Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1776
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: 35285
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.37
Found at i:2100 original size:2 final size:2
Alignment explanation
Indices: 2093--2125 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2083 AGGTTTCAAA
2093 AT 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 AT A
2126 CACATATTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3767 original size:2 final size:2
Alignment explanation
Indices: 3760--3798 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3750 GAGATTTCCT
3760 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3799 GAGCAATGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4624 original size:14 final size:13
Alignment explanation
Indices: 4605--4638 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
4595 CTTTTTTTTA
4605 AAAAAAAAAAATCT
1 AAAAAAAAAAAT-T
*
4619 AAAAAAAAGAATT
1 AAAAAAAAAAATT
4632 AAAAAAA
1 AAAAAAA
4639 TCAACAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAAAAAAAAATT
Found at i:7018 original size:3 final size:3
Alignment explanation
Indices: 7010--7054 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
7000 ATATATACTT
7010 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7055 ATTGTTTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:8264 original size:20 final size:20
Alignment explanation
Indices: 8223--8264 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
8213 AAAATTGGAA
***
8223 AATGATTTTCAAAATGTTAC
1 AATGATTTTCAAAATAAAAC
8243 AATGATTTTCAAAATAAAAC
1 AATGATTTTCAAAATAAAAC
8263 AA
1 AA
8265 ATGCTTGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (20 bp):
AATGATTTTCAAAATAAAAC
Found at i:16667 original size:24 final size:24
Alignment explanation
Indices: 16619--16668 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
16609 TCTTGAAAAT
*
16619 TTTTATTTATTAAATCTTAATTAA
1 TTTTATTTATTAAATCTTAAATAA
16643 TTTTATTT-TTAAAGT-TATAAATAA
1 TTTTATTTATTAAA-TCT-TAAATAA
16667 TT
1 TT
16669 AATCATACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTTATTTATTAAATCTTAAATAA
Found at i:17677 original size:32 final size:32
Alignment explanation
Indices: 17641--17707 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
17631 AATAGCTACG
17641 AACTACTTTGATATGATAGAAAGCTAAAATCA
1 AACTACTTTGATATGATAGAAAGCTAAAATCA
17673 AACTACTTTGATATGATAGAAAGCTAAAATCA
1 AACTACTTTGATATGATAGAAAGCTAAAATCA
17705 AAC
1 AAC
17708 GATGAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (32 bp):
AACTACTTTGATATGATAGAAAGCTAAAATCA
Found at i:21839 original size:12 final size:13
Alignment explanation
Indices: 21822--21856 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
21812 CTTTGTTCCA
21822 TTTCTTTTTTT-T
1 TTTCTTTTTTTCT
21834 TTTCTTTTTTTCT
1 TTTCTTTTTTTCT
*
21847 TTTATTTTTT
1 TTTCTTTTTT
21857 ACCAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTCTTTTTTTCT
Found at i:23510 original size:95 final size:92
Alignment explanation
Indices: 23301--23513 Score: 246
Period size: 92 Copynumber: 2.3 Consensus size: 92
23291 TGTAGTATTA
* * * *
23301 TCAAACGCATGCGACGGGATTTACATCAAAGTATAATCTAATAAATAAGTGATTTTTTTATGAAT
1 TCAAACGCATGCGACGGGATTTACATCAAAATATAATCCAACAAATAAGTAATTTTTTTATGAAT
* * * *
23366 TTTTTGAAAAAAAATGATTGTATTTTG
66 TTCTTAAAAAAAAATGAGTGAATTTTG
** * * * * *
23393 TCAAATACGTGTGACGAGATTTATATTAAAATATAATCCAACAAATAAGTAACTTTTTTTAATGA
1 TCAAACGCATGCGACGGGATTTACATCAAAATATAATCCAACAAATAAGTAA-TTTTTTT-ATGA
*
23458 ATTTCTTAAAAAAAATATGGGTGAATTTTG
64 ATTTCTTAAAAAAAA-ATGAGTGAATTTTG
*
23488 TCAAACGCATGCGGCGGGATTTACAT
1 TCAAACGCATGCGACGGGATTTACAT
23514 AAGACTTCTT
Statistics
Matches: 95, Mismatches: 23, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
92 41 0.43
93 7 0.07
94 17 0.18
95 30 0.32
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (92 bp):
TCAAACGCATGCGACGGGATTTACATCAAAATATAATCCAACAAATAAGTAATTTTTTTATGAAT
TTCTTAAAAAAAAATGAGTGAATTTTG
Found at i:23930 original size:52 final size:52
Alignment explanation
Indices: 23874--23972 Score: 189
Period size: 52 Copynumber: 1.9 Consensus size: 52
23864 AAAATAAAAA
23874 ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGATTAAT
1 ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGATTAAT
*
23926 ATATTTTTCATATTATGGATATTAATAGACATAAGTTATATAATAGA
1 ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGA
23973 ATATAAATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (52 bp):
ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGATTAAT
Found at i:25304 original size:13 final size:14
Alignment explanation
Indices: 25286--25316 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
25276 CAACAATTTT
25286 AATAAA-ATGTATA
1 AATAAAGATGTATA
25299 AATAAAGATGTATA
1 AATAAAGATGTATA
25313 AATA
1 AATA
25317 TATAGACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (14 bp):
AATAAAGATGTATA
Found at i:26237 original size:2 final size:2
Alignment explanation
Indices: 26225--26264 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
26215 ATTAAAAATA
26225 AT AT A- AT AT AT AT A- AGT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A
26265 AGAAAACCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 32 0.91
3 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:27161 original size:191 final size:190
Alignment explanation
Indices: 26750--27307 Score: 726
Period size: 191 Copynumber: 2.9 Consensus size: 190
26740 TGCGATAAGC
* * *
26750 TTTATATTAAAATATAATTTAATAAATAAGTGATCATTTTTAATGAAATTTTGAAAAAAATAATA
1 TTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTG-AAAAAA-AATA
** * * * * *
26815 TAATTACTTTTTATCGAACATATGAAGTGAGGTTTATATTAAAGTATAATTTAATAAATAAGT-G
64 TGGTTACCTTTTATCAAACGTATGAGGTGGGGTTTATATTAAAGTATAATTTAATAAATAAGTAG
* * * *
26879 ATCCTTTTTAATGAAATTTTAAAAAAAAATATGACTGCCTTTTATCAGATGTGTACGGCAAGT
129 -TCCTTTTTAATGAAATTTTGAAAAAAAATATGACTGCCTTTTATCAGACGCGTACGACAAGT
* *
26942 TTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATAAAATTTTGAAAAACAATATG
1 TTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGAAAAAAAATATG
*
27007 GTTACCTTTTATCAAACGTATGAGGTGGGGTTTATATTAAAGTATAATTTAATAAATGAGTAGT-
66 GTTACCTTTTATCAAACGTATGAGGTGGGGTTTATATTAAAGTATAATTTAATAAATAAGTAGTC
* * * **
27071 CTTTTCTAATGAAATTTTGGAAGAAAAATAT-AGCTGTCTTTTATTAGACGCGTGTGACAAGT
131 CTTTT-TAATGAAATTTT-GAAAAAAAATATGA-CTGCCTTTTATCAGACGCGTACGACAAGT
* *
27133 TTTATAATAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTAAAAAAAAATATG
1 TTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGAAAAAAAATATG
* ** * * * * *
27198 GATGTCTTTTATGAAACGTATGAGATGGGGTTTATATTAAAATATAATTTAATAAATAAATAATC
66 GTTACCTTTTATCAAACGTATGAGGTGGGGTTTATATTAAAGTATAATTTAATAAATAAGTAGTC
* *
27263 CTTTTTAATGAAACTTTGAAAAAAAATTATGACTACCTTTTATCA
131 CTTTTTAATGAAATTTTGAAAAAAAA-TATGACTGCCTTTTATCA
27308 AAGATATGAG
Statistics
Matches: 319, Mismatches: 40, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
189 5 0.02
190 81 0.25
191 178 0.56
192 55 0.17
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (190 bp):
TTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGAAAAAAAATATG
GTTACCTTTTATCAAACGTATGAGGTGGGGTTTATATTAAAGTATAATTTAATAAATAAGTAGTC
CTTTTTAATGAAATTTTGAAAAAAAATATGACTGCCTTTTATCAGACGCGTACGACAAGT
Found at i:27373 original size:96 final size:96
Alignment explanation
Indices: 26750--27354 Score: 570
Period size: 95 Copynumber: 6.3 Consensus size: 96
26740 TGCGATAAGC
*
26750 TTTATATTAAAATATAATTTAATAAATAAGTGATCATTTTTAATGAAATTTTGAAAAAAATAATA
1 TTTATATTAAAGTATAATTTAATAAATAAGTGATCATTTTTAATGAAATTTTGAAAAAAA-AATA
* * * * * * *
26815 TAATTACTTTTTATCGAACATATGAAGTGAGG
65 TGACTACCTTTTATCAAAGATATGAGGTGGGG
*
26847 TTTATATTAAAGTATAATTTAATAAATAAGTGATCCTTTTTAATGAAATTTT-AAAAAAAAATAT
1 TTTATATTAAAGTATAATTTAATAAATAAGTGATCATTTTTAATGAAATTTTGAAAAAAAAATAT
* * *** *
26911 GACTGCCTTTTATC--AGATGTGTACGGCAAGT
66 GACTACCTTTTATCAAAGATATG-A-GGTGGGG
* * * *
26942 TTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATAAAATTTTG-AAAAACAATAT
1 TTTATATTAAAGTATAATTTAATAAATAAGTGATCATTTTTAATGAAATTTTGAAAAAAAAATAT
**
27006 GGTTACCTTTTATCAAACG-TATGAGGTGGGG
66 GACTACCTTTTATCAAA-GATATGAGGTGGGG
* * *
27037 TTTATATTAAAGTATAATTTAATAAATGAGT-AGTC-TTTTCTAATGAAATTTTGGAAGAAAAAT
1 TTTATATTAAAGTATAATTTAATAAATAAGTGA-TCATTTT-TAATGAAATTTTGAAAAAAAAAT
** * * * * *** *
27100 AT-AGCTGTCTTTTATTAGACGCGTGTGA--CAAGT
64 ATGA-CTACCTTTTATCA-AAG-ATATGAGGTGGGG
* * *
27133 TTTATAATAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTT-AAAAAAAAATAT
1 TTTATATTAAAGTATAATTTAATAAATAAGTGATCATTTTTAATGAAATTTTGAAAAAAAAATAT
** * *
27197 GGA-TGTCTTTTATGAAACG-TATGAGATGGGG
66 -GACTACCTTTTATCAAA-GATATGAGGTGGGG
* * * * * *
27228 TTTATATTAAAATATAATTTAATAAATAAATAATCCTTTTTAATGAAACTTTGAAAAAAAATTAT
1 TTTATATTAAAGTATAATTTAATAAATAAGTGATCATTTTTAATGAAATTTTGAAAAAAAAATAT
*
27293 GACTACCTTTTATCAAAGATATGAGGTGGGA
66 GACTACCTTTTATCAAAGATATGAGGTGGGG
* *
27324 TTTATATTAAAATATAATTTAAAAAATAAGT
1 TTTATATTAAAGTATAATTTAATAAATAAGT
27355 TATCCTTTCT
Statistics
Matches: 418, Mismatches: 67, Indels: 47
0.79 0.13 0.09
Matches are distributed among these distances:
93 9 0.02
94 7 0.02
95 204 0.49
96 132 0.32
97 61 0.15
98 5 0.01
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (96 bp):
TTTATATTAAAGTATAATTTAATAAATAAGTGATCATTTTTAATGAAATTTTGAAAAAAAAATAT
GACTACCTTTTATCAAAGATATGAGGTGGGG
Found at i:27860 original size:36 final size:37
Alignment explanation
Indices: 27790--27860 Score: 85
Period size: 38 Copynumber: 1.9 Consensus size: 37
27780 AGTTTTGATT
*
27790 TATAAAATATAAAAATACTAAATAATTAATAATTTAAA
1 TATAAAATATAAAAATAC-AAATAATTAAAAATTTAAA
27828 TATAAAATA-AATAAATA-AAACTAA-TAAAAATTT
1 TATAAAATATAA-AAATACAAA-TAATTAAAAATTT
27861 TAAAAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
36 11 0.37
37 5 0.17
38 14 0.47
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (37 bp):
TATAAAATATAAAAATACAAATAATTAAAAATTTAAA
Found at i:28078 original size:24 final size:25
Alignment explanation
Indices: 28035--28083 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
28025 TAGGATATAA
*
28035 AAAAATAAAAAATAATTCAAAAAAT
1 AAAAATAAAAAATAAGTCAAAAAAT
*
28060 AAAAATAAAGAA-AAGTCAAAAAAT
1 AAAAATAAAAAATAAGTCAAAAAAT
28084 TCTTAACCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (25 bp):
AAAAATAAAAAATAAGTCAAAAAAT
Found at i:32205 original size:12 final size:12
Alignment explanation
Indices: 32190--32229 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
32180 AAACTTTTTT
32190 AAAAAATAATTG
1 AAAAAATAATTG
*
32202 AAAAAATAAAT-
1 AAAAAATAATTG
32213 -AAAAATAATTG
1 AAAAAATAATTG
32224 AAAAAA
1 AAAAAA
32230 AGGAACAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (12 bp):
AAAAAATAATTG
Done.