Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2909
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: 41314
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:6091 original size:10 final size:10
Alignment explanation
Indices: 6076--6100 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6066 CCATAATTTA
6076 TGATACAAAT
1 TGATACAAAT
6086 TGATACAAAT
1 TGATACAAAT
6096 TGATA
1 TGATA
6101 ATGGGTTAGG
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:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (10 bp):
TGATACAAAT
Found at i:6136 original size:26 final size:26
Alignment explanation
Indices: 6096--6203 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
6086 TGATACAAAT
6096 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
6122 TGACAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
6148 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
6174 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
6200 TGAT
1 TGAT
6204 GGGAATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:8230 original size:137 final size:136
Alignment explanation
Indices: 7976--8245 Score: 504
Period size: 137 Copynumber: 2.0 Consensus size: 136
7966 GTGGGTTGAG
*
7976 TATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTTATCTGAATAAGGG
1 TATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTTATCTGAATAAGGG
8041 GCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCTAGTACCACTGTTACCCAAATGGG
66 GCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCTAGTACCACTGTTACCCAAATGGG
8106 CTTGCA
131 CTTGCA
8112 TATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTTATCTGAATAAGG
1 TATG-TTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTTATCTGAATAAGG
**
8177 GGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCTAGTACCACTGTTACCTGAATGG
65 GGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCTAGTACCACTGTTACCCAAATGG
8242 GCTT
130 GCTT
8246 AGGCCCAATG
Statistics
Matches: 130, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
136 4 0.03
137 126 0.97
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (136 bp):
TATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTTATCTGAATAAGGG
GCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCTAGTACCACTGTTACCCAAATGGG
CTTGCA
Found at i:8250 original size:64 final size:64
Alignment explanation
Indices: 8039--8252 Score: 145
Period size: 64 Copynumber: 3.2 Consensus size: 64
8029 TCTGAATAAG
**
8039 GGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCTAGTACCACTGTTACCCAAAT
1 GGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCTAGTACCACTGTTACCTGAAT
* ** * * *
8103 GGGCT--TGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCC-A-T---AC
1 GGGCTAAGGCCCA-GTTTA-T--TG-T--A---A-TCTGAAAAGGG-CTCT-GGCCTAGTACCAC
*
8161 TGTTATCTGAAT
53 TGTTACCTGAAT
8173 AAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCTAGTACCACTGTTACCTGA
1 ---GGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCTAGTACCACTGTTACCTGA
8238 AT
63 AT
*
8240 GGGCTTAGGCCCA
1 GGGCTAAGGCCCA
8253 ATGGGCTTGA
Statistics
Matches: 110, Mismatches: 17, Indels: 46
0.64 0.10 0.27
Matches are distributed among these distances:
62 7 0.06
63 9 0.08
64 28 0.25
65 1 0.01
66 2 0.02
67 14 0.13
68 1 0.01
69 1 0.01
70 12 0.11
71 2 0.02
72 1 0.01
73 16 0.15
74 9 0.08
75 7 0.06
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (64 bp):
GGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCTAGTACCACTGTTACCTGAAT
Found at i:10726 original size:40 final size:40
Alignment explanation
Indices: 10643--10750 Score: 105
Period size: 40 Copynumber: 2.7 Consensus size: 40
10633 ATATTGAGCT
* * * *
10643 TTTAGTGGTGCTTTTTTAAAAACGCCGCTATAGGTACACC
1 TTTAGCGGCGCTTTTTAAAAAACGCCGCTATAGCTACACC
* *
10683 TTTAGCTGCGCTTTTTAAAAAACGCCGCTAATA-CT-CTATC
1 TTTAGCGGCGCTTTTTAAAAAACGCCGCT-ATAGCTAC-ACC
*
10723 TTTAGCGGTG-TTTTTAAAAAAGCGCCGC
1 TTTAGCGGCGCTTTTTAAAAAA-CGCCGC
10751 AAAAAGTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
39 12 0.21
40 42 0.74
41 3 0.05
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (40 bp):
TTTAGCGGCGCTTTTTAAAAAACGCCGCTATAGCTACACC
Found at i:11090 original size:21 final size:21
Alignment explanation
Indices: 11042--11099 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
11032 GTTTATGGAA
* *
11042 TATGGGTTTAGGGATTACAGTT
1 TATGGG-TTAGGGTTTAAAGTT
*
11064 TA-GGGTTGGGGTTTAAAGTT
1 TATGGGTTAGGGTTTAAAGTT
*
11084 TATGGGTAAGGGTTTA
1 TATGGGTTAGGGTTTA
11100 GGGTTAAGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 14 0.47
21 14 0.47
22 2 0.07
ACGTcount: A:0.22, C:0.02, G:0.36, T:0.40
Consensus pattern (21 bp):
TATGGGTTAGGGTTTAAAGTT
Found at i:11102 original size:7 final size:7
Alignment explanation
Indices: 11045--11184 Score: 68
Period size: 7 Copynumber: 20.0 Consensus size: 7
11035 TATGGAATAT
11045 GGGTTTA
1 GGGTTTA
*
11052 GGGATTA
1 GGGTTTA
**
11059 CAGTTTA
1 GGGTTTA
*
11066 GGG-TTG
1 GGGTTTA
11072 GGGTTTA
1 GGGTTTA
**
11079 AAGTTTA
1 GGGTTTA
*
11086 TGGG-TAA
1 -GGGTTTA
11093 GGGTTTA
1 GGGTTTA
*
11100 GGGTTAA
1 GGGTTTA
11107 GGGTTTA
1 GGGTTTA
* *
11114 TGTTTTA
1 GGGTTTA
*
11121 GGATTTA
1 GGGTTTA
*
11128 AGGTTTA
1 GGGTTTA
*
11135 TGGTTTA
1 GGGTTTA
**
11142 GGGACTA
1 GGGTTTA
*
11149 GGGATTA
1 GGGTTTA
*
11156 GGGATTA
1 GGGTTTA
*
11163 GGGATTA
1 GGGTTTA
* *
11170 AGGATTA
1 GGGTTTA
11177 GGAGTTTA
1 GG-GTTTA
11185 TGATTTAGAT
Statistics
Matches: 99, Mismatches: 30, Indels: 7
0.73 0.22 0.05
Matches are distributed among these distances:
6 8 0.08
7 86 0.87
8 5 0.05
ACGTcount: A:0.24, C:0.01, G:0.36, T:0.38
Consensus pattern (7 bp):
GGGTTTA
Found at i:11451 original size:14 final size:15
Alignment explanation
Indices: 11426--11463 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
11416 TTTATGATGA
11426 ATTATGGGTTTAGGG
1 ATTATGGGTTTAGGG
11441 ATTAT-GGTTTAGGG
1 ATTATGGGTTTAGGG
*
11455 TTTA-GGGTT
1 ATTATGGGTT
11464 GGAGTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (15 bp):
ATTATGGGTTTAGGG
Found at i:11458 original size:7 final size:7
Alignment explanation
Indices: 11431--11544 Score: 63
Period size: 7 Copynumber: 16.1 Consensus size: 7
11421 GATGAATTAT
11431 GGGTTTA
1 GGGTTTA
*
11438 GGGATTA
1 GGGTTTA
*
11445 TGGTTTA
1 GGGTTTA
11452 GGGTTTA
1 GGGTTTA
11459 GGG-TT-
1 GGGTTTA
11464 GGAGTTTA
1 GG-GTTTA
** *
11472 AAGTGTA
1 GGGTTTA
11479 GGGGTTTA
1 -GGGTTTA
*
11487 GGGTTAA
1 GGGTTTA
*
11494 GTGTTTA
1 GGGTTTA
11501 GGGTTTA
1 GGGTTTA
**
11508 GTATTTA
1 GGGTTTA
* *
11515 TAGG-ATA
1 -GGGTTTA
*
11522 GGGATTA
1 GGGTTTA
11529 GAGGTTTA
1 G-GGTTTA
11537 GGGTTTA
1 GGGTTTA
11544 G
1 G
11545 ATTAATTAGT
Statistics
Matches: 77, Mismatches: 23, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
5 2 0.03
6 5 0.06
7 60 0.78
8 10 0.13
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (7 bp):
GGGTTTA
Found at i:12812 original size:15 final size:15
Alignment explanation
Indices: 12792--12842 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
12782 GGGGCATGAG
12792 TTAGGGGTTAGGGGT
1 TTAGGGGTTAGGGGT
**
12807 TTAGGGGTTAAGGCAT
1 TTAGGGGTT-AGGGGT
* *
12823 TAAGGGGATAGGGGT
1 TTAGGGGTTAGGGGT
12838 TTAGG
1 TTAGG
12843 TTAATTAGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.22, C:0.02, G:0.47, T:0.29
Consensus pattern (15 bp):
TTAGGGGTTAGGGGT
Found at i:13008 original size:16 final size:16
Alignment explanation
Indices: 12955--13008 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 16
12945 ATATTAAATC
*
12955 ATTTCAAATTTTAAAG
1 ATTTCAAATTTTCAAG
12971 ATTTCAAATTTTC-A-
1 ATTTCAAATTTTCAAG
12985 A--T--AATTTTCAAG
1 ATTTCAAATTTTCAAG
12997 ATTTCAAATTTT
1 ATTTCAAATTTT
13009 ATCTAATTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
10 7 0.23
11 1 0.03
12 2 0.06
14 2 0.06
15 1 0.03
16 18 0.58
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (16 bp):
ATTTCAAATTTTCAAG
Found at i:16340 original size:22 final size:23
Alignment explanation
Indices: 16289--16341 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
16279 AGAAAAGCAT
*
16289 TTTAT-GTGTTAAATGTTGAAAA
1 TTTATGGTGTTAAATGCTGAAAA
*
16311 TTTA-GGTGTTAAATGCTG-CAA
1 TTTATGGTGTTAAATGCTGAAAA
16332 TTTATGGTGT
1 TTTATGGTGT
16342 CTGAAAGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.28, C:0.04, G:0.23, T:0.45
Consensus pattern (23 bp):
TTTATGGTGTTAAATGCTGAAAA
Found at i:19124 original size:43 final size:43
Alignment explanation
Indices: 18992--19280 Score: 276
Period size: 43 Copynumber: 6.6 Consensus size: 43
18982 GTGGCTCTAT
* * *
18992 AGAACATGACCTTTAGCGATGTTTTTCCCACAAAC-CCAGCTAA
1 AGAACATGACCTTTAGCGACGCTTTCCCCACAAACGCC-GCTAA
* * * *
19035 ATAACATGACGTTTAGTGGCAGAGGCATTTTCCCCACAAACGCCGCTAT
1 AGAACATGACCTTTA---GC-GACGC--TTTCCCCACAAACGCCGCTAA
* * * *
19084 AGAACATGACCTTTAGCGGCGTTTTTCCTACAAACGCCGCTAA
1 AGAACATGACCTTTAGCGACGCTTTCCCCACAAACGCCGCTAA
* *
19127 AGATCATGACCTTTAGCTG-CACTTTCCCCACAAACGCCGCTAA
1 AGAACATGACCTTTAGC-GACGCTTTCCCCACAAACGCCGCTAA
* * * **
19170 AGAACATGACCTTTAGCAACGCTATCCCTACAAAAACCGCTAA
1 AGAACATGACCTTTAGCGACGCTTTCCCCACAAACGCCGCTAA
* ** **
19213 AGAACATGATCTTTAGCGACGCTTTCCCCACAAACATCATTAA
1 AGAACATGACCTTTAGCGACGCTTTCCCCACAAACGCCGCTAA
*
19256 AGAACATGACCTTTAGCGACTCTTT
1 AGAACATGACCTTTAGCGACGCTTT
19281 TGCTAAAAGT
Statistics
Matches: 201, Mismatches: 36, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
43 160 0.80
44 1 0.00
45 2 0.01
46 4 0.02
47 3 0.01
49 29 0.14
50 2 0.01
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (43 bp):
AGAACATGACCTTTAGCGACGCTTTCCCCACAAACGCCGCTAA
Found at i:25005 original size:21 final size:21
Alignment explanation
Indices: 24981--25021 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
24971 CATCTGCTCA
* *
24981 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
25002 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
25022 TCGCTGTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:30858 original size:28 final size:28
Alignment explanation
Indices: 30827--30882 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
30817 TTTCTAATTA
* *
30827 AATTCAATTTT-AATCCTTTTTATATTTT
1 AATT-AATTTTAAATACTTTATATATTTT
*
30855 AATTTATTTTAAATACTTTATATATTTT
1 AATTAATTTTAAATACTTTATATATTTT
30883 TATAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (28 bp):
AATTAATTTTAAATACTTTATATATTTT
Found at i:30890 original size:21 final size:22
Alignment explanation
Indices: 30864--30905 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
30854 TAATTTATTT
30864 TAAATACT-TTATATATTTTTA
1 TAAATACTATTATATATTTTTA
*
30885 TAAATATTAGTTATATATTTT
1 TAAATACTA-TTATATATTTT
30906 ATTATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TAAATACTATTATATATTTTTA
Found at i:30910 original size:12 final size:12
Alignment explanation
Indices: 30872--30973 Score: 67
Period size: 10 Copynumber: 8.9 Consensus size: 12
30862 TTTAAATACT
30872 TTATATA-TTT-
1 TTATATATTTTA
* *
30882 TTATAAATATTA
1 TTATATATTTTA
30894 GTTATATATTTTA
1 -TTATATATTTTA
30907 TTATATATTTTA
1 TTATATATTTTA
* *
30919 TCTATAAATTATA
1 T-TATATATTTTA
*
30932 -T-TATATTATA
1 TTATATATTTTA
30942 -TATTATATTTTA
1 TTA-TATATTTTA
*
30954 -TATAT-TTCT-
1 TTATATATTTTA
30963 TTATATATTTT
1 TTATATATTTT
30974 TATAAAATCG
Statistics
Matches: 74, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
10 23 0.31
11 9 0.12
12 23 0.31
13 19 0.26
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (12 bp):
TTATATATTTTA
Found at i:30919 original size:21 final size:21
Alignment explanation
Indices: 30847--30973 Score: 59
Period size: 21 Copynumber: 5.8 Consensus size: 21
30837 TAATCCTTTT
30847 TATATTTTA-AT-TTATT-TTA
1 TATATTTTATATATT-TTATTA
* *
30866 AATACTTTATATATTTT-TATA
1 TATATTTTATATATTTTAT-TA
*
30887 AATATTAGTTATATATTTTATTA
1 TATATT--TTATATATTTTATTA
*
30910 TATATTTTATCTATAAATTATATTA
1 TATATTTTA--TAT--ATTTTATTA
*
30935 TAT-TATATATTATATTTTA-TA
1 TATAT-TTTA-TATATTTTATTA
*
30956 TATTTCTTTATATATTTT
1 TATAT-TTTATATATTTT
30974 TATAAAATCG
Statistics
Matches: 86, Mismatches: 10, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
19 7 0.08
20 5 0.06
21 25 0.29
22 9 0.10
23 21 0.24
24 5 0.06
25 14 0.16
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (21 bp):
TATATTTTATATATTTTATTA
Found at i:30956 original size:14 final size:13
Alignment explanation
Indices: 30928--30971 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
30918 ATCTATAAAT
30928 TATATTATA-TTA
1 TATATTATATTTA
30940 TATATTATATTTTA
1 TATATTATA-TTTA
*
30954 TATATT-TCTTTA
1 TATATTATATTTA
30966 TATATT
1 TATATT
30972 TTTATAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 19 0.66
13 1 0.03
14 9 0.31
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATTATATTTA
Found at i:31302 original size:27 final size:26
Alignment explanation
Indices: 31272--31328 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
31262 TAATATTCCT
*
31272 TATAATATCTATCTTTCTTATATTTTA-
1 TATAATATCTAT-TTTATT-TATTTTAC
* *
31299 TATATTATTTATTTTATTTATTTTAC
1 TATAATATCTATTTTATTTATTTTAC
31325 TATA
1 TATA
31329 TTTTATATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 7 0.27
26 9 0.35
27 10 0.38
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (26 bp):
TATAATATCTATTTTATTTATTTTAC
Found at i:31332 original size:10 final size:9
Alignment explanation
Indices: 31290--31336 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
31280 CTATCTTTCT
31290 TATATTTTA
1 TATATTTTA
31299 TATA--TTA
1 TATATTTTA
*
31306 TTTATTTTA
1 TATATTTTA
*
31315 TTTATTTTA
1 TATATTTTA
31324 CTATATTTTA
1 -TATATTTTA
31334 TAT
1 TAT
31337 GCAAATTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 6 0.18
9 19 0.58
10 8 0.24
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (9 bp):
TATATTTTA
Done.