Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3049
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: 31519
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:304 original size:44 final size:45
Alignment explanation
Indices: 203--357 Score: 133
Period size: 44 Copynumber: 3.4 Consensus size: 45
193 TTGGATTATC
* * *
203 ACATATATACACTTTTC-CATTCATCACATCCGG-CAATAGGCTTTACT
1 ACATATATACA--TTTCACATTCATCACAT-CGGCCATTAGGCCTGA-T
250 CACATATATACATTTCACA-TCATCCACA-C-G-CATTAGGCCTGGAT
1 -ACATATATACATTTCACATTCAT-CACATCGGCCATTAGGCCT-GAT
* *
294 ACAGTATATACACTTCACATTCATCACATCGGCCATTAGGCCTTAT
1 ACA-TATATACATTTCACATTCATCACATCGGCCATTAGGCCTGAT
*
340 ACATAAATACACTTTCAC
1 ACATATATACA-TTTCAC
358 CATTACCATC
Statistics
Matches: 91, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
43 3 0.03
44 28 0.31
45 14 0.15
46 19 0.21
47 16 0.18
48 11 0.12
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.30
Consensus pattern (45 bp):
ACATATATACATTTCACATTCATCACATCGGCCATTAGGCCTGAT
Found at i:4741 original size:40 final size:40
Alignment explanation
Indices: 4697--4915 Score: 368
Period size: 40 Copynumber: 5.5 Consensus size: 40
4687 TCTTCGAGGT
* * * *
4697 TTAGCACGGATATATTACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
*
4737 TTAGCCCGGATACATCACTAGCACGAATGCTCCTCGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
4777 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
4817 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
4857 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCTGGG-C
1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTC-GGGAC
*
4897 TTAGCCCGGAAATATCACT
1 TTAGCCCGGATATATCACT
4916 CTCAATTCTC
Statistics
Matches: 171, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
40 168 0.98
41 3 0.02
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
Found at i:7220 original size:40 final size:39
Alignment explanation
Indices: 7183--7274 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
7173 GCTACTCGTT
*
7183 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
7223 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
7262 CAAATGCCTTCGG
1 CAAATGCCTTCGG
7275 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:7254 original size:39 final size:40
Alignment explanation
Indices: 7164--7324 Score: 170
Period size: 40 Copynumber: 4.0 Consensus size: 40
7154 CGGAATTTAA
** *
7164 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
7204 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
7243 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
7283 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
7323 CC
1 CC
7325 AGACATCATT
Statistics
Matches: 102, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.31
40 55 0.54
41 12 0.12
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:10379 original size:29 final size:29
Alignment explanation
Indices: 10346--10452 Score: 105
Period size: 29 Copynumber: 3.7 Consensus size: 29
10336 TAAAGGTGAT
10346 TTGGGCCTAATGGGCCATATGAATATGGA
1 TTGGGCCTAATGGGCCATATGAATATGGA
* *
10375 TTGGGCCTGATGGGCCATATGAATGT-GA
1 TTGGGCCTAATGGGCCATATGAATATGGA
* * *
10403 TTTAGGCCTGATAGGCCATAT-AA-ATGAGA
1 -TTGGGCCTAATGGGCCATATGAATATG-GA
*
10432 TTGGGCC-AAGTGGGGCATATG
1 TTGGGCCTAA-TGGGCCATATG
10453 CATGTATGTA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
27 2 0.03
28 18 0.28
29 44 0.69
ACGTcount: A:0.26, C:0.14, G:0.33, T:0.27
Consensus pattern (29 bp):
TTGGGCCTAATGGGCCATATGAATATGGA
Found at i:14927 original size:29 final size:29
Alignment explanation
Indices: 14895--14987 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 29
14885 TAAAGGTGAT
*
14895 TTGGGCCT-ACTAGGCTATATGAATATGAA
1 TTGGGCCTGA-TAGGCCATATGAATATGAA
* * *
14924 TTGGGCTTGATGGGCCATATGAATGTGAA
1 TTGGGCCTGATAGGCCATATGAATATGAA
*
14953 TTGGGCCTGATAGGCCTTAT-AA-ATGAGA
1 TTGGGCCTGATAGGCCATATGAATATGA-A
14981 TTGGGCC
1 TTGGGCC
14988 AAGTGGGGCA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
27 3 0.06
28 10 0.19
29 40 0.74
30 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (29 bp):
TTGGGCCTGATAGGCCATATGAATATGAA
Found at i:21617 original size:39 final size:40
Alignment explanation
Indices: 21500--21682 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 40
21490 GCTACTCATT
*
21500 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
21540 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
21580 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
21619 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
21660 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
21683 AACATCATTC
Statistics
Matches: 121, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 74 0.61
41 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:21668 original size:79 final size:80
Alignment explanation
Indices: 21500--21682 Score: 203
Period size: 79 Copynumber: 2.3 Consensus size: 80
21490 GCTACTCATT
* *
21500 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAA-GCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
21565 ATTTAGTAACTCGCAC
65 ATATAGTAACTAGCAC
* * ** *
21581 CAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCTG
1 CAAAGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* *
21643 GATATGGTCACTTAGCA-
64 GATATAGTAAC-TAGCAC
21660 CAAAGCCTTCGGGACTTAGCCCG
1 CAAAGCCTTCGGGACTTAGCCCG
21683 AACATCATTC
Statistics
Matches: 86, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
78 4 0.05
79 57 0.66
80 22 0.26
81 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTAGCAC
Found at i:28610 original size:39 final size:41
Alignment explanation
Indices: 28509--28689 Score: 188
Period size: 39 Copynumber: 4.6 Consensus size: 41
28499 TTGAATGATG
* *
28509 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
28549 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
28589 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAG-T--TAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
28625 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
28664 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28690 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 8, Indels: 24
0.79 0.05 0.16
Matches are distributed among these distances:
36 22 0.18
37 11 0.09
38 2 0.02
39 40 0.33
40 33 0.27
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:28680 original size:76 final size:80
Alignment explanation
Indices: 28510--28689 Score: 214
Period size: 76 Copynumber: 2.3 Consensus size: 80
28500 TGAATGATGT
28510 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGA-CATATCCGGACTAAGATCCGAAGGCATTT
*
28574 GTGCGAGATACTAATT
65 GTGCGAGATACTAATA
* * **
28590 CCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTA-A-ATCCGGGTTAAG-TCCCGAAGGCA-TT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACATATCCGGACTAAGAT-CCGAAGGCATTT
*
28649 GTGCGAGTTACT-ATAA
65 GTGCGAGATACTAAT-A
*
28665 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28690 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 7, Indels: 12
0.82 0.06 0.11
Matches are distributed among these distances:
74 2 0.02
75 23 0.26
76 33 0.37
77 1 0.01
79 13 0.15
80 17 0.19
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACATATCCGGACTAAGATCCGAAGGCATTTG
TGCGAGATACTAATA
Done.