Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 9 of 214
Found at i:2723009 original size:15 final size:15
Alignment explanation
Indices: 2722971--2723016 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
2722961 GTTTCGTCTC
*
2722971 TTCTATTCTGTTTCTT
1 TTCTATTCT-TTTTTT
2722987 TTCT-TTCTTTTTTT
1 TTCTATTCTTTTTTT
2723001 TTCTATTCTTTCTTTT
1 TTCTATTCTTT-TTTT
2723017 GTTTTATGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 9 0.33
15 10 0.37
16 8 0.30
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.76
Consensus pattern (15 bp):
TTCTATTCTTTTTTT
Found at i:2723038 original size:5 final size:5
Alignment explanation
Indices: 2723025--2723097 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
2723015 TTGTTTTATG
2723025 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
2723073 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
2723098 TTTTTTAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:2723050 original size:19 final size:19
Alignment explanation
Indices: 2723026--2723068 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2723016 TGTTTTATGT
2723026 ATATATATAAT-ATAATATA
1 ATATAT-TAATAATAATATA
2723045 ATATATTAATAATAATATA
1 ATATATTAATAATAATATA
2723064 ATATA
1 ATATA
2723069 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAATAATAATATA
Found at i:2723078 original size:24 final size:25
Alignment explanation
Indices: 2723032--2723096 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
2723022 ATGTATATAT
* *
2723032 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
2723056 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
2723081 TTACTATAATATAATA
1 ATAATATAATATAATA
2723097 TTTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 13 0.38
26 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:2729558 original size:22 final size:23
Alignment explanation
Indices: 2729515--2729558 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
2729505 TTATCATTGT
* **
2729515 TATAAAAAATATTTAATTATAAC
1 TATAAAAAATAATTAAAAATAAC
2729538 TATAAAAAA-AATTAAAAATAA
1 TATAAAAAATAATTAAAAATAA
2729559 TTATCATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
TATAAAAAATAATTAAAAATAAC
Found at i:2729824 original size:21 final size:21
Alignment explanation
Indices: 2729800--2729852 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2729790 CATTGTTTCT
*
2729800 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
*
2729821 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
2729842 AATCTCACCGC
1 AATCTCACCGC
2729853 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.40, G:0.09, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:2742832 original size:21 final size:21
Alignment explanation
Indices: 2742785--2742832 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2742775 TTTCGTTTGC
*
2742785 TATTCTGTTTCTTTTCTTCTA
1 TATTTTGTTTCTTTTCTTCTA
* *
2742806 TCTTTTGTTTC-TTTCTTTCTT
1 TATTTTGTTTCTTTTC-TTCTA
2742827 TATTTT
1 TATTTT
2742833 ACTTACTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.73
Consensus pattern (21 bp):
TATTTTGTTTCTTTTCTTCTA
Found at i:2743018 original size:24 final size:25
Alignment explanation
Indices: 2742976--2743022 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2742966 TATTTGTTAC
* *
2742976 AATTTAATTTATTTTATAACATAAT
1 AATTTAATTAATTTAATAACATAAT
2743001 AATTTAA-TAATTTAATAACATA
1 AATTTAATTAATTTAATAACATA
2743023 TTTTAACACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTTAATTAATTTAATAACATAAT
Found at i:2745402 original size:24 final size:23
Alignment explanation
Indices: 2745361--2745407 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
2745351 TATTCATGGG
2745361 ACATTTAAAGTAAGGTAAGTAATA
1 ACATTTAAAGTAAGGTAAG-AATA
*
2745385 ACATTTGAAATTAA-GTAAGAATA
1 ACATTT-AAAGTAAGGTAAGAATA
2745408 TGTGTGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 11 0.52
25 6 0.29
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (23 bp):
ACATTTAAAGTAAGGTAAGAATA
Found at i:2745759 original size:21 final size:23
Alignment explanation
Indices: 2745717--2745759 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2745707 TATTATTCCG
*
2745717 GGTGTGTTTAGGTTGGATATTCT
1 GGTGTGTTTAGGGTGGATATTCT
2745740 GGTGTGTTT-GGGTGGA-ATTC
1 GGTGTGTTTAGGGTGGATATTC
2745760 GCGTATCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.12, C:0.05, G:0.40, T:0.44
Consensus pattern (23 bp):
GGTGTGTTTAGGGTGGATATTCT
Found at i:2747676 original size:19 final size:19
Alignment explanation
Indices: 2747612--2747678 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
2747602 CATAAGTATT
* *
2747612 TATTTATACACATATTAAA
1 TATTTTTACATATATTAAA
*
2747631 TATTTTT-TATAT-TTATAA
1 TATTTTTACATATATTA-AA
2747649 GTATTTTTTTACATATATTAAA
1 -TA--TTTTTACATATATTAAA
2747671 TATTTTTA
1 TATTTTTA
2747679 AAAATATCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
17 3 0.08
18 5 0.13
19 14 0.37
21 7 0.18
22 6 0.16
23 3 0.08
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (19 bp):
TATTTTTACATATATTAAA
Found at i:2747676 original size:20 final size:20
Alignment explanation
Indices: 2747618--2747677 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2747608 TATTTATTTA
*
2747618 TACACATATTAAATATTTTT
1 TACATATATTAAATATTTTT
* * *
2747638 TATATTTA-TAAGTATTTTTT
1 TACATATATTAAATA-TTTTT
2747658 TACATATATTAAATATTTTT
1 TACATATATTAAATATTTTT
2747678 AAAAATATCG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 5 0.16
20 21 0.68
21 5 0.16
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (20 bp):
TACATATATTAAATATTTTT
Found at i:2748232 original size:32 final size:32
Alignment explanation
Indices: 2748170--2748232 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
2748160 CCATAAACTT
* *
2748170 ATAAACTAATTACTTGAATTTAGTAGCTCATG
1 ATAAACTAATTAATTGAATTTAGTAACTCATG
* *
2748202 ATAAATTAATTAATTTAATTT-GATAACTCAT
1 ATAAACTAATTAATTGAATTTAG-TAACTCAT
2748233 ATTGATTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (32 bp):
ATAAACTAATTAATTGAATTTAGTAACTCATG
Found at i:2749793 original size:16 final size:17
Alignment explanation
Indices: 2749762--2749799 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2749752 GCGTTTCTTC
*
2749762 TTCTTCCATTTCTTTGT
1 TTCTTCCATCTCTTTGT
2749779 TTCTTCCA-CTCTTTGT
1 TTCTTCCATCTCTTTGT
2749795 TTCTT
1 TTCTT
2749800 TCCGACGCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.05, C:0.26, G:0.05, T:0.63
Consensus pattern (17 bp):
TTCTTCCATCTCTTTGT
Found at i:2760199 original size:5 final size:6
Alignment explanation
Indices: 2760182--2760223 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
2760172 ATTTTTTTCG
*
2760182 ATAAAA ATAAAA ATAAAA AT-AAA ATAAATA CTAAAA AGTAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAA-A ATAAAA A-TAAA
2760224 TAGCTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 5 0.16
6 17 0.55
7 9 0.29
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:2760207 original size:17 final size:19
Alignment explanation
Indices: 2760185--2760223 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
2760175 TTTTTCGATA
2760185 AAAATAAA-AATAAAAA-T
1 AAAATAAATAATAAAAAGT
*
2760202 AAAATAAATACTAAAAAGT
1 AAAATAAATAATAAAAAGT
2760221 AAA
1 AAA
2760224 TAGCTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 7 0.37
19 4 0.21
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (19 bp):
AAAATAAATAATAAAAAGT
Found at i:2763434 original size:18 final size:18
Alignment explanation
Indices: 2763413--2763455 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2763403 TATTCATCTA
**
2763413 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
2763431 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
2763449 AACCCAA
1 AACCCAA
2763456 CCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:2766601 original size:14 final size:15
Alignment explanation
Indices: 2766582--2766624 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
2766572 TTAACCCAAT
2766582 ATTTTATTTATTAA-
1 ATTTTATTTATTAAC
*
2766596 ATTTTATATTTTTAAC
1 ATTTTAT-TTATTAAC
2766612 A-TTTATTTATTAA
1 ATTTTATTTATTAA
2766625 GTTTAGGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 13 0.52
15 11 0.44
16 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTATTTATTAAC
Found at i:2768374 original size:28 final size:28
Alignment explanation
Indices: 2768343--2768407 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
2768333 ATAAAAATTA
2768343 ACCAAAATATTATAAC-TTTTTT-TTATTT
1 ACCAAAATATT-T-ACTTTTTTTATTATTT
2768371 ACCAAAATA-TTACTTTTTTTATTATTT
1 ACCAAAATATTTACTTTTTTTATTATTT
*
2768398 ACGAAAATAT
1 ACCAAAATAT
2768408 ACCAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 2 0.06
26 7 0.21
27 15 0.45
28 9 0.27
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (28 bp):
ACCAAAATATTTACTTTTTTTATTATTT
Found at i:2768507 original size:27 final size:27
Alignment explanation
Indices: 2768477--2768555 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
2768467 GGCCAATCGC
* *
2768477 ATTGGCGACACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
* *
2768504 ATTGGTGGCACCAATGGTGCCAAAGTG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
2768531 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
2768556 GACTAAAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.30, C:0.22, G:0.32, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGAG
Found at i:2768656 original size:19 final size:19
Alignment explanation
Indices: 2768629--2768698 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
2768619 TCAACTCATT
*
2768629 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
2768648 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
2768666 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
2768685 TTTTAATTTAATAA
1 TTTTAATTTAATAA
2768699 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:2768679 original size:37 final size:37
Alignment explanation
Indices: 2768634--2768704 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
2768624 TCATTTTTTT
2768634 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
2768671 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
2768705 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:2768961 original size:18 final size:19
Alignment explanation
Indices: 2768924--2768962 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2768914 TCAACTCATT
* *
2768924 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACACTA
2768943 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACACTA
2768961 TT
1 TT
2768963 AAGTAATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAATTTAATAACACTA
Found at i:2769199 original size:19 final size:19
Alignment explanation
Indices: 2769177--2769246 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
2769167 TTCAACTCAT
*
2769177 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
2769196 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
2769214 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
2769233 TTTTAATTTAATAA
1 TTTTAATTTAATAA
2769247 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:2769226 original size:37 final size:37
Alignment explanation
Indices: 2769182--2769252 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
2769172 CTCATTTTTT
2769182 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
2769219 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
2769253 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:2769502 original size:18 final size:18
Alignment explanation
Indices: 2769481--2769540 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
2769471 TTTAATATCT
2769481 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
* * *
2769499 CTATTCTCATTTAATAACT
1 CTATTTTAATTTAATAA-A
2769518 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
2769536 CTATT
1 CTATT
2769541 AAGTAATACT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 20 0.57
19 15 0.43
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (18 bp):
CTATTTTAATTTAATAAA
Found at i:2769520 original size:37 final size:37
Alignment explanation
Indices: 2769470--2769540 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
2769460 TCGTTTTTTT
*
2769470 ATTTAATATCTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
2769507 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
2769541 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:2769534 original size:19 final size:19
Alignment explanation
Indices: 2769465--2769534 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
2769455 TCAACTCGTT
* *
2769465 TTTTTATTTAATATCTCTA
1 TTTTAATTTAATAACTCTA
*
2769484 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
2769502 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
2769521 TTTTAATTTAATAA
1 TTTTAATTTAATAA
2769535 ACTATTAAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 15 0.36
19 27 0.64
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:2769626 original size:288 final size:289
Alignment explanation
Indices: 2768929--2769806 Score: 1634
Period size: 288 Copynumber: 3.0 Consensus size: 289
2768919 TCATTTTTTT
2768929 ATTTAATAACTCTATTTTAATTTAATAAACTATTAAGTAATACTTAATTTTTTTAAATTAAAATA
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTAAGTAATACTTAATTTTTTTAAATTAAAATA
*
2768994 GAGTTATTAAATGAGAGAATTCTAATTAAGTGACCATTTGCCGTTTTAAGGACCTGAAATGCAAA
66 GAGTTATTAAATGAGAGAATTCTAATTAAGTGACCATTTGCCGTTTTAAGGACCTGACATGCAAA
*
2769059 TTTACCATTTTGAATTTTGAAAGTGAATTGCTGTTGTGCGCACTAAAATTGAAATGTGGCTAATT
131 TTTACCATTTTGAATTTTGAAAGTGAATTGCTGCTGT-CGCACTAAAATTGAAATGTGGCTAATT
*
2769124 GCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAACTCATTTTTTATTTAAT
195 GCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAACTCTTTTTTTATTTAAT
2769189 AACTCTATTTTAATTTAATAAACTATTCTC
260 AACTCTATTTTAATTTAATAAACTATTCTC
2769219 ATTTAATAACTCTATTTTAATTTAATAAACTATTAAGTAATACTTAATTTTTTTAAATTAAAATA
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTAAGTAATACTTAATTTTTTTAAATTAAAATA
2769284 GAGTTATTAAATGAGAGAATTCTAATTAAGTGACCATTTGCCGTTTTAAGGACCTGACATGCAAA
66 GAGTTATTAAATGAGAGAATTCTAATTAAGTGACCATTTGCCGTTTTAAGGACCTGACATGCAAA
2769349 TTTACCATTTTGAATTTTGAAAGTGAATTGCTGCTGT-G-ACTAAAATTGAAATGTGGCTAATTG
131 TTTACCATTTTGAATTTTGAAAGTGAATTGCTGCTGTCGCACTAAAATTGAAATGTGGCTAATTG
2769412 CCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAACTCGTTTTTTTATTTAAT
196 CCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAACTC-TTTTTTTATTTAAT
*
2769477 ATCTCTATTTTAATTTAATAAACTATTCTC
260 AACTCTATTTTAATTTAATAAACTATTCTC
2769507 ATTTAATAACTCTATTTTAATTTAATAAACTATTAAGTAATACTTAATTTTTTTAAATTAAAATA
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTAAGTAATACTTAATTTTTTTAAATTAAAATA
2769572 GAGTTATTAAATGAGAGAATTCTAATTAAGTGACCATTTGCCGTTTTAAGGACCTGACATGCAAA
66 GAGTTATTAAATGAGAGAATTCTAATTAAGTGACCATTTGCCGTTTTAAGGACCTGACATGCAAA
*
2769637 TTTACTATTTTGAATTTTGAAAGTGAATTGCTGCTGCTGTGCGCACTAAAATTGAAATGTGGCTA
131 TTTACCATTTTGAATTTTGAAAGTGAA-T--TGCTGCTGT-CGCACTAAAATTGAAATGTGGCTA
2769702 ATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAACTCATTTTTTTATT
192 ATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAACTC-TTTTTTTATT
2769767 TAATAACTCTATTTTAATTTAATAAACTATTCTC
256 TAATAACTCTATTTTAATTTAATAAACTATTCTC
2769801 ATTTAA
1 ATTTAA
2769807 ATTAAAATAG
Statistics
Matches: 574, Mismatches: 7, Indels: 10
0.97 0.01 0.02
Matches are distributed among these distances:
287 75 0.13
288 199 0.35
289 1 0.00
290 165 0.29
291 9 0.02
293 1 0.00
294 124 0.22
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (289 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTAAGTAATACTTAATTTTTTTAAATTAAAATA
GAGTTATTAAATGAGAGAATTCTAATTAAGTGACCATTTGCCGTTTTAAGGACCTGACATGCAAA
TTTACCATTTTGAATTTTGAAAGTGAATTGCTGCTGTCGCACTAAAATTGAAATGTGGCTAATTG
CCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAACTCTTTTTTTATTTAATA
ACTCTATTTTAATTTAATAAACTATTCTC
Found at i:2769796 original size:18 final size:19
Alignment explanation
Indices: 2769759--2769797 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2769749 TCAACTCATT
* *
2769759 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACACTA
2769778 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACACTA
2769796 TT
1 TT
2769798 CTCATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAATTTAATAACACTA
Found at i:2769804 original size:18 final size:19
Alignment explanation
Indices: 2769764--2769806 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2769754 TCATTTTTTT
* *
2769764 ATTTAATAACTCTATTTTA
1 ATTTAATAACACTATTCTA
*
2769783 ATTTAATAA-ACTATTCTC
1 ATTTAATAACACTATTCTA
2769801 ATTTAA
1 ATTTAA
2769807 ATTAAAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAATAACACTATTCTA
Found at i:2769866 original size:18 final size:19
Alignment explanation
Indices: 2769803--2769861 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
2769793 CTATTCTCAT
2769803 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
2769822 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
2769840 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
2769859 TTA
1 TTA
2769862 CTTAATTAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:2770098 original size:37 final size:37
Alignment explanation
Indices: 2770056--2770126 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
2770046 AGCATTACTT
2770056 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
2770093 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
2770127 AAAAAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.39
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:2770131 original size:19 final size:19
Alignment explanation
Indices: 2770062--2770130 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
2770052 ACTTAATAGT
2770062 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
2770081 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
2770099 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
2770118 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
2770131 AAATGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:2770236 original size:27 final size:27
Alignment explanation
Indices: 2770205--2770256 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2770195 CATTTTAGTC
2770205 CTTTGGCACCATTGGTGCCACCAATCT
1 CTTTGGCACCATTGGTGCCACCAATCT
* *
2770232 CTTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCACCAAT
2770257 GTGATTGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.33, G:0.21, T:0.31
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCACCAATCT
Found at i:2770264 original size:27 final size:27
Alignment explanation
Indices: 2770207--2770265 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
2770197 TTTTAGTCCT
*
2770207 TTGGCACCATTGGTGCCACCAATCTCT
1 TTGGCACCATTGGTGCCACCAATCTCA
* * * *
2770234 TTGGCACCTTTGGTGCCGCCAATGTGA
1 TTGGCACCATTGGTGCCACCAATCTCA
2770261 TTGGC
1 TTGGC
2770266 CTGATCAGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.29, G:0.25, T:0.31
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCACCAATCTCA
Found at i:2770368 original size:27 final size:24
Alignment explanation
Indices: 2770316--2770376 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 24
2770306 TTTTTTTGGT
* *
2770316 ATATTTTCGTAAATAAAAAAAGTA
1 ATATTTTGGTAAATAAAAAAAATA
2770340 ATATTTTGGTAAATAAAAAAAATTATA
1 ATATTTTGGTAAAT-AAAAAAA--ATA
2770367 ATATTTTGGT
1 ATATTTTGGT
2770377 TAATTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 13 0.41
25 7 0.22
27 12 0.38
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (24 bp):
ATATTTTGGTAAATAAAAAAAATA
Found at i:2770765 original size:19 final size:20
Alignment explanation
Indices: 2770743--2770808 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 20
2770733 AATAAATTCT
*
2770743 AAAATTTATAT-TTTTAAAA
1 AAAATTTATATAATTTAAAA
2770762 AAAA-TTATATAATTTAAAA
1 AAAATTTATATAATTTAAAA
* * * *
2770781 AAAATCTAAAGAATATATAAA
1 AAAATTTATATAATTTA-AAA
2770802 AAAATTT
1 AAAATTT
2770809 GAAAATTTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
18 6 0.16
19 15 0.39
20 8 0.21
21 9 0.24
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAATTTATATAATTTAAAA
Found at i:2779535 original size:18 final size:18
Alignment explanation
Indices: 2779512--2779597 Score: 127
Period size: 18 Copynumber: 4.8 Consensus size: 18
2779502 CGTTTACGGT
2779512 ACTATTCACGTATATGGC
1 ACTATTCACGTATATGGC
* *
2779530 ACTATTCACGTATATAGT
1 ACTATTCACGTATATGGC
2779548 ACTATTCACGTATATGGC
1 ACTATTCACGTATATGGC
* *
2779566 ACTATTCACGTATACGGT
1 ACTATTCACGTATATGGC
*
2779584 ACTGTTCACGTATA
1 ACTATTCACGTATA
2779598 CAGTAGTTGG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (18 bp):
ACTATTCACGTATATGGC
Found at i:2779557 original size:36 final size:36
Alignment explanation
Indices: 2779510--2779597 Score: 149
Period size: 36 Copynumber: 2.4 Consensus size: 36
2779500 ACCGTTTACG
*
2779510 GTACTATTCACGTATATGGCACTATTCACGTATATA
1 GTACTATTCACGTATATGGCACTATTCACGTATACA
*
2779546 GTACTATTCACGTATATGGCACTATTCACGTATACG
1 GTACTATTCACGTATATGGCACTATTCACGTATACA
*
2779582 GTACTGTTCACGTATA
1 GTACTATTCACGTATA
2779598 CAGTAGTTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (36 bp):
GTACTATTCACGTATATGGCACTATTCACGTATACA
Found at i:2788102 original size:31 final size:32
Alignment explanation
Indices: 2788053--2788121 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
2788043 TTTAAAGGTG
*
2788053 TATAA-TTAAATCAAAATTAAAATTTTAAGTA
1 TATAATTTAAACCAAAATTAAAATTTTAAGTA
* * * *
2788084 TA-AATTTAAACCACAATTAGAGTTTTATGTA
1 TATAATTTAAACCAAAATTAAAATTTTAAGTA
2788115 TATAATT
1 TATAATT
2788122 GAACCAATTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 2 0.06
31 25 0.81
32 4 0.13
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (32 bp):
TATAATTTAAACCAAAATTAAAATTTTAAGTA
Found at i:2796568 original size:90 final size:90
Alignment explanation
Indices: 2796415--2796590 Score: 289
Period size: 90 Copynumber: 2.0 Consensus size: 90
2796405 GAGTTGAGGT
* * * *
2796415 TACAAAATTAATGCGACGAATAACATGTAACTCATAAATGATAAGTTTTGAATGGTCGTTTCCAT
1 TACAAAATTAATGCAACAAATAACATATAACTCATAAATGATAAGTTCTGAATGGTCGTTTCCAT
2796480 CCAACATACGTTGCTTTTGTAGTCC
66 CCAACATACGTTGCTTTTGTAGTCC
* *
2796505 TACAAAATTAATGCAACAAATAACATATAACTCGTAAATGATAAGTTCTGAATGGTCTTTTCCAT
1 TACAAAATTAATGCAACAAATAACATATAACTCATAAATGATAAGTTCTGAATGGTCGTTTCCAT
*
2796570 CCAACATATGTTGCTTTTGTA
66 CCAACATACGTTGCTTTTGTA
2796591 ATCCAGGTAC
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (90 bp):
TACAAAATTAATGCAACAAATAACATATAACTCATAAATGATAAGTTCTGAATGGTCGTTTCCAT
CCAACATACGTTGCTTTTGTAGTCC
Found at i:2798990 original size:24 final size:24
Alignment explanation
Indices: 2798944--2798996 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2798934 CTGTATCTTT
*
2798944 TTAATAATAATTATTAAATAATTA
1 TTAATAATAATAATTAAATAATTA
*
2798968 TTAATAA-AATAATTAATTCAATTA
1 TTAATAATAATAATTAAAT-AATTA
2798992 TTAAT
1 TTAAT
2798997 CTAAATCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TTAATAATAATAATTAAATAATTA
Found at i:2800853 original size:48 final size:49
Alignment explanation
Indices: 2800788--2801391 Score: 561
Period size: 50 Copynumber: 12.5 Consensus size: 49
2800778 TACAAAAATT
* * * * *
2800788 GAAAAAAAAA-TTGGGTGTTGGCCTATCAATGACCAGTACCAGTA-TAC
1 GAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTAC
* * *
2800835 GAAAAAAAAATTTAGGTG-TTGCCTTGTCAATGGCCGGAACCAGTA-TAC
1 GAAAAAAAAATTTGGGTGCTGGCC-TGTCAATGGCCGGCACCAGTAGTAC
* * * * **
2800883 GAAAAAAAATTTTGGGTGCTAGCTTGTCAATGGCTGGCACCACCAGTAC
1 GAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTAC
* * * * *
2800932 GAAACAAAAAAATTGGGTGCTGGACTATCAATGGCCTGCACCAGCAGTAC
1 GAAA-AAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTAC
* * * **
2800982 AAAAAAAAAATTTTGTGTGCTGGCCTATCAATGGCCGGCACCACCAGTAC
1 GAAAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTAC
* *
2801032 GAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGTCGGCACCAGCAGTAC
1 GAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTAC
* * ** *
2801081 --AAAAAAAATGTTGGGGTGCTGGCTTGTCAATGGTCGGCACCAACAATAC
1 GAAAAAAAAAT-TT-GGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTAC
* *
2801130 GGAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGTCGGCACCAGTA-TAC
1 -GAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTAC
* * * *
2801179 -AAAAAAAAATTTGGGTGCTGACCTGTTAATGGTCTGCACCAGTA-TAC
1 GAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTAC
* ** * *
2801226 GAAAAAAAAATTTGAGTGCCAGCCTGTCAATGGACGACACCAGTAGTAC
1 GAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTAC
* * *
2801275 GAAAAAAGAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACTAGTAG-AT
1 GAAAAAA-AAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTAC
* * * * * * *
2801324 G-AAAAAAAA-CTGGGTGCTGGCCTGTTAATCGTCAGCACTAG-CGTA-
1 GAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTAC
* *
2801369 TAAAAAAAAATTTTGGTGCTGGC
1 GAAAAAAAAATTTGGGTGCTGGC
2801392 AATTTATCAA
Statistics
Matches: 469, Mismatches: 71, Indels: 34
0.82 0.12 0.06
Matches are distributed among these distances:
45 1 0.00
46 35 0.07
47 79 0.17
48 102 0.22
49 99 0.21
50 143 0.30
51 2 0.00
52 8 0.02
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (49 bp):
GAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTAC
Found at i:2800967 original size:98 final size:97
Alignment explanation
Indices: 2800832--2801391 Score: 523
Period size: 98 Copynumber: 5.8 Consensus size: 97
2800822 AGTACCAGTA
* * *
2800832 TACGAAAAAAAAATTTAGGTG-TTGCCTTGTCAATGGCCGGAACCAGTA-TACGAAAAAAAATTT
1 TACGAAAAAAAAATTTGGGTGCTGGCC-TGTCAATGGCCGGCACCAGTAGTAC-AAAAAAAATTT
* *
2800895 TGGGTGCTAGCTTGTCAATGGCTGGCACCACCAG
64 TGGGTGCTGGCCTGTCAATGGCTGGCACCACCAG
* * * * *
2800929 TACGAAACAAAAAAATTGGGTGCTGGACTATCAATGGCCTGCACCAGCAGTACAAAAAAAAAATT
1 TACGAAA-AAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTAC--AAAAAAAATT
* * *
2800994 TTGTGTGCTGGCCTATCAATGGCCGGCACCACCAG
63 TTGGGTGCTGGCCTGTCAATGGCTGGCACCACCAG
* * *
2801029 TACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGTCGGCACCAGCAGTACAAAAAAAATGTTG
1 TACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTACAAAAAAAAT-TTT
* * *
2801094 GGGTGCTGGCTTGTCAATGG-TCGGCACCAACAA
65 GGGTGCTGGCCTGTCAATGGCT-GGCACCACCAG
* * *
2801127 TACGGAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGTCGGCACCAGTA-TACAAAAAAAAATTT
1 TAC-GAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTACAAAAAAAATTTT
* * **
2801191 GGGTGCTGACCTGTTAATGGTCT-GCACCAGTA-
65 GGGTGCTGGCCTGTCAATGG-CTGGCACCACCAG
* ** * * *
2801223 TACGAAAAAAAAATTTGAGTGCCAGCCTGTCAATGGACGACACCAGTAGTACGAAAAAAGAAATT
1 TACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTAC-AAAAAA-AATTT
* * * **
2801288 TAGGTGCTGGCCTGTCAATGGCCGGCACTAGTAG
64 TGGGTGCTGGCCTGTCAATGGCTGGCACCACCAG
* * * * * * *
2801322 -ATG-AAAAAAAA-CTGGGTGCTGGCCTGTTAATCGTCAGCACTAGCGTA-TA-AAAAAAAATTT
1 TACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCA--GTAGTACAAAAAAAATTT
2801382 T-GGTGCTGGC
64 TGGGTGCTGGC
2801392 AATTTATCAA
Statistics
Matches: 389, Mismatches: 58, Indels: 36
0.81 0.12 0.07
Matches are distributed among these distances:
93 9 0.02
94 5 0.01
95 45 0.12
96 27 0.07
97 59 0.15
98 107 0.28
99 90 0.23
100 47 0.12
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (97 bp):
TACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCAGTAGTACAAAAAAAATTTTG
GGTGCTGGCCTGTCAATGGCTGGCACCACCAG
Found at i:2804362 original size:21 final size:23
Alignment explanation
Indices: 2804338--2804399 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 23
2804328 AAAGTAAATT
2804338 AAATTTTAA-TGAAATGAGG-GA
1 AAATTTTAATTGAAATGAGGAGA
*
2804359 AAATTTTAATTTAAATGAGGAGAAA
1 AAATTTTAATTGAAATGAGGAG--A
2804384 AAATTTTGAATTGAAA
1 AAATTTT-AATTGAAA
2804400 ATAGAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 9 0.26
22 9 0.26
23 1 0.03
25 8 0.24
26 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (23 bp):
AAATTTTAATTGAAATGAGGAGA
Found at i:2804506 original size:19 final size:19
Alignment explanation
Indices: 2804484--2804523 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2804474 CGGAAAAAGT
*
2804484 TAAATTTAAATTAAAAAAA
1 TAAATTGAAATTAAAAAAA
*
2804503 TAAATTGAAATTGAAAAAA
1 TAAATTGAAATTAAAAAAA
2804522 TA
1 TA
2804524 TATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
TAAATTGAAATTAAAAAAA
Found at i:2808457 original size:95 final size:94
Alignment explanation
Indices: 2808328--2808540 Score: 266
Period size: 95 Copynumber: 2.2 Consensus size: 94
2808318 GACTATTAGA
* * **
2808328 AGGCCAGCACCTACTTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCTTGCACCCAAATTT
1 AGGCTAGCACCCA-TTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACCCAAATTT
*
2808393 TTTTTTCGTACTACTGGTG-TCGCCCATTGAC
65 TTTTTTCGTA-TACTGCTGCT-GCCCATTGAC
* * * *
2808424 AGGCTAGCACCCATTTTTTTTCGTATTGGTGGTGCCGGCTATTGACAGGCCAGCACCTAAATTTT
1 AGGCTAGCACCCATTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTT
*
2808489 TTTTTCGTATACTGCTGCTGGCCATTGAC
66 TTTTTCGTATACTGCTGCTGCCCATTGAC
* *
2808518 AAGTTAGCACCCAAATTTTTTTT
1 AGGCTAGCACCC--ATTTTTTTT
2808541 TTTTTTTAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
94 26 0.25
95 56 0.55
96 20 0.20
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (94 bp):
AGGCTAGCACCCATTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTT
TTTTTCGTATACTGCTGCTGCCCATTGAC
Found at i:2808542 original size:49 final size:49
Alignment explanation
Indices: 2808342--2808541 Score: 246
Period size: 49 Copynumber: 4.2 Consensus size: 49
2808332 CAGCACCTAC
* *
2808342 TTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCTTGCACCCAAAT
1 TTTTTTTTCGTACTACTGGTGCCGGCCATTGACAGGCTAGCACCCAAAT
* *
2808391 TTTTTTTTCGTACTACTGGTGTCGCCCATTGACAGGCTAGCACCC--A-
1 TTTTTTTTCGTACTACTGGTGCCGGCCATTGACAGGCTAGCACCCAAAT
* ** * * *
2808437 TTTTTTTTCGTATTGGTGGTGCCGGCTATTGACAGGCCAGCACCTAAAT
1 TTTTTTTTCGTACTACTGGTGCCGGCCATTGACAGGCTAGCACCCAAAT
* * * *
2808486 TTTTTTTTCGTA-TACTGCTGCTGGCCATTGACAAGTTAGCACCCAAAT
1 TTTTTTTTCGTACTACTGGTGCCGGCCATTGACAGGCTAGCACCCAAAT
2808534 TTTTTTTT
1 TTTTTTTT
2808542 TTTTTTAAAT
Statistics
Matches: 127, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
46 37 0.29
47 1 0.01
48 36 0.28
49 53 0.42
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (49 bp):
TTTTTTTTCGTACTACTGGTGCCGGCCATTGACAGGCTAGCACCCAAAT
Found at i:2815953 original size:197 final size:196
Alignment explanation
Indices: 2815593--2815958 Score: 418
Period size: 197 Copynumber: 1.9 Consensus size: 196
2815583 ATTTGCTAAG
* * * * * * **
2815593 GCCTCTTAATGCCCGAACTCGCTAAAAAGCACTACCAATGAAGGAATTACCCAACAACAATGGTC
1 GCCTCTTAAGGCCCCAACTAGCTAAAAAGCACTACCAACGAAGCAACTACCCAACAACAATGAAC
* * * *
2815658 TTCCAAAGACCCTAATGTTGTTTTTGGTAAAGCCTTTTAAGGCTCTAGTGTTCTGCCAGGTAAGG
66 TTCCAAAGACCCTAATGTTGTTTTTGGTAAAGCCTTTTAAAGCTCTAGTGCTCTGCCAAGCAAGG
**
2815723 CCTCTTAAGGCCCTAAACTGACTTCTGGCGTAGGCCTTTCGAGTGCCTTATTATTGTTTTCAACA
131 CCTCTTAAGGCCCT-AACTGACTTCCAGCGTAGGCCTTTCGAGTGCCTTATTATTGTTTTCAACA
2815788 AA
195 AA
* * *
2815790 GCCTCTTAAGGCCCCAACTAGCTAAAAAGTGACTACCAACGAAGCAACTATCTAACAACAAT-AA
1 GCCTCTTAAGGCCCCAACTAGCTAAAAAG-CACTACCAACGAAGCAACTACCCAACAACAATGAA
* * * *
2815854 CTTGCC-AAGGCCCTAGTG-TGATTTTTGGTGAAGCCTTTTAAAGCTCTAGTGC-CTCGTCAAGC
65 CTT-CCAAAGACCCTAATGTTG-TTTTTGGTAAAGCCTTTTAAAGCTCTAGTGCTCT-GCCAAGC
* * *
2815916 GAGGCCTCTTAAGGCCCT-AGTGCCATTTCCAGCGTAGGCCTTT
127 AAGGCCTCTTAAGGCCCTAACTG--ACTTCCAGCGTAGGCCTTT
2815959 TGAGGGATCC
Statistics
Matches: 139, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
195 3 0.02
196 4 0.03
197 104 0.75
198 28 0.20
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (196 bp):
GCCTCTTAAGGCCCCAACTAGCTAAAAAGCACTACCAACGAAGCAACTACCCAACAACAATGAAC
TTCCAAAGACCCTAATGTTGTTTTTGGTAAAGCCTTTTAAAGCTCTAGTGCTCTGCCAAGCAAGG
CCTCTTAAGGCCCTAACTGACTTCCAGCGTAGGCCTTTCGAGTGCCTTATTATTGTTTTCAACAA
A
Found at i:2816315 original size:60 final size:60
Alignment explanation
Indices: 2816219--2816365 Score: 163
Period size: 60 Copynumber: 2.5 Consensus size: 60
2816209 ATAAAGACAG
* * * * * *
2816219 CATTGGAGAGTTCATTGTATATGTACCCTTATGGAGTTCACTCA-T-TGATACGAACCCCTT
1 CATTGGAGAGTTCATTATATATCTATCCTTACGGAGTTAACTCACTCAGATA--AACCCCTT
* ** *
2816279 CATTGGAGAGTTCATTATGTATCTATTGTTACGGAGTTAACTCACTCAGGTAAACCCCTT
1 CATTGGAGAGTTCATTATATATCTATCCTTACGGAGTTAACTCACTCAGATAAACCCCTT
*
2816339 CATTGAAGAGTTCATTATATATCTATC
1 CATTGGAGAGTTCATTATATATCTATC
2816366 TTTTTTATTC
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
60 68 0.94
61 1 0.01
62 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (60 bp):
CATTGGAGAGTTCATTATATATCTATCCTTACGGAGTTAACTCACTCAGATAAACCCCTT
Found at i:2818556 original size:12 final size:11
Alignment explanation
Indices: 2818528--2818579 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 11
2818518 ATATACTAAA
*
2818528 TAAAATAATAA
1 TAAAATAATAT
2818539 TAAAATAATATT
1 TAAAATAATA-T
2818551 TAAAAT-A-A-
1 TAAAATAATAT
2818559 TAAAATAATATT
1 TAAAATAATA-T
2818571 TAAAATAAT
1 TAAAATAAT
2818580 TAATCTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
8 6 0.17
9 1 0.03
10 2 0.06
11 11 0.31
12 15 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAATAATAT
Found at i:2818559 original size:20 final size:20
Alignment explanation
Indices: 2818534--2818579 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
2818524 TAAATAAAAT
2818534 AATAATAAAATAATATTTAA
1 AATAATAAAATAATATTTAA
2818554 AATAATAAAATAATATTTAA
1 AATAATAAAATAATATTTAA
2818574 AATAAT
1 AATAAT
2818580 TAATCTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AATAATAAAATAATATTTAA
Found at i:2819043 original size:23 final size:23
Alignment explanation
Indices: 2819014--2819062 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2819004 CTTTCTTAAT
* **
2819014 GTAGTAATTTTCGAGGTATTACA
1 GTAGTAATTTTCAAAATATTACA
2819037 GTAGTAATTTTCAAAATATTACA
1 GTAGTAATTTTCAAAATATTACA
2819060 GTA
1 GTA
2819063 TATATAGTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (23 bp):
GTAGTAATTTTCAAAATATTACA
Found at i:2823009 original size:11 final size:11
Alignment explanation
Indices: 2822993--2823037 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 11
2822983 ATATTTTTAA
2822993 AAAAATTATAT
1 AAAAATTATAT
2823004 AAAAATAATAATAAT
1 AAAAAT--T-AT-AT
2823019 AAAAATTATAT
1 AAAAATTATAT
2823030 AAAAATTA
1 AAAAATTA
2823038 ATACGGTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 16 0.53
12 2 0.07
13 2 0.07
14 2 0.07
15 8 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAATTATAT
Found at i:2823509 original size:26 final size:26
Alignment explanation
Indices: 2823478--2823554 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 26
2823468 GCCCATTTTT
* *
2823478 AATAAACATTAAAAAATTATTTTAAA
1 AATAAAAATTAAAAAAATATTTTAAA
** *
2823504 AATAAAAAATTTTAAAAGTA-TTTAAA
1 AAT-AAAAATTAAAAAAATATTTTAAA
*
2823530 ATTAAAAATTAAAAAAATATATTTA
1 AATAAAAATTAAAAAAATAT-TTTA
2823555 TTATATTCGG
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
25 13 0.32
26 11 0.28
27 16 0.40
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (26 bp):
AATAAAAATTAAAAAAATATTTTAAA
Found at i:2823552 original size:27 final size:27
Alignment explanation
Indices: 2823480--2823554 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 27
2823470 CCATTTTTAA
* *
2823480 TAAACATTAAAAAATTAT-TTTAAAAAT
1 TAAAAATTAAAAAAATATATTT-AAAAT
* ** *
2823507 AAAAAATT-TTAAAA-GTATTTAAAAT
1 TAAAAATTAAAAAAATATATTTAAAAT
2823532 TAAAAATTAAAAAAATATATTTA
1 TAAAAATTAAAAAAATATATTTA
2823555 TTATATTCGG
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
25 13 0.37
26 10 0.29
27 12 0.34
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (27 bp):
TAAAAATTAAAAAAATATATTTAAAAT
Found at i:2830896 original size:5 final size:6
Alignment explanation
Indices: 2830880--2830905 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2830870 ACTAAATTCT
2830880 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
2830906 GAGGGACAAA
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:2833031 original size:43 final size:42
Alignment explanation
Indices: 2832982--2833099 Score: 146
Period size: 43 Copynumber: 2.7 Consensus size: 42
2832972 ATAATTTCGT
*
2832982 TGAACTTGAGTGATTCAGATTGTGATTAATATATATTTTCGGA
1 TGAACTTAAGTGATTCAGATTGTGATTAATATATATTTT-GGA
* * *
2833025 TGAACTTAAGTGATTCAGATTGTGATCAAATATGTATTTTTGA
1 TGAACTTAAGTGATTCAGATTGTGAT-TAATATATATTTTGGA
* *
2833068 TGAACTTTTAAGTGACTCAAATTGTGATTAAT
1 TGAAC--TTAAGTGATTCAGATTGTGATTAAT
2833100 TTTGGGGTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
43 32 0.49
44 14 0.22
45 19 0.29
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.42
Consensus pattern (42 bp):
TGAACTTAAGTGATTCAGATTGTGATTAATATATATTTTGGA
Found at i:2852701 original size:46 final size:44
Alignment explanation
Indices: 2852600--2852961 Score: 371
Period size: 46 Copynumber: 8.6 Consensus size: 44
2852590 TACGTATGAT
*
2852600 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTA-GCTAC
2852643 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-A-GCTAC
* *
2852689 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-A-GCTAC
*
2852735 TACTTATCACTTTGTCACTTGATCAGATAA--GTA--TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
*
2852771 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
*
2852807 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT--AGCTAC
*
2852853 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
*
2852889 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT--AGCTAC
* *
2852935 CACTTATCACTTTATCCCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
2852962 AGTACTCAAA
Statistics
Matches: 283, Mismatches: 13, Indels: 43
0.83 0.04 0.13
Matches are distributed among these distances:
36 92 0.33
38 5 0.02
39 1 0.00
40 5 0.02
41 1 0.00
42 6 0.02
43 11 0.04
44 10 0.04
45 20 0.07
46 132 0.47
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (44 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
Found at i:2852777 original size:36 final size:36
Alignment explanation
Indices: 2852736--2852925 Score: 245
Period size: 36 Copynumber: 5.0 Consensus size: 36
2852726 TAAGGCTAAT
*
2852736 ACTTATCACTTTGTCACTTGATCAGATAAGTATAGC
1 ACTTATCACTTTTTCACTTGATCAGATAAGTATAGC
2852772 ACTTATCACTTTTTCACTTGATCAGATAAGTATAGC
1 ACTTATCACTTTTTCACTTGATCAGATAAGTATAGC
2852808 ACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
1 ACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG----C
* * *
2852854 ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 ACTTATCACTTTTTCACTTGATCAGATAAGTATAGC
*
2852890 ACTTATCACTTTTTCACTTGATCAGATAAGTGTAGC
1 ACTTATCACTTTTTCACTTGATCAGATAAGTATAGC
2852926 TAAAGCTACC
Statistics
Matches: 138, Mismatches: 6, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
36 99 0.72
38 3 0.02
40 3 0.02
42 3 0.02
44 2 0.01
46 28 0.20
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (36 bp):
ACTTATCACTTTTTCACTTGATCAGATAAGTATAGC
Found at i:2852857 original size:82 final size:82
Alignment explanation
Indices: 2852643--2852961 Score: 397
Period size: 82 Copynumber: 3.9 Consensus size: 82
2852633 GCTAGGCTAC
* *
2852643 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
2852708 TGATCAGATAAGTGTAGCTAAGG
66 TGATCAGATAA--GTA--T-A-G
*
2852731 CTAATACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG----CACTTATCACTTTTT
1 C----ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTAT
2852786 CACTTGATCAGATAAGTATAG
62 CACTTGATCAGATAAGTATAG
* * *
2852807 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
*
2852872 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTATAG
* *
2852889 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCCCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
2852954 TGATCAGA
66 TGATCAGA
2852962 AGTACTCAAA
Statistics
Matches: 209, Mismatches: 8, Indels: 34
0.83 0.03 0.14
Matches are distributed among these distances:
72 28 0.13
74 3 0.01
76 3 0.01
77 1 0.00
78 3 0.01
80 3 0.01
82 133 0.64
86 1 0.00
88 2 0.01
90 3 0.01
92 29 0.14
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (82 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
TGATCAGATAAGTATAG
Found at i:2852897 original size:118 final size:118
Alignment explanation
Indices: 2852689--2852925 Score: 411
Period size: 118 Copynumber: 2.0 Consensus size: 118
2852679 CTAAGGCTAC
* *
2852689 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAATACTTATCACTTTGTCACT
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
2852754 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
66 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
* * *
2852807 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
* *
2852872 TGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
66 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
2852925 C
1 C
2852926 TAAAGCTACC
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 112 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (118 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:2863101 original size:24 final size:24
Alignment explanation
Indices: 2863074--2863120 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2863064 GGTTTAAGCT
*
2863074 ATGTTTTGGTATGTAGT-TTAGTTA
1 ATGTTGTGGTATGT-GTATTAGTTA
2863098 ATGTTGTGGTATGTGTATTAGTT
1 ATGTTGTGGTATGTGTATTAGTT
2863121 TTAAAGCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (24 bp):
ATGTTGTGGTATGTGTATTAGTTA
Found at i:2866116 original size:44 final size:44
Alignment explanation
Indices: 2866053--2866143 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
2866043 AACTTTGTTT
* *
2866053 TTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTAATTAATGTAGGTTATTTTAATA
2866097 TTAGTTTCCCACTTAAACTCTAATTAATGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTAATTAATGTAGGTTATTTTAATA
2866141 TTA
1 TTA
2866144 TTTGACCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACTCTAATTAATGTAGGTTATTTTAATA
Found at i:2867206 original size:50 final size:50
Alignment explanation
Indices: 2867151--2867306 Score: 151
Period size: 50 Copynumber: 3.2 Consensus size: 50
2867141 TACCACAAAG
*
2867151 GCATCTAAGTAAAAAAAACATAATTGATGCAATTCAAATGTTCAATACAA
1 GCATCTAAGTAAAAAAAACATAATTGATGCAATTCAAATGTTCAACACAA
* * * * ** * * *
2867201 GCATCTAAG-CATAATACCATAATCAATGCAAAT--GA-GTT-ACCACAAA
1 GCATCTAAGTAAAAAAAACATAATTGATGCAATTCAAATGTTCAACAC-AA
* *
2867247 GGCATCTAAGTAAAGAAAACATAATTGATGCAGTTCAAATGTTCAACACAA
1 -GCATCTAAGTAAAAAAAACATAATTGATGCAATTCAAATGTTCAACACAA
2867298 GCATCTAAG
1 GCATCTAAG
2867307 CATAATACCA
Statistics
Matches: 78, Mismatches: 21, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
45 3 0.04
46 5 0.06
47 10 0.13
48 15 0.19
49 17 0.22
50 19 0.24
51 5 0.06
52 4 0.05
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (50 bp):
GCATCTAAGTAAAAAAAACATAATTGATGCAATTCAAATGTTCAACACAA
Found at i:2867241 original size:97 final size:97
Alignment explanation
Indices: 2867131--2867361 Score: 410
Period size: 97 Copynumber: 2.4 Consensus size: 97
2867121 TTAAAAAGAG
*
2867131 GCAAATGAATTACCACAAAGGCATCTAAGTAAAAAAAACATAATTGATGCAATTCAAATGTTCAA
1 GCAAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAACATAATTGATGCAATTCAAATGTTCAA
*
2867196 TACAAGCATCTAAGCATAATACCATAATCAAT
66 CACAAGCATCTAAGCATAATACCATAATCAAT
* *
2867228 GCAAATGAGTTACCACAAAGGCATCTAAGTAAAGAAAACATAATTGATGCAGTTCAAATGTTCAA
1 GCAAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAACATAATTGATGCAATTCAAATGTTCAA
2867293 CACAAGCATCTAAGCATAATACCATAATCAAT
66 CACAAGCATCTAAGCATAATACCATAATCAAT
*
2867325 GCAAATGAGTTACCACAAAGG-ATTTAAGTAAAAAAAA
1 GCAAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAA
2867362 AACATAAAGG
Statistics
Matches: 128, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
96 14 0.11
97 114 0.89
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.23
Consensus pattern (97 bp):
GCAAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAACATAATTGATGCAATTCAAATGTTCAA
CACAAGCATCTAAGCATAATACCATAATCAAT
Found at i:2867377 original size:26 final size:26
Alignment explanation
Indices: 2867341--2867394 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
2867331 GAGTTACCAC
2867341 AAAGGATTTAAGTAAAAAAAAAACAT
1 AAAGGATTTAAGTAAAAAAAAAACAT
2867367 AAAGGATTTAAGTAAAAAAAAAACAT
1 AAAGGATTTAAGTAAAAAAAAAACAT
2867393 AA
1 AA
2867395 TTGATGCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.67, C:0.04, G:0.11, T:0.19
Consensus pattern (26 bp):
AAAGGATTTAAGTAAAAAAAAAACAT
Found at i:2867913 original size:22 final size:22
Alignment explanation
Indices: 2867869--2867912 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2867859 TAGAAGGAGG
2867869 AGAAGCAAGAAACAAGCAAAAA
1 AGAAGCAAGAAACAAGCAAAAA
*
2867891 AGAAGCAAGAAGCAA-CAAAAA
1 AGAAGCAAGAAACAAGCAAAAA
2867912 A
1 A
2867913 AATTTAAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.68, C:0.14, G:0.18, T:0.00
Consensus pattern (22 bp):
AGAAGCAAGAAACAAGCAAAAA
Found at i:2868570 original size:28 final size:27
Alignment explanation
Indices: 2868538--2868600 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
2868528 TTTAATATTA
*
2868538 AAATAATACA-AAAATTCATTTATAATTT
1 AAATAATA-ATAAAATTCA-GTATAATTT
* *
2868566 GAATAATAATATAATTCAGTATAATTT
1 AAATAATAATAAAATTCAGTATAATTT
2868593 AAATAATA
1 AAATAATA
2868601 TTACTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (27 bp):
AAATAATAATAAAATTCAGTATAATTT
Found at i:2870494 original size:44 final size:44
Alignment explanation
Indices: 2870444--2870758 Score: 160
Period size: 44 Copynumber: 7.2 Consensus size: 44
2870434 CCAGTAATTC
*
2870444 TATCTCCCTGAGCAGCAGTGGAATAGATTAAAGATTTCAGATAT
1 TATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTTCAGATAT
* * * * * ** ** * *
2870488 TGTCTCCCTAAGCAGTAGTGGGACAGATCAAAGATGGCGGATTT
1 TATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTTCAGATAT
* ** * * *
2870532 TACCTCCCTGAAGTTGCAGTGGAGTATATTGAAG---CCAG-TAATT
1 TATCTCCCTG-AGCAGCAGTGGAATAGATTGAAGATTTCAGAT-A-T
*
2870575 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATAT
1 -TATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTTCAGATAT
* * * * * ** ** * *
2870620 TGTCTCCCTAAGCAGTAGTGGGACAGATCAAAGATGGCGGATTT
1 TATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTTCAGATAT
* ** * * *
2870664 TACCTCCCTGAAGTTGCAGTGGAGTATATTGAAG---CCAG-TAATT
1 TATCTCCCTG-AGCAGCAGTGGAATAGATTGAAGATTTCAGAT-A-T
*
2870707 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATAT
1 -TATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTTCAGATAT
*
2870752 TGTCTCC
1 TATCTCC
2870759 AGTAGTGGGA
Statistics
Matches: 188, Mismatches: 67, Indels: 32
0.66 0.23 0.11
Matches are distributed among these distances:
41 2 0.01
42 4 0.02
43 38 0.20
44 104 0.55
45 30 0.16
46 8 0.04
47 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTTCAGATAT
Found at i:2870538 original size:132 final size:132
Alignment explanation
Indices: 2870379--2871235 Score: 1133
Period size: 132 Copynumber: 6.5 Consensus size: 132
2870369 GACAACGAAG
* * *
2870379 CAGATCAAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTAATTC
1 CAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* *
2870444 TATCTCCCTGAGCAGCAGTGGAATAGATTAAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGG
66 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGG
2870509 GA
131 GA
* * *
2870511 CAGATCAAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTAATTC
1 CAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
2870576 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGG
66 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGG
2870641 GA
131 GA
* * *
2870643 CAGATCAAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTAATTC
1 CAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
2870708 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCT--C----CAGTAGTGG
66 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGG
2870767 GA
131 GA
* * *
2870769 CAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* * *
2870834 TA-CTTCCCTGGGCAGCAGTGGAATAGATTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAGTG
66 TATC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTG
2870898 AGG-
130 -GGA
* * * * * *
2870901 CAGATCAAAGAGGGTGAATGTTACCTTCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* * * *
2870966 TA-CTTCCCTGGGCAGAAGTGGAATAGATGGAAGATTTCAGATCTTTTCTCCCTAAGCAGTAGTG
66 TATC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTG
*
2871030 GAA
130 GGA
* * ** * *
2871033 CATATTAAAGATGATGGATTTTACCTCCCT-ATGGTTACAATGGAGTAAATTGAAGCCAGTAATT
1 CAGATCAAAGATGGCGGATTTTACCTCCCTGA-GGTTACAGTGGAGTACATTGAAGCCAGTAATT
* * * * * * ** * *
2871097 CTATCTTCCTAGGCAACAGTGGAATAGATTGAAGACTACAGATCTCATCTCCTTAGGCAGTAGTG
65 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTG
*
2871162 GAA
130 GGA
* * * * * *
2871165 TAGATCGAAGATTGCAGATTTTACCTCCCTGAGGTTACAATGGAGTACATTGAAGCAAGT-ATTC
1 CAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATT-
2871229 CTATCTC
65 CTATCTC
2871236 TTTGAAGTTG
Statistics
Matches: 660, Mismatches: 52, Indels: 26
0.89 0.07 0.04
Matches are distributed among these distances:
125 1 0.00
126 114 0.17
128 1 0.00
130 1 0.00
131 4 0.01
132 535 0.81
133 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (132 bp):
CAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGG
GA
Found at i:2871098 original size:390 final size:394
Alignment explanation
Indices: 2870379--2871235 Score: 1144
Period size: 390 Copynumber: 2.2 Consensus size: 394
2870369 GACAACGAAG
* * * * *
2870379 CAGATCAAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTAATTC
1 CAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
*
2870444 TATCTCCCTGAGCAGCAGTGGAATAGATTAAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGG
66 TATCTCCCTGAGCAGCAGTGGAATAGATTAAAGATTACAGATATTGTCTCCCTAAGCAGTAGTGG
* * * * *
2870509 GACAGATCAAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTAAT
131 GACAGATCAAAGAGGGCGAATGTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
2870574 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGT
196 TCTATCTCCCTGGGCAGAAGTGGAATAGATGGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGT
* * * * *
2870639 GGGACAGATCAAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTA
261 GGAACAGATCAAAGATGACGGATTTTACCTCCCTGAAGTTACAATGGAGTAAATTGAAGCCAGTA
* * * * *
2870704 ATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATAT-TGT-C-T-CCAGTAGT
326 ATTCTATCTCCCTAGGCAACAGTGGAATAGATTGAAGACTACAGATATATCTCCTTACCAGTAGT
*
2870765 GGGA
391 GGAA
*
2870769 CAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* *
2870834 TA-CTTCCCTGGGCAGCAGTGGAATAGATTGAAA-ATTACAGATCTTGTCTCCCTAAGCAGTAGT
66 TATC-TCCCTGAGCAGCAGTGGAATAGATT-AAAGATTACAGATATTGTCTCCCTAAGCAGTAGT
* * **
2870897 GAGG-CAGATCAAAGAGGGTGAATGTTACCTTCCTGTGGTTACAGTGGAGTACATTGAAGCCAGT
129 G-GGACAGATCAAAGAGGGCGAATGTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGT
* *
2870961 AATTCTA-CTTCCCTGGGCAGAAGTGGAATAGATGGAAGATTTCAGATCTTTTCTCCCTAAGCAG
193 AATTCTATC-TCCCTGGGCAGAAGTGGAATAGATGGAAGATTTCAGATATTGTCTCCCTAAGCAG
* * * *
2871025 TAGTGGAACATATTAAAGATGATGGATTTTACCTCCCT-ATGGTTACAATGGAGTAAATTGAAGC
257 TAGTGGAACAGATCAAAGATGACGGATTTTACCTCCCTGA-AGTTACAATGGAGTAAATTGAAGC
* * *
2871089 CAGTAATTCTATCTTCCTAGGCAACAGTGGAATAGATTGAAGACTACAGATCTCATCTCCTTAGG
321 CAGTAATTCTATCTCCCTAGGCAACAGTGGAATAGATTGAAGACTACAGATAT-ATCTCCTTA-C
2871154 CAGTAGTGGAA
384 CAGTAGTGGAA
* * * *
2871165 TAGATCGAAGAT--TGCAGATTTTACCTCCCTGAGGTTACAATGGAGTACATTGAAGCAAGT-AT
1 CAGATCAAAGATGGTG-A-ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
2871227 TCCTATCTC
64 T-CTATCTC
2871236 TTTGAAGTTG
Statistics
Matches: 407, Mismatches: 45, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
389 3 0.01
390 323 0.79
391 5 0.01
392 2 0.00
393 1 0.00
394 3 0.01
395 4 0.01
396 65 0.16
397 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (394 bp):
CAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
TATCTCCCTGAGCAGCAGTGGAATAGATTAAAGATTACAGATATTGTCTCCCTAAGCAGTAGTGG
GACAGATCAAAGAGGGCGAATGTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTATCTCCCTGGGCAGAAGTGGAATAGATGGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGT
GGAACAGATCAAAGATGACGGATTTTACCTCCCTGAAGTTACAATGGAGTAAATTGAAGCCAGTA
ATTCTATCTCCCTAGGCAACAGTGGAATAGATTGAAGACTACAGATATATCTCCTTACCAGTAGT
GGAA
Found at i:2875313 original size:60 final size:60
Alignment explanation
Indices: 2875249--2875534 Score: 321
Period size: 60 Copynumber: 4.9 Consensus size: 60
2875239 TACCGTACTG
** * *
2875249 CTATTTTTTTTCTGGCAACTTTTTTGCTGCCTCTTCATGATCTCTTTGCCACCCCTGCTA
1 CTATTTTTTTTCTGGCAACTGCTTTGCTGCCTCTTCACGATCTCTTTGCAACCCCTGCTA
* *
2875309 CTATTATTTTTTTCT-GCAACTGCTTTGCTGCCTCTTCACGTATCTC--TGCAACCCTTGCTG
1 CTA-T-TTTTTTTCTGGCAACTGCTTTGCTGCCTCTTCACG-ATCTCTTTGCAACCCCTGCTA
*
2875369 CTA--TTTTTT-TGGCAACTGCTTTGCTGTCTCTTCACG-TCTCTTTGCAACCCCTGCTA
1 CTATTTTTTTTCTGGCAACTGCTTTGCTGCCTCTTCACGATCTCTTTGCAACCCCTGCTA
* *
2875425 CTATTATTTTTTTCT-GCAACTGCTTT-CTTGCCTCTTCACGTATCTC--TGCAACCCTTGCTG
1 CTA-T-TTTTTTTCTGGCAACTGCTTTGC-TGCCTCTTCACG-ATCTCTTTGCAACCCCTGCTA
*
2875485 CTA-TGTTTTT-TGGCAACTGCTTTGCTGCCTCTTCACG-TCTCTTTGCAACC
1 CTATTTTTTTTCTGGCAACTGCTTTGCTGCCTCTTCACGATCTCTTTGCAACC
2875535 TCTACTGATT
Statistics
Matches: 195, Mismatches: 13, Indels: 39
0.79 0.05 0.16
Matches are distributed among these distances:
54 4 0.02
55 5 0.03
56 46 0.24
57 36 0.18
58 1 0.01
59 1 0.01
60 60 0.31
61 24 0.12
62 18 0.09
ACGTcount: A:0.13, C:0.30, G:0.13, T:0.44
Consensus pattern (60 bp):
CTATTTTTTTTCTGGCAACTGCTTTGCTGCCTCTTCACGATCTCTTTGCAACCCCTGCTA
Found at i:2875531 original size:117 final size:116
Alignment explanation
Indices: 2875254--2875534 Score: 474
Period size: 116 Copynumber: 2.4 Consensus size: 116
2875244 TACTGCTATT
** * *
2875254 TTTTTTCTGGCAACTTTTTTGCTGCCTCTTCATGATCTCTTTGCCACCCCTGCTACTATTATTTT
1 TTTTTT-TGGCAACTGCTTTGCTGCCTCTTCACG-TCTCTTTGCAACCCCTGCTACTATTATTTT
2875319 TTTCTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCTTGCTGCTA
64 TTTCTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCTTGCTGCTA
*
2875372 TTTTTTTGGCAACTGCTTTGCTGTCTCTTCACGTCTCTTTGCAACCCCTGCTACTATTATTTTTT
1 TTTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACCCCTGCTACTATTATTTTTT
2875437 TCTGCAACTGCTTT-CTTGCCTCTTCACGTATCTCTGCAACCCTTGCTGCTA
66 TCTGCAACTGCTTTGC-TGCCTCTTCACGTATCTCTGCAACCCTTGCTGCTA
2875488 TGTTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACC
1 T-TTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACC
2875535 TCTACTGATT
Statistics
Matches: 155, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
115 1 0.01
116 81 0.52
117 67 0.43
118 6 0.04
ACGTcount: A:0.12, C:0.30, G:0.14, T:0.44
Consensus pattern (116 bp):
TTTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACCCCTGCTACTATTATTTTTT
TCTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCTTGCTGCTA
Found at i:2879272 original size:9 final size:9
Alignment explanation
Indices: 2879258--2879282 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2879248 ACTTAAATTT
2879258 TAAATTAAA
1 TAAATTAAA
2879267 TAAATTAAA
1 TAAATTAAA
2879276 TAAATTA
1 TAAATTA
2879283 TTGAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TAAATTAAA
Found at i:2882648 original size:6 final size:6
Alignment explanation
Indices: 2882639--2882672 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2882629 ACTATAAGAA
* *
2882639 GGTTGG GGTTAA GGTTAG GGTTAG GGTTAG GGTT
1 GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG GGTT
2882673 GAGGTAGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.15, C:0.00, G:0.50, T:0.35
Consensus pattern (6 bp):
GGTTAG
Found at i:2882654 original size:12 final size:12
Alignment explanation
Indices: 2882637--2882677 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2882627 AAACTATAAG
*
2882637 AAGGTTGGGGTT
1 AAGGTTAGGGTT
2882649 AAGGTTAGGGTT
1 AAGGTTAGGGTT
*
2882661 AGGGTTAGGGTT
1 AAGGTTAGGGTT
*
2882673 GAGGT
1 AAGGT
2882678 AGATGAGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.49, T:0.32
Consensus pattern (12 bp):
AAGGTTAGGGTT
Found at i:2883286 original size:98 final size:99
Alignment explanation
Indices: 2883115--2883404 Score: 435
Period size: 99 Copynumber: 2.9 Consensus size: 99
2883105 TTAAAAAGAG
*
2883115 GCAAATGAATTACCAC-AAAGGCATCTAAGTAAAAAAAAAAACATAATTGATGCAGTTCAAATGT
1 GCAAATGAGTTACCACAAAAGGCATCTAAGT--AAAAAAAAACATAATTGATGCAGTTCAAATGT
* * *
2883179 TCAATACAAGCATTTAAGCATAATACGATAATCGAT
64 TCAATACAAGCATCTAAGCATAATACCATAATCAAT
*
2883215 GCAAATGAGTTACCACAAAAGGCATCTAAGT-AAAGAAAACATAATTGATGCAGTTCAAATGTTC
1 GCAAATGAGTTACCACAAAAGGCATCTAAGTAAAAAAAAACATAATTGATGCAGTTCAAATGTTC
2883279 AATACAAGCATCTAAGCATAATACCCATAATCAAT
66 AATACAAGCATCTAAGCATAATA-CCATAATCAAT
* * *
2883314 GCAAATGAGTTACCACAAAA-G-ATTTAAGTAAAAAAAAACCATAATTGTTGCAATTCAAATGTT
1 GCAAATGAGTTACCACAAAAGGCATCTAAGTAAAAAAAAA-CATAATTGATGCAGTTCAAATGTT
*
2883377 TAATACAAGCATCTAAGCATAATACCAT
65 CAATACAAGCATCTAAGCATAATACCAT
2883405 GATTGACGGA
Statistics
Matches: 176, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
97 7 0.04
98 66 0.38
99 74 0.42
100 15 0.09
101 14 0.08
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.24
Consensus pattern (99 bp):
GCAAATGAGTTACCACAAAAGGCATCTAAGTAAAAAAAAACATAATTGATGCAGTTCAAATGTTC
AATACAAGCATCTAAGCATAATACCATAATCAAT
Found at i:2883540 original size:4 final size:4
Alignment explanation
Indices: 2883531--2883565 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
2883521 AAGTTTGTGG
2883531 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2883566 GATAAACAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2884566 original size:27 final size:29
Alignment explanation
Indices: 2884535--2884596 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 29
2884525 TTTAATATTA
*
2884535 AAATAATACAA-A-AATTCATTATAATTT
1 AAATAATACAATATAATTCAGTATAATTT
*
2884562 GAAT-A-ACAATATAATTCAGTATAATTT
1 AAATAATACAATATAATTCAGTATAATTT
2884589 AAATAATA
1 AAATAATA
2884597 TTACTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 4 0.14
26 2 0.07
27 20 0.71
28 1 0.04
29 1 0.04
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (29 bp):
AAATAATACAATATAATTCAGTATAATTT
Found at i:2885689 original size:40 final size:40
Alignment explanation
Indices: 2885634--2885717 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
2885624 TTGAAAGTCT
2885634 ATTTCAAGCAACTCAGAATATATATTTTTCTATTATTTCC
1 ATTTCAAGCAACTCAGAATATATATTTTTCTATTATTTCC
2885674 ATTTCAAGCAACTCAGAATATATATTTTTCTATTATTTCC
1 ATTTCAAGCAACTCAGAATATATATTTTTCTATTATTTCC
2885714 ATTT
1 ATTT
2885718 TAACCTAACC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.46
Consensus pattern (40 bp):
ATTTCAAGCAACTCAGAATATATATTTTTCTATTATTTCC
Found at i:2886648 original size:60 final size:59
Alignment explanation
Indices: 2886551--2886728 Score: 227
Period size: 60 Copynumber: 3.0 Consensus size: 59
2886541 CTCTGCCCTG
* * * *
2886551 CTGCTATTATTTTTTTTTTGGCAACTTCTTT-TCTGCCTCTTCACATCTCTTTGCAACCC
1 CTGCTACTATTTTTTTTCTGGCAACTGCTTTGT-TGCCTCTTCACGTCTCTTTGCAACCC
* *
2886610 CTGCTACTATTATTTTTTCTGGCAACTGCTTTGTTGCCTCTTCACGTATCTCTGCAACCC
1 CTGCTACTATT-TTTTTTCTGGCAACTGCTTTGTTGCCTCTTCACGTCTCTTTGCAACCC
* * * *
2886670 CTGCTGCTA-TTTTTTTC-GACAACTGCTTTGCTCCCTCTTCACGTCTCTTTGCAACCC
1 CTGCTACTATTTTTTTTCTGGCAACTGCTTTGTTGCCTCTTCACGTCTCTTTGCAACCC
2886727 CT
1 CT
2886729 ACTGATTTGC
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
57 37 0.35
58 7 0.07
59 11 0.10
60 49 0.47
61 1 0.01
ACGTcount: A:0.13, C:0.31, G:0.11, T:0.44
Consensus pattern (59 bp):
CTGCTACTATTTTTTTTCTGGCAACTGCTTTGTTGCCTCTTCACGTCTCTTTGCAACCC
Found at i:2891060 original size:31 final size:31
Alignment explanation
Indices: 2891007--2891065 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2890997 TTAAAAATTA
* * * *
2891007 TCAAATAAGGGCTTAACTTTTTTGAAAGTGT
1 TCAAATAAGGGATAAACCTTTTTAAAAGTGT
2891038 TCAAATAAGGGATAAACCTTTTTAAAAG
1 TCAAATAAGGGATAAACCTTTTTAAAAG
2891066 AACTCAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (31 bp):
TCAAATAAGGGATAAACCTTTTTAAAAGTGT
Found at i:2892041 original size:13 final size:13
Alignment explanation
Indices: 2891971--2892043 Score: 55
Period size: 13 Copynumber: 5.7 Consensus size: 13
2891961 ACAAATAATA
*
2891971 TTAAATAATATAT
1 TTAAATATTATAT
*
2891984 TCTAAATACTATA-
1 T-TAAATATTATAT
*
2891997 TAAAATATTATA-
1 TTAAATATTATAT
2892009 --AAATATGTACTAT
1 TTAAATAT-TA-TAT
2892022 TTAAATATTATAT
1 TTAAATATTATAT
*
2892035 TTTAATATT
1 TTAAATATT
2892044 GTAAAATACT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.12
11 2 0.04
12 11 0.22
13 13 0.26
14 12 0.24
15 6 0.12
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (13 bp):
TTAAATATTATAT
Found at i:2893380 original size:25 final size:23
Alignment explanation
Indices: 2893350--2893406 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
2893340 ATTAGTTAAT
**
2893350 TAGTATTATTAAGGTTTTTTTTTAG
1 TAGTATTATT-A-GTTTTTTAGTAG
*
2893375 TAGTATAATTAGTTTTTTAGTAG
1 TAGTATTATTAGTTTTTTAGTAG
2893398 TAGT-TTATT
1 TAGTATTATT
2893407 TGTGTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 4 0.14
23 14 0.50
24 1 0.04
25 9 0.32
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (23 bp):
TAGTATTATTAGTTTTTTAGTAG
Found at i:2896247 original size:18 final size:19
Alignment explanation
Indices: 2896218--2896258 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2896208 GACAAAAAGG
* *
2896218 TTTTACTTTTTTTATTTTA
1 TTTTACTTTTTTAATGTTA
2896237 TTTTA-TTTTTTAATGTTA
1 TTTTACTTTTTTAATGTTA
2896255 TTTT
1 TTTT
2896259 CTTGTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTACTTTTTTAATGTTA
Found at i:2896288 original size:11 final size:11
Alignment explanation
Indices: 2896274--2896314 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
2896264 TGTTTTCTCC
2896274 CTATTTTGCTA
1 CTATTTTGCTA
*
2896285 CTATTTTACTA
1 CTATTTTGCTA
* *
2896296 TTATGTTGCTA
1 CTATTTTGCTA
2896307 CTATTTTG
1 CTATTTTG
2896315 TTGTTATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:2896413 original size:30 final size:30
Alignment explanation
Indices: 2896351--2896413 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2896341 ACTTATTTTA
*
2896351 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAACGCAT
* *
2896381 TTGTTAATTTTGTTATTATTTTAGACGTAT
1 TTGTTAATTTTGTTATTATTTTAAACGCAT
2896411 TTG
1 TTG
2896414 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.03, G:0.14, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAACGCAT
Found at i:2897199 original size:17 final size:17
Alignment explanation
Indices: 2897179--2897212 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2897169 TACCTATTTC
*
2897179 ATTATGTATTATATTAT
1 ATTATATATTATATTAT
*
2897196 ATTATATTTTATATTAT
1 ATTATATATTATATTAT
2897213 TTGGTTAAAA
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:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTATATATTATATTAT
Found at i:2902123 original size:21 final size:21
Alignment explanation
Indices: 2902098--2902171 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
2902088 CAACACATAA
*
2902098 GTGCCTGAAATGACACGCGAG
1 GTGCCTGAAATGACACACGAG
* *
2902119 ATGCCTGATATGACACACGAG
1 GTGCCTGAAATGACACACGAG
* *
2902140 GTGCCTGATACGACACACGAG
1 GTGCCTGAAATGACACACGAG
*
2902161 GTGCCTAAAAT
1 GTGCCTGAAAT
2902172 ATGACACATA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (21 bp):
GTGCCTGAAATGACACACGAG
Found at i:2902897 original size:5 final size:5
Alignment explanation
Indices: 2902887--2902914 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2902877 AATTCTCCCT
2902887 TTTTC TTTTC TTTTC TTTTC TTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTT
2902915 CCCCTTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:2902922 original size:16 final size:16
Alignment explanation
Indices: 2902888--2902931 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2902878 ATTCTCCCTT
* *
2902888 TTTCTTTTCTTT-TCT
1 TTTCTTTTCTTTCCCC
2902903 TTTCTTTTCTTTCCCC
1 TTTCTTTTCTTTCCCC
*
2902919 TTTCCTTTCTTTC
1 TTTCTTTTCTTTC
2902932 TTCTTCGCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTCTTTTCTTTCCCC
Found at i:2905655 original size:18 final size:18
Alignment explanation
Indices: 2905618--2905656 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2905608 AAAATTATTA
* **
2905618 AAAAATAATAAAATGTAT
1 AAAAATAAAAAAATACAT
2905636 AAAAATAAAAAAATACAT
1 AAAAATAAAAAAATACAT
2905654 AAA
1 AAA
2905657 TTAAAACTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
AAAAATAAAAAAATACAT
Found at i:2905837 original size:27 final size:26
Alignment explanation
Indices: 2905806--2905869 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 26
2905796 TTTATCAAGG
*
2905806 TTATTAGTTTATCGATAAATGAATATT
1 TTATTAATTTATCGATAAATGAATA-T
* *
2905833 TTATTAATTAATCGATAAATTAATAT
1 TTATTAATTTATCGATAAATGAATAT
2905859 TTATTAATTTA
1 TTATTAATTTA
2905870 GAGAATATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 11 0.33
27 22 0.67
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (26 bp):
TTATTAATTTATCGATAAATGAATAT
Found at i:2910762 original size:24 final size:24
Alignment explanation
Indices: 2910718--2910764 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2910708 ATTAAAATGG
2910718 ATTGATTTAGTATGTGATGAATTT
1 ATTGATTTAGTATGTGATGAATTT
2910742 ATTGAATTTA-TAT-TGATTGAATT
1 ATTG-ATTTAGTATGTGA-TGAATT
2910765 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGATTTAGTATGTGATGAATTT
Found at i:2914489 original size:29 final size:30
Alignment explanation
Indices: 2914447--2914521 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 30
2914437 AAAATGGAGT
*
2914447 TTTAGGTTCCTTAAAAGTTAG-AAAAAAAA
1 TTTAGGTCCCTTAAAAGTTAGTAAAAAAAA
*
2914476 TTTAGGTCCCTTAAAAGTTGGTAAAAAAAA
1 TTTAGGTCCCTTAAAAGTTAGTAAAAAAAA
* *
2914506 TTT-GGGCCTTTAAAAG
1 TTTAGGTCCCTTAAAAG
2914522 CTAAATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 30 0.73
30 11 0.27
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.32
Consensus pattern (30 bp):
TTTAGGTCCCTTAAAAGTTAGTAAAAAAAA
Found at i:2917787 original size:22 final size:22
Alignment explanation
Indices: 2917755--2917796 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2917745 AATAATTCAA
2917755 AAAATTATAAAAATATAAAATT
1 AAAATTATAAAAATATAAAATT
*
2917777 AAAATTTTAAAAATATAAAA
1 AAAATTATAAAAATATAAAA
2917797 AGTTCATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATTATAAAAATATAAAATT
Found at i:2918040 original size:22 final size:22
Alignment explanation
Indices: 2917981--2918034 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
2917971 TGTTAATTTA
* * *
2917981 TTTTATTTTAATTTGGGTTTTG
1 TTTTAATTTAAGTTGTGTTTTG
*
2918003 TTTTTATTTAAGTTGTGTTTTG
1 TTTTAATTTAAGTTGTGTTTTG
2918025 TTTTAATTTA
1 TTTTAATTTA
2918035 TATTGTAGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.69
Consensus pattern (22 bp):
TTTTAATTTAAGTTGTGTTTTG
Found at i:2922013 original size:21 final size:22
Alignment explanation
Indices: 2921964--2922014 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
2921954 ATTAGAAAAA
*
2921964 TGATTTAAGATGAAATATGAAC
1 TGATTTAAGATGAAATATCAAC
* * *
2921986 CGATTTAAGATG-AATTTCAAT
1 TGATTTAAGATGAAATATCAAC
2922007 TGATTTAA
1 TGATTTAA
2922015 ATGTGTTGAC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (22 bp):
TGATTTAAGATGAAATATCAAC
Found at i:2922234 original size:18 final size:19
Alignment explanation
Indices: 2922199--2922234 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2922189 TTAAAAGTTA
2922199 TATAAATATAAAAAAATCT
1 TATAAATATAAAAAAATCT
*
2922218 TATAAATA-AACAAAATC
1 TATAAATATAAAAAAATC
2922235 AGAATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (19 bp):
TATAAATATAAAAAAATCT
Found at i:2928187 original size:12 final size:12
Alignment explanation
Indices: 2928170--2928195 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2928160 TAGATCAAGA
2928170 AACGAACAAACC
1 AACGAACAAACC
2928182 AACGAACAAACC
1 AACGAACAAACC
2928194 AA
1 AA
2928196 ACTTGAATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.31, G:0.08, T:0.00
Consensus pattern (12 bp):
AACGAACAAACC
Found at i:2931217 original size:27 final size:27
Alignment explanation
Indices: 2931179--2931272 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 27
2931169 GGAGGGTTTG
* *
2931179 TGATTGGCGGCACCAAAGGTGCC-TAAC
1 TGATTGGCGGCACCGATGGTGCCAT-AC
2931206 TGATTGGCGGCACCGATGGTGCCATAC
1 TGATTGGCGGCACCGATGGTGCCATAC
*
2931233 TGGTTGGCGGCACCGATGGTGCCATAC
1 TGATTGGCGGCACCGATGGTGCCATAC
*
2931260 TGATTGGTGGCAC
1 TGATTGGCGGCAC
2931273 TACTCGTGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 60 0.98
28 1 0.02
ACGTcount: A:0.19, C:0.24, G:0.34, T:0.22
Consensus pattern (27 bp):
TGATTGGCGGCACCGATGGTGCCATAC
Found at i:2932411 original size:18 final size:18
Alignment explanation
Indices: 2932388--2932425 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2932378 GGTTAGTGAT
2932388 GAAGAAGAAGGTGGTGGC
1 GAAGAAGAAGGTGGTGGC
*
2932406 GAAGAAGAATGTGGTGGC
1 GAAGAAGAAGGTGGTGGC
2932424 GA
1 GA
2932426 TCATTGGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.47, T:0.13
Consensus pattern (18 bp):
GAAGAAGAAGGTGGTGGC
Found at i:2937210 original size:162 final size:161
Alignment explanation
Indices: 2937008--2937530 Score: 547
Period size: 162 Copynumber: 3.3 Consensus size: 161
2936998 ATAATTTCTA
* * *
2937008 ATTTTATAATTTTACATTATTTCAGTGCATAATATTTGAAATTTATTAATTTAGTATGTTTTTTA
1 ATTTTATTATTTTACATTATTTCAGTGCATATTGTTTGAAATTTATTAATTTAGTATGTTTTTTA
*
2937073 AATTAATTTGTTGTAAGAAAAAAACTCTTATCCTTGCCCTTTGCTCGTATTATTTTCCCGATTTT
66 AATTAATTTGATGTAAGAAAAAAACTCTTATCCTTGCCCTTTGCTCGTATTATTTTCCCGATTTT
2937138 TATTACTTTCAATAAAAATATTTTATTTTCGT
131 TATTACTTT-AATAAAAATATTTTATTTTCGT
* * * * * *
2937170 ATTTTATTATTTTATATTATTTTAGTGCATTTTGTTTGAAATATTTGTATTAA-TTATTTTTGAA
1 ATTTTATTATTTTACATTATTTCAGTGCATATTGTTTG-AA-A-TT-TATTAATTTA-GTATG-T
* * * ** * *
2937234 TTTTTAAA--AA----ATGT-AGTAATACACTCTTA--CTTCGGCTATTTGTTCGTATTTTTTTA
60 TTTTTAAATTAATTTGATGTAAGAAAAAAACTCTTATCCTT--GCCCTTTGCTCGTATTATTTT-
* * ** *
2937290 TCCG-TATTATATTA-TTT--TAAAAATATCGTAATTTC-T
122 CCCGAT-TTTTATTACTTTAATAAAAATATTTTATTTTCGT
* *
2937326 AATTTTATCATTTTACATTATTTCAGTGCATAATT-TTTGAAATTTATTAATTTAGTGTGTTTTT
1 -ATTTTATTATTTTACATTATTTCAGTGCAT-ATTGTTTGAAATTTATTAATTTAGTATGTTTTT
* *
2937390 TAAATTAATTTGGTGTAAGAAAAAAACTCTTATCCCTGCCCTTTGCTCGTATTATTTTCCCGATT
64 TAAATTAATTTGATGTAAGAAAAAAACTCTTATCCTTGCCCTTTGCTCGTATTATTTTCCCGATT
2937455 TTTATTACTTTTAATAAAAATATTTTATTTTCGT
129 TTTATTAC-TTTAATAAAAATATTTTATTTTCGT
* * *
2937489 ATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAAT
1 ATTTTATTATTTTACATTATTTCAGTGCATATTGTTTGAAAT
2937531 ATTTGTATTA
Statistics
Matches: 285, Mismatches: 47, Indels: 58
0.73 0.12 0.15
Matches are distributed among these distances:
152 8 0.03
153 9 0.03
154 7 0.02
155 1 0.00
156 3 0.01
157 46 0.16
158 18 0.06
159 30 0.11
160 36 0.13
161 17 0.06
162 82 0.29
163 3 0.01
164 1 0.00
165 7 0.02
166 9 0.03
167 8 0.03
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (161 bp):
ATTTTATTATTTTACATTATTTCAGTGCATATTGTTTGAAATTTATTAATTTAGTATGTTTTTTA
AATTAATTTGATGTAAGAAAAAAACTCTTATCCTTGCCCTTTGCTCGTATTATTTTCCCGATTTT
TATTACTTTAATAAAAATATTTTATTTTCGT
Found at i:2937507 original size:319 final size:321
Alignment explanation
Indices: 2936918--2937547 Score: 1138
Period size: 319 Copynumber: 2.0 Consensus size: 321
2936908 GCAAGTTGAA
2936918 AAAAAAAGTTAGTAATACACTCTTACTTCGACTATTTGTTCGTATTTTTTTATCCGCATTATATT
1 AAAAAAAGTTAGTAATACACTCTTACTTCGACTATTTGTTCGTATTTTTTTATCCGCATTATATT
2936983 ATTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATAATATTTGAA
66 ATTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATAATATTTGAA
* *
2937048 ATTTATTAATTTAGTATGTTTTTTAAATTAATTTGTTGTAAGAAAAAAACTCTTATCCTTGCCCT
131 ATTTATTAATTTAGTATGTTTTTTAAATTAATTTGGTGTAAGAAAAAAACTCTTATCCCTGCCCT
2937113 TTGCTCGTATTATTTTCCCGATTTTTATTACTTTCAATAAAAATATTTTATTTTCGTATTTTATT
196 TTGCTCGTATTATTTTCCCGATTTTTATTACTTTCAATAAAAATATTTTATTTTCGTATTTTATT
* *
2937178 ATTTTATATTATTTTAGTGCATTTTGTTTGAAATATTTGTATTAATTATTTTTGAATTTTT
261 ATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTTTGAATTTTT
* * *
2937239 AAAAAATG-TAGTAATACACTCTTACTTCGGCTATTTGTTCGTATTTTTTTATCCGTATTATATT
1 AAAAAAAGTTAGTAATACACTCTTACTTCGACTATTTGTTCGTATTTTTTTATCCGCATTATATT
* * *
2937303 ATTTT-AAAAATATCGTAATTTCTAATTTTATCATTTTACATTATTTCAGTGCATAATTTTTGAA
66 ATTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATAATATTTGAA
*
2937367 ATTTATTAATTTAGTGTGTTTTTTAAATTAATTTGGTGTAAGAAAAAAACTCTTATCCCTGCCCT
131 ATTTATTAATTTAGTATGTTTTTTAAATTAATTTGGTGTAAGAAAAAAACTCTTATCCCTGCCCT
*
2937432 TTGCTCGTATTATTTTCCCGATTTTTATTACTTTTAATAAAAATATTTTATTTTCGTATTTTATT
196 TTGCTCGTATTATTTTCCCGATTTTTATTACTTTCAATAAAAATATTTTATTTTCGTATTTTATT
2937497 ATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTT
261 ATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTT
2937548 CTGACTTCGG
Statistics
Matches: 297, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
319 231 0.78
320 59 0.20
321 7 0.02
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (321 bp):
AAAAAAAGTTAGTAATACACTCTTACTTCGACTATTTGTTCGTATTTTTTTATCCGCATTATATT
ATTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATAATATTTGAA
ATTTATTAATTTAGTATGTTTTTTAAATTAATTTGGTGTAAGAAAAAAACTCTTATCCCTGCCCT
TTGCTCGTATTATTTTCCCGATTTTTATTACTTTCAATAAAAATATTTTATTTTCGTATTTTATT
ATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTTTGAATTTTT
Found at i:2938086 original size:27 final size:27
Alignment explanation
Indices: 2938044--2938111 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
2938034 TTATAAGGTT
* *
2938044 GGTGCCGCTAACCAG-TATGGCACCGTC
1 GGTGCCGCCAATCAGTTA-GGCACCGTC
* *
2938071 GGTGCCGCCAATCAGTTAGGCACCTTT
1 GGTGCCGCCAATCAGTTAGGCACCGTC
2938098 GGTGCCGCCAATCA
1 GGTGCCGCCAATCA
2938112 CAAACCCTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 34 0.94
28 2 0.06
ACGTcount: A:0.19, C:0.32, G:0.28, T:0.21
Consensus pattern (27 bp):
GGTGCCGCCAATCAGTTAGGCACCGTC
Found at i:2947407 original size:28 final size:29
Alignment explanation
Indices: 2947376--2947448 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 29
2947366 AAATACGTAC
* * * *
2947376 GTATCTATGTCTATATAGATTA-TAAAAT
1 GTATGTATGTATATATAAATTACAAAAAT
2947404 GTATGTATGTATATATAAATTACAAAAAT
1 GTATGTATGTATATATAAATTACAAAAAT
2947433 GTATGTATGTATATAT
1 GTATGTATGTATATAT
2947449 GTAATTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 19 0.47
29 21 0.52
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.42
Consensus pattern (29 bp):
GTATGTATGTATATATAAATTACAAAAAT
Found at i:2947441 original size:29 final size:28
Alignment explanation
Indices: 2947376--2947457 Score: 101
Period size: 29 Copynumber: 2.9 Consensus size: 28
2947366 AAATACGTAC
* * * *
2947376 GTATCTATGTCTATATAGATTATAAAAT
1 GTATGTATGTATATATAAATTAAAAAAT
2947404 GTATGTATGTATATATAAATTACAAAAAT
1 GTATGTATGTATATATAAATTA-AAAAAT
*
2947433 GTATGTATGTATATATGTAATTAAA
1 GTATGTATGTATATAT-AAATTAAA
2947458 TTTAAAATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
28 19 0.40
29 23 0.49
30 5 0.11
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (28 bp):
GTATGTATGTATATATAAATTAAAAAAT
Found at i:2952465 original size:43 final size:43
Alignment explanation
Indices: 2952386--2952468 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
2952376 TCATATTTCA
* * * *
2952386 TTTCTCATCTCATAATCATTTTTCGTATTTGTCATTTCAATAT
1 TTTCTCATCTCATAATCAATTCTCATATTTGCCATTTCAATAT
* *
2952429 TTTCTCATCTCATATTCAATTCTCATCTTTGCCATTTCAA
1 TTTCTCATCTCATAATCAATTCTCATATTTGCCATTTCAA
2952469 AATCAATCAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.23, C:0.23, G:0.04, T:0.51
Consensus pattern (43 bp):
TTTCTCATCTCATAATCAATTCTCATATTTGCCATTTCAATAT
Found at i:2961715 original size:3 final size:3
Alignment explanation
Indices: 2961707--2961746 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2961697 TTGATGACAG
2961707 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2961747 TGATAGTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2962163 original size:31 final size:31
Alignment explanation
Indices: 2962115--2962179 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
2962105 CTTGATATAT
2962115 TTTGGTAACAATGATAATGATAACTTTTTAA
1 TTTGGTAACAATGATAATGATAACTTTTTAA
* *
2962146 TTTGTTAACAATTATAATGATAACTTTTTAA
1 TTTGGTAACAATGATAATGATAACTTTTTAA
2962177 TTT
1 TTT
2962180 ATTATTTGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (31 bp):
TTTGGTAACAATGATAATGATAACTTTTTAA
Found at i:2965130 original size:12 final size:12
Alignment explanation
Indices: 2965113--2965140 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2965103 ATAGAAGGAA
2965113 TAAACAGATCTT
1 TAAACAGATCTT
2965125 TAAACAGATCTT
1 TAAACAGATCTT
2965137 TAAA
1 TAAA
2965141 TATGTCCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (12 bp):
TAAACAGATCTT
Found at i:2966051 original size:13 final size:13
Alignment explanation
Indices: 2966035--2966059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2966025 ATCACACTTT
2966035 TCAAAAATATTTC
1 TCAAAAATATTTC
2966048 TCAAAAATATTT
1 TCAAAAATATTT
2966060 TTCCACAACA
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:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
TCAAAAATATTTC
Found at i:2998354 original size:25 final size:26
Alignment explanation
Indices: 2998309--2998366 Score: 84
Period size: 24 Copynumber: 2.3 Consensus size: 26
2998299 TATTTAAGTT
*
2998309 TATATATTGCAATAAAAAT-AATT-A
1 TATATATTGAAATAAAAATAAATTGA
2998333 TATATATTGAATATAAAAATAAATTGA
1 TATATATTGAA-ATAAAAATAAATTGA
2998360 TATATAT
1 TATATAT
2998367 ATTTTTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 10 0.33
25 8 0.27
26 4 0.13
27 8 0.27
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (26 bp):
TATATATTGAAATAAAAATAAATTGA
Found at i:3001509 original size:34 final size:35
Alignment explanation
Indices: 3001471--3001537 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3001461 CAGTAAAATA
*
3001471 TTTTCCGTAAAATAATTT-TTGAAAAATATTTTAC
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
*
3001505 TTTTCTGTAAAATAATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTT
3001538 CTGATGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
Found at i:3001541 original size:14 final size:15
Alignment explanation
Indices: 3001465--3001541 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
3001455 GATTGCCAGT
* *
3001465 AAAAT-ATTTTCCGT
1 AAAATAATTTTCTGA
3001479 AAAATAATTTT-TGA
1 AAAATAATTTTCTGA
*
3001493 AAAATATTTTACTTTTCTGT
1 AAAATA----A-TTTTCTGA
*
3001513 AAAATAATTTACTGA
1 AAAATAATTTTCTGA
3001528 AAAAT-ATTTTCTGA
1 AAAATAATTTTCTGA
3001542 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 20 0.40
15 16 0.32
16 1 0.02
18 1 0.02
19 4 0.08
20 8 0.16
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (15 bp):
AAAATAATTTTCTGA
Found at i:3008441 original size:21 final size:20
Alignment explanation
Indices: 3008399--3008437 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3008389 TTTTGTCTAT
3008399 AAACATTTACAAGTCATTTA
1 AAACATTTACAAGTCATTTA
*
3008419 AAACACTTTAGAA-TCATTT
1 AAACA-TTTACAAGTCATTT
3008438 TAAATTGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (20 bp):
AAACATTTACAAGTCATTTA
Found at i:3012042 original size:20 final size:20
Alignment explanation
Indices: 3011988--3012044 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
3011978 TAGGGGACCA
*
3011988 TTAACTTAAGTAAAATAAGGT
1 TTAA-TTAAGTAAATTAAGGT
*
3012009 TTAATTAATTAAATTAAGG-
1 TTAATTAAGTAAATTAAGGT
3012028 TTAATTAAGCTAAATTA
1 TTAATTAAG-TAAATTA
3012045 TAATTTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.25
20 20 0.62
21 4 0.12
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.39
Consensus pattern (20 bp):
TTAATTAAGTAAATTAAGGT
Found at i:3013122 original size:20 final size:19
Alignment explanation
Indices: 3013093--3013148 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
3013083 AGATTATGTT
*
3013093 CTAGTATGCACTTCGTGTG
1 CTAGTATGCACTTTGTGTG
*
3013112 CTAGATATGCA-TTTATGTG
1 CTAG-TATGCACTTTGTGTG
*
3013131 CCAGTATGCACTTTGTGT
1 CTAGTATGCACTTTGTGT
3013149 ACCAGGTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 6 0.19
19 19 0.61
20 6 0.19
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (19 bp):
CTAGTATGCACTTTGTGTG
Done.