Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1137
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: 24247
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:844 original size:3 final size:3
Alignment explanation
Indices: 836--876 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
826 TCATTTAACT
836 ATA ATA AT- ATA ATA A-A TATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
877 GATTTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 3 0.09
3 31 0.89
4 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2455 original size:6 final size:6
Alignment explanation
Indices: 2444--2481 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
2434 AGAACAAAGT
* *
2444 TTTGGC TTTGGC TTTGGC TTCGGC TTCGGC TTTGGC TT
1 TTTGGC TTTGGC TTTGGC TTTGGC TTTGGC TTTGGC TT
2482 CATGTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.21, G:0.32, T:0.47
Consensus pattern (6 bp):
TTTGGC
Found at i:3724 original size:24 final size:21
Alignment explanation
Indices: 3673--3732 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 21
3663 TATCCAATTT
3673 AAATTATT-TTTAAAA-TAATA
1 AAATT-TTATTTAAAATTAATA
3693 AAATTTTATTTAAAATTAATTA
1 AAATTTTATTTAAAATTAA-TA
*
3715 TAAATATTTATATAAAAT
1 -AAAT-TTTATTTAAAAT
3733 ATTTTTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 2 0.06
20 12 0.35
21 3 0.09
22 2 0.06
23 4 0.12
24 11 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATTTTATTTAAAATTAATA
Found at i:4552 original size:16 final size:17
Alignment explanation
Indices: 4531--4562 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4521 TTATAATAAG
4531 TAAAAAACTT-AAACAA
1 TAAAAAACTTGAAACAA
4547 TAAAAAACTTGAAACA
1 TAAAAAACTTGAAACA
4563 TTTAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.66, C:0.12, G:0.03, T:0.19
Consensus pattern (17 bp):
TAAAAAACTTGAAACAA
Found at i:9867 original size:25 final size:27
Alignment explanation
Indices: 9810--9867 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 27
9800 TATAATGATC
* * *
9810 CATTTTTATAATTAATAATATTTTTCT
1 CATTTTTATAATAAATAAGATTTTTAT
9837 CA-TTTTA-AATAAATAAGATTTTTAT
1 CATTTTTATAATAAATAAGATTTTTAT
9862 -ATTTTT
1 CATTTTT
9868 GAAAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 1 0.04
25 19 0.70
26 5 0.19
27 2 0.07
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (27 bp):
CATTTTTATAATAAATAAGATTTTTAT
Found at i:13500 original size:22 final size:22
Alignment explanation
Indices: 13455--13500 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
13445 CCATGCAAGA
*
13455 TTTGGATATCACCACTAAAGCC
1 TTTGGATATCACCACGAAAGCC
13477 TTTGGATATCACCATCGAAA-CC
1 TTTGGATATCACCA-CGAAAGCC
13499 TT
1 TT
13501 GAATGTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (22 bp):
TTTGGATATCACCACGAAAGCC
Found at i:13539 original size:87 final size:87
Alignment explanation
Indices: 13443--13702 Score: 373
Period size: 87 Copynumber: 3.0 Consensus size: 87
13433 TCAAAGACTG
* *
13443 GTCCATGCAAGA-TTTGGATATCACCACTAAAGCCTTTGGATATCACCATCGAAACCTTGAATGT
1 GTCCATGCAAGATTTTGGATATCACCACTAAAGCCTTTAGATATCACCATCAAAACCTTGAATGT
* *
13507 GAAAATCCTTTTTGAATGCTTCA
66 GAAATTCTTTTTTGAATGCTT-A
13530 GTCCATGCAA-ATTTTGGATATCACCACTAAAGCCTTTAGATATCACCAAT-AAAACCTTGAATG
1 GTCCATGCAAGATTTTGGATATCACCACTAAAGCCTTTAGATATCACC-ATCAAAACCTTGAATG
* *
13593 TGAAGTTCTTTTTTGAATGCTTT
65 TGAAATTCTTTTTTGAATGCTTA
** * * *
13616 GATTTATGCAAGATTTTGGATATCACCACTAGAGCCTTTAAATATCACCACCAAAACCTTGAATG
1 G-TCCATGCAAGATTTTGGATATCACCACTAAAGCCTTTAGATATCACCATCAAAACCTTGAATG
13681 TGAAATTCTTTTTTGAATGCTT
65 TGAAATTCTTTTTTGAATGCTT
13703 TGGCTATTGC
Statistics
Matches: 156, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
86 2 0.01
87 83 0.53
88 71 0.46
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (87 bp):
GTCCATGCAAGATTTTGGATATCACCACTAAAGCCTTTAGATATCACCATCAAAACCTTGAATGT
GAAATTCTTTTTTGAATGCTTA
Found at i:13574 original size:22 final size:22
Alignment explanation
Indices: 13546--13587 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
13536 GCAAATTTTG
* *
13546 GATATCACCACTAAAGCCTTTA
1 GATATCACCAATAAAACCTTTA
13568 GATATCACCAATAAAACCTT
1 GATATCACCAATAAAACCTT
13588 GAATGTGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (22 bp):
GATATCACCAATAAAACCTTTA
Found at i:14611 original size:17 final size:17
Alignment explanation
Indices: 14589--14621 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
14579 TTTTATCTAT
14589 TTATAT-TTATATTTAAA
1 TTATATATT-TATTTAAA
14606 TTATATATTTATTTAA
1 TTATATATTTATTTAA
14622 TATTTTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATATTTATTTAAA
Found at i:16236 original size:8 final size:8
Alignment explanation
Indices: 16225--16264 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
16215 AAACTAGAAA
16225 AAAAAAAG
1 AAAAAAAG
16233 AAAAATAA-
1 AAAAA-AAG
16241 AAAAAAGAG
1 AAAAAA-AG
16250 AAAAAAAG
1 AAAAAAAG
16258 AAAAAAA
1 AAAAAAA
16265 AGGAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 1 0.03
8 20 0.69
9 8 0.28
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:16242 original size:15 final size:15
Alignment explanation
Indices: 16222--16262 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
16212 AAAAAACTAG
16222 AAAAAAAAAAGA-AA
1 AAAAAAAAAAGAGAA
16236 AATAAAAAAAAGAGAA
1 AA-AAAAAAAAGAGAA
16252 AAAAAGAAAAA
1 AAAAA-AAAAA
16263 AAAGGAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.08
15 13 0.54
16 9 0.38
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAAGAGAA
Found at i:16244 original size:17 final size:16
Alignment explanation
Indices: 16222--16266 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
16212 AAAAAACTAG
16222 AAAAAAAAAAGAAAAA
1 AAAAAAAAAAGAAAAA
*
16238 TAAAAAAAAGAGAAAAA
1 -AAAAAAAAAAGAAAAA
16255 AAGAAAAAAAAG
1 AA-AAAAAAAAG
16267 GAAAGTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 2 0.08
17 23 0.92
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAAGAAAAA
Found at i:17018 original size:58 final size:57
Alignment explanation
Indices: 16903--17042 Score: 156
Period size: 58 Copynumber: 2.4 Consensus size: 57
16893 CACATTAAAT
* ** * * *
16903 ATTACTATGTCATTTCATGCATTTAATTACATTTAATTCATTTTCTATAGTTTAGAA
1 ATTATTATGTCATTTCATGCATTTAAAGACATTGAAGTCATTTTCTATAGTATAGAA
*
16960 ATTATTATGTCATTTCATGCATGTTAAAGATATTGAAGTCATTTTCTAT-GATATAGAA
1 ATTATTATGTCATTTCATGCAT-TTAAAGACATTGAAGTCATTTTCTATAG-TATAGAA
* * *
17018 ACTTTTTTTGTCATTTCATGAATTT
1 A-TTATTATGTCATTTCATGCATTT
17043 TAATGGCATT
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
57 22 0.31
58 30 0.43
59 18 0.26
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.49
Consensus pattern (57 bp):
ATTATTATGTCATTTCATGCATTTAAAGACATTGAAGTCATTTTCTATAGTATAGAA
Found at i:17059 original size:59 final size:58
Alignment explanation
Indices: 16903--17062 Score: 171
Period size: 59 Copynumber: 2.8 Consensus size: 58
16893 CACATTAAAT
* * * *
16903 ATTACTATGTCATTTCATGCA-TTTAATTACATTTAATTCATTTTCTATAGTTTAGAA
1 ATTATTATGTCATTTCATGCATTTTAATGACATTTAAGTCATTTTCTATAGTATAGAA
* * * *
16960 ATTATTATGTCATTTCATGCATGTTAAAGATATTGAAGTCATTTTCTAT-GATATAGAA
1 ATTATTATGTCATTTCATGCATTTTAATGACATTTAAGTCATTTTCTATAG-TATAGAA
* * * * *
17018 ACTTTTTTTGTCATTTCATGAATTTTAATGGCATTTTAGTCATTT
1 A-TTATTATGTCATTTCATGCATTTTAATGACATTTAAGTCATTT
17063 CTCATGACTT
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
57 21 0.25
58 28 0.34
59 34 0.41
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (58 bp):
ATTATTATGTCATTTCATGCATTTTAATGACATTTAAGTCATTTTCTATAGTATAGAA
Found at i:17199 original size:58 final size:58
Alignment explanation
Indices: 17122--17277 Score: 147
Period size: 58 Copynumber: 2.7 Consensus size: 58
17112 TGTCAATTTT
* ** * * * *
17122 CATGATTTAGGACCATTTATGTATTCCCATGTATTTTAAGG-CCATTATAGTTATTTGC
1 CATGTTTTAGGATTATTTATGTATT-TCATGTATTTTAAGGACCATTATAATAACTTGC
* * * *
17180 CATGTTTTAGGATTATTTATGCAATTTCATGCATTTT-AGGATCATTTTAATAACTTGC
1 CATGTTTTAGGATTATTTATG-TATTTCATGTATTTTAAGGACCATTATAATAACTTGC
*
17238 AATGTTTTAAGGATT-TTTATGTAATTTCATGTATTTTAAG
1 CATGTTTT-AGGATTATTTATGT-ATTTCATGTATTTTAAG
17278 ACTATTTTGG
Statistics
Matches: 79, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
57 3 0.04
58 65 0.82
59 11 0.14
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.47
Consensus pattern (58 bp):
CATGTTTTAGGATTATTTATGTATTTCATGTATTTTAAGGACCATTATAATAACTTGC
Found at i:17274 original size:29 final size:27
Alignment explanation
Indices: 17180--17275 Score: 72
Period size: 29 Copynumber: 3.4 Consensus size: 27
17170 AGTTATTTGC
*
17180 CATG-TTTTAGGATTATTTATGCAATTT
1 CATGATTTTAGGATT-TTTATGTAATTT
* *
17207 CATGCATTTTAGGATCATTTTA-ATAACTTG
1 CATG-ATTTTAGGAT--TTTTATGTAA-TTT
17237 CAATG-TTTTAAGGATTTTTATGTAATTT
1 C-ATGATTTT-AGGATTTTTATGTAATTT
17265 CATGTATTTTA
1 CATG-ATTTTA
17276 AGACTATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 19
0.69 0.06 0.24
Matches are distributed among these distances:
27 7 0.13
28 9 0.17
29 22 0.41
30 12 0.22
31 4 0.07
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (27 bp):
CATGATTTTAGGATTTTTATGTAATTT
Found at i:17285 original size:58 final size:58
Alignment explanation
Indices: 17149--17285 Score: 152
Period size: 58 Copynumber: 2.4 Consensus size: 58
17139 TATGTATTCC
* * * * * * *
17149 CATGTATTTTAAGGCCATTATAGTTATTTGCCATGTTTTAGGATTATTTATGCAATTT
1 CATGTATTTTAAGACTATTTTAATAACTTGCAATGTTTTAGGATTATTTATGCAATTT
* * *
17207 CATGCATTTTAGGA-TCATTTTAATAACTTGCAATGTTTTAAGGATT-TTTATGTAATTT
1 CATGTATTTTAAGACT-ATTTTAATAACTTGCAATGTTTT-AGGATTATTTATGCAATTT
17265 CATGTATTTTAAGACTATTTT
1 CATGTATTTTAAGACTATTTT
17286 GGTCATTTTC
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
58 57 0.89
59 7 0.11
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (58 bp):
CATGTATTTTAAGACTATTTTAATAACTTGCAATGTTTTAGGATTATTTATGCAATTT
Found at i:19843 original size:20 final size:20
Alignment explanation
Indices: 19795--19832 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19785 AGGACAATGT
*
19795 ATCGATATAATTCTTCATGC
1 ATCGATACAATTCTTCATGC
19815 ATCGATACAATTCTTCAT
1 ATCGATACAATTCTTCAT
19833 TTATTGATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (20 bp):
ATCGATACAATTCTTCATGC
Found at i:19950 original size:19 final size:19
Alignment explanation
Indices: 19905--19955 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
19895 ACTACCAGTT
*
19905 TCATGTATCGATACAATTG
1 TCATGTATCGATACAAGTG
19924 TGCATGTATCGATAC-AGTG
1 T-CATGTATCGATACAAGTG
19943 ATCATGTATCGAT
1 -TCATGTATCGAT
19956 TCATTGTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (19 bp):
TCATGTATCGATACAAGTG
Found at i:22571 original size:16 final size:16
Alignment explanation
Indices: 22552--22582 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
22542 TAGTATCGAA
22552 CCTAAATTGTATCAAT
1 CCTAAATTGTATCAAT
22568 CCTAAATTGTATCAA
1 CCTAAATTGTATCAA
22583 ACAAGTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (16 bp):
CCTAAATTGTATCAAT
Done.