Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3009
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: 24844
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:923 original size:16 final size:16
Alignment explanation
Indices: 902--934 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
892 TTTGTTTACC
902 TCACTAATTAACAAGA
1 TCACTAATTAACAAGA
918 TCACTAATTAACAAGA
1 TCACTAATTAACAAGA
934 T
1 T
935 GTATGTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.27
Consensus pattern (16 bp):
TCACTAATTAACAAGA
Found at i:3707 original size:31 final size:31
Alignment explanation
Indices: 3672--3741 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
3662 CTTGTCACTT
* * *
3672 GTAGCCGAAGCTATCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTATTCACTAATCAA
* * *
3703 GTAGCCGGAGCTACCATTTTTCACTAATCAA
1 GTAGCCGAAGCTACCACTATTCACTAATCAA
3734 GTAGCCGA
1 GTAGCCGA
3742 TGATCAGATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTATTCACTAATCAA
Found at i:3763 original size:46 final size:46
Alignment explanation
Indices: 3696--3787 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
3686 CACTATTCAC
* * *
3696 TGATCAGGTAGCCGGAGCTACCATTTTTCACTAATCAAGTAGCCGA
1 TGATCAGATAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGA
* * *
3742 TGATCAGATAGCCGAAGCTACCACTTTTCATTGATCAGGTAGCCGA
1 TGATCAGATAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGA
3788 AGTTACCACT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (46 bp):
TGATCAGATAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGA
Found at i:3785 original size:31 final size:31
Alignment explanation
Indices: 3742--3800 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3732 AAGTAGCCGA
3742 TGATCAGATAGCCGAAGCTACCACTTTTCAT
1 TGATCAGATAGCCGAAGCTACCACTTTTCAT
* *
3773 TGATCAGGTAGCCGAAGTTACCACTTTT
1 TGATCAGATAGCCGAAGCTACCACTTTT
3801 TACTTGCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (31 bp):
TGATCAGATAGCCGAAGCTACCACTTTTCAT
Found at i:3867 original size:50 final size:50
Alignment explanation
Indices: 3780--4106 Score: 546
Period size: 50 Copynumber: 6.5 Consensus size: 50
3770 CATTGATCAG
* * * * *
3780 GTAGCCGAAGTTACCACTTTTTACTTGCCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
*
3831 GTAGCTGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
3881 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCTTTGATCAAATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
3931 GTAGCCGAAACTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
3981 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
4031 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
4081 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
4107 GTTGCCATGG
Statistics
Matches: 261, Mismatches: 15, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
50 240 0.92
51 21 0.08
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:8659 original size:27 final size:28
Alignment explanation
Indices: 8595--8663 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 28
8585 GAATATCCAA
*
8595 CCCAAACACACCCGGAATATTATAAATCCT
1 CCCAAACACA-CCGG-ATATAATAAATCCT
*
8625 -CCATAACACACCGG-TATAATATATCCT
1 CCCA-AACACACCGGATATAATAAATCCT
8652 CCCAAACACACC
1 CCCAAACACACC
8664 AATAAGGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 19 0.54
28 3 0.09
29 7 0.20
30 6 0.17
ACGTcount: A:0.39, C:0.36, G:0.06, T:0.19
Consensus pattern (28 bp):
CCCAAACACACCGGATATAATAAATCCT
Found at i:9733 original size:12 final size:12
Alignment explanation
Indices: 9718--9748 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
9708 TTCTCTTTTA
9718 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
9730 TTTTTCTTTCTC
1 TTTTTCTTTCCC
9742 TTTTTCT
1 TTTTTCT
9749 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:20016 original size:29 final size:30
Alignment explanation
Indices: 19957--20014 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
19947 TCCGAGCCTT
*
19957 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
19987 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
20015 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:20244 original size:13 final size:13
Alignment explanation
Indices: 20226--20257 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
20216 TTTCCAGCAA
20226 TTATGAATTTATT
1 TTATGAATTTATT
20239 TTATGAATTTATT
1 TTATGAATTTATT
*
20252 TGATGA
1 TTATGA
20258 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:20465 original size:50 final size:50
Alignment explanation
Indices: 20352--20593 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
20342 ATTTGGGTAA
* * *
20352 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
20408 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
20458 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
20508 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
20558 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
20594 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:20541 original size:100 final size:103
Alignment explanation
Indices: 20352--20601 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
20342 ATTTGGGTAA
20352 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
20417 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
20458 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
20520 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
20558 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
20602 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:22417 original size:2 final size:2
Alignment explanation
Indices: 22410--22470 Score: 79
Period size: 2 Copynumber: 30.5 Consensus size: 2
22400 ATTAAGGGGG
* *
22410 CT CT CT CT CT CT CT CT CT CT -T CT CT CT CT CA AT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
22451 CT CT CT CGT CT CT CG CT CT C
1 CT CT CT C-T CT CT CT CT CT C
22471 GCCTTTTAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.94
3 2 0.04
ACGTcount: A:0.03, C:0.48, G:0.03, T:0.46
Consensus pattern (2 bp):
CT
Done.