Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003337.1 Hibiscus syriacus cultivar Beakdansim tig00007026_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: 92738
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:381 original size:52 final size:53
Alignment explanation
Indices: 266--370 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
256 TTTAACATAA
*
266 TTTCCATTTTTTGTGGCATTCTTAAAGAAAATTTCTTGAATTGTTACTACAAG
1 TTTCCATTTTTTGTGGCATTCTTAAAGAAAAATTCTTGAATTGTTACTACAAG
319 TTTCCATTTTTT-TGGCATTCTTAAAAGAAAAATTCTTGAATTGTTACTACAA
1 TTTCCATTTTTTGTGGCATTCTT-AAAGAAAAATTCTTGAATTGTTACTACAA
371 TTTTTGTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 10 0.20
53 40 0.80
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (53 bp):
TTTCCATTTTTTGTGGCATTCTTAAAGAAAAATTCTTGAATTGTTACTACAAG
Found at i:9840 original size:24 final size:24
Alignment explanation
Indices: 9809--9864 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
9799 TTACATTTTA
9809 AAACATACTATAAGGTATCAAAAT
1 AAACATACTATAAGGTATCAAAAT
*
9833 AAACATACTATATGGTATCAAAAT
1 AAACATACTATAAGGTATCAAAAT
9857 AAACATAC
1 AAACATAC
9865 ATGACAGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (24 bp):
AAACATACTATAAGGTATCAAAAT
Found at i:10412 original size:32 final size:32
Alignment explanation
Indices: 10375--10465 Score: 121
Period size: 32 Copynumber: 2.8 Consensus size: 32
10365 TGACATTGAC
*
10375 ACTGTTATGCATTATCTGAATACAACAGTAACT
1 ACTGTTGTGCATTATCTGAATACAACAGTAA-T
* *
10408 -CTGTTGTTCATTATCTGAATACAACATTAAT
1 ACTGTTGTGCATTATCTGAATACAACAGTAAT
* *
10439 ACTGTTGTGCATTATTTGAATGCAACA
1 ACTGTTGTGCATTATCTGAATACAACA
10466 CTGCTAGTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
31 1 0.02
32 50 0.98
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (32 bp):
ACTGTTGTGCATTATCTGAATACAACAGTAAT
Found at i:21688 original size:15 final size:15
Alignment explanation
Indices: 21665--21706 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
21655 AAATATTTGT
*
21665 TTTACAATTGATAAA
1 TTTAAAATTGATAAA
21680 TTTAAAATTGATAAA
1 TTTAAAATTGATAAA
21695 TTTAAAA-TGATA
1 TTTAAAATTGATA
21707 TATCAGAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (15 bp):
TTTAAAATTGATAAA
Found at i:23390 original size:64 final size:62
Alignment explanation
Indices: 23308--23464 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 62
23298 TTCAGTATGT
* * * *
23308 ATCGATGCACAGGAAGTGCATCGATGCACCCCTTAAAAATGGAAATATCGAA-TGCAATTAGTGC
1 ATCGATGCATAGGGAGTGCATCGATGCACCCCTT-AAAATGAAAACATCGAAGTGC--TTAGTGC
* * * * *
23372 ATCGATGCATAGGGAGTGCATCGATACACCCCCTTAAGATTAAAACATCGAAGGTGCTTTGTGT
1 ATCGATGCATAGGGAGTGCATCGATGCA-CCCCTTAAAATGAAAACATCGAA-GTGCTTAGTGC
23436 ATCGATGCAT-GGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGG-AGTGCATCGATGCAC
23465 ATGTTAAGGG
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
63 4 0.05
64 66 0.84
65 6 0.08
66 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (62 bp):
ATCGATGCATAGGGAGTGCATCGATGCACCCCTTAAAATGAAAACATCGAAGTGCTTAGTGC
Found at i:24577 original size:2 final size:2
Alignment explanation
Indices: 24570--24605 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
24560 AGGTAAAATG
24570 AT AT AT AT AT AT AT AT AT AT AT A- ACT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
24606 TACTATGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24610 original size:14 final size:14
Alignment explanation
Indices: 24570--24611 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
24560 AGGTAAAATG
24570 ATATATATA-TA-T
1 ATATATATATTACT
*
24582 ATATATATATAACT
1 ATATATATATTACT
24596 ATATATATATTACT
1 ATATATATATTACT
24610 AT
1 AT
24612 GAGTTGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 9 0.35
13 1 0.04
14 16 0.62
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATATATATTACT
Found at i:25180 original size:23 final size:23
Alignment explanation
Indices: 25112--25172 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
25102 ACATTTTATA
*
25112 TGGCACTTCGGTGCAATTCTATG
1 TGGCACTTCGGTGCAATTCTACG
*
25135 TGGAACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
25158 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
25173 TTTATACGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:27509 original size:17 final size:17
Alignment explanation
Indices: 27487--27520 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27477 ATGGACAAAG
27487 GAAAATGCAGAATAGAA
1 GAAAATGCAGAATAGAA
27504 GAAAATGCAGAATAGAA
1 GAAAATGCAGAATAGAA
27521 AGAGAGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.24, T:0.12
Consensus pattern (17 bp):
GAAAATGCAGAATAGAA
Found at i:27968 original size:16 final size:16
Alignment explanation
Indices: 27947--27987 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
27937 TCCAGAGTTC
27947 TCTTCTTCTCATTTCT
1 TCTTCTTCTCATTTCT
*
27963 TCTTCTTCTCCTTTCT
1 TCTTCTTCTCATTTCT
27979 TCTTCTTCT
1 TCTTCTTCT
27988 TCACGTGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.63
Consensus pattern (16 bp):
TCTTCTTCTCATTTCT
Found at i:28952 original size:90 final size:90
Alignment explanation
Indices: 28792--28969 Score: 257
Period size: 90 Copynumber: 2.0 Consensus size: 90
28782 CCTAACACAC
* * * * *
28792 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTAAAATTAATTAAATATAT
* * *
28857 GTTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* *
28882 CCTTTTATATCCAAGTTACCCTAATTATATCAGGGATTTTATTATTTAAAATTAATTAAATATAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTAAAATTAATTAAATATAT
*
28947 ATTTAATTAGTTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
28970 TTCGGGATTA
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 77 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTAAAATTAATTAAATATAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:31297 original size:2 final size:2
Alignment explanation
Indices: 31290--31358 Score: 129
Period size: 2 Copynumber: 34.0 Consensus size: 2
31280 AGGTAAAATG
31290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31332 AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT
31359 GACTATGAGT
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 64 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31905 original size:23 final size:23
Alignment explanation
Indices: 31871--31930 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
31861 CATTTTATAT
31871 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
31894 GGCACTTTGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
* *
31917 GGCATTTCAGTGCA
1 GGCACTTCGGTGCA
31931 TTTATACAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:43784 original size:18 final size:18
Alignment explanation
Indices: 43761--43806 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
43751 GACCGACTAT
*
43761 TCTTCTTCTTCAACCCCA
1 TCTTCTTCTTCAACCCAA
*
43779 TCTTCTTCCTCAACCCAA
1 TCTTCTTCTTCAACCCAA
43797 TC-TCTTCTTC
1 TCTTCTTCTTC
43807 TTTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.15, C:0.43, G:0.00, T:0.41
Consensus pattern (18 bp):
TCTTCTTCTTCAACCCAA
Found at i:44429 original size:17 final size:18
Alignment explanation
Indices: 44407--44440 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44397 AAAGAAAGAA
44407 GAAGAAGATG-GGTTGAG
1 GAAGAAGATGTGGTTGAG
*
44424 GAAGAATATGTGGTTGA
1 GAAGAAGATGTGGTTGA
44441 TTAATTGTAA
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:0.35, C:0.00, G:0.41, T:0.24
Consensus pattern (18 bp):
GAAGAAGATGTGGTTGAG
Found at i:49740 original size:2 final size:2
Alignment explanation
Indices: 49733--49758 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
49723 TTTTAAACAA
49733 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
49759 GACTAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49887 original size:20 final size:19
Alignment explanation
Indices: 49864--49905 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
49854 GATTAAATTG
*
49864 AAAAATATAAAAATTAATAA
1 AAAAAAATAAAAATT-ATAA
*
49884 AAAAAAATGAAAATTATAA
1 AAAAAAATAAAAATTATAA
49903 AAA
1 AAA
49906 TCAATGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAAAAATAAAAATTATAA
Found at i:51392 original size:3 final size:3
Alignment explanation
Indices: 51384--51436 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
51374 AATTATTTAT
* * * *
51384 TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TTA TAA AAA TAA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
51431 TAA TAA
1 TAA TAA
51437 AACGGGACAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:51413 original size:20 final size:20
Alignment explanation
Indices: 51388--51425 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
51378 ATTTATTAAT
*
51388 AATAATAATAATAATAATAA
1 AATAATAATAAAAATAATAA
*
51408 AATAATTATAAAAATAAT
1 AATAATAATAAAAATAAT
51426 TATTATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAATAATAAAAATAATAA
Found at i:53219 original size:32 final size:32
Alignment explanation
Indices: 53183--53275 Score: 118
Period size: 32 Copynumber: 2.9 Consensus size: 32
53173 AATTTTGGAT
53183 GTGACACGTGTCACTTAACATGA-TTTTTAGAC
1 GTGACACGTGTCACTTAACA-GAGTTTTTAGAC
* * * *
53215 GTGACATGTGTCATTTAAC-GAATTTTTTTGAC
1 GTGACACGTGTCACTTAACAG-AGTTTTTAGAC
53247 GTGACACGTGTCACTTAACAGAGTTTTTA
1 GTGACACGTGTCACTTAACAGAGTTTTTA
53276 ACAGTAGGTA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
30 1 0.02
31 1 0.02
32 48 0.94
33 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (32 bp):
GTGACACGTGTCACTTAACAGAGTTTTTAGAC
Found at i:55084 original size:27 final size:27
Alignment explanation
Indices: 55054--55105 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
55044 TAATGGATAA
55054 AGTTTCTTGGGAGTAGTTGCAAAGCTC
1 AGTTTCTTGGGAGTAGTTGCAAAGCTC
*
55081 AGTTTCTTGGGGGTAGTTGCAAAGC
1 AGTTTCTTGGGAGTAGTTGCAAAGC
55106 CCTTAAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.13, G:0.33, T:0.33
Consensus pattern (27 bp):
AGTTTCTTGGGAGTAGTTGCAAAGCTC
Found at i:56290 original size:22 final size:22
Alignment explanation
Indices: 56262--56315 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
56252 ATTAAATCCC
56262 TATTTTTATTGAATAAAAATAA
1 TATTTTTATTGAATAAAAATAA
56284 TATTTTTATTGAATAAAAATAA
1 TATTTTTATTGAATAAAAATAA
*
56306 CATTTTTATT
1 TATTTTTATT
56316 ATTTCAGTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (22 bp):
TATTTTTATTGAATAAAAATAA
Found at i:57447 original size:2 final size:2
Alignment explanation
Indices: 57440--57476 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
57430 ACCGAATTTA
57440 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57477 AATAGTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60008 original size:19 final size:20
Alignment explanation
Indices: 59981--60018 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
59971 TTAGGGTTGA
59981 GAGACGGGAGA-GCAGAGAG
1 GAGACGGGAGAGGCAGAGAG
*
60000 GAGATGGGAGAGGCAGAGA
1 GAGACGGGAGAGGCAGAGA
60019 ACGGCGAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.08, G:0.53, T:0.03
Consensus pattern (20 bp):
GAGACGGGAGAGGCAGAGAG
Found at i:62131 original size:23 final size:23
Alignment explanation
Indices: 62104--62151 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
62094 CTGGGTACAT
62104 TTCTTATGTTTACGAGTGAAACA
1 TTCTTATGTTTACGAGTGAAACA
62127 TTCTTATGTTTACGAGTGAAACA
1 TTCTTATGTTTACGAGTGAAACA
62150 TT
1 TT
62152 GAGTTTCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (23 bp):
TTCTTATGTTTACGAGTGAAACA
Found at i:62902 original size:21 final size:21
Alignment explanation
Indices: 62878--63036 Score: 209
Period size: 21 Copynumber: 7.6 Consensus size: 21
62868 TTGTACCAAG
*
62878 GACGAGAAGAGCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
62899 GACGAGAATG-TCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
62920 GACGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
*
62941 GACGAGAAGGCCATTCATCAA
1 GACGAGAAGACCATTCATCAA
62962 GACGAGAAGACCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
62983 GACGAGAAGACCTTTCAT-AA
1 GACGAGAAGACCATTCATCAA
* *
63003 CGACGAGAAGACC-TTCGTAAA
1 -GACGAGAAGACCATTCATCAA
63024 GACGAGAAGACCA
1 GACGAGAAGACCA
63037 CATCACATGG
Statistics
Matches: 128, Mismatches: 5, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
20 19 0.15
21 108 0.84
22 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (21 bp):
GACGAGAAGACCATTCATCAA
Found at i:65589 original size:12 final size:11
Alignment explanation
Indices: 65559--65636 Score: 59
Period size: 11 Copynumber: 6.5 Consensus size: 11
65549 GTCATTATGT
*
65559 AGAAAGAGAAA
1 AGAAAAAGAAA
*
65570 AGGAAAAGAAA
1 AGAAAAAGAAA
65581 AGAAGAAAGAAA
1 AGAA-AAAGAAA
65593 AGAAAAATTGAAA
1 AGAAAAA--GAAA
65606 ATGAGGAAAATGAAA
1 A-GA--AAAA-GAAA
*
65621 AGAAAATG-AA
1 AGAAAAAGAAA
65631 AGAAAA
1 AGAAAA
65637 TCGATCAAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
10 8 0.14
11 16 0.28
12 14 0.25
13 5 0.09
14 4 0.07
15 6 0.11
16 4 0.07
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:65605 original size:17 final size:17
Alignment explanation
Indices: 65559--65598 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
65549 GTCATTATGT
*
65559 AGAAAGAGAA-AAGGAAA
1 AGAAA-AGAAGAAAGAAA
65576 AGAAAAGAAGAAAGAAA
1 AGAAAAGAAGAAAGAAA
65593 AGAAAA
1 AGAAAA
65599 ATTGAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AGAAAAGAAGAAAGAAA
Found at i:67108 original size:124 final size:125
Alignment explanation
Indices: 66888--67148 Score: 373
Period size: 124 Copynumber: 2.1 Consensus size: 125
66878 AAGTTGTGAT
* * * *
66888 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCGGACCAAGGAGGCCTGAA
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATACAGACCAAGAAGACCTGAA
* *
66953 GAATGAGCCTTATAATTTGAGGTGATGGGGCATTTTGAAGGCCCATACCAGT-TAAGATA
66 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTCTGAAGGCCCATACCAGTATAAGATA
* **
67012 ATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGATGAGATACAGACCAAGAAGACCTTG-
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATACAGACCAAGAAGACC-TGA
* * * *
67076 AGAATGAGCCTTACAATTTGAGGTGTTGGGGCATTCTGAAGGCCCGTACTAGTATAAGATG
65 AGAATGAGCCTTACAATTTGAGGTGATGGGGCATTCTGAAGGCCCATACCAGTATAAGATA
*
67137 ATGTTGCGGCAC
1 ATGTTGGGGCAC
67149 TAGTGAAGGC
Statistics
Matches: 120, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
124 102 0.85
125 18 0.15
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (125 bp):
ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATACAGACCAAGAAGACCTGAA
GAATGAGCCTTACAATTTGAGGTGATGGGGCATTCTGAAGGCCCATACCAGTATAAGATA
Found at i:68287 original size:36 final size:36
Alignment explanation
Indices: 68183--68278 Score: 138
Period size: 36 Copynumber: 2.7 Consensus size: 36
68173 GAGAGGAGAT
* * *
68183 TGAAGCAGTCCATCTTAAGCATTCACCGAAGAATAA
1 TGAAGCAATCCATCTTAAGCCTTCACCGAAGAGTAA
* *
68219 TGAAGCAAGCCATCTTAAGCCTTCACCGAAGAGTAG
1 TGAAGCAATCCATCTTAAGCCTTCACCGAAGAGTAA
*
68255 TGAAGCAATCCATTTTAAGCCTTC
1 TGAAGCAATCCATCTTAAGCCTTC
68279 TCAAAAGAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (36 bp):
TGAAGCAATCCATCTTAAGCCTTCACCGAAGAGTAA
Found at i:68692 original size:51 final size:51
Alignment explanation
Indices: 68637--69524 Score: 1012
Period size: 51 Copynumber: 16.9 Consensus size: 51
68627 GAAGCAAATG
*
68637 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGGACCCGTTTA
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTA
* * *
68688 AAGATTTTCGAGTTCTATACTCCCTGGAGAAAGAGGGAACGAACCCGTTTG
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTA
* * * *
68739 AAGATGTCCGAGTTCTGTACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTA
* *
68790 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGATGGAGAGAACCCGTTTGAA
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTT--A
* * *
68843 GAAGATGTCCGAGTTCTATACTCCCTG-AGAAAGAGGGAGCGAACCCGTTTG
1 -AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTA
* *
68894 AAGA-TGTCAGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG
1 AAGATTTTC-GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTA
* * * * *
68945 AAGATTTTTGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCACTTGCA
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCC-GTT-TA
* * * *
68998 GAATATTGTTCGAGTTCTATACTCCTTGAAGAAAGAGGGAGCGGACCCGTTTG
1 -AAGATT-TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTA
* * *
69051 AAGATGTCCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTA
* * * * *
69102 AAGATTTTTGAGTTCCATACTCCCTAAAGAAAGAGGGAACGAACCCGCTTGCA
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG-TT-TA
* * *
69155 GAATATTGTTCGAGTTCTATACTCCTTGAAGAAAGAGGGAGCGAACCCGTTTG
1 -AAGATT-TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTA
* * *
69208 AAGATGTCCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTA
* * * * * *
69259 AAGATTTTTGAGTTCCATACTCCCTAAAGAAAAAGGGAGTGAACCCGCTTGCA
1 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG-TT-TA
* *
69312 GAAGATTGTTCGAATTCCATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAA
1 -AAGATT-TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTT--A
* * *
69367 GAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCAGTTAGCA
1 -AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTT--TA
* *
69421 GAAGATTCTT-GAGTTCTATACTCCCTGAA-ACAATAGGGAGCGAACCCGTTAGCA
1 -AAGATT-TTCGAGTTCTATACTCCCTGAAGA-AAGAGGGAGCGAACCCGTT--TA
*
69475 GAAGATTATTCGAGTTCTATACTCCCTGAA-ACAATAGGGAGCGAACCCGT
1 -AAGATT-TTCGAGTTCTATACTCCCTGAAGA-AAGAGGGAGCGAACCCGT
69525 CCCCAGAAGA
Statistics
Matches: 724, Mismatches: 88, Indels: 46
0.84 0.10 0.05
Matches are distributed among these distances:
49 1 0.00
50 21 0.03
51 367 0.51
52 16 0.02
53 22 0.03
54 142 0.20
55 155 0.21
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (51 bp):
AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTA
Found at i:69031 original size:106 final size:103
Alignment explanation
Indices: 68635--69593 Score: 1069
Period size: 106 Copynumber: 9.1 Consensus size: 103
68625 GTGAAGCAAA
*
68635 TGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGGACCCGTTTA-AAGATT-TTCG
1 TGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG-TTAGAAGATTGTTCG
* *
68698 AGTTCTATACTCCCTGGAGAAAGAGGGAACGAACCCGTT
65 AGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTT
* * * *
68737 TGAAGATGTCCGAGTTCTGTACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATT-TTCGA
1 TGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTAGAAGATTGTTCGA
* *
68801 GTTCTATACTCCCTGAAGAAAGATGGAGAGAACCCGTT
66 GTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTT
* * *
68839 TGAAGAAGATGTCCGAGTTCTATACTCCCTG-AGAAAGAGGGAGCGAACCCGTTTGAAGA-TG-T
1 T---GAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTAGAAGATTGTT
68901 CAGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTT
63 C-GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTT
* * * * *
68943 TGAAGATTTTTGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCACTTGCAGAATATTGTT
1 TGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCC-GTT--AGAAGATTGTT
* *
69008 CGAGTTCTATACTCCTTGAAGAAAGAGGGAGCGGACCCGTT
63 CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTT
* * * *
69049 TGAAGATGTCCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATT-TTTGA
1 TGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTAGAAGATTGTTCGA
* * *
69113 GTTCCATACTCCCTAAAGAAAGAGGGAACGAACCCGCTT
66 GTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG-TT
* * * * *
69152 GCAGAATATTGTTCGAGTTCTATACTCCTTGAAGAAAGAGGGAGCGAACCCGTTTGAAGA-TGTC
1 --TGAAGATT-TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTAGAAGATTGTT
69216 CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTT
63 CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTT
* * * * *
69257 TGAAGATTTTTGAGTTCCATACTCCCTAAAGAAAAAGGGAGTGAACCCGCTTGCAGAAGATTGTT
1 TGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG-TT--AGAAGATTGTT
* *
69322 CGAATTCCATACTCCCTGAAGAAAGAGGGAGCGAACCCGTT
63 CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTT
* *
69363 TGAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCAGTTAGCAGAAGATT
1 T---GAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTT---AGAAGATT
* *
69428 CTT-GAGTTCTATACTCCCTGAA-ACAATAGGGAGCGAACCCGTT
60 GTTCGAGTTCTATACTCCCTGAAGA-AAGAGGGAGCGAACCCGTT
* * *
69471 AGCAGAAGATTATTCGAGTTCTATACTCCCTGAA-ACAATAGGGAGCGAACCCGTCCCCAGAAGA
1 ---TGAAGATT-TTCGAGTTCTATACTCCCTGAAGA-AAGAGGGAGCGAACCCGT---TAGAAGA
* * ** * *
69535 TTCTTCAAGTTCTATGTTCCCTGAA-ACGATAGGGAGCGAACCCGATTT
58 TTGTTCGAGTTCTATACTCCCTGAAGA-AAGAGGGAGCGAACCCG--TT
69583 TGAAGAATTTT
1 TGAAG-ATTTT
69594 TCAAGTCTCA
Statistics
Matches: 740, Mismatches: 79, Indels: 69
0.83 0.09 0.08
Matches are distributed among these distances:
101 24 0.03
102 180 0.24
103 21 0.03
104 67 0.09
105 45 0.06
106 209 0.28
107 3 0.00
108 44 0.06
109 108 0.15
110 37 0.05
112 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (103 bp):
TGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTAGAAGATTGTTCGA
GTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTT
Found at i:69099 original size:157 final size:157
Alignment explanation
Indices: 68635--69524 Score: 1303
Period size: 157 Copynumber: 5.7 Consensus size: 157
68625 GTGAAGCAAA
* * * * *
68635 TGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGGACCCG-TT-TA-AAGATT-TT
1 TGAAGATTTTTGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGCTTGCAGAAGATTGTT
* * *
68696 CGAGTTCTATACTCCCTGGAGAAAGAGGGAACGAACCCGTTTGAAGATGTCCGAGTTCTGTACTC
66 CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCTATACTC
68761 CCTGAAGAAAGAGGGAGCGAACCCGTT
131 CCTGAAGAAAGAGGGAGCGAACCCGTT
* * * * * * * *
68788 TGAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGATGGAGAGAACCCGTTTGAAGAAGA-TGTC
1 TGAAGATTTTTGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGCTTGCAGAAGATTGTT
*
68852 CGAGTTCTATACTCCCTG-AGAAAGAGGGAGCGAACCCGTTTGAAGATGTCAGAGTTCTATACTC
66 CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCTATACTC
68916 CCTGAAGAAAGAGGGAGCGAACCCGTT
131 CCTGAAGAAAGAGGGAGCGAACCCGTT
* *
68943 TGAAGATTTTTGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCACTTGCAGAATATTGTT
1 TGAAGATTTTTGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGCTTGCAGAAGATTGTT
* *
69008 CGAGTTCTATACTCCTTGAAGAAAGAGGGAGCGGACCCGTTTGAAGATGTCCGAGTTCTATACTC
66 CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCTATACTC
69073 CCTGAAGAAAGAGGGAGCGAACCCGTT
131 CCTGAAGAAAGAGGGAGCGAACCCGTT
* *
69100 TGAAGATTTTTGAGTTCCATACTCCCTAAAGAAAGAGGGAACGAACCCGCTTGCAGAATATTGTT
1 TGAAGATTTTTGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGCTTGCAGAAGATTGTT
*
69165 CGAGTTCTATACTCCTTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCTATACTC
66 CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCTATACTC
69230 CCTGAAGAAAGAGGGAGCGAACCCGTT
131 CCTGAAGAAAGAGGGAGCGAACCCGTT
* *
69257 TGAAGATTTTTGAGTTCCATACTCCCTAAAGAAAAAGGGAGTGAACCCGCTTGCAGAAGATTGTT
1 TGAAGATTTTTGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGCTTGCAGAAGATTGTT
* * *
69322 CGAATTCCATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATA
66 CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTT---GAAGATGTCCGAGTTCTATA
*
69387 CTCCCTGAAGAAAGAGGGAGCGAACCAGTT
128 CTCCCTGAAGAAAGAGGGAGCGAACCCGTT
* * * * *
69417 AGCAGAAGATTCTTGAGTTCTATACTCCCTGAAA-CAATAGGGAGCGAACCCG-TTAGCAGAAGA
1 ---TGAAGATTTTTGAGTTCCATACTCCCT-AAAGAAAGAGGGAGCGAACCCGCTT-GCAGAAGA
* *
69480 TTATTCGAGTTCTATACTCCCTGAA-ACAATAGGGAGCGAACCCGT
61 TTGTTCGAGTTCTATACTCCCTGAAGA-AAGAGGGAGCGAACCCGT
69525 CCCCAGAAGA
Statistics
Matches: 679, Mismatches: 43, Indels: 20
0.92 0.06 0.03
Matches are distributed among these distances:
153 46 0.07
154 2 0.00
155 123 0.18
156 43 0.06
157 325 0.48
160 48 0.07
162 3 0.00
163 86 0.13
164 3 0.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (157 bp):
TGAAGATTTTTGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGCTTGCAGAAGATTGTT
CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCTATACTC
CCTGAAGAAAGAGGGAGCGAACCCGTT
Found at i:71263 original size:19 final size:20
Alignment explanation
Indices: 71236--71273 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
71226 TTAGGGTTGA
71236 GAGACGGGAGA-GCAGAGAG
1 GAGACGGGAGAGGCAGAGAG
*
71255 GAGATGGGAGAGGCAGAGA
1 GAGACGGGAGAGGCAGAGA
71274 ATGGCGAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.08, G:0.53, T:0.03
Consensus pattern (20 bp):
GAGACGGGAGAGGCAGAGAG
Found at i:73315 original size:2 final size:2
Alignment explanation
Indices: 73308--73337 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
73298 TAATTATTTA
73308 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73338 TAGGGTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73498 original size:26 final size:26
Alignment explanation
Indices: 73462--73514 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
73452 AAACAATGTG
*
73462 TGACATTCATTGAAATGCACCACTAA
1 TGACATGCATTGAAATGCACCACTAA
*
73488 TGACATGCATTGAAATGTACCACTAA
1 TGACATGCATTGAAATGCACCACTAA
73514 T
1 T
73515 ATAAATTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (26 bp):
TGACATGCATTGAAATGCACCACTAA
Found at i:73824 original size:21 final size:21
Alignment explanation
Indices: 73795--73834 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
73785 AAAATATATG
*
73795 AAAATAAATTATTTTTAAAATT
1 AAAATAAA-TATTTTCAAAATT
73817 AAAA-AAATATTTTCAAAA
1 AAAATAAATATTTTCAAAA
73835 AAATCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 3 0.18
22 4 0.24
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATAAATATTTTCAAAATT
Found at i:73836 original size:14 final size:16
Alignment explanation
Indices: 73817--73849 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
73807 TTTTAAAATT
73817 AAAAAAAT-ATTT-TC
1 AAAAAAATCATTTATC
73831 AAAAAAATCATTTATC
1 AAAAAAATCATTTATC
73847 AAA
1 AAA
73850 CAATGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAAAATCATTTATC
Found at i:75216 original size:54 final size:54
Alignment explanation
Indices: 75116--75238 Score: 149
Period size: 54 Copynumber: 2.3 Consensus size: 54
75106 CCTTAATTAT
* * *
75116 GGTATCGATAACCTTAAAACATCGAATGTCAGATTGGTACCAGTACCTTGGGGA
1 GGTATCGATACCCTTAAAACATCGAATGTCAGATTGGTACCAGTACCATGAGGA
* * * * *
75170 GGTATCGATACCCTTATAACATCGAATGTTA-TTTCGGTATCGGTACCATGAGGA
1 GGTATCGATACCCTTAAAACATCGAATGTCAGATT-GGTACCAGTACCATGAGGA
*
75224 GGTATTGATACCCTT
1 GGTATCGATACCCTT
75239 GAAGGGTGGT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 2 0.03
54 57 0.97
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (54 bp):
GGTATCGATACCCTTAAAACATCGAATGTCAGATTGGTACCAGTACCATGAGGA
Found at i:75656 original size:21 final size:21
Alignment explanation
Indices: 75626--75676 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
75616 ATGTTATAGA
* *
75626 AATGTAAACTTTGAATAAGTG
1 AATGTGAACTTTGAACAAGTG
*
75647 AATGTGAACTTTGAACCAGTG
1 AATGTGAACTTTGAACAAGTG
75668 AATGTGAAC
1 AATGTGAAC
75677 AAACTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (21 bp):
AATGTGAACTTTGAACAAGTG
Found at i:75835 original size:21 final size:21
Alignment explanation
Indices: 75809--75858 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
75799 GTCGAGGGTT
75809 TTATGTGGTCA-TCTGGGACAA
1 TTATGTGGTCATTC-GGGACAA
*
75830 TTATGTGCTCATTCGGGACAA
1 TTATGTGGTCATTCGGGACAA
*
75851 ATATGTGG
1 TTATGTGG
75859 CACTTTGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (21 bp):
TTATGTGGTCATTCGGGACAA
Found at i:75878 original size:23 final size:23
Alignment explanation
Indices: 75852--75900 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
75842 TCGGGACAAA
* **
75852 TATGTGGCACTTTGGTGCAAACC
1 TATGTAGCACTTCAGTGCAAACC
75875 TATGTAGCACTTCAGTGCAAACC
1 TATGTAGCACTTCAGTGCAAACC
75898 TAT
1 TAT
75901 ATGGTTATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (23 bp):
TATGTAGCACTTCAGTGCAAACC
Found at i:82113 original size:21 final size:21
Alignment explanation
Indices: 82055--82114 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
82045 CTGTTGAGAG
*
82055 TGGTATCGATACCGTAAGGGA
1 TGGTATCGATACCTTAAGGGA
* *
82076 TGGGTATCGATAACTTAA-TGA
1 T-GGTATCGATACCTTAAGGGA
82097 TGGTATCGATACCCTTAA
1 TGGTATCGATA-CCTTAA
82115 AACATCTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 10 0.30
21 9 0.27
22 14 0.42
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (21 bp):
TGGTATCGATACCTTAAGGGA
Found at i:82217 original size:54 final size:54
Alignment explanation
Indices: 82101--82220 Score: 125
Period size: 54 Copynumber: 2.2 Consensus size: 54
82091 TAATGATGGT
* * * *
82101 ATCGATACCCTTAAAACATCTAATGCCAGATTGGCATCGGTACCTTGGGGAGGT
1 ATCGATACCCTTAAAACATCGAATGCCAGATTGGCATCGGTACCATGAGGAGGC
** * ** * *
82155 ATTTATACCCTTATAACATCGAATGTTA-TTTCGGTATCGGTACCATGAGGAGGC
1 ATCGATACCCTTAAAACATCGAATGCCAGATT-GGCATCGGTACCATGAGGAGGC
82209 ATCGATACCCTT
1 ATCGATACCCTT
82221 GAAGGGTGGT
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
53 2 0.04
54 50 0.96
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (54 bp):
ATCGATACCCTTAAAACATCGAATGCCAGATTGGCATCGGTACCATGAGGAGGC
Found at i:82638 original size:21 final size:21
Alignment explanation
Indices: 82608--82658 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
82598 ATGTTATAGA
* *
82608 AATGTAAACTTTAAATAAGTG
1 AATGTGAACTTTAAACAAGTG
* *
82629 AATGTGAACTTTGAACCAGTG
1 AATGTGAACTTTAAACAAGTG
82650 AATGTGAAC
1 AATGTGAAC
82659 AAACTTTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (21 bp):
AATGTGAACTTTAAACAAGTG
Found at i:85593 original size:21 final size:20
Alignment explanation
Indices: 85569--85607 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
85559 ATATTAATAA
85569 TAAAATTTAAAAATAATGAGT
1 TAAAATTTAAAAA-AATGAGT
*
85590 TAAATTTTAAAAAAATGA
1 TAAAATTTAAAAAAATGA
85608 ATAAAACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (20 bp):
TAAAATTTAAAAAAATGAGT
Found at i:88514 original size:20 final size:20
Alignment explanation
Indices: 88491--88569 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
88481 ATCGATACTA
*
88491 TAAGGGTAGTATTGGTACCT
1 TAAGGGTAGTATCGGTACCT
* * *
88511 TAAGGATGGTATCGATA-CT
1 TAAGGGTAGTATCGGTACCT
88530 GTAAGGGTAGTATCGGTACCT
1 -TAAGGGTAGTATCGGTACCT
* * *
88551 TAAGGATGGTATCGATACC
1 TAAGGGTAGTATCGGTACC
88570 CTTGAAATAT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 2 0.04
20 43 0.91
21 2 0.04
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (20 bp):
TAAGGGTAGTATCGGTACCT
Found at i:88529 original size:40 final size:40
Alignment explanation
Indices: 88478--88568 Score: 164
Period size: 40 Copynumber: 2.3 Consensus size: 40
88468 TTGTTGAAGA
*
88478 GGTATCGATACTATAAGGGTAGTATTGGTACCTTAAGGAT
1 GGTATCGATACTATAAGGGTAGTATCGGTACCTTAAGGAT
*
88518 GGTATCGATACTGTAAGGGTAGTATCGGTACCTTAAGGAT
1 GGTATCGATACTATAAGGGTAGTATCGGTACCTTAAGGAT
88558 GGTATCGATAC
1 GGTATCGATAC
88569 CCTTGAAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.31
Consensus pattern (40 bp):
GGTATCGATACTATAAGGGTAGTATCGGTACCTTAAGGAT
Found at i:89568 original size:18 final size:18
Alignment explanation
Indices: 89545--89589 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
89535 TATGTGGTCC
* *
89545 TTCGGGACATAGTAGTCT
1 TTCGGGACATAATAGTCA
89563 TTCGGGACATAATAGTCA
1 TTCGGGACATAATAGTCA
89581 TTCGGGACA
1 TTCGGGACA
89590 AATTCTACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (18 bp):
TTCGGGACATAATAGTCA
Found at i:92637 original size:20 final size:20
Alignment explanation
Indices: 92583--92660 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
92573 GAATATTTTG
92583 TAAGGGTAGTATCGATACTTGT
1 TAAGGGTAGTATCGATA-TT-T
*
92605 TAA-AG-AGGTATCGATATTT
1 TAAGGGTA-GTATCGATATTT
* **
92624 TAAGGGTAGTATCGGTACCT
1 TAAGGGTAGTATCGATATTT
* *
92644 TAAGGATGGTATCGATA
1 TAAGGGTAGTATCGATA
92661 CCTTGAAACT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
19 4 0.09
20 27 0.60
21 11 0.24
22 3 0.07
ACGTcount: A:0.31, C:0.09, G:0.27, T:0.33
Consensus pattern (20 bp):
TAAGGGTAGTATCGATATTT
Found at i:92662 original size:20 final size:20
Alignment explanation
Indices: 92611--92664 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
92601 TTGTTAAAGA
** *
92611 GGTATCGATATTTTAAGGGT
1 GGTATCGATACCTTAAGGAT
* *
92631 AGTATCGGTACCTTAAGGAT
1 GGTATCGATACCTTAAGGAT
92651 GGTATCGATACCTT
1 GGTATCGATACCTT
92665 GAAACTAATG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (20 bp):
GGTATCGATACCTTAAGGAT
Done.