Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001838.1 Hibiscus syriacus cultivar Beakdansim tig00003721_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: 3924084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 18
Found at i:2332674 original size:24 final size:24
Alignment explanation
Indices: 2332647--2332705 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
2332637 TTCTTTTTGA
*
2332647 TTTTTGTTCTTTCTT-TTTTTTTCT
1 TTTTTGTT-TTTCTTCTTCTTTTCT
2332671 TTTTCT-TTTTT-TTGCTTCTTTTCT
1 TTTT-TGTTTTTCTT-CTTCTTTTCT
2332695 TTTTTGTTTTT
1 TTTTTGTTTTT
2332706 TCCCTTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
22 2 0.07
23 4 0.13
24 23 0.77
25 1 0.03
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (24 bp):
TTTTTGTTTTTCTTCTTCTTTTCT
Found at i:2332675 original size:16 final size:16
Alignment explanation
Indices: 2332634--2332699 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
2332624 TTTTTGTCCC
**
2332634 TTTTTCTTTTTGATTT
1 TTTTTCTTTTTCTTTT
*
2332650 TTGTTC--TTTCTTTT
1 TTTTTCTTTTTCTTTT
2332664 TTTTTCTTTTTCTTTT
1 TTTTTCTTTTTCTTTT
*
2332680 TTTTGCTTCTTTTCTTTT
1 TTTTTC-T-TTTTCTTTT
2332698 TT
1 TT
2332700 GTTTTTTCCC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
14 11 0.27
16 18 0.44
17 1 0.02
18 11 0.27
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTTTCTTTT
Found at i:2332681 original size:30 final size:30
Alignment explanation
Indices: 2332634--2332719 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
2332624 TTTTTGTCCC
*
2332634 TTTTTCTTTTTGATTTTTGTTCTTTCTTTT
1 TTTTTCTTTTTCATTTTTGTTCTTTCTTTT
*
2332664 TTTTTCTTTTTCTTTTTTTTGCTTCTTTTCTTTT
1 TTTTTCTTTTTC--ATTTTTG-TTC-TTTCTTTT
* * *
2332698 TTGTT-TTTTCCCTTTTTGTTCT
1 TTTTTCTTTTTCATTTTTGTTCT
2332720 GATTAAATCT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
29 1 0.02
30 14 0.30
31 6 0.13
32 6 0.13
33 8 0.17
34 12 0.26
ACGTcount: A:0.01, C:0.14, G:0.06, T:0.79
Consensus pattern (30 bp):
TTTTTCTTTTTCATTTTTGTTCTTTCTTTT
Found at i:2332700 original size:16 final size:15
Alignment explanation
Indices: 2332647--2332719 Score: 69
Period size: 14 Copynumber: 4.7 Consensus size: 15
2332637 TTCTTTTTGA
2332647 TTTTTGTTC-TTTCT
1 TTTTTGTTCTTTTCT
*
2332661 TTTTTTTTCTTTTTCTTT
1 TTTTTGTTC-TTTTC--T
2332679 TTTTTGCTTCTTTTCT
1 TTTTTG-TTCTTTTCT
*
2332695 TTTTTGTT-TTTTCCC
1 TTTTTGTTCTTTT-CT
2332710 TTTTTGTTCT
1 TTTTTGTTCT
2332720 GATTAAATCT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
14 12 0.24
15 11 0.22
16 12 0.24
18 11 0.22
19 3 0.06
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.79
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Found at i:2336149 original size:19 final size:19
Alignment explanation
Indices: 2336116--2336152 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2336106 TGCAGATGAT
2336116 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
2336135 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
2336153 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:2338657 original size:28 final size:28
Alignment explanation
Indices: 2338617--2338671 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2338607 ATGCAAAATG
2338617 TAAATAAACATATATACATTATAATTTA
1 TAAATAAACATATATACATTATAATTTA
* * **
2338645 TAAATATATATATATTTATTATAATTT
1 TAAATAAACATATATACATTATAATTT
2338672 GCAAATTAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (28 bp):
TAAATAAACATATATACATTATAATTTA
Found at i:2342592 original size:74 final size:74
Alignment explanation
Indices: 2342454--2342592 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 74
2342444 TTCGGGACAA
* * * * *
2342454 CAATAGTGGCGTTTTTTTGACAAACGCCGCAATAGGTCCATCTATAGTAGCATTTTTTTCAAAAA
1 CAATAGTGGCGTTTTTCTGACAAACGCCGCAAGAAGTCCATCTATAGTAGCATTTATTGCAAAAA
2342519 AAGCCACAG
66 AAGCCACAG
* * * * *
2342528 CAATAGTGGTGTTTTTCTGATAAACGCCGCAAGAAGTCCATCTATAGTGGCGTTTATTGGAAAAA
1 CAATAGTGGCGTTTTTCTGACAAACGCCGCAAGAAGTCCATCTATAGTAGCATTTATTGCAAAAA
2342593 TGACACTATA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
74 55 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (74 bp):
CAATAGTGGCGTTTTTCTGACAAACGCCGCAAGAAGTCCATCTATAGTAGCATTTATTGCAAAAA
AAGCCACAG
Found at i:2346195 original size:15 final size:15
Alignment explanation
Indices: 2346175--2346210 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
2346165 ACCAATGAAC
2346175 GGAAAGAGAGGAGAA
1 GGAAAGAGAGGAGAA
*
2346190 GGAAAGAGAGGAGGA
1 GGAAAGAGAGGAGAA
2346205 GGAAAG
1 GGAAAG
2346211 TGAAAGGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (15 bp):
GGAAAGAGAGGAGAA
Found at i:2348065 original size:22 final size:22
Alignment explanation
Indices: 2348040--2348081 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2348030 CTTTGATCGA
*
2348040 TCTAACCGTTAACTTTGACTAG
1 TCTAACCATTAACTTTGACTAG
* *
2348062 TCTAGCCATTGACTTTGACT
1 TCTAACCATTAACTTTGACT
2348082 TTGACAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (22 bp):
TCTAACCATTAACTTTGACTAG
Found at i:2349703 original size:35 final size:35
Alignment explanation
Indices: 2349663--2349802 Score: 113
Period size: 35 Copynumber: 4.0 Consensus size: 35
2349653 GAAGTCTCTG
*
2349663 TAGGTTCAGTTCGATCAAACTGGTAATTCCTTATA
1 TAGGTTCAGTCCGATCAAACTGGTAATTCCTTATA
* * **
2349698 TAGGTTCA-TACCAATCAAATTGGTAATTCCTTACGG
1 TAGGTTCAGT-CCGATCAAACTGGTAATTCCTTA-TA
* * * * *
2349734 CATGTTCAG-CTCGGTCAAATTGCTAATTCCTTATA
1 TAGGTTCAGTC-CGATCAAACTGGTAATTCCTTATA
* ** *
2349769 TAGGTTCAGACCGATTGAGCTGGTAATTCCTTAT
1 TAGGTTCAGTCCGATCAAACTGGTAATTCCTTAT
2349803 GGATCTAAGG
Statistics
Matches: 80, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
34 1 0.01
35 53 0.66
36 26 0.32
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (35 bp):
TAGGTTCAGTCCGATCAAACTGGTAATTCCTTATA
Found at i:2349793 original size:71 final size:71
Alignment explanation
Indices: 2349666--2349801 Score: 182
Period size: 71 Copynumber: 1.9 Consensus size: 71
2349656 GTCTCTGTAG
* * * *
2349666 GTTCAGTTCGATCAAACTGGTAATTCCTTATATAGGTTCATACCAATCAAATTGGTAATTCCTTA
1 GTTCAGCTCGATCAAACTGCTAATTCCTTATATAGGTTCAGACCAATCAAACTGGTAATTCCTTA
2349731 CGGCAT
66 CGGCAT
* * * ** *
2349737 GTTCAGCTCGGTCAAATTGCTAATTCCTTATATAGGTTCAGACCGATTGAGCTGGTAATTCCTTA
1 GTTCAGCTCGATCAAACTGCTAATTCCTTATATAGGTTCAGACCAATCAAACTGGTAATTCCTTA
2349802 TGGATCTAAG
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
71 55 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (71 bp):
GTTCAGCTCGATCAAACTGCTAATTCCTTATATAGGTTCAGACCAATCAAACTGGTAATTCCTTA
CGGCAT
Found at i:2353044 original size:24 final size:24
Alignment explanation
Indices: 2353012--2353074 Score: 110
Period size: 24 Copynumber: 2.6 Consensus size: 24
2353002 ATGCATAGAT
2353012 AGTGCATCGATGCACACGTTAAGG
1 AGTGCATCGATGCACACGTTAAGG
2353036 AGTGCATCGATGCACACGTTAAGG
1 AGTGCATCGATGCACACGTTAAGG
2353060 -GATGCATCGATGCAC
1 AG-TGCATCGATGCAC
2353075 TATATAGTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 1 0.03
24 37 0.97
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.21
Consensus pattern (24 bp):
AGTGCATCGATGCACACGTTAAGG
Found at i:2353643 original size:18 final size:18
Alignment explanation
Indices: 2353620--2353690 Score: 115
Period size: 18 Copynumber: 3.9 Consensus size: 18
2353610 AGGGATAATC
2353620 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
2353638 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCGGGACAT
*
2353656 AGTGGTTCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
2353674 AGTTGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
2353691 AATATTCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2353944 original size:35 final size:36
Alignment explanation
Indices: 2353898--2353969 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
2353888 TTGCAATGTC
2353898 CTAGGGATTG-A-TAGTGTATGTTCATGATATTATTG
1 CTAGGGATTGAAGTAGTGTATG-TCATGATATTATTG
2353933 CTAGGGATTGATAGTAGTGTATGTCATGATATTATTG
1 CTAGGGATTGA-AGTAGTGTATGTCATGATATTATTG
2353970 TTATATGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 10 0.29
37 15 0.44
38 9 0.26
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.42
Consensus pattern (36 bp):
CTAGGGATTGAAGTAGTGTATGTCATGATATTATTG
Found at i:2356651 original size:21 final size:21
Alignment explanation
Indices: 2356625--2356671 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
2356615 ATACTGTCAA
2356625 TGAAAGTTGATTCAT-CTACCT
1 TGAAAGTTGATTCATCCT-CCT
2356646 TGAAAGTTGATTCATCCTCCT
1 TGAAAGTTGATTCATCCTCCT
2356667 TGAAA
1 TGAAA
2356672 ATTAATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (21 bp):
TGAAAGTTGATTCATCCTCCT
Found at i:2357459 original size:183 final size:183
Alignment explanation
Indices: 2357151--2357514 Score: 712
Period size: 183 Copynumber: 2.0 Consensus size: 183
2357141 CACTTTCTAG
2357151 GTCCTCGCAAACTGCTTTTAGTAGCAAGAAACAACACATCGTGTAGAGAGGGATGGCCTGAAAGA
1 GTCCTCGCAAACTGCTTTTAGTAGCAAGAAACAACACATCGTGTAGAGAGGGATGGCCTGAAAGA
2357216 CAACATTGACATATACATCCTTACCACCTTGTGAAAACATTCGAGTACTCCATGAATGAACTCAC
66 CAACATTGACATATACATCCTTACCACCTTGTGAAAACATTCGAGTACTCCATGAATGAACTCAC
2357281 -ACAATAATCGTTCCTTTAAACTCAAGAATGCACCCATGCTTGTTTCTTCCGTC
131 AACAATAATCGTTCCTTTAAACTCAAGAATGCA-CCATGCTTGTTTCTTCCGTC
2357334 GTCCTCGCAAACTGCTTTTAGTAGCAAGAAACAACACATCGTGTAGAGAGGGATGGCCTGAAAGA
1 GTCCTCGCAAACTGCTTTTAGTAGCAAGAAACAACACATCGTGTAGAGAGGGATGGCCTGAAAGA
2357399 CAACATTGACATATACATCCTTACCACCTTGTGAAAACATTCGAGTACTCCATGAATGAACTCAC
66 CAACATTGACATATACATCCTTACCACCTTGTGAAAACATTCGAGTACTCCATGAATGAACTCAC
2357464 AACAATAATCGTTCCTTTAAACTCAAGAATGCACCATGCTTGTTTCTTCCG
131 AACAATAATCGTTCCTTTAAACTCAAGAATGCACCATGCTTGTTTCTTCCG
2357515 ATCATTGCTT
Statistics
Matches: 180, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
183 148 0.82
184 32 0.18
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (183 bp):
GTCCTCGCAAACTGCTTTTAGTAGCAAGAAACAACACATCGTGTAGAGAGGGATGGCCTGAAAGA
CAACATTGACATATACATCCTTACCACCTTGTGAAAACATTCGAGTACTCCATGAATGAACTCAC
AACAATAATCGTTCCTTTAAACTCAAGAATGCACCATGCTTGTTTCTTCCGTC
Found at i:2360982 original size:32 final size:32
Alignment explanation
Indices: 2360936--2361018 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
2360926 TACTGTGAAT
* * *
2360936 TATCTAAATACAATATTGACGCT-CTTGTGCAC
1 TATCTGAATGCAATATTGACGCTAC-TATGCAC
* *
2360968 TATCTGAATGCAATATTGACTCTACTATGCAT
1 TATCTGAATGCAATATTGACGCTACTATGCAC
*
2361000 TATTTGAATGCAATATTGA
1 TATCTGAATGCAATATTGA
2361019 ACTTGATGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
32 43 0.98
33 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (32 bp):
TATCTGAATGCAATATTGACGCTACTATGCAC
Found at i:2366396 original size:25 final size:25
Alignment explanation
Indices: 2366368--2366417 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
2366358 CATATAGTAA
2366368 TATAAGTTTACCAAAATATTCAGAG
1 TATAAGTTTACCAAAATATTCAGAG
2366393 TATAAGTTTACCAAAATATTCAGAG
1 TATAAGTTTACCAAAATATTCAGAG
2366418 CATACACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (25 bp):
TATAAGTTTACCAAAATATTCAGAG
Found at i:2366865 original size:23 final size:22
Alignment explanation
Indices: 2366834--2366902 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
2366824 CACCACAGCT
*
2366834 CGTATAATTGCACCTAAGTGCCA
1 CGTAGAATTGCACCT-AGTGCCA
* * *
2366857 CTTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACC-TAGTGCCA
2366880 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACC-TAGTGCCA
2366903 TATAACAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (22 bp):
CGTAGAATTGCACCTAGTGCCA
Found at i:2367049 original size:103 final size:103
Alignment explanation
Indices: 2366918--2367135 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
2366908 CAATGTCCAT
* *
2366918 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
* *
2366983 GACCTCACACATGTTCCAAAGAATACATATATGTTCCG
66 GACCTCACACATATTCCAAAGAATACATATATGTCCCG
2367021 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
*
2367086 GACCTCACACATATTCTAAAGAATACATATATGTCCCG
66 GACCTCACACATATTCCAAAGAATACATATATGTCCCG
2367124 AAGGACCACATA
1 AAGGACCACATA
2367136 GACCCTCTAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
GACCTCACACATATTCCAAAGAATACATATATGTCCCG
Found at i:2367704 original size:21 final size:21
Alignment explanation
Indices: 2367680--2367722 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2367670 TCATATTCGT
*
2367680 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
2367701 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
2367722 T
1 T
2367723 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:2373687 original size:23 final size:23
Alignment explanation
Indices: 2373661--2373724 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
2373651 CAGCTCGTAT
* * *
2373661 AATTGCACCTAAGTGCTACTTAG
1 AATTGCACCGAAGTGCCACATAG
* *
2373684 AATTGCACCGGAGTGCCGCATAG
1 AATTGCACCGAAGTGCCACATAG
*
2373707 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
2373725 TATAATAATG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.23
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:2373913 original size:103 final size:103
Alignment explanation
Indices: 2373740--2373957 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
2373730 TAATGTCCAT
* * *
2373740 AAGGACCACATATCATTCCTTAAGAATCATGTACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
2373805 AACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
2373843 AAGGACCACATATCATTCCTTAAGAATCATATTCATATACCAAGGATCAAGTAGGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
*
2373908 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACCTCACACATGTTCCAAAGAATACATATATGTCCCG
2373946 AAGGACCACATA
1 AAGGACCACATA
2373958 GACCCTCTAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
AACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:2374476 original size:19 final size:20
Alignment explanation
Indices: 2374439--2374476 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2374429 TTTTTCATTA
*
2374439 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
2374459 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
2374477 TCTAGCGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:2374528 original size:21 final size:21
Alignment explanation
Indices: 2374504--2374546 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2374494 TCATATTCAT
* *
2374504 TTGAGGGGGTATTGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
2374525 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
2374546 T
1 T
2374547 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.35
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:2376582 original size:21 final size:21
Alignment explanation
Indices: 2376552--2376614 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
2376542 ATATGAAATT
*
2376552 TATCCCGAAGGACCTCATGTA
1 TATCCCGAAGGACCTCATATA
* * *
2376573 TGTTCCGAAGGACCTCGTATA
1 TATCCCGAAGGACCTCATATA
2376594 TATCCCGAAGGACCTCATATA
1 TATCCCGAAGGACCTCATATA
2376615 ACCCTCGACT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (21 bp):
TATCCCGAAGGACCTCATATA
Found at i:2378391 original size:17 final size:17
Alignment explanation
Indices: 2378350--2378421 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
2378340 ATTCATGCAT
2378350 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
2378367 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
2378385 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
2378402 CTAGTTCATTTATTAGA
1 CTAGTTCATTAATTAAA
2378419 CTA
1 CTA
2378422 ACTCTTAACT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
17 33 0.72
18 13 0.28
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:2385728 original size:191 final size:192
Alignment explanation
Indices: 2385404--2385791 Score: 742
Period size: 191 Copynumber: 2.0 Consensus size: 192
2385394 ATATGCTTAA
2385404 ATATTTATATGTTCTACAAATCCATATCATCAATAATTCAACATATATTCAGATACTCATATCAT
1 ATATTTATATGTTCTACAAATCCATATCATCAATAATTCAACATATATTCAGATACTCATATCAT
2385469 TTTTCTTATAATCATGTATGTCTTATCACATACCATGTATCACATGTACATATAATCAATTATAT
66 TTTTCTTATAATCATGTATGTCTTATCACATACCATGTATCACATGTACATATAATCAATTATAT
2385534 CATGTC-TAGCTTATGTTGTTTGATTATGTTCACATGGATCATATAACATATGTCAAAACAT
131 CATGTCATAGCTTATGTTGTTTGATTATGTTCACATGGATCATATAACATATGTCAAAACAT
*
2385595 ATATTTATATGTTCTACAAATCCATATCATCAATAATTCAACATATATTCATATACTCATATCAT
1 ATATTTATATGTTCTACAAATCCATATCATCAATAATTCAACATATATTCAGATACTCATATCAT
2385660 TTTTCTTATAATCATGTATGTCTTATCACATACCATGTATCACATGTACATATAATCAATTATAT
66 TTTTCTTATAATCATGTATGTCTTATCACATACCATGTATCACATGTACATATAATCAATTATAT
2385725 CATGTCATATAGCTTATGTTGTTTGATTATGTTCACATGGATCATATAACATATGTCAAAACAT
131 CATGTC--ATAGCTTATGTTGTTTGATTATGTTCACATGGATCATATAACATATGTCAAAACAT
2385789 ATA
1 ATA
2385792 AACATATAAC
Statistics
Matches: 193, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
191 135 0.70
194 58 0.30
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.40
Consensus pattern (192 bp):
ATATTTATATGTTCTACAAATCCATATCATCAATAATTCAACATATATTCAGATACTCATATCAT
TTTTCTTATAATCATGTATGTCTTATCACATACCATGTATCACATGTACATATAATCAATTATAT
CATGTCATAGCTTATGTTGTTTGATTATGTTCACATGGATCATATAACATATGTCAAAACAT
Found at i:2386112 original size:147 final size:147
Alignment explanation
Indices: 2385883--2386183 Score: 595
Period size: 147 Copynumber: 2.1 Consensus size: 147
2385873 GAAATAGACT
2385883 TATC-ACAAGTCTTATTTCCATAAAACTACATCTATACTATAACATGCACTCACCTTAGCCACAC
1 TATCTACAAGTCTTATTTCCATAAAACTACATCTATACTATAACATGCACTCACCTTAGCCACAC
2385947 TGAATCCAAATCAACTTCTATGGCTTTATCCTTCTTAATCGATTCTAACTCTTCAGTCGTTCTAG
66 TGAATCCAAATCAACTTCTATGGCTTTATCCTTCTTAATCGATTCTAACTCTTCAGTCGTTCTAG
2386012 AACTTGCTTATGCTCGA
131 AACTTGCTTATGCTCGA
2386029 TATCTACAAGTCTTATTTCCATAAAACTACATCTATACTATAACATGCACTCACCTTAGCCACAC
1 TATCTACAAGTCTTATTTCCATAAAACTACATCTATACTATAACATGCACTCACCTTAGCCACAC
2386094 TGAATCCAAATCAACTTCTATGGCTTTATCCTTCTTAATCGATTCTAACTCTTCAGTCGTTCTAG
66 TGAATCCAAATCAACTTCTATGGCTTTATCCTTCTTAATCGATTCTAACTCTTCAGTCGTTCTAG
2386159 AACTTGCTTATGCTCGA
131 AACTTGCTTATGCTCGA
2386176 TATCTACA
1 TATCTACA
2386184 CAATCATACA
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
146 4 0.03
147 150 0.97
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.35
Consensus pattern (147 bp):
TATCTACAAGTCTTATTTCCATAAAACTACATCTATACTATAACATGCACTCACCTTAGCCACAC
TGAATCCAAATCAACTTCTATGGCTTTATCCTTCTTAATCGATTCTAACTCTTCAGTCGTTCTAG
AACTTGCTTATGCTCGA
Found at i:2388480 original size:19 final size:16
Alignment explanation
Indices: 2388445--2388478 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2388435 TGATGGCACA
2388445 GGAGGAGAAATTAGGT
1 GGAGGAGAAATTAGGT
2388461 GGAGGAGAAATTAGGT
1 GGAGGAGAAATTAGGT
2388477 GG
1 GG
2388479 TGCAGTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.47, T:0.18
Consensus pattern (16 bp):
GGAGGAGAAATTAGGT
Found at i:2389297 original size:23 final size:23
Alignment explanation
Indices: 2389237--2389300 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
2389227 CAGCTCGTAT
**
2389237 AAATGCACCGAAGTGCCATGTAG
1 AAATGCACCGAAGTGCCACATAG
* *
2389260 AATTGCA-CTATAGTGCCACATAG
1 AAATGCACCGA-AGTGCCACATAG
2389283 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
2389301 TATAAGATTG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 2 0.06
23 29 0.88
24 2 0.06
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:2390229 original size:45 final size:45
Alignment explanation
Indices: 2390147--2390366 Score: 388
Period size: 45 Copynumber: 4.9 Consensus size: 45
2390137 CATTTATCCC
*
2390147 ATATACTTACCATTTATTACCATAAGCTTGTAAGCTTATTTTACCA
1 ATATACTTACCATTTATT-CCATAAGCTCGTAAGCTTATTTTACCA
2390193 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
* *
2390238 ATATACTTACCATTTATTCCATAGGCTCATAAGCTTATTTTACCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
2390283 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
*
2390328 ATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
2390367 GCCAGTTTTT
Statistics
Matches: 168, Mismatches: 6, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
44 27 0.16
45 123 0.73
46 18 0.11
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.40
Consensus pattern (45 bp):
ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
Found at i:2392948 original size:35 final size:35
Alignment explanation
Indices: 2392907--2392980 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
2392897 CATATAATCA
2392907 CATAGTAATATAATATTTCATATGATCTCATAGGT
1 CATAGTAATATAATATTTCATATGATCTCATAGGT
2392942 CATAGTAATATAATATTTCATATGATCTCATAGGT
1 CATAGTAATATAATATTTCATATGATCTCATAGGT
2392977 CATA
1 CATA
2392981 TCGCATAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (35 bp):
CATAGTAATATAATATTTCATATGATCTCATAGGT
Found at i:2392981 original size:17 final size:17
Alignment explanation
Indices: 2392924--2392981 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
2392914 ATATAATATT
2392924 TCATATGATCTCATAGG
1 TCATATGATCTCATAGG
* * * **
2392941 TCATAGTAATATAATATT
1 TCATA-TGATCTCATAGG
2392959 TCATATGATCTCATAGG
1 TCATATGATCTCATAGG
2392976 TCATAT
1 TCATAT
2392982 CGCATAGATT
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (17 bp):
TCATATGATCTCATAGG
Found at i:2397104 original size:55 final size:55
Alignment explanation
Indices: 2397037--2397167 Score: 156
Period size: 55 Copynumber: 2.4 Consensus size: 55
2397027 GCATTCAGAT
* ** *
2397037 GATTCATGAAGAAGAACATTTGACGAATGAAGAAATTTGAACCTGACTGAAGAAC
1 GATTCATAAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAAC
* * * *
2397092 GATTCATAAAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGACC
1 GATTCATAAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAAC
* *
2397147 GATCCACAAAGAA-AGACATCC
1 GATTCATAAAGAAGA-ACATCC
2397168 TGAAGATGTT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (55 bp):
GATTCATAAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAAC
Found at i:2397949 original size:72 final size:72
Alignment explanation
Indices: 2397829--2397979 Score: 248
Period size: 72 Copynumber: 2.1 Consensus size: 72
2397819 CCCTATTACA
* * *
2397829 CAAGAAAATATGAAGACTTCGGGTGAGAATATGAATGTTAGTGATGCAGCCAATGTGATGATAGC
1 CAAGAACAGATGAAGACTTCGAGTGAGAATATGAATGTTAGTGATGCAGCCAATGTGATGATAGC
2397894 AAATGAT
66 AAATGAT
* *
2397901 CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
1 CAAGAACAGATGAAGACTTCGAGTGAGAATATGAATGTTAGTGATGCAGCCAATGTGATGATAGC
*
2397966 AATTGAT
66 AAATGAT
2397973 CAAGAAC
1 CAAGAAC
2397980 CTATTAGGGG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (72 bp):
CAAGAACAGATGAAGACTTCGAGTGAGAATATGAATGTTAGTGATGCAGCCAATGTGATGATAGC
AAATGAT
Found at i:2401619 original size:125 final size:125
Alignment explanation
Indices: 2401387--2401620 Score: 319
Period size: 125 Copynumber: 1.9 Consensus size: 125
2401377 GGCATGAATA
** *
2401387 AACCCACATCATGTTGAGATGACAAGATTTGGACCAAGGAGCCATGAAGAATGAGCCTTACAAAT
1 AACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGCCATGAAGAATGAGCCTTACAAAT
* * *
2401452 TGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATGAGATAATGTCGGGGTACGATTG
66 TGAGGTGATGGGGAATTTTGAAGGCCCGTACCAGAATAAGATAATGTCGGGGTACGATTG
* * * *
2401512 AACCCACATCATGTTGAGATGATAAGATTCAGACCAAGAAGGCATTGAA-AATGAGCCTTATAAT
1 AACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGCCA-TGAAGAATGAGCCTTACAAA
* * *
2401576 TTGAGGTGTTGGGGAATTTTGAAGGCTCTTACCTA-AATAAGATAA
65 TTGAGGTGATGGGGAATTTTGAAGGCCCGTACC-AGAATAAGATAA
2401621 CGTTGCGGCA
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
125 89 0.95
126 5 0.05
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (125 bp):
AACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGCCATGAAGAATGAGCCTTACAAAT
TGAGGTGATGGGGAATTTTGAAGGCCCGTACCAGAATAAGATAATGTCGGGGTACGATTG
Found at i:2402500 original size:37 final size:36
Alignment explanation
Indices: 2402413--2402518 Score: 115
Period size: 36 Copynumber: 2.9 Consensus size: 36
2402403 GGCAAAGTCG
* *
2402413 AGCCTTCACCAAAGATTAGTGAAGCAAACCATCTTA
1 AGCCTTCACCGAAGAGTAGTGAAGCAAACCATCTTA
* * *
2402449 AGCCTTCACCGAAGAGTAGTGAAGCATATCCTTTTTA
1 AGCCTTCACCGAAGAGTAGTGAAGCA-AACCATCTTA
* * *
2402486 AGCCTTCTCGGAAGAGT-GTTGGAGCAAACCATC
1 AGCCTTCACCGAAGAGTAG-TGAAGCAAACCATC
2402519 AGACTATCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
36 29 0.51
37 28 0.49
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (36 bp):
AGCCTTCACCGAAGAGTAGTGAAGCAAACCATCTTA
Found at i:2402877 original size:37 final size:37
Alignment explanation
Indices: 2402817--2402896 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
2402807 TTCAACCTTC
* *
2402817 GAAGCAAATCAAACTTAAGTCTTCACGAGAGAGTAGT
1 GAAGCAAATCAAACTTAAGTCTTCACAAGAAAGTAGT
* *
2402854 GAAGCAAATC-ATCTATAATTCTTCACAAGAAAGTAGT
1 GAAGCAAATCAAACT-TAAGTCTTCACAAGAAAGTAGT
*
2402891 AAAGCA
1 GAAGCA
2402897 GAAGAAGATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 3 0.08
37 34 0.92
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (37 bp):
GAAGCAAATCAAACTTAAGTCTTCACAAGAAAGTAGT
Found at i:2402974 original size:54 final size:54
Alignment explanation
Indices: 2402896--2403624 Score: 1179
Period size: 54 Copynumber: 13.5 Consensus size: 54
2402886 GTAGTAAAGC
* * *
2402896 AGAAGAAGATGTTCGAGTTTCATACTCCCTAGAGAAAGAGGGAACGAACCAGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
2402950 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCAGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
2403004 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * *
2403058 AGAAGAAGATGTTCGAGTTCCATACTCCTTAGAGAAAGAGGGAGCGAATCTGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
2403112 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGATAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
2403166 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGGGCGAACCAGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
**
2403220 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGAAAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
2403274 AGAAGAAGATGTTCGAGTTCCATACTCCTTAGAGAAAGAGGGAGCGAATCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
2403328 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGATAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * * *
2403382 AGAAGAAGATGTTCGAGTTTCATACTCCCTAGAGAAAGAGGGGGTGAACCAGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
2403436 AGAAGAAGATGTTCGAGTTTCATACTCCCTAGAGAAAGAGGGAGAGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * *
2403490 AGAAGAAGATGTTCGAGTTTCATACTCCTTAGAGAAAGAGGGAGCGAATCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
2403544 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGATAAAGAGGGAGTGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * *
2403598 AAAAGAAGACGTTTGAGTTCCATACTC
1 AGAAGAAGATGTTCGAGTTCCATACTC
2403625 TCTGAAGTAA
Statistics
Matches: 628, Mismatches: 47, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 628 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (54 bp):
AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
Found at i:2403787 original size:56 final size:55
Alignment explanation
Indices: 2403619--2403859 Score: 257
Period size: 56 Copynumber: 4.5 Consensus size: 55
2403609 TTTGAGTTCC
* * * * *
2403619 ATACTCTCTGAAGTAATAGAGAGCGGACACGTTTGTTAAAGA---TT-GAGTCCT
1 ATACTCTCTGAAGGAATAGAGAGCAGACACGTTTATTGAAGATTGTTCGAGTCTT
*
2403670 ATACTCTCTGAAGGAATAGGGAGCAGAC-CTGTTTATTGAAGATT-TTCCGAGT-TCT
1 ATACTCTCTGAAGGAATAGAGAGCAGACAC-GTTTATTGAAGATTGTT-CGAGTCT-T
* * *
2403725 ATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTCAAGTCTT
1 ATACTCTCTGAAGGAATAGAGAGCAGACACG-TTTATTGAAGATTGTTCGAGTCTT
* * *
2403781 AAACTCTCTGAATGAATAGAGAGTAGACACGTTTA-TGAAGATTGTTCGAGTCTT
1 ATACTCTCTGAAGGAATAGAGAGCAGACACGTTTATTGAAGATTGTTCGAGTCTT
*
2403835 ATACT-TCCTAAAGGAATAGAGAGCA
1 ATACTCT-CTGAAGGAATAGAGAGCA
2403860 TGCTCGTCAT
Statistics
Matches: 160, Mismatches: 19, Indels: 19
0.81 0.10 0.10
Matches are distributed among these distances:
50 1 0.01
51 35 0.22
53 3 0.02
54 37 0.23
55 36 0.22
56 45 0.28
57 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (55 bp):
ATACTCTCTGAAGGAATAGAGAGCAGACACGTTTATTGAAGATTGTTCGAGTCTT
Found at i:2404415 original size:146 final size:144
Alignment explanation
Indices: 2404153--2404442 Score: 546
Period size: 146 Copynumber: 2.0 Consensus size: 144
2404143 ACGTTGGTTT
2404153 TGACAGTATGTAAGTGGGGAGGGATATCAACAATGAACACCACAACGAAGAGAGGACACAGGCAA
1 TGACAGTATGTAAGTGGGGAGGGATATCAACAATGAACACCACAACGAAGAGAGGACACAGGCAA
2404218 GAAGAAAAAAAAGAAAAAAAAACGATCTGGAGAAACAAGAGAGTATACTGTAAATCCACTCCCGG
66 GAAGAAAAAAAAGAAAAAAAAACGATCTGGAGAAACAAGAGAGTATACTGTAAATCCACTCCCGG
2404283 ATATTCAAAACAAA
131 ATATTCAAAACAAA
2404297 TGACAGTATTGTAAGTGGGGAGGGATATCAACAATTGAACACCACAACGAAGAGAGGACACAGGC
1 TGACAGTA-TGTAAGTGGGGAGGGATATCAACAA-TGAACACCACAACGAAGAGAGGACACAGGC
2404362 -AGAAGAGAAAAAAAGAAAAAAAAACGATCTGGAGAAACAAGAGAGTATACTGTAAATCCACTCC
64 AAGAAGA-AAAAAAAGAAAAAAAAACGATCTGGAGAAACAAGAGAGTATACTGTAAATCCACTCC
2404426 CGGATATTCAAAACAAA
128 CGGATATTCAAAACAAA
2404443 GGGCAAATTG
Statistics
Matches: 143, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
144 8 0.06
145 31 0.22
146 104 0.73
ACGTcount: A:0.48, C:0.16, G:0.22, T:0.14
Consensus pattern (144 bp):
TGACAGTATGTAAGTGGGGAGGGATATCAACAATGAACACCACAACGAAGAGAGGACACAGGCAA
GAAGAAAAAAAAGAAAAAAAAACGATCTGGAGAAACAAGAGAGTATACTGTAAATCCACTCCCGG
ATATTCAAAACAAA
Found at i:2407794 original size:20 final size:20
Alignment explanation
Indices: 2407769--2407807 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2407759 TTCCTTTAGG
2407769 GGGTATC-GATACCCTCCTTA
1 GGGTATCAG-TACCCTCCTTA
2407789 GGGTATCAGTACCCTCCTT
1 GGGTATCAGTACCCTCCTT
2407808 GCATTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.18, C:0.31, G:0.21, T:0.31
Consensus pattern (20 bp):
GGGTATCAGTACCCTCCTTA
Found at i:2409493 original size:25 final size:25
Alignment explanation
Indices: 2409457--2409508 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
2409447 TAAGAAAATT
2409457 TAGTTAATGATT-TATAAATTTAAAA
1 TAGTTAATGATTATAT-AATTTAAAA
*
2409482 TAGTATAA-GATTATATATTTTAAAA
1 TAGT-TAATGATTATATAATTTAAAA
2409507 TA
1 TA
2409509 TAGTTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (25 bp):
TAGTTAATGATTATATAATTTAAAA
Found at i:2409520 original size:26 final size:27
Alignment explanation
Indices: 2409451--2409520 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 27
2409441 ATTATTTAAG
*
2409451 AAAATTTAGTTAATGATT-TATAAATTT
1 AAAATATAGTTAAT-ATTATATAAATTT
* *
2409478 -AAA-ATAGTATAAGATTATAT-ATTTT
1 AAAATATAGT-TAATATTATATAAATTT
2409503 AAAATATAGTTAATATTA
1 AAAATATAGTTAATATTA
2409521 GATTTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
25 11 0.31
26 19 0.54
27 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (27 bp):
AAAATATAGTTAATATTATATAAATTT
Found at i:2409541 original size:48 final size:50
Alignment explanation
Indices: 2409474--2409568 Score: 133
Period size: 48 Copynumber: 1.9 Consensus size: 50
2409464 TGATTTATAA
*
2409474 ATTTAAAATAGTATAAGATTAT-ATATTTTAAAA-TATAGTTAATATTAG
1 ATTTAAAATAATATAAGATTATAATATTTTAAAACTATAGTTAATATTAG
* *
2409522 ATTTAAAATAATA-ATAGATTTTAATATTTTAAAACTATATTTAATAT
1 ATTTAAAATAATATA-AGATTATAATATTTTAAAACTATAGTTAATAT
2409569 GTACAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 1 0.02
48 18 0.44
49 11 0.27
50 11 0.27
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.45
Consensus pattern (50 bp):
ATTTAAAATAATATAAGATTATAATATTTTAAAACTATAGTTAATATTAG
Found at i:2411974 original size:23 final size:23
Alignment explanation
Indices: 2411948--2412025 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 23
2411938 AAAATGAAAA
2411948 TAATAATAAAATAATATTTAAAT
1 TAATAATAAAATAATATTTAAAT
* * *
2411971 TAATAACTTAAA-CATATTGAAAT
1 TAATAA-TAAAATAATATTTAAAT
*
2411994 TAA-AATAATAATAATA-AT-AA-
1 TAATAATAA-AATAATATTTAAAT
2412014 TAATAATAAAAT
1 TAATAATAAAAT
2412026 TTAAGATACA
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
20 6 0.14
21 9 0.20
22 4 0.09
23 21 0.48
24 4 0.09
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.35
Consensus pattern (23 bp):
TAATAATAAAATAATATTTAAAT
Found at i:2412005 original size:3 final size:3
Alignment explanation
Indices: 2411997--2412022 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2411987 TTGAAATTAA
2411997 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2412023 AATTTAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2412234 original size:18 final size:19
Alignment explanation
Indices: 2412199--2412235 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2412189 CACAGAATGT
2412199 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2412219 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2412236 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2413636 original size:25 final size:25
Alignment explanation
Indices: 2413608--2413664 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
2413598 GCGACATGGA
2413608 TAGGGTTATAAAACCCTAAATGCAT
1 TAGGGTTATAAAACCCTAAATGCAT
2413633 TAGGGTTATAAAACCCTAAATGCAT
1 TAGGGTTATAAAACCCTAAATGCAT
2413658 TAGGGTT
1 TAGGGTT
2413665 TGGATCTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (25 bp):
TAGGGTTATAAAACCCTAAATGCAT
Found at i:2419307 original size:56 final size:56
Alignment explanation
Indices: 2419229--2419346 Score: 157
Period size: 56 Copynumber: 2.1 Consensus size: 56
2419219 TATTGCATTT
* * * *
2419229 TTGCATTTGCATTTATGTGTATGCACTAACTTGTTTTCCTTGTGCTTATCATTTTC
1 TTGCATTTACATTTATCTGTATGAACTAACTTGTTGTCCTTGTGCTTATCATTTTC
* * *
2419285 TTGCATTTACA-TTATCTAGTATGAACTAACTTGTTGTCCTTGTTCTTTTCTTTTTC
1 TTGCATTTACATTTATCT-GTATGAACTAACTTGTTGTCCTTGTGCTTATCATTTTC
2419341 TTGCAT
1 TTGCAT
2419347 CATGTGGTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
55 5 0.09
56 49 0.91
ACGTcount: A:0.17, C:0.18, G:0.13, T:0.53
Consensus pattern (56 bp):
TTGCATTTACATTTATCTGTATGAACTAACTTGTTGTCCTTGTGCTTATCATTTTC
Found at i:2426079 original size:21 final size:21
Alignment explanation
Indices: 2426055--2426132 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
2426045 CCTTCGGGAT
*
2426055 ATATATGTAATCCTTTGGAAC
1 ATATATGTGATCCTTTGGAAC
* * * *
2426076 ATATATATGATTCTTCGAAAC
1 ATATATGTGATCCTTTGGAAC
* * * *
2426097 ATATATTTGGTCATTTGGAAT
1 ATATATGTGATCCTTTGGAAC
2426118 ATATATGTGATCCTT
1 ATATATGTGATCCTT
2426133 AAGGAGTGGT
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (21 bp):
ATATATGTGATCCTTTGGAAC
Found at i:2426187 original size:23 final size:21
Alignment explanation
Indices: 2426140--2426197 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 21
2426130 CTTAAGGAGT
* * *
2426140 GGTCTTTCGGGACATCTATGT
1 GGTCATTCGGGACATCTACGC
*
2426161 GGTCCTTCGGGACATTTCTACGC
1 GGTCATTCGGGACA--TCTACGC
2426184 GGTCATTCGGGACA
1 GGTCATTCGGGACA
2426198 AATTCTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 13 0.42
23 18 0.58
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
GGTCATTCGGGACATCTACGC
Found at i:2430352 original size:41 final size:42
Alignment explanation
Indices: 2430269--2430355 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 42
2430259 GGGCCATCAG
* * * *
2430269 TAAGTCTTTCGAGCATGATGATTAAATCATTTGGGTCATCTA
1 TAAGTCTTTCAAGCAAGATGATTAAATCATTCGGATCATCTA
*
2430311 TAAGTCTTTCAAGCAAGATGA-TAAGTCATTCGGATCATCTA
1 TAAGTCTTTCAAGCAAGATGATTAAATCATTCGGATCATCTA
2430352 TAAG
1 TAAG
2430356 ACCTTGGGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 21 0.52
42 19 0.47
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (42 bp):
TAAGTCTTTCAAGCAAGATGATTAAATCATTCGGATCATCTA
Found at i:2432898 original size:47 final size:47
Alignment explanation
Indices: 2432774--2432907 Score: 132
Period size: 47 Copynumber: 2.9 Consensus size: 47
2432764 CTAACTTTTA
**
2432774 TTTTATTTTATTTTTATGATACTAACGGCT-ACCACTAACTCTTAAC
1 TTTTATTTTATTTTTATGATACTAACAACTAACCACTAACTCTTAAC
* * * * *
2432820 TTTTATTTTATTTTCAT-TTA-TAACTTTACTAAACTCTAACTAC-TAAC
1 TTTTATTTTATTTTTATGATACTAAC--AACTAACCACTAACT-CTTAAC
* *
2432867 TTTTATTTTATTTTTATGCTACTAACAACTAACCGCTAACT
1 TTTTATTTTATTTTTATGATACTAACAACTAACCACTAACT
2432908 GTTCACTCTT
Statistics
Matches: 71, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
44 4 0.06
45 2 0.03
46 18 0.25
47 40 0.56
48 3 0.04
49 4 0.06
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.48
Consensus pattern (47 bp):
TTTTATTTTATTTTTATGATACTAACAACTAACCACTAACTCTTAAC
Found at i:2432935 original size:101 final size:102
Alignment explanation
Indices: 2432811--2432996 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
2432801 GCTACCACTA
* *
2432811 ACTCTTAACTTTTATTTTATTTTCATTTATAACTTTACTAAACTCTAACTACTAAC-TTTTATTT
1 ACTCTTAACTTTTACTTTATTTTCATTTATAACTTTACTAAACTCTAACCACTAACTTTTTATTT
*
2432875 TATTTTTATGCTACTAACAACTAACCGCTAACTGTTC
66 TACTTTTATGCTACTAACAACTAACCGCTAACTGTTC
* * *
2432912 ACTCTTAACTTTTACTTTATTTTCATTTCTAACTTTACTAACCTCTGACCACTAACTTATTTTAT
1 ACTCTTAACTTTTACTTTATTTTCATTTATAACTTTACTAAACTCTAACCACTAAC-T-TTTTAT
*
2432977 TTTACTTTTATGTTACTAAC
64 TTTACTTTTATGCTACTAAC
2432997 TGCTAACTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 51 0.68
104 24 0.32
ACGTcount: A:0.28, C:0.20, G:0.03, T:0.49
Consensus pattern (102 bp):
ACTCTTAACTTTTACTTTATTTTCATTTATAACTTTACTAAACTCTAACCACTAACTTTTTATTT
TACTTTTATGCTACTAACAACTAACCGCTAACTGTTC
Found at i:2434445 original size:32 final size:31
Alignment explanation
Indices: 2434326--2434450 Score: 94
Period size: 31 Copynumber: 4.0 Consensus size: 31
2434316 AACCTCGGCA
* * * *
2434326 ACTGTCCATAGGTCCCGAAGAACCTAGGTAA-
1 ACTGTCCATA-TTTCCGTAGAACATAGGTAAT
* *
2434357 AATGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATAT-TTCCGTAGAACATAGGTAAT
* * *
2434388 ACTATCCATATGTCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATTTC-CGTAGA-ACATAGGTAAT
*
2434420 TCTGTCCATATATTCCGTAGAACATAGGTAA
1 ACTGTCCATAT-TTCCGTAGAACATAGGTAA
2434451 ACCCTCGACT
Statistics
Matches: 72, Mismatches: 15, Indels: 13
0.72 0.15 0.13
Matches are distributed among these distances:
30 5 0.07
31 40 0.56
32 23 0.32
33 4 0.06
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (31 bp):
ACTGTCCATATTTCCGTAGAACATAGGTAAT
Found at i:2434735 original size:2 final size:2
Alignment explanation
Indices: 2434728--2434798 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
2434718 ATATTATCCA
2434728 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 AT
2434769 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
2434799 TAACATGTCA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2435517 original size:64 final size:63
Alignment explanation
Indices: 2435394--2435530 Score: 161
Period size: 64 Copynumber: 2.2 Consensus size: 63
2435384 TCTTTAACTT
* * *
2435394 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACATTCGATGTTTTCATTTTAA-AGA
* * * * *
2435458 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTACATTCGATG-TTTCTTCTTTAAAGA
1 GTGCATCGATGCACTACC-CATGCATCGATACACCAATCACATTCGATGTTTTCAT-TTTAAAGA
2435521 GTGCATCGAT
1 GTGCATCGAT
2435531 ACACATTGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
63 18 0.29
64 45 0.71
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACCAATCACATTCGATGTTTTCATTTTAAAGA
Found at i:2437260 original size:61 final size:61
Alignment explanation
Indices: 2437165--2437290 Score: 243
Period size: 61 Copynumber: 2.1 Consensus size: 61
2437155 TTCCTTTCTG
*
2437165 GAAGAATTTGGATTTGAATGTTTTGTAGAGTAGTAGAAAGAAGAGCAGTTCCAATGAAGCT
1 GAAGAATTTGGATTTGAATGATTTGTAGAGTAGTAGAAAGAAGAGCAGTTCCAATGAAGCT
2437226 GAAGAATTTGGATTTGAATGATTTGTAGAGTAGTAGAAAGAAGAGCAGTTCCAATGAAGCT
1 GAAGAATTTGGATTTGAATGATTTGTAGAGTAGTAGAAAGAAGAGCAGTTCCAATGAAGCT
2437287 GAAG
1 GAAG
2437291 CATCTGCGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.28
Consensus pattern (61 bp):
GAAGAATTTGGATTTGAATGATTTGTAGAGTAGTAGAAAGAAGAGCAGTTCCAATGAAGCT
Found at i:2438753 original size:35 final size:36
Alignment explanation
Indices: 2438707--2438790 Score: 152
Period size: 35 Copynumber: 2.4 Consensus size: 36
2438697 ATCCAACAAT
*
2438707 AATGAATCTTTAAATATATATTATTCCGAATTT-AA
1 AATGAATCTTTAAATATAGATTATTCCGAATTTAAA
2438742 AATGAATCTTTAAATATAGATTATTCCGAATTTAAA
1 AATGAATCTTTAAATATAGATTATTCCGAATTTAAA
2438778 AATGAATCTTTAA
1 AATGAATCTTTAA
2438791 GTTAAATTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
35 32 0.68
36 15 0.32
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (36 bp):
AATGAATCTTTAAATATAGATTATTCCGAATTTAAA
Found at i:2441259 original size:32 final size:32
Alignment explanation
Indices: 2441212--2441277 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
2441202 TGAGTACATG
* *
2441212 ATGATACGATGGATACGGTTAGAACAACCCAT
1 ATGATACAATGGATACAGTTAGAACAACCCAT
*
2441244 ATGATACAATTGATACAGTTAGAACAACCCAT
1 ATGATACAATGGATACAGTTAGAACAACCCAT
2441276 AT
1 AT
2441278 CTCTGAGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (32 bp):
ATGATACAATGGATACAGTTAGAACAACCCAT
Found at i:2449553 original size:2 final size:2
Alignment explanation
Indices: 2449546--2449573 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2449536 AACAACCCAT
2449546 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
2449574 GTTTACTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2456688 original size:21 final size:21
Alignment explanation
Indices: 2456659--2456705 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2456649 GTCTTTGGGC
*
2456659 CCCTAAATAATATTTCTAAAT
1 CCCTTAATAATATTTCTAAAT
2456680 CCCTTAATAATATTTCTAAAT
1 CCCTTAATAATATTTCTAAAT
2456701 CCCTT
1 CCCTT
2456706 GGGTTTCCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.40
Consensus pattern (21 bp):
CCCTTAATAATATTTCTAAAT
Found at i:2456898 original size:18 final size:18
Alignment explanation
Indices: 2456875--2456920 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2456865 CACTCTTAAG
2456875 CTAGGGTATCGATACTAT
1 CTAGGGTATCGATACTAT
2456893 CTAGGGTATCGATACTAT
1 CTAGGGTATCGATACTAT
* *
2456911 GTAGAGTATC
1 CTAGGGTATC
2456921 AAAACTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (18 bp):
CTAGGGTATCGATACTAT
Found at i:2459203 original size:30 final size:30
Alignment explanation
Indices: 2459167--2459227 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2459157 AGATGTTGAT
2459167 TCTAGTTGTTGCTTTTATCATATTTTAGTG
1 TCTAGTTGTTGCTTTTATCATATTTTAGTG
*
2459197 TCTAGTTGTTTCTTTTATCATATTTTAGTG
1 TCTAGTTGTTGCTTTTATCATATTTTAGTG
2459227 T
1 T
2459228 GGAGATTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.16, C:0.10, G:0.15, T:0.59
Consensus pattern (30 bp):
TCTAGTTGTTGCTTTTATCATATTTTAGTG
Found at i:2460000 original size:69 final size:70
Alignment explanation
Indices: 2459889--2460029 Score: 266
Period size: 69 Copynumber: 2.0 Consensus size: 70
2459879 AGGATAATTG
*
2459889 GATATGAAAGACATGGTTAGGAAAGAGTAATATATGTGTTTTTGTATTAATGTTTCATTCGAGA-
1 GATATGAAAGACATGCTTAGGAAAGAGTAATATATGTGTTTTTGTATTAATGTTTCATTCGAGAT
2459953 TATAC
66 TATAC
2459958 GATATGAAAGACATGCTTAGGAAAGAGTAATATATGTGTTTTTGTATTAATGTTTCATTCGAGAT
1 GATATGAAAGACATGCTTAGGAAAGAGTAATATATGTGTTTTTGTATTAATGTTTCATTCGAGAT
2460023 TATAC
66 TATAC
2460028 GA
1 GA
2460030 GGTTTGGATA
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 63 0.90
70 7 0.10
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (70 bp):
GATATGAAAGACATGCTTAGGAAAGAGTAATATATGTGTTTTTGTATTAATGTTTCATTCGAGAT
TATAC
Found at i:2460926 original size:21 final size:21
Alignment explanation
Indices: 2460905--2460979 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
2460895 ACCTTGCAAG
2460905 GGATCGATCCCTTTTC-AAAA
1 GGATCGATCCCTTTTCAAAAA
*** *
2460925 GGATCGATCCCCCGTGAAAAA
1 GGATCGATCCCTTTTCAAAAA
*
2460946 TGATCGATCCC-TTTCAAGAAA
1 GGATCGATCCCTTTTCAA-AAA
*
2460967 AGATCGATCCCTT
1 GGATCGATCCCTT
2460980 CACTGTTTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 15 0.35
21 27 0.63
22 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (21 bp):
GGATCGATCCCTTTTCAAAAA
Found at i:2463928 original size:63 final size:63
Alignment explanation
Indices: 2463848--2463970 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 63
2463838 GAAACTAGAC
* * * *
2463848 TCAAATAAGAATCTATCCATATAAGACATTTCTTCTAGTTCAATTTGTACAATTTATGGTAAA
1 TCAAATAAGAATATATCCATATAAGACACTTCGTCTAGTTCAATATGTACAATTTATGGTAAA
*
2463911 TCAAATAAGAATATATCCATATAAGGCACTTCGTCTAGTTCAATATGTACAATTTATGGT
1 TCAAATAAGAATATATCCATATAAGACACTTCGTCTAGTTCAATATGTACAATTTATGGT
2463971 GAATTTTCAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (63 bp):
TCAAATAAGAATATATCCATATAAGACACTTCGTCTAGTTCAATATGTACAATTTATGGTAAA
Found at i:2466191 original size:20 final size:22
Alignment explanation
Indices: 2466166--2466219 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
2466156 ACCTTGCAAG
2466166 GGATCGATCCCTTTTC-A-AAA
1 GGATCGATCCCTTTTCAAGAAA
2466186 GGATCGATCCC-TTTCAAGAAA
1 GGATCGATCCCTTTTCAAGAAA
*
2466207 AGATCGATCCCTT
1 GGATCGATCCCTT
2466220 CACTGTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 4 0.13
20 12 0.40
21 13 0.43
22 1 0.03
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (22 bp):
GGATCGATCCCTTTTCAAGAAA
Found at i:2469494 original size:63 final size:63
Alignment explanation
Indices: 2469414--2469536 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 63
2469404 GAAACTAGAC
* * * *
2469414 TCAAATAAGAATCTATCCATATAAGACATTTCTTCTAGTTCAATTTGTACAATTTATGGTAAA
1 TCAAATAAGAATATATCCATATAAGACACTTCGTCTAGTTCAATATGTACAATTTATGGTAAA
*
2469477 TCAAATAAGAATATATCCATATAAGGCACTTCGTCTAGTTCAATATGTACAATTTATGGT
1 TCAAATAAGAATATATCCATATAAGACACTTCGTCTAGTTCAATATGTACAATTTATGGT
2469537 GAATTTTCAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (63 bp):
TCAAATAAGAATATATCCATATAAGACACTTCGTCTAGTTCAATATGTACAATTTATGGTAAA
Found at i:2485972 original size:29 final size:29
Alignment explanation
Indices: 2485939--2486016 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
2485929 TCCTTTATTC
*
2485939 TTTTACCCAA-AGGTATTTAGCCTTTCATA
1 TTTTACCCAACA-GTATTTAACCTTTCATA
* * *
2485968 TTTTACTCAACAGTGTTTAACCTTTCATC
1 TTTTACCCAACAGTATTTAACCTTTCATA
* *
2485997 TTTTACTCAACAGTGTTTAA
1 TTTTACCCAACAGTATTTAA
2486017 TTGTTCTTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 43 0.98
30 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.44
Consensus pattern (29 bp):
TTTTACCCAACAGTATTTAACCTTTCATA
Found at i:2486130 original size:81 final size:81
Alignment explanation
Indices: 2485995--2486148 Score: 245
Period size: 81 Copynumber: 1.9 Consensus size: 81
2485985 TAACCTTTCA
* * * *
2485995 TCTTTTACTCAACAGTGTTTAATTGTTCTTCTAACTGACATAATTGACACATTTCTGCCAATTGC
1 TCTTTTACTCAACAGTATTTAACTGTTCATCTAACTGACATAATTGACACATTTCTGCCAAATGC
*
2486060 ACAGTTAGACAGTTAT
66 ACAATTAGACAGTTAT
* *
2486076 TCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
1 TCTTTTACTCAACAGTATTTAACTGTTCATCTAACTGACATAATTGACACATTTCTGCCAAATGC
2486141 ACAATTAG
66 ACAATTAG
2486149 GCCTCTTAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (81 bp):
TCTTTTACTCAACAGTATTTAACTGTTCATCTAACTGACATAATTGACACATTTCTGCCAAATGC
ACAATTAGACAGTTAT
Found at i:2486633 original size:45 final size:44
Alignment explanation
Indices: 2486584--2486808 Score: 236
Period size: 45 Copynumber: 5.5 Consensus size: 44
2486574 TTTTATGTCG
*
2486584 ATAATGCCCCCATATGCATTTCAGCTATGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAGCTAT-GCATCCTTTCATGCCA
* *
2486629 ATAATGCACCCATATGCA-TT-A--T-T---T-CTTTTATGCTGA
1 ATAATGCACCCATATGCATTTCAGCTATGCATCCTTTCATGC-CA
2486665 A-AATGCACCCATATGCATTTCAGCTATGTCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAGCTATG-CATCCTTTCATGCCA
*
2486709 ATAATGCACCCATATGCA-TT-A--T-T---T-CTTTTATGCCA
1 ATAATGCACCCATATGCATTTCAGCTATGCATCCTTTCATGCCA
*
2486744 TTAATGCACCCATATGCATTTCAGCTATGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAGCTAT-GCATCCTTTCATGCCA
2486789 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
2486809 ATTCTTTTAT
Statistics
Matches: 149, Mismatches: 9, Indels: 44
0.74 0.04 0.22
Matches are distributed among these distances:
35 51 0.34
36 8 0.05
37 2 0.01
39 2 0.01
40 4 0.03
41 2 0.01
43 2 0.01
44 8 0.05
45 70 0.47
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (44 bp):
ATAATGCACCCATATGCATTTCAGCTATGCATCCTTTCATGCCA
Found at i:2486670 original size:35 final size:34
Alignment explanation
Indices: 2486618--2486763 Score: 139
Period size: 35 Copynumber: 3.9 Consensus size: 34
2486608 CTATGGCATC
*
2486618 CTTTCATGCCAATAATGCACCCATATGCATTATTT
1 CTTTTATGCCAA-AATGCACCCATATGCATTATTT
*
2486653 CTTTTATGCTGAAAATGCACCCATATGCATTTCAGCTATGT
1 CTTTTATGC-CAAAATGCACCCATATGCA-TT-A--T-T-T
2486694 CATCCTTTCATGCCAATAATGCACCCATATGCATTATTT
1 C-T--TTT-ATGCCAA-AATGCACCCATATGCATTATTT
*
2486733 CTTTTATGCCATTAATGCACCCATATGCATT
1 CTTTTATGCCA-AAATGCACCCATATGCATT
2486764 TCAGCTATGG
Statistics
Matches: 94, Mismatches: 4, Indels: 26
0.76 0.03 0.21
Matches are distributed among these distances:
35 48 0.51
36 7 0.07
37 1 0.01
38 1 0.01
39 3 0.03
40 2 0.02
41 3 0.03
42 1 0.01
43 1 0.01
44 7 0.07
45 20 0.21
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.37
Consensus pattern (34 bp):
CTTTTATGCCAAAATGCACCCATATGCATTATTT
Found at i:2486698 original size:80 final size:79
Alignment explanation
Indices: 2486534--2486818 Score: 475
Period size: 80 Copynumber: 3.6 Consensus size: 79
2486524 ATGCCTTAAT
* *
2486534 GCATCCTTTCATGCCAACAATGCACCCATATGCATTATTCTTTTATG-TCGATAATGCCCCCATA
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCT-GATAATGCACCCATA
2486598 TGCATTTCAGCTATG
65 TGCATTTCAGCTATG
*
2486613 GCATCCTTTCATGCCAATAATGCACCCATATGCATTATTTCTTTTATGCTGAAAATGCACCCATA
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTA-TTCTTTTATGCTGATAATGCACCCATA
2486678 TGCATTTCAGCTATG
65 TGCATTTCAGCTATG
* *
2486693 TCATCCTTTCATGCCAATAATGCACCCATATGCATTATTTCTTTTATGC-CATTAATGCACCCAT
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTA-TTCTTTTATGCTGA-TAATGCACCCAT
2486757 ATGCATTTCAGCTATG
64 ATGCATTTCAGCTATG
2486773 GCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTAT
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTAT
2486819 TCATTTATTC
Statistics
Matches: 196, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
79 46 0.23
80 149 0.76
81 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.36
Consensus pattern (79 bp):
GCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGATAATGCACCCATAT
GCATTTCAGCTATG
Found at i:2487386 original size:95 final size:96
Alignment explanation
Indices: 2487249--2487444 Score: 265
Period size: 95 Copynumber: 2.1 Consensus size: 96
2487239 CCTAGTACCG
* * * * * *
2487249 ATACT-TCTATATTGTGGTACCGATACCCCATTACGGTATCGATACTAATTTTAGGTTCT-ATGT
1 ATACTATCTATATTATGGTACCAATACCCCATTACGATATCGATACCAATTTTAGCTT-TGATGA
2487312 TG-TCTGGTATCGATACCCTTACCATGGTATCA
65 TGCT-TGGTATCGATACCCTTACCATGGTATCA
* *
2487344 ATACTATC-ATATTATGGTACCAATACCCCCTTCCGATATCGATACCAATTTTAGCTTTGATGAT
1 ATACTATCTATATTATGGTACCAATACCCCATTACGATATCGATACCAATTTTAGCTTTGATGAT
*
2487408 GCTTGGTATCGATACCCTTACCATGGTATCG
66 GCTTGGTATCGATACCCTTACCATGGTATCA
2487439 ATACTA
1 ATACTA
2487445 CCTCGTCAGT
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
94 1 0.01
95 85 0.96
96 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.36
Consensus pattern (96 bp):
ATACTATCTATATTATGGTACCAATACCCCATTACGATATCGATACCAATTTTAGCTTTGATGAT
GCTTGGTATCGATACCCTTACCATGGTATCA
Found at i:2503843 original size:21 final size:23
Alignment explanation
Indices: 2503798--2503850 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
2503788 CATATAAGTA
2503798 TAAATTAATTAAAAATTAAAAGG
1 TAAATTAATTAAAAATTAAAAGG
* *
2503821 TAAATT-ATTTAAAA-TAAAGGG
1 TAAATTAATTAAAAATTAAAAGG
*
2503842 TAAACTAAT
1 TAAATTAAT
2503851 CAGTGACCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 11 0.42
22 9 0.35
23 6 0.23
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (23 bp):
TAAATTAATTAAAAATTAAAAGG
Found at i:2505234 original size:28 final size:28
Alignment explanation
Indices: 2505193--2505258 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
2505183 TAATCGGATG
2505193 GTGACACATGTTATTACACTTGACACC-
1 GTGACACATGTTATTACACTTGACACCA
2505220 GATGACACATGTTATTACACTTGACACCA
1 G-TGACACATGTTATTACACTTGACACCA
2505249 GTGACACATG
1 GTGACACATG
2505259 ACACCATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
27 1 0.03
28 35 0.95
29 1 0.03
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (28 bp):
GTGACACATGTTATTACACTTGACACCA
Found at i:2505875 original size:31 final size:32
Alignment explanation
Indices: 2505836--2505916 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
2505826 GGACAAATGA
*
2505836 AAAT-ATTAT-TATTTTTAAAAA-TTTAAGTTC
1 AAATAATTATGTA-TTTAAAAAATTTTAAGTTC
*
2505866 AAATAATTATGTATTTAAAAAATTTTAAGTTT
1 AAATAATTATGTATTTAAAAAATTTTAAGTTC
*
2505898 AAATAATTACGTATTTAAA
1 AAATAATTATGTATTTAAA
2505917 GTATGCGTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
30 4 0.09
31 13 0.29
32 28 0.62
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (32 bp):
AAATAATTATGTATTTAAAAAATTTTAAGTTC
Found at i:2506955 original size:28 final size:25
Alignment explanation
Indices: 2506924--2506975 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
2506914 ATTTCAAAAT
2506924 TATAATTATTAGAAAAAAATAATTTATA
1 TATAATTA-TA-AAAAAAAT-ATTTATA
* *
2506952 TATATTTATAAATAAAATATTTAT
1 TATAATTATAAAAAAAATATTTAT
2506976 TTATTTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 7 0.32
27 2 0.09
28 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TATAATTATAAAAAAAATATTTATA
Found at i:2506982 original size:23 final size:26
Alignment explanation
Indices: 2506932--2506988 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
2506922 ATTATAATTA
2506932 TTAGAAA-AAAATAATTTATATATAT
1 TTAGAAATAAAATAATTTATATATAT
*
2506957 TTATAAATAAAAT-ATTTAT-T-TAT
1 TTAGAAATAAAATAATTTATATATAT
2506980 TTAGAAATA
1 TTAGAAATA
2506989 TCAGAAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 11 0.38
24 1 0.03
25 12 0.41
26 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
TTAGAAATAAAATAATTTATATATAT
Found at i:2508631 original size:3 final size:3
Alignment explanation
Indices: 2508625--2508673 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
2508615 TAATATTTAT
2508625 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
2508669 TAA TA
1 TAA TA
2508674 TTTAAATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2508990 original size:17 final size:17
Alignment explanation
Indices: 2508968--2509026 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
2508958 TTGAACAAGC
2508968 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
2508985 TCTTCTTC-TTCAGATG-AGT
1 TCTTC-TCATT--G-TGAACT
*
2509004 TCTTCTCATTATGAACT
1 TCTTCTCATTGTGAACT
2509021 TCTTCT
1 TCTTCT
2509027 TCTTCAGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 2 0.06
17 15 0.45
18 4 0.12
19 10 0.30
20 2 0.06
ACGTcount: A:0.17, C:0.24, G:0.10, T:0.49
Consensus pattern (17 bp):
TCTTCTCATTGTGAACT
Found at i:2509008 original size:36 final size:36
Alignment explanation
Indices: 2508968--2509057 Score: 171
Period size: 36 Copynumber: 2.5 Consensus size: 36
2508958 TTGAACAAGC
*
2508968 TCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
2509004 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
2509040 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
2509058 TCTCTGGAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.48
Consensus pattern (36 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
Found at i:2509053 original size:16 final size:16
Alignment explanation
Indices: 2508998--2509053 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
2508988 TCTTCTTCAG
2508998 ATGAGTTCTTCTCATT
1 ATGAGTTCTTCTCATT
*
2509014 ATGAACTTCTTCTTC-TT
1 ATG-AGTTCTTC-TCATT
2509031 CAGATGAGTTCTTCTCATT
1 ---ATGAGTTCTTCTCATT
2509050 ATGA
1 ATGA
2509054 ACTTTCTCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 7 0.22
17 9 0.28
18 4 0.12
19 9 0.28
20 3 0.09
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.46
Consensus pattern (16 bp):
ATGAGTTCTTCTCATT
Found at i:2509155 original size:34 final size:36
Alignment explanation
Indices: 2509112--2509203 Score: 152
Period size: 36 Copynumber: 2.6 Consensus size: 36
2509102 GTTGAACAAA
2509112 TTCTTCTCATTATGAATTTCTTC-T-TTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTATTCAGATGAG
*
2509146 TTCTTCTCATTATGAACTTCTTCTTATTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTATTCAGATGAG
2509182 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAA-TTTCT
2509204 CTGGAAAAGC
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
34 22 0.42
35 1 0.02
36 26 0.49
37 4 0.08
ACGTcount: A:0.21, C:0.20, G:0.10, T:0.50
Consensus pattern (36 bp):
TTCTTCTCATTATGAATTTCTTCTTATTCAGATGAG
Found at i:2509166 original size:143 final size:145
Alignment explanation
Indices: 2508951--2509312 Score: 584
Period size: 143 Copynumber: 2.5 Consensus size: 145
2508941 TAGAATTATG
* * * *
2508951 CAAAAGATTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* *
2509016 GAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCTATCA
66 GAACTTCTTCTTATTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
2509081 AGTGATGGATTTGAA
131 AGTGATGGATTTGAA
*
2509096 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTC-T-TTCAGATGAGTTCTTCTCATTAT
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
2509159 GAACTTCTTCTTATTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
66 GAACTTCTTCTTATTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
*
2509224 AGTGATGGTTTTGAA
131 AGTGATGGATTTGAA
* *
2509239 CAAAAAGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGAGTTCTTCTCA
2509304 TTATGAACT
62 TTATGAACT
2509313 CTACCTGGCA
Statistics
Matches: 200, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
143 129 0.64
144 1 0.00
145 35 0.17
146 5 0.03
147 1 0.00
148 1 0.00
149 28 0.14
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (145 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTCTTCTTATTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
AGTGATGGATTTGAA
Found at i:2509343 original size:113 final size:113
Alignment explanation
Indices: 2509144--2509464 Score: 420
Period size: 113 Copynumber: 2.9 Consensus size: 113
2509134 CTTTCAGATG
* *
2509144 AGTTCTTCTCATTATGAA---CTTCTT-CTTATTCAGATGAGTTCTTCTCATTATGAACT-TTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-
* * * *
2509204 CTGGAAAAGCTGATCCATCAAGTGATGGTTTTGAACAAAAAGTTGAACA
65 CTGGAAATGTTGATCCATCAAATGATGGTTTTAAACAAAAAGTTGAACA
*
2509253 AGTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
* ** *
2509318 TGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACA
66 TGGAAATGTTGATCCATCAAATGATGGTTTTAAACAAAAAGTTGAACA
* * * *
2509366 AGTTCTTCTCATTATGAACTT-TCCCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTCGAA
1 AGTTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
**
2509430 CTGGAAATGTTGATCCATTGAATGATGGATTTTAA
65 CTGGAAATGTTGATCCATCAAATGATGG-TTTTAA
2509465 TCTTTGCTAA
Statistics
Matches: 183, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
109 17 0.09
112 7 0.04
113 153 0.84
114 6 0.03
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
TGGAAATGTTGATCCATCAAATGATGGTTTTAAACAAAAAGTTGAACA
Found at i:2510355 original size:114 final size:115
Alignment explanation
Indices: 2510155--2510610 Score: 781
Period size: 115 Copynumber: 4.0 Consensus size: 115
2510145 CATGCAGTTC
* * * *
2510155 ATCTTTTAATTCCAATGATTGG-TTCTGTGGTTCCTACCAAACCAGATCAGATAACTCAAAGAAC
1 ATCTTTCAAATCCAATGATTGGTTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
*
2510219 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTATACTATGAGCACATTT
66 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATTT
* *
2510269 ATCTTTCAAATCCAATGATTGG-TTCTGTGGTTCCTACCAAACCAGATCAGATAACTCAAAGAAC
1 ATCTTTCAAATCCAATGATTGGTTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
* *
2510333 ACTTCCAGAAGATGCTATTGGGTATTCTTATTTGTACTATGAGCACATTT
66 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATTT
* *
2510383 ATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACTAGATCAGATAACTCAAAGAAC
1 ATCTTTCAAATCCAATGATTGGTTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
2510448 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATTT
66 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATTT
* *
2510498 ATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCATATCAGATAACTCAAAGAAC
1 ATCTTTCAAATCCAATGATTGGTTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
2510563 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACAT
66 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACAT
2510611 GGCACTTGCT
Statistics
Matches: 329, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
114 132 0.40
115 197 0.60
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (115 bp):
ATCTTTCAAATCCAATGATTGGTTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATTT
Found at i:2511896 original size:10 final size:10
Alignment explanation
Indices: 2511881--2511923 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
2511871 CTTGACCCCC
2511881 TTTTTTCTTT
1 TTTTTTCTTT
2511891 TTTTTTC-TT
1 TTTTTTCTTT
*
2511900 TGTTTTCTTT
1 TTTTTTCTTT
*
2511910 TTTGTTCTTT
1 TTTTTTCTTT
2511920 TTTT
1 TTTT
2511924 CTTCAAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.86
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:2511905 original size:19 final size:18
Alignment explanation
Indices: 2511881--2511926 Score: 74
Period size: 19 Copynumber: 2.5 Consensus size: 18
2511871 CTTGACCCCC
*
2511881 TTTTTTCTTTTTTTTTCT
1 TTTTTTCTTTTTTGTTCT
2511899 TTGTTTTCTTTTTTGTTCT
1 TT-TTTTCTTTTTTGTTCT
2511918 TTTTTTCTT
1 TTTTTTCTT
2511927 CAAACATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.85
Consensus pattern (18 bp):
TTTTTTCTTTTTTGTTCT
Found at i:2515469 original size:18 final size:19
Alignment explanation
Indices: 2515443--2515479 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2515433 ATTTATGAAA
*
2515443 TAAATAAATGTAAA-AATG
1 TAAAAAAATGTAAAGAATG
2515461 TAAAAAAATGTAAAGAATG
1 TAAAAAAATGTAAAGAATG
2515480 ATTGCCATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (19 bp):
TAAAAAAATGTAAAGAATG
Found at i:2519283 original size:15 final size:15
Alignment explanation
Indices: 2519260--2519291 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2519250 TGAAATGAAT
2519260 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
2519275 AATGTATGTATGCAA
1 AATGAATGTATGCAA
2519290 AA
1 AA
2519292 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:2523131 original size:28 final size:25
Alignment explanation
Indices: 2523100--2523151 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
2523090 ATTTCAAAAT
2523100 TATAATTATTAGAAAAAAATAATTTATA
1 TATAATTA-TA-AAAAAAAT-ATTTATA
* *
2523128 TATATTTATAAATAAAATATTTAT
1 TATAATTATAAAAAAAATATTTAT
2523152 TTATTTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 7 0.32
27 2 0.09
28 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TATAATTATAAAAAAAATATTTATA
Found at i:2523158 original size:23 final size:26
Alignment explanation
Indices: 2523108--2523164 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
2523098 ATTATAATTA
2523108 TTAGAAA-AAAATAATTTATATATAT
1 TTAGAAATAAAATAATTTATATATAT
*
2523133 TTATAAATAAAAT-ATTTAT-T-TAT
1 TTAGAAATAAAATAATTTATATATAT
2523156 TTAGAAATA
1 TTAGAAATA
2523165 TCAGAAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 11 0.38
24 1 0.03
25 12 0.41
26 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
TTAGAAATAAAATAATTTATATATAT
Found at i:2524727 original size:3 final size:3
Alignment explanation
Indices: 2524721--2524757 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
2524711 TAATATTTAT
2524721 TAA TAA TAA -AA TAA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
2524758 TTTAAATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 25 0.81
4 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2526777 original size:83 final size:83
Alignment explanation
Indices: 2526664--2526835 Score: 272
Period size: 83 Copynumber: 2.1 Consensus size: 83
2526654 CGTTAAATTC
* *
2526664 TTAACAACCATATCAAAACGACATCATTTTGGTGAGGTTTCTATGTCAACAACCATCAACCATGT
1 TTAACAACCAGATCAAAACGACATCATTTTGGCGAGGTTTCTATGTCAACAACCATCAACCATGT
* *
2526729 CATCGTGTCATTGATAAT
66 CATCGTGTAATTAATAAT
* * * *
2526747 TTAACAACTAGATCAAAACGACATCGTTTTGGCGAGGTTTCTATGTCAACAACCGTCAGCCATGT
1 TTAACAACCAGATCAAAACGACATCATTTTGGCGAGGTTTCTATGTCAACAACCATCAACCATGT
2526812 CATCGTGTAATTAATAAT
66 CATCGTGTAATTAATAAT
2526830 TTAACA
1 TTAACA
2526836 GTTCAGTGGT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (83 bp):
TTAACAACCAGATCAAAACGACATCATTTTGGCGAGGTTTCTATGTCAACAACCATCAACCATGT
CATCGTGTAATTAATAAT
Found at i:2527144 original size:29 final size:29
Alignment explanation
Indices: 2527110--2527179 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 29
2527100 TATTTTTTAG
*
2527110 ATTTAATTAGAAAATTTTATAATTTATAA
1 ATTTAATTAGAAAATGTTATAATTTATAA
2527139 ATTTAATTAGAAAATGTTATAATTTATAA
1 ATTTAATTAGAAAATGTTATAATTTATAA
2527168 A-TTAATTTAGAA
1 ATTTAA-TTAGAA
2527180 TTTCAATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 4 0.10
29 35 0.90
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (29 bp):
ATTTAATTAGAAAATGTTATAATTTATAA
Found at i:2528509 original size:9 final size:9
Alignment explanation
Indices: 2528472--2528517 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
2528462 TATATAATTT
2528472 TAATATT-A
1 TAATATTAA
2528480 -AATATT-A
1 TAATATTAA
2528487 TAATATTATAA
1 TAATA-T-TAA
2528498 TAATATTAA
1 TAATATTAA
2528507 TAATATTAA
1 TAATATTAA
2528516 TA
1 TA
2528518 TTAAATTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.21
8 4 0.12
9 15 0.44
10 2 0.06
11 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TAATATTAA
Found at i:2528516 original size:26 final size:26
Alignment explanation
Indices: 2528434--2528520 Score: 81
Period size: 26 Copynumber: 3.4 Consensus size: 26
2528424 TTACTTTAGG
*
2528434 ATTATTATTATAA-AATATTAAT-AT
1 ATTAATATTATAATAATATTAATAAT
* * ** *
2528458 AATTTATATAATTTTAATATTAAATATT
1 -ATTAATATTATAATAATATT-AATAAT
2528486 A-TAATATTATAATAATATTAATAAT
1 ATTAATATTATAATAATATTAATAAT
2528511 ATTAATATTA
1 ATTAATATTA
2528521 AATTTTCAAT
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
25 14 0.30
26 28 0.60
27 4 0.09
28 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTAATATTATAATAATATTAATAAT
Found at i:2528537 original size:41 final size:42
Alignment explanation
Indices: 2528447--2528537 Score: 111
Period size: 41 Copynumber: 2.2 Consensus size: 42
2528437 ATTATTATAA
* *
2528447 AATATTAAT-ATAATTTATATAATTTTAATATTAAATATTAT
1 AATATTTATAATAATTTATATAATATTAATATTAAATATTAT
2528488 AATA-TTATAATAATATTA-ATAATATTAATATTAAAT-TT-T
1 AATATTTATAATAAT-TTATATAATATTAATATTAAATATTAT
2528527 CAATATTTATA
1 -AATATTTATA
2528538 TTAAGTTGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
39 1 0.02
40 9 0.20
41 31 0.70
42 3 0.07
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (42 bp):
AATATTTATAATAATTTATATAATATTAATATTAAATATTAT
Found at i:2539812 original size:36 final size:36
Alignment explanation
Indices: 2539765--2539980 Score: 387
Period size: 36 Copynumber: 6.0 Consensus size: 36
2539755 TTATTCTTAA
*
2539765 GCAAATCAAGCCTTCACAAAAGAGTATTGAAGCAAT
1 GCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCAAT
2539801 GCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCAAT
1 GCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCAAT
*
2539837 ACAAATCAAGCCTTCACAAAAGAGTAGTGAAGCAAT
1 GCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCAAT
*
2539873 GCAAATCAAGTCTTCACAAAAGAGTAGTGAAGCAAT
1 GCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCAAT
2539909 GCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCAAT
1 GCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCAAT
*
2539945 GCAAATCAAGTCTTCACAAAAAGAGTAGTGAAGCAA
1 GCAAATCAAGCCTTCAC-AAAAGAGTAGTGAAGCAA
2539981 GATCATATCA
Statistics
Matches: 173, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
36 155 0.90
37 18 0.10
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.18
Consensus pattern (36 bp):
GCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCAAT
Found at i:2540168 original size:18 final size:18
Alignment explanation
Indices: 2540145--2540179 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2540135 CTGAGTGACG
2540145 TTTATA-TATATTATTATA
1 TTTATATTATA-TATTATA
2540163 TTTATATTATATATTAT
1 TTTATATTATATATTAT
2540180 TATATACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATATTATATATTATA
Found at i:2540197 original size:21 final size:21
Alignment explanation
Indices: 2540152--2540197 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2540142 ACGTTTATAT
** * *
2540152 ATATTATTATATTTATATTAT
1 ATATTATTATATACATAATAA
2540173 ATATTATTATATACATAATAA
1 ATATTATTATATACATAATAA
2540194 ATAT
1 ATAT
2540198 AATGAATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATTATTATATACATAATAA
Found at i:2540779 original size:22 final size:22
Alignment explanation
Indices: 2540744--2540793 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2540734 ACCGAGAGCA
* *
2540744 AGAG-AACAACAACCAAGCAAC
1 AGAGAAACAAAAACCAACCAAC
*
2540765 ATAGAAACAAAAACCAACCAAC
1 AGAGAAACAAAAACCAACCAAC
2540787 AGAGAAA
1 AGAGAAA
2540794 ATAGAGAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.62, C:0.24, G:0.12, T:0.02
Consensus pattern (22 bp):
AGAGAAACAAAAACCAACCAAC
Found at i:2542896 original size:238 final size:240
Alignment explanation
Indices: 2542608--2543086 Score: 935
Period size: 238 Copynumber: 2.0 Consensus size: 240
2542598 CTAGAAAAGA
2542608 CCAGATCTCCTCAACAAGAATGAGTAATGTCATCTTCAAAATCAAATCATTTATAGGCATTTAGA
1 CCAGATCTCCTCAACAAGAATGAGTAATGTCATCTTCAAAATCAAATCATTTATAGGCATTTAGA
2542673 CTTCCTCAACACGAAGGGACTATGTTGTCTTCAGACACATGATCACTCAAATGCGACT-ACGTCC
66 CTTCCTCAACACGAAGGGACTATGTTGTCTTCAGACACATGATCACTCAAATGCGACTAACGTCC
2542737 TCATCACGAAGGAACAAAGTCATTTCCAAATTCTTTACCCTCAAGAAAA-GATTCAAGTTTTAGA
131 TCATCACGAAGGAACAAAGTCATTTCCAAATTCTTTACCCTCAAGAAAAGGATTCAAGTTTTAGA
2542801 TTCAGAGCGATCATCAAGGCTGGAAAAAATAGTGTCCTTGGTCTT
196 TTCAGAGCGATCATCAAGGCTGGAAAAAATAGTGTCCTTGGTCTT
2542846 CCAGATCTCCTCAACAAGAATGAGTAATGTCATCTTCAAAATCAAATCATTTATAGGCATTTAGA
1 CCAGATCTCCTCAACAAGAATGAGTAATGTCATCTTCAAAATCAAATCATTTATAGGCATTTAGA
2542911 CTTCCTCAACACGAAGGGACTATGTTGTCTTCAGACACATGATCACTCAAATGCGACTAGACGTC
66 CTTCCTCAACACGAAGGGACTATGTTGTCTTCAGACACATGATCACTCAAATGCGACTA-ACGTC
2542976 CTCATCACGAAGGAACAAAGTCATTTCCAAATTCTTTACCCTCAAGAAAAGGATTCAAGTTTTAG
130 CTCATCACGAAGGAACAAAGTCATTTCCAAATTCTTTACCCTCAAGAAAAGGATTCAAGTTTTAG
2543041 ATTCAGAGCGATCATCAAGGCTGGAAAAAATAGTGTCCTTGGTCTT
195 ATTCAGAGCGATCATCAAGGCTGGAAAAAATAGTGTCCTTGGTCTT
2543087 TTCCCTATTC
Statistics
Matches: 238, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
238 123 0.52
240 55 0.23
241 60 0.25
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (240 bp):
CCAGATCTCCTCAACAAGAATGAGTAATGTCATCTTCAAAATCAAATCATTTATAGGCATTTAGA
CTTCCTCAACACGAAGGGACTATGTTGTCTTCAGACACATGATCACTCAAATGCGACTAACGTCC
TCATCACGAAGGAACAAAGTCATTTCCAAATTCTTTACCCTCAAGAAAAGGATTCAAGTTTTAGA
TTCAGAGCGATCATCAAGGCTGGAAAAAATAGTGTCCTTGGTCTT
Found at i:2543202 original size:23 final size:25
Alignment explanation
Indices: 2543161--2543222 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 25
2543151 GGCTTTTCAA
*
2543161 TTTAATATTATTAGATTATTTATAGT
1 TTTAATATTATTAGATTATGTATA-T
2543187 TTTAA-ATT-TTA-ATTATGTATAT
1 TTTAATATTATTAGATTATGTATAT
2543209 TTTAATTATTATTA
1 TTTAA-TATTATTA
2543223 ATATGTGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 6 0.19
23 9 0.28
24 6 0.19
25 6 0.19
26 5 0.16
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (25 bp):
TTTAATATTATTAGATTATGTATAT
Found at i:2544660 original size:55 final size:55
Alignment explanation
Indices: 2544576--2544684 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
2544566 ATGGTACCTC
2544576 GGACATGTTAATGCGAGAGCCAATTCAGATTACTCCCTAAATTAAAGGACTATGT
1 GGACATGTTAATGCGAGAGCCAATTCAGATTACTCCCTAAATTAAAGGACTATGT
* *
2544631 GGACATGTTAATGCGAGATCCAATTCAGATTACTCCCTAAATTTAAGGACTATG
1 GGACATGTTAATGCGAGAGCCAATTCAGATTACTCCCTAAATTAAAGGACTATG
2544685 GTGTGAGACA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (55 bp):
GGACATGTTAATGCGAGAGCCAATTCAGATTACTCCCTAAATTAAAGGACTATGT
Found at i:2545730 original size:15 final size:15
Alignment explanation
Indices: 2545698--2545726 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2545688 ATAAATACTG
2545698 GTAAAACTAAACTAA
1 GTAAAACTAAACTAA
2545713 GTAAAA-TAAACTAA
1 GTAAAACTAAACTAA
2545727 AGTAGTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (15 bp):
GTAAAACTAAACTAA
Found at i:2546541 original size:17 final size:18
Alignment explanation
Indices: 2546508--2546573 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
2546498 AATCTACGTC
2546508 TGATAACTGTAAAACATA
1 TGATAACTGTAAAACATA
*
2546526 TGATAATTGT-AAACATA
1 TGATAACTGTAAAACATA
* *
2546543 TGATAAATG-AAAATCATT
1 TGATAACTGTAAAA-CATA
*
2546561 TGATAACTATAAA
1 TGATAACTGTAAA
2546574 TTTTTAGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 18 0.45
18 19 0.47
19 3 0.08
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (18 bp):
TGATAACTGTAAAACATA
Found at i:2548548 original size:20 final size:20
Alignment explanation
Indices: 2548503--2548545 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2548493 TTTTATACCA
* *
2548503 TTTTATAAAATCATTGAATT
1 TTTTGTAAAATTATTGAATT
2548523 TTTTGTAAAATTATT-AATT
1 TTTTGTAAAATTATTGAATT
2548542 TTTT
1 TTTT
2548546 TGTTAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTGTAAAATTATTGAATT
Found at i:2554731 original size:18 final size:18
Alignment explanation
Indices: 2554708--2554753 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
2554698 ATCTATGTCT
2554708 GATAACTGTAAAACATAA
1 GATAACTGTAAAACATAA
* *
2554726 GATAACT-T-TAACATAT
1 GATAACTGTAAAACATAA
2554742 GATAACTG-AAAA
1 GATAACTGTAAAA
2554754 TCATCTGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
16 13 0.57
17 3 0.13
18 7 0.30
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26
Consensus pattern (18 bp):
GATAACTGTAAAACATAA
Found at i:2554764 original size:34 final size:33
Alignment explanation
Indices: 2554707--2554774 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 33
2554697 AATCTATGTC
*
2554707 TGATAACTGTAAAACATAAGATAACTTTAACATA
1 TGATAACTGTAAAACATAAGATAACTATAA-ATA
**
2554741 TGATAACTG-AAAATCATCTGATAACTATAAATA
1 TGATAACTGTAAAA-CATAAGATAACTATAAATA
2554774 T
1 T
2554775 TTAGAATTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 8 0.27
34 22 0.73
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.31
Consensus pattern (33 bp):
TGATAACTGTAAAACATAAGATAACTATAAATA
Found at i:2554772 original size:18 final size:18
Alignment explanation
Indices: 2554707--2554772 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
2554697 AATCTATGTC
* *
2554707 TGATAACTGTAAAACATA
1 TGATAACTATAAATCATA
* *
2554725 AGATAACT-TTAA-CATA
1 TGATAACTATAAATCATA
*
2554741 TGATAACTGA-AAATCATC
1 TGATAACT-ATAAATCATA
2554759 TGATAACTATAAAT
1 TGATAACTATAAAT
2554773 ATTTAGAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
16 11 0.28
17 6 0.15
18 22 0.56
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.30
Consensus pattern (18 bp):
TGATAACTATAAATCATA
Found at i:2556261 original size:2 final size:2
Alignment explanation
Indices: 2556256--2556284 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2556246 ATAATAAAAA
2556256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2556285 AAATAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2561773 original size:30 final size:30
Alignment explanation
Indices: 2561739--2561798 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2561729 GACAAAAGGC
2561739 ATTCAACTATATGAAAATGTACCAAAGGGA
1 ATTCAACTATATGAAAATGTACCAAAGGGA
* * * *
2561769 ATTCATCTGTATGCAAATGTACTAAAGGGA
1 ATTCAACTATATGAAAATGTACCAAAGGGA
2561799 CATGCAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (30 bp):
ATTCAACTATATGAAAATGTACCAAAGGGA
Found at i:2567408 original size:15 final size:16
Alignment explanation
Indices: 2567379--2567408 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2567369 TGAAGAAAAC
2567379 AAGGAAAATAAGAAGA
1 AAGGAAAATAAGAAGA
2567395 AAGGAAAA-AAGAAG
1 AAGGAAAATAAGAAG
2567409 GAGGTGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (16 bp):
AAGGAAAATAAGAAGA
Found at i:2567931 original size:19 final size:19
Alignment explanation
Indices: 2567895--2567931 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2567885 TGAAAATGAT
*
2567895 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
2567914 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
2567932 ATGAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:2570224 original size:21 final size:22
Alignment explanation
Indices: 2570194--2570246 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
2570184 AGCATATTTG
*
2570194 AAAAT-AAAACTT-AAAATAAA
1 AAAATGAAAACTTGAAAAGAAA
2570214 AAAATGAAAACTTGAAAAGAAA
1 AAAATGAAAACTTGAAAAGAAA
*
2570236 AGAAAAGAAAA
1 A-AAATGAAAA
2570247 GAGAGAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 8 0.29
23 8 0.29
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (22 bp):
AAAATGAAAACTTGAAAAGAAA
Done.