Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008639.1 Hibiscus syriacus cultivar Beakdansim tig00111614_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: 1076872
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:345777 original size:2 final size:2
Alignment explanation
Indices: 345772--345816 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
345762 TTTTTATTAT
345772 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
345813 TA TA
1 TA TA
345817 ATGTATTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:346339 original size:1 final size:1
Alignment explanation
Indices: 346333--346367 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
346323 ACAGAATTTT
346333 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
346368 CCTCTCCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:355503 original size:16 final size:17
Alignment explanation
Indices: 355472--355504 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
355462 GCTGATTCGA
*
355472 GAATTGATGCGTTGGTG
1 GAATTGAAGCGTTGGTG
355489 GAATTGAAG-GTTGGTG
1 GAATTGAAGCGTTGGTG
355505 ACAACTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.03, G:0.42, T:0.33
Consensus pattern (17 bp):
GAATTGAAGCGTTGGTG
Found at i:356325 original size:6 final size:6
Alignment explanation
Indices: 356314--356350 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
356304 AGAGGAGGTT
356314 GATGGA GATGGA GATGGA GATGGA GATGGA GA-GGA GA
1 GATGGA GATGGA GATGGA GATGGA GATGGA GATGGA GA
356351 GAAAGACGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.35, C:0.00, G:0.51, T:0.14
Consensus pattern (6 bp):
GATGGA
Found at i:365885 original size:16 final size:15
Alignment explanation
Indices: 365833--365887 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 15
365823 GAATCTTCGT
365833 CTTTAATTTGATTTTTA
1 CTTTAA-TT-ATTTTTA
365850 CTTT-ATT-TTATTTA
1 CTTTAATTATT-TTTA
365864 -TTTAATTATTTTTA
1 CTTTAATTATTTTTA
365878 TCTTTAATTA
1 -CTTTAATTA
365888 CTTCAATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 5 0.15
14 11 0.33
15 4 0.12
16 9 0.27
17 4 0.12
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.67
Consensus pattern (15 bp):
CTTTAATTATTTTTA
Found at i:379307 original size:23 final size:23
Alignment explanation
Indices: 379281--379349 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
379271 CACCACAGCT
*
379281 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
379304 CGTAGAATTGCATCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
379327 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
379350 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:379825 original size:25 final size:25
Alignment explanation
Indices: 379791--379846 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
379781 TCATATAACA
*
379791 CATAGAAACACCTAGAACACTTTCT
1 CATAGCAACACCTAGAACACTTTCT
* *
379816 CATAGCAACACTTAGAATACTTTCT
1 CATAGCAACACCTAGAACACTTTCT
379841 CATAGC
1 CATAGC
379847 TTATATCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.27, G:0.09, T:0.27
Consensus pattern (25 bp):
CATAGCAACACCTAGAACACTTTCT
Found at i:383630 original size:23 final size:23
Alignment explanation
Indices: 383604--383667 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
383594 CAGCTTGTAT
383604 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
383627 AATTGCACCGGAGTACCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
383650 AATTGCACTGTAGTGCCA
1 AATTGCACCGAAGTGCCA
383668 TATAATAATG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:384633 original size:20 final size:20
Alignment explanation
Indices: 384610--384655 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
384600 CTCTTTATAA
384610 ACATCTATTTCTATTTCCCT
1 ACATCTATTTCTATTTCCCT
*
384630 ACATCTATTTCTATTTTCCT
1 ACATCTATTTCTATTTCCCT
384650 ACATCT
1 ACATCT
384656 CTCGACTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.28, G:0.00, T:0.50
Consensus pattern (20 bp):
ACATCTATTTCTATTTCCCT
Found at i:389870 original size:17 final size:17
Alignment explanation
Indices: 389848--389881 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
389838 TTATACATAC
389848 CATCACTAACTTTACTT
1 CATCACTAACTTTACTT
389865 CATCACTAACTTTACTT
1 CATCACTAACTTTACTT
389882 AGGTGACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (17 bp):
CATCACTAACTTTACTT
Found at i:405022 original size:13 final size:14
Alignment explanation
Indices: 405004--405042 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
404994 ACAGTTGAGG
405004 TATATATA-ATATT
1 TATATATATATATT
405017 TATATA-ATATATT
1 TATATATATATATT
405030 TACTATATATATA
1 TA-TATATATATA
405043 GATATGGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.04
13 13 0.57
14 4 0.17
15 5 0.22
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATATATATATT
Found at i:407872 original size:24 final size:24
Alignment explanation
Indices: 407845--407890 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
407835 TTTGGGAATG
*
407845 GAGAAAGAAGGTTTAGGGATTCTA
1 GAGAAAGAAGGGTTAGGGATTCTA
407869 GAGAAAGAAGGGTTAGGGATTC
1 GAGAAAGAAGGGTTAGGGATTC
407891 GGGAGAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.37, T:0.22
Consensus pattern (24 bp):
GAGAAAGAAGGGTTAGGGATTCTA
Found at i:407896 original size:24 final size:24
Alignment explanation
Indices: 407844--407896 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
407834 ATTTGGGAAT
* *
407844 GGAGAAAGAAGGTTTAGGGATTCT
1 GGAGAAAGAAGGGTTAGGGATTCG
*
407868 AGAGAAAGAAGGGTTAGGGATTCG
1 GGAGAAAGAAGGGTTAGGGATTCG
407892 GGAGA
1 GGAGA
407897 GTAAATTGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.42, T:0.19
Consensus pattern (24 bp):
GGAGAAAGAAGGGTTAGGGATTCG
Found at i:413035 original size:24 final size:24
Alignment explanation
Indices: 412981--413028 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
412971 TGATTTGGGA
* *
412981 ATGGAGAAAGGAGGGTTAGGGATT
1 ATGGAGAAAGAAGGGTTAAGGATT
413005 ATGGAGAAAGAAGGGTTAAGGATT
1 ATGGAGAAAGAAGGGTTAAGGATT
413029 CAGGAGAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.21
Consensus pattern (24 bp):
ATGGAGAAAGAAGGGTTAAGGATT
Found at i:413601 original size:2 final size:2
Alignment explanation
Indices: 413594--413644 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
413584 AATCAACCAT
413594 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
413636 TA TA TA TA T
1 TA TA TA TA T
413645 TTCTGGTTCC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:413833 original size:3 final size:3
Alignment explanation
Indices: 413825--413850 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
413815 TTCCTCTTAT
413825 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
413851 TTGCCACGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:416771 original size:37 final size:39
Alignment explanation
Indices: 416730--416805 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
416720 AAGATGAACA
416730 AGCATCTC-A-ACTCTCTATGCATCTTTACCATTTGAAT
1 AGCATCTCAATACTCTCTATGCATCTTTACCATTTGAAT
416767 AGCATCTCAATACTCTCTATGCATCTTTACCATTTGAAT
1 AGCATCTCAATACTCTCTATGCATCTTTACCATTTGAAT
416806 GTGCACTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 8 0.22
38 1 0.03
39 28 0.76
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (39 bp):
AGCATCTCAATACTCTCTATGCATCTTTACCATTTGAAT
Found at i:417149 original size:3 final size:3
Alignment explanation
Indices: 417141--417186 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
417131 CCTTCAGCGC
417141 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
417187 ATCCTCAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:418344 original size:35 final size:35
Alignment explanation
Indices: 418298--418376 Score: 158
Period size: 35 Copynumber: 2.3 Consensus size: 35
418288 TAAATAAATA
418298 CATAAATATATAGTTGAACAGTATTTATATGCAGT
1 CATAAATATATAGTTGAACAGTATTTATATGCAGT
418333 CATAAATATATAGTTGAACAGTATTTATATGCAGT
1 CATAAATATATAGTTGAACAGTATTTATATGCAGT
418368 CATAAATAT
1 CATAAATAT
418377 CATTAATATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.37
Consensus pattern (35 bp):
CATAAATATATAGTTGAACAGTATTTATATGCAGT
Found at i:420358 original size:216 final size:215
Alignment explanation
Indices: 419961--420565 Score: 796
Period size: 216 Copynumber: 2.8 Consensus size: 215
419951 CTTGTTTCGA
* * * * *
419961 GAGGAAATGAAAATG-TTTTCTCTTAGAAGTCCTTACAGTCTTGCTAGTTTGTTTAATGATCCTA
1 GAGGAAATGAACA-GATTTTCTCCTAGAAGTCCCTACAGCCTTGCTAGTTTGTTTAGTGATCCTA
* ** * *
420025 ATTTCTTGGAGGAAAATCTGGAGTCG-GTCTTCGACGAGAAAGGGGGGGATGGCATGGAACATGG
65 ATTTCTTGGAAGAAAATCTGGAGTCGAG-AAT-GA-GAG--AGGGAGGAATGGCATGGAACATGG
* *
420089 AGGAGGGAGTTCCTTCAATAGTAAGACAAAAAATGATCGAGCACTTCCGAAGTCGCTGTTGAGTG
125 AGGAGGGAGTTCCTTCAATATTAAGACAAAAAATGATCGAGCACTTCCGAAGTCGCGGTTGAGTG
420154 ATAGCTTTCAACGACAGTCAGCAAGG
190 ATAGCTTTCAACGACAGTCAGCAAGG
* *
420180 GAGGAAGTGAACAGATTTTCTCCTAGAAGTCCCTACGGCCTTGCTAGTTTGTTTAGTGATCCTAA
1 GAGGAAATGAACAGATTTTCTCCTAGAAGTCCCTACAGCCTTGCTAGTTTGTTTAGTGATCCTAA
*
420245 TTTCTTGGACGAAAATCTGGAGTCGAAGAATGAGAGAGGGAGGAATGGCATGGAACATGGAGGAG
66 TTTCTTGGAAGAAAATCTGGAGTCG-AGAATGAGAGAGGGAGGAATGGCATGGAACATGGAGGAG
*
420310 GGAGTTCCTTCAATATTAACACAAAAAATGATCGAGCACTTCCGAAGTCGCGGTTGAGTGATAGC
130 GGAGTTCCTTCAATATTAAGACAAAAAATGATCGAGCACTTCCGAAGTCGCGGTTGAGTGATAGC
*
420375 TTTCAACGACAGTCAGTAAGG
195 TTTCAACGACAGTCAGCAAGG
*
420396 GAGGAAATGAACAGATTTTCTCCTAGAAGTCCCTA-TGCTCTTGCTAGTTTGTTTAGTGATCCTA
1 GAGGAAATGAACAGATTTTCTCCTAGAAGTCCCTACAGC-CTTGCTAGTTTGTTTAGTGATCCTA
* * * * * * *
420460 ACTTCTTGGAAGAAATTCCGCAGTCAGTATTCGAA-GAGAAAGGAAGGAATAGCATGGAACAT--
65 ATTTCTTGGAAGAAAATCTGGAGTC-G-A---GAATGAGAGAGGGAGGAATGGCATGGAACATGG
*
420522 -GGAGGGAGTTCCTTTAATATTAAGAC--AAAATGATCGAGCACTTC
125 AGGAGGGAGTTCCTTCAATATTAAGACAAAAAATGATCGAGCACTTC
420566 GTGGTACGTG
Statistics
Matches: 349, Mismatches: 29, Indels: 21
0.87 0.07 0.05
Matches are distributed among these distances:
214 18 0.05
215 2 0.01
216 212 0.61
217 2 0.01
218 4 0.01
219 106 0.30
220 4 0.01
221 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (215 bp):
GAGGAAATGAACAGATTTTCTCCTAGAAGTCCCTACAGCCTTGCTAGTTTGTTTAGTGATCCTAA
TTTCTTGGAAGAAAATCTGGAGTCGAGAATGAGAGAGGGAGGAATGGCATGGAACATGGAGGAGG
GAGTTCCTTCAATATTAAGACAAAAAATGATCGAGCACTTCCGAAGTCGCGGTTGAGTGATAGCT
TTCAACGACAGTCAGCAAGG
Found at i:420663 original size:9 final size:9
Alignment explanation
Indices: 420611--420676 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
420601 TTTTATTTTT
420611 TATTATTAA
1 TATTATTAA
*
420620 TA--ATCAA
1 TATTATTAA
*
420627 TATTATTAT
1 TATTATTAA
*
420636 TATTATTAT
1 TATTATTAA
420645 TATTTATTAA
1 TA-TTATTAA
420655 TATTATTAA
1 TATTATTAA
420664 CT-TTATT-A
1 -TATTATTAA
420672 TATTA
1 TATTA
420677 CAGACCCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
7 7 0.15
8 4 0.08
9 28 0.58
10 9 0.19
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (9 bp):
TATTATTAA
Found at i:420669 original size:28 final size:27
Alignment explanation
Indices: 420609--420672 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
420599 GTTTTTATTT
*
420609 TTTATTATTAATAATCAATATTATTAT
1 TTTATTATTAATAATCAATATTATTAC
* * *
420636 TATTATTATTATTTATTAATATTATTAAC
1 T-TTATTATTAATAATCAATATTATT-AC
420665 TTTATTAT
1 TTTATTAT
420673 ATTACAGACC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 1 0.03
28 28 0.90
29 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTATTATTAATAATCAATATTATTAC
Found at i:420672 original size:3 final size:3
Alignment explanation
Indices: 420627--420662 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
420617 TAATAATCAA
*
420627 TAT TAT TAT TAT TAT TAT TATT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA
420663 ACTTTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:422361 original size:145 final size:145
Alignment explanation
Indices: 422212--422512 Score: 355
Period size: 145 Copynumber: 2.1 Consensus size: 145
422202 AAAAATCCCA
* *
422212 TTTATAAATT-TA-AT-TTTATATAAATTACTTA-TAAGAAAAATAATCATATT-TTAATATTTA
1 TTTATAAATTATATATATTAATATAAATTAATTATTAAGAAAAAT-AT--T-TTATTAATATTTA
* *
422272 TTTATTTTATAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCCTTTTCTGATA-TTCT
62 TTTATTTT-TAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCATTTTATGATATTTCT
422336 CAAATAAATAAATATCC-TATT
126 -AAATAAATAAATA-CCTTATT
* ** ***
422357 TTTATAAATTATATATATTAATTTATTTTAATTATTTTTAAAAATATTTTATTAATATTTATTTA
1 TTTATAAATTATATATATTAATATAAATTAATTATTAAGAAAAATATTTTATTAATATTTATTTA
* * *
422422 TTTTTAATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAATTCATTTTATGATATTTCTAAGTA
66 TTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCATTTTATGATATTTCTAAATA
422487 AATAAATACCTTATT
131 AATAAATACCTTATT
422502 TATATATAAAT
1 T-T-TATAAAT
422513 ATTCTCTTAA
Statistics
Matches: 134, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
144 2 0.01
145 76 0.57
146 26 0.19
147 9 0.07
148 14 0.10
149 7 0.05
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (145 bp):
TTTATAAATTATATATATTAATATAAATTAATTATTAAGAAAAATATTTTATTAATATTTATTTA
TTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCATTTTATGATATTTCTAAATA
AATAAATACCTTATT
Found at i:422556 original size:145 final size:145
Alignment explanation
Indices: 422262--422558 Score: 354
Period size: 145 Copynumber: 2.0 Consensus size: 145
422252 TAATCATATT
* *
422262 TTAATATTTATTTATTTTATAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCCTTTTC
1 TTAATATTTATTTATTTTATAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCATTTTA
* * * *
422327 TGATATTCTCAAATAAATAAATATCCTATTTTTATAAATTATATATATTAATTTATTTTAATTAT
66 TGATATTCTCAAATAAATAAATATCCTATTTTTATAAATTATATATATTAAATTATATTAATAAA
* * **
422392 TTTTAAAAATATTTTA
131 TTTGAAAAACA-TGGA
* *
422408 TTAATATTTATTTATTTT-TAATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAATTCATTTTA
1 TTAATATTTATTTATTTTATAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCATTTTA
* * *
422472 TGATATT-TCTAAGTAAATAAATA-CCTTATTTATATATAAA-TAT-TCTCTTAAAATTATATTA
66 TGATATTCTC-AAATAAATAAATATCC-TATTT-T-TATAAATTATATATATT-AAATTATATTA
422533 ATAAATTTGAAATAACA-GGA
126 ATAAATTTGAAA-AACATGGA
422553 TTAATA
1 TTAATA
422559 ATTAAATATA
Statistics
Matches: 130, Mismatches: 15, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
144 4 0.03
145 77 0.59
146 40 0.31
147 9 0.07
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (145 bp):
TTAATATTTATTTATTTTATAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCATTTTA
TGATATTCTCAAATAAATAAATATCCTATTTTTATAAATTATATATATTAAATTATATTAATAAA
TTTGAAAAACATGGA
Found at i:423048 original size:17 final size:18
Alignment explanation
Indices: 423013--423050 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
423003 TCCTTTCAAA
*
423013 ATTTTTATATATACTTATT
1 ATTTTCATATATAC-TATT
423032 ATTTTCATATATA-TATT
1 ATTTTCATATATACTATT
423049 AT
1 AT
423051 CTATTAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTCATATATACTATT
Found at i:433771 original size:16 final size:15
Alignment explanation
Indices: 433750--433825 Score: 92
Period size: 15 Copynumber: 5.3 Consensus size: 15
433740 CTTGAAGAAG
433750 AAAAAAATGAAAATGAA
1 AAAAAAATG-AAATG-A
433767 AAAAAAATGAAATGA
1 AAAAAAATGAAATGA
433782 AAAAAAATGAAATGA
1 AAAAAAATGAAATGA
433797 AAAAAAA--AAA-G-
1 AAAAAAATGAAATGA
433808 AAAAAAATG--ATGA
1 AAAAAAATGAAATGA
433821 AAAAA
1 AAAAA
433826 GATATAGAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
11 8 0.15
12 2 0.04
13 8 0.15
15 23 0.42
16 5 0.09
17 9 0.16
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.11
Consensus pattern (15 bp):
AAAAAAATGAAATGA
Found at i:433788 original size:26 final size:25
Alignment explanation
Indices: 433759--433825 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 25
433749 GAAAAAAATG
* *
433759 AAAATGAAAAAAAAATGAAATGAAAA
1 AAAATGAAAAAAAAA-AAAAAGAAAA
433785 AAAATGAAATGAAAAAAAAAAAGAAAA
1 AAAATGAAA--AAAAAAAAAAAGAAAA
433812 AAATGATGAAAAAA
1 AAA--ATGAAAAAA
433826 GATATAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 9 0.26
27 14 0.40
28 6 0.17
29 6 0.17
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (25 bp):
AAAATGAAAAAAAAAAAAAAGAAAA
Found at i:433805 original size:32 final size:32
Alignment explanation
Indices: 433750--433810 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
433740 CTTGAAGAAG
*
433750 AAAAAAATGAAAATGAAAAAAAAATGAAATGA
1 AAAAAAATGAAAATGAAAAAAAAAAGAAATGA
433782 AAAAAAATG-AAATGAAAAAAAAAAAGAAA
1 AAAAAAATGAAAATG-AAAAAAAAAAGAAA
433811 AAAATGATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (32 bp):
AAAAAAATGAAAATGAAAAAAAAAAGAAATGA
Found at i:433810 original size:17 final size:16
Alignment explanation
Indices: 433750--433804 Score: 94
Period size: 15 Copynumber: 3.4 Consensus size: 16
433740 CTTGAAGAAG
433750 AAAAAAATGAAAATGAA
1 AAAAAAATG-AAATGAA
433767 AAAAAAATGAAATG-A
1 AAAAAAATGAAATGAA
433782 AAAAAAATGAAATGAA
1 AAAAAAATGAAATGAA
433798 AAAAAAA
1 AAAAAAA
433805 AAGAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
15 15 0.41
16 13 0.35
17 9 0.24
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (16 bp):
AAAAAAATGAAATGAA
Found at i:434208 original size:18 final size:18
Alignment explanation
Indices: 434182--434219 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
434172 CAAGATTATC
*
434182 TTTTTGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
434200 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
434218 TT
1 TT
434220 CTTTCACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTTCGAAATTCAATTTA
Found at i:437067 original size:137 final size:136
Alignment explanation
Indices: 436794--437067 Score: 313
Period size: 137 Copynumber: 2.0 Consensus size: 136
436784 ATAGATCAGC
* * *
436794 ATCAACATTTCCAGAAGTATTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGGATTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAATTCAAAA
* * * ** * **
436859 TGAGAAGAACTTGTTCAACATTGTCTTAATTCATCACATATAAAGCTGAATTAACAACCCCTCTT
66 TGAGAAGAACTTGTTCAACATTGCCATAATTCATCACAGATAAAAATAAATTAACAACCCCTCAG
*
436924 TTGAAA
131 TGGAAA
* *
436930 ATCAGCATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAATGAGAAGAAATTCAAA
1 ATCAACATTTCCAGAAGGA-TTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAATTCAAA
* * * *
436995 ATGAGAAGAATTTGTTCAACTTTTTGCCAT-ATTACATCACAGA-AGAAAATAAATTATC-ATCC
65 ATGAGAAGAACTTGTTCAAC--ATTGCCATAATT-CATCACAGATA-AAAATAAATTAACAACCC
437057 C-CAGTGGAAA
126 CTCAGTGGAAA
437067 A
1 A
437068 ATAAATACCT
Statistics
Matches: 115, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
136 17 0.15
137 68 0.59
138 8 0.07
139 22 0.19
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.27
Consensus pattern (136 bp):
ATCAACATTTCCAGAAGGATTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAATTCAAAA
TGAGAAGAACTTGTTCAACATTGCCATAATTCATCACAGATAAAAATAAATTAACAACCCCTCAG
TGGAAA
Found at i:437832 original size:57 final size:57
Alignment explanation
Indices: 437722--437837 Score: 144
Period size: 57 Copynumber: 2.0 Consensus size: 57
437712 AACAGTCATG
* * * *
437722 GAGGAAATGAACAGGTTTTCTCCTAGAACTCCTTATGGTATTGCTGATCTGTTTCGT
1 GAGGAAATGAAAAGGTTTTCTCCGAGAACTCCATATGGTATTGCTGATCTGTTTAGT
* * * *
437779 GAGGAAATGAAAATGTTTTCTCCGAGAAGTCCATATGGTCTTGCT-AGTTTGTTTAGT
1 GAGGAAATGAAAAGGTTTTCTCCGAGAACTCCATATGGTATTGCTGA-TCTGTTTAGT
437836 GA
1 GA
437838 TAGTAACTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
56 1 0.02
57 49 0.98
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (57 bp):
GAGGAAATGAAAAGGTTTTCTCCGAGAACTCCATATGGTATTGCTGATCTGTTTAGT
Found at i:438544 original size:103 final size:103
Alignment explanation
Indices: 438365--438570 Score: 403
Period size: 103 Copynumber: 2.0 Consensus size: 103
438355 TTCAGTAATC
*
438365 CTAATTTCTTGGACGAAAATACGGAGTCGGTCTTCGATGAGGAAGGGAGGAATAGCATGGAACAT
1 CTAATTTCTTGGACAAAAATACGGAGTCGGTCTTCGATGAGGAAGGGAGGAATAGCATGGAACAT
438430 GGAGGGAGTTCCTCCAATATCGAGATGGCAAGTGATCG
66 GGAGGGAGTTCCTCCAATATCGAGATGGCAAGTGATCG
438468 CTAATTTCTTGGACAAAAATACGGAGTCGGTCTTCGATGAGGAAGGGAGGAATAGCATGGAACAT
1 CTAATTTCTTGGACAAAAATACGGAGTCGGTCTTCGATGAGGAAGGGAGGAATAGCATGGAACAT
438533 GGAGGGAGTTCCTCCAATATCGAGATGGCAAGTGATCG
66 GGAGGGAGTTCCTCCAATATCGAGATGGCAAGTGATCG
438571 TGCGCTTGAT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.31, C:0.16, G:0.32, T:0.22
Consensus pattern (103 bp):
CTAATTTCTTGGACAAAAATACGGAGTCGGTCTTCGATGAGGAAGGGAGGAATAGCATGGAACAT
GGAGGGAGTTCCTCCAATATCGAGATGGCAAGTGATCG
Found at i:438719 original size:57 final size:57
Alignment explanation
Indices: 438629--438738 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 57
438619 GTCTGGAAGG
* *
438629 GAGGAAATGGACAGGTTTTCTCCTAGAACTCCTTATGGTATTGCTAATTTGTTCCGC
1 GAGGAAATGAAAAGGTTTTCTCCTAGAACTCCTTATGGTATTGCTAATTTGTTCCGC
* * * * *
438686 GAGGAAATGAAAATGTTTTCTCCTAGAAGTCCTTATGGTCTTTCTAGTTTGTT
1 GAGGAAATGAAAAGGTTTTCTCCTAGAACTCCTTATGGTATTGCTAATTTGTT
438739 TAGTAATCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (57 bp):
GAGGAAATGAAAAGGTTTTCTCCTAGAACTCCTTATGGTATTGCTAATTTGTTCCGC
Found at i:438795 original size:382 final size:380
Alignment explanation
Indices: 438083--438836 Score: 1055
Period size: 382 Copynumber: 2.0 Consensus size: 380
438073 TTTTCTCCAA
* ** * *
438083 GATCGTAATTTCTTTGATGAAAATCCGAAGTCGATCTTTGACGAGGAAGGGAGAAACGACATGGA
1 GATCGTAATTTCTTGGACAAAAATACGAAGTCGATCTTCGACGAGGAAGGGAGAAACGACATGGA
* * * ** *
438148 ACATGTAGGGAGTTCCTCCAATAAAGAGATGGCAAATGATGGAGCACTTGCTGGTATGAATTCAC
66 ACATGGAGGGAGTTCCTCCAATAAAGAGATGGCAAATGATCGAGCACTTGATAATACGAATTCAC
438213 TGTCAAGTGATAGCTCTCAAGAACAGTGGGAAGGGAGGAAATGGACAACTTTTCACCTAGAACTC
131 TGTCAAGTGATAGCTCTCAAGAACAGTGGGAAGGGAGGAAATGGACAACTTTTCACCTAGAACTC
* *
438278 CTTATGGTATTGCTAATTTGTTTCGTGAAGAAATGAAAATGTTTTCTCCCAGAAGTCCATATGGT
196 CTTATGGTATTGCTAATTTGTTCCGCGAAGAAATGAAAATGTTTTCTCCCAGAAGTCCATATGGT
* * *
438343 CTTGCTAGTTTGTTCAGTAATCCTAATTTCTTGGACGAAAATACGGAGTCGGTCTTCGATGAGGA
261 CTTGCTAGTTTGTTCAGTAATCCTAATTTCTTGGACGAAAATACGAAGACGGTCTTCGATGAGAA
* * * *
438408 AGGGAGGAATAGCATGGAACATGGAGGGAGTTCCTCCAATATCGAGATGGCAAGT
326 AGGGAGGAATAACATGGAACATGGAGAGAGTTACTCCAACATCGAGATGGCAAGT
* * *
438463 GATCGCTAATTTCTTGGACAAAAATACGGAGTCGGTCTTCGATGAGGAAGGGAGGAATA-G-CAT
1 GATCG-TAATTTCTTGGACAAAAATACGAAGTCGATCTTCGACGAGGAAGGGA-GAA-ACGACAT
** * * *
438526 GGAACATGGAGGGAGTTCCTCCAATATCGAGATGGCAAGTGATCGTGCGCTTGATAATACGAATT
63 GGAACATGGAGGGAGTTCCTCCAATAAAGAGATGGCAAATGATCGAGCACTTGATAATACGAATT
** * * * ** *
438591 GTCTGTCGAGTGATAGCTTTCAAGAACAGTCTGGAAGGGAGGAAATGGACAGGTTTTCTCCTAGA
128 CACTGTCAAGTGATAGCTCTCAAGAACAGT-GGGAAGGGAGGAAATGGACAACTTTTCACCTAGA
* * *
438656 ACTCCTTATGGTATTGCTAATTTGTTCCGCGAGGAAATGAAAATGTTTTCTCCTAGAAGTCCTTA
192 ACTCCTTATGGTATTGCTAATTTGTTCCGCGAAGAAATGAAAATGTTTTCTCCCAGAAGTCCATA
* * * *
438721 TGGTCTTTCTAGTTTGTTTAGTAATCCTAATTTCTTGGATGAAAGT-CTGAAGACGGTCTTCGAT
257 TGGTCTTGCTAGTTTGTTCAGTAATCCTAATTTCTTGGACGAAAATAC-GAAGACGGTCTTCGAT
438785 GAGAAAGGGAGGAATAACATGGAACATGGAGAGAGTTACTCCAACATCGAGA
321 GAGAAAGGGAGGAATAACATGGAACATGGAGAGAGTTACTCCAACATCGAGA
438837 CGGTAAATGA
Statistics
Matches: 326, Mismatches: 43, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
380 5 0.02
381 123 0.38
382 197 0.60
383 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (380 bp):
GATCGTAATTTCTTGGACAAAAATACGAAGTCGATCTTCGACGAGGAAGGGAGAAACGACATGGA
ACATGGAGGGAGTTCCTCCAATAAAGAGATGGCAAATGATCGAGCACTTGATAATACGAATTCAC
TGTCAAGTGATAGCTCTCAAGAACAGTGGGAAGGGAGGAAATGGACAACTTTTCACCTAGAACTC
CTTATGGTATTGCTAATTTGTTCCGCGAAGAAATGAAAATGTTTTCTCCCAGAAGTCCATATGGT
CTTGCTAGTTTGTTCAGTAATCCTAATTTCTTGGACGAAAATACGAAGACGGTCTTCGATGAGAA
AGGGAGGAATAACATGGAACATGGAGAGAGTTACTCCAACATCGAGATGGCAAGT
Found at i:441864 original size:32 final size:32
Alignment explanation
Indices: 441828--441891 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
441818 TAAAGTCGGT
*
441828 CCAAATATGTCCTAATATTGGATTAATCAACA
1 CCAAATATGTCCTAATATTCGATTAATCAACA
*
441860 CCAAATATGTCTTAATATTCGATTAATCAACA
1 CCAAATATGTCCTAATATTCGATTAATCAACA
441892 TTTTTAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.33
Consensus pattern (32 bp):
CCAAATATGTCCTAATATTCGATTAATCAACA
Found at i:442012 original size:22 final size:22
Alignment explanation
Indices: 441993--442045 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
441983 AATTCCTTAA
*
441993 TGAAACCAACGTTTTCCCTTGT
1 TGAAACCAACGCTTTCCCTTGT
*
442015 TGAAACCAATGCTTTCCCTTGT
1 TGAAACCAACGCTTTCCCTTGT
442037 TGAAACCAA
1 TGAAACCAA
442046 AGCCATCTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (22 bp):
TGAAACCAACGCTTTCCCTTGT
Found at i:447265 original size:37 final size:37
Alignment explanation
Indices: 447212--447287 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 37
447202 TGAACCATTT
* * *
447212 TCAAAATAAGTGTCTAGATAAACGCTTGTTATTCTTA
1 TCAAAATAAGTGTCTAGATAAACACATGCTATTCTTA
* *
447249 TCAAAATGAGTTTCTAGATAAACACATGCTATTCTTA
1 TCAAAATAAGTGTCTAGATAAACACATGCTATTCTTA
447286 TC
1 TC
447288 TTTTAATTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (37 bp):
TCAAAATAAGTGTCTAGATAAACACATGCTATTCTTA
Found at i:451180 original size:21 final size:21
Alignment explanation
Indices: 451154--451193 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
451144 AGACAAGTAG
* *
451154 TACTCCATAGCAGGTGGAGCA
1 TACTCCAAAACAGGTGGAGCA
451175 TACTCCAAAACAGGTGGAG
1 TACTCCAAAACAGGTGGAG
451194 TTTCAGCAGA
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:0.33, C:0.23, G:0.28, T:0.17
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGCA
Found at i:454616 original size:17 final size:17
Alignment explanation
Indices: 454568--454618 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
454558 TACTAAAATT
* *
454568 AAATAAAACAAAAT-AA
1 AAATAAAATAGAATAAA
**
454584 AAATAAAATATCATAAA
1 AAATAAAATAGAATAAA
*
454601 AAATAAGATAGAATAAA
1 AAATAAAATAGAATAAA
454618 A
1 A
454619 TATTACTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (17 bp):
AAATAAAATAGAATAAA
Found at i:456547 original size:3 final size:3
Alignment explanation
Indices: 456529--456570 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
456519 ATAACCTGAA
*
456529 AAT AAT AAA AATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
456571 ATCCCATGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.94
4 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:457502 original size:36 final size:36
Alignment explanation
Indices: 457462--457530 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
457452 GTGATTGGAA
*
457462 TGTAAATTTTGTAGTTTGGGGACTAAAGTATAAAGT
1 TGTAAATTTTGTAGTTTGGGGACTAAAATATAAAGT
457498 TGTAAATTTTGTAGTTTGGGGACTAAAATATAA
1 TGTAAATTTTGTAGTTTGGGGACTAAAATATAA
457531 TTTTTCAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (36 bp):
TGTAAATTTTGTAGTTTGGGGACTAAAATATAAAGT
Found at i:458650 original size:32 final size:32
Alignment explanation
Indices: 458609--458672 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
458599 CCAAAGTTGG
*
458609 ATTAAGTTCGAGGGTGCAAGGAATATAATAAT
1 ATTAAGTTCGAGGATGCAAGGAATATAATAAT
*
458641 ATTAAGTTCGAGGATGCAAGGAATATAGTAAT
1 ATTAAGTTCGAGGATGCAAGGAATATAATAAT
458673 TAAAGTGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.41, C:0.06, G:0.25, T:0.28
Consensus pattern (32 bp):
ATTAAGTTCGAGGATGCAAGGAATATAATAAT
Found at i:460745 original size:13 final size:13
Alignment explanation
Indices: 460727--460770 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
460717 AGCATTGTGA
460727 AAAGAAAATAATG
1 AAAGAAAATAATG
460740 AAAGAAAATAATG
1 AAAGAAAATAATG
*
460753 AAAGAAAATAAAG
1 AAAGAAAATAATG
460766 AAAGA
1 AAAGA
460771 TGGAGATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (13 bp):
AAAGAAAATAATG
Found at i:461637 original size:15 final size:15
Alignment explanation
Indices: 461628--461664 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
461618 TTTAATATAA
461628 GAAAAATTAAAGAAT
1 GAAAAATTAAAGAAT
*
461643 GAAAAATT-GAG-AT
1 GAAAAATTAAAGAAT
461656 GAAAAATTA
1 GAAAAATTA
461665 TATAGTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 10 0.50
14 2 0.10
15 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.16, T:0.22
Consensus pattern (15 bp):
GAAAAATTAAAGAAT
Found at i:468596 original size:20 final size:20
Alignment explanation
Indices: 468571--468608 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
468561 TTTTAGTGCA
*
468571 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
468591 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
468609 TTTGAAGGGG
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:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:471577 original size:12 final size:12
Alignment explanation
Indices: 471554--471591 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 12
471544 AAGAAAAACT
471554 AGAATC-AAGAG
1 AGAATCAAAGAG
471565 AGAATCAAAGAGAG
1 AGAATC-AA-AGAG
471579 AGAATCAAAGAG
1 AGAATCAAAGAG
471591 A
1 A
471592 AAGCATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.25
12 5 0.21
13 3 0.12
14 10 0.42
ACGTcount: A:0.58, C:0.08, G:0.26, T:0.08
Consensus pattern (12 bp):
AGAATCAAAGAG
Found at i:471580 original size:14 final size:14
Alignment explanation
Indices: 471561--471601 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
471551 ACTAGAATCA
471561 AGAGAGAATCAAAG
1 AGAGAGAATCAAAG
471575 AGAGAGAATCAAAG
1 AGAGAGAATCAAAG
* *
471589 AGAAAGCATCAAA
1 AGAGAGAATCAAA
471602 CCTCAAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.59, C:0.10, G:0.24, T:0.07
Consensus pattern (14 bp):
AGAGAGAATCAAAG
Found at i:476890 original size:19 final size:19
Alignment explanation
Indices: 476841--476883 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
476831 TTATTAAAAC
476841 TTATAAGATGGTTTCCTAA
1 TTATAAGATGGTTTCCTAA
476860 TTATAAGATGGTTTCCTAA
1 TTATAAGATGGTTTCCTAA
476879 TTATA
1 TTATA
476884 GTATGGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (19 bp):
TTATAAGATGGTTTCCTAA
Found at i:477228 original size:28 final size:28
Alignment explanation
Indices: 477191--477251 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
477181 TTTGATAACT
477191 TAATTAAAATATTTCAAACTTTGTAGAG
1 TAATTAAAATATTTCAAACTTTGTAGAG
477219 TAATTAAAATATTTCAAACTTTGTAGAG
1 TAATTAAAATATTTCAAACTTTGTAGAG
477247 TAATT
1 TAATT
477252 TACAAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.41
Consensus pattern (28 bp):
TAATTAAAATATTTCAAACTTTGTAGAG
Found at i:480625 original size:31 final size:31
Alignment explanation
Indices: 480587--480711 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
480577 CCCGAAGGAC
* * *
480587 CAGTCCATA-GATTTCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCTCGAAGAACATAGGTAAA
*
480618 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCTCGAAGAACATAGGTAAA
480649 CAGTCCATATGTCTCGAAGAACATAGGTAAA
1 CAGTCCATATGTCTCGAAGAACATAGGTAAA
*
480680 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCTCGAAGAACATAGGTAAA
480711 C
1 C
480712 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTCTCGAAGAACATAGGTAAA
Found at i:487791 original size:6 final size:6
Alignment explanation
Indices: 487780--487804 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
487770 GTCTTGGTGT
487780 AAAGCC AAAGCC AAAGCC AAAGCC A
1 AAAGCC AAAGCC AAAGCC AAAGCC A
487805 CCGCCTTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGCC
Found at i:490221 original size:27 final size:27
Alignment explanation
Indices: 490181--490235 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
490171 TTTGGACATT
490181 TATTTTCCAATGTTGAGAACTTAAAAA
1 TATTTTCCAATGTTGAGAACTTAAAAA
*
490208 TATTTTCCATTGTTGAGAACTTAAAAA
1 TATTTTCCAATGTTGAGAACTTAAAAA
490235 T
1 T
490236 CAGAAAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (27 bp):
TATTTTCCAATGTTGAGAACTTAAAAA
Found at i:491472 original size:56 final size:56
Alignment explanation
Indices: 491388--491497 Score: 211
Period size: 56 Copynumber: 2.0 Consensus size: 56
491378 AACCAAATTG
*
491388 AAAAAATGCATGAAATGAAATCAAGAAAAATAACAACCATATAATACCTTCTGGGA
1 AAAAAATGAATGAAATGAAATCAAGAAAAATAACAACCATATAATACCTTCTGGGA
491444 AAAAAATGAATGAAATGAAATCAAGAAAAATAACAACCATATAATACCTTCTGG
1 AAAAAATGAATGAAATGAAATCAAGAAAAATAACAACCATATAATACCTTCTGG
491498 ATCACCCGAC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.55, C:0.14, G:0.12, T:0.20
Consensus pattern (56 bp):
AAAAAATGAATGAAATGAAATCAAGAAAAATAACAACCATATAATACCTTCTGGGA
Found at i:495462 original size:14 final size:14
Alignment explanation
Indices: 495421--495459 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
495411 TGGTTTTGAA
*
495421 TTAGGGTTTTA-GT
1 TTAGGGTTTAAGGT
495434 TTAGGGTTTAAGGT
1 TTAGGGTTTAAGGT
495448 TTAGGG-TTAAGG
1 TTAGGGTTTAAGG
495460 GTTAAAGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.44
Consensus pattern (14 bp):
TTAGGGTTTAAGGT
Found at i:495641 original size:51 final size:51
Alignment explanation
Indices: 495582--495691 Score: 121
Period size: 51 Copynumber: 2.2 Consensus size: 51
495572 TGAGTGATTT
* * *
495582 TAGGTTAAAATGGTATAGTGTTCGTTAAGGTGAAAGCGGTGAAGGATTTTG
1 TAGGTTAAAATGGTATAGGGTTCGTTAAGGTGAAAGCGGTCAAGGATTGTG
* * ** * * * *
495633 TAGGTTAAAGTGGTTTAGGGTTTTTTAATGTGAGAGTGGTCAAGGGTTGTG
1 TAGGTTAAAATGGTATAGGGTTCGTTAAGGTGAAAGCGGTCAAGGATTGTG
495684 TAGGTTAA
1 TAGGTTAA
495692 TTTATGTAGG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.26, C:0.03, G:0.35, T:0.36
Consensus pattern (51 bp):
TAGGTTAAAATGGTATAGGGTTCGTTAAGGTGAAAGCGGTCAAGGATTGTG
Found at i:498673 original size:22 final size:22
Alignment explanation
Indices: 498645--498694 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
498635 CTCATTTTCA
498645 GAGAATATAGGTTTGAGAGTTT
1 GAGAATATAGGTTTGAGAGTTT
498667 GAGAATATAGGTTTGAGAGTTT
1 GAGAATATAGGTTTGAGAGTTT
498689 GAGAAT
1 GAGAAT
498695 TTCTCCATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (22 bp):
GAGAATATAGGTTTGAGAGTTT
Found at i:499657 original size:18 final size:18
Alignment explanation
Indices: 499634--499670 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
499624 TGAATTTTAA
*
499634 AAACATTTAACAAACATT
1 AAACATTTAAAAAACATT
499652 AAACATTTAAAAAACATT
1 AAACATTTAAAAAACATT
499670 A
1 A
499671 GAAAATTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (18 bp):
AAACATTTAAAAAACATT
Found at i:500125 original size:21 final size:21
Alignment explanation
Indices: 500096--500162 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
500086 GGTGTCATAA
* *
500096 AACCCTGCGAGCTAGGAATGT
1 AACCTTGCGGGCTAGGAATGT
* *
500117 AACCTTGCGGGCTGGGTATGT
1 AACCTTGCGGGCTAGGAATGT
* * *
500138 ACCCTTGTGGGCTAGGAATAT
1 AACCTTGCGGGCTAGGAATGT
500159 AACC
1 AACC
500163 CTGCAGTGGT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (21 bp):
AACCTTGCGGGCTAGGAATGT
Found at i:502015 original size:23 final size:24
Alignment explanation
Indices: 501987--502043 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
501977 TTTAAATATA
501987 TAATAATTATATAA-A-TATTATTT
1 TAATAATTATATAACATTATT-TTT
**
502010 TAATAAAAATATAACATTATTTTT
1 TAATAATTATATAACATTATTTTT
*
502034 AAATAATTAT
1 TAATAATTAT
502044 TTATAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 12 0.44
24 11 0.41
25 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATAATTATATAACATTATTTTT
Found at i:502020 original size:36 final size:36
Alignment explanation
Indices: 501980--502073 Score: 86
Period size: 36 Copynumber: 2.6 Consensus size: 36
501970 TAATAAATTT
501980 AAATATATAATAATTATATAAAT-ATTATTT-TAATAA
1 AAATATATAATAATT-TATAAATAATTATTTATAA-AA
* *
502016 AAATATA-ACATTATTTTTAAATAATTATTTATAAAA
1 AAATATATA-ATAATTTATAAATAATTATTTATAAAA
* * *
502052 AAAAATGTAATAACTTTTTAAA
1 AAATATATAATAA-TTTATAAA
502074 GAAAATATAC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
35 7 0.15
36 29 0.60
37 12 0.25
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (36 bp):
AAATATATAATAATTTATAAATAATTATTTATAAAA
Found at i:502807 original size:6 final size:6
Alignment explanation
Indices: 502798--502822 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
502788 GGGATGATAA
502798 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
502823 AAAACCGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:502922 original size:12 final size:13
Alignment explanation
Indices: 502886--502935 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
502876 GCCCCGATTA
502886 CCCGATTACCCGG
1 CCCGATTACCCGG
502899 CCCGATTACCCGG
1 CCCGATTACCCGG
*
502912 CCCGA-TACCCGA
1 CCCGATTACCCGG
502924 CCCGA-TACCCGG
1 CCCGATTACCCGG
502936 GTATTCATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
12 17 0.49
13 18 0.51
ACGTcount: A:0.18, C:0.48, G:0.22, T:0.12
Consensus pattern (13 bp):
CCCGATTACCCGG
Found at i:502927 original size:25 final size:25
Alignment explanation
Indices: 502886--502935 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
502876 GCCCCGATTA
*
502886 CCCGATTACCCGGCCCGATTACCCGG
1 CCCGATTACCCGACCCGA-TACCCGG
502912 CCCGA-TACCCGACCCGATACCCGG
1 CCCGATTACCCGACCCGATACCCGG
502936 GTATTCATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 11 0.48
26 5 0.22
ACGTcount: A:0.18, C:0.48, G:0.22, T:0.12
Consensus pattern (25 bp):
CCCGATTACCCGACCCGATACCCGG
Found at i:505622 original size:29 final size:29
Alignment explanation
Indices: 505590--505647 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
505580 TTGTTTAATC
505590 AGTTTCTAATTTGTATCTTGTATTTATTT
1 AGTTTCTAATTTGTATCTTGTATTTATTT
*
505619 AGTTTCTAATTTGTATGTTGTATTTATTT
1 AGTTTCTAATTTGTATCTTGTATTTATTT
505648 CAGTCTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.21, C:0.05, G:0.12, T:0.62
Consensus pattern (29 bp):
AGTTTCTAATTTGTATCTTGTATTTATTT
Found at i:506897 original size:20 final size:20
Alignment explanation
Indices: 506872--506909 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
506862 CTATATGAGT
506872 TTGTTTTATTTATCTTTTGA
1 TTGTTTTATTTATCTTTTGA
*
506892 TTGTTTTATTTATGTTTT
1 TTGTTTTATTTATCTTTT
506910 AAATGTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.11, T:0.74
Consensus pattern (20 bp):
TTGTTTTATTTATCTTTTGA
Found at i:509769 original size:38 final size:37
Alignment explanation
Indices: 509712--509800 Score: 144
Period size: 38 Copynumber: 2.4 Consensus size: 37
509702 CCTAAACCCG
509712 AACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGACCTGACCCGAATATCACACTT-AAAA
*
509750 AACTCGACCCGA-CTCGACCCGAATATCACACTTAAAA
1 AACCCGACCCGACCT-GACCCGAATATCACACTTAAAA
509787 AACCCGACCCGACC
1 AACCCGACCCGACC
509801 CGAACAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
37 17 0.36
38 30 0.64
ACGTcount: A:0.37, C:0.39, G:0.11, T:0.12
Consensus pattern (37 bp):
AACCCGACCCGACCTGACCCGAATATCACACTTAAAA
Found at i:510017 original size:33 final size:32
Alignment explanation
Indices: 509969--510045 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 32
509959 TTTTCACCCT
509969 AAACCCGAACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGAATATCACACTT-AAA
510003 AAACCCGACCCGACCCGAATATCACACTTAAA
1 AAACCCGACCCGACCCGAATATCACACTTAAA
*
510035 AAGCCCGACCC
1 AAACCCGACCC
510046 AAACAAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
32 13 0.31
33 22 0.52
34 7 0.17
ACGTcount: A:0.40, C:0.39, G:0.10, T:0.10
Consensus pattern (32 bp):
AAACCCGACCCGACCCGAATATCACACTTAAA
Found at i:514340 original size:43 final size:44
Alignment explanation
Indices: 514293--514563 Score: 197
Period size: 43 Copynumber: 6.3 Consensus size: 44
514283 AGGCTTAAAC
*
514293 TATAAAAGTAAAAAGT-ATGATTGAAAAAATTAGAGACCCCAAT
1 TATAAAAGTAAAAAGTGATGATTGAAAAAATTAGAGACCTCAAT
* *
514336 TATAAAGGTAAAAAGTGAT-ATT-ATAAAAA-TAGGAGA-ATCAAT
1 TATAAAAGTAAAAAGTGATGATTGA-AAAAATTA-GAGACCTCAAT
* * * * * *
514378 TTTAAATGTAAAAAGTGA-GATTGAAAAAAATAGGGGCCTAAAT
1 TATAAAAGTAAAAAGTGATGATTGAAAAAATTAGAGACCTCAAT
** * * *
514421 TATATGAGTAAAAAATG-GGATTGAAAAAATTAGAGACCTTAAT
1 TATAAAAGTAAAAAGTGATGATTGAAAAAATTAGAGACCTCAAT
* * * * *
514464 TATAAAGGTAAAAAGTGAT-ATTGAAAAAA-AACAGGAGCTTAAT
1 TATAAAAGTAAAAAGTGATGATTGAAAAAATTAGA-GACCTCAAT
* * * *
514507 TATAAAGGTACAAGGTGA-GATT-AAAAAACTTAG-GATCATCAAT
1 TATAAAAGTAAAAAGTGATGATTGAAAAAA-TTAGAGA-CCTCAAT
*
514550 TATAAATGTAAAAA
1 TATAAAAGTAAAAA
514564 AAATAAAATT
Statistics
Matches: 178, Mismatches: 36, Indels: 28
0.74 0.15 0.12
Matches are distributed among these distances:
42 43 0.24
43 132 0.74
44 3 0.02
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.25
Consensus pattern (44 bp):
TATAAAAGTAAAAAGTGATGATTGAAAAAATTAGAGACCTCAAT
Found at i:514534 original size:86 final size:86
Alignment explanation
Indices: 514293--514563 Score: 241
Period size: 86 Copynumber: 3.2 Consensus size: 86
514283 AGGCTTAAAC
* ** ** *
514293 TATAAAAGTAAAAAGT-ATGATTGAAAAAATTA-GAGACCCCAATTATAAAGGTAAAAAGTGATA
1 TATAAATGTAAAAAGTGA-GATTGAAAAAAACAGGAG-CCTAAATTATAAAGGTAAAAAGTGAGA
*
514356 TTATAAAAA-TAGGAGA-ATCAAT
64 TTAAAAAAATTA-GAGACATCAAT
* * * * * *
514378 TTTAAATGTAAAAAGTGAGATTGAAAAAAATAGGGGCCTAAATTAT-ATGAGTAAAAAATGGGAT
1 TATAAATGTAAAAAGTGAGATTGAAAAAAACAGGAGCCTAAATTATAAAG-GTAAAAAGTGAGAT
* * *
514442 TGAAAAAATTAGAGACCTTAAT
65 TAAAAAAATTAGAGACATCAAT
* * * * *
514464 TATAAAGGTAAAAAGTGATATTGAAAAAAAACAGGAG-CTTAATTATAAAGGTACAAGGTGAGAT
1 TATAAATGTAAAAAGTGAGATTG-AAAAAAACAGGAGCCTAAATTATAAAGGTAAAAAGTGAGAT
*
514528 TAAAAAACTTAG-GATCATCAAT
65 TAAAAAAATTAGAGA-CATCAAT
514550 TATAAATGTAAAAA
1 TATAAATGTAAAAA
514564 AAATAAAATT
Statistics
Matches: 148, Mismatches: 30, Indels: 15
0.77 0.16 0.08
Matches are distributed among these distances:
84 2 0.01
85 58 0.39
86 75 0.51
87 13 0.09
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.25
Consensus pattern (86 bp):
TATAAATGTAAAAAGTGAGATTGAAAAAAACAGGAGCCTAAATTATAAAGGTAAAAAGTGAGATT
AAAAAAATTAGAGACATCAAT
Found at i:514563 original size:128 final size:127
Alignment explanation
Indices: 514288--514563 Score: 304
Period size: 128 Copynumber: 2.1 Consensus size: 127
514278 ATTAGAGGCT
* *
514288 TAAACTATAAAAGTAAAAAGTATGATTGAAAAAATTAGAGACCCCAATTATAAAGGTAAAAAGTG
1 TAAATTAT-AAAGTAAAAAGTAGGATTGAAAAAATTAGAGACCCCAATTATAAAGGTAAAAAGTG
* * * * * *
514353 ATATTATAAAAATAGGAGAATCAATTTTAAATGTAAAAAGTGAGATTGAAAAAAATAGGGGCC
65 ATATTAAAAAAACAGGAGAATCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAATAGGAGCA
* * * **
514416 TAAATTATATGAGTAAAAAATGGGATTGAAAAAATTAGAGACCTTAATTATAAAGGTAAAAAGTG
1 TAAATTATA-AAGTAAAAAGTAGGATTGAAAAAATTAGAGACCCCAATTATAAAGGTAAAAAGTG
* * * * * *
514481 ATATTGAAAAAAAACAGGAG-CTTAATTATAAAGGTACAAGGTGAGATT-AAAAAACTTAGGATC
65 ATATT--AAAAAAACAGGAGAATCAATTATAAAGGTAAAAAGTGAGATTGAAAAAA-ATAGGAGC
514544 A
127 A
*
514545 TCAATTATAAATGTAAAAA
1 TAAATTATAAA-GTAAAAA
514564 AAATAAAATT
Statistics
Matches: 122, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
127 1 0.01
128 68 0.56
129 42 0.34
130 11 0.09
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.25
Consensus pattern (127 bp):
TAAATTATAAAGTAAAAAGTAGGATTGAAAAAATTAGAGACCCCAATTATAAAGGTAAAAAGTGA
TATTAAAAAAACAGGAGAATCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAATAGGAGCA
Found at i:517087 original size:21 final size:21
Alignment explanation
Indices: 517061--517105 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
517051 GATTTCTGGG
* *
517061 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
517082 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
517103 CAA
1 CAA
517106 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:517661 original size:23 final size:24
Alignment explanation
Indices: 517618--517664 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
517608 ATATGGCCTG
*
517618 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
517642 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
517665 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:517879 original size:31 final size:31
Alignment explanation
Indices: 517841--517984 Score: 234
Period size: 31 Copynumber: 4.6 Consensus size: 31
517831 AAGGTCGAGG
*
517841 GTTTACCTATGTTCTTCAGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
517872 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
517903 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
517934 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
517965 GATTACCTAGGTTCTTCGGA
1 GTTTACCTATGTTCTTCGGA
517985 TTCTATGGAC
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:520976 original size:12 final size:13
Alignment explanation
Indices: 520952--520980 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
520942 AAATGAAAAA
520952 AAATGCAAAATGT
1 AAATGCAAAATGT
520965 AAATGC-AAATGT
1 AAATGCAAAATGT
520977 AAAT
1 AAAT
520981 ATAAAAATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (13 bp):
AAATGCAAAATGT
Found at i:520979 original size:37 final size:35
Alignment explanation
Indices: 520914--520987 Score: 85
Period size: 37 Copynumber: 2.1 Consensus size: 35
520904 ATGCAAATGC
*
520914 AAAAATGAAAATATAAATATAAACGTAAAAATGAAA
1 AAAAATGAAAATATAAATACAAACGTAAAAAT-AAA
* * * *
520950 AAAAATGCAAAATGTAAATGCAAATGTAAATATAAA
1 AAAAATG-AAAATATAAATACAAACGTAAAAATAAA
520986 AA
1 AA
520988 TGCAAATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 12 0.38
37 20 0.62
ACGTcount: A:0.66, C:0.04, G:0.09, T:0.20
Consensus pattern (35 bp):
AAAAATGAAAATATAAATACAAACGTAAAAATAAA
Found at i:523554 original size:27 final size:29
Alignment explanation
Indices: 523514--523588 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
523504 TCTTTGATAT
* *
523514 TAAAAATAAACAAATATTAT-TA-ATTTA
1 TAAAAATAAACAAATAATATATATATTAA
* *
523541 TAAAATTAATCAAATAATATATATATTAA
1 TAAAAATAAACAAATAATATATATATTAA
523570 TAAAAATAAA-ATAATAATA
1 TAAAAATAAACA-AATAATA
523589 CTAATTAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 17 0.44
28 3 0.08
29 19 0.49
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.35
Consensus pattern (29 bp):
TAAAAATAAACAAATAATATATATATTAA
Found at i:523690 original size:26 final size:26
Alignment explanation
Indices: 523640--523691 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
523630 ACTAAATATA
* *
523640 AAAAGTAATAAAACTTGTAATTAAAT
1 AAAAGTAATAAAACTAGTAACTAAAT
* *
523666 AAAAGTATTAAAACTAGTGACTAAAT
1 AAAAGTAATAAAACTAGTAACTAAAT
523692 TATAACATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.56, C:0.06, G:0.10, T:0.29
Consensus pattern (26 bp):
AAAAGTAATAAAACTAGTAACTAAAT
Found at i:527046 original size:16 final size:16
Alignment explanation
Indices: 527025--527055 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
527015 CGACTTGAAA
*
527025 GAAAATTAAAGAAAAC
1 GAAAATAAAAGAAAAC
527041 GAAAATAAAAGAAAA
1 GAAAATAAAAGAAAA
527056 TAATTTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (16 bp):
GAAAATAAAAGAAAAC
Found at i:528777 original size:9 final size:9
Alignment explanation
Indices: 528763--528787 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
528753 TGAGTAATTA
528763 TATTTTGAC
1 TATTTTGAC
528772 TATTTTGAC
1 TATTTTGAC
528781 TATTTTG
1 TATTTTG
528788 TGAAATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.08, G:0.12, T:0.60
Consensus pattern (9 bp):
TATTTTGAC
Found at i:529246 original size:20 final size:21
Alignment explanation
Indices: 529221--529260 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
529211 TCAGAAATGT
* *
529221 TAAAAA-ATTAATGTTTTAAG
1 TAAAAATAATAATATTTTAAG
529241 TAAAAATAATAATATTTTAA
1 TAAAAATAATAATATTTTAA
529261 ATAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAG
Found at i:537815 original size:2 final size:2
Alignment explanation
Indices: 537808--537846 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
537798 TCGTCCTATT
537808 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
537847 ATTTAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:537901 original size:27 final size:26
Alignment explanation
Indices: 537859--537925 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
537849 TTAAAAATAC
*
537859 TTTTAAAATATATATATATAATATAG
1 TTTTAAAATATTTATATATAATATAG
*
537885 TTTTAAAAATATTTATATATTATATAG
1 TTTT-AAAATATTTATATATAATATAG
*
537912 TTTTTAAAACATTT
1 -TTTTAAAATATTT
537926 TGAAAATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.11
27 28 0.78
28 4 0.11
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (26 bp):
TTTTAAAATATTTATATATAATATAG
Found at i:537909 original size:64 final size:63
Alignment explanation
Indices: 537829--538096 Score: 209
Period size: 64 Copynumber: 4.1 Consensus size: 63
537819 ATATATATAT
* *
537829 ATATATATATATTATATAATTTAAAAATAC-TTTT-AAAATATATATATATAATATAGTTTTAAA
1 ATATTTATATATTATATAATTTAAAAA-ACATTTTGAAAATAAATATA-AT-ATATAGTTTTAAA
537892 A
63 A
* **
537893 ATATTTATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGTTTTTAAAA
1 ATATTTATATATTATATAATTTAAAAAACATTTTGAAAATAAATATAATATATAG-TTTTAAAA
* * ** * * *
537957 TATTTTTAAAAATATATATTATATAGTTTTTAAAATATTTTAAAAATAAATATAATATATAATTT
1 -A-TATT-----TATATATTATATAATTTAAAAAACATTTTGAAAATAAATATAATATAT-AGTT
538022 TTAAAA
58 TTAAAA
** * ** * * *
538028 CA-AAGTATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAA
1 -ATATTTATATATTATATAATTTAAAAAACATTTTGAAAATAAATATAATATATAGTTTTAAAA
*
538091 ACATTT
1 ATATTT
538097 TAAAAAATTT
Statistics
Matches: 174, Mismatches: 18, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 18 0.10
64 84 0.48
65 12 0.07
66 3 0.02
71 55 0.32
72 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.46
Consensus pattern (63 bp):
ATATTTATATATTATATAATTTAAAAAACATTTTGAAAATAAATATAATATATAGTTTTAAAA
Found at i:537939 original size:36 final size:36
Alignment explanation
Indices: 537899--538288 Score: 338
Period size: 36 Copynumber: 10.9 Consensus size: 36
537889 AAAAATATTT
537899 ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
1 ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
* * * *
537935 ATATAATATATAGTTTTTAAAATATTTTTAAAA-AT
1 ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
* *
537970 ATATATTATATAGTTTTTAAAATATTTTAAAAATAA
1 ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
* * *
538006 ATATAATATATAATTTTTAAAAC------AAAGT--
1 ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
*
538034 ATATATTATATAGTTTTTAAAACATTTTAAAAATAA
1 ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
* * * **
538070 ATATAATATATAATTTTTAAAACATTTTAAAAAATTT
1 ATATATTATATAGTTTTTAAAACATTTT-GAAAATAA
* * *
538107 ATATATTAAATATTTTTTAAAACACTTTGAAAATAA
1 ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
* * ***
538143 ATATGA-TATATAATTTTTAAAACAATTTTAAAAACGT
1 ATAT-ATTATATAGTTTTTAAAAC-ATTTTGAAAATAA
* *
538180 ATATATTATATAGTTTTTAAAAAATATTTTGAAAAACATAT
1 ATATATTATATAGTTTTT--AAAACATTTTG--AAA-ATAA
* *
538221 ATATATTATATAGTTTTGAAATCATTTTGAAAACT--
1 ATATATTATATAGTTTTTAAAACATTTTGAAAA-TAA
* *
538256 -TATAATATATAGTTTTAAAAACATTTTTGAAAA
1 ATATATTATATAGTTTTTAAAACA-TTTTGAAAA
538289 CTATATAATT
Statistics
Matches: 291, Mismatches: 43, Indels: 41
0.78 0.11 0.11
Matches are distributed among these distances:
28 21 0.07
30 4 0.01
34 24 0.08
35 41 0.14
36 103 0.35
37 58 0.20
38 5 0.02
39 13 0.04
40 3 0.01
41 19 0.07
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (36 bp):
ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
Found at i:537964 original size:11 final size:11
Alignment explanation
Indices: 537948--538004 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
537938 TAATATATAG
537948 TTTTTAAAATA
1 TTTTTAAAATA
537959 TTTTTAAAAATA
1 TTTTT-AAAATA
* *
537971 TATATT-ATATA
1 T-TTTTAAAATA
537982 GTTTTTAAAATA
1 -TTTTTAAAATA
*
537994 TTTTAAAAATA
1 TTTTTAAAATA
538005 AATATAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
11 22 0.59
12 12 0.32
13 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (11 bp):
TTTTTAAAATA
Found at i:537998 original size:135 final size:135
Alignment explanation
Indices: 537833--538167 Score: 430
Period size: 135 Copynumber: 2.5 Consensus size: 135
537823 ATATATATAT
* * * *
537833 ATATATATTATATAATTTAAAAATACTTTTAAAATATATATATATAATATAGTTTTAAAA-ATAT
1 ATATATATTATATATTTTTAAAATACTTTTAAAATATATATATATAATATATTTTTAAAACA-AA
* * * *
537897 TTATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGTTTTTAAAATATTT
65 GTATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAAACATTT
*
537962 TTAAAA
130 TAAAAA
*
537968 ATATATATTATATAGTTTTTAAAATA-TTTTAAAA-ATAAATATA-ATATATAATTTTTAAAACA
1 ATATATATTATATA-TTTTTAAAATACTTTTAAAATATATATATATA-ATAT-ATTTTTAAAACA
538030 AAGTATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAAACAT
63 AAGTATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAAACAT
538095 TTTAAAAA
128 TTTAAAAA
* * * *
538103 ATTTATATATTAAATATTTTTTAAAACACTTTGAAAATAAATATGATAT-ATA-ATTTTTAAAAC
1 A--TATATATTATATA-TTTTTAAAATACTTTTAAAATATATAT-ATATAATATATTTTTAAAAC
538166 AA
62 AA
538168 TTTTAAAAAC
Statistics
Matches: 174, Mismatches: 16, Indels: 18
0.84 0.08 0.09
Matches are distributed among these distances:
133 1 0.01
134 12 0.07
135 99 0.57
136 10 0.06
137 35 0.20
138 7 0.04
139 7 0.04
140 3 0.02
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (135 bp):
ATATATATTATATATTTTTAAAATACTTTTAAAATATATATATATAATATATTTTTAAAACAAAG
TATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAAACATTTT
AAAAA
Found at i:538024 original size:26 final size:27
Alignment explanation
Indices: 537994--538057 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
537984 TTTTAAAATA
537994 TTTTAAAA-ATAA-ATATAATATATAAT
1 TTTTAAAACA-AAGATATAATATATAAT
* *
538020 TTTTAAAACAAAGTATATATTATATAGT
1 TTTTAAAACAAAG-ATATAATATATAAT
538048 TTTTAAAACA
1 TTTTAAAACA
538058 TTTTAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 10 0.30
27 1 0.03
28 22 0.67
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (27 bp):
TTTTAAAACAAAGATATAATATATAAT
Found at i:538225 original size:73 final size:73
Alignment explanation
Indices: 538032--538288 Score: 283
Period size: 73 Copynumber: 3.5 Consensus size: 73
538022 TTAAAACAAA
*
538032 GTATATATTATATAGTTTTT-AAAACATTTTAAAAATAAATATAATATATAATTTTTAAAACATT
1 GTATATATTATATAGTTTTTAAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACATT
*
538096 TTAAAAAAT
66 TT-AAAAAC
* * * * *
538105 TTATATATTAAATA-TTTTTTAAAACACTTTGAAAATAAATATGATATATAATTTTTAAAACAAT
1 GTATATATTATATAGTTTTTAAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAAC-AT
538169 TTTAAAAAC
65 TTTAAAAAC
* * *
538178 GTATATATTATATAGTTTTTAAAAAATATTTTGAAAA-ACATATATATATTATATAGTTTTGAAA
1 GTATATATTATATAGTTTTT-AAAAACATTTTGAAAATA-A-ATATA-A-TATATAATTTTTAAA
* *
538242 TCATTTTGAAAAC
61 ACATTTTAAAAAC
*
538255 -T-TATAATATATAG-TTTTAAAAACATTTTTGAAAA
1 GTATATATTATATAGTTTTTAAAAACA-TTTTGAAAA
538289 CTATATAATT
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
72 5 0.03
73 73 0.46
74 24 0.15
75 25 0.16
76 5 0.03
77 11 0.07
78 14 0.09
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.44
Consensus pattern (73 bp):
GTATATATTATATAGTTTTTAAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACATT
TTAAAAAC
Found at i:538264 original size:41 final size:40
Alignment explanation
Indices: 538024--538295 Score: 166
Period size: 37 Copynumber: 7.3 Consensus size: 40
538014 TATAATTTTT
* *
538024 AAAACAAAGTATATATTATATAGTTTTT-AAAACATTTT--
1 AAAACATA-TATATATTATATAGTTTTTAAAAATATTTTGA
* * * *
538062 AAAA-ATAAATATAATATATAATTTTT-AAAACATTTT-A
1 AAAACATATATATATTATATAGTTTTTAAAAATATTTTGA
* * * * *
538099 AAAA-ATTTATATATTAAATA-TTTTTTAAAACACTTTGA
1 AAAACATATATATATTATATAGTTTTTAAAAATATTTTGA
538137 AAATA-A-ATATGATA-TATA-A-TTTTTAAAACA-ATTTT-A
1 AAA-ACATATAT-ATATTATATAGTTTTTAAAA-ATATTTTGA
*
538173 AAAAC--GTATATATTATATAGTTTTTAAAAAATATTTTGA
1 AAAACATATATATATTATATAGTTTTT-AAAAATATTTTGA
*
538212 AAAACATATATATATTATATAG-TTTT-GAAATCATTTTG-
1 AAAACATATATATATTATATAGTTTTTAAAAAT-ATTTTGA
*
538250 AAAAC-T-TATA-A-TATATAG-TTTTAAAAACATTTTTG-
1 AAAACATATATATATTATATAGTTTTTAAAAATA-TTTTGA
538285 AAAAC-TATATA
1 AAAACATATATA
538296 ATTTTGAAAA
Statistics
Matches: 197, Mismatches: 18, Indels: 40
0.77 0.07 0.16
Matches are distributed among these distances:
34 15 0.08
35 23 0.12
36 44 0.22
37 47 0.24
38 33 0.17
39 17 0.09
40 4 0.02
41 14 0.07
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (40 bp):
AAAACATATATATATTATATAGTTTTTAAAAATATTTTGA
Found at i:538294 original size:29 final size:28
Alignment explanation
Indices: 538259--538352 Score: 111
Period size: 30 Copynumber: 3.3 Consensus size: 28
538249 GAAAACTTAT
*
538259 AATATATAGTTTTAAAAACATTTTTGAA
1 AATATATAATTTTAAAAACATTTTTGAA
* *
538287 AACTATATAATTTTGAAAACATTTTTTAAA
1 AA-TATATAATTTTAAAAACA-TTTTTGAA
538317 ATATATATAATTTTAAAATAC--TTTTGAA
1 A-ATATATAATTTTAAAA-ACATTTTTGAA
538345 AATATATA
1 AATATATA
538353 TTATATAGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
27 7 0.12
28 9 0.16
29 16 0.28
30 22 0.39
31 3 0.05
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (28 bp):
AATATATAATTTTAAAAACATTTTTGAA
Found at i:538324 original size:30 final size:29
Alignment explanation
Indices: 538260--538353 Score: 118
Period size: 29 Copynumber: 3.2 Consensus size: 29
538250 AAAACTTATA
*
538260 ATATATAGTTTTAAAAACATTTTTGAAAA-
1 ATATATAATTTT-AAAACATTTTTGAAAAT
* *
538289 CTATATAATTTTGAAAACATTTTTTAAAAT
1 ATATATAATTTT-AAAACATTTTTGAAAAT
* *
538319 ATATATAATTTTAAAATACTTTTGAAAAT
1 ATATATAATTTTAAAACATTTTTGAAAAT
538348 ATATAT
1 ATATAT
538354 TATATAGTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 45 0.80
30 11 0.20
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (29 bp):
ATATATAATTTTAAAACATTTTTGAAAAT
Found at i:538378 original size:23 final size:24
Alignment explanation
Indices: 538338--538382 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
538328 TTTAAAATAC
* *
538338 TTTTGAAAATATATATTATATAGT
1 TTTTGAAAATAAAAATTATATAGT
538362 TTTTGAAAA-AAAAATTATATA
1 TTTTGAAAATAAAAATTATATA
538383 TAATAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (24 bp):
TTTTGAAAATAAAAATTATATAGT
Found at i:538439 original size:15 final size:14
Alignment explanation
Indices: 538413--538455 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 14
538403 TCGTTGTTAT
538413 TTATTTTTATTTT-
1 TTATTTTTATTTTA
*
538426 TTA-TTTTATTATTT
1 TTATTTTTATT-TTA
538440 TTATTTTTATTTTA
1 TTATTTTTATTTTA
538454 TT
1 TT
538456 TTCCTGATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 7 0.27
13 5 0.19
14 7 0.27
15 7 0.27
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTATTTTTATTTTA
Found at i:538446 original size:20 final size:21
Alignment explanation
Indices: 538413--538455 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
538403 TCGTTGTTAT
538413 TTATTTTTATTTTTTATTTTA
1 TTATTTTTATTTTTTATTTTA
538434 TTATTTTTA-TTTTTATTTTA
1 TTATTTTTATTTTTTATTTTA
538454 TT
1 TT
538456 TTCCTGATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (21 bp):
TTATTTTTATTTTTTATTTTA
Found at i:539413 original size:4 final size:4
Alignment explanation
Indices: 539390--539463 Score: 62
Period size: 4 Copynumber: 17.8 Consensus size: 4
539380 TTGTTTATGC
* *
539390 ATTT ATTT AATTT TTCTT ATTT ATTT ATTT ATTT ATTT -TTAT TTTT ATTT
1 ATTT ATTT -ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATT-T ATTT ATTT
*
539440 CTTT GATTT ATTT -TTT ATATT ATT
1 ATTT -ATTT ATTT ATTT AT-TT ATT
539464 ATTATTTTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
3 5 0.09
4 37 0.64
5 16 0.28
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:539415 original size:22 final size:22
Alignment explanation
Indices: 539390--539451 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
539380 TTGTTTATGC
539390 ATTTATTTAATTT-TTCTTATTT
1 ATTTATTT-ATTTATTCTTATTT
*
539412 ATTTATTTATTTATTTTTATTTTT
1 ATTTATTTATTTATTCTTA--TTT
*
539436 ATTTCTTTGATTTATT
1 ATTTATTT-ATTTATT
539452 TTTTATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 4 0.12
22 13 0.38
24 10 0.29
25 7 0.21
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (22 bp):
ATTTATTTATTTATTCTTATTT
Found at i:539430 original size:18 final size:18
Alignment explanation
Indices: 539390--539472 Score: 63
Period size: 18 Copynumber: 4.8 Consensus size: 18
539380 TTGTTTATGC
*
539390 ATTTATTTAATTTTT-CTT
1 ATTTATTT-ATTTTTATTT
539408 ATTTATTTA--TTTATTT
1 ATTTATTTATTTTTATTT
539424 A-TT-TTTATTTTTATTT
1 ATTTATTTATTTTTATTT
*
539440 CTTTGATTTATTTTTTATATT
1 ATTT-ATTTA-TTTTTAT-TT
539461 A-TTA-TTATTTTT
1 ATTTATTTATTTTT
539473 CTATTCACTT
Statistics
Matches: 54, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
14 4 0.07
15 5 0.09
16 10 0.19
17 8 0.15
18 11 0.20
19 5 0.09
20 9 0.17
21 2 0.04
ACGTcount: A:0.22, C:0.02, G:0.01, T:0.75
Consensus pattern (18 bp):
ATTTATTTATTTTTATTT
Found at i:539448 original size:25 final size:25
Alignment explanation
Indices: 539390--539454 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
539380 TTGTTTATGC
*
539390 ATTTATTTAATTTTTCTTATTTATTT
1 ATTTATTT-ATTTTTATTATTTATTT
539416 ATTTATTTATTTTTATT-TTTATTT
1 ATTTATTTATTTTTATTATTTATTT
*
539440 CTTTGATTTATTTTT
1 ATTT-ATTTATTTTT
539455 TATATTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 10 0.28
25 18 0.50
26 8 0.22
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (25 bp):
ATTTATTTATTTTTATTATTTATTT
Found at i:539460 original size:28 final size:28
Alignment explanation
Indices: 539390--539470 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 28
539380 TTGTTTATGC
* *
539390 ATTTATTTAATT-T-TTCTTATTTATTT
1 ATTTATTTATTTATATTATTATTTATTT
* * *
539416 ATTTATTTATTTTTATTTTTATTTCTTT
1 ATTTATTTATTTATATTATTATTTATTT
539444 GATTTATTT-TTTATATTATTA-TTATTT
1 -ATTTATTTATTTATATTATTATTTATTT
539471 TTCTATTCAC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
26 11 0.24
27 6 0.13
28 21 0.46
29 8 0.17
ACGTcount: A:0.22, C:0.02, G:0.01, T:0.74
Consensus pattern (28 bp):
ATTTATTTATTTATATTATTATTTATTT
Found at i:539470 original size:51 final size:48
Alignment explanation
Indices: 539394--539554 Score: 143
Period size: 50 Copynumber: 3.2 Consensus size: 48
539384 TTATGCATTT
539394 ATTTAATTTTTCTTAT-TTATTTATTTATTTATTTTTATTTTTATTTCTTTG
1 ATTT-ATTTTT-TTATATTA-TTATTTATTTATTTTTATTTTT-TTTCTTTG
*
539445 ATTTA-TTTTTTATATTATTA-TTATTT-TTCTATTCACTTTTTTTCCTTTG
1 ATTTATTTTTTTATATTATTATTTATTTATT-T-TT-A-TTTTTTTTCTTTG
* * *
539494 ATTTATTTTCTTTATATTACTA-TTATTTTATTTTTATTCTTTTTTATTTT
1 ATTTATTTT-TTTATATTATTATTTA-TTTATTTTTATT-TTTTTTCTTTG
*
539544 ATTTCTTTTTT
1 ATTTATTTTTT
539555 CTTTTTTTCT
Statistics
Matches: 94, Mismatches: 6, Indels: 22
0.77 0.05 0.18
Matches are distributed among these distances:
46 2 0.02
47 7 0.07
48 9 0.10
49 24 0.26
50 26 0.28
51 20 0.21
52 4 0.04
53 2 0.02
ACGTcount: A:0.19, C:0.07, G:0.01, T:0.73
Consensus pattern (48 bp):
ATTTATTTTTTTATATTATTATTTATTTATTTTTATTTTTTTTCTTTG
Found at i:539538 original size:16 final size:16
Alignment explanation
Indices: 539519--539567 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
539509 ATTACTATTA
539519 TTTTATTTTTATTCTT
1 TTTTATTTTTATTCTT
539535 TTTTA-TTTTATTTCTT
1 TTTTATTTTTA-TTCTT
*
539551 TTTTCTTTTT-TTCTT
1 TTTTATTTTTATTCTT
539566 TT
1 TT
539568 CATTTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 12 0.40
16 14 0.47
17 4 0.13
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTATTTTTATTCTT
Found at i:539541 original size:21 final size:23
Alignment explanation
Indices: 539516--539561 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
539506 TATATTACTA
539516 TTATTTTA-TT-TTTATTCTTTT
1 TTATTTTATTTCTTTATTCTTTT
*
539537 TTATTTTATTTCTTTTTTCTTTT
1 TTATTTTATTTCTTTATTCTTTT
539560 TT
1 TT
539562 TCTTTTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 2 0.09
23 12 0.55
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.83
Consensus pattern (23 bp):
TTATTTTATTTCTTTATTCTTTT
Found at i:539574 original size:15 final size:14
Alignment explanation
Indices: 539446--539576 Score: 64
Period size: 15 Copynumber: 8.8 Consensus size: 14
539436 ATTTCTTTGA
* *
539446 TTTATTTTTTATAT
1 TTTATTTTTTTTCT
*
539460 TATTATTATTTTTCT
1 T-TTATTTTTTTTCT
* *
539475 ATTCACTTTTTTTCCT
1 -TTTA-TTTTTTTTCT
* *
539491 TTGATTTATTTTCT
1 TTTATTTTTTTTCT
** * *
539505 TTATATTACTATTAT
1 TT-TATTTTTTTTCT
*
539520 TTTATTTTTATTCTTT
1 TTTATTTTT-TT-TCT
*
539536 TTTATTTTATTTCT
1 TTTATTTTTTTTCT
*
539550 TTTTTCTTTTTTTCT
1 TTTAT-TTTTTTTCT
539565 TTTCATTTTTTT
1 TTT-ATTTTTTT
539577 ACTTATTTTC
Statistics
Matches: 86, Mismatches: 23, Indels: 15
0.69 0.19 0.12
Matches are distributed among these distances:
14 22 0.26
15 44 0.51
16 20 0.23
ACGTcount: A:0.15, C:0.09, G:0.01, T:0.75
Consensus pattern (14 bp):
TTTATTTTTTTTCT
Found at i:540378 original size:18 final size:18
Alignment explanation
Indices: 540355--540392 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
540345 TATTTTATTA
540355 ATATTTATATATGATGTG
1 ATATTTATATATGATGTG
*
540373 ATATTTATGTATGATGTG
1 ATATTTATATATGATGTG
540391 AT
1 AT
540393 TTTTTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (18 bp):
ATATTTATATATGATGTG
Found at i:540643 original size:29 final size:29
Alignment explanation
Indices: 540593--540653 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
540583 AAAGCATCGG
540593 AATATTTTTTAATTTAATTATAATTTTAGA
1 AATATTTTTTAATTTAATTATAATTTTA-A
*
540623 AATATTTTTT-GTTTCAA-TATAATTTTAA
1 AATATTTTTTAATTT-AATTATAATTTTAA
540651 AAT
1 AAT
540654 TTTAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 4 0.14
29 13 0.45
30 12 0.41
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (29 bp):
AATATTTTTTAATTTAATTATAATTTTAA
Found at i:540942 original size:19 final size:19
Alignment explanation
Indices: 540918--540974 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 19
540908 ACACAAAGTA
*
540918 ACGGAACCGTTGGTCAATG
1 ACGGAAACGTTGGTCAATG
540937 ACGGAAAACGTTGGTCAATG
1 ACGG-AAACGTTGGTCAATG
*
540957 ACGGAAAACATTGGTCAA
1 ACGG-AAACGTTGGTCAA
540975 ATAATCTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 4 0.11
20 31 0.89
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (19 bp):
ACGGAAACGTTGGTCAATG
Found at i:540950 original size:20 final size:20
Alignment explanation
Indices: 540925--540974 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
540915 GTAACGGAAC
540925 CGTTGGTCAATGACGGAAAA
1 CGTTGGTCAATGACGGAAAA
540945 CGTTGGTCAATGACGGAAAA
1 CGTTGGTCAATGACGGAAAA
*
540965 CATTGGTCAA
1 CGTTGGTCAA
540975 ATAATCTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (20 bp):
CGTTGGTCAATGACGGAAAA
Found at i:541404 original size:21 final size:23
Alignment explanation
Indices: 541367--541419 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
541357 CTCTATATAT
* *
541367 TATTTTT-TTCAATT-AAATTAC
1 TATTTTTATTCAATTAAAAATAA
*
541388 TATTTTTATTGAA-TAAAAATAA
1 TATTTTTATTCAATTAAAAATAA
541410 TATTTTTATT
1 TATTTTTATT
541420 ATTATTTCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (23 bp):
TATTTTTATTCAATTAAAAATAA
Found at i:542476 original size:2 final size:2
Alignment explanation
Indices: 542469--542500 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
542459 CACAATGTCC
542469 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
542501 GAGTATTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:542659 original size:102 final size:102
Alignment explanation
Indices: 542534--542734 Score: 269
Period size: 102 Copynumber: 2.0 Consensus size: 102
542524 ACTTTTTCGA
* * * *
542534 ACATGTACTATTATGTATTCACCTCAAACTAATAAAAA-TAATTTATATTATTTTTTAAATCTAT
1 ACATGGACTACTATATATTCACCTCAAACTAATAAAAAGTAATTTATATTATCTTTTAAATCTA-
*
542598 TTTTTGAATTTAATATATGTATCAAATTTAATAAATTG
65 TTTTTGAATTTAATATATGTATCAAACTTAATAAATTG
** * * *
542636 ACATGGACTACTATATATTCACCTCGTACTAATAAAAAGTCATTTATATTATCTTTTAGATTTAT
1 ACATGGACTACTATATATTCACCTCAAACTAATAAAAAGTAATTTATATTATCTTTTAAATCTAT
* * *
542701 TTTTGAATTTAATATTTTTATCGAACTTAATAAA
66 TTTTGAATTTAATATATGTATCAAACTTAATAAA
542735 ATATAAGAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
102 64 0.75
103 21 0.25
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.45
Consensus pattern (102 bp):
ACATGGACTACTATATATTCACCTCAAACTAATAAAAAGTAATTTATATTATCTTTTAAATCTAT
TTTTGAATTTAATATATGTATCAAACTTAATAAATTG
Found at i:551835 original size:23 final size:23
Alignment explanation
Indices: 551803--551853 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
551793 GTGTTCGTTT
*
551803 ATTTATTGTTCACAAACATGTTC
1 ATTTAATGTTCACAAACATGTTC
* *
551826 ATTTAATGTTCGCGAACATGTTC
1 ATTTAATGTTCACAAACATGTTC
551849 ATTTA
1 ATTTA
551854 TACGTTAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (23 bp):
ATTTAATGTTCACAAACATGTTC
Found at i:551899 original size:70 final size:70
Alignment explanation
Indices: 551823--551970 Score: 233
Period size: 70 Copynumber: 2.1 Consensus size: 70
551813 CACAAACATG
* * *
551823 TTCATTTAATGTTCGCGAACATGTTCATTTATACGTTAATGAACGTGTTCATGAATATGTTCGTT
1 TTCATTTAATGTTCGCGAACATATTCATTTATACGTTAACGAACGTGTTCATGAACATGTTCGTT
*
551888 TAGCA
66 TAACA
* *
551893 TTCATTTAATGTTCGCGAACATATTCGTTTATATGTTAACGAACGTGTTCATGAACATGTTCGTT
1 TTCATTTAATGTTCGCGAACATATTCATTTATACGTTAACGAACGTGTTCATGAACATGTTCGTT
*
551958 TAACG
66 TAACA
551963 TTCATTTA
1 TTCATTTA
551971 GTGCTCGTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (70 bp):
TTCATTTAATGTTCGCGAACATATTCATTTATACGTTAACGAACGTGTTCATGAACATGTTCGTT
TAACA
Found at i:557982 original size:10 final size:10
Alignment explanation
Indices: 557969--557995 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
557959 ATCCTTTTTC
557969 TTGCTTTGTA
1 TTGCTTTGTA
557979 TTGCTTTGTA
1 TTGCTTTGTA
557989 TTGCTTT
1 TTGCTTT
557996 CTTCGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.11, G:0.19, T:0.63
Consensus pattern (10 bp):
TTGCTTTGTA
Found at i:560182 original size:74 final size:73
Alignment explanation
Indices: 560058--560267 Score: 330
Period size: 74 Copynumber: 2.8 Consensus size: 73
560048 TACTCCATCA
* *
560058 CAGCAAATCAAGCCGCAATTGAAAGACCAGAGCCTTATTAGCACCTATAAAATAGAAAAAAAAAT
1 CAGCAAATCAAGCCGTAATTGAAAGACCAG-GCCTTATTAGCACCGATAAAATAGAAAAAAAAAT
560123 CCTTATAGT
65 CCTTATAGT
****
560132 CAGCAAATCAAGCCGTAATTGAAAGACCATGGCCTTATTAGCACCGATAAAATAGGGGGAAAAAT
1 CAGCAAATCAAGCCGTAATTGAAAGACCA-GGCCTTATTAGCACCGATAAAATAGAAAAAAAAAT
560197 CCTTATAGT
65 CCTTATAGT
*
560206 CAACAAATCAAGCCGTAATTGAAAGACCAGGGCCTTATTAGCACCGATAAAATAGAAAAAAA
1 CAGCAAATCAAGCCGTAATTGAAAGACCA-GGCCTTATTAGCACCGATAAAATAGAAAAAAA
560268 CTAAAAATTG
Statistics
Matches: 123, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
74 122 0.99
75 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.20
Consensus pattern (73 bp):
CAGCAAATCAAGCCGTAATTGAAAGACCAGGCCTTATTAGCACCGATAAAATAGAAAAAAAAATC
CTTATAGT
Found at i:560830 original size:2 final size:2
Alignment explanation
Indices: 560823--560852 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
560813 CTTTTTAATG
560823 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
560853 CACACGCGCG
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):
TA
Found at i:561061 original size:5 final size:5
Alignment explanation
Indices: 561037--561082 Score: 69
Period size: 5 Copynumber: 9.4 Consensus size: 5
561027 TAGAGATAAA
561037 AATAT AATGAT AA-A- AATAT AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AAT-AT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AA
561083 CAAATATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 30 0.79
6 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:563438 original size:18 final size:16
Alignment explanation
Indices: 563415--563464 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 16
563405 GTTCCTCTAC
563415 TTATTTTTATTTACTTAT
1 TTATTTTTATTT--TTAT
563433 TTATTTTATTATTTTTAT
1 TTA-TTT-TTATTTTTAT
563451 TTATTTTATATTTT
1 TTATTTT-TATTTT
563465 ATTCCCTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.03
17 9 0.31
18 10 0.34
19 3 0.10
20 6 0.21
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTTATTTTTAT
Found at i:563448 original size:26 final size:25
Alignment explanation
Indices: 563415--563467 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
563405 GTTCCTCTAC
563415 TTATTTTTATTTACTTATT-TATTTTA
1 TTATTTTTATTTA-TT-TTATATTTTA
563441 TTATTTTTATTTATTTTATATTTTA
1 TTATTTTTATTTATTTTATATTTTA
563466 TT
1 TT
563468 CCCTTCTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 2 0.08
25 11 0.42
26 13 0.50
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (25 bp):
TTATTTTTATTTATTTTATATTTTA
Done.