Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023881.1 Corchorus olitorius cultivar O-4 contig23914, whole genome shotgun sequence
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: 66154
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:730 original size:328 final size:325
Alignment explanation
Indices: 1--1385 Score: 1212
Period size: 327 Copynumber: 4.2 Consensus size: 325
* * * *
1 TTACATGATTTTTTGGCGCCAAGTCTCATTAAA-ATATCTATATTTATCTAACAAAATAC-CATT
1 TTACATGA-TTTTTGGCGCCAAGACTCATTAAATA-ATC-ATATTCATCTAACCAAAT-CTCAAT
* * * * ** *
64 CTCATTGGATTTAACAATTTTTTTTTTTACCAGCATCAAAAATC-TATTTCGATTTAATTA-AAA
62 CACATT-GATTTAA-GA---TTTTTTTTACGAGCTTC-TGAATCTTGTTTCGATTTAATTAGAAA
* * *
127 -AATT-ATGAAAAATATAGGAAATTCGATATTAGAAG-CGTGAAAAGCCTTTCAATATTTATGGA
121 TAATTCA-GAAAAATATAGGAAATTCGATATTAGAAGTCGTG---AGCCTTTCAATCTTTTTGAA
* * *
189 GTTGAATTACATATTTATTATGAGTATTTTGTACAAAAATTGAAGAAAAATCTTT-AGGGTAAAT
182 GTTAAATTATATATTTATTATGAGTATTTTGTACAAAAATTGAAGAAAAATCTTTCA-GGTCAAT
* * * * *
253 TTTTTCAAAATTTTAGCCGAAATCATGTACTATTA-CATAACGATTTTTGTCTAAAAACGCTTTA
246 TTTTGCAATATTTTAGCTGAAATCATGTACTA--ACCATCACGATTTTTGGCTAAAAACGCTTTA
* *
317 CAGAACTCCGGCTCAGTT
309 CGGAAC-CCAGCTCAGTT
** * * * **
335 TTGTATGATTTTTGGCACCAAGACTCATTGAATAATCATATTCATCTAACCAAATATCACCCACA
1 TTACATGATTTTTGGCGCCAAGACTCATTAAATAATCATATTCATCTAACCAAATCTCAATCACA
*
400 TTGTATTTAAGATTTTTTTTACGAGCTTCTGAATCTTTTTTCGATTTAATTAGAAATTAATTCAG
66 TTG-ATTTAAGATTTTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATTAGAAA-TAATTCAG
* *
465 AAAAATATAAGAAATTCGATATTAGAAGTC-TG-GCCTTTCAATCTTTTTCAAGTTAAATTATAT
129 AAAAATATAGGAAATTCGATATTAGAAGTCGTGAGCCTTTCAATCTTTTTGAAGTTAAATTATAT
* ** * *
528 ATTTATTATAAGTATTTTGTACACTAATTGAAAAAAAAATCTGTCAGGTCAATTTTTGCAATATT
194 ATTTATTATGAGTATTTTGTACAAAAATTG-AAGAAAAATCTTTCAGGTCAATTTTTGCAATATT
* ** * * * **
593 TTAGCTGATATGGTGTACTAACCATCACGGTTTTTGGCTAAAAACACGTTACGGGGTCCCAGCTT
258 TTAGCTGAAATCATGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTAC-GGAACCCAGC-T
*
658 C-TTT
321 CAGTT
* * * *
662 TTATATGATTTTTGGCGGCAA-ACCTCATTAAAATATAT-TTATTTATCTAACCAAATCTCAATC
1 TTACATGATTTTTGGCGCCAAGA-CTCATT-AAATA-ATCATATTCATCTAACCAAATCTCAATC
* * * *
725 ACATTGGATATAAGAATTTTTTTTTTTTTTACCAGCATCAGAAATC-TGTTTCGATTTAATTAGA
63 ACATT-GATTTAAG-A------TTTTTTTTACGAGCTTCTG-AATCTTGTTTCGATTTAATTAGA
* * * * * *
789 AATTAATTCGGAAAATTATAGGAAAATCAATATTAGAA-ACGTGAAAAACCTTTCAATCTTTTTG
119 AA-TAATTCAGAAAAATATAGGAAATTCGATATTAGAAGTCGTG---AGCCTTTCAATCTTTTTG
** * * * *
853 GCGTTGAAA-TATACATTTATTATGAGTATTTTGTACAAATATTAAAGAAAAATCTTTC-GGTTA
180 AAGTT-AAATTATATATTTATTATGAGTATTTTGTACAAAAATTGAAGAAAAATCTTTCAGGTCA
* * ** *
916 A-------AA-A-TTTAGCTGAAATCATGTACTAACTAGCACGATTTTTGTTTAAAAACGCATTA
244 ATTTTTGCAATATTTTAGCTGAAATCATGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTA
* *
972 CGGAACTCTGACTCAGTT
309 CGGAACCCAG-CTCAGTT
* * * **
990 TTGCATGATTTTTGACGCCAAGACTCATTGAATAATCCATATTCATCTAACCAAATCTCAGGCAC
1 TTACATGATTTTTGGCGCCAAGACTCATTAAATAAT-CATATTCATCTAACCAAATCTCAATCAC
* * * *
1055 ATTAGATTTAAGATTTTATTTTACGAGTTTCTGAACCTTGTTTCAATTTAATTATAAATATATTC
65 ATT-GATTTAAGATTTT-TTTTACGAGCTTCTGAATCTTGTTTCGATTTAATTAGAAATA-ATTC
* * *
1120 GGAAAAATATAGGAAATTCGATATTAGAAGT-GT--GCCTTTCAATCTTTTTGACGTTGAATTAT
127 AGAAAAATATAGGAAATTCGATATTAGAAGTCGTGAGCCTTTCAATCTTTTTGAAGTTAAATTAT
* *
1182 ATATTTATTATGAGTATTTTGTACAAAAATTGAAGAAGAATCTTTCAGGTCAATTTTTGCAATGT
192 ATATTTATTATGAGTATTTTGTACAAAAATTGAAGAAAAATCTTTCAGGTCAATTTTTGCAATAT
* * * * ** *
1247 TTTAACTGATATCATGTACTAATCATCACGGTTTTTGGCTAAAAACGCTTTACGGGGTCCCAACT
257 TTTAGCTGAAATCATGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTAC-GGAACCCAGCT
*
1312 TAGTT
321 CAGTT
** * *
1317 TTACCGGATTTTTGGCGCCAAGTCTCATTAAA-ATATCTATATTTATCTAACCAAATCTCAATCA
1 TTACATGATTTTTGGCGCCAAGACTCATTAAATA-ATC-ATATTCATCTAACCAAATCTCAATCA
1381 CATTG
64 CATTG
1386 GAGAGATAGC
Statistics
Matches: 847, Mismatches: 149, Indels: 118
0.76 0.13 0.11
Matches are distributed among these distances:
316 2 0.00
317 65 0.08
318 5 0.01
321 9 0.01
322 61 0.07
325 2 0.00
326 7 0.01
327 228 0.27
328 218 0.26
329 10 0.01
330 2 0.00
331 36 0.04
332 31 0.04
333 24 0.03
334 8 0.01
335 68 0.08
336 4 0.00
337 5 0.01
338 12 0.01
339 47 0.06
340 3 0.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (325 bp):
TTACATGATTTTTGGCGCCAAGACTCATTAAATAATCATATTCATCTAACCAAATCTCAATCACA
TTGATTTAAGATTTTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATTAGAAATAATTCAGAA
AAATATAGGAAATTCGATATTAGAAGTCGTGAGCCTTTCAATCTTTTTGAAGTTAAATTATATAT
TTATTATGAGTATTTTGTACAAAAATTGAAGAAAAATCTTTCAGGTCAATTTTTGCAATATTTTA
GCTGAAATCATGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTACGGAACCCAGCTCAGTT
Found at i:1289 original size:655 final size:652
Alignment explanation
Indices: 1--1387 Score: 1867
Period size: 655 Copynumber: 2.1 Consensus size: 652
* *
1 TTACATGATTTTTTGGCGCCAAGTCTCATTAAAATATCTATATTTATCTAACAAAATAC-CATTC
1 TTACATGA-TTTTTGGCGCCAAGTCTCATTAAAATATCTATATTTATCTAACCAAAT-CTCAATC
* *
65 TCATTGGATTTAACAATTTTTTTTTTTACCAGCATCAAAAATCTATTTCGATTTAATTAAAAAAT
64 ACATTGGATATAACAATTTTTTTTTTTACCAGCATCAAAAATCTATTTCGATTTAATTAAAAAAT
* * * * *
130 TATGAAAAATATAGGAAATTCGATATTAGAAGCGTGAAAAGCCTTTCAATATTTATGGAGTTGAA
129 TAGGAAAAATATAGGAAAATCAATATTAGAAACGTGAAAAACCTTTCAATATTTATGGAGTTGAA
* * * *
195 TTACATATTTATTATGAGTATTTTGTACAAAAATTGAAGAAAAATCTTTAGGGTAAATTTTTTCA
194 ATACACATTTATTATGAGTATTTTGTACAAAAATTAAAGAAAAATCTTTACGG-------TTTCA
* *
260 AAATTTTAGCCGAAATCATGTACTATTACATAACGATTTTTGTCTAAAAACGCTTTACAGAACTC
252 AAAATTTAGCCGAAATCATGTACTA-TACATAACGATTTTTGTCTAAAAACGCATTACAGAACTC
* * *
325 CGGCTCAGTTTTGTATGATTTTTGGCACCAAGACTCATTGAATAATCATATTCATCTAACCAAAT
316 CGACTCAGTTTTGCATGATTTTTGACACCAAGACTCATTGAATAATCATATTCATCTAACCAAAT
* * *
390 ATCACCCACATTGTATTTAAGATTTTTTTTACGAGCTTCTGAATCTTTTTTCGATTTAATTAGAA
381 ATCACCCACATTGTATTTAAGATTTTTTTTACGAGCTTCTGAACCTTGTTTCAATTTAATTAGAA
455 ATTAATTCAGAAAAATATAAGAAATTCGATATTAGAAGTCTGGCCTTTCAATCTTTTTCAAGTTA
446 ATTAATTCAGAAAAATATAAGAAATTCGATATTAGAAGTCTGGCCTTTCAATCTTTTTCAAGTTA
**
520 AATTATATATTTATTATAAGTATTTTGTACACTAATTGAAAAAAAAATCTGTCAGGTCAATTTTT
511 AATTATATATTTATTATAAGTATTTTGTACAAAAATTGAAAAAAAAATCTGTCAGGTCAATTTTT
* **
585 GCAATATTTTAGCTGATATGGTGTACTAACCATCACGGTTTTTGGCTAAAAACACGTTACGGGGT
576 GCAATATTTTAACTGATATCATGTACTAACCATCACGGTTTTTGGCTAAAAACACGTTACGGGGT
* **
650 CCCAGCTTCTTT
641 CCCAACTTAGTT
* * ** * *
662 TTATATGATTTTTGGCGGCAAACCTCATTAAAATATATTTATTTATCTAACCAAATCTCAATCAC
1 TTACATGATTTTTGGCGCCAAGTCTCATTAAAATATCTATATTTATCTAACCAAATCTCAATCAC
* * *
727 ATTGGATATAAGAATTTTTTTTTTTTTTACCAGCATCAGAAATCTGTTTCGATTTAATTAGAAAT
66 ATTGGATATAACAA---TTTTTTTTTTTACCAGCATCAAAAATCTATTTCGATTTAATTA-AAA-
* * * * *
792 TAATTCGGAAAATTATAGGAAAATCAATATTAGAAACGTGAAAAACCTTTCAATCTTTTTGGCGT
126 -AATTAGGAAAAATATAGGAAAATCAATATTAGAAACGTGAAAAACCTTTCAATATTTATGGAGT
* *
857 TGAAATATACATTTATTATGAGTATTTTGTACAAATATTAAAGAAAAATCTTT-CGG-TT-AAAA
190 TGAAATACACATTTATTATGAGTATTTTGTACAAAAATTAAAGAAAAATCTTTACGGTTTCAAAA
* * * *
919 ATTTAGCTGAAATCATGTACTA-AC-TAGCACGATTTTTGTTTAAAAACGCATTACGGAACTCTG
255 ATTTAGCCGAAATCATGTACTATACATA--ACGATTTTTGTCTAAAAACGCATTACAGAACTCCG
* *
982 ACTCAGTTTTGCATGATTTTTGACGCCAAGACTCATTGAATAATCCATATTCATCTAACCAAATC
318 ACTCAGTTTTGCATGATTTTTGACACCAAGACTCATTGAATAAT-CATATTCATCTAACCAAATA
** * *
1047 TCAGGCACATTAG-ATTTAAGATTTTATTTTACGAGTTTCTGAACCTTGTTTCAATTTAATTATA
382 TCACCCACATT-GTATTTAAGATTTT-TTTTACGAGCTTCTGAACCTTGTTTCAATTTAATTAGA
* * * * *
1111 AA-TATATTCGGAAAAATATAGGAAATTCGATATTAGAAGTGT-GCCTTTCAATCTTTTTGACGT
445 AATTA-ATTCAGAAAAATATAAGAAATTCGATATTAGAAGTCTGGCCTTTCAATCTTTTTCAAGT
* * * * *
1174 TGAATTATATATTTATTATGAGTATTTTGTACAAAAATTG-AAGAAGAATCTTTCAGGTCAATTT
509 TAAATTATATATTTATTATAAGTATTTTGTACAAAAATTGAAAAAAAAATCTGTCAGGTCAATTT
* * * *
1238 TTGCAATGTTTTAACTGATATCATGTACTAATCATCACGGTTTTTGGCTAAAAACGCTTTACGGG
574 TTGCAATATTTTAACTGATATCATGTACTAACCATCACGGTTTTTGGCTAAAAACACGTTACGGG
1303 GTCCCAACTTAGTT
639 GTCCCAACTTAGTT
**
1317 TTACCGGATTTTTGGCGCCAAGTCTCATTAAAATATCTATATTTATCTAACCAAATCTCAATCAC
1 TTACATGATTTTTGGCGCCAAGTCTCATTAAAATATCTATATTTATCTAACCAAATCTCAATCAC
1382 ATTGGA
66 ATTGGA
1388 GAGATAGCTC
Statistics
Matches: 636, Mismatches: 77, Indels: 32
0.85 0.10 0.04
Matches are distributed among these distances:
653 2 0.00
654 2 0.00
655 224 0.35
656 121 0.19
657 72 0.11
659 1 0.00
660 59 0.09
661 7 0.01
663 41 0.06
664 3 0.00
665 2 0.00
666 102 0.16
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (652 bp):
TTACATGATTTTTGGCGCCAAGTCTCATTAAAATATCTATATTTATCTAACCAAATCTCAATCAC
ATTGGATATAACAATTTTTTTTTTTACCAGCATCAAAAATCTATTTCGATTTAATTAAAAAATTA
GGAAAAATATAGGAAAATCAATATTAGAAACGTGAAAAACCTTTCAATATTTATGGAGTTGAAAT
ACACATTTATTATGAGTATTTTGTACAAAAATTAAAGAAAAATCTTTACGGTTTCAAAAATTTAG
CCGAAATCATGTACTATACATAACGATTTTTGTCTAAAAACGCATTACAGAACTCCGACTCAGTT
TTGCATGATTTTTGACACCAAGACTCATTGAATAATCATATTCATCTAACCAAATATCACCCACA
TTGTATTTAAGATTTTTTTTACGAGCTTCTGAACCTTGTTTCAATTTAATTAGAAATTAATTCAG
AAAAATATAAGAAATTCGATATTAGAAGTCTGGCCTTTCAATCTTTTTCAAGTTAAATTATATAT
TTATTATAAGTATTTTGTACAAAAATTGAAAAAAAAATCTGTCAGGTCAATTTTTGCAATATTTT
AACTGATATCATGTACTAACCATCACGGTTTTTGGCTAAAAACACGTTACGGGGTCCCAACTTAG
TT
Found at i:1496 original size:50 final size:51
Alignment explanation
Indices: 1409--1527 Score: 123
Period size: 50 Copynumber: 2.4 Consensus size: 51
1399 CATCGGTCAC
* * * * *
1409 TTTTTTAATTGTTTGGGGAGACAGCTCCCATCGGTCTCCTAATTACTA-AA
1 TTTTTTAAATATTTGGAGAGACAGCTCCCATCAGTCTCCTAAATACTACAA
* * * * *
1459 TTTTTTAAATATTTGGAGAGATAGTTCTCATCAGTCTCTTAAATACTACAC
1 TTTTTTAAATATTTGGAGAGACAGCTCCCATCAGTCTCCTAAATACTACAA
* *
1510 TTTTTAAAACATTTGGAG
1 TTTTTTAAATATTTGGAG
1528 TTATAACAGG
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
50 39 0.70
51 17 0.30
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (51 bp):
TTTTTTAAATATTTGGAGAGACAGCTCCCATCAGTCTCCTAAATACTACAA
Found at i:4820 original size:14 final size:14
Alignment explanation
Indices: 4801--4827 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4791 CTTTCCCTAT
4801 ATAATATACCACAC
1 ATAATATACCACAC
4815 ATAATATACCACA
1 ATAATATACCACA
4828 AAGAGTTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (14 bp):
ATAATATACCACAC
Found at i:6235 original size:36 final size:36
Alignment explanation
Indices: 6188--6261 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
6178 CTCAAAGATA
6188 AAAGTTCGTGTTATTATGCCAACATGGGTTTGGATC
1 AAAGTTCGTGTTATTATGCCAACATGGGTTTGGATC
**
6224 AAAGTTCGTGTTATTATGTTAACATGGGTTTGGATC
1 AAAGTTCGTGTTATTATGCCAACATGGGTTTGGATC
6260 AA
1 AA
6262 GTGGTAAGCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (36 bp):
AAAGTTCGTGTTATTATGCCAACATGGGTTTGGATC
Found at i:16419 original size:13 final size:13
Alignment explanation
Indices: 16401--16441 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
16391 TCATGATATA
16401 ATCATATAGGAGT
1 ATCATATAGGAGT
*
16414 ATCATATAGAAGT
1 ATCATATAGGAGT
16427 ATCATATAGGAGT
1 ATCATATAGGAGT
16440 AT
1 AT
16442 ATACTCTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (13 bp):
ATCATATAGGAGT
Found at i:27271 original size:19 final size:19
Alignment explanation
Indices: 27247--27283 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
27237 CTCATCTGTA
27247 ATCGTTTCACCACCGTTTG
1 ATCGTTTCACCACCGTTTG
*
27266 ATCGTTTCACCATCGTTT
1 ATCGTTTCACCACCGTTT
27284 TGGGACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.30, G:0.14, T:0.41
Consensus pattern (19 bp):
ATCGTTTCACCACCGTTTG
Found at i:27378 original size:19 final size:20
Alignment explanation
Indices: 27331--27391 Score: 97
Period size: 19 Copynumber: 3.0 Consensus size: 20
27321 ATCGCTGCTC
27331 TAATAATCTCATCTGTACAG
1 TAATAATCTCATCTGTACAG
*
27351 TACATAATCTAATCTGTACAG
1 TA-ATAATCTCATCTGTACAG
27372 T-ATAATCTCATCTGTACAG
1 TAATAATCTCATCTGTACAG
27391 T
1 T
27392 TGCCAAACAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 18 0.47
20 2 0.05
21 18 0.47
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (20 bp):
TAATAATCTCATCTGTACAG
Found at i:29333 original size:6 final size:6
Alignment explanation
Indices: 29332--29357 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
29322 AAACAAAAAC
29332 AAGACA AAGACA AAGACA AAGACA AA
1 AAGACA AAGACA AAGACA AAGACA AA
29358 AGAAGACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.00
Consensus pattern (6 bp):
AAGACA
Found at i:38997 original size:11 final size:11
Alignment explanation
Indices: 38981--39011 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
38971 CTTTTGCATG
38981 GCGCCCACAAA
1 GCGCCCACAAA
38992 GCGCCCACAAA
1 GCGCCCACAAA
39003 GCGCCCACA
1 GCGCCCACA
39012 GCTGTTAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.32, C:0.48, G:0.19, T:0.00
Consensus pattern (11 bp):
GCGCCCACAAA
Found at i:41352 original size:3 final size:3
Alignment explanation
Indices: 41344--41371 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
41334 TCTCAAAAAC
41344 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
41372 CATTTCCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:44176 original size:46 final size:46
Alignment explanation
Indices: 44105--44196 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
44095 AACAACATAA
44105 GAGAGGGATTTGAATCCTCGCCATAACTCATGAAAATGAGATTCCT
1 GAGAGGGATTTGAATCCTCGCCATAACTCATGAAAATGAGATTCCT
*
44151 GAGAGGGATTTGAATCCTCGTCATAACTCATGAAAATGAGATTCCT
1 GAGAGGGATTTGAATCCTCGCCATAACTCATGAAAATGAGATTCCT
44197 AACTACGTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (46 bp):
GAGAGGGATTTGAATCCTCGCCATAACTCATGAAAATGAGATTCCT
Found at i:51071 original size:3 final size:3
Alignment explanation
Indices: 51065--51099 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
51055 AAAAAAAAAA
*
51065 AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
51100 CCCATTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:54243 original size:21 final size:21
Alignment explanation
Indices: 54214--54258 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
54204 TTGACATTGT
*
54214 TTAGGTACTATACAGATCAAA
1 TTAGATACTATACAGATCAAA
* *
54235 TTAGATACTGTACAGATGAAA
1 TTAGATACTATACAGATCAAA
54256 TTA
1 TTA
54259 TTAGAGCAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (21 bp):
TTAGATACTATACAGATCAAA
Found at i:59101 original size:24 final size:25
Alignment explanation
Indices: 59056--59102 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
59046 TTGTTGGTAG
59056 AAAAAATACGAGTAATATATTTAAA
1 AAAAAATACGAGTAATATATTTAAA
59081 AAAAAATACGAGTAATA-ATTTA
1 AAAAAATACGAGTAATATATTTA
59103 TTTAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.28
Consensus pattern (25 bp):
AAAAAATACGAGTAATATATTTAAA
Done.