Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold814
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: 18284
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Found at i:2657 original size:12 final size:11
Alignment explanation
Indices: 2631--2727 Score: 79
Period size: 12 Copynumber: 8.3 Consensus size: 11
2621 TTGAATCTTC
*
2631 TTATTTTTTTAT
1 TTATTTTATT-T
2643 TTATTCTTATTT
1 TTATT-TTATTT
2655 TTATTTTATTT
1 TTATTTTATTT
2666 ATTATTTTATTT
1 -TTATTTTATTT
2678 TTATTTT-TCTT
1 TTATTTTAT-TT
2689 TTGATTTTTATTT
1 TT-A-TTTTATTT
* * *
2702 TCATTTCAATT
1 TTATTTTATTT
*
2713 TTATTATTTTTT
1 TTATT-TTATTT
2725 TTA
1 TTA
2728 AAAGACATAT
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
10 1 0.01
11 27 0.39
12 30 0.43
13 11 0.16
14 1 0.01
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (11 bp):
TTATTTTATTT
Found at i:2697 original size:7 final size:6
Alignment explanation
Indices: 2631--2707 Score: 79
Period size: 6 Copynumber: 13.0 Consensus size: 6
2621 TTGAATCTTC
*
2631 TTATTT TT-TTAT TTATTC TTATTT TTA-TT TTATTT ATTA-TT TTATTT
1 TTATTT TTATT-T TTATTT TTATTT TTATTT TTATTT -TTATTT TTATTT
* * *
2678 TTATTT TTCTTT TGATTT TTATTT TCATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT
2708 CAATTTTATT
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
5 10 0.17
6 44 0.75
7 5 0.08
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:2702 original size:18 final size:17
Alignment explanation
Indices: 2631--2727 Score: 79
Period size: 18 Copynumber: 5.5 Consensus size: 17
2621 TTGAATCTTC
* *
2631 TTATTTTTTTATTTATTC
1 TTATTTTATT-TTTATTT
2649 TTATTTT-TATTTTATTT
1 TTATTTTAT-TTTTATTT
2666 ATTATTTTATTTTTATTT
1 -TTATTTTATTTTTATTT
*
2684 TTCTTTTGATTTTTATTT
1 TTATTTT-ATTTTTATTT
* * *
2702 TCATTTCAATTTTATTAT
1 TTATTTTATTTTTATT-T
*
2720 TTTTTTTA
1 TTATTTTA
2728 AAAGACATAT
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
17 21 0.32
18 43 0.66
19 1 0.02
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (17 bp):
TTATTTTATTTTTATTT
Found at i:2714 original size:17 final size:17
Alignment explanation
Indices: 2657--2717 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
2647 TCTTATTTTT
* *
2657 ATTTTATTTATTATTTTA
1 ATTTTATTT-TCATTTCA
* * *
2675 TTTTTATTTTTCTTTTGA
1 ATTTTA-TTTTCATTTCA
*
2693 TTTTTATTTTCATTTCA
1 ATTTTATTTTCATTTCA
2710 ATTTTATT
1 ATTTTATT
2718 ATTTTTTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
17 16 0.46
18 16 0.46
19 3 0.09
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.74
Consensus pattern (17 bp):
ATTTTATTTTCATTTCA
Found at i:5638 original size:13 final size:13
Alignment explanation
Indices: 5620--5644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5610 ATTAAATTAT
5620 TAATTAGTTTAAA
1 TAATTAGTTTAAA
5633 TAATTAGTTTAA
1 TAATTAGTTTAA
5645 TAAACAAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TAATTAGTTTAAA
Found at i:12011 original size:40 final size:39
Alignment explanation
Indices: 11954--12183 Score: 293
Period size: 40 Copynumber: 5.8 Consensus size: 39
11944 GGATATAGCT
* * *
11954 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
11994 ACTTGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAA-TGCCTTCGGGACTTAGCCCGGATTTAGTA
*
12034 ACTCACACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
12073 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATTTAGTA
* ** *
12113 ACTCGAACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
12152 ACTAGCGCAGATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACA-ATGCCTTCGGGACTTAGCCCGG
12184 TTATCATCCA
Statistics
Matches: 171, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.01
39 69 0.40
40 99 0.58
41 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:12061 original size:79 final size:79
Alignment explanation
Indices: 11961--12183 Score: 294
Period size: 79 Copynumber: 2.8 Consensus size: 79
11951 GCTACTCGCT
* * *
11961 CAAATGCCTTCGGGACATAGCCCGGTTAGAGTAACTTGCACAATTGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCACAA-TGCCTTCGGGACTTAGCCCGG
12026 ATTTAGTAACTC--A
65 ATTTAGTAACTCGAA
*
12039 CACAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
1 CA-AATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTAGCAC-AATGCCTTCGGGACTTAGCCC
12103 GGATTTAGTAACTCGAA
63 GGATTTAGTAACTCGAA
* * *
12120 CAAATGCCTTCGGGACTT-GCCCGG-AACTAGTCACTAGCGCAGATGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTAGCACA-ATGCCTTCGGGACTTAGCCCG
12183 G
64 G
12184 TTATCATCCA
Statistics
Matches: 130, Mismatches: 7, Indels: 15
0.86 0.05 0.10
Matches are distributed among these distances:
78 3 0.02
79 104 0.80
80 20 0.15
81 3 0.02
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCACAATGCCTTCGGGACTTAGCCCGGA
TTTAGTAACTCGAA
Found at i:12166 original size:119 final size:119
Alignment explanation
Indices: 11954--12183 Score: 322
Period size: 119 Copynumber: 1.9 Consensus size: 119
11944 GGATATAGCT
* * * *
11954 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTAGAGTAACTTGCACAATTGCCTTCGGGACTT
1 ACTCGCACAAATGCCTTCGGGACATAGCCCGGTTAGAGTAACTCGAACAAATGCCTTCGGGACTT
**
12019 AGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
66 AGCCCGGAACTAGTAACTCACACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
12073 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGAACAAATGCCTTCGGGACT
1 ACTCGCACAAATGCCTTCGGGACATAGCCCGG-TTAGAGTAACTCGAACAAATGCCTTCGGGACT
* *
12137 T-GCCCGGAACTAGTCACT-AGCGCAGATGCCTTCGGGACTTAGCCCGG
65 TAGCCCGGAACTAGTAACTCA-CACA-ATGCCTTCGGGACTTAGCCCGG
12184 TTATCATCCA
Statistics
Matches: 98, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
117 1 0.01
118 17 0.17
119 78 0.80
120 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (119 bp):
ACTCGCACAAATGCCTTCGGGACATAGCCCGGTTAGAGTAACTCGAACAAATGCCTTCGGGACTT
AGCCCGGAACTAGTAACTCACACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Done.