Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008357.1 Hibiscus syriacus cultivar Beakdansim tig00111096_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: 1459476
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:313624 original size:14 final size:16
Alignment explanation
Indices: 313597--313629 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
313587 ATATATATAA
313597 TAAATAATATTTATTT
1 TAAATAATATTTATTT
313613 TAAATAA-A-TTATTT
1 TAAATAATATTTATTT
313627 TAA
1 TAA
313630 TATTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATAATATTTATTT
Found at i:313646 original size:14 final size:12
Alignment explanation
Indices: 313601--313639 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
313591 ATATAATAAA
313601 TAATATTTATTT
1 TAATATTTATTT
*
313613 TAAATAAATTATTT
1 T-AAT-ATTTATTT
313627 TAATATTTATTT
1 TAATATTTATTT
313639 T
1 T
313640 TCAATATCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 9 0.39
13 6 0.26
14 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TAATATTTATTT
Found at i:314356 original size:15 final size:13
Alignment explanation
Indices: 314336--314373 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
314326 ATGTTTTATT
314336 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
314351 TTATTTTATTTCA
1 TTATTTTATTTCA
314364 TTA-TTTATTT
1 TTATTTTATTT
314374 TACTGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:317691 original size:8 final size:8
Alignment explanation
Indices: 317678--317702 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
317668 TTTATGAATA
317678 ATTTTATT
1 ATTTTATT
317686 ATTTTATT
1 ATTTTATT
317694 ATTTTATT
1 ATTTTATT
317702 A
1 A
317703 AGATAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
ATTTTATT
Found at i:321434 original size:10 final size:10
Alignment explanation
Indices: 321419--321451 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
321409 GCAATCATTC
321419 TTTACATTTT
1 TTTACATTTT
321429 TTTACA-TTT
1 TTTACATTTT
*
321438 TTTACATTTA
1 TTTACATTTT
321448 TTTA
1 TTTA
321452 TTTCATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTACATTTT
Found at i:321441 original size:19 final size:19
Alignment explanation
Indices: 321414--321451 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
321404 ACATGGCAAT
*
321414 CATTCTTTACATTTTTTTA
1 CATTCTTTACATTTATTTA
*
321433 CATTTTTTACATTTATTTA
1 CATTCTTTACATTTATTTA
321452 TTTCATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (19 bp):
CATTCTTTACATTTATTTA
Found at i:324986 original size:11 final size:11
Alignment explanation
Indices: 324970--325032 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
324960 ATGCTTGAAG
324970 AAAAAAGAAAA
1 AAAAAAGAAAA
*
324981 AAAAAAGAGAA
1 AAAAAAGAAAA
324992 AAAAAAGAAAA
1 AAAAAAGAAAA
* *
325003 GAAAAATAAATA
1 AAAAAAGAAA-A
325015 AAAAAAGAAAA
1 AAAAAAGAAAA
325026 AAGAAAA
1 AA-AAAA
325033 AGAGAAAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
11 31 0.70
12 13 0.30
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:324991 original size:13 final size:13
Alignment explanation
Indices: 324970--325050 Score: 59
Period size: 12 Copynumber: 6.5 Consensus size: 13
324960 ATGCTTGAAG
324970 AAAAA-AGAAAAA
1 AAAAAGAGAAAAA
324982 AAAAAGAG---AA
1 AAAAAGAGAAAAA
*
324992 AAAAA-AGAAAAG
1 AAAAAGAGAAAAA
* *
325004 AAAAATA-AATAA
1 AAAAAGAGAAAAA
325016 AAAAAGA-AAAAA
1 AAAAAGAGAAAAA
325028 GAAAAAGAGAAAAGA
1 -AAAAAGAGAAAA-A
325043 AGAAAAGA
1 A-AAAAGA
325051 AAGGGGGTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
9 2 0.04
10 7 0.13
12 24 0.44
13 10 0.18
14 5 0.09
15 7 0.13
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (13 bp):
AAAAAGAGAAAAA
Found at i:324997 original size:15 final size:15
Alignment explanation
Indices: 324977--325050 Score: 78
Period size: 15 Copynumber: 4.8 Consensus size: 15
324967 AAGAAAAAAG
324977 AAAAAAAAAAGAGAA
1 AAAAAAAAAAGAGAA
324992 AAAAAAGAAAAGA-AA
1 AAAAAA-AAAAGAGAA
*
325007 AATAAATAAAAAAAGAA
1 AA-AAA-AAAAAGAGAA
*
325024 AAAAGAAAAAGAGAA
1 AAAAAAAAAAGAGAA
* *
325039 AAGAAGAAAAGA
1 AAAAAAAAAAGA
325051 AAGGGGGTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
15 28 0.57
16 16 0.33
17 5 0.10
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAGAGAA
Found at i:325051 original size:13 final size:12
Alignment explanation
Indices: 324970--325040 Score: 62
Period size: 11 Copynumber: 6.2 Consensus size: 12
324960 ATGCTTGAAG
324970 AAAAAAGAA-AA
1 AAAAAAGAAGAA
324981 AAAAAAG-AGAA
1 AAAAAAGAAGAA
324992 AAAAAAGAA-AA
1 AAAAAAGAAGAA
* *
325003 GAAAAATAA-ATA
1 AAAAAAGAAGA-A
*
325015 AAAAAAGAAAAA
1 AAAAAAGAAGAA
325027 AGAAAAAG-AGAA
1 A-AAAAAGAAGAA
325039 AA
1 AA
325041 GAAGAAAAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
10 1 0.02
11 27 0.54
12 15 0.30
13 7 0.14
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (12 bp):
AAAAAAGAAGAA
Found at i:325052 original size:13 final size:12
Alignment explanation
Indices: 324967--325052 Score: 81
Period size: 13 Copynumber: 7.1 Consensus size: 12
324957 ATTATGCTTG
324967 AAGAAAAAAGAA
1 AAGAAAAAAGAA
*
324979 AA-AAAAAAGAG
1 AAGAAAAAAGAA
324990 AA-AAAAAAGAA
1 AAGAAAAAAGAA
325001 AAGAAAAATA-AA
1 AAGAAAAA-AGAA
*
325013 TAA-AAAAAGAAAA
1 -AAGAAAAA-AGAA
325026 AAGAAAAAGAGAA
1 AAGAAAAA-AGAA
325039 AAGAAGAAAAGAA
1 AAGAA-AAAAGAA
325052 A
1 A
325053 GGGGGTCAAG
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
11 20 0.31
12 17 0.27
13 24 0.38
14 3 0.05
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (12 bp):
AAGAAAAAAGAA
Found at i:326418 original size:83 final size:84
Alignment explanation
Indices: 326190--326658 Score: 657
Period size: 83 Copynumber: 5.6 Consensus size: 84
326180 TAACTGGAAC
* ** *
326190 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA
* * *
326255 CTAGTTATTGAATTTAGAA
66 CCAATCATTGAATTTAGAA
* * *
326274 AGATGAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
1 AGATGAATGTG-CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
326339 AACCAATCATTGAATTTAG-A
64 AACCAATCATTGAATTTAGAA
326359 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA
326424 CCAATCATTGAATTTAG-A
66 CCAATCATTGAATTTAGAA
**
326442 AGATGAATGTGCTCATAGCATCTTCTATAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA
*
326507 CCAATCATTGAATTTTGAA
66 CCAATCATTGAATTTAGAA
* **
326526 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGGTA-AA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA
326589 -C--T-ATTGAATTTAGAA
66 CCAATCATTGAATTTAGAA
* * *
326604 AGATGAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCTGATCTGAT
1 AGATGAATGTG-CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGT-T-ATCTGAT
326659 TCAGTAGGAA
Statistics
Matches: 353, Mismatches: 25, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
78 21 0.06
79 3 0.01
80 29 0.08
81 2 0.01
82 9 0.03
83 153 0.43
84 63 0.18
85 12 0.03
86 61 0.17
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.36
Consensus pattern (84 bp):
AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA
CCAATCATTGAATTTAGAA
Found at i:326658 original size:166 final size:165
Alignment explanation
Indices: 326190--326658 Score: 723
Period size: 166 Copynumber: 2.8 Consensus size: 165
326180 TAACTGGAAC
326190 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT-AAA
326255 CTAGTTATTGAATTTAGAAAGATGAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
65 C-A--TATTGAATTTAGAAAGATGAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
326320 ATCTGATCTGGTTAGACAGAACCAATCATTGAATTTAGA
127 ATCTGATCTGGTTAGACAGAACCAATCATTGAATTTAGA
* **
326359 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-AA
* * * **
326424 CCAATCATTGAATTTAG-AAGATGAATGTG-CTC-ATAGCATCTTCTATAAGTGTTCTTTGAGTT
65 -C-AT-ATTGAATTTAGAAAGATGAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
*
326486 ATCTGATCTGGTTAGACAGAACCAATCATTGAATTTTGAA
127 ATCTGATCTGGTTAGACAGAACCAATCATTGAATTTAG-A
326526 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGGTAAAC
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAC
326590 -TATTGAATTTAGAAAGATGAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCTGAT
66 ATATTGAATTTAGAAAGATGAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT-T-AT
326654 CTGAT
129 CTGAT
326659 TCAGTAGGAA
Statistics
Matches: 273, Mismatches: 18, Indels: 21
0.88 0.06 0.07
Matches are distributed among these distances:
161 11 0.04
162 11 0.04
163 2 0.01
164 28 0.10
165 3 0.01
166 77 0.28
167 56 0.21
168 12 0.04
169 71 0.26
170 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.36
Consensus pattern (165 bp):
AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAC
ATATTGAATTTAGAAAGATGAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
GATCTGGTTAGACAGAACCAATCATTGAATTTAGA
Found at i:327520 original size:111 final size:113
Alignment explanation
Indices: 327352--328015 Score: 909
Period size: 112 Copynumber: 5.9 Consensus size: 113
327342 AGATTCAAAT
* * *
327352 ATCATTTGATAGATTAGCTTTTCCAGA-AAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCAATTGATGGATTATCTTTTCCAGAGAAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
327416 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTACCTAAATTC
65 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACCTAAATTC
* *
327464 ATCAATTGATGGATTATTTTTTTCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*** *
327528 GAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGGTTTGAATTC
66 GAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTT-ACCTAAATTC
* * * * *
327577 ATC-ATTGAGGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCAATTGATGGATTATCTTTTCCAGAGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
*
327640 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTAAATTC
62 GGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACCTAAATTC
* *
327692 ATCAAATGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCA--TGAAGAA-G--
1 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*** *
327752 GAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGGTTTGAATTC
66 GAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTT-ACCTAAATTC
* *
327801 ATCAATTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* **
327866 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTTGATTC
66 GAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACCTAAATTC
*
327914 ATCAATTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAA
1 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * *
327978 GAAGAAGTTCGTAATAAGAAGAACTTGTTCAACTTTTT
66 GAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTT
328016 GCATAATTCT
Statistics
Matches: 485, Mismatches: 51, Indels: 32
0.85 0.09 0.06
Matches are distributed among these distances:
108 37 0.08
109 54 0.11
110 1 0.00
111 82 0.17
112 113 0.23
113 61 0.13
114 38 0.08
115 10 0.02
116 86 0.18
117 3 0.01
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (113 bp):
ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACCTAAATTC
Found at i:328338 original size:3 final size:3
Alignment explanation
Indices: 328330--328420 Score: 146
Period size: 3 Copynumber: 30.0 Consensus size: 3
328320 TTATCCATAT
328330 TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
328376 TTA TTA TTA TTA TTA TCA TCA TCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
328421 AATATATTAA
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
3 82 0.96
4 3 0.04
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:329338 original size:182 final size:180
Alignment explanation
Indices: 329009--329372 Score: 660
Period size: 182 Copynumber: 2.0 Consensus size: 180
328999 GAAGAGAGCT
329009 TACTCTGTCATCGGAGAACCCAACCGTCGCCGGGATACACGAAAACGAAGGTATTTTGTAGATCT
1 TACTCTGTCATCGGAGAACCCAACCGTCGCC-GGATACACGAAAACGAAGGTATTTTGTAGATCT
329074 GCTCCGATTGGGAGCTTTTTAAGGAAAAACACCGGAAACGGTTTTTAGACCGTCCCGATCTATAT
65 GCTCCGATTGGGAGCTTTTTAAGGAAAAACACCGGAAACGGTTTTTAGACCGTCCCGATCTATAT
329139 TTTGGTGGATTTTTGTAATTTCCGGCCACCATTAACGGTGGCCGGCAGCGG
130 TTTGGTGGATTTTTGTAATTTCCGGCCACCATTAACGGTGGCCGGCAGCGG
*
329190 TACTCTGTCATCGGAGACCCCAACCGTCGCC-GATACACGAAAACCGAAGGTATTTTGTAGATCT
1 TACTCTGTCATCGGAGAACCCAACCGTCGCCGGATACACGAAAA-CGAAGGTATTTTGTAGATCT
329254 GCTCCGATTGGGAGCTTTTTAAGGAAAAGAACACCGGAAACGG-TTTTAGACCGTCCCCGATCTA
65 GCTCCGATTGGGAGCTTTTTAAGG-AAA-AACACCGGAAACGGTTTTTAGACCGT-CCCGATCTA
329318 TATTTTGGTGGATTTTTGTAATTTCCGGCCACCATTAACGGTGGCCGGCAGCGG
127 TATTTTGGTGGATTTTTGTAATTTCCGGCCACCATTAACGGTGGCCGGCAGCGG
329372 T
1 T
329373 GGTCGGAGCC
Statistics
Matches: 178, Mismatches: 1, Indels: 7
0.96 0.01 0.04
Matches are distributed among these distances:
179 12 0.07
180 44 0.25
181 44 0.25
182 78 0.44
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (180 bp):
TACTCTGTCATCGGAGAACCCAACCGTCGCCGGATACACGAAAACGAAGGTATTTTGTAGATCTG
CTCCGATTGGGAGCTTTTTAAGGAAAAACACCGGAAACGGTTTTTAGACCGTCCCGATCTATATT
TTGGTGGATTTTTGTAATTTCCGGCCACCATTAACGGTGGCCGGCAGCGG
Found at i:332468 original size:57 final size:57
Alignment explanation
Indices: 332404--332515 Score: 152
Period size: 57 Copynumber: 2.0 Consensus size: 57
332394 AACGGACATG
* * * *
332404 AACGGAGTAGGTTAATATTTGTTTATTTAATTTTAATCTAATAAATGAACGAACACA
1 AACGGAGTAGATTAATATTTGTTCATTTAATTTTAACCGAATAAATGAACGAACACA
* ** *
332461 AACGGAGTATATTCTTATTTGTTCATTTAATTTTAACCGAATAAATGAATGAACA
1 AACGGAGTAGATTAATATTTGTTCATTTAATTTTAACCGAATAAATGAACGAACA
332516 GAACATAAAC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (57 bp):
AACGGAGTAGATTAATATTTGTTCATTTAATTTTAACCGAATAAATGAACGAACACA
Found at i:332644 original size:24 final size:22
Alignment explanation
Indices: 332617--332682 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 22
332607 TAAATGAATG
332617 AACATAAACGAACGAATGTAAAAA
1 AACATAAA--AACGAATGTAAAAA
*
332641 AACATAATAAACGAACGTAAACAA
1 AACATAA-AAACGAATGTAAA-AA
332665 ACACA-AATAAACGAATGT
1 A-ACATAA-AAACGAATGT
332683 GAATACTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
23 11 0.30
24 22 0.59
25 4 0.11
ACGTcount: A:0.61, C:0.15, G:0.11, T:0.14
Consensus pattern (22 bp):
AACATAAAAACGAATGTAAAAA
Found at i:332660 original size:23 final size:24
Alignment explanation
Indices: 332627--332679 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
332617 AACATAAACG
*
332627 AACGAATGTAAA-AAA-ACATAATA
1 AACGAACGTAAACAAACACA-AATA
332650 AACGAACGTAAACAAACACAAATA
1 AACGAACGTAAACAAACACAAATA
332674 AACGAA
1 AACGAA
332680 TGTGAATACT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 11 0.41
24 13 0.48
25 3 0.11
ACGTcount: A:0.64, C:0.15, G:0.09, T:0.11
Consensus pattern (24 bp):
AACGAACGTAAACAAACACAAATA
Found at i:333860 original size:43 final size:42
Alignment explanation
Indices: 333812--333893 Score: 121
Period size: 41 Copynumber: 1.9 Consensus size: 42
333802 TTACACTATA
*
333812 TTATTATATTCCTATTAGTTATATATATATATAC-ATATTTCTT
1 TTATTACA-TCCTATTA-TTATATATATATATACTATATTTCTT
*
333855 TTATTACATGCTATTATTATATATATATATACTATATTT
1 TTATTACATCCTATTATTATATATATATATACTATATTT
333894 GCCTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 16 0.44
42 13 0.36
43 7 0.19
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (42 bp):
TTATTACATCCTATTATTATATATATATATACTATATTTCTT
Found at i:333911 original size:41 final size:41
Alignment explanation
Indices: 333824--333913 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
333814 ATTATATTCC
* *
333824 TATTAGTTATATATATATATACATATTTCTTTTATTACATGC
1 TATTA-TTATATATATATATACATATTTCCTTTATTACATGA
*
333866 TATTATTATATATATATATACTATATTTGCCTTT-TTATAT-A
1 TATTATTATATATATATATAC-ATATTT-CCTTTATTACATGA
333907 TATTATT
1 TATTATT
333914 TTCTTTGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
41 23 0.53
42 16 0.37
43 4 0.09
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (41 bp):
TATTATTATATATATATATACATATTTCCTTTATTACATGA
Found at i:333988 original size:22 final size:22
Alignment explanation
Indices: 333955--333998 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
333945 TCATTTACTA
*
333955 TTATTTATATTTTTATATTTTT
1 TTATTTATATTTTCATATTTTT
*
333977 TTATTTGA-ATTTTCGTATTTTT
1 TTATTT-ATATTTTCATATTTTT
333999 CCTTGTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (22 bp):
TTATTTATATTTTCATATTTTT
Found at i:344410 original size:1 final size:1
Alignment explanation
Indices: 344404--344429 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
344394 TCCTAAGTTG
344404 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
344430 CGTTTAGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:344471 original size:63 final size:63
Alignment explanation
Indices: 344370--344490 Score: 183
Period size: 63 Copynumber: 1.9 Consensus size: 63
344360 AATACTTCGC
* *
344370 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAAAAAAAAAAAAAAAAAAACGT
1 TTAGGATGAAAACCCGAGAGGGCGCCCTAAATTGAAAAAAAAAAAAAAAAAAAAAAAAAACGT
*
344433 TTAGGGTGAAAACCCG-GAAGGGCGCCCTAAAATT-AAAAAAAAAAAAAAAAAAAAAAAA
1 TTAGGATGAAAACCCGAG-AGGGCGCCCT-AAATTGAAAAAAAAAAAAAAAAAAAAAAAA
344491 GAAAAGAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.59, C:0.12, G:0.18, T:0.12
Consensus pattern (63 bp):
TTAGGATGAAAACCCGAGAGGGCGCCCTAAATTGAAAAAAAAAAAAAAAAAAAAAAAAAACGT
Found at i:344473 original size:1 final size:1
Alignment explanation
Indices: 344467--344500 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
344457 CCCTAAAATT
* *
344467 AAAAAAAAAAAAAAAAAAAAAAAAGAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
344501 TAAGGTGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:345602 original size:106 final size:105
Alignment explanation
Indices: 345231--345759 Score: 934
Period size: 106 Copynumber: 5.0 Consensus size: 105
345221 AGGTTTTACC
*
345231 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
345296 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
345336 CAGAGCCAATTTCAACTTCACAACGAAGGATATT-GACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
345400 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
*
345440 CATAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
345505 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ACTTCTCAATTT
* *
345546 CAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
345611 GCGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ACTTCTCAATTT
* *
345652 CAGAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
345717 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
345757 CAG
1 CAG
345760 CTCCACAACG
Statistics
Matches: 405, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
104 100 0.25
105 105 0.26
106 200 0.49
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
Found at i:345855 original size:20 final size:20
Alignment explanation
Indices: 345817--345858 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
345807 CCAGAACTCT
*
345817 GAGTTCGATTTCAGCTTCAC
1 GAGTTCGATTTCAACTTCAC
* *
345837 GAGTTTGATTTCAATTTCAC
1 GAGTTCGATTTCAACTTCAC
345857 GA
1 GA
345859 CGAAGGATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:347120 original size:31 final size:30
Alignment explanation
Indices: 347022--347125 Score: 86
Period size: 30 Copynumber: 3.3 Consensus size: 30
347012 CAAACTGCGT
347022 TTTGGCTCCCTCTGTTTTGAAAAACATTCAA
1 TTTGG-TCCCTCTGTTTTGAAAAACATTCAA
* * ** *
347053 TTTGGTCCC-CAAATCGGTTGGGTAAAC-TTCAT
1 TTTGGTCCCTC---T-GTTTTGAAAAACATTCAA
*
347085 TTTGGCTCCCTCTGTTTTGAAAAACATTTAA
1 TTTGG-TCCCTCTGTTTTGAAAAACATTCAA
347116 TTTGGTCCCT
1 TTTGGTCCCT
347126 AAATCGGTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
29 1 0.02
30 17 0.31
31 14 0.25
32 10 0.18
33 12 0.22
34 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (30 bp):
TTTGGTCCCTCTGTTTTGAAAAACATTCAA
Found at i:347964 original size:10 final size:10
Alignment explanation
Indices: 347945--347979 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
347935 AACAAACACA
*
347945 ATAAATAAAC
1 ATAAACAAAC
347955 ATAAACAAAC
1 ATAAACAAAC
*
347965 ATAAACGAAC
1 ATAAACAAAC
347975 ATAAA
1 ATAAA
347980 TAAAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.69, C:0.14, G:0.03, T:0.14
Consensus pattern (10 bp):
ATAAACAAAC
Found at i:348201 original size:24 final size:24
Alignment explanation
Indices: 348174--348232 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
348164 GCATATAAAC
*
348174 AAACGAACATAAATGAACGAACAT
1 AAACGAACATAAATGAAAGAACAT
348198 AAACGAACATAAATGAAAGAACAT
1 AAACGAACATAAATGAAAGAACAT
348222 AAACGAACATA
1 AAACGAACATA
348233 TTACCGAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.61, C:0.15, G:0.12, T:0.12
Consensus pattern (24 bp):
AAACGAACATAAATGAAAGAACAT
Found at i:348219 original size:14 final size:14
Alignment explanation
Indices: 348154--348229 Score: 70
Period size: 14 Copynumber: 5.7 Consensus size: 14
348144 TGGGTTAAAT
* *
348154 ATAAATGAACGCAT
1 ATAAATGAACGAAC
**
348168 ATAAACAAACGAAC
1 ATAAATGAACGAAC
348182 ATAAATGAACGAAC
1 ATAAATGAACGAAC
348196 AT--A--AACGAAC
1 ATAAATGAACGAAC
*
348206 ATAAATGAAAGAAC
1 ATAAATGAACGAAC
*
348220 ATAAACGAAC
1 ATAAATGAAC
348230 ATATTACCGA
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
10 9 0.18
12 2 0.04
14 38 0.78
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.13
Consensus pattern (14 bp):
ATAAATGAACGAAC
Found at i:350726 original size:23 final size:24
Alignment explanation
Indices: 350686--350731 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
350676 CCCCCTCGAA
*
350686 TCTCTCTGTAGTTTTTCTATTTTCT
1 TCTCTCTGTA-TTATTCTATTTTCT
*
350711 TCTCTCTGT-TTATTCTCTTTT
1 TCTCTCTGTATTATTCTATTTT
350732 TTCCAAGTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
25 9 0.47
ACGTcount: A:0.07, C:0.22, G:0.07, T:0.65
Consensus pattern (24 bp):
TCTCTCTGTATTATTCTATTTTCT
Found at i:351172 original size:3 final size:3
Alignment explanation
Indices: 351164--351206 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
351154 TTAAAATGAT
351164 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TTAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA T
351207 TTTTTTATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:351801 original size:31 final size:31
Alignment explanation
Indices: 351756--351867 Score: 93
Period size: 31 Copynumber: 3.5 Consensus size: 31
351746 AGATAAAATT
351756 TGTTTCAA-AGGAAACAAACTCAAAGATGACG
1 TGTTTCAAGA-GAAACAAACTCAAAGATGACG
*** * *
351787 TGTTTCAAGAGAAACTGTCTCAAGGGA-GACAAAATT
1 TGTTTCAAGAGAAACAAACTCAA-AGATGAC-----G
351823 TGTTTCAAGAGAAACAAACTCAAAGATGACG
1 TGTTTCAAGAGAAACAAACTCAAAGATGACG
*
351854 TGTTTCATGAGAAA
1 TGTTTCAAGAGAAA
351868 TTGTCTCAAG
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
31 34 0.55
32 3 0.05
35 2 0.03
36 23 0.37
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (31 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGACG
Found at i:351821 original size:67 final size:67
Alignment explanation
Indices: 351626--352165 Score: 599
Period size: 67 Copynumber: 8.2 Consensus size: 67
351616 AGGGATAATG
* * ** *
351626 GTTTCAAGAGAAACTGA-CTCACAGATGA--TGCTTCAAGAGAAGTTGTCTCAAGAGAGACAAAA
1 GTTTCAAGAGAAAC-GATCTCAAAGATGAGGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
*
351688 TTC
65 TTT
* * * *
351691 ATTTCAAGTGAAACGATCTCAAAGATG-GGTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAAT
1 GTTTCAAGAGAAACGATCTCAAAGATGAGGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
351755 TT
66 TT
* * *
351757 GTTTCAA-AGGAAACAAACTCAAAGATGACGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1 GTTTCAAGA-GAAACGATCTCAAAGATGAGGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
351821 TTT
65 TTT
* * * * *
351824 GTTTCAAGAGAAACAAACTCAAAGATGACGTGTTTCATGAGAAATTGTCTCAAGGGAGACAAAAT
1 GTTTCAAGAGAAACGATCTCAAAGATGAGGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
351889 TT
66 TT
* * *
351891 GTTTCAA-ATGAAATGATCTCAAAGAT-AGGTGATTCAAGAGAAACTGTCTTAAGGGAGACAAAA
1 GTTTCAAGA-GAAACGATCTCAAAGATGAGGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
*
351954 TTC
65 TTT
* * *
351957 ATTTCAAGAGAAACGATTTCAAAG-T----T-TTTCTTAAG-GAAGACTGTCACAAGGGAGACAA
1 GTTTCAAGAGAAACGATCTCAAAGATGAGGTGTTTC--AAGAGAA-ACTGTCTCAAGGGAGACAA
352015 AATTT
63 AATTT
* * * * *
352020 GTTTCAAGAGAAACAAACTCAAAGATGATGTGTTTCATGAGAAATTGTCTCAAGGGAGACAAAAT
1 GTTTCAAGAGAAACGATCTCAAAGATGAGGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
352085 TT
66 TT
* *
352087 GTTTCAA-ATGAAATGATCTCAAAGAT-AGGTGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAA
1 GTTTCAAGA-GAAACGATCTCAAAGATGAGGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
*
352150 TTC
65 TTT
*
352153 ATTTCAAGAGAAA
1 GTTTCAAGAGAAA
352166 TAATTTCAAA
Statistics
Matches: 406, Mismatches: 49, Indels: 39
0.82 0.10 0.08
Matches are distributed among these distances:
61 3 0.01
62 4 0.01
63 44 0.11
64 3 0.01
65 22 0.05
66 154 0.38
67 167 0.41
68 5 0.01
69 4 0.01
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (67 bp):
GTTTCAAGAGAAACGATCTCAAAGATGAGGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
TT
Found at i:352055 original size:196 final size:195
Alignment explanation
Indices: 351626--352219 Score: 838
Period size: 196 Copynumber: 3.0 Consensus size: 195
351616 AGGGATAATG
** * * * * *
351626 GTTTCAAGAGAAACTGACTCACAGATGA-TGCTTCAAGAGAAGTTGTCTCAAGAGAGACAAAATT
1 GTTTCAAGAGAAACAAACTCAAAGATGAGTGTTTCATGAGAAATTGTCTCAAGGGAGACAAAATT
** * * * * * *
351690 CATTTCAAGTGAAACGATCTCAAAGATGGGTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAAT
66 TGTTTCAAATGAAATGATCTCAAAGATAGGTGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAAT
** **
351755 TTGTTTCAA-AGGAAACAAACTCAAAGATGACGTGTTTC--AAGAGAA-ACTGTCTCAAGGGAGA
131 TCATTTCAAGA-GAAACAATTTCAAAG-T----T-TTTCTTAAG-GAAGACTGTCTCAAGGGAGA
351816 CAAAATTT
188 CAAAATTT
351824 GTTTCAAGAGAAACAAACTCAAAGATGACGTGTTTCATGAGAAATTGTCTCAAGGGAGACAAAAT
1 GTTTCAAGAGAAACAAACTCAAAGATGA-GTGTTTCATGAGAAATTGTCTCAAGGGAGACAAAAT
*
351889 TTGTTTCAAATGAAATGATCTCAAAGATAGGTGATTCAAGAGAAACTGTCTTAAGGGAGACAAAA
65 TTGTTTCAAATGAAATGATCTCAAAGATAGGTGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAA
* *
351954 TTCATTTCAAGAGAAACGATTTCAAAGTTTTTCTTAAGGAAGACTGTCACAAGGGAGACAAAATT
130 TTCATTTCAAGAGAAACAATTTCAAAGTTTTTCTTAAGGAAGACTGTCTCAAGGGAGACAAAATT
352019 T
195 T
352020 GTTTCAAGAGAAACAAACTCAAAGATGATGTGTTTCATGAGAAATTGTCTCAAGGGAGACAAAAT
1 GTTTCAAGAGAAACAAACTCAAAGATGA-GTGTTTCATGAGAAATTGTCTCAAGGGAGACAAAAT
352085 TTGTTTCAAATGAAATGATCTCAAAGATAGGTGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAA
65 TTGTTTCAAATGAAATGATCTCAAAGATAGGTGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAA
* * *
352150 TTCATTTCAAGAGAAATAATTTCAAAGTTTTTCTTAAGGAAGACTGTCTCAAGTGAGACAAAGTT
130 TTCATTTCAAGAGAAACAATTTCAAAGTTTTTCTTAAGGAAGACTGTCTCAAGGGAGACAAAATT
352215 T
195 T
352216 GTTT
1 GTTT
352220 TTAGAAAAAC
Statistics
Matches: 361, Mismatches: 29, Indels: 14
0.89 0.07 0.03
Matches are distributed among these distances:
194 4 0.01
195 4 0.01
196 219 0.61
198 25 0.07
199 1 0.00
200 107 0.30
201 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.27
Consensus pattern (195 bp):
GTTTCAAGAGAAACAAACTCAAAGATGAGTGTTTCATGAGAAATTGTCTCAAGGGAGACAAAATT
TGTTTCAAATGAAATGATCTCAAAGATAGGTGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAAT
TCATTTCAAGAGAAACAATTTCAAAGTTTTTCTTAAGGAAGACTGTCTCAAGGGAGACAAAATTT
Found at i:352345 original size:36 final size:37
Alignment explanation
Indices: 352289--352384 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 37
352279 CATCTCAAAG
* *
352289 GAAAAA-TGTCTTAAGTGAGACGAAATTTG-TTTTGA
1 GAAAAATTGTCTTAAGCGAGACGAAATTTGTTTTTAA
* *
352324 GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAA
1 GAAAAATTGTCTTAAGCGAGACGAAATTTGTTTTTAA
* * *
352361 GAAATATTGTATTTAGCGAGACGA
1 GAAAAATTGTCTTAAGCGAGACGA
352385 CCCTTTGTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 6 0.12
36 20 0.40
37 24 0.48
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (37 bp):
GAAAAATTGTCTTAAGCGAGACGAAATTTGTTTTTAA
Found at i:358847 original size:23 final size:23
Alignment explanation
Indices: 358804--358848 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
358794 GTGGTGTGAA
* *
358804 GGAATAAAATAATCTAGAATATC
1 GGAATAAAATAATCCAAAATATC
358827 GGAATAAAATAATCCAAAATAT
1 GGAATAAAATAATCCAAAATAT
358849 ATTCATTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.56, C:0.09, G:0.11, T:0.24
Consensus pattern (23 bp):
GGAATAAAATAATCCAAAATATC
Found at i:383662 original size:61 final size:61
Alignment explanation
Indices: 383567--383726 Score: 257
Period size: 61 Copynumber: 2.6 Consensus size: 61
383557 ACCGTAGTGC
* * **
383567 TATGACACATAAGTTTGTGCCCACCACCTGCACTAAGTTTACACTCTAGTGCTAATCCGGA
1 TATGACACATAAGGTTGTGCCCACCACCTGCACTAAGTTTACACTCTAGTACTAATCCAAA
* *
383628 TATGACACATAAGGTTGTGCCCACCACTTGCACTAAGTTTACACTCTAGTACTGATCCAAA
1 TATGACACATAAGGTTGTGCCCACCACCTGCACTAAGTTTACACTCTAGTACTAATCCAAA
*
383689 TATGACACATAAGGTCGTGCCCACCACCTGCACTAAGT
1 TATGACACATAAGGTTGTGCCCACCACCTGCACTAAGT
383727 GTCCTTACAC
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 91 1.00
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (61 bp):
TATGACACATAAGGTTGTGCCCACCACCTGCACTAAGTTTACACTCTAGTACTAATCCAAA
Found at i:393928 original size:3 final size:3
Alignment explanation
Indices: 393914--393974 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
393904 TTTTTTCATT
* ** *
393914 TTA TTT TTA TTA TTA AAA TTA TCA TTA TTA TTA TGTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA
393960 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
393975 AAAAATAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:395304 original size:16 final size:16
Alignment explanation
Indices: 395263--395298 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
395253 TTGCTTTTAA
395263 ATTTATTT-TAAATATT
1 ATTTATTTAT-AATATT
395279 ATTTATTTATAATATT
1 ATTTATTTATAATATT
395295 ATTT
1 ATTT
395299 TGTTATTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTATTTATAATATT
Found at i:395321 original size:17 final size:17
Alignment explanation
Indices: 395301--395334 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
395291 TATTATTTTG
395301 TTATTACTTTT-ATATTA
1 TTATTA-TTTTCATATTA
395318 TTATTATTTTCATATTA
1 TTATTATTTTCATATTA
395335 GTCACATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTCATATTA
Found at i:395347 original size:2 final size:2
Alignment explanation
Indices: 395340--395386 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
395330 TATTAGTCAC
395340 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
395382 AT AT A
1 AT AT A
395387 AAATAATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:402322 original size:114 final size:114
Alignment explanation
Indices: 402119--402339 Score: 336
Period size: 114 Copynumber: 1.9 Consensus size: 114
402109 GTGTTATGTT
* * *
402119 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGAATCTTCTGGAAATGATCTTTGAGTTATCTAATCTG
** * *
402184 GTTTGGTATGAACCCCAAAGCCAATCATTAGATTTGAAAGATAAATTTG
66 GTTCAGTAGGAACCCCAAAGCCAATCATTAGAATTGAAAGATAAATTTG
*
402233 CTCATAGTAGAAATAAGGAGACCCAATAGAATCTTCTGGAAGTGATCTTTGAGTTATCTAATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGAATCTTCTGGAAATGATCTTTGAGTTATCTAATCTG
* *
402298 GTTCAGTAGGAACCCCAGAA-CCAATTATTGGAATTGAAAGAT
66 GTTCAGTAGGAACCCCA-AAGCCAATCATTAGAATTGAAAGAT
402340 GAACTGCATG
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
114 94 0.98
115 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGAATCTTCTGGAAATGATCTTTGAGTTATCTAATCTG
GTTCAGTAGGAACCCCAAAGCCAATCATTAGAATTGAAAGATAAATTTG
Found at i:402546 original size:31 final size:31
Alignment explanation
Indices: 402508--402571 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
402498 GCACATATAA
402508 AATCTGTCAACTCTGCAATTGATGAATTCAG
1 AATCTGTCAACTCTGCAATTGATGAATTCAG
402539 AATCTGTCAACTCTGCAATTGATGAATTCAG
1 AATCTGTCAACTCTGCAATTGATGAATTCAG
402570 AA
1 AA
402572 CAAATCTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (31 bp):
AATCTGTCAACTCTGCAATTGATGAATTCAG
Found at i:404970 original size:22 final size:22
Alignment explanation
Indices: 404941--404995 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
404931 ATCTACACTC
404941 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
404963 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
404985 TTCAAAGATGA
1 TTCAAAGATGA
404996 AAGCTTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:405822 original size:73 final size:73
Alignment explanation
Indices: 405702--405985 Score: 514
Period size: 73 Copynumber: 3.9 Consensus size: 73
405692 GGATGTTTTC
*
405702 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTT
1 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTT
405767 CACTCGAA
66 CACTCGAA
*
405775 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGAAAGTTT
1 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTT
405840 CACTCGAA
66 CACTCGAA
* *
405848 ACGGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAATAAAATTTGTCTCGCTTGAGACAGTTT
1 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTT
405913 CACTCGAA
66 CACTCGAA
*
405921 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAGATTTGTCTCACTTGAGACAGTT
1 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTTGTCTCGCTTGAGACAGTT
405986 ATTTCGAGTT
Statistics
Matches: 202, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
73 181 0.90
74 21 0.10
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (73 bp):
ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTT
CACTCGAA
Found at i:405960 original size:37 final size:36
Alignment explanation
Indices: 405706--405980 Score: 235
Period size: 37 Copynumber: 7.5 Consensus size: 36
405696 GTTTTCACAG
405706 AACTTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 AACTTTATCTCACTTGAGATTGTTTTTCTTAAAACA
* * * ** ** **
405742 AATTTTGTCTCGCTTGAGACAGTTTCACTCGAAACA
1 AACTTTATCTCACTTGAGATTGTTTTTCTTAAAACA
405778 GAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 -AACTTTATCTCACTTGAGATTGTTTTTCTTAAAACA
* * * ** ** ** *
405815 AAATTTGTCTCGCTTGAGAAAGTTTCACTCGAAACGG
1 AACTTTATCTCACTTGAGATTGTTTTTCTTAAAAC-A
*
405852 AACTTTATCTCACTTGAGATTGTTTTTCTTAAAATA
1 AACTTTATCTCACTTGAGATTGTTTTTCTTAAAACA
* * * ** ** **
405888 AAATTTGTCTCGCTTGAGACAGTTTCACTCGAAACA
1 AACTTTATCTCACTTGAGATTGTTTTTCTTAAAACA
405924 GAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 -AACTTTATCTCACTTGAGATTGTTTTTCTTAAAACA
* *
405961 AAGATTTGTCTCACTTGAGA
1 AA-CTTTATCTCACTTGAGA
405981 CAGTTATTTC
Statistics
Matches: 175, Mismatches: 60, Indels: 7
0.72 0.25 0.03
Matches are distributed among these distances:
36 81 0.46
37 94 0.54
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (36 bp):
AACTTTATCTCACTTGAGATTGTTTTTCTTAAAACA
Found at i:406402 original size:3 final size:3
Alignment explanation
Indices: 406388--406448 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
406378 ATTTTTCATT
* ** *
406388 TTA TTT TTA TTA TTA AAA TTA TCA TTA TTA TTA TGTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA
406434 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
406449 AAAAATAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:407733 original size:27 final size:28
Alignment explanation
Indices: 407702--407755 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
407692 TTTGCAATTT
*
407702 AATATTATTTCTTT-TAA-ATTTATTTTA
1 AATATTATTTATTTATAATA-TTATTTTA
407729 AATATTATTTATTTATAATATTATTTT
1 AATATTATTTATTTATAATATTATTTT
407756 GTTATTACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 13 0.54
28 10 0.42
29 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
AATATTATTTATTTATAATATTATTTTA
Found at i:407760 original size:16 final size:16
Alignment explanation
Indices: 407719--407754 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
407709 TTTCTTTTAA
407719 ATTTATTT-TAAATATT
1 ATTTATTTAT-AATATT
407735 ATTTATTTATAATATT
1 ATTTATTTATAATATT
407751 ATTT
1 ATTT
407755 TGTTATTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTATTTATAATATT
Found at i:407816 original size:2 final size:2
Alignment explanation
Indices: 407809--407850 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
407799 CACATAAATA
407809 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
407851 TTTAAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:428484 original size:3 final size:3
Alignment explanation
Indices: 428476--428507 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
428466 TTTGTTTCTT
428476 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
428508 TTTGTATGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:439757 original size:3 final size:3
Alignment explanation
Indices: 439749--439773 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
439739 GTACTTTATT
439749 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
439774 TTAAAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:440022 original size:45 final size:45
Alignment explanation
Indices: 439964--440691 Score: 1199
Period size: 45 Copynumber: 16.2 Consensus size: 45
439954 GCTCGGAAGA
* * *
439964 CTTACAAATGACCCGAAGGCTTTGAAAACATCATGCACTAAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
* *
440009 CTTATAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
* * *
440054 CTTACAGATGACCTGAAGGTTTTGGATACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
* *
440099 CTTATAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
* *
440144 CTAACAGATGACCCGAAGGTTTTGGAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
* *
440189 CTTATAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
* *
440234 CTTATAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
* *
440279 CTTACAGATGACCCAAAGGTTTTGGAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
* * *
440324 CTTACAGATGACCCAAAGGTTTTGAAAACTTCATGCACTGAAGAT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
*
440369 CTTACAGATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
* *
440414 CTTACACATGACTCGAAGGTTTTGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
*
440459 CTTATAGATGACCCGAAGGTTTTG--AACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
*
440502 CTTACAGTTGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
*
440547 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGCT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
440592 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
440637 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
440682 CTTACAGATG
1 CTTACAGATG
440692 TGGGAAATAG
Statistics
Matches: 640, Mismatches: 41, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
43 41 0.06
45 599 0.94
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (45 bp):
CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
Found at i:440186 original size:25 final size:24
Alignment explanation
Indices: 440023--440681 Score: 122
Period size: 20 Copynumber: 29.2 Consensus size: 24
440013 TAGATGACCC
*
440023 GAAGGCTTTGAAAACATCATGCACT
1 GAAGGTTTTG-AAACATCATGCACT
* *
440048 GAAGGTCTT---ACA-GATG-ACCT
1 GAAGGTTTTGAAACATCATGCA-CT
*
440068 GAAGGTTTTGGATACATCATGCACT
1 GAAGGTTTT-GAAACATCATGCACT
* * * * *
440093 GAAGGTCTT-ATAGATGA--C-CC
1 GAAGGTTTTGAAACATCATGCACT
*
440113 AAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTG-AAACATCATGCACT
* * *
440138 GAAGG-TCT--AACA-GATG-ACCC
1 GAAGGTTTTGAAACATCATGCA-CT
440158 GAAGGTTTTGGAAACATCATGCACT
1 GAAGGTTTT-GAAACATCATGCACT
* * * * *
440183 GAAGGTCTT-ATAGATGA--C-CC
1 GAAGGTTTTGAAACATCATGCACT
*
440203 AAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTG-AAACATCATGCACT
* * * * *
440228 GAAGGTCTT-ATAGATGA--C-CC
1 GAAGGTTTTGAAACATCATGCACT
*
440248 AAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTG-AAACATCATGCACT
* * *
440273 GAAGGTCTT---ACA-GATG-ACCC
1 GAAGGTTTTGAAACATCATGCA-CT
*
440293 AAAGGTTTTGGAAACATCATGCACT
1 GAAGGTTTT-GAAACATCATGCACT
* * *
440318 GAAGGTCTT---ACA-GATG-ACCC
1 GAAGGTTTTGAAACATCATGCA-CT
* *
440338 AAAGGTTTTGAAAACTTCATGCACT
1 GAAGGTTTTG-AAACATCATGCACT
* * *
440363 GAAGATCTT---ACA-GATG-ACCT
1 GAAGGTTTTGAAACATCATGCA-CT
440383 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTG-AAACATCATGCACT
*
440408 GAAGGTCTT---ACA-CATG-ACT
1 GAAGGTTTTGAAACATCATGCACT
440427 CGAAGGTTTTGAAAACATCATGCACT
1 -GAAGGTTTTG-AAACATCATGCACT
* * * * *
440453 GAAGGTCTT-ATAGATGA--C-CC
1 GAAGGTTTTGAAACATCATGCACT
440473 GAAGGTTTTG-AACATCATGCACT
1 GAAGGTTTTGAAACATCATGCACT
* *
440496 GAAGGTCTT---ACAGT--TG-ACCC
1 GAAGGTTTTGAAACA-TCATGCA-CT
440516 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTG-AAACATCATGCACT
* * *
440541 GAAGGTCTT---ACA-GATG-ACCC
1 GAAGGTTTTGAAACATCATGCA-CT
440561 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTG-AAACATCATGCACT
* * * *
440586 GAAGCTCTT---ACA-GATG-ACCC
1 GAAGGTTTTGAAACATCATGCA-CT
440606 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTG-AAACATCATGCACT
* * *
440631 GAAGGTCTT---ACA-GATG-ACCC
1 GAAGGTTTTGAAACATCATGCA-CT
440651 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTG-AAACATCATGCACT
440676 GAAGGT
1 GAAGGT
440682 CTTACAGATG
Statistics
Matches: 437, Mismatches: 106, Indels: 182
0.60 0.15 0.25
Matches are distributed among these distances:
19 12 0.03
20 151 0.35
21 36 0.08
22 17 0.04
23 31 0.07
24 35 0.08
25 143 0.33
26 12 0.03
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (24 bp):
GAAGGTTTTGAAACATCATGCACT
Found at i:441393 original size:22 final size:22
Alignment explanation
Indices: 441368--441418 Score: 88
Period size: 20 Copynumber: 2.4 Consensus size: 22
441358 TAAAGTTTTT
441368 ATCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
441390 ATCTTTG--AAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
441410 ATCTTTGAA
1 ATCTTTGAA
441419 GAATGTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 20 0.74
22 7 0.26
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATCTATC
Found at i:441904 original size:54 final size:52
Alignment explanation
Indices: 441772--441904 Score: 142
Period size: 53 Copynumber: 2.5 Consensus size: 52
441762 ATAATCATTG
* * *
441772 GTTCATAAAACATTGGACAACTCATTCATCCTGCTGAATCTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTGCTGAATCTTCTGCACAGAT
* * * * * *
441824 GTTTTGTAAAACATTTGATAATACATTCATCCTTTCATGTGA-CTTCTGCCCAGAT
1 G-TTCGTAAAACATTTGACAACACATTCATCC-TGC-TG-AATCTTCTGCACAGAT
441879 GTTCGTAAAACATTTGACAACACATT
1 GTTCGTAAAACATTTGACAACACATT
441905 AATATTTTCT
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
52 1 0.02
53 24 0.37
54 24 0.37
55 15 0.23
56 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (52 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTGCTGAATCTTCTGCACAGAT
Found at i:441924 original size:54 final size:55
Alignment explanation
Indices: 441811--441924 Score: 140
Period size: 54 Copynumber: 2.1 Consensus size: 55
441801 CCTGCTGAAT
* * * * *
441811 CTTCTGCACAGATGTTTTGTAAAACATTTGATAATACATTCATCCTTTCATGTGA
1 CTTCTGCACAGATGTTTCGTAAAACATTTGACAACACATTAATACTTTCATGTGA
* * * *
441866 CTTCTGCCCAGATG-TTCGTAAAACATTTGACAACACATTAATATTTTCTTGTGG
1 CTTCTGCACAGATGTTTCGTAAAACATTTGACAACACATTAATACTTTCATGTGA
441920 CTTCT
1 CTTCT
441925 TCCCTAATTC
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
54 37 0.74
55 13 0.26
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (55 bp):
CTTCTGCACAGATGTTTCGTAAAACATTTGACAACACATTAATACTTTCATGTGA
Found at i:447321 original size:42 final size:42
Alignment explanation
Indices: 447262--447345 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
447252 TTAGTTTTGT
* * * ** *
447262 CATTTGCTCTTTTGAATCATCTTGGAATTTTTTTGCTTGATC
1 CATTTGCTCATTTGAATCACCCTGGAACCTTTTTACTTGATC
*
447304 CATTTGTTCATTTGAATCACCCTGGAACCTTTTTACTTGATC
1 CATTTGCTCATTTGAATCACCCTGGAACCTTTTTACTTGATC
447346 AATCATCTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.19, C:0.20, G:0.13, T:0.48
Consensus pattern (42 bp):
CATTTGCTCATTTGAATCACCCTGGAACCTTTTTACTTGATC
Found at i:447663 original size:26 final size:28
Alignment explanation
Indices: 447634--447695 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
447624 CAAATTGTGC
*
447634 AATGCAAAATTAAACAT-AAAAG-TACG-
1 AATGCAAAATGAAA-ATGAAAAGATACGA
*
447660 AATGCAAAATGAAAATGCAAAGATACGA
1 AATGCAAAATGAAAATGAAAAGATACGA
447688 AATGCAAA
1 AATGCAAA
447696 TGCATGTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 17 0.55
27 4 0.13
28 8 0.26
ACGTcount: A:0.58, C:0.11, G:0.15, T:0.16
Consensus pattern (28 bp):
AATGCAAAATGAAAATGAAAAGATACGA
Found at i:447840 original size:43 final size:43
Alignment explanation
Indices: 447776--447866 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
447766 GTACATCGAA
*
447776 CAAAACTTTACATATATGGGATAACTTTCATTCCTAACTTCTC
1 CAAAACTTTACATATAGGGGATAACTTTCATTCCTAACTTCTC
447819 CAAAACTTTACATATAGGGGATAACTTTCATTCCTAACTTCTC
1 CAAAACTTTACATATAGGGGATAACTTTCATTCCTAACTTCTC
447862 CAAAA
1 CAAAA
447867 ATAAGTTAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (43 bp):
CAAAACTTTACATATAGGGGATAACTTTCATTCCTAACTTCTC
Found at i:450222 original size:20 final size:21
Alignment explanation
Indices: 450199--450243 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
450189 CTAAACAATG
450199 AATAAAATAAATAAAAT-TAA
1 AATAAAATAAATAAAATGTAA
* * *
450219 AATAACATGATTAAAATGTAA
1 AATAAAATAAATAAAATGTAA
450240 AATA
1 AATA
450244 TCTAAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (21 bp):
AATAAAATAAATAAAATGTAA
Found at i:451553 original size:3 final size:3
Alignment explanation
Indices: 451545--451611 Score: 71
Period size: 3 Copynumber: 22.3 Consensus size: 3
451535 GTATTTTATT
* * * * *
451545 TAA TAA TAA TAA TAA TAA TAA TCA TCA TAT TTA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
451593 TTA TAA AAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
451612 TTAAAAATGG
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:454438 original size:2 final size:2
Alignment explanation
Indices: 454431--454460 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
454421 TGCCTCATCC
454431 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
454461 GCGTTTGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:458822 original size:2 final size:2
Alignment explanation
Indices: 458815--458840 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
458805 ATAGTGTTAA
458815 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
458841 GTAGATGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:459369 original size:42 final size:42
Alignment explanation
Indices: 459322--459402 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
459312 ATCGAGGCTG
* ** * *
459322 TAAGAACAGTATCGGTACTTTATGAATAGTATCGATACTGAC
1 TAAGAACAATATCGGTACTGGATGAACAATATCGATACTGAC
459364 TAAGAACAATATCGGTACTGGATGAACAATATCGATACT
1 TAAGAACAATATCGGTACTGGATGAACAATATCGATACT
459403 AAATGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (42 bp):
TAAGAACAATATCGGTACTGGATGAACAATATCGATACTGAC
Found at i:459412 original size:20 final size:20
Alignment explanation
Indices: 459367--459412 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
459357 TACTGACTAA
* **
459367 GAACAATATCGGTACTGGAT
1 GAACAATATCGATACTAAAT
459387 GAACAATATCGATACTAAAT
1 GAACAATATCGATACTAAAT
*
459407 GCACAA
1 GAACAA
459413 AATGGTCCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (20 bp):
GAACAATATCGATACTAAAT
Found at i:463054 original size:89 final size:89
Alignment explanation
Indices: 462903--463080 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
462893 TTGAGGTTCT
462903 TTGGTGGCCTCTATAATTATATTGTCTAAAGTTATTTCTAACATAGTTGGATTTAGAATTTTGTC
1 TTGGTGGCCTCTATAATTATATTGTCTAAAGTTATTTCTAACATAGTTGGATTTAGAATTTTGTC
462968 CTATTTGTTCCAACTTTGTTAAAA
66 CTATTTGTTCCAACTTTGTTAAAA
462992 TTGGTGGCCTCTATAATTATATTGTCTAAAGTTATTTCTAACATAGTTGGATTTAGAATTTTGTC
1 TTGGTGGCCTCTATAATTATATTGTCTAAAGTTATTTCTAACATAGTTGGATTTAGAATTTTGTC
463057 CTATTTGTTCCAACTTTGTTAAAA
66 CTATTTGTTCCAACTTTGTTAAAA
463081 GAAGCTTTAA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (89 bp):
TTGGTGGCCTCTATAATTATATTGTCTAAAGTTATTTCTAACATAGTTGGATTTAGAATTTTGTC
CTATTTGTTCCAACTTTGTTAAAA
Found at i:467090 original size:22 final size:21
Alignment explanation
Indices: 467059--467100 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
467049 GTTATAAGGC
* *
467059 TATCGGTACTACTATTTAGTAG
1 TATCGATACTA-TATATAGTAG
467081 TATCGATACTATATATAGTA
1 TATCGATACTATATATAGTA
467101 TCGGTACCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (21 bp):
TATCGATACTATATATAGTAG
Found at i:467101 original size:18 final size:19
Alignment explanation
Indices: 467068--467103 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
467058 CTATCGGTAC
*
467068 TACTATTTAGTAGTATCGA
1 TACTATATAGTAGTATCGA
467087 TACTATATA-TAGTATCG
1 TACTATATAGTAGTATCG
467104 GTACCATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (19 bp):
TACTATATAGTAGTATCGA
Found at i:471365 original size:20 final size:20
Alignment explanation
Indices: 471337--471375 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
471327 CTAGAAAAAT
*
471337 GATCAATCCCTTTGACAAAG
1 GATCAATCCCTTGGACAAAG
*
471357 GATCGATCCCTTGGACAAA
1 GATCAATCCCTTGGACAAA
471376 AGTGAGTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (20 bp):
GATCAATCCCTTGGACAAAG
Found at i:476943 original size:37 final size:36
Alignment explanation
Indices: 476900--477007 Score: 103
Period size: 39 Copynumber: 2.9 Consensus size: 36
476890 AAAGTAATAT
476900 TTAAAATATATTAAAAATAATAATAATAAAAATTAA
1 TTAAAATATATTAAAAATAATAATAATAAAAATTAA
* *
476936 GTTAAAATATAACTAAACAATGACTAA-AATAAAAATTAA
1 -TTAAAATAT-ATTAAA-AAT-AATAATAATAAAAATTAA
* *
476975 TAAATAATAAATGTAAAACA-AATAATAATAAAA
1 TTAA-AATATAT-TAAAA-ATAATAATAATAAAA
477008 CTTGTAAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
37 13 0.22
38 17 0.29
39 24 0.41
40 4 0.07
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.28
Consensus pattern (36 bp):
TTAAAATATATTAAAAATAATAATAATAAAAATTAA
Found at i:478339 original size:3 final size:3
Alignment explanation
Indices: 478331--478427 Score: 51
Period size: 3 Copynumber: 32.7 Consensus size: 3
478321 TAAAATTATT
* * * * *
478331 TAA TAA TAA TAA TATA TAA TTA TTA TTA TAT TAA TTA TATA TAA TAAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA
* * *
478379 TAA TAA T-A TAA TAA T-T TAA TTA TTA TAA TAA T-A TAA -AA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
478423 TAA TA
1 TAA TA
478428 TTTAAATAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
2 9 0.12
3 55 0.73
4 11 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:478370 original size:25 final size:24
Alignment explanation
Indices: 478324--478421 Score: 85
Period size: 25 Copynumber: 4.1 Consensus size: 24
478314 TATGAAATAA
478324 AATTATTTAATAATAATAATATAT
1 AATTATTTAATAATAATAATATAT
* * *
478348 AATTATTATTATATTAATTATATAT
1 AATTATT-TAATAATAATAATATAT
** *
478373 AA-TAAATAATAAT-ATAATAATTT
1 AATTATTTAATAATAATAAT-ATAT
*
478396 AATTATTATAATAAT-ATAAAATAT
1 AATTATT-TAATAATAATAATATAT
478420 AA
1 AA
478422 ATAATATTTA
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
22 4 0.07
23 10 0.18
24 16 0.28
25 27 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AATTATTTAATAATAATAATATAT
Found at i:478401 original size:45 final size:42
Alignment explanation
Indices: 478320--478427 Score: 79
Period size: 44 Copynumber: 2.6 Consensus size: 42
478310 GTAATATGAA
* *
478320 ATAA-AATTATTTAATAAT-AATAAT-ATATAATTATTATTA-T
1 ATAATAATTATAT-ATAATAAATAATAATAT-ATAATTATTATT
478360 AT--TAATTATATATAATAAATAATAATATAATAATTTAATTATT
1 ATAATAATTATATATAATAAATAATAATAT-ATAA-TT-ATTATT
*
478403 ATAATAA-TATA-AAATATAAATAATA
1 ATAATAATTATATATA-ATAAATAATA
478428 TTTAAATAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
38 5 0.09
39 13 0.23
40 10 0.18
41 2 0.04
42 4 0.07
43 5 0.09
44 14 0.25
45 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (42 bp):
ATAATAATTATATATAATAAATAATAATATATAATTATTATT
Found at i:478944 original size:124 final size:122
Alignment explanation
Indices: 478634--479083 Score: 478
Period size: 124 Copynumber: 3.8 Consensus size: 122
478624 TCTGTGATGT
* *
478634 AATCTAGC-AAAGGTTGAACAAGCTCTTCTCATTGTGAA---CTTCTT-ATTCTTCAGATGAGTT
1 AATC-AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
* * * *
478694 CTTCTTATTATGAACTCTT-TCTGGAAATA-TTGATACTGATCTATCTCTTTCTTTGATAG
65 CTTCTCATTATGAACT-TTCTCTGGAAA-AGTTGAT-CTGATCTATCTCCTTATATGATAG
* * ** *
478753 AATCA-AACAAATGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTT
1 AATCAGCA-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
*
478817 CTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTATGTGATAG
65 CTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT-CTGATCTATCTCCTTATATGATAG
* * *
478876 AGTCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTT
1 AATCA-GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
* * * * *
478941 CTTCTTATTATCAACTTTCTATGGAAAAGTTGA--T--TC-A--T-C-GA-ATGATGG
65 CTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCTGATCTATCTCCTTATATGATAG
*
478989 ATTCGAGCAAAAGGTTGAACAAG---TTCTCATTATGAA-TTCTTC-TCCTTCTTCAGATGAGTT
1 AATC-AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
479049 CTTCTCATTATGAACTTTCTCTGGAAAAGTTGATC
65 CTTCTCATTATGAACTTTCTCTGGAAAAGTTGATC
479084 CATCGAATGA
Statistics
Matches: 286, Mismatches: 32, Indels: 35
0.81 0.09 0.10
Matches are distributed among these distances:
108 48 0.17
109 5 0.02
110 13 0.05
113 24 0.08
114 2 0.01
115 1 0.00
116 1 0.00
118 2 0.01
119 32 0.11
121 1 0.00
122 9 0.03
123 67 0.23
124 80 0.28
125 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (122 bp):
AATCAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
TTCTCATTATGAACTTTCTCTGGAAAAGTTGATCTGATCTATCTCCTTATATGATAG
Found at i:479052 original size:108 final size:111
Alignment explanation
Indices: 478882--479099 Score: 343
Period size: 108 Copynumber: 2.0 Consensus size: 111
478872 ATAGAGTCAT
* * *
478882 GCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAG--CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
478947 ATTATCAACTTTCTATGGAAAAGTTGATTCATCGAATGATGGATTCGA
64 ATTATCAACTTTCTATGGAAAAGTTGATCCATCGAATGATGGATTCGA
478995 GCAAAAGGTTGAACAAG-TTCTCATTATGAA-TTCTTC-TCCTTCTTCAGATGAGTTCTTCTCAT
1 GCAAAAGGTTGAACAAGCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
479057 TATGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGGATT
66 TATCAACTTTCTATGGAAAAGTTGATCCATCGAATGATGGATT
479100 TGAATCTTTG
Statistics
Matches: 99, Mismatches: 6, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
108 65 0.66
109 5 0.05
110 13 0.13
113 16 0.16
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (111 bp):
GCAAAAGGTTGAACAAGCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATCAACTTTCTATGGAAAAGTTGATCCATCGAATGATGGATTCGA
Found at i:480073 original size:274 final size:274
Alignment explanation
Indices: 479577--480127 Score: 1057
Period size: 274 Copynumber: 2.0 Consensus size: 274
479567 TTTTCAATAG
*
479577 TCATAAAGATGTGGTTTGGATTCATCAATTGCAGAGTTGACAGATTTTATATGTGCTGGTCAAAT
1 TCATAAAGATGTGGTTTGGATTCATCAACTGCAGAGTTGACAGATTTTATATGTGCTGGTCAAAT
479642 GGCTAAAGCTGCTGACACACTTCTTCCGGTAAAAGATGGGAAGCCATTATGCAATGATCCCAATT
66 GGCTAAAGCTGCTGACACACTTCTTCCGGTAAAAGATGGGAAGCCATTATGCAATGATCCCAATT
*
479707 ACAAGAAAAAATGAAACTTGGGCTATGATTTTCTTAGAAAAAGAAGAAGCAGAAGTAGCTTGAAA
131 ACAAGAAAAAATGAAACTTGGGCTATGATTTTCTTAGAAAAAGAAGAAGCAGAAGTAGCATGAAA
*
479772 AGAAGCTTCTTAATGAAGACGATCATGCAGTTCATCCTCATAATCCAATGATTGGTTTTGGAGTT
196 AGAAGCTTCTTAATGAAGACAATCATGCAGTTCATCCTCATAATCCAATGATTGGTTTTGGAGTT
479837 CCTACTGAACCAGA
261 CCTACTGAACCAGA
479851 TCATAAAGATGTGGTTTGGATTCATCAACTGCAGAGTTGACAGATTTTATATGTGCTGGTCAAAT
1 TCATAAAGATGTGGTTTGGATTCATCAACTGCAGAGTTGACAGATTTTATATGTGCTGGTCAAAT
479916 GGCTAAAGCTGCTGACACACTTCTTCCGGTAAAAGATGGGAAGCCATTATGCAATGATCCCAATT
66 GGCTAAAGCTGCTGACACACTTCTTCCGGTAAAAGATGGGAAGCCATTATGCAATGATCCCAATT
*
479981 ACAAGAAAAAATGAAACTTGGGCTATGCTTTTCTTAGAAAAAGAAGAAGCAGAAGTAGCATGAAA
131 ACAAGAAAAAATGAAACTTGGGCTATGATTTTCTTAGAAAAAGAAGAAGCAGAAGTAGCATGAAA
*
480046 AGAAGCTTCTTAATGAAGACAATCATGCAGTTCATCCTCCTAATCCAATGATTGGTTTTGGAGTT
196 AGAAGCTTCTTAATGAAGACAATCATGCAGTTCATCCTCATAATCCAATGATTGGTTTTGGAGTT
480111 CCTACTGAACCAGA
261 CCTACTGAACCAGA
480125 TCA
1 TCA
480128 GATAACTCAA
Statistics
Matches: 272, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
274 272 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (274 bp):
TCATAAAGATGTGGTTTGGATTCATCAACTGCAGAGTTGACAGATTTTATATGTGCTGGTCAAAT
GGCTAAAGCTGCTGACACACTTCTTCCGGTAAAAGATGGGAAGCCATTATGCAATGATCCCAATT
ACAAGAAAAAATGAAACTTGGGCTATGATTTTCTTAGAAAAAGAAGAAGCAGAAGTAGCATGAAA
AGAAGCTTCTTAATGAAGACAATCATGCAGTTCATCCTCATAATCCAATGATTGGTTTTGGAGTT
CCTACTGAACCAGA
Found at i:487917 original size:13 final size:13
Alignment explanation
Indices: 487901--487934 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
487891 TATACATAAA
487901 GAATGCAATGAAT
1 GAATGCAATGAAT
487914 GAATGCAATGAAT
1 GAATGCAATGAAT
*
487927 GTATGCAA
1 GAATGCAA
487935 AAGGTATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.24
Consensus pattern (13 bp):
GAATGCAATGAAT
Found at i:491441 original size:28 final size:26
Alignment explanation
Indices: 491386--491442 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
491376 AAATATTAAT
*
491386 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
491412 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
491440 AAA
1 AAA
491443 TTTTGAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 8 0.31
27 1 0.04
28 17 0.65
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:492357 original size:35 final size:36
Alignment explanation
Indices: 492305--492391 Score: 94
Period size: 35 Copynumber: 2.5 Consensus size: 36
492295 TAAAAATAAT
* *
492305 ATAAA-AATAAGTTAAAAT-ATACTAA-ACAATGACTAA
1 ATAAATAATAA-TTAAAATAATAATAATAAAATG--TAA
492341 ATAAATAA-AATTAAAATAATAATAATAAAATGTAA
1 ATAAATAATAATTAAAATAATAATAATAAAATGTAA
492376 ATAAATAATAA-TAAAA
1 ATAAATAATAATTAAAA
492392 CTTGTAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
35 23 0.51
36 15 0.33
37 7 0.16
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (36 bp):
ATAAATAATAATTAAAATAATAATAATAAAATGTAA
Found at i:492411 original size:23 final size:21
Alignment explanation
Indices: 492344--492404 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
492334 TGACTAAATA
492344 AATAAAAT-TAAA-ATAATAAT
1 AATAAAATGTAAATA-AATAAT
492364 AATAAAATGTAAATAAATAAT
1 AATAAAATGTAAATAAATAAT
492385 AATAAAACTTGTAAATAAAT
1 AATAAAA--TGTAAATAAAT
492405 GAAAATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.22
21 17 0.46
22 1 0.03
23 11 0.30
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.30
Consensus pattern (21 bp):
AATAAAATGTAAATAAATAAT
Found at i:493592 original size:20 final size:21
Alignment explanation
Indices: 493577--493646 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
493567 TGTAATATTA
493577 AATAA-AATTATT-TAATAAT
1 AATAATAATTATTATAATAAT
493596 AATAATAATTATTATAATAAT
1 AATAATAATTATTATAATAAT
* *
493617 AATAATAATAATAATAATAAT
1 AATAATAATTATTATAATAAT
493638 -ATAAATAAT
1 AAT-AATAAT
493647 ATTTAAATGA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.11
20 9 0.20
21 32 0.70
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAATAATTATTATAATAAT
Found at i:493597 original size:3 final size:3
Alignment explanation
Indices: 493589--493647 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
493579 TAAAATTATT
* *
493589 TAA TAA TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
493637 T-A TAAA TAA TA
1 TAA T-AA TAA TA
493648 TTTAAATGAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.92
4 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:497085 original size:15 final size:15
Alignment explanation
Indices: 497065--497106 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
497055 TTAGTTGGGC
*
497065 GGGCGGATGTGGGGA
1 GGGCGGATGCGGGGA
*
497080 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGA
*
497095 GGGTGGATGCGG
1 GGGCGGATGCGG
497107 TGCGGATGCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.67, T:0.12
Consensus pattern (15 bp):
GGGCGGATGCGGGGA
Found at i:499385 original size:12 final size:13
Alignment explanation
Indices: 499368--499396 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
499358 TATAAGTACA
499368 TTTTTA-TAATAT
1 TTTTTATTAATAT
499380 TTTTTATTAATAT
1 TTTTTATTAATAT
499393 TTTT
1 TTTT
499397 ATGAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTATTAATAT
Found at i:506731 original size:56 final size:52
Alignment explanation
Indices: 506628--506736 Score: 173
Period size: 56 Copynumber: 2.0 Consensus size: 52
506618 ATATATATTT
*
506628 ATTCATATTGTTAATAGTTTGCCGTGATAGGATGATAAGGATGACAAGGGTG
1 ATTCATATTGTTAATAGTTTGCCGTGATAAGATGATAAGGATGACAAGGGTG
506680 ATTCATATTGTTAATAGTTTGCCATGAATGATAAGATGATAAGGATGACAAGGGTG
1 ATTCATATTGTTAATAGTTTGCC--G--TGATAAGATGATAAGGATGACAAGGGTG
506736 A
1 A
506737 ATGCGTAGGC
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
52 23 0.44
54 1 0.02
56 28 0.54
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (52 bp):
ATTCATATTGTTAATAGTTTGCCGTGATAAGATGATAAGGATGACAAGGGTG
Found at i:516376 original size:21 final size:21
Alignment explanation
Indices: 516343--516382 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
516333 CTGAAATCAT
516343 TTAATCATTATTCTTAGCTCC
1 TTAATCATTATTCTTAGCTCC
516364 TTAAT-ATTAATTCTTAGCT
1 TTAATCATT-ATTCTTAGCT
516383 TTAATACCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50
Consensus pattern (21 bp):
TTAATCATTATTCTTAGCTCC
Found at i:518182 original size:15 final size:15
Alignment explanation
Indices: 518164--518193 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
518154 GCATCATGGG
518164 AATGAGCAATGCAAT
1 AATGAGCAATGCAAT
*
518179 AATGAGCGATGCAAT
1 AATGAGCAATGCAAT
518194 GTACTTACGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.20
Consensus pattern (15 bp):
AATGAGCAATGCAAT
Found at i:533538 original size:137 final size:137
Alignment explanation
Indices: 533292--533565 Score: 548
Period size: 137 Copynumber: 2.0 Consensus size: 137
533282 AAACAAGTTG
533292 CTATCGCATTCCCATACTTCTCACACACATAACATATAGTAGGTAACCCCTCATACTCTACACTT
1 CTATCGCATTCCCATACTTCTCACACACATAACATATAGTAGGTAACCCCTCATACTCTACACTT
533357 TAGTATATATCATCTATCATCATACAAGGAACCAAAGGCTTATCCAGATTCTAAGCGAGCAAATC
66 TAGTATATATCATCTATCATCATACAAGGAACCAAAGGCTTATCCAGATTCTAAGCGAGCAAATC
533422 GTTCGCA
131 GTTCGCA
533429 CTATCGCATTCCCATACTTCTCACACACATAACATATAGTAGGTAACCCCTCATACTCTACACTT
1 CTATCGCATTCCCATACTTCTCACACACATAACATATAGTAGGTAACCCCTCATACTCTACACTT
533494 TAGTATATATCATCTATCATCATACAAGGAACCAAAGGCTTATCCAGATTCTAAGCGAGCAAATC
66 TAGTATATATCATCTATCATCATACAAGGAACCAAAGGCTTATCCAGATTCTAAGCGAGCAAATC
533559 GTTCGCA
131 GTTCGCA
533566 TTTGTCTTTT
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
137 137 1.00
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.28
Consensus pattern (137 bp):
CTATCGCATTCCCATACTTCTCACACACATAACATATAGTAGGTAACCCCTCATACTCTACACTT
TAGTATATATCATCTATCATCATACAAGGAACCAAAGGCTTATCCAGATTCTAAGCGAGCAAATC
GTTCGCA
Found at i:536929 original size:23 final size:22
Alignment explanation
Indices: 536901--536967 Score: 89
Period size: 23 Copynumber: 3.0 Consensus size: 22
536891 GCTGCCTCCG
536901 AGCCATCACTCGAGCCGCCGCC
1 AGCCATCACTCGAGCCGCCGCC
* * *
536923 ACGCCATCACTTGAGCCTCCGTCG
1 A-GCCATCACTCGAGCCGCCG-CC
536947 AGCCATCACTCGAGCCGCCGC
1 AGCCATCACTCGAGCCGCCGC
536968 TGAAGCCATC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
22 2 0.05
23 34 0.89
24 2 0.05
ACGTcount: A:0.18, C:0.46, G:0.22, T:0.13
Consensus pattern (22 bp):
AGCCATCACTCGAGCCGCCGCC
Found at i:537703 original size:145 final size:145
Alignment explanation
Indices: 537535--537816 Score: 519
Period size: 145 Copynumber: 1.9 Consensus size: 145
537525 CCCATTTGGC
* *
537535 AACCTACGTTGTGACTTTATGTTTTATAATATTTTTTATATAATAATGCAAGCCTATTTGTATAT
1 AACCTACGTTGTAACTTTATGTTTTATAATATTTTTTATATAATAATGCAAGCCTATATGTATAT
* *
537600 ATTAATTGAATGTTAGTTATTAACATTTGACTTTTGTTACATTGTTGTTTGTGTATGAAATTGGA
66 ATTAATTGAATGTTAGCTATTAACATTAGACTTTTGTTACATTGTTGTTTGTGTATGAAATTGGA
537665 TTATTTGGCATTAGT
131 TTATTTGGCATTAGT
537680 AACCTACGTTGTAACTTTATGTTTTATAATATTTTTTATATAATAATGCAAGCCTATATGTATAT
1 AACCTACGTTGTAACTTTATGTTTTATAATATTTTTTATATAATAATGCAAGCCTATATGTATAT
*
537745 ATTAATTGAATGTTAGCTATTAACATTAGACTTTTGTTACATTGTTGTTTGTTTATGAAATTGGA
66 ATTAATTGAATGTTAGCTATTAACATTAGACTTTTGTTACATTGTTGTTTGTGTATGAAATTGGA
537810 TTATTTG
131 TTATTTG
537817 ATTATGTGAG
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
145 132 1.00
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (145 bp):
AACCTACGTTGTAACTTTATGTTTTATAATATTTTTTATATAATAATGCAAGCCTATATGTATAT
ATTAATTGAATGTTAGCTATTAACATTAGACTTTTGTTACATTGTTGTTTGTGTATGAAATTGGA
TTATTTGGCATTAGT
Found at i:541750 original size:20 final size:21
Alignment explanation
Indices: 541711--541758 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
541701 CACCGAAGTG
* *
541711 CCACACAATTGTCCCGAAGGA
1 CCACATAATTGTCCCAAAGGA
541732 CCACATAATT-TCCCAAAGGA
1 CCACATAATTGTCCCAAAGGA
541752 CCACATA
1 CCACATA
541759 GACCCTCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.38, C:0.33, G:0.12, T:0.17
Consensus pattern (21 bp):
CCACATAATTGTCCCAAAGGA
Found at i:542525 original size:55 final size:55
Alignment explanation
Indices: 542459--542602 Score: 198
Period size: 55 Copynumber: 2.6 Consensus size: 55
542449 TCATACTTGG
* * *
542459 GGGTATCGATACACTCCTCAATATACCGATACACAAATAGCACTCGATGTTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAGAACTCGATGTTTTGA
* * * * *
542514 GGGTATCGATACACTCCTTAGTGTATCGATACACAAATGGAATTTGATGTTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAGAACTCGATGTTTTGA
* *
542569 GGGTATTGATATACTCCTCAGTGTACCGATACAC
1 GGGTATCGATACACTCCTCAGTGTACCGATACAC
542603 TCATACAAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 77 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (55 bp):
GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAGAACTCGATGTTTTGA
Found at i:548525 original size:42 final size:41
Alignment explanation
Indices: 548479--548619 Score: 149
Period size: 41 Copynumber: 3.4 Consensus size: 41
548469 TTTTGAGCAT
548479 GATGATTAAATCCTTCGAGTTATCTGTAAGCCTTTAGAACAA
1 GATGA-TAAATCCTTCGAGTTATCTGTAAGCCTTTAGAACAA
* * * ** ** * * *
548521 GATGATAAGTCCATCGGGCCATCCATAAGACC-TTCGAGCAT
1 GATGATAAATCCTTCGAGTTATCTGTAAG-CCTTTAGAACAA
548562 GATGATTAAATCCTTCGAGTTATCTGTAAGCCTTTAGAACAA
1 GATGA-TAAATCCTTCGAGTTATCTGTAAGCCTTTAGAACAA
*
548604 GATGATAAGTCCTTCG
1 GATGATAAATCCTTCG
548620 GGCCATCCAT
Statistics
Matches: 75, Mismatches: 21, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
41 40 0.53
42 35 0.47
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (41 bp):
GATGATAAATCCTTCGAGTTATCTGTAAGCCTTTAGAACAA
Found at i:548567 original size:41 final size:42
Alignment explanation
Indices: 548505--548635 Score: 142
Period size: 41 Copynumber: 3.2 Consensus size: 42
548495 GAGTTATCTG
*
548505 TAAG-CCTTTAGAACAAGATGATAAGTCCATCGGGCCATCCA
1 TAAGACCTTTAGAACAAGATGATAAGTCCTTCGGGCCATCCA
* * * * * ** **
548546 TAAGACC-TTCGAGCATGATGATTAAATCCTTCGAGTTATCTG
1 TAAGACCTTTAGAACAAGATGA-TAAGTCCTTCGGGCCATCCA
548588 TAAG-CCTTTAGAACAAGATGATAAGTCCTTCGGGCCATCCA
1 TAAGACCTTTAGAACAAGATGATAAGTCCTTCGGGCCATCCA
548629 TAAGACC
1 TAAGACC
548636 ATGGGGTAGG
Statistics
Matches: 67, Mismatches: 19, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
41 35 0.52
42 32 0.48
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (42 bp):
TAAGACCTTTAGAACAAGATGATAAGTCCTTCGGGCCATCCA
Found at i:548601 original size:83 final size:83
Alignment explanation
Indices: 548473--548635 Score: 317
Period size: 83 Copynumber: 2.0 Consensus size: 83
548463 TAAGTCTTTT
548473 GAGCATGATGATTAAATCCTTCGAGTTATCTGTAAGCCTTTAGAACAAGATGATAAGTCCATCGG
1 GAGCATGATGATTAAATCCTTCGAGTTATCTGTAAGCCTTTAGAACAAGATGATAAGTCCATCGG
548538 GCCATCCATAAGACCTTC
66 GCCATCCATAAGACCTTC
*
548556 GAGCATGATGATTAAATCCTTCGAGTTATCTGTAAGCCTTTAGAACAAGATGATAAGTCCTTCGG
1 GAGCATGATGATTAAATCCTTCGAGTTATCTGTAAGCCTTTAGAACAAGATGATAAGTCCATCGG
548621 GCCATCCATAAGACC
66 GCCATCCATAAGACC
548636 ATGGGGTAGG
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (83 bp):
GAGCATGATGATTAAATCCTTCGAGTTATCTGTAAGCCTTTAGAACAAGATGATAAGTCCATCGG
GCCATCCATAAGACCTTC
Found at i:549453 original size:21 final size:19
Alignment explanation
Indices: 549417--549525 Score: 92
Period size: 21 Copynumber: 5.3 Consensus size: 19
549407 AATGCGATTT
*
549417 TCCAAATTCATTGCGATAG
1 TCCAAATTCGTTGCGATAG
* *
549436 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
549459 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* * *
549478 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
549501 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
549520 TCCAAA
1 TCCAAA
549526 ATCGCAACGA
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
19 23 0.32
21 31 0.44
23 17 0.24
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:549473 original size:42 final size:42
Alignment explanation
Indices: 549409--549524 Score: 200
Period size: 42 Copynumber: 2.8 Consensus size: 42
549399 AGATTCGCAA
*
549409 TGCGA-TT-TTCCAAATTCATTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
*
549449 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
549491 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
549525 AATCGCAACG
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
40 5 0.07
41 2 0.03
42 64 0.90
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:549625 original size:6 final size:6
Alignment explanation
Indices: 549614--549655 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
549604 GACACGTATT
*
549614 ACCACG ACCACG ACCACG ACCACT ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
549656 CGAGACGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 14 0.41
6 20 0.59
ACGTcount: A:0.29, C:0.55, G:0.14, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:550465 original size:42 final size:42
Alignment explanation
Indices: 550413--550535 Score: 180
Period size: 42 Copynumber: 3.0 Consensus size: 42
550403 CGTTGCGATT
550413 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAAC
* *
550455 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAAC
*
550497 TTGGACTATCGCAATGCGAATAT-G--TAAATCGCAATGCGA
1 TTGGACTATCGCAA--CGAATTTGGAATAAATCGCAATGCGA
550536 TAGTCGAAGT
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
41 14 0.19
42 54 0.73
43 1 0.01
44 5 0.07
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAAC
Found at i:550507 original size:21 final size:20
Alignment explanation
Indices: 550413--550516 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 20
550403 CGTTGCGATT
*
550413 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
550432 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
* *
550455 TTGGACTATCGCAA-CAAAT
1 TTGGACTATCGCAAGCGAAC
*
550474 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
550497 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAA-GCGAA
550517 TATGTAAATC
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
19 15 0.22
21 33 0.49
23 19 0.28
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:552539 original size:2 final size:2
Alignment explanation
Indices: 552532--552586 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
552522 TTTACACAAA
552532 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
552574 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
552587 CATGCGAGGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:553030 original size:19 final size:19
Alignment explanation
Indices: 553008--553073 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
552998 ATAATTATTT
553008 ATATAAAAATTCATCGATA
1 ATATAAAAATTCATCGATA
** *
553027 ATATATTTAAATATAAATC-ATTT
1 ATATA---AAA-ATTCATCGA-TA
553050 ATATAAAAATTCATCGATA
1 ATATAAAAATTCATCGATA
553069 ATATA
1 ATATA
553074 TTATTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
19 16 0.46
20 4 0.11
22 4 0.11
23 11 0.31
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.38
Consensus pattern (19 bp):
ATATAAAAATTCATCGATA
Found at i:553031 original size:21 final size:21
Alignment explanation
Indices: 553007--553074 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
552997 AATAATTATT
553007 TATATAAAAATTCATCGATAA
1 TATATAAAAATTCATCGATAA
* ** *
553028 TATATTTAAATATAAATC-AT-T
1 TATA--TAAAAATTCATCGATAA
553049 TATATAAAAATTCATCGATAA
1 TATATAAAAATTCATCGATAA
553070 TATAT
1 TATAT
553075 TATTTTATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
19 9 0.26
20 2 0.06
21 13 0.37
22 2 0.06
23 9 0.26
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (21 bp):
TATATAAAAATTCATCGATAA
Found at i:553050 original size:42 final size:42
Alignment explanation
Indices: 552985--553075 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
552975 TGAAATTTTA
*
552985 AATAT-TTTAAATAATAATTATTTATATAAAAATTCATCGAT
1 AATATATTTAAATAATAATCATTTATATAAAAATTCATCGAT
553026 AATATATTTAAAT-ATAAATCATTTATATAAAAATTCATCGAT
1 AATATATTTAAATAAT-AATCATTTATATAAAAATTCATCGAT
553068 AATATATT
1 AATATATT
553076 ATTTTATTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
41 7 0.15
42 40 0.85
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (42 bp):
AATATATTTAAATAATAATCATTTATATAAAAATTCATCGAT
Found at i:553123 original size:23 final size:26
Alignment explanation
Indices: 553066--553123 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
553056 AAATTCATCG
553066 ATAATATATTATTTTATTATTTAAAT
1 ATAATATATTATTTTATTATTTAAAT
*
553092 ATATCATATATTA-TTT-TTATTTTAAT
1 ATA--ATATATTATTTTATTATTTAAAT
553118 -TAATAT
1 ATAATAT
553124 TAAATTTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
25 2 0.07
26 12 0.41
27 3 0.10
28 8 0.28
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
ATAATATATTATTTTATTATTTAAAT
Found at i:553781 original size:7 final size:7
Alignment explanation
Indices: 553769--553803 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
553759 TTCAAAGAAT
553769 TCAAGCA
1 TCAAGCA
553776 TCAAGCA
1 TCAAGCA
*
553783 TCAAGAA
1 TCAAGCA
*
553790 TCAAGAA
1 TCAAGCA
553797 TCAAGCA
1 TCAAGCA
553804 AATATCAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.49, C:0.23, G:0.14, T:0.14
Consensus pattern (7 bp):
TCAAGCA
Found at i:553792 original size:14 final size:14
Alignment explanation
Indices: 553763--553803 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
553753 AAGTTTTTCA
553763 AAGAATTCAAGCATC
1 AAGAA-TCAAGCATC
* *
553778 AAGCATCAAGAATC
1 AAGAATCAAGCATC
553792 AAGAATCAAGCA
1 AAGAATCAAGCA
553804 AATATCAGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.51, C:0.20, G:0.15, T:0.15
Consensus pattern (14 bp):
AAGAATCAAGCATC
Found at i:553799 original size:21 final size:22
Alignment explanation
Indices: 553763--553803 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
553753 AAGTTTTTCA
*
553763 AAGAATTCAAGCATCAAGCATC
1 AAGAATTCAAGAATCAAGCATC
553785 AAGAA-TCAAGAATCAAGCA
1 AAGAATTCAAGAATCAAGCA
553804 AATATCAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.20, G:0.15, T:0.15
Consensus pattern (22 bp):
AAGAATTCAAGAATCAAGCATC
Found at i:556192 original size:24 final size:25
Alignment explanation
Indices: 556138--556192 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
556128 GAACTCAAAA
*
556138 AAAAAATTAGAAGCTCGATTGAAGC
1 AAAAAATTAGAAGCTCGATTAAAGC
** * *
556163 CTAAAATTCG-AGTTCGATTAAAGC
1 AAAAAATTAGAAGCTCGATTAAAGC
556187 AAAAAA
1 AAAAAA
556193 ATAGTTCGCT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (25 bp):
AAAAAATTAGAAGCTCGATTAAAGC
Found at i:556773 original size:13 final size:13
Alignment explanation
Indices: 556752--556784 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
556742 GAAGGAAAAT
*
556752 TTATGATAAACAA
1 TTATCATAAACAA
556765 TTATCATAAACAA
1 TTATCATAAACAA
556778 TTATCAT
1 TTATCAT
556785 TTTTCACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (13 bp):
TTATCATAAACAA
Found at i:559617 original size:12 final size:12
Alignment explanation
Indices: 559602--559682 Score: 78
Period size: 12 Copynumber: 6.7 Consensus size: 12
559592 TTCTGGCCTG
*
559602 TAATAATATATT
1 TAATAATATATA
559614 TAATAATATATA
1 TAATAATATATA
559626 T-AT-ATATATA
1 TAATAATATATA
559636 TATATATATATATA
1 TA-ATA-ATATATA
* *
559650 TTAATAATAAAAA
1 -TAATAATATATA
559663 TAATAATA-ATAA
1 TAATAATATAT-A
559675 TAATAATA
1 TAATAATA
559683 AAAGTAATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
10 8 0.14
11 3 0.05
12 31 0.53
13 5 0.08
14 10 0.17
15 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATAATATATA
Found at i:559624 original size:2 final size:2
Alignment explanation
Indices: 559607--559650 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
559597 GCCTGTAATA
*
559607 AT AT AT TT A- AT A- 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
559647 AT AT
1 AT AT
559651 TAATAATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:559666 original size:9 final size:9
Alignment explanation
Indices: 559614--559695 Score: 67
Period size: 9 Copynumber: 8.3 Consensus size: 9
559604 ATAATATATT
559614 TAATAATATA
1 TAATAATA-A
559624 TATATATATATA
1 TA-ATA-ATA-A
559636 TATATATATATA
1 TA-ATA-ATA-A
*
559648 TATTAATAA
1 TAATAATAA
*
559657 TAAAAATAA
1 TAATAATAA
559666 TAATAATAA
1 TAATAATAA
559675 TAATAATAA
1 TAATAATAA
559684 -AAGTAATAA
1 TAA-TAATAA
559693 TAA
1 TAA
559696 AAGTAAAATG
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
8 2 0.03
9 31 0.48
10 7 0.11
11 5 0.08
12 19 0.30
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (9 bp):
TAATAATAA
Found at i:559683 original size:12 final size:12
Alignment explanation
Indices: 559614--559695 Score: 67
Period size: 12 Copynumber: 6.2 Consensus size: 12
559604 ATAATATATT
559614 TAATAATATATATA
1 TAATAATA-ATA-A
559628 TATATATATATATATA
1 TA-ATA-ATA-ATA-A
*
559644 TATATATTAATAA
1 TA-ATAATAATAA
*
559657 TAAAAATAATAA
1 TAATAATAATAA
559669 TAATAATAATAA
1 TAATAATAATAA
559681 TAA-AAGTAATAA
1 TAATAA-TAATAA
559693 TAA
1 TAA
559696 AAGTAAAATG
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
11 2 0.03
12 31 0.51
13 3 0.05
14 5 0.08
15 5 0.08
16 15 0.25
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (12 bp):
TAATAATAATAA
Found at i:559709 original size:12 final size:12
Alignment explanation
Indices: 559651--559701 Score: 77
Period size: 12 Copynumber: 4.2 Consensus size: 12
559641 ATATATATAT
*
559651 TAATAATAAAAA
1 TAATAATAAAAG
559663 TAATAATAATAA-
1 TAATAATAA-AAG
559675 TAATAATAAAAG
1 TAATAATAAAAG
559687 TAATAATAAAAG
1 TAATAATAAAAG
559699 TAA
1 TAA
559702 AATGAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (12 bp):
TAATAATAAAAG
Found at i:560081 original size:45 final size:45
Alignment explanation
Indices: 560017--560594 Score: 883
Period size: 45 Copynumber: 12.9 Consensus size: 45
560007 AAAAGCTCCT
*
560017 GAAGGCTTTGAAAACATCATACACTGAAGGGCTTACAGATGACCC
1 GAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
* *
560062 GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACTC
1 GAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
* **
560107 GGAGATTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
1 GAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
*
560152 GAAGGCTTTGAAAACATCATGCACTAAAGGGCTTACAGATGACCC
1 GAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
* *
560197 GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTATAGATGACCC
1 GAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
*
560242 GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
1 GAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
* *
560287 GAAGGCTTTGAAAACATCATGCATTGAAGGGCTTACAGATGACCT
1 GAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
560332 GAAGGCTTTG-AAA-A-CATGCACTGAAGGGCTTACAGATGACCC
1 GAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
* * *
560374 GAAGGCTTTGAAAACATCATCCACTTAAGGGCTTACATATGACCC
1 GAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
* * *
560419 GAAGGCTTTAAAAATATCATGCACTGAATGGCTTACAGATGACCC
1 GAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
* * *
560464 AAAGGCTTTGAAAACATTATCCACTGAAGGGCTTACAGATGACCC
1 GAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
* * * * *
560509 AAAAGTTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCT
1 GAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
* *
560554 GAAGGTTTTGAAAACATCATGCACTGAAGGTCTTACAGATG
1 GAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
560595 TGGGAAATAG
Statistics
Matches: 486, Mismatches: 44, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
42 36 0.07
43 4 0.01
44 4 0.01
45 442 0.91
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (45 bp):
GAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
Found at i:560336 original size:20 final size:20
Alignment explanation
Indices: 560311--560378 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
560301 CATCATGCAT
560311 TGAAGGGCTTACAGATGACC
1 TGAAGGGCTTACAGATGACC
* *
560331 TGAA-GGCTTTGAAAACATG-CAC
1 TGAAGGGC-TT--ACAGATGAC-C
560353 TGAAGGGCTTACAGATGACC
1 TGAAGGGCTTACAGATGACC
*
560373 CGAAGG
1 TGAAGG
560379 CTTTGAAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
19 3 0.08
20 17 0.46
21 2 0.05
22 12 0.32
23 3 0.08
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.19
Consensus pattern (20 bp):
TGAAGGGCTTACAGATGACC
Done.