Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2915
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: 21102
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:3850 original size:23 final size:23
Alignment explanation
Indices: 3824--3868 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3814 GTTCAAAATT
*
3824 TTAAAATAAACAATATATATGAG
1 TTAAAACAAACAATATATATGAG
*
3847 TTAAAACAAATAATATATATGA
1 TTAAAACAAACAATATATATGA
3869 ATGTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAAACAAACAATATATATGAG
Found at i:3957 original size:24 final size:24
Alignment explanation
Indices: 3917--4168 Score: 181
Period size: 24 Copynumber: 10.8 Consensus size: 24
3907 TGAATTGGAT
* *
3917 AATTTACAATAACTAATATATAATA
1 AATTTAAAATAA-TAATATATGATA
*
3942 AATTTGAAATAATAATATAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
3966 AATTTAAAA-AAT--T-TGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
*
3986 AATTCTAAAATAATCATACT-TGATA
1 AATT-TAAAATAATAATA-TATGATA
** * *
4011 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
*
4035 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* *
4056 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
** **
4080 AATTTAAAATAATGTTA-ACAATA
1 AATTTAAAATAATAATATATGATA
4103 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
4126 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
*
4150 AATCTAAAATAATAATATA
1 AATTTAAAATAATAATATA
4169 CAATACACTT
Statistics
Matches: 181, Mismatches: 26, Indels: 41
0.73 0.10 0.17
Matches are distributed among these distances:
20 5 0.03
21 18 0.10
22 17 0.09
23 48 0.27
24 77 0.43
25 15 0.08
26 1 0.01
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:4012 original size:69 final size:69
Alignment explanation
Indices: 3939--4173 Score: 214
Period size: 69 Copynumber: 3.4 Consensus size: 69
3929 CTAATATATA
* *
3939 ATAAATTTGAAATAATAATATAT-ATAAAATTTAAAAA-ATTTGATGAT-AATTCTAAAATA-AT
1 ATAAATTTAAAATAATAATATATAAT-AAATTTAAAAATA-TTAATGATAAATT-TAAAATAGAT
*
4000 CATACTTG
63 -ATACATG
** * *
4008 ATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
1 ATAAATTTAAAATAATAATATATAATAAATTTAAAAATATTAATGATAAATTTAAAATAGATATA
4073 CATG
66 CATG
** * * *
4077 ATAAATTTAAAATAATGTTA-ACAATAAATTTAAAATAATAATATTGATAAA-TTACAAATA-AT
1 ATAAATTTAAAATAATAATATATAATAAATTT-AAA-AATATTAATGATAAATTTA-AAATAGAT
*
4139 AAAACATG
63 -ATACATG
* *
4147 ATAAATCTAAAATAATAATATACAATA
1 ATAAATTTAAAATAATAATATATAATA
4174 CACTTAGATA
Statistics
Matches: 138, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
68 10 0.07
69 72 0.52
70 50 0.36
71 6 0.04
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (69 bp):
ATAAATTTAAAATAATAATATATAATAAATTTAAAAATATTAATGATAAATTTAAAATAGATATA
CATG
Found at i:4151 original size:47 final size:48
Alignment explanation
Indices: 3917--4167 Score: 129
Period size: 45 Copynumber: 5.4 Consensus size: 48
3907 TGAATTGGAT
* * * * *
3917 AATTTACAATAACTAATATATAATAAATTTGAAATAAT-AATATAT-ATAA
1 AATTTAAAATAA-TAATAT-TGATAAATTTAAAATAATGAAAACATGAT-A
* * * *
3966 AATTTAAAA-AAT-TTGA-TGAT-AATTCTAAAATAAT-CATACTTGATA
1 AATTTAAAATAATAAT-ATTGATAAATT-TAAAATAATGAAAACATGATA
** * * **
4011 AATCCAAAATAATAGTATATAATAAATTT-AAA-AAT-ATTA-ATGATA
1 AATTTAAAATAATAATAT-TGATAAATTTAAAATAATGAAAACATGATA
* * **
4056 AATTTGAAATAGAT-ATACATGATAAATTTAAAATAATGTTAACA--ATA
1 AATTTAAAATA-ATAATA-TTGATAAATTTAAAATAATGAAAACATGATA
4103 AATTTAAAATAATAATATTGATAAA-TTACAAATAAT-AAAACATGATA
1 AATTTAAAATAATAATATTGATAAATTTA-AAATAATGAAAACATGATA
*
4150 AATCTAAAATAATAATAT
1 AATTTAAAATAATAATAT
4168 ACAATACACT
Statistics
Matches: 157, Mismatches: 27, Indels: 38
0.71 0.12 0.17
Matches are distributed among these distances:
44 4 0.03
45 54 0.34
46 33 0.21
47 45 0.29
48 8 0.05
49 13 0.08
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (48 bp):
AATTTAAAATAATAATATTGATAAATTTAAAATAATGAAAACATGATA
Found at i:4185 original size:70 final size:69
Alignment explanation
Indices: 4006--4173 Score: 187
Period size: 70 Copynumber: 2.4 Consensus size: 69
3996 TAATCATACT
* * * * * **
4006 TGATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATA
1 TGATAAATCTAAAATAATAATATACAATAAATTTAATAATAATAATGATAAATTACAAATAGATA
*
4071 TACA
66 AACA
* ** *
4075 TGATAAATTTAAAATAATGTTA-ACAATAAATTTAAAATAATAATATTGATAAATTACAAATA-A
1 TGATAAATCTAAAATAATAATATACAATAAATTT--AATAATAATAATGATAAATTACAAATAGA
4138 TAAAACA
64 T-AAACA
4145 TGATAAATCTAAAATAATAATATACAATA
1 TGATAAATCTAAAATAATAATATACAATA
4174 CACTTAGATA
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
68 10 0.12
69 20 0.25
70 45 0.56
71 6 0.07
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (69 bp):
TGATAAATCTAAAATAATAATATACAATAAATTTAATAATAATAATGATAAATTACAAATAGATA
AACA
Found at i:5027 original size:23 final size:22
Alignment explanation
Indices: 5000--5044 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4990 AATTTAAATC
5000 TCTAAGATTACAAAATCTTATCT
1 TCTAAGATTAC-AAATCTTATCT
* *
5023 TCTAAGATTGCATATCTTATCT
1 TCTAAGATTACAAATCTTATCT
5045 AAGATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (22 bp):
TCTAAGATTACAAATCTTATCT
Found at i:5047 original size:19 final size:19
Alignment explanation
Indices: 5023--5078 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
5013 AATCTTATCT
*
5023 TCTAAGATTGCATATCTTA
1 TCTAAGATTGCATATCCTA
5042 TCTAAGATTGCATATCCTA
1 TCTAAGATTGCATATCCTA
5061 TCTAAGATTGCATATCCT
1 TCTAAGATTGCATATCCT
5079 TTTTCAAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCCTA
Found at i:5484 original size:51 final size:50
Alignment explanation
Indices: 5394--5520 Score: 130
Period size: 51 Copynumber: 2.5 Consensus size: 50
5384 CAATGAGATG
* * *
5394 AGATTCGTTGCCTTCAACTTTAATCTGCTCTGCTACAACGCCAGGGAAATA
1 AGATTCGCTGCCTTCAGCTTTAATCTGCTCT-CTACAACGCCAAGGAAATA
* * *
5445 AGATTCGCTGCCTTCAGCTTTAATCTG-TTTCATTGCAACGCCAAGGAGATA
1 AGATTCGCTGCCTTCAGCTTTAATCTGCTCTC--TACAACGCCAAGGAAATA
* * **
5496 GGATTTGCTGTATTCAGCTTTAATC
1 AGATTCGCTGCCTTCAGCTTTAATC
5521 CACTCCACTT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
49 1 0.02
50 2 0.03
51 61 0.95
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (50 bp):
AGATTCGCTGCCTTCAGCTTTAATCTGCTCTCTACAACGCCAAGGAAATA
Found at i:5534 original size:21 final size:21
Alignment explanation
Indices: 5508--5550 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5498 ATTTGCTGTA
*
5508 TTCAGCTTTAATCCACTCCAC
1 TTCAGCTTTAACCCACTCCAC
*
5529 TTCAGCTTTAACCCATTCCAC
1 TTCAGCTTTAACCCACTCCAC
5550 T
1 T
5551 GCAACACTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.37, G:0.05, T:0.35
Consensus pattern (21 bp):
TTCAGCTTTAACCCACTCCAC
Found at i:5637 original size:123 final size:123
Alignment explanation
Indices: 5436--5658 Score: 275
Period size: 123 Copynumber: 1.8 Consensus size: 123
5426 CTACAACGCC
* * * * * *
5436 AGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTTCATTGCAACGCCAAGGAGATAGGATT
1 AGGGAAACAAGATTCGCTACCTTCAGCTTTAATCTGTTCCACTACAACGCCAAAGAGATAGGATT
* * ** *
5501 TGCTGTATTCAGCTTTAATCCACTCCACTTCAGCTTTAACCCATTCCACTGCAACACT
66 CGCTGCACACAGCTTTAATCCACTCCACCTCAGCTTTAACCCATTCCACTGCAACACT
* * * * *
5559 AGGGAAACAAGATTCGCTACCTTTATCTTTAATTTGTTCCACTATAATGCCAAAGAGATAGGATT
1 AGGGAAACAAGATTCGCTACCTTCAGCTTTAATCTGTTCCACTACAACGCCAAAGAGATAGGATT
* **
5624 CGCTGCCCACAGCTTTAATCTGCTCCACCTCAGCT
66 CGCTGCACACAGCTTTAATCCACTCCACCTCAGCT
5659 ATTCCAAGTC
Statistics
Matches: 81, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
123 81 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.30
Consensus pattern (123 bp):
AGGGAAACAAGATTCGCTACCTTCAGCTTTAATCTGTTCCACTACAACGCCAAAGAGATAGGATT
CGCTGCACACAGCTTTAATCCACTCCACCTCAGCTTTAACCCATTCCACTGCAACACT
Found at i:5935 original size:46 final size:46
Alignment explanation
Indices: 5863--6032 Score: 268
Period size: 46 Copynumber: 3.7 Consensus size: 46
5853 CCACTGCAAT
* * *
5863 GCCAAGGAAATGAGATTCACAACCCTCAGCTTTAATCTACTACGAC
1 GCCATGGAAATGAGATTCGCTACCCTCAGCTTTAATCTACTACGAC
* *
5909 GTCATGGAAATGAGATTCGCTGCCCTCAGCTTTAATCTACTACGAC
1 GCCATGGAAATGAGATTCGCTACCCTCAGCTTTAATCTACTACGAC
* *
5955 GCCATGGAAATGAGACTCGCTGCCCTCAGCTTTAATCTACTACGAC
1 GCCATGGAAATGAGATTCGCTACCCTCAGCTTTAATCTACTACGAC
*
6001 GCCATGGAAATGAGATTCGCTACCCACAGCTT
1 GCCATGGAAATGAGATTCGCTACCCTCAGCTT
6033 CAATTTATTC
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 114 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (46 bp):
GCCATGGAAATGAGATTCGCTACCCTCAGCTTTAATCTACTACGAC
Found at i:6874 original size:12 final size:12
Alignment explanation
Indices: 6857--6881 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6847 TGACAACAAA
6857 ATCTGAAGGGAT
1 ATCTGAAGGGAT
6869 ATCTGAAGGGAT
1 ATCTGAAGGGAT
6881 A
1 A
6882 GTCTCAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (12 bp):
ATCTGAAGGGAT
Found at i:8415 original size:21 final size:20
Alignment explanation
Indices: 8370--8438 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
8360 CCTTGGCCTC
* **
8370 TCATTTTCCTTTCTTTTTTTT
1 TCATTTTCTTTTC-TTTTTCA
8391 TCATTTTCTTTTCTTTTTCCA
1 TCATTTTCTTTTCTTTTT-CA
*
8412 TCATTTTCATTTTCATTTTCA
1 TCATTTTC-TTTTCTTTTTCA
8433 T-ATTTT
1 TCATTTT
8439 GATTTTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 10 0.24
21 23 0.55
22 9 0.21
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.70
Consensus pattern (20 bp):
TCATTTTCTTTTCTTTTTCA
Found at i:10972 original size:16 final size:16
Alignment explanation
Indices: 10947--10981 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
10937 TTCTATGATG
*
10947 AAATGCCATGCAGTCA
1 AAATGCCATGCAGCCA
*
10963 AAATGTCATGCAGCCA
1 AAATGCCATGCAGCCA
10979 AAA
1 AAA
10982 CAAAACAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (16 bp):
AAATGCCATGCAGCCA
Found at i:12415 original size:23 final size:23
Alignment explanation
Indices: 12389--12442 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
12379 GTTCAAAATT
*
12389 TTAAAATAAACAATATATATGAG
1 TTAAAATAAACAATATATATGAA
* * *
12412 TTAAAACAAATAATTTATATGAA
1 TTAAAATAAACAATATATATGAA
12435 TGTAAAAT
1 T-TAAAAT
12443 TTAATACAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (23 bp):
TTAAAATAAACAATATATATGAA
Found at i:12631 original size:46 final size:46
Alignment explanation
Indices: 12581--12670 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 46
12571 GATAAATCCA
* **
12581 AAATAAATAGTATATAATAAATTTAAA-AATATTAATTATAAATTTG
1 AAATAAATA-TACATAATAAATTTAAATAATATTAAAAATAAATTTG
* * *
12627 AAATAGATATACATGATAAATTTAAATAATGTTAAAAATAAATT
1 AAATAAATATACATAATAAATTTAAATAATATTAAAAATAAATT
12671 AAAATAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
45 15 0.41
46 22 0.59
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.37
Consensus pattern (46 bp):
AAATAAATATACATAATAAATTTAAATAATATTAAAAATAAATTTG
Found at i:12676 original size:45 final size:44
Alignment explanation
Indices: 12597--12729 Score: 119
Period size: 45 Copynumber: 2.9 Consensus size: 44
12587 ATAGTATATA
** *
12597 ATAAATTTAAAAATATTAATTATAAATTTGAAATAGAT-ATACATG
1 ATAAATTTAAAAATATTAAAAATAAATTTAAAATA-ATAATA-ATG
* *
12642 ATAAATTTAAATAATGTTAAAAATAAA-TTAAAATAATAATATTG
1 ATAAATTTAAA-AATATTAAAAATAAATTTAAAATAATAATAATG
* *
12686 ATAAA-TTACAAAATATAAAACATGATAAATCTAAAATAATAATA
1 ATAAATTTA-AAAATATTAAA-A--ATAAATTTAAAATAATAATA
12730 TACATACACT
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
43 10 0.14
44 12 0.16
45 21 0.29
46 17 0.23
47 13 0.18
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.34
Consensus pattern (44 bp):
ATAAATTTAAAAATATTAAAAATAAATTTAAAATAATAATAATG
Found at i:12727 original size:24 final size:22
Alignment explanation
Indices: 12639--12727 Score: 67
Period size: 22 Copynumber: 3.9 Consensus size: 22
12629 ATAGATATAC
* *
12639 ATGATAAATTTAAATAATGTTAAA
1 ATGATAAATTAAAATAA--TAAAA
*
12663 A--ATAAATTAAAATAATAATA
1 ATGATAAATTAAAATAATAAAA
*
12683 TTGATAAATTACAAA-ATATAAAA
1 ATGATAAATTA-AAATA-ATAAAA
12706 CATGATAAATCTAAAATAATAA
1 -ATGATAAAT-TAAAATAATAA
12728 TATACATACA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
20 3 0.06
22 22 0.42
23 8 0.15
24 16 0.31
25 3 0.06
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.31
Consensus pattern (22 bp):
ATGATAAATTAAAATAATAAAA
Found at i:17621 original size:21 final size:20
Alignment explanation
Indices: 17584--17627 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
17574 TTTTACGATT
* *
17584 TATTTTTATGTGCTTTTTAA
1 TATTTTTATGTGATTTTAAA
*
17604 TATTTTTATATTGATTTTAAA
1 TATTTTTAT-GTGATTTTAAA
17625 TAT
1 TAT
17628 GTAGTTCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (20 bp):
TATTTTTATGTGATTTTAAA
Done.