Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold999
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: 16574
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:6682 original size:79 final size:81
Alignment explanation
Indices: 6561--6745 Score: 252
Period size: 79 Copynumber: 2.3 Consensus size: 81
6551 GCTACTCGTT
* *
6561 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
6625 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
6641 CAAATGCCTTCGGGACTTAACCCGGAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
6705 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
6721 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
6746 CATCATTCAA
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
78 3 0.03
79 58 0.62
80 32 0.34
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:6745 original size:40 final size:40
Alignment explanation
Indices: 6542--6745 Score: 254
Period size: 40 Copynumber: 5.1 Consensus size: 40
6532 CGGAATTTAA
** *
6542 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
6582 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
6622 CCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
6662 CCGGAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
6701 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
6741 CCGGA
1 CCGGA
6746 CATCATTCAA
Statistics
Matches: 146, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
38 3 0.02
39 34 0.23
40 98 0.67
41 11 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:12028 original size:41 final size:38
Alignment explanation
Indices: 11969--12072 Score: 129
Period size: 38 Copynumber: 2.7 Consensus size: 38
11959 CTCGAATGAT
*
11969 ATCCGGGCTAAGTCCCGAAGGCTTTTGCGCTAAGCGACTAC
1 ATCCGGGCTAAGTCCCGAAGGCATTTGCGCT-A--GACTAC
* * *
12010 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGACTAT
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGCGCTAGACTAC
12048 ATCCGGGCTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATT
12073 ATGCTAGTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
37 1 0.02
38 27 0.48
40 1 0.02
41 26 0.46
42 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (38 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGCGCTAGACTAC
Found at i:12059 original size:38 final size:39
Alignment explanation
Indices: 11967--12108 Score: 155
Period size: 41 Copynumber: 3.6 Consensus size: 39
11957 TACTCGAATG
* *
11967 ATATCCGGGCTAAGTCCCGAAGGCTTTTGCGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AG-GACT
* *
12008 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTA-GACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGGACT
* *
12046 ATATCCGGGCTAAGTCCCGAAGGCA-TTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-GACT
* *
12085 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
12109 CTTGTGCGAG
Statistics
Matches: 87, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
37 8 0.09
38 25 0.29
39 25 0.29
40 1 0.01
41 27 0.31
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGGACT
Found at i:12128 original size:39 final size:39
Alignment explanation
Indices: 11967--12144 Score: 132
Period size: 39 Copynumber: 4.6 Consensus size: 39
11957 TACTCGAATG
* * *
11967 ATATCCGGGCTAAGTCCCGAAGGC-TTTTGCGCTAAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTATGCG---AGTGACT
* * * * *
12008 ACATCCGGACTAAGATCCGAAGGCATT-TGTG-CTAGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTATGCGAGT-GACT
* * *
12046 ATATCCGGGCTAAGTCCCGAAGGCATTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTATGCGAGTGACT
* * * **
12085 ATATCCGGGTTAAGACCCGAAGGCCTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTATGCGAGTGACT
12124 ATATCC-GGCTAA-ACCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
12145 ATGCTTGATT
Statistics
Matches: 108, Mismatches: 24, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
37 1 0.01
38 39 0.36
39 42 0.39
40 1 0.01
41 23 0.21
42 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTATGCGAGTGACT
Done.