Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1065
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: 37456
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:428 original size:46 final size:46
Alignment explanation
Indices: 328--542 Score: 263
Period size: 46 Copynumber: 4.6 Consensus size: 46
318 AGGGGTTCAC
*
328 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAG-G--TATATATGTGATAAGGCCGAATGGCCGATGTGATG
*
377 AATGTGAAA-GTATATATGTGATAAGGCCGGAATAGCCGATGTGATG
1 AATGTGAAAGGTATATATGTGATAAGGCC-GAATGGCCGATGTGATG
* *
423 AATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAG-GTATATATGTGATAAGGCCGAATGGCCGATGTGATG
* * * *
470 -ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAATGTGATG
1 AATGTGAAAG-GTATATATGTGATAAGGCCGAATGGCCGATGTGATG
* *
516 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAG-GTATATATGTGATAAG
543 TCCCGAAGGG
Statistics
Matches: 148, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
45 18 0.12
46 64 0.43
47 39 0.26
48 18 0.12
49 9 0.06
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (46 bp):
AATGTGAAAGGTATATATGTGATAAGGCCGAATGGCCGATGTGATG
Found at i:512 original size:93 final size:93
Alignment explanation
Indices: 328--542 Score: 308
Period size: 93 Copynumber: 2.3 Consensus size: 93
318 AGGGGTTCAC
328 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATA
* *
393 TGTGATAAGGCCGGAATAGCCGATGTGATG
64 TGTGACAAGGCCGGAATAGCCAATGTGATG
*
423 AATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATG-ATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA--GTATATA
* * *
487 TGTGACAGGGCC-GAGTGGCCAATGTGATG
64 TGTGACAAGGCCGGAATAGCCAATGTGATG
* *
516 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
543 TCCCGAAGGG
Statistics
Matches: 109, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
92 8 0.07
93 72 0.66
94 17 0.16
95 12 0.11
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (93 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATATG
TGACAAGGCCGGAATAGCCAATGTGATG
Found at i:10147 original size:19 final size:20
Alignment explanation
Indices: 10106--10154 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
10096 CTTGCTGACA
*
10106 TTTTCTTTTTATTTCGATATT
1 TTTTC-TTTTATTTCAATATT
*
10127 TTTTCTTTTCTTTCAAT-TT
1 TTTTCTTTTATTTCAATATT
10146 TTTTCTTTT
1 TTTTCTTTT
10155 TTCTGCACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 11 0.42
20 10 0.38
21 5 0.19
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTCTTTTATTTCAATATT
Found at i:10158 original size:21 final size:21
Alignment explanation
Indices: 10106--10155 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
10096 CTTGCTGACA
* *
10106 TTTTCTTTTTATTTCGATATT
1 TTTTCTTTTTCTTTCAATATT
10127 TTTTC-TTTTCTTTCAAT-TT
1 TTTTCTTTTTCTTTCAATATT
10146 TTTTCTTTTT
1 TTTTCTTTTT
10156 TCTGCACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 7 0.27
20 14 0.54
21 5 0.19
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTCTTTTTCTTTCAATATT
Found at i:14638 original size:37 final size:37
Alignment explanation
Indices: 14580--14684 Score: 174
Period size: 37 Copynumber: 2.8 Consensus size: 37
14570 GCTCAGACGA
* * *
14580 AATCTCCACATGAAGTTATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
14617 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
*
14654 AATCTCCACACGTAGTCATCGAGTCTTACCC
1 AATCTCCACACGTAGTCATCGGGTCTTACCC
14685 AGAATATATT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:15086 original size:53 final size:51
Alignment explanation
Indices: 14898--15266 Score: 455
Period size: 47 Copynumber: 7.5 Consensus size: 51
14888 ACACGTTTCG
* *
14898 CATTAGCCATTCGGCCTTA-C-CACATATAT-T-CATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATATATACATGTTCACATTCATCA
* *
14945 CATTGGCCATTCGGCCTTAT--C-T-CATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATATATACATGTTCACATTCATCA
* * *
14992 CATTGGCCATTCAGCCTTATCAC----ACATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATATATACATGTTCACATTCATCA
*
15039 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--CATATATATATACATGTTCACATTCATCA
15092 CATTGGCCATTCGGCCTTATCACGCATATATATATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--CATATATATATACATGTTCACATTCATCA
* * **
15145 AATTGGCCATTCGGCCTTATCAC----ACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATATATACATGTTCACATTCATCA
* **
15192 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATATATACATGTTCACATTCATCA
15243 CATTGGCCATTCGGCCTTATCACA
1 CATTGGCCATTCGGCCTTATCACA
15267 CATACGCATG
Statistics
Matches: 287, Mismatches: 20, Indels: 26
0.86 0.06 0.08
Matches are distributed among these distances:
45 4 0.01
46 1 0.00
47 142 0.49
49 2 0.01
51 44 0.15
53 94 0.33
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.33
Consensus pattern (51 bp):
CATTGGCCATTCGGCCTTATCACATATATATATACATGTTCACATTCATCA
Found at i:15193 original size:153 final size:150
Alignment explanation
Indices: 14898--15271 Score: 568
Period size: 153 Copynumber: 2.5 Consensus size: 150
14888 ACACGTTTCG
* *
14898 CATTAGCCATTCGGCCTTA-C-CACATATAT-T-CATGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATATATATACAGGTTCACATTCATCACATTGGCCATTCGG
* *
14959 CCTTAT---C-T-CATATATGCATGTTCACATTCATCACATTGGCCATTCAGCCTTATCACACAT
66 CCTTATCACCATACATATATACATGTTCACATTCATCAAATTGGCCATTCAGCCTTATCACACAT
*
15019 ATGCATGTTCACATTCATCA
131 ACGCATGTTCACATTCATCA
*
15039 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCACATTGGCCATTC
1 CATTGGCCATTCGGCCTTATCA--CACATATATATACAGGTTCACATTCATCACATTGGCCATTC
* *
15104 GGCCTTATCACGCATATATATATACATGTTCACATTCATCAAATTGGCCATTCGGCCTTATCACA
64 GGCCTTATCAC-CATACATATATACATGTTCACATTCATCAAATTGGCCATTCAGCCTTATCACA
15169 CATACGCATGTTCACATTCATCA
128 CATACGCATGTTCACATTCATCA
*
15192 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATATATATACAGGTTCACATTCATCACATTGGCCATTCGG
15257 CCTTATCACACATAC
66 CCTTATCAC-CATAC
15272 GCATGTTCAC
Statistics
Matches: 209, Mismatches: 12, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
141 18 0.09
142 1 0.00
145 8 0.04
146 1 0.00
147 36 0.17
151 55 0.26
152 1 0.00
153 89 0.43
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (150 bp):
CATTGGCCATTCGGCCTTATCACACATATATATACAGGTTCACATTCATCACATTGGCCATTCGG
CCTTATCACCATACATATATACATGTTCACATTCATCAAATTGGCCATTCAGCCTTATCACACAT
ACGCATGTTCACATTCATCA
Found at i:20606 original size:14 final size:14
Alignment explanation
Indices: 20587--20614 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20577 CATTCCGAAG
20587 TATATATATACATA
1 TATATATATACATA
20601 TATATATATACATA
1 TATATATATACATA
20615 AGTATGCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TATATATATACATA
Found at i:21129 original size:28 final size:28
Alignment explanation
Indices: 21061--21158 Score: 126
Period size: 27 Copynumber: 3.5 Consensus size: 28
21051 CATGAGATTG
* * * *
21061 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
21090 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
21118 GCACTAAGTGTGCGA-CTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
21145 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
21159 GACTTAATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 24 0.38
28 21 0.33
29 18 0.29
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:21145 original size:27 final size:27
Alignment explanation
Indices: 21089--21171 Score: 114
Period size: 27 Copynumber: 3.0 Consensus size: 27
21079 TAAATTGTAC
*
21089 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGATTATAT
21117 AGCACTAAGTGTGCGACTTGATTATAT
1 AGCACTAAGTGTGCGACTTGATTATAT
* *
21144 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGATTATAT
21171 A
1 A
21172 CTTTTGAATC
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
27 30 0.59
28 21 0.41
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGATTATAT
Found at i:22776 original size:40 final size:40
Alignment explanation
Indices: 22744--23135 Score: 631
Period size: 40 Copynumber: 9.8 Consensus size: 40
22734 CCAGCATGAT
* * *
22744 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
22784 TGCTCTTCGGAACTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
22824 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
22864 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
22904 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
22944 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
22984 TGCTCTTCGGGATTTAGCCCGGATATATCACTAACACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
23024 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
23064 TGCTCTTTGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
23104 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACT
23136 CTCAATTCTC
Statistics
Matches: 323, Mismatches: 29, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 323 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:24463 original size:37 final size:37
Alignment explanation
Indices: 24405--24475 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
24395 GCTCAGACGA
* *
24405 AATCTCCACATGAAGTTATCGGGTCTTACCCGGACAT
1 AATCTCCACACGAAGTCATCGGGTCTTACCCGGACAT
*
24442 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AATCTCCACACGAAGTCATCGGGTCTTACCCGGA
24476 ATATATTTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (37 bp):
AATCTCCACACGAAGTCATCGGGTCTTACCCGGACAT
Found at i:24745 original size:47 final size:47
Alignment explanation
Indices: 24688--25028 Score: 412
Period size: 47 Copynumber: 7.0 Consensus size: 47
24678 ACACGTTTCG
* * *
24688 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* * *
24735 CATTAGCCATTCGACCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* * *
24782 CATTGGTCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
24829 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C----ATATATGCATGTTCACATTCATCA
* * *
24882 CATTGGCCATGCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* **
24929 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTAT--CAC--ATATATGCATGTTCACATTCATCA
* * *
24980 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATACATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
25027 CA
1 CA
25029 GTAAAATCCT
Statistics
Matches: 252, Mismatches: 32, Indels: 20
0.83 0.11 0.07
Matches are distributed among these distances:
47 164 0.65
49 7 0.03
51 40 0.16
53 41 0.16
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.31
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:24878 original size:147 final size:148
Alignment explanation
Indices: 24688--25007 Score: 447
Period size: 147 Copynumber: 2.2 Consensus size: 148
24678 ACACGTTTCG
* * *
24688 CATTAGCCATTCGGCCTTA-C-CAC--ATATAT-T-CATGTTCACATTCATCACATTAGCCATTC
1 CATTGGCCATTCGGCCTTATCACACATATATATATACAGGTTCACATTCATCACATTAGCCATGC
* * * * *
24747 GACCTTATCTCATATATGCATGTTCACATTCATCACATTGGTCATTCGGCCTTATCACACATACG
66 GACCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACA
24812 CAT-GTTCACATTCATCA
131 CATGGTTCACATTCATCA
* *
24829 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCACATTGGCCATGC
1 CATTGGCCATTCGGCCTTATCACACATATATATATACAGGTTCACATTCATCACATTAGCCATGC
* *
24894 GGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATA
66 GACCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACA
*
24959 TATACGGGTTCACATTCATCA
131 CAT---GGTTCACATTCATCA
24980 CATTGGCCATTCGGCCTTATCACACATA
1 CATTGGCCATTCGGCCTTATCACACATA
25008 CGCATGTTCA
Statistics
Matches: 155, Mismatches: 14, Indels: 10
0.87 0.08 0.06
Matches are distributed among these distances:
141 18 0.12
142 1 0.01
143 2 0.01
145 6 0.04
146 1 0.01
147 86 0.55
151 41 0.26
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (148 bp):
CATTGGCCATTCGGCCTTATCACACATATATATATACAGGTTCACATTCATCACATTAGCCATGC
GACCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACA
CATGGTTCACATTCATCA
Found at i:24902 original size:100 final size:98
Alignment explanation
Indices: 24688--25028 Score: 501
Period size: 100 Copynumber: 3.5 Consensus size: 98
24678 ACACGTTTCG
* * * ** * *
24688 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTAGCCATTCGACCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * *
24753 AT--C-T-CATATATGCATGTTCACATTCATCA
66 ATCACATATATATATACAGGTTCACATTCATCA
*
24782 CATTGGTCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
24847 ATCACGCATATATATATACAGGTTCACATTCATCA
66 ATCA--CATATATATATACAGGTTCACATTCATCA
*
24882 CATTGGCCATGCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
* *
24947 ATCACACATATATATACGGGTTCACATTCATCA
66 ATCACATATATATATACAGGTTCACATTCATCA
*
24980 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATACATCACA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACA
25029 GTAAAATCCT
Statistics
Matches: 224, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
94 59 0.26
98 75 0.33
99 1 0.00
100 89 0.40
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.31
Consensus pattern (98 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCACATATATATATACAGGTTCACATTCATCA
Done.