Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2653
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: 30102
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:6315 original size:47 final size:47
Alignment explanation
Indices: 6261--6530 Score: 425
Period size: 47 Copynumber: 5.7 Consensus size: 47
6251 TTAGGATTCT
* * *
6261 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
6308 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
6355 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
6402 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
6449 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
6496 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
6531 TCCCGAAGGG
Statistics
Matches: 209, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
46 1 0.00
47 208 1.00
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:6704 original size:36 final size:37
Alignment explanation
Indices: 6649--6726 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 37
6639 CCGAGCTCTA
* *
6649 AAGACCCGATGACTACGTGTGG-GATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
6685 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
6722 AAGAC
1 AAGAC
6727 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 20 0.53
37 18 0.47
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:8637 original size:43 final size:43
Alignment explanation
Indices: 8589--8691 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
8579 TTGGTTTTCA
8589 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
8632 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
8675 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
8692 TTGAAATGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:8740 original size:28 final size:29
Alignment explanation
Indices: 8673--8745 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
8663 GTTGTGAGAT
* *
8673 TGGCACTAAGTGTGCGGGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATACA
*
8702 TGGCACTAAGTGTG-GAG-TTTAAAGTACA
1 TGGCACTAAGTGTGCGAGCTTGAAA-TACA
8730 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
8746 TGGTTGATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 5 0.13
28 19 0.49
29 15 0.38
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATACA
Found at i:9131 original size:40 final size:39
Alignment explanation
Indices: 9094--9277 Score: 235
Period size: 40 Copynumber: 4.6 Consensus size: 39
9084 CTAAGTGACC
9094 ATATCCGGACTAAGTTCGAAGAGCATTCGTGCTAGTGAT
1 ATATCCGGACTAAGTTCGAAGAGCATTCGTGCTAGTGAT
*
9133 GTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
1 ATATCCGGACTAAGTT-CGAAGAGCATTCGTGCTAGTGAT
*
9173 GTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
1 ATATCCGGACTAAGTT-CGAAGAGCATTCGTGCTAGTGAT
*** * *
9213 ATATCCGTG-CTAAACCCCGAAGAGCATTCGTGCTGGTGTT
1 ATATCCG-GACT-AAGTTCGAAGAGCATTCGTGCTAGTGAT
* * *
9253 ATATCCGGGCTAGGTCCGAAGAGCA
1 ATATCCGGACTAAGTTCGAAGAGCA
9278 ATCATGCTGG
Statistics
Matches: 131, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 27 0.21
40 101 0.77
41 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (39 bp):
ATATCCGGACTAAGTTCGAAGAGCATTCGTGCTAGTGAT
Found at i:9218 original size:80 final size:80
Alignment explanation
Indices: 9069--9277 Score: 257
Period size: 80 Copynumber: 2.6 Consensus size: 80
9059 CGGGCTAAGT
* *
9069 CCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGTT-CGAAGAGCATTCGTGCTAGTG
1 CCCGAAGAGCATTCGTGCT-AGTGA-TATATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTG
* **
9131 ATGTATCCG-GACTAAGT
64 ATATATCCGTG-CTAAAC
* *
9148 TCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
1 CCCGAAGAGCATTCGTGCTAGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
9213 ATATCCGTGCTAAAC
66 ATATCCGTGCTAAAC
* * * *
9228 CCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCT-AGGTCCGAAGAGCA
1 CCCGAAGAGCATTCGTGCTAGTGATATATCCGGACTAAGTTCCGAAGAGCA
9278 ATCATGCTGG
Statistics
Matches: 113, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
79 34 0.30
80 71 0.63
81 8 0.07
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
CCCGAAGAGCATTCGTGCTAGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
ATATCCGTGCTAAAC
Found at i:12667 original size:47 final size:47
Alignment explanation
Indices: 12613--12976 Score: 545
Period size: 47 Copynumber: 7.7 Consensus size: 47
12603 TTAGGATTCT
* * *
12613 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
*
12660 ATGTGATGAATGTGAAAGTGTATATACACGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATAT--ATGTGATAAGGCCTAATGGCCG
12709 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
12756 ATGTGATAAATGTGAAAGTGTATATCTGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
12803 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
12850 ATGTGAT-AATGTGAAAGTGTATATATGTGAT-AGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
12895 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
12942 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
12977 TCCCAAAGGG
Statistics
Matches: 291, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
45 21 0.07
46 48 0.16
47 177 0.61
49 45 0.15
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:12920 original size:186 final size:189
Alignment explanation
Indices: 12613--12976 Score: 556
Period size: 186 Copynumber: 1.9 Consensus size: 189
12603 TTAGGATTCT
*
12613 ATGTGATGGATGTGAACATGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
12678 TGTATATACACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
66 TGTATATA-ACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAA
* * * **
12743 GGCCTAATGGCCGATGTGATAAATGTGAAAGTGTATATCTGTGATAAGGCCTAATAGCCG
130 GGCCGAATGGCCAACGTGATAAATGTGAAAGTGTATAAATGTGATAAGGCCTAATAGCCG
* *
12803 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT-AATGTGAAA
1 ATGTGATGAATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
* *
12866 GTGTATAT-ATGTGAT-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAG
65 GTGTATATAACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAA
* **
12929 GGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
130 GGCCGAATGGCCAACGTGATAAATGTGAAAGTGTATAAATGTGATAAG
12977 TCCCAAAGGG
Statistics
Matches: 159, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
186 86 0.54
187 6 0.04
189 18 0.11
190 49 0.31
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.28
Consensus pattern (189 bp):
ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATAACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAG
GCCGAATGGCCAACGTGATAAATGTGAAAGTGTATAAATGTGATAAGGCCTAATAGCCG
Found at i:13151 original size:37 final size:37
Alignment explanation
Indices: 13098--13173 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
13088 AGCTCTAAAT
* * *
13098 ACCCGATGACTACGTGTGGGGATTTTGTCCGGGTAAG
1 ACCCGATAACTACGTGTGGAGATTATGTCCGGGTAAG
*
13135 ACCCGATAACTTCGTGTGGAGATTATGTCCGGGTAAG
1 ACCCGATAACTACGTGTGGAGATTATGTCCGGGTAAG
13172 AC
1 AC
13174 TTCTTAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (37 bp):
ACCCGATAACTACGTGTGGAGATTATGTCCGGGTAAG
Found at i:23434 original size:40 final size:39
Alignment explanation
Indices: 23329--23512 Score: 237
Period size: 40 Copynumber: 4.6 Consensus size: 39
23319 GCTACTCGTT
*
23329 CAAATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATT-TAGTAACTCGCA
*
23368 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
*
23407 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
23447 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
23488 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
23513 CATCATTCAA
Statistics
Matches: 131, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
39 48 0.37
40 72 0.55
41 11 0.08
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:23459 original size:79 final size:82
Alignment explanation
Indices: 23329--23512 Score: 254
Period size: 79 Copynumber: 2.3 Consensus size: 82
23319 GCTACTCGTT
*
23329 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
23391 GATTTAGTAAC-TCGCA
66 GATATAGTAACTTAGCA
* **
23407 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
23471 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
23488 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
23513 CATCATTCAA
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
78 11 0.12
79 37 0.40
80 37 0.40
81 8 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:29976 original size:27 final size:27
Alignment explanation
Indices: 29945--30088 Score: 137
Period size: 27 Copynumber: 5.3 Consensus size: 27
29935 TATTGAGCCC
* * *
29945 CACACTCAATGCTATATAATCAACTCG
1 CACACTTAGTGCTACATAATCAACTCG
* *
29972 CACACTTAGTGCTACGTAATCAAATCG
1 CACACTTAGTGCTACATAATCAACTCG
*
29999 CACACTTAGTGCTACATAGTCAACTTCG
1 CACACTTAGTGCTACATAATCAAC-TCG
** ** *
30027 CACACTTAGTGCCGCATGGTCAATTCG
1 CACACTTAGTGCTACATAATCAACTCG
* **
30054 CACACTTAGTGC-ATCATATTCATTTCG
1 CACACTTAGTGCTA-CATAATCAACTCG
30081 CACACTTA
1 CACACTTA
30089 TGCAATCTCC
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
27 76 0.77
28 23 0.23
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (27 bp):
CACACTTAGTGCTACATAATCAACTCG
Found at i:30055 original size:55 final size:55
Alignment explanation
Indices: 29945--30088 Score: 150
Period size: 55 Copynumber: 2.7 Consensus size: 55
29935 TATTGAGCCC
* * * * *
29945 CACACTCAATGCTATATAATCAAC-TCGCACACTTAGTGCTACGTAATCAAATCG
1 CACACTTAGTGCTACATAATCAACTTCGCACACTTAGTGCCACATAATCAAATCG
* * ** *
29999 CACACTTAGTGCTACATAGTCAACTTCGCACACTTAGTGCCGCATGGTCAATTCG
1 CACACTTAGTGCTACATAATCAACTTCGCACACTTAGTGCCACATAATCAAATCG
* *
30054 CACACTTAGTGC-ATCATATTC-ATTTCGCACACTTA
1 CACACTTAGTGCTA-CATAATCAACTTCGCACACTTA
30089 TGCAATCTCC
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 34 0.45
55 42 0.55
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (55 bp):
CACACTTAGTGCTACATAATCAACTTCGCACACTTAGTGCCACATAATCAAATCG
Done.