT
*
39693030 AAAATTACTAAAATA
66 AAAATTACCAAAATA
* * *
39693045 CCCTCGAAAGGTAAAATTACCAAAATACCCTCGAAGGGTAAAATTTTTGAAATACCTTCAAAAGA
1 CCC-CGAAAGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTATCGAAATACCTTCAAAAGA
39693110 TAAAATTACCAAAATA
65 TAAAATTACCAAAATA
* * * *
39693126 CCCCTGAAGGGTAAAATTATCGAGATACCCCCGAAGGGTAAAAT
1 CCCC-GAAAGGTAAAATTACCGAAATACCCTCGAAGGGTAAAAT
39693170 GATTGTTATT
Statistics
Matches: 109, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
80 4 0.04
81 105 0.96
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (80 bp):
CCCCGAAAGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTATCGAAATACCTTCAAAAGAT
AAAATTACCAAAATA
Found at i:39693601 original size:32 final size:30
Alignment explanation
Indices: 39693527--39693601 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 30
39693517 TAACTGCATT
*
39693527 GTACTGATTACTGTTTTGGGCTAGGGCCCAC
1 GTACTG-TTACTGTTTTGGGCTAGGCCCCAC
39693558 -TCACTGTTACTGTTTTGGGCTTA-GCCCACAC
1 GT-ACTGTTACTGTTTTGGGC-TAGGCCC-CAC
39693589 GGTACTGTTACTG
1 -GTACTGTTACTG
39693602 AATATGGCTC
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
30 18 0.47
31 9 0.24
32 10 0.26
33 1 0.03
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (30 bp):
GTACTGTTACTGTTTTGGGCTAGGCCCCAC
Found at i:39694096 original size:20 final size:20
Alignment explanation
Indices: 39694071--39694111 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
39694061 CCAAAATTAG
39694071 GAAACGACTTTTATCAACAA
1 GAAACGACTTTTATCAACAA
*
39694091 GAAACGAGTTTTATCAACAA
1 GAAACGACTTTTATCAACAA
39694111 G
1 G
39694112 TCTAAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (20 bp):
GAAACGACTTTTATCAACAA
Found at i:39699403 original size:20 final size:20
Alignment explanation
Indices: 39699378--39699416 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
39699368 TAAACGCAAA
39699378 TGAGCTTAA-AATGAGCTGAT
1 TGAGC-TAAGAATGAGCTGAT
*
39699398 TGAGCTAAGAGTGAGCTGA
1 TGAGCTAAGAATGAGCTGA
39699417 ATGAACTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.26
Consensus pattern (20 bp):
TGAGCTAAGAATGAGCTGAT
Found at i:39701351 original size:17 final size:19
Alignment explanation
Indices: 39701319--39701368 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
39701309 GAACACACTC
*
39701319 TCTTCCTTCATCTTTTC-TTT
1 TCTT-CTTC-TCTTTTCAGTT
39701339 TCTTCTT-TCTTTTCAGTT
1 TCTTCTTCTCTTTTCAGTT
39701357 TCTTCTTCTCTT
1 TCTTCTTCTCTT
39701369 GTTGCCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.26
18 9 0.33
19 7 0.26
20 4 0.15
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.66
Consensus pattern (19 bp):
TCTTCTTCTCTTTTCAGTT
Found at i:39702316 original size:27 final size:27
Alignment explanation
Indices: 39702274--39702449 Score: 205
Period size: 27 Copynumber: 6.5 Consensus size: 27
39702264 TACGAATCGT
*
39702274 GGGTAAAATGACTGAAATACCCTCGAA
1 GGGTAAAATTACTGAAATACCCTCGAA
* **
39702301 GGGTAAAATTATTGAAATACCCTTAAA
1 GGGTAAAATTACTGAAATACCCTCGAA
* *
39702328 AGGTAAAATTACTGAAATACACTCGAA
1 GGGTAAAATTACTGAAATACCCTCGAA
**
39702355 GAATAAAATTA-TCGAAATACCCTCGAA
1 GGGTAAAATTACT-GAAATACCCTCGAA
*
39702382 GGGTAAAATTACTGAAATACCC-CTAAA
1 GGGTAAAATTACTGAAATACCCTC-GAA
*
39702409 GGGTAAAATTACTGAGATACCC-CTGAA
1 GGGTAAAATTACTGAAATACCCTC-GAA
*
39702436 GGGTAAAATGACTG
1 GGGTAAAATTACTG
39702450 TTATACCCCT
Statistics
Matches: 127, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.02
27 124 0.98
28 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (27 bp):
GGGTAAAATTACTGAAATACCCTCGAA
Found at i:39702457 original size:81 final size:81
Alignment explanation
Indices: 39702274--39702449 Score: 248
Period size: 81 Copynumber: 2.2 Consensus size: 81
39702264 TACGAATCGT
* *
39702274 GGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATTATTGAAATACCCTTAAAAGGTAAAATTA
1 GGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCTAAAAGGTAAAATTA
39702339 CTGAAATACACTCGAA
66 CTGAAATACACTCGAA
** * *
39702355 GAATAAAATTA-TCGAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCTAAAGGGTAAAATT
1 GGGTAAAATGACT-GAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCTAAAAGGTAAAATT
* *
39702419 ACTGAGATAC-CCCTGAA
65 ACTGAAATACACTC-GAA
39702436 GGGTAAAATGACTG
1 GGGTAAAATGACTG
39702450 TTATACCCCT
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
80 3 0.04
81 77 0.95
82 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (81 bp):
GGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATTACTGAAATACCCCTAAAAGGTAAAATTA
CTGAAATACACTCGAA
Found at i:39702682 original size:26 final size:26
Alignment explanation
Indices: 39702627--39702699 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
39702617 ACATATACTG
* ** * *
39702627 TTACTGGCAGCCTTGCTGTATTATTG
1 TTACTGGCAGCTTTGCTGCGTCATTA
39702653 TTACTGGCAGCTTTGCTGCGTCATTA
1 TTACTGGCAGCTTTGCTGCGTCATTA
* *
39702679 TTACTGGTAGCTCTGCTGCGT
1 TTACTGGCAGCTTTGCTGCGT
39702700 TATTGGTGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.40
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCGTCATTA
Found at i:39707038 original size:13 final size:13
Alignment explanation
Indices: 39707022--39707071 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
39707012 TTTAAACCAA
39707022 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
* *
39707035 ACTTCTCAAAAGC
1 ACTTTTCAAAAAC
* *
39707048 ACTTTTCTATAAC
1 ACTTTTCAAAAAC
39707061 ACTTTTCAAAA
1 ACTTTTCAAAA
39707072 GTATTGCCAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:39707061 original size:26 final size:26
Alignment explanation
Indices: 39707022--39707072 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
39707012 TTTAAACCAA
39707022 ACTTTTCAAAAACACTTCTCAAAAGC
1 ACTTTTCAAAAACACTTCTCAAAAGC
* * *
39707048 ACTTTTCTATAACACTTTTCAAAAG
1 ACTTTTCAAAAACACTTCTCAAAAG
39707073 TATTGCCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (26 bp):
ACTTTTCAAAAACACTTCTCAAAAGC
Found at i:39707365 original size:7 final size:7
Alignment explanation
Indices: 39707355--39707390 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
39707345 ATAATTTTCA
39707355 AAAATTT
1 AAAATTT
39707362 AAAATTT
1 AAAATTT
39707369 AAAATTT
1 AAAATTT
39707376 AAAATTT
1 AAAATTT
39707383 AAAATTT
1 AAAATTT
39707390 A
1 A
39707391 GTATTTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAAATTT
Found at i:39712376 original size:50 final size:50
Alignment explanation
Indices: 39712310--39712498 Score: 218
Period size: 51 Copynumber: 3.7 Consensus size: 50
39712300 ATTATTATCA
* * *
39712310 TTCGATACACGTAGTAGCCTTCACATAGTACTACACATGTGATCAAACTT
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAACTT
* * * *
39712360 TTCGGTTCACGTAGTAGCCTGCACATAATACTACACACGTGACCAAAGCCT
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAA-CTT
* * * *
39712411 TCCGGTACACATAGTAGACTGCACATAGTACTACACATGTGACCATTA-TCT
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA-AACT-T
* * *
39712462 ATCGATACACGTAGTAGCCTGCACTTAGTACTACACA
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACA
39712499 CGTGTTTATA
Statistics
Matches: 115, Mismatches: 21, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
50 41 0.36
51 73 0.63
52 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (50 bp):
TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAACTT
Found at i:39714970 original size:14 final size:14
Alignment explanation
Indices: 39714951--39714988 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
39714941 CTAGAAAAGT
39714951 AAATCATTTTTCAG
1 AAATCATTTTTCAG
*
39714965 AAATCATTTTTCGG
1 AAATCATTTTTCAG
*
39714979 AAAACATTTT
1 AAATCATTTT
39714989 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (14 bp):
AAATCATTTTTCAG
Found at i:39717403 original size:12 final size:12
Alignment explanation
Indices: 39717386--39717411 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39717376 TTAAAATATG
39717386 TTAGTTTTATCA
1 TTAGTTTTATCA
39717398 TTAGTTTTATCA
1 TTAGTTTTATCA
39717410 TT
1 TT
39717412 TATCAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (12 bp):
TTAGTTTTATCA
Found at i:39719051 original size:6 final size:6
Alignment explanation
Indices: 39719040--39719103 Score: 92
Period size: 6 Copynumber: 10.3 Consensus size: 6
39719030 GAAGTTTAAG
* *
39719040 AAATAA AAATAAA AAATAA AAAAAA ATAAAAA AAATAA AAATAA AAATAA
1 AAATAA AAAT-AA AAATAA AAATAA A-AATAA AAATAA AAATAA AAATAA
39719090 AAATAA AAATAA AA
1 AAATAA AAATAA AA
39719104 GAAATAAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
6 42 0.78
7 12 0.22
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAATAA
Found at i:39719065 original size:12 final size:12
Alignment explanation
Indices: 39719044--39719113 Score: 77
Period size: 12 Copynumber: 5.5 Consensus size: 12
39719034 TTTAAGAAAT
39719044 AAAAATAAAAAA
1 AAAAATAAAAAA
*
39719056 TAAAAAAAAATAAA
1 -AAAAATAAA-AAA
*
39719070 AAAAATAAAAAT
1 AAAAATAAAAAA
*
39719082 AAAAATAAAAAT
1 AAAAATAAAAAA
39719094 AAAAATAAAAGAA
1 AAAAATAAAA-AA
39719107 ATAAAAT
1 A-AAAAT
39719114 CAATGATCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
12 24 0.48
13 18 0.36
14 8 0.16
ACGTcount: A:0.84, C:0.00, G:0.01, T:0.14
Consensus pattern (12 bp):
AAAAATAAAAAA
Found at i:39719083 original size:38 final size:38
Alignment explanation
Indices: 39719040--39719113 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 38
39719030 GAAGTTTAAG
*
39719040 AAATAAAAATAAAAAATAAAAA-AAAATAAAAAAAATAA
1 AAATAAAAAT-AAAAATAAAAATAAAAGAAAAAAAATAA
*
39719078 AAATAAAAATAAAAATAAAAATAAAAGAAATAAAAT
1 AAATAAAAATAAAAATAAAAATAAAAGAAAAAAAAT
39719114 CAATGATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 11 0.33
38 22 0.67
ACGTcount: A:0.84, C:0.00, G:0.01, T:0.15
Consensus pattern (38 bp):
AAATAAAAATAAAAATAAAAATAAAAGAAAAAAAATAA
Found at i:39719113 original size:32 final size:32
Alignment explanation
Indices: 39719037--39719112 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 32
39719027 AAAGAAGTTT
39719037 AAGAAATAAAAATAAAAAATAAAAAAAAATAA
1 AAGAAATAAAAATAAAAAATAAAAAAAAATAA
*
39719069 AAAAAATAAAAAT-AAAAATAAAAATAAAAATAA
1 AAGAAATAAAAATAAAAAAT-AAAA-AAAAATAA
39719102 AAGAAATAAAA
1 AAGAAATAAAA
39719113 TCAATGATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
31 6 0.15
32 16 0.40
33 18 0.45
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (32 bp):
AAGAAATAAAAATAAAAAATAAAAAAAAATAA
Found at i:39727639 original size:29 final size:29
Alignment explanation
Indices: 39727607--39727675 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
39727597 GCCACAAAGC
* *
39727607 CTCACATATATCAAATTTCT-CCACTAGAG
1 CTCACATATA-AAAAATTCTGCCACTAGAG
* * *
39727636 CTCATATATAAAAAATTCTGCCACTGGGG
1 CTCACATATAAAAAATTCTGCCACTAGAG
39727665 CTCACATATAA
1 CTCACATATAA
39727676 TAGAAAAGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 7 0.21
29 26 0.79
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (29 bp):
CTCACATATAAAAAATTCTGCCACTAGAG
Found at i:39749963 original size:50 final size:50
Alignment explanation
Indices: 39749909--39750007 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
39749899 AGGATTAATC
* *
39749909 AAGATGCAAACTAAATAAACAAATGAGTTACGTAATGCATAACATAATTT
1 AAGATGCAAACTAAATAAACAAAGGAGTTACATAATGCATAACATAATTT
* * * *
39749959 AAGATGCAAACTTAATTAACATAGGAGTTACATAATGCATGACATAATT
1 AAGATGCAAACTAAATAAACAAAGGAGTTACATAATGCATAACATAATT
39750008 AAAACACAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.27
Consensus pattern (50 bp):
AAGATGCAAACTAAATAAACAAAGGAGTTACATAATGCATAACATAATTT
Found at i:39777814 original size:29 final size:29
Alignment explanation
Indices: 39777773--39777831 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
39777763 TCCTTTCTCC
*
39777773 TCCTCCTTGCTATTCTGTCTTTCTATTTT
1 TCCTCCTTGCTATTCTGTCTATCTATTTT
39777802 TCCTCCTTGCTATTCTGTCTATCTATTTT
1 TCCTCCTTGCTATTCTGTCTATCTATTTT
39777831 T
1 T
39777832 TCTATTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.08, C:0.27, G:0.07, T:0.58
Consensus pattern (29 bp):
TCCTCCTTGCTATTCTGTCTATCTATTTT
Found at i:39778780 original size:1 final size:1
Alignment explanation
Indices: 39778774--39778799 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
39778764 TTTGATCTCC
39778774 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
39778800 GCCTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:39796762 original size:39 final size:39
Alignment explanation
Indices: 39796708--39796877 Score: 250
Period size: 39 Copynumber: 4.4 Consensus size: 39
39796698 GACGGCAAAA
*
39796708 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCATGT
1 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
* * * * * *
39796747 AAGTGTGATTAGGGGTACCGAAGTACAATAAGGACACAT
1 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
* *
39796786 AAGTGCGATCAGGGGTATCGAAGTACAATAGGGGCACGT
1 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
*
39796825 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCATGT
1 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
39796864 AAGTGCGATCAGGG
1 AAGTGCGATCAGGG
39796878 TATAATTATA
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 115 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.17
Consensus pattern (39 bp):
AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
Found at i:39796828 original size:19 final size:19
Alignment explanation
Indices: 39796806--39796867 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
39796796 AGGGGTATCG
39796806 AAGTACAATAGGGGCACGT
1 AAGTACAATAGGGGCACGT
* * *
39796825 AAGTGCGATCAGGGGTACCG-
1 AAGTACAAT-AGGGGCA-CGT
* *
39796845 AAGTACAACAGGGGCATGT
1 AAGTACAATAGGGGCACGT
39796864 AAGT
1 AAGT
39796868 GCGATCAGGG
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 1 0.03
19 17 0.53
20 12 0.38
21 2 0.06
ACGTcount: A:0.34, C:0.16, G:0.34, T:0.16
Consensus pattern (19 bp):
AAGTACAATAGGGGCACGT
Found at i:39796848 original size:20 final size:20
Alignment explanation
Indices: 39796708--39796848 Score: 76
Period size: 20 Copynumber: 7.2 Consensus size: 20
39796698 GACGGCAAAA
39796708 AAGTGCGATCAGGGGTACCG
1 AAGTGCGATCAGGGGTACCG
* * * *
39796728 AAGTAC-AACAGGGGCA-TG
1 AAGTGCGATCAGGGGTACCG
* *
39796746 TAAGTGTGATTAGGGGTACCG
1 -AAGTGCGATCAGGGGTACCG
* * * ** **
39796767 AAGTACAAT-AAGGACACAT
1 AAGTGCGATCAGGGGTACCG
*
39796786 AAGTGCGATCAGGGGTATCG
1 AAGTGCGATCAGGGGTACCG
* * *
39796806 AAGTACAAT-AGGGGCA-CG
1 AAGTGCGATCAGGGGTACCG
39796824 TAAGTGCGATCAGGGGTACCG
1 -AAGTGCGATCAGGGGTACCG
39796845 AAGT
1 AAGT
39796849 ACAACAGGGG
Statistics
Matches: 82, Mismatches: 32, Indels: 14
0.64 0.25 0.11
Matches are distributed among these distances:
18 3 0.04
19 37 0.45
20 39 0.48
21 3 0.04
ACGTcount: A:0.33, C:0.16, G:0.34, T:0.18
Consensus pattern (20 bp):
AAGTGCGATCAGGGGTACCG
Found at i:39805942 original size:17 final size:17
Alignment explanation
Indices: 39805922--39805954 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
39805912 TAGAATTAGG
39805922 TTGAGAAAATAATTTAA
1 TTGAGAAAATAATTTAA
39805939 TTGAGAAAATAATTTA
1 TTGAGAAAATAATTTA
39805955 GTTAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (17 bp):
TTGAGAAAATAATTTAA
Found at i:39808742 original size:249 final size:250
Alignment explanation
Indices: 39808104--39809103 Score: 1215
Period size: 249 Copynumber: 4.0 Consensus size: 250
39808094 TATTCGTTTG
* *
39808104 TAAACTTGTAATTTTTTTTGAAAAGATTGAAGAATAAAACAAATTCATGGATTACATTAATATAC
1 TAAACTTGTAA-TTTTTTCGAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATAC
* * * * **
39808169 TTTGTATGATTGTCCTCGTACGGTTTTTGCACGCAAAGCAAAATGGAAGCAAATGTTGGTCATTG
65 TTTTTATGATTTTCCTCGTACGGTTTTTGCACACAAAGAAAAATGGAAGCAAATGTTACTCATTG
** * * * *
39808234 GTTGTCTAAAATTTAAACTAATACTAAGC-AGTATTATATGGCCGGATTGTAATACAGAAAGACA
130 GTTGTCTAACGTTTAAACTAATACTAATCGA-TATTACATGGCCGGATCGTAATACAGAAAAACA
* * * * *
39808298 ACTTACATTACTCGATGAAACTTAACATGTCCTTAGTCTAATCGAAAACGAGCAAAC
194 ACTTATATTAGTAGATGAAACTTAACATGTCCTTAATCTAATCGGAAACGAGCAAAC
* *
39808355 TAAAATTGTAATTTTTTCGAAAAGATTGAATAATAAAACAAATCCATGGATTACATTAATATA-T
1 TAAACTTGTAATTTTTTCGAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATACT
* * ** * * *
39808419 TTTGTATGACTTTCCTTGTATAGTTTTTGCAGGA-AAAGAAAAATGGAAGAAAATGTTGCTCATT
66 TTT-TATGATTTTCCTCGTACGGTTTTTGCA-CACAAAGAAAAATGGAAGCAAATGTTACTCATT
* * ** *
39808483 GGTTGTCTAACGTTTAAACTAATACTAATCGACATTACATGACTAGATCGTAATATAGAAAAACA
129 GGTTGTCTAACGTTTAAACTAATACTAATCGATATTACATGGCCGGATCGTAATACAGAAAAACA
* * *
39808548 ACTTATATTAGTAGATGAAACTTAACATGTCCTTAATCTAATCAGAAATGAGCAAAA
194 ACTTATATTAGTAGATGAAACTTAACATGTCCTTAATCTAATCGGAAACGAGCAAAC
*
39808605 TAAACTTGTAA-TTTTTCAAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATACT
1 TAAACTTGTAATTTTTTCGAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATACT
* * * * * *
39808669 TTTTACGATTTTCCTCATACGGTTTTTGCATACAAAGGAAAATGGAAGCAAATGCTACTTATTGG
66 TTTTATGATTTTCCTCGTACGGTTTTTGCACACAAAGAAAAATGGAAGCAAATGTTACTCATTGG
* * * *
39808734 TTGTCTAACGTTTAAACTAATACTAAGT-GGTATTACATGGCCGGATTGTAATATAGAAAGACAA
131 TTGTCTAACGTTTAAACTAATACTAA-TCGATATTACATGGCCGGATCGTAATACAGAAAAACAA
* * * * * *
39808798 CTTATATTAGTAGACGGAACTTAACATGTCCTTAACCCAATTGGAAATGAGCAAAC
195 CTTATATTAGTAGATGAAACTTAACATGTCCTTAATCTAATCGGAAACGAGCAAAC
* * *
39808854 TAAACTTGTAATTTTTTTTTTGAAAAGATTAAATAATAAATA-AAATTCTTGGATTACATTAATA
1 TAAACTTGTAA---TTTTTTCGAAAAGATTGAATAATAAA-ACAAATTCATGGATTACATTAATA
* * * *
39808918 TACATTTTATGATTTTCCTTGTACGGTTTTTGCACGCAAAGAAAAATGAAAGCAAATGTTACTCA
62 TACTTTTTATGATTTTCCTCGTACGGTTTTTGCACACAAAGAAAAATGGAAGCAAATGTTACTCA
* * * *
39808983 TTGGTTGTCTAACGTTTAAACTAATACTAAACGGTATTAAATGGCTGGATCGTAATACA-AAAAG
127 TTGGTTGTCTAACGTTTAAACTAATACTAATCGATATTACATGGCCGGATCGTAATACAGAAAA-
* * * * * *
39809047 ACAACTAATATTAGTA-TTCGAAACTAAACATGACTTTAGTCTAATCGGAAACGAGCA
191 ACAACTTATATTAGTAGAT-GAAACTTAACATGTCCTTAATCTAATCGGAAACGAGCA
39809104 TACCGATTGA
Statistics
Matches: 640, Mismatches: 95, Indels: 26
0.84 0.12 0.03
Matches are distributed among these distances:
248 1 0.00
249 215 0.34
250 214 0.33
251 11 0.02
252 3 0.00
253 195 0.30
254 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (250 bp):
TAAACTTGTAATTTTTTCGAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATACT
TTTTATGATTTTCCTCGTACGGTTTTTGCACACAAAGAAAAATGGAAGCAAATGTTACTCATTGG
TTGTCTAACGTTTAAACTAATACTAATCGATATTACATGGCCGGATCGTAATACAGAAAAACAAC
TTATATTAGTAGATGAAACTTAACATGTCCTTAATCTAATCGGAAACGAGCAAAC
Found at i:39808868 original size:499 final size:501
Alignment explanation
Indices: 39808104--39809103 Score: 1355
Period size: 499 Copynumber: 2.0 Consensus size: 501
39808094 TATTCGTTTG
**
39808104 TAAACTTGTAATTTTTTTTGAAAAGATTGAAGAATAAAACAAATTCATGGATTACATTAATATAC
1 TAAACTTGTAA-TTTTTTCAAAAAGATTGAAGAATAAAACAAATTCATGGATTACATTAATATAC
* * * * **
39808169 TTTGTATGATTGTCCTCGTACGGTTTTTGCACGCAAAGCAAAATGGAAGCAAATGTTGGTCATTG
65 TTTGTACGATTGTCCTCATACGGTTTTTGCACACAAAGCAAAATGGAAGCAAATGCTACTCATTG
*
39808234 GTTGTCTAAAATTTAAACTAATACTAAGCAGTATTATATGGCCGGATTGTAATACAGAAAGACAA
130 GTTGTCTAAAATTTAAACTAATACTAAGCAGTATTACATGGCCGGATTGTAATACAGAAAGACAA
* * ** *
39808299 CTTACATTACTCGATGAAACTTAACATGTCCTTAGTCTAATCGAAAACGAGCAAACTAAAATTGT
195 CTTACATTACTAGACGAAACTTAACATGTCCTTAACCCAATCGAAAACGAGCAAACTAAAATTGT
* *
39808364 AA-TTTTTTCGAAAAGATTGAATAATAAA-ACAAATCCATGGATTACATTAATATA-TTTTGTAT
260 AATTTTTTTCGAAAAGATTAAATAATAAATA-AAATCCATGGATTACATTAATATACATTT-TAT
* * * *
39808426 GACTTTCCTTGTATAGTTTTTGCAGGAAAAGAAAAATGGAAGAAAATGTTGCTCATTGGTTGTCT
323 GACTTTCCTTGTACAGTTTTTGCACGAAAAGAAAAATGAAAGAAAATGTTACTCATTGGTTGTCT
* * * *
39808491 AACGTTTAAACTAATACTAATCGACATTACATGACTAGATCGTAATATAGAAAA-ACAACTTATA
388 AACGTTTAAACTAATACTAAACGACATTAAATGACTAGATCGTAATACA-AAAAGACAACTAATA
* * *
39808555 TTAGTAGAT-GAAACTTAACATGTCCTTAATCTAATCAGAAATGAGCAAAA
452 TTAGTA-ATCGAAACTAAACATGACCTTAATCTAATCAGAAACGAGCAAAA
*
39808605 TAAACTTGTAA-TTTTTCAAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATACT
1 TAAACTTGTAATTTTTTCAAAAAGATTGAAGAATAAAACAAATTCATGGATTACATTAATATACT
* * * * *
39808669 TTTTACGATTTTCCTCATACGGTTTTTGCATACAAAGGAAAATGGAAGCAAATGCTACTTATTGG
66 TTGTACGATTGTCCTCATACGGTTTTTGCACACAAAGCAAAATGGAAGCAAATGCTACTCATTGG
** ** *
39808734 TTGTCTAACGTTTAAACTAATACTAAGTGGTATTACATGGCCGGATTGTAATATAGAAAGACAAC
131 TTGTCTAAAATTTAAACTAATACTAAGCAGTATTACATGGCCGGATTGTAATACAGAAAGACAAC
* * * * * * *
39808799 TTATATTAGTAGACGGAACTTAACATGTCCTTAACCCAATTGGAAATGAGCAAACTAAACTTGTA
196 TTACATTACTAGACGAAACTTAACATGTCCTTAACCCAATCGAAAACGAGCAAACTAAAATTGTA
* * *
39808864 ATTTTTTTTTTGAAAAGATTAAATAATAAATAAAATTCTTGGATTACATTAATATACATTTTATG
261 A--TTTTTTTCGAAAAGATTAAATAATAAATAAAATCCATGGATTACATTAATATACATTTTATG
* * * *
39808929 ATTTTCCTTGTACGGTTTTTGCACGCAAAGAAAAATGAAAGCAAATGTTACTCATTGGTTGTCTA
324 ACTTTCCTTGTACAGTTTTTGCACGAAAAGAAAAATGAAAGAAAATGTTACTCATTGGTTGTCTA
** * *
39808994 ACGTTTAAACTAATACTAAACGGTATTAAATGGCTGGATCGTAATACAAAAAGACAACTAATATT
389 ACGTTTAAACTAATACTAAACGACATTAAATGACTAGATCGTAATACAAAAAGACAACTAATATT
* * * *
39809059 AGTATTCGAAACTAAACATGACTTTAGTCTAATCGGAAACGAGCA
454 AGTAATCGAAACTAAACATGACCTTAATCTAATCAGAAACGAGCA
39809104 TACCGATTGA
Statistics
Matches: 432, Mismatches: 60, Indels: 13
0.86 0.12 0.03
Matches are distributed among these distances:
499 217 0.50
501 16 0.04
502 195 0.45
503 4 0.01
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (501 bp):
TAAACTTGTAATTTTTTCAAAAAGATTGAAGAATAAAACAAATTCATGGATTACATTAATATACT
TTGTACGATTGTCCTCATACGGTTTTTGCACACAAAGCAAAATGGAAGCAAATGCTACTCATTGG
TTGTCTAAAATTTAAACTAATACTAAGCAGTATTACATGGCCGGATTGTAATACAGAAAGACAAC
TTACATTACTAGACGAAACTTAACATGTCCTTAACCCAATCGAAAACGAGCAAACTAAAATTGTA
ATTTTTTTCGAAAAGATTAAATAATAAATAAAATCCATGGATTACATTAATATACATTTTATGAC
TTTCCTTGTACAGTTTTTGCACGAAAAGAAAAATGAAAGAAAATGTTACTCATTGGTTGTCTAAC
GTTTAAACTAATACTAAACGACATTAAATGACTAGATCGTAATACAAAAAGACAACTAATATTAG
TAATCGAAACTAAACATGACCTTAATCTAATCAGAAACGAGCAAAA
Found at i:39812252 original size:46 final size:46
Alignment explanation
Indices: 39812164--39812334 Score: 283
Period size: 46 Copynumber: 3.8 Consensus size: 46
39812154 TGGAATGAAA
* *
39812164 GTATGGTATTTTAGTAAAG--AACCATACTCAGTTGTGAAAAGTAG
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAG
*
39812208 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAGAAGTAG
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAG
*
39812254 GTATGGTATTTCAGTAACGAAAACCATACTGAGTTGTGAAAAGTAG
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAG
*
39812300 GTATGGTATTTCAGTGAAGAAAACCATACTGAGTT
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
39812335 ATAGCATTGT
Statistics
Matches: 118, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
44 18 0.15
46 100 0.85
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (46 bp):
GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAG
Found at i:39829463 original size:132 final size:132
Alignment explanation
Indices: 39829241--39829500 Score: 389
Period size: 132 Copynumber: 2.0 Consensus size: 132
39829231 AAAATAAAGA
* *
39829241 GACTTTTATTCTCTAAAAATTAAATATATTTTCCGGAATAACTATTCTATCGGTTTCTATTTGAG
1 GACTTTTATTCTCTAAAAATTAAATATATTTTCCGGAATAACGATTCTATCGGTTTCTATTTAAG
*
39829306 AAAAGAATTTTTCTTTTCACTTCAAAAGAAAAGAAAACTATTTCTAATTTCTGTGTTTGATTCAA
66 AAAAGAATTTTTCTTTTCACCTCAAAAGAAAAGAAAACTATTTCTAATTTCTGTGTTTGATTCAA
39829371 AT
131 AT
* * *
39829373 GACTTTTATTCTCTAAGAATTAAATATATTTTTCGGAATAACGATTCTATCTGTCTT-TATTTAA
1 GACTTTTATTCTCTAAAAATTAAATATATTTTCCGGAATAACGATTCTATCGGT-TTCTATTTAA
* * * * *
39829437 GAAGAGAA-TTTTCATTTTCACCTCAAAAGAAAATAAAGCTATTTCTAGTTTTTGTGTTTGATTC
65 GAAAAGAATTTTTC-TTTTCACCTCAAAAGAAAAGAAAACTATTTCTAATTTCTGTGTTTGATTC
39829501 GATTTGATTG
Statistics
Matches: 115, Mismatches: 11, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
131 5 0.04
132 108 0.94
133 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (132 bp):
GACTTTTATTCTCTAAAAATTAAATATATTTTCCGGAATAACGATTCTATCGGTTTCTATTTAAG
AAAAGAATTTTTCTTTTCACCTCAAAAGAAAAGAAAACTATTTCTAATTTCTGTGTTTGATTCAA
AT
Found at i:39834271 original size:18 final size:18
Alignment explanation
Indices: 39834250--39834308 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
39834240 GAAACCCATA
39834250 TTATTATGCGAACCTTTG
1 TTATTATGCGAACCTTTG
* *
39834268 TTATTATGC-AAACTTACG
1 TTATTATGCGAACCTT-TG
* * *
39834286 TTTTTATGTGAACCTATG
1 TTATTATGCGAACCTTTG
39834304 TTATT
1 TTATT
39834309 TTCCGAACCC
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
17 5 0.16
18 22 0.71
19 4 0.13
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (18 bp):
TTATTATGCGAACCTTTG
Found at i:39834335 original size:36 final size:36
Alignment explanation
Indices: 39834241--39834335 Score: 91
Period size: 36 Copynumber: 2.6 Consensus size: 36
39834231 TCTTTTTTCG
** * *
39834241 AAACCCATATTATTATGCGAACCTTTGTTATTATGC
1 AAACCCACGTTATTATGCGAACCTATGTTATTATCC
** * * *
39834277 AAACTTACGTTTTTATGTGAACCTATGTTATTTTCC
1 AAACCCACGTTATTATGCGAACCTATGTTATTATCC
* *
39834313 GAACCCACGTTATTGTGCGAACC
1 AAACCCACGTTATTATGCGAACC
39834336 CTAACATTAA
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (36 bp):
AAACCCACGTTATTATGCGAACCTATGTTATTATCC
Found at i:39836868 original size:44 final size:42
Alignment explanation
Indices: 39836818--39836930 Score: 118
Period size: 44 Copynumber: 2.6 Consensus size: 42
39836808 GGTGCTTCGG
* *** *
39836818 TGGCATTCTATTAACCTTTATGGTGTATTTTGATTTGGCCTTTA
1 TGGCATTCTATTAGCCTTTATGGCACATTTT-A-TTAGCCTTTA
*
39836862 TGGCATTCTGATCTAGCCTTTGTGGCACATTTTATTAGCCTTTA
1 TGGCATTCT-AT-TAGCCTTTATGGCACATTTTATTAGCCTTTA
* *
39836906 TGGCATTCTACTAGCCTTTGTGGCA
1 TGGCATTCTATTAGCCTTTATGGCA
39836931 TGTTCTATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 14 0.23
43 1 0.02
44 27 0.45
45 3 0.05
46 15 0.25
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (42 bp):
TGGCATTCTATTAGCCTTTATGGCACATTTTATTAGCCTTTA
Found at i:39836880 original size:22 final size:21
Alignment explanation
Indices: 39836855--39836931 Score: 86
Period size: 20 Copynumber: 3.6 Consensus size: 21
39836845 TTTTGATTTG
39836855 GCCTTTATGGCATTCTGATCTA
1 GCCTTTATGGCATTCT-ATCTA
* *
39836877 GCCTTTGTGGCACATTTTAT-TA
1 GCCTTTATGG--CATTCTATCTA
39836899 GCCTTTATGGCATTCTA-CTA
1 GCCTTTATGGCATTCTATCTA
*
39836919 GCCTTTGTGGCAT
1 GCCTTTATGGCAT
39836932 GTTCTATATG
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
20 20 0.43
22 20 0.43
23 2 0.04
24 5 0.11
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (21 bp):
GCCTTTATGGCATTCTATCTA
Found at i:39838973 original size:19 final size:19
Alignment explanation
Indices: 39838949--39838988 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
39838939 ACATAAAATA
*
39838949 AACTAAGTAAAAACTTAAG
1 AACTAAATAAAAACTTAAG
39838968 AACTAAATAAAAACTTAAG
1 AACTAAATAAAAACTTAAG
39838987 AA
1 AA
39838989 TCAATCCCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.20
Consensus pattern (19 bp):
AACTAAATAAAAACTTAAG
Found at i:39842676 original size:12 final size:12
Alignment explanation
Indices: 39842659--39842693 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
39842649 TTGGCCCGCC
39842659 TATATTAATTTT
1 TATATTAATTTT
*
39842671 TATATTATTTTT
1 TATATTAATTTT
39842683 TATA-TAATTTT
1 TATATTAATTTT
39842694 AAAATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:39844657 original size:69 final size:69
Alignment explanation
Indices: 39844527--39844668 Score: 178
Period size: 69 Copynumber: 2.1 Consensus size: 69
39844517 ACTGCCTTTG
* ****
39844527 GTTTCCTCCTTTCGTCTCTACTCAGCTGCTACACTCTATTGTTGCCTTTGGATCTCTACACCATT
1 GTTTCCTCCTTTCGTCCCTACTCAGCTGCTACACTCTATTGTTGCCTCCAAATCTCTACACCATT
39844592 TAGA
66 TAGA
* * * *
39844596 GTTTCCTCCTTTCGTCCCTACTCAGTTGCTACCCTTTATTGTTGCCTCCAAATCT-TCACACCCT
1 GTTTCCTCCTTTCGTCCCTACTCAGCTGCTACACTCTATTGTTGCCTCCAAATCTCT-ACACCAT
*
39844660 TTAGG
65 TTAGA
39844665 GTTT
1 GTTT
39844669 TTCCTCTTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
68 1 0.02
69 61 0.98
ACGTcount: A:0.15, C:0.32, G:0.13, T:0.41
Consensus pattern (69 bp):
GTTTCCTCCTTTCGTCCCTACTCAGCTGCTACACTCTATTGTTGCCTCCAAATCTCTACACCATT
TAGA
Found at i:39846754 original size:26 final size:26
Alignment explanation
Indices: 39846718--39846808 Score: 182
Period size: 26 Copynumber: 3.5 Consensus size: 26
39846708 TTACATCAAC
39846718 GCTCACACGAGCTATGAAATGGGTCT
1 GCTCACACGAGCTATGAAATGGGTCT
39846744 GCTCACACGAGCTATGAAATGGGTCT
1 GCTCACACGAGCTATGAAATGGGTCT
39846770 GCTCACACGAGCTATGAAATGGGTCT
1 GCTCACACGAGCTATGAAATGGGTCT
39846796 GCTCACACGAGCT
1 GCTCACACGAGCT
39846809 GTGGGTCGAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 65 1.00
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.22
Consensus pattern (26 bp):
GCTCACACGAGCTATGAAATGGGTCT
Found at i:39852031 original size:22 final size:22
Alignment explanation
Indices: 39852001--39852599 Score: 533
Period size: 23 Copynumber: 27.0 Consensus size: 22
39851991 AGGATGCTAG
39852001 TTAAGGGTTTAGGG-TTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
39852022 TTCAAGGGTTTAGGGTTTTTAAT
1 TT-AAGGGTTTAGGGTTTTTAAT
* **** *
39852045 TAAATTAAATTAGGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
*
39852068 TTAAGGGCTTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
39852091 TTAAGGGTTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** *
39852113 TAAATTAGTTTAGGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
*
39852136 TTAAGGGCTTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
39852159 TTAAGGGTTTA-GGTTTTATAAT
1 TTAAGGGTTTAGGGTTTT-TAAT
*
39852181 TTAAGGG-TTAGGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAT
*
39852202 TTAATGGTTTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
*
39852225 TTAAGGGTTTATGGTTTTTAA-
1 TTAAGGGTTTAGGGTTTTTAAT
*
39852246 -T---GG-TTAGGGTTTTTAAA
1 TTAAGGGTTTAGGGTTTTTAAT
39852263 TTAAGGGTTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** *
39852285 TAAATTAGTTTAGGG-TTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
39852307 TTAAGGGTTTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
*
39852330 TTAAGAGTTTAGGGTTTTTAAGT
1 TTAAGGGTTTAGGGTTTTTAA-T
* ****** *** *
39852353 AATAACTCAAAAAAATTTCTATTTTAT
1 -TTAA--GGGTTTAGGGT-T-TTTAAT
39852380 TTAAGGG-TTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
* *
39852402 TTAAGAGTTTAAGGTTTTTAACT
1 TTAAGGGTTTAGGGTTTTTAA-T
39852425 TTAAGGGTTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* *
39852447 TTAATGG-TTAGGGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAT
* *
39852468 TTAAGGGTTTAGGG-TCTTAAG
1 TTAAGGGTTTAGGGTTTTTAAT
39852489 TTAAGGGTTTAGGGTTTTTAACT
1 TTAAGGGTTTAGGGTTTTTAA-T
39852512 TTAAGGGTTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* ** *
39852534 TAAATTAGTTTAGGG-TTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
39852556 TTAAGGGTTTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
*
39852579 TTAAGAGTTTAGGGTTTTTAA
1 TTAAGGGTTTAGGGTTTTTAA
39852600 GTAATAACTC
Statistics
Matches: 466, Mismatches: 80, Indels: 62
0.77 0.13 0.10
Matches are distributed among these distances:
16 12 0.03
17 2 0.00
18 1 0.00
20 1 0.00
21 75 0.16
22 154 0.33
23 206 0.44
24 3 0.01
26 6 0.01
27 2 0.00
28 4 0.01
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (22 bp):
TTAAGGGTTTAGGGTTTTTAAT
Found at i:39852074 original size:45 final size:44
Alignment explanation
Indices: 39852009--39852578 Score: 254
Period size: 44 Copynumber: 12.8 Consensus size: 44
39851999 AGTTAAGGGT
39852009 TTAGGG-TTTTAATTTCAAGGGTTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTTTTAATTT-AAGGGTTTAGGGTTTTTAATTAAATT-AA
* * * ****
39852054 TTAGGGTTTTTAAGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGT
1 TTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAA-TTAAATTAA
* ** ****
39852099 TTAGGGTTTTTAATTAAATTAGTTTAGGGTTTTTAAGTT-AAGGGC
1 TTAGGGTTTTTAATTTAA-GGGTTTAGGGTTTTTAA-TTAAATTAA
* ***
39852144 TTAGGGTTTTTAATTTTAAGGGTTTA-GGTTTTATAATTTAA-GGG
1 TTAGGGTTTTTAA-TTTAAGGGTTTAGGGTTTT-TAATTAAATTAA
* *
39852188 TTAGGGTTTTTAAGTTAATGGTTTAGGGTTTTTAATT---TT-A
1 TTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAA
* * **
39852228 --AGGGTTTATGGT-TTTTAATGG-TTAGGGTTTTTAAATTAAGGGT--
1 TTAGGGTTT-T--TAATTTAAGGGTTTAGGGTTTTT-AATTAA-ATTAA
* ** **
39852271 TTAGGGTTTTTAATTAAATTAGTTTAGGG-TTTTAAGTTAAGGGT--
1 TTAGGGTTTTTAATTTAA-GGGTTTAGGGTTTTTAA-TTAA-ATTAA
* * *
39852315 TTAGGGTTTTTAATTTTAAGAGTTTAGGGTTTTTAAGTAATAACTCAAA
1 TTAGGGTTTTTAA-TTTAAGGGTTTAGGGTTTTTAA-T--TAAAT-TAA
** *** * *
39852364 AAAATTTCTATTTTATTTAAGGG-TTAGGGTTTTTAATTTTAAGAGT--
1 TTAGGGT-T-TTTAATTTAAGGGTTTAGGGTTTTTAA--TTAA-ATTAA
* * **
39852410 TTAAGGTTTTTAACTTTAAGGGTTTAGGGTTTTTAATTTAA-TGG
1 TTAGGGTTTTTAA-TTTAAGGGTTTAGGGTTTTTAATTAAATTAA
* * **
39852454 TTAGGGTTTTTAAGTTAAGGGTTTAGGG-TCTTAAGTTAAGGGT--
1 TTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAA-TTAA-ATTAA
*
39852497 TTAGGGTTTTTAACTTTAAGGGTTTAGGGTTTTTAATTAAATTAGT
1 TTAGGGTTTTTAA-TTTAAGGGTTTAGGGTTTTTAATTAAATTA-A
*
39852543 TTAGGG-TTTTAAGTTAAGGGTTTAGGGTTTTTAATT
1 TTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATT
39852579 TTAAGAGTTT
Statistics
Matches: 420, Mismatches: 60, Indels: 91
0.74 0.11 0.16
Matches are distributed among these distances:
38 7 0.02
39 12 0.03
40 11 0.03
41 1 0.00
42 7 0.02
43 53 0.13
44 127 0.30
45 114 0.27
46 54 0.13
47 3 0.01
48 3 0.01
49 15 0.04
50 9 0.02
51 4 0.01
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (44 bp):
TTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTAAATTAA
Found at i:39852107 original size:68 final size:68
Alignment explanation
Indices: 39851999--39852246 Score: 362
Period size: 68 Copynumber: 3.7 Consensus size: 68
39851989 GCAGGATGCT
* *
39851999 AGTTAAGGGTTTAGGG-TTTTAATTTCAAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTT
1 AGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTT
39852063 TTA
66 TTA
**
39852066 AGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTAGGGTTT
1 AGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTT
39852131 TTA
66 TTA
* *
39852134 AGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTA-GG-TTTT-A-TAATTTAAGGGTTAGGGT
1 AGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTAGGGTTTTTAATTAAATTAA--ATTAGGGT
39852195 TTTTA
64 TTTTA
* * *
39852200 AGTTAATGGTTTAGGGTTTTTAATTTTAAGGGTTTATGGTTTTTAAT
1 AGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTAGGGTTTTTAAT
39852247 GGTTAGGGTT
Statistics
Matches: 165, Mismatches: 9, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
64 6 0.04
65 1 0.01
66 50 0.30
67 19 0.12
68 88 0.53
69 1 0.01
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.48
Consensus pattern (68 bp):
AGTTAAGGGCTTAGGGTTTTTAATTTTAAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTT
TTA
Found at i:39852256 original size:16 final size:17
Alignment explanation
Indices: 39852223--39852261 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
39852213 GGGTTTTTAA
*
39852223 TTTTAAGGGTTTATGGT
1 TTTTAAGGGTTTAGGGT
*
39852240 TTTTAATGG-TTAGGGT
1 TTTTAAGGGTTTAGGGT
39852256 TTTTAA
1 TTTTAA
39852262 ATTAAGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.54
Consensus pattern (17 bp):
TTTTAAGGGTTTAGGGT
Found at i:39852369 original size:105 final size:103
Alignment explanation
Indices: 39852159--39852445 Score: 233
Period size: 105 Copynumber: 2.8 Consensus size: 103
39852149 GTTTTTAATT
* * *
39852159 TTAAGGGTTTAGGTTTTATAATTTAAGGGTTAGGGTTTTTAAGTTAATGGTTTAGGGTTTTTAAT
1 TTAAGGGTTTAGGTTTTATAATTAAAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAT
* * ** ****
39852224 TTTAAGGGTTTATGGTTTTTAATGGTTAGGGTTTTTAAA
66 TTTAAGAGTTTAGGGTTTTTAA-GGTTAGACTAAAAAAA
*
39852263 TTAAGGGTTTAGGGTTTT-TAATTAAATTAGTTTAGGG-TTTTAAGTTAAGGGTTTAGGGTTTTT
1 TTAAGGGTTTA-GGTTTTATAATTAAA--AGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTT
39852326 AATTTTAAGAGTTTAGGGTTTTTAA-GTAATA-ACTCAAAAAAA
63 AATTTTAAGAGTTTAGGGTTTTTAAGGT--TAGACT-AAAAAAA
* * * * *
39852368 TT-----TCTA--TTTTAT--TT-AAGGGTTAGGGTTTTTAATTTTAAGAGTTTAAGGTTTTTAA
1 TTAAGGGTTTAGGTTTTATAATTAAAAGGTTAGGGTTTTTAA-GTTAAGGGTTTAGGGTTTTTAA
* *
39852423 CTTTAAGGGTTTAGGGTTTTTAA
65 TTTTAAGAGTTTAGGGTTTTTAA
39852446 TTTAATGGTT
Statistics
Matches: 154, Mismatches: 20, Indels: 27
0.77 0.10 0.13
Matches are distributed among these distances:
93 7 0.05
94 6 0.04
95 42 0.27
96 2 0.01
97 4 0.03
98 1 0.01
100 3 0.02
103 2 0.01
104 19 0.12
105 61 0.40
106 7 0.05
ACGTcount: A:0.27, C:0.01, G:0.23, T:0.48
Consensus pattern (103 bp):
TTAAGGGTTTAGGTTTTATAATTAAAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAT
TTTAAGAGTTTAGGGTTTTTAAGGTTAGACTAAAAAAA
Found at i:39852474 original size:205 final size:198
Alignment explanation
Indices: 39852179--39852556 Score: 514
Period size: 205 Copynumber: 1.9 Consensus size: 198
39852169 AGGTTTTATA
* * *
39852179 ATTTAAGGGTTAGGGTTTTTAAGTTAATGGTTTAGGGTTTTTAATTTTAAGGGTTTATGGTTTTT
1 ATTTAAGGGTTAGGGTTTTTAAGTTAATGGTTTAAGGTTTTTAACTTTAAGGGTTTAGGGTTTTT
* *
39852244 AATGGTTAGGGTTTTTAAATTAAGGGTTTAGGGTTTTTAA-TTAAATTAGTTTAGGG-TTTTAA-
66 AATGGTTAGGGTTTTTAAATTAAGGGTTTAGGG-TCTTAAGTT-AA-GAGTTTAGGGTTTTTAAC
*
39852306 GTTAAGGGTTTAGGGTTTTTAATTTTAA-GAGTTTAGGGTTTTTAAGTAATAACTCAAAAAAATT
128 GTTAAGGGTTTAGGGTTTTTAA-TTAAATGAGTTTAGGG-TTTTAAGTAATAACTCAAAAAAATT
39852370 TCTATTTT
191 TCTATTTT
*
39852378 ATTTAAGGGTTAGGGTTTTTAATTTTAA-GAGTTTAAGGTTTTTAACTTTAAGGGTTTAGGGTTT
1 ATTTAAGGGTTAGGGTTTTTAA-GTTAATG-GTTTAAGGTTTTTAACTTTAAGGGTTTAGGG---
* *
39852442 TTAATTTAATGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTCTTAAGTTAAGGGTTTAGGGTTTT
61 TT--TTTAATGGTTAGGGTTTTTAAATTAAGGGTTTAGGGTCTTAAGTTAAGAGTTTAGGGTTTT
* *
39852507 TAACTTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTAGGGTTTTAAGT
124 TAACGTTAAGGGTTTAGGGTTTTTAATTAAATGAGTTTAGGGTTTTAAGT
39852557 TAAGGGTTTA
Statistics
Matches: 157, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
199 23 0.15
200 32 0.20
203 10 0.06
204 25 0.16
205 67 0.43
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (198 bp):
ATTTAAGGGTTAGGGTTTTTAAGTTAATGGTTTAAGGTTTTTAACTTTAAGGGTTTAGGGTTTTT
AATGGTTAGGGTTTTTAAATTAAGGGTTTAGGGTCTTAAGTTAAGAGTTTAGGGTTTTTAACGTT
AAGGGTTTAGGGTTTTTAATTAAATGAGTTTAGGGTTTTAAGTAATAACTCAAAAAAATTTCTAT
TTT
Found at i:39852805 original size:21 final size:21
Alignment explanation
Indices: 39852767--39852807 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39852757 TTGTCCAGCT
*
39852767 TCCGGCGGCGGTTGTGGTTCC
1 TCCGGCGGCGGTTCTGGTTCC
39852788 TCCGGCGG-GGATTCTGGTTC
1 TCCGGCGGCGG-TTCTGGTTC
39852808 TTTCGGTACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.02, C:0.27, G:0.41, T:0.29
Consensus pattern (21 bp):
TCCGGCGGCGGTTCTGGTTCC
Found at i:39853756 original size:7 final size:7
Alignment explanation
Indices: 39853746--39853771 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39853736 TTATATACAT
39853746 AATACTA
1 AATACTA
39853753 AATACTA
1 AATACTA
39853760 AATACTA
1 AATACTA
39853767 AATAC
1 AATAC
39853772 CAATCAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:39853978 original size:20 final size:20
Alignment explanation
Indices: 39853941--39853978 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39853931 TTTATTTTTA
*
39853941 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
39853961 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
39853979 TTCCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:39862871 original size:23 final size:23
Alignment explanation
Indices: 39862845--39863074 Score: 142
Period size: 23 Copynumber: 10.1 Consensus size: 23
39862835 ACAAATATTG
* * *
39862845 AATACGCTACATAGGCATTATAA
1 AATACGCCACAAAGGCATTACAA
* * ** *
39862868 AATACACCACAAAAGCATTGTAG
1 AATACGCCACAAAGGCATTACAA
* *
39862891 AATAAGCCACATAA-GCATTGCAA
1 AATACGCCACA-AAGGCATTACAA
* ** * *
39862914 AATACACCACAAAGAAAATACAT
1 AATACGCCACAAAGGCATTACAA
* * * *
39862937 AATAAGCCACATAGGCATTGCAT
1 AATACGCCACAAAGGCATTACAA
* *
39862960 AATATGCCACAAATGCATTACAA
1 AATACGCCACAAAGGCATTACAA
* * ** *
39862983 AATATGCCACATAGGCATTGTAG
1 AATACGCCACAAAGGCATTACAA
* *
39863006 AATACACCATAAAGGCATTACAA
1 AATACGCCACAAAGGCATTACAA
* * * *
39863029 AATATGCTACAAAGGCATTATAG
1 AATACGCCACAAAGGCATTACAA
39863052 AATACGCCACAAAGGC-TT-CAA
1 AATACGCCACAAAGGCATTACAA
39863073 AA
1 AA
39863075 GTAACTTACC
Statistics
Matches: 154, Mismatches: 51, Indels: 6
0.73 0.24 0.03
Matches are distributed among these distances:
21 3 0.02
22 4 0.03
23 145 0.94
24 2 0.01
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (23 bp):
AATACGCCACAAAGGCATTACAA
Found at i:39862916 original size:46 final size:46
Alignment explanation
Indices: 39862853--39863047 Score: 185
Period size: 46 Copynumber: 4.2 Consensus size: 46
39862843 TGAATACGCT
** ** *
39862853 ACATAGGCATTATAAAATACACCACAAAAGCATTGTAGAATAAGCC
1 ACATAGGCATTGCAAAATACACCACAAAAGCATTACAAAATAAGCC
* * * *
39862899 ACATAAGCATTGCAAAATACACCAC-AAAGAAAATACATAATAAGCC
1 ACATAGGCATTGCAAAATACACCACAAAAG-CATTACAAAATAAGCC
* ** * *
39862945 ACATAGGCATTGCATAATATGCCACAAATGCATTACAAAATATGCC
1 ACATAGGCATTGCAAAATACACCACAAAAGCATTACAAAATAAGCC
* * * * * *
39862991 ACATAGGCATTGTAGAATACACCATAAAGGCATTACAAAATATGCT
1 ACATAGGCATTGCAAAATACACCACAAAAGCATTACAAAATAAGCC
*
39863037 ACAAAGGCATT
1 ACATAGGCATT
39863048 ATAGAATACG
Statistics
Matches: 122, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
45 4 0.03
46 115 0.94
47 3 0.02
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.21
Consensus pattern (46 bp):
ACATAGGCATTGCAAAATACACCACAAAAGCATTACAAAATAAGCC
Found at i:39863053 original size:46 final size:46
Alignment explanation
Indices: 39862857--39863074 Score: 172
Period size: 46 Copynumber: 4.8 Consensus size: 46
39862847 TACGCTACAT
* * ** * *
39862857 AGGCATTATAAAATACACCACAAAAGCATTGTAGAATAAGCCACATA
1 AGGCATTATAGAATACACCACAAAGGCATTACAAAATATGCCACA-A
** * ** * * * *
39862904 A-GCATTGCAAAATACACCACAAAGAAAATACATAATAAGCCACAT
1 AGGCATTATAGAATACACCACAAAGGCATTACAAAATATGCCACAA
** * ** * *
39862949 AGGCATTGCATAATATGCCACAAATGCATTACAAAATATGCCACAT
1 AGGCATTATAGAATACACCACAAAGGCATTACAAAATATGCCACAA
* * *
39862995 AGGCATTGTAGAATACACCATAAAGGCATTACAAAATATGCTACAA
1 AGGCATTATAGAATACACCACAAAGGCATTACAAAATATGCCACAA
*
39863041 AGGCATTATAGAATACGCCACAAAGGC-TT-CAAAA
1 AGGCATTATAGAATACACCACAAAGGCATTACAAAA
39863075 GTAACTTACC
Statistics
Matches: 140, Mismatches: 30, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
44 5 0.04
45 3 0.02
46 131 0.94
47 1 0.01
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (46 bp):
AGGCATTATAGAATACACCACAAAGGCATTACAAAATATGCCACAA
Found at i:39863061 original size:92 final size:92
Alignment explanation
Indices: 39862845--39863064 Score: 233
Period size: 92 Copynumber: 2.4 Consensus size: 92
39862835 ACAAATATTG
* * ** *
39862845 AATACGCTACATAGGCATTATAAAATACACCACAAAAGCATTGTAGAATAAGCCACATAAGCATT
1 AATAAGCTACATAGGCATTATAAAATACGCCACAAAAGCATTACAAAATAAGCCACATAAGCATT
*
39862910 GCAAAATACACCACAAAGAAAATACAT
66 GCAAAATACACCACAAAGAAAATACAA
* ** * * * * *
39862937 AATAAGCCACATAGGCATTGCATAATATGCCACAAATGCATTACAAAATATGCCACATAGGCATT
1 AATAAGCTACATAGGCATTATAAAATACGCCACAAAAGCATTACAAAATAAGCCACATAAGCATT
* * * ** *
39863002 GTAGAATACACCATAAAGGCATTACAA
66 GCAAAATACACCACAAAGAAAATACAA
* * *
39863029 AATATGCTACAAAGGCATTATAGAATACGCCACAAA
1 AATAAGCTACATAGGCATTATAAAATACGCCACAAA
39863065 GGCTTCAAAA
Statistics
Matches: 101, Mismatches: 27, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
92 101 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (92 bp):
AATAAGCTACATAGGCATTATAAAATACGCCACAAAAGCATTACAAAATAAGCCACATAAGCATT
GCAAAATACACCACAAAGAAAATACAA
Found at i:39881151 original size:23 final size:23
Alignment explanation
Indices: 39881071--39881204 Score: 117
Period size: 23 Copynumber: 5.8 Consensus size: 23
39881061 TGAGTACACT
* * *
39881071 ACATAGGTATTGCAGAATTCACC
1 ACATAGGCATTGCAGAATACGCC
* * * *
39881094 ACAAAGGCATTACAAAATACGCT
1 ACATAGGCATTGCAGAATACGCC
*
39881117 ACAAAGGCATTGCAGAATACGCC
1 ACATAGGCATTGCAGAATACGCC
* * * * *
39881140 ATATAGGTATTGTAGAATATGTC
1 ACATAGGCATTGCAGAATACGCC
* *
39881163 AC-TAAGGCATTACATAATACGCC
1 ACAT-AGGCATTGCAGAATACGCC
39881186 ACATAGGCATTGCAGAATA
1 ACATAGGCATTGCAGAATA
39881205 TGCTAAAAGT
Statistics
Matches: 84, Mismatches: 25, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
22 1 0.01
23 82 0.98
24 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (23 bp):
ACATAGGCATTGCAGAATACGCC
Found at i:39888749 original size:28 final size:28
Alignment explanation
Indices: 39888667--39888799 Score: 160
Period size: 28 Copynumber: 4.6 Consensus size: 28
39888657 CAGCCCTATT
39888667 CAATGACAGTAA-AGTGTGGGCCTTAGCC
1 CAAT-ACAGTAACAGTGTGGGCCTTAGCC
*
39888695 TAATACAGTAACAGTACAGTGTGGGCCTTAGCC
1 CAATACAGT---A--ACAGTGTGGGCCTTAGCC
* *
39888728 CAATATAGTAACAGTGTAGGCCTTAGCC
1 CAATACAGTAACAGTGTGGGCCTTAGCC
* *
39888756 CAATACAGTAACAATGTGGGCTTTAGCC
1 CAATACAGTAACAGTGTGGGCCTTAGCC
39888784 CAATACAGTAACAGTG
1 CAATACAGTAACAGTG
39888800 CAGTGCAATA
Statistics
Matches: 90, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
27 5 0.06
28 59 0.66
30 2 0.02
32 1 0.01
33 23 0.26
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (28 bp):
CAATACAGTAACAGTGTGGGCCTTAGCC
Found at i:39888798 original size:56 final size:59
Alignment explanation
Indices: 39888667--39888799 Score: 175
Period size: 61 Copynumber: 2.3 Consensus size: 59
39888657 CAGCCCTATT
* *
39888667 CAATGACAGTAA-AGTGTGGGCCTTAGCCTAATACAGTAACAGTACAGTGTGGGCCTTAGCC
1 CAAT-ACAGTAACAGTGTAGGCCTTAGCCCAATACAGTAACA--ACAGTGTGGGCCTTAGCC
* *
39888728 CAATATAGTAACAGTGTAGGCCTTAGCCCAATACAGTAAC-A-A-TGTGGGCTTTAGCC
1 CAATACAGTAACAGTGTAGGCCTTAGCCCAATACAGTAACAACAGTGTGGGCCTTAGCC
39888784 CAATACAGTAACAGTG
1 CAATACAGTAACAGTG
39888800 CAGTGCAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
56 28 0.42
57 1 0.02
58 1 0.02
60 6 0.09
61 30 0.45
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (59 bp):
CAATACAGTAACAGTGTAGGCCTTAGCCCAATACAGTAACAACAGTGTGGGCCTTAGCC
Found at i:39889313 original size:81 final size:79
Alignment explanation
Indices: 39889178--39889413 Score: 287
Period size: 81 Copynumber: 2.9 Consensus size: 79
39889168 TTATCTCCTA
** * *
39889178 GGGGTATAACAGTTATTTTACCTTATGGGGATATTTCGATCATTTTACCCTATAGGGGTATTTCG
1 GGGGTATTTCAGTCATTTTACCTTATGGGG-TATTTCGGTCATTTTACCCTATAGGGGTATTTCG
39889243 ATCAATTTTCCCTATG
65 ATC-ATTTTCCCTATG
* *
39889259 GGGGTATTT-TGATCATTTTAGCC-TATGAGGGTATTTCGGTCATTTTACCCTATAGGAGTATTT
1 GGGGTATTTCAG-TCATTTTA-CCTTATG-GGGTATTTCGGTCATTTTACCCTATAGGGGTATTT
*
39889322 CGATCATTTTAACCTATG
63 CGATCATTTT-CCCTATG
* * * * *
39889340 GGTGTATTTCAGTTATTTTACCTTATGGGGGTATTTTGGTCATTTTACACTATGGGGGTATTTCG
1 GGGGTATTTCAGTCATTTTACCTTAT-GGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCG
39889405 ATCATTTTC
65 ATCATTTTC
39889414 ATCTATTAGG
Statistics
Matches: 133, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
80 8 0.06
81 118 0.89
82 7 0.05
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (79 bp):
GGGGTATTTCAGTCATTTTACCTTATGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGA
TCATTTTCCCTATG
Found at i:39889419 original size:27 final size:26
Alignment explanation
Indices: 39889192--39889412 Score: 246
Period size: 27 Copynumber: 8.2 Consensus size: 26
39889182 TATAACAGTT
*
39889192 ATTTTACCTTATGGGGATATTTCGATC
1 ATTTTACC-TATGGGGGTATTTCGATC
*
39889219 ATTTTACCCTATAGGGGTATTTCGATC
1 ATTTTA-CCTATGGGGGTATTTCGATC
* *
39889246 AATTTTCCCTATGGGGGTATTTTGATC
1 -ATTTTACCTATGGGGGTATTTCGATC
* *
39889273 ATTTTAGCCTATGAGGGTATTTCGGTC
1 ATTTTA-CCTATGGGGGTATTTCGATC
* *
39889300 ATTTTACCCTATAGGAGTATTTCGATC
1 ATTTTA-CCTATGGGGGTATTTCGATC
* *
39889327 ATTTTAACCTATGGGTGTATTTC-AGTT
1 ATTTT-ACCTATGGGGGTATTTCGA-TC
* *
39889354 ATTTTACCTTATGGGGGTATTTTGGTC
1 ATTTTACC-TATGGGGGTATTTCGATC
39889381 ATTTTACACTATGGGGGTATTTCGATC
1 ATTTTAC-CTATGGGGGTATTTCGATC
39889408 ATTTT
1 ATTTT
39889413 CATCTATTAG
Statistics
Matches: 163, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
26 9 0.06
27 145 0.89
28 9 0.06
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.44
Consensus pattern (26 bp):
ATTTTACCTATGGGGGTATTTCGATC
Found at i:39892156 original size:28 final size:28
Alignment explanation
Indices: 39892112--39892345 Score: 298
Period size: 28 Copynumber: 8.4 Consensus size: 28
39892102 CTATTCAGTG
39892112 ACAGT-ACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* * *
39892139 ATAGTTACAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* *
39892167 ACAGTAATAATGTGGGCCTT-GCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* * *
39892194 ACAGTAATAATGTGGGCCTTAGCCTAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
39892222 ACAG-AATCAGTGTGGGCCTTAGCCCAAT
1 ACAGTAA-CAGTGTGGGCCTTAGCCCAAT
* *
39892250 ACAG-AATCAGTGGGGGCCTTAGCTCAAT
1 ACAGTAA-CAGTGTGGGCCTTAGCCCAAT
39892278 ACAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
*
39892306 ACAG-AATCGGTGTGGGCCTTAGCCCAAT
1 ACAGTAA-CAGTGTGGGCCTTAGCCCAAT
*
39892334 ACAGTAATAGTG
1 ACAGTAACAGTG
39892346 CAGCGCAATA
Statistics
Matches: 185, Mismatches: 16, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
27 35 0.19
28 146 0.79
29 4 0.02
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAT
Found at i:39892307 original size:84 final size:83
Alignment explanation
Indices: 39892112--39892345 Score: 330
Period size: 84 Copynumber: 2.8 Consensus size: 83
39892102 CTATTCAGTG
* * *
39892112 ACAGT-ACAGTGTGGGCCTTAGCCCAATATAG-TTACAATGTGGGCCTTAGCCCAATACAGTAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAATACAGAAT-CAGTGTGGGCCTTAGCCCAATACAGTAAT
* *
39892175 AATGTGGGCCTTGCCCAAT
65 AGTGGGGGCCTTGCCCAAT
* * *
39892194 ACAGTAATAATGTGGGCCTTAGCCTAATACAGAATCAGTGTGGGCCTTAGCCCAATACAG-AATC
1 ACAGTAACAGTGTGGGCCTTAGCCCAATACAGAATCAGTGTGGGCCTTAGCCCAATACAGTAAT-
*
39892258 AGTGGGGGCCTTAGCTCAAT
65 AGTGGGGGCCTT-GCCCAAT
*
39892278 ACAGTAACAGTGTGGGCCTTAGCCCAATACAGAATCGGTGTGGGCCTTAGCCCAATACAGTAATA
1 ACAGTAACAGTGTGGGCCTTAGCCCAATACAGAATCAGTGTGGGCCTTAGCCCAATACAGTAATA
39892343 GTG
66 GTG
39892346 CAGCGCAATA
Statistics
Matches: 134, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
82 8 0.06
83 56 0.42
84 67 0.50
85 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (83 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAATACAGAATCAGTGTGGGCCTTAGCCCAATACAGTAATA
GTGGGGGCCTTGCCCAAT
Found at i:39892506 original size:26 final size:26
Alignment explanation
Indices: 39892452--39892527 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
39892442 ACCAATATCA
* * * **
39892452 CAGCAAAGCTGCTAGTAATAGCACCG
1 CAGCAAAGCTGCCAGTAACAGTATTG
* *
39892478 CAGCAGAGCTGCCAGTATCAGTATTG
1 CAGCAAAGCTGCCAGTAACAGTATTG
*
39892504 CAGCAAAGTTGCCAGTAACAGTAT
1 CAGCAAAGCTGCCAGTAACAGTAT
39892528 ATGTGCCAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (26 bp):
CAGCAAAGCTGCCAGTAACAGTATTG
Found at i:39893154 original size:27 final size:27
Alignment explanation
Indices: 39892759--39893144 Score: 363
Period size: 27 Copynumber: 14.4 Consensus size: 27
39892749 GGGTATAATA
* * *
39892759 GTCATTTTACCCTCTAGGCGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTTG
* * **
39892786 ATTATTTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATAGGGGTATTTTG
* *
39892813 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTTG
*
39892840 GTCATTTTA-CCT-T-GGGGTATTTTT
1 GTCATTTTACCCTATAGGGGTATTTTG
* *
39892864 GTCATTTTACCTTAT-GGTGGTATTTTT
1 GTCATTTTACCCTATAGG-GGTATTTTG
* *
39892891 TTCATTTTACCCTAT-GGGGAATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
* * *
39892917 GCCATTTTATCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
* * *
39892944 CTCATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTACCCTATAGGGGTATTTTG
39892971 GTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
* *
39892998 CTCATTTTACCCTAT-GGGAGTATTTCG
1 GTCATTTTACCCTATAGGG-GTATTTTG
* * **
39893025 GTCATTTTACCTTATGGGGGTATTTCA
1 GTCATTTTACCCTATAGGGGTATTTTG
* **
39893052 GTCATTTTACCCTATAGGGGTATGTCA
1 GTCATTTTACCCTATAGGGGTATTTTG
* *** *
39893079 GTCATTTT-CATCTATTAGGGGTAAAATA
1 GTCATTTTAC-CCTA-TAGGGGTATTTTG
* *
39893107 GACATTTTACCCTTTAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
39893134 GTCATTTTACC
1 GTCATTTTACC
39893145 TATTTGGGGT
Statistics
Matches: 302, Mismatches: 48, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
24 18 0.06
25 3 0.01
26 29 0.10
27 230 0.76
28 21 0.07
29 1 0.00
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTTG
Found at i:39901033 original size:25 final size:26
Alignment explanation
Indices: 39901004--39901067 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
39900994 TTAATTAGTA
*
39901004 TAAAATATT-AATAATTCAAT-AAAT
1 TAAAATATTAAATAATTAAATAAAAT
39901028 TGAAAA-ATTAAATAATTAAATAAAAT
1 T-AAAATATTAAATAATTAAATAAAAT
*
39901054 TAAAATATTCAATA
1 TAAAATATTAAATA
39901068 CTTGGTGGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.12
25 18 0.53
26 12 0.35
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (26 bp):
TAAAATATTAAATAATTAAATAAAAT
Found at i:39906722 original size:22 final size:19
Alignment explanation
Indices: 39906683--39906724 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
39906673 TGCAAAGCTG
39906683 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
39906702 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
39906724 A
1 A
39906725 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:39914196 original size:6 final size:6
Alignment explanation
Indices: 39914173--39914213 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
39914163 TATTTAACCC
*
39914173 AAATT- AAATT- AGATTA AAATTA AAATTA AAATTA AAATTA A
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA A
39914214 TTATATTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
5 9 0.27
6 24 0.73
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (6 bp):
AAATTA
Found at i:39918231 original size:21 final size:21
Alignment explanation
Indices: 39918207--39918253 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
39918197 AGGTTAACAG
*
39918207 AATGCCATAAAAGCCATACAA
1 AATGCCACAAAAGCCATACAA
* *
39918228 AATGCCACAAAGGCCATACAG
1 AATGCCACAAAAGCCATACAA
39918249 AATGC
1 AATGC
39918254 ATTATAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.26, G:0.15, T:0.13
Consensus pattern (21 bp):
AATGCCACAAAAGCCATACAA
Found at i:39924878 original size:3 final size:3
Alignment explanation
Indices: 39924864--39924893 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
39924854 TTGTATTTAA
*
39924864 TGT TGT TAT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
39924894 CTACATTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.00, G:0.30, T:0.67
Consensus pattern (3 bp):
TGT
Found at i:39926624 original size:27 final size:27
Alignment explanation
Indices: 39926594--39926682 Score: 133
Period size: 27 Copynumber: 3.3 Consensus size: 27
39926584 TGTAAACACG
*
39926594 TCATGAAAGAAATGTCTTTGTGGTGAA
1 TCATGAAAGAAATGCCTTTGTGGTGAA
*
39926621 TCATGAAAGAAATGCCTTTGTGGCGAA
1 TCATGAAAGAAATGCCTTTGTGGTGAA
* *
39926648 TCATGAAAGAAAAGCCTTGGTGGTGAA
1 TCATGAAAGAAATGCCTTTGTGGTGAA
*
39926675 TTATGAAA
1 TCATGAAA
39926683 AGAATTTTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (27 bp):
TCATGAAAGAAATGCCTTTGTGGTGAA
Done.