Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2009
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: 46148
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:328 original size:76 final size:74
Alignment explanation
Indices: 169--383 Score: 236
Period size: 76 Copynumber: 2.8 Consensus size: 74
159 TATTCGAATG
* * *
169 ATATCCGGGCCTAAGTCCCGAAGGCATTTGTGCTATTGGCATAAATCCGGCTCAGTCTCG-AGGC
1 ATATCC-GG-CTAAGTCCCGAAGGCA-TTGTGCTAGT-GC-TATAT-CGGCTAAGTC-CGAAGGC
233 ATTTGTGCTATTGACT
59 ATTTGTGCTATTGACT
* *
249 ATATCCGAGCTAAGTCACGAAGGCATT-TGCTAGTGACTATATCGGGCTAAGTCCGAAGGCTTTT
1 ATATCCG-GCTAAGTCCCGAAGGCATTGTGCTAGTG-CTATATC-GGCTAAGTCCGAAGGCATTT
313 GTGCTATTGACT
63 GTGCTATTGACT
* * *
325 ATATCCGGCTAAGACCCGAAGGCATTGTGCGAGTTTGCTATATCGGCTAAATCCGAAGG
1 ATATCCGGCTAAGTCCCGAAGGCATTGTGCTAG--TGCTATATCGGCTAAGTCCGAAGG
384 TACTTGGGTT
Statistics
Matches: 119, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
75 20 0.17
76 58 0.49
77 14 0.12
78 4 0.03
79 16 0.13
80 7 0.06
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (74 bp):
ATATCCGGCTAAGTCCCGAAGGCATTGTGCTAGTGCTATATCGGCTAAGTCCGAAGGCATTTGTG
CTATTGACT
Found at i:366 original size:39 final size:38
Alignment explanation
Indices: 169--383 Score: 208
Period size: 38 Copynumber: 5.6 Consensus size: 38
159 TATTCGAATG
*
169 ATATCCGGGCCTAAGTCCCGAAGGCATTTGTGCTATTGGCAT
1 ATATCC-GG-CTAAGTCCCGAAGGCA-TTGTGCTATTGAC-T
* * *
211 AAATCCGGCTCAGTCTCG-AGGCATTTGTGCTATTGACT
1 ATATCCGGCTAAGTCCCGAAGGCA-TTGTGCTATTGACT
* *
249 ATATCCGAGCTAAGTCACGAAGGCATT-TGCTAGTGACT
1 ATATCCG-GCTAAGTCCCGAAGGCATTGTGCTATTGACT
* *
287 ATATCGGGCTAAGT-CCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGCTAAGTCCCGAAGGC-ATTGTGCTATTGACT
* *
325 ATATCCGGCTAAGACCCGAAGGCATTGTGCGAGTTTG-CT
1 ATATCCGGCTAAGTCCCGAAGGCATTGTGCTA--TTGACT
*
364 ATAT-CGGCTAAAT-CCGAAGG
1 ATATCCGGCTAAGTCCCGAAGG
384 TACTTGGGTT
Statistics
Matches: 148, Mismatches: 18, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
36 7 0.05
37 16 0.11
38 59 0.40
39 43 0.29
40 16 0.11
41 2 0.01
42 5 0.03
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (38 bp):
ATATCCGGCTAAGTCCCGAAGGCATTGTGCTATTGACT
Found at i:8356 original size:40 final size:40
Alignment explanation
Indices: 8295--8516 Score: 322
Period size: 40 Copynumber: 5.6 Consensus size: 40
8285 TATTCGAATG
*
8295 ATATCCGGGCTAAGTTCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* *
8335 ATATCCGGGCTAAGTCTCGAAGGCATTTGTGCTACTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* * * *
8375 ATATCCGAGCTAAGTCACGAAGGCATTTTTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
8415 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* *
8455 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-TTGACT
*
8495 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
8517 TACTTGGGTT
Statistics
Matches: 164, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 14 0.09
40 146 0.89
41 4 0.02
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
Found at i:12951 original size:10 final size:10
Alignment explanation
Indices: 12936--12960 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12926 ATATTATATA
12936 TATTTTTTAT
1 TATTTTTTAT
12946 TATTTTTTAT
1 TATTTTTTAT
12956 TATTT
1 TATTT
12961 ACCCATATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:23483 original size:29 final size:30
Alignment explanation
Indices: 23427--23506 Score: 74
Period size: 31 Copynumber: 2.6 Consensus size: 30
23417 AATTAAACCA
*
23427 AAATTAAAGTATGGTGTATACAAATGC-ATC
1 AAATTAAAGT-TGATGTATACAAATGCAATC
* *
23457 AAATTAAAGTTGATGTATAGC-ATTGCAAATT
1 AAATTAAAGTTGATGTATA-CAAATGC-AATC
* *
23488 ATATTAAAGTTCATGTATA
1 AAATTAAAGTTGATGTATA
23507 ATTTTAGTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 12 0.29
30 11 0.26
31 19 0.45
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (30 bp):
AAATTAAAGTTGATGTATACAAATGCAATC
Found at i:25687 original size:46 final size:48
Alignment explanation
Indices: 25511--25690 Score: 195
Period size: 48 Copynumber: 3.8 Consensus size: 48
25501 AAGCTGACGC
* * * **
25511 CATGTCCCAGACAAGCCTTACACTAGCTTGTC-TATCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGC-TCACATATCTCGAGGCCGATG
* * *
25559 CATGTCCCAAACATGTCTTACACTGGCTTAAATATCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCACATATCTCGAGGCCGATG
* * * *
25607 CATGTCCCAGACATGTCTTACATTGGCTCTCATAT-T-GTGGCTGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCACATATCTCGAGGCCGATG
* * *
25653 CATGTGCCAGACATGTCTTACACTAGCACACATATCTC
1 CATGTCCCAGACATGTCTTACACTGGCTCACATATCTC
25691 CCAATATCAA
Statistics
Matches: 110, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
46 38 0.35
47 3 0.03
48 69 0.63
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTGGCTCACATATCTCGAGGCCGATG
Found at i:29695 original size:11 final size:11
Alignment explanation
Indices: 29679--29703 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29669 CTGTGTGTTC
29679 TTTATTTTATT
1 TTTATTTTATT
29690 TTTATTTTATT
1 TTTATTTTATT
29701 TTT
1 TTT
29704 TTAAACAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:33794 original size:29 final size:29
Alignment explanation
Indices: 33731--33798 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
33721 TAATCAACCG
*
33731 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
33760 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
33789 CGCACACTTA
1 CGCACACTTA
33799 CCTTTTCTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:33968 original size:29 final size:29
Alignment explanation
Indices: 33905--33972 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
33895 TAATCAACCG
33905 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
33934 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
33963 CGCACACTTA
1 CGCACACTTA
33973 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:34113 original size:29 final size:30
Alignment explanation
Indices: 34074--34152 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
34064 CTTAATAATC
34074 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
* *
34104 AACTCGCACACTCAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
34133 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
34153 ATCTCATGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 31 0.76
30 4 0.10
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:34146 original size:174 final size:174
Alignment explanation
Indices: 33620--34121 Score: 923
Period size: 174 Copynumber: 2.9 Consensus size: 174
33610 AACTCAAGGT
* *
33620 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
33685 GAAAATATATATTGAGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
33750 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
33794 ACTTACCTTTTCTGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
33859 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
33924 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
33968 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTTGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
34033 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
* *
34098 ACTTTAAACTCGCACACTCAGTGC
131 ACTTTAAACTCACACACTTAGTGC
34122 TGTACAATTT
Statistics
Matches: 316, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 316 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:42072 original size:28 final size:29
Alignment explanation
Indices: 42009--42075 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
41999 TAATCAACCG
*
42009 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
42038 CACACACTTAGTG-CATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
42066 CGCACACTTA
1 CGCACACTTA
42076 CCTTTTCCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
27 3 0.09
28 17 0.53
29 12 0.38
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:42242 original size:29 final size:28
Alignment explanation
Indices: 42180--42246 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
42170 AAATCAACCG
42180 CGCACACTTAGTGCATGCACTTTAAACT
1 CGCACACTTAGTGCATGCACTTTAAACT
* **
42208 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTG-CATGCACTTT-AAACT
42237 CGCACACTTA
1 CGCACACTTA
42247 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 15 0.45
29 18 0.55
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCATGCACTTTAAACT
Found at i:42260 original size:171 final size:173
Alignment explanation
Indices: 41899--42395 Score: 903
Period size: 171 Copynumber: 2.9 Consensus size: 173
41889 AACTCAAGGT
* *
41899 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCA-CCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
41963 GAAAATATATATTGAGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTG-GTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
42028 ACTTTAAACTCACACACTTAGTG-CATGCATTTCAAGTTCGCAC
130 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
42071 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
42136 GAAAATATATATTGGTTCGCACACATAGTGCTCAA-AATCAACCGCGCACACTTAGTG-CATGCA
66 GAAAATATATATTGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGTA
42199 CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
42242 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
42307 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATT-GGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
*
42372 ACTTTAAACTCGCACACTTAGTGC
130 ACTTTAAACTCACACACTTAGTGC
42396 TGTACAATTT
Statistics
Matches: 313, Mismatches: 7, Indels: 8
0.95 0.02 0.02
Matches are distributed among these distances:
170 27 0.09
171 120 0.38
172 83 0.27
173 56 0.18
174 27 0.09
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (173 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGTA
CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:42387 original size:29 final size:30
Alignment explanation
Indices: 42348--42426 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
42338 CTTAATAATC
42348 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
42378 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
42407 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
42427 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Done.