Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012701.1 Corchorus olitorius cultivar O-4 contig12734, 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: 45681
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1101 original size:251 final size:253
Alignment explanation
Indices: 647--1160 Score: 899
Period size: 251 Copynumber: 2.0 Consensus size: 253
637 TCTTTTTTTT
*
647 AAAAAAAAATTCAATAAAATAAAATATATTTAAAAAATATTTAATTTTTATTCCACGTGTCACCT
1 AAAATAAAATTCAATAAAATAAAATATATTTAAAAAATATTTAATTTTTATTCCACGTGTCACCT
*
712 GCCACGTTAGCAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGCAT
66 GCCACGTCAGCAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGCAT
*
777 GCTAACGTGAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAAGAAAAAAAA
131 GCTAACGTAAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAAGAAAAAAAA
* *
842 GTACAGGGACCAAAGTCAACATTTTGTATAGTACAGGGACCTCCCGGATACTTTTACC
196 GTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCGGATACTTTTACC
* *
900 AAAATAAATTTCAATAAAATAAAATATA-TTAAAAAA-ATTTAATTTTTATTCCACGTGTCATCT
1 AAAATAAAATTCAATAAAATAAAATATATTTAAAAAATATTTAATTTTTATTCCACGTGTCACCT
963 GCCACGTCAGCAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGCAT
66 GCCACGTCAGCAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGCAT
1028 GCTAACGTAAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGT-AGAAAAAAAA
131 GCTAACGTAAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAAG-AAAAAAA
* * *
1092 AGTACAGGGACCAAAATCAATATTTCGTATAGTACATGGACCTCCCGGGTACTTTTACC
195 AGTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCGGATACTTTTACC
*
1151 AGAATAAAAT
1 AAAATAAAAT
1161 ATATCTCCTC
Statistics
Matches: 248, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
250 2 0.01
251 212 0.85
252 8 0.03
253 26 0.10
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (253 bp):
AAAATAAAATTCAATAAAATAAAATATATTTAAAAAATATTTAATTTTTATTCCACGTGTCACCT
GCCACGTCAGCAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGCAT
GCTAACGTAAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAAGAAAAAAAA
GTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCGGATACTTTTACC
Found at i:4241 original size:92 final size:94
Alignment explanation
Indices: 4111--4291 Score: 287
Period size: 92 Copynumber: 1.9 Consensus size: 94
4101 TGTCACGAGC
*
4111 TAATTCGGAGACAAACTCAGTCACTCACAAATAAAATATTAAAAATAGATATAACTTTAAATT-A
1 TAATTCGGAGACAAACTCAGCCACTCACAAATAAAATATTAAAAATAGATATAACTTTAAATTAA
4175 AAACTA-TCAAAAAAATTGGTTACACGACT
66 AAAC-AGTCAAAAAAATTGGTTACACGACT
* * *
4204 TAATTGGGAGACAAACTCA-CCACTCACAAGTAAAATATTAAAATTAGATATAACTTTAAATTAA
1 TAATTCGGAGACAAACTCAGCCACTCACAAATAAAATATTAAAAATAGATATAACTTTAAATTAA
*
4268 AAACAGTCATAAAAATTGGTTACA
66 AAACAGTCAAAAAAATTGGTTACA
4292 AATTAAACTC
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
92 41 0.51
93 40 0.49
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.27
Consensus pattern (94 bp):
TAATTCGGAGACAAACTCAGCCACTCACAAATAAAATATTAAAAATAGATATAACTTTAAATTAA
AAACAGTCAAAAAAATTGGTTACACGACT
Found at i:6756 original size:21 final size:21
Alignment explanation
Indices: 6724--6763 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6714 AACAGACCAG
*
6724 GTCCTGGTCAGGATTTGTCAA
1 GTCCTGGTCAGGACTTGTCAA
6745 GTCCTAGG-CAGGACTTGTC
1 GTCCT-GGTCAGGACTTGTC
6764 CTATTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (21 bp):
GTCCTGGTCAGGACTTGTCAA
Found at i:11054 original size:20 final size:21
Alignment explanation
Indices: 11029--11067 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11019 AACAGACCAG
*
11029 GTCCT-GGCAGGAGTTGTCAA
1 GTCCTGGGCAGGACTTGTCAA
11049 GTCCTGGGCAGGACTTGTC
1 GTCCTGGGCAGGACTTGTC
11068 CTGTTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.15, C:0.23, G:0.36, T:0.26
Consensus pattern (21 bp):
GTCCTGGGCAGGACTTGTCAA
Found at i:12730 original size:41 final size:41
Alignment explanation
Indices: 12668--12752 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
12658 CCAAACAAAT
*
12668 ACAATTGAAATCTCATTACACCCGAAACAAACAATCTCATA
1 ACAATTGAAATCTCATAACACCCGAAACAAACAATCTCATA
12709 ACAATTGAAATCTCATAACACCCGAAACAAACAATCTCATA
1 ACAATTGAAATCTCATAACACCCGAAACAAACAATCTCATA
12750 ACA
1 ACA
12753 CCCGCTCTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.48, C:0.27, G:0.05, T:0.20
Consensus pattern (41 bp):
ACAATTGAAATCTCATAACACCCGAAACAAACAATCTCATA
Found at i:13005 original size:148 final size:146
Alignment explanation
Indices: 12685--13081 Score: 660
Period size: 148 Copynumber: 2.7 Consensus size: 146
12675 AAATCTCATT
12685 ACACCCGAAACAAACAATCTCATAACAATTGAAATCTCATAACACCCGAAACAAACAATCTCATA
1 ACACCCGAAACAAACAATCTCATAACAATTGAAATCTCATAACACCCGAAACAAACAATCTCATA
* * *
12750 ACACCCGCTC-T---T-GAACCTAGAAACTATACCTACCTACAAACCTAAAAACAAACAAACAAA
66 ACACCCGCTCTTAACTAGAAACTAGAAACTATATCTACCTACAAACCAAAAAACAAACAAACAAA
*
12810 CAAATTACATATTATA
131 CAAATTACAAATTATA
12826 ACACCCGAAACAAACAATCTCATAACAATTGAAATCTCATAACACCCGAAACAAACAATCTCATA
1 ACACCCGAAACAAACAATCTCATAACAATTGAAATCTCATAACACCCGAAACAAACAATCTCATA
*
12891 ACACGCGCTCTTAAACCTAGAAACTAGAAACTATATCTACCTACAAACCAAAAAACAAACAAACA
66 ACACCCGCTCTT-AA-CTAGAAACTAGAAACTATATCTACCTACAAACCAAAAAACAAACAAACA
12956 AACAAATTACAAATTATA
129 AACAAATTACAAATTATA
12974 ACACCCGAAACAAACAATCTCATAACAATTGAAATCTCATAACACCCGAAACAAACAATCTCATA
1 ACACCCGAAACAAACAATCTCATAACAATTGAAATCTCATAACACCCGAAACAAACAATCTCATA
* *
13039 ACACCCGCTCTTGAACTTAGAAATTAGAAACTATGTCTACCTA
66 ACACCCGCTCTT-AAC-TAGAAACTAGAAACTATATCTACCTA
13082 AATTAAAATC
Statistics
Matches: 239, Mismatches: 9, Indels: 9
0.93 0.04 0.04
Matches are distributed among these distances:
141 74 0.31
142 1 0.00
147 2 0.01
148 162 0.68
ACGTcount: A:0.48, C:0.27, G:0.05, T:0.19
Consensus pattern (146 bp):
ACACCCGAAACAAACAATCTCATAACAATTGAAATCTCATAACACCCGAAACAAACAATCTCATA
ACACCCGCTCTTAACTAGAAACTAGAAACTATATCTACCTACAAACCAAAAAACAAACAAACAAA
CAAATTACAAATTATA
Found at i:17183 original size:23 final size:23
Alignment explanation
Indices: 17157--17209 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
17147 GGGGGGGAGA
17157 GAGAAGAAGGGCAAACTTGGAAG
1 GAGAAGAAGGGCAAACTTGGAAG
17180 GAGAAGAAGGGCAAACTTGGAAG
1 GAGAAGAAGGGCAAACTTGGAAG
*
17203 CAGAAGA
1 GAGAAGA
17210 TAAAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.45, C:0.09, G:0.38, T:0.08
Consensus pattern (23 bp):
GAGAAGAAGGGCAAACTTGGAAG
Found at i:18936 original size:24 final size:25
Alignment explanation
Indices: 18904--18951 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
18894 GCCCCAACAT
*
18904 ATTTAAATTA-AATATTTTAATAAA
1 ATTTAAATTATAAAATTTTAATAAA
*
18928 ATTTAAATTATAAAATTTTGATAA
1 ATTTAAATTATAAAATTTTAATAA
18952 CCTTCATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
ATTTAAATTATAAAATTTTAATAAA
Found at i:18964 original size:22 final size:22
Alignment explanation
Indices: 18936--19439 Score: 101
Period size: 22 Copynumber: 22.9 Consensus size: 22
18926 AAATTTAAAT
18936 TATAAAATTTTGATAACCTTCA
1 TATAAAATTTTGATAACCTTCA
18958 TATAAAATTTTGATAA--TTACA
1 TATAAAATTTTGATAACCTT-CA
* * ***
18979 TTATAAAGTTTTTATAATGAT-A
1 -TATAAAATTTTGATAACCTTCA
* * * *
19001 CTATAGAATTTCGAGAACCTCCA
1 -TATAAAATTTTGATAACCTTCA
* * *
19024 TATGAAATTTTGTTAA-CTTCCC
1 TATAAAATTTTGATAACCTT-CA
* * *
19046 TATAAAATTTTG-TTACACTCCC
1 TATAAAATTTTGATAAC-CTTCA
* * *
19068 TATTAAAATTTTAATAACC-ACC
1 TA-TAAAATTTTGATAACCTTCA
* *
19090 TAATGAAATTTTGATAACCTCCCA
1 T-ATAAAATTTTGATAACCT-TCA
* * * *
19114 -ATGAAATATTGGTAAACGC-ACA
1 TATAAAATTTTGAT-AAC-CTTCA
* *
19136 TTATGAAATTTTGATAACCTTCC
1 -TATAAAATTTTGATAACCTTCA
* ** * * *
19159 GATAAAATACTGGTAATC-ACA
1 TATAAAATTTTGATAACCTTCA
* * *
19180 TTATGAAATTTTGATAAACTTCC
1 -TATAAAATTTTGATAACCTTCA
* ** * * *
19203 GATAAAATAGTGGTAATC-ACA
1 TATAAAATTTTGATAACCTTCA
* *
19224 TTATAAAATTTTGATAACCATACC
1 -TATAAAATTTTGATAACC-TTCA
* *
19248 TATGAAATTGTGAT-ACC-TCA
1 TATAAAATTTTGATAACCTTCA
* *
19268 TTATGAAATTTTTATAAACCTCTC-
1 -TATAAAATTTTGAT-AACCT-TCA
19292 TATAAAATTTTGATAACC-TCTA
1 TATAAAATTTTGATAACCTTC-A
* *
19314 TTTGAAATTTT-ATAACC-TC-
1 TATAAAATTTTGATAACCTTCA
* * * *
19333 -ATGAAATTTTGAAAACC-ACC
1 TATAAAATTTTGATAACCTTCA
* * *
19353 TCATGAAATTTTGATAACCATCG
1 T-ATAAAATTTTGATAACCTTCA
* * * *
19376 TATGAAATTTTGATAACATCCT
1 TATAAAATTTTGATAACCTTCA
* * * * *
19398 TATAAATTTTTTTATAATCTCCT
1 TATAAA-ATTTTGATAACCTTCA
*
19421 TATAAAATTTTGTTAACCT
1 TATAAAATTTTGATAACCT
19440 CCTACGAATT
Statistics
Matches: 350, Mismatches: 96, Indels: 72
0.68 0.19 0.14
Matches are distributed among these distances:
18 9 0.03
19 6 0.02
20 5 0.01
21 28 0.08
22 212 0.61
23 69 0.20
24 19 0.05
25 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (22 bp):
TATAAAATTTTGATAACCTTCA
Found at i:19270 original size:44 final size:43
Alignment explanation
Indices: 19007--20125 Score: 382
Period size: 44 Copynumber: 25.1 Consensus size: 43
18997 GATACTATAG
* * * * ** *
19007 AATTTCGAGAACCTCCATATGAAATTTTGTTAACTTCCCTATAA
1 AATTTTGATAACCTCC-TATGAAATTTTGATAACCTCATTATGA
* * * * * *
19051 AATTTTG-TTACACTCCCTATTAAAATTTTAATAACCACCTAATGA
1 AATTTTGATAAC-CT-CCTA-TGAAATTTTGATAACCTCATTATGA
* * * *
19096 AATTTTGATAACCTCCCAATGAAATATTGGTAAACGCACATTATGA
1 AATTTTGATAACCT-CCTATGAAATTTTGAT-AAC-CTCATTATGA
* * ** * * *
19142 AATTTTGATAACCTTCCGATAAAATACTGGTAATCACATTATGA
1 AATTTTGATAACC-TCCTATGAAATTTTGATAACCTCATTATGA
* * * ** * * * *
19186 AATTTTGATAAACTTCCGATAAAATAGTGGTAATCACATTATAA
1 AATTTTGAT-AACCTCCTATGAAATTTTGATAACCTCATTATGA
*
19230 AATTTTGATAACCATACCTATGAAATTGTGAT-ACCTCATTATGA
1 AATTTTGATAACC-T-CCTATGAAATTTTGATAACCTCATTATGA
* *
19274 AATTTTTATAAACCTCTCTATAAAATTTTGATAACCTCTATT-TGA
1 AATTTTGAT-AACCTC-CTATGAAATTTTGATAACCTC-ATTATGA
* * * *
19319 AATTTT-ATAACCT-C-ATGAAATTTTGAAAACCACCTCATGA
1 AATTTTGATAACCTCCTATGAAATTTTGATAACCTCATTATGA
* * *
19359 AATTTTGATAACCATCGTATGAAATTTTGATAACATCCTTAT-A
1 AATTTTGATAACC-TCCTATGAAATTTTGATAACCTCATTATGA
* * * * * *
19402 AATTTTTTTATAATCTCCTTATAAAATTTTGTTAACCTC-CTACGA
1 AA--TTTTGATAACCTCC-TATGAAATTTTGATAACCTCATTATGA
* * *** * * *
19447 ATTTTTTATTTATAAGAACACTATTAAAATTTGATAACCCCCA--ATGA
1 A---ATT-TTGATAACCTC-CTATGAAATTTTGATAA-CCTCATTATGA
* * * ** * * *
19494 AATTTTGATAATTAACTACACCATCAAATTACGATAACTTGC-CTGTGA
1 AATTTTGAT-A--ACCT-C-CTATGAAATTTTGATAACCT-CATTATGA
* * * * * * **
19542 AATTTTGTTAATCTCCCTCTAAAATTTCGATAGCCTCACCATGA
1 AATTTTGATAACCT-CCTATGAAATTTTGATAACCTCATTATGA
* * ** * *
19586 AATTTTGATAACCACACTATGAAATTTTGATAATCTCCGTCTAA
1 AATTTTGATAACCTC-CTATGAAATTTTGATAACCTCATTATGA
* * *
19630 AATTTCGATAACCTCCCCATGAAATTTTGTTAACCTC--TATGA
1 AATTTTGATAACCT-CCTATGAAATTTTGATAACCTCATTATGA
* * * * * ** *
19672 AATTGTGATCA-TTACACTATGAAAATTTGGTAACAACACT-TGA
1 AATTTTGATAACCT-C-CTATGAAATTTTGATAACCTCATTATGA
* * *
19715 AATTTTGATAAACTCACTCTATCTCACTATGTAAATTTT-ATAAGCACACTATGA
1 AATTTTGAT--A---A--C---CTC-CTATG-AAATTTTGATAACCTCATTATGA
* * *
19769 AATTTTGAAAATCTTCCTATGAAATTTTGATAACCTCCA-TATAA
1 AATTTTGATAA-CCTCCTATGAAATTTTGATAACCT-CATTATGA
* * * *
19813 AATTTCGATAATCATCCTATGAAATTTTGATAACCAGC-GTATGA
1 AATTTTGATAA-CCTCCTATGAAATTTTGATAACC-TCATTATGA
*
19857 AATTTT-AGTAACCTCCCTATGAAATTTTGATAA-C-C-TTCTG-
1 AATTTTGA-TAACCT-CCTATGAAATTTTGATAACCTCATTATGA
* *
19897 AATTTCGATAACCTACTTATGAAATTTTGATAACCTCCA-TATGA
1 AATTTTGATAACCT-CCTATGAAATTTTGATAACCT-CATTATGA
* * *
19941 AATTTTGATAACATCCTTATGAAATTTTATTTTAATAACCTCCTTATGA
1 AATTTTGATAACCTCC-TATG-AA----ATTTTGATAACCTCATTATGA
* * * *
19990 AATTTTGATAACATCCCATGAAATTATGATAA-CT-ATACTATAA
1 AATTTTGATAACCTCCTATGAAATTTTGATAACCTCAT--TATGA
* * * * * *
20033 AATTTTAATATCCTACCTATGAAATTTTGGTAACCTTACTATAA
1 AATTTTGATAACCT-CCTATGAAATTTTGATAACCTCATTATGA
* * * * *
20077 AATTTTGATAACCACACTATGAAATTTTGAGAACCACAGTATAA
1 AATTTTGATAACCTC-CTATGAAATTTTGATAACCTCATTATGA
20121 AATTT
1 AATTT
20126 GAGTGACCAC
Statistics
Matches: 826, Mismatches: 168, Indels: 162
0.71 0.15 0.14
Matches are distributed among these distances:
39 1 0.00
40 53 0.06
41 16 0.02
42 30 0.04
43 71 0.09
44 365 0.44
45 111 0.13
46 45 0.05
47 44 0.05
48 22 0.03
49 34 0.04
52 1 0.00
53 15 0.02
54 18 0.02
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (43 bp):
AATTTTGATAACCTCCTATGAAATTTTGATAACCTCATTATGA
Found at i:19370 original size:62 final size:64
Alignment explanation
Indices: 19225--19392 Score: 186
Period size: 62 Copynumber: 2.6 Consensus size: 64
19215 GTAATCACAT
* * * *
19225 TATAAAATTTTGATAACCATACCTATGAAATTGTGAT-ACCTCATTATGAAATTTTTATAAACCT
1 TATAAAATTTTGATAACCAT-CGTATGAAATTTTGATAACCTC---ATGAAATTTTGATAAACCC
19289 CTC
62 CTC
19292 TATAAAATTTTGATAACC-TC-TATTTGAAATTTT-ATAACCTCATGAAATTTTGA-AAACCACC
1 TATAAAATTTTGATAACCATCGTA--TGAAATTTTGATAACCTCATGAAATTTTGATAAACC-CC
19353 TC
63 TC
*
19355 -ATGAAATTTTGATAACCATCGTATGAAATTTTGATAAC
1 TATAAAATTTTGATAACCATCGTATGAAATTTTGATAAC
19393 ATCCTTATAA
Statistics
Matches: 90, Mismatches: 4, Indels: 18
0.80 0.04 0.16
Matches are distributed among these distances:
62 30 0.33
63 21 0.23
64 4 0.04
65 3 0.03
66 14 0.16
67 18 0.20
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (64 bp):
TATAAAATTTTGATAACCATCGTATGAAATTTTGATAACCTCATGAAATTTTGATAAACCCCTC
Found at i:19414 original size:23 final size:23
Alignment explanation
Indices: 19383--19431 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
19373 TCGTATGAAA
*
19383 TTTTGATAA-CATCCTTATAAATT
1 TTTTGATAATC-TCCTTATAAAAT
*
19406 TTTTTATAATCTCCTTATAAAAT
1 TTTTGATAATCTCCTTATAAAAT
19429 TTT
1 TTT
19432 GTTAACCTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTTGATAATCTCCTTATAAAAT
Found at i:19441 original size:22 final size:22
Alignment explanation
Indices: 19007--19442 Score: 196
Period size: 22 Copynumber: 19.8 Consensus size: 22
18997 GATACTATAG
* * *
19007 AATTTCGAGAACCTCCATATGA
1 AATTTTGATAACCTCCTTATGA
* * * *
19029 AATTTTGTTAACTTCCCTATAA
1 AATTTTGATAACCTCCTTATGA
* * *
19051 AATTTTG-TTACACTCCCTATTAA
1 AATTTTGATAAC-CTCCTTA-TGA
* * *
19074 AATTTTAATAACCACCTAATGA
1 AATTTTGATAACCTCCTTATGA
**
19096 AATTTTGATAACCTCCCAATGA
1 AATTTTGATAACCTCCTTATGA
* * * *
19118 AATATTGGTAAACGCACATTATGA
1 AATTTTGAT-AAC-CTCCTTATGA
* *
19142 AATTTTGATAACCTTCC-GATAA
1 AATTTTGATAACC-TCCTTATGA
** * * * *
19164 AATACTGGTAATCACATTATGA
1 AATTTTGATAACCTCCTTATGA
* * *
19186 AATTTTGATAAACTTCC-GATAA
1 AATTTTGAT-AACCTCCTTATGA
** * * * * *
19208 AATAGTGGTAATCACATTATAA
1 AATTTTGATAACCTCCTTATGA
19230 AATTTTGATAACCATACC-TATGA
1 AATTTTGATAACC-T-CCTTATGA
* *
19253 AATTGTGAT-ACCTCATTATGA
1 AATTTTGATAACCTCCTTATGA
* *
19274 AATTTTTATAAACCT-CTCTATAA
1 AATTTTGAT-AACCTCCT-TATGA
*
19297 AATTTTGATAACCT-CTATTTGA
1 AATTTTGATAACCTCCT-TATGA
19319 AATTTT-ATAACCT-C--ATGA
1 AATTTTGATAACCTCCTTATGA
* * *
19337 AATTTTGAAAACCACCTCATGA
1 AATTTTGATAACCTCCTTATGA
*
19359 AATTTTGATAACCAT-CGTATGA
1 AATTTTGATAACC-TCCTTATGA
*
19381 AATTTTGATAACATCCTTAT-A
1 AATTTTGATAACCTCCTTATGA
* * *
19402 AATTTTTTTATAATCTCCTTATAA
1 AA--TTTTGATAACCTCCTTATGA
*
19426 AATTTTGTTAACCTCCT
1 AATTTTGATAACCTCCT
19443 ACGAATTTTT
Statistics
Matches: 304, Mismatches: 86, Indels: 48
0.69 0.20 0.11
Matches are distributed among these distances:
18 9 0.03
19 5 0.02
20 2 0.01
21 32 0.11
22 170 0.56
23 66 0.22
24 20 0.07
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACCTCCTTATGA
Found at i:19588 original size:22 final size:22
Alignment explanation
Indices: 19563--19666 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 22
19553 TCTCCCTCTA
*
19563 AAATTTCGATAGCCTCACCATG
1 AAATTTCGATAACCTCACCATG
* * *
19585 AAATTTTGATAACCACACTATG
1 AAATTTCGATAACCTCACCATG
* * *
19607 AAATTTTGATAATCTC-CGTC-TA
1 AAATTTCGATAACCTCAC--CATG
*
19629 AAATTTCGATAACCTCCCCATG
1 AAATTTCGATAACCTCACCATG
* *
19651 AAATTTTGTTAACCTC
1 AAATTTCGATAACCTC
19667 TATGAAATTG
Statistics
Matches: 65, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
21 2 0.03
22 62 0.95
23 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.34
Consensus pattern (22 bp):
AAATTTCGATAACCTCACCATG
Found at i:19589 original size:66 final size:66
Alignment explanation
Indices: 19512--19655 Score: 182
Period size: 66 Copynumber: 2.2 Consensus size: 66
19502 TAATTAACTA
* ** * * *
19512 CACCATCAAATTACGATAACTTGC-CTGTGAAATTTTGTTAATCTCCCTCTAAAATTTCGATAGC
1 CACCATGAAATTACGATAAC-CACACTATGAAATTTTGATAATCTCCCTCTAAAATTTCGATAAC
19576 CT
65 CT
** *
19578 CACCATGAAATTTTGATAACCACACTATGAAATTTTGATAATCTCCGTCTAAAATTTCGATAACC
1 CACCATGAAATTACGATAACCACACTATGAAATTTTGATAATCTCCCTCTAAAATTTCGATAACC
19643 T
66 T
*
19644 CCCCATGAAATT
1 CACCATGAAATT
19656 TTGTTAACCT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
65 1 0.01
66 66 0.99
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (66 bp):
CACCATGAAATTACGATAACCACACTATGAAATTTTGATAATCTCCCTCTAAAATTTCGATAACC
T
Found at i:19656 original size:66 final size:64
Alignment explanation
Indices: 19539--19680 Score: 203
Period size: 66 Copynumber: 2.2 Consensus size: 64
19529 AACTTGCCTG
* *
19539 TGAAATTTTGTTAATCTCCCTCTAAAATTTCGATAGCCTCACCATGAAATTTTGATAACCACACT
1 TGAAATTTTGATAATCTCCCTCTAAAATTTCGATAACCTCACCATGAAATTTTGATAA-C-CACT
19604 A
64 A
* * * *
19605 TGAAATTTTGATAATCTCCGTCTAAAATTTCGATAACCTCCCCATGAAATTTTGTTAACCTCTA
1 TGAAATTTTGATAATCTCCCTCTAAAATTTCGATAACCTCACCATGAAATTTTGATAACCACTA
*
19669 TGAAATTGTGAT
1 TGAAATTTTGAT
19681 CATTACACTA
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
64 15 0.22
65 1 0.01
66 53 0.77
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (64 bp):
TGAAATTTTGATAATCTCCCTCTAAAATTTCGATAACCTCACCATGAAATTTTGATAACCACTA
Found at i:19788 original size:22 final size:22
Alignment explanation
Indices: 19763--20111 Score: 254
Period size: 22 Copynumber: 15.9 Consensus size: 22
19753 TATAAGCACA
* *
19763 CTATGAAATTTTGAAAATCTTC
1 CTATGAAATTTTGATAACCTTC
19785 CTATGAAATTTTGATAACC-TC
1 CTATGAAATTTTGATAACCTTC
* * * *
19806 CATATAAAATTTCGATAATCATC
1 C-TATGAAATTTTGATAACCTTC
**
19829 CTATGAAATTTTGATAACCAGC
1 CTATGAAATTTTGATAACCTTC
* *
19851 GTATGAAATTTT-AGTAACCTCC
1 CTATGAAATTTTGA-TAACCTTC
19873 CTATGAAATTTTGATAACCTT-
1 CTATGAAATTTTGATAACCTTC
* *
19894 C--TG-AATTTCGATAACCTAC
1 CTATGAAATTTTGATAACCTTC
*
19913 TTATGAAATTTTGATAACC-TC
1 CTATGAAATTTTGATAACCTTC
*
19934 CATATGAAATTTTGATAA-CATC
1 C-TATGAAATTTTGATAACCTTC
*
19956 CTTATGAAATTTTATTTTAATAACC-TC
1 C-TATG-AA----ATTTTGATAACCTTC
*
19983 CTTATGAAATTTTGATAA-CATC
1 C-TATGAAATTTTGATAACCTTC
* * *
20005 CCATGAAATTATGATAA-CTATA
1 CTATGAAATTTTGATAACCT-TC
* * * *
20027 CTATAAAATTTTAATATCCTAC
1 CTATGAAATTTTGATAACCTTC
* *
20049 CTATGAAATTTTGGTAACCTTA
1 CTATGAAATTTTGATAACCTTC
* *
20071 CTATAAAATTTTGATAACC-AC
1 CTATGAAATTTTGATAACCTTC
*
20092 ACTATGAAATTTTGAGAACC
1 -CTATGAAATTTTGATAACC
20112 ACAGTATAAA
Statistics
Matches: 261, Mismatches: 46, Indels: 40
0.75 0.13 0.12
Matches are distributed among these distances:
18 13 0.05
19 2 0.01
21 25 0.10
22 193 0.74
23 8 0.03
26 2 0.01
27 17 0.07
28 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCTTC
Found at i:19984 original size:27 final size:27
Alignment explanation
Indices: 19942--19995 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
19932 TCCATATGAA
*
19942 ATTTTGATAACATCCTTATGAAATTTT
1 ATTTTAATAACATCCTTATGAAATTTT
*
19969 ATTTTAATAACCTCCTTATGAAATTTT
1 ATTTTAATAACATCCTTATGAAATTTT
19996 GATAACATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (27 bp):
ATTTTAATAACATCCTTATGAAATTTT
Found at i:19992 original size:49 final size:48
Alignment explanation
Indices: 19920--20014 Score: 154
Period size: 49 Copynumber: 2.0 Consensus size: 48
19910 TACTTATGAA
* *
19920 ATTTTGATAACCTCCATATGAAATTTTGATAACATCCTTATGAAATTTT
1 ATTTTAATAACCTCCATATGAAATTTTGATAACATCC-CATGAAATTTT
*
19969 ATTTTAATAACCTCCTTATGAAATTTTGATAACATCCCATGAAATT
1 ATTTTAATAACCTCCATATGAAATTTTGATAACATCCCATGAAATT
20015 ATGATAACTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
48 8 0.19
49 35 0.81
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (48 bp):
ATTTTAATAACCTCCATATGAAATTTTGATAACATCCCATGAAATTTT
Found at i:20112 original size:22 final size:23
Alignment explanation
Indices: 19739--20148 Score: 132
Period size: 22 Copynumber: 18.6 Consensus size: 23
19729 CACTCTATCT
*
19739 CACTATGTAAATTTT-A-TAAGCA
1 CACTATG-AAATTTTGAGTAACCA
* **
19761 CACTATGAAATTTTGA-AAATCTT
1 CACTATGAAATTTTGAGTAA-CCA
*
19784 C-CTATGAAATTTTGA-TAACCT
1 CACTATGAAATTTTGAGTAACCA
* * *
19805 C-CATATAAAATTTCGA-TAATCA
1 CAC-TATGAAATTTTGAGTAACCA
19827 TC-CTATGAAATTTTGA-TAACCA
1 -CACTATGAAATTTTGAGTAACCA
* *
19849 GC-GTATGAAATTTT-AGTAACCT
1 -CACTATGAAATTTTGAGTAACCA
*
19871 CCCTATGAAATTTTGA-TAA-C-
1 CACTATGAAATTTTGAGTAACCA
* * *
19891 C-TTCTG-AATTTCGA-TAACCTA
1 CACTATGAAATTTTGAGTAACC-A
* *
19912 C-TTATGAAATTTTGA-TAACCT
1 CACTATGAAATTTTGAGTAACCA
19933 C-CATATGAAATTTTGA-TAA-CA
1 CAC-TATGAAATTTTGAGTAACCA
* * *
19954 TC-CTTATGAAATTTTATTTTAATAACCT
1 -CAC-TATGAAA---T-TTTGAGTAACCA
19982 C-CTTATGAAATTTTGA-TAA-CA
1 CAC-TATGAAATTTTGAGTAACCA
* * *
20003 TC-CCATGAAATTATGA-TAACTA
1 -CACTATGAAATTTTGAGTAACCA
* * * *
20025 TACTATAAAATTTT-AATATCCTA
1 CACTATGAAATTTTGAGTAACC-A
*
20048 C-CTATGAAATTTTG-GTAACCT
1 CACTATGAAATTTTGAGTAACCA
* *
20069 TACTATAAAATTTTGA-TAACCA
1 CACTATGAAATTTTGAGTAACCA
20091 CACTATGAAATTTTGAG-AACCA
1 CACTATGAAATTTTGAGTAACCA
* * *
20113 CAGTAT-AAAATTTGAGTGACCA
1 CACTATGAAATTTTGAGTAACCA
* *
20135 CACAATGAATTTTT
1 CACTATGAAATTTT
20149 AACTTCCAAA
Statistics
Matches: 302, Mismatches: 56, Indels: 59
0.72 0.13 0.14
Matches are distributed among these distances:
18 10 0.03
19 4 0.01
20 1 0.00
21 46 0.15
22 207 0.69
23 14 0.05
24 1 0.00
25 1 0.00
26 4 0.01
27 13 0.04
28 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (23 bp):
CACTATGAAATTTTGAGTAACCA
Found at i:22043 original size:125 final size:125
Alignment explanation
Indices: 21824--22356 Score: 736
Period size: 125 Copynumber: 4.3 Consensus size: 125
21814 ACTATATCGG
* * * * *
21824 CGTTTGTAAGTGTCGGAACAAATTCTTCATATCATTTGATTTCTACGTATTCCGACATTTGTAAG
1 CGTTTGCAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACGTATTCCGACATTTGTAAG
* * *
21889 CGTTGGTATAGATATTATATCGTGACATTTATTAAACGTCGCTATAAAACACTATACCAA
66 CGTTGGTATAGATATTATATCATGGCATTTATTAAACGTCGCTATAGAACACTATACCAA
* *
21949 CGTTTGCAAAAGTCGGAACAAGTTCTTCACATCATTTGATTTCGACGTATGCCGACATTTGTAAG
1 CGTTTGCAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACGTATTCCGACATTTGTAAG
* **
22014 TGTTGGTATAGATATTATATCATGGCATTTATTAAACGTCGCTATAGAACACTATACTGA
66 CGTTGGTATAGATATTATATCATGGCATTTATTAAACGTCGCTATAGAACACTATACCAA
* * * *
22074 TGTTTGCAAATGTTGGAACAACTTCTTCACATCATTTGATTTCGACGTATTCCGATATTTGTAAG
1 CGTTTGCAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACGTATTCCGACATTTGTAAG
** ***
22139 CGTTAATATAGATATTATATCACATCATTTATTAAACGTCGCTATAGAACACTATACCAA
66 CGTTGGTATAGATATTATATCATGGCATTTATTAAACGTCGCTATAGAACACTATACCAA
*
22199 CGTTTGCAAATGTCGGAACAAGTTCTTCACATCATTTG-----G-CGTATTCCGACATTTCTAAG
1 CGTTTGCAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACGTATTCCGACATTTGTAAG
* * * * *
22258 CGTTGGTATAGATATCATATCGTGGCATTTATTAAACATCGTTATAGAACACTATACCGA
66 CGTTGGTATAGATATTATATCATGGCATTTATTAAACGTCGCTATAGAACACTATACCAA
* * * *
22318 CATTTGCAAATGTTGTAACAAGTTGTTCACATCATTTGA
1 CGTTTGCAAATGTCGGAACAAGTTCTTCACATCATTTGA
22357 ATTGGTTCCT
Statistics
Matches: 361, Mismatches: 46, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
119 102 0.28
120 1 0.00
125 258 0.71
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (125 bp):
CGTTTGCAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACGTATTCCGACATTTGTAAG
CGTTGGTATAGATATTATATCATGGCATTTATTAAACGTCGCTATAGAACACTATACCAA
Found at i:25385 original size:19 final size:17
Alignment explanation
Indices: 25360--25413 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
25350 CTGCCACGTC
25360 ATATTTTTTGATTAAAAAA
1 ATATTTTTT--TTAAAAAA
*
25379 TTA-TTTTTTTAAAAAA
1 ATATTTTTTTTAAAAAA
25395 ATATTTTTTTTTAAAAAA
1 ATA-TTTTTTTTAAAAAA
25413 A
1 A
25414 AATTGGGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 10 0.32
18 19 0.61
19 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
ATATTTTTTTTAAAAAA
Found at i:25392 original size:16 final size:16
Alignment explanation
Indices: 25371--25404 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
25361 TATTTTTTGA
*
25371 TTAAAAAATTATTTTT
1 TTAAAAAAATATTTTT
25387 TTAAAAAAATATTTTT
1 TTAAAAAAATATTTTT
25403 TT
1 TT
25405 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAAAAAAATATTTTT
Found at i:25394 original size:18 final size:17
Alignment explanation
Indices: 25373--25414 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
25363 TTTTTTGATT
25373 AAAAAATTATTTTTTTAA
1 AAAAAATT-TTTTTTTAA
25391 AAAAATATTTTTTTTTAA
1 AAAAA-ATTTTTTTTTAA
25409 AAAAAA
1 AAAAAA
25415 ATTGGGTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.04
18 19 0.83
19 3 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAAAATTTTTTTTTAA
Found at i:26394 original size:19 final size:17
Alignment explanation
Indices: 26370--26411 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
26360 ACCCAAGTTT
26370 TTTTTTTTAAAAAAATATA
1 TTTTTTTT-AAAAAATA-A
26389 TTTTTTTTAAAAAATAA
1 TTTTTTTTAAAAAATAA
26406 TTTTTT
1 TTTTTT
26412 AATCAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 7 0.30
18 8 0.35
19 8 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTTTTAAAAAATAA
Found at i:26419 original size:18 final size:18
Alignment explanation
Indices: 26372--26424 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 18
26362 CCAAGTTTTT
26372 TTTTTTAA-AAAAATATA
1 TTTTTTAATAAAAATATA
*
26389 TTTTTT-TTAAAAA-ATAA
1 TTTTTTAATAAAAATAT-A
26406 TTTTTTAATCAAAAA-ATA
1 TTTTTTAAT-AAAAATATA
26424 T
1 T
26425 GACGTGGCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 2 0.07
17 18 0.60
18 3 0.10
19 7 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTTTAATAAAAATATA
Found at i:26419 original size:19 final size:18
Alignment explanation
Indices: 26371--26424 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
26361 CCCAAGTTTT
*
26371 TTTTTTTAAAAAAATATA
1 TTTTTTTCAAAAAATATA
*
26389 TTTTTTTTAAAAAATA-A
1 TTTTTTTCAAAAAATATA
26406 TTTTTTAATCAAAAAATAT
1 TTTTTT--TCAAAAAATAT
26425 GACGTGGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 7 0.23
18 15 0.48
19 9 0.29
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTTTTCAAAAAATATA
Found at i:30086 original size:178 final size:177
Alignment explanation
Indices: 29715--30101 Score: 481
Period size: 178 Copynumber: 2.2 Consensus size: 177
29705 GTTTGGCTAA
* * * * * *
29715 ACGGTCTATTTAACATTATATAATTTTCTCTCCGGTTATCCGATCAAGGTGATTTAAGTGTCTAT
1 ACGGTCTATTTAATATTATATAATTTT-GCTCCAGATATCCGATCAAGATGATTCAAGTGTCTAT
* *
29780 TAAAAGATTGTTCCATGATCTACAACTTTTATGAAGGACTCGAAAACTAAATTAAATGTTTCAAG
65 TAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCAAAAACTAAATTAAATGTTTCAAG
* * *
29845 TATCAAAAATGCTTCCGAAAAAATTGTTGTTTCAGTTTACGGGAATAG
130 TATAAAAAATGCTTCCGAAAAAATTGTTGTTTCAGTTAACGGAAATAG
** * * * * ** *
29893 ACTATCCACTTAATATTATATAACTTTTGCTCCAGATGTCTGATTGAGATGATTCAAGTGTCTCT
1 ACGGTCTATTTAATATTATATAA-TTTTGCTCCAGATATCCGATCAAGATGATTCAAGTGTCTAT
* *
29958 TGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCAAAAACTAAATTAAATG-TTCAAG
65 TAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCAAAAACTAAATTAAATGTTTCAA-
* * *
30022 GTATAAAAAATGCTTCC-AAAGAATTAGTTGTTTCGGTTAATGGAAATAG
129 GTATAAAAAATGCTTCCGAAAAAATT-GTTGTTTCAGTTAACGGAAATAG
*
30071 ACGGTCTATTTAATATTACATAATTTGTGCT
1 ACGGTCTATTTAATATTATATAATTT-TGCT
30102 TATGGTGGAA
Statistics
Matches: 175, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
177 15 0.09
178 156 0.89
179 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (177 bp):
ACGGTCTATTTAATATTATATAATTTTGCTCCAGATATCCGATCAAGATGATTCAAGTGTCTATT
AAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCAAAAACTAAATTAAATGTTTCAAGT
ATAAAAAATGCTTCCGAAAAAATTGTTGTTTCAGTTAACGGAAATAG
Found at i:30481 original size:33 final size:33
Alignment explanation
Indices: 30444--30511 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
30434 CTAGTAGCTC
*
30444 ATAACAGTGTGAAGTGAAGTTACAAGAAAACCA
1 ATAACAGGGTGAAGTGAAGTTACAAGAAAACCA
30477 ATAACAGGGTGAAGTGAAGTTACAAGAAAACCA
1 ATAACAGGGTGAAGTGAAGTTACAAGAAAACCA
30510 AT
1 AT
30512 CAAAAGGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.12, G:0.22, T:0.18
Consensus pattern (33 bp):
ATAACAGGGTGAAGTGAAGTTACAAGAAAACCA
Found at i:38881 original size:21 final size:21
Alignment explanation
Indices: 38855--38905 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
38845 CGCCCATTCG
* *
38855 CCGTGCCATCACCGGTTAATC
1 CCGTGCCATCACCGATTAAGC
*
38876 CCGTGCCACCACCGATTAAGC
1 CCGTGCCATCACCGATTAAGC
38897 CCGTGCCAT
1 CCGTGCCAT
38906 ACCCTTTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.41, G:0.20, T:0.20
Consensus pattern (21 bp):
CCGTGCCATCACCGATTAAGC
Found at i:43883 original size:45 final size:44
Alignment explanation
Indices: 43827--43937 Score: 120
Period size: 43 Copynumber: 2.5 Consensus size: 44
43817 GAATTGATTG
* * *
43827 GTACCGATGGTGATGAGCAATCACACCATCAG-GACAAAGAGGTTA
1 GTACTGATGGTGA-GAGCAATCACACCATC-GTGACAAAGAAGTGA
* *
43872 GTACTGATGGTGAG-GAAATCACACCATCGTGACAGAGAAGTGA
1 GTACTGATGGTGAGAGCAATCACACCATCGTGACAAAGAAGTGA
43915 GTA-TCGATGGTGAGAAGCAATCA
1 GTACT-GATGGTGAG-AGCAATCA
43938 TATAAAACTC
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
42 2 0.04
43 35 0.62
44 1 0.02
45 18 0.32
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (44 bp):
GTACTGATGGTGAGAGCAATCACACCATCGTGACAAAGAAGTGA
Done.