Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold844
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: 32174
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Found at i:3360 original size:29 final size:32
Alignment explanation
Indices: 3319--3406 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 32
3309 TGGTTCGTGA
* *
3319 ATAAATTTATTTAA-TTTAAATGAAT-AA-AT
1 ATAAATATATTTAATTTTAAATAAATGAACAT
*
3348 ATAAATATGTTTAATTTTAAATAAATGAACAT
1 ATAAATATATTTAATTTTAAATAAATGAACAT
*
3380 A-AAATATAAATTTAAATTTTTAATAAA
1 ATAAATAT--ATTT-AATTTTAAATAAA
3407 AATAAACAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
29 12 0.25
30 10 0.21
31 8 0.17
32 3 0.06
33 3 0.06
34 12 0.25
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.42
Consensus pattern (32 bp):
ATAAATATATTTAATTTTAAATAAATGAACAT
Found at i:6260 original size:110 final size:110
Alignment explanation
Indices: 6056--6270 Score: 292
Period size: 110 Copynumber: 2.0 Consensus size: 110
6046 CTATTATACG
* * *
6056 TAGGTTAGATAATAAATAGTTTTATAATTAATAATTGATTAAAATAGAAATATATAAAAATTAAG
1 TAGGTTAGATAAAAAATAGTTTTATAATTAATAATTGATTAAAATAGAAATACACAAAAATTAAG
* ** *
6121 AAAAAAAGGGTTTTTAAAGTCTGGTTCATTAGGAACCATTAAATA
66 AAAAAAAGGGTGTCAAAAATCTGGTTCATTAGGAACCATTAAATA
*
6166 TAGGTTAGATATGAAAAATAGTTTTATAATTAATAATTGATTAAAAT-GGAA-ACACAAAAATTA
1 TAGGTTAGATA--AAAAATAGTTTTATAATTAATAATTGATTAAAATAGAAATACACAAAAATTA
* *
6229 CGAAAAAAAAGGG-GTCAAAAATCTGGTTCATTTGGAACCATT
64 AG-AAAAAAAGGGTGTCAAAAATCTGGTTCATTAGGAACCATT
6271 TGAATGTGAC
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
110 46 0.50
111 13 0.14
112 33 0.36
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (110 bp):
TAGGTTAGATAAAAAATAGTTTTATAATTAATAATTGATTAAAATAGAAATACACAAAAATTAAG
AAAAAAAGGGTGTCAAAAATCTGGTTCATTAGGAACCATTAAATA
Found at i:6407 original size:21 final size:20
Alignment explanation
Indices: 6360--6410 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
6350 TATAATTTTT
* *
6360 ATATAATTAATATTTTAATA
1 ATATAATTATTAATTTAATA
*
6380 ATTTAATTATTAAATTTAATA
1 ATATAATTATT-AATTTAATA
6401 ATATAATTAT
1 ATATAATTAT
6411 ATTTATTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATAATTATTAATTTAATA
Found at i:6505 original size:32 final size:29
Alignment explanation
Indices: 6448--6506 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 29
6438 TAATTTAATA
*
6448 TTTTTATTATATTAAATAAAAATATTTAT
1 TTTTTAATATATTAAATAAAAATATTTAT
6477 TTTTTAATATATTTATAATTAAAAATATTT
1 TTTTTAATATA-TTA-AA-TAAAAATATTT
6507 TAATAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.38
30 3 0.12
31 2 0.08
32 11 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTTTAATATATTAAATAAAAATATTTAT
Found at i:6518 original size:15 final size:16
Alignment explanation
Indices: 6464--6510 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
6454 TTATATTAAA
**
6464 TAAAAATATTTATTTT
1 TAAAAATATTTATAAT
* *
6480 TTAATATATTTATAAT
1 TAAAAATATTTATAAT
6496 TAAAAATATTT-TAAT
1 TAAAAATATTTATAAT
6511 AAATAATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAAAATATTTATAAT
Found at i:6546 original size:25 final size:25
Alignment explanation
Indices: 6477--6546 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
6467 AAATATTTAT
* *
6477 TTTTTAATATATTTATAATTAAAAA
1 TTTTTAATTTATTAATAATTAAAAA
* * *
6502 TATTTTAA-TAAATAATAATTAAATA
1 T-TTTTAATTTATTAATAATTAAAAA
*
6527 TTTTTAATTTATTAAAAATT
1 TTTTTAATTTATTAATAATT
6547 TGATAAGTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
24 6 0.17
25 23 0.66
26 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTTTAATTTATTAATAATTAAAAA
Found at i:10527 original size:17 final size:17
Alignment explanation
Indices: 10474--10535 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
10464 AAATATAAAC
10474 ATATTAAAATTTATATAAAT
1 ATATTAAAATTTATAT---T
**
10494 ATATTATTA-TTATTATT
1 ATATTAAAATTTA-TATT
10511 ATATTAAAATTTATATT
1 ATATTAAAATTTATATT
10528 ATATTAAA
1 ATATTAAA
10536 TATAATATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
17 20 0.56
18 3 0.08
19 3 0.08
20 10 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTAAAATTTATATT
Found at i:10954 original size:15 final size:15
Alignment explanation
Indices: 10934--10987 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
10924 CGTATAAAAT
10934 TAATTTATTTTTATA
1 TAATTTATTTTTATA
10949 TAATTTTAATTTTTATA
1 TAA-TTT-ATTTTTATA
* *
10966 TAATTTATCTTTATT
1 TAATTTATTTTTATA
10981 TAATTTA
1 TAATTTA
10988 ATTATCATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 17 0.49
16 6 0.17
17 12 0.34
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
TAATTTATTTTTATA
Found at i:12146 original size:23 final size:24
Alignment explanation
Indices: 12119--12168 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
12109 AAAAGTACAT
*
12119 TATCTTTTTCTTCATTTTTTT-TA
1 TATCTTTTCCTTCATTTTTTTCTA
12142 TATCTTTTCCTTCATTTTTTTCTA
1 TATCTTTTCCTTCATTTTTTTCTA
12166 TAT
1 TAT
12169 AATATAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (24 bp):
TATCTTTTCCTTCATTTTTTTCTA
Found at i:12331 original size:21 final size:21
Alignment explanation
Indices: 12307--12373 Score: 89
Period size: 21 Copynumber: 3.0 Consensus size: 21
12297 ATGTTTGGTG
12307 AAAACAAAAAGAAAGAAAAAA
1 AAAACAAAAAGAAAGAAAAAA
12328 AAAACAAAAAGAAAGAAAAAA
1 AAAACAAAAAGAAAGAAAAAA
* *
12349 AGAAAGGAGAAAAAAAAGAAAAAA
1 A-AAA-CA-AAAAGAAAGAAAAAA
12373 A
1 A
12374 TTATATATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
21 22 0.54
22 3 0.07
23 1 0.02
24 15 0.37
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (21 bp):
AAAACAAAAAGAAAGAAAAAA
Found at i:12338 original size:17 final size:17
Alignment explanation
Indices: 12318--12365 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
12308 AAACAAAAAG
12318 AAAGAAAAAAAAAACAA
1 AAAGAAAAAAAAAACAA
*
12335 AAAGAAAGAAAAAAAGAA
1 AAAGAAA-AAAAAAACAA
*
12353 AGGAGAAAAAAAA
1 A-AAGAAAAAAAA
12366 GAAAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 15 0.56
19 5 0.19
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAAAACAA
Found at i:12793 original size:11 final size:11
Alignment explanation
Indices: 12777--12810 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
12767 GAAAAAGTTG
12777 AAAAGAAAAAA
1 AAAAGAAAAAA
*
12788 AAAAGAAAAAG
1 AAAAGAAAAAA
12799 AAAAGAAAAAA
1 AAAAGAAAAAA
12810 A
1 A
12811 GGAGAGAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:13374 original size:15 final size:14
Alignment explanation
Indices: 13350--13385 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
13340 TTTATTTGAT
13350 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
13364 AAAAGAAAGAAAAAG
1 AAAA-AAAGAAAAAG
13379 AAAAAAA
1 AAAAAAA
13386 TTTATGCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:13629 original size:23 final size:22
Alignment explanation
Indices: 13590--13643 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
13580 AGTAAAATAA
13590 AATTATATAAATTTCTACATGTT
1 AATTAT-TAAATTTCTACATGTT
* * *
13613 AATTATTATATTATCTATATTTT
1 AATTATTAAATT-TCTACATGTT
13636 AATATATT
1 AAT-TATT
13644 TGTATATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 17 0.65
24 4 0.15
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (22 bp):
AATTATTAAATTTCTACATGTT
Found at i:13919 original size:16 final size:16
Alignment explanation
Indices: 13898--13939 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
13888 TATTTTAAAC
*
13898 TAATTTTTTTTAATTA
1 TAATTTTATTTAATTA
13914 TAATTTTATTTAATTTA
1 TAATTTTATTTAA-TTA
*
13931 AAATTTTAT
1 TAATTTTAT
13940 AAATATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATTTTATTTAATTA
Found at i:13948 original size:17 final size:18
Alignment explanation
Indices: 13910--13955 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
13900 ATTTTTTTTA
* *
13910 ATTATAATTTTATTTAAT
1 ATTAAAATTTTATTAAAT
13928 -TTAAAATTTTA-TAAAT
1 ATTAAAATTTTATTAAAT
13944 ATTAAAACTTTT
1 ATTAAAA-TTTT
13956 CTACGAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTAAAATTTTATTAAAT
Found at i:14314 original size:42 final size:41
Alignment explanation
Indices: 14267--14355 Score: 117
Period size: 41 Copynumber: 2.1 Consensus size: 41
14257 GGTTTGAAAG
*
14267 TTTATATTATTATTTA-AAATAATATTATAAATAAAAAATATT
1 TTTATATTAATATTTATAAATAA-ATT-TAAATAAAAAATATT
* * *
14309 TTTATATTAATATTTATAATTAAATTTAAGTAAATAATATT
1 TTTATATTAATATTTATAAATAAATTTAAATAAAAAATATT
14350 TTTATA
1 TTTATA
14356 ATATAATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 19 0.45
42 18 0.43
43 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (41 bp):
TTTATATTAATATTTATAAATAAATTTAAATAAAAAATATT
Found at i:16131 original size:2 final size:2
Alignment explanation
Indices: 16124--16162 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
16114 AATTAATGTG
16124 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
16163 TTGACCATCT
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:18678 original size:2 final size:2
Alignment explanation
Indices: 18671--18700 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18661 AATAACCTGA
*
18671 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18701 TAATTCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19946 original size:2 final size:2
Alignment explanation
Indices: 19939--19986 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
19929 ATTAGGATGA
* * *
19939 AT AT AT AT AT AT AT AT AT GT GT GT 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
19981 AT AT AT
1 AT AT AT
19987 CTGTTAAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20109 original size:20 final size:20
Alignment explanation
Indices: 20084--20125 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
20074 TTAAATTGCA
20084 TTTTAATTTAGAATTTATAT
1 TTTTAATTTAGAATTTATAT
20104 TTTTAATTTAGAATTTATAT
1 TTTTAATTTAGAATTTATAT
20124 TT
1 TT
20126 GATGAGCTGA
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:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTAATTTAGAATTTATAT
Found at i:21345 original size:15 final size:16
Alignment explanation
Indices: 21321--21353 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
21311 TAAATAAATC
21321 TTATTAATAATAA-AA
1 TTATTAATAATAATAA
*
21336 TTATTTATAATAATAA
1 TTATTAATAATAATAA
21352 TT
1 TT
21354 TAAGAACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATTAATAATAATAA
Found at i:22001 original size:23 final size:22
Alignment explanation
Indices: 21959--22003 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
21949 AAAGTTATTC
*
21959 AAATTTTTTAATTATTTATTTT
1 AAATTTTTTAATTATATATTTT
21981 AAATTATTTT-ATTAATATATTTT
1 AAATT-TTTTAATT-ATATATTTT
22004 GAATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
AAATTTTTTAATTATATATTTT
Found at i:22099 original size:14 final size:14
Alignment explanation
Indices: 22065--22115 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
22055 TATTTTACTA
22065 TTTAATATAAATATAAT
1 TTTAATAT--ATAT-AT
22082 TTTAATATATATAT
1 TTTAATATATATAT
*
22096 TTTAATTTA-ATACT
1 TTTAATATATATA-T
22110 TTTAAT
1 TTTAAT
22116 GATTATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 3 0.09
14 17 0.53
15 4 0.12
17 8 0.25
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAATATATATAT
Found at i:22100 original size:31 final size:31
Alignment explanation
Indices: 21986--22101 Score: 80
Period size: 31 Copynumber: 3.7 Consensus size: 31
21976 ATTTTAAATT
*
21986 ATTTTATTA-ATATATTTTGAATATAAATATA
1 ATTTTAATATATATATTTT-AATATAAATATA
* *
22017 ATTTTAATAATGTATAATTATT-AT-TTAATATA
1 ATTTTAAT-ATATAT-ATT-TTAATATAAATATA
** * *
22049 A-ACTCATAT-TTTACTATTTAATATAAATATA
1 ATTTTAATATATATA-T-TTTAATATAAATATA
22080 ATTTTAATATATATATTTTAAT
1 ATTTTAATATATATATTTTAAT
22102 TTAATACTTT
Statistics
Matches: 63, Mismatches: 12, Indels: 20
0.66 0.13 0.21
Matches are distributed among these distances:
28 1 0.02
29 5 0.08
30 5 0.08
31 24 0.38
32 15 0.24
33 8 0.13
34 3 0.05
35 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (31 bp):
ATTTTAATATATATATTTTAATATAAATATA
Found at i:24028 original size:10 final size:10
Alignment explanation
Indices: 23997--24068 Score: 57
Period size: 10 Copynumber: 7.6 Consensus size: 10
23987 AAAAAAAGAA
23997 AAATTTATTT
1 AAATTTATTT
24007 AAA---ATTT
1 AAATTTATTT
*
24014 TAATTTATTT
1 AAATTTATTT
*
24024 AAA-TTATTA
1 AAATTTATTT
24033 AAATTTATTT
1 AAATTTATTT
24043 --ATTTAAATTT
1 AAATTT--ATTT
*
24053 TAATTTATTT
1 AAATTTATTT
24063 AAATTT
1 AAATTT
24069 TAATCAAACT
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
7 6 0.12
8 4 0.08
9 8 0.16
10 27 0.55
12 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
AAATTTATTT
Found at i:24046 original size:23 final size:22
Alignment explanation
Indices: 24004--24063 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
23994 GAAAAATTTA
24004 TTTAAAATTTTAATTTATTTAAAT
1 TTTAAAA-TTT-ATTTATTTAAAT
24028 TATTAAAATTTATTTATTTAAAT
1 T-TTAAAATTTATTTATTTAAAT
24051 TTT--AATTTATTTA
1 TTTAAAATTTATTTA
24064 AATTTTAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.29
22 2 0.06
23 13 0.37
24 4 0.11
25 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTAAAATTTATTTATTTAAAT
Found at i:24060 original size:16 final size:16
Alignment explanation
Indices: 23998--24072 Score: 78
Period size: 16 Copynumber: 4.2 Consensus size: 16
23988 AAAAAAGAAA
23998 AATTTATTTAAAATTTT
1 AATTTATTT-AAATTTT
24015 AATTTATTTAAATTATT
1 AATTTATTTAAATT-TT
24032 AAAATTTATTTATTTAAATTTT
1 ---A---ATTTATTTAAATTTT
24054 AATTTATTTAAATTTT
1 AATTTATTTAAATTTT
24070 AAT
1 AAT
24073 CAAACTTCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
16 23 0.45
17 11 0.22
19 1 0.02
20 1 0.02
22 2 0.04
23 13 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTATTTAAATTTT
Found at i:24106 original size:27 final size:27
Alignment explanation
Indices: 24068--24122 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
24058 TATTTAAATT
24068 TTAATCAAACTTCTACAGATCGCATGA
1 TTAATCAAACTTCTACAGATCGCATGA
24095 TTAATCAAACTTCTACAGATCGCATGA
1 TTAATCAAACTTCTACAGATCGCATGA
24122 T
1 T
24123 CGCATTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (27 bp):
TTAATCAAACTTCTACAGATCGCATGA
Found at i:24688 original size:94 final size:93
Alignment explanation
Indices: 24512--24695 Score: 314
Period size: 94 Copynumber: 2.0 Consensus size: 93
24502 ATATTATTAA
*
24512 GCTCCGCGTGAAACACGTGCAAAAATTATTAGGTGAGGTTTGAGAGATTTTCGGTCACAAAAACC
1 GCTCCACGTGAAACACGTGCAAAAATTATTAGGTGAGGTTTGAGAGATTTTCGGTCACAAAAACC
24577 ATGTTGAAAATACTAAATCTTGTCCTTG
66 ATGTTGAAAATACTAAATCTTGTCCTTG
* *
24605 GCTCCACGTGAAACACGTGGAATAATTATTAGGTGAGGTTTGAGGAGATTTTCGGTCACAAAAAC
1 GCTCCACGTGAAACACGTGCAAAAATTATTAGGTGAGGTTTGA-GAGATTTTCGGTCACAAAAAC
* *
24670 CATGTTGAGAATACTAAATGTTGTCC
65 CATGTTGAAAATACTAAATCTTGTCC
24696 CTTCCGAGTT
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
93 40 0.47
94 45 0.53
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (93 bp):
GCTCCACGTGAAACACGTGCAAAAATTATTAGGTGAGGTTTGAGAGATTTTCGGTCACAAAAACC
ATGTTGAAAATACTAAATCTTGTCCTTG
Found at i:24907 original size:19 final size:19
Alignment explanation
Indices: 24864--24918 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
24854 ATTTTAATAA
*
24864 TATAATATATTTAATTTAT
1 TATAATATATTAAATTTAT
24883 TGATAATATA-TAAATTTAT
1 T-ATAATATATTAAATTTAT
*
24902 GTATAAATTTATTAAAT
1 -TAT-AATATATTAAAT
24919 ATAAATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 11 0.37
20 14 0.47
21 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
TATAATATATTAAATTTAT
Found at i:24975 original size:2 final size:2
Alignment explanation
Indices: 24970--25004 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
24960 TTGTTCTTTG
24970 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 A
25005 ATTTGTACAA
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27648 original size:5 final size:5
Alignment explanation
Indices: 27638--27677 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
27628 CTTTATCTTT
*
27638 TTTTC TTTTC -TTTC TTTTC TTTTC TTGTTT TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC
27678 CCTTTCTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.13
5 23 0.74
6 4 0.13
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:27655 original size:14 final size:13
Alignment explanation
Indices: 27627--27669 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 13
27617 TTTTTATTTA
27627 TCTTTATCTTTTTT
1 TCTTT-TCTTTTTT
27641 TCTTTTCTTTCTTT
1 TCTTTTCTTT-TTT
27655 TCTTTTCTTGTTTT
1 TCTTTTCTT-TTTT
27669 T
1 T
27670 TTCTTTTCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.19
14 21 0.78
15 1 0.04
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (13 bp):
TCTTTTCTTTTTT
Found at i:27683 original size:22 final size:22
Alignment explanation
Indices: 27643--27685 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
27633 TCTTTTTTTC
*
27643 TTTTCTTTCTTTTCTTTTCTTG
1 TTTTCTTTCTTTTCCTTTCTTG
27665 TTTT-TTTCTTTTCCCTTTCTT
1 TTTTCTTTCTTTT-CCTTTCTT
27686 TCTCCCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTCTTTCTTTTCCTTTCTTG
Found at i:30632 original size:2 final size:2
Alignment explanation
Indices: 30625--30651 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30615 TGTTTTGCTT
30625 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 T
30652 GTTTGCTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.