Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002993.1 Hibiscus syriacus cultivar Beakdansim tig00006189_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: 104730
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:865 original size:15 final size:15
Alignment explanation
Indices: 845--880 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
835 ATTCTAGGTG
845 AAAATAT-ATTATTAT
1 AAAATATAATTATT-T
860 AAAATATAATTATTT
1 AAAATATAATTATTT
875 AAAATA
1 AAAATA
881 ATATAGCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAATATAATTATTT
Found at i:964 original size:5 final size:5
Alignment explanation
Indices: 954--1062 Score: 112
Period size: 5 Copynumber: 21.8 Consensus size: 5
944 CGAGATCATA
954 ATTAT ATTAT A-TAT ATTAT ATTAT ATATAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT ATTAT ATTAT ATTAT ATTAT
* * * * * * * * *
1004 ATTAT ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
*
1054 ATTAC ATTA
1 ATTAT ATTA
1063 CATTTTTTGT
Statistics
Matches: 101, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
4 4 0.04
5 92 0.91
6 5 0.05
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (5 bp):
ATTAT
Found at i:968 original size:2 final size:2
Alignment explanation
Indices: 956--1010 Score: 54
Period size: 2 Copynumber: 31.5 Consensus size: 2
946 AGATCATAAT
956 TA TA T- TA TA TA TA T- TA TA T- TA TA TA TA TA T- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
993 TA T- TA TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1011 TACATTACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
1 8 0.18
2 37 0.82
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:1063 original size:5 final size:5
Alignment explanation
Indices: 984--1066 Score: 121
Period size: 5 Copynumber: 16.6 Consensus size: 5
974 TTATATATAT
* * * * *
984 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAC ATTAC ATTAC ATTAC ATTAC
1 ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC
1034 ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATT
1 ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATT
1067 TTTTGTTGCT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 77 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (5 bp):
ATTAC
Found at i:3666 original size:18 final size:18
Alignment explanation
Indices: 3631--3701 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 18
3621 ATCCAGCTTG
3631 AAATAATATATTTTTTAA
1 AAATAATATATTTTTTAA
*
3649 AAATATTAT-TTTTATTAA
1 AAATAATATATTTT-TTAA
*
3667 ATAAAAATATGAATTTAATTTAAA
1 A-AATAATAT--ATTT--TTT-AA
3691 AAATAATATAT
1 AAATAATATAT
3702 AAAAGAGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
17 4 0.10
18 13 0.32
19 6 0.15
21 2 0.05
22 3 0.07
23 9 0.22
24 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (18 bp):
AAATAATATATTTTTTAA
Found at i:3689 original size:23 final size:22
Alignment explanation
Indices: 3646--3699 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
3636 ATATATTTTT
* * *
3646 TAAAAATATTATTTTTATTAAA
1 TAAAAATATGAATTTAATTAAA
3668 TAAAAATATGAATTTAATTTAAA
1 TAAAAATATGAATTTAA-TTAAA
3691 -AAATAATAT
1 TAAA-AATAT
3700 ATAAAAGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAAATATGAATTTAATTAAA
Found at i:4674 original size:2 final size:2
Alignment explanation
Indices: 4667--4700 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4657 TATGTGATCA
4667 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
4701 GATTTTTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5580 original size:38 final size:37
Alignment explanation
Indices: 5529--5609 Score: 117
Period size: 38 Copynumber: 2.2 Consensus size: 37
5519 GCATTATTTC
*
5529 TTAAAATTTAAATATAATTATTTTATTTTGATTTAAT
1 TTAAAACTTAAATATAATTATTTTATTTTGATTTAAT
* * *
5566 ATTAAAACTTAAATATAATTATTTTGTTTTGTTTTGAT
1 -TTAAAACTTAAATATAATTATTTTATTTTGATTTAAT
5604 TTAAAA
1 TTAAAA
5610 AATAGTATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 6 0.15
38 33 0.85
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (37 bp):
TTAAAACTTAAATATAATTATTTTATTTTGATTTAAT
Found at i:7306 original size:28 final size:28
Alignment explanation
Indices: 7275--7331 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
7265 TTTTTTGAAT
*
7275 TATTGATAATTTA-ATAATATATTTTAAA
1 TATTGATAACTTATATAAT-TATTTTAAA
* *
7303 TATTGGTAACTTATTTAATTATTTTAAA
1 TATTGATAACTTATATAATTATTTTAAA
7331 T
1 T
7332 CAAGAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (28 bp):
TATTGATAACTTATATAATTATTTTAAA
Found at i:11793 original size:14 final size:14
Alignment explanation
Indices: 11774--11820 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
11764 ACATGGCCAT
*
11774 TTTCACTTATATCA-
1 TTTCACATATA-CAC
11788 TTTCACATATACAC
1 TTTCACATATACAC
11802 TTTCACATATACAC
1 TTTCACATATACAC
11816 TTTCA
1 TTTCA
11821 TATCACATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 2 0.06
14 29 0.94
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTCACATATACAC
Found at i:12433 original size:20 final size:20
Alignment explanation
Indices: 12405--12481 Score: 59
Period size: 20 Copynumber: 3.7 Consensus size: 20
12395 TTTCCCTCGA
12405 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
* *
12425 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATACATTC--T-AC
* *
12448 ATGTGCATCGATGCATTAC-CC
1 A-GTGCATCGATACATT-CTAC
12469 A-TGCATCGATACA
1 AGTGCATCGATACA
12482 CAAATCACCT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
19 11 0.23
20 15 0.32
21 2 0.04
22 1 0.02
23 3 0.06
24 14 0.30
25 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:12462 original size:24 final size:20
Alignment explanation
Indices: 12405--12464 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 20
12395 TTTCCCTCGA
*
12405 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
12425 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
12448 ATGTGCATCGATGCATT
1 A-GTGCATCGATGCATT
12465 ACCCATGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 15 0.45
22 1 0.03
23 3 0.09
24 14 0.42
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:20008 original size:183 final size:183
Alignment explanation
Indices: 19695--20029 Score: 429
Period size: 183 Copynumber: 1.8 Consensus size: 183
19685 TGAACCAAAC
* * * *
19695 GATTCACTTGATCCATTGCCATATCCTTCATAGGTGACATTACTATGAACTCCCTCTCTCATTCT
1 GATTCACCTGATCCATTGCCAAATCCTTCATACGTGACATTACGATGAACTCCCTCTCTCATTCT
* * * * *
19760 CCCTGATCTCGAACATGGAGGAATCGGGGAACCTAAAACGTCACTCCCATCGAATTTCGCCAAAT
66 CCCAGATCTCGAACATGGAGGAATCGAGGAACCTAAAACATCACTCCCATCAAACTTCGCCAAAT
*
19825 TTTCAGAACCTAAATCACCAAATGCCTCACCTCTACTCTTATTAGAAGCAGAA
131 TTTCAGAACCCAAATCACCAAATGCCTCACCTCTACTCTTATTAGAAGCAGAA
* * * * *
19878 GATTCACCTGATCCATTGTCAAATCCTTCATACGTTACATTACGATGAACTCTCTCTTTCCTTCT
1 GATTCACCTGATCCATTGCCAAATCCTTCATACGTGACATTACGATGAACTCCCTCTCTCATTCT
* * * * * * * *
19943 TCCAGATCTCGAGCGCT-GAGGGATTGAGGAACCTAAAACATCACTCTCATTAAACTTCTCCAAA
66 CCCAGATCTCGAAC-ATGGAGGAATCGAGGAACCTAAAACATCACTCCCATCAAACTTCGCCAAA
* *
20007 TTTTCCGAACCCAAATTACCAAA
130 TTTTCAGAACCCAAATCACCAAA
20030 ACTCTTATTA
Statistics
Matches: 126, Mismatches: 25, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
183 125 0.99
184 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.29
Consensus pattern (183 bp):
GATTCACCTGATCCATTGCCAAATCCTTCATACGTGACATTACGATGAACTCCCTCTCTCATTCT
CCCAGATCTCGAACATGGAGGAATCGAGGAACCTAAAACATCACTCCCATCAAACTTCGCCAAAT
TTTCAGAACCCAAATCACCAAATGCCTCACCTCTACTCTTATTAGAAGCAGAA
Found at i:20170 original size:198 final size:200
Alignment explanation
Indices: 19868--20341 Score: 530
Period size: 198 Copynumber: 2.3 Consensus size: 200
19858 TACTCTTATT
* * * * *
19868 AGAAGCAGAAGATTCACCTGATCCATTGTCAAATCCTTCATACGTTACATTACGATGAACTCTCT
1 AGAACCAGAAGATTCACTTGATCCATTGT-AAATCCTTCATATGTGACATTACTATGAACTCTCT
* * * * **
19933 CTTTCCTTCTTCCAGATCTCGAGCGCTGAGGGATTGAGGAACCTAAAACATCACTCTCATTAAAC
65 CTCTCATTCTTCCAGATCTCAAACGCTGAGAAATTGAGGAACCTAAAACATCACTCTCATTAAA-
* * * *
19998 T-TCTCCAAATTTTCCGAACCCAAATTAC-CAA-A-ACTCTTATTAGAACTATCCGACGAATCCT
129 TATCTCCAAATTTTCAGAACCCAAATCACAAAACACACTCTTATTAGAACTATCCGACGAATCAT
20059 TCATTTG
194 TCATTTG
* * *
20066 TGAACCTGAAGATTCACTTGATCGATT-TATATATCCTTCATATGTGACATTACTATGAACTCTC
1 AGAACCAGAAGATTCACTTGATCCATTGTA-A-ATCCTTCATATGTGACATTACTATGAACTCTC
*
20130 AT-TCTCATTCTTCCAGATCTCAAACGCTGA-AAATTTGAGGAACCTAAAACATCAGTCTCATTA
64 -TCTCTCATTCTTCCAGATCTCAAACGCTGAGAAA-TTGAGGAACCTAAAACATCACTCTCATTA
*
20193 GATATCTCCAAATTTTCAGAACCCAAATCACAAAATCCCTTACCTCTACTCTTATTAGAACTATC
127 AATATCTCCAAATTTTCAGAACCCAAATCACAAAA---C--A---C-ACTCTTATTAGAACTATC
20258 CGACGAATCATTCATTTG
183 CGACGAATCATTCATTTG
* * * * *
20276 AGAACCAGAAGATTCACTCGAGCCATTGTCAGATCCTTGATATGTGACATTACTACGAACTCTCT
1 AGAACCAGAAGATTCACTTGATCCATTGT-AAATCCTTCATATGTGACATTACTATGAACTCTCT
20341 C
65 C
20342 GTCCCTCCTT
Statistics
Matches: 228, Mismatches: 28, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
196 1 0.00
197 4 0.02
198 129 0.57
199 3 0.01
205 1 0.00
209 1 0.00
210 87 0.38
211 1 0.00
212 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.31
Consensus pattern (200 bp):
AGAACCAGAAGATTCACTTGATCCATTGTAAATCCTTCATATGTGACATTACTATGAACTCTCTC
TCTCATTCTTCCAGATCTCAAACGCTGAGAAATTGAGGAACCTAAAACATCACTCTCATTAAATA
TCTCCAAATTTTCAGAACCCAAATCACAAAACACACTCTTATTAGAACTATCCGACGAATCATTC
ATTTG
Found at i:20392 original size:210 final size:211
Alignment explanation
Indices: 20030--20499 Score: 499
Period size: 210 Copynumber: 2.2 Consensus size: 211
20020 AATTACCAAA
* * * *
20030 ACTCTTATTAGAACTATCCGACGAATCCTTCATTTGTGAACCTGAAGATTCACTTGATCGATTTA
1 ACTCTTATTAGAACTATCCGACGAATCCTTCATTTGTGAACCAGAAGATTCACTCGAGCCATTTA
* * * * *
20095 TATATCCTTCATATGTGACATTACTATGAACTCTCATTCTCATTCTTCCAGATCTCAAACGCTGA
66 CAGATCCTTCATATGTGACATTACTACGAACTCTCATTCTCATCCTTCCAGATCTCAAACGCCGA
* * * * *
20160 AAATTTGAGGAACCTAAAACATCAGTCTCA-TTAGA-TAT-CTCCAAATTTTCAGAACCCAAATC
131 AAATTCGAGGAACCTAAAACATCACTCTCATTTA-ACT-TCCTCCAAATTTCCAGAACCAAAACC
*
20222 ACAAAATCCCTTACCTCT
194 ACAAAATCCCCTACCTCT
* *
20240 ACTCTTATTAGAACTATCCGACGAATCATTCATTTGAGAACCAGAAGATTCACTCGAGCCATTGT
1 ACTCTTATTAGAACTATCCGACGAATCCTTCATTTGTGAACCAGAAGATTCACTCGAGCCATT-T
* * * * *
20305 -CAGATCCTTGATATGTGACATTACTACGAACTCTC--TCGTCCCTCCTTCTAGATCTCGAAGGC
65 ACAGATCCTTCATATGTGACATTACTACGAACTCTCATTC-T-CATCCTTCCAGATCTCAAACGC
* ** *
20367 CGAGTAA-TCG-GGAAATGTAAAACATCACTCTCATTTAACTTCCCCTCCAAATTTCCAGAAGCA
128 CGA-AAATTCGAGG-AACCTAAAACATCACTCTCATTTAACTT--CCTCCAAATTTCCAGAACCA
* *
20430 AAACCACCAAATCCCCTATCTCT
189 AAACCACAAAATCCCCTACCTCT
* ** *
20453 ACTCTCATTAGAACCT-TGTGACGAATCCTTCATATGTGAACCAGAAG
1 ACTCTTATTAGAA-CTATCCGACGAATCCTTCATTTGTGAACCAGAAG
20500 GTTCGTTTGA
Statistics
Matches: 215, Mismatches: 34, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
208 2 0.01
209 3 0.01
210 128 0.60
211 7 0.03
213 73 0.34
214 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.30
Consensus pattern (211 bp):
ACTCTTATTAGAACTATCCGACGAATCCTTCATTTGTGAACCAGAAGATTCACTCGAGCCATTTA
CAGATCCTTCATATGTGACATTACTACGAACTCTCATTCTCATCCTTCCAGATCTCAAACGCCGA
AAATTCGAGGAACCTAAAACATCACTCTCATTTAACTTCCTCCAAATTTCCAGAACCAAAACCAC
AAAATCCCCTACCTCT
Found at i:22955 original size:17 final size:18
Alignment explanation
Indices: 22933--22967 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22923 ATTTTGTTTA
22933 TATT-AAAATATAATTTC
1 TATTAAAAATATAATTTC
22950 TATTAAAAAATATAATTT
1 TATT-AAAAATATAATTT
22968 TATATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
19 12 0.75
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTAAAAATATAATTTC
Found at i:29021 original size:16 final size:18
Alignment explanation
Indices: 28989--29024 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
28979 AATGTAATAT
28989 TTTATATTTTATATTTTA
1 TTTATATTTTATATTTTA
29007 TTTAT-TTTTAT-TTTTA
1 TTTATATTTTATATTTTA
29023 TT
1 TT
29025 AATAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTATATTTTATATTTTA
Found at i:35270 original size:20 final size:20
Alignment explanation
Indices: 35231--35270 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
35221 AACAGAATGT
*
35231 AAGATTATCAGTAGGAATAA
1 AAGATTATCAGTAGAAATAA
35251 AAGATTATCAG-AGAATATAA
1 AAGATTATCAGTAGAA-ATAA
35271 TTACTGGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.53, C:0.05, G:0.17, T:0.25
Consensus pattern (20 bp):
AAGATTATCAGTAGAAATAA
Found at i:35486 original size:36 final size:36
Alignment explanation
Indices: 35415--35487 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
35405 GTTAGAAAAT
* *
35415 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
35451 ATTTATATAATTTT-TTTATAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTAAAAATCATAAA
35487 A
1 A
35488 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
Found at i:36844 original size:19 final size:18
Alignment explanation
Indices: 36817--36855 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
36807 AATTTAATCT
*
36817 TAATTAATATGAACCTTAA
1 TAATAAATATGAACC-TAA
*
36836 TAATAAATATTAACCTAA
1 TAATAAATATGAACCTAA
36854 TA
1 TA
36856 TAATTTAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (18 bp):
TAATAAATATGAACCTAA
Found at i:41839 original size:122 final size:122
Alignment explanation
Indices: 41562--42028 Score: 715
Period size: 123 Copynumber: 3.8 Consensus size: 122
41552 ATTAACCCAT
* * *
41562 CAATCA-AGAAGTGACACGTGTCAATACATGGTCATGACACGTGTCATTCATGCCACATGTCACC
1 CAATCATAG-AGTGACACGTGTCAATACATGGTCATGACACATGTCATTCGTGCCACGTGTCACC
*
41626 ACGTAATTGGAGAATTTTTTATTAATTTGAA-TTATTTAACTAAATTTATTTTCTACC
65 ACGTAATTGGAGAATTTTTTATTAATTTTAATTTATTTAACTAAATTTATTTTCTACC
* *
41683 CAATCATAGAGTGACACGTGTCAATACATGGTCATGGCACATTTCATTCGTGCCACGTGTCACCA
1 CAATCATAGAGTGACACGTGTCAATACATGGTCATGACACATGTCATTCGTGCCACGTGTCACCA
* *
41748 CGTAATTGGAGAATTTTTTATTAATTTAAATTTATTTAACTAAATTTATTTTCTATC
66 CGTAATTGGAGAATTTTTTATTAATTTTAATTTATTTAACTAAATTTATTTTCTACC
* * * * * *
41805 TAATCATAGAGCGACACATGTCAATACATGGTCATGACACTTATCATTCGTGTCACGTGTCACCA
1 CAATCATAGAGTGACACGTGTCAATACATGGTCATGACACATGTCATTCGTGCCACGTGTCACCA
* * *
41870 CGTAATTGGAGGATTTTTTTATTAATTTTTATTTATTTAACTAAATTTGTTTTCTACC
66 CGTAATTGGA-GAATTTTTTATTAATTTTAATTTATTTAACTAAATTTATTTTCTACC
* *
41928 CAATCATAGAGTGACACGTGTTAATACATGGTCATGACCCATGTCATTCGTGCCACGTGTCACCA
1 CAATCATAGAGTGACACGTGTCAATACATGGTCATGACACATGTCATTCGTGCCACGTGTCACCA
*
41993 CGTAATTGGAGGA-TTTTTATTAATTTTAATTTATTT
66 CGTAATTGGAGAATTTTTTATTAATTTTAATTTATTT
42029 TCTACCCAAT
Statistics
Matches: 313, Mismatches: 30, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
121 108 0.35
122 96 0.31
123 109 0.35
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (122 bp):
CAATCATAGAGTGACACGTGTCAATACATGGTCATGACACATGTCATTCGTGCCACGTGTCACCA
CGTAATTGGAGAATTTTTTATTAATTTTAATTTATTTAACTAAATTTATTTTCTACC
Found at i:41954 original size:123 final size:122
Alignment explanation
Indices: 41562--42028 Score: 708
Period size: 121 Copynumber: 3.8 Consensus size: 122
41552 ATTAACCCAT
* * *
41562 CAATCA-AGAAGTGACACGTGTCAATACATGGTCATGACACGTGTCATTCATGCCACATGTCACC
1 CAATCATAG-AGTGACACGTGTCAATACATGGTCATGACACTTGTCATTCGTGCCACGTGTCACC
*
41626 ACGTAATTGGAGAATTTTTTATTAATTTGAA-TTATTTAACTAAATTTATTTTCTACC
65 ACGTAATTGGAGAATTTTTTATTAATTTTAATTTATTTAACTAAATTTATTTTCTACC
*
41683 CAATCATAGAGTGACACGTGTCAATACATGGTCATGGCACATT-TCATTCGTGCCACGTGTCACC
1 CAATCATAGAGTGACACGTGTCAATACATGGTCATGACAC-TTGTCATTCGTGCCACGTGTCACC
* *
41747 ACGTAATTGGAGAATTTTTTATTAATTTAAATTTATTTAACTAAATTTATTTTCTATC
65 ACGTAATTGGAGAATTTTTTATTAATTTTAATTTATTTAACTAAATTTATTTTCTACC
* * * * *
41805 TAATCATAGAGCGACACATGTCAATACATGGTCATGACACTTATCATTCGTGTCACGTGTCACCA
1 CAATCATAGAGTGACACGTGTCAATACATGGTCATGACACTTGTCATTCGTGCCACGTGTCACCA
* * *
41870 CGTAATTGGAGGATTTTTTTATTAATTTTTATTTATTTAACTAAATTTGTTTTCTACC
66 CGTAATTGGA-GAATTTTTTATTAATTTTAATTTATTTAACTAAATTTATTTTCTACC
* * *
41928 CAATCATAGAGTGACACGTGTTAATACATGGTCATGACCCATGTCATTCGTGCCACGTGTCACCA
1 CAATCATAGAGTGACACGTGTCAATACATGGTCATGACACTTGTCATTCGTGCCACGTGTCACCA
*
41993 CGTAATTGGAGGA-TTTTTATTAATTTTAATTTATTT
66 CGTAATTGGAGAATTTTTTATTAATTTTAATTTATTT
42029 TCTACCCAAT
Statistics
Matches: 314, Mismatches: 27, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
121 109 0.35
122 96 0.31
123 109 0.35
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (122 bp):
CAATCATAGAGTGACACGTGTCAATACATGGTCATGACACTTGTCATTCGTGCCACGTGTCACCA
CGTAATTGGAGAATTTTTTATTAATTTTAATTTATTTAACTAAATTTATTTTCTACC
Found at i:49321 original size:25 final size:23
Alignment explanation
Indices: 49293--49374 Score: 67
Period size: 25 Copynumber: 3.4 Consensus size: 23
49283 GTATAAATTC
* *
49293 TTAAATTCATAATATTTTATATATA
1 TTAAATTAAAAATATTTT-T-TATA
*
49318 TTAACTTAAAAATATTTTTTATA
1 TTAAATTAAAAATATTTTTTATA
*
49341 TTAACTTATTAAATATATTTTTT-TA
1 TTAA---ATTAAAAATATTTTTTATA
*
49366 TTAACTTAA
1 TTAAATTAA
49375 TTTAAAAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
22 4 0.08
23 8 0.17
24 1 0.02
25 21 0.44
26 14 0.29
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAAATTAAAAATATTTTTTATA
Found at i:49344 original size:23 final size:23
Alignment explanation
Indices: 49303--49374 Score: 92
Period size: 25 Copynumber: 3.0 Consensus size: 23
49293 TTAAATTCAT
49303 AATATTTTATATATATTAACTTAAA
1 AATATTTT-T-TATATTAACTTAAA
49328 AATATTTTTTATATTAACTTATTAA
1 AATATTTTTTATATTAACTTA--AA
49353 ATATATTTTTT-TATTAACTTAA
1 A-ATATTTTTTATATTAACTTAA
49375 TTTAAAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
23 13 0.30
24 1 0.02
25 21 0.48
26 9 0.20
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATTTTTTATATTAACTTAAA
Found at i:49388 original size:25 final size:25
Alignment explanation
Indices: 49303--49390 Score: 83
Period size: 25 Copynumber: 3.4 Consensus size: 25
49293 TTAAATTCAT
49303 AATATTTTATA-TATA-TTAACTTAAA
1 AATATTTTATATTA-ACTTAA-TTAAA
49328 AATATTTTTTATATTAACTT-ATTAAA
1 AATA--TTTTATATTAACTTAATTAAA
* *
49354 TATATTTTTTTATTAACTTAATTTAAA
1 AATA-TTTTATATTAACTTAA-TTAAA
49381 AATATTTTAT
1 AATATTTTAT
49391 TTTTATTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
25 18 0.34
26 14 0.26
27 17 0.32
28 4 0.08
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (25 bp):
AATATTTTATATTAACTTAATTAAA
Found at i:49590 original size:32 final size:31
Alignment explanation
Indices: 49544--49609 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
49534 TAATCATGTA
*
49544 TTAATTATATAAAAACAAAAATGA-TCATATC
1 TTAATTAAATAAAAACAAAAATGACT-ATATC
* *
49575 TTAATTAAATAAAAAACGAAAGTGACTATATC
1 TTAATTAAAT-AAAAACAAAAATGACTATATC
49607 TTA
1 TTA
49610 TATTTTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 9 0.30
32 20 0.67
33 1 0.03
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (31 bp):
TTAATTAAATAAAAACAAAAATGACTATATC
Found at i:51264 original size:72 final size:73
Alignment explanation
Indices: 51142--51281 Score: 219
Period size: 72 Copynumber: 1.9 Consensus size: 73
51132 AATCAAATAT
*
51142 TTTTTGTTAAACTAAATTATATAACATTTTAAAATACTTTCTCCGTCCAATAATTTGT-TATTAT
1 TTTTTGTTAAACTAAATTATATAACATTTTAAAATACTTTCTCCGCCCAATAATTTGTATATTAT
51206 ATTAAACA
66 ATTAAACA
* * * * *
51214 TTTTTGTTAAATTGAATTATATAATATTTTAAAATGCTTTCTCCGCCCAATAATTTGTATCTTAT
1 TTTTTGTTAAACTAAATTATATAACATTTTAAAATACTTTCTCCGCCCAATAATTTGTATATTAT
51279 ATT
66 ATT
51282 GATTATATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 53 0.87
73 8 0.13
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (73 bp):
TTTTTGTTAAACTAAATTATATAACATTTTAAAATACTTTCTCCGCCCAATAATTTGTATATTAT
ATTAAACA
Found at i:60825 original size:186 final size:186
Alignment explanation
Indices: 60498--60889 Score: 680
Period size: 186 Copynumber: 2.1 Consensus size: 186
60488 ATTTCGAATT
* * *
60498 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAACAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
*
60562 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
66 ATTATAAAATAAAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
* *
60627 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGAGCTTAGCCCATATGTTA
131 TTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGAGCTAAGCCCATATGTTA
60683 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
*
60748 ATTATAAAATAAAAAATTTATAT-AATTTTTGTAATTAATTAATATTGATTTAGGTTTAAAAGTT
66 ATTATAAAATAAAAAATTTATATAAATTTTT-TAATTAATTAATATTGATTTAAGTTTAAAAGTT
*
60812 ATTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTAAGCCCATATGTTA
130 ATTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGAGCTAAGCCCATATGTTA
*
60869 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
60890 AATTTCGGTT
Statistics
Matches: 196, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
185 14 0.07
186 182 0.93
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
TTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGAGCTAAGCCCATATGTTA
Found at i:61188 original size:20 final size:20
Alignment explanation
Indices: 61162--61206 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
61152 ATACACCTTA
61162 ATAATAAATATTAACCTAAT
1 ATAATAAATATTAACCTAAT
* *
61182 GTAATAAATATTAACTTAAT
1 ATAATAAATATTAACCTAAT
61202 ATAAT
1 ATAAT
61207 TTAATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (20 bp):
ATAATAAATATTAACCTAAT
Found at i:62219 original size:22 final size:21
Alignment explanation
Indices: 62178--62219 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
62168 AACGCGTTAA
*
62178 AAATTAAAATAATTCAAAAAC
1 AAATTAAAATAATGCAAAAAC
62199 AAATATAAAATAACTGCAAAA
1 AAAT-TAAAATAA-TGCAAAA
62220 TTTCTCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 8 0.44
23 6 0.33
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.21
Consensus pattern (21 bp):
AAATTAAAATAATGCAAAAAC
Found at i:67755 original size:2 final size:2
Alignment explanation
Indices: 67702--67744 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
67692 TAAAAAAACA
67702 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
67744 A
1 A
67745 AAGCAATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:68027 original size:6 final size:6
Alignment explanation
Indices: 68016--68089 Score: 76
Period size: 6 Copynumber: 12.3 Consensus size: 6
68006 CAAGAATTCA
* * * *
68016 ATGTAT ATGTAT ATGTAC ATGTAC ATGTAC ATGTAC ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
* * * *
68064 ATATAT ATATAT ATATAT ATATAT AT
1 ATGTAT ATGTAT ATGTAT ATGTAT AT
68090 ATAGAGAGAG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (6 bp):
ATGTAT
Found at i:68068 original size:2 final size:2
Alignment explanation
Indices: 68055--68092 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
68045 CATGTACATG
*
68055 TA TA TG 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
68093 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:68097 original size:2 final size:2
Alignment explanation
Indices: 68092--68116 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
68082 ATATATATAT
68092 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 A
68117 ATAAGTTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:74411 original size:30 final size:30
Alignment explanation
Indices: 74375--74454 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
74365 ACACGTGAAT
*
74375 TTTAGATATAATATTAATTTGA-TCTTAAAC
1 TTTAGATA-AATATTAATTTGACCCTTAAAC
*
74405 TTTAGATGAAATATTATTTTGACCCTTAAAC
1 TTTAGAT-AAATATTAATTTGACCCTTAAAC
** *
74436 AATAGATAAATATCAATTT
1 TTTAGATAAATATTAATTT
74455 AACTATTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
30 29 0.69
31 13 0.31
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.42
Consensus pattern (30 bp):
TTTAGATAAATATTAATTTGACCCTTAAAC
Found at i:75827 original size:2 final size:2
Alignment explanation
Indices: 75820--75861 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
75810 GGAAGGTGGT
75820 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
75862 CAGCTGCGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:81931 original size:24 final size:24
Alignment explanation
Indices: 81900--81987 Score: 106
Period size: 24 Copynumber: 3.5 Consensus size: 24
81890 AAATTGAATG
*
81900 ACCGGTTTTTTTACCGGATTAAAA
1 ACCGGTTTTTTTACCGGATAAAAA
81924 ACCGGTTTTTTTCTAACCGGATAAAAA
1 ACCGG-TTTTTT-T-ACCGGATAAAAA
* *
81951 ACC-GATTTTTTATCCGTATAAAAA
1 ACCGGTTTTTTTA-CCGGATAAAAA
81975 ACCGGTTTTTTTA
1 ACCGGTTTTTTTA
81988 AAAAACCGGT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
23 1 0.02
24 19 0.35
25 19 0.35
26 2 0.04
27 14 0.25
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (24 bp):
ACCGGTTTTTTTACCGGATAAAAA
Found at i:82004 original size:16 final size:17
Alignment explanation
Indices: 81969--82002 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
81959 TTTATCCGTA
81969 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
81986 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
82003 AACCGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
TAAAAAACCGGTTTTTT
Found at i:82024 original size:39 final size:41
Alignment explanation
Indices: 81945--82041 Score: 126
Period size: 39 Copynumber: 2.4 Consensus size: 41
81935 TCTAACCGGA
* * *
81945 TAAAAAACCGATTTTTTATCCGTATAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTTAACCGTATAAAAAACCAGTTTTTT
*
81986 TAAAAAACCGGTTTTTTAACCG-A-AAAAATCCAGTTTTTT
1 TAAAAAACCGGTTTTTTAACCGTATAAAAAACCAGTTTTTT
**
82025 TTTAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
82042 GCAAACCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
39 29 0.58
40 1 0.02
41 20 0.40
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.40
Consensus pattern (41 bp):
TAAAAAACCGGTTTTTTAACCGTATAAAAAACCAGTTTTTT
Found at i:84817 original size:6 final size:6
Alignment explanation
Indices: 84806--84830 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
84796 CACGTATTAA
84806 CACGAC CACGAC CACGAC CACGAC C
1 CACGAC CACGAC CACGAC CACGAC C
84831 CAAGACAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:85592 original size:41 final size:41
Alignment explanation
Indices: 85535--85686 Score: 223
Period size: 41 Copynumber: 3.7 Consensus size: 41
85525 GGTCGTGGTC
* *
85535 GAATCGCAACGTGAACTTCGCCTGTCGCAACGAATTGGAAT
1 GAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAAT
*
85576 GAATCGCAACGCGAACTTCGCCTATCGCAACGATTTGGAAT
1 GAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAAT
*
85617 GAATCGCAACGCGAACTTCGCATATCGCAACGAATTTGGAAT
1 GAATCGCAACGCGAACTTCGCCTATCGCAACGAA-TTGGAAT
* * * *
85659 AAATCGCAATGCGAATTTCGACTATCGC
1 GAATCGCAACGCGAACTTCGCCTATCGC
85687 GTTGCGAATC
Statistics
Matches: 100, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 70 0.70
42 30 0.30
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (41 bp):
GAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAAT
Found at i:85664 original size:21 final size:21
Alignment explanation
Indices: 85559--85676 Score: 70
Period size: 21 Copynumber: 5.7 Consensus size: 21
85549 ACTTCGCCTG
85559 TCGCAA-CGAA-TTGGAATGAA
1 TCGCAAGCGAATTTGGAAT-AA
* * **
85579 TCGCAACGCGAACTTCGCCT-A
1 TCGCAA-GCGAATTTGGAATAA
85600 TCGCAA-CG-ATTTGGAATGAA
1 TCGCAAGCGAATTTGGAAT-AA
* * *
85620 TCGCAACGCGAACTTCGCAT-A
1 TCGCAA-GCGAATTTGGAATAA
85641 TCGCAA-CGAATTTGGAATAAA
1 TCGCAAGCGAATTTGGAAT-AA
85662 TCGCAATGCGAATTT
1 TCGCAA-GCGAATTT
85677 CGACTATCGC
Statistics
Matches: 73, Mismatches: 13, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
18 5 0.07
19 11 0.15
20 13 0.18
21 21 0.29
22 6 0.08
23 17 0.23
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (21 bp):
TCGCAAGCGAATTTGGAATAA
Found at i:85685 original size:21 final size:21
Alignment explanation
Indices: 85619--85695 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
85609 TTTGGAATGA
* *
85619 ATCGCAACGCGAACTTCG-CAT
1 ATCGCAATGCGAATTTCGAC-T
* *
85640 ATCGCAA--CGAATTTGGAAT
1 ATCGCAATGCGAATTTCGACT
85659 AAATCGCAATGCGAATTTCGACT
1 --ATCGCAATGCGAATTTCGACT
**
85682 ATCGCGTTGCGAAT
1 ATCGCAATGCGAAT
85696 CTGGAAACTG
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
19 8 0.18
21 26 0.59
23 10 0.23
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (21 bp):
ATCGCAATGCGAATTTCGACT
Found at i:89064 original size:38 final size:39
Alignment explanation
Indices: 88994--89070 Score: 147
Period size: 38 Copynumber: 2.0 Consensus size: 39
88984 GATATATAAT
88994 ACTCTTGTTACCTTATATCTTTTTAAAATAGTATGCAAC
1 ACTCTTGTTACCTTATATCTTTTTAAAATAGTATGCAAC
89033 ACTCTTGTTACCTTATAT-TTTTTAAAATAGTATGCAAC
1 ACTCTTGTTACCTTATATCTTTTTAAAATAGTATGCAAC
89071 GATTACGAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 20 0.53
39 18 0.47
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (39 bp):
ACTCTTGTTACCTTATATCTTTTTAAAATAGTATGCAAC
Found at i:93699 original size:30 final size:30
Alignment explanation
Indices: 93663--93734 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
93653 CCCACAGGAC
*
93663 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
93693 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
93723 CTGTCCATAGGT
1 CTATCCAGAGGT
93735 TCCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:93759 original size:31 final size:30
Alignment explanation
Indices: 93721--93845 Score: 137
Period size: 31 Copynumber: 4.0 Consensus size: 30
93711 GATCCTCGGC
* *
93721 AACTGTCCATAGGTTCCGAAGAACCTAGGT
1 AACTGTCCATATGTTCCGAAGAACATAGGT
**
93751 GAACTGTCCATATGTTCCTTAGAACATAGGT
1 -AACTGTCCATATGTTCCGAAGAACATAGGT
93782 ATACTGTCCATATG-TCTCGAA-AGACATAGGT
1 A-ACTGTCCATATGTTC-CGAAGA-ACATAGGT
*
93813 AATTCTGTCCATATGTTCCGTAGAACATAGGT
1 AA--CTGTCCATATGTTCCGAAGAACATAGGT
93845 A
1 A
93846 CCCTCGACTC
Statistics
Matches: 80, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
30 5 0.06
31 49 0.61
32 23 0.29
33 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (30 bp):
AACTGTCCATATGTTCCGAAGAACATAGGT
Found at i:94703 original size:23 final size:23
Alignment explanation
Indices: 94677--94721 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
94667 CACCACATCT
*
94677 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
94700 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
94722 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:94864 original size:25 final size:26
Alignment explanation
Indices: 94829--94879 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
94819 CAAAGAATAT
94829 ATATATATCCCGAAGGACCGCGTAGA
1 ATATATATCCCGAAGGACCGCGTAGA
94855 ATAT-TATCCCGAAGGACCGCGTAGA
1 ATATATATCCCGAAGGACCGCGTAGA
94880 CCCTCTACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (26 bp):
ATATATATCCCGAAGGACCGCGTAGA
Found at i:96568 original size:21 final size:21
Alignment explanation
Indices: 96544--96587 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
96534 TTTTGTTCGT
* *
96544 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
96565 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
96586 TT
1 TT
96588 ACCCAGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:97925 original size:21 final size:21
Alignment explanation
Indices: 97895--97935 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
97885 TTTTATTCGC
* *
97895 TTGAAGGGGTATCGGTTCCCT
1 TTGAAGGGGTACCGATTCCCT
*
97916 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
97936 CTAGCCCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.22, G:0.29, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCT
Found at i:102291 original size:31 final size:31
Alignment explanation
Indices: 102256--102343 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
102246 GTGAACGTCC
*
102256 CATATGTTCCTTAGAACATAGGTATAATGTA
1 CATATGTTCCATAGAACATAGGTATAATGTA
* * * *
102287 CATATGTCTCGAAAG-ACATAGGTAATTATGTC
1 CATATGT-TCCATAGAACATAGGT-ATAATGTA
*
102319 CATATGTTCCGTAGAAACATAGGTA
1 CATATGTTCCATAG-AACATAGGTA
102344 CCTCGACTCT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
31 19 0.42
32 18 0.40
33 8 0.18
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (31 bp):
CATATGTTCCATAGAACATAGGTATAATGTA
Done.