Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 108 of 141
Found at i:35024618 original size:13 final size:12
Alignment explanation
Indices: 35024595--35024628 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
35024585 CATTTTTACT
35024595 TTTTCATTTTTCA
1 TTTTCA-TTTTCA
35024608 TTTCTCATTTTCA
1 TTT-TCATTTTCA
35024621 TTTTCATT
1 TTTTCATT
35024629 CTTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 12 0.60
14 3 0.15
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTCATTTTCA
Found at i:35025575 original size:23 final size:21
Alignment explanation
Indices: 35025537--35025613 Score: 66
Period size: 23 Copynumber: 3.5 Consensus size: 21
35025527 TTGACATTGA
*
35025537 TTTTGATTTTTC-TTTTTTCTT
1 TTTTCATTTTTCATTTTTT-TT
* *
35025558 CTTTTCGTTTTTGATTTTGATTTT
1 -TTTTCATTTTTCATTTT--TTTT
*
35025582 TTTTCATTTTTCATTTTTTTA
1 TTTTCATTTTTCATTTTTTTT
*
35025603 TTTTGATTTTT
1 TTTTCATTTTT
35025614 TTCATCTAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 13 0.29
22 9 0.20
23 19 0.42
24 2 0.04
25 2 0.04
ACGTcount: A:0.09, C:0.08, G:0.06, T:0.77
Consensus pattern (21 bp):
TTTTCATTTTTCATTTTTTTT
Found at i:35025584 original size:16 final size:15
Alignment explanation
Indices: 35025565--35025615 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
35025555 CTTCTTTTCG
*
35025565 TTTTTGATTTTGATT
1 TTTTTTATTTTGATT
*
35025580 TTTTTTCATTTTTCA-T
1 TTTTTT-A-TTTTGATT
35025596 TTTTTTATTTTGATT
1 TTTTTTATTTTGATT
35025611 TTTTT
1 TTTTT
35025616 CATCTAGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 5 0.17
15 12 0.40
16 8 0.27
17 5 0.17
ACGTcount: A:0.12, C:0.04, G:0.06, T:0.78
Consensus pattern (15 bp):
TTTTTTATTTTGATT
Found at i:35025696 original size:142 final size:142
Alignment explanation
Indices: 35025446--35025728 Score: 505
Period size: 143 Copynumber: 2.0 Consensus size: 142
35025436 TTTTTGTCCT
35025446 TTTTTCATTTTTTTATTTTGATTTTTTTCATCTAGATTTTTCTCTTTTTTCATTCTTATTTCTTT
1 TTTTTCATTTTTTTATTTTGATTTTTTTCATCTAGATTTTTCTCTTTTTTCATTCTTATTTCTTT
35025511 TTCTCTTATTTTCATTTTGACATTGATTTTGATTTTTCTTTTTTCTTC-TTTTCGTTTTTGATTT
66 TTCTCTTATTTTCATTTTGACATTGATTTTGATTTTTCTTTTTTCTTCATTTT-GTTTTTGATTT
35025575 TGATTTTTTTTCA
130 TGATTTTTTTTCA
*
35025588 TTTTTCATTTTTTTATTTTGATTTTTTTCATCTAGATTTTTCTCTTTTTTTCATTCTTCTTTCTT
1 TTTTTCATTTTTTTATTTTGATTTTTTTCATCTAGATTTTTCTC-TTTTTTCATTCTTATTTCTT
* * *
35025653 TTTCTCTTATTTTTATTTTGACCTTGATTTTGATTTTTCTTTTTTCTTCATTTTGTTTTTTATTT
65 TTTCTCTTATTTTCATTTTGACATTGATTTTGATTTTTCTTTTTTCTTCATTTTGTTTTTGATTT
35025718 TGATTTTTTTT
130 TGATTTTTTTT
35025729 GAATTGGATC
Statistics
Matches: 135, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
142 44 0.33
143 87 0.64
144 4 0.03
ACGTcount: A:0.11, C:0.12, G:0.05, T:0.72
Consensus pattern (142 bp):
TTTTTCATTTTTTTATTTTGATTTTTTTCATCTAGATTTTTCTCTTTTTTCATTCTTATTTCTTT
TTCTCTTATTTTCATTTTGACATTGATTTTGATTTTTCTTTTTTCTTCATTTTGTTTTTGATTTT
GATTTTTTTTCA
Found at i:35027770 original size:20 final size:20
Alignment explanation
Indices: 35027745--35027782 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35027735 ATTCGCTCTA
35027745 ATTTTTCCAACCTTTGTTCT
1 ATTTTTCCAACCTTTGTTCT
*
35027765 ATTTTTCTAACCTTTGTT
1 ATTTTTCCAACCTTTGTT
35027783 TGGATACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (20 bp):
ATTTTTCCAACCTTTGTTCT
Found at i:35030177 original size:3 final size:3
Alignment explanation
Indices: 35030162--35030191 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
35030152 AAAATAAAAC
*
35030162 TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35030192 CATTAAAATA
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:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:35030180 original size:15 final size:15
Alignment explanation
Indices: 35030154--35030217 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
35030144 AATAAAGGAA
*
35030154 AATAA-AACTAATAAC
1 AATAATAAC-AATAAT
*
35030169 AATAATAATAATAAT
1 AATAATAACAATAAT
*
35030184 AATAATAACATTAA-
1 AATAATAACAATAAT
*
35030198 AATAATTAACTA-AAT
1 AATAA-TAACAATAAT
35030213 AATAA
1 AATAA
35030218 AATTGCTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
14 7 0.17
15 31 0.77
16 2 0.05
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (15 bp):
AATAATAACAATAAT
Found at i:35032756 original size:9 final size:9
Alignment explanation
Indices: 35032727--35032756 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
35032717 ATGTGTAGGA
35032727 TTATTTTTT
1 TTATTTTTT
35032736 TTATCTTTTT
1 TTAT-TTTTT
35032746 TTATTTTTT
1 TTATTTTTT
35032755 TT
1 TT
35032757 TTGTCTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (9 bp):
TTATTTTTT
Found at i:35050293 original size:18 final size:20
Alignment explanation
Indices: 35050267--35050303 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35050257 CAGACACTCC
35050267 ATGTGC-TTTCT-TCTTTTT
1 ATGTGCTTTTCTCTCTTTTT
*
35050285 ATGTTCTTTTCTCTCTTTT
1 ATGTGCTTTTCTCTCTTTT
35050304 ATAACGTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 5 0.31
20 6 0.38
ACGTcount: A:0.05, C:0.19, G:0.08, T:0.68
Consensus pattern (20 bp):
ATGTGCTTTTCTCTCTTTTT
Found at i:35050423 original size:18 final size:18
Alignment explanation
Indices: 35050402--35050453 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
35050392 TATCAATAGA
*
35050402 ATAAATTTAATTTTATTT
1 ATAAATTTAATTTAATTT
35050420 ATAAATTT-ATTTAATTT
1 ATAAATTTAATTTAATTT
*
35050437 ATTAAATATAATTTAAT
1 A-TAAATTTAATTTAAT
35050454 GGTTGTGAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 9 0.30
18 14 0.47
19 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATAAATTTAATTTAATTT
Found at i:35052062 original size:3 final size:3
Alignment explanation
Indices: 35052056--35052091 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
35052046 ATTATTAAGT
35052056 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35052092 TTAAAAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35052173 original size:17 final size:18
Alignment explanation
Indices: 35052151--35052184 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35052141 AGCAAAACGG
35052151 GAAAAAAGA-AAAGAAAA
1 GAAAAAAGAGAAAGAAAA
*
35052168 GAAAAAGGAGAAAGAAA
1 GAAAAAAGAGAAAGAAA
35052185 CAACGAAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
GAAAAAAGAGAAAGAAAA
Found at i:35060538 original size:18 final size:20
Alignment explanation
Indices: 35060512--35060548 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35060502 CAGACACTCC
35060512 ATGTGC-TTTCT-TCTTTTT
1 ATGTGCTTTTCTCTCTTTTT
*
35060530 ATGTTCTTTTCTCTCTTTT
1 ATGTGCTTTTCTCTCTTTT
35060549 ATAACGTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 5 0.31
20 6 0.38
ACGTcount: A:0.05, C:0.19, G:0.08, T:0.68
Consensus pattern (20 bp):
ATGTGCTTTTCTCTCTTTTT
Found at i:35060668 original size:18 final size:18
Alignment explanation
Indices: 35060647--35060698 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
35060637 TATCAATAGA
*
35060647 ATAAATTTAATTTTATTT
1 ATAAATTTAATTTAATTT
35060665 ATAAATTT-ATTTAATTT
1 ATAAATTTAATTTAATTT
*
35060682 ATTAAATATAATTTAAT
1 A-TAAATTTAATTTAAT
35060699 GGTTGTGAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 9 0.30
18 14 0.47
19 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATAAATTTAATTTAATTT
Found at i:35062307 original size:3 final size:3
Alignment explanation
Indices: 35062301--35062336 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
35062291 ATTATTAAGT
35062301 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35062337 TTAAAAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35062418 original size:17 final size:18
Alignment explanation
Indices: 35062396--35062429 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35062386 AGCAAAACGG
35062396 GAAAAAAGA-AAAGAAAA
1 GAAAAAAGAGAAAGAAAA
*
35062413 GAAAAAGGAGAAAGAAA
1 GAAAAAAGAGAAAGAAA
35062430 CAACGAAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
GAAAAAAGAGAAAGAAAA
Found at i:35070804 original size:19 final size:19
Alignment explanation
Indices: 35070780--35070825 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
35070770 TTGAACTTGA
*
35070780 AAATTGGACCTGAGATCGT
1 AAATTGGACATGAGATCGT
*
35070799 AAATTGGGCATGAGATCGT
1 AAATTGGACATGAGATCGT
35070818 AAATTGGA
1 AAATTGGA
35070826 TCTGGGAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (19 bp):
AAATTGGACATGAGATCGT
Found at i:35074840 original size:3 final size:3
Alignment explanation
Indices: 35074832--35074882 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
35074822 TATCTGGTAC
35074832 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
35074880 GAA
1 GAA
35074883 ATAAAGATGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:35077647 original size:3 final size:3
Alignment explanation
Indices: 35077639--35077674 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
35077629 TTTTTCTCTT
* *
35077639 CTC CTC CTC CTC CCC CTC TTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
35077675 ATCATCATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:35077699 original size:3 final size:3
Alignment explanation
Indices: 35077693--35077750 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
35077683 TATCATTATT
* *
35077693 TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC -TC TGC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
35077740 TTC TTT TTC TT
1 TTC TTC TTC TT
35077751 TTATTTCCCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:35094991 original size:23 final size:23
Alignment explanation
Indices: 35094961--35095006 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
35094951 TGGTACTCAC
35094961 CTTTTACAAGAAAAAAATATTAA
1 CTTTTACAAGAAAAAAATATTAA
35094984 CTTTTACAAGAAAAAAATATTAA
1 CTTTTACAAGAAAAAAATATTAA
35095007 ATTAATCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (23 bp):
CTTTTACAAGAAAAAAATATTAA
Found at i:35102381 original size:22 final size:23
Alignment explanation
Indices: 35102338--35102381 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
35102328 AAACACGCAA
*
35102338 AGTAGAAGAAAATAATGCAAAAC
1 AGTAGAAGAAAATAATGAAAAAC
35102361 AGTAGAA-AAAATAGAT-AAAAA
1 AGTAGAAGAAAATA-ATGAAAAA
35102382 TATATTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.66, C:0.05, G:0.16, T:0.14
Consensus pattern (23 bp):
AGTAGAAGAAAATAATGAAAAAC
Found at i:35102531 original size:22 final size:22
Alignment explanation
Indices: 35102498--35102540 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35102488 GATTCAAAGG
*
35102498 TTGCTTTCTTATTTTTGTTTTT
1 TTGCTTTCTTATTTTTATTTTT
35102520 TTGC-TTCGTTATTTTTATTTT
1 TTGCTTTC-TTATTTTTATTTT
35102541 ATTTTCGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.07, C:0.09, G:0.09, T:0.74
Consensus pattern (22 bp):
TTGCTTTCTTATTTTTATTTTT
Found at i:35103471 original size:62 final size:59
Alignment explanation
Indices: 35103393--35103517 Score: 169
Period size: 62 Copynumber: 2.1 Consensus size: 59
35103383 TCTATACATA
* * *
35103393 TTTTTAATTTTCATATATACATACTTTATATCTTACATCATTATATATCTTTATATACGCAT
1 TTTTTAATTTTCATATATACATACCTTACATCTT--AT-ATTATATATCTTTATACACGCAT
* * *
35103455 TTTTTAATTTTCATATATATATACCTTGCATCTTATATTATATATCTTTATACACGTAT
1 TTTTTAATTTTCATATATACATACCTTACATCTTATATTATATATCTTTATACACGCAT
35103514 TTTT
1 TTTT
35103518 AAACTCATGT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 25 0.44
60 2 0.04
62 30 0.53
ACGTcount: A:0.30, C:0.14, G:0.02, T:0.54
Consensus pattern (59 bp):
TTTTTAATTTTCATATATACATACCTTACATCTTATATTATATATCTTTATACACGCAT
Found at i:35104537 original size:107 final size:106
Alignment explanation
Indices: 35104391--35104588 Score: 290
Period size: 107 Copynumber: 1.9 Consensus size: 106
35104381 AATAATAATA
* * *
35104391 AAGGCAATATTTTGCATTTGGAAATTCGAGAAAGCGTGCCCTAATGTGTTGGGTTTCAATTTTTT
1 AAGGCAATATTTTGAATTTGGAAATTCGAGAAAGCGTGCCCTAATGTGCTAGGTTTCAATTTTTT
* *
35104456 TGTTCGACCGAATAGCCAAATATCCTTTAAAATTTCAAAGT
66 CGTTCGACCAAATAGCCAAATATCCTTTAAAATTTCAAAGT
* **
35104497 AAGGCAATATTTTGAAGTTTGGAAATTCGAGGAAA-TGTGCCCTAATGTGCTAGGTTTTGATTTT
1 AAGGCAATATTTTGAA-TTTGGAAATTCGA-GAAAGCGTGCCCTAATGTGCTAGGTTTCAATTTT
*
35104561 TTCGTTTGACCAAATAGCCAAATATCCT
64 TTCGTTCGACCAAATAGCCAAATATCCT
35104589 CTTATATCTT
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
106 15 0.19
107 62 0.77
108 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.36
Consensus pattern (106 bp):
AAGGCAATATTTTGAATTTGGAAATTCGAGAAAGCGTGCCCTAATGTGCTAGGTTTCAATTTTTT
CGTTCGACCAAATAGCCAAATATCCTTTAAAATTTCAAAGT
Found at i:35111859 original size:1 final size:1
Alignment explanation
Indices: 35111853--35111882 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
35111843 TCTTTCTTTC
35111853 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
35111883 GCATTACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:35116713 original size:7 final size:7
Alignment explanation
Indices: 35116701--35116734 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
35116691 AAATACTCAT
35116701 ATATCCA
1 ATATCCA
35116708 ATATCCA
1 ATATCCA
*
35116715 TTATCCA
1 ATATCCA
35116722 ATATCCA
1 ATATCCA
35116729 ATATCC
1 ATATCC
35116735 GAAACCCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.38, C:0.29, G:0.00, T:0.32
Consensus pattern (7 bp):
ATATCCA
Found at i:35118147 original size:3 final size:3
Alignment explanation
Indices: 35118139--35118234 Score: 174
Period size: 3 Copynumber: 32.0 Consensus size: 3
35118129 ACAAAATTGC
35118139 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
35118187 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
35118235 TGTGTGTGTG
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:35121670 original size:54 final size:55
Alignment explanation
Indices: 35121556--35121697 Score: 146
Period size: 54 Copynumber: 2.6 Consensus size: 55
35121546 TCCCAGCCCA
* * * * *
35121556 TGTAACTCACTGA-TTTAGGTCACATGGTCGTGTCATAGGCCGTATGCCAGGCCG
1 TGTAACTCACTAACTTAATGTCACATGGTCGTGTCATAGGCCGTATGCCAGACAG
* * * * *
35121610 TGTAACTCTCTAACTT-GTGTCACATGGTCGTGTCATAGGCCGTGTGCTAGATAG
1 TGTAACTCACTAACTTAATGTCACATGGTCGTGTCATAGGCCGTATGCCAGACAG
* * *
35121664 TTTAACTCACTGACTTAAT-ACACATGGTCGTGTC
1 TGTAACTCACTAACTTAATGTCACATGGTCGTGTC
35121698 TTAGACTGTG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
54 69 0.96
55 3 0.04
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.32
Consensus pattern (55 bp):
TGTAACTCACTAACTTAATGTCACATGGTCGTGTCATAGGCCGTATGCCAGACAG
Found at i:35130370 original size:66 final size:65
Alignment explanation
Indices: 35130249--35130371 Score: 142
Period size: 66 Copynumber: 1.9 Consensus size: 65
35130239 TGATGCGTGT
** * * **
35130249 ACAACCCAATTTTGCCCAGACCCAAATGGCCCATTACCTAATAACCCACCTAAACCCAACAAACA
1 ACAACCCAATTCGGCCCAAACCCAAATGGCCCATTACCTAATAACCAACAGAAACCCAACAAACA
*
35130314 ACAACCCAATTCGGCCCAAAACCCGAATGGCCCATTAACCT-A-AACCTAACAGAAACCC
1 ACAACCCAATTCGGCCC-AAACCCAAATGGCCCATT-ACCTAATAACC-AACAGAAACCC
35130372 TAGCAGAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
65 19 0.40
66 25 0.52
67 4 0.08
ACGTcount: A:0.40, C:0.38, G:0.08, T:0.14
Consensus pattern (65 bp):
ACAACCCAATTCGGCCCAAACCCAAATGGCCCATTACCTAATAACCAACAGAAACCCAACAAACA
Found at i:35130696 original size:13 final size:13
Alignment explanation
Indices: 35130661--35130709 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
35130651 ATAAGCTCTA
*
35130661 TTTTCCCTTTTAT
1 TTTTCCTTTTTAT
**
35130674 TTTTTATTTTTAT
1 TTTTCCTTTTTAT
35130687 TTTTCCTTTTT-T
1 TTTTCCTTTTTAT
35130699 TCTTTCCTTTT
1 T-TTTCCTTTT
35130710 AAAACTGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 2 0.07
13 28 0.93
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTCCTTTTTAT
Found at i:35130709 original size:25 final size:25
Alignment explanation
Indices: 35130659--35130710 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
35130649 GTATAAGCTC
*
35130659 TATTTTCCCTTTTATTTTTTATTTT
1 TATTTTCCCTTTTATTTTTTACTTT
* *
35130684 TATTTTTCCTTTT-TTTCTTTCCTTT
1 TATTTTCCCTTTTATTT-TTTACTTT
35130709 TA
1 TA
35130711 AAACTGTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (25 bp):
TATTTTCCCTTTTATTTTTTACTTT
Found at i:35130751 original size:17 final size:17
Alignment explanation
Indices: 35130726--35130763 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
35130716 GTTTGCTTTC
*
35130726 TTTATTTTTATTTTATT
1 TTTACTTTTATTTTATT
*
35130743 TTTACTTTTCTTTTATT
1 TTTACTTTTATTTTATT
35130760 TTTA
1 TTTA
35130764 AAAAAACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTACTTTTATTTTATT
Found at i:35136080 original size:6 final size:6
Alignment explanation
Indices: 35136071--35136113 Score: 68
Period size: 6 Copynumber: 6.8 Consensus size: 6
35136061 AAAATAGAAA
35136071 AAAAAG AAAAAAG AAAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG -AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
35136114 AAGGAGAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.64
7 13 0.36
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:35136080 original size:7 final size:7
Alignment explanation
Indices: 35136070--35136114 Score: 69
Period size: 7 Copynumber: 6.9 Consensus size: 7
35136060 AAAAATAGAA
35136070 AAAAAAG
1 AAAAAAG
35136077 AAAAAAG
1 AAAAAAG
35136084 AAAAAAG
1 AAAAAAG
35136091 -AAAAAG
1 AAAAAAG
35136097 -AAAAAG
1 AAAAAAG
35136103 -AAAAAG
1 AAAAAAG
35136109 AAAAAA
1 AAAAAA
35136115 AGGAGAGGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 18 0.49
7 19 0.51
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:35136087 original size:12 final size:11
Alignment explanation
Indices: 35136060--35136113 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 11
35136050 AATCAAAGCC
*
35136060 AAAAATAGAAA
1 AAAAAAAGAAA
35136071 AAAAAGAA-AAA
1 AAAAA-AAGAAA
35136082 AGAAAAAAGAAA
1 A-AAAAAAGAAA
35136094 AAGAAAAAGAAA
1 AA-AAAAAGAAA
35136106 AAGAAAAA
1 AA-AAAAA
35136114 AAGGAGAGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
11 12 0.32
12 26 0.68
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:35138264 original size:85 final size:85
Alignment explanation
Indices: 35138118--35139857 Score: 2246
Period size: 85 Copynumber: 20.3 Consensus size: 85
35138108 AGAACAAATT
* * * *
35138118 AGCAGATCGAAAACAAGCCTTGCATTCATTGGTTACAGTGGAGCTGGTTAAAGAAGTAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
**
35138183 CCTTCCTGCGTTAACAGTGA
66 CCTTCCTGCGTTAACACCGA
* * * *
35138203 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAGCAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
* *
35138268 CCTTCCTGC-ATAACAGCGA
66 CCTTCCTGCGTTAACACCGA
* * * * *
35138287 AGCAGATCGAAAACAAAGTCTTGCCTTCATTGGTTACAATGGAGCTGGTTAAAGAAGTAGATCTT
1 AGCAGATCGAAAAC-AAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTT
*
35138352 GCCTTCCTGCGTTAACAGCGA
65 GCCTTCCTGCGTTAACACCGA
35138373 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
* **
35138438 CCTTCCTGCATTAACAGTGA
66 CCTTCCTGCGTTAACACCGA
35138458 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
35138523 CCTTCCTGCGTTAACACCGA
66 CCTTCCTGCGTTAACACCGA
*
35138543 AGCAGATCGTAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
35138608 CCTTCCTGCGTTAACACCGA
66 CCTTCCTGCGTTAACACCGA
*
35138628 AGCAGATCGTAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
35138693 CCTTCCTGCGTTAACACCGA
66 CCTTCCTGCGTTAACACCGA
*
35138713 AGCAGATCGTAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
35138778 CCTTCCTGCGTTAACACCGA
66 CCTTCCTGCGTTAACACCGA
*
35138798 AGCAGATCGTAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
35138863 CCTTCCTGCGTTAACACCGA
66 CCTTCCTGCGTTAACACCGA
*
35138883 AGCAGATCGTAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
35138948 CCTTCCTGCGTTAACACCGA
66 CCTTCCTGCGTTAACACCGA
*
35138968 AGCAGATCGTAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
35139033 CCTTCCTGCGTTAACACCGA
66 CCTTCCTGCGTTAACACCGA
*
35139053 AGCAGATCGTAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
35139118 CCTTCCTGCGTTAACACCGA
66 CCTTCCTGCGTTAACACCGA
*
35139138 AGCAGATCGTAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
35139203 CCTTCCTGCGTTAACACCGA
66 CCTTCCTGCGTTAACACCGA
*
35139223 AGCAGATCGTAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
35139288 CCTTCCTGCGTTAACACCGA
66 CCTTCCTGCGTTAACACCGA
*
35139308 AGCAGATCGTAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
** * *
35139373 CCTTCCTGCAATGACAGCGA
66 CCTTCCTGCGTTAACACCGA
* * * * * *
35139393 AGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATT--TTG-A-TGGAGCTGGTTGAAGTCAA-A
1 AGCAGATCGAA-A-ACAAGCCTTG-C-CT-TC-ATTGGTTGCAGTAGAGCTGTTTAAAG--AAGT
* ** * * *
35139453 AGATCTTGCCTTTCTGTATTGACAGCAA
58 AGATCTTGCCTTCCTGCGTTAACACCGA
* * * * * * * * **
35139481 AGCAGGTCAAAAACACAAACCTTGCCTCTC-TCGGTTG-TGATGGAGCTGGTTGAAGACAAAAGA
1 AGCAGATC-GAAA-ACAAGCCTTGCCT-TCATTGGTTGCAG-TAGAGCTGTTTAAAGA-AGTAGA
** * *
35139544 TCTTGCCTTCCTGTATTGACAGCGA
61 TCTTGCCTTCCTGCGTTAACACCGA
* * * * * * * **
35139569 AGCAGGTCGAAGACACAAACCTTGCCTCTC-TCGGTTG-TGATGGAGCTGGTTGAAGACAAAAGA
1 AGCAGATCGAA-A-ACAAGCCTTGCCT-TCATTGGTTGCAG-TAGAGCTGTTTAAAGA-AGTAGA
* ** * *
35139632 TCTTGCCTTTCTGTATTGACAGCGA
61 TCTTGCCTTCCTGCGTTAACACCGA
* * * * * * * **
35139657 AGCAGGTCGAAGACACAAACCTTGCCTCTC-TCGGTTG-TGATGGAGCTGGTTGAAGACAAAAGA
1 AGCAGATCGAA-A-ACAAGCCTTGCCT-TCATTGGTTGCAG-TAGAGCTGTTTAAAGA-AGTAGA
* * *
35139720 TCTTGCCTTCCTGCATTGACAGCGA
61 TCTTGCCTTCCTGCGTTAACACCGA
* * * * * * *
35139745 AGCA-AGTCGAAAACACAAACCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGAT
1 AGCAGA-TCG-AAA-ACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGA-AGTAGAT
* * * *
35139809 ATTGCCTTCCTACGTTAATAGCGA
62 CTTGCCTTCCTGCGTTAACACCGA
*
35139833 AGCAGATCGAAAACAAACCTTGCCT
1 AGCAGATCGAAAACAAGCCTTGCCT
35139858 CTCTCAGTTG
Statistics
Matches: 1578, Mismatches: 54, Indels: 45
0.94 0.03 0.03
Matches are distributed among these distances:
84 23 0.01
85 1129 0.72
86 46 0.03
87 29 0.02
88 333 0.21
89 13 0.01
90 2 0.00
91 3 0.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (85 bp):
AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTAGAGCTGTTTAAAGAAGTAGATCTTG
CCTTCCTGCGTTAACACCGA
Found at i:35139461 original size:44 final size:43
Alignment explanation
Indices: 35139413--35139727 Score: 212
Period size: 44 Copynumber: 7.2 Consensus size: 43
35139403 AGACACAAAC
*
35139413 CTTGCCTCTCTCGATTTTGATGGAGCTGGTTGAAGTCAAAAGAT
1 CTTGCCTCTCTCG-TTTTGATGGAGCTGGTTGAAGACAAAAGAT
* * * * * ** * * *
35139457 CTTGCCTTTCT-GTATTGACAGCAAAGCAGGTCAAAAACACAA-AC
1 CTTGCCTCTCTCGTTTTGA-TG--GAGCTGGTTGAAGACAAAAGAT
*
35139501 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTC-GTTTTGATGGAGCTGGTTGAAGACAAAAGAT
* * * * * *
35139545 CTTGCCT-TC-CTGTATTGACAGCGAAGCAGGTCGAAGACACAA-AC
1 CTTGCCTCTCTC-GTTTTGA-TG-G-AGCTGGTTGAAGACAAAAGAT
*
35139589 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTC-GTTTTGATGGAGCTGGTTGAAGACAAAAGAT
* * * * * * *
35139633 CTTGCCTTTCT-GTATTGACAGCGAAGCAGGTCGAAGACACAA-AC
1 CTTGCCTCTCTCGTTTTGA-TG-G-AGCTGGTTGAAGACAAAAGAT
*
35139677 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTC-GTTTTGATGGAGCTGGTTGAAGACAAAAGAT
35139721 CTTGCCT
1 CTTGCCT
35139728 TCCTGCATTG
Statistics
Matches: 199, Mismatches: 54, Indels: 36
0.69 0.19 0.12
Matches are distributed among these distances:
42 16 0.08
43 49 0.25
44 71 0.36
45 47 0.24
46 16 0.08
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (43 bp):
CTTGCCTCTCTCGTTTTGATGGAGCTGGTTGAAGACAAAAGAT
Found at i:35139553 original size:176 final size:174
Alignment explanation
Indices: 35139365--35139898 Score: 761
Period size: 176 Copynumber: 3.0 Consensus size: 174
35139355 TTAAAGAAGT
*
35139365 AGATCTTGCCTTCCTGCAATGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATTT
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCG-TTT
*
35139430 TGATGGAGCTGGTTGAAGTCAAAAGATCTTGCCTTTCTGTATTGACAGCAAAGCAGGTCAAAAAC
65 TGATGGAGCTGGTTGAAGTCAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTC-AAAAC
35139495 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAA
129 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAA
* *
35139541 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTC-GTTT
* *
35139606 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAAGAC
65 TGATGGAGCTGGTTGAAGTCAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTC-AAAAC
35139671 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAA
129 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAA
* * *
35139717 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAAGTCGAAAACACAAACCTTGCCTC-CATCG-GT
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTC-TCGTTT
** * * *** * * * *
35139780 TGCAGTGGAGCTGGTTGAAGAT-AGCAGATATTGCCTTCCTACGTTAATAGCGAAGCAGATCGAA
65 TG-A-TGGAGCTGGTTGAAG-TCAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCAAA
* *
35139844 A-ACAAACCTTGCCTCTCTCAGTTGTGATAGAGCTGGTTGAAGACAAA
127 ACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAA
*
35139891 TGATCTTG
1 AGATCTTG
35139899 TTTCAAATCA
Statistics
Matches: 325, Mismatches: 28, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
174 53 0.16
175 5 0.02
176 266 0.82
177 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.25
Consensus pattern (174 bp):
AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGTTTT
GATGGAGCTGGTTGAAGTCAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCAAAACAC
AAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAA
Found at i:35140729 original size:154 final size:155
Alignment explanation
Indices: 35140449--35140759 Score: 579
Period size: 154 Copynumber: 2.0 Consensus size: 155
35140439 TAAATTCCAC
*
35140449 TTTCAAACTCTGAAATCCAAGTTGAATCCAGGCAATGGGAACTCAGTTAATAAGTTTGAAACTCT
1 TTTCAAACTCTGAAATCCAAGTTGAATCCAGACAATGGGAACTCAGTTAATAAGTTTGAAACTCT
35140514 TCAACACCCAGCTACATTGCGGGGTCGACATTTATATTACCGGGTTTTTTACTGGAATAA-TTTT
66 TCAACACCCAGCTACATTGCGGGGTCGACATTTATATTACCGGGTTTTTTACTGGAATAATTTTT
35140578 AAAAAAAATTATATACTGAAATAGG
131 AAAAAAAATTATATACTGAAATAGG
* *
35140603 TTTCAAACTCTGAAATCCAAGTTGAATCCAGACAATGGGAACTGAGTTAATAGGTTTGAAACTCT
1 TTTCAAACTCTGAAATCCAAGTTGAATCCAGACAATGGGAACTCAGTTAATAAGTTTGAAACTCT
*
35140668 TCAACACCCAGTTACATTGCGGGGTCGACATTTATATTACCGGGTTTTTTACTGGAATAATTTTT
66 TCAACACCCAGCTACATTGCGGGGTCGACATTTATATTACCGGGTTTTTTACTGGAATAATTTTT
35140733 AAAAAAAATTATATACTGAAATAGG
131 AAAAAAAATTATATACTGAAATAGG
35140758 TT
1 TT
35140760 GTCAGATAGA
Statistics
Matches: 152, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
154 121 0.80
155 31 0.20
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (155 bp):
TTTCAAACTCTGAAATCCAAGTTGAATCCAGACAATGGGAACTCAGTTAATAAGTTTGAAACTCT
TCAACACCCAGCTACATTGCGGGGTCGACATTTATATTACCGGGTTTTTTACTGGAATAATTTTT
AAAAAAAATTATATACTGAAATAGG
Found at i:35140871 original size:49 final size:50
Alignment explanation
Indices: 35140789--35140897 Score: 166
Period size: 49 Copynumber: 2.2 Consensus size: 50
35140779 GAAATGGTCT
35140789 TTTTTTTAATGGAGCCTATCTGAAAAGCGCCAATGAATATTTTATATT-A
1 TTTTTTTAATGGAGCCTATCTGAAAAGCGCCAATGAATATTTTATATTAA
* * * * *
35140838 TTTTTTTAATGGCGCCTATCTGATAGGCTCCAATGAATTTTTTATATTAA
1 TTTTTTTAATGGAGCCTATCTGAAAAGCGCCAATGAATATTTTATATTAA
35140888 TTTTTTTAAT
1 TTTTTTTAAT
35140898 AAAATGTCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 43 0.80
50 11 0.20
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (50 bp):
TTTTTTTAATGGAGCCTATCTGAAAAGCGCCAATGAATATTTTATATTAA
Found at i:35141518 original size:39 final size:40
Alignment explanation
Indices: 35141459--35141548 Score: 137
Period size: 39 Copynumber: 2.2 Consensus size: 40
35141449 AAAATTTATA
* *
35141459 TTTAATACAATAAAACATTTATTATATTTAT-TTGTGTTT
1 TTTAATATAATAAAACATTTATTATATTTATATAGTGTTT
*
35141498 TTTAATATAATAAAATATTTATTATATTTATAATAGTGTTT
1 TTTAATATAATAAAACATTTATTATATTTAT-ATAGTGTTT
35141539 TTTAATATAA
1 TTTAATATAA
35141549 ATACTTTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 29 0.63
41 17 0.37
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (40 bp):
TTTAATATAATAAAACATTTATTATATTTATATAGTGTTT
Found at i:35141851 original size:14 final size:14
Alignment explanation
Indices: 35141832--35141870 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
35141822 GAATGATTTT
35141832 TTCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
35141846 TTCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
*
35141860 TCCTTTCTCTT
1 TTC-TTCTCTT
35141871 TTTTCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TTCTTCTCTTCTTC
Found at i:35142055 original size:24 final size:25
Alignment explanation
Indices: 35142010--35142057 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
35142000 TTTATATTTA
*
35142010 AATATTTTTAATAAAAATAAAAAAT
1 AATATTTTTAATAAAAACAAAAAAT
* *
35142035 AATA-TTTTAATCAAACCAAAAAA
1 AATATTTTTAATAAAAACAAAAAA
35142058 AAATTAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (25 bp):
AATATTTTTAATAAAAACAAAAAAT
Found at i:35142698 original size:45 final size:45
Alignment explanation
Indices: 35142648--35142787 Score: 208
Period size: 45 Copynumber: 3.0 Consensus size: 45
35142638 CGGAGGGAAA
* * *
35142648 GGAGGGTATGGAGGTGGGCACGGAGGGTATGGTGGTGGTGGCCAC
1 GGAGGGTATGGTGGTGGCCACGGAGGATATGGTGGTGGTGGCCAC
35142693 GGAGGGTATGGTGGTGGCCACGGAGGATATGGTGGTGGTGGCCAC
1 GGAGGGTATGGTGGTGGCCACGGAGGATATGGTGGTGGTGGCCAC
* *
35142738 GGAGGATACGGTGGTGGTGGCCACGGAGGATACGGTGGTGGTGGCCAC
1 GGAGGGTA---TGGTGGTGGCCACGGAGGATATGGTGGTGGTGGCCAC
35142786 GG
1 GG
35142788 CGGTCACGGT
Statistics
Matches: 87, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
45 49 0.56
48 38 0.44
ACGTcount: A:0.16, C:0.14, G:0.53, T:0.18
Consensus pattern (45 bp):
GGAGGGTATGGTGGTGGCCACGGAGGATATGGTGGTGGTGGCCAC
Found at i:35142799 original size:24 final size:24
Alignment explanation
Indices: 35142660--35142787 Score: 190
Period size: 24 Copynumber: 5.5 Consensus size: 24
35142650 AGGGTATGGA
* * *
35142660 GGTGGGCACGGAGGGTATGGTGGT
1 GGTGGCCACGGAGGATACGGTGGT
*
35142684 GGTGGCCACGGAGGGTA---TGGT
1 GGTGGCCACGGAGGATACGGTGGT
*
35142705 GGTGGCCACGGAGGATATGGTGGT
1 GGTGGCCACGGAGGATACGGTGGT
35142729 GGTGGCCACGGAGGATACGGTGGT
1 GGTGGCCACGGAGGATACGGTGGT
35142753 GGTGGCCACGGAGGATACGGTGGT
1 GGTGGCCACGGAGGATACGGTGGT
35142777 GGTGGCCACGG
1 GGTGGCCACGG
35142788 CGGTCACGGT
Statistics
Matches: 98, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
21 20 0.20
24 78 0.80
ACGTcount: A:0.15, C:0.15, G:0.52, T:0.18
Consensus pattern (24 bp):
GGTGGCCACGGAGGATACGGTGGT
Found at i:35147731 original size:16 final size:16
Alignment explanation
Indices: 35147710--35147743 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
35147700 CAAAATCTCA
35147710 ATTTAATT-TTTAATTT
1 ATTTAATTATTT-ATTT
35147726 ATTTAATTATTTATTT
1 ATTTAATTATTTATTT
35147742 AT
1 AT
35147744 GATGTTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTAATTATTTATTT
Found at i:35149119 original size:5 final size:5
Alignment explanation
Indices: 35149093--35149132 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
35149083 ATGTTTTAAA
* *
35149093 TATAT TAATAT TTTAA TATAT TATAT TATAT TATAT TATA
1 TATAT T-ATAT TATAT TATAT TATAT TATAT TATAT TATA
35149133 NATGTAATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:35149454 original size:15 final size:15
Alignment explanation
Indices: 35149434--35149485 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
35149424 TATGTTTTAT
35149434 ATATTATTTTATATC
1 ATATTATTTTATATC
35149449 ATATTATTTTATATC
1 ATATTATTTTATATC
* * *
35149464 ATATTGTATTATATT
1 ATATTATTTTATATC
35149479 ATATTAT
1 ATATTAT
35149486 ATTAAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (15 bp):
ATATTATTTTATATC
Found at i:35149473 original size:5 final size:5
Alignment explanation
Indices: 35149433--35149489 Score: 69
Period size: 5 Copynumber: 11.4 Consensus size: 5
35149423 TTATGTTTTA
* * * * *
35149433 TATAT TATTT TATAT CATAT TATTT TATAT CATAT TGTAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
35149483 TATAT TA
1 TATAT TA
35149490 AATAAAATAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:35150109 original size:23 final size:24
Alignment explanation
Indices: 35150074--35150118 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
35150064 AATATGGCAA
35150074 GAAATTAAGTAGAAAAG-AAGTAT
1 GAAATTAAGTAGAAAAGTAAGTAT
35150097 GAAA-TAAGCTAGAAAAGTAAGT
1 GAAATTAAG-TAGAAAAGTAAGT
35150119 GAGCTTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (24 bp):
GAAATTAAGTAGAAAAGTAAGTAT
Found at i:35162406 original size:18 final size:17
Alignment explanation
Indices: 35162378--35162412 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35162368 NNNNNNNAGA
*
35162378 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
35162395 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
35162413 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:35162669 original size:16 final size:16
Alignment explanation
Indices: 35162648--35162683 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
35162638 AATTTACTAT
35162648 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
35162664 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
35162680 TACA
1 TACA
35162684 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:35162968 original size:30 final size:31
Alignment explanation
Indices: 35162916--35163016 Score: 102
Period size: 30 Copynumber: 3.3 Consensus size: 31
35162906 ATATTTTATG
* *
35162916 TATCATTATATTAAATTATTTAAATATGATT
1 TATCATTATATTAAAATATTTAAATATCATT
35162947 TATCATTATA-TAAAATATTTAAATATCATT
1 TATCATTATATTAAAATATTTAAATATCATT
* * *
35162977 TCTTATTGTATTTAAAAT-TTTAAA-AT-ATT
1 TATCATTATA-TTAAAATATTTAAATATCATT
35163006 TCATCTATTAT
1 T-ATC-ATTAT
35163017 TAAATTTACA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
29 4 0.07
30 28 0.48
31 20 0.34
32 6 0.10
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (31 bp):
TATCATTATATTAAAATATTTAAATATCATT
Found at i:35163512 original size:28 final size:27
Alignment explanation
Indices: 35163460--35163513 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 27
35163450 TCATAGTGTG
*
35163460 AAAATAAAGGAAACTTTTAAAAAAATTC
1 AAAATAAAGGAAAC-TCTAAAAAAATTC
35163488 AAAATAATAGGAAA-TCTAAAGAAAAT
1 AAAATAA-AGGAAACTCTAAA-AAAAT
35163514 GAAATACCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 5 0.22
28 12 0.52
29 6 0.26
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.22
Consensus pattern (27 bp):
AAAATAAAGGAAACTCTAAAAAAATTC
Found at i:35164939 original size:43 final size:43
Alignment explanation
Indices: 35164863--35165036 Score: 140
Period size: 43 Copynumber: 4.1 Consensus size: 43
35164853 GCCGCTATAA
* * *
35164863 AACATGACATTTAGCGGCG-TTTCTCACAAAAACGCCACTATAG
1 AACATGACATTTAGCGGTGCTTTCTC-CACAAACGCCACTAAAG
* * * *
35164906 AACATAACATTTAGCGGTGCTTTTTCCACAAACGACGCTAAAG
1 AACATGACATTTAGCGGTGCTTTCTCCACAAACGCCACTAAAG
* * * * *
35164949 AACATGACCTTTAACAGTGCTTTCCCCACAAACTCCACTAAAG
1 AACATGACATTTAGCGGTGCTTTCTCCACAAACGCCACTAAAG
* * * * * * *
35164992 AATATG--A-TTAGTGGCGCTTTCCCCACAAACACCGCTAAAT
1 AACATGACATTTAGCGGTGCTTTCTCCACAAACGCCACTAAAG
35165032 AACAT
1 AACAT
35165037 TATCTTTAGC
Statistics
Matches: 104, Mismatches: 26, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
40 30 0.29
43 69 0.66
44 5 0.05
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (43 bp):
AACATGACATTTAGCGGTGCTTTCTCCACAAACGCCACTAAAG
Found at i:35173836 original size:45 final size:43
Alignment explanation
Indices: 35173783--35173973 Score: 285
Period size: 45 Copynumber: 4.4 Consensus size: 43
35173773 ATCCAAAGTT
35173783 TTATGTAAGTTATGATATGATATATATTTATGTAAATTATGTAAA
1 TTATGTAAGTTATGATATGATATATATTTATGT--ATTATGTAAA
* * *
35173828 TTATGTAAGTTATGATATGATGT-TTTTTATGTATTATGTAAG
1 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAA
35173870 TTATGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAAA
1 TTATGTAAGTTATGATATGATATATATTTATGT-A-TTATGTAAA
* * *
35173915 TTATGTAATTTATGATATGATATATATTTATGTATTATGCAAG
1 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAA
35173958 TTATGTAAGTTATGAT
1 TTATGTAAGTTATGAT
35173974 CCAATGTTTT
Statistics
Matches: 133, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
42 31 0.23
43 30 0.23
44 10 0.08
45 62 0.47
ACGTcount: A:0.35, C:0.01, G:0.16, T:0.49
Consensus pattern (43 bp):
TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAA
Found at i:35173910 original size:87 final size:88
Alignment explanation
Indices: 35173783--35173973 Score: 330
Period size: 87 Copynumber: 2.2 Consensus size: 88
35173773 ATCCAAAGTT
35173783 TTATGTAAGTTATGATATGATATATATTTATGTAAATTATGTAAATTATGTAAGTTATGATATGA
1 TTATGTAAGTTATGATATGATATATATTTATGTAAATTATGTAAATTATGTAAGTTATGATATGA
* * *
35173848 TGT-TTTTTATGTATTATGTAAG
66 TATATATTTATGTATTATGCAAG
* *
35173870 TTATGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAAATTATGTAATTTATGATATGA
1 TTATGTAAGTTATGATATGATATATATTTATGTAAATTATGTAAATTATGTAAGTTATGATATGA
35173935 TATATATTTATGTATTATGCAAG
66 TATATATTTATGTATTATGCAAG
35173958 TTATGTAAGTTATGAT
1 TTATGTAAGTTATGAT
35173974 CCAATGTTTT
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
87 65 0.66
88 33 0.34
ACGTcount: A:0.35, C:0.01, G:0.16, T:0.49
Consensus pattern (88 bp):
TTATGTAAGTTATGATATGATATATATTTATGTAAATTATGTAAATTATGTAAGTTATGATATGA
TATATATTTATGTATTATGCAAG
Found at i:35173967 original size:9 final size:9
Alignment explanation
Indices: 35173783--35173971 Score: 90
Period size: 9 Copynumber: 21.6 Consensus size: 9
35173773 ATCCAAAGTT
35173783 TTATGTAAG
1 TTATGTAAG
*
35173792 TTATGATATG
1 TTATG-TAAG
* * *
35173802 ATATAT-AT
1 TTATGTAAG
*
35173810 TTATGTAAA
1 TTATGTAAG
*
35173819 TTATGTAAA
1 TTATGTAAG
35173828 TTATGTAAG
1 TTATGTAAG
35173837 TTATG-ATA-
1 TTATGTA-AG
* ***
35173845 TGATGTTTT
1 TTATGTAAG
35173854 TTATGT-A-
1 TTATGTAAG
35173861 TTATGTAAG
1 TTATGTAAG
35173870 TTATGTAAG
1 TTATGTAAG
*
35173879 TTATGATATG
1 TTATG-TAAG
* * *
35173889 ATATAT-AT
1 TTATGTAAG
35173897 TTATGTAAG
1 TTATGTAAG
*
35173906 TTATGTAAA
1 TTATGTAAG
*
35173915 TTATGTAAT
1 TTATGTAAG
*
35173924 TTATGATATG
1 TTATG-TAAG
* * *
35173934 ATATAT-AT
1 TTATGTAAG
35173942 TTATGT-A-
1 TTATGTAAG
*
35173949 TTATGCAAG
1 TTATGTAAG
35173958 TTATGTAAG
1 TTATGTAAG
35173967 TTATG
1 TTATG
35173972 ATCCAATGTT
Statistics
Matches: 134, Mismatches: 34, Indels: 24
0.70 0.18 0.12
Matches are distributed among these distances:
7 11 0.08
8 20 0.15
9 86 0.64
10 17 0.13
ACGTcount: A:0.35, C:0.01, G:0.16, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:35174649 original size:13 final size:14
Alignment explanation
Indices: 35174626--35174660 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
35174616 GATACAGAGA
35174626 ACAGAATCAGATAT
1 ACAGAATCAGATAT
*
35174640 GCAGAA-CAGATAT
1 ACAGAATCAGATAT
35174653 ACAGAATC
1 ACAGAATC
35174661 CTACCACCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (14 bp):
ACAGAATCAGATAT
Found at i:35177119 original size:72 final size:72
Alignment explanation
Indices: 35177038--35177256 Score: 235
Period size: 72 Copynumber: 3.1 Consensus size: 72
35177028 AAATGGTTCC
* * * * * *
35177038 ACTTAATATCAAAACTCAATAAGTTGAACTAAATTAACCTTTTTTAAAATTCATAATTGAACAAG
1 ACTTAATATCAAAACTTAATAAATTGAACTAAATTAACCTTTTTAAAAATTCATAATTAAATAAA
*
35177103 CGTTTTT
66 CGATTTT
** ** * * * *
35177110 ACTTAATATCAAATTTTAATAAATCAAACTAAATTAAGC-TTCTGAAAATGT-ATAACTAAATAA
1 ACTTAATATCAAAACTTAATAAATTGAACTAAATTAACCTTTTTAAAAAT-TCATAATTAAATAA
* *
35177173 ACGGTTTC
65 ACGATTTT
* **
35177181 GCTTAATATCAAAACTTAATAAATTGAACTAAATTAACCTTTTTAAAAACACATAATTAAATAAA
1 ACTTAATATCAAAACTTAATAAATTGAACTAAATTAACCTTTTTAAAAATTCATAATTAAATAAA
35177246 CGATTTT
66 CGATTTT
35177253 ACTT
1 ACTT
35177257 GATAATTAAT
Statistics
Matches: 115, Mismatches: 29, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
71 55 0.48
72 60 0.52
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (72 bp):
ACTTAATATCAAAACTTAATAAATTGAACTAAATTAACCTTTTTAAAAATTCATAATTAAATAAA
CGATTTT
Found at i:35177630 original size:12 final size:12
Alignment explanation
Indices: 35177613--35177643 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
35177603 CAAAAGCATG
35177613 CTCCATTCTCAA
1 CTCCATTCTCAA
*
35177625 CTCCATTCTCGA
1 CTCCATTCTCAA
35177637 CTCCATT
1 CTCCATT
35177644 TACAACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.42, G:0.03, T:0.35
Consensus pattern (12 bp):
CTCCATTCTCAA
Found at i:35179206 original size:22 final size:22
Alignment explanation
Indices: 35179163--35179206 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
35179153 AACATATAAT
*
35179163 TAAATTAATCAAAATTTACAAA
1 TAAATTAATCAAAAATTACAAA
*
35179185 TAAA-TAATCCAAAAATTGCAAA
1 TAAATTAAT-CAAAAATTACAAA
35179207 CAGCAGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAATTAATCAAAAATTACAAA
Found at i:35184068 original size:27 final size:27
Alignment explanation
Indices: 35184038--35184090 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
35184028 TGGAGGTTAT
35184038 GGAGGATACGGAGGGCGCGGTGGGTAC
1 GGAGGATACGGAGGGCGCGGTGGGTAC
*
35184065 GGAGGATACGGAGGGCGTGGTGGGTA
1 GGAGGATACGGAGGGCGCGGTGGGTA
35184091 TGGTGGTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.11, G:0.57, T:0.13
Consensus pattern (27 bp):
GGAGGATACGGAGGGCGCGGTGGGTAC
Found at i:35185111 original size:30 final size:29
Alignment explanation
Indices: 35185048--35185111 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
35185038 ACTACAAGTT
** * *
35185048 AGTCTTTGTACTTTTATTTTTAAGAATTT
1 AGTCTTTGTACTTTTAAATTTAAAAATTA
*
35185077 AGTCTTTTTACTTTTCAAATTTAAAAATTA
1 AGTCTTTGTACTTTT-AAATTTAAAAATTA
35185107 AGTCT
1 AGTCT
35185112 AACTGTTGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (29 bp):
AGTCTTTGTACTTTTAAATTTAAAAATTA
Found at i:35185858 original size:32 final size:32
Alignment explanation
Indices: 35185809--35185877 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
35185799 TATATATATA
* *
35185809 TAAAT-TTTTTTAGATAAATTCATG-TACCAAT
1 TAAATATTTTCTAAATAAATT-ATGATACCAAT
35185840 TAAATATTTTCTAAATAAATTATGATACCAAT
1 TAAATATTTTCTAAATAAATTATGATACCAAT
35185872 TAAATA
1 TAAATA
35185878 CTTATAGGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 8 0.24
32 26 0.76
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (32 bp):
TAAATATTTTCTAAATAAATTATGATACCAAT
Found at i:35186073 original size:28 final size:28
Alignment explanation
Indices: 35186038--35186103 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
35186028 ATAAAAAATA
*
35186038 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTTATTT
35186066 ACCAAAATATTATAAATTTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTTATTT
35186094 ACCAAAATAT
1 ACCAAAATAT
35186104 ACCAAAAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (28 bp):
ACCAAAATATTATAAATTTTTTTTATTT
Found at i:35186183 original size:27 final size:27
Alignment explanation
Indices: 35186144--35186202 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
35186134 GCCTGATCAG
35186144 GCCAATCACATTGGAGGCACCAAAGGT
1 GCCAATCACATTGGAGGCACCAAAGGT
* * * *
35186171 GCCAATGAGATTGGCGGCACCAATGGT
1 GCCAATCACATTGGAGGCACCAAAGGT
35186198 GCCAA
1 GCCAA
35186203 AGGACTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.29, T:0.15
Consensus pattern (27 bp):
GCCAATCACATTGGAGGCACCAAAGGT
Found at i:35187786 original size:113 final size:115
Alignment explanation
Indices: 35187595--35187895 Score: 482
Period size: 113 Copynumber: 2.6 Consensus size: 115
35187585 CACTTTCAAA
35187595 ATTCAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAGAAAATTACATTTTAGTCCTTTG
1 ATTCAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAGAAAATTACATTTTAGTCCTTTG
35187660 GCACCATTGGTGCCACCAATCTCATTGGCACCTTTGGCAGCAATTCAC-T
66 GCACCATTGGTGCCACCAATCTCATTGGCACCTTTGGCAGCAATTCACTT
35187709 -TTCAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAGAAAATTACATTTTAGTCCTTTG
1 ATTCAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAGAAAATTACATTTTAGTCCTTTG
35187773 GCACCATTGGTGCCACCAATCTCATTGGCACCTTTGGCAGCAATTCACTTT
66 GCACCATTGGTGCCACCAATCTCATTGGCACCTTTGGCAGCAATTCAC-TT
* * * *
35187824 CAAAATTCAAAATCGTAAATTTACATGTCAGGTCTTTAAAACTGTA-AAAAGTTACATTTTAGTC
1 ----ATTCAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAGAAAA-TTACATTTTAGTC
*
35187888 ATTTGGCA
61 CTTTGGCA
35187896 ATCTCATTGG
Statistics
Matches: 174, Mismatches: 5, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
113 112 0.64
115 1 0.01
119 4 0.02
120 57 0.33
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (115 bp):
ATTCAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTGCAGAAAATTACATTTTAGTCCTTTG
GCACCATTGGTGCCACCAATCTCATTGGCACCTTTGGCAGCAATTCACTT
Found at i:35187973 original size:98 final size:100
Alignment explanation
Indices: 35187789--35187993 Score: 306
Period size: 98 Copynumber: 2.0 Consensus size: 100
35187779 TTGGTGCCAC
35187789 CAATCTCATTGGCACCTTTGGCAGCAATTCACTTTCAAAATTCAAAATCGTAAATTTACATGTCA
1 CAATCTCATTGGCACCTTTGGCAGCAATTCAC-TT----ATTCAAAATCGTAAATTTACATGTCA
*
35187854 GGTCTTTAAAACTGTAAAAAGTTACATTTTAGTCATTTGG
61 GGTCCTTAAAACTGTAAAAAGTTACATTTTAGTCATTTGG
* *
35187894 CAATCTCATTGGCACCTTTGGCAGCAATTCAC-T-TTCAAAATGGTAAATTTGCATGTCAGGTCC
1 CAATCTCATTGGCACCTTTGGCAGCAATTCACTTATTCAAAATCGTAAATTTACATGTCAGGTCC
* *
35187957 TTAAAACTGTAGAAAGTTACATTTTAGTCCTTTGG
66 TTAAAACTGTAAAAAGTTACATTTTAGTCATTTGG
35187992 CA
1 CA
35187994 CCATTGGTGC
Statistics
Matches: 95, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
98 62 0.65
103 1 0.01
105 32 0.34
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (100 bp):
CAATCTCATTGGCACCTTTGGCAGCAATTCACTTATTCAAAATCGTAAATTTACATGTCAGGTCC
TTAAAACTGTAAAAAGTTACATTTTAGTCATTTGG
Found at i:35188027 original size:27 final size:27
Alignment explanation
Indices: 35187988--35188046 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
35187978 TTTTAGTCCT
35187988 TTGGCACCATTGGTGCCGCCAATCTCA
1 TTGGCACCATTGGTGCCGCCAATCTCA
* * * *
35188015 TTGGCACCTTTGGTGCCTCCAATGTGA
1 TTGGCACCATTGGTGCCGCCAATCTCA
35188042 TTGGC
1 TTGGC
35188047 CTGATCAGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.29, G:0.25, T:0.31
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:35188122 original size:29 final size:30
Alignment explanation
Indices: 35188096--35188163 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
35188086 TTTTTTTAGT
*
35188096 ATATTTTGGTAAACAAAA-AAAATTTTATA
1 ATATTTTGATAAACAAAATAAAATTTTATA
* *
35188125 ATATTTTGATAAATAAAATAAAA-GTTATA
1 ATATTTTGATAAACAAAATAAAATTTTATA
35188154 ATATTTTGAT
1 ATATTTTGAT
35188164 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 31 0.89
30 4 0.11
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.41
Consensus pattern (30 bp):
ATATTTTGATAAACAAAATAAAATTTTATA
Found at i:35191050 original size:214 final size:215
Alignment explanation
Indices: 35190671--35191099 Score: 851
Period size: 214 Copynumber: 2.0 Consensus size: 215
35190661 ATTCTTATTT
35190671 CAAAGTGTGAATTTTAATTGTGATTTTAGTTATTCATTTTGATTTGGCTTATATTGTTTTATAAT
1 CAAAGTGTGAATTTTAATTGTGATTTTAGTTATTCATTTTGATTTGGCTTATATTGTTTTATAAT
35190736 ATGTTTTTAAATATAATAATTATGTTAACACATTACATTTTTACAACAATATCAATAATTTTTAA
66 ATGTTTTTAAATATAATAATTATGTTAACACATTACATTTTTACAACAATATCAATAATTTTTAA
35190801 AACCTTAAATTATTATAGTAGGTGAATAAAATTCATTCCGGTTGAGTTTTAATTTAGTTCGTATT
131 AACCTTAAATTATTATAGTAGGTGAATAAAATTCATTCCGGTTGAGTTTTAATTTAGTTCGTATT
35190866 AATATTATTGTCGGTGCAAG
196 AATATTATTGTCGGTGCAAG
35190886 CAAAGTGTG-ATTTTAATTGTGATTTTAGTTATTCATTTTGATTTGGCTTATATTGTTTTATAAT
1 CAAAGTGTGAATTTTAATTGTGATTTTAGTTATTCATTTTGATTTGGCTTATATTGTTTTATAAT
35190950 ATGTTTTTAAATATAATAATTATGTTAACACATTACATTTTTACAACAATATCAATAATTTTTAA
66 ATGTTTTTAAATATAATAATTATGTTAACACATTACATTTTTACAACAATATCAATAATTTTTAA
35191015 AACCTTAAATTATTATAGTAGGTGAATAAAATTCATTCCGGTTGAGTTTTAATTTAGTTCGTATT
131 AACCTTAAATTATTATAGTAGGTGAATAAAATTCATTCCGGTTGAGTTTTAATTTAGTTCGTATT
35191080 AATATTATTGTCGGTGCAAG
196 AATATTATTGTCGGTGCAAG
35191100 AGAACCTAAA
Statistics
Matches: 214, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
214 205 0.96
215 9 0.04
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (215 bp):
CAAAGTGTGAATTTTAATTGTGATTTTAGTTATTCATTTTGATTTGGCTTATATTGTTTTATAAT
ATGTTTTTAAATATAATAATTATGTTAACACATTACATTTTTACAACAATATCAATAATTTTTAA
AACCTTAAATTATTATAGTAGGTGAATAAAATTCATTCCGGTTGAGTTTTAATTTAGTTCGTATT
AATATTATTGTCGGTGCAAG
Found at i:35194065 original size:15 final size:14
Alignment explanation
Indices: 35194039--35194076 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
35194029 TTAAAAAAGT
*
35194039 AAATTATTTTTTAG
1 AAATTATTTTTTTG
35194053 AAATTATTTTTTTG
1 AAATTATTTTTTTG
*
35194067 AAAATATTTT
1 AAATTATTTT
35194077 ACTGCAAATA
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:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
AAATTATTTTTTTG
Found at i:35194906 original size:34 final size:34
Alignment explanation
Indices: 35194831--35194907 Score: 82
Period size: 34 Copynumber: 2.3 Consensus size: 34
35194821 TTACTATAAT
* * * * * *
35194831 TAATAATTAGTTATTAATTAATATTTTTTTACTT
1 TAATGATTAGTTAGTAATTAACATCTTTCTACTG
* *
35194865 TATTGATTGGTTAGTAATTAACATCTTTCTACTG
1 TAATGATTAGTTAGTAATTAACATCTTTCTACTG
35194899 TAATGATTA
1 TAATGATTA
35194908 AGAATTAGTT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.52
Consensus pattern (34 bp):
TAATGATTAGTTAGTAATTAACATCTTTCTACTG
Found at i:35195001 original size:27 final size:26
Alignment explanation
Indices: 35194971--35195046 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 26
35194961 ATATTTTTAT
35194971 TATTGTATTATTATTAAATATTATAAG
1 TATT-TATTATTATTAAATATTATAAG
* *
35194998 TATTATTATTATCATTAAAGA-TATAAG
1 TA-T-TTATTATTATTAAATATTATAAG
35195025 TA-TTATTATTATTCAACATATT
1 TATTTATTATTATT-AA-ATATT
35195047 TTTATTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
24 10 0.25
25 2 0.05
26 2 0.05
27 11 0.28
28 14 0.35
29 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (26 bp):
TATTTATTATTATTAAATATTATAAG
Found at i:35195055 original size:27 final size:25
Alignment explanation
Indices: 35194961--35195057 Score: 70
Period size: 27 Copynumber: 3.6 Consensus size: 25
35194951 ATTGTTAAAC
35194961 ATATTTTTATTATTGTATTATTATTAA
1 ATATTTTTATTA-T-TATTATTATTAA
* *
35194988 ATATTATAAGTATTATTATTATCATTAA
1 ATATT-T--TTATTATTATTATTATTAA
* * * *
35195016 AGA-TATAAGTATTATTATTATTCAA
1 ATATTTTTATTATTATTATTATT-AA
35195041 CATATTTTTATTATTAT
1 -ATATTTTTATTATTAT
35195058 AGGATTATTG
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
24 13 0.25
25 2 0.04
26 2 0.04
27 15 0.29
28 14 0.27
29 1 0.02
30 5 0.10
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (25 bp):
ATATTTTTATTATTATTATTATTAA
Found at i:35198457 original size:18 final size:19
Alignment explanation
Indices: 35198434--35198478 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
35198424 AAATGTACTA
*
35198434 ATTAATTT-TTTGGACCGC
1 ATTAATTTGTTTGGACCAC
*
35198452 ATTAATTTGTTTGGACCAT
1 ATTAATTTGTTTGGACCAC
35198471 ATTAATTT
1 ATTAATTT
35198479 AAGATCTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (19 bp):
ATTAATTTGTTTGGACCAC
Found at i:35203649 original size:21 final size:21
Alignment explanation
Indices: 35203625--35203665 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
35203615 TAATACTCAC
35203625 CCTACAACACCTAATTCTTAA
1 CCTACAACACCTAATTCTTAA
*
35203646 CCTACAACACCTACTTCTTA
1 CCTACAACACCTAATTCTTA
35203666 GTTTAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (21 bp):
CCTACAACACCTAATTCTTAA
Found at i:35207623 original size:17 final size:17
Alignment explanation
Indices: 35207601--35207633 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35207591 TTCTATTGTA
35207601 TTTCATTTAAATAAAAC
1 TTTCATTTAAATAAAAC
35207618 TTTCATTTAAATAAAA
1 TTTCATTTAAATAAAA
35207634 AATTGAAAAC
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:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTCATTTAAATAAAAC
Found at i:35209227 original size:5 final size:5
Alignment explanation
Indices: 35209212--35209317 Score: 203
Period size: 5 Copynumber: 21.0 Consensus size: 5
35209202 ATATAGCTAG
35209212 TTATAT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
1 TTAT-T TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
35209263 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
35209313 TTATT
1 TTATT
35209318 GAGTTTTGGA
Statistics
Matches: 100, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 96 0.96
6 4 0.04
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:35211551 original size:38 final size:38
Alignment explanation
Indices: 35211498--35211726 Score: 449
Period size: 38 Copynumber: 6.0 Consensus size: 38
35211488 TTATTTAAGC
35211498 AAACTCTACTATAACATCATTTCCATACTTTTTCAACA
1 AAACTCTACTATAACATCATTTCCATACTTTTTCAACA
*
35211536 ATACTCTACTATAACATCATTTCCATACTTTTTCAACA
1 AAACTCTACTATAACATCATTTCCATACTTTTTCAACA
35211574 AAACTCTACTATAACATCATTTCCATACTTTTTCAACA
1 AAACTCTACTATAACATCATTTCCATACTTTTTCAACA
35211612 AAACTCTACTATAACATCATTTCCATACTTTTTCAACA
1 AAACTCTACTATAACATCATTTCCATACTTTTTCAACA
35211650 AAACTCTACTATAACATCATTTCCATACTTTTTCAACA
1 AAACTCTACTATAACATCATTTCCATACTTTTTCAACA
35211688 AAACTCTACTATAACATCATTTCCATACTTTTTCAACA
1 AAACTCTACTATAACATCATTTCCATACTTTTTCAACA
35211726 A
1 A
35211727 TAACAAACTT
Statistics
Matches: 189, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 189 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (38 bp):
AAACTCTACTATAACATCATTTCCATACTTTTTCAACA
Found at i:35211564 original size:19 final size:19
Alignment explanation
Indices: 35211504--35211564 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
35211494 AAGCAAACTC
35211504 TACTATAACATCATTTCCA
1 TACTATAACATCATTTCCA
* ** * * *
35211523 TACTTTTTCAACAATACTC-
1 TACTATAACATCATTTC-CA
35211542 TACTATAACATCATTTCCA
1 TACTATAACATCATTTCCA
35211561 TACT
1 TACT
35211565 TTTTCAACAA
Statistics
Matches: 28, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
18 1 0.04
19 26 0.93
20 1 0.04
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.39
Consensus pattern (19 bp):
TACTATAACATCATTTCCA
Found at i:35221517 original size:30 final size:30
Alignment explanation
Indices: 35221481--35221537 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
35221471 TGTCCACTTC
*
35221481 TCCCAGATTGGTACTTAAGGTTTTTTTTTG
1 TCCCAGATTAGTACTTAAGGTTTTTTTTTG
35221511 TCCCAGATTAGTACTTAAGGTTTTTTT
1 TCCCAGATTAGTACTTAAGGTTTTTTT
35221538 CCGTTAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (30 bp):
TCCCAGATTAGTACTTAAGGTTTTTTTTTG
Found at i:35221849 original size:26 final size:26
Alignment explanation
Indices: 35221813--35221870 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
35221803 ACTTTTTTGG
*
35221813 CTCCAAAGTGGCTCTTAGTTGTTTCT
1 CTCCATAGTGGCTCTTAGTTGTTTCT
35221839 CTCCATAGTGGCTCTTAGTTGTTTCT
1 CTCCATAGTGGCTCTTAGTTGTTTCT
35221865 CTCCAT
1 CTCCAT
35221871 TCCCTCTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.14, C:0.26, G:0.17, T:0.43
Consensus pattern (26 bp):
CTCCATAGTGGCTCTTAGTTGTTTCT
Found at i:35228088 original size:38 final size:39
Alignment explanation
Indices: 35228033--35228134 Score: 145
Period size: 41 Copynumber: 2.6 Consensus size: 39
35228023 CACTCTACTA
35228033 AGTACATGTTGAA-CATGTCTACTACTAC-TGTTGAATTG
1 AGTACATGTT-AAGCATGTCTACTACTACTTGTTGAATTG
35228071 AGTACATGTTAAGCATGTCTACTACTACTATTGTTGAATTG
1 AGTACATGTTAAGCATGTCTACTACTAC--TTGTTGAATTG
* *
35228112 AATACATGTTAAGCATGGCTACT
1 AGTACATGTTAAGCATGTCTACT
35228135 GTTTCTGCAC
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
37 2 0.03
38 25 0.43
41 31 0.53
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (39 bp):
AGTACATGTTAAGCATGTCTACTACTACTTGTTGAATTG
Found at i:35230934 original size:201 final size:202
Alignment explanation
Indices: 35230578--35230980 Score: 799
Period size: 201 Copynumber: 2.0 Consensus size: 202
35230568 ATATTTTGTA
35230578 TATTATAATATCAATTAATTTTACTTTTGAAAATGAAGATCTTTTATTTTTTTTATTATTTATTT
1 TATTATAATATCAATTAATTTTACTTTTGAAAATGAAGATCTTTTATTTTTTTTATTATTTATTT
35230643 ACAATAATGCTTAACATGTAAAACTGTAAAATCACATGACGGTGGGTTTTGGGGAGTGAATTACA
66 ACAATAATGCTTAACATGTAAAACTGTAAAATCACATGACGGTGGGTTTTGGGGAGTGAATTACA
35230708 TTCATGTCCTTCTTGGCTGTCCCTACTAAAACGCGTCCACTTTATTTATTTTTTTAATGCCAAAA
131 TTCATGTCCTTCTTGGCTGTCCCTACTAAAACGCGTCCACTTTATTTATTTTTTTAATGCCAAAA
35230773 TTGACGC
196 TTGACGC
35230780 TATTATAATA-CAATTAATTTTACTTTTGAAAATGAAGATCTTTTATTTTTTTTATTATTTATTT
1 TATTATAATATCAATTAATTTTACTTTTGAAAATGAAGATCTTTTATTTTTTTTATTATTTATTT
35230844 ACAATAATGCTTAACATGTAAAACTGTAAAATCACATGACGGTGGGTTTTGGGGAGTGAATTACA
66 ACAATAATGCTTAACATGTAAAACTGTAAAATCACATGACGGTGGGTTTTGGGGAGTGAATTACA
35230909 TTCATGTCCTTCTTGGCTGTCCCTACTAAAACGCGTCCACTTTATTTATTTTTTTAATGCCAAAA
131 TTCATGTCCTTCTTGGCTGTCCCTACTAAAACGCGTCCACTTTATTTATTTTTTTAATGCCAAAA
35230974 TTGACGC
196 TTGACGC
35230981 CTCCCATGGT
Statistics
Matches: 201, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
201 191 0.95
202 10 0.05
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (202 bp):
TATTATAATATCAATTAATTTTACTTTTGAAAATGAAGATCTTTTATTTTTTTTATTATTTATTT
ACAATAATGCTTAACATGTAAAACTGTAAAATCACATGACGGTGGGTTTTGGGGAGTGAATTACA
TTCATGTCCTTCTTGGCTGTCCCTACTAAAACGCGTCCACTTTATTTATTTTTTTAATGCCAAAA
TTGACGC
Found at i:35231974 original size:9 final size:9
Alignment explanation
Indices: 35231960--35231988 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
35231950 ATAGTTGCAC
35231960 TAAATTATT
1 TAAATTATT
35231969 TAAATTATT
1 TAAATTATT
35231978 TAAATTATT
1 TAAATTATT
35231987 TA
1 TA
35231989 TAATACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAAATTATT
Found at i:35231999 original size:18 final size:18
Alignment explanation
Indices: 35231959--35232003 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
35231949 TATAGTTGCA
*
35231959 CTAAATTATTTAAATTAT
1 CTAAATTATTTAAATTAC
*
35231977 TTAAATTATTTATAA-TAC
1 CTAAATTATTTA-AATTAC
35231995 CTAAATTAT
1 CTAAATTAT
35232004 CCCTATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (18 bp):
CTAAATTATTTAAATTAC
Found at i:35232531 original size:15 final size:15
Alignment explanation
Indices: 35232507--35232544 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
35232497 AAAACCCTAA
*
35232507 AAACCTTAAAATCTT
1 AAACCCTAAAATCTT
35232522 AAACCCTAAAATCTT
1 AAACCCTAAAATCTT
*
35232537 AAAACCTA
1 AAACCCTA
35232545 CAAGTCAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (15 bp):
AAACCCTAAAATCTT
Found at i:35233028 original size:18 final size:19
Alignment explanation
Indices: 35233005--35233042 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
35232995 CTGTTTAACT
*
35233005 TATAAA-AAAAAGAAATTA
1 TATAAATAAAAACAAATTA
*
35233023 TATAAATCAAAACAAATTA
1 TATAAATAAAAACAAATTA
35233042 T
1 T
35233043 CCCTTCGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (19 bp):
TATAAATAAAAACAAATTA
Found at i:35241661 original size:3 final size:3
Alignment explanation
Indices: 35241653--35241691 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
35241643 AAACACCAAA
35241653 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
35241692 TGATAGGAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:35250131 original size:26 final size:26
Alignment explanation
Indices: 35250085--35250162 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 26
35250075 TTAAAAATTA
*
35250085 AAAAATTA-AAAAATATATAATTATTT
1 AAAAATTATAAAAAAAT-TAATTATTT
35250111 AAAAATTATAAAAAAATTAATGT-TTT
1 AAAAATTATAAAAAAATTAAT-TATTT
* * *
35250137 TAATATTTTAAAAAATAATTAATTAT
1 AAAAATTAT-AAAAA-AATTAATTAT
35250163 CAACGTAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
26 21 0.49
27 14 0.33
28 8 0.19
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (26 bp):
AAAAATTATAAAAAAATTAATTATTT
Found at i:35252047 original size:20 final size:19
Alignment explanation
Indices: 35252022--35252074 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
35252012 AAGTAAAATA
35252022 TTAAAATAAAAATAATATAT
1 TTAAAATAAAAAT-ATATAT
* *
35252042 TTAAAAT-CAAATTTATAT
1 TTAAAATAAAAATATATAT
35252060 TTAACATATAAAAAT
1 TTAA-A-ATAAAAAT
35252075 TATTAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 5 0.19
20 9 0.33
21 4 0.15
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAAAATAAAAATATATAT
Found at i:35252077 original size:20 final size:18
Alignment explanation
Indices: 35252022--35252077 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
35252012 AAGTAAAATA
35252022 TTAAAATAAAAATAATATAT
1 TTAAAATAAAAAT--TATAT
* *
35252042 TTAAAATCAAATTTATAT
1 TTAAAATAAAAATTATAT
35252060 TTAACATATAAAAATTAT
1 TTAA-A-ATAAAAATTAT
35252078 TAAAAAAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 9 0.30
19 1 0.03
20 20 0.67
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAAATAAAAATTATAT
Found at i:35252647 original size:19 final size:18
Alignment explanation
Indices: 35252615--35252651 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
35252605 TCAATTGCTT
35252615 TTAATTTTATTTAATTAA
1 TTAATTTTATTTAATTAA
*
35252633 TTAATTTTTTATTAATTAA
1 TTAATTTTAT-TTAATTAA
35252652 AAATAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAATTTTATTTAATTAA
Found at i:35253878 original size:27 final size:28
Alignment explanation
Indices: 35253807--35253880 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
35253797 ATTAATTTTT
**
35253807 TTAAAATT-TTTAAAAATTTAAAAATAA
1 TTAAAATTATTTAAAAAAGTAAAAATAA
**
35253834 -TAAAAGTTATTTTTAAAAGTAAAAA-AA
1 TTAAAA-TTATTTAAAAAAGTAAAAATAA
35253861 TTAAAATTATTTAAAAAAGT
1 TTAAAATTATTTAAAAAAGT
35253881 GTCAAAATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 5 0.13
27 16 0.42
28 17 0.45
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (28 bp):
TTAAAATTATTTAAAAAAGTAAAAATAA
Found at i:35255864 original size:21 final size:22
Alignment explanation
Indices: 35255815--35255864 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
35255805 AATCAAACTT
*
35255815 AATATT-ATTATATTTTTTATA
1 AATATTAATTATATTTTTTAAA
*
35255836 AATATTAATTTTA-TTTTTAAA
1 AATATTAATTATATTTTTTAAA
35255857 AATATTAA
1 AATATTAA
35255865 AATATTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATATTAATTATATTTTTTAAA
Found at i:35259793 original size:34 final size:34
Alignment explanation
Indices: 35259732--35259798 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
35259722 TCAGTTTAGT
* * *
35259732 TGGGCCTTTGCCCATTGCAGTATCAGTATCAGTG
1 TGGGCCTTAGCCCATTACAGTATCAGTAACAGTG
35259766 TGGGCCTTAGCCCATTACAGTGA-CAGTAACAGT
1 TGGGCCTTAGCCCATTACAGT-ATCAGTAACAGT
35259799 TCAGATATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 28 0.97
35 1 0.03
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.28
Consensus pattern (34 bp):
TGGGCCTTAGCCCATTACAGTATCAGTAACAGTG
Found at i:35260105 original size:27 final size:26
Alignment explanation
Indices: 35260065--35260136 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
35260055 ATAACATAAA
*
35260065 GCAT-ACAGTTATTTTATAACATAGGG
1 GCATAACAGTCATTTTATAACAT-GGG
** *
35260091 GCATAACAGTCATTTTACCACGTGGG
1 GCATAACAGTCATTTTATAACATGGG
*
35260117 GACATAACAATCATTTTATA
1 G-CATAACAGTCATTTTATA
35260137 TCAGTTTGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 8 0.22
27 29 0.78
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (26 bp):
GCATAACAGTCATTTTATAACATGGG
Found at i:35260257 original size:9 final size:9
Alignment explanation
Indices: 35260242--35260304 Score: 108
Period size: 9 Copynumber: 7.0 Consensus size: 9
35260232 GGCCCAGGCC
35260242 CATAATTTA
1 CATAATTTA
*
35260251 AATAATTTA
1 CATAATTTA
35260260 CATAATTTA
1 CATAATTTA
35260269 CATAATTTA
1 CATAATTTA
35260278 CATAATTTA
1 CATAATTTA
35260287 CATAATTTA
1 CATAATTTA
*
35260296 CATCATTTA
1 CATAATTTA
35260305 GCACTTGTGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (9 bp):
CATAATTTA
Found at i:35261863 original size:23 final size:23
Alignment explanation
Indices: 35261837--35261907 Score: 133
Period size: 23 Copynumber: 3.1 Consensus size: 23
35261827 GGAGCTGTCT
*
35261837 TTGATGACCAATGTTCGAATCCC
1 TTGATGACCAGTGTTCGAATCCC
35261860 TTGATGACCAGTGTTCGAATCCC
1 TTGATGACCAGTGTTCGAATCCC
35261883 TTGATGACCAGTGTTCGAATCCC
1 TTGATGACCAGTGTTCGAATCCC
35261906 TT
1 TT
35261908 CCCTCTCATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (23 bp):
TTGATGACCAGTGTTCGAATCCC
Found at i:35262597 original size:16 final size:16
Alignment explanation
Indices: 35262561--35262600 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
35262551 AGACCACTTC
*
35262561 CTTTCCTTTTTTCTCT
1 CTTTCTTTTTTTCTCT
*
35262577 -ATTCTTTTTTTCTCT
1 CTTTCTTTTTTTCTCT
35262592 CTTTCTTTT
1 CTTTCTTTT
35262601 AGCAAGAGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (16 bp):
CTTTCTTTTTTTCTCT
Found at i:35268740 original size:20 final size:20
Alignment explanation
Indices: 35268713--35268764 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
35268703 ACAAAAGTGC
* *
35268713 GTAT-AGGAGCACGAATGTG
1 GTATCAGGAGCACGAAAGTA
*
35268732 GTATCAGGAGTACGAAAGTA
1 GTATCAGGAGCACGAAAGTA
*
35268752 CTATCAGGAGCAC
1 GTATCAGGAGCAC
35268765 TTATTCAGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (20 bp):
GTATCAGGAGCACGAAAGTA
Found at i:35270208 original size:21 final size:21
Alignment explanation
Indices: 35270180--35270232 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
35270170 ATTGCTAAAT
35270180 AAAA-TGCTTTTGAGCTTTTC
1 AAAAGTGCTTTTGAGCTTTTC
35270200 AAAAGTGCTTTTGAGCTTTTC
1 AAAAGTGCTTTTGAGCTTTTC
35270221 AAAAGTGCTTTT
1 AAAAGTGCTTTT
35270233 AGAACAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (21 bp):
AAAAGTGCTTTTGAGCTTTTC
Found at i:35270526 original size:12 final size:12
Alignment explanation
Indices: 35270495--35270520 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35270485 AATTTCATTT
35270495 AATATTAATATA
1 AATATTAATATA
35270507 AATATTAATATA
1 AATATTAATATA
35270519 AA
1 AA
35270521 ATTTAAATTT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATTAATATA
Found at i:35270608 original size:71 final size:72
Alignment explanation
Indices: 35270532--35270674 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 72
35270522 TTTAAATTTA
35270532 TTACTATATTTTTTGAAAATATTTATGTATTTTATATATTTCTTTAA-TTTTTTTAGAATTAGGA
1 TTACTATATTTTTTGAAAATATTTATGTATTTTATATATTTCTTTAATTTTTTTTAGAATTAGGA
35270596 ACAAATT
66 ACAAATT
35270603 TTACTATATTTTTTGAAAATATTTATGTATTTTATATATTTCTTTAATTTTTTTTAGAATTAGGA
1 TTACTATATTTTTTGAAAATATTTATGTATTTTATATATTTCTTTAATTTTTTTTAGAATTAGGA
35270668 ACAAATT
66 ACAAATT
35270675 CTATTTGTAA
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 47 0.66
72 24 0.34
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (72 bp):
TTACTATATTTTTTGAAAATATTTATGTATTTTATATATTTCTTTAATTTTTTTTAGAATTAGGA
ACAAATT
Found at i:35275066 original size:340 final size:339
Alignment explanation
Indices: 35274415--35275093 Score: 1169
Period size: 340 Copynumber: 2.0 Consensus size: 339
35274405 GTGGAATGAC
*
35274415 TTCGTGACTAAATGAATTTATAATTAATAGGAAAAAACTAGAACTTAATTATAAATCATTTGAGC
1 TTCGCGACTAAATGAATTTATAATTAATAGGAAAAAACTAGAACTTAATTATAAATCATTTGAGC
* *
35274480 CCTAATTACATATGTGCAATCGATCTCTCTAGTAGCTAGTTGAAACCAAAAATAAATTGCTTATA
66 CCTAATTACATATGTCCAATCGATCTCTCTAGTAGCTAGTTGAAACAAAAAATAAATTGCTTATA
*
35274545 GAATTAAATGAAAAGAAATGGATAGAAATGATAAAGTTAAAAAAATAGGTTACGTTCGGAAATGA
131 GAATTAAATGAAAAGAAATGGATAGAAATGATAAAGTTAAAAAAATAGGTTACATTCGGAAATGA
* *
35274610 ATATGGTATCTCATTAAGTATGAAAATGACCTGATAATTAATTTAAGTTTTTGAATTATTATTTA
196 ATATGGTATCTCACTAAGTATGAAAATGACATGATAATTAATTTAAGTTTTTGAATTATTATTTA
*
35274675 ATCAAACAATTGAAGTTTGAAAAATGGAATTAAATTAATTGGTCATTTGAATTCATTGAATATGA
261 ATCAAACAATTGAAGTTTGAAAAATGGAATTAAATTAATTGGTCATTTGAATTCATTGAAAATGA
35274740 AAATTAAATATATT
326 AAATTAAATATATT
35274754 TTCGCGACTAAATGAATTTATAATTAATAGGTAAAAAACTAGAACTTAATTATAAATCATTTGAG
1 TTCGCGACTAAATGAATTTATAATTAATAGG-AAAAAACTAGAACTTAATTATAAATCATTTGAG
* * * *
35274819 CCTTAATTACATATGTCCAATCGATCTCTCTGGTAGCTTGTTGAAACAAAAAATGAATTGCTTAT
65 CCCTAATTACATATGTCCAATCGATCTCTCTAGTAGCTAGTTGAAACAAAAAATAAATTGCTTAT
* * * *
35274884 AGAATTAAATGAAAAGAAATGGATAGAAATGGTAAAGTTAAAGAAATGGGTTGCATTCGGAAATG
130 AGAATTAAATGAAAAGAAATGGATAGAAATGATAAAGTTAAAAAAATAGGTTACATTCGGAAATG
* *
35274949 AATATGTTATCTCACTAAGTATGAAAATGACATGATGATTAATTTAAGTTTTTGAATTATTATTT
195 AATATGGTATCTCACTAAGTATGAAAATGACATGATAATTAATTTAAGTTTTTGAATTATTATTT
* **
35275014 AATCAAATAATTGAAGTTTGAAAAATGGAATTAAATTAATTGGTCATTTGAATTTGTTGAAAATG
260 AATCAAACAATTGAAGTTTGAAAAATGGAATTAAATTAATTGGTCATTTGAATTCATTGAAAATG
35275079 AAAATTAAATATATT
325 AAAATTAAATATATT
35275094 GTCTCATAGA
Statistics
Matches: 319, Mismatches: 20, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
339 30 0.09
340 289 0.91
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.35
Consensus pattern (339 bp):
TTCGCGACTAAATGAATTTATAATTAATAGGAAAAAACTAGAACTTAATTATAAATCATTTGAGC
CCTAATTACATATGTCCAATCGATCTCTCTAGTAGCTAGTTGAAACAAAAAATAAATTGCTTATA
GAATTAAATGAAAAGAAATGGATAGAAATGATAAAGTTAAAAAAATAGGTTACATTCGGAAATGA
ATATGGTATCTCACTAAGTATGAAAATGACATGATAATTAATTTAAGTTTTTGAATTATTATTTA
ATCAAACAATTGAAGTTTGAAAAATGGAATTAAATTAATTGGTCATTTGAATTCATTGAAAATGA
AAATTAAATATATT
Found at i:35275156 original size:16 final size:17
Alignment explanation
Indices: 35275128--35275164 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
35275118 GTTGCCATGA
*
35275128 AATTGAGAAAATTATTT
1 AATTGAGAAAATTAATT
35275145 AATTGA-AAAATTAATT
1 AATTGAGAAAATTAATT
35275161 AATT
1 AATT
35275165 TAATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (17 bp):
AATTGAGAAAATTAATT
Found at i:35276596 original size:6 final size:6
Alignment explanation
Indices: 35276585--35276644 Score: 75
Period size: 6 Copynumber: 9.8 Consensus size: 6
35276575 ATTTTTCTCA
* * * *
35276585 AAATGG AAATGG AAATGG AAATAG AAATGG AAATAG AAAGGG AAATGA
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
35276633 AAATGAG AAATG
1 AAATG-G AAATG
35276645 ATTCATTTGC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
6 40 0.89
7 5 0.11
ACGTcount: A:0.57, C:0.00, G:0.28, T:0.15
Consensus pattern (6 bp):
AAATGG
Found at i:35280986 original size:22 final size:22
Alignment explanation
Indices: 35280961--35281036 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
35280951 TGTTGTTTTC
35280961 TTAGCACTTCGGTACTCTTTGT
1 TTAGCACTTCGGTACTCTTTGT
* * * *
35280983 TTAGCATTTTGGTACTCTCTAT
1 TTAGCACTTCGGTACTCTTTGT
* * *
35281005 TTAGCACTTTGATGCTCTTTGT
1 TTAGCACTTCGGTACTCTTTGT
* *
35281027 TCAACACTTC
1 TTAGCACTTC
35281037 AGTGTTCTCC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.17, C:0.22, G:0.14, T:0.46
Consensus pattern (22 bp):
TTAGCACTTCGGTACTCTTTGT
Found at i:35291498 original size:21 final size:21
Alignment explanation
Indices: 35291456--35291499 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35291446 TTGATTCTGG
* *
35291456 TGTGGATGCATCTGGCTTTGT
1 TGTGGATGAATCTGGCTGTGT
35291477 TGTGGATGAATCTGAG-TGTGT
1 TGTGGATGAATCTG-GCTGTGT
35291498 TG
1 TG
35291500 ATTATAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.14, C:0.09, G:0.36, T:0.41
Consensus pattern (21 bp):
TGTGGATGAATCTGGCTGTGT
Found at i:35297056 original size:30 final size:30
Alignment explanation
Indices: 35297018--35297081 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
35297008 AACTTATTTT
35297018 ATTT-TTAATTTTGTTATTATTTTAAAGAC
1 ATTTGTTAATTTTGTTATTATTTTAAAGAC
*
35297047 ATTTGTTAATTTTGTTATTATTTTAGAGAC
1 ATTTGTTAATTTTGTTATTATTTTAAAGAC
35297077 ATTTG
1 ATTTG
35297082 CTTGTTAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 4 0.12
30 29 0.88
ACGTcount: A:0.28, C:0.03, G:0.11, T:0.58
Consensus pattern (30 bp):
ATTTGTTAATTTTGTTATTATTTTAAAGAC
Found at i:35306685 original size:40 final size:40
Alignment explanation
Indices: 35306626--35307121 Score: 688
Period size: 40 Copynumber: 12.4 Consensus size: 40
35306616 CAGATTAACA
* *
35306626 AAACACACCAGACAGAAGCTCATAAGAGCTAATCCAACCG
1 AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCG
* * * *
35306666 AAATACACCAAACAGAAGCTCATAAGAGTTGATCAAACTG
1 AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCG
* * * *
35306706 AAACACGCCAAACA-AATACTCATAAAAGCTGATCCAATCG
1 AAACACACCAAACAGAA-GCTCATAAGAGCTGATCCAACCG
* * *
35306746 AAACACACCAAACATAAGCTCATAAGGGCTGTTCCAACCG
1 AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCG
* *
35306786 AAACACGCCAAACAGAAGCTTATAAGAGCTGATCCAACCG
1 AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCG
* **
35306826 AATCATGCCAAACAGAAGCTCATAAGAGCTGATCCAACCG
1 AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCG
* * * **
35306866 AAACACGCCAAATAGAAGCTCATAAGAGCTAATCCAACTA
1 AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCG
* * * *
35306906 AAACACGCCAAACAGAAGCTCATAAAAGCTGGTCCAACCA
1 AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCG
* *
35306946 AAACACGCCAAACAGAAGTTCATAAGAGCTGATCCAACCG
1 AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCG
35306986 AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCG
1 AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCG
35307026 AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCG
1 AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCG
*
35307066 AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCA
1 AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCG
**
35307106 AAACATGCCAAACAGA
1 AAACACACCAAACAGA
35307122 GAGTATAAAA
Statistics
Matches: 406, Mismatches: 48, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
39 2 0.00
40 402 0.99
41 2 0.00
ACGTcount: A:0.45, C:0.28, G:0.15, T:0.12
Consensus pattern (40 bp):
AAACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCG
Found at i:35308069 original size:20 final size:20
Alignment explanation
Indices: 35308046--35308090 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
35308036 ATGAAATAAC
35308046 CACACGTTTTAATCAATACA
1 CACACGTTTTAATCAATACA
35308066 CACACGTTTTAATCAATACA
1 CACACGTTTTAATCAATACA
35308086 CACAC
1 CACAC
35308091 TAACATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.29, G:0.04, T:0.27
Consensus pattern (20 bp):
CACACGTTTTAATCAATACA
Found at i:35308086 original size:18 final size:19
Alignment explanation
Indices: 35308040--35308090 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 19
35308030 TCGAAAATGA
35308040 AATAACCACACGTTTTAATC
1 AATAA-CACACGTTTTAATC
35308060 AATACACACACGTTTTAATC
1 AATA-ACACACGTTTTAATC
35308080 AATACACACAC
1 AATA-ACACAC
35308091 TAACATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.27, G:0.04, T:0.25
Consensus pattern (19 bp):
AATAACACACGTTTTAATC
Found at i:35315744 original size:16 final size:18
Alignment explanation
Indices: 35315716--35315749 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
35315706 TTAGAATTGG
35315716 ATTGAGAAAATT-ATTTA
1 ATTGAGAAAATTAATTTA
35315733 ATTGAG-AAATTAATTTA
1 ATTGAGAAAATTAATTTA
35315750 GTTAATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (18 bp):
ATTGAGAAAATTAATTTA
Found at i:35319031 original size:58 final size:59
Alignment explanation
Indices: 35318937--35319052 Score: 155
Period size: 58 Copynumber: 2.0 Consensus size: 59
35318927 TTTTTTCTTT
* * * * *
35318937 TTCATTTTCATTTTGGATAAAACCACATTCATTTCCAAAT-TATT-TCATTTCTTCATTA
1 TTCATTTTCATTTTGGAGAAAACCACAATAAATTCCAAATGT-TTCTCATTTCTCCATTA
*
35318995 TTCATTTTCATTTTGGAGAAAACCATAATAAATTCCAAATGTTTCTCATTTCTCCATT
1 TTCATTTTCATTTTGGAGAAAACCACAATAAATTCCAAATGTTTCTCATTTCTCCATT
35319053 TTTACCATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 37 0.74
59 13 0.26
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (59 bp):
TTCATTTTCATTTTGGAGAAAACCACAATAAATTCCAAATGTTTCTCATTTCTCCATTA
Found at i:35320418 original size:41 final size:41
Alignment explanation
Indices: 35320372--35320475 Score: 131
Period size: 41 Copynumber: 2.5 Consensus size: 41
35320362 AAGGTTGTTT
* *
35320372 CTACCATGTTGATATTGCAAAGTTCAGAATGGTCCCTTCTC
1 CTACCATGTTAATATTGCAAAGTTCAGAATGGGCCCTTCTC
* *
35320413 CTACCATGTTAATGTTGCAAAGTTCAGAATGGGCCCTCCT-
1 CTACCATGTTAATATTGCAAAGTTCAGAATGGGCCCTTCTC
*
35320453 CTCGCCATGTTAA-AGTTGCAAAG
1 CT-ACCATGTTAATA-TTGCAAAG
35320476 GTTCTTCCCG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
40 2 0.04
41 53 0.96
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (41 bp):
CTACCATGTTAATATTGCAAAGTTCAGAATGGGCCCTTCTC
Found at i:35320551 original size:70 final size:70
Alignment explanation
Indices: 35320416--35320749 Score: 382
Period size: 70 Copynumber: 4.8 Consensus size: 70
35320406 CCTTCTCCTA
* * ** * * * *
35320416 CCATGTTAATGTTGCAAAGTTCAGAATGGGCCCTCCTCTCGCCATGTTAAAGTTGCAAAGGTTCT
1 CCATGTTGATGGTGCAAAGTTTGGAATGGGCCCTCCTCTCACCATGTTGAAGTTGAAAAAGTTCT
35320481 TCCCG
66 TCCCG
* * * * *
35320486 CCATTTTGATGGTGCAAAGTTTGGAATGGGCTCTCCTTTCACCATGTTGAAGTTGTAAAATTTCT
1 CCATGTTGATGGTGCAAAGTTTGGAATGGGCCCTCCTCTCACCATGTTGAAGTTGAAAAAGTTCT
**
35320551 TCTTG
66 TCCCG
* **
35320556 CCATGTTGATGGTGCAAAGTTTAGAATGGGTTCTCCTCTCACCATGTTGAAGTTGAAAAAGTTCT
1 CCATGTTGATGGTGCAAAGTTTGGAATGGGCCCTCCTCTCACCATGTTGAAGTTGAAAAAGTTCT
*
35320621 TCCTG
66 TCCCG
* * * *
35320626 CCATGTTGATGGTGCATAGTTTGAAATAGACCCTCCTCTCACCATGTTGAA-TTGAAAAAGTTCT
1 CCATGTTGATGGTGCAAAGTTTGGAATGGGCCCTCCTCTCACCATGTTGAAGTTGAAAAAGTTCT
* *
35320690 TCTCA
66 TCCCG
* * * ** *
35320695 CCATGATGATGGTGCAAAGTTTGGAATAGGACCTGTTTTCACCATGTTGAAGTTG
1 CCATGTTGATGGTGCAAAGTTTGGAATGGGCCCTCCTCTCACCATGTTGAAGTTG
35320750 CAAAGGTCTT
Statistics
Matches: 224, Mismatches: 39, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
69 58 0.26
70 166 0.74
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (70 bp):
CCATGTTGATGGTGCAAAGTTTGGAATGGGCCCTCCTCTCACCATGTTGAAGTTGAAAAAGTTCT
TCCCG
Done.