Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001976.1 Hibiscus syriacus cultivar Beakdansim tig00004004_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: 915387
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:513335 original size:11 final size:11
Alignment explanation
Indices: 513311--513368 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
513301 TCACTTTTTA
*
513311 AAAAAT-CAAC
1 AAAAATGCAAT
513321 AAAAATGCAAT
1 AAAAATGCAAT
* *
513332 AAAAAAGGAATT
1 AAAAATGCAA-T
513344 AAAAATG-AAT
1 AAAAATGCAAT
*
513354 -AAAATTCAAT
1 AAAAATGCAAT
513364 AAAAA
1 AAAAA
513369 AAGAATGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 5 0.13
10 10 0.26
11 17 0.44
12 7 0.18
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (11 bp):
AAAAATGCAAT
Found at i:513934 original size:338 final size:338
Alignment explanation
Indices: 513529--514148 Score: 960
Period size: 338 Copynumber: 1.8 Consensus size: 338
513519 CTGTTGTTAA
513529 AATAATAATTCATTTGATCTCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTA
1 AATAATAATTCATTTGATCTCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTA
* * *
513594 AACAATTAATTTTAAAAGTCAATAAATTTTTTAAAAATATCTAAAATTTATAATTTTTTAAATTA
66 AACAATTAATTTTAAAAGTCAATAAATTTTTCAAAAATATATAAAAATTATAATTTTTTAAATTA
* * * *
513659 TAAAATACTTATCATCATCATCATCATCATTTTGTAAAATAAATAATGGTTATAAAAATTTTATA
131 TAAAATACTTATCACCATCATCATCATCATTTTGTAAAAAAAATAATAGTTATAAAAATTTCATA
* * * * *
513724 AAATTATTGATATTTTAAAATATTTACCATCAAAATTTTTC-TATACTAAATTATACA-TATTGT
196 AAATTATTCATATTTTAAAATACTGACCATC-AAAGTTTTCATATACTAAATTATA-AGTATGGT
* *
513787 ATAATTTCATGCAAAAATCTAAATAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTTAA
259 ATAATTTCATGAAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTTAA
513852 AAATAATAATTAATG
324 AAATAATAATTAATG
*
513867 AATAATAATTCATTTGATC-CTTCAATTGTAATTACAAGTTTATTTTAATATTTTTT-TATATTT
1 AATAATAATTCATTTGATCTC-TCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATAT-TTT
*
513930 TAAACAATTAATTTTAAAAGTCAATAGATTTTTCAAAAATATATAAAAATTATAATTTTTTAAAT
64 TAAACAATTAATTTTAAAAGTCAATAAATTTTTCAAAAATATATAAAAATTATAATTTTTTAAAT
* * * * *
513995 TATAAAATATTTATTACCATCATCATTATCATTTTGTAAAAAAAATACTAGTTATAAAACTTTCA
129 TATAAAATACTTATCACCATCATCATCATCATTTTGTAAAAAAAATAATAGTTATAAAAATTTCA
*
514060 TAAAATTATTCATATTTTAAAATACTGACCCTCAAAGTTTTCATATACTAAATTATAAGTATGGT
194 TAAAATTATTCATATTTTAAAATACTGACCATCAAAGTTTTCATATACTAAATTATAAGTATGGT
* *
514125 GTAATTTTATGAAAAAATCAAAAT
259 ATAATTTCATGAAAAAATCAAAAT
514149 TTATCGAGTT
Statistics
Matches: 254, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
337 13 0.05
338 241 0.95
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (338 bp):
AATAATAATTCATTTGATCTCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTA
AACAATTAATTTTAAAAGTCAATAAATTTTTCAAAAATATATAAAAATTATAATTTTTTAAATTA
TAAAATACTTATCACCATCATCATCATCATTTTGTAAAAAAAATAATAGTTATAAAAATTTCATA
AAATTATTCATATTTTAAAATACTGACCATCAAAGTTTTCATATACTAAATTATAAGTATGGTAT
AATTTCATGAAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTTAAAA
ATAATAATTAATG
Found at i:520290 original size:20 final size:20
Alignment explanation
Indices: 520246--520533 Score: 245
Period size: 20 Copynumber: 14.2 Consensus size: 20
520236 AATGACCAAC
**
520246 AAAATCGCAACGCGA-TATC
1 AAAATCGCAACGCGATTAAG
520265 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
* *
520285 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
520305 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
520325 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
520346 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
520367 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* *
520388 AAGAATCGCAATGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
520409 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
520431 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
520449 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
520471 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
520489 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
520511 --AATCGCAACGCGATTAAT
1 AAAATCGCAACGCGATTAAG
520529 AAAAT
1 AAAAT
520534 GAGTAAATTC
Statistics
Matches: 222, Mismatches: 25, Indels: 43
0.77 0.09 0.15
Matches are distributed among these distances:
18 9 0.04
19 15 0.07
20 150 0.68
21 13 0.06
22 35 0.16
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:520316 original size:40 final size:40
Alignment explanation
Indices: 520246--520533 Score: 343
Period size: 40 Copynumber: 7.1 Consensus size: 40
520236 AATGACCAAC
520246 AAAATCGCAACGCGATAT-CAA-AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGA-ATCCAAGAATCGCAACGCGATTAAG
* *** *
520285 AAAATCGCAACGTTGAAAAGAA-AATCGCAACG-G-TCAAAAG
1 AAAATCGCAACG-CGAATCCAAGAATCGCAACGCGAT--TAAG
*
520325 AAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGA-A-TCCAAGAATCGCAACGCGATTAAG
* * * *
520367 AGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGA--ATCCAAGAATCGCAACGCGATTAAG
*
520409 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGAATCCAAGAATCGCAACGCGATTAAG
*
520449 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGAATCCAAGAATCGCAACGCGATTAAG
* *
520489 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAT
1 AAAATCGCAACGCGAATCCAAGAATCGCAACGCGATTAAG
520529 AAAAT
1 AAAAT
520534 GAGTAAATTC
Statistics
Matches: 221, Mismatches: 18, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
38 1 0.00
39 16 0.07
40 137 0.62
41 2 0.01
42 63 0.29
43 1 0.00
44 1 0.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (40 bp):
AAAATCGCAACGCGAATCCAAGAATCGCAACGCGATTAAG
Found at i:520640 original size:6 final size:6
Alignment explanation
Indices: 520629--520709 Score: 162
Period size: 6 Copynumber: 13.5 Consensus size: 6
520619 GACACGTATT
520629 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
520677 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
520710 CGAGACGAGA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 75 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:521280 original size:6 final size:6
Alignment explanation
Indices: 521203--521378 Score: 261
Period size: 6 Copynumber: 31.5 Consensus size: 6
521193 TCTCGTCTCG
521203 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT -GTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
521244 -GTCGT -GTCGT -GTCGT -GTCGT -GTCGT -GTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
521286 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
521334 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
521379 AATACGTGTC
Statistics
Matches: 169, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
5 65 0.38
6 104 0.62
ACGTcount: A:0.00, C:0.18, G:0.50, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:521503 original size:20 final size:20
Alignment explanation
Indices: 521478--521697 Score: 184
Period size: 20 Copynumber: 10.8 Consensus size: 20
521468 TCATTTTCTA
521478 AATCGCGTTGCGATTCTCTG
1 AATCGCGTTGCGATTCTCTG
521498 AATCGCGTTGCGATTCT-TGG
1 AATCGCGTTGCGATTCTCT-G
521518 AAGATCGCGTTGCGATTCTCTG
1 -A-ATCGCGTTGCGATTCTCTG
521540 AATCGCGTTGCGATTCTCTG
1 AATCGCGTTGCGATTCTCTG
521560 AATCGCGTTGCGATTCT-TGG
1 AATCGCGTTGCGATTCTCT-G
* * *
521580 AAGATCGCATTGCGATTTTATG
1 -A-ATCGCGTTGCGATTCTCTG
*
521602 AATCGCATTGCGATTCT-TGG
1 AATCGCGTTGCGATTCTCT-G
521622 ATGATCGCGTTGCGA-TCTTCT-
1 A--ATCGCGTTGCGATTC-TCTG
** * * * *
521643 TTTCAACGTTGCGCTTTTCTA
1 AATC-GCGTTGCGATTCTCTG
*
521664 AATCGCGTTGCGGTT-T-TG
1 AATCGCGTTGCGATTCTCTG
521682 ATATCGCGTTGCGATT
1 A-ATCGCGTTGCGATT
521698 TTGTTGGTCA
Statistics
Matches: 168, Mismatches: 15, Indels: 35
0.77 0.07 0.16
Matches are distributed among these distances:
18 2 0.01
19 19 0.11
20 91 0.54
21 9 0.05
22 44 0.26
23 3 0.02
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTCTG
Found at i:521538 original size:42 final size:40
Alignment explanation
Indices: 521478--521697 Score: 184
Period size: 42 Copynumber: 5.4 Consensus size: 40
521468 TCATTTTCTA
521478 AATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCT-TGG
1 AATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCT-G
521518 AAGATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCTG
1 -A-ATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCTG
* * *
521560 AATCGCGTTGCGATTCT-TGGAAGATCGCATTGCGATTTTATG
1 AATCGCGTTGCGATTCTCT-G-A-ATCGCGTTGCGATTCTCTG
*
521602 AATCGCATTGCGATTCT-TGGATGATCGCGTTGCGA-TCTTCT-
1 AATCGCGTTGCGATTCTCT-GA--ATCGCGTTGCGATTC-TCTG
** * * * * *
521643 TTTCAACGTTGCGCTTTTCTAAATCGCGTTGCGGTT-T-TG
1 AATC-GCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCTG
521682 ATATCGCGTTGCGATT
1 A-ATCGCGTTGCGATT
521698 TTGTTGGTCA
Statistics
Matches: 148, Mismatches: 19, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
38 1 0.01
39 11 0.07
40 30 0.20
41 8 0.05
42 96 0.65
43 2 0.01
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (40 bp):
AATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCTG
Found at i:521554 original size:62 final size:62
Alignment explanation
Indices: 521478--521637 Score: 250
Period size: 62 Copynumber: 2.5 Consensus size: 62
521468 TCATTTTCTA
* *
521478 AATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTCTG
1 AATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTTGGAAGATCGCATTGCGATTCTATG
*
521540 AATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTTGGAAGATCGCATTGCGATTTTATG
1 AATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTTGGAAGATCGCATTGCGATTCTATG
*
521602 AATCGCATTGCGATTCT-TGGATGATCGCGTTGCGAT
1 AATCGCGTTGCGATTCTCT-GA--ATCGCGTTGCGAT
521638 CTTCTTTTCA
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
61 1 0.01
62 77 0.85
64 13 0.14
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (62 bp):
AATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTTGGAAGATCGCATTGCGATTCTATG
Found at i:529562 original size:30 final size:31
Alignment explanation
Indices: 529519--529576 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
529509 CATTTAAAAT
* *
529519 ATATTTATTAATATTCTAATAATATAATATA
1 ATATTTATTAATATTATAATAAAATAATATA
529550 ATATTT-TTAATATTATAATAAAATAAT
1 ATATTTATTAATATTATAATAAAATAAT
529577 CAATTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (31 bp):
ATATTTATTAATATTATAATAAAATAATATA
Found at i:529566 original size:22 final size:21
Alignment explanation
Indices: 529527--529574 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
529517 ATATATTTAT
529527 TAATATTCTAATAATATAATA
1 TAATATTCTAATAATATAATA
* *
529548 TAATATTTTTAATATTATAATA
1 TAATA-TTCTAATAATATAATA
*
529570 AAATA
1 TAATA
529575 ATCAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATATTCTAATAATATAATA
Found at i:529643 original size:29 final size:29
Alignment explanation
Indices: 529537--529644 Score: 80
Period size: 29 Copynumber: 3.8 Consensus size: 29
529527 TAATATTCTA
*
529537 ATAATATAATATAATATTTTTAAT-AT-T
1 ATAATATAATATAATAATTTTAATAATAT
* * *
529564 ATAATAAAATAATCAATTATATTAATAATAT
1 ATAATATAAT-AT-AATAATTTTAATAATAT
* ** *
529595 A-AGATATTATATTTTTATTTTAATAATAT
1 ATA-ATATAATATAATAATTTTAATAATAT
*
529624 ATAATA-AATATAATAAATTTA
1 ATAATATAATATAATAATTTTA
529645 TATTTTTATT
Statistics
Matches: 61, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
27 9 0.15
28 12 0.20
29 27 0.44
30 6 0.10
31 7 0.11
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
ATAATATAATATAATAATTTTAATAATAT
Found at i:529673 original size:39 final size:37
Alignment explanation
Indices: 529582--529673 Score: 87
Period size: 41 Copynumber: 2.4 Consensus size: 37
529572 ATAATCAATT
* *
529582 ATATTAATAATATAAGATATTATATTTTTATTTTAATA
1 ATATAAATAATATAAGAAATTATATTTTTATTTT-ATA
* *
529620 ATATATAATAAATATAATAAATTTATATTTTTATTAATT-TC
1 ATATA-AAT-AATATAAGAAA-TTATATTTTTATT--TTATA
529661 ATATAAATAATAT
1 ATATAAATAATAT
529674 TAAATTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
38 4 0.09
39 8 0.18
40 12 0.27
41 19 0.42
43 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (37 bp):
ATATAAATAATATAAGAAATTATATTTTTATTTTATA
Found at i:529701 original size:19 final size:18
Alignment explanation
Indices: 529666--529745 Score: 58
Period size: 19 Copynumber: 4.3 Consensus size: 18
529656 ATTTCATATA
*
529666 AATAATATTAA-ATTATT
1 AATAATAATAATATTATT
529683 AATAATGAATAATATTATT
1 AATAAT-AATAATATTATT
* *
529702 TAT-ATATTTAATATTAATAT
1 AATAATA-ATAATATT-AT-T
529722 AATAATCTAATAATATT-TT
1 AATAA--TAATAATATTATT
529741 AATAA
1 AATAA
529746 AGATATTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
17 7 0.14
18 13 0.26
19 16 0.32
20 4 0.08
21 1 0.02
22 7 0.14
23 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (18 bp):
AATAATAATAATATTATT
Found at i:529914 original size:20 final size:19
Alignment explanation
Indices: 529868--529917 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
529858 AATAAAATTA
529868 TAAAAATAATTTTAATAAT
1 TAAAAATAATTTTAATAAT
* * *
529887 AAATAAATTATTTTAATATTT
1 TAA-AAATAATTTTAATA-AT
529908 TAAAAATAAT
1 TAAAAATAAT
529918 AACATTAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAAATAATTTTAATAAT
Found at i:531514 original size:40 final size:40
Alignment explanation
Indices: 531430--531517 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
531420 TTCCACAAGC
* * * *
531430 TTCTAGAGAGTTCTACACTTCTATAAAATTCTCCGAAATA
1 TTCTAGAAAATTCTACACTTCTATAAAACTCTCAGAAATA
*
531470 TTCTAGAAAATTCTACACTTCTCCATAAAACTCT-AG-AATT
1 TTCTAGAAAATTCTACACTTCT--ATAAAACTCTCAGAAATA
531510 TTCTAGAA
1 TTCTAGAA
531518 TATTTCCAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 31 0.76
41 1 0.02
42 9 0.22
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.35
Consensus pattern (40 bp):
TTCTAGAAAATTCTACACTTCTATAAAACTCTCAGAAATA
Found at i:543599 original size:2 final size:2
Alignment explanation
Indices: 543594--543619 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
543584 TATGTGTGGG
543594 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
543620 GCATTGTGCC
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):
TA
Found at i:544348 original size:3 final size:3
Alignment explanation
Indices: 544342--544371 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
544332 TTTTAAAGGC
544342 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
544372 TTTTAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:544563 original size:60 final size:59
Alignment explanation
Indices: 544487--544637 Score: 155
Period size: 60 Copynumber: 2.5 Consensus size: 59
544477 GTCCCTAAAC
* *
544487 CTTTTAATATTCTAATTTCATCC-CTAAATTAAGACTATT-ATTTTAAATTAGTCCTCAAA
1 CTTTTAATATTCTAATTTCATCCTC-AAACTAAGA-TATTCATTCTAAATTAGTCCTCAAA
* * * *
544546 CTTTTGAATATTTTAATTTCATCCTCAAACTATGATATTCATTCTAAATTGGTCCTCAAG
1 CTTTT-AATATTCTAATTTCATCCTCAAACTAAGATATTCATTCTAAATTAGTCCTCAAA
* * *
544606 CTTTTTTCACATTCCAATTTCATCC-CAAACTA
1 C--TTTTAATATTCTAATTTCATCCTCAAACTA
544638 TACATATATA
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
59 9 0.12
60 49 0.64
61 15 0.19
62 4 0.05
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.43
Consensus pattern (59 bp):
CTTTTAATATTCTAATTTCATCCTCAAACTAAGATATTCATTCTAAATTAGTCCTCAAA
Found at i:544866 original size:60 final size:60
Alignment explanation
Indices: 544779--544914 Score: 148
Period size: 60 Copynumber: 2.3 Consensus size: 60
544769 ATAAATTTAG
* ** * * *
544779 AATATTCAAATGTTTGGGGACTGATTTAGAAAAA-AGGTCATAATTTATGGATGAAATTAA
1 AATATTCAAAAGTTTAAGAACTAATTTAGAAAAAGA-GTCATAATTTAGGGATGAAATTAA
** * *
544839 AATATTCAAAAGTTTAAGAACTAATTTAGAATGAGAGTCATAGTTTAGGGATGAAATTGA
1 AATATTCAAAAGTTTAAGAACTAATTTAGAAAAAGAGTCATAATTTAGGGATGAAATTAA
* *
544899 AATATTAAAAAATTTA
1 AATATTCAAAAGTTTA
544915 GTGACCAATT
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
60 62 0.98
61 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (60 bp):
AATATTCAAAAGTTTAAGAACTAATTTAGAAAAAGAGTCATAATTTAGGGATGAAATTAA
Found at i:544925 original size:60 final size:60
Alignment explanation
Indices: 544815--544945 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 60
544805 TAGAAAAAAG
* * * * * *
544815 GTCATAATTTATGGATGAAATTAAAATATTCAAAAGTTTAAGAACTAATTTAGAA-TGAGA
1 GTCATAGTTTAGGGATGAAATTAAAATATTAAAAAATTTAAGAACCAATTTA-AACCGAGA
* *
544875 GTCATAGTTTAGGGATGAAATTGAAATATTAAAAAATTT-AGTGACCAATTTAAACCGAGA
1 GTCATAGTTTAGGGATGAAATTAAAATATTAAAAAATTTAAG-AACCAATTTAAACCGAGA
*
544935 GTTATAGTTTA
1 GTCATAGTTTA
544946 AAAAGTCTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
59 4 0.07
60 56 0.93
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.34
Consensus pattern (60 bp):
GTCATAGTTTAGGGATGAAATTAAAATATTAAAAAATTTAAGAACCAATTTAAACCGAGA
Found at i:548542 original size:181 final size:182
Alignment explanation
Indices: 548238--548601 Score: 721
Period size: 181 Copynumber: 2.0 Consensus size: 182
548228 TTCCTACTAG
548238 ATGACTAATACCATTCAGAAGAAGTTCAAAGTATCTTCAACCCAACTTCTCTATCAGTCTTGCCC
1 ATGACTAATACCATTCAGAAGAAGTTCAAAGTATCTTCAACCCAACTTCTCTATCAGTCTTGCCC
548303 TTACCAGGCATTAACTTTGTTCACCATTGGCCCATTCCTGGATGGGCTTTTGACCAACCTGAATG
66 TTACCAGGCATTAACTTTGTTCACCATTGGCCCATTCCTGGATGGGCTTTTGACCAACCTGAATG
548368 TTTTTGCTTTCAAGTATACCCCTCAAGTGCTGGTAAAGAATCA-TGCTTACA
131 TTTTTGCTTTCAAGTATACCCCTCAAGTGCTGGTAAAGAATCATTGCTTACA
548419 ATGACTAATACCATTCAGAAGAAGTTCAAAGTATCTTCAACCCAACTTCTCTATCAGTCTTGCCC
1 ATGACTAATACCATTCAGAAGAAGTTCAAAGTATCTTCAACCCAACTTCTCTATCAGTCTTGCCC
548484 TTACCAGGCATTAACTTTGTTCACCATTGGCCCATTCCTGGATGGGCTTTTGACCAACCTGAATG
66 TTACCAGGCATTAACTTTGTTCACCATTGGCCCATTCCTGGATGGGCTTTTGACCAACCTGAATG
548549 TTTTTGCTTTCAAGTATACCCCTCAAGTGCTGGTAAAGAATCATTGCTTACA
131 TTTTTGCTTTCAAGTATACCCCTCAAGTGCTGGTAAAGAATCATTGCTTACA
548601 A
1 A
548602 ATTCCTGCCC
Statistics
Matches: 182, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
181 173 0.95
182 9 0.05
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.32
Consensus pattern (182 bp):
ATGACTAATACCATTCAGAAGAAGTTCAAAGTATCTTCAACCCAACTTCTCTATCAGTCTTGCCC
TTACCAGGCATTAACTTTGTTCACCATTGGCCCATTCCTGGATGGGCTTTTGACCAACCTGAATG
TTTTTGCTTTCAAGTATACCCCTCAAGTGCTGGTAAAGAATCATTGCTTACA
Found at i:554890 original size:18 final size:17
Alignment explanation
Indices: 554863--554897 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
554853 ATTAATTAAT
*
554863 ATTAATTAATAAAATTTA
1 ATTAAATAAT-AAATTTA
554881 ATTAAATAATAAATTTA
1 ATTAAATAATAAATTTA
554898 TTTATTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTAAATAATAAATTTA
Found at i:558037 original size:24 final size:23
Alignment explanation
Indices: 558002--558047 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
557992 TATGTCATGA
*
558002 AAAATTTCTTTAAAAAAAAAAAC
1 AAAATTACTTTAAAAAAAAAAAC
* *
558025 AAAATTACATTTAATATAAAAAA
1 AAAATTAC-TTTAAAAAAAAAAA
558048 TATTATATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAATTACTTTAAAAAAAAAAAC
Found at i:558298 original size:2 final size:2
Alignment explanation
Indices: 558291--558319 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
558281 AATAAGTGAG
558291 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
558320 GAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:587075 original size:2 final size:2
Alignment explanation
Indices: 587070--587115 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
587060 AATATATGTG
587070 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
587112 AT AT
1 AT AT
587116 GTTTTCTGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:590307 original size:31 final size:31
Alignment explanation
Indices: 590258--590334 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
590248 TTTTGGTTGG
* *
590258 ATTTAAGAGTTAAATTGATATATTATCTAAA
1 ATTTAAGGGTCAAATTGATATATTATCTAAA
* *
590289 GTTT-AGGGATCAAATTGATATTTTATCTAAA
1 ATTTAAGGG-TCAAATTGATATATTATCTAAA
590320 ATTTAAGGGTCAAAT
1 ATTTAAGGGTCAAAT
590335 AAAAAAGTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
30 3 0.08
31 32 0.82
32 4 0.10
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.40
Consensus pattern (31 bp):
ATTTAAGGGTCAAATTGATATATTATCTAAA
Found at i:595934 original size:64 final size:62
Alignment explanation
Indices: 595866--596046 Score: 193
Period size: 64 Copynumber: 2.8 Consensus size: 62
595856 TTGGAACACT
*
595866 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCA-CAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
595930 TGATGCATCGATGCA-TGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCACAAG--TGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * * *
595994 AGAGTGCATCGATGCATAGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCACA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
596047 CAATTAATTC
Statistics
Matches: 98, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
64 54 0.55
65 42 0.43
67 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (62 bp):
TGATGCATCGATGCACAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:596086 original size:65 final size:64
Alignment explanation
Indices: 595888--596095 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 64
595878 GCACCAAGTG
* *
595888 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGAC-TG
595952 -
64 A
* *
595952 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATAGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGACT
596014 GA
63 GA
* * * *
596016 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGACT
596080 GA
63 GA
*
596082 TGCATCGGTGCATG
1 TGCATCGATGCATG
596096 CCTTTGAATA
Statistics
Matches: 123, Mismatches: 10, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
63 10 0.08
64 45 0.37
65 64 0.52
66 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:596286 original size:20 final size:21
Alignment explanation
Indices: 596263--596302 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
596253 GAATCGAATA
596263 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
596283 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
596303 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:597977 original size:21 final size:21
Alignment explanation
Indices: 597921--597984 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
597911 TCAATAAGCC
* *
597921 ATTAGGA-GCTTGAGGATCAGG
1 ATTAGGATG-TTGAGGAACGGG
* **
597942 ATTAGGTTGAGGAGGAACGGG
1 ATTAGGATGTTGAGGAACGGG
597963 ATTAGGATGTTGAGGAACGGG
1 ATTAGGATGTTGAGGAACGGG
597984 A
1 A
597985 GGACGGTTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.42, T:0.22
Consensus pattern (21 bp):
ATTAGGATGTTGAGGAACGGG
Found at i:602416 original size:21 final size:20
Alignment explanation
Indices: 602374--602417 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
602364 TCAAAAGAAG
*
602374 TTTTATGATCATCAATTTTC
1 TTTTATGATCATCAATTATC
602394 TTTTGATGATCATC-ATTGATC
1 TTTT-ATGATCATCAATT-ATC
602415 TTT
1 TTT
602418 GAAAGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTATGATCATCAATTATC
Found at i:602571 original size:22 final size:21
Alignment explanation
Indices: 602529--602568 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
602519 GAGTTTGTTT
*
602529 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
602550 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
602569 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:604563 original size:64 final size:63
Alignment explanation
Indices: 604495--604724 Score: 221
Period size: 64 Copynumber: 3.6 Consensus size: 63
604485 TTGGAACACT
* ***
604495 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
604559 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * * * *
604623 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAAT-TC
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATAGC
*
604686 A
63 C
* *
604687 TCGATGCATCGATGCATGGACTGATGCATCGGTGCATG
1 T-GATGCATCGATGCATGGAGTG-TGCATCGATGCATG
604725 CCTTTGAATA
Statistics
Matches: 138, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
63 4 0.03
64 70 0.51
65 64 0.46
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:604647 original size:19 final size:19
Alignment explanation
Indices: 604623--604673 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
604613 GAAAATATTC
604623 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
604642 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
604661 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
604674 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:604715 original size:65 final size:64
Alignment explanation
Indices: 604517--604724 Score: 230
Period size: 65 Copynumber: 3.2 Consensus size: 64
604507 GCACCAAGTG
* *
604517 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGAC-TG
604581 -
64 A
*
604581 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGACT
604643 GA
63 GA
* * * *
604645 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGACT
604709 GA
63 GA
*
604711 TGCATCGGTGCATG
1 TGCATCGATGCATG
604725 CCTTTGAATA
Statistics
Matches: 125, Mismatches: 8, Indels: 21
0.81 0.05 0.14
Matches are distributed among these distances:
63 10 0.08
64 46 0.37
65 65 0.52
66 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:604915 original size:20 final size:21
Alignment explanation
Indices: 604892--604931 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
604882 GAATCGAATA
604892 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
604912 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
604932 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:611795 original size:14 final size:13
Alignment explanation
Indices: 611761--611804 Score: 63
Period size: 12 Copynumber: 3.4 Consensus size: 13
611751 AATTTAAATT
611761 TATTATTATTATA
1 TATTATTATTATA
611774 -ATTATTATTATA
1 TATTATTATTATA
*
611786 TATTATTTATTAAA
1 TATTA-TTATTATA
611800 TATTA
1 TATTA
611805 CAAAGCCCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 12 0.43
13 4 0.14
14 12 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TATTATTATTATA
Found at i:613076 original size:16 final size:16
Alignment explanation
Indices: 613057--613112 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 16
613047 TTACTTTTTA
613057 TATTTAATTTTAATTT
1 TATTTAATTTTAATTT
613073 TATTT-ATTTTACTCATTGTT
1 TATTTAATTTTA---A-T-TT
613093 TATTTATATTTTAATTT
1 TATTTA-ATTTTAATTT
613110 TAT
1 TAT
613113 ATGTTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 6 0.18
16 5 0.15
17 5 0.15
18 2 0.06
19 2 0.06
20 7 0.21
22 6 0.18
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (16 bp):
TATTTAATTTTAATTT
Found at i:613126 original size:37 final size:36
Alignment explanation
Indices: 613057--613126 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 36
613047 TTACTTTTTA
* * *
613057 TATTTAATTTTAATTTTATTTATTTTACTCATTGTT
1 TATTTAATTTTAATTTTATATATTTAAATCATTGTT
*
613093 TATTTATATTTTAATTTTATATGTTTAAATCATT
1 TATTTA-ATTTTAATTTTATATATTTAAATCATT
613127 ATTTTCATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 6 0.21
37 23 0.79
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (36 bp):
TATTTAATTTTAATTTTATATATTTAAATCATTGTT
Found at i:613311 original size:31 final size:33
Alignment explanation
Indices: 613276--613338 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
613266 ATAATTAAAC
613276 ATTATAAAAATTAT-A-ATTTAGTTTTATTTAA
1 ATTATAAAAATTATAATATTTAGTTTTATTTAA
* * *
613307 ATTATTAAAATTTTAATATTTATTTTTATTTA
1 ATTATAAAAATTATAATATTTAGTTTTATTTA
613339 TTAATATCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 12 0.44
32 1 0.04
33 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (33 bp):
ATTATAAAAATTATAATATTTAGTTTTATTTAA
Found at i:627946 original size:2 final size:2
Alignment explanation
Indices: 627939--627966 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
627929 ATAAACACAA
627939 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
627967 CAAGATCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:631252 original size:2 final size:2
Alignment explanation
Indices: 631245--631324 Score: 115
Period size: 2 Copynumber: 40.0 Consensus size: 2
631235 TAGGCTTACC
* * *
631245 AT AT AT AT AT AT AT GT GT AT AT AT AT AT AT AT GT 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
* *
631287 AT AT AT GT AT AT AT AT AT AT AT GT 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
631325 GTGTTCTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:631268 original size:18 final size:16
Alignment explanation
Indices: 631246--631326 Score: 153
Period size: 16 Copynumber: 5.1 Consensus size: 16
631236 AGGCTTACCA
*
631246 TATATATATATATGTG
1 TATATATATATATATG
631262 TATATATATATATATG
1 TATATATATATATATG
631278 TATATATATATATATG
1 TATATATATATATATG
631294 TATATATATATATATG
1 TATATATATATATATG
631310 TATATATATATATATG
1 TATATATATATATATG
631326 T
1 T
631327 GTTCTTTTCA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 64 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (16 bp):
TATATATATATATATG
Found at i:632227 original size:21 final size:21
Alignment explanation
Indices: 632201--632249 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
632191 TGACTATCGT
632201 ATTGCGATTTCCCAAATTCGC
1 ATTGCGATTTCCCAAATTCGC
* *
632222 ATTGCGATTTTCCTAATTCGC
1 ATTGCGATTTCCCAAATTCGC
*
632243 AATGCGA
1 ATTGCGA
632250 ATATGTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (21 bp):
ATTGCGATTTCCCAAATTCGC
Found at i:632264 original size:20 final size:20
Alignment explanation
Indices: 632239--632325 Score: 102
Period size: 20 Copynumber: 4.3 Consensus size: 20
632229 TTTTCCTAAT
632239 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
* * *
632259 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATAT-GTAAA
* *
632280 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATATGTAAA
* *
632300 TCACAATGCGAATCTGTAAA
1 TCGCAATGCGAATATGTAAA
632320 TCGCAA
1 TCGCAA
632326 CGAGATTCTG
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 38 0.72
21 15 0.28
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:632284 original size:41 final size:40
Alignment explanation
Indices: 632239--632325 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 40
632229 TTTTCCTAAT
* * *
632239 TCGCAATGCGAATATGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCACAACGCGAATCT-GAAAA
* * *
632280 TCGCAATGCGATTACGTAAATCACAATGCGAATCTGTAAA
1 TCGCAATGCGAATACGTAAATCACAACGCGAATCTGAAAA
632320 TCGCAA
1 TCGCAA
632326 CGAGATTCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 10 0.25
41 30 0.75
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCACAACGCGAATCTGAAAA
Found at i:632335 original size:20 final size:20
Alignment explanation
Indices: 632239--632335 Score: 72
Period size: 20 Copynumber: 4.8 Consensus size: 20
632229 TTTTCCTAAT
* * *
632239 TCGCAATGCGAATATGTAAA
1 TCGCAACGCGATTCTGTAAA
*
632259 TCGCAACGCGAATT-TGGAAAA
1 TCGCAACGCG-ATTCT-GTAAA
*
632280 TCGCAATGCGATTAC-GTAAA
1 TCGCAACGCGATT-CTGTAAA
* * *
632300 TCACAATGCGAATCTGTAAA
1 TCGCAACGCGATTCTGTAAA
*
632320 TCGCAACGAGATTCTG
1 TCGCAACGCGATTCTG
632336 ACTATCGCAA
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
19 1 0.02
20 45 0.74
21 15 0.25
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATTCTGTAAA
Found at i:633214 original size:24 final size:24
Alignment explanation
Indices: 633187--633240 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
633177 GTATTCGAAA
633187 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
633211 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
633235 TTTGAT
1 TTTGAT
633241 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:635127 original size:21 final size:20
Alignment explanation
Indices: 635100--635175 Score: 109
Period size: 20 Copynumber: 3.8 Consensus size: 20
635090 CGCAACGTGA
635100 ATATGACTATCGCAACACGG
1 ATATGACTATCGCAACACGG
635120 ACTATGACTATCGCAACACGG
1 A-TATGACTATCGCAACACGG
* *
635141 AAATGACTATCGCAACGCGG
1 ATATGACTATCGCAACACGG
635161 A-ATTGACTATCGCAA
1 ATA-TGACTATCGCAA
635176 TGCGAAATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.02
20 31 0.60
21 20 0.38
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
ATATGACTATCGCAACACGG
Found at i:635184 original size:20 final size:20
Alignment explanation
Indices: 635088--635184 Score: 90
Period size: 20 Copynumber: 4.8 Consensus size: 20
635078 CAACGCGGAA
*
635088 ATCGCAACGTG-AATATGACT
1 ATCGCAACGCGAAAT-TGACT
* * *
635108 ATCGCAACACGGACTATGACT
1 ATCGCAACGCGAAAT-TGACT
*
635129 ATCGCAACACGGAAA-TGACT
1 ATCGCAACGC-GAAATTGACT
*
635149 ATCGCAACGCGGAATTGACT
1 ATCGCAACGCGAAATTGACT
*
635169 ATCGCAATGCGAAATT
1 ATCGCAACGCGAAATT
635185 AAACAAGCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.05
20 42 0.65
21 18 0.28
22 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAATTGACT
Found at i:636707 original size:42 final size:42
Alignment explanation
Indices: 636628--636720 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
636618 CCTCTTCAAC
* * *
636628 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
636670 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
636712 GATGACAGG
1 GATGACAGG
636721 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:637231 original size:20 final size:20
Alignment explanation
Indices: 637208--637266 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
637198 AAATCACAAC
*
637208 GCGAAAATGATTATCGCAAT
1 GCGAAAATGACTATCGCAAT
*
637228 GCGAAAATAACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
**
637248 GCGAATTTGACTATCGCAA
1 GCGAAAATGACTATCGCAA
637267 CGAGAGAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (20 bp):
GCGAAAATGACTATCGCAAT
Found at i:637341 original size:20 final size:20
Alignment explanation
Indices: 637316--637456 Score: 195
Period size: 20 Copynumber: 7.3 Consensus size: 20
637306 TCTTTCGTTA
**
637316 CGATAGTCAAATTCGCATTG
1 CGATAGTCATTTTCGCATTG
637336 CGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
637356 CGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
*
637376 CGATAGTCATTTTTGCATTG
1 CGATAGTCATTTTCGCATTG
*
637396 CGAT--TC--TCTCG--TTG
1 CGATAGTCATTTTCGCATTG
*
637410 CGATAGTCATTTTCGCGTTG
1 CGATAGTCATTTTCGCATTG
637430 CGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
637450 CGATAGT
1 CGATAGT
637457 AAACTATTCT
Statistics
Matches: 108, Mismatches: 7, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
14 7 0.06
16 5 0.05
18 6 0.06
20 90 0.83
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
CGATAGTCATTTTCGCATTG
Found at i:639378 original size:20 final size:20
Alignment explanation
Indices: 639353--639407 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
639343 GCAAAACTTT
*
639353 AAATCGTAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
639373 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
639393 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
639408 TTTGACTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.13
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:639413 original size:20 final size:20
Alignment explanation
Indices: 639364--639424 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
639354 AATCGTAACA
** *
639364 CGAAAATGAAAATCGCAACA
1 CGAAAATGACTATCGCAACG
639384 CGAAAATGACTATCGCAACG
1 CGAAAATGACTATCGCAACG
**
639404 CGAATTTGACTATCGCAACG
1 CGAAAATGACTATCGCAACG
639424 C
1 C
639425 AAGAATCGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.16
Consensus pattern (20 bp):
CGAAAATGACTATCGCAACG
Found at i:639463 original size:33 final size:34
Alignment explanation
Indices: 639395--639467 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
639385 GAAAATGACT
* **
639395 ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
*
639429 ATCGCAACGCGAA-ATGAAAATCGCAATG-ACAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCA-AGA
639462 ATCGCA
1 ATCGCA
639468 TTGCGATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.59
34 13 0.38
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (34 bp):
ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
Found at i:646381 original size:26 final size:26
Alignment explanation
Indices: 646350--646405 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
646340 TGGTTACAAA
* * * *
646350 AAATTGAATGATTAGATTACAATTTT
1 AAATTGAATCATAAAATTAAAATTTT
*
646376 AAATTGAGTCATAAAATTAAAATTTT
1 AAATTGAATCATAAAATTAAAATTTT
646402 AAAT
1 AAAT
646406 CTTATGCACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (26 bp):
AAATTGAATCATAAAATTAAAATTTT
Found at i:656787 original size:28 final size:29
Alignment explanation
Indices: 656755--656836 Score: 114
Period size: 31 Copynumber: 2.8 Consensus size: 29
656745 ATAAGTCCTT
656755 AAACTT-TCTAAAAAA-CAATTATGCCATC
1 AAACTTATC-AAAAAATCAATTATGCCATC
656783 AAACTTAGTCAAAAAAATCAATTATGCCATC
1 AAACTTA-TC-AAAAAATCAATTATGCCATC
656814 AAACTTAGTCAAAAAATCAATTA
1 AAACTTA-TCAAAAAATCAATTA
656837 AGATTATCTA
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
28 6 0.12
30 21 0.42
31 23 0.46
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.27
Consensus pattern (29 bp):
AAACTTATCAAAAAATCAATTATGCCATC
Found at i:656828 original size:30 final size:31
Alignment explanation
Indices: 656764--656836 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
656754 TAAACTTTCT
656764 AAAAAA-CAATTATGCCATCAAACTTAGTCA
1 AAAAAATCAATTATGCCATCAAACTTAGTCA
656794 AAAAAATCAATTATGCCATCAAACTTAGTC-
1 AAAAAATCAATTATGCCATCAAACTTAGTCA
656824 AAAAAATCAATTA
1 AAAAAATCAATTA
656837 AGATTATCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 19 0.45
31 23 0.55
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (31 bp):
AAAAAATCAATTATGCCATCAAACTTAGTCA
Found at i:657468 original size:27 final size:27
Alignment explanation
Indices: 657405--657479 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
657395 ATGTTTTTTA
* *
657405 ATTTTCAAAAAATAAAAA-ATAAAAAAT
1 ATTTTCTAAAAACAAAAATA-AAAAAAT
657432 ATTTTCTAAAAACAAAAATAAAAAAAT
1 ATTTTCTAAAAACAAAAATAAAAAAAT
* * *
657459 ATTTTTTAAAACCAAACATAA
1 ATTTTCTAAAAACAAAAATAA
657480 CATTTTTCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 41 0.98
28 1 0.02
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (27 bp):
ATTTTCTAAAAACAAAAATAAAAAAAT
Found at i:659581 original size:6 final size:6
Alignment explanation
Indices: 659570--659610 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
659560 ATTAAAGATT
659570 AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAA
1 AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAA
659611 AAAGAGAGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
AGGAAG
Found at i:661793 original size:33 final size:32
Alignment explanation
Indices: 661756--661854 Score: 119
Period size: 22 Copynumber: 3.4 Consensus size: 32
661746 CAATCCATAT
661756 TTTAAAATAAATCAATTCATACTAATAAAATTA
1 TTTAAAATAAATCAATTCATACTAAT-AAATTA
661789 TTTAAAATAAATCAA-T--T-C--AT--A-T-
1 TTTAAAATAAATCAATTCATACTAATAAATTA
661811 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
661843 TTTAAAATAAAT
1 TTTAAAATAAAT
661855 TATTTTAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 21
0.73 0.00 0.27
Matches are distributed among these distances:
22 15 0.27
23 2 0.04
24 1 0.02
25 1 0.02
26 1 0.02
27 2 0.04
28 2 0.04
29 1 0.02
30 2 0.04
31 1 0.02
32 13 0.23
33 15 0.27
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (32 bp):
TTTAAAATAAATCAATTCATACTAATAAATTA
Found at i:661810 original size:55 final size:54
Alignment explanation
Indices: 661741--661854 Score: 210
Period size: 55 Copynumber: 2.1 Consensus size: 54
661731 TGTTCTTAAC
661741 TAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAAATTATTTAAAA
1 TAAATCAATCCATATTTTAAAATAAATCAATTCATACTAAT-AAATTATTTAAAA
*
661796 TAAATCAATTCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAA
1 TAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAA
661850 TAAAT
1 TAAAT
661855 TATTTTAAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
54 18 0.31
55 40 0.69
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (54 bp):
TAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAA
Found at i:661863 original size:15 final size:15
Alignment explanation
Indices: 661834--661946 Score: 101
Period size: 15 Copynumber: 7.5 Consensus size: 15
661824 AATTCATACT
661834 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
661848 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
661863 AATAAATCAATCTATATTTAT
1 AAT--A--AAT-TAT-TTTAA
*
661884 AATAATTTA-TTTAA
1 AATAAATTATTTTAA
* *
661898 AGTAAATTATTTTAT
1 AATAAATTATTTTAA
661913 AAT-AA--ATTTTAA
1 AATAAATTATTTTAA
661925 AATAAATTATTTTAA
1 AATAAATTATTTTAA
661940 AATAAAT
1 AATAAAT
661947 AACCTTATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
12 9 0.11
13 2 0.03
14 22 0.28
15 28 0.35
16 2 0.03
17 3 0.04
19 4 0.05
20 3 0.04
21 7 0.09
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:661904 original size:50 final size:47
Alignment explanation
Indices: 661753--661946 Score: 177
Period size: 50 Copynumber: 4.0 Consensus size: 47
661743 AATCAATCCA
*
661753 TATTTTAAAATAAATCAATTCATACTAATAAAATTATTTAAAATAAATCAATT
1 TATTTTAAAATAAATCAATTCATAATAAT-AAATTATTTAAAAT--A--AA-T
*
661806 CATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAAT
1 --TATTTTAAAATAAATCAATTCATAATAATAAATTATTTAAAATAAAT
* *
661855 TATTTTAAAATAAATCAA-TCTATATTTATAATAATTTATTTAAAGTAAAT
1 TATTTTAAAATAAATCAATTC-ATA---ATAATAAATTATTTAAAATAAAT
*
661905 TATTTTATAATAAAT---TT--TAA-AATAAATTATTTTAAAATAAAT
1 TATTTTAAAATAAATCAATTCATAATAATAAATTA-TTTAAAATAAAT
661947 AACCTTATTA
Statistics
Matches: 127, Mismatches: 6, Indels: 25
0.80 0.04 0.16
Matches are distributed among these distances:
41 8 0.06
42 12 0.09
45 2 0.02
46 2 0.02
47 21 0.17
48 1 0.01
49 1 0.01
50 36 0.28
52 1 0.01
54 14 0.11
55 29 0.23
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.43
Consensus pattern (47 bp):
TATTTTAAAATAAATCAATTCATAATAATAAATTATTTAAAATAAAT
Found at i:661930 original size:27 final size:28
Alignment explanation
Indices: 661834--661947 Score: 97
Period size: 27 Copynumber: 3.8 Consensus size: 28
661824 AATTCATACT
*
661834 AATAAATTA-TTTAAAATAAATTATTTTAA
1 AATAAATTATTTTATAATAAA-TA-TTTAA
*
661863 AATAAATCAATCTATATTTATAATAATTTATTTAA
1 AAT--A--AAT-TAT-TTTATAATAA-ATATTTAA
*
661898 AGTAAATTATTTTATAATAAAT-TTTAA
1 AATAAATTATTTTATAATAAATATTTAA
*
661925 AATAAATTATTTTAAAATAAATA
1 AATAAATTATTTTATAATAAATA
661948 ACCTTATTAA
Statistics
Matches: 70, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
27 25 0.36
28 1 0.01
29 13 0.19
30 3 0.04
31 4 0.06
33 4 0.06
34 2 0.03
35 7 0.10
36 11 0.16
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.45
Consensus pattern (28 bp):
AATAAATTATTTTATAATAAATATTTAA
Found at i:662582 original size:23 final size:23
Alignment explanation
Indices: 662556--662599 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
662546 AAACGTTCAA
* * *
662556 TCACTTTTGCAGTCATTGGTGAG
1 TCACATTTGCAATAATTGGTGAG
662579 TCACATTTGCAATAATTGGTG
1 TCACATTTGCAATAATTGGTG
662600 CTAGAATCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (23 bp):
TCACATTTGCAATAATTGGTGAG
Found at i:667284 original size:24 final size:24
Alignment explanation
Indices: 667257--667365 Score: 123
Period size: 24 Copynumber: 4.5 Consensus size: 24
667247 AAACGGAGAT
* *
667257 ATCAAAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
667281 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
667305 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
667329 GTAATG-TATCAGAACAGAATTCA-
1 ATCA-GAAATCAGAACAGAATTCAG
667352 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
667366 TAAAATATTT
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
23 1 0.01
24 68 0.97
25 1 0.01
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:667328 original size:12 final size:12
Alignment explanation
Indices: 667269--667328 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
667259 CAAAAATCAA
667269 AACAGAATTCAG
1 AACAGAATTCAG
*
667281 ATCAG-ATATCAG
1 AACAGAAT-TCAG
*
667293 AACAGAATCCAG
1 AACAGAATTCAG
* *
667305 ATCAGAAATCAG
1 AACAGAATTCAG
667317 AACAGAATTCAG
1 AACAGAATTCAG
667329 GTAATGTATC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 2 0.05
12 34 0.89
13 2 0.05
ACGTcount: A:0.48, C:0.18, G:0.17, T:0.17
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:667339 original size:48 final size:47
Alignment explanation
Indices: 667257--667365 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 47
667247 AAACGGAGAT
* * *
667257 ATCAAAAATCAAAACAGAATTCAGATCAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCA
* *
667304 GATCAGAAATCAGAACAGAATTCAGGTAATG-TATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGATAA-GATATCAGAACAGAATCCA
667352 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
667366 TAAAATATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
47 1 0.02
48 52 0.96
49 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCA
Found at i:675705 original size:4 final size:4
Alignment explanation
Indices: 675696--675751 Score: 98
Period size: 4 Copynumber: 14.5 Consensus size: 4
675686 GTTTGCTAAT
675696 AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG A--G AGGG
1 AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG
675742 AGGG AGGG AG
1 AGGG AGGG AG
675752 AGTTGAGTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
4 48 0.96
ACGTcount: A:0.27, C:0.00, G:0.73, T:0.00
Consensus pattern (4 bp):
AGGG
Found at i:682262 original size:118 final size:118
Alignment explanation
Indices: 682119--682354 Score: 454
Period size: 118 Copynumber: 2.0 Consensus size: 118
682109 ATAATAATTG
*
682119 AGTGATCAAAACATAGACTAAGTAATAAGTGGGTGATCAAATAAGTAGTTTACCCTTAAATCAAT
1 AGTGATCAAAACATAGACCAAGTAATAAGTGGGTGATCAAATAAGTAGTTTACCCTTAAATCAAT
682184 TGAGTCAAGGTTTAATATTAAATCAATATTAATAAAATTGTTGTAGTTTAGGA
66 TGAGTCAAGGTTTAATATTAAATCAATATTAATAAAATTGTTGTAGTTTAGGA
*
682237 AGTGATCAAAACATAGACCAAGTAATAGGTGGGTGATCAAATAAGTAGTTTACCCTTAAATCAAT
1 AGTGATCAAAACATAGACCAAGTAATAAGTGGGTGATCAAATAAGTAGTTTACCCTTAAATCAAT
682302 TGAGTCAAGGTTTAATATTAAATCAATATTAATAAAATTGTTGTAGTTTAGGA
66 TGAGTCAAGGTTTAATATTAAATCAATATTAATAAAATTGTTGTAGTTTAGGA
682355 GTTAGTAAGC
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 116 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (118 bp):
AGTGATCAAAACATAGACCAAGTAATAAGTGGGTGATCAAATAAGTAGTTTACCCTTAAATCAAT
TGAGTCAAGGTTTAATATTAAATCAATATTAATAAAATTGTTGTAGTTTAGGA
Found at i:682608 original size:2 final size:2
Alignment explanation
Indices: 682603--682630 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
682593 ATATGAAGAA
682603 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
682631 CGTATAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:683955 original size:24 final size:24
Alignment explanation
Indices: 683923--683987 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
683913 TTGTTAGGAT
683923 GATGAATTTTTAAAATTTTAAAAG
1 GATGAATTTTTAAAATTTTAAAAG
683947 GATGAATTTTTAAAATTTTAAAAG
1 GATGAATTTTTAAAATTTTAAAAG
* * *
683971 AATAAATTTATAAAATT
1 GATGAATTTTTAAAATT
683988 CTAAGAACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (24 bp):
GATGAATTTTTAAAATTTTAAAAG
Found at i:686817 original size:23 final size:23
Alignment explanation
Indices: 686774--686818 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
686764 ACATATTAGG
**
686774 TAACGCTTATATAATGTAATAGA
1 TAACGCTTATATAATAAAATAGA
*
686797 TAACGTTTATATAATAAAATAG
1 TAACGCTTATATAATAAAATAG
686819 GTATTTAACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.36
Consensus pattern (23 bp):
TAACGCTTATATAATAAAATAGA
Found at i:689105 original size:120 final size:118
Alignment explanation
Indices: 688894--689138 Score: 384
Period size: 120 Copynumber: 2.1 Consensus size: 118
688884 ATTTTCTTCC
*
688894 ATTCTGGATATAAAGTACCGACACAATAAAAACGTGTCGACATAGGTTGTAGACCTATTCGCTAA
1 ATTCTGGACATAAAGTACCGACACAATAAAAACGTGTCGACATAGGTTGTAGACCTATTCGCTAA
*
688959 TAAAACCGGTATACTTATACCAGTTATATTACAAAATTATCTAGTAGATTATA
66 TAAAACCGGTATACTTATACCAGTTATATTACAAAATTATCTAGTACATTATA
* * *
689012 ATTCTGGACATAAAGTACCGACACAAAATTAAAAGGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACAC--AATAAAAACGTGTCGACATAGGTTGTAGACCTATTCGCT
* * *
689077 CAA-AAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATA
64 -AATAAAACCGGTATACTTATACCAGTTATATTACAAAATTATCTAGTACATTATA
689132 ATTCTGG
1 ATTCTGG
689139 GTTCCGATGT
Statistics
Matches: 116, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
118 23 0.20
120 91 0.78
121 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (118 bp):
ATTCTGGACATAAAGTACCGACACAATAAAAACGTGTCGACATAGGTTGTAGACCTATTCGCTAA
TAAAACCGGTATACTTATACCAGTTATATTACAAAATTATCTAGTACATTATA
Found at i:689320 original size:183 final size:183
Alignment explanation
Indices: 689012--689600 Score: 1029
Period size: 183 Copynumber: 3.2 Consensus size: 183
689002 GTAGATTATA
* *
689012 ATTCTGGACATAAAGTACCGACACAAAATTAAAAGGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
*
689077 CAAAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
689142 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
689195 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATAGAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
*
689260 CATAAAACCGGTATATTTATAGCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
689325 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
689378 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
689443 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
* * * * *
689508 CCGATGTTTTTTCAA--TCGACACGTTTTGAAAAGGTATCGACACATATTTCTTCC
131 CCGATG---TGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
689562 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
689601 GAAAACTTTG
Statistics
Matches: 389, Mismatches: 14, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
183 310 0.80
184 75 0.19
186 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (183 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
Found at i:690825 original size:200 final size:200
Alignment explanation
Indices: 690482--691054 Score: 1017
Period size: 200 Copynumber: 2.9 Consensus size: 200
690472 AGTTTGAATG
* * *
690482 TCGACACATTATGGTTGCACCATGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
1 TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
* *
690547 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
66 AAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
690612 TGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATAT
131 TGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATAT
690677 ATGGA
196 ATGGA
*
690682 TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGATACAAACTAC
1 TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
* *
690747 AAAAGTGTCGATACATTAATTAGACCTATTCTCTCATAAAACTGGTATACTTGTACCGGTTAGAT
66 AAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
*
690812 TGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATAT
131 TGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATAT
690877 ATGGA
196 ATGGA
*
690882 TCGACACTTTATTGTTGCAACCTGTTTGCCATTCATTCTGGACC-AAAATATCGACACAAACTAC
1 TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
*
690946 AAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGAT
66 AAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
*
691011 TG-AAAATTACCTA-TACATTATACTTTTGGGTTTCGATGTTTATG
131 TGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATG
691055 ATCTTTATGG
Statistics
Matches: 357, Mismatches: 16, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
197 29 0.08
198 11 0.03
199 83 0.23
200 234 0.66
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (200 bp):
TCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC
AAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
TGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATAT
ATGGA
Found at i:691338 original size:18 final size:18
Alignment explanation
Indices: 691315--691375 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 18
691305 TCTCATTCAT
*
691315 AATTATATTCACATACAA
1 AATTATAATCACATACAA
*
691333 AATTATAAATCGCATACAA
1 AATTAT-AATCACATACAA
**
691352 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
691371 AATTA
1 AATTA
691376 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:691350 original size:19 final size:19
Alignment explanation
Indices: 691326--691375 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
691316 ATTATATTCA
691326 CATACAAAATTATAAATCG
1 CATACAAAATTATAAATCG
*
691345 CATACAAAATTATAAATCT
1 CATACAAAATTATAAATCG
*
691364 TATACAAAATTA
1 CATACAAAATTA
691376 ACCCTACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (19 bp):
CATACAAAATTATAAATCG
Found at i:693085 original size:21 final size:22
Alignment explanation
Indices: 693055--693098 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
693045 TGATCTCCTT
*
693055 CATCCCAGTA-TTATCAACCAC
1 CATCCAAGTATTTATCAACCAC
693076 CATCCAAGTATTTATCAACCAC
1 CATCCAAGTATTTATCAACCAC
693098 C
1 C
693099 CCTTCACCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.34, C:0.36, G:0.05, T:0.25
Consensus pattern (22 bp):
CATCCAAGTATTTATCAACCAC
Found at i:693219 original size:33 final size:33
Alignment explanation
Indices: 693182--693247 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
693172 CATCTTAATA
*
693182 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* * *
693215 TCACCCCTCAACACCTCTATTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
693248 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:693304 original size:21 final size:21
Alignment explanation
Indices: 693279--693343 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
693269 CCCCTTATGC
* *
693279 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
693300 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
693321 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
693342 CT
1 CT
693344 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:695566 original size:20 final size:19
Alignment explanation
Indices: 695520--695566 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
695510 TCCGGTATCG
695520 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
695539 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
695560 TTTTACC
1 TTTTACC
695567 TGTTATATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:695937 original size:182 final size:178
Alignment explanation
Indices: 695487--695957 Score: 672
Period size: 179 Copynumber: 2.6 Consensus size: 178
695477 CGTATTTACG
*
695487 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
695552 TATCATATTTTTACCTGTTATATTGTTGTGGATCGATATATTTTTTTTAAAGTATCGACACATAG
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTTTAAAAGTATCGACACATAG
*
695617 GCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
130 GAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
695666 AAAGTATCGACACTTTCAATATATTCGGTAACATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
695731 TATCATATTTTTACTTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACAC---AT
** * *
695796 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCTTTATATT
128 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * ** *
695848 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
695913 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
695958 AATTTGGATC
Statistics
Matches: 259, Mismatches: 29, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
178 19 0.07
179 97 0.37
181 47 0.18
182 96 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (178 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATAGG
AGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:695971 original size:182 final size:178
Alignment explanation
Indices: 695487--695972 Score: 636
Period size: 182 Copynumber: 2.7 Consensus size: 178
695477 CGTATTTACG
*
695487 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
695552 TATCATATTTTTACCTGTTATATTGTTGTGGATCGATATATTTTT--TTTAAAGTATCGACACAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAATTT---GTATCGACACAT
*
695615 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
128 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
695666 AAAGTATCGACACTTTCAATATATTCGGTAACATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * **
695731 TATCATATTTTTACTTGGTATATCGTTTTGGATCGATACATTTTTTAA-AAGTATCGACACTTTA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTTAATTTGTATCGACAC---A
** * *
695795 TAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCTTTATATT
127 TAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * ** *
695848 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
695913 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTTAATTTGGATCGACAC
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAATTTGTATCGACAC
695973 GAACCGACAA
Statistics
Matches: 266, Mismatches: 33, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
178 10 0.04
179 97 0.36
180 5 0.02
181 54 0.20
182 100 0.38
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (178 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAATTTGTATCGACACATAGG
AGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:697474 original size:24 final size:24
Alignment explanation
Indices: 697432--697479 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
697422 TTAAACAAAC
* *
697432 ATATAAACGAACATGTTCGTGAAT
1 ATATAAACGAACATATTCGCGAAT
697456 ATATAAACAGAA-ATATTCGCGAAT
1 ATATAAAC-GAACATATTCGCGAAT
697480 GATTAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (24 bp):
ATATAAACGAACATATTCGCGAAT
Found at i:698558 original size:26 final size:24
Alignment explanation
Indices: 698496--698558 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
698486 CATTTTAATC
698496 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
698520 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
698543 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
698559 AAATTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:698559 original size:8 final size:8
Alignment explanation
Indices: 698542--698582 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
698532 TTAATATTTC
*
698542 TAATAATA
1 TAATATTA
698550 TAATATTA
1 TAATATTA
698558 TAA-ATT-
1 TAATATTA
698564 TAATATTA
1 TAATATTA
*
698572 TAATAATA
1 TAATATTA
698580 TAA
1 TAA
698583 GATAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 3 0.10
7 6 0.21
8 20 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
TAATATTA
Found at i:698622 original size:22 final size:24
Alignment explanation
Indices: 698578--698639 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
698568 ATTATAATAA
* *
698578 TATAAGATAAT-ATTTTAATATTT
1 TATAAAATAATAATATTAATATTT
698601 TA-AAAATAATAATATTAA-ATTT
1 TATAAAATAATAATATTAATATTT
*
698623 TATAAAATAATATTATT
1 TATAAAATAATAATATT
698640 TATTGTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TATAAAATAATAATATTAATATTT
Found at i:698629 original size:23 final size:23
Alignment explanation
Indices: 698564--698639 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
698554 ATTATAAATT
** *
698564 TAATATTATAATAATATAAGATAA
1 TAATATTA-AATTTTATAAAATAA
*
698588 T-ATTTTAATATTTTA-AAAATAA
1 TAATATTAA-ATTTTATAAAATAA
698610 TAATATTAAATTTTATAAAATAA
1 TAATATTAAATTTTATAAAATAA
*
698633 TATTATT
1 TAATATT
698640 TATTGTATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
22 14 0.33
23 28 0.65
24 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (23 bp):
TAATATTAAATTTTATAAAATAA
Found at i:710654 original size:17 final size:17
Alignment explanation
Indices: 710631--710676 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
710621 TGTGTATGAT
*
710631 GGAATTGAAAGGAATAA
1 GGAATTGAAAGGAAGAA
*
710648 TGAATTGAAAGGAAGAA
1 GGAATTGAAAGGAAGAA
710665 GGAATT-AAAGGA
1 GGAATTGAAAGGA
710677 CAATAGAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.52, C:0.00, G:0.30, T:0.17
Consensus pattern (17 bp):
GGAATTGAAAGGAAGAA
Found at i:711930 original size:29 final size:29
Alignment explanation
Indices: 711857--711958 Score: 149
Period size: 29 Copynumber: 3.7 Consensus size: 29
711847 GTGATATGAG
711857 AATGACATGAGCTACATGAT--CAAGAG-
1 AATGACATGAGCTACATGATCACAAGAGA
*
711883 AATGACACGAGCTACATGATCACAAGAGA
1 AATGACATGAGCTACATGATCACAAGAGA
* *
711912 AATGACATGAACTATATGATCACAAGAGA
1 AATGACATGAGCTACATGATCACAAGAGA
711941 AATGACATGAG-TACATGA
1 AATGACATGAGCTACATGA
711959 ACATATAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 19 0.28
28 12 0.18
29 36 0.54
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.19
Consensus pattern (29 bp):
AATGACATGAGCTACATGATCACAAGAGA
Found at i:714300 original size:103 final size:107
Alignment explanation
Indices: 714113--714326 Score: 337
Period size: 111 Copynumber: 2.0 Consensus size: 107
714103 ATTACAAAAA
*
714113 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAA-TT--ATTA
* *
714178 AATTAAAACGTTAAAATGTTATCGTATCAGCAAAGTGTAGAGATAT
63 AATTAAAAC-TTAAAATGTTACCGTATCAGCAAAGTGTAAAGATAT
714224 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAA-T-TTAAAT
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTATTAAAT
714287 T-AAA-TTAAAATGTTACCGTATCAGCAAAGTGTAAAGATAT
66 TAAAACTTAAAATGTTACCGTATCAGCAAAGTGTAAAGATAT
714327 ATGATTTTCA
Statistics
Matches: 100, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
103 34 0.34
105 3 0.03
106 7 0.07
109 1 0.01
111 55 0.55
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.36
Consensus pattern (107 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTATTAAAT
TAAAACTTAAAATGTTACCGTATCAGCAAAGTGTAAAGATAT
Found at i:714410 original size:17 final size:18
Alignment explanation
Indices: 714390--714423 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
714380 ATTATATTAA
714390 TAAAATA-TTAAATAAAG
1 TAAAATATTTAAATAAAG
714407 TAAAATATTTAAATAAA
1 TAAAATATTTAAATAAA
714424 TTATATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
TAAAATATTTAAATAAAG
Found at i:714877 original size:2 final size:2
Alignment explanation
Indices: 714870--714918 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
714860 TTTATATGTG
714870 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
714912 TA TA TA T
1 TA TA TA T
714919 GATTGTCGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:719721 original size:23 final size:23
Alignment explanation
Indices: 719671--719715 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
719661 CGTCTATTTT
*
719671 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
719694 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
719716 TGTTATTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:720475 original size:16 final size:17
Alignment explanation
Indices: 720454--720487 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
720444 AGGTGTCACA
*
720454 TTGACTT-TTTAAAACT
1 TTGACTTGTTGAAAACT
720470 TTGACTTGTTGAAAACT
1 TTGACTTGTTGAAAACT
720487 T
1 T
720488 ATTGAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
TTGACTTGTTGAAAACT
Found at i:721089 original size:23 final size:22
Alignment explanation
Indices: 721049--721100 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
721039 CACCGAAATG
*
721049 CCACATA-TTTGTCTCGAAGGA
1 CCACATAGTTTGTCCCGAAGGA
721070 CCACATAGGTTTGTCCCGAAGGA
1 CCACATA-GTTTGTCCCGAAGGA
*
721093 CAACATAG
1 CCACATAG
721101 AACCCTCGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 7 0.26
22 1 0.04
23 19 0.70
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (22 bp):
CCACATAGTTTGTCCCGAAGGA
Found at i:722996 original size:21 final size:21
Alignment explanation
Indices: 722972--723014 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
722962 AAAATAATAC
722972 TAAATAAATTGAAGAGAA-AAA
1 TAAATAAATT-AAGAGAACAAA
722993 TAAATAAATTAAGAGAACAAA
1 TAAATAAATTAAGAGAACAAA
723014 T
1 T
723015 GTTAAAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.21
Consensus pattern (21 bp):
TAAATAAATTAAGAGAACAAA
Found at i:725193 original size:106 final size:106
Alignment explanation
Indices: 725065--726463 Score: 2198
Period size: 106 Copynumber: 13.3 Consensus size: 106
725055 ATATTGTTCC
*
725065 GAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
725130 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
725171 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
725236 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
725277 GAGTCCAATATCCTTCGCTGTGAAGTTTAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
725342 CAAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
725383 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
725448 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
725489 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGTGAAGTTGTTTATTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
725554 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
725595 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
725660 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
725701 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAAGTTGTTTATTAACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTGTTGACA
*
725765 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * * *
725807 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGATATGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
725872 CCAGCGGTCCATTCGTCGTGAAATTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
725913 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTCCGAAATTG-GAAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC-TCTGAAATTGAG-AAGTTGTTTGTTGAC
725977 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
726020 GAGTTCAATAT--TTTGC--T---G-TG--A---GCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
726072 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTTCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
726113 GAGTCCAATATTCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
726178 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
726219 GAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
726284 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
726325 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
726390 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
726431 GAGTCCAATATCCTTCGATGTGAAGTTGAAATT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
726464 TGACTCTAAA
Statistics
Matches: 1200, Mismatches: 75, Indels: 36
0.92 0.06 0.03
Matches are distributed among these distances:
93 76 0.06
94 3 0.00
95 3 0.00
97 2 0.00
99 2 0.00
100 2 0.00
101 2 0.00
103 2 0.00
105 4 0.00
106 1030 0.86
107 74 0.06
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:727733 original size:19 final size:18
Alignment explanation
Indices: 727701--727755 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
727691 TTTGTCCCTT
*
727701 TTTCTTTTTCTTTTGTTC
1 TTTCTTTTTCTTTTCTTC
*
727719 TTTCTTTTTTGTTTTCTTC
1 TTTC-TTTTTCTTTTCTTC
727738 TTT-TTTGCTTCTTTTCTT
1 TTTCTTT--TTCTTTTCTT
727756 TTTTTGGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 3 0.10
18 4 0.13
19 24 0.77
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTCTTTTTCTTTTCTTC
Found at i:727734 original size:30 final size:31
Alignment explanation
Indices: 727700--727759 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
727690 TTTTGTCCCT
*
727700 TTTTCTTTTTCTTTTG-TTC-TTTCTTTTTTG
1 TTTTCTTCTT-TTTTGCTTCTTTTCTTTTTTG
727730 TTTTCTTCTTTTTTGCTTCTTTTCTTTTTT
1 TTTTCTTCTTTTTTGCTTCTTTTCTTTTTT
727760 TGGTTTTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 5 0.19
30 12 0.44
31 10 0.37
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (31 bp):
TTTTCTTCTTTTTTGCTTCTTTTCTTTTTTG
Found at i:727742 original size:14 final size:14
Alignment explanation
Indices: 727702--727759 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
727692 TTGTCCCTTT
727702 TTCTTT-TTCTTTTG
1 TTCTTTCTT-TTTTG
727716 TTCTTTCTTTTTTG
1 TTCTTTCTTTTTTG
*
727730 TTTTCTTCTTTTTTG
1 TTCT-TTCTTTTTTG
727745 CTTCTTTTCTTTTTT
1 -TTC-TTTCTTTTTT
727760 TGGTTTTTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
14 14 0.37
15 12 0.32
16 11 0.29
17 1 0.03
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (14 bp):
TTCTTTCTTTTTTG
Found at i:729013 original size:25 final size:25
Alignment explanation
Indices: 728976--729024 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
728966 CATGTTTATA
*
728976 AAAATGCTTAAAATGAATGTAGATGC
1 AAAATGCTAAAAATGAATG-AGATGC
*
729002 AAAATGC-AAAAATGCATGAGATG
1 AAAATGCTAAAAATGAATGAGATG
729025 TTCGAGGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 9 0.43
26 7 0.33
ACGTcount: A:0.49, C:0.08, G:0.20, T:0.22
Consensus pattern (25 bp):
AAAATGCTAAAAATGAATGAGATGC
Found at i:730775 original size:21 final size:21
Alignment explanation
Indices: 730751--730793 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
730741 AAAACAATAC
730751 TAAATAAATTAAAGAGAA-AAA
1 TAAATAAATT-AAGAGAACAAA
730772 TAAATAAATTAAGAGAACAAA
1 TAAATAAATTAAGAGAACAAA
730793 T
1 T
730794 GTTAAAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.21
Consensus pattern (21 bp):
TAAATAAATTAAGAGAACAAA
Found at i:732367 original size:2 final size:2
Alignment explanation
Indices: 732360--732396 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
732350 ATAACACATA
732360 AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
732397 TAAATATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:747421 original size:692 final size:691
Alignment explanation
Indices: 746102--747481 Score: 2643
Period size: 692 Copynumber: 2.0 Consensus size: 691
746092 AGTGGTGTTG
*
746102 GGGGCATTCTAAGAGTTGAGGATGGCTCGGTGGTGGGTTCTTTCCAAGAGGCTGCTGGTCCAGGT
1 GGGGCATTCTAAGAGTTGAGGATGGCTCGGTGGTGGGTTCTTTCCAAGAGGCTGCTAGTCCAGGT
* *
746167 CCTCCTATTTTGATAGAGCTTATGGCAATTAAAAAGGGTTTAACTCTCTTTGCTTTGATTTAGCA
66 CCTCCTATTTTGATAGAGCTTATGGCAATTAAAAAGGGTTTAACTCTCTTTGCTTCGATTCAGCA
*
746232 GCGGTTTAAGGAACGTTTAATTGTTGAATCTGACAGTAAACTAGCAGTGGATTGGGTCAAGAACA
131 GCGGTTTAAGGAACGTTTAATTGTTGAATCTGACAATAAACTAGCAGTGGATTGGGTCAAGAACA
746297 ATGATCGTTGTTCCTATGTCTACGTAGACTTTGTGAAAGACATTGTTACTAAGTTAAGAGGTTTG
196 ATGATCGTTGTTCCTATGTCTACGTAGACTTTGTGAAAGACATTGTTACTAAGTTAAGAGGTTTG
746362 AAGGGTATTATTAGATGGGTTGCTAGGTCAGCCAATGTTGAGGCTGACAACTTAGCTAAGGCTGG
261 AAGGGTATTATTAGATGGGTTGCTAGGTCAGCCAATGTTGAGGCTGACAACTTAGCTAAGGCTGG
746427 TATTGCTAGTTTCACTGTTTTGGTTAGGTTATCGTTTAGGCTTTGGGTTGGTTATTGTAAAGGGA
326 TATTGCTAGTTTCACTGTTTTGGTTAGGTTATCGTTTAGGCTTTGGGTTGGTTATTGTAAAGGGA
746492 GCTTGTATGTTTGTTTCTTAAGAATTATGTAACTTTCGGGTATTAATGAATTATAAAACACTCTT
391 GCTTGTATGTTTGTTTCTTAAGAATTATGTAACTTTCGGGTATTAATGAATTATAAAACACTCTT
*
746557 TTCCTCCTTCCGCTGATTAAGGAGCACCTTGTGATCCATTAATCATGAAGGGGGCTTTTAATGAG
456 TTCATCCTTCCGCTGATTAAGGAGCACCTTGTGATCCATTAATCATGAAGGGGGCTTTTAATGAG
746622 GCCTACCATTCCTATAAAAAAACAATATCTTTCCTAATTTTTTTAACATGATTCATACACAATTT
521 GCCTACCATTCCTATAAAAAAACAATATCTTTCCTAATTTTTTTAACATGATTCATACACAATTT
746687 GCTGTGAAATACAAAAGATTTTTCTAATCAAGTTCTTTCAACCTTTTTCAAGATAAAGGAATTAT
586 GCTGTGAAATACAAAAGATTTTTCTAATCAAGTTCTTTCAACCTTTTTCAAGATAAAGGAATTAT
746752 TCATGAATTCTCATGCGTGATCACTCCACAATAAAATGGTT
651 TCATGAATTCTCATGCGTGATCACTCCACAATAAAATGGTT
746793 GGGGCATTCTAAGAGTTGAGGATGGCTCGGTGGTGGGTTCTTTCCAAGAGGCTGCTAGTCCAGGT
1 GGGGCATTCTAAGAGTTGAGGATGGCTCGGTGGTGGGTTCTTTCCAAGAGGCTGCTAGTCCAGGT
*
746858 CCTCCTATTTTGATAGAGCTTATGGCAATTAAAAAGGGTTTAACTTTCTTTGCTTCGATTCAGCA
66 CCTCCTATTTTGATAGAGCTTATGGCAATTAAAAAGGGTTTAACTCTCTTTGCTTCGATTCAGCA
746923 GCGGTTTAAGGAACGTTTAATTGTTGAATCTGACAATAAACTAGCAGTGGATTGGGTCAAGAACA
131 GCGGTTTAAGGAACGTTTAATTGTTGAATCTGACAATAAACTAGCAGTGGATTGGGTCAAGAACA
*
746988 ATGATCGTTGTTCCTATGTCTACGTAGACTTTGTGAAAGACATTGTTACTAAGTTAAGAGGTTTT
196 ATGATCGTTGTTCCTATGTCTACGTAGACTTTGTGAAAGACATTGTTACTAAGTTAAGAGGTTTG
747053 AAGGGTATTATTAGATGGGTTGCTAGGTCAGCCAATGTTGAGGCTGACAACTTAGCTAAGGCTGG
261 AAGGGTATTATTAGATGGGTTGCTAGGTCAGCCAATGTTGAGGCTGACAACTTAGCTAAGGCTGG
747118 TATTGGCTAGTTTCACTGTTTTGGTTAGGTTATCGTTTAGGCTTTGGGTTGGTTATTGTAAAGGG
326 TATT-GCTAGTTTCACTGTTTTGGTTAGGTTATCGTTTAGGCTTTGGGTTGGTTATTGTAAAGGG
* **
747183 AGCTTGTATGTTTGTTTCTTAAGAATTATGTAACTTTCTGGTATTAATGAATTATAAGGCACTCT
390 AGCTTGTATGTTTGTTTCTTAAGAATTATGTAACTTTCGGGTATTAATGAATTATAAAACACTCT
*
747248 TTTCATCCTTCCGCTGATTAAGGAGCACCTTGTGATCCATTAATCATGAAGGGGGCTTTTAATGG
455 TTTCATCCTTCCGCTGATTAAGGAGCACCTTGTGATCCATTAATCATGAAGGGGGCTTTTAATGA
747313 GGCCTACCATTCCTATAAAAAAACAATATCTTTCCTAATTTTTTTAACATGATTCATACACAATT
520 GGCCTACCATTCCTATAAAAAAACAATATCTTTCCTAATTTTTTTAACATGATTCATACACAATT
*
747378 TGCTGTGAAATACAAAAGATTTTTCTAATCAAGTTCTTTCAACCTTTTTCAGGATAAAGGAATTA
585 TGCTGTGAAATACAAAAGATTTTTCTAATCAAGTTCTTTCAACCTTTTTCAAGATAAAGGAATTA
747443 TTCATGAATTCTCATGCGTGATCACTCCACAATAAAATG
650 TTCATGAATTCTCATGCGTGATCACTCCACAATAAAATG
747482 AGGTAGCTAA
Statistics
Matches: 676, Mismatches: 12, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
691 323 0.48
692 353 0.52
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (691 bp):
GGGGCATTCTAAGAGTTGAGGATGGCTCGGTGGTGGGTTCTTTCCAAGAGGCTGCTAGTCCAGGT
CCTCCTATTTTGATAGAGCTTATGGCAATTAAAAAGGGTTTAACTCTCTTTGCTTCGATTCAGCA
GCGGTTTAAGGAACGTTTAATTGTTGAATCTGACAATAAACTAGCAGTGGATTGGGTCAAGAACA
ATGATCGTTGTTCCTATGTCTACGTAGACTTTGTGAAAGACATTGTTACTAAGTTAAGAGGTTTG
AAGGGTATTATTAGATGGGTTGCTAGGTCAGCCAATGTTGAGGCTGACAACTTAGCTAAGGCTGG
TATTGCTAGTTTCACTGTTTTGGTTAGGTTATCGTTTAGGCTTTGGGTTGGTTATTGTAAAGGGA
GCTTGTATGTTTGTTTCTTAAGAATTATGTAACTTTCGGGTATTAATGAATTATAAAACACTCTT
TTCATCCTTCCGCTGATTAAGGAGCACCTTGTGATCCATTAATCATGAAGGGGGCTTTTAATGAG
GCCTACCATTCCTATAAAAAAACAATATCTTTCCTAATTTTTTTAACATGATTCATACACAATTT
GCTGTGAAATACAAAAGATTTTTCTAATCAAGTTCTTTCAACCTTTTTCAAGATAAAGGAATTAT
TCATGAATTCTCATGCGTGATCACTCCACAATAAAATGGTT
Found at i:747766 original size:18 final size:18
Alignment explanation
Indices: 747743--747779 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
747733 GAAGATAGTT
*
747743 AGACCCGCAAACTATTAA
1 AGACCCACAAACTATTAA
747761 AGACCCACAAACTATTAA
1 AGACCCACAAACTATTAA
747779 A
1 A
747780 TGCATTTTCA
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:0.49, C:0.27, G:0.08, T:0.16
Consensus pattern (18 bp):
AGACCCACAAACTATTAA
Found at i:752975 original size:15 final size:15
Alignment explanation
Indices: 752955--752993 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
752945 CAGATTTTAA
752955 TTTTGAACATTCTCC
1 TTTTGAACATTCTCC
752970 TTTTGAACATTCTCC
1 TTTTGAACATTCTCC
*
752985 TTCTGAACA
1 TTTTGAACA
752994 CCACCCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.08, T:0.44
Consensus pattern (15 bp):
TTTTGAACATTCTCC
Found at i:757466 original size:20 final size:20
Alignment explanation
Indices: 757441--757531 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
757431 TAAATTAAAT
*
757441 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
757461 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
757481 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
757493 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
757513 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
757532 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:757518 original size:52 final size:52
Alignment explanation
Indices: 757440--757587 Score: 271
Period size: 53 Copynumber: 2.8 Consensus size: 52
757430 CTAAATTAAA
*
757440 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
757492 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
757545 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATT
757588 ATGTTGCTAA
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 8 0.09
52 35 0.37
53 51 0.54
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:757571 original size:20 final size:20
Alignment explanation
Indices: 757546--757585 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
757536 TCTATTAGTT
*
757546 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
757566 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
757586 TTATGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:762178 original size:20 final size:20
Alignment explanation
Indices: 762153--762243 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
762143 TAAATTAAAT
*
762153 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
762173 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
762193 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
762205 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
762225 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
762244 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:762230 original size:52 final size:52
Alignment explanation
Indices: 762152--762299 Score: 271
Period size: 53 Copynumber: 2.8 Consensus size: 52
762142 CTAAATTAAA
*
762152 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
762204 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
762257 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATT
762300 ATGTTGCTAA
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 8 0.09
52 35 0.37
53 51 0.54
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:762283 original size:20 final size:20
Alignment explanation
Indices: 762258--762297 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
762248 TCTATTAGTT
*
762258 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
762278 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
762298 TTATGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:769281 original size:127 final size:127
Alignment explanation
Indices: 769055--769299 Score: 382
Period size: 127 Copynumber: 1.9 Consensus size: 127
769045 TGTTAACTCT
* * * *
769055 TGATTCTGCTCATGTATGGGTTAAGCTTTGGCATGTGTCATTGGAGTTATTTTCTCAAAGATGAC
1 TGATTCTGCTCATGCATGGGTTAAGCTTTAGCATGTGCCATTGGAGTTATTTTCTCAAAGAGGAC
* *
769120 TTGGTTATATTGCGAGTGTGCTTGGTAGGCCTTTGTACACAGATAGAGCTACAGGGAGCACC
66 TTGGTTATATTACGAGTGCGCTTGGTAGGCCTTTGTACACAGATAGAGCTACAGGGAGCACC
* * *
769182 TGATTTTGCTCCTGCATGGGTTAAGCTTTAGCGTGTGCCATTGGAGTTATTTTCTCAAAGAGGAC
1 TGATTCTGCTCATGCATGGGTTAAGCTTTAGCATGTGCCATTGGAGTTATTTTCTCAAAGAGGAC
* * *
769247 TTGGTTATATTACGAGTGCGCTTGGTTGGCCTTTGTACACATATCGAGCTACA
66 TTGGTTATATTACGAGTGCGCTTGGTAGGCCTTTGTACACAGATAGAGCTACA
769300 ACATTGAAGA
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
127 106 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.36
Consensus pattern (127 bp):
TGATTCTGCTCATGCATGGGTTAAGCTTTAGCATGTGCCATTGGAGTTATTTTCTCAAAGAGGAC
TTGGTTATATTACGAGTGCGCTTGGTAGGCCTTTGTACACAGATAGAGCTACAGGGAGCACC
Found at i:772574 original size:31 final size:31
Alignment explanation
Indices: 772486--772578 Score: 116
Period size: 31 Copynumber: 3.0 Consensus size: 31
772476 AGGGTCGAGG
* * * *
772486 GTTTACCTATATTCTTCGGGACATATAGATT
1 GTTTAACTATGTTCTTCGGGACATATGGACT
772517 GTTT-ACATATGTTCTTCGGGACATATGGACT
1 GTTTAAC-TATGTTCTTCGGGACATATGGACT
* *
772548 GTTTAACTATGTTCTTCGGAATATATGGACT
1 GTTTAACTATGTTCTTCGGGACATATGGACT
772579 AGTCATTCGG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
30 1 0.02
31 51 0.94
32 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (31 bp):
GTTTAACTATGTTCTTCGGGACATATGGACT
Found at i:777100 original size:31 final size:31
Alignment explanation
Indices: 777062--777186 Score: 178
Period size: 31 Copynumber: 4.0 Consensus size: 31
777052 AGGGTCGAGG
* *
777062 GTTTACCTATATTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
777093 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
777124 ATTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* * * *
777155 GATTACCTAGGTTCTTTGGAACCTATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
777186 G
1 G
777187 GTCATTCATG
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 86 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Done.