Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1080
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: 28637
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Found at i:2650 original size:40 final size:40
Alignment explanation
Indices: 2556--2780 Score: 290
Period size: 40 Copynumber: 5.6 Consensus size: 40
2546 TATTCGAATG
* *
2556 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACT
* * * * *
2597 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
* *
2637 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* *
2677 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
2717 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
*
2757 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
2781 CTTGCGCAAG
Statistics
Matches: 159, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 129 0.81
41 29 0.18
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:2736 original size:80 final size:80
Alignment explanation
Indices: 2556--2816 Score: 303
Period size: 80 Copynumber: 3.3 Consensus size: 80
2546 TATTCGAATG
* * * *
2556 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAAGACCCGAAGGC
*
2621 ATTCGTGCGAGTTGCT
65 ATTCGTGCGAGTCGCT
* * * *
2637 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAAACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* *
2702 TTTGTGCTAG-CGACT
66 TTCGTGCGAGTCG-CT
* * * *
2717 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACCACATCCGGGCTAAGACCCGAAGGCC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* * * *
2782 TT-GCGCAAGTAGTT
66 TTCGTGCGAGTCGCT
*
2796 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
2817 ATTACTTGAG
Statistics
Matches: 154, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
78 14 0.09
79 13 0.08
80 95 0.62
81 32 0.21
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCGCT
Found at i:10803 original size:40 final size:40
Alignment explanation
Indices: 10709--10933 Score: 290
Period size: 40 Copynumber: 5.6 Consensus size: 40
10699 TATTCGAATG
* *
10709 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACT
* * * * *
10750 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
* *
10790 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* *
10830 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
10870 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
*
10910 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
10934 CTTGCGCAAG
Statistics
Matches: 159, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 129 0.81
41 29 0.18
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:10889 original size:80 final size:80
Alignment explanation
Indices: 10709--10969 Score: 303
Period size: 80 Copynumber: 3.3 Consensus size: 80
10699 TATTCGAATG
* * * *
10709 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAAGACCCGAAGGC
*
10774 ATTCGTGCGAGTTGCT
65 ATTCGTGCGAGTCGCT
* * * *
10790 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAAACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* *
10855 TTTGTGCTAG-CGACT
66 TTCGTGCGAGTCG-CT
* * * *
10870 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACCACATCCGGGCTAAGACCCGAAGGCC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* * * *
10935 TT-GCGCAAGTAGTT
66 TTCGTGCGAGTCGCT
*
10949 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
10970 ATTACTTGAG
Statistics
Matches: 154, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
78 14 0.09
79 13 0.08
80 95 0.62
81 32 0.21
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCGCT
Found at i:17600 original size:22 final size:22
Alignment explanation
Indices: 17570--17620 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
17560 TGTTAGGAGA
* *
17570 AAATAAGGGTATAAAATAAGAGG
1 AAAT-AGGGTAAAAAATAAAAGG
*
17593 GAATAGGGTAAAAAATAAAAGG
1 AAATAGGGTAAAAAATAAAAGG
17615 AAATAG
1 AAATAG
17621 ATGAAAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.16
Consensus pattern (22 bp):
AAATAGGGTAAAAAATAAAAGG
Found at i:23507 original size:1 final size:1
Alignment explanation
Indices: 23501--23537 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
23491 TTTATGTTAA
*
23501 TTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
23538 GATACTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Done.