Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007930.1 Hibiscus syriacus cultivar Beakdansim tig00110338_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: 2280901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 12
Found at i:511598 original size:19 final size:19
Alignment explanation
Indices: 511576--511729 Score: 118
Period size: 19 Copynumber: 8.8 Consensus size: 19
511566 GAAACCAAAA
511576 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
511595 TCGCGTTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
511611 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
511628 TCGCATT--G---TTC-TG
1 TCGCATTGCGATTTTCATT
511641 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
**
511658 TCGCATTGCGATTTTGGTT
1 TCGCATTGCGATTTTCATT
**
511677 TCGCATTGCGATTTTGGTT
1 TCGCATTGCGATTTTCATT
* * *
511696 TCTCGTTGCGATTCTCATT
1 TCGCATTGCGATTTTCATT
*
511715 TCGCGTTGCGATTTT
1 TCGCATTGCGATTTT
511730 AAGTTTTCGT
Statistics
Matches: 108, Mismatches: 14, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.02
13 5 0.05
14 9 0.08
16 10 0.09
17 12 0.11
19 70 0.65
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:511623 original size:33 final size:33
Alignment explanation
Indices: 511581--511670 Score: 141
Period size: 30 Copynumber: 2.8 Consensus size: 33
511571 CAAAATCGCA
*
511581 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
511614 TTGCGATTTTCATTTCGCATT--G-TTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
511644 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
511671 TTGGTTTCGC
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
30 28 0.54
31 1 0.02
32 1 0.02
33 22 0.42
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:513804 original size:19 final size:18
Alignment explanation
Indices: 513780--513875 Score: 107
Period size: 19 Copynumber: 5.5 Consensus size: 18
513770 AAAAATGACT
513780 ATCGCAATGCGGAAATGAA
1 ATCGCAATGC-GAAATGAA
513799 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
513818 ATCGCAA--CG--A-GAA
1 ATCGCAATGCGAAATGAA
513831 ATCGC-ATGCG-AATGAAA
1 ATCGCAATGCGAAATG-AA
513848 ATCGCAATGCGGAAATGAA
1 ATCGCAATGC-GAAATGAA
513867 ATCGCAATG
1 ATCGCAATG
513876 AGAGAATCGC
Statistics
Matches: 68, Mismatches: 0, Indels: 18
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.01
13 7 0.10
14 3 0.04
15 2 0.03
16 1 0.01
17 9 0.13
18 10 0.15
19 31 0.46
20 4 0.06
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.16
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:513847 original size:30 final size:32
Alignment explanation
Indices: 513796--513854 Score: 104
Period size: 30 Copynumber: 1.9 Consensus size: 32
513786 ATGCGGAAAT
513796 GAAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAAATCGCAATGCGAAATGAAAATCGCAACGA
513828 GAAATCGC-ATGCG-AATGAAAATCGCAA
1 GAAATCGCAATGCGAAATGAAAATCGCAA
513855 TGCGGAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 14 0.52
31 5 0.19
32 8 0.30
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (32 bp):
GAAATCGCAATGCGAAATGAAAATCGCAACGA
Found at i:513852 original size:49 final size:50
Alignment explanation
Indices: 513780--513892 Score: 160
Period size: 49 Copynumber: 2.2 Consensus size: 50
513770 AAAAATGACT
513780 ATCGCAATGCGGAAATGAAATCGCAATGC-GAAATGAAAATCGCAACGAGA-A
1 ATCGCAATGC-G-AATGAAATCGCAATGCGGAAATG-AAATCGCAACGAGAGA
*
513831 ATCGC-ATGCGAATGAAAATCGCAATGCGGAAATGAAATCGCAATGAGAGA
1 ATCGCAATGCGAATG-AAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
513881 ATCGCAATGCGA
1 ATCGCAATGCGA
513893 TTTTCATTTC
Statistics
Matches: 57, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
48 4 0.07
49 26 0.46
50 16 0.28
51 11 0.19
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (50 bp):
ATCGCAATGCGAATGAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
Found at i:513951 original size:53 final size:52
Alignment explanation
Indices: 513888--514105 Score: 302
Period size: 53 Copynumber: 4.1 Consensus size: 52
513878 AGAATCGCAA
513888 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
513941 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTACGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
513994 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
514052 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
514099 TGCGATT
1 TGCGATT
514106 GTAATTTCCG
Statistics
Matches: 154, Mismatches: 5, Indels: 18
0.87 0.03 0.10
Matches are distributed among these distances:
47 8 0.05
49 2 0.01
50 2 0.01
51 3 0.02
52 9 0.06
53 109 0.71
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.08
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:513968 original size:72 final size:71
Alignment explanation
Indices: 513882--514091 Score: 255
Period size: 72 Copynumber: 2.9 Consensus size: 71
513872 AATGAGAGAA
* * *
513882 TCGCAATGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCA-TTGCGATTCTCTCGTTGCG
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCCG-ATTTGC-ATT-TCGCATTGCG
513945 ATTTTCATT
63 ATTTTCATT
* * * *
513954 TCGCATTGCGATTTTCATTTCCGCATTACGATTCTCTC-GTTGCGATTTTCATTTCGCATTGCGA
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATT-T-TCATTTCCGATTTGCATTTCGCATTGCGA
514018 TTTTCATT
64 TTTTCATT
** *
514026 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-TTCCGATTTGCATTTCGCATTGCGAT
514091 T
65 T
514092 CTCTCGTTGC
Statistics
Matches: 122, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
70 2 0.02
71 1 0.01
72 94 0.77
73 15 0.12
74 8 0.07
75 2 0.02
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.45
Consensus pattern (71 bp):
TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCCGATTTGCATTTCGCATTGCGATT
TTCATT
Found at i:516386 original size:12 final size:12
Alignment explanation
Indices: 516369--516393 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
516359 TCTTCGGGGA
516369 CTTTTTCTTCTT
1 CTTTTTCTTCTT
516381 CTTTTTCTTCTT
1 CTTTTTCTTCTT
516393 C
1 C
516394 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:517324 original size:20 final size:20
Alignment explanation
Indices: 517296--517486 Score: 233
Period size: 20 Copynumber: 9.6 Consensus size: 20
517286 AAATTTCAGT
* * * *
517296 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
517316 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
517336 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
517356 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
517376 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
517396 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
517416 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
517436 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
517456 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
517476 GTTGCGATTTA
1 GTTGCGATTTA
517487 TGTGTTCGCG
Statistics
Matches: 151, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
19 3 0.02
20 146 0.97
21 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:517496 original size:20 final size:20
Alignment explanation
Indices: 517473--517524 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
517463 TTTACGGATA
* *
517473 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTT-TCATATT
*
517493 CGCGTTGTGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
517513 CGCGTTGCGATT
1 CGCGTTGCGATT
517525 CTGGAAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.12, C:0.17, G:0.27, T:0.44
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:517950 original size:21 final size:20
Alignment explanation
Indices: 517924--517962 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
517914 TTAGATAATT
517924 TTTAAAAAATTATTTAAAAAA
1 TTTAAAAAATTA-TTAAAAAA
*
517945 TTTAAAATATTATTAAAA
1 TTTAAAAAATTATTAAAA
517963 TTAAACCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTAAAAAATTATTAAAAAA
Found at i:520759 original size:12 final size:12
Alignment explanation
Indices: 520742--520780 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
520732 CCGTAAAAGA
*
520742 ATGACATGTGTT
1 ATGACACGTGTT
520754 ATGACACACGTGTT
1 ATG--ACACGTGTT
520768 ATGACACGTGTT
1 ATGACACGTGTT
520780 A
1 A
520781 GTATGAACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 13 0.54
14 11 0.46
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.33
Consensus pattern (12 bp):
ATGACACGTGTT
Found at i:520910 original size:15 final size:15
Alignment explanation
Indices: 520890--520919 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
520880 AATTTATAAT
520890 AAATATGTTTTGTTA
1 AAATATGTTTTGTTA
520905 AAATATGTTTTGTTA
1 AAATATGTTTTGTTA
520920 TTTTAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
AAATATGTTTTGTTA
Found at i:521733 original size:10 final size:10
Alignment explanation
Indices: 521705--521734 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
521695 GGACCGGCTG
*
521705 AAAACCGGAA
1 AAAACCGGGA
521715 AAAACCGGGA
1 AAAACCGGGA
521725 AAAACCGGGA
1 AAAACCGGGA
521735 TTTTTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.20, G:0.27, T:0.00
Consensus pattern (10 bp):
AAAACCGGGA
Found at i:522271 original size:14 final size:14
Alignment explanation
Indices: 522252--522278 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
522242 ATTTATTTTT
522252 TAATTATAGTTATA
1 TAATTATAGTTATA
522266 TAATTATAGTTAT
1 TAATTATAGTTAT
522279 TATTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TAATTATAGTTATA
Found at i:523360 original size:14 final size:14
Alignment explanation
Indices: 523341--523400 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
523331 CATTCGGTAA
*
523341 TATGTTCATTTATT
1 TATGTTCATTCATT
*
523355 TATGTTCGTTCATT
1 TATGTTCATTCATT
* *
523369 TA--TTCGTTCGTT
1 TATGTTCATTCATT
* *
523381 TATGTGCGTTCATT
1 TATGTTCATTCATT
523395 TATGTT
1 TATGTT
523401 TAGTCCAATC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
12 11 0.29
14 27 0.71
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (14 bp):
TATGTTCATTCATT
Found at i:523376 original size:12 final size:12
Alignment explanation
Indices: 523359--523397 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
523349 TTTATTTATG
523359 TTCGTTCATTTA
1 TTCGTTCATTTA
*
523371 TTCGTTCGTTTA
1 TTCGTTCATTTA
523383 TGTGCGTTCATTTA
1 T-T-CGTTCATTTA
523397 T
1 T
523398 GTTTAGTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 12 0.52
13 1 0.04
14 10 0.43
ACGTcount: A:0.13, C:0.15, G:0.15, T:0.56
Consensus pattern (12 bp):
TTCGTTCATTTA
Found at i:523610 original size:23 final size:23
Alignment explanation
Indices: 523580--523635 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
523570 ATTCATTTAA
*
523580 GTTCGTTTATGTTCATTTATTGT
1 GTTCGTTTATGTTCACTTATTGT
* *
523603 GTTCGTTTACGTTCGCTTATTGT
1 GTTCGTTTATGTTCACTTATTGT
523626 GTTCGTTTAT
1 GTTCGTTTAT
523636 CATTTAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.11, C:0.12, G:0.20, T:0.57
Consensus pattern (23 bp):
GTTCGTTTATGTTCACTTATTGT
Found at i:524652 original size:20 final size:19
Alignment explanation
Indices: 524627--524696 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
524617 GCGAAGTTCG
524627 CGTTGCGATCCATTCCAAAT
1 CGTTGCGAT-CATTCCAAAT
* * *
524647 CGTTGCGAT-AGTCGAAGTT
1 CGTTGCGATCATTCCAA-AT
524666 CACGTTGCGATTCATTCCAAAT
1 --CGTTGCGA-TCATTCCAAAT
524688 CGTTGCGAT
1 CGTTGCGAT
524697 AGGCGAAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
18 5 0.13
19 2 0.05
20 17 0.44
21 8 0.21
22 2 0.05
23 5 0.13
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.31
Consensus pattern (19 bp):
CGTTGCGATCATTCCAAAT
Found at i:524663 original size:41 final size:41
Alignment explanation
Indices: 524568--524710 Score: 214
Period size: 41 Copynumber: 3.5 Consensus size: 41
524558 GATTCGCAAC
* * *
524568 GCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
* *
524610 GCAATAGGCGAAGTTCGCGTTGCGATCCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
* *
524651 GCGATAGTCGAAGTTCACGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
524692 GCGATAGGCGAAGTTCGCG
1 GCGATAGGCGAAGTTCGCG
524711 AATATTTTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 59 0.66
42 31 0.34
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (41 bp):
GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
Found at i:531181 original size:19 final size:20
Alignment explanation
Indices: 531130--531189 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 20
531120 GATTCCCCTG
531130 TGGGGGAATCGGTTCCCCTTCAA
1 TGGGGG-ATCGGTT-CCC-TCAA
* *
531153 AGGGGAATCGGTTCCCTC-A
1 TGGGGGATCGGTTCCCTCAA
*
531172 TGGGGGATCGATTCCCTC
1 TGGGGGATCGGTTCCCTC
531190 TGCACCAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 16 0.50
20 2 0.06
21 3 0.09
22 7 0.22
23 4 0.12
ACGTcount: A:0.17, C:0.27, G:0.32, T:0.25
Consensus pattern (20 bp):
TGGGGGATCGGTTCCCTCAA
Found at i:537404 original size:20 final size:20
Alignment explanation
Indices: 537375--537426 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
537365 TATTGAAGTA
* *
537375 GTATCAATACTGATATGG-AG
1 GTATCGATACTGAGA-GGAAG
**
537395 GTATCGATACCAAGAGGAAG
1 GTATCGATACTGAGAGGAAG
537415 GTATCGATACTG
1 GTATCGATACTG
537427 TAATTAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (20 bp):
GTATCGATACTGAGAGGAAG
Found at i:537927 original size:28 final size:30
Alignment explanation
Indices: 537858--537928 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
537848 TATTAATATG
* *
537858 TGAATGTGTTATATGTGAAAATGCTTTACA
1 TGAATGTGTTCTATGTGAAAATGCGTTACA
* *
537888 TGAATGTGTTCTATGTGAAGA-G-GTTATA
1 TGAATGTGTTCTATGTGAAAATGCGTTACA
537916 TGAATGTGTTCTA
1 TGAATGTGTTCTA
537929 AATTAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 17 0.46
29 1 0.03
30 19 0.51
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.41
Consensus pattern (30 bp):
TGAATGTGTTCTATGTGAAAATGCGTTACA
Found at i:544787 original size:30 final size:30
Alignment explanation
Indices: 544751--544829 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
544741 TATTAATATG
544751 TGAATGTGTTATATGTGAAAATGCTTTACA
1 TGAATGTGTTATATGTGAAAATGCTTTACA
* * *
544781 TGAATGTGTTCTATGTGAAGATGCTTTATA
1 TGAATGTGTTATATGTGAAAATGCTTTACA
* * *
544811 TGAATATGTTGTACGTGAA
1 TGAATGTGTTATATGTGAA
544830 TAAAATATAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.30, C:0.06, G:0.23, T:0.41
Consensus pattern (30 bp):
TGAATGTGTTATATGTGAAAATGCTTTACA
Found at i:549308 original size:21 final size:21
Alignment explanation
Indices: 549279--549320 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
549269 AGGCGTAAAC
549279 ATAATGTATCGATACTTATTAT
1 ATAATGTATCGATACTT-TTAT
549301 ATAA-GTATCGATACTTTTAT
1 ATAATGTATCGATACTTTTAT
549321 TTCAATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (21 bp):
ATAATGTATCGATACTTTTAT
Found at i:549529 original size:20 final size:20
Alignment explanation
Indices: 549484--549529 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
549474 GTAAACATAA
*
549484 AGTATCGATACTTTTTGTAT
1 AGTATCGATACTTTTAGTAT
*
549504 AGGTATCGATACTTTTAGTCT
1 A-GTATCGATACTTTTAGTAT
549525 AGTAT
1 AGTAT
549530 TCTTCTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (20 bp):
AGTATCGATACTTTTAGTAT
Found at i:549649 original size:199 final size:199
Alignment explanation
Indices: 549191--550901 Score: 1778
Period size: 197 Copynumber: 8.5 Consensus size: 199
549181 TGATACTTAG
* * ** *
549191 AATTTTGAAA-AGTATTACTTTAAAGTAATACATAAATTTACAATGTAAACGGTAAAAATCTACC
1 AATTTTGAAACCG-ATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACC
* * * * * *
549255 GATTTAATGTTAATAGGCGTAAACATAATGTATCGATACTTATTATATAAGTATCGATACTTTTA
65 GGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTA
* * * * * * *
549320 TTTCAATATACATCTCAAACAATTTGCACTCAAAAAAGTATCGAT--ACATGTATAACAAGTATC
130 GTCCAATATTCTTCTC-AATAATTTGCACGC-ACAAAGTATCGATACACATGTAT-A-AAGTATC
** *
549383 GATACTTAT
191 GATACGCAA
*
549392 AATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACAG
1 AATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACCG
549457 GTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAG
66 GTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAG
* *
549522 TCTAGTATTCTTCTCAATAACTTT-CACGCACAAAGTATCGATACACATGTA-ACAAGTATCGAT
131 TCCAATATTCTTCTCAATAA-TTTGCACGCACAAAGTATCGATACACATGTATA-AAGTATCGAT
*
549585 ACACAA
194 ACGCAA
* * * * **
549591 AATTCTGAAACTGATTACTTTAAAGTTATAGGTAAATTTATAATGTCAACATTAAAAGTCTACCG
1 AATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACCG
* * * *
549656 ATTTAATGATAATAGGCGTAAACATAAAGTATCTATAC-CTTTGTATAGGTATTGATACTTTTAG
66 GTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAG
* * * * * **
549720 TCCAACATGT-TTCTGAACAATTTACACGCACAAAGTATCGATACACATGTA-ACATGTATATAT
131 TCCAATAT-TCTTCTCAATAATTTGCACGCACAAAGTATCGATACACATGTATA-AAGTATCGAT
**
549783 ACGTGA
194 ACGCAA
* * *
549789 AATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTCAACAGTAAAAGTCTATCG
1 AATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACCG
* *
549854 GTTTAATGATAATAGGCATAAACATAAAGTATCGATACTTTTTGTATAGGTATCTATACTTTTAG
66 GTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAG
* * * *
549919 TCCAATATGCTTCTCAACAATTT--ACACAGAAAGTATCGATACACATGTA-ACAAGTATCGATA
131 TCCAATATTCTTCTCAATAATTTGCACGCACAAAGTATCGATACACATGTATA-AAGTATCGATA
**
549981 CGCGG
195 CGCAA
* * *
549986 AATTTTAAAACCGATTACTTTAAAGTTATAGGTAAATTTATAA-GTTAACGGTAAAAGTCTACCG
1 AATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACCG
* * * * *
550050 ATTTAATGATAATAGGCGTAAACATCAAGTATTGATACTTTTTGT-TAGATATCGATACTTGTAG
66 GTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAG
* * *
550114 TCCAGTATAT-TTCTCAATAATTTGCACGCACAAAGTATCGATACACATGTATAAAATATCAATA
131 TCCAATAT-TCTTCTCAATAATTTGCACGCACAAAGTATCGATACACATGTATAAAGTATCGATA
**
550178 CGCGG
195 CGCAA
* * * *
550183 ATTTTTGAAACCGATTACTTTAAGGTTATAGGTAAATTTACAATGTAAACGATAAAAGTCTACCA
1 AATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACCG
* *
550248 GTTT-A--AT-ATAGGCGTAAACATCAAA-TATTGATACTTTTAGTATAGGTATCGATACTTTTA
66 GTTTAATGATAATAGGCGTAAACAT-AAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTA
** * * *
550308 GTATAATATGCTTCTCAACAATTTGCACGCACAAAGTATTTCGATACACATATATAAAGTATCGA
130 GTCCAATATTCTTCTCAATAATTTGCACGCACAAAGTA--TCGATACACATGTATAAAGTATCGA
*
550373 AACGCAA
193 TACGCAA
* **
550380 AATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTCAACGGTAAAAGTCTAGTG
1 AATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACCG
* * **
550445 GTTTAATGATAATAGGCGTAAACATCAGGTATCGATACTTTTTGTATAATTATCGATACTTTTTG
66 GTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATAC---TT-
* * *
550510 TATAGGCATCGATACTTTTAGTTCAATATGCTTCTCAACAATTTGCACGCA-AAAGGTATAGATA
127 T-TA-G--TC----C----A-AT--AT-T-CTTCTCAATAATTTGCACGCACAAA-GTATCGATA
* *
550574 CACATGTATAAAGTATCGGTACACAA
174 CACATGTATAAAGTATCGATACGCAA
* * * * *
550600 AATTTCGAAACCGATTACTTAAAAATTATAGGTAAATTTACAATGTCAATGGTAAAAGTCTACCG
1 AATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACCG
* * * * * * * * * *
550665 GTATATTGATAATAGGAGTAAATATCAAGTATTGATACTTTCTATATAAGTATCGATACTTTTAT
66 GTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAG
* * * *
550730 TCCATTATGCTTCTCAAATAATTTGCACGCA-AAATGTATCTATACACATATATAAAGTATCGAT
131 TCCAATATTCTTCTC-AATAATTTGCACGCACAAA-GTATCGATACACATGTATAAAGTATCGAT
** *
550794 ACTTAT
194 ACGCAA
* * * * *
550800 AATTTCGAAA-TGTATTACTGT-AAGGTACTAGGTTAATTTACAATG-AAACGGTAAAAGTCTAC
1 AATTTTGAAACCG-ATTACTTTAAAGTTA-TAGGTAAATTTACAATGTAAACGGTAAAAGTCTAC
* * * * *
550862 AGGTATAATGATAATAGACATAAACATCAAGTATCGATAC
64 CGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATAC
550902 ACATGTATAA
Statistics
Matches: 1290, Mismatches: 172, Indels: 98
0.83 0.11 0.06
Matches are distributed among these distances:
194 29 0.02
195 87 0.07
196 59 0.05
197 247 0.19
198 194 0.15
199 223 0.17
200 88 0.07
201 177 0.14
202 1 0.00
203 2 0.00
204 3 0.00
205 1 0.00
206 2 0.00
207 1 0.00
208 1 0.00
209 1 0.00
212 2 0.00
215 2 0.00
216 1 0.00
217 3 0.00
218 1 0.00
220 138 0.11
221 3 0.00
222 24 0.02
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (199 bp):
AATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACCG
GTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAG
TCCAATATTCTTCTCAATAATTTGCACGCACAAAGTATCGATACACATGTATAAAGTATCGATAC
GCAA
Found at i:550500 original size:21 final size:21
Alignment explanation
Indices: 550473--550528 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
550463 TAAACATCAG
550473 GTATCGATACTTTTTGTATAA
1 GTATCGATACTTTTTGTATAA
* *
550494 TTATCGATACTTTTTGTATAG
1 GTATCGATACTTTTTGTATAA
*
550515 GCATCGATACTTTT
1 GTATCGATACTTTT
550529 AGTTCAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.48
Consensus pattern (21 bp):
GTATCGATACTTTTTGTATAA
Found at i:550661 original size:220 final size:221
Alignment explanation
Indices: 550277--550728 Score: 658
Period size: 220 Copynumber: 2.0 Consensus size: 221
550267 ATCAAATATT
*
550277 GATACTTTTAGTATAGGTATCGATACTTTTAGTATAATATGCTTCTCAACAATTTGCACGCACAA
1 GATACTTTTAGTATAGGCATCGATACTTTTAGTATAATATGCTTCTCAACAATTTGCACGCACAA
* * * * *
550342 AGTATTTCGATACACATATATAAAGTATCGAAACGCAAAATTTTGAAACCGATTACTTTAAAGTT
66 AGTA-TTAGATACACATATATAAAGTATCGAAACACAAAATTTCGAAACCGATTACTTAAAAATT
** * *
550407 ATAGGTAAATTTACAATGTCAACGGTAAAAGTCTAGTGGTTTAATGATAATAGGCGTAAACATCA
130 ATAGGTAAATTTACAATGTCAACGGTAAAAGTCTACCGGTATAATGATAATAGGAGTAAACATCA
* * * *
550472 GGTATCGATACTTTTTGTATAATTATC
195 AGTATCGATACTTTCTATATAAGTATC
*
550499 GATACTTTTTGTATAGGCATCGATACTTTTAGT-TCAATATGCTTCTCAACAATTTGCACGCA-A
1 GATACTTTTAGTATAGGCATCGATACTTTTAGTAT-AATATGCTTCTCAACAATTTGCACGCACA
* **
550562 AAGGTA-TAGATACACATGTATAAAGTATCGGTACACAAAATTTCGAAACCGATTACTTAAAAAT
65 AA-GTATTAGATACACATATATAAAGTATCGAAACACAAAATTTCGAAACCGATTACTTAAAAAT
* * *
550626 TATAGGTAAATTTACAATGTCAATGGTAAAAGTCTACCGGTATATTGATAATAGGAGTAAATATC
129 TATAGGTAAATTTACAATGTCAACGGTAAAAGTCTACCGGTATAATGATAATAGGAGTAAACATC
*
550691 AAGTATTGATACTTTCTATATAAGTATC
194 AAGTATCGATACTTTCTATATAAGTATC
550719 GATACTTTTA
1 GATACTTTTA
550729 TTCCATTATG
Statistics
Matches: 205, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
220 140 0.68
221 4 0.02
222 61 0.30
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (221 bp):
GATACTTTTAGTATAGGCATCGATACTTTTAGTATAATATGCTTCTCAACAATTTGCACGCACAA
AGTATTAGATACACATATATAAAGTATCGAAACACAAAATTTCGAAACCGATTACTTAAAAATTA
TAGGTAAATTTACAATGTCAACGGTAAAAGTCTACCGGTATAATGATAATAGGAGTAAACATCAA
GTATCGATACTTTCTATATAAGTATC
Found at i:550715 original size:21 final size:22
Alignment explanation
Indices: 550686--550726 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
550676 ATAGGAGTAA
*
550686 ATATCAAGTATTGATACTTTCT
1 ATATCAAGTATCGATACTTTCT
550708 ATAT-AAGTATCGATACTTT
1 ATATCAAGTATCGATACTTT
550727 TATTCCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (22 bp):
ATATCAAGTATCGATACTTTCT
Found at i:550841 original size:200 final size:197
Alignment explanation
Indices: 550495--550901 Score: 489
Period size: 199 Copynumber: 2.0 Consensus size: 197
550485 TTTGTATAAT
* * *
550495 TATCGATACTTTTTGTATAGGCATCGATACTTTTAGTTCAATATGCTTCTCAACAATTTGCACGC
1 TATCGATACTTTCTATATAAGCATCGATACTTTTAGTTCAATATGCTTCTCAACAATTTGCACGC
* *
550560 AAAAGGTATAGATACACATGTATAAAGTATCGGTACACAAAATTTCGAAACCGATTACTTAAAAA
66 AAAAGGTATAGATACACATATATAAAGTATCGATACACAAAATTTCGAAACCGATTACTT-AAAA
* * * * * * *
550625 TTATAGGTAAATTTACAATGTCAATGGTAAAAGTCTACCGGTATATTGATAATAGGA-GTAAATA
130 GTATAGGTAAATTTACAATG-AAACGGTAAAAGTCTACAGGTATAATGATAATA-GACATAAACA
550689 TCAAG
193 TCAAG
* * * *
550694 TATTGATACTTTCTATATAAGTATCGATACTTTTA-TTCCATTATGCTTCTCAAATAATTTGCAC
1 TATCGATACTTTCTATATAAGCATCGATACTTTTAGTT-CAATATGCTTCTC-AACAATTTGCAC
* ** ** * *
550758 GCAAAATGTATCTATACACATATATAAAGTATCGATACTTATAATTTCGAAA-TGTATTACTGT-
64 GCAAAAGGTATAGATACACATATATAAAGTATCGATACACAAAATTTCGAAACCG-ATTACT-TA
* *
550821 AAGGTACTAGGTTAATTTACAATGAAACGGTAAAAGTCTACAGGTATAATGATAATAGACATAAA
127 AAAGTA-TAGGTAAATTTACAATGAAACGGTAAAAGTCTACAGGTATAATGATAATAGACATAAA
550886 CATCAAG
191 CATCAAG
550893 TATCGATAC
1 TATCGATAC
550902 ACATGTATAA
Statistics
Matches: 176, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
198 4 0.02
199 94 0.53
200 77 0.44
201 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (197 bp):
TATCGATACTTTCTATATAAGCATCGATACTTTTAGTTCAATATGCTTCTCAACAATTTGCACGC
AAAAGGTATAGATACACATATATAAAGTATCGATACACAAAATTTCGAAACCGATTACTTAAAAG
TATAGGTAAATTTACAATGAAACGGTAAAAGTCTACAGGTATAATGATAATAGACATAAACATCA
AG
Found at i:551285 original size:118 final size:116
Alignment explanation
Indices: 551114--551505 Score: 324
Period size: 118 Copynumber: 3.4 Consensus size: 116
551104 TTGATAACAA
* * ** * * * *
551114 ATCACGTAATTAACCCATTTTGTTATAGTTAGATTTCTAATGCCCCATTAGCTTTTAATAGGCGC
1 ATCA-GTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATAAGCTTTAAATAGGCGC
551179 TACGTATTACATTAAATAAACACTACTTGTTATGTTATTATGGTTGATAATGT
65 TAC-TATTACATTAAATAAACACTACTTGTTATGTTATTATGGTTGATAATGT
* * * **
551232 GTCGAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTACATAAGCTTAAAATTTG-G-
1 ATC-AGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATAAGCTTTAAATAGGCGC
** * * * * ***
551295 TAAC-ATT---TTAGGTGATAC-CTA----ATATGTTAATAAT-ATTGATAACAA
65 T-ACTATTACATTAAAT-AAACACTACTTGTTATGTT-ATTATGGTTGATAATGT
* * * *
551340 ATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAA-GATCCCATCAGCTTTAAACAGACG
1 ATC-AGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCT-CCATAAGCTTTAAATAGGCG
* *
551404 CTACCTATTACATTAAATTAACACTACTTGTTATGTTATTACGGTTGATAATGTT
64 CTA-CTATTACATTAAATAAACACTACTTGTTATGTTATTATGGTTGATAATG-T
* * *
551459 TTCAGTAATTAACTTATTTTGTTATCGTCGGATTTCTAAGGCACCAT
1 ATCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCAT
551506 CAGATTAAAC
Statistics
Matches: 207, Mismatches: 47, Indels: 40
0.70 0.16 0.14
Matches are distributed among these distances:
107 2 0.01
108 62 0.30
109 6 0.03
110 2 0.01
111 3 0.01
112 7 0.03
113 5 0.02
114 7 0.03
115 3 0.01
116 1 0.00
117 6 0.03
118 99 0.48
119 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (116 bp):
ATCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATAAGCTTTAAATAGGCGCT
ACTATTACATTAAATAAACACTACTTGTTATGTTATTATGGTTGATAATGT
Found at i:551482 original size:226 final size:225
Alignment explanation
Indices: 551088--551696 Score: 843
Period size: 226 Copynumber: 2.7 Consensus size: 225
551078 ATATAATCGG
* * *
551088 TAATATGTTGATAATATTGATAACAAATCACGTAATTAACCCATTTTGTTATAGTTAGATTTCTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATAGTCAGATTTCTA
* * * * * *
551153 ATGCCCCATTAGCTTTTAATAGGCGCTACGTATTACATTAAATAAACACTACTTGTTATGTTATT
66 A-GTCCCATCAGCTTTAAAAAGGCGCTACCTATTACATTAAATTAACACTACTTGTTATGTTATT
* *
551218 ATGGTTGATAATG-TGTCGAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTA-CATA
130 AAGGTTGATAATGTTTTC-AGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGC-ACCATA
* *
551281 AGCTTAAAATTTGGTAACATTTTAGGTGATACC
193 AGATTAAAATTTGGTAACATTTTAGGCGATACC
* * *
551314 TAATATGTTAATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATAGTCAGATTTCTA
* *
551379 AGATCCCATCAGCTTTAAACAGACGCTACCTATTACATTAAATTAACACTACTTGTTATGTTATT
66 AG-TCCCATCAGCTTTAAAAAGGCGCTACCTATTACATTAAATTAACACTACTTGTTATGTTATT
* * *
551444 ACGGTTGATAATGTTTTCAGTAATTAACTTATTTTGTTATCGTCGGATTTCTAAGGCACCATCAG
130 AAGGTTGATAATGTTTTCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCACCATAAG
* * *
551509 ATTAAACTTTGGTAATATTTTAGGCGTTACC
195 ATTAAAATTTGGTAACATTTTAGGCGATACC
*
551540 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTATTATTA-TCAGATTT-T
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTA-TAGTCAGATTTCT
* * * *
551603 AAGTCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACA-TAAGCGCAACTTG-TATGTTA
65 AAGT-CCCATCAGCTTTAAAAAGGCGCTACCTATTACATTAAATTAA-CACTACTTGTTATGTTA
*
551666 TTAAGGTTGATAATGTTTCCAGTAATTAACC
128 TTAAGGTTGATAATGTTTTCAGTAATTAACC
551697 GGTTATGTTA
Statistics
Matches: 342, Mismatches: 35, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
224 39 0.11
225 47 0.14
226 252 0.74
227 4 0.01
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (225 bp):
TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATAGTCAGATTTCTA
AGTCCCATCAGCTTTAAAAAGGCGCTACCTATTACATTAAATTAACACTACTTGTTATGTTATTA
AGGTTGATAATGTTTTCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCACCATAAGA
TTAAAATTTGGTAACATTTTAGGCGATACC
Found at i:556767 original size:14 final size:13
Alignment explanation
Indices: 556742--556776 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
556732 TAACTTTTTG
556742 GTCAACGGTCAAA
1 GTCAACGGTCAAA
556755 GTCAACTGGTCAAA
1 GTCAAC-GGTCAAA
556769 GTCAACGG
1 GTCAACGG
556777 GTTGACTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (13 bp):
GTCAACGGTCAAA
Found at i:559526 original size:19 final size:19
Alignment explanation
Indices: 559498--559534 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
559488 AGTATTTTGA
559498 CATGCCCGATGCACCAATC
1 CATGCCCGATGCACCAATC
* *
559517 CATGCTCGATGCATCAAT
1 CATGCCCGATGCACCAAT
559535 TAATTTCTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.35, G:0.16, T:0.22
Consensus pattern (19 bp):
CATGCCCGATGCACCAATC
Found at i:568255 original size:45 final size:46
Alignment explanation
Indices: 568206--568296 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
568196 GAACATCGAA
* * *
568206 TGCATTTTATGCATTGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAAACCATGCATCGATGCACTCAG
* *
568251 TGCATTTGATTCATCGATGCACAAAACTATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAAACCATGCATCGATGCACTCAG
568297 ACTTTTTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 19 0.47
46 21 0.52
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAAACCATGCATCGATGCACTCAG
Found at i:573265 original size:24 final size:24
Alignment explanation
Indices: 573238--573284 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
573228 CCGATTATGA
573238 TTCTCATCTTAAAATAAAAGGGGG
1 TTCTCATCTTAAAATAAAAGGGGG
573262 TTCTCATCTTAAAATAAAAGGGG
1 TTCTCATCTTAAAATAAAAGGGG
573285 TAAACCGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (24 bp):
TTCTCATCTTAAAATAAAAGGGGG
Found at i:573854 original size:25 final size:27
Alignment explanation
Indices: 573820--573882 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
573810 GTGCATGTTA
*
573820 ATTTCTGCTTC-TT-TTGTCTGCTATC
1 ATTTCAGCTTCTTTGTTGTCTGCTATC
573845 ATTTCAGCTTCTTTGTTGTCTGCTATC
1 ATTTCAGCTTCTTTGTTGTCTGCTATC
573872 ATTTCAGCTTC
1 ATTTCAGCTTC
573883 ATGGAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 10 0.29
26 2 0.06
27 23 0.66
ACGTcount: A:0.11, C:0.24, G:0.13, T:0.52
Consensus pattern (27 bp):
ATTTCAGCTTCTTTGTTGTCTGCTATC
Found at i:576366 original size:21 final size:21
Alignment explanation
Indices: 576249--576386 Score: 61
Period size: 20 Copynumber: 6.7 Consensus size: 21
576239 ACGCGAAATA
**
576249 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
576269 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
* *
576289 ACAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* * ** *
576310 AAAATTGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* *
576331 AAATTCG-AATTGCGATTTTCC
1 AAAATCGCAA-CGCGATTTTCC
* * *
576352 AAAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
576372 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
576387 ACACATAAAT
Statistics
Matches: 86, Mismatches: 26, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
19 1 0.01
20 41 0.48
21 40 0.47
22 4 0.05
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:576418 original size:20 final size:20
Alignment explanation
Indices: 576353--576602 Score: 222
Period size: 20 Copynumber: 12.5 Consensus size: 20
576343 CGATTTTCCA
* ** *
576353 AAATCGCAACGCGAATATGA
1 AAATCGCAACGTGAATCCGT
* *
576373 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGTGAATC-CGT
*
576393 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
576413 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
576433 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
576453 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
576473 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
*
576493 AAATCGCAACGAT-AATCTGT
1 AAATCGCAACG-TGAATCCGT
576513 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
576533 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
576553 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
576573 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
*
576593 AAATCACAAC
1 AAATCGCAAC
576603 ACTGAAATTT
Statistics
Matches: 199, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
20 198 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGTGAATCCGT
Found at i:577322 original size:24 final size:24
Alignment explanation
Indices: 577283--577329 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
577273 AAATTTGCTC
577283 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
577307 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
577330 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:579759 original size:33 final size:34
Alignment explanation
Indices: 579708--579981 Score: 240
Period size: 33 Copynumber: 7.8 Consensus size: 34
579698 CGGAAATTAC
* *
579708 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
579741 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
579775 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* *
579813 AATCGCAACGA-GAGAATCGCAATGCGAAATG-A
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
* * *
579845 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AAT-GAA
*
579884 AAT-GCGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
* *
579916 AATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
*
579950 AATCGCAATGCGAAATGAAAATCGCATTGCGA
1 AATCGCAA--C--AATGAAAATCGCAATGCGA
579982 TTCTCTCGTT
Statistics
Matches: 198, Mismatches: 20, Indels: 41
0.76 0.08 0.16
Matches are distributed among these distances:
31 1 0.01
32 16 0.08
33 73 0.37
34 34 0.17
36 4 0.02
37 13 0.07
38 25 0.13
39 32 0.16
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:579791 original size:19 final size:19
Alignment explanation
Indices: 579722--579981 Score: 310
Period size: 19 Copynumber: 14.7 Consensus size: 19
579712 GCAACGAGAG
579722 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
579741 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
579755 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
579775 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
579794 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
579813 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
579827 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
579845 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
579864 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
579878 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
579897 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
579916 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
579930 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
579950 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
579969 AATCGCATTGCGA
1 AATCGCAATGCGA
579982 TTCTCTCGTT
Statistics
Matches: 209, Mismatches: 9, Indels: 46
0.79 0.03 0.17
Matches are distributed among these distances:
14 42 0.20
15 3 0.01
16 6 0.03
17 8 0.04
18 19 0.09
19 102 0.49
20 29 0.14
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:580015 original size:53 final size:52
Alignment explanation
Indices: 579952--580067 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
579942 GAAATGAAAA
*
579952 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
580004 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
580057 TCGCATTGCGA
1 TCGCATTGCGA
580068 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:580084 original size:52 final size:53
Alignment explanation
Indices: 579971--580087 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
579961 GAAATGAAAA
579971 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
580024 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
580076 TCGCATTGCGAT
1 TCGCATTGCGAT
580088 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:580095 original size:19 final size:19
Alignment explanation
Indices: 579990--580087 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
579980 GATTCTCTCG
579990 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
580010 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
580029 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
580043 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
580062 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
580081 TTGCGAT
1 TTGCGAT
580088 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:580210 original size:13 final size:14
Alignment explanation
Indices: 580194--580229 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
580184 CATCAATTAC
580194 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
580207 ACAAATCATCTTTT
1 ACAAATCAACTTTT
580221 ACAAATCAA
1 ACAAATCAA
580230 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:582220 original size:14 final size:14
Alignment explanation
Indices: 582201--582257 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
582191 GCGAAATGAA
*
582201 AATCGCAACGACAG
1 AATCGCAACGAAAG
582215 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
582232 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
582248 AATCGCAACG
1 AATCGCAACG
582258 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:582228 original size:33 final size:33
Alignment explanation
Indices: 582182--582273 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
582172 GCGAAACCAA
*
582182 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
582215 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
582248 AATCGCAACGCGAAATG-AAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
582274 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 9 0.16
33 47 0.84
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:582239 original size:19 final size:19
Alignment explanation
Indices: 582145--582278 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
582135 TAGTTTACTT
* *
582145 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
582165 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
582184 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
582203 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
582217 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
582236 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
582250 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
582268 TCGCAATGCGA
1 TCGCAACGCGA
582279 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
18 12 0.12
19 35 0.36
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:582296 original size:19 final size:19
Alignment explanation
Indices: 582274--582402 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
582264 GAAATCGCAA
582274 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
582293 TGCGA-TCT--TAT--CGT
1 TGCGATTTTGGTTTCGCGT
582307 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
582326 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
582340 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
582359 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
582378 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
582398 TGCGA
1 TGCGA
582403 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 3 0.03
17 3 0.03
18 3 0.03
19 45 0.51
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:582316 original size:33 final size:33
Alignment explanation
Indices: 582274--582365 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
582264 GAAATCGCAA
582274 TGCGATTTTGGTTTCGCGTTGCGA-TCTTATCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TATCGT
*
582307 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTATCGT
**
582340 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
582366 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTATCGT
Found at i:582605 original size:93 final size:93
Alignment explanation
Indices: 582446--582919 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
582436 TTGAATGGAT
582446 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
582511 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
582539 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
582604 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
582632 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
582697 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
582725 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
582790 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
582818 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
582883 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
582911 AAATTTACT
1 AAATTTACT
582920 AAGCAATCTA
Statistics
Matches: 378, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 378 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:584645 original size:14 final size:14
Alignment explanation
Indices: 584626--584715 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
584616 TTGAAATGAA
584626 AATCGCAACGAGAG
1 AATCGCAACGAGAG
584640 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
584657 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
584673 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
584692 AATCGCAACGAGAG
1 AATCGCAACGAGAG
584706 AATCGCAACG
1 AATCGCAACG
584716 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:584663 original size:33 final size:33
Alignment explanation
Indices: 584618--584732 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
584608 TCTTTTGGTT
584618 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
584651 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
584684 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
584717 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
584733 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:584664 original size:19 final size:18
Alignment explanation
Indices: 584625--584737 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
584615 GTTGAAATGA
584625 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
584640 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
584657 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
584673 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
584690 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
584706 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
584723 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
584738 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:584755 original size:19 final size:18
Alignment explanation
Indices: 584733--584791 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
584723 AAAATCGCAA
584733 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
584752 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
584766 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
584785 TGCGATT
1 TGCGATT
584792 CTCTCGTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 11 0.34
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.56
ACGTcount: A:0.08, C:0.19, G:0.27, T:0.46
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:584781 original size:33 final size:33
Alignment explanation
Indices: 584733--584813 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
584723 AAAATCGCAA
** *
584733 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
584766 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
584799 TGCGCTTTTCATTTC
1 TGCGATTTTCATTTC
584814 TCTCGTTGCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.07, C:0.22, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:584849 original size:41 final size:41
Alignment explanation
Indices: 584789--584866 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
584779 TCGCGTTGCG
* *
584789 ATTCTCTCGTTGCGCTTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
584830 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
584867 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:584865 original size:21 final size:21
Alignment explanation
Indices: 584790--584865 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
584780 CGCGTTGCGA
*
584790 TTCTCTCGTTGCGCTTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
584811 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
584831 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
584852 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
584866 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:584992 original size:33 final size:33
Alignment explanation
Indices: 584945--585015 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
584935 AATACTAACT
* *
584945 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
584978 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
585011 TGAAA
1 TGAAA
585016 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:585249 original size:22 final size:22
Alignment explanation
Indices: 585197--585251 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
585187 TGGTTGTGAG
**
585197 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
585219 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
585241 GGATTTCTTCG
1 GGATTTCTTCG
585252 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:585422 original size:20 final size:20
Alignment explanation
Indices: 585397--585590 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
585387 CTTTAAATAT
585397 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
585417 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
585439 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
585458 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
585478 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
585498 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
585518 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
585538 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
585558 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
585578 CGCGTTGCGATTT
1 CGCGTTGCGATTT
585591 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:585584 original size:60 final size:60
Alignment explanation
Indices: 585397--585590 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
585387 CTTTAAATAT
**
585397 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
585458 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
585518 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
585578 CGCGTTGCGATTT
1 CGCGTTGCGATTT
585591 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:585607 original size:21 final size:21
Alignment explanation
Indices: 585577--585659 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
585567 ATTTTCATAT
*
585577 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
585598 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
585619 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
585640 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
585660 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:585650 original size:42 final size:43
Alignment explanation
Indices: 585557--585655 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
585547 ATTTATGTGT
* *
585557 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
585598 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
585640 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
585656 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:587390 original size:76 final size:72
Alignment explanation
Indices: 587258--587403 Score: 238
Period size: 76 Copynumber: 2.0 Consensus size: 72
587248 AATAGTTGGA
*
587258 AAAGGAAAACTTGTATTCTTCATTATTTAAATTATATATTACATGATCCTTGGAGGGGTCGACCC
1 AAAGGAAAACTTGTATTCTTCATTATTTAAATTATATATTACAAGATCCTTGGAGGGGTCGACCC
587323 AATAACT
66 AATAACT
*
587330 AAAGGAAAACTTGTATTCTTCATTATTTATTTAAATTATATATTACAAGATCTTTGGAGGGGTCG
1 AAAGGAAAACTTGTATTCTTC---A-TTATTTAAATTATATATTACAAGATCCTTGGAGGGGTCG
587395 ACCCAATAA
62 ACCCAATAA
587404 TTAAGAGAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
72 21 0.31
75 1 0.01
76 46 0.68
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Consensus pattern (72 bp):
AAAGGAAAACTTGTATTCTTCATTATTTAAATTATATATTACAAGATCCTTGGAGGGGTCGACCC
AATAACT
Found at i:592656 original size:3 final size:3
Alignment explanation
Indices: 592650--592691 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
592640 TATTTGCTTA
*
592650 TAT TAT TAT TAT TAT TAT TAT TA- TGT TA- TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
592692 AATAATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 3 0.09
3 32 0.91
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:594164 original size:20 final size:20
Alignment explanation
Indices: 594139--594231 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
594129 TTTTCCCAAT
*
594139 TCGCAATGTGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
594159 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
594180 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
594200 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
594221 TCGCAATGCGA
1 TCGCAATGCGA
594232 TACTGACTAT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 26 0.46
21 31 0.54
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:594182 original size:21 final size:21
Alignment explanation
Indices: 594156--594231 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
594146 GTGAATAAGT
594156 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
594177 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
594197 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
594218 AAATCGCAATGCGA
1 AAATCGCAACGCGA
594232 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:594196 original size:41 final size:41
Alignment explanation
Indices: 594139--594231 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
594129 TTTTCCCAAT
*
594139 TCGCAATGTGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
594180 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
594221 TCGCAATGCGA
1 TCGCAATGCGA
594232 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:594244 original size:41 final size:41
Alignment explanation
Indices: 594158--594292 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
594148 GAATAAGTAA
* *
594158 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
594199 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
594240 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
594281 TTCGCAACGCGA
1 ATCGCAACGCGA
594293 TTTACATAGC
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:594266 original size:21 final size:20
Alignment explanation
Indices: 594217--594267 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
594207 GCGAATTGGG
* *
594217 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
594237 ACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
594258 AAAATCGCAA
1 AAAATCGCAA
594268 CGAGATACTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:594892 original size:20 final size:19
Alignment explanation
Indices: 594853--594997 Score: 147
Period size: 20 Copynumber: 7.7 Consensus size: 19
594843 TAATCGCAAC
594853 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
*
594872 GCGATTTTTATTTCGCGGTT
1 GCGATTTTCATTTCGC-GTT
594892 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
* *
594911 GCGATTGTC---T-G-GTC
1 GCGATTTTCATTTCGCGTT
**
594925 GCGATAGTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
**
594944 GCGATAGTCATTTCCGCGTT
1 GCGATTTTCATTT-CGCGTT
* *
594964 GCGATTCTCATTATCTCGTT
1 GCGATTTTCATT-TCGCGTT
594984 GCGATTTTCATTTC
1 GCGATTTTCATTTC
594998 AACCAAAAGA
Statistics
Matches: 108, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 43 0.40
20 50 0.46
21 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.43
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:594927 original size:39 final size:39
Alignment explanation
Indices: 594853--594927 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
594843 TAATCGCAAC
* **
594853 GCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGGTT
1 GCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGGTT
594892 GCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 GCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
594928 ATAGTCATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 30 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.20, G:0.27, T:0.44
Consensus pattern (39 bp):
GCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGGTT
Found at i:597055 original size:42 final size:42
Alignment explanation
Indices: 596995--597117 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
596985 GCCCGACTCG
* * *
596995 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
597037 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
597079 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
597118 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:597075 original size:21 final size:21
Alignment explanation
Indices: 597051--597117 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
597041 TCATTCCTCG
597051 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
597072 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
597093 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
597114 AGAG
1 AGAG
597118 CCCGATTCAC
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:598486 original size:14 final size:14
Alignment explanation
Indices: 598467--598502 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
598457 ATTGTTTAAT
598467 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
598481 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
598495 TGATTTGT
1 TGATTTGT
598503 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:598703 original size:19 final size:19
Alignment explanation
Indices: 598681--598831 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
598671 CGAAATTAAA
598681 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
598700 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
598715 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
598733 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
598747 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
598766 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
598781 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
598799 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
598818 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
598832 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:598727 original size:33 final size:32
Alignment explanation
Indices: 598685--598811 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
598675 ATTAAATTCG
598685 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
598718 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
598751 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
598784 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
598812 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:598774 original size:66 final size:66
Alignment explanation
Indices: 598678--598810 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
598668 ACGCGAAATT
*
598678 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
598743 G
66 G
*
598744 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
598809 G
66 G
598810 A
1 A
598811 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:601119 original size:12 final size:12
Alignment explanation
Indices: 601102--601126 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
601092 TCTTCGGGGA
601102 CTTTTTCTTCTT
1 CTTTTTCTTCTT
601114 CTTTTTCTTCTT
1 CTTTTTCTTCTT
601126 C
1 C
601127 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:601335 original size:24 final size:24
Alignment explanation
Indices: 601301--601354 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
601291 CTGAAACATC
* *
601301 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
601325 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
601349 ATCAAA
1 ATCAAA
601355 TTTTGAATAC
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:602439 original size:20 final size:20
Alignment explanation
Indices: 602414--602471 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
602404 ATTCATTTGA
602414 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
602434 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
602454 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
602472 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:602514 original size:14 final size:14
Alignment explanation
Indices: 602495--602581 Score: 66
Period size: 14 Copynumber: 5.5 Consensus size: 14
602485 GAAAATCGCA
602495 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
602509 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
602526 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
* *
602542 TTGCGATAGCCATTTCGCA
1 TTGCGAT-----TTTCTCG
602561 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
602575 TTGCGAT
1 TTGCGAT
602582 AGCCATTTCG
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 30 0.51
16 3 0.05
17 3 0.05
19 23 0.39
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.45
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:602514 original size:33 final size:33
Alignment explanation
Indices: 602490--602600 Score: 163
Period size: 33 Copynumber: 3.4 Consensus size: 33
602480 GAAATGAAAA
* *
602490 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATATGCATT
602523 TCGCATTGCGATTTTCTCGTTGCGATA-GCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATATG-CATT
602556 TCGCATTGCGATTTTCTCGTTGCGATA-GCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATATG-CATT
*
602589 TCGCGTTGCGAT
1 TCGCATTGCGAT
602601 AGTCTGTTTT
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.41
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATATGCATT
Found at i:602557 original size:19 final size:19
Alignment explanation
Indices: 602535--602602 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
602525 GCATTGCGAT
*
602535 TTTCTCGTTGCGATAGCCA
1 TTTCGCGTTGCGATAGCCA
*
602554 TTTCGCATTGCGAT-----
1 TTTCGCGTTGCGATAGCCA
*
602568 TTTCTCGTTGCGATAGCCA
1 TTTCGCGTTGCGATAGCCA
602587 TTTCGCGTTGCGATAG
1 TTTCGCGTTGCGATAG
602603 TCTGTTTTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
14 12 0.31
19 27 0.69
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGCCA
Found at i:604623 original size:20 final size:19
Alignment explanation
Indices: 604588--604654 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
604578 GAAACTTAAA
*
604588 ATCGCAAAGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
604607 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
604627 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
604646 ATCGCAACG
1 ATCGCAACG
604655 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:604649 original size:19 final size:19
Alignment explanation
Indices: 604569--604686 Score: 86
Period size: 20 Copynumber: 6.4 Consensus size: 19
604559 TAGTTTACTT
* *
604569 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
604589 TCGCAAAGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
604608 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
604628 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
604647 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
604661 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
604679 TCGCAACG
1 TCGCAACG
604687 ACAAAATCGC
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.15
19 24 0.30
20 28 0.35
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:604662 original size:14 final size:14
Alignment explanation
Indices: 604643--604700 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
604633 ATGCGAAATG
604643 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
604657 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
604673 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
604689 AAAATCGCAACG
1 AAAATCGCAACG
604701 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:604685 original size:32 final size:33
Alignment explanation
Indices: 604627--604705 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
604617 GGAAATGGCT
*
604627 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
604660 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
604692 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
604706 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:604753 original size:14 final size:14
Alignment explanation
Indices: 604734--604791 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
604724 TTTCATTTCG
604734 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
604748 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
604764 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
604780 CGTTGCGATTTT
1 CGTTGCGATTTT
604792 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:604798 original size:33 final size:33
Alignment explanation
Indices: 604717--604807 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
604707 ACAAATCGCA
*
604717 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
604750 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
604782 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
604808 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:604826 original size:20 final size:19
Alignment explanation
Indices: 604792--604846 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
604782 TTGCGATTTT
*
604792 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
604811 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
604831 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
604847 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:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:605345 original size:18 final size:18
Alignment explanation
Indices: 605319--605364 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
605309 GTCGATCAGA
*
605319 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
605337 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
605355 TGATGGCTCT
1 TGATGGCTCT
605365 CGAAGTGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.15, G:0.43, T:0.28
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:607240 original size:20 final size:20
Alignment explanation
Indices: 607215--607267 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
607205 GATTATGTAT
*
607215 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
607235 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
607255 TATCTCGTTGCGA
1 TATCGCGTTGCGA
607268 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:607304 original size:20 final size:20
Alignment explanation
Indices: 607195--607309 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
607185 CGCTTTGAAA
*
607195 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
607216 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
607236 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
607256 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
*
607277 ACCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
607297 ATCGCATTGCGAT
1 ATCGCATTGCGAT
607310 TTCCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 49 0.66
21 23 0.31
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:607328 original size:41 final size:41
Alignment explanation
Indices: 607298--607390 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 41
607288 ATAGTCAGTA
* *
607298 TCGCATTGCGATTTCCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTCCCCAATTCGCGTTGCGATTCACGTAT
* * * *
607339 TCGCATTGCGATTTTCCCAATTCGCTTTGCGATTTACTTAT
1 TCGCATTGCGATTTCCCCAATTCGCGTTGCGATTCACGTAT
607380 TCGCATTGCGA
1 TCGCATTGCGA
607391 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTCCCCAATTCGCGTTGCGATTCACGTAT
Found at i:607342 original size:20 final size:20
Alignment explanation
Indices: 607298--607390 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
607288 ATAGTCAGTA
* **
607298 TCGCATTGCGATTTCCCCAAT
1 TCGCATTGCGATTT-ACTTAT
*
607319 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
607339 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
607360 TCGCTTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
607380 TCGCATTGCGA
1 TCGCATTGCGA
607391 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:608028 original size:98 final size:98
Alignment explanation
Indices: 607826--608029 Score: 222
Period size: 98 Copynumber: 2.1 Consensus size: 98
607816 TATAAGCATG
*
607826 TTTTAATTTAATATTAAAGAAAATGACTGTCTTAAAGCACCTAGAAGTCCGTTTTCTGATTTTTT
1 TTTT-ATTTAATATTAAAGAAAATGACTGTCTTAAAGCACCTAGAAGTCCGTTTTCTGATTTTCT
* ** * **
607891 TACTCTATAAAATATATACTATTTTTTTATTAATA
65 TAATAAATAAAATATATA-TATTTATAAATTAATA
*
607926 -TTTATTTAATA-TAGAAGAAAA-GAGCTGTCTTAAGGCACCTAGAAGTCC-TTTTCTGATATTT
1 TTTTATTTAATATTA-AAGAAAATGA-CTGTCTTAAAGCACCTAGAAGTCCGTTTTCTGAT-TTT
*
607987 CTTAATAAAT-AAATATCT-TATTTATAAATTAATAGA
63 CTTAATAAATAAAATATATATATTTATAAATTAAT--A
608023 TTTTATT
1 TTTTATT
608030 AAAGATACTA
Statistics
Matches: 89, Mismatches: 9, Indels: 14
0.79 0.08 0.12
Matches are distributed among these distances:
95 12 0.13
97 21 0.24
98 53 0.60
99 3 0.03
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.44
Consensus pattern (98 bp):
TTTTATTTAATATTAAAGAAAATGACTGTCTTAAAGCACCTAGAAGTCCGTTTTCTGATTTTCTT
AATAAATAAAATATATATATTTATAAATTAATA
Found at i:611400 original size:15 final size:15
Alignment explanation
Indices: 611380--611408 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
611370 GGGATCAATA
611380 CATTTTGCATACATG
1 CATTTTGCATACATG
611395 CATTTTGCATACAT
1 CATTTTGCATACAT
611409 TAATTATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (15 bp):
CATTTTGCATACATG
Found at i:619174 original size:21 final size:20
Alignment explanation
Indices: 619122--619209 Score: 97
Period size: 20 Copynumber: 4.2 Consensus size: 20
619112 ATTTATTAAT
*
619122 AAATTCTAAGTTTATTTTCTCT-
1 AAATTC-AA-TTTATTTT-TTTG
619144 AAATTCAATTTATTATTTTTG
1 AAATTCAATTTATT-TTTTTG
*
619165 AAATTTAATTTATTTTTTTG
1 AAATTCAATTTATTTTTTTG
*
619185 AAATTCAATTTATTCTTTTG
1 AAATTCAATTTATTTTTTTG
619205 TAAAT
1 -AAAT
619210 GGATTAACAT
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
20 32 0.54
21 21 0.36
22 6 0.10
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.57
Consensus pattern (20 bp):
AAATTCAATTTATTTTTTTG
Found at i:619189 original size:41 final size:43
Alignment explanation
Indices: 619122--619203 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 43
619112 ATTTATTAAT
619122 AAATTCTAAGTTTATTTTCTCTAAATTCAATTTATTATTTTTG
1 AAATTCTAAGTTTATTTTCTCTAAATTCAATTTATTATTTTTG
* *
619165 AAATT-TAA-TTTATTTT-TTTGAAATTCAATTTATTCTTTT
1 AAATTCTAAGTTTATTTTCTCT-AAATTCAATTTATTATTTT
619204 GTAAATGGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
40 2 0.06
41 26 0.72
42 3 0.08
43 5 0.14
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (43 bp):
AAATTCTAAGTTTATTTTCTCTAAATTCAATTTATTATTTTTG
Found at i:620550 original size:113 final size:113
Alignment explanation
Indices: 620335--620626 Score: 401
Period size: 113 Copynumber: 2.6 Consensus size: 113
620325 TAGCAAAGAT
* *
620335 TCAAATCCATCAC--AATGGATCAACATTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTG
* * * *
620397 AAGAAGGAAGAAGAAGTTCATATTGAGAAGAGCTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTATTCAACCTTTTGC
* *
620446 TCAAATCCATCACTTGATGGACCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
620511 AGAAGGAAGAATAAATTCATAATGAGAAGAATTTATTCAACTTTTTGT
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTATTCAACCTTTTGC
** * * *
620559 TTGAATTCATCATTTGATGGATCAGCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
620624 AGA
66 AGA
620627 GAAGAGTTTG
Statistics
Matches: 159, Mismatches: 19, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
111 13 0.08
113 144 0.91
114 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTATTCAACCTTTTGC
Found at i:620760 original size:20 final size:20
Alignment explanation
Indices: 620698--620761 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
620688 TTTTCAGAAG
620698 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
620718 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
620737 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
620757 GTTCA
1 GTTCA
620762 ACTTTTTGTA
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:620780 original size:121 final size:122
Alignment explanation
Indices: 620625--620856 Score: 333
Period size: 121 Copynumber: 1.9 Consensus size: 122
620615 CTCATCTGAA
**
620625 GAGAAGAGTTTGTTCAACCTTCTGCATGACTCTATCACAG-AAGAAGATAGATCAACATCAACAT
1 GAGAAGAACTTGTTCAACCTTCTGCATGACTCTATCACAGAAAG-AGATAGATCAACATCAACAT
* * * *
620689 TTTCAGAAG-GTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAAT
65 TTCCAGAAGAATTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAAT
* * * * *
620746 GAGAAGAACTTGTTCAACTTTTTGTATGATTCTATCACAGAAAGAGATAGATCATCATCAACATT
1 GAGAAGAACTTGTTCAACCTTCTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATT
620811 TCCAGAAGAAATTCATAATGAGAAGAACTCATCTGAAGAGAAAGAA
66 TCCAGAAG-AATTCATAATGAGAAGAACTCATCTGAAGAGAAAGAA
620857 CTTGTTCAAC
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
121 61 0.63
122 3 0.03
123 33 0.34
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (122 bp):
GAGAAGAACTTGTTCAACCTTCTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATT
TCCAGAAGAATTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAAT
Found at i:622964 original size:98 final size:96
Alignment explanation
Indices: 622762--622965 Score: 204
Period size: 98 Copynumber: 2.1 Consensus size: 96
622752 TATAAGCATG
*
622762 TTTTAATTTAATATTAAAGAAAAAGACTGACTTAAAGCACCTAGAAGTCCGTTTTCTGATTTTTT
1 TTTT-ATTTAATATTAAAGAAAAAGACTGACTTAAAGCACCTAGAAGTCCGTTTTCTGATTTTCT
* **
622827 TACTCTATAAAATATATACTAATTTTTTATTAATA
65 TA--C-ATAAAAAATATACTAATTTTAAATTAATA
* *
622862 -TTTATTTAATA-TAGAAGAAAATAG-CTGTCTTAAGGCACCTAGAAGTCC-TTTTCTGATATTT
1 TTTTATTTAATATTA-AAGAAAA-AGACTGACTTAAAGCACCTAGAAGTCCGTTTTCTGAT-TTT
*
622923 CTTA-ATAAATAAATAT-CTTATTTATAAATTAATAGA
63 CTTACATAAA-AAATATACTAATTT-TAAATTAAT--A
622959 TTTTATT
1 TTTTATT
622966 AAAGATACTA
Statistics
Matches: 89, Mismatches: 7, Indels: 18
0.78 0.06 0.16
Matches are distributed among these distances:
94 11 0.12
95 12 0.13
97 12 0.13
98 49 0.55
99 5 0.06
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (96 bp):
TTTTATTTAATATTAAAGAAAAAGACTGACTTAAAGCACCTAGAAGTCCGTTTTCTGATTTTCTT
ACATAAAAAATATACTAATTTTAAATTAATA
Found at i:631765 original size:29 final size:29
Alignment explanation
Indices: 631733--631828 Score: 72
Period size: 29 Copynumber: 3.2 Consensus size: 29
631723 AAATTGGTCC
631733 CTAAACTTTTAAATATTTTAATTTTATCT
1 CTAAACTTTTAAATATTTTAATTTTATCT
* * *
631762 CTAAAC-TATGAATATCGTTCTAA-ATTAGTC-
1 CTAAACTTTTAAATAT--TT-TAATTTTA-TCT
* *
631792 CTTAAACTTTTAAATATTTCAATTTCATCT
1 C-TAAACTTTTAAATATTTTAATTTTATCT
*
631822 CCAAACT
1 CTAAACT
631829 ATGGTCTTCA
Statistics
Matches: 50, Mismatches: 9, Indels: 16
0.67 0.12 0.21
Matches are distributed among these distances:
28 7 0.14
29 15 0.30
30 11 0.22
31 10 0.20
32 7 0.14
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (29 bp):
CTAAACTTTTAAATATTTTAATTTTATCT
Found at i:631843 original size:60 final size:60
Alignment explanation
Indices: 631723--631862 Score: 174
Period size: 60 Copynumber: 2.3 Consensus size: 60
631713 TCTTAATTTC
* * * *
631723 AAATTGGTCCCTAAACTTTTAAATATTTTAATTTTATCTCTAAACTATGAATATCGTTCT
1 AAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATCTCCAAACTATGAATATCATTCT
* * * *
631783 AAATTAGTCCTTAAACTTTTAAATATTTCAATTTCATCTCCAAACTATG-GTCTTCATTCT
1 AAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATCTCCAAACTATGAAT-ATCATTCT
* *
631843 AAGTTGGTCCCCAAACTTTT
1 AAATTGGTCCCTAAACTTTT
631863 TGAACATTCC
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
59 1 0.01
60 66 0.99
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (60 bp):
AAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATCTCCAAACTATGAATATCATTCT
Found at i:632087 original size:60 final size:59
Alignment explanation
Indices: 632010--632158 Score: 158
Period size: 60 Copynumber: 2.5 Consensus size: 59
632000 GATGAATTTG
* * *
632010 AGGATGAAATT-TGAATATTTAAAAGTTTAGAGAATAATTTAGAAAAAGTGTCATAGTTT
1 AGGATGAAATTAT-AATATTTAAAAGTTTAAAGAATAAGTTAGAAAAAGAGTCATAGTTT
* * ** *
632069 AAGGATGAAATTATAATATTCAAAAGTTTAAAGATTAAGTTAGAACGAGAGTTATAGTTT
1 -AGGATGAAATTATAATATTTAAAAGTTTAAAGAATAAGTTAGAAAAAGAGTCATAGTTT
* * *
632129 AGGGTAAAATTGA-AATATTTAAAAATTTAA
1 AGGATGAAATT-ATAATATTTAAAAGTTTAA
632159 GGATCAATTT
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
59 24 0.32
60 50 0.67
61 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.34
Consensus pattern (59 bp):
AGGATGAAATTATAATATTTAAAAGTTTAAAGAATAAGTTAGAAAAAGAGTCATAGTTT
Found at i:632754 original size:18 final size:20
Alignment explanation
Indices: 632716--632755 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
632706 CACGGAATGT
632716 AAGATTACCAGTGGAAATAA
1 AAGATTACCAGTGGAAATAA
632736 AAGATTACCAG-GG-AATAA
1 AAGATTACCAGTGGAAATAA
632754 AA
1 AA
632756 TTACTGGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 2 0.10
20 11 0.55
ACGTcount: A:0.53, C:0.10, G:0.20, T:0.17
Consensus pattern (20 bp):
AAGATTACCAGTGGAAATAA
Found at i:634853 original size:21 final size:21
Alignment explanation
Indices: 634827--634866 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
634817 CAAAAAGGGT
634827 AGTATC-AGTACTACCATGAGG
1 AGTATCGA-TACTACCATGAGG
*
634848 AGTATCGATACTACTATGA
1 AGTATCGATACTACCATGA
634867 AAAATAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (21 bp):
AGTATCGATACTACCATGAGG
Found at i:634909 original size:24 final size:24
Alignment explanation
Indices: 634848--634912 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
634838 TACCATGAGG
* *
634848 AGTATCGATACTACTATGAAAAAT
1 AGTATCTATACTATTATGAAAAAT
634872 AGTATCTATACTATTATGAAAAAT
1 AGTATCTATACTATTATGAAAAAT
634896 AGTATCTATACTATTAT
1 AGTATCTATACTATTAT
634913 ACTTAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (24 bp):
AGTATCTATACTATTATGAAAAAT
Found at i:635420 original size:29 final size:27
Alignment explanation
Indices: 635387--635448 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 27
635377 CCGAAATATT
635387 ATAAAAATCGCAAT-AAA-CATCCAAAGAGC
1 ATAAAAATC-C-ATCAAACCATCC-AA-AGC
635416 ATAAAAATCCATCAAACCATCCAAAGC
1 ATAAAAATCCATCAAACCATCCAAAGC
635443 ATAAAA
1 ATAAAA
635449 TAAATAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
27 11 0.35
28 6 0.19
29 14 0.45
ACGTcount: A:0.56, C:0.23, G:0.06, T:0.15
Consensus pattern (27 bp):
ATAAAAATCCATCAAACCATCCAAAGC
Found at i:649093 original size:23 final size:23
Alignment explanation
Indices: 649048--649099 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
649038 GTCGAGGGTT
* ***
649048 CTTCGAGACAATTCTATGTGGTC
1 CTTCGGGACAATTCTACACGGTC
649071 CTTCGGGACAATTCTACACGGTC
1 CTTCGGGACAATTCTACACGGTC
649094 CTTCGG
1 CTTCGG
649100 TGCATAATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (23 bp):
CTTCGGGACAATTCTACACGGTC
Found at i:649125 original size:24 final size:24
Alignment explanation
Indices: 649098--649186 Score: 124
Period size: 24 Copynumber: 3.7 Consensus size: 24
649088 ACGGTCCTTC
* *
649098 GGTGCATAATCTATGTGGCACTTT
1 GGTGCATATTCTACGTGGCACTTT
*
649122 GGTGCATATTCTACGTAGCACTTT
1 GGTGCATATTCTACGTGGCACTTT
*
649146 GGTGCATATTCTACGTGGCACTTC
1 GGTGCATATTCTACGTGGCACTTT
* *
649170 GGTGCAAATTTTACGTG
1 GGTGCATATTCTACGTG
649187 ACAATTTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (24 bp):
GGTGCATATTCTACGTGGCACTTT
Found at i:652743 original size:14 final size:14
Alignment explanation
Indices: 652724--652755 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
652714 ATCAAGGCTT
652724 AGCGCCGGGCGAAA
1 AGCGCCGGGCGAAA
*
652738 AGCGCCGGGTGAAA
1 AGCGCCGGGCGAAA
652752 AGCG
1 AGCG
652756 ACTAGATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.44, T:0.03
Consensus pattern (14 bp):
AGCGCCGGGCGAAA
Found at i:655919 original size:16 final size:17
Alignment explanation
Indices: 655882--655920 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
655872 TATCAAAAGA
* *
655882 ATATTTTTTTTCTTTCT
1 ATATTTTTTTTATTTAT
655899 ATATTTTTTTTATTTAT
1 ATATTTTTTTTATTTAT
655916 -TATTT
1 ATATTT
655921 AAGAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (17 bp):
ATATTTTTTTTATTTAT
Found at i:658558 original size:23 final size:23
Alignment explanation
Indices: 658500--658547 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
658490 TGTCTAGGCA
* *
658500 TGCTCCTAGGCACGCCTCCGCCT
1 TGCTCCTAGGCATGCCTCCACCT
658523 TGCTCCTAGGCATGCCTCCACCT
1 TGCTCCTAGGCATGCCTCCACCT
658546 TG
1 TG
658548 TGCCTAAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.10, C:0.44, G:0.21, T:0.25
Consensus pattern (23 bp):
TGCTCCTAGGCATGCCTCCACCT
Found at i:670749 original size:25 final size:25
Alignment explanation
Indices: 670721--670769 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
670711 AAATAAATAA
*
670721 TAAAAATTTAAGAGATATAAAATTT
1 TAAAAATTTAAAAGATATAAAATTT
*
670746 TAAAATTTTAAAAGATATAAAATT
1 TAAAAATTTAAAAGATATAAAATT
670770 ATATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (25 bp):
TAAAAATTTAAAAGATATAAAATTT
Done.