Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3145
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: 65746
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3855 original size:5 final size:5
Alignment explanation
Indices: 3845--3881 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
3835 TTAACTAAGT
3845 AAATA AAAT- AAATA AAAT- AAATA AAATAA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAAT-A AAATA AAA
3882 CTGTACAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.28
5 16 0.55
6 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:3858 original size:9 final size:9
Alignment explanation
Indices: 3844--3874 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
3834 TTTAACTAAG
3844 TAAATAAAA
1 TAAATAAAA
3853 TAAATAAAA
1 TAAATAAAA
3862 TAAATAAAA
1 TAAATAAAA
3871 TAAA
1 TAAA
3875 AATAAAACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
TAAATAAAA
Found at i:12363 original size:12 final size:13
Alignment explanation
Indices: 12346--12377 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
12336 ACTAAGTAAG
12346 TAAATAAATA-AA
1 TAAATAAATATAA
12358 TAAATAAATATAA
1 TAAATAAATATAA
12371 -AAATAAA
1 TAAATAAA
12378 ACTTTACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 17 0.89
13 2 0.11
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAATAAATATAA
Found at i:14451 original size:20 final size:19
Alignment explanation
Indices: 14428--14492 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
14418 AAGCTCAAAC
14428 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
14448 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
14468 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
14488 GAGCT
1 GAGCT
14493 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:16304 original size:33 final size:33
Alignment explanation
Indices: 16266--16328 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
16256 GATTACTCAC
16266 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
16299 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
16329 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:16355 original size:27 final size:27
Alignment explanation
Indices: 16325--16422 Score: 78
Period size: 27 Copynumber: 3.6 Consensus size: 27
16315 TCAAGCTCTC
16325 TTTCAATTTCTTTTTTCGCTTTTTCTT
1 TTTCAATTTCTTTTTTCGCTTTTTCTT
*
16352 TTTCAATTTTCTTTTCTT--CATTTTCTT
1 TTTCAA-TTTCTTTT-TTCGCTTTTTCTT
* *
16379 TTTC--TCTCATTTTTCGATTTCTTTTTCTT
1 TTTCAATTTCTTTTTTCG----CTTTTTCTT
*
16408 TTGCAATTTCTTTTT
1 TTTCAATTTCTTTTT
16423 CTTCTTCGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
23 2 0.04
24 6 0.11
27 18 0.33
28 8 0.15
29 13 0.24
31 7 0.13
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.69
Consensus pattern (27 bp):
TTTCAATTTCTTTTTTCGCTTTTTCTT
Found at i:16381 original size:15 final size:15
Alignment explanation
Indices: 16345--16391 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 15
16335 TTTTTTCGCT
*
16345 TTTTCTTTTTC--AA
1 TTTTCTTTTTCTTCA
16358 TTTTC-TTTTCTTCA
1 TTTTCTTTTTCTTCA
16372 TTTTCTTTTTCTCTCA
1 TTTTCTTTTTCT-TCA
16388 TTTT
1 TTTT
16392 TCGATTTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 5 0.17
13 5 0.17
14 6 0.21
15 6 0.21
16 7 0.24
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTCTTTTTCTTCA
Found at i:16390 original size:16 final size:14
Alignment explanation
Indices: 16345--16391 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
16335 TTTTTTCGCT
16345 TTTTC-TTT-TTCAA
1 TTTTCTTTTCTTC-A
16358 TTTTCTTTTCTTCA
1 TTTTCTTTTCTTCA
16372 TTTTCTTTTTCTCTCA
1 TTTTC-TTTTCT-TCA
16388 TTTT
1 TTTT
16392 TCGATTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.17
14 9 0.30
15 9 0.30
16 7 0.23
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCTTTTCTTCA
Found at i:16435 original size:18 final size:17
Alignment explanation
Indices: 16389--16446 Score: 71
Period size: 18 Copynumber: 3.3 Consensus size: 17
16379 TTTCTCTCAT
16389 TTTTCGATTTCTTTTTC
1 TTTTCGATTTCTTTTTC
*
16406 TTTTGCAATTTCTTTTTC
1 TTTT-CGATTTCTTTTTC
* *
16424 TTCTTCGTTTTCTTTTTG
1 TT-TTCGATTTCTTTTTC
16442 TTTTC
1 TTTTC
16447 TTTCAATTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
17 7 0.20
18 26 0.74
19 2 0.06
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (17 bp):
TTTTCGATTTCTTTTTC
Found at i:16462 original size:6 final size:6
Alignment explanation
Indices: 16343--16449 Score: 58
Period size: 6 Copynumber: 17.7 Consensus size: 6
16333 TCTTTTTTCG
* * *
16343 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT C--TCT CATTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT C-TTTTT
** * ** * *
16393 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
16441 -GTTTT CTTT
1 CTTTTT CTTT
16450 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 23, Indels: 12
0.67 0.21 0.11
Matches are distributed among these distances:
4 3 0.04
5 4 0.06
6 50 0.69
7 12 0.17
8 3 0.04
ACGTcount: A:0.07, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:17504 original size:16 final size:15
Alignment explanation
Indices: 17459--17507 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
17449 CTCGCAAGAC
17459 TTTTCACTTCTTTTT
1 TTTTCACTTCTTTTT
*
17474 TTTTAAC-TCGATTTTT
1 TTTTCACTTC--TTTTT
*
17490 TTGTCACTTCTTTTT
1 TTTTCACTTCTTTTT
17505 TTT
1 TTT
17508 AAATTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 2 0.07
15 13 0.48
16 10 0.37
17 2 0.07
ACGTcount: A:0.10, C:0.16, G:0.04, T:0.69
Consensus pattern (15 bp):
TTTTCACTTCTTTTT
Found at i:18971 original size:30 final size:30
Alignment explanation
Indices: 18911--18972 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
18901 TCAGCTGAAC
* * *
18911 AAACATTAATATAATTTAGACACACTAATT
1 AAACATAAATATAAATTAGACAAACTAATT
*
18941 AAACATAAAT-TAAATTAGACAAATTAAATT
1 AAACATAAATATAAATTAGACAAACT-AATT
18971 AA
1 AA
18973 CAAGACACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (30 bp):
AAACATAAATATAAATTAGACAAACTAATT
Found at i:19121 original size:20 final size:19
Alignment explanation
Indices: 19098--19162 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
19088 AAGCTCAAAC
19098 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
19118 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
19138 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
19158 GAGCT
1 GAGCT
19163 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:19915 original size:30 final size:30
Alignment explanation
Indices: 19881--19977 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19871 AGCTCACTCC
*
19881 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * *
19911 TAGCTCAACTTTAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
19941 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
19971 TAGCTCA
1 TAGCTCA
19978 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 47 0.90
31 5 0.10
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:22344 original size:20 final size:20
Alignment explanation
Indices: 22321--22368 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
22311 AGCTCCGTCC
22321 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
22341 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
22361 AGCTCAAC
1 AGCTCAAC
22369 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:27222 original size:30 final size:30
Alignment explanation
Indices: 27188--27284 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
27178 TAAACTAAAA
* *
27188 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
27218 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
27248 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
27278 TGAGCTA
1 TGAGCTA
27285 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 47 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:28165 original size:22 final size:22
Alignment explanation
Indices: 28114--28179 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
28104 GGTATTTGGG
* *
28114 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
28135 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
28157 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
28180 TCAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:31092 original size:12 final size:12
Alignment explanation
Indices: 31077--31107 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
31067 TTCTTTTTGC
31077 TTTTCAAAGGCT
1 TTTTCAAAGGCT
31089 TTTTCAAAGGCT
1 TTTTCAAAGGCT
31101 TTTTCAA
1 TTTTCAA
31108 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:31165 original size:5 final size:5
Alignment explanation
Indices: 31155--31211 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
31145 CTCTTGCCTC
*
31155 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
31202 TCTTT TCTTT
1 TCTTT TCTTT
31212 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:31195 original size:15 final size:14
Alignment explanation
Indices: 31155--31211 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
31145 CTCTTGCCTC
*
31155 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
31170 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
31185 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
31202 TCTTTTCTTT
1 TCTTTTCTTT
31212 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:31212 original size:21 final size:21
Alignment explanation
Indices: 31155--31222 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
31145 CTCTTGCCTC
* *
31155 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
31176 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
31197 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
31217 CTCTTT
1 -TCTTT
31223 ACAAAAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:33777 original size:30 final size:30
Alignment explanation
Indices: 33743--33839 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
33733 TAAACTAAAA
* *
33743 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
33773 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
33803 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
33833 TGAGCTA
1 TGAGCTA
33840 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 47 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:35411 original size:15 final size:15
Alignment explanation
Indices: 35391--35441 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
35381 CGTATCTTGA
35391 GTTTCTTTATTCTGG
1 GTTTCTTTATTCTGG
*
35406 GTTTCTCTA-TCTTGG
1 GTTTCTTTATTC-TGG
*
35421 ATTTCTTTATTC-GG
1 GTTTCTTTATTCTGG
*
35435 TTTTCTT
1 GTTTCTT
35442 GTTATCTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 10 0.33
15 18 0.60
16 2 0.07
ACGTcount: A:0.08, C:0.16, G:0.16, T:0.61
Consensus pattern (15 bp):
GTTTCTTTATTCTGG
Found at i:35418 original size:30 final size:29
Alignment explanation
Indices: 35383--35440 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
35373 TATAGTATCG
35383 TATCTT-GAGTTTCTTTATTCTGGGTTTCTC
1 TATCTTGGA-TTTCTTTATTC-GGGTTTCTC
*
35413 TATCTTGGATTTCTTTATTCGGTTTTCT
1 TATCTTGGATTTCTTTATTCGGGTTTCT
35441 TGTTATCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.27
30 17 0.65
31 2 0.08
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.59
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGGTTTCTC
Found at i:38741 original size:21 final size:21
Alignment explanation
Indices: 38717--38765 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
38707 AAAAATTCGA
**
38717 AAAAAAATAAAAAAAAAGTTT
1 AAAAAAATAAAAAAAAACCTT
* *
38738 AAAAAATTAGAAAAAAACCTT
1 AAAAAAATAAAAAAAAACCTT
38759 AAAAAAA
1 AAAAAAA
38766 ATTTTGACCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (21 bp):
AAAAAAATAAAAAAAAACCTT
Found at i:39633 original size:25 final size:25
Alignment explanation
Indices: 39599--39654 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
39589 AAGGGATTGG
39599 ATCTTCTAGATACATTCATGCATGA
1 ATCTTCTAGATACATTCATGCATGA
39624 ATCTTCTAGATACATTCATGCATGA
1 ATCTTCTAGATACATTCATGCATGA
39649 ATCTTC
1 ATCTTC
39655 ATCATTCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (25 bp):
ATCTTCTAGATACATTCATGCATGA
Found at i:39660 original size:21 final size:23
Alignment explanation
Indices: 39599--39664 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 23
39589 AAGGGATTGG
39599 ATCTTCTAGATACATTCATGCATGA
1 ATCTTC-A-ATACATTCATGCATGA
39624 ATCTTCTAGATACATTCATGCATGA
1 ATCTTC-A-ATACATTCATGCATGA
39649 ATCTTC-AT-CATTCATG
1 ATCTTCAATACATTCATG
39665 TAACCGAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.20
22 2 0.05
25 31 0.76
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (23 bp):
ATCTTCAATACATTCATGCATGA
Found at i:40493 original size:14 final size:15
Alignment explanation
Indices: 40451--40495 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
40441 TTTTATTGCT
*
40451 TCTCTTTTCTTTTGA
1 TCTCTTTTCTTTTCA
40466 TCTCCTTTTACTTTTCA
1 TCT-CTTTT-CTTTTCA
40483 TCT-TTTTCTTTTC
1 TCTCTTTTCTTTTC
40496 TCGTCTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
16 5 0.19
17 9 0.33
ACGTcount: A:0.07, C:0.24, G:0.02, T:0.67
Consensus pattern (15 bp):
TCTCTTTTCTTTTCA
Found at i:43149 original size:30 final size:30
Alignment explanation
Indices: 43064--43151 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
43054 TAAACTAAAA
* * *
43064 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGG
* * * * *
43094 TGAGCTGAGATTAAACTCCTAAGCTGAAGG
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGG
*
43124 TGAGCTAAGGTTTAGCTCGTGAGCTGAA
1 TGAGCTAAGATTTAGCTCGTGAGCTGAA
43152 TATAAGCTAG
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGG
Found at i:43263 original size:10 final size:10
Alignment explanation
Indices: 43248--43305 Score: 55
Period size: 10 Copynumber: 5.8 Consensus size: 10
43238 GCTGGAAACG
43248 AGCTTGGATC
1 AGCTTGGATC
* *
43258 AGCTTGCAAC
1 AGCTTGGATC
* * *
43268 ATGTTTCGAAC
1 A-GCTTGGATC
43279 -GCTTGGATC
1 AGCTTGGATC
43288 AGCTTGGATC
1 AGCTTGGATC
43298 AGCTTGGA
1 AGCTTGGA
43306 AAAGGTAAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
9 6 0.16
10 26 0.68
11 6 0.16
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (10 bp):
AGCTTGGATC
Found at i:59287 original size:10 final size:10
Alignment explanation
Indices: 59272--59298 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
59262 GTTTACCTTT
59272 TCCAAGCTGA
1 TCCAAGCTGA
59282 TCCAAGCTGA
1 TCCAAGCTGA
59292 TCCAAGC
1 TCCAAGC
59299 GTTCGAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.19
Consensus pattern (10 bp):
TCCAAGCTGA
Found at i:59461 original size:30 final size:30
Alignment explanation
Indices: 59427--59514 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
59417 CTAGCTTATA
*
59427 TTCAGCTCACGAGCTAAACCTTAGCTCACC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * *
59457 TTCAGCTTAGGAGTTTAATCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* *
59487 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAACCTTAGCTCA
59515 TTTTAGTTTA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:62093 original size:14 final size:15
Alignment explanation
Indices: 62076--62120 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
62066 AAGAAGACGA
62076 GAAAAGAAAA-AGAT
1 GAAAAGAAAAGAGAT
62090 GAAAAGTAAAAGGAGAT
1 GAAAAG-AAAA-GAGAT
*
62107 CAAAAGAAAAGAGA
1 GAAAAGAAAAGAGA
62121 AGCAATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.22
15 8 0.30
16 4 0.15
17 9 0.33
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (15 bp):
GAAAAGAAAAGAGAT
Found at i:62941 original size:25 final size:25
Alignment explanation
Indices: 62913--62965 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
62903 CATGAATGAT
62913 GAAGATTCATGCATGAATGTATCTA
1 GAAGATTCATGCATGAATGTATCTA
62938 GAAGATTCATGCATGAATGTATCTA
1 GAAGATTCATGCATGAATGTATCTA
62963 GAA
1 GAA
62966 AATCCAATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (25 bp):
GAAGATTCATGCATGAATGTATCTA
Found at i:63846 original size:20 final size:20
Alignment explanation
Indices: 63800--63846 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
63790 GGTCAAAATT
**
63800 TTTTTTTAAGGTTTTTTCTA
1 TTTTTTTAAACTTTTTTCTA
* *
63820 ATTTTTTAAACTTTTTTTTA
1 TTTTTTTAAACTTTTTTCTA
63840 TTTTTTT
1 TTTTTTT
63847 TCGAATTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (20 bp):
TTTTTTTAAACTTTTTTCTA
Done.