Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007741.1 Hibiscus syriacus cultivar Beakdansim tig00110004_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: 1550271
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:277722 original size:35 final size:34
Alignment explanation
Indices: 277643--277729 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 34
277633 GCTCTGATTA
* * *
277643 AGTTAGTAATTCCTTAAATAGGTTCAACTCGATC
1 AGTTGGTAATTCCTTATATAGGGTCAACTCGATC
* * *
277677 AATTGATAATTACTTATATAGGGTCAACATCGATC
1 AGTTGGTAATTCCTTATATAGGGTCAAC-TCGATC
277712 AGTTGGTAATTCCTTATA
1 AGTTGGTAATTCCTTATA
277730 GACCTAAGGC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
34 22 0.51
35 21 0.49
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (34 bp):
AGTTGGTAATTCCTTATATAGGGTCAACTCGATC
Found at i:281504 original size:22 final size:22
Alignment explanation
Indices: 281474--281515 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
281464 CGATCAACCA
* *
281474 GTCATAGTCAACGGTCTGACTG
1 GTCAAAGTCAACGGTATGACTG
281496 GTCAAAGTCAACGGTATGAC
1 GTCAAAGTCAACGGTATGAC
281516 CGATCACCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (22 bp):
GTCAAAGTCAACGGTATGACTG
Found at i:283681 original size:31 final size:31
Alignment explanation
Indices: 283610--283684 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
283600 TTGGGTCCTG
* **
283610 AGAGCCTACCCAAGAAAGTTCTTGGGGCCAC
1 AGAGTCTACCCAAGAAAAATCTTGGGGCCAC
*
283641 -G-GTCTTACCCAAGAAAAATCTTTGGGCCAC
1 AGAGTC-TACCCAAGAAAAATCTTGGGGCCAC
283671 AGAGTCTACCCAAG
1 AGAGTCTACCCAAG
283685 GGTCATCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 2 0.05
30 23 0.62
31 9 0.24
32 3 0.08
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.19
Consensus pattern (31 bp):
AGAGTCTACCCAAGAAAAATCTTGGGGCCAC
Found at i:286586 original size:22 final size:22
Alignment explanation
Indices: 286517--286586 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
286507 GACTTTATAG
* * *
286517 GTCAAAGTCAATGATCAGACCA
1 GTCAAAGTCAACGGTCTGACCA
* **
286539 GTCATAGTCAACGGTCTGACTG
1 GTCAAAGTCAACGGTCTGACCA
*
286561 GTCAAAGTGAACGGTCTGACCA
1 GTCAAAGTCAACGGTCTGACCA
286583 GTCA
1 GTCA
286587 CCGGTAAATA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.21
Consensus pattern (22 bp):
GTCAAAGTCAACGGTCTGACCA
Found at i:286671 original size:23 final size:23
Alignment explanation
Indices: 286644--286692 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
286634 TAGTTGGGAA
286644 GGCGGGTGGGGCTGACCGGTTCG
1 GGCGGGTGGGGCTGACCGGTTCG
286667 GGCGGGTGGGGCTGACCGGTTCG
1 GGCGGGTGGGGCTGACCGGTTCG
286690 GGC
1 GGC
286693 CGGCCTAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.04, C:0.22, G:0.57, T:0.16
Consensus pattern (23 bp):
GGCGGGTGGGGCTGACCGGTTCG
Found at i:292269 original size:23 final size:22
Alignment explanation
Indices: 292220--292269 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
292210 GATCTGGTAG
*
292220 GTCAAAGTCAACAGTCTGACCA
1 GTCAAAGTCAACAGTCAGACCA
* * *
292242 ATCAAAGATCAACGGTCAGACTA
1 GTCAAAG-TCAACAGTCAGACCA
292265 GTCAA
1 GTCAA
292270 TGGTAAGACT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (22 bp):
GTCAAAGTCAACAGTCAGACCA
Found at i:293345 original size:19 final size:19
Alignment explanation
Indices: 293321--293361 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
293311 TGGTTGGAAA
*
293321 ATTGACACCATTGTTGAAC
1 ATTGACACCATTGTAGAAC
293340 ATTGACACCATTGTAGAAC
1 ATTGACACCATTGTAGAAC
293359 ATT
1 ATT
293362 ATAACTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (19 bp):
ATTGACACCATTGTAGAAC
Found at i:301402 original size:22 final size:22
Alignment explanation
Indices: 301377--301422 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
301367 AAAGCTTTCG
301377 TCTTTGAAAAAAGAATCTATCA
1 TCTTTGAAAAAAGAATCTATCA
*
301399 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAAAGAATCTATCA
301421 TC
1 TC
301423 CTTGCAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (22 bp):
TCTTTGAAAAAAGAATCTATCA
Found at i:307698 original size:19 final size:19
Alignment explanation
Indices: 307674--307711 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
307664 AAAGTAAAAT
307674 TACTAAT-ATTAATTAATTA
1 TACTAATAATTAA-TAATTA
307693 TACTAATAATTAATAATTA
1 TACTAATAATTAATAATTA
307712 AAGAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
TACTAATAATTAATAATTA
Found at i:316088 original size:19 final size:19
Alignment explanation
Indices: 316038--316094 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
316028 CTAGGTTATT
316038 CAATGCATGGGCGGCTGAAAA
1 CAATGCATGGGCGGCT--AAA
316059 CAA-G--TGTGGCGGCTAAA
1 CAATGCATG-GGCGGCTAAA
316076 CAATGCATGGGCGGCTAAA
1 CAATGCATGGGCGGCTAAA
316095 TGGTCAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
17 6 0.19
18 3 0.09
19 17 0.53
20 3 0.09
21 3 0.09
ACGTcount: A:0.32, C:0.19, G:0.33, T:0.16
Consensus pattern (19 bp):
CAATGCATGGGCGGCTAAA
Found at i:329841 original size:13 final size:13
Alignment explanation
Indices: 329817--329865 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
329807 GCTAAATGAA
329817 CGTCATAAATGTG
1 CGTCATAAATGTG
329830 CGTCATAAATGTG
1 CGTCATAAATGTG
* * * **
329843 TGTAAAAAATGCA
1 CGTCATAAATGTG
329856 CGTCATAAAT
1 CGTCATAAAT
329866 TTATGACGCA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (13 bp):
CGTCATAAATGTG
Found at i:335310 original size:16 final size:16
Alignment explanation
Indices: 335289--335321 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
335279 TTTGAAAAAT
335289 ATTTTTATAAA-ATTTA
1 ATTTTTA-AAACATTTA
335305 ATTTTTAAAACATTTA
1 ATTTTTAAAACATTTA
335321 A
1 A
335322 AATAATTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTTAAAACATTTA
Found at i:335371 original size:3 final size:3
Alignment explanation
Indices: 335363--335423 Score: 52
Period size: 3 Copynumber: 19.0 Consensus size: 3
335353 CCATTTGTTT
* *
335363 TTA TTA TTA TTA -TA TTA TTC GTA TTA TTTA TTTA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA T-TA TTA TTA TTA
335410 TATA TATA TTA TTA
1 T-TA T-TA TTA TTA
335424 AATAAATAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 2 0.04
3 31 0.62
4 17 0.34
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:335380 original size:11 final size:11
Alignment explanation
Indices: 335364--335421 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 11
335354 CATTTGTTTT
335364 TATTATTATTA
1 TATTATTATTA
335375 TATTATTCGTATTA
1 TATTA-T--TATTA
335389 T-TTATT-TATA
1 TATTATTAT-TA
335399 TATTATTATTA
1 TATTATTATTA
335410 TA-TATATATTA
1 TATTAT-TATTA
335421 T
1 T
335422 TAAATAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
9 1 0.03
10 7 0.17
11 20 0.50
12 3 0.08
13 3 0.08
14 6 0.15
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTATTATTA
Found at i:335404 original size:15 final size:15
Alignment explanation
Indices: 335373--335422 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 15
335363 TTATTATTAT
**
335373 TATATTATTCGTAT-
1 TATATTATTTATATA
335387 TAT-TTATTTATATA
1 TATATTATTTATATA
335401 T-TATTA-TTATATA
1 TATATTATTTATATA
335414 TATATTATT
1 TATATTATT
335423 AAATAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 17 0.57
14 12 0.40
15 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (15 bp):
TATATTATTTATATA
Found at i:335410 original size:17 final size:17
Alignment explanation
Indices: 335364--335423 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
335354 CATTTGTTTT
335364 TATTATTATTATATTAT-
1 TATTATTATTAT-TTATA
**
335381 TCGTATTATTTATTTATA
1 TATTATTA-TTATTTATA
*
335399 TATTATTATTATATATA
1 TATTATTATTATTTATA
335416 TATTATTA
1 TATTATTA
335424 AATAAATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 26 0.72
18 10 0.28
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TATTATTATTATTTATA
Found at i:336825 original size:17 final size:19
Alignment explanation
Indices: 336796--336837 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
336786 ATTTAATTTT
336796 ATAA-ATTACTTTTAA-AA
1 ATAATATTACTTTTAATAA
*
336813 ATAATATTA-TTTTAATAT
1 ATAATATTACTTTTAATAA
336831 ATAATAT
1 ATAATAT
336838 CAATATTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAATATTACTTTTAATAA
Found at i:336981 original size:27 final size:27
Alignment explanation
Indices: 336929--336981 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
336919 TAAATTATAT
*
336929 ATAAATATATTTTTATATTATTTTTAG
1 ATAAATATATTTTTATATTATATTTAG
336956 ATAAATAT-TTTATTAATATT-TATTTA
1 ATAAATATATTT-TT-ATATTATATTTA
336982 TTCTTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 3 0.13
27 15 0.65
28 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
ATAAATATATTTTTATATTATATTTAG
Found at i:340931 original size:15 final size:15
Alignment explanation
Indices: 340911--340942 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
340901 GATCAATACC
340911 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
340926 TTTTGCATACATTCA
1 TTTTGCATACATGCA
340941 TT
1 TT
340943 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:350856 original size:113 final size:113
Alignment explanation
Indices: 350658--351112 Score: 481
Period size: 113 Copynumber: 4.0 Consensus size: 113
350648 TTTCAAAGAT
* * * *
350658 TCGAATCCATCATTCGATGGATCAAC-TGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTG
1 TCGAATTCATCACTCGATGGATCAACAT-TGCCAGAGGAAGTTCATAATGAGAAGAACTCATCTG
* *
350722 AAGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
350771 TCGAATTCATCACTTGATGGATCAGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTG
1 TCGAATTCATCACTCGATGGATCAACATTGCCAGAGGA-AGTTCATAATGAGAAGAACTCATCTG
* * *
350835 AAGAAGTAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * *
350884 TTGAATTCATTACTCGATGGATCAACTTTTCCAGAGGAAGTTCATAATAATAAGAACTCATCTGA
1 TCGAATTCATCACTCGATGGATCAACATTGCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGA
*
350949 AG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * * * * *
350995 TTGATTATATCATAGAAGGAGATAGATCAGCATCAACATTTCGAGAAG-TGTTCATAATGAGAAG
1 TCGA--AT-TCAT-----CA-CTCGAT--GGATCAACATTGCCAGAGGAAGTTCATAATGAGAAG
* *
351059 AACTCATTTGAAGAAGG-AGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTT
55 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
351113 AATTTAATTC
Statistics
Matches: 289, Mismatches: 37, Indels: 23
0.83 0.11 0.07
Matches are distributed among these distances:
111 8 0.03
112 37 0.13
113 154 0.53
114 7 0.02
119 1 0.00
120 4 0.01
121 59 0.20
122 19 0.07
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
TCGAATTCATCACTCGATGGATCAACATTGCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:351425 original size:3 final size:3
Alignment explanation
Indices: 351412--351500 Score: 94
Period size: 3 Copynumber: 29.3 Consensus size: 3
351402 ATTTGTTTTC
*
351412 ATT AAT ATT ATT ATT ATT A-T ATT ATT ATT CA-T ATT ATT -TT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT A-TT
* *
351456 ATAT ATT TTT ATT ATAT ATT ATT ATT ATT AAT ATT ATT ATT ATT A
1 AT-T ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT A
351501 AATAAATAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 14
0.78 0.06 0.15
Matches are distributed among these distances:
2 5 0.07
3 58 0.79
4 10 0.14
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:352770 original size:3 final size:3
Alignment explanation
Indices: 352762--352799 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
352752 AGTATATTTA
*
352762 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
352800 AAATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:356669 original size:186 final size:189
Alignment explanation
Indices: 356438--356844 Score: 640
Period size: 186 Copynumber: 2.2 Consensus size: 189
356428 TAACTGAGTT
* *
356438 AACCACATGCTCTGAGTGAAATGGTTGTGCCATATAACTTCTATTGTCTGAGAGTTGTTCCGTCT
1 AACCACATGCTCTGAGTGAAATGGTTGAGCCATATAACCTCTATTGTCTGAGAGTTGTTCCGTCT
*
356503 GATCAAGATTATAGATAAATTAACAAAGGATTATATAATGTAGTGTAAATAGGTTATAATTGATA
66 GATCAAGATTATAGATAAATTAACAAAGGATTATATAATGTAGTGTAAATAGATTATAATTGATA
* * *
356568 GGCATATAGTGGGAGGTTACCATTCCAATATGATCATTGACTTGATTTG-T-CTGA-AC
131 CGCATATAGTGGGAGGTTACCATTCCAATACGACCATTGACTTGATTTGCTGCTGAGAC
* ** *
356624 AACCACATGTTCTGAGTGAAATGGTTGAGCTGTATAACCTCTATTGTGTGAGAGTTGTTCCGTCT
1 AACCACATGCTCTGAGTGAAATGGTTGAGCCATATAACCTCTATTGTCTGAGAGTTGTTCCGTCT
* *
356689 GATCAAGATTATAGATAAATTAACAAATGATTATATAATGTAGTGTAAATAGATTATAATTGATT
66 GATCAAGATTATAGATAAATTAACAAAGGATTATATAATGTAGTGTAAATAGATTATAATTGATA
**
356754 CGCATATAGTGGGAGGTTACCATTCCAATACGACCATTGACTTGATTTGCTTGGACTGAGTT
131 CGCATATAGTGGGAGGTTACCATTCCAATACGACCATTGACTTGATTTGC-T-G-CTGAGAC
356816 AACCACATGCTCTGAGTGAAATGGTTGAG
1 AACCACATGCTCTGAGTGAAATGGTTGAG
356845 TCGAGTAACC
Statistics
Matches: 200, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
186 167 0.83
188 1 0.00
191 4 0.02
192 28 0.14
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (189 bp):
AACCACATGCTCTGAGTGAAATGGTTGAGCCATATAACCTCTATTGTCTGAGAGTTGTTCCGTCT
GATCAAGATTATAGATAAATTAACAAAGGATTATATAATGTAGTGTAAATAGATTATAATTGATA
CGCATATAGTGGGAGGTTACCATTCCAATACGACCATTGACTTGATTTGCTGCTGAGAC
Found at i:356991 original size:126 final size:126
Alignment explanation
Indices: 356788--357020 Score: 324
Period size: 126 Copynumber: 1.8 Consensus size: 126
356778 CCAATACGAC
* * * * * *
356788 CATTGACTTGATTTGCTTGGACTGAGTTAACCACATGCTCTGAGTGAAATGGTTGAGTCGAGTAA
1 CATTGACCTGATTTGCTTGAACTGAGCTAACCACATGCTCCGAGTGAAACGGTTGAGTCGAATAA
* * *
356853 CCTGCATTTTGTGGGACCTCTTTCGTCTGATCAAGATGAGAGGTTACCAGTCTAGTGAGAT
66 CCTCCATTTTGTGGGACATCTTTCGCCTGATCAAGATGAGAGGTTACCAGTCTAGTGAGAT
* *
356914 CATTGACCTGATTTGTTTGAACTGAGCTAATCC-CATGCTCCGAGTGAAACGGTTGAGTTGAATA
1 CATTGACCTGATTTGCTTGAACTGAGCTAA-CCACATGCTCCGAGTGAAACGGTTGAGTCGAATA
* * *
356978 ACCTCCATTTTGTGTGACATTTTTTGCCTGATCAAGATGAGAG
65 ACCTCCATTTTGTGGGACATCTTTCGCCTGATCAAGATGAGAG
357021 ATAAATTAAC
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
126 90 0.98
127 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (126 bp):
CATTGACCTGATTTGCTTGAACTGAGCTAACCACATGCTCCGAGTGAAACGGTTGAGTCGAATAA
CCTCCATTTTGTGGGACATCTTTCGCCTGATCAAGATGAGAGGTTACCAGTCTAGTGAGAT
Found at i:358297 original size:12 final size:11
Alignment explanation
Indices: 358282--358318 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
358272 ATTACTTACC
358282 TAATTTAATATT
1 TAATTTAAT-TT
358294 TAATTTAATTTT
1 TAATTTAA-TTT
358306 TAATTTAATTT
1 TAATTTAATTT
358317 TA
1 TA
358319 GGATAAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 5 0.21
12 18 0.75
13 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TAATTTAATTT
Found at i:361570 original size:59 final size:59
Alignment explanation
Indices: 361475--361656 Score: 210
Period size: 59 Copynumber: 3.1 Consensus size: 59
361465 TGCATTATCT
* *
361475 ATCCTCAAACTATAACTCTTATTTTAAATTGATCCTTAAACTTTTGAA-ATTCCAATTTC
1 ATCCTCAAACTATGACTCTCATTTTAAATTG-TCCTTAAACTTTTGAACATTCCAATTTC
* *
361534 ATCCTCAAACTATGACTCTCATTTTAAATTAGTCCTTAAACTTTTGAACATTCTAATATC
1 ATCCTCAAACTATGACTCTCATTTTAAATT-GTCCTTAAACTTTTGAACATTCCAATTTC
* * * * *
361594 ATCCTTAAATTATGATTCTC-TTTCTAAATTGGTCC-CAAACTTTTGAATC-TTCCAATTTT
1 ATCCTCAAACTATGACTCTCATTT-TAAATT-GTCCTTAAACTTTTGAA-CATTCCAATTTC
361653 ATCC
1 ATCC
361657 AAAAATTCAT
Statistics
Matches: 107, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
59 69 0.64
60 38 0.36
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.42
Consensus pattern (59 bp):
ATCCTCAAACTATGACTCTCATTTTAAATTGTCCTTAAACTTTTGAACATTCCAATTTC
Found at i:372315 original size:57 final size:56
Alignment explanation
Indices: 372244--372354 Score: 141
Period size: 56 Copynumber: 2.0 Consensus size: 56
372234 CCATTTGACG
** * * *
372244 TAGGAGCCTCCCTAAGGGAATACCATAGGTTCATAAGGACTTACACTAGCCGAAGAA
1 TAGGAGCCAACCTAAGGGAACA-CATAGGTCCATAAGGACTTACACTAGACGAAGAA
* * *
372301 TAGGAGCCAACCTAAGGGAACACTTTGGTCCATAAGGACTTACTCTAGACGAAG
1 TAGGAGCCAACCTAAGGGAACACATAGGTCCATAAGGACTTACACTAGACGAAG
372355 CGTATGAGCC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
56 27 0.59
57 19 0.41
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (56 bp):
TAGGAGCCAACCTAAGGGAACACATAGGTCCATAAGGACTTACACTAGACGAAGAA
Found at i:373652 original size:13 final size:11
Alignment explanation
Indices: 373611--373657 Score: 58
Period size: 11 Copynumber: 4.0 Consensus size: 11
373601 CTCAAAGGTA
373611 TTTTCATCAAT
1 TTTTCATCAAT
*
373622 TTTTCATCATT
1 TTTTCATCAAT
373633 TTTTCATCCAAT
1 TTTTCAT-CAAT
373645 TGTTTCATGCAAT
1 T-TTTCAT-CAAT
373658 AAATCATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
11 17 0.55
12 4 0.13
13 10 0.32
ACGTcount: A:0.23, C:0.19, G:0.04, T:0.53
Consensus pattern (11 bp):
TTTTCATCAAT
Found at i:374074 original size:26 final size:27
Alignment explanation
Indices: 374019--374096 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 27
374009 ATTTGATTTT
*
374019 AATTTTAATATTAATTTTTTAA-A-TA
1 AATTATAATATTAATTTTTTAATATTA
374044 AATTA-AATATTAATTTTTTAATATTA
1 AATTATAATATTAATTTTTTAATATTA
*
374070 TATTATAGATATTAA--TTTTAATATTA
1 AATTATA-ATATTAATTTTTTAATATTA
374096 A
1 A
374097 TTTTTAAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
24 16 0.35
25 5 0.11
26 17 0.37
27 1 0.02
28 7 0.15
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
AATTATAATATTAATTTTTTAATATTA
Found at i:374127 original size:62 final size:64
Alignment explanation
Indices: 373998--374152 Score: 257
Period size: 62 Copynumber: 2.5 Consensus size: 64
373988 TTATGTTTAA
*
373998 TTTT-ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
374059 TTTTAATATTATATTATAGATATTAATTTTAATATTAA-TTTTTAAATAAATTAAATATT-ATT
1 TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
374121 TTTTAATATTATATTATAGATATTTAATTTTA
1 TTTTAATATTATATTATAGATA-TTAATTTTA
374153 TATCATATAA
Statistics
Matches: 89, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
61 4 0.04
62 35 0.39
63 31 0.35
64 19 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (64 bp):
TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
Found at i:374207 original size:20 final size:19
Alignment explanation
Indices: 374147--374208 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
374137 TAGATATTTA
*
374147 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
374166 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
374184 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
374204 ATTTT
1 ATTTT
374209 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:392154 original size:15 final size:15
Alignment explanation
Indices: 392134--392165 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
392124 GTATGCTCCT
392134 ACCGATGTAGGTTTG
1 ACCGATGTAGGTTTG
392149 ACCGATGTAGGTTTG
1 ACCGATGTAGGTTTG
392164 AC
1 AC
392166 GCCTGAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (15 bp):
ACCGATGTAGGTTTG
Found at i:394250 original size:80 final size:81
Alignment explanation
Indices: 394117--394331 Score: 279
Period size: 80 Copynumber: 2.7 Consensus size: 81
394107 AATAAAAGGT
* * * *
394117 TAAATGCCTAATTGTGCCTTTGGCAGAAAGGTGCCAATAATACAAGTTAGATGAAAGGTTAAATG
1 TAAATGCCTAACTGTGCATTTGGCAGAAAGGTTCCAATAATGCAAGTTAGATGAAAGGTTAAATG
* *
394182 CCTT-AGATGAAACAC
66 CCTTCAAAGGAAACAC
* * * *
394197 TAAATGCGTATCTGTGCATTTGGAAGAAAGGTTCCAATAATGCTAGTTAGATGAAAGGTTAAATG
1 TAAATGCCTAACTGTGCATTTGGCAGAAAGGTTCCAATAATGCAAGTTAGATGAAAGGTTAAATG
***
394262 CCTTCAAAGGAAAGGT
66 CCTTCAAAGGAAACAC
* *
394278 TAAATTCCTAACTGTGCATTTTGGCAGAAAGGTTCCATTAATGCAAGTTAGATG
1 TAAATGCCTAACTGTGCA-TTTGGCAGAAAGGTTCCAATAATGCAAGTTAGATG
394332 TAAAACAGTG
Statistics
Matches: 114, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
80 61 0.54
81 21 0.18
82 32 0.28
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (81 bp):
TAAATGCCTAACTGTGCATTTGGCAGAAAGGTTCCAATAATGCAAGTTAGATGAAAGGTTAAATG
CCTTCAAAGGAAACAC
Found at i:402947 original size:23 final size:23
Alignment explanation
Indices: 402902--402947 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
402892 TAAAGTCAAT
* *
402902 GGTCAAAGTCAACGGGTGGACTC
1 GGTCAAAGTCAACGAGTGCACTC
* *
402925 GGTCAAAGTCAATGAGTTCACTC
1 GGTCAAAGTCAACGAGTGCACTC
402948 AGTGAGTTGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (23 bp):
GGTCAAAGTCAACGAGTGCACTC
Found at i:422396 original size:31 final size:31
Alignment explanation
Indices: 422329--422388 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
422319 CAATTTAAGG
*
422329 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
422360 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
422389 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:422570 original size:21 final size:21
Alignment explanation
Indices: 422544--422585 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
422534 ATTTGAATAT
*
422544 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
422565 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
422586 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:422907 original size:34 final size:32
Alignment explanation
Indices: 422869--422938 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
422859 TTTTGAAAAG
*
422869 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
422903 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
422935 GGGA
1 GGGA
422939 GTTTTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:429546 original size:30 final size:30
Alignment explanation
Indices: 429506--429566 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
429496 TTGATCCAAG
429506 AAGGATGTGTAGTCACTTATGAGACTCGTT
1 AAGGATGTGTAGTCACTTATGAGACTCGTT
* *
429536 AAGGGTGTGTAGTCACTTATGAGGCTCGTT
1 AAGGATGTGTAGTCACTTATGAGACTCGTT
429566 A
1 A
429567 GCTTAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.33
Consensus pattern (30 bp):
AAGGATGTGTAGTCACTTATGAGACTCGTT
Found at i:438435 original size:12 final size:12
Alignment explanation
Indices: 438418--438446 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
438408 CACTTCCCTC
438418 TTTCACTTTCTA
1 TTTCACTTTCTA
438430 TTTCACTTTCTA
1 TTTCACTTTCTA
438442 TTTCA
1 TTTCA
438447 GTCGTTCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTCACTTTCTA
Found at i:441853 original size:24 final size:21
Alignment explanation
Indices: 441778--441874 Score: 149
Period size: 21 Copynumber: 4.6 Consensus size: 21
441768 ATTTACCGTG
* *
441778 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGTCGTCGCGGACGCT
* *
441799 ATTGCAGTCGTCGCTGACGCT
1 ATTGCGGTCGTCGCGGACGCT
441820 ATTGCGGTCGTCGCGGACGCT
1 ATTGCGGTCGTCGCGGACGCT
441841 ATTGCGGTCGTCGCGGACGCT
1 ATTGCGGTCGTCGCGGACGCT
*
441862 ATTGCGGCCGTCG
1 ATTGCGGTCGTCG
441875 TGGGTAACTC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.09, C:0.30, G:0.37, T:0.24
Consensus pattern (21 bp):
ATTGCGGTCGTCGCGGACGCT
Found at i:447364 original size:21 final size:18
Alignment explanation
Indices: 447340--447378 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
447330 CGATACCCCT
447340 CTCTCGTCCTTCGTCTTCTCC
1 CTCTCG-CCTTC--CTTCTCC
447361 CTCTCGCCTTCCTTCTCC
1 CTCTCGCCTTCCTTCTCC
447379 AACCGTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.00, C:0.51, G:0.08, T:0.41
Consensus pattern (18 bp):
CTCTCGCCTTCCTTCTCC
Found at i:452188 original size:10 final size:11
Alignment explanation
Indices: 452162--452191 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
452152 CGGTAAATGG
452162 TTGATAATACT
1 TTGATAATACT
452173 TTGATAATAC-
1 TTGATAATACT
452183 TTGATAATA
1 TTGATAATA
452192 TAATCATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (11 bp):
TTGATAATACT
Found at i:457620 original size:39 final size:36
Alignment explanation
Indices: 457531--457639 Score: 130
Period size: 39 Copynumber: 3.0 Consensus size: 36
457521 ACTGTATATT
* * * *
457531 TGTCCCGAAGGA-AACTATGTCCTGAAGGACTACTA
1 TGTCCCAAAGGACCACTATGTCCCGAAGGACCACTA
*
457566 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TGTCCCAAAGGACCACTATGTCCCGAAGGACCACT-A
*
457603 TTTGTCCCAAATGACCACTATGTCCCGAAGGACCACT
1 --TGTCCCAAAGGACCACTATGTCCCGAAGGACCACT
457640 CCTTAAGAAC
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
35 12 0.18
36 19 0.29
37 1 0.02
39 33 0.51
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (36 bp):
TGTCCCAAAGGACCACTATGTCCCGAAGGACCACTA
Found at i:457636 original size:18 final size:18
Alignment explanation
Indices: 457531--457639 Score: 139
Period size: 18 Copynumber: 5.9 Consensus size: 18
457521 ACTGTATATT
*
457531 TGTCCCGAAGGA-AACTA
1 TGTCCCGAAGGACCACTA
* *
457548 TGTCCTGAAGGACTACTA
1 TGTCCCGAAGGACCACTA
457566 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
457584 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
457603 TTTGTCCCAAATGACCACTA
1 --TGTCCCGAAGGACCACTA
457623 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
457640 CCTTAAGAAC
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
17 11 0.14
18 52 0.65
19 1 0.01
20 1 0.01
21 15 0.19
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:462201 original size:13 final size:13
Alignment explanation
Indices: 462183--462208 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
462173 GTGTGTGTGC
462183 ATATATATATATA
1 ATATATATATATA
462196 ATATATATATATA
1 ATATATATATATA
462209 TAGTGTTCAC
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:462527 original size:18 final size:18
Alignment explanation
Indices: 462504--462613 Score: 130
Period size: 18 Copynumber: 5.9 Consensus size: 18
462494 ACTGTATATT
462504 TGTCCCAAAGGACCACTA
1 TGTCCCAAAGGACCACTA
* *
462522 TGTCCCGAAGGACTACTA
1 TGTCCCAAAGGACCACTA
* *
462540 TATCCCGAAGGACCACTA
1 TGTCCCAAAGGACCACTA
462558 TGTCCCAAAGGACCACTGA
1 TGTCCCAAAGGACCACT-A
* *
462577 TTTATCCCAAATGACCACTA
1 --TGTCCCAAAGGACCACTA
*
462597 TGTCCCGAAGGACCACT
1 TGTCCCAAAGGACCACT
462614 CCTTAAGAAC
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
18 61 0.78
19 1 0.01
20 1 0.01
21 15 0.19
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:462594 original size:39 final size:38
Alignment explanation
Indices: 462500--462613 Score: 160
Period size: 39 Copynumber: 3.0 Consensus size: 38
462490 GGGCACTGTA
* *
462500 TATTTGTCCCAAAGGACCACTATGTCCCGAAGGACTAC
1 TATTTATCCCAAAGGACCACTATGTCCCGAAGGACCAC
* *
462538 TA--TATCCCGAAGGACCACTATGTCCCAAAGGACCAC
1 TATTTATCCCAAAGGACCACTATGTCCCGAAGGACCAC
*
462574 TGATTTATCCCAAATGACCACTATGTCCCGAAGGACCAC
1 T-ATTTATCCCAAAGGACCACTATGTCCCGAAGGACCAC
462613 T
1 T
462614 CCTTAAGAAC
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
36 31 0.47
37 1 0.02
38 2 0.03
39 32 0.48
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (38 bp):
TATTTATCCCAAAGGACCACTATGTCCCGAAGGACCAC
Found at i:466562 original size:40 final size:42
Alignment explanation
Indices: 466497--466576 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
466487 TATTAATATT
*
466497 TAATATAAATTTATATTTTTAAATAA-A-TTAATTATATAAA
1 TAATATAAATTTATATTTTTAAATAATATTTAAATATATAAA
*
466537 TAATATAGATATTTTTA-TTTT-AATAATATTTAAATATATA
1 TAATATA-A-ATTTATATTTTTAAATAATATTTAAATATATA
466577 TTTTAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
40 12 0.35
41 6 0.18
42 16 0.47
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (42 bp):
TAATATAAATTTATATTTTTAAATAATATTTAAATATATAAA
Found at i:466587 original size:26 final size:26
Alignment explanation
Indices: 466558--466611 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
466548 TTTTTATTTT
466558 AATAATATT-TAAATATATATTTTAAA
1 AATAATATTATAAATA-ATATTTTAAA
* *
466584 AATATTATTATAATTAATATTTTAAA
1 AATAATATTATAAATAATATTTTAAA
466610 AA
1 AA
466612 ATATAACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AATAATATTATAAATAATATTTTAAA
Found at i:466650 original size:18 final size:18
Alignment explanation
Indices: 466588--466652 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 18
466578 TTTAAAAATA
*
466588 TTATTATAATTAATAT-T
1 TTATAATAATTAATATAT
*
466605 TTA-AAAAATATAACTATTACT
1 TTATAATAAT-TAA-TA-TA-T
466626 TTAATAATAATTAATATAT
1 TT-ATAATAATTAATATAT
466645 TTATAATA
1 TTATAATA
466653 TTTTATTTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
16 4 0.11
17 6 0.16
18 8 0.21
19 4 0.11
20 2 0.05
21 5 0.13
22 4 0.11
23 5 0.13
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
TTATAATAATTAATATAT
Found at i:466924 original size:14 final size:14
Alignment explanation
Indices: 466892--466918 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
466882 AATGTAATTC
466892 ATTTTACGGAAAAA
1 ATTTTACGGAAAAA
466906 ATTTTACGGAAAA
1 ATTTTACGGAAAA
466919 CGTTTTCCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (14 bp):
ATTTTACGGAAAAA
Found at i:466958 original size:20 final size:20
Alignment explanation
Indices: 466921--466959 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
466911 ACGGAAAACG
**
466921 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
466941 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
466960 CAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:466975 original size:15 final size:15
Alignment explanation
Indices: 466933--466978 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
466923 TTCCAGAAAT
466933 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
466948 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
466962 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
466977 GT
1 GT
466979 TCCAGTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:466996 original size:21 final size:21
Alignment explanation
Indices: 466957--466996 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
466947 AGAATTCAAA
**
466957 TTCCAGTAATTCATTTTCCAG
1 TTCCAGTAATTCAAATTCCAG
466978 TTCCAGTAATTCAAATTCC
1 TTCCAGTAATTCAAATTCC
466997 GTAATTCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (21 bp):
TTCCAGTAATTCAAATTCCAG
Found at i:467382 original size:60 final size:60
Alignment explanation
Indices: 467304--467447 Score: 159
Period size: 59 Copynumber: 2.4 Consensus size: 60
467294 CTTGGAGACT
* * * * **
467304 AATTTAGAACAA-AGGTCATAGTTTGAGGGAT-AATTTGAAATTTTCAAAAGTTTGGGGAAC
1 AATTTAGAATAAGA-GTCATAGTTTGAGGGATGAAATTAAAATGTT-AAAAGTTTAAGGAAC
** *
467364 AATTTAGAATGGGAGTCATAGTTT-AGGGATGAAATTAAAATGTTAAAAGTTTAAGGATC
1 AATTTAGAATAAGAGTCATAGTTTGAGGGATGAAATTAAAATGTTAAAAGTTTAAGGAAC
*
467423 AATTTAGAATAAGAGTCATAATTTG
1 AATTTAGAATAAGAGTCATAGTTTG
467448 GGAATGTATA
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
59 39 0.57
60 29 0.42
61 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (60 bp):
AATTTAGAATAAGAGTCATAGTTTGAGGGATGAAATTAAAATGTTAAAAGTTTAAGGAAC
Found at i:467789 original size:19 final size:19
Alignment explanation
Indices: 467754--467793 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
467744 CTGAAAACTG
*
467754 AAAATAAAAAGTATTCTTAA
1 AAAATAAAAACTATTC-TAA
467774 AAAATAAAAACT-TTCTAA
1 AAAATAAAAACTATTCTAA
467792 AA
1 AA
467794 GCAATCAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 3 0.16
20 11 0.58
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAATAAAAACTATTCTAA
Found at i:473441 original size:11 final size:11
Alignment explanation
Indices: 473425--473449 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
473415 TTTTAAACTA
473425 ATATATATTTT
1 ATATATATTTT
473436 ATATATATTTT
1 ATATATATTTT
473447 ATA
1 ATA
473450 ACTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATATATTTT
Found at i:473834 original size:20 final size:19
Alignment explanation
Indices: 473768--473879 Score: 98
Period size: 20 Copynumber: 5.6 Consensus size: 19
473758 AAATAACCAA
* *
473768 CGAATTCGCAACTCAATTT
1 CGAATTCGCAACACAGTTT
***
473787 CGAATTCGCAACACAAACT
1 CGAATTCGCAACACAGTTT
*
473806 CTAATTTCGCAACACAGTTT
1 CGAA-TTCGCAACACAGTTT
473826 CCGAATTCGCAACACAGAATTT
1 -CGAATTCGCAACACAG--TTT
* **
473848 GGAATTCGCAACACAGAAGT
1 CGAATTCGCAACACAG-TTT
473868 CGAATTCGCAAC
1 CGAATTCGCAAC
473880 TCTAATTTGA
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
19 19 0.25
20 37 0.48
21 18 0.23
22 3 0.04
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (19 bp):
CGAATTCGCAACACAGTTT
Found at i:473872 original size:41 final size:40
Alignment explanation
Indices: 473769--473879 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 40
473759 AATAACCAAC
*
473769 GAATTCGCAACTCA-ATTTCGAATTCGCAACACAAACTCT
1 GAATTCGCAACACAGATTTCGAATTCGCAACACAAACTCT
*
473808 -AATTTCGCAACACAG-TTTCCGAATTCGCAACACAGAA-TTT
1 GAA-TTCGCAACACAGATTT-CGAATTCGCAACACA-AACTCT
**
473848 GGAATTCGCAACACAGAAGTCGAATTCGCAAC
1 -GAATTCGCAACACAGATTTCGAATTCGCAAC
473880 TCTAATTTGA
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
38 2 0.03
39 13 0.21
40 17 0.28
41 26 0.43
42 3 0.05
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.23
Consensus pattern (40 bp):
GAATTCGCAACACAGATTTCGAATTCGCAACACAAACTCT
Found at i:473956 original size:40 final size:40
Alignment explanation
Indices: 473872--474001 Score: 118
Period size: 40 Copynumber: 3.2 Consensus size: 40
473862 AGAAGTCGAA
* * * * * *
473872 TTCGCAACTCTAATTTGACAATTTCGCAACACAAATTTCTTT
1 TTCGCAACTCGATTTTTA-AATTT-GCAACACGAGTTTCATT
*
473914 TTCGCAACTCGATTTTTAAATTTGCAACACGAGTTTCCTT
1 TTCGCAACTCGATTTTTAAATTTGCAACACGAGTTTCATT
** * * *
473954 TTCGCAACAAGATTTTCT-AATTCGTAACGCGAGTTTCATT
1 TTCGCAACTCGATTTT-TAAATTTGCAACACGAGTTTCATT
473994 TTCGCAAC
1 TTCGCAAC
474002 AGGAATTTCG
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
40 54 0.72
41 6 0.08
42 15 0.20
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (40 bp):
TTCGCAACTCGATTTTTAAATTTGCAACACGAGTTTCATT
Found at i:473960 original size:20 final size:20
Alignment explanation
Indices: 473937--474021 Score: 73
Period size: 20 Copynumber: 4.2 Consensus size: 20
473927 TTTTAAATTT
473937 GCAACACGAGTTTCCTTTTC
1 GCAACACGAGTTTCCTTTTC
* * *
473957 GCAACAAGA-TTTTCTAATTC
1 GCAACACGAGTTTCCT-TTTC
* * *
473977 GTAACGCGAGTTTCATTTTC
1 GCAACACGAGTTTCCTTTTC
* * *
473997 GCAACAGGAATTTCGTTTTC
1 GCAACACGAGTTTCCTTTTC
474017 GCAAC
1 GCAAC
474022 TCGATTTTTG
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
19 5 0.10
20 40 0.82
21 4 0.08
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (20 bp):
GCAACACGAGTTTCCTTTTC
Found at i:474002 original size:40 final size:40
Alignment explanation
Indices: 473894--474002 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 40
473884 ATTTGACAAT
* * * **
473894 TTCGCAACACAAATTTCTTTTTCGCAACTCGATTTTTAAA
1 TTCGCAACACGAGTTTCATTTTCGCAACAAGATTTTTAAA
* *
473934 TTTGCAACACGAGTTTCCTTTTCGCAACAAGATTTTCT-AA
1 TTCGCAACACGAGTTTCATTTTCGCAACAAGATTTT-TAAA
* *
473974 TTCGTAACGCGAGTTTCATTTTCGCAACA
1 TTCGCAACACGAGTTTCATTTTCGCAACA
474003 GGAATTTCGT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 57 0.98
41 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (40 bp):
TTCGCAACACGAGTTTCATTTTCGCAACAAGATTTTTAAA
Found at i:474043 original size:60 final size:60
Alignment explanation
Indices: 473932--474063 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 60
473922 TCGATTTTTA
* * * *
473932 AATTT-GCAACACGAGTTTCCTTTTCGCAACAAGATTTTCTAATTCGTAACGCGAGTTTC
1 AATTTCGCAACACGAATTTCCTTTTCGCAACAAGATTTTCTAATTCGCAACGCAAATTTC
* * * ** * *
473991 ATTTTCGCAACAGGAATTTCGTTTTCGCAACTCGATTTT-TGAATTTGCAACGCAAATTTT
1 AATTTCGCAACACGAATTTCCTTTTCGCAACAAGATTTTCT-AATTCGCAACGCAAATTTC
474051 AATTTCGCAACAC
1 AATTTCGCAACAC
474064 ATCTTTTAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
59 5 0.09
60 53 0.91
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.36
Consensus pattern (60 bp):
AATTTCGCAACACGAATTTCCTTTTCGCAACAAGATTTTCTAATTCGCAACGCAAATTTC
Found at i:474070 original size:20 final size:20
Alignment explanation
Indices: 474047--474084 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
474037 GCAACGCAAA
474047 TTTTAATTTCGCAACACATC
1 TTTTAATTTCGCAACACATC
474067 TTTTAATTTCGCAACACA
1 TTTTAATTTCGCAACACA
474085 AATATTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (20 bp):
TTTTAATTTCGCAACACATC
Found at i:474874 original size:20 final size:20
Alignment explanation
Indices: 474851--474929 Score: 77
Period size: 20 Copynumber: 4.0 Consensus size: 20
474841 TTATTTCAAG
*
474851 AAAATCAAATTCGCAACTAA
1 AAAATCAAATTCGCAACTCA
* * *
474871 AAAATCGAATTCGCAATTCG
1 AAAATCAAATTCGCAACTCA
* * *
474891 AAACTTAAATTCGCAACTCT
1 AAAATCAAATTCGCAACTCA
* *
474911 TAAATAAAATTCGCAACTC
1 AAAATCAAATTCGCAACTC
474930 GAATTTCATT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.46, C:0.22, G:0.08, T:0.25
Consensus pattern (20 bp):
AAAATCAAATTCGCAACTCA
Found at i:474966 original size:20 final size:20
Alignment explanation
Indices: 474933--474996 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
474923 GCAACTCGAA
* *
474933 TTTCATTTTGGAGTTGCGAT
1 TTTCATTTTCGAGTTACGAT
** *
474953 TTTTGTTTTCGAGTTACGAA
1 TTTCATTTTCGAGTTACGAT
*
474973 TTTCATTTTTGAGTTACGAT
1 TTTCATTTTCGAGTTACGAT
474993 TTTC
1 TTTC
474997 GTATTGCGAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.17, C:0.11, G:0.19, T:0.53
Consensus pattern (20 bp):
TTTCATTTTCGAGTTACGAT
Found at i:475007 original size:34 final size:34
Alignment explanation
Indices: 474958--475043 Score: 120
Period size: 34 Copynumber: 2.5 Consensus size: 34
474948 GCGATTTTTG
*
474958 TTTTCG-AGTTACGAATTTCATTTTTGAGTTACGA
1 TTTTCGTA-TTACGAATTTCATTTTCGAGTTACGA
* *
474992 TTTTCGTATTGCGAATTTCATTTTCGAGTTGCGA
1 TTTTCGTATTACGAATTTCATTTTCGAGTTACGA
*
475026 TTTTCGTGTTACGAATTT
1 TTTTCGTATTACGAATTT
475044 AAGTTTCTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 45 0.98
35 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.49
Consensus pattern (34 bp):
TTTTCGTATTACGAATTTCATTTTCGAGTTACGA
Found at i:475014 original size:20 final size:20
Alignment explanation
Indices: 474991--475030 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
474981 TTGAGTTACG
474991 ATTTTCGTA-TTGCGAATTTC
1 ATTTTCG-AGTTGCGAATTTC
*
475011 ATTTTCGAGTTGCGATTTTC
1 ATTTTCGAGTTGCGAATTTC
475031 GTGTTACGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.50
Consensus pattern (20 bp):
ATTTTCGAGTTGCGAATTTC
Found at i:475660 original size:60 final size:60
Alignment explanation
Indices: 475595--475737 Score: 171
Period size: 60 Copynumber: 2.4 Consensus size: 60
475585 ATTGATTTTT
* * * * *
475595 GAAATTTAAATTTGCGTTGCGAATTCGAAAATCGAGTTGTGAAAACAAAATTCGCATTGC
1 GAAATTTAAACTCGCGTTGCGAATTAGAAAATCGAGTTGCGAAAACAAAACTCGCATTGC
* * **
475655 GAAATTGAAACTCGCGTTGCGAATTAGAAAATCGAGTTGCGAAAACGAAACTCGTGTTGC
1 GAAATTTAAACTCGCGTTGCGAATTAGAAAATCGAGTTGCGAAAACAAAACTCGCATTGC
* *
475715 G-AATTTAAAAATCGAGTTGCGAA
1 GAAATTT-AAACTCGCGTTGCGAA
475738 AAAGAAATTC
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
59 4 0.06
60 66 0.94
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (60 bp):
GAAATTTAAACTCGCGTTGCGAATTAGAAAATCGAGTTGCGAAAACAAAACTCGCATTGC
Found at i:475713 original size:20 final size:20
Alignment explanation
Indices: 475610--475744 Score: 87
Period size: 20 Copynumber: 6.8 Consensus size: 20
475600 TTAAATTTGC
**
475610 GTTGCGAATTCGAAAATCGA
1 GTTGCGAAAACGAAAATCGA
*
475630 GTTGTGAAAAC-AAAATTCGCA
1 GTTGCGAAAACGAAAA-TCG-A
** * *
475651 -TTGCGAAATTGAAACTCGC
1 GTTGCGAAAACGAAAATCGA
*
475670 GTTGCGAATTA-GAAAATCGA
1 GTTGCGAA-AACGAAAATCGA
* *
475690 GTTGCGAAAACGAAACTCGT
1 GTTGCGAAAACGAAAATCGA
****
475710 GTTGCGAATTTAAAAATCGA
1 GTTGCGAAAACGAAAATCGA
*
475730 GTTGCGAAAAAGAAA
1 GTTGCGAAAACGAAA
475745 TTCGTTTTGC
Statistics
Matches: 84, Mismatches: 25, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
19 5 0.06
20 75 0.89
21 4 0.05
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (20 bp):
GTTGCGAAAACGAAAATCGA
Found at i:475779 original size:42 final size:40
Alignment explanation
Indices: 475651--475779 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 40
475641 AAAATTCGCA
** *
475651 TTGCGAAATTGAAACTCGCGTTGCGAA-TTAGAAAATCGAG
1 TTGCGAAAAAGAAACTCGTGTTGCGAATTTA-AAAATCGAG
*
475691 TTGCGAAAACGAAACTCGTGTTGCGAATTTAAAAATCGAG
1 TTGCGAAAAAGAAACTCGTGTTGCGAATTTAAAAATCGAG
* * * *
475731 TTGCGAAAAAGAAATTCGTTTTGCGCAATTGTCAAATTCGAG
1 TTGCGAAAAAGAAACTCGTGTTGCG-AATT-TAAAAATCGAG
475773 TTGCGAA
1 TTGCGAA
475780 TTCGTCTAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
40 55 0.71
41 7 0.09
42 16 0.21
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (40 bp):
TTGCGAAAAAGAAACTCGTGTTGCGAATTTAAAAATCGAG
Found at i:476658 original size:2 final size:2
Alignment explanation
Indices: 476651--476681 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
476641 GATAAAAATT
476651 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
476682 GCAGTTCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:478287 original size:32 final size:35
Alignment explanation
Indices: 478241--478316 Score: 86
Period size: 38 Copynumber: 2.2 Consensus size: 35
478231 CTTTATTTTG
*
478241 TTCGGGTCGGGTC-GG-G-TTTTTTAAGTGTGATA
1 TTCGGGTCGAGTCGGGAGATTTTTTAAGTGTGATA
*
478273 TTCGGGTTGAGTCGGGTCAGATTTTTTTAAGTGTGATA
1 TTCGGGTCGAGTCGGG--AGA-TTTTTTAAGTGTGATA
478311 TTCGGG
1 TTCGGG
478317 CCGGGCCGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
32 11 0.31
33 2 0.06
36 1 0.03
38 22 0.61
ACGTcount: A:0.14, C:0.09, G:0.36, T:0.41
Consensus pattern (35 bp):
TTCGGGTCGAGTCGGGAGATTTTTTAAGTGTGATA
Found at i:480472 original size:20 final size:20
Alignment explanation
Indices: 480444--480497 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
480434 AAATCCAAGA
*
480444 GATCGATCCTTTTTCAAGGG
1 GATCGATCCTTTTTCAAAGG
* *
480464 GATCAATCCTTTGGTCAAAGG
1 GATCGATCCTTT-TTCAAAGG
480485 GATCGATCCTTTT
1 GATCGATCCTTTT
480498 GCTTAGGAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
GATCGATCCTTTTTCAAAGG
Found at i:488159 original size:10 final size:10
Alignment explanation
Indices: 488140--488251 Score: 65
Period size: 10 Copynumber: 11.1 Consensus size: 10
488130 AAACACACAT
488140 AAAA-AAAGA
1 AAAAGAAAGA
488149 AAAAGAAAGA
1 AAAAGAAAGA
*
488159 AAGAAAAAAGA
1 AA-AAGAAAGA
488170 AAAA-AATAG-
1 AAAAGAA-AGA
*
488179 GAAAGAATAGGA
1 AAAAGAA-A-GA
*
488191 AAAA-ACATAAA
1 AAAAGA-A-AGA
488202 AAAAG-AAGA
1 AAAAGAAAGA
*
488211 AAAAAATAAGA
1 AAAAGA-AAGA
*
488222 AAAAAAAAGA
1 AAAAGAAAGA
*
488232 AAAATAAA-A
1 AAAAGAAAGA
488241 AAAAGAAAGA
1 AAAAGAAAGA
488251 A
1 A
488252 GAAAATAGAT
Statistics
Matches: 84, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
9 23 0.27
10 29 0.35
11 26 0.31
12 6 0.07
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.04
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:488165 original size:21 final size:20
Alignment explanation
Indices: 488141--488256 Score: 85
Period size: 21 Copynumber: 5.5 Consensus size: 20
488131 AACACACATA
488141 AAAAAAGAAAAAGAAAGAAAG
1 AAAAAAGAAAAA-AAAGAAAG
488162 AAAAAAGAAAAAAATAGGAAAG
1 AAAAAAGAAAAAAA-A-GAAAG
* * * *
488184 -AATAGGAAAAAACATAAA-
1 AAAAAAGAAAAAAAAGAAAG
488202 AAAAGAAGAAAAAAATAAGAAA-
1 AAAA-AAG-AAAAAA-AAGAAAG
*
488224 AAAAAAGAAAAATAAAAAAAAG
1 AAAAAAG-AAAA-AAAAGAAAG
*
488246 AAAGAAGAAAA
1 AAAAAAGAAAA
488257 TAGATAGATC
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
19 5 0.06
20 5 0.06
21 46 0.60
22 21 0.27
ACGTcount: A:0.80, C:0.01, G:0.15, T:0.04
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAGAAAG
Found at i:488211 original size:41 final size:39
Alignment explanation
Indices: 488140--488259 Score: 114
Period size: 41 Copynumber: 2.9 Consensus size: 39
488130 AAACACACAT
* *
488140 AAAAAAAGAAAAAGAAAGAAAGAAAAAAGAAAAAAATAGGAA
1 AAAAAAAGAAAAA-CAA-AAA-AAAGAAGAAAAAAATAGGAA
* * * *
488182 AGAATAGGAAAAAACATAAAAAAAGAAGAAAAAAATAAGAA
1 AAAAAAAG-AAAAACA-AAAAAAAGAAGAAAAAAATAGGAA
* *
488223 AAAAAAAGAAAAATAAAAAAAAGAAAGAAGAAAATAG
1 AAAAAAAGAAAAACAAAAAAAAG-AAGAAAAAAATAG
488260 ATAGATCCAA
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
39 8 0.13
40 17 0.27
41 23 0.37
42 9 0.14
43 6 0.10
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.05
Consensus pattern (39 bp):
AAAAAAAGAAAAACAAAAAAAAGAAGAAAAAAATAGGAA
Found at i:490005 original size:2 final size:2
Alignment explanation
Indices: 489998--490053 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
489988 TAAGTGTATT
489998 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
490040 CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA
490054 TAGGGAAACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:490261 original size:54 final size:53
Alignment explanation
Indices: 490195--490499 Score: 260
Period size: 54 Copynumber: 5.8 Consensus size: 53
490185 ACTAATGAGT
* * * * *
490195 TTTTAAATAAACTAAGTCTAATTTTCAGAAGTTTCTTGACGATTTTTAAATGAG
1 TTTTAAAGAAACTAAGCCTAATTTTCAGAAGTTTCTTGATG-TTTTCAAATGAA
* * * * *
490249 TTTTAAAGAAACTATGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAAAGAA
1 TTTTAAAGAAACTAAGCCTAATTTTCAGAAGTTTCTTGATG-TTTTCAAATGAA
* * * ** * *
490303 CTTTAAA-AAATTAAGCCTAATTTTTAGGGGTTTCATGACGTTTTCAAATGAA
1 TTTTAAAGAAACTAAGCCTAATTTTCAGAAGTTTCTTGATGTTTTCAAATGAA
* * * *
490355 TTTCAAATAAGCTAAGCCTGATTTTCA-AGAGTTTCTTGATG-TTTCAAATGAA
1 TTTTAAAGAAACTAAGCCTAATTTTCAGA-AGTTTCTTGATGTTTTCAAATGAA
* * * * * * *
490407 TTTCAAAGAAATTAAGCATATTTTTTATG-GGTTTCTTGATGTTTTCAAATAAA
1 TTTTAAAGAAACTAAGCCTAATTTTCA-GAAGTTTCTTGATGTTTTCAAATGAA
* *
490460 TTTTTAAAGAATCTAAGCCTAATTTT-AGAGGTTTCTTGAT
1 -TTTTAAAGAAACTAAGCCTAATTTTCAGAAGTTTCTTGAT
490500 AACTGTAAAT
Statistics
Matches: 202, Mismatches: 42, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
52 58 0.29
53 70 0.35
54 74 0.37
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (53 bp):
TTTTAAAGAAACTAAGCCTAATTTTCAGAAGTTTCTTGATGTTTTCAAATGAA
Found at i:490371 original size:53 final size:53
Alignment explanation
Indices: 490203--490499 Score: 233
Period size: 53 Copynumber: 5.6 Consensus size: 53
490193 GTTTTTAAAT
* * ** * * * *
490203 AAACTAAGTCTAATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGTTTTAAAG
1 AAACTAAGCCTAATTTTTAGGGGTTTCTTGATG-TTTTCAAATGAATTTCAAAG
* * * * ** * *
490257 AAACTATGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAAAGAACTTT-AAA-
1 AAACTAAGCCTAATTTTTAGGGGTTTCTTGATG-TTTTCAAATGAA-TTTCAAAG
* * * *
490310 AAATTAAGCCTAATTTTTAGGGGTTTCATGACGTTTTCAAATGAATTTCAAAT
1 AAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTCAAAG
* * * * *
490363 AAGCTAAGCCTGATTTTCAAGAGTTTCTTGATG-TTTCAAATGAATTTCAAAG
1 AAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTCAAAG
* * * * * *
490415 AAATTAAGCATATTTTTTATGGGTTTCTTGATGTTTTCAAATAAATTTTTAAAG
1 AAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA-TTTCAAAG
* *
490469 AATCTAAGCCTAA-TTTTAGAGGTTTCTTGAT
1 AAACTAAGCCTAATTTTTAGGGGTTTCTTGAT
490500 AACTGTAAAT
Statistics
Matches: 197, Mismatches: 41, Indels: 11
0.79 0.16 0.04
Matches are distributed among these distances:
51 3 0.02
52 56 0.28
53 75 0.38
54 60 0.30
55 3 0.02
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (53 bp):
AAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTCAAAG
Found at i:490452 original size:105 final size:104
Alignment explanation
Indices: 490225--490499 Score: 304
Period size: 106 Copynumber: 2.6 Consensus size: 104
490215 ATTTTCAGAA
* * * *
490225 GTTTCTTGACGATTTTTAAATGAGTTTTAAAGAAACTATGTCTGATTTTCAGAAGTTTCTTGATG
1 GTTTCTTGACG-TTTTCAAATGAATTTTAAAGAAACTAAGCCTGATTTTCAG-AGTTTCTTGATG
* *
490290 ATTTTTAAAAGAACTTTAAAAAATTAAGCCTAATTTTTAGGG
64 A-TTTCAAAAGAACTTTAAAAAATTAAGCATAATTTTTAGGG
* * * *
490332 GTTTCATGACGTTTTCAAATGAATTTCAAATAAGCTAAGCCTGATTTTCAAGAGTTTCTTGATG-
1 GTTTCTTGACGTTTTCAAATGAATTTTAAAGAAACTAAGCCTGATTTTC-AGAGTTTCTTGATGA
* * *
490396 TTTCAAATGAA-TTTCAAAGAAATTAAGCATATTTTTTATGG
65 TTTCAAAAGAACTTT-AAA-AAATTAAGCATAATTTTTAGGG
* * * *
490437 GTTTCTTGATGTTTTCAAATAAATTTTTAAAGAATCTAAGCCTAATTTT-AGAGGTTTCTTGAT
1 GTTTCTTGACGTTTTCAAATGAA-TTTTAAAGAAACTAAGCCTGATTTTCAGA-GTTTCTTGAT
490500 AACTGTAAAT
Statistics
Matches: 143, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
103 3 0.02
104 15 0.10
105 49 0.34
106 64 0.45
107 12 0.08
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (104 bp):
GTTTCTTGACGTTTTCAAATGAATTTTAAAGAAACTAAGCCTGATTTTCAGAGTTTCTTGATGAT
TTCAAAAGAACTTTAAAAAATTAAGCATAATTTTTAGGG
Found at i:490666 original size:18 final size:18
Alignment explanation
Indices: 490643--490680 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
490633 CCAAGAAAAG
*
490643 AATGAAGGCTGCTCTAGC
1 AATGAAGACTGCTCTAGC
*
490661 AATGAAGACTGCTCTTGC
1 AATGAAGACTGCTCTAGC
490679 AA
1 AA
490681 CCAATTCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (18 bp):
AATGAAGACTGCTCTAGC
Found at i:490753 original size:21 final size:19
Alignment explanation
Indices: 490721--490762 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
490711 TTACACATGA
490721 ATTTGCATATTTGCATTATAC
1 ATTTGCATATTT-CA-TATAC
490742 ATTT-CATCATTTCATATAC
1 ATTTGCAT-ATTTCATATAC
490761 AT
1 AT
490763 GGTAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.35
20 5 0.25
21 8 0.40
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.48
Consensus pattern (19 bp):
ATTTGCATATTTCATATAC
Found at i:491529 original size:139 final size:134
Alignment explanation
Indices: 491233--491871 Score: 660
Period size: 136 Copynumber: 4.7 Consensus size: 134
491223 GGGTAAACCA
* * * *
491233 ATCAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCTGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTTCAT
* * * *
491298 AATGAGAAGAACTTGTT-AACCTTATCTCGATTCATCGCATATGTAGTTGAATCAGCAACACCTT
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCA-C-AACAT-T--TTGAATCAGCAACACCTC
491362 ACTTGAGGG
126 ACTTGAGGG
* * * *
491371 ATTAAAATTTCCAGTGGAGAGTTCATAATGAGAAGTACTCATCCGATAAGAGAGAAGAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTTCAT
* *
491436 AATAAGAAGAACTTGTTCAATCTTAGCTCGATTCATC-ACATATGGAGTTGAATCAGCAACACCT
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCA-CAACAT-T----TTGAATCAGCAACACCT
*
491500 CACTCGAGGG
125 CACTTGAGGG
* *
491510 ATCAATATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCG-ATAAGGGAGAAGAAGTTCA
* * * * ** * ** * *
491575 TAATGAGAAGAGCTTGTACGACCTATCA-CTTGATTCACGGCATTTCGAATCAGTGACGCCTCGC
65 TAATGAGAAGAACTTGTTCAACCT-T-AGCTCGATTCACAACATTTTGAATCAGCAACACCTCAC
491639 TTGAGGG
128 TTGAGGG
* * * *
491646 AAT-GACATTT-CAGATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAATAAGTT
1 -ATCAACATTTCCAG-TGGAGAGTTCATAATGAGAAGAACTCATCCGATA-AGGGAGAAGAAGTT
* * * * * * *
491709 CATAATGAAAAGAGCTTGTTCGACATATTGCTCGATTCACAACACTTCT-AATTAGCAACACCTC
63 CATAATGAGAAGAACTTGTTCAACCT-TAGCTCGATTCACAACA-TTTTGAATCAGCAACACCTC
*
491773 GCTTGAGGG
126 ACTTGAGGG
* * * *
491782 ATTAACATTTCCAGTGGAGAGTTCGTAATGAGAAGAAATCATCCGATAAAGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTTCAT
*
491847 AATGATAAGAACTTGTTCAACCTTA
66 AATGAGAAGAACTTGTTCAACCTTA
491872 TCTTGTTTCC
Statistics
Matches: 424, Mismatches: 63, Indels: 32
0.82 0.12 0.06
Matches are distributed among these distances:
134 1 0.00
135 41 0.10
136 161 0.38
137 11 0.03
138 73 0.17
139 86 0.20
140 38 0.09
141 12 0.03
142 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (134 bp):
ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCACAACATTTTGAATCAGCAACACCTCACTTG
AGGG
Found at i:493387 original size:23 final size:24
Alignment explanation
Indices: 493360--493416 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
493350 TATTGTATTT
493360 TTTATGTTTTAG-TCACTGTTTTA
1 TTTATGTTTTAGTTCACTGTTTTA
* * *
493383 TTTATGATTT-GTTCATTGTTTTT
1 TTTATGTTTTAGTTCACTGTTTTA
*
493406 TTTATATTTTA
1 TTTATGTTTTA
493417 TTATGTTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.18, C:0.05, G:0.11, T:0.67
Consensus pattern (24 bp):
TTTATGTTTTAGTTCACTGTTTTA
Found at i:495135 original size:36 final size:36
Alignment explanation
Indices: 494943--495134 Score: 258
Period size: 36 Copynumber: 5.2 Consensus size: 36
494933 TCACTTGAAT
* **
494943 ATTGGAAAAAATGCTCAAATTAGGTTTTTTCCAATTGAAT
1 ATTGG-AAAAATGCTCAAATTAGG-TTTTTCC-ACT-AGC
*
494983 ATTGGAAAAATGCTCAAATTAGGTATTTCCACTAGC
1 ATTGGAAAAATGCTCAAATTAGGTTTTTCCACTAGC
* *
495019 ATTGGAAAAATACTCAATTTAGGTTTTTCCACTAGC
1 ATTGGAAAAATGCTCAAATTAGGTTTTTCCACTAGC
*
495055 ATTGGAAAAATGCTCAATTTAGGTTTTTCCACTAGC
1 ATTGGAAAAATGCTCAAATTAGGTTTTTCCACTAGC
* * *
495091 ATTGGAAATATGCTGAAATTAGGTTTTTCCACTAGT
1 ATTGGAAAAATGCTCAAATTAGGTTTTTCCACTAGC
495127 ATTGGAAA
1 ATTGGAAA
495135 TGATGATTTT
Statistics
Matches: 140, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
36 109 0.78
37 2 0.01
38 6 0.04
39 18 0.13
40 5 0.04
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (36 bp):
ATTGGAAAAATGCTCAAATTAGGTTTTTCCACTAGC
Found at i:496574 original size:192 final size:193
Alignment explanation
Indices: 496247--496632 Score: 747
Period size: 192 Copynumber: 2.0 Consensus size: 193
496237 AAGAAGATCG
496247 TTAAATGAGAGAATCAAGACAATAAGATAAAACCTCATAAGGCTACCAACTTCAAGAAGTCATGA
1 TTAAATGAGAGAATCAAGACAATAAGATAAAACCTCATAAGGCTACCAACTTCAAGAAGTCATGA
496312 AAGGCCAAACCTGAAGGAAAGATGTTCAAGTGCTATGTATGTGGTTTAGCCCGCCACAAAGCTTA
66 AAGGCCAAACCTGAAGGAAAGATGTTCAAGTGCTATGTATGTGGTTTAGCCCGCCACAAAGCTTA
496377 CTAATGCCAACACCACTCAGACCACCAGAATG-AACAAGCCACAGATACACGTTGTAGAAAAA
131 CTAATGCCAACACCACTCAGACCACCAGAATGAAACAAGCCACAGATACACGTTGTAGAAAAA
496439 TTAAATGAGAGAATCAAGACAATAAGATAAAACCTCATAAGGCTACCAACTTCAAGAAGTCATGA
1 TTAAATGAGAGAATCAAGACAATAAGATAAAACCTCATAAGGCTACCAACTTCAAGAAGTCATGA
*
496504 AAGGCCAAACCTGAAGGAAAGATGTTCAAGTGCTATGTATGTGGTTTAGCCGGCCACAAAGCTTA
66 AAGGCCAAACCTGAAGGAAAGATGTTCAAGTGCTATGTATGTGGTTTAGCCCGCCACAAAGCTTA
496569 CTAATGCCAACACCACTCAGACCACCAGAATGACAACAAGCCACAGATACACGTTGTAGAAAAA
131 CTAATGCCAACACCACTCAGACCACCAGAATGA-AACAAGCCACAGATACACGTTGTAGAAAAA
496633 GATGATGAAA
Statistics
Matches: 191, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
192 161 0.84
194 30 0.16
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (193 bp):
TTAAATGAGAGAATCAAGACAATAAGATAAAACCTCATAAGGCTACCAACTTCAAGAAGTCATGA
AAGGCCAAACCTGAAGGAAAGATGTTCAAGTGCTATGTATGTGGTTTAGCCCGCCACAAAGCTTA
CTAATGCCAACACCACTCAGACCACCAGAATGAAACAAGCCACAGATACACGTTGTAGAAAAA
Found at i:500794 original size:71 final size:74
Alignment explanation
Indices: 500661--500808 Score: 212
Period size: 71 Copynumber: 2.0 Consensus size: 74
500651 AATATTGGAA
* *
500661 AAAAATGCTCAAATTAGGTTTTTCCACTTGAATATTGGAAAAATGCTCAAATTAGATATTTCCAC
1 AAAAATGCTCAAATTAGGTTTTTACACTTGAACATTGGAAAAATGCTCAAATTAGATATTTCCAC
500726 TAGCATTGG
66 TAGCATTGG
* * * *
500735 AAAAATGCTCAAATTAGG-TTTTACAC-T-AGCATTGGAAATATGCTCAAATTAGGTTTTTCCAC
1 AAAAATGCTCAAATTAGGTTTTTACACTTGAACATTGGAAAAATGCTCAAATTAGATATTTCCAC
*
500797 TAGTATTGG
66 TAGCATTGG
500806 AAA
1 AAA
500809 TGACGATTTG
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
71 41 0.61
72 1 0.01
73 7 0.10
74 18 0.27
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (74 bp):
AAAAATGCTCAAATTAGGTTTTTACACTTGAACATTGGAAAAATGCTCAAATTAGATATTTCCAC
TAGCATTGG
Found at i:500809 original size:36 final size:36
Alignment explanation
Indices: 500661--500808 Score: 208
Period size: 36 Copynumber: 4.1 Consensus size: 36
500651 AATATTGGAA
**
500661 AAAAATGCTCAAATTAGGTTTTTCCACTTGAATATTGG
1 AAAAATGCTCAAATTAGGTTTTTCCAC-T-AGCATTGG
* *
500699 AAAAATGCTCAAATTAGATATTTCCACTAGCATTGG
1 AAAAATGCTCAAATTAGGTTTTTCCACTAGCATTGG
*
500735 AAAAATGCTCAAATTAGG-TTTTACACTAGCATTGG
1 AAAAATGCTCAAATTAGGTTTTTCCACTAGCATTGG
* *
500770 AAATATGCTCAAATTAGGTTTTTCCACTAGTATTGG
1 AAAAATGCTCAAATTAGGTTTTTCCACTAGCATTGG
500806 AAA
1 AAA
500809 TGACGATTTG
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
35 32 0.32
36 41 0.41
37 1 0.01
38 25 0.25
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (36 bp):
AAAAATGCTCAAATTAGGTTTTTCCACTAGCATTGG
Found at i:514201 original size:17 final size:17
Alignment explanation
Indices: 514175--514212 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
514165 ATTCGTATCT
*
514175 GGGTCTTGTACGGGTTG
1 GGGTCGTGTACGGGTTG
514192 GGGTCGTGTACGGGTTG
1 GGGTCGTGTACGGGTTG
514209 GGGT
1 GGGT
514213 GTTACATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.11, G:0.53, T:0.32
Consensus pattern (17 bp):
GGGTCGTGTACGGGTTG
Found at i:542504 original size:13 final size:13
Alignment explanation
Indices: 542486--542524 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
542476 GCCATAAATC
542486 TATGACGCGCATT
1 TATGACGCGCATT
**
542499 TATGACATGCATT
1 TATGACGCGCATT
542512 TATGACGCGCATT
1 TATGACGCGCATT
542525 GCGTGTCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:542588 original size:98 final size:97
Alignment explanation
Indices: 542430--542674 Score: 267
Period size: 98 Copynumber: 2.5 Consensus size: 97
542420 ACAAATACGC
* * * * * *
542430 GTCATTGAAGCCACCGTCATAAATCTCAGATGACACGCAATTGTGTGCCATAAATCTATGACGCG
1 GTCATTGAAGCCCCCGTCATAAA--TAAGATGACACACATTTGTGTGTCATAAATCTATGACACG
* * * * *
542495 CATTTATGACATGCATTTATGACGCGCATTGCGT
64 CATTTATGACATACATTTACGACGCACATTACAT
* *
542529 GTCATTGAAGCCCCCTTCATAAATGAAGATGACACACATTTGTGTGTCATAAATTTATGACACGC
1 GTCATTGAAGCCCCCGTCATAAAT-AAGATGACACACATTTGTGTGTCATAAATCTATGACACGC
* **
542594 ATTTATGACTTACATTTACGACTTACATTACAT
65 ATTTATGACATACATTTACGACGCACATTACAT
* * *
542627 GTCATTGAAGCACACGTCATTAAA-AAGGATGACACACATTCGTGTGTC
1 GTCATTGAAGCCCCCGTCA-TAAATAA-GATGACACACATTTGTGTGTC
542675 GTGATTGTAT
Statistics
Matches: 123, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
97 3 0.02
98 95 0.77
99 25 0.20
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (97 bp):
GTCATTGAAGCCCCCGTCATAAATAAGATGACACACATTTGTGTGTCATAAATCTATGACACGCA
TTTATGACATACATTTACGACGCACATTACAT
Found at i:542609 original size:13 final size:13
Alignment explanation
Indices: 542593--542622 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
542583 TTATGACACG
*
542593 CATTTATGACTTA
1 CATTTACGACTTA
542606 CATTTACGACTTA
1 CATTTACGACTTA
542619 CATT
1 CATT
542623 ACATGTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (13 bp):
CATTTACGACTTA
Found at i:546183 original size:36 final size:36
Alignment explanation
Indices: 546133--546231 Score: 153
Period size: 36 Copynumber: 2.8 Consensus size: 36
546123 CAGGAGATAA
* * *
546133 TTATTCTTCTAAATATCTCATGCATCTATGGTATAG
1 TTATTCTTCAAAATATCTCATGCATCTAGGGTACAG
* *
546169 TTATTCTTCGAAATATCTCATGAATCTAGGGTACAG
1 TTATTCTTCAAAATATCTCATGCATCTAGGGTACAG
546205 TTATTCTTCAAAATATCTCATGCATCT
1 TTATTCTTCAAAATATCTCATGCATCT
546232 GAGGCGTTTC
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.41
Consensus pattern (36 bp):
TTATTCTTCAAAATATCTCATGCATCTAGGGTACAG
Found at i:549183 original size:24 final size:24
Alignment explanation
Indices: 549156--549230 Score: 89
Period size: 24 Copynumber: 3.2 Consensus size: 24
549146 CAAAGTGCCA
549156 CGTAGAATTTGTCCCGAAGGACCG
1 CGTAGAATTTGTCCCGAAGGACCG
* * *
549180 CGTAGAATTTGTCACGAATGACCA
1 CGTAGAATTTGTCCCGAAGGACCG
** *
549204 TATAG-ATTTGACCCGAAGGACCG
1 CGTAGAATTTGTCCCGAAGGACCG
549227 CGTA
1 CGTA
549231 AAATCCTCGA
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 16 0.40
24 24 0.60
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (24 bp):
CGTAGAATTTGTCCCGAAGGACCG
Found at i:554334 original size:181 final size:182
Alignment explanation
Indices: 554028--554392 Score: 660
Period size: 181 Copynumber: 2.0 Consensus size: 182
554018 AATCTCTTAT
554028 TCTTAGCTTCATTCATACCCTCAAACTTATTATCACTTATCCTAGCTAACTTACCTCCATAATTC
1 TCTTAGCTTCATTCATACCCTC-AACTTATTATCACTTATCCTAGCTAACTTACCTCCATAATTC
*
554093 CCCTTATAACATCTAAATTTCTCCATAGAACACTTAGAACTCAAAATCACACCAAATATTCAAAC
65 CCCTTATAACATCTAAATTTCTCCATAGAACACTTAGAACTAAAAATCACACCAAATATTCAAAC
*
554158 ATGTTTTTAATCTTTTCTAATACTTCTAACTTCTTAATTAGACCCTTGAAAAG
130 ATGTTTTTAATCCTTTCTAATACTTCTAACTTCTTAATTAGACCCTTGAAAAG
*
554211 TCTTAGCTTCATTCATACCCTC-ACTTATTATCATTTATCCTAGCTAACTTACCTCCATAATTCC
1 TCTTAGCTTCATTCATACCCTCAACTTATTATCACTTATCCTAGCTAACTTACCTCCATAATTCC
**
554275 CCTTATAACATCTAAATTTCTTTATAGAACACTTAGAACTAAAAATCACACCAAATATTCAAACA
66 CCTTATAACATCTAAATTTCTCCATAGAACACTTAGAACTAAAAATCACACCAAATATTCAAACA
*
554340 TGTTTTTAATCCTTTCTAATACTTCTAACTTCTTAATTAGACCCTTGACAAG
131 TGTTTTTAATCCTTTCTAATACTTCTAACTTCTTAATTAGACCCTTGAAAAG
554392 T
1 T
554393 TAAAAATATC
Statistics
Matches: 176, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
181 154 0.88
183 22 0.12
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.37
Consensus pattern (182 bp):
TCTTAGCTTCATTCATACCCTCAACTTATTATCACTTATCCTAGCTAACTTACCTCCATAATTCC
CCTTATAACATCTAAATTTCTCCATAGAACACTTAGAACTAAAAATCACACCAAATATTCAAACA
TGTTTTTAATCCTTTCTAATACTTCTAACTTCTTAATTAGACCCTTGAAAAG
Found at i:555303 original size:23 final size:24
Alignment explanation
Indices: 555257--555303 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
555247 TATAACTTTT
*
555257 CAAAAAAAGTCAACTTTTGGTCAA
1 CAAAAAAAGTCAACTGTTGGTCAA
*
555281 CAAACAAAGTCAAC-GTTGGTCAA
1 CAAAAAAAGTCAACTGTTGGTCAA
555304 TGCTGATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (24 bp):
CAAAAAAAGTCAACTGTTGGTCAA
Found at i:556730 original size:15 final size:16
Alignment explanation
Indices: 556710--556739 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
556700 CTTCAATAAG
556710 AGATTAAA-AATTAAA
1 AGATTAAATAATTAAA
556725 AGATTAAATAATTAA
1 AGATTAAATAATTAA
556740 TGACTATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (16 bp):
AGATTAAATAATTAAA
Found at i:557993 original size:23 final size:23
Alignment explanation
Indices: 557954--557998 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
557944 TTGGAATATA
*
557954 TATGTGGTCCTTAAGGAGATTTC
1 TATGTGGTCCTTAAGGACATTTC
557977 TATGTGGTCCTCT-AGGACATTT
1 TATGTGGTCCT-TAAGGACATTT
557999 TATATGGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (23 bp):
TATGTGGTCCTTAAGGACATTTC
Found at i:561506 original size:11 final size:11
Alignment explanation
Indices: 561490--561521 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
561480 TCAGGTTCTC
561490 ATTTATTATTA
1 ATTTATTATTA
561501 ATTTATTA-TA
1 ATTTATTATTA
561511 A-TTATTATTA
1 ATTTATTATTA
561521 A
1 A
561522 CAATATACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 6 0.30
10 6 0.30
11 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTATTATTA
Found at i:564107 original size:156 final size:154
Alignment explanation
Indices: 563778--564131 Score: 371
Period size: 156 Copynumber: 2.3 Consensus size: 154
563768 GCCTTTGAGA
* * * *
563778 TGTTTTTCACAAAACAAATTTCGTCTCGCTTAAGACGATTTT-AATTAAATTTTGAAAATTTTGA
1 TGTTTTTCTCAAAACAAATTTCGTCTCGCTTAAGACAATTTTCCATCAAATTTTGAAAATTTTGA
* * *
563842 AACAAAATTGATCTCCCTTGAAATTGTTTCTTTCAAAACAAACTTCGTCTCTCTTGAGACAATTT
66 AAAAAAATTGATCT-CCTTGAAATTGTTTCCTTCAAAACAAACTTCGTCTCGCTTGAGACAATTT
563907 CTCTTGAAACACAAATCCTCGTGAT
130 CTCTTGAAACACAAATCCTCGTGAT
* * * *
563932 TGTTTATCTCGAAACAAATTTCGTCTCGCTTAAGACAATTTTCCA-CCAATTTTGAAATTTTTGC
1 TGTTTTTCTCAAAACAAATTTCGTCTCGCTTAAGACAATTTTCCATCAAATTTTGAAAATTTTG-
* * *
563996 ACCTGAAAAAAATTGATCT-CTTGAGATTGTTTCCCTT-GAAAC-AATTTCGTCTCGCTTGAGAC
65 A----AAAAAAATTGATCTCCTTGAAATTGTTT-CCTTCAAAACAAACTTCGTCTCGCTTGAGAC
* * ** * *
564058 ATTTTCTTTTGAAACTTAAA-CAT-TTGATAT
125 AATTTCTCTTGAAACACAAATCCTCGTG--AT
* * *
564088 TGTTTTTCTCAAAACAAATTTCGTCTCACTTGAGACCATTTTCC
1 TGTTTTTCTCAAAACAAATTTCGTCTCGCTTAAGACAATTTTCC
564132 TTAAGACACA
Statistics
Matches: 166, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
154 55 0.33
155 4 0.02
156 75 0.45
157 16 0.10
158 3 0.02
159 13 0.08
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (154 bp):
TGTTTTTCTCAAAACAAATTTCGTCTCGCTTAAGACAATTTTCCATCAAATTTTGAAAATTTTGA
AAAAAAATTGATCTCCTTGAAATTGTTTCCTTCAAAACAAACTTCGTCTCGCTTGAGACAATTTC
TCTTGAAACACAAATCCTCGTGAT
Found at i:564120 original size:66 final size:64
Alignment explanation
Indices: 564034--564189 Score: 208
Period size: 65 Copynumber: 2.4 Consensus size: 64
564024 GTTTCCCTTG
* ** *
564034 AAAC-AATTTCGTCTCGCTTGAGACATTTTCTTTTGAA-ACTTAAACATTTGATATTGTTTTTCT
1 AAACAAATTTCGTCTCGCTTGAGACATTTTC-CTT-AAGACACAAACATTTGAGA-TGTTTTTCT
564097 CA
63 CA
*
564099 AAACAAATTTCGTCTCACTTGAGACCATTTTCCTTAAGACACAAACATTTGAGATGTTTTTCTCA
1 AAACAAATTTCGTCTCGCTTGAGA-CATTTTCCTTAAGACACAAACATTTGAGATGTTTTTCTCA
*
564164 AAACAAATTTTGTCTCGCTTGAGACA
1 AAACAAATTTCGTCTCGCTTGAGACA
564190 GATCTTCACA
Statistics
Matches: 81, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
64 2 0.02
65 39 0.48
66 33 0.41
67 7 0.09
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (64 bp):
AAACAAATTTCGTCTCGCTTGAGACATTTTCCTTAAGACACAAACATTTGAGATGTTTTTCTCA
Found at i:564512 original size:81 final size:81
Alignment explanation
Indices: 564409--564578 Score: 270
Period size: 81 Copynumber: 2.1 Consensus size: 81
564399 AAGTTTTGTC
* *
564409 TCTCTTGAGACAGTTTCTCTTGAAACATAAA-CAATTGAGATTGTTTCCCTTGAAACAAATTTTG
1 TCTCTTGAGACAGTTTCCCTTGAAACAGAAATC-ATTGAGATTGTTTCCCTTGAAACAAATTTTG
*
564473 TCTCGCTAGAGATAGTT
65 TCTCGCTAGAGACAGTT
* *
564490 TCTCTTGAGACATTTTCCCTTGAAACAGAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGT
1 TCTCTTGAGACAGTTTCCCTTGAAACAGAAATCATTGAGATTGTTTCCCTTGAAACAAATTTTGT
*
564555 CTCGCTTGAGACAGTT
66 CTCGCTAGAGACAGTT
564571 TCTCTTGA
1 TCTCTTGA
564579 AACAAATTAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
81 81 0.99
82 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (81 bp):
TCTCTTGAGACAGTTTCCCTTGAAACAGAAATCATTGAGATTGTTTCCCTTGAAACAAATTTTGT
CTCGCTAGAGACAGTT
Found at i:564837 original size:140 final size:139
Alignment explanation
Indices: 564581--565012 Score: 541
Period size: 140 Copynumber: 3.1 Consensus size: 139
564571 TCTCTTGAAA
* * * *
564581 CAAATTATCCCTAATGATGGCTAGACATCTTCATCACGTAGGAACAATATCATCCA-TCGACCAG
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACT-GACCAG
* ** ** * *
564645 ATCTCCTCATCGCATAGGAGCAGCGTCATCCCCAGATAATCAGACTTACTCATCATGTAGGAATC
65 ATCTCCTCATCACATAGGAGCAAAGTCATCCTTAGATAA-CAGACTTCCTCATCACGTAGGAATC
564710 GTGTTGTCTCC
129 GTGTTGTCTCC
* * * *
564721 CAAATTTTCCCTAAAGATGGCTAAACGTCCTCATCACGTAGGAACAATGTCATCCACTGAACAAA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACTGACCAGA
* * * *
564786 TCTCCTTATCACGTAGGAGGAAAGTCATTCTTAGATAACCAGACTTCCTCATCACGTAGGAAAT-
66 TCTCCTCATCACATAGGAGCAAAGTCATCCTTAGATAA-CAGACTTCCTCATCACGTAGG-AATC
564850 GTGTTGTCTCC
129 GTGTTGTCTCC
* *
564861 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACTGACCAGA
* * * *
564926 TCTCCTCATCACATAGGAGCAGCA-TCACCCTTAGATAACAGATTTCTTCATCACGTAGGAATCG
66 TCTCCTCATCACATAGGAGCA-AAGTCATCCTTAGATAACAGACTTCCTCATCACGTAGGAATCG
*
564990 TGTTATCT-C
130 TGTTGTCTCC
*
564999 CAAATT-TACCTAAA
1 CAAATTATCCCTAAA
565013 ACGACCAGAA
Statistics
Matches: 252, Mismatches: 36, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
137 7 0.03
138 10 0.04
139 27 0.11
140 203 0.81
141 5 0.02
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (139 bp):
CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACTGACCAGA
TCTCCTCATCACATAGGAGCAAAGTCATCCTTAGATAACAGACTTCCTCATCACGTAGGAATCGT
GTTGTCTCC
Found at i:565318 original size:3 final size:3
Alignment explanation
Indices: 565310--565375 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
565300 GTTCTCATTT
565310 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
565358 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
565376 CAATATACTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:566542 original size:14 final size:14
Alignment explanation
Indices: 566510--566543 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
566500 TTATCCTGAC
566510 TTTTATGTTAATAA
1 TTTTATGTTAATAA
* *
566524 ATTTATGTTAATAT
1 TTTTATGTTAATAA
566538 TTTTAT
1 TTTTAT
566544 ATTTAATGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (14 bp):
TTTTATGTTAATAA
Found at i:572436 original size:20 final size:21
Alignment explanation
Indices: 572406--572445 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
572396 AGCCGTTGGG
572406 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
*
572427 GCCT-ATGGTATGGATACTA
1 GCCTGATGGTATCGATACTA
572446 CTATACAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:573438 original size:30 final size:31
Alignment explanation
Indices: 573404--573475 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 31
573394 GGCTAAGAAA
*
573404 ATATACATATACATAAATATTTTTTT-AAAT
1 ATATATATATACATAAATATTTTTTTAAAAT
*
573434 ATATATATATATATAAATATTTTTTTAAAAT
1 ATATATATATACATAAATATTTTTTTAAAAT
573465 ATATATATATA
1 ATATATATATA
573476 TATACACCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 24 0.62
31 15 0.38
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (31 bp):
ATATATATATACATAAATATTTTTTTAAAAT
Found at i:574168 original size:37 final size:37
Alignment explanation
Indices: 574092--574164 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 37
574082 TTTTTATATT
* *
574092 TTTAATTTTGTAAAAAATATTATATAACTATTATGAA
1 TTTAATTTTGTAAAAAATATTATATAAATATTATAAA
* *
574129 TTTAATTTTTTAAAGAAA-A-TATATAAATATTTTAAA
1 TTTAATTTTGTAAA-AAATATTATATAAATATTATAAA
574165 ATTTGTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
36 14 0.45
37 14 0.45
38 3 0.10
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAATATTATATAAATATTATAAA
Found at i:574191 original size:18 final size:17
Alignment explanation
Indices: 574144--574192 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
574134 TTTTTTAAAG
*
574144 AAAATATATAAATATTTT
1 AAAATATAT-AATATTAT
* *
574162 AAAATTTGTAATATTAT
1 AAAATATATAATATTAT
574179 ACAAATATATAATA
1 A-AAATATATAATA
574193 AGGACAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
AAAATATATAATATTAT
Found at i:574350 original size:20 final size:20
Alignment explanation
Indices: 574314--574351 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
574304 ATCCTATTCT
**
574314 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
574334 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
574352 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:574915 original size:29 final size:28
Alignment explanation
Indices: 574872--574927 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
574862 AAATTATGGA
574872 AATTAAAGGCAGAAAT-TAACATAACAAG
1 AATTAAAGGCAGAAATGTAA-ATAACAAG
*
574900 AATTAAAAGGTAGAAATGTAAATAACAA
1 AATT-AAAGGCAGAAATGTAAATAACAA
574928 AAAATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 18 0.72
30 3 0.12
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.20
Consensus pattern (28 bp):
AATTAAAGGCAGAAATGTAAATAACAAG
Found at i:575075 original size:22 final size:21
Alignment explanation
Indices: 575050--575106 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
575040 AGTTTTAAGG
575050 GTTAGTAATTAGAAGTTAGTAA
1 GTTAGTAATTAGAAGTTAG-AA
** *
575072 GTTAGTGGTTAAAAGTTAGAA
1 GTTAGTAATTAGAAGTTAGAA
* *
575093 ATTAATAATTAGAA
1 GTTAGTAATTAGAA
575107 TTTTACCTAG
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (21 bp):
GTTAGTAATTAGAAGTTAGAA
Found at i:580336 original size:19 final size:20
Alignment explanation
Indices: 580312--580349 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
580302 AATTATTTGG
580312 TTAGTTAGACTGTT-GTTAA
1 TTAGTTAGACTGTTAGTTAA
*
580331 TTAGTTAGATTGTTAGTTA
1 TTAGTTAGACTGTTAGTTA
580350 GGCTAGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (20 bp):
TTAGTTAGACTGTTAGTTAA
Found at i:588672 original size:34 final size:33
Alignment explanation
Indices: 588613--588681 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
588603 TTAGGGTTAT
**
588613 AATAAAAAAATAAAATAAATTAAATTAAAATTA
1 AATAAAAAAATAAAATAAAAGAAATTAAAATTA
*
588646 AATAAATAAAA-AGAAATAAAAGAAATTCAAATTA
1 AATAAA-AAAATA-AAATAAAAGAAATTAAAATTA
588680 AA
1 AA
588682 AGGGTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 7 0.23
34 24 0.77
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.23
Consensus pattern (33 bp):
AATAAAAAAATAAAATAAAAGAAATTAAAATTA
Found at i:589844 original size:41 final size:40
Alignment explanation
Indices: 589774--589851 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 40
589764 GGACCTGAAA
589774 TAAAATAAATAAATTAATAAATATAAATATAAATATAAGG
1 TAAAATAAATAAATTAATAAATATAAATATAAATATAAGG
*
589814 TAAAATAAATAACATTAATATAATAT-AATATATATATA
1 TAAAATAAATAA-ATTAATA-AATATAAATATAAATATA
589852 CACTAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 12 0.34
41 18 0.51
42 5 0.14
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (40 bp):
TAAAATAAATAAATTAATAAATATAAATATAAATATAAGG
Found at i:589848 original size:2 final size:2
Alignment explanation
Indices: 589831--590110 Score: 143
Period size: 2 Copynumber: 144.5 Consensus size: 2
589821 AATAACATTA
* * *
589831 AT AT A- AT AT A- AT AT AT AT AT AC ACT AA AT A- AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * *
589871 AT AA AT AT AGT AA AT AT AT AT TT AT AT -T AT A- AT AT AT AA AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
589912 AT A- AT A- AT AA AT AT A- AC AT AT AC A- AT AT AT AT ACT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T
* *
589952 AT AG A- AT AT AT AT AT AGT AT A- AT AT AT ACT AA AT AT ACT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT A-T AT
* * * *
589993 AT A- AT AA AT A- AT AT AT AT A- AA AT AT ACT AA AT AT AT AC ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T
*
590034 AT AT AA AT A- AT AT AT ACT AT AT AT AT AT AT -T A- AT AT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
*
590073 A- AT A- AT AT AT CAT AT A- AT AT AT ACT AT AC AT AT AT AT A
1 AT AT AT AT AT AT -AT AT AT AT AT AT A-T AT AT AT AT AT AT A
590111 AAATAAAAAA
Statistics
Matches: 213, Mismatches: 32, Indels: 66
0.68 0.10 0.21
Matches are distributed among these distances:
1 21 0.10
2 170 0.80
3 22 0.10
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (2 bp):
AT
Found at i:589888 original size:41 final size:38
Alignment explanation
Indices: 589862--590093 Score: 117
Period size: 39 Copynumber: 5.9 Consensus size: 38
589852 CACTAAATAA
** *
589862 TATATAAATATAAATATAGTAAATATATATTTATATTATAA
1 TATATAAATAT-AATA-A-TAAATATATATACATATAATAA
*
589903 TATATAAATATAATAAT-AA-ATATA-ACATAT-ACAA
1 TATATAAATATAATAATAAATATATATACATATAATAA
* * *
589937 TATATATACTATACT-ATAGAATATATATATAGTATAAT-A
1 TATATA-AATATAATAATA-AATATATATACA-TATAATAA
* * *
589976 TATACTAAATATACT-ATATAATAAATAATATATATAA-AA
1 TATA-TAAATATAATAATA-AATATAT-ATACATATAATAA
590015 TATACTAAATATATACACTATATAAATAATATATAC-TAT-ATATA
1 TATA-T-AA-ATATA-A-TA-ATAAAT-ATATATACATATAATA-A
*
590059 TATATTAATATAATAATAATATATCATATA-ATATA
1 TATATAAATATAATAATAA-ATAT-ATATACATATA
590094 TACTATACAT
Statistics
Matches: 154, Mismatches: 14, Indels: 47
0.72 0.07 0.22
Matches are distributed among these distances:
34 11 0.07
35 10 0.06
36 7 0.05
37 7 0.05
38 9 0.06
39 49 0.32
40 15 0.10
41 21 0.14
42 2 0.01
43 6 0.04
44 11 0.07
45 6 0.04
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (38 bp):
TATATAAATATAATAATAAATATATATACATATAATAA
Found at i:589932 original size:7 final size:6
Alignment explanation
Indices: 589773--589940 Score: 73
Period size: 6 Copynumber: 27.5 Consensus size: 6
589763 TGGACCTGAA
* *
589773 ATAAA- ATAAAT A-AATT AATAAAT ATAAAT ATAAAT ATAAGGT A-AAAT
1 ATAAAT ATAAAT ATAAAT -ATAAAT ATAAAT ATAAAT ATAA-AT ATAAAT
* * * * * * *
589820 AAATAAC ATTAAT AT-AAT AT-AAT ATATAT ATACA- CTAAAT A-ATAT
1 ATA-AAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
* * *
589865 ATAAAT ATAAATAT AGTAAAT ATATAT TTATATT ATAATAT ATAAAT AT-AAT
1 ATAAAT AT-AA-AT A-TAAAT ATAAAT ATA-AAT ATAA-AT ATAAAT ATAAAT
589917 AATAAAT ATAACAT ATACAAT ATA
1 -ATAAAT ATAA-AT ATA-AAT ATA
589941 TATACTATAC
Statistics
Matches: 124, Mismatches: 21, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
5 30 0.24
6 53 0.43
7 34 0.27
8 6 0.05
9 1 0.01
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (6 bp):
ATAAAT
Found at i:589995 original size:116 final size:115
Alignment explanation
Indices: 589840--590117 Score: 268
Period size: 116 Copynumber: 2.4 Consensus size: 115
589830 AATATAATAT
* * *
589840 AATATATATATACACTAAATAATATA-TAAATATAAATATAGTAAATATATATTTATATTATAAT
1 AATATATATATATA-T-AAT-ATATACTAAATATAAATATAATAAATA-ATA--TATA-TAAAAT
* *
589904 ATA-TAAATATAATA-A-TA-A-ATATAACATATACAATATATATACTA-TACTAT-AG
59 ATACTAAATAT-ATACACTATATAAATAACATATACAATATATATA-TATTAATATAAG
*
589956 AATATATATATAGTATAATATATACTAAATATACTATATAATAAATAATATATATAAAATATACT
1 AATATATATATA-TATAATATATACTAAATATA-AATATAATAAATAATATATATAAAATATACT
* * *
590021 AAATATATACACTATATAAATAATATATACTATATATATATATTAATATAAT
64 AAATATATACACTATATAAATAACATATACAATATATATATATTAATATAAG
* *
590073 AATA-ATATATCATATAATATATACTATACATATATATAAAATAAA
1 AATATATATAT-ATATAATATATACTA-A-ATATAAATATAATAAA
590118 AAAGGGTTGG
Statistics
Matches: 139, Mismatches: 10, Indels: 25
0.80 0.06 0.14
Matches are distributed among these distances:
112 11 0.08
113 12 0.09
114 7 0.05
115 17 0.12
116 69 0.50
117 18 0.13
118 5 0.04
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.38
Consensus pattern (115 bp):
AATATATATATATATAATATATACTAAATATAAATATAATAAATAATATATATAAAATATACTAA
ATATATACACTATATAAATAACATATACAATATATATATATTAATATAAG
Done.