Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005967.1 Hibiscus syriacus cultivar Beakdansim tig00014016_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: 63431
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:8586 original size:17 final size:17
Alignment explanation
Indices: 8560--8611 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
8550 ATATGACTAC
8560 ATAATAATATAATAATA
1 ATAATAATATAATAATA
* * *
8577 ATAATTATATATTAAAA
1 ATAATAATATAATAATA
*
8594 ATAA-ACATATAAAAATA
1 ATAATA-ATATAATAATA
8611 A
1 A
8612 ATATAACTAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAATAATATAATAATA
Found at i:13210 original size:48 final size:48
Alignment explanation
Indices: 13139--13233 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
13129 AAAATAATGG
*
13139 CACTCTTTGAATCAGAAAGTGTTGCCTATGGTGGCATCAACACAGCAA
1 CACTCTTTGAATCAGAAAGTGTTGCCTATGGTGGCACCAACACAGCAA
*
13187 CACTCTTTGAATCAGAAAGTGTTGTCTATGGTGGCACCAACACAGCA
1 CACTCTTTGAATCAGAAAGTGTTGCCTATGGTGGCACCAACACAGCA
13234 GCACCGGCAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (48 bp):
CACTCTTTGAATCAGAAAGTGTTGCCTATGGTGGCACCAACACAGCAA
Found at i:14463 original size:2 final size:2
Alignment explanation
Indices: 14456--14480 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14446 AGGTAACTCG
14456 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
14481 GATGAACGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15312 original size:20 final size:19
Alignment explanation
Indices: 15295--15332 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
15285 AAATTTAATT
*
15295 TTTTTAAATAATTATTAAAA
1 TTTTCAAATAATT-TTAAAA
15315 TTTTCAAATAATTTTAAA
1 TTTTCAAATAATTTTAAA
15333 TGATAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTCAAATAATTTTAAAA
Found at i:15491 original size:23 final size:22
Alignment explanation
Indices: 15459--15503 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
15449 AATTTTTAAA
15459 TTTTAATAATTTTAA-AAATATT
1 TTTTAATAA-TTTAATAAATATT
15481 TTTTACATAATTTAATAAATATT
1 TTTTA-ATAATTTAATAAATATT
15504 ATATAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTAATAATTTAATAAATATT
Found at i:15500 original size:41 final size:41
Alignment explanation
Indices: 15416--15524 Score: 100
Period size: 41 Copynumber: 2.6 Consensus size: 41
15406 ATTTATCATT
*
15416 ATTTATAATAATTTAAAATAATAATATTTTTATAATTTTTAA
1 ATTT-TAATAATTTAAAATAATAATATTTTTATAATTTATAA
*
15458 ATTTTAATAATTTTAAA-AAT-AT-TTTTTACATAATTTAATAA
1 ATTTTAATAATTTAAAATAATAATATTTTT--ATAATTT-ATAA
* *
15499 ATATTATATAA-TTAATAATAAAAATA
1 ATTTTA-ATAATTTAA-AATAATAATA
15525 GATCAACAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
38 5 0.09
39 2 0.04
40 10 0.19
41 23 0.43
42 10 0.19
43 2 0.04
44 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (41 bp):
ATTTTAATAATTTAAAATAATAATATTTTTATAATTTATAA
Found at i:27750 original size:21 final size:21
Alignment explanation
Indices: 27724--27768 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27714 GATTTCTGGG
* *
27724 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
27745 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
27766 CAA
1 CAA
27769 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:28991 original size:32 final size:32
Alignment explanation
Indices: 28950--29046 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
28940 GAGTCGAGGG
28950 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
28982 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
29013 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
29045 TT
1 TT
29047 ACTTAGGTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:29070 original size:31 final size:31
Alignment explanation
Indices: 28949--29076 Score: 134
Period size: 31 Copynumber: 4.1 Consensus size: 31
28939 AGAGTCGAGG
28949 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
28980 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
29012 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * * * *
29043 GTTTACTTAGGTTCTTCGGGACCTATGGATA
1 GTTTACCTATGTTCTACGGAACATATGGACA
29074 GTT
1 GTT
29077 ACCGAGGATC
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 52 0.65
32 28 0.35
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:29102 original size:30 final size:30
Alignment explanation
Indices: 29062--29134 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
29052 GGTTCTTCGG
29062 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTATGGATAGTTACCGAGGATCTTTAT
*
29092 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTATGGATAGTTACCGAGGATCTTTAT
*
29122 GACCTTTGGATAG
1 GACCTATGGATAG
29135 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (30 bp):
GACCTATGGATAGTTACCGAGGATCTTTAT
Found at i:32229 original size:21 final size:21
Alignment explanation
Indices: 32192--32236 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
32182 GATTTCTGGG
*
32192 CAAGGGGAATCAGTACCCATT
1 CAAGGGGAACCAGTACCCATT
*
32213 CAAGGGGAACC-GATACCCCTT
1 CAAGGGGAACCAG-TACCCATT
32234 CAA
1 CAA
32237 ACGAACAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCAGTACCCATT
Found at i:32706 original size:21 final size:22
Alignment explanation
Indices: 32682--32725 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
32672 TAATTACATA
*
32682 AGAAGGTTAT-GAAGTTATATG
1 AGAAGATTATAGAAGTTATATG
*
32703 AGAAGATTATAGGAGTTATATG
1 AGAAGATTATAGAAGTTATATG
32725 A
1 A
32726 AATTGATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (22 bp):
AGAAGATTATAGAAGTTATATG
Found at i:33531 original size:31 final size:31
Alignment explanation
Indices: 33410--33537 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
33400 AGAGTCGAGG
33410 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
33441 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
33473 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * * *
33504 GTTTACCTAGGTTCTTCGGGACCTATGGATA
1 GTTTACCTATGTTCTACGGAACATATGGACA
33535 GTT
1 GTT
33538 ACCGAGGATC
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
31 53 0.65
32 28 0.35
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:33557 original size:30 final size:30
Alignment explanation
Indices: 33523--33595 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
33513 GGTTCTTCGG
*
33523 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
33553 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
33583 GACCTCTGGATAG
1 GACCTCTGGATAG
33596 GTCCTTCGGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:35709 original size:48 final size:48
Alignment explanation
Indices: 35636--35730 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
35626 TTGATGAAGT
35636 ACGAGACATCTACTCGATATACGTATGTATATGTATGTTTATGTATAC
1 ACGAGACATCTACTCGATATACGTATGTATATGTATGTTTATGTATAC
* * * *
35684 ACGAGACATCTCCTCGATATGCGTATGTATGTGTGTGTTTATGTATA
1 ACGAGACATCTACTCGATATACGTATGTATATGTATGTTTATGTATA
35731 TACCCAAGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (48 bp):
ACGAGACATCTACTCGATATACGTATGTATATGTATGTTTATGTATAC
Found at i:36558 original size:31 final size:32
Alignment explanation
Indices: 36502--36567 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
36492 GCTTAATAAG
* *
36502 CTTAACGAGCAACGACTCGAGCAATAAATTTT
1 CTTAACGAGCAACAACTAGAGCAATAAATTTT
*
36534 CTTAACGAG-AACAAGTAGAGCAATAAATTTT
1 CTTAACGAGCAACAACTAGAGCAATAAATTTT
36565 CTT
1 CTT
36568 TACAAGCACG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (32 bp):
CTTAACGAGCAACAACTAGAGCAATAAATTTT
Found at i:37055 original size:78 final size:78
Alignment explanation
Indices: 36973--37130 Score: 203
Period size: 78 Copynumber: 2.0 Consensus size: 78
36963 TAGAAAAAAC
* *
36973 AACATTTTAAG-TAGCACCCAATATTAACATTTCCGGT-AAAAAAATAATAATTTAGATAACGCT
1 AACATTTT-AGTTAGCACCCAATATTAACATTTCCAGTAAAAAAAAT-ATAATTTAAATAACGCT
* *
37036 TTACCAGAAATGTTA
64 TTACCAAAAATATTA
* * * * *
37051 AACATTTTAGTTAGCACCTAATATTAACATTTCTAGTAAAAAAAATATATTTTAAATAGCGTTTT
1 AACATTTTAGTTAGCACCCAATATTAACATTTCCAGTAAAAAAAATATAATTTAAATAACGCTTT
37116 ACCAAAAATATTA
66 ACCAAAAATATTA
37129 AA
1 AA
37131 AAATATTAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
77 2 0.03
78 59 0.86
79 8 0.12
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (78 bp):
AACATTTTAGTTAGCACCCAATATTAACATTTCCAGTAAAAAAAATATAATTTAAATAACGCTTT
ACCAAAAATATTA
Found at i:40222 original size:23 final size:24
Alignment explanation
Indices: 40192--40238 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
40182 GGAATAACAA
40192 TGCCAGTGATTGGTGA-TTAAAAG
1 TGCCAGTGATTGGTGATTTAAAAG
40215 TGCCAGTGATTGGTGATTTAAAAG
1 TGCCAGTGATTGGTGATTTAAAAG
40239 ATTCTTATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (24 bp):
TGCCAGTGATTGGTGATTTAAAAG
Found at i:41706 original size:19 final size:19
Alignment explanation
Indices: 41670--41707 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
41660 CAGAAACATC
*
41670 AAAAAGAACAACTTTGAAA
1 AAAAAGAACAACTATGAAA
41689 AAAAAGAACATAC-ATGAAA
1 AAAAAGAACA-ACTATGAAA
41708 CTTGCGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.66, C:0.11, G:0.11, T:0.13
Consensus pattern (19 bp):
AAAAAGAACAACTATGAAA
Found at i:46797 original size:18 final size:18
Alignment explanation
Indices: 46774--46809 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
46764 AAGCAAAAGG
*
46774 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
46792 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
46810 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:47121 original size:20 final size:20
Alignment explanation
Indices: 47075--47179 Score: 84
Period size: 20 Copynumber: 5.2 Consensus size: 20
47065 AAATCGCAAC
* * *
47075 GCGAAGTTGACTTTCGCATT
1 GCGAATTTGACTTTCACGTT
* * *
47095 ACAAATTTGGCTTTCACGTT
1 GCGAATTTGACTTTCACGTT
**
47115 GCGAATTTGACTTTTGCGTT
1 GCGAATTTGACTTTCACGTT
* * ***
47135 GCGAATTTGACTATCGCAAC
1 GCGAATTTGACTTTCACGTT
*
47155 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCACGTT
47175 GCGAA
1 GCGAA
47180 AGTGTACCTT
Statistics
Matches: 65, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
GCGAATTTGACTTTCACGTT
Found at i:47142 original size:40 final size:40
Alignment explanation
Indices: 47071--47179 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
47061 CTCGAAATCG
* * * * * *
47071 CAACGCGAAGTTGACTTTCGCATTACAAATTTGGCTTTCA
1 CAACGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCA
*** * *
47111 CGTTGCGAATTTGACTTTTGCGTTGCGAATTTGACTATCG
1 CAACGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCA
47151 CAACGCGAATTTGACTTTCGCGTTGCGAA
1 CAACGCGAATTTGACTTTCGCGTTGCGAA
47180 AGTGTACCTT
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (40 bp):
CAACGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCA
Found at i:47322 original size:14 final size:14
Alignment explanation
Indices: 47303--47339 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
47293 CATCAATTAA
47303 ACAAATCAACTTTT
1 ACAAATCAACTTTT
47317 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
47331 TCAAATCAA
1 ACAAATCAA
47340 TTAAACAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:47375 original size:78 final size:77
Alignment explanation
Indices: 47239--47399 Score: 250
Period size: 78 Copynumber: 2.1 Consensus size: 77
47229 CTTTAAAACA
*
47239 ACAAATTAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
47304 CAAATCAACTTTT
66 CAAATCAAC-TTT
* *** * *
47317 ACAAATCAACTTTTTCAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
47382 CAAATCAACTTT
66 CAAATCAACTTT
47394 ACAAAT
1 ACAAAT
47400 ACATCAATTT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
77 9 0.12
78 67 0.88
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.30
Consensus pattern (77 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAA
CAAATCAACTTT
Found at i:48792 original size:21 final size:21
Alignment explanation
Indices: 48771--48869 Score: 119
Period size: 21 Copynumber: 4.7 Consensus size: 21
48761 AGGGACCAGG
* * *
48771 GGCCTCTTGAACGGTGGGAGG
1 GGCCTCTTGAACGATAGGAGA
* * *
48792 GGCCTCTTGAAGGAT-GATAGT
1 GGCCTCTTGAACGATAG-GAGA
*
48813 GGCCTCTTGAATGATAGGAGA
1 GGCCTCTTGAACGATAGGAGA
48834 GGCCTCTTGAACGATAGGAGA
1 GGCCTCTTGAACGATAGGAGA
48855 GGCCTCTTGAACGAT
1 GGCCTCTTGAACGAT
48870 GACAGGTGCT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
20 1 0.01
21 66 0.97
22 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.35, T:0.23
Consensus pattern (21 bp):
GGCCTCTTGAACGATAGGAGA
Found at i:51478 original size:19 final size:20
Alignment explanation
Indices: 51456--51493 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
51446 AATATTGTGT
51456 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
51475 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
51494 CGTGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:51741 original size:22 final size:22
Alignment explanation
Indices: 51716--51765 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
51706 ATGAAGATAA
51716 ATGGATTTCACCAGAGATGGGG
1 ATGGATTTCACCAGAGATGGGG
** *
51738 ATGGATTTCGTCGGAGATGGGG
1 ATGGATTTCACCAGAGATGGGG
*
51760 ACGGAT
1 ATGGAT
51766 GTCGCCGTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.40, T:0.24
Consensus pattern (22 bp):
ATGGATTTCACCAGAGATGGGG
Found at i:51892 original size:420 final size:421
Alignment explanation
Indices: 51107--51932 Score: 1438
Period size: 420 Copynumber: 2.0 Consensus size: 421
51097 AATTTACTAA
*
51107 GCAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAATA
1 GCAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAACA
51172 TGAAAAATCTAATAATAATACAAAAATTTCAAAATAAAAATAATTAAAAAACTAACCCTCAGTGG
66 TGAAAAATCTAATAATAATACAAAAATTTCAAAATAAAAATAATTAAAAAACTAACCCTCAGTGG
* *
51237 TTGATTTTCCATTTCTGACCGTGAATGGTTGTGAGGGTGGCTCTGAGAGATGAAGATAGACGGAT
131 TTGATTTTCCATTTCTGACCATGAATGGTTGTGAGGGTGGCTCTGAGAGATGAAGATAAACGGAT
* * *
51302 TTCGCCGGAGATAAGGACGAATTTCATCGGAGATGGGGACGGATGTCGCCGTAGAGAGTGAGAGA
196 TTCACCAGAGATAAGGACGAATTTCATCGGAGATGGGGACGGATGTCGCCGTAGAGAGTAAGAGA
* * * *
51367 TGGAGATGGGACTGAGTTGTGATTTAGGGTTTTAGGTTATAATTTACGATTATATTGTATATATT
261 TGAAGATGAGACTGAGTTGTGATTTAGGGTTTTAGGTTATAATTTACGATTATACTATATATATT
*
51432 TGTGTTGCGAAATAAATATTGTGTTTCGAATTCGAAAAT-AAAATTCGCGTTGCGAAAATAAACG
326 TGTGTTGCGAAATAAATATTGTGTTTCGAATTCAAAAATAAAAATTCGCGTTGCGAAAATAAACG
*
51496 TGCTTTGCGAATTTGACTTCTGTCCAAATTC
391 CGCTTTGCGAATTTGACTTCTGTCCAAATTC
*
51527 GCAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAGCA
1 GCAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAACA
*
51592 TGAAAAATCTAATAATAATACAAAAATTTCAAAATAAAAATAATTAAAAAACTAACCCTCGGTGG
66 TGAAAAATCTAATAATAATACAAAAATTTCAAAATAAAAATAATTAAAAAACTAACCCTCAGTGG
*
51657 TTGATTTTCCATTTCTGACCATGAATGGTTGTGAGGGTGGCTCTGAGAGATGAAGATAAATGGAT
131 TTGATTTTCCATTTCTGACCATGAATGGTTGTGAGGGTGGCTCTGAGAGATGAAGATAAACGGAT
** * * *
51722 TTCACCAGAGATGGGGATGGATTTCGTCGGAGATGGGGACGGATGTCGCCGTAGAGAGTAAGAGA
196 TTCACCAGAGATAAGGACGAATTTCATCGGAGATGGGGACGGATGTCGCCGTAGAGAGTAAGAGA
* *
51787 TGAAGATGAGACTGAGTTGTGATTTAGGGTTTTAGGTTATGATTTACGATTATACTATTTATATT
261 TGAAGATGAGACTGAGTTGTGATTTAGGGTTTTAGGTTATAATTTACGATTATACTATATATATT
*
51852 TGTGTTGCGAAATAAATATTGTGTTTCGAATTCAAAAATAAAAATTCGCGTTGCGAAAATAAATG
326 TGTGTTGCGAAATAAATATTGTGTTTCGAATTCAAAAATAAAAATTCGCGTTGCGAAAATAAACG
51917 CGCTTTGCGAATTTGA
391 CGCTTTGCGAATTTGA
51933 ATTGTGTTGC
Statistics
Matches: 382, Mismatches: 23, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
420 343 0.90
421 39 0.10
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (421 bp):
GCAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAACA
TGAAAAATCTAATAATAATACAAAAATTTCAAAATAAAAATAATTAAAAAACTAACCCTCAGTGG
TTGATTTTCCATTTCTGACCATGAATGGTTGTGAGGGTGGCTCTGAGAGATGAAGATAAACGGAT
TTCACCAGAGATAAGGACGAATTTCATCGGAGATGGGGACGGATGTCGCCGTAGAGAGTAAGAGA
TGAAGATGAGACTGAGTTGTGATTTAGGGTTTTAGGTTATAATTTACGATTATACTATATATATT
TGTGTTGCGAAATAAATATTGTGTTTCGAATTCAAAAATAAAAATTCGCGTTGCGAAAATAAACG
CGCTTTGCGAATTTGACTTCTGTCCAAATTC
Found at i:51947 original size:18 final size:20
Alignment explanation
Indices: 51921--51969 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
51911 TAAATGCGCT
51921 TTGCGAATTTGA-AT-TGTG
1 TTGCGAATTTGACATATGTG
* *
51939 TTGCAAATTTGACTTATGTG
1 TTGCGAATTTGACATATGTG
51959 TTGCGAATTTG
1 TTGCGAATTTG
51970 GAAACTGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 11 0.42
19 1 0.04
20 14 0.54
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTGACATATGTG
Found at i:58816 original size:11 final size:12
Alignment explanation
Indices: 58788--58820 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
58778 GTATTATGAA
58788 TTTTCAAATATTG
1 TTTTCAAATA-TG
58801 TTTTCAAATA-G
1 TTTTCAAATATG
58812 TTTTCAAAT
1 TTTTCAAAT
58821 TTTCCCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (12 bp):
TTTTCAAATATG
Done.