Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold458
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: 516756
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 3
Found at i:157191 original size:58 final size:57
Alignment explanation
Indices: 156888--157184 Score: 348
Period size: 56 Copynumber: 5.2 Consensus size: 57
156878 CACCGACTTG
* * * *
156888 TGTGGGCTTTGAAAA-GATACTACTAACTTGTGGGCTTTGACAAGGATGCTACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTAACTTGTGGGCTTTGA-AAGGGTGCCACTGACT
* * * * *
156945 TGTGAGCTTTGAAAAGGATGCCACTAACTTGTGAGCTTTTAAAAAGGATGCCACTGACC
1 TGTGGGCTTTGAAAAGGATGCCACTAACTTGTGGGC-TTT-GAAAGGGTGCCACTGACT
* * * * * *
157004 TGTGGGCTTCGAAAA-AATGCAACTATCTTATGGGCTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* **
157060 TGTGGGCTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAATGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
157116 TGTGAGCTTTGAAAGGGTATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGG-ATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACT
157174 TGTGGGCTTTG
1 TGTGGGCTTTG
157185 GAAGGGTGCT
Statistics
Matches: 202, Mismatches: 32, Indels: 11
0.82 0.13 0.04
Matches are distributed among these distances:
56 77 0.38
57 17 0.08
58 77 0.38
59 30 0.15
60 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (57 bp):
TGTGGGCTTTGAAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:160483 original size:20 final size:20
Alignment explanation
Indices: 160436--160510 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
160426 AAAAAGACAT
*
160436 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
160455 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
160476 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
160496 AATGTATCGATACAT
1 AATGTATCGATACAT
160511 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:160504 original size:40 final size:39
Alignment explanation
Indices: 160433--160510 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
160423 GGTAAAAAGA
* *
160433 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
160472 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
160511 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:161087 original size:32 final size:32
Alignment explanation
Indices: 161038--161698 Score: 910
Period size: 32 Copynumber: 21.2 Consensus size: 32
161028 AATATGGTGA
* * **
161038 TTTGAAAAGGGTTGCCACTGACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
161070 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
161102 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
161134 TTTGGAATGGGTTGCCACCGACTTGTGTGGGT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
161166 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
161198 TTTGAAATGGGTTGCCACCGAGTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
161230 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
161262 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
161294 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
161326 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
161358 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
161390 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
161422 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
161454 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
161486 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
161518 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* **
161550 TTTGGAAT-GG-TGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * * *
161578 TCTGAAAAGAG-TGCCACTGGC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
161607 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
* ** *
161636 TTTGAAA--GGATGCCAATGA-GT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
161664 TTTGAAA-GGG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
161692 TTTGAAA
1 TTTGAAA
161699 GGGATGAACA
Statistics
Matches: 593, Mismatches: 30, Indels: 16
0.93 0.05 0.03
Matches are distributed among these distances:
27 1 0.00
28 60 0.10
29 51 0.09
30 8 0.01
31 2 0.00
32 471 0.79
ACGTcount: A:0.16, C:0.18, G:0.35, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:162947 original size:13 final size:13
Alignment explanation
Indices: 162931--162967 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
162921 TTTTTTGCTA
162931 TTTTTTTTTTTTG
1 TTTTTTTTTTTTG
*
162944 TTTTTTTGTTTTG
1 TTTTTTTTTTTTG
162957 TTTTTTTTTTT
1 TTTTTTTTTTT
162968 GGGTGTAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:165631 original size:33 final size:33
Alignment explanation
Indices: 165594--165660 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
165584 TTTAACGATT
165594 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
165627 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
165660 T
1 T
165661 TTAAGCTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:165632 original size:13 final size:13
Alignment explanation
Indices: 165614--165638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
165604 CATAAAATGT
165614 TGTATCGATACAA
1 TGTATCGATACAA
165627 TGTATCGATACA
1 TGTATCGATACA
165639 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:165719 original size:13 final size:13
Alignment explanation
Indices: 165701--165725 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
165691 ATTACTCAAA
165701 TGTATCGATACAT
1 TGTATCGATACAT
165714 TGTATCGATACA
1 TGTATCGATACA
165726 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:165760 original size:87 final size:83
Alignment explanation
Indices: 165614--165794 Score: 195
Period size: 87 Copynumber: 2.1 Consensus size: 83
165604 CATAAAATGT
* ** *
165614 TGTATCGATACAATGTATCGATACATATTTTTTTGTATCGATACAATTTAAGCTATTGCCAAAAA
1 TGTATCGATACAATGTATCGATACATA-TTCTTTGTATCGATACAATGCAAGCAATTGCC--AAA
*
165679 ATGTATCGATACATTACTCAAA
63 ATGTATCGATACATT-CTAAAA
* * * *
165701 TGTATCGATACATTGTATCGATACACTGA-TCTTTGTATCGATAC-ATGCAGGCAATTTGCCCAG
1 TGTATCGATACAATGTATCGATACA-T-ATTCTTTGTATCGATACAATGCAAGCAA-TTGCCAAA
*
165764 ATGTATCGATACATTTTAAAA
63 ATGTATCGATACATTCTAAAA
165785 TGTATCGATA
1 TGTATCGATA
165795 TATGCAGGCA
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
84 14 0.17
85 16 0.20
86 6 0.07
87 43 0.53
88 1 0.01
89 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (83 bp):
TGTATCGATACAATGTATCGATACATATTCTTTGTATCGATACAATGCAAGCAATTGCCAAAATG
TATCGATACATTCTAAAA
Found at i:165827 original size:52 final size:52
Alignment explanation
Indices: 165734--165857 Score: 198
Period size: 52 Copynumber: 2.4 Consensus size: 52
165724 CACTGATCTT
*
165734 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
*
165785 TGTATCGATATATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
165837 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
165858 CTTTTCATAT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 18 0.27
52 46 0.69
53 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:179454 original size:18 final size:18
Alignment explanation
Indices: 179431--179486 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 18
179421 ATATTTTTAT
179431 ATAATTGATTTTATATAA
1 ATAATTGATTTTATATAA
* *
179449 ATAATTAATTTCATATCTAA
1 ATAATTGATTT--TATATAA
179469 A-ATATTGATTTTA-ATAA
1 ATA-ATTGATTTTATATAA
179486 A
1 A
179487 GAAATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 4 0.13
18 12 0.39
19 1 0.03
20 14 0.45
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (18 bp):
ATAATTGATTTTATATAA
Found at i:187515 original size:21 final size:21
Alignment explanation
Indices: 187461--187532 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
187451 ATTAATATAT
187461 TTTAAGTATTT-AATATTAATA
1 TTTAA-TATTTAAATATTAATA
* *
187482 --AAATATTTTAATATTAA-A
1 TTTAATATTTAAATATTAATA
*
187500 TATTATTATTTAAATATTAATA
1 T-TTAATATTTAAATATTAATA
187522 TTTAATATTTA
1 TTTAATATTTA
187533 TGTTAATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
18 6 0.15
19 10 0.24
21 23 0.56
22 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (21 bp):
TTTAATATTTAAATATTAATA
Found at i:187531 original size:7 final size:7
Alignment explanation
Indices: 187461--187532 Score: 55
Period size: 7 Copynumber: 10.6 Consensus size: 7
187451 ATTAATATAT
187461 TTTAAGTA
1 TTTAA-TA
187469 TTTAATA
1 TTTAATA
187476 -TTAATA
1 TTTAATA
*
187482 --AAATA
1 TTTAATA
187487 TTTTAATA
1 -TTTAATA
*
187495 TTAAATA
1 TTTAATA
*
187502 -TTATTA
1 TTTAATA
187508 TTTAA-A
1 TTTAATA
187514 TATTAATA
1 T-TTAATA
187522 TTTAATA
1 TTTAATA
187529 TTTA
1 TTTA
187533 TGTTAATATT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
5 4 0.08
6 12 0.23
7 25 0.48
8 11 0.21
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (7 bp):
TTTAATA
Found at i:191395 original size:19 final size:19
Alignment explanation
Indices: 191371--191431 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
191361 TTCTTATTTA
191371 TTTATTTACTCATTTTATT
1 TTTATTTACTCATTTTATT
* *
191390 TTTATTTTCTTA-TTTA--
1 TTTATTTACTCATTTTATT
191406 TTTATTTACTCATTTTATT
1 TTTATTTACTCATTTTATT
191425 TTTATTT
1 TTTATTT
191432 CATCCTTACT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 10 0.29
17 4 0.11
18 4 0.11
19 17 0.49
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATTTACTCATTTTATT
Found at i:191404 original size:35 final size:35
Alignment explanation
Indices: 191353--191431 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
191343 AATTCAACAC
*
191353 TTTTGATTTTCTTATTTATTTATTTACTCATTTTA
1 TTTTTATTTTCTTATTTATTTATTTACTCATTTTA
191388 TTTTTATTTTCTTATTTATTTATTTACTCATTTTA
1 TTTTTATTTTCTTATTTATTTATTTACTCATTTTA
191423 TTTTTATTT
1 TTTTTATTT
191432 CATCCTTACT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.19, C:0.08, G:0.01, T:0.72
Consensus pattern (35 bp):
TTTTTATTTTCTTATTTATTTATTTACTCATTTTA
Found at i:193620 original size:130 final size:130
Alignment explanation
Indices: 193436--193682 Score: 359
Period size: 130 Copynumber: 1.9 Consensus size: 130
193426 TGGGTATGTA
* *
193436 TAATTTTGAAAAATTTAAGGGTTAAAGTGCGGTTTTAAAAGTTTTAGGGCCAAAGTGAAATTTCA
1 TAATTTTGAAAAATTTAAGGGTCAAAGTGCGATTTTAAAAGTTTTAGGGCCAAAGTGAAATTTCA
*
193501 AAAAGTTTCGGGTAAGAATAAAATTTTAAAAAGTTTAGAGGTCAAAGTGTAAGTTCAAAAAAATG
66 AAAAGTTTCAGGTAAGAATAAAATTTTAAAAAGTTTAGAGGTCAAAGTGTAAGTTCAAAAAAATG
* * * * * *
193566 TAATTTTGAGAAGTTTAGGGGTCAAAGTGTGATTTTAAAAGTTTTGGGGTCAAAGTGAAATTTCA
1 TAATTTTGAAAAATTTAAGGGTCAAAGTGCGATTTTAAAAGTTTTAGGGCCAAAGTGAAATTTCA
* * * * * *
193631 AAAAGTTTTAGGTCAGAATGAAATTTTAAAAGGTTTTGGGGTCAAAGTGTAA
66 AAAAGTTTCAGGTAAGAATAAAATTTTAAAAAGTTTAGAGGTCAAAGTGTAA
193683 TTTTTAAAAG
Statistics
Matches: 102, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
130 102 1.00
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (130 bp):
TAATTTTGAAAAATTTAAGGGTCAAAGTGCGATTTTAAAAGTTTTAGGGCCAAAGTGAAATTTCA
AAAAGTTTCAGGTAAGAATAAAATTTTAAAAAGTTTAGAGGTCAAAGTGTAAGTTCAAAAAAATG
Found at i:193637 original size:57 final size:55
Alignment explanation
Indices: 193576--193724 Score: 165
Period size: 57 Copynumber: 2.6 Consensus size: 55
193566 TAATTTTGAG
*
193576 AAGTTTAGGGGTCAAAGTGTGATTTTAAAAGTTTTGGGGTCAAAGTGAAATTTCAAA
1 AAGTTTA-GGGTCAAA-TGTAATTTTAAAAGTTTTGGGGTCAAAGTGAAATTTCAAA
* * **
193633 AAGTTTTA-GGTCAGAATGAAATTTTAAAAGGTTTTGGGGTCAAAGTGTAATTTTTAA
1 AAG-TTTAGGGTCA-AATGTAATTTTAAAA-GTTTTGGGGTCAAAGTGAAATTTCAAA
* *
193690 AAGTTTAAGGGTTAAAATGTAATTTTAAAAATTTT
1 AAGTTT-AGGG-TCAAATGTAATTTTAAAAGTTTT
193725 AAGGATTTGG
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
56 19 0.24
57 37 0.47
58 20 0.26
59 2 0.03
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (55 bp):
AAGTTTAGGGTCAAATGTAATTTTAAAAGTTTTGGGGTCAAAGTGAAATTTCAAA
Found at i:193684 original size:29 final size:28
Alignment explanation
Indices: 193564--193724 Score: 155
Period size: 28 Copynumber: 5.6 Consensus size: 28
193554 TTCAAAAAAA
* *
193564 TGTAATTTTGAGAAGTTTAGGGGTCAAAG
1 TGTAATTTT-AAAAGTTTTGGGGTCAAAG
*
193593 TGTGATTTTAAAAGTTTTGGGGTCAAAG
1 TGTAATTTTAAAAGTTTTGGGGTCAAAG
* * *
193621 TGAAATTTCAAAAAGTTTT-AGGTCAGAA-
1 TGTAATTT-TAAAAGTTTTGGGGTCA-AAG
*
193649 TGAAATTTTAAAAGGTTTTGGGGTCAAAG
1 TGTAATTTTAAAA-GTTTTGGGGTCAAAG
** * *
193678 TGTAATTTTTAAAAGTTTAAGGGTTAAAA
1 TGTAA-TTTTAAAAGTTTTGGGGTCAAAG
*
193707 TGTAATTTTAAAAATTTT
1 TGTAATTTTAAAAGTTTT
193725 AAGGATTTGG
Statistics
Matches: 110, Mismatches: 16, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
27 4 0.04
28 54 0.49
29 44 0.40
30 8 0.07
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (28 bp):
TGTAATTTTAAAAGTTTTGGGGTCAAAG
Found at i:199125 original size:79 final size:80
Alignment explanation
Indices: 198964--199137 Score: 210
Period size: 79 Copynumber: 2.2 Consensus size: 80
198954 GAATTTTAGT
* * * * * *** *
198964 GTAAAAATAGGGATAGAGTATCTTCTCAGAGATGGTGGGGTTAGAGTATCCTTGTAGATAAAAAC
1 GTAAAAATGGGGTTGGAATATCCTCTCAGAGATGGTGGGGTTAGAGTATCCTCAAAGATAAAAAA
*
199029 TTTAGTGTTTTGAAA
66 TTCAGTGTTTTGAAA
*
199044 GTAAAAATGGGGTTGGAATATCCTCTCAGAGATGGT-GGGTTGGAGTATTCC-CAAAGATAAAAA
1 GTAAAAATGGGGTTGGAATATCCTCTCAGAGATGGTGGGGTTAGAGTA-TCCTCAAAGATAAAAA
199107 ATTCAGTGTTTT-AGAA
65 ATTCAGTGTTTTGA-AA
199123 GTAAAAATGGGGTTG
1 GTAAAAATGGGGTTG
199138 AAGTGCCATC
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
78 1 0.01
79 46 0.57
80 34 0.42
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (80 bp):
GTAAAAATGGGGTTGGAATATCCTCTCAGAGATGGTGGGGTTAGAGTATCCTCAAAGATAAAAAA
TTCAGTGTTTTGAAA
Found at i:200977 original size:19 final size:21
Alignment explanation
Indices: 200929--200981 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
200919 AATTTCTACA
200929 ATTTGTATCGATACAAACAGT
1 ATTTGTATCGATACAAACAGT
** *
200950 AAATGTATCGATACATA-AGT
1 ATTTGTATCGATACAAACAGT
200970 -TTTGTATCGATA
1 ATTTGTATCGATA
200982 TAATGTATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 10 0.37
20 3 0.11
21 14 0.52
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (21 bp):
ATTTGTATCGATACAAACAGT
Found at i:201046 original size:20 final size:21
Alignment explanation
Indices: 201021--201079 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
201011 ACTGCCAAGG
201021 AAATGTATCGATACATTAAT-
1 AAATGTATCGATACATTAATC
***
201041 AAATGTATCGATACATGCTTC
1 AAATGTATCGATACATTAATC
201062 AAATTGTATCGATACATT
1 AAA-TGTATCGATACATT
201080 TCTCATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 17 0.52
21 3 0.09
22 13 0.39
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.36
Consensus pattern (21 bp):
AAATGTATCGATACATTAATC
Found at i:206130 original size:31 final size:31
Alignment explanation
Indices: 205986--207392 Score: 477
Period size: 31 Copynumber: 45.0 Consensus size: 31
205976 GGACAAACAA
* *
205986 AAAG-AAGAAAATGTCCTGCTCTTTAAGGA-
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* *
206015 TAA-AAAGAAAAACGTCCTGCTCTTTGAA-GAC
1 AAAGAAAG-AAAACGTCTTGCTCTTT-AAGGAC
* * * * * * *
206046 GAAGAATGGAAACATCTTACTTTTTGAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
*
206077 AAAGAAAGAAAGAAAATGTCTTGCTCTTTAAGGAC
1 ----AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* *
206112 AAA-AAAGGAAAACATCTTGTTCTTTAAGGAC
1 AAAGAAA-GAAAACGTCTTGCTCTTTAAGGAC
* * * * * *
206143 TAAGGAAA-AAAATGTCCTACTCTTTGAGGAT
1 -AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* *
206174 AAAGAAAGAAAACATCTTGCTCTTTGAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* * *
206205 AAAGGAAA-AAAACATCTTGATCTTTGAA-GAT
1 AAA-GAAAGAAAACGTCTTGCTCTTT-AAGGAC
* * *
206236 AAAGAAAGAAAATGTCCTGCTCTTTGAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* * * *
206267 ATAGAAAAGAAAATGTCCTCCTCTTTGAA-GAC
1 AAAG-AAAGAAAACGTCTTGCTCTTT-AAGGAC
* *
206299 AAAGAAAGAAAACGTCTTACTCTTTAAAGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
*** * * * * *
206330 AAAGGGGGAAAATGTCCTACTTTTTTAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* * *
206361 AAAGAAAGAAAACGTCCTG-TCTTTGAGGAA
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* * * * * *
206391 AAAGAAAGAAAATGCCCTACTCTTTGAGGCC
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* * ** * *
206422 AAAGACAA-AAATAC--CCTACTCTTGGAGTAT
1 AAAGA-AAGAAA-ACGTCTTGCTCTTTAAGGAC
* * ** * *
206452 AAAGAAAGAAAACATCATATTCTTTGAGTAC
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* * * * *
206483 AAA-AAA-AAAACATCTAGCTTTTTGAGGAT
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* ** *
206512 AAAGGAAA-AAAACATCCGGCTCTTTGAGGAC
1 AAA-GAAAGAAAACGTCTTGCTCTTTAAGGAC
** * * *
206543 AAAGGAAA-AAAAATTC-TACTCTTTGAGGAT
1 AAA-GAAAGAAAACGTCTTGCTCTTTAAGGAC
* * * * *
206573 AAAAAAAGAAAGCGTCATGCTCTTTGAGAAC
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* * * * *
206604 AAAGAAAGAAAGCGT-TCAGCTTTTTTAGGAA
1 AAAGAAAGAAAACGTCT-TGCTCTTTAAGGAC
** * * *
206635 AAAGAAAGAAAGAAAATACCCTACTTTTTAAGGAC
1 AAAGAAAG-AA-AACGT--CTTGCTCTTTAAGGAC
* *
206670 AAAGAAAGAAAACATCTTGCTCTTTGAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* *
206701 AAAGAAAGAAAAATGTCTTG-TTTTTAAGGAC
1 AAAGAAAG-AAAACGTCTTGCTCTTTAAGGAC
* * * * * *
206732 AAAGAGAA-AATATGTCATACTCTCTGAGGAC
1 AAAGA-AAGAAAACGTCTTGCTCTTTAAGGAC
* * *
206763 AAAGCAAA-AAAATGTCTTGCTCTTTAAAGAT
1 AAAG-AAAGAAAACGTCTTGCTCTTTAAGGAC
* * * * *
206794 AAAGAATGAAAACATTTTGCTTTTTTAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* *
206825 AAAGAAAGGAAAATGTCTTGCTCTTTGAGGAC
1 AAAGAAA-GAAAACGTCTTGCTCTTTAAGGAC
* * * * *
206857 -AA-AAA-AAAATGTCCTACTTTTTAAGGAT
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
** * * *
206885 AAAGAAA-AAAATATCCTGCTCTTTGAGGAT
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* *
206915 AATGAAAGAAAACGTCCTGCTCTTTAAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* * **
206946 AAAGAAAGAAAACAT-TCTACTCTTTAAGGGT
1 AAAGAAAGAAAACGTCT-TGCTCTTTAAGGAC
* * *
206977 AAATAAAAGAAAACATCTTACTCTTTAAGGA-
1 AAA-GAAAGAAAACGTCTTGCTCTTTAAGGAC
* * * **
207008 AAATAAAGAAAACATCTTGTTCTTTAACCTGCTC
1 AAAGAAAGAAAACGTCTTGCTCTTTAA---GGAC
* * *** * ****
207042 TTTGAGGACAAAGAAATGAAAACAT-CT-TGCTCTTTGA-
1 ----A-AAGAAAGAAA--ACGTCTTGCTCT--TTAAGGAC
** * * *
207079 GGACAAAGAAATGAAAACATCTTGCTCTTTGAGGAC
1 AAAGAAA-----GAAAACGTCTTGCTCTTTAAGGAC
* **
207115 AAAGAAAGAAAACATCTTATTCTTTAAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
** * * ** * * *
207146 AAAGGGAGAAAACATCCTATTTTTTTAGGAT
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* * ** * *
207177 AAAAAAAGAAAATGTCTCACTCTTTGAGGAT
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* * * *
207208 AAAGAAAGGAAAACATCTTGCTTTTTGAGTAC
1 AAAGAAA-GAAAACGTCTTGCTCTTTAAGGAC
** *
207240 AAAG-AA-AAAACGTCTTATTCTTTGAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* * *
207269 AAGGAAAGGAAAACGTCCTGCTCTTTGAGGAC
1 AAAGAAA-GAAAACGTCTTGCTCTTTAAGGAC
* * * * *
207301 AAAGAAAGAAAATGTCCTACTCTTTGAGGAT
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
*
207332 AAAGAAAGAAAATGTCTTGCTCTTTAAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
* * *
207363 AAAGAAAGCAAATGTCCTGCTCTTTAAGGA
1 AAAGAAAGAAAACGTCTTGCTCTTTAAGGA
207393 TAAATAATAA
Statistics
Matches: 1053, Mismatches: 251, Indels: 146
0.73 0.17 0.10
Matches are distributed among these distances:
28 18 0.02
29 54 0.05
30 165 0.16
31 579 0.55
32 148 0.14
33 12 0.01
34 2 0.00
35 48 0.05
36 6 0.01
37 5 0.00
38 1 0.00
39 9 0.01
40 1 0.00
41 5 0.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (31 bp):
AAAGAAAGAAAACGTCTTGCTCTTTAAGGAC
Found at i:206185 original size:62 final size:63
Alignment explanation
Indices: 205986--207392 Score: 693
Period size: 62 Copynumber: 22.5 Consensus size: 63
205976 GGACAAACAA
* * * * * * *
205986 AAAG-AAGAAAATGTCCTGCTCTTTAAGGA-TAA--AAAGAAAAACGTCCTGCTCTTTGAAGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAG-AAAATGTCCTACTCTTTGAGGAC
* * * * * * * * *
206046 GAAGAATGGAAACATCTTACTTTTTGAGGACAAAGAAAGAAAGAAAATGTCTTGCTCTTTAAGGA
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAG---GAAAGAAAATGTCCTACTCTTTGAGGA
206111 C
63 C
* * * * *
206112 AAA-AAAGGAAAACATCTTGTTCTTTAAGGACTAAGGAAA-AAAATGTCCTACTCTTTGAGGAT
1 AAAGAAA-GAAAACGTCTTGCTCTTTGAGGACAAAGGAAAGAAAATGTCCTACTCTTTGAGGAC
* ** * * *
206174 AAAGAAAGAAAACATCTTGCTCTTTGAGGACAAAGGAAA-AAAACATCTTGA-TCTTTGAAGAT
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAGAAAATGTCCT-ACTCTTTGAGGAC
* * * * * *
206236 AAAGAAAGAAAATGTCCTGCTCTTTGAGGACATAGAAAAGAAAATGTCCTCCTCTTTGAAGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAGAAAATGTCCTACTCTTTGAGGAC
* * * ** * *
206299 AAAGAAAGAAAACGTCTTACTCTTTAAAGACAAAGG-GGGAAAATGTCCTACTTTTTTAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAGAAAATGTCCTACTCTTTGAGGAC
* * * *
206361 AAAGAAAGAAAACGTCCTG-TCTTTGAGGA-AAAAGAAAGAAAATGCCCTACTCTTTGAGGCC
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAGAAAATGTCCTACTCTTTGAGGAC
* * * * * ** * * *
206422 AAAGACAA-AAATAC--CCTACTCTTGGAGTATAAA-GAAAGAAAACATCATATTCTTTGAGTAC
1 AAAGA-AAGAAA-ACGTCTTGCTCTTTGAGGACAAAGGAAAGAAAATGTCCTACTCTTTGAGGAC
* * * * ** **
206483 AAA-AAA-AAAACATCTAGCTTTTTGAGGATAAAGGAAA-AAAACATCCGGCTCTTTGAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAGAAAATGTCCTACTCTTTGAGGAC
** * * * ** * * *
206543 AAAGGAAA-AAAAATTC-TACTCTTTGAGGATAAA-AAAAGAAAGCGTCATGCTCTTTGAGAAC
1 AAA-GAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAGAAAATGTCCTACTCTTTGAGGAC
* * * * * ** * *
206604 AAAGAAAGAAAGCGT-TCAGCTTTTTTAGGAAAAAGAAAGAAAGAAAATACCCTACTTTTTAAGG
1 AAAGAAAGAAAACGTCT-TGCTCTTTGAGGACAAAG---GAAAGAAAATGTCCTACTCTTTGAGG
206668 AC
62 AC
* ** * *
206670 AAAGAAAGAAAACATCTTGCTCTTTGAGGACAAA-GAAAGAAAAATGT-CTTGTTTTTAAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAG-AAAATGTCCTACTCTTTGAGGAC
* * * * * * * * * * *
206732 AAAGAGAA-AATATGTCATACTCTCTGAGGACAAAGCAAA-AAAATGTCTTGCTCTTTAAAGAT
1 AAAGA-AAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAGAAAATGTCCTACTCTTTGAGGAC
* * * * * * *
206794 AAAGAATGAAAACATTTTGCTTTTTTAGGACAAA-GAAAGGAAAATGTCTTGCTCTTTGAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAA-GAAAATGTCCTACTCTTTGAGGAC
* * * * * * * * *
206857 -AA-AAA-AAAATGTCCTACTTTTTAAGGATAAA-GAAA-AAAATATCCTGCTCTTTGAGGAT
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAGAAAATGTCCTACTCTTTGAGGAC
* * * ** * * **
206915 AATGAAAGAAAACGTCCTGCTCTTTAAGGACAAA-GAAAGAAAACATTCTACTCTTTAAGGGT
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAGAAAATGTCCTACTCTTTGAGGAC
* * * * * *
206977 AAATAAAAGAAAACATCTTACTCTTTAAGGA-AAA-TAAAGAAAACATCTTGTTCTTTAACCTGC
1 AAA-GAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAG-AAA-A---TG-----T--CCTAC
207040 TCTTTGAGGAC
53 TCTTTGAGGAC
* ** * *
207051 AAAGAAATGAAAACATCTTGCTCTTTGAGGACAAA-GAAATGAAAACATCTTGCTCTTTGAGGAC
1 AAAGAAA-GAAAACGTCTTGCTCTTTGAGGACAAAGGAAA-GAAAATGTCCTACTCTTTGAGGAC
* ** * * ** * * * *
207115 AAAGAAAGAAAACATCTTATTCTTTAAGGACAAAGG-GAGAAAACATCCTATTTTTTTAGGAT
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAGAAAATGTCCTACTCTTTGAGGAC
* * ** * ** * * * *
207177 AAAAAAAGAAAATGTCTCACTCTTTGAGGATAAA-GAAAGGAAAACATCTTGCTTTTTGAGTAC
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAA-GAAAATGTCCTACTCTTTGAGGAC
** * *
207240 AAAG-AA-AAAACGTCTTATTCTTTGAGGAC-AAGGAAAGGAAAACGTCCTGCTCTTTGAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAA-GAAAATGTCCTACTCTTTGAGGAC
* * * * * * *
207301 AAAGAAAGAAAATGTCCTACTCTTTGAGGATAAA-GAAAGAAAATGTCTTGCTCTTTAAGGAC
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAGAAAATGTCCTACTCTTTGAGGAC
* * * *
207363 AAAGAAAGCAAATGTCCTGCTCTTTAAGGA
1 AAAGAAAGAAAACGTCTTGCTCTTTGAGGA
207393 TAAATAATAA
Statistics
Matches: 1044, Mismatches: 238, Indels: 128
0.74 0.17 0.09
Matches are distributed among these distances:
58 22 0.02
59 6 0.01
60 80 0.08
61 216 0.21
62 370 0.35
63 179 0.17
64 26 0.02
65 2 0.00
66 88 0.08
67 5 0.00
72 1 0.00
73 3 0.00
74 36 0.03
75 9 0.01
76 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (63 bp):
AAAGAAAGAAAACGTCTTGCTCTTTGAGGACAAAGGAAAGAAAATGTCCTACTCTTTGAGGAC
Found at i:206989 original size:152 final size:154
Alignment explanation
Indices: 206138--207019 Score: 435
Period size: 152 Copynumber: 5.7 Consensus size: 154
206128 TTGTTCTTTA
* * * * * * * * * *
206138 AGGACTAAGGAAAAAAATGTCCTACTCTTTGAGGATAAAGAAAGAAAACA-TCTTGCTCTTTGAG
1 AGGACAAAGCAAAAAAACGTCCTGCTCTTTAAAGACAAAGAAAGAAAACATTC-TACTTTTTAAG
* * * * * * *
206202 GACAAAGGAAA-AAAACATCTTGATCTTTGAAGATAAAGAAAG-AAAATGTCCTGCTCTTTGAGG
65 GACAAA-AAAAGAAAACATCTTGCTCTTTGAGGA-CAAGAAAGAAAAATGT-CTACTTTTTAAGG
* * * * * *
206265 ACATAGAAAAGAAAATGTCCTCCTCTTTG
127 ACAAAGAGAA-AAAATATCATACTCTCTG
* * * *** ** * *
206294 AAGACAAAG-AAAGAAAACGTCTTACTCTTTAAAGACAAAGGGGGAAAATGTCCTACTTTTTTAG
1 AGGACAAAGCAAA-AAAACGTCCTGCTCTTTAAAGACAAAGAAAGAAAACATTCTACTTTTTAAG
* * * * * * * *
206358 GACAAAGAAAGAAAACGTCCTG-TCTTTGAGGAAAAAGAAAG-AAAATGCCCTACTCTTTGAGGC
65 GACAAAAAAAGAAAACATCTTGCTCTTTGAGG-ACAAGAAAGAAAAATG-TCTACTTTTTAAGGA
* * *
206421 CAAAGA-CAAAAATACCCTACTCT-TGG
128 CAAAGAGAAAAAATATCATACTCTCT-G
* * * * ** * *
206447 AGTATAAAG-AAAGAAAACATCATATTCTTT-GAGTACAAA-AAA-AAAACA-TCTAGCTTTTTG
1 AGGACAAAGCAAA-AAAACGTCCTGCTCTTTAAAG-ACAAAGAAAGAAAACATTCTA-CTTTTTA
* * ** * *
206507 AGGATAAAGGAAA-AAAACATCCGGCTCTTTGAGGACAAAGGAAA-AAAAAT-TCTACTCTTTGA
63 AGGACAAA-AAAAGAAAACATCTTGCTCTTTGAGGAC-AA-GAAAGAAAAATGTCTACTTTTTAA
* ** * *
206569 GGATAAA-A-AAAGAAAGCGTCATGCTCTTTG
125 GGACAAAGAGAAA-AAA-TATCATACTCTCTG
* * * * * * * * **
206599 AGAACAAAG-AAAGAAAGCGTTCAGCTTTTTTAGGAAAAAGAAAGAAAGAAAATACCCTACTTTT
1 AGGACAAAGCAAA-AAAACGTCCTGC-TCTTT---AAAGACAAAGAAAGAAAACATTCTACTTTT
* **
206663 TAAGGACAAAGAAAGAAAACATCTTGCTCTTTGAGGACAAAGAAAGAAAAATGTCTTGTTTTTAA
61 TAAGGACAAAAAAAGAAAACATCTTGCTCTTTGAGGAC-AAGAAAGAAAAATGTCTACTTTTTAA
* *
206728 GGACAAAGAGAAAATATGTCATACTCTCTG
125 GGACAAAGAGAAAAAATATCATACTCTCTG
* * * * * * *
206758 AGGACAAAGCAAAAAAATGTCTTGCTCTTTAAAGATAAAGAATGAAAACATTTTGCTTTTTTAGG
1 AGGACAAAGCAAAAAAACGTCCTGCTCTTTAAAGACAAAGAAAGAAAACATTCTACTTTTTAAGG
* ** *
206823 ACAAAGAAAGGAAAATGTCTTGCTCTTTGAGGAC-A-AAA-AAAAATGTCCTACTTTTTAAGGAT
66 ACAAA-AAAAGAAAACATCTTGCTCTTTGAGGACAAGAAAGAAAAATGT-CTACTTTTTAAGGAC
* * *
206885 AAAGA-AAAAAATATCCTGCTCTTTG
129 AAAGAGAAAAAATATCATACTCTCTG
* * * *
206910 AGGATAATG-AAAGAAAACGTCCTGCTCTTTAAGGACAAAGAAAGAAAACATTCTACTCTTTAAG
1 AGGACAAAGCAAA-AAAACGTCCTGCTCTTTAAAGACAAAGAAAGAAAACATTCTACTTTTTAAG
** * * * *
206974 GGTAAATAAAAGAAAACATCTTACTCTTTAAGGAAAATAAAGAAAA
65 GACAAA-AAAAGAAAACATCTTGCTCTTTGAGGACAAGAAAGAAAA
207020 CATCTTGTTC
Statistics
Matches: 560, Mismatches: 130, Indels: 73
0.73 0.17 0.10
Matches are distributed among these distances:
150 6 0.01
151 49 0.09
152 139 0.25
153 77 0.14
154 5 0.01
155 81 0.14
156 86 0.15
157 13 0.02
158 52 0.09
159 43 0.08
160 6 0.01
161 3 0.01
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (154 bp):
AGGACAAAGCAAAAAAACGTCCTGCTCTTTAAAGACAAAGAAAGAAAACATTCTACTTTTTAAGG
ACAAAAAAAGAAAACATCTTGCTCTTTGAGGACAAGAAAGAAAAATGTCTACTTTTTAAGGACAA
AGAGAAAAAATATCATACTCTCTG
Found at i:212456 original size:37 final size:37
Alignment explanation
Indices: 212415--212488 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
212405 AACGGGAACA
212415 AGTAGGACTTTCTAATAGAAGGCAGCAGAAATATAGT
1 AGTAGGACTTTCTAATAGAAGGCAGCAGAAATATAGT
212452 AGTAGGACTTTCTAATAGAAGGCAGCAGAAATATAGT
1 AGTAGGACTTTCTAATAGAAGGCAGCAGAAATATAGT
212489 CATACAAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (37 bp):
AGTAGGACTTTCTAATAGAAGGCAGCAGAAATATAGT
Found at i:213840 original size:43 final size:42
Alignment explanation
Indices: 213736--213845 Score: 114
Period size: 43 Copynumber: 2.5 Consensus size: 42
213726 AGCTTAAAAA
213736 GCCACTAAATATTTAAATTTAGTGGCATTTTCGAAGTATAAAC
1 GCCACTAAATA-TTAAATTTAGTGGCATTTTCGAAGTATAAAC
* * * ** *
213779 GCCACTAAGTACATAAATTGAGTGGTGTTTT-TAAGCTATAAAC
1 GCCACTAAATA-TTAAATTTAGTGGCATTTTCGAAG-TATAAAC
*
213822 GTCACTAAATATTCAAATTTAGTG
1 GCCACTAAATATT-AAATTTAGTG
213846 ACGTTTACCA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
42 4 0.07
43 50 0.93
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (42 bp):
GCCACTAAATATTAAATTTAGTGGCATTTTCGAAGTATAAAC
Found at i:227993 original size:18 final size:18
Alignment explanation
Indices: 227946--227993 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
227936 GCTTGTACAT
*
227946 AAATTTCTTTGATGAATG
1 AAATTTGTTTGATGAATG
227964 AAATTATGTTTGATGAATG
1 AAATT-TGTTTGATGAATG
227983 AAATTTGTTTG
1 AAATTTGTTTG
227994 TCTTGCTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (18 bp):
AAATTTGTTTGATGAATG
Found at i:230201 original size:18 final size:18
Alignment explanation
Indices: 230178--230226 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
230168 TGTACAATTG
230178 ATTTTATATAAAA-AGTTA
1 ATTTTATATAAAATA-TTA
230196 ATTTTATATCTAAAATATTA
1 ATTTTATA--TAAAATATTA
230216 ATTTTA-ATAAA
1 ATTTTATATAAA
230227 TAAATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 4 0.14
18 8 0.29
19 1 0.04
20 14 0.50
21 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTTATATAAAATATTA
Found at i:231080 original size:2 final size:2
Alignment explanation
Indices: 231075--231102 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
231065 TCTATATCCC
231075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
231103 ATTTAATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:233765 original size:22 final size:23
Alignment explanation
Indices: 233739--233783 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
233729 ATATAAAAAT
233739 ATAAA-TATATTAAATTAT-TATA
1 ATAAATTATA-TAAATTATATATA
233761 ATAAATTATATAAATTATATATA
1 ATAAATTATATAAATTATATATA
233784 TATTCTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATAAATTATATAAATTATATATA
Found at i:234156 original size:2 final size:2
Alignment explanation
Indices: 234149--234176 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
234139 GGTGACAAGC
234149 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
234177 TCCATCGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:234240 original size:2 final size:2
Alignment explanation
Indices: 234233--234259 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
234223 ACATGCACAA
234233 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
234260 ATTCAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:237250 original size:50 final size:50
Alignment explanation
Indices: 237193--237292 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
237183 AGATTATTGT
* *
237193 TATTAAGAGATTATTATTAGAGATATTTTTCTTAAGAAGAGAATAAGAAC
1 TATTAAGAGATTATTATCAGAGATATTTTTCTTAAGAAGAGAAGAAGAAC
237243 TATTAAGAGATTATTATCAGAGATATTTTTCTTAAGAAGAGAAGAAGAAC
1 TATTAAGAGATTATTATCAGAGATATTTTTCTTAAGAAGAGAAGAAGAAC
237293 AAGAAGACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (50 bp):
TATTAAGAGATTATTATCAGAGATATTTTTCTTAAGAAGAGAAGAAGAAC
Found at i:239871 original size:2 final size:2
Alignment explanation
Indices: 239864--239895 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
239854 TACGATAAGC
239864 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
239896 TCTATAAATC
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:241175 original size:27 final size:28
Alignment explanation
Indices: 241141--241215 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 28
241131 GCCACCCATT
*
241141 TGTTTGTCAAAAATGGTGGTTT-TTTTG
1 TGTTTGTCAAAAATGGTGGTTTCCTTTG
241168 TGTTTGTCAAAAATGGTGGTTTCCTTTG
1 TGTTTGTCAAAAATGGTGGTTTCCTTTG
* *
241196 TATTTGACAAATAAT-GTGGT
1 TGTTTGTCAAA-AATGGTGGT
241216 GGAACCAGCG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 22 0.51
28 18 0.42
29 3 0.07
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.47
Consensus pattern (28 bp):
TGTTTGTCAAAAATGGTGGTTTCCTTTG
Found at i:241514 original size:25 final size:25
Alignment explanation
Indices: 241452--241521 Score: 92
Period size: 24 Copynumber: 2.8 Consensus size: 25
241442 AATAAAAATT
*
241452 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
241476 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
241501 AGCCTA-C-ATATTTGACAAATA
1 AGCC-ACCAAT-TTTGACAAATA
241522 CAAAGGAAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
24 21 0.50
25 20 0.48
26 1 0.02
ACGTcount: A:0.46, C:0.24, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:246081 original size:25 final size:25
Alignment explanation
Indices: 246019--246088 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
246009 AATAAAAATT
*
246019 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
246043 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
246068 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
246089 CAAAGGAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:246146 original size:24 final size:27
Alignment explanation
Indices: 246073--246143 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
246063 AAACAAGCCT
* *
246073 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
246101 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
*
246128 CCATTTTTGATAAACA
1 CCATTTTTGACAAACA
246144 AATGGGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:252403 original size:16 final size:16
Alignment explanation
Indices: 252384--252442 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
252374 AAAAGGTTTG
*
252384 AATCTAAAAAAATCTA
1 AATCTAAAAAAATCCA
**
252400 AATCTAAAATTATCCA
1 AATCTAAAAAAATCCA
* *
252416 AATCCAAAAAAAACCCA
1 AAT-CTAAAAAAATCCA
*
252433 AACCTAAAAA
1 AATCTAAAAA
252443 CTCTCAATTT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
16 22 0.67
17 11 0.33
ACGTcount: A:0.61, C:0.20, G:0.00, T:0.19
Consensus pattern (16 bp):
AATCTAAAAAAATCCA
Found at i:254061 original size:2 final size:2
Alignment explanation
Indices: 254043--254085 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
254033 TTAATTGAAC
* * *
254043 AT AT GT AT AT AT GT AT AT AT AT AT AT AT AT GT 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 AT
254085 A
1 A
254086 AAAATATTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (2 bp):
AT
Found at i:255616 original size:23 final size:26
Alignment explanation
Indices: 255579--255640 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
255569 AAATTAATTT
**
255579 TAATAAAATAAAATTAT-AT-AA-AA
1 TAATAAAATTTAATTATAATAAATAA
* *
255602 TTATAAAATTTAATTTTAATAAATAA
1 TAATAAAATTTAATTATAATAAATAA
255628 TAATAAAATTTAA
1 TAATAAAATTTAA
255641 AATTATTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 13 0.42
24 2 0.06
25 2 0.06
26 14 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
TAATAAAATTTAATTATAATAAATAA
Found at i:255888 original size:2 final size:2
Alignment explanation
Indices: 255881--255906 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
255871 AATTCCAAAA
255881 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
255907 TCTTTTGTTA
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:256354 original size:2 final size:2
Alignment explanation
Indices: 256347--256375 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
256337 ACGTGCACAA
256347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
256376 AAATTCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:265971 original size:1 final size:1
Alignment explanation
Indices: 265961--266059 Score: 81
Period size: 1 Copynumber: 99.0 Consensus size: 1
265951 TGGCAATTGG
* * * ** * * * **
265961 AAAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
266026 GAAAAAAAAAAAACAAAAAAACAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
266060 GTGAAGATTT
Statistics
Matches: 76, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.87, C:0.06, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:266055 original size:30 final size:30
Alignment explanation
Indices: 265959--266046 Score: 167
Period size: 30 Copynumber: 2.9 Consensus size: 30
265949 CATGGCAATT
265959 GGAAAAAGAAAAAAACAAAACAAAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAAAA
265989 GGAAAAAGAAAAAAACAAAACAAAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAAAA
*
266019 GGAAAAAGAAAAAAAAAAAACAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAA
266047 CAAAAAAAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (30 bp):
GGAAAAAGAAAAAAACAAAACAAAAAAAAA
Found at i:269926 original size:30 final size:30
Alignment explanation
Indices: 269890--269950 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
269880 GCTCTAGCAT
269890 ATATTCC-CCTTCTATTATAGATGGAATAAA
1 ATATTCCTCC-TCTATTATAGATGGAATAAA
269920 ATATTCCTCCTCTATTATAGATGGAATAAA
1 ATATTCCTCCTCTATTATAGATGGAATAAA
269950 A
1 A
269951 GCTTGTTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (30 bp):
ATATTCCTCCTCTATTATAGATGGAATAAA
Found at i:271634 original size:37 final size:37
Alignment explanation
Indices: 271570--271641 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
271560 CTCTTTATAA
* ** *
271570 TCAATGAAATCTGAATTAGGTAGGATTAACTTTTATT
1 TCAATGAAATCTGAATAAAATAAGATTAACTTTTATT
*
271607 TCAATGAAATCTGAATAAAATAAGATTAATTTTTA
1 TCAATGAAATCTGAATAAAATAAGATTAACTTTTA
271642 AAATTTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (37 bp):
TCAATGAAATCTGAATAAAATAAGATTAACTTTTATT
Found at i:274873 original size:155 final size:154
Alignment explanation
Indices: 274681--274988 Score: 476
Period size: 155 Copynumber: 2.0 Consensus size: 154
274671 CATAATTAAG
* ** * * *
274681 TTTATTTATGAGTAAATATTCTTAATAGAAAAAAAATCTTAGTGATCAAATAATTGTCTTTATAA
1 TTTATTTATAAGTAAATAGCCTTAACAGAAAAAAAATCTTAGCGATCAAATAATTATCTTTATAA
* * * *
274746 ATATAGAAGGATCTTAACTTTTAAAATTAAAATGAAAGAGATGTAAACCTTATGAGTTCTCATTA
66 ATATAGAAGGATCTTAACTTTTAAAATTAAAATAAAAGAAATGTAAACCCTATGAATTCTCATTA
274811 AAGAAA-AGGATTTGTAACTTTATA
131 AA-AAAGAGGATTTGTAACTTTATA
*
274835 TTTATTTAATAAGTAAATAGCCTTAACA-AAAAAGAAATCTTAGCGATCAAATAATTATTTTTAT
1 TTTATTT-ATAAGTAAATAGCCTTAACAGAAAAA-AAATCTTAGCGATCAAATAATTATCTTTAT
274899 AAATATAGAAGGATCTTAACTTTTAAAATTAAAATAAAAGAAATGTAAACCCTATGAATTCTCAT
64 AAATATAGAAGGATCTTAACTTTTAAAATTAAAATAAAAGAAATGTAAACCCTATGAATTCTCAT
274964 TAAAAAAGAGGATTTGTAACTTTAT
129 TAAAAAAGAGGATTTGTAACTTTAT
274989 TGTAACTTTT
Statistics
Matches: 140, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
154 15 0.11
155 125 0.89
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (154 bp):
TTTATTTATAAGTAAATAGCCTTAACAGAAAAAAAATCTTAGCGATCAAATAATTATCTTTATAA
ATATAGAAGGATCTTAACTTTTAAAATTAAAATAAAAGAAATGTAAACCCTATGAATTCTCATTA
AAAAAGAGGATTTGTAACTTTATA
Found at i:275982 original size:3 final size:3
Alignment explanation
Indices: 275976--276011 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
275966 TATCATTCAT
275976 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
276012 ATTATTGCAT
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):
TAA
Found at i:278068 original size:23 final size:24
Alignment explanation
Indices: 278042--278086 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
278032 GTGAAATAAT
278042 AAATAAATAATAAAAAT-TATTTA
1 AAATAAATAATAAAAATATATTTA
* *
278065 AAATACATATTAAAAATATATT
1 AAATAAATAATAAAAATATATT
278087 ATGAATTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATAAATAATAAAAATATATTTA
Found at i:278867 original size:18 final size:19
Alignment explanation
Indices: 278846--278886 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
278836 AATTAATATC
* *
278846 AAAATCATTCCTAA-TAAA
1 AAAATCATGCCCAATTAAA
278864 AAAATCATGCCCAATTAAA
1 AAAATCATGCCCAATTAAA
278883 AAAA
1 AAAA
278887 GGCCCTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.59, C:0.17, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAATCATGCCCAATTAAA
Found at i:279122 original size:24 final size:24
Alignment explanation
Indices: 279094--279142 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
279084 TTTAATATTT
279094 GAGATTATTAAGGTTTGATTTCGG
1 GAGATTATTAAGGTTTGATTTCGG
279118 GAGATTATTAAGGTTTGATTTCGG
1 GAGATTATTAAGGTTTGATTTCGG
279142 G
1 G
279143 TCACGAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.04, G:0.31, T:0.41
Consensus pattern (24 bp):
GAGATTATTAAGGTTTGATTTCGG
Found at i:279289 original size:17 final size:16
Alignment explanation
Indices: 279267--279315 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 16
279257 AGTTACAAAT
279267 TATTTTTAAAATAATAA
1 TATTTTTAAAATAAT-A
279284 TATTTTATATTAAATAATA
1 TATTTT-TA--AAATAATA
279303 TATTTGTTAAAAT
1 TATTT-TTAAAAT
279316 GACAGGGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 10 0.36
18 2 0.07
19 8 0.29
20 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TATTTTTAAAATAATA
Found at i:280346 original size:30 final size:32
Alignment explanation
Indices: 280283--280346 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
280273 AATGCAAATG
* *
280283 TGTCAAAATTTAAATAAAACTAATTATTAACT
1 TGTCAAAATTTAAATAAAACTAAATAATAACT
* *
280315 TGTCGAAATTTATAT-AAA-TAAATAATAACT
1 TGTCAAAATTTAAATAAAACTAAATAATAACT
280345 TG
1 TG
280347 ACTACGATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 12 0.43
31 3 0.11
32 13 0.46
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (32 bp):
TGTCAAAATTTAAATAAAACTAAATAATAACT
Found at i:280613 original size:20 final size:18
Alignment explanation
Indices: 280567--280625 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
280557 TTTTTTGTAC
280567 AATTGATTTTATATAAAA
1 AATTGATTTTATATAAAA
*
280585 AATTAATTTTATATCTAAAA
1 AATTGATTTTATA--TAAAA
*
280605 TATTGATTTTA-ATAAATA
1 AATTGATTTTATATAAA-A
280623 AAT
1 AAT
280626 ATATTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.12
18 15 0.44
19 1 0.03
20 14 0.41
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (18 bp):
AATTGATTTTATATAAAA
Found at i:281007 original size:16 final size:16
Alignment explanation
Indices: 280986--281022 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
280976 GAACTCAAAT
*
280986 TCAAAACGGTCTAAAC
1 TCAAAACAGTCTAAAC
281002 TCAAAACAGTCTAAAC
1 TCAAAACAGTCTAAAC
281018 T-AAAA
1 TCAAAA
281023 AACGTCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.51, C:0.22, G:0.08, T:0.19
Consensus pattern (16 bp):
TCAAAACAGTCTAAAC
Found at i:281511 original size:2 final size:2
Alignment explanation
Indices: 281506--281539 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
281496 ATATTCTTTG
* *
281506 AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
281540 CTTATTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:282641 original size:2 final size:2
Alignment explanation
Indices: 282634--282669 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
282624 GATTAATTGA
282634 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
282670 TTCAATGGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:284348 original size:13 final size:14
Alignment explanation
Indices: 284330--284363 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
284320 TACCGTAAAA
284330 TTTGAAAA-CATTT
1 TTTGAAAATCATTT
284343 TTTGAAAATCATTT
1 TTTGAAAATCATTT
*
284357 TGTGAAA
1 TTTGAAA
284364 GAAATGAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (14 bp):
TTTGAAAATCATTT
Found at i:284887 original size:16 final size:16
Alignment explanation
Indices: 284809--284890 Score: 52
Period size: 16 Copynumber: 5.4 Consensus size: 16
284799 TTTAAAATTT
284809 AAATTA-AATTAT-TA
1 AAATTATAATTATATA
*
284823 TAA-TA-AATTATATA
1 AAATTATAATTATATA
*
284837 AAATATTTAATT-TA-A
1 AAAT-TATAATTATATA
** *
284852 AAATTATTTTTA-AAA
1 AAATTATAATTATATA
284867 TAAATTATAATTATATA
1 -AAATTATAATTATATA
284884 AAATTAT
1 AAATTAT
284891 CAAATTTAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
13 8 0.16
14 11 0.22
15 6 0.12
16 20 0.39
17 6 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTATAATTATATA
Found at i:285349 original size:26 final size:27
Alignment explanation
Indices: 285320--285371 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
285310 ATATTTATAT
285320 ATTTT-TTAATTAAATT-TAAATTAAAA
1 ATTTTATT-ATTAAATTATAAATTAAAA
*
285346 ATTTTATTATTAAATTATAATTTAAA
1 ATTTTATTATTAAATTATAAATTAAA
285372 CTAATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTTTATTATTAAATTATAAATTAAAA
Found at i:285563 original size:2 final size:2
Alignment explanation
Indices: 285556--285590 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
285546 TGATGCTAAG
285556 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
285591 TCCATCGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:285710 original size:77 final size:77
Alignment explanation
Indices: 285601--285752 Score: 252
Period size: 77 Copynumber: 2.0 Consensus size: 77
285591 TCCATCGATG
* **
285601 ATTGAGGTTGAATGTATACTTCAGAAAAGAGGATGATGACAAGCACAAATATTTATATATATATA
1 ATTGAGGTTGAATATATACTTCAGAAAAGAGGATGATGACAAGCACAAATAAATATATATATATA
285666 TATATATATAAA
66 TATATATATAAA
*
285678 ATTGAGGTTGAATATATGCTTCA-AAAAGGAGGATGATGACAAGCACAAATAAATATATATATAT
1 ATTGAGGTTGAATATATACTTCAGAAAA-GAGGATGATGACAAGCACAAATAAATATATATATAT
285742 ATATATATATA
65 ATATATATATA
285753 TATATATATA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
76 4 0.06
77 66 0.94
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.32
Consensus pattern (77 bp):
ATTGAGGTTGAATATATACTTCAGAAAAGAGGATGATGACAAGCACAAATAAATATATATATATA
TATATATATAAA
Found at i:285737 original size:2 final size:2
Alignment explanation
Indices: 285730--285764 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
285720 GCACAAATAA
285730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
285765 ATTAATTGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:287270 original size:2 final size:2
Alignment explanation
Indices: 287265--287300 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
287255 GATGACAAGC
287265 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
287301 TCCATCGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:287799 original size:24 final size:24
Alignment explanation
Indices: 287763--287808 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
287753 ATAAGATTTT
* *
287763 ATTTTTTTTATTTTTTTTAAATTC
1 ATTTATTTGATTTTTTTTAAATTC
287787 ATTTATTTGATTTTTTTTAAAT
1 ATTTATTTGATTTTTTTTAAAT
287809 CAATTCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (24 bp):
ATTTATTTGATTTTTTTTAAATTC
Found at i:288710 original size:2 final size:2
Alignment explanation
Indices: 288705--288732 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
288695 GATGATAAGC
288705 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
288733 TCTATAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:288913 original size:19 final size:20
Alignment explanation
Indices: 288868--288914 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
288858 TGCTAACTAA
*
288868 TAAAATTTAAACAACCTAAT
1 TAAAATTTAAACAACATAAT
**
288888 T-TTATTTAAACAA-ATAAT
1 TAAAATTTAAACAACATAAT
288906 TAAAATTTA
1 TAAAATTTA
288915 TAAATACAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 3
0.72 0.17 0.10
Matches are distributed among these distances:
18 5 0.24
19 15 0.71
20 1 0.05
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAATTTAAACAACATAAT
Found at i:289680 original size:2 final size:2
Alignment explanation
Indices: 289673--289705 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
289663 CTAAAATAAC
289673 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
289706 ATCAAAACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:290740 original size:14 final size:13
Alignment explanation
Indices: 290683--290734 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
290673 TTAAGTCTTT
290683 AATATTAATA-TA
1 AATATTAATATTA
* *
290695 ATATTTTAGTATTA
1 A-ATATTAATATTA
*
290709 AATATTATTATTAA
1 AATATTAATATT-A
290723 AATATTAATATT
1 AATATTAATATT
290735 TTAATAAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 1 0.03
13 16 0.50
14 15 0.47
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (13 bp):
AATATTAATATTA
Found at i:290785 original size:26 final size:25
Alignment explanation
Indices: 290728--290792 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
290718 ATTAAAATAT
*
290728 TAATATTTTAATAAGAAATAGCTTTT
1 TAATATTTTAATAAGAAATA-CTTTA
*
290754 TAATATTTTAATAATAAATA-TTTAA
1 TAATATTTTAATAAGAAATACTTT-A
*
290779 TATATATGTTAATA
1 TA-ATATTTTAATA
290793 TTGCTCCATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.09
25 2 0.06
26 29 0.85
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (25 bp):
TAATATTTTAATAAGAAATACTTTA
Found at i:291013 original size:30 final size:30
Alignment explanation
Indices: 290977--291037 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
290967 GCTCAAGCAT
*
290977 ATATTCC-CTTTCTATTATAGATGGAATAAA
1 ATATTCCTC-TTCCATTATAGATGGAATAAA
*
291007 ATATTCCTCTTCCATTATATATGGAATAAA
1 ATATTCCTCTTCCATTATAGATGGAATAAA
291037 A
1 A
291038 GCTTGTCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (30 bp):
ATATTCCTCTTCCATTATAGATGGAATAAA
Found at i:292419 original size:39 final size:39
Alignment explanation
Indices: 292358--292438 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
292348 CTCCAACCAT
* *
292358 TCACTCCTCCACAAGATTAGCTCATCATCAATTGGAAAA
1 TCACTCCTCCACAAAATCAGCTCATCATCAATTGGAAAA
*
292397 TCACTCTTCCACAAAATCAGCTCATCATCAATTGGAAAA
1 TCACTCCTCCACAAAATCAGCTCATCATCAATTGGAAAA
292436 TCA
1 TCA
292439 TTGACTCCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.37, C:0.28, G:0.09, T:0.26
Consensus pattern (39 bp):
TCACTCCTCCACAAAATCAGCTCATCATCAATTGGAAAA
Found at i:295830 original size:20 final size:20
Alignment explanation
Indices: 295755--295832 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
295745 AAAAACCCAG
* *
295755 ATGTATCGATACAATGATAA
1 ATGTATCGATACATTTATAA
*
295775 ATGTATCGATACAATTTGA-AGC
1 ATGTATCGATAC-ATTT-ATA-A
* *
295797 ATGTATCCATACATTTATTA
1 ATGTATCGATACATTTATAA
295817 ATGTATCGATACATTT
1 ATGTATCGATACATTT
295833 CTTTGGCAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
20 28 0.60
21 7 0.15
22 12 0.26
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTTATAA
Found at i:300805 original size:23 final size:23
Alignment explanation
Indices: 300779--300844 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 23
300769 CCTCCACAAG
300779 ATCAGCTCATCATCAATTGGAAA
1 ATCAGCTCATCATCAATTGGAAA
* *
300802 ATCA-CTC--C-TCCA---CAAA
1 ATCAGCTCATCATCAATTGGAAA
300818 ATCAGCTCATCATCAATTGGAAA
1 ATCAGCTCATCATCAATTGGAAA
300841 ATCA
1 ATCA
300845 TTGACTCCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
16 7 0.22
17 3 0.09
19 4 0.12
20 4 0.12
22 3 0.09
23 11 0.34
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (23 bp):
ATCAGCTCATCATCAATTGGAAA
Found at i:300807 original size:39 final size:39
Alignment explanation
Indices: 300764--300844 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
300754 CTCCAGCCAT
*
300764 TCACTCCTCCACAAGATCAGCTCATCATCAATTGGAAAA
1 TCACTCCTCCACAAAATCAGCTCATCATCAATTGGAAAA
300803 TCACTCCTCCACAAAATCAGCTCATCATCAATTGGAAAA
1 TCACTCCTCCACAAAATCAGCTCATCATCAATTGGAAAA
300842 TCA
1 TCA
300845 TTGACTCCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.37, C:0.31, G:0.09, T:0.23
Consensus pattern (39 bp):
TCACTCCTCCACAAAATCAGCTCATCATCAATTGGAAAA
Found at i:305424 original size:12 final size:12
Alignment explanation
Indices: 305397--305429 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
305387 TGGATACCCT
305397 ATTATA-TTATA
1 ATTATATTTATA
*
305408 CTTATATTTATA
1 ATTATATTTATA
305420 ATTATATTTA
1 ATTATATTTA
305430 CATTTATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTATATTTATA
Found at i:305425 original size:18 final size:17
Alignment explanation
Indices: 305398--305441 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
305388 GGATACCCTA
*
305398 TTATATTATACTTATAT
1 TTATATTATACTTACAT
*
305415 TTATAATTATATTTACAT
1 TTAT-ATTATACTTACAT
305433 TTATGATTA
1 TTAT-ATTA
305442 GATGTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (17 bp):
TTATATTATACTTACAT
Found at i:308365 original size:18 final size:20
Alignment explanation
Indices: 308321--308373 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
308311 AATTTTAGTT
*
308321 TATTATTTA-TTTTTTACTC
1 TATTATTTATTTTTTTAATC
308340 TATT-TTTATTTTTTTAAT-
1 TATTATTTATTTTTTTAATC
308358 T-TTATTTATTTCTTTT
1 TATTATTTATTT-TTTT
308374 TCTGATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 2 0.07
18 12 0.40
19 16 0.53
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (20 bp):
TATTATTTATTTTTTTAATC
Found at i:309282 original size:37 final size:37
Alignment explanation
Indices: 309217--309306 Score: 110
Period size: 37 Copynumber: 2.5 Consensus size: 37
309207 TTGCCTACCC
* * * * *
309217 TACCCATTATCCA-ACCCATTTAATCATTCACTTAGA
1 TACCTATTATCCAGCCCCATTGAACCATTCACTTAAA
309253 TACCTATTATCCAGCCCCATTGAACCATTCACTTAAA
1 TACCTATTATCCAGCCCCATTGAACCATTCACTTAAA
* *
309290 TGCCTATTATTCAGCCC
1 TACCTATTATCCAGCCC
309307 TAATTTATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 12 0.26
37 34 0.74
ACGTcount: A:0.30, C:0.32, G:0.06, T:0.32
Consensus pattern (37 bp):
TACCTATTATCCAGCCCCATTGAACCATTCACTTAAA
Found at i:311224 original size:17 final size:17
Alignment explanation
Indices: 311175--311229 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
311165 ATAAATATCT
* *
311175 TAAAATCTATATAATTA
1 TAAAATTTATATAAATA
311192 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
311207 TAAAATTTATATAAATA
1 TAAAATTTATATAAATA
311224 TAAAAT
1 TAAAAT
311230 ATTTTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 3 0.09
15 6 0.19
16 6 0.19
17 14 0.44
18 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:311271 original size:15 final size:15
Alignment explanation
Indices: 311182--311271 Score: 60
Period size: 15 Copynumber: 5.9 Consensus size: 15
311172 TCTTAAAATC
* *
311182 TATATAATTATAAAT
1 TATATAAATATAAAA
311197 TAT-TAATATATAAAA
1 TATATAA-ATATAAAA
311212 TTTATATAAATATAAAA
1 --TATATAAATATAAAA
* * *
311229 TATTTTAAAT-TTAAC
1 TA-TATAAATATAAAA
*
311244 TATA-ATATGATAAAA
1 TATATAAAT-ATAAAA
311259 TATATAAATATAA
1 TATATAAATATAA
311272 CATAAATATA
Statistics
Matches: 57, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
13 3 0.05
14 4 0.07
15 27 0.47
16 9 0.16
17 11 0.19
18 3 0.05
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (15 bp):
TATATAAATATAAAA
Found at i:311272 original size:29 final size:29
Alignment explanation
Indices: 311216--311285 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
311206 ATAAAATTTA
* *
311216 TATAA-ATATAAAATATTTTAAATTTAAC
1 TATAATATATAAAATATTATAAATATAAC
311244 TATAATATGATAAAATA-TATAAATATAAC
1 TATAATAT-ATAAAATATTATAAATATAAC
311273 -ATAAATATATAAA
1 TAT-AATATATAAA
311286 TTATCAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 12 0.32
29 17 0.46
30 8 0.22
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (29 bp):
TATAATATATAAAATATTATAAATATAAC
Found at i:311813 original size:21 final size:21
Alignment explanation
Indices: 311789--311828 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
311779 AATTAAAAAT
311789 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
311810 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
311829 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:314921 original size:14 final size:14
Alignment explanation
Indices: 314902--314928 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
314892 AACAAGCAAA
314902 CAATAAAAGAAAAT
1 CAATAAAAGAAAAT
314916 CAATAAAAGAAAA
1 CAATAAAAGAAAA
314929 AAGATGGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.11
Consensus pattern (14 bp):
CAATAAAAGAAAAT
Found at i:319043 original size:17 final size:16
Alignment explanation
Indices: 318979--319055 Score: 91
Period size: 16 Copynumber: 4.7 Consensus size: 16
318969 TAATCAAATA
*
318979 TAAAATAATTTGATTT
1 TAAAATAATTTAATTT
*
318995 TAAAATAATTTAAATT
1 TAAAATAATTTAATTT
* *
319011 TGAAATGATTTAAATTT
1 TAAAATAATTT-AATTT
319028 TAAAATAATCTTAATTT
1 TAAAATAAT-TTAATTT
*
319045 AAAAATAATTT
1 TAAAATAATTT
319056 TTTTTTTCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
16 25 0.49
17 24 0.47
18 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (16 bp):
TAAAATAATTTAATTT
Found at i:319751 original size:20 final size:19
Alignment explanation
Indices: 319714--319777 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
319704 TTAATTATTT
*
319714 ATTATATTTAAT-ATTAAA
1 ATTATTTTTAATAATTAAA
319732 ATTATTTTTAAATAATTAAA
1 ATTATTTTT-AATAATTAAA
* *
319752 ATTTTATTTTAATAAAT-AA
1 ATTAT-TTTTAATAATTAAA
319771 ATTATTT
1 ATTATTT
319778 CAACATATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 10 0.26
19 9 0.23
20 16 0.41
21 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTATTTTTAATAATTAAA
Found at i:322985 original size:2 final size:2
Alignment explanation
Indices: 322980--323024 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
322970 ATATATATAT
*
322980 AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
323022 AG A
1 AG A
323025 ATGATTGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:323968 original size:2 final size:2
Alignment explanation
Indices: 323961--323985 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
323951 ATATTTTAAC
323961 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
323986 TCAGATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:324273 original size:16 final size:17
Alignment explanation
Indices: 324203--324273 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 17
324193 TATAAGACAG
*
324203 TTTGAATTTGAAAA-AG
1 TTTGAATTTGAAAATAA
* * *
324219 GTT-AAATTGAAAATTA
1 TTTGAATTTGAAAATAA
*
324235 TTTGAATTT-AAAATGA
1 TTTGAATTTGAAAATAA
**
324251 TACGAATTTGAAAA-AA
1 TTTGAATTTGAAAATAA
324267 TTTGAAT
1 TTTGAAT
324274 CTAATATGAT
Statistics
Matches: 40, Mismatches: 12, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
15 9 0.22
16 23 0.57
17 8 0.20
ACGTcount: A:0.46, C:0.01, G:0.14, T:0.38
Consensus pattern (17 bp):
TTTGAATTTGAAAATAA
Found at i:325383 original size:32 final size:32
Alignment explanation
Indices: 325346--325409 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
325336 AAATTAAATG
325346 ATATATTTAGGTTTAAATTAAATGTTACGAGC
1 ATATATTTAGGTTTAAATTAAATGTTACGAGC
*
325378 ATATATTTAGGTTTAAATTAAATGTTAGGAGC
1 ATATATTTAGGTTTAAATTAAATGTTACGAGC
325410 TTTCTTAGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.41
Consensus pattern (32 bp):
ATATATTTAGGTTTAAATTAAATGTTACGAGC
Found at i:325720 original size:13 final size:13
Alignment explanation
Indices: 325698--325757 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 13
325688 TTGGGCTTAA
*
325698 ATATTAAAATAAT
1 ATATTTAAATAAT
*
325711 ATATTTAAATTAT
1 ATATTTAAATAAT
** *
325724 A-AAATATATAA-
1 ATATTTAAATAAT
*
325735 ATATTAAAATAAT
1 ATATTTAAATAAT
325748 ATATTTAAAT
1 ATATTTAAAT
325758 TTAAATTTAA
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
11 1 0.03
12 12 0.35
13 21 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATTTAAATAAT
Found at i:325720 original size:21 final size:21
Alignment explanation
Indices: 325694--325762 Score: 87
Period size: 18 Copynumber: 3.6 Consensus size: 21
325684 TGTTTTGGGC
325694 TTAAATATTAAAATAATATAT
1 TTAAATATTAAAATAATATAT
*
325715 TT-AA-ATTATAA-AATATA-
1 TTAAATATTAAAATAATATAT
325732 -TAAATATTAAAATAATATAT
1 TTAAATATTAAAATAATATAT
325752 TTAAAT-TTAAA
1 TTAAATATTAAA
325763 TTTAATTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
16 1 0.02
17 2 0.05
18 12 0.29
19 12 0.29
20 7 0.17
21 7 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAATATTAAAATAATATAT
Found at i:325730 original size:16 final size:15
Alignment explanation
Indices: 325695--325786 Score: 54
Period size: 14 Copynumber: 6.5 Consensus size: 15
325685 GTTTTGGGCT
325695 TAAATATTAAAATA-A
1 TAAATA-TAAAATATA
* * *
325710 TATATTTAAATTATA
1 TAAATATAAAATATA
325725 -AAATATATAAATAT-
1 TAAATATA-AAATATA
* *
325739 TAAA-ATAATATATT
1 TAAATATAAAATATA
*
325753 TAAAT-TTAAAT-T-
1 TAAATATAAAATATA
*
325765 TAATTATAAAATATA
1 TAAATATAAAATATA
325780 TAAATAT
1 TAAATAT
325787 TAACATAAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
12 4 0.07
13 11 0.19
14 23 0.40
15 19 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAATATAAAATATA
Found at i:325768 original size:21 final size:21
Alignment explanation
Indices: 325694--325776 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
325684 TGTTTTGGGC
* *
325694 TTAAATATTAAAATA-ATATAT
1 TTAAAT-TTAATATATATAAAT
*
325715 TTAAATTATAAAATATATAAAT
1 TTAAATT-TAATATATATAAAT
* *
325737 ATTAAA-ATAATATATTTAAAT
1 -TTAAATTTAATATATATAAAT
325758 TTAAATTTAAT-TATA-AAAT
1 TTAAATTTAATATATATAAAT
325777 ATATAAATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
19 4 0.08
20 9 0.17
21 29 0.56
22 5 0.10
23 5 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAATTTAATATATATAAAT
Found at i:326617 original size:12 final size:13
Alignment explanation
Indices: 326594--326627 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
326584 TCATGGGAGT
326594 ATTTTTATAAATA
1 ATTTTTATAAATA
326607 ATTTTTA-AAATA
1 ATTTTTATAAATA
*
326619 TTTTTTATA
1 ATTTTTATA
326628 TCTTAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTTATAAATA
Found at i:327300 original size:15 final size:15
Alignment explanation
Indices: 327280--327333 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
327270 CAATCGTATC
327280 ATAAAAATAATATAA
1 ATAAAAATAATATAA
327295 ATAAAAA-ATATATAAA
1 ATAAAAATA-ATAT-AA
*
327311 ATAAAAATAAATAAAA
1 ATAAAAAT-AATATAA
327327 ATAAAAA
1 ATAAAAA
327334 AATTACCACG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 1 0.03
15 11 0.32
16 18 0.53
17 3 0.09
18 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
ATAAAAATAATATAA
Found at i:327303 original size:16 final size:16
Alignment explanation
Indices: 327282--327334 Score: 65
Period size: 15 Copynumber: 3.3 Consensus size: 16
327272 ATCGTATCAT
327282 AAAAATAATATAAATA
1 AAAAATAATATAAATA
327298 AAAAAT-ATATAAA-A
1 AAAAATAATATAAATA
*
327312 TAAAAATAAATAAAAATA
1 -AAAAAT-AATATAAATA
327330 AAAAA
1 AAAAA
327335 ATTACCACGT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.03
15 13 0.41
16 6 0.19
17 11 0.34
18 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATAATATAAATA
Found at i:327917 original size:2 final size:2
Alignment explanation
Indices: 327910--327939 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
327900 TTTATTTCCT
327910 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
327940 CTTCAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:334342 original size:23 final size:24
Alignment explanation
Indices: 334316--334363 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
334306 AACACATAAT
334316 AAAAATAAA-TT-TTATATTAAATA
1 AAAAATAAATTTATTAT-TTAAATA
334339 AAAAATAAATTTATTATTTAAATA
1 AAAAATAAATTTATTATTTAAATA
334363 A
1 A
334364 TAATTTACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.39
24 10 0.43
25 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAAATAAATTTATTATTTAAATA
Found at i:334359 original size:24 final size:23
Alignment explanation
Indices: 334316--334363 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 23
334306 AACACATAAT
334316 AAAAATAAATTTTATATTAAATA
1 AAAAATAAATTTTATATTAAATA
334339 AAAAATAAA-TTTATTATTTAAATA
1 AAAAATAAATTTTA-TA-TTAAATA
334363 A
1 A
334364 TAATTTACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.17
23 11 0.48
24 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAAATAAATTTTATATTAAATA
Found at i:335047 original size:25 final size:25
Alignment explanation
Indices: 335009--335056 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
334999 TTGGACATGA
*
335009 TAAATATATGATAAGAAAAAAATAAT
1 TAAATATATAATAA-AAAAAAATAAT
*
335035 TAAA-ATATAATAAAAAATAATA
1 TAAATATATAATAAAAAAAAATA
335057 CGATATAAAT
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:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (25 bp):
TAAATATATAATAAAAAAAAATAAT
Found at i:335468 original size:18 final size:18
Alignment explanation
Indices: 335431--335465 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
335421 ATATTTTAAA
*
335431 ATTAATATAATATAAATT
1 ATTAATATAATAAAAATT
335449 ATTAATA-AATAAAAATT
1 ATTAATATAATAAAAATT
335466 TATCTGTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTAATATAATAAAAATT
Found at i:336760 original size:3 final size:3
Alignment explanation
Indices: 336747--336782 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
336737 CTTCTTCTTT
*
336747 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
336783 ATTTTTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:338385 original size:219 final size:219
Alignment explanation
Indices: 337798--338475 Score: 842
Period size: 219 Copynumber: 3.1 Consensus size: 219
337788 TTTTTATATA
* * *
337798 TATTTAGATTTAGGACTTTTTACAATGAGTTCAAAGAAAACGAGCTCCGTGGTTGTATTAAATGG
1 TATTTAGATGTAGGACTTTTTACTATGAGTTCAAAGAAAACGAGCTCCGTGGTTGTATGAAATGG
** * * * * * *
337863 TTATTTCCATGGACTTTGATACTCTTCATACTGTTTTGACTTGGATTGACTCAATTGCGCTCTTG
66 TTATTTTGATGGAATTTGATACTCTTCGTATTGTTTTGACTTGGATTGACTTAATTGTGCACTTG
* * * * * * * * *
337928 CATAGGCTTTGCGTCAAGCTTCGTTATCGATATCAGTGTTATTGCTATGAATCAAAACCCGGAAA
131 TATAGGCTCTGCTTTAAGCTTCGTTATTGATAACAGTATTATTGCTATGCATCAAAACCTGGAAA
* *
337993 CCTGCAAGT-TCAGTGTATTTTTCT
196 CCTGCAAGTCT-AGGGTTTTTTTCT
* *** ** *
338017 TATTGAGATGTAGGAGGCTTTGGTATGAGTTCAAAGAAAACGAGCTCCGTGGTTTCTATGAAATG
1 TATTTAGATGTAGGACTTTTTACTATGAGTTCAAAGAAAACGAGCTCCGTGG-TTGTATGAAATG
* * *
338082 GCTATTTTGAT-GAATTTTGATACTCCTCGTATTGTTTTGACTTGGATTGA-TTCACTTGTGCAC
65 GTTATTTTGATGGAA-TTTGATACTCTTCGTATTGTTTTGACTTGGATTGACTT-AATTGTGCAC
* * * * *
338145 TTGTATATGCTCTGCTTTAAGCTTCGTTATTGACAAAATTATTATTGCTATGCGTCAAAACCTGG
128 TTGTATAGGCTCTGCTTTAAGCTTCGTTATTGATAACAGTATTATTGCTATGCATCAAAACCTGG
* *
338210 ATACATGCAAGTCTAGGGTTTTTTTCT
193 AAACCTGCAAGTCTAGGGTTTTTTTCT
* * *
338237 TATTTA-ATTGTAGGACTTTTTACTATGAGTTCAACGAAAAAGAGCTCCATGGTTGTATGAAATG
1 TATTTAGA-TGTAGGACTTTTTACTATGAGTTCAAAGAAAACGAGCTCCGTGGTTGTATGAAATG
* * * *
338301 GTTATTTTGATGGAATCTGATACTCTTCGTATTCTTTTGACTTGTATCGACTTAATTGTGCACTT
65 GTTATTTTGATGGAATTTGATACTCTTCGTATTGTTTTGACTTGGATTGACTTAATTGTGCACTT
* *
338366 GTATAGGCTCTGCTTTAAGCTTCGTTATTGATAACGGTATTATTGCTATGCCTCAAAACCTGGAA
130 GTATAGGCTCTGCTTTAAGCTTCGTTATTGATAACAGTATTATTGCTATGCATCAAAACCTGGAA
*
338431 ACCTGCAAGTCTAGGGTTTTCTTCT
195 ACCTGCAAGTCTAGGGTTTTTTTCT
338456 TATTTAGATGTAGGACTTTT
1 TATTTAGATGTAGGACTTTT
338476 ATGAGTTCAA
Statistics
Matches: 386, Mismatches: 65, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
219 209 0.54
220 176 0.46
221 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (219 bp):
TATTTAGATGTAGGACTTTTTACTATGAGTTCAAAGAAAACGAGCTCCGTGGTTGTATGAAATGG
TTATTTTGATGGAATTTGATACTCTTCGTATTGTTTTGACTTGGATTGACTTAATTGTGCACTTG
TATAGGCTCTGCTTTAAGCTTCGTTATTGATAACAGTATTATTGCTATGCATCAAAACCTGGAAA
CCTGCAAGTCTAGGGTTTTTTTCT
Found at i:340648 original size:30 final size:30
Alignment explanation
Indices: 340612--340671 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
340602 TTTTTAATAC
340612 ATTCAAATAAA-TATTAATTTTTAAATTTTT
1 ATTCAAATAAATTATTAATTTTT-AATTTTT
*
340642 ATTCAAATAAATTTTTAATTTTTAATTTTT
1 ATTCAAATAAATTATTAATTTTTAATTTTT
340672 GAATTATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
ATTCAAATAAATTATTAATTTTTAATTTTT
Found at i:342209 original size:15 final size:14
Alignment explanation
Indices: 342169--342202 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
342159 ATATTCAATC
*
342169 TTAAATAATTTTTA
1 TTAATTAATTTTTA
342183 TTAATTAATTTTTA
1 TTAATTAATTTTTA
342197 -TAATTA
1 TTAATTA
342203 GAATTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAATTAATTTTTA
Found at i:344832 original size:23 final size:24
Alignment explanation
Indices: 344788--344835 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
344778 ATCTGTTGCT
*
344788 TTTATTTTTTTGGGGAATTTTATTTA
1 TTTATTTTTTT--GGAAATTTATTTA
344814 TTTATTTTTTT-GAAATTTATTT
1 TTTATTTTTTTGGAAATTTATTT
344836 GACTGAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
26 11 0.52
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (24 bp):
TTTATTTTTTTGGAAATTTATTTA
Found at i:345990 original size:14 final size:14
Alignment explanation
Indices: 345971--345999 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
345961 CCACTTTTTG
345971 TGTAAAATTGATTA
1 TGTAAAATTGATTA
345985 TGTAAAATTGATTA
1 TGTAAAATTGATTA
345999 T
1 T
346000 ATGAAACTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (14 bp):
TGTAAAATTGATTA
Found at i:351749 original size:12 final size:12
Alignment explanation
Indices: 351732--351763 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
351722 ACAGAAAATT
351732 AATTAATTAATC
1 AATTAATTAATC
*
351744 AATTAATCAATC
1 AATTAATTAATC
351756 AATTAATT
1 AATTAATT
351764 CAATTGTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (12 bp):
AATTAATTAATC
Found at i:352585 original size:2 final size:2
Alignment explanation
Indices: 352578--352606 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
352568 TCTTTTTCAA
352578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
352607 AGTCAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:353132 original size:13 final size:13
Alignment explanation
Indices: 353114--353138 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
353104 AAAATTACTT
353114 TTATTTTTAATTA
1 TTATTTTTAATTA
353127 TTATTTTTAATT
1 TTATTTTTAATT
353139 TTTTTTGTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTTTAATTA
Found at i:353848 original size:14 final size:14
Alignment explanation
Indices: 353824--353861 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
353814 AATAAAATTA
353824 TTAAT-TAATATAT
1 TTAATATAATATAT
*
353837 TTAATATAATATTT
1 TTAATATAATATAT
*
353851 TTAATAAAATA
1 TTAATATAATA
353862 ATATATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAATATAATATAT
Found at i:354910 original size:2 final size:2
Alignment explanation
Indices: 354903--354937 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
354893 AAATAGGAGA
354903 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
354938 GTACAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:355913 original size:2 final size:2
Alignment explanation
Indices: 355906--355949 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
355896 CTTGAAATGA
* *
355906 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
355948 AT
1 AT
355950 GGAGCTTGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:361086 original size:17 final size:17
Alignment explanation
Indices: 361047--361087 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
361037 AATTAAATTT
**
361047 AAAAATATTAAAAGATC
1 AAAAATATTAAAAGAAA
*
361064 ATAAATATTAAAAGAAA
1 AAAAATATTAAAAGAAA
361081 AAAAATA
1 AAAAATA
361088 GTGGGATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (17 bp):
AAAAATATTAAAAGAAA
Found at i:362457 original size:16 final size:17
Alignment explanation
Indices: 362436--362469 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
362426 TTATTTAAAA
362436 TATATTAAAATTT-TAT
1 TATATTAAAATTTATAT
*
362452 TATATTAATATTTATAT
1 TATATTAAAATTTATAT
362469 T
1 T
362470 TTTCATAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATTAAAATTTATAT
Found at i:362910 original size:26 final size:26
Alignment explanation
Indices: 362881--362932 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
362871 TAGTTGAAAC
362881 TGACTAGGCAGCAATGTTGCAGAAGT
1 TGACTAGGCAGCAATGTTGCAGAAGT
362907 TGACTAGGCAGCAATGTTGCAGAAGT
1 TGACTAGGCAGCAATGTTGCAGAAGT
362933 GAATCGGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (26 bp):
TGACTAGGCAGCAATGTTGCAGAAGT
Found at i:370354 original size:18 final size:17
Alignment explanation
Indices: 370331--370365 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
370321 TATAAAGTTG
370331 ATTACAAAAAGTAACAAA
1 ATTACAAAAAGT-ACAAA
370349 ATTACAAAAAGTACAAA
1 ATTACAAAAAGTACAAA
370366 TTATTCATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (17 bp):
ATTACAAAAAGTACAAA
Found at i:376548 original size:16 final size:16
Alignment explanation
Indices: 376529--376577 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
376519 GGACTCGGAC
376529 CATTTTGAGTTTGAGT
1 CATTTTGAGTTTGAGT
* * * *
376545 CATTTTAAATTCGAAT
1 CATTTTGAGTTTGAGT
376561 CATTTTTGAGTTTGAGT
1 CA-TTTTGAGTTTGAGT
376578 TAGTCAATTT
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.49
Consensus pattern (16 bp):
CATTTTGAGTTTGAGT
Done.