Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008335.1 Hibiscus syriacus cultivar Beakdansim tig00111052_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: 54517
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:119 original size:20 final size:20
Alignment explanation
Indices: 96--147 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
86 AACGCGATCC
96 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
116 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
136 CCAAAATCGCAA
1 CCAGAATCGCAA
148 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:245 original size:20 final size:19
Alignment explanation
Indices: 220--390 Score: 112
Period size: 20 Copynumber: 8.7 Consensus size: 19
210 CGCGAATATG
*
220 AAATCGCAACGCGAACACAT
1 AAATCGCAACGCGAAC-CGT
*
240 AAATCGCAA-GCGTATCCGT
1 AAATCGCAACGCG-AACCGT
* *
259 -AATCGCAACGTGTATCCGT
1 AAATCGCAACGCG-AACCGT
***
278 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCG-AACCGT
* * *
298 AAATCGCAATGCGTATCGT
1 AAATCGCAACGCGAACCGT
* *
317 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCG-AACCGT
** * *
337 AAATCGCAACGATAATACAT
1 AAATCGCAACGCGAA-CCGT
*
357 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCG-AACCGT
377 AAATCGCAACGCGA
1 AAATCGCAACGCGA
391 TATTTAAAGC
Statistics
Matches: 118, Mismatches: 27, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
18 8 0.07
19 29 0.25
20 80 0.68
21 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (19 bp):
AAATCGCAACGCGAACCGT
Found at i:335 original size:59 final size:58
Alignment explanation
Indices: 220--389 Score: 209
Period size: 59 Copynumber: 2.9 Consensus size: 58
210 CGCGAATATG
** * *
220 AAATCGCAACGCGAACACATAAATCGCAAGCGTATCCGTAATCGCAACGTGTATCCGT
1 AAATCGCAACGATAATACATAAATCGCAAGCGTATCCGTAATCGCAACGCGTATCCGT
* ***
278 AAATCGCAACGCGT-ATGGGTAAATCGCAATGCGTAT-CGTATATCGCAACGCGTATCCGT
1 AAATCGCAACG-ATAATACATAAATCGCAA-GCGTATCCGTA-ATCGCAACGCGTATCCGT
337 AAATCGCAACGATAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AAATCGCAACGATAATACATAAATCGCAA-GCGTATCCGT-AATCGCAACGCG
390 ATATTTAAAG
Statistics
Matches: 94, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
58 27 0.29
59 52 0.55
60 14 0.15
61 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (58 bp):
AAATCGCAACGATAATACATAAATCGCAAGCGTATCCGTAATCGCAACGCGTATCCGT
Found at i:366 original size:79 final size:77
Alignment explanation
Indices: 242--385 Score: 209
Period size: 79 Copynumber: 1.8 Consensus size: 77
232 GAACACATAA
* * * **
242 ATCGCAAGCGTATCCGTAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAA
1 ATCGCAAGCGTATCCGTAATCGCAACGTGAATACATAAATCGCAACGCGTATCCGTAAATCGCAA
307 TGCGTATCGTAT
66 TGCGTATCGTAT
319 ATCGCAACGCGTATCCGTAAATCGCAACGAT-AATACATAAATCGCAACGCGTATCCGTAAATCG
1 ATCGCAA-GCGTATCCGT-AATCGCAACG-TGAATACATAAATCGCAACGCGTATCCGTAAATCG
383 CAA
63 CAA
386 CGCGATATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
77 7 0.12
78 10 0.17
79 41 0.69
80 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (77 bp):
ATCGCAAGCGTATCCGTAATCGCAACGTGAATACATAAATCGCAACGCGTATCCGTAAATCGCAA
TGCGTATCGTAT
Found at i:797 original size:31 final size:33
Alignment explanation
Indices: 762--830 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
752 TTCACTTAGA
* *
762 TTTCATTTCGCGTT-C-GTTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
793 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
826 TTTCA
1 TTTCA
831 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 14 0.41
32 1 0.03
33 19 0.56
ACGTcount: A:0.09, C:0.23, G:0.19, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
Found at i:962 original size:22 final size:20
Alignment explanation
Indices: 908--963 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
898 TTTGCAGAAG
*
908 AGTCGCAACGAGATAAATGA
1 AGTCGCAACGAGAGAAATGA
*
928 AATCGCAACGAGAG-AATGA
1 AGTCGCAACGAGAGAAATGA
*
947 CTGTCGCAACGAGAGAA
1 -AGTCGCAACGAGAGAA
964 TCGCAACGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 5 0.17
20 24 0.80
21 1 0.03
ACGTcount: A:0.43, C:0.18, G:0.27, T:0.12
Consensus pattern (20 bp):
AGTCGCAACGAGAGAAATGA
Found at i:969 original size:14 final size:14
Alignment explanation
Indices: 950--1004 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
940 AGAATGACTG
950 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
964 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
983 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
997 TCGCAACG
1 TCGCAACG
1005 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1017 original size:33 final size:33
Alignment explanation
Indices: 950--1020 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
940 AGAATGACTG
***
950 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
983 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1016 TCGCA
1 TCGCA
1021 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1038 original size:19 final size:19
Alignment explanation
Indices: 1016--1113 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1006 GAAACCAAAA
*
1016 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1035 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1049 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1068 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1082 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1101 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1114 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1057 original size:14 final size:14
Alignment explanation
Indices: 1038--1127 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1028 TTTCATTTCG
1038 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1052 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1071 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1085 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1102 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1118 CGTTGCGATT
1 CGTTGCGATT
1128 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1063 original size:33 final size:33
Alignment explanation
Indices: 1021--1135 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1011 CAAAATCGCA
1021 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1054 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1087 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1120 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1136 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3047 original size:93 final size:93
Alignment explanation
Indices: 2806--3268 Score: 779
Period size: 91 Copynumber: 5.1 Consensus size: 93
2796 TAGATTGCTT
2806 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
2871 TTTGTCTT-TGTTTGTCTTTTGGTTG-A
66 TTTGTCTTGTTTTTGTCTTTTGGTTGAA
2897 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2960 -TTGTCGTTGTTTTTGTCTTTTGGTTGAA
66 TTTGTC-TTGTTTTTGTCTTTTGGTTGAA
2988 AGTAAATTTGTTCGGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTGTTCGG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
3053 A-TTGTCTT-TGTTTTGTCTTTTGG-TGAA
65 ATTTGTCTTGT-TTTTGTCTTTTGGTTGAA
3080 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3145 TTTGTCTT-TGTTTTGTCTTTTTGGTTGAA
66 TTTGTCTTGT-TTTTGTC-TTTTGGTTGAA
3174 AGTAAATTTGTTCGGTTGCTGCCAATT-TGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
3238 TTTGTCTT-TGTTTGTCTTTTGG-TGAA
66 TTTGTCTTGTTTTTGTCTTTTGGTTGAA
3264 AGTAA
1 AGTAA
3269 TTTATCCATT
Statistics
Matches: 360, Mismatches: 2, Indels: 21
0.94 0.01 0.05
Matches are distributed among these distances:
88 5 0.01
89 4 0.01
90 54 0.15
91 104 0.29
92 59 0.16
93 96 0.27
94 38 0.11
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTGTTTTTGTCTTTTGGTTGAA
Found at i:3113 original size:183 final size:185
Alignment explanation
Indices: 2806--3268 Score: 832
Period size: 183 Copynumber: 2.5 Consensus size: 185
2796 TAGATTGCTT
2806 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2871 TTTGTCTTTGTTTGTCTTTTGGTTG-AAGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTG
66 TTTGTCTTTGTTTGTCTTTTGG-TGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
2934 TGTATTCTTTAACACTGTGAAATA-TA-TTGTCGTTGTTTTTGTC-TTTTGGTTGAA
130 TGTATTCTTTAACACTGTGAAATAGTATTTGTCGTTG-TTTTGTCTTTTTGGTTGAA
2988 AGTAAATTTGTTCGGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTGTTCGG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
3053 A-TTGTCTTTGTTTTGTCTTTTGGTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65 ATTTGTCTTTG-TTTGTCTTTTGGTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
3117 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTTGGTTGAA
129 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCGTTGTTTTGTCTTTTTGGTTGAA
3174 AGTAAATTTGTTCGGTTGCTGCCAATT-TGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3238 TTTGTCTTTGTTTGTCTTTTGGTGAAAGTAA
66 TTTGTCTTTGTTTGTCTTTTGGTGAAAGTAA
3269 TTTATCCATT
Statistics
Matches: 272, Mismatches: 1, Indels: 14
0.95 0.00 0.05
Matches are distributed among these distances:
182 26 0.10
183 95 0.35
184 87 0.32
185 30 0.11
186 34 0.12
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTGTCTTTTGGTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
GTATTCTTTAACACTGTGAAATAGTATTTGTCGTTGTTTTGTCTTTTTGGTTGAA
Found at i:3338 original size:19 final size:19
Alignment explanation
Indices: 3314--3447 Score: 117
Period size: 19 Copynumber: 7.6 Consensus size: 19
3304 TAGTTTACTT
* *
3314 TCGCAACACGAAACTAAAA
1 TCGCAACGCGAAACCAAAA
3333 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3352 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3371 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
3385 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
3404 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
**
3418 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3437 TCGCAATGCGA
1 TCGCAACGCGA
3448 TTTTCATTTC
Statistics
Matches: 94, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
14 19 0.20
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 63 0.67
ACGTcount: A:0.46, C:0.27, G:0.19, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:3392 original size:33 final size:32
Alignment explanation
Indices: 3349--3442 Score: 152
Period size: 33 Copynumber: 2.9 Consensus size: 32
3339 CGCGAAACCA
3349 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAATGAAAATCGCAACGAC
**
3381 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAATGAAAATCGCAACGAC
3414 AAGATCGCAACGCGAAATGAAAATCGCAA
1 AA-ATCGCAACGCGAAATGAAAATCGCAA
3443 TGCGATTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.47, C:0.26, G:0.19, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:3439 original size:52 final size:51
Alignment explanation
Indices: 3314--3447 Score: 141
Period size: 52 Copynumber: 2.6 Consensus size: 51
3304 TAGTTTACTT
3314 TCGCAACACGAAACT-AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
3365 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAATGA-A-AATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
* *
3418 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAACACGAAATGAAAATCGCAACGCGA
3448 TTTTCATTTC
Statistics
Matches: 67, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
49 3 0.04
50 6 0.09
51 2 0.03
52 43 0.64
53 4 0.06
54 7 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.27, G:0.19, T:0.09
Consensus pattern (51 bp):
TCGCAACACGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:3465 original size:19 final size:19
Alignment explanation
Indices: 3443--3570 Score: 98
Period size: 19 Copynumber: 7.3 Consensus size: 19
3433 AAAATCGCAA
**
3443 TGCGATTTTCATTTCTTGT
1 TGCGATTTTCATTTCGCGT
3462 TGCGA--TTC-TTT--CGT
1 TGCGATTTTCATTTCGCGT
*
3476 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCGT
*
3495 TGCGA--TTC-TGT--CG-
1 TGCGATTTTCATTTCGCGT
3508 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
**
3527 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
* *
3546 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
3566 TGCGA
1 TGCGA
3571 AAGTAAACTA
Statistics
Matches: 87, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
13 5 0.06
14 8 0.09
15 3 0.03
16 10 0.11
17 9 0.10
18 2 0.02
19 38 0.44
20 12 0.14
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:3517 original size:32 final size:33
Alignment explanation
Indices: 3443--3533 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
3433 AAAATCGCAA
** *
3443 TGCGATTTTCATTTCTTGTTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
*
3476 TGCGATTTTCATTTCGCATTGCGATTCTGTCG-
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
3508 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCGTTGCGATT
3534 TTGGTTTCGC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 25 0.47
33 28 0.53
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
Found at i:5471 original size:14 final size:14
Alignment explanation
Indices: 5452--5487 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5442 GATTGTTAAT
5452 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
5466 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
5480 TGATTTGT
1 TGATTTGT
5488 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5667 original size:19 final size:19
Alignment explanation
Indices: 5593--5692 Score: 124
Period size: 19 Copynumber: 5.6 Consensus size: 19
5583 CAAAATGACT
*
5593 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5612 ATCGCAATGCG-AATGAAA
1 ATCGCAATGCGAAATGAAA
*
5630 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
5644 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5663 ATCGCAATGCAGAAATG-AA
1 ATCGCAATGC-GAAATGAAA
5682 ATCGCAATGCG
1 ATCGCAATGCG
5693 TTTATAATTT
Statistics
Matches: 72, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 4 0.06
18 16 0.22
19 35 0.49
20 6 0.08
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5744 original size:18 final size:18
Alignment explanation
Indices: 5699--5992 Score: 297
Period size: 18 Copynumber: 17.1 Consensus size: 18
5689 TGCGTTTATA
5699 ATTTCGCATTGCGA-TT-
1 ATTTCGCATTGCGATTTC
*
5715 ATCTCG--TTGCGATTTC
1 ATTTCGCATTGCGATTTC
5731 ATTTCGCATTGCGATTTC
1 ATTTCGCATTGCGATTTC
5749 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
5766 -TTTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
5782 ATTTCGCATTGCGATTTC
1 ATTTCGCATTGCGATTTC
5800 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
* *
5819 A-TTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA-TTTC
5837 ATTTCGCATTGCGA-TT-
1 ATTTCGCATTGCGATTTC
* *
5853 ATGTCG-GTT-CGATTTTC
1 ATTTCGCATTGCGA-TTTC
5870 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
5889 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
*
5906 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
5922 ATTTCGCATTGCGATTTC
1 ATTTCGCATTGCGATTTC
5940 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
*
5957 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
* *
5973 ATTTCGCGTTGCGTTTTC
1 ATTTCGCATTGCGATTTC
5991 AT
1 AT
5993 GTTGGGATTT
Statistics
Matches: 238, Mismatches: 14, Indels: 50
0.79 0.05 0.17
Matches are distributed among these distances:
14 27 0.11
15 4 0.02
16 39 0.16
17 29 0.12
18 84 0.35
19 55 0.23
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (18 bp):
ATTTCGCATTGCGATTTC
Found at i:5901 original size:140 final size:135
Alignment explanation
Indices: 5689--6020 Score: 478
Period size: 140 Copynumber: 2.4 Consensus size: 135
5679 GAAATCGCAA
5689 TGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGA-TTTCATTTCGCATTGCGA-TTTCAT
1 TGCGATTT-TAATTTCGCATTGCGATTAT-TCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
*
5751 TTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATT
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATT
*
5816 TTCATTCGTAT
129 CTC--TCG--T
5827 TGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTTTAATTTCGCATTGCGATTAT-TC-GTTGCGATTTTCATTTCGCATTGCGATTTTCAT
5891 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATT
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATT
5956 CTCTCGT
129 CTCTCGT
* * * *
5963 TGCGATTTTCATTTCGCGTTGCG-TT-TTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTAATTTCGCATTGCGATTATTC--GTTGCGATTTTCATTTCGCATTGCGATT
6021 GTATTTTCCG
Statistics
Matches: 180, Mismatches: 8, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
133 2 0.01
134 4 0.02
135 24 0.13
136 22 0.12
138 32 0.18
139 24 0.13
140 72 0.40
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.46
Consensus pattern (135 bp):
TGCGATTTTAATTTCGCATTGCGATTATTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATTCT
CTCGT
Found at i:5960 original size:51 final size:52
Alignment explanation
Indices: 5721--5992 Score: 330
Period size: 51 Copynumber: 5.2 Consensus size: 52
5711 GATTATCTCG
*
5721 TTGCGA-TTTCATTTCGCATTGCGATTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
5771 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATTTTCA-TTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
5826 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
5878 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
5930 TTGCGA-TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
5981 TTGCG-TTTTCAT
1 TTGCGATTTTCAT
5993 GTTGGGATTT
Statistics
Matches: 204, Mismatches: 8, Indels: 19
0.88 0.03 0.08
Matches are distributed among these distances:
50 6 0.03
51 103 0.50
52 58 0.28
53 10 0.05
54 3 0.01
55 24 0.12
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:8519 original size:24 final size:24
Alignment explanation
Indices: 8485--8531 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
8475 CTGAAACATC
8485 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
8509 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
8532 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:9227 original size:20 final size:20
Alignment explanation
Indices: 9199--9564 Score: 431
Period size: 20 Copynumber: 18.4 Consensus size: 20
9189 AAATTTCAGT
* * * *
9199 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
9219 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
9239 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
9259 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
9279 GTTGCGA-TTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9298 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
9318 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
9338 GTTGCGA-TTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9357 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9377 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
9397 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
9417 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9437 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
9457 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
9477 GTTGCGA-TTACGGATACAC
1 GTTGCGATTTACGGATACGC
9496 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
9516 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
9536 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
9556 GTTGCGATT
1 GTTGCGATT
9565 ATGGAAAATC
Statistics
Matches: 303, Mismatches: 32, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
18 2 0.01
19 52 0.17
20 244 0.81
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:9369 original size:79 final size:80
Alignment explanation
Indices: 9199--9545 Score: 438
Period size: 79 Copynumber: 4.4 Consensus size: 80
9189 AAATTTCAGT
* * * * * * *
9199 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCTCGTTG
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGA-TACTCGTTGCGATTTACGGATACGCGTTG
*
9263 CGATTTACGGATTA-TC
65 CGATTTACGGA-TACGC
9279 GTTGCGA-TTACGGATACGCGTTGCGATTTACGGATTA-TCGTTGCGATTTACGGATACGCGTTG
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGA-TACTCGTTGCGATTTACGGATACGCGTTG
9342 CGA-TTACGGATACGC
65 CGATTTACGGATACGC
* * *
9357 ATTGCGATTTACGGATACGCGTTGCGATTTACGGATACACGTTGCGGTTTACGGATACGCGTTGC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATACTCGTTGCGATTTACGGATACGCGTTGC
9422 GATTTACGGATACGC
66 GATTTACGGATACGC
* * ** * *
9437 GTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGA-TTACGGATACACGTTGC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATACTCGTTGCGATTTACGGATACGCGTTGC
9501 GATTTACGGATACGC
66 GATTTACGGATACGC
* *
9516 GTTGCGATTTATGTG-TTCGCGTTGCGATTT
1 GTTGCGATTTACG-GATACGCGTTGCGATTT
9546 TCATATTCGC
Statistics
Matches: 239, Mismatches: 23, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
77 2 0.01
78 16 0.07
79 162 0.68
80 59 0.25
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (80 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTACGGATACTCGTTGCGATTTACGGATACGCGTTGC
GATTTACGGATACGC
Found at i:9913 original size:18 final size:21
Alignment explanation
Indices: 9873--9913 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 21
9863 AGGTATTTAG
*
9873 GGTTTGTTTGATTATTGTGTT
1 GGTTTGTTTGATTATTGTATT
9894 GGTTT-TTT-ATT-TTGTATT
1 GGTTTGTTTGATTATTGTATT
9912 GG
1 GG
9914 GTTTCAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 8 0.42
19 3 0.16
20 3 0.16
21 5 0.26
ACGTcount: A:0.10, C:0.00, G:0.27, T:0.63
Consensus pattern (21 bp):
GGTTTGTTTGATTATTGTATT
Found at i:11586 original size:2 final size:2
Alignment explanation
Indices: 11579--11604 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11569 GTGAATATGC
11579 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
11605 TCCTTTCTAT
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:15048 original size:73 final size:74
Alignment explanation
Indices: 14945--15142 Score: 232
Period size: 73 Copynumber: 2.7 Consensus size: 74
14935 TGCAGACGGT
* *
14945 TTTTTGAAAATATGTATATAATATA-G-TTTTTCTAAAACATTTTTGAAAACTATAATATATAGT
1 TTTTAGAAAATA--TATATAATATATGATTTTT-AAAAACATTTTTGAAAACTATAATATATAGT
15008 TTTT-AAAAT-A
63 TTTTGAAAATGA
15018 TTTTAGAAAATATATATAATATATGATTTTTAAAAAGCATTTTT-AAAACTTATAATATATAGTT
1 TTTTAGAAAATATATATAATATATGATTTTTAAAAA-CATTTTTGAAAAC-TATAATATATAGTT
*
15082 TTTGAAAATGT
64 TTTGAAAATGA
* * * *
15093 TTTTA-AAACT-TATATAATATAT-AATTTTAAAAACATTTTTGGAAATTATA
1 TTTTAGAAAATATATATAATATATGATTTTTAAAAACATTTTTGAAAACTATA
15143 TAGTTTTAAA
Statistics
Matches: 111, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
71 22 0.20
72 23 0.21
73 52 0.47
74 9 0.08
75 5 0.05
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (74 bp):
TTTTAGAAAATATATATAATATATGATTTTTAAAAACATTTTTGAAAACTATAATATATAGTTTT
TGAAAATGA
Found at i:15162 original size:32 final size:32
Alignment explanation
Indices: 15121--15209 Score: 133
Period size: 32 Copynumber: 2.8 Consensus size: 32
15111 ATATAATTTT
*
15121 AAAAACATTTTTGGAAATTATATAGTTTTAAA
1 AAAAACATTTTTGAAAATTATATAGTTTTAAA
***
15153 AAAAACATTTTTGAAAATTATATAGTTTTTTT
1 AAAAACATTTTTGAAAATTATATAGTTTTAAA
15185 AAAAACATTTTTGAAAATTTATATA
1 AAAAACATTTTTGAAAA-TTATATA
15210 ATATATAGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 45 0.87
33 7 0.13
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (32 bp):
AAAAACATTTTTGAAAATTATATAGTTTTAAA
Found at i:15262 original size:40 final size:38
Alignment explanation
Indices: 15137--15265 Score: 121
Period size: 40 Copynumber: 3.5 Consensus size: 38
15127 ATTTTTGGAA
* *
15137 ATTATATAGTTTTAAAAAAAACATTTTTGAAAA-TTAT
1 ATTATATAGTTTTTAAAAAAACATTTTTAAAAATTTAT
*
15174 A-TAGT-T--TTTTT--AAAAACATTTTTGAAAATTTAT
1 ATTA-TATAGTTTTTAAAAAAACATTTTTAAAAATTTAT
15207 ATAATATATAG-TTTTAAAAGAAACATTTTTAAAAAATTTAT
1 AT--TATATAGTTTTTAAAA-AAACATTTTT-AAAAATTTAT
*
15248 ATTATATTGTTTTTAAAA
1 ATTATATAGTTTTTAAAA
15266 TATTTTTCAT
Statistics
Matches: 76, Mismatches: 3, Indels: 23
0.75 0.03 0.23
Matches are distributed among these distances:
32 17 0.22
33 5 0.07
34 4 0.05
35 1 0.01
36 6 0.08
37 6 0.08
39 8 0.11
40 18 0.24
41 11 0.14
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (38 bp):
ATTATATAGTTTTTAAAAAAACATTTTTAAAAATTTAT
Found at i:15288 original size:19 final size:19
Alignment explanation
Indices: 15266--15311 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
15256 GTTTTTAAAA
15266 TATTTTTCATATGTA-TTA-T
1 TATTTTTCAT-T-TATTTATT
*
15285 TATTTCTCATTTATTTATT
1 TATTTTTCATTTATTTATT
15304 TATTTTTC
1 TATTTTTC
15312 TTTCTTCTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.09
18 4 0.17
19 17 0.74
ACGTcount: A:0.22, C:0.09, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTTCATTTATTTATT
Found at i:18066 original size:15 final size:15
Alignment explanation
Indices: 18046--18075 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18036 CTCTATGCGA
18046 CTCTTCGTCATCTTC
1 CTCTTCGTCATCTTC
*
18061 CTCTTCTTCATCTTC
1 CTCTTCGTCATCTTC
18076 TATCAACTTA
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:0.07, C:0.40, G:0.03, T:0.50
Consensus pattern (15 bp):
CTCTTCGTCATCTTC
Found at i:29698 original size:26 final size:26
Alignment explanation
Indices: 29668--29730 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
29658 ATACATATCA
*
29668 TGTCATCACTTTGAACATATAAGATT
1 TGTCATCACTTTGAACATATAAGACT
29694 TGTCATCACTTTGAACATATAAGACT
1 TGTCATCACTTTGAACATATAAGACT
29720 TGTCATCACTT
1 TGTCATCACTT
29731 ATGTACATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (26 bp):
TGTCATCACTTTGAACATATAAGACT
Found at i:41275 original size:19 final size:19
Alignment explanation
Indices: 41251--41291 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
41241 GCCATACTGG
41251 TTTTCCCT-TAATATCTTAA
1 TTTTCCCTATAATATC-TAA
*
41270 TTTTCCCTATAATTTCTAA
1 TTTTCCCTATAATATCTAA
41289 TTT
1 TTT
41292 GTGCAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTCCCTATAATATCTAA
Found at i:42420 original size:15 final size:15
Alignment explanation
Indices: 42400--42436 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
42390 TGAGACATTA
*
42400 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
42415 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
42430 CCCGCCC
1 CCCGCCC
42437 AACTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:47401 original size:21 final size:22
Alignment explanation
Indices: 47375--47422 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
47365 CGATAAAAAA
47375 TTTTACCTAAAATATT-ATAAT
1 TTTTACCTAAAATATTAATAAT
*
47396 TTTTACCTAAAATATTAATATT
1 TTTTACCTAAAATATTAATAAT
47418 TTTTA
1 TTTTA
47423 AAAAATTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTACCTAAAATATTAATAAT
Found at i:49524 original size:21 final size:21
Alignment explanation
Indices: 49498--49537 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
49488 TGGAGCGCAT
* *
49498 GGAGGAACTATCATCTCCACC
1 GGAGGAACCATCATATCCACC
49519 GGAGGAACCATCATATCCA
1 GGAGGAACCATCATATCCA
49538 TCAGAAGAAC
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:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (21 bp):
GGAGGAACCATCATATCCACC
Done.