Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 8 of 325
Found at i:2263134 original size:17 final size:18
Alignment explanation
Indices: 2263085--2263134 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 18
2263075 TGTTATTGTG
*
2263085 AAATTATATTAAAATTTAA
1 AAATTATATTTAAA-TTAA
*
2263104 AAATTA-AATT-AATT-A
1 AAATTATATTTAAATTAA
2263119 AAATTATATTTAAATT
1 AAATTATATTTAAATT
2263135 CATTAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
15 7 0.27
16 5 0.19
17 6 0.23
18 2 0.08
19 6 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTATATTTAAATTAA
Found at i:2264430 original size:9 final size:9
Alignment explanation
Indices: 2264416--2264464 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
2264406 AAAACTTGTC
2264416 TTTAATAAT
1 TTTAATAAT
2264425 TTTAATAATT
1 TTTAATAA-T
*
2264435 TTTAATTAT
1 TTTAATAAT
*
2264444 TGATAAT-AT
1 T-TTAATAAT
2264453 TTTAATAAT
1 TTTAATAAT
2264462 TTT
1 TTT
2264465 TTTCATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 4 0.12
9 18 0.53
10 12 0.35
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (9 bp):
TTTAATAAT
Found at i:2265503 original size:13 final size:13
Alignment explanation
Indices: 2265460--2265504 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
2265450 TAATAATATA
* *
2265460 TTAATTGATCATT
1 TTAATTTATAATT
* *
2265473 TTAAATTATTATT
1 TTAATTTATAATT
2265486 TTAATTTATAATT
1 TTAATTTATAATT
2265499 TTAATT
1 TTAATT
2265505 GAAATTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (13 bp):
TTAATTTATAATT
Found at i:2268149 original size:69 final size:70
Alignment explanation
Indices: 2268069--2268209 Score: 239
Period size: 69 Copynumber: 2.0 Consensus size: 70
2268059 AATTTTACCC
* *
2268069 AAGCCCGACCCGAATAAAAATGTTAAAACCCAAAGTAGCAACATAATAGTAAAATAGTAGCAAAA
1 AAGCCCAACCCGAATAAAAATGTTAAAACCCAAAGTAACAACATAATAGTAAAATAGTAGCAAAA
2268134 -AAAA
66 TAAAA
* *
2268138 AAGCCCAACCCGAATAAAAATGTTAAAACCTAAAGTAATAACATAATAGTAAAATAGTAGCAAAA
1 AAGCCCAACCCGAATAAAAATGTTAAAACCCAAAGTAACAACATAATAGTAAAATAGTAGCAAAA
2268203 TAAAA
66 TAAAA
2268208 AA
1 AA
2268210 AAAACAATAA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 61 0.91
70 6 0.09
ACGTcount: A:0.57, C:0.16, G:0.11, T:0.16
Consensus pattern (70 bp):
AAGCCCAACCCGAATAAAAATGTTAAAACCCAAAGTAACAACATAATAGTAAAATAGTAGCAAAA
TAAAA
Found at i:2281733 original size:21 final size:21
Alignment explanation
Indices: 2281709--2281772 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2281699 GTCTTCGTCA
*
2281709 TGTTCCAAGGATGCATAATAG
1 TGTTCCAAGGATGTATAATAG
* *
2281730 TGTTGC-A-GAT-TAT-ATGG
1 TGTTCCAAGGATGTATAATAG
2281747 TTGTTCCAAGGATGTATAATAG
1 -TGTTCCAAGGATGTATAATAG
2281769 TGTT
1 TGTT
2281773 GCAGGTTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 3 0.09
18 7 0.21
19 4 0.12
20 4 0.12
21 12 0.36
22 3 0.09
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (21 bp):
TGTTCCAAGGATGTATAATAG
Found at i:2281766 original size:39 final size:39
Alignment explanation
Indices: 2281709--2281787 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
2281699 GTCTTCGTCA
2281709 TGTTCCAAGGATGCATAATAGTGTTGCAGATTATATGGT
1 TGTTCCAAGGATGCATAATAGTGTTGCAGATTATATGGT
* *
2281748 TGTTCCAAGGATGTATAATAGTGTTGCAGGTTATATGGT
1 TGTTCCAAGGATGCATAATAGTGTTGCAGATTATATGGT
2281787 T
1 T
2281788 AAGTATGTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.38
Consensus pattern (39 bp):
TGTTCCAAGGATGCATAATAGTGTTGCAGATTATATGGT
Found at i:2282917 original size:10 final size:10
Alignment explanation
Indices: 2282904--2282987 Score: 52
Period size: 10 Copynumber: 8.6 Consensus size: 10
2282894 ATTGTTAAAA
2282904 ATAAAATATT
1 ATAAAATATT
2282914 ATAAAAT-TT
1 ATAAAATATT
* *
2282923 CTACTAA-ATT
1 ATA-AAATATT
2282933 ATAAAA-ATTT
1 ATAAAATA-TT
*
2282943 ATAAAAT-TA
1 ATAAAATATT
2282952 ATAAAATATAT
1 ATAAAATAT-T
* * *
2282963 TTAAAAAAAT
1 ATAAAATATT
2282973 -TAAAATATT
1 ATAAAATATT
2282982 ATAAAA
1 ATAAAA
2282988 ACATATTAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
9 22 0.39
10 28 0.50
11 6 0.11
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (10 bp):
ATAAAATATT
Found at i:2282997 original size:21 final size:22
Alignment explanation
Indices: 2282953--2283014 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
2282943 ATAAAATTAA
*
2282953 TAAAATATATTTAAAAA-A-AT
1 TAAAATATATATAAAAACATAT
2282973 TAAAATAT-TATAAAAACATAT
1 TAAAATATATATAAAAACATAT
*
2282994 TAAAAT-TCTATAAAAATCATA
1 TAAAATATATATAAAAA-CATA
2283015 AAAAATGTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 7 0.19
20 10 0.27
21 16 0.43
22 4 0.11
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAAATATATATAAAAACATAT
Found at i:2283019 original size:21 final size:21
Alignment explanation
Indices: 2282981--2283020 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2282971 ATTAAAATAT
*
2282981 TATAAAAACATATTAAAATTC
1 TATAAAAACATATAAAAATTC
2283002 TATAAAAATCATA-AAAAAT
1 TATAAAAA-CATATAAAAAT
2283021 GTAAAACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
TATAAAAACATATAAAAATTC
Found at i:2283543 original size:21 final size:20
Alignment explanation
Indices: 2283517--2283559 Score: 77
Period size: 21 Copynumber: 2.1 Consensus size: 20
2283507 TTATATCAAA
2283517 TTTATAAGTTTTTCAATATTT
1 TTTATAAGTTTTTCAA-ATTT
2283538 TTTATAAGTTTTTCAAATTT
1 TTTATAAGTTTTTCAAATTT
2283558 TT
1 TT
2283560 ATTATCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTATAAGTTTTTCAAATTT
Found at i:2284551 original size:19 final size:20
Alignment explanation
Indices: 2284502--2284553 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
2284492 CAAGCAAGAT
*
2284502 TTTTTTTA-AATACAAATAA
1 TTTTTTTATAATTCAAATAA
*
2284521 TTTTTTAGATAATTC-AATAA
1 TTTTTT-TATAATTCAAATAA
2284541 TTTTTTTATAATT
1 TTTTTTTATAATT
2284554 TTTTTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 12 0.43
20 12 0.43
21 4 0.14
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTTTATAATTCAAATAA
Found at i:2291020 original size:33 final size:33
Alignment explanation
Indices: 2290983--2291048 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
2290973 TCCTACACGA
*
2290983 ATGGTGGATTAAAATGTCAAATTCTTCTATTTT
1 ATGGTGGATTAAAATGTCAAATTCTTCCATTTT
2291016 ATGGTGGATTAAAATGTCAAATTCTTCCATTTT
1 ATGGTGGATTAAAATGTCAAATTCTTCCATTTT
2291049 TTAAATTGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (33 bp):
ATGGTGGATTAAAATGTCAAATTCTTCCATTTT
Found at i:2305637 original size:20 final size:21
Alignment explanation
Indices: 2305614--2305653 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2305604 TAAGCGGGAA
2305614 TCAAA-TTTTATTATTTTAAT
1 TCAAATTTTTATTATTTTAAT
2305634 TCAAATTTTTATTATTTTAA
1 TCAAATTTTTATTATTTTAA
2305654 AGAATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TCAAATTTTTATTATTTTAAT
Found at i:2310534 original size:18 final size:19
Alignment explanation
Indices: 2310511--2310550 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2310501 ATTATAAAGG
2310511 AAATTTAT-AAAATCATTA
1 AAATTTATAAAAATCATTA
*
2310529 AAATTTATAAAAATTATTA
1 AAATTTATAAAAATCATTA
2310548 AAA
1 AAA
2310551 ACATATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTTATAAAAATCATTA
Found at i:2312838 original size:13 final size:13
Alignment explanation
Indices: 2312817--2312858 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
2312807 GATTTTAAAT
*
2312817 AAAATTTAAATAG
1 AAAAATTAAATAG
2312830 AAAAATT-AATAG
1 AAAAATTAAATAG
2312842 AAAAATATAAATA-
1 AAAAAT-TAAATAG
2312855 AAAA
1 AAAA
2312859 TTTGTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 11 0.42
13 11 0.42
14 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (13 bp):
AAAAATTAAATAG
Found at i:2313328 original size:53 final size:53
Alignment explanation
Indices: 2313258--2313380 Score: 210
Period size: 53 Copynumber: 2.3 Consensus size: 53
2313248 ATTTTAATAT
* *
2313258 TTTTTTCAATTTGATACCTGAGTTAGACATTAATGTTTGTTTTAGTATGTAAA
1 TTTTTTAAATTTTATACCTGAGTTAGACATTAATGTTTGTTTTAGTATGTAAA
* *
2313311 TTTTTTAAATTTTATACCTGAGTTAGACATTAATGTTTTTTTTAGTATGTAAG
1 TTTTTTAAATTTTATACCTGAGTTAGACATTAATGTTTGTTTTAGTATGTAAA
2313364 TTTTTTAAATTTTATAC
1 TTTTTTAAATTTTATAC
2313381 TTGAATTTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 66 1.00
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (53 bp):
TTTTTTAAATTTTATACCTGAGTTAGACATTAATGTTTGTTTTAGTATGTAAA
Found at i:2314959 original size:19 final size:19
Alignment explanation
Indices: 2314910--2314947 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2314900 AAATATTCAC
2314910 ATGATTAAAAAAATTAAAG
1 ATGATTAAAAAAATTAAAG
*
2314929 ATGAATAGAAAAAATTAAA
1 ATGATTA-AAAAAATTAAA
2314948 TTGACTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (19 bp):
ATGATTAAAAAAATTAAAG
Found at i:2316447 original size:6 final size:6
Alignment explanation
Indices: 2316436--2316461 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2316426 TAAAGATTTC
2316436 GCCTTT GCCTTT GCCTTT GCCTTT GC
1 GCCTTT GCCTTT GCCTTT GCCTTT GC
2316462 TTGTTTGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.19, T:0.46
Consensus pattern (6 bp):
GCCTTT
Found at i:2318883 original size:24 final size:25
Alignment explanation
Indices: 2318848--2318894 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2318838 AAGTCAAATA
2318848 TAATCTTATAAGA-TATTATCCCCT
1 TAATCTTATAAGATTATTATCCCCT
* *
2318872 TAATCTTCTAAGATTATTTTCCC
1 TAATCTTATAAGATTATTATCCC
2318895 TATTTACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (25 bp):
TAATCTTATAAGATTATTATCCCCT
Found at i:2325459 original size:22 final size:19
Alignment explanation
Indices: 2325437--2325483 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
2325427 TTAAAAATAT
2325437 TATTTTTATACTTTTTAATTA
1 TATTTTTATA--TTTTAATTA
*
2325458 T-TTTTTATATTTTATTTAA
1 TATTTTTATATTTTAATT-A
2325477 TATTTTT
1 TATTTTT
2325484 TTGAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 7 0.30
19 2 0.09
20 13 0.57
21 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTTTTATATTTTAATTA
Found at i:2325484 original size:22 final size:20
Alignment explanation
Indices: 2325432--2325485 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
2325422 AAAGCTTAAA
2325432 AATATTATTTTTATACTTTTT
1 AATATT-TTTTTATACTTTTT
*
2325453 AAT-TATTTTTTATATTTTATTT
1 AATAT-TTTTTTATA-CTT-TTT
2325475 AATATTTTTTT
1 AATATTTTTTT
2325486 GAAATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 9 0.32
21 6 0.21
22 12 0.43
23 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
AATATTTTTTTATACTTTTT
Found at i:2326380 original size:10 final size:9
Alignment explanation
Indices: 2326358--2326426 Score: 77
Period size: 10 Copynumber: 7.2 Consensus size: 9
2326348 AAACGATTAT
*
2326358 AAATAAAAA
1 AAATATAAA
2326367 AAATATAGAA
1 AAATATA-AA
2326377 AAATATATTAA
1 AAATATA--AA
2326388 AAATATATAA
1 AAATATA-AA
2326398 AAATA-AAA
1 AAATATAAA
2326406 AAATGATAAA
1 AAAT-ATAAA
2326416 AAATATAAA
1 AAATATAAA
2326425 AA
1 AA
2326427 TTACTAAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
8 6 0.11
9 15 0.28
10 24 0.44
11 9 0.17
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (9 bp):
AAATATAAA
Found at i:2326389 original size:40 final size:39
Alignment explanation
Indices: 2326345--2326422 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
2326335 ATTTTTCCCA
*
2326345 TAAAAACGAT-TATAAATAAAAAAAAT-ATAGAAAAATATAT
1 TAAAAA-GATATAAAAAT-AAAAAAATGATA-AAAAATATAT
*
2326385 TAAAAATATATAAAAATAAAAAAATGATAAAAAATATA
1 TAAAAAGATATAAAAATAAAAAAATGATAAAAAATATA
2326423 AAAATTACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 19 0.56
40 15 0.44
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (39 bp):
TAAAAAGATATAAAAATAAAAAAATGATAAAAAATATAT
Found at i:2326434 original size:10 final size:9
Alignment explanation
Indices: 2326365--2326570 Score: 91
Period size: 10 Copynumber: 21.6 Consensus size: 9
2326355 TATAAATAAA
*
2326365 AAAAATATAG
1 AAAAAT-TAT
2326375 AAAAATATATT
1 AAAAAT-TA-T
2326386 AAAAATATAT
1 AAAAAT-TAT
*
2326396 AAAAA-TAA
1 AAAAATTAT
*
2326404 AAAAATGAT
1 AAAAATTAT
*
2326413 AAAAAATAT
1 AAAAATTAT
2326422 AAAAATTACT
1 AAAAATTA-T
* *
2326432 AAATATTAG
1 AAAAATTAT
2326441 AAAATATTA-
1 AAAA-ATTAT
2326450 AAAAA--AT
1 AAAAATTAT
* *
2326457 GAAAACTAAT
1 -AAAAATTAT
* *
2326467 ATCAACTTAT
1 A-AAAATTAT
2326477 AAAAATTAT
1 AAAAATTAT
2326486 AAAAAATTTAT
1 -AAAAA-TTAT
2326497 AAAGAATTAT
1 AAA-AATTAT
*
2326507 AAATATTAT
1 AAAAATTAT
2326516 AAAACATCTA-
1 AAAA-AT-TAT
* *
2326526 ATAAATTCT
1 AAAAATTAT
2326535 AATAAATTATT
1 AA-AAATTA-T
2326546 AAGAAAATTAT
1 -A-AAAATTAT
2326557 -AAAATTAAT
1 AAAAATT-AT
2326566 AAAAA
1 AAAAA
2326571 CATATTAAAT
Statistics
Matches: 154, Mismatches: 21, Indels: 42
0.71 0.10 0.19
Matches are distributed among these distances:
6 1 0.01
8 19 0.12
9 42 0.27
10 65 0.42
11 19 0.12
12 7 0.05
13 1 0.01
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:2326435 original size:26 final size:26
Alignment explanation
Indices: 2326375--2326453 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
2326365 AAAAATATAG
*
2326375 AAAAATATATTAAAAATATATAAAAAT
1 AAAAAAATATTAAAAA-ATATAAAAAT
2326402 AAAAAAATGA-TAAAAAATATAAAAAT
1 AAAAAAAT-ATTAAAAAATATAAAAAT
* ** *
2326428 TACTAAATATTAGAAAATATTAAAAA
1 AAAAAAATATTAAAAAATA-TAAAAA
2326454 AATGAAAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
25 1 0.02
26 23 0.52
27 19 0.43
28 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.27
Consensus pattern (26 bp):
AAAAAAATATTAAAAAATATAAAAAT
Found at i:2327092 original size:9 final size:10
Alignment explanation
Indices: 2327071--2327128 Score: 64
Period size: 10 Copynumber: 5.6 Consensus size: 10
2327061 TTTATATCAA
2327071 TTTTAATATT
1 TTTTAATATT
2327081 TTTTAATATT
1 TTTTAATATT
*
2327091 TTTTTATAATT
1 TTTTAAT-ATT
2327102 TTTTACA-ATT
1 TTTTA-ATATT
*
2327112 CTTTTATTATT
1 -TTTTAATATT
2327123 TTTTAA
1 TTTTAA
2327129 AAATTCTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
10 24 0.60
11 15 0.38
12 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTAATATT
Found at i:2327093 original size:11 final size:11
Alignment explanation
Indices: 2327071--2327126 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
2327061 TTTATATCAA
2327071 TTTTAATA-TT
1 TTTTAATATTT
2327081 TTTTAATATTT
1 TTTTAATATTT
*
2327092 TTTT-ATAATT
1 TTTTAATATTT
*
2327102 TTTTACA-ATTC
1 TTTTA-ATATTT
*
2327113 TTTTATTATTT
1 TTTTAATATTT
2327124 TTT
1 TTT
2327127 AAAAATTCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 17 0.46
11 19 0.51
12 1 0.03
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTAATATTT
Found at i:2327095 original size:21 final size:20
Alignment explanation
Indices: 2327071--2327129 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
2327061 TTTATATCAA
2327071 TTTTAATATTTTTTAATATT-
1 TTTTAATATTTTTTAA-ATTC
*
2327091 TTTTTATAATTTTTTACAATTC
1 TTTTAAT-ATTTTTTA-AATTC
*
2327113 TTTTATTATTTTTTAAA
1 TTTTAATATTTTTTAAA
2327130 AATTCTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 8 0.24
21 19 0.58
22 6 0.18
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTAATATTTTTTAAATTC
Found at i:2327263 original size:21 final size:20
Alignment explanation
Indices: 2327239--2327281 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
2327229 AATTTTAATA
2327239 TTTATAATATTTATAAATTTT
1 TTTATAATATTTAT-AATTTT
* *
2327260 TTTATAATTTTTATGATTTT
1 TTTATAATATTTATAATTTT
2327280 TT
1 TT
2327282 ATGGAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTATAATATTTATAATTTT
Found at i:2327270 original size:9 final size:9
Alignment explanation
Indices: 2327187--2327280 Score: 50
Period size: 9 Copynumber: 10.1 Consensus size: 9
2327177 TATAAAAAAA
2327187 TATAATTTAT
1 TATAATTT-T
*
2327197 TATAATTCT
1 TATAATTTT
*
2327206 TATCATTTT
1 TATAATTTT
* *
2327215 AATAAGTTTA
1 TATAA-TTTT
2327225 TATCAA--TT
1 TAT-AATTTT
*
2327233 T-TAATATT
1 TATAATTTT
*
2327241 TATAATATT
1 TATAATTTT
2327250 TATAAATTTTTT
1 TAT-AA--TTTT
2327262 TATAATTTT
1 TATAATTTT
*
2327271 TATGATTTT
1 TATAATTTT
2327280 T
1 T
2327281 TATGGAAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
6 2 0.03
7 1 0.02
8 5 0.08
9 34 0.52
10 14 0.21
11 4 0.06
12 6 0.09
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (9 bp):
TATAATTTT
Found at i:2328745 original size:31 final size:31
Alignment explanation
Indices: 2328678--2328770 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
2328668 GTTAGTCCTC
*
2328678 AAACTTGACAATTGTTCCCATATTAGAGCTT
1 AAACTTGACAATTATTCCCATATTAGAGCTT
* * *
2328709 GAACTTGATAATTATTCCCATATT-GGGACTT
1 AAACTTGACAATTATTCCCATATTAGAG-CTT
* * * * *
2328740 AAACTTGGCAATTGTTTCCACATTGGAGCTT
1 AAACTTGACAATTATTCCCATATTAGAGCTT
2328771 GAACATACTC
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
30 2 0.04
31 45 0.92
32 2 0.04
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (31 bp):
AAACTTGACAATTATTCCCATATTAGAGCTT
Found at i:2338687 original size:12 final size:12
Alignment explanation
Indices: 2338670--2338694 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2338660 ATATTTAAAG
2338670 TTTATGATTGTT
1 TTTATGATTGTT
2338682 TTTATGATTGTT
1 TTTATGATTGTT
2338694 T
1 T
2338695 CTCTTAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (12 bp):
TTTATGATTGTT
Found at i:2340089 original size:23 final size:23
Alignment explanation
Indices: 2340045--2340087 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2340035 ATACAAAAAG
2340045 TTTTCAAAAAATTTAGAAAAATC
1 TTTTCAAAAAATTTAGAAAAATC
*
2340068 TTTTTAAAAAA-TTAGAAAAA
1 TTTTCAAAAAATTTAGAAAAA
2340088 ATATATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (23 bp):
TTTTCAAAAAATTTAGAAAAATC
Found at i:2354689 original size:21 final size:21
Alignment explanation
Indices: 2354665--2354705 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2354655 TATCCAAATA
*
2354665 ATAATAATAAAATAGTAGCAT
1 ATAATAACAAAATAGTAGCAT
* *
2354686 ATAATAGCAAAATGGTAGCA
1 ATAATAACAAAATAGTAGCA
2354706 AAACAATGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (21 bp):
ATAATAACAAAATAGTAGCAT
Found at i:2357416 original size:18 final size:18
Alignment explanation
Indices: 2357393--2357479 Score: 111
Period size: 18 Copynumber: 4.8 Consensus size: 18
2357383 CGTTTATGGT
*
2357393 ACTATTTACGTATACGGC
1 ACTATTCACGTATACGGC
* * *
2357411 ACTATTTATGTATACGGT
1 ACTATTCACGTATACGGC
2357429 ACTATTCACGTATACGGC
1 ACTATTCACGTATACGGC
* *
2357447 ACTATTCACGTATATGGT
1 ACTATTCACGTATACGGC
*
2357465 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
2357480 AGTAGTTGGG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.36
Consensus pattern (18 bp):
ACTATTCACGTATACGGC
Found at i:2357440 original size:36 final size:36
Alignment explanation
Indices: 2357390--2357479 Score: 135
Period size: 36 Copynumber: 2.5 Consensus size: 36
2357380 GACCGTTTAT
* * *
2357390 GGTACTATTTACGTATACGGCACTATTTATGTATAC
1 GGTACTATTCACGTATACGGCACTATTCACGTATAC
*
2357426 GGTACTATTCACGTATACGGCACTATTCACGTATAT
1 GGTACTATTCACGTATACGGCACTATTCACGTATAC
*
2357462 GGTACTGTTCACGTATAC
1 GGTACTATTCACGTATAC
2357480 AGTAGTTGGG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (36 bp):
GGTACTATTCACGTATACGGCACTATTCACGTATAC
Found at i:2370432 original size:133 final size:132
Alignment explanation
Indices: 2370189--2370520 Score: 404
Period size: 133 Copynumber: 2.5 Consensus size: 132
2370179 ATAATTATTC
* *
2370189 AAAAATTCTTTAAAACGAAGGCAATGTTCGATGTTTGACAATTCGAGGAATCGTGCCCTACCGTG
1 AAAAATTCTTTAAAACGAAGGAAATGTTCAATGTTTGACAATTCGAGGAATCGTGCCCTACCGTG
* * * *
2370254 CTGGGTTGCAATTTCTCATTCGTTCAAAATAATCGAATATTCCTTTGGAATTTCAGTCATGTCTT
66 CTGGGTTGCAATTTCCCATTCGTTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATGT-TT
2370319 TAA
130 TAA
* * * * *
2370322 AAAAATTCTTTAAAACGATGGAAATGTTCAATGTTTGGCAATTCGGGGAATTGTGCCCTATCGTG
1 AAAAATTCTTTAAAACGAAGGAAATGTTCAATGTTTGACAATTCGAGGAATCGTGCCCTACCGTG
* *
2370387 CTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATGTTTT
66 CTGGGTTGCAATTTCCCATTCGTTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATGTTTT
2370452 --
131 AA
* * * * * ** * * * *
2370452 CAAAATTC--TAAAA-TAAAGCAATGCTCAATGCCTAAAAATTCGAGGAATCGTGCCCTACTGTA
1 AAAAATTCTTTAAAACGAAGGAAATGTTCAATGTTTGACAATTCGAGGAATCGTGCCCTACCGTG
2370514 CTGGGTT
66 CTGGGTT
2370521 TATATTTTTT
Statistics
Matches: 170, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
127 41 0.24
128 5 0.03
130 7 0.04
132 3 0.02
133 114 0.67
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (132 bp):
AAAAATTCTTTAAAACGAAGGAAATGTTCAATGTTTGACAATTCGAGGAATCGTGCCCTACCGTG
CTGGGTTGCAATTTCCCATTCGTTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATGTTTT
AA
Found at i:2371300 original size:16 final size:16
Alignment explanation
Indices: 2371279--2371312 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2371269 TTATTACCAC
*
2371279 ATAGAACATCACATCA
1 ATAGAAAATCACATCA
*
2371295 ATAGAAAATGACATCA
1 ATAGAAAATCACATCA
2371311 AT
1 AT
2371313 TTATAAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.18, G:0.09, T:0.21
Consensus pattern (16 bp):
ATAGAAAATCACATCA
Found at i:2371853 original size:22 final size:23
Alignment explanation
Indices: 2371806--2371859 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
2371796 AATTTATGAA
2371806 TTTAATTATTTAATGTATATTCAC
1 TTTAATTATTT-ATGTATATTCAC
*
2371830 TTTTAATTATTT-T-TATATTTAC
1 -TTTAATTATTTATGTATATTCAC
2371852 TTTAATTA
1 TTTAATTA
2371860 AATTAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 8 0.29
22 8 0.29
23 1 0.04
25 11 0.39
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTAATTATTTATGTATATTCAC
Found at i:2373208 original size:18 final size:18
Alignment explanation
Indices: 2373185--2373220 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2373175 CTCAACGCTT
2373185 GGATCTCGAACTCATCTA
1 GGATCTCGAACTCATCTA
2373203 GGATCTCGAACTCATCTA
1 GGATCTCGAACTCATCTA
2373221 TCAAATCTTC
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:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (18 bp):
GGATCTCGAACTCATCTA
Found at i:2373732 original size:17 final size:17
Alignment explanation
Indices: 2373710--2373748 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2373700 TCTATTTAAC
* * *
2373710 ATAAAAATATACAACAA
1 ATAAAAAAAAACAAAAA
2373727 ATAAAAAAAAACAAAAA
1 ATAAAAAAAAACAAAAA
2373744 ATAAA
1 ATAAA
2373749 TTTTTTACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (17 bp):
ATAAAAAAAAACAAAAA
Found at i:2373869 original size:11 final size:11
Alignment explanation
Indices: 2373853--2373886 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
2373843 TTCCCCCCTC
2373853 CCTTCTCTCTT
1 CCTTCTCTCTT
2373864 CCTTCTCTCTT
1 CCTTCTCTCTT
*
2373875 CCCTCTCTCTT
1 CCTTCTCTCTT
2373886 C
1 C
2373887 TTTTTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (11 bp):
CCTTCTCTCTT
Found at i:2373884 original size:22 final size:23
Alignment explanation
Indices: 2373851--2373904 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
2373841 CCTTCCCCCC
2373851 TCCCTTCTCTCTTCCTTCTCTC-T
1 TCCC-TCTCTCTTCCTTCTCTCTT
* * *
2373874 TCCCTCTCTCTTCTTTTTTTCTT
1 TCCCTCTCTCTTCCTTCTCTCTT
2373897 TCCCTCTC
1 TCCCTCTC
2373905 CCCAAATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (23 bp):
TCCCTCTCTCTTCCTTCTCTCTT
Found at i:2374368 original size:6 final size:6
Alignment explanation
Indices: 2374368--2374401 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
2374358 TTATTAGTAT
2374368 TATTAG TATTAG TATTAG TATTATG TATTAG TAT
1 TATTAG TATTAG TATTAG TATTA-G TATTAG TAT
2374402 ATATTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (6 bp):
TATTAG
Found at i:2375313 original size:38 final size:37
Alignment explanation
Indices: 2375229--2375323 Score: 97
Period size: 38 Copynumber: 2.5 Consensus size: 37
2375219 TATACGTACT
*
2375229 TATACATACTTAAATATATTTTTCATATTTCATAATTC
1 TATACATACTTAAATATATTTTGCATATTT-ATAATTC
* *
2375267 T-TATATACTTACATATATTTATGCATATTT-TACA-TC
1 TATACATACTTAAATATATTT-TGCATATTTATA-ATTC
*
2375303 ATATACATACTTATATATATT
1 -TATACATACTTAAATATATT
2375324 CTTTATATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
36 4 0.08
37 19 0.40
38 25 0.52
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (37 bp):
TATACATACTTAAATATATTTTGCATATTTATAATTC
Found at i:2379418 original size:41 final size:39
Alignment explanation
Indices: 2379366--2379466 Score: 105
Period size: 41 Copynumber: 2.5 Consensus size: 39
2379356 AATAAAAAAT
*
2379366 AAAATACTAAAAAATTATTAAAAATTAGAAACACAACATATA
1 AAAATAGTAAAAAATTATTAAAAATT-GAAA-A-AACATATA
***
2379408 AAAAT-GTAAAAAAATATATTTAAAAATTGAAAAATTTTATA
1 AAAATAGT-AAAAAAT-TA-TTAAAAATTGAAAAAACATATA
2379449 AAAATAGTAAAAAATTAT
1 AAAATAGTAAAAAATTAT
2379467 AAATTTTATA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
39 1 0.02
40 2 0.04
41 18 0.35
42 15 0.29
43 6 0.12
44 9 0.18
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (39 bp):
AAAATAGTAAAAAATTATTAAAAATTGAAAAAACATATA
Found at i:2379486 original size:27 final size:27
Alignment explanation
Indices: 2379429--2379524 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 27
2379419 AAATATATTT
* * *
2379429 AAAAATTGAAAAATTTTATAAAAATAGTA
1 AAAAATT-ATAAATTTTATAGAATTA-TA
2379458 AAAAATTATAAATTTTATAGAATTATA
1 AAAAATTATAAATTTTATAGAATTATA
*
2379485 AAAAAATATAAATTTGTA-AGAAAATTATA
1 AAAAATTATAAATTT-TATAG--AATTATA
*
2379514 CAAAATT-TAAA
1 AAAAATTATAAA
2379525 GAAATATAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
27 18 0.31
28 21 0.36
29 19 0.33
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.33
Consensus pattern (27 bp):
AAAAATTATAAATTTTATAGAATTATA
Found at i:2379513 original size:29 final size:27
Alignment explanation
Indices: 2379439--2379499 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
2379429 AAAAATTGAA
* * *
2379439 AAATTTTATAAAAATAGTAAAAAATTAT
1 AAATTTTATAGAATTA-TAAAAAAATAT
2379467 AAATTTTATAGAATTATAAAAAAATAT
1 AAATTTTATAGAATTATAAAAAAATAT
2379494 AAATTT
1 AAATTT
2379500 GTAAGAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (27 bp):
AAATTTTATAGAATTATAAAAAAATAT
Found at i:2379557 original size:38 final size:39
Alignment explanation
Indices: 2379478--2379560 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 39
2379468 AATTTTATAG
* *
2379478 AATTATAAAAAAATATAAATTTGTAAGAAAATTATACAA
1 AATTATAAAAAAATATAAATTTATAAGAAAATTACACAA
*
2379517 AATT-TAAAGAAATATAAATTTCATAA-AGAAATTACA-AA
1 AATTATAAAAAAATATAAATTT-ATAAGA-AAATTACACAA
2379555 AATTAT
1 AATTAT
2379561 CATACTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
38 23 0.61
39 15 0.39
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (39 bp):
AATTATAAAAAAATATAAATTTATAAGAAAATTACACAA
Found at i:2380527 original size:23 final size:21
Alignment explanation
Indices: 2380501--2380542 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
2380491 AAATTATTAT
2380501 ATAAATGATATTTAATATATAAC
1 ATAAA-GA-ATTTAATATATAAC
*
2380524 ATAAAGACTTTAATATATA
1 ATAAAGAATTTAATATATA
2380543 TAAGAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ATAAAGAATTTAATATATAAC
Found at i:2385550 original size:10 final size:10
Alignment explanation
Indices: 2385535--2385563 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2385525 ATGTAATTTA
2385535 GGGACTTTTT
1 GGGACTTTTT
2385545 GGGACTTTTT
1 GGGACTTTTT
2385555 GGGACTTTT
1 GGGACTTTT
2385564 GCTTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.31, T:0.48
Consensus pattern (10 bp):
GGGACTTTTT
Found at i:2386093 original size:28 final size:28
Alignment explanation
Indices: 2386061--2386116 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
2386051 GGAAAAGAAC
2386061 GTCAAACTAAAAAAAACTCCTTTTTCAA
1 GTCAAACTAAAAAAAACTCCTTTTTCAA
*
2386089 GTCAAATTAAAAAAAACTCCTTTTTCAA
1 GTCAAACTAAAAAAAACTCCTTTTTCAA
2386117 ATTTTAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (28 bp):
GTCAAACTAAAAAAAACTCCTTTTTCAA
Found at i:2386385 original size:31 final size:31
Alignment explanation
Indices: 2386350--2386414 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
2386340 GGGTATTACA
* **
2386350 ATTCAAAAGTTTTCATTTAAGTCACTGAACT
1 ATTCAAAAGTTTTCATTTAAATCACCAAACT
*
2386381 ATTCAAAAGTTTTTATTTAAATCACCAAACT
1 ATTCAAAAGTTTTCATTTAAATCACCAAACT
2386412 ATT
1 ATT
2386415 AAGTTTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.40
Consensus pattern (31 bp):
ATTCAAAAGTTTTCATTTAAATCACCAAACT
Found at i:2388562 original size:19 final size:18
Alignment explanation
Indices: 2388526--2388573 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
2388516 AGAAAGTTAT
*
2388526 AGAGAAAGAAACGTGAAA
1 AGAGAAAGAAACGAGAAA
2388544 GAGAGAAAGAAA-GAAGAAA
1 -AGAGAAAGAAACG-AGAAA
*
2388563 AGAAAAAGAAA
1 AGAGAAAGAAA
2388574 AAGGGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.69, C:0.02, G:0.27, T:0.02
Consensus pattern (18 bp):
AGAGAAAGAAACGAGAAA
Found at i:2389314 original size:28 final size:28
Alignment explanation
Indices: 2389266--2389320 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
2389256 GTATACATGT
* *
2389266 GTGAAATTGAATTGTATAATGATTTGTG
1 GTGAAATTGAATTGTAGAATGAATTGTG
*
2389294 GTGAATTTGAAATTGT-GAATGAATTGT
1 GTGAAATTG-AATTGTAGAATGAATTGT
2389321 TATTGCGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (28 bp):
GTGAAATTGAATTGTAGAATGAATTGTG
Found at i:2392481 original size:14 final size:15
Alignment explanation
Indices: 2392455--2392484 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2392445 TAATTATCAC
2392455 TTAATTAATATTAAT
1 TTAATTAATATTAAT
2392470 TTAATT-ATATTAAT
1 TTAATTAATATTAAT
2392484 T
1 T
2392485 ATTATTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAATTAATATTAAT
Found at i:2400295 original size:30 final size:31
Alignment explanation
Indices: 2400235--2400300 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
2400225 ACAATTTGGC
*
2400235 CATTAAACTATTCAAAAGTTTTCATTTAAGT
1 CATTGAACTATTCAAAAGTTTTCATTTAAGT
* * *
2400266 CATTGAACTGTTCAAGAGTTTT-TTTTAAGT
1 CATTGAACTATTCAAAAGTTTTCATTTAAGT
2400296 CATTG
1 CATTG
2400301 GGTTGTTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (31 bp):
CATTGAACTATTCAAAAGTTTTCATTTAAGT
Found at i:2402604 original size:31 final size:31
Alignment explanation
Indices: 2402565--2402631 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
2402555 AAAATTAATA
2402565 ATTT-AGTTATTAAACTATTC-AAAAATTTCT
1 ATTTAAGTTATTAAACTATTCAAAAAATTT-T
*
2402595 ATTTAAGTTATTGAACTATTCAAAAAATTTT
1 ATTTAAGTTATTAAACTATTCAAAAAATTTT
2402626 ATTTAA
1 ATTTAA
2402632 ATTACTTGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 4 0.12
31 22 0.65
32 8 0.24
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.46
Consensus pattern (31 bp):
ATTTAAGTTATTAAACTATTCAAAAAATTTT
Found at i:2403593 original size:25 final size:26
Alignment explanation
Indices: 2403554--2403606 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
2403544 AAATTCGTTT
*
2403554 TTATTATTTGAAATTTAATTT-TTTA
1 TTATTATTAGAAATTTAATTTATTTA
* *
2403579 TTATTATTAGGAATTTGATTTATTTA
1 TTATTATTAGAAATTTAATTTATTTA
2403605 TT
1 TT
2403607 TTCTAGAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (26 bp):
TTATTATTAGAAATTTAATTTATTTA
Found at i:2408890 original size:31 final size:30
Alignment explanation
Indices: 2408837--2408919 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 30
2408827 TTAGATTTTT
* *
2408837 TTTTGAAAT-TTTTATCATTTTTAAAAATATA
1 TTTTGAAATATTTTGT-AATTTTAAAAAT-TA
2408868 TATATT-AAATATTTTG-AATTTTAAAAATTA
1 T-T-TTGAAATATTTTGTAATTTTAAAAATTA
*
2408898 TTTTGAATTATTTTGTAATTTT
1 TTTTGAAATATTTTGTAATTTT
2408920 TGTTGAGAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
28 2 0.05
29 10 0.23
30 9 0.20
31 12 0.27
32 5 0.11
33 6 0.14
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (30 bp):
TTTTGAAATATTTTGTAATTTTAAAAATTA
Found at i:2409259 original size:21 final size:21
Alignment explanation
Indices: 2409235--2409276 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2409225 TTTTATAAGT
2409235 GTGATTGTAAAATGTATTATG
1 GTGATTGTAAAATGTATTATG
2409256 GTGATTGTAAAATGTATTATG
1 GTGATTGTAAAATGTATTATG
2409277 TTGTGGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (21 bp):
GTGATTGTAAAATGTATTATG
Found at i:2409725 original size:18 final size:20
Alignment explanation
Indices: 2409685--2409726 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
2409675 TCTCTTAACA
*
2409685 AAAATTTCAAAATAATTTTT
1 AAAATTTCAAAATAATTTAT
2409705 AAAA-TTCAAAAT-ATTTAT
1 AAAATTTCAAAATAATTTAT
2409723 AAAA
1 AAAA
2409727 ATTTAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 8 0.38
20 4 0.19
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTTCAAAATAATTTAT
Found at i:2409727 original size:19 final size:19
Alignment explanation
Indices: 2409684--2409729 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2409674 TTCTCTTAAC
2409684 AAAAATTTCAAAATAATTTT
1 AAAAA-TTCAAAATAATTTT
*
2409704 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
2409723 AAAAATT
1 AAAAATT
2409730 TAATATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.17
19 15 0.65
20 4 0.17
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:2409791 original size:21 final size:21
Alignment explanation
Indices: 2409749--2409792 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2409739 ATATTTTTTT
*** *
2409749 AAAAATTCTAATTTTTTTTAA
1 AAAAATTCTAAAAATTTCTAA
2409770 AAAAATTCTAAAAATTTCTAA
1 AAAAATTCTAAAAATTTCTAA
2409791 AA
1 AA
2409793 TAATAATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAATTCTAAAAATTTCTAA
Found at i:2417362 original size:3 final size:3
Alignment explanation
Indices: 2417354--2417388 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
2417344 ACATAGTTTA
*
2417354 TAT TAT TAT TAT TAT AAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2417389 ACGTTGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2417636 original size:103 final size:103
Alignment explanation
Indices: 2417457--2417663 Score: 333
Period size: 103 Copynumber: 2.0 Consensus size: 103
2417447 AAATTTTACA
* * *
2417457 TAGAAAATTTTTATCGAGAAAAATCATGGTTAAAGGAAGAGAAATTCATTAATGTTGAAAAACAA
1 TAGAAAATTTTTATCGAGAAAAATCATGGTCAAAGGAAGAGAAATTCACTAATATTGAAAAACAA
* * *
2417522 CAATGCAAGAGGTTTTCAATTACATATATTTTTAAGGG
66 CAACGCAAGAGGTTTTCAATTACACACATTTTTAAGGG
*
2417560 TAGAAAATTTTTATCGAGAAAAATCATGGTCAAAGGAAGAGAAATTTACTAATATTGAAAAACAA
1 TAGAAAATTTTTATCGAGAAAAATCATGGTCAAAGGAAGAGAAATTCACTAATATTGAAAAACAA
* *
2417625 CAACGCAAGAGGTTTTCGATTACACACGTTTTTAAGGG
66 CAACGCAAGAGGTTTTCAATTACACACATTTTTAAGGG
2417663 T
1 T
2417664 TAAACGACCA
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (103 bp):
TAGAAAATTTTTATCGAGAAAAATCATGGTCAAAGGAAGAGAAATTCACTAATATTGAAAAACAA
CAACGCAAGAGGTTTTCAATTACACACATTTTTAAGGG
Found at i:2419129 original size:20 final size:21
Alignment explanation
Indices: 2419104--2419168 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
2419094 TAAAATTTCA
*
2419104 AAAAAATTATAAGAATTATTTT
1 AAAAAATTATAAAAATTA-TTT
*
2419126 AAAAAA-T-GAAAAATTATTT
1 AAAAAATTATAAAAATTATTT
* *
2419145 AAAAAATTATAAAAAATAATT
1 AAAAAATTATAAAAATTATTT
2419166 AAA
1 AAA
2419169 TTTTGACATA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 9 0.25
20 8 0.22
21 13 0.36
22 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (21 bp):
AAAAAATTATAAAAATTATTT
Found at i:2436614 original size:16 final size:15
Alignment explanation
Indices: 2436576--2436614 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2436566 AAATTAATCC
*
2436576 AAATATATATTCTTA
1 AAATATATATTATTA
2436591 AAATTATATATTATATA
1 AAA-TATATATTAT-TA
2436608 AAATATA
1 AAATATA
2436615 AATCTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 13 0.62
17 5 0.24
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATATATATTATTA
Found at i:2437699 original size:16 final size:18
Alignment explanation
Indices: 2437678--2437717 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
2437668 TTAAAATTAT
2437678 AAAATATTCA-A-AAATA
1 AAAATATTCATAGAAATA
*
2437694 AAAATATTCATAGAAATT
1 AAAATATTCATAGAAATA
2437712 AAAATA
1 AAAATA
2437718 AAGTACATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 1 0.05
18 10 0.48
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAATATTCATAGAAATA
Found at i:2438917 original size:66 final size:66
Alignment explanation
Indices: 2438811--2438940 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
2438801 TATGAGCTGG
**
2438811 TACCAAAATCGAGTCCTAAACAAGCAGATCTAATTTTAACAATTAGAACAATAACAATGAAAATT
1 TACCAAAATCGAGTCCTAAACAAGCAGATCTAATTTTAACAACCAGAACAATAACAATGAAAATT
2438876 A
66 A
*
2438877 TACCAAAATCGAGTCCTAAACAAGCAGATCTAATTTTAACAACCGGAACAATAACAATGAAAAT
1 TACCAAAATCGAGTCCTAAACAAGCAGATCTAATTTTAACAACCAGAACAATAACAATGAAAAT
2438941 GATGCATAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.49, C:0.18, G:0.10, T:0.22
Consensus pattern (66 bp):
TACCAAAATCGAGTCCTAAACAAGCAGATCTAATTTTAACAACCAGAACAATAACAATGAAAATT
A
Found at i:2440620 original size:17 final size:17
Alignment explanation
Indices: 2440600--2440633 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2440590 AGGTTTAAGT
2440600 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
**
2440617 TTAAATTTTTTAATTAA
1 TTAAAAATTTTAATTAA
2440634 AAATCTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:2454439 original size:2 final size:2
Alignment explanation
Indices: 2454432--2454463 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2454422 TGTTAGGAGG
2454432 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2454464 TGGGAAGTTG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2458007 original size:53 final size:53
Alignment explanation
Indices: 2457922--2458039 Score: 164
Period size: 53 Copynumber: 2.2 Consensus size: 53
2457912 ATTTTTAACA
* * *
2457922 TAAATTTAGTAATGAGTGGATTAAGATTTACAAACCTATAAAAATGAAGTGAT
1 TAAATTTACTAATGAGTGGATTAAGATATACAAACCTATAAAAATGAAGTGAC
* * * * *
2457975 TAAATTCACTAATGATTGGATTAAGATATACAAAGCTATAAAAATGCATTGAC
1 TAAATTTACTAATGAGTGGATTAAGATATACAAACCTATAAAAATGAAGTGAC
2458028 TAAATTTACTAA
1 TAAATTTACTAA
2458040 AGAAAAAGTA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (53 bp):
TAAATTTACTAATGAGTGGATTAAGATATACAAACCTATAAAAATGAAGTGAC
Found at i:2460241 original size:26 final size:26
Alignment explanation
Indices: 2460210--2460263 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
2460200 GCGTGCGTAT
2460210 ATATATGTGTATATATAAGCTATAGAAC
1 ATAT-TGTGTATATAT-AGCTATAGAAC
*
2460238 ATATTGTGTGTATATAGCTATAGAAC
1 ATATTGTGTATATATAGCTATAGAAC
2460264 TTCCTTTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 11 0.44
27 10 0.40
28 4 0.16
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (26 bp):
ATATTGTGTATATATAGCTATAGAAC
Found at i:2460842 original size:24 final size:24
Alignment explanation
Indices: 2460815--2460862 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2460805 CAAGACATGT
2460815 CACTCAAATACTCGAAACAAGGTC
1 CACTCAAATACTCGAAACAAGGTC
2460839 CACTCAAATACTCGAAACAAGGTC
1 CACTCAAATACTCGAAACAAGGTC
2460863 AAATTCTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.29, G:0.12, T:0.17
Consensus pattern (24 bp):
CACTCAAATACTCGAAACAAGGTC
Found at i:2465196 original size:25 final size:25
Alignment explanation
Indices: 2465166--2465219 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
2465156 AATTCTCCCA
*
2465166 TATTT-ATTTTTAAAAATATAATTTT
1 TATTTAATATTTAAAAATAT-ATTTT
**
2465191 TATTTAATATTTAATTATATATTTT
1 TATTTAATATTTAAAAATATATTTT
2465216 TATT
1 TATT
2465220 AAAATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTTAATATTTAAAAATATATTTT
Found at i:2468099 original size:31 final size:31
Alignment explanation
Indices: 2468064--2468129 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
2468054 AATAGTCTAG
2468064 TGACTTAAATAAAAACTTTTGAATAATTCAA
1 TGACTTAAATAAAAACTTTTGAATAATTCAA
* * * *
2468095 TGACTTAAATGAAAATTTTTGAATAGTTCAT
1 TGACTTAAATAAAAACTTTTGAATAATTCAA
2468126 TGAC
1 TGAC
2468130 CAATTTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAATTCAA
Found at i:2471264 original size:25 final size:25
Alignment explanation
Indices: 2471217--2471265 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2471207 AGATAAGAAT
*
2471217 GAAAATAAAGAAAATAAAGTTAAAA
1 GAAAATAAAGAAAATAAAATTAAAA
2471242 GAAAATAAA-AAAATAAGAATTAAA
1 GAAAATAAAGAAAATAA-AATTAAA
2471266 TTGCTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.16
Consensus pattern (25 bp):
GAAAATAAAGAAAATAAAATTAAAA
Found at i:2474184 original size:13 final size:13
Alignment explanation
Indices: 2474166--2474190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2474156 AAATACACCA
2474166 AAACATATCAAAG
1 AAACATATCAAAG
2474179 AAACATATCAAA
1 AAACATATCAAA
2474191 ACAACTACAG
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:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAACATATCAAAG
Found at i:2481764 original size:18 final size:21
Alignment explanation
Indices: 2481741--2481789 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 21
2481731 CATGTTAGCG
2481741 AATAAAATATT-TA-ATATA-
1 AATAAAATATTATATATATAT
2481759 AAT-AAATAATTATATATATAT
1 AATAAAAT-ATTATATATATAT
2481780 AATAAAATAT
1 AATAAAATAT
2481790 AAATAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.15
18 6 0.23
19 2 0.08
20 5 0.19
21 5 0.19
22 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAAAATATTATATATATAT
Found at i:2481789 original size:16 final size:16
Alignment explanation
Indices: 2481753--2481800 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2481743 TAAAATATTT
2481753 AATATAAATA-AATAA
1 AATATAAATAGAATAA
* * *
2481768 TTATATATATATAATAA
1 -AATATAAATAGAATAA
2481785 AATATAAATAGAATAA
1 AATATAAATAGAATAA
2481801 GTTTACATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 21 0.81
17 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AATATAAATAGAATAA
Found at i:2483982 original size:13 final size:14
Alignment explanation
Indices: 2483959--2483988 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2483949 AATTGATTAA
2483959 AACTAAAATTAACT
1 AACTAAAATTAACT
2483973 AACT-AAATTAACT
1 AACTAAAATTAACT
2483986 AAC
1 AAC
2483989 GAGTGTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.27
Consensus pattern (14 bp):
AACTAAAATTAACT
Found at i:2490354 original size:21 final size:21
Alignment explanation
Indices: 2490313--2490354 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2490303 AACTTTTTAA
*
2490313 CCTGAACCTTGAATCCTGAAT
1 CCTGAACCTTGAATCCAGAAT
*
2490334 CCTGAACCTTGAATTCAGAAT
1 CCTGAACCTTGAATCCAGAAT
2490355 ATGAAACCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (21 bp):
CCTGAACCTTGAATCCAGAAT
Found at i:2491694 original size:15 final size:15
Alignment explanation
Indices: 2491674--2491703 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2491664 TGAAAGAGGG
2491674 AAGAAGAAGACTAAA
1 AAGAAGAAGACTAAA
*
2491689 AAGAAGAAGATTAAA
1 AAGAAGAAGACTAAA
2491704 TCATTTCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.20, T:0.10
Consensus pattern (15 bp):
AAGAAGAAGACTAAA
Found at i:2491719 original size:4 final size:4
Alignment explanation
Indices: 2491710--2491745 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
2491700 TAAATCATTT
2491710 CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
2491746 TGTATAGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:2506874 original size:41 final size:41
Alignment explanation
Indices: 2506705--2506879 Score: 280
Period size: 41 Copynumber: 4.3 Consensus size: 41
2506695 GTTTGGAATT
* *
2506705 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
2506746 GGTGATCT-AATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
2506786 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
2506827 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
2506868 GGTGATCCGAAT
1 GGTGATCTGAAT
2506880 ATGATGAATT
Statistics
Matches: 123, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
40 37 0.30
41 86 0.70
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
Found at i:2514109 original size:19 final size:19
Alignment explanation
Indices: 2514085--2514121 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2514075 TTAATGTGCG
*
2514085 AATATATGTATATGTGTGT
1 AATATATATATATGTGTGT
2514104 AATATATATATATGTGTG
1 AATATATATATATGTGTG
2514122 GATCGAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (19 bp):
AATATATATATATGTGTGT
Found at i:2514397 original size:41 final size:41
Alignment explanation
Indices: 2514335--2514510 Score: 271
Period size: 41 Copynumber: 4.3 Consensus size: 41
2514325 GTTTGGAATT
* *
2514335 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
2514376 GGTGATCTAAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
2514417 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
2514458 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
2514499 GATGATCCGAAT
1 GGTGATCTGAAT
2514511 ATGATGAATT
Statistics
Matches: 122, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 122 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.23
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
Found at i:2514472 original size:82 final size:82
Alignment explanation
Indices: 2514335--2514504 Score: 322
Period size: 82 Copynumber: 2.1 Consensus size: 82
2514325 GTTTGGAATT
2514335 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
2514400 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
*
2514417 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
2514482 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
*
2514499 GATGAT
1 GGTGAT
2514505 CCGAATATGA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 86 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (82 bp):
GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
CTAGCAGGCTAAGTGCC
Found at i:2516238 original size:19 final size:19
Alignment explanation
Indices: 2516214--2516257 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
2516204 CATACTAAGA
2516214 TAAGAATAAAAATTAGAAT
1 TAAGAATAAAAATTAGAAT
2516233 TAAGAATAAAAATTAGAAT
1 TAAGAATAAAAATTAGAAT
2516252 TAAGAA
1 TAAGAA
2516258 ATTGAACCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (19 bp):
TAAGAATAAAAATTAGAAT
Found at i:2517708 original size:15 final size:16
Alignment explanation
Indices: 2517688--2517721 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2517678 TAATCTTTTA
2517688 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
2517703 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
2517719 AAA
1 AAA
2517722 ACTATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Found at i:2519552 original size:21 final size:21
Alignment explanation
Indices: 2519520--2519577 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
2519510 ATATATTTGC
2519520 ATTAATATTAATATATTTTA-TA
1 ATTAA-ATTAAT-TATTTTATTA
*
2519542 ATTAAATTAATTTTTTTATTA
1 ATTAAATTAATTATTTTATTA
*
2519563 TTTAAATTAAATTAT
1 ATTAAATT-AATTAT
2519578 GGATAGATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 6 0.19
21 15 0.48
22 10 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTAAATTAATTATTTTATTA
Found at i:2520205 original size:19 final size:20
Alignment explanation
Indices: 2520181--2520219 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2520171 TGATTAAATT
2520181 ATATTAAAT-TAAAATATAA
1 ATATTAAATCTAAAATATAA
*
2520200 ATATTAAATCTTAAATATAA
1 ATATTAAATCTAAAATATAA
2520220 GAATAGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATTAAATCTAAAATATAA
Found at i:2523941 original size:13 final size:14
Alignment explanation
Indices: 2523912--2523946 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2523902 TTTGAGGCTA
*
2523912 TAAATTATAATTTT
1 TAAATTATAATTAT
2523926 TAAATT-TAATTAT
1 TAAATTATAATTAT
2523939 TAAATTAT
1 TAAATTAT
2523947 TAATATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAAATTATAATTAT
Found at i:2523964 original size:28 final size:27
Alignment explanation
Indices: 2523912--2523965 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
2523902 TTTGAGGCTA
**
2523912 TAAATTATAATTTTTAAATTTAATTAT
1 TAAATTATAATTTTTAAATGAAATTAT
2523939 TAAATTATTAATATTTTAAA-GAAATTA
1 TAAATTA-TAAT-TTTTAAATGAAATTA
2523966 AAAATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 9 0.39
29 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TAAATTATAATTTTTAAATGAAATTAT
Found at i:2529009 original size:20 final size:20
Alignment explanation
Indices: 2528971--2529010 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2528961 TTTTAATTCA
*
2528971 CTAAACCCCAAACTTGAACC
1 CTAAACCCCAAACTCGAACC
2528991 CTAAA-CCCAAACCTCGAACC
1 CTAAACCCCAAA-CTCGAACC
2529011 TCAAACCCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.40, C:0.42, G:0.05, T:0.12
Consensus pattern (20 bp):
CTAAACCCCAAACTCGAACC
Found at i:2532459 original size:86 final size:85
Alignment explanation
Indices: 2532369--2532548 Score: 344
Period size: 86 Copynumber: 2.1 Consensus size: 85
2532359 AATATAATTG
2532369 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
1 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAA-ATGAAACCTGTT
2532434 TGTTAAGTATTAATGTTGATA
65 TGTTAAGTATTAATGTTGATA
2532455 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAAATGAAACCTGTTT
1 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAAATGAAACCTGTTT
2532520 GTTAAGTATTAATGTTGATA
66 GTTAAGTATTAATGTTGATA
2532540 TAATT-TTAT
1 TAATTATTAT
2532549 GTGGAGAGAA
Statistics
Matches: 94, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
84 4 0.04
85 38 0.40
86 52 0.55
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.48
Consensus pattern (85 bp):
TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAAATGAAACCTGTTT
GTTAAGTATTAATGTTGATA
Found at i:2532690 original size:51 final size:50
Alignment explanation
Indices: 2532615--2532717 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 50
2532605 TATACGTAAA
2532615 AATTATCATACACCAACAATGTTTTTTAGGGTA-AATAACATTAAACCAAC
1 AATTATCATACACCAACAATGTTTTTTAGGG-ACAATAACATTAAACCAAC
2532665 AATTATACATACACCAACAATGTTTTTTAGGGACAATAACATTAAACCAAC
1 AATTAT-CATACACCAACAATGTTTTTTAGGGACAATAACATTAAACCAAC
2532716 AA
1 AA
2532718 GTAATTTTAG
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
50 7 0.14
51 44 0.86
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (50 bp):
AATTATCATACACCAACAATGTTTTTTAGGGACAATAACATTAAACCAAC
Found at i:2532726 original size:33 final size:34
Alignment explanation
Indices: 2532663--2532773 Score: 115
Period size: 33 Copynumber: 3.4 Consensus size: 34
2532653 CATTAAACCA
* *
2532663 ACAATTATACATACACCAACAATGT-TTTTTAGGG
1 ACAATTATACATAAACCAACAA-GTAATTTTAGGG
2532697 ACAA-TA-ACATTAAACCAACAAGTAATTTTA-GG
1 ACAATTATACA-TAAACCAACAAGTAATTTTAGGG
* * *
2532729 TCAATTATACATACACCAACAATTAATTTTA-GG
1 ACAATTATACATAAACCAACAAGTAATTTTAGGG
*
2532762 TCAATTATACAT
1 ACAATTATACAT
2532774 GCTTTATAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
32 10 0.15
33 51 0.75
34 7 0.10
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (34 bp):
ACAATTATACATAAACCAACAAGTAATTTTAGGG
Found at i:2535918 original size:18 final size:17
Alignment explanation
Indices: 2535890--2535924 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2535880 ATTATTAAGA
*
2535890 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
2535907 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
2535925 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:2536084 original size:121 final size:120
Alignment explanation
Indices: 2535799--2536182 Score: 716
Period size: 120 Copynumber: 3.2 Consensus size: 120
2535789 TTTTCAAGTT
2535799 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
2535864 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
*
2535919 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
2535984 TAATATAAGAATATT-ATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAAT--TATTAAGAATTTTATTAAATTATATATTTTAATTAAA
2536040 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
2536105 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
2536160 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
2536183 TAAATATGAT
Statistics
Matches: 255, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
119 2 0.01
120 137 0.54
121 114 0.45
122 2 0.01
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
Found at i:2536159 original size:18 final size:17
Alignment explanation
Indices: 2536131--2536165 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2536121 ATTATTAAGA
*
2536131 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
2536148 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
2536166 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:2536380 original size:44 final size:45
Alignment explanation
Indices: 2536330--2536420 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
2536320 ACCTCTATTC
* * *
2536330 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
2536374 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
2536419 CA
1 CA
2536421 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:2536422 original size:16 final size:16
Alignment explanation
Indices: 2536401--2536469 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
2536391 GATTAGCTAT
2536401 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2536417 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
2536434 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
2536450 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
2536466 TACA
1 TACA
2536470 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:2536443 original size:33 final size:32
Alignment explanation
Indices: 2536401--2536469 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
2536391 GATTAGCTAT
2536401 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
2536434 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
2536466 TACA
1 TACA
2536470 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:2541964 original size:17 final size:17
Alignment explanation
Indices: 2541942--2541974 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2541932 TATCATTGCT
*
2541942 TTTTTCTTTTAATTTTC
1 TTTTTCATTTAATTTTC
2541959 TTTTTCATTTAATTTT
1 TTTTTCATTTAATTTT
2541975 GGTACTTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCATTTAATTTTC
Found at i:2544344 original size:25 final size:26
Alignment explanation
Indices: 2544295--2544349 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
2544285 AATGATGACG
2544295 AAAACAATAATAATAGCAATAGTA-T
1 AAAACAATAATAATAGCAATAGTATT
* *
2544320 AAAACGATAATAATA-CATATGGTATT
1 AAAACAATAATAATAGCA-ATAGTATT
2544346 AAAA
1 AAAA
2544350 TATATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 2 0.08
25 19 0.73
26 5 0.19
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.25
Consensus pattern (26 bp):
AAAACAATAATAATAGCAATAGTATT
Found at i:2547285 original size:43 final size:44
Alignment explanation
Indices: 2547218--2547304 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
2547208 GGAGACGAGA
* * *
2547218 TCTGTAATTTTCAGCCTATTACCCTACTGCTTAGGGGGTTAAGG
1 TCTGTAAATTTCAACCTATTACCCTACTGCTTAGGGGCTTAAGG
*
2547262 TCTGTAAATTT-AACCTGTTACCCTACTGCTTAGGGGCTTAAGG
1 TCTGTAAATTTCAACCTATTACCCTACTGCTTAGGGGCTTAAGG
2547305 CTTGGTGAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 29 0.74
44 10 0.26
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (44 bp):
TCTGTAAATTTCAACCTATTACCCTACTGCTTAGGGGCTTAAGG
Found at i:2550572 original size:16 final size:16
Alignment explanation
Indices: 2550551--2550584 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2550541 TCTGAGTACG
2550551 TGGTGGAGGTAACTCT
1 TGGTGGAGGTAACTCT
2550567 TGGTGGAGGTAACTCT
1 TGGTGGAGGTAACTCT
2550583 TG
1 TG
2550585 TATGGCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.38, T:0.32
Consensus pattern (16 bp):
TGGTGGAGGTAACTCT
Found at i:2559258 original size:25 final size:26
Alignment explanation
Indices: 2559209--2559263 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
2559199 AATGATGACG
2559209 AAAACAATAATAATAGCAATAGTA-T
1 AAAACAATAATAATAGCAATAGTATT
* *
2559234 AAAACGATAATAATA-CATATGGTATT
1 AAAACAATAATAATAGCA-ATAGTATT
2559260 AAAA
1 AAAA
2559264 TATATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 2 0.08
25 19 0.73
26 5 0.19
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.25
Consensus pattern (26 bp):
AAAACAATAATAATAGCAATAGTATT
Found at i:2561850 original size:31 final size:31
Alignment explanation
Indices: 2561784--2561853 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
2561774 TTCAGCCCAC
*
2561784 TTCAGTCCCTAATGTTATCAAACGCTCCCGA
1 TTCAGTCCCTAATGTTATCAAACGCTCCAGA
* *
2561815 TTCAGTTCCTAATGTTATCAAACGTTCCTAG-
1 TTCAGTCCCTAATGTTATCAAACGCTCC-AGA
2561846 TTCAGTCC
1 TTCAGTCC
2561854 TTTAGATGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.34
Consensus pattern (31 bp):
TTCAGTCCCTAATGTTATCAAACGCTCCAGA
Found at i:2562816 original size:18 final size:17
Alignment explanation
Indices: 2562759--2562816 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
2562749 TTTAATAAAA
*
2562759 TTTATTACTTTTTTATAT
1 TTTATAACTTTTTTA-AT
2562777 TTATATATA-TTTTTATAAT
1 TT-TATA-ACTTTTT-TAAT
2562796 TTTATAACTTTTTTAAGT
1 TTTATAACTTTTTTAA-T
2562814 TTT
1 TTT
2562817 TGATAATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
17 4 0.12
18 15 0.44
19 12 0.35
20 3 0.09
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATAACTTTTTTAAT
Found at i:2562826 original size:37 final size:36
Alignment explanation
Indices: 2562735--2562844 Score: 98
Period size: 37 Copynumber: 3.0 Consensus size: 36
2562725 AAAATTTCTA
* * *
2562735 ATATTTTTAAAATTTTTAATAAAATTTATTACTTTTTT
1 ATATTTATATAATTTTT-AT-AAATTTATAACTTTTTT
*
2562773 ATATTTATATATATTTTTATAATTTTATAACTTTTTT
1 ATATTTATATA-ATTTTTATAAATTTATAACTTTTTT
* * *
2562810 A-AGTTTTTGATAATTTTAATAAATTTA-AAATTTTT
1 ATA-TTTAT-ATAATTTTTATAAATTTATAACTTTTT
2562845 AAAGAATTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
36 8 0.13
37 33 0.54
38 14 0.23
39 6 0.10
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (36 bp):
ATATTTATATAATTTTTATAAATTTATAACTTTTTT
Found at i:2564088 original size:10 final size:10
Alignment explanation
Indices: 2564052--2564100 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
2564042 AATAATTAAT
2564052 TAATTTTTTAA
1 TAATTTTTT-A
*
2564063 TACTTTTTTA
1 TAATTTTTTA
*
2564073 T-TTTTTTTA
1 TAATTTTTTA
*
2564082 TAATTTTTAA
1 TAATTTTTTA
2564092 TAATTTTTT
1 TAATTTTTT
2564101 GAATTTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
9 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:2568188 original size:21 final size:21
Alignment explanation
Indices: 2568162--2568202 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2568152 AGACGAGCAA
* *
2568162 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2568183 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2568203 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2575617 original size:7 final size:7
Alignment explanation
Indices: 2575607--2575633 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2575597 AGTTATATAT
2575607 TTTAAAA
1 TTTAAAA
2575614 TTTAAAA
1 TTTAAAA
2575621 TTTAAAA
1 TTTAAAA
2575628 TTTAAA
1 TTTAAA
2575634 CTCCAGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTTAAAA
Found at i:2581821 original size:2 final size:2
Alignment explanation
Indices: 2581814--2581838 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2581804 TGTTTTTCCC
2581814 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 A
2581839 AAAGTGTGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2588616 original size:20 final size:18
Alignment explanation
Indices: 2588556--2588632 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 18
2588546 ATTTAGAAAC
* *
2588556 TATAAAAAATTTACAATAT
1 TATAAAAAATATA-AAAAT
* *
2588575 TGTAAAAAAATATAAAATT
1 TAT-AAAAAATATAAAAAT
*
2588594 TATTAAAAATCATAAAAGAT
1 TATAAAAAAT-ATAAAA-AT
2588614 TATAAAAAATAGTAAAAAT
1 TATAAAAAATA-TAAAAAT
2588633 ATATTGCATC
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
18 6 0.13
19 16 0.35
20 24 0.52
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (18 bp):
TATAAAAAATATAAAAAT
Found at i:2596146 original size:23 final size:23
Alignment explanation
Indices: 2596116--2596161 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2596106 TTAAATCATA
2596116 ACATTAATAGAAAATAACCTGGC
1 ACATTAATAGAAAATAACCTGGC
2596139 ACATTAATAGAAAATAACCTGGC
1 ACATTAATAGAAAATAACCTGGC
2596162 TGGATGCGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (23 bp):
ACATTAATAGAAAATAACCTGGC
Found at i:2596503 original size:31 final size:27
Alignment explanation
Indices: 2596439--2596504 Score: 69
Period size: 31 Copynumber: 2.3 Consensus size: 27
2596429 TATTTTTCTC
2596439 AATTTTTAAAGTTAGGACTAAATTGAT
1 AATTTTTAAAGTTAGGACTAAATTGAT
* *
2596466 AGATTTTGTAAATGTTGAGGACTAAGTTTATT
1 A-ATTTT-TAAA-GTT-AGGACTAAATTGA-T
2596498 AATTTTT
1 AATTTTT
2596505 TTTGAATTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
27 1 0.03
28 5 0.16
29 4 0.12
30 4 0.12
31 16 0.50
32 2 0.06
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (27 bp):
AATTTTTAAAGTTAGGACTAAATTGAT
Done.