Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1983
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: 18279
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Found at i:11020 original size:28 final size:26
Alignment explanation
Indices: 10959--11035 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 26
10949 GTTTGGAGAT
* *
10959 AATAACGGGGTTGGAGTGTTCCCTCGA
1 AATAAC-GGGTTGGAGTATCCCCTCGA
10986 AAGTAACAGGGTTGGAGTATCCCCAAT-GA
1 AA-TAAC-GGGTTGGAGTATCCCC--TCGA
11015 AATAACGAGGTTGGAGTATCC
1 AATAACG-GGTTGGAGTATCC
11036 TCGATTGTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 3 0.07
28 35 0.81
29 4 0.09
30 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (26 bp):
AATAACGGGTTGGAGTATCCCCTCGA
Found at i:11084 original size:52 final size:51
Alignment explanation
Indices: 11018--11203 Score: 164
Period size: 52 Copynumber: 3.6 Consensus size: 51
11008 CCAATGAAAT
* * *
11018 AACGAGGTTGGAGTATCCTCGATTGTGAAAAAATGGTATTTTTGGAAATAA
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAAATGGTATTTTTGGAAATAA
* * * * * * *
11069 AATCAGAGTTGGAGTAT-CCCGATTAAAGGAAAATTGGT-GTTTTGAAAATAA
1 AA-CGGGGTTGGAGTATCCCCGATT-ATGAAAAAATGGTATTTTTGGAAATAA
* * * *
11120 AACTGGGGTTGAAGTATCCCCGATTGTGAAAAAAT--TAGTGTTTTAGCAATAA
1 AAC-GGGGTTGGAGTATCCCCGATTATGAAAAAATGGTA-T-TTTTGGAAATAA
11172 AACCGGGGTTGGAGTATCCCCGATTATGAAAA
1 AA-CGGGGTTGGAGTATCCCCGATTATGAAAA
11204 TCAATATTTT
Statistics
Matches: 104, Mismatches: 23, Indels: 15
0.73 0.16 0.11
Matches are distributed among these distances:
49 1 0.01
50 1 0.01
51 37 0.36
52 64 0.62
53 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (51 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAAAATGGTATTTTTGGAAATAA
Found at i:11144 original size:103 final size:101
Alignment explanation
Indices: 11023--11347 Score: 294
Period size: 103 Copynumber: 3.2 Consensus size: 101
11013 GAAATAACGA
* *
11023 GGTTGGAGTATCCTCGATTGTGAAAAAATGGTAT-TTTTGGAAATAAAATCAGAGTTGGAGTATC
1 GGTT-GAGTATCCCCGATTGTGAAAAAAT-GTATGTTTTAGAAATAAAATCAGAGTTGGAGTATC
*
11087 CCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACT-G-G
64 CCGATT-AA-GAAAATTAGTGTTTTGAAAAT-AAACTCGAG
* * * *
11126 GGTTGAAGTATCCCCGATTGTGAAAAAAT-TAGTGTTTTAGCAATAAAACCGGGGTTGGAGTATC
1 GGTTG-AGTATCCCCGATTGTGAAAAAATGTA-TGTTTTAGAAATAAAATCAGAGTTGGAGTAT-
* * * * *
11190 CCCGATTATGAAAATCAATATTTTGAAAATAAAGTCGAG
63 CCCGATTAAGAAAATTAGTGTTTTGAAAATAAACTCGAG
* * * * *
11229 GTTTGAGTATTCCC-A--ATGAAAAATTG-ATGTTTTAGAGATAAAATCAGAGTTGGAGTATCCC
1 GGTTGAGTATCCCCGATTGTGAAAAAATGTATGTTTTAGAAATAAAATCAGAGTTGGAGTATCCC
11290 TGATTATAGAAAATTAGTGTTTTG-AAATGAAA-TCG-G
66 -GATTA-AGAAAATTAGTGTTTTGAAAAT-AAACTCGAG
* *
11326 AGTTGGGATATCCCCGATTGTG
1 GGTTGAG-TATCCCCGATTGTG
11348 GAGAATCGAG
Statistics
Matches: 178, Mismatches: 30, Indels: 30
0.75 0.13 0.13
Matches are distributed among these distances:
97 8 0.04
98 44 0.25
99 26 0.15
101 9 0.05
102 28 0.16
103 56 0.31
104 7 0.04
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (101 bp):
GGTTGAGTATCCCCGATTGTGAAAAAATGTATGTTTTAGAAATAAAATCAGAGTTGGAGTATCCC
GATTAAGAAAATTAGTGTTTTGAAAATAAACTCGAG
Found at i:11329 original size:50 final size:51
Alignment explanation
Indices: 11057--11344 Score: 215
Period size: 50 Copynumber: 5.7 Consensus size: 51
11047 AAAATGGTAT
* * * *
11057 TTTTGGAAATAAAATCAGAGTTGGAGTAT-CCCGATTAAAGGAAAATTGGTG
1 TTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTATA-GAAAATTAGTG
* * * *
11108 TTTT-GAAAATAAAA-CTGGGGTTGAAGTATCCCCGATTGTGAAAAAATTAGTG
1 TTTTAG-AAATAAAATC-GGAGTTGGAGTATCCCCGATTAT-AGAAAATTAGTG
* * * * * *
11160 TTTTAGCAATAAAACCGGGGTTGGAGTATCCCCGATTAT-GAAAATCAATA
1 TTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATTAGTG
* * *
11210 TTTT-GAAAATAAAGTC-GAGGTTTGAGTATTCCC-A--AT-GAAAAATT-GATG
1 TTTTAG-AAATAAAATCGGA-GTTGGAGTATCCCCGATTATAG-AAAATTAG-TG
* * *
11258 TTTTAGAGATAAAATCAGAGTTGGAGTATCCCTGATTATAGAAAATTAGTG
1 TTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATTAGTG
*
11309 TTTT-GAAATGAAATCGGAGTTGG-GATATCCCCGATT
1 TTTTAGAAATAAAATCGGAGTTGGAG-TATCCCCGATT
11345 GTGGAGAATC
Statistics
Matches: 187, Mismatches: 32, Indels: 37
0.73 0.12 0.14
Matches are distributed among these distances:
47 3 0.02
48 29 0.16
49 8 0.04
50 58 0.31
51 36 0.19
52 50 0.27
53 3 0.02
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (51 bp):
TTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATTAGTG
Found at i:13644 original size:22 final size:20
Alignment explanation
Indices: 13600--13644 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
13590 AAAATGCCTG
*
13600 AATGTATCGATACAGTGTAA
1 AATGTATCGATACAGGGTAA
*
13620 AATGTATCGATCATCTGGGTAA
1 AATGTATCGAT-A-CAGGGTAA
13642 AAT
1 AAT
13645 TTCCAAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 1 0.05
22 9 0.43
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACAGGGTAA
Found at i:15054 original size:59 final size:59
Alignment explanation
Indices: 13905--15052 Score: 1871
Period size: 59 Copynumber: 19.5 Consensus size: 59
13895 GAGATTTTCT
* ** * *
13905 AAGGCGTCCTGCTCTTTGAGGACTGAAAAATTCCACCAACTTGTGTGGGCTTTAAAAGGAG
1 AAGGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAA
* * *
13966 AAGGCGTTCTGGTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTT---A-AA
1 AAGGCGTCCCGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
* * * * *
14022 ATGG-GTCCTGCTTTTTGGGGACGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAA
1 AAGGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAA
* * *
14082 AAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
1 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
14141 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
1 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
* *
14200 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTTAAACAA
1 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
*
14259 AAGGCGTCCCGCTCTTTGAGGACTGGAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
1 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
14318 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG-A
1 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
14376 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
1 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
*
14435 AAGGCGTCCCGCTCTTTGAGGACTGAAGTTGCCACCAACTTGTGTGGGCTTTAAAAGAA
1 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
*
14494 AAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
1 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
14553 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
1 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
* *
14612 AAGGCGTCCCGCTTTTTGAAGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
1 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
*
14671 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAA
1 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
14730 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
1 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
*
14789 AAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
1 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
*
14848 AAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
1 AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
* **
14907 AAGGCATCCCGCTCTTTGAGGACTGGAAAATGCCACCAAC-TGTGTGGGCTTTAAAAGAA
1 AAGGCGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
** *
14966 AAGGCGTCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAATAGAA
1 AAGGCGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
*
15026 AAGGCGTCCCGCTCTTTAAGGACTGAA
1 AAGGCGTCCCGCTCTTTGAGGACTGAA
15053 AAGCAGAAGG
Statistics
Matches: 1032, Mismatches: 42, Indels: 28
0.94 0.04 0.03
Matches are distributed among these distances:
53 1 0.00
54 2 0.00
55 38 0.04
56 4 0.00
58 59 0.06
59 780 0.76
60 85 0.08
61 60 0.06
62 2 0.00
63 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (59 bp):
AAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
Found at i:16033 original size:16 final size:17
Alignment explanation
Indices: 16009--16064 Score: 69
Period size: 16 Copynumber: 3.3 Consensus size: 17
15999 CTTAAGCAGA
*
16009 TTTTCTTTTTTTTTTG-
1 TTTTGTTTTTTTTTTGT
*
16025 TTTTGTTTTGTTTTTGT
1 TTTTGTTTTTTTTTTGT
*
16042 TTTTGTTTTTTTTCTTTT
1 TTTTGTTTTTTTT-TTGT
16060 TTTTG
1 TTTTG
16065 AAGAGAAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 14 0.41
17 12 0.35
18 8 0.24
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.86
Consensus pattern (17 bp):
TTTTGTTTTTTTTTTGT
Done.