Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2038
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: 44263
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:13419 original size:174 final size:170
Alignment explanation
Indices: 13104--13432 Score: 430
Period size: 174 Copynumber: 1.9 Consensus size: 170
13094 GTTCATAATA
* * *
13104 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGAT
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGAT
* *
13169 TACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTC
66 TACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTC
13234 TTATCTCCCTG-AGATTACAGTGGAACAGACCAAAGAATTT
131 TTATCTCCCTGAAGA-TACAGTGGAACAGACCAAAGAATTT
* *
13274 CAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGA-AG
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGA-
* * * * * * *
13337 TTACAGTGGAGTGGATTAAAATAAAGGATTTTATCTCTCTGAGGTTACAGCAGAGTAGGTCGCAT
65 TTACAATGGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACAT
* *
13402 CAAGTCTTATTTCCCTGAAGATGCAGTGGAA
125 CAAGTCTTATCTCCCTGAAGATACAGTGGAA
13433 TAGATTGAAA
Statistics
Matches: 136, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
168 1 0.01
169 27 0.20
170 43 0.32
174 62 0.46
175 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (170 bp):
CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGAT
TACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTC
TTATCTCCCTGAAGATACAGTGGAACAGACCAAAGAATTT
Found at i:15147 original size:19 final size:21
Alignment explanation
Indices: 15123--15164 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
15113 ATCCCGCTTT
*
15123 TATTTATTTA-ATAT-TTATA
1 TATTTATATACATATATTATA
15142 TATTTATATACATATATTATA
1 TATTTATATACATATATTATA
15163 TA
1 TA
15165 ATATTTATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 4 0.20
21 7 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTATATACATATATTATA
Found at i:22373 original size:17 final size:16
Alignment explanation
Indices: 22350--22394 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
22340 ATTGAAGCGG
22350 ATTTTTTTAATTTTTA
1 ATTTTTTTAATTTTTA
* *
22366 AGTTTTTTTAAATTTTG
1 A-TTTTTTTAATTTTTA
22383 ATATTTTTTAAT
1 AT-TTTTTTAAT
22395 CAGATTGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 22 0.92
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (16 bp):
ATTTTTTTAATTTTTA
Found at i:25505 original size:25 final size:24
Alignment explanation
Indices: 25454--25505 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
25444 CACAACTTAA
* *
25454 AAATTAATTTAAAATTATTTATTT
1 AAATTAATTTAAAATTATTAATAT
25478 AAATTCAATTTATAAA-TATTAATAT
1 AAATT-AATTTA-AAATTATTAATAT
25503 AAA
1 AAA
25506 CTATTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.21
25 16 0.67
26 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATTAATTTAAAATTATTAATAT
Found at i:32423 original size:5 final size:5
Alignment explanation
Indices: 32413--32440 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
32403 GAGGTAGTCC
32413 TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TAT
32441 ATGTCATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:35051 original size:29 final size:28
Alignment explanation
Indices: 34989--35053 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
34979 ATAAAATTGC
* *
34989 TAAAATATGGGCTAAATCGAAATAAAAA
1 TAAAATATGGGCGAAATCGAAAGAAAAA
* *
35017 TGAAAATGTAGGGCGAAATTGAAAGAAAAA
1 T-AAAATAT-GGGCGAAATCGAAAGAAAAA
35047 TAAAATA
1 TAAAATA
35054 AAAGGGACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.03
29 11 0.37
30 18 0.60
ACGTcount: A:0.57, C:0.05, G:0.18, T:0.20
Consensus pattern (28 bp):
TAAAATATGGGCGAAATCGAAAGAAAAA
Found at i:36724 original size:44 final size:42
Alignment explanation
Indices: 36662--37078 Score: 179
Period size: 44 Copynumber: 9.6 Consensus size: 42
36652 GATCTACTCT
* *
36662 ACTGTAACTTCAGAGAGATAAGATCCTTAGT-TTTAATCCGCTCC
1 ACTGTAA-TTCAGGGAGATAAGATCC-TA-TCTTCAATCCGCTCC
* * *
36706 ACTGTAATATCAGGGAGATAGGATTACTATCTTCAATCTGCTCC
1 ACTGTAAT-TCAGGGAGATAAGA-TCCTATCTTCAATCCGCTCC
** ***
36750 ACTGTAATCTCAGGGAGATAAGAT-CTGAAATTCTTCGGTCTATTCC
1 ACTGTAAT-TCAGGGAGATAAGATCCT---A-TCTTCAATCCGCTCC
* * * * ** *
36796 ACTATAATCTCAGGGAAATAAGA-CCTGA-C-ACGATCTACTCT
1 ACTGTAAT-TCAGGGAGATAAGATCCT-ATCTTCAATCCGCTCC
* * * *
36837 GCTGTAACTTCAGAGAGATAAGATCCT-TCATTTTAATTCGCTCC
1 ACTGTAA-TTCAGGGAGATAAGATCCTATC--TTCAATCCGCTCC
* * * * *
36881 ACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTCC
1 ACTGTAAT-TCAGGGAGATAAGA-TCCTATCTTCAATCCGCTCC
* * * ** *
36925 GCTGTAATCTCAGGGAGATAAGAT-CTGA-C-ACGATCTACTCT
1 ACTGTAAT-TCAGGGAGATAAGATCCT-ATCTTCAATCCGCTCC
* * *
36966 ACTGTAACTTCAGAGAGATAAGATCCTTTAT-TTTAATCCACTCC
1 ACTGTAA-TTCAGGGAGATAAGATCC--TATCTTCAATCCGCTCC
* * *
37010 ACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCC
1 ACTGTAAT-TCAGGGAGATAAGA-TCCTATCTTCAATCCGCTCC
* *
37054 GCAGTAATCTCAGGGAGATAAGATC
1 ACTGTAAT-TCAGGGAGATAAGATC
37079 TGAAATTCTT
Statistics
Matches: 284, Mismatches: 62, Indels: 55
0.71 0.15 0.14
Matches are distributed among these distances:
41 54 0.19
42 12 0.04
43 12 0.04
44 163 0.57
45 8 0.03
46 35 0.12
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (42 bp):
ACTGTAATTCAGGGAGATAAGATCCTATCTTCAATCCGCTCC
Found at i:36768 original size:175 final size:174
Alignment explanation
Indices: 36479--36952 Score: 718
Period size: 175 Copynumber: 2.7 Consensus size: 174
36469 AATCTGAGGT
* * * *
36479 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTTTTTTTAATCCACTCCATTG-AA-CTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATC-CTTATTTTAATCCGCTCCACTGTAATCTC
*
36542 AAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
65 AGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
* * * * ***
36607 CTTCGGTCTGCTCTACTGTAATCTCAAAGAGATAAGACCTGGTGC
130 CTTCGGTCTACTCCACTATAATCTCAAAGAAATAAGACCTGACAC
*
36652 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTAGTTTTAATCCGCTCCACTGTAATATC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTA-TTTTAATCCGCTCCACTGTAATCTC
* *
36717 AGGGAGATAGGATTACTATCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATT
65 AGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
* **
36782 CTTCGGTCTATTCCACTATAATCTCAGGGAAATAAGACCTGACAC
130 CTTCGGTCTACTCCACTATAATCTCAAAGAAATAAGACCTGACAC
* * *
36827 GATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATTCGCTCCACTGTAATCTT
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTT-ATTTTAATCCGCTCCACTGTAATCTC
36892 AGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
65 AGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
36953 CACGATCTAC
Statistics
Matches: 273, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
172 2 0.01
173 51 0.19
174 2 0.01
175 217 0.79
176 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (174 bp):
GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTATTTTAATCCGCTCCACTGTAATCTCA
GGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTC
TTCGGTCTACTCCACTATAATCTCAAAGAAATAAGACCTGACAC
Found at i:36971 original size:129 final size:129
Alignment explanation
Indices: 36800--37081 Score: 483
Period size: 129 Copynumber: 2.2 Consensus size: 129
36790 TATTCCACTA
* * *
36800 TAATCTCAGGGAAATAAGACCTGACACGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTT
1 TAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTT
* * * *
36865 CATTTTAATTCGCTCCACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTG
66 CATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCAG
36929 TAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTT
1 TAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTT
* *
36994 TATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCAG
66 CATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCAG
37058 TAATCTCAGGGAGATAAGATCTGA
1 TAATCTCAGGGAGATAAGATCTGA
37082 AATTCTTCGG
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 144 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (129 bp):
TAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTT
CATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCAG
Done.