Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1026
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: 24902
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Found at i:629 original size:38 final size:40
Alignment explanation
Indices: 566--780 Score: 295
Period size: 38 Copynumber: 5.6 Consensus size: 40
556 CGGATGATAA
* * *
566 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGAGTA-AT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
605 TCGGGCTAAG-CCCG-AGGCATTTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTTGTGCGAGTTACTATAT
*
644 CCGGGCTAAGT--CGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
682 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
722 CCGGGCTAAGT-CC-AAGGCATTTG-GCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
759 CCGGGCTAAGTCCC-AAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
781 GAATAGGTAT
Statistics
Matches: 163, Mismatches: 6, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
37 30 0.18
38 68 0.42
39 27 0.17
40 38 0.23
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:697 original size:78 final size:78
Alignment explanation
Indices: 562--780 Score: 311
Period size: 78 Copynumber: 2.8 Consensus size: 78
552 TATTCGGATG
* * * **
562 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGAGTA-ATTCGGGCTAAG-CCCGAGGCAT
1 ATAACCGGGCTAAGT--CGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAGGCAT
625 TTTGTGCGAGTTACT
64 TTTGTGCGAGTTACT
*
640 ATATCCGGGCTAAGTCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCA-T
1 ATAACCGGGCTAAGTCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCG-AGGCATT
704 TTGTGCGAGTTACT
65 TTGTGCGAGTTACT
* *
718 ATAACCGGGCTAAGTCCAAGGCATTTG-GCGAGTTACTATAACCGGGCTAAGTCCCAAGGCATT
1 ATAACCGGGCTAAGTCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAGGCATT
781 GAATAGGTAT
Statistics
Matches: 128, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
76 26 0.20
77 39 0.30
78 58 0.45
79 5 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (78 bp):
ATAACCGGGCTAAGTCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAGGCATTT
TGTGCGAGTTACT
Found at i:777 original size:116 final size:116
Alignment explanation
Indices: 562--780 Score: 325
Period size: 116 Copynumber: 1.9 Consensus size: 116
552 TATTCGGATG
* * ** *
562 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGAGTAATTCGGGCTAAGCCCGAGGCATTT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAACCGGGCTAAGCCCAAGGCATTT
* *
627 TGTGCGAGTTACTATATCCGGGCTAAGTCGAAGGCATTTGTGCGAGTTACT
66 TGTGCGAGTTACTATAACCGGGCTAAGTCCAAGGCATTTGTGCGAGTTACT
* *
678 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCAAGGCA-T
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTA-AACCGGGCTAAGCCCAAGGCATT
742 TTG-GCGAGTTACTATAACCGGGCTAAGTCCCAAGGCATT
65 TTGTGCGAGTTACTATAACCGGGCTAAGT-CCAAGGCATT
781 GAATAGGTAT
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
115 24 0.26
116 51 0.55
117 17 0.18
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (116 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAACCGGGCTAAGCCCAAGGCATTT
TGTGCGAGTTACTATAACCGGGCTAAGTCCAAGGCATTTGTGCGAGTTACT
Found at i:8641 original size:40 final size:40
Alignment explanation
Indices: 8538--8753 Score: 314
Period size: 40 Copynumber: 5.5 Consensus size: 40
8528 TGGATGATAA
* *
8538 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-AT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
8577 TCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
8616 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
8656 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
8696 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
8736 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
8754 TACTTGGTTT
Statistics
Matches: 164, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
38 24 0.15
39 36 0.22
40 104 0.63
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:15352 original size:40 final size:40
Alignment explanation
Indices: 15292--15475 Score: 239
Period size: 40 Copynumber: 4.6 Consensus size: 40
15282 TATTCGAATG
*
15292 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
15332 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * *
15372 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
15412 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
15452 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
15476 CTTGTGCGAG
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
39 1 0.01
40 122 0.97
41 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:15425 original size:80 final size:80
Alignment explanation
Indices: 15292--15475 Score: 264
Period size: 80 Copynumber: 2.3 Consensus size: 80
15282 TATTCGAATG
* * *
15292 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAG-TCCCGAAGGC
* *
15356 ATTTGTGCGAGTTG-CT
65 ATTTATGCGAG-TGACC
* *
15372 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
*
15437 TTTATGCTAGTGACC
66 TTTATGCGAGTGACC
15452 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
15476 CTTGTGCGAG
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
79 3 0.03
80 91 0.97
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
TTTATGCGAGTGACC
Found at i:16300 original size:11 final size:11
Alignment explanation
Indices: 16275--16312 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16265 GGAATGGAAT
16275 TAAATAGTGAA
1 TAAATAGTGAA
*
16286 TAAATTA-TGAT
1 TAAA-TAGTGAA
16297 TAAATAGTGAA
1 TAAATAGTGAA
16308 TAAAT
1 TAAAT
16313 TATGTAATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 2 0.09
11 19 0.83
12 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (11 bp):
TAAATAGTGAA
Found at i:16301 original size:22 final size:22
Alignment explanation
Indices: 16273--16316 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
16263 TAGGAATGGA
16273 ATTAAATAGTGAATAAATTATG
1 ATTAAATAGTGAATAAATTATG
16295 ATTAAATAGTGAATAAATTATG
1 ATTAAATAGTGAATAAATTATG
16317 TAATCGAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (22 bp):
ATTAAATAGTGAATAAATTATG
Found at i:21123 original size:19 final size:19
Alignment explanation
Indices: 21099--21139 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
21089 AAAGATATTG
21099 AGTATCAGGTGGGAGACAA
1 AGTATCAGGTGGGAGACAA
21118 AGTATCAGGTGGGAGACAA
1 AGTATCAGGTGGGAGACAA
21137 AGT
1 AGT
21140 GTTTCTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.10, G:0.37, T:0.17
Consensus pattern (19 bp):
AGTATCAGGTGGGAGACAA
Found at i:23388 original size:38 final size:39
Alignment explanation
Indices: 23292--23478 Score: 172
Period size: 39 Copynumber: 4.9 Consensus size: 39
23282 TTATCGAATG
* ** * *
23292 ATATCCGGGCTAAG-TCCGAAGGGTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAA-GGCATTGTGCGAGTGACT
* *
23331 ATATCCGGACTAAG-TCCGAAGGCATTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTGTGCGAG-TGACT
* *
23369 ATAT-CGGGCTAAGACCCGAAGGCATTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGACT
* * * *
23407 ATATCCGGGCTAAGTCCCGAAGGCATTTATGC-AGTGCCC
1 ATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGAGTGACT
*
23446 ATATCCGGGC--AGACCCGAAGGCCTTGTGCGAGT
1 ATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGT
23479 TGTTATGTCC
Statistics
Matches: 125, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
36 5 0.04
37 23 0.18
38 38 0.30
39 54 0.43
40 5 0.04
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGACT
Found at i:23420 original size:76 final size:76
Alignment explanation
Indices: 23320--23474 Score: 201
Period size: 76 Copynumber: 2.0 Consensus size: 76
23310 AAGGGTTTTA
* * *
23320 TGCTAGTGACTATATCCGGACTAAGT-CCGAAGGCA-TTGTGCGAGTTG-CTATAT-CGGGCTAA
1 TGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCATTTATGC-AG-TGCCCATATCCGGGC--A
23381 GACCCGAAGGCATTG
62 GACCCGAAGGCATTG
*
23396 TGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCATTTATGCAGTGCCCATATCCGGGCAGACC
1 TGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCATTTATGCAGTGCCCATATCCGGGCAGACC
*
23461 CGAAGGCCTTG
66 CGAAGGCATTG
23472 TGC
1 TGC
23475 GAGTTGTTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
76 44 0.63
77 16 0.23
78 10 0.14
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.23
Consensus pattern (76 bp):
TGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCATTTATGCAGTGCCCATATCCGGGCAGACC
CGAAGGCATTG
Done.