Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015440.1 Corchorus olitorius cultivar O-4 contig15473, 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: 123737
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--34 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35 AACAATCCCC
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):
TA
Found at i:2295 original size:32 final size:32
Alignment explanation
Indices: 2254--2320 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
2244 AATATTCAAG
2254 ACACCCCAAACCAACTAATTCCTGATTTAAAA
1 ACACCCCAAACCAACTAATTCCTGATTTAAAA
2286 ACACCCCAAACCAACTAATTCCTGATTTAAAA
1 ACACCCCAAACCAACTAATTCCTGATTTAAAA
2318 ACA
1 ACA
2321 GTTCAAGCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.45, C:0.31, G:0.03, T:0.21
Consensus pattern (32 bp):
ACACCCCAAACCAACTAATTCCTGATTTAAAA
Found at i:6911 original size:13 final size:13
Alignment explanation
Indices: 6893--6917 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6883 GATAGTCAAC
6893 AAACCGACTTCGT
1 AAACCGACTTCGT
6906 AAACCGACTTCG
1 AAACCGACTTCG
6918 GCTGATTTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (13 bp):
AAACCGACTTCGT
Found at i:8715 original size:31 final size:31
Alignment explanation
Indices: 8617--8740 Score: 144
Period size: 31 Copynumber: 4.1 Consensus size: 31
8607 GGTGTACGAC
8617 GTGGCACGCCACGTGCACCAAAAAGTGACAT
1 GTGGCACGCCACGTGCACCAAAAAGTGACAT
* *** *
8648 GTAGCACGCCACGTGTGTCAAAGAGTGACAT
1 GTGGCACGCCACGTGCACCAAAAAGTGACAT
*
8679 GTGGCACGCCACGTGCACCAAAAAGTGACAC
1 GTGGCACGCCACGTGCACCAAAAAGTGACAT
* * * *
8710 ATGGCATGCCACATGCA-CAAAAA-TAACAT
1 GTGGCACGCCACGTGCACCAAAAAGTGACAT
8739 GT
1 GT
8741 ACTAGTCCAT
Statistics
Matches: 76, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
29 5 0.07
30 6 0.08
31 65 0.86
ACGTcount: A:0.34, C:0.27, G:0.24, T:0.15
Consensus pattern (31 bp):
GTGGCACGCCACGTGCACCAAAAAGTGACAT
Found at i:13675 original size:21 final size:20
Alignment explanation
Indices: 13632--13680 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
13622 GAACTCGAAG
*
13632 TTTATTTATTTATTGTTTTT
1 TTTATTTATTTATTGTTTGT
13652 TTTAGTTTATTTATT-TATTGT
1 TTTA-TTTATTTATTGT-TTGT
13673 TTT-TTTAT
1 TTTATTTAT
13681 ATTTACAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 5 0.19
21 16 0.62
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (20 bp):
TTTATTTATTTATTGTTTGT
Found at i:13685 original size:25 final size:25
Alignment explanation
Indices: 13630--13678 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
13620 GAGAACTCGA
13630 AGTTTATTTATTTATTGTTTTTTTT
1 AGTTTATTTATTTATTGTTTTTTTT
13655 AGTTTATTTATTTATTGTTTTTTT
1 AGTTTATTTATTTATTGTTTTTTT
13679 ATATTTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (25 bp):
AGTTTATTTATTTATTGTTTTTTTT
Found at i:17766 original size:18 final size:18
Alignment explanation
Indices: 17740--17778 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
17730 GTAAATATTG
*
17740 TACATCCAAACTTTTGTA
1 TACAACCAAACTTTTGTA
17758 TACAACCAAACTTTTGTA
1 TACAACCAAACTTTTGTA
17776 TAC
1 TAC
17779 TGTTGGAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (18 bp):
TACAACCAAACTTTTGTA
Found at i:18764 original size:42 final size:42
Alignment explanation
Indices: 18717--18802 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
18707 TGAAAGAAGA
* * *
18717 TACTTTGATTACATAA-AGTTGTCATAATTCGAACCTAATCAC
1 TACTTTAATTACATAAGA-TTGTCATAATTCAAACCCAATCAC
* *
18759 TACTTTAATTACCTAAGATTGTCTTAATTCAAACCCAATCAC
1 TACTTTAATTACATAAGATTGTCATAATTCAAACCCAATCAC
18801 TA
1 TA
18803 AAATCAAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
42 37 0.97
43 1 0.03
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (42 bp):
TACTTTAATTACATAAGATTGTCATAATTCAAACCCAATCAC
Found at i:20484 original size:15 final size:14
Alignment explanation
Indices: 20464--20493 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
20454 AATTGTGATA
20464 ATTAATTTTATATTT
1 ATTAATTTTA-ATTT
20479 ATTAATTTTAATTT
1 ATTAATTTTAATTT
20493 A
1 A
20494 CATGAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTAATTTTAATTT
Found at i:25610 original size:36 final size:36
Alignment explanation
Indices: 25570--25639 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
25560 TGACAGTTGT
*
25570 TCATTTAGAAGCAGGAGTGCTAGAATACGAGTATAA
1 TCATTTAGAAGAAGGAGTGCTAGAATACGAGTATAA
* * *
25606 TCATTTAGAAGAAGGATTGCTAGGATATGAGTAT
1 TCATTTAGAAGAAGGAGTGCTAGAATACGAGTAT
25640 GATCGACTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.29
Consensus pattern (36 bp):
TCATTTAGAAGAAGGAGTGCTAGAATACGAGTATAA
Found at i:33163 original size:21 final size:21
Alignment explanation
Indices: 33137--33180 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
33127 TCTGCATCAA
33137 ATAAGAAAGAACCAGACTAGG
1 ATAAGAAAGAACCAGACTAGG
33158 ATAAGAAAGAACCAGACTAGG
1 ATAAGAAAGAACCAGACTAGG
33179 AT
1 AT
33181 GCTTAATGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.23, T:0.11
Consensus pattern (21 bp):
ATAAGAAAGAACCAGACTAGG
Found at i:33330 original size:235 final size:235
Alignment explanation
Indices: 32919--33370 Score: 868
Period size: 235 Copynumber: 1.9 Consensus size: 235
32909 ACATATCCCA
32919 TAGGATAAGAAAGAACCAGACTAGGATGCTTAATGCCAATATAAAGTTATAAAATGCAAAGTAGA
1 TAGGATAAGAAAGAACCAGACTAGGATGCTTAATGCCAATATAAAGTTATAAAATGCAAAGTAGA
32984 CTTAAAGCCCTAATACTTGGAAAATAAACAAAATCCTCAAATAGCCTTGATTATTTAAATTCGCT
66 CTTAAAGCCCTAATACTTGGAAAATAAACAAAATCCTCAAATAGCCTTGATTATTTAAATTCGCT
33049 AAATTGCTAACTCTATAAAAGTTTGCAAGGACATAATAACAGTGTTAAGTTTTTCATCATCAGTT
131 AAATTGCTAACTCTATAAAAGTTTGCAAGGACATAATAACAGTGTTAAGTTTTTCATCATCAGTT
33114 AGCCTCTTTGCACTCTGCATCAAATAAGAAAGAACCAGAC
196 AGCCTCTTTGCACTCTGCATCAAATAAGAAAGAACCAGAC
*
33154 TAGGATAAGAAAGAACCAGACTAGGATGCTTAATGCCAATATAAAGTTATAAAGTGCAAAGTAGA
1 TAGGATAAGAAAGAACCAGACTAGGATGCTTAATGCCAATATAAAGTTATAAAATGCAAAGTAGA
33219 CTTAAAGCCCTAATACTTGGAAAATAAACAAAATCCTCAAATAGCCTTGATTATTTAAATTCGCT
66 CTTAAAGCCCTAATACTTGGAAAATAAACAAAATCCTCAAATAGCCTTGATTATTTAAATTCGCT
* *
33284 AAATTGCTAACTCTTTAAAAGTTTGCAAGGACATGATAACAGTGTTAAGTTTTTCATCATCAGTT
131 AAATTGCTAACTCTATAAAAGTTTGCAAGGACATAATAACAGTGTTAAGTTTTTCATCATCAGTT
*
33349 AGCCTCTTTGCATTCTGCATCA
196 AGCCTCTTTGCACTCTGCATCA
33371 GATAGTTGCT
Statistics
Matches: 213, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
235 213 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (235 bp):
TAGGATAAGAAAGAACCAGACTAGGATGCTTAATGCCAATATAAAGTTATAAAATGCAAAGTAGA
CTTAAAGCCCTAATACTTGGAAAATAAACAAAATCCTCAAATAGCCTTGATTATTTAAATTCGCT
AAATTGCTAACTCTATAAAAGTTTGCAAGGACATAATAACAGTGTTAAGTTTTTCATCATCAGTT
AGCCTCTTTGCACTCTGCATCAAATAAGAAAGAACCAGAC
Found at i:36514 original size:64 final size:64
Alignment explanation
Indices: 36412--36533 Score: 201
Period size: 64 Copynumber: 1.9 Consensus size: 64
36402 TTTAGCCTTA
* *
36412 GCCAATTCTCGAAAATTTTCCTCAATTTTTTGCTACAATACTCGTAAAAAATATATGAAGCGTG
1 GCCAATTCTCGAAAATTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATATATGAAGCGTG
*
36476 GCCAATTCTTGAAAATTTTCCTCAATTTTTGG-TCACAATACTCATAAAAAATATATGA
1 GCCAATTCTCGAAAATTTTCCTCAATTTTTGGCT-ACAATACTCATAAAAAATATATGA
36534 TTCAAAGCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 1 0.02
64 53 0.98
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (64 bp):
GCCAATTCTCGAAAATTTTCCTCAATTTTTGGCTACAATACTCATAAAAAATATATGAAGCGTG
Found at i:37100 original size:333 final size:334
Alignment explanation
Indices: 36487--37143 Score: 815
Period size: 333 Copynumber: 2.0 Consensus size: 334
36477 CCAATTCTTG
* * * *
36487 AAAATTTTCCTCAATTTTTGGTCACAATACTCATAAAAAATATATGATTCAAAGCAAAAAAGATT
1 AAAATTTTCCTCAATTTTTGGTCACAATAATCAGAAAAAATATATAATTCAAACCAAAAAAGATT
* * *
36552 AAAGGATTTTTCAAGCATCTAATATCGCTTTTCCAATTTTTTCTGAATTAATTTCTGACTAAATC
66 AAAGGATTTTTCAACCATCTAATATCGCTTTTCCAATCTTTTCTGAATTAATTTCTAACTAAATC
* * * * * * *
36617 GAAATATTATTTAGATTCTCGTAAAAATAAATCCTTAAATCCAACATGGTTGAGATTTGGTAAGA
131 GAAACATGATTCAGATGCTCGTAAAAACAAATCATTAAATCCAACATGGTCGAGATTTGGTAAGA
* * * *
36682 TGCATATAGATATTTCAAGGAGTTTAGGAGCCAAAAATCAAGCAAAACTGAGTTAGGGCCCTGGA
196 TGAATATAGATATTTCAAGAAGTCTAGGAGCCAAAAATCAAGCAAAACTGAGTTAGGGCCCTGAA
* * * *
36747 ACGCATTTTTAGTCAAAAACCGTGATGATTAGTACATGATTTCGGAT-GAATTTTGCAAAAAAAA
261 ACGCATTTTTAGGCAAAAACCGTGATGAGTAGTACACGATTTCGGATAAAATTTTGCAAAAAAAA
36811 AAGATCCCA
326 AAGATCCCA
* *
36820 AAAATTCTTCCTCAATTTTT-GTCCACAATAATCAGGAAAAATATATAATTCAACTCCAAAAAA-
1 AAAATT-TTCCTCAATTTTTGGT-CACAATAATCAGAAAAAATATATAATTCAA-ACCAAAAAAG
* * * * *
36883 ATTGAAGGGCTTTTT-AACCATCTAATATCGCTTTTCCTA-CTTTTCTGAATTAATTTTTAATTA
63 ATT-AAAGGATTTTTCAACCATCTAATATCGCTTTTCCAATCTTTTCTGAATTAATTTCTAACTA
* * ** * *
36946 AATCGAAACATGATTCAGATGCTTGTATAAACAAATCATTAAATCCAATGTGGTCGGGATTTGTT
127 AATCGAAACATGATTCAGATGCTCGTAAAAACAAATCATTAAATCCAACATGGTCGAGATTTGGT
* * * * * *
37011 TAGATGAATATAGATATTTCATGAAGTCTGGGCGCCAAAAATGAAGCAAAACTGAG-TCGCGGCC
192 AAGATGAATATAGATATTTCAAGAAGTCTAGGAGCCAAAAATCAAGCAAAACTGAGTTAG-GGCC
* * *
37075 AC-GAAACGCGTTTTTAGGCAAAAACCGTGATGGGTAGTACACGATTTCGGCTAAAATTTTGCAA
256 -CTGAAACGCATTTTTAGGCAAAAACCGTGATGAGTAGTACACGATTTCGGATAAAATTTTGCAA
37139 AAAAA
320 AAAAA
37144 TATCCGAAAA
Statistics
Matches: 273, Mismatches: 44, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
332 2 0.01
333 175 0.64
334 80 0.29
335 16 0.06
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (334 bp):
AAAATTTTCCTCAATTTTTGGTCACAATAATCAGAAAAAATATATAATTCAAACCAAAAAAGATT
AAAGGATTTTTCAACCATCTAATATCGCTTTTCCAATCTTTTCTGAATTAATTTCTAACTAAATC
GAAACATGATTCAGATGCTCGTAAAAACAAATCATTAAATCCAACATGGTCGAGATTTGGTAAGA
TGAATATAGATATTTCAAGAAGTCTAGGAGCCAAAAATCAAGCAAAACTGAGTTAGGGCCCTGAA
ACGCATTTTTAGGCAAAAACCGTGATGAGTAGTACACGATTTCGGATAAAATTTTGCAAAAAAAA
AAGATCCCA
Found at i:37590 original size:22 final size:22
Alignment explanation
Indices: 37549--37590 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
37539 TGCTGCTTAA
*
37549 GCACGTCGGTCGCGCTGTGCCG
1 GCACGTCGGTCGCGCCGTGCCG
* *
37571 GCACGTGGGTCGTGCCGTGC
1 GCACGTCGGTCGCGCCGTGC
37591 TAGCCCATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.05, C:0.33, G:0.43, T:0.19
Consensus pattern (22 bp):
GCACGTCGGTCGCGCCGTGCCG
Found at i:38795 original size:333 final size:333
Alignment explanation
Indices: 37764--42779 Score: 6439
Period size: 333 Copynumber: 15.2 Consensus size: 333
37754 CTGGACGCAA
* * * * *
37764 AAAAATCAAGCAAAACTGAGTCGGGGCTCCAGAACGCGTTTTTAGCCAAAAACCCTGATAGTTAG
1 AAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
* *
37829 TACACGATTTCGGCTAAAATTTTGCAAAAAAAGATCCGAAAAATATTTTCTCAATTTTTGACCAC
66 TACACGATTTCGGCTAAAATTTTGCAAAAATAGATCCGAAAAATATTTCCTCAATTTTTGACCAC
37894 AATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAATA
131 AATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAATA
* *
37959 TCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAATATGATTCAGATGGTCGTAA
196 TCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGCTCGTAA
* * *
38024 AAATAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTCCATGGAGTA
261 AAACAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGGAGTC
38089 TGGGCGCC
326 TGGGCGCC
* ** *
38097 AAAAATCAAGCAAAACTGAGTCGGGGTGCCGGAACGCGTTTTTAGCCAGAAACCGTGATGGTTAG
1 AAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
*
38162 TACACGATTTCGGCTAAAATTTTGCAAAAATAGATCCGAAAAATA-TTACTCAATTTTTGA-CAG
66 TACACGATTTCGGCTAAAATTTTGCAAAAATAGATCCGAAAAATATTTCCTCAATTTTTGACCA-
*
38225 CAATTCTCATATAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAAT
130 CAATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAAT
* *
38290 ATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAATATGATTCAGATGGTCGTA
195 ATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGCTCGTA
* *
38355 AAAATAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTCCATGGAGT
260 AAAACAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGGAGT
*
38420 ATGGGCGCC
325 CTGGGCGCC
* * *
38429 AAAAATCAAGCAAAACTGAGTCGGGGTCCCGGAAC-CAGTTTTTAGCCAAAAACTGTGATGGTTA
1 AAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGC-GTTTTTAGCCAAAAACCGTGATGGTTA
* * * **
38493 GTACACGATTTCGGCTAAAATTTTACAAAAATAGATCCCAAAAATATTTACTCAATTTTTGAGAA
65 GTACACGATTTCGGCTAAAATTTTGCAAAAATAGATCCGAAAAATATTTCCTCAATTTTTGACCA
* ** *
38558 CAATTCTCATAAAAATATATATAATTCAACGCCAACAAGATTGAAGGGCTTTTCAAGCATATAAT
130 CAATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAAT
* * * * * * *
38623 ATTGCTTTTCCAAATTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTCGGATGCTCGTA
195 ATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGCTCGTA
* * * * * *
38688 AATACAAATCCTTAAATCCATTGTGGCCGAGATTCGGTTATATGAATATAGATATTTCATGGAGT
260 AAAACAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGGAGT
** *
38753 CT-TTCTGCA
325 CTGGGC-GCC
* * * *
38762 AAAAATCAAGCAAAACTGAGTCGATGCCCCGGAACGCGTTTTTAGCCAAAAACAGTGATCGTTAA
1 AAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
*
38827 TACACGATTTCGGCTAAAATTTTGCAGAAAAT-GACCCGAAAAATATTTCCTCAATTTTTTG-CC
66 TACACGATTTCGGCTAAAATTTTGCA-AAAATAGATCCGAAAAATATTTCCTCAA-TTTTTGACC
* * * *
38890 A-AATACTTAT-AAAA-ATATATAATTAAACGCCAAAAAGATTGAAGGTCTTTTTGAGCATCTAA
129 ACAATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAA
*
38952 TATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGGTCGT
194 TATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGCTCGT
* * *
39017 AAAAAGAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGACGAATATAGATATTCCATGGAG
259 AAAAACAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGGAG
*
39082 TATGGGCGCC
324 TCTGGGCGCC
* *
39092 AAAAATCAAGCAAAACTGAGTCGTGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
1 AAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
* * *
39157 TACACGATTTCGGCTAAAATTTTGCAGAAAAT-GACCCGAAAAGTATTTCCTCAATTTTTGACTA
66 TACACGATTTCGGCTAAAATTTTGCA-AAAATAGATCCGAAAAATATTTCCTCAATTTTTGACCA
* * * * *
39221 CAATACTTAT-AAAA-ATATATAATTAAACGCCAAAAAGATTGAAGGTCTTTTAGAGCATCTAAT
130 CAATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAAT
* *
39284 ATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTTATTAAATCGAAACATGATTCCGATGCTCGTA
195 ATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGCTCGTA
* * * * *
39349 AAAGCAAATCCTTATAACAAATGTGGCC-ATGATTCAGTTAGATGAATATAGATACTTCATGGAG
260 AAAACAAATCCTTAAAACCAATGCGGCCGA-GATTCAGTTAGATGAATATAGATATTTCATGGAG
39413 TCTGGGCGCC
324 TCTGGGCGCC
* * *
39423 AAAAATCAAGCAAAACTGAGTCGA-ACCCCGAAACGCATTTTTAGCCAAAAAACCGTGATGGTTA
1 AAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGCC-AAAAACCGTGATGGTTA
* * * *
39487 GTACACGATTTCGACTAGAATTTTGCAAAAA-ATATCCGAAAAATATTTTTCCTCAATTTTTTAC
65 GTACACGATTTCGGCTAAAATTTTGCAAAAATAGATCCGAAAAATA--TTTCCTCAATTTTTGAC
* * * *
39551 CACAGTTCCCATAAAAATATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTTGAGCAACTA
128 CACAATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTA
* * * *
39616 ATATCGGTTTTCCTGTTTTTTCTGAG-TAATTTTTCATTAAATCGAAACATGATTCAGATGGTCG
193 ATATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGCTCG
* *
39680 TAAAAAGAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTCCATGGA
258 TAAAAACAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGGA
*
39745 GTATGGGCGCC
323 GTCTGGGCGCC
* * *
39756 AAAAATCAAGTAAAACTGAGTC-ATGGTCCCGGAACGCGTTTTTGGCCAAAAACCGTGATGGTTA
1 AAAAATCAAGCAAAACTGAGTCGA-GGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* *
39820 GTACACGATTTCGGCTAAAATTTTGCAAAAAAAAATATCCGAAAAATATTTCCTCAATATTTT-A
65 GTACACGATTTCGGCTAAAATTTTGC--AAAAATAGATCCGAAAAATATTTCCTCAAT-TTTTGA
* *
39884 CCACAATTCTCAT-AAAATATGTATAATTCAACGCCAAAAAGTTTGAAGGGCTTTTTGAGCATCT
127 CCACAATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCT
* *
39948 AATATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTTATTAAATCGAAACATAATTCAGATGCTC
192 AATATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGCTC
* * * * * * * *
40013 GTTAAAATAAATCCTTCAACCCATTGTGGCCGAGATTCACTTACATGAATATAGATATTTCATGG
257 GTAAAAACAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGG
* *
40078 AGTCTGGCCGCA
322 AGTCTGGGCGCC
**
40090 AAAAATCAAGCAAAACTGAGTCG-GGTCCTTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
1 AAAAATCAAGCAAAACTGAGTCGAGG-CCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* * **
40154 GTACACGATTTCGGCTAAAATTTTGCAGAAAAT-GACCCGAAAAATTTTTCCTCAATTTTTTTTC
65 GTACACGATTTCGGCTAAAATTTTGCA-AAAATAGATCCGAAAAATATTTCCTCAA-TTTTTGAC
* * *
40218 CACAATACTTAT-AAAA-ATATATAATTAAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTA
128 CACAATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTA
* * *
40281 ATATTGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAAATGGTCG
193 ATATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGCTCG
* * * ** * * *
40346 GAAAAACAAATCCTTAAATCCAATACGGCTAATATTCATTTAGATGAATATAGATATTCCATGGA
258 TAAAAACAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGGA
* *
40411 GTATGGGTGCC
323 GTCTGGGCGCC
* *
40422 AAAAATCAAGCAAAACTGAGTCTG-GGCTCCAGAACGCG----T------------T--T--TTA
1 AAAAATCAAGCAAAACTGAGTC-GAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* *
40466 GTACACGATTTCGGCTAAAATTTTGCAAAAAAAGATCCAAAAAATA-TT-CTCAATTTTTGACCA
65 GTACACGATTTCGGCTAAAATTTTGCAAAAATAGATCCGAAAAATATTTCCTCAATTTTTGACCA
* *
40529 AAATTCTCATAAAAATATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTTGAGCATCTAAT
130 CAATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAAT
* * * *
40594 ATCGTTTTTCCTGTTTTTT-TGAGTTAATTTTTCATTAAATAGAAACATGATTCAGATGGTCGTA
195 ATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGCTCGTA
* * * * *
40658 AAAAGAAATTCTTAAAACCAATGCGGCCGATATTCAGTTAGATGAATATGGATATTCCATGGAG-
260 AAAACAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGGAGT
40722 CATGGGCGCC
325 C-TGGGCGCC
* ** * *
40732 AAAAATCAAGCAAAACTGAGTCGTGATCCCGGAACGCGTTTTTAGCCAACAACCGTGATGGTTTG
1 AAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
* * * *
40797 TACACGATTTCGGCTAAAATTTTACAAAAAAAATATCTGAAAAATATTTCCTCAATATTTT-ACC
66 TACACGATTTCGGCTAAAATTTTGC-AAAAATAGATCCGAAAAATATTTCCTCAAT-TTTTGACC
* *
40861 ACAATTCTTATAAAAATATGTATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAA
129 ACAATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAA
*
40926 TATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTTATTAAATCGAAACATGATTCAGATGCTCGT
194 TATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGCTCGT
* * * * * * * *
40991 TAAAATAAATGCTTAAACCCATTGTGGCCGAGATTCTGTTATATGAATATAGATATTTCATGGAG
259 AAAAACAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGGAG
* *
41056 TCTGGCCGCA
324 TCTGGGCGCC
* * * * *
41066 AAAAATCAAGCCAAACTGAGTCGAGGCCCTGGAACGCGTATTTAGCCATAAACCGTGATGGTTAC
1 AAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
** * * * *
41131 TACACGATTTCACCTAAAATTTTGCAAAAGTAGATCCGAAAAATATTTACTCAATTTTTGACAAA
66 TACACGATTTCGGCTAAAATTTTGCAAAAATAGATCCGAAAAATATTTCCTCAATTTTTGACCAC
* * * ** *
41196 AATTCTCATAAAAATATATATAATTCAATGCCAACAATATTGAAGGGCTTTTCAAGCATATAATA
131 AATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAATA
* * * * * *
41261 TTGCTTTTCCAATTTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTCGGATGCTCGTAA
196 TCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGCTCGTAA
* * * * *
41326 AAAC-AATCCTTAAATCCATTGTGGCCGAGATTCAGTTATATGAATATAGATATTTCATGGAGTT
261 AAACAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGGAGTC
* *
41390 TGGCCGCA
326 TGGGCGCC
* *
41398 AAAAATCAAGCAAAACTGAGCCGAGGCCCCGGAACGCGATTTTAGCCAAAAACCGTGATGGTTAG
1 AAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
* * * *
41463 TACACGATTTCGTCTAAAATTTTGCAAAAATAGATCCGAAAAATATTTTTGCTCAATTTTTTACA
66 TACACGATTTCGGCTAAAATTTTGCAAAAATAGATCCGAAAAATA--TTTCCTCAATTTTTGACC
* ** *
41528 ACAATTCTCATAAAAATATATATAATTCAACGCCAACAAGATTGAAGGGCTTTTCAAGCATATAA
129 ACAATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAA
* * * * * *
41593 TATTGTTTTTCCAATTTTATCTGAATTAATTTCTGATTAAATCGAAACATGATTC-GAATGCTTG
194 TATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAG-ATGCTCG
* * * *
41657 TAAAATCAATTCCTTAAAACCAATGCGGCCAAGATTCAGTTAGATGAATATAGATATTTCGTGGA
258 TAAAAACAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGGA
41722 GTCTGGGCGCC
323 GTCTGGGCGCC
** * *
41733 AAAAATCAAGCAAAACTGAGTCG-GAGCCCCAAAACGCATTTTTAGCCAAAAAACTGTGATGGTT
1 AAAAATCAAGCAAAACTGAGTCGAG-GCCCCGGAACGCGTTTTTAGCC-AAAAACCGTGATGGTT
* * * *
41797 AGTACACGATTTCGACTAAAATTTTGCAAAAAAATATCCGAAAAATATTTCCTCAATTTTTTACC
64 AGTACACGATTTCGGCTAAAATTTTGCAAAAATAGATCCGAAAAATATTTCCTCAATTTTTGACC
* * *
41862 ACAATTCTCATAAATATATATATATATATATAATTCAACGTCAAAAAATATTGAAGGGC-TTTTA
129 ACAATTCTC----ATA-A-A-A-ATATATATAATTCAACG-CCAAAAAGATTGAAGGGCTTTTTG
* * *
41926 AGCATCTAATATCATTTTTTCCTATTTTTTCTGAATTAATTTCTTATTAAATCGAAACATGATTC
185 AGCATCTAATATC-GTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTC
* * * *
41991 AAATGCTCGTAAAAACAAATCCTTAAAATCTATGCGGCCAAGATTCAGTTAGATGAATATAGATA
249 AGATGCTCGTAAAAACAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATA
* * *
42056 TTCCATGGAGTATGGGTGCC
314 TTTCATGGAGTCTGGGCGCC
* *
42076 AAAAATCAAGCAAAACTGTGTCAGAGG-CCCGGAACGTGTTTTTAGCCAAAAA-C----------
1 AAAAATCAAGCAAAACTGAGTC-GAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* * *
42129 ---CACGATTTCGGCTAAAATTTTGCAAATATGGATCCGAAAAATATTTCTTCAATTTTTGACCA
65 GTACACGATTTCGGCTAAAATTTTGCAAAAATAGATCCGAAAAATATTTCCTCAATTTTTGACCA
* * * * * * ** *
42191 CAATTCTCCTAATAATGTATATAATTCAACACCAACAAGATTGAAGAGCTTTTCAAGCATATAAT
130 CAATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAAT
* * * * * * *
42256 ATCGCTTTTCCTATTTTTTCTAAATTTATTTCTAATTAAACCGAAACATGATTCGGATGCTCGTA
195 ATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGCTCGTA
* * * *
42321 AAAACAAATCTTTAAATCCAATGTGGCCGAGATTCGGTTAGATGAATATAGATATTTCATGGAGT
260 AAAACAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGGAGT
* * *
42386 CTGGCCTCA
325 CTGGGCGCC
* ** *
42395 AAAAATCAAGCAAAACTGAGTCGGGGCCTTGGAACGCGTTTTTAGCCAAAAACGGTGATGGTTAG
1 AAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
* * * *
42460 TACACGATTTTGGCGTAAAATTTTGCAAAAAAAGATCCGAAAATTTTTTCCTCAATTTTTGACCA
66 TACACGATTTCGGC-TAAAATTTTGCAAAAATAGATCCGAAAAATATTTCCTCAATTTTTGACCA
* * * *
42525 AAATTCTCATAAAAATATATATAATAT-AATGCCAGAAAGATTGAAGGGCTTTTCGAGCATCTAA
130 CAATTCTCATAAAAATATATATAAT-TCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAA
* * * * * *
42589 TATCGTTTTTCCTATTTTTT-TGAATTAATTGCTGATTAAGTCGAATCATGATTCAGATGCTCGC
194 TATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGCTCGT
* * * * *
42653 AAAAACAAATCCTTAAATCCAATGTGGCCGAGATTC-GCTTAGATTAATATAGGTATTTCTTGGA
259 AAAAACAAATCCTTAAAACCAATGCGGCCGAGATTCAG-TTAGATGAATATAGATATTTCATGGA
* *
42717 CTCTGGGTGCC
323 GTCTGGGCGCC
* *
42728 AAAAATCAAGCAAAACTGAGTCGAGGCCTCGAAACGCGTTTTTAGCCAAAAA
1 AAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGCCAAAAA
42780 ATTATGGTTA
Statistics
Matches: 4121, Mismatches: 460, Indels: 204
0.86 0.10 0.04
Matches are distributed among these distances:
309 16 0.00
310 145 0.04
311 70 0.02
312 40 0.01
314 2 0.00
316 1 0.00
318 3 0.00
319 172 0.04
320 31 0.01
321 1 0.00
323 1 0.00
324 2 0.00
326 1 0.00
328 65 0.02
329 6 0.00
330 333 0.08
331 276 0.07
332 739 0.18
333 1054 0.26
334 762 0.18
335 109 0.03
336 73 0.02
338 3 0.00
339 1 0.00
340 1 0.00
341 1 0.00
342 37 0.01
343 173 0.04
344 2 0.00
345 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (333 bp):
AAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
TACACGATTTCGGCTAAAATTTTGCAAAAATAGATCCGAAAAATATTTCCTCAATTTTTGACCAC
AATTCTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTGAGCATCTAATA
TCGTTTTTCCTATTTTTTCTGAGTTAATTTCTCATTAAATCGAAACATGATTCAGATGCTCGTAA
AAACAAATCCTTAAAACCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGGAGTC
TGGGCGCC
Found at i:42873 original size:662 final size:658
Alignment explanation
Indices: 40463--42830 Score: 2759
Period size: 662 Copynumber: 3.6 Consensus size: 658
40453 GAACGCGTTT
* *
40463 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAAAAGATCCAAAAAATA-TT-CTCAATTTTTGA
1 TTAGTACACGATTTCGACTAAAATTTTGCAAAAAAAGATCCGAAAAATATTTCCTCAATTTTTGA
* **
40526 CCAAAATTCTCATAAAAATATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTTGAGCATCT
66 CCAAAATTCTCATAAAAATATATATAATTCAATGCCAAAAATATTGAAGGGCTTTTCAAGCATCT
* * * * * *
40591 AATATCGTTTTTCCTGTTTTTT-TGAGTTAATTTTTCATTAAATAGAAACATGATTCAGATGGTC
131 AATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTCAGATGCTC
* * * * *
40655 GTAAAAAGAAATTCTTAAAACCAATGCGGCCGATATTCAGTTAGATGAATATGGATATTCCATGG
196 GTAAAAACAAATCCTTAAATCCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTCCATGG
* *
40720 AGC-ATGGGCGCCAAAAATCAAGCAAAACTGAGTCGTGATCCCGGAACGCGTTTTTAGCCAACAA
261 A-CTATGGGCGCCAAAAATCAAGCAAAACTGAGTCGAG-GCCCGGAACGCGTTTTTAGCCAA-AA
* * * * * * * ** *
40784 CCGTGATGGTTTGTACACGATTTCGGCTAAAATTTTACAAAAAAAATATCTGAAAAATATTTCCT
323 ACATGATGGTTAGCACA-AATGTC-G--AAAATTTTAC-AAAAATAGGTCCGAAAAATATTTCCT
* * * *
40849 CAATATTTTACCACAATTCTTATAAAAATATGTATAATTCAACGCCAAAAAGATTGAAGGGCTTT
383 CAATA-TTTAACACAATTCTCATAAAAATATATATAATTCAACGCCAACAAGATTGAAGGGCTTT
** * * *
40914 TTGAGCATCTAATATCGTTTTTCCTATTTTTTCTGAGTTAATTTCTTATTAAATCGAAACATGAT
447 TCAAGCATATAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACATGAT
* * * * * * *
40979 TCAGATGCTCGTTAAAATAAATGCTTAAACCCATTGTGGCCGAGATTCTGTTATATGAATATAGA
512 TCGGATGCTCGTAAAAACAAAT-CTTAAAACCAATGTGGCCGAGATTCAGTTAGATGAATATAGA
* * *
41044 TATTTCATGGAGTCTGGCCGCAAAAAATCAAGCCAAACTGAGTCGAGGCCCTGGAACGCGTATTT
576 TATTTCATGGAGTCTGGCCGCAAAAAATCAAGCAAAACTGAGTCGGGGCCCTGGAACGCGTTTTT
*
41109 AGCCATAAACCGTGATGG
641 AGCCAAAAACCGTGATGG
* ** *
41127 TTACTACACGATTTC-ACCTAAAATTTTGCAAAAGTAGATCCGAAAAATATTTACTCAATTTTTG
1 TTAGTACACGATTTCGA-CTAAAATTTTGCAAAAAAAGATCCGAAAAATATTTCCTCAATTTTTG
* * *
41191 ACAAAAATTCTCATAAAAATATATATAATTCAATGCCAACAATATTGAAGGGCTTTTCAAGCATA
65 ACCAAAATTCTCATAAAAATATATATAATTCAATGCCAAAAATATTGAAGGGCTTTTCAAGCATC
* * * *
41256 TAATATTGCTTTTCCAATTTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTCGGATGCT
130 TAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTCAGATGCT
* * * *
41321 CGTAAAAAC-AATCCTTAAATCCATTGTGGCCGAGATTCAGTTATATGAATATAGATATTTCATG
195 CGTAAAAACAAATCCTTAAATCCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTCCATG
* * * * * *
41385 GAGTTTGGCCGCAAAAAATCAAGCAAAACTGAGCCGAGGCCCCGGAACGCGATTTTAGCCAAAAA
260 GACTATGGGCGCCAAAAATCAAGCAAAACTGAGTCGAGG-CCCGGAACGCGTTTTTAGCCAAAAA
* ** * * * *
41450 CCGTGATGGTTAGTACACGATTTCGTCTAAAATTTTGCAAAAATAGATCCGAAAAATATTTTTGC
324 -CATGATGGTTAG--CAC-AAAT-GTCGAAAATTTTACAAAAATAGGTCCGAAAAATA--TTTCC
* *
41515 TCAATTTTTTACAACAATTCTCATAAAAATATATATAATTCAACGCCAACAAGATTGAAGGGCTT
382 TCAATATTTAAC-ACAATTCTCATAAAAATATATATAATTCAACGCCAACAAGATTGAAGGGCTT
* * * *
41580 TTCAAGCATATAATATTGTTTTTCCAATTTTATCTGAATTAATTTCTGATTAAATCGAAACATGA
446 TTCAAGCATATAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACATGA
* * * * * *
41645 TTCGAATGCTTGTAAAATCAATTCCTTAAAACCAATGCGGCCAAGATTCAGTTAGATGAATATAG
511 TTCGGATGCTCGTAAAAACAAAT-CTTAAAACCAATGTGGCCGAGATTCAGTTAGATGAATATAG
* * * * *** *
41710 ATATTTCGTGGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGTCGGAGCCCCAAAACGCATTTT
575 ATATTTCATGGAGTCTGGCCGCAAAAAATCAAGCAAAACTGAGTCGGGGCCCTGGAACGCGTTTT
*
41775 TAGCCAAAAAACTGTGATGG
640 TAGCC-AAAAACCGTGATGG
* *
41795 TTAGTACACGATTTCGACTAAAATTTTGCAAAAAAATATCCGAAAAATATTTCCTCAATTTTTTA
1 TTAGTACACGATTTCGACTAAAATTTTGCAAAAAAAGATCCGAAAAATATTTCCTCAATTTTTGA
* * *
41860 CCACAATTCTCATAAATATATATATATATATATAATTCAACGTCAAAAAATATTGAAGGGCTTTT
66 CCAAAATTCTC----ATA-A-A-A-ATATATATAATTCAATG-CCAAAAATATTGAAGGGCTTTT
* *
41925 -AAGCATCTAATATCATTTTTTCCTATTTTTTCTGAATTAATTTCTTATTAAATCGAAACATGAT
122 CAAGCATCTAATATC-GTTTTTCCTATTTTTTCTGAATTAATTTCTGATTAAATCGAAACATGAT
* * *
41989 TCAAATGCTCGTAAAAACAAATCCTTAAAAT-CTATGCGGCCAAGATTCAGTTAGATGAATATAG
186 TCAGATGCTCGTAAAAACAAATCCTT-AAATCCAATGCGGCCGAGATTCAGTTAGATGAATATAG
* * * *
42053 ATATTCCATGGAGTATGGGTGCCAAAAATCAAGCAAAACTGTGTCAGAGGCCCGGAACGTGTTTT
250 ATATTCCATGGACTATGGGCGCCAAAAATCAAGCAAAACTGAGTC-GAGGCCCGGAACGCGTTTT
* * * * *
42118 TAGCCAAAAACCACGAT--TT----C----GGCTAAAATTTTGCAAATAT-GGATCCGAAAAATA
314 TAGCCAAAAA-CATGATGGTTAGCACAAATGTCGAAAATTTTACAAAAATAGG-TCCGAAAAATA
* * * * * * *
42172 TTTCTTCAATTTTTGACCACAATTCTCCTAATAATGTATATAATTCAACACCAACAAGATTGAAG
377 TTTCCTCAATATTT-AACACAATTCTCATAAAAATATATATAATTCAACGCCAACAAGATTGAAG
* * * * *
42237 AGCTTTTCAAGCATATAATATCGCTTTTCCTATTTTTTCTAAATTTATTTCTAATTAAACCGAAA
441 GGCTTTTCAAGCATATAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAA
* *
42302 CATGATTCGGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCCGAGATTCGGTTAGATGAA
506 CATGATTCGGATGCTCGTAAAAACAAATC-TTAAAACCAATGTGGCCGAGATTCAGTTAGATGAA
* *
42367 TATAGATATTTCATGGAGTCTGGCCTCAAAAAATCAAGCAAAACTGAGTCGGGGCCTTGGAACGC
570 TATAGATATTTCATGGAGTCTGGCCGCAAAAAATCAAGCAAAACTGAGTCGGGGCCCTGGAACGC
*
42432 GTTTTTAGCCAAAAACGGTGATGG
635 GTTTTTAGCCAAAAACCGTGATGG
* * * *
42456 TTAGTACACGATTTTGGCGTAAAATTTTGCAAAAAAAGATCCGAAAATTTTTTCCTCAATTTTTG
1 TTAGTACACGATTTCGAC-TAAAATTTTGCAAAAAAAGATCCGAAAAATATTTCCTCAATTTTTG
* * *
42521 ACCAAAATTCTCATAAAAATATATATAATAT-AATGCCAGAAAGATTGAAGGGCTTTTCGAGCAT
65 ACCAAAATTCTCATAAAAATATATATAAT-TCAATGCCAAAAATATTGAAGGGCTTTTCAAGCAT
* * *
42585 CTAATATCGTTTTTCCTATTTTTT-TGAATTAATTGCTGATTAAGTCGAATCATGATTCAGATGC
129 CTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTCAGATGC
* * * * * *
42649 TCGCAAAAACAAATCCTTAAATCCAATGTGGCCGAGATTC-GCTTAGATTAATATAGGTATTTCT
194 TCGTAAAAACAAATCCTTAAATCCAATGCGGCCGAGATTCAG-TTAGATGAATATAGATATTCCA
* * *
42713 TGGACTCTGGGTGCCAAAAATCAAGCAAAACTGAGTCGAGGCCTCGAAACGCGTTTTTAGCCAAA
258 TGGACTATGGGCGCCAAAAATCAAGCAAAACTGAGTCGAGGCC-CGGAACGCGTTTTTAGCCAAA
* * * * *
42778 AA-ATTATGGTTAGCCCAAAATGTC-CAAATTTTAACAAAAATAGGCCCTAAAAA
322 AACATGATGGTTAGCAC-AAATGTCGAAAATTTT-ACAAAAATAGGTCCGAAAAA
42831 GCCCATTTCC
Statistics
Matches: 1449, Mismatches: 204, Indels: 105
0.82 0.12 0.06
Matches are distributed among these distances:
650 3 0.00
651 11 0.01
652 141 0.10
653 34 0.02
654 27 0.02
655 2 0.00
656 2 0.00
657 1 0.00
658 3 0.00
660 7 0.00
661 45 0.03
662 286 0.20
663 2 0.00
664 72 0.05
665 21 0.01
666 212 0.15
667 268 0.18
668 81 0.06
669 4 0.00
670 1 0.00
672 3 0.00
673 1 0.00
674 1 0.00
675 1 0.00
676 30 0.02
677 81 0.06
678 101 0.07
679 8 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (658 bp):
TTAGTACACGATTTCGACTAAAATTTTGCAAAAAAAGATCCGAAAAATATTTCCTCAATTTTTGA
CCAAAATTCTCATAAAAATATATATAATTCAATGCCAAAAATATTGAAGGGCTTTTCAAGCATCT
AATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTCAGATGCTC
GTAAAAACAAATCCTTAAATCCAATGCGGCCGAGATTCAGTTAGATGAATATAGATATTCCATGG
ACTATGGGCGCCAAAAATCAAGCAAAACTGAGTCGAGGCCCGGAACGCGTTTTTAGCCAAAAACA
TGATGGTTAGCACAAATGTCGAAAATTTTACAAAAATAGGTCCGAAAAATATTTCCTCAATATTT
AACACAATTCTCATAAAAATATATATAATTCAACGCCAACAAGATTGAAGGGCTTTTCAAGCATA
TAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACATGATTCGGATGCT
CGTAAAAACAAATCTTAAAACCAATGTGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGG
AGTCTGGCCGCAAAAAATCAAGCAAAACTGAGTCGGGGCCCTGGAACGCGTTTTTAGCCAAAAAC
CGTGATGG
Found at i:45527 original size:20 final size:20
Alignment explanation
Indices: 45498--45568 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
45488 CGGCACATTC
*
45498 ACATTTAACTTTCCCAATTG
1 ACATTGAACTTTCCCAATTG
* ** *
45518 ACATTGAACTTGCCTTATTC
1 ACATTGAACTTTCCCAATTG
** *
45538 ACATCCAACTTTCCCAAATG
1 ACATTGAACTTTCCCAATTG
45558 ACATTGAACTT
1 ACATTGAACTT
45569 GCCTTAATTC
Statistics
Matches: 37, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35
Consensus pattern (20 bp):
ACATTGAACTTTCCCAATTG
Found at i:45539 original size:40 final size:41
Alignment explanation
Indices: 45494--45823 Score: 270
Period size: 32 Copynumber: 9.2 Consensus size: 41
45484 CACGCGGCAC
** *
45494 ATTCACATTTAACTTTCCCAATTGACATTGAACTTGCCTT-
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
45534 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
45575 ATT--CA--C-A---T-CCAAATGACATTGAAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTG-AACTTGCCTTA
45608 ATT--CA--C-A---T-CCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
*
45640 A-TCACATCCAACTTTCCCAAATAACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
45680 ATT--CA--C-A---T-CCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
*
45712 ATT--CA--C-A---T-CCAAACGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
45744 ATT--CA--C-A---T-CCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
45776 A-TCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
45816 ATTCACAT
1 ATTCACAT
45824 TGGCCCTCGA
Statistics
Matches: 261, Mismatches: 7, Indels: 43
0.84 0.02 0.14
Matches are distributed among these distances:
31 2 0.01
32 111 0.43
33 38 0.15
35 2 0.01
36 4 0.02
37 2 0.01
39 6 0.02
40 86 0.33
41 10 0.04
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.32
Consensus pattern (41 bp):
ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
Found at i:45592 original size:32 final size:32
Alignment explanation
Indices: 45551--45823 Score: 357
Period size: 32 Copynumber: 8.0 Consensus size: 32
45541 TCCAACTTTC
45551 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
45583 CCAAATGACATTGAAACTTGCCTTAATTCACAT
1 CCAAATGACATTG-AACTTGCCTTAATTCACAT
*
45616 CCAAATGACATTGAACTTGCCTTAATCACATCCAACTTT
1 CCAAATGACATTGAACTTGCCTTAAT----T-C-AC-AT
*
45655 CCCAAATAACATTGAACTTGCCTTAATTCACAT
1 -CCAAATGACATTGAACTTGCCTTAATTCACAT
45688 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
*
45720 CCAAACGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
*
45752 CCAAATGACATTGAACTTGCCTTAATCACATCCAACTTT
1 CCAAATGACATTGAACTTGCCTTAAT----T-C-AC-AT
45791 CCCAAATGACATTGAACTTGCCTTAATTCACAT
1 -CCAAATGACATTGAACTTGCCTTAATTCACAT
45824 TGGCCCTCGA
Statistics
Matches: 216, Mismatches: 8, Indels: 33
0.84 0.03 0.13
Matches are distributed among these distances:
32 113 0.52
33 34 0.16
34 4 0.02
35 2 0.01
36 4 0.02
37 2 0.01
38 4 0.02
39 2 0.01
40 51 0.24
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.30
Consensus pattern (32 bp):
CCAAATGACATTGAACTTGCCTTAATTCACAT
Found at i:45652 original size:20 final size:20
Alignment explanation
Indices: 45629--45691 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
45619 AATGACATTG
45629 AACTTGCCTTAATCACATCC
1 AACTTGCCTTAATCACATCC
* ** * **
45649 AACTTTCCCAAATAACATTG
1 AACTTGCCTTAATCACATCC
45669 AACTTGCCTTAATTCACATCC
1 AACTTGCCTTAA-TCACATCC
45690 AA
1 AA
45692 ATGACATTGA
Statistics
Matches: 30, Mismatches: 12, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (20 bp):
AACTTGCCTTAATCACATCC
Found at i:45698 original size:105 final size:104
Alignment explanation
Indices: 45511--45755 Score: 436
Period size: 105 Copynumber: 2.3 Consensus size: 104
45501 TTTAACTTTC
* * *
45511 CCAATTGACATTGAACTTGCCTTATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTAA
1 CCAAATGACATTGAACTTGCCTTAATCACATCCAACTTTCCCAAATAACATTGAACTTGCCTTAA
45576 TTCACATCCAAATGACATTGAAACTTGCCTTAATTCACAT
66 TTCACATCCAAATGACATTG-AACTTGCCTTAATTCACAT
45616 CCAAATGACATTGAACTTGCCTTAATCACATCCAACTTTCCCAAATAACATTGAACTTGCCTTAA
1 CCAAATGACATTGAACTTGCCTTAATCACATCCAACTTTCCCAAATAACATTGAACTTGCCTTAA
45681 TTCACATCCAAATGACATTGAACTTGCCTTAATTCACAT
66 TTCACATCCAAATGACATTGAACTTGCCTTAATTCACAT
*
45720 CCAAACGACATTGAACTTGCCTTAATTCACATCCAA
1 CCAAATGACATTGAACTTGCCTTAA-TCACATCCAA
45756 ATGACATTGA
Statistics
Matches: 135, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
104 43 0.32
105 92 0.68
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (104 bp):
CCAAATGACATTGAACTTGCCTTAATCACATCCAACTTTCCCAAATAACATTGAACTTGCCTTAA
TTCACATCCAAATGACATTGAACTTGCCTTAATTCACAT
Found at i:45788 original size:20 final size:20
Alignment explanation
Indices: 45765--45823 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
45755 AATGACATTG
45765 AACTTGCCTTAATCACATCC
1 AACTTGCCTTAATCACATCC
* ** * **
45785 AACTTTCCCAAATGACATTG
1 AACTTGCCTTAATCACATCC
45805 AACTTGCCTTAATTCACAT
1 AACTTGCCTTAA-TCACAT
45824 TGGCCCTCGA
Statistics
Matches: 28, Mismatches: 10, Indels: 1
0.72 0.26 0.03
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (20 bp):
AACTTGCCTTAATCACATCC
Found at i:45796 original size:104 final size:101
Alignment explanation
Indices: 45517--45823 Score: 381
Period size: 104 Copynumber: 2.9 Consensus size: 101
45507 TTTCCCAATT
* * *
45517 GACATTGAACTTGCCTTATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTAATTCACA
1 GACATTGAACTTGCCTTA---ATATCCAACTATCCCAAATAACATTGAACTTGCCTTAATTCACA
*
45582 TCCAAATGACATTGAAACTTGCCTTAATTCACATCCAAAT
63 TCCAAATGACATTG-AACTTGCCTTAATTCACATCCAAAC
*
45622 GACATTGAACTTGCCTTAATCACATCCAACTTTCCCAAATAACATTGAACTTGCCTTAATTCACA
1 GACATTGAACTTGCCTTAAT---ATCCAACTATCCCAAATAACATTGAACTTGCCTTAATTCACA
45687 TCCAAATGACATTGAACTTGCCTTAATTCACATCCAAAC
63 TCCAAATGACATTGAACTTGCCTTAATTCACATCCAAAC
*
45726 GACATTGAACTTGCCTTAAT-T-C-AC-AT-CCAAATGACATTGAACTTGCCTTAATCACATCCA
1 GACATTGAACTTGCCTTAATATCCAACTATCCCAAATAACATTGAACTTGCCTTAAT----T-C-
*
45786 ACTTTCCCAAATGACATTGAACTTGCCTTAATTCACAT
60 AC-AT-CCAAATGACATTGAACTTGCCTTAATTCACAT
45824 TGGCCCTCGA
Statistics
Matches: 185, Mismatches: 6, Indels: 23
0.86 0.03 0.11
Matches are distributed among these distances:
96 25 0.14
97 1 0.01
98 2 0.01
99 1 0.01
100 2 0.01
101 1 0.01
102 3 0.02
103 1 0.01
104 76 0.41
105 73 0.39
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (101 bp):
GACATTGAACTTGCCTTAATATCCAACTATCCCAAATAACATTGAACTTGCCTTAATTCACATCC
AAATGACATTGAACTTGCCTTAATTCACATCCAAAC
Found at i:45796 original size:136 final size:137
Alignment explanation
Indices: 45551--45823 Score: 521
Period size: 136 Copynumber: 2.0 Consensus size: 137
45541 TCCAACTTTC
*
45551 CCAAATGACATTGAACTTGCCTTAATTCACATCCAAATGACATTGAAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACATCCAAACGACATTGAAACTTGCCTTAATTCACAT
45616 CCAAATGACATTGAACTTGCCTTAATCACATCCAACTTTCCCAAATAACATTGAACTTGCCTTAA
66 CCAAATGACATTGAACTTGCCTTAATCACATCCAACTTTCCCAAATAACATTGAACTTGCCTTAA
45681 TTCACAT
131 TTCACAT
45688 CCAAATGACATTGAACTTGCCTTAATTCACATCCAAACGACATTG-AACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACATCCAAACGACATTGAAACTTGCCTTAATTCACAT
*
45752 CCAAATGACATTGAACTTGCCTTAATCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTAA
66 CCAAATGACATTGAACTTGCCTTAATCACATCCAACTTTCCCAAATAACATTGAACTTGCCTTAA
45817 TTCACAT
131 TTCACAT
45824 TGGCCCTCGA
Statistics
Matches: 134, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
136 90 0.67
137 44 0.33
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.30
Consensus pattern (137 bp):
CCAAATGACATTGAACTTGCCTTAATTCACATCCAAACGACATTGAAACTTGCCTTAATTCACAT
CCAAATGACATTGAACTTGCCTTAATCACATCCAACTTTCCCAAATAACATTGAACTTGCCTTAA
TTCACAT
Found at i:57962 original size:19 final size:18
Alignment explanation
Indices: 57899--57962 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 18
57889 TAGTATAATA
* *
57899 AATAAAATATTTTGTAAC
1 AATAATATATTATGTAAC
*
57917 AATAATATA-TATGTACC
1 AATAATATATTATGTAAC
* *
57934 AA-AAGAATATTGCTGTAAC
1 AATAA-TATATT-ATGTAAC
57953 AATAATATAT
1 AATAATATAT
57963 AAGCAATAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
16 2 0.06
17 11 0.31
18 9 0.26
19 11 0.31
20 2 0.06
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (18 bp):
AATAATATATTATGTAAC
Found at i:59817 original size:12 final size:12
Alignment explanation
Indices: 59800--59824 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59790 TCTATATATC
59800 TTGTTATGGCTT
1 TTGTTATGGCTT
59812 TTGTTATGGCTT
1 TTGTTATGGCTT
59824 T
1 T
59825 CATGGATCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.24, T:0.60
Consensus pattern (12 bp):
TTGTTATGGCTT
Found at i:63039 original size:17 final size:17
Alignment explanation
Indices: 63011--63059 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
63001 GATCACCCCC
* **
63011 AAATCACTAGTGATTTA
1 AAATCACCAGTGATGCA
*
63028 AGATCACCAGTGATGCA
1 AAATCACCAGTGATGCA
63045 AAATCACCAGTGATG
1 AAATCACCAGTGATG
63060 ATCACCTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (17 bp):
AAATCACCAGTGATGCA
Found at i:63406 original size:42 final size:42
Alignment explanation
Indices: 63346--63425 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
63336 TTTCCAGAAA
* *
63346 GAAATGAGGAGTAGATTTCCCTTTCAAGGAAAGAAAAAAAAG
1 GAAATGAAGAGTAAATTTCCCTTTCAAGGAAAGAAAAAAAAG
*
63388 GAAATGAAGAGTAAATTTCCGTTTCAAGGAAAGAAAAA
1 GAAATGAAGAGTAAATTTCCCTTTCAAGGAAAGAAAAA
63426 TGGTAATTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.49, C:0.09, G:0.23, T:0.20
Consensus pattern (42 bp):
GAAATGAAGAGTAAATTTCCCTTTCAAGGAAAGAAAAAAAAG
Found at i:64727 original size:17 final size:17
Alignment explanation
Indices: 64692--64741 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
64682 AAGATTTGAG
*
64692 AAACATTACTAGTAATA
1 AAACATTACTAGTCATA
*
64709 AAACATTACTAGTCCTA
1 AAACATTACTAGTCATA
**
64726 AATTATTACTAGTCAT
1 AAACATTACTAGTCAT
64742 GTGATATGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (17 bp):
AAACATTACTAGTCATA
Found at i:69226 original size:44 final size:44
Alignment explanation
Indices: 69176--69266 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
69166 TGAAGAAATG
**
69176 TTTGGG-CAGTAATCGGGCCAATGTTGATCCATGATATTGACAAA
1 TTTGGGCCA-TAATCGGGCCAATGTTGATCCATGATAAAGACAAA
*
69220 TTTGGGCCATAATTGGGCCAATGTTGATCCATGATAAAGACAAA
1 TTTGGGCCATAATCGGGCCAATGTTGATCCATGATAAAGACAAA
69264 TTT
1 TTT
69267 TGGGACAGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 41 0.95
45 2 0.05
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (44 bp):
TTTGGGCCATAATCGGGCCAATGTTGATCCATGATAAAGACAAA
Found at i:69251 original size:22 final size:22
Alignment explanation
Indices: 69185--69251 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
69175 GTTTGGGCAG
*
69185 TAATCGGGCCAATGTTGATCCA
1 TAATTGGGCCAATGTTGATCCA
* * **
69207 TGATATT-GACAAAT-TTGGGCCA
1 T-A-ATTGGGCCAATGTTGATCCA
69229 TAATTGGGCCAATGTTGATCCA
1 TAATTGGGCCAATGTTGATCCA
69251 T
1 T
69252 GATAAAGACA
Statistics
Matches: 32, Mismatches: 9, Indels: 8
0.65 0.18 0.16
Matches are distributed among these distances:
20 3 0.09
21 6 0.19
22 15 0.47
23 6 0.19
24 2 0.06
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (22 bp):
TAATTGGGCCAATGTTGATCCA
Found at i:71935 original size:21 final size:21
Alignment explanation
Indices: 71911--71956 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
71901 TACCCATCCC
* *
71911 AAGAAGCTCTTGGTTCATCAA
1 AAGAAGATCTTGGATCATCAA
*
71932 AAGAATATCTTGGATCATCAA
1 AAGAAGATCTTGGATCATCAA
71953 AAGA
1 AAGA
71957 CATTCTTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (21 bp):
AAGAAGATCTTGGATCATCAA
Found at i:71963 original size:21 final size:21
Alignment explanation
Indices: 71918--71984 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
71908 CCCAAGAAGC
*
71918 TCTTGGTTCATCAAAAGA-AT
1 TCTTGGATCATCAAAAGACAT
71938 ATCTTGGATCATCAAAAGACAT
1 -TCTTGGATCATCAAAAGACAT
*
71960 TCTT-GCTGCATCAAAAGACAT
1 TCTTGGAT-CATCAAAAGACAT
71981 TCTT
1 TCTT
71985 CCTGCATCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Consensus pattern (21 bp):
TCTTGGATCATCAAAAGACAT
Found at i:71989 original size:21 final size:21
Alignment explanation
Indices: 71947--71994 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
71937 TATCTTGGAT
*
71947 CATCAAAAGACATTCTTGCTG
1 CATCAAAAGACATTCTTCCTG
71968 CATCAAAAGACATTCTTCCTG
1 CATCAAAAGACATTCTTCCTG
71989 CATCAA
1 CATCAA
71995 GTGAAAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.27
Consensus pattern (21 bp):
CATCAAAAGACATTCTTCCTG
Found at i:93218 original size:20 final size:22
Alignment explanation
Indices: 93193--93232 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
93183 TTGGGTTGAA
93193 CAGC-TTG-AGAAGGAGAGAAC
1 CAGCTTTGAAGAAGGAGAGAAC
93213 CAGCTTTGAAGAAGGAGAGA
1 CAGCTTTGAAGAAGGAGAGA
93233 GGAGCGGCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 11 0.61
ACGTcount: A:0.40, C:0.12, G:0.35, T:0.12
Consensus pattern (22 bp):
CAGCTTTGAAGAAGGAGAGAAC
Found at i:97419 original size:12 final size:12
Alignment explanation
Indices: 97402--97429 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
97392 TGCAAAAATA
97402 TTTATATTTATC
1 TTTATATTTATC
97414 TTTATATTTATC
1 TTTATATTTATC
97426 TTTA
1 TTTA
97430 ATAATTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATATTTATC
Found at i:98721 original size:72 final size:72
Alignment explanation
Indices: 98604--98748 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
98594 ATTATCTCAG
98604 CCATGGTGTTCAGGCAAAAGCTTTTCTGATATTTTCACTTAGAATACCTAGGCTGTAGGTTACTT
1 CCATGGTGTTCAGGCAAAAGCTTTTCTGATATTTTCACTTAGAATACCTAGGCTGTAGGTTACTT
98669 AAGGACT
66 AAGGACT
98676 CCATGGTGTTCAGGCAAAAGCTTTTCTGATATTTTCACTTAGAATACCTAGGCTGTAGGTTACTT
1 CCATGGTGTTCAGGCAAAAGCTTTTCTGATATTTTCACTTAGAATACCTAGGCTGTAGGTTACTT
98741 AAGGACT
66 AAGGACT
98748 C
1 C
98749 TGCTGGTTTG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (72 bp):
CCATGGTGTTCAGGCAAAAGCTTTTCTGATATTTTCACTTAGAATACCTAGGCTGTAGGTTACTT
AAGGACT
Found at i:105500 original size:19 final size:20
Alignment explanation
Indices: 105473--105510 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
105463 GTTAAAAACA
105473 AAATAAAAACTACCCATTAT
1 AAATAAAAACTACCCATTAT
105493 AAAT-AAAACTACCCATTA
1 AAATAAAAACTACCCATTA
105511 AAGGATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (20 bp):
AAATAAAAACTACCCATTAT
Found at i:110379 original size:30 final size:30
Alignment explanation
Indices: 110343--110403 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
110333 TTAGTAAGAT
*
110343 ATTAAAATTTGAGGGTATAAGA-AGAAAGTC
1 ATTAAAATTTGAGGATATAAGAGA-AAAGTC
110373 ATTAAAATTTGAGGATATAAGAGAAAAGTC
1 ATTAAAATTTGAGGATATAAGAGAAAAGTC
110403 A
1 A
110404 AGATAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.21, T:0.26
Consensus pattern (30 bp):
ATTAAAATTTGAGGATATAAGAGAAAAGTC
Done.