Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1263
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: 33660
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1309 original size:21 final size:21
Alignment explanation
Indices: 1279--1326 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
1269 TTCCAAAAAG
*
1279 CAAAAACAAGAACACA-AGAA
1 CAAAAACAAGAACAAACAGAA
*
1299 CAAAAATCAAGAAGAAACAGAA
1 CAAAAA-CAAGAACAAACAGAA
1321 CAAAAA
1 CAAAAA
1327 ATAACGTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 8 0.33
22 10 0.42
ACGTcount: A:0.71, C:0.17, G:0.10, T:0.02
Consensus pattern (21 bp):
CAAAAACAAGAACAAACAGAA
Found at i:2479 original size:26 final size:26
Alignment explanation
Indices: 2450--2557 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
2440 TGGTACAAAT
2450 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
2476 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2502 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
2528 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2554 TGAT
1 TGAT
2558 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:10054 original size:29 final size:29
Alignment explanation
Indices: 10021--10079 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
10011 ATAGTAGTAA
10021 CATAGTTTGTCTGGCAAAGTATAATCCGT
1 CATAGTTTGTCTGGCAAAGTATAATCCGT
10050 CATAGTTTGTCTGGCAAAGTATAATCCGT
1 CATAGTTTGTCTGGCAAAGTATAATCCGT
10079 C
1 C
10080 CAATGACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (29 bp):
CATAGTTTGTCTGGCAAAGTATAATCCGT
Found at i:11533 original size:27 final size:27
Alignment explanation
Indices: 11503--11563 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
11493 AGCACGTTAG
11503 GAAAGGAAAGACTAT-ATGGCACAAT-AT
1 GAAAGGAAAGACT-TGATGGCA-AATCAT
* * *
11530 GAAATGAATGACTTGATGGTAAATCAT
1 GAAAGGAAAGACTTGATGGCAAATCAT
11557 GAAAGGA
1 GAAAGGA
11564 TAGCATCTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.46, C:0.08, G:0.25, T:0.21
Consensus pattern (27 bp):
GAAAGGAAAGACTTGATGGCAAATCAT
Found at i:16256 original size:40 final size:40
Alignment explanation
Indices: 16147--16274 Score: 147
Period size: 40 Copynumber: 3.2 Consensus size: 40
16137 CCTTCGGAGT
*
16147 TTAG-CCGGATATAGCCACTAGCTCAAACGCCTTCGGGAC
1 TTAGCCCGGATATAGCCACTAGCTCAAATGCCTTCGGGAC
* ** * *
16186 TTAGCCCGGATATAG-TAGCTCCCACGAATGCCTTCGGGAC
1 TTAGCCCGGATATAGCCA-CTAGCTCAAATGCCTTCGGGAC
16226 TTAGCCCGGA-ATTAGCCACTAGCTCAAATG-CTCTCGGGAC
1 TTAGCCCGGATA-TAGCCACTAGCTCAAATGCCT-TCGGGAC
16266 TTAGCCCGG
1 TTAGCCCGG
16275 TTATCATCCG
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
39 8 0.11
40 64 0.88
41 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.24, T:0.22
Consensus pattern (40 bp):
TTAGCCCGGATATAGCCACTAGCTCAAATGCCTTCGGGAC
Found at i:24202 original size:40 final size:40
Alignment explanation
Indices: 24158--24381 Score: 256
Period size: 40 Copynumber: 5.6 Consensus size: 40
24148 GCCACTAGCT
* * * *
24158 CAAATGCCTTCGGGACTTGGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCA
*
24198 CAAATGCCTTCGGGACTTAGCCCGG-TATAATAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCA
*
24237 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCA
* * * *
24277 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCCCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCA
* * *** * *
24317 CGAATGCCTTCGGGACTTAGCCTGGA-ATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAATAACTCGCA
24357 CAAATG-CTCTCGGGACTTAGCCCGG
1 CAAATGCCT-TCGGGACTTAGCCCGG
24382 TTATCATCCG
Statistics
Matches: 161, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
39 39 0.24
40 122 0.76
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCA
Found at i:24260 original size:79 final size:78
Alignment explanation
Indices: 24158--24382 Score: 263
Period size: 79 Copynumber: 2.8 Consensus size: 78
24148 GCCACTAGCT
* *
24158 CAAATGCCTTCGGGACTTGGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
24223 TATAATAACTCACA
65 TATAATAACTCACA
* * * *
24237 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGCACAAACGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
* * *
24302 ATATAGTAGCTCCCA
65 -TATAATAACTCACA
* * * ** *
24317 CGAATGCCTTCGGGACTTAGCCTGGAATTAGCCACTAGCTCAAATG-CTCTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTAGCACAAATGCCT-TCGGGACTTAGCCCG
24381 GT
64 GT
24383 TATCATCCGA
Statistics
Matches: 124, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
79 63 0.51
80 61 0.49
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGT
ATAATAACTCACA
Found at i:27297 original size:43 final size:43
Alignment explanation
Indices: 27178--27299 Score: 154
Period size: 43 Copynumber: 2.8 Consensus size: 43
27168 TCACATATTG
* * * * **
27178 ATGCCACTGTCCTAGACAAGGTCTTACACGAAATCATAATATG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCATAATACA
* *
27221 ATGCCAATGTCCCAGACATTGTCTTACACGTAATCTTAATACA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCATAATACA
* *
27264 ATGCCAATGTCCCGGACATGGTCTTACATGTAATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
27300 CAACTTGATA
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCATAATACA
Found at i:30793 original size:42 final size:42
Alignment explanation
Indices: 30747--30900 Score: 184
Period size: 42 Copynumber: 3.6 Consensus size: 42
30737 TAAGACTATG
* * * *
30747 TGTAATACCATATCTAGGATATGGCATCTATATGGGACTTCG
1 TGTAAGACCATATCTAGGATATGGCATCGATATGAGACTTCA
*
30789 TGTAAGACCATATCTAGGATATGGCATCGATATGATACTTCA
1 TGTAAGACCATATCTAGGATATGGCATCGATATGAGACTTCA
* * * * *
30831 TGCAAGACCATAGCTAGGCTATTGGCATCGATACGAGA-TCCCA
1 TGTAAGACCATATCTAGGATA-TGGCATCGATATGAGACT-TCA
*
30874 TGTAAGACCATATCTGGGATATGGCAT
1 TGTAAGACCATATCTAGGATATGGCAT
30901 TGTTATAGTA
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 62 0.65
43 33 0.35
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATATCTAGGATATGGCATCGATATGAGACTTCA
Done.