Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold534
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: 20596
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:2752 original size:20 final size:20
Alignment explanation
Indices: 2727--2766 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2717 TGCTTTCTCT
2727 TTCAAATAGAACCTAAAAGC
1 TTCAAATAGAACCTAAAAGC
2747 TTCAAATAGAACCTAAAAGC
1 TTCAAATAGAACCTAAAAGC
2767 ATAGATGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.20, G:0.10, T:0.20
Consensus pattern (20 bp):
TTCAAATAGAACCTAAAAGC
Found at i:12316 original size:33 final size:33
Alignment explanation
Indices: 12276--12344 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
12266 CCGTTACAAG
* *
12276 CAATGTATCGATACAATT-CATCATGTATCGATA
1 CAATGTATCAATAC-ATTGCACCATGTATCGATA
*
12309 CAATGTATCAATACATTGTACCATGTATCGATA
1 CAATGTATCAATACATTGCACCATGTATCGATA
12342 CAA
1 CAA
12345 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.32
Consensus pattern (33 bp):
CAATGTATCAATACATTGCACCATGTATCGATA
Found at i:12417 original size:19 final size:19
Alignment explanation
Indices: 12373--12428 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
12363 CTGCCAATTT
**
12373 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
12393 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
12412 CATGTATCGATACAATG
1 CATGTATCGATACAATG
12429 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:12431 original size:13 final size:13
Alignment explanation
Indices: 12413--12438 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12403 TACAATGAAC
12413 ATGTATCGATACA
1 ATGTATCGATACA
12426 ATGTATCGATACA
1 ATGTATCGATACA
12439 TCTGGGTGTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:15397 original size:80 final size:80
Alignment explanation
Indices: 15307--15794 Score: 478
Period size: 80 Copynumber: 6.2 Consensus size: 80
15297 GGAGATAGTC
* ** * *
15307 GGGTTAGAGTATCCCCAAAGATGGAAAATTT-TTATTTTTAGAAGTAAAAACTAGGTTGGAGTAT
1 GGGTTGGAGTATCCCCGTAGATGGAAAATTTGATATTTTTAGAAGTAAAAA-TGGGTTGGAGTAT
*
15371 CCCCTCAAAAATGGCA
65 CCCCTCAAAAATGGCG
* * *
15387 AGGTTGGAGTATCTCCGTAGATGGAAAATTTGATA-TTTTAGAAATAAAAATGGGGTTGGAGTAT
1 GGGTTGGAGTATCCCCGTAGATGGAAAATTTGATATTTTTAGAAGTAAAAAT-GGGTTGGAGTAT
* * **
15451 TCTCTCGAAAAA-GATG
65 CCCCTC-AAAAATGGCG
* ** *
15467 GTGTTGGAGTATCCTTGTAGATGGAAAATTTGATATTTTTAGAAGTAACAAT--G--GG-G--TC
1 GGGTTGGAGTATCCCCGTAGATGGAAAATTTGATATTTTTAGAAGTAAAAATGGGTTGGAGTATC
*
15525 CCCTC-AAAATGGTG
66 CCCTCAAAAATGGCG
** * * * * * *
15539 GGGTTGGAGTATCCTTGAAGATGGAAAGTTTAATATTCTTAGGAGT-AAAATGGGGTTAGAGTAT
1 GGGTTGGAGTATCCCCGTAGATGGAAAATTTGATATTTTTAGAAGTAAAAAT-GGGTTGGAGTAT
15603 CCCCTCAAAAATGGCG
65 CCCCTCAAAAATGGCG
* * * *
15619 GGGTTGGAGTATCCCCTTAGATGGAAACTTTGATATTTTTAGAAGTAAAAAACGGGGTTAGAGTA
1 GGGTTGGAGTATCCCCGTAGATGGAAAATTTGATATTTTTAGAAGT-AAAAA-TGGGTTGGAGTA
*
15684 TCCCCTCAAAAATGGTG
64 TCCCCTCAAAAATGGCG
* **
15701 GGGTTGGAGTATCCCCGTAGATGGAAAATTTGATATTTTTAGATGTAAAAAATCGGGTTAAAGTA
1 GGGTTGGAGTATCCCCGTAGATGGAAAATTTGATATTTTTAGAAGT-AAAAAT-GGGTTGGAGTA
* * * *
15766 TCCCCTTAGAAATCGTG
64 TCCCCTCAAAAATGGCG
15783 GGGTTGGAGTAT
1 GGGTTGGAGTAT
15795 TCACTTTTAA
Statistics
Matches: 340, Mismatches: 50, Indels: 34
0.80 0.12 0.08
Matches are distributed among these distances:
71 8 0.02
72 43 0.13
73 5 0.01
74 1 0.00
75 1 0.00
76 3 0.01
77 1 0.00
78 1 0.00
79 8 0.02
80 132 0.39
81 21 0.06
82 116 0.34
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (80 bp):
GGGTTGGAGTATCCCCGTAGATGGAAAATTTGATATTTTTAGAAGTAAAAATGGGTTGGAGTATC
CCCTCAAAAATGGCG
Found at i:15589 original size:152 final size:153
Alignment explanation
Indices: 15307--15794 Score: 378
Period size: 152 Copynumber: 3.1 Consensus size: 153
15297 GGAGATAGTC
* ** * *
15307 GGGTTAGAGTATCCCCAAAGATGGAAAATTT-TTATTTTTAGAAGTAAAAACTAGGTTGGAGTAT
1 GGGTTGGAGTATCCCCTTAGATGGAAAATTTGATATTTTTAGAAGTAACAA-T--G--GG-G--T
* *
15371 CCCCTCAAAAATGGCAAGGTTGGAGTATCTCCGTAGATGGAAAATTTGATATTTTAGAAATAAAA
58 CCCCTCAAAAATGGCAAGGTTGGAGTATCTCCGAAGATGGAAAATTTAATATTTTAGAAATAAAA
* * * *
15436 ATGGGGTTGGAGTATTCTCTCGAAAAA-GATG
123 ATGGGGTTAGAGTATCCCCTC-AAAAATGACG
* *
15467 GTGTTGGAGTAT-CCTTGTAGATGGAAAATTTGATATTTTTAGAAGTAACAATGGGGTCCCCTC-
1 GGGTTGGAGTATCCCCT-TAGATGGAAAATTTGATATTTTTAGAAGTAACAATGGGGTCCCCTCA
*** * * * *
15530 AAAATGGTGGGGTTGGAGTATC-CTTGAAGATGGAAAGTTTAATATTCTTAGGAGT-AAAATGGG
65 AAAATGGCAAGGTTGGAGTATCTC-CGAAGATGGAAAATTTAATATT-TTAGAAATAAAAATGGG
*
15593 GTTAGAGTATCCCCTCAAAAATGGCG
128 GTTAGAGTATCCCCTCAAAAATGACG
* * *
15619 GGGTTGGAGTATCCCCTTAGATGGAAACTTTGATATTTTTAGAAGTAAAAAACGGGGTTAGAGTA
1 GGGTTGGAGTATCCCCTTAGATGGAAAATTTGATATTTTTAGAAGT-AACAA--TGG---G-G--
*** * * * **
15684 TCCCCTCAAAAATGGTGGGGTTGGAGTATCCCCGTAGATGGAAAATTTGATATTTTTAGATGTAA
57 TCCCCTCAAAAATGGCAAGGTTGGAGTATCTCCGAAGATGGAAAATTTAATA-TTTTAGAAAT-A
* * * * *
15749 AAAATCGGGTTAAAGTATCCCCTTAGAAATCG-TG
120 AAAATGGGGTTAGAGTATCCCCTCAAAAAT-GACG
15783 GGGTTGGAGTAT
1 GGGTTGGAGTAT
15795 TCACTTTTAA
Statistics
Matches: 270, Mismatches: 37, Indels: 38
0.78 0.11 0.11
Matches are distributed among these distances:
151 6 0.02
152 99 0.37
153 20 0.07
155 3 0.01
156 2 0.01
158 2 0.01
159 3 0.01
160 24 0.09
161 24 0.09
162 44 0.16
163 3 0.01
164 39 0.14
165 1 0.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (153 bp):
GGGTTGGAGTATCCCCTTAGATGGAAAATTTGATATTTTTAGAAGTAACAATGGGGTCCCCTCAA
AAATGGCAAGGTTGGAGTATCTCCGAAGATGGAAAATTTAATATTTTAGAAATAAAAATGGGGTT
AGAGTATCCCCTCAAAAATGACG
Found at i:15690 original size:82 final size:82
Alignment explanation
Indices: 15523--15794 Score: 358
Period size: 82 Copynumber: 3.4 Consensus size: 82
15513 AACAATGGGG
* * * *
15523 TCCCCTC-AAAATGGTGGGGTTGGAGTAT--CCTTGAAGATGGAAAGTTTAATATTCTTAGGAGT
1 TCCCCTCAAAAATGGTGGGGTTGGAGTATCCCCTT--AGATGGAAAATTTGATATTTTTAGAAGT
*
15585 --AAAATGGGGTTAGAGTA
64 AAAAAACGGGGTTAGAGTA
* *
15602 TCCCCTCAAAAATGGCGGGGTTGGAGTATCCCCTTAGATGGAAACTTTGATATTTTTAGAAGTAA
1 TCCCCTCAAAAATGGTGGGGTTGGAGTATCCCCTTAGATGGAAAATTTGATATTTTTAGAAGTAA
15667 AAAACGGGGTTAGAGTA
66 AAAACGGGGTTAGAGTA
* *
15684 TCCCCTCAAAAATGGTGGGGTTGGAGTATCCCCGTAGATGGAAAATTTGATATTTTTAGATGTAA
1 TCCCCTCAAAAATGGTGGGGTTGGAGTATCCCCTTAGATGGAAAATTTGATATTTTTAGAAGTAA
*
15749 AAAATC-GGGTTAAAGTA
66 AAAA-CGGGGTTAGAGTA
* * *
15766 TCCCCTTAGAAATCGTGGGGTTGGAGTAT
1 TCCCCTCAAAAATGGTGGGGTTGGAGTAT
15795 TCACTTTTAA
Statistics
Matches: 173, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
79 7 0.04
80 44 0.25
82 121 0.70
83 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.30
Consensus pattern (82 bp):
TCCCCTCAAAAATGGTGGGGTTGGAGTATCCCCTTAGATGGAAAATTTGATATTTTTAGAAGTAA
AAAACGGGGTTAGAGTA
Found at i:18259 original size:51 final size:52
Alignment explanation
Indices: 18140--18278 Score: 147
Period size: 52 Copynumber: 2.7 Consensus size: 52
18130 GATTGCTTTC
* * ** * *
18140 ATGTATCGATACATTGAGGAATGTATCGATACATTCAGGTCAAAAACCTAGA
1 ATGTATCGATACAATAAAAAATGTATCGATACATTTAGGTCAAAAACCCAGA
* * * *
18192 ATGTATCGATATAATAAATAATTGTATCGATACATTTGGGT-TAAAACCCA-A
1 ATGTATCGATACAATAAA-AAATGTATCGATACATTTAGGTCAAAAACCCAGA
* *
18243 ATGTGTCGATACAATAAAAAATGTATTGATACATTT
1 ATGTATCGATACAATAAAAAATGTATCGATACATTT
18279 CTTTTCAGCA
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
50 16 0.22
51 17 0.24
52 21 0.29
53 18 0.25
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (52 bp):
ATGTATCGATACAATAAAAAATGTATCGATACATTTAGGTCAAAAACCCAGA
Found at i:20198 original size:153 final size:154
Alignment explanation
Indices: 19906--20578 Score: 754
Period size: 153 Copynumber: 4.4 Consensus size: 154
19896 ACAAATAAGA
* * * * * * * *
19906 TGAACCTATTCTAAATACCCACCTTCGGCATAAAAGC-GAACTTGGTGCCAACCAAGGAGTTGGT
1 TGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAG-ACCTAGTGACAACCTAGGACTCGAT
* * * * **
19970 TCTAAAAAATTATGAAAATACCCCAAGAGG-GACCTTCGACATAACAGTGCCTGATACCTTTAAA
65 TCTAAAAAATTATGAAAATGCACCTAGAGGATACCTTCGACATAACAGTGCCTGATACCCCTAAA
* ** *
20034 GGACTTAAAAAGGAAATAAATGGGT
130 GGACTTAAAAAGGATATGGATGGGG
* * * * *
20059 TGAACCTATTCTAAATACCCACCTTTGGCATAAAAGCGGACCTAGTGACAACCTAGGACTTGGTT
1 TGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGACCTAGTGACAACCTAGGACTCGATT
* *
20124 CTAAAAAACTATGAAAATGCACCTAGAGGATACTTTCGACATAACAGTGCCTGATACCCCTAAAG
66 CTAAAAAATTATGAAAATGCACCTAGAGGATACCTTCGACATAACAGTGCCTGATACCCCTAAAG
20189 GACTT-AAAAGGATATGGATGGGG
131 GACTTAAAAAGGATATGGATGGGG
* * * *
20212 TGAACCTATCCTAAATACCCACCTTCAGCATAAAAGTAAACCTAGTGACAACCCAGGACTCGATT
1 TGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGACCTAGTGACAACCTAGGACTCGATT
** * * * ** * *
20277 -TTTAAAATTAAGAAAATGC-CCTTAGGGGATACCCTCGATGTAATAGTGCCTGATACCCTTAAA
66 CTAAAAAATTATGAAAATGCACC-TAGAGGATACCTTCGACATAACAGTGCCTGATACCCCTAAA
20340 GGACTTAAAAAGGATATGGAT-GGG
130 GGACTTAAAAAGGATATGGATGGGG
* ** * *
20364 TGAACCTATCCTAAATACCCACTTTCAACACAAAAGTAGACC-AGTGACAACCTAGGACTCGATT
1 TGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGACCTAGTGACAACCTAGGACTCGATT
* * * ** * * * * *
20428 TTGAAAAATTACG-AGGTGCATCTAGGGGATACCTTCAACGTAACAGTGCCTGATACCCCTAAAA
66 CTAAAAAATTATGAAAATGCACCTAGAGGATACCTTCGACATAACAGTGCCTGATACCCCTAAAG
* *
20492 GACTTAAAAAGGGTCTGGATGGGG
131 GACTTAAAAAGGATATGGATGGGG
*
20516 TGAA-CTATCCTAAATGCCCACCTTCGGCATAAAAGCAGACCTAGTGACAA-CTAGGACTCGATT
1 TGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGACCTAGTGACAACCTAGGACTCGATT
20579 ATTGAAATAA
Statistics
Matches: 449, Mismatches: 63, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
151 125 0.28
152 121 0.27
153 166 0.37
154 37 0.08
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (154 bp):
TGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGACCTAGTGACAACCTAGGACTCGATT
CTAAAAAATTATGAAAATGCACCTAGAGGATACCTTCGACATAACAGTGCCTGATACCCCTAAAG
GACTTAAAAAGGATATGGATGGGG
Found at i:20548 original size:303 final size:304
Alignment explanation
Indices: 20015--20596 Score: 796
Period size: 303 Copynumber: 1.9 Consensus size: 304
20005 TCGACATAAC
* *
20015 AGTGCCTGATACCTTTAAAGGACTTAAAAAGGAAATAAATGGGTTGAACCTATTCTAAATACCCA
1 AGTGCCTGATACCCTTAAAGGACTTAAAAAGGAAATAAATGGGTTGAACCTATCCTAAATACCCA
** * * * * *
20080 CCTTTGGCATAAAAGCGGACCTAGTGACAACCTAGGACTTGGTTCTAAAAAACTATGAAAATGCA
66 CCTTTAACACAAAAGCAGACCTAGTGACAACCTAGGACTCGATTCTAAAAAACTACGAAAATGCA
* * *
20145 CCTAGAGGATACTTTCGACATAACAGTGCCTGATACCCCTAAAGGACTTAAAAGGATATGGATGG
131 CCTAGAGGATACCTTCAACATAACAGTGCCTGATACCCCTAAAAGACTTAAAAGGATATGGATGG
*
20210 GGTGAACCTATCCTAAATACCCACCTTCAGCATAAAAGTAAACCTAGTGACAACCCAGGACTCGA
196 GGTGAACCTATCCTAAATACCCACCTTCAGCATAAAAGCAAACCTAGTGACAA-CCAGGACTCGA
*
20275 TTTTTAAAATTAAGAAAATGCCCTTAGGGGATACCCTCGATGTAAT
260 TTATTAAAA-TAAGAAAATGCCCTTAGGGGATACCCTCGATGTAAT
* **
20321 AGTGCCTGATACCCTTAAAGGACTTAAAAAGGATATGGATGGG-TGAACCTATCCTAAATACCCA
1 AGTGCCTGATACCCTTAAAGGACTTAAAAAGGAAATAAATGGGTTGAACCTATCCTAAATACCCA
* * * * **
20385 -CTTTCAACACAAAAGTAGACC-AGTGACAACCTAGGACTCGATTTTGAAAAATTACG-AGGTGC
66 CCTTT-AACACAAAAGCAGACCTAGTGACAACCTAGGACTCGATTCTAAAAAACTACGAAAATGC
* * * * *
20447 ATCTAGGGGATACCTTCAACGTAACAGTGCCTGATACCCCTAAAAGACTTAAAAAGGGTCTGGAT
130 ACCTAGAGGATACCTTCAACATAACAGTGCCTGATACCCCTAAAAGACTT-AAAAGGATATGGAT
* * * *
20512 GGGGTGAA-CTATCCTAAATGCCCACCTTCGGCATAAAAGCAGACCTAGTGACAACTAGGACTCG
194 GGGGTGAACCTATCCTAAATACCCACCTTCAGCATAAAAGCAAACCTAGTGACAACCAGGACTCG
*
20576 ATTATTGAAATAAGAAAATGC
259 ATTATTAAAATAAGAAAATGC
Statistics
Matches: 241, Mismatches: 33, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
301 11 0.05
302 17 0.07
303 90 0.37
304 53 0.22
305 31 0.13
306 39 0.16
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (304 bp):
AGTGCCTGATACCCTTAAAGGACTTAAAAAGGAAATAAATGGGTTGAACCTATCCTAAATACCCA
CCTTTAACACAAAAGCAGACCTAGTGACAACCTAGGACTCGATTCTAAAAAACTACGAAAATGCA
CCTAGAGGATACCTTCAACATAACAGTGCCTGATACCCCTAAAAGACTTAAAAGGATATGGATGG
GGTGAACCTATCCTAAATACCCACCTTCAGCATAAAAGCAAACCTAGTGACAACCAGGACTCGAT
TATTAAAATAAGAAAATGCCCTTAGGGGATACCCTCGATGTAAT
Done.