Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3528
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: 25385
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Found at i:1813 original size:22 final size:23
Alignment explanation
Indices: 1781--1828 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
1771 CACCGGTTCC
*
1781 TTCGGCTAATGAT-CCAATTAAT
1 TTCGGCCAATGATCCCAATTAAT
1803 TTCGGCCAATGATCCCAATTAAT
1 TTCGGCCAATGATCCCAATTAAT
1826 TTC
1 TTC
1829 TACTCAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.35
Consensus pattern (23 bp):
TTCGGCCAATGATCCCAATTAAT
Found at i:5475 original size:40 final size:40
Alignment explanation
Indices: 5377--5605 Score: 305
Period size: 39 Copynumber: 6.0 Consensus size: 40
5367 TCCTCGTTCA
* * * * *
5377 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
5416 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
5456 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
5496 AATGCCTTCGGGACTTAACCCGGA-TTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
5535 AATGCCTTCGGGACTTAACCCGGATTT-AT--CTCGCAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
5571 AATG-CTTC-GGACTTAA-CCGGATTTAGTATCTCGCA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
5606 GGCTTCGGAT
Statistics
Matches: 175, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
33 8 0.05
34 9 0.05
35 4 0.02
36 10 0.06
37 7 0.04
39 75 0.43
40 62 0.35
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:5478 original size:79 final size:78
Alignment explanation
Indices: 5377--5595 Score: 306
Period size: 79 Copynumber: 2.8 Consensus size: 78
5367 TCCTCGTTCA
* * * * *
5377 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAACCCGGATTTA-TAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
5442 TAACAACTCGCACG
65 TAACAACTCGCACG
*
5456 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA-
1 AATGCCTTCGGGACTTAACCCGGATTT-ATAACTCGCAC-AATGCCTTCGGGACTTAACCCGGAT
*
5520 TTAATAACTCGCACG
64 TTAACAACTCGCACG
5535 AATGCCTTCGGGACTTAACCCGGATTTAT--CTCGCACAATG-CTTC-GGACTTAA-CCGGATTT
1 AATGCCTTCGGGACTTAACCCGGATTTATAACTCGCACAATGCCTTCGGGACTTAACCCGGATTT
5595 A
66 A
5596 GTATCTCGCA
Statistics
Matches: 129, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
72 5 0.04
73 11 0.09
74 4 0.03
75 4 0.03
76 7 0.05
78 2 0.02
79 72 0.56
80 24 0.19
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (78 bp):
AATGCCTTCGGGACTTAACCCGGATTTATAACTCGCACAATGCCTTCGGGACTTAACCCGGATTT
AACAACTCGCACG
Found at i:13422 original size:40 final size:40
Alignment explanation
Indices: 13324--13586 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
13314 TCCTCGTTCA
* * * * *
13324 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
13363 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
13403 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
13443 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
13483 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
13523 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
13563 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
13587 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:21219 original size:38 final size:39
Alignment explanation
Indices: 21164--21350 Score: 261
Period size: 38 Copynumber: 4.8 Consensus size: 39
21154 GAATGATATC
*
21164 CGGGTTAGGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
21203 CGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTAATT
1 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
21241 CGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAAT
1 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
21279 CCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTATAAC
1 -CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AAT
* * *
21320 CGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGT
21351 AGCTATATCC
Statistics
Matches: 131, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
38 61 0.47
39 17 0.13
40 51 0.39
41 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (39 bp):
CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:21310 original size:40 final size:40
Alignment explanation
Indices: 21161--21366 Score: 264
Period size: 40 Copynumber: 5.3 Consensus size: 40
21151 TTCGAATGAT
*
21161 ATCCGGGTTAGGTCCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
21201 AT-CGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACT-A
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
* * *
21238 ATTCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
*
21277 ATCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTATA
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
* * * *
21318 A-CCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCTAT
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAA
21357 ATCC-GGTTAA
1 ATCCGGGTTAA
21367 ATTACAAGGT
Statistics
Matches: 145, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
37 3 0.02
38 55 0.38
39 27 0.19
40 58 0.40
41 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Done.