Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012853.1 Corchorus capsularis cultivar CVL-1 contig12874, 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: 110095
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:7946 original size:1 final size:1
Alignment explanation
Indices: 7942--7966 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
7932 TTTCTTTCTC
7942 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
7967 GGCTAAGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16218 original size:396 final size:395
Alignment explanation
Indices: 15271--16270 Score: 1316
Period size: 396 Copynumber: 2.5 Consensus size: 395
15261 TCAAATCACT
* * * * **
15271 TTATATAATTTTTCTTATAGAATTATTATACAATACACTTTTCAGTGTAAATTTTACACTCCCTA
1 TTATATAA-TTTTCTTATAGGATTATTATACAATACGC-TGTCAGTGTAAATTTTAGACT-TTTA
* * * *
15336 AACGGGTTAAGAAATTGACACA-ATGCCCCATTTCAT-AGTCAATTAAATATTTAATATTAATAC
63 AGCGGGTTAAGAAGTTGACACATAT--CACATTTCATCA-TCAATTAAATATATAATATTAATAC
* ** * * *
15399 ATATTCCTTAAGGGGACACATGTCAACCC-T-------GCATATGTAGTCTGTTAAATTCGACTG
125 ATATTCCTTAAGGAGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCGACTG
* * * ** * ** *
15456 AC--AGTATAGTATAATTTTTCTTATAAGATTATTATATAATCCATTGTCAGTGTAAATTTTGGA
190 ACGGTGTATTGTATAATTTTTCTTATAAGATTATTATACAATAAACTGTCAAAGTAAATTTTGCA
* * * *
15519 CTATATAAGCGGGTTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTA
255 CTACATAAACGGGTTAAGAAGTTGACA-ACACCCCATTTCATAATTAATTAAATATATAATATTA
*
15584 ATACATATCTTCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTTTGCTAAAATCC
319 ATACATATCCTCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTTTGCTAAAATCC
15649 ACTGACGGTGTA
384 ACTGACGGTGTA
15661 TTATATAATTTCTCTTATAGGATTATTATACAATACGCTGTCAGTGTAAATTTTAGAC-TTTAAG
1 TTATATAATTT-TCTTATAGGATTATTATACAATACGCTGTCAGTGTAAATTTTAGACTTTTAAG
* *
15725 CGGGTTAAGAAGTTGACACATACCTA-ATTTCATCATTAATTAAATATATAATATTAATACATAT
65 CGGGTTAAGAAGTTGACACATATC-ACATTTCATCATCAATTAAATATATAATATTAATACATAT
* *
15789 TCCTTAA-GAGGACACATGTCAACCTTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACG
129 TCCTTAAGGA-GACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCGACTGACG
* * *
15853 GTGTATTGTATAATTGTTCTTATAGGATTATTATACAATAAACTGTCAAAGTAAATTTTGCACTC
193 GTGTATTGTATAATTTTTCTTATAAGATTATTATACAATAAACTGTCAAAGTAAATTTTGCACTA
*
15918 CATAAACGGGTTGAGAAGTTGAC-ACACCCCATTTCATAATTAATTAAATATATAATATTAATAC
258 CATAAACGGGTTAAGAAGTTGACAACACCCCATTTCATAATTAATTAAATATATAATATTAATAC
* * * *
15982 ATATTCCT-TAAGGGGACACATGTCAACCCTTAAA-GCCGTTATGTGCAGTTTGCTAAACTCCAC
323 ATA-TCCTCTAAGGGGACACATGTCAACCCTTAAACCCCG-CACGTGCAGTTTGCTAAAATCCAC
16045 TGACGGTGTA
386 TGACGGTGTA
* * *
16055 TTGTATAATTGTTCTTATAGGATTATTATACAACACGCTGTCTGTGTAAATTTTAGACTTTATAA
1 TTATATAATT-TTCTTATAGGATTATTATACAATACGCTGTCAGTGTAAATTTTAGACTTT-TAA
*
16120 GCGGGTTAAGAAGTTTACACATATCACATTTCATCATCAATTAAATATATAATATTAATACATAT
64 GCGGGTTAAGAAGTTGACACATATCACATTTCATCATCAATTAAATATATAATATTAATACATAT
*
16185 TCCCTAAGGAGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCGACTGACGG
129 TCCTTAAGGAGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCGACTGACGG
*
16250 TGTATTGGATAATTTTTCTTA
194 TGTATTGTATAATTTTTCTTA
16271 AGTTATACCA
Statistics
Matches: 535, Mismatches: 53, Indels: 38
0.85 0.08 0.06
Matches are distributed among these distances:
385 1 0.00
386 56 0.10
387 24 0.04
388 1 0.00
389 21 0.04
390 32 0.06
393 3 0.01
394 175 0.33
395 7 0.01
396 213 0.40
397 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (395 bp):
TTATATAATTTTCTTATAGGATTATTATACAATACGCTGTCAGTGTAAATTTTAGACTTTTAAGC
GGGTTAAGAAGTTGACACATATCACATTTCATCATCAATTAAATATATAATATTAATACATATTC
CTTAAGGAGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCGACTGACGGTG
TATTGTATAATTTTTCTTATAAGATTATTATACAATAAACTGTCAAAGTAAATTTTGCACTACAT
AAACGGGTTAAGAAGTTGACAACACCCCATTTCATAATTAATTAAATATATAATATTAATACATA
TCCTCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTTTGCTAAAATCCACTGACG
GTGTA
Found at i:16237 original size:199 final size:199
Alignment explanation
Indices: 15274--16270 Score: 1263
Period size: 197 Copynumber: 5.1 Consensus size: 199
15264 AATCACTTTA
* * * ** *
15274 TATAATTTTTCTTATAGAATTATTATACAATACACTTTTCAGTGTAAATTTTACACTCCCTAAAC
1 TATAATTTTTCTTATAGGATTATTATACAATACAC-TGTCAGTGTAAATTTTAGACTCTATAAGC
* * * * *
15339 GGGTTAAGAAATTGACACAATGCCCCATTTCATAGTCAATTAAATATTTAATATTAATACATATT
65 GGGTTAAGAAGTTGACAC-ATACCCCATTTCATAATTAATTAAATATATAATATTAATACATATT
** * * * * *
15404 CCTTAAGGGGACACATGTCAACCC-T-------GCATATGTAGTCTGTTAAATTCGACTGAC--A
129 CCTTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGT
*
15459 GTATAG
194 GTATTG
* * * * * *
15465 TATAATTTTTCTTATAAGATTATTATATAATCCATTGTCAGTGTAAATTTTGGACTATATAAGCG
1 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTAGACTCTATAAGCG
* * *
15530 GGTTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATA-TCT
66 GGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATATAATATTAATACATATTCC
* *
15594 TCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTTTGCTAAAATCCACTGACGGTG
131 T-TAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTG
*
15659 TATTA
195 TATTG
* *
15664 TATAATTTCTCTTATAGGATTATTATACAATACGCTGTCAGTGTAAATTTTAGACT-T-TAAGCG
1 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTAGACTCTATAAGCG
** *
15727 GGTTAAGAAGTTGACACATACCTAATTTCATCATTAATTAAATATATAATATTAATACATATTCC
66 GGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATATAATATTAATACATATTCC
* *
15792 TTAAGAGGACACATGTCAACCTTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGT
131 TTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGT
15857 ATTG
196 ATTG
* * ** * *
15861 TATAATTGTTCTTATAGGATTATTATACAATAAACTGTCAAAGTAAATTTT-GCACTCCATAAAC
1 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTAG-ACTCTATAAGC
*
15925 GGGTTGAGAAGTTGACAC--ACCCCATTTCATAATTAATTAAATATATAATATTAATACATATTC
65 GGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATATAATATTAATACATATTC
* * * *
15988 CTTAAGGGGACACATGTCAACCCTTAAA-GCCGTTATGTGCAGTTTGCTAAACTCCACTGACGGT
130 CTTAAGGGGACACATGTCAACCCTTAAACCCCG-CACGTGCAGTCTGCTAAACTCCACTGACGGT
16052 GTATTG
194 GTATTG
* * * * *
16058 TATAATTGTTCTTATAGGATTATTATACAACACGCTGTCTGTGTAAATTTTAGACTTTATAAGCG
1 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTAGACTCTATAAGCG
* * * * *
16123 GGTTAAGAAGTTTACACATATCACATTTCATCATCAATTAAATATATAATATTAATACATATTCC
66 GGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATATAATATTAATACATATTCC
* * *
16188 CTAAGGAGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCGACTGACGGTGT
131 TTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGT
16253 ATTG
196 ATTG
*
16257 GATAATTTTTCTTA
1 TATAATTTTTCTTA
16271 AGTTATACCA
Statistics
Matches: 698, Mismatches: 88, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
188 3 0.00
189 62 0.09
190 39 0.06
191 30 0.04
196 4 0.01
197 366 0.52
198 5 0.01
199 186 0.27
200 3 0.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.35
Consensus pattern (199 bp):
TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTAGACTCTATAAGCG
GGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATATAATATTAATACATATTCC
TTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGT
ATTG
Found at i:17887 original size:13 final size:13
Alignment explanation
Indices: 17871--17895 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17861 AGTGATTATT
17871 GAAAAAAGAAAAA
1 GAAAAAAGAAAAA
17884 GAAAAAAGAAAA
1 GAAAAAAGAAAA
17896 TTGAGAGTGT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
GAAAAAAGAAAAA
Found at i:18966 original size:2 final size:2
Alignment explanation
Indices: 18959--18994 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
18949 CCGAATCATG
*
18959 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18995 ATAAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18974 original size:10 final size:10
Alignment explanation
Indices: 18959--19000 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
18949 CCGAATCATG
18959 ATATATATAA
1 ATATATATAA
*
18969 ATATATATAT
1 ATATATATAA
*
18979 ATATATATAT
1 ATATATATAA
18989 AT-TATAATAA
1 ATATAT-ATAA
18999 AT
1 AT
19001 TTTATTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 3 0.10
10 26 0.90
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
ATATATATAA
Found at i:20040 original size:21 final size:20
Alignment explanation
Indices: 20016--20054 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
20006 ATATTTTATT
20016 AATAAATATTTTCTTTAAAAA
1 AATAAATATTTT-TTTAAAAA
20037 AATAAATATTTTTTTAAA
1 AATAAATATTTTTTTAAA
20055 TATAGAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAAATATTTTTTTAAAAA
Found at i:20167 original size:6 final size:6
Alignment explanation
Indices: 20156--20189 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
20146 TAAATATATT
20156 TAAATA TAAATATA TAAATA TAAATA TAAATA TA
1 TAAATA T-AA-ATA TAAATA TAAATA TAAATA TA
20190 TTGTTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 18 0.69
7 4 0.15
8 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:20190 original size:14 final size:15
Alignment explanation
Indices: 20146--20183 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
20136 TAATCTAATC
20146 TAAATATATTTAAATA
1 TAAATATA-TTAAATA
20162 TAAATATA-TAAATA
1 TAAATATATTAAATA
20176 TAAATATA
1 TAAATATA
20184 AATATATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.64
16 8 0.36
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAATATATTAAATA
Found at i:21438 original size:199 final size:199
Alignment explanation
Indices: 21098--22736 Score: 1976
Period size: 199 Copynumber: 8.3 Consensus size: 199
21088 TTAAACTAAG
* * * *
21098 GATTATTATACAATATATTGTCAGTGTAAATCTTAGACTCCATAAGCGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* *
21163 ATACCCCATTTCATAATTAATTAAATATTTGATATTAATACATATTCCCTAAGGGGACACATGTC
66 ATACCCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
** *
21228 AACCCTTAAACCCCGTGCGTGCAGTCTGCTAAACTCCACTAACGGTGTATTGTATAATTTTTTTT
131 AACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTTT
21293 ATAT
196 ATAT
* * **
21297 GATTATTATACAATACACTGTAAGTGTAAATCTTAAACTCCATAAGCGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* * ** *
21362 ATGCCCTAATTCATAATTAATTAAATATAAAATATTAATACATACTCCCTAAGGGGACACATGTC
66 ATACCCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
* ** *
21427 AACTCTTAAACCCCGTGCGTGCAGTCTGCTAAACTCCACTGATGGTGTATTGTATAATTTTTTTT
131 AACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTTT
21492 ATAT
196 ATAT
*
21496 GATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCAT-A------T----AG-T---AC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
*
21546 ---CCC-ATTTCATAATTAATTAAATATTTAATATTAATACATATTCCTTAAGGGGACACATGTC
66 ATACCCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
* ** * * *
21607 AACGCTTAAACCATGCACGTGCAGTCAGCTAAAATCCACTGATGGTGTATTGTATAATTTTTTTT
131 AACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTTT
21672 AT-T
196 ATAT
* * *
21675 GGATTATTATACAATACACTGTCAGTGTAAATCTTGAACTCCATAAGTGGGTTAAGAAGTTGACA
1 -GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACA
* * * *
21740 TATACCCTATTTCGTAATTAATTAAATATAAATTAATAATAATACATATTCCCTAAGGAGACACA
65 CATACCCTATTTCATAATTAATTAAATAT---TTAATATTAATACATATTCCCTAAGGGGACACA
* ** *
21805 TGTCAACCCTTAAACCTCGCGTGTGCAGTCTGCTAAACTCCACTGACGGTGCATTGTATAATTTT
127 TGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTT
21870 TTTTATAT
192 TTTTATAT
* * * * * * *
21878 GGTTATT-TACAATACACCGTTAGTATAAATTTTGCACACCATAAGCGGGTTAAGAAGTTGACAG
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* ** *
21942 ATACCCTATTTCACAATTAATTAAAATATAAAATATTAATACATATATTCCCTAAGGGAACACAT
66 ATACCCTATTTCATAATTAATT-AAATATTTAATATTAATAC--ATATTCCCTAAGGGGACACAT
* * * *
22007 ATCAACCCTTAAAGCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTATATAA--TAT
128 GTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTT
22070 TTTATAT
193 TTTATAT
* * *
22077 GATTATTATACAATACATTGTCAGTGTAAATTTTGGATTCCATAAGTGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
22142 ATA-CCTCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGT
66 ATACCCT-ATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGT
* * * * * *
22206 CAACCCCTGAACCCCGCATGTGCAGTCTGCT--ACTCCACTGACAGTGTATTGCT-TAATTCTTC
130 CAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTG-TATAATTTTTT
*
22268 TTATAA
194 TTATAT
* * * *
22274 GATTATTATACAATACACTGTTAGTATAAATTTTGGACTCCATAGGTGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* *
22339 ACACCGC-ATTTCATAATTAATTAAATATTTGATATTAATACATATTCCCTAAGGGGACACATGT
66 ATACC-CTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGT
* ** * * * * * * * * * *
22403 CAACCTTTAAATACTGTACATGCAGTCTGCTAAAATTCATTAACGG-GAACTGTATAATTTTTCT
130 CAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTT
*
22467 TATAA
195 TATAT
* *
22472 GATTATTATACAATACACTATCAGTGTAAATTTTGGACTCCATAATCGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* * * *
22537 ATACCCCATTTC---A-TAATTAAATATTTAATATTAATATATATTCCCTAAGGGTACACATGTT
66 ATACCCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
* * *
22598 AACCCTTAAAGTTAAACTCCGCACGTGCAGTCTACTAAACTCCACTAACGGTGTATTGTATAAAT
131 AACCC------TTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTAT-AAT
*
22663 TTTCTTATATAT
189 TTT-TTTTATAT
* * *
22675 AGAATTATTATACAATACACTGTCAGTGTAAAATTTGGACACTATAAGCGGGTTAAGAAGTT
1 -G-ATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTT
22737 TTTGTACCAA
Statistics
Matches: 1239, Mismatches: 152, Indels: 92
0.84 0.10 0.06
Matches are distributed among these distances:
179 1 0.00
180 153 0.12
181 4 0.00
184 2 0.00
187 2 0.00
188 2 0.00
191 2 0.00
192 2 0.00
194 48 0.04
195 23 0.02
196 1 0.00
197 196 0.16
198 91 0.07
199 297 0.24
200 96 0.08
201 148 0.12
202 110 0.09
203 6 0.00
204 1 0.00
205 54 0.04
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (199 bp):
GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
ATACCCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
AACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTTT
ATAT
Found at i:21993 original size:201 final size:199
Alignment explanation
Indices: 21543--22736 Score: 1414
Period size: 197 Copynumber: 6.0 Consensus size: 199
21533 CTCCATATAG
* *
21543 TACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCTTAAGGGGACACATGTCA
1 TACCCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCA
* * * *
21608 ACGCTTAAACCAT-GCACGTGCAGTCAGCTAAAATCCACTGATGGTGTATTGTATAATTTTTTTT
66 ACCCTTAAACC-TCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTTT
* * *
21672 AT-TGGATTATTATACAATACACTGTCAGTGTAAATCTTGAACTCCATAAGTGGGTTAAGAAGTT
130 ATAT-GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTT
*
21736 GACATA
194 GACACA
* * *
21742 TACCCTATTTCGTAATTAATTAAATATAAATTAATAATAATACATATTCCCTAAGGAGACACATG
1 TACCCTATTTCATAATTAATTAAATAT---TTAATATTAATACATATTCCCTAAGGGGACACATG
** *
21807 TCAACCCTTAAACCTCGCGTGTGCAGTCTGCTAAACTCCACTGACGGTGCATTGTATAATTTTTT
63 TCAACCCTTAAACCTCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTT
* * * * * *
21872 TTATATGGTTATT-TACAATACACCGTTAGTATAAATTTTGCACACCATAAGCGGGTTAAGAAGT
128 TTATATGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGT
*
21936 TGACAGA
193 TGACACA
* ** * *
21943 TACCCTATTTCACAATTAATTAAAATATAAAATATTAATACATATATTCCCTAAGGGAACACATA
1 TACCCTATTTCATAATTAATT-AAATATTTAATATTAATAC--ATATTCCCTAAGGGGACACATG
* *
22008 TCAACCCTTAAAGCC-CGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTATATAA--TAT
63 TCAACCCTTAAA-CCTCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTT
* * *
22070 TTTATATGATTATTATACAATACATTGTCAGTGTAAATTTTGGATTCCATAAGTGGGTTAAGAAG
127 TTTATATGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAG
22135 TTGACACA
192 TTGACACA
22143 TA-CCTCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
1 TACCCT-ATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
* * * * * * *
22207 AACCCCTGAACCCCGCATGTGCAGTCTGCT--ACTCCACTGACAGTGTATTGCT-TAATTCTTCT
65 AACCCTTAAACCTCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTG-TATAATTTTTTT
* * * * *
22269 TATAAGATTATTATACAATACACTGTTAGTATAAATTTTGGACTCCATAGGTGGGTTAAGAAGTT
129 TATATGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTT
22334 GACACA
194 GACACA
* *
22340 CACCGC-ATTTCATAATTAATTAAATATTTGATATTAATACATATTCCCTAAGGGGACACATGTC
1 TACC-CTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
* * * * * * * * * * *
22404 AACCTTTAAATACT-GTACATGCAGTCTGCTAAAATTCATTAACGG-GAACTGTATAATTTTTCT
65 AACCCTTAAA-CCTCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTT
* * *
22467 TATAAGATTATTATACAATACACTATCAGTGTAAATTTTGGACTCCATAATCGGGTTAAGAAGTT
129 TATATGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTT
22532 GACACA
194 GACACA
* * * *
22538 TACCCCATTTC---A-TAATTAAATATTTAATATTAATATATATTCCCTAAGGGTACACATGTTA
1 TACCCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCA
* * *
22599 ACCCTTAAAGTTAAACTCCGCACGTGCAGTCTACTAAACTCCACTAACGGTGTATTGTATAAATT
66 ACCCTT--A---AACCT-CGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTAT-AATT
* * * *
22664 TTCTTATATATAGAATTATTATACAATACACTGTCAGTGTAAAATTTGGACACTATAAGCGGGTT
124 TT-TTTTATAT-G-ATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTT
22729 AAGAAGTT
186 AAGAAGTT
22737 TTTGTACCAA
Statistics
Matches: 852, Mismatches: 109, Indels: 62
0.83 0.11 0.06
Matches are distributed among these distances:
194 50 0.06
195 22 0.03
196 4 0.00
197 193 0.23
198 91 0.11
199 81 0.10
200 90 0.11
201 148 0.17
202 112 0.13
203 6 0.01
204 1 0.00
205 54 0.06
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (199 bp):
TACCCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCA
ACCCTTAAACCTCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTTTA
TATGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGA
CACA
Found at i:22692 original size:600 final size:595
Alignment explanation
Indices: 21098--22736 Score: 1789
Period size: 581 Copynumber: 2.8 Consensus size: 595
21088 TTAAACTAAG
* * * *
21098 GATTATTATACAATATATTGTCAGTGTAAATCTT-AGACTCCATAAGCGGGTTAAGAAGTTGACA
1 GATTATTATACAATACACTGTCAGTATAAATCTTGA-ACTCCATAAGTGGGTTAAGAAGTTGACA
* * * * *
21162 CATACCCCATTTCATAATTAATTAAATAT-TTGATATTAATACATATTCCCTAAGGGGACACATG
65 CACACCCTATTTCATAATTAATTAAATATATTAATAATAATACATATTCCCTAAGGAGACACATG
* * ** * * * * *
21226 TCAACCCTTAAACCCCGTGCGTGCAGTCTGCTAAACTCCACTAACGGTGTATTGTATAATTTTTT
130 TCAACCCTTAAAACTCGCACATGCAGTCTGCTAAAATCCACTAACGGTGAACTGTATAATTTTTC
* ** * * * ** *
21291 TTATATGATTATTATACAATACACTGTAAGTGTAAATCTTAAACTCCATAAGCGGGTTAAGAAGT
195 TTATAAGATTATT-TACAATACACCATCAGTATAAATTTTGCACACCATAAGCGGGTTAAGAAGT
* * * * * * *
21356 TGACACATGCCCTAATTCATAATTAATT-AAATATAAAATATTAAT-ACATACTCCCTAAGGGGA
259 TGACACATACCC-CATTTACAATTAATTAAAATATAAAATATTAATAATATATTCCCTAAGGGAA
* * * ** * * * *
21419 CACATGTCAACTCTTAAACCCCGTGCGTGCAGTCTGCTAAACTCCACTGATGGTGTATTGTATAA
323 CACATATCAACCCTTAAAGCCCGCACGTGCAGTCTACTAAACTCCACTAACGGTGTATTATATAA
* * * *
21484 TTTTTTTTATATGATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCAT-A------T-
388 --TATTTTATATGATTATTATACAATACACTGTCAGTGTAAAATTTGGACACCATAAGCGGGTTA
*
21541 ---A---G-----TACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCTTAAG
451 AGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAG
* * * **
21595 GGGACACATGTCAACGCTTAAACCATGCACGTGCAGTCAGCTAAAATCCACTGATGGTGTATTGT
516 GGGACACATGTCAACCCCTAAACCACGCACGTGCAGTCAGCT-AAATCCACTGACAGTGTATTGT
* * **
21660 ATAATTTTTTTTATTG
580 ATAATTCTTCTTATAA
* *
21676 GATTATTATACAATACACTGTCAGTGTAAATCTTGAACTCCATAAGTGGGTTAAGAAGTTGACAT
1 GATTATTATACAATACACTGTCAGTATAAATCTTGAACTCCATAAGTGGGTTAAGAAGTTGACAC
* *
21741 ATACCCTATTTCGTAATTAATTAAATATAAATTAATAATAATACATATTCCCTAAGGAGACACAT
66 ACACCCTATTTCATAATTAATTAAATAT--ATTAATAATAATACATATTCCCTAAGGAGACACAT
* *** * * * *
21806 GTCAACCCTTAAACCTCGCGTGTGCAGTCTGCTAAACTCCACTGACGGTGCATTGTATAATTTTT
129 GTCAACCCTTAAAACTCGCACATGCAGTCTGCTAAAATCCACTAACGGTGAACTGTATAATTTTT
* * * * *
21871 TTTATATGGTTATTTACAATACACCGTTAGTATAAATTTTGCACACCATAAGCGGGTTAAGAAGT
194 CTTATAAGATTATTTACAATACACCATCAGTATAAATTTTGCACACCATAAGCGGGTTAAGAAGT
* *
21936 TGACAGATACCCTATTTCACAATTAATTAAAATATAAAATATTAATACATATATTCCCTAAGGGA
259 TGACACATACCCCATTT-ACAATTAATTAAAATATAAAATATTAATA-ATATATTCCCTAAGGGA
* *
22001 ACACATATCAACCCTTAAAGCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTATATA
322 ACACATATCAACCCTTAAAGCCCGCACGTGCAGTCTACTAAACTCCACTAACGGTGTATTATATA
* * ** *
22066 ATATTTTATATGATTATTATACAATACATTGTCAGTGTAAATTTTGGATTCCATAAGTGGGTTAA
387 ATATTTTATATGATTATTATACAATACACTGTCAGTGTAAAATTTGGACACCATAAGCGGGTTAA
*
22131 GAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGG
452 GAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGG
* * * * *
22196 GGACACATGTCAACCCCTGAACCCCGCATGTGCAGTCTGCT-ACTCCACTGACAGTGTATTGCT-
517 GGACACATGTCAACCCCTAAACCACGCACGTGCAGTCAGCTAAATCCACTGACAGTGTATTG-TA
22259 TAATTCTTCTTATAA
581 TAATTCTTCTTATAA
* * * *
22274 GATTATTATACAATACACTGTTAGTATAAATTTTGGACTCCATAGGTGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTATAAATCTTGAACTCCATAAGTGGGTTAAGAAGTTGACAC
* * *
22339 ACACCGC-ATTTCATAATTAATTAAATAT-TTGATATTAATACATATTCCCTAAGGGGACACATG
66 ACACC-CTATTTCATAATTAATTAAATATATTAATAATAATACATATTCCCTAAGGAGACACATG
* * * *
22402 TCAACCTTTAAATACT-GTACATGCAGTCTGCTAAAATTCATTAACGG-GAACTGTATAATTTTT
130 TCAACCCTTAAA-ACTCGCACATGCAGTCTGCTAAAATCCACTAACGGTGAACTGTATAATTTTT
* * * * *
22465 CTTATAAGATTATTATACAATACACTATCAGTGTAAATTTTGGACTCCATAATCGGGTTAAGAAG
194 CTTATAAGATTATT-TACAATACACCATCAGTATAAATTTTGCACACCATAAGCGGGTTAAGAAG
** *
22530 TTGACACATACCCCATTT-C-A-TAATT-AAATATTTAATATTAAT-ATATATTCCCTAAGGGTA
258 TTGACACATACCCCATTTACAATTAATTAAAATATAAAATATTAATAATATATTCCCTAAGGGAA
* *
22590 CACATGTTAACCCTTAAAGTTAAACTCCGCACGTGCAGTCTACTAAACTCCACTAACGGTGTATT
323 CACATATCAACCCTTAAAG-----C-CCGCACGTGCAGTCTACTAAACTCCACTAACGGTGTATT
* * *
22655 GTATAAATTTTCTTATATATAGAATTATTATACAATACACTGTCAGTGTAAAATTTGGACACTAT
382 ATAT-AA-TAT-TT-TATAT-G-ATTATTATACAATACACTGTCAGTGTAAAATTTGGACACCAT
22720 AAGCGGGTTAAGAAGTT
441 AAGCGGGTTAAGAAGTT
22737 TTTGTACCAA
Statistics
Matches: 911, Mismatches: 107, Indels: 64
0.84 0.10 0.06
Matches are distributed among these distances:
578 85 0.09
579 4 0.00
580 63 0.07
581 170 0.19
582 1 0.00
583 73 0.08
588 35 0.04
590 15 0.02
591 5 0.01
592 2 0.00
593 2 0.00
594 65 0.07
595 128 0.14
596 4 0.00
597 2 0.00
598 116 0.13
599 3 0.00
600 138 0.15
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (595 bp):
GATTATTATACAATACACTGTCAGTATAAATCTTGAACTCCATAAGTGGGTTAAGAAGTTGACAC
ACACCCTATTTCATAATTAATTAAATATATTAATAATAATACATATTCCCTAAGGAGACACATGT
CAACCCTTAAAACTCGCACATGCAGTCTGCTAAAATCCACTAACGGTGAACTGTATAATTTTTCT
TATAAGATTATTTACAATACACCATCAGTATAAATTTTGCACACCATAAGCGGGTTAAGAAGTTG
ACACATACCCCATTTACAATTAATTAAAATATAAAATATTAATAATATATTCCCTAAGGGAACAC
ATATCAACCCTTAAAGCCCGCACGTGCAGTCTACTAAACTCCACTAACGGTGTATTATATAATAT
TTTATATGATTATTATACAATACACTGTCAGTGTAAAATTTGGACACCATAAGCGGGTTAAGAAG
TTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGAC
ACATGTCAACCCCTAAACCACGCACGTGCAGTCAGCTAAATCCACTGACAGTGTATTGTATAATT
CTTCTTATAA
Found at i:24452 original size:2 final size:2
Alignment explanation
Indices: 24427--24470 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
24417 TGTTGTAGCA
*
24427 AT AT -T AT AT AT -T A- AT -T AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24465 AT AT AT
1 AT AT AT
24471 CAATTGACTG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
1 4 0.11
2 32 0.89
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33086 original size:15 final size:15
Alignment explanation
Indices: 33066--33095 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33056 AGAAGATTTA
33066 ATATTCGTATGAAAT
1 ATATTCGTATGAAAT
*
33081 ATATTCTTATGAAAT
1 ATATTCGTATGAAAT
33096 TAAATTATGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (15 bp):
ATATTCGTATGAAAT
Found at i:48600 original size:7 final size:7
Alignment explanation
Indices: 48588--48621 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
48578 AAATATTGTG
*
48588 AAAAAAA
1 AAAAAAC
48595 AAAAAAC
1 AAAAAAC
48602 AAAAAAC
1 AAAAAAC
48609 AAAAAAC
1 AAAAAAC
48616 AAAAAA
1 AAAAAA
48622 GAATGGGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:49297 original size:15 final size:16
Alignment explanation
Indices: 49265--49308 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
49255 AAGCTAAATC
49265 CTCTTCTTTCTTTCTTT
1 CTCTTCTTT-TTTCTTT
*
49282 CT-TTCTTTTTTTTTT
1 CTCTTCTTTTTTCTTT
49297 CTCTCTCTTTTT
1 CTCT-TCTTTTT
49309 CATCCATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 8 0.33
16 7 0.29
17 9 0.38
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
CTCTTCTTTTTTCTTT
Found at i:52217 original size:13 final size:13
Alignment explanation
Indices: 52184--52216 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
52174 TGCTATCTTC
*
52184 TTCTTCTTCTTTT
1 TTCTTTTTCTTTT
52197 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
52210 TT-TTTTT
1 TTCTTTTT
52217 TTAAATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTCTTTTTCTTTT
Found at i:55669 original size:61 final size:61
Alignment explanation
Indices: 55574--55688 Score: 194
Period size: 61 Copynumber: 1.9 Consensus size: 61
55564 AACTCCCACA
* *
55574 GACTCGAGTAGGATCATTACTCCATCAGTTGAGCTAACAACTTGGGTGCTTATACGGCACG
1 GACTCGAGTAGGATCATTACTCCACCAGTTGAGCTAACAACTTGAGTGCTTATACGGCACG
* *
55635 GACTCGAGTAGGATTATTACTCCACCAGTTGAGCTAACAACTTGAGTGTTTATA
1 GACTCGAGTAGGATCATTACTCCACCAGTTGAGCTAACAACTTGAGTGCTTATA
55689 ATCGTACTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.29
Consensus pattern (61 bp):
GACTCGAGTAGGATCATTACTCCACCAGTTGAGCTAACAACTTGAGTGCTTATACGGCACG
Found at i:58276 original size:19 final size:19
Alignment explanation
Indices: 58207--58283 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 19
58197 CGTAATAATT
58207 ATTTATATCTTTTAGTAAC
1 ATTTATATCTTTTAGTAAC
* **
58226 ATTTAGAATCTCAT-GT-A-
1 ATTTA-TATCTTTTAGTAAC
* *
58243 ATCT-TAT-TATTAGTAAC
1 ATTTATATCTTTTAGTAAC
58260 ATTTATATCTTTTAGTAAC
1 ATTTATATCTTTTAGTAAC
58279 ATTTA
1 ATTTA
58284 GAATCTCATA
Statistics
Matches: 43, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
14 2 0.05
15 4 0.09
16 1 0.02
17 6 0.14
18 4 0.09
19 21 0.49
20 5 0.12
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.49
Consensus pattern (19 bp):
ATTTATATCTTTTAGTAAC
Found at i:67833 original size:3 final size:3
Alignment explanation
Indices: 67825--67880 Score: 78
Period size: 3 Copynumber: 18.3 Consensus size: 3
67815 CTTCTGCCAT
*
67825 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- ATC TTC TTGAC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT--C
67874 TTC TTC T
1 TTC TTC T
67881 ATATTATGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 1 0.02
3 44 0.92
5 3 0.06
ACGTcount: A:0.04, C:0.30, G:0.02, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:70565 original size:74 final size:74
Alignment explanation
Indices: 70487--70638 Score: 236
Period size: 74 Copynumber: 2.1 Consensus size: 74
70477 TGGTCTTTTC
* *
70487 ACACTTTTCAGG-TGACTAAAAAGCCCCTCTATGAGTTTCTCCTATTCCTTTTCCTTCTACCCTT
1 ACACTTTTC-GGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTA-CCTT
70551 TTTT-GTAATT
64 TTTTCGTAATT
* *
70561 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCTTTTTCCTTTTACCTTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCTTTT
70626 TTCGTAATT
66 TTCGTAATT
70635 ACAC
1 ACAC
70639 ATTCCTTAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
73 10 0.14
74 62 0.86
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (74 bp):
ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCTTTT
TTCGTAATT
Found at i:74580 original size:109 final size:109
Alignment explanation
Indices: 74384--74658 Score: 439
Period size: 109 Copynumber: 2.5 Consensus size: 109
74374 ACTATTATAG
* *
74384 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
74449 TATTTTTACACAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACACAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
74498 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
74563 TTAC-CAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACAC-AAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
74607 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
74659 TAATTTTTTT
Statistics
Matches: 156, Mismatches: 3, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
108 8 0.05
109 122 0.78
110 3 0.02
111 2 0.01
114 21 0.13
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACACAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:86159 original size:24 final size:24
Alignment explanation
Indices: 86127--86174 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
86117 ACTATGAGGA
86127 TAAAGTTCTCCCAACAATAGTTTT
1 TAAAGTTCTCCCAACAATAGTTTT
86151 TAAAGTTCTCCCAACAATAGTTTT
1 TAAAGTTCTCCCAACAATAGTTTT
86175 CTTTTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (24 bp):
TAAAGTTCTCCCAACAATAGTTTT
Found at i:86401 original size:28 final size:29
Alignment explanation
Indices: 86364--86424 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
86354 TCGGTTTATT
* *
86364 TTTTTATTTTATAATAATTTAATTAAACC
1 TTTTTATTTTACAATAATTTAATTAAACA
* *
86393 TTTTT-TTTTGCATTAATTTAATTAAACA
1 TTTTTATTTTACAATAATTTAATTAAACA
86421 TTTT
1 TTTT
86425 AATTCATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTTATTTTACAATAATTTAATTAAACA
Found at i:99807 original size:28 final size:28
Alignment explanation
Indices: 99769--99822 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
99759 CATACACATG
99769 ATTATCATGATTACACCTAACATCTTTT
1 ATTATCATGATTACACCTAACATCTTTT
*
99797 ATTATCATGATTAGACCTAACATCTT
1 ATTATCATGATTACACCTAACATCTT
99823 CTATAGTCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (28 bp):
ATTATCATGATTACACCTAACATCTTTT
Found at i:109876 original size:22 final size:20
Alignment explanation
Indices: 109836--109880 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
109826 ACTTAACCTC
109836 TGTATATAATATACAATACA
1 TGTATATAATATACAATACA
*
109856 TGTATATATATATACCCATACA
1 TGTATATA-ATATA-CAATACA
109878 TGT
1 TGT
109881 TGATTTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 5 0.23
22 9 0.41
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (20 bp):
TGTATATAATATACAATACA
Done.