Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1319
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: 22332
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Found at i:1511 original size:39 final size:39
Alignment explanation
Indices: 1437--1617 Score: 201
Period size: 39 Copynumber: 4.6 Consensus size: 39
1427 ACTCCTCGTT
**
1437 CAAATGCCTTCGGGAGATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATT-TAGTAACTCGCA
*
1477 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* *
1516 CAAATGCCTTC-G-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
1553 CAAATGCCTTCGGATCTTAGTCCGGATAT-GTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
1593 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
1618 CATCATTCAA
Statistics
Matches: 122, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
37 33 0.27
38 2 0.02
39 52 0.43
40 35 0.29
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:1551 original size:37 final size:38
Alignment explanation
Indices: 1465--1564 Score: 157
Period size: 37 Copynumber: 2.6 Consensus size: 38
1455 AGCCCGGTTA
*
1465 TAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTC-GACTTAACCCGGAAT
*
1504 TAGTAACTCGCACAAATGCCTTCG-CTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGACTTAACCCGGAAT
*
1541 TAGTATCTCGCACAAATGCCTTCG
1 TAGTAACTCGCACAAATGCCTTCG
1565 GATCTTAGTC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
37 34 0.59
38 1 0.02
39 23 0.40
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (38 bp):
TAGTAACTCGCACAAATGCCTTCGACTTAACCCGGAAT
Found at i:1601 original size:76 final size:78
Alignment explanation
Indices: 1437--1617 Score: 201
Period size: 76 Copynumber: 2.3 Consensus size: 78
1427 ACTCCTCGTT
** *
1437 CAAATGCCTTCGGGAGATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGACTTAACCCGG
1 CAAATGCCTTC-GGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGACTTAACCCGG
* *
1501 ATTTAGTAACTCGCA
64 ATATAGTAACTAGCA
* **
1516 CAAATGCCTTC-G-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 CAAATGCCTTCGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGA-CTTAACCCGGA
*
1579 TAT-GTCACTTAGCA
65 TATAGTAAC-TAGCA
1593 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
1618 CATCATTCAA
Statistics
Matches: 87, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
76 43 0.49
77 21 0.24
78 1 0.01
79 22 0.25
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGAT
ATAGTAACTAGCA
Found at i:9196 original size:79 final size:81
Alignment explanation
Indices: 9094--9278 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
9084 GCTCCTCGTT
* *
9094 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
9157 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
9174 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
9238 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
9254 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9279 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:9278 original size:40 final size:40
Alignment explanation
Indices: 9094--9278 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
9084 GCTCCTCGTT
* *
9094 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
9134 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
9174 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
9213 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
9254 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9279 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:11003 original size:93 final size:93
Alignment explanation
Indices: 10844--11015 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
10834 CGCCCATAAG
*
10844 CGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCA
10909 ACAAGTTCGGATGCCTAGTTACATCTCA
66 ACAAGTTCGGATGCCTAGTTACATCTCA
* *
10937 CGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTGAACTCAGACTCAACTC
*
11001 AACGAGTTCGGATGC
65 AACAAGTTCGGATGC
11016 TCAATCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACAAGTTCGGATGCCTAGTTACATCTCA
Found at i:11010 original size:46 final size:46
Alignment explanation
Indices: 10837--11012 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
10827 TGTCACACGC
* *
10837 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* * * *
10883 CCATAAGTGAACTCAGACTCAACTCAACAAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
10933 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
10976 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
11013 TGCTCAATCA
Statistics
Matches: 107, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 59 0.55
47 27 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:18464 original size:46 final size:46
Alignment explanation
Indices: 18397--18525 Score: 206
Period size: 46 Copynumber: 2.8 Consensus size: 46
18387 TGTAACCCGC
* *
18397 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCAT
*
18443 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
18489 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
18526 TGCTCAACCA
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
45 2 0.03
46 77 0.97
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:18544 original size:46 final size:45
Alignment explanation
Indices: 18405--18544 Score: 133
Period size: 46 Copynumber: 3.0 Consensus size: 45
18395 GCCCATAAGC
* * * *
18405 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTC-GCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTC-GGATGCTCACCATCC-T-AGT
*** *
18451 GAACTCGGACTCAACTCAACGAGTTCGGACATTC-GCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T-AGT
18497 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-ACCATCCTAGT
18543 GA
1 GA
18545 CATGTCACTT
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
45 2 0.02
46 77 0.91
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCCTAGT
Done.