Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004912.1 Hibiscus syriacus cultivar Beakdansim tig00011061_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: 80529
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:9695 original size:29 final size:29
Alignment explanation
Indices: 9654--9730 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
9644 ATTTTTTTAA
* *
9654 AATTACGAAAATAGCACCCTTTTCCAAAT
1 AATTACCAGAATAGCACCCTTTTCCAAAT
* * *
9683 AATTACCAGAATAACAACCTTTTCTAAAT
1 AATTACCAGAATAGCACCCTTTTCCAAAT
9712 AATTACCAGAATAGCACCC
1 AATTACCAGAATAGCACCC
9731 GGTTAACGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.43, C:0.25, G:0.06, T:0.26
Consensus pattern (29 bp):
AATTACCAGAATAGCACCCTTTTCCAAAT
Found at i:16843 original size:29 final size:29
Alignment explanation
Indices: 16799--16953 Score: 110
Period size: 29 Copynumber: 5.6 Consensus size: 29
16789 ATCATTTTCA
* *
16799 AAAACAATTACCAAAATATCACAATTTTT
1 AAAATAATTACCAAAATATCACACTTTTT
* **
16828 AAAATAATTACTAAAATATCA-TTTTTTT
1 AAAATAATTACCAAAATATCACACTTTTT
* * *
16856 TAAA-AATTA-CTAAAT-T---ATTTTTT
1 AAAATAATTACCAAAATATCACACTTTTT
* * *
16879 AAAAAAATTACGAAAATAACAC-CTTTTT
1 AAAATAATTACCAAAATATCACACTTTTT
* * * *
16907 AAAATAATTACCAGAATAGCACCCTTTTC
1 AAAATAATTACCAAAATATCACACTTTTT
*
16936 CAAATAATTACCAAAATA
1 AAAATAATTACCAAAATA
16954 GCATCTGAAC
Statistics
Matches: 99, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
23 9 0.09
24 5 0.05
25 5 0.05
26 4 0.04
27 5 0.05
28 31 0.31
29 40 0.40
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATAATTACCAAAATATCACACTTTTT
Found at i:16884 original size:24 final size:27
Alignment explanation
Indices: 16789--16917 Score: 104
Period size: 27 Copynumber: 4.8 Consensus size: 27
16779 CGAAAATAGC
* *
16789 ATCA-TTTTCAAAAACAATTACCAAAAT
1 ATCATTTTTTAAAAA-AATTACTAAAAT
* *
16816 ATCACAATTTTTAAAATAATTACTAAAAT
1 AT--CATTTTTTAAAAAAATTACTAAAAT
**
16845 ATCATTTTTTTTAAAAATTACT-AAAT
1 ATCATTTTTTAAAAAAATTACTAAAAT
*
16871 -T-ATTTTTTAAAAAAATTACGAAAAT
1 ATCATTTTTTAAAAAAATTACTAAAAT
* * *
16896 AACACCTTTTTAAAATAATTAC
1 ATCA-TTTTTTAAAAAAATTAC
16918 CAGAATAGCA
Statistics
Matches: 82, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
24 16 0.20
25 5 0.06
26 4 0.05
27 19 0.23
28 15 0.18
29 15 0.18
30 8 0.10
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.39
Consensus pattern (27 bp):
ATCATTTTTTAAAAAAATTACTAAAAT
Found at i:16909 original size:28 final size:29
Alignment explanation
Indices: 16874--16953 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 29
16864 ACTAAATTAT
* *
16874 TTTTTAAAAAAATTACGAAAATAACA-CC
1 TTTTTAAAATAATTACCAAAATAACACCC
* *
16902 TTTTTAAAATAATTACCAGAATAGCACCC
1 TTTTTAAAATAATTACCAAAATAACACCC
**
16931 TTTTCCAAATAATTACCAAAATA
1 TTTTTAAAATAATTACCAAAATA
16954 GCATCTGAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 22 0.50
29 22 0.50
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.31
Consensus pattern (29 bp):
TTTTTAAAATAATTACCAAAATAACACCC
Found at i:22365 original size:15 final size:15
Alignment explanation
Indices: 22345--22426 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
22335 TTCCAGAAAA
22345 TGAATTACTGGAATT
1 TGAATTACTGGAATT
22360 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
22375 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
*
22390 TGAATTACTGAAATT
1 TGAATTACTGGAATT
**
22405 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
22419 TGAATTAC
1 TGAATTAC
22427 ATTTCTGTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 11 0.19
15 47 0.81
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:22379 original size:30 final size:30
Alignment explanation
Indices: 22345--22426 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
22335 TTCCAGAAAA
** *
22345 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGAAATT
22375 TGAATTACTGGAAAATGAATTACTGAAATT
1 TGAATTACTGGAAAATGAATTACTGAAATT
22405 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
22427 ATTTCTGTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGAAATT
Found at i:22405 original size:45 final size:44
Alignment explanation
Indices: 22340--22426 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 44
22330 TGGTTTTCCA
* **
22340 GAAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGAAATTTGAATT-CTGGAAAATGAATTACTG
22385 GAAAATGAATTACTGAAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGAAATTTGAATTCTGGAAAATGAATTAC
22427 ATTTCTGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.33
Consensus pattern (44 bp):
GAAAATGAATTACTGAAATTTGAATTCTGGAAAATGAATTACTG
Found at i:22432 original size:20 final size:20
Alignment explanation
Indices: 22409--22478 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
22399 GAAATTTGAA
22409 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
22429 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
22449 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
22469 TTCTGGAAAA
1 TTCTGGAAAA
22479 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:22690 original size:28 final size:27
Alignment explanation
Indices: 22635--22699 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
22625 TTTACTAAAA
*
22635 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAATATTAT
22663 TCATTATTAAATATATAAAAAA-ATTTAT
1 T-ATTATTAAATATATAAAAAATA-TTAT
22691 TATATATTA
1 TAT-TATTA
22700 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.09
28 24 0.73
29 6 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAATATTAT
Found at i:22725 original size:31 final size:32
Alignment explanation
Indices: 22635--22732 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 32
22625 TTTACTAAAA
*
22635 TATTATTGAAATATAT--AAATA-ATATTAT-T
1 TATTATT-AAATATATAAAAAAATATATTATAT
* *
22664 CATTATTAAATATATAAAAAAATTTATTATA-
1 TATTATTAAATATATAAAAAAATATATTATAT
*
22695 TATTATTAAA-ATA-AAAATATAATATCTTATAT
1 TATTATTAAATATATAAAA-A-AATATATTATAT
22727 TATTAT
1 TATTAT
22733 AATAATTGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 8 0.14
29 10 0.18
30 8 0.14
31 24 0.43
32 6 0.11
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (32 bp):
TATTATTAAATATATAAAAAAATATATTATAT
Found at i:22772 original size:28 final size:27
Alignment explanation
Indices: 22688--22796 Score: 82
Period size: 28 Copynumber: 4.0 Consensus size: 27
22678 TAAAAAAATT
* *
22688 TATTATATATTATTAAAATAAAAATATAA
1 TATTATATAATATTAAAAT--AAATATTA
* * *
22717 TATCT-TATATTATTATAATAATTGATTA
1 TAT-TATATAATATTAAAATAAAT-ATTA
*
22745 TTTTATATAATATTAAAATATAATATTA
1 TATTATATAATATTAAAATA-AATATTA
22773 TATTAT-TAAATATT--AATAAATATT
1 TATTATAT-AATATTAAAATAAATATT
22797 TTAAATATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
25 6 0.09
26 4 0.06
27 5 0.07
28 33 0.49
29 18 0.27
30 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
TATTATATAATATTAAAATAAATATTA
Found at i:22779 original size:21 final size:21
Alignment explanation
Indices: 22750--22790 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22740 GATTATTTTA
22750 TATAATATTAAA-ATATAATAT
1 TATAATATTAAATAT-TAATAT
*
22771 TATATTATTAAATATTAATA
1 TATAATATTAAATATTAATA
22791 AATATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATAATATTAAATATTAATAT
Found at i:22803 original size:9 final size:10
Alignment explanation
Indices: 22772--22809 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
22762 ATATAATATT
22772 ATATTATTAA
1 ATATTATTAA
*
22782 ATATTAATAA
1 ATATTATTAA
22792 ATATT-TTAA
1 ATATTATTAA
22801 ATATT-TTAA
1 ATATTATTAA
22810 TAATTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 12 0.46
10 14 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATTATTAA
Found at i:23057 original size:42 final size:42
Alignment explanation
Indices: 22994--23095 Score: 186
Period size: 42 Copynumber: 2.4 Consensus size: 42
22984 ATGAATTACA
*
22994 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
23036 TTCTGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
23078 TTCCGGAAAACGAATTAC
1 TTCCGGAAAACGAATTAC
23096 ACGGGAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.19
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:33860 original size:27 final size:30
Alignment explanation
Indices: 33805--33861 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
33795 ATGAAAGATA
*
33805 GGTTAAATTGATTTTTTTTGTCGAGTTCAAT
1 GGTTAAATTGATGTTTTTTGTC-AGTTCAAT
33836 GGTTAAATTG-TGTTTTTT-T-AGTTCAA
1 GGTTAAATTGATGTTTTTTGTCAGTTCAA
33862 AGAAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 7 0.28
29 1 0.04
30 7 0.28
31 10 0.40
ACGTcount: A:0.23, C:0.05, G:0.19, T:0.53
Consensus pattern (30 bp):
GGTTAAATTGATGTTTTTTGTCAGTTCAAT
Found at i:34342 original size:22 final size:20
Alignment explanation
Indices: 34295--34356 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 20
34285 TTTACTCAGT
*
34295 AATTTAATTTTTAAAATTTTTA
1 AATTTAATTTTT--TATTTTTA
34317 AATTT-ATTTATTTATTTTTA
1 AATTTAATTT-TTTATTTTTA
34337 GTAATTTAATTTTTTATTTT
1 --AATTTAATTTTTTATTTT
34357 ATATTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 7 0.20
21 4 0.11
22 20 0.57
23 4 0.11
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
AATTTAATTTTTTATTTTTA
Found at i:41269 original size:19 final size:19
Alignment explanation
Indices: 41245--41329 Score: 170
Period size: 19 Copynumber: 4.5 Consensus size: 19
41235 CAATTAATGG
41245 ATCGATGCATAAGGAGTGC
1 ATCGATGCATAAGGAGTGC
41264 ATCGATGCATAAGGAGTGC
1 ATCGATGCATAAGGAGTGC
41283 ATCGATGCATAAGGAGTGC
1 ATCGATGCATAAGGAGTGC
41302 ATCGATGCATAAGGAGTGC
1 ATCGATGCATAAGGAGTGC
41321 ATCGATGCA
1 ATCGATGCA
41330 CATGTTAAGG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 66 1.00
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.21
Consensus pattern (19 bp):
ATCGATGCATAAGGAGTGC
Found at i:42853 original size:23 final size:23
Alignment explanation
Indices: 42819--42887 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
42809 CAACCTTATA
42819 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* *
42842 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
42865 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
42888 AACTGTGGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:46383 original size:24 final size:22
Alignment explanation
Indices: 46355--46419 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 22
46345 CATCGATACA
46355 TAAGGAGTGCATCGATGCACATG
1 TAAGGAGTGCATCGATGCAC-TG
* *
46378 TTAAGGGGTGCATCGATACACTG
1 -TAAGGAGTGCATCGATGCACTG
*
46401 T-A-GAATGCATCGATGCACT
1 TAAGGAGTGCATCGATGCACT
46420 TCAAGGGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 14 0.39
21 1 0.03
22 1 0.03
23 2 0.06
24 18 0.50
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (22 bp):
TAAGGAGTGCATCGATGCACTG
Found at i:47895 original size:23 final size:23
Alignment explanation
Indices: 47869--47929 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
47859 TATGGCAGTT
47869 CGGTGCATTTCTACGCGGCACTA
1 CGGTGCATTTCTACGCGGCACTA
* * *
47892 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCATTTCTACGCGGCACTA
*
47915 CGGTGCATTTATACG
1 CGGTGCATTTCTACG
47930 AGCTGTGGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
CGGTGCATTTCTACGCGGCACTA
Found at i:52036 original size:18 final size:17
Alignment explanation
Indices: 52013--52046 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
52003 CTACTATTAG
52013 TGAACCGGTCAGAATCGT
1 TGAACCGGTCA-AATCGT
*
52031 TGAACCGTTCAAATCG
1 TGAACCGGTCAAATCG
52047 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (17 bp):
TGAACCGGTCAAATCGT
Found at i:64059 original size:2 final size:2
Alignment explanation
Indices: 64052--64093 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
64042 TGTTTGTACT
64052 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
64094 GAGAGAGAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:72678 original size:22 final size:22
Alignment explanation
Indices: 72634--72679 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
72624 TTATGTGTGA
72634 TTGTTGTCGTAACAAAAATAAT
1 TTGTTGTCGTAACAAAAATAAT
*
72656 TTGTCTGTCGTAATAAAAA-AAT
1 TTGT-TGTCGTAACAAAAATAAT
72678 TT
1 TT
72680 ACTTTTACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (22 bp):
TTGTTGTCGTAACAAAAATAAT
Found at i:75825 original size:27 final size:23
Alignment explanation
Indices: 75771--75815 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
75761 GCATATTAGG
**
75771 TAACGCTTATATAATGTAATAGA
1 TAACGCTTATATAATAAAATAGA
75794 TAACGCTTATATAATAAAATAG
1 TAACGCTTATATAATAAAATAG
75816 GTATTTAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (23 bp):
TAACGCTTATATAATAAAATAGA
Found at i:79505 original size:183 final size:183
Alignment explanation
Indices: 79197--79569 Score: 683
Period size: 183 Copynumber: 2.0 Consensus size: 183
79187 TTAAAATTAG
*
79197 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTATAGACCTATTCGCTCATAAAACCGGTATATTT
* *
79262 ATACCGGTTATATAACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATAACAAAATTATCTATTACATTATAATTCTAGGTTCCGATATGTAAATGTCGA
* *
79327 CACTTTTTGACAATGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTATGGACATAAAGTAC
79380 CGACACAATATTAAAAAGTGTCGATATAGGTTATAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTATAGACCTATTCGCTCATAAAACCGGTATATTT
*
79445 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTAGGTTCCGATATGTAAATGTCGA
66 ATACCGGTTATATAACAAAATTATCTATTACATTATAATTCTAGGTTCCGATATGTAAATGTCGA
*
79510 CACTTTTTGACAAGGTATTGACACATTTTTCTTCCATTATGGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTATGGACATAAAGTAC
79563 CGACACA
1 CGACACA
79570 TTTATACCTA
Statistics
Matches: 183, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 183 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (183 bp):
CGACACAATATTAAAAAGTGTCGATATAGGTTATAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATAACAAAATTATCTATTACATTATAATTCTAGGTTCCGATATGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTATGGACATAAAGTAC
Found at i:80337 original size:198 final size:200
Alignment explanation
Indices: 79678--80529 Score: 1347
Period size: 198 Copynumber: 4.4 Consensus size: 200
79668 ACATTAAACG
* * * * *
79678 GTGTCGATACA-TATATATACCAATTCTCTCATAAAACTGGTATACTTGTA-CGGTTAGATTGAA
1 GTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAA
79741 AAATTACCTATTACATTATACTTATGGGTTTCGATG-TTATCGGATCGACAC-TTTT-TATATGG
66 AAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGG
* *
79803 ATCGACACTTTATTATTGCACCTTG-TTGCCA-T--TTCTGGACCAAAAATAT---CACAAAC-A
131 ATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTA
79860 CAAAA
196 CAAAA
79865 GTGTCGATACATTATTTAGACCTATTCTCTCATAAAACC-GTATACTTGTACCGA-TAGATTGAA
1 GTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAA
* *
79928 AAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACA-TTTTTATATATGG
66 AAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGG
* *
79992 ATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATTGACACAAACTA
131 ATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTA
*
80057 -TAAA
196 CAAAA
* *
80061 GTGTCGATATATTA-TTAGACCTATTCTCTCATAAAATCGGTATACTTGTACCGATTAGATTGAA
1 GTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAA
*
80125 AAATTACCTATTACA-TATACTTATGGGTTTCGATGTTTATCGGATCGATACTTTTTATATATGG
66 AAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGG
* *
80189 ATCGACACTTTATTGTTGCACCCTGTTTTTCCATTCA-T-TGGACAAAAAATATCGACACAAACT
131 ATCGACACTTTATTGTTGCACCCTG-TTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
80252 ACAAAA
195 ACAAAA
80258 GTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAA
1 GTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAA
80323 AAATTACCTATTACATTATACTTATGGGTTTTCGATGTTTATCGGATCGACACTTTTTATATATG
66 AAATTACCTATTACATTATACTTATGGG-TTTCGATGTTTATCGGATCGACACTTTTTATATATG
*
80388 GATCGACACTTTATTGTTGCACCTTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
130 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
80453 ACAAAA
195 ACAAAA
*
80459 GTGTCGATACATTATTTAGACCTA-T-TCTCATAAAATCGGTATACTTGTA-CGATTAGATTGAA
1 GTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAA
80521 AAATTACCT
66 AAATTACCT
Statistics
Matches: 614, Mismatches: 28, Indels: 35
0.91 0.04 0.05
Matches are distributed among these distances:
187 66 0.11
188 42 0.07
189 29 0.05
190 6 0.01
191 1 0.00
193 17 0.03
195 23 0.04
196 94 0.15
197 79 0.13
198 96 0.16
199 45 0.07
200 62 0.10
201 54 0.09
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (200 bp):
GTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAA
AAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGG
ATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTA
CAAAA
Found at i:80435 original size:397 final size:384
Alignment explanation
Indices: 79678--80529 Score: 1349
Period size: 397 Copynumber: 2.2 Consensus size: 384
79668 ACATTAAACG
* * *
79678 GTGTCGATACA-TATATATACCAATTCTCTCATAAAA-CTGGTATACTTGTACGGTTAGATTGAA
1 GTGTCGATACATTAT-TAGACCTATTCTCTCATAAAATC-GGTATACTTGTACGATTAGATTGAA
79741 AAATTACCTATTACATTATACTTATGGGTTTCGATGTTATCGGATCGACACTTTTTATATGGATC
64 AAATTACCTATTACATTATACTTATGGGTTTCGATGTTATCGGATCGACACTTTTTATATGGATC
*
79806 GACACTTTATTATTGCACCTTGTTGCCATTTCTGGACCAAAAATATCACAAACACAAAAGTGTCG
129 GACACTTTATTATTGCACCTTGTTGCCATTTCTGGACAAAAAATATCACAAACACAAAAGTGTCG
79871 ATACATTATTTAGACCTATTCTCTCATAAAACCGTATACTTGTACCGATAGATTGAAAAATTACC
194 ATACATTATTTAGACCTATTCTCTCATAAAACCGTATACTTGTACCGATAGATTGAAAAATTACC
* *
79936 TATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACATTTTTATATATGGATCGACACT
259 TATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACATTTTTATATATGGATCGACACT
* *
80001 TTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATTGACACAAACTA-TAAA
324 TTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAA
*
80061 GTGTCGATATATTATTAGACCTATTCTCTCATAAAATCGGTATACTTGTACCGATTAGATTGAAA
1 GTGTCGATACATTATTAGACCTATTCTCTCATAAAATCGGTATACTTGTA-CGATTAGATTGAAA
*
80126 AATTACCTATTACA-TATACTTATGGGTTTCGATGTTTATCGGATCGATACTTTTTATATATGGA
65 AATTACCTATTACATTATACTTATGGGTTTCGATG-TTATCGGATCGACAC-TTTT-TATATGGA
* * *
80190 TCGACACTTTATTGTTGCACCCTGTTTTTCCA-TTCATTGGACAAAAAATATCGACACAAACTAC
127 TCGACACTTTATTATTGCA-CCT-TGTTGCCATTTC--TGGACAAAAAATAT---CACAAAC-AC
80254 AAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGAT
184 AAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACC-GTATACTTGTACCGA-TAGAT
80319 TGAAAAATTACCTATTACATTATACTTATGGGTTTTCGATGTTTATCGGATCGACACTTTTTATA
247 TGAAAAATTACCTATTACATTATACTTATGGG-TTTCGATGTTTATCGGATCGACA-TTTTTATA
* *
80384 TATGGATCGACACTTTATTGTTGCACCTTGTTTGCCATTCATTCTGGACCAAAAATATCGACACA
310 TATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACA
80449 AACTACAAAA
375 AACTACAAAA
80459 GTGTCGATACATTATTTAGACCTA-T-TCTCATAAAATCGGTATACTTGTACGATTAGATTGAAA
1 GTGTCGATACATTA-TTAGACCTATTCTCTCATAAAATCGGTATACTTGTACGATTAGATTGAAA
80522 AATTACCT
65 AATTACCT
Statistics
Matches: 433, Mismatches: 16, Indels: 27
0.91 0.03 0.06
Matches are distributed among these distances:
383 61 0.14
384 45 0.10
385 4 0.01
386 26 0.06
387 6 0.01
388 6 0.01
389 13 0.03
392 7 0.02
393 45 0.10
394 15 0.03
395 36 0.08
396 44 0.10
397 99 0.23
398 17 0.04
399 9 0.02
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (384 bp):
GTGTCGATACATTATTAGACCTATTCTCTCATAAAATCGGTATACTTGTACGATTAGATTGAAAA
ATTACCTATTACATTATACTTATGGGTTTCGATGTTATCGGATCGACACTTTTTATATGGATCGA
CACTTTATTATTGCACCTTGTTGCCATTTCTGGACAAAAAATATCACAAACACAAAAGTGTCGAT
ACATTATTTAGACCTATTCTCTCATAAAACCGTATACTTGTACCGATAGATTGAAAAATTACCTA
TTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACATTTTTATATATGGATCGACACTTT
ATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAA
Done.