Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004244.1 Hibiscus syriacus cultivar Beakdansim tig00009303_pilon, 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: 155556
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:548 original size:11 final size:12
Alignment explanation
Indices: 532--560 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
522 TAGAAAAATA
532 CTAACTC-TCAC
1 CTAACTCTTCAC
543 CTAACTCTTCAC
1 CTAACTCTTCAC
555 CTAACT
1 CTAACT
561 AAATTGATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.28, C:0.41, G:0.00, T:0.31
Consensus pattern (12 bp):
CTAACTCTTCAC
Found at i:10968 original size:66 final size:62
Alignment explanation
Indices: 10815--10934 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 62
10805 AAGTATTTTC
* * *
10815 ATCTTTTTAACTTTGAATATTAAATATAATTGTATACTTTTGTATATTTCAAATTAAAATAAT
1 ATCTATTTAAGTTTGAATATTAAA-ATAATTGTATACTTTTGAATATTTCAAATTAAAATAAT
* *
10878 ATCTATTTAAGTTTGAATGA-TAAAATGAGTT-TAT-CTTTTGAATATTTTAAATTAAAA
1 ATCTATTTAAGTTTGAAT-ATTAAAAT-AATTGTATACTTTTGAATATTTCAAATTAAAA
10935 GATATTATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
61 21 0.42
62 5 0.10
63 23 0.46
64 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (62 bp):
ATCTATTTAAGTTTGAATATTAAAATAATTGTATACTTTTGAATATTTCAAATTAAAATAAT
Found at i:12542 original size:12 final size:13
Alignment explanation
Indices: 12499--12542 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
12489 TACTTTATAT
12499 ATTAATTATAATC
1 ATTAATTATAATC
12512 ATTATATTATAAATC
1 ATTA-ATTAT-AATC
12527 -TTAA-TATAATC
1 ATTAATTATAATC
12538 ATTAA
1 ATTAA
12543 ATTAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
11 4 0.14
12 7 0.25
13 5 0.18
14 8 0.29
15 4 0.14
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTAATTATAATC
Found at i:12580 original size:15 final size:14
Alignment explanation
Indices: 12538--12584 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
12528 TAATATAATC
12538 ATTAAAT-TAATTTT
1 ATTAAATAT-ATTTT
*
12552 ATTAAATATTTTTT
1 ATTAAATATATTTT
*
12566 ATTTAATATGATTTT
1 ATTAAATAT-ATTTT
12581 ATTA
1 ATTA
12585 GATTATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 19 0.70
15 8 0.30
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTAAATATATTTT
Found at i:12674 original size:23 final size:25
Alignment explanation
Indices: 12639--12684 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
12629 TGTGTACTAA
12639 TTAATTAATAA-TTT-AAATATAAT
1 TTAATTAATAATTTTAAAATATAAT
12662 TTAACTTAA-AATTTTAAAATATA
1 TTAA-TTAATAATTTTAAAATATA
12685 TATAAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAATTAATAATTTTAAAATATAAT
Found at i:13321 original size:12 final size:12
Alignment explanation
Indices: 13269--13335 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
13259 TAATGATAAA
*
13269 TATATATACACT
1 TATATATATACT
*
13281 TATGTATATACT
1 TATATATATACT
* *
13293 TACATACAT--T
1 TATATATATACT
13303 GTATATATATAC-
1 -TATATATATACT
13315 T-TATATATACT
1 TATATATATACT
*
13326 TATACATATA
1 TATATATATA
13336 TATTTGTATA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
10 10 0.24
11 9 0.21
12 23 0.55
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (12 bp):
TATATATATACT
Found at i:19229 original size:21 final size:21
Alignment explanation
Indices: 19205--19268 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
19195 TACATACATC
19205 ATACATATATACTTATATATT
1 ATACATATATACTTATATATT
*
19226 ATACTTATATATATTTATATA-T
1 ATAC--ATATATACTTATATATT
* *
19248 ATTATATACATACTTATATAT
1 A-TACATATATACTTATATAT
19269 AGATTCTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
21 17 0.49
22 2 0.06
23 16 0.46
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (21 bp):
ATACATATATACTTATATATT
Found at i:19230 original size:13 final size:13
Alignment explanation
Indices: 19212--19237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19202 ATCATACATA
19212 TATACTTATATAT
1 TATACTTATATAT
19225 TATACTTATATAT
1 TATACTTATATAT
19238 ATTTATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TATACTTATATAT
Found at i:19269 original size:21 final size:23
Alignment explanation
Indices: 19205--19296 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 23
19195 TACATACATC
*
19205 ATAC-ATATATACTTATATAT-T
1 ATACTATACATACTTATATATAT
* *
19226 ATACTTATATATATTTATATATAT
1 ATAC-TATACATACTTATATATAT
*
19250 -TA-TATACATACTTATATATAG
1 ATACTATACATACTTATATATAT
* * * *
19271 ATTCTTTTATATACATATATATAT
1 ATAC-TATACATACTTATATATAT
19295 AT
1 AT
19297 GTGTACGTGT
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
21 20 0.36
22 1 0.02
23 17 0.30
24 18 0.32
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.50
Consensus pattern (23 bp):
ATACTATACATACTTATATATAT
Found at i:19282 original size:58 final size:58
Alignment explanation
Indices: 19167--19294 Score: 147
Period size: 58 Copynumber: 2.3 Consensus size: 58
19157 TCCATTCATA
* * * *
19167 TATACTTGTATATATTTATATATTTGTGTACATACATCATACATATATACTTATATAT
1 TATACTTATATATATTTATATATTTATATACATACATCATACATAGATACTTATATAT
* * *
19225 TATACTTATATATATTTATATATATTATATACATAC-TTATATATAGATTCTT-T-TA-
1 TATACTTATATATATTTATATAT-TTATATACATACATCATACATAGATACTTATATAT
*
19280 TATACATATATATAT
1 TATACTTATATATAT
19295 ATGTGTACGT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
55 14 0.23
56 2 0.03
57 1 0.02
58 34 0.56
59 10 0.16
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (58 bp):
TATACTTATATATATTTATATATTTATATACATACATCATACATAGATACTTATATAT
Found at i:19375 original size:23 final size:24
Alignment explanation
Indices: 19211--19447 Score: 87
Period size: 23 Copynumber: 10.2 Consensus size: 24
19201 CATCATACAT
*
19211 ATATACTTATATAT-TATACT-TAT
1 ATATACTTATATATATATA-TATAC
*
19234 ATATATTTATATATAT-TATATAC
1 ATATACTTATATATATATATATAC
* * **
19257 --ATACTTATATATAGAT-TCTTTT
1 ATATACTTATATATATATAT-ATAC
* * *
19279 ATATACATATATATATATGTGTAC
1 ATATACTTATATATATATATATAC
* * *
19303 GTGT-GTGTA-AT-TATATATATA-
1 ATATACT-TATATATATATATATAC
* * * *
19324 AGTATACATATACATAAATATA-AT
1 A-TATACTTATATATATATATATAC
*
19348 GTATACTTATATATATAT-TATAC
1 ATATACTTATATATATATATATAC
*
19371 ATATACTTATGTATA-ATATATACC
1 ATATACTTATATATATATATATA-C
*
19395 ATA-A-TGTATA-ATTTATACTTATA-
1 ATATACT-TATATATATATA--TATAC
*
19418 AGTATACTTATAT-TATATATATAT
1 A-TATACTTATATATATATATATAC
19442 ATATAC
1 ATATAC
19448 ACACTTATAG
Statistics
Matches: 155, Mismatches: 34, Indels: 50
0.65 0.14 0.21
Matches are distributed among these distances:
21 13 0.08
22 22 0.14
23 70 0.45
24 34 0.22
25 15 0.10
26 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (24 bp):
ATATACTTATATATATATATATAC
Found at i:19422 original size:19 final size:19
Alignment explanation
Indices: 19320--19534 Score: 65
Period size: 19 Copynumber: 10.9 Consensus size: 19
19310 TAATTATATA
*
19320 TATAAGTAT-ACATATAC-
1 TATAAGTATAATATATACT
* *
19337 -ATAAATATAATGTATACT
1 TATAAGTATAATATATACT
19355 TATATA-TATATTATACATATACT
1 TATA-AGTATA--AT--ATATACT
19378 TAT--GTATAATATATAC-
1 TATAAGTATAATATATACT
* *
19394 CATAATGTATAATTTATACT
1 TATAA-GTATAATATATACT
19414 TATAAGTATACTTATATTATA-T
1 TATAAGTATA---ATA-TATACT
*
19436 ATATATA-TATACACACTTATAGC-
1 -TATA-AGTATA-ATA--TATA-CT
*
19459 TACAAGTATAATGTATATA-T
1 TATAAGTATAA--TATATACT
19479 TATAAGTATAATATATACT
1 TATAAGTATAATATATACT
* * * *
19498 TAAAAGTATTATGTATAGT
1 TATAAGTATAATATATACT
* *
19517 TTTATGTATATATATATA
1 TATAAGTATA-ATATATA
19535 TATATATATA
Statistics
Matches: 148, Mismatches: 22, Indels: 53
0.66 0.10 0.24
Matches are distributed among these distances:
16 9 0.06
17 12 0.08
18 6 0.04
19 48 0.32
20 21 0.14
21 14 0.09
22 15 0.10
23 22 0.15
24 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (19 bp):
TATAAGTATAATATATACT
Found at i:19487 original size:20 final size:21
Alignment explanation
Indices: 19462--19514 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 21
19452 TTATAGCTAC
*
19462 AAGTATAATGTATATA-TTAT
1 AAGTATAATGTATATACTTAA
19482 AAGTATAA--TATATACTTAA
1 AAGTATAATGTATATACTTAA
*
19501 AAGTATTATGTATA
1 AAGTATAATGTATA
19515 GTTTTATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 8 0.29
21 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (21 bp):
AAGTATAATGTATATACTTAA
Found at i:19530 original size:2 final size:2
Alignment explanation
Indices: 19523--19567 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
19513 TAGTTTTATG
19523 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19565 TA T
1 TA T
19568 TAAAATTGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19799 original size:70 final size:70
Alignment explanation
Indices: 19698--19835 Score: 215
Period size: 70 Copynumber: 2.0 Consensus size: 70
19688 AGTTAAATAT
*
19698 TAATTTATGCAATTTAGTCTTTAAAATTATATTTGTATATGAAATTAACACATACTTATTTATAT
1 TAATTTATGCAATTTAGTCCTTAAAATTATATTTGTATATGAAATTAACACATACTTATTTATAT
19763 TTTTG
66 TTTTG
* * * *
19768 TAATTTACTTCAATTTTGTCCTT-AAATTATATTTGTATATGAAATTGACCCATACTTATTTATA
1 TAATTTA-TGCAATTTAGTCCTTAAAATTATATTTGTATATGAAATTAACACATACTTATTTATA
19832 TTTT
65 TTTT
19836 GATTTAGTCC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
70 50 0.81
71 12 0.19
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (70 bp):
TAATTTATGCAATTTAGTCCTTAAAATTATATTTGTATATGAAATTAACACATACTTATTTATAT
TTTTG
Found at i:29466 original size:17 final size:18
Alignment explanation
Indices: 29423--29463 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
29413 AATTTATATT
29423 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
29440 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
29458 ATTAAA
1 AGTAAA
29464 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:30041 original size:74 final size:75
Alignment explanation
Indices: 29917--30066 Score: 275
Period size: 74 Copynumber: 2.0 Consensus size: 75
29907 AACAGGCTTG
*
29917 TATGCAAATATGCCCAAAAAACCATACCCTAGAAAAGAAAGTGATTTGCAGAGAAAATAAAGCAA
1 TATGCAAATATGCCCAAAAAACCATACCCTAGAAAAGAAAGTGATTTGCAGAGAAAATAAAGAAA
29982 TTTATTAATA
66 TTTATTAATA
*
29992 TATGCAAATATGCCCAAAAAACCATGCCCT-GAAAAGAAAGTGATTTGCAGAGAAAATAAAGAAA
1 TATGCAAATATGCCCAAAAAACCATACCCTAGAAAAGAAAGTGATTTGCAGAGAAAATAAAGAAA
30056 TTTATTAATA
66 TTTATTAATA
30066 T
1 T
30067 TATATATTAC
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
74 44 0.60
75 29 0.40
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (75 bp):
TATGCAAATATGCCCAAAAAACCATACCCTAGAAAAGAAAGTGATTTGCAGAGAAAATAAAGAAA
TTTATTAATA
Found at i:41204 original size:3 final size:3
Alignment explanation
Indices: 41187--41257 Score: 99
Period size: 3 Copynumber: 23.3 Consensus size: 3
41177 ATATTATAAA
*
41187 TAT TAAT TA- TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
41232 TAT TAT TAT TAT TAA TATT TAT TAT T
1 TAT TAT TAT TAT TAT TA-T TAT TAT T
41258 TTACATTTGC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
2 2 0.03
3 54 0.89
4 5 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:41250 original size:9 final size:9
Alignment explanation
Indices: 41176--41245 Score: 79
Period size: 9 Copynumber: 7.8 Consensus size: 9
41166 CGGGCTTAAA
*
41176 AATATTATA
1 AATATTATT
41185 AATATTAATT
1 AATATT-ATT
41195 -ATATTATT
1 AATATTATT
*
41203 ATTATTATT
1 AATATTATT
41212 AATATTATT
1 AATATTATT
*
41221 ATTATTATT
1 AATATTATT
*
41230 ATTATTATT
1 AATATTATT
*
41239 ATTATTA
1 AATATTA
41246 ATATTTATTA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
8 3 0.05
9 50 0.91
10 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
AATATTATT
Found at i:47152 original size:24 final size:23
Alignment explanation
Indices: 47125--47169 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
47115 ACACCCTGCA
47125 TTTT-GCATATGCATCATTTATTGT
1 TTTTCGCA-ATGCATC-TTTATTGT
*
47149 TTTTCGCAATGTATCTTTATT
1 TTTTCGCAATGCATCTTTATT
47170 TTTCTTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.32
24 10 0.53
25 3 0.16
ACGTcount: A:0.20, C:0.13, G:0.11, T:0.56
Consensus pattern (23 bp):
TTTTCGCAATGCATCTTTATTGT
Found at i:55702 original size:55 final size:55
Alignment explanation
Indices: 55636--56080 Score: 390
Period size: 55 Copynumber: 8.2 Consensus size: 55
55626 GTGAAGCAAA
* * *
55636 TGAAGATTGTTCGAGTCTTATACTCTTTGAACAAATAGAGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * * * *
55691 TGAAGATTGTTCAAGTCTCATACTCTCTTAAGCAATAGGGAGCAGACATGAATAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * *
55746 TGAAAATTGTTCGAGTCTAATACTCTCTAAAGAAATAGGGAGCAGACACGAATGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * *
55801 TGAAAATTATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * *
55856 TGAAGGTTGTTCAAGTCATATACTCTCTGAAGAAATAGGGAGCGGACACGTTTGAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG-T
* * * *
55912 TGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATGGGGAGCGGACAC-ATTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGT
* * * * * ** *
55963 TGAAGA-T-TT--AGTCCTATACTCTCTGAAGGAATAGAGAACGGACTTG-TTTT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * * * *
56013 ATGAAGATTGTTTGAGTTTTATACTCCCTGAAGCAAA-AGGGAGCAAACCCAATGGT
1 -TGAAGATTGTTCGAGTCTTATACTCTCTGAAG-AAATAGGGAGCAGACACGATTGT
*
56069 CGAAGATTGTTC
1 TGAAGATTGTTC
56081 AAAGAAGAGG
Statistics
Matches: 322, Mismatches: 57, Indels: 22
0.80 0.14 0.05
Matches are distributed among these distances:
50 3 0.01
51 44 0.14
52 39 0.12
53 4 0.01
55 222 0.69
56 10 0.03
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
Found at i:56018 original size:51 final size:51
Alignment explanation
Indices: 55813--56022 Score: 226
Period size: 51 Copynumber: 4.0 Consensus size: 51
55803 AAAATTATTC
* * *
55813 GAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT-TGAAGGTT
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTT-TATGAAGATT
* * *
55864 GTTCAAGTCATATACTCTCTGAAGAAATAGGGAGCGGACACGTTTGATTGAAGATT
1 G----AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTTA-TGAAGATT
* *
55920 GAGTCCTATACTCTCTGAAGGAATGGGGAGCGGACACATTTGT-TGAAGATT
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTT-TATGAAGATT
* * * **
55971 TAGTCCTATACTCTCTGAAGGAATAGAGAACGGACTTGTTTTATGAAGATT
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTTATGAAGATT
56022 G
1 G
56023 TTTGAGTTTT
Statistics
Matches: 133, Mismatches: 18, Indels: 16
0.80 0.11 0.10
Matches are distributed among these distances:
50 1 0.01
51 51 0.38
52 36 0.27
55 37 0.28
56 8 0.06
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (51 bp):
GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTTATGAAGATT
Found at i:59372 original size:26 final size:26
Alignment explanation
Indices: 59342--59401 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
59332 ATAACCAATG
*
59342 CCATAAAATAATGGAAGGGTCAAACC
1 CCATAAAATAATGAAAGGGTCAAACC
*
59368 CCATAAAATAATGAAAGGGTCAAACT
1 CCATAAAATAATGAAAGGGTCAAACC
59394 CCATAAAA
1 CCATAAAA
59402 CAAATACAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.50, C:0.18, G:0.15, T:0.17
Consensus pattern (26 bp):
CCATAAAATAATGAAAGGGTCAAACC
Found at i:60467 original size:26 final size:25
Alignment explanation
Indices: 60417--60467 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
60407 TTTATTTTCT
*
60417 TTTTCTATAAAATTTTTTAAGTTTA
1 TTTTCTATAAAATTTTTAAAGTTTA
*
60442 TTTTCTCA-AAAATTTTATAAATTTTA
1 TTTTCT-ATAAAATTTT-TAAAGTTTA
60468 AATTAAGCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTTCTATAAAATTTTTAAAGTTTA
Found at i:60730 original size:14 final size:14
Alignment explanation
Indices: 60711--60753 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
60701 ATGACTGTAT
60711 GAGACAGTGCAGTA
1 GAGACAGTGCAGTA
60725 GAGACAGTGCAGTA
1 GAGACAGTGCAGTA
*
60739 GAGACAGGGCAGTA
1 GAGACAGTGCAGTA
60753 G
1 G
60754 GGACGGTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.35, C:0.14, G:0.40, T:0.12
Consensus pattern (14 bp):
GAGACAGTGCAGTA
Found at i:60988 original size:21 final size:21
Alignment explanation
Indices: 60962--61005 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
60952 AAACACTGCG
60962 CATTGCCCTTTGCCCAAAAGC
1 CATTGCCCTTTGCCCAAAAGC
60983 CATTGCCCTTTGCCCAAAAGC
1 CATTGCCCTTTGCCCAAAAGC
61004 CA
1 CA
61006 AAAAAAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.39, G:0.14, T:0.23
Consensus pattern (21 bp):
CATTGCCCTTTGCCCAAAAGC
Found at i:73561 original size:12 final size:12
Alignment explanation
Indices: 73544--73569 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
73534 AATCTCTCAT
73544 ATAGGTATTACA
1 ATAGGTATTACA
73556 ATAGGTATTACA
1 ATAGGTATTACA
73568 AT
1 AT
73570 TTGACAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (12 bp):
ATAGGTATTACA
Found at i:76426 original size:3 final size:3
Alignment explanation
Indices: 76418--76446 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
76408 ACTAGGCAGC
76418 GCT GCT GCT GCT GCT GCT GCT GCT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GC
76447 CTCCTGGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.34, T:0.31
Consensus pattern (3 bp):
GCT
Found at i:79029 original size:29 final size:29
Alignment explanation
Indices: 78987--79115 Score: 143
Period size: 29 Copynumber: 4.4 Consensus size: 29
78977 ACAAGATGGA
* * *
78987 GATATAATCACATACAGAGTCAGGACGGG
1 GATATAATCCCATACAAAATCAGGACGGG
* * *
79016 GATATCATCTCATACAAAATCAAGACGGG
1 GATATAATCCCATACAAAATCAGGACGGG
* * *
79045 GATATAATCCCACACAGAA-CTAGGACGAG
1 GATATAATCCCATACAAAATC-AGGACGGG
**
79074 GATATAATCCCATACAAAATCAGGGTGGG
1 GATATAATCCCATACAAAATCAGGACGGG
79103 GATATAATCCCAT
1 GATATAATCCCAT
79116 GCAGAATAAA
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
28 1 0.01
29 80 0.98
30 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (29 bp):
GATATAATCCCATACAAAATCAGGACGGG
Found at i:79049 original size:58 final size:58
Alignment explanation
Indices: 78978--79121 Score: 173
Period size: 58 Copynumber: 2.5 Consensus size: 58
78968 CAAAAAGAAA
* * * * * *
78978 CAAGATGGAGATATAATCACATACAG-AGTCAGGACGGGGATATCATCTCATACAAAAT
1 CAAGATGGGGATATAATCCCATACAGAACT-AGGACGAGGATATAATCCCATACAAAAT
* *
79036 CAAGACGGGGATATAATCCCACACAGAACTAGGACGAGGATATAATCCCATACAAAAT
1 CAAGATGGGGATATAATCCCATACAGAACTAGGACGAGGATATAATCCCATACAAAAT
* * *
79094 CAGGGTGGGGATATAATCCCATGCAGAA
1 CAAGATGGGGATATAATCCCATACAGAA
79122 TAAAAAAATG
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
58 70 0.97
59 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.18
Consensus pattern (58 bp):
CAAGATGGGGATATAATCCCATACAGAACTAGGACGAGGATATAATCCCATACAAAAT
Found at i:82724 original size:50 final size:50
Alignment explanation
Indices: 82649--82774 Score: 173
Period size: 50 Copynumber: 2.5 Consensus size: 50
82639 GGACATTCCT
* * * *
82649 TCCGAAGAGGATCCCAATCATAAATAGAAATC-AGAATAAAGATATAACTC
1 TCCGAAGATGATCCCAAACAAAAATAGAAATCGA-AATAAAGATATAACCC
**
82699 TCCGAAGATGATCCCAAACAAAAATAGAAATCGAAATGGAGATATAACCC
1 TCCGAAGATGATCCCAAACAAAAATAGAAATCGAAATAAAGATATAACCC
*
82749 TCCGAAGATGATCCCAAACAGAAATA
1 TCCGAAGATGATCCCAAACAAAAATA
82775 TGATAGGGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 67 0.99
51 1 0.01
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (50 bp):
TCCGAAGATGATCCCAAACAAAAATAGAAATCGAAATAAAGATATAACCC
Found at i:82883 original size:28 final size:29
Alignment explanation
Indices: 82776--82889 Score: 140
Period size: 29 Copynumber: 4.0 Consensus size: 29
82766 ACAGAAATAT
* * *
82776 GATAGGGATATAAACCCATACAGAATGAG
1 GATAGGGATATAATCCCATGCAGAATCAG
*
82805 GATGGGGATATAATCCCATGCAGAATCAG
1 GATAGGGATATAATCCCATGCAGAATCAG
* * *
82834 GTTAGGGAAATAATCTCATGCAGAATCAG
1 GATAGGGATATAATCCCATGCAGAATCAG
* *
82863 GAT-GTGATATAATCTCATGCAGAATCA
1 GATAGGGATATAATCCCATGCAGAATCA
82890 AAAATGTATC
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
28 22 0.30
29 52 0.70
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.23
Consensus pattern (29 bp):
GATAGGGATATAATCCCATGCAGAATCAG
Found at i:85666 original size:6 final size:6
Alignment explanation
Indices: 85655--85713 Score: 91
Period size: 6 Copynumber: 9.8 Consensus size: 6
85645 GGCTCGGCTT
* * *
85655 GTGGTC GTGGTC GTGGTT GAGGTC GTGGTC GTGGTT GTGGTC GTGGTC
1 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
85703 GTGGTC GTGGT
1 GTGGTC GTGGT
85714 AATACGTGTC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.02, C:0.12, G:0.51, T:0.36
Consensus pattern (6 bp):
GTGGTC
Found at i:85712 original size:18 final size:18
Alignment explanation
Indices: 85653--85713 Score: 104
Period size: 18 Copynumber: 3.4 Consensus size: 18
85643 TCGGCTCGGC
85653 TTGTGGTCGTGGTCGTGG
1 TTGTGGTCGTGGTCGTGG
*
85671 TTGAGGTCGTGGTCGTGG
1 TTGTGGTCGTGGTCGTGG
85689 TTGTGGTCGTGGTCGTGG
1 TTGTGGTCGTGGTCGTGG
*
85707 TCGTGGT
1 TTGTGGT
85714 AATACGTGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.02, C:0.11, G:0.49, T:0.38
Consensus pattern (18 bp):
TTGTGGTCGTGGTCGTGG
Found at i:87680 original size:17 final size:19
Alignment explanation
Indices: 87643--87680 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
87633 TCTTTTTTTC
*
87643 TTTCGAACAGTCTCTCTTT
1 TTTCGAACAGTCTCGCTTT
87662 TTTCGAACAG-CT-GCTTT
1 TTTCGAACAGTCTCGCTTT
87679 TT
1 TT
87681 GTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.16, C:0.24, G:0.13, T:0.47
Consensus pattern (19 bp):
TTTCGAACAGTCTCGCTTT
Found at i:87695 original size:14 final size:14
Alignment explanation
Indices: 87676--87702 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
87666 GAACAGCTGC
87676 TTTTTGTTTTTTTT
1 TTTTTGTTTTTTTT
87690 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
87703 CATTCAACAT
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:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (14 bp):
TTTTTGTTTTTTTT
Found at i:88569 original size:13 final size:12
Alignment explanation
Indices: 88550--88583 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
88540 TGCTTAATCG
88550 AAAAAAAATAAA
1 AAAAAAAATAAA
*
88562 AGAAAAAATAAA
1 AAAAAAAATAAA
*
88574 AATAAAAATA
1 AAAAAAAATA
88584 TAACGGAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAAAAAATAAA
Found at i:101141 original size:6 final size:6
Alignment explanation
Indices: 101130--101190 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
101120 TCGGCTCGGC
* * *
101130 TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
*
101178 TTGTGG TCGTGG T
1 TCGTGG TCGTGG T
101191 AATACGTGTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.05, C:0.15, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:101490 original size:22 final size:22
Alignment explanation
Indices: 101465--101519 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
101455 TCAGGAGTTA
* *
101465 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
101487 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
101509 CGGGAGTTATA
1 CAGGAGTTATA
101520 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:105980 original size:31 final size:31
Alignment explanation
Indices: 105945--106007 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 31
105935 ATATAATATT
105945 TAATTATT-TTTATTTTTATTTAATTAAGATG
1 TAATT-TTATTTATTTTTATTTAATTAAGATG
105976 TAATTTTATTTATTTTTATTTAATTAAGATG
1 TAATTTTATTTATTTTTATTTAATTAAGATG
106007 T
1 T
106008 GGTTATTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (31 bp):
TAATTTTATTTATTTTTATTTAATTAAGATG
Found at i:107149 original size:21 final size:21
Alignment explanation
Indices: 107125--107164 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
107115 AAAAAATTAT
* *
107125 TTAAAATATTATTATTTTTAC
1 TTAAAACATTAATATTTTTAC
107146 TTAAAACATTAATATTTTT
1 TTAAAACATTAATATTTTT
107165 TAATATTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAAAACATTAATATTTTTAC
Found at i:124714 original size:30 final size:30
Alignment explanation
Indices: 124670--124751 Score: 148
Period size: 30 Copynumber: 2.8 Consensus size: 30
124660 AAAAATTAAG
*
124670 TAATTAAT-TAAAAAAATCAAATATTTTAT
1 TAATTAATCTAAAAAATTCAAATATTTTAT
124699 TAATTAATCTAAAAAATTCAAATATTTTAT
1 TAATTAATCTAAAAAATTCAAATATTTTAT
124729 TAATTAATCTAAAAAATTCAAAT
1 TAATTAATCTAAAAAATTCAAAT
124752 TTTAAATAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 8 0.16
30 43 0.84
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (30 bp):
TAATTAATCTAAAAAATTCAAATATTTTAT
Found at i:125019 original size:21 final size:21
Alignment explanation
Indices: 124993--125045 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
124983 GTTTTCAGAT
124993 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
125014 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
125035 TCGCAATGCGA
1 TCGCAACGCGA
125046 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:125104 original size:40 final size:42
Alignment explanation
Indices: 125049--125159 Score: 154
Period size: 40 Copynumber: 2.7 Consensus size: 42
125039 AATGCGATTT
125049 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTG-CA-ATAA
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGTCATATAA
* * * * * *
125089 TCCAAGTTCGTTGCGATAGTCGAAGTCCGCGTTGTGATTTAT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGTCATATAA
125131 TCCAAATTCGTTGCGATAGTCCAAGTTCG
1 TCCAAATTCGTTGCGATAGTCCAAGTTCG
125160 TTGCGATAGT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
40 31 0.52
41 1 0.02
42 28 0.47
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (42 bp):
TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGTCATATAA
Found at i:125143 original size:61 final size:61
Alignment explanation
Indices: 125078--125215 Score: 240
Period size: 61 Copynumber: 2.3 Consensus size: 61
125068 TCCAAGTTCG
* * *
125078 CGTTGCAATAATCCAAGTTCGTTGCGATAGTCGAAGTCCGCGTTGTGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTCCGCGTTGGGATTTATTCCAAATT
*
125139 CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGGGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTCCGCGTTGGGATTTATTCCAAATT
125200 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
125216 AATCGCAACG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 73 1.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
CGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTCCGCGTTGGGATTTATTCCAAATT
Found at i:125216 original size:19 final size:19
Alignment explanation
Indices: 125049--125215 Score: 136
Period size: 19 Copynumber: 8.3 Consensus size: 19
125039 AATGCGATTT
*
125049 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
125068 TCCAAGTTCGCGTTGCAATAA
1 TCCAAGTT--CGTTGCGATAG
125089 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* * * *
125108 TCGAAGTCCGCGTTGTGATTTAT
1 TCCAAGT--TCGTTGCGA--TAG
*
125131 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
125150 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* * *
125169 TCGAAGTTCGCGTTGGGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
125192 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
125211 TCCAA
1 TCCAA
125216 AATCGCAACG
Statistics
Matches: 116, Mismatches: 22, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
19 56 0.48
21 45 0.39
23 15 0.13
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:126127 original size:42 final size:42
Alignment explanation
Indices: 126068--126244 Score: 236
Period size: 42 Copynumber: 4.3 Consensus size: 42
126058 TGCGATTTTG
126068 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
126110 GACTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
126152 GACTATCGCAACAAATTTGG-A-AAATCGCAACACGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * * *
126192 GACTATCGCAACGCGAACTTGGACT--ATCGCAATGCGAACTTG
1 GACTATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTC
126234 GACTATCGCAA
1 GACTATCGCAA
126245 TGCAAATATG
Statistics
Matches: 119, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
40 28 0.24
41 1 0.01
42 90 0.76
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:126204 original size:82 final size:83
Alignment explanation
Indices: 126065--126244 Score: 258
Period size: 82 Copynumber: 2.2 Consensus size: 83
126055 CGTTGCGATT
* * *
126065 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA-CGAATTTG
1 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAACCGAACTTG
*
126129 TAATAAATCGCAACGCGAAC
66 GAAT--ATCGCAACGCGAAC
126149 TTGGACTATCGCAACAAATTTGG-A-AAATCGCAACACGAACTTCGACTATCGCAACGCGAACTT
1 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAAC-CGAACTT
* *
126212 GGACTATCGCAATGCGAAC
65 GGAATATCGCAACGCGAAC
126231 TTGGACTATCGCAA
1 TTGGACTATCGCAA
126245 TGCAAATATG
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
82 56 0.64
83 1 0.01
84 31 0.35
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (83 bp):
TTGGACTATCGCAACAAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAACCGAACTTG
GAATATCGCAACGCGAAC
Found at i:126247 original size:21 final size:21
Alignment explanation
Indices: 126065--126244 Score: 165
Period size: 21 Copynumber: 8.7 Consensus size: 21
126055 CGTTGCGATT
*
126065 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
126084 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
126107 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
126126 TTGTAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
126149 TTGGACTATCGCAA--CAAAT
1 TTGGACTATCGCAACGCGAAC
** *
126168 TTGGAAAATCGCAACACGAAC
1 TTGGACTATCGCAACGCGAAC
*
126189 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
126210 TTGGACTATCGCAATGCGAAC
1 TTGGACTATCGCAACGCGAAC
126231 TTGGACTATCGCAA
1 TTGGACTATCGCAA
126245 TGCAAATATG
Statistics
Matches: 128, Mismatches: 23, Indels: 18
0.76 0.14 0.11
Matches are distributed among these distances:
19 29 0.23
21 81 0.63
23 18 0.14
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:127341 original size:3 final size:3
Alignment explanation
Indices: 127329--127369 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
127319 ATTAGCTGCC
127329 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
127370 CAAACACCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:128389 original size:3 final size:3
Alignment explanation
Indices: 128383--128450 Score: 59
Period size: 3 Copynumber: 22.0 Consensus size: 3
128373 CCATTTGTTT
* *
128383 TTA TTA TGTTA TTA TTA TT- TTA TTTA TCA CTA TTA TTA TT- TTA TTA
1 TTA TTA T-T-A TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
*
128429 TTA TTA TTAA TTA ATA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA
128451 CAAACAGATC
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
2 4 0.08
3 39 0.74
4 8 0.15
5 2 0.04
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:128397 original size:11 final size:11
Alignment explanation
Indices: 128383--128435 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
128373 CCATTTGTTT
*
128383 TTATTATGTTA
1 TTATTATATTA
*
128394 TTATTATTTTA
1 TTATTATATTA
*
128405 TTTATCACTATTA
1 -TTATTA-TATTA
*
128418 TTATTTTATTA
1 TTATTATATTA
128429 TTATTAT
1 TTATTAT
128436 TAATTAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 21 0.62
12 9 0.26
13 4 0.12
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (11 bp):
TTATTATATTA
Found at i:130621 original size:2 final size:2
Alignment explanation
Indices: 130614--130642 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
130604 TTTCAAAATT
130614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
130643 TATTTTCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:133977 original size:15 final size:15
Alignment explanation
Indices: 133957--133988 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
133947 GATCAATACC
133957 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
133972 TTTTGCATACATTCA
1 TTTTGCATACATGCA
133987 TT
1 TT
133989 ATTTATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:138273 original size:20 final size:20
Alignment explanation
Indices: 138250--138292 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
138240 AATCCACCAC
*
138250 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
138270 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
138290 ATG
1 ATG
138293 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:140923 original size:19 final size:20
Alignment explanation
Indices: 140899--140937 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
140889 AGAGGAAACT
140899 AGAAAGTG-AAAGTAAAAAG
1 AGAAAGTGAAAAGTAAAAAG
140918 AGAAAGTGAAAAGTAAAAAG
1 AGAAAGTGAAAAGTAAAAAG
140938 TAAGTGGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.26, T:0.10
Consensus pattern (20 bp):
AGAAAGTGAAAAGTAAAAAG
Found at i:148635 original size:10 final size:10
Alignment explanation
Indices: 148622--148664 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
148612 ATGCAACTAT
148622 ATGCTCCTAA
1 ATGCTCCTAA
148632 ATGCAT-CTAA
1 ATGC-TCCTAA
*
148642 ATGGTCCTAA
1 ATGCTCCTAA
*
148652 ATGGTCCTAA
1 ATGCTCCTAA
148662 ATG
1 ATG
148665 GGCTCTTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 1 0.03
10 28 0.93
11 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (10 bp):
ATGCTCCTAA
Found at i:148635 original size:20 final size:20
Alignment explanation
Indices: 148612--148654 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
148602 AATCCTCCAC
*
148612 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
148632 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
148652 ATG
1 ATG
148655 GTCCTAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:148665 original size:10 final size:10
Alignment explanation
Indices: 148638--148665 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
148628 CTAAATGCAT
148638 CTAAATGGTC
1 CTAAATGGTC
148648 CTAAATGGTC
1 CTAAATGGTC
148658 CTAAATGG
1 CTAAATGG
148666 GCTCTTAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (10 bp):
CTAAATGGTC
Found at i:153542 original size:20 final size:19
Alignment explanation
Indices: 153519--153567 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
153509 ATGCTTGAAG
153519 AAGAAAAAATAAATAAAAAA
1 AAGAAAAAATAAA-AAAAAA
* *
153539 AAGAAAAAAGAAAAGAAAA
1 AAGAAAAAATAAAAAAAAA
153558 AAGAAAAAAT
1 AAGAAAAAAT
153568 TTTGAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (19 bp):
AAGAAAAAATAAAAAAAAA
Found at i:153552 original size:12 final size:12
Alignment explanation
Indices: 153533--153564 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
153523 AAAAATAAAT
153533 AAAA-AAAAGAA
1 AAAAGAAAAGAA
153544 AAAAGAAAAGAA
1 AAAAGAAAAGAA
153556 AAAAGAAAA
1 AAAAGAAAA
153565 AATTTTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:153585 original size:7 final size:7
Alignment explanation
Indices: 153519--153566 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
153509 ATGCTTGAAG
153519 AAGAAAA
1 AAGAAAA
* *
153526 AATAAAT
1 AAGAAAA
153533 AA-AAAA
1 AAGAAAA
153539 AAGAAAA
1 AAGAAAA
153546 AAG--AA
1 AAGAAAA
153551 AAGAAAA
1 AAGAAAA
153558 AAGAAAA
1 AAGAAAA
153565 AA
1 AA
153567 TTTTGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
5 5 0.14
6 5 0.14
7 25 0.71
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.04
Consensus pattern (7 bp):
AAGAAAA
Found at i:155518 original size:112 final size:113
Alignment explanation
Indices: 155303--155556 Score: 327
Period size: 112 Copynumber: 2.3 Consensus size: 113
155293 AGAACTCAAG
* * **
155303 AAGAAATTCATAATGAGAAGAATTTGTTCAAATTTTTTGTTTGAATTCATCACCCAATGGATCAA
1 AAGAAGTTCATAATGAGAAGAACTTGTTCAAACCTTTTGTTTGAATTCATCACCCAATGGATCAA
* *
155368 CATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAATAAGGAAA
66 CATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA-AAGGAAA
* * **
155417 AAGAAGTTCATAATGAGAAGAACTTGTT-TAACCTTTTGTTTGAATTCATTACTTAATGGATC-A
1 AAGAAGTTCATAATGAGAAGAACTTGTTCAAACCTTTTGTTTGAATTCATCACCCAATGGATCAA
* * * *
155480 C-TTCTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAG
66 CATT-GCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAA
*
155528 AAGAAG-TCATAATGAGAAGAGCTTGTTCA
1 AAGAAGTTCATAATGAGAAGAACTTGTTCA
Statistics
Matches: 122, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
110 20 0.16
111 13 0.11
112 35 0.29
113 28 0.23
114 26 0.21
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.30
Consensus pattern (113 bp):
AAGAAGTTCATAATGAGAAGAACTTGTTCAAACCTTTTGTTTGAATTCATCACCCAATGGATCAA
CATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAA
Done.