Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold116
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: 1263769
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 4928 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:561215 original size:19 final size:18
Alignment explanation
Indices: 561167--561216 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
561157 TTATCTTATG
*
561167 TAAAAAATAATTAAAATA
1 TAAATAATAATTAAAATA
561185 T-AATAA-AA-TAAAATA
1 TAAATAATAATTAAAATA
*
561200 TAAATAATAATTTAAAT
1 TAAATAATAATTAAAAT
561217 TTATGAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 8 0.30
16 7 0.26
17 6 0.22
18 6 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAATAATAATTAAAATA
Found at i:561230 original size:18 final size:18
Alignment explanation
Indices: 561205--561253 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
561195 AAATATAAAT
561205 AATA-ATTTAAATTTATG
1 AATATATTTAAATTTATG
* *
561222 AATATATTTAAATATATT
1 AATATATTTAAATTTATG
561240 AATAT-TTTAAATTT
1 AATATATTTAAATTT
561254 TATATAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
AATATATTTAAATTTATG
Found at i:563738 original size:64 final size:64
Alignment explanation
Indices: 563607--563726 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 64
563597 CCATATTTGA
563607 GGATAGATGCATGGATTGAAAGGTCTCTGGCTCTCAGCAGGGACAAACTACATATCCATCCCCT
1 GGATAGATGCATGGATTGAAAGGTCTCTGGCTCTCAGCAGGGACAAACTACATATCCATCCCCT
* * * * *
563671 GGATAGGTGCATGGATTGAAAGGTCTTTGGCTCGT-TGCCGGGACAAACTACGTATC
1 GGATAGATGCATGGATTGAAAGGTCTCTGGCTC-TCAGCAGGGACAAACTACATATC
563727 TCTCCTGTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
64 49 0.98
65 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (64 bp):
GGATAGATGCATGGATTGAAAGGTCTCTGGCTCTCAGCAGGGACAAACTACATATCCATCCCCT
Found at i:568390 original size:12 final size:11
Alignment explanation
Indices: 568368--568410 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
568358 TGATATATTT
*
568368 ATTTATTTTTA
1 ATTTTTTTTTA
568379 ATTTTCTTTTTA
1 ATTTT-TTTTTA
*
568391 ATTTTTTTTAA
1 ATTTTTTTTTA
568402 ATTTTTTTT
1 ATTTTTTTT
568411 AAAAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (11 bp):
ATTTTTTTTTA
Found at i:576898 original size:25 final size:25
Alignment explanation
Indices: 576851--576898 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
576841 TATCATTAAA
*
576851 ATTAAATATTTTAATATATTATTTT
1 ATTAAATATTTTAATATAGTATTTT
* * *
576876 ATTATATATTTTACTTTAGTATT
1 ATTAAATATTTTAATATAGTATT
576899 ATTTTTTACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
ATTAAATATTTTAATATAGTATTTT
Found at i:577841 original size:20 final size:22
Alignment explanation
Indices: 577809--577861 Score: 78
Period size: 20 Copynumber: 2.6 Consensus size: 22
577799 TTGATATTAT
577809 TTTTAATATAAAAATAA-AAAA
1 TTTTAATATAAAAATAATAAAA
577830 TTTTAA-ATAAAAATAATAAAA
1 TTTTAATATAAAAATAATAAAA
577851 --TTAATATAAAA
1 TTTTAATATAAAA
577862 TTTTAATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.13
20 16 0.53
21 10 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TTTTAATATAAAAATAATAAAA
Found at i:578302 original size:23 final size:22
Alignment explanation
Indices: 578254--578295 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
578244 AAGCATGACT
578254 AAAAAGAATTTTATTTGTTACA
1 AAAAAGAATTTTATTTGTTACA
578276 AAAAAGAATTTTATTTGTTA
1 AAAAAGAATTTTATTTGTTA
578296 GGCAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (22 bp):
AAAAAGAATTTTATTTGTTACA
Found at i:579575 original size:6 final size:6
Alignment explanation
Indices: 579566--579607 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
579556 ATATTAAGAG
579566 TATAAA TATAAA TAT-AA TATAAA TTATTAAA TATAAA TATAA
1 TATAAA TATAAA TATAAA TATAAA -TA-TAAA TATAAA TATAA
579608 TAATATGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 5 0.15
6 20 0.61
7 4 0.12
8 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TATAAA
Found at i:579586 original size:11 final size:11
Alignment explanation
Indices: 579570--579609 Score: 53
Period size: 11 Copynumber: 3.4 Consensus size: 11
579560 TAAGAGTATA
579570 AATATAAATAT
1 AATATAAATAT
579581 AATATAAATTATT
1 AATATAAA-TA-T
579594 AAATATAAATAT
1 -AATATAAATAT
579606 AATA
1 AATA
579610 ATATGTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 12 0.46
12 3 0.12
13 3 0.12
14 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATAAATAT
Found at i:587394 original size:2 final size:2
Alignment explanation
Indices: 587389--587416 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
587379 AAAGTAACAT
587389 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
587417 CACCCTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:590768 original size:2 final size:2
Alignment explanation
Indices: 590761--590786 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
590751 AACGGAAAAT
590761 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
590787 GATACACACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:605216 original size:2 final size:2
Alignment explanation
Indices: 605209--605257 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
605199 TTTGATATCC
605209 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
605251 CC CT CT C
1 CT CT CT C
605258 GCATAAGAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:613057 original size:18 final size:17
Alignment explanation
Indices: 613010--613092 Score: 57
Period size: 17 Copynumber: 4.9 Consensus size: 17
613000 ATATATTTTA
*
613010 AAATTTATATAAA-A-T
1 AAATTTAAATAAATATT
* *
613025 AAATTATTAATATAT-TT
1 AAATT-TAAATAAATATT
*
613042 AAATTTAAATAAATATA
1 AAATTTAAATAAATATT
613059 AAATTTTTAAAT-AATATT
1 AAA--TTTAAATAAATATT
*
613077 ATAATATAAATAAATA
1 A-AATTTAAATAAATA
613093 ATACTAATAC
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
15 5 0.10
16 12 0.23
17 16 0.31
18 10 0.19
19 9 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTTAAATAAATATT
Found at i:613090 original size:21 final size:20
Alignment explanation
Indices: 613066--613111 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
613056 ATAAAATTTT
613066 TAAATAATATTATAATA-TAAA
1 TAAATAATA--ATAATACTAAA
*
613087 TAAATAATACTAATACTAAA
1 TAAATAATAATAATACTAAA
613107 TAAAT
1 TAAAT
613112 TTACGAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.22
20 9 0.39
21 9 0.39
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATAATAATAATACTAAA
Found at i:614155 original size:2 final size:2
Alignment explanation
Indices: 614148--614183 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
614138 ATGAACTCTT
614148 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
614184 TATTTCAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:614363 original size:2 final size:2
Alignment explanation
Indices: 614358--614382 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
614348 TTTACTAGAA
614358 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
614383 AAATTAGCCA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:622726 original size:3 final size:3
Alignment explanation
Indices: 622718--622759 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
622708 TTTCAAAAGG
* * *
622718 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ACA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
622760 TAAAAATCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:628409 original size:24 final size:24
Alignment explanation
Indices: 628375--628428 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
628365 TCATAGATTC
628375 TTGTGTTCAGTCACTAGTGTTAGAT
1 TTGT-TTCAGTCACTAGTGTTAGAT
*
628400 TTGTTTCAGTTACTAGTGTTAGAT
1 TTGTTTCAGTCACTAGTGTTAGAT
628424 TTGTT
1 TTGTT
628429 AAATCCTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.19, C:0.09, G:0.22, T:0.50
Consensus pattern (24 bp):
TTGTTTCAGTCACTAGTGTTAGAT
Found at i:630901 original size:2 final size:2
Alignment explanation
Indices: 630889--630923 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
630879 TGCCTAGAAA
630889 CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
630924 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:633783 original size:15 final size:14
Alignment explanation
Indices: 633748--633793 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
633738 ATATAAATTT
*
633748 TTTAAAAATAAATATA
1 TTTAAATATAAA-A-A
633764 TTTAAATATTAAAAA
1 TTTAAATA-TAAAAA
633779 TTTAAATATAAAAA
1 TTTAAATATAAAAA
633793 T
1 T
633794 ATATTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 7 0.25
15 9 0.32
16 8 0.29
17 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTTAAATATAAAAA
Found at i:634551 original size:16 final size:14
Alignment explanation
Indices: 634495--634553 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 14
634485 TATTATGATT
*
634495 ATTAATTATAATAAT
1 ATTAATTATAA-AAA
*
634510 ATTTATTAT-AAAA
1 ATTAATTATAAAAA
*
634523 ATTAATAATAAAAA
1 ATTAATTATAAAAA
634537 ATTAAAATTATAAAAA
1 ATT--AATTATAAAAA
634553 A
1 A
634554 ATTATAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
13 9 0.25
14 8 0.22
15 8 0.22
16 11 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTAATTATAAAAA
Found at i:637304 original size:16 final size:16
Alignment explanation
Indices: 637279--637309 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
637269 CTCGCCGATA
*
637279 TTTTCTTTTTTTTTCT
1 TTTTCATTTTTTTTCT
637295 TTTTCATTTTTTTTC
1 TTTTCATTTTTTTTC
637310 CTTCTACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCATTTTTTTTCT
Found at i:638570 original size:21 final size:21
Alignment explanation
Indices: 638527--638571 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
638517 TGATATAGGG
* *
638527 AGGATGTCATTTGATGCAGCA
1 AGGATGTCATTAGATGCACCA
638548 AGGATGTCATTAGATG-ATCCA
1 AGGATGTCATTAGATGCA-CCA
638569 AGG
1 AGG
638572 TATTCTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (21 bp):
AGGATGTCATTAGATGCACCA
Found at i:647348 original size:28 final size:28
Alignment explanation
Indices: 647293--647363 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
647283 GAATAAAGCT
** **
647293 GGGGTTGGAGTATCCCCTCGGAGGTAAC
1 GGGGTTGGAGTATCCCCGAGGAAATAAC
*
647321 GGGGTTGGAGTATCCCCGATGAAATAAC
1 GGGGTTGGAGTATCCCCGAGGAAATAAC
*
647349 GAGGTTGGAGTATCC
1 GGGGTTGGAGTATCC
647364 TCAATTGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGAGGAAATAAC
Found at i:647509 original size:51 final size:50
Alignment explanation
Indices: 647351--647516 Score: 179
Period size: 52 Copynumber: 3.2 Consensus size: 50
647341 GAAATAACGA
* * *
647351 GGTTGGAGTATCCTCAATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTTGGAAATAAAACCG
** * * *
647402 GAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAGCCGG
1 G-GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGGAAATAAAACC-G
* * *
647455 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGATTTGGAAATAAAACCTG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACC-G
*
647506 GGTTGTAGTAT
1 GGTTGGAGTAT
647517 TCCCTCGAAG
Statistics
Matches: 94, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
51 34 0.36
52 47 0.50
53 13 0.14
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.31
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACCG
Found at i:647549 original size:79 final size:79
Alignment explanation
Indices: 647454--647631 Score: 209
Period size: 79 Copynumber: 2.2 Consensus size: 79
647444 AATAAAGCCG
* * * * *
647454 GGGTTGGAGTATCCCCGATTGTGAA-AAATCGATGA-TTTGGAAATAAAACCTGGG-TTGTAGTA
1 GGGTTGGAGTATCCCCGATTAT-AAGAAATCAAT-ATTTTAGAAATAAAACCGGGGATTGGAGTA
* * *
647516 TTCCCTCGAAGATAAC
64 TCCCCTCAAAAATAAC
* *
647532 GAGGTTGGAGTATCCCCGATTATAAGAAATTAATATTTTAGAAATAAAGCCGGGGATTGGAGTAT
1 G-GGTTGGAGTATCCCCGATTATAAGAAATCAATATTTTAGAAATAAAACCGGGGATTGGAGTAT
647597 CCCCTCAAAAATAAC
65 CCCCTCAAAAATAAC
647612 GGAGTTGGAGTATCCCCGAT
1 GG-GTTGGAGTATCCCCGAT
647632 GATTAACGGG
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
78 4 0.05
79 43 0.51
80 38 0.45
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCGATTATAAGAAATCAATATTTTAGAAATAAAACCGGGGATTGGAGTATC
CCCTCAAAAATAAC
Found at i:647646 original size:27 final size:27
Alignment explanation
Indices: 647608--647660 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
647598 CCCTCAAAAA
647608 TAACGGAGTTGGAGTATCCCCGATGAT
1 TAACGGAGTTGGAGTATCCCCGATGAT
* *
647635 TAACGGGGTTGGAGTATCCTCGATGA
1 TAACGGAGTTGGAGTATCCCCGATGA
647661 AAAATTGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (27 bp):
TAACGGAGTTGGAGTATCCCCGATGAT
Found at i:647725 original size:51 final size:51
Alignment explanation
Indices: 647661--647759 Score: 150
Period size: 51 Copynumber: 1.9 Consensus size: 51
647651 TCCTCGATGA
647661 AAAATTGATGTTTT-AGAAATAAAATCGGAGTT-GGAGTATCCCCGATTATAG
1 AAAATTGATGTTTTGA-AAATAAAATCGGAGTTGGGA-TATCCCCGATTATAG
647712 AAAATT-AGTGTTTTGAAAATAAAATCGGAGTTGGGATATCCCCGATTA
1 AAAATTGA-TGTTTTGAAAATAAAATCGGAGTTGGGATATCCCCGATTA
647760 CGGAGAATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
50 1 0.02
51 40 0.89
52 4 0.09
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (51 bp):
AAAATTGATGTTTTGAAAATAAAATCGGAGTTGGGATATCCCCGATTATAG
Found at i:648881 original size:94 final size:94
Alignment explanation
Indices: 648720--648907 Score: 367
Period size: 94 Copynumber: 2.0 Consensus size: 94
648710 AGATTATCTC
648720 ACCATGAATCCAGATTTGAAATTTTCTATTTCCCCAAGGTTGGAAAACCAACTCATAAAAGCCAT
1 ACCATGAATCCAGATTTGAAATTTTCTATTTCCCCAAGGTTGGAAAACCAACTCATAAAAGCCAT
*
648785 AAGTTCATGTTATTCTCCATGTATGGGAG
66 AAGTTCATGTTATTCTCCATGTATAGGAG
648814 ACCATGAATCCAGATTTGAAATTTTCTATTTCCCCAAGGTTGGAAAACCAACTCATAAAAGCCAT
1 ACCATGAATCCAGATTTGAAATTTTCTATTTCCCCAAGGTTGGAAAACCAACTCATAAAAGCCAT
648879 AAGTTCATGTTATTCTCCATGTATAGGAG
66 AAGTTCATGTTATTCTCCATGTATAGGAG
648908 GTAGCATGAG
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (94 bp):
ACCATGAATCCAGATTTGAAATTTTCTATTTCCCCAAGGTTGGAAAACCAACTCATAAAAGCCAT
AAGTTCATGTTATTCTCCATGTATAGGAG
Found at i:650238 original size:13 final size:13
Alignment explanation
Indices: 650220--650245 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
650210 CAAAGAATAG
650220 ATGTATCGATACA
1 ATGTATCGATACA
650233 ATGTATCGATACA
1 ATGTATCGATACA
650246 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:650242 original size:34 final size:33
Alignment explanation
Indices: 650199--650265 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
650189 AACTTCCTAG
*
650199 ATGTATCGATACAAAGAATAGATGTATCGATACA
1 ATGTATCGATACAAAGAA-AAATGTATCGATACA
*
650233 ATGTATCGATACACAGAAAAATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
650266 TTTCCTTGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 14 0.45
34 17 0.55
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATACA
Found at i:650321 original size:19 final size:19
Alignment explanation
Indices: 650297--650369 Score: 92
Period size: 19 Copynumber: 3.7 Consensus size: 19
650287 AGCGATACAT
650297 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
650316 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
** *
650335 TGTATCGATACATTTACTGAA
1 TGTATCGATACA-AAACT-TA
650356 TGTATCGATACAAA
1 TGTATCGATACAAA
650370 TTATTGGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 30 0.65
20 3 0.07
21 13 0.28
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:656631 original size:16 final size:16
Alignment explanation
Indices: 656566--656631 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 16
656556 TAATACTTAA
* *
656566 TTTAAGTTTGAATTAT
1 TTTAAATTTAAATTAT
** *
656582 TTTAGGTTCAAATTAT
1 TTTAAATTTAAATTAT
* * *
656598 TTTAGATTTAGATCAT
1 TTTAAATTTAAATTAT
656614 TTTAAATTTAAATTAT
1 TTTAAATTTAAATTAT
656630 TT
1 TT
656632 CAAGTTTCAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (16 bp):
TTTAAATTTAAATTAT
Found at i:662528 original size:3 final size:3
Alignment explanation
Indices: 662520--662551 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
662510 TTGTTCACCC
662520 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
662552 ACTTGGCTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:663016 original size:20 final size:20
Alignment explanation
Indices: 662980--663029 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
662970 TTATTATTAT
662980 TTTTATTTATATATGT-AAA
1 TTTTATTTATATATGTAAAA
662999 TTTTATTTAT-TAATTGTAAAA
1 TTTTATTTATAT-A-TGTAAAA
663020 TTTATATTTA
1 TTT-TATTTA
663030 AGAATGATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.04
19 11 0.41
20 3 0.11
21 6 0.22
22 6 0.22
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTATTTATATATGTAAAA
Found at i:663423 original size:15 final size:14
Alignment explanation
Indices: 663409--663457 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
663399 TTTTTTAATA
663409 ATTTATATTTAAAT
1 ATTTATATTTAAAT
* *
663423 ATTTATTAATTAAAA
1 ATTTA-TATTTAAAT
*
663438 ATTTATATTCAAAT
1 ATTTATATTTAAAT
663452 ATTTAT
1 ATTTAT
663458 TAAATGATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTATATTTAAAT
Found at i:663445 original size:29 final size:29
Alignment explanation
Indices: 663403--663460 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
663393 TCCATCTTTT
* *
663403 TTAATAATTTATATTTAAATATTTATTAA
1 TTAAAAATTTATATTCAAATATTTATTAA
663432 TTAAAAATTTATATTCAAATATTTATTAA
1 TTAAAAATTTATATTCAAATATTTATTAA
663461 ATGATTAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TTAAAAATTTATATTCAAATATTTATTAA
Found at i:664751 original size:2 final size:2
Alignment explanation
Indices: 664744--664776 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
664734 TACAACTTAC
664744 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
664777 ACTCAAGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:665570 original size:5 final size:5
Alignment explanation
Indices: 665560--665584 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
665550 CCAAGGTTGG
665560 TCGAT TCGAT TCGAT TCGAT TCGAT
1 TCGAT TCGAT TCGAT TCGAT TCGAT
665585 CGTCAAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
TCGAT
Found at i:668462 original size:29 final size:29
Alignment explanation
Indices: 668428--668485 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
668418 GGGGAGGGCC
668428 GGAGCTGGAGCAGGAGGAGTGAGAGAATA
1 GGAGCTGGAGCAGGAGGAGTGAGAGAATA
668457 GGAGCTGGAGCAGGAGGAGTGAGAGAATA
1 GGAGCTGGAGCAGGAGGAGTGAGAGAATA
668486 TATTATAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.48, T:0.10
Consensus pattern (29 bp):
GGAGCTGGAGCAGGAGGAGTGAGAGAATA
Found at i:672027 original size:2 final size:2
Alignment explanation
Indices: 672020--672058 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
672010 TATTAGAATC
*
672020 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
672059 AATTAAAAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:672750 original size:15 final size:15
Alignment explanation
Indices: 672720--672749 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
672710 ATAGTAAACA
672720 TAAATATTAAGATTT
1 TAAATATTAAGATTT
672735 TAAATATTAA-ATTT
1 TAAATATTAAGATTT
672749 T
1 T
672750 TTTTATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TAAATATTAAGATTT
Found at i:695849 original size:12 final size:12
Alignment explanation
Indices: 695812--695841 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
695802 TTAATATATA
695812 TATATATTATGTT
1 TATATATTAT-TT
695825 TATATATTATTT
1 TATATATTATTT
695837 TATAT
1 TATAT
695842 TTACTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (12 bp):
TATATATTATTT
Found at i:696489 original size:3 final size:3
Alignment explanation
Indices: 696481--696505 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
696471 ATATATATAT
696481 GTA GTA GTA GTA GTA GTA GTA GTA G
1 GTA GTA GTA GTA GTA GTA GTA GTA G
696506 AGTTTCTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GTA
Found at i:697596 original size:35 final size:35
Alignment explanation
Indices: 697521--697605 Score: 84
Period size: 35 Copynumber: 2.4 Consensus size: 35
697511 TCATAGTGAA
* **
697521 AAAATTATAAATATTAAAATTTAAATTAAATTTTATT
1 AAAATT-T-AATATTAAAATATAAATTAAATTAAATT
*
697558 AAAATATT-ATATTAATATATAAATT-AATTAAATAT
1 AAAAT-TTAATATTAAAATATAAATTAAATTAAAT-T
697593 AAAATTTAATATT
1 AAAATTTAATATT
697606 GAAGTTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
34 8 0.20
35 26 0.63
37 6 0.15
38 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (35 bp):
AAAATTTAATATTAAAATATAAATTAAATTAAATT
Found at i:697601 original size:29 final size:29
Alignment explanation
Indices: 697528--697615 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 29
697518 GAAAAAATTA
*
697528 TAAATATTAAAATTTAA-ATTAAATTTTAT
1 TAAATA-TAAAATTTAATATTAAATTTAAT
**
697557 TAAA-ATATTATATTAATATATAAA-TTAAT
1 TAAATATAAAAT-TTAATAT-TAAATTTAAT
* *
697586 TAAATATAAAATTTAATATTGAAGTTAAT
1 TAAATATAAAATTTAATATTAAATTTAAT
697615 T
1 T
697616 TTATTGTCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
27 4 0.08
28 8 0.17
29 27 0.56
30 9 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
TAAATATAAAATTTAATATTAAATTTAAT
Found at i:704978 original size:18 final size:18
Alignment explanation
Indices: 704931--704978 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
704921 ATCTAATTAC
704931 TAATATTTAA-AATATTT
1 TAATATTTAATAATATTT
704948 T-ATATTTATATAA-ATTT
1 TAATATTTA-ATAATATTT
704965 TAATATATTAATAA
1 TAATAT-TTAATAA
704979 CTAACATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 7 0.26
17 7 0.26
18 10 0.37
19 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATATTTAATAATATTT
Found at i:705002 original size:38 final size:37
Alignment explanation
Indices: 704960--705034 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
704950 TATTTATATA
704960 AATTTTAATATATTAATAACTA-ACATTATATTAATTTT
1 AATTTTAATATATTAAT-ACTATACA-TATATTAATTTT
** * *
704998 AATTTTTTTATATTTATATTATACATATATTAATTTT
1 AATTTTAATATATTAATACTATACATATATTAATTTT
705035 TTTAACGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 15 0.47
38 17 0.53
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (37 bp):
AATTTTAATATATTAATACTATACATATATTAATTTT
Found at i:708127 original size:5 final size:5
Alignment explanation
Indices: 708117--708141 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
708107 GCCGCACGGG
708117 AAACC AAACC AAACC AAACC AAACC
1 AAACC AAACC AAACC AAACC AAACC
708142 CACCAAACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACC
Found at i:708655 original size:61 final size:63
Alignment explanation
Indices: 708589--708710 Score: 158
Period size: 61 Copynumber: 1.9 Consensus size: 63
708579 TTGTTAATCA
* * *
708589 AATTAAATTAATATTAATTAATTTAATTTAATTTT-TTAATC-ACTAATTTAATTATTTGAGT
1 AATTAAAATAATATTAATTAATTCAATTGAATTTTATTAATCAACTAATTTAATTATTTGAGT
* * *
708650 AATTAAAATAATTTTAATTAATTCAATTGATTTTTCATTAATCAAATTAATTTAATTATTT
1 AATTAAAATAATATTAATTAATTCAATTGAATTTT-ATTAATC-AACTAATTTAATTATTT
708711 AATTTTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
61 30 0.59
63 6 0.12
65 15 0.29
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (63 bp):
AATTAAAATAATATTAATTAATTCAATTGAATTTTATTAATCAACTAATTTAATTATTTGAGT
Found at i:708697 original size:20 final size:20
Alignment explanation
Indices: 708661--708702 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
708651 ATTAAAATAA
*
708661 TTTTAATTAATTCAATTGAT
1 TTTTAATTAATTCAATTAAT
*
708681 TTTTCATTAA-TCAAATTAAT
1 TTTTAATTAATTC-AATTAAT
708701 TT
1 TT
708703 AATTATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTTAATTAATTCAATTAAT
Found at i:708712 original size:8 final size:9
Alignment explanation
Indices: 708589--708714 Score: 55
Period size: 9 Copynumber: 14.0 Consensus size: 9
708579 TTGTTAATCA
*
708589 AATTAAATT
1 AATTTAATT
708598 AATATTAATT
1 AAT-TTAATT
708608 AATTTAATTT
1 AATTTAA-TT
*
708618 AATTT-TTT
1 AATTTAATT
* *
708626 AA--TCACT
1 AATTTAATT
708633 AATTTAATT
1 AATTTAATT
* *
708642 -ATTTGAGT
1 AATTTAATT
* *
708650 AATTAAAAT
1 AATTTAATT
708659 AATTTTAATT
1 AA-TTTAATT
*
708669 AATTCAATT
1 AATTTAATT
* *
708678 GATTTTTCATT
1 -A-ATTTAATT
**
708689 AATCAAATT
1 AATTTAATT
708698 AATTTAATT
1 AATTTAATT
708707 -ATTTAATT
1 AATTTAATT
708715 TTTTTTAAAT
Statistics
Matches: 85, Mismatches: 23, Indels: 19
0.67 0.18 0.15
Matches are distributed among these distances:
6 1 0.01
7 3 0.04
8 18 0.21
9 34 0.40
10 24 0.28
11 5 0.06
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (9 bp):
AATTTAATT
Found at i:709522 original size:28 final size:28
Alignment explanation
Indices: 709490--709550 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
709480 TTGAGTCATC
* *
709490 TTTATT-TAGAATATATTAAAATTTAATT
1 TTTATTATAAAATATATTAAAAGTT-ATT
709518 TTTATTATAAAATATATTAAAAGTTATT
1 TTTATTATAAAATATATTAAAAGTTATT
709546 TTTAT
1 TTTAT
709551 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 14 0.47
29 16 0.53
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (28 bp):
TTTATTATAAAATATATTAAAAGTTATT
Found at i:714039 original size:12 final size:12
Alignment explanation
Indices: 714010--714046 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
714000 GTTCAGTATA
714010 AAATATTTATTT
1 AAATATTTATTT
714022 AAAT-TTT-TTT
1 AAATATTTATTT
714032 AAATATTTATTT
1 AAATATTTATTT
714044 AAA
1 AAA
714047 AAATTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 7 0.30
11 6 0.26
12 10 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
AAATATTTATTT
Found at i:718088 original size:17 final size:18
Alignment explanation
Indices: 718068--718115 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
718058 TATATTAAAT
* *
718068 ATAAATATTTTAAATA-A
1 ATAAATAATTAAAATATA
718085 ATAAA-AATTAAAATATA
1 ATAAATAATTAAAATATA
*
718102 ATAAATAATGAAAA
1 ATAAATAATTAAAA
718116 AAATGAGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 8 0.31
17 11 0.42
18 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
ATAAATAATTAAAATATA
Found at i:718679 original size:26 final size:26
Alignment explanation
Indices: 718650--718706 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
718640 TATGAATGAT
*
718650 TAAAATAAAATTTAAATATTTAATTA
1 TAAAATAAAATTTAAATATTAAATTA
** *
718676 TAAAATTTATTTTAAATATTAAATTA
1 TAAAATAAAATTTAAATATTAAATTA
718702 TAAAA
1 TAAAA
718707 AAATATAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAAATAAAATTTAAATATTAAATTA
Found at i:718683 original size:13 final size:14
Alignment explanation
Indices: 718658--718705 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
718648 ATTAAAATAA
718658 AATT-TAAATATTT
1 AATTATAAATATTT
718671 AATTATAAA-ATTT
1 AATTATAAATATTT
* *
718684 -ATTTTAAATATTA
1 AATTATAAATATTT
718697 AATTATAAA
1 AATTATAAA
718706 AAAATATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 7 0.24
13 11 0.38
14 11 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTATAAATATTT
Found at i:721172 original size:39 final size:39
Alignment explanation
Indices: 721115--721192 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
721105 TTAGTGGCTG
**
721115 GTCAGCTATTCTGTGTTCACAAATAAACTTCCTAATTTC
1 GTCAGCTATTCTACGTTCACAAATAAACTTCCTAATTTC
*
721154 GTCAGCTATTCTACGTTCACAAATAAACTTTCTAATTTC
1 GTCAGCTATTCTACGTTCACAAATAAACTTCCTAATTTC
721193 CTTTTCTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.38
Consensus pattern (39 bp):
GTCAGCTATTCTACGTTCACAAATAAACTTCCTAATTTC
Found at i:721390 original size:2 final size:2
Alignment explanation
Indices: 721383--721420 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
721373 CTTGGCATAC
*
721383 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
721421 ATCCCGTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:729760 original size:2 final size:2
Alignment explanation
Indices: 729753--729780 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
729743 AACCTTTTAC
729753 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
729781 GTTAAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:731276 original size:2 final size:2
Alignment explanation
Indices: 731271--731304 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
731261 CAATGGAGGA
731271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
731305 GATTGAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:731674 original size:2 final size:2
Alignment explanation
Indices: 731667--731712 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
731657 GCAGAATCTC
* * *
731667 TA TA TA TA TA TG TG TA TG TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
731708 TA TA T
1 TA TA T
731713 GGAACTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (2 bp):
TA
Found at i:731705 original size:13 final size:13
Alignment explanation
Indices: 731687--731712 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
731677 TGTGTATGTA
731687 TATATATATATAT
1 TATATATATATAT
731700 TATATATATATAT
1 TATATATATATAT
731713 GGAACTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:732080 original size:17 final size:17
Alignment explanation
Indices: 732060--732104 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
732050 ATATTTTCAT
*
732060 TAAATAAATTTTAATTA
1 TAAAAAAATTTTAATTA
*
732077 TAAAAAAGATTTTAATTT
1 TAAAAAA-ATTTTAATTA
732095 TAAAAAAATT
1 TAAAAAAATT
732105 ACAAATTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAAAAAATTTTAATTA
Found at i:733401 original size:3 final size:3
Alignment explanation
Indices: 733393--733424 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
733383 TGAAAAGAGC
733393 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
733425 CAACATGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:736157 original size:17 final size:19
Alignment explanation
Indices: 736124--736174 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
736114 ATTATTAGTT
* *
736124 TAATATATAAATTTTT-TTA
1 TAATA-ATATATTTTTATGA
736143 TAATTAATATATTTTTATGA
1 TAA-TAATATATTTTTATGA
736163 TAATAATATATT
1 TAATAATATATT
736175 AAATAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TAATAATATATTTTTATGA
Found at i:737007 original size:4 final size:4
Alignment explanation
Indices: 736998--737039 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
736988 ATGTAGAATG
736998 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA
737040 ACTTAGCTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (4 bp):
TAGA
Found at i:740052 original size:23 final size:23
Alignment explanation
Indices: 740004--740052 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
739994 ATTGATTTAT
*
740004 TTTATTAAAATAATATTATATGA
1 TTTATTAAAATAATATAATATGA
740027 TTTATTAATAAT-ATATAAATAT-A
1 TTTATTAA-AATAATAT-AATATGA
740050 TTT
1 TTT
740053 TTTTTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTATTAAAATAATATAATATGA
Found at i:750523 original size:3 final size:3
Alignment explanation
Indices: 750517--750542 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
750507 CAACAACAAC
750517 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
750543 GCTTTGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:753832 original size:2 final size:2
Alignment explanation
Indices: 753825--753858 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
753815 GACATTAACA
753825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
753859 GTAATGAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:754108 original size:39 final size:39
Alignment explanation
Indices: 754065--754161 Score: 158
Period size: 39 Copynumber: 2.5 Consensus size: 39
754055 TTAGGACCAT
* * *
754065 TAAATCAATATTTGAAAATCAATTTCTTCAATAAATAAA
1 TAAATAAAAATTTGAAAATCAATTTCTTCAAAAAATAAA
*
754104 TAAATAAAAATTTGAAAGTCAATTTCTTCAAAAAATAAA
1 TAAATAAAAATTTGAAAATCAATTTCTTCAAAAAATAAA
754143 TAAATAAAAATTTGAAAAT
1 TAAATAAAAATTTGAAAAT
754162 AAATATACGT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (39 bp):
TAAATAAAAATTTGAAAATCAATTTCTTCAAAAAATAAA
Found at i:754182 original size:39 final size:39
Alignment explanation
Indices: 754065--754172 Score: 117
Period size: 39 Copynumber: 2.7 Consensus size: 39
754055 TTAGGACCAT
* * * * * *
754065 TAAATCAATATTTGAAAATCAATTTCTTCAATAAATAAA
1 TAAATAAAAATTTGAAAATAAATTACGTCAAAAAATAAA
* * * *
754104 TAAATAAAAATTTGAAAGTCAATTTCTTCAAAAAATAAA
1 TAAATAAAAATTTGAAAATAAATTACGTCAAAAAATAAA
754143 TAAATAAAAATTTGAAAATAAATATACGTC
1 TAAATAAAAATTTGAAAATAAAT-TACGTC
754173 TAGAATAAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 56 0.93
40 4 0.07
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (39 bp):
TAAATAAAAATTTGAAAATAAATTACGTCAAAAAATAAA
Found at i:754364 original size:2 final size:2
Alignment explanation
Indices: 754357--754394 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
754347 GCAAAAATCA
754357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
754395 GTTAGCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:755766 original size:6 final size:6
Alignment explanation
Indices: 755757--755839 Score: 54
Period size: 6 Copynumber: 14.7 Consensus size: 6
755747 TTTATTTTAA
* *
755757 TTAAAT TTAAA- -TAAATT TTTAAT TTAAAT TTAAA- -TAAAT TTATAT
1 TTAAAT TTAAAT TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * *
755802 TTATAT TT-AA- TTAAAT AT-ATT TTAAAT ATTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT TTAA
755840 TTATTTCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
4 10 0.17
5 6 0.10
6 35 0.58
7 9 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:755787 original size:23 final size:23
Alignment explanation
Indices: 755751--755817 Score: 93
Period size: 22 Copynumber: 3.0 Consensus size: 23
755741 TATTTTTTTA
755751 TTTTAA-TTAAATTTAAATAAAT
1 TTTTAATTTAAATTTAAATAAAT
755773 TTTTAATTTAAATTTAAATAAAT
1 TTTTAATTTAAATTTAAATAAAT
* * *
755796 TTAT-ATTTATATTTAATTAAAT
1 TTTTAATTTAAATTTAAATAAAT
755818 ATATTTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 22 0.54
23 19 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTAATTTAAATTTAAATAAAT
Found at i:755833 original size:22 final size:22
Alignment explanation
Indices: 755757--755835 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
755747 TTTATTTTAA
* *
755757 TTAAATTTAAATAAATTTTTAAT
1 TTAAATTTAAATAAATATAT-AT
*
755780 TTAAATTTAAATAAATTTATAT
1 TTAAATTTAAATAAATATATAT
* *
755802 TTATATTTAATTAAATATAT-T
1 TTAAATTTAAATAAATATATAT
755823 TTAAATATTAAAT
1 TTAAAT-TTAAAT
755836 TTAATTATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
21 6 0.12
22 24 0.49
23 19 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAATTTAAATAAATATATAT
Found at i:767447 original size:2 final size:2
Alignment explanation
Indices: 767440--767478 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
767430 TAGGAGTTTC
767440 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
767479 GCTTGCCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:771665 original size:2 final size:2
Alignment explanation
Indices: 771658--771693 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
771648 CCATAAATCA
771658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
771694 GGATGAAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:778620 original size:20 final size:19
Alignment explanation
Indices: 778597--778635 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
778587 AGGGATACAA
*
778597 GAGAAGGATGAGGGATGCTT
1 GAGAAGGAGGAGGGA-GCTT
*
778617 GAGAGGGAGGAGGGAGCTT
1 GAGAAGGAGGAGGGAGCTT
778636 CCTTTTATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.05, G:0.51, T:0.15
Consensus pattern (19 bp):
GAGAAGGAGGAGGGAGCTT
Found at i:778705 original size:24 final size:25
Alignment explanation
Indices: 778678--778747 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
778668 AATAAAAATT
*
778678 AGCCACCAATTTTGACAAAC-AACA
1 AGCCACCAATTTTGACAAACAAAAA
*
778702 AGCCA-TAATTTTTGACAAACAAAAA
1 AGCCACCAA-TTTTGACAAACAAAAA
*
778727 AGAACCACCATTTTTGACAAA
1 AG--CCACCAATTTTGACAAA
778748 TACAAAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 16 0.43
25 5 0.14
27 13 0.35
28 1 0.03
ACGTcount: A:0.47, C:0.23, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAACAAAAA
Found at i:778747 original size:27 final size:27
Alignment explanation
Indices: 778680--778776 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
778670 TAAAAATTAG
* *
778680 CCACCAATTTTGACAAAC-AACAAG--
1 CCACCATTTTTGACAAACAAAAAAGAA
**
778704 CCATAATTTTTGACAAACAAAAAAGAA
1 CCACCATTTTTGACAAACAAAAAAGAA
* *
778731 CCACCATTTTTGACAAA-TACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAAG-AA
*
778758 CCACCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
778777 CATAGTGGCT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
24 15 0.26
25 5 0.09
26 5 0.09
27 33 0.57
ACGTcount: A:0.46, C:0.24, G:0.08, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAAGAA
Found at i:778795 original size:24 final size:25
Alignment explanation
Indices: 778764--778821 Score: 82
Period size: 24 Copynumber: 2.3 Consensus size: 25
778754 GTAACCACCA
*
778764 TTGTTGACAAACACATA-GTGGCTT
1 TTGTTGACAAACACAAAGGTGGCTT
*
778788 TTGTTGACAAACACAAAGGGTGGTTT
1 TTGTTGACAAACACAAA-GGTGGCTT
778814 TTGTTGAC
1 TTGTTGAC
778822 TAGCCACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 16 0.53
26 14 0.47
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (25 bp):
TTGTTGACAAACACAAAGGTGGCTT
Found at i:780711 original size:21 final size:22
Alignment explanation
Indices: 780685--780730 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
780675 ATCTGTTGAA
* *
780685 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGTGGAGTACT
780706 ACTCCACCTGCTGTGGAGTACT
1 ACTCCACCTGCTGTGGAGTACT
780728 ACT
1 ACT
780731 TGTCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTACT
Found at i:783217 original size:20 final size:19
Alignment explanation
Indices: 783194--783232 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
783184 AGGGATACAA
*
783194 GAGAAGGATGAGGGATGCTT
1 GAGAAGGAGGAGGGA-GCTT
*
783214 GAGAGGGAGGAGGGAGCTT
1 GAGAAGGAGGAGGGAGCTT
783233 CCTTTTATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.05, G:0.51, T:0.15
Consensus pattern (19 bp):
GAGAAGGAGGAGGGAGCTT
Found at i:783302 original size:24 final size:24
Alignment explanation
Indices: 783275--783320 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
783265 AATAAAAATT
783275 AGCCACCAA-TTTTGACAAACAACA
1 AGCCA-CAATTTTTGACAAACAACA
*
783299 AGCCATAATTTTTGACAAACAA
1 AGCCACAATTTTTGACAAACAA
783321 AAAAGAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.46, C:0.24, G:0.09, T:0.22
Consensus pattern (24 bp):
AGCCACAATTTTTGACAAACAACA
Found at i:783344 original size:27 final size:28
Alignment explanation
Indices: 783306--783373 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
783296 ACAAGCCATA
783306 ATTTTTGACAAACAAAAAAG-AACCACC
1 ATTTTTGACAAACAAAAAAGTAACCACC
* * *
783333 ATTTTTTACAAA-TACAAAGTAACCACC
1 ATTTTTGACAAACAAAAAAGTAACCACC
*
783360 ATTGTTGACAAACA
1 ATTTTTGACAAACA
783374 CATGGTGGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
26 5 0.15
27 28 0.85
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.25
Consensus pattern (28 bp):
ATTTTTGACAAACAAAAAAGTAACCACC
Found at i:783389 original size:24 final size:25
Alignment explanation
Indices: 783361--783418 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
783351 GTAACCACCA
*
783361 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
*
783385 TTGTTGACAAACACAAAGGGTGGTTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
783411 TTGTTGAC
1 TTGTTGAC
783419 TAGCCACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.47
26 16 0.53
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:785759 original size:2 final size:2
Alignment explanation
Indices: 785752--785783 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
785742 TCTTCTCTTT
785752 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
785784 AGATTTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:792908 original size:2 final size:2
Alignment explanation
Indices: 792901--792925 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
792891 ACTATTTATT
792901 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
792926 GTAGATGCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:794630 original size:67 final size:67
Alignment explanation
Indices: 794522--794657 Score: 272
Period size: 67 Copynumber: 2.0 Consensus size: 67
794512 ATTCTTGCCG
794522 GGTAAGTTTGGTGTTAATAACATCATTGATCCAATTAGTGTGGTTATAGATGACCAGCAAATAAT
1 GGTAAGTTTGGTGTTAATAACATCATTGATCCAATTAGTGTGGTTATAGATGACCAGCAAATAAT
794587 CA
66 CA
794589 GGTAAGTTTGGTGTTAATAACATCATTGATCCAATTAGTGTGGTTATAGATGACCAGCAAATAAT
1 GGTAAGTTTGGTGTTAATAACATCATTGATCCAATTAGTGTGGTTATAGATGACCAGCAAATAAT
794654 CA
66 CA
794656 GG
1 GG
794658 CAATACCATA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (67 bp):
GGTAAGTTTGGTGTTAATAACATCATTGATCCAATTAGTGTGGTTATAGATGACCAGCAAATAAT
CA
Found at i:798202 original size:18 final size:18
Alignment explanation
Indices: 798159--798213 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
798149 CCTTAACCAA
* *
798159 CCAAATCCAGATCTAGAT
1 CCAAATCCAGATCCAAAT
* *
798177 TCAGATCCAGATCCAAAT
1 CCAAATCCAGATCCAAAT
*
798195 CCAAATCCAAATCCAAAT
1 CCAAATCCAGATCCAAAT
798213 C
1 C
798214 TGGGAATTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.42, C:0.31, G:0.07, T:0.20
Consensus pattern (18 bp):
CCAAATCCAGATCCAAAT
Found at i:798210 original size:6 final size:6
Alignment explanation
Indices: 798181--798213 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
798171 CTAGATTCAG
*
798181 ATCCAG ATCCAA ATCCAA ATCCAA ATCCAA ATC
1 ATCCAA ATCCAA ATCCAA ATCCAA ATCCAA ATC
798214 TGGGAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.45, C:0.33, G:0.03, T:0.18
Consensus pattern (6 bp):
ATCCAA
Found at i:805483 original size:3 final size:3
Alignment explanation
Indices: 805475--805517 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
805465 AGGTCAAGAG
805475 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
805518 AAATGATGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:807345 original size:2 final size:2
Alignment explanation
Indices: 807338--807362 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
807328 AATTGAACTT
807338 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
807363 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:808974 original size:24 final size:25
Alignment explanation
Indices: 808945--809019 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 25
808935 AATTAATTCG
*
808945 TATAATTATTTTTAAAATATAA-TAT
1 TATAATTATATTT-AAATATAATTAT
808970 T-TAA-TATATTTAAATATAATTAT
1 TATAATTATATTTAAATATAATTAT
*
808993 TATAA-TATGA--TAAATATGATTAT
1 TATAATTAT-ATTTAAATATAATTAT
809016 TATA
1 TATA
809020 TCTGTAAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
22 8 0.18
23 26 0.58
24 9 0.20
25 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (25 bp):
TATAATTATATTTAAATATAATTAT
Found at i:809006 original size:23 final size:23
Alignment explanation
Indices: 808959--809019 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
808949 ATTATTTTTA
808959 AAATATAA-TATT-TAATATATTT
1 AAATATAATTATTATAATATA-TT
808981 AAATATAATTATTATAATATGA-T
1 AAATATAATTATTATAATAT-ATT
*
809004 AAATATGATTATTATA
1 AAATATAATTATTATA
809020 TCTGTAAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
22 8 0.23
23 20 0.57
24 6 0.17
25 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (23 bp):
AAATATAATTATTATAATATATT
Found at i:812399 original size:11 final size:11
Alignment explanation
Indices: 812383--812419 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
812373 AAAGGTTAAA
812383 AAAAAAAAGAG
1 AAAAAAAAGAG
812394 AAAAAAAAGA-
1 AAAAAAAAGAG
*
812404 AAGAAAAAG-G
1 AAAAAAAAGAG
812414 AAAAAA
1 AAAAAA
812420 CTCATCGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:813234 original size:41 final size:39
Alignment explanation
Indices: 813146--813237 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 39
813136 TTAATTGTAT
* *
813146 TTATTTAAATTTATTTTTGATTTAAAATATAAATTTTAAA
1 TTATTTAAATTAATTTTT-ATTTAAAATATAAAATTTAAA
813186 TTATTTAAATTAATTTATT-TTTATAAATA-AATAATTTAAA
1 TTATTTAAATTAATTT-TTATTTA-AAATATAA-AATTTAAA
813226 TCTATTTAAATT
1 T-TATTTAAATT
813238 TATTCATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
39 6 0.13
40 28 0.61
41 12 0.26
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (39 bp):
TTATTTAAATTAATTTTTATTTAAAATATAAAATTTAAA
Found at i:813240 original size:31 final size:31
Alignment explanation
Indices: 813182--813240 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
813172 ATATAAATTT
* **
813182 TAAATTATTTAAATTAATTTATTTTTATAAA
1 TAAATAATTTAAATTAATTTAAATTTATAAA
813213 TAAATAATTTAAATCT-ATTTAAATTTAT
1 TAAATAATTTAAAT-TAATTTAAATTTAT
813241 TCATATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.96
32 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (31 bp):
TAAATAATTTAAATTAATTTAAATTTATAAA
Found at i:822742 original size:5 final size:5
Alignment explanation
Indices: 822732--822761 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
822722 GTTGAAGACG
*
822732 CTTTC CTTTC CTTTC CTTTC CTTTT CTTTC
1 CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC
822762 TTTGTCCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (5 bp):
CTTTC
Found at i:822860 original size:25 final size:25
Alignment explanation
Indices: 822827--822877 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
822817 TAAATCATTA
* *
822827 TAAATTAAAATTTTATTAT-TTTATT
1 TAAAATAAAATTAT-TTATATTTATT
822852 TAAAATAAAATTATTTATATTTATT
1 TAAAATAAAATTATTTATATTTATT
822877 T
1 T
822878 TCAAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TAAAATAAAATTATTTATATTTATT
Found at i:832306 original size:2 final size:2
Alignment explanation
Indices: 832299--832329 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
832289 GTTAATAGTC
832299 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
832330 GATGATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:834037 original size:3 final size:3
Alignment explanation
Indices: 834029--834053 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
834019 AAACAAGGGA
834029 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
834054 GGTATTTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:835297 original size:2 final size:2
Alignment explanation
Indices: 835290--835326 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
835280 ACATTAGCAC
835290 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
835327 TGTACTCAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:841262 original size:27 final size:28
Alignment explanation
Indices: 841232--841288 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
841222 AATTATTTAT
841232 TATTTAAATTAAA-TTAATTT-ATAAAAA
1 TATTT-AATTAAATTTAATTTAATAAAAA
* *
841259 TATTTATTTAAATTTAATTTAATATAAA
1 TATTTAATTAAATTTAATTTAATAAAAA
841287 TA
1 TA
841289 AATATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.23
27 12 0.46
28 8 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TATTTAATTAAATTTAATTTAATAAAAA
Found at i:841292 original size:32 final size:31
Alignment explanation
Indices: 841231--841296 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
841221 AAATTATTTA
*
841231 TTATTTAAATTAAATTAATTTATAAAAATAT
1 TTATTTAAATTAAATTAATATATAAAAATAT
*
841262 TTATTTAAATTTAATTTAATATA-AATAAATAT
1 TTATTTAAA-TTAAATTAATATATAA-AAATAT
841294 TTA
1 TTA
841297 AATCATGACC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 11 0.35
32 20 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
TTATTTAAATTAAATTAATATATAAAAATAT
Found at i:841296 original size:28 final size:27
Alignment explanation
Indices: 841240--841299 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
841230 ATTATTTAAA
**
841240 TTAAA-TTAATTTATAAAAATATTTAT
1 TTAAATTTAATTTATAAAAATAAATAT
*
841266 TTAAATTTAATTTAATATAAATAAATAT
1 TTAAATTTAATTT-ATAAAAATAAATAT
841294 TTAAAT
1 TTAAAT
841300 CATGACCTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 5 0.17
27 7 0.24
28 17 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TTAAATTTAATTTATAAAAATAAATAT
Found at i:844199 original size:8 final size:8
Alignment explanation
Indices: 844182--844213 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
844172 GGGCAGGAAA
844182 AAAAAAAG
1 AAAAAAAG
*
844190 AAAGAAAG
1 AAAAAAAG
844198 AAAAAAAG
1 AAAAAAAG
844206 AAAAAAAG
1 AAAAAAAG
844214 GGATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:844203 original size:16 final size:16
Alignment explanation
Indices: 844178--844213 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
844168 TTTTGGGCAG
844178 GAAA-AAAAAAAGAAA
1 GAAAGAAAAAAAGAAA
844193 GAAAGAAAAAAAGAAA
1 GAAAGAAAAAAAGAAA
*
844209 AAAAG
1 GAAAG
844214 GGATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAAAAGAAA
Found at i:844245 original size:22 final size:24
Alignment explanation
Indices: 844218--844270 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
844208 AAAAAGGGAT
* *
844218 TTTTTTTATAT-TTATAT-TTATA
1 TTTTTTTATATATAAAATATTATA
844240 TTTTTTTATATATAAAATATTATA
1 TTTTTTTATATATAAAATATTATA
844264 TTTTTTT
1 TTTTTTT
844271 TACATCTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 11 0.41
23 4 0.15
24 12 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTTTTATATATAAAATATTATA
Found at i:844856 original size:23 final size:23
Alignment explanation
Indices: 844812--844858 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
844802 TTGTGTCATA
*
844812 TTTATATTATTTTTATGCTGTAT
1 TTTATATTATTTTTATACTGTAT
*
844835 TTTA-ATTATTCTTTATATTGTAT
1 TTTATATTATT-TTTATACTGTAT
844858 T
1 T
844859 CATATCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.66
Consensus pattern (23 bp):
TTTATATTATTTTTATACTGTAT
Found at i:845127 original size:18 final size:17
Alignment explanation
Indices: 845096--845159 Score: 55
Period size: 18 Copynumber: 3.8 Consensus size: 17
845086 TTATTTTTTG
845096 TATA-AAATATTTTAAATT
1 TATATAAATA-TTT-AATT
845114 TATATAAATATTT-A--
1 TATATAAATATTTAATT
* *
845128 TATATTAATAATTTATTT
1 TATATAAAT-ATTTAATT
845146 TATATAAATATTTA
1 TATATAAATATTTA
845160 TATGTTTGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
14 8 0.21
15 4 0.11
16 1 0.03
17 5 0.13
18 15 0.39
19 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATAAATATTTAATT
Found at i:845973 original size:17 final size:17
Alignment explanation
Indices: 845952--846017 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
845942 TTTTTGTATC
845952 ATATTATATTTTAA-TT
1 ATATTATATTTTAATTT
* *
845968 ATTATTTTAATATTATATTT
1 A-TATTAT-ATTTTA-ATTT
*
845988 ATGTTATATTTTAATTT
1 ATATTATATTTTAATTT
*
846005 ATCTTATATTTTA
1 ATATTATATTTTA
846018 TATAAATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
16 1 0.03
17 21 0.52
18 10 0.25
19 5 0.12
20 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTAATTT
Found at i:846006 original size:12 final size:12
Alignment explanation
Indices: 845955--846020 Score: 57
Period size: 12 Copynumber: 5.5 Consensus size: 12
845945 TTGTATCATA
845955 TTATATTTTAA-
1 TTATATTTTAAT
845966 TTATTATTTTAAT
1 TTA-TATTTTAAT
845979 ATTATA-TTT-AT
1 -TTATATTTTAAT
845990 GTTATATTTTAAT
1 -TTATATTTTAAT
* * *
846003 TTATCTTATATT
1 TTATATTTTAAT
846015 TTATAT
1 TTATAT
846021 AAATTTTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
11 10 0.22
12 28 0.62
13 4 0.09
14 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (12 bp):
TTATATTTTAAT
Found at i:846242 original size:12 final size:12
Alignment explanation
Indices: 846223--846287 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
846213 TTTTACATTT
846223 AAAAAGAAAGAA
1 AAAAAGAAAGAA
*
846235 ATAAAGAAA-AA
1 AAAAAGAAAGAA
*
846246 AAAAAGGAAGAA
1 AAAAAGAAAGAA
*
846258 AGGACAAG--AGAA
1 A--AAAAGAAAGAA
846270 AAAAAGGAAAGAA
1 AAAAA-GAAAGAA
846283 AAAAA
1 AAAAA
846288 TATTGATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
10 3 0.07
11 10 0.24
12 16 0.38
13 9 0.21
14 4 0.10
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAGAA
Found at i:846259 original size:19 final size:19
Alignment explanation
Indices: 846223--846287 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
846213 TTTTACATTT
* *
846223 AAAAAGAAAGAAATAAAGA
1 AAAAAAAAAGAAAGAAAGA
*
846242 AAAAAAAAAGGAAGAAAGGA
1 AAAAAAAAAGAAAGAAA-GA
* *
846262 CAAGAGAAAAA-AAGGAAAGA
1 -AA-AAAAAAAGAAAGAAAGA
846282 AAAAAA
1 AAAAAA
846288 TATTGATATT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
18 3 0.08
19 16 0.44
20 4 0.11
21 7 0.19
22 6 0.17
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAGAAAGAAAGA
Found at i:846302 original size:12 final size:12
Alignment explanation
Indices: 846287--846372 Score: 51
Period size: 12 Copynumber: 7.3 Consensus size: 12
846277 AAAGAAAAAA
*
846287 ATATTGATATTT
1 ATATTAATATTT
*
846299 ATATTAATTTTT
1 ATATTAATATTT
*
846311 ATATTAAAATATT
1 ATATTAATAT-TT
846324 ATATT--T-TTAT
1 ATATTAATATT-T
846334 ATATTAATAATTT
1 ATATTAAT-ATTT
846347 AT-TT--TATTT
1 ATATTAATATTT
846356 CATATATAAT-TTT
1 -ATAT-TAATATTT
846369 ATAT
1 ATAT
846373 GTATGTATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 22
0.68 0.06 0.26
Matches are distributed among these distances:
9 5 0.09
10 10 0.17
11 1 0.02
12 26 0.45
13 13 0.22
14 3 0.05
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (12 bp):
ATATTAATATTT
Found at i:846340 original size:23 final size:24
Alignment explanation
Indices: 846299--846362 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
846289 ATTGATATTT
846299 ATATTA-A-TTTT-TATATTAA-A
1 ATATTATATTTTTATATATTAATA
846319 ATATTATATTTTTATATATTAATA
1 ATATTATATTTTTATATATTAATA
*
846343 AT-TTATTTTATTTCATATAT
1 ATATTATATT-TTT-ATATAT
846363 AATTTTATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 6 0.16
21 1 0.03
22 4 0.11
23 14 0.38
24 6 0.16
25 6 0.16
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
ATATTATATTTTTATATATTAATA
Found at i:846342 original size:21 final size:21
Alignment explanation
Indices: 846293--846351 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
846283 AAAAATATTG
*
846293 ATATTTATATTA-ATTTTTAT
1 ATATTAATATTATATTTTTAT
*
846313 AT-TAAAATATTATATTTTTAT
1 ATAT-TAATATTATATTTTTAT
846334 ATATTAATAATT-TATTTT
1 ATATTAAT-ATTATATTTT
846352 ATTTCATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.03
20 8 0.25
21 19 0.59
22 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTAATATTATATTTTTAT
Found at i:846880 original size:11 final size:12
Alignment explanation
Indices: 846849--846898 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
846839 CATGTCATAT
846849 TTATTTTTTATA
1 TTATTTTTTATA
*
846861 TTATGTTTTA-A
1 TTATTTTTTATA
*
846872 TTATTTTTTATG
1 TTATTTTTTATA
*
846884 TCATATTTTTATA
1 TTAT-TTTTTATA
846897 TT
1 TT
846899 TTATATATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
11 10 0.33
12 12 0.40
13 8 0.27
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (12 bp):
TTATTTTTTATA
Done.