Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold300
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: 35763
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2208 original size:16 final size:16
Alignment explanation
Indices: 2159--2210 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
2149 TAGCTTCTTC
**
2159 TTTTTTTTCACGAAAA
1 TTTTTTTTCACGAATT
2175 TTTTTTTTCACGAATT
1 TTTTTTTTCACGAATT
2191 TTTTTTTTCACG-ATT
1 TTTTTTTTCACGAATT
2206 TTTTT
1 TTTTT
2211 CAACTTGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 8 0.24
16 26 0.76
ACGTcount: A:0.19, C:0.12, G:0.06, T:0.63
Consensus pattern (16 bp):
TTTTTTTTCACGAATT
Found at i:2266 original size:11 final size:11
Alignment explanation
Indices: 2250--2290 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
2240 ATGGAAACCA
2250 AATTTTTTTTG
1 AATTTTTTTTG
2261 AATTTTTTTTG
1 AATTTTTTTTG
2272 AA-TTTTTTTG
1 AATTTTTTTTG
2282 AATTTTTTT
1 AATTTTTTT
2291 GAAGAAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.34
11 19 0.66
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:2268 original size:10 final size:10
Alignment explanation
Indices: 2253--2293 Score: 73
Period size: 10 Copynumber: 4.0 Consensus size: 10
2243 GAAACCAAAT
2253 TTTTTTTGAA
1 TTTTTTTGAA
2263 TTTTTTTTGAA
1 -TTTTTTTGAA
2274 TTTTTTTGAA
1 TTTTTTTGAA
2284 TTTTTTTGAA
1 TTTTTTTGAA
2294 GAAAACTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 20 0.67
11 10 0.33
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.71
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:3320 original size:21 final size:23
Alignment explanation
Indices: 3275--3321 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3265 TCACCTGCAA
* *
3275 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
3298 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
3319 TAA
1 TAA
3322 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:26400 original size:27 final size:27
Alignment explanation
Indices: 26369--26546 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
26359 TAAATTGTAC
*
26369 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
26396 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
26422 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
26450 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
26477 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
26505 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
26532 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
26547 GACTTAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:26430 original size:54 final size:55
Alignment explanation
Indices: 26369--26546 Score: 236
Period size: 54 Copynumber: 3.3 Consensus size: 55
26359 TAAATTGTAC
* **
26369 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* * * *
26424 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* *
26477 AGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
*
26532 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
26547 GACTTAATAT
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:33224 original size:53 final size:53
Alignment explanation
Indices: 33124--33227 Score: 156
Period size: 53 Copynumber: 2.0 Consensus size: 53
33114 AAGGAAAAAC
** *
33124 AAAAAAAAATGTTCATCTTTTATCTCCTTGGCCGAATGTTCTAAAGAAGAAAG
1 AAAAAAAAATGTTCATCTTTTATCTCCTTGGCCGAAAATGCTAAAGAAGAAAG
*
33177 AAAAAAAATTGTTCATCTTTTATCATCCTTGGCCGAAAATGCT-AAGAAGAA
1 AAAAAAAAATGTTCATCTTTTATC-TCCTTGGCCGAAAATGCTAAAGAAGAA
33228 GGGGGAAGGG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 31 0.67
54 15 0.33
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (53 bp):
AAAAAAAAATGTTCATCTTTTATCTCCTTGGCCGAAAATGCTAAAGAAGAAAG
Found at i:34291 original size:27 final size:27
Alignment explanation
Indices: 34260--34437 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
34250 TAAATTGTAC
*
34260 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
34287 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
34313 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
34341 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
34368 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
34396 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
34423 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
34438 GACTTAATAT
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 25 0.19
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:34321 original size:54 final size:55
Alignment explanation
Indices: 34260--34437 Score: 227
Period size: 54 Copynumber: 3.3 Consensus size: 55
34250 TAAATTGTAC
* **
34260 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
* * ** *
34315 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
* *
34368 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
*
34423 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
34438 GACTTAATAT
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
53 1 0.01
54 60 0.57
55 45 0.42
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
Done.