Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold884
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: 53483
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:8588 original size:43 final size:43
Alignment explanation
Indices: 8465--8588 Score: 169
Period size: 43 Copynumber: 2.9 Consensus size: 43
8455 TTATAGAAAT
* * * *
8465 AAACGCCACTAAATGTCATG-TTCTTTAGCGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGGTCATGACT-TTTAGCGGCGCTTTTCCCAC
* *
8508 AAACGCCGCTAAAGGTCATGACTTTTAGCAGCACTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGACTTTTAGCGGCGCTTTTCCCAC
*
8551 AAACGCCGCTATAGGTCATGACTTTTAGCGGCGCTTTT
1 AAACGCCGCTAAAGGTCATGACTTTTAGCGGCGCTTTT
8589 TGGTTTTAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
43 70 0.99
44 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGACTTTTAGCGGCGCTTTTCCCAC
Found at i:8964 original size:13 final size:13
Alignment explanation
Indices: 8946--9011 Score: 87
Period size: 13 Copynumber: 5.1 Consensus size: 13
8936 AGTTTGGCAA
8946 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
8959 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
* * *
8972 TGATGTGGAAAAG
1 TGCTTTTGAAAAG
*
8985 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
8998 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
9011 T
1 T
9012 TTAGTTTAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:19742 original size:3 final size:3
Alignment explanation
Indices: 19730--19774 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
19720 TATAATCTCA
19730 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
19775 GGGTAACGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:21756 original size:17 final size:17
Alignment explanation
Indices: 21734--21779 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
21724 TAAGGCAAAC
21734 TTCAATTTTAGTAAAAT
1 TTCAATTTTAGTAAAAT
** * *
21751 TTCAATAATGGTAAAGT
1 TTCAATTTTAGTAAAAT
21768 TTCAATTTTAGT
1 TTCAATTTTAGT
21780 TCCTGTGTCA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (17 bp):
TTCAATTTTAGTAAAAT
Found at i:22528 original size:17 final size:18
Alignment explanation
Indices: 22487--22528 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
22477 TAATTTTTGA
22487 ATTAG-TTCTTCAAAATG
1 ATTAGCTTCTTCAAAATG
* *
22504 ATTTGCTTCTT-AAATTG
1 ATTAGCTTCTTCAAAATG
22521 ATTAGCTT
1 ATTAGCTT
22529 TCATTGCAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (18 bp):
ATTAGCTTCTTCAAAATG
Found at i:22837 original size:156 final size:156
Alignment explanation
Indices: 22553--22864 Score: 615
Period size: 156 Copynumber: 2.0 Consensus size: 156
22543 CATTTGATTG
22553 GAAATTTAATATTTGCATTGTAAAAAATATTGATTTTTATTGAGATTTTTGTATCTGTCCTAGAA
1 GAAATTTAATATTTGCATTGTAAAAAATATTGATTTTTATTGAGATTTTTGTATCTGTCCTAGAA
22618 AGTGTTAAGTTATCTATTTATATGATATGTACATTGTTTATAGATGTGACATCGTAGGTAGATCC
66 AGTGTTAAGTTATCTATTTATATGATATGTACATTGTTTATAGATGTGACATCGTAGGTAGATCC
22683 CCATGTATTTTAACACTTGTCCTATT
131 CCATGTATTTTAACACTTGTCCTATT
22709 GAAATTTAATATTTGCATTGTAAAAAATATTGATTTTTATTGAGATTTTTGTATCTGTCCTAGAA
1 GAAATTTAATATTTGCATTGTAAAAAATATTGATTTTTATTGAGATTTTTGTATCTGTCCTAGAA
*
22774 AGTGTTAAGTTATCTATTTATATGATATGTATATTGTTTATAGATGTGACATCGTAGGTAGATCC
66 AGTGTTAAGTTATCTATTTATATGATATGTACATTGTTTATAGATGTGACATCGTAGGTAGATCC
22839 CCATGTATTTTAACACTTGTCCTATT
131 CCATGTATTTTAACACTTGTCCTATT
22865 CTAATATTAA
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 155 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (156 bp):
GAAATTTAATATTTGCATTGTAAAAAATATTGATTTTTATTGAGATTTTTGTATCTGTCCTAGAA
AGTGTTAAGTTATCTATTTATATGATATGTACATTGTTTATAGATGTGACATCGTAGGTAGATCC
CCATGTATTTTAACACTTGTCCTATT
Found at i:23145 original size:21 final size:21
Alignment explanation
Indices: 23119--23164 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
23109 GGGTTCTGAA
*
23119 AATAACATAAAATGTGGAAAT
1 AATAACACAAAATGTGGAAAT
23140 AATAACACAAAATGTGGAAAT
1 AATAACACAAAATGTGGAAAT
23161 AATA
1 AATA
23165 GATAGGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.22
Consensus pattern (21 bp):
AATAACACAAAATGTGGAAAT
Found at i:26027 original size:14 final size:14
Alignment explanation
Indices: 26008--26041 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
25998 AGTTGTTGGC
26008 TGTATATATATGTA
1 TGTATATATATGTA
26022 TGTATATATATGTA
1 TGTATATATATGTA
*
26036 TATATA
1 TGTATA
26042 AGCAATTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (14 bp):
TGTATATATATGTA
Found at i:27640 original size:26 final size:25
Alignment explanation
Indices: 27588--27642 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
27578 AATTTTAAAA
* * *
27588 TATTTTTAAAATACTTTTTATTTTT
1 TATTTTTAAAATAATTTTTAGTGTT
*
27613 TATTTTTAAAATAAATTTTTGGTGTT
1 TATTTTTAAAAT-AATTTTTAGTGTT
27639 TATT
1 TATT
27643 AAAAAAATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (25 bp):
TATTTTTAAAATAATTTTTAGTGTT
Found at i:29857 original size:15 final size:17
Alignment explanation
Indices: 29834--29865 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
29824 ATTCACGTAT
29834 AAATAT-AAATAGAAAA
1 AAATATAAAATAGAAAA
29850 AAAT-TAAAATAGAAAA
1 AAATATAAAATAGAAAA
29866 TATTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.07
16 14 0.93
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (17 bp):
AAATATAAAATAGAAAA
Found at i:33551 original size:3 final size:3
Alignment explanation
Indices: 33539--33578 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
33529 TATAATCTCA
33539 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
33579 AGGAGAAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:34184 original size:44 final size:45
Alignment explanation
Indices: 34109--34234 Score: 137
Period size: 44 Copynumber: 2.8 Consensus size: 45
34099 TATGGCGGAT
* * ** *
34109 CTTATCTTCCTGAAGTTGTAGTGGAGTAGATTGAAGCCAAC-AGC
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGCCAACGAAC
** * * *
34153 CTTATCTCCCTGAAGTTGCAGCAGAACAGATTGAAGACAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGCCAACGAAC
* *
34198 CTTATTTCCCTGAAGATGCAGTGGAACAGATTGAAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGC
34235 TACAAATTAT
Statistics
Matches: 66, Mismatches: 15, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
44 33 0.50
45 33 0.50
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGCCAACGAAC
Found at i:35686 original size:3 final size:3
Alignment explanation
Indices: 35674--35707 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
35664 TATAATCTCA
35674 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
35708 AGGAGAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:37631 original size:17 final size:17
Alignment explanation
Indices: 37609--37654 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
37599 TAAGGCAAAC
37609 TTCAATTTTAGTAAAAT
1 TTCAATTTTAGTAAAAT
** * *
37626 TTCAATAATGGTAAAGT
1 TTCAATTTTAGTAAAAT
37643 TTCAATTTTAGT
1 TTCAATTTTAGT
37655 TCCTATGTTA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (17 bp):
TTCAATTTTAGTAAAAT
Found at i:38043 original size:30 final size:29
Alignment explanation
Indices: 37994--38057 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
37984 CATATATTTG
* **
37994 AATTTTTAAATTTAAAAAATTGAGGGACTA
1 AATTTTTAAAATTAAAAAATT-AAAGACTA
38024 AATTTTTAAAAATT-AAAAATTAAAGACTA
1 AATTTTT-AAAATTAAAAAATTAAAGACTA
38053 AATTT
1 AATTT
38058 CAATTGTACA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 11 0.37
30 14 0.47
31 5 0.17
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.38
Consensus pattern (29 bp):
AATTTTTAAAATTAAAAAATTAAAGACTA
Found at i:38285 original size:20 final size:20
Alignment explanation
Indices: 38260--38309 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
38250 TGGCTTAAAA
38260 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
38280 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
38297 GTGGTAGTGGATT
1 TTGGTAGTGGATT
38310 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:42913 original size:20 final size:20
Alignment explanation
Indices: 42888--42937 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
42878 TGGCTTAAAA
42888 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
42908 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
42925 GTGGTAGTGGATT
1 TTGGTAGTGGATT
42938 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:43926 original size:17 final size:18
Alignment explanation
Indices: 43885--43926 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
43875 TAATTTTTGA
43885 ATTAG-TTCTTCAAAATG
1 ATTAGCTTCTTCAAAATG
* *
43902 ATTTGCTTCTT-AAATTG
1 ATTAGCTTCTTCAAAATG
43919 ATTAGCTT
1 ATTAGCTT
43927 TCATTGCAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (18 bp):
ATTAGCTTCTTCAAAATG
Found at i:44388 original size:21 final size:21
Alignment explanation
Indices: 44362--44407 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
44352 GGGTTCTGAA
*
44362 AATAACATAAAATGTGGAAAT
1 AATAACACAAAATGTGGAAAT
44383 AATAACACAAAATGTGGAAAT
1 AATAACACAAAATGTGGAAAT
44404 AATA
1 AATA
44408 GATAGGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.22
Consensus pattern (21 bp):
AATAACACAAAATGTGGAAAT
Done.