Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014822.1 Corchorus capsularis cultivar CVL-1 contig14843, 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: 14736
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:1151 original size:19 final size:20
Alignment explanation
Indices: 1110--1151 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
1100 TTGCAAGCTA
* *
1110 AAAGCCCAAAACCCAATATT
1 AAAGCCCAAAACCCAAAAGT
*
1130 AAAG-CCAAAGCCCAAAAGT
1 AAAGCCCAAAACCCAAAAGT
1149 AAA
1 AAA
1152 ACGACACTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.55, C:0.26, G:0.10, T:0.10
Consensus pattern (20 bp):
AAAGCCCAAAACCCAAAAGT
Found at i:5529 original size:431 final size:435
Alignment explanation
Indices: 4889--5707 Score: 1109
Period size: 431 Copynumber: 1.9 Consensus size: 435
4879 TAGTTTTTTG
* * * * *
4889 TCCACATGTCCAATTGAAGTTATTGAAGTGTCAGTTAAAAGGTTATTGCATGATTTACGACTTCT
1 TCCACATGTCCAATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTACTGCATAATCTACGACTTCT
* * * *
4954 ATGAAGGACCCAAAAGCTAAATTTGATCTACGAGTTTCGTTAAGGGTTCAAAAGGGAATTTTTAT
66 ATGAAGAACCCAAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTAT
* *
5019 GTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGGATTATTGATCAAATGACCCTCATACTT
131 GTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTATTGATCAAATCACCCTCATACTT
* * *
5084 TTATACTTTATACTACTTAGTCCTTTACAAATTCTA-T-CTT-A-ATCGCTTTA-TTTTTTCTTT
196 TTATACTTTATACTACTT--TCCTTTACAAATTCTATTACTTGATAACACTTCATTTTTTTCTTT
* * * * *
5144 AA-TCTTTGTTCTATTTGTCCGATTAAGTTGATTCATGTGTCTATTAAAAGACAATTTCATAATC
259 AATTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTATCTATTAAAAGACAATTTCATAATC
* * *
5208 TACATA-TTTCATGAAGGATTCAAAAGCAAATTTTTATGTTTCAATTCAAAAAAATGCTTCCTAA
324 TACA-ACTTTCATGAAAGACTCAAAAGCAAATTTTTATATTTCAATTCAAAAAAATGCTTCCTAA
5272 ATGTGGTCGTTTCAATTGTTGGTCTATTTAATACCATATAATTTTCGA
388 ATGTGGTCGTTTCAATTGTTGGTCTATTTAATACCATATAATTTTCGA
* * *
5320 TCCACATGTGCAATTAAAGTTATTCAAGTGTCGGTTAAAAAGGTTACTGTATAATCTACGACTT-
1 TCCACATGTCCAATTAAAGTTATTCAAGTGTCAGTT-AAAAGGTTACTGCATAATCTACGACTTC
* * * *
5384 TCATGAAGAACCCGAAAG-TTAATTTGATCTATGAGTTTCATGAAGGGTTCAATAGGAAATTTTT
65 T-ATGAAGAACCCAAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTT
*
5448 ATGTTTCAAGATCTCCATTAACAAATATTTTCTTATTTGAATTAGTT-ATCAAATCACCCTCATA
129 ATGTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTA-TTGATCAAATCACCCTCATA
* *
5512 CTTTTCTATTTTATACTACTTTCCTTTACAAATTCTATTTTACTTGATTTAACACTTCATTTTTT
193 CTTTTATACTTTATACTACTTTCCTTTACAAATTCTA--TTACTTGA--TAACACTTCATTTTTT
* **
5577 TTTTTAATTTTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTATCTATTAAAAGGTAATTT
254 TCTTTAA--TTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTATCTATTAAAAGACAATTT
* * * *
5642 TATGATCTACAACTTTCATGAAAGACTCAAAAGCTAATTTTTATATTTCAATTCTAAAAAATGCT
317 CATAATCTACAACTTTCATGAAAGACTCAAAAGCAAATTTTTATATTTCAATTCAAAAAAATGCT
5707 T
382 T
5708 TTGAAATTTT
Statistics
Matches: 333, Mismatches: 39, Indels: 22
0.85 0.10 0.06
Matches are distributed among these distances:
429 16 0.05
431 150 0.45
432 40 0.12
433 3 0.01
434 1 0.00
437 6 0.02
438 11 0.03
440 1 0.00
441 105 0.32
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (435 bp):
TCCACATGTCCAATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTACTGCATAATCTACGACTTCT
ATGAAGAACCCAAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTAT
GTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTATTGATCAAATCACCCTCATACTT
TTATACTTTATACTACTTTCCTTTACAAATTCTATTACTTGATAACACTTCATTTTTTTCTTTAA
TTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTATCTATTAAAAGACAATTTCATAATCTA
CAACTTTCATGAAAGACTCAAAAGCAAATTTTTATATTTCAATTCAAAAAAATGCTTCCTAAATG
TGGTCGTTTCAATTGTTGGTCTATTTAATACCATATAATTTTCGA
Found at i:6911 original size:198 final size:200
Alignment explanation
Indices: 6554--6938 Score: 549
Period size: 198 Copynumber: 1.9 Consensus size: 200
6544 TATAATAAGG
* * * *
6554 ATTATTATACAAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTGAGAAGTTGACAC
1 ATTATTATACAAATACACTGTCAATGTAAATTTTGAACTCCATAACCGGGTTAAAAAGTTGACAC
* *** * *
6619 ATACCCCCATTTCATAATTAATTAAATATTTGATATTAATACATATTCCTTAAGGGGACACATGT
66 ATACCCCCATTTCATAATAAATTAAATATAAAATATTAATACATATTCCCTAAGAGGACACATGT
* * * * *
6684 CAACCCTTAAACCATGTGCGTACAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTT
131 CAACCCTTAAACCACGGGCGTAAAGTCTGCTAAACTCCACTGACAGTGTATTATATAATTTTTTT
6749 ATAGA
196 ATAGA
*
6754 ATTATTATAC-AATACACTGTCAGTGTAAATTTTGAACTCCATAACCGGGTTAAAAAGTTGACAC
1 ATTATTATACAAATACACTGTCAATGTAAATTTTGAACTCCATAACCGGGTTAAAAAGTTGACAC
* * * *
6818 TTA-CCCTATTTCATGATAAATTAGATATAAAATATTAATACATATTCCCTAAGAGGACACATGT
66 ATACCCCCATTTCATAATAAATTAAATATAAAATATTAATACATATTCCCTAAGAGGACACATGT
* * *
6882 CAATCCTTAAGCCCCGGGCGTAAAGTCTGCTAAACTCCACTGACAGTGTATTATATA
131 CAACCCTTAAACCACGGGCGTAAAGTCTGCTAAACTCCACTGACAGTGTATTATATA
6939 CAATGTCAGT
Statistics
Matches: 162, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
198 101 0.62
199 51 0.31
200 10 0.06
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (200 bp):
ATTATTATACAAATACACTGTCAATGTAAATTTTGAACTCCATAACCGGGTTAAAAAGTTGACAC
ATACCCCCATTTCATAATAAATTAAATATAAAATATTAATACATATTCCCTAAGAGGACACATGT
CAACCCTTAAACCACGGGCGTAAAGTCTGCTAAACTCCACTGACAGTGTATTATATAATTTTTTT
ATAGA
Found at i:7434 original size:14 final size:14
Alignment explanation
Indices: 7415--7442 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
7405 GCATATTAAC
7415 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
7429 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
7443 ATTAATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:7614 original size:20 final size:20
Alignment explanation
Indices: 7589--7627 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
7579 AAATACAAGG
7589 CATTTGATTTACAAATTGGA
1 CATTTGATTTACAAATTGGA
*
7609 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
7628 TGCTCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Found at i:9118 original size:17 final size:17
Alignment explanation
Indices: 9098--9131 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9088 CTCTCTCTGG
*
9098 ATTCTTTCACTCTCTTC
1 ATTCTCTCACTCTCTTC
*
9115 ATTCTCTGACTCTCTTC
1 ATTCTCTCACTCTCTTC
9132 CCTTCTTCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.35, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTCTCTCACTCTCTTC
Found at i:9890 original size:40 final size:41
Alignment explanation
Indices: 9846--9924 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
9836 TGAAGATGTG
*
9846 ATCTTTA-GCTAAAAGATGAAACTTTTAATTGATTTATATA
1 ATCTTTATGCTAAAAGATGAAACTTTTAATTGACTTATATA
* *
9886 ATCTTTATGTTAAAAGATGAAATTTTTAATTGACTTATA
1 ATCTTTATGCTAAAAGATGAAACTTTTAATTGACTTATA
9925 ATAAAAATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 7 0.20
41 28 0.80
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.44
Consensus pattern (41 bp):
ATCTTTATGCTAAAAGATGAAACTTTTAATTGACTTATATA
Found at i:10055 original size:30 final size:30
Alignment explanation
Indices: 9958--10057 Score: 112
Period size: 30 Copynumber: 3.3 Consensus size: 30
9948 GAAGATGAGG
* *
9958 TCTTTAAGTAATTTGTAAACAAAGATTGGA
1 TCTTTAAGTAATTTGTAAATAAAGATTGAA
* * *
9988 TTTTTAAGTAATGTT-TAAGTGAAAGATTGAG
1 TCTTTAAGTAAT-TTGTAAAT-AAAGATTGAA
*
10019 TCTTTAAGTAATTTGTAAATAAAGATTAAA
1 TCTTTAAGTAATTTGTAAATAAAGATTGAA
*
10049 TGTTTAAGT
1 TCTTTAAGT
10058 GAAAGATTGA
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
30 32 0.56
31 25 0.44
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.41
Consensus pattern (30 bp):
TCTTTAAGTAATTTGTAAATAAAGATTGAA
Found at i:10073 original size:50 final size:52
Alignment explanation
Indices: 9997--10113 Score: 184
Period size: 51 Copynumber: 2.3 Consensus size: 52
9987 ATTTTTAAGT
*
9997 AATGTTTAAGTGAAAGATTGAGTC-TTTAAGTAATTTGTAAATAAAGATT-A
1 AATGTTTAAGTGAAAGATTGAATCTTTTAAGTAATTTGTAAATAAAGATTGA
*
10047 AATGTTTAAGTGAAAGATTGAATCTTTTAAGTAATTTGTGAATAAAGATTGA
1 AATGTTTAAGTGAAAGATTGAATCTTTTAAGTAATTTGTAAATAAAGATTGA
*
10099 AATTTTTTAAGTGAA
1 AA-TGTTTAAGTGAA
10114 TGATGAAATT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
50 23 0.38
51 24 0.39
52 3 0.05
53 11 0.18
ACGTcount: A:0.41, C:0.02, G:0.18, T:0.39
Consensus pattern (52 bp):
AATGTTTAAGTGAAAGATTGAATCTTTTAAGTAATTTGTAAATAAAGATTGA
Found at i:11130 original size:49 final size:49
Alignment explanation
Indices: 11066--11300 Score: 267
Period size: 49 Copynumber: 4.8 Consensus size: 49
11056 TGTCAAATGA
* * * * *
11066 CCAAAATGCCACTTCCTGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTT
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCTTTATTTATTC
* * * *
11115 CCAAAAAGCCCCTTCCCAGTCGGAAGGTCACAGTTTTCCTTT-CTTATTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTT-CTTTATTTATTC
* * * *
11164 CCAAAATGCCCCTTCCCGGTCGAAAGGTCCCTGTTCTCTTTATTTGTTTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCTTTATTT-ATTC
* * *
11214 CCAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCTTTCTTTATTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCTTTATTTATTC
* * *
11263 CCAAAATGCCCTTTCCCAGTCGGAAGGT-CTAGTTTTCT
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCT
11301 CTTCACATTT
Statistics
Matches: 154, Mismatches: 29, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
48 13 0.08
49 95 0.62
50 46 0.30
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (49 bp):
CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCTTTATTTATTC
Found at i:11271 original size:99 final size:98
Alignment explanation
Indices: 11066--11291 Score: 328
Period size: 99 Copynumber: 2.3 Consensus size: 98
11056 TGTCAAATGA
* * *
11066 CCAAAATGCCACTTCCTGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCAAAAAGCCCCTTCC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTCTCTTTATTTGTTTCCAAAAAGCCCCTTCC
11131 CAGTCGGAAGGTCACAGTTTTCCTTTCTTATTC
66 CAGTCGGAAGGTCACAGTTTTCCTTTCTTATTC
* *
11164 CCAAAATGCCCCTTCCCGGTCGAAAGGTCCCTGTTCTCTTTATTTGTTTCCCAAAATGCCCCTTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTCTCTTTATTTGTTT-CCAAAAAGCCCCTTC
** * *
11229 CTGGTTGGAAGGTCCCAGTTTT-CTTTCTTTATTC
65 CCAGTCGGAAGGTCACAGTTTTCCTTTC-TTATTC
* *
11263 CCAAAATGCCCTTTCCCAGTCGGAAGGTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTC
11292 TAGTTTTCTC
Statistics
Matches: 114, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
98 50 0.44
99 64 0.56
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.35
Consensus pattern (98 bp):
CCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTCTCTTTATTTGTTTCCAAAAAGCCCCTTCC
CAGTCGGAAGGTCACAGTTTTCCTTTCTTATTC
Found at i:12632 original size:395 final size:393
Alignment explanation
Indices: 11726--13060 Score: 1737
Period size: 395 Copynumber: 3.4 Consensus size: 393
11716 CACGTTTCGA
* *
11726 CATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTACTA
1 CATAAACGGGTTAAGAAGTTGACACATACCCCATTTC---A-TAATTAAATATTTAATATTAATA
* * *
11791 CATATTTCCTAAGGGGATACATGTCAACACTT-AA--ACCACGCACGTGCAGTCTGCTAAACTCC
62 CATATTCCCTAAGCGGATACATGTCAACCCTTAAAGTACC-CGCACGTGCAGTCTGCTAAACTCC
* * * *
11853 ATTAACTG-TGTATTGCATAATTTTTCTTATAGGATTATTATACAATACACTATCAGCACAAATT
126 ACTGAC-GATGTATTGCATAATTTTTCTTATAGGATTATTATACAATACACTATCAGTATAAATT
* *
11917 TTGGACTCCATAAGCGAGTTAAGAAGTTGACACATACCCGATTTCATGATTAATAAAATATTTAA
190 TTGGACTCCATAAGCGAGTTAAGAAGTTGACACATACCCTATTTCATGATTAATTAAATATTTAA
* **
11982 TATTAATACATATTCCCTAAGGGGACACATGACAACCCTTAAATCTTACACGTGCAGTCTGCTAA
255 TATTAATACATATTCCCTAAGGGGACACATGACAACCCTTAAA-CCTGGACGTGCAGTCTGCTAA
* *
12047 AATCCACTGACAGGCATTGTATAATTTTTCTTATAGGATTATTATACAATACATTGT--A--T-A
319 AATCCACTGACAGGTATTGTAT-ATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAA
12107 ATTTTGGACTC
383 ATTTTGGACTC
* *
12118 CATAAACGGGTTGAGAAGTTGACACATACCCCATTTCATAATTAAATATTTGATATTAATACATA
1 CATAAACGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAAATATTTAATATTAATACATA
* * * *
12183 TTCCCTAAACGTATACATGTCAACCCTTAAAGTTAAACCCCGCATGTACAGTCTGCTAAACTCCA
66 TTCCCTAAGCGGATACATGTCAACCCTTAAAG-T--A-CCCGCACGTGCAGTCTGCTAAACTCCA
* ** * * * * *
12248 CTGACGATATATTATATAATTTTTTTTATAGAATTATTACACAATACACTGTCAGTGTAAATTTT
127 CTGACGATGTATTGCATAATTTTTCTTATAGGATTATTATACAATACACTATCAGTATAAA-TTT
* * * * ** **
12313 TGGACTCCATAACCGTGTTAAGAAGTTGACACATACCCTATTTCATAATAAATTTGATATAAAAT
191 TGGACTCCATAAGCGAGTTAAGAAGTTGACACATACCCTATTTCATGATTAATTAAATATTTAAT
* * * * **
12378 ATTAAAACATATTCCCTAAGAGGACACATGTCAACCCTTAAGCCTCGGGTGTGCAGTCTGCTAAA
256 ATTAATACATATTCCCTAAGGGGACACATGACAACCCTTAAACCT-GGACGTGCAGTCTGCTAAA
* *
12443 CTCCACTGACAGTGTATTGTAT-TTTTT-TTATATGATTATTATACAATACACTGTCAATGTAAA
320 ATCCACTGACAG-GTATTGTATATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAA
12506 TTTTGGACTC
384 TTTTGGACTC
* * *
12516 CATAAGCGGGTTAA-AAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTACTA
1 CATAAACGGGTTAAGAAGTTGACACATACCCCATTTC---A-TAATTAAATATTTAATATTAATA
*
12580 CATATTCCCTAAGGGGATACATGTCAACCCTTAAA-T-CCCGCACGTGCAGTCTGCTAAACTCCA
62 CATATTCCCTAAGCGGATACATGTCAACCCTTAAAGTACCCGCACGTGCAGTCTGCTAAACTCCA
* *
12643 CTGACTATGTATTGCATTATTTTTCTTATAGGATTATTATACAATACACTATCAGTATAAATTTT
127 CTGACGATGTATTGCATAATTTTTCTTATAGGATTATTATACAATACACTATCAGTATAAATTTT
* *
12708 GAACTCCATAAGCGAGTTAAGAAGTTGACATATA-CCTCATTTCATGATTAATTAAATATTTAAT
192 GGACTCCATAAGCGAGTTAAGAAGTTGACACATACCCT-ATTTCATGATTAATTAAATATTTAAT
*
12772 ATTAATACATATTCCCTAAGGGGACACATGACAACCCTTAAATCCTGGACGTACAGTCTGCTAAA
256 ATTAATACATATTCCCTAAGGGGACACATGACAACCCTTAAA-CCTGGACGTGCAGTCTGCTAAA
* * * *
12837 ATCAACTGACAGATATTATATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAA
320 ATCCACTGACAGGTATTGTAT-ATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAA
*
12902 TTTTGGACTT
384 TTTTGGACTC
12912 CATAAACGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAAATATTTAATATTAATACATA
1 CATAAACGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAAATATTTAATATTAATACATA
* * *
12977 TTCCCTAAGCGTACACATGTCAACCCTTAAAGTTAAACCCCGCACGTGCAGTCTGCTAAACTCTA
66 TTCCCTAAGCGGATACATGTCAACCCTTAAAG-T--A-CCCGCACGTGCAGTCTGCTAAACTCCA
* * *
13042 ATGACGGTGTATTGTATAA
127 CTGACGATGTATTGCATAA
13061 ATTTGATTAA
Statistics
Matches: 809, Mismatches: 102, Indels: 57
0.84 0.11 0.06
Matches are distributed among these distances:
388 48 0.06
389 3 0.00
392 35 0.04
393 90 0.11
394 197 0.24
395 210 0.26
396 64 0.08
397 43 0.05
398 24 0.03
399 41 0.05
400 1 0.00
401 53 0.07
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (393 bp):
CATAAACGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAAATATTTAATATTAATACATA
TTCCCTAAGCGGATACATGTCAACCCTTAAAGTACCCGCACGTGCAGTCTGCTAAACTCCACTGA
CGATGTATTGCATAATTTTTCTTATAGGATTATTATACAATACACTATCAGTATAAATTTTGGAC
TCCATAAGCGAGTTAAGAAGTTGACACATACCCTATTTCATGATTAATTAAATATTTAATATTAA
TACATATTCCCTAAGGGGACACATGACAACCCTTAAACCTGGACGTGCAGTCTGCTAAAATCCAC
TGACAGGTATTGTATATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGGA
CTC
Found at i:12787 original size:199 final size:198
Alignment explanation
Indices: 11726--13060 Score: 1621
Period size: 199 Copynumber: 6.7 Consensus size: 198
11716 CACGTTTCGA
*
11726 CATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTACTA
1 CATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATA
* * * *
11791 CATATTTCCTAAGGGGATACATGTCAACACTTAAA-CCACGCACGTGCAGTCTGCTAAACTCCAT
66 CATATTCCCTAAGGGGACACATGTCAACCCTTAAATCC-CGCACGTGCAGTCTGCTAAACTCCAC
* * * * * *
11855 TAACTGTGTATTGCATAATTTTTCTTATAGGATTATTATACAATACACTATCAGCACAAATTTTG
130 TGAC-ATGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTATAAATTTTG
11920 GACTC
194 GACTC
* * * *
11925 CATAAGCGAGTTAAGAAGTTGACACATACCCGATTTCATGATTAATAAAATATTTAATATTAATA
1 CATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATA
* *** *
11990 CATATTCCCTAAGGGGACACATGACAACCCTTAAATCTTACACGTGCAGTCTGCTAAAATCCACT
66 CATATTCCCTAAGGGGACACATGTCAACCCTTAAATCCCGCACGTGCAGTCTGCTAAACTCCACT
* *
12055 GACAGGCATTGTATAATTTTTCTTATAGGATTATTATACAATACA-T-T--GTAT-AATTTTGGA
131 GACATGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTATAAATTTTGGA
12115 CTC
196 CTC
* * *
12118 CATAAACGGGTTGAGAAGTTGACACATACCCCATTTC---A-TAATTAAATATTTGATATTAATA
1 CATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATA
** * * * *
12179 CATATTCCCTAAACGTATACATGTCAACCCTTAAAGTTAAACCCCGCATGTACAGTCTGCTAAAC
66 CATATTCCCTAAGGGGACACATGTCAACCCTTAAA--T----CCCGCACGTGCAGTCTGCTAAAC
* * * * * *
12244 TCCACTGACGATATATTATATAATTTTTTTTATAGAATTATTACACAATACACTGTCAGTGTAAA
125 TCCACTGAC-ATGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTATAAA
12309 TTTTTGGACTC
189 -TTTTGGACTC
* * * * ** ** *
12320 CATAACCGTGTTAAGAAGTTGACACATACCCTATTTCATAATAAATTTGATATAAAATATTAAAA
1 CATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATA
* * ***
12385 CATATTCCCTAAGAGGACACATGTCAACCCTT-AAGCCTCGGGTGTGCAGTCTGCTAAACTCCAC
66 CATATTCCCTAAGGGGACACATGTCAACCCTTAAATCC-CGCACGTGCAGTCTGCTAAACTCCAC
* * *
12449 TGACAGTGTATTGTAT--TTTTT-TTATATGATTATTATACAATACACTGTCAATGTAAATTTTG
130 TGACA-TGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTATAAATTTTG
12511 GACTC
194 GACTC
* *
12516 CATAAGCGGGTTAA-AAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTACTA
1 CATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATA
*
12580 CATATTCCCTAAGGGGATACATGTCAACCCTTAAATCCCGCACGTGCAGTCTGCTAAACTCCACT
66 CATATTCCCTAAGGGGACACATGTCAACCCTTAAATCCCGCACGTGCAGTCTGCTAAACTCCACT
* * * *
12645 GACTATGTATTGCATTATTTTTCTTATAGGATTATTATACAATACACTATCAGTATAAATTTTGA
131 GAC-ATGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTATAAATTTTGG
12710 ACTC
195 ACTC
* * * *
12714 CATAAGCGAGTTAAGAAGTTGACATATACCTCATTTCATGATTAATTAAATATTTAATATTAATA
1 CATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATA
* * * * * *
12779 CATATTCCCTAAGGGGACACATGACAACCCTTAAATCCTGGACGTACAGTCTGCTAAAATCAACT
66 CATATTCCCTAAGGGGACACATGTCAACCCTTAAATCCCGCACGTGCAGTCTGCTAAACTCCACT
* *
12844 GACA-GATATTATATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGG
131 GACATG-TATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTATAAATTTTGG
*
12908 ACTT
195 ACTC
*
12912 CATAAACGGGTTAAGAAGTTGACACATACCCCATTTC---A-TAATTAAATATTTAATATTAATA
1 CATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATA
* *
12973 CATATTCCCTAAGCGTACACATGTCAACCCTTAAAGTTAAACCCCGCACGTGCAGTCTGCTAAAC
66 CATATTCCCTAAGGGGACACATGTCAACCCTTAAA--T----CCCGCACGTGCAGTCTGCTAAAC
* * *
13038 TCTAATGACGGTGTATTGTATAA
125 TCCACTGAC-ATGTATTGTATAA
13061 ATTTGATTAA
Statistics
Matches: 974, Mismatches: 127, Indels: 68
0.83 0.11 0.06
Matches are distributed among these distances:
189 51 0.05
190 1 0.00
191 1 0.00
193 45 0.05
194 57 0.06
195 134 0.14
196 64 0.07
197 40 0.04
198 187 0.19
199 227 0.23
200 65 0.07
201 11 0.01
202 44 0.05
205 3 0.00
206 44 0.05
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (198 bp):
CATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATA
CATATTCCCTAAGGGGACACATGTCAACCCTTAAATCCCGCACGTGCAGTCTGCTAAACTCCACT
GACATGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTATAAATTTTGGA
CTC
Found at i:14409 original size:2 final size:2
Alignment explanation
Indices: 14402--14432 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14392 AATTAAGTAC
14402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14433 CACACACACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.