Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2628
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: 27760
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:393 original size:20 final size:21
Alignment explanation
Indices: 362--401 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
352 TCCTGTTCTG
362 CGCCTCCCTCGCTGCTGCCTT
1 CGCCTCCCTCGCTGCTGCCTT
383 CGCCT-CCTCGCTGCTGCCT
1 CGCCTCCCTCGCTGCTGCCT
402 CCGCTCTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.00, C:0.53, G:0.20, T:0.28
Consensus pattern (21 bp):
CGCCTCCCTCGCTGCTGCCTT
Found at i:3535 original size:21 final size:21
Alignment explanation
Indices: 3509--3550 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3499 TGTCAAAGCG
3509 GCTCGATCTTGTACTTTTTCA
1 GCTCGATCTTGTACTTTTTCA
3530 GCTCGATCTTGTACTTTTTCA
1 GCTCGATCTTGTACTTTTTCA
3551 ATTCTTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.48
Consensus pattern (21 bp):
GCTCGATCTTGTACTTTTTCA
Found at i:8378 original size:133 final size:133
Alignment explanation
Indices: 8140--8391 Score: 477
Period size: 133 Copynumber: 1.9 Consensus size: 133
8130 GAATTCAACA
8140 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
*
8205 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAAAACATCTAAATAACCAAAATATAACAATTTT
8270 ATT
131 ATT
* *
8273 ATATAAAACGTGAGCAACAAGACAGCATTAAACTCTTAAATCAATCTAAGTCCACATTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
8338 TAAGTTGGATAGAAACATGAAAACAGACCAAAAAAACATCTAAATAACCAAAAT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAAAACATCTAAATAACCAAAAT
8392 GGAATCACCA
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 116 1.00
ACGTcount: A:0.52, C:0.18, G:0.10, T:0.20
Consensus pattern (133 bp):
ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
TAAGTTGGATAGAAACATGAAAACAGACCAAAAAAACATCTAAATAACCAAAATATAACAATTTT
ATT
Found at i:11019 original size:15 final size:15
Alignment explanation
Indices: 10999--11030 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10989 AAATAATAAT
*
10999 TTATATATATTTATC
1 TTATATACATTTATC
11014 TTATATACATTTATC
1 TTATATACATTTATC
11029 TT
1 TT
11031 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:11909 original size:14 final size:14
Alignment explanation
Indices: 11890--11929 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
11880 ATTAAACCTG
* *
11890 CTTAAACCATATAT
1 CTTAAACCATAAAC
11904 CTTAAACCATAAAC
1 CTTAAACCATAAAC
*
11918 CTTAAACTATAA
1 CTTAAACCATAA
11930 TGATAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (14 bp):
CTTAAACCATAAAC
Found at i:13805 original size:29 final size:29
Alignment explanation
Indices: 13770--13843 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
13760 GTTGTGAGAT
* *
13770 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
13799 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
13828 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
13844 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:21661 original size:29 final size:29
Alignment explanation
Indices: 21626--21699 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
21616 GTTGTGAGAT
* *
21626 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
21655 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
21684 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
21700 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:23370 original size:41 final size:41
Alignment explanation
Indices: 23307--23390 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
23297 GGGTGTTACA
* **
23307 GTTTTACCTAAAGCACCGCTAATGCTCTAGTTTTTAGCGGC
1 GTTTTACCGAAAGCACAACTAATGCTCTAGTTTTTAGCGGC
* *
23348 GTTTTACCGAAAGCGCAACTAATGCTCTGGTTTTTAGCGGC
1 GTTTTACCGAAAGCACAACTAATGCTCTAGTTTTTAGCGGC
23389 GT
1 GT
23391 GTAACACCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (41 bp):
GTTTTACCGAAAGCACAACTAATGCTCTAGTTTTTAGCGGC
Found at i:23872 original size:19 final size:19
Alignment explanation
Indices: 23836--23874 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
23826 TTTTCATCAT
* *
23836 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
23855 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
23874 A
1 A
23875 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:24375 original size:55 final size:56
Alignment explanation
Indices: 24310--24424 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
24300 AGCATGGCTG
* * *
24310 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
24366 CCAGA-ACAGATATACGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
24421 CCAG
1 CCAG
24425 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.57
56 21 0.41
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (56 bp):
CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:24421 original size:28 final size:27
Alignment explanation
Indices: 24335--24424 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
24325 GTGACAGAGT
*
24335 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
** *
24364 CACCAGAACAGAT-ATACGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
24391 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
24419 CACCAG
1 CACCAG
24425 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:24577 original size:28 final size:28
Alignment explanation
Indices: 24530--24591 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
24520 AAATTAACCC
*
24530 TAGGGGTATAGAGGTCATTTTGCATACA
1 TAGGGGTATAGAGGTAATTTTGCATACA
24558 TAGGGGTATA-ATGGTAATTTTGCATACA
1 TAGGGGTATAGA-GGTAATTTTGCATACA
24586 TAGGGG
1 TAGGGG
24592 GTACTCTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.29, C:0.08, G:0.31, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTGCATACA
Done.