Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold303
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: 26785
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Found at i:5377 original size:39 final size:40
Alignment explanation
Indices: 5332--5556 Score: 242
Period size: 40 Copynumber: 5.7 Consensus size: 40
5322 GCTCCTCGTT
* * * *
5332 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
5372 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
5411 CGAATGCCTTCGGGACTTAACCCGGATTTAGTACCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
5451 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
5491 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
5532 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
5557 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
39 39 0.25
40 104 0.66
41 15 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:5565 original size:41 final size:41
Alignment explanation
Indices: 5488--5565 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
5478 TTTGTATCTC
* * *
5488 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
5529 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
5566 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:13306 original size:39 final size:40
Alignment explanation
Indices: 13261--13484 Score: 242
Period size: 40 Copynumber: 5.7 Consensus size: 40
13251 GCTCCTCGTT
* * * *
13261 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
13301 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
13340 CGAATGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
13379 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
13419 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
13460 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
13485 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
39 70 0.45
40 76 0.48
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:13364 original size:79 final size:77
Alignment explanation
Indices: 13261--13484 Score: 252
Period size: 79 Copynumber: 2.8 Consensus size: 77
13251 GCTCCTCGTT
* * *
13261 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCACACAAAGCCTTCGGGACTTAACCCGGA
13326 TTTAATAACTCGCA
65 TTT-ATAACTCGCA
* * * *
13340 CGAATGCCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCACACAAA-GCCTTCGGGACTTAACCCGG-
* *
13405 ATTTGTATCTCGCA
64 ATTTATAACTCGCA
* * * * *
13419 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-ACTCA-CACAAAGCCTTCGGGACTTAACCCG
13483 GA
63 GA
13485 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
78 12 0.10
79 79 0.65
80 25 0.20
81 6 0.05
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCACACAAAGCCTTCGGGACTTAACCCGGAT
TTATAACTCGCA
Found at i:13493 original size:41 final size:41
Alignment explanation
Indices: 13416--13493 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
13406 TTTGTATCTC
* * *
13416 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
13457 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
13494 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:18075 original size:64 final size:66
Alignment explanation
Indices: 17994--18155 Score: 177
Period size: 67 Copynumber: 2.5 Consensus size: 66
17984 AGACATTATG
* * * * * *
17994 ATGTAGCTAGGTTGCATGGGTGATACTA-TG-TGTACACCATGTAGACAAGAGAGTTACGGGATA
1 ATGTAGCTAGGTCGCATGGGTGGTACTAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATA
*
18057 T
66 A
* * *
18058 ATGTAGCTAGGTCGCATGTGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA-GTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
18123 AA
65 AA
* *
18125 AT-TGGCTAGGTCACATGGGTGGTACTGAGTG
1 ATGTAGCTAGGTCGCATGGGTGGTACT-AGTG
18156 TTCTCCATGT
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
64 23 0.29
66 24 0.30
67 32 0.41
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.25
Consensus pattern (66 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATA
A
Found at i:22226 original size:68 final size:66
Alignment explanation
Indices: 22154--22325 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
22144 CATCATGTGT
* * * *
22154 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
22217 TGTAG
62 TGTAG
** * *
22222 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
22287 AG
65 AG
* * * *
22289 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
22326 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:22259 original size:64 final size:64
Alignment explanation
Indices: 22178--22361 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
22168 AGACATTATG
* * *
22178 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
22242 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
22307 AA
63 AA
* * *
22309 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
22362 CGAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 33 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:26478 original size:27 final size:28
Alignment explanation
Indices: 26447--26506 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
26437 TGGAAATGTT
26447 TTGGATAATTA-TTGATTGGTGAAATTG
1 TTGGATAATTACTTGATTGGTGAAATTG
26474 TTGGATAATTACTTGATTGGTGAAATTG
1 TTGGATAATTACTTGATTGGTGAAATTG
26502 TTGGA
1 TTGGA
26507 AAAGAGAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 11 0.34
28 21 0.66
ACGTcount: A:0.28, C:0.02, G:0.27, T:0.43
Consensus pattern (28 bp):
TTGGATAATTACTTGATTGGTGAAATTG
Found at i:26676 original size:68 final size:66
Alignment explanation
Indices: 26604--26775 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
26594 CATCATGTGT
* * * *
26604 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
26667 TGTAG
62 TGTAG
** * *
26672 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
26737 AG
65 AG
* * * *
26739 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
26776 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:26709 original size:64 final size:66
Alignment explanation
Indices: 26628--26784 Score: 194
Period size: 67 Copynumber: 2.4 Consensus size: 66
26618 AGACATTATG
* * * *
26628 ATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGGGATA
1 ATGTAGCTAGGTCGCATGGGTGGTACTAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATA
*
26691 T
66 A
* * *
26692 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA-GTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
26757 AA
65 AA
* *
26759 AT-TGGCTAGGTCACATGGGTGGTACT
1 ATGTAGCTAGGTCGCATGGGTGGTACT
26785 G
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 24 0.31
66 21 0.27
67 32 0.42
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.24
Consensus pattern (66 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATA
A
Done.