Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3089
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: 28104
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:835 original size:40 final size:40
Alignment explanation
Indices: 783--1021 Score: 191
Period size: 41 Copynumber: 5.8 Consensus size: 40
773 ATAACTACTT
* *
783 GCACAAAGGCCTTCGGGTCTTAGCCCGGATATGGGT-ACTGA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT-AGTCACT-A
* * *
824 GCAC-GATGCCTTCGCGGACTTAGCCCGGATATAGTCGCTA
1 GCACAAATGCCTTCG-GGTCTTAGCCCGGATATAGTCACTA
* *
864 GCACAAATGCCTTTCGGGTCTTAGCCCGGATTATAATCGCTA
1 GCACAAATGCC-TTCGGGTCTTAGCCCGGA-TATAGTCACTA
* *
906 GCCGACAAATGCCTTCGGGTCTTTAGCCCAGATATAG-CAACTC
1 G-C-ACAAATGCCTTCGGGTC-TTAGCCCGGATATAGTC-ACTA
* * * * * *
949 GTACGAATGCCTTCGGATCTTAGTCTGGTTATAGTCCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT-CACTA
*
990 -CACAAA-GCCTTCGGGACTTAGCCGGCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCC--CGGATAT
1022 CATTCGAATA
Statistics
Matches: 158, Mismatches: 27, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
39 14 0.09
40 30 0.19
41 63 0.40
42 17 0.11
43 16 0.10
44 18 0.11
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGTCACTA
Found at i:2791 original size:44 final size:43
Alignment explanation
Indices: 2647--2809 Score: 134
Period size: 44 Copynumber: 3.6 Consensus size: 43
2637 GCAATAAGCG
* * *
2647 ACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCGCATGCATAAGTGA
1 ACTCGGACTCAACTCAACGAGTTCGGAC---T-CG-ATACATAAGTGA
* * * *
2695 ACTCGGACTCAACTCAA-GAGTTCGGATGCTAGTTACATTTCA-CGA
1 ACTCGGACTCAACTCAACGAGTTCGGA--CTCGATACA--TAAGTGA
* *
2740 TCT-GGACTCAACTCAACGAGTTCGGACATCGATCCATAAGTGA
1 ACTCGGACTCAACTCAACGAGTTCGGAC-TCGATACATAAGTGA
2783 ACTCGGACTCAACTCAACGAGTTCGGA
1 ACTCGGACTCAACTCAACGAGTTCGGA
2810 TGCTCAGCCA
Statistics
Matches: 93, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 44 0.47
45 14 0.15
46 3 0.03
47 7 0.08
48 17 0.18
49 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (43 bp):
ACTCGGACTCAACTCAACGAGTTCGGACTCGATACATAAGTGA
Found at i:10281 original size:93 final size:93
Alignment explanation
Indices: 10122--10293 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
10112 CGCCCATAAG
* *
10122 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
10187 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
10215 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
10280 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
10294 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:10290 original size:46 final size:46
Alignment explanation
Indices: 10115--10290 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
10105 TGTAACCCGC
* * *
10115 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
10161 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
10211 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
10254 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
10291 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:11885 original size:38 final size:38
Alignment explanation
Indices: 11834--11923 Score: 164
Period size: 38 Copynumber: 2.4 Consensus size: 38
11824 TGCTTACCTA
11834 TGGCCGAACATACACATCAACTTATGTACTCAGT-CATG
1 TGGCCGAACATACACATCAACTTATGTACTCA-TCCATG
11872 TGGCCGAACATACACATCAACTTATGTACTCATCCATG
1 TGGCCGAACATACACATCAACTTATGTACTCATCCATG
11910 TGGCCGAACATACA
1 TGGCCGAACATACA
11924 TGTCTATGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
37 1 0.02
38 50 0.98
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (38 bp):
TGGCCGAACATACACATCAACTTATGTACTCATCCATG
Found at i:17469 original size:40 final size:40
Alignment explanation
Indices: 17385--17608 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
17375 TTGAATGATG
* * * *
17385 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
17425 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
17465 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
17503 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
17543 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
17584 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
17609 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 25 0.15
39 19 0.12
40 111 0.67
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:17603 original size:80 final size:80
Alignment explanation
Indices: 17385--17608 Score: 296
Period size: 78 Copynumber: 2.8 Consensus size: 80
17375 TTGAATGATG
* * * * *
17385 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
17448 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
*
17465 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
*
17527 TGTGCGAGTTACTAAA
65 TGTGCGAGATACTAAA
* *
17543 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
17608 G
66 G
17609 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
77 2 0.02
78 49 0.39
79 25 0.20
80 49 0.39
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:25411 original size:40 final size:40
Alignment explanation
Indices: 25327--25550 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
25317 TTGAATGATG
* * * *
25327 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
25367 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
25407 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
25446 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
25486 TCC-GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
25526 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
25551 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
39 71 0.43
40 86 0.52
41 8 0.05
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:25463 original size:79 final size:80
Alignment explanation
Indices: 25327--25550 Score: 296
Period size: 79 Copynumber: 2.8 Consensus size: 80
25317 TTGAATGATG
* * * * *
25327 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCAT
*
25390 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
*
25407 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
*
25471 GTGCGAGTTACTAAA
66 GTGCGAGATACTAAA
* *
25486 TCC-GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
25549 TG
65 TG
25551 AACGAGGAGC
Statistics
Matches: 129, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
78 7 0.05
79 102 0.79
80 20 0.16
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:25568 original size:79 final size:79
Alignment explanation
Indices: 25334--25583 Score: 251
Period size: 79 Copynumber: 3.2 Consensus size: 79
25324 ATGTCCGGGC
* * * * * **
25334 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCATTTGAACG
* *
25397 AGAT-ACTAATTCCGGGC
64 AG-TGACTAAATCC-GGT
* **
25414 TAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG
*
25478 TTACTAAATCCGGT
66 TGACTAAATCCGGT
*
25492 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGA
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGA
*
25556 G-GAGCTATATCCGGT
65 GTGA-CTAAATCCGGT
* *
25571 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
25584 TACGTGATTT
Statistics
Matches: 148, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
78 9 0.06
79 126 0.85
80 13 0.09
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG
TGACTAAATCCGGT
Done.