Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3225
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: 51912
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Found at i:271 original size:26 final size:27
Alignment explanation
Indices: 234--372 Score: 107
Period size: 26 Copynumber: 5.3 Consensus size: 27
224 AGCACTATGT
234 CGATTT-ACTATGTCGCACT-AGTGTG
1 CGATTTGACTATGTCGCACTAAGTGTG
*
259 CGATTTGACTATGTC-AACTAAGTGTG
1 CGATTTGACTATGTCGCACTAAGTGTG
* *
285 CGA-ATGAATGATGAGT-GCACTAAGTGTG
1 CGATTTGACT-AT--GTCGCACTAAGTGTG
* * *
313 CGAATTGACCATG-CTGCCCTAAGT-TG
1 CGATTTGACTATGTC-GCACTAAGTGTG
*
339 CGAGTTTGACTATGTAGCAC-AAGTGTG
1 CGA-TTTGACTATGTCGCACTAAGTGTG
366 CG-TTTGA
1 CGATTTGA
373 TTACGTTAGC
Statistics
Matches: 90, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
25 18 0.20
26 29 0.32
27 23 0.26
28 17 0.19
29 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (27 bp):
CGATTTGACTATGTCGCACTAAGTGTG
Found at i:8679 original size:27 final size:27
Alignment explanation
Indices: 8649--8849 Score: 251
Period size: 27 Copynumber: 7.4 Consensus size: 27
8639 TGAGTCCGCT
* * * *
8649 CACTCAGTGCTATATAATCAACTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* *
8676 CACTTAGTGCTACGTAATCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
8703 CACTTAGTGCTACATAGTCAAACTCGCA
1 CACTTAGTGCTACATAGTCAAA-TCGCA
** * *
8731 CACTTAGTGCCGCATGGTCAATTCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
* **
8758 CACTTAGTGC-ATCATATTCATTTCGCA
1 CACTTAGTGCTA-CATAGTCAAATCGCA
*
8785 CACTTAGTGCAACATAGTCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
8812 CACTTAGTGCTACATAGTCAAATCGCA
1 CACTTAGTGCTACATAGTCAAATCGCA
8839 CACTTAGTGCT
1 CACTTAGTGCT
8850 GTACAATTTA
Statistics
Matches: 153, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
27 129 0.84
28 24 0.16
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (27 bp):
CACTTAGTGCTACATAGTCAAATCGCA
Found at i:15377 original size:50 final size:49
Alignment explanation
Indices: 15262--15437 Score: 190
Period size: 50 Copynumber: 3.5 Consensus size: 49
15252 TGAGGTCGCA
* * * * * *
15262 TGTGTAGTACTAAGTGCAGGCTACCATGCGTACCCGATAAATTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAT-AATT-GGTCACG
* **
15313 TGTGTAGTATTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATT-GGTCACG
* * * ** *
15363 TGTGTAGTACTAAGTGCAGGATACTACATGTATCGGATAATTGGTTTCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATTGGTCACG
15412 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
15438 TGCGTACCAG
Statistics
Matches: 105, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
49 29 0.28
50 44 0.42
51 32 0.30
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATTGGTCACG
Found at i:20991 original size:14 final size:15
Alignment explanation
Indices: 20967--20998 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
20957 CTGCATGATA
20967 TTTCTTTCTCCTCCT
1 TTTCTTTCTCCTCCT
20982 TTTC-TTCTCCTCCT
1 TTTCTTTCTCCTCCT
20996 TTT
1 TTT
20999 ATTTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTCTTTCTCCTCCT
Found at i:28268 original size:27 final size:27
Alignment explanation
Indices: 28206--28294 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 27
28196 GGAAAAATGG
* * * *
28206 TAATTTTACCCCACAAGGGTATCTCG-
1 TAATTCTACCCTACAGGGGTATTTCGA
28232 TAATTCTACCCTACAGGGGTATTTCGA
1 TAATTCTACCCTACAGGGGTATTTCGA
* *
28259 TATTTCTACCTTACAGGGGTATTTCGA
1 TAATTCTACCCTACAGGGGTATTTCGA
28286 TAATTCTAC
1 TAATTCTAC
28295 AACTTATCCA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 22 0.40
27 33 0.60
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (27 bp):
TAATTCTACCCTACAGGGGTATTTCGA
Found at i:31318 original size:20 final size:22
Alignment explanation
Indices: 31285--31327 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
31275 GAACAAATAT
*
31285 ATATGTGTGGCGAAG-CACCAG
1 ATATGTGTGACGAAGTCACCAG
31306 ATAT-TGTGACGAAGTCACCAG
1 ATATGTGTGACGAAGTCACCAG
31327 A
1 A
31328 ACAGATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.21
Consensus pattern (22 bp):
ATATGTGTGACGAAGTCACCAG
Found at i:31332 original size:26 final size:27
Alignment explanation
Indices: 31303--31354 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
31293 GGCGAAGCAC
*
31303 CAGATAT-TGTGACGAAGTCACCAGAA
1 CAGATATATGTGACGAAGCCACCAGAA
* *
31329 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATATATGTGACGAAGCCACCAGA
31355 TTGCACGAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (27 bp):
CAGATATATGTGACGAAGCCACCAGAA
Found at i:31351 original size:27 final size:26
Alignment explanation
Indices: 31252--31354 Score: 68
Period size: 26 Copynumber: 4.0 Consensus size: 26
31242 TGGCTAAACC
*
31252 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGGCGAGGCCACCAGAA
* * * * * *
31278 CAAATATATAT-GTGTGGCGA--AGCAC
1 CAGATAT-TGTGGCGAGGCCACCAG-AA
* * *
31303 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGGCGAGGCCACCAGAA
31329 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGGCGAGGCCACCAGA
31355 TTGCACGAGG
Statistics
Matches: 52, Mismatches: 19, Indels: 11
0.63 0.23 0.13
Matches are distributed among these distances:
24 4 0.08
25 10 0.19
26 19 0.37
27 19 0.37
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCGAGGCCACCAGAA
Found at i:32092 original size:27 final size:27
Alignment explanation
Indices: 32005--32094 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 27
31995 GGCAAAATGG
* * * * * *
32005 TAATTTTACCCTACAAGGGAATCTCGG
1 TAATTCTACCTTACAGGGGTATTTCGA
32032 TAATTCTACCTTACAGGGGTATTTC-A
1 TAATTCTACCTTACAGGGGTATTTCGA
*
32058 GTATTTCTACCTTACAGGGGTATTTCGA
1 -TAATTCTACCTTACAGGGGTATTTCGA
32086 TAATTCTAC
1 TAATTCTAC
32095 AACTTATCCA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
27 52 0.98
28 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (27 bp):
TAATTCTACCTTACAGGGGTATTTCGA
Found at i:36842 original size:63 final size:62
Alignment explanation
Indices: 36726--36860 Score: 166
Period size: 63 Copynumber: 2.1 Consensus size: 62
36716 CATGGGTGTC
* * *
36726 TGTCAGGACATGTAACTCACTTTTTAGGAATTAGAGTCACACGGGCTAGAGACACGGGCGTT
1 TGTCAGGCCATGTAACTCACTTTTTAGGAATTAGAGTCACACGGGCTAAAGACACGGGCGTG
* * *
36788 TGTCTAGGCCATGTAACTCACTATTTT-GGAATTAGTGTCTCACAGGGC-AAAGACACGGGTGTG
1 TGTC-AGGCCATGTAACTCACT-TTTTAGGAATTAGAGTCACAC-GGGCTAAAGACACGGGCGTG
36851 TGTCAAGGCC
1 TGTC-AGGCC
36861 GTGTGAGAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
62 4 0.06
63 51 0.81
64 8 0.13
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (62 bp):
TGTCAGGCCATGTAACTCACTTTTTAGGAATTAGAGTCACACGGGCTAAAGACACGGGCGTG
Found at i:40139 original size:40 final size:39
Alignment explanation
Indices: 40088--40239 Score: 171
Period size: 40 Copynumber: 3.8 Consensus size: 39
40078 GGATATAGCC
*
40088 ACTAGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
1 ACTAGCACAAATGCCTTCGGGACTTAGCCCGG-TATAGTA
* * *
40128 ACTTGCACAAATGCCTTTGGGACTTAGCCCGGTATAATA
1 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTATAGTA
* * * **
40167 ACTCGCACAAATGCCTTCGGGACTTACCCCGGAATTAGCC
1 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTA-TAGTA
* *
40207 ACTAGCTCAAATG-CTCTCAGGACTTAGCCCGGT
1 ACTAGCACAAATGCCT-TCGGGACTTAGCCCGGT
40240 TATCATCCGA
Statistics
Matches: 94, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 38 0.40
40 56 0.60
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTATAGTA
Found at i:48367 original size:40 final size:38
Alignment explanation
Indices: 48323--48417 Score: 110
Period size: 37 Copynumber: 2.6 Consensus size: 38
48313 GCCACTAGCT
* *
48323 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAATAACTCG-A
*
48363 CAAATGCCTT-GTGA-TTAGCCCGGTATAATAACTCGA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGA
48399 -AAA--CCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
48418 AATAGTAGCT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
33 4 0.08
34 3 0.06
35 9 0.18
36 1 0.02
37 10 0.20
38 9 0.18
39 3 0.06
40 10 0.20
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.26
Consensus pattern (38 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGA
Done.