Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1092
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: 31558
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Found at i:1683 original size:28 final size:26
Alignment explanation
Indices: 1588--1687 Score: 96
Period size: 27 Copynumber: 3.7 Consensus size: 26
1578 CATGGCTACC
* * *
1588 AGAATAGATATTGTGACAGAGTCACCA
1 AGAACAGATATTGTGGCAGAGCCA-CA
*
1615 A-ATACAGATATTGTGGCAGAGCCACC
1 AGA-ACAGATATTGTGGCAGAGCCACA
1641 AGAACAGATATTTGTGGC-GTAGCCACTA
1 AGAACAGATA-TTGTGGCAG-AGCCAC-A
1669 AGAACAGATAGTTGTGGCA
1 AGAACAGATA-TTGTGGCA
1688 TAGGCACCAG
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
26 11 0.18
27 33 0.54
28 17 0.28
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (26 bp):
AGAACAGATATTGTGGCAGAGCCACA
Found at i:6038 original size:26 final size:26
Alignment explanation
Indices: 6002--6054 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
5992 AAAAAATCCG
6002 AATCCAGTTACCAGTACCAAGCCTGC
1 AATCCAGTTACCAGTACCAAGCCTGC
6028 AATCCAGTTACCAGTACCAAGCCTGC
1 AATCCAGTTACCAGTACCAAGCCTGC
6054 A
1 A
6055 GGGCTTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.34, G:0.15, T:0.19
Consensus pattern (26 bp):
AATCCAGTTACCAGTACCAAGCCTGC
Found at i:8415 original size:20 final size:19
Alignment explanation
Indices: 8392--8438 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
8382 TATTTCTTAA
8392 AATTAAAACTCAATTCTACC
1 AATTAAAACTCAATTC-ACC
* *
8412 AATTCAAAACTCCATTCAGC
1 AATT-AAAACTCAATTCACC
8432 AATTAAA
1 AATTAAA
8439 CATGAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 11 0.46
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (19 bp):
AATTAAAACTCAATTCACC
Found at i:9825 original size:30 final size:29
Alignment explanation
Indices: 9782--9845 Score: 110
Period size: 30 Copynumber: 2.2 Consensus size: 29
9772 AAAGCAGCCG
*
9782 AAGCTAGTTAAATCGCATACTTAGTGCCA
1 AAGCTAGTTAAATCGCACACTTAGTGCCA
9811 AAGCTAGTTTAAATCGCACACTTAGTGCCA
1 AAGCTAG-TTAAATCGCACACTTAGTGCCA
9841 AAGCT
1 AAGCT
9846 TCCGATTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 7 0.21
30 26 0.79
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (29 bp):
AAGCTAGTTAAATCGCACACTTAGTGCCA
Found at i:11162 original size:27 final size:27
Alignment explanation
Indices: 11121--11174 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
11111 TGTCATGTGA
* *
11121 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
11148 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
11175 GGTTGTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:11500 original size:49 final size:50
Alignment explanation
Indices: 11419--11614 Score: 232
Period size: 50 Copynumber: 3.9 Consensus size: 50
11409 ATCTATTGTG
* * *
11419 AGGTCACGTGTATAGTACTAAATGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * * *
11469 -GGTCGCATGTGTAGTATTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * **
11519 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
11569 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT
11615 GGCCTTGTCT
Statistics
Matches: 121, Mismatches: 23, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
49 39 0.32
50 45 0.37
51 37 0.31
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (50 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:14341 original size:7 final size:7
Alignment explanation
Indices: 14329--14386 Score: 82
Period size: 7 Copynumber: 8.4 Consensus size: 7
14319 GTTATCACAA
14329 AGGGTTT
1 AGGGTTT
14336 AGGGTTT
1 AGGGTTT
14343 AGGGTTT
1 AGGGTTT
*
14350 AAGGTTT
1 AGGGTTT
*
14357 AGTG-TT
1 AGGGTTT
*
14363 AGTGTTT
1 AGGGTTT
14370 AGGGTTT
1 AGGGTTT
14377 AGGGTTT
1 AGGGTTT
14384 AGG
1 AGG
14387 CTCATAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
6 6 0.13
7 40 0.87
ACGTcount: A:0.17, C:0.00, G:0.40, T:0.43
Consensus pattern (7 bp):
AGGGTTT
Found at i:14372 original size:27 final size:27
Alignment explanation
Indices: 14334--14385 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
14324 CACAAAGGGT
14334 TTAGGGTTTAGGGTTTAAGGTTTAGTG
1 TTAGGGTTTAGGGTTTAAGGTTTAGTG
* *
14361 TTAGTGTTTAGGGTTTAGGGTTTAG
1 TTAGGGTTTAGGGTTTAAGGTTTAG
14386 GCTCATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.46
Consensus pattern (27 bp):
TTAGGGTTTAGGGTTTAAGGTTTAGTG
Found at i:16763 original size:50 final size:50
Alignment explanation
Indices: 16531--16973 Score: 329
Period size: 50 Copynumber: 8.7 Consensus size: 50
16521 ATCGAAGCTC
* * * * *
16531 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACAGATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * * *
16581 TCTGGTGTACACGTAGTAGCCTACACTTAGTACTAAACACGTGACTTATCCA
1 TCT-G-GTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * ** * * ** *
16633 TATGATACATATAGCAGCTTGCACTTAGTACTACACACGTGATCGAAGTTAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCTA-TCAA
* * * * * *
16685 T-AGGTGCACATGGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * * * *
16734 TCCGGTACACGTGGTAGCCTACACTTAGTACTACACACGTGACCTGTCCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * * * * *
16784 TCTGATACACGTAGTAGCCTGCACTTAGTACTGCACACATGA-TTGAAACTA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT--ATCAA
* * * * * *
16835 T-TGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGGCCTAACAA
1 TCT-GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* *
16885 TCTAGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACCTA--AA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * * *
16933 ACTGTCTTAAACACATAGTAGCCTGCACATAGTACTACACA
1 TCTG--GT--ACACGTAGTAGCCTGCACTTAGTACTACACA
16974 TGTGTTCTCA
Statistics
Matches: 305, Mismatches: 74, Indels: 26
0.75 0.18 0.06
Matches are distributed among these distances:
48 4 0.01
49 5 0.02
50 155 0.51
51 70 0.23
52 71 0.23
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
Found at i:16842 original size:101 final size:101
Alignment explanation
Indices: 16534--16922 Score: 254
Period size: 101 Copynumber: 3.8 Consensus size: 101
16524 GAAGCTCTCT
* * * * * *
16534 GGTACGCATAGTAGCCTGCACTTAGTACTACAGATGCGACCTATCAATCTGGTGTACACGTAGTA
1 GGTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAACAATCT--AGTACACGTAGTA
* * * *
16599 GCCTACACTTAGTACTAAACACGTGACTT--ATCCATAT-
64 GCCTACACTTAGTACTACACACATGA-TTGAAACTAT-TG
* * * * * * * * * * * *
16636 GATACATATAGCAGCTTGCACTTAGTACTACACACGTGATCGAAGTTAA--TAGGTGCACATGGT
1 GGTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAA--CAATCTA-GTACACGTAGT
* *** * * * **
16699 AGCCTGCACTTAGTACTACACATGCGACCT--ATCAATCC
63 AGCCTACACTTAGTACTACACACATGA-TTGAAACTATTG
* * * ** *
16737 GGTACACGTGGTAGCCTACACTTAGTACTACACACGTGACCTGTCCATCT-GATACACGTAGTAG
1 GGTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAACAATCTAG-TACACGTAGTAG
* *
16801 CCTGCACTTAGTACTGCACACATGATTGAAACTATTG
65 CCTACACTTAGTACTACACACATGATTGAAACTATTG
* * * *
16838 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGGCCTAACAATCTAGTACACGTAGTAGC
1 GGTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAACAATCTAGTACACGTAGTAGC
16903 CTACACTTAGTACTACACAC
66 CTACACTTAGTACTACACAC
16923 GTGACCTAAA
Statistics
Matches: 217, Mismatches: 60, Indels: 21
0.73 0.20 0.07
Matches are distributed among these distances:
99 3 0.01
100 30 0.14
101 147 0.68
102 35 0.16
104 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (101 bp):
GGTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAACAATCTAGTACACGTAGTAGC
CTACACTTAGTACTACACACATGATTGAAACTATTG
Found at i:16973 original size:151 final size:149
Alignment explanation
Indices: 16534--16975 Score: 551
Period size: 151 Copynumber: 2.9 Consensus size: 149
16524 GAAGCTCTCT
* *
16534 GGTACGCATAGTAGCCTGCACTTAGTACTACAGATGCGACCTATCAATCTGGTGTACACGTAGTA
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCT--AGTACACGTAGTA
* * * * * *
16599 GCCTACACTTAGTACTAAACACGTGACTTATCCATATGATACATATAGCAGCTTGCACTTAGTAC
64 GCCTACACTTAGTACTACACACGTGACCTATCCATCTGATACACATAGTAGCCTGCACTTAGTAC
**
16664 TACACACGTGATCGAAGTTAATA
129 TACACA--TGATCGAAACTAATA
* * * ** *
16687 GGTGCACATGGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCCGGTACACGTGGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACACGTAGTAGC
* *
16752 CTACACTTAGTACTACACACGTGACCTGTCCATCTGATACACGTAGTAGCCTGCACTTAGTACTG
66 CTACACTTAGTACTACACACGTGACCTATCCATCTGATACACATAGTAGCCTGCACTTAGTACT-
* * *
16817 CACACATGATTGAAACTATTG
130 -ACACATGATCGAAACTAATA
* *
16838 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGGCCTAACAATCTAGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACACGTAGTAGC
* ** * * *
16903 CTACACTTAGTACTACACACGTGACCTAAAACTGTCTTAAACACATAGTAGCCTGCACATAGTAC
66 CTACACTTAGTACTACACACGTGACCT--ATCCATCTGATACACATAGTAGCCTGCACTTAGTAC
16968 TACACATG
129 TACACATG
16976 TGTTCTCACA
Statistics
Matches: 249, Mismatches: 36, Indels: 10
0.84 0.12 0.03
Matches are distributed among these distances:
151 170 0.68
153 79 0.32
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (149 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACACGTAGTAGC
CTACACTTAGTACTACACACGTGACCTATCCATCTGATACACATAGTAGCCTGCACTTAGTACTA
CACATGATCGAAACTAATA
Found at i:22172 original size:40 final size:39
Alignment explanation
Indices: 22128--22272 Score: 209
Period size: 40 Copynumber: 3.6 Consensus size: 39
22118 GCTCCTCGTT
* * * *
22128 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCATCGGGACTTAACCCGGTT-TAGTAACTCGCA
*
22168 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCATCGGGACTTAACCCGG-TTTAGTAACTCGCA
*
22208 CAAATGCCATCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCATCGGGACTTAACCC-GGTTTAGTAACTCGCA
22248 CAAATGCCATCGGGACTTAACCCGG
1 CAAATGCCATCGGGACTTAACCCGG
22273 AACATTCTAC
Statistics
Matches: 97, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
39 1 0.01
40 93 0.96
41 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (39 bp):
CAAATGCCATCGGGACTTAACCCGGTTTAGTAACTCGCA
Found at i:29638 original size:118 final size:120
Alignment explanation
Indices: 29455--29678 Score: 296
Period size: 118 Copynumber: 1.9 Consensus size: 120
29445 GCTCCTCGTT
*
29455 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
29520 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
29575 CAAATGCCTTCGGG-CTTA-CCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
29636 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
29679 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
117 4 0.04
118 62 0.68
119 11 0.12
120 14 0.15
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:29678 original size:40 final size:40
Alignment explanation
Indices: 29455--29678 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
29445 GCTCCTCGTT
* *
29455 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
29495 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
29535 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
29575 CAAATGCCTTCGGG-CTTA-CCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
29613 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
29654 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29679 CATCATTCAA
Statistics
Matches: 165, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
37 2 0.01
38 28 0.17
39 8 0.05
40 115 0.70
41 12 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Done.