Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002042.1 Hibiscus syriacus cultivar Beakdansim tig00004163_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: 124983
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3947 original size:20 final size:21
Alignment explanation
Indices: 3919--3959 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3909 TTATGAAATG
*
3919 AGAAAAATG-AATTTAATTTA
1 AGAAAAATGAAATTCAATTTA
*
3939 AGAATAATGAAATTCAATTTA
1 AGAAAAATGAAATTCAATTTA
3960 TTTGTTGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (21 bp):
AGAAAAATGAAATTCAATTTA
Found at i:4390 original size:28 final size:26
Alignment explanation
Indices: 4350--4409 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 26
4340 GGGTCGAGTC
4350 GGTCGGTTTTTTAAGTGTGATATTCG
1 GGTCGGTTTTTTAAGTGTGATATTCG
* *
4376 GGTCGGATCTTTTTAAGTTTGATATTTG
1 GGTCGG-T-TTTTTAAGTGTGATATTCG
4404 GGTCGG
1 GGTCGG
4410 GTTCGGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 6 0.20
27 1 0.03
28 23 0.77
ACGTcount: A:0.15, C:0.08, G:0.32, T:0.45
Consensus pattern (26 bp):
GGTCGGTTTTTTAAGTGTGATATTCG
Found at i:4980 original size:18 final size:17
Alignment explanation
Indices: 4935--4981 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
4925 TATGAAATTG
*
4935 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
4952 GATTTCAATTCCTTCACA
1 GATTCCAATTCC-TCACA
*
4970 TATTCCAATTCC
1 GATTCCAATTCC
4982 CTCATAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.28, C:0.30, G:0.06, T:0.36
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:5529 original size:20 final size:21
Alignment explanation
Indices: 5504--5543 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5494 AATACAAGAA
5504 AATAAAAGTTAACT-ATTTTT
1 AATAAAAGTTAACTAATTTTT
*
5524 AATAAATGTTAACTAATTTT
1 AATAAAAGTTAACTAATTTT
5544 GAAGCAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (21 bp):
AATAAAAGTTAACTAATTTTT
Found at i:19528 original size:19 final size:19
Alignment explanation
Indices: 19506--19543 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19496 GATAATAATG
19506 AGATTATATGTATTCAAAC
1 AGATTATATGTATTCAAAC
19525 AGATTATATGTATTCAAAC
1 AGATTATATGTATTCAAAC
19544 TAAGAACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
AGATTATATGTATTCAAAC
Found at i:26481 original size:2 final size:2
Alignment explanation
Indices: 26474--26503 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
26464 AAATACATAC
26474 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
26504 GAAAGAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27814 original size:2 final size:2
Alignment explanation
Indices: 27807--27843 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
27797 TTGTTTGAGC
27807 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27844 GATGAAGACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29393 original size:2 final size:2
Alignment explanation
Indices: 29388--29423 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
29378 TTAGTGTTAT
29388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29424 TTCTATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:29504 original size:20 final size:20
Alignment explanation
Indices: 29479--29516 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29469 TTTTTGATTA
29479 TTTTACTTATATATATATGT
1 TTTTACTTATATATATATGT
* *
29499 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
29517 TTTACTCATT
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:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTACTTATATATATATGT
Found at i:29548 original size:16 final size:18
Alignment explanation
Indices: 29527--29561 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
29517 TTTACTCATT
29527 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
29543 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
29561 T
1 T
29562 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:32818 original size:8 final size:8
Alignment explanation
Indices: 32747--32848 Score: 66
Period size: 8 Copynumber: 12.5 Consensus size: 8
32737 AATCAAGAAC
32747 AAAAAAGA
1 AAAAAAGA
*
32755 AAAGAAGCA
1 AAAAAAG-A
32764 AAAAAAGCA
1 AAAAAAG-A
32773 AAAAAA-A
1 AAAAAAGA
32780 AAACAAAG-
1 AAA-AAAGA
**
32788 AAGCAAGA
1 AAAAAAGA
*
32796 GAAACAAGA
1 -AAAAAAGA
*
32805 ACAAAAGA
1 AAAAAAGA
32813 AAAAAAGA
1 AAAAAAGA
*
32821 GAAAAAGA
1 AAAAAAGA
*
32829 GAAAAAA-T
1 -AAAAAAGA
*
32837 CAAAAAGA
1 AAAAAAGA
32845 AAAA
1 AAAA
32849 GGGACAAAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
7 12 0.16
8 34 0.47
9 27 0.37
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.01
Consensus pattern (8 bp):
AAAAAAGA
Found at i:32820 original size:16 final size:15
Alignment explanation
Indices: 32747--32848 Score: 78
Period size: 16 Copynumber: 6.3 Consensus size: 15
32737 AATCAAGAAC
32747 AAAAAAGAAAAGAAGCA
1 AAAAAAGAAAA-AAG-A
*
32764 AAAAAAGCAAAAAAAA
1 AAAAAAG-AAAAAAGA
**
32780 AAACAAAGAAGCAAGA
1 AAA-AAAGAAAAAAGA
*
32796 GAAACAAGAACAAAAGA
1 -AAAAAAGAA-AAAAGA
32813 AAAAAAGAGAAAAAGA
1 AAAAAAGA-AAAAAGA
**
32829 GAAAAAATCAAAAAGA
1 -AAAAAAGAAAAAAGA
32845 AAAA
1 AAAA
32849 GGGACAAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
15 4 0.06
16 34 0.49
17 27 0.39
18 4 0.06
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.01
Consensus pattern (15 bp):
AAAAAAGAAAAAAGA
Found at i:32857 original size:22 final size:23
Alignment explanation
Indices: 32815--32858 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
32805 ACAAAAGAAA
32815 AAAAGAGAAAAAGAGAAAAAATC
1 AAAAGAGAAAAAGAGAAAAAATC
*
32838 AAAA-AGAAAAAGGGACAAAAA
1 AAAAGAGAAAAAGAGA-AAAAA
32859 GCACATGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.75, C:0.05, G:0.18, T:0.02
Consensus pattern (23 bp):
AAAAGAGAAAAAGAGAAAAAATC
Found at i:33511 original size:22 final size:22
Alignment explanation
Indices: 33483--33533 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
33473 CCCCATCAAT
33483 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
* *
33505 CCTTTGAGCATCAAATGCTAAA
1 CCTTTGAGCATCAAATACCAAA
33527 CCTTTGA
1 CCTTTGA
33534 CCAAACACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:34560 original size:36 final size:36
Alignment explanation
Indices: 34452--34575 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
34442 ATTGAAAACA
* * *
34452 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
* *
34488 TTTCCCTTGGAACTAAGTTTT-GTCTCTCTTAAGACAG
1 TTTCCCTTGAAAC-AA-TTTTCGTCTCTCTTGAGACAG
* *
34525 TTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
34561 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
34576 AACCTTTGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.05
36 41 0.55
37 27 0.36
38 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
Found at i:34638 original size:65 final size:67
Alignment explanation
Indices: 34551--34691 Score: 180
Period size: 67 Copynumber: 2.1 Consensus size: 67
34541 TTTCGTCTAT
* ** *
34551 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAAC-AATTTTTTTC
1 CTTGAGACAGTTACCCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACAAATTTTGTT-
34613 TCC
65 TCC
* * *
34616 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTACCCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACA-AATTTTGTT
34681 TCC
65 TCC
34684 CTTGAGAC
1 CTTGAGAC
34692 CGTTTCTCAT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
65 17 0.26
66 2 0.03
67 27 0.42
68 11 0.17
69 8 0.12
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.38
Consensus pattern (67 bp):
CTTGAGACAGTTACCCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACAAATTTTGTTT
CC
Found at i:35535 original size:105 final size:105
Alignment explanation
Indices: 35351--36074 Score: 1158
Period size: 105 Copynumber: 7.0 Consensus size: 105
35341 GCACTCGAGG
* * ** *
35351 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
35416 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
35457 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
35522 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
35562 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT---CAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
35624 ACCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
35664 CAATGCAAGTTCAAATTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
35729 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* **
35769 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
35834 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
35874 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
35939 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
35979 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
36039 TTCAATTTCAACTTCACGACGGAGGATATTGGACTC
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTC
36075 TGAACAATGC
Statistics
Matches: 586, Mismatches: 29, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
100 37 0.06
101 1 0.00
102 99 0.17
103 2 0.00
104 2 0.00
105 406 0.69
106 39 0.07
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:35715 original size:207 final size:208
Alignment explanation
Indices: 35351--36074 Score: 1143
Period size: 207 Copynumber: 3.5 Consensus size: 208
35341 GCACTCGAGG
* * ** *
35351 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT--AC-AACAACTTCTCAATTTCAG
*
35416 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
63 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACG
* *
35481 AAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAG
128 AAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
35546 GATATTGGACTTCAGA
193 GATATTGGACTTCAGA
* *
35562 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT-CAACAACTTCTCAATTTCAGAAC
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTACAACAACTTCTCAATTTCAGAGC
* * *
35626 CAATTTCAACTTCACAATGAAGGATATTGGACTTCAGACAATGCAAGTTCAAATTCACGACGAAG
66 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAG
35691 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
131 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
35756 ATTGGACTTCAGA
196 ATTGGACTTCAGA
* **
35769 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT--ACAACAACTTCTCAATTTCAGA
35834 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGA
64 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGA
* *
35899 AGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
129 AGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
*
35964 ATATTGGACTCCAGA
194 ATATTGGACTTCAGA
* *
35979 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT-CAACAAAATT-TC-A-TTCAGAT
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTACAAC-AACTTCTCAATTTCAGAG
* * *
36040 TCAATTTCAACTTCACGACGGAGGATATTGGACTC
65 CCAATTTCAACTTCACAACGAAGGATATTGGACTC
36075 TGAACAATGC
Statistics
Matches: 477, Mismatches: 32, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
205 36 0.08
206 1 0.00
207 203 0.43
208 5 0.01
210 197 0.41
211 35 0.07
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (208 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTACAACAACTTCTCAATTTCAGAGC
CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAG
GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
ATTGGACTTCAGA
Found at i:37288 original size:2 final size:2
Alignment explanation
Indices: 37283--37337 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
37273 TTAGTGTTAT
37283 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
*
37325 TA TA TT TA TA TA T
1 TA TA TA TA TA TA T
37338 TTTCTATTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:37456 original size:39 final size:39
Alignment explanation
Indices: 37381--37457 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
37371 TTTTGATTTT
* *
37381 TTTTTTGATTATTTTACTTATATATATATATGTTTTTAC
1 TTTTTTGATTATTTTACTCATATATATATATATTTTTAC
* * *
37420 TTTTTT-ATATATTTTACTCATTTATTTATCTATTTTTA
1 TTTTTTGAT-TATTTTACTCATATATATATATATTTTTA
37458 TATTTATCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 2 0.06
39 30 0.94
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (39 bp):
TTTTTTGATTATTTTACTCATATATATATATATTTTTAC
Found at i:37463 original size:16 final size:18
Alignment explanation
Indices: 37442--37476 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
37432 TTTACTCATT
37442 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
37458 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
37476 T
1 T
37477 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:38102 original size:60 final size:61
Alignment explanation
Indices: 38009--38173 Score: 210
Period size: 60 Copynumber: 2.7 Consensus size: 61
37999 GTTGCGACAC
* * *
38009 AAATTAGTCTTTAAACTTTTG-ACTACTTTAATTTCATCCCTAAATC-ATGACTCTCATTCT
1 AAATTAGTCTTTAAACTTTTGAAC-ATTTTAATTTCATCCCTAAATCTACGACACTCATTCT
*
38069 AAATTAGTCTTTAAACTTTTGAACATTTTAATTTCATCCCTAAA-CTACGACACTCTTTCT
1 AAATTAGTCTTTAAACTTTTGAACATTTTAATTTCATCCCTAAATCTACGACACTCATTCT
*** * * *
38129 AAATTAGTCCCCAAAATTTTGAATATTTTAATTTCATCCCAAAAT
1 AAATTAGTCTTTAAACTTTTGAACATTTTAATTTCATCCCTAAAT
38174 TCATCCTAAT
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
59 1 0.01
60 89 0.97
61 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (61 bp):
AAATTAGTCTTTAAACTTTTGAACATTTTAATTTCATCCCTAAATCTACGACACTCATTCT
Found at i:41171 original size:3 final size:3
Alignment explanation
Indices: 41163--41257 Score: 190
Period size: 3 Copynumber: 31.7 Consensus size: 3
41153 GGTAGGGAGA
41163 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41211 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41258 ATGATTGTTA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:49901 original size:31 final size:29
Alignment explanation
Indices: 49863--49930 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
49853 CTTTGGATGC
49863 ATTGAATTGGGAAAGAAAAAGAAGAAATTAT
1 ATTGAATTGGGAAA-AAAAAG-AGAAATTAT
* ** *
49894 ATTGAATTTGGTCAAACAAGAGAAATTAT
1 ATTGAATTGGGAAAAAAAAGAGAAATTAT
49923 ATTGAATT
1 ATTGAATT
49931 TGGTCAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 17 0.52
30 5 0.15
31 11 0.33
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.29
Consensus pattern (29 bp):
ATTGAATTGGGAAAAAAAAGAGAAATTAT
Found at i:49921 original size:29 final size:29
Alignment explanation
Indices: 49885--49944 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
49875 AAGAAAAAGA
49885 AGAAATTATATTGAATTTGGTCAAACAAG
1 AGAAATTATATTGAATTTGGTCAAACAAG
49914 AGAAATTATATTGAATTTGGTCAAACAAG
1 AGAAATTATATTGAATTTGGTCAAACAAG
49943 AG
1 AG
49945 TTAAACGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (29 bp):
AGAAATTATATTGAATTTGGTCAAACAAG
Found at i:51056 original size:20 final size:20
Alignment explanation
Indices: 51031--51080 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
51021 CAACTGGTAA
51031 TATCGATACTACCTAGAGAG
1 TATCGATACTACCTAGAGAG
51051 TATCGATACTACCTAGAGAG
1 TATCGATACTACCTAGAGAG
51071 TATCGATACT
1 TATCGATACT
51081 TCTCTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (20 bp):
TATCGATACTACCTAGAGAG
Found at i:52559 original size:2 final size:2
Alignment explanation
Indices: 52552--52585 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
52542 GTCACTTGTC
*
52552 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52586 TCCAATCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:53620 original size:3 final size:3
Alignment explanation
Indices: 53612--53642 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
53602 TTTTACCCAC
53612 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
53643 AATATATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:53669 original size:14 final size:13
Alignment explanation
Indices: 53641--53677 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
53631 TTATTATTAT
53641 TAAATATATTAAA
1 TAAATATATTAAA
53654 TAAATATATATAAA
1 TAAATATAT-TAAA
53668 TAAATA-ATTA
1 TAAATATATTA
53678 CAGACCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 11 0.48
14 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAATATATTAAA
Found at i:67915 original size:83 final size:83
Alignment explanation
Indices: 67634--68267 Score: 1039
Period size: 83 Copynumber: 7.7 Consensus size: 83
67624 AATTAAATGA
*
67634 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
67698 AA-CAATCATTGAGTTTAG
65 AACCAATCATTGAGTTTAG
67716 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
67780 AA-CAATCATTGAGTTTAG
65 AACCAATCATTGAGTTTAG
*
67798 AAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AAGATGAATTTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
*
67862 AACCCATCATTGAGTTTAG
65 AACCAATCATTGAGTTTAG
*
67881 AAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AAGATGAATTTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
* * *
67945 AACCCATCATTGAATTTGG
65 AACCAATCATTGAGTTTAG
*
67964 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
* *
68029 ACCAATCATTGAATTTGG
66 ACCAATCATTGAGTTTAG
*
68047 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
68112 ACCAATCATTGAGTTTAG
66 ACCAATCATTGAGTTTAG
*
68130 AAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AAGATGAATTTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
* *
68194 AACCAATCATTGAATTTGG
65 AACCAATCATTGAGTTTAG
*
68213 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
68268 ATTCAGTAGG
Statistics
Matches: 530, Mismatches: 16, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
81 1 0.00
82 140 0.26
83 387 0.73
84 2 0.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (83 bp):
AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACCAATCATTGAGTTTAG
Found at i:69214 original size:114 final size:113
Alignment explanation
Indices: 69006--69650 Score: 909
Period size: 114 Copynumber: 5.6 Consensus size: 113
68996 GATTTAAATC
* * * *
69006 CATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * **
69071 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATT
* * *
69119 CATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATC-ATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * * *
69184 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATT
* * *
69233 CATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATC-ATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
69298 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGTTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATT
* * *
69347 CATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
1 CATCATTTGATGGATCATCATTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGA
69411 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATT
62 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATT
* * *
69463 CATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
1 CATCATTTGATGGATCATCATTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGA
69527 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATT
62 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATT
** * *
69579 CATCATTTGATGGATCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG
1 CATCATTTGATGGATCATCATTTCCAG-AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
69644 -AGAAGAA
65 AAGAAGAA
69651 TTTATTCAAT
Statistics
Matches: 496, Mismatches: 29, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
112 3 0.01
113 46 0.09
114 224 0.45
115 2 0.00
116 202 0.41
117 17 0.03
118 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (113 bp):
CATCATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATT
Found at i:69793 original size:3 final size:3
Alignment explanation
Indices: 69787--69847 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
69777 TTTTACCCAC
*
69787 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
69835 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
69848 AAAATATTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:79591 original size:7 final size:7
Alignment explanation
Indices: 79579--79618 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
79569 TATGAAATAT
79579 ATATAAA
1 ATATAAA
79586 ATATAAA
1 ATATAAA
79593 ATAT-AA
1 ATATAAA
79599 ATATTAAA
1 ATA-TAAA
79607 AT-TAAA
1 ATATAAA
79613 AT-TAAA
1 ATATAAA
79619 CTATTAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 15 0.48
7 12 0.39
8 4 0.13
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
ATATAAA
Found at i:79598 original size:14 final size:14
Alignment explanation
Indices: 79579--79618 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
79569 TATGAAATAT
79579 ATATAAAATATAAA
1 ATATAAAATATAAA
79593 ATAT-AAATATTAAA
1 ATATAAAATA-TAAA
79607 AT-TAAAAT-TAAA
1 ATATAAAATATAAA
79619 CTATTAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.17
13 6 0.25
14 14 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATAAAATATAAA
Found at i:79612 original size:20 final size:20
Alignment explanation
Indices: 79577--79630 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
79567 ATTATGAAAT
79577 ATATATAAAATATAAAATATAA
1 ATAT-TAAAATATAAAAT-TAA
79599 ATATTAAAAT-TAAAATTAA
1 ATATTAAAATATAAAATTAA
*
79618 ACTATTAACATAT
1 A-TATTAAAATAT
79631 TCTGTTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 7 0.24
22 4 0.14
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATTAAAATATAAAATTAA
Found at i:88019 original size:22 final size:22
Alignment explanation
Indices: 87994--88051 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
87984 CTGTACAAAT
**
87994 TTAATGAATGGTACTATGAACA
1 TTAATGAACAGTACTATGAACA
*
88016 TTAATGAACAGTACTGTGAACA
1 TTAATGAACAGTACTATGAACA
* *
88038 GTAATGGACAGTAC
1 TTAATGAACAGTAC
88052 CGTTGCTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.28
Consensus pattern (22 bp):
TTAATGAACAGTACTATGAACA
Found at i:88115 original size:21 final size:21
Alignment explanation
Indices: 88089--88146 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
88079 CAGGAGTATT
88089 GATACCCTGCTACAGTGTACC
1 GATACCCTGCTACAGTGTACC
*
88110 GATACCCTGCTACAGTGTACT
1 GATACCCTGCTACAGTGTACC
*
88131 GATACCCTGTTACAGT
1 GATACCCTGCTACAGT
88147 AATTTCGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (21 bp):
GATACCCTGCTACAGTGTACC
Found at i:88741 original size:22 final size:23
Alignment explanation
Indices: 88716--88759 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
88706 AATTAAGTTT
88716 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
88738 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
88760 TCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:94680 original size:20 final size:21
Alignment explanation
Indices: 94656--94735 Score: 83
Period size: 20 Copynumber: 3.8 Consensus size: 21
94646 TTAATGTAGA
94656 GGGAATCGATTCCCCCTTTA-
1 GGGAATCGATTCCCCCTTTAG
*
94676 GGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATTCCCCCTTT--AG
**
94699 GGGAA-CTGATTCCCCCCATAG
1 GGGAATC-GATTCCCCCTTTAG
*
94720 GGGAATCGATACCCCC
1 GGGAATCGATTCCCCC
94736 ATGGGGTTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
20 18 0.35
21 15 0.29
22 3 0.06
23 15 0.29
ACGTcount: A:0.23, C:0.33, G:0.24, T:0.21
Consensus pattern (21 bp):
GGGAATCGATTCCCCCTTTAG
Found at i:95152 original size:26 final size:27
Alignment explanation
Indices: 95103--95154 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
95093 GAATTTTCCC
*
95103 AAAAAAATTGTAAATTTTCGAAATTAA
1 AAAAAAAATGTAAATTTTCGAAATTAA
*
95130 AAAAAAAATGTTAATTTTC-AAATTA
1 AAAAAAAATGTAAATTTTCGAAATTA
95155 TTGTGTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (27 bp):
AAAAAAAATGTAAATTTTCGAAATTAA
Found at i:96725 original size:17 final size:17
Alignment explanation
Indices: 96689--96733 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
96679 GTTTTAACTT
*
96689 TTTGAATATTTTGGAATG
1 TTTGAAT-TTGTGGAATG
*
96707 TTTGAATTTGTGGATTG
1 TTTGAATTTGTGGAATG
*
96724 TTTGACTTTG
1 TTTGAATTTG
96734 AATTTGTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.20, C:0.02, G:0.24, T:0.53
Consensus pattern (17 bp):
TTTGAATTTGTGGAATG
Found at i:100928 original size:31 final size:31
Alignment explanation
Indices: 100893--100960 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
100883 CGGTTACGTC
*
100893 GGGGACCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
** *
100924 GGGGACTGTATTGCAAACATACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
100955 GGGGAC
1 GGGGAC
100961 TGTATTGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:100961 original size:31 final size:31
Alignment explanation
Indices: 100901--100967 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
100891 TCGGGGACCA
*
100901 TATTGCAAACGGACTAAATGTTGGGGGACTG
1 TATTGCAAACAGACTAAATGTTGGGGGACTG
*
100932 TATTGCAAACATACTAAATGTTGGGGGACTG
1 TATTGCAAACAGACTAAATGTTGGGGGACTG
100963 TATTG
1 TATTG
100968 AAAATTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (31 bp):
TATTGCAAACAGACTAAATGTTGGGGGACTG
Found at i:101511 original size:13 final size:13
Alignment explanation
Indices: 101493--101520 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
101483 GTATCAAATT
101493 TTATAAAATTTCA
1 TTATAAAATTTCA
101506 TTATAAAATTTCA
1 TTATAAAATTTCA
101519 TT
1 TT
101521 CTTAAAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (13 bp):
TTATAAAATTTCA
Found at i:111547 original size:81 final size:80
Alignment explanation
Indices: 111454--111614 Score: 270
Period size: 81 Copynumber: 2.0 Consensus size: 80
111444 CAACAGCCTG
*
111454 CATAATTAACTCTTAAAGAACCTCAAACCATGACACGTGGTAAAATAATATCACAAAATATCCTG
1 CATAATTAACTCTTAAAGAACCTCAAACCATGACACGTGATAAAATAATATCAC-AAA-ATCCTG
111519 ATCCTT-AAAGCATAAA
64 ATCCTTCAAAGCATAAA
*
111535 CATAATTAACTCTTAAAGAACCTCAAACCATGACACGTGATATAATAATATCACAAAATCCTGAT
1 CATAATTAACTCTTAAAGAACCTCAAACCATGACACGTGATAAAATAATATCACAAAATCCTGAT
*
111600 CCTTCAAAGCCTAAA
66 CCTTCAAAGCATAAA
111615 AGGGTTAAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
79 12 0.16
80 12 0.16
81 52 0.68
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (80 bp):
CATAATTAACTCTTAAAGAACCTCAAACCATGACACGTGATAAAATAATATCACAAAATCCTGAT
CCTTCAAAGCATAAA
Found at i:112237 original size:2 final size:2
Alignment explanation
Indices: 112230--112264 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
112220 CAAACAAGAA
112230 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
112265 ATTTGAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:113223 original size:14 final size:14
Alignment explanation
Indices: 113204--113231 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
113194 CAACCTCTTT
113204 ATCTTTGTTTTGGC
1 ATCTTTGTTTTGGC
113218 ATCTTTGTTTTGGC
1 ATCTTTGTTTTGGC
113232 CAACCACGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.14, G:0.21, T:0.57
Consensus pattern (14 bp):
ATCTTTGTTTTGGC
Done.