Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1175
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: 49065
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2831 original size:23 final size:22
Alignment explanation
Indices: 2779--2831 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
2769 TCCACGTCTT
*
2779 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
2801 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
2824 TTTCTTTT
1 TTTCTTTT
2832 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:7868 original size:30 final size:31
Alignment explanation
Indices: 7834--7930 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
7824 AGCTCACTCC
*
7834 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
7864 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
7894 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
7924 TAGCTCA
1 TAGCTCA
7931 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:8820 original size:22 final size:20
Alignment explanation
Indices: 8788--8836 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
8778 GCCAAATTTA
8788 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
8811 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
8831 TGAACA
1 TGAACA
8837 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:10783 original size:12 final size:12
Alignment explanation
Indices: 10775--10799 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10765 TTTGAAAAGC
10775 AAAAAGAAAATG
1 AAAAAGAAAATG
10787 AAAAAGAAAATG
1 AAAAAGAAAATG
10799 A
1 A
10800 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:10796 original size:18 final size:18
Alignment explanation
Indices: 10769--10824 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
10759 AAAGCCTTTG
10769 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
10788 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
10806 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
10823 AA
1 AA
10825 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:10809 original size:30 final size:31
Alignment explanation
Indices: 10775--10856 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
10765 TTTGAAAAGC
*
10775 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
10805 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
10835 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
10857 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:12652 original size:30 final size:30
Alignment explanation
Indices: 12566--12663 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
12556 TTAAACTAAA
* *
12566 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
12596 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
12626 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
12656 ATGAGCTA
1 ATGAGCTA
12664 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:14400 original size:20 final size:19
Alignment explanation
Indices: 14377--14441 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
14367 AAGCTCAAAC
14377 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
14397 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
14417 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
14437 GAGCT
1 GAGCT
14442 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:16252 original size:33 final size:33
Alignment explanation
Indices: 16214--16276 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
16204 GATTACTCAC
16214 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
16247 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
16277 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:16321 original size:17 final size:18
Alignment explanation
Indices: 16291--16332 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
16281 TCTTTTTTCG
*
16291 CTTTTTC-TTTTCAATTT
1 CTTTTTCATTCTCAATTT
16308 -TTTTTCATTCTCAATTT
1 CTTTTTCATTCTCAATTT
16325 CTTTTTCA
1 CTTTTTCA
16333 ATTTTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 9 0.41
18 7 0.32
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (18 bp):
CTTTTTCATTCTCAATTT
Found at i:16334 original size:29 final size:27
Alignment explanation
Indices: 16294--16358 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
16284 TTTTTCGCTT
16294 TTTC-TTTTCAATTTT-TTTTCATTCTCAA
1 TTTCTTTTTCAATTTTCTTTTC--T-TCAA
*
16322 TTTCTTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
16349 TTTCTTTTTC
1 TTTCTTTTTC
16359 TCTCACTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
27 13 0.38
28 5 0.15
29 11 0.32
30 5 0.15
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:16386 original size:18 final size:17
Alignment explanation
Indices: 16365--16422 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
16355 TTTCTCTCAC
16365 TTTTTCGATTTCTTTTT
1 TTTTTCGATTTCTTTTT
* *
16382 ATTTTGCAATTTCTTTTT
1 -TTTTTCGATTTCTTTTT
* *
16400 CTTTTCGTTTTCTTTTT
1 TTTTTCGATTTCTTTTT
*
16417 GTTTTC
1 TTTTTC
16423 TTTCAATTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
17 18 0.55
18 15 0.45
ACGTcount: A:0.07, C:0.14, G:0.07, T:0.72
Consensus pattern (17 bp):
TTTTTCGATTTCTTTTT
Found at i:16410 original size:11 final size:11
Alignment explanation
Indices: 16391--16425 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
16381 TATTTTGCAA
*
16391 TTTCTTTTTCT
1 TTTCGTTTTCT
16402 TTTCGTTTTCT
1 TTTCGTTTTCT
*
16413 TTTTGTTTTCT
1 TTTCGTTTTCT
16424 TT
1 TT
16426 CAATTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (11 bp):
TTTCGTTTTCT
Found at i:16438 original size:6 final size:6
Alignment explanation
Indices: 16322--16425 Score: 50
Period size: 6 Copynumber: 17.2 Consensus size: 6
16312 TCATTCTCAA
* * * ** **
16322 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTT TTTCGA
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* * ** * *
16373 TTTCTT TTTATT TTGCAA TTTCTT TTTC-T TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
16419 TTTCTT T
1 TTTCTT T
16426 CAATTTCTTT
Statistics
Matches: 68, Mismatches: 26, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
5 9 0.13
6 47 0.69
7 9 0.13
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:17483 original size:20 final size:20
Alignment explanation
Indices: 17437--17483 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
17427 AGCTCGTTTC
*
17437 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
17457 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
17477 CAGCTCA
1 CAGCTCA
17484 ATCTTAACCT
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:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:19045 original size:10 final size:9
Alignment explanation
Indices: 19030--19065 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
19020 AGAAGTGAGC
19030 AAAAAAAGA
1 AAAAAAAGA
19039 AAAAAAAGTA
1 AAAAAAAG-A
19049 AAAAAAAGA
1 AAAAAAAGA
19058 ACAAAAAA
1 A-AAAAAA
19066 AGTGAAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:19073 original size:10 final size:10
Alignment explanation
Indices: 19030--19073 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
19020 AGAAGTGAGC
19030 AAAAAAAG-A
1 AAAAAAAGTA
19039 AAAAAAAGTA
1 AAAAAAAGTA
*
19049 AAAAAAAGAA
1 AAAAAAAGTA
19059 CAAAAAAAGTGA
1 -AAAAAAAGT-A
19071 AAA
1 AAA
19074 GTCTTGCGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 8 0.27
10 10 0.33
11 11 0.37
12 1 0.03
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.05
Consensus pattern (10 bp):
AAAAAAAGTA
Found at i:19073 original size:22 final size:20
Alignment explanation
Indices: 19015--19073 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 20
19005 GAAATTCAAA
19015 AAAAAAGAAGTGAGCAAAAAAAG
1 AAAAAA-AAGTGA--AAAAAAAG
19038 AAAAAAAAGT-AAAAAAAAG
1 AAAAAAAAGTGAAAAAAAAG
19057 AACAAAAAAAGTGAAAA
1 -A-AAAAAAAGTGAAAA
19074 GTCTTGCGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
19 8 0.24
20 1 0.03
21 10 0.30
22 8 0.24
23 6 0.18
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAAAAAAGTGAAAAAAAAG
Found at i:21934 original size:20 final size:20
Alignment explanation
Indices: 21888--21934 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
21878 AGCTCGTTTC
*
21888 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
21908 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
21928 CAGCTCA
1 CAGCTCA
21935 ATCTTAACCC
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:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:23453 original size:23 final size:22
Alignment explanation
Indices: 23427--23492 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
23417 TTTTAACTCA
23427 ATTTTTTTGTCACTTTTTTTTTG
1 ATTTTTTT-TCACTTTTTTTTTG
* *
23450 ATTTTTTTTGAATATTTTTTTTG
1 ATTTTTTTTCACT-TTTTTTTTG
* * *
23473 AATTTCTTCTCTCTTTTTTT
1 -ATTTTTTTTCACTTTTTTT
23493 AAATCCAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
22 3 0.09
23 23 0.68
24 8 0.24
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.73
Consensus pattern (22 bp):
ATTTTTTTTCACTTTTTTTTTG
Found at i:23466 original size:13 final size:13
Alignment explanation
Indices: 23450--23475 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23440 TTTTTTTTTG
23450 ATTTTTTTTGAAT
1 ATTTTTTTTGAAT
23463 ATTTTTTTTGAAT
1 ATTTTTTTTGAAT
23476 TTCTTCTCTC
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:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (13 bp):
ATTTTTTTTGAAT
Found at i:25119 original size:20 final size:19
Alignment explanation
Indices: 25096--25160 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
25086 AAGCTCAAAC
25096 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
25116 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * *
25136 AAGCTCATGTGAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
25156 GAGCT
1 GAGCT
25161 GGGAAAAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 31 0.84
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:25120 original size:10 final size:10
Alignment explanation
Indices: 25096--25160 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
25086 AAGCTCAAAC
*
25096 GAGCTAAAGT
1 GAGCTAAATT
*
25106 AAGCTAAATT
1 GAGCTAAATT
*
25116 GAGCTCAAA-C
1 GAGCT-AAATT
25126 GAGCTAAATT
1 GAGCTAAATT
* *
25136 AAGCT-CATGT
1 GAGCTAAAT-T
25146 GAGCTAAATT
1 GAGCTAAATT
25156 GAGCT
1 GAGCT
25161 GGGAAAAACT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
9 5 0.12
10 32 0.76
11 5 0.12
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (10 bp):
GAGCTAAATT
Found at i:26574 original size:20 final size:20
Alignment explanation
Indices: 26551--26597 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
26541 GGGTTAAGAT
*
26551 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
26571 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
26591 TGAGCTG
1 TGAGCTG
26598 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:28318 original size:48 final size:48
Alignment explanation
Indices: 28266--28371 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
28256 TTGTCTTTTC
*
28266 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
28314 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
28362 TTTCTTTTTC
1 TTTCTTTTTC
28372 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:29465 original size:12 final size:12
Alignment explanation
Indices: 29450--29487 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
29440 TTTTTTTTCC
*
29450 TTTTTTTTCG-A
1 TTTTTTTTTGAA
29461 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
29473 TTTTTTTCTGAA
1 TTTTTTTTTGAA
29485 TTT
1 TTT
29488 CTTCTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:32032 original size:75 final size:76
Alignment explanation
Indices: 31910--32168 Score: 312
Period size: 75 Copynumber: 3.3 Consensus size: 76
31900 TTGAATGATG
*
31910 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-A-C-TATCCGGACTAAGATCCGAAGGCAT
31973 TTGTGCGAGATACATA
61 TTGTGCGAGATACATA
*
31989 TCCGGACTAAG-CCGAAGGCATTTGTGCGAGATACTATCCGGACTAAGATCCGAAGGCATTTGTG
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTATCCGGACTAAGATCCGAAGGCATTTGTG
32053 CGAGATAC-TAA
66 CGAGATACAT-A
* **
32064 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACT--ATCCGGACTAAGAT-CCGAAGGCATTT
*
32128 GTGCGAGTTACTATA
63 GTGCGAGATAC-ATA
* *
32143 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
32169 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 9, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
74 1 0.01
75 49 0.30
76 24 0.15
77 10 0.06
78 41 0.25
79 21 0.13
80 15 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (76 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTATCCGGACTAAGATCCGAAGGCATTTGTG
CGAGATACATA
Found at i:32051 original size:38 final size:37
Alignment explanation
Indices: 31948--32168 Score: 273
Period size: 38 Copynumber: 5.7 Consensus size: 37
31938 TAAGTGACCA
31948 TATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATAC
1 TATCCGGACTAAG-TCCGAAGGCATTTGTGCGAGATAC
31986 ATATCCGGACTAAG-CCGAAGGCATTTGTGCGAGATAC
1 -TATCCGGACTAAGTCCGAAGGCATTTGTGCGAGATAC
32023 TATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATAC
1 TATCCGGACTAAG-TCCGAAGGCATTTGTGCGAGATAC
* * *
32061 TAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTAC
1 T-ATCCGGACTAAGTCCGAAGGCATTTGTGCGAGATAC
** *
32099 TAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTAC
1 T--ATCCGGACTAAGT-CCGAAGGCATTTGTGCGAGATAC
* *
32139 TATAACCGGGCTATGTCCCGAAGGCATTTG
1 TAT--CCGGACTAAGT-CCGAAGGCATTTG
32169 AACGAGGAGC
Statistics
Matches: 168, Mismatches: 7, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
36 13 0.08
37 23 0.14
38 49 0.29
39 36 0.21
40 47 0.28
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (37 bp):
TATCCGGACTAAGTCCGAAGGCATTTGTGCGAGATAC
Found at i:32130 original size:40 final size:40
Alignment explanation
Indices: 31910--32168 Score: 290
Period size: 40 Copynumber: 6.7 Consensus size: 40
31900 TTGAATGATG
* * *
31910 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
* *
31950 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-ATA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
31989 TCCGGACTAAG--CCGAAGGCATTTGTGCGAGATACT--A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
*
32025 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
32064 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
32103 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTA-AA
*
32144 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
32169 AACGAGGAGC
Statistics
Matches: 201, Mismatches: 7, Indels: 22
0.87 0.03 0.10
Matches are distributed among these distances:
36 12 0.06
37 23 0.11
38 47 0.23
39 37 0.18
40 69 0.34
41 12 0.06
42 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:39009 original size:39 final size:38
Alignment explanation
Indices: 38922--39182 Score: 278
Period size: 39 Copynumber: 6.7 Consensus size: 38
38912 TTGAATGATG
* *
38922 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGACTAAGT-CCGAAGGCATTTGTGCGAGA-T-A-CATA
38962 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACATA
1 TCCGGACTAAG-TCCGAAGGCATTTGTGCGAGATACATA
39001 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACATA
1 TCCGGACTAAG-TCCGAAGGCATTTGTGCGAGATACATA
39040 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATAC-TAA
1 TCCGGACTAAG-TCCGAAGGCATTTGTGCGAGATACAT-A
* * *
39079 TTCC-GAGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 -TCCGGA-CTAAGTCCGAAGGCATTTGTGCGAGATAC-ATA
* ** *
39119 TCTGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGACTAAGTCCGAAGGCATTTGTGCGAGATAC-ATA
* * *
39158 ACCGGGCTATGTCCGAAGGCATTTG
1 TCCGGACTAAGTCCGAAGGCATTTG
39183 AACGAGAGCT
Statistics
Matches: 198, Mismatches: 14, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.01
39 157 0.79
40 29 0.15
41 10 0.05
42 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (38 bp):
TCCGGACTAAGTCCGAAGGCATTTGTGCGAGATACATA
Found at i:42244 original size:12 final size:12
Alignment explanation
Indices: 42227--42272 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
42217 CGTAGCTTCG
42227 AAAAAAAAAGTT
1 AAAAAAAAAGTT
42239 AAAAAAAAAGTT
1 AAAAAAAAAGTT
*
42251 TAAAAAAAA-TT
1 AAAAAAAAAGTT
42262 GCAAAAAAAAA
1 --AAAAAAAAA
42273 ATTGCATACG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
11 2 0.07
12 20 0.67
13 8 0.27
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAAAAAAAGTT
Found at i:42245 original size:13 final size:13
Alignment explanation
Indices: 42227--42259 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
42217 CGTAGCTTCG
42227 AAAAAAAAAG-TT
1 AAAAAAAAAGTTT
42239 AAAAAAAAAGTTT
1 AAAAAAAAAGTTT
42252 AAAAAAAA
1 AAAAAAAA
42260 TTGCAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (13 bp):
AAAAAAAAAGTTT
Found at i:42269 original size:14 final size:14
Alignment explanation
Indices: 42252--42278 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42242 AAAAAAGTTT
42252 AAAAAAAATTGCAA
1 AAAAAAAATTGCAA
42266 AAAAAAAATTGCA
1 AAAAAAAATTGCA
42279 TACGGTCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAAAAAATTGCAA
Found at i:44555 original size:24 final size:25
Alignment explanation
Indices: 44528--44581 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
44518 ATGAGTGATA
*
44528 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
44552 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
44576 AAAAAA
1 AAAAAA
44582 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Done.