Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005349.1 Hibiscus syriacus cultivar Beakdansim tig00012136_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: 1796274
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 1 of 8
Found at i:826 original size:14 final size:14
Alignment explanation
Indices: 797--825 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
787 GTGAGCTCTC
797 TTCTTTTCTTTCTT
1 TTCTTTTCTTTCTT
811 TTCTTTTCTTT-TT
1 TTCTTTTCTTTCTT
824 TT
1 TT
826 TTTGTAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTTCTTTCTT
Found at i:4625 original size:10 final size:10
Alignment explanation
Indices: 4596--4659 Score: 62
Period size: 10 Copynumber: 6.6 Consensus size: 10
4586 GATGCTGGAA
4596 AACCGGTTTG
1 AACCGGTTTG
*
4606 -ACCAGTTTTG
1 AACC-GGTTTG
4616 AACCGGTTTG
1 AACCGGTTTG
*
4626 -ACCGGTCTG
1 AACCGGTTTG
*
4635 AACCGGGTTG
1 AACCGGTTTG
*
4645 -ACCGGTCTG
1 AACCGGTTTG
4654 AACCGG
1 AACCGG
4660 GTTAACCTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
9 18 0.42
10 22 0.51
11 3 0.07
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:4638 original size:19 final size:19
Alignment explanation
Indices: 4596--4659 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
4586 GATGCTGGAA
* *
4596 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
4616 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
4635 AACCGGGTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
4654 AACCGG
1 AACCGG
4660 GTTAACCTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 28 0.68
20 13 0.32
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:4698 original size:17 final size:17
Alignment explanation
Indices: 4676--4731 Score: 94
Period size: 17 Copynumber: 3.3 Consensus size: 17
4666 CTGACCCGAC
4676 TGACCCGACCCGACTGT
1 TGACCCGACCCGACTGT
*
4693 TGACCCGGCCCGACTGT
1 TGACCCGACCCGACTGT
*
4710 TGACCCGACCCGACCGT
1 TGACCCGACCCGACTGT
4727 TGACC
1 TGACC
4732 GTTGACCGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.16, C:0.43, G:0.25, T:0.16
Consensus pattern (17 bp):
TGACCCGACCCGACTGT
Found at i:4733 original size:7 final size:7
Alignment explanation
Indices: 4721--4751 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
4711 GACCCGACCC
4721 GACCGTT
1 GACCGTT
4728 GACCGTT
1 GACCGTT
4735 GACCGTT
1 GACCGTT
4742 GACCGTT
1 GACCGTT
4749 GAC
1 GAC
4752 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:11130 original size:17 final size:17
Alignment explanation
Indices: 11105--11141 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
11095 GATGATTAAT
11105 TTAGATAAACTTAATTA
1 TTAGATAAACTTAATTA
*
11122 TTAGTTAAACTTAATTA
1 TTAGATAAACTTAATTA
11139 TTA
1 TTA
11142 AAAAATCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (17 bp):
TTAGATAAACTTAATTA
Found at i:24688 original size:18 final size:17
Alignment explanation
Indices: 24665--24712 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
24655 ACACATATAC
24665 CATCATTATCATCATCAA
1 CATCATTATCATCATC-A
* *
24683 CATCATTATCATGATCT
1 CATCATTATCATCATCA
24700 CTATCATTATCAT
1 C-ATCATTATCAT
24713 TAACCCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (17 bp):
CATCATTATCATCATCA
Found at i:25551 original size:25 final size:25
Alignment explanation
Indices: 25523--25582 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
25513 GCTCTATAAC
25523 TTATCTCACAGTTTTACATAATCAT
1 TTATCTCACAGTTTTACATAATCAT
25548 TTATCTCACAGTTTTACATAATCAT
1 TTATCTCACAGTTTTACATAATCAT
25573 TTATCTCACA
1 TTATCTCACA
25583 CTATTTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (25 bp):
TTATCTCACAGTTTTACATAATCAT
Found at i:29532 original size:18 final size:19
Alignment explanation
Indices: 29509--29546 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
29499 CGGTTGTTCT
*
29509 GGAACTGGTGCT-GGACTG
1 GGAACTGCTGCTGGGACTG
29527 GGAACTGCTGCTGGGACTG
1 GGAACTGCTGCTGGGACTG
29546 G
1 G
29547 CGGGGCTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.16, C:0.18, G:0.45, T:0.21
Consensus pattern (19 bp):
GGAACTGCTGCTGGGACTG
Found at i:36678 original size:30 final size:30
Alignment explanation
Indices: 36642--36707 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
36632 AACCAACATT
*
36642 AACTTTTTAAA-ATTATCATTTTGGTC-CCTA
1 AACTTTTTAAAGATTAT-ACTTTGGTCACC-A
*
36672 AACTTTTTAAAGTTTATACTTTGGTCACCA
1 AACTTTTTAAAGATTATACTTTGGTCACCA
36702 AACTTT
1 AACTTT
36708 ACAAAATCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (30 bp):
AACTTTTTAAAGATTATACTTTGGTCACCA
Found at i:38349 original size:60 final size:60
Alignment explanation
Indices: 38272--38384 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
38262 AATGGTCCCT
* * * * *
38272 GACTATAGGGTGATGCTTCGTTGAGTCTCTCGACTATTAAAAGTTATAAAATGATCTTTC
1 GACTATAGGGTGATGCTTCGTTCAGTCCCCCGACTATCAAAAGTTACAAAATGATCTTTC
* * *
38332 GACTATAGGGTGTTGCTTTGTTCAGTCCCCCGACTATCGAAAGTTACAAAATG
1 GACTATAGGGTGATGCTTCGTTCAGTCCCCCGACTATCAAAAGTTACAAAATG
38385 GTTATCCAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (60 bp):
GACTATAGGGTGATGCTTCGTTCAGTCCCCCGACTATCAAAAGTTACAAAATGATCTTTC
Found at i:38397 original size:60 final size:60
Alignment explanation
Indices: 38273--38397 Score: 135
Period size: 60 Copynumber: 2.1 Consensus size: 60
38263 ATGGTCCCTG
* * * * * * *
38273 ACTATAGGGTGATGCTTCGTTGAGTCTCTCGACTATTAAAAGTTATAAAATGATCTTTCG
1 ACTATAGGGTGATGCTTCGTTCAGTCCCCCGACTATCAAAAGTTACAAAATGATCTTCCA
* * * *
38333 ACTATAGGGTGTTGCTTTGTTCAGTCCCCCGACTATCGAAAGTTACAAAATGGT-TATCCA
1 ACTATAGGGTGATGCTTCGTTCAGTCCCCCGACTATCAAAAGTTACAAAATGATCT-TCCA
38393 ACTAT
1 ACTAT
38398 TTAGCATGTT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
59 1 0.02
60 52 0.98
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (60 bp):
ACTATAGGGTGATGCTTCGTTCAGTCCCCCGACTATCAAAAGTTACAAAATGATCTTCCA
Found at i:38704 original size:60 final size:60
Alignment explanation
Indices: 38585--38705 Score: 140
Period size: 60 Copynumber: 2.0 Consensus size: 60
38575 TCAGATGGTC
* * * * *
38585 ATTTTGTAACTTTTAATAGTTGGAGGACTTGACAAAGAAACATCTTATAGTTGAAGGACT
1 ATTTTATAACTTTTAATAGTCGGAGGACTTAACAAAGAAACATCTTATAATCGAAGGACT
*
38645 ATTTTATAACTTTTAATAGTC-GAGAGACTTAACAAA-ACAACA-CATTATAATCGAGGGACT
1 ATTTTATAACTTTTAATAGTCGGAG-GACTTAACAAAGA-AACATC-TTATAATCGAAGGACT
38705 A
1 A
38706 CTTGTGTACT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
59 5 0.10
60 47 0.90
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTCGGAGGACTTAACAAAGAAACATCTTATAATCGAAGGACT
Found at i:42770 original size:2 final size:2
Alignment explanation
Indices: 42758--42788 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
42748 TAATATAATG
42758 AT AT A- 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
42789 CGATAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45215 original size:10 final size:10
Alignment explanation
Indices: 45202--45244 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
45192 CAAACGGATG
45202 TAAACGAACA
1 TAAACGAACA
45212 TAAACGAACACAA
1 TAAACG-A-AC-A
*
45225 TAAACGAACG
1 TAAACGAACA
45235 TAAACGAACA
1 TAAACGAACA
45245 CAGATGAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 15 0.54
11 3 0.11
12 3 0.11
13 7 0.25
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
TAAACGAACA
Found at i:45262 original size:24 final size:24
Alignment explanation
Indices: 45163--45262 Score: 107
Period size: 24 Copynumber: 4.2 Consensus size: 24
45153 CATTTAAACG
* *
45163 ATAAACGAACACAAATGAAAGAAC
1 ATAAACGAACACAGATGAACGAAC
*
45187 ATAAAC-AA-ACGGATGTAAACGAAC
1 ATAAACGAACACAGATG--AACGAAC
*
45211 ATAAACGAACACA-ATAAACGAAC
1 ATAAACGAACACAGATGAACGAAC
* *
45234 GTAAACGAACACAGATGAACGTAC
1 ATAAACGAACACAGATGAACGAAC
45258 ATAAA
1 ATAAA
45263 TTAATTTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
22 5 0.08
23 21 0.34
24 30 0.48
25 4 0.06
26 2 0.03
ACGTcount: A:0.57, C:0.18, G:0.14, T:0.11
Consensus pattern (24 bp):
ATAAACGAACACAGATGAACGAAC
Found at i:51948 original size:23 final size:23
Alignment explanation
Indices: 51899--51941 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
51889 TCTCAATGGT
* *
51899 TCTATCTTTATGACACGATTTCC
1 TCTACCTTCATGACACGATTTCC
51922 TCTACCTTCATGACAC-ATTT
1 TCTACCTTCATGACACGATTT
51942 TTCTCTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (23 bp):
TCTACCTTCATGACACGATTTCC
Found at i:54663 original size:2 final size:2
Alignment explanation
Indices: 54656--54688 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
54646 TGAGAAACCA
*
54656 TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
54689 TCTAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:62170 original size:30 final size:30
Alignment explanation
Indices: 62113--62182 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
62103 TATGAGTTAG
* *
62113 ATTAGTATTTTATGTAAAGTTTAAGGTCAA
1 ATTAATATTTTATCTAAAGTTTAAGGTCAA
*
62143 ATTAATATTTTGTCTAAA-TTTAGAGGTCAA
1 ATTAATATTTTATCTAAAGTTTA-AGGTCAA
*
62173 ATTAAAATTT
1 ATTAATATTT
62183 AACCATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 4 0.11
30 31 0.89
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (30 bp):
ATTAATATTTTATCTAAAGTTTAAGGTCAA
Found at i:66719 original size:3 final size:3
Alignment explanation
Indices: 66711--66752 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
66701 TTCACTATCA
* * *
66711 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAC TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
66753 ATACAACAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:70734 original size:17 final size:17
Alignment explanation
Indices: 70712--70754 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
70702 TAACTTTATT
*
70712 TAAATTATTATTATAAA
1 TAAATTATTAATATAAA
*
70729 TAAATTTTTAATATAAA
1 TAAATTATTAATATAAA
70746 TATAATTAT
1 TA-AATTAT
70755 AAATGAGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAATTATTAATATAAA
Found at i:74171 original size:15 final size:16
Alignment explanation
Indices: 74151--74180 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
74141 GATATAAAAA
74151 AATATTTTTT-TATTG
1 AATATTTTTTGTATTG
74166 AATATTTTTTGTATT
1 AATATTTTTTGTATT
74181 TTTATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (16 bp):
AATATTTTTTGTATTG
Found at i:75091 original size:224 final size:226
Alignment explanation
Indices: 74654--75097 Score: 752
Period size: 224 Copynumber: 2.0 Consensus size: 226
74644 GTAAATTATC
* * *
74654 TATCCTTTTTATAAAAGTGTCAATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCAATACTTATTTCACTGTGAAAATACATTTATTATTATATTTAGT
**
74719 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAATT
74784 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
74849 AAACATAAATTACATAACTTTCAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAGTATA
* *
74881 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTG-AAA-ACATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCAATACTTATTTCACTG-TGAAAATACATTTATTATTATATTTAG
*
74944 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA-AAT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAAT
* *
75008 TTGTGT-AATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
75072 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
75098 GCAGTTATAA
Statistics
Matches: 206, Mismatches: 10, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
223 4 0.02
224 78 0.38
225 7 0.03
226 77 0.37
227 38 0.18
228 2 0.01
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTGTCAATACTTATTTCACTGTGAAAATACATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAATT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAGTATA
Found at i:75184 original size:20 final size:19
Alignment explanation
Indices: 75161--75206 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
75151 CGATATACCA
75161 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
75181 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
75201 GGTAAA
1 GGTAAA
75207 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:75375 original size:17 final size:19
Alignment explanation
Indices: 75336--75378 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
75326 CAGGTAAAAT
75336 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
75356 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
75373 ATGATA
1 ATGATA
75379 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:77653 original size:21 final size:21
Alignment explanation
Indices: 77606--77670 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
77596 AAGACAATCA
* *
77606 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
77628 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
77648 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
77669 AG
1 AG
77671 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:79899 original size:183 final size:183
Alignment explanation
Indices: 79591--80400 Score: 1503
Period size: 183 Copynumber: 4.4 Consensus size: 183
79581 CTTTCAACAT
** * * *
79591 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
79656 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
79721 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* * *
79774 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
79839 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
79904 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
79957 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
80022 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
80087 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* * * *
80140 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACAGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
80205 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
80270 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
80323 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
*
80388 TGTCTACAACCTA
66 GGTCTACAACCTA
80401 AAATGTGTCG
Statistics
Matches: 607, Mismatches: 20, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 607 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:82893 original size:28 final size:23
Alignment explanation
Indices: 82837--82890 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
82827 TAACTACAAG
*
82837 TATATAATGTAATAGGTATCGTT
1 TATATAATGTAATAGGTAGCGTT
*
82860 TATATAATGTAATAGGTAGCGCT
1 TATATAATGTAATAGGTAGCGTT
82883 TATATAAT
1 TATATAAT
82891 ATATTGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.41
Consensus pattern (23 bp):
TATATAATGTAATAGGTAGCGTT
Found at i:83343 original size:18 final size:18
Alignment explanation
Indices: 83322--83358 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
83312 GTAATTGGAG
83322 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
83340 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
83358 T
1 T
83359 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:83366 original size:24 final size:24
Alignment explanation
Indices: 83314--83360 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
83304 TTTCATATGT
* *
83314 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
83338 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
83361 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:83658 original size:39 final size:39
Alignment explanation
Indices: 83615--83701 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
83605 TCCGATGCTC
* *
83615 ATCAAAATCCGAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
83654 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
83693 ATCAAAATC
1 ATCAAAATC
83702 TACAACTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:84153 original size:23 final size:23
Alignment explanation
Indices: 84122--84194 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
84112 ATAGGTAAAA
*
84122 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
84145 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
84168 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
84191 ATAT
1 ATAT
84195 TGTAATGTGT
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:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:84581 original size:23 final size:23
Alignment explanation
Indices: 84555--84627 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
84545 AATAGGTAAA
*
84555 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
84578 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
84601 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
84624 ATAT
1 ATAT
84628 TGTAAAGTGT
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:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:85000 original size:433 final size:434
Alignment explanation
Indices: 83909--85000 Score: 1893
Period size: 435 Copynumber: 2.5 Consensus size: 434
83899 TTATCTTTGG
*
83909 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTT
1 TTAA-GTTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTT
83974 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAA
65 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAAA
*
84039 TTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAGGTATGGACACTT
129 TTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTT
* *
84104 TCAATATAATAGGTAA-AAATAT-GA-TGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGT
194 TCAATATAATA--TAAGTAATATAAATTGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGT
*
84166 TTATATAATGTAATAGGTAGTGGTTATATTGTAATGTGTCTATCCTTTTTATAAAAGTGTCCATA
257 TTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATA
84231 CTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTAAGTGAGTTTTAAGATTTTAATTT
322 CTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTAAGTGAGTTTTAAGATTTTAATTT
84296 AGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATAT
387 AGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATAT
* *
84344 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATATT
1 TTAA-GTTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTT
84409 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
65 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
84474 TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTT
130 TGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTT
*
84539 CAATATAATAGGTAA--AATAT-GA-TGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTT
195 CAATATAATA--TAAGTAATATAAATTGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTT
84600 TATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATAC
258 TATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATAC
* *
84665 -TTTTTCACTGTTGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTA
323 TTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTAAGTGAGTTTTAAGATTTTAATTTA
84729 GTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA-
388 GTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATAT
*
84775 TT-A-TTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTT
1 TTAAGTTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTTT
*
84838 TGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-CAAAAAATT
66 TGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
84902 GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTC
131 GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTC
84967 AATATAATATAATGTAATAGGTAAATTTGTAATA
196 AATATAATATAA-GTAATA--TAAA-TTGTAATA
85001 CTATCGGTAT
Statistics
Matches: 639, Mismatches: 10, Indels: 18
0.96 0.01 0.03
Matches are distributed among these distances:
425 3 0.00
427 82 0.13
428 116 0.18
430 2 0.00
431 3 0.00
432 108 0.17
433 117 0.18
434 88 0.14
435 120 0.19
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (434 bp):
TTAAGTTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTTT
TGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTC
AATATAATATAAGTAATATAAATTGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTAT
ATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTT
TTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTAAGTGAGTTTTAAGATTTTAATTTAGTA
ATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATAT
Found at i:90821 original size:19 final size:19
Alignment explanation
Indices: 90797--90834 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
90787 ACACTCGAAG
*
90797 TTAATTTTATGGGCTTAAA
1 TTAATTTTAAGGGCTTAAA
*
90816 TTAATTTTAAGTGCTTAAA
1 TTAATTTTAAGGGCTTAAA
90835 GAATTTGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.47
Consensus pattern (19 bp):
TTAATTTTAAGGGCTTAAA
Found at i:91401 original size:2 final size:2
Alignment explanation
Indices: 91396--91429 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
91386 AAAACTAAAT
91396 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
91430 ACACTGGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:94225 original size:60 final size:60
Alignment explanation
Indices: 94105--94225 Score: 138
Period size: 60 Copynumber: 2.0 Consensus size: 60
94095 TCAGATGATC
* * * * * * *
94105 ATTTTGTAACTTTTAATAGTCGGAGGACTTGACAAAGAAACATCTTGTAGTTGAATGACT
1 ATTTTATAACTTTTAATAGTCGGAGGACTTGAAAAAAAAACATCTTATAATCGAAGGACT
*
94165 ATTTTATAACTTTTAATAGTC-GAGGGACTT-AAAAAAATAACATCTTATAATCGAGGGACT
1 ATTTTATAACTTTTAATAGTCGGA-GGACTTGAAAAAAA-AACATCTTATAATCGAAGGACT
94225 A
1 A
94226 CTTGTGTACT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 7 0.14
60 44 0.86
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTCGGAGGACTTGAAAAAAAAACATCTTATAATCGAAGGACT
Found at i:104339 original size:14 final size:14
Alignment explanation
Indices: 104310--104365 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
104300 CGTTCGTGAA
104310 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
104326 CGTTCATTTA---T
1 CGTTCATTTATGTT
104337 -GTTCATTTATGTT
1 CGTTCATTTATGTT
104350 CGTTCATTTATGTT
1 CGTTCATTTATGTT
104364 CG
1 CG
104366 AACAGAGGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 1 0.03
14 17 0.47
15 3 0.08
16 5 0.14
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.54
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:104352 original size:24 final size:26
Alignment explanation
Indices: 104311--104366 Score: 98
Period size: 24 Copynumber: 2.2 Consensus size: 26
104301 GTTCGTGAAC
104311 GTTCGATTATATGTTCGTTCATTTAT
1 GTTCGATTATATGTTCGTTCATTTAT
104337 GTTC-ATT-TATGTTCGTTCATTTAT
1 GTTCGATTATATGTTCGTTCATTTAT
104361 GTTCGA
1 GTTCGA
104367 ACAGAGGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 21 0.72
25 4 0.14
26 4 0.14
ACGTcount: A:0.18, C:0.12, G:0.16, T:0.54
Consensus pattern (26 bp):
GTTCGATTATATGTTCGTTCATTTAT
Found at i:104664 original size:14 final size:13
Alignment explanation
Indices: 104623--104681 Score: 54
Period size: 13 Copynumber: 4.7 Consensus size: 13
104613 TTGTGTTTGT
*
104623 GTTTGTGTTGTTC
1 GTTTATGTTGTTC
104636 GTTTAT-TGTGTTC
1 GTTTATGT-TGTTC
104649 GTTTATGTTCGTTC
1 GTTTATGTT-GTTC
*
104663 G-TT-CG-TGTTC
1 GTTTATGTTGTTC
104673 GTTTATGTT
1 GTTTATGTT
104682 CGTTTATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
10 5 0.14
11 3 0.08
12 3 0.08
13 20 0.54
14 6 0.16
ACGTcount: A:0.05, C:0.10, G:0.25, T:0.59
Consensus pattern (13 bp):
GTTTATGTTGTTC
Found at i:104982 original size:3 final size:3
Alignment explanation
Indices: 104974--105025 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
104964 ACAAGTTGCA
104974 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
105022 ATT A
1 ATT A
105026 ATTTGGATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:105105 original size:3 final size:3
Alignment explanation
Indices: 105099--105144 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
105089 TTGCATCATC
*
105099 ATT ATT ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
105145 GGGGACAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:106570 original size:10 final size:10
Alignment explanation
Indices: 106557--106599 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
106547 CAAACGGATG
106557 TAAACGAACA
1 TAAACGAACA
106567 TAAACGAACACAA
1 TAAACG-A-AC-A
*
106580 TAAACGAACG
1 TAAACGAACA
106590 TAAACGAACA
1 TAAACGAACA
106600 CAGATGAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 15 0.54
11 3 0.11
12 3 0.11
13 7 0.25
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
TAAACGAACA
Found at i:106617 original size:24 final size:24
Alignment explanation
Indices: 106518--106617 Score: 107
Period size: 24 Copynumber: 4.2 Consensus size: 24
106508 CATTTAAATG
* *
106518 ATAAACGAACACAAATGAAAGAAC
1 ATAAACGAACACAGATGAACGAAC
*
106542 ATAAAC-AA-ACGGATGTAAACGAAC
1 ATAAACGAACACAGATG--AACGAAC
*
106566 ATAAACGAACACA-ATAAACGAAC
1 ATAAACGAACACAGATGAACGAAC
* *
106589 GTAAACGAACACAGATGAACGAAA
1 ATAAACGAACACAGATGAACGAAC
106613 ATAAA
1 ATAAA
106618 TGAAAATATA
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
22 5 0.08
23 21 0.34
24 30 0.48
25 4 0.06
26 2 0.03
ACGTcount: A:0.59, C:0.17, G:0.14, T:0.10
Consensus pattern (24 bp):
ATAAACGAACACAGATGAACGAAC
Found at i:106819 original size:24 final size:24
Alignment explanation
Indices: 106787--106864 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
106777 GATTGGGCTA
* *
106787 AACATAAATGAGCGCACATAAACG
1 AACATAAATGAACGAACATAAACG
* **
106811 AACATAAATGAATGAATGTAAACG
1 AACATAAATGAACGAACATAAACG
* * *
106835 AACATAAATGTATGAACATAAACA
1 AACATAAATGAACGAACATAAACG
106859 AACATA
1 AACATA
106865 TTACCGTTCA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.55, C:0.14, G:0.13, T:0.18
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:111047 original size:23 final size:23
Alignment explanation
Indices: 110998--111040 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
110988 TCTCAATGGT
* *
110998 TCTATCTTTATGACACGATTTCC
1 TCTACCTTCATGACACGATTTCC
111021 TCTACCTTCATGACAC-ATTT
1 TCTACCTTCATGACACGATTT
111041 TTCTCTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (23 bp):
TCTACCTTCATGACACGATTTCC
Found at i:118815 original size:447 final size:445
Alignment explanation
Indices: 117839--118728 Score: 1235
Period size: 448 Copynumber: 2.0 Consensus size: 445
117829 ATCTTCTTAG
* * * ** * * * *
117839 GCTAATTATTTTTAAATTCATCTTTTAGTTCAACTAATAACTGTTAAGTGGTCTCATCTCACATT
1 GCTAATGATTTTGAAATTCAGCCATTA-TTCAACTAATAACGGATAAG-GGTCCCATCTCATATT
* *
117904 AGCTTCATTTGA-AGTTTGTTTTGTCTTTGTATTCAATTTTAGGGCCTCTGCACCAATTGCTATT
64 AGCCTCA-TCGACAGTTTGTTTTGTCTTTGTATTCAATTTTAGGGCCTCTGCACCAATTGCTATT
* *
117968 AGTTTTAGGTTGGATGATCAACATAACTACCTTCTATTTGTTTAAGACTTTTTGGACTTTACCTT
128 AGTTCTAGGTTGGATGATCAACAGAACTACCTTCTATTTGTTTAAGACTTTTTGGACTTTACCTT
*
118033 TCAACAATGGTAATGTACTTATGCATCCTTCTTACCTGCAGCCAAATCAAATTTTTACTCACCCT
193 TCAACAATGGTAATGTACTTATGCATCCTTCTTACCTGCAACCAAATCAAATTTTTACTCACCCT
*
118098 GGGTTCGCTGGACCAGGATCCGTTGATGTCCTCCACTTTTGGACTGACTGAATCTAATGGAAAAA
258 GGGTTCGCTGGACCAGGATCCGTTGATGTCCTCCACTTTTGGAATGACTGAATCTAATGGAAAAA
*
118163 AATACATATTCTGCATAATGAAGGTGCTAAAACATGGAATGATAGCATTTATGTCAGCCTAGTAT
323 AATACATATTCTGCACAATGAAGGTGCTAAAACATGGAATGATAGCATTTATGTCAGCCTAGTAT
* * * * * * *
118228 GCTACCTTCAGGCTTTTTTCCAGTGACTTACAAAGCTCATTTATTTTATATCTTCTTAG
388 GCTACCTTCAGGCCTTTTTCCAGTGACTTACAAAGCTCATTTACTTGACATATAC-TAA
* * ** * * *
118287 GCTAATGATTTTTAAATTCATCTTTTAGTTCAACTAATAACTGTTAAGTGGTCTCATCTCATATT
1 GCTAATGATTTTGAAATTCAGCCATTA-TTCAACTAATAACGGATAAG-GGTCCCATCTCATATT
* ** *
118352 AGCTTCATTTACAGTTTGTTTTGTCTTTGTATTCAATTTTAGGGCCTCTGCACCTATTGCTATTA
64 AGCCTCATCGACAGTTTGTTTTGTCTTTGTATTCAATTTTAGGGCCTCTGCACCAATTGCTATTA
* *
118417 GTTCTAGGTTGGGTGATCAACAGAACTACCTTCTATTTGTTTAAGCCTTTTT-GACTTTACCTTT
129 GTTCTAGGTTGGATGATCAACAGAACTACCTTCTATTTGTTTAAGACTTTTTGGACTTTACCTTT
* * * * *
118481 GAACCATGGTAATGTACTTATGCATCTTTCTTACCTGCAACCGAATCAAATTTTTACTCACCTTG
194 CAACAATGGTAATGTACTTATGCATCCTTCTTACCTGCAACCAAATCAAATTTTTACTCACCCTG
*
118546 GGTTCGCTGGACCTGGATCCGTTGATGTCCTCCACTTTTGGAATGACTGAATCTAATGGAAAAAA
259 GGTTCGCTGGACCAGGATCCGTTGATGTCCTCCACTTTTGGAATGACTGAATCTAATGGAAAAAA
* *
118611 ATACATATTCTGCACAATGAAGGTGGTTATGCTACAACATGGAATGGTAGCATTTATGTCAGCCT
324 ATACATATTCTGCACAATGAA---GG---TGCTAAAACATGGAATGATAGCATTTATGTCAGCCT
* * *
118676 AGTGTGCTACCTTCAGGCCTTTTTCCAGTGACTTACAAATCTCATTTGCTTGA
383 AGTATGCTACCTTCAGGCCTTTTTCCAGTGACTTACAAAGCTCATTTACTTGA
118729 GCAATACAAT
Statistics
Matches: 410, Mismatches: 25, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
447 157 0.38
448 170 0.41
450 2 0.00
453 81 0.20
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (445 bp):
GCTAATGATTTTGAAATTCAGCCATTATTCAACTAATAACGGATAAGGGTCCCATCTCATATTAG
CCTCATCGACAGTTTGTTTTGTCTTTGTATTCAATTTTAGGGCCTCTGCACCAATTGCTATTAGT
TCTAGGTTGGATGATCAACAGAACTACCTTCTATTTGTTTAAGACTTTTTGGACTTTACCTTTCA
ACAATGGTAATGTACTTATGCATCCTTCTTACCTGCAACCAAATCAAATTTTTACTCACCCTGGG
TTCGCTGGACCAGGATCCGTTGATGTCCTCCACTTTTGGAATGACTGAATCTAATGGAAAAAAAT
ACATATTCTGCACAATGAAGGTGCTAAAACATGGAATGATAGCATTTATGTCAGCCTAGTATGCT
ACCTTCAGGCCTTTTTCCAGTGACTTACAAAGCTCATTTACTTGACATATACTAA
Found at i:118941 original size:20 final size:20
Alignment explanation
Indices: 118918--118956 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
118908 TTTTACAAAT
118918 ATTATATTAGGTCTACATTG
1 ATTATATTAGGTCTACATTG
118938 ATTATATTAGGTCTACATT
1 ATTATATTAGGTCTACATT
118957 TCTCAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (20 bp):
ATTATATTAGGTCTACATTG
Found at i:127599 original size:31 final size:31
Alignment explanation
Indices: 127561--127685 Score: 180
Period size: 31 Copynumber: 4.0 Consensus size: 31
127551 CCCGAAGGAC
* * *
127561 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
127592 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
127623 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
127654 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
127685 C
1 C
127686 CCTCGACCCT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:127986 original size:23 final size:24
Alignment explanation
Indices: 127960--128006 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
127950 ATATACTTGT
*
127960 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
127983 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
128007 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:128668 original size:21 final size:21
Alignment explanation
Indices: 128638--128682 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
128628 ATTCTGTCGT
* *
128638 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
128659 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
128680 TTG
1 TTG
128683 CCCAGAACTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:136497 original size:10 final size:10
Alignment explanation
Indices: 136484--136537 Score: 63
Period size: 10 Copynumber: 5.1 Consensus size: 10
136474 GTGTTTGTGT
136484 TGTTCGTTTA
1 TGTTCGTTTA
*
136494 TGTTTGTTTA
1 TGTTCGTTTA
136504 TGTTCGTTTA
1 TGTTCGTTTA
*
136514 TTGTGTTCGTTAA
1 ---TGTTCGTTTA
136527 TGTTCGTTTA
1 TGTTCGTTTA
136537 T
1 T
136538 TTATTAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
10 28 0.76
13 9 0.24
ACGTcount: A:0.11, C:0.07, G:0.20, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:136520 original size:23 final size:23
Alignment explanation
Indices: 136473--136538 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
136463 GTTTTTTGTG
*
136473 TGTGTTTGTGT-TGTTCGTTTA-
1 TGTGTTTGTTTATGTTCGTTTAT
136494 --TGTTTGTTTATGTTCGTTTAT
1 TGTGTTTGTTTATGTTCGTTTAT
* *
136515 TGTGTTCGTTAATGTTCGTTTAT
1 TGTGTTTGTTTATGTTCGTTTAT
136538 T
1 T
136539 TATTAAATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
19 8 0.21
20 10 0.26
23 20 0.53
ACGTcount: A:0.09, C:0.06, G:0.23, T:0.62
Consensus pattern (23 bp):
TGTGTTTGTTTATGTTCGTTTAT
Found at i:136626 original size:16 final size:16
Alignment explanation
Indices: 136605--136635 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
136595 AAAAATTTTG
136605 TTCGTTTATATTCGTA
1 TTCGTTTATATTCGTA
*
136621 TTCGTTTATGTTCGT
1 TTCGTTTATATTCGT
136636 TTATTTATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.58
Consensus pattern (16 bp):
TTCGTTTATATTCGTA
Found at i:137112 original size:17 final size:17
Alignment explanation
Indices: 137090--137124 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
137080 GGGATCAAAT
137090 TCTAAATGTATGAAGGG
1 TCTAAATGTATGAAGGG
137107 TCTAAATGTATGAAGGG
1 TCTAAATGTATGAAGGG
137124 T
1 T
137125 ATAGGGATTT
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:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (17 bp):
TCTAAATGTATGAAGGG
Found at i:146641 original size:16 final size:16
Alignment explanation
Indices: 146596--146653 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
146586 AGTAAGCGCT
***
146596 GAATGATTTAAATATT
1 GAATGATTTAAATGCA
*
146612 GAATGATTTAAATGCG
1 GAATGATTTAAATGCA
146628 GAATGATTTAAATGCA
1 GAATGATTTAAATGCA
*
146644 AAATGATTTA
1 GAATGATTTA
146654 GAGATTATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.36
Consensus pattern (16 bp):
GAATGATTTAAATGCA
Found at i:147664 original size:16 final size:16
Alignment explanation
Indices: 147643--147676 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
147633 TGATTAAGCA
147643 CTGAATGATTCAAATG
1 CTGAATGATTCAAATG
*
147659 CTGAATGATTCAGATG
1 CTGAATGATTCAAATG
147675 CT
1 CT
147677 ATGTATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (16 bp):
CTGAATGATTCAAATG
Found at i:149024 original size:15 final size:16
Alignment explanation
Indices: 148986--149026 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
148976 ACAGAGCCTC
*
148986 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
149002 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
149018 T-AATCATTC
1 TGAATCATTC
149027 TGAAGTAAAC
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:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:152642 original size:31 final size:31
Alignment explanation
Indices: 152607--152665 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
152597 GAGAAGAGGT
152607 GAATCATACCTAGAGCATTAGGGAGAGTAGG
1 GAATCATACCTAGAGCATTAGGGAGAGTAGG
*
152638 GAATCATACCTATAGCATTAGGGAGAGT
1 GAATCATACCTAGAGCATTAGGGAGAGT
152666 CTAAGGTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.22
Consensus pattern (31 bp):
GAATCATACCTAGAGCATTAGGGAGAGTAGG
Found at i:159445 original size:2 final size:2
Alignment explanation
Indices: 159440--159474 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
159430 TATGTATGCA
*
159440 AT AT AT AT A- AT AT AT AT AT CT 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
159475 GACCAATCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:164025 original size:3 final size:3
Alignment explanation
Indices: 164017--164070 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
164007 ACAAGTTGCA
164017 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
164065 A-T ATT A
1 ATT ATT A
164071 ATTTGGATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:164147 original size:3 final size:3
Alignment explanation
Indices: 164139--164193 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
164129 AACAAGTTGC
164139 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
164187 ATT ATT A
1 ATT ATT A
164194 GTGGACAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:164297 original size:3 final size:3
Alignment explanation
Indices: 164289--164348 Score: 111
Period size: 3 Copynumber: 19.7 Consensus size: 3
164279 ACAAGTTGCA
164289 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
164335 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
164349 GTGGACAGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:164610 original size:10 final size:10
Alignment explanation
Indices: 164595--164660 Score: 60
Period size: 10 Copynumber: 5.9 Consensus size: 10
164585 GTTTGTGTTA
164595 TTCGTTTATG
1 TTCGTTTATG
164605 TTCGTTTATTGTG
1 TTCGTTTA---TG
164618 TTCGTTTATG
1 TTCGTTTATG
*
164628 TTCGTTCGTTCGTG
1 TTCG-T--TT-ATG
164642 TTCGTTTATG
1 TTCGTTTATG
164652 TTCGTTTAT
1 TTCGTTTAT
164661 TTATTTAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
10 25 0.53
11 3 0.06
13 13 0.28
14 6 0.13
ACGTcount: A:0.08, C:0.12, G:0.21, T:0.59
Consensus pattern (10 bp):
TTCGTTTATG
Found at i:164611 original size:23 final size:23
Alignment explanation
Indices: 164595--164658 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 23
164585 GTTTGTGTTA
*
164595 TTCGTTTATGTTCGTTTATTGTG
1 TTCGTTTATGTTCGTTTGTTGTG
*
164618 TTCGTTTATGTTCGTTCGTTCGTG
1 TTCGTTTATGTTCGTTTGTT-GTG
164642 TTCGTTTATGTTCGTTT
1 TTCGTTTATGTTCGTTT
164659 ATTTATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.06, C:0.12, G:0.22, T:0.59
Consensus pattern (23 bp):
TTCGTTTATGTTCGTTTGTTGTG
Found at i:165040 original size:3 final size:3
Alignment explanation
Indices: 165032--165086 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
165022 AACAAGTTGC
165032 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
165080 ATT ATT A
1 ATT ATT A
165087 GTGGACAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:165189 original size:3 final size:3
Alignment explanation
Indices: 165181--165214 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
165171 AACAAGTTGC
165181 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
165215 GTGGACAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:165299 original size:18 final size:16
Alignment explanation
Indices: 165276--165308 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
165266 AACAAACATC
165276 ATAT-TATTATCATAA
1 ATATATATTATCATAA
165291 ATA-ATATTATCATAA
1 ATATATATTATCATAA
165306 ATA
1 ATA
165309 ATAATATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATATTATCATAA
Found at i:165300 original size:15 final size:15
Alignment explanation
Indices: 165280--165311 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
165270 AACATCATAT
165280 TATTATCATAAATAA
1 TATTATCATAAATAA
165295 TATTATCATAAATAA
1 TATTATCATAAATAA
165310 TA
1 TA
165312 ATATTCAAAT
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:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
TATTATCATAAATAA
Found at i:166696 original size:13 final size:14
Alignment explanation
Indices: 166678--166720 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
166668 GCAAACGAAT
166678 ATAAACGAACAC-A
1 ATAAACGAACACAA
*
166691 ATAAACAAACACAA
1 ATAAACGAACACAA
* *
166705 ATGAACGAACATAA
1 ATAAACGAACACAA
166719 AT
1 AT
166721 GAAAATAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.63, C:0.19, G:0.07, T:0.12
Consensus pattern (14 bp):
ATAAACGAACACAA
Found at i:166912 original size:20 final size:20
Alignment explanation
Indices: 166899--166978 Score: 61
Period size: 24 Copynumber: 3.6 Consensus size: 20
166889 AACATAAATG
*
166899 AACGCACATAAACAAACATA
1 AACGAACATAAACAAACATA
*
166919 AACGAACATAAATGAACGAACATA
1 AACGAACAT--A--AACAAACATA
*
166943 AACGAACATAAATGAACGAACATA
1 AACGAACAT--A--AACAAACATA
166967 AACGAACATAAA
1 AACGAACATAAA
166979 TGTATGAACA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
20 10 0.19
22 2 0.04
24 42 0.78
ACGTcount: A:0.60, C:0.19, G:0.10, T:0.11
Consensus pattern (20 bp):
AACGAACATAAACAAACATA
Found at i:166928 original size:34 final size:34
Alignment explanation
Indices: 166889--166978 Score: 119
Period size: 34 Copynumber: 2.6 Consensus size: 34
166879 GATTAGGCTA
*
166889 AACATAAATGAACGCACATAAACAAACATAAACG
1 AACATAAATGAACGAACATAAACAAACATAAACG
* *
166923 AACATAAATGAACGAACATAAACGAACATAAATG
1 AACATAAATGAACGAACATAAACAAACATAAACG
* *
166957 AACGA-ACATAAACGAACATAAA
1 AAC-ATAAATGAACGAACATAAA
166979 TGTATGAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
34 49 0.98
35 1 0.02
ACGTcount: A:0.60, C:0.18, G:0.10, T:0.12
Consensus pattern (34 bp):
AACATAAATGAACGAACATAAACAAACATAAACG
Found at i:166940 original size:24 final size:24
Alignment explanation
Indices: 166913--167000 Score: 149
Period size: 24 Copynumber: 3.7 Consensus size: 24
166903 CACATAAACA
166913 AACATAAACGAACATAAATGAACG
1 AACATAAACGAACATAAATGAACG
166937 AACATAAACGAACATAAATGAACG
1 AACATAAACGAACATAAATGAACG
* *
166961 AACATAAACGAACATAAATGTATG
1 AACATAAACGAACATAAATGAACG
*
166985 AACATAAATGAACATA
1 AACATAAACGAACATA
167001 CTATCGAACG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.58, C:0.15, G:0.11, T:0.16
Consensus pattern (24 bp):
AACATAAACGAACATAAATGAACG
Found at i:166968 original size:14 final size:14
Alignment explanation
Indices: 166919--166997 Score: 84
Period size: 14 Copynumber: 6.2 Consensus size: 14
166909 AACAAACATA
166919 AACGAACATAAATG
1 AACGAACATAAATG
166933 AACGAACAT--A--
1 AACGAACATAAATG
166943 AACGAACATAAATG
1 AACGAACATAAATG
166957 AACGAACAT--A--
1 AACGAACATAAATG
166967 AACGAACATAAATG
1 AACGAACATAAATG
* *
166981 TATGAACATAAATG
1 AACGAACATAAATG
166995 AAC
1 AAC
166998 ATACTATCGA
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
10 18 0.34
12 4 0.08
14 31 0.58
ACGTcount: A:0.57, C:0.15, G:0.13, T:0.15
Consensus pattern (14 bp):
AACGAACATAAATG
Found at i:172511 original size:2 final size:2
Alignment explanation
Indices: 172504--172597 Score: 172
Period size: 2 Copynumber: 47.5 Consensus size: 2
172494 TGAGAAACCA
172504 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
172545 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
172587 TC TC TC CC TC T
1 TC TC TC TC TC T
172598 TCTAATTTTT
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 88 0.99
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:175772 original size:27 final size:27
Alignment explanation
Indices: 175730--175851 Score: 212
Period size: 27 Copynumber: 4.6 Consensus size: 27
175720 TTGTAGGAAT
175730 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
175755 TATAGAGATATGATTTGTTTCCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
175782 TATAGAGATATGATTTGTTTCCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
175809 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
175836 TATAGAGATATGATTT
1 TATAGAGATATGATTT
175852 TGTAAATAGA
Statistics
Matches: 93, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
25 7 0.08
27 86 0.92
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:179612 original size:27 final size:27
Alignment explanation
Indices: 179570--179664 Score: 167
Period size: 27 Copynumber: 3.6 Consensus size: 27
179560 GTGTAGGAAT
179570 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
179595 TATAGAGATATGATTTGTTTCCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
179622 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
179649 TATAGAGATATGATTT
1 TATAGAGATATGATTT
179665 TGTAAATAGA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
25 7 0.11
27 59 0.89
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:181337 original size:17 final size:17
Alignment explanation
Indices: 181294--181329 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
181284 TAAAGGTGTG
181294 TTTATTTTTCTATCTTC
1 TTTATTTTTCTATCTTC
181311 TTTATTTTTCTATCTTC
1 TTTATTTTTCTATCTTC
181328 TT
1 TT
181330 CTTTTTTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTTTCTATCTTC
Found at i:182085 original size:41 final size:41
Alignment explanation
Indices: 182040--182121 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
182030 AGTTTAGGAG
182040 GCAGTGTTCCAACTGCGATATGCCCCAATGATGTGTTTCAA
1 GCAGTGTTCCAACTGCGATATGCCCCAATGATGTGTTTCAA
182081 GCAGTGTTCCAACTGCGATATGCCCCAATGATGTGTTTCAA
1 GCAGTGTTCCAACTGCGATATGCCCCAATGATGTGTTTCAA
182122 CTACCCAGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (41 bp):
GCAGTGTTCCAACTGCGATATGCCCCAATGATGTGTTTCAA
Found at i:185345 original size:121 final size:122
Alignment explanation
Indices: 185130--185368 Score: 417
Period size: 121 Copynumber: 2.0 Consensus size: 122
185120 GCCCTAATGG
** *
185130 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGGCCGTAGCCCTCCGGCATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
185195 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGACCA
66 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGACCA
* * *
185252 TACATATGTAGATTATGGTACGAAACTACCATTGG-CATACAATGAACGTAGCCCTCCAGCATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
185316 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTG
66 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTG
185369 GACTCTTTAA
Statistics
Matches: 111, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
121 79 0.71
122 32 0.29
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (122 bp):
TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGACCA
Found at i:186855 original size:10 final size:10
Alignment explanation
Indices: 186840--186914 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
186830 CATTTAATAA
186840 ATAAACGAAC
1 ATAAACGAAC
186850 ATAAACGAAC
1 ATAAACGAAC
186860 ----ACGAAC
1 ATAAACGAAC
186866 ATAAACGAAC
1 ATAAACGAAC
** *
186876 ACGAAC-ATAA
1 ATAAACGA-AC
186886 ATGAACACGAAC
1 AT-AA-ACGAAC
186898 ATAAACGAAC
1 ATAAACGAAC
186908 ATAAACG
1 ATAAACG
186915 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:186865 original size:16 final size:16
Alignment explanation
Indices: 186844--186908 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
186834 TAATAAATAA
186844 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
186860 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
186876 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
186892 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
186908 A
1 A
186909 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:187676 original size:14 final size:14
Alignment explanation
Indices: 187659--187714 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
187649 AATGAACATA
187659 AACGAACATAATCG
1 AACGAACATAATCG
187673 AACGAACAT-A---
1 AACGAACATAATCG
* *
187683 AACAAACATAACCG
1 AACGAACATAATCG
187697 AACGAACATAATCG
1 AACGAACATAATCG
187711 AACG
1 AACG
187715 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:187679 original size:24 final size:24
Alignment explanation
Indices: 187639--187713 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
187629 GATTGAGTTA
*
187639 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
187663 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* *
187687 AACATAACCGAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
187711 AAC
1 AAC
187714 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:188903 original size:6 final size:6
Alignment explanation
Indices: 188892--188919 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
188882 AACAGACGAC
188892 GATGAA GATGAA GATGAA GATGAA GATG
1 GATGAA GATGAA GATGAA GATGAA GATG
188920 GGCGACGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.36, T:0.18
Consensus pattern (6 bp):
GATGAA
Found at i:200157 original size:37 final size:37
Alignment explanation
Indices: 200105--200190 Score: 145
Period size: 37 Copynumber: 2.3 Consensus size: 37
200095 TTTTGTTCGG
200105 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
* * *
200142 GTCGGATCGGTTTTTTTAAGTGTGATATTCGGGTCGG
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
200179 GTCGGGTCGGGT
1 GTCGGGTCGGGT
200191 CGAGTTCGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.12, C:0.12, G:0.40, T:0.37
Consensus pattern (37 bp):
GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:205054 original size:26 final size:28
Alignment explanation
Indices: 204994--205055 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
204984 GAGTATTGCT
*
204994 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
205025 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
205051 GAGCT
1 GAGCT
205056 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:205690 original size:121 final size:122
Alignment explanation
Indices: 205475--205714 Score: 419
Period size: 121 Copynumber: 2.0 Consensus size: 122
205465 TCCCTAATGG
** *
205475 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGGCCGTAGCCCTCCGACATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAACATTC
205540 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
66 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
* * *
205597 TACATATGTAGATTATGGTACGAAACTACCATTGG-CATACAATGAACGTAGCCCTCCAACATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAACATTC
205661 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGG
66 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGG
205715 ACTCTTTAAG
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
121 80 0.71
122 32 0.29
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (122 bp):
TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAACATTC
TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
Found at i:215825 original size:36 final size:36
Alignment explanation
Indices: 215778--215852 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
215768 TCTTTAGAAG
215778 CATGAGACTCAATAAAATAGTGTTATAGTCGAAAAT
1 CATGAGACTCAATAAAATAGTGTTATAGTCGAAAAT
215814 CATGAGACTCAATAAAATAGTGTTATAGTCGAAAAT
1 CATGAGACTCAATAAAATAGTGTTATAGTCGAAAAT
215850 CAT
1 CAT
215853 TTATATACTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (36 bp):
CATGAGACTCAATAAAATAGTGTTATAGTCGAAAAT
Found at i:216241 original size:21 final size:21
Alignment explanation
Indices: 216217--216281 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
216207 GATTCGCATT
216217 GCGATAGTCCAAAATCGCAAC
1 GCGATAGTCCAAAATCGCAAC
* * * * **
216238 GCGAT-TTTCAGATTCGCATT
1 GCGATAGTCCAAAATCGCAAC
216258 GCGATAGTCCAAAATCGCAAC
1 GCGATAGTCCAAAATCGCAAC
216279 GCG
1 GCG
216282 GTTTTAAGAT
Statistics
Matches: 31, Mismatches: 12, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22
Consensus pattern (21 bp):
GCGATAGTCCAAAATCGCAAC
Found at i:216254 original size:41 final size:41
Alignment explanation
Indices: 216149--216303 Score: 211
Period size: 41 Copynumber: 3.6 Consensus size: 41
216139 ATTTCGCGTT
*
216149 GCGATTTTCCAGATTCGCATTGCGATAGTCTAAAATCGCAACAC
1 GCGATTTT-CAGATTCGCATTGCGATAGTCCAAAATCGC-A-AC
216193 GGTTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
1 ----GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
216238 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
* * *
216279 GCGGTTTTAAGATTTGCATTGCGAT
1 GCGATTTTCAGATTCGCATTGCGAT
216304 TTTCAGATTC
Statistics
Matches: 103, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
41 63 0.61
45 2 0.02
46 1 0.01
47 29 0.28
48 8 0.08
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (41 bp):
GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
Found at i:216306 original size:61 final size:61
Alignment explanation
Indices: 216238--216364 Score: 236
Period size: 61 Copynumber: 2.1 Consensus size: 61
216228 AAATCGCAAC
*
216238 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTTGCATT
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATT
216299 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATT
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATT
*
216360 ACGAT
1 GCGAT
216365 AGTATAAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (61 bp):
GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATT
Found at i:216324 original size:102 final size:102
Alignment explanation
Indices: 216195--216405 Score: 350
Period size: 102 Copynumber: 2.1 Consensus size: 102
216185 CGCAACACGG
* *
216195 TTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTCAGATTCGCATTGC
1 TTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTAAGATTCGCATTAC
* * *
216260 GATAGTCCAAAATCGCAACGCGGTTTTAAGATTTGCA
66 GATAGTACAAAATCGCAACGCGATTTTAAGATTCGCA
*
216297 TTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATTAC
1 TTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTAAGATTCGCATTAC
* *
216362 GATAGTATAAAATCGCAACGCGATTTTCAGATTCGCA
66 GATAGTACAAAATCGCAACGCGATTTTAAGATTCGCA
216399 TTGCGAT
1 TTGCGAT
216406 AGTCCAAAAT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (102 bp):
TTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTAAGATTCGCATTAC
GATAGTACAAAATCGCAACGCGATTTTAAGATTCGCA
Found at i:216353 original size:41 final size:41
Alignment explanation
Indices: 216299--216466 Score: 264
Period size: 41 Copynumber: 4.1 Consensus size: 41
216289 GATTTGCATT
216299 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
* * * **
216340 GCGGTTTTAAGATTCGCATTACGATAGTATAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
*
216381 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAA
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
**
216422 GCGATTTTCAGATTCGCATTGCGATAGTTGAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
216463 GCGA
1 GCGA
216467 CTGGTGGTAT
Statistics
Matches: 113, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 113 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (41 bp):
GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
Found at i:216435 original size:143 final size:147
Alignment explanation
Indices: 216141--216446 Score: 458
Period size: 143 Copynumber: 2.1 Consensus size: 147
216131 ATGGCCCCAT
* * *
216141 TTCGCGTTGCGATTTTCCAGATTCGCATTGCGATAGTCTAAAATCGCAACACGGTTGCGATTTTC
1 TTCGCATTGCGATTTTCCAGATTCGCATTGCGATAGTCCAAAATCGCAACAC-G--GCGATTTTA
* *
216206 AGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAA
63 AGATTCGCATTACGATAGTACAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAA
* *
216271 ATCGCAACGCGGTTTTAAGA
128 ATCGCAAAGCGATTTTAAGA
* *
216291 TTTGCATTGCGATTTT-CAGATTCGCATTGCGATAGTCCAAAATCGC-A-AC-GCGGTTTTAAGA
1 TTCGCATTGCGATTTTCCAGATTCGCATTGCGATAGTCCAAAATCGCAACACGGCGATTTTAAGA
*
216352 TTCGCATTACGATAGTATAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATC
66 TTCGCATTACGATAGTACAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATC
*
216417 GCAAAGCGATTTTCAGA
131 GCAAAGCGATTTTAAGA
216434 TTCGCATTGCGAT
1 TTCGCATTGCGAT
216447 AGTTGAAAAT
Statistics
Matches: 144, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
143 98 0.68
147 2 0.01
148 1 0.01
149 29 0.20
150 14 0.10
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (147 bp):
TTCGCATTGCGATTTTCCAGATTCGCATTGCGATAGTCCAAAATCGCAACACGGCGATTTTAAGA
TTCGCATTACGATAGTACAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATC
GCAAAGCGATTTTAAGA
Found at i:216556 original size:6 final size:6
Alignment explanation
Indices: 216545--216569 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
216535 GACACGTATT
216545 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
216570 TATTATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:223900 original size:37 final size:37
Alignment explanation
Indices: 223848--223926 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
223838 TTTTGTTCGG
*
223848 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCGA
* *
223885 GTCGGATCGGTTTTTTTAAGTGTGATATTCGGGTCGG
1 GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCGA
223922 GTCGG
1 GTCGG
223927 GTCGAGTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.13, C:0.11, G:0.38, T:0.38
Consensus pattern (37 bp):
GTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:224088 original size:305 final size:300
Alignment explanation
Indices: 223579--224189 Score: 1034
Period size: 305 Copynumber: 2.0 Consensus size: 300
223569 CTTTATTTTG
* *
223579 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTCGGGTTCGGGTTTAGGGTGA
1 GTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTCGAGTTCGGGTTTAGGGTGA
*
223644 AAAAAACCGGACCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATA
66 AAAAAACCGGACCGACCCAAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATA
*
223709 ATACCCCTCTATATATTTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATT
131 ATACCCCTC---ATATTTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATT
223774 ATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATA-T-TCGGGTCGGGTCGGGTGAAACTTT
193 A-TT----TCGGGTCGGGTCGGATTTCTAATTCATATATTGTCGGGTCGGGTCGGGTGAAACTTT
*
223837 ATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
253 ATTTTGTTCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCGA
*
223885 GTCGGATC-GGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGA
1 GTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTCGAGTTCGGGTTTAGGGTGA
223949 AAAAAACCGGACCGACCCAAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATA
66 AAAAAACCGGACCGACCCAAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATA
224014 ATACCCCTC-T-TTTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATT
131 ATACCCCTCATATTTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATT
224077 TCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTCGGGTGAAACTTTATTTT
196 TCGGGTCGGGTCGGATTTCTAATTCATATATT---GTCGGGTCGGGTCGGGTGAAACTTTATTTT
224142 GTTCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCGA
258 GTTCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCGA
224185 GTCGG
1 GTCGG
224190 GAAACAAAAA
Statistics
Matches: 294, Mismatches: 6, Indels: 16
0.93 0.02 0.05
Matches are distributed among these distances:
295 30 0.10
296 1 0.00
299 2 0.01
300 126 0.43
301 1 0.00
305 127 0.43
306 7 0.02
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.38
Consensus pattern (300 bp):
GTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTCGAGTTCGGGTTTAGGGTGA
AAAAAACCGGACCGACCCAAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATA
ATACCCCTCATATTTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATT
TCGGGTCGGGTCGGATTTCTAATTCATATATTGTCGGGTCGGGTCGGGTGAAACTTTATTTTGTT
CGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:228828 original size:26 final size:28
Alignment explanation
Indices: 228768--228829 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
228758 GAGTATTGCT
*
228768 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
228799 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
228825 GAGCT
1 GAGCT
228830 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:229467 original size:121 final size:122
Alignment explanation
Indices: 229252--229491 Score: 419
Period size: 121 Copynumber: 2.0 Consensus size: 122
229242 TCCCTAATGG
** *
229252 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGGCCGTAGCCCTCCGACATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAACATTC
229317 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
66 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
* * *
229374 TACATATGTAGATTATGGTACGAAACTACCATTGG-CATACAATGAACGTAGCCCTCCAACATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAACATTC
229438 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGG
66 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGG
229492 ACTCTTTAAG
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
121 80 0.71
122 32 0.29
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (122 bp):
TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAACATTC
TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
Found at i:239508 original size:41 final size:41
Alignment explanation
Indices: 239403--239557 Score: 220
Period size: 41 Copynumber: 3.6 Consensus size: 41
239393 ATTTCGCGTT
*
239403 GCGATTTTCAAGATTCGCATTGCGATAGTCTAAAATCGCAACGC
1 GCGATTTTC-AGATTCGCATTGCGATAGTCCAAAATCGCAA--C
239447 GGTTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
1 ----GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
239492 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
* *
239533 GCGGTTTTAAGATTCGCATTGCGAT
1 GCGATTTTCAGATTCGCATTGCGAT
239558 TTTCCGATTC
Statistics
Matches: 104, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
41 64 0.62
45 1 0.01
47 30 0.29
48 9 0.09
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (41 bp):
GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
Found at i:239557 original size:61 final size:61
Alignment explanation
Indices: 239492--239618 Score: 236
Period size: 61 Copynumber: 2.1 Consensus size: 61
239482 AAATCGCAAC
239492 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATT
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATT
* *
239553 GCGATTTTCCGATTCGCATTGCTATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATT
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATT
239614 GCGAT
1 GCGAT
239619 AGTATAAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (61 bp):
GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATT
Found at i:239580 original size:102 final size:102
Alignment explanation
Indices: 239449--239659 Score: 350
Period size: 102 Copynumber: 2.1 Consensus size: 102
239439 CGCAACGCGG
*
239449 TTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTCAGATTCGCATTGC
1 TTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTAAGATTCGCATTGC
* *
239514 GATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCA
66 GATAGTACAAAATCGCAACGCGATTTTAAGATTCGCA
* * *
239551 TTGCGATTTTCCGATTCGCATTGCTATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATTGC
1 TTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTAAGATTCGCATTGC
* *
239616 GATAGTATAAAATCGCAACGCGATTTTCAGATTCGCA
66 GATAGTACAAAATCGCAACGCGATTTTAAGATTCGCA
239653 TTGCGAT
1 TTGCGAT
239660 AGTCCAAAAT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (102 bp):
TTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTAAGATTCGCATTGC
GATAGTACAAAATCGCAACGCGATTTTAAGATTCGCA
Found at i:239591 original size:41 final size:41
Alignment explanation
Indices: 239553--239720 Score: 264
Period size: 41 Copynumber: 4.1 Consensus size: 41
239543 GATTCGCATT
* *
239553 GCGATTTTCCGATTCGCATTGCTATAGTCCAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
* * **
239594 GCGGTTTTAAGATTCGCATTGCGATAGTATAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
239635 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
**
239676 GCGATTTTCAGATTCGCATTGCGATAGTTGAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
239717 GCGA
1 GCGA
239721 CTGGTGGTAT
Statistics
Matches: 115, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 115 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (41 bp):
GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
Found at i:239678 original size:143 final size:147
Alignment explanation
Indices: 239395--239700 Score: 476
Period size: 143 Copynumber: 2.1 Consensus size: 147
239385 ATGGCCCCAT
* * *
239395 TTCGCGTTGCGATTTTCAAGATTCGCATTGCGATAGTCTAAAATCGCAACGCGGTTGCGATTTTC
1 TTCGCATTGCGATTTTCAAGATTCGCATTGCGATAGTCCAAAATCGCAACGC-G--GCGATTTTA
*
239460 AGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAA
63 AGATTCGCATTGCGATAGTACAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAA
*
239525 ATCGCAACGCGGTTTTAAGA
128 ATCGCAACGCGATTTTAAGA
* *
239545 TTCGCATTGCGATTTTC-CGATTCGCATTGCTATAGTCCAAAATCGCAACGC-G-G-TTTTAAGA
1 TTCGCATTGCGATTTTCAAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGCGATTTTAAGA
*
239606 TTCGCATTGCGATAGTATAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATC
66 TTCGCATTGCGATAGTACAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATC
*
239671 GCAACGCGATTTTCAGA
131 GCAACGCGATTTTAAGA
239688 TTCGCATTGCGAT
1 TTCGCATTGCGAT
239701 AGTTGAAAAT
Statistics
Matches: 147, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
143 98 0.67
144 1 0.01
145 1 0.01
149 31 0.21
150 16 0.11
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (147 bp):
TTCGCATTGCGATTTTCAAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGCGATTTTAAGA
TTCGCATTGCGATAGTACAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATC
GCAACGCGATTTTAAGA
Found at i:239714 original size:21 final size:21
Alignment explanation
Indices: 239464--239714 Score: 97
Period size: 20 Copynumber: 12.2 Consensus size: 21
239454 ATTTTCAGAT
*
239464 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTTCAAAA
** * * *
239485 TCGCAACGCGAT-TTTCAGAT
1 TCGCATTGCGATAGTTCAAAA
*
239505 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTTCAAAA
** * * *
239526 TCGCAACGCGGT--TTTAAGAT
1 TCGCATTGCGATAGTTCAA-AA
* ** *
239546 TCGCATTGCGAT-TTTCCGAT
1 TCGCATTGCGATAGTTCAAAA
* *
239566 TCGCATTGCTATAGTCCAAAA
1 TCGCATTGCGATAGTTCAAAA
** * * *
239587 TCGCAACGCGGT--TTTAAGAT
1 TCGCATTGCGATAGTTCAA-AA
239607 TCGCATTGCGATAGTAT-AAAA
1 TCGCATTGCGATAGT-TCAAAA
** * * *
239628 TCGCAACGCGAT-TTTCAGAT
1 TCGCATTGCGATAGTTCAAAA
*
239648 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTTCAAAA
** * * *
239669 TCGCAACGCGAT-TTTCAGAT
1 TCGCATTGCGATAGTTCAAAA
*
239689 TCGCATTGCGATAGTTGAAAA
1 TCGCATTGCGATAGTTCAAAA
239710 TCGCA
1 TCGCA
239715 ACGCGACTGG
Statistics
Matches: 155, Mismatches: 64, Indels: 22
0.64 0.27 0.09
Matches are distributed among these distances:
19 7 0.05
20 74 0.48
21 70 0.45
22 3 0.02
23 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (21 bp):
TCGCATTGCGATAGTTCAAAA
Found at i:239810 original size:6 final size:6
Alignment explanation
Indices: 239799--239829 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
239789 GACACGTATT
239799 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
239830 TATTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:244043 original size:37 final size:37
Alignment explanation
Indices: 243991--244076 Score: 145
Period size: 37 Copynumber: 2.3 Consensus size: 37
243981 TTTTGTTCGG
243991 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
* * *
244028 GTCGGATCGGTTTTTTTAAGTGTGATATTCGGGTCGG
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
244065 GTCGGGTCGGGT
1 GTCGGGTCGGGT
244077 CGAGTTCGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.12, C:0.12, G:0.40, T:0.37
Consensus pattern (37 bp):
GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:244266 original size:304 final size:296
Alignment explanation
Indices: 243724--244336 Score: 964
Period size: 304 Copynumber: 2.0 Consensus size: 296
243714 CTTTATTTTG
*
243724 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTCGGGTTCGGGTTTAGGGTGA
1 GTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTCGGGTTCGGGTTTAGGGTGA
243789 AAAAAACCGGACCGACCCGAAAATATATATAATTTTACCTTATATTTAGGAATAATTACAATAAT
66 AAAAAACCGGACCGACCCGAAAATATATATAATTTTACCTTATATTTAGGAATAATTACAATAAT
*
243854 ACCCCTCTATATATTTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTAT
131 ACCCCTC-----ATTTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTAT
243919 TTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTT
191 TT---GTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTT
* *
243984 TGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
253 TGTTCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCAGGTCGA
*
244028 GTCGGATC-GGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTCGGGTCGAGTTCGGGTTTAG
1 GTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTC--G--G-GTTCGGGTTTAG
*
244092 GGTGAAAAAAACCGGACCGACCCGAATATATATATAATTTTACCTTATATATTTAGGAATAATTA
61 GGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTTTACC-T-TATATTTAGGAATAATTA
244157 CAATAATACCCCTC-TTTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATT
124 CAATAATACCCCTCATTTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATT
244221 A-TT-TCGGGTCGGGTCGGATTTCTAATTCATATATTCGAGTCGGGTCGGGTCGGGTGAAACTTT
189 ATTTGTCGGGTCGGGTCGGATTTCTAATTCATATA-T----TCGGGTCGGGTCGGGTGAAACTTT
244284 ATTTTGTTCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCAGGTCGA
249 ATTTTGTTCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCAGGTCGA
244332 GTCGG
1 GTCGG
244337 GAAACAAAAA
Statistics
Matches: 291, Mismatches: 6, Indels: 24
0.91 0.02 0.07
Matches are distributed among these distances:
299 30 0.10
300 1 0.00
303 38 0.13
304 132 0.45
305 1 0.00
307 1 0.00
308 55 0.19
309 1 0.00
310 32 0.11
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.38
Consensus pattern (296 bp):
GTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGTCGGGTTCGGGTTTAGGGTGA
AAAAAACCGGACCGACCCGAAAATATATATAATTTTACCTTATATTTAGGAATAATTACAATAAT
ACCCCTCATTTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTGTC
GGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGG
TCGGGTCGAGTTTTTTAAGTGTGATATTCAGGTCGA
Found at i:248976 original size:26 final size:28
Alignment explanation
Indices: 248916--248977 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
248906 GAGTATTGCT
*
248916 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
248947 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
248973 GAGCT
1 GAGCT
248978 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:249608 original size:121 final size:122
Alignment explanation
Indices: 249393--249632 Score: 419
Period size: 121 Copynumber: 2.0 Consensus size: 122
249383 TCCCTAATGG
** *
249393 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGGCCGTAGCCCTCCGACATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAACATTC
249458 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
66 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
* * *
249515 TACATATGTAGATTATGGTACGAAACTACCATTGG-CATACAATGAACGTAGCCCTCCAACATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAACATTC
249579 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGG
66 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGG
249633 ACTCTTTAAG
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
121 80 0.71
122 32 0.29
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (122 bp):
TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAACATTC
TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
Found at i:260493 original size:51 final size:51
Alignment explanation
Indices: 260417--260515 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 51
260407 TCCCTTCTTC
*
260417 GAATCTTCTTGCATGTTCTGCATATGGAGAAAAGACCTCCTTTTCCACGAA
1 GAATCTTCTTGCATGTTATGCATATGGAGAAAAGACCTCCTTTTCCACGAA
260468 GAATCTTCTTGCATGTTATGCATATGGAGAAAAGACCTCCTTTTCCAC
1 GAATCTTCTTGCATGTTATGCATATGGAGAAAAGACCTCCTTTTCCAC
260516 ATTTGATGGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (51 bp):
GAATCTTCTTGCATGTTATGCATATGGAGAAAAGACCTCCTTTTCCACGAA
Found at i:264671 original size:41 final size:41
Alignment explanation
Indices: 264566--264720 Score: 220
Period size: 41 Copynumber: 3.6 Consensus size: 41
264556 ATTTCGCGTT
*
264566 GCGATTTTCAAGATTCGCATTGCGATAGTCTAAAATCGCAACGC
1 GCGATTTTC-AGATTCGCATTGCGATAGTCCAAAATCGCAA--C
264610 GGTTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
1 ----GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
264655 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
* *
264696 GCGGTTTTAAGATTCGCATTGCGAT
1 GCGATTTTCAGATTCGCATTGCGAT
264721 TTTCCGATTC
Statistics
Matches: 104, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
41 64 0.62
45 1 0.01
47 30 0.29
48 9 0.09
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (41 bp):
GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
Found at i:264720 original size:61 final size:61
Alignment explanation
Indices: 264655--264781 Score: 245
Period size: 61 Copynumber: 2.1 Consensus size: 61
264645 AAATCGCAAC
264655 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATT
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATT
*
264716 GCGATTTTCCGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATT
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATT
264777 GCGAT
1 GCGAT
264782 AGTATAAAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (61 bp):
GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATT
Found at i:264741 original size:102 final size:102
Alignment explanation
Indices: 264612--264822 Score: 359
Period size: 102 Copynumber: 2.1 Consensus size: 102
264602 CGCAACGCGG
*
264612 TTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTCAGATTCGCATTGC
1 TTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTAAGATTCGCATTGC
* *
264677 GATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCA
66 GATAGTACAAAATCGCAACGCGATTTTAAGATTCGCA
* *
264714 TTGCGATTTTCCGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATTGC
1 TTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTAAGATTCGCATTGC
* *
264779 GATAGTATAAAATCGCAACGCGATTTTCAGATTCGCA
66 GATAGTACAAAATCGCAACGCGATTTTAAGATTCGCA
264816 TTGCGAT
1 TTGCGAT
264823 AGTCCAAAAT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (102 bp):
TTGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTAAGATTCGCATTGC
GATAGTACAAAATCGCAACGCGATTTTAAGATTCGCA
Found at i:264754 original size:41 final size:41
Alignment explanation
Indices: 264716--264883 Score: 273
Period size: 41 Copynumber: 4.1 Consensus size: 41
264706 GATTCGCATT
*
264716 GCGATTTTCCGATTCGCATTGCGATAGTCCAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
* * **
264757 GCGGTTTTAAGATTCGCATTGCGATAGTATAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
264798 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
**
264839 GCGATTTTCAGATTCGCATTGCGATAGTTGAAAATCGCAAC
1 GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
264880 GCGA
1 GCGA
264884 CTGGTGGTAT
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 116 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (41 bp):
GCGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAAC
Found at i:264815 original size:61 final size:61
Alignment explanation
Indices: 264675--264802 Score: 177
Period size: 61 Copynumber: 2.1 Consensus size: 61
264665 GATTCGCATT
* ** * **
264675 GCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATTGCGATTTTCCGATTCGCATT
1 GCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATTGCGATTATCAAAATCGCAAC
264736 GCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATTGCGATAGTAT-AAAATCGCAAC
1 GCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATTGCGAT--TATCAAAATCGCAAC
264798 GCGAT
1 GCGAT
264803 TTTCAGATTC
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
61 46 0.78
62 11 0.19
63 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (61 bp):
GCGATAGTCCAAAATCGCAACGCGGTTTTAAGATTCGCATTGCGATTATCAAAATCGCAAC
Found at i:264841 original size:143 final size:147
Alignment explanation
Indices: 264558--264863 Score: 485
Period size: 143 Copynumber: 2.1 Consensus size: 147
264548 ATGGCCCCAT
* * *
264558 TTCGCGTTGCGATTTTCAAGATTCGCATTGCGATAGTCTAAAATCGCAACGCGGTTGCGATTTTC
1 TTCGCATTGCGATTTTCAAGATTCGCATTGCGATAGTCCAAAATCGCAACGC-G--GCGATTTTA
*
264623 AGATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAA
63 AGATTCGCATTGCGATAGTACAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAA
*
264688 ATCGCAACGCGGTTTTAAGA
128 ATCGCAACGCGATTTTAAGA
*
264708 TTCGCATTGCGATTTTC-CGATTCGCATTGCGATAGTCCAAAATCGCAACGC-G-G-TTTTAAGA
1 TTCGCATTGCGATTTTCAAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGCGATTTTAAGA
*
264769 TTCGCATTGCGATAGTATAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATC
66 TTCGCATTGCGATAGTACAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATC
*
264834 GCAACGCGATTTTCAGA
131 GCAACGCGATTTTAAGA
264851 TTCGCATTGCGAT
1 TTCGCATTGCGAT
264864 AGTTGAAAAT
Statistics
Matches: 148, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
143 98 0.66
144 1 0.01
145 1 0.01
149 32 0.22
150 16 0.11
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (147 bp):
TTCGCATTGCGATTTTCAAGATTCGCATTGCGATAGTCCAAAATCGCAACGCGGCGATTTTAAGA
TTCGCATTGCGATAGTACAAAATCGCAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAAATC
GCAACGCGATTTTAAGA
Found at i:264877 original size:21 final size:21
Alignment explanation
Indices: 264627--264877 Score: 106
Period size: 20 Copynumber: 12.2 Consensus size: 21
264617 ATTTTCAGAT
*
264627 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTTCAAAA
** * * *
264648 TCGCAACGCGAT-TTTCAGAT
1 TCGCATTGCGATAGTTCAAAA
*
264668 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTTCAAAA
** * * *
264689 TCGCAACGCGGT--TTTAAGAT
1 TCGCATTGCGATAGTTCAA-AA
* ** *
264709 TCGCATTGCGAT-TTTCCGAT
1 TCGCATTGCGATAGTTCAAAA
*
264729 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTTCAAAA
** * * *
264750 TCGCAACGCGGT--TTTAAGAT
1 TCGCATTGCGATAGTTCAA-AA
264770 TCGCATTGCGATAGTAT-AAAA
1 TCGCATTGCGATAGT-TCAAAA
** * * *
264791 TCGCAACGCGAT-TTTCAGAT
1 TCGCATTGCGATAGTTCAAAA
*
264811 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTTCAAAA
** * * *
264832 TCGCAACGCGAT-TTTCAGAT
1 TCGCATTGCGATAGTTCAAAA
*
264852 TCGCATTGCGATAGTTGAAAA
1 TCGCATTGCGATAGTTCAAAA
264873 TCGCA
1 TCGCA
264878 ACGCGACTGG
Statistics
Matches: 157, Mismatches: 62, Indels: 22
0.65 0.26 0.09
Matches are distributed among these distances:
19 7 0.04
20 75 0.48
21 71 0.45
22 3 0.02
23 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTTCAAAA
Found at i:264973 original size:6 final size:6
Alignment explanation
Indices: 264962--264992 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
264952 GACACGTATT
264962 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
264993 TATTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Done.