Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2223
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: 15165
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:318 original size:13 final size:13
Alignment explanation
Indices: 300--325 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
290 AATTTTTTTG
300 TGTATCGATACAT
1 TGTATCGATACAT
313 TGTATCGATACAT
1 TGTATCGATACAT
326 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:336 original size:32 final size:34
Alignment explanation
Indices: 279--343 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
269 TACAAGCCAA
*
279 TGTATCGATACAATTTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTATTTTGTGTATCGATACAT
313 TGTATCGATAC-A-TATTTTGTGTATCGATACA
1 TGTATCGATACAATTATTTTGTGTATCGATACA
344 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 18 0.60
33 1 0.03
34 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (34 bp):
TGTATCGATACAATTATTTTGTGTATCGATACAT
Found at i:448 original size:20 final size:20
Alignment explanation
Indices: 395--450 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
385 ACATCTTTTT
*
395 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
415 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
434 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
451 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:2641 original size:20 final size:20
Alignment explanation
Indices: 2616--2687 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
2606 TTAAAAGCCA
2616 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATTTTGGG
2636 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATTTTGGG
** *
2656 ATGTATCGATACAACTTGTG
1 ATGTATCGATACATTTTGGG
2676 -TGTATCGATACA
1 ATGTATCGATACA
2688 AACAGTTAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 12 0.24
20 37 0.76
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTTTGGG
Found at i:5074 original size:147 final size:147
Alignment explanation
Indices: 4807--5081 Score: 326
Period size: 147 Copynumber: 1.9 Consensus size: 147
4797 TTTCTAAGTT
** * *
4807 TATAATTTTTAAAATTCCTCAAATATTATTGTTTAATTCATATTAAATCAGTTTTGAAAATTTAA
1 TATAATTTCCAAAATTCCTCAAATATTATTGTCTAATTAATATTAAATCAGTTTTGAAAATTTAA
* ** *
4872 TTCATTTTATTAGTTTAGGAATTTTACCTGTTATTGAAATGCGGAGTTTTCTACTTCGTAAATTT
66 TTCAGTTTACAAGTTTAGGAATTTTACCTGTTATTCAAATGCGGAGTTTTCTACTTCGTAAATTT
4937 CCTTGGAAGCATTTTTC
131 CCTTGGAAGCATTTTTC
* * *
4954 TATAATTTCCAAAATTCTTCAAATATTATTGTCTAA-TAATGTTAAATTAGTTTTGAAAATTTCA
1 TATAATTTCCAAAATTCCTCAAATATTATTGTCTAATTAATATTAAATCAGTTTTGAAAATTT-A
* * * * *
5018 GTTTAGTTTACAAGTTTTA-GAATATTT-TCTGTT-TTCAAGATATC-GAGTTTTCTACTTTGTA
65 ATTCAGTTTACAAG-TTTAGGAAT-TTTACCTGTTATTCAA-AT-GCGGAGTTTTCTACTTCGTA
5079 AAT
126 AAT
5082 ATCATTGGTT
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
146 27 0.25
147 72 0.67
148 8 0.07
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.48
Consensus pattern (147 bp):
TATAATTTCCAAAATTCCTCAAATATTATTGTCTAATTAATATTAAATCAGTTTTGAAAATTTAA
TTCAGTTTACAAGTTTAGGAATTTTACCTGTTATTCAAATGCGGAGTTTTCTACTTCGTAAATTT
CCTTGGAAGCATTTTTC
Found at i:5513 original size:10 final size:10
Alignment explanation
Indices: 5479--5522 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
5469 AAATATCACC
5479 AATTTTACAT
1 AATTTTACAT
** *
5489 AATCGATAAAT
1 AAT-TTTACAT
5500 AATTTTACAT
1 AATTTTACAT
5510 AATTTTACAT
1 AATTTTACAT
5520 AAT
1 AAT
5523 CCATAAAAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
10 20 0.74
11 7 0.26
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (10 bp):
AATTTTACAT
Found at i:7436 original size:22 final size:23
Alignment explanation
Indices: 7406--7449 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
7396 TGAATTTCAG
*
7406 ATATGATTTTGGTG-TTAATTATA
1 ATATGA-TTTGATGTTTAATTATA
7429 ATAT-ATTTGATGTTTAATTAT
1 ATATGATTTGATGTTTAATTAT
7450 GTGTTCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (23 bp):
ATATGATTTGATGTTTAATTATA
Found at i:7963 original size:155 final size:157
Alignment explanation
Indices: 7744--8105 Score: 412
Period size: 163 Copynumber: 2.3 Consensus size: 157
7734 ATCTTTCGAG
* * * * ***
7744 TACTTTTACGTTGAAGGTATACC-CAAAGGTATTTTCGTAATATTTTAGAATTGAGTCTTAGGTT
1 TACTTTTACGTCGAAGGTATACCTTAAAGGTATTTTTGTAATTTTTTAGAAGCAAGTCTTAGGTT
** * * *
7808 GTCATTGGGACGCTTTTATGCTGAAGG-TGT-GCATTTAGGATAGGTTTATCCCATTTATGATC-
66 GTCACCGAGACGCTTTTATGCTAAAGGATGTAGCATTTAGGATAGGTTCATCCCATTTATGATCA
*
7870 TTTTT-AGTATCCATTAGGGTTATCGGGA
131 TTTTTAAG--TCCATTAGGGTTACCGGGA
* *
7898 TACTTTTATGTCGAAGGTATACCTTAAAGGTATTTTTGTAATTTTTTAGAAGCAAGTTTTAGGTT
1 TACTTTTACGTCGAAGGTATACCTTAAAGGTATTTTTGTAATTTTTTAGAAGCAAGTCTTAGGTT
* *
7963 GTCACCGAGATGCTTTTATGCTAAAGGTATACATTTAGGCATTTAGGATAGGTTCATCCCATTTA
66 GTCACCGAGACGCTTTTATGCTAAAGG-----ATGTA-GCATTTAGGATAGGTTCATCCCATTTA
*
8028 TGATCATTTTTAAGTCCTTTAGGGTTACCGGGA
125 TGATCATTTTTAAGTCCATTAGGGTTACCGGGA
* * *
8061 TACTTTTACATCGAAGGTATATCTTAGAGGTA-TTTTGATAATTTT
1 TACTTTTACGTCGAAGGTATACCTTAAAGGTATTTTTG-TAATTTT
8106 GCATTAGAAC
Statistics
Matches: 174, Mismatches: 22, Indels: 15
0.82 0.10 0.07
Matches are distributed among these distances:
154 21 0.12
155 56 0.32
161 2 0.01
162 5 0.03
163 83 0.48
164 5 0.03
165 2 0.01
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (157 bp):
TACTTTTACGTCGAAGGTATACCTTAAAGGTATTTTTGTAATTTTTTAGAAGCAAGTCTTAGGTT
GTCACCGAGACGCTTTTATGCTAAAGGATGTAGCATTTAGGATAGGTTCATCCCATTTATGATCA
TTTTTAAGTCCATTAGGGTTACCGGGA
Found at i:10728 original size:12 final size:12
Alignment explanation
Indices: 10711--10745 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
10701 CACTTATTTG
10711 CATACATGCATA
1 CATACATGCATA
10723 CATACATGCATA
1 CATACATGCATA
10735 CATACATGCAT
1 CATACATGCAT
10746 TTGTTCATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (12 bp):
CATACATGCATA
Found at i:11406 original size:16 final size:17
Alignment explanation
Indices: 11382--11413 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11372 GATGAAGAGA
11382 AAAAGGGAAAAAGAAAG
1 AAAAGGGAAAAAGAAAG
11399 AAAA-GGAAAAAGAAA
1 AAAAGGGAAAAAGAAA
11414 ATTTAGTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AAAAGGGAAAAAGAAAG
Found at i:13758 original size:1 final size:1
Alignment explanation
Indices: 13752--13866 Score: 77
Period size: 1 Copynumber: 115.0 Consensus size: 1
13742 GGCGTCCTCC
* ** * ** ** *
13752 AAAAAAAAAAAACAAAAAAAAAATGAAAAAAACAAAAAAAATGAATGAAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * *
13817 ACAAAAGAAAAAAAAAACAAAAACAATAAAAAAACAAACAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13867 GGGGGTCCGG
Statistics
Matches: 83, Mismatches: 31, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 83 1.00
ACGTcount: A:0.85, C:0.08, G:0.03, T:0.03
Consensus pattern (1 bp):
A
Found at i:13803 original size:33 final size:31
Alignment explanation
Indices: 13751--13866 Score: 124
Period size: 33 Copynumber: 3.5 Consensus size: 31
13741 CGGCGTCCTC
13751 CAAAAAAAAAAAACAAAAAAAAAATGAAAAAAA
1 CAAAAAAAAAAAA-AAAAAAAAAAT-AAAAAAA
* *
13784 CAAAAAAAATGAATGAAAAAAAAAAACAAAAAAA
1 CAAAAAAAA--AA-AAAAAAAAAAAATAAAAAAA
*
13818 CAAAAGAAAAAAAAAACAAAAACAATAAAAAAA
1 CAAAA-AAAAAAAAAA-AAAAAAAATAAAAAAA
* *
13851 CAAACAAAAACAAAAA
1 CAAAAAAAAAAAAAAA
13867 GGGGGTCCGG
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
31 1 0.01
32 12 0.17
33 29 0.41
34 12 0.17
35 16 0.23
36 1 0.01
ACGTcount: A:0.84, C:0.09, G:0.03, T:0.03
Consensus pattern (31 bp):
CAAAAAAAAAAAAAAAAAAAAAATAAAAAAA
Found at i:13803 original size:46 final size:44
Alignment explanation
Indices: 13753--13867 Score: 151
Period size: 46 Copynumber: 2.5 Consensus size: 44
13743 GCGTCCTCCA
* *
13753 AAAAAAAAAAACAAAAAAAAAATGAAAAAAACAAA-AAAAATGAAT
1 AAAAAAAAAAACAAAAAAAAAAAGAAAAAAA-AAACAAAAA-CAAT
13798 GAAAAAAAAAAACAAAAAAACAAAAGAAAAAAAAAACAAAAACAAT
1 -AAAAAAAAAAACAAAAAAA-AAAAGAAAAAAAAAACAAAAACAAT
* *
13844 AAAAAAACAAACAAAAACAAAAAG
1 AAAAAAAAAAACAAAAAAAAAAAG
13868 GGGGTCCGGA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
44 5 0.08
45 17 0.27
46 25 0.40
47 16 0.25
ACGTcount: A:0.84, C:0.08, G:0.04, T:0.03
Consensus pattern (44 bp):
AAAAAAAAAAACAAAAAAAAAAAGAAAAAAAAAACAAAAACAAT
Found at i:13861 original size:21 final size:22
Alignment explanation
Indices: 13757--13863 Score: 116
Period size: 20 Copynumber: 4.9 Consensus size: 22
13747 CCTCCAAAAA
13757 AAAAAAACAAA-AAAAA-AATG
1 AAAAAAACAAACAAAAACAATG
*
13777 AAAAAAACAAA-AAAAATGAATG
1 AAAAAAACAAACAAAAA-CAATG
* *
13799 AAAAAAAAAAACAAAAAAACAAAAG
1 AAAAAAACAAAC--AAAAAC-AATG
13824 AAAAAAA-AAACAAAAACAAT-
1 AAAAAAACAAACAAAAACAATG
13844 AAAAAAACAAACAAAAACAA
1 AAAAAAACAAACAAAAACAA
13864 AAAGGGGGTC
Statistics
Matches: 76, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
20 23 0.30
21 14 0.18
22 20 0.26
24 4 0.05
25 15 0.20
ACGTcount: A:0.84, C:0.08, G:0.04, T:0.04
Consensus pattern (22 bp):
AAAAAAACAAACAAAAACAATG
Done.