Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold515
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: 66640
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:1886 original size:21 final size:22
Alignment explanation
Indices: 1849--1891 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1839 AATAGCTACG
*
1849 TAAAAAATTTCAGAAA-TAAAA
1 TAAAAAAATTCAGAAATTAAAA
1870 TAAAAAAATTC-GAAAATTAAAA
1 TAAAAAAATTCAG-AAATTAAAA
1892 ATATACATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 13 0.68
22 5 0.26
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (22 bp):
TAAAAAAATTCAGAAATTAAAA
Found at i:2294 original size:14 final size:14
Alignment explanation
Indices: 2275--2304 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2265 TTTTCAGAGA
*
2275 TTGTGAGGTTTTCT
1 TTGTGAGGTCTTCT
2289 TTGTGAGGTCTTCT
1 TTGTGAGGTCTTCT
2303 TT
1 TT
2305 TTAATGTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.10, G:0.27, T:0.57
Consensus pattern (14 bp):
TTGTGAGGTCTTCT
Found at i:4049 original size:18 final size:19
Alignment explanation
Indices: 4008--4049 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
3998 CAAAACGAGA
* *
4008 GAAAAAGAAAAGTGAAAAT
1 GAAAAAGAAAAGTAAAAAG
4027 G-AAAAGAAAAG-AAAAAG
1 GAAAAAGAAAAGTAAAAAG
4044 GAAAAA
1 GAAAAA
4050 AGGATAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 5 0.25
18 14 0.70
19 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (19 bp):
GAAAAAGAAAAGTAAAAAG
Found at i:8082 original size:23 final size:22
Alignment explanation
Indices: 8030--8082 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
8020 TCCACGTCTT
*
8030 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
8052 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
8075 TTTCTTTT
1 TTTCTTTT
8083 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:10433 original size:10 final size:10
Alignment explanation
Indices: 10418--10444 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
10408 CTAAGTAAAT
10418 AAATAAATAA
1 AAATAAATAA
10428 AAATAAATAA
1 AAATAAATAA
10438 AAATAAA
1 AAATAAA
10445 ACTTTACAAC
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAATAAATAA
Found at i:11842 original size:23 final size:22
Alignment explanation
Indices: 11790--11842 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
11780 TCCACGTCTT
*
11790 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
11812 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
11835 TTTCTTTT
1 TTTCTTTT
11843 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:17338 original size:18 final size:18
Alignment explanation
Indices: 17315--17351 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17305 CTCTTTTTGC
17315 TCTTTTTC-ATTCTCTTTT
1 TCTTTTTCGATT-TCTTTT
17333 TCTTTTTCGATTTCTTTT
1 TCTTTTTCGATTTCTTTT
17351 T
1 T
17352 GTCTTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.05, C:0.19, G:0.03, T:0.73
Consensus pattern (18 bp):
TCTTTTTCGATTTCTTTT
Found at i:20345 original size:52 final size:52
Alignment explanation
Indices: 20262--20362 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
20252 TAAGGAAAAG
*
20262 TAATGGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
20314 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
20363 TATGTGCATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:29955 original size:20 final size:20
Alignment explanation
Indices: 29909--29955 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
29899 AGCTCGTTTC
*
29909 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
29929 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
29949 CAGCTCA
1 CAGCTCA
29956 ATCTAACCTA
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:45250 original size:47 final size:47
Alignment explanation
Indices: 45196--45880 Score: 1199
Period size: 47 Copynumber: 14.6 Consensus size: 47
45186 TATTTGAATA
45196 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
45243 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATC
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
45290 AATGTGAAATTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
45337 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
45384 AATGTGAAAGTGTATATATGTGATAAGGTCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
45431 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
45478 AATGTGAAAGTGTATATATGTGATAAGTCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
45525 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
45572 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
45619 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
45666 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
45713 AATGTGAACGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
45760 AATGTGAAAGTGTATATATGTGATAAGGTCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * *
45807 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
45854 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
45881 TCCCGAAGGG
Statistics
Matches: 613, Mismatches: 25, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 613 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:47279 original size:16 final size:15
Alignment explanation
Indices: 47260--47289 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
47250 AGTATCAATT
47260 TTTGATTGGTGATGAC
1 TTTGATTGG-GATGAC
47276 TTTGATTGGGATGA
1 TTTGATTGGGATGA
47290 TGGATTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
TTTGATTGGGATGAC
Found at i:49126 original size:27 final size:27
Alignment explanation
Indices: 49053--49201 Score: 230
Period size: 27 Copynumber: 5.6 Consensus size: 27
49043 TAAATTGTAC
49053 AGCACTAAGTGTGCGA-TTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
49079 -GCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
49106 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* *
49133 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* *
49160 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
49187 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
49202 GACTAATATA
Statistics
Matches: 115, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.13
27 84 0.73
28 16 0.14
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.32
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:57169 original size:28 final size:27
Alignment explanation
Indices: 57060--57212 Score: 211
Period size: 27 Copynumber: 5.6 Consensus size: 27
57050 TAAATTGTGC
*
57060 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
57087 -GCACTAAGTGTGCGAGTTTGACTAATGTT
1 AGCACTAAGTGTGCGAG-TTGACT-ATG-T
57116 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
57143 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
*
57171 AGCACTAAGTGTGCGAGTTGA-TATAAT
1 AGCACTAAGTGTGCGAGTTGACTAT-GT
*
57198 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
57213 GACTTAATAT
Statistics
Matches: 116, Mismatches: 4, Indels: 12
0.88 0.03 0.09
Matches are distributed among these distances:
26 18 0.16
27 43 0.37
28 32 0.28
29 7 0.06
30 16 0.14
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:57190 original size:55 final size:57
Alignment explanation
Indices: 57060--57212 Score: 233
Period size: 55 Copynumber: 2.7 Consensus size: 57
57050 TAAATTGTGC
*
57060 AGCACTAAGTGTGCGAATTGACTATGT-GCACTAAGTGTGCGAGTTTGACTAATGTT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTAATGTT
*
57116 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGA-TTATG-T
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTAATGTT
* *
57171 AGCACTAAGTGTGCGAGTTGA-TATAATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTAT-GTAGCACTAAGTGTGCG
57213 GACTTAATAT
Statistics
Matches: 91, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
54 3 0.03
55 37 0.41
56 30 0.33
57 21 0.23
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (57 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTAATGTT
Found at i:62171 original size:21 final size:22
Alignment explanation
Indices: 62147--62187 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
62137 AGTTGTAAAG
*
62147 TTTTATTTTTATTTA-TTTATT
1 TTTTATTTTTACTTAGTTTATT
62168 TTTTATTTTTACTTAGTTTA
1 TTTTATTTTTACTTAGTTTA
62188 ATAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTATTTTTACTTAGTTTATT
Done.