Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001902.1 Hibiscus syriacus cultivar Beakdansim tig00003853_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: 166863
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4602 original size:13 final size:13
Alignment explanation
Indices: 4584--4612 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4574 AAATCGTTGG
4584 AACTTAGATTTTA
1 AACTTAGATTTTA
4597 AACTTAGATTTTA
1 AACTTAGATTTTA
4610 AAC
1 AAC
4613 CGTATCAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (13 bp):
AACTTAGATTTTA
Found at i:10486 original size:2 final size:2
Alignment explanation
Indices: 10479--10527 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
10469 AACCGCTGTG
10479 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10521 TA TA TA T
1 TA TA TA T
10528 CCATCCGTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13993 original size:17 final size:17
Alignment explanation
Indices: 13971--14009 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
13961 AACGGTCAAC
13971 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
13988 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
14005 GGTCA
1 GGTCA
14010 GACCGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:14029 original size:19 final size:19
Alignment explanation
Indices: 14007--14104 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 19
13997 TCGGGTCGGG
14007 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* *
14026 TCAGACCAGTCAAATCGGT
1 TCAGACCGGTCAAACCGGT
*
14045 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
* *
14064 TCAAACCGGTCAGAACTGGT
1 TCAGACCGGTCA-AACCGGT
* * *
14084 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
14104 T
1 T
14105 TCCAGAAGCC
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.05
19 35 0.56
20 15 0.24
21 9 0.15
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:14061 original size:10 final size:10
Alignment explanation
Indices: 14011--14104 Score: 72
Period size: 9 Copynumber: 9.7 Consensus size: 10
14001 GTCGGGTCAG
14011 ACCGG-TCAA
1 ACCGGTTCAA
*
14020 ACCGGTTCAG
1 ACCGGTTCAA
*
14030 ACCAG-TCAA
1 ACCGGTTCAA
* *
14039 ATCGGTTCGA
1 ACCGGTTCAA
*
14049 ACCGGTTGAA
1 ACCGGTTCAA
14059 ACCGG-TCAA
1 ACCGGTTCAA
14068 ACCGG-TCAGA
1 ACCGGTTCA-A
* *
14078 ACTGGTTGAAA
1 ACCGGTT-CAA
14089 ACCGGTT-AA
1 ACCGGTTCAA
14098 ACCGGTT
1 ACCGGTT
14105 TCCAGAAGCC
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
9 31 0.46
10 27 0.40
11 8 0.12
12 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:21395 original size:17 final size:17
Alignment explanation
Indices: 21373--21407 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21363 GTCAACGATG
21373 AACGGTCGGGTCGGGTC
1 AACGGTCGGGTCGGGTC
21390 AACGGTCGGGTCGGGTC
1 AACGGTCGGGTCGGGTC
21407 A
1 A
21408 GACCGGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (17 bp):
AACGGTCGGGTCGGGTC
Found at i:21452 original size:19 final size:19
Alignment explanation
Indices: 21405--21444 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
21395 TCGGGTCGGG
21405 TCAGACCGGTCAAATTGGT
1 TCAGACCGGTCAAATTGGT
21424 TCAGACCGGTCAAATTGGT
1 TCAGACCGGTCAAATTGGT
21443 TC
1 TC
21445 GAACCGGTTG
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:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (19 bp):
TCAGACCGGTCAAATTGGT
Found at i:21459 original size:10 final size:10
Alignment explanation
Indices: 21421--21502 Score: 55
Period size: 9 Copynumber: 8.4 Consensus size: 10
21411 CGGTCAAATT
*
21421 GGTTCAGACC
1 GGTTCAAACC
**
21431 GG-TCAAATT
1 GGTTCAAACC
*
21440 GGTTCGAACC
1 GGTTCAAACC
*
21450 GGTTGAAACC
1 GGTTCAAACC
21460 GG-TCAAACC
1 GGTTCAAACC
*
21469 GG-TCAGAACT
1 GGTTCA-AACC
*
21479 GGTTGAAAACC
1 GGTT-CAAACC
21490 GGTT-AAACC
1 GGTTCAAACC
21499 GGTT
1 GGTT
21503 TCCAGCAGCC
Statistics
Matches: 56, Mismatches: 12, Indels: 9
0.73 0.16 0.12
Matches are distributed among these distances:
9 26 0.46
10 21 0.38
11 8 0.14
12 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (10 bp):
GGTTCAAACC
Found at i:21460 original size:29 final size:30
Alignment explanation
Indices: 21428--21501 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
21418 ATTGGTTCAG
**
21428 ACCGGTCAAATTGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
*
21457 ACCGGTCAAACCGGTCAGAACTGGTTGAAA
1 ACCGGTCAAACCGGTCAGAACCGGTTGAAA
*
21487 ACCGGTTAAACCGGT
1 ACCGGTCAAACCGGT
21502 TTCCAGCAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 2 0.05
29 21 0.54
30 16 0.41
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (30 bp):
ACCGGTCAAACCGGTCAGAACCGGTTGAAA
Found at i:28789 original size:12 final size:12
Alignment explanation
Indices: 28751--28800 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
28741 AACGGTCAAC
28751 GGTCAACGGTCG
1 GGTCAACGGTCG
*
28763 GGTC--GGGTCG
1 GGTCAACGGTCG
*
28773 GGTCAACGGTTG
1 GGTCAACGGTCG
28785 GGTCAACGGTCG
1 GGTCAACGGTCG
28797 GGTC
1 GGTC
28801 GGGTCAGACC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 9 0.28
12 23 0.72
ACGTcount: A:0.12, C:0.22, G:0.46, T:0.20
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:28862 original size:11 final size:9
Alignment explanation
Indices: 28808--28873 Score: 51
Period size: 10 Copynumber: 6.8 Consensus size: 9
28798 GTCGGGTCAG
*
28808 ACCGGTCAA
1 ACCGGTTAA
*
28817 ACCGGTTCGA
1 ACCGGTT-AA
28827 ACCGGTTGAA
1 ACCGGTT-AA
* *
28837 ATCGGTCAGA
1 ACCGGTTA-A
28847 ACCGGTTGAAA
1 ACCGGTT--AA
28858 ACCGGTTAA
1 ACCGGTTAA
28867 ACCGGTT
1 ACCGGTT
28874 TCCAGCAGCC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
9 16 0.36
10 20 0.44
11 8 0.18
12 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:28869 original size:20 final size:19
Alignment explanation
Indices: 28815--28873 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
28805 CAGACCGGTC
*
28815 AAACCGGTTCGAACCGGTTG
1 AAACCGGTT-AAACCGGTTG
* *
28835 AAATCGGTCAGAACCGGTTG
1 AAACCGGTTA-AACCGGTTG
28855 AAAACCGGTTAAACCGGTT
1 -AAACCGGTTAAACCGGTT
28874 TCCAGCAGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 24 0.75
21 8 0.25
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (19 bp):
AAACCGGTTAAACCGGTTG
Found at i:28873 original size:9 final size:10
Alignment explanation
Indices: 28815--28873 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
28805 CAGACCGGTC
28815 AAACCGGTTCG
1 AAACCGGTT-G
28826 -AACCGGTTG
1 AAACCGGTTG
* *
28835 AAATCGG-TC
1 AAACCGGTTG
28844 AGAACCGGTTG
1 A-AACCGGTTG
28855 AAAACCGGTT-
1 -AAACCGGTTG
28865 AAACCGGTT
1 AAACCGGTT
28874 TCCAGCAGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
9 12 0.30
10 18 0.45
11 9 0.22
12 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (10 bp):
AAACCGGTTG
Found at i:31649 original size:20 final size:20
Alignment explanation
Indices: 31601--31649 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
31591 TGGACTTATG
**
31601 TCTTCAAAATTCTTCTAACA
1 TCTTCAAAGCTCTTCTAACA
*
31621 TTTTCAAAGCTCTTCTAACA
1 TCTTCAAAGCTCTTCTAACA
31641 TCTTCAAAG
1 TCTTCAAAG
31650 AACCATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (20 bp):
TCTTCAAAGCTCTTCTAACA
Found at i:31806 original size:31 final size:30
Alignment explanation
Indices: 31760--31839 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
31750 ATCGATAATA
*
31760 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAA-TATTTTATAATCATTTA-ATAAATT
* *
31791 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATCATTTAATAAATT
31822 TAATAAGTATTTTATAAT
1 TAATAA-TATTTTATAAT
31840 TTTTAAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 36 0.86
32 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTATAATCATTTAATAAATT
Found at i:31817 original size:19 final size:20
Alignment explanation
Indices: 31793--31842 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
31783 GATAAATTTA
*
31793 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
31812 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
31833 TT-ATAATTTT
1 TTAATAATTTT
31843 TAAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:32600 original size:31 final size:30
Alignment explanation
Indices: 32565--32651 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
32555 TCAATAAAGT
32565 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
32596 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
32627 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
32652 TATTATCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:32627 original size:20 final size:20
Alignment explanation
Indices: 32560--32627 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
32550 TTTCATCAAT
*
32560 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
32578 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
32599 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
32618 ATAA-ATTTAT
1 A-AAGATTTAT
32628 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:33159 original size:22 final size:20
Alignment explanation
Indices: 33118--33160 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
33108 TCGCACATAA
*
33118 TTTTATTTAATTAAAATTAT
1 TTTTATTTAAATAAAATTAT
33138 TTTTATTTTAAATATAAATTAT
1 TTTTA-TTTAAATA-AAATTAT
33160 T
1 T
33161 GATCATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
22 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATTTAAATAAAATTAT
Found at i:33426 original size:60 final size:60
Alignment explanation
Indices: 33354--33470 Score: 216
Period size: 60 Copynumber: 1.9 Consensus size: 60
33344 AAAAGCATAC
*
33354 TATTATTATAATATTAATTATCTTTCCTTTTTCTAATTAAATTAATATAAAAATAAATGT
1 TATTATTATAATATTAATTATCTTTCATTTTTCTAATTAAATTAATATAAAAATAAATGT
*
33414 TATTATTATAATATTAATTATCTTTCATTTTTCTAATTAAATTAATATAAGAATAAA
1 TATTATTATAATATTAATTATCTTTCATTTTTCTAATTAAATTAATATAAAAATAAA
33471 CATAGTATCT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.50
Consensus pattern (60 bp):
TATTATTATAATATTAATTATCTTTCATTTTTCTAATTAAATTAATATAAAAATAAATGT
Found at i:35311 original size:228 final size:228
Alignment explanation
Indices: 34376--35313 Score: 925
Period size: 228 Copynumber: 4.1 Consensus size: 228
34366 TGATTAATAG
* * * * * *
34376 ATGCAAATCTTTGTTAAA-ACCCTCACTGGCAAGACCATCACCCTT-GAGGTGGAGAGTTCGGAC
1 ATGCAAATCTTTG-TAAAGACTCTTACTGGAAAGACCATCA-CCTTGGAGGTTGAAAGTTCAGAC
* * * *
34439 ACCATTGACAATGTGAAGGCAAAGATCCAAGACAAGGAAGGAATACCCCCAGACCAGCAGAGGCT
64 ACCATTGACAATGTGAAGGCAAAGATCCAAGACAAAGAAGGAATCCCCCCAGACCAACAAAGGCT
* * * ** *
34504 TATCTTTGCTGGCAAGCAACTCGAAGATGGTCGAACACTGGCCGACTACAACATCCAGAAA-GAG
129 TATCTTTGCAGGAAAGCAACTTGAAGATGGAAGAACACTGGCCGACTATAACATCCA-AAAGGAG
* * *
34568 TCCACACTCCACCTGGTGCTTCGACTTCGAGGTGGT
193 TCCACTCTCCACCTGGTGCTTCGCCTTCGTGGTGGT
* * * * * * *
34604 ATGCAAATCTTTGTCAAGCCTCTCACTGGAAAGACGATTACCTTGGAGGTTGAAAGCTCCGACAC
1 ATGCAAATCTTTGTAAAGACTCTTACTGGAAAGACCATCACCTTGGAGGTTGAAAGTTCAGACAC
* * * * * * * * * * *
34669 TACTGATAATGTCAAGGCTAAGATCCAAGATAAAGAAGGAATCCCTCAAGATCAACAGAGGTTTA
66 CATTGACAATGTGAAGGCAAAGATCCAAGACAAAGAAGGAATCCCCCCAGACCAACAAAGGCTTA
* * ** * * *
34734 TCTTTGCTGGAAAGCAGCTTGAAGATGGTCGGACACTGGCTGACTATAACATCCAGAAGGAGTCC
131 TCTTTGCAGGAAAGCAACTTGAAGATGGAAGAACACTGGCCGACTATAACATCCAAAAGGAGTCC
* * * *
34799 ACCCTCCACCTAGTGCTTCGTCTTCGTGGTGGC
196 ACTCTCCACCTGGTGCTTCGCCTTCGTGGTGGT
* * * * *
34832 ATGCAAATCTTTGTCAAGACTCTTACTGGAAAGACAATTACCTTGGAGGTTGAGAGTTCAGATAC
1 ATGCAAATCTTTGTAAAGACTCTTACTGGAAAGACCATCACCTTGGAGGTTGAAAGTTCAGACAC
* * * * * * *
34897 CATTGATAATGTGAAAGCCAAA-ATTCAGGACAAAGAAGGAATTCCACCAGACCAACAAA-GATT
66 CATTGACAATGTG-AAGGCAAAGATCCAAGACAAAGAAGGAATCCCCCCAGACCAACAAAGGCTT
* * * * * * *
34960 GATTTTTGCAGGAAAACAGCTTGAAGATGGAAGAACTCTTGCCGATTATAATATCCAAAAGGAGT
130 -ATCTTTGCAGGAAAGCAACTTGAAGATGGAAGAACACTGGCCGACTATAACATCCAAAAGGAGT
* ** * * *
35025 CTACTCTCCATTTGGTTCTCCGCCTTCGTGGAGGT
194 CCACTCTCCACCTGGTGCTTCGCCTTCGTGGTGGT
* * * *
35060 ATGCATATCTTTGTGAAGACTCTTACTGGAAAGACCATCACTTTGGAAGTTGAAAGTTCAGACAC
1 ATGCAAATCTTTGTAAAGACTCTTACTGGAAAGACCATCACCTTGGAGGTTGAAAGTTCAGACAC
* * * * * *
35125 AATTGACAATGTGAAGGCAAAGATCCAAGACAAGGAGGGTATCCCCCCAGACCAGCAAAGGCTCA
66 CATTGACAATGTGAAGGCAAAGATCCAAGACAAAGAAGGAATCCCCCCAGACCAACAAAGGCTTA
* * * ** * * *
35190 TTTTTGCAGGCAAGCAACTTGAAGATGGAAGGACGTTGGCTGACTATAATATCCAAAAGGAGTCA
131 TCTTTGCAGGAAAGCAACTTGAAGATGGAAGAACACTGGCCGACTATAACATCCAAAAGGAGTCC
* * *
35255 ACTCTTCACTTGGTG-TTGCGCCTGCGTGGTGGT
196 ACTCTCCACCTGGTGCTT-CGCCTTCGTGGTGGT
*
35288 ATGCAGATCTTTGTAAAGACTCTTAC
1 ATGCAAATCTTTGTAAAGACTCTTAC
35314 AGTTTTGCTC
Statistics
Matches: 585, Mismatches: 117, Indels: 16
0.81 0.16 0.02
Matches are distributed among these distances:
227 20 0.03
228 557 0.95
229 8 0.01
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (228 bp):
ATGCAAATCTTTGTAAAGACTCTTACTGGAAAGACCATCACCTTGGAGGTTGAAAGTTCAGACAC
CATTGACAATGTGAAGGCAAAGATCCAAGACAAAGAAGGAATCCCCCCAGACCAACAAAGGCTTA
TCTTTGCAGGAAAGCAACTTGAAGATGGAAGAACACTGGCCGACTATAACATCCAAAAGGAGTCC
ACTCTCCACCTGGTGCTTCGCCTTCGTGGTGGT
Found at i:48156 original size:13 final size:12
Alignment explanation
Indices: 48122--48150 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
48112 AGAATGCTGG
48122 AAAAAAAT-AAT
1 AAAAAAATAAAT
48133 AAAAAAATAAAT
1 AAAAAAATAAAT
48145 AAAAAA
1 AAAAAA
48151 GGTAAAGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAATAAAT
Found at i:48339 original size:21 final size:23
Alignment explanation
Indices: 48313--48375 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
48303 TCTTTAATCA
* *
48313 ATTTAAAT-TTTAAAAT-ATTAT
1 ATTTAAATATTAAAAATAATAAT
48334 ATTTAAATAATTAAAAATAATAAT
1 ATTTAAAT-ATTAAAAATAATAAT
48358 ATTTAAACTATTCAAAAA
1 ATTTAAA-TATT-AAAAA
48376 AATTCATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 8 0.23
23 7 0.20
24 14 0.40
25 6 0.17
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTTAAATATTAAAAATAATAAT
Found at i:50833 original size:7 final size:7
Alignment explanation
Indices: 50821--50846 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
50811 TCTGGCTTTA
50821 ACTCCTC
1 ACTCCTC
50828 ACTCCTC
1 ACTCCTC
50835 ACTCCTC
1 ACTCCTC
50842 ACTCC
1 ACTCC
50847 ATAGTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.58, G:0.00, T:0.27
Consensus pattern (7 bp):
ACTCCTC
Found at i:57281 original size:21 final size:21
Alignment explanation
Indices: 57255--57294 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
57245 CAGAACCCCA
*
57255 GGGGGGTATC-GATTCCCCTGT
1 GGGGGGAATCGGA-TCCCCTGT
57276 GGGGGGAATCGGATCCCCT
1 GGGGGGAATCGGATCCCCT
57295 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.12, C:0.25, G:0.40, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGGATCCCCTGT
Found at i:57326 original size:21 final size:23
Alignment explanation
Indices: 57275--57326 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
57265 GATTCCCCTG
57275 TGGGGGGAATCGGATCCCCTTCA
1 TGGGGGGAATCGGATCCCCTTCA
** *
57298 AAGGGGGAATCGG-TTCCC-TCA
1 TGGGGGGAATCGGATCCCCTTCA
57319 TGGGGGGA
1 TGGGGGGA
57327 TTGATTCACT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 9 0.38
22 4 0.17
23 11 0.46
ACGTcount: A:0.19, C:0.21, G:0.40, T:0.19
Consensus pattern (23 bp):
TGGGGGGAATCGGATCCCCTTCA
Found at i:61177 original size:22 final size:21
Alignment explanation
Indices: 61135--61174 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
61125 GAGTTTGTTT
*
61135 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
61156 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
61175 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:66163 original size:20 final size:20
Alignment explanation
Indices: 66118--66175 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
66108 GCATGGGTAG
66118 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
66142 TGCATTGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
66162 TGCATCGATGCACT
1 TGCATCGATGCACT
66176 TCAATGGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:70238 original size:20 final size:20
Alignment explanation
Indices: 70193--70250 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
70183 GCATGGGTAG
70193 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
70217 TGCATTGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
70237 TGCATCGATGCACT
1 TGCATCGATGCACT
70251 TCAAGGGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:73799 original size:18 final size:18
Alignment explanation
Indices: 73776--73815 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
73766 AAAGGCGATG
*
73776 GCGGCATCATATATGGTT
1 GCGGCATCATAAATGGTT
73794 GCGGCATCATAAATGGTT
1 GCGGCATCATAAATGGTT
73812 GCGG
1 GCGG
73816 TGGCTACTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.28
Consensus pattern (18 bp):
GCGGCATCATAAATGGTT
Found at i:75538 original size:17 final size:18
Alignment explanation
Indices: 75495--75535 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
75485 AAATTATATT
75495 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
75512 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
75530 ATTAAA
1 AGTAAA
75536 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:79970 original size:181 final size:182
Alignment explanation
Indices: 79635--80107 Score: 651
Period size: 181 Copynumber: 2.6 Consensus size: 182
79625 GATCCAAATT
* * * ** **
79635 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGCCAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * *
79700 AAACCGGTAAAGCGCTACCGGATACATTTAAATTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
79765 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTAGATACTTTTA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTAGATACTTTAA
* * *
79817 AAAAATGTATCGATCCAAAACGATATACCAAGTAAAAATATGATAAAACCGATAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
79882 AAACCGGTAAAACGTTACTGTATATATTGAAAGTGTCAATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** * *
79946 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTAGATACTTTAA
* * * *
79998 AAAAATATATCGATCCACAACGATATAACATGTAAAAATATGATAAAATCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
80063 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
80108 CGTAAGTACG
Statistics
Matches: 253, Mismatches: 38, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
181 162 0.64
182 91 0.36
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTAGATACTTTAA
Found at i:82327 original size:21 final size:21
Alignment explanation
Indices: 82301--82341 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
82291 AAGACAATCA
82301 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
* *
82322 AGAGTCGAAGATACACTTGA
1 AGAGTCGAAGAGAAACTTGA
82342 GAGGCATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAT
Found at i:82421 original size:33 final size:33
Alignment explanation
Indices: 82378--82443 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
82368 AAATAGATGG
*
82378 AGTGGCGAAAGAAG-TAGAGGTGTTGAGGGGTGA
1 AGTGGCGAAAGAAGTTAG-GGTGTTAAGGGGTGA
* * *
82411 AGTGGTGAAAGGAGTTCGGGTGTTAAGGGGTGA
1 AGTGGCGAAAGAAGTTAGGGTGTTAAGGGGTGA
82444 TATTAAGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.27, C:0.03, G:0.48, T:0.21
Consensus pattern (33 bp):
AGTGGCGAAAGAAGTTAGGGTGTTAAGGGGTGA
Found at i:84258 original size:19 final size:19
Alignment explanation
Indices: 84234--84282 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
84224 AATGTAGGGT
84234 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
84253 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
84272 TAATTTTGTAT
1 TAATTTTGTAT
84283 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:84746 original size:200 final size:200
Alignment explanation
Indices: 84395--85158 Score: 1350
Period size: 200 Copynumber: 3.8 Consensus size: 200
84385 AATTTACAAT
84395 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
84460 CAAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
84525 ATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTATAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
84590 AATGA
196 AATGA
* *
84595 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCTATACATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
84660 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
84725 ATGAGAGAATAGGTATAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTATAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
84790 AATGA
196 AATGA
*
84795 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATAAATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
84860 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
84925 ATGAGAGAATAAGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
131 ATGAGAGAATAGGTATAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
84990 AATGA
196 AATGA
**
84995 ATGGCAAACAAAGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
85060 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCTGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
85125 ATGAGAGAATTGGTATATAAT-ATGTATCGACACT
131 ATGAGAGAATAGGTATA-AATAATGTGTCGACACT
85159 GTGTATATTA
Statistics
Matches: 541, Mismatches: 22, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
200 538 0.99
201 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTATAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:85457 original size:23 final size:21
Alignment explanation
Indices: 85414--85457 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
85404 ATTACATAAC
*
85414 TTTAAAAAAGTATCGATCTTT
1 TTTAAAAAAGTATCGAACTTT
*
85435 TTTATAAAAAGTATGGACACTTT
1 TTTA-AAAAAGTATCGA-ACTTT
85458 CAATATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (21 bp):
TTTAAAAAAGTATCGAACTTT
Found at i:85506 original size:23 final size:23
Alignment explanation
Indices: 85475--85547 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
85465 ATAGGTAAAA
*
85475 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
85498 ATATAATGTAATAAGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
85521 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
85544 ATAT
1 ATAT
85548 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:85992 original size:23 final size:23
Alignment explanation
Indices: 85960--86032 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
85950 ATAGGTAAAA
* *
85960 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
85983 ATATAGTGTAATATGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
86006 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
86029 ATAT
1 ATAT
86033 TGTAAAGTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:86091 original size:485 final size:486
Alignment explanation
Indices: 85182--86435 Score: 2230
Period size: 485 Copynumber: 2.6 Consensus size: 486
85172 GCGTCTAATG
* *
85182 ATTTA-TTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACA
1 ATTTATTTTTTTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACA
* *
85246 TATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATC
66 TATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATC
* * * *
85311 AAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTATAAGTGGAAAACATG
131 AAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATT
*
85376 AAACACTATTTAAAAAATTAAAACATAAATTACATAACTTT-AAAAAAGTATCGATCTTTTTTAT
196 AAACACTA-TTAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCTTTTTTAT
* *
85440 AAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAAT
260 AAAAAATATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCACTTATATAAT
85505 GTAATAAGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTA
325 GTAATAAGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTA
*
85570 TAAAAGTGTCCATACTTATTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTTAGTGAGTTT
390 TAAAAGTGTCCATACTTATTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTT
85635 TAAGATATCAATTTAGTAATTATATGTATCTA
455 TAAGATATCAATTTAGTAATTATATGTATCTA
85667 ATTTATTTTTTTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATA-TACA
1 ATTTATTTTTTTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACA
85731 TATTTATTATTATCTTTGGTTAATATTGTT-AATTTAAATTCTAAATATTATTTTATAAAATATC
66 TATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATC
*
85795 AAAACAATCAAATGATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATT
131 AAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATT
*
85860 AAACACTATTAAAAAATTTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTAT
196 AAACACTATTAAAAAA-TTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCTTTTTTAT
* *
85925 AAAAAATATGGACACTTTTAATATAATAGGTAAAAATATGATGTAATAGGTAGCACTTATATAGT
260 AAAAAATATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCACTTATATAAT
*
85990 GTAATATGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTA
325 GTAATAAGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTA
86055 TAAAAGTGTCCATACTTATTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTT
390 TAAAAGTGTCCATACTTATTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTT
86120 TAAGATATCAATTTAGTAATTATATGTATCTA
455 TAAGATATCAATTTAGTAATTATATGTATCTA
86152 ATGATT-TATTTTTTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATATT
1 AT--TTAT-TTTTTTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATATT
86216 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
63 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
*
86281 ATTAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
128 ATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
*
86346 ATTAAACACTATTAAAAAAATTGAAATATAAATTACATAACTTTAAAAAAAGTATCGATCTTTTT
193 ATTAAACACTATT-AAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCTTTTT
*
86411 TATGAAAAAATATAGACACTTTCAA
257 TAT-AAAAAATATGGACACTTTCAA
86436 CATATTATAA
Statistics
Matches: 736, Mismatches: 23, Indels: 15
0.95 0.03 0.02
Matches are distributed among these distances:
483 8 0.01
484 123 0.17
485 284 0.39
486 53 0.07
487 56 0.08
488 34 0.05
489 153 0.21
490 25 0.03
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (486 bp):
ATTTATTTTTTTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACA
TATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATC
AAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATT
AAACACTATTAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCTTTTTTATA
AAAAATATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCACTTATATAATG
TAATAAGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTAT
AAAAGTGTCCATACTTATTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
AAGATATCAATTTAGTAATTATATGTATCTA
Found at i:86538 original size:23 final size:23
Alignment explanation
Indices: 86509--86556 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
86499 AAATAGGTCA
*
86509 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAGTACATT
*
86532 ATATAAGCGCTACCTAGTATATT
1 ATATAAGCGCTACCTAGTACATT
86555 AT
1 AT
86557 TGTACTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTAGTACATT
Found at i:88525 original size:15 final size:15
Alignment explanation
Indices: 88505--88536 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
88495 TTAAACACAA
88505 TAATGGAAATTCTTC
1 TAATGGAAATTCTTC
88520 TAATGGAAATTCTTC
1 TAATGGAAATTCTTC
88535 TA
1 TA
88537 GCATAAACCT
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:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (15 bp):
TAATGGAAATTCTTC
Found at i:89147 original size:24 final size:24
Alignment explanation
Indices: 89108--89154 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
89098 ATATGATATT
*
89108 ATTTATATTTAGATATTATGTAAAA
1 ATTTATATTTAAATATT-TGTAAAA
89133 ATTTAT-TTTAAATATTTGTAAA
1 ATTTATATTTAAATATTTGTAAA
89155 CTCACATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 9 0.43
25 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (24 bp):
ATTTATATTTAAATATTTGTAAAA
Found at i:97044 original size:2 final size:2
Alignment explanation
Indices: 97037--97075 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
97027 CAATTAGATT
97037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
97076 TATTTTTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:97294 original size:2 final size:2
Alignment explanation
Indices: 97287--97327 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
97277 GTAAGTATCG
97287 AT AT AT AT AT 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 AT AT AT AT AT A
97328 AGTGTCCATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:100649 original size:4 final size:4
Alignment explanation
Indices: 100642--100681 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
100632 TATATATATA
100642 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
100682 AAACTAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:103974 original size:18 final size:18
Alignment explanation
Indices: 103947--103981 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
103937 AACTTTACTG
103947 CAAACAGACTAAATGTTA
1 CAAACAGACTAAATGTTA
*
103965 CAAACGGACTAAATGTT
1 CAAACAGACTAAATGTT
103982 GGGGGACCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (18 bp):
CAAACAGACTAAATGTTA
Found at i:104092 original size:31 final size:31
Alignment explanation
Indices: 103966--104085 Score: 141
Period size: 31 Copynumber: 3.7 Consensus size: 31
103956 TAAATGTTAC
*
103966 AAACGGACTAAATGTTGGGGGACCATATTGA
1 AAACGGACTAAATGTTAGGGGACCATATTGA
* * * *
103997 AAACAGACTAAATGTTACATCGAGAACCATATTGT
1 AAACGGACTAAATGTT--A--GGGGACCATATTGA
* *
104032 AAACGGACTAAATATTGGGGGACCATATTGA
1 AAACGGACTAAATGTTAGGGGACCATATTGA
104063 AAACGGACTAAATGTTAGGGGAC
1 AAACGGACTAAATGTTAGGGGAC
104086 TTTATTGGAA
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
31 47 0.65
35 25 0.35
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (31 bp):
AAACGGACTAAATGTTAGGGGACCATATTGA
Found at i:106955 original size:24 final size:24
Alignment explanation
Indices: 106928--106981 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
106918 CGTTCATTTA
106928 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * * *
106952 CGTTTGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
106976 CGTTCG
1 CGTTCG
106982 ATTATGTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.09, C:0.15, G:0.28, T:0.48
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:106960 original size:14 final size:14
Alignment explanation
Indices: 106938--106970 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
106928 CGTTCGTGAA
*
106938 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
106952 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
106966 CGTTT
1 CGTTT
106971 ATGTTCGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.27, T:0.55
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:106986 original size:24 final size:24
Alignment explanation
Indices: 106939--107013 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
106929 GTTCGTGAAC
* * *
106939 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
106963 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
* *
106987 GTTTGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
107011 GTT
1 GTT
107014 TAACACAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 1 0.02
24 44 0.98
ACGTcount: A:0.12, C:0.09, G:0.21, T:0.57
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:107757 original size:10 final size:10
Alignment explanation
Indices: 107738--107812 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
107728 GGGTCTCCAA
107738 CGTTTATGTT
1 CGTTTATGTT
*
107748 CGTTTGTGTT
1 CGTTTATGTT
107758 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
107769 ATGTTCGTGTT
1 -CGTTTATGTT
107780 CGTTTATGTT
1 CGTTTATGTT
107790 CG----TGTT
1 CGTTTATGTT
107796 CGTTTATGTT
1 CGTTTATGTT
107806 CGTTTAT
1 CGTTTAT
107813 TTATTAAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 6 0.12
10 33 0.67
11 7 0.14
12 3 0.06
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:107773 original size:16 final size:16
Alignment explanation
Indices: 107744--107808 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
107734 CCAACGTTTA
*
107744 TGTTCGTTTGTGTTCG
1 TGTTCGTTTATGTTCG
*
107760 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
107776 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
107792 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
107808 T
1 T
107809 TTATTTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.06, C:0.12, G:0.25, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:107899 original size:16 final size:16
Alignment explanation
Indices: 107878--107910 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
107868 AAAAAAAATT
107878 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
107894 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
107910 T
1 T
107911 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:112865 original size:16 final size:16
Alignment explanation
Indices: 112844--112878 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
112834 AGATCGGTTA
112844 AAGGGTAATCAAATCC
1 AAGGGTAATCAAATCC
112860 AAGGGTAATCAAATCC
1 AAGGGTAATCAAATCC
112876 AAG
1 AAG
112879 CCTTTGTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (16 bp):
AAGGGTAATCAAATCC
Found at i:112904 original size:2 final size:2
Alignment explanation
Indices: 112897--112933 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
112887 CACATATTTA
112897 AT AT AT 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 AT AT AT A
112934 AATTAATAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:115574 original size:40 final size:40
Alignment explanation
Indices: 115493--115621 Score: 116
Period size: 41 Copynumber: 3.1 Consensus size: 40
115483 GAAAATGATT
** * * *
115493 AAATTAGGGGTTTTAATTTTAAAAATTAAAATAGAG-TTTAA
1 AAATTAGGGGCCTCAATTTT-AAAGTTAAAA-AGAGATTAAA
115534 AAATTAGGGGCCTCAATTTTAAAGTTAAAAAGAGAATTAAA
1 AAATTAGGGGCCTCAATTTTAAAGTTAAAAAGAG-ATTAAA
* * *
115575 AAATTAGGAGCCTCAATTAATAAAGGTAAAAAGTGAGATTGAAA
1 AAATTAGGGGCCTCAATT-TTAAAGTTAAAAA--GAGATT-AAA
115619 AAA
1 AAA
115622 AAAATTAGGG
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
39 4 0.05
40 9 0.12
41 38 0.51
42 11 0.15
43 3 0.04
44 9 0.12
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.29
Consensus pattern (40 bp):
AAATTAGGGGCCTCAATTTTAAAGTTAAAAAGAGATTAAA
Found at i:115706 original size:21 final size:20
Alignment explanation
Indices: 115682--115732 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
115672 AAAAGTCTCA
* *
115682 ATTATAAAGATAAAATATATT
1 ATTATAAAAATAAAAAATA-T
115703 ATTATAAAAATAAAAAATAT
1 ATTATAAAAATAAAAAATAT
*
115723 AATATAAAAA
1 ATTATAAAAA
115733 ATAGGGACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
ATTATAAAAATAAAAAATAT
Found at i:115733 original size:21 final size:23
Alignment explanation
Indices: 115693--115735 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
115683 TTATAAAGAT
*
115693 AAAATATATTATTATAAAAATAA
1 AAAATATAATATTATAAAAATAA
115716 AAAATATAATA-TA-AAAAATA
1 AAAATATAATATTATAAAAATA
115736 GGGACCCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 10 0.53
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
AAAATATAATATTATAAAAATAA
Found at i:116390 original size:3 final size:3
Alignment explanation
Indices: 116382--116460 Score: 158
Period size: 3 Copynumber: 26.3 Consensus size: 3
116372 ATTTGTCCCG
116382 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
116430 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
116461 CATAGAACTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:116886 original size:8 final size:10
Alignment explanation
Indices: 116859--116887 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
116849 TGGAAAGAGA
116859 TGAAATATAT
1 TGAAATATAT
116869 TGAAATATAT
1 TGAAATATAT
116879 TGAAATATA
1 TGAAATATA
116888 AAAAAATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (10 bp):
TGAAATATAT
Found at i:119551 original size:16 final size:16
Alignment explanation
Indices: 119518--119558 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
119508 GTTTATTTTA
119518 GAATGATT-AAATACT
1 GAATGATTCAAATACT
**
119533 GAATGATTCAAATGTT
1 GAATGATTCAAATACT
119549 GAATGATTCA
1 GAATGATTCA
119559 GAGTCTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (16 bp):
GAATGATTCAAATACT
Found at i:120909 original size:46 final size:45
Alignment explanation
Indices: 120838--120924 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 45
120828 TAAATATTTA
* * *
120838 TGATATTTACATTTTCGGTAGAAAAAATAACATTTTAGGTAGCGTC
1 TGATATTAACATTTTCGGTAAAAAAAATAA-ATTTTAAGTAGCGTC
*
120884 TGATATTAATATTTTCGGTAAAAAAAATAAATTTTAAGTAG
1 TGATATTAACATTTTCGGTAAAAAAAATAAATTTTAAGTAG
120925 TGCTCTACCG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 10 0.27
46 27 0.73
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (45 bp):
TGATATTAACATTTTCGGTAAAAAAAATAAATTTTAAGTAGCGTC
Found at i:122012 original size:2 final size:2
Alignment explanation
Indices: 122005--122047 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
121995 GATACCTAGG
122005 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
122047 A
1 A
122048 AATCGGGACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:127195 original size:31 final size:30
Alignment explanation
Indices: 127160--127240 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
127150 ATTTAATTAC
*
127160 AAAATATGT-ATTGAAGTTATTAAATTCG-TAT
1 AAAATA-GTCATTAAAGTTA-TAAATT-GTTAT
*
127191 AAAATAGTCATTAAATTTATAAATTGTTAT
1 AAAATAGTCATTAAAGTTATAAATTGTTAT
* * *
127221 AAAATAATCTTTAAATTTAT
1 AAAATAGTCATTAAAGTTAT
127241 TAAAATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 1 0.02
30 29 0.66
31 14 0.32
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (30 bp):
AAAATAGTCATTAAAGTTATAAATTGTTAT
Found at i:127215 original size:30 final size:30
Alignment explanation
Indices: 127180--127240 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
127170 TTGAAGTTAT
*
127180 TAAATTCG-TATAAAATAGTCATTAAATTTA
1 TAAATT-GTTATAAAATAATCATTAAATTTA
*
127210 TAAATTGTTATAAAATAATCTTTAAATTTA
1 TAAATTGTTATAAAATAATCATTAAATTTA
127240 T
1 T
127241 TAAAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (30 bp):
TAAATTGTTATAAAATAATCATTAAATTTA
Found at i:127251 original size:30 final size:30
Alignment explanation
Indices: 127188--127251 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
127178 ATTAAATTCG
* *
127188 TATAAAATAGTCATTAAATTTATAAATTGT
1 TATAAAATAATCATTAAATTTATAAAATGT
*
127218 TATAAAATAATCTTTAAATTTATTAAAAT-T
1 TATAAAATAATCATTAAATTTA-TAAAATGT
127248 TATA
1 TATA
127252 GTTATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (30 bp):
TATAAAATAATCATTAAATTTATAAAATGT
Found at i:128156 original size:33 final size:33
Alignment explanation
Indices: 128114--128187 Score: 139
Period size: 33 Copynumber: 2.2 Consensus size: 33
128104 GTTTTTATAT
*
128114 GGAGAGTGAACGGTGCGTGGGGTCCAAAGAGCA
1 GGAGAGTGAACGGTGCATGGGGTCCAAAGAGCA
128147 GGAGAGTGAACGGTGCATGGGGTCCAAAGAGCA
1 GGAGAGTGAACGGTGCATGGGGTCCAAAGAGCA
128180 GGAGAGTG
1 GGAGAGTG
128188 GCAGCTGGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.28, C:0.14, G:0.46, T:0.12
Consensus pattern (33 bp):
GGAGAGTGAACGGTGCATGGGGTCCAAAGAGCA
Found at i:138059 original size:26 final size:26
Alignment explanation
Indices: 138012--138061 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
138002 AAAATTAAAT
*
138012 TATTTTCATTAATAATTCAACTTTTA
1 TATTTTCATTAATAAATCAACTTTTA
*
138038 TATTTTTATTAATTAAAT-AACTTT
1 TATTTTCATTAA-TAAATCAACTTT
138062 ATCAGAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (26 bp):
TATTTTCATTAATAAATCAACTTTTA
Found at i:143695 original size:33 final size:33
Alignment explanation
Indices: 143653--143733 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 33
143643 CAGGGGAGGA
* * *
143653 ACAAAAATCAAAATCCACTGAAACAACCCAAAG
1 ACAACAATCAAAATCCAATGAAACAACACAAAG
* *
143686 GCAACAATCAAAAGCCAATGAAACAACACAAAG
1 ACAACAATCAAAATCCAATGAAACAACACAAAG
*
143719 ACAACAATCGAAATC
1 ACAACAATCAAAATC
143734 TCACCCCCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.57, C:0.26, G:0.09, T:0.09
Consensus pattern (33 bp):
ACAACAATCAAAATCCAATGAAACAACACAAAG
Found at i:155561 original size:50 final size:52
Alignment explanation
Indices: 155441--155564 Score: 173
Period size: 50 Copynumber: 2.4 Consensus size: 52
155431 CACGTAGGGG
* *
155441 TATAACGCGGATCAGGAACCGC-ACTATACCTTTACTCCCGACATAATTTTA
1 TATAGCGCGGATCAGGTACCGCGACTATACCTTTACTCCCGACATAATTTTA
** *
155492 TATAGCGCGGGGCAGGTACCGCGAC-ATACCTTTACT-CTGACATAATTTTA
1 TATAGCGCGGATCAGGTACCGCGACTATACCTTTACTCCCGACATAATTTTA
*
155542 TATAGCGCGGATCATGTACCGCG
1 TATAGCGCGGATCAGGTACCGCG
155565 TTTTGTATAA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 33 0.52
51 29 0.45
52 2 0.03
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (52 bp):
TATAGCGCGGATCAGGTACCGCGACTATACCTTTACTCCCGACATAATTTTA
Found at i:159669 original size:18 final size:18
Alignment explanation
Indices: 159646--159680 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
159636 GCAATGGCGG
*
159646 CATCATATATGGTTGCGA
1 CATCATATATGGCTGCGA
159664 CATCATATATGGCTGCG
1 CATCATATATGGCTGCG
159681 GTGGCTACTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (18 bp):
CATCATATATGGCTGCGA
Found at i:161450 original size:20 final size:19
Alignment explanation
Indices: 161422--161460 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
161412 ACCTTAAAAG
*
161422 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTGAGA-AAATTT
161442 AGAGAATTTGAGAAAATTT
1 AGAGAATTTGAGAAAATTT
161461 GGTGTGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (19 bp):
AGAGAATTTGAGAAAATTT
Found at i:161627 original size:50 final size:51
Alignment explanation
Indices: 161573--161699 Score: 166
Period size: 51 Copynumber: 2.5 Consensus size: 51
161563 AGATATACAG
* * * ** **
161573 GTATAGCGCGTTGCAGGGGCCGCGTTATA-CCCATGTGGCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACATGGCGCCAAATCACC
* *
161623 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACATGGTGCCAAATCATC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACATGGCGCCAAATCACC
161674 GTATAGCGCGGTGCAGGGGGCGCGCT
1 GTATAGCGCGGTGCAGGGGGCGCGCT
161700 TTACTGATAA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 26 0.39
51 41 0.61
ACGTcount: A:0.17, C:0.29, G:0.35, T:0.18
Consensus pattern (51 bp):
GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACATGGCGCCAAATCACC
Done.