Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5660.1
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: 19699
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:2533 original size:17 final size:18
Alignment explanation
Indices: 2511--2548 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
2501 TTTAAATTTT
2511 TTTTTGTAATTTTTC-AA
1 TTTTTGTAATTTTTCGAA
*
2528 TTTTTGTGATTTTTCGAA
1 TTTTTGTAATTTTTCGAA
2546 TTT
1 TTT
2549 CCCTTTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.18, C:0.05, G:0.11, T:0.66
Consensus pattern (18 bp):
TTTTTGTAATTTTTCGAA
Found at i:11712 original size:37 final size:37
Alignment explanation
Indices: 11648--11804 Score: 199
Period size: 37 Copynumber: 4.0 Consensus size: 37
11638 TACGTATGAT
*
11648 CACTTATCAC-TTGTCCCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
11684 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
11721 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AGC
*
11764 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 ---CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
11804 C
1 C
11805 GAAGCTATCA
Statistics
Matches: 107, Mismatches: 4, Indels: 19
0.82 0.03 0.15
Matches are distributed among these distances:
36 10 0.09
37 54 0.50
39 2 0.02
40 4 0.04
41 1 0.01
42 1 0.01
43 3 0.03
44 2 0.02
46 30 0.28
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:11774 original size:46 final size:46
Alignment explanation
Indices: 11721--11989 Score: 331
Period size: 46 Copynumber: 5.6 Consensus size: 46
11711 TAAGTGTAGC
* **
11721 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
11767 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
11813 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
11865 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
11911 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
11963 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
11990 AGTACTCAAA
Statistics
Matches: 198, Mismatches: 13, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
46 111 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:11840 original size:52 final size:52
Alignment explanation
Indices: 11764--11983 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
11754 TAGCTAAAGC
* *
11764 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
11817 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
11869 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
11915 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
11967 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
11984 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:11886 original size:98 final size:98
Alignment explanation
Indices: 11721--11989 Score: 448
Period size: 98 Copynumber: 2.7 Consensus size: 98
11711 TAAGTGTAGC
* * *
11721 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
11786 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
11820 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
11885 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * *
11918 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
11983 GATCAGA
66 GATCAGA
11990 AGTACTCAAA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 150 0.94
99 9 0.06
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:15171 original size:49 final size:49
Alignment explanation
Indices: 15116--15261 Score: 220
Period size: 49 Copynumber: 3.0 Consensus size: 49
15106 TTCGTTTTCT
* * *
15116 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACAAATCACATAC
* *
15165 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACTTAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACAAATCACATAC
* *
15214 CGATGCCACAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACA-AATCACAT
15262 GTTCACATGT
Statistics
Matches: 87, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
49 81 0.93
50 6 0.07
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.23
Consensus pattern (49 bp):
CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACAAATCACATAC
Done.