Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2487
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: 33896
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Found at i:28 original size:1 final size:1
Alignment explanation
Indices: 22--50 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
12 CTATCTATCT
22 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
51 TCTCAAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2644 original size:77 final size:80
Alignment explanation
Indices: 2520--2701 Score: 230
Period size: 77 Copynumber: 2.3 Consensus size: 80
2510 GCTACTCGTT
* *
2520 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGG-CTTAGCCCGGATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
2584 GATTTAGTAAC-TCGCA
64 GATATAGTAACTTAGCA
**
2600 CAAATG-CTTCGGGCTTAGCCCGGAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
2663 TATGGTCACTTAGCA
66 TATAGTAACTTAGCA
*
2678 CAAA-GCCTTCGGACTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGA
2702 CATCATTCAA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
76 3 0.03
77 39 0.43
78 35 0.39
79 7 0.08
80 6 0.07
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (80 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCA
Found at i:2695 original size:39 final size:38
Alignment explanation
Indices: 2520--2701 Score: 215
Period size: 40 Copynumber: 4.7 Consensus size: 38
2510 GCTACTCGTT
* *
2520 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGAT-TAGTAACTCGCA
*
2560 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGA-TTAGTAACTCGCA
*
2600 CAAATG-CTTCGGGCTTAGCCCGGATTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTAGTAACTCGCA
* * * *
2637 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGAT-TAGTAAC-TCGCA
2678 CAAA-GCCTTCGGACTTAGCCCGGA
1 CAAATGCCTTCGGACTTAGCCCGGA
2702 CATCATTCAA
Statistics
Matches: 126, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
37 19 0.15
38 18 0.14
39 25 0.20
40 55 0.44
41 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (38 bp):
CAAATGCCTTCGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:10459 original size:40 final size:40
Alignment explanation
Indices: 10422--10527 Score: 162
Period size: 40 Copynumber: 2.7 Consensus size: 40
10412 GCTACTCGTT
*
10422 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
*
10462 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
10502 CAAATGCCTTCGGGACTTAA-CCGGAT
1 CAAATGCCTTCGGGACATAACCCGGAT
10528 ATGGAGATGG
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
39 6 0.10
40 55 0.87
41 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:12195 original size:16 final size:16
Alignment explanation
Indices: 12174--12204 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12164 TATATTTTTC
*
12174 ATTTGCATCATATATG
1 ATTTGCAACATATATG
12190 ATTTGCAACATATAT
1 ATTTGCAACATATAT
12205 CAAATAACCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (16 bp):
ATTTGCAACATATATG
Found at i:12497 original size:43 final size:42
Alignment explanation
Indices: 12358--12512 Score: 129
Period size: 43 Copynumber: 3.7 Consensus size: 42
12348 ATATCGTACA
* *
12358 ATGCCAACGTCCTAGACATGGTCTTACACGCT-ATCACATATCG
1 ATGCCAACATCCCAGACATGGTCTTACA--CTAATCACATATCG
* * * * *
12401 ATGCC-ACTGTCCTAGACAGGGTCTTACACGAATCAAATA-CG
1 ATGCCAAC-ATCCCAGACATGGTCTTACACTAATCACATATCG
* * * * *
12442 ATGACGATATCCCAAACATGATCTTACACATAATCACATATCG
1 ATGCCAACATCCCAGACATGGTCTTACAC-TAATCACATATCG
12485 ATGCCAACATCCCAGA-AGTGGTCTTACA
1 ATGCCAACATCCCAGACA-TGGTCTTACA
12513 TGGGAACACA
Statistics
Matches: 89, Mismatches: 17, Indels: 12
0.75 0.14 0.10
Matches are distributed among these distances:
41 23 0.26
42 19 0.21
43 47 0.53
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (42 bp):
ATGCCAACATCCCAGACATGGTCTTACACTAATCACATATCG
Found at i:15296 original size:28 final size:28
Alignment explanation
Indices: 15256--15314 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
15246 ATTATCGAAC
* *
15256 CATCATCATACATATCCATATGCGCATT
1 CATCATCAGACATATCCATATGCACATT
*
15284 CATCATCAGACATATTCATATGCACATT
1 CATCATCAGACATATCCATATGCACATT
15312 CAT
1 CAT
15315 TGCACGCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (28 bp):
CATCATCAGACATATCCATATGCACATT
Found at i:18300 original size:79 final size:80
Alignment explanation
Indices: 18139--18361 Score: 242
Period size: 79 Copynumber: 2.8 Consensus size: 80
18129 TTGAATGATG
* * * * *
18139 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCGGACTAAGAT-CCGAAGGCA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATAACCGGGCTAAG-TCCCGAAGGCA
*
18201 TTTGTGCGAGATACTAAA
63 TTCGTGCGAGATACTAAA
*
18219 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA-ACCGGGCTAAGTCCCGAAGGCAT
*
18281 TCGTGCGAGTTACTAAA
64 TCGTGCGAGATACTAAA
** * * *
18298 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGATACTATAACCGGGCTAAGTCCCGAAGGCATT
18362 TGAACGAGGA
Statistics
Matches: 123, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
78 1 0.01
79 67 0.54
80 44 0.36
81 10 0.08
82 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGATACTATAACCGGGCTAAGTCCCGAAGGCATTC
GTGCGAGATACTAAA
Found at i:18331 original size:40 final size:40
Alignment explanation
Indices: 18139--18363 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
18129 TTGAATGATG
* * * *
18139 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
18179 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
18219 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
18259 TCCGGGCTAAG-CCCGAAGGCATTCGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
18298 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
18339 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
18364 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 120 0.73
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:18362 original size:119 final size:120
Alignment explanation
Indices: 18139--18363 Score: 280
Period size: 119 Copynumber: 1.9 Consensus size: 120
18129 TTGAATGATG
* *
18139 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTCGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
18204 GTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
66 GTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
* * * **
18259 TCCGGGCTAAG-CCCGAAGGCATTCGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTCGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
18321 TTGTGTGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTG
64 TTGTGCGAGATACTA-AATCCGGACTAAGAT-CCGAAGGCATTTG
18364 AACGAGGAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
118 2 0.02
119 69 0.77
120 19 0.21
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCTTCGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:18385 original size:79 final size:78
Alignment explanation
Indices: 18146--18396 Score: 233
Period size: 79 Copynumber: 3.2 Consensus size: 78
18136 ATGTCCGGGC
* * * *
18146 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGCATTTGTG-TGAGTTACTATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCG
* *
18209 AGATACTAAATCCGGAC
64 AG-GACTAAATCCGG-T
* * *
18226 TAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCATTCGTGCG
1 TAAG-TCCCGAAGGCATTTGTGTGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCG
*
18288 AGTTACTAAATCCGGGT
64 AG-GACTAAATCC-GGT
* * **
18305 TAAGTCCCGAAGGCATTTGTGTGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG
1 TAAGTCCCGAAGGCATTTGTGTGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
*
18370 GAGCTATATCCGGT
66 GA-CTAAATCCGGT
* *
18384 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
18397 TGCGTGATTT
Statistics
Matches: 142, Mismatches: 20, Indels: 19
0.78 0.11 0.10
Matches are distributed among these distances:
78 1 0.01
79 80 0.56
80 54 0.38
81 7 0.05
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (78 bp):
TAAGTCCCGAAGGCATTTGTGTGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
GACTAAATCCGGT
Found at i:21635 original size:79 final size:81
Alignment explanation
Indices: 21511--21694 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
21501 GCTACTCGTT
* *
21511 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTC-GGATCTTAACCCG
* *
21574 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
21590 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCAC-AATGCCTTCGGATCTTAACCCG
* *
21653 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
21670 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
21695 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 48 0.53
80 19 0.21
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:21694 original size:40 final size:40
Alignment explanation
Indices: 21492--21694 Score: 229
Period size: 39 Copynumber: 5.1 Consensus size: 40
21482 CGGAATTTAA
** *
21492 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
21532 CCGGTTATAGTAACTCGCAC-AATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
21571 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
21610 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
21650 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
21690 CCGGA
1 CCGGA
21695 CATCATTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
38 2 0.01
39 68 0.49
40 57 0.41
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.