Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2203
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: 10432
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Found at i:2701 original size:18 final size:18
Alignment explanation
Indices: 2672--2749 Score: 120
Period size: 18 Copynumber: 4.3 Consensus size: 18
2662 GTCACGATCG
*
2672 ATATCGTCACTATCATCA
1 ATATCGTCACTAGCATCA
* *
2690 ATAGCTTCACTAGCATCA
1 ATATCGTCACTAGCATCA
2708 ATATCGTCACTAGCATCA
1 ATATCGTCACTAGCATCA
*
2726 ATATCGTCACTATCATCA
1 ATATCGTCACTAGCATCA
2744 ATATCG
1 ATATCG
2750 ATATCATCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.31
Consensus pattern (18 bp):
ATATCGTCACTAGCATCA
Found at i:2719 original size:36 final size:36
Alignment explanation
Indices: 2672--2761 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 36
2662 GTCACGATCG
*
2672 ATATCGTCACTATCATCAATAGCTTCACTAGCATCA
1 ATATCGTCACTATCATCAATAGCGTCACTAGCATCA
* * *
2708 ATATCGTCACTAGCATCAATATCGTCACTATCATCA
1 ATATCGTCACTATCATCAATAGCGTCACTAGCATCA
2744 ATATCG--A-TATCATCAATA
1 ATATCGTCACTATCATCAATA
2762 AGAAAACCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
33 10 0.20
34 1 0.02
36 38 0.78
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.31
Consensus pattern (36 bp):
ATATCGTCACTATCATCAATAGCGTCACTAGCATCA
Found at i:2748 original size:9 final size:9
Alignment explanation
Indices: 2672--2748 Score: 55
Period size: 9 Copynumber: 8.6 Consensus size: 9
2662 GTCACGATCG
*
2672 ATATCGTCA
1 ATATCATCA
*
2681 CTATCATCA
1 ATATCATCA
* *
2690 ATAGCTTCA
1 ATATCATCA
* *
2699 CTAGCATCA
1 ATATCATCA
*
2708 ATATCGTCA
1 ATATCATCA
* *
2717 CTAGCATCA
1 ATATCATCA
*
2726 ATATCGTCA
1 ATATCATCA
*
2735 CTATCATCA
1 ATATCATCA
2744 ATATC
1 ATATC
2749 GATATCATCA
Statistics
Matches: 49, Mismatches: 19, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (9 bp):
ATATCATCA
Found at i:2754 original size:15 final size:17
Alignment explanation
Indices: 2672--2761 Score: 94
Period size: 18 Copynumber: 5.2 Consensus size: 17
2662 GTCACGATCG
2672 ATATCGTCACTATCATCA
1 ATATCG-CACTATCATCA
* * *
2690 ATAGCTTCACTAGCATCA
1 ATATC-GCACTATCATCA
*
2708 ATATCGTCACTAGCATCA
1 ATATCG-CACTATCATCA
2726 ATATCGTCACTATCATCA
1 ATATCG-CACTATCATCA
2744 ATATCG-A-TATCATCA
1 ATATCGCACTATCATCA
2759 ATA
1 ATA
2762 AGAAAACCTT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
15 11 0.17
16 1 0.02
18 52 0.81
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.31
Consensus pattern (17 bp):
ATATCGCACTATCATCA
Found at i:5209 original size:24 final size:21
Alignment explanation
Indices: 5129--5196 Score: 86
Period size: 20 Copynumber: 3.3 Consensus size: 21
5119 CTCACAAAGA
* * *
5129 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
5149 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
5170 -AAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
5190 AAAAAGA
1 AAAAAGA
5197 AACGAAGTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 25 0.61
21 16 0.39
ACGTcount: A:0.54, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:10288 original size:24 final size:22
Alignment explanation
Indices: 10252--10307 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
10242 TTCTCCTTTT
*
10252 CCCCCCCTTCTTTCCTTCCCCTCC
1 CCCCCCCTCCTTTCC--CCCCTCC
10276 CCCCCCCTCCTTTCCCCCCTCC
1 CCCCCCCTCCTTTCCCCCCTCC
*
10298 CCCCCTCTCC
1 CCCCCCCTCC
10308 CCCTTTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 16 0.53
24 14 0.47
ACGTcount: A:0.00, C:0.73, G:0.00, T:0.27
Consensus pattern (22 bp):
CCCCCCCTCCTTTCCCCCCTCC
Found at i:10290 original size:20 final size:20
Alignment explanation
Indices: 10251--10304 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 20
10241 CTTCTCCTTT
*
10251 TCCCCCCCTTCTTTCCTTCCCC
1 TCCCCCCCTCCTTTCC--CCCC
10273 TCCCCCCCCCTCCTTTCCCCCC
1 T--CCCCCCCTCCTTTCCCCCC
10295 TCCCCCCCTC
1 TCCCCCCCTC
10305 TCCCCCTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 9 0.31
22 6 0.21
24 14 0.48
ACGTcount: A:0.00, C:0.72, G:0.00, T:0.28
Consensus pattern (20 bp):
TCCCCCCCTCCTTTCCCCCC
Done.