Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002070.1 Hibiscus syriacus cultivar Beakdansim tig00004227_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: 812484
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:6782 original size:18 final size:18
Alignment explanation
Indices: 6756--6803 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
6746 GCACATGTAC
6756 CATCATTATCATCATCAA
1 CATCATTATCATCATCAA
* *
6774 CATCTTTATCATTATCAA
1 CATCATTATCATCATCAA
* *
6792 TATTATTATCAT
1 CATCATTATCAT
6804 TTATCCCTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (18 bp):
CATCATTATCATCATCAA
Found at i:10101 original size:28 final size:26
Alignment explanation
Indices: 10034--10087 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
10024 AATCTCCAAG
10034 CTATCCACTTCCAACATCACTTGTCT
1 CTATCCACTTCCAACATCACTTGTCT
10060 CTATCCACTTCCAACATCACTTGTCT
1 CTATCCACTTCCAACATCACTTGTCT
10086 CT
1 CT
10088 CACCAAGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.39, G:0.04, T:0.35
Consensus pattern (26 bp):
CTATCCACTTCCAACATCACTTGTCT
Found at i:32384 original size:14 final size:14
Alignment explanation
Indices: 32365--32418 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
32355 TAATAAGTTC
32365 ATTTATGTTCATTT
1 ATTTATGTTCATTT
*
32379 ATTTATGTTCGTTCT
1 ATTTATGTTCATT-T
* *
32394 -TTTATGTTCGTTC
1 ATTTATGTTCATTT
*
32407 GTTTATGTTCAT
1 ATTTATGTTCAT
32419 CTACTTTCGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 34 0.97
15 1 0.03
ACGTcount: A:0.15, C:0.11, G:0.13, T:0.61
Consensus pattern (14 bp):
ATTTATGTTCATTT
Found at i:32401 original size:28 final size:28
Alignment explanation
Indices: 32361--32416 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
32351 TTGGTAATAA
*
32361 GTTCATTTATGTTCATTTATTTATGTTC
1 GTTCATTTATGTTCATTCATTTATGTTC
* * *
32389 GTTCTTTTATGTTCGTTCGTTTATGTTC
1 GTTCATTTATGTTCATTCATTTATGTTC
32417 ATCTACTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.61
Consensus pattern (28 bp):
GTTCATTTATGTTCATTCATTTATGTTC
Found at i:32634 original size:10 final size:10
Alignment explanation
Indices: 32619--32721 Score: 62
Period size: 10 Copynumber: 9.2 Consensus size: 10
32609 GAAAAAAACA
32619 TTTATGTTCG
1 TTTATGTTCG
*
32629 TTTATGTTCATT
1 TTTATGTTC--G
*
32641 TATTATGTTTG
1 T-TTATGTTCG
32652 TTTATGTTCGTTCG
1 TTTA---T-GTTCG
* *
32666 TTTGTGTTCA
1 TTTATGTTCG
*
32676 TTTACGTTCG
1 TTTATGTTCG
32686 TTTATGTTCG
1 TTTATGTTCG
32696 TTTACATCAGTTCG
1 TTT--AT--GTTCG
32710 TTTATGTTCG
1 TTTATGTTCG
32720 TT
1 TT
32722 CATTTGCGTT
Statistics
Matches: 72, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
10 42 0.58
11 2 0.03
12 5 0.07
13 8 0.11
14 15 0.21
ACGTcount: A:0.13, C:0.12, G:0.17, T:0.58
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:32642 original size:20 final size:20
Alignment explanation
Indices: 32617--32718 Score: 70
Period size: 20 Copynumber: 5.0 Consensus size: 20
32607 AAGAAAAAAA
32617 CATTTATGTTCGTTTATGTT
1 CATTTATGTTCGTTTATGTT
32637 CATTTAT-TAT-G-TT-TGTT
1 CATTTATGT-TCGTTTATGTT
* * *
32654 TATGTT-CGTTCGTTTGTGTT
1 CAT-TTATGTTCGTTTATGTT
*
32674 CATTTACGTTCGTTTATGTT
1 CATTTATGTTCGTTTATGTT
*
32694 CGTTTACATCAGTTCGTTTATGTT
1 CATTT--AT--GTTCGTTTATGTT
32718 C
1 C
32719 GTTCATTTGC
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
17 7 0.11
18 6 0.09
19 6 0.09
20 31 0.48
22 1 0.02
24 14 0.22
ACGTcount: A:0.14, C:0.13, G:0.17, T:0.57
Consensus pattern (20 bp):
CATTTATGTTCGTTTATGTT
Found at i:32732 original size:24 final size:23
Alignment explanation
Indices: 32643--32738 Score: 83
Period size: 24 Copynumber: 4.2 Consensus size: 23
32633 TGTTCATTTA
* *
32643 TTATGTTTGTTTATGTTCGTTCG-
1 TTATGTTCGTTCAT-TTCGTTCGT
32666 TT-TG-T-GTTCATTTACGTTCGT
1 TTATGTTCGTTCATTT-CGTTCGT
* **
32687 TTATGTTCGTTTACATCAGTTCGT
1 TTATGTTCGTTCATTTC-GTTCGT
32711 TTATGTTCGTTCATTTGCGTTCGT
1 TTATGTTCGTTCATTT-CGTTCGT
32735 TTAT
1 TTAT
32739 CATTTAAATG
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
19 2 0.03
20 11 0.19
21 3 0.05
22 4 0.07
23 4 0.07
24 34 0.58
25 1 0.02
ACGTcount: A:0.11, C:0.14, G:0.19, T:0.56
Consensus pattern (23 bp):
TTATGTTCGTTCATTTCGTTCGT
Found at i:33564 original size:29 final size:30
Alignment explanation
Indices: 33531--33588 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
33521 TAAAGTTTGG
*
33531 AAAAGTGTAGAGATCAAAAG-GTAATTTTT
1 AAAAGTGTAGAGACCAAAAGTGTAATTTTT
* *
33560 AAAAGTTTAGGGACCAAAAGTGTAATTTT
1 AAAAGTGTAGAGACCAAAAGTGTAATTTT
33589 AGAAATTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (30 bp):
AAAAGTGTAGAGACCAAAAGTGTAATTTTT
Found at i:36265 original size:39 final size:39
Alignment explanation
Indices: 36210--36372 Score: 220
Period size: 39 Copynumber: 4.2 Consensus size: 39
36200 AAGTATACTA
* *
36210 GTGCATATGGTAGGCACGACCTTATGTGCAAGCACTTCG
1 GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCG
* *
36249 GTGCATATGGTGGGCACGACCTTATGTGTAAGCATTTCA
1 GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCG
* * * *
36288 GTGCATATTGTGGACACGACCTTATGTGTAAGAACTTTG
1 GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCG
* * *
36327 GTGCATATGGTGGGTATGACC-TATGTGTAAGCACTACG
1 GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCG
36365 GTGCATAT
1 GTGCATAT
36373 ATTTGACTCG
Statistics
Matches: 107, Mismatches: 17, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
38 22 0.21
39 85 0.79
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (39 bp):
GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCG
Found at i:41506 original size:46 final size:46
Alignment explanation
Indices: 41148--41496 Score: 493
Period size: 46 Copynumber: 7.6 Consensus size: 46
41138 AAATTCCTTT
* *
41148 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGATGCATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
*
41194 GGCATGAAAGAATGCCATAAATGAAAATGCATAACGGTGCATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
* *
41240 GGCATGAAAGGATGCCATAAATGAAAATGCCTAATGGTGCATTA-C
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
* * * *
41285 AGGTATGAAAGGATACCATAAATGAAAATGGATAACGGTGTATTATC
1 -GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
* *
41332 AGTATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
* * * *
41378 GGCATGAGAGGATGCCACAAATCAAAATGTATAACGGTGCATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
* * * *
41424 GACATGAAATGATGTCATAAATGAAAATGCATAATGGTGCATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
**
41470 GGCATGAAAGGATGCCACCAATGAAAA
1 GGCATGAAAGGATGCCATAAATGAAAA
41497 AACATAATGG
Statistics
Matches: 266, Mismatches: 35, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
45 1 0.00
46 264 0.99
47 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23
Consensus pattern (46 bp):
GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
Found at i:46322 original size:17 final size:18
Alignment explanation
Indices: 46300--46343 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
46290 GTATTATTAA
46300 AAGTATA-AATGTTAGAG
1 AAGTATACAATGTTAGAG
46317 AAGTATACTAATGTTAGAG
1 AAGTATAC-AATGTTAGAG
46336 AAGTATAC
1 AAGTATAC
46344 TAACATTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 7 0.28
19 18 0.72
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
AAGTATACAATGTTAGAG
Found at i:46331 original size:19 final size:19
Alignment explanation
Indices: 46307--46346 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
46297 TAAAAGTATA
46307 AATGTTAGAGAAGTATACT
1 AATGTTAGAGAAGTATACT
46326 AATGTTAGAGAAGTATACT
1 AATGTTAGAGAAGTATACT
46345 AA
1 AA
46347 CATTTAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (19 bp):
AATGTTAGAGAAGTATACT
Found at i:47255 original size:46 final size:46
Alignment explanation
Indices: 46721--47254 Score: 649
Period size: 46 Copynumber: 11.6 Consensus size: 46
46711 AAATGCCTTT
*
46721 GGCATGAAAAGATGCCATAAATGAAAATGCATAACGGTGCATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
* *
46767 GGCATGAAAGGATGCCATAAATGAAAGTGCATAATGGTGCATTA-C
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
* *
46812 TGGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCTTTATA
1 -GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
* *
46859 GGTATGAAAGGAGGCCATAAATGAAAATGCATAACGGTGCATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
** * * * *
46905 GATATGAAAGGATGCCATAAATGAAAATGAATAATGGTTCCTTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
* * *
46951 GGCATGAAAAGATGCCATAAATGAAAATGCATAATGATGCATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
* *
46997 GGCATGAAAGGATGCCATAAATGAAAATGCATAACAAG-GCATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAAC-GGTGCATTATC
* * * * *
47043 GACATGAAAGGATGCCAAAAATGAAAATGTATAACAGTGTATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
** * * * *
47089 AACATGAAAGAATGTCATAAATGAAAATGTATAACGGTTCATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
** * ** *
47135 GATATGAAAGGATGCCATAAATGAAAATGGATAATAGTACATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
** * *
47181 GGCATGAAAAAATGCCATAAATGAAAATACATAACGATGCATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
** **
47227 AACATGAAAGGATGCCACGAATGAAAAT
1 GGCATGAAAGGATGCCATAAATGAAAAT
47255 ATGTAATGGT
Statistics
Matches: 419, Mismatches: 65, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
45 3 0.01
46 416 0.99
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (46 bp):
GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC
Found at i:47947 original size:25 final size:25
Alignment explanation
Indices: 47919--47969 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
47909 AAATGTATAT
*
47919 GGGAAATTAGTGTTACAGTTCGGGA
1 GGGAAATGAGTGTTACAGTTCGGGA
47944 GGGAAATGAGTGTTACAGTTCGGGA
1 GGGAAATGAGTGTTACAGTTCGGGA
47969 G
1 G
47970 TCAATCACGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.08, G:0.39, T:0.25
Consensus pattern (25 bp):
GGGAAATGAGTGTTACAGTTCGGGA
Found at i:50599 original size:18 final size:18
Alignment explanation
Indices: 50550--50587 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
50540 ATATTCTAAC
50550 ATGCAAACTATATAGTCT
1 ATGCAAACTATATAGTCT
50568 ATGCAAACTATATAGTCT
1 ATGCAAACTATATAGTCT
50586 AT
1 AT
50588 AGTAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (18 bp):
ATGCAAACTATATAGTCT
Found at i:52213 original size:7 final size:7
Alignment explanation
Indices: 52189--52226 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
52179 TTTATTTCTA
*
52189 TTTCTAT
1 TTTCTCT
52196 TTT-TC-
1 TTTCTCT
52201 TTTCTCT
1 TTTCTCT
52208 TTTCTCT
1 TTTCTCT
52215 TTTCTCT
1 TTTCTCT
52222 TTTCT
1 TTTCT
52227 GCATTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 3 0.11
6 3 0.11
7 22 0.79
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTCTCT
Found at i:52218 original size:14 final size:13
Alignment explanation
Indices: 52183--52226 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 13
52173 TCTTCTTTTA
* *
52183 TTTCTATTTCTAT
1 TTTCTCTTTCTCT
52196 TTT-TCTTTCTCT
1 TTTCTCTTTCTCT
52208 TTTCTCTTTTCTCT
1 TTTCTC-TTTCTCT
52222 TTTCT
1 TTTCT
52227 GCATTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 10 0.37
13 5 0.19
14 12 0.44
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTCTCTTTCTCT
Found at i:54364 original size:20 final size:19
Alignment explanation
Indices: 54343--54417 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
54333 TTTTTACATC
*
54343 TTCTTTCTATTCTTTTTTT
1 TTCTTTTTATTCTTTTTTT
** *
54362 CTT-TTTTTCCTCTTTTCTT
1 -TTCTTTTTATTCTTTTTTT
*
54381 TTCTTTTTCTTCTTTTGTTT
1 TTCTTTTTATTCTTTT-TTT
54401 TTCTTTTTCATTCTTTT
1 TTCTTTTT-ATTCTTTT
54418 CCTTCTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 2 0.04
19 24 0.53
20 12 0.27
21 7 0.16
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (19 bp):
TTCTTTTTATTCTTTTTTT
Found at i:54377 original size:19 final size:19
Alignment explanation
Indices: 54353--54414 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 19
54343 TTCTTTCTAT
54353 TCTTTTTTTCTTTTT-TTCC
1 TCTTTTTTTCTTTTTCTT-C
54372 TCTTTTCTTTTCTTTTTCTTC
1 TC-TTT-TTTTCTTTTTCTTC
*
54393 TTTTGTTTTTCTTTTTCATTC
1 TCTT-TTTTTCTTTTTC-TTC
54414 T
1 T
54415 TTTCCTTCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
19 2 0.05
20 16 0.43
21 17 0.46
22 2 0.05
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (19 bp):
TCTTTTTTTCTTTTTCTTC
Found at i:54414 original size:21 final size:19
Alignment explanation
Indices: 54352--54417 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 19
54342 CTTCTTTCTA
54352 TTCTTTTTTTCTT-TTTTTC
1 TTCTTTTTTT-TTCTTTTTC
* *
54371 CTCTTTTCTTTTCTTTTTC
1 TTCTTTTTTTTTCTTTTTC
54390 TTCTTTTGTTTTTCTTTTTC
1 TTCTTTT-TTTTTCTTTTTC
54410 ATTCTTTT
1 -TTCTTTT
54418 CCTTCTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.05
19 20 0.50
20 11 0.28
21 7 0.17
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (19 bp):
TTCTTTTTTTTTCTTTTTC
Found at i:54415 original size:30 final size:30
Alignment explanation
Indices: 54341--54436 Score: 99
Period size: 31 Copynumber: 3.1 Consensus size: 30
54331 ATTTTTTACA
54341 TCTTCTTTCTATTCTTTTT-TTC-TTTTTTT
1 TCTT-TTTCTATTCTTTTTCTTCTTTTTTTT
* *
54370 CCTCTTTTCTTTTCTTTTTCTTCTTTTGTTTT
1 TCT-TTTTCTATTCTTTTTCTTCTTTT-TTTT
*
54402 TCTTTTTC-ATTCTTTTCCTTCTATTTTATTT
1 TCTTTTTCTATTCTTTTTCTTCT-TTTT-TTT
54433 TCTT
1 TCTT
54437 CTTCAAGCAT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
29 15 0.27
30 17 0.30
31 18 0.32
32 6 0.11
ACGTcount: A:0.04, C:0.20, G:0.01, T:0.75
Consensus pattern (30 bp):
TCTTTTTCTATTCTTTTTCTTCTTTTTTTT
Found at i:75174 original size:29 final size:31
Alignment explanation
Indices: 75127--75189 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
75117 AAAAATTTGA
* *
75127 TTAGTAACCAAAATGTAAA-TTTTG-AAAGT
1 TTAGTAACCAAAATATAAAGTTTGGAAAAGT
* *
75156 TTAGTAGCCAAAGTATAAAGTTTGGAAAAGT
1 TTAGTAACCAAAATATAAAGTTTGGAAAAGT
75187 TTA
1 TTA
75190 TGGACCGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.57
30 4 0.14
31 8 0.29
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.33
Consensus pattern (31 bp):
TTAGTAACCAAAATATAAAGTTTGGAAAAGT
Found at i:75217 original size:30 final size:30
Alignment explanation
Indices: 75181--75250 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
75171 TAAAGTTTGG
* *
75181 AAAAGTTTATGGACCGAAAAG-GTATTTTTT
1 AAAAGTTTAGGGACC-AAAAGTGTAATTTTT
75211 AAAAGTTTAGGGACCAAAAGTGTAATTTTT
1 AAAAGTTTAGGGACCAAAAGTGTAATTTTT
75241 AAAA-TTTAGG
1 AAAAGTTTAGG
75251 TGTTTTAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 11 0.30
30 26 0.70
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (30 bp):
AAAAGTTTAGGGACCAAAAGTGTAATTTTT
Found at i:76758 original size:2 final size:2
Alignment explanation
Indices: 76751--76796 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
76741 TGATTCATTC
76751 AT AT AT AT AT AT 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 AT AT AT AT AT AT
76793 AT AT
1 AT AT
76797 CAATTCCCGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79051 original size:16 final size:17
Alignment explanation
Indices: 79030--79078 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
79020 TGTAGCCCTT
79030 TGAAAATACATGTTAA-
1 TGAAAATACATGTTAAG
*
79046 TGAAAATGCATGTCTTTAAG
1 TGAAAATACATG---TTAAG
79066 TGAAAATACATGT
1 TGAAAATACATGT
79079 CCTTGAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 11 0.41
17 1 0.04
19 4 0.15
20 11 0.41
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (17 bp):
TGAAAATACATGTTAAG
Found at i:79094 original size:21 final size:19
Alignment explanation
Indices: 79030--79091 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
79020 TGTAGCCCTT
79030 TGAAAATACATG--TT-AA
1 TGAAAATACATGTCTTGAA
* *
79046 TGAAAATGCATGTCTTTAA
1 TGAAAATACATGTCTTGAA
79065 GTGAAAATACATGTCCTTGAA
1 -TGAAAATACATGT-CTTGAA
79086 TGAAAA
1 TGAAAA
79092 ATAAGGTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
16 11 0.29
18 2 0.05
19 2 0.05
20 18 0.47
21 5 0.13
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.31
Consensus pattern (19 bp):
TGAAAATACATGTCTTGAA
Found at i:83191 original size:15 final size:16
Alignment explanation
Indices: 83158--83237 Score: 51
Period size: 16 Copynumber: 5.1 Consensus size: 16
83148 TGTTAGAGGG
*
83158 AAAAATGAATAAATGA
1 AAAAATGAATAAATAA
*
83174 AAAAATGAA-GAATAA
1 AAAAATGAATAAATAA
*
83189 AAATAA-GTAA-AAAAAA
1 AAA-AATG-AATAAATAA
*
83205 ATAAAACGAA-AAATAA
1 A-AAAATGAATAAATAA
* *
83221 ATAAATAAATAAATAA
1 AAAAATGAATAAATAA
83237 A
1 A
83238 TGAAATATTA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
15 13 0.25
16 35 0.69
17 3 0.06
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.16
Consensus pattern (16 bp):
AAAAATGAATAAATAA
Found at i:83222 original size:4 final size:4
Alignment explanation
Indices: 83215--83244 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
83205 ATAAAACGAA
83215 AAAT AAAT AAAT AAAT AAAT AAAT GAAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A
83245 TTAAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:83257 original size:2 final size:2
Alignment explanation
Indices: 83250--83280 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
83240 AAATATTAAA
83250 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
83281 AATGAGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:83628 original size:23 final size:23
Alignment explanation
Indices: 83597--83640 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
83587 ACCAAATGAA
83597 TATAAATAAATAAAAA-ATATATG
1 TATAAAT-AATAAAAATATATATG
*
83620 TATATATAATAAAAATATATA
1 TATAAATAATAAAAATATATA
83641 GTGCAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
TATAAATAATAAAAATATATATG
Found at i:84203 original size:37 final size:37
Alignment explanation
Indices: 84110--84211 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
84100 GTGCTTGTGG
* * * * * *
84110 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAATTTT
1 ATCCTATTTTTAGGAGTTTGAATACTAGCAAAATTCT
*
84147 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATACTAGCAAAATTCT
*
84184 ATCCTATTTTTAGGAGTTTGAATTCTAG
1 ATCCTATTTTTAGGAGTTTGAATACTAG
84212 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATACTAGCAAAATTCT
Found at i:85215 original size:106 final size:105
Alignment explanation
Indices: 84899--85530 Score: 839
Period size: 106 Copynumber: 6.0 Consensus size: 105
84889 GCATTGTTCC
* * * * * *
84899 GAGTCTAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAA-CGGGAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAATTGTTTATTGACAA
* * *
84962 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
85003 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAAAT-TTTGTTGACAAT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTGTTTATTGACAAC
* * ** *
85063 CAGCCGCCCCTTCATCGTGAAGTTGGGCTTGTGTTGTCTTG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* *
85104 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-TTGTTTATTGACAA
* *
85168 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
65 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
85209 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGTCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AATTGTTTATTGACAA
*
85274 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
85315 GAGTCCAATATCCTTAGTTGTGAAGTTGAATTTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AATTGTTTATTGACAA
*
85380 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
85421 AAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-TTGTTTATTGACAA
* * *
85486 CCAGCCGTCCCTTCGTCATGAAGTTGAACTTGTGTTGTCTC
65 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
85527 GAGT
1 GAGT
85531 GACACGATAT
Statistics
Matches: 470, Mismatches: 47, Indels: 20
0.88 0.09 0.04
Matches are distributed among these distances:
100 79 0.17
101 8 0.02
102 1 0.00
103 2 0.00
104 38 0.08
105 7 0.01
106 333 0.71
107 2 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTGTTTATTGACAAC
CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:85849 original size:115 final size:115
Alignment explanation
Indices: 85708--85937 Score: 451
Period size: 115 Copynumber: 2.0 Consensus size: 115
85698 TTATGAAGTT
85708 TGGCTTCGAGCTAGATATCCTTCGTCATGAAGTTGAAATCCACTATCGAGCAAATTGTGTTGTTT
1 TGGCTTCGAGCTAGATATCCTTCGTCATGAAGTTGAAATCCACTATCGAGCAAATTGTGTTGTTT
85773 CGAGAGAAACTTTCAATCTGTCGAGTTGGTCGAAGTGTAGCTTCTTGCTG
66 CGAGAGAAACTTTCAATCTGTCGAGTTGGTCGAAGTGTAGCTTCTTGCTG
*
85823 TGGCTTCGAGCTAGATATCCTTCGTCATGAAGTTGAAATCCACTCTCGAGCAAATTGTGTTGTTT
1 TGGCTTCGAGCTAGATATCCTTCGTCATGAAGTTGAAATCCACTATCGAGCAAATTGTGTTGTTT
85888 CGAGAGAAACTTTCAATCTGTCGAGTTGGTCGAAGTGTAGCTTCTTGCTG
66 CGAGAGAAACTTTCAATCTGTCGAGTTGGTCGAAGTGTAGCTTCTTGCTG
85938 CTGAGTTAAG
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 114 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (115 bp):
TGGCTTCGAGCTAGATATCCTTCGTCATGAAGTTGAAATCCACTATCGAGCAAATTGTGTTGTTT
CGAGAGAAACTTTCAATCTGTCGAGTTGGTCGAAGTGTAGCTTCTTGCTG
Found at i:86385 original size:24 final size:24
Alignment explanation
Indices: 86357--86417 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
86347 AATATCAATA
*
86357 AAGAGTTTCGAAAGATGTTTAATC
1 AAGAGTTTTGAAAGATGTTTAATC
*
86381 AAGAGTTTTGAAAGATGTTTAATT
1 AAGAGTTTTGAAAGATGTTTAATC
*
86405 AAAAGTTTTGAAA
1 AAGAGTTTTGAAA
86418 ATATTGTCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (24 bp):
AAGAGTTTTGAAAGATGTTTAATC
Found at i:86623 original size:22 final size:22
Alignment explanation
Indices: 86598--86674 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
86588 TATTATTTGG
*
86598 TCAAAGGTTTGGCATTTAATGC
1 TCAAAGGTTTGGCATTTGATGC
86620 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
86642 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
86664 TCAACGGTTTG
1 TCAAAGGTTTG
86675 ATGGGATAGC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:87311 original size:14 final size:14
Alignment explanation
Indices: 87309--87365 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 14
87299 GTTCTTTCTT
87309 TTTCTTTTGTT-TTC
1 TTTCTTTT-TTGTTC
87323 -TTCTTTTTTGCTTC
1 TTTCTTTTTTG-TTC
*
87337 TTTTCTTTTTTGTTT
1 -TTTCTTTTTTGTTC
87352 TTTC-TTTTTGTTC
1 TTTCTTTTTTGTTC
87365 T
1 T
87366 GATTAAATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
12 2 0.05
13 16 0.43
14 7 0.19
15 2 0.05
16 10 0.27
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTCTTTTTTGTTC
Found at i:87316 original size:19 final size:19
Alignment explanation
Indices: 87295--87330 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
87285 TCCTTTTGAT
87295 TTTTGTTCT-TTCTTTTTC
1 TTTTGTTCTCTTCTTTTTC
*
87313 TTTTGTTTTCTTCTTTTT
1 TTTTGTTCTCTTCTTTTT
87331 TGCTTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.81
Consensus pattern (19 bp):
TTTTGTTCTCTTCTTTTTC
Found at i:87324 original size:16 final size:16
Alignment explanation
Indices: 87303--87359 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 16
87293 ATTTTTGTTC
87303 TTTCTTTTTCTTTTGT
1 TTTCTTTTTCTTTTGT
*
87319 TTTCTTCTT-TTTTG-
1 TTTCTTTTTCTTTTGT
*
87333 CTTC-TTTTCTTTT-T
1 TTTCTTTTTCTTTTGT
*
87347 TGT-TTTTTCTTTT
1 TTTCTTTTTCTTTT
87360 TGTTCTGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
13 3 0.09
14 17 0.52
15 5 0.15
16 8 0.24
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (16 bp):
TTTCTTTTTCTTTTGT
Found at i:87340 original size:30 final size:30
Alignment explanation
Indices: 87304--87360 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
87294 TTTTTGTTCT
87304 TTCTTTT-TCTTTTGTTTTCTTCTTTTTTGC
1 TTCTTTTCTCTTTTGTTTT-TTCTTTTTTGC
*
87334 TTCTTTTCTTTTTTGTTTTTTCTTTTT
1 TTCTTTTCTCTTTTGTTTTTTCTTTTT
87361 GTTCTGATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (30 bp):
TTCTTTTCTCTTTTGTTTTTTCTTTTTTGC
Found at i:91771 original size:24 final size:23
Alignment explanation
Indices: 91744--91793 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
91734 AATGAAGAAT
*
91744 AAAAATAAGTAAAAAAATTAAAGG
1 AAAAATAAATAAAAAAA-TAAAGG
* *
91768 AAAAATAAATAAATAAATAAATG
1 AAAAATAAATAAAAAAATAAAGG
91791 AAA
1 AAA
91794 TATTAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (23 bp):
AAAAATAAATAAAAAAATAAAGG
Found at i:92113 original size:19 final size:19
Alignment explanation
Indices: 92091--92128 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
92081 AAAAAAGTTT
92091 ATATA-TATAAAAATAATAA
1 ATATAGTATAAAAA-AATAA
*
92110 ATATAGTATTAAAAAATAA
1 ATATAGTATAAAAAAATAA
92129 CCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
ATATAGTATAAAAAAATAA
Found at i:92751 original size:37 final size:37
Alignment explanation
Indices: 92658--92754 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
92648 GTGCTTGTGG
* * * *
92658 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
* *
92695 ATCCTATTTTTAGGAGTTTGAATCTTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
92732 ATCCTATTTTTAGGAGTTTGAAT
1 ATCCTATTTTTAGGAGTTTGAAT
92755 TCTAGTAGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
Found at i:99416 original size:18 final size:18
Alignment explanation
Indices: 99384--99421 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
99374 AAATATTTAC
99384 ATTTTAAACATAAATTTT
1 ATTTTAAACATAAATTTT
99402 ATTTTGAAACA-AAATTTT
1 ATTTT-AAACATAAATTTT
99420 AT
1 AT
99422 CTCACTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTTTAAACATAAATTTT
Found at i:99461 original size:36 final size:39
Alignment explanation
Indices: 99412--99523 Score: 128
Period size: 38 Copynumber: 3.0 Consensus size: 39
99402 ATTTTGAAAC
*
99412 AAAATTTTATCTCACTTGAGATAGTTTTC-CTT-AAAAT
1 AAAATTTCATCTCACTTGAGATAGTTTTCTCTTGAAAAT
* *
99449 AAAA-TTCATCTCACTCGAGACAG-TTTCTCTTGAAACA-
1 AAAATTTCATCTCACTTGAGATAGTTTTCTCTTGAAA-AT
* *
99486 AAAATTTCATCTCCCTTTAGATA-TTTTCTCTTGAAAAT
1 AAAATTTCATCTCACTTGAGATAGTTTTCTCTTGAAAAT
99524 TTTTCGAGAT
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
35 4 0.06
36 19 0.31
37 12 0.19
38 27 0.44
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (39 bp):
AAAATTTCATCTCACTTGAGATAGTTTTCTCTTGAAAAT
Found at i:99983 original size:36 final size:37
Alignment explanation
Indices: 99924--100100 Score: 88
Period size: 36 Copynumber: 5.1 Consensus size: 37
99914 AAACTTTAAC
* * *
99924 ATTGTTTTTCTTAAAGCAAAATTTCATCTCACTTGAG
1 ATTGTTCTTCCTAAAACAAAATTTCATCTCACTTGAG
* **
99961 ATTGTTCTTCCTAAAAC-AAATTTTATCTTGCTTGAG
1 ATTGTTCTTCCTAAAACAAAATTTCATCTCACTTGAG
** * * **
99997 ACAGTT-TCTCATGAAACTCAA----A-CT---TTGAG
1 ATTGTTCT-TCCTAAAACAAAATTTCATCTCACTTGAG
* * * *
100026 ATTGTTTTTCTTAAAACAAAATTTTATCTCACTTGGG
1 ATTGTTCTTCCTAAAACAAAATTTCATCTCACTTGAG
** * *
100063 ATTGTAGTTCTTAAAAC-AAATTTCGTCTCACTTGAG
1 ATTGTTCTTCCTAAAACAAAATTTCATCTCACTTGAG
100099 AT
1 AT
100101 AGTTTCTCAT
Statistics
Matches: 106, Mismatches: 23, Indels: 23
0.70 0.15 0.15
Matches are distributed among these distances:
29 18 0.17
30 1 0.01
32 2 0.02
33 2 0.02
34 2 0.02
35 1 0.01
36 45 0.42
37 35 0.33
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (37 bp):
ATTGTTCTTCCTAAAACAAAATTTCATCTCACTTGAG
Found at i:99998 original size:102 final size:102
Alignment explanation
Indices: 99815--100194 Score: 496
Period size: 102 Copynumber: 3.7 Consensus size: 102
99805 TTTTATCTCT
* * * *
99815 CTTT-AGATT-TTTTTATTACAACAAAATTTCATCTCACTTGAGAGATTATTGTTCTTAAAACAA
1 CTTTAAGATTGTTTTTCTTAAAACAAAATTTCATCTCACTT--GAGATTGTTGTTCCTAAAACAA
* * *
99878 ATTTTGTCTCGCTCGAGACAGTTTCTCATGAAACTAAAA
64 ATTTTATCTCGCTTGAGACAGTTTCTCATGAAACTCAAA
* * *
99917 CTTTAACATTGTTTTTCTTAAAGCAAAATTTCATCTCACTTGAGATTGTTCTTCCTAAAACAAAT
1 CTTTAAGATTGTTTTTCTTAAAACAAAATTTCATCTCACTTGAGATTGTTGTTCCTAAAACAAAT
*
99982 TTTATCTTGCTTGAGACAGTTTCTCATGAAACTCAAA
66 TTTATCTCGCTTGAGACAGTTTCTCATGAAACTCAAA
* * * * *
100019 CTTTGAGATTGTTTTTCTTAAAACAAAATTTTATCTCACTTGGGATTGTAGTTCTTAAAACAAAT
1 CTTTAAGATTGTTTTTCTTAAAACAAAATTTCATCTCACTTGAGATTGTTGTTCCTAAAACAAAT
** * *
100084 TTCGTCTCACTTGAGATAGTTTCTCATGAAACTCAAA
66 TTTATCTCGCTTGAGACAGTTTCTCATGAAACTCAAA
* * *
100121 CTTTAAGATTATTTTTCTTAAAACAAAATTTCATCTCACATGAGATTGTT-TTTCTAAAAAACAA
1 CTTTAAGATTGTTTTTCTTAAAACAAAATTTCATCTCACTTGAGATTGTTGTTCCT--AAAACAA
100185 ATTTTATCTC
64 ATTTTATCTC
100195 ACTGGATATT
Statistics
Matches: 240, Mismatches: 34, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
101 3 0.01
102 191 0.80
103 19 0.08
104 27 0.11
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.41
Consensus pattern (102 bp):
CTTTAAGATTGTTTTTCTTAAAACAAAATTTCATCTCACTTGAGATTGTTGTTCCTAAAACAAAT
TTTATCTCGCTTGAGACAGTTTCTCATGAAACTCAAA
Found at i:100187 original size:37 final size:37
Alignment explanation
Indices: 100126--100212 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
100116 TCAAACTTTA
* *
100126 AGATTATTTTTCTTAAAACAAAATTTCATCTCACAT-G
1 AGATTGTTTTTCTAAAAACAAAATTTCATCTCAC-TGG
*
100163 AGATTGTTTTTCTAAAAA-ACAAATTTTATCTCACTGG
1 AGATTGTTTTTCTAAAAACA-AAATTTCATCTCACTGG
*
100200 ATATTGTTTTTCT
1 AGATTGTTTTTCT
100213 TGAAACTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
36 2 0.05
37 42 0.95
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (37 bp):
AGATTGTTTTTCTAAAAACAAAATTTCATCTCACTGG
Found at i:100289 original size:139 final size:139
Alignment explanation
Indices: 100022--100287 Score: 306
Period size: 139 Copynumber: 1.9 Consensus size: 139
100012 ACTCAAACTT
*
100022 TGAGATTGTTTTTCTTAAAACAAAATTTTATCTCACTTGGGATTGTAGTTCTTAAAACAAATTTC
1 TGAGATTGTTTTTCTAAAAACAAAATTTTATCTCACTTGGGATTGTAGTTCTTAAAACAAATTTC
* * * * *
100087 GTCTCACTTGAGATAGTTTCTCATGAAACTCAAACTTTAAGATTATTTTTCTTAAAACAAAATTT
66 GTCTCACTTGAGACAGTTTCTCATGAAACTCAAACATTAACATCATTTCTCTTAAAACAAAATTT
100152 CATCTCACA
131 CATCTCACA
* ** * *
100161 TGAGATTGTTTTTCTAAAAA-ACAAATTTTATCTCAC-TGGATATTGTTTTTCTTGAAACTAATT
1 TGAGATTGTTTTTCTAAAAACA-AAATTTTATCTCACTTGG-GATTGTAGTTCTTAAAACAAATT
* * ** * *
100224 TTGTCTCACTCT-CGACAGTTTCTTTTGAAA-TCCAAAGCATTGACATCATTTCTCTTGAAACAA
64 TCGTCTCACT-TGAGACAGTTTCTCATGAAACT-CAAA-CATTAACATCATTTCTCTTAAAACAA
100287 A
126 A
100288 TTGTGTATTG
Statistics
Matches: 105, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
138 5 0.05
139 78 0.74
140 22 0.21
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41
Consensus pattern (139 bp):
TGAGATTGTTTTTCTAAAAACAAAATTTTATCTCACTTGGGATTGTAGTTCTTAAAACAAATTTC
GTCTCACTTGAGACAGTTTCTCATGAAACTCAAACATTAACATCATTTCTCTTAAAACAAAATTT
CATCTCACA
Found at i:103711 original size:48 final size:48
Alignment explanation
Indices: 103643--103740 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
103633 ATTTATGTTT
* *
103643 TGATGAGAATTTTATTTTAGAATTTGTTATTATCATTTGAATGACTTA
1 TGATGAGAATTTTATTTTAGAATTTGTTATTATCATTTCAATAACTTA
103691 TGATGAGAATTTTATTTTAGAATTTGTTATTATCATTTCAATAACTTA
1 TGATGAGAATTTTATTTTAGAATTTGTTATTATCATTTCAATAACTTA
103739 TG
1 TG
103741 TGACATTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (48 bp):
TGATGAGAATTTTATTTTAGAATTTGTTATTATCATTTCAATAACTTA
Found at i:104294 original size:23 final size:22
Alignment explanation
Indices: 104251--104295 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
104241 TTTTTGCAAA
*
104251 TTTTGCATATTTTCGTTTGTCT
1 TTTTGCATATTTTCGTCTGTCT
104273 TTTTGGCATATTTTAC-TCTGTCT
1 TTTT-GCATATTTT-CGTCTGTCT
104296 CGTGGCACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 15 0.75
24 1 0.05
ACGTcount: A:0.11, C:0.16, G:0.13, T:0.60
Consensus pattern (22 bp):
TTTTGCATATTTTCGTCTGTCT
Found at i:119033 original size:47 final size:47
Alignment explanation
Indices: 118981--119185 Score: 337
Period size: 47 Copynumber: 4.4 Consensus size: 47
118971 TCATTTATCT
* *
118981 CATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAATTC
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
*
119028 CATAAGCTCGTAAGCTTATTTTATCAACATACTTACCATTTAAATTC
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
*
119075 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTT
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
*
119122 CATAAGCTCGTAAGCTTATTTTATCAATATACTTGCCA-TT--ATT-
1 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
119165 CATAAGCTCGTAAGCTTATTT
1 CATAAGCTCGTAAGCTTATTT
119186 ACATACTTAC
Statistics
Matches: 153, Mismatches: 5, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
43 21 0.14
44 3 0.02
46 2 0.01
47 127 0.83
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.40
Consensus pattern (47 bp):
CATAAGCTCGTAAGCTTATTTTATCAATATACTTACCATTTAAATTC
Found at i:119390 original size:61 final size:61
Alignment explanation
Indices: 119295--119409 Score: 194
Period size: 61 Copynumber: 1.9 Consensus size: 61
119285 GTAGTGCTAA
*
119295 ACCTACACTAAGCTTACGCCATAATGCTAATCTGGATATGACACATAAGGTCGTGCCCACC
1 ACCTACACTAAGCTTACGCCATAATGCTAATCTGGACATGACACATAAGGTCGTGCCCACC
* * *
119356 ACCTACACTAAGCTTACGCTATAATGCTAATCTGGACATGATACATTAGGTCGT
1 ACCTACACTAAGCTTACGCCATAATGCTAATCTGGACATGACACATAAGGTCGT
119410 ATCCACCTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (61 bp):
ACCTACACTAAGCTTACGCCATAATGCTAATCTGGACATGACACATAAGGTCGTGCCCACC
Found at i:120394 original size:29 final size:28
Alignment explanation
Indices: 120328--120395 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
120318 AGGTTCTTCA
* *
120328 TCAATTTTCCAAAATTTACGAATTGATC
1 TCAATTTTTCAAAATTTACGAAATGATC
* *
120356 TCCAACTTTTCAAAGA-TTACGAAATGGTCC
1 T-CAATTTTTCAAA-ATTTACGAAATGAT-C
120386 TCAATTTTTC
1 TCAATTTTTC
120396 TAAGGTTGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 1 0.03
29 28 0.88
30 3 0.09
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (28 bp):
TCAATTTTTCAAAATTTACGAAATGATC
Found at i:121234 original size:30 final size:30
Alignment explanation
Indices: 121198--121255 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
121188 TTTGGTCCCT
*
121198 AAACTTT-CCAAAGTTTATACTTTGATCACC
1 AAACTTTACCAAA-TTTATAATTTGATCACC
121228 AAACTTTACCAAATTTATAATTTGATCA
1 AAACTTTACCAAATTTATAATTTGATCA
121256 TTAAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (30 bp):
AAACTTTACCAAATTTATAATTTGATCACC
Found at i:128532 original size:172 final size:172
Alignment explanation
Indices: 128229--128562 Score: 553
Period size: 172 Copynumber: 1.9 Consensus size: 172
128219 TCTCCTTTTA
*
128229 AACTTGGAAAACTTTCCATCTTTTTTCGATGTTAAGAGAAGTACTACCGTTTGTCTACTTCAGTT
1 AACTTGGAAAACTTTCCATCTTTTTTCGATGTTAAGAGAAGTACAACCGTTTGTCTACTTCAGTT
* * * * *
128294 TTCAGATGACGAATCTTTGGAGATATCTATTAACCTCAGGGGACGAATGTCTGTTGCAGCGATTA
66 TTCAAATGACAAATCTTTGGAGAGATCTATTAACCTCAGGGGACGAATGCCTATTGCAGCGATTA
128359 CACACATCAAGACGAATTCATTTCTAAGACAACTCTTCTATT
131 CACACATCAAGACGAATTCATTTCTAAGACAACTCTTCTATT
*
128401 AACTTGGAAAGCTTTCCATCTTTTTTCGATGTTAAGAGAAGTACAACCGTTTGTCTACTTC-GAT
1 AACTTGGAAAACTTTCCATCTTTTTTCGATGTTAAGAGAAGTACAACCGTTTGTCTACTTCAG-T
* * *
128465 TTTCAAATGACAAATCTTTGGAGAGATCTATTGACCTCTGGGGACGAATGCCTATTGCAGTGATT
65 TTTCAAATGACAAATCTTTGGAGAGATCTATTAACCTCAGGGGACGAATGCCTATTGCAGCGATT
*
128530 ACACACATTAAGACGAATTCATTTCTAAGACAA
130 ACACACATCAAGACGAATTCATTTCTAAGACAA
128563 TGATTATACC
Statistics
Matches: 150, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
171 1 0.01
172 149 0.99
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (172 bp):
AACTTGGAAAACTTTCCATCTTTTTTCGATGTTAAGAGAAGTACAACCGTTTGTCTACTTCAGTT
TTCAAATGACAAATCTTTGGAGAGATCTATTAACCTCAGGGGACGAATGCCTATTGCAGCGATTA
CACACATCAAGACGAATTCATTTCTAAGACAACTCTTCTATT
Found at i:132363 original size:36 final size:35
Alignment explanation
Indices: 132304--132444 Score: 194
Period size: 36 Copynumber: 3.9 Consensus size: 35
132294 TGATGAAGAA
* *
132304 GAACGAAAGGAAGCATTGACACTTTCGATTCAAAGT
1 GAACG-AAGGAAGCATCGGCACTTTCGATTCAAAGT
* *
132340 GAACAGAAGAAAGCATCGGCACTTTCGATTC-AAGAA
1 GAAC-GAAGGAAGCATCGGCACTTTCGATTCAAAG-T
132376 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
1 GAACG-AAGGAAGCATCGGCACTTTCGATTCAAAGT
132412 GAACGGAAGGAAGCATCGGCACTTTCGATTCAA
1 GAAC-GAAGGAAGCATCGGCACTTTCGATTCAA
132445 TTATTCATCT
Statistics
Matches: 94, Mismatches: 6, Indels: 10
0.85 0.05 0.09
Matches are distributed among these distances:
35 4 0.04
36 85 0.90
37 5 0.05
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (35 bp):
GAACGAAGGAAGCATCGGCACTTTCGATTCAAAGT
Found at i:132385 original size:72 final size:72
Alignment explanation
Indices: 132299--132444 Score: 256
Period size: 72 Copynumber: 2.0 Consensus size: 72
132289 GAAGGTGATG
*
132299 AAGAAGAACGAAAGGAAGCATTGACACTTTCGATTCAAAGTGAACAGAAGAAAGCATCGGCACTT
1 AAGAAGAACGAAAGGAAGCATCGACACTTTCGATTCAAAGTGAACAGAAGAAAGCATCGGCACTT
132364 TCGATTC
66 TCGATTC
* * *
132371 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTT
1 AAGAAGAACGAAAGGAAGCATCGACACTTTCGATTCAAAGTGAACAGAAGAAAGCATCGGCACTT
132436 TCGATTC
66 TCGATTC
132443 AA
1 AA
132445 TTATTCATCT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (72 bp):
AAGAAGAACGAAAGGAAGCATCGACACTTTCGATTCAAAGTGAACAGAAGAAAGCATCGGCACTT
TCGATTC
Found at i:133774 original size:38 final size:38
Alignment explanation
Indices: 133723--133796 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
133713 ATCTAACTTG
133723 AATAATATACACGAAATTAAGATAACCGTTTAACATTA
1 AATAATATACACGAAATTAAGATAACCGTTTAACATTA
* *
133761 AATAATATACACGAAATTAATATAACCGTTTTACAT
1 AATAATATACACGAAATTAAGATAACCGTTTAACAT
133797 GTAATTCTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.31
Consensus pattern (38 bp):
AATAATATACACGAAATTAAGATAACCGTTTAACATTA
Found at i:133942 original size:38 final size:37
Alignment explanation
Indices: 133900--134003 Score: 127
Period size: 38 Copynumber: 2.7 Consensus size: 37
133890 GTATGTAGTT
133900 TAAAATATTATTTTTTTCATAATATTTTCCATTGAACC
1 TAAAATATTATTTTTTT-ATAATATTTTCCATTGAACC
* * *
133938 TAAAATATTAATTTTCTTATAACATTTTCGATTGAACC
1 TAAAATATT-ATTTTTTTATAATATTTTCCATTGAACC
* * *
133976 TAAAATGTTATCTTCTTTGTAATATTTT
1 TAAAATATTAT-TTTTTTATAATATTTT
134004 AAGTTATAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
37 2 0.04
38 47 0.84
39 7 0.12
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.50
Consensus pattern (37 bp):
TAAAATATTATTTTTTTATAATATTTTCCATTGAACC
Found at i:142936 original size:24 final size:24
Alignment explanation
Indices: 142909--142955 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
142899 TTCCTTTCTT
142909 TAGTTTTTCTTCACATGGAATCAA
1 TAGTTTTTCTTCACATGGAATCAA
*
142933 TAGTTTTTCTTCACTTGGAATCA
1 TAGTTTTTCTTCACATGGAATCA
142956 CTTGTTGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.45
Consensus pattern (24 bp):
TAGTTTTTCTTCACATGGAATCAA
Found at i:148237 original size:23 final size:23
Alignment explanation
Indices: 148204--148271 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
148194 CATCTTATAT
*
148204 GGCACTTCGGTGTATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
148227 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
148250 GGCATTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
148272 AGCTGTGGTA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:148853 original size:27 final size:27
Alignment explanation
Indices: 148820--148884 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
148810 TAGGAATTAT
148820 AGATATGATTTGTTACCATTCCTATAA
1 AGATATGATTTGTTACCATTCCTATAA
*
148847 AGATATGATTTGTTACCATTCCTATAG
1 AGATATGATTTGTTACCATTCCTATAA
148874 AGATATGATTT
1 AGATATGATTT
148885 TGTAAATAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (27 bp):
AGATATGATTTGTTACCATTCCTATAA
Found at i:152828 original size:27 final size:27
Alignment explanation
Indices: 152786--152853 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
152776 GTGTAGGAAT
152786 TATAGAG--ATGATTTGTTACCAATCC
1 TATAGAGATATGATTTGTTACCAATCC
*
152811 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCAATCC
152838 TATAGAGATATGATTT
1 TATAGAGATATGATTT
152854 TGTAAATAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 7 0.17
27 33 0.82
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCAATCC
Found at i:156437 original size:19 final size:18
Alignment explanation
Indices: 156415--156482 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 18
156405 TTGATTTAAA
156415 AAAATAAAATTTAAATATT
1 AAAATAAAATTTAAATA-T
*
156434 AAAATGAAA--TAAA-AT
1 AAAATAAAATTTAAATAT
156449 AATAATAATAATTTAAATACT
1 AA-AATAA-AATTTAAATA-T
*
156470 AAATATATAATTT
1 AAA-ATAAAATTT
156483 TAAAAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
15 3 0.08
16 5 0.13
17 6 0.15
19 12 0.31
20 7 0.18
21 6 0.15
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (18 bp):
AAAATAAAATTTAAATAT
Found at i:157380 original size:25 final size:23
Alignment explanation
Indices: 157352--157417 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
157342 TCATCCTTGT
*
157352 GTATATAATATATTTATATTGTATA
1 GTATATAATATA-TGATATT-TATA
* *
157377 GTATGTATTATATGATATTTATA
1 GTATATAATATATGATATTTATA
* *
157400 TTATATAATACAT-ATATT
1 GTATATAATATATGATATT
157418 ATATTATGAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 5 0.15
23 13 0.38
24 6 0.18
25 10 0.29
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.52
Consensus pattern (23 bp):
GTATATAATATATGATATTTATA
Found at i:157403 original size:16 final size:16
Alignment explanation
Indices: 157382--157421 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
157372 GTATAGTATG
* **
157382 TATTATATGATATTTA
1 TATTATATAATACATA
157398 TATTATATAATACATA
1 TATTATATAATACATA
157414 TATTATAT
1 TATTATAT
157422 TATGATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
TATTATATAATACATA
Found at i:162375 original size:19 final size:20
Alignment explanation
Indices: 162351--162401 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
162341 CGGCCAGGAG
*
162351 CATGTATTTTCATT-AAAGT
1 CATGTATTTTCATTAAAAAT
162370 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
162390 CATGTATTTTCA
1 CATGTATTTTCA
162402 AAGGGATTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:167545 original size:15 final size:15
Alignment explanation
Indices: 167520--167554 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
167510 TGCTTCAACT
167520 TCTTT-CTTTTCTTC
1 TCTTTGCTTTTCTTC
167534 TCTTTGCTTTTCTTC
1 TCTTTGCTTTTCTTC
*
167549 TTTTTG
1 TCTTTG
167555 AATGCCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.00, C:0.23, G:0.06, T:0.71
Consensus pattern (15 bp):
TCTTTGCTTTTCTTC
Found at i:167570 original size:27 final size:27
Alignment explanation
Indices: 167540--167601 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
167530 CTTCTCTTTG
*
167540 CTTTTCTTCTTTTTGAATGC-CAAATTT
1 CTTTTCTTCTTTTGGAATGCTC-AATTT
*
167567 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTC-TTCTTTTGGAATGC-TCAATTT
167595 CTTTTCT
1 CTTTTCT
167602 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 7 0.24
29 5 0.17
ACGTcount: A:0.13, C:0.19, G:0.10, T:0.58
Consensus pattern (27 bp):
CTTTTCTTCTTTTGGAATGCTCAATTT
Found at i:178217 original size:19 final size:20
Alignment explanation
Indices: 178195--178232 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
178185 TTATTTTTAG
*
178195 TTTAAATGA-CTTTTTTTTC
1 TTTAAATCATCTTTTTTTTC
*
178214 TTTACATCATCTTTTTTTT
1 TTTAAATCATCTTTTTTTT
178233 TCACTTTGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.18, C:0.13, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTAAATCATCTTTTTTTTC
Found at i:182360 original size:22 final size:20
Alignment explanation
Indices: 182312--182360 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
182302 TTTTGTTTTT
*
182312 TAATTTTGAAATATCTTTCT
1 TAATTTTGAAATATCTTTCA
*
182332 TATATTTTGAAAATAATTTTTCA
1 TA-ATTTTG-AAAT-ATCTTTCA
182355 TAATTT
1 TAATTT
182361 GAAGCCAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.08
21 6 0.25
22 8 0.33
23 8 0.33
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (20 bp):
TAATTTTGAAATATCTTTCA
Found at i:187551 original size:45 final size:45
Alignment explanation
Indices: 187500--187590 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
187490 AGAAAGTTAA
187500 CTTAAATGCAAGTAACTTAACCATTTTGTGCATTATTAATCGTTT
1 CTTAAATGCAAGTAACTTAACCATTTTGTGCATTATTAATCGTTT
*
187545 CTTAAATGCAAGTCACTTAACCATTTTGTGCATTATTAATCGTTT
1 CTTAAATGCAAGTAACTTAACCATTTTGTGCATTATTAATCGTTT
187590 C
1 C
187591 ATGCTTCCTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.42
Consensus pattern (45 bp):
CTTAAATGCAAGTAACTTAACCATTTTGTGCATTATTAATCGTTT
Found at i:191616 original size:45 final size:44
Alignment explanation
Indices: 191567--191916 Score: 235
Period size: 45 Copynumber: 7.9 Consensus size: 44
191557 CTTCTCCGTG
* * * *
191567 AGAAATTAAAGAAGGACAACACTAAAAAATTGACTCCTCTTTACA
1 AGAAAGTAAAGAATGACATCACTAAAAGATTGACTCCTCTTT-CA
* * * * *
191612 AGAAAGTCAA-AATGACATCATTGAAAGATTGACTCCTCTTCGCG
1 AGAAAGTAAAGAATGACATCACTAAAAGATTGACTCCTCTT-TCA
* *
191656 AGAAAGTCAAGAATGACATTACTAAAAGATTGACTCCTCTTCTCA
1 AGAAAGTAAAGAATGACATCACTAAAAGATTGACTCCTCTT-TCA
* * ** * * *
191701 AGAAAGTAAAAAATAACATCGTTGAAAGATTGA-ACCTC-TTCGTG
1 AGAAAGTAAAGAATGACATCACTAAAAGATTGACTCCTCTTTC--A
* * * * *
191745 AGAAAGTCAAGAATGAAACCACTAACAA-ATTGACTCCTCTTCCCG
1 AGAAAGTAAAGAATGACATCACTAA-AAGATTGACTCCTCTT-TCA
* * * * * *
191790 AGAAAGTCAATAA-GAACATTACTAAAAGATTAACTCCTCTTCGCG
1 AGAAAGTAAAGAATG-ACATCACTAAAAGATTGACTCCTCTT-TCA
* * * * *
191835 AGAAAGTCAAGAATGACATCAATAAAAGTTTGACTCCTCGTTGCG
1 AGAAAGTAAAGAATGACATCACTAAAAGATTGACTCCTC-TTTCA
* * *
191880 AGAAAGTCAAGAATGAGATCAAT-AAAGATTGACTCCT
1 AGAAAGTAAAGAATGACATCACTAAAAGATTGACTCCT
191917 GTTCGTGAGA
Statistics
Matches: 247, Mismatches: 46, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
42 2 0.01
43 1 0.00
44 78 0.32
45 161 0.65
46 4 0.02
47 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.24
Consensus pattern (44 bp):
AGAAAGTAAAGAATGACATCACTAAAAGATTGACTCCTCTTTCA
Found at i:191695 original size:89 final size:89
Alignment explanation
Indices: 191547--191934 Score: 401
Period size: 89 Copynumber: 4.4 Consensus size: 89
191537 GCAATACTGA
* * * * * * *
191547 AAAG-TTGACTCTTCTCCGTGAGAAATTAAAGAAGGACAACACTAAAAAATTGACTCCTCTTTAC
1 AAAGATTGACTCCTCTTCGTGAGAAAGTCAAGAATGACATCACTAAAAGATTGACTCCTCTTT-C
191611 AAGAAAGTCAA-AATGACATCATTG
65 AAGAAAGTCAAGAATGACATCATTG
* *
191635 AAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAATGACATTACTAAAAGATTGACTCCTCTTCTC
1 AAAGATTGACTCCTCTTCGTGAGAAAGTCAAGAATGACATCACTAAAAGATTGACTCCTCTT-TC
* * * *
191700 AAGAAAGTAAAAAATAACATCGTTG
65 AAGAAAGTCAAGAATGACATCATTG
* * * *
191725 AAAGATTGA-ACCTCTTCGTGAGAAAGTCAAGAATGAAACCACTAACAA-ATTGACTCCTCTTCC
1 AAAGATTGACTCCTCTTCGTGAGAAAGTCAAGAATGACATCACTAA-AAGATTGACTCCTCTT-T
* * * * *
191788 CGAGAAAGTCAATAA-GAACATTACTA
64 CAAGAAAGTCAAGAATG-ACATCATTG
* * * * *
191814 AAAGATTAACTCCTCTTCGCGAGAAAGTCAAGAATGACATCAATAAAAGTTTGACTCCTCGTTGC
1 AAAGATTGACTCCTCTTCGTGAGAAAGTCAAGAATGACATCACTAAAAGATTGACTCCTC-TTTC
* * *
191879 GAGAAAGTCAAGAATGAGATCAAT-
65 AAGAAAGTCAAGAATGACATCATTG
*
191903 AAAGATTGACTCCTGTTCGTGAGAAAGTCAAG
1 AAAGATTGACTCCTCTTCGTGAGAAAGTCAAG
191935 TTGAGGTTTT
Statistics
Matches: 250, Mismatches: 41, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
88 4 0.02
89 160 0.64
90 83 0.33
91 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (89 bp):
AAAGATTGACTCCTCTTCGTGAGAAAGTCAAGAATGACATCACTAAAAGATTGACTCCTCTTTCA
AGAAAGTCAAGAATGACATCATTG
Found at i:191777 original size:134 final size:134
Alignment explanation
Indices: 191589--191934 Score: 367
Period size: 134 Copynumber: 2.6 Consensus size: 134
191579 AGGACAACAC
* * * * * * * * *
191589 TAAAAAATTGACTCCTCTTTACAAGAAAGTCAA-AATGACATCATTGAAAGATTGACTCCTCTTC
1 TAAAAGATTGACACCTCGTTGCGAGAAAGTCAAGAATGAAACCAAT-AAAAATTGACTCCTCTTC
* *
191653 GCGAGAAAGTCAAGAATG-ACATTACTAAAAGATTGACTCCTCTTCTCAAGAAAGTAAAAAATAA
65 GCGAGAAAGTCAAGAA-GAACATTACTAAAAGATTAACTCCTCTTCGCAAGAAAGTAAAAAATAA
**
191717 CATCGT
129 CATCAA
* * *
191723 TGAAAGATTGA-ACCTC-TTCGTGAGAAAGTCAAGAATGAAACCACTAACAAATTGACTCCTCTT
1 TAAAAGATTGACACCTCGTT-GCGAGAAAGTCAAGAATGAAACCAATAA-AAATTGACTCCTCTT
* * * * * *
191786 CCCGAGAAAGTCAATAAGAACATTACTAAAAGATTAACTCCTCTTCGCGAGAAAGTCAAGAATGA
64 CGCGAGAAAGTCAAGAAGAACATTACTAAAAGATTAACTCCTCTTCGCAAGAAAGTAAAAAATAA
191851 CATCAA
129 CATCAA
* * * * * *
191857 TAAAAGTTTGACTCCTCGTTGCGAGAAAGTCAAGAATGAGATCAATAAAGATTGACTCCTGTTCG
1 TAAAAGATTGACACCTCGTTGCGAGAAAGTCAAGAATGAAACCAATAAAAATTGACTCCTCTTCG
*
191922 TGAGAAAGTCAAG
66 CGAGAAAGTCAAG
191935 TTGAGGTTTT
Statistics
Matches: 174, Mismatches: 32, Indels: 12
0.80 0.15 0.06
Matches are distributed among these distances:
132 2 0.01
133 17 0.10
134 125 0.72
135 28 0.16
136 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (134 bp):
TAAAAGATTGACACCTCGTTGCGAGAAAGTCAAGAATGAAACCAATAAAAATTGACTCCTCTTCG
CGAGAAAGTCAAGAAGAACATTACTAAAAGATTAACTCCTCTTCGCAAGAAAGTAAAAAATAACA
TCAA
Found at i:192070 original size:74 final size:74
Alignment explanation
Indices: 191961--192105 Score: 200
Period size: 74 Copynumber: 2.0 Consensus size: 74
191951 AACGATTTTG
* * * * *
191961 AGAATGACTAAAATGAATTTCTAGAGAAACGATCCTAAGAAGGACTATAACGAATTTCTAGAGAA
1 AGAATGACTAAAATGAATTTATAGAGAAACAATCCTAAGAAGAACTAAAACGAATTTATAGAGAA
192026 ACAATCTTA
66 ACAATCTTA
* * * *
192035 AGAATGACTAAAATGAATTTATAGTGAAACAATCCTAATAAGAATTAAAATGAATTTATAGAGAA
1 AGAATGACTAAAATGAATTTATAGAGAAACAATCCTAAGAAGAACTAAAACGAATTTATAGAGAA
*
192100 ATAATC
66 ACAATC
192106 CAAAGAAGGA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
74 61 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.26
Consensus pattern (74 bp):
AGAATGACTAAAATGAATTTATAGAGAAACAATCCTAAGAAGAACTAAAACGAATTTATAGAGAA
ACAATCTTA
Found at i:192106 original size:37 final size:36
Alignment explanation
Indices: 191961--192118 Score: 172
Period size: 37 Copynumber: 4.2 Consensus size: 36
191951 AACGATTTTG
* *
191961 AGAATGACTAAAATGAATTTCTAGAGAAACGATCCTA
1 AGAA-GACTAAAATGAATTTATAGAGAAACAATCCTA
* * * *
191998 AGAAGGACTATAACGAATTTCTAGAGAAACAATCTTA
1 AGAA-GACTAAAATGAATTTATAGAGAAACAATCCTA
*
192035 AGAATGACTAAAATGAATTTATAGTGAAACAATCCTA
1 AGAA-GACTAAAATGAATTTATAGAGAAACAATCCTA
* * * *
192072 ATAAGAATTAAAATGAATTTATAGAGAAATAATCCAA
1 AGAAG-ACTAAAATGAATTTATAGAGAAACAATCCTA
192109 AGAAGGACTA
1 AGAA-GACTA
192119 GAGTGAGGTT
Statistics
Matches: 101, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
36 1 0.01
37 99 0.98
38 1 0.01
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (36 bp):
AGAAGACTAAAATGAATTTATAGAGAAACAATCCTA
Found at i:192608 original size:26 final size:25
Alignment explanation
Indices: 192578--192648 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
192568 AAATTCAATG
* *
192578 AAGAAGTTTTGAAAAATGTTTGATAA
1 AAGAA-TTTTGAAAAATATTCGATAA
* *
192604 AAGAATTTTAAAAAATATTCGATGA
1 AAGAATTTTGAAAAATATTCGATAA
*
192629 AATAATTTTTGAAAAATATT
1 AAGAA-TTTTGAAAAATATT
192649 ACCCTTTAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 20 0.53
26 18 0.47
ACGTcount: A:0.49, C:0.01, G:0.13, T:0.37
Consensus pattern (25 bp):
AAGAATTTTGAAAAATATTCGATAA
Found at i:193208 original size:24 final size:22
Alignment explanation
Indices: 193181--193237 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
193171 TCATCATTCA
*
193181 TTTTTCTTTTCTTTTCTGTTTTT
1 TTTTTCTTTTCTTCTCT-TTTTT
193204 GTTTTT-TTTATCTTCTCTTTTTT
1 -TTTTTCTTT-TCTTCTCTTTTTT
193227 TTTCTTCTTTT
1 TTT-TTCTTTT
193238 TACCTCTCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 3 0.10
23 11 0.38
24 15 0.52
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.81
Consensus pattern (22 bp):
TTTTTCTTTTCTTCTCTTTTTT
Found at i:193224 original size:15 final size:14
Alignment explanation
Indices: 193205--193238 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
193195 TCTGTTTTTG
193205 TTTTTTTTATCTTC
1 TTTTTTTTATCTTC
*
193219 TCTTTTTTTTTCTTC
1 T-TTTTTTTATCTTC
193234 TTTTT
1 TTTTT
193239 ACCTCTCGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTTTATCTTC
Found at i:193567 original size:174 final size:174
Alignment explanation
Indices: 193257--193594 Score: 498
Period size: 174 Copynumber: 1.9 Consensus size: 174
193247 TTTATTTCAC
*
193257 TTACCTCAAGGAATTCATCGCTCACAATTAATGTCACGATTTGAATATAACCAATTCATGAAGCT
1 TTACCTCAAGGAATTCATCGCTCACAATTAATGTCACGATTTGAATATAACCAATTCATAAAGCT
* * * * * *
193322 CAGACTTACCTCAATAGCTGCTTGAAATTACCTTCAAGTTATCATCTTAATGCTTTCAAGGGAAC
66 CAAACTTACCTCAATAACTGCTTGAAATTACCTTCAAATTATCAGCTTAATACTTTCAACGGAAC
*
193387 GGCCCCATTTTATTACACTCACCTATCACTATTTCATTAATTTT
131 GGCCCCATTTTATGACACTCACCTATCACTATTTCATTAATTTT
* * * * *
193431 TTACCTCAGGGAATTCATTGCATCACAATTAATGTCACGGTTTGAATATAA-CACTTTATAAAGC
1 TTACCTCAAGGAATTCATCGC-TCACAATTAATGTCACGATTTGAATATAACCAATTCATAAAGC
* * *
193495 TCAAACTTACCTCAATAACTGCTTGAAATTACCTTCAAATTATTAGCTTAATACTTTTAACGGAG
65 TCAAACTTACCTCAATAACTGCTTGAAATTACCTTCAAATTATCAGCTTAATACTTTCAACGGAA
* *
193560 TGGCCCCATTTTATGACACTCATCTATCACTATTT
130 CGGCCCCATTTTATGACACTCACCTATCACTATTT
193595 TTTAACTTTT
Statistics
Matches: 145, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
174 117 0.81
175 28 0.19
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (174 bp):
TTACCTCAAGGAATTCATCGCTCACAATTAATGTCACGATTTGAATATAACCAATTCATAAAGCT
CAAACTTACCTCAATAACTGCTTGAAATTACCTTCAAATTATCAGCTTAATACTTTCAACGGAAC
GGCCCCATTTTATGACACTCACCTATCACTATTTCATTAATTTT
Found at i:200840 original size:24 final size:25
Alignment explanation
Indices: 200808--200854 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
200798 CTATTCTTTC
200808 ACTTCAATCAAGC-TCGAATTTTAG
1 ACTTCAATCAAGCTTCGAATTTTAG
* *
200832 ACTTCAATCGAGCTTCTAATTTT
1 ACTTCAATCAAGCTTCGAATTTT
200855 TTTTTAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (25 bp):
ACTTCAATCAAGCTTCGAATTTTAG
Found at i:203374 original size:20 final size:20
Alignment explanation
Indices: 203349--203394 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
203339 TCACATCTCA
*
203349 ATCCTCCCTGTAAATACTCC
1 ATCCTCCCTATAAATACTCC
203369 ATCCTCCCTATAAATACTCC
1 ATCCTCCCTATAAATACTCC
203389 ATCCTC
1 ATCCTC
203395 AATCACTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.41, G:0.02, T:0.30
Consensus pattern (20 bp):
ATCCTCCCTATAAATACTCC
Found at i:205752 original size:21 final size:21
Alignment explanation
Indices: 205716--205767 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
205706 ACCTGCTCAG
* * *
205716 GATGACGACGACGACGACGAG
1 GATGATGACAACGACGACGAC
*
205737 GGTGATGACAACGACGACGAC
1 GATGATGACAACGACGACGAC
205758 GATGATGACA
1 GATGATGACA
205768 GCGAGGAGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.21, G:0.35, T:0.10
Consensus pattern (21 bp):
GATGATGACAACGACGACGAC
Found at i:210137 original size:42 final size:40
Alignment explanation
Indices: 210041--210156 Score: 135
Period size: 42 Copynumber: 2.9 Consensus size: 40
210031 ATAACCAACG
*
210041 AATTCGCAACTCA-ATTTCGAATTCGCAACACAAAAGCCA
1 AATTCGCAACTCAGTTTTCGAATTCGCAACACAAAAGCCA
* * ** *
210080 AATTCGAAACACAGTTTTCGAATTCGCAACACGAATTTGTCA
1 AATTCGCAACTCAGTTTTCGAATTCGCAACAC-AA-AAGCCA
* *
210122 AATTCGCAACTCAGTTTTCAAATTCGCAACTCAAA
1 AATTCGCAACTCAGTTTTCGAATTCGCAACACAAA
210157 TTCGGATTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
39 11 0.17
40 17 0.27
41 4 0.06
42 31 0.49
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (40 bp):
AATTCGCAACTCAGTTTTCGAATTCGCAACACAAAAGCCA
Found at i:210154 original size:20 final size:20
Alignment explanation
Indices: 210078--210151 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
210068 ACACAAAAGC
*
210078 CAAATTCGAAACACAGTTTT
1 CAAATTCGCAACACAGTTTT
* *
210098 CGAATTCGCAACACGAATTTGT
1 CAAATTCGCAACAC-AGTTT-T
*
210120 CAAATTCGCAACTCAGTTTT
1 CAAATTCGCAACACAGTTTT
210140 CAAATTCGCAAC
1 CAAATTCGCAAC
210152 TCAAATTCGG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 25 0.54
21 8 0.17
22 13 0.28
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAACACAGTTTT
Found at i:210468 original size:19 final size:19
Alignment explanation
Indices: 210444--210494 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
210434 AAACGCGGTA
*
210444 AAATTCGCAACTCATTTTT
1 AAATTCGCAACTCATTTTC
210463 AAATTCGCAACTCATTTTC
1 AAATTCGCAACTCATTTTC
*
210482 AAATTCGCTACTC
1 AAATTCGCAACTC
210495 GAATTCACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.37
Consensus pattern (19 bp):
AAATTCGCAACTCATTTTC
Found at i:210759 original size:321 final size:323
Alignment explanation
Indices: 210121--210769 Score: 1043
Period size: 321 Copynumber: 2.0 Consensus size: 323
210111 CGAATTTGTC
* * * *
210121 AAATTCGCAACTCAGTTTTCAAATTCGCAACTCAAATTCGGATTTTACAACTCGAATTGCCAATT
1 AAATTCGCAACTCAGTTTTCAAATTCGCAACTCAAATTCGAAATTCACAACTCGAATTACCAATT
210186 TCGCAACTCAATTGTACCGCATTTACCTATATAACTAATTATAACCGGTCAAAATAACGATGTTT
66 TCGCAACTCAATTGTACCGCATTTACCTATATAACTAATTATAACCGGTCAAAATAACGATGTTT
** * * *
210251 TCGATTATTTTTTTACTGGTTTTGTTAACAATTCAATTTAAAAATATATACATGATATTATTAAA
131 TAAATCATTTTTTTACAGATTTTGTTAACAATTCAATTTAAAAATATATACATGATATTATTAAA
210316 AAAATATTAAAATTATTATTTTGAAATTTATTTTTCTTTTTTTGTCATTTTGTTACAATATGTAA
196 AAAATATTAAAATTATTATTTTGAAATTTATTTTTCTTTTTTTGTCATTTTGTTACAATATGTAA
* *
210381 CTTAAATTCTGCAACTTACATCAAAGCATTGGTTTATAATTACCTATATAGGTAAACGCGGTA
261 CTTAAATTCTGCAACTTACATCAAAGCATTGATTTATAATTACCTATATAAGTAAACGCGGTA
* ** * *
210444 AAATTCGCAACTCA-TTTTTAAATTCGCAACTCATTTTC-AAATTCGCTACTCGAATTCACCAAT
1 AAATTCGCAACTCAGTTTTCAAATTCGCAACTCAAATTCGAAATTCACAACTCGAATT-ACCAAT
* * * ** * *
210507 TTCGCAACTCAATTTTACTGCGTTTACCTATATAGGTAATTTTAACCGGTCAAAATAATGATGTT
65 TTCGCAACTCAATTGTACCGCATTTACCTATATAACTAATTATAACCGGTCAAAATAACGATGTT
*
210572 TTAAATCATTTTTTTACAGATTTTGTTAATAATTCAATTTAAAAATATATACATGATATTATT-A
130 TTAAATCATTTTTTTACAGATTTTGTTAACAATTCAATTTAAAAATATATACATGATATTATTAA
210636 AAAAATATTAAAATTATTATTTTGAAATTTATTTTTCTTTTTTTGTCATTTTGTTACAATATGTA
195 AAAAATATTAAAATTATTATTTTGAAATTTATTTTTCTTTTTTTGTCATTTTGTTACAATATGTA
*
210701 ACTTAAATTCTGCAACTTGCATCAAAGCATTGATTTATAATTACCTATATAAGTAAACGCGGTA
260 ACTTAAATTCTGCAACTTACATCAAAGCATTGATTTATAATTACCTATATAAGTAAACGCGGTA
210765 AAATT
1 AAATT
210770 GAATTACGAA
Statistics
Matches: 300, Mismatches: 25, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
321 145 0.48
322 141 0.47
323 14 0.05
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.41
Consensus pattern (323 bp):
AAATTCGCAACTCAGTTTTCAAATTCGCAACTCAAATTCGAAATTCACAACTCGAATTACCAATT
TCGCAACTCAATTGTACCGCATTTACCTATATAACTAATTATAACCGGTCAAAATAACGATGTTT
TAAATCATTTTTTTACAGATTTTGTTAACAATTCAATTTAAAAATATATACATGATATTATTAAA
AAAATATTAAAATTATTATTTTGAAATTTATTTTTCTTTTTTTGTCATTTTGTTACAATATGTAA
CTTAAATTCTGCAACTTACATCAAAGCATTGATTTATAATTACCTATATAAGTAAACGCGGTA
Found at i:211401 original size:25 final size:24
Alignment explanation
Indices: 211354--211401 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
211344 ATTTATACAC
* *
211354 TTTTTAATAAAATTTATATATAAT
1 TTTTTAATAAAATTTAAAGATAAT
*
211378 TTTTTTATAAAATTTAAAAGATAA
1 TTTTTAATAAAATTT-AAAGATAA
211402 ATGGGTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTTAATAAAATTTAAAGATAAT
Found at i:218220 original size:17 final size:17
Alignment explanation
Indices: 218186--218237 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
218176 ACCGGACAAA
*
218186 TTTATTATTTTAAAGAG
1 TTTATTAATTTAAAGAG
**
218203 TTTATTAATTTACCGAG
1 TTTATTAATTTAAAGAG
*
218220 --TATTAATTAAAAGAG
1 TTTATTAATTTAAAGAG
218235 TTT
1 TTT
218238 CTACTGTATA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 12 0.44
17 15 0.56
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (17 bp):
TTTATTAATTTAAAGAG
Found at i:218448 original size:32 final size:32
Alignment explanation
Indices: 218407--218486 Score: 151
Period size: 32 Copynumber: 2.5 Consensus size: 32
218397 AATATTTGAA
*
218407 AGACTCTTAAAATTTTCTAAAATTATATCTCT
1 AGACTCTTAAAATTATCTAAAATTATATCTCT
218439 AGACTCTTAAAATTATCTAAAATTATATCTCT
1 AGACTCTTAAAATTATCTAAAATTATATCTCT
218471 AGACTCTTAAAATTAT
1 AGACTCTTAAAATTAT
218487 TAATTTCAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.41
Consensus pattern (32 bp):
AGACTCTTAAAATTATCTAAAATTATATCTCT
Found at i:224060 original size:54 final size:55
Alignment explanation
Indices: 223952--224071 Score: 161
Period size: 56 Copynumber: 2.2 Consensus size: 55
223942 GACTAATATC
* *
223952 AAAATATACCTAAAAAATTCCCTGGGAATCACAAGAATCACACTGTAAACGAACCA
1 AAAATCTACCTAAAAAATTCCCTGAGAATCACAAGAAT-ACACTGTAAACGAACCA
* * * * *
224008 AAAATCTACCTAAAATATTCCCTGAGATTCACAAGCAT-GACTGTAAAGGAACCA
1 AAAATCTACCTAAAAAATTCCCTGAGAATCACAAGAATACACTGTAAACGAACCA
224062 AAAATCTACC
1 AAAATCTACC
224072 CGGATTCTCA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 24 0.42
56 33 0.58
ACGTcount: A:0.46, C:0.23, G:0.11, T:0.20
Consensus pattern (55 bp):
AAAATCTACCTAAAAAATTCCCTGAGAATCACAAGAATACACTGTAAACGAACCA
Found at i:232938 original size:15 final size:15
Alignment explanation
Indices: 232920--232955 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
232910 AAACACGCAC
232920 GCACGCACTACGCGT
1 GCACGCACTACGCGT
232935 GCACGCACTACGCGT
1 GCACGCACTACGCGT
232950 GCACGC
1 GCACGC
232956 GCACACACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.42, G:0.28, T:0.11
Consensus pattern (15 bp):
GCACGCACTACGCGT
Found at i:237991 original size:122 final size:122
Alignment explanation
Indices: 237772--238024 Score: 461
Period size: 122 Copynumber: 2.1 Consensus size: 122
237762 AAATACATGC
237772 ATGAAATTATACATGGATGTTTTATACATCATCAGGAAGACTTGCGATAAGTCGACCTTGTTTTA
1 ATGAAATTATACATGGATGTTTTATACATCATCAGGAAGACTTGCGATAAGTCGACCTTGTTTTA
* *
237837 TCAGCATGATATTATATCATATTTTTATAAACTGACATGACATTGATATGTCAGAGT
66 TCAGCATGATATTATATCATATTTTTAGAAACTAACATGACATTGATATGTCAGAGT
* *
237894 ATGAAATTATACATGGATGTTTTATACATCATCAGGAAGACTTGCGATAAGTTGGCCTTGTTTTA
1 ATGAAATTATACATGGATGTTTTATACATCATCAGGAAGACTTGCGATAAGTCGACCTTGTTTTA
*
237959 TCAGCATGATATTATATCATATTTTTAGAAACTAACATGACATTGATATGTCATAGT
66 TCAGCATGATATTATATCATATTTTTAGAAACTAACATGACATTGATATGTCAGAGT
238016 ATGAAATTA
1 ATGAAATTA
238025 AAATGCATTG
Statistics
Matches: 126, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
122 126 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (122 bp):
ATGAAATTATACATGGATGTTTTATACATCATCAGGAAGACTTGCGATAAGTCGACCTTGTTTTA
TCAGCATGATATTATATCATATTTTTAGAAACTAACATGACATTGATATGTCAGAGT
Found at i:238329 original size:58 final size:59
Alignment explanation
Indices: 238211--238346 Score: 186
Period size: 58 Copynumber: 2.3 Consensus size: 59
238201 CAGTAGGCTG
** *
238211 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACATATGGTGGACACGACCTTATGTGT
* * *
238270 CATATTCGGGACTATACTTAAGGATACCTAGTACA-ATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACATATGGTGGACACGACCTTATGTGT
*
238328 CATACTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
238347 CGGTGCTTAT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
57 2 0.03
58 34 0.52
59 30 0.45
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACATATGGTGGACACGACCTTATGTGT
Found at i:242559 original size:12 final size:12
Alignment explanation
Indices: 242542--242566 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
242532 GGTTGACGAC
242542 ACAGCACCCATA
1 ACAGCACCCATA
242554 ACAGCACCCATA
1 ACAGCACCCATA
242566 A
1 A
242567 TCTTGGGGAG
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:0.44, C:0.40, G:0.08, T:0.08
Consensus pattern (12 bp):
ACAGCACCCATA
Found at i:252311 original size:18 final size:19
Alignment explanation
Indices: 252270--252311 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
252260 TCTGTCCTCC
* *
252270 ATGGTTAAACGAATACTGA
1 ATGGTAAAACGAATAATGA
*
252289 TTGGTAAAAC-AATAATGA
1 ATGGTAAAACGAATAATGA
252307 ATGGT
1 ATGGT
252312 CCTCCTATCA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (19 bp):
ATGGTAAAACGAATAATGA
Found at i:254325 original size:28 final size:28
Alignment explanation
Indices: 254271--254325 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
254261 TTGGCTTGCT
*
254271 TTCTCTTTTTGAATTTCTTTTTCTTTTC
1 TTCTCTTTTTGAATTTCTTTTTATTTTC
* *
254299 TTCT-TTTTTGAGTTTTTTTCTTATTTT
1 TTCTCTTTTTGAATTTCTTT-TTATTTT
254326 GTCTTTTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.07, C:0.13, G:0.05, T:0.75
Consensus pattern (28 bp):
TTCTCTTTTTGAATTTCTTTTTATTTTC
Found at i:257117 original size:26 final size:27
Alignment explanation
Indices: 257079--257129 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
257069 CGTTGCTTTC
257079 AAGTACTGACTCAACAACATAATGTTT
1 AAGTACTGACTCAACAACATAATGTTT
* *
257106 AAGTAC-GACTCAACGATATAATGT
1 AAGTACTGACTCAACAACATAATGT
257130 AAACGGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (27 bp):
AAGTACTGACTCAACAACATAATGTTT
Found at i:257744 original size:11 final size:11
Alignment explanation
Indices: 257728--257761 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
257718 AATATTCAAC
257728 TATTCAAATAG
1 TATTCAAATAG
257739 TATTCAAATAG
1 TATTCAAATAG
257750 TATTCAAATAG
1 TATTCAAATAG
257761 T
1 T
257762 TCTATTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (11 bp):
TATTCAAATAG
Found at i:259102 original size:20 final size:20
Alignment explanation
Indices: 259077--259115 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
259067 AAATCTTACA
259077 TGGGGGTATCGGTACCCTCT
1 TGGGGGTATCGGTACCCTCT
*
259097 TGGGGGTATTGGTACCCTC
1 TGGGGGTATCGGTACCCTC
259116 CGAGCAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.23, G:0.36, T:0.31
Consensus pattern (20 bp):
TGGGGGTATCGGTACCCTCT
Found at i:259115 original size:75 final size:75
Alignment explanation
Indices: 259002--259169 Score: 275
Period size: 75 Copynumber: 2.3 Consensus size: 75
258992 CCATTATGAG
* *
259002 ATGGGGGTAACGGTA-CCTCCTAGGGGTATCGGTACCCTCCGAGCAATCTATTATTTCTCGGAGT
1 ATGGGGGTATCGGTACCCTCCTAGGGGTATCGGTACCCTCCGAGCAATCTATTATTTCTCGGAGC
259066 CAAATCTTAC
66 CAAATCTTAC
* * * *
259076 ATGGGGGTATCGGTACCCTCTTGGGGGTATTGGTACCCTCCGAGCAATCTGTTATTTCTCGGAGC
1 ATGGGGGTATCGGTACCCTCCTAGGGGTATCGGTACCCTCCGAGCAATCTATTATTTCTCGGAGC
259141 CAAATCTTAC
66 CAAATCTTAC
259151 ATGGGGGTATCGGTACCCT
1 ATGGGGGTATCGGTACCCT
259170 TCAAGCAATC
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
74 14 0.16
75 73 0.84
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (75 bp):
ATGGGGGTATCGGTACCCTCCTAGGGGTATCGGTACCCTCCGAGCAATCTATTATTTCTCGGAGC
CAAATCTTAC
Found at i:259655 original size:28 final size:28
Alignment explanation
Indices: 259623--259680 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
259613 AATTCAAAAA
259623 CTTAATATGTTGTATTTTAATAGTTGTG
1 CTTAATATGTTGTATTTTAATAGTTGTG
* *
259651 CTTAATCTTTTGTATTTTAATAGTTGTG
1 CTTAATATGTTGTATTTTAATAGTTGTG
259679 CT
1 CT
259681 AGCTGCTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.22, C:0.07, G:0.16, T:0.55
Consensus pattern (28 bp):
CTTAATATGTTGTATTTTAATAGTTGTG
Found at i:261977 original size:21 final size:20
Alignment explanation
Indices: 261939--261979 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
261929 CTATGAACAG
*
261939 TGGGGGAATCAGTTCCCATA
1 TGGGGGAATCAGTACCCATA
*
261959 TGGGGGAATCGGTAACCCATA
1 TGGGGGAATCAGT-ACCCATA
261980 AGAATTCTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22
Consensus pattern (20 bp):
TGGGGGAATCAGTACCCATA
Found at i:262442 original size:44 final size:44
Alignment explanation
Indices: 262391--262598 Score: 294
Period size: 44 Copynumber: 4.7 Consensus size: 44
262381 TAAGCTCGTA
* * *
262391 ATTTTACCAATATACTTACCATTTGTCGATAAGTTCATAAGCTT
1 ATTTTACCAATATACTTACCATTTATCCATAAGCTCATAAGCTT
* *
262435 ATTTTACCATTATACTTACCATTTATTCATAAGCT-AGTAAGCTT
1 ATTTTACCAATATACTTACCATTTATCCATAAGCTCA-TAAGCTT
*
262479 ATTTTACCAATATACTTACCATTTATCCATAAGCTCGTAAGCTT
1 ATTTTACCAATATACTTACCATTTATCCATAAGCTCATAAGCTT
*
262523 ATTTTACCAATATACTTACCATTTATCCATAAGCTCGTAAGCTT
1 ATTTTACCAATATACTTACCATTTATCCATAAGCTCATAAGCTT
* * *
262567 ATTTTTCCAATACACTTGCCA-TTATTCCATAA
1 ATTTTACCAATATACTTACCATTTA-TCCATAA
262599 CCATATACCA
Statistics
Matches: 150, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
43 4 0.03
44 146 0.97
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (44 bp):
ATTTTACCAATATACTTACCATTTATCCATAAGCTCATAAGCTT
Found at i:262526 original size:24 final size:24
Alignment explanation
Indices: 262499--262575 Score: 60
Period size: 24 Copynumber: 3.4 Consensus size: 24
262489 TATACTTACC
262499 ATTTATCCATAAGCTCGTAAGCTT
1 ATTTATCCATAAGCTCGTAAGCTT
*
262523 ATTT-TACCAATATA-CT--T-A-C-C
1 ATTTAT-CC-ATA-AGCTCGTAAGCTT
262543 ATTTATCCATAAGCTCGTAAGCTT
1 ATTTATCCATAAGCTCGTAAGCTT
*
262567 ATTTTTCCA
1 ATTTATCCA
262576 ATACACTTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 20
0.63 0.05 0.32
Matches are distributed among these distances:
18 1 0.03
19 5 0.12
20 6 0.15
21 3 0.08
22 2 0.05
23 3 0.08
24 14 0.35
25 5 0.12
26 1 0.03
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (24 bp):
ATTTATCCATAAGCTCGTAAGCTT
Found at i:265652 original size:765 final size:764
Alignment explanation
Indices: 264183--265714 Score: 2760
Period size: 765 Copynumber: 2.0 Consensus size: 764
264173 GAACCCTAGT
* *
264183 AATATTCATGTGAAAATGTAGAGAATTGAAAGTAGAATATTTATCCTAACTACACTGAGTCTAAT
1 AATATTCATGTCAAAATGTAGAGAATTGAAAGTAGAATATTTATCCTAACTACACCGAGTCTAAT
*
264248 TCTCAAGAAATAGCTTCAAAATTGAAACTAAAAATGTTTACCTTTCTTTCTTGAAAATGTCGGCC
66 TCTCAAGAAATAGCTTCAAAATTGAAACTAAAAATGTTTACCTTTCTTGCTTGAAAATGTCGGCC
*
264313 CTTGGAGGAAGAAGAACTGGAAATGATCTTCCATGATTGATATTTAATGATAAATAAATCTATCA
131 CTTGGAGGAAGAAGAACTGGAAATGATCGTCCATGATTGATATTTAATGATAAATAAATCTATCA
* *
264378 CATGGCAATATATATTATGATGGCATTTTTTTATTCAATCCAATAGGAATTTCCATTTTTTCCAT
196 CATGGCAATATATATTATGATGACATTTTTTTATTCAATCCAATAGGAATTTCCATTTTTGCCAT
264443 TAATGAATTTCCATATTCACCATAAAACCAAGCCATCTGATCATTATCAATTTACAAAGTCAAAT
261 TAATGAATTTCCATATTCACCATAAAACCAAGCCATCTGATCATTATCAATTTACAAAGTCAAAT
* *
264508 ATGAATTAATTTGACTTTCATTACCAAATTTCCCCTTGAATTTCCAAAAAATTGCGTTTTAGTCA
326 ATAAATTAATTTGACTTTCATTACCAAATATCCCCTTGAATTTCCAAAAAATTGCGTTTTAGTCA
* *
264573 CTAAATTCCGCAGTTTCGATTAAATCTGAAAAATTGCACAATTCAAAACCAAATTTCTCTGATCT
391 CTAAATTCCACAATTTCGATTAAATCTGAAAAATTGCACAATTCAAAACCAAATTTCTCTGATCT
* *
264638 AAATTATTAAAATAATATTTCCAAACATTTTATAACATCCTTCAAATTTTTGTAACATTCCAATT
456 AAATTATTAAAATAATATTTCCAAACATTTAATAACATCCTTCAAATTTTTATAACATTCCAATT
* *
264703 AGATCCGAATTTCTGATTCCTTATCGGCTTTAACCCTTTCTAATTTTTCTTCACTAAAATTCTAA
521 AGATCCGAATTTCCGATTCCTTATCGGCTTTAACCCTTTCTAATTTTTCTTCACTAAAATTCCAA
264768 ATCCAAATATATGATCTCTATAAAACCCCACTCTCAAGAGTAAACCATCTATTTATGGAATAAAA
586 ATCCAAATATATGATCTCTATAAAACCCCACTCTCAAGAGTAAACCATCTATTTATGGAATAAAA
264833 TTCTTTTTAGGAAATTATCACTTAATTCCCTAAACGTTTTCCCAATTTTCTACTTTGACCATCAA
651 TTCTTTTTAGGAAATTATCACTTAATTCCCTAAACGTTTTCCCAATTTTCTACTTTGACCATCAA
264898 ACTTTCAAAATTTTCATTTTGGTAATTGTCTAAATTTTTGGGGTATTAC
716 ACTTTCAAAATTTTCATTTTGGTAATTGTCTAAATTTTTGGGGTATTAC
*
264947 AATATTCATGTCAAAATGTAGAGAATTGAAAGTAGAATATTTTTCCTAACTACACCGAGTCTAAT
1 AATATTCATGTCAAAATGTAGAGAATTGAAAGTAGAATATTTATCCTAACTACACCGAGTCTAAT
* *
265012 TCTGAAGAAATAGCTTCAAAATTGAAACTAAAAATGTTTACCTTTCTTGCTTGAAAGTGTCGGCC
66 TCTCAAGAAATAGCTTCAAAATTGAAACTAAAAATGTTTACCTTTCTTGCTTGAAAATGTCGGCC
* *
265077 CTTGGAGGAAGAAGAAGCTTGAAAT-ACTCGTCCTTGATTGATATTTAATGATAAATAAATCTAT
131 CTTGGAGGAAGAAGAA-CTGGAAATGA-TCGTCCATGATTGATATTTAATGATAAATAAATCTAT
265141 CACATGGCAATATATATTATGATGACATTTTTTTATTCAATCCAATAGGAATTTCCATTTTTGCC
194 CACATGGCAATATATATTATGATGACATTTTTTTATTCAATCCAATAGGAATTTCCATTTTTGCC
265206 ATTAATGAATTTCCATATTCACCATAAAACCAAGCCATCTGATCATTATCAATTTACAAAGTCAA
259 ATTAATGAATTTCCATATTCACCATAAAACCAAGCCATCTGATCATTATCAATTTACAAAGTCAA
* *
265271 ATATAAATTAATTTGACTTTCATTTCCGAATATCCCCTTGAATTTCCAAAAAATTGCGTTTTAGT
324 ATATAAATTAATTTGACTTTCATTACCAAATATCCCCTTGAATTTCCAAAAAATTGCGTTTTAGT
* *
265336 CACTAAATTCCACAATTTCGATTAAATCTGAAAAATTGCACAATTCCAAGCCAAATTTCTCTGAT
389 CACTAAATTCCACAATTTCGATTAAATCTGAAAAATTGCACAATTCAAAACCAAATTTCTCTGAT
* *
265401 CTAAATTATTAAAATAATATTTCCAAACATTTAATAACATCTTTCAAATTTTTATAACTTTCCAA
454 CTAAATTATTAAAATAATATTTCCAAACATTTAATAACATCCTTCAAATTTTTATAACATTCCAA
* *
265466 TTCGATCCGAATTTCCGATTCCTTATCGGCTTTAACCCTTTCTAATTTTTCTTTACTAAAATTCC
519 TTAGATCCGAATTTCCGATTCCTTATCGGCTTTAACCCTTTCTAATTTTTCTTCACTAAAATTCC
265531 AAATCCAAATATATGATCTCTATAAAACCCCACTCTCAAGAGTAAACCATCTATTTATGGAATAA
584 AAATCCAAATATATGATCTCTATAAAACCCCACTCTCAAGAGTAAACCATCTATTTATGGAATAA
* * *
265596 AATTCTTTTTAGGAAATTATCACTTAATTCCCTAAACTTTTTCCTAATTTTCTACTTTGATCATC
649 AATTCTTTTTAGGAAATTATCACTTAATTCCCTAAACGTTTTCCCAATTTTCTACTTTGACCATC
*
265661 AAACTTTCAAAATTTTCATTTTGGTCATTGTCTAAATTTTTGGGGTATTAC
714 AAACTTTCAAAATTTTCATTTTGGTAATTGTCTAAATTTTTGGGGTATTAC
265712 AAT
1 AAT
265715 TCTCCTCTCC
Statistics
Matches: 735, Mismatches: 31, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
764 141 0.19
765 594 0.81
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (764 bp):
AATATTCATGTCAAAATGTAGAGAATTGAAAGTAGAATATTTATCCTAACTACACCGAGTCTAAT
TCTCAAGAAATAGCTTCAAAATTGAAACTAAAAATGTTTACCTTTCTTGCTTGAAAATGTCGGCC
CTTGGAGGAAGAAGAACTGGAAATGATCGTCCATGATTGATATTTAATGATAAATAAATCTATCA
CATGGCAATATATATTATGATGACATTTTTTTATTCAATCCAATAGGAATTTCCATTTTTGCCAT
TAATGAATTTCCATATTCACCATAAAACCAAGCCATCTGATCATTATCAATTTACAAAGTCAAAT
ATAAATTAATTTGACTTTCATTACCAAATATCCCCTTGAATTTCCAAAAAATTGCGTTTTAGTCA
CTAAATTCCACAATTTCGATTAAATCTGAAAAATTGCACAATTCAAAACCAAATTTCTCTGATCT
AAATTATTAAAATAATATTTCCAAACATTTAATAACATCCTTCAAATTTTTATAACATTCCAATT
AGATCCGAATTTCCGATTCCTTATCGGCTTTAACCCTTTCTAATTTTTCTTCACTAAAATTCCAA
ATCCAAATATATGATCTCTATAAAACCCCACTCTCAAGAGTAAACCATCTATTTATGGAATAAAA
TTCTTTTTAGGAAATTATCACTTAATTCCCTAAACGTTTTCCCAATTTTCTACTTTGACCATCAA
ACTTTCAAAATTTTCATTTTGGTAATTGTCTAAATTTTTGGGGTATTAC
Found at i:268168 original size:21 final size:20
Alignment explanation
Indices: 268130--268168 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
268120 ACAATAACAG
* *
268130 TGGGGGAATCGGTTCCCAAA
1 TGGGGGAATCGATCCCCAAA
268150 TGGGGGAATCGATACCCCA
1 TGGGGGAATCGAT-CCCCA
268169 TAAGAAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.26, C:0.23, G:0.33, T:0.18
Consensus pattern (20 bp):
TGGGGGAATCGATCCCCAAA
Found at i:268648 original size:87 final size:88
Alignment explanation
Indices: 268532--268769 Score: 345
Period size: 87 Copynumber: 2.7 Consensus size: 88
268522 TTTGCAATAT
*
268532 TTACCATTTAATACCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATCCATAAGC
1 TTACCATTT-AT-CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATCCATAAGC
* * *
268597 TCGTATGCTTATTTTACCATTATAC
64 TCATAAGCTTATTTTACCAATATAC
268622 TTACCA-TTATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATCCATAAGCTC
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATCCATAAGCTC
* *
268686 ATAAGCTTATTTTACGAATATAT
66 ATAAGCTTATTTTACCAATATAC
* * * *
268709 TTTCCATTTATCCATAAGCTCGTAAGCTTATTTTTCCAATACACTTGCCA-TTATTCCATAA
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTA-TCCATAA
268770 CCATATACCA
Statistics
Matches: 136, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
87 79 0.58
88 49 0.36
89 2 0.01
90 6 0.04
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (88 bp):
TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATCCATAAGCTC
ATAAGCTTATTTTACCAATATAC
Found at i:268760 original size:44 final size:44
Alignment explanation
Indices: 268532--268769 Score: 345
Period size: 44 Copynumber: 5.4 Consensus size: 44
268522 TTTGCAATAT
*
268532 TTACCATTTAATACCATAAGCTCATAAGCTTATTTTACCAATATAC
1 TTACCATTT-AT-CCATAAGCTCGTAAGCTTATTTTACCAATATAC
* *
268578 TTACCATTTATCCATAAGCTCGTATGCTTATTTTACCATTATAC
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATATAC
268622 TTACCA-TTATCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATATAC
* * *
268665 TTACCATTTATCCATAAGCTCATAAGCTTATTTTACGAATATAT
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATATAC
* * *
268709 TTTCCATTTATCCATAAGCTCGTAAGCTTATTTTTCCAATACAC
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
268753 TTGCCA-TTATTCCATAA
1 TTACCATTTA-TCCATAA
268770 CCATATACCA
Statistics
Matches: 175, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
43 44 0.25
44 120 0.69
45 2 0.01
46 9 0.05
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (44 bp):
TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:275337 original size:16 final size:16
Alignment explanation
Indices: 275316--275349 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
275306 AAAACGATAG
*
275316 CATTGAAAATCATTTT
1 CATTGAAAATAATTTT
275332 CATTGAAAATAATTTT
1 CATTGAAAATAATTTT
275348 CA
1 CA
275350 CTAAAATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (16 bp):
CATTGAAAATAATTTT
Found at i:275357 original size:15 final size:16
Alignment explanation
Indices: 275319--275357 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
275309 ACGATAGCAT
* *
275319 TGAAAATCATTTTCAT
1 TGAAAATAATTTTCAC
275335 TGAAAATAATTTTCAC
1 TGAAAATAATTTTCAC
275351 T-AAAATA
1 TGAAAATA
275358 CTAGATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.38
Consensus pattern (16 bp):
TGAAAATAATTTTCAC
Found at i:281185 original size:22 final size:21
Alignment explanation
Indices: 281149--281189 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
281139 CATCTATATT
281149 TCATCATCAACACCATCAACA
1 TCATCATCAACACCATCAACA
*
281170 TCATCCATCAAGACCATCAA
1 TCAT-CATCAACACCATCAA
281190 TTCCGCAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.37, G:0.02, T:0.20
Consensus pattern (21 bp):
TCATCATCAACACCATCAACA
Found at i:284644 original size:20 final size:20
Alignment explanation
Indices: 284605--284675 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
284595 CTACCAAGAG
*
284605 CATGTATCTTCATT-AAAAT
1 CATGTATTTTCATTAAAAAT
284624 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
284644 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
284664 CATGTATTTTCA
1 CATGTATTTTCA
284676 AAGGGGTTTC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 13 0.26
20 37 0.74
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:289319 original size:70 final size:70
Alignment explanation
Indices: 289148--289308 Score: 259
Period size: 70 Copynumber: 2.3 Consensus size: 70
289138 GGATGTGAGC
** ** *
289148 TTCTAATGCACATAAATTCTGAACCTCACCCTGACCTCTTAAGGATCCAAAATAGACTGAGGTTT
1 TTCTAATGCATGTAAATTCTGAACCTCACCCTGACCTCTTAAGGATCCAAAATAGACCAAGGGTT
289213 ATAAG
66 ATAAG
* *
289218 TTCTGATGCATGTAAATTCTGAACCTCACCCTGACCTCTTGAGGATCCAAAATAGACCAAGGGTT
1 TTCTAATGCATGTAAATTCTGAACCTCACCCTGACCTCTTAAGGATCCAAAATAGACCAAGGGTT
289283 ATAAG
66 ATAAG
289288 TTCTAATGCATGTAAATTCTG
1 TTCTAATGCATGTAAATTCTG
289309 GTTCTTACCC
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 83 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (70 bp):
TTCTAATGCATGTAAATTCTGAACCTCACCCTGACCTCTTAAGGATCCAAAATAGACCAAGGGTT
ATAAG
Found at i:291174 original size:14 final size:14
Alignment explanation
Indices: 291155--291197 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
291145 GTTTTCTTTT
291155 TTCATT-TCCATTTC
1 TTCATTCTCCA-TTC
*
291169 TTCATTCTTCATTC
1 TTCATTCTCCATTC
*
291183 TTCATTCTTCATTC
1 TTCATTCTCCATTC
291197 T
1 T
291198 CAAGCTTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 24 0.89
15 3 0.11
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (14 bp):
TTCATTCTCCATTC
Found at i:291176 original size:7 final size:7
Alignment explanation
Indices: 291166--291197 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
291156 TCATTTCCAT
291166 TTCTTCA
1 TTCTTCA
291173 TTCTTCA
1 TTCTTCA
291180 TTCTTCA
1 TTCTTCA
291187 TTCTTCA
1 TTCTTCA
291194 TTCT
1 TTCT
291198 CAAGCTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.59
Consensus pattern (7 bp):
TTCTTCA
Found at i:291181 original size:21 final size:21
Alignment explanation
Indices: 291155--291197 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
291145 GTTTTCTTTT
291155 TTCATT-TCCATTTCTTCATTC
1 TTCATTCTCCA-TTCTTCATTC
*
291176 TTCATTCTTCATTCTTCATTC
1 TTCATTCTCCATTCTTCATTC
291197 T
1 T
291198 CAAGCTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (21 bp):
TTCATTCTCCATTCTTCATTC
Found at i:292694 original size:2 final size:2
Alignment explanation
Indices: 292687--292715 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
292677 AAAATAATTA
292687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
292716 ATTTATAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:292734 original size:22 final size:22
Alignment explanation
Indices: 292709--292751 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
292699 ATATATATAT
292709 ATATATAATTTA-TAAAAATAAG
1 ATAT-TAATTTATTAAAAATAAG
*
292731 ATATTTATTTATTTAAAAATA
1 ATATTAATTTA-TTAAAAATA
292752 TCAAAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 4 0.22
23 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATTAATTTATTAAAAATAAG
Done.