Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3496
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: 18389
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Found at i:2350 original size:44 final size:44
Alignment explanation
Indices: 2292--2439 Score: 146
Period size: 43 Copynumber: 3.4 Consensus size: 44
2282 AATCTGATAT
*
2292 TCGGGCCTC-GGCCTAGCAAGCTT-TAA-GCTGGTGA-ATAATATTA
1 TCGGGCTTCGGGCCTAGCAAGCTTATAATGCTGGTGAGAT-A-A-TA
*
2335 TCGGGCTTCGGGCCTAGC-AGGTTATAATGCTGGTGAGATAATA
1 TCGGGCTTCGGGCCTAGCAAGCTTATAATGCTGGTGAGATAATA
* ** * *
2378 TCGGGCTTCGGGCCTAGCAGGC-TATAATGCCAGTGAAATGATA
1 TCGGGCTTCGGGCCTAGCAAGCTTATAATGCTGGTGAGATAATA
**
2421 TCGGGCTTCAAGCCTAGCA
1 TCGGGCTTCGGGCCTAGCA
2440 GGTGAAATGC
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
43 66 0.73
44 13 0.14
45 9 0.10
46 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (44 bp):
TCGGGCTTCGGGCCTAGCAAGCTTATAATGCTGGTGAGATAATA
Found at i:2380 original size:43 final size:42
Alignment explanation
Indices: 2328--2457 Score: 163
Period size: 43 Copynumber: 3.1 Consensus size: 42
2318 GCTGGTGAAT
* *
2328 AATATTATCGGGCTTCGGGCCTAGCAGGTTATAATGCTGGTG
1 AATAATATCGGGCTTCGGGCCTAGCAGGTTATAATGCCGGTG
* *
2370 AGATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGTG
1 A-ATAATATCGGGCTTCGGGCCTAGCAGGTTATAATGCCGGTG
* ** *
2413 AAATGATATCGGGCTTCAAGCCTAGCAGGTGA-AATGCCGGTG
1 -AATAATATCGGGCTTCGGGCCTAGCAGGTTATAATGCCGGTG
2455 AAT
1 AAT
2458 GAGTTCAGAC
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
41 3 0.04
42 10 0.13
43 62 0.82
44 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.25
Consensus pattern (42 bp):
AATAATATCGGGCTTCGGGCCTAGCAGGTTATAATGCCGGTG
Found at i:7708 original size:50 final size:53
Alignment explanation
Indices: 7645--7752 Score: 163
Period size: 52 Copynumber: 2.1 Consensus size: 53
7635 CAAGGGATGA
7645 GGCAAACTGTCATG-AA-ATGTTGTGTTAATGGAA-AAT-AAATAAG-AGCATG
1 GGCAAACTGTCATGAAACATGTTGTG-TAATGGAAGAATAAAATAAGAAGCATG
7694 GGCAAACATGTCATGAAACATGTTGTGTAATGGAAGAATAAAATAAGAAGCATG
1 GGCAAAC-TGTCATGAAACATGTTGTGTAATGGAAGAATAAAATAAGAAGCATG
7748 GGCAA
1 GGCAA
7753 TAAACTAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
49 7 0.13
50 7 0.13
51 10 0.19
52 11 0.21
53 7 0.13
54 11 0.21
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (53 bp):
GGCAAACTGTCATGAAACATGTTGTGTAATGGAAGAATAAAATAAGAAGCATG
Found at i:9086 original size:40 final size:39
Alignment explanation
Indices: 8998--9179 Score: 185
Period size: 40 Copynumber: 4.6 Consensus size: 39
8988 TTGAATGATG
* * *
8998 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
9036 AT-CGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAT
*
9076 TCCGGGCTAAG-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAT
*
9114 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAT
* * *
9153 AACCGGGCTATGACCCGAAGGCATTTG
1 -TCCGGGCTAAG-TCCGAAGGCATTTG
9180 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
38 43 0.36
39 16 0.13
40 62 0.51
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:9131 original size:78 final size:78
Alignment explanation
Indices: 8998--9179 Score: 201
Period size: 78 Copynumber: 2.3 Consensus size: 78
8988 TTGAATGATG
*
8998 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATATCGGACTAAGATCCGAAGGCATTTG
1 TCCGGGCTAAG-CCGAAGGCATTTGTGCTAAGTGACCAAATCGGACTAAGATCCGAAGGCATTTG
9062 TGCGAGATACTA-A
65 TGCGAGATACTATA
* * * **
9075 TTCCGGGCTAAGCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 -TCCGGGCTAAGCCGAAGGCATTTGTGCTAAGTGACCAAAT-CGGACTAAGAT-CCGAAGGCATT
*
9138 TGTGCGAGTTACTATA
63 TGTGCGAGATACTATA
* *
9154 ACCGGGCTATGACCCGAAGGCATTTG
1 TCCGGGCTA--AGCCGAAGGCATTTG
9180 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
77 17 0.19
78 57 0.64
79 1 0.01
80 14 0.16
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGCTAAGCCGAAGGCATTTGTGCTAAGTGACCAAATCGGACTAAGATCCGAAGGCATTTGT
GCGAGATACTATA
Found at i:14906 original size:55 final size:55
Alignment explanation
Indices: 14830--14939 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
14820 AAAGATGGGC
14830 AACATGTCATGAAACATGTTGTGTT-ATGGAAAAATAAAATAAGAAGCATGGGCAA
1 AACATGTCATGAAACATGTTGTGTTAATGGAAAAAT-AAATAAGAAGCATGGGCAA
*
14885 AACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAATAAGAAGCATGGGCAA
1 AACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAATAAGAAGCATGGGCAA
14940 TAAACTAATA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
55 44 0.83
56 9 0.17
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.24
Consensus pattern (55 bp):
AACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAATAAGAAGCATGGGCAA
Found at i:16427 original size:38 final size:38
Alignment explanation
Indices: 16329--16509 Score: 195
Period size: 38 Copynumber: 4.7 Consensus size: 38
16319 TCGAATGATG
* * *
16329 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTA-A
* * *
16369 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA
*
16408 TTCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTAC-AA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
*
16445 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-A
* * *
16485 ACCGGGCTATGACCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTTG
16510 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
37 11 0.09
38 46 0.38
39 24 0.20
40 32 0.27
41 7 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:16467 original size:76 final size:80
Alignment explanation
Indices: 16330--16509 Score: 219
Period size: 76 Copynumber: 2.3 Consensus size: 80
16320 CGAATGATGT
16330 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAG-CCCGAAGGCATTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
*
16394 GTGCGAGATACTA-AT
65 GTGCGAGATACTATAA
* * * **
16409 TCGGGCTAAGCCCGAAGGCATTTGTGC-GAGTTA-CA-ATCCGGGTTAAG-TCCCGAAGGCATTT
1 CCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTT
*
16470 GTGCGAGTTACTATAA
65 GTGCGAGATACTATAA
* *
16486 CCGGGCTATGACCGAAGGCATTTG
1 CCGGGCTAAGCCCGAAGGCATTTG
16510 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
75 1 0.01
76 34 0.39
77 24 0.27
78 13 0.15
79 16 0.18
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTG
TGCGAGATACTATAA
Found at i:16538 original size:76 final size:75
Alignment explanation
Indices: 16380--16540 Score: 184
Period size: 77 Copynumber: 2.1 Consensus size: 75
16370 CCGGACTAAG
** * **
16380 ATCCGAAGGCATTTGTGCGAGATACTAATTCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACAA
1 ATCCGAAGGCATTTGTGCGAGATACTAAACCGGGCTAAGACCGAAGGCATTTGAACGAGTTACAA
16445 TCCGGGTTAA
66 TCCGGGTTAA
* * *
16455 GTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGACCGAAGGCATTTGAACGAG-TAG
1 AT-CCGAAGGCATTTGTGCGAGATACTA-AACCGGGCTAAGACCGAAGGCATTTGAACGAGTTA-
16519 CTATAT-C-GGTTAA
63 C-A-ATCCGGGTTAA
16532 ATCCGAAGG
1 ATCCGAAGG
16541 TACGTGATTT
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
75 1 0.01
76 33 0.46
77 34 0.47
78 2 0.03
79 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (75 bp):
ATCCGAAGGCATTTGTGCGAGATACTAAACCGGGCTAAGACCGAAGGCATTTGAACGAGTTACAA
TCCGGGTTAA
Done.