Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1350
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: 38627
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5327 original size:27 final size:27
Alignment explanation
Indices: 5297--5474 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
5287 ATATTGAGTC
* * * *
5297 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
5324 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
5351 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
5379 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
5406 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
5433 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
5460 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
5475 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:5436 original size:82 final size:81
Alignment explanation
Indices: 5318--5473 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
5308 TGCTATATAA
* *
5318 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
5383 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
5400 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
5464 CACTTAGTGC
65 CACTTAGTGC
5474 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:11237 original size:40 final size:40
Alignment explanation
Indices: 11182--11366 Score: 266
Period size: 40 Copynumber: 4.6 Consensus size: 40
11172 TATTCGGATG
*
11182 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTCCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
* *
11222 ATATCCGGGATAAGTCCCGAAGGCATTTGTGCTAG-TGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CT
*
11262 ATATCCGGGCGAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC--G-AGTTGCT
*
11305 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
*
11345 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
11367 TACTTGGGTT
Statistics
Matches: 130, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
39 16 0.12
40 77 0.59
41 1 0.01
43 34 0.26
44 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCT
Found at i:11347 original size:83 final size:80
Alignment explanation
Indices: 11182--11366 Score: 266
Period size: 83 Copynumber: 2.3 Consensus size: 80
11172 TATTCGGATG
*
11182 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTCCTATATCCGGGATAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTCCTATACCCGGGATAAGTCCCGAAGGCA
*
11247 TTTGTGCTAGTGACT
66 TTTGTGCGAGTGACT
* * *
11262 ATATCCGGGCGAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCTATACCCGGGCTAAGTCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC--G-AGTTCCTATACCCGGGATAAGTCCCGAAG
11327 GCATTTGTGCGAGTTG-CT
63 GCATTTGTGCGAG-TGACT
*
11345 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
11367 TACTTGGGTT
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
80 31 0.33
82 15 0.16
83 46 0.49
84 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTCCTATACCCGGGATAAGTCCCGAAGGCA
TTTGTGCGAGTGACT
Found at i:20408 original size:43 final size:41
Alignment explanation
Indices: 20361--20502 Score: 128
Period size: 43 Copynumber: 3.3 Consensus size: 41
20351 ATGATACCGA
20361 TGTCCCAGACATGGTCCTTTACATAAATCTTAATCGAGGCCTG
1 TGTCCCAGACATGGT-CTTTACATAAATC-TAATCGAGGCCTG
** ** *
20404 TGTCCCAGACACAGTC-TTACGCGAAATC-AGATACGATGCC-G
1 TGTCCCAGACATGGTCTTTAC-ATAAATCTA-AT-CGAGGCCTG
* *
20445 ATATCCCAGACATGGTCTTATACGTAAATCTCAATCGAGGCCTG
1 -TGTCCCAGACATGGTCTT-TACATAAATCT-AATCGAGGCCTG
20489 TGTCCCAGACATGG
1 TGTCCCAGACATGG
20503 CCTTACACGA
Statistics
Matches: 78, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
40 1 0.01
41 7 0.09
42 25 0.32
43 38 0.49
44 6 0.08
45 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (41 bp):
TGTCCCAGACATGGTCTTTACATAAATCTAATCGAGGCCTG
Found at i:20421 original size:85 final size:85
Alignment explanation
Indices: 20332--20499 Score: 266
Period size: 85 Copynumber: 2.0 Consensus size: 85
20322 CGTAGATAGG
* * *
20332 GTCTTACACGAAATCAGATATGATACCGATGTCCCAGACATGGTCCTT-TACATAAATCTTAATC
1 GTCTTACACGAAATCAGATACGATACCGATATCCCAGACATGGT-CTTATACATAAATCTCAATC
20396 GAGGCCTGTGTCCCAGACACA
65 GAGGCCTGTGTCCCAGACACA
* * *
20417 GTCTTACGCGAAATCAGATACGATGCCGATATCCCAGACATGGTCTTATACGTAAATCTCAATCG
1 GTCTTACACGAAATCAGATACGATACCGATATCCCAGACATGGTCTTATACATAAATCTCAATCG
20482 AGGCCTGTGTCCCAGACA
66 AGGCCTGTGTCCCAGACA
20500 TGGCCTTACA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
84 3 0.04
85 73 0.96
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (85 bp):
GTCTTACACGAAATCAGATACGATACCGATATCCCAGACATGGTCTTATACATAAATCTCAATCG
AGGCCTGTGTCCCAGACACA
Found at i:20463 original size:42 final size:41
Alignment explanation
Indices: 20331--20464 Score: 112
Period size: 42 Copynumber: 3.2 Consensus size: 41
20321 TCGTAGATAG
* *
20331 GGTCTTACACGAAATCAGATATGATACCGATGTCCCAGACAT
1 GGTCTTAC-CGAAATCAGATACGATGCCGATGTCCCAGACAT
** * *
20373 GGTCCTTTACATAAATCTTA-AT-CGAGGCCTG-TGTCCCAGACAC
1 GGT-C-TTACCGAAATC--AGATACGATGCC-GATGTCCCAGACAT
* *
20416 AGTCTTACGCGAAATCAGATACGATGCCGATATCCCAGACAT
1 GGTCTTAC-CGAAATCAGATACGATGCCGATGTCCCAGACAT
20458 GGTCTTA
1 GGTCTTA
20465 TACGTAAATC
Statistics
Matches: 70, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
40 1 0.01
41 7 0.10
42 31 0.44
43 23 0.33
44 7 0.10
45 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (41 bp):
GGTCTTACCGAAATCAGATACGATGCCGATGTCCCAGACAT
Found at i:27776 original size:42 final size:42
Alignment explanation
Indices: 27674--27825 Score: 137
Period size: 43 Copynumber: 3.6 Consensus size: 42
27664 TACAATATCG
* * * *
27674 ATGTCCTAGACGTGGTCTTACATGTAATTCAATACCGATGCCT
1 ATGTCCCAGACATGGTCTTACACGTAAATCAATA-CGATGCCT
* * * * *
27717 CTGTCCCAAATAGGGTCTTACACG-AAATCAAATACGATGCCA
1 ATGTCCCAGACATGGTCTTACACGTAAATC-AATACGATGCCT
* *
27759 ATGTCCCAGACATGGTCTTATACGTAAATCTCAAT-CGAGGCCT
1 ATGTCCCAGACATGGTCTTACACGTAAA--TCAATACGATGCCT
* *
27802 GTGTCCCAGACAAGGTCTTACACG
1 ATGTCCCAGACATGGTCTTACACG
27826 ATATCTCAGA
Statistics
Matches: 86, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
42 30 0.35
43 51 0.59
44 3 0.03
45 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (42 bp):
ATGTCCCAGACATGGTCTTACACGTAAATCAATACGATGCCT
Found at i:28179 original size:14 final size:14
Alignment explanation
Indices: 28160--28189 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28150 TTAGGGCACT
28160 TTACATTTTAACTC
1 TTACATTTTAACTC
*
28174 TTACATTTTCACTC
1 TTACATTTTAACTC
28188 TT
1 TT
28190 TGATAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.53
Consensus pattern (14 bp):
TTACATTTTAACTC
Found at i:28909 original size:22 final size:22
Alignment explanation
Indices: 28882--28934 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
28872 CATAATTAAG
28882 CACAGAAATAGACAAATTAAAT
1 CACAGAAATAGACAAATTAAAT
28904 CACAGAAATAGACAAATTAAAT
1 CACAGAAATAGACAAATTAAAT
28926 CACAGAAAT
1 CACAGAAAT
28935 TTTCACAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.58, C:0.15, G:0.09, T:0.17
Consensus pattern (22 bp):
CACAGAAATAGACAAATTAAAT
Found at i:33646 original size:27 final size:27
Alignment explanation
Indices: 33615--33792 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
33605 TAAATTGTAC
33615 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
33642 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
33668 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
33696 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
33724 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
33751 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
33778 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
33793 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:33729 original size:82 final size:81
Alignment explanation
Indices: 33616--33771 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
33606 AAATTGTACA
* *
33616 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
33680 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
33697 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
33762 TGCGAGTTGA
65 TGCGAATTGA
33772 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:33783 original size:82 final size:81
Alignment explanation
Indices: 33612--33792 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
33602 GATTAAATTG
* *
33612 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
33677 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
33693 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
33757 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
33775 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
33793 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.