Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1073
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: 48013
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Found at i:140 original size:32 final size:32
Alignment explanation
Indices: 104--171 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
94 ATTAGAGAAG
* * * *
104 TTTTATATGAATTTACTAATTATTTTAGTGAT
1 TTTTACATGAATTCACTAATCAATTTAGTGAT
* *
136 TTTTACGTGAATTCATTAATCAATTTAGTGAT
1 TTTTACATGAATTCACTAATCAATTTAGTGAT
168 TTTT
1 TTTT
172 CGTTAATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.54
Consensus pattern (32 bp):
TTTTACATGAATTCACTAATCAATTTAGTGAT
Found at i:229 original size:27 final size:29
Alignment explanation
Indices: 178--239 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
168 TTTTCGTTAA
178 TTAAAATAATAATATTTTAATAA-TTTAT
1 TTAAAATAATAATATTTTAATAATTTTAT
* *
206 TTAAATTAATCATATTTTAA-AATTTTAT
1 TTAAAATAATAATATTTTAATAATTTTAT
234 TTAAAA
1 TTAAAA
240 ATTAATAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 28 0.93
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
TTAAAATAATAATATTTTAATAATTTTAT
Found at i:2237 original size:14 final size:13
Alignment explanation
Indices: 2214--2267 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 13
2204 AATTGAATGA
2214 TTTAATTAAAAAT
1 TTTAATTAAAAAT
2227 TTTATATTAAATAAAT
1 TTTA-ATT-AA-AAAT
*
2243 ATTAATATAAAAAT
1 TTTAAT-TAAAAAT
2257 TTTATATTAAA
1 TTTA-ATTAAA
2268 TAAATATTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 4 0.12
14 14 0.41
15 8 0.24
16 8 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAATTAAAAAT
Found at i:2241 original size:18 final size:18
Alignment explanation
Indices: 2215--2320 Score: 70
Period size: 18 Copynumber: 6.3 Consensus size: 18
2205 ATTGAATGAT
* *
2215 TTAATTAAAAATTTTATA
1 TTAAATAAAAATATTATA
2233 TTAAAT--AAATATTA-A
1 TTAAATAAAAATATTATA
*
2248 -T--ATAAAAATTTTATA
1 TTAAATAAAAATATTATA
*
2263 TTAAAT--AAATATTAGA
1 TTAAATAAAAATATTATA
*
2279 TTATATAAAAA-ATTTATA
1 TTAAATAAAAATA-TTATA
*
2297 TTACATAAAATATATTA-A
1 TTAAATAAAA-ATATTATA
2315 TTAAAT
1 TTAAAT
2321 GATATAATTT
Statistics
Matches: 68, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
12 2 0.03
14 8 0.12
15 2 0.03
16 21 0.31
17 1 0.01
18 29 0.43
19 4 0.06
20 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (18 bp):
TTAAATAAAAATATTATA
Found at i:2253 original size:16 final size:17
Alignment explanation
Indices: 2230--2305 Score: 58
Period size: 15 Copynumber: 4.7 Consensus size: 17
2220 TAAAAATTTT
2230 ATATTAAATAAATATTA
1 ATATTAAATAAATATTA
*
2247 ATA-T-AA-AAAT-TTT
1 ATATTAAATAAATATTA
2260 ATATTAAATAAATATTA
1 ATATTAAATAAATATTA
2277 GATTATATAAA-AAAT-TT-
1 -A-TAT-TAAATAAATATTA
*
2294 ATATTACATAAA
1 ATATTAAATAAA
2306 ATATATTAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 18
0.70 0.04 0.26
Matches are distributed among these distances:
13 5 0.10
14 8 0.17
15 10 0.21
16 6 0.12
17 5 0.10
18 3 0.06
19 7 0.15
20 4 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (17 bp):
ATATTAAATAAATATTA
Found at i:2285 original size:34 final size:30
Alignment explanation
Indices: 2215--2305 Score: 121
Period size: 30 Copynumber: 2.9 Consensus size: 30
2205 ATTGAATGAT
2215 TTAAT-TAAAAATTTTATATTAAATAAATA
1 TTAATATAAAAATTTTATATTAAATAAATA
2244 TTAATATAAAAATTTTATATTAAATAAATA
1 TTAATATAAAAATTTTATATTAAATAAATA
* *
2274 TTAGATTATATAAAAAATTTATATTACATAAA
1 TT--A--ATATAAAAATTTTATATTAAATAAA
2306 ATATATTAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
29 5 0.09
30 26 0.47
32 1 0.02
34 23 0.42
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (30 bp):
TTAATATAAAAATTTTATATTAAATAAATA
Found at i:2306 original size:16 final size:16
Alignment explanation
Indices: 2222--2319 Score: 55
Period size: 14 Copynumber: 6.2 Consensus size: 16
2212 GATTTAATTA
2222 AAAATTTTATATTAAAT
1 AAAA-TTTATATTAAAT
*
2239 AAATATTAATA-T-AA-
1 AAA-ATTTATATTAAAT
*
2253 AAATTTTATATTAAAT
1 AAAATTTATATTAAAT
* *
2269 -AAATATTAGATTATATAA
1 AAAAT-TTATATTA-A-AT
*
2287 AAAATTTATATTACAT
1 AAAATTTATATTAAAT
*
2303 AAAA--TATATTAATT
1 AAAATTTATATTAAAT
2317 AAA
1 AAA
2320 TGATATAATT
Statistics
Matches: 62, Mismatches: 11, Indels: 19
0.67 0.12 0.21
Matches are distributed among these distances:
13 5 0.08
14 15 0.24
15 7 0.11
16 13 0.21
17 9 0.15
18 9 0.15
19 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (16 bp):
AAAATTTATATTAAAT
Found at i:2644 original size:7 final size:7
Alignment explanation
Indices: 2621--2671 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
2611 TTGAAAAATA
2621 ATTTTAT
1 ATTTTAT
*
2628 ATCTTAT
1 ATTTTAT
2635 ATTTTAT
1 ATTTTAT
*
2642 ATTTTAA
1 ATTTTAT
2649 ATTTTGAT
1 ATTTT-AT
2657 ATTTCTAT
1 ATTT-TAT
*
2665 TTTTTAT
1 ATTTTAT
2672 GAGTTTTGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
7 26 0.70
8 10 0.27
9 1 0.03
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (7 bp):
ATTTTAT
Found at i:4346 original size:13 final size:12
Alignment explanation
Indices: 4313--4374 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
4303 TGGTTACTTT
*
4313 TTTTGTTTTTTA
1 TTTTGATTTTTA
4325 TTTTGATTTTTA
1 TTTTGATTTTTA
* *
4337 TTATTTATTTATA
1 TT-TTGATTTTTA
* *
4350 TTTTAATTCTT-
1 TTTTGATTTTTA
*
4361 TTCTGATTTTTA
1 TTTTGATTTTTA
4373 TT
1 TT
4375 AAAAAAATAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
11 8 0.21
12 21 0.54
13 10 0.26
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTTGATTTTTA
Found at i:5025 original size:1 final size:1
Alignment explanation
Indices: 5019--5057 Score: 60
Period size: 1 Copynumber: 39.0 Consensus size: 1
5009 TCTCCTCCCT
* *
5019 CCCCCCCACCCCCCCCCCCACCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
5058 ACGGAAACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.05, C:0.95, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:5036 original size:12 final size:12
Alignment explanation
Indices: 5019--5057 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
5009 TCTCCTCCCT
5019 CCCCCCCACCCC
1 CCCCCCCACCCC
5031 CCCCCCCACCCC
1 CCCCCCCACCCC
5043 CCCCCCC-CCCC
1 CCCCCCCACCCC
5054 CCCC
1 CCCC
5058 ACGGAAACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.05, C:0.95, G:0.00, T:0.00
Consensus pattern (12 bp):
CCCCCCCACCCC
Found at i:5044 original size:20 final size:20
Alignment explanation
Indices: 5019--5059 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5009 TCTCCTCCCT
5019 CCCCCCCACCCCCCCCCCCA
1 CCCCCCCACCCCCCCCCCCA
*
5039 CCCCCCCCCCCCCCCCCCCA
1 CCCCCCCACCCCCCCCCCCA
5059 C
1 C
5060 GGAAACCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.07, C:0.93, G:0.00, T:0.00
Consensus pattern (20 bp):
CCCCCCCACCCCCCCCCCCA
Found at i:8205 original size:80 final size:83
Alignment explanation
Indices: 8070--8230 Score: 292
Period size: 82 Copynumber: 2.0 Consensus size: 83
8060 CATAGTCTCA
8070 GGTGCTCGGTAAACATGCTAATTTCACGTCACCCACTCTCATTACATTCTCC-TTTTCTTTTTAA
1 GGTGCTCGGTAAACATGCTAATTTCACGTCACCCACTCTCATTACATTCTCCTTTTTCTTTTTAA
8134 TATTTATTATTGTGACTC
66 TATTTATTATTGTGACTC
8152 GGTGCTCGGTAAAC-TGCTAATTTCACGTCA-CCACTCTCATTACATTCTCCTTTTTTCTTTTTA
1 GGTGCTCGGTAAACATGCTAATTTCACGTCACCCACTCTCATTACATTCTCC-TTTTTCTTTTTA
8215 ATATTTATTATTGTGA
65 ATATTTATTATTGTGA
8231 AATAATATTT
Statistics
Matches: 77, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
80 20 0.26
81 16 0.21
82 41 0.53
ACGTcount: A:0.22, C:0.23, G:0.11, T:0.44
Consensus pattern (83 bp):
GGTGCTCGGTAAACATGCTAATTTCACGTCACCCACTCTCATTACATTCTCCTTTTTCTTTTTAA
TATTTATTATTGTGACTC
Found at i:11322 original size:2 final size:2
Alignment explanation
Indices: 11317--11346 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11307 TATGTGTGTG
*
11317 TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11347 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:12991 original size:273 final size:270
Alignment explanation
Indices: 12506--13052 Score: 1040
Period size: 273 Copynumber: 2.0 Consensus size: 270
12496 TCTTCTGCAG
12506 AAACTAGCGGTAAGCCCTTGTTTATTGACTGTTTGGAATCTTTCATAGCTGATGTCAGCCCAGTG
1 AAACTAGCGGTAAGCCCTTGTTTATTGACTGTTTGGAATCTTTCATAGCTGATGTCAGCCCAGTG
12571 TTTTTAGTTTAGATCATAACATTTCCCCTACTAAAATGATATTAATCTGGTGGGCTTGCTCTGTT
66 TTTTTAGTTTAGATCATAACATTTCCCCTACTAAAATGATATTAATCTGGTGGGCTTGCTCTGTT
12636 TCTCTTTAACATGCCCATCTTTTTAATGAACAATTTCTCGGTAGTAAAATATTAAAGGAAGTAGT
131 TCTCTTTAACATGCCCATCTTTTTAATGAACAATTTCTCGGTAGTAAAATATTAAAGGAAGTAGT
12701 AACATGCCCAACCTTAATGCAAGGTTTATGCCAGATTATCAGAATATATTTCACTAACTTGTTAA
196 AACATGCCCAACCTTAATGCAAGGTTTATGCCAGATTATCAGAATATATTTCACTAACTTGTT-A
12766 GTCATTACATT
260 GTCATTACATT
*
12777 AAACTAGCGGTAAGCCCTTGTTTATTGACTGTTTGGAATCTTTCATAGCTGATGTCAGCCACTGT
1 AAACTAGCGGTAAGCCCTTGTTTATTGACTGTTTGGAATCTTTCATAGCTGATGTCAGCC-CAGT
*
12842 GTTTTTAGTTTAGATCATAACATTTCCCTTACTAAAAATGATATTAATCTGGTGGGCTTGCTCTG
65 GTTTTTAGTTTAGATCATAACATTTCCCCTACT-AAAATGATATTAATCTGGTGGGCTTGCTCTG
*
12907 TTTCTCTTTAACATGCCCATCTTTTTAATGAACAATTTCTCGGTAGTAAATTATTAAAGGAAGTA
129 TTTCTCTTTAACATGCCCATCTTTTTAATGAACAATTTCTCGGTAGTAAAATATTAAAGGAAGTA
12972 GTAACATGCCCAACCTTAATGCAAGGTTTATGCCAGATTATCAGAATATATTTCACTAACTTGTT
194 GTAACATGCCCAACCTTAATGCAAGGTTTATGCCAGATTATCAGAATATATTTCACTAACTTGTT
13037 AGTCATTACATT
259 AGTCATTACATT
13049 AAAC
1 AAAC
13053 AGGAGTTTGA
Statistics
Matches: 271, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
271 60 0.22
272 51 0.19
273 160 0.59
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (270 bp):
AAACTAGCGGTAAGCCCTTGTTTATTGACTGTTTGGAATCTTTCATAGCTGATGTCAGCCCAGTG
TTTTTAGTTTAGATCATAACATTTCCCCTACTAAAATGATATTAATCTGGTGGGCTTGCTCTGTT
TCTCTTTAACATGCCCATCTTTTTAATGAACAATTTCTCGGTAGTAAAATATTAAAGGAAGTAGT
AACATGCCCAACCTTAATGCAAGGTTTATGCCAGATTATCAGAATATATTTCACTAACTTGTTAG
TCATTACATT
Found at i:19530 original size:2 final size:2
Alignment explanation
Indices: 19523--19569 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
19513 AGGTTTAGCT
19523 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19565 TC TC T
1 TC TC T
19570 TTCCCCTCCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:21390 original size:18 final size:16
Alignment explanation
Indices: 21370--21400 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21360 TTTATTGCTA
21370 TATATTTTAATTTTCC
1 TATATTTTAATTTTCC
21386 TATATTTTAATTTTC
1 TATATTTTAATTTTC
21401 TTTTTTCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATTTTAATTTTCC
Found at i:21405 original size:76 final size:77
Alignment explanation
Indices: 21311--21462 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 77
21301 CTTTTTTTAT
21311 TATTATTAATTTTCTTTTTTCCTATCTTTAGATATCATTATTTTTGTTTTTTATTGCTATATATT
1 TATTATTAATTTTCTTTTTTCCTATCTTTAGATATCATTATTTTTGTTTTTTATTGCTATATATT
21376 TTAATTTTCCTA
66 TTAATTTTCCTA
21388 TATT-TTAATTTTCTTTTTTCCTATCTTTAGATATCATTATTTTTGTTTTTTATTGCTATATATT
1 TATTATTAATTTTCTTTTTTCCTATCTTTAGATATCATTATTTTTGTTTTTTATTGCTATATATT
21452 TTAATTTTCCT
66 TTAATTTTCCT
21463 GTAAGTTTAC
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 71 0.95
77 4 0.05
ACGTcount: A:0.21, C:0.11, G:0.04, T:0.64
Consensus pattern (77 bp):
TATTATTAATTTTCTTTTTTCCTATCTTTAGATATCATTATTTTTGTTTTTTATTGCTATATATT
TTAATTTTCCTA
Found at i:32410 original size:14 final size:14
Alignment explanation
Indices: 32391--32441 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
32381 TATAGTAAAA
32391 TATATTTTAATTTT
1 TATATTTTAATTTT
*
32405 TATATTATTAAATTT
1 TATATT-TTAATTTT
* *
32420 AATATTTTAATCTT
1 TATATTTTAATTTT
32434 TATATTTT
1 TATATTTT
32442 TTAAAATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TATATTTTAATTTT
Found at i:33956 original size:14 final size:14
Alignment explanation
Indices: 33939--33988 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
33929 TTATATTTTA
*
33939 AAAATATAAATACT
1 AAAATATAAATATT
33953 AAAATAATAAAT-TT
1 AAAAT-ATAAATATT
*
33967 AATAATATAAAAATT
1 AA-AATATAAATATT
33982 AAAATAT
1 AAAATAT
33989 TTTTTCACCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAATATAAATATT
Found at i:45915 original size:58 final size:59
Alignment explanation
Indices: 45850--45967 Score: 184
Period size: 58 Copynumber: 2.0 Consensus size: 59
45840 AATGTCATGC
* *
45850 TATGTCTTGGAATTAGAAATTACTTGTTTCTGTATTTGC-AGGCATAAACAGATCCTGT
1 TATGTCTTAGAATTAGAAATTACTTGTTTCTGTATTGGCGAGGCATAAACAGATCCTGT
* *
45908 TATGTCTTAGAATTGGAAATTACTTGTTTCTGTATTGGCGGGGGCATAAACAGATCCTGT
1 TATGTCTTAGAATTAGAAATTACTTGTTTCTGTATTGGC-GAGGCATAAACAGATCCTGT
45968 AACCGGGGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 36 0.67
60 18 0.33
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (59 bp):
TATGTCTTAGAATTAGAAATTACTTGTTTCTGTATTGGCGAGGCATAAACAGATCCTGT
Done.