Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1685
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: 59500
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:26660 original size:27 final size:27
Alignment explanation
Indices: 26630--26814 Score: 115
Period size: 27 Copynumber: 6.9 Consensus size: 27
26620 GACCCTCGAC
**
26630 TTGTAAAATTATTGAAATACCCCCGGG
1 TTGTAAAATTATTGAAATACCCCCAAG
* * * * *
26657 TTGTAAAATTACTAAAATACCTCTAAT
1 TTGTAAAATTATTGAAATACCCCCAAG
* * * *
26684 TTGTGAAATTATCGAAATACCCTCAAT
1 TTGTAAAATTATTGAAATACCCCCAAG
* * * * *
26711 TTGTTAAATCAGTGAAATACCCCCGAC
1 TTGTAAAATTATTGAAATACCCCCAAG
* *
26738 TTGTAAAATTATTGAAGTACCCCC-GG
1 TTGTAAAATTATTGAAATACCCCCAAG
* **
26764 TTGGTAAAATTACTT-AAATAACCTTATAG
1 TT-GTAAAATTA-TTGAAATACCCCCA-AG
* *
26793 -TGTAAAATTACTGAAAGACCCC
1 TTGTAAAATTATTGAAATACCCC
26815 TGTAGGGTAA
Statistics
Matches: 117, Mismatches: 36, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
26 3 0.03
27 110 0.94
28 3 0.03
29 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.31
Consensus pattern (27 bp):
TTGTAAAATTATTGAAATACCCCCAAG
Found at i:26747 original size:54 final size:54
Alignment explanation
Indices: 26621--26783 Score: 139
Period size: 54 Copynumber: 3.0 Consensus size: 54
26611 GTTCGTTAAG
* ** *
26621 ACCCTCGACTTGTAAAATTATTGAAATACCCCCGGGTTGTAAAATTACTAAAAT
1 ACCCCCGACTTGTAAAATTATTGAAATACCCCCAAGTTGTAAAATCACTAAAAT
* ** * * * * * * * *
26675 ACCTCTAATTTGTGAAATTATCGAAATACCCTCAATTTGTTAAATCAGTGAAAT
1 ACCCCCGACTTGTAAAATTATTGAAATACCCCCAAGTTGTAAAATCACTAAAAT
* * * *
26729 ACCCCCGACTTGTAAAATTATTGAAGTACCCCC-GGTTGGTAAAATTACTTAAAT
1 ACCCCCGACTTGTAAAATTATTGAAATACCCCCAAGTT-GTAAAATCACTAAAAT
26783 A
1 A
26784 ACCTTATAGT
Statistics
Matches: 79, Mismatches: 29, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
53 2 0.03
54 77 0.97
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (54 bp):
ACCCCCGACTTGTAAAATTATTGAAATACCCCCAAGTTGTAAAATCACTAAAAT
Found at i:26824 original size:27 final size:27
Alignment explanation
Indices: 26766--26827 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
26756 ACCCCCGGTT
* * *
26766 GGTAAAATTACTTAAATAACCTTATAG
1 GGTAAAATTACTGAAAGAACCCTATAG
* * *
26793 TGTAAAATTACTGAAAGACCCCTGTAG
1 GGTAAAATTACTGAAAGAACCCTATAG
26820 GGTAAAAT
1 GGTAAAAT
26828 GGTTGTTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (27 bp):
GGTAAAATTACTGAAAGAACCCTATAG
Found at i:28804 original size:12 final size:12
Alignment explanation
Indices: 28779--28813 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28769 CTCATTAGGA
*
28779 TTTAATTTAATC
1 TTTAATTCAATC
*
28791 TTTTATTCAATC
1 TTTAATTCAATC
28803 TTTAATTCAAT
1 TTTAATTCAAT
28814 TTACACAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTAATTCAATC
Found at i:46087 original size:46 final size:46
Alignment explanation
Indices: 46037--46209 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
46027 TGGTTGAGCA
*
46037 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
46083 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
46130 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
46176 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
46210 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:46193 original size:93 final size:93
Alignment explanation
Indices: 46034--46204 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
46024 GGATGGTTGA
* *
46034 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
46099 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
46127 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
46192 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
46205 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:46471 original size:19 final size:20
Alignment explanation
Indices: 46434--46471 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
46424 ATAAGGTGGT
46434 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
46454 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
46472 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:55109 original size:23 final size:22
Alignment explanation
Indices: 55083--55159 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
55073 AATAAAATAA
*
55083 AAAAATAAAAGCAAAAGAAATTT
1 AAAAATAAAA-CAAAAGAAAATT
* * *
55106 AAAACTAAAACAACATAAAATT
1 AAAAATAAAACAAAAGAAAATT
*
55128 AAAAATAAAA-ATAAATAAAATAT
1 AAAAATAAAACA-AAAGAAAAT-T
*
55151 AAAACTAAA
1 AAAAATAAA
55160 TCTGAAATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
21 1 0.02
22 26 0.58
23 18 0.40
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (22 bp):
AAAAATAAAACAAAAGAAAATT
Found at i:55129 original size:22 final size:22
Alignment explanation
Indices: 55104--55159 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
55094 CAAAAGAAAT
*
55104 TTAAAACTAAAACA-ACATAAAA
1 TTAAAACTAAAA-ATAAATAAAA
*
55126 TTAAAAATAAAAATAAATAAAA
1 TTAAAACTAAAAATAAATAAAA
55148 TATAAAACTAAA
1 T-TAAAACTAAA
55160 TCTGAAATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 19 0.66
23 9 0.31
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (22 bp):
TTAAAACTAAAAATAAATAAAA
Found at i:55143 original size:17 final size:18
Alignment explanation
Indices: 55123--55160 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
55113 AAACAACATA
55123 AAATTAAAA-ATAAAAAT
1 AAATTAAAATATAAAAAT
*
55140 AAA-TAAAATATAAAACT
1 AAATTAAAATATAAAAAT
55157 AAAT
1 AAAT
55161 CTGAAATCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATTAAAATATAAAAAT
Done.