Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2294
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: 24221
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:3410 original size:47 final size:47
Alignment explanation
Indices: 3347--3910 Score: 922
Period size: 47 Copynumber: 12.1 Consensus size: 47
3337 GAAATGATAG
*
3347 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
3394 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3441 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
3488 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
3533 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3578 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
3625 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
3672 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
3719 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
3766 TAAGGCCTAACGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3813 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
** * * * * * * *
3860 -CGGTGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAG-GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3907 TAAG
1 TAAG
3911 TCCCGAAGGG
Statistics
Matches: 489, Mismatches: 24, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
45 89 0.18
46 1 0.00
47 398 0.81
48 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:3510 original size:22 final size:22
Alignment explanation
Indices: 3482--3600 Score: 62
Period size: 22 Copynumber: 5.3 Consensus size: 22
3472 AAGTGTATAT
3482 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
* *** ***
3504 ATGTGATGAATGTGAAAGTGTATG
1 ATGTGAT-AAGGCCTAA-TGGCCG
3528 -TGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
* *** ***
3549 ATGTGATGAATGTGAAAGTGTATG
1 ATGTGAT-AAGGCCTAA-TGGCCG
3573 -TGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
3594 ATGTGAT
1 ATGTGAT
3601 GAATGTGAAA
Statistics
Matches: 63, Mismatches: 28, Indels: 12
0.61 0.27 0.12
Matches are distributed among these distances:
21 6 0.10
22 29 0.46
23 22 0.35
24 6 0.10
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCG
Found at i:3532 original size:23 final size:23
Alignment explanation
Indices: 3505--3578 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
3495 TAATGGCCGA
3505 TGTGATGAATGTGAAAGTGTATG
1 TGTGATGAATGTGAAAGTGTATG
* *** ***
3528 TGTGAT-AAGGCCTAA-TGGCCG
1 TGTGATGAATGTGAAAGTGTATG
3549 ATGTGATGAATGTGAAAGTGTATG
1 -TGTGATGAATGTGAAAGTGTATG
3573 TGTGAT
1 TGTGAT
3579 AAGGCCTAAT
Statistics
Matches: 34, Mismatches: 14, Indels: 6
0.63 0.26 0.11
Matches are distributed among these distances:
21 3 0.09
22 11 0.32
23 17 0.50
24 3 0.09
ACGTcount: A:0.28, C:0.05, G:0.34, T:0.32
Consensus pattern (23 bp):
TGTGATGAATGTGAAAGTGTATG
Found at i:4085 original size:37 final size:37
Alignment explanation
Indices: 4029--4107 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
4019 CCGAGCTCTA
* *
4029 AAGACCCAATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCAATAACTACGTGTGGAG-ATTATGTCCGGGT
* *
4066 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCAATAACTACGTGTGGAGATTATGTCCGGGT
4103 AAGAC
1 AAGAC
4108 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (37 bp):
AAGACCCAATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:6020 original size:43 final size:43
Alignment explanation
Indices: 5972--6074 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
5962 TTGGTTTTCA
5972 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
6015 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
6058 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
6075 TTGAAATGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:6091 original size:29 final size:29
Alignment explanation
Indices: 6056--6129 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
6046 GTTGTGAGAT
* *
6056 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
* *
6085 TGGCACTAAGTGTACGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
6114 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
6130 TGGTTGATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.13
29 34 0.87
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:6564 original size:40 final size:40
Alignment explanation
Indices: 6517--6833 Score: 436
Period size: 40 Copynumber: 7.9 Consensus size: 40
6507 GAGTTACTAA
*
6517 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGAGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* *
6557 ATTCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
6597 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* *
6637 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* *
6677 ATCCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * *
6717 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* ** * * * * *
6757 ATCCGTGCTAAACCCCAAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * * *
6797 ATCCGGGCTAGGTCCCGAAGAGTAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
6834 CGTGTATTCG
Statistics
Matches: 248, Mismatches: 29, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 248 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
Found at i:6575 original size:80 final size:80
Alignment explanation
Indices: 6438--6833 Score: 449
Period size: 80 Copynumber: 5.0 Consensus size: 80
6428 TCGAATGATG
** ** *
6438 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAG-GC
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TGTATCCGGGCTAAG-TCCCGAAGAGC
** * * *
6499 ATTGGTGCGAGTTACTAAA
63 ATTCATGCTAGTGA-TATA
* *
6518 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGAGATGTATTCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
* *
6583 CATGCTAGCGATGTA
66 CATGCTAGTGATATA
*
6598 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
6663 CATGCTAGTGATATA
66 CATGCTAGTGATATA
* * *
6678 TCCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
*
6743 CGTGCTAGTGATATA
66 CATGCTAGTGATATA
* ** * * * * * * * *
6758 TCCGTGCTAAACCCCAAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGTAAT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
*
6823 CATGCTGGTGA
66 CATGCTAGTGA
6834 CGTGTATTCG
Statistics
Matches: 276, Mismatches: 36, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
79 1 0.00
80 252 0.91
81 17 0.06
82 6 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
CATGCTAGTGATATA
Found at i:10222 original size:47 final size:47
Alignment explanation
Indices: 10159--10446 Score: 522
Period size: 47 Copynumber: 6.1 Consensus size: 47
10149 GAAATGATAG
* *
10159 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
10206 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
10253 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
10300 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
10347 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
10394 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
10441 TAAGGC
1 TAAGGC
10447 GTGAAAGTGT
Statistics
Matches: 231, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 231 1.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.30
Consensus pattern (47 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:10453 original size:26 final size:26
Alignment explanation
Indices: 10421--10472 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
10411 TGTGATGAAT
10421 GTGAAAGTGTATATATGTGATAAGGC
1 GTGAAAGTGTATATATGTGATAAGGC
10447 GTGAAAGTGTATATATGTGATAAGGC
1 GTGAAAGTGTATATATGTGATAAGGC
10473 CTAATGGCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.31, T:0.31
Consensus pattern (26 bp):
GTGAAAGTGTATATATGTGATAAGGC
Found at i:10460 original size:73 final size:73
Alignment explanation
Indices: 10374--10519 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
10364 TGTGATGAAT
10374 GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT
*
10439 GATAAGGC
66 AATAAGGC
*
10447 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT
10512 AATAAGGC
66 AATAAGGC
10520 CTAATGGCCG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.30
Consensus pattern (73 bp):
GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT
AATAAGGC
Found at i:10481 original size:120 final size:120
Alignment explanation
Indices: 10327--10566 Score: 444
Period size: 120 Copynumber: 2.0 Consensus size: 120
10317 TGTGATGAAT
*
10327 GTGAAAGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
* *
10392 GATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
66 AATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGC
10447 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
*
10512 AATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGC
66 AATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGC
10567 CTAATGGCCG
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 116 1.00
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.30
Consensus pattern (120 bp):
GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
AATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGC
Found at i:10500 original size:47 final size:47
Alignment explanation
Indices: 10447--10705 Score: 419
Period size: 47 Copynumber: 5.5 Consensus size: 47
10437 GTGATAAGGC
10447 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
*
10494 GTGAAAGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
*
10541 GTGAAAGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
10588 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
*** * * * *
10635 GTGAAAGTGTATATATGTGACGGGGCCGAGTGGCCAATGTGATGGAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
* *
10682 GTGAAAGTGCATAAATGTGATAAG
1 GTGAAAGTGTATATATGTGATAAG
10706 TCCCGAAGGG
Statistics
Matches: 198, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 198 1.00
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
Found at i:10556 original size:167 final size:167
Alignment explanation
Indices: 10280--10613 Score: 623
Period size: 167 Copynumber: 2.0 Consensus size: 167
10270 TGTGATGAAT
*
10280 GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT
* *
10345 GATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
66 AATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATAGCCG
10410 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
131 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
*
10447 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT
*
10512 AATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATGGCCG
66 AATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATAGCCG
10577 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
131 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
10614 CTAATGGCCG
Statistics
Matches: 162, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
167 162 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (167 bp):
GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT
AATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATAGCCG
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
Found at i:10602 original size:214 final size:214
Alignment explanation
Indices: 10233--10654 Score: 790
Period size: 214 Copynumber: 2.0 Consensus size: 214
10223 TGTGATGAAT
10233 GTGAAAGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GTGAAAGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
* * *
10298 GATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATGGCCG
66 AATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATGGCCG
10363 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
131 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
10428 TGTATATATGTGATAAGGC
196 TGTATATATGTGATAAGGC
*
10447 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GTGAAAGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
*
10512 AATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATGGCCG
66 AATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATGGCCG
*
10577 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
131 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
10642 TGTATATATGTGA
196 TGTATATATGTGA
10655 CGGGGCCGAG
Statistics
Matches: 202, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
214 202 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (214 bp):
GTGAAAGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
AATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATGGCCG
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGC
Found at i:10650 original size:261 final size:261
Alignment explanation
Indices: 10186--10705 Score: 905
Period size: 261 Copynumber: 2.0 Consensus size: 261
10176 TGTGATGAAT
*
10186 GTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT
*
10251 AATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
66 AATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATAGCCG
*
10316 ATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
131 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
* * * * *
10381 TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
196 TGTATATATGTGACAAGGCCGAATAGCCAATGTGATGAATGTGAAAGTGCATAAATGTGATAAGG
10446 C
261 C
*
10447 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT
*
10512 AATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATGGCCG
66 AATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATAGCCG
10577 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
131 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
** * * *
10642 TGTATATATGTGACGGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCATAAATGTGATAAG
196 TGTATATATGTGACAAGGCCGAATAGCCAATGTGATGAATGTGAAAGTGCATAAATGTGATAAG
10706 TCCCGAAGGG
Statistics
Matches: 244, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
261 244 1.00
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (261 bp):
GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT
AATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAATAAGGCCTAATAGCCG
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGACAAGGCCGAATAGCCAATGTGATGAATGTGAAAGTGCATAAATGTGATAAGG
C
Found at i:10880 original size:37 final size:37
Alignment explanation
Indices: 10824--10902 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
10814 CCGAGCTCTA
* *
10824 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
10861 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
10898 AAGAC
1 AAGAC
10903 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:14983 original size:41 final size:40
Alignment explanation
Indices: 14856--15000 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
14846 CTCGCACAAG
* * * * *
14856 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
14896 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
14936 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
14977 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
15001 TATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:17406 original size:120 final size:119
Alignment explanation
Indices: 17148--17457 Score: 350
Period size: 120 Copynumber: 2.6 Consensus size: 119
17138 TTGCAGCGTC
* * * * * *
17148 TTTCAAAAACTGCCGCTAATGGTCGGCCTATAGTGGCGTTTTTTAAAAAGGTCGCTTATGCTTGA
1 TTTCAAAAAGTGCCGCTAATGGTCGACCTATAGTGGCGTTTTTCAAAAAGGCCGCTAATGCTCGA
* * * * * * *
17213 TCTGTAGCGGCATTTTTCAAAAAGCATAGCTAATGGTCAACCTATAGCGGCGTT
66 TCTATAGCAGCATTTTTCAAAAAGCACAGCTAATGCTCAACCTATAGAGACATT
* * * * *
17267 TTTTAAAAAGCGCCGCTAATGGTCTACCTATAGCGACGTTTTTCAAAAAGCGCCGCTAATGCTCG
1 TTTCAAAAAGTGCCGCTAATGGTCGACCTATAGTGGCGTTTTTCAAAAAG-GCCGCTAATGCTCG
* * * * *
17332 ATCTATAGCAGCGTTTTTCAAAAAGCGCAGCTAATGCTCGATCTGTAGAGACATT
65 ATCTATAGCAGCATTTTTCAAAAAGCACAGCTAATGCTCAACCTATAGAGACATT
* * * * *
17387 TTTCAGAAAGTGCCACTAATGCTCGATCTATAATGGCGTTTTTCAAAAAGTGCCGCTAATGCTCG
1 TTTCAAAAAGTGCCGCTAATGGTCGACCTATAGTGGCGTTTTTCAAAAAG-GCCGCTAATGCTCG
17452 ATCTAT
65 ATCTAT
17458 GCTAAAAATG
Statistics
Matches: 156, Mismatches: 34, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
119 42 0.27
120 114 0.73
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (119 bp):
TTTCAAAAAGTGCCGCTAATGGTCGACCTATAGTGGCGTTTTTCAAAAAGGCCGCTAATGCTCGA
TCTATAGCAGCATTTTTCAAAAAGCACAGCTAATGCTCAACCTATAGAGACATT
Found at i:17448 original size:40 final size:40
Alignment explanation
Indices: 17143--17457 Score: 301
Period size: 40 Copynumber: 7.9 Consensus size: 40
17133 ATTTTTTGCA
* * ** *
17143 GCGTCTTTCAAAAA-CTGCCGCTAATGGTCGGCCTATAGTG
1 GCGTTTTTCAAAAAGC-GCCGCTAATGCTCGATCTATAGCG
* * * * *
17183 GCGTTTTTTAAAAAG-GTCGCTTATGCTTGATCTGTAGCG
1 GCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCG
* *** * * *
17222 GCATTTTTCAAAAAGCATAGCTAATGGTCAACCTATAGCG
1 GCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCG
* * * *
17262 GCGTTTTTTAAAAAGCGCCGCTAATGGTCTACCTATAGCG
1 GCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCG
* *
17302 ACGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCA
1 GCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCG
* * *
17342 GCGTTTTTCAAAAAGCGCAGCTAATGCTCGATCTGTAGAG
1 GCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCG
* * * * * **
17382 ACATTTTTCAGAAAGTGCCACTAATGCTCGATCTATAATG
1 GCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCG
*
17422 GCGTTTTTCAAAAAGTGCCGCTAATGCTCGATCTAT
1 GCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTAT
17458 GCTAAAAATG
Statistics
Matches: 223, Mismatches: 50, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
39 29 0.13
40 194 0.87
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (40 bp):
GCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCG
Found at i:23922 original size:17 final size:17
Alignment explanation
Indices: 23900--23933 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
23890 AATGTTTCTA
*
23900 ATTCAAAATTAATATAT
1 ATTCAAAAGTAATATAT
23917 ATTCAAAAGTAATATAT
1 ATTCAAAAGTAATATAT
23934 TTCTTTCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTCAAAAGTAATATAT
Found at i:23972 original size:9 final size:9
Alignment explanation
Indices: 23958--24208 Score: 96
Period size: 9 Copynumber: 29.1 Consensus size: 9
23948 CCAGCAACTC
23958 ACATAATTT
1 ACATAATTT
23967 ACATAATTT
1 ACATAATTT
23976 ACATAA--T
1 ACATAATTT
*
23983 ACATAACTT
1 ACATAATTT
23992 ACATAATTT
1 ACATAATTT
*
24001 --A-AAGTT
1 ACATAATTT
24007 -CA-AATTT
1 ACATAATTT
*
24014 -CATAACTT
1 ACATAATTT
24022 ACATAATTT
1 ACATAATTT
* *
24031 ACTTAACTT
1 ACATAATTT
24040 ACATAA--T
1 ACATAATTT
* *
24047 ACATGACTT
1 ACATAATTT
24056 ACATAATTT
1 ACATAATTT
*
24065 AAAGATCAAATTT
1 --ACAT--AATTT
*
24078 -CATAACTT
1 ACATAATTT
*
24086 ACATGA--T
1 ACATAATTT
*
24093 ACATAACTT
1 ACATAATTT
*
24102 ATATAATTT
1 ACATAATTT
24111 AAAGACCA-AATTT
1 ----A-CATAATTT
*
24124 -CATAAGTT
1 ACATAATTT
24132 ACATAATTT
1 ACATAATTT
24141 ACATAATTT
1 ACATAATTT
24150 ACATAATAATT
1 ACATAAT--TT
* *
24161 -TA-AAGTT
1 ACATAATTT
24168 -CA-AATTT
1 ACATAATTT
*
24175 -CATAACTT
1 ACATAATTT
24183 ACATAA--T
1 ACATAATTT
*
24190 ACATAACTT
1 ACATAATTT
24199 ACATAATTT
1 ACATAATTT
24208 A
1 A
24209 AAGATCAAAA
Statistics
Matches: 188, Mismatches: 27, Indels: 54
0.70 0.10 0.20
Matches are distributed among these distances:
6 4 0.02
7 45 0.24
8 16 0.09
9 103 0.55
10 3 0.02
11 5 0.03
13 11 0.06
14 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (9 bp):
ACATAATTT
Found at i:23987 original size:16 final size:16
Alignment explanation
Indices: 23966--24062 Score: 83
Period size: 16 Copynumber: 6.1 Consensus size: 16
23956 TCACATAATT
*
23966 TACATAATTTACATAA
1 TACATAACTTACATAA
23982 TACATAACTTACATAA
1 TACATAACTTACATAA
** *
23998 TTTA-AAGTT-CA-AA
1 TACATAACTTACATAA
*
24011 TTTCATAACTTACATAA
1 -TACATAACTTACATAA
*
24028 TTTACTTAACTTACATAA
1 --TACATAACTTACATAA
*
24046 TACATGACTTACATAA
1 TACATAACTTACATAA
24062 T
1 T
24063 TTAAAGATCA
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
13 2 0.03
14 5 0.08
15 8 0.12
16 34 0.52
17 2 0.03
18 15 0.23
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.38
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:24001 original size:34 final size:34
Alignment explanation
Indices: 23953--24065 Score: 128
Period size: 34 Copynumber: 3.4 Consensus size: 34
23943 GTTCACCAGC
* *
23953 AACTCACATAATTTACATAATTTACATAATACAT
1 AACTTACATAATTTACATAACTTACATAATACAT
* *
23987 AACTTACATAATTT--A-AAGTT-CA-AATTTCAT
1 AACTTACATAATTTACATAACTTACATAA-TACAT
*
24017 AACTTACATAATTTACTTAACTTACATAATACAT
1 AACTTACATAATTTACATAACTTACATAATACAT
*
24051 GACTTACATAATTTA
1 AACTTACATAATTTA
24066 AAGATCAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
29 2 0.03
30 20 0.30
31 4 0.06
32 1 0.02
33 4 0.06
34 33 0.50
35 2 0.03
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (34 bp):
AACTTACATAATTTACATAACTTACATAATACAT
Found at i:24020 original size:30 final size:30
Alignment explanation
Indices: 23984--24089 Score: 124
Period size: 30 Copynumber: 3.4 Consensus size: 30
23974 TTACATAATA
23984 CATAACTTACATAATTTAAAGTTCAAATTT
1 CATAACTTACATAATTTAAAGTTCAAATTT
* *
24014 CATAACTTACATAATTTACTTAACTTACATAA-TA
1 CATAACTTACATAATTTA---AAGTT-CA-AATTT
* *
24048 CATGACTTACATAATTTAAAGATCAAATTT
1 CATAACTTACATAATTTAAAGTTCAAATTT
24078 CATAACTTACAT
1 CATAACTTACAT
24090 GATACATAAC
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
29 2 0.03
30 32 0.51
31 3 0.05
33 4 0.06
34 20 0.32
35 2 0.03
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (30 bp):
CATAACTTACATAATTTAAAGTTCAAATTT
Found at i:24042 original size:64 final size:64
Alignment explanation
Indices: 23953--24108 Score: 235
Period size: 64 Copynumber: 2.5 Consensus size: 64
23943 GTTCACCAGC
* * *
23953 AACTCACATAATTTACATAATTTACATAATACATAACTTACATAATTTAAAGTTCAAATTTCAT
1 AACTTACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCAT
* *
24017 AACTTACATAATTTACTTAACTTACATAATACATGACTTACATAATTTAAAGATCAAATTTCAT
1 AACTTACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCAT
* *
24081 AACTTACATGA--TACATAACTTATATAAT
1 AACTTACATAATTTACATAACTTACATAAT
24109 TTAAAGACCA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
62 15 0.18
64 69 0.82
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.37
Consensus pattern (64 bp):
AACTTACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCAT
Found at i:24095 original size:46 final size:46
Alignment explanation
Indices: 24034--24217 Score: 260
Period size: 46 Copynumber: 3.9 Consensus size: 46
24024 ATAATTTACT
*
24034 TAACTTACATAATACATGACTTACATAATTTAAAGATCAAATTTCA
1 TAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCA
* * *
24080 TAACTTACATGATACATAACTTATATAATTTAAAGACCAAATTTCA
1 TAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCA
* * *
24126 TAAGTTACATAATTTACATAATTTACATAATAATTTAAAGTTCAAATTTCA
1 TAACTTACATAA--TACATAACTTAC---ATAATTTAAAGATCAAATTTCA
24177 TAACTTACATAATACATAACTTACATAATTTAAAGATCAAA
1 TAACTTACATAATACATAACTTACATAATTTAAAGATCAAA
24218 ATTC
Statistics
Matches: 120, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
46 68 0.57
48 10 0.08
49 11 0.09
51 31 0.26
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.36
Consensus pattern (46 bp):
TAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCA
Found at i:24196 original size:16 final size:16
Alignment explanation
Indices: 24175--24205 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
24165 GTTCAAATTT
24175 CATAACTTACATAATA
1 CATAACTTACATAATA
24191 CATAACTTACATAAT
1 CATAACTTACATAAT
24206 TTAAAGATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (16 bp):
CATAACTTACATAATA
Done.