Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1866
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: 12685
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Found at i:4972 original size:20 final size:19
Alignment explanation
Indices: 4943--5016 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
4933 TTTTAACTAG
4943 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAA-A
* * *
4963 ATGAATCGATAAATTCAAA
1 ATGTATCGATACATTGAAA
*
4982 CATTTATCGATACATTGAAAA
1 -ATGTATCGATACATTG-AAA
5003 ATGTATCGATACAT
1 ATGTATCGATACAT
5017 ATGGGTAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 40 0.91
21 3 0.07
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (19 bp):
ATGTATCGATACATTGAAA
Found at i:6009 original size:28 final size:28
Alignment explanation
Indices: 5930--6550 Score: 622
Period size: 28 Copynumber: 21.9 Consensus size: 28
5920 TAAAAAAAAT
*
5930 GTGCCACTAACTTGTGTGGGCTTTGAAAAGAG
1 GTGCCACTGAC-T-TGTGGGCTTTG-AAAG-G
* *
5962 TTGCCACCGACTTCTGTGGGCTTTGAAAGG
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGG
* **
5992 GTGCCACTAACTTGTGGGCTTTGATGGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
6020 GTGCCACTGACTTGTGGGCTTTGAAGGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
6048 GTACCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * * *
6076 GTACTACTGACTTGTGGGATTCGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * *
6104 GTACCACTAACTTATGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
** *
6132 GTATCACTAACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
6160 GTGCCACTAACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * *
6188 GTGCCACTGAGTTGTGGGATTTGGAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
6216 GTGCCACTGATTTGTGCGGGCTTTGAAAAAGT
1 GTGCCACTGACTTGT--GGGCTTTG--AAAGG
* * **
6248 ATGCCACTTACTTGTGGGCTTTGAAACA
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
6276 GTGCCACTAACTTGTGGGCTTTGTAAA-G
1 GTGCCACTGACTTGTGGGCTTTG-AAAGG
* * *
6304 ATGCCACTGACTTGTGGTCTTTTG-AAGAA
1 GTGCCACTGACTTGTGGGC-TTTGAAAG-G
* * * *
6333 ATGCCACTAACTTATGGGTTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
6361 ATGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * * *
6389 ATGCCACTAACTTGTAGGCTTTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
6417 GTGCCACTGACTTATGGGCTTTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * *
6445 ATGCCACT-ACTTATGGGCTTT-CAA-G
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * **
6470 ATGCCACTAACTTGTGGGCTTTGAAATT
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
6498 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
6526 ATGCCACTGACCTGTGGGCTTTGAA
1 GTGCCACTGACTTGTGGGCTTTGAA
6551 GAGATGAACG
Statistics
Matches: 506, Mismatches: 71, Indels: 28
0.84 0.12 0.05
Matches are distributed among these distances:
25 9 0.02
26 14 0.03
27 17 0.03
28 376 0.74
29 26 0.05
30 24 0.05
31 4 0.01
32 36 0.07
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (28 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGG
Found at i:6411 original size:229 final size:221
Alignment explanation
Indices: 5931--6552 Score: 627
Period size: 229 Copynumber: 2.7 Consensus size: 221
5921 AAAAAAAATG
* * * * * *
5931 TGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCGACTTCTGTGGGCTTTGAAAGGGTGC
1 TGCCACTAAC-T-TGTAGGCTTTGAAAAG-G-TGCCACTGAC-T-TATGGGATTTGAAAAGATGC
* ** * * *** * *
5996 CACTAACTTGTGGGCTTTGATGGGGTGCCACTGACTTGTGGGCTTTGAAGGGGTACCACTGACTT
60 CACT-ACTTATGGGCTTT-A-AAGATGCCACTAACTTGTGGGCTTTGAAACAGTGCCACTAACTT
* * * * * * ** *
6061 GTGGGCTTTGAAAGGGTACTACTGACTTGTGGGATTCGAA-AGGGTACCACTAACTTATGGGCTT
122 GTGGGCTTTGAAAGGATGCCACTGACCTGTGGGCTTTGAAGA-AATGCCACTAACTTATGGGCTT
* * *
6125 TGAAAGGGTATCACTAACTTGTGGGCTTTGAAAGGG
186 TGAAAGGATACCACTAACTTGTGGGCTTTGAAAGGA
* * * * * * *
6161 TGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGAGTTGTGGGATTTGGAAGGGTGCCACTGA
1 TGCCACTAACTTGTAGGCTTTGAAAAGGTGCCACTGACTTATGGGATTTGAAAAGATGCCACT-A
* * *
6226 TTTGTGCGGGCTTTGAAAAAGTATGCCACTTACTTGTGGGCTTTGAAACAGTGCCACTAACTTGT
65 CTTAT--GGGCTTT---AAAG-ATGCCACTAACTTGTGGGCTTTGAAACAGTGCCACTAACTTGT
* * *
6291 GGGCTTTGTAAA-GATGCCACTGACTTGTGGTCTTTTGAAGAAATGCCACTAACTTATGGGTTTT
124 GGGCTTTG-AAAGGATGCCACTGACCTGTGGGC-TTTGAAGAAATGCCACTAACTTATGGGCTTT
* *
6355 GAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGA
187 GAAAGGATACCACTAACTTGTGGGCTTTGAAAGGA
*
6390 TGCCACTAACTTGTAGGCTTTGAAAAGGTGCCACTGACTTATGGGCTTTGAAAAGATGCCACTAC
1 TGCCACTAACTTGTAGGCTTTGAAAAGGTGCCACTGACTTATGGGATTTGAAAAGATGCCACTAC
* ** *
6455 TTATGGGCTTTCAAGATGCCACTAACTTGTGGGCTTTGAAATTGTGCCACTGACTTGTGGGCTTT
66 TTATGGGCTTTAAAGATGCCACTAACTTGTGGGCTTTGAAACAGTGCCACTAACTTGTGGGCTTT
6520 GAAAGGATGCCACTGACCTGTGGGCTTTGAAGA
131 GAAAGGATGCCACTGACCTGTGGGCTTTGAAGA
6553 GATGAACGTT
Statistics
Matches: 334, Mismatches: 49, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
221 11 0.03
222 65 0.19
223 3 0.01
224 27 0.08
225 1 0.00
226 22 0.07
227 2 0.01
228 79 0.24
229 113 0.34
230 11 0.03
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (221 bp):
TGCCACTAACTTGTAGGCTTTGAAAAGGTGCCACTGACTTATGGGATTTGAAAAGATGCCACTAC
TTATGGGCTTTAAAGATGCCACTAACTTGTGGGCTTTGAAACAGTGCCACTAACTTGTGGGCTTT
GAAAGGATGCCACTGACCTGTGGGCTTTGAAGAAATGCCACTAACTTATGGGCTTTGAAAGGATA
CCACTAACTTGTGGGCTTTGAAAGGA
Done.