Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1992
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: 39291
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:5213 original size:7 final size:7
Alignment explanation
Indices: 5131--5212 Score: 94
Period size: 7 Copynumber: 11.9 Consensus size: 7
5121 AGAATTAAGA
5131 ATTGAGG
1 ATTGAGG
*
5138 ATTGGGG
1 ATTGAGG
5145 ATTGAGG
1 ATTGAGG
5152 ATTGAGG
1 ATTGAGG
*
5159 ATTGAGA
1 ATTGAGG
* **
5166 AATGAAA
1 ATTGAGG
5173 ATTGAGG
1 ATTGAGG
5180 ATTGA-G
1 ATTGAGG
*
5186 ATTTAGG
1 ATTGAGG
5193 ATTGAGG
1 ATTGAGG
*
5200 ATTGAGT
1 ATTGAGG
5207 ATTGAG
1 ATTGAG
5213 TTAAAAAAAC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
6 5 0.08
7 58 0.92
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (7 bp):
ATTGAGG
Found at i:20003 original size:16 final size:18
Alignment explanation
Indices: 19971--20005 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
19961 CATAATTAAA
19971 TTAATTTATATAAATATT
1 TTAATTTATATAAATATT
19989 TTAATTT-TA-AAATATT
1 TTAATTTATATAAATATT
20005 T
1 T
20006 AAGTAAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 2 0.12
18 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAATTTATATAAATATT
Found at i:22970 original size:72 final size:72
Alignment explanation
Indices: 22798--22959 Score: 245
Period size: 72 Copynumber: 2.2 Consensus size: 72
22788 GAAGAGTTTG
** * *
22798 AAACAGTTGGACCTATCCAATAACCAAATTCTTGGTCCTATTCCTTCTACCTTGGGCAACTTAAC
1 AAACAGTTGGACCTATCCAATAACCAAATTAGTGGTCCTATCCCTTCTACCTTGGGCAAATTAAC
22863 CAATTTA
66 CAATTTA
* *
22870 AAA-ATGTTGAACCTATCCAAAAACCAAATTAGTGGTCCTATCCCTTCTACCTTGGGCAAATTAA
1 AAACA-GTTGGACCTATCCAATAACCAAATTAGTGGTCCTATCCCTTCTACCTTGGGCAAATTAA
22934 CCAATTTA
65 CCAATTTA
*
22942 AAACAGTTGGACTTATCC
1 AAACAGTTGGACCTATCC
22960 TTTAATCAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
71 1 0.01
72 78 0.98
73 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (72 bp):
AAACAGTTGGACCTATCCAATAACCAAATTAGTGGTCCTATCCCTTCTACCTTGGGCAAATTAAC
CAATTTA
Found at i:22988 original size:72 final size:72
Alignment explanation
Indices: 22803--22997 Score: 178
Period size: 72 Copynumber: 2.7 Consensus size: 72
22793 GTTTGAAACA
* * * * * *
22803 GTTGGACCTATCCAATAACCAAATTC-TTGGTCCTATTCCTTCTACCTTGGGCAACTTAACCAAT
1 GTTGAACCTATCCAAAAACCAAA-TCACTGGGCCAATTCCTTCTACCTTGGGCAAATTAACCAAT
22867 TTAAAAAT
65 TTAAAAAT
* * * * *
22875 GTTGAACCTATCCAAAAACCAAATTAGTGGTCCTATCCCTTCTACCTTGGGCAAATTAACCAATT
1 GTTGAACCTATCCAAAAACCAAATCACTGGGCCAATTCCTTCTACCTTGGGCAAATTAACCAATT
22940 TAAAACA-
66 TAAAA-AT
* * *** * * * *
22947 GTTGGACTTATCCTTTAATCAAATCACTGGGGCAATTCCTTCAACTTTGGG
1 GTTGAACCTATCCAAAAACCAAATCACTGGGCCAATTCCTTCTACCTTGGG
22998 TCGCTTAACC
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
71 1 0.01
72 99 0.98
73 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (72 bp):
GTTGAACCTATCCAAAAACCAAATCACTGGGCCAATTCCTTCTACCTTGGGCAAATTAACCAATT
TAAAAAT
Found at i:28998 original size:16 final size:17
Alignment explanation
Indices: 28968--29008 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
28958 ATAGGTTCAA
28968 TTATTAAATTATTTA-TT
1 TTATT-AATTATTTACTT
*
28985 TTATTAATTGTTTACTT
1 TTATTAATTATTTACTT
29002 TT-TTAAT
1 TTATTAAT
29009 AATTATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
TTATTAATTATTTACTT
Found at i:30066 original size:24 final size:24
Alignment explanation
Indices: 30038--30086 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
30028 CATGCATTCC
30038 ATAGCACCTCAAATGGGTGCCACG
1 ATAGCACCTCAAATGGGTGCCACG
*
30062 ATAGCACCTCAAATGGGTGTCACG
1 ATAGCACCTCAAATGGGTGCCACG
30086 A
1 A
30087 CACGCCAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (24 bp):
ATAGCACCTCAAATGGGTGCCACG
Found at i:31304 original size:10 final size:9
Alignment explanation
Indices: 31279--31423 Score: 60
Period size: 10 Copynumber: 15.0 Consensus size: 9
31269 ATGATAACAA
*
31279 ATAAAAATCA
1 ATAAAAAT-T
*
31289 ATAAAAGTT
1 ATAAAAATT
31298 ATAAAAATT
1 ATAAAAATT
**
31307 ATTAAATTTT
1 A-TAAAAATT
31317 ATTAAAAA-T
1 A-TAAAAATT
31326 ATAAAAAATT
1 AT-AAAAATT
**
31336 ATTTAAATTTT
1 A--TAAAAATT
*
31347 AGTAACAATT
1 A-TAAAAATT
*
31357 AGAAAAAATT
1 A-TAAAAATT
31367 ATAAAAATCT
1 ATAAAAAT-T
31377 -TAAAAATT
1 ATAAAAATT
*
31385 ATAGAATATAT
1 ATA-AAAAT-T
* *
31396 AGAAATAAAT
1 ATAAA-AATT
31406 ATAAAAATT
1 ATAAAAATT
*
31415 ATAAGAATT
1 ATAAAAATT
31424 CAAGGTAGTT
Statistics
Matches: 102, Mismatches: 23, Indels: 21
0.70 0.16 0.14
Matches are distributed among these distances:
8 2 0.02
9 42 0.41
10 47 0.46
11 10 0.10
12 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:31344 original size:30 final size:31
Alignment explanation
Indices: 31300--31368 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
31290 TAAAAGTTAT
* *
31300 AAAAATTA-TTAAATTTTATTAA-AAATATA
1 AAAAATTATTTAAATTTTAGTAACAAATAGA
*
31329 AAAAATTATTTAAATTTTAGTAACAATTAGA
1 AAAAATTATTTAAATTTTAGTAACAAATAGA
31360 AAAAATTAT
1 AAAAATTAT
31369 AAAAATCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 8 0.23
30 13 0.37
31 14 0.40
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (31 bp):
AAAAATTATTTAAATTTTAGTAACAAATAGA
Found at i:31362 original size:29 final size:29
Alignment explanation
Indices: 31300--31368 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
31290 TAAAAGTTAT
*
31300 AAAAATTATTAAATTTTATTAAAAATATA
1 AAAAATTATTAAATTTTAGTAAAAATATA
* *
31329 AAAAATTATTTAAATTTTAGTAACAATTAGA
1 AAAAATTA-TTAAATTTTAGTAA-AAATATA
31360 AAAAATTAT
1 AAAAATTAT
31369 AAAAATCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 8 0.23
30 14 0.40
31 13 0.37
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAAATTATTAAATTTTAGTAAAAATATA
Found at i:32086 original size:40 final size:40
Alignment explanation
Indices: 32042--32117 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
32032 ATTTGGAGAA
* * *
32042 AAAACGCTGCTAAAAATCAAGTATTAGCGGCGCTTTAAAT
1 AAAACGCCGCTAAAAACCAAGCATTAGCGGCGCTTTAAAT
* *
32082 AAAACGCCGCTAAAGACCGAGCATTAGCGGCGCTTT
1 AAAACGCCGCTAAAAACCAAGCATTAGCGGCGCTTT
32118 CCTAAAAGCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (40 bp):
AAAACGCCGCTAAAAACCAAGCATTAGCGGCGCTTTAAAT
Found at i:32143 original size:39 final size:40
Alignment explanation
Indices: 32064--32147 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
32054 AAAATCAAGT
* *
32064 ATTAGCGGCGCTTTAAATAAAACGCCGCTAAAGACCGAGC
1 ATTAGCGGCGCTTTAAATAAAACGCCGCCAAAGAACGAGC
** *
32104 ATTAGCGGCGCTTT-CCTAAAAGCGCCGCCAAA-AATGAGC
1 ATTAGCGGCGCTTTAAATAAAA-CGCCGCCAAAGAACGAGC
32143 ATTAG
1 ATTAG
32148 TGGCATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
39 15 0.39
40 23 0.61
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (40 bp):
ATTAGCGGCGCTTTAAATAAAACGCCGCCAAAGAACGAGC
Found at i:32298 original size:41 final size:41
Alignment explanation
Indices: 32241--32491 Score: 378
Period size: 41 Copynumber: 6.1 Consensus size: 41
32231 AACAGTTTTA
* * *
32241 AAAGCGACGCTAATGCTC-GGAGCTTTAGCGGCATTTTTGAC
1 AAAGCGCCGCTAATGCTCAGG-CCTTTAGCGGCGTTTTTGAC
*
32282 AAAGCGCTGCTAATGCTCAGGCCTTTAGCGGCGTTTTTGAC
1 AAAGCGCCGCTAATGCTCAGGCCTTTAGCGGCGTTTTTGAC
* *
32323 GAAGCGCCGCTAATACTCAGGCCTTTAGCGGCGTTTTTGAC
1 AAAGCGCCGCTAATGCTCAGGCCTTTAGCGGCGTTTTTGAC
* * * *
32364 GAAGCACCGCTAATGCTCAGGCCTTTAGCGGTGTTTTTGAG
1 AAAGCGCCGCTAATGCTCAGGCCTTTAGCGGCGTTTTTGAC
*
32405 AAAGCGCCGCTAATGCTCAGGCCTTTAGCGGCGTTTTTGAG
1 AAAGCGCCGCTAATGCTCAGGCCTTTAGCGGCGTTTTTGAC
*
32446 AAAGCGCCGCTAATGCTCAGGCCTTTAGCGGCGTTTTTGAA
1 AAAGCGCCGCTAATGCTCAGGCCTTTAGCGGCGTTTTTGAC
32487 AAAGC
1 AAAGC
32492 ACCCCTAAAA
Statistics
Matches: 194, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
41 192 0.99
42 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (41 bp):
AAAGCGCCGCTAATGCTCAGGCCTTTAGCGGCGTTTTTGAC
Found at i:32965 original size:13 final size:13
Alignment explanation
Indices: 32930--32979 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
32920 AGGGTTGTGA
32930 TTTAGGGGTTAAGGG
1 TTTA-GGGTT-AGGG
32945 -TTAGGGGTTAGGG
1 TTTA-GGGTTAGGG
32958 ATTT-GGGTTAGGG
1 -TTTAGGGTTAGGG
32971 TTTAGGGTT
1 TTTAGGGTT
32980 TAGATTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.09
13 18 0.56
14 9 0.28
15 2 0.06
ACGTcount: A:0.16, C:0.00, G:0.46, T:0.38
Consensus pattern (13 bp):
TTTAGGGTTAGGG
Found at i:33070 original size:20 final size:21
Alignment explanation
Indices: 33034--33086 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
33024 GGGGTTAGTA
*
33034 GTTAGGGGTTAGGGGTTTGGG
1 GTTAGGGGTTAGGGGTTGGGG
33055 GTTAGGGGTT-GGGGTTGGGG
1 GTTAGGGGTTAGGGGTTGGGG
*
33075 GTTAGAGGTTAG
1 GTTAGGGGTTAG
33087 AGTTAGTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.11, C:0.00, G:0.57, T:0.32
Consensus pattern (21 bp):
GTTAGGGGTTAGGGGTTGGGG
Found at i:33088 original size:7 final size:7
Alignment explanation
Indices: 33021--33086 Score: 80
Period size: 7 Copynumber: 9.6 Consensus size: 7
33011 TAAATAAGGT
33021 TTAGGGG
1 TTAGGGG
**
33028 TTAGTAG
1 TTAGGGG
33035 TTAGGGG
1 TTAGGGG
33042 TTAGGGG
1 TTAGGGG
*
33049 TTTGGGG
1 TTAGGGG
33056 TTAGGGG
1 TTAGGGG
33063 TT-GGGG
1 TTAGGGG
*
33069 TTGGGGG
1 TTAGGGG
*
33076 TTAGAGG
1 TTAGGGG
33083 TTAG
1 TTAG
33087 AGTTAGTGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
6 6 0.12
7 44 0.88
ACGTcount: A:0.14, C:0.00, G:0.53, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Done.