Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6905.1
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: 9076
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1965 original size:51 final size:51
Alignment explanation
Indices: 1889--1995 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 51
1879 ACGCGGACCA
*
1889 AGATCGAGTTGCCAAGTCACGAGAAACTCTTACGAAAGATCCTAGACGAAC
1 AGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGATCCTAGACGAAC
*
1940 AGATCGATTTGCCAAGTCACGAGAAACTCCTACGAAAGATCCTAGACGAAC
1 AGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGATCCTAGACGAAC
1991 AGATC
1 AGATC
1996 TGAAATCAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (51 bp):
AGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGATCCTAGACGAAC
Found at i:4095 original size:27 final size:27
Alignment explanation
Indices: 4064--4241 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
4054 TAAATTGTAC
4064 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
4091 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
4117 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
4145 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
4173 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
4200 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
**
4227 AGCACTGGGTGTGCG
1 AGCACTAAGTGTGCG
4242 GACTCAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:4178 original size:82 final size:81
Alignment explanation
Indices: 4065--4220 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
4055 AAATTGTACA
* *
4065 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
4129 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
4146 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
4211 TGCGAGTTGA
65 TGCGAATTGA
4221 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:6495 original size:177 final size:177
Alignment explanation
Indices: 6199--6559 Score: 713
Period size: 177 Copynumber: 2.0 Consensus size: 177
6189 ATGAAGAAAT
6199 TTCTTGATTGGGCTGGATTTTGGTTATTGGGCCTCGCCTTCAAGAATTTGGGCTCGTGATCCATC
1 TTCTTGATTGGGCTGGATTTTGGTTATTGGGCCTCGCCTTCAAGAATTTGGGCTCGTGATCCATC
*
6264 TCCTACCAAAATTGGGTCGTTGATGCTCGTAATGGAGATCCAATGCGTTTTGGCTGCAAGATTTG
66 TCCTACCAAAATTGGGTCGTTGATGCTCGTAATGGAGATCCAATGCATTTTGGCTGCAAGATTTG
6329 GTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGA
131 GTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGA
6376 TTCTTGATTGGGCTGGATTTTGGTTATTGGGCCTCGCCTTCAAGAATTTGGGCTCGTGATCCATC
1 TTCTTGATTGGGCTGGATTTTGGTTATTGGGCCTCGCCTTCAAGAATTTGGGCTCGTGATCCATC
6441 TCCTACCAAAATTGGGTCGTTGATGCTCGTAATGGAGATCCAATGCATTTTGGCTGCAAGATTTG
66 TCCTACCAAAATTGGGTCGTTGATGCTCGTAATGGAGATCCAATGCATTTTGGCTGCAAGATTTG
6506 GTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGA
131 GTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGA
6553 TTCTTGA
1 TTCTTGA
6560 AATCTCTTTG
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
177 183 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (177 bp):
TTCTTGATTGGGCTGGATTTTGGTTATTGGGCCTCGCCTTCAAGAATTTGGGCTCGTGATCCATC
TCCTACCAAAATTGGGTCGTTGATGCTCGTAATGGAGATCCAATGCATTTTGGCTGCAAGATTTG
GTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGA
Found at i:8069 original size:23 final size:22
Alignment explanation
Indices: 8018--8070 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
8008 CCTCGTCTTT
*
8018 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
8040 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
8063 TTCTTTTC
1 TTCTTTTC
8071 AATTTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.19
23 14 0.54
24 5 0.19
ACGTcount: A:0.09, C:0.25, G:0.02, T:0.64
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Done.