Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008549.1 Hibiscus syriacus cultivar Beakdansim tig00111441_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: 316982
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:176484 original size:60 final size:60
Alignment explanation
Indices: 176385--176534 Score: 149
Period size: 60 Copynumber: 2.5 Consensus size: 60
176375 GATGAAGTTG
* * * * * * * **
176385 GGAATGAAATTGGAACATTTAAAAGCTTGAGGACAAATTTAGAAAGATTGTCAAAATTGA
1 GGAATGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAGAAAGAGAGTCAAAATTGA
* * ** *
176445 GGAATG-AATCTAGAATGTTCAAAAGTTTAAAGACTAATTTAGAATGAGAGTCGTAATTTA
1 GGAATGAAAT-TAGAATATTCAAAAGTTTAAAGACTAATTTAGAAAGAGAGTCAAAATTGA
*
176505 GGGATGAAATTAGAATATTCAAAAGTTTAA
1 GGAATGAAATTAGAATATTCAAAAGTTTAA
176535 GGATCCATTT
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
59 3 0.04
60 66 0.92
61 3 0.04
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (60 bp):
GGAATGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAGAAAGAGAGTCAAAATTGA
Found at i:180578 original size:22 final size:22
Alignment explanation
Indices: 180553--180610 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
180543 TCGGTTAAAG
180553 TCAAAGTCAACGGTCAGACC-A
1 TCAAAGTCAACGGTCAGACCGA
* *
180574 TTCAAAGTCAACTGTCTGACCGA
1 -TCAAAGTCAACGGTCAGACCGA
*
180597 TCAAGGTCAACGGT
1 TCAAAGTCAACGGT
180611 TCGGGTTGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.21
Consensus pattern (22 bp):
TCAAAGTCAACGGTCAGACCGA
Found at i:180774 original size:23 final size:22
Alignment explanation
Indices: 180742--180788 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
180732 CCAAAATTAG
180742 TCCAATATCACCAATAAACCAA
1 TCCAATATCACCAATAAACCAA
*
180764 TCCAACTATCACCAATCAACCAA
1 TCCAA-TATCACCAATAAACCAA
180787 TC
1 TC
180789 GTTAACTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (22 bp):
TCCAATATCACCAATAAACCAA
Found at i:184159 original size:21 final size:22
Alignment explanation
Indices: 184135--184178 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
184125 AACAAGCGTC
*
184135 ATAATTGTCAA-ATAAATAAAT
1 ATAATTCTCAATATAAATAAAT
*
184156 ATAATTCTCAATTTAAATAAAT
1 ATAATTCTCAATATAAATAAAT
184178 A
1 A
184179 AAATAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAATTCTCAATATAAATAAAT
Found at i:198564 original size:20 final size:20
Alignment explanation
Indices: 198541--198694 Score: 247
Period size: 20 Copynumber: 7.7 Consensus size: 20
198531 TGCGAACACA
198541 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
198561 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
198581 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
198601 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
198621 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
198641 TAAATCGCAACG-ATAATCAG
1 TAAATCGCAACGCGT-ATCCG
198661 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
198681 TAAATCGCAACGCG
1 TAAATCGCAACGCG
198695 ATTTTTAAAG
Statistics
Matches: 122, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
19 1 0.01
20 120 0.98
21 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:198566 original size:40 final size:40
Alignment explanation
Indices: 198503--198690 Score: 211
Period size: 40 Copynumber: 4.7 Consensus size: 40
198493 GATTTTCAAG
* ** * *
198503 AATCGCAACGCGAATATGAAAATCGTAATGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAATGCGTAAC-CATA
* * * *
198543 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAATGCGTAACCATA
* *
198583 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAATGCGTAACCATA
* *
198623 TATCGCAACGCGTATCCGTAAATCGCAA--CGATAATCAGTA
1 AATCGCAACGCGTATCCGTAAATCGCAATGCG-TAACCA-TA
198663 AATCGCAACGCGTATCCGTAAATCGCAA
1 AATCGCAACGCGTATCCGTAAATCGCAA
198691 CGCGATTTTT
Statistics
Matches: 129, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
38 2 0.02
39 3 0.02
40 122 0.95
41 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAATGCGTAACCATA
Found at i:198586 original size:60 final size:59
Alignment explanation
Indices: 198503--198694 Score: 219
Period size: 60 Copynumber: 3.2 Consensus size: 59
198493 GATTTTCAAG
* ** * *
198503 AATCGCAACGCGAATATGAAAATCGTAATGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAA-GCGAACACATAAATCGCAACGCGTATCCGTA
* * * *
198563 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAA-GCG-AACACATAAATCGCAACGCGTATCCGTA
*
198623 TATCGCAACGCGTATCCGTAAATCGCAA-CGATA-ATCAGTAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAAGCGA-ACA-CA-TAAATCGCAACGCGTATCCGTA
198683 AATCGCAACGCG
1 AATCGCAACGCG
198695 ATTTTTAAAG
Statistics
Matches: 111, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
57 1 0.01
58 2 0.02
59 1 0.01
60 105 0.95
61 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (59 bp):
AATCGCAACGCGTATCCGTAAATCGCAAGCGAACACATAAATCGCAACGCGTATCCGTA
Found at i:199113 original size:33 final size:33
Alignment explanation
Indices: 199074--199144 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
199064 TTCACTTAGA
199074 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
***
199107 TTTCATTTCGCGTTGTTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
199140 TTTCA
1 TTTCA
199145 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:199294 original size:21 final size:21
Alignment explanation
Indices: 199224--199297 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
199214 TGCAGAAGAG
* *
199224 TCGCAACTAGATAAATGAAAA
1 TCGCAACGAGAAAAATGAAAA
* **
199245 TCGCAACGTG-AAAATGACTA
1 TCGCAACGAGAAAAATGAAAA
199265 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAAAAATGAAAA
199287 TCGCAACGAGA
1 TCGCAACGAGA
199298 GAATCGCAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 9 0.21
21 24 0.56
22 10 0.23
ACGTcount: A:0.47, C:0.18, G:0.19, T:0.16
Consensus pattern (21 bp):
TCGCAACGAGAAAAATGAAAA
Found at i:199304 original size:14 final size:14
Alignment explanation
Indices: 199285--199341 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
199275 GAAAAATGAA
199285 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
199299 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
199318 AATCGCAACGAGAG
1 AATCGCAACGAGAG
199332 AATCGCAACG
1 AATCGCAACG
199342 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:199316 original size:33 final size:33
Alignment explanation
Indices: 199278--199355 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
199268 GCAACGAGAA
199278 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
199311 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
199344 AAACCAAAATCG
1 AAATGAAAATCG
199356 TATTGCGATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:199394 original size:14 final size:14
Alignment explanation
Indices: 199375--199431 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
199365 TTTCATTTCA
199375 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
199389 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
199408 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
199422 CGTTGCGATT
1 CGTTGCGATT
199432 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:199400 original size:33 final size:33
Alignment explanation
Indices: 199358--199481 Score: 158
Period size: 33 Copynumber: 3.5 Consensus size: 33
199348 CAAAATCGTA
199358 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
*
199391 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
*
199424 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCACGTT--G-C-G--ATTCTCTCG
199465 TTGCGATTTTCATTTCA
1 TTGCGATTTTCATTTCA
199482 ACCAAAAGAC
Statistics
Matches: 80, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 44 0.55
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.26
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
Found at i:199442 original size:21 final size:21
Alignment explanation
Indices: 199416--199480 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
199406 CGCGTTGCGA
199416 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
199437 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
199457 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
199478 TTC
1 TTC
199481 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:201449 original size:93 final size:93
Alignment explanation
Indices: 201163--201476 Score: 587
Period size: 93 Copynumber: 3.4 Consensus size: 93
201153 TAGATTGCTT
* *
201163 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTC
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
201228 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
201256 AGTAAATTTGTTTGGTTGCTGCCAATTCTGCTAAAC--TGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
201319 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
201347 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
201412 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
201440 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
201477 AATACCCTGA
Statistics
Matches: 215, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
91 89 0.41
93 126 0.59
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:201616 original size:19 final size:19
Alignment explanation
Indices: 201574--201727 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
201564 TAGTTTACTT
* *
201574 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
201594 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
201613 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
201632 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
201651 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
201665 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
201684 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
201698 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
201717 TCGCAATGCGA
1 TCGCAACGCGA
201728 TTTTGGTTTC
Statistics
Matches: 109, Mismatches: 15, Indels: 21
0.75 0.10 0.14
Matches are distributed among these distances:
14 18 0.17
15 1 0.01
16 7 0.06
17 7 0.06
18 1 0.01
19 63 0.58
20 12 0.11
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:201668 original size:14 final size:14
Alignment explanation
Indices: 201649--201705 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
201639 GCGAAATGAA
*
201649 AATCGCAACGACAG
1 AATCGCAACGAAAG
201663 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
201680 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
201696 AATCGCAACG
1 AATCGCAACG
201706 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:201676 original size:33 final size:33
Alignment explanation
Indices: 201592--201722 Score: 181
Period size: 33 Copynumber: 3.8 Consensus size: 33
201582 CGAAACTTAA
* *
201592 AATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAATGAAAATCGCAAC--G--A-CAG
201630 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
201663 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
201696 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
201723 TGCGATTTTG
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
33 59 0.67
34 1 0.01
36 1 0.01
38 27 0.31
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:201719 original size:52 final size:51
Alignment explanation
Indices: 201591--201727 Score: 141
Period size: 52 Copynumber: 2.6 Consensus size: 51
201581 ACGAAACTTA
* * * *
201591 AAATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAAAATCGCAACGCG
1 AAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAG
* ** * * **
201642 AAAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AAATCGCAACGCGAAATGA-A-AATCGCAATGCGAAACCAAAATCGCAACGAG
201694 AGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 A-AATCGCAACGCGAAATGAAAATCGCAATGCGA
201728 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
50 9 0.14
51 4 0.06
52 40 0.61
53 4 0.06
54 9 0.14
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (51 bp):
AAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAG
Found at i:201758 original size:14 final size:14
Alignment explanation
Indices: 201739--201797 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
201729 TTTGGTTTCG
201739 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
201753 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
201770 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
201786 CGTTGCGATTTT
1 CGTTGCGATTTT
201798 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:201765 original size:33 final size:33
Alignment explanation
Indices: 201723--201846 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
201713 AAAATCGCAA
*
201723 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
201756 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
201789 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
201822 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
201847 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:201777 original size:19 final size:18
Alignment explanation
Indices: 201723--201814 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
201713 AAAATCGCAA
201723 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
201742 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
201756 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
201775 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
201789 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
201808 TGCGATT
1 TGCGATT
201815 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:201824 original size:14 final size:14
Alignment explanation
Indices: 201772--201828 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
201762 TTTGGTTTCG
*
201772 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
201786 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
201805 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
201819 CGTTGCGATT
1 CGTTGCGATT
201829 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:202324 original size:21 final size:21
Alignment explanation
Indices: 202300--202366 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
202290 TCATTCCTCG
202300 AGAGTCCCCTCCCACCATTCA
1 AGAGTCCCCTCCCACCATTCA
* * ** * *
202321 AGAGGCCACTGTCATCATTGA
1 AGAGTCCCCTCCCACCATTCA
202342 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCATTCA
202363 AGAG
1 AGAG
202367 CCCGATTCAC
Statistics
Matches: 33, Mismatches: 12, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.27, C:0.36, G:0.18, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCATTCA
Found at i:203788 original size:14 final size:14
Alignment explanation
Indices: 203769--203804 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
203759 ATTGTTTAAT
203769 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
203783 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
203797 TGATTTGT
1 TGATTTGT
203805 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:203919 original size:19 final size:19
Alignment explanation
Indices: 203895--203982 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
203885 GCATTATGTT
203895 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
203914 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
203931 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
203947 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
203966 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
203983 CGAGAGAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.48
20 16 0.26
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:203986 original size:53 final size:52
Alignment explanation
Indices: 203895--204001 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 52
203885 GCATTATGTT
203895 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
203947 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
204000 GA
1 GA
204002 TTTCGCATTG
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 19 0.35
53 35 0.65
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (52 bp):
GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:204062 original size:33 final size:33
Alignment explanation
Indices: 203991--204174 Score: 160
Period size: 33 Copynumber: 5.4 Consensus size: 33
203981 AACGAGAGAA
* * *
203991 TCGCAATGCGATT-TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
204023 TCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
* *
204057 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 TCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TCATT
* * * **
204097 GCG-ATTTTC-ATT-TCGCAATGCGATTTTCATT
1 TCGCA-TTGCGATTCTCTCGTTGCGATTTTCATT
204128 TCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
204162 TCGCATTGCGATT
1 TCGCATTGCGATT
204175 TTCATTTCCG
Statistics
Matches: 121, Mismatches: 17, Indels: 27
0.73 0.10 0.16
Matches are distributed among these distances:
31 4 0.03
32 7 0.06
33 44 0.36
34 35 0.29
35 5 0.04
36 4 0.03
37 2 0.02
38 8 0.07
39 3 0.02
40 9 0.07
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.43
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:204124 original size:105 final size:106
Alignment explanation
Indices: 204001--204227 Score: 411
Period size: 105 Copynumber: 2.2 Consensus size: 106
203991 TCGCAATGCG
204001 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
204066 GATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTC
66 GATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTC
*
204106 ATTTCGCAATGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
* * *
204171 GATTTTCATTTCCGCATTGCGATTTTCTTGTTGGGATTTTC
66 GATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTC
204212 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
204228 CTCTCGTTGC
Statistics
Matches: 116, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
105 75 0.65
106 41 0.35
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (106 bp):
ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
GATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:204157 original size:53 final size:53
Alignment explanation
Indices: 204001--204227 Score: 411
Period size: 53 Copynumber: 4.3 Consensus size: 53
203991 TCGCAATGCG
204001 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTC
204054 ATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTC
*
204106 ATTTCGCAATGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTC
* * *
204159 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGTTGGGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTC
204212 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
204228 CTCTCGTTGC
Statistics
Matches: 168, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
52 51 0.30
53 117 0.70
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:204225 original size:33 final size:33
Alignment explanation
Indices: 204062--204241 Score: 166
Period size: 33 Copynumber: 5.2 Consensus size: 33
204052 TCATTTCGCA
* *
204062 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCTTG
* *
204095 TTGCGATTTTCATTTCGCAATGCGATTTTCAT-
1 TTGCGATTTTCATTTCGCATTGCGATTTTCTTG
* * * *
204127 TTCCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCG
1 TTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC--TT-G
204165 CATTGCGATTTTCATTTCCGCATTGCGATTTTCTTG
1 --TTGCGATTTTCATTT-CGCATTGCGATTTTCTTG
* * *
204201 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCTTG
204234 TTGCGATT
1 TTGCGATT
204242 GTAATTTCCG
Statistics
Matches: 118, Mismatches: 18, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
32 7 0.06
33 55 0.47
34 27 0.23
36 2 0.02
37 2 0.02
38 1 0.01
39 17 0.14
40 7 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCTTG
Found at i:204256 original size:53 final size:53
Alignment explanation
Indices: 204001--204260 Score: 259
Period size: 53 Copynumber: 4.9 Consensus size: 53
203991 TCGCAATGCG
* *
204001 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGA-TTCTC-TCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTC-CGT-GTTGCGATTTTC
* *
204054 ATTTCGCATTGCGATTTTCA-TTTCGCATTGCGA-TTCTC-TCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTC-CGT-GTTGCGATTTTC
* * *
204106 ATTTCGCAATGCGATTTTCATTTCCGCATTGCGA-TTCTC-TCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTC-CGT-GTTGCGATTTTC
* * * * *
204159 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGTTGGGATTTTC
1 ATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTCCGTGTTGCGATTTTC
* *
204212 ATTTCGCATTGCGATTCTCTC-GTTGCG-ATTGTAATTTCCGTGTTGCGAT
1 ATTTCGCATTGCGATT-T-TCAGTTCCGCATTGCAATTTCCGTGTTGCGAT
204261 AGTCAAATGC
Statistics
Matches: 189, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
52 50 0.26
53 129 0.68
54 8 0.04
55 2 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.45
Consensus pattern (53 bp):
ATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTCCGTGTTGCGATTTTC
Found at i:206539 original size:12 final size:12
Alignment explanation
Indices: 206522--206546 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
206512 TCTTCGGGGA
206522 CTTTTTCTTCTT
1 CTTTTTCTTCTT
206534 CTTTTTCTTCTT
1 CTTTTTCTTCTT
206546 C
1 C
206547 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:206755 original size:24 final size:24
Alignment explanation
Indices: 206721--206767 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
206711 CTGAAACATC
206721 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
206745 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
206768 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:207488 original size:20 final size:20
Alignment explanation
Indices: 207460--207689 Score: 243
Period size: 20 Copynumber: 11.5 Consensus size: 20
207450 AAATTTCAGT
* * * *
207460 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
207480 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
207500 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
* *
207520 GTTGCGATTTACTGATTA-TC
1 GTTGCGATTTACGGA-TACGC
207540 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
207560 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
207580 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
207600 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
207620 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
207640 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* *
207660 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
207680 GTTGCGATTT
1 GTTGCGATTT
207690 TTCATATTCG
Statistics
Matches: 188, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
19 3 0.02
20 182 0.97
21 3 0.02
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:207721 original size:21 final size:20
Alignment explanation
Indices: 207697--207773 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 20
207687 TTTTTCATAT
207697 TCGCATTGCGATTCTGTAAAA
1 TCGCATTGCGATT-TGTAAAA
* **
207718 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCG-ATTTGTAAAA
207739 TCGCATTGCGA-TTGTCAAGAA
1 TCGCATTGCGATTTGT-AA-AA
*
207760 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
207774 TGGAAACTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.09
20 2 0.04
21 34 0.76
22 5 0.11
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (20 bp):
TCGCATTGCGATTTGTAAAA
Found at i:207770 original size:42 final size:44
Alignment explanation
Indices: 207676--207775 Score: 104
Period size: 42 Copynumber: 2.4 Consensus size: 44
207666 ATTTATGTGT
*
207676 TCGCGTTGCG-ATTT-TTCATATTCGCATTGCGATTCTGTAAAA
1 TCGCGTTGCGAATTTGTACATATTCGCATTGCGATTCTGTAAAA
**
207718 TCGCAATGCGAATTTGTAC-TA-TCGCATTGCGA-T-TGTCAAGAA
1 TCGCGTTGCGAATTTGTACATATTCGCATTGCGATTCTGT-AA-AA
*
207760 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
207776 GAAACTGGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
40 3 0.06
41 3 0.06
42 34 0.71
43 6 0.12
44 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (44 bp):
TCGCGTTGCGAATTTGTACATATTCGCATTGCGATTCTGTAAAA
Found at i:209068 original size:24 final size:24
Alignment explanation
Indices: 209041--209094 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
209031 CGTTCATTTA
209041 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * * *
209065 CGTTTGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
209089 CGTTCG
1 CGTTCG
209095 ATTATGTTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.09, C:0.15, G:0.28, T:0.48
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:209073 original size:14 final size:14
Alignment explanation
Indices: 209051--209083 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
209041 CGTTCGTGAA
*
209051 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
209065 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
209079 CGTTT
1 CGTTT
209084 ATGTTCGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.27, T:0.55
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:209093 original size:14 final size:14
Alignment explanation
Indices: 209076--209116 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
209066 GTTTGGTTAT
209076 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
209090 GTTCGATTATGTTC
1 GTTCGTTTATGTTC
* *
209104 ATTCATTTATGTT
1 GTTCGTTTATGTT
209117 TAACACAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.15, C:0.12, G:0.17, T:0.56
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:209099 original size:24 final size:24
Alignment explanation
Indices: 209052--209103 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
209042 GTTCGTGAAC
* *
209052 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGGTTATGTTCGTTCGATTAT
*
209076 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGGTTATGTTCGTTCGATTAT
209100 GTTC
1 GTTC
209104 ATTCATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.10, C:0.12, G:0.25, T:0.54
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTCGATTAT
Found at i:209857 original size:10 final size:10
Alignment explanation
Indices: 209842--209916 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
209832 GGGTCTCCAA
209842 CGTTTATGTT
1 CGTTTATGTT
209852 CGTTTATGTT
1 CGTTTATGTT
209862 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
209873 ATGTTCGTGTT
1 -CGTTTATGTT
209884 CGTTTATGTT
1 CGTTTATGTT
209894 CG----TGTT
1 CGTTTATGTT
209900 CGTTTATGTT
1 CGTTTATGTT
209910 CGTTTAT
1 CGTTTAT
209917 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:209873 original size:16 final size:16
Alignment explanation
Indices: 209848--209912 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
209838 CCAACGTTTA
209848 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
209864 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
209880 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
209896 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
209912 T
1 T
209913 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:212199 original size:13 final size:13
Alignment explanation
Indices: 212181--212210 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
212171 TAAACAAGAT
212181 GATACTATTTTTA
1 GATACTATTTTTA
212194 GATACTATTTTTA
1 GATACTATTTTTA
212207 GATA
1 GATA
212211 ATATCTCCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (13 bp):
GATACTATTTTTA
Found at i:228952 original size:37 final size:39
Alignment explanation
Indices: 228874--228953 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 39
228864 AACAAGTTAG
* *
228874 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAATATTTATATATTTTCTTTAAAAAATTGAAAATCAT
*
228913 AAAAT-TTATATATATTTT-TTTATAAAATTGAAAAT-AT
1 AAAATATT-TATATATTTTCTTTAAAAAATTGAAAATCAT
228950 AAAA
1 AAAA
228954 AGGTTTAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 6 0.16
38 16 0.43
39 15 0.41
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (39 bp):
AAAATATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Found at i:230877 original size:29 final size:30
Alignment explanation
Indices: 230825--230884 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
230815 AGGCAGAGAT
*
230825 AGAATATTTATTTTAGGGTGTCAAATTTAG
1 AGAAAATTTATTTTAGGGTGTCAAATTTAG
230855 AGAAAATTTATTTT-GGGTGTCAAATTTAG
1 AGAAAATTTATTTTAGGGTGTCAAATTTAG
230884 A
1 A
230885 AGTTGTAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (30 bp):
AGAAAATTTATTTTAGGGTGTCAAATTTAG
Found at i:234647 original size:3 final size:3
Alignment explanation
Indices: 234639--234667 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
234629 AGGGGTGGGC
234639 AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
234668 AAAGAAAGTA
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:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:236750 original size:28 final size:27
Alignment explanation
Indices: 236709--236761 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
236699 ATAATTAAAT
236709 TTATCAAACTATTATAAAATGTATTACC
1 TTATCAAACTATTATAAAATG-ATTACC
* * *
236737 TTATTAAATTATTATTAAATGATTA
1 TTATCAAACTATTATAAAATGATTA
236762 TTAAATTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (27 bp):
TTATCAAACTATTATAAAATGATTACC
Found at i:236753 original size:11 final size:11
Alignment explanation
Indices: 236737--236768 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
236727 ATGTATTACC
236737 TTATTAAATTA
1 TTATTAAATTA
*
236748 TTATTAAATGA
1 TTATTAAATTA
236759 TTATTAAATT
1 TTATTAAATT
236769 TTGTAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTATTAAATTA
Found at i:239147 original size:24 final size:24
Alignment explanation
Indices: 239120--239328 Score: 165
Period size: 24 Copynumber: 8.7 Consensus size: 24
239110 ATGAGGTTGG
*
239120 AGACTCATTCCGAGATGGGATTGA
1 AGACTCGTTCCGAGATGGGATTGA
* *
239144 AGACTCATTCCTAGATGAGG-TTGA
1 AGACTCGTTCCGAGATG-GGATTGA
* *
239168 AGACTTGTTCCTAGAT-GGAGTTGA
1 AGACTCGTTCCGAGATGGGA-TTGA
* *
239192 AGACTCGTTCCAAGATGGGGTTGA
1 AGACTCGTTCCGAGATGGGATTGA
* * * *
239216 ATACTCGGTCAGAGATGGGGTTGA
1 AGACTCGTTCCGAGATGGGATTGA
* * *
239240 AGACTCGGTCGGAGATGGGGTTGA
1 AGACTCGTTCCGAGATGGGATTGA
* *
239264 AGTA-TCGGTCGGAGATGAGG-TTGA
1 AG-ACTCGTTCCGAGATG-GGATTGA
** *
239288 AGACTCGACCCGAGATGGGATCGA
1 AGACTCGTTCCGAGATGGGATTGA
* *
239312 AGACTCATTCCTAGATG
1 AGACTCGTTCCGAGATG
239329 CGGTGAAGAG
Statistics
Matches: 157, Mismatches: 20, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
22 2 0.01
23 3 0.02
24 145 0.92
25 7 0.04
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (24 bp):
AGACTCGTTCCGAGATGGGATTGA
Found at i:239197 original size:72 final size:72
Alignment explanation
Indices: 239106--239244 Score: 172
Period size: 72 Copynumber: 1.9 Consensus size: 72
239096 CGAACTTTTA
* * * **
239106 CTAGATGAGGTTGGAGACTCATTCCGAGATGGGATTGAAGACTCATTCCTAGATGAGGTTGAAGA
1 CTAGATGAGGTTGAAGACTCATTCCAAGATGGGATTGAAGACTCAGTCAGAGATGAGGTTGAAGA
239171 CTTGTTC
66 CTTGTTC
* * * * *
239178 CTAGATG-GAGTTGAAGACTCGTTCCAAGATGGGGTTGAATACTCGGTCAGAGATGGGGTTGAAG
1 CTAGATGAG-GTTGAAGACTCATTCCAAGATGGGATTGAAGACTCAGTCAGAGATGAGGTTGAAG
239242 ACT
65 ACT
239245 CGGTCGGAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
71 1 0.02
72 55 0.98
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (72 bp):
CTAGATGAGGTTGAAGACTCATTCCAAGATGGGATTGAAGACTCAGTCAGAGATGAGGTTGAAGA
CTTGTTC
Found at i:241661 original size:28 final size:28
Alignment explanation
Indices: 241628--241682 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
241618 ATTTAAGAAC
241628 AAGATTGAAAGGAATCATGGATTAACTA
1 AAGATTGAAAGGAATCATGGATTAACTA
241656 AAGATTGAAAGGAATCATGGATTAACT
1 AAGATTGAAAGGAATCATGGATTAACT
241683 CAAGTTAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.07, G:0.22, T:0.25
Consensus pattern (28 bp):
AAGATTGAAAGGAATCATGGATTAACTA
Found at i:245334 original size:60 final size:60
Alignment explanation
Indices: 245255--245418 Score: 156
Period size: 60 Copynumber: 2.7 Consensus size: 60
245245 TGGAAGATTC
** * **
245255 AAAAGTTTGGGGACCAATTTATAAA-GAGGATCATAATTT-AGGGATGAAATTAGAA-TGTT
1 AAAAGTTTAAGGACTAATTTA-AAATGAGGATCATAATTTGA-GGATGAAATTAGAACACTT
* ** * *
245314 CGAAAGTTTAAGGACTAATTTAAAATGAGTCTCATAGTTTGAGTATGAAATTAGAACACTT
1 -AAAAGTTTAAGGACTAATTTAAAATGAGGATCATAATTTGAGGATGAAATTAGAACACTT
**
245375 AAAAGTTTAAGGA-TCAATTTAAAATGAGGATCATGGTTTGAGGA
1 AAAAGTTTAAGGACT-AATTTAAAATGAGGATCATAATTTGAGGA
245419 CATATGATGC
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
59 4 0.05
60 78 0.92
61 3 0.04
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (60 bp):
AAAAGTTTAAGGACTAATTTAAAATGAGGATCATAATTTGAGGATGAAATTAGAACACTT
Found at i:254731 original size:34 final size:35
Alignment explanation
Indices: 254683--254749 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
254673 TATTATTTAT
* *
254683 AATTTTTGTTATTCAACATATGTGAGAATGGGTAG
1 AATTTTTGTTATTCAACAGATGTGAAAATGGGTAG
254718 AATTTTT-TTATTCAACAGATGTGAAAATGGGT
1 AATTTTTGTTATTCAACAGATGTGAAAATGGGT
254750 GTGCTGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 23 0.77
35 7 0.23
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (35 bp):
AATTTTTGTTATTCAACAGATGTGAAAATGGGTAG
Found at i:259944 original size:3 final size:3
Alignment explanation
Indices: 259938--259963 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
259928 AGAAGAGTAC
259938 GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GA
259964 AGAAGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:259986 original size:36 final size:36
Alignment explanation
Indices: 259941--260044 Score: 147
Period size: 36 Copynumber: 2.9 Consensus size: 36
259931 AGAGTACGAG
*
259941 GAGGAGGAGGAGGAGGAGGAGGAAGAAGAAGAATAT
1 GAGGTGGAGGAGGAGGAGGAGGAAGAAGAAGAATAT
* * *
259977 GGGGTGGAGGAGGAGGAGAAGGAAGAAGAAGAGTAT
1 GAGGTGGAGGAGGAGGAGGAGGAAGAAGAAGAATAT
260013 GAGGTGGAGGAGGAAAGGA-GAGGAAGAAGAAG
1 GAGGTGGAGGAGG--AGGAGGAGGAAGAAGAAG
260045 TAGAAGAAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
36 44 0.73
37 12 0.20
38 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.52, T:0.06
Consensus pattern (36 bp):
GAGGTGGAGGAGGAGGAGGAGGAAGAAGAAGAATAT
Found at i:265922 original size:144 final size:143
Alignment explanation
Indices: 265658--265932 Score: 484
Period size: 144 Copynumber: 1.9 Consensus size: 143
265648 GATGATCGTT
265658 AAATTTTTAACGAAAAAAGGACGAGGTTGGAACATAATGAATAGCGAGTGACTATTTGTAACTTT
1 AAATTTTTAACGAAAAAAGGACGAGGTTGGAACATAATGAATAGCGAGTGACTATTTGTAACTTT
*
265723 AATAGTTGAGGGACTACAAAATAATATCTTCTAGTCAGTGGATTATTTTTTAACTTTTAATAGTC
66 AATAGTTGAGGGACTACAAAATAATATCTTATAGTCAGTGGATTATTTTTTAACTTTTAATAGTC
265788 AGGAAGACTCAAA
131 AGGAAGACTCAAA
265801 AAATTTTTAACGAAAAAAGGACGA-GTTGGAACAT-ATGAATAGTCGAGTGACTATTTGTAACTT
1 AAATTTTTAACGAAAAAAGGACGAGGTTGGAACATAATGAATAG-CGAGTGACTATTTGTAAC-T
265864 TTAATAGTTGA-GGACTACACAAAATAATATCTTATAGTCAGTGGATTATTTTTTAACTTTTAAT
64 TTAATAGTTGAGGGACT--ACAAAATAATATCTTATAGTCAGTGGATTATTTTTTAACTTTTAAT
265928 AGTCA
127 AGTCA
265933 AAGACCAATA
Statistics
Matches: 127, Mismatches: 1, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
141 8 0.06
142 33 0.26
143 36 0.28
144 50 0.39
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (143 bp):
AAATTTTTAACGAAAAAAGGACGAGGTTGGAACATAATGAATAGCGAGTGACTATTTGTAACTTT
AATAGTTGAGGGACTACAAAATAATATCTTATAGTCAGTGGATTATTTTTTAACTTTTAATAGTC
AGGAAGACTCAAA
Found at i:270746 original size:17 final size:18
Alignment explanation
Indices: 270718--270753 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
270708 CGTTTACTCG
270718 ACTCGAAAAGATTAAATT
1 ACTCGAAAAGATTAAATT
270736 ACTCG-AAAGATTAAATT
1 ACTCGAAAAGATTAAATT
270753 A
1 A
270754 AATTGATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (18 bp):
ACTCGAAAAGATTAAATT
Found at i:271447 original size:13 final size:13
Alignment explanation
Indices: 271429--271455 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
271419 CCCTGTCTCA
271429 CGTACTTAAATAT
1 CGTACTTAAATAT
271442 CGTACTTAAATAT
1 CGTACTTAAATAT
271455 C
1 C
271456 CTAGATTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (13 bp):
CGTACTTAAATAT
Found at i:275879 original size:22 final size:22
Alignment explanation
Indices: 275838--275912 Score: 89
Period size: 22 Copynumber: 3.3 Consensus size: 22
275828 AAAATACAGT
275838 ATGAACAGTACCATATGAACAATA
1 ATGAACAGTA-C-TATGAACAATA
*
275862 ATGAACAGTATTATGAACAGA-A
1 ATGAACAGTACTATGAACA-ATA
* *
275884 ATGAACAGTACTATTAACATTA
1 ATGAACAGTACTATGAACAATA
275906 ATGAACA
1 ATGAACA
275913 ATAATGTCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
22 34 0.76
23 1 0.02
24 10 0.22
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.24
Consensus pattern (22 bp):
ATGAACAGTACTATGAACAATA
Found at i:275925 original size:44 final size:46
Alignment explanation
Indices: 275838--275925 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 46
275828 AAAATACAGT
* * *
275838 ATGAACAGTACCATATGAACAATAATGAACAGTATTATGAACAGAA
1 ATGAACAGTACCATATGAACAATAATGAACAATAATATCAACAGAA
* * *
275884 ATGAACAGTA-C-TATTAACATTAATGAACAATAATGTCAACAG
1 ATGAACAGTACCATATGAACAATAATGAACAATAATATCAACAG
275926 TACTCAAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
44 25 0.69
45 1 0.03
46 10 0.28
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (46 bp):
ATGAACAGTACCATATGAACAATAATGAACAATAATATCAACAGAA
Found at i:276448 original size:20 final size:22
Alignment explanation
Indices: 276430--276470 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
276420 CACTCATATT
276430 TCTTAT-CTCTTGTTCATATAA
1 TCTTATGCTCTTGTTCATATAA
*
276451 TCTTATGCTCTT-ATCATATA
1 TCTTATGCTCTTGTTCATATA
276471 TATTATGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.20, G:0.05, T:0.51
Consensus pattern (22 bp):
TCTTATGCTCTTGTTCATATAA
Found at i:277930 original size:21 final size:21
Alignment explanation
Indices: 277904--277945 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
277894 CCAGAATGGG
*
277904 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
277925 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
277946 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:278073 original size:19 final size:19
Alignment explanation
Indices: 278049--278115 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
278039 GAGCCTCGGG
*
278049 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
*
278068 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* *
278087 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
278106 TTACTATTCA
1 TTACTGTTCA
278116 TAAAAACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:278237 original size:31 final size:31
Alignment explanation
Indices: 278178--278267 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
278168 TAAATTTGAA
278178 TAAATTCAATT-AAGTCC-AAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
278206 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
278237 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
278268 CCTTAAATTG
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
28 11 0.19
29 6 0.10
30 4 0.07
31 38 0.64
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:281226 original size:134 final size:134
Alignment explanation
Indices: 281078--281561 Score: 554
Period size: 131 Copynumber: 3.7 Consensus size: 134
281068 GATATCTGGA
* * *
281078 GGTGACTCGACTCCTACATGATGAGGAGGTCTGGTCAGTGGATGACACGGTTCTTACGTGATGAG
1 GGTGACTCGACTCCTACGTGATGAGGAGATCTGGTCAGTGGATGACACGGTTCCTACGTGATGAG
* * * * *
281143 GATGATATGCCATCTTTAGGGATGATGATAACTCAGTTCCTACGCGATGAGGATGACTGGTTAGC
66 GACGACATGCCATCTTTAGGGATGATGATAACACAGTTCCTACGTGATGAGGATGACTGGTTATC
*
281208 TAGG
131 TAAG
* * * * * *
281212 GGTGACTCGGCTCCTTCGTGATGAGGAGGTCTGGTTAGTAGATGACACGGTTCCTACGTGATGAA
1 GGTGACTCGACTCCTACGTGATGAGGAGATCTGGTCAGTGGATGACACGGTTCCTACGTGATGAG
* * **
281277 GACAACAAGCCATCTTTAGGGAT-A--ATAACACAGTTCCTACGTGATGAGGATGGTTGGTTATC
66 GACGACATGCCATCTTTAGGGATGATGATAACACAGTTCCTACGTGATGAGGATGACTGGTTATC
281339 TAAG
131 TAAG
* * * *
281343 GGTGACGCAACTCCTATGTGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAG
1 GGTGACTCGACTCCTACGTGATGAGGAGATCTGGTCAGTGGATGACACGGTTCCTACGTGATGAG
* * *
281408 GATGACA-GACCATCTTTA--GA-GATGATAACAC-GATTCCTACGTGATAAGGATGACTGATTA
66 GACGACATG-CCATCTTTAGGGATGATGATAACACAG-TTCCTACGTGATGAGGATGACTGGTTA
281468 TCTAAG
129 TCTAAG
* * * ** * * *
281474 GGTGACACCG-CTCTTACGTGACGAGGAGATCTGGTTGGTGGATGAAACAGTTCCTACATGATGA
1 GGTGAC-TCGACTCCTACGTGATGAGGAGATCTGGTCAGTGGATGACACGGTTCCTACGTGATGA
* *
281538 GAACGACATACCATCTTTAGGGAT
65 GGACGACATGCCATCTTTAGGGAT
281562 TTGTTCCTAC
Statistics
Matches: 295, Mismatches: 45, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
129 3 0.01
130 2 0.01
131 209 0.71
132 1 0.00
133 3 0.01
134 77 0.26
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (134 bp):
GGTGACTCGACTCCTACGTGATGAGGAGATCTGGTCAGTGGATGACACGGTTCCTACGTGATGAG
GACGACATGCCATCTTTAGGGATGATGATAACACAGTTCCTACGTGATGAGGATGACTGGTTATC
TAAG
Found at i:281580 original size:41 final size:41
Alignment explanation
Indices: 281523--281607 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
281513 GGATGAAACA
281523 GTTCCTACATGATGAGAACGACATACCATCTTTAGGGATTT
1 GTTCCTACATGATGAGAACGACATACCATCTTTAGGGATTT
*
281564 GTTCCTACATGATGAGAATGACATACCATCTTTAGGGATTT
1 GTTCCTACATGATGAGAACGACATACCATCTTTAGGGATTT
281605 GTT
1 GTT
281608 TCAAGGGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (41 bp):
GTTCCTACATGATGAGAACGACATACCATCTTTAGGGATTT
Found at i:282035 original size:36 final size:37
Alignment explanation
Indices: 281957--282042 Score: 95
Period size: 36 Copynumber: 2.3 Consensus size: 37
281947 AATAACTTTG
* * *
281957 AAATTTGTATTTCGAGAGAAAATGTCTTAAGTGAGACA
1 AAATTTGT-TTTCGAGAGAAAATATCTCAAGCGAGACA
*
281995 AAATTTGTTTT-GAGA-AAAATTATCTCAAGCGATACA
1 AAATTTGTTTTCGAGAGAAAA-TATCTCAAGCGAGACA
*
282031 AAATTTATTTTC
1 AAATTTGTTTTC
282043 ATAAAAGCGT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
35 4 0.10
36 26 0.63
37 3 0.07
38 8 0.20
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (37 bp):
AAATTTGTTTTCGAGAGAAAATATCTCAAGCGAGACA
Found at i:282384 original size:16 final size:16
Alignment explanation
Indices: 282363--282393 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
282353 ATTTCATGTA
*
282363 TATGTATGTATTGATG
1 TATGTATATATTGATG
282379 TATGTATATATTGAT
1 TATGTATATATTGAT
282394 CTGTGAGGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (16 bp):
TATGTATATATTGATG
Found at i:284497 original size:744 final size:745
Alignment explanation
Indices: 283061--284919 Score: 3348
Period size: 744 Copynumber: 2.5 Consensus size: 745
283051 TCGGTCTAAA
* *
283061 AATGAGATTTCTGAGTGCTCA-TGTGAGTTGTTCAACTATAACAGATGTTCCTCAACTCCCTTAT
1 AATGAGATTTCTAAGTGCT-AGTGTGAGTTGTTCAACTATAACAGGTGTTCCTCAACTCCCTTAT
* * * * *
283125 TCCATATTCACTGAAACTCATTGTTTAGTAAATTCGAATTAATCTGTCACTGTTTAGCTAGCTGA
65 TCCATATTCACCGAAACTCATTGTTTAGTAAATTCGAATTAATTTGCCATTGTTTGGCTAGCTGA
*
283190 ATTCAACTTTATTGTACATATATATTAAAATTGCCTTTGTTAGGCTAACTGAAGGATTCATGTCA
130 ATTCAGCTTTATTGTACATATATATTAAAATTGCCTTTGTTAGGCTAACTGAAGGATTCATGTCA
*
283255 TCACAAAGTCTTCAACTTGACAATCACAGTGGAGCAAACACCGAATTGCCAAGTACCCGATCAAT
195 TCACAAAGTCTTCGACTTGACAATCACAGTGGAGCAAACACCGAATTGCCAAGTACCCGATCAAT
*
283320 GTCATGGTTTGAATGTAATATATTCATAAAGCCAGAGCTTTCGTGTTTCCTCTATAACCAATTGC
260 GTCATGGTTTGAATGTAATATATTCATAAAGCCAGAGCTTTCGTGTTTCCTC-ATAACCAATTAC
*
283385 TTTAGCGGAATAGCTCAACTTTATTGAATATATATATATATATATTCATTTTTTTGGTATACGAA
324 TTTAGCGGAATAGCTCAGCTTTATTGAATATATATATATATATATTCATTTTTTTGGTATACGAA
*
283450 TTCCATTTATTAAGCTTACTAAGGAGAAACTGTTATAGTCCATGTTTGTTGAAGGTAAAAAAATC
389 TTCCATTTATTAAGCTTACCAAGGAGAAACTGTTATAGTCCATGTTTGTTGAAGGTAAAAAAATC
283515 TCATCGTTAGAGTTCAATTCCCAAGAAACTGACCTAAACTAGATTCACATACTTGACCATTCCAT
454 TCATCGTTAGAGTTCAATTCCCAAGAAACTGACCTAAACTAGATTCACATACTTGACCATTCCAT
*
283580 CTAAAAAGATCATGATCATCATTGAATGTCATCAACAGAAGTTAAAAACCAATTAGGTTTGCAAT
519 CTAAAAAGATCATGATCAACATTGAATGTCATCAACAGAAGTTAAAAACCAATTAGGTTTGCAAT
*
283645 CTCATGTGCTAGTTGCCCCATTTTGTTCGTTTAAACATACCTGAATACCAAACCCTTGATGGACT
584 CTCATGTGCTAGTTGCCCCATTTTGTTCGTTTAAACATACATGAATACCAAACCCTTGATGGACT
283710 CTTCATGAGAAGAGAAACTAGTTAGGTCTCTGCATGAGAAGGGTATGTATTGGTATATCTTTAGA
649 CTTCATGAGAAGAGAAACTAGTTAGGTCTCTGCATGAGAAGGGTATGTATTGGTATATCTTTAGA
*
283775 TTAAGATCAAGGGGTCCTTGTTTTGCTAGTTG
714 TTAAGATCAAGGGGTCCTTGTTTTGCTAGCTG
283807 AATGAGATTTCTAAGTGCTAGTGTGAGTTGTTCAACTATAACAGGTGTTCCTCAACTCCCTTATT
1 AATGAGATTTCTAAGTGCTAGTGTGAGTTGTTCAACTATAACAGGTGTTCCTCAACTCCCTTATT
283872 CCATATTCACCGAAACTCATTGTTTAGTAAATTCGAATTAATTTGCCATTGTTTGGCTAGCTGAA
66 CCATATTCACCGAAACTCATTGTTTAGTAAATTCGAATTAATTTGCCATTGTTTGGCTAGCTGAA
283937 TTCAGCTTTATTGTACATATATATTAAAATTGCCTTTGTTAGGCTAACTGAAGGATTCATGTCAT
131 TTCAGCTTTATTGTACATATATATTAAAATTGCCTTTGTTAGGCTAACTGAAGGATTCATGTCAT
* * *
284002 CACAAATTCTTCGACTTGACAATCACAGTGGAACAAACACTGAATTGCCAAGTACCCGATCAATG
196 CACAAAGTCTTCGACTTGACAATCACAGTGGAGCAAACACCGAATTGCCAAGTACCCGATCAATG
284067 TCATGGTTTGAATGTAATATATTCATAAAGCCAGAGCTTTCGTGTTTCCTC-TAACCAATTACTT
261 TCATGGTTTGAATGTAATATATTCATAAAGCCAGAGCTTTCGTGTTTCCTCATAACCAATTACTT
* * *
284131 CAGCAGAATAGCTCAGCTTTATTGAATATATATATATATATATTCATTTTTTTGGTATACGGATT
326 TAGCGGAATAGCTCAGCTTTATTGAATATATATATATATATATTCATTTTTTTGGTATACGAATT
*
284196 CCATTTATTAAGCTTACCAAGGAGAAACTGTTATAGTCCATGTTTTTTGAAGGTAAAAAAATCTC
391 CCATTTATTAAGCTTACCAAGGAGAAACTGTTATAGTCCATGTTTGTTGAAGGTAAAAAAATCTC
* *
284261 ATCGTTAGAGTTCAATTCCCAAGAAACTGACCTAAACTAGATTCACATATTTGACCATTCTATCT
456 ATCGTTAGAGTTCAATTCCCAAGAAACTGACCTAAACTAGATTCACATACTTGACCATTCCATCT
* *
284326 GAAAAGATCATGATCAACATTGAATGTCATCAACAGAAG-TAAAAACCAATTAGTTTTGCAATCT
521 AAAAAGATCATGATCAACATTGAATGTCATCAACAGAAGTTAAAAACCAATTAGGTTTGCAATCT
*
284390 CATGTGCTAGTTGCCCCATTTTGTTCTTTTAACACATACATGAATACCAAACCCTTGATGGACTC
586 CATGTGCTAGTTGCCCCATTTTGTTCGTTTAA-ACATACATGAATACCAAACCCTTGATGGACTC
284455 TTCATGAGAAGAGAAACTAGTTAGGTCTCTGCATGAGAAGGGTATGTATTGGTATATCTTTAGAT
650 TTCATGAGAAGAGAAACTAGTTAGGTCTCTGCATGAGAAGGGTATGTATTGGTATATCTTTAGAT
284520 TAAGATCAAGGGGTCCTTGTTTTGCTAGCTG
715 TAAGATCAAGGGGTCCTTGTTTTGCTAGCTG
*
284551 AATGAGATTTCTAAGTGCTCGTGTGAGTTGTTCAACTATAACAGGTGTTCCTCAACTCCCTTATT
1 AATGAGATTTCTAAGTGCTAGTGTGAGTTGTTCAACTATAACAGGTGTTCCTCAACTCCCTTATT
* * *
284616 CCATATTCATCGAAACTCATTGTTTAGTAAATTCGAATTAATTTGCCATTGTTTGGATAGTTGAA
66 CCATATTCACCGAAACTCATTGTTTAGTAAATTCGAATTAATTTGCCATTGTTTGGCTAGCTGAA
* *
284681 TTCAGCTTTATTGTACATATATATTAGAATTTCCTTTGTTAGGCTAACTGAAGGATTCATGTCAT
131 TTCAGCTTTATTGTACATATATATTAAAATTGCCTTTGTTAGGCTAACTGAAGGATTCATGTCAT
284746 CACAAAGTCTTCGACTTGACAATCACAGTGGAGCAAACACCGAATTGCCAAGTACCCGATCAATG
196 CACAAAGTCTTCGACTTGACAATCACAGTGGAGCAAACACCGAATTGCCAAGTACCCGATCAATG
284811 TCATGGTTTGAATGTAATATATTCATAAAGCCAGAGCTTTCGTGTTTCCTCTATAACCAATTGA-
261 TCATGGTTTGAATGTAATATATTCATAAAGCCAGAGCTTTCGTGTTTCCTC-ATAACCAATT-AC
284875 TTTAGCGGAATAGCTCAGCTTTATTGAATATATATATATATATAT
324 TTTAGCGGAATAGCTCAGCTTTATTGAATATATATATATATATAT
284920 ATTGTTCACT
Statistics
Matches: 1070, Mismatches: 38, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
743 55 0.05
744 664 0.62
745 1 0.00
746 349 0.33
747 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (745 bp):
AATGAGATTTCTAAGTGCTAGTGTGAGTTGTTCAACTATAACAGGTGTTCCTCAACTCCCTTATT
CCATATTCACCGAAACTCATTGTTTAGTAAATTCGAATTAATTTGCCATTGTTTGGCTAGCTGAA
TTCAGCTTTATTGTACATATATATTAAAATTGCCTTTGTTAGGCTAACTGAAGGATTCATGTCAT
CACAAAGTCTTCGACTTGACAATCACAGTGGAGCAAACACCGAATTGCCAAGTACCCGATCAATG
TCATGGTTTGAATGTAATATATTCATAAAGCCAGAGCTTTCGTGTTTCCTCATAACCAATTACTT
TAGCGGAATAGCTCAGCTTTATTGAATATATATATATATATATTCATTTTTTTGGTATACGAATT
CCATTTATTAAGCTTACCAAGGAGAAACTGTTATAGTCCATGTTTGTTGAAGGTAAAAAAATCTC
ATCGTTAGAGTTCAATTCCCAAGAAACTGACCTAAACTAGATTCACATACTTGACCATTCCATCT
AAAAAGATCATGATCAACATTGAATGTCATCAACAGAAGTTAAAAACCAATTAGGTTTGCAATCT
CATGTGCTAGTTGCCCCATTTTGTTCGTTTAAACATACATGAATACCAAACCCTTGATGGACTCT
TCATGAGAAGAGAAACTAGTTAGGTCTCTGCATGAGAAGGGTATGTATTGGTATATCTTTAGATT
AAGATCAAGGGGTCCTTGTTTTGCTAGCTG
Found at i:285390 original size:21 final size:21
Alignment explanation
Indices: 285363--285409 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
285353 CTACAATTCT
285363 CAATGGTGTGCACTGAGCTCC
1 CAATGGTGTGCACTGAGCTCC
*
285384 TAATGGTGTGCACTGAGCTCC
1 CAATGGTGTGCACTGAGCTCC
285405 CAATG
1 CAATG
285410 TGATAGATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.26
Consensus pattern (21 bp):
CAATGGTGTGCACTGAGCTCC
Found at i:292483 original size:50 final size:50
Alignment explanation
Indices: 292408--292508 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
292398 ATTTGAAACC
*
292408 ACTGCTGTTGAAACCACTAATCCAACAGACTTGCTGGATTATACTTATAA
1 ACTGCTGTTGAAACCACTAATCCAACAGACTTGCTGGATTATACTGATAA
* * * *
292458 ACTGCTGTTGAAACCATTATTCCAACCGACTTGCTGGATTCTACTGATAA
1 ACTGCTGTTGAAACCACTAATCCAACAGACTTGCTGGATTATACTGATAA
292508 A
1 A
292509 AATATGTTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (50 bp):
ACTGCTGTTGAAACCACTAATCCAACAGACTTGCTGGATTATACTGATAA
Found at i:307806 original size:28 final size:29
Alignment explanation
Indices: 307747--307822 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 29
307737 CAGGGCCCCT
* *
307747 ATTTTTTGTATTTATAATCAGAGCTCTCA
1 ATTTTTTATATTTATAATCAGAACTCTCA
*
307776 ATTTTCTTATATTTATAATTAGAAC-C-CA
1 ATTTT-TTATATTTATAATCAGAACTCTCA
307804 A-TTTTTATAATTTCATAAT
1 ATTTTTTAT-ATTT-ATAAT
307823 ATTTTTAGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 4 0.10
27 7 0.17
28 8 0.20
29 6 0.15
30 16 0.39
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (29 bp):
ATTTTTTATATTTATAATCAGAACTCTCA
Found at i:311431 original size:2 final size:2
Alignment explanation
Indices: 311424--311453 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
311414 AACCATTTGC
311424 AT AT AT AT AT AT 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
311454 GTGTATTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:314278 original size:22 final size:22
Alignment explanation
Indices: 314253--314295 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
314243 GAGGAAAAAG
* *
314253 ACAATGAAAATAAATAAATAAA
1 ACAAAGAAAACAAATAAATAAA
*
314275 ACAAAGAAAACACATAAATAA
1 ACAAAGAAAACAAATAAATAA
314296 CACGAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.72, C:0.09, G:0.05, T:0.14
Consensus pattern (22 bp):
ACAAAGAAAACAAATAAATAAA
Found at i:314776 original size:22 final size:22
Alignment explanation
Indices: 314735--314784 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
314725 ATATATATAT
314735 AAATAAAAAATAAAGTATAAAT-G
1 AAATAAAAAATAAAG-AT-AATGG
314758 AAATAAAAAATAATA-ATAATGG
1 AAATAAAAAATAA-AGATAATGG
314780 AAATA
1 AAATA
314785 TAAGTAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
23 13 0.52
24 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (22 bp):
AAATAAAAAATAAAGATAATGG
Found at i:315294 original size:35 final size:35
Alignment explanation
Indices: 315255--315326 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
315245 TAAAAAAACC
*
315255 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
315290 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
315325 CT
1 CT
315327 TCTTTGTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (35 bp):
CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:315905 original size:109 final size:110
Alignment explanation
Indices: 315774--316220 Score: 749
Period size: 109 Copynumber: 4.1 Consensus size: 110
315764 ATCCAATACA
**
315774 AGTTGAAATC-GACTCTGAAATTGGGAAGTTGTTTGTTGACAACCAACCGTCCCTTCGTTGTGAA
1 AGTTGAAATCGGACTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAA
315838 GTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGG
66 GTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGG
*
315883 AGTTGAAATCGGA-TCTGAAATTGGGAAGTTGTTTGTTGACAACCAGTCGTCCCTTCATTGTGAA
1 AGTTGAAATCGGACTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAA
*
315947 GTTAAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGG
66 GTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGG
*
315992 AGTTGAAATC-GACTCTGAAATTGGGAAGTTGTTTATTGACAACCAGTCGTCCCTTCGTTGTGAA
1 AGTTGAAATCGGACTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAA
*
316056 GTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCATCGTGG
66 GTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGG
* * * *
316101 AATTGAAATCGG-CTCTGAAATTGAGAAGTTGTTTGTCGACAACCAGTTGTCCCTTCGTTGTGAA
1 AGTTGAAATCGGACTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAA
*
316165 GTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCTCTGTCGTGG
66 GTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGG
* *
316210 GGTTAAAATCG
1 AGTTGAAATCG
316221 CGGATGGCCC
Statistics
Matches: 317, Mismatches: 18, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
108 2 0.01
109 312 0.98
110 3 0.01
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (110 bp):
AGTTGAAATCGGACTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAA
GTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGG
Done.