Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011238.1 Corchorus capsularis cultivar CVL-1 contig11259, 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: 20154
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:6066 original size:19 final size:19
Alignment explanation
Indices: 6024--6066 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
6014 TCCTAAAATT
*
6024 AAAAATTGTTTTTGCAAAA
1 AAAAAGTGTTTTTGCAAAA
*
6043 GAAAAGTGTTTTT-CTAAAA
1 AAAAAGTGTTTTTGC-AAAA
6062 AAAAA
1 AAAAA
6067 AGGTTTTCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.33
Consensus pattern (19 bp):
AAAAAGTGTTTTTGCAAAA
Found at i:7437 original size:35 final size:35
Alignment explanation
Indices: 7209--7451 Score: 287
Period size: 35 Copynumber: 6.9 Consensus size: 35
7199 TTATCTCTTA
*
7209 TTGACCTAGGGCGGTCTTCCTTC-GATTTATTTCAG
1 TTGACCTAGGGCGGTCTTTCTTCAG-TTTATTTCAG
* * *
7244 TTGACCCAGGGCGGTCTTTCGTCAATTTATTTCAG
1 TTGACCTAGGGCGGTCTTTCTTCAGTTTATTTCAG
*
7279 TTGACCTAGGGCGGTCTTTC-GCTAGTTTATTTCAG
1 TTGACCTAGGGCGGTCTTTCTTC-AGTTTATTTCAG
*
7314 TTGACCTAGGGTGGTCTTTCTTCAGTTTA-TTCGAG
1 TTGACCTAGGGCGGTCTTTCTTCAGTTTATTTC-AG
* * *
7349 TGGACCGAGGGCGGTCTTTCTTCAGTTAATTTCAG
1 TTGACCTAGGGCGGTCTTTCTTCAGTTTATTTCAG
* ** *
7384 TTGACCCAGGGCGGTCTTTCTTTTGTTTATTTTAG
1 TTGACCTAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
7419 TTGA-TTCAGGGCGGTCTTTCATCAGTTTATTTC
1 TTGACCT-AGGGCGGTCTTTCTTCAGTTTATTTC
7452 GATCCAGGGA
Statistics
Matches: 177, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
34 4 0.02
35 169 0.95
36 4 0.02
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (35 bp):
TTGACCTAGGGCGGTCTTTCTTCAGTTTATTTCAG
Found at i:7542 original size:34 final size:34
Alignment explanation
Indices: 7499--7569 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
7489 ATCCAAATGA
* *
7499 TCCAGGGTGGTCTTTATCAGATTATTCCGTTTGG
1 TCCAGGGTGGTCTTCATCAGAGTATTCCGTTTGG
**
7533 TCCAGGGTGGTCTTCATCAGAGTATTTTGTTTGG
1 TCCAGGGTGGTCTTCATCAGAGTATTCCGTTTGG
7567 TCC
1 TCC
7570 GGGCAGTTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.14, C:0.18, G:0.27, T:0.41
Consensus pattern (34 bp):
TCCAGGGTGGTCTTCATCAGAGTATTCCGTTTGG
Found at i:8196 original size:338 final size:338
Alignment explanation
Indices: 7570--8243 Score: 1070
Period size: 338 Copynumber: 2.0 Consensus size: 338
7560 TGTTTGGTCC
* * * *
7570 GGGCAGTTGGTAAAACCTCCGGATATCATTTCATTTCATCAAATTTTTCATCAAAGATCCATGAT
1 GGGCAATTGGTAAAACCTCCGGATACCACTTCATTTCATCAAATTTTTCATCAAAAATCCATGAT
*
7635 TAATTTTAAAATCATTGTTAAAGGTCTCTATTCAAAGTTTGCATTGTAAGTCCTCCGGGCACAAA
66 TAATTTTAAAATCATTGTTAAAGGTCTCTATTCAAAGTTTGCATTGTAAGACCTCCGGGCACAAA
*
7700 CTCAGAAACCTCCAGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGATACT
131 CTCAGAAACCTCCAGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGATACC
* *
7765 ATTCTATTTCATTAAGTTTTTCATCAAAAATTCCTGTTTAAGTTTTAAAATCCATGTTAAAGGTC
196 ATTCTATTTCATCAAGTTTTTCATCAAAAATTCATGTTTAAGTTTTAAAATCCATGTTAAAGGTC
* * *
7830 TCTATTAAGAGTTTGCATTGGTAAGACCTCCGGACACAAATTCAGAAACCTCCGGGTTTTAATTT
261 TCTATTAAGAGTTTGCATTGGTAAGACCTCCGCACACAAATTCAGAAACCTCCGGGTATTAATTC
7895 TGATAAGTCCTTT
326 TGATAAGTCCTTT
* * * * *
7908 GGGCAATTGGTAAAACCTCCGGGTACCACTTCATTTCATTAAGTTTTTCATCAAAAATTCATGTT
1 GGGCAATTGGTAAAACCTCCGGATACCACTTCATTTCATCAAATTTTTCATCAAAAATCCATGAT
*
7973 TAAGTTTTAAAATCCTTGTTAAAGGTCTCTATT-AAGAGTTTGCATTGGTAAGACCTCCGGGCAC
66 TAA-TTTTAAAATCATTGTTAAAGGTCTCTATTCAA-AGTTTGCATT-GTAAGACCTCCGGGCAC
* *
8037 AAACTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGT
128 AAACTCAGAAACCTCCAGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGAT
*
8102 ACCATT-TCATTTCATCAAG-TTTTCAT-AAAAGATTCATGTTTAAG-TTTAAAATCCTTGTTAA
193 ACCATTCT-ATTTCATCAAGTTTTTCATCAAAA-ATTCATGTTTAAGTTTTAAAATCCATGTTAA
* *
8163 AGGTCTCTATTGAGAGTTTGCATTGGTAAGACCTCCGCACACAATTTCAGAAACCTCCGGGTATT
256 AGGTCTCTATTAAGAGTTTGCATTGGTAAGACCTCCGCACACAAATTCAGAAACCTCCGGGTATT
8228 AATTCTGATAAGTCCT
321 AATTCTGATAAGTCCT
8244 CCAAGTATTT
Statistics
Matches: 309, Mismatches: 22, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
338 157 0.51
339 58 0.19
340 94 0.30
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (338 bp):
GGGCAATTGGTAAAACCTCCGGATACCACTTCATTTCATCAAATTTTTCATCAAAAATCCATGAT
TAATTTTAAAATCATTGTTAAAGGTCTCTATTCAAAGTTTGCATTGTAAGACCTCCGGGCACAAA
CTCAGAAACCTCCAGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGATACC
ATTCTATTTCATCAAGTTTTTCATCAAAAATTCATGTTTAAGTTTTAAAATCCATGTTAAAGGTC
TCTATTAAGAGTTTGCATTGGTAAGACCTCCGCACACAAATTCAGAAACCTCCGGGTATTAATTC
TGATAAGTCCTTT
Found at i:8268 original size:168 final size:170
Alignment explanation
Indices: 7567--8245 Score: 1012
Period size: 170 Copynumber: 4.0 Consensus size: 170
7557 TTTTGTTTGG
* * * * * * *
7567 TCCGGGCAGTTGGTAAAACCTCCGGATATCATTTCATTTCATCAAATTTTTCATCAAAGATCCAT
1 TCCGGGCAATTGATAAAACCTCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAAAAATTCAT
* * * *
7632 GATTAA-TTTTAAAATCATTGTTAAAGGTCTCTATTCAA-AGTTTGCATT-GTAAGTCCTCCGGG
66 GTTTAAGTTTTAAAATCCTTGTTAAAGGTCTCTATT-AAGAGTTTGCATTGGTAAGACCTCCGGA
*
7694 CACAAACTCAGAAACCTCCAGGTATTAATTCTGATAAGTCC
130 CACAAACTCAGAAACCTCCGGGTATTAATTCTGATAAGTCC
* * * *
7735 TCCGGGCAATTGATAAAACCTCCGGATACTA-TTCTATTTCATTAAGTTTTTCATCAAAAATTCC
1 TCCGGGCAATTGATAAAACCTCCGGGTACCATTTC-ATTTCATCAAGTTTTTCATCAAAAATTCA
*
7799 TGTTTAAGTTTTAAAATCCATGTTAAAGGTCTCTATTAAGAGTTTGCATTGGTAAGACCTCCGGA
65 TGTTTAAGTTTTAAAATCCTTGTTAAAGGTCTCTATTAAGAGTTTGCATTGGTAAGACCTCCGGA
* * *
7864 CACAAATTCAGAAACCTCCGGGTTTTAATTTTGATAAGTCC
130 CACAAACTCAGAAACCTCCGGGTATTAATTCTGATAAGTCC
** * * *
7905 TTTGGGCAATTGGTAAAACCTCCGGGTACCACTTCATTTCATTAAGTTTTTCATCAAAAATTCAT
1 TCCGGGCAATTGATAAAACCTCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAAAAATTCAT
*
7970 GTTTAAGTTTTAAAATCCTTGTTAAAGGTCTCTATTAAGAGTTTGCATTGGTAAGACCTCCGGGC
66 GTTTAAGTTTTAAAATCCTTGTTAAAGGTCTCTATTAAGAGTTTGCATTGGTAAGACCTCCGGAC
8035 ACAAACTCAGAAACCTCCGGGTATTAATTCTGATAAGTCC
131 ACAAACTCAGAAACCTCCGGGTATTAATTCTGATAAGTCC
8075 TCCGGGCAATTGATAAAACCTCCGGGTACCATTTCATTTCATCAAG-TTTTCAT-AAAAGATTCA
1 TCCGGGCAATTGATAAAACCTCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAAAA-ATTCA
* *
8138 TGTTTAAG-TTTAAAATCCTTGTTAAAGGTCTCTATTGAGAGTTTGCATTGGTAAGACCTCCGCA
65 TGTTTAAGTTTTAAAATCCTTGTTAAAGGTCTCTATTAAGAGTTTGCATTGGTAAGACCTCCGGA
**
8202 CACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAGTCC
130 CACAAACTCAGAAACCTCCGGGTATTAATTCTGATAAGTCC
8243 TCC
1 TCC
8246 AAGTATTTCA
Statistics
Matches: 466, Mismatches: 39, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
167 3 0.01
168 158 0.34
169 57 0.12
170 245 0.53
171 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (170 bp):
TCCGGGCAATTGATAAAACCTCCGGGTACCATTTCATTTCATCAAGTTTTTCATCAAAAATTCAT
GTTTAAGTTTTAAAATCCTTGTTAAAGGTCTCTATTAAGAGTTTGCATTGGTAAGACCTCCGGAC
ACAAACTCAGAAACCTCCGGGTATTAATTCTGATAAGTCC
Found at i:8340 original size:38 final size:38
Alignment explanation
Indices: 8297--8607 Score: 269
Period size: 38 Copynumber: 8.4 Consensus size: 38
8287 AGAACTATTC
* * *
8297 TGCTTTATCAGTTTATTTCAATCATGATTTAGGATCTT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* * *
8335 TGCTTTATTA-TTTAATTTCAAT-C--A--T--GATTAT
1 TGCTTTATCAGTTT-ATTTTAATCCTGATTTAGGATCAT
**
8366 TGCTTTATGGGTTTATTTTAATCCTGATTTAGGATCAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* * * * *
8404 TGTTTTATCAATTTATGTTACTCCTGATCTAGGATCAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* *
8442 TGCTTTATAAGTTAATTTTAATCCTGATTTAGGATCAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* * * * * *
8480 TGATTTATCAATTTATGTTAATTCTGATCTAGGAGCAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* * * *
8518 TGCTTTATAAGTTAATTTTAATCCTGGTTTAGGACCAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* * * **
8556 TGATTTATTAATACATTTTAATCCTGATTTAGGATCAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* *
8594 TGATTAATCAGTTT
1 TGCTTTATCAGTTT
8608 CTCCCTGACT
Statistics
Matches: 213, Mismatches: 51, Indels: 18
0.76 0.18 0.06
Matches are distributed among these distances:
31 19 0.09
32 4 0.02
33 1 0.00
34 1 0.00
35 1 0.00
36 1 0.00
37 3 0.01
38 183 0.86
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.48
Consensus pattern (38 bp):
TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
Found at i:8449 original size:76 final size:76
Alignment explanation
Indices: 8364--8595 Score: 338
Period size: 76 Copynumber: 3.1 Consensus size: 76
8354 AATCATGATT
** * * *
8364 ATTGCTTTATGGGTTTATTTTAATCCTGATTTAGGATCATTGTTTTATCAATTTATGTTACTCCT
1 ATTGCTTTATAAGTTAATTTTAATCCTGATTTAGGATCATTGATTTATCAATTTATGTTAATCCT
8429 GATCTAGGATC
66 GATCTAGGATC
*
8440 ATTGCTTTATAAGTTAATTTTAATCCTGATTTAGGATCATTGATTTATCAATTTATGTTAATTCT
1 ATTGCTTTATAAGTTAATTTTAATCCTGATTTAGGATCATTGATTTATCAATTTATGTTAATCCT
*
8505 GATCTAGGAGC
66 GATCTAGGATC
* * * ** *
8516 ATTGCTTTATAAGTTAATTTTAATCCTGGTTTAGGACCATTGATTTATTAATACATTTTAATCCT
1 ATTGCTTTATAAGTTAATTTTAATCCTGATTTAGGATCATTGATTTATCAATTTATGTTAATCCT
*
8581 GATTTAGGATC
66 GATCTAGGATC
8592 ATTG
1 ATTG
8596 ATTAATCAGT
Statistics
Matches: 140, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 140 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.47
Consensus pattern (76 bp):
ATTGCTTTATAAGTTAATTTTAATCCTGATTTAGGATCATTGATTTATCAATTTATGTTAATCCT
GATCTAGGATC
Found at i:8999 original size:63 final size:63
Alignment explanation
Indices: 8908--9576 Score: 516
Period size: 63 Copynumber: 11.0 Consensus size: 63
8898 CTGTTTGAGA
* * * ** *
8908 GTTTCATTTTAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTTATTTCCAAAATCTT
1 GTTTCA-TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCA-ATCTGAAGTCTT
* ** * * * ** * *
8973 G-TTCTTTTCAAATCCTAATCGAGGTCTCCAGTCAAGAGTTTCTTGTTTCAACTCCAAAATCAT
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCTGAAGTCTT
9036 G-TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTGAAGTCTT
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTGAAGTCTT
*
9098 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGATTTTCTTGTTTCAATCTGAAGTCTT
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTGAAGTCTT
*
9161 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGATTTTCTTGTTTCAATCTGAAGTCTT
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTGAAGTCTT
* * *
9224 GTTTCATTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAG-----T-TATCAATTCT-AAGTCCT
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCTGAAGTCTT
* * * * **
9281 ATTACATTTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAG-----T-TATCAATTCT-AAGTCCA
1 GTTTCA-TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCTGAAGTCTT
* * ***
9339 GTTTCATTTTCAAATCCT-ATTCGAGGTCTCTAATCGAGAGTTT-TCAATTCAA----AA-TCTT
1 GTTTCA-TTTCAAATCCTGCTT-GAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTGAAGTCTT
* * * * *
9397 GTTTCGTTTTTAAATCCTGATCGAGGTCTCTAGTCGAGAG-----T-TTTCAAT-TCCAAGT-TT
1 GTTTC-ATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCT-GAAGTCTT
* * * *
9454 AGTTTCATTTCCAAATCCTGCTTGAGGCCTTTAGTGGAGAG-----T-TTTCAATC-CACAGTCT
1 -GTTTCATTT-CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTGA-AGTCT
9512 T
63 T
** * * * *
9513 GTTTTGTTTTCAAATCCTGCTCGAGGTCTCTAGCCGAGAGTTTC-TGTTTCAATCTAAAATCTT
1 G-TTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTGAAGTCTT
9576 G
1 G
9577 CTTGAGAGTT
Statistics
Matches: 515, Mismatches: 60, Indels: 60
0.81 0.09 0.09
Matches are distributed among these distances:
53 5 0.01
57 25 0.05
58 188 0.37
59 12 0.02
62 9 0.02
63 271 0.53
64 4 0.01
65 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (63 bp):
GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTGAAGTCTT
Found at i:9309 original size:58 final size:58
Alignment explanation
Indices: 9037--9555 Score: 428
Period size: 58 Copynumber: 8.7 Consensus size: 58
9027 CAAAATCATG
* * *
9037 TTCA-TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCTGAAGTCTTGT
1 TTCATTTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAG-----T-TTTCAATTC-CAAGTCTTAT
* * * *
9100 TTCA-TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGATTTTCTTGTTTCAA-TCTGAAGTCTTGT
1 TTCATTTTCAAATCCTGCTCGAGGTCTCTAGTCGAGA-----GT-TTTCAATTC-CAAGTCTTAT
* * * *
9163 TTCA-TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGATTTTCTTGTTTCAA-TCTGAAGTCTTGT
1 TTCATTTTCAAATCCTGCTCGAGGTCTCTAGTCGAGA-----GT-TTTCAATTC-CAAGTCTTAT
* * *
9226 TTCA-TTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTATCAATTCTAAGTCCTAT
1 TTCATTTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTTCAATTCCAAGTCTTAT
* * * *
9283 TACATTTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTATCAATTCTAAGTC-CAGT
1 TTCATTTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTTCAATTCCAAGTCTTA-T
** * * * *
9341 TTCATTTTCAAATCCTATTCGAGGTCTCTAATCGAGAGTTTTCAATTCAAAATCTTGT
1 TTCATTTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTTCAATTCCAAGTCTTAT
* * *
9399 TTCGTTTTTAAATCCTGATCGAGGTCTCTAGTCGAGAGTTTTCAATTCCAAGT-TTAGT
1 TTCATTTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTTCAATTCCAAGTCTTA-T
* * * * * *
9457 TTCATTTCCAAATCCTGCTTGAGGCCTTTAGTGGAGAGTTTTCAA-TCCACAGTCTTGT
1 TTCATTTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTTCAATTCCA-AGTCTTAT
** *
9515 TTTGTTTTCAAATCCTGCTCGAGGTCTCTAGCCGAGAGTTT
1 TTCATTTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTT
9556 CTGTTTCAAT
Statistics
Matches: 401, Mismatches: 43, Indels: 29
0.85 0.09 0.06
Matches are distributed among these distances:
57 22 0.05
58 222 0.55
59 2 0.00
63 155 0.39
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (58 bp):
TTCATTTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTTCAATTCCAAGTCTTAT
Found at i:16289 original size:11 final size:13
Alignment explanation
Indices: 16260--16284 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16250 TTGAAGAAGG
16260 AGAAGAGAGAAAT
1 AGAAGAGAGAAAT
16273 AGAAGAGAGAAA
1 AGAAGAGAGAAA
16285 GAAGAAAGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (13 bp):
AGAAGAGAGAAAT
Found at i:17267 original size:40 final size:41
Alignment explanation
Indices: 17206--17282 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 41
17196 AGTTTTCTAT
*
17206 TTAAGCAATTCCAAGAGAAGACTTTTGGAAAATAAAAATTC
1 TTAAGCAATTCCAAGAAAAGACTTTTGGAAAATAAAAATTC
17247 TTAA-CAATTCCAAGAAAAGACTTTTGGAAAATAAAA
1 TTAAGCAATTCCAAGAAAAGACTTTTGGAAAATAAAA
17283 GTTTTTAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 31 0.89
41 4 0.11
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.26
Consensus pattern (41 bp):
TTAAGCAATTCCAAGAAAAGACTTTTGGAAAATAAAAATTC
Found at i:18024 original size:16 final size:16
Alignment explanation
Indices: 18003--18040 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
17993 TTTAATTTCA
*
18003 TAATTTGCTTAGGAAT
1 TAATTTACTTAGGAAT
*
18019 TAATTTATTTAGGAAT
1 TAATTTACTTAGGAAT
18035 TAATTT
1 TAATTT
18041 TATTTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (16 bp):
TAATTTACTTAGGAAT
Found at i:18472 original size:18 final size:18
Alignment explanation
Indices: 18449--18483 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18439 ATTATTTTCT
*
18449 TTATCTATCTATTTATTA
1 TTATCTATCTATCTATTA
18467 TTATCTATCTATCTATT
1 TTATCTATCTATCTATT
18484 TATCTACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATCTATCTATCTATTA
Found at i:18575 original size:17 final size:17
Alignment explanation
Indices: 18553--18592 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
18543 TAGTATTTAT
*
18553 TATTATCTATTTAGTAC
1 TATTATCTATTTAATAC
*
18570 TATTATCTGTTTAATAC
1 TATTATCTATTTAATAC
18587 TATTAT
1 TATTAT
18593 TTATCTATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (17 bp):
TATTATCTATTTAATAC
Found at i:19240 original size:20 final size:20
Alignment explanation
Indices: 19217--19255 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19207 TTTTTTGTCT
*
19217 TTTTTGTTTTGTTT-TTTGAA
1 TTTTTATTTT-TTTATTTGAA
19237 TTTTTATTTTTTTATTTGA
1 TTTTTATTTTTTTATTTGA
19256 TTGTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (20 bp):
TTTTTATTTTTTTATTTGAA
Done.