Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold126
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: 2080828
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 191490 characters in sequence are not A, C, G, or T
File 13 of 13
Found at i:2064959 original size:13 final size:13
Alignment explanation
Indices: 2064941--2065000 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 13
2064931 ACAAAGATCC
2064941 ATGTATCGATACA
1 ATGTATCGATACA
2064954 ATGTATCGATACA
1 ATGTATCGATACA
2064967 CA-G-A---A-A-A
1 -ATGTATCGATACA
2064974 ATGTATCGATACA
1 ATGTATCGATACA
*
2064987 TTGTATCGATACA
1 ATGTATCGATACA
2065000 A
1 A
2065001 AACTTATGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
6 1 0.03
7 2 0.05
8 2 0.05
9 1 0.03
11 1 0.03
12 2 0.05
13 27 0.73
14 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2064962 original size:33 final size:32
Alignment explanation
Indices: 2064920--2065019 Score: 121
Period size: 33 Copynumber: 3.1 Consensus size: 32
2064910 AAAATTTCCA
*
2064920 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGA-CAATGTATCGATAC
* *
2064953 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAG-ACAATGTATCGATAC
* *
2064986 ATTGTATCGATACAAA-ACTTATGTATCGATAC
1 AATGTATCGATACAAAGAC-AATGTATCGATAC
2065018 AA
1 AA
2065020 ATTGTTGAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
31 1 0.02
32 13 0.23
33 42 0.74
34 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (32 bp):
AATGTATCGATACAAAGACAATGTATCGATAC
Found at i:2065726 original size:29 final size:29
Alignment explanation
Indices: 2065693--2065782 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
2065683 CTTTGAGGAC
2065693 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
* ** *
2065722 TGAAAAGGGGTCCTGC-TCTT-TG-GGGAC--
1 TG-AAAGGTG-CCACCAACTTGTGTGGG-CTT
2065749 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
2065778 TGAAA
1 TGAAA
2065783 AGAAAAAGCA
Statistics
Matches: 45, Mismatches: 8, Indels: 16
0.65 0.12 0.23
Matches are distributed among these distances:
25 3 0.07
26 9 0.20
27 5 0.11
28 6 0.13
29 10 0.22
30 9 0.20
31 3 0.07
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (29 bp):
TGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:2065933 original size:59 final size:59
Alignment explanation
Indices: 2065395--2066438 Score: 1359
Period size: 59 Copynumber: 17.9 Consensus size: 59
2065385 ATAAAGTGTA
* * * * * *
2065395 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
2065450 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** *
2065505 TCCTGCTCTTTGAAGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
** *
2065560 TCCTGCTCTTTG-GGAACTGAAAAATGCCACCAACTTGTGTGGGC-TT---CG-AAAGG-G
1 TCCTGCTCTTTGAGG-ACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * *
2065614 ATCCTACTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 -TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
*
2065676 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----GAAAAGGGG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
2065732 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
* * *
2065793 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGCGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
* *
2065854 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
2065913 TCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
2065972 TCTTGCTCTTTGAGGATTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
2066031 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
2066090 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
2066149 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
2066208 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
2066267 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** ** *
2066326 TCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGGGAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
*
2066387 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCATCTTGTGTGGGCTTTAAAAG
1 TCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
2066439 GTGTCCTGCT
Statistics
Matches: 907, Mismatches: 56, Indels: 47
0.90 0.06 0.05
Matches are distributed among these distances:
53 1 0.00
54 5 0.01
55 174 0.19
56 57 0.06
57 1 0.00
59 427 0.47
60 56 0.06
61 182 0.20
62 4 0.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (59 bp):
TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
Found at i:2067475 original size:11 final size:11
Alignment explanation
Indices: 2067444--2067498 Score: 74
Period size: 11 Copynumber: 4.8 Consensus size: 11
2067434 CTTTTCTCTC
*
2067444 TTTTTCTTTGT
1 TTTTTTTTTGT
2067455 TTTGTTTTTTGT
1 TTT-TTTTTTGT
*
2067467 TTTTTTTTTGC
1 TTTTTTTTTGT
2067478 TTTTTTTTTGT
1 TTTTTTTTTGT
2067489 TTTGTTTTTT
1 TTT-TTTTTT
2067499 TTGAAGAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
11 23 0.59
12 16 0.41
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:2067484 original size:27 final size:27
Alignment explanation
Indices: 2067444--2067500 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
2067434 CTTTTCTCTC
2067444 TTTTTCTTTGTTTTGTT-TTTTGTTTTT
1 TTTTTCTTTGTTTT-TTGTTTTGTTTTT
2067471 TTTTTGCTTT-TTTTTTGTTTTGTTTTT
1 TTTTT-CTTTGTTTTTTGTTTTGTTTTT
2067498 TTT
1 TTT
2067501 GAAGAGAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 2 0.07
27 22 0.79
28 4 0.14
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.86
Consensus pattern (27 bp):
TTTTTCTTTGTTTTTTGTTTTGTTTTT
Found at i:2079996 original size:28 final size:28
Alignment explanation
Indices: 2079956--2080027 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
2079946 AGAAAAAAAT
* ** *
2079956 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2079984 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2080012 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
2080028 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:2080086 original size:53 final size:52
Alignment explanation
Indices: 2080020--2080141 Score: 138
Period size: 51 Copynumber: 2.3 Consensus size: 52
2080010 AACGAGGTTG
* * * * *
2080020 GAGTATCCTCGATTGTGAAAAAATTGGTATTTTTGGAAATAAAGTCGGAGTTA
1 GAGTATCCCCGATTGTGAAAAAATTAGT-GTTTTGAAAATAAAATCGGAGTTA
* * *
2080073 GAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAAAAAATTAGTGTTTTGAAAATAAAATCGGAGTTA
*
2080124 GAATATCCCCGCATTGTG
1 GAGTATCCCCG-ATTGTG
2080142 GAGAATTGAG
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
51 30 0.53
52 13 0.23
53 14 0.25
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (52 bp):
GAGTATCCCCGATTGTGAAAAAATTAGTGTTTTGAAAATAAAATCGGAGTTA
Done.