Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2272
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: 24337
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1735 original size:40 final size:40
Alignment explanation
Indices: 1656--1831 Score: 232
Period size: 40 Copynumber: 4.5 Consensus size: 40
1646 CGGATGATAA
* * * *
1656 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * *
1696 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
1736 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1776 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
1816 CC-GGCTAA-ATCCGAAG
1 CCGGGCTAAGACCCGAAG
1832 ATACTTGGGT
Statistics
Matches: 119, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
38 7 0.06
39 8 0.07
40 102 0.86
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:1794 original size:80 final size:80
Alignment explanation
Indices: 1656--1831 Score: 259
Period size: 80 Copynumber: 2.2 Consensus size: 80
1646 CGGATGATAA
* * *
1656 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
1 CCGGGCTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
*
1721 TGCTAG-TGATTATAT
66 TGCGAGTTG-TTATAT
* * *
1736 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
1801 TGCGAGTTGTTATAT
66 TGCGAGTTGTTATAT
1816 CC-GGCTAA-ATCCGAAG
1 CCGGGCTAAGATCCGAAG
1832 ATACTTGGGT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
78 7 0.08
79 6 0.07
80 72 0.83
81 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
TGCGAGTTGTTATAT
Found at i:9664 original size:40 final size:40
Alignment explanation
Indices: 9609--9786 Score: 254
Period size: 40 Copynumber: 4.5 Consensus size: 40
9599 CGGATGATAA
* *
9609 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
9649 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
9689 CCGGGCTACGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
9729 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
9769 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
9787 TACTTGGGTT
Statistics
Matches: 127, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
39 17 0.13
40 109 0.86
41 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:14459 original size:29 final size:29
Alignment explanation
Indices: 14427--14487 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
14417 CACACGCCTG
* *
14427 TGTGGGTAGGCTATGTGGTCACAAGCCCA
1 TGTGGGTAGGCCATGTAGTCACAAGCCCA
* *
14456 TGTGGGTAGGCCATGTAGTCACACGGCCA
1 TGTGGGTAGGCCATGTAGTCACAAGCCCA
14485 TGT
1 TGT
14488 CCCTAACCCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.20, C:0.21, G:0.34, T:0.25
Consensus pattern (29 bp):
TGTGGGTAGGCCATGTAGTCACAAGCCCA
Found at i:16474 original size:49 final size:48
Alignment explanation
Indices: 16401--16588 Score: 232
Period size: 49 Copynumber: 3.8 Consensus size: 48
16391 TAGCTGAAGC
*
16401 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
* * *
16449 TAATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACAG
1 T-ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAA
* * * *
16500 TTTTTAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTAA
1 TATCT-GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
** *
16549 TTATCCAGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 -TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
16589 CGTGACCTCA
Statistics
Matches: 118, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
48 1 0.01
49 72 0.61
50 6 0.05
51 39 0.33
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (48 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
Found at i:16520 original size:100 final size:100
Alignment explanation
Indices: 16406--16593 Score: 331
Period size: 100 Copynumber: 1.9 Consensus size: 100
16396 GAAGCTATCT
**
16406 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACATAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACATAGTAGCC
16471 TGCACTTAGTACTACACACGTGATCACAGTTTTTA
66 TGCACTTAGTACTACACACGTGATCACAGTTTTTA
* * *
16506 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTAATTATCCAGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACATAGTAGCC
16571 TGCACTTAGTACTACACACGTGA
66 TGCACTTAGTACTACACACGTGA
16594 CCTCACAATA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 83 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACATAGTAGCC
TGCACTTAGTACTACACACGTGATCACAGTTTTTA
Found at i:18752 original size:43 final size:42
Alignment explanation
Indices: 18690--18811 Score: 154
Period size: 43 Copynumber: 2.9 Consensus size: 42
18680 TACCATACCA
* ****
18690 ATGCCATATCCAAGATATGGTCTTACATGGGATCTCATATAG
1 ATGCCATATCCCAGATATGGTCTTACACAAAATCTCATATAG
* *
18732 ATGCCATTATCCCAGCTATGGTCTTACACAAAATCTCATATCG
1 ATGCCA-TATCCCAGATATGGTCTTACACAAAATCTCATATAG
**
18775 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACACAAAATCTCA
18812 ACTAACCCTA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
42 34 0.49
43 35 0.51
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACAAAATCTCATATAG
Done.