Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2320
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: 53204
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Found at i:84 original size:3 final size:3
Alignment explanation
Indices: 78--122 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
68 TTTTAAAACT
78 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
123 ATCTTTCTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2023 original size:15 final size:16
Alignment explanation
Indices: 2003--2041 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1993 CTCCACTGAC
*
2003 TATTTTTTTAT-AATT
1 TATTTTTTCATAAATT
*
2018 TATTTTTACATAAATT
1 TATTTTTTCATAAATT
2034 TATTTTTT
1 TATTTTTT
2042 ATTTAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTTTTCATAAATT
Found at i:3341 original size:21 final size:22
Alignment explanation
Indices: 3312--3356 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
3302 AACTTTGAAG
*
3312 ATAAATTTTTAT-ATTTTAAAA
1 ATAAATTTTAATAATTTTAAAA
* *
3333 ATAATTTTTAATAATTTTTAAA
1 ATAAATTTTAATAATTTTAAAA
3355 AT
1 AT
3357 TTTAAATTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATAAATTTTAATAATTTTAAAA
Found at i:3355 original size:22 final size:20
Alignment explanation
Indices: 3315--3356 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
3305 TTTGAAGATA
3315 AATTTTTATATTTTAAAAAT
1 AATTTTTATATTTTAAAAAT
*
3335 AATTTTTAATAATTTTTAAAAT
1 AATTTTT-AT-ATTTTAAAAAT
3357 TTTAAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 2 0.11
22 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTTTATATTTTAAAAAT
Found at i:3641 original size:13 final size:13
Alignment explanation
Indices: 3623--3653 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3613 TTGCCACCAA
3623 AAAAATAAAAAAT
1 AAAAATAAAAAAT
*
3636 AAAAATAAAAATT
1 AAAAATAAAAAAT
3649 AAAAA
1 AAAAA
3654 GAGAGAGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:6717 original size:2 final size:2
Alignment explanation
Indices: 6710--6745 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6700 TTATCTAATA
6710 AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6746 CTTACCTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7170 original size:18 final size:18
Alignment explanation
Indices: 7147--7190 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
7137 ATAAGTGTAA
7147 AATTAATTAATTTTAATT
1 AATTAATTAATTTTAATT
* *
7165 AATTAATTATTTTTATTT
1 AATTAATTAATTTTAATT
*
7183 TATTAATT
1 AATTAATT
7191 TTTTATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTAATTAATTTTAATT
Found at i:7187 original size:22 final size:23
Alignment explanation
Indices: 7156--7199 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
7146 AAATTAATTA
7156 ATTTTAATTAATTAATTATTTTT
1 ATTTTAATTAATTAATTATTTTT
**
7179 ATTTT-ATTAATTTTTTATTTT
1 ATTTTAATTAATTAATTATTTT
7200 AATTAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTTAATTAATTAATTATTTTT
Found at i:7195 original size:16 final size:17
Alignment explanation
Indices: 7163--7205 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
7153 TTAATTTTAA
7163 TTAATTAATTATTTTTATT
1 TTAATTAA-T-TTTTTATT
7182 TT-ATTAATTTTTTATT
1 TTAATTAATTTTTTATT
7198 TTAATTAA
1 TTAATTAA
7206 ACATAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 10 0.43
17 6 0.26
18 5 0.22
19 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTAATTAATTTTTTATT
Found at i:7397 original size:18 final size:18
Alignment explanation
Indices: 7363--7397 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7353 ATTTAAATAG
* *
7363 ATATAAAATAATTTATAA
1 ATATAAAAAAATATATAA
7381 ATATAAAAAAATATATA
1 ATATAAAAAAATATATA
7398 TTTATTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATAAAAAAATATATAA
Found at i:10013 original size:2 final size:2
Alignment explanation
Indices: 10006--10041 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
9996 GATTCAAATA
10006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10042 GTCGAATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10896 original size:14 final size:14
Alignment explanation
Indices: 10859--10898 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
10849 TTTCACCTTT
10859 TTTTTA-AATTAAA
1 TTTTTATAATTAAA
10872 TTTTTATTAATTAAA
1 TTTTTA-TAATTAAA
10887 TTTTTATAATTA
1 TTTTTATAATTA
10899 GTATGTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.24
14 6 0.24
15 13 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTTATAATTAAA
Found at i:11424 original size:17 final size:17
Alignment explanation
Indices: 11397--11429 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11387 TTCTTAATAT
11397 AATATTTAATA-AACTA
1 AATATTTAATATAACTA
11413 AATATGTTAATATAACT
1 AATAT-TTAATATAACT
11430 TTCTCGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (17 bp):
AATATTTAATATAACTA
Found at i:11510 original size:34 final size:34
Alignment explanation
Indices: 11472--11587 Score: 119
Period size: 34 Copynumber: 3.4 Consensus size: 34
11462 ATTGATATTC
* * *
11472 ATAATTCATGAATCTTTATGCTACAAGAATGTCT
1 ATAATTCATGAATCTTCATGATACATGAATGTCT
* *
11506 ATAATGCATGAAT-TTCAT-ATTACATGAATGCCT
1 ATAATTCATGAATCTTCATGA-TACATGAATGTCT
* * * *
11539 ATAATTTATGAATCTTCATGATATATGAATATCA
1 ATAATTCATGAATCTTCATGATACATGAATGTCT
*
11573 ATAATTCATAAATCT
1 ATAATTCATGAATCT
11588 CTGTAATACA
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
33 26 0.39
34 39 0.59
35 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (34 bp):
ATAATTCATGAATCTTCATGATACATGAATGTCT
Found at i:11541 original size:33 final size:34
Alignment explanation
Indices: 11472--11557 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 34
11462 ATTGATATTC
* * ** *
11472 ATAATTCATGAATCTTTATGCTACAAGAATGTCT
1 ATAATGCATGAATCTTCATATTACAAGAATGCCT
*
11506 ATAATGCATGAAT-TTCATATTACATGAATGCCT
1 ATAATGCATGAATCTTCATATTACAAGAATGCCT
**
11539 ATAATTTATGAATCTTCAT
1 ATAATGCATGAATCTTCAT
11558 GATATATGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 26 0.60
34 17 0.40
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (34 bp):
ATAATGCATGAATCTTCATATTACAAGAATGCCT
Found at i:12123 original size:19 final size:19
Alignment explanation
Indices: 12099--12139 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
12089 AAATAAAATC
*
12099 TTTAATTGAACCGAAATAT
1 TTTAATTGAACCAAAATAT
*
12118 TTTAATTGAACCAAAATGT
1 TTTAATTGAACCAAAATAT
12137 TTT
1 TTT
12140 TATCAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (19 bp):
TTTAATTGAACCAAAATAT
Found at i:12834 original size:73 final size:73
Alignment explanation
Indices: 12698--12840 Score: 159
Period size: 73 Copynumber: 2.0 Consensus size: 73
12688 ATGGTAACGC
* * ** *
12698 ATTTATTAAATCAACTGACTATTTTTTATTTTAAACTGAATTTCAACTTATTTATTATATTAATT
1 ATTTATTAAATCAACTGACTATTTTCTATTTTAAACTGAAATTCAACTTATAAATAATATTAATT
*
12763 TTAAATGT
66 ATAAATGT
*
12771 ATTTATTAAATCAA-TGTA-TAATTTTCTATTTTAAACT-AAATT-AACTGTATAAATCAATTTT
1 ATTTATTAAATCAACTG-ACT-ATTTTCTATTTTAAACTGAAATTCAACT-TATAAAT-AATATT
12832 AATTATAAA
62 AATTATAAA
12841 ATAAATTATA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
71 4 0.07
72 12 0.20
73 43 0.73
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (73 bp):
ATTTATTAAATCAACTGACTATTTTCTATTTTAAACTGAAATTCAACTTATAAATAATATTAATT
ATAAATGT
Found at i:14294 original size:2 final size:2
Alignment explanation
Indices: 14287--14323 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
14277 TCCACATTGT
14287 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
14324 TAACATGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17270 original size:19 final size:19
Alignment explanation
Indices: 17246--17294 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
17236 TACTATAAGA
*
17246 AAGAAAAAAAAAAAGTAAT
1 AAGAAAAAAAAAAAGTAAC
17265 AAG-AAAAAAAAAAGTAAC
1 AAGAAAAAAAAAAAGTAAC
17283 AAGAAAATAAAA
1 AAGAAAA-AAAA
17295 GAGAACCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 17 0.63
19 6 0.22
20 4 0.15
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.08
Consensus pattern (19 bp):
AAGAAAAAAAAAAAGTAAC
Found at i:18861 original size:33 final size:32
Alignment explanation
Indices: 18824--18887 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 32
18814 TATTTAAAAT
* *
18824 ATAAATAAAT-TATTTTATATTTATTATTTTTAA
1 ATAAATAAATATAATTTA-ATTCA-TATTTTTAA
*
18857 ATAAATTAATATAATTTAATTCATATTTTTA
1 ATAAATAAATATAATTTAATTCATATTTTTA
18888 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 8 0.30
33 13 0.48
34 6 0.22
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (32 bp):
ATAAATAAATATAATTTAATTCATATTTTTAA
Found at i:19321 original size:4 final size:4
Alignment explanation
Indices: 19312--19336 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
19302 TTTCTGAAGA
19312 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
19337 TATTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:20036 original size:2 final size:2
Alignment explanation
Indices: 20029--20053 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20019 AATATTAATA
20029 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
20054 GTTTTTTGTC
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:22102 original size:5 final size:5
Alignment explanation
Indices: 22094--22118 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
22084 CTGTTGGGGA
22094 GGAGG GGAGG GGAGG GGAGG GGAGG
1 GGAGG GGAGG GGAGG GGAGG GGAGG
22119 TGTGGTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (5 bp):
GGAGG
Found at i:24198 original size:23 final size:23
Alignment explanation
Indices: 24172--24226 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
24162 AATTTAGACA
24172 TGCCATTACTGATAATGCCATCT
1 TGCCATTACTGATAATGCCATCT
*
24195 TGCCATTACTGATAATGCCGTCT
1 TGCCATTACTGATAATGCCATCT
*
24218 TACCATTAC
1 TGCCATTAC
24227 CACCATGTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (23 bp):
TGCCATTACTGATAATGCCATCT
Found at i:25619 original size:16 final size:17
Alignment explanation
Indices: 25587--25620 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25577 TAAATATAAT
*
25587 TAAATATCTTATAATTA
1 TAAATATATTATAATTA
25604 TAAATATATT-TAATTA
1 TAAATATATTATAATTA
25620 T
1 T
25621 TTTTAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATATATTATAATTA
Found at i:27114 original size:23 final size:23
Alignment explanation
Indices: 27084--27130 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
27074 AAACAAAAAC
27084 AAAAAAAGAAAATTATTGGCAAA
1 AAAAAAAGAAAATTATTGGCAAA
27107 AAAAAAAGAAAATTATTGGCAAA
1 AAAAAAAGAAAATTATTGGCAAA
27130 A
1 A
27131 CAATAGACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.66, C:0.04, G:0.13, T:0.17
Consensus pattern (23 bp):
AAAAAAAGAAAATTATTGGCAAA
Found at i:28296 original size:27 final size:28
Alignment explanation
Indices: 28253--28316 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
28243 CACTTGTATT
* *
28253 AATAAAAAATTATTATTTTA-ATTTTAAA
1 AATAAAAAATGATTATTTTAGA-ATTAAA
28281 AATAAAAAATGA-TATTTTAGGAATTAAA
1 AATAAAAAATGATTATTTTA-GAATTAAA
28309 AATAAAAA
1 AATAAAAA
28317 TATTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 7 0.22
28 24 0.75
29 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (28 bp):
AATAAAAAATGATTATTTTAGAATTAAA
Found at i:28474 original size:31 final size:30
Alignment explanation
Indices: 28413--28474 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
28403 TAAAATATTT
*
28413 TAAATATTAAATATATAATTTTAATAATAAA
1 TAAATATTAAATATATAATATT-ATAATAAA
28444 TAAATATTAAATATAATAAATATT-TAATAAA
1 TAAATATTAAATAT-AT-AATATTATAATAAA
28475 AGTATGCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 21 0.75
32 2 0.07
33 5 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
TAAATATTAAATATATAATATTATAATAAA
Found at i:33903 original size:17 final size:18
Alignment explanation
Indices: 33882--33947 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 18
33872 TTTTATTTTT
33882 TATTTTTTAA-AATTTTAA
1 TATTTTTTAATAA-TTTAA
33900 -A-TTTTTAATAATTTAA
1 TATTTTTTAATAATTTAA
33916 TA-TTTTT-AT-ATTTAA
1 TATTTTTTAATAATTTAA
*
33931 TTTATTTTTAAT-ATTTA
1 TAT-TTTTTAATAATTTA
33948 CATCATAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
15 7 0.17
16 14 0.33
17 14 0.33
18 7 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTTTTAATAATTTAA
Found at i:33904 original size:16 final size:17
Alignment explanation
Indices: 33885--33947 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
33875 TATTTTTTAT
33885 TTTTTAA-AATTTTAA-A
1 TTTTTAATAA-TTTAATA
33901 TTTTTAATAATTTAATA
1 TTTTTAATAATTTAATA
33918 TTTTT-AT-ATTTAATTTA
1 TTTTTAATAATTTAA--TA
33935 TTTTTAAT-ATTTA
1 TTTTTAATAATTTA
33948 CATCATAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.14
16 14 0.33
17 15 0.36
18 7 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTTAATAATTTAATA
Found at i:33933 original size:20 final size:18
Alignment explanation
Indices: 33900--33947 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
33890 AAAATTTTAA
33900 ATTTTTAATAATTTAA--T
1 ATTTTTAAT-ATTTAATTT
33917 ATTTTT-ATATTTAATTT
1 ATTTTTAATATTTAATTT
33934 ATTTTTAATATTTA
1 ATTTTTAATATTTA
33948 CATCATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.21
16 2 0.07
17 13 0.46
18 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTAATATTTAATTT
Found at i:33998 original size:29 final size:25
Alignment explanation
Indices: 33964--34022 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 25
33954 AATATTATAT
*
33964 TTATATGATATAATTATATAAATATAAA
1 TTATATGAAATAATT-TA-AAA-ATAAA
*
33992 TATATATTAAATAATTTAAAAATAAA
1 T-TATATGAAATAATTTAAAAATAAA
34018 TTATA
1 TTATA
34023 CAAAACTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 4 0.14
26 6 0.21
27 3 0.11
28 3 0.11
29 12 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
TTATATGAAATAATTTAAAAATAAA
Found at i:34128 original size:29 final size:28
Alignment explanation
Indices: 34071--34132 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
34061 TTTTTATAAA
* ** *
34071 TAAATTTTATTTTTTATTTATTTTTTTT
1 TAAATTTAATTTTTTATTTAAATTCTTT
34099 TAAATTTAATATTTTTATTTAAATTCTTT
1 TAAATTTAAT-TTTTTATTTAAATTCTTT
34128 TAAAT
1 TAAAT
34133 AAATTACATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 9 0.31
29 20 0.69
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (28 bp):
TAAATTTAATTTTTTATTTAAATTCTTT
Found at i:35575 original size:2 final size:2
Alignment explanation
Indices: 35568--35592 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35558 GTCGACATAC
35568 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
35593 GATTCATTTG
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:36126 original size:17 final size:18
Alignment explanation
Indices: 36100--36134 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
36090 TATTCAAAAT
*
36100 TTTTTAAAATTTATATAA
1 TTTTTAAAATTTAAATAA
36118 TTTTT-AAATTTAAATAA
1 TTTTTAAAATTTAAATAA
36135 ATAACTAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTTAAAATTTAAATAA
Found at i:37344 original size:2 final size:2
Alignment explanation
Indices: 37337--37361 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37327 ACAGCGAATC
37337 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
37362 ATCTTTTAAA
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:40601 original size:4 final size:4
Alignment explanation
Indices: 40592--40620 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
40582 AAATAATCTG
40592 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
40621 TTTTTTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:40999 original size:15 final size:15
Alignment explanation
Indices: 40981--41037 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
40971 AAAACATACT
40981 AAAAAAAATATTATG
1 AAAAAAAATATTATG
*
40996 AAAAAAAAACACTTTAT-
1 -AAAAAAAATA--TTATG
*
41013 TAAAAAAATATTATG
1 AAAAAAAATATTATG
*
41028 AATAAAAATA
1 AAAAAAAATA
41038 AATAAATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
14 4 0.12
15 8 0.24
16 17 0.52
18 4 0.12
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.26
Consensus pattern (15 bp):
AAAAAAAATATTATG
Found at i:41035 original size:18 final size:18
Alignment explanation
Indices: 40980--41041 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
40970 AAAAACATAC
40980 TAAAAAAAATATTATGAA
1 TAAAAAAAATATTATGAA
40998 -AAAAAAACACT-TTAT---
1 TAAAAAAA-A-TATTATGAA
41013 T-AAAAAAATATTATGAA
1 TAAAAAAAATATTATGAA
41030 TAAAAATAAATA
1 TAAAAA-AAATA
41042 AATAAAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 17
0.67 0.00 0.33
Matches are distributed among these distances:
13 1 0.03
14 5 0.14
15 6 0.17
17 8 0.23
18 9 0.26
19 6 0.17
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (18 bp):
TAAAAAAAATATTATGAA
Found at i:41367 original size:14 final size:14
Alignment explanation
Indices: 41350--41382 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
41340 TAAGTTTTTT
41350 TTTTAAAATTTTAA
1 TTTTAAAATTTTAA
*
41364 TTTTAAATTTTTAA
1 TTTTAAAATTTTAA
41378 TTTTA
1 TTTTA
41383 TTAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAAAATTTTAA
Found at i:44653 original size:3 final size:3
Alignment explanation
Indices: 44645--44735 Score: 155
Period size: 3 Copynumber: 30.3 Consensus size: 3
44635 TTTTAGCACC
* *
44645 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
44693 ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
44736 AAGTAGTTTC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:44960 original size:21 final size:21
Alignment explanation
Indices: 44934--44993 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
44924 AATTTTATTT
*
44934 TTAATTTTATATTTTAA-AATA
1 TTAATTTTATATATTAATAA-A
*
44955 TTAATTTTTTATATTAATAAA
1 TTAATTTTATATATTAATAAA
44976 -TAGATTTTATATAATTAA
1 TTA-ATTTTATAT-ATTAA
44994 ATTTAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 2 0.06
21 24 0.73
22 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTAATTTTATATATTAATAAA
Found at i:46068 original size:19 final size:20
Alignment explanation
Indices: 46035--46073 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
46025 TTTATATTTA
**
46035 AATATAAAATGTT-AATATT
1 AATATAAAAAATTAAATATT
46054 AATATAAAAAATTAAATATT
1 AATATAAAAAATTAAATATT
46074 TTAATATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AATATAAAAAATTAAATATT
Found at i:46098 original size:27 final size:28
Alignment explanation
Indices: 45991--46098 Score: 86
Period size: 27 Copynumber: 4.1 Consensus size: 28
45981 AACTTGATTG
* *
45991 TATTTAAAT-TATATTTAATTAATAAAA
1 TATTTTAATATATATTTAAATAATAAAA
* *
46018 T-TTTTTATTTATATTTAAAT-AT-AAA
1 TATTTTAATATATATTTAAATAATAAAA
* * * *
46043 -ATGTTAATAT-TAATATAAAAAATTAAA
1 TATTTTAATATAT-ATTTAAATAATAAAA
46070 TATTTTAATATAT-TTTAAATAATAAAA
1 TATTTTAATATATATTTAAATAATAAAA
46097 TA
1 TA
46099 AATTTTTGAA
Statistics
Matches: 62, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
24 1 0.02
25 15 0.24
26 9 0.15
27 27 0.44
28 9 0.15
29 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATATATATTTAAATAATAAAA
Found at i:46111 original size:31 final size:32
Alignment explanation
Indices: 46052--46112 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 32
46042 AATGTTAATA
46052 TTAATATAAAAAATTAAATATTTTAATATATT
1 TTAATATAAAAAATTAAATATTTTAATATATT
46084 TTAA-ATAATAAAA-TAAAT-TTTTGAATATA
1 TTAATATAA-AAAATTAAATATTTT-AATATA
46113 AACACACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 4 0.15
31 15 0.56
32 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (32 bp):
TTAATATAAAAAATTAAATATTTTAATATATT
Found at i:47225 original size:4 final size:4
Alignment explanation
Indices: 47214--47243 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
47204 AAAATAAAAG
47214 TAAA -AAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
47244 TTGCTCATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:48333 original size:35 final size:35
Alignment explanation
Indices: 48294--48369 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
48284 TTTGAGTATT
48294 TTTTATTTTCTTTTAAAATA-TTTCCTTAATTTTC
1 TTTTATTTTCTTTTAAAATACTTTCCTTAATTTTC
*** *
48328 ATTTTA-TTTCTTTTACTTTACTTTCCTTTATTTTC
1 -TTTTATTTTCTTTTAAAATACTTTCCTTAATTTTC
48363 TTTTATT
1 TTTTATT
48370 ATCGTTTATC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
34 16 0.46
35 19 0.54
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.68
Consensus pattern (35 bp):
TTTTATTTTCTTTTAAAATACTTTCCTTAATTTTC
Found at i:49919 original size:12 final size:12
Alignment explanation
Indices: 49902--49935 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
49892 ATAAGACTTG
49902 ATAATATTAAAC
1 ATAATATTAAAC
*
49914 ATAATA-TAAAT
1 ATAATATTAAAC
49925 ATAATATTAAA
1 ATAATATTAAA
49936 AAATAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATATTAAAC
Found at i:49950 original size:24 final size:23
Alignment explanation
Indices: 49902--49946 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
49892 ATAAGACTTG
*
49902 ATAATATTAAACATAATATAAAT
1 ATAATATTAAAAATAATATAAAT
49925 ATAATATTAAAAAATAAT-TAAA
1 ATAATATT-AAAAATAATATAAA
49947 ATATGATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAATATTAAAAATAATATAAAT
Found at i:50084 original size:13 final size:13
Alignment explanation
Indices: 50066--50091 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50056 ATTATGATAT
50066 AATAAAATATAAA
1 AATAAAATATAAA
50079 AATAAAATATAAA
1 AATAAAATATAAA
50092 TACATAAATC
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAAATATAAA
Found at i:51399 original size:2 final size:2
Alignment explanation
Indices: 51392--51422 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
51382 TATAATATTC
51392 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51423 AAAATTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52027 original size:9 final size:9
Alignment explanation
Indices: 52013--52048 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
52003 CCCTGACCAC
52013 ATTTTTTTA
1 ATTTTTTTA
52022 A-TTTTTTA
1 ATTTTTTTA
52030 ATTTTTTTTA
1 A-TTTTTTTA
52040 ATTTTTTTA
1 ATTTTTTTA
52049 TCAATGGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.32
9 9 0.36
10 8 0.32
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:52036 original size:10 final size:10
Alignment explanation
Indices: 52014--52047 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
52004 CCTGACCACA
52014 TTTTTTTAA-
1 TTTTTTTAAT
52023 -TTTTTTAAT
1 TTTTTTTAAT
52032 TTTTTTTAAT
1 TTTTTTTAAT
52042 TTTTTT
1 TTTTTT
52048 ATCAATGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
10 15 0.65
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTAAT
Found at i:52422 original size:21 final size:21
Alignment explanation
Indices: 52398--52437 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
52388 ATTATTATGC
* *
52398 AATTATTTAATTAAAAAATGA
1 AATTATATAAATAAAAAATGA
52419 AATTATATAAATAAAAAAT
1 AATTATATAAATAAAAAAT
52438 TTTTCATCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
AATTATATAAATAAAAAATGA
Found at i:52735 original size:2 final size:2
Alignment explanation
Indices: 52715--52759 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
52705 ATTGATTTAA
* *
52715 AT AT AA AT AT A- AA 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
52756 AT AT
1 AT AT
52760 TAGTAGAACG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Done.