Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020754.1 Corchorus olitorius cultivar O-4 contig20787, 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: 77598
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--39 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40 TCTAGTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:124 original size:14 final size:14
Alignment explanation
Indices: 88--115 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
78 GTTTTGATTA
88 AAACATATTTTAAG
1 AAACATATTTTAAG
102 AAACATATTTTAAG
1 AAACATATTTTAAG
116 TTACATATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
AAACATATTTTAAG
Found at i:1921 original size:332 final size:326
Alignment explanation
Indices: 782--2579 Score: 1407
Period size: 332 Copynumber: 5.4 Consensus size: 326
772 AGCCAGACAG
* ** * * * *
782 AAAACCGTGATGGTTAGTATACGATTTCAACTAAAAAGTTTGCAAAAATTGACCTGAAAAATTTT
1 AAAACCGTGATGGTTA-TACACGATTTCGGCT-AAAATTTTGCAAAAATTCACCAGAAAATTTTT
* * * * * * * * * *
847 TCCTCGATTTCTAGCGAAAATAATCATAAAAAATATATAATTCAATG-CAAAAAAATTGAAAGCC
64 TCCTCAATTTTTGGC-TAAATACTCAT--GAAATATATAATTCAACGCCAAAAAGATTGAAGGAC
* * * * *
911 TTTTTCAGGTTTCTAATATAGTTTTTC-CTATTTTATTTCCA-AATTAATTTCTGATTAAATCGA
126 -TTTTCACGCTTCTAATATCGTTTTTCAC-A-TTT-TTT-CAGAATTAATTTTTAATTAAATCGA
* * * ** * * *
974 AATAAAATTTAGAAACTCGCAAAAACAAATCCTTAAATACAATGTGGCTGAGATTTGGTTAGATG
186 AACAAGATTCAGATGCTCG-TAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATG
* * * * * *
1039 AATATAAATATATTTTAAGGAGTCTTGA-CGCCAAAAATCATGAAAAACTGACA-CAGG-GCCCC
250 AATAT--AGATATTTCAA-GAGTC-TGAGCACCAAAAATCATGCAAAATTGA-ATC-GGTGCTCC
* **
1101 GAAACTCGTTTTTAGGAAAAAAA
309 GAAACGCGTTTTTA-G----CCA
* * * * * * *
1124 AAAACCATGATGG---TACAAGATTTCGGCTAAAAATTTTGCAAAAAATGACCCGGAATACTTTT
1 AAAACCGTGATGGTTATACACGATTTCGGCT-AAAATTTTGCAAAAATTCA-CCAGAAAATTTTT
* * * * * *
1186 T-CTCCATTTTTAGCCACAATAGTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGC
64 TCCTCAATTTTTGGCTA-AATACTCAT--GAAATATATAATTCAACGCCAAAAAGATTGAAGGAC
**
1250 TTCCCACGCTTCTAATATCGTTTTTC-CTATTTTTTTC-GAATTAATTTTTAATTAAATCGAAAC
126 TTTTCACGCTTCTAATATCGTTTTTCAC-A-TTTTTTCAGAATTAATTTTTAATTAAATCGAAAC
* *
1313 AAGATTC-GAATGCTCGTAAAATCAAATCATTAAATCCAATGTGGCTAAGATTTTG-TTAGATGA
189 AAGATTCAG-ATGCTCGTAAAA-CAAATCCTTAAATCCAATGTGGCTGAGA-TTTGATTAGATGA
* * * *
1376 ATATAGATATTTCAATGAGTTTTG-GCACCAAAAACCATGCAAAACTGACAT-GG-GATCCCGAA
251 ATATAGATATTTCAA-GAG-TCTGAGCACCAAAAATCATGCAAAATTGA-ATCGGTGCT-CCGAA
* *
1438 ACGCATTTTTAGCTAA
312 ACGCGTTTTTAGC-CA
* * * * *
1454 AAAACCGTGAT--TGATACACGATTTCCGCTAAAATTTTGCAAAAATTTACCCG-AAATATTTTC
1 AAAACCGTGATGGTTATACACGATTTCGGCTAAAATTTTGCAAAAATTCACCAGAAAATTTTTTC
* * * * * *
1516 CTCAATTTTTAGCCACAATACTCATAAAAAAAATATAATTCAACGCCAAAAAGTTTGGAGGACTT
66 CTCAATTTTTGGCTA-AATACTCAT--GAAATATATAATTCAACGCCAAAAAGATTGAAGGACTT
* * * * *
1581 TTCACGCTTTTAATATCATTTTTCACA-TTTTTCAGAATTGATTTCTAATTAAATCGAAACAACA
128 TTCACGCTTCTAATATCGTTTTTCACATTTTTTCAGAATTAATTTTTAATTAAATCGAAACAAGA
* * *
1645 TTCAGATGGTCGTAAAAGAAATCTTTAAA-CTCAATGTGGCTGAGATTTGATTAGATGAATATAG
193 TTCAGATGCTCGTAAAACAAATCCTTAAATC-CAATGTGGCTGAGATTTGATTAGATGAATATAG
* * * * *
1709 ATGTTTCAAGAAGTCTCAGCTCCAAAAATCATGCAAAATT-AAGTCGGTGCTCCAAAACTCGTTT
257 ATATTTCAAG-AGTCTGAGCACCAAAAATCATGCAAAATTGAA-TCGGTGCTCCGAAACGCGTTT
1773 TTAGCCA
320 TTAGCCA
* * *
1780 AAAACCGTGATGGTTAGTACATGATTTCGGCTGAAATTTTGCAAAAAAATCACCAGAAAATTTTT
1 AAAACCGTGATGGTTA-TACACGATTTCGGCTAAAATTTTGC-AAAAATTCACCAGAAAA-TTTT
* * * *
1845 TTCCTCAATTTTTGGCTAAACTACTCATGAATTATATATAATTTAATGCGAAAAAGATTGGAGGA
63 TTCCTCAATTTTTGGCTAAA-TACTCATGAA--ATATATAATTCAACGCCAAAAAGATTGAAGGA
* * ** *
1910 CTTTTCACGCTTTTCATATCGTTTTTCGTA-GTTTT-ATGAATTAATTTTTAATTAAATCGAAAC
125 CTTTTCACGCTTCTAATATCGTTTTTCACATTTTTTCA-GAATTAATTTTTAATTAAATCGAAAC
* * * *
1973 AAAATTCAGATGCTCGTAAAAAAAATCCTTAAATGCAATGTTGCTGAGATTTGATTAGATGAATA
189 AAGATTCAGATGCTCGTAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
* * * * * *
2038 TGGATATCTCAAGGAGTCTGAGCACCAAAAATAATGCAAAATTGACCTGGGTCGCT--GGAACGC
254 TAGATATTTCAA-GAGTCTGAGCACCAAAAATCATGCAAAATTGA-ATCGGT-GCTCCGAAACGC
2101 GTTTTTAGCCA
316 GTTTTTAGCCA
* * * *
2112 AAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCGGAAAGA-TATT
1 AAAACCGTGATGGTTA-TACACGATTTCGGCTAAAATTTTGCAAAAATTCACCAGAAA-ATTTTT
* * * * **
2176 TCCTCAATTTTTGGCTAAAATACTCATAAGAAATATATAATTCAACACCAAGAATATTAAAGGGT
64 TCCTCAATTTTTGGCT-AAATACTCAT--GAAATATATAATTCAACGCCAAAAAGATTGAAGGAC
* * * *
2241 TTTTTACGGTTCTAATATCGTTTTTCATATTTTTTCAGAATTAATTTATAATTAAATCGAAACAA
126 TTTTCACGCTTCTAATATCGTTTTTCACATTTTTTCAGAATTAATTTTTAATTAAATCGAAACAA
*
2306 GATTCATATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT
191 GATTCAGATGCTCGT-AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT
* * * * * *
2371 AGATATTTCAAGTAGTCTTG-G-AGTCAAAAATCATGCAGAATTGAACCAGGT-CCCCGGAACTC
255 AGATATTTCAAG-AGTC-TGAGCA-CCAAAAATCATGCAAAATTGAATC-GGTGCTCCGAAACGC
*
2433 CTTTTTAGCCA
316 GTTTTTAGCCA
* ** * * * * *
2444 AAAACTGTGATGGTTTGTTAGTACATAATTTTGGTTAAAATTTTGCAAAAGTGGAT-ACGAG-AG
1 AAAACCGTGAT-G---GTTA-TACACGATTTCGGCTAAAATTTTGCAAAAAT---TCACCAGAAA
* * * *
2507 A-TTTCTCCTCAATTTTTGGCTAAAATACTCATAAAAATATATAATTCAACGTCAAAATGATTGA
58 ATTTTTTCCTCAATTTTTGGCT-AAATACTCAT-GAAATATATAATTCAACGCCAAAAAGATTGA
2571 ATGG-CTTTT
121 A-GGACTTTT
2580 TACGGTTTTT
Statistics
Matches: 1209, Mismatches: 185, Indels: 131
0.79 0.12 0.09
Matches are distributed among these distances:
325 1 0.00
326 22 0.02
327 89 0.07
328 51 0.04
329 106 0.09
330 116 0.10
331 81 0.07
332 365 0.30
333 13 0.01
334 53 0.04
335 36 0.03
336 131 0.11
337 9 0.01
338 98 0.08
339 26 0.02
342 12 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (326 bp):
AAAACCGTGATGGTTATACACGATTTCGGCTAAAATTTTGCAAAAATTCACCAGAAAATTTTTTC
CTCAATTTTTGGCTAAATACTCATGAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTC
ACGCTTCTAATATCGTTTTTCACATTTTTTCAGAATTAATTTTTAATTAAATCGAAACAAGATTC
AGATGCTCGTAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
TTCAAGAGTCTGAGCACCAAAAATCATGCAAAATTGAATCGGTGCTCCGAAACGCGTTTTTAGCC
A
Found at i:7899 original size:27 final size:27
Alignment explanation
Indices: 7861--7912 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
7851 TTTCTGAGGA
*
7861 CTGATGAACATCAAGAACAGCAGAAGG
1 CTGATGAACATCAAAAACAGCAGAAGG
7888 CTGATGAACATCAAAAACAGCAGAA
1 CTGATGAACATCAAAAACAGCAGAA
7913 TTTTCTGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.12
Consensus pattern (27 bp):
CTGATGAACATCAAAAACAGCAGAAGG
Found at i:14640 original size:76 final size:80
Alignment explanation
Indices: 14463--14645 Score: 223
Period size: 83 Copynumber: 2.3 Consensus size: 80
14453 TATAAACACA
* *
14463 TACAAAA-TCAAAGCAGCCAAAATAGAGATTAACATAATAATTTTAATTGAATAAATAAATGGAG
1 TACAAAAGT-AAAGCAACCAAAATAGAGATTAACATAATAATTTTAAGTGAAT--ATAAATGGAG
*
14527 ATTTAAGGATCCATGGGAC
63 ATTCAAGGA-CCATGGGAC
* * * *
14546 TACAAAATTAAAGCAACCAAAATGGAGATTAACATAATACTTTTTAGTG-AT-TAAATGGAGATT
1 TACAAAAGTAAAGCAACCAAAATAGAGATTAACATAATAATTTTAAGTGAATATAAATGGAGATT
14609 CAAGGA-CAT-GGAC
66 CAAGGACCATGGGAC
*
14622 TATAAAAGTAAAGCAACCAAAATA
1 TACAAAAGTAAAGCAACCAAAATA
14646 AATAATGTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
76 25 0.28
77 3 0.03
79 17 0.19
82 2 0.02
83 42 0.47
84 1 0.01
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (80 bp):
TACAAAAGTAAAGCAACCAAAATAGAGATTAACATAATAATTTTAAGTGAATATAAATGGAGATT
CAAGGACCATGGGAC
Found at i:14765 original size:39 final size:39
Alignment explanation
Indices: 14722--14800 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
14712 CTTCCACCAC
*
14722 AAATGCAAGTTTAGGGGAGATTAATCTAAATTAACTAAT
1 AAATGCAAGTTTAGGGGAGATTAACCTAAATTAACTAAT
14761 AAATGCAAGTTTAGGGGAGATTAACCTAAATTAACTAAT
1 AAATGCAAGTTTAGGGGAGATTAACCTAAATTAACTAAT
14800 A
1 A
14801 CTAACATCAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (39 bp):
AAATGCAAGTTTAGGGGAGATTAACCTAAATTAACTAAT
Found at i:14922 original size:6 final size:6
Alignment explanation
Indices: 14900--15142 Score: 84
Period size: 6 Copynumber: 42.0 Consensus size: 6
14890 CTAACCCTAA
* * * ** * ** *
14900 TTCACC TTCACC TTCATC TTCATC ATCATC CCCTTC ACCACC TTCATC
1 TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC
* ** * ** *
14948 TTCATC TTCA-C --CACC TTCATC TTCATC CCCTTC ACCACC TTCATC
1 TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC
* * * *
14993 TTCATC TTCA-C --CACC TTCATC TTCACC TTCACC TTCTAATC --CACC
1 TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC TTC--ATC TTCATC
* * *
15038 TTCATC TTCATC TTCACC TTCACC TTCTAATC --CACC TTCATC TTCATC
1 TTCATC TTCATC TTCATC TTCATC TTC--ATC TTCATC TTCATC TTCATC
* * * *
15086 TTCA-C --CACC TTCATC TTCACC TTCACC TTCTAATC --CACC TTCATC
1 TTCATC TTCATC TTCATC TTCATC TTCATC TTC--ATC TTCATC TTCATC
15131 TTCATC TTCATC
1 TTCATC TTCATC
15143 AGAAACAATC
Statistics
Matches: 181, Mismatches: 35, Indels: 42
0.70 0.14 0.16
Matches are distributed among these distances:
3 6 0.03
4 9 0.05
5 3 0.02
6 157 0.87
8 6 0.03
ACGTcount: A:0.19, C:0.44, G:0.00, T:0.37
Consensus pattern (6 bp):
TTCATC
Found at i:14944 original size:30 final size:30
Alignment explanation
Indices: 14908--15098 Score: 107
Period size: 30 Copynumber: 6.0 Consensus size: 30
14898 AATTCACCTT
14908 CACCTTCATCTTCATCATCATCC-CCTTCAC
1 CACCTTCATCTTCATCATCA-CCACCTTCAC
*
14938 CACCTTCATCTTCATCTTCACCACCTTCATC
1 CACCTTCATCTTCATCATCACCACCTTCA-C
* ** * ** *
14969 TTCATCCCCTTCACCACCTTCATCTTCATCTTCAC
1 --CA---CCTTCATCTTCATCATCACCACCTTCAC
* * ** *
15004 CACCTTCATCTTCACCTTCACCTTC-TAATC
1 CACCTTCATCTTCATCATCACCACCTTCA-C
*
15034 CACCTTCATCTTCATCTTCACCTTCACCTTCTAATC
1 CACCTTCATCTTCATCATCA-C--CACCTTC--A-C
*
15070 CACCTTCATCTTCATCTTCACCACCTTCA
1 CACCTTCATCTTCATCATCACCACCTTCA
15099 TCTTCACCTT
Statistics
Matches: 124, Mismatches: 23, Indels: 27
0.71 0.13 0.16
Matches are distributed among these distances:
29 4 0.03
30 59 0.48
31 3 0.02
33 13 0.10
34 1 0.01
35 2 0.02
36 42 0.34
ACGTcount: A:0.19, C:0.45, G:0.00, T:0.36
Consensus pattern (30 bp):
CACCTTCATCTTCATCATCACCACCTTCAC
Found at i:14946 original size:21 final size:21
Alignment explanation
Indices: 14922--15112 Score: 190
Period size: 21 Copynumber: 8.8 Consensus size: 21
14912 TTCATCTTCA
* *
14922 TCATCATCCCCTTCACCACCT
1 TCATCTTCACCTTCACCACCT
*
14943 TCATCTTCATCTTCACCACCT
1 TCATCTTCACCTTCACCACCT
14964 TCATCTTCATCCCCTTCACCACCT
1 TCATCTTCA---CCTTCACCACCT
*
14988 TCATCTTCATCTTCACCACCT
1 TCATCTTCACCTTCACCACCT
**
15009 TCATCTTCACCTTCACCTTC-
1 TCATCTTCACCTTCACCACCT
* *
15029 TAATC--CACCTTCATCTTCATCT
1 TCATCTTCACCTTCA-C--CACCT
*
15051 TCACCTTCACCTTCTAATCCACCT
1 TCATCTTCACCTTC--A-CCACCT
*
15075 TCATCTTCATCTTCACCACCT
1 TCATCTTCACCTTCACCACCT
15096 TCATCTTCACCTTCACC
1 TCATCTTCACCTTCACC
15113 TTCTAATCCA
Statistics
Matches: 143, Mismatches: 16, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
18 8 0.06
19 1 0.01
20 4 0.03
21 80 0.56
22 4 0.03
24 43 0.30
26 3 0.02
ACGTcount: A:0.19, C:0.45, G:0.00, T:0.36
Consensus pattern (21 bp):
TCATCTTCACCTTCACCACCT
Found at i:14968 original size:45 final size:45
Alignment explanation
Indices: 14917--15140 Score: 223
Period size: 45 Copynumber: 4.9 Consensus size: 45
14907 TCACCTTCAT
*
14917 CTTCATCATCATCCCCTTCACCACCTTCATCTTCATCTTCACCAC
1 CTTCATCTTCATCCCCTTCACCACCTTCATCTTCATCTTCACCAC
14962 CTTCATCTTCATCCCCTTCACCACCTTCATCTTCATCTTCACCAC
1 CTTCATCTTCATCCCCTTCACCACCTTCATCTTCATCTTCACCAC
*
15007 CTTCATCTTCACCTTCACCTTCTAATCCACCTTCATCTTCATCTT---CAC
1 CTTCATCTTCA---TCCCCTTC--A-CCACCTTCATCTTCATCTTCACCAC
* **
15055 CTTCACCTTC-T---AAT--CCACCTTCATCTTCATCTTCACCAC
1 CTTCATCTTCATCCCCTTCACCACCTTCATCTTCATCTTCACCAC
*
15094 CTTCATCTTCACCTTCACCTTCTAATCCACCTTCATCTTCATCTTCA
1 CTTCATCTTCA---TCCCCTTC--A-CCACCTTCATCTTCATCTTCA
15141 TCAGAAACAA
Statistics
Matches: 150, Mismatches: 8, Indels: 36
0.77 0.04 0.19
Matches are distributed among these distances:
36 19 0.13
39 12 0.08
41 1 0.01
43 1 0.01
44 1 0.01
45 55 0.37
46 1 0.01
48 19 0.13
50 1 0.01
51 40 0.27
ACGTcount: A:0.19, C:0.44, G:0.00, T:0.37
Consensus pattern (45 bp):
CTTCATCTTCATCCCCTTCACCACCTTCATCTTCATCTTCACCAC
Found at i:15047 original size:36 final size:36
Alignment explanation
Indices: 15007--15091 Score: 170
Period size: 36 Copynumber: 2.4 Consensus size: 36
14997 TCTTCACCAC
15007 CTTCATCTTCACCTTCACCTTCTAATCCACCTTCAT
1 CTTCATCTTCACCTTCACCTTCTAATCCACCTTCAT
15043 CTTCATCTTCACCTTCACCTTCTAATCCACCTTCAT
1 CTTCATCTTCACCTTCACCTTCTAATCCACCTTCAT
15079 CTTCATCTTCACC
1 CTTCATCTTCACC
15092 ACCTTCATCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.19, C:0.42, G:0.00, T:0.39
Consensus pattern (36 bp):
CTTCATCTTCACCTTCACCTTCTAATCCACCTTCAT
Found at i:15059 original size:87 final size:86
Alignment explanation
Indices: 14982--15140 Score: 309
Period size: 87 Copynumber: 1.8 Consensus size: 86
14972 ATCCCCTTCA
14982 CCACCTTCATCTTCATCTTCACCACCTTCATCTTCACCTTCACCTTCTAATCCACCTTCATCTTC
1 CCACCTTCATCTTCATCTTCACCACCTTCATCTTCACCTTCACCTTCTAATCCACCTTCATCTTC
15047 ATCTTCACCTTCACCTTCTAAT
66 ATCTTCACCTTCACCTTC-AAT
15069 CCACCTTCATCTTCATCTTCACCACCTTCATCTTCACCTTCACCTTCTAATCCACCTTCATCTTC
1 CCACCTTCATCTTCATCTTCACCACCTTCATCTTCACCTTCACCTTCTAATCCACCTTCATCTTC
15134 ATCTTCA
66 ATCTTCA
15141 TCAGAAACAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.19, C:0.43, G:0.00, T:0.38
Consensus pattern (86 bp):
CCACCTTCATCTTCATCTTCACCACCTTCATCTTCACCTTCACCTTCTAATCCACCTTCATCTTC
ATCTTCACCTTCACCTTCAAT
Found at i:15140 original size:30 final size:30
Alignment explanation
Indices: 14986--15091 Score: 119
Period size: 36 Copynumber: 3.4 Consensus size: 30
14976 CCTTCACCAC
*
14986 CTTCATCTTCATCTTC--A-CCACCTTCAT
1 CTTCATCTTCACCTTCTAATCCACCTTCAT
*
15013 CTTCACCTTCACCTTCTAATCCACCTTCAT
1 CTTCATCTTCACCTTCTAATCCACCTTCAT
15043 CTTCATCTTCACCTTCACCTTCTAATCCACCTTCAT
1 CTTCA---T---CTTCACCTTCTAATCCACCTTCAT
15079 CTTCATCTTCACC
1 CTTCATCTTCACC
15092 ACCTTCATCT
Statistics
Matches: 67, Mismatches: 3, Indels: 15
0.79 0.04 0.18
Matches are distributed among these distances:
27 14 0.21
29 1 0.01
30 22 0.33
33 1 0.01
36 29 0.43
ACGTcount: A:0.19, C:0.42, G:0.00, T:0.39
Consensus pattern (30 bp):
CTTCATCTTCACCTTCTAATCCACCTTCAT
Found at i:15140 original size:51 final size:53
Alignment explanation
Indices: 14982--15112 Score: 144
Period size: 57 Copynumber: 2.4 Consensus size: 53
14972 ATCCCCTTCA
14982 CCACCTTCATCTTCATCTTCA-CCACCTTCATCTTCACCTTCACCTTC-TAAT
1 CCACCTTCATCTTCATCTTCACCCACCTTCATCTTCACCTTCACCTTCATAAT
* **
15033 CCACCTTCATCTTCATCTTCACCTTCACCTTCTAATC--CACCTTCATCTTCATCTT
1 CCACCTTCATCTTCATCTTCACC--CACCTTC--ATCTTCACCTTCACCTTCATAAT
*
15088 CACCACCTTCATCTTCACCTTCACC
1 --CCACCTTCATCTTCATCTTCACC
15113 TTCTAATCCA
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
51 21 0.31
52 1 0.01
54 19 0.28
55 2 0.03
56 3 0.04
57 22 0.32
ACGTcount: A:0.19, C:0.44, G:0.00, T:0.37
Consensus pattern (53 bp):
CCACCTTCATCTTCATCTTCACCCACCTTCATCTTCACCTTCACCTTCATAAT
Found at i:17508 original size:23 final size:22
Alignment explanation
Indices: 17482--17529 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 22
17472 TTTACTATCT
17482 TAAAT-ATAATATATATTATTAAA
1 TAAATAATAA-ATATATT-TTAAA
17505 TAAATAATAAATATATTTTAAA
1 TAAATAATAAATATATTTTAAA
17527 TAA
1 TAA
17530 TAAATAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 8 0.33
23 12 0.50
24 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATAATAAATATATTTTAAA
Found at i:17513 original size:21 final size:21
Alignment explanation
Indices: 17487--17537 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
17477 TATCTTAAAT
17487 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
17508 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
17529 ATAAATAAT
1 AT-AATAAT
17538 GAGTTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 11 0.41
22 9 0.33
23 7 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:21307 original size:331 final size:331
Alignment explanation
Indices: 20374--22527 Score: 2116
Period size: 332 Copynumber: 6.5 Consensus size: 331
20364 CATGATGGTT
* **
20374 AAAA-TGACCAGAAAGGA-TTTTCCT-AATTTTTTGGAAAAAATACTCAT--AAAATATATAATT
1 AAAATTGACCAGAAA-GATTTTTCCTCAA-TTTTTAGCTAAAATACTCATAAAAAATATATAATT
* * * * * *
20434 CAATGCCAGAAGGATT-AGAGGAATTTTCACGCTTTTAATATCATTTTTCATATTTTTCTGAATT
64 CAACGCCAAAAAGATTGAAAGG-CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATT
* * * *
20498 AATTTCAAATTAAATCGAAACAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGC
128 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * *
20563 CTGACATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA-T
193 CTGAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTCGGCGCCAAAAATCATGCAAAACT
* * *** ** *
20627 AGAGTCGTGGTCATAGAACGCGTTTTTAG-CGAAAAACTGTGATGGTTTCTGCACGATTTCGGCT
258 -GAGTCGGGGCCCCGGAACGCGTTTTTAGCCG-AAAACTGTGATGGTTAGTACACGATTTCGGCT
* *
20691 GAAACTTTGCA
321 AAAATTTTGCA
* *
20702 AAAATTGAGCC-GAAAGATATTTCCTCAATTTTT-GTCTAAAATACTCGTAAGAAAAATATATAA
1 AAAATTGA-CCAGAAAGATTTTTCCTCAATTTTTAG-CTAAAATACTCAT-A-AAAAATATATAA
** ** * ** *
20765 TTCAACATCAAAAAGATTGATCGGGCTTTTAACGCTCCTAATA-------T--TATTTTTCCGAA
62 TTCAACGCCAAAAAGATTGA-AAGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAA
*
20821 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATCAAATCCTTAAATCTAATG
126 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-CAAATCCTTAAATCCAATG
* * * * *
20886 TGGTTGATATTTGGTTAGATGAATATAGATATTTCAAAGAGTCTTGGCACCAAAAATCATGCAAA
190 TGGCTGAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTCGGCGCCAAAAATCATGCAAA
* * * *
20951 ACTGAGTC--GGCCCTGAAACGCGTTTTTAGCCGAAAATTGTGATGGTTAGTACATGATTTCGGC
255 ACTGAGTCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGTACACGATTTCGGC
*
21014 GAAAATTTTGCA
320 TAAAATTTTGCA
* * * *
21026 AAACTTGATTC-GAAAGATTTTTCCTCAATTTCTT-GCGAAAATACTTATAAAAAATATATAATT
1 AAAATTGA-CCAGAAAGATTTTTCCTCAATTT-TTAGCTAAAATACTCATAAAAAATATATAATT
* * * * *
21089 CAATGCCAAAAAAATTTAAAGCCTTTTTCACGCTTTTAATATCATTTTTCATATTTTTCTGAATT
64 CAACGCCAAAAAGATTGAAAGGC-TTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATT
* * *
21154 AATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATTCAATGTGG
128 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * *** * *
21219 CTGAGATTTAATTATATGAATTTAGATATTTC-AAGAAGTCTCGATACAAAAAATCATGCAATAC
193 CTGAGATTTGATTAGATGAATATAGATATTTCAAAG-AGTCTCGGCGCCAAAAATCATGCAAAAC
* * * *
21283 TGAGTC-GAGCCCCGGAATGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACAATTTCGGCTA
257 TGAGTCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGTACACGATTTCGGCTA
21347 AAATTTTGCA
322 AAATTTTGCA
* * * * * * *
21357 AAAATTGACCTGAAAAATTTTTTCCGTCAATTTTTGGCTAAAAAACTCATTATATATATATAATT
1 AAAATTGACCAGAAAGA-TTTTTCC-TCAATTTTTAGCTAAAATACTCATAAAAAATATATAATT
* * *
21422 TAACGCCAAAGAGATTG-GAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATT
64 CAACGCCAAAAAGATTGAAAGG-CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATT
* * * * * * *
21486 AGTTTCCAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCGATTTTG
128 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * * *
21551 CTGAGATTTTATTAAATGAATATGGATATCTCAAAGAGTCTTGGCGGCAAAAATCATGCAAAACT
193 CTGAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTCGGCGCCAAAAATCATGCAAAACT
* * * * * * * * * *
21616 TAGTCGGGGCCCCGGAACGCGTTTTAAACCAAAAACCGTGATGATTATTACACGATTTTGGTTAG
258 GAGTCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGTACACGATTTCGGCTAA
21681 AATTTTGCA
323 AATTTTGCA
* * * * * *
21690 AAAATTGACTAGAAAG-TTATTTCCTCATTTTTTAGCCACAATACTCGTAAAAATTATATAATTC
1 AAAATTGACCAGAAAGATT-TTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTC
* * * * * * *
21754 TACGCCAAAAAGATTGAAGGGATTTTCATGCTTTTAATATCGTTTTTCCTATTATTTTTCAAGTT
65 AACGCCAAAAAGATTGAAAGGCTTTTCACGCTTTTAATATCGTTTTTCATATT-TTTCTGAA-TT
* * *** *
21819 AAATTT-TAATTAAATCGAAACATGATTCAGATGCTTGT-TTTACAAATCCTTAAATGCAATGTG
128 -AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * **
21882 GCTGAGATTTGGTTAGATGAATGTAGATATTTCAAGGAGTCTCGGCGCAAAAAAATCATGCAACT
192 GCTGAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTCGGCGC-CAAAAATCATGCAAAA
** * * ** * * * * *
21947 CTGAACCGGGGCCCCAGAACGTGTTTTT--CCG-TGA-TTTGA--CTAACGTACACAATTTCGGA
256 CTGAGTCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTA-GTACACGATTTCGGC
*
22006 TAATATTTTGCA
320 TAAAATTTTGCA
* * *
22018 AAAATTGACCAGAAATATTTTTCCTCAATTTTT-GTCTAAAATACTCATAAAATATATATAATTT
1 AAAATTGACCAGAAAGATTTTTCCTCAATTTTTAG-CTAAAATACTCATAAAAAATATATAATTC
* * * *
22082 AACTCCAAAAAAAATTG-GAGGACTTTTCACGCTTTTAATATCGTTATTCATATTTTTCTGAATT
65 AACGCC-AAAAAGATTGAAAGG-CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATT
* * * *
22146 AATTTTTACTTAAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATGCAATGTGG
128 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * *
22211 TTGAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTTGACGCCAAAAATTATGCAAAACT
193 CTGAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTCGGCGCCAAAAATCATGCAAAACT
** * * * ** * * *
22276 GAACCGGGGCCTCGAAACACGTTTTTAGCAAAAAAAAATTGTGATTGTTAGTACACGATTTCAGC
258 GAGTCGGGGCCCCGGAACGCGTTTTTAGC---CGAAAACTGTGATGGTTAGTACACGATTTCGGC
*
22341 CAAAATTTTGCA
320 TAAAATTTTGCA
* * * * *
22353 AAAAATGACCAGAAAAATATTTCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCA
1 AAAATTGACCAGAAAGATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCA
* * * *
22418 ACACCAAAAAAATTG-AAGAGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCTGAATT
66 ACGCCAAAAAGATTGAAAG-GCTTTTCACGCTTTTAATATCGTTTTT-C-ATATTTTTCTGAATT
* * * * *
22482 AATTTCTAATTAAAACGAAACATGATTTAGATGTTTGTAAAAACAA
128 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
22528 TGACTGGGAT
Statistics
Matches: 1491, Mismatches: 275, Indels: 112
0.79 0.15 0.06
Matches are distributed among these distances:
321 2 0.00
322 41 0.03
323 1 0.00
324 89 0.06
325 58 0.04
326 86 0.06
327 71 0.05
328 153 0.10
329 75 0.05
330 80 0.05
331 201 0.13
332 228 0.15
333 206 0.14
334 59 0.04
335 86 0.06
336 55 0.04
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (331 bp):
AAAATTGACCAGAAAGATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCA
ACGCCAAAAAGATTGAAAGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAAT
TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
AGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTCGGCGCCAAAAATCATGCAAAACTGAG
TCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAT
TTTGCA
Found at i:27534 original size:18 final size:18
Alignment explanation
Indices: 27511--27545 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
27501 TCTGTCCGTT
27511 CATCGAAGGAGTACTTAC
1 CATCGAAGGAGTACTTAC
27529 CATCGAAGGAGTACTTA
1 CATCGAAGGAGTACTTA
27546 AACTGCAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (18 bp):
CATCGAAGGAGTACTTAC
Found at i:28425 original size:21 final size:21
Alignment explanation
Indices: 28410--28452 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28400 AAAGAGATTC
28410 TTATTAATTTGGAAGAAAAGA
1 TTATTAATTTGGAAGAAAAGA
28431 TTATTAATTTGGAAGAAAAGA
1 TTATTAATTTGGAAGAAAAGA
28452 T
1 T
28453 ACATAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.35
Consensus pattern (21 bp):
TTATTAATTTGGAAGAAAAGA
Found at i:38320 original size:24 final size:24
Alignment explanation
Indices: 38236--38312 Score: 118
Period size: 24 Copynumber: 3.2 Consensus size: 24
38226 CGGCAAAGGT
38236 GGAGGAGGTGGTGGAAAAGGCGGC
1 GGAGGAGGTGGTGGAAAAGGCGGC
* *
38260 GGAGGAGGTGGTGGCAAGGGCGGC
1 GGAGGAGGTGGTGGAAAAGGCGGC
* *
38284 GGAGGAGGAGGTGGAAAAGGCGGG
1 GGAGGAGGTGGTGGAAAAGGCGGC
38308 GGAGG
1 GGAGG
38313 TGGCGGTGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.23, C:0.08, G:0.62, T:0.06
Consensus pattern (24 bp):
GGAGGAGGTGGTGGAAAAGGCGGC
Found at i:38336 original size:48 final size:46
Alignment explanation
Indices: 38230--38336 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 46
38220 AATGGGCGGC
* *
38230 AAAGGTGGAGGAGGTGGTGGAAAAGGCGGCGGAGGAGGTGGTGGCA
1 AAAGGTGGAGGAGGAGGTGGAAAAGGCGGCGGAGGAGGCGGTGGCA
** * * *
38276 AGGGCGGCGGAGGAGGAGGTGGAAAAGGCGGGGGAGGTGGCGGTGCTGCA
1 A--AAGGTGGAGGAGGAGGTGGAAAAGGCGGCGGAGGAGGCGGTG--GCA
38326 AAAGGTGGAGG
1 AAAGGTGGAGG
38337 CGGGGGTTCT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
46 1 0.02
48 42 0.89
50 4 0.09
ACGTcount: A:0.24, C:0.08, G:0.58, T:0.09
Consensus pattern (46 bp):
AAAGGTGGAGGAGGAGGTGGAAAAGGCGGCGGAGGAGGCGGTGGCA
Found at i:46915 original size:2 final size:2
Alignment explanation
Indices: 46908--46938 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46898 AGATCTTGCA
46908 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
46939 GTCCCCTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:66762 original size:72 final size:73
Alignment explanation
Indices: 66639--66788 Score: 266
Period size: 72 Copynumber: 2.1 Consensus size: 73
66629 AGACTCTCCT
*
66639 ACCAGCTTAATAGAGATAGTTAAAGTCACCCTAAAGTTCTAGCTCTAAAACAGACGATCTTATTC
1 ACCAGCTTAATAGAGATAGTTAAAGTCAACCTAAAGTTCTAGCTCTAAAACAGACGATCTTATTC
66704 AAAAGACA
66 AAAAGACA
* *
66712 ACCAGCTTAATAGAGATAGTT-AAGTTAACCTAAAGTTCTAGCTCTAAAACAGACGATTTTATTC
1 ACCAGCTTAATAGAGATAGTTAAAGTCAACCTAAAGTTCTAGCTCTAAAACAGACGATCTTATTC
66776 AAAAGACA
66 AAAAGACA
66784 ACCAG
1 ACCAG
66789 TTGAGTAATA
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 53 0.72
73 21 0.28
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.25
Consensus pattern (73 bp):
ACCAGCTTAATAGAGATAGTTAAAGTCAACCTAAAGTTCTAGCTCTAAAACAGACGATCTTATTC
AAAAGACA
Found at i:68851 original size:205 final size:205
Alignment explanation
Indices: 68499--68908 Score: 820
Period size: 205 Copynumber: 2.0 Consensus size: 205
68489 TAAAAATACA
68499 AAACAAAATAAAAAGTACCCATTTTAAATAAAACTACCTATTGGAGGATAAATAAAAATATTTAA
1 AAACAAAATAAAAAGTACCCATTTTAAATAAAACTACCTATTGGAGGATAAATAAAAATATTTAA
68564 ATTTTATTTATATGATTTTAAAAAAACTAACCATTTAAAGAGAAAAAAACTTCCAAAAACTACTC
66 ATTTTATTTATATGATTTTAAAAAAACTAACCATTTAAAGAGAAAAAAACTTCCAAAAACTACTC
68629 ACGTAGTGAGTGCCCTGAGTCTTGTAAGGGAAGAAATCTTAACCTCATTTTCTATTTCAAAATGT
131 ACGTAGTGAGTGCCCTGAGTCTTGTAAGGGAAGAAATCTTAACCTCATTTTCTATTTCAAAATGT
68694 CCTGTTTTAC
196 CCTGTTTTAC
68704 AAACAAAATAAAAAGTACCCATTTTAAATAAAACTACCTATTGGAGGATAAATAAAAATATTTAA
1 AAACAAAATAAAAAGTACCCATTTTAAATAAAACTACCTATTGGAGGATAAATAAAAATATTTAA
68769 ATTTTATTTATATGATTTTAAAAAAACTAACCATTTAAAGAGAAAAAAACTTCCAAAAACTACTC
66 ATTTTATTTATATGATTTTAAAAAAACTAACCATTTAAAGAGAAAAAAACTTCCAAAAACTACTC
68834 ACGTAGTGAGTGCCCTGAGTCTTGTAAGGGAAGAAATCTTAACCTCATTTTCTATTTCAAAATGT
131 ACGTAGTGAGTGCCCTGAGTCTTGTAAGGGAAGAAATCTTAACCTCATTTTCTATTTCAAAATGT
68899 CCTGTTTTAC
196 CCTGTTTTAC
68909 TCCTATTTTT
Statistics
Matches: 205, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 205 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.32
Consensus pattern (205 bp):
AAACAAAATAAAAAGTACCCATTTTAAATAAAACTACCTATTGGAGGATAAATAAAAATATTTAA
ATTTTATTTATATGATTTTAAAAAAACTAACCATTTAAAGAGAAAAAAACTTCCAAAAACTACTC
ACGTAGTGAGTGCCCTGAGTCTTGTAAGGGAAGAAATCTTAACCTCATTTTCTATTTCAAAATGT
CCTGTTTTAC
Found at i:69182 original size:19 final size:20
Alignment explanation
Indices: 69155--69192 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
69145 ATACAAAACA
*
69155 AAATAAAAAGTACCCATTTT
1 AAATAAAAACTACCCATTTT
*
69175 AAAT-AAAACTACCTATTT
1 AAATAAAAACTACCCATTT
69193 GAGGATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.32
Consensus pattern (20 bp):
AAATAAAAACTACCCATTTT
Found at i:69658 original size:445 final size:446
Alignment explanation
Indices: 68704--69747 Score: 2027
Period size: 445 Copynumber: 2.3 Consensus size: 446
68694 CCTGTTTTAC
68704 AAACAAAATAAAAAGTACCCATTTTAAATAAAACTACCTATTGGAGGATAAATAAAAATATTTAA
1 AAACAAAATAAAAAGTACCCATTTTAAATAAAACTACCTATTGGAGGATAAATAAAAATATTTAA
68769 ATTTTATTTATATGATTTTAAAAAAACTAACCATTTAAAGAGAAAAAAACTTCCAAAAACTACTC
66 ATTTTATTTATATGATTTTAAAAAAACTAACCATTTAAAGAGAAAAAAACTTCCAAAAACTACTC
* *
68834 ACGTAGTGAGTGCCCTGAGTCTTGTAAGGGAAGAAATCTTAACCTCATTTTCTATTTCAAAATGT
131 ACGTAGTGAGTGCCCTGTGTCTTGTAAGGGAAGAAATCCTAACCTCATTTTCTATTTCAAAATGT
68899 CCTGTTTTACTCCTATTTTTGGCATTCAAACAAAGGATTATATTAATATCTCAAAAAAACCAAGT
196 CCTGTTTTACTCCTATTTTTGGCATTCAAACAAAGGATTATATTAATATCTCAAAAAAACCAAGT
* *
68964 ACAAAGAGTTCCATTTTCAAGCCAAATTGACAACATAGAAAACCCTTCAAAATTGCCTAAAAGAC
261 ACAAAGAGTTCCATTTCCAAGCCAAATAGACAACATAGAAAACCCTTCAAAATTGCCTAAAAGAC
69029 TAAAGCAGAAAAGAGAAGAAATTATGGTAGAGCATCCACAGCATCTATACTAATTATAAAGCCAA
326 TAAAGCAGAAAAGAGAAGAAATTATGGTAGAGCATCCACAGCATCTATACTAATTATAAAGCCAA
69094 GTCCTGAGTTTGTGTCACGAGTTGACTCAGATACAAAATCAGTTTTTAAAAATACA
391 GTCCTGAGTTTGTGTCACGAGTTGACTCAGATACAAAATCAGTTTTTAAAAATACA
*
69150 AAACAAAATAAAAAGTACCCATTTTAAATAAAACTACCTATTTGAGGATAAATAAAAATATTTAA
1 AAACAAAATAAAAAGTACCCATTTTAAATAAAACTACCTATTGGAGGATAAATAAAAATATTTAA
69215 ATTTTATTTATATGATTTTAAAAAAACTAACCATTTAAAGAGAAAAAAACTTCCAAAAACTACTC
66 ATTTTATTTATATGATTTTAAAAAAACTAACCATTTAAAGAGAAAAAAACTTCCAAAAACTACTC
69280 ACGTAGTGAGTGCCCTGTGTCTTGTAAGGGAAGAAATCCTAACCTCATTTTCTATTTCAAAATGT
131 ACGTAGTGAGTGCCCTGTGTCTTGTAAGGGAAGAAATCCTAACCTCATTTTCTATTTCAAAATGT
69345 CCTGTTTTACTCCTATTTTTGGCATTCAAACAAAGGATTATATTAATATCTCAAAAAAACCAAGT
196 CCTGTTTTACTCCTATTTTTGGCATTCAAACAAAGGATTATATTAATATCTCAAAAAAACCAAGT
69410 ACAAAGAGTTCCA-TTCCAAGCCAAATAGACAACATAGAAAACCCTTCAAAATTGCCTAAAAGAC
261 ACAAAGAGTTCCATTTCCAAGCCAAATAGACAACATAGAAAACCCTTCAAAATTGCCTAAAAGAC
69474 TAAAGCAGAAAAGAGAAGAAATTATGGTAGAGCATCCACAGCATCTATACTAATTATAAAGCCAA
326 TAAAGCAGAAAAGAGAAGAAATTATGGTAGAGCATCCACAGCATCTATACTAATTATAAAGCCAA
*
69539 GTCCTGAGTTTGTGTCACGAGTTGACTCAGATACAAAATCAGTTTTTAAATATACA
391 GTCCTGAGTTTGTGTCACGAGTTGACTCAGATACAAAATCAGTTTTTAAAAATACA
69595 AAACAAAATAAAAAGTACCCATTTTAAATAAAACTACCTATTGGAGGATAAATAAAAATATTTAA
1 AAACAAAATAAAAAGTACCCATTTTAAATAAAACTACCTATTGGAGGATAAATAAAAATATTTAA
69660 ATTTTATTTATATGATTTTAAAAAAACTAACCATTTAAAGAGAAAAAAACTTCCAAAAACTACTC
66 ATTTTATTTATATGATTTTAAAAAAACTAACCATTTAAAGAGAAAAAAACTTCCAAAAACTACTC
69725 ACGTAGTGAGTGCCCTGTGTCTT
131 ACGTAGTGAGTGCCCTGTGTCTT
69748 ACTATTATAA
Statistics
Matches: 591, Mismatches: 7, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
445 321 0.54
446 270 0.46
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (446 bp):
AAACAAAATAAAAAGTACCCATTTTAAATAAAACTACCTATTGGAGGATAAATAAAAATATTTAA
ATTTTATTTATATGATTTTAAAAAAACTAACCATTTAAAGAGAAAAAAACTTCCAAAAACTACTC
ACGTAGTGAGTGCCCTGTGTCTTGTAAGGGAAGAAATCCTAACCTCATTTTCTATTTCAAAATGT
CCTGTTTTACTCCTATTTTTGGCATTCAAACAAAGGATTATATTAATATCTCAAAAAAACCAAGT
ACAAAGAGTTCCATTTCCAAGCCAAATAGACAACATAGAAAACCCTTCAAAATTGCCTAAAAGAC
TAAAGCAGAAAAGAGAAGAAATTATGGTAGAGCATCCACAGCATCTATACTAATTATAAAGCCAA
GTCCTGAGTTTGTGTCACGAGTTGACTCAGATACAAAATCAGTTTTTAAAAATACA
Found at i:70249 original size:16 final size:15
Alignment explanation
Indices: 70216--70245 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
70206 TAAAAAACAG
70216 TAAAGAGATATTAAA
1 TAAAGAGATATTAAA
70231 TAAAGAGATATTAAA
1 TAAAGAGATATTAAA
70246 ATAACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (15 bp):
TAAAGAGATATTAAA
Found at i:72251 original size:15 final size:15
Alignment explanation
Indices: 72231--72261 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
72221 AATAAAAAAC
*
72231 AATAAAGAGATATTA
1 AATAAAAAGATATTA
72246 AATAAAAAGATATTA
1 AATAAAAAGATATTA
72261 A
1 A
72262 CACAACAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (15 bp):
AATAAAAAGATATTA
Found at i:73379 original size:15 final size:15
Alignment explanation
Indices: 73359--73388 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
73349 AATAAAAAAC
73359 AATAAAGAGATATTA
1 AATAAAGAGATATTA
73374 AATAAAGAGATATTA
1 AATAAAGAGATATTA
73389 TTAAGACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (15 bp):
AATAAAGAGATATTA
Found at i:74475 original size:14 final size:15
Alignment explanation
Indices: 74456--74486 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
74446 CCTAAAAAAC
74456 AATAAAGAGAT-TTA
1 AATAAAGAGATATTA
74470 AATAAAGAGATATTA
1 AATAAAGAGATATTA
74485 AA
1 AA
74487 ATAACAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (15 bp):
AATAAAGAGATATTA
Found at i:75624 original size:16 final size:15
Alignment explanation
Indices: 75589--75620 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
75579 AATAAAAAAC
75589 AATAAAGAGATATTA
1 AATAAAGAGATATTA
75604 AATAAAGAGATATTA
1 AATAAAGAGATATTA
75619 AA
1 AA
75621 ATAACAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (15 bp):
AATAAAGAGATATTA
Found at i:77348 original size:39 final size:42
Alignment explanation
Indices: 77267--77381 Score: 164
Period size: 39 Copynumber: 2.7 Consensus size: 42
77257 GTTTAGAGAA
77267 TTGCGAAGGCAAGAGAGAAGGGGAGGCTTTTAGATGAGGATTTGG
1 TTGCGAAGGCAAGAGAGAAGGGGAGGC-TTT--ATGAGGATTTGG
*
77312 TTGCGAAGGCAAGAGAGAGGGGGAGGCTTT-T-A-GATTTGG
1 TTGCGAAGGCAAGAGAGAAGGGGAGGCTTTATGAGGATTTGG
*
77351 TTGCGAAGGCAAGAGGGAAGGGGAGGCTTTA
1 TTGCGAAGGCAAGAGAGAAGGGGAGGCTTTA
77382 AAAGGATGTT
Statistics
Matches: 66, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
39 35 0.53
40 1 0.02
41 1 0.02
44 3 0.05
45 26 0.39
ACGTcount: A:0.28, C:0.08, G:0.43, T:0.21
Consensus pattern (42 bp):
TTGCGAAGGCAAGAGAGAAGGGGAGGCTTTATGAGGATTTGG
Done.