Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2495
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: 23109
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Found at i:577 original size:39 final size:38
Alignment explanation
Indices: 454--587 Score: 159
Period size: 39 Copynumber: 3.6 Consensus size: 38
444 TGATGTTTAT
*
454 CGGACTT-A-GTCCACAGGCTATGTGCTGGAATTATATC
1 CGGACTTAAGGTCCGCAGGCTATGTGCT-GAATTATATC
* *
491 AGGACTTAGGGTCCGCA-GCTATGTGCTGAA-TATATC
1 CGGACTTAAGGTCCGCAGGCTATGTGCTGAATTATATC
* * *
527 CGAACTTAAGGTCCGCAGGCTATGTACTAGAATTATAAC
1 CGGACTTAAGGTCCGCAGGCTATGTGCT-GAATTATATC
*
566 CGGACTTAAGGTCTGCAGGCTA
1 CGGACTTAAGGTCCGCAGGCTA
588 CTGCTAGAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
36 20 0.24
37 18 0.22
38 13 0.16
39 31 0.38
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (38 bp):
CGGACTTAAGGTCCGCAGGCTATGTGCTGAATTATATC
Found at i:3348 original size:26 final size:26
Alignment explanation
Indices: 3319--3369 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
3309 CCAACACACC
* *
3319 AATATCGTAGCAAAGATGCCAGTAAT
1 AATATCGCAGCAAAGATACCAGTAAT
*
3345 AATATCGCAGCAAAGCTACCAGTAA
1 AATATCGCAGCAAAGATACCAGTAA
3370 CAGTAATGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.20
Consensus pattern (26 bp):
AATATCGCAGCAAAGATACCAGTAAT
Found at i:11262 original size:47 final size:48
Alignment explanation
Indices: 11193--11569 Score: 311
Period size: 47 Copynumber: 8.0 Consensus size: 48
11183 CATGACATTG
*
11193 GTTGATATGTGTGCCAGTGTAAGAACATGTCTGGGACATGG-ATCGGA
1 GTTGATATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGA
* * *
11240 GTTGATATGTGTGCTAGTGTAAGACCATGTCTGGGGCATGGCATCGGC
1 GTTGATATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGA
* * * * *
11288 G--CATTATGAGAGCCAGTGTAAGACCATCT-TAGGACATGGCAT-GG-
1 GTTGA-TATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGA
*** * * *
11332 GCCACATTATGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATC--A
1 G-TTGA-TATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGA
* *
11380 GTAATGATATGTGTGCTAGTGTAAAGACCATGTTTGGGACATGGCATCGGCCA
1 GT--TGATATGTGTGCCAGTGT-AAGACCATGTCTGGGACATGGCATCGG--A
* * *
11433 CATT-ATA---G-GCCAGTGTAAGACCATGTCTGTGACATGGCATCAGA
1 -GTTGATATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGA
* * * *
11477 GTTAATATGTGTGCTAGTATAAGACCATGTCT-GGACATGGCATTGGCA
1 GTTGATATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-A
*
11525 -TTGATATGTGTGCTAGTGT-AGACCATGTCTAGGG-CATGGCATCGG
1 GTTGATATGTGTGCCAGTGTAAGACCATGTCT-GGGACATGGCATCGG
11570 TAATTGACGC
Statistics
Matches: 272, Mismatches: 34, Indels: 48
0.77 0.10 0.14
Matches are distributed among these distances:
43 2 0.01
44 5 0.02
45 2 0.01
46 47 0.17
47 132 0.49
48 54 0.20
49 24 0.09
51 3 0.01
52 1 0.00
53 1 0.00
54 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (48 bp):
GTTGATATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGA
Found at i:11449 original size:142 final size:139
Alignment explanation
Indices: 11205--11569 Score: 404
Period size: 142 Copynumber: 2.6 Consensus size: 139
11195 TGATATGTGT
*
11205 GCCAGTGTAAGAACATGTCTGGGACATGG-ATCGGAGT-TGATATGTGTGCTAGTGTAAGACCAT
1 GCCAGTGTAAGACCATGTCT-GGACATGGCATC--AGTATGATATGTGTGCTAGTGTAAGACCAT
* *
11268 GTCTGGGGCATGGCATCGGCGCATTATGAGAGCCAGTGTAAGACCATCT-TAG-GACATGGCAT-
63 GT-TTGGGCATGGCATCGGCACATTATGAGAGCCAGTGTAAGACCATCTCT-GTGACATGGCATA
*
11330 GGGCCACATTATGAGA
126 GAGCCA-A-TATGAGA
11346 GCCAGTGTAAGACCATGTCTAGGACATGGCATCAGTAATGATATGTGTGCTAGTGTAAAGACCAT
1 GCCAGTGTAAGACCATGTCT-GGACATGGCATCAGT-ATGATATGTGTGCTAGTGT-AAGACCAT
*
11411 GTTTGGGACATGGCATCGGCCACATTAT-AG-GCCAGTGTAAGACCATGTCTGTGACATGGCATC
63 GTTTGGG-CATGGCATCGG-CACATTATGAGAGCCAGTGTAAGACCATCTCTGTGACATGGCAT-
** * *
11474 AGAGTTAATATGTGT
125 AGAGCCAATATGAGA
* * ** *
11489 GCTAGTATAAGACCATGTCTGGACATGGCATTGGCATTGATATGTGTGCTAGTGT-AGACCATGT
1 GCCAGTGTAAGACCATGTCTGGACATGGCATCAGTA-TGATATGTGTGCTAGTGTAAGACCATGT
*
11553 CTAGGGCATGGCATCGG
65 -TTGGGCATGGCATCGG
11570 TAATTGACGC
Statistics
Matches: 196, Mismatches: 16, Indels: 25
0.83 0.07 0.11
Matches are distributed among these distances:
140 23 0.12
141 32 0.16
142 73 0.37
143 57 0.29
144 8 0.04
145 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (139 bp):
GCCAGTGTAAGACCATGTCTGGACATGGCATCAGTATGATATGTGTGCTAGTGTAAGACCATGTT
TGGGCATGGCATCGGCACATTATGAGAGCCAGTGTAAGACCATCTCTGTGACATGGCATAGAGCC
AATATGAGA
Found at i:11459 original size:95 final size:95
Alignment explanation
Indices: 11255--11519 Score: 317
Period size: 95 Copynumber: 2.8 Consensus size: 95
11245 TATGTGTGCT
* * * * * * * *
11255 AGTGTAAGACCATGTCTGGGGCATGGCATCGGCGCAT--TATGAGAGCCAGTGTAAGACCATCTT
1 AGTGTAAGACCATGTCTGTGACATGGCATCAGAG-ATAATATGTGTGCTAGTGTAAGACCATGTT
* *
11318 AGGACATGGCATGGGCCACATTATGAGAGCC
65 TGGACATGGCATCGGCCACATTATGAGAGCC
*
11349 AGTGTAAGACCATGTCTAG-GACATGGCATCAGTA-ATGATATGTGTGCTAGTGTAAAGACCATG
1 AGTGTAAGACCATGTCT-GTGACATGGCATCAG-AGATAATATGTGTGCTAGTGT-AAGACCATG
11412 TTTGGGACATGGCATCGGCCACATTAT-AG-GCC
63 TTT-GGACATGGCATCGGCCACATTATGAGAGCC
* * *
11444 AGTGTAAGACCATGTCTGTGACATGGCATCAGAGTTAATATGTGTGCTAGTATAAGACCATGTCT
1 AGTGTAAGACCATGTCTGTGACATGGCATCAGAGATAATATGTGTGCTAGTGTAAGACCATGTTT
11509 GGACATGGCAT
66 GGACATGGCAT
11520 TGGCATTGAT
Statistics
Matches: 150, Mismatches: 13, Indels: 17
0.83 0.07 0.09
Matches are distributed among these distances:
93 13 0.09
94 41 0.27
95 62 0.41
96 12 0.08
97 22 0.15
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (95 bp):
AGTGTAAGACCATGTCTGTGACATGGCATCAGAGATAATATGTGTGCTAGTGTAAGACCATGTTT
GGACATGGCATCGGCCACATTATGAGAGCC
Found at i:12921 original size:39 final size:37
Alignment explanation
Indices: 12878--13091 Score: 148
Period size: 39 Copynumber: 5.5 Consensus size: 37
12868 AAATCACGTA
* *
12878 CCTTCGGAATTTAACCGGATATAGCT-ACTCGTTCAAATG
1 CCTTCGGGACTTAACCGGATATAG-TAACTCG--CAAATG
* * *
12917 CCTTCGGGACATAGCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCGGATATAGTAACTCG--CAAATG
*
12956 CCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATG
1 CCTTCGGGACTTAA-CCGGATATAGTAACTCGCA-AATG
* *
12995 CCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAATG
1 CCTTCGGGACTTA-ACCGGATA-TAGTAACTCGCA-AATG
* * * * *
13033 CCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAAG
1 CCTTCGGGA-CTTA-ACCGGATATAGTAAC-TCGCA-AATG
*
13073 CCTTCGGGACTTAGCCGGA
1 CCTTCGGGACTTAACCGGA
13092 CATCATTCAA
Statistics
Matches: 144, Mismatches: 21, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
37 2 0.01
38 33 0.23
39 73 0.51
40 33 0.23
41 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (37 bp):
CCTTCGGGACTTAACCGGATATAGTAACTCGCAAATG
Found at i:13026 original size:38 final size:39
Alignment explanation
Indices: 12913--13088 Score: 198
Period size: 39 Copynumber: 4.5 Consensus size: 39
12903 TACTCGTTCA
*
12913 AATGCCTTCGGGACATAG-CCGG-TTATAGTAACTCGCAC
1 AATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCAC
*
12951 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
* *
12991 AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCAC
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
* * * * *
13029 AATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC
1 AATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCAC
*
13069 AAAGCCTTCGGGACTTAGCC
1 AATGCCTTCGGGACTTAGCC
13089 GGACATCATT
Statistics
Matches: 117, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
37 2 0.02
38 32 0.27
39 42 0.36
40 36 0.31
41 5 0.04
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
Found at i:21526 original size:46 final size:47
Alignment explanation
Indices: 21436--21552 Score: 148
Period size: 46 Copynumber: 2.5 Consensus size: 47
21426 TGTGTGCTTG
* * * *
21436 TGTAAGACCATGTCTGGGACATGGCATCGGCCATATTATGGAGCCAA
1 TGTAAGACCATGTCTAGGACATGGAATCAGCCACATTATGGAGCCAA
* * *
21483 TGTAAGATCATGT-TTGGACATGGAATCAGCCACATT-TGAGAGCCAG
1 TGTAAGACCATGTCTAGGACATGGAATCAGCCACATTATG-GAGCCAA
21529 TGTAAGACCATGTCTAGGACATGG
1 TGTAAGACCATGTCTAGGACATGG
21553 CATCGGTGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 2 0.03
46 37 0.62
47 21 0.35
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (47 bp):
TGTAAGACCATGTCTAGGACATGGAATCAGCCACATTATGGAGCCAA
Found at i:21582 original size:48 final size:48
Alignment explanation
Indices: 21423--21744 Score: 183
Period size: 48 Copynumber: 6.8 Consensus size: 48
21413 ACATTTGTTG
* * **
21423 ATATGTGTGCTTGTGTAAGACCATGTCTGGGACATGGCATCGGCCATA
1 ATATGTGTACTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTA
* * * * * * * *
21471 TTATG-G-AGCCAATGTAAGATCATGT-TTGGACATGGAATCAGC--CA
1 ATATGTGTA-CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTA
* * * * *
21515 CATTTGAG-AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGTGTTA
1 -ATATGTGTA-CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTA
* * * * ***
21564 ATATGTGTACTAGTGTAAGACCATGTGTGGAACATGGCCTAGGCCAGA
1 ATATGTGTACTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTA
* * * * * * *
21612 GTATGAG-AGCCAGTGTAAGACCATG-ATGGGACATGGCATCAGTGTTG
1 ATATGTGTA-CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTA
* * * * * *
21659 ATATGTGTGCTACTGTAAGACAATGTTTGGGACATGCCATCGGCGTTG
1 ATATGTGTACTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTA
* * * *
21707 ATATGTTTGCTAGTGTAAGACCGTGTCTGGGGCATGGC
1 ATATGTGTACTAGTGTAAGACCATGTCTGGGACATGGC
21745 GTCGACAATT
Statistics
Matches: 203, Mismatches: 61, Indels: 20
0.71 0.21 0.07
Matches are distributed among these distances:
44 1 0.00
45 3 0.01
46 32 0.16
47 58 0.29
48 107 0.53
49 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (48 bp):
ATATGTGTACTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTA
Found at i:21728 original size:95 final size:96
Alignment explanation
Indices: 21519--21694 Score: 264
Period size: 95 Copynumber: 1.8 Consensus size: 96
21509 CAGCCACATT
* * *
21519 TGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGTGTTAATATGTGTACTAGTGTAAGA
1 TGAGAGCCAGTGTAAGACCATGTATAGGACATGGCATCAGTGTTAATATGTGTACTACTGTAAGA
*
21584 CCATGTGTGGAACATGGCCTAGGCCAGAGTA
66 CAATGTGTGGAACATGGCCTAGGCCAGAGTA
* * *
21615 TGAGAGCCAGTGTAAGACCATG-ATGGGACATGGCATCAGTGTTGATATGTGTGCTACTGTAAGA
1 TGAGAGCCAGTGTAAGACCATGTATAGGACATGGCATCAGTGTTAATATGTGTACTACTGTAAGA
* *
21679 CAATGTTTGGGACATG
66 CAATGTGTGGAACATG
21695 CCATCGGCGT
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
95 49 0.69
96 22 0.31
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (96 bp):
TGAGAGCCAGTGTAAGACCATGTATAGGACATGGCATCAGTGTTAATATGTGTACTACTGTAAGA
CAATGTGTGGAACATGGCCTAGGCCAGAGTA
Found at i:21743 original size:143 final size:141
Alignment explanation
Indices: 21419--21744 Score: 355
Period size: 143 Copynumber: 2.3 Consensus size: 141
21409 CATGACATTT
* * * *
21419 GTTGATATGTGTGCTTGTGTAAGACCATGTCTGGGACATGGCATCGGCCATATTATGGAGCCAAT
1 GTTGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATAGGCCAGAGTATGGAGCCAAT
* * * * * *
21484 GTAAGATCATGTTTGGACATGGAATCAGCCACATTTGAGAGCCAGTGTAAGACCATGTCTAGGAC
66 GTAAGACCATGATGGGACATGGAATCAGCCACATATGAGAGCCACTGTAAGACAATGTCTAGGAC
* *
21549 ATGGCATCGGT
131 ATGCCATCGGC
* * * * * *
21560 GTTAATATGTGTACTAGTGTAAGACCATGTGTGGAACATGGCCTAGGCCAGAGTATGAGAGCCAG
1 GTTGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATAGGCCAGAGTATG-GAGCCAA
* **** * * * * *
21625 TGTAAGACCATGATGGGACATGGCATCAGTGTTGATATGTGTGCTACTGTAAGACAATGTTTGGG
65 TGTAAGACCATGATGGGACATGGAATCAG-CCACATATGAGAGCCACTGTAAGACAATGTCTAGG
21690 ACATGCCATCGGC
129 ACATGCCATCGGC
* * *
21703 GTTGATATGTTTGCTAGTGTAAGACCGTGTCTGGGGCATGGC
1 GTTGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGC
21745 GTCGACAATT
Statistics
Matches: 148, Mismatches: 35, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
141 48 0.32
142 31 0.21
143 69 0.47
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (141 bp):
GTTGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATAGGCCAGAGTATGGAGCCAAT
GTAAGACCATGATGGGACATGGAATCAGCCACATATGAGAGCCACTGTAAGACAATGTCTAGGAC
ATGCCATCGGC
Done.