Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_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: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 37
Found at i:12009 original size:2 final size:2
Alignment explanation
Indices: 12002--12093 Score: 184
Period size: 2 Copynumber: 46.0 Consensus size: 2
11992 TCAAATAATT
12002 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12044 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12086 TA TA TA TA
1 TA TA TA TA
12094 AAAGAACTTG
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 90 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15461 original size:20 final size:18
Alignment explanation
Indices: 15436--15474 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
15426 AATATAAAAA
15436 TAAATAAAATTGTATTATAT
1 TAAATAAAATT-T-TTATAT
*
15456 TAAATAACATTTTTATAT
1 TAAATAAAATTTTTATAT
15474 T
1 T
15475 GATCTTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
20 10 0.56
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
TAAATAAAATTTTTATAT
Found at i:23668 original size:23 final size:24
Alignment explanation
Indices: 23642--23696 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
23632 TACATGATAT
* *
23642 AAATATATAT-TTATTAAA-ATAAC
1 AAATAAATATATTA-TAAATATAAA
23665 AAATAAATATATTATAAATATAAA
1 AAATAAATATATTATAAATATAAA
23689 AAATAAAT
1 AAATAAAT
23697 CAAATCGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATAAATATATTATAAATATAAA
Found at i:26530 original size:25 final size:26
Alignment explanation
Indices: 26492--26557 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 26
26482 TTCTAAGGTA
*
26492 TATTTTATTATATTTTTAATATTTT-G
1 TATTTAATT-TATTTTTAATATTTTAG
*
26518 TATTTAATTTA--TTTAATATTTTACT
1 TATTTAATTTATTTTTAATATTTTA-G
26543 TATTTAATTT-TTTTT
1 TATTTAATTTATTTTT
26558 CAGATATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 11 0.32
25 12 0.35
26 11 0.32
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (26 bp):
TATTTAATTTATTTTTAATATTTTAG
Found at i:36212 original size:3 final size:3
Alignment explanation
Indices: 36204--36228 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
36194 ATGAAAATTA
36204 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
36229 GCAAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:39578 original size:21 final size:20
Alignment explanation
Indices: 39535--39578 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
39525 AAAATAATTG
*
39535 AATTTAATAAAATATCATTA
1 AATTTAATAAAATATCATAA
* *
39555 AATTTTATCAAAATATTATAA
1 AATTTAAT-AAAATATCATAA
39576 AAT
1 AAT
39579 AATAATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTAATAAAATATCATAA
Found at i:43145 original size:16 final size:16
Alignment explanation
Indices: 43115--43153 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
43105 ATCATAATTT
*
43115 TAATTT-AATTTTTAA
1 TAATTTAAAATTTTAA
43130 TAATTTAAAATTTTAA
1 TAATTTAAAATTTTAA
*
43146 TAAGTTAA
1 TAATTTAA
43154 TATACATGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TAATTTAAAATTTTAA
Found at i:50271 original size:58 final size:58
Alignment explanation
Indices: 50206--50361 Score: 240
Period size: 58 Copynumber: 2.7 Consensus size: 58
50196 TACACTTTTT
* * *
50206 ATTCTAAATTAGTTTTTAAACTTTTAAATATTTCAATTTTATCCTTAAACTATGACTC
1 ATTCTAAATTAGTTCTCAAACTTTTAAATATTTCAATTTTATCCCTAAACTATGACTC
*
50264 ATTCTAAATTAGTTCTCAAACTTTTAAATATTTCAATTTAATCCCTAAACTATGACTC
1 ATTCTAAATTAGTTCTCAAACTTTTAAATATTTCAATTTTATCCCTAAACTATGACTC
* * * *
50322 ATTCTAAATTAGTCCTCAAACTTTTTAACATTTCAGTTTT
1 ATTCTAAATTAGTTCTCAAACTTTTAAATATTTCAATTTT
50362 GTTTTCACAC
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 89 1.00
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.46
Consensus pattern (58 bp):
ATTCTAAATTAGTTCTCAAACTTTTAAATATTTCAATTTTATCCCTAAACTATGACTC
Found at i:50284 original size:29 final size:29
Alignment explanation
Indices: 50252--50343 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
50242 TTTTATCCTT
50252 AAACTATGACTCATTCTAAATTAGTTCTC
1 AAACTATGACTCATTCTAAATTAGTTCTC
* * * * * *
50281 AAACTTTTAAAT-ATT-TCAATTTA-ATCCC
1 AAAC-TATGACTCATTCT-AAATTAGTTCTC
*
50309 TAAACTATGACTCATTCTAAATTAGTCCTC
1 -AAACTATGACTCATTCTAAATTAGTTCTC
50339 AAACT
1 AAACT
50344 TTTTAACATT
Statistics
Matches: 44, Mismatches: 13, Indels: 12
0.64 0.19 0.17
Matches are distributed among these distances:
28 8 0.18
29 29 0.66
30 7 0.16
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.38
Consensus pattern (29 bp):
AAACTATGACTCATTCTAAATTAGTTCTC
Found at i:50433 original size:2 final size:2
Alignment explanation
Indices: 50426--50470 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
50416 CAATTCATCC
50426 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50468 TA T
1 TA T
50471 GCTAATCACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55585 original size:23 final size:23
Alignment explanation
Indices: 55550--55595 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
55540 GAGACTGAAT
*
55550 TTATAATATTTTAAGAGAA-AAAA
1 TTATAATAGTTTAA-AGAATAAAA
*
55573 TTATAATGGTTTAAAGAATAAAA
1 TTATAATAGTTTAAAGAATAAAA
55596 GTAAATTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (23 bp):
TTATAATAGTTTAAAGAATAAAA
Found at i:56858 original size:37 final size:37
Alignment explanation
Indices: 56817--56896 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 37
56807 CTTTCGAAGT
56817 TGGATGTCAGCAGCAAAAGCATGCCTCTAGAATTGAG
1 TGGATGTCAGCAGCAAAAGCATGCCTCTAGAATTGAG
*
56854 TGGATGTTAGCAGCAAAAGCATGCCTCTAGAATTGAG
1 TGGATGTCAGCAGCAAAAGCATGCCTCTAGAATTGAG
*
56891 AGGATG
1 TGGATG
56897 AGTCCATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (37 bp):
TGGATGTCAGCAGCAAAAGCATGCCTCTAGAATTGAG
Found at i:60189 original size:16 final size:18
Alignment explanation
Indices: 60155--60191 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
60145 TTAATATTTA
*
60155 AATTAGATATCTTTTATT
1 AATTAGATATCTTTAATT
60173 AATTAGATA-C-TTAATT
1 AATTAGATATCTTTAATT
60189 AAT
1 AAT
60192 CTTAGTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 1 0.06
18 9 0.50
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
AATTAGATATCTTTAATT
Found at i:62550 original size:32 final size:29
Alignment explanation
Indices: 62490--62593 Score: 154
Period size: 29 Copynumber: 3.5 Consensus size: 29
62480 GGACGCACCG
62490 GATTCATAATGCTCTTTTCTTTAATAAAA
1 GATTCATAATGCTCTTTTCTTTAATAAAA
*
62519 GATTCATAATGCTCTTTCTGAATTTAATAAAA
1 GATTCATAATGCTCTTT-T--CTTTAATAAAA
* *
62551 GACTCATAATGCTCTTTTCTTTAACAAAA
1 GATTCATAATGCTCTTTTCTTTAATAAAA
62580 GATTCATAATGCTC
1 GATTCATAATGCTC
62594 ACTGTATACA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
29 39 0.58
30 1 0.01
31 1 0.01
32 26 0.39
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (29 bp):
GATTCATAATGCTCTTTTCTTTAATAAAA
Found at i:64641 original size:29 final size:29
Alignment explanation
Indices: 64607--64673 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
64597 CATATTAAAC
* *
64607 AATAATTAAGAATTGAGTTTTAATTTAAT
1 AATAATTAAGAATTAAATTTTAATTTAAT
64636 AATAATTAAGAATTAAATTTTAATTTAAT
1 AATAATTAAGAATTAAATTTTAATTTAAT
64665 AATAATTAA
1 AATAATTAA
64674 CAATCTTCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (29 bp):
AATAATTAAGAATTAAATTTTAATTTAAT
Found at i:67303 original size:24 final size:24
Alignment explanation
Indices: 67276--67332 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
67266 ATTGAAATCC
67276 AATTTCATCAAGAGAGGGAAAGTA
1 AATTTCATCAAGAGAGGGAAAGTA
* * *
67300 AATTCCATTAAGGGAGGGAAAGTA
1 AATTTCATCAAGAGAGGGAAAGTA
67324 AATTTCATC
1 AATTTCATC
67333 CATAACATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.25
Consensus pattern (24 bp):
AATTTCATCAAGAGAGGGAAAGTA
Found at i:67496 original size:28 final size:28
Alignment explanation
Indices: 67456--67590 Score: 236
Period size: 28 Copynumber: 4.9 Consensus size: 28
67446 CGGGTCGGGG
67456 TTTTTAAGTGTGATATTCGGGTCGAGTT
1 TTTTTAAGTGTGATATTCGGGTCGAGTT
*
67484 TTTTTAAGTGTGATATTCGGGTCGGGTT
1 TTTTTAAGTGTGATATTCGGGTCGAGTT
*
67512 TTTTTAAGTGTGATATTCGGGTCGGGTT
1 TTTTTAAGTGTGATATTCGGGTCGAGTT
*
67540 TTTTTAAGTGTGATATTCGGGTC-AGGT
1 TTTTTAAGTGTGATATTCGGGTCGAGTT
67567 TTTTTAAGTGTGATATTCGGGTCG
1 TTTTTAAGTGTGATATTCGGGTCG
67591 GGTTCGGGTT
Statistics
Matches: 103, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
27 25 0.24
28 78 0.76
ACGTcount: A:0.16, C:0.07, G:0.30, T:0.46
Consensus pattern (28 bp):
TTTTTAAGTGTGATATTCGGGTCGAGTT
Found at i:67754 original size:28 final size:28
Alignment explanation
Indices: 67718--67775 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
67708 TTTTTACACT
67718 GTTTTTTTAACTGTGATATTCGGGTCGG
1 GTTTTTTTAACTGTGATATTCGGGTCGG
* *
67746 GTTTTTTTAAGTGTGATGTTCGGGTCGG
1 GTTTTTTTAACTGTGATATTCGGGTCGG
67774 GT
1 GT
67776 CGGATCAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.12, C:0.09, G:0.33, T:0.47
Consensus pattern (28 bp):
GTTTTTTTAACTGTGATATTCGGGTCGG
Found at i:68189 original size:16 final size:16
Alignment explanation
Indices: 68164--68210 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
68154 TTTCAGATTA
*
68164 AGATTTCAATTCCTAC
1 AGATTCCAATTCCTAC
*
68180 AGATTCCAATTCTTTTAC
1 AGATTCCAATTC--CTAC
68198 AGATTCCAATTCC
1 AGATTCCAATTCC
68211 CTCATAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 11 0.42
18 15 0.58
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.38
Consensus pattern (16 bp):
AGATTCCAATTCCTAC
Found at i:71153 original size:16 final size:17
Alignment explanation
Indices: 71118--71161 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
71108 ATGGAATTAA
71118 AAAAATAATATTATTGT
1 AAAAATAATATTATTGT
71135 AAAAAT-ATAATTATT-T
1 AAAAATAAT-ATTATTGT
71151 -AAAATAATATT
1 AAAAATAATATT
71162 TAATTGTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.32
16 5 0.20
17 12 0.48
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AAAAATAATATTATTGT
Found at i:86593 original size:28 final size:29
Alignment explanation
Indices: 86540--86594 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
86530 ATGAGATACA
86540 TGAGATACATATCAATTTAAGGATTATAT
1 TGAGATACATATCAATTTAAGGATTATAT
*
86569 TGAGATACATAT-AATTTGAGGATTAT
1 TGAGATACATATCAATTTAAGGATTAT
86595 CATGTGCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.38
Consensus pattern (29 bp):
TGAGATACATATCAATTTAAGGATTATAT
Found at i:90389 original size:117 final size:116
Alignment explanation
Indices: 90072--90393 Score: 366
Period size: 117 Copynumber: 2.8 Consensus size: 116
90062 AACCAGATCC
* * * * *
90072 TGGTTCACCTTCTCACTTGCAAGGTACACGCCATTCCGTCGATCGATCCCCACGATCA--TCACT
1 TGGTTCACCCTCTCCCTTGCAAGGTACTCGCCATTCTGTCGATCGATCCCCACGATCATCTCTCT
* * *
90135 TAACTCGAAGCCGACGATTGATC-GAGGATCGCCGAAGGTTGATCCGGAACG
66 TAACTCGAAGCC-ACGATTGATCGGAGGACCGCCAAAGGTTGAGCCGGAACG
* * * * * * *
90186 TGGTTCGCCCTCTCCCTTGCGAGGTACTCGCCATT-TGGTTGATCGGTCTCCTCGATCATCACCT
1 TGGTTCACCCTCTCCCTTGCAAGGTACTCGCCATTCT-GTCGATCGATCCCCACGATCATC-TCT
** *
90250 CTTAACTCGAAGCTGGCAATTGATCGGAGG-CCGCCAAAGGTTGAGCCGGAACG
64 CTTAACTCGAAGC-CACGATTGATCGGAGGACCGCCAAAGGTTGAGCCGGAACG
* * *
90303 TGGTTTACCCTCTCCCTTGCAAGGTACTCGCCATTCTGTCGACCCATCCCCACGATCATCGTCTC
1 TGGTTCACCCTCTCCCTTGCAAGGTACTCGCCATTCTGTCGATCGATCCCCACGATCATC-TCTC
90368 TTAACTCGAAGCCATCGATTGATCGG
65 TTAACTCGAAGCCA-CGATTGATCGG
90394 GGATCACCAA
Statistics
Matches: 168, Mismatches: 32, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
114 47 0.28
117 116 0.69
118 5 0.03
ACGTcount: A:0.20, C:0.32, G:0.23, T:0.25
Consensus pattern (116 bp):
TGGTTCACCCTCTCCCTTGCAAGGTACTCGCCATTCTGTCGATCGATCCCCACGATCATCTCTCT
TAACTCGAAGCCACGATTGATCGGAGGACCGCCAAAGGTTGAGCCGGAACG
Found at i:93908 original size:20 final size:20
Alignment explanation
Indices: 93885--93936 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
93875 AACGCGATCC
93885 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
93905 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
93925 CCAAAATCGCAA
1 CCAGAATCGCAA
93937 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:93953 original size:21 final size:20
Alignment explanation
Indices: 93926--94024 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
93916 AATCAGTTTC
93926 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
93947 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
93968 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
93988 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
94009 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
94025 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:94053 original size:20 final size:20
Alignment explanation
Indices: 93991--94184 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
93981 CGATTTTCCA
* ** *
93991 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
94011 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
94031 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
94051 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
94071 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
94091 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
94111 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
94131 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
94151 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
94172 AAATCGCAACGCG
1 AAATCGCAACGCG
94185 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:94075 original size:60 final size:60
Alignment explanation
Indices: 93991--94184 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
93981 CGATTTTCCA
* ** * *
93991 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
94051 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
94111 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
94172 AAATCGCAACGCG
1 AAATCGCAACGCG
94185 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:94605 original size:33 final size:33
Alignment explanation
Indices: 94566--94636 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
94556 TTCACTTAGA
*
94566 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
94599 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
94632 TTTCA
1 TTTCA
94637 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:94798 original size:14 final size:14
Alignment explanation
Indices: 94779--94868 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
94769 TTTGGTTTCG
94779 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
94793 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
94812 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
94826 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
94843 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
94859 CGTTGCGATT
1 CGTTGCGATT
94869 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:94804 original size:33 final size:33
Alignment explanation
Indices: 94762--94876 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
94752 GACTGTCGCA
**
94762 TTGCGATTTTGGTTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
94795 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
94828 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
94861 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
94877 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:96804 original size:185 final size:186
Alignment explanation
Indices: 96575--97046 Score: 930
Period size: 185 Copynumber: 2.5 Consensus size: 186
96565 TAGATTGCTT
96575 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
96640 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
96705 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
96760 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
96824 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
96889 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
96945 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
97010 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
97047 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
184 92 0.32
185 154 0.54
186 39 0.14
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:96981 original size:93 final size:93
Alignment explanation
Indices: 96575--97046 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
96565 TAGATTGCTT
96575 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
96640 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
96668 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
96732 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
96760 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
96824 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
96852 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
96917 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
96945 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
97010 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
97038 AGTAAATTT
1 AGTAAATTT
97047 ATCCATTCAA
Statistics
Matches: 378, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.49
93 194 0.51
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:97130 original size:19 final size:19
Alignment explanation
Indices: 97090--97218 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
97080 TAGTTTACTT
* *
97090 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
97110 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
97129 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
97148 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
97162 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
97181 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
97195 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
97214 TCGCA
1 TCGCA
97219 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:97169 original size:33 final size:32
Alignment explanation
Indices: 97126--97218 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
97116 CGCGAAACCA
**
97126 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
97158 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
97191 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
97219 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:97216 original size:52 final size:52
Alignment explanation
Indices: 97090--97218 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
97080 TAGTTTACTT
**
97090 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
97142 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
97195 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
97219 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:97236 original size:19 final size:19
Alignment explanation
Indices: 97214--97348 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
97204 GAAACCAAAA
*
97214 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
97233 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
97249 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
97266 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
97282 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
97299 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
97318 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
97338 TCGTGTTGCGA
1 TCGCGTTGCGA
97349 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:97255 original size:14 final size:14
Alignment explanation
Indices: 97236--97292 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
97226 TTTCATTTCG
97236 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
97250 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
97267 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
97283 CGTTGCGATT
1 CGTTGCGATT
97293 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:97261 original size:33 final size:33
Alignment explanation
Indices: 97219--97311 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
97209 CAAAATCGCA
*
97219 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
97252 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
97285 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
97312 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:99209 original size:38 final size:38
Alignment explanation
Indices: 99166--99238 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
99156 AATTGATTGT
*
99166 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
99204 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
99239 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:99225 original size:19 final size:19
Alignment explanation
Indices: 99161--99225 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
99151 AGTTTAATTG
*
99161 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
99180 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
99198 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
99218 ATTGATTT
1 ATTGATTT
99226 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:99239 original size:14 final size:14
Alignment explanation
Indices: 99220--99255 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
99210 ATTGTTTAAT
99220 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
99234 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
99248 TGATTTGT
1 TGATTTGT
99256 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:99378 original size:19 final size:19
Alignment explanation
Indices: 99362--99463 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
99352 AAAAATGACT
99362 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
99381 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
99400 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
99414 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
99433 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
99453 ATCGCAATGCG
1 ATCGCAATGCG
99464 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:99516 original size:19 final size:19
Alignment explanation
Indices: 99492--99817 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
99482 GATTATCTCG
99492 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
99511 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
99530 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
99544 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
99563 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
99582 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
99601 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
99620 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
99639 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
99653 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
99672 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
99691 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
99705 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
99724 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
99743 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
99757 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
99777 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
99791 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
99810 TTGCGATT
1 TTGCGATT
99818 GTATTTTCCG
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 3 0.01
19 160 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:99532 original size:52 final size:52
Alignment explanation
Indices: 99470--99789 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
99460 TGCGTTTATA
*
99470 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
99522 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
99574 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
99631 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
99683 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
99735 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
99788 AT
1 AT
99790 GTTGGGATTT
Statistics
Matches: 257, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 182 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:99567 original size:71 final size:72
Alignment explanation
Indices: 99492--99817 Score: 389
Period size: 71 Copynumber: 4.6 Consensus size: 72
99482 GATTATCTCG
99492 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
99556 TTTCGCA
66 TTTCGCA
* *
99563 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGATT
99628 TTCATTTCGCA
62 TTCATTTCGCA
*
99639 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATT
*
99697 TTC-TCTCG--
62 TTCATTTCGCA
*
99705 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
99769 TTTCCGCA
66 TTT-CGCA
* *
99777 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
99818 GTATTTTCCG
Statistics
Matches: 227, Mismatches: 11, Indels: 38
0.82 0.04 0.14
Matches are distributed among these distances:
66 12 0.05
67 25 0.11
68 14 0.06
69 13 0.06
70 3 0.01
71 109 0.48
72 12 0.05
73 6 0.03
74 8 0.04
76 25 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
TTTCGCA
Found at i:99735 original size:161 final size:157
Alignment explanation
Indices: 99470--99789 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
99460 TGCGTTTATA
99470 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
99535 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
99600 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
99631 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
99696 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
99761 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
99788 AT
1 AT
99790 GTTGGGATTT
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 116 0.75
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:99761 original size:33 final size:33
Alignment explanation
Indices: 99511--99817 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
99501 TCATTTCGCA
*
99511 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
99544 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
99580 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
99618 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
99653 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
99689 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
99724 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
99757 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
99791 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
99818 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 87 0.37
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:102141 original size:12 final size:12
Alignment explanation
Indices: 102124--102148 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
102114 TCTTCGGGGA
102124 CTTTTTCTTCTT
1 CTTTTTCTTCTT
102136 CTTTTTCTTCTT
1 CTTTTTCTTCTT
102148 C
1 C
102149 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:103071 original size:20 final size:20
Alignment explanation
Indices: 103043--103411 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
103033 AAATTTCAGT
* * * *
103043 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
103063 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
103083 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
103103 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
103123 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
103143 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
103163 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
103183 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
103203 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
103223 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
103243 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
103263 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
103283 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
103303 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
103323 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
103343 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
103363 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
103383 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
103403 GTTGCGATT
1 GTTGCGATT
103412 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:117234 original size:20 final size:21
Alignment explanation
Indices: 117209--117301 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
117199 TTTTCCCAAT
*
117209 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
117229 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
117250 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
117270 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
117291 TCGCAATGCGA
1 TCGCAATGCGA
117302 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:117254 original size:41 final size:41
Alignment explanation
Indices: 117209--117301 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
117199 TTTTCCCAAT
117209 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
117250 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
117291 TCGCAATGCGA
1 TCGCAATGCGA
117302 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:117314 original size:41 final size:41
Alignment explanation
Indices: 117228--117362 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
117218 GAATAAGTAA
** *
117228 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
117269 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
117310 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
117351 TTCGCAACGCGA
1 ATCGCAACGCGA
117363 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:117315 original size:20 final size:20
Alignment explanation
Indices: 117290--117383 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
117280 AATTGGGAAA
*
117290 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
117310 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
117331 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
117351 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
117371 TTCGCAACGCGAT
1 ATCGCAACGCGAT
117384 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:117937 original size:19 final size:19
Alignment explanation
Indices: 117899--117965 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
117889 TTCGAGAATG
117899 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
117919 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
117938 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
117957 AAAATCGCA
1 AAAATCGCA
117966 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:117983 original size:19 final size:19
Alignment explanation
Indices: 117961--118110 Score: 175
Period size: 19 Copynumber: 8.1 Consensus size: 19
117951 GAAACCAAAA
*
117961 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
117980 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
117999 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
118018 TCGCGTTACGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
118037 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
118053 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
118070 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
118089 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
118109 TC
1 TC
118111 AACCAAAAGA
Statistics
Matches: 112, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 81 0.72
20 17 0.15
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:120172 original size:42 final size:42
Alignment explanation
Indices: 120110--120232 Score: 124
Period size: 42 Copynumber: 2.9 Consensus size: 42
120100 GCCCGACTCG
* * * *
120110 CCTATCATTCCTCAATAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
*
120152 CCTATCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * * * *
120194 ACTGTCA-TCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATTC-CTCAAGA-GTCCACTCCCACCGTTCAAGAG
120233 CCCGATTCAC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.03
42 62 0.91
43 4 0.06
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:120195 original size:21 final size:21
Alignment explanation
Indices: 120166--120232 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
120156 TCATTCCTCG
*
120166 AGAGTCCACTCCCACCGTTCA
1 AGAGGCCACTCCCACCGTTCA
** * *
120187 AGAGGCCACTGTCATCGTTGA
1 AGAGGCCACTCCCACCGTTCA
*
120208 AGAGGTCC-CTCCCACCATTCA
1 AGAGG-CCACTCCCACCGTTCA
120229 AGAG
1 AGAG
120233 CCCGATTCAC
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
21 33 0.94
22 2 0.06
ACGTcount: A:0.25, C:0.34, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGGCCACTCCCACCGTTCA
Found at i:121607 original size:14 final size:14
Alignment explanation
Indices: 121588--121623 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
121578 TTTGTTTAAT
121588 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
121602 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
121616 TGATTTGT
1 TGATTTGT
121624 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:121825 original size:19 final size:19
Alignment explanation
Indices: 121803--121933 Score: 112
Period size: 19 Copynumber: 7.7 Consensus size: 19
121793 CGAAATTAAA
*
121803 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
121822 TTCGCATTGCGA--TTCA-
1 TTCGCATTGCGATTTTCAT
*
121838 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
121855 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
*
121869 TTAGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
121888 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
121904 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
121921 TTCGCATTGCGAT
1 TTCGCATTGCGAT
121934 AGTAATTTCC
Statistics
Matches: 88, Mismatches: 9, Indels: 30
0.69 0.07 0.24
Matches are distributed among these distances:
14 24 0.27
16 14 0.16
17 14 0.16
19 36 0.41
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:121849 original size:33 final size:33
Alignment explanation
Indices: 121807--121933 Score: 195
Period size: 33 Copynumber: 3.8 Consensus size: 33
121797 ATTAAATTCG
121807 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
*
121840 CGTTGCGATTTTCATTTCGCATTGCGAAATT-A-G
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCACT
* *
121873 CATTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
121906 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
121934 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.92
34 1 0.01
35 3 0.04
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:121896 original size:66 final size:66
Alignment explanation
Indices: 121800--121932 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
121790 ACGCGAAATT
* *
121800 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGCATTGC
121865 G
66 G
*
121866 AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGCATTGC
121931 G
66 G
121932 A
1 A
121933 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (66 bp):
AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:124279 original size:20 final size:20
Alignment explanation
Indices: 124254--124311 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
124244 ATTCATTTGA
124254 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
124274 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
124294 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
124312 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:124354 original size:14 final size:14
Alignment explanation
Indices: 124335--124392 Score: 71
Period size: 14 Copynumber: 3.8 Consensus size: 14
124325 GAAAATCGCA
124335 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
124349 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
124366 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
124382 TTGCGATTTTC
1 TTGCGATTTTC
124393 ATTTCGCATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 22 0.56
16 3 0.08
17 3 0.08
19 11 0.28
ACGTcount: A:0.10, C:0.21, G:0.19, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:124354 original size:33 final size:33
Alignment explanation
Indices: 124317--124387 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
124307 AAAATCGCAA
124317 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
124350 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
124383 TGCGA
1 TGCGA
124388 TTTTCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:124371 original size:19 final size:19
Alignment explanation
Indices: 124330--124464 Score: 173
Period size: 19 Copynumber: 7.6 Consensus size: 19
124320 GAAATGAAAA
124330 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
124346 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
124363 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
124379 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
124396 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
124415 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
*
124434 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
124453 TCGCGTTGCGAT
1 TCGCATTGCGAT
124465 AGTCTGTTTT
Statistics
Matches: 105, Mismatches: 4, Indels: 17
0.83 0.03 0.13
Matches are distributed among these distances:
14 22 0.21
16 6 0.06
17 6 0.06
19 71 0.68
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:124435 original size:38 final size:33
Alignment explanation
Indices: 124330--124447 Score: 182
Period size: 33 Copynumber: 3.4 Consensus size: 33
124320 GAAATGAAAA
124330 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
124363 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
124396 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
124434 TCGCATTGCGATTT
1 TCGCATTGCGATTT
124448 CCATTTCGCG
Statistics
Matches: 79, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
33 49 0.62
36 3 0.04
38 27 0.34
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:124453 original size:38 final size:36
Alignment explanation
Indices: 124330--124464 Score: 165
Period size: 33 Copynumber: 3.8 Consensus size: 36
124320 GAAATGAAAA
*
124330 TCGCATTGCGATTT--TCTCG-TTGCGATTTTCATT
1 TCGCATTGCGATTTCATTTCGCTTGCGATTTTCATT
*
124363 TCGCATTGCGATTT--TCTCG-TTGCGATTTTCATT
1 TCGCATTGCGATTTCATTTCGCTTGCGATTTTCATT
*
124396 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTTATT
1 TCGCATTGCGA-TTTCATTTCGC-TTGCGATTTTCATT
124434 TCGCATTGCGATTTCCATTTCGCGTTGCGAT
1 TCGCATTGCGATTT-CATTTCGC-TTGCGAT
124465 AGTCTGTTTT
Statistics
Matches: 93, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
33 44 0.47
34 3 0.03
36 4 0.04
37 3 0.03
38 39 0.42
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (36 bp):
TCGCATTGCGATTTCATTTCGCTTGCGATTTTCATT
Found at i:126489 original size:20 final size:19
Alignment explanation
Indices: 126457--126520 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
126447 TCTTAAAATT
126457 GCAACGCGAAATGACTATC
1 GCAACGCGAAATGACTATC
*
126476 GCAACGCGGAAATGGCTATC
1 GCAACGC-GAAATGACTATC
* **
126496 GCAATGCGAAATGAAAATC
1 GCAACGCGAAATGACTATC
126515 GCAACG
1 GCAACG
126521 ACAAAATCGC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 21 0.55
20 17 0.45
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.14
Consensus pattern (19 bp):
GCAACGCGAAATGACTATC
Found at i:126528 original size:14 final size:14
Alignment explanation
Indices: 126509--126566 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
126499 ATGCGAAATG
126509 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
126523 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
126539 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
126555 AAAATCGCAACG
1 AAAATCGCAACG
126567 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:126538 original size:33 final size:33
Alignment explanation
Indices: 126493--126585 Score: 145
Period size: 32 Copynumber: 2.8 Consensus size: 33
126483 GGAAATGGCT
*
126493 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
126526 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
126558 ATCGCAACGCGAAA-CACAAATCGCAACG
1 ATCGCAACGCGAAATGA-AAATCGCAACG
126586 CGAAACACAA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
32 30 0.54
33 26 0.46
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:126607 original size:19 final size:19
Alignment explanation
Indices: 126524--126601 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 19
126514 CGCAACGACA
**
126524 AAATCGCAACGCGAAA-TG
1 AAATCGCAACGCGAAACAC
126542 AAATCGCAA--CG--ACA-
1 AAATCGCAACGCGAAACAC
126556 AAATCGCAACGCGAAACAC
1 AAATCGCAACGCGAAACAC
126575 AAATCGCAACGCGAAACAC
1 AAATCGCAACGCGAAACAC
126594 AAATCGCA
1 AAATCGCA
126602 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
14 10 0.19
16 4 0.08
18 12 0.23
19 27 0.51
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (19 bp):
AAATCGCAACGCGAAACAC
Found at i:126638 original size:14 final size:14
Alignment explanation
Indices: 126619--126676 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
126609 TTTCATTTCG
126619 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
126633 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
126649 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
126665 CGTTGCGATTTT
1 CGTTGCGATTTT
126677 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:126649 original size:32 final size:33
Alignment explanation
Indices: 126602--126684 Score: 159
Period size: 32 Copynumber: 2.5 Consensus size: 33
126592 ACAAATCGCA
126602 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
126635 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
126667 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
126685 ATTGTGATAG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
32 32 0.65
33 17 0.35
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:126701 original size:19 final size:19
Alignment explanation
Indices: 126677--126722 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
126667 TTGCGATTTT
*
126677 CATTTCGCATTGTGATAGC
1 CATTTCGCATTGCGATAGC
* *
126696 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTGCGATAGC
126716 CATTTCG
1 CATTTCG
126723 TGTTGCGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:126729 original size:19 final size:19
Alignment explanation
Indices: 126665--126730 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
126655 GCGATTTTGT
**
126665 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
126684 CATTGTGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
126704 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
126723 TGTTGCGA
1 CGTTGCGA
126731 AAGTAAACTA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 21 0.57
20 16 0.43
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:128807 original size:22 final size:22
Alignment explanation
Indices: 128782--128825 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
128772 GATTTAGATA
128782 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
128804 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
128826 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:129106 original size:20 final size:20
Alignment explanation
Indices: 128993--129106 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 20
128983 CGCTTTGAAA
128993 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * * *
129013 ATCGCGTTGTGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* * *
129033 ATCGCGTTACGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
129053 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
129074 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
129094 ATCGCATTGCGAT
1 ATCGCATTGCGAT
129107 TTTCCCAATT
Statistics
Matches: 73, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 52 0.71
21 12 0.16
22 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:129124 original size:21 final size:21
Alignment explanation
Indices: 129095--129187 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
129085 ATAGTAAGTA
129095 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
129116 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
129136 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
129157 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
129177 TCGCATTGCGA
1 TCGCATTGCGA
129188 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:129125 original size:41 final size:41
Alignment explanation
Indices: 129034--129168 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
129024 AAAGTCAGTA
* * * * ** *
129034 TCGCGTTACGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
129074 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
129116 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
129157 TCGCGTTGCGAT
1 TCGCGTTGCGAT
129169 TTACTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:129169 original size:41 final size:41
Alignment explanation
Indices: 129095--129187 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
129085 ATAGTAAGTA
129095 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
129136 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
129177 TCGCATTGCGA
1 TCGCATTGCGA
129188 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:129687 original size:18 final size:19
Alignment explanation
Indices: 129645--129688 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
129635 TTTGGTTCAC
*
129645 GGAATATAAGATTACCAGT
1 GGAATAAAAGATTACCAGT
*
129664 GTGAATAAAAGATTACTAG-
1 G-GAATAAAAGATTACCAGT
129683 GGAATA
1 GGAATA
129689 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 2 0.09
20 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGT
Found at i:129827 original size:18 final size:18
Alignment explanation
Indices: 129804--129851 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
129794 AAATTGTCTT
*
129804 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
129822 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
129839 TATTTATATATTT
1 TA-TTATATATTT
129852 TCTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:132500 original size:117 final size:117
Alignment explanation
Indices: 132333--132543 Score: 287
Period size: 117 Copynumber: 1.8 Consensus size: 117
132323 AAGTCCAGTC
* * * * * * * * *
132333 TATGAAAAATCTGAAGTTTCAGAGGATTCCTATGTTTATGGAAATTCAGATGCATATGGATCTAC
1 TATGAAAAAACAGAAGTTTCAGAGGATTCCTATGTTAAAGAAAATCCAGATGAATACGAATCTAC
* *
132398 ACTGGATGAGAGCTCTGAATCACAAGAAAATGAAGATAATGAGTCTTCTGTT
66 ACCGGACGAGAGCTCTGAATCACAAGAAAATGAAGATAATGAGTCTTCTGTT
* * *
132450 TATGAAAAAACAGAAGTTTCGGAGGGTTCCTATGTTAAAGAAAATCCAGATGAATACGAATCTCC
1 TATGAAAAAACAGAAGTTTCAGAGGATTCCTATGTTAAAGAAAATCCAGATGAATACGAATCTAC
*
132515 ACCGGACGAGAGCTCTGAATCGCAAGAAA
66 ACCGGACGAGAGCTCTGAATCACAAGAAA
132544 GTTCTAGTTT
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
117 79 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (117 bp):
TATGAAAAAACAGAAGTTTCAGAGGATTCCTATGTTAAAGAAAATCCAGATGAATACGAATCTAC
ACCGGACGAGAGCTCTGAATCACAAGAAAATGAAGATAATGAGTCTTCTGTT
Found at i:139465 original size:22 final size:23
Alignment explanation
Indices: 139423--139470 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
139413 TTAATTTCTG
**
139423 TTTGGGTGTTATTTGTGTAAA-A
1 TTTGGGTGTTATTTGCATAAATA
139445 TTTGGGTGTTAGTTT-CATAAATA
1 TTTGGGTGTTA-TTTGCATAAATA
139468 TTT
1 TTT
139471 ATAGAAGACG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.23, C:0.02, G:0.23, T:0.52
Consensus pattern (23 bp):
TTTGGGTGTTATTTGCATAAATA
Found at i:140199 original size:26 final size:26
Alignment explanation
Indices: 140170--140257 Score: 149
Period size: 26 Copynumber: 3.4 Consensus size: 26
140160 CAAGTTGTGT
* *
140170 GATTTGTGATAAAGAAATCAGCCATG
1 GATTTGTAACAAAGAAATCAGCCATG
*
140196 GATTTGTAACAAAGAAATCAACCATG
1 GATTTGTAACAAAGAAATCAGCCATG
140222 GATTTGTAACAAAGAAATCAGCCATG
1 GATTTGTAACAAAGAAATCAGCCATG
140248 GATTTGTAAC
1 GATTTGTAAC
140258 TTATATTTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 58 1.00
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (26 bp):
GATTTGTAACAAAGAAATCAGCCATG
Found at i:142466 original size:32 final size:31
Alignment explanation
Indices: 142394--142468 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
142384 CTAATGTGAC
*
142394 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCTCTGCGGCCCTAAGATCAT
** *
142425 TCTCGGGTAGGCTCTGCGGCCCTAAGATGTAT
1 TCTTAGGTAGGCTCTGCGGCCCTAAGAT-CAT
142457 TCTTAGGTAGGC
1 TCTTAGGTAGGC
142469 CCCGTGGCCC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 25 0.68
32 12 0.32
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCTCTGCGGCCCTAAGATCAT
Found at i:143564 original size:35 final size:36
Alignment explanation
Indices: 143481--143575 Score: 122
Period size: 35 Copynumber: 2.7 Consensus size: 36
143471 AATGGATTAT
* ** *
143481 GAATTTGGGG-TTAGGCATGTAATTAAAGTATTTTTG
1 GAATTTGGGGTTTA-GAATGTAATTAAAACATTTTTA
*
143517 GAATTTGAGGTTTAGAATGTAATTAAAACA-TTTTA
1 GAATTTGGGGTTTAGAATGTAATTAAAACATTTTTA
143552 GAATTTGGGGTTTAGAATGTAATT
1 GAATTTGGGGTTTAGAATGTAATT
143576 GATGAATGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
35 27 0.52
36 22 0.42
37 3 0.06
ACGTcount: A:0.33, C:0.02, G:0.24, T:0.41
Consensus pattern (36 bp):
GAATTTGGGGTTTAGAATGTAATTAAAACATTTTTA
Found at i:156356 original size:20 final size:20
Alignment explanation
Indices: 156331--156384 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
156321 AATTGGGAAA
*
156331 ATCGCAATACGATACTGACT
1 ATCGCAATGCGATACTGACT
*
156351 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
156371 ATCGCAATGCGATA
1 ATCGCAATGCGATA
156385 ATACAAAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:156429 original size:20 final size:20
Alignment explanation
Indices: 156396--156445 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
156386 TACAAAAGCG
* *
156396 CAACGAGATACTGACTTTCA
1 CAACGCGATTCTGACTTTCA
*
156416 CAACGCGATTCTGACTTTCG
1 CAACGCGATTCTGACTTTCA
156436 CAACGCGATT
1 CAACGCGATT
156446 TACATAGCGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (20 bp):
CAACGCGATTCTGACTTTCA
Found at i:157065 original size:20 final size:20
Alignment explanation
Indices: 157042--157088 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
157032 GTTGTGATAG
157042 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
157062 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
157082 TCATTTC
1 TCATTTC
157089 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:159159 original size:42 final size:42
Alignment explanation
Indices: 159099--159221 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
159089 GCCCAACTCA
* * *
159099 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
159141 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
159183 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
159222 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:159179 original size:21 final size:21
Alignment explanation
Indices: 159155--159221 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
159145 TCATTCCTCG
159155 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
159176 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
159197 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
159218 AGAG
1 AGAG
159222 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:160598 original size:14 final size:14
Alignment explanation
Indices: 160579--160614 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
160569 ATTGTTTAAT
160579 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
160593 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
160607 TGATTTGT
1 TGATTTGT
160615 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:160781 original size:19 final size:19
Alignment explanation
Indices: 160759--160909 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
160749 CGAAATTAAA
160759 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
160778 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
160793 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
160811 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
160825 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
160844 TTCGTATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
160859 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
160877 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
160896 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
160910 AGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:160805 original size:33 final size:32
Alignment explanation
Indices: 160763--160889 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
160753 ATTAAATTCG
160763 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
160796 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
160829 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
160862 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
160890 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:160841 original size:66 final size:66
Alignment explanation
Indices: 160756--160888 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
160746 ACGCGAAATT
*
160756 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
160821 G
66 G
* *
160822 AAATTAGCGTTGCGATTTTCATTTCGTATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
160887 G
66 G
160888 A
1 A
160889 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:162723 original size:12 final size:12
Alignment explanation
Indices: 162706--162742 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
162696 TCTCCGGGGA
162706 CTTTTTCTTCTT
1 CTTTTTCTTCTT
*
162718 CTTTTTCTTATT
1 CTTTTTCTTCTT
162730 CTTTTTCTTCTT
1 CTTTTTCTTCTT
162742 C
1 C
162743 AGGATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:163784 original size:20 final size:21
Alignment explanation
Indices: 163759--163810 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
163749 TTTTCCTAAT
*
163759 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
163779 TCGCAATGCGAATTTTGAAAA
1 TCGCAATGCGAATTAAGAAAA
163800 TCGCAATGCGA
1 TCGCAATGCGA
163811 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:163884 original size:20 final size:20
Alignment explanation
Indices: 163776--163886 Score: 80
Period size: 20 Copynumber: 5.5 Consensus size: 20
163766 GCGAATAAGT
*
163776 AAATCGCAATGCGA-ATTTTGA
1 AAATCGCAA--CGAGATTCTGA
* * *
163797 AAATCGCAATGCGATACTGA
1 AAATCGCAACGAGATTCTGA
** ** *
163817 CTATCGCAACGAGATAATACA
1 AAATCGCAACGAGATTCT-GA
163838 AAATCGCAACGAGATTCTGA
1 AAATCGCAACGAGATTCTGA
***
163858 CTTTCGCAACGAGATTCTGA
1 AAATCGCAACGAGATTCTGA
163878 AAATCGCAA
1 AAATCGCAA
163887 TCATCTTCAA
Statistics
Matches: 67, Mismatches: 21, Indels: 5
0.72 0.23 0.05
Matches are distributed among these distances:
19 1 0.01
20 42 0.63
21 24 0.36
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.23
Consensus pattern (20 bp):
AAATCGCAACGAGATTCTGA
Found at i:164187 original size:20 final size:20
Alignment explanation
Indices: 164104--164187 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
164094 GGGGAAATCC
164104 CAACGCGAAAATGGCTATCG
1 CAACGCGAAAATGGCTATCG
*
164124 CAATGCGAAAATGGCTATCG
1 CAACGCGAAAATGGCTATCG
** ***
164144 CAATTCG-AAATGAAAAATCG
1 CAACGCGAAAATG-GCTATCG
164164 CAACGCGAAAATGGCTATCG
1 CAACGCGAAAATGGCTATCG
164184 CAAC
1 CAAC
164188 TAGAAAATCG
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
19 5 0.10
20 42 0.81
21 5 0.10
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
CAACGCGAAAATGGCTATCG
Found at i:164199 original size:34 final size:38
Alignment explanation
Indices: 164120--164207 Score: 112
Period size: 40 Copynumber: 2.4 Consensus size: 38
164110 GAAAATGGCT
164120 ATCGCAATGCGAAAATGGCTATCGCAATTCGAAATGAAAA
1 ATCGCAATGCGAAAATGGCTATCGCAA-TC-AAATGAAAA
* *
164160 ATCGCAACGCGAAAATGGCTATCGCAA-C-TA-G-AAA
1 ATCGCAATGCGAAAATGGCTATCGCAATCAAATGAAAA
164194 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
164208 TGAAAATCGC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 16 0.36
35 1 0.02
36 1 0.02
38 1 0.02
40 26 0.58
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.17
Consensus pattern (38 bp):
ATCGCAATGCGAAAATGGCTATCGCAATCAAATGAAAA
Found at i:164255 original size:19 final size:19
Alignment explanation
Indices: 164214--164281 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
164204 GAAATGAAAA
164214 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
164230 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
164247 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
164266 TCGCATTACGATTTTC
1 TCGCATTGCGATTTTC
164282 TCGTTGCCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:164437 original size:14 final size:14
Alignment explanation
Indices: 164418--164454 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
164408 CATCAATTAA
164418 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
164432 ACAAATCATCTTTT
1 ACAAATCAACATTT
164446 ACAAATCAA
1 ACAAATCAA
164455 TTAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:166343 original size:20 final size:19
Alignment explanation
Indices: 166320--166387 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
166310 GAAACTTAAA
166320 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
166340 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
166360 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
166379 ATCGCAACG
1 ATCGCAACG
166388 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:166395 original size:14 final size:14
Alignment explanation
Indices: 166376--166432 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
166366 ATGCGAAATG
166376 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
166390 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
166409 AAAATCGCAACGAC
1 AAAATCGCAACGAC
166423 AAAATCGCAA
1 AAAATCGCAA
166433 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:166402 original size:33 final size:33
Alignment explanation
Indices: 166360--166452 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
166350 GGAAATGGCT
166360 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
166393 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
166426 ATCGCAATGCGAAATG-AAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
166453 CGAAACACAA
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 11 0.18
33 49 0.82
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:166466 original size:19 final size:18
Alignment explanation
Indices: 166424--166468 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
166414 CGCAACGACA
* **
166424 AAATCGCAATGCGAAATG
1 AAATCGCAACGCGAAAAC
166442 AAATCGCAACGCGAAACAC
1 AAATCGCAACGCGAAA-AC
166461 AAATCGCA
1 AAATCGCA
166469 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAAAAC
Found at i:166474 original size:19 final size:18
Alignment explanation
Indices: 166391--166474 Score: 61
Period size: 19 Copynumber: 4.8 Consensus size: 18
166381 CGCAACGACA
166391 AAATCGCAATGCGAAATGA-
1 AAATCGCAATGCGAAA--AC
*
166410 AAATCGCAA--CG-ACA-
1 AAATCGCAATGCGAAAAC
**
166424 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAAAC
*
166442 AAATCGCAACGCGAAACAC
1 AAATCGCAATGCGAAA-AC
*
166461 AAATCGCATTGCGA
1 AAATCGCAATGCGA
166475 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
14 10 0.19
16 3 0.06
17 3 0.06
18 15 0.29
19 21 0.40
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (18 bp):
AAATCGCAATGCGAAAAC
Found at i:166501 original size:19 final size:19
Alignment explanation
Indices: 166464--166522 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
166454 GAAACACAAA
**
166464 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATAGTCATT
*
166483 TCGCATTGCGATAGCCATT
1 TCGCATTGCGATAGTCATT
*
166502 TCCGCGTTGCGATAGTCATT
1 T-CGCATTGCGATAGTCATT
166522 T
1 T
166523 TCGTGTTGCG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (19 bp):
TCGCATTGCGATAGTCATT
Found at i:166513 original size:20 final size:19
Alignment explanation
Indices: 166479--166533 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
166469 TTGCGATTTT
*
166479 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
166498 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
166518 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
166534 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:167041 original size:18 final size:18
Alignment explanation
Indices: 167015--167059 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
167005 GTCGATCAGA
*
167015 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
167033 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
167051 TGATGGCTC
1 TGATGGCTC
167060 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:168422 original size:20 final size:20
Alignment explanation
Indices: 168399--168436 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
168389 AACACAAAAA
168399 TGACTATCACAACACGAATT
1 TGACTATCACAACACGAATT
* *
168419 TGACTATCGCAACGCGAA
1 TGACTATCACAACACGAA
168437 ACTAAAATCA
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:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (20 bp):
TGACTATCACAACACGAATT
Found at i:168700 original size:20 final size:21
Alignment explanation
Indices: 168675--168723 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
168665 TCTGAGAGAT
*
168675 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGAATTTCGCC
*
168695 GGAGATGGAGACGAATTTCGTC
1 GGAGAT-GAGACGAATTTCGCC
168717 GGAGATG
1 GGAGATG
168724 GGTGAGAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 1 0.04
22 18 0.72
ACGTcount: A:0.27, C:0.14, G:0.39, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGAATTTCGCC
Found at i:168712 original size:22 final size:22
Alignment explanation
Indices: 168681--168724 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
168671 AGATGGAGAT
*
168681 AGACGGATTTCGCCGGAGATGG
1 AGACGAATTTCGCCGGAGATGG
*
168703 AGACGAATTTCGTCGGAGATGG
1 AGACGAATTTCGCCGGAGATGG
168725 GTGAGAGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.16, G:0.39, T:0.20
Consensus pattern (22 bp):
AGACGAATTTCGCCGGAGATGG
Found at i:168999 original size:20 final size:20
Alignment explanation
Indices: 168893--169027 Score: 130
Period size: 20 Copynumber: 6.7 Consensus size: 20
168883 CGCTTTGAAA
*
168893 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
168914 ATCGCATTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
168934 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
168954 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
168975 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
168995 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
169015 ATCGCATTGCGAT
1 ATCGCATTGCGAT
169028 TTTCCTAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 65 0.68
21 24 0.25
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:169045 original size:21 final size:21
Alignment explanation
Indices: 169016--169088 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
169006 ATAGTCAGTA
169016 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* * *
169037 TCGCGTTGCGATTTACCCAAT
1 TCGCATTGCGATTTTCCTAAT
* * *
169058 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCTAAT
169078 TCGCATTGCGA
1 TCGCATTGCGA
169089 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:169048 original size:61 final size:61
Alignment explanation
Indices: 168893--169030 Score: 204
Period size: 61 Copynumber: 2.3 Consensus size: 61
168883 CGCTTTGAAA
* * * *
168893 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * * *
168954 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
169015 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
169031 CCTAATTCGC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:182278 original size:6 final size:6
Alignment explanation
Indices: 182267--182294 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
182257 TTTCCATAGG
182267 AAATAT AAATAT AAATAT AAATAT AAAT
1 AAATAT AAATAT AAATAT AAATAT AAAT
182295 TTTATATTAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:193523 original size:12 final size:12
Alignment explanation
Indices: 193495--193531 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
193485 TTTGGTAATC
193495 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
193508 CCCGCCCCGATA
1 CCCGCCCCGATA
*
193520 CCCGACCCGATA
1 CCCGCCCCGATA
193532 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.19, C:0.54, G:0.16, T:0.11
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:193604 original size:19 final size:19
Alignment explanation
Indices: 193580--193619 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
193570 AATAAATTTA
193580 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
193599 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
193618 AT
1 AT
193620 ATATATATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:193674 original size:12 final size:12
Alignment explanation
Indices: 193626--193679 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
193616 ATATATATAT
*
193626 ATACCCGGCCCG
1 ATACCCGGCCCA
*
193638 ATTCCCGGCCCA
1 ATACCCGGCCCA
*
193650 ATA-CCGACCCA
1 ATACCCGGCCCA
193661 ATACCCGGCCCA
1 ATACCCGGCCCA
193673 ATACCCG
1 ATACCCG
193680 TTTAAATAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
11 10 0.28
12 26 0.72
ACGTcount: A:0.24, C:0.48, G:0.17, T:0.11
Consensus pattern (12 bp):
ATACCCGGCCCA
Done.