Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1002
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: 47153
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Found at i:4462 original size:40 final size:40
Alignment explanation
Indices: 4388--4610 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
4378 GCTCCTCGTT
*
4388 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
4427 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
4467 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
4507 C-AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
4545 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
4586 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
4611 CATCATTCAA
Statistics
Matches: 164, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
38 25 0.15
39 32 0.20
40 94 0.57
41 13 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:4551 original size:78 final size:78
Alignment explanation
Indices: 4388--4610 Score: 288
Period size: 78 Copynumber: 2.8 Consensus size: 78
4378 GCTCCTCGTT
* *
4388 CAAATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGACTTAGCCCGGATT-TAGTAACTCGCAC-AATGCCTTCGGGACTTAGCCCGG
*
4452 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
4467 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTAACTCGCACAATGCCTTCGGGACTTAGCCCGGA
*
4531 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * * *
4545 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAATGCCTTCGGGACTTAGCCCGG
4610 A
64 A
4611 CATCATTCAA
Statistics
Matches: 127, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
77 3 0.02
78 48 0.38
79 39 0.31
80 35 0.28
81 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:4570 original size:118 final size:118
Alignment explanation
Indices: 4390--4610 Score: 295
Period size: 118 Copynumber: 1.9 Consensus size: 118
4380 TCCTCGTTCA
* *
4390 AATGCCTTCGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATA
*
4455 TAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
66 TAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * * **
4508 AATGCCTTCGGGCTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGA
1 AATGCCTTCGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
* * *
4571 TATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 TATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
4611 CATCATTCAA
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
117 4 0.04
118 77 0.87
119 8 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (118 bp):
AATGCCTTCGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATA
TAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:8834 original size:52 final size:50
Alignment explanation
Indices: 8756--8894 Score: 170
Period size: 50 Copynumber: 2.7 Consensus size: 50
8746 GTTGTGAGAA
* * ** *
8756 CACGTGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAAATGGTTTTAGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTAAGTGTACAAAATGG--TTAGGC
* * *
8808 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGC
1 CACGTGTGTAGTACTAAGTGCAGGCTACTAAGTGTACAAAATGGTTAGGC
* *
8858 CGCATGTGTAGTACTAAGTGCAGGCTACTAAGTGTAC
1 CACGTGTGTAGTACTAAGTGCAGGCTACTAAGTGTAC
8895 CCGATAGCTT
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 39 0.51
52 38 0.49
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (50 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTAAGTGTACAAAATGGTTAGGC
Found at i:16055 original size:21 final size:21
Alignment explanation
Indices: 16029--16069 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16019 GTTTGGTTGG
*
16029 TGAGAAAACTAAAGAAAATGA
1 TGAGAAAAATAAAGAAAATGA
*
16050 TGAGAAAAATGAAGAAAATG
1 TGAGAAAAATAAAGAAAATG
16070 GATTTCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.61, C:0.02, G:0.22, T:0.15
Consensus pattern (21 bp):
TGAGAAAAATAAAGAAAATGA
Found at i:21321 original size:35 final size:35
Alignment explanation
Indices: 21278--21391 Score: 140
Period size: 35 Copynumber: 3.3 Consensus size: 35
21268 CATACGTAAG
21278 TACATGTGAGCTTATATTGAACTTGTATATTCGGC
1 TACATGTGAGCTTATATTGAACTTGTATATTCGGC
* * * **
21313 TGCATGTGAGGTTATATTGAACTTG-AGTATTTGAT
1 TACATGTGAGCTTATATTGAACTTGTA-TATTCGGC
* *
21348 TACATGTGAGCTTATATTAAACTTGTATATTCGGT
1 TACATGTGAGCTTATATTGAACTTGTATATTCGGC
*
21383 TATATGTGA
1 TACATGTGA
21392 AGTTATCTTG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 1 0.02
35 64 0.97
36 1 0.02
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (35 bp):
TACATGTGAGCTTATATTGAACTTGTATATTCGGC
Found at i:28621 original size:35 final size:35
Alignment explanation
Indices: 28509--28622 Score: 158
Period size: 35 Copynumber: 3.3 Consensus size: 35
28499 CATAGGTAAG
*
28509 TACATGTGAGCTTATATTGAACTTGTATATTCAGT
1 TACATGTGAGCTTATATTGAACTTGTATATTCGGT
* * * *
28544 TGCATGTGAGGTTATATTGAACTTG-AGTATTTGAT
1 TACATGTGAGCTTATATTGAACTTGTA-TATTCGGT
28579 TACATGTGAGCTTATATTGAACTTGTATATTCGGT
1 TACATGTGAGCTTATATTGAACTTGTATATTCGGT
*
28614 TATATGTGA
1 TACATGTGA
28623 AGTTATCTTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
34 1 0.01
35 65 0.97
36 1 0.01
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (35 bp):
TACATGTGAGCTTATATTGAACTTGTATATTCGGT
Found at i:37299 original size:40 final size:40
Alignment explanation
Indices: 37244--37427 Score: 235
Period size: 40 Copynumber: 4.5 Consensus size: 40
37234 TATTCGGATG
37244 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
37284 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * * * *
37327 ATACCCGGGCTAAGTCCCGAAGGCATTTATGCTACTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
37367 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
37407 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
37428 ATACTTGGGT
Statistics
Matches: 123, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
39 13 0.11
40 74 0.60
41 1 0.01
43 35 0.28
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:37387 original size:83 final size:80
Alignment explanation
Indices: 37248--37427 Score: 254
Period size: 83 Copynumber: 2.2 Consensus size: 80
37238 CGGATGATAT
* * * * *
37248 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCTGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTATGCAACTGACTATATCCGGGCTAAGACCCGAAGGCATTTG
37313 TGCGAGTAGTTGCTATAC
66 TGC--G-AGTTGCTATAC
*
37331 CCGGGCTAAGTCCCGAAGGCATTTATGCTACTGACTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTATGCAACTGACTATATCCGGGCTAAGACCCGAAGGCATTTG
*
37396 TGCGAGTTGCTATAT
66 TGCGAGTTGCTATAC
*
37411 CC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAG
37428 ATACTTGGGT
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
79 14 0.16
80 12 0.13
81 1 0.01
83 62 0.70
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTATGCAACTGACTATATCCGGGCTAAGACCCGAAGGCATTTG
TGCGAGTTGCTATAC
Found at i:45337 original size:39 final size:40
Alignment explanation
Indices: 45282--45500 Score: 245
Period size: 39 Copynumber: 5.5 Consensus size: 40
45272 TTATTCGATG
45282 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
45322 ATATCC-GGCTAAGTCCCGAAGGCATTT-TGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
45363 ATA-CCTAGGCTAAGT-CCGAAGGCA-TTGTGCTAGTGACT
1 ATATCC-GGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
45401 ATAT-CGGGCTAAGTCCCGAAGGCATTTATGCTACTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
45440 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
45480 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
45501 ATACTTGGGT
Statistics
Matches: 154, Mismatches: 15, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
37 8 0.05
38 21 0.14
39 51 0.33
40 45 0.29
41 21 0.14
42 8 0.05
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:45470 original size:79 final size:78
Alignment explanation
Indices: 45282--45500 Score: 259
Period size: 79 Copynumber: 2.8 Consensus size: 78
45272 TTATTCGATG
*
45282 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGCTAAGTCCCGAAGGCAT
1 ATATCCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTGACTATATCCGGCTAAGTCCCGAAGGCAT
*
45347 TTTGCGAGTAGTTGCT
65 TTTGC--GTAGCTGCT
* * * *
45363 ATA-CCTAGGCTAAGTCCGAAGGCA-TTGTGCTAGTGACTATATCGGGCTAAGTCCCGAAGGCAT
1 ATATCC-GGGCTAAGCCCGAAGGCATTTGTGCAAGTGACTATATCCGGCTAAGTCCCGAAGGCAT
45426 TTATGC-TA-CTGACT
65 TT-TGCGTAGCTG-CT
* *
45440 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCCGGCTAAATCCCGAAG
1 ATATCCGGGCTAAG-CCCGAAGGCATTTGTGCAAG-TGACTATATCCGGCTAAGTCCCGAAG
45501 ATACTTGGGT
Statistics
Matches: 120, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
76 2 0.02
77 14 0.12
78 11 0.09
79 67 0.56
80 16 0.13
81 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (78 bp):
ATATCCGGGCTAAGCCCGAAGGCATTTGTGCAAGTGACTATATCCGGCTAAGTCCCGAAGGCATT
TTGCGTAGCTGCT
Done.