Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 38 of 438
Found at i:9397708 original size:28 final size:29
Alignment explanation
Indices: 9397677--9397736 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
9397667 GATTTTTAGT
*
9397677 AAAAATGCATATT-AGGGATTAAATTGAG
1 AAAAATGCAAATTGAGGGATTAAATTGAG
* * * *
9397705 AAAAGTGTAAATTGAGGGGTTAAATTGTG
1 AAAAATGCAAATTGAGGGATTAAATTGAG
9397734 AAA
1 AAA
9397737 TAGATAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.28
Consensus pattern (29 bp):
AAAAATGCAAATTGAGGGATTAAATTGAG
Found at i:9404610 original size:19 final size:22
Alignment explanation
Indices: 9404571--9404611 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 22
9404561 CTTATTTCTA
9404571 TTATTACTCTTAGTATATTATT
1 TTATTACTCTTAGTATATTATT
9404593 TTATT-CTCTTA-T-TATTATT
1 TTATTACTCTTAGTATATTATT
9404612 GCTTTCTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 1 0.05
21 6 0.32
22 5 0.26
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATTACTCTTAGTATATTATT
Found at i:9406185 original size:25 final size:25
Alignment explanation
Indices: 9406123--9406178 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
9406113 TTTCATTCCT
9406123 ATATTCTCTGTTTCTTCTTGCTACC
1 ATATTCTCTGTTTCTTCTTGCTACC
*
9406148 ATATTCTTTGTTTCTTCTTGCTACC
1 ATATTCTCTGTTTCTTCTTGCTACC
9406173 ATATTC
1 ATATTC
9406179 ACAGTTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.14, C:0.25, G:0.07, T:0.54
Consensus pattern (25 bp):
ATATTCTCTGTTTCTTCTTGCTACC
Found at i:9410763 original size:32 final size:32
Alignment explanation
Indices: 9410727--9410854 Score: 211
Period size: 32 Copynumber: 4.0 Consensus size: 32
9410717 TATAACTATG
9410727 CTACTTTTTTATATGTAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
9410759 CTACTTTTTCATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
9410791 CTACTTTTTTATATGTGAACCTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
*
9410823 CTACTTTTTTATATGTAAACCTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
9410855 ATTTTTTATG
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 89 1.00
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.45
Consensus pattern (32 bp):
CTACTTTTTTATATGTAAAACTAATGTATGAT
Found at i:9412915 original size:21 final size:21
Alignment explanation
Indices: 9412863--9412917 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
9412853 ACCGCTGTTT
** *
9412863 CTAATCTCATAGCTACAGTAT
1 CTAATCTCACCGCTACAGTAA
*
9412884 CCAATCTCACCGCTACAGTAA
1 CTAATCTCACCGCTACAGTAA
9412905 CTAATCTCACCGC
1 CTAATCTCACCGC
9412918 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.35, G:0.09, T:0.25
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAA
Found at i:9413523 original size:17 final size:18
Alignment explanation
Indices: 9413496--9413530 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
9413486 CATTGAGTCC
9413496 GATTATTTTTATGTTTAT
1 GATTATTTTTATGTTTAT
*
9413514 GATT-TTTTTATTTTTAT
1 GATTATTTTTATGTTTAT
9413531 CTTGTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (18 bp):
GATTATTTTTATGTTTAT
Found at i:9413557 original size:7 final size:6
Alignment explanation
Indices: 9413498--9413578 Score: 69
Period size: 6 Copynumber: 13.7 Consensus size: 6
9413488 TTGAGTCCGA
* ** *
9413498 TTATTT TTATGT TTATGA TT-TTT TTATTT TTATCTT GTA-TT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTAT-TT TTATTT TTATTT
* *
9413545 TCT-TTT TTATTT TTAGTT TTATTT TTCTTT TTAT
1 T-TATTT TTATTT TTATTT TTATTT TTATTT TTAT
9413579 GTCTATTTTG
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
5 8 0.13
6 47 0.78
7 5 0.08
ACGTcount: A:0.15, C:0.04, G:0.05, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:9418671 original size:22 final size:20
Alignment explanation
Indices: 9418640--9418679 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9418630 ATATAAGATC
9418640 TATATCTATCTCTGAATTTGCA
1 TATATCTA--TCTGAATTTGCA
*
9418662 TATATGTATCTGAATTTG
1 TATATCTATCTGAATTTG
9418680 TATTTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TATATCTATCTGAATTTGCA
Found at i:9428402 original size:18 final size:19
Alignment explanation
Indices: 9428354--9428404 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 19
9428344 ATATATTAAT
*
9428354 TTTTTATTT-T-TAATTCA
1 TTTTTATTTATATAAATCA
*
9428371 TTTTTAATTA-ATAAATCA
1 TTTTTATTTATATAAATCA
9428389 -TTTTATTTATATAAAT
1 TTTTTATTTATATAAAT
9428405 AAAATAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTATTTATATAAATCA
Found at i:9428488 original size:86 final size:89
Alignment explanation
Indices: 9428371--9428538 Score: 236
Period size: 86 Copynumber: 1.9 Consensus size: 89
9428361 TTTTAATTCA
*
9428371 TTTTTAATTAATAAATCATTTTATTTATATAAATAAAATAATAAATATGTAATTATAT-ATAAAA
1 TTTTTAATTAAT-AATCATTTTATTTATATAAATAAAATAATAAATATATAATTATATAATAAAA
9428435 T-TATATATTATTATGTTAAAAATAC
65 TATATA-ATTATTATGTTAAAAATAC
* * * *
9428460 TTTTTAATTAAT-AT-TTTTTATTTGTATAAATAAATTAATAATTATATAATTATATAATAAAAT
1 TTTTTAATTAATAATCATTTTATTTATATAAATAAAATAATAAATATATAATTATATAATAAAAT
*
9428523 ATATAATTTTTATGTT
66 ATATAATTATTATGTT
9428539 TATCATTGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
86 36 0.51
87 19 0.27
88 4 0.06
89 12 0.17
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.50
Consensus pattern (89 bp):
TTTTTAATTAATAATCATTTTATTTATATAAATAAAATAATAAATATATAATTATATAATAAAAT
ATATAATTATTATGTTAAAAATAC
Found at i:9428580 original size:16 final size:18
Alignment explanation
Indices: 9428559--9428593 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
9428549 TTAAATATAT
9428559 TTATTT-TATAA-AAAAA
1 TTATTTATATAATAAAAA
9428575 TTATTTATATAATAAAAA
1 TTATTTATATAATAAAAA
9428593 T
1 T
9428594 AAGGGCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 5 0.29
18 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATTTATATAATAAAAA
Found at i:9428581 original size:20 final size:21
Alignment explanation
Indices: 9428551--9428592 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
9428541 TCATTGTGTT
* *
9428551 AAATATATTTATTTTATAAAA
1 AAATATATTTATATAATAAAA
9428572 AAAT-TATTTATATAATAAAA
1 AAATATATTTATATAATAAAA
9428592 A
1 A
9428593 TAAGGGCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATATATTTATATAATAAAA
Found at i:9429206 original size:16 final size:17
Alignment explanation
Indices: 9429185--9429216 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
9429175 ATGCCACGTG
9429185 AATTATTT-ATATTTTA
1 AATTATTTAATATTTTA
9429201 AATTATTTAATATTTT
1 AATTATTTAATATTTT
9429217 TTAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTATTTAATATTTTA
Found at i:9435742 original size:18 final size:18
Alignment explanation
Indices: 9435719--9435753 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
9435709 TGTTTTTTTG
9435719 AAAAAGGGCAAGAAAATA
1 AAAAAGGGCAAGAAAATA
9435737 AAAAAGGGCAAGAAAAT
1 AAAAAGGGCAAGAAAAT
9435754 GCTTGCCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.66, C:0.06, G:0.23, T:0.06
Consensus pattern (18 bp):
AAAAAGGGCAAGAAAATA
Found at i:9436445 original size:23 final size:22
Alignment explanation
Indices: 9436390--9436449 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
9436380 ACTATTATAA
*
9436390 TGTTACTATTTTGTTGTTATTG
1 TGTTACTATTTTATTGTTATTG
* * *
9436412 TATAACTTATTTTATTGTTAATTT
1 TGTTAC-TATTTTATTGTT-ATTG
9436436 TGTTACTATTTTAT
1 TGTTACTATTTTAT
9436450 AGGCATTTAC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 4 0.13
23 19 0.63
24 7 0.23
ACGTcount: A:0.22, C:0.05, G:0.10, T:0.63
Consensus pattern (22 bp):
TGTTACTATTTTATTGTTATTG
Found at i:9436579 original size:35 final size:34
Alignment explanation
Indices: 9436497--9436580 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 34
9436487 ATTTAAATAT
9436497 ACATATATAT-TTTTAATTTATTTTTAATTTGTTG
1 ACATATATATATTTTAA-TTATTTTTAATTTGTTG
* * * *
9436531 AGAAATATTTATTTTAA-TATTTTTAATATTTTTG
1 ACATATATATATTTTAATTATTTTTAAT-TTGTTG
9436565 ACATATTATATATTTT
1 ACATA-TATATATTTT
9436581 TAAAAATTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
33 10 0.25
34 15 0.38
35 15 0.38
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (34 bp):
ACATATATATATTTTAATTATTTTTAATTTGTTG
Found at i:9437710 original size:18 final size:20
Alignment explanation
Indices: 9437684--9437726 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9437674 AAACATAATT
9437684 TTTTATTTAA-A-AAATATA
1 TTTTATTTAATATAAATATA
* *
9437702 TTTTCTTTAATATATATATA
1 TTTTATTTAATATAAATATA
9437722 TTTTA
1 TTTTA
9437727 AAAAATCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 9 0.45
19 1 0.05
20 10 0.50
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTATTTAATATAAATATA
Found at i:9438287 original size:138 final size:137
Alignment explanation
Indices: 9438062--9438309 Score: 331
Period size: 138 Copynumber: 1.8 Consensus size: 137
9438052 AATAGTGTAA
* * *
9438062 TGTACATTCTTTTATTAATGATATGCAACCTAAACCTTAAACGTGAAACTAATTTTATGGTAGAA
1 TGTACATTCTTTTATTAATGATATGCAACCTAAACCTTAAACGTGAAACTAACTCTATGATAGAA
*
9438127 TATAATATATACAATTAACATTATGA-AATTAAGATAGATTATTAAAACATGTATCCATGTATAT
66 TATAATATATACAATTAACATTAT-ATAATGAAGATAGATTATTAAAACATGTATCCATGTATAT
9438191 CACTTTGT
130 CACTTTGT
* * * *
9438199 TGTACATT-TTTATATTAATGATATGTAAGCTTAAACAC-TAAACGTGTAATTAACTCTATGATA
1 TGTACATTCTTT-TATTAATGATATGCAA-CCTAAAC-CTTAAACGTGAAACTAACTCTATGATA
* * * *
9438262 GATTATAATATATATAATTAGCATTATATAATGAAGTTAGATTATTAA
63 GAATATAATATATACAATTAACATTATATAATGAAGATAGATTATTAA
9438310 TTATATGTAA
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
136 3 0.03
137 24 0.25
138 67 0.71
139 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (137 bp):
TGTACATTCTTTTATTAATGATATGCAACCTAAACCTTAAACGTGAAACTAACTCTATGATAGAA
TATAATATATACAATTAACATTATATAATGAAGATAGATTATTAAAACATGTATCCATGTATATC
ACTTTGT
Found at i:9441647 original size:25 final size:25
Alignment explanation
Indices: 9441613--9441662 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
9441603 TCGTTTGGAG
9441613 GAAGGTGCGTCTGTGCATGAACACT
1 GAAGGTGCGTCTGTGCATGAACACT
9441638 GAAGGTGCGTCTGTGCATGAACACT
1 GAAGGTGCGTCTGTGCATGAACACT
9441663 TAACTGTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (25 bp):
GAAGGTGCGTCTGTGCATGAACACT
Found at i:9445766 original size:22 final size:22
Alignment explanation
Indices: 9445741--9445789 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
9445731 AAAAGAAGTC
* *
9445741 TAAACCCTAAGAGAAAGAAAAA
1 TAAACCCAAAAAGAAAGAAAAA
**
9445763 TAAACTGAAAAAGAAAGAAAAA
1 TAAACCCAAAAAGAAAGAAAAA
9445785 TAAAC
1 TAAAC
9445790 TGAAAACTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.67, C:0.10, G:0.12, T:0.10
Consensus pattern (22 bp):
TAAACCCAAAAAGAAAGAAAAA
Found at i:9445774 original size:12 final size:12
Alignment explanation
Indices: 9445757--9445800 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
9445747 CTAAGAGAAA
9445757 GAAAAATAAACT
1 GAAAAATAAACT
*
9445769 GAAAAAGAAA--
1 GAAAAATAAACT
9445779 GAAAAATAAACT
1 GAAAAATAAACT
*
9445791 GAAAACTAAA
1 GAAAAATAAA
9445801 TTTTACAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.70, C:0.07, G:0.11, T:0.11
Consensus pattern (12 bp):
GAAAAATAAACT
Found at i:9445790 original size:22 final size:22
Alignment explanation
Indices: 9445752--9445795 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
9445742 AAACCCTAAG
9445752 AGAAAGAAAAATAAACTGAAAA
1 AGAAAGAAAAATAAACTGAAAA
9445774 AGAAAGAAAAATAAACTGAAAA
1 AGAAAGAAAAATAAACTGAAAA
9445796 CTAAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.09
Consensus pattern (22 bp):
AGAAAGAAAAATAAACTGAAAA
Found at i:9458405 original size:2 final size:2
Alignment explanation
Indices: 9458398--9458437 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9458388 ACCAGAACAG
9458398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9458438 GTGGCGAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9459190 original size:27 final size:28
Alignment explanation
Indices: 9459129--9459191 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
9459119 GTCATTTACG
*
9459129 CACAAGGGGCAAAATAGTCATTTAACACC
1 CACAA-GGGCAAAATAGTAATTTAACACC
* * *
9459158 C-TAAGGGCAAAATGGTAATTTTAC-CC
1 CACAAGGGCAAAATAGTAATTTAACACC
9459184 CACAAGGG
1 CACAAGGG
9459192 TATCTCGGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
26 3 0.11
27 22 0.79
28 2 0.07
29 1 0.04
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (28 bp):
CACAAGGGCAAAATAGTAATTTAACACC
Found at i:9459201 original size:27 final size:27
Alignment explanation
Indices: 9459171--9459289 Score: 150
Period size: 27 Copynumber: 4.4 Consensus size: 27
9459161 AGGGCAAAAT
* *
9459171 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* * *
9459198 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
9459225 GGT-ATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
* *
9459252 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
*
9459279 GATAATTTTAC
1 GGTAATTTTAC
9459290 AAACCAGGGG
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
26 3 0.04
27 72 0.92
28 3 0.04
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTTTACCCTACAAGGGTATTTC
Found at i:9459243 original size:54 final size:53
Alignment explanation
Indices: 9459175--9459289 Score: 176
Period size: 54 Copynumber: 2.1 Consensus size: 53
9459165 CAAAATGGTA
*
9459175 ATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCGGT
1 ATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGGT
* * *
9459228 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGAT
1 ATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGGT
9459282 AATTTTAC
1 -ATTTTAC
9459290 AAACCAGGGG
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
53 4 0.07
54 48 0.86
55 4 0.07
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (53 bp):
ATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGGT
Found at i:9459311 original size:54 final size:53
Alignment explanation
Indices: 9459171--9459366 Score: 162
Period size: 54 Copynumber: 3.6 Consensus size: 53
9459161 AGGGCAAAAT
** * * *
9459171 GGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTTTA-CAAACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
** *
9459225 GGT-ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTT-TA-CAAACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
* * * * ** *
9459279 GATAATTTTACAAACCAGGGGTATTTTAGTAATTTTA-CAAACTAGGGGTATTTT
1 GGTAATTTTACAAA-CAAGGGTATTTCAGTAATTCTACCCTAC-AGGGGTATTTC
* * *
9459333 GGTAATTTTACTGATCGAGGGTATTTCAGTAATT
1 GGTAATTTTAC-AAACAAGGGTATTTCAGTAATT
9459367 TTGTAAATTG
Statistics
Matches: 118, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
53 9 0.08
54 104 0.88
55 5 0.04
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (53 bp):
GGTAATTTTACAAACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
Found at i:9459354 original size:27 final size:27
Alignment explanation
Indices: 9459268--9459368 Score: 107
Period size: 27 Copynumber: 3.7 Consensus size: 27
9459258 TCTACCCTAC
* *
9459268 AGGGGTA-TTTCGATAATTTTACAAACC
1 AGGGGTATTTTAG-TAATTTTACAAACG
*
9459295 AGGGGTATTTTAGTAATTTTACAAACT
1 AGGGGTATTTTAGTAATTTTACAAACG
* * *
9459322 AGGGGTATTTTGGTAATTTTACTGATCG
1 AGGGGTATTTTAGTAATTTTAC-AAACG
*
9459350 A-GGGTATTTCAGTAATTTT
1 AGGGGTATTTTAGTAATTTT
9459369 GTAAATTGAG
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
27 57 0.89
28 7 0.11
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.41
Consensus pattern (27 bp):
AGGGGTATTTTAGTAATTTTACAAACG
Found at i:9459391 original size:54 final size:52
Alignment explanation
Indices: 9459346--9459569 Score: 209
Period size: 54 Copynumber: 4.2 Consensus size: 52
9459336 AATTTTACTG
** * *
9459346 ATCGAGGGTATTTCAGTAATTTTGTAAATTGAGGGTAAAACGGTAATTCTGTAA
1 ATCGAGGGTAAATCAGTAATTCTGTAAATCGAGGGTAAAACGGTAATT-T-TAA
* **
9459400 ATCGAGGGTAAAATGA-TAATTCTGTAAATCGAGGGTAAAACAATAATTCTATAA
1 ATCGAGGGT-AAATCAGTAATTCTGTAAATCGAGGGTAAAACGGTAATT-T-TAA
* * * * *
9459454 ATCGAGGGTAAAAT-GGTAATTTTATAAATCGAGTGTAAAATGGTAATTCTGTAA
1 ATCGAGGGT-AAATCAGTAATTCTGTAAATCGAGGGTAAAACGGTAATT-T-TAA
* * *
9459508 ATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAATGGTAATTTTACA
1 ATCGAGGGTAAATCAGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTA-A
9459561 AGTCGAGGG
1 A-TCGAGGG
9459570 CATTTCAGTA
Statistics
Matches: 143, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
52 2 0.01
53 6 0.04
54 132 0.92
55 3 0.02
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (52 bp):
ATCGAGGGTAAATCAGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTAA
Found at i:9459420 original size:81 final size:81
Alignment explanation
Indices: 9459359--9459569 Score: 305
Period size: 81 Copynumber: 2.6 Consensus size: 81
9459349 GAGGGTATTT
* * * *
9459359 CAGTAATTTTGTAAATTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGATAATTCTG
1 CAGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGATAATTCTG
9459424 TAAATCGAGGGTAAAA
66 TAAATCGAGGGTAAAA
* * * * *
9459440 CAATAATTCTATAAATCGAGGGTAAAATGGTAATTTTATAAATCGAGTGTAAAATGGTAATTCTG
1 CAGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGATAATTCTG
9459505 TAAATCGAGGGTAAAA
66 TAAATCGAGGGTAAAA
* * * *
9459521 CAGTAATTCTGTAAATCAAGGGTAAAATGGTAATTTTACAAGTCGAGGG
1 CAGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGG
9459570 CATTTCAGTA
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 115 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (81 bp):
CAGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGATAATTCTG
TAAATCGAGGGTAAAA
Found at i:9459569 original size:27 final size:27
Alignment explanation
Indices: 9459361--9459555 Score: 264
Period size: 27 Copynumber: 7.2 Consensus size: 27
9459351 GGGTATTTCA
* * *
9459361 GTAATTTTGTAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
9459388 GTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* **
9459415 ATAATTCTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
9459442 ATAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* * *
9459469 GTAATTTTATAAATCGAGTGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
**
9459496 GTAATTCTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
9459523 GTAATTCTGTAAATCAAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
9459550 GTAATT
1 GTAATT
9459556 TTACAAGTCG
Statistics
Matches: 148, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 148 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.31
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATG
Found at i:9469597 original size:18 final size:18
Alignment explanation
Indices: 9469576--9469627 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
9469566 AGGAAACTGA
9469576 TGTTGTCGAAGAAGAAGT
1 TGTTGTCGAAGAAGAAGT
** *
9469594 TGTTGTCGAAGCGGTAGT
1 TGTTGTCGAAGAAGAAGT
9469612 TGTTG-CTGAAGAAGAA
1 TGTTGTC-GAAGAAGAA
9469628 AAAGTTGCTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.29, C:0.08, G:0.35, T:0.29
Consensus pattern (18 bp):
TGTTGTCGAAGAAGAAGT
Found at i:9480176 original size:27 final size:27
Alignment explanation
Indices: 9480117--9480188 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
9480107 AATGCCTTAT
*
9480117 TGGTGTGCTTGGGAGGATATGATATAC
1 TGGTGTGTTTGGGAGGATATGATATAC
** *
9480144 CAGTGTGTTTGGGAGGCTAT-ATTATAC
1 TGGTGTGTTTGGGAGGATATGA-TATAC
9480171 TGGTGTGTTAT-GGAGGAT
1 TGGTGTGTT-TGGGAGGAT
9480189 TTATATTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 1 0.03
27 34 0.94
28 1 0.03
ACGTcount: A:0.21, C:0.07, G:0.36, T:0.36
Consensus pattern (27 bp):
TGGTGTGTTTGGGAGGATATGATATAC
Found at i:9485900 original size:24 final size:24
Alignment explanation
Indices: 9485870--9485921 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
9485860 TTGTGGAAGG
* *
9485870 TATGTATGTATGTGCTT-TTGTGTA
1 TATGTATGGATGTG-TTCATGTGTA
9485894 TATGTATGGATGTGTTCATGTGTA
1 TATGTATGGATGTGTTCATGTGTA
9485918 TATG
1 TATG
9485922 GGTATGAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.19, C:0.04, G:0.27, T:0.50
Consensus pattern (24 bp):
TATGTATGGATGTGTTCATGTGTA
Found at i:9492523 original size:18 final size:19
Alignment explanation
Indices: 9492481--9492525 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
9492471 CAGAATTTAT
* *
9492481 TAAAAAATATTTAATATTA
1 TAAAAATTATTTAATATAA
*
9492500 TGAAAATTATTTAAT-TAA
1 TAAAAATTATTTAATATAA
9492518 TAAAAATT
1 TAAAAATT
9492526 TCACATATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAAAATTATTTAATATAA
Found at i:9495443 original size:11 final size:11
Alignment explanation
Indices: 9495429--9495469 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
9495419 TGTTTTCTCC
9495429 CTATTTTGCTA
1 CTATTTTGCTA
*
9495440 CTATTTTACTA
1 CTATTTTGCTA
* *
9495451 TTATGTTGCTA
1 CTATTTTGCTA
9495462 CTATTTTG
1 CTATTTTG
9495470 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:9495540 original size:30 final size:30
Alignment explanation
Indices: 9495506--9495568 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
9495496 ACTTATTTTA
9495506 TTGTTAATTTTGTTCA-TATTTTAAAGACAT
1 TTGTTAATTTTGTT-ATTATTTTAAAGACAT
*
9495536 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
9495566 TTG
1 TTG
9495569 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.27, C:0.05, G:0.13, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:9521411 original size:27 final size:27
Alignment explanation
Indices: 9521339--9521414 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
9521329 TCGGCGGACT
* *
9521339 TGTTGGTGTACACCATATCACCAAACT
1 TGTTGGTGTACACCATCTCACCAAACC
* * * * *
9521366 TATTGGCGTACAACATCTCGCCAGACC
1 TGTTGGTGTACACCATCTCACCAAACC
*
9521393 TGTTGGTGTACACCGTCTCACC
1 TGTTGGTGTACACCATCTCACC
9521415 GGACATATTA
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (27 bp):
TGTTGGTGTACACCATCTCACCAAACC
Found at i:9521414 original size:54 final size:55
Alignment explanation
Indices: 9521339--9521446 Score: 137
Period size: 54 Copynumber: 2.0 Consensus size: 55
9521329 TCGGCGGACT
*
9521339 TGTTGGTGTACACCATATCACCAAACTTATT-GGCGTACAACATCTCGCCAGACC
1 TGTTGGTGTACACCATATCACCAAACATATTAGGCGTACAACATCTCGCCAGACC
* * ** * * *
9521393 TGTTGGTGTACACCGTCTCACCGGACATATTAGGCGTATACCATCTCGCTAGAC
1 TGTTGGTGTACACCATATCACCAAACATATTAGGCGTACAACATCTCGCCAGAC
9521447 TTACTGGTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
54 26 0.58
55 19 0.42
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (55 bp):
TGTTGGTGTACACCATATCACCAAACATATTAGGCGTACAACATCTCGCCAGACC
Found at i:9521455 original size:55 final size:54
Alignment explanation
Indices: 9521342--9521463 Score: 127
Period size: 55 Copynumber: 2.2 Consensus size: 54
9521332 GCGGACTTGT
* **
9521342 TGGTGTACACCATATCACCAAACTTATTGGCGTACAACATCTCGCCAGACCTGT
1 TGGTGTACACCATATCACCAAACATATTGGCGTACAACATCTCGCCAGACCTAC
* * ** * * * *
9521396 TGGTGTACACCGTCTCACCGGACATATTAGGCGTATACCATCTCGCTAGACTTAC
1 TGGTGTACACCATATCACCAAACATATT-GGCGTACAACATCTCGCCAGACCTAC
*
9521451 TGGTGTATACCAT
1 TGGTGTACACCAT
9521464 CTTGCCAGAC
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
54 23 0.43
55 31 0.57
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (54 bp):
TGGTGTACACCATATCACCAAACATATTGGCGTACAACATCTCGCCAGACCTAC
Found at i:9522202 original size:20 final size:20
Alignment explanation
Indices: 9522177--9522217 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
9522167 ACTAAAATAT
9522177 AAAATTGTGAAATTTGATGA
1 AAAATTGTGAAATTTGATGA
* *
9522197 AAAATTTTGAAATTTTATGA
1 AAAATTGTGAAATTTGATGA
9522217 A
1 A
9522218 TATATGTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (20 bp):
AAAATTGTGAAATTTGATGA
Found at i:9525271 original size:127 final size:128
Alignment explanation
Indices: 9525045--9525300 Score: 505
Period size: 127 Copynumber: 2.0 Consensus size: 128
9525035 TAAGCTTCAT
9525045 TTTAAATTATATCTATGTTTATGAGTTCGTTTTAGCTTAATCTAGCTAGCCAGGTGTCAATTTGT
1 TTTAAATTATATCTATGTTTATGAGTTCGTTTTAGCTTAATCTAGCTAGCCAGGTGTCAATTTGT
9525110 AAAAATGTTAAAGGATGAGGGTTATGCCATGAATTTTCTTGAA-TTTTTTTGGTGTTAAGTGA
66 AAAAATGTTAAAGGATGAGGGTTATGCCATGAATTTTCTTGAATTTTTTTTGGTGTTAAGTGA
9525172 TTTAAATTATATCTATGTTTATGAGTTCGTTTTAGCTTAATCTAGCTAGCCAGGTGTCAATTTGT
1 TTTAAATTATATCTATGTTTATGAGTTCGTTTTAGCTTAATCTAGCTAGCCAGGTGTCAATTTGT
9525237 AAAAATGTTAAAGGATGAGGGTTATGCCATGAATTTTCTTGAATTTTTTTTGGTGTTAAGTGA
66 AAAAATGTTAAAGGATGAGGGTTATGCCATGAATTTTCTTGAATTTTTTTTGGTGTTAAGTGA
9525300 T
1 T
9525301 AGATTATGAA
Statistics
Matches: 128, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
127 108 0.84
128 20 0.16
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (128 bp):
TTTAAATTATATCTATGTTTATGAGTTCGTTTTAGCTTAATCTAGCTAGCCAGGTGTCAATTTGT
AAAAATGTTAAAGGATGAGGGTTATGCCATGAATTTTCTTGAATTTTTTTTGGTGTTAAGTGA
Found at i:9526505 original size:19 final size:19
Alignment explanation
Indices: 9526481--9526518 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9526471 AAACAGACTC
9526481 GTAAATATTTATTAAAAAT
1 GTAAATATTTATTAAAAAT
9526500 GTAAATATTTATTAAAAAT
1 GTAAATATTTATTAAAAAT
9526519 ATTTACGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
GTAAATATTTATTAAAAAT
Found at i:9529736 original size:21 final size:20
Alignment explanation
Indices: 9529708--9529746 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
9529698 TCCTAGACTT
*
9529708 TCCTAATTGTTTCAAATTAG
1 TCCTAATTGCTTCAAATTAG
*
9529728 TCCTAAATTGCTTCTAATT
1 TCCT-AATTGCTTCAAATT
9529747 TATTTTTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (20 bp):
TCCTAATTGCTTCAAATTAG
Found at i:9532916 original size:20 final size:20
Alignment explanation
Indices: 9532891--9532940 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
9532881 TTAAGTAACC
9532891 ATTCATTACTTAATTATTTT
1 ATTCATTACTTAATTATTTT
9532911 ATTCATTACTTAATTATTTT
1 ATTCATTACTTAATTATTTT
*
9532931 AATCA-TACTT
1 ATTCATTACTT
9532941 TCATTAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 5 0.17
20 24 0.83
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTCATTACTTAATTATTTT
Found at i:9535067 original size:63 final size:62
Alignment explanation
Indices: 9534964--9535124 Score: 225
Period size: 63 Copynumber: 2.5 Consensus size: 62
9534954 TGCACCAGGT
* **
9534964 GAATCAAATGCCTGCTTTGCAACATCCTTCTGCTCGAAGTTCTGTTCGTTGGAAGGAGGAGGA
1 GAATCAAATGCC-GCTTTGCAACATCCTTCTGCTCGAAGTTATGTTCGTTGGAACCAGGAGGA
* *
9535027 GAATCAAATGCTCGCTTCGCAACATCCTTCTG-TTGCAAGTTATGTTCGTTGGAACCAGGAGGA
1 GAATCAAATGC-CGCTTTGCAACATCCTTCTGCTCG-AAGTTATGTTCGTTGGAACCAGGAGGA
*
9535090 GAATCAAATGCCCGCTTTGCAACATCCTTCCGCTC
1 GAATCAAATG-CCGCTTTGCAACATCCTTCTGCTC
9535125 ATAGCTGTGA
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
62 2 0.02
63 81 0.94
64 3 0.03
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (62 bp):
GAATCAAATGCCGCTTTGCAACATCCTTCTGCTCGAAGTTATGTTCGTTGGAACCAGGAGGA
Found at i:9535287 original size:21 final size:21
Alignment explanation
Indices: 9535261--9535300 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9535251 ACTCCTACTC
* *
9535261 CTACTCCTACTCCTACTCCTA
1 CTACTCCAACTCCGACTCCTA
9535282 CTACTCCAACTCCGACTCC
1 CTACTCCAACTCCGACTCC
9535301 CACTGCGGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.50, G:0.03, T:0.28
Consensus pattern (21 bp):
CTACTCCAACTCCGACTCCTA
Found at i:9535299 original size:12 final size:12
Alignment explanation
Indices: 9535249--9535300 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
9535239 GCTTCTGCTT
9535249 CGACTCCTACTC
1 CGACTCCTACTC
*
9535261 CTACTCCTACTC
1 CGACTCCTACTC
*
9535273 CTACTCCTACT-
1 CGACTCCTACTC
*
9535284 --ACTCCAACTC
1 CGACTCCTACTC
9535294 CGACTCC
1 CGACTCC
9535301 CACTGCGGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 8 0.23
12 27 0.77
ACGTcount: A:0.19, C:0.50, G:0.04, T:0.27
Consensus pattern (12 bp):
CGACTCCTACTC
Found at i:9535300 original size:6 final size:6
Alignment explanation
Indices: 9535251--9535283 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
9535241 TTCTGCTTCG
9535251 ACTCCT ACTCCT ACTCCT ACTCCT ACTCCT ACT
1 ACTCCT ACTCCT ACTCCT ACTCCT ACTCCT ACT
9535284 ACTCCAACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.48, G:0.00, T:0.33
Consensus pattern (6 bp):
ACTCCT
Found at i:9535315 original size:6 final size:6
Alignment explanation
Indices: 9535306--9535333 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
9535296 ACTCCCACTG
9535306 CGGCTA CGGCTA CGGCTA CGGCTA CGGC
1 CGGCTA CGGCTA CGGCTA CGGCTA CGGC
9535334 GCCAAGTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.36, G:0.36, T:0.14
Consensus pattern (6 bp):
CGGCTA
Found at i:9535661 original size:33 final size:33
Alignment explanation
Indices: 9535624--9535712 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
9535614 ACCGCCAAAA
* * *
9535624 CCATCTCTCATGCCACCACGTCCACCAAAGCCC
1 CCATCCCTCATTCCACCACGGCCACCAAAGCCC
*
9535657 CCATCCCTCATTCCACCACGGCCACCAAAGCCT
1 CCATCCCTCATTCCACCACGGCCACCAAAGCCC
9535690 CCATCCCTCATTCCACCACGGCC
1 CCATCCCTCATTCCACCACGGCC
9535713 TCCAGAATCC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.22, C:0.53, G:0.09, T:0.16
Consensus pattern (33 bp):
CCATCCCTCATTCCACCACGGCCACCAAAGCCC
Found at i:9538280 original size:217 final size:217
Alignment explanation
Indices: 9538013--9538445 Score: 769
Period size: 217 Copynumber: 2.0 Consensus size: 217
9538003 ATCTTCAAAT
9538013 CTTATGAATGGTGCTGGAACGTTGTCTCCCTATGCAATTTAATAAACAATCAAAGTCATGAATAA
1 CTTATGAATGGTGCTGGAACGTTGTCTCCCTATGCAATTTAATAAACAATCAAAGTCATGAATAA
*
9538078 TCTTAAATTGGCAAAATGAATCATTTCCTCACCATTAAAACAAAGACAACTCTTCAAATATTGTA
66 TCTTAAATTGGCAAAATGAATCATTTCCTCACCATTAAAACAAAGAAAACTCTTCAAATATTGTA
9538143 ATGGAAGAACAATAAAGTGAGAATTAAAAAGAACAAGGCACAAAGCAATAGATTTTCAAAGAA-T
131 ATGGAAGAACAATAAAGTGAGAATTAAAAAGAACAAGGCACAAAGCAATAGATTTTCAAA-AATT
*
9538207 GATATTTGTCAAACACCCTTCCC
195 GATATTTATCAAACACCCTTCCC
*
9538230 CTTATGAATGGTGCTGGAATGTTGTCTCCCTATGCAATTTAATAAACAATCAAAGTCATGAATAA
1 CTTATGAATGGTGCTGGAACGTTGTCTCCCTATGCAATTTAATAAACAATCAAAGTCATGAATAA
*
9538295 TCTTAAATTGGCAAAATGAATCATTTCTTCACCATTAAAACAAAGAAAACTCTTCAAATATTGTA
66 TCTTAAATTGGCAAAATGAATCATTTCCTCACCATTAAAACAAAGAAAACTCTTCAAATATTGTA
* * *
9538360 ATGGAAGAACACTTAAGTGAGAATTAAAAAGAACAAGGCGCAAAGCAATAGATTTTCAAAAATTG
131 ATGGAAGAACAATAAAGTGAGAATTAAAAAGAACAAGGCACAAAGCAATAGATTTTCAAAAATTG
* *
9538425 ATATTTATCCAACCCCCTTCC
196 ATATTTATCAAACACCCTTCC
9538446 TCTTCAGCAG
Statistics
Matches: 206, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
216 2 0.01
217 204 0.99
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (217 bp):
CTTATGAATGGTGCTGGAACGTTGTCTCCCTATGCAATTTAATAAACAATCAAAGTCATGAATAA
TCTTAAATTGGCAAAATGAATCATTTCCTCACCATTAAAACAAAGAAAACTCTTCAAATATTGTA
ATGGAAGAACAATAAAGTGAGAATTAAAAAGAACAAGGCACAAAGCAATAGATTTTCAAAAATTG
ATATTTATCAAACACCCTTCCC
Found at i:9542695 original size:8 final size:7
Alignment explanation
Indices: 9542655--9542691 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
9542645 CGAGAAGAAG
9542655 AAAATGA
1 AAAATGA
9542662 AAAATGA
1 AAAATGA
9542669 AAAATGA
1 AAAATGA
9542676 AAAATGA
1 AAAATGA
9542683 ATAAATGA
1 A-AAATGA
9542691 A
1 A
9542692 TAAAGAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (7 bp):
AAAATGA
Found at i:9542869 original size:59 final size:58
Alignment explanation
Indices: 9542797--9542918 Score: 235
Period size: 59 Copynumber: 2.1 Consensus size: 58
9542787 GAAATTCCAT
9542797 GTAATCCAGTGTTTATACTTTAACGGTTCAATGATTAAAAAATGCATTTGGATAGTTTA
1 GTAATCCAGTGTTTATACTTTAACGGTTCAATGATT-AAAAATGCATTTGGATAGTTTA
9542856 GTAATCCAGTGTTTATACTTTAACGGTTCAATGATTAAAAATGCATTTGGATAGTTTA
1 GTAATCCAGTGTTTATACTTTAACGGTTCAATGATTAAAAATGCATTTGGATAGTTTA
9542914 GTAAT
1 GTAAT
9542919 TAAATTAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 27 0.43
59 36 0.57
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (58 bp):
GTAATCCAGTGTTTATACTTTAACGGTTCAATGATTAAAAATGCATTTGGATAGTTTA
Found at i:9543254 original size:18 final size:18
Alignment explanation
Indices: 9543216--9543254 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9543206 ATTGCTTCTC
* *
9543216 AAAAGCACTTTTGGGACA
1 AAAAACACTTTTGAGACA
*
9543234 AAAAACACTTTTGAGATA
1 AAAAACACTTTTGAGACA
9543252 AAA
1 AAA
9543255 GAATTGATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (18 bp):
AAAAACACTTTTGAGACA
Found at i:9546383 original size:42 final size:40
Alignment explanation
Indices: 9546302--9546381 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
9546292 ACTACGTTTG
*
9546302 GCACTTAGTGTGCGTTTCAGAATAGCTTCGGCTATATATA
1 GCACTTAGTGTGCGATTCAGAATAGCTTCGGCTATATATA
* *
9546342 GCACTTAGTGTGTGAATT-AGAATAGCTTCGGCTACATATA
1 GCACTTAGTGTGCG-ATTCAGAATAGCTTCGGCTATATATA
9546382 TATATGGTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 34 0.94
41 2 0.06
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34
Consensus pattern (40 bp):
GCACTTAGTGTGCGATTCAGAATAGCTTCGGCTATATATA
Found at i:9546394 original size:46 final size:47
Alignment explanation
Indices: 9546334--9546422 Score: 119
Period size: 46 Copynumber: 1.9 Consensus size: 47
9546324 TAGCTTCGGC
* *
9546334 TATATATAGCACTTAGTGTGTGA-A-TTAGAATAGCTTCGGCTACATA
1 TATATATAGCACTTAGTGTGCGAGACTGAG-ATAGCTTCGGCTACATA
* *
9546380 TATATATGGTACTTAGTGTGCGAGACTGAGATAGCTTCGGCTA
1 TATATATAGCACTTAGTGTGCGAGACTGAGATAGCTTCGGCTA
9546423 TGAAAGGCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 20 0.54
47 14 0.38
48 3 0.08
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (47 bp):
TATATATAGCACTTAGTGTGCGAGACTGAGATAGCTTCGGCTACATA
Found at i:9547214 original size:13 final size:13
Alignment explanation
Indices: 9547196--9547221 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9547186 ATATGTATTG
9547196 AACTGGTACCATT
1 AACTGGTACCATT
9547209 AACTGGTACCATT
1 AACTGGTACCATT
9547222 TTGGTTGCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
AACTGGTACCATT
Found at i:9548863 original size:15 final size:14
Alignment explanation
Indices: 9548823--9548912 Score: 74
Period size: 15 Copynumber: 6.1 Consensus size: 14
9548813 CTGTGCATAA
9548823 CCCTATGG-AGAACT
1 CCCTATGGCA-AACT
*
9548837 CCCTTATAGCAAACT
1 CCC-TATGGCAAACT
9548852 CACCTATGGCAAACT
1 C-CCTATGGCAAACT
**
9548867 CCCTATGGTGAACT
1 CCCTATGGCAAACT
** *
9548881 CCTCTATGGTGAGCT
1 CC-CTATGGCAAACT
9548896 CACCTATGGCAAACT
1 C-CCTATGGCAAACT
9548911 CC
1 CC
9548913 TTTATAGAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
14 17 0.27
15 42 0.67
16 4 0.06
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (14 bp):
CCCTATGGCAAACT
Found at i:9552480 original size:3 final size:3
Alignment explanation
Indices: 9552467--9552548 Score: 155
Period size: 3 Copynumber: 27.0 Consensus size: 3
9552457 TTTGAAACTA
9552467 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9552513 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9552549 GGTAAAAGGT
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
3 75 0.96
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:9555243 original size:37 final size:37
Alignment explanation
Indices: 9555146--9555243 Score: 99
Period size: 37 Copynumber: 2.6 Consensus size: 37
9555136 TAATCCCTGT
** *
9555146 TTTGGCGTGCTTTCGATTGGATTAGCTATTCGGAGCA
1 TTTGGCGTGCTTTCGGGTGGATTAGCTATTAGGAGCA
* * * * *
9555183 ATTGGCGTG-TTATCTGGTAGATTAGCTCTTATGAGCA
1 TTTGGCGTGCTT-TCGGGTGGATTAGCTATTAGGAGCA
*
9555220 TTTGGCATGCTTTCGGGTGGATTA
1 TTTGGCGTGCTTTCGGGTGGATTA
9555244 ATGTGCTCGT
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
36 2 0.04
37 43 0.91
38 2 0.04
ACGTcount: A:0.17, C:0.14, G:0.30, T:0.39
Consensus pattern (37 bp):
TTTGGCGTGCTTTCGGGTGGATTAGCTATTAGGAGCA
Found at i:9556383 original size:17 final size:19
Alignment explanation
Indices: 9556358--9556395 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
9556348 TTTTGAAATT
9556358 TTTCATATTTT-CTTAAAA
1 TTTCATATTTTGCTTAAAA
*
9556376 TTTC-TATTTTGCTTCAAA
1 TTTCATATTTTGCTTAAAA
9556394 TT
1 TT
9556396 GATCTCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTCATATTTTGCTTAAAA
Found at i:9559084 original size:27 final size:27
Alignment explanation
Indices: 9559039--9559090 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
9559029 TCAATTTGAT
* *
9559039 AAAATGACTGTTCTGCCCTTATGTGGC
1 AAAATGACTATTCTACCCTTATGTGGC
*
9559066 AAAATGACTATTTTACCCTTATGTG
1 AAAATGACTATTCTACCCTTATGTG
9559091 ACATTTGCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (27 bp):
AAAATGACTATTCTACCCTTATGTGGC
Found at i:9559125 original size:27 final size:27
Alignment explanation
Indices: 9559094--9559342 Score: 268
Period size: 27 Copynumber: 9.2 Consensus size: 27
9559084 TTATGTGACA
* *
9559094 TTTGCCCTTCTGTGGGAAAATGACTGT
1 TTTGCCCTTATGTGGTAAAATGACTGT
* * *
9559121 TTTGCCCGTATGTGGTAAAATGATTAT
1 TTTGCCCTTATGTGGTAAAATGACTGT
*
9559148 TTTGCCCTTGTGTGGTAAAATGA-TAGT
1 TTTGCCCTTATGTGGTAAAATGACT-GT
* *
9559175 TTTGCCCTTATGTGGCAAAATGATTGT
1 TTTGCCCTTATGTGGTAAAATGACTGT
* * * * *
9559202 TCTT-CCATTGTATGGTAAAATAACAGT
1 T-TTGCCCTTATGTGGTAAAATGACTGT
*** *
9559229 TTTGCCCTTATGTCAAAAAATGACGGT
1 TTTGCCCTTATGTGGTAAAATGACTGT
*
9559256 TTTGCCCTTATGTGGTAAAATGACTTT
1 TTTGCCCTTATGTGGTAAAATGACTGT
* *
9559283 TTTGCCCTTGTGTGGTAAAATGACAGT
1 TTTGCCCTTATGTGGTAAAATGACTGT
* *
9559310 TTCGCCCTTATGTGGTAAAATGATTGT
1 TTTGCCCTTATGTGGTAAAATGACTGT
9559337 TTTGCC
1 TTTGCC
9559343 ATTACATGGT
Statistics
Matches: 180, Mismatches: 38, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
26 3 0.02
27 174 0.97
28 3 0.02
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (27 bp):
TTTGCCCTTATGTGGTAAAATGACTGT
Found at i:9559376 original size:54 final size:54
Alignment explanation
Indices: 9559094--9559377 Score: 153
Period size: 54 Copynumber: 5.3 Consensus size: 54
9559084 TTATGTGACA
* * * ** ** *
9559094 TTTGCCCTTCTGTGGGAAAATGACTGTTTTGCCCGTATGTGGTAAAATGATTA-T
1 TTTGCCCTTATGTGGTAAAATGACTTTTTTGCCATTACATGGTAAAATGA-CAGT
* * * ** * **
9559148 TTTGCCCTTGTGTGGTAAAATGA-TAGTTTTGCCCTTATGTGGCAAAATGATTGT
1 TTTGCCCTTATGTGGTAAAATGACT-TTTTTGCCATTACATGGTAAAATGACAGT
* * * * ** * ** *** *
9559202 TCTT-CCATTGTATGGTAAAATAACAGTTTTGCCCTTATGTCAAAAAATGACGGT
1 T-TTGCCCTTATGTGGTAAAATGACTTTTTTGCCATTACATGGTAAAATGACAGT
* ***
9559256 TTTGCCCTTATGTGGTAAAATGACTTTTTTGCCCTTGTGTGGTAAAATGACAGT
1 TTTGCCCTTATGTGGTAAAATGACTTTTTTGCCATTACATGGTAAAATGACAGT
* ** *
9559310 TTCGCCCTTATGTGGTAAAATGA-TTGTTTTGCCATTACATGGTAAGCTGACCGT
1 TTTGCCCTTATGTGGTAAAATGACTT-TTTTGCCATTACATGGTAAAATGACAGT
* *
9559364 TTTACCCCTATGTG
1 TTTGCCCTTATGTG
9559378 ATGTATGTTT
Statistics
Matches: 188, Mismatches: 36, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
53 6 0.03
54 180 0.96
55 2 0.01
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (54 bp):
TTTGCCCTTATGTGGTAAAATGACTTTTTTGCCATTACATGGTAAAATGACAGT
Found at i:9569354 original size:35 final size:35
Alignment explanation
Indices: 9569305--9569374 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
9569295 AATTATAAAG
*
9569305 TTAATTAAGTTTTAGGGACCAAATTTTGTAACACC
1 TTAATTAAGCTTTAGGGACCAAATTTTGTAACACC
9569340 TTAATTAAGCTTTAGGGACCAAATTTTGTAACACC
1 TTAATTAAGCTTTAGGGACCAAATTTTGTAACACC
9569375 CCTTTACCCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (35 bp):
TTAATTAAGCTTTAGGGACCAAATTTTGTAACACC
Found at i:9571325 original size:25 final size:25
Alignment explanation
Indices: 9571250--9571325 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
9571240 ATTCCAAAAA
* *
9571250 TAATATTATTTTAATAGTTTAATAT
1 TAATAATATTTTAATAATTTAATAT
* * *
9571275 TAA-ATATAATTTAAT-ACTT-ATCT
1 TAATA-ATATTTTAATAATTTAATAT
*
9571298 TAATAATATTTTACTAATTTAATAT
1 TAATAATATTTTAATAATTTAATAT
9571323 TAA
1 TAA
9571326 AGTGATTATC
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
23 14 0.37
24 7 0.18
25 17 0.45
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (25 bp):
TAATAATATTTTAATAATTTAATAT
Found at i:9578089 original size:17 final size:17
Alignment explanation
Indices: 9578053--9578086 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9578043 TAAAAGAGTT
*
9578053 AATTAGGATTAAATTGG
1 AATTAGGAATAAATTGG
9578070 AATTAGGAAATAAATTG
1 AATTAGG-AATAAATTG
9578087 AATAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (17 bp):
AATTAGGAATAAATTGG
Found at i:9578625 original size:27 final size:27
Alignment explanation
Indices: 9578587--9578682 Score: 88
Period size: 27 Copynumber: 3.4 Consensus size: 27
9578577 ATGCCTTATT
9578587 GGTGTGTTTGGGAGGATATGA-TATACC
1 GGTGTGTTTGGGAGGATAT-ATTATACC
* * *
9578614 GGTGTGTTTGGGAAGCTATATTATACT
1 GGTGTGTTTGGGAGGATATATTATACC
* *
9578641 GGTGTGTTAT-GGAGGATTTATATTATTTCG
1 GGTGTGTT-TGGGAGGA--TATATTA-TACC
9578671 GGTGTGTTTGGG
1 GGTGTGTTTGGG
9578683 TTGGATATTC
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
26 1 0.02
27 34 0.61
28 1 0.02
29 8 0.14
30 12 0.21
ACGTcount: A:0.19, C:0.05, G:0.35, T:0.41
Consensus pattern (27 bp):
GGTGTGTTTGGGAGGATATATTATACC
Found at i:9580378 original size:35 final size:35
Alignment explanation
Indices: 9580337--9580433 Score: 99
Period size: 35 Copynumber: 2.7 Consensus size: 35
9580327 CATAGGTAAG
*
9580337 TACATGTAAGCTTATATTGAACTTGT-GTATTCGGT
1 TACATGTAAGCTTATATTGAA-TTGTAGTATTCGAT
* * * * *
9580372 TGCATGTGAGGTTATATTGAATTTTAGTATTTGAT
1 TACATGTAAGCTTATATTGAATTGTAGTATTCGAT
9580407 TACATGTGAA-CTTATATTGAAATTGTA
1 TACATGT-AAGCTTATATTG-AATTGTA
9580434 TACTCGGATA
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
34 3 0.06
35 39 0.80
36 7 0.14
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (35 bp):
TACATGTAAGCTTATATTGAATTGTAGTATTCGAT
Found at i:9582061 original size:2 final size:2
Alignment explanation
Indices: 9582056--9582081 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9582046 ATATAAGTTC
9582056 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9582082 TTGTATAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9582958 original size:44 final size:44
Alignment explanation
Indices: 9582895--9582982 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
9582885 TGAAGATAAC
9582895 ACACTTATAATAAGGTCATTGGATGAGCACTGATCGATTTGCTT
1 ACACTTATAATAAGGTCATTGGATGAGCACTGATCGATTTGCTT
*
9582939 ACACTTATAATAAGGTCATTGGATGAGCACTGATTGATTTGCTT
1 ACACTTATAATAAGGTCATTGGATGAGCACTGATCGATTTGCTT
9582983 TCCTAATGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (44 bp):
ACACTTATAATAAGGTCATTGGATGAGCACTGATCGATTTGCTT
Found at i:9583279 original size:57 final size:58
Alignment explanation
Indices: 9583200--9583314 Score: 187
Period size: 57 Copynumber: 2.0 Consensus size: 58
9583190 TGAAATGGTG
9583200 AAATAGAAAAATAGGAAACATTTGGAAATGATTATAGTTTTCTCCAAAATAAAAATGA
1 AAATAGAAAAATAGGAAACATTTGGAAATGATTATAGTTTTCTCCAAAATAAAAATGA
* * * *
9583258 AAATGGAAAAAT-GGAATCATTTGGAAATTATTATAGTTTTCTCCAAAATGAAAATGA
1 AAATAGAAAAATAGGAAACATTTGGAAATGATTATAGTTTTCTCCAAAATAAAAATGA
9583315 CTTGAAAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 42 0.79
58 11 0.21
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.30
Consensus pattern (58 bp):
AAATAGAAAAATAGGAAACATTTGGAAATGATTATAGTTTTCTCCAAAATAAAAATGA
Found at i:9584361 original size:28 final size:28
Alignment explanation
Indices: 9584324--9584378 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
9584314 TAATAGAAAG
9584324 AAAGTTTAGCTTAATTTGTTTAACTGAA
1 AAAGTTTAGCTTAATTTGTTTAACTGAA
*
9584352 AAAGTTTAGCTTAATTTGTTTAGCTGA
1 AAAGTTTAGCTTAATTTGTTTAACTGA
9584379 TAATTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (28 bp):
AAAGTTTAGCTTAATTTGTTTAACTGAA
Found at i:9584372 original size:14 final size:14
Alignment explanation
Indices: 9584327--9584376 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
9584317 TAGAAAGAAA
9584327 GTTTAGCTTAATTT
1 GTTTAGCTTAATTT
* * ***
9584341 GTTTAACTGAAAAA
1 GTTTAGCTTAATTT
9584355 GTTTAGCTTAATTT
1 GTTTAGCTTAATTT
9584369 GTTTAGCT
1 GTTTAGCT
9584377 GATAATTTAA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (14 bp):
GTTTAGCTTAATTT
Found at i:9585755 original size:17 final size:18
Alignment explanation
Indices: 9585735--9585772 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
9585725 TGTAAAAAAT
*
9585735 AAACTTATGAAAAAT-AA
1 AAACTAATGAAAAATCAA
*
9585752 AAACTAATTAAAAATCAA
1 AAACTAATGAAAAATCAA
9585770 AAA
1 AAA
9585773 TAAAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.21
Consensus pattern (18 bp):
AAACTAATGAAAAATCAA
Found at i:9587422 original size:16 final size:16
Alignment explanation
Indices: 9587399--9587434 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
9587389 AATAAACAAT
9587399 TAAATAAATT-GGAAA
1 TAAATAAATTGGGAAA
9587414 TAAATTAAATTGGGAAA
1 TAAA-TAAATTGGGAAA
9587431 TAAA
1 TAAA
9587435 CTTGGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 6 0.32
17 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (16 bp):
TAAATAAATTGGGAAA
Found at i:9594074 original size:22 final size:21
Alignment explanation
Indices: 9594042--9594090 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
9594032 TTTTTATCAT
*
9594042 ATTACTAAATTAACTTTAAGAATA
1 ATTA-TAATTTAA-TTTAA-AATA
*
9594066 ATTATAATTTAATTTAAAATT
1 ATTATAATTTAATTTAAAATA
9594087 ATTA
1 ATTA
9594091 GTTTAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 5 0.22
23 7 0.30
24 4 0.17
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTATAATTTAATTTAAAATA
Found at i:9595367 original size:9 final size:9
Alignment explanation
Indices: 9595353--9595419 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
9595343 ATTTAAAGTC
9595353 TTTTTTTTA
1 TTTTTTTTA
9595362 --TTTTTTA
1 TTTTTTTTA
**
9595369 TTTTAATTA
1 TTTTTTTTA
9595378 TTATTTTTTA
1 TT-TTTTTTA
*
9595388 CTTTTTTCATA
1 -TTTTTT-TTA
9595399 TTTTTTTTA
1 TTTTTTTTA
*
9595408 TGTTTTTTA
1 TTTTTTTTA
9595417 TTT
1 TTT
9595420 AAAATATGGA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
7 7 0.16
9 19 0.42
10 15 0.33
11 4 0.09
ACGTcount: A:0.16, C:0.03, G:0.01, T:0.79
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:9595620 original size:21 final size:20
Alignment explanation
Indices: 9595596--9595644 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
9595586 AAAAAATACA
**
9595596 AAAATTTAATGTATCAAAATT
1 AAAATTTAAAATAT-AAAATT
*
9595617 AAAATTTAAAATATAAATTT
1 AAAATTTAAAATATAAAATT
9595637 AAAATTTA
1 AAAATTTA
9595645 TATGCGTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAATTTAAAATATAAAATT
Found at i:9596238 original size:24 final size:24
Alignment explanation
Indices: 9596201--9596281 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
9596191 ATTTTATTTT
9596201 TATTTTTAAAAATATTTAAAATATTA
1 TATTTTT--AAATATTTAAAATATTA
* *
9596227 TATTTTTCAATATTATTAAATA-TA
1 TATTTTTAAATATT-TAAAATATTA
* * *
9596251 CATATTTAAATATTTATATATATTTA
1 TATTTTTAAATATTTA-AAATA-TTA
9596277 TATTT
1 TATTT
9596282 ATTTATATAA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
23 1 0.02
24 23 0.55
25 6 0.14
26 12 0.29
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTTTTAAATATTTAAAATATTA
Found at i:9596275 original size:10 final size:10
Alignment explanation
Indices: 9596247--9596290 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
9596237 TATTATTAAA
*
9596247 TATACATATT
1 TATATATATT
9596257 TA-A-ATATT
1 TATATATATT
9596265 TATATATATT
1 TATATATATT
*
9596275 TATATTTATT
1 TATATATATT
9596285 TATATA
1 TATATA
9596291 ATAAATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 7 0.23
9 2 0.07
10 21 0.70
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (10 bp):
TATATATATT
Found at i:9596299 original size:16 final size:16
Alignment explanation
Indices: 9596280--9596340 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 16
9596270 ATATTTATAT
9596280 TTATTTATATAATAAA
1 TTATTTATATAATAAA
*
9596296 TTATTAATATAATAAA
1 TTATTTATATAATAAA
9596312 TATAATTTATTATTTTAATAAA
1 T-T-ATTTA-TA---TAATAAA
9596334 TTATTTA
1 TTATTTA
9596341 ATATTTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 16 0.43
17 1 0.03
18 4 0.11
19 2 0.05
20 5 0.14
21 1 0.03
22 8 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTTATATAATAAA
Found at i:9596306 original size:34 final size:34
Alignment explanation
Indices: 9596268--9596366 Score: 78
Period size: 38 Copynumber: 2.8 Consensus size: 34
9596258 AAATATTTAT
9596268 ATATATTTATATTTATTTATATAATAAATTATTA
1 ATATATTTATATTTATTTATATAATAAATTATTA
* * *
9596302 ATATAATAAATATAATTTA-TTATTTTAATAAATTATTT
1 ATAT-AT--TTAT-ATTTATTTA-TATAATAAATTATTA
*
9596340 A-ATATTTAAATTTTATTT-TAATAATAA
1 ATATATTTATA-TTTATTTAT-ATAATAA
9596367 TTTTTTTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
33 2 0.04
34 16 0.31
35 4 0.08
36 2 0.04
37 8 0.16
38 19 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
ATATATTTATATTTATTTATATAATAAATTATTA
Found at i:9596316 original size:22 final size:22
Alignment explanation
Indices: 9596291--9596334 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9596281 TATTTATATA
9596291 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
9596313 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
9596335 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:9596350 original size:38 final size:43
Alignment explanation
Indices: 9596253--9596350 Score: 109
Period size: 38 Copynumber: 2.4 Consensus size: 43
9596243 TAAATATACA
* *
9596253 TATTTAAATATTTATATATATTTATATTTATTTATATAATAAAT
1 TATTT-AATATTTAAATATAATTATATTTATTTATATAATAAAT
*
9596297 TA-TTAATATAATAAATATAATT-TA-TTA-TT-T-TAATAAAT
1 TATTTAATAT-TTAAATATAATTATATTTATTTATATAATAAAT
9596335 TATTTAATATTTAAAT
1 TATTTAATATTTAAAT
9596351 TTTATTTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
38 15 0.31
39 8 0.17
40 2 0.04
41 3 0.06
42 7 0.15
43 11 0.23
44 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (43 bp):
TATTTAATATTTAAATATAATTATATTTATTTATATAATAAAT
Found at i:9596375 original size:15 final size:15
Alignment explanation
Indices: 9596355--9596385 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9596345 TTAAATTTTA
*
9596355 TTTTAATAATAATTT
1 TTTTAAAAATAATTT
9596370 TTTTAAAAATAATTT
1 TTTTAAAAATAATTT
9596385 T
1 T
9596386 AAATAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTAAAAATAATTT
Found at i:9599867 original size:22 final size:21
Alignment explanation
Indices: 9599832--9599875 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
9599822 TATCTAAATT
*
9599832 TTAAATTTTGAAAATTAAGAAA
1 TTAAATTTTGAAAAATAA-AAA
9599854 TTAAATTTCT-AAAAATAAAAA
1 TTAAATTT-TGAAAAATAAAAA
9599875 T
1 T
9599876 AAAAGTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 15 0.75
23 1 0.05
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (21 bp):
TTAAATTTTGAAAAATAAAAA
Found at i:9601133 original size:18 final size:18
Alignment explanation
Indices: 9601092--9601135 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
9601082 ATCGATTCTT
*
9601092 AGTTCAAATAGTTTGACT
1 AGTTCAAATAGTTTGACC
*
9601110 AATTCAAATAGTTTGACC
1 AGTTCAAATAGTTTGACC
9601128 AGTTCAAA
1 AGTTCAAA
9601136 ACAATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (18 bp):
AGTTCAAATAGTTTGACC
Found at i:9603896 original size:2 final size:2
Alignment explanation
Indices: 9603891--9603922 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9603881 TATTTTAAGG
9603891 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9603923 TACATTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9605104 original size:18 final size:18
Alignment explanation
Indices: 9605081--9605133 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
9605071 AAAAACACAA
9605081 AGAAAATCAATAGCAATC
1 AGAAAATCAATAGCAATC
*
9605099 AG-AAA--AACA-CAA--
1 AGAAAATCAATAGCAATC
9605111 AGAAAATCAATAGCAATC
1 AGAAAATCAATAGCAATC
9605129 AGAAA
1 AGAAA
9605134 TCTGATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
12 2 0.07
13 3 0.11
14 3 0.11
15 6 0.22
16 3 0.11
17 3 0.11
18 7 0.26
ACGTcount: A:0.62, C:0.15, G:0.11, T:0.11
Consensus pattern (18 bp):
AGAAAATCAATAGCAATC
Found at i:9605105 original size:30 final size:30
Alignment explanation
Indices: 9605071--9605133 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
9605061 AATACAACAA
9605071 AAAAACACAAAGAAAATCAATAGCAATCAG
1 AAAAACACAAAGAAAATCAATAGCAATCAG
9605101 AAAAACACAAAGAAAATCAATAGCAATCAG
1 AAAAACACAAAGAAAATCAATAGCAATCAG
9605131 AAA
1 AAA
9605134 TCTGATTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.65, C:0.16, G:0.10, T:0.10
Consensus pattern (30 bp):
AAAAACACAAAGAAAATCAATAGCAATCAG
Found at i:9605825 original size:28 final size:28
Alignment explanation
Indices: 9605793--9605846 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
9605783 CCTTTTAATT
9605793 TTACTTTTATTTCAATTAATTTTTTTGG
1 TTACTTTTATTTCAATTAATTTTTTTGG
9605821 TTACTTTTATTTCAATTAATTTTTTT
1 TTACTTTTATTTCAATTAATTTTTTT
9605847 TTGGTTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (28 bp):
TTACTTTTATTTCAATTAATTTTTTTGG
Found at i:9605860 original size:28 final size:27
Alignment explanation
Indices: 9605801--9605860 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 27
9605791 TTTTACTTTT
*
9605801 ATTTCAATTAATTTTTTTGGTTACTTTT
1 ATTTCAATTAATTTTTTTGGTTAC-TTC
9605829 ATTTCAATTAATTTTTTTTTGGTTA-TTC
1 ATTTCAATTAA--TTTTTTTGGTTACTTC
9605857 ATTT
1 ATTT
9605861 TTTTTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 17 0.59
30 12 0.41
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.65
Consensus pattern (27 bp):
ATTTCAATTAATTTTTTTGGTTACTTC
Found at i:9607125 original size:125 final size:125
Alignment explanation
Indices: 9606715--9607150 Score: 473
Period size: 125 Copynumber: 3.4 Consensus size: 125
9606705 CTTAAGGAAT
* * *
9606715 TATTTCGTGTTT-GAAGGTCTGAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTTCGTTC-A
1 TATTTCGTATTTAGAA-GTTTGAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTTCATTCGA
* * * *
9606778 GCTAAAATACGGAATATCCTTTGGAAATTTCGTCCCTGTTTT-TAAAAAAAATTAAAATGAGGCA
65 -CTAAAATACGGAATATCCTTTCGAAATTTCATCCATGTTTTCT----TAAATTAAAATGAGGCA
9606842 A
125 A
* * * * * * *
9606843 TATTTCGTATTTGGGGAGTTTGAGAGATCATGCTCAATCGTACTGGGTTTCGTTTTTTCATTCGA
1 TATTTCGTATTT-AGAAGTTTGAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTTCATTCGA
* * * * * *
9606908 CTAAAATATGGAATATCCTTTTTTGAAATTTCATCCACGCTTTCTTAAACTAAAACGAGGCAA
65 CTAAAATACGGAATATCC--TTTCGAAATTTCATCCATGTTTTCTTAAATTAAAATGAGGCAA
* * * *
9606971 TATTTCGTGTTTAGAAGTTTGGGAGATCGTGCCCAATCATGCTGGGTTTCGATTTTTCATTCGAC
1 TATTTCGTATTTAGAAGTTTGAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTTCATTCGAC
* * * *
9607036 TAAGATACGGAATATCCTCTCGACATTTCATCCATATTTTCTTAAATTAAAATGAGGCAA
66 TAAAATACGGAATATCCTTTCGAAATTTCATCCATGTTTTCTTAAATTAAAATGAGGCAA
* * * * *
9607096 TATTTCGTATTTAGAAATTCGATAAATCGTGCCCAATCGTGTTGGGTTGCGATTT
1 TATTTCGTATTTAGAAGTTTGAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTT
9607151 ACCGCTTGGT
Statistics
Matches: 256, Mismatches: 46, Indels: 15
0.81 0.15 0.05
Matches are distributed among these distances:
125 81 0.32
127 60 0.23
128 37 0.14
129 56 0.22
130 3 0.01
131 18 0.07
132 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (125 bp):
TATTTCGTATTTAGAAGTTTGAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTTCATTCGAC
TAAAATACGGAATATCCTTTCGAAATTTCATCCATGTTTTCTTAAATTAAAATGAGGCAA
Found at i:9607189 original size:125 final size:125
Alignment explanation
Indices: 9606830--9607190 Score: 276
Period size: 125 Copynumber: 2.9 Consensus size: 125
9606820 TAAAAAAAAT
* * * * * * * * * * *
9606830 TAAAATGAGGCAATATTTCGTATTTGGGGAGTTTGAGAGATCATGCTCAATCGTACTGGGTTTCG
1 TAAAACGAGGCAATATTTCGTATTT-AGAAATTCGAGAAATCGTGCCCAATCATGCTGGGTTGCG
* ** * *** *
9606895 TTTTTTCATTCGACTAAAATATGGAATATCCTTTTTTGAAATTTCATCCACGCTTTCTTAAAC
65 ATTTACCATTCGACTAAGATACCAAATAT-C-TTTTTGAAATTTCATCCACACTTTCTTAAAC
* * * * * *
9606958 TAAAACGAGGCAATATTTCGTGTTTAGAAGTTTGGGAGATCGTGCCCAATCATGCTGGGTTTCGA
1 TAAAACGAGGCAATATTTCGTATTTAGAAATTCGAGAAATCGTGCCCAATCATGCTGGGTTGCGA
** ** * * * * * * *
9607023 TTTTTCATTCGACTAAGATACGGAATATCCTCTCGACATTTCATCCATATTTTCTTAAAT
66 TTTACCATTCGACTAAGATACCAAATATCTTTTTGAAATTTCATCCACACTTTCTTAAAC
* * * *
9607083 TAAAATGAGGCAATATTTCGTATTTAGAAATTCGATAAATCGTGCCCAATCGTGTTGGGTTGCGA
1 TAAAACGAGGCAATATTTCGTATTTAGAAATTCGAGAAATCGTGCCCAATCATGCTGGGTTGCGA
* * *
9607148 TTTACCGCTTGGTC-AA-ATAACCAAATATCTTTTTGAAATTTCA
66 TTTACC-ATTCGACTAAGAT-ACCAAATATCTTTTTGAAATTTCA
9607191 AATGCATGAG
Statistics
Matches: 190, Mismatches: 41, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
124 2 0.01
125 102 0.54
126 5 0.03
127 58 0.31
128 23 0.12
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (125 bp):
TAAAACGAGGCAATATTTCGTATTTAGAAATTCGAGAAATCGTGCCCAATCATGCTGGGTTGCGA
TTTACCATTCGACTAAGATACCAAATATCTTTTTGAAATTTCATCCACACTTTCTTAAAC
Found at i:9616683 original size:45 final size:44
Alignment explanation
Indices: 9616623--9616708 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 44
9616613 ACTTCACCTG
*
9616623 AAAAAGGAAAGGCCAAGGCGAAAACTCGAAAAGGGCGCTTTAAA
1 AAAAAGGAAAGGCCAAGGCGAAAACCCGAAAAGGGCGCTTTAAA
* *
9616667 AAAAATGGAGAGGCCAAGGCGAAAACCCGCAAAGGGCGCTTT
1 AAAAA-GGAAAGGCCAAGGCGAAAACCCGAAAAGGGCGCTTT
9616709 GAGTTGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 5 0.13
45 33 0.87
ACGTcount: A:0.43, C:0.19, G:0.29, T:0.09
Consensus pattern (44 bp):
AAAAAGGAAAGGCCAAGGCGAAAACCCGAAAAGGGCGCTTTAAA
Found at i:9617839 original size:132 final size:132
Alignment explanation
Indices: 9617604--9617899 Score: 466
Period size: 132 Copynumber: 2.2 Consensus size: 132
9617594 AAATGGCGAG
9617604 TCTTATCTCCATGTATCGGCTGTGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAACA
1 TCTTATCTCCATGTATCGGCTGTGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAACA
* * * *
9617669 AGAGAGCAGGTTAAAGATACGAGCCTTGACCCCCTAAGCAGTAGGGTAACATGCTAAAAATTATA
66 AGAGAGCAGATTAAAGATACGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACA
*
9617734 GA
131 AA
* * *
9617736 TCTTATCTCTATGTATCGGTTGTGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCA
1 TCTTATCTCCATGTATCGGCTGTGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAACA
* * * *
9617801 AGAGAGCAGATTGAAGATACGAGCCTTAACCTCTTAAGCAGTAGGGTAACAGGCTACAAATTACA
66 AGAGAGCAGATTAAAGATACGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACA
9617866 AA
131 AA
* *
9617868 TCTTATCTCCATGTATCGGCTATAGAGCAGAT
1 TCTTATCTCCATGTATCGGCTGTGGAGCAGAT
9617900 CAAAAATGGC
Statistics
Matches: 148, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 148 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (132 bp):
TCTTATCTCCATGTATCGGCTGTGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAACA
AGAGAGCAGATTAAAGATACGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACA
AA
Found at i:9618060 original size:177 final size:177
Alignment explanation
Indices: 9617736--9618076 Score: 558
Period size: 177 Copynumber: 1.9 Consensus size: 177
9617726 AAATTATAGA
* * * *
9617736 TCTTATCTCTATGTATCGGTTGTGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCA
1 TCTTATATCTATATATCGGCTATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCA
* *
9617801 AGAGAGCAGATTGAAGATACGAGCCTTAACCTCTTAAGCAGTAGGGTAACAGGCTACAAATTACA
66 AGAGAGCAGATTGAAGATACGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTACAAATTACA
*
9617866 AATCTTATCTCCATGTATCGGCTATAGAGCAGATCAAAAATGGCAAG
131 AATCTTATCTCCATGTATCAGCTATAGAGCAGATCAAAAATGGCAAG
*
9617913 TCTTATATCTATATATCGGCTATGGAGTAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCA
1 TCTTATATCTATATATCGGCTATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCA
* *
9617978 AGAGAGCAGGTTGAAGATACGAGCCTTGACCCCCCTAAGCAGTA-GGTAACAGGCTACAAATTAC
66 AGAGAGCAGATTGAAGATACGAGCCTT-AACCCCCTAAGCAGTAGGGTAACAGGCTACAAATTAC
* *
9618042 AGATCTTATCTCCATGTATCAGCTATGGAGCAGAT
130 AAATCTTATCTCCATGTATCAGCTATAGAGCAGAT
9618077 TTTAGCCATC
Statistics
Matches: 151, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
177 138 0.91
178 13 0.09
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (177 bp):
TCTTATATCTATATATCGGCTATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCA
AGAGAGCAGATTGAAGATACGAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTACAAATTACA
AATCTTATCTCCATGTATCAGCTATAGAGCAGATCAAAAATGGCAAG
Found at i:9618073 original size:309 final size:307
Alignment explanation
Indices: 9617492--9618361 Score: 1294
Period size: 309 Copynumber: 2.8 Consensus size: 307
9617482 TAAACAGTAG
* * * * * * *
9617492 GAGAACAGATCGAAGGTAGCGAGCCTTAACCCCCTAAGCCGTAGGGTAATAGGCTGTAAATTA-A
1 GAGAGCAGATTGAAGATA-CGAGCCTTAA-CCCTTAAGCAGTAGGGTAACAGGCTGCAAATTACA
* * *
9617556 AGCTCTTATCTCCATGTATCGGCTATGGAGCAAATCGAAAATGGCGAGTCTTATCTCCATGTATC
64 A-ATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCGAGTCTTATCTCTATGTATC
* * *
9617621 GGCTGTGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAACAAGAGAGCAGGTTAAAGA
128 GGCTATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGA
* * *
9617686 TACGAGCCTTGACCCCCTAAGCAGTAGGGTAACATGCTAAAAATTATAGATCTTATCTCTATGTA
193 TACGAGCCTTGACCCCCTAAGCAGTAGGGTAACAGGCT-AAAATTACAGATCTTATCTCCATGTA
* * *
9617751 TCGGTTGTGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAA
257 TCAGCTATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAA
*
9617802 GAGAGCAGATTGAAGATACGAGCCTTAACCTCTTAAGCAGTAGGGTAACAGGCTACAAATTACAA
1 GAGAGCAGATTGAAGATACGAGCCTTAACC-CTTAAGCAGTAGGGTAACAGGCTGCAAATTACAA
* * * * *
9617867 ATCTTATCTCCATGTATCGGCTATAGAGCAGATCAAAAATGGCAAGTCTTATATCTATATATCGG
65 ATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCGAGTCTTATCTCTATGTATCGG
*
9617932 CTATGGAGTAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATA
130 CTATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATA
9617997 CGAGCCTTGACCCCCCTAAGCAGTA-GGTAACAGGCTACAAATTACAGATCTTATCTCCATGTAT
195 CGAGCCTTGA-CCCCCTAAGCAGTAGGGTAACAGGCTA-AAATTACAGATCTTATCTCCATGTAT
9618061 CAGCTATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAA
258 CAGCTATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAA
* *
9618111 GAGAGCAGATTGAAGATACGAGCCTTAACCCTCTAAGTAGTAGGGTAACAGGCTGCAAATTACAG
1 GAGAGCAGATTGAAGATACGAGCCTTAACCCT-TAAGCAGTAGGGTAACAGGCTGCAAATTACAA
* *
9618176 ATCTTATCTCCATGTATCGGCTATGGAGCAGATCGGAAATGGTGAGTCTTATCTCTATGTATCGG
65 ATCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCGAGTCTTATCTCTATGTATCGG
* * * *
9618241 CTATAGAGCAGATTTTAGTCACCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGTTTGAAGATA
130 CTATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATA
* * * * *
9618306 TGAGCCTTAACCCCCTAAGCAGTAGGGTGACAGGCTGAAAATTGCAAATCTTATCT
195 CGAGCCTTGACCCCCTAAGCAGTAGGGTAACAGGCT-AAAATTACAGATCTTATCT
9618362 TCCAGAAGTC
Statistics
Matches: 507, Mismatches: 46, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
308 19 0.04
309 456 0.90
310 32 0.06
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (307 bp):
GAGAGCAGATTGAAGATACGAGCCTTAACCCTTAAGCAGTAGGGTAACAGGCTGCAAATTACAAA
TCTTATCTCCATGTATCGGCTATGGAGCAGATCGAAAATGGCGAGTCTTATCTCTATGTATCGGC
TATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATAC
GAGCCTTGACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCATGTATCAG
CTATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAA
Found at i:9618158 original size:132 final size:132
Alignment explanation
Indices: 9617926--9618208 Score: 487
Period size: 132 Copynumber: 2.1 Consensus size: 132
9617916 TATATCTATA
* *
9617926 TATCGGCTATGGAGTAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTG
1 TATCGGCTATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGATTG
*
9617991 AAGATACGAGCCTTGACCCCCCTAAGCAGTAGGTAACAGGCTACAAATTACAGATCTTATCTCCA
66 AAGATACGAGCCTTGAACCCCCTAAGCAGTAGGTAACAGGCTACAAATTACAGATCTTATCTCCA
9618056 TG
131 TG
*
9618058 TATCAGCTATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGATTG
1 TATCGGCTATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGATTG
* * *
9618123 AAGATACGAGCCTT-AACCCTCTAAGTAGTAGGGTAACAGGCTGCAAATTACAGATCTTATCTCC
66 AAGATACGAGCCTTGAACCCCCTAAGCAGTA-GGTAACAGGCTACAAATTACAGATCTTATCTCC
9618187 ATG
130 ATG
9618190 TATCGGCTATGGAGCAGAT
1 TATCGGCTATGGAGCAGAT
9618209 CGGAAATGGT
Statistics
Matches: 142, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
131 13 0.09
132 129 0.91
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (132 bp):
TATCGGCTATGGAGCAGATTTTAGCCATCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGATTG
AAGATACGAGCCTTGAACCCCCTAAGCAGTAGGTAACAGGCTACAAATTACAGATCTTATCTCCA
TG
Found at i:9621023 original size:125 final size:124
Alignment explanation
Indices: 9620667--9621070 Score: 407
Period size: 125 Copynumber: 3.2 Consensus size: 124
9620657 AGGTCTGAGA
* * * * *
9620667 AATCGTGTTGGGTTTCGATTTTTCGTTCAGCTAAAATAC-AGAATATCCTTTGGAAATTTCGTCC
1 AATCGTGCTGGGTTTCGATTTTTC-TTTAACTAAAATACGA-AATATCCTTTCGAAATTTCATCC
* * * * * *
9620731 ATGTTTTTTTAAAAAAATTAAAATGAAGCAATATTTCATATTTGGGGAGTTTGAGAGATCATGCC
64 ATGTTTTATT----AAATTAAAATGAGGCAATATTTCGTATTT-AGAAGTTTGAGAGATCGTGCC
9620796 C
124 C
* * * * *
9620797 AATCGTGTTGGGTTTCGTTTTTTTCCTTTAACTAAAATATGGAATATCCTTTTTTGAAATTTCAT
1 AATCGTGCTGGGTTTCG-ATTTTT-CTTTAACTAAAATACGAAATATCC--TTTCGAAATTTCAT
* * * * * *
9620862 CCACGCTTTCTTAAACTAAAATGAGGCAATATTTCGTGTTTAGAAGTTTGGGAGATCGTGCCC
62 CCATGTTTTATTAAATTAAAATGAGGCAATATTTCGTATTTAGAAGTTTGAGAGATCGTGCCC
* * *
9620925 AATCGTGCAT-GGTTTCGATTTTTCATTTGACTAAGATACGAAATATCCTTTCGACATTTCATCC
1 AATCGTGC-TGGGTTTCGATTTTTC-TTTAACTAAAATACGAAATATCCTTTCGAAATTTCATCC
* * * *
9620989 ATGTTTTATTAAATTAAAATGAGGCAATATTTCGTATTTAGAAATTCGATAAATCGTGCCC
64 ATGTTTTATTAAATTAAAATGAGGCAATATTTCGTATTTAGAAGTTTGAGAGATCGTGCCC
*
9621050 AATCGTGCTGGGTTGCGATTT
1 AATCGTGCTGGGTTTCGATTT
9621071 ACCGCTTGGT
Statistics
Matches: 229, Mismatches: 37, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
124 1 0.00
125 83 0.36
126 1 0.00
127 24 0.10
128 32 0.14
129 26 0.11
130 17 0.07
131 23 0.10
132 1 0.00
133 21 0.09
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (124 bp):
AATCGTGCTGGGTTTCGATTTTTCTTTAACTAAAATACGAAATATCCTTTCGAAATTTCATCCAT
GTTTTATTAAATTAAAATGAGGCAATATTTCGTATTTAGAAGTTTGAGAGATCGTGCCC
Found at i:9621094 original size:125 final size:125
Alignment explanation
Indices: 9620852--9621110 Score: 299
Period size: 125 Copynumber: 2.1 Consensus size: 125
9620842 ATCCTTTTTT
* * * * * *
9620852 GAAATTTCATCCACGCTTTCTTAAACTAAAATGAGGCAATATTTCGTGTTTAGAAGTTTGGGAGA
1 GAAATTTCATCCACGCTTTATTAAACTAAAATGAGGCAATATTTCGTATTTAGAAATTCGAGAAA
* ** * *
9620917 TCGTGCCCAATCGTGCATGGTTTCGATTTTTCATTTGACTAAGATACGAAATATCCTTTC
66 TCGTGCCCAATCGTGCATGGTTGCGATTTACCATTGGACTAAGATACCAAATATCCTTTC
* * * * *
9620977 GACATTTCATCCATGTTTTATTAAATTAAAATGAGGCAATATTTCGTATTTAGAAATTCGATAAA
1 GAAATTTCATCCACGCTTTATTAAACTAAAATGAGGCAATATTTCGTATTTAGAAATTCGAGAAA
* * *
9621042 TCGTGCCCAATCGTGC-TGGGTTGCGATTTACCGCTTGGTC-AA-ATAACCAAATATCCTTTT
66 TCGTGCCCAATCGTGCAT-GGTTGCGATTTACC-ATTGGACTAAGAT-ACCAAATATCCTTTC
9621102 GAAATTTCA
1 GAAATTTCA
9621111 AATGCATGAG
Statistics
Matches: 111, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
124 3 0.03
125 104 0.94
126 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (125 bp):
GAAATTTCATCCACGCTTTATTAAACTAAAATGAGGCAATATTTCGTATTTAGAAATTCGAGAAA
TCGTGCCCAATCGTGCATGGTTGCGATTTACCATTGGACTAAGATACCAAATATCCTTTC
Found at i:9631827 original size:15 final size:15
Alignment explanation
Indices: 9631807--9631837 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9631797 TAAAGAGCCG
9631807 TCACTGGACAGTTTA
1 TCACTGGACAGTTTA
*
9631822 TCACTGGATAGTTTA
1 TCACTGGACAGTTTA
9631837 T
1 T
9631838 GTCATGACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (15 bp):
TCACTGGACAGTTTA
Found at i:9633414 original size:18 final size:18
Alignment explanation
Indices: 9633391--9633426 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
9633381 ATTGGTTCCA
9633391 CCTAATCTAACTTAATTG
1 CCTAATCTAACTTAATTG
9633409 CCTAATCTAACTTAATTG
1 CCTAATCTAACTTAATTG
9633427 TAAGGAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (18 bp):
CCTAATCTAACTTAATTG
Found at i:9635009 original size:25 final size:24
Alignment explanation
Indices: 9634988--9635063 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
9634978 TATTAAAAGA
*
9634988 TATATATATATATATATATAAAATG
1 TATACATA-ATATATATATAAAATG
*
9635013 TATACATAATATA-ATATTAAAATA
1 TATACATAATATATATA-TAAAATG
* ** *
9635037 TTTACATGGTATATACATAATAATG
1 TATACATAATATATATATAA-AATG
9635062 TA
1 TA
9635064 AAAAATAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
23 3 0.08
24 24 0.60
25 13 0.32
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (24 bp):
TATACATAATATATATATAAAATG
Found at i:9635639 original size:39 final size:38
Alignment explanation
Indices: 9635551--9635699 Score: 192
Period size: 38 Copynumber: 3.9 Consensus size: 38
9635541 ATTCCACTCC
* * * *
9635551 CCCCATGCTACTTTGTTTTATTATTAATCAAAAAC-ACT
1 CCCCATACTATTTTGTTTTATTGTTAAT-TAAAACTACT
* * *
9635589 CCCCATGCTATTTTATTTTATTGTTAATTAAAACTATTT
1 CCCCATACTATTTTGTTTTATTGTTAATTAAAACTA-CT
9635628 CCCCATACTATTTTGTTTTATTGTTAATTAAAACTACT
1 CCCCATACTATTTTGTTTTATTGTTAATTAAAACTACT
* *
9635666 CCTCATACTATTTTGTTTTATTATTAATTAAAAC
1 CCCCATACTATTTTGTTTTATTGTTAATTAAAAC
9635700 CATACTTTAT
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
37 5 0.05
38 59 0.60
39 35 0.35
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (38 bp):
CCCCATACTATTTTGTTTTATTGTTAATTAAAACTACT
Found at i:9635649 original size:77 final size:77
Alignment explanation
Indices: 9635551--9635699 Score: 210
Period size: 77 Copynumber: 1.9 Consensus size: 77
9635541 ATTCCACTCC
* * *
9635551 CCCCATGCTACTTTGTTTTATTATTAATCAAAAAC-ACTCCCCATGCTATTTTATTTTATTGTTA
1 CCCCATACTACTTTGTTTTATTATTAAT-AAAAACTACTCCCCATACTATTTTATTTTATTATTA
9635615 ATTAAAACTATTT
65 ATTAAAACTATTT
* * * * *
9635628 CCCCATACTATTTTGTTTTATTGTTAATTAAAACTACTCCTCATACTATTTTGTTTTATTATTAA
1 CCCCATACTACTTTGTTTTATTATTAATAAAAACTACTCCCCATACTATTTTATTTTATTATTAA
9635693 TTAAAAC
66 TTAAAAC
9635700 CATACTTTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
76 5 0.08
77 58 0.92
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (77 bp):
CCCCATACTACTTTGTTTTATTATTAATAAAAACTACTCCCCATACTATTTTATTTTATTATTAA
TTAAAACTATTT
Found at i:9635740 original size:21 final size:21
Alignment explanation
Indices: 9635715--9635777 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
9635705 TTTATTTTCT
*
9635715 TTTTTTTATCATAAAAAAAACC
1 TTTTTTTAT-ATAAAAAAAACA
9635737 TTTTTTTATATAAAAAAAACA
1 TTTTTTTATATAAAAAAAACA
9635758 TTTTTTTA-A-AAAAAACAACA
1 TTTTTTTATATAAAAAA-AACA
9635778 AAAAAAGAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 6 0.15
20 5 0.13
21 19 0.49
22 9 0.23
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTTTTTATATAAAAAAAACA
Found at i:9636979 original size:45 final size:45
Alignment explanation
Indices: 9636929--9637014 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
9636919 CGATATCTGC
*
9636929 TATCTTTGATCTGCCCCCCGTCTACTACAAAGACGCCAAATCTAT
1 TATCTTTGATCTGCCCCCCGTCTAATACAAAGACGCCAAATCTAT
* * *
9636974 TATCTTTGATCTGCTCCCCGTCTAATACAGATACGCCAAAT
1 TATCTTTGATCTGCCCCCCGTCTAATACAAAGACGCCAAAT
9637015 TTGCTTCTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.30
Consensus pattern (45 bp):
TATCTTTGATCTGCCCCCCGTCTAATACAAAGACGCCAAATCTAT
Found at i:9637596 original size:210 final size:210
Alignment explanation
Indices: 9637231--9638079 Score: 1184
Period size: 210 Copynumber: 4.1 Consensus size: 210
9637221 GATGCCAAAC
** * **
9637231 CATCTTGGATCCACTTCAGCATAAACATCCGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCA
1 CATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCTCTCCATCA
* *
9637296 AAGTGAAGATGTCAAACTTTGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTT
66 AAGTGAAGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTT
* * *
9637361 GCTTCATCGAAAACACGTGAAAGCCAAATCAGCTATATCTTCGATCTGTTCCCTACCGAAATACA
131 GCTTCATCGTAAACACGTGAAAGCCAAATCAACTATATCTTCGATCTGCTCCCTACCG-AATACA
9637426 GAGAGATAAGATCTGT
195 GAGAGATAAGATCTGT
* *
9637442 CATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTAAGATCTGCAATGTGTCTGC-CTTCCATC
1 CATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCTC-TCCATC
* *
9637506 AAAGTGGAA-ATGCCAGACTTCGATTTGTTC-CTGACAATACAGAGACGACAAATCATCTTAGAT
65 AAAGT-GAAGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGAT
* * *
9637569 TTGCTTCATCGTAAACACGTAAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCTGCCGAATAC
129 TTGCTTCATCGTAAACACGTGAAAGCCAAATCAACTATATCTTCGATCTGCTCCCTACCGAATAC
9637634 AGAGAGATAAGATCTGT
194 AGAGAGATAAGATCTGT
*
9637651 CATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTAAGATCTGCTATGTGTCTGC-CTTCCATC
1 CATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCTC-TCCATC
* *
9637715 AAAGTGGAA-ATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGAT
65 AAAGT-GAAGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGAT
* * * * * * ** *
9637779 TTGTTTCAACGTAAACACGTGAAAGCCAAATCAACTATGTCTTCGATTTGTTCCTTA-TAAACAC
129 TTGCTTCATCGTAAACACGTGAAAGCCAAATCAACTATATCTTCGATCTGCTCCCTACCGAATAC
9637843 A-AGA-ATGCCAA-A-C---
194 AGAGAGAT---AAGATCTGT
* * * *
9637856 CATCTTGTATCCGCTTCAGCATAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCTCTCTATCA
1 CATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCTCTCCATCA
*
9637921 AAGTGAAGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGACAACAAATCATCTTAGATTT
66 AAGTGAAGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTT
* * **
9637986 GCTTCATCGTAAACACGTGAAAGCCAAATCAACTATATCTTTGATATGCTCCCCGCCGAATACAG
131 GCTTCATCGTAAACACGTGAAAGCCAAATCAACTATATCTTCGATCTGCTCCCTACCGAATACAG
9638051 AGAGATAAGATCTGT
196 AGAGATAAGATCTGT
*
9638066 CATCTTAGATCTGC
1 CATCTTGGATCTGC
9638080 CCCGATGAAG
Statistics
Matches: 571, Mismatches: 51, Indels: 33
0.87 0.08 0.05
Matches are distributed among these distances:
204 3 0.01
205 164 0.29
206 7 0.01
207 6 0.01
208 6 0.01
209 121 0.21
210 184 0.32
211 77 0.13
212 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (210 bp):
CATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCTCTCCATCA
AAGTGAAGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTT
GCTTCATCGTAAACACGTGAAAGCCAAATCAACTATATCTTCGATCTGCTCCCTACCGAATACAG
AGAGATAAGATCTGT
Found at i:9637944 original size:205 final size:207
Alignment explanation
Indices: 9637112--9638026 Score: 1110
Period size: 205 Copynumber: 4.4 Consensus size: 207
9637102 CTGCTTCTTT
* * * * * *
9637112 GATTTGTTCCCTGACAATACAGAGATGCCAAATCATCTTAGGTTTGCTTTGA-CGTAAGCACGTG
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGC-TTCATCGTAAACACGTG
* * * * *
9637176 AAAGCCAAATCAACTATGA--TTCGATTTGCTCCTTGTAAGCATA-AG-GATGCCAA-A-C-CAT
65 AAAGCCAAATCAACTAT-ATCTTCGATCTGTTCCTTATAAACACAGAGAGAT---AAGATCTCAT
* * **
9637234 CTTGGATCCACTTCAGCATAAACATCCGAAGGCGAGATCTGCTATGTGTCTG-CTCTCCATCAAA
126 CTTGGATCCGCTTCAGCATAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCCT-TCCATCAAA
* *
9637298 GT-GAAGATGTCAAACTTT
190 GTGGAA-ATGCCAAACTTC
* *
9637316 GATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGAAAACACGTGA
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGA
* * * *
9637381 AAGCCAAATCAGCTATATCTTCGATCTGTTCCCTACCGAAATACAGAGAGATAAGATCTGTCATC
66 AAGCCAAATCAACTATATCTTCGATCTGTTCCTTA--TAAACACAGAGAGATAAGATC--TCATC
* * *
9637446 TTGGATCTGCTTCAGCGTAAACATCTGAAGGTAAGATCTGCAATGTGTCTGCCTTCCATCAAAGT
127 TTGGATCCGCTTCAGCATAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCCTTCCATCAAAGT
*
9637511 GGAAATGCCAGACTTC
192 GGAAATGCCAAACTTC
*
9637527 GATTTGTTC-CTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTAA
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGA
* * **** *
9637591 AAGCCAAATCAGCTATATCTTCGATCTGCTCCCTGCCGAATACAGAGAGATAAGATCTGTCATCT
66 AAGCCAAATCAACTATATCTTCGATCTG-TTCCTTATAAACACAGAGAGATAAGATC--TCATCT
* *
9637656 TGGATCTGCTTCAGCGTAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCCTTCCATCAAAGTG
128 TGGATCCGCTTCAGCATAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCCTTCCATCAAAGTG
*
9637721 GAAATGCCAGACTTC
193 GAAATGCCAAACTTC
* *
9637736 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGTTTCAACGTAAACACGTGA
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGA
* *
9637801 AAGCCAAATCAACTATGTCTTCGATTTGTTCCTTATAAACACA-AGA-ATGCCAA-A-C-CATCT
66 AAGCCAAATCAACTATATCTTCGATCTGTTCCTTATAAACACAGAGAGAT---AAGATCTCATCT
* * *
9637861 TGTATCCGCTTCAGCATAAACATCTGAAGGTCAGATCTGCTATGTGTCTG-CTCTCTATCAAAGT
128 TGGATCCGCTTCAGCATAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCCT-TCCATCAAAGT
9637925 -GAAGATGCCAAACTTC
192 GGAA-ATGCCAAACTTC
* *
9637941 GATTCGTTCTCTGACAATACAGAGACAACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGA
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGA
9638006 AAGCCAAATCAACTATATCTT
66 AAGCCAAATCAACTATATCTT
9638027 TGATATGCTC
Statistics
Matches: 630, Mismatches: 60, Indels: 41
0.86 0.08 0.06
Matches are distributed among these distances:
203 4 0.01
204 73 0.12
205 165 0.26
206 2 0.00
207 7 0.01
208 7 0.01
209 128 0.20
210 160 0.25
211 79 0.13
212 5 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (207 bp):
GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGA
AAGCCAAATCAACTATATCTTCGATCTGTTCCTTATAAACACAGAGAGATAAGATCTCATCTTGG
ATCCGCTTCAGCATAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCCTTCCATCAAAGTGGAA
ATGCCAAACTTC
Found at i:9646092 original size:13 final size:15
Alignment explanation
Indices: 9646062--9646092 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
9646052 TTCCAGATTT
9646062 TCTTTTCTACCTCTC
1 TCTTTTCTACCTCTC
9646077 TCTTTTCTACCTCTC
1 TCTTTTCTACCTCTC
9646092 T
1 T
9646093 GGAAAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTTTTCTACCTCTC
Found at i:9646178 original size:15 final size:14
Alignment explanation
Indices: 9646136--9646185 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
9646126 ATAACCTTGA
*
9646136 ATGCAAATGATGTG
1 ATGCAAATGATGAG
9646150 ATG-AAATGTTATGAG
1 ATGCAAATG--ATGAG
9646165 ATGCAAATGCATGA-
1 ATGCAAATG-ATGAG
9646179 ATGCAAA
1 ATGCAAA
9646186 AAGAATATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 11 0.35
16 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (14 bp):
ATGCAAATGATGAG
Found at i:9650602 original size:37 final size:39
Alignment explanation
Indices: 9650558--9650706 Score: 203
Period size: 39 Copynumber: 3.9 Consensus size: 39
9650548 ATTCCACTCC
* * *
9650558 CCCCATGCTACTTTGTTTTATTATTAATAAAAAC-A-CT
1 CCCCATACTATTTTGTTTTATTATTAATTAAAACTACCT
* * **
9650595 CCCCATGCTATTTTGTTTTATTGTTAATTAAAACTATTT
1 CCCCATACTATTTTGTTTTATTATTAATTAAAACTACCT
*
9650634 CCCCATACTATTTTGTTTTATTGTTAATTAAAACTACCT
1 CCCCATACTATTTTGTTTTATTATTAATTAAAACTACCT
*
9650673 CCTCATACTATTTTGTTTTATTATTAATTAAAAC
1 CCCCATACTATTTTGTTTTATTATTAATTAAAAC
9650707 CATACTTTAT
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
37 31 0.31
38 1 0.01
39 69 0.68
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (39 bp):
CCCCATACTATTTTGTTTTATTATTAATTAAAACTACCT
Found at i:9660858 original size:32 final size:31
Alignment explanation
Indices: 9660822--9660883 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
9660812 AAAGCACTTA
*
9660822 ACATTTTAGTGACTTAAATAAAAAACTTTTGC
1 ACATTTCAGTGACTTAAAT-AAAAACTTTTGC
**
9660854 ACATTTCAGTGGTTTAAATAAAAACTTTTG
1 ACATTTCAGTGACTTAAATAAAAACTTTTG
9660884 AATAGTCCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (31 bp):
ACATTTCAGTGACTTAAATAAAAACTTTTGC
Found at i:9660895 original size:31 final size:32
Alignment explanation
Indices: 9660835--9660895 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
9660825 TTTTAGTGAC
* * *
9660835 TTAAATAAAAAACTTTTGCACATTTCAGTGGT
1 TTAAATAAAAAACTTTTGAACAGTCCAGTGGT
*
9660867 TTAAAT-AAAAACTTTTGAATAGTCCAGTG
1 TTAAATAAAAAACTTTTGAACAGTCCAGTG
9660896 ATCATTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (32 bp):
TTAAATAAAAAACTTTTGAACAGTCCAGTGGT
Found at i:9662633 original size:26 final size:24
Alignment explanation
Indices: 9662603--9662650 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
9662593 GCAAGGGAAT
*
9662603 AGGGAAAGGAAATGAGGAAAAATGCA
1 AGGG-AAGGAAAAGA-GAAAAATGCA
*
9662629 AGGGAATGAAAAGAGAAAAATG
1 AGGGAAGGAAAAGAGAAAAATG
9662651 AGAAAGAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 8 0.40
26 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.33, T:0.08
Consensus pattern (24 bp):
AGGGAAGGAAAAGAGAAAAATGCA
Found at i:9667270 original size:32 final size:32
Alignment explanation
Indices: 9667229--9667290 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
9667219 TTTCCTTAAT
9667229 TTATTCACAATTCAATATCAATAAACTATAAG
1 TTATTCACAATTCAATATCAATAAACTATAAG
9667261 TTATTCACAATTCAATATCAATAAACTATA
1 TTATTCACAATTCAATATCAATAAACTATA
9667291 TTCAACTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (32 bp):
TTATTCACAATTCAATATCAATAAACTATAAG
Found at i:9667737 original size:23 final size:22
Alignment explanation
Indices: 9667710--9667759 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
9667700 TGCCTAAAAC
9667710 GACACACGAGGTGCCTG-ATAT
1 GACACACGAGGTGCCTGAATAT
9667731 GACACACGAGGTGCCTGAAATAT
1 GACACACGAGGTGCCTG-AATAT
9667754 GACACA
1 GACACA
9667760 TAAAGTGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 17 0.63
23 10 0.37
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (22 bp):
GACACACGAGGTGCCTGAATAT
Done.