Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2922
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: 43028
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:2438 original size:24 final size:25
Alignment explanation
Indices: 2411--2462 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
2401 GCCTAGCCTC
*
2411 TTTTAAT-AACTGGGGTAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
*
2435 TTTTAGTAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
2460 TTT
1 TTT
2463 CGCACTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:2537 original size:21 final size:21
Alignment explanation
Indices: 2513--2570 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
2503 AATGAGTATT
*
2513 TCATAGCATATCATGTGCATC
1 TCATAGCATATCATGTGCATA
*
2534 TCATAACATATCATGTGCATA
1 TCATAGCATATCATGTGCATA
*
2555 TTAT-GTCATATCATGT
1 TCATAG-CATATCATGT
2571 ATAAAATATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (21 bp):
TCATAGCATATCATGTGCATA
Found at i:2564 original size:10 final size:11
Alignment explanation
Indices: 2518--2570 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
2508 GTATTTCATA
2518 GCATATCATGT
1 GCATATCATGT
* *
2529 GCATCTCAT-A
1 GCATATCATGT
*
2539 ACATATCATGT
1 GCATATCATGT
*
2550 GCATATTATGT
1 GCATATCATGT
2561 -CATATCATGT
1 GCATATCATGT
2571 ATAAAATATC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (11 bp):
GCATATCATGT
Found at i:2634 original size:25 final size:25
Alignment explanation
Indices: 2606--2653 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2596 ATAATTAAAC
* * *
2606 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAAGGGTAAAATAGTCATTTTTA
2631 CCTAAGGGTAAAATAGTCATTTT
1 CCTAAGGGTAAAATAGTCATTTT
2654 CCATATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (25 bp):
CCTAAGGGTAAAATAGTCATTTTTA
Found at i:5028 original size:46 final size:44
Alignment explanation
Indices: 4885--5054 Score: 137
Period size: 46 Copynumber: 3.7 Consensus size: 44
4875 ATTGTGGGCT
* **
4885 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATTATGAGAACC
1 AGTGTAAGACATGTCTGGGACATGCATC-GGCACGA-TATGA-AGTC
* * * *
4931 AGTGTAAGACTATGTCTGGGAGATGGATCGGCATCGAAACG-AGTGC
1 AGTGTAAGAC-ATGTCTGGGACATGCATCGGCA-CGATATGAAGT-C
*
4977 TAGTGTAAGACATGTCTGGCACATGCATCGGCTACGATATGATAGTC
1 -AGTGTAAGACATGTCTGGGACATGCATCGGC-ACGATATGA-AGTC
* *
5024 AGTGTAAGACCATGTCTTGGATATGGCATCG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCG
5055 ACTTGAGATA
Statistics
Matches: 99, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
45 1 0.01
46 46 0.46
47 42 0.42
48 10 0.10
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCACGATATGAAGTC
Found at i:5075 original size:93 final size:92
Alignment explanation
Indices: 4885--5099 Score: 222
Period size: 93 Copynumber: 2.3 Consensus size: 92
4875 ATTGTGGGCT
* *
4885 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAACCAGTGTAAGACTATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAACCAGTGTAAGACCATGTCTGG
* *
4950 GAGATGGATCGGCATCGAAACGAGTGCT
66 GAGATGGATCGACATCGAAACGAG-GCA
* * * ** *
4978 AGTGTAAGACATGTCTGGCACATGCATCGGCTACGA-TATGATAGTCAGTGTAAGACCATGTCTT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAACCAGTGTAAGACCATGTCTG
* * *
5042 GGATATGGCATCGAC-TTGAGATATGA-GCA
65 GGAGATGG-ATCGACATCGA-A-ACGAGGCA
*
5071 AGTGTAAGAC-TGTTTGGGACATGGCATCG
1 AGTGTAAGACATGTCTGGGACAT-GCATCG
5100 ACATCCTACC
Statistics
Matches: 102, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
92 10 0.10
93 82 0.80
94 7 0.07
95 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (92 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAACCAGTGTAAGACCATGTCTGG
GAGATGGATCGACATCGAAACGAGGCA
Found at i:5941 original size:31 final size:31
Alignment explanation
Indices: 5903--5964 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
5893 AAATAAAAAG
5903 AAAGAAAAAGAGTTTGAGACATTCGGCTATT
1 AAAGAAAAAGAGTTTGAGACATTCGGCTATT
5934 AAAGAAAAAGAGTTTGAGACATTCGGCTATT
1 AAAGAAAAAGAGTTTGAGACATTCGGCTATT
5965 TGAAAGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.26
Consensus pattern (31 bp):
AAAGAAAAAGAGTTTGAGACATTCGGCTATT
Found at i:6132 original size:15 final size:15
Alignment explanation
Indices: 6112--6149 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
6102 TTATTGAAGA
6112 TATGTTTTGGGTTAG
1 TATGTTTTGGGTTAG
6127 TATGTTTTGGGTTAG
1 TATGTTTTGGGTTAG
6142 TAT-TTTTG
1 TATGTTTTG
6150 ATGAATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.13, C:0.00, G:0.29, T:0.58
Consensus pattern (15 bp):
TATGTTTTGGGTTAG
Found at i:6783 original size:43 final size:42
Alignment explanation
Indices: 6719--6887 Score: 144
Period size: 43 Copynumber: 4.0 Consensus size: 42
6709 AGGATTTCCG
* * * *
6719 ATATGTGATCTCTGTAAGATCAGGTCTGGGACATTGGCATCA
1 ATATGTGATTTCAGTAAGACCATGTCTGGGACATTGGCATCA
* * *
6761 ATATGTGATTTCGAGTAAGATCATGTTTGGGACATCGGCATCGTA
1 ATATGTGATTTC-AGTAAGACCATGTCTGGGACATTGGCATC--A
* * * *
6806 AT-TGTGA-TTCGTGTAAGACCCTGTCTGGGACAGTGGCATCG
1 ATATGTGATTTC-AGTAAGACCATGTCTGGGACATTGGCATCA
* * * *
6847 ACATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 ATATGTGATTTCA-GTAAGACCATGTCTGGGACATTGGCAT
6888 TGTATGATAT
Statistics
Matches: 102, Mismatches: 19, Indels: 11
0.77 0.14 0.08
Matches are distributed among these distances:
41 1 0.01
42 16 0.16
43 77 0.75
44 5 0.05
45 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (42 bp):
ATATGTGATTTCAGTAAGACCATGTCTGGGACATTGGCATCA
Found at i:26054 original size:44 final size:43
Alignment explanation
Indices: 25969--26058 Score: 119
Period size: 44 Copynumber: 2.1 Consensus size: 43
25959 ATAAATGTAA
* * * *
25969 ATTATAATTATAATTATTTTAAATGTGTAATTATCACAATTTCT
1 ATTATAATTATAATTATTTGAAATGTATAATTATAAAAATTT-T
26013 ATTA-AATTATAATTATTGTGAAATGTATAATTATAAAAATTTT
1 ATTATAATTATAATTATT-TGAAATGTATAATTATAAAAATTTT
26056 ATT
1 ATT
26059 TTATGCCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
43 17 0.41
44 24 0.59
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (43 bp):
ATTATAATTATAATTATTTGAAATGTATAATTATAAAAATTTT
Found at i:31319 original size:48 final size:48
Alignment explanation
Indices: 31173--31393 Score: 228
Period size: 48 Copynumber: 4.6 Consensus size: 48
31163 GAATTTTCCA
** * * * * * * *
31173 ATGCCATGTCTTAGACATGGTCTGAAATTGGCTCACATGTCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATGGTGGCCG
* * ** * ** *
31221 ATGCCATGTCCCAGACGTGGTCTTACACTAGCTCTTGTCTCAAT-GTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAT-GGTGGCCG
* *
31269 ATGCCATATCCCAGACATGGTCTTACACTGGCTCTCCTATGGTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATGGTGGCCG
* *
31317 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAAGGTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATGGTGGCCG
*
31365 ATTCCATGTCCCAGACATGGTCTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
31394 AGCACACACA
Statistics
Matches: 141, Mismatches: 30, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
47 1 0.01
48 140 0.99
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATGGTGGCCG
Found at i:34200 original size:3 final size:3
Alignment explanation
Indices: 34194--34251 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
34184 ATGATGAAAT
*
34194 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
34242 AGA AGA AGA A
1 AGA AGA AGA A
34252 AAACAAAAGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:36637 original size:46 final size:46
Alignment explanation
Indices: 36587--36759 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
36577 TGGTTGAGCA
36587 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
36633 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
36678 CATCTGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
36726 TGCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
36760 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 59 0.57
47 27 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:36743 original size:93 final size:93
Alignment explanation
Indices: 36584--36754 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
36574 GGATGGTTGA
* *
36584 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
36649 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* * *
36677 GCATCTGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTGCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
36742 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
36755 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:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:41142 original size:18 final size:18
Alignment explanation
Indices: 41119--41158 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
41109 GTTTATAGTA
41119 AGGGCATTTTGGTCATTT
1 AGGGCATTTTGGTCATTT
41137 AGGGCATTTTGGTCATTT
1 AGGGCATTTTGGTCATTT
41155 AGGG
1 AGGG
41159 GTAAAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.10, G:0.33, T:0.40
Consensus pattern (18 bp):
AGGGCATTTTGGTCATTT
Done.