Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1184
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: 60716
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:1851 original size:20 final size:20
Alignment explanation
Indices: 1828--1867 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1818 TTATTTACTG
*
1828 TTAAAGTTATATATTTAATA
1 TTAAAATTATATATTTAATA
* *
1848 TTAAAATTTTATTTTTAATA
1 TTAAAATTATATATTTAATA
1868 CAACTAACCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTAAAATTATATATTTAATA
Found at i:3190 original size:14 final size:14
Alignment explanation
Indices: 3173--3225 Score: 51
Period size: 13 Copynumber: 4.0 Consensus size: 14
3163 ATTTTATCAT
*
3173 TTTAATTTTTTATA
1 TTTAATTATTTATA
3187 TTTAA-TATTTATA
1 TTTAATTATTTATA
*
3200 ATTAA-TATTTATCA
1 TTTAATTATTTAT-A
3214 --TAATTATTTATA
1 TTTAATTATTTATA
3226 ATAATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 4 0.11
13 25 0.71
14 6 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTAATTATTTATA
Found at i:3199 original size:13 final size:13
Alignment explanation
Indices: 3181--3232 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
3171 ATTTTAATTT
*
3181 TTTATATTTAATA
1 TTTATAATTAATA
3194 TTTATAATTAATA
1 TTTATAATTAATA
*
3207 TTTATCA-TAATTA
1 TTTATAATTAA-TA
3220 TTTATAA-TAATA
1 TTTATAATTAATA
3232 T
1 T
3233 ATATTACGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
12 6 0.17
13 29 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTATAATTAATA
Found at i:3693 original size:13 final size:13
Alignment explanation
Indices: 3675--3699 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3665 ATCACTTAAA
3675 TGTATCGATACAT
1 TGTATCGATACAT
3688 TGTATCGATACA
1 TGTATCGATACA
3700 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3764 original size:52 final size:52
Alignment explanation
Indices: 3708--3888 Score: 326
Period size: 52 Copynumber: 3.5 Consensus size: 52
3698 CACTGATCTT
*
3708 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3760 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
3812 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3864 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
3889 TCATATTTCG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:7686 original size:17 final size:17
Alignment explanation
Indices: 7664--7699 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
7654 TATTCAATAT
7664 TAAATAT-ATATTAAAAA
1 TAAATATCA-ATTAAAAA
7681 TAAATATCAATTAAAAA
1 TAAATATCAATTAAAAA
7698 TA
1 TA
7700 TTTTTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAATATCAATTAAAAA
Found at i:13245 original size:22 final size:22
Alignment explanation
Indices: 13220--13263 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
13210 CACTGGCACC
13220 GTGCTCGTGTCATTAATTCCTA
1 GTGCTCGTGTCATTAATTCCTA
13242 GTGCTCGTGTCATTAATTCCTA
1 GTGCTCGTGTCATTAATTCCTA
13264 CTGAAACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (22 bp):
GTGCTCGTGTCATTAATTCCTA
Found at i:13406 original size:23 final size:27
Alignment explanation
Indices: 13382--13453 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 27
13372 AAATAATCTT
* *
13382 TTATTTAATATAATTAATAAATTTTTTA
1 TTATATAATA-AATTAATAAATTTTATA
**
13410 TTATATAATAAATTAATAAA-CATATA
1 TTATATAATAAATTAATAAATTTTATA
* *
13436 TTTTATAATCAATTAATA
1 TTATATAATAAATTAATA
13454 TGATTAATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 19 0.50
27 10 0.26
28 9 0.24
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (27 bp):
TTATATAATAAATTAATAAATTTTATA
Found at i:13617 original size:29 final size:28
Alignment explanation
Indices: 13566--13636 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 28
13556 TTGTTTCTAT
*
13566 TTTTAATTTATTTTTTAAAATAAATATAAA
1 TTTTAA-TTATATTTTAAAATAAATAT-AA
*
13596 TTTTAATTATATTTTAATATAAATATAA
1 TTTTAATTATATTTTAAAATAAATATAA
13624 TTTTAATATATAT
1 TTTTAAT-TATAT
13637 ATATATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 9 0.24
29 23 0.61
30 6 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TTTTAATTATATTTTAAAATAAATATAA
Found at i:13628 original size:17 final size:17
Alignment explanation
Indices: 13606--13671 Score: 78
Period size: 17 Copynumber: 3.5 Consensus size: 17
13596 TTTTAATTAT
13606 ATTTTAATATAAATATA
1 ATTTTAATATAAATATA
13623 ATTTTAATATATATATATA
1 ATTTTAATATA-A-ATATA
13642 TTATTACTTAATATAAATATA
1 --ATT--TTAATATAAATATA
13663 ATTTTAATA
1 ATTTTAATA
13672 ATTTTTAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
17 17 0.40
18 1 0.02
19 8 0.19
21 8 0.19
22 1 0.02
23 8 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTAATATAAATATA
Found at i:13642 original size:21 final size:22
Alignment explanation
Indices: 13612--13662 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
13602 TTATATTTTA
*
13612 ATATAAATATAATT-TTAATAT
1 ATATATATATAATTATTAATAT
*
13633 ATATATATATTATTACTTAATAT
1 ATATATATATAATTA-TTAATAT
*
13656 AAATATA
1 ATATATA
13663 ATTTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.48
23 13 0.52
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATATATATAATTATTAATAT
Found at i:14001 original size:2 final size:2
Alignment explanation
Indices: 13994--14032 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
13984 CAATTAAGAG
13994 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14033 GGACTTTAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14546 original size:22 final size:22
Alignment explanation
Indices: 14468--14546 Score: 61
Period size: 24 Copynumber: 3.4 Consensus size: 22
14458 AATAATTTTA
*
14468 AATACATATAAAAATATAAATTTT
1 AATA-ATATAAAAATATATA-TTT
* * *
14492 TATGAATATAAAAATAATATAATA
1 AAT-AATATAAAAAT-ATATATTT
*
14516 AATATTAT-AAAATATATATTT
1 AATAATATAAAAATATATATTT
14537 AATACATATA
1 AATA-ATATA
14547 TCATATTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
21 10 0.24
22 8 0.19
23 4 0.10
24 15 0.36
25 5 0.12
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (22 bp):
AATAATATAAAAATATATATTT
Found at i:14577 original size:17 final size:17
Alignment explanation
Indices: 14555--14602 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
14545 TATCATATTT
14555 TTATTTAATATTTTAAA
1 TTATTTAATATTTTAAA
* *
14572 TTATTTAATAATTTATA
1 TTATTTAATATTTTAAA
*
14589 TTATGTTTATATTT
1 TTAT-TTAATATTT
14603 ACATAATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TTATTTAATATTTTAAA
Found at i:14990 original size:18 final size:17
Alignment explanation
Indices: 14935--15000 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 17
14925 AAGCGGTATT
14935 ATTTTAT-TTTAATTAA
1 ATTTTATATTTAATTAA
* *
14951 ATTTTA-AATTATTTATA
1 ATTTTATATTTAATTA-A
14968 ATTTTATATTTAAATTAA
1 ATTTTATATTT-AATTAA
14986 ATTTTATCATTTAAT
1 ATTTTAT-ATTTAAT
15001 ATTAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 12 0.29
17 7 0.17
18 14 0.34
19 8 0.20
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATATTTAATTAA
Found at i:15002 original size:26 final size:23
Alignment explanation
Indices: 14966--15014 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 23
14956 AAATTATTTA
14966 TAATTTTAT-ATTTAA-ATT-A-
1 TAATTTTATAATTTAATATTAAT
*
14985 -AATTTTATCATTTAATATTAAT
1 TAATTTTATAATTTAATATTAAT
15007 TAATTTTA
1 TAATTTTA
15015 AGTTAAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 8 0.32
19 6 0.24
20 3 0.12
21 1 0.04
23 7 0.28
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TAATTTTATAATTTAATATTAAT
Found at i:15007 original size:19 final size:17
Alignment explanation
Indices: 14966--15007 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 17
14956 AAATTATTTA
14966 TAATTTTATATTTAAAT
1 TAATTTTATATTTAAAT
14983 TAAATTTTATCATTTAATAT
1 T-AATTTTAT-ATTTAA-AT
15003 TAATT
1 TAATT
15008 AATTTTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.05
18 8 0.36
19 10 0.45
20 3 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATTTTATATTTAAAT
Found at i:16072 original size:21 final size:23
Alignment explanation
Indices: 16029--16073 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
16019 TATTATTAAA
16029 ATATTATTTTAATATTAATATTT
1 ATATTATTTTAATATTAATATTT
16052 ATATT-TTTT-ATAATTAA-ATTT
1 ATATTATTTTAAT-ATTAATATTT
16073 A
1 A
16074 AATAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATATTATTTTAATATTAATATTT
Found at i:16845 original size:2 final size:2
Alignment explanation
Indices: 16838--16862 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16828 TAAAATTCAG
16838 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16863 AAAGAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17348 original size:2 final size:2
Alignment explanation
Indices: 17343--17375 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
17333 ATATATATAT
*
17343 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
17376 AATTCTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17651 original size:22 final size:22
Alignment explanation
Indices: 17607--17653 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
17597 TTGCATGCTC
* **
17607 TTATATTATATATGTTTCGCTA
1 TTATATAATATATGTTGAGCTA
*
17629 TTATATAATATATGTTGATCTA
1 TTATATAATATATGTTGAGCTA
17651 TTA
1 TTA
17654 AATTTATAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (22 bp):
TTATATAATATATGTTGAGCTA
Found at i:18552 original size:14 final size:14
Alignment explanation
Indices: 18533--18571 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
18523 TTCGTTAATA
18533 ATATATAAATTTAT
1 ATATATAAATTTAT
*
18547 ATATATATATTTAT
1 ATATATAAATTTAT
* *
18561 TTATTTAAATT
1 ATATATAAATT
18572 AATTTATCTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATATAAATTTAT
Found at i:19608 original size:2 final size:2
Alignment explanation
Indices: 19601--19639 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19591 TTAAGGGCCA
19601 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19640 GGGGTGAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20627 original size:2 final size:2
Alignment explanation
Indices: 20620--20648 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20610 GGTCAGAATG
20620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20649 GAAAAAGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21357 original size:2 final size:2
Alignment explanation
Indices: 21350--21384 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
21340 AATGGAAATC
21350 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 A
21385 AAAGAGGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21625 original size:20 final size:20
Alignment explanation
Indices: 21600--21652 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
21590 GATTCAAAAA
* *
21600 TTAATTTAATTTTATATATT
1 TTAATTTAATTTTACATAAT
*
21620 TTAA-TTATTTTTTACATAAT
1 TTAATTTA-ATTTTACATAAT
21640 TTATATTTAATTT
1 TTA-ATTTAATTT
21653 CTTTTCAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 3 0.12
20 16 0.62
21 4 0.15
22 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTAATTTAATTTTACATAAT
Found at i:22455 original size:14 final size:15
Alignment explanation
Indices: 22438--22471 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
22428 TAATAATTAA
22438 ATATAT-AAAAAATT
1 ATATATCAAAAAATT
*
22452 ATATATCAAAAAGTT
1 ATATATCAAAAAATT
22467 ATATA
1 ATATA
22472 CACTCATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (15 bp):
ATATATCAAAAAATT
Found at i:23677 original size:31 final size:31
Alignment explanation
Indices: 23642--23719 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 31
23632 ATTTTTATAT
23642 TTTTTAAAATTATTTTAAA-TAATAAAATAAA
1 TTTTTAAAATTATTTTAAACTAATAAAA-AAA
* *
23673 TTTTTAAATTTA-CTTAAACTTAATAAAAAAA
1 TTTTTAAAATTATTTTAAAC-TAATAAAAAAA
*
23704 -ATTTAAAA-TATTTTAA
1 TTTTTAAAATTATTTTAA
23720 CTTATAATCC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 2 0.05
30 15 0.38
31 14 0.36
32 8 0.21
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (31 bp):
TTTTTAAAATTATTTTAAACTAATAAAAAAA
Found at i:24144 original size:21 final size:24
Alignment explanation
Indices: 24102--24147 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
24092 TATTAAAAGA
*
24102 AAATATTTAATATATTTAAATTTT
1 AAATATTTAATATATGTAAATTTT
*
24126 AAAT-TTTAATAT-TGTAATTTTT
1 AAATATTTAATATATGTAAATTTT
24148 TTATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 8 0.40
24 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
AAATATTTAATATATGTAAATTTT
Found at i:24693 original size:31 final size:31
Alignment explanation
Indices: 24645--24705 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
24635 ATCATTAATA
*
24645 ATCATACTTAATAAATTTCATTGTCAAGATT
1 ATCATAATTAATAAATTTCATTGTCAAGATT
24676 ATCATAATTAACT-AATTTCATTGTCAAGAT
1 ATCATAATTAA-TAAATTTCATTGTCAAGAT
24706 GAAATGGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (31 bp):
ATCATAATTAATAAATTTCATTGTCAAGATT
Found at i:25832 original size:30 final size:31
Alignment explanation
Indices: 25781--25840 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
25771 AAGATTATTT
*
25781 ATTATTATAATATTTTAAAAAATTAAAAATA
1 ATTATTATAATATTTTAAAAAAGTAAAAATA
* *
25812 ATTATTA-ATTATTTTTAAAAAGTAAAAAT
1 ATTATTATAATATTTTAAAAAAGTAAAAAT
25841 CACCTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (31 bp):
ATTATTATAATATTTTAAAAAAGTAAAAATA
Found at i:25891 original size:15 final size:14
Alignment explanation
Indices: 25864--25909 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
25854 AATTTAGAAA
25864 TAAAATT-TATTTT
1 TAAAATTATATTTT
25877 TAATAATTATA-TTT
1 TAA-AATTATATTTT
*
25891 TAAAATTATATCTT
1 TAAAATTATATTTT
25905 TAAAA
1 TAAAA
25910 AATTTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 10 0.34
14 17 0.59
15 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
TAAAATTATATTTT
Found at i:25910 original size:15 final size:14
Alignment explanation
Indices: 25864--25910 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
25854 AATTTAGAAA
*
25864 TAAAATTTAT-TTT
1 TAAAAATTATATTT
*
25877 TAATAATTATATTT
1 TAAAAATTATATTT
25891 T-AAAATTATATCTT
1 TAAAAATTATAT-TT
25905 TAAAAA
1 TAAAAA
25911 ATTTTAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 17 0.61
14 7 0.25
15 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
TAAAAATTATATTT
Found at i:26156 original size:14 final size:14
Alignment explanation
Indices: 26137--26164 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
26127 TTGCATCACA
26137 CATCTCTCTCTCTC
1 CATCTCTCTCTCTC
26151 CATCTCTCTCTCTC
1 CATCTCTCTCTCTC
26165 TCTACCAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.50, G:0.00, T:0.43
Consensus pattern (14 bp):
CATCTCTCTCTCTC
Found at i:28726 original size:47 final size:47
Alignment explanation
Indices: 28658--28748 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
28648 ACAACCCATA
*
28658 AAAACTCAACAATAAAGAAATAAAAAAACATAAATTTTAATGTAGTT
1 AAAACTCAACAATAAAGAAATAAAAAAACACAAATTTTAATGTAGTT
* * * *
28705 AAAATTCAATAATAAAGAAATAAAAGAACACAAATTTTATTGTA
1 AAAACTCAACAATAAAGAAATAAAAAAACACAAATTTTAATGTA
28749 ATTTAGTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.59, C:0.08, G:0.07, T:0.26
Consensus pattern (47 bp):
AAAACTCAACAATAAAGAAATAAAAAAACACAAATTTTAATGTAGTT
Found at i:29699 original size:24 final size:23
Alignment explanation
Indices: 29672--29755 Score: 64
Period size: 25 Copynumber: 3.6 Consensus size: 23
29662 ACATATCTCA
29672 AAAT-TTATATAATATAAATTATAT
1 AAATATTATA-AATAT-AATTATAT
* *
29696 AAATATTTTAAATATAATTATAAC
1 AAATATTATAAATATAATTAT-AT
** * *
29720 ATAATAAAATATATATAATAATAT
1 A-AATATTATAAATATAATTATAT
29744 AAATA-TATAAAT
1 AAATATTATAAAT
29756 TATCAAAGCA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
22 5 0.11
23 10 0.21
24 13 0.28
25 19 0.40
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATATTATAAATATAATTATAT
Found at i:29751 original size:8 final size:8
Alignment explanation
Indices: 29683--29755 Score: 55
Period size: 8 Copynumber: 9.0 Consensus size: 8
29673 AATTTATATA
29683 ATATAAATT
1 ATATAAA-T
29692 ATATAAAT
1 ATATAAAT
* *
29700 ATTTTAA-
1 ATATAAAT
29707 ATAT-AAT
1 ATATAAAT
29714 -TATAACAT
1 ATATAA-AT
29722 A-ATAAAAT
1 ATAT-AAAT
29730 ATATATAAT
1 ATATA-AAT
29739 AATATAAAT
1 -ATATAAAT
29748 ATATAAAT
1 ATATAAAT
29756 TATCAAAGCA
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
6 5 0.09
7 4 0.08
8 22 0.42
9 17 0.32
10 5 0.09
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAAAT
Found at i:30568 original size:21 final size:22
Alignment explanation
Indices: 30544--30590 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
30534 AATCATTCAC
**
30544 ATATATTAATTTA-TTATAATT
1 ATATATTAAAATATTTATAATT
*
30565 ATAT-TTAAAATATTTATATTT
1 ATATATTAAAATATTTATAATT
30586 ATATA
1 ATATA
30591 AATTTTGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATATTAAAATATTTATAATT
Found at i:30601 original size:16 final size:15
Alignment explanation
Indices: 30576--30627 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
30566 TATTTAAAAT
30576 ATTTATATTTATATAA
1 ATTT-TATTTATATAA
30592 ATTTTGATTTAT-TAA
1 ATTTT-ATTTATATAA
*
30607 CATTTTATATCATATAA
1 -ATTTTAT-TTATATAA
30624 ATTT
1 ATTT
30628 AAAATATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
15 6 0.19
16 22 0.71
17 3 0.10
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (15 bp):
ATTTTATTTATATAA
Found at i:32022 original size:10 final size:10
Alignment explanation
Indices: 32007--32055 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
31997 ATATGATGTG
*
32007 AAAAATAGTA
1 AAAAATAATA
32017 AAAAATAAT-
1 AAAAATAATA
*
32026 AAAAATATTA
1 AAAAATAATA
*
32036 TAAAATAATA
1 AAAAATAATA
*
32046 AAATATAATA
1 AAAAATAATA
32056 TAAATACATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
9 8 0.25
10 24 0.75
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (10 bp):
AAAAATAATA
Found at i:32067 original size:20 final size:19
Alignment explanation
Indices: 32007--32059 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
31997 ATATGATGTG
* *
32007 AAAAATAGTAAAAAATAAT
1 AAAAATAATATAAAATAAT
*
32026 AAAAATATTATAAAATAAT
1 AAAAATAATATAAAATAAT
32045 AAAATATAATATAAA
1 AAAA-ATAATATAAA
32060 TACATAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 21 0.70
20 9 0.30
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATAATATAAAATAAT
Found at i:32068 original size:19 final size:19
Alignment explanation
Indices: 32018--32070 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
32008 AAAATAGTAA
* *
32018 AAAATAATAAAAATATTAT
1 AAAATAATAAATATAATAT
32037 AAAATAATAAAATATAATAT
1 AAAATAAT-AAATATAATAT
32057 -AAATACATAAATAT
1 AAAATA-ATAAATAT
32071 CTTAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATAATAAATATAATAT
Found at i:32090 original size:33 final size:31
Alignment explanation
Indices: 32048--32125 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 31
32038 AAATAATAAA
*
32048 ATATAATATAAATACATAAATATCTTAAAATTT
1 ATATAATATAAATA-ATAAA-ATATTAAAATTT
* * *
32081 ATATAATATAACTTATTAAAATATTATAATTT
1 ATATAATATAA-ATAATAAAATATTAAAATTT
32113 ATATAAATATAAA
1 ATAT-AATATAAA
32126 ATATTTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
32 14 0.37
33 22 0.58
34 2 0.05
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (31 bp):
ATATAATATAAATAATAAAATATTAAAATTT
Found at i:32104 original size:20 final size:20
Alignment explanation
Indices: 32081--32124 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
32071 CTTAAAATTT
32081 ATATAATATAACTTAT-TAA
1 ATATAATATAACTTATATAA
* *
32100 A-ATATTATAATTTATATAA
1 ATATAATATAACTTATATAA
32119 ATATAA
1 ATATAA
32125 AATATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
18 12 0.60
19 5 0.25
20 3 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATAATATAACTTATATAA
Found at i:32491 original size:16 final size:15
Alignment explanation
Indices: 32470--32499 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
32460 TTTAAGCATA
32470 AAAATAATATATATAT
1 AAAATAATA-ATATAT
32486 AAAATAATAATATA
1 AAAATAATAATATA
32500 AATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATAATAATATAT
Found at i:32511 original size:11 final size:10
Alignment explanation
Indices: 32473--32520 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 10
32463 AAGCATAAAA
32473 ATAATATATAT
1 ATAA-ATATAT
32484 ATAAAATAATAAT
1 AT-AAAT-AT-AT
32497 ATAAATATGAT
1 ATAAATAT-AT
32508 ATAAATATAT
1 ATAAATATAT
32518 ATA
1 ATA
32521 CGAATGTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
10 5 0.15
11 16 0.48
12 8 0.24
13 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
ATAAATATAT
Found at i:33114 original size:43 final size:40
Alignment explanation
Indices: 33066--33145 Score: 117
Period size: 43 Copynumber: 1.9 Consensus size: 40
33056 ACCATATATG
33066 AGTATATTTGA-ATTATTTTAAGTTATTTTTTTATATATTTTGA
1 AGTATATTT-ATATTATTTTAA---ATTTTTTTATATATTTTGA
33109 AGTATATTTATATTATTTTAAATTTTTTTATATATTT
1 AGTATATTTATATTATTTTAAATTTTTTTATATATTT
33146 AAAAGATCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
40 16 0.44
42 1 0.03
43 19 0.53
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (40 bp):
AGTATATTTATATTATTTTAAATTTTTTTATATATTTTGA
Found at i:33120 original size:20 final size:19
Alignment explanation
Indices: 33095--33145 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
33085 AAGTTATTTT
*
33095 TTTATATATTTTGAAGTATA
1 TTTATATATTTT-AAATATA
* *
33115 TTTATATTATTTTAAATTTT
1 TTTATA-TATTTTAAATATA
33135 TTTATATATTT
1 TTTATATATTT
33146 AAAAGATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.19
20 16 0.59
21 6 0.22
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTATATATTTTAAATATA
Found at i:35883 original size:2 final size:2
Alignment explanation
Indices: 35876--35917 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
35866 ACTTGTCTCA
35876 AT AT 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 AT AT
35918 GAGACAACAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36419 original size:13 final size:13
Alignment explanation
Indices: 36401--36428 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
36391 TGAAATACTT
36401 ATGTCCGACACCC
1 ATGTCCGACACCC
36414 ATGTCCGACACCC
1 ATGTCCGACACCC
36427 AT
1 AT
36429 ATCTTTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.43, G:0.14, T:0.18
Consensus pattern (13 bp):
ATGTCCGACACCC
Found at i:40625 original size:15 final size:15
Alignment explanation
Indices: 40601--40646 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
40591 TGGAGTTGGT
40601 AATTTTTTAAATTTA
1 AATTTTTTAAATTTA
* * *
40616 AATTTGTTAAGTTGA
1 AATTTTTTAAATTTA
40631 AATTTATTTAAATTTA
1 AATTT-TTTAAATTTA
40647 GATTAAATTA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (15 bp):
AATTTTTTAAATTTA
Found at i:40983 original size:16 final size:16
Alignment explanation
Indices: 40964--41014 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
40954 TTTGATCATA
*
40964 TTAAATTTAAACTATT
1 TTAAATTTAAATTATT
*
40980 TTAAGTTTAAATTATT
1 TTAAATTTAAATTATT
40996 TTAAA-TTAAATTATT
1 TTAAATTTAAATTATT
41011 TTAA
1 TTAA
41015 GTTAGAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 14 0.44
16 18 0.56
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
TTAAATTTAAATTATT
Found at i:40983 original size:31 final size:31
Alignment explanation
Indices: 40948--41014 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
40938 CGTGTTAATA
*
40948 TTTAACTTT-GATCATATTAAATTTAAACTAT
1 TTTAACTTTAAATCATATTAAA-TTAAACTAT
* * * *
40979 TTTAAGTTTAAATTATTTTAAATTAAATTAT
1 TTTAACTTTAAATCATATTAAATTAAACTAT
41010 TTTAA
1 TTTAA
41015 GTTAGAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 21 0.70
32 9 0.30
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.52
Consensus pattern (31 bp):
TTTAACTTTAAATCATATTAAATTAAACTAT
Found at i:41006 original size:15 final size:15
Alignment explanation
Indices: 40964--41028 Score: 67
Period size: 16 Copynumber: 4.1 Consensus size: 15
40954 TTTGATCATA
*
40964 TTAAATTTAAACTATT
1 TTAAA-TTAAATTATT
*
40980 TTAAGTTTAAATTATT
1 TTAA-ATTAAATTATT
40996 TTAAATTAAATTATT
1 TTAAATTAAATTATT
* *
41011 TTAAGTTAGAATAATT
1 TTAAATTA-AATTATT
41027 TT
1 TT
41029 TGAGTTCAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
15 17 0.40
16 25 0.60
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (15 bp):
TTAAATTAAATTATT
Found at i:41028 original size:31 final size:32
Alignment explanation
Indices: 40964--41028 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
40954 TTTGATCATA
*
40964 TTAAATTTAAACTATTTTAAGTTTAAATTATT
1 TTAAATTTAAACTATTTTAAGTTTAAATAATT
*
40996 TTAAA-TTAAATTATTTTAAG-TTAGAATAATT
1 TTAAATTTAAACTATTTTAAGTTTA-AATAATT
41027 TT
1 TT
41029 TGAGTTCAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 3 0.10
31 22 0.73
32 5 0.17
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (32 bp):
TTAAATTTAAACTATTTTAAGTTTAAATAATT
Found at i:41769 original size:11 final size:11
Alignment explanation
Indices: 41746--41779 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
41736 AAGAACTTTA
41746 ATTTTATATTTT
1 ATTTTA-ATTTT
41758 ATTTTAATTTT
1 ATTTTAATTTT
*
41769 ATTTAAATTTT
1 ATTTTAATTTT
41780 TTAATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTTTAATTTT
Found at i:44281 original size:23 final size:20
Alignment explanation
Indices: 44255--44322 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 20
44245 GATAAAATAA
44255 TTTTATTATTTTACATATTAAAT
1 TTTTATTATTTTA-A-A-TAAAT
*
44278 TTTTATTATTTTAAATATAT
1 TTTTATTATTTTAAATAAAT
*
44298 TTTTATATATTTT--TTAAAT
1 TTTTAT-TATTTTAAATAAAT
44317 TTTTAT
1 TTTTAT
44323 GATAATAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 10 0.24
20 10 0.24
21 7 0.17
22 1 0.02
23 13 0.32
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATTATTTTAAATAAAT
Found at i:44307 original size:10 final size:10
Alignment explanation
Indices: 44276--44322 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 10
44266 TACATATTAA
44276 ATTTTTAT-T
1 ATTTTTATAT
*
44285 ATTTTAAATAT
1 ATTTT-TATAT
44296 ATTTTTATAT
1 ATTTTTATAT
*
44306 ATTTTT-TAA
1 ATTTTTATAT
44315 ATTTTTAT
1 ATTTTTAT
44323 GATAATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 13 0.41
10 13 0.41
11 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:44818 original size:8 final size:8
Alignment explanation
Indices: 44802--44860 Score: 88
Period size: 8 Copynumber: 7.6 Consensus size: 8
44792 ATATTATTTG
44802 TTTTT-AT
1 TTTTTAAT
44809 TTTTTAAT
1 TTTTTAAT
44817 TTTTTAAT
1 TTTTTAAT
44825 TTTTTAATT
1 TTTTTAA-T
44834 TTTTTAA-
1 TTTTTAAT
44841 TTTTTAA-
1 TTTTTAAT
44848 TTTTTAAT
1 TTTTTAAT
44856 TTTTT
1 TTTTT
44861 TAAAAATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
7 19 0.39
8 22 0.45
9 8 0.16
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTAAT
Found at i:46567 original size:34 final size:32
Alignment explanation
Indices: 46529--46630 Score: 102
Period size: 34 Copynumber: 3.1 Consensus size: 32
46519 GCCAAAATAT
*
46529 TTTAAAAAATTATGTTTAAATTTATTTATATTAA
1 TTTAAAAAATTAT-TTTATATTTATTTATATT-A
*
46563 TTTAAAAGATTATTTTATTATTTA-TTATATTA
1 TTTAAAAAATTATTTTA-TATTTATTTATATTA
*
46595 -TTAAAATATTATTTTTATATTAATATTTATA-TA
1 TTTAAAAAATTA-TTTTATATT--TATTTATATTA
46628 TTT
1 TTT
46631 TTATAATTAA
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
31 14 0.24
32 6 0.10
33 15 0.25
34 24 0.41
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (32 bp):
TTTAAAAAATTATTTTATATTTATTTATATTA
Found at i:46629 original size:22 final size:22
Alignment explanation
Indices: 46604--46645 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
46594 ATTAAAATAT
46604 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
46626 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
46646 AATAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:46686 original size:29 final size:29
Alignment explanation
Indices: 46623--46686 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
46613 ATTAATATTT
46623 ATATATTTTTATAATTAAATTTAAATAAAA
1 ATATATTTTTATAATTAAA-TTAAATAAAA
* *
46653 TTATA-TTTTATTATTAAA-TAATATAAATA
1 ATATATTTTTATAATTAAATTAA-ATAAA-A
46682 ATATA
1 ATATA
46687 ATATAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 3 0.10
28 5 0.17
29 17 0.59
30 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
ATATATTTTTATAATTAAATTAAATAAAA
Found at i:46689 original size:14 final size:14
Alignment explanation
Indices: 46670--46699 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
46660 TTATTATTAA
*
46670 ATAATATAAATAAT
1 ATAATATAAAAAAT
46684 ATAATATAAAAAAT
1 ATAATATAAAAAAT
46698 AT
1 AT
46700 TTATATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATATAAAAAAT
Found at i:56690 original size:28 final size:31
Alignment explanation
Indices: 56644--56701 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
56634 ATTTTAAGCT
56644 TTTATTTTTATTAATTTAGAA-AT-AAAATA
1 TTTATTTTTATTAATTTAGAAGATGAAAATA
*
56673 TTTATTTTTA-TATTTTAGAAGATGAAAAT
1 TTTATTTTTATTAATTTAGAAGATGAAAAT
56702 TAATTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.35
29 12 0.46
30 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (31 bp):
TTTATTTTTATTAATTTAGAAGATGAAAATA
Found at i:59096 original size:13 final size:13
Alignment explanation
Indices: 59078--59107 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
59068 TAGTAAAATG
59078 TATTAAATATAAA
1 TATTAAATATAAA
59091 TATTAAATATAAA
1 TATTAAATATAAA
59104 TATT
1 TATT
59108 TAAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TATTAAATATAAA
Found at i:60251 original size:15 final size:15
Alignment explanation
Indices: 60198--60252 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 15
60188 ACTTTAACAT
60198 AAGTATTTT-GACAC
1 AAGTATTTTCGACAC
* * *
60212 AAATATTCTAG-CAC
1 AAGTATTTTCGACAC
*
60226 AGGTA-TTTCGACAC
1 AAGTATTTTCGACAC
60240 AAGTATTTTCGAC
1 AAGTATTTTCGAC
60253 GTAAATACTT
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
13 3 0.10
14 20 0.65
15 8 0.26
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (15 bp):
AAGTATTTTCGACAC
Done.