Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2416
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: 24604
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Found at i:2030 original size:31 final size:31
Alignment explanation
Indices: 1979--2069 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 31
1969 TAAAAAAATA
*
1979 TAAATA-AAAATAAATCAAATTTAATATATCT
1 TAAATACAAAA-AAATTAAATTTAATATATCT
* *
2010 TAAATACAAAAAAATTAAATTTAAAATATTT
1 TAAATACAAAAAAATTAAATTTAATATATCT
* *
2041 TACAT-CTAAAAAAATTAGAATTAAATATA
1 TAAATAC-AAAAAAATTA-AATTTAATATA
2070 ATCCAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.02
31 37 0.73
32 13 0.25
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.34
Consensus pattern (31 bp):
TAAATACAAAAAAATTAAATTTAATATATCT
Found at i:4855 original size:20 final size:20
Alignment explanation
Indices: 4830--4873 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4820 ATTATTTATC
*
4830 TTTTTTAAAAAAAATTGATT
1 TTTTTTAAAAAAAATTAATT
**
4850 TTTTTTTTAAAAAATTAATT
1 TTTTTTAAAAAAAATTAATT
4870 TTTT
1 TTTT
4874 AAATTGTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTTTAAAAAAAATTAATT
Found at i:12164 original size:14 final size:14
Alignment explanation
Indices: 12145--12188 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
12135 AAAAAAGTGT
12145 AAATAAAAAAAATA
1 AAATAAAAAAAATA
* * *
12159 ATATAACATAAATA
1 AAATAAAAAAAATA
*
12173 AAATAAAAATAATA
1 AAATAAAAAAAATA
12187 AA
1 AA
12189 TATTCAGATC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAAAAAAAATA
Found at i:12916 original size:18 final size:18
Alignment explanation
Indices: 12893--12928 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12883 GTGTGAGATA
12893 ATTATATATTGCTAAATT
1 ATTATATATTGCTAAATT
12911 ATTATATATTGCTAAATT
1 ATTATATATTGCTAAATT
12929 GGAGGTGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTATATATTGCTAAATT
Found at i:13641 original size:308 final size:308
Alignment explanation
Indices: 12949--13850 Score: 1518
Period size: 308 Copynumber: 2.9 Consensus size: 308
12939 AATTGTTGTT
*
12949 ATGTGATTTGTTTGCTGTTGTAGGTTTTTTAGTTTATAATAATAATAATTATTATTATTATTATT
1 ATGTGATTTGTTTGTTGTTGTAGGTTTTTTAGTTTATAATAATAATAA-TA--ATTATTATTATT
* * *
13014 AATGTTTAAAATTATAATAAGATTGTTAAAGTTATTTTCTATTGATGTATATATATATATATATA
63 AATGTTCAAAATTCTAATAAGATTGTTAAAGTTATTTTCTATTG--GTGTATATATATATATATA
13079 TTGTAAATTATTATTAATGTTTGCTGTTGACATGTGATTTGTTTGCTGTTGTAGGTTTTTTAGTT
126 TTGTAAATTATTATTAATGTTTGCTGTTGACATGTGATTTGTTTGCTGTTGTAGGTTTTTTAG-T
*
13144 TATAATAATAATAATAATAATTATTATTATTAATGTTTAAAATTATAATAAGATTGTTAAAGTTA
190 T-T-ATAATAATAATAATAATTATTATTATTAATGTTCAAAATTATAATAAGATTGTTAAAGTTA
*
13209 TTTTCTATTGGTGTATATATATATATATTGTAAATTATTATTAATGTTTGCTGTTGGC
253 TTTTCTATTGGTG--TATATATATATATTGTAAATTATTATTAATGTTTGCTGTTGAC
*
13267 ATGTGATTTGTTTGTTGTTGTAGGTTTTTTAGTTTATAATAATAATAATTATTATTATTATTAAT
1 ATGTGATTTGTTTGTTGTTGTAGGTTTTTTAGTTTATAATAATAATAATAATTATTATTATTAAT
13332 GTTCAAAATTCTAATAAGATTGTTAAAGTTATTTTCTATTGGTGTATATATATATATATATTGTA
66 GTTCAAAATTCTAATAAGATTGTTAAAGTTATTTTCTATTGGTGTATATATATATATATATTGTA
*
13397 AATTATTATTAATGTTTGCTGTTGACATGTGATTTGTTTGTTGTTGTAGGTTTTTTAGTTTATAA
131 AATTATTATTAATGTTTGCTGTTGACATGTGATTTGTTTGCTGTTGTAGGTTTTTTAGTTTATAA
*
13462 TAATAATAATAATTATTATTATTAATGTTCAAAATTCTAATAAGATTGTTAAAGTTATTTTCTAT
196 TAATAATAATAATTATTATTATTAATGTTCAAAATTATAATAAGATTGTTAAAGTTATTTTCTAT
13527 TGGTGTATATATATATATTGTAAATTATTATTAATGTTTGCTGTTGAC
261 TGGTGTATATATATATATTGTAAATTATTATTAATGTTTGCTGTTGAC
13575 ATGTGATTTGTTTGTTGTTGTAGGTTTTTTAGTTTATAATAATAATAATAATTATTATTATTAAT
1 ATGTGATTTGTTTGTTGTTGTAGGTTTTTTAGTTTATAATAATAATAATAATTATTATTATTAAT
* *
13640 GTTCAAAATTCTAAAAAGATTGTTGAAGTTATTTTCTATTGGTG------TATATATATATTGTA
66 GTTCAAAATTCTAATAAGATTGTTAAAGTTATTTTCTATTGGTGTATATATATATATATATTGTA
13699 AATTATTATTAATGTTTGCTGTTGACATGTGATTTGTTTGCTG-T-T-GGTTTTTTA-TATTATA
131 AATTATTATTAATGTTTGCTGTTGACATGTGATTTGTTTGCTGTTGTAGGTTTTTTAGT-TTATA
* *
13760 ATAATAATAATTATTATTATTATTAATGTTCAAAATTATAATAAGATTGTTAAAGTTATTTTTTA
195 ATAATAATAATAATTATTATTATTAATGTTCAAAATTATAATAAGATTGTTAAAGTTATTTTCTA
13825 TTGGTGTATATATATATATTGTAAAT
260 TTGGTGTATATATATATATTGTAAAT
13851 ACTTACAAAA
Statistics
Matches: 567, Mismatches: 16, Indels: 21
0.94 0.03 0.03
Matches are distributed among these distances:
298 1 0.00
299 102 0.18
300 1 0.00
301 1 0.00
302 57 0.10
308 148 0.26
310 72 0.13
311 1 0.00
312 2 0.00
313 80 0.14
315 54 0.10
317 1 0.00
318 47 0.08
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (308 bp):
ATGTGATTTGTTTGTTGTTGTAGGTTTTTTAGTTTATAATAATAATAATAATTATTATTATTAAT
GTTCAAAATTCTAATAAGATTGTTAAAGTTATTTTCTATTGGTGTATATATATATATATATTGTA
AATTATTATTAATGTTTGCTGTTGACATGTGATTTGTTTGCTGTTGTAGGTTTTTTAGTTTATAA
TAATAATAATAATTATTATTATTAATGTTCAAAATTATAATAAGATTGTTAAAGTTATTTTCTAT
TGGTGTATATATATATATTGTAAATTATTATTAATGTTTGCTGTTGAC
Found at i:15608 original size:13 final size:14
Alignment explanation
Indices: 15580--15609 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
15570 TAAATTGAGG
15580 CAGAAAGTGCTTTT
1 CAGAAAGTGCTTTT
15594 CAGAAAGTG-TTTT
1 CAGAAAGTGCTTTT
15607 CAG
1 CAG
15610 CAATTTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (14 bp):
CAGAAAGTGCTTTT
Found at i:22555 original size:167 final size:166
Alignment explanation
Indices: 22349--23442 Score: 927
Period size: 166 Copynumber: 6.7 Consensus size: 166
22339 CTCTTCTCCA
** * *
22349 TAATTTTTTCGAGA-AGATTTTT-TTAATTTTTAATTTTTAAAATTTATCAAATATTAAT-ATTT
1 TAATTTTTTCGAGAGA-ATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATA-TCATCATTT
* * * * * *
22411 ATTTCACATTAAATCAGTTTGTAAAAATTAATTCATTTTTATGAGTTTTT-AAATTTCTCCTTGA
64 ATTTCATATTAATTCAGTTTTTAAAAATTCATTCATTTTCATGAGTTTTTGAAATTTTTCCTTGA
* *
22475 AATTCTTATTTTTTTTCGAAATACGGTGTTTTTTACTTCG
129 AATTC-T-TTTTTTTTCGAAATACGATATTTTTTACTTCG
* * *
22515 TAATTTTTTCGAGAGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATACCATAATTTAT
1 TAATTTTTTCGAGAGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCATCATTTAT
*
22580 TTCATATTAATTAAGTTTTTCAAAAATTCATTCATTTTCATGAGTTTTT--AATTTTTCCTTTTC
66 TTCATATTAATTCAGTTTTT-AAAAATTCATTCATTTTCATGAGTTTTTGAAATTTTTCC---T-
* ** * * * *
22643 TGAAATAC-AGTATTTTC-TACTTCG-TATTTTTT--TTC-
126 TGAAATTCTTTTTTTTTCGAAATACGATATTTTTTACTTCG
*
22678 -AA-------G-G-GAATTTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATCATCATTTA
1 TAATTTTTTCGAGAGAA-TTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCATCATTTA
* * * *
22733 TTTCACATTAA-TCAGTTTTTAAAAATTCATTCATTTTCATTCA-TTTTTG-ATTTTTTTCTTGA
65 TTTCATATTAATTCAGTTTTTAAAAATTCATTCATTTTCA-TGAGTTTTTGAAATTTTTCCTTGA
** *
22795 AATTCTTTTTTTTTCGAAATACGACGTTTTCTACTTCG
129 AATTCTTTTTTTTTCGAAATACGATATTTTTTACTTCG
* * *
22833 TAATTTTTTTCGAGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATATCATCATTTA
1 TAA-TTTTTTCGAGAGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCATCATTTA
* * * ** ** *
22898 TTTCATATTAATTCAATTCTCAAAAATTCATTCATGCTCATGAGTTTTTGATTTTTTTCCTTGGA
65 TTTCATATTAATTCAGTTTTTAAAAATTCATTCATTTTCATGAGTTTTTGAAATTTTTCCTTGAA
* ** *
22963 ACTC-CATTTTTTC-AAATACGATATTTTCTA-TTCCG
130 ATTCTTTTTTTTTCGAAATACGATATTTTTTACTT-CG
* * * * * *
22998 TAAATTTTTTTGA-AGGGATTTTTCTCGTCTTTTTCAATTTTTAAAATTCATCAAATATTTATTA
1 T-AATTTTTTCGAGA-GAATTTTTCTTG-GTTTTT-AATTTTTAAAATTCATCAAATA-TCATCA
* * * **
23062 TTTATTTCTTATCAATTCAG--TTTCAAAATTCATTCATTTTCATGAGTTTTTGTTA-TTTTCCT
61 TTTATTTCATATTAATTCAGTTTTTAAAAATTCATTCATTTTCATGAGTTTTTGAAATTTTTCCT
* *
23124 TGAAATTCTTTTTTTTT-GAAATA-TAGTA-TTTTTACTCCG
126 TGAAATTCTTTTTTTTTCGAAATACGA-TATTTTTTACTTCG
* * *
23163 TAATTTTTTTGAGGGGATTTTTCTTGGTTTTTAATTTTT-AAATTCATCAAATATCATCATTTAT
1 TAATTTTTTCGAGAGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCATCATTTAT
* * * * ** *
23227 TCCATATTAATTCAATTTTTTAAAATTCATTCATTTTCATAAGTTTTTTGATTTTTTTACTTGAA
66 TTCATATTAATTCAGTTTTTAAAAATTCATTCATTTTCATGAG-TTTTTGAAATTTTTCCTTGAA
*
23292 ACTCCTTTTTTTTTTCGAAATACGATATTTTTTAC-TCGG
130 A-TTC-TTTTTTTTTCGAAATACGATATTTTTTACTTC-G
* ** * * * *
23331 TAAATTGTTTCGA-AGAGATTTTTCTCAGTTTTCAAATTTTTATAATTCATTAAACATCATCATT
1 T-AATTTTTTCGAGAGA-ATTTTTCTTGGTTTT-TAATTTTTAAAATTCATCAAATATCATCATT
* ** *
23395 TGA-TTCATATTAAATT-AATTTGAAAAAATTAATTCATTTTCATGAGTT
63 T-ATTTCATATT-AATTCAGTTTTTAAAAATTCATTCATTTTCATGAGTT
23443 ATAATTTTTT
Statistics
Matches: 755, Mismatches: 115, Indels: 112
0.77 0.12 0.11
Matches are distributed among these distances:
149 7 0.01
150 7 0.01
151 4 0.01
152 29 0.04
153 20 0.03
154 57 0.08
155 1 0.00
156 2 0.00
160 20 0.03
161 14 0.02
162 33 0.04
163 12 0.02
164 39 0.05
165 119 0.16
166 125 0.17
167 106 0.14
168 64 0.08
169 22 0.03
170 10 0.01
171 59 0.08
172 5 0.01
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (166 bp):
TAATTTTTTCGAGAGAATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCATCATTTAT
TTCATATTAATTCAGTTTTTAAAAATTCATTCATTTTCATGAGTTTTTGAAATTTTTCCTTGAAA
TTCTTTTTTTTTCGAAATACGATATTTTTTACTTCG
Found at i:22648 original size:152 final size:151
Alignment explanation
Indices: 22487--22772 Score: 423
Period size: 154 Copynumber: 1.9 Consensus size: 151
22477 TTCTTATTTT
* * * * *
22487 TTTTCGAAATACGGTGTTTTTTACTTCGTA-ATTTTTTCGAGAGAA-TTTTTCTTGGTTTTTAAT
1 TTTTCGAAATACAGTATTTTCTACTTCGTATATTTTTTCAAGAGAATTTTTTCTTAGTTTTTAAT
*
22550 TTTTAAAATTCATAAAATACCATAATTTATTTCATATTAATTAAGTTTTTCAAAAATTCATTCAT
66 TTTTAAAATTCATAAAATACCATAATTTATTTCACATTAA-TAAGTTTTT-AAAAATTCATTCAT
22615 TTTCATGAGTTTTTAATTTTTCC
129 TTTCATGAGTTTTTAATTTTTCC
* *
22638 TTTTCTGAAATACAGTATTTTCTACTTCGTATTTTTTTTCAAGGGAATTTTTTCTTAGTTTTTAA
1 TTTTC-GAAATACAGTATTTTCTACTTCGTATATTTTTTCAAGAGAATTTTTTCTTAGTTTTTAA
* * * *
22703 TTTTTAAAATTCATCAAATATCATCATTTATTTCACATTAATCAGTTTTTAAAAATTCATTCATT
65 TTTTTAAAATTCATAAAATACCATAATTTATTTCACATTAATAAGTTTTTAAAAATTCATTCATT
22768 TTCAT
130 TTCAT
22773 TCATTTTTGA
Statistics
Matches: 120, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
151 5 0.04
152 42 0.35
153 20 0.17
154 53 0.44
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (151 bp):
TTTTCGAAATACAGTATTTTCTACTTCGTATATTTTTTCAAGAGAATTTTTTCTTAGTTTTTAAT
TTTTAAAATTCATAAAATACCATAATTTATTTCACATTAATAAGTTTTTAAAAATTCATTCATTT
TCATGAGTTTTTAATTTTTCC
Found at i:23822 original size:24 final size:24
Alignment explanation
Indices: 23769--23842 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
23759 TGGCTGCTGG
* *
23769 AAAAAGAAGAGAGAAAAGAGAGAAA
1 AAAAAG-AGAGAGAAAATAGAAAAA
*
23794 GAAAAGCA-AGAGAAAATAGAAAAA
1 AAAAAG-AGAGAGAAAATAGAAAAA
23818 AAAAAGAGAGAGAAAAATTAGAAAA
1 AAAAAGAGAGAG-AAAA-TAGAAAA
23843 CACTAGCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.02
24 23 0.56
25 10 0.24
26 7 0.17
ACGTcount: A:0.72, C:0.01, G:0.23, T:0.04
Consensus pattern (24 bp):
AAAAAGAGAGAGAAAATAGAAAAA
Found at i:23833 original size:13 final size:12
Alignment explanation
Indices: 23769--23834 Score: 55
Period size: 13 Copynumber: 5.3 Consensus size: 12
23759 TGGCTGCTGG
23769 AAAAAGAAGAGA
1 AAAAAGAAGAGA
*
23781 GAAAAG-AGAGAA
1 AAAAAGAAGAG-A
23793 AGAAAAGCAAGAGA
1 A-AAAAG-AAGAGA
* *
23807 AAATAGAA-AAA
1 AAAAAGAAGAGA
23818 AAAAAGAGAGAGA
1 AAAAAGA-AGAGA
23831 AAAA
1 AAAA
23835 TTAGAAAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
11 12 0.29
12 9 0.21
13 15 0.36
14 2 0.05
15 4 0.10
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.02
Consensus pattern (12 bp):
AAAAAGAAGAGA
Done.