Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold931
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: 39331
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:2327 original size:39 final size:40
Alignment explanation
Indices: 2259--2473 Score: 295
Period size: 39 Copynumber: 5.6 Consensus size: 40
2249 TATTCGAATG
2259 ATATCCGGGCTAAGTCCCGAAGGCA-TTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
2298 ATATCC-GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
2337 A-ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
2376 AAAT--AGGCTAAGT-CCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
2413 ATATCCGGGCTAAG-ACCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
* *
2452 ATAT-CTGGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
2474 TACTTGGGTT
Statistics
Matches: 159, Mismatches: 9, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
37 26 0.16
38 37 0.23
39 92 0.58
40 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:2462 original size:77 final size:79
Alignment explanation
Indices: 2259--2473 Score: 316
Period size: 77 Copynumber: 2.8 Consensus size: 79
2249 TATTCGAATG
*
2259 ATATCCGGGCTAAGTCCCGAAGGCA-TTGTGCTAGTGACTATATCCGGCTAAGTCCCGAAGGCAT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCAGGCTAAGTCCCGAAGGCAT
2323 TTGTGCTAGTGACT
66 TTGTGCTAGTGACT
* *
2337 A-ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAAAT-AGGCTAAGT-CCGAAGGCTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCAGGCTAAGTCCCGAAGGCAT
2399 TTGTGCTAGTGACT
66 TTGTGCTAGTGACT
* * * *
2413 ATATCCGGGCTAAG-ACCGAAGGCATTTGTGCGAGTTG-CTATATCTGGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTATATCAGGCTAAGTCCCGAAGG
2474 TACTTGGGTT
Statistics
Matches: 124, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
76 47 0.38
77 52 0.42
78 25 0.20
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (79 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCAGGCTAAGTCCCGAAGGCAT
TTGTGCTAGTGACT
Found at i:2469 original size:115 final size:115
Alignment explanation
Indices: 2266--2473 Score: 307
Period size: 115 Copynumber: 1.8 Consensus size: 115
2256 ATGATATCCG
* *
2266 GGCTAAGTCCCGAAGGCATTGTGCTAGTGACTATATCCGGCTAAGTCCCGAAGGCATTTGTGCTA
1 GGCTAAGTCCCGAAGGCATTGTGCTAGTGACTATATCCGGCTAAGTACCGAAGGCATTTGTGCGA
*
2331 GTGACTAATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAAATA
66 GTGACTAATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGTGACTAAATA
*
2381 GGCTAAGT-CCGAAGGCTTTTGTGCTAGTGACTATATCCGGGCTAAG-ACCGAAGGCATTTGTGC
1 GGCTAAGTCCCGAAGGC-ATTGTGCTAGTGACTATATCC-GGCTAAGTACCGAAGGCATTTGTGC
*
2444 GAGTTG-CTATAT-CTGGCTAAATCCCGAAGG
64 GAG-TGACTA-ATCCGGGCTAAATCCCGAAGG
2474 TACTTGGGTT
Statistics
Matches: 84, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
114 8 0.10
115 65 0.77
116 11 0.13
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (115 bp):
GGCTAAGTCCCGAAGGCATTGTGCTAGTGACTATATCCGGCTAAGTACCGAAGGCATTTGTGCGA
GTGACTAATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGTGACTAAATA
Found at i:10762 original size:40 final size:40
Alignment explanation
Indices: 10707--10928 Score: 331
Period size: 40 Copynumber: 5.6 Consensus size: 40
10697 TATTCGAATG
*
10707 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
10747 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
10787 AAATCCAGGCTAACTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
10827 AAATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
10867 ATATCCGGGCTACGACCCGAAGGCATTTGTGCGAGCTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
10907 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
10929 TACTTGGGTT
Statistics
Matches: 166, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 13 0.08
40 151 0.91
41 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:23198 original size:30 final size:30
Alignment explanation
Indices: 23164--23230 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
23154 CATTTTGGTC
23164 CCTTTACTACTTTAAATCAAAATCAATTAA
1 CCTTTACTACTTTAAATCAAAATCAATTAA
*
23194 CCTTTACTATTTTAAATCAAAATCAATTAA
1 CCTTTACTACTTTAAATCAAAATCAATTAA
*
23224 CTTTTAC
1 CCTTTAC
23231 CTCTTTTACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (30 bp):
CCTTTACTACTTTAAATCAAAATCAATTAA
Found at i:28937 original size:47 final size:47
Alignment explanation
Indices: 28886--29253 Score: 603
Period size: 47 Copynumber: 7.7 Consensus size: 47
28876 TTAGGATTCT
* * *
28886 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
28933 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
28980 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
29029 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
29076 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
29125 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
29172 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
29219 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
29254 TCCCGAAGGG
Statistics
Matches: 306, Mismatches: 10, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
46 1 0.00
47 212 0.69
49 93 0.30
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:29017 original size:96 final size:96
Alignment explanation
Indices: 28907--29253 Score: 617
Period size: 96 Copynumber: 3.6 Consensus size: 96
28897 GTGAACATGC
*
28907 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
28972 AATGGCCGATGTGATGAATGTGAAAGTGTAT
66 AATGGCCGATGTGATGAATGTGAAAGTGTAT
*
29003 ATATATGTGATAAGGTCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
29068 AATGGCCGATGTGATGAATGTGAAAGTGTAT
66 AATGGCCGATGTGATGAATGTGAAAGTGTAT
29099 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
29164 AATGGCCGATGTGATGAATGTGAAAGTG--T
66 AATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * * *
29193 ATATATGTGATAAGGCCTAATAGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
29254 TCCCGAAGGG
Statistics
Matches: 243, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
94 57 0.23
96 186 0.77
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (96 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
AATGGCCGATGTGATGAATGTGAAAGTGTAT
Found at i:29067 original size:143 final size:141
Alignment explanation
Indices: 28886--29253 Score: 603
Period size: 143 Copynumber: 2.6 Consensus size: 141
28876 TTAGGATTCT
* * *
28886 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
28950 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATA
65 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATA
*
29015 AGGTCTAATGGCCG
128 AGGCCTAATGGCCG
29029 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
29094 TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
66 TG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
29159 GGCCTAATGGCCG
129 GGCCTAATGGCCG
* * * *
29172 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCAACGTGATGGATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
29237 TGTATAAATGTGATAAG
66 TGTATATATGTGATAAG
29254 TCCCGAAGGG
Statistics
Matches: 213, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
141 14 0.07
142 1 0.00
143 151 0.71
145 47 0.22
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (141 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
CCTAATGGCCG
Found at i:29427 original size:37 final size:37
Alignment explanation
Indices: 29371--29449 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
29361 CCGAGCTCTA
* * *
29371 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
* *
29408 AAGATCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
29445 AAGAC
1 AAGAC
29450 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:32560 original size:40 final size:40
Alignment explanation
Indices: 32515--32626 Score: 188
Period size: 40 Copynumber: 2.8 Consensus size: 40
32505 ATAACCACAA
* * *
32515 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
32555 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
32595 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
32627 CATTCAAATG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Done.