Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3660
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: 40627
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1432 original size:11 final size:11
Alignment explanation
Indices: 1416--1456 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
1406 AATAGGTTGG
1416 TGAAAAAAATT
1 TGAAAAAAATT
1427 TGAAAAAAA-T
1 TGAAAAAAATT
**
1437 CAAAAAAAATT
1 TGAAAAAAATT
1448 TGAAAAAAA
1 TGAAAAAAA
1457 ATTCAAGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (11 bp):
TGAAAAAAATT
Found at i:7585 original size:27 final size:28
Alignment explanation
Indices: 7555--7616 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
7545 GATTGAGAGT
* * *
7555 GAAAAAGAAATT-GAAGAAGAAAGAAGA
1 GAAAAAGAAATTAGAAAAAGAAACAAAA
*
7582 GAAAATG-AATTAGAAAAAGAAACAAAA
1 GAAAAAGAAATTAGAAAAAGAAACAAAA
7609 GAAAAAGA
1 GAAAAAGA
7617 CGTGGAAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.69, C:0.02, G:0.21, T:0.08
Consensus pattern (28 bp):
GAAAAAGAAATTAGAAAAAGAAACAAAA
Found at i:18272 original size:23 final size:22
Alignment explanation
Indices: 18220--18272 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
18210 TCCACGTCTT
*
18220 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
18242 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
18265 TTTCTTTT
1 TTTCTTTT
18273 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:20610 original size:4 final size:4
Alignment explanation
Indices: 20601--20631 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
20591 TTAAACTAAG
20601 TAAA TAAA TAAA TAAA TAAA TAAA -AAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
20632 AATAAAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:23961 original size:20 final size:20
Alignment explanation
Indices: 23938--23991 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
23928 AACTAAGAAG
23938 GAGCTGAATGAGCTAAGGA-T
1 GAGCTGAATGAGCT-AGGATT
* *
23958 GAGCTCAATGAGCTATGATT
1 GAGCTGAATGAGCTAGGATT
*
23978 GACCTGAATGAGCT
1 GAGCTGAATGAGCT
23992 TGAAGTAGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (20 bp):
GAGCTGAATGAGCTAGGATT
Found at i:29324 original size:19 final size:19
Alignment explanation
Indices: 29300--29336 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
29290 ACTAGCCAAT
29300 GACAACTCAAGAGTCATTG
1 GACAACTCAAGAGTCATTG
29319 GACAACTCAAGAGTCATT
1 GACAACTCAAGAGTCATT
29337 TTCTAAGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (19 bp):
GACAACTCAAGAGTCATTG
Found at i:31785 original size:24 final size:24
Alignment explanation
Indices: 31758--31807 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
31748 TTAAAACTAC
31758 TTCTAAG-GAAAACTCAAGAGAGAA
1 TTCTAAGAGAAAACTCAA-AGAGAA
*
31782 TTCTTAGAGAAAACTCAAAGAGAA
1 TTCTAAGAGAAAACTCAAAGAGAA
31806 TT
1 TT
31808 TTCACTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (24 bp):
TTCTAAGAGAAAACTCAAAGAGAA
Found at i:37030 original size:8 final size:8
Alignment explanation
Indices: 37008--37040 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
36998 TATATGTAGG
37008 TATAATAA
1 TATAATAA
37016 TAT-ATAA
1 TATAATAA
37023 TATAATAA
1 TATAATAA
*
37031 TAAAATAA
1 TATAATAA
37039 TA
1 TA
37041 ATAACAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TATAATAA
Found at i:37037 original size:23 final size:23
Alignment explanation
Indices: 37011--37060 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
37001 ATGTAGGTAT
* *
37011 AATAATATATAATATAA-TAATAA
1 AATAATA-ATAACAAAATTAATAA
37034 AATAATAATAACAAAATTAATAA
1 AATAATAATAACAAAATTAATAA
37057 AATA
1 AATA
37061 GACTAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
AATAATAATAACAAAATTAATAA
Found at i:37527 original size:21 final size:21
Alignment explanation
Indices: 37501--37576 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
37491 AATCATATCT
37501 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
**
37522 TCTAAGATTACATATATCATA
1 TCTAAGATTGTATATATCATA
* *
37543 TCTAGGATTG--CATATCATA
1 TCTAAGATTGTATATATCATA
37562 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
37577 CCTCGAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 17 0.37
21 29 0.63
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.41
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:37536 original size:19 final size:20
Alignment explanation
Indices: 37480--37570 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 20
37470 ATTAAATCTT
*
37480 TAAGATTACAAAATCATATCTTC
1 TAAGATTACAATATCATA---TC
**
37503 TAAGATTGTATATATCATATC
1 TAAGATTACA-ATATCATATC
37524 TAAGATTACATATATCATATC
1 TAAGATTACA-ATATCATATC
* *
37545 TAGGATTGC-ATATCATATC
1 TAAGATTACAATATCATATC
37564 TAAGATT
1 TAAGATT
37571 GTATATCCTC
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 16 0.27
21 28 0.47
23 8 0.14
24 7 0.12
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (20 bp):
TAAGATTACAATATCATATC
Found at i:37571 original size:19 final size:19
Alignment explanation
Indices: 37514--37577 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
37504 AAGATTGTAT
*
37514 ATATCATATCTAAGATTAC
1 ATATCATATCTAAGATTGC
*
37533 ATATATCATATCTAGGATTGC
1 --ATATCATATCTAAGATTGC
*
37554 ATATCATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
37573 ATATC
1 ATATC
37578 CTCGAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 22 0.56
21 17 0.44
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:38043 original size:132 final size:132
Alignment explanation
Indices: 37862--38389 Score: 903
Period size: 132 Copynumber: 4.0 Consensus size: 132
37852 GACGATAAGA
* * *
37862 CTTGCTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
* *
37927 CCCTACTGCTTAGGGATATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
37992 GG
131 GG
* * *
37994 CTTGGTGGCTTAAATCTGCTTCCCGCTATCTTCGAAAGATAAGATTTGCCGTCTTTGATCTGCTT
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
* *
38059 CACTACTGCTTAGGGATATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGACACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
38124 GG
131 GG
*
38126 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
* *
38191 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTAATCCGCTGCTGCTCATGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
38256 GG
131 GG
* *
38258 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGTTT
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
* *
38323 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGTTGCTACTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
38388 GG
131 GG
38390 TGATGTGACC
Statistics
Matches: 373, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 373 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (132 bp):
CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
GG
Found at i:38210 original size:44 final size:44
Alignment explanation
Indices: 38030--38346 Score: 106
Period size: 44 Copynumber: 7.2 Consensus size: 44
38020 TATCTTCGAA
* * *
38030 AGATAAGATTTGCCGTCTTTGATCTGCTTCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * * * *
38074 ATATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** **** * *
38118 ACACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCATCTTTAATCTGC-T-CCACTACTGCTTAGG-G
*
38162 AGATAAGATTTGCCATCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * ** * * * *
38206 AGATAAGATCTACAATCTTCAACCTAATCCGCTGCTGCTCATGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* ** **** * *
38250 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCATCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * * *
38294 AGATAAGATTTGCCGTCTTTGATCTGTTTCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
38338 AGATAAGAT
1 AGATAAGAT
38347 CTACAATCTT
Statistics
Matches: 179, Mismatches: 82, Indels: 24
0.63 0.29 0.08
Matches are distributed among these distances:
42 11 0.06
43 7 0.04
44 145 0.81
45 8 0.04
46 8 0.04
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (44 bp):
AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
Done.