Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1934
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: 38071
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:12935 original size:20 final size:20
Alignment explanation
Indices: 12888--12935 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
12878 AGTAAGCTCG
12888 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
12908 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
12928 GTTGAGCT
1 GTTGAGCT
12936 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:14619 original size:27 final size:27
Alignment explanation
Indices: 14589--14674 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
14579 TTTTTCAAAC
*
14589 TCTTTTTCAAATTATT-TTTTC-GCTTTT
1 TCTTTTTC-AATT-TTCTTTTCTGCATTT
*
14616 TCTTTTTCAATTTTCTTTTCTTCATTT
1 TCTTTTTCAATTTTCTTTTCTGCATTT
*
14643 TCTTTTTC--TTTTACTTTTTTG-A-TT
1 TCTTTTTCAATTTT-CTTTTCTGCATTT
14667 TCTTTTTC
1 TCTTTTTC
14675 TTGTGCAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
24 10 0.19
25 7 0.13
26 15 0.29
27 20 0.38
ACGTcount: A:0.10, C:0.16, G:0.02, T:0.71
Consensus pattern (27 bp):
TCTTTTTCAATTTTCTTTTCTGCATTT
Found at i:14642 original size:14 final size:14
Alignment explanation
Indices: 14613--14649 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
14603 TTTTTTCGCT
14613 TTTTC-TTTTTCAA
1 TTTTCTTTTTTCAA
14626 TTTTCTTTTCTTC-A
1 TTTTCTTTT-TTCAA
14640 TTTTCTTTTT
1 TTTTCTTTTT
14650 CTTTTACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
14 13 0.59
15 3 0.14
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTTCAA
Found at i:14649 original size:15 final size:15
Alignment explanation
Indices: 14613--14652 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
14603 TTTTTTCGCT
14613 TTTTCTTTTTC--AA
1 TTTTCTTTTTCTTAA
*
14626 TTTTC-TTTTCTTCA
1 TTTTCTTTTTCTTAA
14640 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
14653 TTACTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 5 0.22
13 5 0.22
14 6 0.26
15 7 0.30
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCTTTTTCTTAA
Found at i:14703 original size:7 final size:6
Alignment explanation
Indices: 14611--14709 Score: 74
Period size: 6 Copynumber: 16.0 Consensus size: 6
14601 TATTTTTTCG
* * *
14611 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTTTTA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * * ** *
14662 -TGATTT CTTTTT CTTGTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
14710 GCCTCGCTCT
Statistics
Matches: 70, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
5 1 0.01
6 56 0.80
7 10 0.14
8 3 0.04
ACGTcount: A:0.07, C:0.16, G:0.04, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:14709 original size:18 final size:18
Alignment explanation
Indices: 14611--14709 Score: 83
Period size: 18 Copynumber: 5.3 Consensus size: 18
14601 TATTTTTTCG
14611 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
14630 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* *
14650 CTTTTACTTTTTTGA-TTT
1 CTTTTTC-TTTTTCATTTT
* * *
14668 CTTTTTCTTGTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
14686 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
14704 CTTTTT
1 CTTTTT
14710 GCCTCGCTCT
Statistics
Matches: 62, Mismatches: 14, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
17 4 0.06
18 34 0.55
19 8 0.13
20 8 0.13
21 8 0.13
ACGTcount: A:0.07, C:0.16, G:0.04, T:0.73
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:15767 original size:12 final size:13
Alignment explanation
Indices: 15750--15782 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
15740 TTAAACTAAG
15750 TAAATAAATAA-A
1 TAAATAAATAATA
15762 TAAATAAATAATA
1 TAAATAAATAATA
*
15775 AAAATAAA
1 TAAATAAA
15783 ACTTTACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAATA
Found at i:17180 original size:23 final size:22
Alignment explanation
Indices: 17128--17180 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
17118 TCCACGTCTT
*
17128 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
17150 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
17173 TTTCTTTT
1 TTTCTTTT
17181 TCAACTCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:19296 original size:25 final size:25
Alignment explanation
Indices: 19262--19329 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
19252 CAACTTCTAA
19262 AGAAAACTCAAGAGAGAAATCTTGG
1 AGAAAACTCAAGAGAGAAATCTTGG
19287 AGAAAACTCAAGAGAGAAATCTTGG
1 AGAAAACTCAAGAGAGAAATCTTGG
19312 AGAAAACTCAA-AGA-AAAT
1 AGAAAACTCAAGAGAGAAAT
19330 TCTGCTCTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.09
24 3 0.07
25 36 0.84
ACGTcount: A:0.53, C:0.12, G:0.21, T:0.15
Consensus pattern (25 bp):
AGAAAACTCAAGAGAGAAATCTTGG
Found at i:20382 original size:10 final size:10
Alignment explanation
Indices: 20367--20393 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
20357 ACTTCAAATT
20367 TTTTTTTGAA
1 TTTTTTTGAA
20377 TTTTTTTGAA
1 TTTTTTTGAA
20387 TTTTTTT
1 TTTTTTT
20394 TTCAAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:21958 original size:20 final size:20
Alignment explanation
Indices: 21911--21958 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
21901 AGTAAGCTCG
21911 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
21931 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
21951 GTTGAGCT
1 GTTGAGCT
21959 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:22494 original size:152 final size:152
Alignment explanation
Indices: 22218--22521 Score: 563
Period size: 152 Copynumber: 2.0 Consensus size: 152
22208 AAGAACTTGG
* * *
22218 TGATACGAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGGTGGGCTCACATTGCCACAAGGCC
1 TGATACAAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCAAATTGCCACAAGGCC
22283 CAATAACGAGATCAAAGGCCCGAAAAATGCGGTCCAAACTAAATGGGACCATTCAAGAGCTTGTT
66 CAATAACGAGATCAAAGGCCCGAAAAATGCGGTCCAAACTAAATGGGACCATTCAAGAGCTTGTT
22348 AGCAAGGCCTGAGATGCATACA
131 AGCAAGGCCTGAGATGCATACA
22370 TGATACAAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCAAATTGCCACAAGGCC
1 TGATACAAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCAAATTGCCACAAGGCC
*
22435 CAATAACGAGATCAAAGGCCCGACAAATGCGGTCCAAACTAAATGGGACCATTCAAGAGCTTGTT
66 CAATAACGAGATCAAAGGCCCGAAAAATGCGGTCCAAACTAAATGGGACCATTCAAGAGCTTGTT
*
22500 AGCAAGGCCTTAGATGCATACA
131 AGCAAGGCCTGAGATGCATACA
22522 CGAGAGAACA
Statistics
Matches: 147, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
152 147 1.00
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.18
Consensus pattern (152 bp):
TGATACAAGTCATAAAGGCCCAATCCAAGTTCAAGAACGTGATGGGCTCAAATTGCCACAAGGCC
CAATAACGAGATCAAAGGCCCGAAAAATGCGGTCCAAACTAAATGGGACCATTCAAGAGCTTGTT
AGCAAGGCCTGAGATGCATACA
Found at i:29075 original size:14 final size:15
Alignment explanation
Indices: 29025--29078 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
29015 ACTCTCCTCA
*
29025 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
29040 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
29055 TT-TTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
29068 TTCTTTT-TCTC
1 TTCTTTTCTCTC
29079 GCTCAATAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
13 8 0.23
14 12 0.34
15 15 0.43
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:31168 original size:11 final size:11
Alignment explanation
Indices: 31152--31181 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
31142 GAATACAAAC
31152 TTTTTTTTGAA
1 TTTTTTTTGAA
*
31163 TTTTTTTCGAA
1 TTTTTTTTGAA
31174 TTTTTTTT
1 TTTTTTTT
31182 TACAATCTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.07, T:0.77
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:33992 original size:21 final size:23
Alignment explanation
Indices: 33947--33993 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
33937 TCACCTGCAA
* *
33947 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
33970 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
33991 TAA
1 TAA
33994 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Done.