Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold112
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: 1714866
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 134939 characters in sequence are not A, C, G, or T
File 3 of 11
Found at i:250639 original size:25 final size:25
Alignment explanation
Indices: 250611--250661 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
250601 ATTTTATTTT
*
250611 TAATATAATTATAAAAAAA-TAAAAA
1 TAATATAAATA-AAAAAAAGTAAAAA
*
250636 TAATCTAAATAAAAAAAAGTAAAAA
1 TAATATAAATAAAAAAAAGTAAAAA
250661 T
1 T
250662 TAGCATGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (25 bp):
TAATATAAATAAAAAAAAGTAAAAA
Found at i:252491 original size:18 final size:17
Alignment explanation
Indices: 252448--252491 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
252438 AATACATTAA
252448 ATATTAAATTTAAATTT
1 ATATTAAATTTAAATTT
* *
252465 ACAGATAAATTTAAATTT
1 ATA-TTAAATTTAAATTT
252483 ATTATTAAA
1 A-TATTAAA
252492 AAAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
17 2 0.10
18 18 0.86
19 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
ATATTAAATTTAAATTT
Found at i:252909 original size:17 final size:19
Alignment explanation
Indices: 252873--252909 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
252863 AAAATAATTA
252873 AAACACGATATAAATATAC
1 AAACACGATATAAATATAC
*
252892 AAACA-GAT-TAAATTTAC
1 AAACACGATATAAATATAC
252909 A
1 A
252910 TAAAACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.24
Consensus pattern (19 bp):
AAACACGATATAAATATAC
Found at i:252960 original size:39 final size:39
Alignment explanation
Indices: 252917--252991 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
252907 ACATAAAACA
252917 AATGATTAATGTATCAAATATTATATAAATATTTAAGAT
1 AATGATTAATGTATCAAATATTATATAAATATTTAAGAT
*
252956 AATGATTAATGTATCAAATGTTATATAAATATTTAA
1 AATGATTAATGTATCAAATATTATATAAATATTTAA
252992 TATCTTTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (39 bp):
AATGATTAATGTATCAAATATTATATAAATATTTAAGAT
Found at i:255251 original size:16 final size:16
Alignment explanation
Indices: 255206--255255 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
255196 CATTTAAACC
*
255206 TTAATTATTATTTAT-
1 TTAATTAATATTTATA
* * *
255221 TTTATTAAAAATTATA
1 TTAATTAATATTTATA
255237 TTAATTAATATTTATA
1 TTAATTAATATTTATA
255253 TTA
1 TTA
255256 TATATTTAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATTAATATTTATA
Found at i:255289 original size:20 final size:19
Alignment explanation
Indices: 255266--255307 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
255256 TATATTTAAA
255266 TTTAAATAAAAATATATTAT
1 TTTAAATAAAAAT-TATTAT
* *
255286 TTTAATTTAAAATTATTAT
1 TTTAAATAAAAATTATTAT
255305 TTT
1 TTT
255308 GGATCAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAATAAAAATTATTAT
Found at i:255561 original size:10 final size:10
Alignment explanation
Indices: 255548--255595 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
255538 AAATAATATG
*
255548 AATATATTAT
1 AATATATTAA
255558 AATATA-T-A
1 AATATATTAA
255566 AATATATTAA
1 AATATATTAA
255576 AATATATATAA
1 AATATAT-TAA
*
255587 AATAAATTA
1 AATATATTA
255596 TAAACACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 6 0.18
9 2 0.06
10 16 0.48
11 9 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATATATTAA
Found at i:255569 original size:18 final size:18
Alignment explanation
Indices: 255537--255583 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
255527 ATATTAATGA
*
255537 AAAATAATATGAATATATT
1 AAAAT-ATATAAATATATT
*
255556 ATAATATATAAATATATT
1 AAAATATATAAATATATT
255574 AAAATATATA
1 AAAATATATA
255584 TAAAATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAATATATAAATATATT
Found at i:255769 original size:5 final size:5
Alignment explanation
Indices: 255761--255793 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
255751 TAATGTAATT
255761 TTAAA TTAAA -TAAA TTAAA GTTAAA TTAAA TTA
1 TTAAA TTAAA TTAAA TTAAA -TTAAA TTAAA TTA
255794 TTATAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (5 bp):
TTAAA
Found at i:255787 original size:11 final size:10
Alignment explanation
Indices: 255761--255793 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
255751 TAATGTAATT
255761 TTAAATTAAA
1 TTAAATTAAA
255771 -TAAATTAAA
1 TTAAATTAAA
255780 GTTAAATTAAA
1 -TTAAATTAAA
255791 TTA
1 TTA
255794 TTATAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.43
10 3 0.14
11 9 0.43
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (10 bp):
TTAAATTAAA
Found at i:255897 original size:19 final size:20
Alignment explanation
Indices: 255873--255917 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
255863 ATACGAGAAA
255873 ATATAAACACGTAAAAA-AT
1 ATATAAACACGTAAAAATAT
**
255892 ATATAAGTACGTAAAAATAT
1 ATATAAACACGTAAAAATAT
255912 ATATAA
1 ATATAA
255918 TAAATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (20 bp):
ATATAAACACGTAAAAATAT
Found at i:255913 original size:20 final size:19
Alignment explanation
Indices: 255850--255917 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
255840 AATAATAATT
*
255850 AAAATATGATAAGATACG-AG
1 AAAATAT-ATAAG-TACGTAA
*
255870 AAAATATA-AA-CACGTAA
1 AAAATATATAAGTACGTAA
255887 AAAATATATAAGTACGTAA
1 AAAATATATAAGTACGTAA
255906 AAATATATATAA
1 AAA-ATATATAA
255918 TAAATTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
16 3 0.07
17 9 0.22
18 4 0.10
19 10 0.24
20 15 0.37
ACGTcount: A:0.60, C:0.06, G:0.10, T:0.24
Consensus pattern (19 bp):
AAAATATATAAGTACGTAA
Found at i:256352 original size:25 final size:24
Alignment explanation
Indices: 256305--256356 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
256295 ATTTTTACCC
*
256305 AAAATTCTGATTTTTTGTGTTCATA
1 AAAATTCTGATTTTTTGTCTTCA-A
256330 AAAATTCTGATTTATTT-TCTTCAA
1 AAAATTCTGATTT-TTTGTCTTCAA
256354 AAA
1 AAA
256357 GATAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 4 0.16
25 18 0.72
26 3 0.12
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.48
Consensus pattern (24 bp):
AAAATTCTGATTTTTTGTCTTCAA
Found at i:256931 original size:15 final size:16
Alignment explanation
Indices: 256905--256948 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
256895 TAATTTGGTG
256905 TTTAATATATTT-GAAT
1 TTTAA-ATATTTAGAAT
*
256921 TTTAAATATTTATAAT
1 TTTAAATATTTAGAAT
*
256937 TTTAAAAATTTA
1 TTTAAATATTTA
256949 TATAATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTAAATATTTAGAAT
Found at i:256949 original size:16 final size:16
Alignment explanation
Indices: 256918--256950 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
256908 AATATATTTG
*
256918 AATTTTAAATATTTAT
1 AATTTTAAAAATTTAT
256934 AATTTTAAAAATTTAT
1 AATTTTAAAAATTTAT
256950 A
1 A
256951 TAATTGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTTAAAAATTTAT
Found at i:256952 original size:18 final size:17
Alignment explanation
Indices: 256918--256973 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
256908 AATATATTTG
256918 AATTTTAAATA-TTTAT
1 AATTTTAAATATTTTAT
*
256934 AATTTTAAAAATTTATAT
1 AATTTTAAATATTT-TAT
*
256952 AATTGATAAATATTTTAT
1 AATT-TTAAATATTTTAT
256970 AATT
1 AATT
256974 GGGAAAATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 10 0.29
17 2 0.06
18 14 0.41
19 8 0.24
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
AATTTTAAATATTTTAT
Found at i:260814 original size:13 final size:14
Alignment explanation
Indices: 260796--260829 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
260786 ATTTTAAATT
260796 TTATTAAA-TTATA
1 TTATTAAATTTATA
*
260809 TTATTAAATTTTTA
1 TTATTAAATTTATA
260823 TTATTAA
1 TTATTAA
260830 TAAATTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTAAATTTATA
Found at i:261683 original size:9 final size:9
Alignment explanation
Indices: 261620--261685 Score: 57
Period size: 8 Copynumber: 7.4 Consensus size: 9
261610 TTATATTTGA
261620 TAAATAT-T
1 TAAATATAT
261628 TAAATATAAAT
1 TAAATAT--AT
* *
261639 TTAATATTT
1 TAAATATAT
261648 TAAATATAT
1 TAAATATAT
* *
261657 AAAAAAT-T
1 TAAATATAT
261665 TAAATA-AT
1 TAAATATAT
261673 TAAATATAT
1 TAAATATAT
261682 TAAA
1 TAAA
261686 AATACACTCG
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
8 19 0.42
9 19 0.42
11 7 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAAATATAT
Found at i:261684 original size:17 final size:16
Alignment explanation
Indices: 261620--261685 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 16
261610 TTATATTTGA
261620 TAAATATTTAAATATAAAT
1 TAAATATTT-AA-AT-AAT
*
261639 TTAATATTTTAAATATAT
1 TAAATA-TTTAAATA-AT
* *
261657 AAAAAATTTAAATAAT
1 TAAATATTTAAATAAT
261673 TAAATATATTAAA
1 TAAATAT-TTAAA
261686 AATACACTCG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
16 7 0.18
17 14 0.37
18 7 0.18
19 7 0.18
20 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATATTTAAATAAT
Found at i:271382 original size:2 final size:2
Alignment explanation
Indices: 271377--271403 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
271367 AGCAAAAAAC
271377 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
271404 CACTCCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:271714 original size:13 final size:13
Alignment explanation
Indices: 271682--271731 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
271672 TTTATTAAAT
*
271682 ATTAATTAATTAT
1 ATTAATTAATTAA
*
271695 ATAAATTAATTAA
1 ATTAATTAATTAA
*
271708 ATTAATT-TTTAA
1 ATTAATTAATTAA
*
271720 ATTTATTAATTA
1 ATTAATTAATTA
271732 TTATTAAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTAATTAATTAA
Found at i:272641 original size:12 final size:12
Alignment explanation
Indices: 272620--272661 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
272610 TGGGAGGGGG
*
272620 TTTCTGTTTCTT
1 TTTCTTTTTCTT
272632 TTTCTTTTTCTT
1 TTTCTTTTTCTT
272644 TTTC-TTTTC-T
1 TTTCTTTTTCTT
272654 TTTCTTTT
1 TTTCTTTT
272662 CGATGGGACT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 8 0.29
12 15 0.54
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTCTTTTTCTT
Found at i:272645 original size:5 final size:5
Alignment explanation
Indices: 272620--272662 Score: 50
Period size: 6 Copynumber: 7.8 Consensus size: 5
272610 TGGGAGGGGG
272620 TTTCT GTTTCTT TTTCTT TTTCTT TTTCT TTTCT TTTCT TTTC
1 TTTCT -TTTC-T TTTC-T TTTC-T TTTCT TTTCT TTTCT TTTC
272663 GATGGGACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 15 0.42
6 20 0.56
7 1 0.03
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:272713 original size:2 final size:2
Alignment explanation
Indices: 272703--272769 Score: 89
Period size: 2 Copynumber: 33.5 Consensus size: 2
272693 TTAGTGTGTG
* * *
272703 TA TA CA TA TA TA CA TA TA TA TA TA TA TA CA TA TA 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
* *
272745 TA TA CA TA AA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
272770 GATAAATAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:272873 original size:20 final size:19
Alignment explanation
Indices: 272842--272892 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
272832 GCCATTGCTT
272842 TTTCTTT-A-TTTCTTTTTC
1 TTTCTTTCACTTTC-TTTTC
272860 TTTCTTTCACTTTCTTTTC
1 TTTCTTTCACTTTCTTTTC
*
272879 TTCTCTTTCCCTTT
1 TT-TCTTTCACTTT
272893 GCTTCTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 7 0.24
19 8 0.28
20 14 0.48
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTCTTTCACTTTCTTTTC
Found at i:273302 original size:24 final size:24
Alignment explanation
Indices: 273275--273334 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
273265 ATTATTTTAA
273275 AATTTTATAAAATAAAATC-ATAAT
1 AATTTTATAAAATAAAATCGA-AAT
* * *
273299 AATTTACATTAAATAAACTCGAAAT
1 AATTT-TATAAAATAAAATCGAAAT
273324 AATTGTTATAA
1 AATT-TTATAA
273335 TAAACCAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
24 5 0.18
25 21 0.75
26 2 0.07
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (24 bp):
AATTTTATAAAATAAAATCGAAAT
Found at i:277615 original size:18 final size:18
Alignment explanation
Indices: 277587--277645 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
277577 TATTTTTTAA
277587 AATATTTAATATATAATAT
1 AATA-TTAATATATAATAT
* *
277606 AATATTAATATATATTTT
1 AATATTAATATATAATAT
*
277624 AAAATTAATAT-TAA-AT
1 AATATTAATATATAATAT
277640 AA-ATTA
1 AATATTA
277646 TTAATCTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 4 0.11
16 3 0.09
17 2 0.06
18 22 0.63
19 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATTAATATATAATAT
Found at i:279094 original size:19 final size:17
Alignment explanation
Indices: 279057--279097 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
279047 TATGGGGTTG
279057 ATAATTTTAGATAAAAT
1 ATAATTTTAGATAAAAT
*
279074 ATAATTATTTGATATAAAT
1 ATAATT-TTAGATA-AAAT
279093 ATAAT
1 ATAAT
279098 ATAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 6 0.29
19 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (17 bp):
ATAATTTTAGATAAAAT
Found at i:279109 original size:30 final size:27
Alignment explanation
Indices: 279067--279133 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 27
279057 ATAATTTTAG
*
279067 ATAAAATATAATTATTTGATATAAATATAAT
1 ATAAAA-ATAATTA--TAATATAAA-ATAAT
*
279098 ATAAAAATAATTATAATATAAAATTAT
1 ATAAAAATAATTATAATATAAAATAAT
279125 ATAAAAATA
1 ATAAAAATA
279134 TTACGAATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 13 0.38
28 8 0.24
30 7 0.21
31 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (27 bp):
ATAAAAATAATTATAATATAAAATAAT
Found at i:279112 original size:17 final size:17
Alignment explanation
Indices: 279087--279120 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
279077 ATTATTTGAT
279087 ATAAATATAATATAAAA
1 ATAAATATAATATAAAA
*
279104 ATAATTATAATATAAAA
1 ATAAATATAATATAAAA
279121 TTATATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAATATAATATAAAA
Found at i:279142 original size:27 final size:28
Alignment explanation
Indices: 279085--279142 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
279075 TAATTATTTG
*
279085 ATATAAATATAATATAAAAATAATTATA
1 ATATAAATATAATATAAAAATAATTAGA
*
279113 ATATAAA-ATTATATAAAAAT-ATTACGA
1 ATATAAATATAATATAAAAATAATTA-GA
279140 ATA
1 ATA
279143 CGATATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 4 0.15
27 16 0.59
28 7 0.26
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (28 bp):
ATATAAATATAATATAAAAATAATTAGA
Found at i:279171 original size:19 final size:20
Alignment explanation
Indices: 279125--279176 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
279115 ATAAAATTAT
*
279125 ATAAAAATATTACGAATACG
1 ATAAAAATATTACGAATACA
* * *
279145 ATATAAATA-TATGAATATA
1 ATAAAAATATTACGAATACA
279164 ATAAAAATTATTA
1 ATAAAAA-TATTA
279177 ACACATCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 13 0.52
20 10 0.40
21 2 0.08
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.33
Consensus pattern (20 bp):
ATAAAAATATTACGAATACA
Found at i:281261 original size:15 final size:16
Alignment explanation
Indices: 281237--281272 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
281227 TTTTTTCACT
281237 TTTAAAAAAATTATAA
1 TTTAAAAAAATTATAA
281253 TTTAAAAAAATTATAA
1 TTTAAAAAAATTATAA
281269 TTTA
1 TTTA
281273 TAATTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAAAAAATTATAA
Found at i:283115 original size:66 final size:65
Alignment explanation
Indices: 283044--283267 Score: 207
Period size: 66 Copynumber: 3.4 Consensus size: 65
283034 GAGTGTGATC
** *
283044 ATAAGCTAACTATTATAACCCATTAGCTGGGCCATGAACTAATTATTATAACCCGTTAGTAGGGC
1 ATAAGCTAACTATTATAACCCATTAGCAAGGCCAT-AACTAACTATTATAACCCGTTAGTAGGGC
283109 T
65 T
* * * * * * * *
283110 GTAAGCAAACTATTATAACCCATTAGCAAGGTCATAACTAAACCATTATAATCTGTTAACTA-GA
1 ATAAGCTAACTATTATAACCCATTAGCAAGGCCATAACT-AACTATTATAACCCGTT-AGTAGGG
*
283174 CC
64 CT
* ** * * **
283176 ATACGCTAACTATTATAACCTGTTAGCAAGACCATAAACTAACTATTATAACTCGTTAGGGGGGC
1 ATAAGCTAACTATTATAACCCATTAGCAAGGCCAT-AACTAACTATTATAACCCGTTAGTAGGGC
283241 T
65 T
* * *
283242 CTATGCTAACTATTCTAACCCATTAG
1 ATAAGCTAACTATTATAACCCATTAG
283268 TGGGGCCTTT
Statistics
Matches: 121, Mismatches: 33, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
65 5 0.04
66 109 0.90
67 7 0.06
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (65 bp):
ATAAGCTAACTATTATAACCCATTAGCAAGGCCATAACTAACTATTATAACCCGTTAGTAGGGCT
Found at i:283234 original size:33 final size:33
Alignment explanation
Indices: 283043--283234 Score: 143
Period size: 33 Copynumber: 5.8 Consensus size: 33
283033 TGAGTGTGAT
* * **
283043 CATAAGCTAACTATTATAACCCATTAGCTGGGC
1 CATAAACTAACTATTATAACCCGTTAGCAAGGC
* * * *
283076 CATGAACTAATTATTATAACCCGTTAGTAGGGC
1 CATAAACTAACTATTATAACCCGTTAGCAAGGC
** * * * *
283109 TGTAAGCAAACTATTATAACCCATTAGCAAGGT
1 CATAAACTAACTATTATAACCCGTTAGCAAGGC
* * * * * *
283142 CAT-AACTAAACCATTATAATCTGTTAACTAGAC
1 CATAAACT-AACTATTATAACCCGTTAGCAAGGC
** * *
283175 CATACGCTAACTATTATAACCTGTTAGCAAGAC
1 CATAAACTAACTATTATAACCCGTTAGCAAGGC
*
283208 CATAAACTAACTATTATAACTCGTTAG
1 CATAAACTAACTATTATAACCCGTTAG
283235 GGGGGCTCTA
Statistics
Matches: 119, Mismatches: 38, Indels: 4
0.74 0.24 0.02
Matches are distributed among these distances:
32 2 0.02
33 115 0.97
34 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (33 bp):
CATAAACTAACTATTATAACCCGTTAGCAAGGC
Found at i:283286 original size:32 final size:33
Alignment explanation
Indices: 283214--283327 Score: 142
Period size: 33 Copynumber: 3.5 Consensus size: 33
283204 AGACCATAAA
* *
283214 CTAACTATTATAACTCGTTAGGGGGGCTCTATG
1 CTAACTATTATAACTCATTAGTGGGGCTCTATG
* * *
283247 CTAACTATTCTAACCCATTAGTGGGGC-CTTTG
1 CTAACTATTATAACTCATTAGTGGGGCTCTATG
283279 CTAACTATTATAACTCATTAGTGGGG-TCGTATG
1 CTAACTATTATAACTCATTAGTGGGGCTC-TATG
**
283312 CTAACCGTTATAACTC
1 CTAACTATTATAACTC
283328 TTTACTTTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 29 0.42
33 40 0.58
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (33 bp):
CTAACTATTATAACTCATTAGTGGGGCTCTATG
Found at i:283415 original size:30 final size:30
Alignment explanation
Indices: 283346--283415 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
283336 TTAGCAGGGC
*
283346 CGTAAGCTAACAATTATAACCCCTCGTGGGG
1 CGTAAGCT-ACAATTATAACCCCTAGTGGGG
*
283377 CGTAAGCTACATATTATAACCCTTTAGT-GGG
1 CGTAAGCTACA-ATTATAACCC-CTAGTGGGG
283408 C-TAAGCTA
1 CGTAAGCTA
283416 ACTGTTGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 10 0.29
31 22 0.63
32 3 0.09
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (30 bp):
CGTAAGCTACAATTATAACCCCTAGTGGGG
Found at i:283596 original size:95 final size:95
Alignment explanation
Indices: 283423--283607 Score: 316
Period size: 95 Copynumber: 1.9 Consensus size: 95
283413 CTAACTGTTG
283423 TTACTCATTAGGGCGCGTTAACAGGCTGTAAGCTAAATATTGTAACTCATTAGCGGGGTCATAAG
1 TTACTCATTAGGGCGCGTTAACAGGCTGTAAGCTAAATATTGTAACTCATTAGCGGGGTCATAAG
* * *
283488 CTAGTTTTTGTAACCCGTTAGCAGGTCTTT
66 CTACTTTTGGTAACCCGTCAGCAGGTCTTT
* * *
283518 TTACTCATTAGGGCGCGTTAGCCGGCTGTAAGCTAAATATTGTAACTCATTAGGGGGGTCATAAG
1 TTACTCATTAGGGCGCGTTAACAGGCTGTAAGCTAAATATTGTAACTCATTAGCGGGGTCATAAG
283583 CTACTTTTGGTAACCCGTCAGCAGG
66 CTACTTTTGGTAACCCGTCAGCAGG
283608 GCCAGAAGCT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 84 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (95 bp):
TTACTCATTAGGGCGCGTTAACAGGCTGTAAGCTAAATATTGTAACTCATTAGCGGGGTCATAAG
CTACTTTTGGTAACCCGTCAGCAGGTCTTT
Found at i:283866 original size:33 final size:33
Alignment explanation
Indices: 283757--283875 Score: 102
Period size: 33 Copynumber: 3.6 Consensus size: 33
283747 TTAAGTATGG
* * *
283757 TAACCCGTTAACAGGGCCTTAAGCTAA-TATTA
1 TAACCCATTAGCAGGGCCTTATGCTAACTATTA
*
283789 TGAA-CCATTAGTAAGGG-CTTATGCTAACTATTA
1 T-AACCCATTAG-CAGGGCCTTATGCTAACTATTA
*** **
283822 TAACTTGTTAGCAGGGCCTTATGCTAACTACCA
1 TAACCCATTAGCAGGGCCTTATGCTAACTATTA
283855 TAACCCATTAGC-GGGACCTTA
1 TAACCCATTAGCAGGG-CCTTA
283876 CACTAATTAA
Statistics
Matches: 68, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
32 24 0.35
33 44 0.65
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (33 bp):
TAACCCATTAGCAGGGCCTTATGCTAACTATTA
Found at i:285022 original size:15 final size:15
Alignment explanation
Indices: 285002--285035 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
284992 GATCGAATCC
285002 TTCTATATATTTATA
1 TTCTATATATTTATA
285017 TTCTATATATTTATA
1 TTCTATATATTTATA
285032 TTCT
1 TTCT
285036 CTTTGACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (15 bp):
TTCTATATATTTATA
Found at i:287913 original size:417 final size:417
Alignment explanation
Indices: 287138--289425 Score: 2710
Period size: 417 Copynumber: 5.5 Consensus size: 417
287128 ATGTGGACCT
* * * * * *
287138 TTTATCAGGATCAGAAA-ATTTGACAGTAAGTGCCGAGGCACTTGATAAATCTAGATTTGTCCTC
1 TTTATCAGGATCA-AAATATGTCACTGTAAGTGCCAAGGCACTTAATAAATCTAGATTTGTCCCC
* ** * * * *
287202 AGCGCTGCTGACAACAACATGAAGTTAGGAGATGAGCCTGTTTTGGCCAGACAAGAAGGTAACTC
65 AGTGCTGCTGACAATGACATGAAATTGGGAGATGAGTCTGTTTTGGTCAGACAAGAAGGTAACTC
* * ** * * *
287267 TGGGGAGATTTCAACACTTCGATCTTCAGAAATAAGCTCTGATCTGGTCAAAGTTTCTTTCAC-G
130 TGGGGAGACTTCAACACTTCCATCTTCAGAAATAAGCTCCAATATGGTCAATGTTTCCTTC-CTG
* * * ** *
287331 CATTCTGACTTGAAAGATACCAGAGCATCACATGTAAATAATGAATCTTCAACCGAGGTGGACAG
194 CATTCTGACTTGAAAGATACCAAAGCATCAAATGTAACTAATGAATCTTCAACTAAGGTGGATAG
* ** * * * * * *
287396 CGCCAATGATAGTCTTCCTAAATACACCTTCCAGAGGAAGCGCAAGAAGGAACTGCTTTGTAACC
259 CGTCAATGGCAGACTTCTTAAATGCACCTTCCAGAGGAAGCGCAAGAAGGAACCGCTTAGTAAGC
* * * * *
287461 CTGATGAAAAGACTTCTGAAGAGAGCAGATTAAAGAGGAGGGCTGGGGAGAATGATAATAGTTTG
324 CAGATGAAAAGACTTCTGAAGTGAGCAGTTTAAAGAGGAGGGCTGGGGAGAATGAAAATAGTTTA
* * * *
287526 CAAGAAATTACTAAGTCCAACTTGGATTC
389 CAAGAAACTGCTAAGTCTAACTTGGATCC
* * * *
287555 TTTATCAGGATCAGAAAAAT-TCACTGTAAGTGGCAAGGCGCTTAATAAATCTAGATTTATCCCC
1 TTTATCAGGATCA-AAATATGTCACTGTAAGTGCCAAGGCACTTAATAAATCTAGATTTGTCCCC
* * *
287619 AGTGCTGCTGAAAATGACATGAAATTGGGAGATGAGCCTGTTTTGGTTC-GACAAGAAGATAACT
65 AGTGCTGCTGACAATGACATGAAATTGGGAGATGAGTCTGTTTTGG-TCAGACAAGAAGGTAACT
* * * * *
287683 CTGGGGAGA-TTCCAACACTTCCATCTTCAGAAATGAGCTCCAATTTGGTCAGTGTTTCTTTCTT
129 CTGGGGAGACTT-CAACACTTCCATCTTCAGAAATAAGCTCCAATATGGTCAATGTTTCCTTCCT
* * *
287747 GCATTCTGACTTGAAAGATACCAAAGCATCAAATGCAATTAATGAATCTTCAACTAAGTTGGATA
193 GCATTCTGACTTGAAAGATACCAAAGCATCAAATGTAACTAATGAATCTTCAACTAAGGTGGATA
* * ** * * * * * *
287812 GCATCGATGATAGACTTCCTAAATACACCTTCCTGAGGAAGCGCAAGATGGAACCACTTAGTAAT
258 GCGTCAATGGCAGACTTCTTAAATGCACCTTCCAGAGGAAGCGCAAGAAGGAACCGCTTAGTAAG
*
287877 CCAGATGAAAAGACTTCTGAAGAGAGCAGTTTAAAGAGGAGGGCTGGGGAGAATGAAAATAGTTT
323 CCAGATGAAAAGACTTCTGAAGTGAGCAGTTTAAAGAGGAGGGCTGGGGAGAATGAAAATAGTTT
* *
287942 ACAAGAAACTGTTAAGCCTAACTTGGATCC
388 ACAAGAAACTGCTAAGTCTAACTTGGATCC
* * * *
287972 TTTATCAGGATCAAAATATGTCTCTGAAAGTGCCACGGCACTTAATAGATCTAGATTTGTCCCCA
1 TTTATCAGGATCAAAATATGTCACTGTAAGTGCCAAGGCACTTAATAAATCTAGATTTGTCCCCA
* *
288037 CTGCTGCTGACAATGACATGAAATTGGGAGATGAGTCTGTTTTGGTTAGACAAGAAGGTAACTCT
66 GTGCTGCTGACAATGACATGAAATTGGGAGATGAGTCTGTTTTGGTCAGACAAGAAGGTAACTCT
* * *
288102 GGGGGGACTTCAACCCTTCCATCTTCAGAAATAAGCTCCAGTATGGTCAATGTTTCCTTCGCT-C
131 GGGGAGACTTCAACACTTCCATCTTCAGAAATAAGCTCCAATATGGTCAATGTTTCCTTC-CTGC
* * * *
288166 ATTCTGACTTGAAAGATACCAAAGTATCAGATGTGACTAATGAATCTTCAACTAAGATGGATAGC
195 ATTCTGACTTGAAAGATACCAAAGCATCAAATGTAACTAATGAATCTTCAACTAAGGTGGATAGC
* * * * * *
288231 GTCAACGGCAGACTTTTTAAATGCACCTTCCAGAGGAAGTGCAAGAGGGAACCACTTAGTAAGCT
260 GTCAATGGCAGACTTCTTAAATGCACCTTCCAGAGGAAGCGCAAGAAGGAACCGCTTAGTAAGCC
* * * * *
288296 GGACGAAAAGACTTCTGAAGTGAGCAGTTTAAAGAGGAGGGTTGGGGAGAAAGAAAATAGTTTCC
325 AGATGAAAAGACTTCTGAAGTGAGCAGTTTAAAGAGGAGGGCTGGGGAGAATGAAAATAGTTTAC
* * *
288361 TAGAAACTGCCAAGTCTAACCTGGATCC
390 AAGAAACTGCTAAGTCTAACTTGGATCC
* * * *
288389 TTTATCAGGATCAAAATATGTCTCTATAAGTGCCAAGGCACTTAATAGATCTAGATCTGTCCCCA
1 TTTATCAGGATCAAAATATGTCACTGTAAGTGCCAAGGCACTTAATAAATCTAGATTTGTCCCCA
** * * ***
288454 GTGCTGCTGATGATGACATGAAATTGGGAGACGAGTCTGTTGTGGTCAGACAAGAAGGTTTTTCT
66 GTGCTGCTGACAATGACATGAAATTGGGAGATGAGTCTGTTTTGGTCAGACAAGAAGGTAACTCT
* * *
288519 GGGGAGACTTCAACACCTCCATCTTCAGAGATAAGCTCCAATATGGTCAACGTTTCCTTCACT-C
131 GGGGAGACTTCAACACTTCCATCTTCAGAAATAAGCTCCAATATGGTCAATGTTTCCTTC-CTGC
* * * *
288583 ATTCTGACTTGAAAGATACCAAAGCTTCAAATTTAACCAATGAATCTTCAACTAAGGTGGATAGT
195 ATTCTGACTTGAAAGATACCAAAGCATCAAATGTAACTAATGAATCTTCAACTAAGGTGGATAGC
* * * *
288648 GTCAATGGCAGACTTCTTACATGCACCTTCCAGAGGAAGCACAAAAAGGAACCGCTTGGTAAGCC
260 GTCAATGGCAGACTTCTTAAATGCACCTTCCAGAGGAAGCGCAAGAAGGAACCGCTTAGTAAGCC
* * * * * *
288713 AAATGAAAGGACTTCTGATGTGAGCAGTTTAAAGAGGAGGGCTGGGGAGACTGAAATTAGTTTTC
325 AGATGAAAAGACTTCTGAAGTGAGCAGTTTAAAGAGGAGGGCTGGGGAGAATGAAAATAGTTTAC
* * *
288778 AAGAAACTTCTAAGTCTAGCCTGGATCC
390 AAGAAACTGCTAAGTCTAACTTGGATCC
* * * * *
288806 TTTATCAGGATCACAATATGTCTCTGTAGGTGCCAAGGCACTTAATAGATCTAGATTTGTTCCCA
1 TTTATCAGGATCAAAATATGTCACTGTAAGTGCCAAGGCACTTAATAAATCTAGATTTGTCCCCA
* * * * * *
288871 ATGTTGTTGACGATGACATGAAATTGGGAGACGAGTCTGTTCTGGTCAGACAAGAAGGTAACTCT
66 GTGCTGCTGACAATGACATGAAATTGGGAGATGAGTCTGTTTTGGTCAGACAAGAAGGTAACTCT
* * * *
288936 GGGGAGACTT-TA-A--T--A---TC---------CTCCAATATGTTCAATGTTTCCTTCGTCCA
131 GGGGAGACTTCAACACTTCCATCTTCAGAAATAAGCTCCAATATGGTCAATGTTTCCTTCCTGCA
* * *
288983 TTCTGACTTGAAAGATGCCAAAGCTTCAAATGTAACTAATGAATCTTCAATTAAGGTGGATAGCG
196 TTCTGACTTGAAAGATACCAAAGCATCAAATGTAACTAATGAATCTTCAACTAAGGTGGATAGCG
* * *
289048 TCAATGGCAGACTTCTTAAATGCACCTTCCAGAGGAAGCGCAAGAAGGAACTGCTTAGCATGCCA
261 TCAATGGCAGACTTCTTAAATGCACCTTCCAGAGGAAGCGCAAGAAGGAACCGCTTAGTAAGCCA
* * *
289113 GATGAAAAGACTTCTGAAGTGAGCAGTTTAAAGAGGA---CTTGGGAGAAAGAGAATAGTTTACA
326 GATGAAAAGACTTCTGAAGTGAGCAGTTTAAAGAGGAGGGCTGGGGAGAATGAAAATAGTTTACA
* * *
289175 AGAAGCTGCCAAGTCTGACTTGGATCC
391 AGAAACTGCTAAGTCTAACTTGGATCC
* * * * * **
289202 TTTAT-TGAAATCAAAATATGTCACTGTTAGTGCCATGGCAC-TAGACAAATCCGGATTTGTCCC
1 TTTATCAG-GATCAAAATATGTCACTGTAAGTGCCAAGGCACTTA-ATAAATCTAGATTTGTCCC
* * *
289265 CAGTGCTGCTGAAAATGACGTGAAATTGGGAGATGAGTCTGTTCTGGTCAGACAAGAAGGTAACT
64 CAGTGCTGCTGACAATGACATGAAATTGGGAGATGAGTCTGTTTTGGTCAGACAAGAAGGTAACT
* * * * * * *
289330 CTAGGGTGACTTCAGCATTTCCATCTTCAGAAATAAGCTCTAATATGGTCAATGCTTCCTTCGTG
129 CTGGGGAGACTTCAACACTTCCATCTTCAGAAATAAGCTCCAATATGGTCAATGTTTCCTTCCTG
*
289395 CATTCTGACTTGAAAGATATCAAAGCATCAA
194 CATTCTGACTTGAAAGATACCAAAGCATCAA
289426 CGGAGGTGGA
Statistics
Matches: 1613, Mismatches: 229, Indels: 61
0.85 0.12 0.03
Matches are distributed among these distances:
395 3 0.00
396 154 0.10
398 2 0.00
399 177 0.11
400 1 0.00
402 1 0.00
405 2 0.00
408 2 0.00
411 1 0.00
413 1 0.00
414 52 0.03
415 1 0.00
416 9 0.01
417 1201 0.74
418 6 0.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (417 bp):
TTTATCAGGATCAAAATATGTCACTGTAAGTGCCAAGGCACTTAATAAATCTAGATTTGTCCCCA
GTGCTGCTGACAATGACATGAAATTGGGAGATGAGTCTGTTTTGGTCAGACAAGAAGGTAACTCT
GGGGAGACTTCAACACTTCCATCTTCAGAAATAAGCTCCAATATGGTCAATGTTTCCTTCCTGCA
TTCTGACTTGAAAGATACCAAAGCATCAAATGTAACTAATGAATCTTCAACTAAGGTGGATAGCG
TCAATGGCAGACTTCTTAAATGCACCTTCCAGAGGAAGCGCAAGAAGGAACCGCTTAGTAAGCCA
GATGAAAAGACTTCTGAAGTGAGCAGTTTAAAGAGGAGGGCTGGGGAGAATGAAAATAGTTTACA
AGAAACTGCTAAGTCTAACTTGGATCC
Found at i:294990 original size:21 final size:19
Alignment explanation
Indices: 294965--295012 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
294955 GTTTACATAA
294965 AAATAATTTAAATATTAAAAT
1 AAATAATTTAAA-ATT-AAAT
294986 AAATAATTTTAAAATTAAAT
1 AAATAA-TTTAAAATTAAAT
*
295006 AACTAAT
1 AAATAAT
295013 AAATATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 1 0.04
20 9 0.36
21 9 0.36
22 6 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATAATTTAAAATTAAAT
Found at i:296578 original size:2 final size:2
Alignment explanation
Indices: 296571--296596 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
296561 GTAAGTGTTA
296571 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
296597 TGTTTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:296866 original size:32 final size:32
Alignment explanation
Indices: 296830--296891 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
296820 TATTATGTAT
296830 TTATATAAATTTTAATAGATTAATAATTTATA
1 TTATATAAATTTTAATAGATTAATAATTTATA
* *
296862 TTATATAAATTTTAATATATTCATAATTTA
1 TTATATAAATTTTAATAGATTAATAATTTA
296892 ATATCGTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (32 bp):
TTATATAAATTTTAATAGATTAATAATTTATA
Found at i:296889 original size:17 final size:16
Alignment explanation
Indices: 296837--296895 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
296827 TATTTATATA
*
296837 AATTTTAATAGATTAAT
1 AATTTTAATATATT-AT
*
296854 AATTTATATTATA-TA-
1 AATTT-TAATATATTAT
296869 AATTTTAATATATTCAT
1 AATTTTAATATATT-AT
296886 AA-TTTAATAT
1 AATTTTAATAT
296896 CGTGTTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
14 6 0.17
15 6 0.17
16 10 0.29
17 8 0.23
18 5 0.14
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
AATTTTAATATATTAT
Found at i:298213 original size:29 final size:30
Alignment explanation
Indices: 298180--298239 Score: 113
Period size: 29 Copynumber: 2.0 Consensus size: 30
298170 AATTGGGCAT
298180 TGCTTTTGAGTTCAA-TTTTTTAAAGGTTG
1 TGCTTTTGAGTTCAATTTTTTTAAAGGTTG
298209 TGCTTTTGAGTTCAATTTTTTTAAAGGTTG
1 TGCTTTTGAGTTCAATTTTTTTAAAGGTTG
298239 T
1 T
298240 AGCTCGGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (30 bp):
TGCTTTTGAGTTCAATTTTTTTAAAGGTTG
Found at i:306950 original size:12 final size:12
Alignment explanation
Indices: 306933--306961 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
306923 TAGCAAATAT
306933 TTAATTAACATA
1 TTAATTAACATA
306945 TTAATTAACATA
1 TTAATTAACATA
306957 -TAATT
1 TTAATT
306962 GAATATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (12 bp):
TTAATTAACATA
Found at i:307022 original size:10 final size:10
Alignment explanation
Indices: 307007--307044 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
306997 AACAAGAAAC
307007 AAATAAATTT
1 AAATAAATTT
*
307017 AAATAAATCT
1 AAATAAATTT
307027 AAATAAATTT
1 AAATAAATTT
*
307037 AAACAAAT
1 AAATAAAT
307045 AAACAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATAAATTT
Found at i:307032 original size:20 final size:20
Alignment explanation
Indices: 307007--307044 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
306997 AACAAGAAAC
*
307007 AAATAAATTTAAATAAATCT
1 AAATAAATTTAAACAAATCT
307027 AAATAAATTTAAACAAAT
1 AAATAAATTTAAACAAAT
307045 AAACAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAAATTTAAACAAATCT
Found at i:310017 original size:11 final size:11
Alignment explanation
Indices: 310001--310028 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
309991 CAGGTCTACT
310001 ATAAGATTTTG
1 ATAAGATTTTG
310012 ATAAGATTTTG
1 ATAAGATTTTG
310023 ATAAGA
1 ATAAGA
310029 ATCTATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (11 bp):
ATAAGATTTTG
Found at i:310185 original size:27 final size:26
Alignment explanation
Indices: 310155--310223 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 26
310145 TAAATATTAA
*
310155 TAAAAAATAAAATTTTAATATT-ATTT
1 TAAAAAATAAAATTTTAAT-TTAAATT
* *
310181 TTAAAAATAAAAAATTTAATTTAAATT
1 TAAAAAAT-AAAATTTTAATTTAAATT
*
310208 TAAATAAAAAAAATTT
1 TAAA-AAATAAAATTT
310224 AAACTATGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
26 9 0.26
27 22 0.65
28 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TAAAAAATAAAATTTTAATTTAAATT
Found at i:310209 original size:26 final size:27
Alignment explanation
Indices: 310157--310225 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
310147 AATATTAATA
* **
310157 AAAAAT-AAAATTTTAATATTATTTTT
1 AAAAATAAAAAATTTAATATTAAATTT
310183 AAAAATAAAAAATTTAAT-TTAAATTT
1 AAAAATAAAAAATTTAATATTAAATTT
310209 AAATAA-AAAAAATTTAA
1 AAA-AATAAAAAATTTAA
310226 ACTATGACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 26 0.68
27 12 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AAAAATAAAAAATTTAATATTAAATTT
Found at i:311052 original size:33 final size:33
Alignment explanation
Indices: 311010--311077 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
311000 AAGTAAAGTT
311010 TTTGCTGATCTACCAATCTCCCTTTGAGAAGGG
1 TTTGCTGATCTACCAATCTCCCTTTGAGAAGGG
*
311043 TTTGCTGATCTACCAATCTCTCTTTGAGAAGGG
1 TTTGCTGATCTACCAATCTCCCTTTGAGAAGGG
311076 TT
1 TT
311078 AATGAATGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (33 bp):
TTTGCTGATCTACCAATCTCCCTTTGAGAAGGG
Found at i:311829 original size:12 final size:13
Alignment explanation
Indices: 311798--311839 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
311788 AGTATCGATC
311798 ATATAAAAATATAA
1 ATATAAAAATA-AA
311812 ATATAAAAATAAA
1 ATATAAAAATAAA
311825 A-AT-AAAATAAA
1 ATATAAAAATAAA
311836 ATAT
1 ATAT
311840 GATTAAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.33
12 4 0.15
13 3 0.11
14 11 0.41
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
ATATAAAAATAAA
Found at i:313473 original size:17 final size:17
Alignment explanation
Indices: 313453--313486 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
313443 GCCCCAATGA
*
313453 TTTTTATTTTTTATTTC
1 TTTTCATTTTTTATTTC
*
313470 TTTTCATTTTTTCTTTC
1 TTTTCATTTTTTATTTC
313487 AATTTCAATA
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:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTCATTTTTTATTTC
Found at i:314653 original size:15 final size:15
Alignment explanation
Indices: 314630--314659 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
314620 TAAATATCAT
314630 TCAAATTAAATTAAA
1 TCAAATTAAATTAAA
*
314645 TCAATTTAAATTAAA
1 TCAAATTAAATTAAA
314660 AAAATTTAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
TCAAATTAAATTAAA
Found at i:314665 original size:15 final size:15
Alignment explanation
Indices: 314635--314668 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
314625 ATCATTCAAA
**
314635 TTAAATTAAATCAAT
1 TTAAATTAAAAAAAT
314650 TTAAATTAAAAAAAT
1 TTAAATTAAAAAAAT
314665 TTAA
1 TTAA
314669 GACTCGACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAAATTAAAAAAAT
Found at i:315280 original size:2 final size:2
Alignment explanation
Indices: 315273--315310 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
315263 CTAATTATTA
*
315273 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
315311 GGAAAGAAGA
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:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:316099 original size:30 final size:30
Alignment explanation
Indices: 316065--316122 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
316055 TTAATTTATC
316065 TTAAAAGTTTATTT-AGATATAAATTAAAAG
1 TTAAAAGTTTATTTAAG-TATAAATTAAAAG
*
316095 TTAAAGGTTTATTTAAGTATAAATTAAA
1 TTAAAAGTTTATTTAAGTATAAATTAAA
316123 TGATTCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (30 bp):
TTAAAAGTTTATTTAAGTATAAATTAAAAG
Found at i:318288 original size:13 final size:13
Alignment explanation
Indices: 318269--318306 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
318259 TTTATACATT
318269 ATAAATTATAGA-
1 ATAAATTATAGAC
318281 ATTAAATTATAGAC
1 A-TAAATTATAGAC
318295 ATAAATATATAG
1 ATAAAT-TATAG
318307 CTATTACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.04
13 16 0.70
14 6 0.26
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (13 bp):
ATAAATTATAGAC
Found at i:318858 original size:23 final size:21
Alignment explanation
Indices: 318827--318877 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
318817 TAATTATGAT
*
318827 TATATATTTGAAATGTATACAAA
1 TATAAATTTGAAAT-T-TACAAA
* *
318850 TATAAATTTTAAATTTATAAA
1 TATAAATTTGAAATTTACAAA
318871 TATAAAT
1 TATAAAT
318878 AAGTATTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.48
22 1 0.04
23 12 0.48
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (21 bp):
TATAAATTTGAAATTTACAAA
Found at i:322182 original size:14 final size:13
Alignment explanation
Indices: 322163--322198 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
322153 TCATTTCCAT
322163 TTTTTTTTTTTTAC
1 TTTTTTTTTTTT-C
322177 TTTTTTTCTTTTTC
1 TTTTTTT-TTTTTC
322191 TTTTTTTT
1 TTTTTTTT
322199 ACATTGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 15 0.71
15 5 0.24
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:322189 original size:24 final size:24
Alignment explanation
Indices: 322162--322231 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
322152 CTCATTTCCA
*
322162 TTTTTTTTTTTTTACTTTTTTTCT
1 TTTTTTTTTTTTTACTTTGTTTCT
* *
322186 TTTTCTTTTTTTTACATTGTTTCT
1 TTTTTTTTTTTTTACTTTGTTTCT
*
322210 TTTTTTTTTTTTTGCTTTGTTT
1 TTTTTTTTTTTTTACTTTGTTT
322232 GCTATGTTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.04, C:0.09, G:0.04, T:0.83
Consensus pattern (24 bp):
TTTTTTTTTTTTTACTTTGTTTCT
Found at i:322198 original size:18 final size:18
Alignment explanation
Indices: 322177--322217 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
322167 TTTTTTTTAC
322177 TTTTTTTC-TT-TTTCTT
1 TTTTTTTCATTGTTTCTT
*
322193 TTTTTTACATTGTTTCTT
1 TTTTTTTCATTGTTTCTT
322211 TTTTTTT
1 TTTTTTT
322218 TTTTTGCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 2 0.10
18 12 0.57
ACGTcount: A:0.05, C:0.10, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTTTCATTGTTTCTT
Found at i:326862 original size:1 final size:1
Alignment explanation
Indices: 326856--326937 Score: 74
Period size: 1 Copynumber: 82.0 Consensus size: 1
326846 AAATCTTCAC
* * * * * ** *
326856 TTTTTTTTTTGTTTTTTTTTTCTTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
326921 TTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTT
326938 CCAATTGCCA
Statistics
Matches: 63, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (1 bp):
T
Found at i:326879 original size:27 final size:25
Alignment explanation
Indices: 326856--326937 Score: 119
Period size: 26 Copynumber: 3.1 Consensus size: 25
326846 AAATCTTCAC
326856 TTTTTTTTTTGTTTTTTTTTTCTTT
1 TTTTTTTTTTGTTTTTTTTTTCTTT
326881 TTTTTTGTTTTGTTTTTTTTTTCTTT
1 TTTTTT-TTTTGTTTTTTTTTTCTTT
326907 TTCCTTTTTTTTGTTTTGTTTTTTTCTTT
1 TT--TTTTTTTTG-TTT-TTTTTTTCTTT
326936 TT
1 TT
326938 CCAATTGCCA
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
25 6 0.12
26 21 0.40
27 5 0.10
28 7 0.13
29 13 0.25
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (25 bp):
TTTTTTTTTTGTTTTTTTTTTCTTT
Found at i:326882 original size:21 final size:20
Alignment explanation
Indices: 326856--326937 Score: 92
Period size: 22 Copynumber: 3.8 Consensus size: 20
326846 AAATCTTCAC
*
326856 TTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTCTTTTTTTTT
*
326876 TCTTTTTTTTTGTTTTGTTTTT
1 T-TTTTTTTTTCTTTT-TTTTT
326898 TTTTTCTTTTTCCTTTTTTTTGT
1 TTTTT-TTTTT-CTTTTTTTT-T
326921 TTTGTTTTTTTCTTTTT
1 TTT-TTTTTTTCTTTTT
326938 CCAATTGCCA
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
20 1 0.02
21 18 0.33
22 21 0.38
23 13 0.24
24 2 0.04
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (20 bp):
TTTTTTTTTTCTTTTTTTTT
Found at i:326897 original size:32 final size:31
Alignment explanation
Indices: 326856--326937 Score: 119
Period size: 32 Copynumber: 2.6 Consensus size: 31
326846 AAATCTTCAC
* *
326856 TTTTTTTTTTGTTTTTTTTTTCTTTTTTTTTG
1 TTTTGTTTTT-TTTTTTTTTTCCTTTTTTTTG
326888 TTTTGTTTTTTTTTTCTTTTTCCTTTTTTTTG
1 TTTTGTTTTTTTTTT-TTTTTCCTTTTTTTTG
*
326920 TTTTGTTTTTTTCTTTTT
1 TTTTGTTTTTTTTTTTTT
326938 CCAATTGCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 8 0.17
32 38 0.83
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (31 bp):
TTTTGTTTTTTTTTTTTTTTCCTTTTTTTTG
Found at i:335102 original size:13 final size:13
Alignment explanation
Indices: 335084--335109 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
335074 ACATTTGGTC
335084 ATGTATCGATACA
1 ATGTATCGATACA
335097 ATGTATCGATACA
1 ATGTATCGATACA
335110 TCTTGTATGT
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:335104 original size:33 final size:32
Alignment explanation
Indices: 335062--335129 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
335052 CGTTACAAGC
335062 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCGATA
335095 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
335127 CAA
1 CAA
335130 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 18 0.53
34 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:335216 original size:13 final size:13
Alignment explanation
Indices: 335198--335222 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
335188 TACAGTGGTC
335198 ATGTATCGATACA
1 ATGTATCGATACA
335211 ATGTATCGATAC
1 ATGTATCGATAC
335223 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:335750 original size:33 final size:33
Alignment explanation
Indices: 335695--335764 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
335685 AAAATCCTTT
* *
335695 TTATCTTTAATTTAAAAATATTATAGATTAATA
1 TTATCTTTAATTTAAAAATATTAAAGATAAATA
* * *
335728 TTATCTTTAATTTAACATTATTAAAGATAAATG
1 TTATCTTTAATTTAAAAATATTAAAGATAAATA
335761 TTAT
1 TTAT
335765 TCTTAAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (33 bp):
TTATCTTTAATTTAAAAATATTAAAGATAAATA
Found at i:336351 original size:16 final size:15
Alignment explanation
Indices: 336330--336365 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
336320 TTATTATGAA
*
336330 AAAAATCTAAAAATTT
1 AAAAAT-TAAAAAATT
336346 AAAAATTAAAAAATT
1 AAAAATTAAAAAATT
336361 AAAAA
1 AAAAA
336366 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAAATTAAAAAATT
Found at i:336367 original size:9 final size:8
Alignment explanation
Indices: 336329--336366 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
336319 GTTATTATGA
336329 AAAAAATCT
1 AAAAAAT-T
336338 -AAAAATT
1 AAAAAATT
*
336345 TAAAAATT
1 AAAAAATT
336353 AAAAAATT
1 AAAAAATT
336361 AAAAAA
1 AAAAAA
336367 AAATTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
7 1 0.04
8 26 0.96
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAAAATT
Found at i:340752 original size:14 final size:14
Alignment explanation
Indices: 340733--340761 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
340723 CTTTCTTTTA
340733 ACAAATAATTTGCC
1 ACAAATAATTTGCC
340747 ACAAATAATTTGCC
1 ACAAATAATTTGCC
340761 A
1 A
340762 TCGAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.28
Consensus pattern (14 bp):
ACAAATAATTTGCC
Found at i:344911 original size:65 final size:65
Alignment explanation
Indices: 344830--344960 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
344820 TATCTATTTT
344830 TCGTACTTATTTAGAGTCCGAATAACACATACAACCACTTTATGCTTTCATGTTAGGGTCAATGA
1 TCGTACTTATTTAGAGTCCGAATAACACATACAACCACTTTATGCTTTCATGTTAGGGTCAATGA
344895 TCGTACTTATTTAGAGTCCGAATAACACATACAACCACTTTATGCTTTCATGTTAGGGTCAATGA
1 TCGTACTTATTTAGAGTCCGAATAACACATACAACCACTTTATGCTTTCATGTTAGGGTCAATGA
344960 T
1 T
344961 ATCTGTATTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (65 bp):
TCGTACTTATTTAGAGTCCGAATAACACATACAACCACTTTATGCTTTCATGTTAGGGTCAATGA
Found at i:362221 original size:19 final size:20
Alignment explanation
Indices: 362169--362221 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
362159 ATAAATTTTG
*
362169 ATATATTTAAATATTCGTATT
1 ATAT-TTTAAATATTCGAATT
**
362190 ATATTTT-TTTATT-GAATT
1 ATATTTTAAATATTCGAATT
362208 ATATTTTAAATATT
1 ATATTTTAAATATT
362222 TTTTTATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 11 0.42
19 8 0.31
20 3 0.12
21 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (20 bp):
ATATTTTAAATATTCGAATT
Found at i:364003 original size:19 final size:20
Alignment explanation
Indices: 363976--364027 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
363966 AATAAATATA
*
363976 ATTTTATTTATATTTT-ATT
1 ATTTAATTTATATTTTAATT
*
363995 ATTTAATTTAAATTTTAATT
1 ATTTAATTTATATTTTAATT
*
364015 ATTTATTTTATAT
1 ATTTAATTTATAT
364028 ATATACATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTAATTTATATTTTAATT
Found at i:365274 original size:37 final size:37
Alignment explanation
Indices: 365224--365297 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
365214 CAAGACGTTA
365224 TCGGTGAGAAGGTTGTAAATGCTTCTAAAATATTGAT
1 TCGGTGAGAAGGTTGTAAATGCTTCTAAAATATTGAT
365261 TCGGTGAGAAGGTTGTAAATGCTTCTAAAATATTGAT
1 TCGGTGAGAAGGTTGTAAATGCTTCTAAAATATTGAT
365298 CTCATTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.35
Consensus pattern (37 bp):
TCGGTGAGAAGGTTGTAAATGCTTCTAAAATATTGAT
Found at i:370431 original size:2 final size:2
Alignment explanation
Indices: 370424--370449 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
370414 TTGGATATGG
370424 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
370450 TTCCTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:371588 original size:3 final size:3
Alignment explanation
Indices: 371580--371607 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
371570 AATATTTTTG
371580 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
371608 TTTTTAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:371670 original size:24 final size:23
Alignment explanation
Indices: 371646--371692 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
371636 AATAACATAA
*
371646 TAATAATAATTTTTTAATTATTAAT
1 TAAT-ATAATATTTTAA-TATTAAT
*
371671 TAATTTAATATTTTAATATTAA
1 TAATATAATATTTTAATATTAA
371693 ATATTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TAATATAATATTTTAATATTAAT
Found at i:371688 original size:8 final size:8
Alignment explanation
Indices: 371652--371734 Score: 53
Period size: 8 Copynumber: 10.4 Consensus size: 8
371642 ATAATAATAA
*
371652 TAATTTTT
1 TAATATTT
*
371660 TAAT-TAT
1 TAATATTT
*
371667 TAATTAATT
1 TAA-TATTT
371676 TAATATTT
1 TAATATTT
371684 TAATA-TT
1 TAATATTT
*
371691 AAATATTAT
1 TAATATT-T
* *
371700 TAAAATAT
1 TAATATTT
*
371708 TACTATTT
1 TAATATTT
*
371716 TAATTTTT
1 TAATATTT
*
371724 TAATAATT
1 TAATATTT
371732 TAA
1 TAA
371735 AAATAAAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
7 11 0.20
8 36 0.64
9 9 0.16
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (8 bp):
TAATATTT
Found at i:375397 original size:5 final size:5
Alignment explanation
Indices: 375377--375410 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
375367 TATTGAAATC
* *
375377 ATTTT GTTTC ATTTT ATTTT ATTTT ATTTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
375411 AAAAATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:375960 original size:22 final size:20
Alignment explanation
Indices: 375922--376049 Score: 52
Period size: 19 Copynumber: 6.4 Consensus size: 20
375912 ACAGGAATCA
*
375922 ATAAAAAATTAACTAAATTATT
1 ATAAAAAATTAAATAAA-TA-T
375944 ATAAAAAA-TAATATAAATAT
1 ATAAAAAATTAA-ATAAATAT
* *
375964 ATAAATATATT-AA-AATTA-
1 ATAAA-AAATTAAATAAATAT
* *
375982 ATATAATATATATAATAAATAT
1 ATAAAAAAT-TA-AATAAATAT
* **
376004 AT-TAAAATTTTATAAATAT
1 ATAAAAAATTAAATAAATAT
* ** *
376023 ATAATATTTTAAATAAA-AA
1 ATAAAAAATTAAATAAATAT
376042 ATAAAAAA
1 ATAAAAAA
376050 ATATAAATAT
Statistics
Matches: 79, Mismatches: 18, Indels: 21
0.67 0.15 0.18
Matches are distributed among these distances:
17 4 0.05
18 5 0.06
19 20 0.25
20 18 0.23
21 17 0.22
22 15 0.19
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAAAAAATTAAATAAATAT
Found at i:375967 original size:8 final size:8
Alignment explanation
Indices: 375949--376060 Score: 58
Period size: 8 Copynumber: 13.9 Consensus size: 8
375939 TTATTATAAA
375949 AAATAATAT
1 AAAT-ATAT
375958 AAATATAT
1 AAATATAT
375966 AAATATATT
1 AAATATA-T
375975 AAA-AT-T
1 AAATATAT
375981 -AATATAAT
1 AAATAT-AT
*
375989 ATATATAAT
1 AAATAT-AT
375998 AAATATATT
1 AAATATA-T
*
376007 AAAATTTTAT
1 -AAA-TATAT
376017 AAATATAT
1 AAATATAT
*
376025 -AATATTTT
1 AAATA-TAT
376033 AAATA-A-
1 AAATATAT
*
376039 AAA-ATAA
1 AAATATAT
*
376046 AAAAATAT
1 AAATATAT
376054 AAATATA
1 AAATATA
376061 ATGTTAATAT
Statistics
Matches: 82, Mismatches: 8, Indels: 27
0.70 0.07 0.23
Matches are distributed among these distances:
5 3 0.04
6 7 0.09
7 7 0.09
8 30 0.37
9 28 0.34
10 4 0.05
11 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AAATATAT
Found at i:375980 original size:40 final size:38
Alignment explanation
Indices: 375936--376029 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 38
375926 AAAATTAACT
375936 AAATTATTATAAAAAATAATATAAATATATAAATATATTA
1 AAATTATTAT-AAAAATAATATAAATA-ATAAATATATTA
*
375976 AAATTA--AT----ATAATATATATAATAAATATATTA
1 AAATTATTATAAAAATAATATAAATAATAAATATATTA
376008 AAATT-TTATAAATATATAATAT
1 AAATTATTATAAA-A-ATAATAT
376030 TTTAAATAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 17
0.71 0.02 0.27
Matches are distributed among these distances:
32 17 0.38
33 13 0.29
38 2 0.04
39 7 0.16
40 6 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (38 bp):
AAATTATTATAAAAATAATATAAATAATAAATATATTA
Found at i:376002 original size:49 final size:51
Alignment explanation
Indices: 375926--376024 Score: 118
Period size: 49 Copynumber: 2.0 Consensus size: 51
375916 GAATCAATAA
375926 AAAATTAACTAAATTATTATAAAAAATA-A-TATAAA-TATATAAATATATT
1 AAAATTAACTAAATTATTATAAAAAATATATTA-AAATTATATAAATATATT
* *
375975 AAAATTAA-TATAA-TATATATAATAAATATATTAAAATTTTATAAATATAT
1 AAAATTAACTA-AATTAT-TATAAAAAATATATTAAAATTATATAAATATAT
376025 AATATTTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
48 5 0.12
49 20 0.47
50 4 0.09
51 14 0.33
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (51 bp):
AAAATTAACTAAATTATTATAAAAAATATATTAAAATTATATAAATATATT
Found at i:376005 original size:32 final size:31
Alignment explanation
Indices: 375951--376028 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 31
375941 ATTATAAAAA
*
375951 ATAATATAAATATATAAATATATTAAAATTAAT
1 ATAATATATATA-ATAAATATATTAAAATT-AT
*
375984 ATAATATATATAATAAATATATTAAAATTTT
1 ATAATATATATAATAAATATATTAAAATTAT
376015 ATAA-ATATATAATA
1 ATAATATATATAATA
376029 TTTTAAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
30 10 0.23
31 5 0.12
32 17 0.40
33 11 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
ATAATATATATAATAAATATATTAAAATTAT
Found at i:376020 original size:19 final size:18
Alignment explanation
Indices: 375955--376033 Score: 61
Period size: 19 Copynumber: 4.1 Consensus size: 18
375945 TAAAAAATAA
*
375955 TATAAATATATAAATATAT
1 TATAAATATATAAA-ATTT
*
375974 TA-AAATTAATATAATATATAT
1 TATAAA-T-ATATAA-A-ATTT
*
375995 AATAAATATATTAAAATTT
1 TATAAATATA-TAAAATTT
*
376014 TATAAATATATAATATTT
1 TATAAATATATAAAATTT
376032 TA
1 TA
376034 AATAAAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
18 12 0.24
19 15 0.29
20 10 0.20
21 11 0.22
22 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAATATATAAAATTT
Found at i:376184 original size:20 final size:20
Alignment explanation
Indices: 376161--376257 Score: 63
Period size: 20 Copynumber: 4.7 Consensus size: 20
376151 TCTTTTGATT
* * *
376161 AATATTTTAAGATTTTATAA
1 AATATTTTAAAATATAATAA
*
376181 AATATGTTAAAATATAATAA
1 AATATTTTAAAATATAATAA
376201 AATA-TTTAATAATAAATAATAA
1 AATATTTTAA-AAT--ATAATAA
** *
376223 ATATAAATTAAAAT-TATATTA
1 A-ATATTTTAAAATATA-ATAA
*
376244 AATATGTTAAAATA
1 AATATTTTAAAATA
376258 AAAAATAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
19 4 0.07
20 35 0.57
21 4 0.07
22 8 0.13
23 6 0.10
24 4 0.07
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
AATATTTTAAAATATAATAA
Found at i:376217 original size:24 final size:24
Alignment explanation
Indices: 376190--376300 Score: 76
Period size: 24 Copynumber: 4.8 Consensus size: 24
376180 AAATATGTTA
*
376190 AAATATAATAAAATATTTAATAAT
1 AAATATAATAAAATATTAAATAAT
376214 -AA-ATAAT-AAATA-TAAATTAA-
1 AAATATAATAAAATATTAAA-TAAT
* * * *
376234 AATTATATTAAATATGTTAAAATAAA
1 AAATATAATAAA-ATATT-AAATAAT
376260 AAATA-AATAATAA-ATTAAAATAAT
1 AAATATAATAA-AATATT-AAATAAT
376284 -AATATAATAAAATATTA
1 AAATATAATAAAATATTA
376301 TTTTTAAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 23
0.69 0.08 0.23
Matches are distributed among these distances:
20 3 0.04
21 9 0.13
22 9 0.13
23 11 0.16
24 19 0.28
25 9 0.13
26 8 0.12
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (24 bp):
AAATATAATAAAATATTAAATAAT
Found at i:376218 original size:7 final size:7
Alignment explanation
Indices: 376194--376294 Score: 57
Period size: 7 Copynumber: 14.1 Consensus size: 7
376184 ATGTTAAAAT
376194 ATAATAAA
1 ATAAT-AA
* *
376202 ATATTTA
1 ATAATAA
376209 ATAATAA
1 ATAATAA
376216 ATAATAA
1 ATAATAA
376223 AT-ATAA
1 ATAATAA
376229 ATTAA-AA
1 A-TAATAA
*
376236 TTATATTAA
1 --ATAATAA
* *
376245 ATATGTTA
1 ATA-ATAA
376253 A-AATAA
1 ATAATAA
*
376259 AAAATAA
1 ATAATAA
376266 ATAATAA
1 ATAATAA
*
376273 ATTA-AA
1 ATAATAA
376279 ATAATAA
1 ATAATAA
376286 TATAATAA
1 -ATAATAA
376294 A
1 A
376295 ATATTATTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
6 13 0.18
7 39 0.54
8 17 0.24
9 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (7 bp):
ATAATAA
Found at i:376247 original size:43 final size:45
Alignment explanation
Indices: 376187--376292 Score: 139
Period size: 43 Copynumber: 2.4 Consensus size: 45
376177 ATAAAATATG
*
376187 TTAAAA-TATAATAAAATAT-TTAATAATAAATAATAAAT-ATAAA
1 TTAAAATTATAATAAAATATGTTAA-AATAAAAAATAAATAATAAA
*
376230 TTAAAATTAT-ATTAAATATGTTAAAATAAAAAATAAATAATAAA
1 TTAAAATTATAATAAAATATGTTAAAATAAAAAATAAATAATAAA
* *
376274 TTAAAATAATAATATAATA
1 TTAAAATTATAATAAAATA
376293 AAATATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
43 27 0.50
44 21 0.39
45 6 0.11
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (45 bp):
TTAAAATTATAATAAAATATGTTAAAATAAAAAATAAATAATAAA
Found at i:376286 original size:16 final size:16
Alignment explanation
Indices: 376191--376297 Score: 66
Period size: 16 Copynumber: 6.9 Consensus size: 16
376181 AATATGTTAA
*
376191 AATATAATAAAATATT
1 AATATAATAAAATAAT
*
376207 TA-ATAAT-AAATAAT
1 AATATAATAAAATAAT
*
376221 AA-AT-ATAAATTAA-
1 AATATAATAAAATAAT
* **
376234 AATTATATTAAATATGTT
1 AA-TATAATAAA-ATAAT
*
376252 AAAATAA-AAAATAAAT
1 AATATAATAAAAT-AAT
376268 AATA-AATTAAAATAAT
1 AATATAA-TAAAATAAT
376284 AATATAATAAAATA
1 AATATAATAAAATA
376298 TTATTTTTAA
Statistics
Matches: 68, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
13 4 0.06
14 14 0.21
15 11 0.16
16 26 0.38
17 11 0.16
18 2 0.03
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (16 bp):
AATATAATAAAATAAT
Found at i:376297 original size:10 final size:10
Alignment explanation
Indices: 376177--376298 Score: 65
Period size: 10 Copynumber: 11.9 Consensus size: 10
376167 TTAAGATTTT
*
376177 ATAAAATATG
1 ATAAAATATA
*
376187 TTAAAATATA
1 ATAAAATATA
376197 ATAAAATATTTA
1 ATAAAATA--TA
376209 ATAATAA-ATA
1 ATAA-AATATA
376219 AT-AAATATAA
1 ATAAAATAT-A
376229 ATTAAAAT-TA
1 A-TAAAATATA
* *
376239 TATTAAATATG
1 -ATAAAATATA
*
376250 TTAAAATA-A
1 ATAAAATATA
*
376259 A-AAATAAATA
1 ATAAA-ATATA
* *
376269 ATAAATTAAA
1 ATAAAATATA
376279 ATAATAATATA
1 ATAA-AATATA
376290 ATAAAATAT
1 ATAAAATAT
376299 TATTTTTAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
8 5 0.06
9 5 0.06
10 46 0.55
11 15 0.18
12 11 0.13
13 2 0.02
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (10 bp):
ATAAAATATA
Found at i:376308 original size:63 final size:63
Alignment explanation
Indices: 376180--376301 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
376170 AGATTTTATA
* * * * *
376180 AAATATGTTAAAATATAATAAAATATTTAATAATAAATAATAAATATAAATTAAAATTATATT
1 AAATATGTTAAAATAAAAAAAAATAATAAATAATAAATAATAAATATAAATAAAAATTATATT
*
376243 AAATATGTTAAAATAAAAAATAAATAATAAATTA-AAATAAT-AATAT-AATAAAATATTAT
1 AAATATGTTAAAATAAAAAA-AAATAATAAATAATAAATAATAAATATAAATAAAA-ATTAT
376302 TTTTAAAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
61 6 0.12
62 10 0.20
63 25 0.49
64 10 0.20
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (63 bp):
AAATATGTTAAAATAAAAAAAAATAATAAATAATAAATAATAAATATAAATAAAAATTATATT
Found at i:377089 original size:16 final size:16
Alignment explanation
Indices: 377070--377119 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
377060 TATTTAAATT
377070 ATTATATATTTTAAAA
1 ATTATATATTTTAAAA
* *
377086 ATTATA-ATAATTAATA
1 ATTATATAT-TTTAAAA
*
377102 ATT-TATATTATAAAA
1 ATTATATATTTTAAAA
377117 ATT
1 ATT
377120 TTAATATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTATATATTTTAAAA
Found at i:377114 original size:22 final size:24
Alignment explanation
Indices: 377086--377134 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
377076 TATTTTAAAA
*
377086 ATTATAATAA-TTAATA-ATTTAT
1 ATTATAAAAATTTAATATATTTAT
377108 ATTATAAAAATTTTAATATATTTAT
1 ATTATAAAAA-TTTAATATATTTAT
377133 AT
1 AT
377135 AATATTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 9 0.39
24 6 0.26
25 8 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTATAAAAATTTAATATATTTAT
Found at i:377398 original size:30 final size:29
Alignment explanation
Indices: 377355--377412 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
377345 TTGATTTTTT
377355 TAATATTAAAAAATATATTATTATATAAAA
1 TAATATTAAAAAATATATTATTA-ATAAAA
* * *
377385 TAATTTTACAAAATATTTTATTAATAAA
1 TAATATTAAAAAATATATTATTAATAAA
377413 TTATAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
TAATATTAAAAAATATATTATTAATAAAA
Found at i:378029 original size:6 final size:6
Alignment explanation
Indices: 378014--378056 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
378004 TTAATTCTGT
*
378014 ATTT-A ATTTAA ATTTAA ATTT-A ATTTAA ATTT-A ATTTAT ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT
378057 TAACTTTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
5 14 0.41
6 20 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
ATTTAA
Found at i:378030 original size:11 final size:11
Alignment explanation
Indices: 378014--378056 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
378004 TTAATTCTGT
378014 ATTT-AATTTAA
1 ATTTAAATTT-A
378025 ATTTAAATTTA
1 ATTTAAATTTA
378036 ATTTAAATTTA
1 ATTTAAATTTA
*
378047 ATTTATATTT
1 ATTTAAATTT
378057 TAACTTTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 25 0.83
12 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:378034 original size:17 final size:16
Alignment explanation
Indices: 378014--378056 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
378004 TTAATTCTGT
378014 ATTTAATTTAAATTTAA
1 ATTTAATTTAAATTT-A
378031 ATTTAATTTAAATTTA
1 ATTTAATTTAAATTTA
378047 ATTTATATTT
1 ATTTA-ATTT
378057 TAACTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTAATTTAAATTTA
Found at i:387589 original size:16 final size:16
Alignment explanation
Indices: 387568--387600 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
387558 CATTTGACGA
387568 AATGAAATTTGCATTT
1 AATGAAATTTGCATTT
387584 AATGAAATTTGCATTT
1 AATGAAATTTGCATTT
387600 A
1 A
387601 GATATGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.42
Consensus pattern (16 bp):
AATGAAATTTGCATTT
Found at i:387862 original size:11 final size:12
Alignment explanation
Indices: 387844--387872 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
387834 TTTATCGTGT
387844 TATTTTATATTA
1 TATTTTATATTA
387856 T-TTTTATATTA
1 TATTTTATATTA
387867 TATTTT
1 TATTTT
387873 TATCATCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTTATATTA
Found at i:388136 original size:37 final size:38
Alignment explanation
Indices: 388087--388188 Score: 110
Period size: 37 Copynumber: 2.8 Consensus size: 38
388077 GAGAAAATTA
* *
388087 TATTAACTTATTAATATTTATATGATATAATATAA-AT
1 TATTAACATATTAATATTTATATGAAATAATATAATAT
* *
388124 TATTAACATATTAAAATTTGTAT-AAAT-ATATAATAT
1 TATTAACATATTAATATTTATATGAAATAATATAATAT
388160 T-TTAA-ATA-TAAT-TATTATATGAAATAATA
1 TATTAACATATTAATAT-TTATATGAAATAATA
388189 ATACAATATA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 8 0.15
34 7 0.13
35 13 0.24
36 6 0.11
37 20 0.36
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (38 bp):
TATTAACATATTAATATTTATATGAAATAATATAATAT
Found at i:389796 original size:2 final size:2
Alignment explanation
Indices: 389789--389816 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
389779 AAACAAATAC
389789 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
389817 CAAACTATTG
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:391767 original size:34 final size:34
Alignment explanation
Indices: 391728--391818 Score: 123
Period size: 32 Copynumber: 2.7 Consensus size: 34
391718 TGATAAGAAA
* *
391728 ATAATATAAAATATTTAAATATTTTAAAATTTAT
1 ATAATATAAAATATTTAAATATATCAAAATTTAT
*
391762 ATAATATAAATTA-TT-AATATATCAAAATTTAT
1 ATAATATAAAATATTTAAATATATCAAAATTTAT
391794 ATGAATATAAAATATTTTAAATATA
1 AT-AATATAAAATA-TTTAAATATA
391819 ATTATAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
32 17 0.35
33 12 0.24
34 12 0.24
35 2 0.04
36 6 0.12
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (34 bp):
ATAATATAAAATATTTAAATATATCAAAATTTAT
Found at i:391801 original size:18 final size:16
Alignment explanation
Indices: 391728--391819 Score: 64
Period size: 16 Copynumber: 5.6 Consensus size: 16
391718 TGATAAGAAA
*
391728 ATAATATAAAATATTTAA
1 ATAATAT-AAA-ATTTAT
* *
391746 ATATTTTAAAATTTAT
1 ATAATATAAAATTTAT
*
391762 ATAATATAAATTATTA-
1 ATAATATAAAAT-TTAT
391778 AT-ATATCAAAATTTAT
1 ATAATAT-AAAATTTAT
*
391794 ATGAATATAAAATATTTT
1 AT-AATATAAAAT-TTAT
391812 A-AATATAA
1 ATAATATAA
391820 TTATAATATG
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
15 7 0.12
16 29 0.48
17 11 0.18
18 13 0.22
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (16 bp):
ATAATATAAAATTTAT
Found at i:391965 original size:2 final size:2
Alignment explanation
Indices: 391958--391990 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
391948 TTTGCTTTGG
391958 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
391991 GCTTTGTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:396166 original size:20 final size:19
Alignment explanation
Indices: 396117--396201 Score: 75
Period size: 20 Copynumber: 4.4 Consensus size: 19
396107 ATTAAATTAT
*
396117 ATTTAAATTTAAATAAAATA
1 ATTTAAA-TTAAAAAAAATA
* **
396137 TTTTTTATTAATAAAAAATA
1 ATTTAAATTAA-AAAAAATA
396157 ATTTAAATTAAAATAAACA-A
1 ATTTAAATTAAAA-AAA-ATA
*
396177 ATTTAAATAAAAAAAAAT-
1 ATTTAAATTAAAAAAAATA
396195 ATTTAAA
1 ATTTAAA
396202 CTTGATCTGA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
18 8 0.15
19 9 0.17
20 35 0.66
21 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTAAATTAAAAAAAATA
Found at i:396710 original size:7 final size:7
Alignment explanation
Indices: 396698--396739 Score: 75
Period size: 7 Copynumber: 5.9 Consensus size: 7
396688 ACTACCTGAC
396698 CCTTGAA
1 CCTTGAA
396705 CCTTGAA
1 CCTTGAA
396712 CCTTGAA
1 CCTTGAA
396719 CCTTGAA
1 CCTTGAA
396726 CCTTGAA
1 CCTTGAA
396733 CCGTTGA
1 CC-TTGA
396740 CTAGGAAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 30 0.88
8 4 0.12
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (7 bp):
CCTTGAA
Found at i:396912 original size:27 final size:27
Alignment explanation
Indices: 396859--396913 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
396849 GATCGAAAAG
*
396859 CAATCAAAGAATTCTTTTCAAGTTTTT
1 CAATCAAAGAATTCTCTTCAAGTTTTT
*
396886 CAATCAAAGGGATTCTCTTCAAGTTTTT
1 CAATCAAA-GAATTCTCTTCAAGTTTTT
396914 GCATTCTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (27 bp):
CAATCAAAGAATTCTCTTCAAGTTTTT
Found at i:398601 original size:47 final size:47
Alignment explanation
Indices: 398532--398625 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
398522 TGAAAAAAAA
398532 TGTACCGATAAAAACAACCAACAGTTATAGAACATTTTCCTAGGAGT
1 TGTACCGATAAAAACAACCAACAGTTATAGAACATTTTCCTAGGAGT
*
398579 TGTACCGATAAAAATAACCAACAGTTATAGAACATTTTCCTAGGAGT
1 TGTACCGATAAAAACAACCAACAGTTATAGAACATTTTCCTAGGAGT
398626 AGACTAACAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (47 bp):
TGTACCGATAAAAACAACCAACAGTTATAGAACATTTTCCTAGGAGT
Found at i:401374 original size:17 final size:17
Alignment explanation
Indices: 401326--401375 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
401316 ATTTAAATTG
*
401326 ATTTAATTTTAATTATT
1 ATTTAAATTTAATTATT
* *
401343 ATAT-AATTATTATTATT
1 ATTTAAATT-TAATTATT
401360 ATTTAAATTTAATTAT
1 ATTTAAATTTAATTAT
401376 AAAATATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
16 3 0.12
17 19 0.73
18 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTAAATTTAATTATT
Found at i:401623 original size:32 final size:33
Alignment explanation
Indices: 401560--401624 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
401550 GAAAGCAAAT
* *
401560 ATATAATAGATTTTATATATAATAATATAATAA
1 ATATAATAAATTTTATATATAATAACATAATAA
*
401593 ATAT-ATAAATTTTAT-TATTATAACATTAATAA
1 ATATAATAAATTTTATATATAATAACA-TAATAA
401625 TGAATTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 8 0.29
32 16 0.57
33 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (33 bp):
ATATAATAAATTTTATATATAATAACATAATAA
Found at i:402751 original size:2 final size:2
Alignment explanation
Indices: 402744--402775 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
402734 TACTAAAGGA
402744 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
402776 TGTTTTGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:403042 original size:20 final size:20
Alignment explanation
Indices: 403017--403058 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
403007 AATTTAAACT
403017 TATTAAATGTCACTTTTTAA
1 TATTAAATGTCACTTTTTAA
403037 TATTAAATGTCACTTTTTAA
1 TATTAAATGTCACTTTTTAA
403057 TA
1 TA
403059 AAGATTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.50
Consensus pattern (20 bp):
TATTAAATGTCACTTTTTAA
Found at i:404841 original size:6 final size:6
Alignment explanation
Indices: 404830--404861 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
404820 GTCATGAGAG
*
404830 TGGGAA TGGGAA TGGGAA TGGGAA TGAGAA TG
1 TGGGAA TGGGAA TGGGAA TGGGAA TGGGAA TG
404862 TGAGTGCGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.34, C:0.00, G:0.47, T:0.19
Consensus pattern (6 bp):
TGGGAA
Found at i:406997 original size:14 final size:11
Alignment explanation
Indices: 406965--406992 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
406955 ATATAAATTT
406965 TAATTTATTAA
1 TAATTTATTAA
406976 TAATTTATTAA
1 TAATTTATTAA
406987 TAATTT
1 TAATTT
406993 TTTATATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TAATTTATTAA
Done.