Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002793.1 Hibiscus syriacus cultivar Beakdansim tig00005754_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: 106275
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:7379 original size:16 final size:16
Alignment explanation
Indices: 7346--7379 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7336 ATGAAATAAC
* *
7346 ATGTATATGTGAATAT
1 ATGTATATGAGAAGAT
7362 ATGTATATGAGAAGAT
1 ATGTATATGAGAAGAT
7378 AT
1 AT
7380 AAGAATAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (16 bp):
ATGTATATGAGAAGAT
Found at i:8136 original size:42 final size:42
Alignment explanation
Indices: 8090--8173 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
8080 GAATATAATC
8090 ATATATGTACATGTTTGTATTTGATATATGAATAGAAATATG
1 ATATATGTACATGTTTGTATTTGATATATGAATAGAAATATG
8132 ATATATGTACATGTTTGTATTTGATATATGAATAGAAATATG
1 ATATATGTACATGTTTGTATTTGATATATGAATAGAAATATG
8174 TTTTTTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (42 bp):
ATATATGTACATGTTTGTATTTGATATATGAATAGAAATATG
Found at i:8156 original size:23 final size:23
Alignment explanation
Indices: 8090--8161 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
8080 GAATATAATC
8090 ATATATGTACATGTTTGTATTTG
1 ATATATGTACATGTTTGTATTTG
** *
8113 ATATATG-A-ATAG---AAATATG
1 ATATATGTACAT-GTTTGTATTTG
8132 ATATATGTACATGTTTGTATTTG
1 ATATATGTACATGTTTGTATTTG
8155 ATATATG
1 ATATATG
8162 AATAGAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 11 0.30
20 2 0.05
21 4 0.11
22 2 0.05
23 18 0.49
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.46
Consensus pattern (23 bp):
ATATATGTACATGTTTGTATTTG
Found at i:11078 original size:24 final size:24
Alignment explanation
Indices: 11051--11099 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
11041 ACAAGGAATG
* *
11051 GAAATTTGAAGTTTGAAATCGCCT
1 GAAATTTGAAATTTGAAAACGCCT
11075 GAAATTTGAAATTTGAAAACGCCT
1 GAAATTTGAAATTTGAAAACGCCT
11099 G
1 G
11100 GTTAGAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (24 bp):
GAAATTTGAAATTTGAAAACGCCT
Found at i:17750 original size:18 final size:18
Alignment explanation
Indices: 17700--17741 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
17690 TTATACTCCG
17700 AAAAATCAAAAATCAAAATAA
1 AAAAAT-AAAAA--AAAATAA
17721 AAAAATAAAAAAAAATAA
1 AAAAATAAAAAAAAATAA
17739 AAA
1 AAA
17742 GAATGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
20 5 0.24
21 6 0.29
ACGTcount: A:0.83, C:0.05, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAAATAAAAAAAAATAA
Found at i:19366 original size:21 final size:21
Alignment explanation
Indices: 19341--19391 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
19331 TTGTATGCTT
19341 TTTGATTATCAAGAGAAGCAC
1 TTTGATTATCAAGAGAAGCAC
*
19362 TTTGATTATCAAGAGAAGCTC
1 TTTGATTATCAAGAGAAGCAC
19383 TTTGATTAT
1 TTTGATTAT
19392 TTCCCTTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (21 bp):
TTTGATTATCAAGAGAAGCAC
Found at i:22181 original size:23 final size:23
Alignment explanation
Indices: 22155--22211 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
22145 TGTGACATGT
22155 TCTCTTCCTTTATGGCACGTTTA
1 TCTCTTCCTTTATGGCACGTTTA
* * * *
22178 TCTCTGCCTTTGTGGCATGTTTT
1 TCTCTTCCTTTATGGCACGTTTA
*
22201 TCTCTTTCTTT
1 TCTCTTCCTTT
22212 TGGTAGCTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.07, C:0.25, G:0.14, T:0.54
Consensus pattern (23 bp):
TCTCTTCCTTTATGGCACGTTTA
Found at i:30141 original size:47 final size:47
Alignment explanation
Indices: 30053--30201 Score: 145
Period size: 47 Copynumber: 3.1 Consensus size: 47
30043 ATTTATTATG
* * ** * *
30053 TTAGTGCGAATATGCACTCTTGTATAGTACAACCGTGCACTCCTATA
1 TTAGTGCGAATACGCACTCCTGTATAGTACAATTGTACACTCATATA
*
30100 TTAGTGTGAATACGCACTCCTGTATAGTACAATTGTACACTCATATA
1 TTAGTGCGAATACGCACTCCTGTATAGTACAATTGTACACTCATATA
* ** * * * * * *
30147 TTTGTGCGAACGCACACTCCTATATTAGTACAATTGTGCATTCTTGTA
1 TTAGTGCGAATACGCACTCCTGTA-TAGTACAATTGTACACTCATATA
30195 TTAGTGC
1 TTAGTGC
30202 ATCTGTGCAC
Statistics
Matches: 83, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
47 58 0.70
48 25 0.30
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (47 bp):
TTAGTGCGAATACGCACTCCTGTATAGTACAATTGTACACTCATATA
Found at i:30237 original size:24 final size:24
Alignment explanation
Indices: 30087--30229 Score: 96
Period size: 24 Copynumber: 6.0 Consensus size: 24
30077 TAGTACAACC
*
30087 GTGCACTCCTATATTAGTGTGAA-T
1 GTGCACTCCTATATTAGTG-CAATT
** * *
30111 ACGCACTCCTGTA-TAGTACAATT
1 GTGCACTCCTATATTAGTGCAATT
* * * *
30134 GTACACTCATATATTTGTGCGAA-C
1 GTGCACTCCTATATTAGTGC-AATT
** *
30158 GCACACTCCTATATTAGTACAATT
1 GTGCACTCCTATATTAGTGCAATT
* * *
30182 GTGCATTCTTGTATTAGTGC-ATCT
1 GTGCACTCCTATATTAGTGCAAT-T
30206 GTGCACTCCTATATTAGTGCAATT
1 GTGCACTCCTATATTAGTGCAATT
30230 TTGTACTCTT
Statistics
Matches: 86, Mismatches: 27, Indels: 12
0.69 0.22 0.10
Matches are distributed among these distances:
22 2 0.02
23 17 0.20
24 63 0.73
25 4 0.05
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (24 bp):
GTGCACTCCTATATTAGTGCAATT
Found at i:30261 original size:48 final size:48
Alignment explanation
Indices: 30160--30263 Score: 120
Period size: 48 Copynumber: 2.2 Consensus size: 48
30150 GTGCGAACGC
* * *
30160 ACACTCCTATATTAGTACAATTGTGCATTCTTGTATTAGTGCATCTGT
1 ACACTCCTATATTAGTACAATTGTGCACTCTTGAATTAGTGCATCTAT
* * * * *
30208 GCACTCCTATATTAGTGCAATTTTGTACTCTTGAATTAGTGTAT-TCAT
1 ACACTCCTATATTAGTACAATTGTGCACTCTTGAATTAGTGCATCT-AT
30256 ACACTCCT
1 ACACTCCT
30264 GATTCTAATA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
47 1 0.02
48 45 0.98
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.41
Consensus pattern (48 bp):
ACACTCCTATATTAGTACAATTGTGCACTCTTGAATTAGTGCATCTAT
Found at i:31499 original size:43 final size:43
Alignment explanation
Indices: 31447--31800 Score: 289
Period size: 43 Copynumber: 8.2 Consensus size: 43
31437 ACTTTTTTTT
* ** *
31447 CTTTGTAATTGAGGTTCTTAATTTTTGT-AATCCTACTTTTTAT
1 CTTTATAATTGAGGCCCTTAATTTTT-TCAATCCTACTTTTTAC
*
31490 CTTTATAATTGAGGCCCTTAATTTTTTTCAATCCCA-TTTTTCCAC
1 CTTTATAATTGAGGCCCTTAA-TTTTTTCAATCCTACTTTTT--AC
* * ** * * *
31535 ATTTATAATTGATGATCTTAAGTTTTTCAATCCCACTTTGTAC
1 CTTTATAATTGAGGCCCTTAATTTTTTCAATCCTACTTTTTAC
* *
31578 TTTTATAATTGA-GCTCC-TGATTTTTTCAAT-CTCACTTTTTAC
1 CTTTATAATTGAGGC-CCTTAATTTTTTCAATCCT-ACTTTTTAC
* *
31620 CTTTATAATTGAGGCCCTTAATTTTTTAAAT-CTCATTTTTTTA-
1 CTTTATAATTGAGGCCCTTAATTTTTTCAATCCT-A-CTTTTTAC
*
31663 CTTATATAATCT-AGGCCCCTAATTTTTTCAA-CCTCACTTTTTAC
1 CTT-TATAAT-TGAGGCCCTTAATTTTTTCAATCCT-ACTTTTTAC
* * * *
31707 CTTTAAAATTGAAGCCCCTAATTTTTTTAAT-CTCACTTTTTAC
1 CTTTATAATTGAGGCCCTTAATTTTTTCAATCCT-ACTTTTTAC
* *
31750 CTTTATAATTGAGG-TCTCTAATTTTTTCAATCATACTTTTTTAC
1 CTTTATAATTGAGGCCCT-TAATTTTTTCAATCCTAC-TTTTTAC
*
31794 TTTTATA
1 CTTTATA
31801 GTTTAAGCCC
Statistics
Matches: 257, Mismatches: 35, Indels: 37
0.78 0.11 0.11
Matches are distributed among these distances:
41 1 0.00
42 35 0.14
43 124 0.48
44 74 0.29
45 23 0.09
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (43 bp):
CTTTATAATTGAGGCCCTTAATTTTTTCAATCCTACTTTTTAC
Found at i:31601 original size:130 final size:129
Alignment explanation
Indices: 31465--31781 Score: 367
Period size: 130 Copynumber: 2.4 Consensus size: 129
31455 TTGAGGTTCT
*
31465 TAATTTTTGTAATC-CTACTTTTTATCTTTATAATTGAGGCCCTTAATTTTTTTCAATCCCATTT
1 TAATTTTT-TAATCTC-ACTTTTTACCTTTATAATTGAGGCCCTTAA-TTTTTTCAATCCCATTT
* * * * *
31529 TTCCACATT-TATAAT-TGATGATCTTAAGTTTTTCAATCC-CACTTTGTACTTTTATAATTG-A
63 TTCCAC-TTATATAATCT-AGGACCCTAAGTTTTTCAA-CCTCACTTTGTACCTTTAAAATTGAA
*
31590 GCTCC
125 GCCCC
* * *
31595 TGATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTTAAATCTCATTTTT
1 TAATTTTTT-AATCTCACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTTCAATCCCATTTTT
** * * *
31660 TTACTTATATAATCTAGGCCCCTAATTTTTTCAACCTCACTTTTTACCTTTAAAATTGAAGCCCC
65 CCACTTATATAATCTAGGACCCTAAGTTTTTCAACCTCACTTTGTACCTTTAAAATTGAAGCCCC
*
31725 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGG-TCTCTAATTTTTTCAATC
1 TAA-TTTTTTAATCTCACTTTTTACCTTTATAATTGAGGCCCT-TAATTTTTTCAATC
31782 ATACTTTTTT
Statistics
Matches: 161, Mismatches: 18, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
128 4 0.02
129 60 0.37
130 90 0.56
131 7 0.04
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (129 bp):
TAATTTTTTAATCTCACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTTCAATCCCATTTTTC
CACTTATATAATCTAGGACCCTAAGTTTTTCAACCTCACTTTGTACCTTTAAAATTGAAGCCCC
Found at i:31700 original size:87 final size:86
Alignment explanation
Indices: 31465--31817 Score: 299
Period size: 87 Copynumber: 4.1 Consensus size: 86
31455 TTGAGGTTCT
* *
31465 TAATTTTTGT-AATC-CTACTTTTTATCTTTATAATTGAGGCCCTTAATTTTTTTCAATCC-CA-
1 TAATTTTT-TAAATCTC-ACTTTTTACCTTTATAATTGAGGCCCCTAA-TTTTTTCAA-CCTCAC
* * * ** *
31526 TTTTTCCACATTTATAATTGATGATCT
62 TTTTT--ACCTTTAAAATTGAAGCCCC
* * * * * * * *
31553 TAAGTTTTTCAATCCCACTTTGTACTTTTATAATTGA-GCTCCTGATTTTTTCAATCTCACTTTT
1 TAATTTTTTAAATCTCACTTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAACCTCACTTTT
* * *
31617 TACCTTTATAATTGAGGCCCT
66 TACCTTTAAAATTGAAGCCCC
*
31638 TAATTTTTTAAATCTCATTTTTTTA-CTTATATAATCT-AGGCCCCTAATTTTTTCAACCTCACT
1 TAATTTTTTAAATCTCA-CTTTTTACCTT-TATAAT-TGAGGCCCCTAATTTTTTCAACCTCACT
31701 TTTTACCTTTAAAATTGAAGCCCC
63 TTTTACCTTTAAAATTGAAGCCCC
* * * *
31725 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGGTCTCTAATTTTTTCAATCAT-ACTTT
1 TAATTTTTTAAATCTCACTTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAA-CCTCAC-TT
* * * *
31789 TTTACTTTTATAGTTTAAGCCCC
64 TTTACCTTTAAAATTGAAGCCCC
31812 TAATTT
1 TAATTT
31818 AATCATTTTT
Statistics
Matches: 220, Mismatches: 33, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
85 34 0.15
86 54 0.25
87 102 0.46
88 29 0.13
89 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.50
Consensus pattern (86 bp):
TAATTTTTTAAATCTCACTTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAACCTCACTTTT
TACCTTTAAAATTGAAGCCCC
Found at i:31790 original size:130 final size:129
Alignment explanation
Indices: 31465--31817 Score: 362
Period size: 130 Copynumber: 2.7 Consensus size: 129
31455 TTGAGGTTCT
* * *
31465 TAATTTTTGT-AATC-CTACTTTTTATCTTTATAATTGAGGCCCTTAATTTTTTTCAATCCCA-T
1 TAATTTTT-TCAATCTC-ACTTTTTACCTTTATAATTGAGGCCCTTAA-TTTTTTAAATCTCACT
* * ** * * * *
31527 TTTTCCACATT-TATAAT-TGATGATCTTAAGTTTTTCAATCCCACTTTGTACTTTTATAATTGA
63 TTTT-TAC-TTATATAATCT-AAGCCCCTAATTTTTTCAATCCCACTTTGTACCTTTAAAATTGA
*
31590 GCTCC
125 GCCCC
* *
31595 TGATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTTAAATCTCATTTTT
1 TAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTTAAATCTCACTTTT
* *
31660 TTACTTATATAATCTAGGCCCCTAATTTTTTCAA-CCTCACTTTTTACCTTTAAAATTGAAGCCC
66 TTACTTATATAATCTAAGCCCCTAATTTTTTCAATCC-CACTTTGTACCTTTAAAATTG-AGCCC
31724 C
129 C
* * *
31725 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGG-TCTCTAATTTTTTCAATCAT-ACTT
1 TAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGCCCT-TAATTTTTTAAATC-TCACTT
* * *
31788 TTTTACTTTTATAGTTTAAGCCCCTAATTT
64 TTTTACTTATATAATCTAAGCCCCTAATTT
31818 AATCATTTTT
Statistics
Matches: 191, Mismatches: 23, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
128 4 0.02
129 55 0.29
130 130 0.68
131 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.50
Consensus pattern (129 bp):
TAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGCCCTTAATTTTTTAAATCTCACTTTT
TTACTTATATAATCTAAGCCCCTAATTTTTTCAATCCCACTTTGTACCTTTAAAATTGAGCCCC
Found at i:37562 original size:17 final size:17
Alignment explanation
Indices: 37534--37569 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
37524 TTAATAATAC
37534 ATATATATAA-TTTAAA
1 ATATATATAATTTTAAA
37550 ATATATGATAATTTTAAA
1 ATATAT-ATAATTTTAAA
37568 AT
1 AT
37570 TTTTCAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATATATAATTTTAAA
Found at i:39793 original size:7 final size:8
Alignment explanation
Indices: 39776--39801 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39766 CATAATTATT
39776 AAAAATAA
1 AAAAATAA
39784 AAAAATAA
1 AAAAATAA
39792 AAAAATAA
1 AAAAATAA
39800 AA
1 AA
39802 GTATGTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:41671 original size:12 final size:13
Alignment explanation
Indices: 41656--41711 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 13
41646 TTAAAATATA
41656 TATTATAT-TTAT
1 TATTATATATTAT
*
41668 TATTATATACTA-
1 TATTATATATTAT
*
41680 TAGTATGATTATTAT
1 TATTAT-A-TATTAT
41695 TATTAT-TATTAT
1 TATTATATATTAT
41707 TATTA
1 TATTA
41712 CTAATATCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 24 0.67
13 3 0.08
14 4 0.11
15 5 0.14
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (13 bp):
TATTATATATTAT
Found at i:41672 original size:3 final size:3
Alignment explanation
Indices: 41664--41711 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
41654 TATATTATAT
* * *
41664 TTA TTA TTA TATA CTA -TA GTA TGA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41709 TTA
1 TTA
41712 CTAATATCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:48261 original size:2 final size:2
Alignment explanation
Indices: 48249--48280 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
48239 TCATTTATCC
*
48249 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48281 CCCTAGTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48511 original size:49 final size:48
Alignment explanation
Indices: 48457--48559 Score: 138
Period size: 49 Copynumber: 2.1 Consensus size: 48
48447 CAAACAAAAT
*
48457 GAAAAAAGAGCAA-AAAGA-AAAGGAAAAAGAAAAAAAAAAGAAATTAAA
1 GAAAAAAGAGCAACAAAGACAAA--AAAAAGAAAAAAAAAAGAAAGTAAA
**
48505 GAAAAAAGAGCAACAAAGAGCAAAAAAAAGAAACGAAAAAGAAAGTAAA
1 GAAAAAAGAGCAACAAAGA-CAAAAAAAAGAAAAAAAAAAGAAAGTAAA
48554 GAAAAA
1 GAAAAA
48560 GAAAGTAAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
48 13 0.27
49 33 0.67
51 3 0.06
ACGTcount: A:0.75, C:0.05, G:0.17, T:0.03
Consensus pattern (48 bp):
GAAAAAAGAGCAACAAAGACAAAAAAAAGAAAAAAAAAAGAAAGTAAA
Found at i:48549 original size:15 final size:15
Alignment explanation
Indices: 48526--48575 Score: 77
Period size: 15 Copynumber: 3.4 Consensus size: 15
48516 AACAAAGAGC
48526 AAAAA-AAAG-AAACG
1 AAAAAGAAAGTAAA-G
48540 AAAAAGAAAGTAAAG
1 AAAAAGAAAGTAAAG
48555 AAAAAGAAAGTAAAG
1 AAAAAGAAAGTAAAG
48570 AAAAAG
1 AAAAAG
48576 GGACAATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
14 5 0.15
15 26 0.76
16 3 0.09
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (15 bp):
AAAAAGAAAGTAAAG
Found at i:49699 original size:33 final size:32
Alignment explanation
Indices: 49601--49735 Score: 180
Period size: 32 Copynumber: 4.2 Consensus size: 32
49591 AAGCAATAGA
* *
49601 GGGCATCTTTGAAGATTCAACATCACATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
* * *
49633 AGGTATCTTTGGAGTTTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
49665 GGGCATCTTTAGAGATTCAACATCAAAATGTTG
1 GGGCATCTTTGGAGATTCAACATC-AAATGTTG
* * *
49698 GGGCATCTTTGGAGATTCAATATCGAATATTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
49730 GGGCAT
1 GGGCAT
49736 TCAATATTCT
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
32 59 0.66
33 30 0.34
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATGTTG
Found at i:49731 original size:65 final size:64
Alignment explanation
Indices: 49601--49735 Score: 182
Period size: 65 Copynumber: 2.1 Consensus size: 64
49591 AAGCAATAGA
* * * *
49601 GGGCATCTTTGAAGATTCAACATCACATGTTGAGGTATCTTTGGAGTTTCAACATCAAATGTTG
1 GGGCATCTTTGAAGATTCAACATCAAATGTTGAGGCATCTTTGGAGATTCAACATCAAATATTG
* * *
49665 GGGCATCTTT-AGAGATTCAACATCAAAATGTTGGGGCATCTTTGGAGATTCAATATCGAATATT
1 GGGCATCTTTGA-AGATTCAACATC-AAATGTTGAGGCATCTTTGGAGATTCAACATCAAATATT
49729 G
64 G
49730 GGGCAT
1 GGGCAT
49736 TCAATATTCT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
63 1 0.02
64 22 0.35
65 39 0.63
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (64 bp):
GGGCATCTTTGAAGATTCAACATCAAATGTTGAGGCATCTTTGGAGATTCAACATCAAATATTG
Found at i:49879 original size:34 final size:34
Alignment explanation
Indices: 49841--49929 Score: 142
Period size: 34 Copynumber: 2.6 Consensus size: 34
49831 TTTAATTTTT
*
49841 TTTTGTCTCACTTGAGATAATTTCTCAAAACAAA
1 TTTTGTCTCACTTGAGACAATTTCTCAAAACAAA
49875 TTTTGTCTCACTTGAGACAATTTCTCAAAACAAA
1 TTTTGTCTCACTTGAGACAATTTCTCAAAACAAA
** *
49909 TTCCGTCTCGCTTGAGACAAT
1 TTTTGTCTCACTTGAGACAAT
49930 ATTTCTCTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (34 bp):
TTTTGTCTCACTTGAGACAATTTCTCAAAACAAA
Found at i:50324 original size:35 final size:36
Alignment explanation
Indices: 50256--50543 Score: 184
Period size: 36 Copynumber: 8.1 Consensus size: 36
50246 CGAAATAGAA
50256 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
*
50292 AAATATTGTCTCCCTTGAGAC-GTTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * *
50327 AAATTTTGTCTCCCTTGAGACAATCTCCCTTGAGAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * * * *
50363 --A----GTTTCCCTCGAAACAAATTTTGTCTCCCTTGAGAC
1 AAATTTTGTCTCCCTTGAGAC--A----GTTTCCCTTGAAAC
* * ***** * ** *
50399 --AGTTTCTCTCGAAACAAATTTTGTCTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGA--CAGTTTCCCTTGAAAC
* *
50435 ACATTTTGTCTCCCTTGAGACAGTTTCCATTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
*
50471 AAA-TTTGTCTCTCTTGAGAC-GATTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAG-TTTCCCTTGAAAC
* * *
50506 AAATTTTGTCTCACTTGAGACATTTTCCCTTGAGAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
50542 AA
1 AA
50544 TTTCACTTGA
Statistics
Matches: 197, Mismatches: 37, Indels: 36
0.73 0.14 0.13
Matches are distributed among these distances:
30 11 0.06
32 1 0.01
34 2 0.01
35 65 0.33
36 102 0.52
38 10 0.05
40 6 0.03
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (36 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
Found at i:50371 original size:15 final size:15
Alignment explanation
Indices: 50335--50363 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
50325 ACAAATTTTG
50335 TCTCCCTTGAGACAA
1 TCTCCCTTGAGACAA
50350 TCTCCCTTGAGACA
1 TCTCCCTTGAGACA
50364 GTTTCCCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (15 bp):
TCTCCCTTGAGACAA
Found at i:50377 original size:51 final size:50
Alignment explanation
Indices: 50300--50399 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 50
50290 ACAAATATTG
*
50300 TCTCCCTTGAGACGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAA
1 TCTCCCTTGAGACGTTTCCCTCGAAACAAATTTTGTCTCCCTTGAGACAA
50350 TCTCCCTTGAGACAGTTTCCCTCGAAACAAATTTTGTCTCCCTTGAGACA
1 TCTCCCTTGAGAC-GTTTCCCTCGAAACAAATTTTGTCTCCCTTGAGACA
50400 GTTTCTCTCG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 13 0.27
51 35 0.73
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (50 bp):
TCTCCCTTGAGACGTTTCCCTCGAAACAAATTTTGTCTCCCTTGAGACAA
Found at i:50433 original size:21 final size:21
Alignment explanation
Indices: 50367--50452 Score: 85
Period size: 21 Copynumber: 4.4 Consensus size: 21
50357 TGAGACAGTT
*
50367 TCCCTCGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
* *
50388 TCCCTTGAGAC--A-GTT-TC
1 TCCCTTGAAACAAATTTTGTC
*
50405 T--CTCGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
*
50424 TCCCTTGAAACACATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
50445 TCCCTTGA
1 TCCCTTGA
50453 GACAGTTTCC
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
15 6 0.12
17 4 0.08
18 4 0.08
19 4 0.08
21 33 0.65
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:50455 original size:57 final size:56
Alignment explanation
Indices: 50316--50487 Score: 194
Period size: 57 Copynumber: 3.1 Consensus size: 56
50306 TTGAGACGTT
* * * * * *
50316 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATCTCCCTTGAGAC--A---GTT
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCATCGAAACAAATTTGTC
*
50367 TCCCTCGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTC-TCGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTC-CATCGAAACAAA-TTTGTC
* *
50424 TCCCTTGAAACACATTTTGTCTCCCTTGAGACAGTTTCCATTGAAACAAATTTGTC
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCATCGAAACAAATTTGTC
*
50480 TCTCTTGA
1 TCCCTTGA
50488 GACGATTTCC
Statistics
Matches: 103, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
51 40 0.39
52 1 0.01
53 1 0.01
56 14 0.14
57 47 0.46
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (56 bp):
TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCATCGAAACAAATTTGTC
Found at i:50539 original size:15 final size:15
Alignment explanation
Indices: 50516--50553 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
50506 AAATTTTGTC
*
50516 TCACTTGAGACATTT
1 TCACTTGAGACAATT
*
50531 TCCCTTGAGACAATT
1 TCACTTGAGACAATT
50546 TCACTTGA
1 TCACTTGA
50554 AACGAAAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (15 bp):
TCACTTGAGACAATT
Found at i:50688 original size:43 final size:43
Alignment explanation
Indices: 50626--50952 Score: 334
Period size: 43 Copynumber: 7.3 Consensus size: 43
50616 GCCTGATTTT
* * *
50626 TAGGGGTTTCTTGAAGAAAAGCTTGAGAAACCGTCGTGATATG
1 TAGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATG
* * *
50669 TAGGGGTTTCTTAATGAAAAGCTTGAGGGACCGTCGTGATATG
1 TAGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATG
* *
50712 TAGGGGTTCCTTGATGACAAGCTTGA-AGGACCATCGTGATATG
1 TAGGGGTTTCTTGATGAAAAGCTTGAGA-GACCATCGTGATATG
* *
50755 TAGGGG-TTCTTTGATGACAAGCTTGAGAAACCATCGTGATATG
1 TAGGGGTTTC-TTGATGAAAAGCTTGAGAGACCATCGTGATATG
* * *
50798 TAGGGGTTTCTTGATAAAAAGCTTGAGGGACCATCGTGATATA
1 TAGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATG
* * * *
50841 TAGGGGTTCCTTGATGACAAATTTGATGACAAGCTTAAGAAACCATCTTGATATG
1 TAGGGG----TT--T--C----TTGATGAAAAGCTTGAGAGACCATCGTGATATG
* *
50896 TAGGGGTTTCTTGATGAAAAGTTTGAGGGACCATCGTGATATG
1 TAGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATG
*
50939 TAGGGGTTCCTTGA
1 TAGGGGTTTCTTGA
50953 AGACAAATTT
Statistics
Matches: 238, Mismatches: 30, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
42 2 0.01
43 192 0.81
44 4 0.02
47 3 0.01
49 2 0.01
51 3 0.01
55 32 0.13
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (43 bp):
TAGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATG
Found at i:50856 original size:129 final size:129
Alignment explanation
Indices: 50626--50946 Score: 392
Period size: 129 Copynumber: 2.4 Consensus size: 129
50616 GCCTGATTTT
* *
50626 TAGGGGTTTCTTGAAGAAAAGCTTGAGAAACCGTCGTGATATGTAGGGGTTTCTTAATGAAAAGC
1 TAGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTAATAAAAAGC
* *
50691 TTGAGGGACCGTCGTGATATGTAGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATG
66 TTGAGGGACCATCGTGATATATAGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATG
* * *
50755 TAGGGG-TTCTTTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATAAAAAG
1 TAGGGGTTTC-TTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTAATAAAAAG
**
50819 CTTGAGGGACCATCGTGATATATAGGGGTTCCTTGATGACAAATTTGATGACAAGCTTAAGAAAC
65 CTTGAGGGACCATCGTGATATATAGGGGTTCCTTGATGAC-AAGCT--TG--AAG-----G--AC
*
50884 CATCTTGATATG
118 CATCGTGATATG
* * **
50896 TAGGGGTTTCTTGATGAAAAGTTTGAGGGACCATCGTGATATGTAGGGGTT
1 TAGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTT
50947 CCTTGAAGAC
Statistics
Matches: 164, Mismatches: 14, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
128 3 0.02
129 93 0.57
130 3 0.02
132 2 0.01
134 3 0.02
139 1 0.01
141 56 0.34
142 3 0.02
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.30
Consensus pattern (129 bp):
TAGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTAATAAAAAGC
TTGAGGGACCATCGTGATATATAGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATG
Found at i:50893 original size:98 final size:98
Alignment explanation
Indices: 50764--51000 Score: 361
Period size: 98 Copynumber: 2.4 Consensus size: 98
50754 GTAGGGGTTC
*
50764 TTTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATAAAAAGCTTGAGGGAC
1 TTTGATGACAAGCTTAAGAAACCATCGTGATATGTAGGGGTTTCTTGATAAAAAGCTTGAGGGAC
*
50829 CATCGTGATATATAGGGGTTCCTTGATGACAAA
66 CATCGTGATATATAGGGGTTCCTTGAAGACAAA
* * *
50862 TTTGATGACAAGCTTAAGAAACCATCTTGATATGTAGGGGTTTCTTGATGAAAAGTTTGAGGGAC
1 TTTGATGACAAGCTTAAGAAACCATCGTGATATGTAGGGGTTTCTTGATAAAAAGCTTGAGGGAC
*
50927 CATCGTGATATGTAGGGGTTCCTTGAAGACAAA
66 CATCGTGATATATAGGGGTTCCTTGAAGACAAA
* ** *
50960 TTTGATGA-ATA-CTTGAGGGACCAACGTGATATGTAGGGGTT
1 TTTGATGACA-AGCTTAAGAAACCATCGTGATATGTAGGGGTT
51001 CTTTGGTGAC
Statistics
Matches: 127, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
97 26 0.20
98 101 0.80
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (98 bp):
TTTGATGACAAGCTTAAGAAACCATCGTGATATGTAGGGGTTTCTTGATAAAAAGCTTGAGGGAC
CATCGTGATATATAGGGGTTCCTTGAAGACAAA
Found at i:50964 original size:43 final size:43
Alignment explanation
Indices: 50882--50964 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
50872 AGCTTAAGAA
* * *
50882 ACCATCTTGATATGTAGGGGTTTCTTGATGAAAAGTTTGAGGG
1 ACCATCGTGATATGTAGGGGTTCCTTGAAGAAAAGTTTGAGGG
50925 ACCATCGTGATATGTAGGGGTTCCTTGAAGACAAA-TTTGA
1 ACCATCGTGATATGTAGGGGTTCCTTGAAGA-AAAGTTTGA
50965 TGAATACTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 33 0.92
44 3 0.08
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (43 bp):
ACCATCGTGATATGTAGGGGTTCCTTGAAGAAAAGTTTGAGGG
Found at i:51459 original size:90 final size:90
Alignment explanation
Indices: 51040--51537 Score: 766
Period size: 90 Copynumber: 5.5 Consensus size: 90
51030 ATTTTCAAGA
*
51040 GTTTCTGGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
51105 GATCTAAGAAACTGAGCCTTCGGGG
66 GATCTAAGAAACTGAGCCTTCGGGG
51130 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATG-TTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
* *
51194 GATCTAAGAATCTGAGTCTTCGGGG
66 GATCTAAGAAACTGAGCCTTCGGGG
* *
51219 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTCAGTACAGGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
* * ** *
51284 GATTTAAGAAACTGAGCTTGATTTTCAAGA
66 GATCTAAGAAACTGAGC-----CTTCGGGG
51314 GTTTCTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATG
1 GTTTCTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATG
51379 AGATCTAAGAAACTGAGCCTTCGGGG
65 AGATCTAAGAAACTGAGCCTTCGGGG
* * *
51405 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGTCCTTCAGTGCAAGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
* *
51470 GATTTAAGAAACTAAGCCTTCGGGG
66 GATCTAAGAAACTGAGCCTTCGGGG
* *
51495 GTTTCTTGATTTTTTAAGTCCTTCAGG-CAACCATAAGACCTTC
1 GTTTCTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
51538 GGGCAAAATG
Statistics
Matches: 372, Mismatches: 28, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
89 85 0.23
90 175 0.47
91 29 0.08
95 13 0.03
96 70 0.19
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (90 bp):
GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
GATCTAAGAAACTGAGCCTTCGGGG
Found at i:51737 original size:3 final size:3
Alignment explanation
Indices: 51729--51782 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
51719 TATATTATAT
* * *
51729 TTA TTA TTA TATA CTA -TA GTA TGA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
51774 TTA TTA TTA
1 TTA TTA TTA
51783 CTACTAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.04
3 41 0.91
4 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:51738 original size:12 final size:13
Alignment explanation
Indices: 51721--51782 Score: 62
Period size: 12 Copynumber: 5.2 Consensus size: 13
51711 TTAAAATATA
51721 TATTATAT-TTAT
1 TATTATATATTAT
*
51733 TATTATATACTA-
1 TATTATATATTAT
* *
51745 TAGTAT-GATTAT
1 TATTATATATTAT
51757 TATTAT-TATTAT
1 TATTATATATTAT
51769 TATTAT-TATTAT
1 TATTATATATTAT
51781 TA
1 TA
51783 CTACTAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
11 3 0.07
12 37 0.88
13 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (13 bp):
TATTATATATTAT
Found at i:53077 original size:2 final size:2
Alignment explanation
Indices: 53070--53098 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53060 TGGATTAGTG
53070 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 T
53099 TTTTTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54870 original size:2 final size:2
Alignment explanation
Indices: 54784--54853 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
54774 AATTCAAACA
54784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54826 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
54854 CTTCATGATT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68741 original size:28 final size:28
Alignment explanation
Indices: 68687--68742 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
68677 TGATTTAAAG
* ***
68687 AATAAGGTTATAAATAGTTTTTTTATTA
1 AATAAGATTATAAATAGTTTAGATATTA
68715 AATAAGATTATAAATAGTTTAGATATTA
1 AATAAGATTATAAATAGTTTAGATATTA
68743 TAAATTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (28 bp):
AATAAGATTATAAATAGTTTAGATATTA
Found at i:71740 original size:2 final size:2
Alignment explanation
Indices: 71735--71767 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
71725 TTAATCATTA
71735 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
71768 ACGTTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:72427 original size:26 final size:26
Alignment explanation
Indices: 72370--72427 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
72360 TAGGTAATTT
* *
72370 ATTTTCTTTTTCTATAAAATTTTTTA
1 ATTTTATTTTTCTATAAAATTTTTAA
* *
72396 AGTTTATTTTT-TCTAAAATTTTATAA
1 ATTTTATTTTTCTATAAAATTTT-TAA
72422 ATTTTA
1 ATTTTA
72428 AATTAAGCGG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (26 bp):
ATTTTATTTTTCTATAAAATTTTTAA
Found at i:73866 original size:21 final size:21
Alignment explanation
Indices: 73841--73880 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
73831 CTGTGAATAC
*
73841 ATATATGTATTATATAATATT
1 ATATATATATTATATAATATT
73862 ATATATATATTATATAATA
1 ATATATATATTATATAATA
73881 CAATAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
ATATATATATTATATAATATT
Found at i:73871 original size:11 final size:11
Alignment explanation
Indices: 73841--73877 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
73831 CTGTGAATAC
*
73841 ATATATGTATT
1 ATATATATATT
73852 ATATA-ATATT
1 ATATATATATT
73862 ATATATATATT
1 ATATATATATT
73873 ATATA
1 ATATA
73878 ATACAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (11 bp):
ATATATATATT
Found at i:74522 original size:99 final size:99
Alignment explanation
Indices: 74387--74581 Score: 318
Period size: 99 Copynumber: 2.0 Consensus size: 99
74377 TTGTTTGTTA
* * * * *
74387 ACAGTTAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCATGAGTCTAATATCCTTCGTTG
1 ACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCATGAGTCCAATATCCTTCATTG
*
74452 TGAAGTTGAAATTGACTCTGAGATTGGGAAGTTG
66 TGAAGTTGAAATTGACTCTGAAATTGGGAAGTTG
*
74486 ACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCATTG
1 ACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCATGAGTCCAATATCCTTCATTG
*
74551 TGAAGTTGAAATTGGCTCTGAAATTGGGAAG
66 TGAAGTTGAAATTGACTCTGAAATTGGGAAG
74582 CCCCTTCGTT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 88 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (99 bp):
ACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCATGAGTCCAATATCCTTCATTG
TGAAGTTGAAATTGACTCTGAAATTGGGAAGTTG
Found at i:75683 original size:12 final size:12
Alignment explanation
Indices: 75666--75729 Score: 62
Period size: 12 Copynumber: 5.6 Consensus size: 12
75656 ACCCACCTTA
75666 TTTTTTCTTTTC
1 TTTTTTCTTTTC
*
75678 TTTTTTCTTTTG
1 TTTTTTCTTTTC
*
75690 TTCTTTC-TTT-
1 TTTTTTCTTTTC
*
75700 TTTTCTCTTTTC
1 TTTTTTCTTTTC
* *
75712 -CTTTCCTTTTC
1 TTTTTTCTTTTC
75723 TTTTTTC
1 TTTTTTC
75730 AATTAGGGCG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
10 5 0.12
11 14 0.35
12 21 0.52
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:75703 original size:20 final size:19
Alignment explanation
Indices: 75666--75729 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
75656 ACCCACCTTA
75666 TTTTTTCTTTTCTTTTTTC
1 TTTTTTCTTTTCTTTTTTC
75685 TTTTGTTC-TTTCTTTTTTTC
1 TTTT-TTCTTTTC-TTTTTTC
* * *
75705 TCTTTTCCTTTC-CTTTTC
1 TTTTTTCTTTTCTTTTTTC
75723 TTTTTTC
1 TTTTTTC
75730 AATTAGGGCG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 11 0.28
19 11 0.28
20 17 0.44
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTTTCTTTTCTTTTTTC
Found at i:87786 original size:16 final size:17
Alignment explanation
Indices: 87767--87799 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
87757 ATAATAATTT
87767 CTTAA-TATAAAAAAGG
1 CTTAAGTATAAAAAAGG
*
87783 CTTAAGTATACAAAAGG
1 CTTAAGTATAAAAAAGG
87800 TGCCCAGCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (17 bp):
CTTAAGTATAAAAAAGG
Found at i:89109 original size:21 final size:21
Alignment explanation
Indices: 89058--89110 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
89048 ATTATGACTA
89058 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
89079 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
89100 TCGCAATGCGA
1 TCGCAATGCGA
89111 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:89125 original size:20 final size:21
Alignment explanation
Indices: 89100--89151 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
89090 TTTTCCCAAT
*
89100 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
89120 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
89141 TCGCAATGCGA
1 TCGCAATGCGA
89152 TACTGACTGT
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:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:89227 original size:20 final size:20
Alignment explanation
Indices: 89140--89234 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
89130 AATTTGGAAA
*
89140 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
89160 GTCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
89181 ATCGCAACGCGATACTAACT
1 ATCGCAACGCGATACTGACT
* * *
89201 TTTGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
89221 ATCGCAACGAGATA
1 ATCGCAACGCGATA
89235 ATACAGAATC
Statistics
Matches: 57, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.04
20 39 0.68
21 14 0.25
22 2 0.04
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:91264 original size:20 final size:20
Alignment explanation
Indices: 91239--91327 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
91229 CAACGGGGAA
91239 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
91259 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
91279 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
91299 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGGAAATGACT
91319 ATCGCAACG
1 ATCGCAACG
91328 AGAGAATCGC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 60 0.95
21 3 0.05
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:91360 original size:33 final size:34
Alignment explanation
Indices: 91299--91394 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 34
91289 GGAAATGACT
* ** *
91299 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAGATGAAAATCGCAACGAGAAA
* * *
91333 ATCGCAATGTGAA-TTGAAAATCGCAACGTGAAA
1 ATCGCAATGCGAAGATGAAAATCGCAACGAGAAA
91366 ATCGCAATGCGAAGATGAAAATCGCAACG
1 ATCGCAATGCGAAGATGAAAATCGCAACG
91395 CGAATTTAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 27 0.51
34 26 0.49
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.17
Consensus pattern (34 bp):
ATCGCAATGCGAAGATGAAAATCGCAACGAGAAA
Found at i:91386 original size:20 final size:20
Alignment explanation
Indices: 91361--91398 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
91351 AATCGCAACG
*
91361 TGAAAATCGCAATGCGAAGA
1 TGAAAATCGCAACGCGAAGA
91381 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
91399 TTTAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAGA
Found at i:91421 original size:19 final size:19
Alignment explanation
Indices: 91394--91456 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
91384 AAATCGCAAC
* *
91394 GCGAATTTAGTTTTGCATT
1 GCGATTTTAGTTTCGCATT
*
91413 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCATT
*
91432 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCATT
91451 GCGATT
1 GCGATT
91457 CTCTCGTTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 39 0.98
20 1 0.03
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCATT
Found at i:91615 original size:14 final size:14
Alignment explanation
Indices: 91596--91632 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
91586 CACCAATTAA
91596 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
91610 ACAAATCATCTTTT
1 ACAAATCAACATTT
91624 ACAAATCAA
1 ACAAATCAA
91633 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:93079 original size:42 final size:42
Alignment explanation
Indices: 93033--93125 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
93023 CCTCTTCAAC
* *
93033 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
* * * *
93075 GATGATAGGGGCCTCTTGAATGATTGGAGGGTACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
93117 GATGACAGG
1 GATGACAGG
93126 TGAGTCGGGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.22, C:0.14, G:0.41, T:0.24
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:93084 original size:21 final size:21
Alignment explanation
Indices: 93059--93121 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
93049 TGAACGGTGG
93059 GAGGGGACTCTTGAGGGATGA
1 GAGGGGACTCTTGAGGGATGA
* * **
93080 TAGGGGCCTCTTGAATGATTG-
1 GAGGGGACTCTTGAGGGA-TGA
*
93101 GAGGGTACTCTTGAGGGATGA
1 GAGGGGACTCTTGAGGGATGA
93122 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.22, C:0.11, G:0.41, T:0.25
Consensus pattern (21 bp):
GAGGGGACTCTTGAGGGATGA
Found at i:93451 original size:20 final size:20
Alignment explanation
Indices: 93426--93469 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
93416 AATAGAATCT
*
93426 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGAAACAC
*
93446 GAAACTTAAAATCGAAACGC
1 GAAACTTAAAATCGAAACAC
93466 GAAA
1 GAAA
93470 ATGACTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.20, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGAAACAC
Found at i:93479 original size:20 final size:20
Alignment explanation
Indices: 93456--93524 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
93446 GAAACTTAAA
*
93456 ATCGAAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
93476 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
**
93496 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
93516 ATCGCAACG
1 ATCGCAACG
93525 AGAGAATCGC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:93678 original size:33 final size:34
Alignment explanation
Indices: 93605--93680 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 34
93595 ACTAAATTCG
* * * * *
93605 CATTGCGATTTTCATTTTCGCGTTGCGCTTTTGT
1 CATTGTGATTTTCATTTTCGCATTGCGATTCTCT
*
93639 CGTTGTGATTTTCA-TTTCGCATTGCGATTCTCT
1 CATTGTGATTTTCATTTTCGCATTGCGATTCTCT
93672 CATTGTGAT
1 CATTGTGAT
93681 AGTCAAATTC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
33 23 0.66
34 12 0.34
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.49
Consensus pattern (34 bp):
CATTGTGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:93713 original size:20 final size:20
Alignment explanation
Indices: 93690--93740 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
93680 TAGTCAAATT
93690 CGCGTTGCGATAGCCATTTC
1 CGCGTTGCGATAGCCATTTC
* *
93710 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGATAGCCATTTC
93730 CGCGTTGCGAT
1 CGCGTTGCGAT
93741 TTTAAGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.14, C:0.25, G:0.27, T:0.33
Consensus pattern (20 bp):
CGCGTTGCGATAGCCATTTC
Found at i:95663 original size:20 final size:20
Alignment explanation
Indices: 95596--95663 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
95586 GAAACTTAAA
*
95596 ATCGCAACG-AAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
95615 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
95635 ATCGCAACGCTG-AAATGACT
1 ATCGCAACGC-GAAAATGACT
95655 ATCGCAACG
1 ATCGCAACG
95664 AGATAATTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 8 0.18
20 35 0.80
21 1 0.02
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:95695 original size:18 final size:19
Alignment explanation
Indices: 95672--95721 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
95662 CGAGATAATT
95672 GCAATGCGAATTG-AAATC
1 GCAATGCGAATTGAAAATC
*
95690 GCAATGCGGAAATGAAAATC
1 GCAATGC-GAATTGAAAATC
*
95710 GCAACGCGAATT
1 GCAATGCGAATT
95722 TGGTTTCGCG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 7 0.26
19 9 0.33
20 11 0.41
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (19 bp):
GCAATGCGAATTGAAAATC
Found at i:95801 original size:20 final size:20
Alignment explanation
Indices: 95749--95827 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 20
95739 TCTCTCGTTA
* * *
95749 CGATTGTCATTTCCGCGTTG
1 CGATAGTCATTTTCGTGTTG
95769 CGATAGTCATTTTCGTGTTG
1 CGATAGTCATTTTCGTGTTG
95789 CGATAGTCATTTT-GTCGTTG
1 CGATAGTCATTTTCGT-GTTG
**
95809 CGATTCTCA-TTTCGTGTTG
1 CGATAGTCATTTTCGTGTTG
95828 TGATTCTCGG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.17
20 43 0.83
ACGTcount: A:0.13, C:0.19, G:0.24, T:0.44
Consensus pattern (20 bp):
CGATAGTCATTTTCGTGTTG
Found at i:96198 original size:22 final size:22
Alignment explanation
Indices: 96171--96222 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
96161 AGATGGAGAT
96171 AGACGGATTTCACCGGAGATGG
1 AGACGGATTTCACCGGAGATGG
**
96193 AGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCACCGGAGATGG
*
96215 GGACGGAT
1 AGACGGAT
96223 GTCGCCGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.19
Consensus pattern (22 bp):
AGACGGATTTCACCGGAGATGG
Found at i:96501 original size:20 final size:20
Alignment explanation
Indices: 96415--96509 Score: 93
Period size: 20 Copynumber: 4.7 Consensus size: 20
96405 GATTCTGTAT
*
96415 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * * *
96435 AAACGTGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
96455 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
96476 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
96496 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
96510 TTTCCAAATT
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
19 3 0.05
20 39 0.67
21 14 0.24
22 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:96528 original size:41 final size:41
Alignment explanation
Indices: 96442--96530 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
96432 CAGAAACGTG
* * ** * *
96442 TTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 TTGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCGCA
96483 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT-TCGCA
1 TTGCGATAGTCAGTATCGCATTGCGATTTT-CAAATATCGCA
96524 TTGCGAT
1 TTGCGAT
96531 TTACTTATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 39 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCGCA
Found at i:96542 original size:20 final size:21
Alignment explanation
Indices: 96498--96549 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
96488 ATAGTCAGTA
*
96498 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
96519 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
96539 TCGCATTGCGA
1 TCGCATTGCGA
96550 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:96591 original size:21 final size:22
Alignment explanation
Indices: 96539--96591 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
96529 ATTTACTTAT
96539 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
96560 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
96581 TCGCATTGCGA
1 TCGCATTGCGA
96592 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:103477 original size:13 final size:14
Alignment explanation
Indices: 103453--103487 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
103443 ATTTAAAATT
*
103453 AATATTTGTATATAA
1 AATATTTATATA-AA
103468 AATATTTATATAAA
1 AATATTTATATAAA
103482 AATATT
1 AATATT
103488 ATTAATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
AATATTTATATAAA
Found at i:103841 original size:31 final size:32
Alignment explanation
Indices: 103777--103846 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 32
103767 AAATGTGTTC
103777 AACTAATGATGTGACATATACACATTACTTAA
1 AACTAATGATGTGACATATACACATTACTTAA
103809 AA-TAATGACT-TGACATATA-ACATATAAC-TAA
1 AACTAATGA-TGTGACATATACACAT-T-ACTTAA
103840 AACTAAT
1 AACTAAT
103847 AACGTAGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
30 4 0.12
31 21 0.62
32 9 0.26
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (32 bp):
AACTAATGATGTGACATATACACATTACTTAA
Found at i:105328 original size:32 final size:35
Alignment explanation
Indices: 105279--105359 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
105269 TTTAAATAGT
*
105279 TATTATTTTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTTTATATTAAATAATATTTATATAAA
*
105312 TATTATTTTTTT-TATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATATT-AAATAATATTTATATAAA
*
105347 TATTATTTATTTA
1 TATTATTTTTTTA
105360 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
32 4 0.10
33 12 0.29
34 3 0.07
35 22 0.54
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (35 bp):
TATTATTTTTTTATATTAAATAATATTTATATAAA
Done.