Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001579.1 Hibiscus syriacus cultivar Beakdansim tig00003144_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: 248634
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
File 1 of 2
Found at i:5473 original size:2 final size:2
Alignment explanation
Indices: 5466--5500 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5456 TGGAAGAACA
* *
5466 AG AG AG AG AG AG AG AG AG AG AG AG GG GG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5501 ACGGGAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6283 original size:14 final size:14
Alignment explanation
Indices: 6264--6297 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
6254 ATAGAATATT
*
6264 AATAATGAGAGATA
1 AATAATGAGAGACA
6278 AATAATGAGAGACA
1 AATAATGAGAGACA
6292 AATAAT
1 AATAAT
6298 ATAAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.18, T:0.21
Consensus pattern (14 bp):
AATAATGAGAGACA
Found at i:7915 original size:17 final size:18
Alignment explanation
Indices: 7893--7929 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
7883 TTTATAGATT
7893 AATTTAAAA-TAAAAGTA
1 AATTTAAAATTAAAAGTA
*
7910 AATTTAAAATTAAAATTA
1 AATTTAAAATTAAAAGTA
7928 AA
1 AA
7930 AATTTAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
AATTTAAAATTAAAAGTA
Found at i:13441 original size:22 final size:23
Alignment explanation
Indices: 13413--13460 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
13403 TCACTTTAAA
*
13413 TTATTTAATTAAT-TATTTTCTT
1 TTATTTAATTAATATATTTTATT
*
13435 TTATTTAATTATTATATTTTATT
1 TTATTTAATTAATATATTTTATT
13458 TTA
1 TTA
13461 AAAACACCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
TTATTTAATTAATATATTTTATT
Found at i:13442 original size:18 final size:18
Alignment explanation
Indices: 13416--13458 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
13406 CTTTAAATTA
* * *
13416 TTTAATTAATTATTTTCT
1 TTTATTTAATTATTATAT
13434 TTTATTTAATTATTATAT
1 TTTATTTAATTATTATAT
13452 TTTATTT
1 TTTATTT
13459 TAAAAACACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTATTATAT
Found at i:15489 original size:33 final size:34
Alignment explanation
Indices: 15430--15496 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
15420 CAAGGTATGC
15430 TAGATTTCTTAAAGACTTTTGTACTACAAAAAGA
1 TAGATTTCTTAAAGACTTTTGTACTACAAAAAGA
15464 TAGATTTCTTAAAGAC-TTTGTACTACAAAAAGA
1 TAGATTTCTTAAAGACTTTTGTACTACAAAAAGA
15497 AAGCTTACCG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 17 0.52
34 16 0.48
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (34 bp):
TAGATTTCTTAAAGACTTTTGTACTACAAAAAGA
Found at i:16555 original size:15 final size:15
Alignment explanation
Indices: 16535--16578 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
16525 TTTAGCATAC
16535 TTTATTTCATTTTAA
1 TTTATTTCATTTTAA
* *
16550 TTTATTTCATTCTAT
1 TTTATTTCATTTTAA
*
16565 TTTATTTTATTTTA
1 TTTATTTCATTTTA
16579 TCAGATGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTTCATTTTAA
Found at i:16598 original size:5 final size:5
Alignment explanation
Indices: 16535--16579 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
16525 TTTAGCATAC
* * * *
16535 TTTAT TTCAT TTTAA TTTAT TTCAT TCTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
16580 CAGATGCTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (5 bp):
TTTAT
Found at i:19585 original size:8 final size:8
Alignment explanation
Indices: 19572--19602 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
19562 TATATATTCC
19572 TTATTTTA
1 TTATTTTA
19580 TTATTTTA
1 TTATTTTA
19588 TTATTTTA
1 TTATTTTA
19596 TTATTTT
1 TTATTTT
19603 TCATTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTATTTTA
Found at i:19613 original size:16 final size:16
Alignment explanation
Indices: 19574--19609 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
19564 TATATTCCTT
*
19574 ATTTTATTATTTTATT
1 ATTTTATTATTTTATC
19590 ATTTTATTATTTT-TC
1 ATTTTATTATTTTATC
19605 ATTTT
1 ATTTT
19610 TATTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTATTATTTTATC
Found at i:24432 original size:24 final size:24
Alignment explanation
Indices: 24401--24446 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
24391 AGGTTTCACC
24401 ATTATATCTCTCTATCTTTCCACT
1 ATTATATCTCTCTATCTTTCCACT
*
24425 ATTATATCTCTTTATCTTTCCA
1 ATTATATCTCTCTATCTTTCCA
24447 TCATTCCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.22, C:0.26, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTATATCTCTCTATCTTTCCACT
Found at i:25992 original size:22 final size:22
Alignment explanation
Indices: 25967--26009 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
25957 ACATTAAACT
*
25967 ATAAATTGACCTATTTATAATA
1 ATAAATTAACCTATTTATAATA
* *
25989 ATAAATTAATCTATTTCTAAT
1 ATAAATTAACCTATTTATAAT
26010 CTTATTAATA
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:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (22 bp):
ATAAATTAACCTATTTATAATA
Found at i:27514 original size:2 final size:2
Alignment explanation
Indices: 27507--27532 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27497 GGCTTATCGG
27507 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
27533 TTAATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27980 original size:16 final size:15
Alignment explanation
Indices: 27959--28001 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
27949 ATTACTTATC
*
27959 ATTTTTTTAAATAATT
1 ATTTTTTTAAATAA-A
27975 ATTTTTTT-AATAAA
1 ATTTTTTTAAATAAA
27989 ATTTTTATTAAAT
1 ATTTTT-TTAAAT
28002 CCTGAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 6 0.25
15 7 0.29
16 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTTTTAAATAAA
Found at i:28543 original size:23 final size:23
Alignment explanation
Indices: 28515--28566 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
28505 TGTATTCAAC
28515 ACAAAAAGATTAATTAAATAATA
1 ACAAAAAGATTAATTAAATAATA
*
28538 ATAAAAAGATTAATTAAATAATA
1 ACAAAAAGATTAATTAAATAATA
28561 ACAAAA
1 ACAAAA
28567 TCAAGAGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (23 bp):
ACAAAAAGATTAATTAAATAATA
Found at i:30363 original size:25 final size:25
Alignment explanation
Indices: 30311--30367 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
30301 AAATTTTATG
*
30311 TTAGATGATATGAACTAATAAAATT
1 TTAGAGGATATGAACTAATAAAATT
*
30336 TTAGAGGATGATGAACTTATAAAA-T
1 TTAGAGGAT-ATGAACTAATAAAATT
30361 TTAGAGG
1 TTAGAGG
30368 GCAAAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 16 0.55
26 13 0.45
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (25 bp):
TTAGAGGATATGAACTAATAAAATT
Found at i:31607 original size:31 final size:31
Alignment explanation
Indices: 31572--31662 Score: 173
Period size: 31 Copynumber: 2.9 Consensus size: 31
31562 ACGAATGTGT
31572 GTTGATAGTTTGGTTGGAAAGTGTGTTATGC
1 GTTGATAGTTTGGTTGGAAAGTGTGTTATGC
*
31603 GTTGATGGTTTGGTTGGAAAGTGTGTTATGC
1 GTTGATAGTTTGGTTGGAAAGTGTGTTATGC
31634 GTTGATAGTTTGGTTGGAAAGTGTGTTAT
1 GTTGATAGTTTGGTTGGAAAGTGTGTTAT
31663 TGGATAACAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.19, C:0.02, G:0.36, T:0.43
Consensus pattern (31 bp):
GTTGATAGTTTGGTTGGAAAGTGTGTTATGC
Found at i:33939 original size:14 final size:14
Alignment explanation
Indices: 33920--33952 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
33910 CCCCTTCAGA
33920 CCGATGCGGGTAAC
1 CCGATGCGGGTAAC
33934 CCGATGCGGGTAAC
1 CCGATGCGGGTAAC
33948 CCGAT
1 CCGAT
33953 CCGATCTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.15
Consensus pattern (14 bp):
CCGATGCGGGTAAC
Found at i:34700 original size:24 final size:23
Alignment explanation
Indices: 34642--34705 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
34632 AAACGGAGAT
* * *
34642 ATCATAAATCAAAATAGAATTCAG
1 ATCA-AAATCATAACAGAATCCAG
34666 ATCAAATATCATAACAGAATCCAG
1 ATCAAA-ATCATAACAGAATCCAG
34690 ATCAGAAATCATAACA
1 ATCA-AAATCATAACA
34706 AAATTAAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 2 0.06
24 31 0.89
25 2 0.06
ACGTcount: A:0.53, C:0.17, G:0.08, T:0.22
Consensus pattern (23 bp):
ATCAAAATCATAACAGAATCCAG
Found at i:40255 original size:23 final size:23
Alignment explanation
Indices: 40214--40274 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
40204 CTAATATAAA
*
40214 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
* *
40237 TGCACCGTAGTTCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
40260 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
40275 TATAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:41980 original size:21 final size:21
Alignment explanation
Indices: 41954--41997 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
41944 TTTTTATTCG
* *
41954 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
41975 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
41996 CT
1 CT
41998 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:45069 original size:23 final size:23
Alignment explanation
Indices: 45035--45095 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
45025 CTCATATAAA
* *
45035 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
45058 TGCACCGTAGTGCCGCATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
45081 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
45096 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:48066 original size:23 final size:24
Alignment explanation
Indices: 48040--48092 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
48030 AAACAAAATA
*
48040 TTCTTATACACATA-TCATA-TCTT
1 TTCTTATA-ACATACACATACTCTT
*
48063 TTCTT-TAATATACACATACTCTT
1 TTCTTATAACATACACATACTCTT
48086 TTCTTAT
1 TTCTTAT
48093 CATTTATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 4 0.16
22 6 0.24
23 14 0.56
24 1 0.04
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.51
Consensus pattern (24 bp):
TTCTTATAACATACACATACTCTT
Found at i:50189 original size:23 final size:23
Alignment explanation
Indices: 50155--50215 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
50145 CTCATATAAA
* *
50155 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
50178 TGCACCGTAGTGCCGCATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
50201 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
50216 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:53153 original size:23 final size:24
Alignment explanation
Indices: 53126--53178 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
53116 AAACAAAATC
*
53126 TTCTTATACACATA-TCATA-TCTT
1 TTCTTATA-ACATACACATACTCTT
*
53149 TTCTT-TAATATACACATACTCTT
1 TTCTTATAACATACACATACTCTT
53172 TTCTTAT
1 TTCTTAT
53179 CATTTATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 4 0.16
22 6 0.24
23 14 0.56
24 1 0.04
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.51
Consensus pattern (24 bp):
TTCTTATAACATACACATACTCTT
Found at i:55274 original size:23 final size:23
Alignment explanation
Indices: 55240--55300 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
55230 CTCATATAAA
* *
55240 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
55263 TGCACCGTAGTGCCGCATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
55286 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
55301 TATAATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:60552 original size:2 final size:2
Alignment explanation
Indices: 60545--60585 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
60535 CATACAAATA
60545 AT AT AT AT AT AT AT AT AT AT AT AT -T 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
60586 GATCTAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:62315 original size:189 final size:189
Alignment explanation
Indices: 61986--62375 Score: 663
Period size: 189 Copynumber: 2.1 Consensus size: 189
61976 CAGATTCCCA
* *
61986 GGCAGAATGTATTGGGGCTGATATGCATGTTGTTATTTGTCAGAGCATGGGCAATACTAATGCTT
1 GGCA-AAT-TATTGGGGCTGATACGCATGATGTTATTTGTCAGAGCATGGGCAATACTAATGCTT
* *
62051 TGGAGAAAGCTATTTTGGTGCACATGGGTCATTTAGTGGATTGTTCTGCTGGTTGCGATGGTAAT
64 TGGAGAAAGCTAGTTTGGCGCACATGGGTCATTTAGTGGATTGTTCTGCTGGTTGCGATGGTAAT
* * *
62116 TCGTTAGTGGATTGCAATGTTTTGGATGAATTAAATATGGTGTACGTGGGTCCTACGGATG
129 CCGTTAGTGGATTGCAATATTATGGATGAATTAAATATGGTGTACGTGGGTCCTACGGATG
62177 GGCAAATTATTGGGGCTGATACGCATGATGTTATTTGTCAGAGCATGGGCAATACTAATGCTTTG
1 GGCAAATTATTGGGGCTGATACGCATGATGTTATTTGTCAGAGCATGGGCAATACTAATGCTTTG
62242 GAGAAAGCTAGTTTGGCGCACATGGGTCATTTAGTGGATTGTTCTGCTGGTTGCGATGGTAATCC
66 GAGAAAGCTAGTTTGGCGCACATGGGTCATTTAGTGGATTGTTCTGCTGGTTGCGATGGTAATCC
* * *
62307 GTTAGTGGATTGCAATATTATGGATGATTTAAATATGGTTTACGTGGGTCCTATGGATG
131 GTTAGTGGATTGCAATATTATGGATGAATTAAATATGGTGTACGTGGGTCCTACGGATG
*
62366 GGCTAATTAT
1 GGCAAATTAT
62376 GGCACATGCT
Statistics
Matches: 188, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
189 181 0.96
190 3 0.02
191 4 0.02
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (189 bp):
GGCAAATTATTGGGGCTGATACGCATGATGTTATTTGTCAGAGCATGGGCAATACTAATGCTTTG
GAGAAAGCTAGTTTGGCGCACATGGGTCATTTAGTGGATTGTTCTGCTGGTTGCGATGGTAATCC
GTTAGTGGATTGCAATATTATGGATGAATTAAATATGGTGTACGTGGGTCCTACGGATG
Found at i:63618 original size:2 final size:2
Alignment explanation
Indices: 63611--63636 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63601 AGTGAATCCC
63611 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
63637 CTTGAGATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65253 original size:19 final size:20
Alignment explanation
Indices: 65211--65253 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
65201 ATAGAAGAAA
*
65211 GATTGACAAGAGGATAATTT
1 GATTGACAAGAGGATAAATT
65231 GATTGACAA-A-GATCAAATT
1 GATTGACAAGAGGAT-AAATT
65250 GATT
1 GATT
65254 CATAAACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 9 0.43
20 9 0.43
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (20 bp):
GATTGACAAGAGGATAAATT
Found at i:65722 original size:26 final size:25
Alignment explanation
Indices: 65693--65743 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
65683 AACTTAATTT
*
65693 TTATTAAAGTAGTTTTTTTTTAATAA
1 TTATTAAAGTAG-ATTTTTTTAATAA
* *
65719 TTATTTAGGTAGATTTTTTTAATAA
1 TTATTAAAGTAGATTTTTTTAATAA
65744 ATCTGAAGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (25 bp):
TTATTAAAGTAGATTTTTTTAATAA
Found at i:68799 original size:32 final size:32
Alignment explanation
Indices: 68758--68819 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
68748 AAGTATCTAA
*
68758 AAATAGCAAGTA-CCTAAGAATGACAAGTAGAC
1 AAATAGCAAGCATCC-AAGAATGACAAGTAGAC
* *
68790 AAATGGCAAGCATCCAAGAATGACATGTAG
1 AAATAGCAAGCATCCAAGAATGACAAGTAG
68820 CTAAGAATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (32 bp):
AAATAGCAAGCATCCAAGAATGACAAGTAGAC
Found at i:68836 original size:17 final size:17
Alignment explanation
Indices: 68764--68836 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
68754 CTAAAAATAG
*
68764 CAAGTACCTAAGAATGA
1 CAAGTAGCTAAGAATGA
*
68781 CAAGTAG--ACA-AATGG
1 CAAGTAGCTA-AGAATGA
* * *
68796 CAAGCATCCAAGAATGA
1 CAAGTAGCTAAGAATGA
*
68813 CATGTAGCTAAGAATGA
1 CAAGTAGCTAAGAATGA
68830 CAAGTAG
1 CAAGTAG
68837 ATATCTTGGG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
15 10 0.24
16 2 0.05
17 30 0.71
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.16
Consensus pattern (17 bp):
CAAGTAGCTAAGAATGA
Found at i:69674 original size:183 final size:182
Alignment explanation
Indices: 69353--69727 Score: 700
Period size: 183 Copynumber: 2.1 Consensus size: 182
69343 CTTCTTGGAC
69353 TTTCAACAATCTCCCACTTGAAGACTGATTTTAATCTGTCTTCATACCTCGATCAATGCAGCAGC
1 TTTCAACAATCTCCCACTTGAAGACTGATTTTAATCTGTCTTCATACCTCGATCAATGCAGCAGC
69418 ATTTTGGTCTTGTTACTCTAGCATGCCAACTGAAGCTGAACACAACTTCAGTTTGTCCGTGGTCA
66 ATTTTGGTCTTGTTACTCTAGCATGCCAACTGAAGCTGAACACAACTTCAGTTTGTCCGTGGTCA
* *
69483 CTGTCTTTGTCAA-CATGTCTGCCGGATTTTGAGCTCCACTAATCTTTTAAAG
131 CCGTCTTTGT-AATCATGTCTGCCGGATTTTGAACTCCACTAATCTTTTAAAG
69535 TTTCAACAATCTCCCACTTGAAGACTGATTTTAATCTGTCTTCATACCTCGATCAATGCAGCAGC
1 TTTCAACAATCTCCCACTTGAAGACTGATTTTAATCTGTCTTCATACCTCGATCAATGCAGCAGC
69600 ATTTCTGGTCTTGTTACTCTAGCATGCCAACTGAAGCTGAACACAACTTCAGTTTGTCCGTGGTC
66 ATTT-TGGTCTTGTTACTCTAGCATGCCAACTGAAGCTGAACACAACTTCAGTTTGTCCGTGGTC
69665 ACCGTCTTTGTAATCATGTCTGCCGGATTTTGAACTCCACTAATCTTTTAAAG
130 ACCGTCTTTGTAATCATGTCTGCCGGATTTTGAACTCCACTAATCTTTTAAAG
69718 TTTCAA-AATC
1 TTTCAACAATC
69728 CCAATCTTTC
Statistics
Matches: 189, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
182 75 0.40
183 114 0.60
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (182 bp):
TTTCAACAATCTCCCACTTGAAGACTGATTTTAATCTGTCTTCATACCTCGATCAATGCAGCAGC
ATTTTGGTCTTGTTACTCTAGCATGCCAACTGAAGCTGAACACAACTTCAGTTTGTCCGTGGTCA
CCGTCTTTGTAATCATGTCTGCCGGATTTTGAACTCCACTAATCTTTTAAAG
Found at i:74304 original size:17 final size:16
Alignment explanation
Indices: 74282--74313 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
74272 TGTGTGACAA
74282 TTAATTTAAAACTATTT
1 TTAATTTAAAA-TATTT
74299 TTAATTTAAAATATT
1 TTAATTTAAAATATT
74314 ATTGTTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTTAAAATATTT
Found at i:77310 original size:34 final size:33
Alignment explanation
Indices: 77234--77310 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
77224 TCTTGATTGG
* *
77234 TGGCCAACTTATTGGAAAATTCATCTTAGTTGG
1 TGGCCAACTTATTGGAAAATTCATCTTAGTAGA
* *
77267 TGGCCAACTTATTGGAAAATTCATTTTTGGTAGA
1 TGGCCAACTTATTGGAAAATTCA-TCTTAGTAGA
77301 TGGCCAACTT
1 TGGCCAACTT
77311 TGCATATGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 23 0.59
34 16 0.41
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (33 bp):
TGGCCAACTTATTGGAAAATTCATCTTAGTAGA
Found at i:82047 original size:33 final size:33
Alignment explanation
Indices: 81959--82095 Score: 139
Period size: 33 Copynumber: 4.0 Consensus size: 33
81949 ATTTGACAAG
81959 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTTTGCA
1 TTGGAAAATTCATC-TTGGTAGGTGGCCAAC-TT--A
* * * * *
81996 CATGGGAATTTCATCTTGGTTGGTGGCCAACATA
1 -TTGGAAAATTCATCTTGGTAGGTGGCCAACTTA
* *
82030 TTGGAAAATTCATCTTGGTTGGTGGTCAACTTA
1 TTGGAAAATTCATCTTGGTAGGTGGCCAACTTA
* *
82063 TTGGAAAATTCATATTTGGTAGGTGACCAACTT
1 TTGGAAAATTCAT-CTTGGTAGGTGGCCAACTT
82096 TGCATATGAG
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
33 41 0.49
34 16 0.19
36 1 0.01
37 15 0.18
38 11 0.13
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.36
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTAGGTGGCCAACTTA
Found at i:96130 original size:3 final size:3
Alignment explanation
Indices: 96115--96167 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
96105 ATTTATTTAT
* *
96115 TTA TTA TTC TTA TTA TTA TTA TTA TAA TTA TTA -TA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
96160 TTA TTA TT
1 TTA TTA TT
96168 TAAAAATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:97408 original size:15 final size:15
Alignment explanation
Indices: 97363--97410 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
97353 TTTATTTTTG
*
97363 ATTATTTTTTTATATT
1 ATTATATTTTTA-ATT
97379 -TTATA-TTTTAA-T
1 ATTATATTTTTAATT
97391 ATTATATTTTTAATT
1 ATTATATTTTTAATT
97406 ATTAT
1 ATTAT
97411 TTGCAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 1 0.04
13 6 0.21
14 11 0.39
15 10 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTATATTTTTAATT
Found at i:97423 original size:3 final size:3
Alignment explanation
Indices: 97417--97462 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
97407 TTATTTGCAA
* *
97417 TAT TAT T-T TAT TAT TAT TAT TACT TTT TAT TAT TAT TCT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
97462 T
1 T
97463 TATATAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:97464 original size:19 final size:19
Alignment explanation
Indices: 97417--97465 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
97407 TTATTTGCAA
97417 TATTATTTTATTATTATTAT
1 TATTA-TTTATTATTATTAT
*
97437 TACTT-TTTATTATTATTCT
1 TA-TTATTTATTATTATTAT
97456 TATTATTTAT
1 TATTATTTAT
97466 ATAATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 20 0.77
20 2 0.08
21 2 0.08
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTATTTATTATTATTAT
Found at i:97676 original size:20 final size:19
Alignment explanation
Indices: 97651--97692 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
97641 TTATTTTATA
97651 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
97671 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
97690 AAT
1 AAT
97693 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:97789 original size:29 final size:29
Alignment explanation
Indices: 97748--97806 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 29
97738 ATATTTCTAA
97748 ATAAATAAAATAT-TTTATTT-ATAAATAT
1 ATAAATAAAATATATTT-TTTCATAAATAT
* *
97776 ATAAATTAATATATATTTTTTCATAATTAT
1 ATAAA-TAAAATATATTTTTTCATAAATAT
97806 A
1 A
97807 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 10 0.38
30 11 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (29 bp):
ATAAATAAAATATATTTTTTCATAAATAT
Found at i:99900 original size:14 final size:14
Alignment explanation
Indices: 99861--99915 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
99851 TTTACGTTTG
*
99861 TATTTACATTTACA
1 TATTTACATTTGCA
*
99875 TTTTTACATTTGCA
1 TATTTACATTTGCA
99889 TATTTACATTTGGCA
1 TATTTACATTT-GCA
* *
99904 TCTTTGCATTTG
1 TATTTACATTTG
99916 TATTTTCATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.53
Consensus pattern (14 bp):
TATTTACATTTGCA
Found at i:103488 original size:26 final size:26
Alignment explanation
Indices: 103452--103504 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
103442 TCTTATACTC
103452 ATCCAACAAAGAAAGAA-AAAAGAAAA
1 ATCCAACAAAGAAAGAAGAAAA-AAAA
*
103478 ATCCAGCAAAGAAAGAAGAAAAAAAA
1 ATCCAACAAAGAAAGAAGAAAAAAAA
103504 A
1 A
103505 GAGGAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.72, C:0.11, G:0.13, T:0.04
Consensus pattern (26 bp):
ATCCAACAAAGAAAGAAGAAAAAAAA
Found at i:105856 original size:114 final size:114
Alignment explanation
Indices: 105656--105875 Score: 368
Period size: 114 Copynumber: 1.9 Consensus size: 114
105646 CACGTTCTCG
* * *
105656 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGCTATCTGATCTGGTTC
* * *
105721 GGTATAAACCCTAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTAGAAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
*
105770 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGCTATCTGATCTGGTTC
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGCTATCTGATCTGGTTC
*
105835 GGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
66 GGTAGAAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
105876 CTGCATAATC
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 98 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGCTATCTGATCTGGTTC
GGTAGAAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
Found at i:108436 original size:22 final size:22
Alignment explanation
Indices: 108407--108461 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
108397 ATCTACACTC
108407 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
108429 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
108451 TTCAGAGATGA
1 TTCAAAGATGA
108462 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:109065 original size:110 final size:110
Alignment explanation
Indices: 108900--109853 Score: 1244
Period size: 110 Copynumber: 8.5 Consensus size: 110
108890 TTCAGTTAGA
* * *
108900 GTTCATAATAAAAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCA
1 GTTCATAATAAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
108965 ACCTTTTGCTCGAATTCATCATTCGATGGATCAGCATTGCCAGAAG
65 ACCTTTTGCTCGAATTCATCATTCGATGGATCAGCATTGCCAGAAG
109011 GTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
1 GTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
109076 CCTTTTGCTCGAATTCATCATTCGATGGATCAGCATTGCCAGAAG
66 CCTTTTGCTCGAATTCATCATTCGATGGATCAGCATTGCCAGAAG
* *
109121 GTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
1 GTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
* * * * * * *
109186 CTTTTTGTTTGAATTCATCGTTCGATGGATCATCATTTCAAAAGAAG
66 CCTTTTGCTCGAATTCATCATTCGATGGATCAGCATTGC--CAGAAG
109233 GTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
1 GTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
109298 CCTTTTGCTCGAATTCATCATTCGATGGATCAGCATTGCCAGAAG
66 CCTTTTGCTCGAATTCATCATTCGATGGATCAGCATTGCCAGAAG
* *
109343 GTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAAATTGTTCAA
1 GTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
* * * * * * * *
109408 CTTTTTGTTTGAATTCATCATTAGATGGATCATCATTTCAAAAGAAA
66 CCTTTTGCTCGAATTCATCATTCGATGGATCAGCATTGC--CAGAAG
* * * **
109455 GTTCATAATGAGAAGAACTTATCTGAAAAATGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATAAGAAGAACTTATCTG-AAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
** ** * * * *
109520 ACCTTTTATTTAAATTCATCATTTGATAGATCAACATTGCCAGGTAG
65 ACCTTTTGCTCGAATTCATCATTCGATGGATCAGCATTGCCA-GAAG
* * *
109567 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAATTCATAATAAGAAGAATTTG
1 -GTTCATAATAAGAAGAACT--T-ATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAATTTG
* * * * * *
109632 TTCAACCTTTTGCTCAAATCCATCACTT-GATGAATCAGCTTTTCCAGAGAAA
61 TTCAACCTTTTGCTCGAATTCATCA-TTCGATGGATCAGCATTGCC--AGAAG
* *
109684 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATAAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
* * * * *
109749 ACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAG
65 ACCTTTTGCTCGAATTCATCATTCGATGGATCAGCATTGCCA-GAAG
* * *
109796 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAA
1 -GTTCATAATAAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAA
109854 CTTATCTGAA
Statistics
Matches: 748, Mismatches: 78, Indels: 32
0.87 0.09 0.04
Matches are distributed among these distances:
110 278 0.37
111 28 0.04
112 135 0.18
113 215 0.29
115 3 0.00
116 84 0.11
117 4 0.01
118 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (110 bp):
GTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
CCTTTTGCTCGAATTCATCATTCGATGGATCAGCATTGCCAGAAG
Found at i:109183 original size:20 final size:20
Alignment explanation
Indices: 109121--109184 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
109111 TTGCCAGAAG
109121 GTTCATAATAAGAAGAACTT
1 GTTCATAATAAGAAGAACTT
* * * ***
109141 -ATC-TGAAGAGGAAGAAGAA
1 GTTCAT-AATAAGAAGAACTT
109160 GTTCATAATAAGAAGAACTT
1 GTTCATAATAAGAAGAACTT
109180 GTTCA
1 GTTCA
109185 ACTTTTTGTT
Statistics
Matches: 29, Mismatches: 12, Indels: 6
0.62 0.26 0.13
Matches are distributed among these distances:
18 1 0.03
19 11 0.38
20 16 0.55
21 1 0.03
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (20 bp):
GTTCATAATAAGAAGAACTT
Found at i:109275 original size:222 final size:225
Alignment explanation
Indices: 108868--109856 Score: 1330
Period size: 222 Copynumber: 4.4 Consensus size: 225
108858 GATTTAAATC
** ** ** * *
108868 CATCATTTAATGGATCAACATTTTCAGTTAGAGTTCATAATAAAAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACATTGCCAGGAAGAGTTCATAATAAGAAGAACTTATCTGAAGAAGGA
* * *
108933 AGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCGAATTCATCATTCGATGGATCA
66 AGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATTCGATGGATCA
* * *
108998 GCATTGC--CAGAAGGTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGA
131 GCATTTCAAAAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGA
109061 GAAGAATTTGTTCAACCTTTTGCTCGAATT
196 GAAGAATTTGTTCAACCTTTTGCTCGAATT
*
109091 CATCATTCGATGGATCAGCATTGCCA-GAAG-GTTCATAATAAGAAGAACTTATCTGAAG-AGGA
1 CATCATTCGATGGATCAACATTGCCAGGAAGAGTTCATAATAAGAAGAACTTATCTGAAGAAGGA
* * * *
109153 AGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCGTTCGATGGATCA
66 AGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATTCGATGGATCA
* *
109218 TCATTTCAAAAGAAGGTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGA
131 GCATTTCAAAAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGA
109283 GAAGAATTTGTTCAACCTTTTGCTCGAATT
196 GAAGAATTTGTTCAACCTTTTGCTCGAATT
*
109313 CATCATTCGATGGATCAGCATTGCCA-GAAG-GTTCATAATAAGAAGAACTTATCTGAAG-AGGA
1 CATCATTCGATGGATCAACATTGCCAGGAAGAGTTCATAATAAGAAGAACTTATCTGAAGAAGGA
* * * * *
109375 AGAAGAAGTTCATAATAAGAAGAAATTGTTCAACTTTTTGTTTGAATTCATCATTAGATGGATCA
66 AGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATTCGATGGATCA
* * * *
109440 TCATTTCAAAAGAAAGTTCATAATGAGAAGAACTTATCTGAAAAATGAAGAAGAAGTTCATAATG
131 GCATTTCAAAAGAAAGTTCATAATAAGAAGAACTTATCTG-AAGAGGAAGAAGAAGTTCATAATG
** ** **
109505 AGAAGAGCTTGTTCAACCTTTTATTTAAATT
195 AGAAGAATTTGTTCAACCTTTTGCTCGAATT
* * * *
109536 CATCATTTGATAGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTCGATGGATCAACATTGCCAGGAAGAGTTCATAATAAGAAGAACT--T-ATCTGAAGAA
* * * * *
109601 GGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTT-GATGA
63 GGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCA-TTCGATGG
* * * * *
109665 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
127 ATCAGCATTTCAAAAGAAAGTTCATAATAAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
* *
109730 AATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
191 AATGAGAAGAATTTGTTCAACCTTTTGCTCGAATT
* * * * *
109765 CATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAACATTGCCAGGAAGAGTTCATAATAAGAAGAACTTATCTGAAGAAGGA
*
109830 AGAAGAAGTTCATAATGAGAAGAACTT
66 AGAAGAAGTTCATAATAAGAAGAACTT
109857 ATCTGAAGAG
Statistics
Matches: 693, Mismatches: 62, Indels: 19
0.90 0.08 0.02
Matches are distributed among these distances:
220 67 0.10
221 26 0.04
222 249 0.36
223 91 0.13
224 3 0.00
225 18 0.03
226 36 0.05
227 1 0.00
228 10 0.01
229 190 0.27
230 2 0.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (225 bp):
CATCATTCGATGGATCAACATTGCCAGGAAGAGTTCATAATAAGAAGAACTTATCTGAAGAAGGA
AGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATTCGATGGATCA
GCATTTCAAAAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGA
GAAGAATTTGTTCAACCTTTTGCTCGAATT
Found at i:109882 original size:39 final size:40
Alignment explanation
Indices: 109796--109889 Score: 163
Period size: 40 Copynumber: 2.4 Consensus size: 40
109786 TGCCAGGTAG
109796 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
* *
109836 AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
109875 AGTTCATAATGAGAA
1 AGTTCATAATGAGAA
109890 AATTTTGTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
39 24 0.46
40 28 0.54
ACGTcount: A:0.48, C:0.09, G:0.23, T:0.20
Consensus pattern (40 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
Found at i:110023 original size:124 final size:123
Alignment explanation
Indices: 109830--110150 Score: 425
Period size: 124 Copynumber: 2.6 Consensus size: 123
109820 TGAAGAAAGA
* * * **
109830 AGAAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAAATTT
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAGCT
* * * *
109895 TGTTCAACCTTTTTCATGACTCTATCATAAAAGGAGATAGATCAGCATCAACTTTTCC
66 TGTTCAACCTTTTGCATAACTCTATCACAAAAGGAGATAGATCAGCATCAACATTTCC
*
109953 AG-AGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAG
1 AGAAG-AAGTTCATAATGAGAAGAACTCATCTGAAG-AAGAAGAAGAAGTTCATAATGAGAAGAG
* * * * *
110017 CTTGTTCGACCTTTTGCATAACTCTATCACAGAAGGAGATATATCATCATCAGCATTTCC
64 CTTGTTCAACCTTTTGCATAACTCTATCACAAAAGGAGATAGATCAGCATCAACATTTCC
* * * *
110077 AGAAGGAGTTCACAATGAGAATAACTCATCT---GAAGAAGAAGAAGTTCACAATGAGAAGAGCT
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAGCT
110139 TGTTCAACCTTT
66 TGTTCAACCTTT
110151 GCTAGATTAC
Statistics
Matches: 174, Mismatches: 21, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
120 40 0.23
121 1 0.01
122 2 0.01
123 30 0.17
124 99 0.57
125 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (123 bp):
AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAGCT
TGTTCAACCTTTTGCATAACTCTATCACAAAAGGAGATAGATCAGCATCAACATTTCC
Found at i:110409 original size:9 final size:9
Alignment explanation
Indices: 110383--110434 Score: 61
Period size: 9 Copynumber: 5.8 Consensus size: 9
110373 ATTTATTTAT
110383 TTATTATAA
1 TTATTATAA
* *
110392 TAATAATAA
1 TTATTATAA
110401 TTATTATAA
1 TTATTATAA
110410 TTATTAT-A
1 TTATTATAA
*
110418 TATATTATTA
1 T-TATTATAA
110428 TTATTAT
1 TTATTAT
110435 TAAAAAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
8 2 0.05
9 33 0.89
10 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTATTATAA
Found at i:110415 original size:12 final size:12
Alignment explanation
Indices: 110394--110436 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
110384 TATTATAATA
*
110394 ATAATAATTATT
1 ATAATTATTATT
110406 ATAATTATTA-T
1 ATAATTATTATT
110417 ATATATTATTATT
1 ATA-ATTATTATT
*
110430 ATTATTA
1 ATAATTA
110437 AAAAATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 20 0.74
13 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATAATTATTATT
Found at i:110423 original size:18 final size:18
Alignment explanation
Indices: 110375--110434 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
110365 CCCATTTTAT
*
110375 TTATT-TATTTATTATAA
1 TTATTATATATATTATAA
* *
110392 TAATAATA-ATTATTATAA
1 TTATTATATA-TATTATAA
*
110410 TTATTATATATATTATTA
1 TTATTATATATATTATAA
110428 TTATTAT
1 TTATTAT
110435 TAAAAAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
17 3 0.09
18 30 0.88
19 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATTATATATATTATAA
Found at i:111573 original size:7 final size:7
Alignment explanation
Indices: 111554--111634 Score: 53
Period size: 7 Copynumber: 11.6 Consensus size: 7
111544 AGTACTCTAG
111554 TTTTATAA
1 TTTTAT-A
111562 TTTTATA
1 TTTTATA
111569 TTTTA-A
1 TTTTATA
* *
111575 TCATTCAAA
1 T--TTTATA
111584 TTTTAT-
1 TTTTATA
111590 TTTTGAT-
1 TTTT-ATA
* *
111597 TATTATT
1 TTTTATA
111604 TTTTATA
1 TTTTATA
111611 TTTTATA
1 TTTTATA
111618 TTTTA-A
1 TTTTATA
*
111624 TATTATA
1 TTTTATA
111631 TTTT
1 TTTT
111635 TAATTATTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
6 13 0.22
7 35 0.59
8 9 0.15
9 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (7 bp):
TTTTATA
Found at i:111588 original size:22 final size:21
Alignment explanation
Indices: 111560--111615 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
111550 CTAGTTTTAT
111560 AATTTTATATTTTAATCATTCA
1 AATTTTATATTTTAATCATT-A
* *
111582 AATTTTAT-TTTTGATTATTA
1 AATTTTATATTTTAATCATTA
**
111602 TTTTTTATATTTTA
1 AATTTTATATTTTA
111616 TATTTTAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 7 0.25
21 13 0.46
22 8 0.29
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (21 bp):
AATTTTATATTTTAATCATTA
Found at i:111607 original size:15 final size:14
Alignment explanation
Indices: 111589--111684 Score: 56
Period size: 14 Copynumber: 6.9 Consensus size: 14
111579 TCAAATTTTA
*
111589 TTTTTGATTATTAT
1 TTTTTTATTATTAT
111603 TTTTTATATT-TTA-
1 TTTTT-TATTATTAT
* *
111616 TATTTTAATATTAT
1 TTTTTTATTATTAT
*
111630 ATTTTTA--ATTAT
1 TTTTTTATTATTAT
** *
111642 TATTTGCAATATTAT
1 T-TTTTTATTATTAT
*
111657 TTTATTATTATTAT
1 TTTTTTATTATTAT
111671 TACTTTTTATTATT
1 T--TTTTTATTATT
111685 CTTCTATTAT
Statistics
Matches: 61, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
12 8 0.13
13 11 0.18
14 23 0.38
15 9 0.15
16 10 0.16
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (14 bp):
TTTTTTATTATTAT
Found at i:111608 original size:42 final size:42
Alignment explanation
Indices: 111562--111646 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
111552 AGTTTTATAA
* *
111562 TTTTATATTTTA-ATCATTCAA-ATTTTATTTTTGATTATTATT
1 TTTTATATTTTATAT--TTCAATATTATATTTTTAATTATTATT
*
111604 TTTTATATTTTATATTTTAATATTATATTTTTAATTATTATT
1 TTTTATATTTTATATTTCAATATTATATTTTTAATTATTATT
111646 T
1 T
111647 GCAATATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 4 0.11
42 32 0.84
43 2 0.05
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (42 bp):
TTTTATATTTTATATTTCAATATTATATTTTTAATTATTATT
Found at i:111613 original size:27 final size:26
Alignment explanation
Indices: 111583--111684 Score: 89
Period size: 27 Copynumber: 3.7 Consensus size: 26
111573 AATCATTCAA
*
111583 ATTTTATTTTTGATTATTATTTTTTAT
1 ATTTTATTTTT-AATATTATTTTTTAT
111610 ATTTTATATTTTAATATTATATTTTTA-
1 ATTTTAT-TTTTAATATTAT-TTTTTAT
**
111637 ATTATTATTTGCAATATTATTTTATTATT
1 ATT-TTATTTTTAATATTATTTT-TTA-T
*
111666 ATTATTACTTTTTATTATT
1 ATT-TTA-TTTTTAATATT
111685 CTTCTATTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
26 3 0.05
27 30 0.48
28 14 0.23
29 7 0.11
30 8 0.13
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (26 bp):
ATTTTATTTTTAATATTATTTTTTAT
Found at i:111654 original size:42 final size:43
Alignment explanation
Indices: 111587--111684 Score: 103
Period size: 42 Copynumber: 2.3 Consensus size: 43
111577 ATTCAAATTT
***
111587 TATTTTTGATTATTATTTTTTATATT-TTATATT-TTAATATTA
1 TATTTTT-ATTATTATTTGCAATATTATTATATTATTAATATTA
* *
111629 TATTTTTAATTATTATTTGCAATATTATTTTATTATTATTATTA
1 TATTTTT-ATTATTATTTGCAATATTATTATATTATTAATATTA
*
111673 -CTTTTTATTATT
1 TATTTTTATTATT
111685 CTTCTATTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
42 28 0.60
43 11 0.23
44 8 0.17
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (43 bp):
TATTTTTATTATTATTTGCAATATTATTATATTATTAATATTA
Found at i:111909 original size:20 final size:19
Alignment explanation
Indices: 111884--111925 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
111874 TTATTTTATA
111884 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
111904 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
111923 AAT
1 AAT
111926 ATCAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:113222 original size:2 final size:2
Alignment explanation
Indices: 113215--113243 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
113205 TTGATGTAAG
113215 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
113244 CCTAATTCCT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:116629 original size:75 final size:76
Alignment explanation
Indices: 116562--116725 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 76
116552 AAAAAATAAT
* * *
116562 ATAATATTCTAAATCCTAATTAAAATACT-AAAACTTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
116626 AAAATATAAAA
66 AAAATATAAAA
*
116637 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
* * *
116701 ATAATGTTTAAA
66 AAAAT-ATAAAA
*
116713 ATATTATCCTAAA
1 ATAATATCCTAAA
116726 TTTGAGTTTA
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 32 0.41
76 47 0.59
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
AAAATATAAAA
Found at i:118364 original size:14 final size:15
Alignment explanation
Indices: 118341--118372 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
118331 CGAACCAAAT
118341 CTGTTTTTTTCTGCA
1 CTGTTTTTTTCTGCA
118356 CTGTTTTTTTCTGCA
1 CTGTTTTTTTCTGCA
118371 CT
1 CT
118373 TTATTGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.22, G:0.12, T:0.59
Consensus pattern (15 bp):
CTGTTTTTTTCTGCA
Found at i:124135 original size:20 final size:20
Alignment explanation
Indices: 124110--124147 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
124100 TATATATATT
124110 AAAATAAAATAAAAATAAGA
1 AAAATAAAATAAAAATAAGA
* *
124130 AAAATAATATAATAATAA
1 AAAATAAAATAAAAATAA
124148 ATATTAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (20 bp):
AAAATAAAATAAAAATAAGA
Found at i:145597 original size:3 final size:3
Alignment explanation
Indices: 145591--145657 Score: 93
Period size: 3 Copynumber: 22.0 Consensus size: 3
145581 TTTTTTTAAT
145591 TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TGT- TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TTA
145637 TTA TTA TTA TTAA TTA -TA TTA
1 TTA TTA TTA TT-A TTA TTA TTA
145658 CATTTTGTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
2 3 0.05
3 49 0.83
4 7 0.12
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:152659 original size:16 final size:16
Alignment explanation
Indices: 152640--152689 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
152630 ACAGATTGAG
152640 ATCAATACATACATAC
1 ATCAATACATACATAC
*
152656 ATCAATACATACATAT
1 ATCAATACATACATAC
*
152672 ATCAACACATACATAC
1 ATCAATACATACATAC
152688 AT
1 AT
152690 GTTACATAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (16 bp):
ATCAATACATACATAC
Found at i:152667 original size:20 final size:20
Alignment explanation
Indices: 152644--152689 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
152634 ATTGAGATCA
*
152644 ATACATACATACATCA-ATAC
1 ATACATACAT-CAACACATAC
*
152664 ATACATATATCAACACATAC
1 ATACATACATCAACACATAC
152684 ATACAT
1 ATACAT
152690 GTTACATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (20 bp):
ATACATACATCAACACATAC
Found at i:153029 original size:34 final size:36
Alignment explanation
Indices: 152968--153089 Score: 133
Period size: 37 Copynumber: 3.4 Consensus size: 36
152958 TCTATTGCCT
* *
152968 TTGAGA-ATGTTTTTTTAAAACAAAAATTTTGTCTCGC
1 TTGAGACAT-TTTTTTCAAAA-TAAAATTTTGTCTCGC
** * *
153005 TTGAGACATTTTTTTC-CCA-CAAATTTTGTCTCAC
1 TTGAGACATTTTTTTCAAAATAAAATTTTGTCTCGC
*
153039 TTGAGACAATTTCTTTCAAAATAAAATTTTGTCTCGC
1 TTGAGAC-ATTTTTTTCAAAATAAAATTTTGTCTCGC
153076 TTGAGACATTTTTT
1 TTGAGACATTTTTT
153090 CTCTGAGATA
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
34 20 0.29
35 8 0.11
36 8 0.11
37 32 0.46
38 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (36 bp):
TTGAGACATTTTTTTCAAAATAAAATTTTGTCTCGC
Found at i:153256 original size:104 final size:104
Alignment explanation
Indices: 153069--153500 Score: 527
Period size: 104 Copynumber: 4.1 Consensus size: 104
153059 ATAAAATTTT
* * * *
153069 GTCTCGCTTGAGACATTTTTTCTCTGAGATACAAATTT-AAATTT-GTTATACTTAAAACAAAAT
1 GTCTCGCTTGAGACATTTTTTCTTTGAGATACAAATTTCGAATTTGGTT-CACTTGAAACAAAAT
* *
153132 TAATCTCACTTGAAATTGTTATTTCTCAAAAATAAACTTC
65 TAATCTCACTTGAGATTGTTATTTCTCAAAAACAAACTTC
* * *
153172 GTCTTGCTTGAGACATTTTTTCTTTGAGATACAAATTTCGAGTTTGGTTCACTTGAAATAAAATT
1 GTCTCGCTTGAGACATTTTTTCTTTGAGATACAAATTTCGAATTTGGTTCACTTGAAACAAAATT
*
153237 AATCTCACTTGAGATTGTTATTTCTCAAAAACAAACGTC
66 AATCTCACTTGAGATTGTTATTTCTCAAAAACAAACTTC
* *
153276 GTCTCGCTTGAGACATTTTTTCCTTTGATATACAAATTTCGAATTTGATTCACTTGAAACAAAAA
1 GTCTCGCTTGAGACATTTTTT-CTTTGAGATACAAATTTCGAATTTGGTTCACTTGAAAC-AAAA
*
153341 TTAATCTCTA-TTGAGATTGTTATTTCTTTC-AAAACAAATTTC
64 TTAATCTC-ACTTGAGATTGTTATTTC--TCAAAAACAAACTTC
* ** * * * * *
153383 GCCTCATTTGAGACATTTTTCCTTTGAGAATACAATTTTTGAATTTGTTTCACATT-AAACAAAG
1 GTCTCGCTTGAGACATTTTTTCTTTGAG-ATACAAATTTCGAATTTGGTTCAC-TTGAAACAAAA
* * *
153447 TTGATCTCACTTGAGATCG-T-TTTCTCAAAAACAAACTTT
64 TTAATCTCACTTGAGATTGTTATTTCTCAAAAACAAACTTC
153486 GTCTCGCTTGAGACA
1 GTCTCGCTTGAGACA
153501 ATTTCTCTAA
Statistics
Matches: 285, Mismatches: 33, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
102 2 0.01
103 58 0.20
104 77 0.27
105 39 0.14
106 52 0.18
107 53 0.19
108 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (104 bp):
GTCTCGCTTGAGACATTTTTTCTTTGAGATACAAATTTCGAATTTGGTTCACTTGAAACAAAATT
AATCTCACTTGAGATTGTTATTTCTCAAAAACAAACTTC
Found at i:153473 original size:210 final size:207
Alignment explanation
Indices: 153069--153500 Score: 534
Period size: 210 Copynumber: 2.1 Consensus size: 207
153059 ATAAAATTTT
*
153069 GTCTCGCTTGAGACATTTTTTCTCTGAGATACAAATTTAAATTTGTTATACTTAAAACAAAATTA
1 GTCTCGCTTGAGACATTTTTTCTCTGAGATACAAATTTAAATTTGTTACACTTAAAACAAAATTA
* * ** *
153134 ATCTCACTTGAAATTGTTATTTCTCAAAAATAAACTTCGTCTTGCTTGAGACATTTTTTCTTTGA
66 ATCTCACTTGAAATTGTTATTTCTCAAAAACAAACTTCGCCTCACTTGAGACATTTTTCCTTTGA
* * *
153199 GATACAAATTTCGAGTTTGGTTCACTTGAAATAAAATTAATCTCACTTGAGATTGTTATTTCTCA
131 GATACAAATTTCGAATTTGGTTCACTTGAAACAAAATTAATCTCACTTGAGATCGTTATTTCTCA
153264 AAAACAAACGTC
196 AAAACAAACGTC
* * * *
153276 GTCTCGCTTGAGACATTTTTTCCTTTGATATACAAATTTCGAATTTGATT-CACTTGAAACAAAA
1 GTCTCGCTTGAGACATTTTTT-CTCTGAGATACAAATTT-AAATTTG-TTACACTTAAAAC-AAA
* * *
153340 ATTAATCTCTA-TTGAGATTGTTATTTCTTTC-AAAACAAATTTCGCCTCATTTGAGACATTTTT
62 ATTAATCTC-ACTTGAAATTGTTATTTC--TCAAAAACAAACTTCGCCTCACTTGAGACATTTTT
* * * * *
153403 CCTTTGAGAATACAATTTTTGAATTTGTTTCACATT-AAACAAAGTTGATCTCACTTGAGATCG-
124 CCTTTGAG-ATACAAATTTCGAATTTGGTTCAC-TTGAAACAAAATTAATCTCACTTGAGATCGT
* *
153466 T-TTTCTCAAAAACAAACTTT
187 TATTTCTCAAAAACAAACGTC
153486 GTCTCGCTTGAGACA
1 GTCTCGCTTGAGACA
153501 ATTTCTCTAA
Statistics
Matches: 193, Mismatches: 23, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
207 21 0.11
208 15 0.08
209 14 0.07
210 61 0.32
211 35 0.18
212 45 0.23
213 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (207 bp):
GTCTCGCTTGAGACATTTTTTCTCTGAGATACAAATTTAAATTTGTTACACTTAAAACAAAATTA
ATCTCACTTGAAATTGTTATTTCTCAAAAACAAACTTCGCCTCACTTGAGACATTTTTCCTTTGA
GATACAAATTTCGAATTTGGTTCACTTGAAACAAAATTAATCTCACTTGAGATCGTTATTTCTCA
AAAACAAACGTC
Found at i:153496 original size:36 final size:35
Alignment explanation
Indices: 153439--153576 Score: 152
Period size: 36 Copynumber: 3.8 Consensus size: 35
153429 GTTTCACATT
* **
153439 AAACAAAGTTGATCTCACTTGAGATCGTTTTCTC-AA
1 AAACAAATTTG-TCTCACTTGAGA-CAATTTCTCTAA
*
153475 AAACAAACTTTGTCTCGCTTGAGACAATTTCTCTAA
1 AAACAAA-TTTGTCTCACTTGAGACAATTTCTCTAA
* * **
153511 AAATAATTTTTGTCTCGTTTGAGACAATTTCTCTAA
1 AAACAA-ATTTGTCTCACTTGAGACAATTTCTCTAA
153547 AAACAAATGTTGTCTCACTTGAGACAATTT
1 AAACAAAT-TTGTCTCACTTGAGACAATTT
153577 TCCAAATTAT
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
35 8 0.09
36 76 0.87
37 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (35 bp):
AAACAAATTTGTCTCACTTGAGACAATTTCTCTAA
Found at i:153792 original size:33 final size:33
Alignment explanation
Indices: 153749--153812 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
153739 CAACATTTAC
*
153749 CATCTGTGAGTCTGTTTCCCTTGAAACAAAACT
1 CATCTGTGAGTATGTTTCCCTTGAAACAAAACT
* * **
153782 CATCTTTGAGTATTTTTCTTTTGAAACAAAA
1 CATCTGTGAGTATGTTTCCCTTGAAACAAAA
153813 TTTTGTCTCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (33 bp):
CATCTGTGAGTATGTTTCCCTTGAAACAAAACT
Found at i:154626 original size:65 final size:66
Alignment explanation
Indices: 154478--154634 Score: 169
Period size: 66 Copynumber: 2.4 Consensus size: 66
154468 AGACGTAACC
**** *
154478 CATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGATAGTTTCTTTTTGAGAA
1 CATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTACAATCTCTTGAGATAGCTTCTTTTTGAGAA
154543 A
66 A
* * *
154544 AATCCTTGAGTCTGTTTCTTTGGAAACAAAATTTACAATCT-TTGAG-TCTGCTTC-TTTTGA-A
1 CATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTACAATCTCTTGAGAT-AGCTTCTTTTTGAGA
154605 ACA
65 A-A
* *
154608 TCATCTTTGAGTCGGTTTCTTTTGAAA
1 -CATCTTTGAGTCTGTTTCTTTGGAAA
154635 TCATTATCCC
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
63 2 0.03
64 8 0.11
65 31 0.41
66 35 0.46
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (66 bp):
CATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTACAATCTCTTGAGATAGCTTCTTTTTGAGAA
A
Found at i:155099 original size:8 final size:8
Alignment explanation
Indices: 155086--155120 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
155076 AGACGTGATG
155086 TCTTTTCC
1 TCTTTTCC
155094 TCTTTTCC
1 TCTTTTCC
*
155102 TCTTTGCC
1 TCTTTTCC
155110 -CTTTTCC
1 TCTTTTCC
155117 TCTT
1 TCTT
155121 CGTCCCCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.00, C:0.37, G:0.03, T:0.60
Consensus pattern (8 bp):
TCTTTTCC
Found at i:155285 original size:3 final size:3
Alignment explanation
Indices: 155279--155326 Score: 71
Period size: 3 Copynumber: 15.7 Consensus size: 3
155269 TTTTTTTAAT
155279 TTA TTA TTA TTA TTA TTTA TTA TTA TTA TGT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
155325 TT
1 TT
155327 TATATTACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.02
3 37 0.88
4 4 0.10
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:155382 original size:17 final size:17
Alignment explanation
Indices: 155357--155396 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
155347 AGGCCACCCT
155357 GAAGCCCAAATACAAAG
1 GAAGCCCAAATACAAAG
*
155374 GAAGTCCAAATACAAAG
1 GAAGCCCAAATACAAAG
155391 GAAGCC
1 GAAGCC
155397 TAGTACTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.23, G:0.20, T:0.07
Consensus pattern (17 bp):
GAAGCCCAAATACAAAG
Found at i:156789 original size:15 final size:15
Alignment explanation
Indices: 156769--156802 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
156759 CCGTAGGACC
156769 ACTACATCCCAAAGG
1 ACTACATCCCAAAGG
*
156784 ACTACATCCCGAAGG
1 ACTACATCCCAAAGG
156799 ACTA
1 ACTA
156803 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.32, G:0.15, T:0.15
Consensus pattern (15 bp):
ACTACATCCCAAAGG
Found at i:156951 original size:23 final size:26
Alignment explanation
Indices: 156914--156982 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
156904 TTCTCTTGTG
156914 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
156938 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
156963 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
156983 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:156964 original size:12 final size:12
Alignment explanation
Indices: 156947--156982 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
156937 TATCATGTTC
156947 TCATATCACATG
1 TCATATCACATG
*
156959 TCATATCACATA
1 TCATATCACATG
156971 TCATATCACATG
1 TCATATCACATG
156983 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:157422 original size:64 final size:63
Alignment explanation
Indices: 157354--157495 Score: 171
Period size: 64 Copynumber: 2.2 Consensus size: 63
157344 TATTGCTGGG
* * *
157354 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTA-TT-AATGGGATGCATCGATGCACTACT
1 ATGCATCGATACACCAATTGCATTCGATGTTT-ATTATTTAAAAGAG-TGCATCGATGCAC-ACT
*
157417 T
63 A
* * *
157418 ATGCATCGATACACGAATTGTATTCGATGTTTTTTATTTTAAAAGAGTGCATCGATGCACACTA
1 ATGCATCGATACACCAATTGCATTCGATGTTTATTA-TTTAAAAGAGTGCATCGATGCACACTA
157482 ATGCATCGATACAC
1 ATGCATCGATACAC
157496 ATTCAAACAA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
63 3 0.04
64 46 0.68
65 15 0.22
66 4 0.06
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATACACCAATTGCATTCGATGTTTATTATTTAAAAGAGTGCATCGATGCACACTA
Found at i:162622 original size:15 final size:15
Alignment explanation
Indices: 162599--162633 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
162589 CCGTAGGACC
*
162599 ACTACATCCCGAAGG
1 ACTATATCCCGAAGG
162614 ACTATATCCCGAAGG
1 ACTATATCCCGAAGG
162629 ACTAT
1 ACTAT
162634 TATACCCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (15 bp):
ACTATATCCCGAAGG
Found at i:162781 original size:23 final size:26
Alignment explanation
Indices: 162744--162812 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
162734 TTCTCTTGTG
162744 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
162768 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
162793 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
162813 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:162794 original size:12 final size:12
Alignment explanation
Indices: 162777--162812 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
162767 TATCATGTTC
162777 TCATATCACATG
1 TCATATCACATG
*
162789 TCATATCACATA
1 TCATATCACATG
162801 TCATATCACATG
1 TCATATCACATG
162813 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:163297 original size:64 final size:63
Alignment explanation
Indices: 163120--163346 Score: 215
Period size: 64 Copynumber: 3.5 Consensus size: 63
163110 TAATGAAGGT
* * * * * * **
163120 ATGCATCGATTCACTACTGATGCATCGGTGCATAAA-AGGTATTCAATGTAGTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATA-GCATTCAATGT-TTATTATTAATGGG
* * *
163184 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATAACATTCAATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATAGCATTCAATGTTT-ATTATTAATGGG
* * * **
163248 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCAATGTTTTTTATTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATAGCATTCAATGTTTATTA--TTAATGGG
* * *
163312 AGTGCATCGATGCATTACTAATGCATCGATACACA
1 A-TGCATCGATGCACTACTTATGCATCGATGCACA
163347 TTCAAACAAT
Statistics
Matches: 136, Mismatches: 22, Indels: 9
0.81 0.13 0.05
Matches are distributed among these distances:
63 4 0.03
64 98 0.72
65 34 0.25
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAATAGCATTCAATGTTTATTATTAATGGG
Found at i:168464 original size:15 final size:15
Alignment explanation
Indices: 168444--168507 Score: 119
Period size: 15 Copynumber: 4.3 Consensus size: 15
168434 CCGTAGGACC
168444 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
168459 ACTACATCTCGAAGG
1 ACTACATCCCGAAGG
168474 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
168489 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
168504 ACTA
1 ACTA
168508 TTATACCCTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.34, C:0.31, G:0.19, T:0.16
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:168669 original size:12 final size:12
Alignment explanation
Indices: 168652--168687 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
168642 TATCATGTTC
*
168652 TCATATCATATG
1 TCATATCACATG
*
168664 TCATATCACATA
1 TCATATCACATG
168676 TCATATCACATG
1 TCATATCACATG
168688 AACATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (12 bp):
TCATATCACATG
Found at i:169103 original size:64 final size:64
Alignment explanation
Indices: 168995--169221 Score: 244
Period size: 64 Copynumber: 3.5 Consensus size: 64
168985 TAATGAAGGT
* * ** * **
168995 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT-GTCATTATTAATGGG
* * *
169059 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTGTCATTATTAATGGG
* ** **
169123 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-TTTTTATTTTAA-AA
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTGTCATTA--TTAATGG
169186 G
64 G
* *
169187 AGTGCATCGATGCACTACTAATGCATCGATACACA
1 A-TGCATCGATGCACTACTTATGCATCGATGCACA
169222 TTCAAATAAT
Statistics
Matches: 140, Mismatches: 19, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
63 5 0.04
64 101 0.72
65 34 0.24
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTGTCATTATTAATGGG
Found at i:172102 original size:18 final size:18
Alignment explanation
Indices: 172079--172121 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
172069 ACCACCGTGG
172079 ACCGCCTTCGCCACCAAC
1 ACCGCCTTCGCCACCAAC
172097 ACCGCCTTCGCCACCAAC
1 ACCGCCTTCGCCACCAAC
172115 ACCGCCT
1 ACCGCCT
172122 CAAATACTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.21, C:0.56, G:0.12, T:0.12
Consensus pattern (18 bp):
ACCGCCTTCGCCACCAAC
Found at i:178459 original size:18 final size:18
Alignment explanation
Indices: 178428--178483 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
178418 TTTGCTTTTG
178428 AAAACAAC--TCACTCTC
1 AAAACAACTATCACTCTC
178444 AAAACAACTATCACTCTC
1 AAAACAACTATCACTCTC
178462 AAAACAACTATCACTCTC
1 AAAACAACTATCACTCTC
178480 AAAA
1 AAAA
178484 TAGAAAAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.21
18 30 0.79
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAACAACTATCACTCTC
Found at i:178547 original size:18 final size:18
Alignment explanation
Indices: 178524--178559 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
178514 TCCTCGGTGG
178524 CAACTATCACTCTCAAAA
1 CAACTATCACTCTCAAAA
178542 CAACTATCACTCTCAAAA
1 CAACTATCACTCTCAAAA
178560 TAGAAAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (18 bp):
CAACTATCACTCTCAAAA
Found at i:178574 original size:76 final size:76
Alignment explanation
Indices: 178448--178617 Score: 340
Period size: 76 Copynumber: 2.2 Consensus size: 76
178438 ACTCTCAAAA
178448 CAACTATCACTCTCAAAACAACTATCACTCTCAAAATAGAAAAGCAACGCTTAGAAATGCTGACC
1 CAACTATCACTCTCAAAACAACTATCACTCTCAAAATAGAAAAGCAACGCTTAGAAATGCTGACC
178513 ATCCTCGGTGG
66 ATCCTCGGTGG
178524 CAACTATCACTCTCAAAACAACTATCACTCTCAAAATAGAAAAGCAACGCTTAGAAATGCTGACC
1 CAACTATCACTCTCAAAACAACTATCACTCTCAAAATAGAAAAGCAACGCTTAGAAATGCTGACC
178589 ATCCTCGGTGG
66 ATCCTCGGTGG
178600 CAACTATCACTCTCAAAA
1 CAACTATCACTCTCAAAA
178618 TAGAAAAGCA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 94 1.00
ACGTcount: A:0.39, C:0.28, G:0.12, T:0.21
Consensus pattern (76 bp):
CAACTATCACTCTCAAAACAACTATCACTCTCAAAATAGAAAAGCAACGCTTAGAAATGCTGACC
ATCCTCGGTGG
Found at i:178680 original size:46 final size:46
Alignment explanation
Indices: 178613--178701 Score: 162
Period size: 46 Copynumber: 1.9 Consensus size: 46
178603 CTATCACTCT
178613 CAAAATAGAAAAGCAACGCTTGTTTTGTATCCATCCTCGGTGGATA
1 CAAAATAGAAAAGCAACGCTTGTTTTGTATCCATCCTCGGTGGATA
178659 CAAAA-AGCAAAAGCAACGCTTGTTTTGTATCCATCCTCGGTGG
1 CAAAATAG-AAAAGCAACGCTTGTTTTGTATCCATCCTCGGTGG
178702 TCAGCATTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
45 2 0.05
46 40 0.95
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (46 bp):
CAAAATAGAAAAGCAACGCTTGTTTTGTATCCATCCTCGGTGGATA
Found at i:181766 original size:30 final size:30
Alignment explanation
Indices: 181731--181794 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
181721 AGAACCGGTA
* * *
181731 GAACCGGCTGAGAACCGGCAAAACCGGGGT
1 GAACCGACTGAAAACCGACAAAACCGGGGT
*
181761 GAACCGACTGAAAACCGACAAAACCGGTGT
1 GAACCGACTGAAAACCGACAAAACCGGGGT
181791 GAAC
1 GAAC
181795 TGCCGATTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.30, T:0.08
Consensus pattern (30 bp):
GAACCGACTGAAAACCGACAAAACCGGGGT
Found at i:183942 original size:26 final size:26
Alignment explanation
Indices: 183906--183963 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
183896 TTTTTCTGGT
*
183906 GAGGTAGAGGTGGTCAGATTTATCTC
1 GAGGTAGAGGTGGCCAGATTTATCTC
*
183932 GAGGTAGAGGTGGCCGGATTTATCTC
1 GAGGTAGAGGTGGCCAGATTTATCTC
183958 GAGGTA
1 GAGGTA
183964 AACTTCTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.22, C:0.12, G:0.38, T:0.28
Consensus pattern (26 bp):
GAGGTAGAGGTGGCCAGATTTATCTC
Found at i:187455 original size:91 final size:91
Alignment explanation
Indices: 187325--187506 Score: 328
Period size: 91 Copynumber: 2.0 Consensus size: 91
187315 GAATCGAGCT
*
187325 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATCAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTAT
187390 GAACTCTCCACTGGAAATGTTGATCC
66 GAACTCTCCACTGGAAATGTTGATCC
* * *
187416 AAGGTTGAACAAGTTCTTCTCATTATCAATTTCTTCTCCCTCGTTGGATGAGTTGTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATCAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTAT
187481 GAACTCTCCACTGGAAATGTTGATCC
66 GAACTCTCCACTGGAAATGTTGATCC
187507 CTCGAGTGAG
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 87 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.38
Consensus pattern (91 bp):
AAGGTTGAACAAGTTCTTCTCATTATCAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATGTTGATCC
Found at i:187594 original size:230 final size:230
Alignment explanation
Indices: 187186--187645 Score: 683
Period size: 230 Copynumber: 2.0 Consensus size: 230
187176 GAAACAAGTT
* *
187186 AAGGCTGAACAAGTTCTTCTCATTATGAACTTATTCTCTCTCAACGGATAAGTTCTTCTCATTAT
1 AAGGCTGAACAAGTTCTTCTCATTATCAACTTATTCTCCCTCAACGGATAAGTTCTTCTCATTAT
* *
187251 GAACTTTCCACTGAGAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGCAATG
66 GAACTCTCCACTGAGAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACAATG
*
187316 AATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCT
131 AATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCT
*
187381 TCTCATTATGAACTCTCCACTG-GAAATGTTGATCC
196 TCTCATTATGAACTCTCCACTGAG-AATGTTCATCC
* * * *** * *
187416 AAGGTTGAACAAGTTCTTCTCATTATCAATTTCTTCTCCCTCGTTGGATGAGTTGTTCTCATTAT
1 AAGGCTGAACAAGTTCTTCTCATTATCAACTTATTCTCCCTCAACGGATAAGTTCTTCTCATTAT
* *
187481 GAACTCTCCACTG-GAAATGTTGATCCCTCGAGTGAGGTGTTTGTTGATTCAACTCCATATACGA
66 GAACTCTCCACTGAG-AATGTTGATCCCTCGAGTGAGGTG-TTGCTGATTCAACTCCATATACAA
* * *
187545 TGAATCGATCT-ATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTT
129 TGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTT
* *
187609 CTTTTCATTATGAACTTTCCACTGAGAATGTTCATCC
194 CTTCTCATTATGAACTCTCCACTGAGAATGTTCATCC
187646 CTCGAGTGAG
Statistics
Matches: 206, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
229 1 0.00
230 173 0.84
231 32 0.16
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (230 bp):
AAGGCTGAACAAGTTCTTCTCATTATCAACTTATTCTCCCTCAACGGATAAGTTCTTCTCATTAT
GAACTCTCCACTGAGAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACAATG
AATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCT
TCTCATTATGAACTCTCCACTGAGAATGTTCATCC
Found at i:187701 original size:139 final size:140
Alignment explanation
Indices: 187416--187784 Score: 609
Period size: 139 Copynumber: 2.6 Consensus size: 140
187406 ATGTTGATCC
* * *
187416 AAGGTTGAACAAGTTCTTCTCATTATCAATTTCTTCTCCCTCGTTGGATGAGTTGTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
*
187481 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTTGTTGATTCAACTCCATATACGAT
66 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTTGCTGATTCAACTCCATATACGAT
*
187546 GAATCGATCT
131 GAATCGAGCT
* * *
187556 -ATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTTTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
* *
187620 GAACTTTCCACT-GAGAATGTTCATCCCTCGAGTGAGGTG-TTGCTGATTCAACTCCATATACGA
66 GAACTCTCCACTGGA-AATGTTGATCCCTCGAGTGAGGTGTTTGCTGATTCAACTCCATATACGA
187683 TGAATCGAGCT
130 TGAATCGAGCT
*
187694 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
187759 GAACTCTCCACTGGAAATGTTGATCC
66 GAACTCTCCACTGGAAATGTTGATCC
187785 AAGGTTGAAC
Statistics
Matches: 210, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
138 35 0.17
139 173 0.82
140 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (140 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTTGCTGATTCAACTCCATATACGAT
GAATCGAGCT
Found at i:187794 original size:230 final size:230
Alignment explanation
Indices: 187558--188008 Score: 753
Period size: 230 Copynumber: 2.0 Consensus size: 230
187548 ATCGATCTAT
*
187558 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTT-TCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAATT-TTTCTCATTATGA
* *
187622 ACTTTCCACT-GAGAATGTTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACGATGA
65 ACTCTCCACTAGA-AATATTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACGATGA
*
187686 ATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTT
129 ATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATTGGATGAGTTCTT
*
187751 CTCATTATGAACTCTCCACTGGAAATGTTGATCCAAG
194 CTCATTATGAACTCTCCACTGAAAATGTTGATCCAAG
* *
187788 GTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCGTTGGATGAATTTTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAATTTTTCTCATTATGAA
* **
187853 CTCTCCACTAGAAATATTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAAT
66 CTCTCCACTAGAAATATTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACGATGAAT
* * *
187918 CGAGCTAATGTTGAATAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATTGGTTGAGTTCTTCT
131 CGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATTGGATGAGTTCTTCT
187983 CATTATGAACTCTCCACTGAAAATGT
196 CATTATGAACTCTCCACTGAAAATGT
188009 ATATTGGTTC
Statistics
Matches: 206, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
229 3 0.01
230 201 0.98
231 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (230 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAATTTTTCTCATTATGAA
CTCTCCACTAGAAATATTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACGATGAAT
CGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATTGGATGAGTTCTTCT
CATTATGAACTCTCCACTGAAAATGTTGATCCAAG
Found at i:187824 original size:91 final size:91
Alignment explanation
Indices: 187694--187875 Score: 310
Period size: 91 Copynumber: 2.0 Consensus size: 91
187684 GAATCGAGCT
*
187694 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAATTCTTCTCATTAT
* *
187759 GAACTCTCCACTGGAAATGTTGATCC
66 GAACTCTCCACTAGAAATATTGATCC
* * *
187785 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCGTTGGATGAATTTTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAATTCTTCTCATTAT
187850 GAACTCTCCACTAGAAATATTGATCC
66 GAACTCTCCACTAGAAATATTGATCC
187876 CTCGAGTGAG
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.38
Consensus pattern (91 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAATTCTTCTCATTAT
GAACTCTCCACTAGAAATATTGATCC
Found at i:187875 original size:369 final size:369
Alignment explanation
Indices: 187191--188008 Score: 1388
Period size: 369 Copynumber: 2.2 Consensus size: 369
187181 AAGTTAAGGC
* * * *
187191 TGAACAAGTTCTTCTCATTATGAACTTATTCTCTCTCAACGGATAAGTTCTTCTCATTATGAACT
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACT
* *
187256 TTCCACTGAGAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGCAATGAATCG
66 TTCCACTGAGAATGTTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACAATGAATCG
187321 AGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCA
131 AGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCA
187386 TTATGAACTCTCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATCAATTTCTT
196 TTATGAACTCTCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATCAATTTCTT
* * *
187451 CTCCCTCGTTGGATGAGTTGTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGA
261 CTCCCTCGTTGGATGAATTGTTCTCATTATGAACTCTCCACTAGAAATATTGATCCCTCGAGTGA
* *
187516 GGTGTTTGTTGATTCAACTCCATATACGATGAATCGATCT-ATGT
326 GGTG-TTGCTGATTCAACTCCATATACGATGAATCGAGCTAATGT
* *
187560 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTTTCATTATGAACT
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACT
*
187625 TTCCACTGAGAATGTTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACGATGAATCG
66 TTCCACTGAGAATGTTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACAATGAATCG
187690 AGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCA
131 AGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCA
*
187755 TTATGAACTCTCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTT-T
196 TTATGAACTCTCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATCAA-TTTCT
*
187819 TCTCCCTCGTTGGATGAATTTTTCTCATTATGAACTCTCCACTAGAAATATTGATCCCTCGAGTG
260 TCTCCCTCGTTGGATGAATTGTTCTCATTATGAACTCTCCACTAGAAATATTGATCCCTCGAGTG
**
187884 AGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCTAATGT
325 AGGTGTTGCTGATTCAACTCCATATACGATGAATCGAGCTAATGT
* * * *
187929 TGAATAAGTTCTTCTCATTATAAACTTCTTCTCCCTCATTGGTTGAGTTCTTCTCATTATGAACT
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACT
* *
187994 CTCCACTGAAAATGT
66 TTCCACTGAGAATGT
188009 ATATTGGTTC
Statistics
Matches: 421, Mismatches: 26, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
368 31 0.07
369 387 0.92
370 3 0.01
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (369 bp):
TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACT
TTCCACTGAGAATGTTCATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATACAATGAATCG
AGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCA
TTATGAACTCTCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATCAATTTCTT
CTCCCTCGTTGGATGAATTGTTCTCATTATGAACTCTCCACTAGAAATATTGATCCCTCGAGTGA
GGTGTTGCTGATTCAACTCCATATACGATGAATCGAGCTAATGT
Found at i:189065 original size:227 final size:230
Alignment explanation
Indices: 188667--189116 Score: 737
Period size: 227 Copynumber: 2.0 Consensus size: 230
188657 GAACTGATAT
188667 ACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAACG
1 ACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAACG
*
188732 AGAAGAGCTTGTTCAAACTTAGCTCGATTAATCACATATGGAGTTGAATCAACAACACCTCACTA
66 AGAAGAACTTGTTCAAACTTAGCTCGATTAATCACATATGGAGTTGAATCAACAACACCTCACTA
*
188797 GAGGGATCAACATTTACAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAA
131 GAGGGATCAACATTTACAGTGGAAAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAA
*
188862 TTCATAATGATAAGAACTTGTTCAACCTTGGATCA
196 TTCATAATGAGAAGAACTTGTTCAACCTTGGATCA
* * *
188897 ACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCATTGA-GG-G-AGAAGTTCATAATG
1 ACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAACG
* * * * * *
188959 AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGGATCAGCAACACCTCACTC
66 AGAAGAACTTGTTCAAACTTAGCTCGATTAATCACATATGGAGTTGAATCAACAACACCTCACTA
*
189024 GAGGGATCAACATTCT-CAGTGGAAAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAA
131 GAGGGATCAACATT-TACAGTGGAAAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAA
*
189088 GTTCATAATGAGAAGAACTTGTTCAACCT
195 ATTCATAATGAGAAGAACTTGTTCAACCT
189117 AGCTCGATTC
Statistics
Matches: 205, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
227 158 0.77
228 2 0.01
229 2 0.01
230 43 0.21
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (230 bp):
ACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATAACG
AGAAGAACTTGTTCAAACTTAGCTCGATTAATCACATATGGAGTTGAATCAACAACACCTCACTA
GAGGGATCAACATTTACAGTGGAAAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAA
TTCATAATGAGAAGAACTTGTTCAACCTTGGATCA
Found at i:189171 original size:138 final size:136
Alignment explanation
Indices: 188891--189254 Score: 572
Period size: 138 Copynumber: 2.6 Consensus size: 136
188881 GTTCAACCTT
*
188891 GGATCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCATTGA-GG-G-AGAAGTTC
1 GGATCAACATTTC-AGTGGAGAGTTCATAATGAGAAGAACTCATCCA-CGAGGGAGAAGAAGTTC
*
188953 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGGATCAGCAACACC
64 ATAATGAGAAGAACTTGTTCAACC-TAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACC
189018 TCACTCGAG
128 TCACTCGAG
*
189027 GGATCAACATTCTCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTC
1 GGATCAACATT-TCAGTGGAGAGTTCATAATGAGAAGAACTCATCC-ACGAGGGAGAAGAAGTTC
*
189092 ATAATGAGAAGAACTTGTTCAACCTAGCTCGATTCATCGCATATGGAGTTGAATTAGCAACACCT
64 ATAATGAGAAGAACTTGTTCAACCTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCT
189157 CACTCGAG
129 CACTCGAG
* * *
189165 GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAACAACTCATCCAACAAGGGAGAAAAAGTTC
1 GGATCAACATTT-CAGTGGAGAGTTCATAATGAGAAGAACTCATCC-ACGAGGGAGAAGAAGTTC
*
189230 ATAATGAGAAGAACTTATTCAACCT
64 ATAATGAGAAGAACTTGTTCAACCT
189255 TGGATCAACA
Statistics
Matches: 212, Mismatches: 10, Indels: 10
0.91 0.04 0.04
Matches are distributed among these distances:
136 44 0.21
137 6 0.03
138 130 0.61
139 32 0.15
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (136 bp):
GGATCAACATTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCACGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCA
CTCGAG
Found at i:189321 original size:91 final size:91
Alignment explanation
Indices: 189165--189346 Score: 310
Period size: 91 Copynumber: 2.0 Consensus size: 91
189155 CTCACTCGAG
189165 GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAACAACTCATCCAACAAGGGAGAAAAAGTTC
1 GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAACAACTCATCCAACAAGGGAGAAAAAGTTC
189230 ATAATGAGAAGAACTTATTCAACCTT
66 ATAATGAGAAGAACTTATTCAACCTT
* *** *
189256 GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCATTGAGGGAGAAAATGTTC
1 GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAACAACTCATCCAACAAGGGAGAAAAAGTTC
*
189321 ATAATGAGAAGAACTTGTTCAACCTT
66 ATAATGAGAAGAACTTATTCAACCTT
189347 AGCTCGATTC
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (91 bp):
GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAACAACTCATCCAACAAGGGAGAAAAAGTTC
ATAATGAGAAGAACTTATTCAACCTT
Found at i:189429 original size:230 final size:229
Alignment explanation
Indices: 189027--189485 Score: 737
Period size: 230 Copynumber: 2.0 Consensus size: 229
189017 CTCACTCGAG
189027 GGATCAACATTCTCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTC
1 GGATCAACATTCTCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTC
*
189092 ATAATGAGAAGAACTTGTTCAACCTAGCTCGATTCATCGCATATGGAGTTGAATTAGCAACACCT
66 ATAATGAGAAGAACTTGTTCAACCTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCT
* *
189157 CACTCGAGGGATCAACATTTCCAGTGGAGAGTTCATAATGAGAACAACTCATCCAACAAGGGAGA
131 CACTCGAGGGATCAACATTTCCAGTGGAAAGTTCATAATGAGAACAACTCATCCAACAAGAGAGA
189222 AAAAGTTCATAATGAGAAGAACTTATTCAACCTT
196 AAAAGTTCATAATGAGAAGAACTTATTCAACCTT
* * *
189256 GGATCAACATT-TCCAGTGGAGAGTTCATAATGAGAATAACTCATCC-ATTGAGGGAGAA-AATG
1 GGATCAACATTCT-CAGTGGAAAGTTCATAATGAGAAGAACTCATCCGA-CGAGGGAGAAGAA-G
189318 TTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAAC
63 TTCATAATGAGAAGAACTTGTTCAACC-TAGCTCGATTCATCGCATATGGAGTTGAATCAGCAAC
* * **
189383 ACCTCACTCGAGGGATCAACA-TTCTCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGATGAG
127 ACCTCACTCGAGGGATCAACATTTC-CAGTGGAAAGTTCATAATGAGAACAACTCATCCAACAAG
* *
189447 AGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
191 AGAGAAAAAGTTCATAATGAGAAGAACTTATTCAACCTT
189486 AACTTGTTTC
Statistics
Matches: 213, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
228 4 0.02
229 82 0.38
230 127 0.60
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (229 bp):
GGATCAACATTCTCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCT
CACTCGAGGGATCAACATTTCCAGTGGAAAGTTCATAATGAGAACAACTCATCCAACAAGAGAGA
AAAAGTTCATAATGAGAAGAACTTATTCAACCTT
Found at i:192033 original size:53 final size:53
Alignment explanation
Indices: 191956--192064 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
191946 CACAAAGCTC
191956 AAAACTAGTCTTATCGAACGATCATTGAAGGAGTTCAAAGTTTTATAACATCA
1 AAAACTAGTCTTATCGAACGATCATTGAAGGAGTTCAAAGTTTTATAACATCA
192009 AAAACTAGTCTTATCGAACGATCATTGAAGGAGTTCAAAGTTTTATAACATCA
1 AAAACTAGTCTTATCGAACGATCATTGAAGGAGTTCAAAGTTTTATAACATCA
192062 AAA
1 AAA
192065 GTTTAGATAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (53 bp):
AAAACTAGTCTTATCGAACGATCATTGAAGGAGTTCAAAGTTTTATAACATCA
Found at i:198679 original size:20 final size:20
Alignment explanation
Indices: 198636--198676 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
198626 AGACCATAGT
* *
198636 ATTTTAGAGTTTTAAATTGA
1 ATTTTAGAATTTTAAAGTGA
198656 ATTTTACGAATTTTAAAGTGA
1 ATTTTA-GAATTTTAAAGTGA
198677 TTTATGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (20 bp):
ATTTTAGAATTTTAAAGTGA
Found at i:202205 original size:24 final size:24
Alignment explanation
Indices: 202178--202229 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
202168 TATATTAATA
*
202178 TTTA-ATTTTTATATCTCTTAAATT
1 TTTATATTTTCATAT-TCTTAAATT
*
202202 TTTATATTTTCGTATTCTTAAATT
1 TTTATATTTTCATATTCTTAAATT
202226 TTTA
1 TTTA
202230 CATTCCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTATATTTTCATATTCTTAAATT
Found at i:208611 original size:3 final size:3
Alignment explanation
Indices: 208603--208629 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
208593 GAGGTAAAGA
208603 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
208630 TATGAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:210417 original size:28 final size:28
Alignment explanation
Indices: 210325--210422 Score: 74
Period size: 28 Copynumber: 3.5 Consensus size: 28
210315 TGGATGCTTT
* * *
210325 TTATTTTAATTTGTAAAAAATATAGGGTA
1 TTATTGTAATTTATAAAAATTATA-GGTA
* * * ** *
210354 TTATTGTAATTT-GAAAAATGCAGACCTT
1 TTATTGTAATTTATAAAAAT-TATAGGTA
210382 TTCA-TGTAATTTATAAAAATTATAGGTA
1 TT-ATTGTAATTTATAAAAATTATAGGTA
210410 TTATTGTAATTTA
1 TTATTGTAATTTA
210423 GAGAAGTTTT
Statistics
Matches: 51, Mismatches: 14, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
27 1 0.02
28 30 0.59
29 20 0.39
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (28 bp):
TTATTGTAATTTATAAAAATTATAGGTA
Found at i:210469 original size:29 final size:28
Alignment explanation
Indices: 210386--210485 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 28
210376 GACCTTTTCA
* *
210386 TGTAATTTATAAAAATTATAGGTA-TTAT
1 TGTAATTTATAAAAGTT-TTGGTATTTAT
* * * *
210414 TGTAATTTAGAGAAGTTTT-TTCTTTTAT
1 TGTAATTTATAAAAGTTTTGGT-ATTTAT
210442 TGTAATTTATAAATAGTTTTGGTATTTAT
1 TGTAATTTATAAA-AGTTTTGGTATTTAT
*
210471 TGTAATATTAAAAAA
1 TGTAAT-TTATAAAA
210486 TTGACTTCTA
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 29 0.52
29 18 0.32
30 7 0.12
ACGTcount: A:0.37, C:0.01, G:0.12, T:0.50
Consensus pattern (28 bp):
TGTAATTTATAAAAGTTTTGGTATTTAT
Found at i:212311 original size:29 final size:29
Alignment explanation
Indices: 212277--212335 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
212267 CCTAAATTAA
212277 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
212306 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
212335 T
1 T
212336 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:216995 original size:29 final size:29
Alignment explanation
Indices: 216961--217019 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
216951 CCTAAATTAA
*
216961 TTTGATGTCATTTCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
216990 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
217019 T
1 T
217020 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:221684 original size:19 final size:19
Alignment explanation
Indices: 221631--221687 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 19
221621 TATATATATA
*
221631 TACAAAGACCAAATTCGAT
1 TACAAAGACCAAATTCGAG
*
221650 TAAAGAAAATGACCAAATTCGAG
1 T--A-CAAA-GACCAAATTCGAG
221673 TACAAAGACCAAATT
1 TACAAAGACCAAATT
221688 TACAACATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 10 0.32
20 3 0.10
21 2 0.06
22 3 0.10
23 13 0.42
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (19 bp):
TACAAAGACCAAATTCGAG
Found at i:223228 original size:12 final size:12
Alignment explanation
Indices: 223211--223235 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
223201 CGAAAATTAG
223211 AAAATTTAAATT
1 AAAATTTAAATT
223223 AAAATTTAAATT
1 AAAATTTAAATT
223235 A
1 A
223236 CTCGATTCGA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTTAAATT
Found at i:224736 original size:25 final size:24
Alignment explanation
Indices: 224700--224768 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 24
224690 TTGGACCTGA
224700 AAAAACAA-AATAAATAA-AATAAAT
1 AAAAACAATAATAAA-AATAA-AAAT
224724 -AAAACGAATAATAAAAATAAAAAT
1 AAAAAC-AATAATAAAAATAAAAAT
224748 AAAAACAAATAATAAAAATAA
1 AAAAAC-AATAATAAAAATAA
224769 TTATATATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 5 0.12
24 8 0.20
25 27 0.68
ACGTcount: A:0.78, C:0.04, G:0.01, T:0.16
Consensus pattern (24 bp):
AAAAACAATAATAAAAATAAAAAT
Found at i:224768 original size:9 final size:9
Alignment explanation
Indices: 224706--224769 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
224696 CTGAAAAAAC
224706 AAAATAA-A
1 AAAATAATA
224714 TAAAATAAATA
1 -AAAAT-AATA
**
224725 AAACGAATA
1 AAAATAATA
224734 ATAAA-AATA
1 A-AAATAATA
*
224743 AAAATAAAA
1 AAAATAATA
224752 ACAAATAATA
1 A-AAATAATA
224762 AAAATAAT
1 AAAATAAT
224770 TATATATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
8 3 0.07
9 26 0.58
10 15 0.33
11 1 0.02
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.19
Consensus pattern (9 bp):
AAAATAATA
Found at i:224929 original size:12 final size:12
Alignment explanation
Indices: 224893--224933 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
224883 TATATATTAC
*
224893 ATATATATATAT
1 ATATATATATGT
224905 ATATATATATGT
1 ATATATATATGT
*
224917 ATATATATTTGT
1 ATATATATATGT
224929 ATATA
1 ATATA
224934 AATCAAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (12 bp):
ATATATATATGT
Found at i:224933 original size:2 final size:2
Alignment explanation
Indices: 224883--224924 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
224873 TTTCAAAGAT
* *
224883 TA TA TA T- TA CA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
224924 T
1 T
224925 TTGTATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Done.