Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003948.1 Hibiscus syriacus cultivar Beakdansim tig00008535_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: 161037
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:3769 original size:23 final size:21
Alignment explanation
Indices: 3701--3769 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 21
3691 ATCTATATAG
3701 TTAAT-ATTTTATAATAAG-A
1 TTAATAATTTTATAATAAGTA
*
3720 TTAATAATATTTAT-ATTAGATA
1 TTAATAAT-TTTATAATAAG-TA
3742 TTTAATAAATTTTATAATAAGTTA
1 -TTAAT-AATTTTATAATAAG-TA
3766 TTAA
1 TTAA
3770 ATTTAATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
19 5 0.12
20 6 0.15
21 5 0.12
22 1 0.03
23 14 0.35
24 9 0.22
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
TTAATAATTTTATAATAAGTA
Found at i:3772 original size:20 final size:21
Alignment explanation
Indices: 3702--3773 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 21
3692 TCTATATAGT
3702 TAATATTTTATAATAAGATTAA
1 TAATATTTTATAATAAG-TTAA
*
3724 TAATATTTATATTAGAT-ATTTAA
1 TAATATTT-TA-TA-ATAAGTTAA
*
3747 TAA-ATTTTATAATAAGTTAT
1 TAATATTTTATAATAAGTTAA
3767 TAA-ATTT
1 TAATATTT
3774 AATTTTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 2 0.05
22 12 0.28
23 9 0.21
24 3 0.07
25 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (21 bp):
TAATATTTTATAATAAGTTAA
Found at i:9418 original size:37 final size:39
Alignment explanation
Indices: 9368--9440 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 39
9358 ACAGAGTATT
**
9368 TTGAACGATCATATCAGTATG-AA-AATGTTGGGACGTC
1 TTGAACGATCATATCACCATGAAATAATGTTGGGACGTC
9405 TTGAA-GACTCATATCACCATGAAATAATGTTGGGAC
1 TTGAACGA-TCATATCACCATGAAATAATGTTGGGAC
9441 ATTTAATGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 2 0.06
37 16 0.52
38 2 0.06
39 11 0.35
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (39 bp):
TTGAACGATCATATCACCATGAAATAATGTTGGGACGTC
Found at i:9543 original size:43 final size:44
Alignment explanation
Indices: 9445--9544 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 44
9435 TGGGACATTT
*
9445 AATGTTGGGGCA--TGCTGAAAGCTCATATTAGACAGAAATAATC
1 AATG-TGGGGCATTTGCTGAAAGCTCATATCAGACAGAAATAATC
* * ** *
9488 CATATGAAGCATTTGC-GAAAGCTCATATCAGACAGAAATGATC
1 AATGTGGGGCATTTGCTGAAAGCTCATATCAGACAGAAATAATC
9531 AATGTGGGGCATTT
1 AATGTGGGGCATTT
9545 TGAAGGATCA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
42 5 0.11
43 37 0.82
44 3 0.07
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (44 bp):
AATGTGGGGCATTTGCTGAAAGCTCATATCAGACAGAAATAATC
Found at i:10459 original size:22 final size:22
Alignment explanation
Indices: 10373--10461 Score: 128
Period size: 22 Copynumber: 4.0 Consensus size: 22
10363 TTCTGCAAGA
*
10373 ATGATAGATTCT-TTCT-ACAAG
1 ATGATAGATTCTCTTTTCA-AAG
*
10394 AATGATAGATTCTCTTTTCAATG
1 -ATGATAGATTCTCTTTTCAAAG
10417 ATGATAGATTCTCTTTTCAAAG
1 ATGATAGATTCTCTTTTCAAAG
10439 ATGATAGATTCTCTTTTCAAAG
1 ATGATAGATTCTCTTTTCAAAG
10461 A
1 A
10462 CATAAAGTTA
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
22 56 0.90
23 5 0.08
24 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
ATGATAGATTCTCTTTTCAAAG
Found at i:12856 original size:42 final size:41
Alignment explanation
Indices: 12809--12901 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 41
12799 CATAATTTAT
*
12809 AATTTAATCTATATAGTTAAT-A-TTTTATAATAAGATTAATA
1 AATTTAAT-TAGATAGTTAATAATTTTTATAATAAG-TTAATA
* *
12850 ATATTTATATTAGATATTTAATAATTTTTATAATAAGTTATTA
1 A-ATTTA-ATTAGATAGTTAATAATTTTTATAATAAGTTAATA
12893 AATTTAATT
1 AATTTAATT
12902 TTAAAAGTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
41 4 0.09
42 20 0.44
43 9 0.20
44 12 0.27
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (41 bp):
AATTTAATTAGATAGTTAATAATTTTTATAATAAGTTAATA
Found at i:12893 original size:23 final size:22
Alignment explanation
Indices: 12826--12893 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
12816 TCTATATAGT
12826 TAATATTTTATAATAAG-ATTAA
1 TAAT-TTTTATAATAAGTATTAA
* *
12848 TAATATTTAT-ATTAGATATTTAA
1 TAATTTTTATAATAAG-TA-TTAA
12871 TAATTTTTATAATAAGTTATTAA
1 TAATTTTTATAATAAG-TATTAA
12894 ATTTAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 4 0.11
21 5 0.14
22 5 0.14
23 17 0.46
24 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
TAATTTTTATAATAAGTATTAA
Found at i:27096 original size:15 final size:17
Alignment explanation
Indices: 27056--27098 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
27046 AATATACCCG
*
27056 ATAAAAAAATAAATAAT
1 ATAAAATAATAAATAAT
*
27073 ATGAAATAA-AAATAA-
1 ATAAAATAATAAATAAT
27088 ATAAAATAATA
1 ATAAAATAATA
27099 CATGCTCCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 8 0.36
16 7 0.32
17 7 0.32
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (17 bp):
ATAAAATAATAAATAAT
Found at i:29832 original size:21 final size:21
Alignment explanation
Indices: 29806--29845 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29796 TGCTGAAATT
*
29806 ACTGTAGTAGTGAATCGATGC
1 ACTGTAGCAGTGAATCGATGC
*
29827 ACTGTAGCAGTGCATCGAT
1 ACTGTAGCAGTGAATCGAT
29846 ACACATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
ACTGTAGCAGTGAATCGATGC
Found at i:31444 original size:17 final size:16
Alignment explanation
Indices: 31378--31445 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
31368 GTACTTAACT
31378 AATAATAATCAA-ATACA
1 AATAATAAT-AATATA-A
* * *
31395 AATAATAACAATTTCA
1 AATAATAATAATATAA
*
31411 AATTATAGATAATATAA
1 AATAATA-ATAATATAA
31428 AATAATAATAATAATAA
1 AATAATAATAAT-ATAA
31445 A
1 A
31446 TAGAAAGCTC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
16 14 0.35
17 26 0.65
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.29
Consensus pattern (16 bp):
AATAATAATAATATAA
Found at i:48717 original size:17 final size:18
Alignment explanation
Indices: 48691--48729 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
48681 AAATGTCTTT
*
48691 AAAATGTTTTCAAGA-AA
1 AAAATCTTTTCAAGACAA
*
48708 AAAATCTTTTTAAGACAA
1 AAAATCTTTTCAAGACAA
48726 AAAA
1 AAAA
48730 CGATCTGCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (18 bp):
AAAATCTTTTCAAGACAA
Found at i:50299 original size:36 final size:36
Alignment explanation
Indices: 50251--50334 Score: 141
Period size: 36 Copynumber: 2.3 Consensus size: 36
50241 AATCGAATTA
50251 AACGGGGACGGGGAAAAACCGTTTATGCTAAACGGG
1 AACGGGGACGGGGAAAAACCGTTTATGCTAAACGGG
* * *
50287 GACGGGAACGGGGGAAAACCGTTTATGCTAAACGGG
1 AACGGGGACGGGGAAAAACCGTTTATGCTAAACGGG
50323 AACGGGGACGGG
1 AACGGGGACGGG
50335 TTTGGTAATC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.31, C:0.17, G:0.40, T:0.12
Consensus pattern (36 bp):
AACGGGGACGGGGAAAAACCGTTTATGCTAAACGGG
Found at i:50373 original size:12 final size:12
Alignment explanation
Indices: 50345--50381 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
50335 TTTGGTAATC
*
50345 CCCGCCCCGATTA
1 CCCGGCCCGA-TA
50358 CCCGGCCCGATA
1 CCCGGCCCGATA
50370 CCCGGCCCGATA
1 CCCGGCCCGATA
50382 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.16, C:0.51, G:0.22, T:0.11
Consensus pattern (12 bp):
CCCGGCCCGATA
Found at i:50633 original size:31 final size:31
Alignment explanation
Indices: 50598--50664 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
50588 GTTTTTTAAG
*
50598 CGGGGACGGGTACGAGTTTTTTAAATGGGGA
1 CGGGGACGGGTACGAGTTTTTTAAACGGGGA
*
50629 CGGGGACGGTTACGAGTTTTTTAAACGGGGA
1 CGGGGACGGGTACGAGTTTTTTAAACGGGGA
50660 CGGGG
1 CGGGG
50665 GGACCAATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.21, C:0.12, G:0.43, T:0.24
Consensus pattern (31 bp):
CGGGGACGGGTACGAGTTTTTTAAACGGGGA
Found at i:50656 original size:25 final size:25
Alignment explanation
Indices: 50588--50663 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 25
50578 AATCCCCGCG
*
50588 GTTTTTTAAGCGGGGACGGGTACGA
1 GTTTTTTAAACGGGGACGGGTACGA
*
50613 GTTTTTTAAATGGGGACGGGGACGGTTACGA
1 GTTTTTT-AA-----ACGGGGACGGGTACGA
50644 GTTTTTTAAACGGGGACGGG
1 GTTTTTTAAACGGGGACGGG
50664 GGGACCAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
25 17 0.40
26 2 0.05
30 2 0.05
31 21 0.50
ACGTcount: A:0.21, C:0.11, G:0.39, T:0.29
Consensus pattern (25 bp):
GTTTTTTAAACGGGGACGGGTACGA
Found at i:52020 original size:18 final size:19
Alignment explanation
Indices: 51985--52022 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
51975 CACGGAATGT
51985 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
52005 AAGATTACCA-GGGAATAA
1 AAGATTACCAGGGGAATAA
52023 GATTACTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:53560 original size:58 final size:59
Alignment explanation
Indices: 53468--53652 Score: 187
Period size: 59 Copynumber: 3.1 Consensus size: 59
53458 ACATCATATG
* * * * * *
53468 TCCCTAATCTATGACCCTCATT-TCAAATTGGTCCTT-AACTTTAAATATTTTAATTTCA
1 TCCCTAAACTATGATCTTCATTCT-AAATTAGTCCTTAAACTTTAAACATTTCAATTTCA
* * * *
53526 TCCCTAAACTATGATTTTCATTCTAAATTAGTCCTTAAACTTTTAACATTTCATTTTTA
1 TCCCTAAACTATGATCTTCATTCTAAATTAGTCCTTAAACTTTAAACATTTCAATTTCA
* ** * *
53585 TCCCTAAATTATGATCTTCATTCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTAA
1 TCCCTAAACTATGATCTTCATTCTAAATTAGTCCTTAAAC--TTTAAACATTTCAATTTCA
53646 T-CCTAAA
1 TCCCTAAA
53653 TTATATGTAT
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
58 29 0.27
59 54 0.51
60 6 0.06
61 17 0.16
ACGTcount: A:0.31, C:0.21, G:0.04, T:0.43
Consensus pattern (59 bp):
TCCCTAAACTATGATCTTCATTCTAAATTAGTCCTTAAACTTTAAACATTTCAATTTCA
Found at i:53598 original size:59 final size:59
Alignment explanation
Indices: 53492--53656 Score: 199
Period size: 59 Copynumber: 2.8 Consensus size: 59
53482 CCCTCATTTC
* * * * * * *
53492 AAATTGGTCCTT-AACTTTAAATATTTTAATTTCATCCCTAAACTATGATTTTCATTCT
1 AAATTAGTCCTTAAACTTTTAACATTTCAATTTAATCCCTAAATTATGATCTTCATTCT
* *
53550 AAATTAGTCCTTAAACTTTTAACATTTCATTTTTATCCCTAAATTATGATCTTCATTCT
1 AAATTAGTCCTTAAACTTTTAACATTTCAATTTAATCCCTAAATTATGATCTTCATTCT
**
53609 AAATTAGTCCCCAAACTTTTTGAACATTTCAATTTAAT-CCTAAATTAT
1 AAATTAGTCCTTAAAC-TTTT-AACATTTCAATTTAATCCCTAAATTAT
53657 ATGTATATAC
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
58 11 0.12
59 53 0.58
60 14 0.15
61 14 0.15
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (59 bp):
AAATTAGTCCTTAAACTTTTAACATTTCAATTTAATCCCTAAATTATGATCTTCATTCT
Found at i:60311 original size:29 final size:30
Alignment explanation
Indices: 60278--60342 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
60268 AATTATCATT
* * *
60278 TGGTCAGTGACCTT-CCAAATGTTAGAAAA
1 TGGTCAGTAACCTTCCCAAAAGTTACAAAA
* *
60307 TGGTCATTAAGCTTCCCAAAAGTTACAAAA
1 TGGTCAGTAACCTTCCCAAAAGTTACAAAA
60337 TGGTCA
1 TGGTCA
60343 TTAAAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (30 bp):
TGGTCAGTAACCTTCCCAAAAGTTACAAAA
Found at i:61010 original size:33 final size:34
Alignment explanation
Indices: 60971--61042 Score: 128
Period size: 33 Copynumber: 2.1 Consensus size: 34
60961 CCTTAAAGAA
60971 TTTATGTTTCTTCTAGTTGAAATTTAAG-AATTC
1 TTTATGTTTCTTCTAGTTGAAATTTAAGAAATTC
*
61004 TTTATGTTTCTTCTAGTTGAAATTTAAGAAATTT
1 TTTATGTTTCTTCTAGTTGAAATTTAAGAAATTC
61038 TTTAT
1 TTTAT
61043 CCAAGTTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 28 0.76
34 9 0.24
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.54
Consensus pattern (34 bp):
TTTATGTTTCTTCTAGTTGAAATTTAAGAAATTC
Found at i:69625 original size:53 final size:53
Alignment explanation
Indices: 69556--69709 Score: 290
Period size: 53 Copynumber: 2.9 Consensus size: 53
69546 AGGTAGCAAT
*
69556 CTAAAACTATATCACAAGTCACAACCCAGAAGGTGAAGAGAGAAATACCATTG
1 CTAAAACTCTATCACAAGTCACAACCCAGAAGGTGAAGAGAGAAATACCATTG
69609 CTAAAACTCTATCACAAGTCACAACCCAGAAGGTGAAGAGAGAAATACCATTG
1 CTAAAACTCTATCACAAGTCACAACCCAGAAGGTGAAGAGAGAAATACCATTG
*
69662 CTAAAACTCTATCACAAGTCACAACCCAGAAGGTGAATAGAGAAATAC
1 CTAAAACTCTATCACAAGTCACAACCCAGAAGGTGAAGAGAGAAATAC
69710 AAGGAATGCA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 99 1.00
ACGTcount: A:0.45, C:0.22, G:0.16, T:0.17
Consensus pattern (53 bp):
CTAAAACTCTATCACAAGTCACAACCCAGAAGGTGAAGAGAGAAATACCATTG
Found at i:70802 original size:19 final size:18
Alignment explanation
Indices: 70756--70802 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
70746 GATGAACTGT
70756 TATTCGTACCGAATTTGG
1 TATTCGTACCGAATTTGG
70774 TA-TCTGTACCGAATTTGGG
1 TATTC-GTACCGAATTT-GG
*
70793 TATTCATACC
1 TATTCGTACC
70803 AAAGGCTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 2 0.08
18 13 0.52
19 8 0.32
20 2 0.08
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (18 bp):
TATTCGTACCGAATTTGG
Found at i:72143 original size:27 final size:27
Alignment explanation
Indices: 72107--72162 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
72097 TTAGAGGCCT
*
72107 TTTATAGGTGTACCCATGGTGAGACCC
1 TTTATAGGTGTACCAATGGTGAGACCC
*
72134 TTTATAGGTGTACCAATGGTGAGGCCC
1 TTTATAGGTGTACCAATGGTGAGACCC
72161 TT
1 TT
72163 AGCAAAGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (27 bp):
TTTATAGGTGTACCAATGGTGAGACCC
Found at i:76375 original size:20 final size:20
Alignment explanation
Indices: 76350--76421 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
76340 AGATAAACTA
*
76350 GTATCCATACTAGAGGACTG
1 GTATCCATACCAGAGGACTG
* * *
76370 GTATCCACACCAGATGATTG
1 GTATCCATACCAGAGGACTG
* *
76390 GCATCCATACCAGATGAACTG
1 GTATCCATACCAGA-GGACTG
*
76411 GTATCCGTACC
1 GTATCCATACC
76422 GAATTTAGGT
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 28 0.70
21 12 0.30
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (20 bp):
GTATCCATACCAGAGGACTG
Found at i:86626 original size:40 final size:40
Alignment explanation
Indices: 86581--86659 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
86571 TCGAGGGTTA
*
86581 TAGTGGTCTTTCGGGACATATCCAGTGGTCATTCGGGACG
1 TAGTGGTCCTTCGGGACATATCCAGTGGTCATTCGGGACG
*
86621 TAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGAC
1 TAGTGGTCCTTCGGGACATATCCAGTGGTCATTCGGGAC
86660 AAATATTCAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.16, C:0.23, G:0.32, T:0.29
Consensus pattern (40 bp):
TAGTGGTCCTTCGGGACATATCCAGTGGTCATTCGGGACG
Found at i:86671 original size:24 final size:22
Alignment explanation
Indices: 86582--86660 Score: 103
Period size: 22 Copynumber: 3.8 Consensus size: 22
86572 CGAGGGTTAT
*
86582 AGTGGTCTTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
* *
86604 AGTGGTCATTCGGGAC--GT--
1 AGTGGTCCTTCGGGACATATCC
86622 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
86644 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
86661 AATATTCAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 15 0.31
20 2 0.04
22 32 0.65
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.28
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACATATCC
Found at i:86677 original size:24 final size:22
Alignment explanation
Indices: 86628--86677 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
86618 ACGTAGTGGT
**
86628 CCTTCGGGACATATCCAGTGGT
1 CCTTCGGGACATATCCAGTGCC
*
86650 CCTTCGGGACAAATATTCAGTGCC
1 CCTTCGGGAC--ATATCCAGTGCC
86674 CCTT
1 CCTT
86678 GAGGGTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
24 13 0.57
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (22 bp):
CCTTCGGGACATATCCAGTGCC
Found at i:94554 original size:472 final size:472
Alignment explanation
Indices: 93662--94601 Score: 1763
Period size: 472 Copynumber: 2.0 Consensus size: 472
93652 AAGAGTTTGT
93662 GCTTTATGAAATGATTCCACAACTTCACTTGTGGAAGTAGGCTCTCCCAGTCCACGGTCTTGAGG
1 GCTTTATGAAATGATTCCACAACTTCACTTGTGGAAGTAGGCTCTCCCAGTCCACGGTCTTGAGG
*
93727 CTCATTTGTTGACCATTCCATTGTGTGTCGGGAAGACATAGGTCTTCCTGGATGCCTTGGTAAGT
66 CTCATTTGTTGACCATTCCATTGCGTGTCGGGAAGACATAGGTCTTCCTGGATGCCTTGGTAAGT
* *
93792 TTCATTGTCAGCTTCTTGAGCGAAACTAGCATAGTGGTCTTCAGTAACCTGTAGTTTAAAATAGC
131 TTCATTGTCAGCTTCTTGAGCGAAACTAGCATAGTGGTCTTCAGCAACCTATAGTTTAAAATAGC
*
93857 GATTAATGGCAGTATGAGTAAAACGAATAGAAATGTCGTAAACCACCACGGCATGCTGATTTGGC
196 GATTAATGGCAGTATGAGTAAAACGAATAGAAATGTCGTAAACCACCACGACATGCTGATTTGGC
93922 TCGGTGTTGTTTGAATAAAACTCATTCACTATGGTTGCGTTGACGGCGACGGGATGCTTGGCAAA
261 TCGGTGTTGTTTGAATAAAACTCATTCACTATGGTTGCGTTGACGGCGACGGGATGCTTGGCAAA
*
93987 TTTTTTCCACTTATGTGTGGTGACCACATCGAGCACCTCGCTCCACAAGTCGGTATCCTCCTCCT
326 TTTTTGCCACTTATGTGTGGTGACCACATCGAGCACCTCGCTCCACAAGTCGGTATCCTCCTCCT
*
94052 CGAAGAAGACAAACCCCAACTCAAAAAAGACTCACCGGTTCTTGATAGTTTGGAACCGCTCACGG
391 CGAAGAAGACAAACCCCAACTCAAAAAAGACTCACCGATTCTTGATAGTTTGGAACCGCTCACGG
94117 GTGACATCATCTACAAA
456 GTGACATCATCTACAAA
* *
94134 GCTTTATGAAATGATTCCACAATTTCACTTGTGGAAGTAGTCTCTCCCAGTCCACGGTCTTGAGG
1 GCTTTATGAAATGATTCCACAACTTCACTTGTGGAAGTAGGCTCTCCCAGTCCACGGTCTTGAGG
94199 CTCATTTGTTGACCATTCCATTGCGTGTCGGGAAGACATAGGTCTTCCTGGATGCCTTGGTAAGT
66 CTCATTTGTTGACCATTCCATTGCGTGTCGGGAAGACATAGGTCTTCCTGGATGCCTTGGTAAGT
*
94264 TTCATTGTCATCTTCTTGAGCGAAACTAGCATAGTGGTCTTCAGCAACCTATAGTTTAAAATAGC
131 TTCATTGTCAGCTTCTTGAGCGAAACTAGCATAGTGGTCTTCAGCAACCTATAGTTTAAAATAGC
94329 GATTAATGGCAGTATGAGTAAAACGAATAGAAATGTCGTAAACCACCACGACATGCTGATTTGGC
196 GATTAATGGCAGTATGAGTAAAACGAATAGAAATGTCGTAAACCACCACGACATGCTGATTTGGC
94394 TCGGTGTTGTTTGAATAAAACTCATTCACTATGGTTGCGTTGACGGCGACGGGATGCTTGGCAAA
261 TCGGTGTTGTTTGAATAAAACTCATTCACTATGGTTGCGTTGACGGCGACGGGATGCTTGGCAAA
*
94459 TTTTTGCCACTTATGTGTGGTGACCACATCGAGCACCTCGCTCCACAAGTCGGTATCCTCTTCCT
326 TTTTTGCCACTTATGTGTGGTGACCACATCGAGCACCTCGCTCCACAAGTCGGTATCCTCCTCCT
* **
94524 CGGAGAAGACAAACCCCAACTCGGAAAAGACTCACCGATTCTTGATAGTTTGGAACCGCTCACGG
391 CGAAGAAGACAAACCCCAACTCAAAAAAGACTCACCGATTCTTGATAGTTTGGAACCGCTCACGG
94589 GTGACATCATCTA
456 GTGACATCATCTA
94602 TAAATTGTGG
Statistics
Matches: 455, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
472 455 1.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (472 bp):
GCTTTATGAAATGATTCCACAACTTCACTTGTGGAAGTAGGCTCTCCCAGTCCACGGTCTTGAGG
CTCATTTGTTGACCATTCCATTGCGTGTCGGGAAGACATAGGTCTTCCTGGATGCCTTGGTAAGT
TTCATTGTCAGCTTCTTGAGCGAAACTAGCATAGTGGTCTTCAGCAACCTATAGTTTAAAATAGC
GATTAATGGCAGTATGAGTAAAACGAATAGAAATGTCGTAAACCACCACGACATGCTGATTTGGC
TCGGTGTTGTTTGAATAAAACTCATTCACTATGGTTGCGTTGACGGCGACGGGATGCTTGGCAAA
TTTTTGCCACTTATGTGTGGTGACCACATCGAGCACCTCGCTCCACAAGTCGGTATCCTCCTCCT
CGAAGAAGACAAACCCCAACTCAAAAAAGACTCACCGATTCTTGATAGTTTGGAACCGCTCACGG
GTGACATCATCTACAAA
Found at i:105334 original size:18 final size:18
Alignment explanation
Indices: 105307--105341 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
105297 TCGAGGGTTA
105307 TAGTGATCCTTCGGGACG
1 TAGTGATCCTTCGGGACG
*
105325 TAGTGGTCCTTCGGGAC
1 TAGTGATCCTTCGGGAC
105342 AAATATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (18 bp):
TAGTGATCCTTCGGGACG
Found at i:107703 original size:14 final size:15
Alignment explanation
Indices: 107684--107712 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
107674 CTAGAACTAT
107684 CTTAGTTTA-TTTTA
1 CTTAGTTTAGTTTTA
107698 CTTAGTTTAGTTTTA
1 CTTAGTTTAGTTTTA
107713 TCAGTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (15 bp):
CTTAGTTTAGTTTTA
Found at i:110514 original size:32 final size:32
Alignment explanation
Indices: 110452--110517 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
110442 CTCTTCCAGC
* * *
110452 AAGCCCTACAAAAGCAATTGAAATATGAAAAT
1 AAGCCATACAAAAACAATTCAAATATGAAAAT
*
110484 AAGCCATACAAAAACAGTTCAAAT-TCGAAAAT
1 AAGCCATACAAAAACAATTCAAATAT-GAAAAT
110516 AA
1 AA
110518 ACTCTTACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 1 0.03
32 28 0.97
ACGTcount: A:0.55, C:0.17, G:0.11, T:0.18
Consensus pattern (32 bp):
AAGCCATACAAAAACAATTCAAATATGAAAAT
Found at i:113755 original size:31 final size:30
Alignment explanation
Indices: 113690--113806 Score: 110
Period size: 31 Copynumber: 3.8 Consensus size: 30
113680 AAATTTTAAA
* *
113690 AAAATTGA-AAGTTTAAGTACCAAAACAGATC
1 AAAATTGATAA-TTTAGGTACTAAAACA-ATC
*
113721 AAAATTGATAATTTAGGTACTAAAACATACC
1 AAAATTGATAATTTAGGTACTAAAACA-ATC
* * * *
113752 AAAACTGATAATTTTGTTACTAAAATGAATC
1 AAAATTGATAATTTAGGTACTAAAA-CAATC
* *
113783 AAAATTGATAGTTTATGTACTAAA
1 AAAATTGATAATTTAGGTACTAAA
113807 TGCATTAAGT
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
31 67 0.96
32 3 0.04
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (30 bp):
AAAATTGATAATTTAGGTACTAAAACAATC
Found at i:114357 original size:21 final size:21
Alignment explanation
Indices: 114306--114358 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
114296 ATTATGACTA
114306 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* **
114327 TTGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
114348 TCGCAATGCGA
1 TCGCAATGCGA
114359 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:114373 original size:20 final size:21
Alignment explanation
Indices: 114348--114399 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
114338 TTTTCCCAAT
*
114348 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
114368 TCGCAATACGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
114389 TCGCAATGCGA
1 TCGCAATGCGA
114400 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:114413 original size:20 final size:20
Alignment explanation
Indices: 114388--114523 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
114378 AATTTGGAAA
*
114388 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
114408 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
114429 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
114449 TTCGCAATGCGATGCTGACT
1 ATCGCAACGCGATACTGACT
* * *
114469 TTTGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * **
114489 TTCGCAACGAGATTTTTGACT
1 ATCGCAACGCGA-TACTGACT
*
114510 ATCGCAACGAGATA
1 ATCGCAACGCGATA
114524 ATACAGAATC
Statistics
Matches: 96, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.02
20 59 0.61
21 33 0.34
22 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:115316 original size:24 final size:24
Alignment explanation
Indices: 115265--115318 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
115255 GTATTCGAAA
*
115265 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCAGAC
* *
115289 TTTGATATTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
115313 TTTGAT
1 TTTGAT
115319 GATGTTTCAG
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:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:115510 original size:12 final size:12
Alignment explanation
Indices: 115493--115517 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
115483 ATATAATCCT
115493 GAAGAAGAAAAA
1 GAAGAAGAAAAA
115505 GAAGAAGAAAAA
1 GAAGAAGAAAAA
115517 G
1 G
115518 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:117824 original size:20 final size:20
Alignment explanation
Indices: 117799--117895 Score: 160
Period size: 20 Copynumber: 4.8 Consensus size: 20
117789 CAACGGGGAA
117799 ATCGCAACGC-GAATATGGCT
1 ATCGCAACGCGGAA-ATGGCT
117819 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGGCT
117839 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGGCT
117859 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGGCT
* *
117879 ATCGCAATGCGAAAATG
1 ATCGCAACGCGGAAATG
117896 AAAATCGTAT
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
20 71 0.96
21 3 0.04
ACGTcount: A:0.32, C:0.24, G:0.28, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGGCT
Found at i:117826 original size:34 final size:34
Alignment explanation
Indices: 117783--117874 Score: 96
Period size: 40 Copynumber: 2.5 Consensus size: 34
117773 ATTCATTTGA
117783 CTATCGCAACGGGGAAATCGCAACGC-GAATATGG
1 CTATCGCAACGGGGAAATCGCAACGCGGAA-ATGG
*
117817 CTATCGCAACGCGGAAATGGCTATCGCAACGCGGAAATGG
1 CTATCGCAACG-GGGAA-----ATCGCAACGCGGAAATGG
*
117857 CTATCGCAACGCGGAAAT
1 CTATCGCAACGGGGAAAT
117875 GGCTATCGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
34 13 0.27
35 4 0.08
39 3 0.06
40 25 0.52
41 3 0.06
ACGTcount: A:0.32, C:0.25, G:0.28, T:0.15
Consensus pattern (34 bp):
CTATCGCAACGGGGAAATCGCAACGCGGAAATGG
Found at i:119579 original size:41 final size:42
Alignment explanation
Indices: 119533--119620 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
119523 CCTCTTCAAC
*
119533 GATGAT-AGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGATAAG-GGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
119574 GATGATAAGGGCCTCTTGAATGATTGGAGGGGACTCTTGAGG
1 GATGATAAGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
119616 GATGA
1 GATGA
119621 GAGGTGAGTC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 18 0.43
42 24 0.57
ACGTcount: A:0.22, C:0.12, G:0.41, T:0.25
Consensus pattern (42 bp):
GATGATAAGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:119624 original size:21 final size:21
Alignment explanation
Indices: 119560--119624 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
119550 GAACGGTGGG
*
119560 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* * **
119581 AGGGCCTCTTGAATGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
119602 GGGGACTCTTGAGGGATGAGA
1 GGGGACTCTTGAGGGATGAGA
119623 GG
1 GG
119625 TGAGTCGGGC
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.23, C:0.11, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:120031 original size:20 final size:20
Alignment explanation
Indices: 119987--120054 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
119977 TAATTTTAAA
*
119987 ATCGCAACGCGAAAATGAGT
1 ATCGCAACGCGAAAATGACT
* *
120007 GTCGCAACGCGAAAATGTCT
1 ATCGCAACGCGAAAATGACT
* **
120027 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
120046 ATCGCAACG
1 ATCGCAACG
120055 ACAAAATCAC
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 13 0.33
20 26 0.67
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:120049 original size:19 final size:19
Alignment explanation
Indices: 120027--120085 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
120017 GAAAATGTCT
120027 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
120046 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
120060 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
120079 ATCGCAA
1 ATCGCAA
120086 CGACAAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 9 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.52
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:120062 original size:14 final size:14
Alignment explanation
Indices: 120043--120101 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
120033 ATGCGAAATG
120043 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
120057 AAAATCACAATGCGAAATG
1 AAAATCGCAA--CG--A-C
120076 AAAATCGCAACGAC
1 AAAATCGCAACGAC
120090 AAAATCGCAACG
1 AAAATCGCAACG
120102 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.25
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:120117 original size:33 final size:33
Alignment explanation
Indices: 120027--120106 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
120017 GAAAATGTCT
120027 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
120060 ATCACAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
120093 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
120107 CACAAATCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.49, C:0.23, G:0.17, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:120141 original size:20 final size:20
Alignment explanation
Indices: 120113--120235 Score: 91
Period size: 20 Copynumber: 6.5 Consensus size: 20
120103 GAAACACAAA
*
120113 TCGCATTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
120133 TCGCGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTTCATTT
* *
120152 TCGCATTGCGA--TT--TTG
1 TCGCGTTGCGATTTTCATTT
120168 T--CGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTTCATTT
* ***
120185 TCGCATTGCGATAGCCATTT
1 TCGCGTTGCGATTTTCATTT
* * *
120205 CCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCATTT
*
120225 TCGTGTTGCGA
1 TCGCGTTGCGA
120236 AAGTAAACTA
Statistics
Matches: 77, Mismatches: 18, Indels: 16
0.69 0.16 0.14
Matches are distributed among these distances:
14 7 0.09
16 4 0.05
17 4 0.05
19 22 0.29
20 40 0.52
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATTT
Found at i:120807 original size:18 final size:18
Alignment explanation
Indices: 120784--120831 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
120774 CAGGTCGATC
*
120784 AGGTGATGGCTCTCGGTG
1 AGGTGATAGCTCTCGGTG
*
120802 AGGTGATAGCTCTGGGTG
1 AGGTGATAGCTCTCGGTG
*
120820 TGGTGATAGCTC
1 AGGTGATAGCTC
120832 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.42, T:0.29
Consensus pattern (18 bp):
AGGTGATAGCTCTCGGTG
Found at i:122213 original size:20 final size:20
Alignment explanation
Indices: 122161--122228 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
122151 GAAACTTAAA
**
122161 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
*
122181 ATCGGAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* * **
122201 TTCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
122221 ATCGCAAC
1 ATCGCAAC
122229 GAGAGAATCG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:122519 original size:22 final size:22
Alignment explanation
Indices: 122492--122542 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
122482 GATGGAGATA
122492 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
122514 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
122536 GACGGAT
1 GACGGAT
122543 GTCGCCGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.14, G:0.45, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:122763 original size:20 final size:20
Alignment explanation
Indices: 122735--122848 Score: 131
Period size: 20 Copynumber: 5.7 Consensus size: 20
122725 GATTATGTAT
*
122735 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
122755 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
122775 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
** *
122795 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
122816 TATCGCGTTGCGATAGTTAG
1 TATCGCGTTGCGAAAGTCAG
*
122836 TATCGCATTGCGA
1 TATCGCGTTGCGA
122849 TTTTCCAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
19 3 0.04
20 64 0.77
21 14 0.17
22 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:122852 original size:41 final size:41
Alignment explanation
Indices: 122715--122850 Score: 168
Period size: 41 Copynumber: 3.3 Consensus size: 41
122705 CGCTTTGAAA
* *
122715 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTAAGT
* * *
122756 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTAAGT
* * * *
122796 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTTAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTAAGT
122837 ATCGCATTGCGATT
1 ATCGCATTGCGATT
122851 TTCCAAATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 3 0.04
40 32 0.40
41 44 0.54
42 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTAAGT
Found at i:122868 original size:41 final size:41
Alignment explanation
Indices: 122715--122870 Score: 118
Period size: 41 Copynumber: 3.8 Consensus size: 41
122705 CGCTTTGAAA
* ** * * * *
122715 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTAAGT
* *** * *
122756 ATCGCGTTGCGAAAGTC-AGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTAAGT
* ** * *
122796 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTTAGT
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTAAGT
*
122837 ATCGCATTGCGATTTTCCAAAT-TCGCATTGCGAT
1 ATCGCATTGCGATTTT-CAAATATCGCGTTGCGAT
122871 TTACTTATTC
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
40 33 0.35
41 58 0.62
42 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTAAGT
Found at i:122882 original size:20 final size:21
Alignment explanation
Indices: 122838--122889 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
122828 ATAGTTAGTA
*
122838 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
122859 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
122879 TCGCATTGCGA
1 TCGCATTGCGA
122890 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:122909 original size:21 final size:20
Alignment explanation
Indices: 122879--122931 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
122869 ATTTACTTAT
122879 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
* *
122900 TCGCAATGCGAAATTTGAAAA
1 TCGCATTGCG-AATTGGAAAA
122921 TCGCATTGCGA
1 TCGCATTGCGA
122932 TAGTCATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:123154 original size:21 final size:21
Alignment explanation
Indices: 123125--123166 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
123115 ATATTTATCA
*
123125 TTATATTAATTTGATATAATTT
1 TTATATTAATTTAATA-AATTT
123147 TTAT-TTAATTTAATAAATTT
1 TTATATTAATTTAATAAATTT
123167 AATCATCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTATATTAATTTAATAAATTT
Found at i:129844 original size:18 final size:17
Alignment explanation
Indices: 129811--129844 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
129801 TGCGTGAGGT
*
129811 CCTTTTTTTTAGTTTTC
1 CCTTTTTTTTAATTTTC
129828 CCTTTTTTTCTAATTTT
1 CCTTTTTTT-TAATTTT
129845 TTTTCTCTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.71
Consensus pattern (17 bp):
CCTTTTTTTTAATTTTC
Found at i:133967 original size:65 final size:65
Alignment explanation
Indices: 133897--134030 Score: 162
Period size: 65 Copynumber: 2.1 Consensus size: 65
133887 AGAAAATATT
* **
133897 ACCCTTGGGCTGCACAATTAAAATTATAGCTTTTAATTTC-AAAATAATCGCTTCAAACAAAGGA
1 ACCCTTCGGCTGCACAATTAAAATTATAGCTTTTAA-TTCAAAAATAATAACTTCAAACAAAGGA
133961 A
65 A
* * * * * * *
133962 ACCCTTCGTCTGCAGAATTACAATTATGGGTTTTAATTCAAAAATAATAACTTTAAACAATGGAA
1 ACCCTTCGGCTGCACAATTAAAATTATAGCTTTTAATTCAAAAATAATAACTTCAAACAAAGGAA
134027 ACCC
1 ACCC
134031 ATCATAAATC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 3 0.05
65 55 0.95
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.30
Consensus pattern (65 bp):
ACCCTTCGGCTGCACAATTAAAATTATAGCTTTTAATTCAAAAATAATAACTTCAAACAAAGGAA
Found at i:136289 original size:21 final size:21
Alignment explanation
Indices: 136263--136303 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
136253 ATAGTTTGTG
*
136263 TATCTAGGCTTTTTTTTACAC
1 TATCTAGGCTTTCTTTTACAC
136284 TATCTAGGCTTTCTTTTACA
1 TATCTAGGCTTTCTTTTACA
136304 GATCGGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51
Consensus pattern (21 bp):
TATCTAGGCTTTCTTTTACAC
Found at i:136588 original size:30 final size:30
Alignment explanation
Indices: 136552--136616 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
136542 AATTAGAGAA
136552 ATTTTTTAACAAGACTCGTGTTTATGTCAT
1 ATTTTTTAACAAGACTCGTGTTTATGTCAT
*
136582 ATTTTTTAACGAGACTCGTGTTTATGTCAT
1 ATTTTTTAACAAGACTCGTGTTTATGTCAT
*
136612 GTTTT
1 ATTTT
136617 ATATGCATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.49
Consensus pattern (30 bp):
ATTTTTTAACAAGACTCGTGTTTATGTCAT
Found at i:144540 original size:34 final size:34
Alignment explanation
Indices: 144497--144566 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
144487 CACTGGCACG
144497 AGGCTAATTATTTGCCTTGAAATGGACTATATGT
1 AGGCTAATTATTTGCCTTGAAATGGACTATATGT
144531 AGGCTAATTATTTGCCTTGAAATGGACTATATGT
1 AGGCTAATTATTTGCCTTGAAATGGACTATATGT
144565 AG
1 AG
144567 TATATAACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.37
Consensus pattern (34 bp):
AGGCTAATTATTTGCCTTGAAATGGACTATATGT
Done.