Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000389.1 Hibiscus syriacus cultivar Beakdansim tig00000715_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: 2672246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 15
Found at i:530733 original size:19 final size:19
Alignment explanation
Indices: 530668--530816 Score: 218
Period size: 19 Copynumber: 8.1 Consensus size: 19
530658 GCGAAATTAG
*
530668 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
530687 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
530705 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
530721 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
530740 TTTCGCATTGCAATTTTCA
1 TTTCGCATTGCGATTTTCA
*
530759 TTTCGAATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
530778 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
530797 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
530816 T
1 T
530817 CTTTTCCTCT
Statistics
Matches: 117, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
14 6 0.05
16 7 0.06
17 3 0.03
18 4 0.03
19 85 0.73
20 12 0.10
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:531061 original size:20 final size:20
Alignment explanation
Indices: 531036--531087 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
531026 CATTCATTTG
* *
531036 ACTATCGCAATGCGGAATTA
1 ACTATCGCAACGCGGAAATA
*
531056 ACTATCGCAACGCGGAAATG
1 ACTATCGCAACGCGGAAATA
531076 ACTATCGCAACG
1 ACTATCGCAACG
531088 AGAGAATCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (20 bp):
ACTATCGCAACGCGGAAATA
Found at i:531109 original size:33 final size:34
Alignment explanation
Indices: 531059--531140 Score: 94
Period size: 33 Copynumber: 2.3 Consensus size: 34
531049 GGAATTAACT
**
531059 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGA
*
531093 ATCGCAATGC-GAAATGAAAATCGCAACGAGTATGAAA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAG-A-G--A
531130 ATCGCAACGCG
1 ATCGCAACGCG
531141 AATCGCATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
33 18 0.46
34 10 0.26
35 1 0.03
37 10 0.26
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.13
Consensus pattern (34 bp):
ATCGCAACGCGGAAATGAAAATCGCAACGAGAGA
Found at i:531403 original size:20 final size:20
Alignment explanation
Indices: 531378--531432 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
531368 AGACATTCAT
*
531378 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
531398 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
*
531418 ATGACTATCGCAACG
1 TTGACTATCGCAACG
531433 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:531445 original size:345 final size:344
Alignment explanation
Indices: 530799--531468 Score: 1286
Period size: 345 Copynumber: 1.9 Consensus size: 344
530789 GATTTTCATT
* *
530799 TCGCATTGCGATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCTCAATCACAA
1 TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAA
*
530864 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAATGTTGTATTATGTGTA
66 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTA
530929 TATTATGTGTGAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGC
131 TATTATGTGTGAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGC
530994 TATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAACT
196 TATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAACT
531059 ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGT
261 ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGT
531124 ATGAAAATCGCAACGCGAA
326 ATGAAAATCGCAACGCGAA
531143 TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAA
1 TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAA
*
531208 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGTAAACGTTGTATTATGTGTA
66 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTA
531273 TATTATGTGTGAACTTTTAACATTTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTG
131 TATTATGTGTGAACTTTTAACA-TTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTG
*
531338 CTATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTGAC
195 CTATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAAC
531403 TATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAG
260 TATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAG
531468 T
325 T
531469 GAATCGTAAT
Statistics
Matches: 320, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
344 148 0.46
345 172 0.54
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (344 bp):
TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAA
CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTA
TATTATGTGTGAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGC
TATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAACT
ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGT
ATGAAAATCGCAACGCGAA
Found at i:531492 original size:34 final size:33
Alignment explanation
Indices: 531404--531499 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
531394 GGAATTGACT
* **
531404 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
531438 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
531471 ATCGTAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
531500 CGAAATTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:531578 original size:19 final size:19
Alignment explanation
Indices: 531509--531676 Score: 265
Period size: 19 Copynumber: 9.1 Consensus size: 19
531499 GCGAAATTAG
*
531509 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
531528 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
531546 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
531562 TTTCGCATTGCGTTTTTCA
1 TTTCGCATTGCGATTTTCA
531581 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
531600 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
531619 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
531638 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
531657 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
531676 T
1 T
531677 CTTTTCCTCT
Statistics
Matches: 138, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
14 6 0.04
16 7 0.05
17 3 0.02
18 4 0.03
19 106 0.77
20 12 0.09
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:531919 original size:20 final size:20
Alignment explanation
Indices: 531894--531947 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
531884 AGACATTCAT
**
531894 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACACGGAA
531914 TTGACTATCGCAACACGGAA
1 TTGACTATCGCAACACGGAA
*
531934 ATGACTATCGCAAC
1 TTGACTATCGCAAC
531948 GAGAGAATCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (20 bp):
TTGACTATCGCAACACGGAA
Found at i:531977 original size:33 final size:34
Alignment explanation
Indices: 531940--532015 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
531930 GGAAATGACT
531940 ATCGCAACGAGAGAATCGCAATGC-AAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
* *
531973 ATCGCAACGAGTGAATCGTAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
532007 ATCGCAACG
1 ATCGCAACG
532016 CGAAATTAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 22 0.55
34 18 0.45
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:532342 original size:20 final size:20
Alignment explanation
Indices: 532317--532368 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
532307 CATTCATTTG
* *
532317 ACTATCGCAATGTGGAATTA
1 ACTATCGCAACGTGGAAATA
*
532337 ACTATCGCAACGTGGAAATG
1 ACTATCGCAACGTGGAAATA
532357 ACTATCGCAACG
1 ACTATCGCAACG
532369 AGAGAATCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (20 bp):
ACTATCGCAACGTGGAAATA
Found at i:532397 original size:19 final size:18
Alignment explanation
Indices: 532373--532418 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
532363 GCAACGAGAG
532373 AATCGCAATGCGA-AATGAA
1 AATCGCAA--CGAGAATGAA
*
532392 AATCGCAACGAGTATGAA
1 AATCGCAACGAGAATGAA
532410 AATCGCAAC
1 AATCGCAAC
532419 CCGAATCGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 14 0.56
19 8 0.32
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.15
Consensus pattern (18 bp):
AATCGCAACGAGAATGAA
Found at i:532684 original size:20 final size:20
Alignment explanation
Indices: 532659--532713 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
532649 AGACATTCAT
*
532659 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
532679 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
*
532699 ATGACTATCGCAACG
1 TTGACTATCGCAACG
532714 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:532724 original size:14 final size:14
Alignment explanation
Indices: 532705--532792 Score: 50
Period size: 14 Copynumber: 5.5 Consensus size: 14
532695 GGAAATGACT
532705 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
532719 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
*
532738 ATCGCAACGAGTGA
1 ATCGCAACGAGAGA
*
532752 ATCGCAATGCGAAAATGAAA
1 ATCGCAA--CG---A-GAGA
532772 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
532786 ATCGCAA
1 ATCGCAA
532793 TGCGAAATGA
Statistics
Matches: 57, Mismatches: 6, Indels: 22
0.67 0.07 0.26
Matches are distributed among these distances:
14 26 0.46
15 2 0.04
16 4 0.07
17 2 0.04
18 3 0.05
19 11 0.19
20 9 0.16
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:532735 original size:33 final size:33
Alignment explanation
Indices: 532685--532853 Score: 221
Period size: 33 Copynumber: 4.9 Consensus size: 33
532675 GGAATTGACT
* **
532685 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
532719 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
532752 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCG-AAATGAAAATCGCAACGAGAGA
*
532786 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGA
*
532824 ATCGCAATGCTAAATGAAAATCGCAACGAG
1 ATCGCAATGCGAAATGAAAATCGCAACGAG
532854 TATGAAAATC
Statistics
Matches: 122, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
33 47 0.39
34 42 0.34
35 2 0.02
36 2 0.02
37 1 0.01
38 28 0.23
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:532742 original size:19 final size:19
Alignment explanation
Indices: 532718--532873 Score: 165
Period size: 19 Copynumber: 8.7 Consensus size: 19
532708 GCAACGAGAG
532718 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
532737 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
532751 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
532771 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
532785 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
532804 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
532823 AATCGCAATGCTAAATGAA
1 AATCGCAATGCGAAATGAA
*
532842 AATCGCAA--CGAGTATGAA
1 AATCGCAATGCGA-AATGAA
*
532860 AATCGCAACGCGAA
1 AATCGCAATGCGAA
532874 TCGCATTGCA
Statistics
Matches: 115, Mismatches: 8, Indels: 28
0.76 0.05 0.19
Matches are distributed among these distances:
14 18 0.16
15 1 0.01
16 7 0.06
17 4 0.03
18 19 0.17
19 55 0.48
20 11 0.10
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:532793 original size:67 final size:70
Alignment explanation
Indices: 532685--532853 Score: 238
Period size: 67 Copynumber: 2.4 Consensus size: 70
532675 GGAATTGACT
* * **
532685 ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA-CG-A
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAAGCGAA
*
532748 GTG-A
66 ATGAA
532752 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA-GCGA
532817 AATGAAA
65 AATG-AA
*
532824 ATCGCAATGC-TAAATGAAAATCGCAACGAG
1 ATCGCAATGCGAAAATGAAAATCGCAACGAG
532854 TATGAAAATC
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
67 56 0.62
69 2 0.02
70 3 0.03
71 19 0.21
72 11 0.12
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (70 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAAGCGAA
ATGAA
Found at i:533137 original size:20 final size:20
Alignment explanation
Indices: 533112--533163 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
533102 CATTCATTTG
* *
533112 ACTATCGCAATGCGGAATTA
1 ACTATCGCAACGCGGAAATA
* *
533132 ACTATCGCAACGTGGAAATG
1 ACTATCGCAACGCGGAAATA
533152 ACTATCGCAACG
1 ACTATCGCAACG
533164 AGAGAATCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
ACTATCGCAACGCGGAAATA
Found at i:533482 original size:20 final size:20
Alignment explanation
Indices: 533453--533507 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
533443 AGACATTCAT
* *
533453 TTGACGATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
533473 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
*
533493 ATGACTATCGCAACG
1 TTGACTATCGCAACG
533508 AGAGAATCGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:533529 original size:33 final size:32
Alignment explanation
Indices: 533479--533573 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 32
533469 GGAATTGACT
* *
533479 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGA-AATCGCAACGAGAGA
*
533513 ATCGCAATGCGAAATGAAACTCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAA-TCGCAACGAGAGA
*
533546 ATCGTAATGCGAAAATGAAATCGCAACG
1 ATCGCAATGCG-AAATGAAATCGCAACG
533574 CGAAATTAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
32 1 0.02
33 37 0.67
34 17 0.31
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.15
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGAGAGA
Found at i:533530 original size:344 final size:345
Alignment explanation
Indices: 532823--533543 Score: 1390
Period size: 344 Copynumber: 2.1 Consensus size: 345
532813 GCGAAATGAA
*
532823 AATCGCAATGCTAAATGAAAATCGCAACGAGTATGAAAATCGCAACGCGAATCGCATTGCAATTT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGTATGAAAATCGCAACGCGAATCGCATTGCAATTT
532888 TCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAACCGGCTTCACCTTT
66 TCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAACCGGCTTCACCTTT
532953 TGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTATATTATGTGTGAAC
131 TGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTATATTATGTGTGAAC
533018 TTTTAACATTTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGATAAGTTCA
196 TTTTAACATTTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGATAAGTTCA
* *
533083 GTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAACTATCGCAACGTGGA
261 GTTGTTATCACTTATTAGACATTCATTTGACGATCGCAATGCGGAATTAACTATCGCAACGCGGA
533148 AATGACTATCGCAACGAGAG
326 AATGACTATCGCAACGAGAG
533168 AATCGCAATGCGAAATGAAAATCGCAACGAGTATGAAAATCGCAACGCGAATCGCATTGCAATTT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGTATGAAAATCGCAACGCGAATCGCATTGCAATTT
533233 TCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAACCGGCTTCACCTTT
66 TCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAACCGGCTTCACCTTT
533298 TGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTATATTA-GTGTGAAC
131 TGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTATATTATGTGTGAAC
533362 TTTTAACATTTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGATAAGTTCA
196 TTTTAACATTTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGATAAGTTCA
*
533427 GTTGTTATCACTTATTAGACATTCATTTGACGATCGCAATGCGGAATTGACTATCGCAACGCGGA
261 GTTGTTATCACTTATTAGACATTCATTTGACGATCGCAATGCGGAATTAACTATCGCAACGCGGA
533492 AATGACTATCGCAACGAGAG
326 AATGACTATCGCAACGAGAG
*
533512 AATCGCAATGCGAAATGAAACTCGCAACGAGT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGT
533544 GAATCGTAAT
Statistics
Matches: 371, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
344 186 0.50
345 185 0.50
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (345 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGTATGAAAATCGCAACGCGAATCGCATTGCAATTT
TCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAACCGGCTTCACCTTT
TGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTATATTATGTGTGAAC
TTTTAACATTTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGATAAGTTCA
GTTGTTATCACTTATTAGACATTCATTTGACGATCGCAATGCGGAATTAACTATCGCAACGCGGA
AATGACTATCGCAACGAGAG
Found at i:533538 original size:19 final size:18
Alignment explanation
Indices: 533512--533579 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 18
533502 GCAACGAGAG
533512 AATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGA
*
533530 AACTCGCAA--CG-AGTG-
1 AA-TCGCAATGCGAAATGA
*
533545 AATCGTAATGCGAAAATGA
1 AATCGCAATGCG-AAATGA
*
533564 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
533580 TAGTTTCGCG
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 5 0.13
17 2 0.05
18 9 0.23
19 16 0.41
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (18 bp):
AATCGCAATGCGAAATGA
Found at i:533648 original size:19 final size:19
Alignment explanation
Indices: 533583--533712 Score: 198
Period size: 19 Copynumber: 7.1 Consensus size: 19
533573 GCGAAATTAG
*
533583 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
533602 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
533620 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
533636 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
533655 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
533674 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
533693 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
533712 T
1 T
533713 CTTTTCCTCT
Statistics
Matches: 102, Mismatches: 3, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
14 6 0.06
16 7 0.07
17 3 0.03
18 4 0.04
19 70 0.69
20 12 0.12
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:533957 original size:20 final size:20
Alignment explanation
Indices: 533932--533983 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
533922 CATTCATTTG
* *
533932 ACTATCGCAATGCGGAATTA
1 ACTATCGCAACGCGGAAATA
* *
533952 ACTATCACAACGCGGAAATG
1 ACTATCGCAACGCGGAAATA
533972 ACTATCGCAACG
1 ACTATCGCAACG
533984 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAACGCGGAAATA
Found at i:534297 original size:20 final size:20
Alignment explanation
Indices: 534272--534326 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
534262 AGACATTCAT
* *
534272 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCAGAA
534292 TTGACTATCGCAACGCAGAA
1 TTGACTATCGCAACGCAGAA
**
534312 AAGACTATCGCAACG
1 TTGACTATCGCAACG
534327 AGAGAATCGC
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:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (20 bp):
TTGACTATCGCAACGCAGAA
Found at i:534357 original size:33 final size:34
Alignment explanation
Indices: 534318--534393 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
534308 AGAAAAGACT
*
534318 ATCGCAACGAGAGAATCGCAATGC-CAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
* *
534351 ATCGCAACGAGTGAATCGTAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
534385 ATCGCAACG
1 ATCGCAACG
534394 CGAAATTAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 22 0.56
34 17 0.44
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.14
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:534474 original size:19 final size:19
Alignment explanation
Indices: 534403--534550 Score: 209
Period size: 19 Copynumber: 8.1 Consensus size: 19
534393 GCGAAATTAG
*
534403 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
534422 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
534440 -CTCG--TTGCGA-TTTCA
1 TTTCGCATTGCGATTTTCA
534455 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
534474 TTTCGCATTGCAATTTTCA
1 TTTCGCATTGCGATTTTCA
*
534493 TTTCGAATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
534512 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
534531 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
534550 T
1 T
534551 CTTTTCCTCT
Statistics
Matches: 116, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
14 6 0.05
15 4 0.03
16 6 0.05
18 10 0.09
19 78 0.67
20 12 0.10
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:534795 original size:20 final size:20
Alignment explanation
Indices: 534770--534821 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
534760 CATTCATTTG
* *
534770 ACTATCGCAATGCGGAATTA
1 ACTATCGCAACGCGGAAATA
* *
534790 ACTATCGCAACGTGGAAATG
1 ACTATCGCAACGCGGAAATA
534810 ACTATCGCAACG
1 ACTATCGCAACG
534822 AGAGAATCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
ACTATCGCAACGCGGAAATA
Found at i:535093 original size:344 final size:344
Alignment explanation
Indices: 534533--535201 Score: 1277
Period size: 344 Copynumber: 1.9 Consensus size: 344
534523 GATTTTCATT
* *
534533 TCGCATTGCGATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCTCAATCACAA
1 TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAA
*
534598 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAATGTTGTATTATGTGTA
66 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTA
534663 TATTATGTGTGAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGC
131 TATTATGTGTGAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGC
534728 TATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAACT
196 TATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAACT
*
534793 ATCGCAACGTGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGT
261 ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGT
534858 ATGAAAATCGCAACGCGAA
326 ATGAAAATCGCAACGCGAA
534877 TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAA
1 TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAA
534942 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTA
66 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTA
535007 TATTATGTGTGAACTTTTAACATTTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTG
131 TATTATGTGTGAACTTTTAACA-TTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTG
*
535072 CTATGATAAGTTCAG-TGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTGAC
195 CTATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAAC
535136 TATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAG
260 TATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAG
535201 T
325 T
535202 GAATCGTAAT
Statistics
Matches: 319, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
344 262 0.82
345 57 0.18
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (344 bp):
TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAA
CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTA
TATTATGTGTGAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGC
TATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAACT
ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGT
ATGAAAATCGCAACGCGAA
Found at i:535136 original size:20 final size:20
Alignment explanation
Indices: 535111--535165 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
535101 AGACATTCAT
*
535111 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
535131 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
*
535151 ATGACTATCGCAACG
1 TTGACTATCGCAACG
535166 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:535225 original size:34 final size:33
Alignment explanation
Indices: 535137--535232 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
535127 GGAATTGACT
* **
535137 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
535171 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
535204 ATCGTAATGCGAAAATGAAAATAGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
535233 CGAAATTAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:535310 original size:19 final size:19
Alignment explanation
Indices: 535242--535371 Score: 180
Period size: 19 Copynumber: 7.1 Consensus size: 19
535232 GCGAAATTAG
*
535242 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
535261 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
535279 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
535295 TTTCGCATTGCAATTTTCA
1 TTTCGCATTGCGATTTTCA
*
535314 TTTCGAATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
535333 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
535352 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
535371 T
1 T
535372 CTTTTCCTCT
Statistics
Matches: 98, Mismatches: 7, Indels: 11
0.84 0.06 0.09
Matches are distributed among these distances:
14 6 0.06
16 7 0.07
17 3 0.03
18 4 0.04
19 66 0.67
20 12 0.12
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:535613 original size:20 final size:20
Alignment explanation
Indices: 535588--535639 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
535578 CATTCATTTG
* *
535588 ACTATCGCAATGCGGAATTA
1 ACTATCGCAACGCGGAAATA
* *
535608 ACTATCACAACGCGGAAATG
1 ACTATCGCAACGCGGAAATA
535628 ACTATCGCAACG
1 ACTATCGCAACG
535640 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAACGCGGAAATA
Found at i:535668 original size:33 final size:36
Alignment explanation
Indices: 535615--535693 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 36
535605 TTAACTATCA
**
535615 CAACGCGGAAATGACTATCGCAACGAG-A-G-AATCG
1 CAACGC-GAAATGAAAATCGCAACGAGTATGAAATCG
*
535649 CAATGCGAAATGAAAATCGCAACGAGTATGAAATCG
1 CAACGCGAAATGAAAATCGCAACGAGTATGAAATCG
535685 CAACGCGAA
1 CAACGCGAA
535694 TCGCATTGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 18 0.47
34 6 0.16
35 1 0.03
36 13 0.34
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.13
Consensus pattern (36 bp):
CAACGCGAAATGAAAATCGCAACGAGTATGAAATCG
Found at i:535953 original size:20 final size:20
Alignment explanation
Indices: 535928--535982 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
535918 AGACATTCAT
*
535928 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
535948 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
**
535968 AGGACTATCGCAACG
1 TTGACTATCGCAACG
535983 AGAGAATCGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:536013 original size:33 final size:34
Alignment explanation
Indices: 535974--536049 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
535964 GGAAAGGACT
535974 ATCGCAACGAGAGAATCGCAATGC-AAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
*
536007 ATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
536041 ATCGCAACG
1 ATCGCAACG
536050 CGAAATTAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 23 0.56
34 18 0.44
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:536045 original size:20 final size:20
Alignment explanation
Indices: 535987--536054 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
535977 GCAACGAGAG
535987 AATCGCAATGC-AAAATGAA
1 AATCGCAATGCGAAAATGAA
*
536006 AATCGCAA--CG--AGTG--
1 AATCGCAATGCGAAAATGAA
536020 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
*
536040 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
536055 TTAGTTTCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
14 8 0.21
16 5 0.13
17 1 0.03
18 3 0.08
19 8 0.21
20 14 0.36
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Found at i:536127 original size:19 final size:19
Alignment explanation
Indices: 536059--536188 Score: 180
Period size: 19 Copynumber: 7.1 Consensus size: 19
536049 GCGAAATTAG
*
536059 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
536078 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
536096 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
536112 TTTCGCATTGCAATTTTCA
1 TTTCGCATTGCGATTTTCA
*
536131 TTTCGAATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
536150 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
536169 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
536188 T
1 T
536189 CTTTTCCTCT
Statistics
Matches: 98, Mismatches: 7, Indels: 11
0.84 0.06 0.09
Matches are distributed among these distances:
14 6 0.06
16 7 0.07
17 3 0.03
18 4 0.04
19 66 0.67
20 12 0.12
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:536432 original size:20 final size:20
Alignment explanation
Indices: 536407--536458 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
536397 CATTCATTTG
* *
536407 ACTATCGCAATGCGGAATTA
1 ACTATCGCAACGCGGAAATA
* *
536427 ACTATCGCAACGTGGAAATG
1 ACTATCGCAACGCGGAAATA
536447 ACTATCGCAACG
1 ACTATCGCAACG
536459 AGAGAATCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
ACTATCGCAACGCGGAAATA
Found at i:536485 original size:19 final size:18
Alignment explanation
Indices: 536463--536509 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
536453 GCAACGAGAG
*
536463 AATCGCAATGCAAAATGAA
1 AATCGCAACG-AAAATGAA
**
536482 AATCGCAACGAGTATGAA
1 AATCGCAACGAAAATGAA
536500 AATCGCAACG
1 AATCGCAACG
536510 CGAATCGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (18 bp):
AATCGCAACGAAAATGAA
Found at i:536772 original size:20 final size:20
Alignment explanation
Indices: 536747--536801 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
536737 AGACATTCAT
*
536747 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
536767 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
*
536787 ATGACTATCGCAACG
1 TTGACTATCGCAACG
536802 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:536861 original size:34 final size:33
Alignment explanation
Indices: 536773--536868 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
536763 GGAATTGACT
* **
536773 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
536807 ATCGCAATGCGAAATGAAAATTGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
536840 ATCGTAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
536869 TGAAATTAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 29 0.54
34 25 0.46
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:536943 original size:19 final size:19
Alignment explanation
Indices: 536878--537026 Score: 236
Period size: 19 Copynumber: 8.1 Consensus size: 19
536868 GTGAAATTAG
*
536878 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
536897 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
536915 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
536931 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
536950 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
536969 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
536988 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
537007 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
537026 T
1 T
537027 CTTTTCCTCT
Statistics
Matches: 121, Mismatches: 3, Indels: 11
0.90 0.02 0.08
Matches are distributed among these distances:
14 6 0.05
16 7 0.06
17 3 0.02
18 4 0.03
19 89 0.74
20 12 0.10
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:537270 original size:20 final size:20
Alignment explanation
Indices: 537245--537296 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
537235 CATTCATTTG
* *
537245 ACTATCGCAATGCGGAATTA
1 ACTATCGCAACGCGGAAATA
* *
537265 ACTATCACAACGCGGAAATG
1 ACTATCGCAACGCGGAAATA
537285 ACTATCGCAACG
1 ACTATCGCAACG
537297 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAACGCGGAAATA
Found at i:537325 original size:19 final size:19
Alignment explanation
Indices: 537301--537370 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
537291 GCAACGAGAG
537301 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
537320 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
537339 AATCGCAA--CGAGTATGAA
1 AATCGCAATGCGA-AATGAA
*
537357 AATCGCAACGCGAA
1 AATCGCAATGCGAA
537371 TCGCATTGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.07
18 13 0.28
19 27 0.59
20 3 0.07
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:537627 original size:20 final size:20
Alignment explanation
Indices: 537602--537656 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
537592 AGACATTCAT
*
537602 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
537622 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
**
537642 AGGACTATCGCAACG
1 TTGACTATCGCAACG
537657 AGAGAATCGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:537687 original size:33 final size:34
Alignment explanation
Indices: 537648--537723 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
537638 GGAAAGGACT
537648 ATCGCAACGAGAGAATCGCAATGC-AAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
* *
537681 ATCGCAACGAGTGAATCGTAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
537715 ATCGCAACG
1 ATCGCAACG
537724 CGAAATTAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 22 0.55
34 18 0.45
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:537798 original size:19 final size:19
Alignment explanation
Indices: 537733--537880 Score: 209
Period size: 19 Copynumber: 8.1 Consensus size: 19
537723 GCGAAATTAG
*
537733 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
537752 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
537770 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
537786 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
537805 TTTCGCATTGC-AATTTCA
1 TTTCGCATTGCGATTTTCA
*
537823 TTTCGAATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
537842 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
537861 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
537880 T
1 T
537881 CTTTTCCTCT
Statistics
Matches: 115, Mismatches: 7, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
14 6 0.05
16 7 0.06
17 3 0.03
18 20 0.17
19 67 0.58
20 12 0.10
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:537833 original size:37 final size:38
Alignment explanation
Indices: 537733--537880 Score: 191
Period size: 37 Copynumber: 4.0 Consensus size: 38
537723 GCGAAATTAG
* *
537733 TTTCGCGTTGCGATTTTCATTTTCGCATTGCGA--TTCA
1 TTTCGCATTGCGAATTTCA-TTTCGCATTGCGATTTTCA
* *
537770 -CTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGAATTTCATTTCGCATTGCGATTTTCA
*
537805 TTTCGCATTGC-AATTTCATTTCGAATTGCGATTTTCA
1 TTTCGCATTGCGAATTTCATTTCGCATTGCGATTTTCA
*
537842 TTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGAATTTCATTTCGCATTGCGATTTTCA
537880 T
1 T
537881 CTTTTCCTCT
Statistics
Matches: 99, Mismatches: 6, Indels: 11
0.85 0.05 0.09
Matches are distributed among these distances:
33 13 0.13
34 12 0.12
35 4 0.04
36 6 0.06
37 35 0.35
38 29 0.29
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (38 bp):
TTTCGCATTGCGAATTTCATTTCGCATTGCGATTTTCA
Found at i:537844 original size:56 final size:53
Alignment explanation
Indices: 537733--537876 Score: 218
Period size: 56 Copynumber: 2.7 Consensus size: 53
537723 GCGAAATTAG
*
537733 TTTCGCGTTGCGATTTTCATTTTCGCATTGCGA-TTCACTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA-TTTCGCATTGCGATTTCACTCGTTGCGATTTTCA
* *
537786 TTTCGCATTGCGATTTTCATTTCGCATTGCAATTTCATTTCGAATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCA-CTCG--TTGCGATTTTCA
537842 TTTCGCATTGCGATTTTCATTTCGCATTGCGATTT
1 TTTCGCATTGCGATTTTCATTTCGCATTGCGATTT
537877 TCATCTTTTC
Statistics
Matches: 83, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
52 12 0.14
53 22 0.27
54 3 0.04
56 46 0.55
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.47
Consensus pattern (53 bp):
TTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCACTCGTTGCGATTTTCA
Found at i:538125 original size:20 final size:20
Alignment explanation
Indices: 538100--538151 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
538090 CATTCATTTG
* *
538100 ACTATCGCAATGCGGAATTA
1 ACTATCGCAACGCGGAAATA
*
538120 ACTATCGCAACGCGGAAATG
1 ACTATCGCAACGCGGAAATA
538140 ACTATCGCAACG
1 ACTATCGCAACG
538152 AGAGAATCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (20 bp):
ACTATCGCAACGCGGAAATA
Found at i:538173 original size:33 final size:34
Alignment explanation
Indices: 538123--538204 Score: 94
Period size: 33 Copynumber: 2.3 Consensus size: 34
538113 GGAATTAACT
**
538123 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGA
*
538157 ATCGCAATGC-GAAATGAAAATCGCAACGAGTATGAAA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAG-A-G--A
538194 ATCGCAACGCG
1 ATCGCAACGCG
538205 AATCGCATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
33 18 0.46
34 10 0.26
35 1 0.03
37 10 0.26
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.13
Consensus pattern (34 bp):
ATCGCAACGCGGAAATGAAAATCGCAACGAGAGA
Found at i:538395 original size:344 final size:344
Alignment explanation
Indices: 537863--538531 Score: 1277
Period size: 344 Copynumber: 1.9 Consensus size: 344
537853 GATTTTCATT
* *
537863 TCGCATTGCGATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCTCAATCACAA
1 TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAA
*
537928 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAATGTTGTATTATGTGTA
66 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTA
537993 TATTATGTGTGAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGC
131 TATTATGTGTGAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGC
538058 TATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAACT
196 TATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAACT
538123 ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGT
261 ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGT
538188 ATGAAAATCGCAACGCGAA
326 ATGAAAATCGCAACGCGAA
538207 TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATC-AAATCCCAATCACAA
1 TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAA
*
538271 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGTAAACGTTGTATTATGTGTA
66 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTA
538336 TATTATGTGTGAACTTTTAACATTTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTG
131 TATTATGTGTGAACTTTTAACA-TTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTG
*
538401 CTATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTGAC
195 CTATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAAC
538466 TATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAG
260 TATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAG
538531 T
325 T
538532 GAATCGTAAT
Statistics
Matches: 319, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
343 99 0.31
344 220 0.69
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (344 bp):
TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCCCAATCACAA
CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTA
TATTATGTGTGAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGC
TATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAACT
ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGT
ATGAAAATCGCAACGCGAA
Found at i:538466 original size:20 final size:20
Alignment explanation
Indices: 538441--538495 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
538431 AGACATTCAT
*
538441 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
538461 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
*
538481 ATGACTATCGCAACG
1 TTGACTATCGCAACG
538496 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:538555 original size:34 final size:33
Alignment explanation
Indices: 538467--538562 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
538457 GGAATTGACT
* **
538467 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
538501 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
538534 ATCGTAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
538563 CGAAATTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:538641 original size:19 final size:19
Alignment explanation
Indices: 538572--538739 Score: 265
Period size: 19 Copynumber: 9.1 Consensus size: 19
538562 GCGAAATTAG
*
538572 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
538591 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
538609 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
538625 TTTCGCATTGCGTTTTTCA
1 TTTCGCATTGCGATTTTCA
538644 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
538663 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
538682 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
538701 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
538720 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
538739 T
1 T
538740 CTTTTCCTCT
Statistics
Matches: 138, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
14 6 0.04
16 7 0.05
17 3 0.02
18 4 0.03
19 106 0.77
20 12 0.09
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:538983 original size:20 final size:20
Alignment explanation
Indices: 538958--539009 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
538948 CATTCATTTG
* *
538958 ACTATCGCAATGCGGAATTA
1 ACTATCGCAACGCGGAAATA
* *
538978 ACTATCACAACGCGGAAATG
1 ACTATCGCAACGCGGAAATA
538998 ACTATCGCAACG
1 ACTATCGCAACG
539010 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAACGCGGAAATA
Found at i:539038 original size:19 final size:19
Alignment explanation
Indices: 539014--539059 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
539004 GCAACGAGAG
539014 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
539033 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
539052 AATCGCAA
1 AATCGCAA
539060 CGAGTATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:539070 original size:18 final size:17
Alignment explanation
Indices: 539014--539079 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 17
539004 GCAACGAGAG
539014 AATCGCAATGCGAAATGAA
1 AATCGCAA--CGAAATGAA
539033 AATCGCAATGCGAAATGAA
1 AATCGCAA--CGAAATGAA
*
539052 AATCGCAACGAGTATGAA
1 AATCGCAACGA-AATGAA
*
539070 AATCTCAACG
1 AATCGCAACG
539080 CGAATCGCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
17 3 0.07
18 14 0.32
19 27 0.61
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.17
Consensus pattern (17 bp):
AATCGCAACGAAATGAA
Found at i:539343 original size:20 final size:20
Alignment explanation
Indices: 539318--539372 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
539308 AGACATTCAT
*
539318 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
539338 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
**
539358 AGGACTATCGCAACG
1 TTGACTATCGCAACG
539373 AGAGAATCGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:539403 original size:33 final size:34
Alignment explanation
Indices: 539364--539439 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
539354 GGAAAGGACT
539364 ATCGCAACGAGAGAATCGCAATGC-AAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
* *
539397 ATCGCAACGAGTGAATCGTAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
539431 ATCGCAACG
1 ATCGCAACG
539440 CGAAATTAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 22 0.55
34 18 0.45
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:539514 original size:19 final size:19
Alignment explanation
Indices: 539449--539597 Score: 209
Period size: 19 Copynumber: 8.1 Consensus size: 19
539439 GCGAAATTAG
*
539449 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
539468 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
539486 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
539502 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
**
539521 TTTCGCATTGAAATTTTCA
1 TTTCGCATTGCGATTTTCA
*
539540 TTTCGAATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
539559 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
539578 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
539597 T
1 T
539598 CTTTTCCTCT
Statistics
Matches: 115, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
14 6 0.05
16 7 0.06
17 3 0.03
18 4 0.03
19 83 0.72
20 12 0.10
ACGTcount: A:0.17, C:0.20, G:0.16, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:539842 original size:20 final size:20
Alignment explanation
Indices: 539817--539868 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
539807 CATTCATTTG
* *
539817 ACTATCGCAATGCGGAATTA
1 ACTATCGCAACGCGGAAATA
*
539837 ACTATCGCAACGCGGAAATG
1 ACTATCGCAACGCGGAAATA
539857 ACTATCGCAACG
1 ACTATCGCAACG
539869 AGAGAATCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (20 bp):
ACTATCGCAACGCGGAAATA
Found at i:539923 original size:37 final size:33
Alignment explanation
Indices: 539840--539923 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 33
539830 GGAATTAACT
**
539840 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAACGC-GAAATGAAAATCGCAACGAGAGA
* *
539874 ATCGCAATGCGAAATGAAAATCGCAAGGAGTATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAG-A-G--A
539911 ATCGCAACGCGAA
1 ATCGCAACGCGAA
539924 TCGCATTGCA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
33 17 0.41
34 10 0.24
35 1 0.02
37 13 0.32
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:540184 original size:20 final size:20
Alignment explanation
Indices: 540159--540233 Score: 132
Period size: 20 Copynumber: 3.8 Consensus size: 20
540149 AGACATTCAT
*
540159 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
540179 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
540199 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
*
540219 ATGACTATCGCAACG
1 TTGACTATCGCAACG
540234 AGAGAATCGC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:540262 original size:33 final size:34
Alignment explanation
Indices: 540225--540299 Score: 125
Period size: 33 Copynumber: 2.2 Consensus size: 34
540215 GGAAATGACT
540225 ATCGCAACGAGAGAATCGCAATGC-AAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCAAAAATGAAA
* *
540258 ATCGCAACGAGTGAATCGTAATGCAAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCAAAAATGAAA
540292 ATCGCAAC
1 ATCGCAAC
540300 TCGGAATTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 22 0.56
34 17 0.44
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.15
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCAAAAATGAAA
Found at i:540375 original size:19 final size:19
Alignment explanation
Indices: 540310--540439 Score: 189
Period size: 19 Copynumber: 7.1 Consensus size: 19
540300 TCGGAATTAG
*
540310 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
540329 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
540347 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
540363 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
540382 TTTCGAATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
540401 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
540420 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
540439 T
1 T
540440 CTTTTCCTCT
Statistics
Matches: 100, Mismatches: 5, Indels: 11
0.86 0.04 0.09
Matches are distributed among these distances:
14 6 0.06
16 7 0.07
17 3 0.03
18 4 0.04
19 68 0.68
20 12 0.12
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:540681 original size:20 final size:20
Alignment explanation
Indices: 540656--540710 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
540646 AGACATTCAT
*
540656 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
540676 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
*
540696 ATGACTATCGCAACG
1 TTGACTATCGCAACG
540711 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:540770 original size:34 final size:33
Alignment explanation
Indices: 540682--540777 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
540672 GGAATTGACT
* **
540682 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
540716 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
540749 ATCGTAATGCGAAAATGAAAATAGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
540778 CGAAATTAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:540855 original size:19 final size:19
Alignment explanation
Indices: 540787--540916 Score: 180
Period size: 19 Copynumber: 7.1 Consensus size: 19
540777 GCGAAATTAG
*
540787 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
540806 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
540824 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
540840 TTTCGCATTGCAATTTTCA
1 TTTCGCATTGCGATTTTCA
*
540859 TTTCGAATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
540878 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
540897 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
540916 T
1 T
540917 CTTTTCCTCT
Statistics
Matches: 98, Mismatches: 7, Indels: 11
0.84 0.06 0.09
Matches are distributed among these distances:
14 6 0.06
16 7 0.07
17 3 0.03
18 4 0.04
19 66 0.67
20 12 0.12
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:541073 original size:477 final size:477
Alignment explanation
Indices: 540179--541223 Score: 2000
Period size: 477 Copynumber: 2.2 Consensus size: 477
540169 CAATGCGGAA
*
540179 TTGACTATCGCAACGCGGAATTGACTATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGC
1 TTGACTATCGCAATGCGGAATTGACTATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGC
* * * *
540244 AATGCAAAATGAAAATCGCAACGAGTGAATCGTAATGCAAAAATGAAAATCGCAACTCGGAATTA
66 AATGCGAAATGAAAATCGCAACGAGTGAATCGTAATGCAAAAATGAAAATAGCAACGCGAAATTA
540309 GTTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGCATTGC
131 GTTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGCATTGC
*
540374 GATTTTCATTTCGAATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCA
196 AATTTTCATTTCGAATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCA
540439 TCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCTCAATCACAACCGGCTTCACCTTTTGG
261 TCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCTCAATCACAACCGGCTTCACCTTTTGG
540504 GACTGTTAACTTAGGTGATTTTTAAATGCAAATGTTGTATTATGTGTATATTATGTGTGAACTTT
326 GACTGTTAACTTAGGTGATTTTTAAATGCAAATGTTGTATTATGTGTATATTATGTGTGAACTTT
540569 TAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGATAAGTTCAGTTG
391 TAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGATAAGTTCAGTTG
540634 TTATCACTTATTAGACATTCAT
456 TTATCACTTATTAGACATTCAT
540656 TTGACTATCGCAATGCGGAATTGACTATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGC
1 TTGACTATCGCAATGCGGAATTGACTATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGC
*
540721 AATGCGAAATGAAAATCGCAACGAGTGAATCGTAATGCGAAAATGAAAATAGCAACGCGAAATTA
66 AATGCGAAATGAAAATCGCAACGAGTGAATCGTAATGCAAAAATGAAAATAGCAACGCGAAATTA
540786 GTTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGCATTGC
131 GTTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGCATTGC
540851 AATTTTCATTTCGAATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCA
196 AATTTTCATTTCGAATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCA
540916 TCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCTCAATCACAACCGGCTTCACCTTTTGG
261 TCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCTCAATCACAACCGGCTTCACCTTTTGG
540981 GACTGTTAACTTAGGTGATTTTTAAATGCAAATGTTGTATTATGTGTATATTATGTGTGAACTTT
326 GACTGTTAACTTAGGTGATTTTTAAATGCAAATGTTGTATTATGTGTATATTATGTGTGAACTTT
541046 TAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGATAAGTTCAGTTG
391 TAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGATAAGTTCAGTTG
*
541111 TTATCCCTTATTAGACATTCAT
456 TTATCACTTATTAGACATTCAT
* *
541133 TTGACTATCGCAATGCGGAATTAACTATCACAACGCGGAAATGACTATCGCAACGAGAGAATCGC
1 TTGACTATCGCAATGCGGAATTGACTATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGC
541198 AATGCGAAATGAAAATCGCAACGAGT
66 AATGCGAAATGAAAATCGCAACGAGT
541224 ATGAAAATCG
Statistics
Matches: 558, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
477 558 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (477 bp):
TTGACTATCGCAATGCGGAATTGACTATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGC
AATGCGAAATGAAAATCGCAACGAGTGAATCGTAATGCAAAAATGAAAATAGCAACGCGAAATTA
GTTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGCATTGC
AATTTTCATTTCGAATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCA
TCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCTCAATCACAACCGGCTTCACCTTTTGG
GACTGTTAACTTAGGTGATTTTTAAATGCAAATGTTGTATTATGTGTATATTATGTGTGAACTTT
TAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTATGATAAGTTCAGTTG
TTATCACTTATTAGACATTCAT
Found at i:541161 original size:20 final size:20
Alignment explanation
Indices: 541136--541187 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
541126 CATTCATTTG
* *
541136 ACTATCGCAATGCGGAATTA
1 ACTATCGCAACGCGGAAATA
* *
541156 ACTATCACAACGCGGAAATG
1 ACTATCGCAACGCGGAAATA
541176 ACTATCGCAACG
1 ACTATCGCAACG
541188 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAACGCGGAAATA
Found at i:541503 original size:20 final size:20
Alignment explanation
Indices: 541478--541532 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
541468 AGACATTCAT
*
541478 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
541498 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
**
541518 AGGACTATCGCAACG
1 TTGACTATCGCAACG
541533 AGAGAATCGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:541558 original size:345 final size:344
Alignment explanation
Indices: 540899--541568 Score: 1250
Period size: 345 Copynumber: 1.9 Consensus size: 344
540889 GATTTTCATT
* * *
540899 TCGCATTGCGATTTTCATCTTTTCCTCTACCAAAATATGGATCCTCATCAAAATCTCAATCACAA
1 TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGAATCCTCATCAAAATCCCAATCACAA
*
540964 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAATGTTGTATTATGTGTA
66 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTA
541029 TATTATGTGTGAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGC
131 TATTATGTGTGAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGC
*
541094 TATGATAAGTTCAGTTGTTATCCCTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAACT
196 TATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAACT
* *
541159 ATCACAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGT
261 ATCACAACGCGGAAAGGACTATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGAGT
541224 ATGAAAATCGCAACGCGAA
326 ATGAAAATCGCAACGCGAA
541243 TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGAATCCTCATCAAAATCCCAATCACAA
1 TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGAATCCTCATCAAAATCCCAATCACAA
541308 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTA
66 CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTA
541373 TATTATGTGTGAACTTTTAACATTTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTG
131 TATTATGTGTGAACTTTTAACA-TTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTG
*
541438 CTATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTGAC
195 CTATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAAC
*
541503 TATCGCAACGCGGAAAGGACTATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGAG
260 TATCACAACGCGGAAAGGACTATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGAG
541568 T
325 T
541569 GAATCGCAAT
Statistics
Matches: 316, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
344 148 0.47
345 168 0.53
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (344 bp):
TCGCATTGCAATTTTCATCTTTTCCTCTACCAAAATATGAATCCTCATCAAAATCCCAATCACAA
CCGGCTTCACCTTTTGGGACTGTTAACTTAGGTGATTTTTAAATGCAAACGTTGTATTATGTGTA
TATTATGTGTGAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGC
TATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAATGCGGAATTAACT
ATCACAACGCGGAAAGGACTATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGAGT
ATGAAAATCGCAACGCGAA
Found at i:541563 original size:33 final size:34
Alignment explanation
Indices: 541524--541599 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
541514 GGAAAGGACT
541524 ATCGCAACGAGAGAATCGCAATGC-AAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
*
541557 ATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
541591 ATCGCAACG
1 ATCGCAACG
541600 CGAAATTAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 23 0.56
34 18 0.44
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:541595 original size:20 final size:20
Alignment explanation
Indices: 541537--541604 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
541527 GCAACGAGAG
541537 AATCGCAATGC-AAAATGAA
1 AATCGCAATGCGAAAATGAA
*
541556 AATCGCAA--CG--AGTG--
1 AATCGCAATGCGAAAATGAA
541570 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
*
541590 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
541605 TTAGTTTCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
14 8 0.21
16 5 0.13
17 1 0.03
18 3 0.08
19 8 0.21
20 14 0.36
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Found at i:541634 original size:20 final size:19
Alignment explanation
Indices: 541609--541695 Score: 94
Period size: 20 Copynumber: 4.7 Consensus size: 19
541599 GCGAAATTAG
541609 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
541628 TTTTCGCATTGCGA--TTCA
1 -TTTCGCGTTGCGATTTTCA
*
541646 ---CTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
541662 TTTCGCATTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
541681 TTTTCGCGTTGCGAT
1 -TTTCGCGTTGCGAT
541696 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
14 8 0.15
16 4 0.07
18 4 0.07
19 14 0.25
20 25 0.45
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:545287 original size:14 final size:14
Alignment explanation
Indices: 545268--545324 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
545258 TTGAAATGAA
545268 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
545282 AATCGCAACGTGAAATTAA
1 AATCGCAAC--G--A-GAG
545301 AATCGCAACGAGAG
1 AATCGCAACGAGAG
545315 AATCGCAACG
1 AATCGCAACG
545325 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 20 0.59
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:545303 original size:33 final size:33
Alignment explanation
Indices: 545259--545341 Score: 148
Period size: 33 Copynumber: 2.5 Consensus size: 33
545249 GTCTTTTGGT
545259 TGAAATGAAAATCGCAACGAGAGAATCGCAACG
1 TGAAATGAAAATCGCAACGAGAGAATCGCAACG
*
545292 TGAAATTAAAATCGCAACGAGAGAATCGCAACG
1 TGAAATGAAAATCGCAACGAGAGAATCGCAACG
*
545325 CGAAATGAAAATCGCAA
1 TGAAATGAAAATCGCAA
545342 TGCGATTTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
TGAAATGAAAATCGCAACGAGAGAATCGCAACG
Found at i:545339 original size:19 final size:19
Alignment explanation
Indices: 545282--545346 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
545272 GCAACGAGAG
* *
545282 AATCGCAACGTGAAATTAA
1 AATCGCAACGCGAAATGAA
*
545301 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
545315 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
545334 AATCGCAATGCGA
1 AATCGCAACGCGA
545347 TTTTGGTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 9 0.25
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 22 0.61
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:545397 original size:21 final size:20
Alignment explanation
Indices: 545372--545444 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
545362 GTGATTCTTT
545372 TGTTGCGATTTTCATTTCTC
1 TGTTGCGATTTTCATTTCTC
** * *
545392 TCGTTGCGATAGTCATTTTTG
1 T-GTTGCGATTTTCATTTCTC
545413 TGTTGCGATTTTCATTT-TC
1 TGTTGCGATTTTCATTTCTC
*
545432 ATGTTCCGATTTT
1 -TGTTGCGATTTT
545445 AAGTTTAGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 26 0.60
21 16 0.37
ACGTcount: A:0.12, C:0.16, G:0.18, T:0.53
Consensus pattern (20 bp):
TGTTGCGATTTTCATTTCTC
Found at i:546030 original size:20 final size:20
Alignment explanation
Indices: 546005--546215 Score: 156
Period size: 20 Copynumber: 10.4 Consensus size: 20
545995 CTTTAAAAAT
546005 CGCGTTGCAATTTACGGATA
1 CGCGTTGCAATTTACGGATA
* *
546025 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGC-AATTTACGGATA
* * *
546045 TGTCGTTGCGATTTATGGATA
1 CG-CGTTGCAATTTACGGATA
* *
546066 CGCATTGCGATTTACGGATA
1 CGCGTTGCAATTTACGGATA
* * * *
546086 CGCATTGCGATTTACGTATT
1 CGCGTTGCAATTTACGGATA
* * * *
546106 CTCGTTGCGATTTACGTATT
1 CGCGTTGCAATTTACGGATA
* *
546126 CTCGTTGCGATTTACGGATA
1 CGCGTTGCAATTTACGGATA
* *
546146 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGC-AATTTACGGATA
*
546166 TGTCGTTGCAATTTACGGATA
1 CG-CGTTGCAATTTACGGATA
* *
546187 CACGTTGCGATTTTACGGATA
1 CGCGTTGC-AATTTACGGATA
*
546208 CTCGTTGC
1 CGCGTTGC
546216 GATAGTCAGA
Statistics
Matches: 157, Mismatches: 27, Indels: 13
0.80 0.14 0.07
Matches are distributed among these distances:
20 109 0.69
21 48 0.31
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
CGCGTTGCAATTTACGGATA
Found at i:546065 original size:41 final size:41
Alignment explanation
Indices: 546007--546218 Score: 259
Period size: 41 Copynumber: 5.2 Consensus size: 41
545997 TTAAAAATCG
*
546007 CGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
* * * *
546048 CGTTGCGATTTATGGATACGCATTGCGA-TTTACGGATACG-
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT-TGT
* * * * *
546088 CATTGCGATTTACGTATTCTCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
546128 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
* * * **
546169 CGTTGCAATTTACGGATACACGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
546210 CGTTGCGAT
1 CGTTGCGAT
546219 AGTCAGAATC
Statistics
Matches: 143, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
40 62 0.43
41 81 0.57
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
Found at i:546320 original size:42 final size:42
Alignment explanation
Indices: 546212--546320 Score: 98
Period size: 42 Copynumber: 2.6 Consensus size: 42
546202 CGGATACTCG
* * * *
546212 TTGCGA-TAGTCAGAATCGCGTTGCG-ATTTATATGTTCGCG
1 TTGCGATTATTCAAAATCGCGTTGCGAATTTATATGATCGCA
** ** *
546252 TTGCGATTATGGAAAATCGCAATGCGAATTTGTACT-ATCGCA
1 TTGCGATTATTCAAAATCGCGTTGCGAATTTATA-TGATCGCA
*
546294 TTGCGATTATTCATAATCGCGTTGCGA
1 TTGCGATTATTCAAAATCGCGTTGCGA
546321 TTCTGGGAAC
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
40 6 0.12
41 13 0.25
42 32 0.62
43 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (42 bp):
TTGCGATTATTCAAAATCGCGTTGCGAATTTATATGATCGCA
Found at i:546358 original size:20 final size:19
Alignment explanation
Indices: 546309--546362 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
546299 ATTATTCATA
546309 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
546328 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
546349 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
546363 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:547107 original size:21 final size:21
Alignment explanation
Indices: 547082--547140 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
547072 GTTCGAGTTA
*
547082 CCCGCGACAGCCTCAATAGAG
1 CCCGCGACAGCCGCAATAGAG
* * *
547103 TCCGCGACGGCCGCAATAGCG
1 CCCGCGACAGCCGCAATAGAG
547124 CCCGCGAC-GACCGCAAT
1 CCCGCGACAG-CCGCAAT
547141 CACGGTAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.24, C:0.41, G:0.27, T:0.08
Consensus pattern (21 bp):
CCCGCGACAGCCGCAATAGAG
Found at i:558394 original size:60 final size:60
Alignment explanation
Indices: 558283--558424 Score: 155
Period size: 60 Copynumber: 2.4 Consensus size: 60
558273 AACATAATGA
* *
558283 ATAGTCAGATGATCATTTTATAACTTTTAATAGTTGAGACACTCAACAAAATAATTTTCT
1 ATAGTCAGATGATCATTTTATAACTTTTAATAATTGAGACACTAAACAAAATAATTTTCT
* * * * * *
558343 ATAGTCA-ATGAATTATTTTATAACTTTTAGTAATTTAGAGACTAAATAAAATAA-TATCAT
1 ATAGTCAGATG-ATCATTTTATAACTTTTAATAATTGAGACACTAAACAAAATAATTTTC-T
*
558403 ATAATCAG-TGATCATTTATATA
1 ATAGTCAGATGATCATTT-TATA
558425 TTTTACCCAA
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
59 12 0.18
60 56 0.82
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (60 bp):
ATAGTCAGATGATCATTTTATAACTTTTAATAATTGAGACACTAAACAAAATAATTTTCT
Found at i:558946 original size:20 final size:20
Alignment explanation
Indices: 558921--559013 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
558911 TTTTCCCAAT
558921 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* * ** *
558941 TCGCAACGCAAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
558961 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
558982 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
559003 TCGCAATGCGA
1 TCGCAATGCGA
559014 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:558963 original size:41 final size:41
Alignment explanation
Indices: 558918--559013 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
558908 CGATTTTCCC
558918 AATTCGCAATGCGAATAAGTAAATCGCAACGCAAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCAAATTGGGA
*
558959 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCAAATTGGGA
*
559000 AAATCGCAATGCGA
1 AATTCGCAATGCGA
559014 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCAAATTGGGA
Found at i:559026 original size:41 final size:41
Alignment explanation
Indices: 558940--559074 Score: 114
Period size: 41 Copynumber: 3.3 Consensus size: 41
558930 GAATAAGTAA
* * * *
558940 ATCGCAACGCAAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
558981 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
559022 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
559063 TTCGCAACGCGA
1 ATCGCAACGCGA
559075 TACTGACTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
40 4 0.05
41 72 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:559027 original size:20 final size:20
Alignment explanation
Indices: 559002--559095 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
558992 AATTGGGAAA
*
559002 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
559022 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
559043 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
559063 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
559083 TTCGCAACGCGAT
1 ATCGCAACGCGAT
559096 TTATATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:559673 original size:19 final size:19
Alignment explanation
Indices: 559649--559693 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
559639 GCAACGAGAT
*
559649 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
559668 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
559687 AATCGCA
1 AATCGCA
559694 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:559735 original size:20 final size:19
Alignment explanation
Indices: 559689--559854 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
559679 GAAACCAAAA
*
559689 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
559708 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
559727 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
559747 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
559763 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
559780 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
559794 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
559813 TCCGCGTTGTGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
559833 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
559853 TC
1 TC
559855 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.35
20 47 0.40
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:559770 original size:39 final size:39
Alignment explanation
Indices: 559694--559770 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
559684 CAAAATCGCA
* **
559694 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
559733 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
559771 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:559779 original size:33 final size:33
Alignment explanation
Indices: 559742--559829 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
559732 GTTGCGATTT
* *
559742 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
559775 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
559808 TCATTTCCGCGTTGTGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
559830 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 36 0.72
34 14 0.28
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:561937 original size:21 final size:21
Alignment explanation
Indices: 561913--561979 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
561903 TCATTCCTCG
561913 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
561934 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
561955 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
561976 AGAG
1 AGAG
561980 CCCAATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:561937 original size:42 final size:42
Alignment explanation
Indices: 561857--561979 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
561847 GCCCGACTCG
* * * * * * *
561857 CCTATCATCCCTCAAGATTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
561899 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
561941 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
561980 CCCAATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:563355 original size:14 final size:14
Alignment explanation
Indices: 563336--563371 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
563326 ATTGTTTAAT
563336 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
563350 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
563364 TGATTTGT
1 TGATTTGT
563372 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:563596 original size:33 final size:32
Alignment explanation
Indices: 563554--563746 Score: 273
Period size: 33 Copynumber: 5.9 Consensus size: 32
563544 ATTAAATTCG
563554 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
563587 CGTTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
563620 CGTGGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
563653 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
563686 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
563719 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
563747 AGTAATTTCC
Statistics
Matches: 144, Mismatches: 8, Indels: 16
0.86 0.05 0.10
Matches are distributed among these distances:
31 6 0.04
33 132 0.92
35 6 0.04
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.41
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:563643 original size:66 final size:66
Alignment explanation
Indices: 563547--563745 Score: 371
Period size: 66 Copynumber: 3.0 Consensus size: 66
563537 ACGCGAAATT
563547 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
563612 G
66 G
*
563613 AAATTCGCGTGGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
563678 G
66 G
* *
563679 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
563744 G
66 G
563745 A
1 A
563746 TAGTAATTTC
Statistics
Matches: 129, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 129 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:563983 original size:12 final size:12
Alignment explanation
Indices: 563968--563998 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
563958 ATTTTAAAGA
563968 TGATTGCGATTT
1 TGATTGCGATTT
563980 TGATTGCGATTT
1 TGATTGCGATTT
563992 TGATTGC
1 TGATTGC
563999 CTTTTTCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.10, G:0.26, T:0.48
Consensus pattern (12 bp):
TGATTGCGATTT
Found at i:566068 original size:12 final size:12
Alignment explanation
Indices: 566051--566075 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
566041 TCTTCGGGGA
566051 CTTTTTCTTCTT
1 CTTTTTCTTCTT
566063 CTTTTTCTTCTT
1 CTTTTTCTTCTT
566075 C
1 C
566076 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:566284 original size:24 final size:24
Alignment explanation
Indices: 566250--566303 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
566240 CTGAAATATC
* *
566250 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
566274 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
566298 ATCAAA
1 ATCAAA
566304 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:567388 original size:20 final size:20
Alignment explanation
Indices: 567363--567440 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
567353 ATTCATTTGA
567363 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
567383 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
567403 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
567423 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
567441 CGCAATGAGA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:567500 original size:19 final size:19
Alignment explanation
Indices: 567459--567545 Score: 130
Period size: 19 Copynumber: 4.8 Consensus size: 19
567449 GAAATAAAAA
567459 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
567475 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
567492 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
567511 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
567530 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
567546 TCGTTGCGAT
Statistics
Matches: 64, Mismatches: 2, Indels: 7
0.88 0.03 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 3 0.05
19 47 0.73
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:567501 original size:33 final size:33
Alignment explanation
Indices: 567459--567574 Score: 142
Period size: 33 Copynumber: 3.4 Consensus size: 33
567449 GAAATAAAAA
567459 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
567492 TCGCATTGCGATTTTTATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGA--TTT-TCTCG--TTGCGATTTTCATT
***
567530 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
567563 TCGCGTTGCGAT
1 TCGCATTGCGAT
567575 AGTCTGTTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
33 33 0.46
35 7 0.10
36 7 0.10
38 25 0.35
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:569587 original size:19 final size:18
Alignment explanation
Indices: 569561--569666 Score: 85
Period size: 19 Copynumber: 5.9 Consensus size: 18
569551 ACGAAACTTA
569561 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
* *
569579 ACTATCGCAATGCGGAAATGG
1 A-AATCGCAACGC-GAAAT-G
** * *
569600 CTATCGCAATGCAAAATG
1 AAATCGCAACGCGAAATG
*
569618 AAAATCGCAA--CGACA--
1 -AAATCGCAACGCGAAATG
569633 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
569651 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
569667 CACAAATCGC
Statistics
Matches: 71, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
14 9 0.13
16 4 0.06
17 3 0.04
18 18 0.25
19 20 0.28
20 16 0.23
21 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.13
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:569598 original size:20 final size:19
Alignment explanation
Indices: 569563--569618 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
569553 GAAACTTAAA
*
569563 ATCGCAACGCGAAATGACT
1 ATCGCAATGCGAAATGACT
*
569582 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGACT
*
569602 ATCGCAATGCAAAATGA
1 ATCGCAATGCGAAATGA
569619 AAATCGCAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (19 bp):
ATCGCAATGCGAAATGACT
Found at i:569675 original size:19 final size:18
Alignment explanation
Indices: 569633--569677 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
569623 CGCAACGACA
**
569633 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAAAC
569651 AAATCGCAACGCGAAACAC
1 AAATCGCAACGCGAAA-AC
569670 AAATCGCA
1 AAATCGCA
569678 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (18 bp):
AAATCGCAACGCGAAAAC
Found at i:569714 original size:14 final size:14
Alignment explanation
Indices: 569695--569752 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
569685 TTTCATTTCG
569695 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
569709 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
569725 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
569741 CGTTGTGATTTT
1 CGTTGCGATTTT
569753 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:569759 original size:33 final size:33
Alignment explanation
Indices: 569678--569768 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
569668 ACAAATCGCA
569678 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
569711 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
569743 TTGTGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
569769 AGCCATTTAC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:569787 original size:20 final size:19
Alignment explanation
Indices: 569753--569807 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
569743 TTGTGATTTT
*
569753 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
569772 CATTTACGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
569792 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
569808 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:570306 original size:18 final size:18
Alignment explanation
Indices: 570280--570324 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
570270 GTCGATCAGA
*
570280 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
570298 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
570316 TGATGGCTC
1 TGATGGCTC
570325 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:571669 original size:20 final size:20
Alignment explanation
Indices: 571644--571681 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
571634 AATAGTTTCT
571644 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
571664 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
571682 GAGAGAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:571970 original size:22 final size:22
Alignment explanation
Indices: 571945--571988 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
571935 GATTTAGATA
571945 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
571967 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
571989 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:572201 original size:20 final size:20
Alignment explanation
Indices: 572176--572269 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
572166 GATTATGTAT
572176 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
572196 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
572216 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
572237 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
572257 TATCGCATTGCGA
1 TATCGCGTTGCGA
572270 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:572270 original size:20 final size:20
Alignment explanation
Indices: 572156--572270 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
572146 CGCTTTGAAA
*
572156 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
572177 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
572197 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
572217 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
572238 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
572258 ATCGCATTGCGAT
1 ATCGCATTGCGAT
572271 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:572289 original size:41 final size:41
Alignment explanation
Indices: 572198--572332 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
572188 AAAGTCAGTA
* * * ** *
572198 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
572238 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
572280 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
572321 TCGCGTTGCGAT
1 TCGCGTTGCGAT
572333 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:572303 original size:20 final size:20
Alignment explanation
Indices: 572259--572351 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
572249 ATAGTCAGTA
* **
572259 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
572280 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
572300 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
572321 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
572341 TCGCATTGCGA
1 TCGCATTGCGA
572352 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:572333 original size:41 final size:41
Alignment explanation
Indices: 572259--572354 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
572249 ATAGTCAGTA
*
572259 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
572300 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
572341 TCGCATTGCGAATT
1 TCGCATTGCGAATT
572355 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:578987 original size:25 final size:25
Alignment explanation
Indices: 578922--578987 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
578912 AGATTTATCT
578922 CGAAGGACCACGTA-AAATTTGTCC
1 CGAAGGACCACGTAGAAATTTGTCC
** **
578946 CGAATAACCACCCAGAAATTTGTCC
1 CGAAGGACCACGTAGAAATTTGTCC
* *
578971 TGAAGGACCGCGTAGAA
1 CGAAGGACCACGTAGAA
578988 CCCTCGACTC
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
24 10 0.32
25 21 0.68
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (25 bp):
CGAAGGACCACGTAGAAATTTGTCC
Done.