Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003404.1 Hibiscus syriacus cultivar Beakdansim tig00007170_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 65307
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:713 original size:3 final size:3
Alignment explanation
Indices: 707--780 Score: 91
Period size: 3 Copynumber: 25.0 Consensus size: 3
697 TTTTTATTTT
707 TTA TTA TTTA TT- TTA TTA -TA TTA TTA TT- TTA TTTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* *
751 TTA CTA TTA TTA TTA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
781 CAGGCCCAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
2 6 0.10
3 50 0.81
4 6 0.10
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:743 original size:15 final size:16
Alignment explanation
Indices: 700--773 Score: 89
Period size: 16 Copynumber: 4.5 Consensus size: 16
690 GCCCATTTTT
*
700 TTATTTTTTATTATTTA
1 TTATTATTTATTA-TTA
717 TT-TTATTATATTATTA
1 TTATTATT-TATTATTA
733 TT-TTATTTATTATTA
1 TTATTATTTATTATTA
748 TTATTACTATTATTATTA
1 TTATTA-T-TTATTATTA
766 TTATTATT
1 TTATTATT
774 ACTATTACAG
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
15 10 0.19
16 18 0.35
17 9 0.17
18 15 0.29
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTATTTATTATTA
Found at i:2273 original size:2 final size:2
Alignment explanation
Indices: 2252--2292 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
2242 AAATAAATAA
*
2252 AT AT TT AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2292 A
1 A
2293 CTTTAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6218 original size:15 final size:15
Alignment explanation
Indices: 6198--6227 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6188 TCAATACCTC
6198 TTGCATACATTCATT
1 TTGCATACATTCATT
6213 TTGCATACATTCATT
1 TTGCATACATTCATT
6228 ACTCATTGCA
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:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (15 bp):
TTGCATACATTCATT
Found at i:13608 original size:6 final size:6
Alignment explanation
Indices: 13597--13657 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
13587 ATGCTTGAAG
* *
13597 AAGAAA AAG-AA AAGAAA AA-AAA CAAAAGAA AAG-AA AAGAAA AAGAGA
1 AAGAAA AAGAAA AAGAAA AAGAAA -AAGA-AA AAGAAA AAGAAA AAGAAA
*
13644 AAGAAA AGGAAA AA
1 AAGAAA AAGAAA AA
13658 ATAGAAAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
5 13 0.29
6 27 0.60
7 3 0.07
8 2 0.04
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:13611 original size:5 final size:5
Alignment explanation
Indices: 13601--13670 Score: 72
Period size: 5 Copynumber: 13.8 Consensus size: 5
13591 TTGAAGAAGA
*
13601 AAAAG AAAAG AAAA- AAAAC AAAAG AAAAG AAAAG AAAAAG AGAAAG AAAAGG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG A-AAAG AAAA-G
* *
13653 AAAA- AATAG AAAAT AAAA
1 AAAAG AAAAG AAAAG AAAA
13671 AAGAGGGTCT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
4 7 0.12
5 34 0.61
6 15 0.27
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:13673 original size:27 final size:26
Alignment explanation
Indices: 13601--13674 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
13591 TTGAAGAAGA
*
13601 AAAAGAAAAG--AAAAAAAACAAAAG
1 AAAAGAAAAGAAAAAAAAAAGAAAAG
*
13625 AAAAGAAAAGAAAAAGAGAAAGAAAAGG
1 AAAAGAAAAGAAAAA-AAAAAGAAAA-G
*
13653 AAAA-AATAGAAAATAAAAAAGA
1 AAAAGAAAAGAAAA-AAAAAAGA
13675 GGGTCTAGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 10 0.24
26 3 0.07
27 22 0.54
28 6 0.15
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (26 bp):
AAAAGAAAAGAAAAAAAAAAGAAAAG
Found at i:15002 original size:242 final size:245
Alignment explanation
Indices: 14554--15249 Score: 1041
Period size: 242 Copynumber: 2.8 Consensus size: 245
14544 CTCGATGGAT
* * *
14554 CAACATTTCCAG-GTGGAGTTCATAATGAGAAGAACTCATCTG-AGAAGGAAGAAGAAGTTCATA
1 CAACATTTCCAGAG-AGAATTCATAATGAGAAGAACTCATCTGAAG-AGAAAGAAGAAGTTCATA
* *
14617 ATGAGAAGAACTTGTTCAA-CTTTTTGCTCGACT-TATCATAGAATGAGATAGATCAGCACCAAC
64 AT-AGAAGAACTTGTTCAACCTTTTT-CTCGACTCTATCATAGAAGGAGATAGATCAACACCAAC
* *
14680 ATTTTCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATAATGAGA
127 ATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGA
* **
14745 AGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGGGATAGATCAGCAC
192 AGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGAAGATAGATCAGCAC
14799 CAACATTTCCAGAGAG-ATGT-ATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
1 CAACATTTCCAGAGAGAAT-TCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
* * * *
14862 T-G-AGAACTTATTTAACCTTTTTCTCGACTCTATCACAAAAGGAGATAGATCAACACCAACATT
65 TAGAAGAACTTGTTCAACCTTTTTCTCGACTCTATCATAGAAGGAGATAGATCAACACCAACATT
* *
14925 TCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
130 TCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGA
*
14990 ACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGAAGATAGATCATCAC
195 ACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGAAGATAGATCAGCAC
* * *
15041 CAATATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGA-AGAAGAAAAAGTTCTTAA
1 CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGA-AAGAAGAAGTTCATAA
* *
15105 TGAGAAGAACTTGTTCAACCTTTTTCTCGACTCTATCATAGAAGGAGATAGATCATCATCAACAT
65 T-AGAAGAACTTGTTCAACCTTTTTCTCGACTCTATCATAGAAGGAGATAGATCAACACCAACAT
* *
15170 TTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGAAG
129 TTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAG
*
15235 AACTTGTTCGACCTT
194 AACTTGTTCAACCTT
15250 AACTTGATTA
Statistics
Matches: 410, Mismatches: 30, Indels: 21
0.89 0.07 0.05
Matches are distributed among these distances:
241 18 0.04
242 162 0.40
243 42 0.10
244 41 0.10
245 17 0.04
246 130 0.32
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (245 bp):
CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAAT
AGAAGAACTTGTTCAACCTTTTTCTCGACTCTATCATAGAAGGAGATAGATCAACACCAACATTT
CCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAA
CTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGAAGATAGATCAGCAC
Found at i:15034 original size:123 final size:123
Alignment explanation
Indices: 14554--15249 Score: 1021
Period size: 123 Copynumber: 5.7 Consensus size: 123
14544 CTCGATGGAT
* *
14554 CAACATTTCCAG-GTGGAGTTCATAATGAGAAGAACTCATCTG-AGAAGGAAGAAGAAGTTCATA
1 CAACATTTCCAGAG-AGAATTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATA
* * * *
14617 ATGAGAAGAACTTGTTCAACTTTTTGCTCGACT-TATCATAGAATGAGATAGATCAGCAC
64 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAGATCAGCAC
* * *
14676 CAACATTTTCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATAAT
1 CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* *
14741 GAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGGGATAGATCAGCAC
66 GAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAGATCAGCAC
*
14799 CAACATTTCCAGAGAG-ATGT-ATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
1 CAACATTTCCAGAGAGAAT-TCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * * *
14862 T--G-AGAACTTATTTAACCTTTTTCTCGACTCTATCACAAAAGGAGATAGATCAACAC
65 TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAGATCAGCAC
14918 CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
1 CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* *
14983 GAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGAAGATAGATCATCAC
66 GAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAGATCAGCAC
* * * *
15041 CAATATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAAAAGTTCTTAAT
1 CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* * * * *
15106 GAGAAGAACTTGTTCAACCTTTTTCTCGACTCTATCATAGAAGGAGATAGATCATCAT
66 GAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAGATCAGCAC
* * *
15164 CAACATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAAT
1 CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* *
15229 AAGAAGAACTTGTTCGACCTT
66 GAGAAGAACTTGTTCAACCTT
15250 AACTTGATTA
Statistics
Matches: 526, Mismatches: 39, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
119 65 0.12
120 46 0.09
122 131 0.25
123 284 0.54
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (123 bp):
CAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAGATCAGCAC
Found at i:15609 original size:80 final size:80
Alignment explanation
Indices: 15475--15655 Score: 335
Period size: 80 Copynumber: 2.3 Consensus size: 80
15465 GAGGAAGAAT
*
15475 AAGTTCATAATGTGAAGAACTTGTTCAACCTTTTGCTAGATTTCATCGCAGAAGGAGATAAGTTA
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTAGATTTCATCGCAGAAGGAGATAAGTTA
15540 TCATTCCCAGTGGAA
66 TCATTCCCAGTGGAA
* *
15555 GAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTAGATTTCATCGCAGAAGGAGATATGTTA
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTAGATTTCATCGCAGAAGGAGATAAGTTA
15620 TCATTCCCAGTGGAA
66 TCATTCCCAGTGGAA
15635 AAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACT
15656 AGCCTCAAAG
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 97 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (80 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTAGATTTCATCGCAGAAGGAGATAAGTTA
TCATTCCCAGTGGAA
Found at i:15843 original size:3 final size:3
Alignment explanation
Indices: 15837--15903 Score: 75
Period size: 3 Copynumber: 22.3 Consensus size: 3
15827 CATTTTTTAT
*
15837 TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA TTA TTA TTA TAA TTAA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* *
15883 TTA -AA TTA TTA TTA CTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
15904 AGGTCCAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 3 0.06
3 45 0.83
4 6 0.11
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:15851 original size:15 final size:15
Alignment explanation
Indices: 15831--15876 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
15821 TTTTCCCATT
15831 TTTTATTTATTATTA
1 TTTTATTTATTATTA
15846 TTTTATTTATTATTA
1 TTTTATTTATTATTA
15861 TTATTA-TTATTATTA
1 TT-TTATTTATTATTA
15876 T
1 T
15877 AATTAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 27 0.90
16 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATTTATTATTA
Found at i:17218 original size:15 final size:15
Alignment explanation
Indices: 17184--17231 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
17174 AATGTCCTAC
* *
17184 TTATATAAATTATAT
1 TTATTTAAATTATTT
* *
17199 ATATTTAATTTATTT
1 TTATTTAAATTATTT
17214 TTATTTAAATTATTT
1 TTATTTAAATTATTT
17229 TTA
1 TTA
17232 GAATATTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTTAAATTATTT
Found at i:17410 original size:169 final size:169
Alignment explanation
Indices: 17099--17410 Score: 402
Period size: 169 Copynumber: 1.8 Consensus size: 169
17089 TGAGGATGAT
* *
17099 ATTTATTTTTTAATATTAAGAAAGTGGCTGTCTTAAATTAACTAGATGTCATTTTCTGATATTTT
1 ATTTATTTTTTAATATTAAGAAAATGGCTGTCTTAAAGTAACTAGATGTCATTTTCTGATATTTT
* * * * ** * * *
17164 TAAATAAATAAATGTCCTACTTATATAAATTATATATATTTAATTTATTTTTATTTAAATTATTT
66 TAAATAAATAAATATCCTACTTATATAAATAACATAAAAATAATATATATTTATTTAAATTATTA
* *
17229 TTAGAATATTTTATTAAAAAATATCATATTTTTATTAAA
131 TAAAAATATTTTATTAAAAAATATCATATTTTTATTAAA
*
17268 ATTTATTTTTTAATATTAAGAAAATGGTTGTCTTAAAGTAACTAGATGTCATTTTCTGATATTTT
1 ATTTATTTTTTAATATTAAGAAAATGGCTGTCTTAAAGTAACTAGATGTCATTTTCTGATA-TTT
17333 TAAATAAATAAATAAATATCCTA-TT-TATAAA-AACATAAAAAT-ATATATATTTACTTT-AAT
65 T---TAAATAAATAAATATCCTACTTATATAAATAACATAAAAATAATATATATTTA-TTTAAAT
17393 T-TTATAAAAATTATTTTA
126 TATTATAAAAA-TATTTTA
17411 ATATATTTTC
Statistics
Matches: 123, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
168 6 0.05
169 78 0.63
170 13 0.11
171 6 0.05
172 2 0.02
173 18 0.15
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (169 bp):
ATTTATTTTTTAATATTAAGAAAATGGCTGTCTTAAAGTAACTAGATGTCATTTTCTGATATTTT
TAAATAAATAAATATCCTACTTATATAAATAACATAAAAATAATATATATTTATTTAAATTATTA
TAAAAATATTTTATTAAAAAATATCATATTTTTATTAAA
Found at i:20416 original size:16 final size:16
Alignment explanation
Indices: 20397--20430 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20387 TGATATTAAT
20397 AAATATTAATATATTA
1 AAATATTAATATATTA
* *
20413 AAATTTTAATATTTTA
1 AAATATTAATATATTA
20429 AA
1 AA
20431 TAAAACTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATTAATATATTA
Found at i:20555 original size:2 final size:2
Alignment explanation
Indices: 20548--20601 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
20538 TTATTTTAAA
20548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20590 AT AT AT -T AT AT A
1 AT AT AT AT AT AT A
20602 CTAGATAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20651 original size:19 final size:18
Alignment explanation
Indices: 20610--20652 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
20600 TACTAGATAA
20610 TAATAATAATAATTAAAG
1 TAATAATAATAATTAAAG
*
20628 CAATAATTAA-AATATAAAG
1 TAATAA-TAATAAT-TAAAG
20647 TAATAA
1 TAATAA
20653 CAAAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (18 bp):
TAATAATAATAATTAAAG
Found at i:21214 original size:13 final size:13
Alignment explanation
Indices: 21196--21221 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21186 CGTACTCCGC
21196 CGCCGGCCACCGT
1 CGCCGGCCACCGT
21209 CGCCGGCCACCGT
1 CGCCGGCCACCGT
21222 AAACAGTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.54, G:0.31, T:0.08
Consensus pattern (13 bp):
CGCCGGCCACCGT
Found at i:21892 original size:3 final size:3
Alignment explanation
Indices: 21884--21983 Score: 128
Period size: 3 Copynumber: 32.7 Consensus size: 3
21874 TTATTTATTA
* *
21884 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT TAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * **
21931 TAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21979 AAT AA
1 AAT AA
21984 ATTTAAATGA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
3 79 0.93
4 6 0.07
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:23463 original size:76 final size:76
Alignment explanation
Indices: 22109--23434 Score: 2492
Period size: 76 Copynumber: 17.4 Consensus size: 76
22099 GATGGAAATG
* * * * *
22109 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGATCCGAAGGTTTTTGAAAACATCAAAACGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
22174 TCCCGAAGGCTT
65 TCCCGAAGGCTT
22186 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
22251 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
22262 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
22327 TCCCGAAGGCTT
65 TCCCGAAGGCTT
22339 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
22404 CCCGAAGGCTT
66 CCCGAAGGCTT
*
22415 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
22480 CCCGAAGGCTT
66 CCCGAAGGCTT
*
22491 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
22556 CCCGAAGGCTT
66 CCCGAAGGCTT
22567 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
22632 CCCGAAGGCTT
66 CCCGAAGGCTT
*
22643 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
22708 CCCGAAGGCTT
66 CCCGAAGGCTT
22719 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
22784 CCCGAAGGCTT
66 CCCGAAGGCTT
22795 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
22860 CCCGAAGGCTT
66 CCCGAAGGCTT
*
22871 TTTGGAAACATTATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
22936 CCCGAAGGCTT
66 CCCGAAGGCTT
*
22947 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
23011 CCCGAAGGCTT
66 CCCGAAGGCTT
23022 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
23087 CCCGAAGGCTT
66 CCCGAAGGCTT
23098 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
23163 CCCGAAGGCTT
66 CCCGAAGGCTT
*
23174 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGATAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
23239 CCCGAAGGCTT
66 CCCGAAGGCTT
23250 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
23315 CCCGAAGGCTT
66 CCCGAAGGCTT
*
23326 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
23391 CCCGAAGGCTTT
66 CCCGAAGGC-TT
23403 TTTGGAAACATCATGCACTGAAGGACTTACAG
1 TTTGGAAACATCATGCACTGAAGGACTTACAG
23435 GTGTGAGAAA
Statistics
Matches: 1223, Mismatches: 23, Indels: 6
0.98 0.02 0.00
Matches are distributed among these distances:
75 74 0.06
76 1001 0.82
77 148 0.12
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:24137 original size:22 final size:22
Alignment explanation
Indices: 24112--24166 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
24102 CATAAAGTTT
* *
24112 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAACAGAATCTA
*
24134 TCATCTTTAAAAACAGAATCTA
1 TCATCTTTGAAAACAGAATCTA
24156 TCATCTTTGAA
1 TCATCTTTGAA
24167 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAACAGAATCTA
Found at i:24612 original size:54 final size:54
Alignment explanation
Indices: 24530--24685 Score: 240
Period size: 54 Copynumber: 2.9 Consensus size: 54
24520 AGAATAGCAG
* ***
24530 GTTCGTAAAACATTTGATAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* *
24584 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* *
24638 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTATGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
24686 CAAGAATTCT
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 92 1.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:26629 original size:114 final size:114
Alignment explanation
Indices: 26429--26882 Score: 710
Period size: 114 Copynumber: 4.0 Consensus size: 114
26419 GATCATGCAG
* * ** * * * * *
26429 TTCATCTTTCAACTCCAATGATCAGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAATGA
1 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
26494 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTAATTCCACTATGAGCAAA
* *
26543 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTTAAATA
1 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * * * *
26608 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGGGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTAATTCCACTATGAGCAAA
* *
26657 TTCATCTTTAAAATCCAATGATTGGTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
26722 ACACTTCCAGAAGATGCTATTGGGTCTCTTTAATTCCACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTAATTCCACTATGAGCAAA
26771 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
26836 ACACTTCCAGAAGATGCTATTGGGTCTCTTTAATTCCACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTAATTCCACTATGAGCA
26883 CATGGCACTT
Statistics
Matches: 314, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 314 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTAATTCCACTATGAGCAAA
Found at i:33955 original size:16 final size:16
Alignment explanation
Indices: 33936--33969 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33926 TGATATTAAT
33936 AAATATTAATATATTA
1 AAATATTAATATATTA
* *
33952 AAATTTTAATATTTTA
1 AAATATTAATATATTA
33968 AA
1 AA
33970 TAAAACTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATTAATATATTA
Found at i:34094 original size:2 final size:2
Alignment explanation
Indices: 34087--34130 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
34077 ATTATTTTAA
*
34087 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34129 AT
1 AT
34131 GACTAAGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:34750 original size:13 final size:13
Alignment explanation
Indices: 34732--34757 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34722 CGTACTCCGC
34732 CGCCGGCCACCGT
1 CGCCGGCCACCGT
34745 CGCCGGCCACCGT
1 CGCCGGCCACCGT
34758 AAACAGTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.54, G:0.31, T:0.08
Consensus pattern (13 bp):
CGCCGGCCACCGT
Found at i:35422 original size:3 final size:3
Alignment explanation
Indices: 35414--35519 Score: 149
Period size: 3 Copynumber: 34.7 Consensus size: 3
35404 TTATTTATTA
*
35414 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * **
35461 AAT TAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT TTT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35509 AAT AAT AAT AA
1 AAT AAT AAT AA
35520 ATTTAAATGA
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
3 85 0.93
4 6 0.07
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:35844 original size:31 final size:31
Alignment explanation
Indices: 35800--35930 Score: 93
Period size: 31 Copynumber: 4.1 Consensus size: 31
35790 GAGCCAACAT
*
35800 AAGGTAATGCCTTGGGGCCTTAGAGCCTACCC
1 AAGG-AATACCTTGGGGCCTTAGAGCCTACCC
* * * *
35832 AAGGAATACCTTGAGGTCTTAGAGCCTTCTC
1 AAGGAATACCTTGGGGCCTTAGAGCCTACCC
* * * * *
35863 AAGGAAGCACCTT-GGGTCTTGAGAGCTTATCG
1 AAGGAA-TACCTTGGGGCCTT-AGAGCCTACCC
* * * *
35895 AATGGAATATCTCGGGGCCTAAGAGCTTACCC
1 AA-GGAATACCTTGGGGCCTTAGAGCCTACCC
35927 AAGG
1 AAGG
35931 TTCACCTTAG
Statistics
Matches: 76, Mismatches: 19, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
31 36 0.47
32 31 0.41
33 9 0.12
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (31 bp):
AAGGAATACCTTGGGGCCTTAGAGCCTACCC
Found at i:37994 original size:13 final size:13
Alignment explanation
Indices: 37976--38002 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
37966 ATAGTTAAAA
37976 CAGTCTTCATATG
1 CAGTCTTCATATG
37989 CAGTCTTCATATG
1 CAGTCTTCATATG
38002 C
1 C
38003 TCGTTTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:38039 original size:14 final size:14
Alignment explanation
Indices: 38020--38056 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
38010 TAATGGGGGT
38020 AATCCCTGCGAAAA
1 AATCCCTGCGAAAA
*
38034 AATCCCTGCGTAAA
1 AATCCCTGCGAAAA
*
38048 AATCTCTGC
1 AATCCCTGC
38057 ATATATACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (14 bp):
AATCCCTGCGAAAA
Found at i:43194 original size:216 final size:215
Alignment explanation
Indices: 42818--43514 Score: 1127
Period size: 216 Copynumber: 3.3 Consensus size: 215
42808 ATTTAATAAT
*
42818 TAAATTGAACAAATATGAAATTGCAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
*
42883 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAAGTACTAAATTATA
66 GGATCAAATCGAAATAATTTTAAATTATGATGTTGAAATTAATAC-AAAAAAGTACTAAATTATA
* * * * * *
42948 CCCATTTAAAAAGTTATGGGCCAATTAAAAAAAGAATTAAGTAAAAAGTATAGATCAATTTCATA
130 CCCATTTAAAAAGTTATGGGCCAATTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
43013 TGCAAATAAAATTTGGAGGAC
195 TGCAAATAAAATTTGGAGGAC
* *
43034 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATTAATTAAACGACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
43099 GGATCAAATCGAAATAATTTTAAATTATGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTATGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
43164 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
131 CCATTTAAAAAGTTATGGGCCAA-TTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
43229 TGCAAATAAAATTTGGAGGAC
195 TGCAAATAAAATTTGGAGGAC
* *
43250 TAAATTGAACAAATATAAAATTACAAATAAAAATTTAAATAAACTAAACAACACA-A---A--AG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * * * *
43309 GGATCAAATTGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAATGTACTAAATTATAA
66 GGATCAAATCGAAATAATTTTAAATTATGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
** *
43374 TAATTTAAAAAGTTATAGGCCAATTAATAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
131 CCATTTAAAAAGTTATGGGCCAATTAA-AAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
* *
43439 TACAAATAAAATGTGGAGGAC
195 TGCAAATAAAATTTGGAGGAC
43460 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
43515 AAAGGGATCA
Statistics
Matches: 453, Mismatches: 26, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
209 4 0.01
210 191 0.42
212 1 0.00
215 44 0.10
216 213 0.47
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.28
Consensus pattern (215 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTATGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
CCATTTAAAAAGTTATGGGCCAATTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGAT
GCAAATAAAATTTGGAGGAC
Found at i:43602 original size:2 final size:2
Alignment explanation
Indices: 43597--43706 Score: 75
Period size: 2 Copynumber: 54.5 Consensus size: 2
43587 AAAACAACTA
* * *
43597 AT AT AT AT AT AT AT AT A- AT AT AA ACT AT AT AGT TT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT
* * *
43640 AGT AT AT GT AT -T AT AT AT AT AA ACT AT AT A- AT TT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* *
43682 AT AT AT -T AT GT AT AA ACT AT AT AT A
1 AT AT AT AT AT AT AT AT A-T AT AT AT A
43707 CCATGTATAA
Statistics
Matches: 83, Mismatches: 16, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
1 4 0.05
2 74 0.89
3 5 0.06
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:43627 original size:20 final size:19
Alignment explanation
Indices: 43602--43911 Score: 109
Period size: 20 Copynumber: 15.4 Consensus size: 19
43592 AACTAATATA
43602 TATATATATATAATATAAAC
1 TATATATATAT-ATATAAAC
* *
43622 TATATAGTTTATATATAAAG
1 TATATA-TATATATATAAAC
43642 TATATGTATTATATATATAAAC
1 TATA--TA-TATATATATAAAC
* *
43664 TATATA-ATTTATATATA-
1 TATATATATATATATAAAC
*
43681 TATATAT-TATGTATAAAC
1 TATATATATATATATAAAC
* *
43699 TATATATACCATGTATAAAC
1 TATATATA-TATATATAAAC
43719 TAATACTATATAATTTATATATGAAC
1 T-ATA-TATAT-A--TATATA--AAC
* *
43745 TAT-TGA-ACTATATAGAACC
1 TATAT-ATA-TATATATAAAC
* * *
43764 TACATAGTTTATATATAAAT
1 TATATA-TATATATATAAAC
43784 TATATATGAATTATATATAAAC
1 TATATAT--A-TATATATAAAC
* * **
43806 TATACA-ATTTATATTTA-
1 TATATATATATATATAAAC
*
43823 TATATTATGTATAATTATAAA-
1 TATA-TATATAT-A-TATAAAC
* *
43844 TA-ATATATATTTTATAAAT
1 TATATATATA-TATATAAAC
*
43863 TATATAGTTTATTAATATAAAC
1 TATATA-TATA-T-ATATAAAC
* *
43885 TATATAGTTTATATATATA-
1 TATATA-TATATATATAAAC
43904 TATATATA
1 TATATATA
43912 GTGTATATGA
Statistics
Matches: 220, Mismatches: 39, Indels: 64
0.68 0.12 0.20
Matches are distributed among these distances:
17 17 0.08
18 31 0.14
19 22 0.10
20 56 0.25
21 24 0.11
22 54 0.25
23 3 0.01
24 7 0.03
25 2 0.01
26 4 0.02
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (19 bp):
TATATATATATATATAAAC
Found at i:43659 original size:22 final size:22
Alignment explanation
Indices: 43608--43682 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
43598 TATATATATA
43608 TATATAATATAAACTATA-TAGT
1 TATAT-ATATAAACTATATTAGT
*
43630 T-TATATATAAAGTATATGTA-T
1 TATATATATAAACTATAT-TAGT
* *
43651 TATATATATAAACTATATAATT
1 TATATATATAAACTATATTAGT
43673 TATATATATA
1 TATATATATA
43683 TATATTATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
20 11 0.24
21 6 0.13
22 29 0.63
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (22 bp):
TATATATATAAACTATATTAGT
Found at i:43660 original size:42 final size:44
Alignment explanation
Indices: 43598--43680 Score: 134
Period size: 42 Copynumber: 1.9 Consensus size: 44
43588 AAACAACTAA
*
43598 TATATATATATATATAATATAAACTATATAGTTTATATATAAAG
1 TATATATATATATATAATATAAACTATATAATTTATATATAAAG
*
43642 TATATGTAT-TATAT-ATATAAACTATATAATTTATATATA
1 TATATATATATATATAATATAAACTATATAATTTATATATA
43681 TATATATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 24 0.65
43 5 0.14
44 8 0.22
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (44 bp):
TATATATATATATATAATATAAACTATATAATTTATATATAAAG
Found at i:43786 original size:11 final size:11
Alignment explanation
Indices: 43772--43809 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
43762 CCTACATAGT
43772 TTATATATAAA
1 TTATATATAAA
*
43783 TTATATATGAA
1 TTATATATAAA
43794 TTATATATAAA
1 TTATATATAAA
*
43805 CTATA
1 TTATA
43810 CAATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:43835 original size:17 final size:17
Alignment explanation
Indices: 43815--43868 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
43805 CTATACAATT
* *
43815 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
43832 TATAATTATAAATAATA
1 TATATTTATAAATTATA
43849 TATATTTTATAAATTATA
1 TATA-TTTATAAATTATA
43867 TA
1 TA
43869 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:43888 original size:22 final size:21
Alignment explanation
Indices: 43767--43919 Score: 83
Period size: 22 Copynumber: 7.5 Consensus size: 21
43757 TAGAACCTAC
*
43767 ATAGTTTATATATA-AATTAT
1 ATAGTTTATATATATAAATAT
* *
43787 ATATGAATTATATATA-AACTAT
1 ATA-G-TTTATATATATAAATAT
* * * *
43809 ACAATTTATATTTATATAT-T
1 ATAGTTTATATATATAAATAT
*
43829 AT-GTATA-AT-TATAAATA-
1 ATAGTTTATATATATAAATAT
* *
43846 ATA-TATAT-TTTATAAATTAT
1 ATAGTTTATATATATAAA-TAT
43866 ATAGTTTAT-TAATATAAACTAT
1 ATAGTTTATAT-ATATAAA-TAT
*
43888 ATAGTTTATATATATATATAT
1 ATAGTTTATATATATAAATAT
*
43909 ATAGTGTATAT
1 ATAGTTTATAT
43920 GATTTAGGGT
Statistics
Matches: 104, Mismatches: 17, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
17 13 0.12
18 8 0.08
19 5 0.05
20 16 0.15
21 21 0.20
22 40 0.38
23 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (21 bp):
ATAGTTTATATATATAAATAT
Found at i:43989 original size:6 final size:6
Alignment explanation
Indices: 43978--44014 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
43968 GGGTTCAGGG
43978 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA T
44015 AAACTACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:44062 original size:12 final size:12
Alignment explanation
Indices: 44022--44066 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
44012 TATAAACTAC
*
44022 ATACTATAATTT
1 ATACTATATTTT
*
44034 ATATTTATATTTAT
1 ATA-CTATATTT-T
44048 ATACTATATTTT
1 ATACTATATTTT
44060 ATACTAT
1 ATACTAT
44067 TTATATAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 11 0.39
13 13 0.46
14 4 0.14
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
ATACTATATTTT
Found at i:44069 original size:35 final size:35
Alignment explanation
Indices: 43992--44072 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
43982 TATTTATATT
43992 TATATTTATATTTATATTTATATAAACTACATACTA
1 TATATTTATATTTATATTTATAT-AACTACATACTA
* **
44028 TA-ATTTATATTTATATTTATAT-ACTATATTTTA
1 TATATTTATATTTATATTTATATAACTACATACTA
44061 TACTATTTATAT
1 TA-TATTTATAT
44073 AAACTATAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
33 10 0.25
35 28 0.70
36 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (35 bp):
TATATTTATATTTATATTTATATAACTACATACTA
Found at i:44103 original size:31 final size:31
Alignment explanation
Indices: 44052--44156 Score: 92
Period size: 31 Copynumber: 3.4 Consensus size: 31
44042 ATTTATATAC
44052 TATATTT-TATACTATTTATATAAACTATAGTT
1 TATATTTATATACTA--TATATAAACTATAGTT
*
44084 TATATTTATATACTATATATATGAAATATAGTT
1 TATATTTATATACTATATATA--AACTATAGTT
* * *
44117 TACA--TATGA-ACTATATATATACTAAAGTT
1 TATATTTAT-ATACTATATATAAACTATAGTT
*
44146 GATATTTATAT
1 TATATTTATAT
44157 CTGAACTATA
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
29 9 0.15
30 1 0.02
31 22 0.37
32 8 0.14
33 19 0.32
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (31 bp):
TATATTTATATACTATATATAAACTATAGTT
Found at i:44105 original size:33 final size:33
Alignment explanation
Indices: 44052--44156 Score: 107
Period size: 33 Copynumber: 3.3 Consensus size: 33
44042 ATTTATATAC
*
44052 TATATTT-TATACTATTTATATAAACTATAGTT
1 TATATTTATATACTATATATATAAACTATAGTT
44084 TATATTTATATACTATATATATGAAA-TATAGTT
1 TATATTTATATACTATATATAT-AAACTATAGTT
* *
44117 TACA--TATGA-ACTATATATAT--ACTAAAGTT
1 TATATTTAT-ATACTATATATATAAACTATAGTT
*
44146 GATATTTATAT
1 TATATTTATAT
44157 CTGAACTATA
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
28 1 0.02
29 8 0.13
30 1 0.02
31 17 0.28
32 8 0.13
33 23 0.38
34 3 0.05
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (33 bp):
TATATTTATATACTATATATATAAACTATAGTT
Found at i:44151 original size:62 final size:62
Alignment explanation
Indices: 44068--44294 Score: 203
Period size: 62 Copynumber: 3.6 Consensus size: 62
44058 TTATACTATT
* * *
44068 TATATAAACTATAGTTTATATTTATATACTATATATATGAAATATAGTTTACATATGAACTA
1 TATATATACTATAGTTGATATTTATATACTATATATATAAAATATAGTTTACATATGAACTA
* * * *** * **
44130 TATATATACTAAAGTTGATATTTATAT-CTGA-ACTATAGTTTACATATAAACTATATA-G-TTT
1 TATATATACTATAGTTGATATTTATATACT-ATA-TATA--TAAAATATAGTTTACATATGAACT
44191 A
62 A
44192 TATACTA-ACTATAGTTGATATTTACATATGAACTATATATATAAATTATATAGTTTACATATGA
1 TATA-TATACTATAGTTGATATTT--ATAT--ACTATATATATAAA--ATATAGTTTACATATGA
*
44256 CCTA
59 ACTA
44260 TATATATACTATAGTTGATATTTATATACTATATA
1 TATATATACTATAGTTGATATTTATATACTATATA
44295 ATTTACATAT
Statistics
Matches: 129, Mismatches: 20, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
61 3 0.02
62 50 0.39
63 3 0.02
64 26 0.20
66 19 0.15
67 6 0.05
68 22 0.17
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (62 bp):
TATATATACTATAGTTGATATTTATATACTATATATATAAAATATAGTTTACATATGAACTA
Found at i:44171 original size:18 final size:18
Alignment explanation
Indices: 44150--44212 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
44140 AAAGTTGATA
*
44150 TTTATATCTGAACTATAG
1 TTTATATATGAACTATAG
* *
44168 TTTACATATAAACTATATAG
1 TTTATATATGAAC--TATAG
44188 TTTATATACT-AACTATAG
1 TTTATATA-TGAACTATAG
*
44206 TTGATAT
1 TTTATAT
44213 TTACATATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 21 0.57
20 15 0.41
21 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (18 bp):
TTTATATATGAACTATAG
Found at i:44316 original size:130 final size:121
Alignment explanation
Indices: 44066--44314 Score: 331
Period size: 130 Copynumber: 2.0 Consensus size: 121
44056 TTTTATACTA
* *
44066 TTTATATAAACTATAGTTTATATTTATATACTATATATATGAAATATAGTTTACATATGAACTAT
1 TTTATATAAACTATAGTTGATATTTATATACTATATATATAAAATATAGTTTACATATGAACTAT
*
44131 ATATATACTAAAGTTGATATTTATATCTGAACTATAGTTTACATATAAACTATATAG
66 ATATATACTAAAGTTGATATTTATATCT-AACTATAATTTACATATAAACTATATAG
44188 TTTATATACTAACTATAGTTGATATTTACATATGAACTATATATATAAATTATATAGTTTACATA
1 TTTATATA--AACTATAGTTGATATTT--ATAT--ACTATATATATAAA--ATATAGTTTACATA
* * * *
44253 TGACCTATATATATACTATAGTTGATATTTATATACT-A-TATAATTTACATATGACCTATATA
58 TGAACTATATATATACTAAAGTTGATATTTATAT-CTAACTATAATTTACATATAAACTATATA
44315 TATACTATAG
Statistics
Matches: 111, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
122 8 0.07
124 16 0.14
126 4 0.04
128 34 0.31
129 1 0.01
130 46 0.41
131 2 0.02
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (121 bp):
TTTATATAAACTATAGTTGATATTTATATACTATATATATAAAATATAGTTTACATATGAACTAT
ATATATACTAAAGTTGATATTTATATCTAACTATAATTTACATATAAACTATATAG
Found at i:44344 original size:51 final size:50
Alignment explanation
Indices: 44225--44345 Score: 179
Period size: 51 Copynumber: 2.4 Consensus size: 50
44215 ACATATGAAC
* *
44225 TATATATATAAATTATATAGTTTACATATGACCTATATATATACTATAGT
1 TATATATATAAAATATATAATTTACATATGACCTATATATATACTATAGT
* * *
44275 TGATATTTATATACTATATAATTTACATATGACCTATATATATACTATAGT
1 T-ATATATATAAAATATATAATTTACATATGACCTATATATATACTATAGT
44326 TATACTATATAAAATATATA
1 TATA-TATATAAAATATATA
44346 CTATAGTTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
50 4 0.06
51 58 0.94
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (50 bp):
TATATATATAAAATATATAATTTACATATGACCTATATATATACTATAGT
Found at i:44349 original size:27 final size:27
Alignment explanation
Indices: 44312--44385 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
44302 TATGACCTAT
44312 ATATATACTATAGTTATACTATATAAA
1 ATATATACTATAGTTATACTATATAAA
*
44339 ATATATACTATAGTTATA-T-TAT-AT
1 ATATATACTATAGTTATACTATATAAA
*
44363 ATATAAACTATA--TATACTATATA
1 ATATATACTATAGTTATACTATATA
44386 GTATAATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
22 4 0.10
23 1 0.02
24 15 0.36
25 3 0.07
26 1 0.02
27 18 0.43
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (27 bp):
ATATATACTATAGTTATACTATATAAA
Found at i:44362 original size:20 final size:19
Alignment explanation
Indices: 44260--44365 Score: 69
Period size: 20 Copynumber: 5.4 Consensus size: 19
44250 ATATGACCTA
44260 TATATATACTATAGTTGATAT
1 TATATATACTATA-TT-ATAT
*
44281 T-TATATACTATATAAT-T
1 TATATATACTATATTATAT
* *
44298 TACATATGACCTATATATATAC
1 TATATAT-A-CTATAT-TATAT
44320 TATAGTTATACTATA-TA-A-
1 TATA--TATACTATATTATAT
*
44338 AATATATACTATAGTTATAT
1 TATATATACTATA-TTATAT
44358 TATATATA
1 TATATATA
44366 TAAACTATAT
Statistics
Matches: 67, Mismatches: 7, Indels: 23
0.69 0.07 0.24
Matches are distributed among these distances:
16 9 0.13
17 2 0.03
18 11 0.16
19 4 0.06
20 26 0.39
21 3 0.04
22 8 0.12
23 1 0.01
24 3 0.04
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (19 bp):
TATATATACTATATTATAT
Found at i:44467 original size:22 final size:22
Alignment explanation
Indices: 44442--44483 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
44432 ACTATAGTTG
44442 ATAATTATATACGATA-TATAAA
1 ATAATT-TATACGATAGTATAAA
*
44464 ATAATTTATACTATAGTATA
1 ATAATTTATACGATAGTATA
44484 TATAAACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (22 bp):
ATAATTTATACGATAGTATAAA
Found at i:44548 original size:18 final size:18
Alignment explanation
Indices: 44475--44686 Score: 146
Period size: 18 Copynumber: 12.2 Consensus size: 18
44465 TAATTTATAC
*
44475 TATAGTATATATAAACAA
1 TATAGTATATATAAACTA
44493 TATA--ATATAT-AACTA
1 TATAGTATATATAAACTA
44508 TATA-TATAGT-T---C-A
1 TATAGTATA-TATAAACTA
44521 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
*
44538 TATAATATATAT-AACTA
1 TATAGTATATATAAACTA
*
44555 TATGGTATATATAAACTA
1 TATAGTATATATAAACTA
*
44573 TATGGTATATATAAACTA
1 TATAGTATATATAAACTA
* * **
44591 TACACTATATAT-ATTTCA
1 TATAGTATATATAAACT-A
44609 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
* * *
44626 TATATTATATAGTTCATTAGTA
1 TATAGTATATA--T-A-AACTA
*
44648 TATA-TAATGTATAAACTA
1 TATAGT-ATATATAAACTA
*
44666 TATAGTATATGTAAACTA
1 TATAGTATATATAAACTA
44684 TAT
1 TAT
44687 TAGTGTACTA
Statistics
Matches: 154, Mismatches: 21, Indels: 38
0.72 0.10 0.18
Matches are distributed among these distances:
12 3 0.02
13 7 0.05
14 1 0.01
15 8 0.05
16 11 0.07
17 30 0.19
18 77 0.50
19 2 0.01
20 2 0.01
21 2 0.01
22 11 0.07
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.42
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:44563 original size:35 final size:36
Alignment explanation
Indices: 44524--44686 Score: 116
Period size: 35 Copynumber: 4.5 Consensus size: 36
44514 TAGTTCATTA
44524 GTATATATAAACTATATAATATATAT-AACTATATG
1 GTATATATAAACTATATAATATATATAAACTATATG
** **
44559 GTATATATAAACTATATGGTATATATAAACTATACA
1 GTATATATAAACTATATAATATATATAAACTATATG
* ** * *
44595 CTATATAT-ATTTCAT-TAGTATATATAAACTATATA
1 GTATATATAAACT-ATATAATATATATAAACTATATG
* ** * * *
44630 TTATATAGTTCATTAGTATATATAATGTATAAACTATATA
1 GTATATA-TAAACTA-TATA-AT-ATATATAAACTATATG
*
44670 GTATATGTAAACTATAT
1 GTATATATAAACTATAT
44687 TAGTGTACTA
Statistics
Matches: 101, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
35 50 0.50
36 18 0.18
37 3 0.03
38 5 0.05
39 5 0.05
40 20 0.20
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (36 bp):
GTATATATAAACTATATAATATATATAAACTATATG
Found at i:44635 original size:53 final size:53
Alignment explanation
Indices: 44475--44686 Score: 156
Period size: 53 Copynumber: 4.1 Consensus size: 53
44465 TAATTTATAC
* *
44475 TATAGTATATATAAACAATA-TA-ATATATAACTATATA-TATAGT-T---C-A
1 TATAGTATATATAAACTATACAATATATATAACTATATAGTATA-TATAAACTA
* *
44521 T-TAGTATATATAAACTATATAATATATATAACTATATGGTATATATAAACTA
1 TATAGTATATATAAACTATACAATATATATAACTATATAGTATATATAAACTA
* * **
44573 TATGGTATATATAAACTATACACTATATATATTTCAT-TAGTATATATAAACTA
1 TATAGTATATATAAACTATACAATATATATAACT-ATATAGTATATATAAACTA
* ** * * * *
44626 TATATTATATAGTTCATTAGTATATATAATGTATAAACTATATAGTATATGTAAACTA
1 TATAGTATATA-TAAACTA-TACA-AT-ATATAT-AACTATATAGTATATATAAACTA
44684 TAT
1 TAT
44687 TAGTGTACTA
Statistics
Matches: 130, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
45 17 0.13
46 2 0.02
47 15 0.12
48 5 0.04
51 1 0.01
52 2 0.02
53 51 0.39
54 6 0.05
55 3 0.02
56 1 0.01
57 7 0.05
58 20 0.15
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.42
Consensus pattern (53 bp):
TATAGTATATATAAACTATACAATATATATAACTATATAGTATATATAAACTA
Found at i:44652 original size:88 final size:91
Alignment explanation
Indices: 44508--44685 Score: 222
Period size: 88 Copynumber: 2.0 Consensus size: 91
44498 TATATAACTA
*
44508 TATATATAGTTCATTAGTATATATAAACTATATAATATATATAACTAT-ATGGTAT-A-TATAAA
1 TATATATAGTTCATTAGTATATATAAACTATATAATATATATAACTATAATGATATAAGTATAAA
*
44570 CTATATGGTATATATAAACTATACAC
66 CTATATAGTATATATAAACTATACAC
* * * *
44596 TATATATATTTCATTAGTATATATAAACTATATATTATATAGTTCATTAGT-AT-ATATAATGTA
1 TATATATAGTTCATTAGTATATATAAACTATATAATATATA--TAACTA-TAATGATATAA-GTA
*
44659 TAAACTATATAGTATATGTAAACTATA
62 TAAACTATATAGTATATATAAACTATA
44686 TTAGTGTACT
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
88 39 0.51
90 7 0.09
91 4 0.05
93 27 0.35
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (91 bp):
TATATATAGTTCATTAGTATATATAAACTATATAATATATATAACTATAATGATATAAGTATAAA
CTATATAGTATATATAAACTATACAC
Found at i:44670 original size:33 final size:33
Alignment explanation
Indices: 44577--44671 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
44567 AAACTATATG
* *
44577 GTATATATAAACTATACACTATATATATTTCATTA
1 GTATATATAAACTATAAAC--TATATAGTTCATTA
* *
44612 GTATATATAAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATAAACTATATAGTTCATTA
**
44645 GTATATATAATGTATAAACTATATAGT
1 GTATATATAAACTATAAACTATATAGT
44672 ATATGTAAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
33 36 0.68
35 17 0.32
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (33 bp):
GTATATATAAACTATAAACTATATAGTTCATTA
Found at i:44722 original size:21 final size:21
Alignment explanation
Indices: 44697--44749 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
44687 TAGTGTACTA
* *
44697 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
*
44718 TATAGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
44739 TATAGTTTATA
1 TATAGTTTATA
44750 TTAATGTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:44762 original size:20 final size:21
Alignment explanation
Indices: 44682--44778 Score: 72
Period size: 22 Copynumber: 4.5 Consensus size: 21
44672 ATATGTAAAC
*
44682 TATATTAGTGTACTATATAGTT
1 TATATTAATGTAC-ATATAGTT
* * * *
44704 TATACTTTAT-AACCTATAGTA
1 TATA-TTAATGTACATATAGTT
* **
44725 TATAATTTATAAAC-TATAGTT
1 TAT-ATTAATGTACATATAGTT
44746 TATATTAATGTACTATATAGTT
1 TATATTAATGTAC-ATATAGTT
44768 TATATTAATGT
1 TATATTAATGT
44779 TAATTATCTT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
20 7 0.11
21 23 0.38
22 28 0.46
23 3 0.05
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.48
Consensus pattern (21 bp):
TATATTAATGTACATATAGTT
Found at i:44810 original size:15 final size:15
Alignment explanation
Indices: 44760--44982 Score: 99
Period size: 15 Copynumber: 14.5 Consensus size: 15
44750 TTAATGTACT
*
44760 ATATAGTTTATATTA
1 ATATAATTTATATTA
* *
44775 ATGTTAA-TTATCTTA
1 AT-ATAATTTATATTA
44790 ACTATAATTTATATTA
1 A-TATAATTTATATTA
* *
44806 ATATAGTATATAGTTTA
1 ATATAATTTATA--TTA
44823 A-ACTAGA-TTATATTA
1 ATA-TA-ATTTATATTA
*
44838 ATATAAATTATA--A
1 ATATAATTTATATTA
*
44851 ACTATAATTTATA-GA
1 A-TATAATTTATATTA
* *
44866 CTATATTTTATATTA
1 ATATAATTTATATTA
*
44881 ATATTAATTATAAATTA
1 ATA-TAATT-TATATTA
*
44898 TAAACTAGA-TTATATTA
1 -ATA-TA-ATTTATATTA
*
44915 ATATAAGTTAATATTA
1 ATATAA-TTTATATTA
44931 ATATTAA-TTATATTA
1 ATA-TAATTTATATTA
*
44946 ATATTAA-TTATAAT-
1 ATA-TAATTTATATTA
*
44960 ATATAA-TTATTTTA
1 ATATAATTTATATTA
44974 ATATTAATT
1 ATA-TAATT
44983 ATAAATAGTT
Statistics
Matches: 161, Mismatches: 25, Indels: 43
0.70 0.11 0.19
Matches are distributed among these distances:
13 10 0.06
14 28 0.17
15 62 0.39
16 30 0.19
17 25 0.16
18 5 0.03
19 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (15 bp):
ATATAATTTATATTA
Found at i:44873 original size:13 final size:14
Alignment explanation
Indices: 44839--44877 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
44829 ATTATATTAA
*
44839 TATAAATTATAAAC
1 TATAATTTATAAAC
*
44853 TATAATTTATAGAC
1 TATAATTTATAAAC
*
44867 TATATTTTATA
1 TATAATTTATA
44878 TTAATATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (14 bp):
TATAATTTATAAAC
Found at i:44931 original size:6 final size:6
Alignment explanation
Indices: 44909--44981 Score: 50
Period size: 6 Copynumber: 12.3 Consensus size: 6
44899 AAACTAGATT
*
44909 ATATTA ATA-TA A-GTTA ATATTA ATATT- A-ATT- ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
44952 AT-TATA ATATATA ATTATTTTA ATATTA AT
1 ATAT-TA ATAT-TA A-TA--TTA ATATTA AT
44982 TATAAATAGT
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
4 4 0.07
5 11 0.20
6 28 0.50
7 5 0.09
8 4 0.07
9 3 0.05
10 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (6 bp):
ATATTA
Found at i:44941 original size:43 final size:41
Alignment explanation
Indices: 44861--45003 Score: 127
Period size: 43 Copynumber: 3.5 Consensus size: 41
44851 ACTATAATTT
* * *
44861 ATAGACTATATT-TTAT-ATTAATATTAATTATAAATTATAA
1 ATAGATTATATTAATATAATTAATATTAA-TATTAATTATAA
44901 ACTAGATTATATTAATATAAGTTAATATTAATATTAATTATATTA
1 A-TAGATTATATTAATATAA-TTAATATTAATATTAATTATA--A
* * *
44946 ATATTAATTATAAT-ATATAATT-ATTTTAATATTAATTATAA
1 ATA--GATTATATTAATATAATTAATATTAATATTAATTATAA
44987 ATAG-TT-TATTAATATAA
1 ATAGATTATATTAATATAA
45004 ATTTTATAGG
Statistics
Matches: 86, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
37 3 0.03
38 8 0.09
40 1 0.01
41 14 0.16
42 3 0.03
43 28 0.33
44 14 0.16
45 8 0.09
46 7 0.08
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (41 bp):
ATAGATTATATTAATATAATTAATATTAATATTAATTATAA
Found at i:44975 original size:28 final size:27
Alignment explanation
Indices: 44881--45006 Score: 100
Period size: 28 Copynumber: 4.6 Consensus size: 27
44871 TTTTATATTA
* *
44881 ATATTAATTATAAATTATAA-ACTAGATT
1 ATATTAA-TATTAATTATAATATTA-ATT
44909 ATATTAATA-TAAGTTAATATTAATATTAATT
1 ATATTAATATTAA--T--TA-TAATATTAATT
44940 ATATTAATATTAATTATAATATATAATT
1 ATATTAATATTAATTATAATAT-TAATT
* *
44968 ATTTTAATATTAATTATAA-A-TAGTT
1 ATATTAATATTAATTATAATATTAATT
*
44993 -TATTAATATAAATT
1 ATATTAATATTAATT
45007 TTATAGGAAT
Statistics
Matches: 84, Mismatches: 6, Indels: 20
0.76 0.05 0.18
Matches are distributed among these distances:
24 12 0.14
25 4 0.05
26 2 0.02
27 9 0.11
28 33 0.39
30 3 0.04
31 15 0.18
32 6 0.07
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (27 bp):
ATATTAATATTAATTATAATATTAATT
Found at i:45122 original size:5 final size:5
Alignment explanation
Indices: 45112--45136 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
45102 GTTCAGCATC
45112 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
45137 CAAATGATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:47430 original size:23 final size:23
Alignment explanation
Indices: 47403--47459 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
47393 CTTAATGCAG
*
47403 GATGCTTGTTGAATCGATGCAAT
1 GATGCTTGTTGAATCGATACAAT
* * * *
47426 GATGCTTGCTGAATTGGTACATT
1 GATGCTTGTTGAATCGATACAAT
47449 GATGCTTGTTG
1 GATGCTTGTTG
47460 TTGCTGCTGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.39
Consensus pattern (23 bp):
GATGCTTGTTGAATCGATACAAT
Found at i:48189 original size:51 final size:51
Alignment explanation
Indices: 48134--48230 Score: 167
Period size: 51 Copynumber: 1.9 Consensus size: 51
48124 ATATAAAACT
* * *
48134 AAATTTTAAAAAGTAATCATATTAATTTAATTATCATAATAATTTATGATA
1 AAATTTCAAAAAGTAACCACATTAATTTAATTATCATAATAATTTATGATA
48185 AAATTTCAAAAAGTAACCACATTAATTTAATTATCATAATAATTTA
1 AAATTTCAAAAAGTAACCACATTAATTTAATTATCATAATAATTTA
48231 ATTATAATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.40
Consensus pattern (51 bp):
AAATTTCAAAAAGTAACCACATTAATTTAATTATCATAATAATTTATGATA
Found at i:48385 original size:16 final size:16
Alignment explanation
Indices: 48351--48389 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
48341 TGAGTCAATT
* *
48351 ACAGATCAGGTTCATA
1 ACAGGTCAGGTTCAAA
*
48367 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
48383 ACAGGTC
1 ACAGGTC
48390 GGGTAATACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:49151 original size:48 final size:50
Alignment explanation
Indices: 49039--49157 Score: 138
Period size: 50 Copynumber: 2.4 Consensus size: 50
49029 AGGAAAGTGC
* *
49039 CCCCTGCACCGCGCTATACGCTGATTTGGCGCAACGTAGAGTATAGCGCG
1 CCCCTGAACCGCGCTATACGCTGATCTGGCGCAACGTAGAGTATAGCGCG
* * * *
49089 CCCCTGAACCGCGCTATACGTTGA-CTGG-GCACACGTGGGGTATAGCG-T
1 CCCCTGAACCGCGCTATACGCTGATCTGGCGCA-ACGTAGAGTATAGCGCG
49137 CCCCTGATA-CGCGCTATACGC
1 CCCCTGA-ACCGCGCTATACGC
49158 CACGTAGGGG
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
48 21 0.35
49 17 0.28
50 22 0.37
ACGTcount: A:0.19, C:0.33, G:0.28, T:0.20
Consensus pattern (50 bp):
CCCCTGAACCGCGCTATACGCTGATCTGGCGCAACGTAGAGTATAGCGCG
Found at i:53059 original size:6 final size:6
Alignment explanation
Indices: 53043--53096 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
53033 ACTCCTCGCT
* * *
53043 GTCATC ATCATC GTCATC GTCGTC GTCA-C --CATC GTCATC GTCGTC
1 GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC
*
53088 GTCGTC GTC
1 GTCATC GTC
53097 GTCCTGAGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
3 2 0.05
4 1 0.03
5 1 0.03
6 36 0.90
ACGTcount: A:0.13, C:0.35, G:0.20, T:0.31
Consensus pattern (6 bp):
GTCATC
Found at i:53075 original size:21 final size:21
Alignment explanation
Indices: 53051--53090 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
53041 CTGTCATCAT
53051 CATCGTCATCGTCGTCGTCAC
1 CATCGTCATCGTCGTCGTCAC
53072 CATCGTCATCGTCGTCGTC
1 CATCGTCATCGTCGTCGTC
53091 GTCGTCGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.38, G:0.20, T:0.30
Consensus pattern (21 bp):
CATCGTCATCGTCGTCGTCAC
Found at i:53465 original size:18 final size:18
Alignment explanation
Indices: 53442--53476 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
53432 GCGATGGCGG
53442 CATCATATATGGCTGCGA
1 CATCATATATGGCTGCGA
53460 CATCATATATGGCTGCG
1 CATCATATATGGCTGCG
53477 GTGGCTGCTG
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:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (18 bp):
CATCATATATGGCTGCGA
Found at i:55108 original size:111 final size:111
Alignment explanation
Indices: 54975--55196 Score: 381
Period size: 111 Copynumber: 2.0 Consensus size: 111
54965 ATTACAAAAA
* * * * *
54975 TTAATTCTTAATCTAATAATCATGCATTAAATGAATTAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCATAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
55040 AATTAAAATGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAATGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
55086 TTAATTCATAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCATAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
55151 AATTAAAATGTTAAAATGTTACCGTATCAGTAAAGTGTAGAGATAT
66 AATTAAAATGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
55197 ATGATTTCCA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCATAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAATGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:55536 original size:50 final size:49
Alignment explanation
Indices: 55482--55606 Score: 162
Period size: 50 Copynumber: 2.5 Consensus size: 49
55472 AGATATCCAA
*
55482 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAGATCACC
1 GTATAGCGCGG-TCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
* * * *
55532 GTATATCGCGGGGCAGGGGGCGCGCTATACTCACGTGGCGCCAAATCAGC
1 GTATAGCGC-GGTCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
*
55582 TTATAGCGCGGTGC-GGGGGCGCGCT
1 GTATAGCGCGGT-CAGGGGGCGCGCT
55607 TTCCTGCTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
49 13 0.20
50 50 0.77
51 2 0.03
ACGTcount: A:0.18, C:0.29, G:0.38, T:0.16
Consensus pattern (49 bp):
GTATAGCGCGGTCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:55916 original size:15 final size:15
Alignment explanation
Indices: 55893--55926 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
55883 ATAACCCGAC
55893 CCGATCCTATCCTAT
1 CCGATCCTATCCTAT
* *
55908 CCTATCCTATCCGAT
1 CCGATCCTATCCTAT
55923 CCGA
1 CCGA
55927 ATAGTTAATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.21, C:0.41, G:0.09, T:0.29
Consensus pattern (15 bp):
CCGATCCTATCCTAT
Done.