Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2786
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: 45038
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Found at i:533 original size:38 final size:38
Alignment explanation
Indices: 469--602 Score: 148
Period size: 38 Copynumber: 3.5 Consensus size: 38
459 TTACGAAGTC
469 CGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAT
1 CGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATAT
*
507 CGGGCTAAGTCCCGAAGGCATGGTGCGAGTTACTATAT
1 CGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATAT
* *
545 CCGGGGGC-ATGTCCCGAAGGCATTGAGCGAG-TAGCTATAT
1 -C--GGGCTAAGTCCCGAAGGCATTGTGCGAGTTA-CTATAT
* * *
585 CAGGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
603 TTACTTGCTT
Statistics
Matches: 82, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
37 2 0.02
38 37 0.45
39 13 0.16
40 26 0.32
41 4 0.05
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (38 bp):
CGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATAT
Found at i:8566 original size:40 final size:40
Alignment explanation
Indices: 8471--8688 Score: 293
Period size: 40 Copynumber: 5.5 Consensus size: 40
8461 TGGATGATAA
*
8471 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
* *
8512 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
8552 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
8592 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
8632 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
8671 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
8689 TACTTGGCTT
Statistics
Matches: 162, Mismatches: 12, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
38 15 0.09
39 15 0.09
40 104 0.64
41 24 0.15
42 4 0.02
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:13686 original size:40 final size:40
Alignment explanation
Indices: 13619--13795 Score: 225
Period size: 40 Copynumber: 4.5 Consensus size: 40
13609 ACCCAAGTAT
*
13619 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
13658 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * * *
13698 CTTCGGGTCTTAGCCCGGATATAATC-ATTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
13738 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
13778 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
13796 TTATCATCCG
Statistics
Matches: 118, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 102 0.86
41 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:17365 original size:40 final size:40
Alignment explanation
Indices: 17221--17556 Score: 434
Period size: 40 Copynumber: 8.5 Consensus size: 40
17211 CGGATGATAA
* * * *
17221 CCGGGCTAAGTCTCAAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* * *
17261 CTGGGCTAAG-CCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
17300 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
17339 CCGGGGTAAGTACCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
17379 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
*
17420 -CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
17459 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
17499 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
17539 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
17557 TACTTGGTTT
Statistics
Matches: 271, Mismatches: 20, Indels: 11
0.90 0.07 0.04
Matches are distributed among these distances:
39 87 0.32
40 183 0.68
41 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:22587 original size:47 final size:48
Alignment explanation
Indices: 22518--22634 Score: 132
Period size: 48 Copynumber: 2.5 Consensus size: 48
22508 GTTGCTACAG
* **
22518 TGTGCCTATGTAAGACCATGTCTAGGA-ATGGCATCGGGGATGATATT
1 TGTGCCTATGTAAGACCATGTCTAGGACATGCCATCGACGATGATATT
* *
22565 TGTGCC-AGTGTAAGACCATGTCTGGGACATGCCATCGACGATGATATG
1 TGTGCCTA-TGTAAGACCATGTCTAGGACATGCCATCGACGATGATATT
**
22613 TG-GATTCATGTAAGACCATGTC
1 TGTGCCT-ATGTAAGACCATGTC
22635 GGGGAAATGG
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
46 1 0.02
47 25 0.42
48 32 0.54
49 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (48 bp):
TGTGCCTATGTAAGACCATGTCTAGGACATGCCATCGACGATGATATT
Found at i:24192 original size:22 final size:22
Alignment explanation
Indices: 24167--24216 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
24157 CACGCAGGGT
* *
24167 CACACGGGCGTGTCCTTTGGAC
1 CACACGGGAGTGTCCTTCGGAC
24189 CACACGGGAGTGTCCTTCGGAC
1 CACACGGGAGTGTCCTTCGGAC
24211 CACACG
1 CACACG
24217 AGCGCGTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.34, G:0.30, T:0.18
Consensus pattern (22 bp):
CACACGGGAGTGTCCTTCGGAC
Found at i:26718 original size:16 final size:17
Alignment explanation
Indices: 26687--26720 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
26677 TGGTAAATTT
26687 ACATTTAATTATGTTATA
1 ACATTTAA-TATGTTATA
26705 ACATTTAA-ATGTTATA
1 ACATTTAATATGTTATA
26721 TGCATGGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (17 bp):
ACATTTAATATGTTATA
Found at i:29664 original size:43 final size:43
Alignment explanation
Indices: 29594--29697 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 43
29584 AATTTGGGGT
* * * *
29594 CACACGGCCAAGTCACACGCCCGTGTCCTGGGGCCGTGTCCTA
1 CACACGGCCAAGTCACACACCCATGTCCCGGGGCCATGTCCTA
29637 CACACGGCCAAGTCACACACCCATGTCCCGGGGCCATGTCCTA
1 CACACGGCCAAGTCACACACCCATGTCCCGGGGCCATGTCCTA
* * *
29680 CACATGGCAAAGACACAC
1 CACACGGCCAAGTCACAC
29698 GGCCGTGTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.24, C:0.39, G:0.23, T:0.13
Consensus pattern (43 bp):
CACACGGCCAAGTCACACACCCATGTCCCGGGGCCATGTCCTA
Found at i:32360 original size:54 final size:54
Alignment explanation
Indices: 32179--32470 Score: 293
Period size: 55 Copynumber: 5.4 Consensus size: 54
32169 TTAGGGTTTC
* *
32179 AGGATACCAAGTAAGACCATGGAAAGGCATGGCATTGGTAAGTTCTATAAGGCA
1 AGGATACCATGTAAGACCATGCAAAGGCATGGCATTGGTAAGTTCTATAAGGCA
* * * * * * *
32233 AGGAAATCATGTAAGACCATGTCAAA-ACATGGCATTGATAAACTACTATAAAGCA
1 AGGATACCATGTAAGACCATG-CAAAGGCATGGCATTGGT-AAGTTCTATAAGGCA
* * *
32288 AAGATCCCATGTAAGACCATGGAAAGGCATGGCATTGGTAAGTTCTATAAGGCA
1 AGGATACCATGTAAGACCATGCAAAGGCATGGCATTGGTAAGTTCTATAAGGCA
* * * * * * *
32342 AGGAAATCATGTAAGACCATGTCAAA-ACATGGCATTGATAAACTACTATAAAGCA
1 AGGATACCATGTAAGACCATG-CAAAGGCATGGCATTGGT-AAGTTCTATAAGGCA
* * * * * *
32397 AAGATCCCATGTAAGACCATGCCAAGGCTTGGCAATGGTGAGTTC-ATAAGGCA
1 AGGATACCATGTAAGACCATGCAAAGGCATGGCATTGGTAAGTTCTATAAGGCA
*
32450 AGGATACCACGTAAGACCATG
1 AGGATACCATGTAAGACCATG
32471 TCAAGACATG
Statistics
Matches: 187, Mismatches: 45, Indels: 13
0.76 0.18 0.05
Matches are distributed among these distances:
53 25 0.13
54 78 0.42
55 84 0.45
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (54 bp):
AGGATACCATGTAAGACCATGCAAAGGCATGGCATTGGTAAGTTCTATAAGGCA
Found at i:32380 original size:109 final size:109
Alignment explanation
Indices: 32189--32480 Score: 496
Period size: 109 Copynumber: 2.7 Consensus size: 109
32179 AGGATACCAA
32189 GTAAGACCATGGAAAGGCATGGCATTGGTAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATG
1 GTAAGACCATGGAAAGGCATGGCATTGGTAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATG
32254 TCAAAACATGGCATTGATAAACTACTATAAAGCAAAGATCCCAT
66 TCAAAACATGGCATTGATAAACTACTATAAAGCAAAGATCCCAT
32298 GTAAGACCATGGAAAGGCATGGCATTGGTAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATG
1 GTAAGACCATGGAAAGGCATGGCATTGGTAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATG
32363 TCAAAACATGGCATTGATAAACTACTATAAAGCAAAGATCCCAT
66 TCAAAACATGGCATTGATAAACTACTATAAAGCAAAGATCCCAT
** * * * * * *
32407 GTAAGACCATGCCAAGGCTTGGCAATGGTGAGTTC-ATAAGGCAAGGATACCACGTAAGACCATG
1 GTAAGACCATGGAAAGGCATGGCATTGGTAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATG
*
32471 TCAAGACATG
66 TCAAAACATG
32481 ACAATGGTAA
Statistics
Matches: 174, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
108 35 0.20
109 139 0.80
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (109 bp):
GTAAGACCATGGAAAGGCATGGCATTGGTAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATG
TCAAAACATGGCATTGATAAACTACTATAAAGCAAAGATCCCAT
Done.