Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001115.1 Hibiscus syriacus cultivar Beakdansim tig00002199_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: 63909
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:2217 original size:17 final size:17
Alignment explanation
Indices: 2207--2242 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2197 TTAATAAAGT
2207 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
2224 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
2241 TA
1 TA
2243 ACTCTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:2803 original size:16 final size:17
Alignment explanation
Indices: 2767--2833 Score: 70
Period size: 16 Copynumber: 4.2 Consensus size: 17
2757 ATTCATGCAT
*
2767 CTAGTT-ATTAATTAAG
1 CTAGTTCATTAATTAAA
*
2783 TTAGTT-ATTAATTAAA
1 CTAGTTCATTAATTAAA
* *
2799 CTAGTTCA-TCATCAAA
1 CTAGTTCATTAATTAAA
2815 CTAGTTCATT-ATTAAA
1 CTAGTTCATTAATTAAA
2831 CTA
1 CTA
2834 ACTCTTAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
16 41 0.95
17 2 0.05
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:8379 original size:17 final size:17
Alignment explanation
Indices: 8359--8394 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
8349 TTAATAAAGT
8359 TAGTTCATTCATTAAAC
1 TAGTTCATTCATTAAAC
*
8376 TAGTTCATTTATTAAAC
1 TAGTTCATTCATTAAAC
8393 TA
1 TA
8395 ACTCTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (17 bp):
TAGTTCATTCATTAAAC
Found at i:13824 original size:21 final size:21
Alignment explanation
Indices: 13800--13842 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
13790 TCCAAATCAA
*
13800 ACATATAAATTCCGAAAAATT
1 ACATATAAATTCAGAAAAATT
*
13821 ACATATAAATTCATAAAAATT
1 ACATATAAATTCAGAAAAATT
13842 A
1 A
13843 ACCTTTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (21 bp):
ACATATAAATTCAGAAAAATT
Found at i:14141 original size:18 final size:19
Alignment explanation
Indices: 14127--14162 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
14117 TTTAATATAT
14127 AACCTAAC-TAAAATAATA
1 AACCTAACATAAAATAATA
*
14145 AACCTAACATAAATTAAT
1 AACCTAACATAAAATAAT
14163 CTTCTTCAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.17, G:0.00, T:0.25
Consensus pattern (19 bp):
AACCTAACATAAAATAATA
Found at i:16174 original size:55 final size:55
Alignment explanation
Indices: 16115--16663 Score: 613
Period size: 55 Copynumber: 10.0 Consensus size: 55
16105 ACACTTGAAA
*
16115 AATCTTCAGAAAACGGGTTTGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAC
1 AATCTTCAGAAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAC
* * * *
16170 AATCTTCTAAAAAACGGGTTTGCTCCCTATTTTTTCAGGGTGTATAGAACTCGAAC
1 AATCTTC-AGAAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAC
* * * * * *
16226 AATGATT-TGGAAATGGGTCCGCTCCCTATTCTTTCAGGGAGTATAGAACTCTAAC
1 AAT-CTTCAGAAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAC
* * * * *
16281 AATCTTCTGAAAATGGGTTCACTCCCTATTCTTTCAGGGATTATAGAACTCAAAC
1 AATCTTCAGAAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAC
* * * *
16336 AATCTTCTA-AAAACGGGTTTGCTCCCTAATCTTTC-GAGGAGTATAAAACTCGAAT
1 AATCTTC-AGAAAACGGGTTCGCTCCCTATTCTTTCAG-GGAGTATAGAACTCGAAC
* ** * * * *
16391 AATATTTTGAAAACGAGTTCGCTCCATATTCCTTCAGGGAGTATAGAACTCGAAA
1 AATCTTCAGAAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAC
* * * * *
16446 AATATTCTGAAAACGAGTTCGCTCCCTATTCTTTCAGGGATTATAGAACTCGAAT
1 AATCTTCAGAAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAC
*
16501 AATCTTCTA-AAAATGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAC
1 AATCTTC-AGAAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAC
* ** * *
16556 AATATTTTGAAAATGGGTTCTCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAC
1 AATCTTCAGAAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAC
* * * * * *
16611 AATCTTCAGCAAACGTG-TCTGCTCACTATTATTTCAAGGAGTATAGGACTCGA
1 AATCTTCAGAAAACGGGTTC-GCTCCCTATTCTTTCAGGGAGTATAGAACTCGA
16664 TCTTGATTTT
Statistics
Matches: 420, Mismatches: 64, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
54 5 0.01
55 364 0.87
56 49 0.12
57 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (55 bp):
AATCTTCAGAAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAC
Found at i:16456 original size:165 final size:165
Alignment explanation
Indices: 16111--16663 Score: 743
Period size: 165 Copynumber: 3.3 Consensus size: 165
16101 AGTGACACTT
* * *
16111 GAAAAATCTTCAGAAAACGGGTTTGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTT
1 GAAAAATCTTCTGAAAACGGGTTCGCTCCCTATTCTTTCAGGGATTATAGAACTCGAACAATCTT
* * *
16176 CTAAAAAACGGGTTTGCTCCCTATTTTTTCAGGGTGTATAGAACTCGAACAATGA-TTTGGAAAT
66 CT-AAAAACGGGTTTGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAAT-ATTTTGAAAAT
*
16240 GGGTCCGCTCCCTATTCTTTCAGGGAGTATAGAACTC
129 GGGTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTC
* * * * *
16277 TAACAATCTTCTGAAAATGGGTTCACTCCCTATTCTTTCAGGGATTATAGAACTCAAACAATCTT
1 GAAAAATCTTCTGAAAACGGGTTCGCTCCCTATTCTTTCAGGGATTATAGAACTCGAACAATCTT
* * * *
16342 CTAAAAACGGGTTTGCTCCCTAATCTTTC-GAGGAGTATAAAACTCGAATAATATTTTGAAAACG
66 CTAAAAACGGGTTTGCTCCCTATTCTTTCAG-GGAGTATAGAACTCGAACAATATTTTGAAAATG
* * *
16406 AGTTCGCTCCATATTCCTTCAGGGAGTATAGAACTC
130 GGTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTC
* * *
16442 GAAAAATATTCTGAAAACGAGTTCGCTCCCTATTCTTTCAGGGATTATAGAACTCGAATAATCTT
1 GAAAAATCTTCTGAAAACGGGTTCGCTCCCTATTCTTTCAGGGATTATAGAACTCGAACAATCTT
* *
16507 CTAAAAATGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATATTTTGAAAATGG
66 CTAAAAACGGGTTTGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATATTTTGAAAATGG
*
16572 GTTCTCTCCCTATTCTTTCAGGGAGTATAGAACTC
131 GTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTC
* * * * * * * * *
16607 GAACAATCTTCAGCAAACGTG-TCTGCTCACTATTATTTCAAGGAGTATAGGACTCGA
1 GAAAAATCTTCTGAAAACGGGTTC-GCTCCCTATTCTTTCAGGGATTATAGAACTCGA
16664 TCTTGATTTT
Statistics
Matches: 336, Mismatches: 47, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
164 4 0.01
165 272 0.81
166 60 0.18
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (165 bp):
GAAAAATCTTCTGAAAACGGGTTCGCTCCCTATTCTTTCAGGGATTATAGAACTCGAACAATCTT
CTAAAAACGGGTTTGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATATTTTGAAAATGG
GTTCGCTCCCTATTCTTTCAGGGAGTATAGAACTC
Found at i:16757 original size:36 final size:36
Alignment explanation
Indices: 16667--16849 Score: 242
Period size: 36 Copynumber: 5.1 Consensus size: 36
16657 GACTCGATCT
* * *
16667 TGATTTTCTTCACTACTCTTCCTTGAAGGCTTATACA
1 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTA-AGA
* *
16704 TGATTTGCTCCACTACTCTTCCATGAAGGCTTAAGA
1 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
* * * *
16740 CGATTTGCTTCATTACTCTTTCGTGAAGGCTTAAAA
1 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
* *
16776 TGATTTGCTTCATTACTATTCCGTGAAGGCTTAAGA
1 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
16812 TGATTTGCTTCACTA-TACTTCCGTGAAGGCTTAAGA
1 TGATTTGCTTCACTACT-CTTCCGTGAAGGCTTAAGA
16848 TG
1 TG
16850 GCATGGAGAA
Statistics
Matches: 129, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
35 1 0.01
36 98 0.76
37 30 0.23
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (36 bp):
TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
Found at i:20620 original size:20 final size:20
Alignment explanation
Indices: 20582--20619 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
20572 TATAAATGAA
20582 TAAGAATGCAATGCAAAAAT
1 TAAGAATGCAATGCAAAAAT
*
20602 TAAG-ATGCATTGCAAAAA
1 TAAGAATGCAATGCAAAAA
20620 AAGTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.21
Consensus pattern (20 bp):
TAAGAATGCAATGCAAAAAT
Found at i:24889 original size:37 final size:37
Alignment explanation
Indices: 24839--24925 Score: 129
Period size: 37 Copynumber: 2.4 Consensus size: 37
24829 TCCCCTAATG
** * *
24839 AAAAACTGGCCTCCTCTCTATCTGGTTGTTAACTGCT
1 AAAAACTAACCTCCTCTATATATGGTTGTTAACTGCT
24876 AAAAACTAACCTCCTCTATATATGGTTGTTAACTGCT
1 AAAAACTAACCTCCTCTATATATGGTTGTTAACTGCT
*
24913 AAAAACCAACCTC
1 AAAAACTAACCTC
24926 GATTCTTCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.31
Consensus pattern (37 bp):
AAAAACTAACCTCCTCTATATATGGTTGTTAACTGCT
Found at i:31713 original size:19 final size:18
Alignment explanation
Indices: 31689--31751 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
31679 TTGTTTTGCT
31689 TTTCTTTTCTTTGCTTGAG
1 TTTCTTTTCTTT-CTTGAG
* **
31708 TTTCTTGTT-TTTATGTGCT
1 TTTCTT-TTCTTTCT-TGAG
31727 TTTCTTTTCTTTACTTGAG
1 TTTCTTTTCTTT-CTTGAG
31746 TTTCTT
1 TTTCTT
31752 ATTTTTTGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
18 3 0.09
19 28 0.82
20 3 0.09
ACGTcount: A:0.06, C:0.14, G:0.13, T:0.67
Consensus pattern (18 bp):
TTTCTTTTCTTTCTTGAG
Found at i:31727 original size:38 final size:37
Alignment explanation
Indices: 31685--31771 Score: 138
Period size: 38 Copynumber: 2.3 Consensus size: 37
31675 TCTTTTGTTT
* *
31685 TGCTTTTCTTTTCTTTGCTTGAGTTTCTTGTTTTTATG
1 TGCTTTTCTTTTCTTTACTTGAGTTTCTTATTTTT-TG
31723 TGCTTTTCTTTTCTTTACTTGAGTTTCTTATTTTTTG
1 TGCTTTTCTTTTCTTTACTTGAGTTTCTTATTTTTTG
*
31760 TGATTTTCTTTT
1 TGCTTTTCTTTT
31772 GTTTTTGTAC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
37 13 0.28
38 33 0.72
ACGTcount: A:0.07, C:0.13, G:0.13, T:0.68
Consensus pattern (37 bp):
TGCTTTTCTTTTCTTTACTTGAGTTTCTTATTTTTTG
Found at i:35401 original size:11 final size:11
Alignment explanation
Indices: 35387--35423 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
35377 ATGTTATATG
35387 TACTTAATAGA
1 TACTTAATAGA
35398 TACTTAATATG-
1 TACTTAATA-GA
35409 TACTTAATAGA
1 TACTTAATAGA
35420 TACT
1 TACT
35424 ATTGAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.04
11 22 0.92
12 1 0.04
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (11 bp):
TACTTAATAGA
Found at i:35407 original size:22 final size:22
Alignment explanation
Indices: 35382--35423 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
35372 TTTGTATGTT
35382 ATATGTACTTAATAGATACTTA
1 ATATGTACTTAATAGATACTTA
35404 ATATGTACTTAATAGATACT
1 ATATGTACTTAATAGATACT
35424 ATTGAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (22 bp):
ATATGTACTTAATAGATACTTA
Found at i:35947 original size:2 final size:2
Alignment explanation
Indices: 35940--35967 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35930 TCTTTCTATG
35940 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35968 CATGTATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36736 original size:12 final size:12
Alignment explanation
Indices: 36719--36746 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
36709 TGATTATTTC
36719 TTGTGTCATTGA
1 TTGTGTCATTGA
36731 TTGTGTCATTGA
1 TTGTGTCATTGA
36743 TTGT
1 TTGT
36747 TAGAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.07, G:0.25, T:0.54
Consensus pattern (12 bp):
TTGTGTCATTGA
Found at i:43009 original size:15 final size:15
Alignment explanation
Indices: 42989--43018 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
42979 TGGTATCTAT
42989 GGTATCGATACCCCC
1 GGTATCGATACCCCC
43004 GGTATCGATACCCCC
1 GGTATCGATACCCCC
43019 TGGCTGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (15 bp):
GGTATCGATACCCCC
Found at i:44305 original size:19 final size:20
Alignment explanation
Indices: 44281--44328 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
44271 AATGATTTTC
*
44281 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
44300 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
44320 TTTTGAAAA
1 TTTTGAAAA
44329 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:45599 original size:29 final size:31
Alignment explanation
Indices: 45546--45605 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
45536 TACTTTAAGG
45546 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
45577 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
45606 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:45793 original size:16 final size:15
Alignment explanation
Indices: 45764--45793 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45754 ACCCCCCCAT
45764 GGTATCGATACCCCC
1 GGTATCGATACCCCC
*
45779 GGTATTGATACCCCC
1 GGTATCGATACCCCC
45794 AGGGGTATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.23
Consensus pattern (15 bp):
GGTATCGATACCCCC
Found at i:45867 original size:21 final size:21
Alignment explanation
Indices: 45841--45881 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
45831 ATTTGAATTT
45841 TATGAAGGGGTACCGATACCA
1 TATGAAGGGGTACCGATACCA
*
45862 TATGAATGGGTACCGATACC
1 TATGAAGGGGTACCGATACC
45882 CCCTGTACGG
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:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TATGAAGGGGTACCGATACCA
Found at i:49723 original size:60 final size:59
Alignment explanation
Indices: 49655--49835 Score: 209
Period size: 60 Copynumber: 3.0 Consensus size: 59
49645 TGAATTTGGG
* * * *
49655 GATGAAATTTGAATATTTAAAAGTTTAGGGACCAATTTTGAATGAGGGTCTTAGTTTGA
1 GATGAAATTAGAATATTTAAAAGTTTAGGGACTAATTTAGAATGAGGGTCATAGTTTGA
* * * * * **
49714 TGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAGTTTCATAGTTTGA
1 -GATGAAATTAGAATATTTAAAAGTTTAGGGACTAATTTAGAATGAGGGTCATAGTTTGA
* * * *
49774 GAATGGAATTAGAATATTTAAAACTTTAGTGACTAGTTTAGAATGAGGGTCATAGTTTGA
1 G-ATGAAATTAGAATATTTAAAAGTTTAGGGACTAATTTAGAATGAGGGTCATAGTTTGA
49834 GA
1 GA
49836 ATATATAATA
Statistics
Matches: 99, Mismatches: 21, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
59 2 0.02
60 97 0.98
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (59 bp):
GATGAAATTAGAATATTTAAAAGTTTAGGGACTAATTTAGAATGAGGGTCATAGTTTGA
Found at i:53256 original size:48 final size:48
Alignment explanation
Indices: 53199--53323 Score: 169
Period size: 48 Copynumber: 2.6 Consensus size: 48
53189 TGCTATGTAC
* **
53199 CATTCATAGTAGCACCACCGTCACACATTCGTCAGACGTGCTAATTAT
1 CATTAATAGTAGCACCACCGTCACACAAACGTCAGACGTGCTAATTAT
* * *
53247 CATTAATAGTAGCACCATCATCACACAAACGTCAGATGTGCTAATTAT
1 CATTAATAGTAGCACCACCGTCACACAAACGTCAGACGTGCTAATTAT
* * *
53295 AATTAATAATAGTACCACCGTCACACAAA
1 CATTAATAGTAGCACCACCGTCACACAAA
53324 AAACAAGCGT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.26
Consensus pattern (48 bp):
CATTAATAGTAGCACCACCGTCACACAAACGTCAGACGTGCTAATTAT
Found at i:54091 original size:22 final size:21
Alignment explanation
Indices: 54065--54116 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
54055 ATAATCAAGC
*
54065 ATTCTAAAACATTACTCTTCA
1 ATTCTAAAACATTACACTTCA
** *
54086 ACTTCTAATCCATTCCACTTCA
1 A-TTCTAAAACATTACACTTCA
54108 ATTCTAAAA
1 ATTCTAAAA
54117 TTTCCATATT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (21 bp):
ATTCTAAAACATTACACTTCA
Found at i:58493 original size:35 final size:35
Alignment explanation
Indices: 58446--58548 Score: 154
Period size: 35 Copynumber: 2.9 Consensus size: 35
58436 ATTTATAAGT
*
58446 TGGTGATAATATAGGCGTGATATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGATGGAATA
* *
58481 TGGTGATGATATAGGCGT-ACAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGA-TATGGTGATGGAATA
58516 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGA
58549 CAGATTGTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
34 1 0.02
35 48 0.79
36 12 0.20
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGAATA
Found at i:61811 original size:24 final size:24
Alignment explanation
Indices: 61764--61811 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
61754 TAGAAAAGGT
* *
61764 TAAGAAAAGGATAAAGTAATGAAA
1 TAAGAAAAGGATAAAGAAAAGAAA
61788 TAAGAAAA-GATGAAAGAAAAGAAA
1 TAAGAAAAGGAT-AAAGAAAAGAAA
61812 ATGAAATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (24 bp):
TAAGAAAAGGATAAAGAAAAGAAA
Found at i:62452 original size:12 final size:12
Alignment explanation
Indices: 62435--62488 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
62425 TATAGGCGTG
62435 ATATGGTGATGA
1 ATATGGTGATGA
62447 ATATGGTGATG-
1 ATATGGTGATGA
*
62458 ATATAGGCG-TGA
1 ATAT-GGTGATGA
62470 CA-ATGGTGATGA
1 -ATATGGTGATGA
62482 ACTATGG
1 A-TATGG
62489 ATATAGGCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
11 10 0.29
12 19 0.56
13 5 0.15
ACGTcount: A:0.31, C:0.06, G:0.33, T:0.30
Consensus pattern (12 bp):
ATATGGTGATGA
Found at i:62462 original size:34 final size:35
Alignment explanation
Indices: 62416--62511 Score: 114
Period size: 31 Copynumber: 2.9 Consensus size: 35
62406 ATTTATAAGT
*
62416 TGGTGATAATATAGGCGTGATATGGTGATGAA-TA
1 TGGTGATGATATAGGCGTGATATGGTGATGAACTA
*
62450 TGGTGATGATATAGGCGTGACAATGGTGATGAACTA
1 TGGTGATGATATAGGCGTGA-TATGGTGATGAACTA
62486 ---TG--GATATAGGCGTGATAATGGTGATG
1 TGGTGATGATATAGGCGTGAT-ATGGTGATG
62512 GACATATGTA
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
31 22 0.39
33 2 0.04
34 19 0.34
35 11 0.20
36 2 0.04
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.30
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGAACTA
Done.