Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003998.1 Hibiscus syriacus cultivar Beakdansim tig00008713_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: 47095
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:533 original size:104 final size:105
Alignment explanation
Indices: 1--777 Score: 1239
Period size: 104 Copynumber: 7.5 Consensus size: 105
1 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG-TGAAA-TGGCTCTGAAATTGAG
1 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
64 AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
66 AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
104 TGAACTTTCGTTGTCTGGGGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGAG
1 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
*
168 AAA-CTTTGTTGAC-ACCAGCGGTCCCTTCGTCGTGAAGT
66 AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
206 TGAACTTGCG-TGTCT-GAGTCCAATATCC-TCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
1 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
268 AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
66 AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* * *
308 TGAACTTTCGTTGTCTGGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGAG
1 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
*
373 AAACGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
66 AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
413 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTATGAGGTTGAAATTGGCTCTGAAATTGAG
1 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
478 AAA-GTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
66 AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
517 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCTG-AATTGGA
1 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GA
*
581 GAAATGTTTGGTGACAACCAGCGG-CCCTTC-TCGTGAAGT
65 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
620 TGAACTTGCGTCG--TGGGGTCC-ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGGA
1 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GA
* * *
681 GAAATGTTTGGTGACAATCAGCGGT-CCTTCGTCATG-AGT
65 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
**
720 TGAACTTTGCGTTGTCTATAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 TGAAC-TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
778 GTAAAACCTG
Statistics
Matches: 630, Mismatches: 28, Indels: 31
0.91 0.04 0.04
Matches are distributed among these distances:
99 3 0.00
100 120 0.19
101 32 0.05
102 75 0.12
103 81 0.13
104 166 0.26
105 153 0.24
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
Found at i:745 original size:204 final size:208
Alignment explanation
Indices: 1--777 Score: 1226
Period size: 204 Copynumber: 3.8 Consensus size: 208
1 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG-TGAAA-TGGCTCTGAAATTGAG
1 TGAACTTGCGTTG-CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
*
64 AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTTCGTTGTCTGGGGTCCAA
65 AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTTCGTTGTCTGGAGTCCAA
*
129 TATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACTTTGTTGAC-ACCAGCGGTCC
130 TATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAAGTTTGTTGACAACCAGCGGTCC
192 CTTCGTCGTGAAGT
195 CTTCGTCGTGAAGT
206 TGAACTTGCG-TGTCT-GAGTCCAATATCC-TCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
1 TGAACTTGCGTTG-CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
*
268 AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTTCGTTGTCTGGGGTCCAA
65 AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTTCGTTGTCTGGAGTCCAA
*
333 TATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGAGAAACGTTTGTTGACAACCAGCGGTC
130 TATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-GTTTGTTGACAACCAGCGGTC
398 CCTTCGTCGTGAAGT
194 CCTTCGTCGTGAAGT
* *
413 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTATGAGGTTGAAATTGGCTCTGAAATTGAG
1 TGAACTTGCGTTG-CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
*
478 AAA-GTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
65 AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTTCGTTGTCTGGAGTCCAA
* *
542 TATCCTTCGTTGTGAAGTTGAGATTGGCTCTG-AATTGGAGAAATGTTTGGTGACAACCAGCGG-
130 TATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAA-GTTTGTTGACAACCAGCGGT
605 CCCTTC-TCGTGAAGT
193 CCCTTCGTCGTGAAGT
* *
620 TGAACTTGCGTCG-TGGGGTCC-ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGGAG
1 TGAACTTGCGTTGCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAG
* * * **
682 AAATGTTTGGTGACAATCAGCGGT-CCTTCGTCATG-AGTTGAACTTTGCGTTGTCTATAGTCCA
65 AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTT-CGTTGTCTGGAGTCCA
745 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
129 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
778 GTAAAACCTG
Statistics
Matches: 539, Mismatches: 21, Indels: 25
0.92 0.04 0.04
Matches are distributed among these distances:
202 11 0.02
203 32 0.06
204 188 0.35
205 67 0.12
206 9 0.02
207 56 0.10
208 15 0.03
209 126 0.23
210 35 0.06
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (208 bp):
TGAACTTGCGTTGCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
AATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTTCGTTGTCTGGAGTCCAAT
ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAAGTTTGTTGACAACCAGCGGTCCC
TTCGTCGTGAAGT
Found at i:1598 original size:56 final size:56
Alignment explanation
Indices: 1523--1631 Score: 148
Period size: 56 Copynumber: 1.9 Consensus size: 56
1513 TTTTCTCTTC
* * *
1523 TTTTTCTTTTTCTTTTTTTT-AATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTCTTTTTCTTTTTTTTCAACTTAGGACGCCCTCTC-GGTTTTCACCCTAAACG
* * *
1579 TTTTTTTTTTTTTTTTTTTTCAACTTAGGACGCCCTCTCGGTTTTCATCCTAA
1 TTTTTCTTTTTCTTTTTTTTCAACTTAGGACGCCCTCTCGGTTTTCACCCTAA
1632 GCGAAATATT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
56 31 0.67
57 15 0.33
ACGTcount: A:0.13, C:0.21, G:0.12, T:0.54
Consensus pattern (56 bp):
TTTTTCTTTTTCTTTTTTTTCAACTTAGGACGCCCTCTCGGTTTTCACCCTAAACG
Found at i:11916 original size:19 final size:19
Alignment explanation
Indices: 11886--11942 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
11876 AAAAGAAGAA
*
11886 AATATAATAAAATATAAAT
1 AATAAAATAAAATATAAAT
* * * *
11905 GGATAAAAAAAAATACACAT
1 -AATAAAATAAAATATAAAT
11925 AATAAAATAAAATATAAA
1 AATAAAATAAAATATAAA
11943 GCAATGAAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATATAAAT
Found at i:12043 original size:14 final size:14
Alignment explanation
Indices: 12026--12052 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12016 AAAAATAGTA
12026 ATGAAATAATAATG
1 ATGAAATAATAATG
12040 ATGAAATAATAAT
1 ATGAAATAATAAT
12053 AAAATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (14 bp):
ATGAAATAATAATG
Found at i:12170 original size:21 final size:21
Alignment explanation
Indices: 12138--12178 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12128 TACGTATATA
*
12138 ATAAAAATATAATATGATAGC
1 ATAAAAATATAATATAATAGC
12159 ATAAATAA-ATAATATAATAG
1 ATAAA-AATATAATATAATAG
12179 TAAAAAGCAA
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:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (21 bp):
ATAAAAATATAATATAATAGC
Found at i:17702 original size:31 final size:31
Alignment explanation
Indices: 17667--17755 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
17657 ATCATTAATG
17667 TTATCGATTTGAAACAAATTGGTCACTAACA
1 TTATCGATTTGAAACAAATTGGTCACTAACA
* *
17698 TTATCGATTT-ATAATAGATTGGTCACTAACA
1 TTATCGATTTGA-AACAAATTGGTCACTAACA
* *
17729 TAATCGATTTGTAACAAATTGGTCACT
1 TTATCGATTTGAAACAAATTGGTCACT
17756 CAATTTTAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (31 bp):
TTATCGATTTGAAACAAATTGGTCACTAACA
Found at i:29249 original size:34 final size:34
Alignment explanation
Indices: 29206--29272 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
29196 TGTTAGAGAG
29206 ATACAAACATGCATGTGTATGTTTACATAGCTAC
1 ATACAAACATGCATGTGTATGTTTACATAGCTAC
*
29240 ATACAAACATGCATGTTTATGTTTACATAGCTA
1 ATACAAACATGCATGTGTATGTTTACATAGCTA
29273 TGTATACACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (34 bp):
ATACAAACATGCATGTGTATGTTTACATAGCTAC
Found at i:29633 original size:20 final size:20
Alignment explanation
Indices: 29608--29648 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
29598 TAGTTTGCCT
*
29608 TAGAATAATCAAATATCTAG
1 TAGAATAATAAAATATCTAG
*
29628 TAGAATAATAAAATATTTAG
1 TAGAATAATAAAATATCTAG
29648 T
1 T
29649 CTTCTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (20 bp):
TAGAATAATAAAATATCTAG
Found at i:33717 original size:13 final size:13
Alignment explanation
Indices: 33699--33735 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
33689 GTTACAACCC
33699 GACCCGACCCGTT
1 GACCCGACCCGTT
*
33712 GACCCGACCGGTT
1 GACCCGACCCGTT
33725 GACCCGACCCG
1 GACCCGACCCG
33736 ACCAAATGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.46, G:0.27, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:33718 original size:18 final size:17
Alignment explanation
Indices: 33695--33738 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 17
33685 ACCGGTTACA
33695 ACCCGACCCGACCCGTTG
1 ACCCGACCCGA-CCGTTG
33713 ACCCGA-CCG---GTTG
1 ACCCGACCCGACCGTTG
33726 ACCCGACCCGACC
1 ACCCGACCCGACC
33739 AAATGACCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 9
0.71 0.00 0.29
Matches are distributed among these distances:
13 10 0.45
14 3 0.14
17 3 0.14
18 6 0.27
ACGTcount: A:0.18, C:0.50, G:0.23, T:0.09
Consensus pattern (17 bp):
ACCCGACCCGACCGTTG
Found at i:36368 original size:57 final size:57
Alignment explanation
Indices: 36293--36456 Score: 229
Period size: 57 Copynumber: 2.9 Consensus size: 57
36283 TATAGTTGGA
* * *
36293 GGAAGAATACTTGTAGGTTCCCCAGCTTTGTGCTGAGAGCCTTATTGTTCGTGACGG
1 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTATTGTTCGTGACGG
**
36350 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTATAATTCGTGACGG
1 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTATTGTTCGTGACGG
** * * * *
36407 GGTTGAATAATTACAGGCTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTC
1 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTATTGTTC
36457 ATACTTGCAA
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 94 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.32
Consensus pattern (57 bp):
GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTATTGTTCGTGACGG
Found at i:39968 original size:22 final size:21
Alignment explanation
Indices: 39915--39972 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
39905 ATAATAAACC
*
39915 AAAGAGAAAAGAAAAAAGTTA
1 AAAGAGAAAATAAAAAAGTTA
39936 ATAA-A-ATAAATAAAATAAGTTA
1 A-AAGAGA-AAATAAAA-AAGTTA
39958 AAAGAGAAAATAAAA
1 AAAGAGAAAATAAAA
39973 GATTGATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
20 1 0.03
21 11 0.35
22 18 0.58
23 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (21 bp):
AAAGAGAAAATAAAAAAGTTA
Found at i:40019 original size:15 final size:16
Alignment explanation
Indices: 39999--40032 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39989 AAGGAGTAGG
39999 AAAAATAA-AAACAAA
1 AAAAATAATAAACAAA
*
40014 AAAAATAATAAATAAA
1 AAAAATAATAAACAAA
40030 AAA
1 AAA
40033 TATATCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAATAATAAACAAA
Found at i:40111 original size:20 final size:21
Alignment explanation
Indices: 40088--40126 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40078 TTTAGGGAAA
40088 AAAT-AAAAAAAACAAAAAAC
1 AAATGAAAAAAAACAAAAAAC
* *
40108 AAATGAAATAAAATAAAAA
1 AAATGAAAAAAAACAAAAA
40127 CTAAAAAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (21 bp):
AAATGAAAAAAAACAAAAAAC
Found at i:40407 original size:26 final size:26
Alignment explanation
Indices: 40371--40431 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
40361 GAGGGGAGTG
40371 CAAAACGGCGTAGCTTCATTTGGCAC
1 CAAAACGGCGTAGCTTCATTTGGCAC
*
40397 CAAAACGGCGTAGCTTCGTTTGGCAC
1 CAAAACGGCGTAGCTTCATTTGGCAC
40423 CAAAACGGC
1 CAAAACGGC
40432 ACCGTTTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (26 bp):
CAAAACGGCGTAGCTTCATTTGGCAC
Found at i:40917 original size:3 final size:3
Alignment explanation
Indices: 40900--40942 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
40890 AATTAAAATA
40900 AAT AA- AAT GAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40943 TACTAAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:41098 original size:38 final size:37
Alignment explanation
Indices: 40970--41256 Score: 242
Period size: 37 Copynumber: 8.2 Consensus size: 37
40960 ATAATATATA
40970 TTTCAAAATAT-TTTTT-AAACTATATA-T-TAT-A--
1 TTTCAAAA-ATGTTTTTAAAACTATATACTATATAAGT
* **
41001 TTT-AAAAA-GTTTTCAAAACTATATGTTATAT-AGT
1 TTTCAAAAATGTTTTTAAAACTATATACTATATAAGT
41035 TTTC-AAAATG-TTTTAAAA--ATAT--TATATAAGT
1 TTTCAAAAATGTTTTTAAAACTATATACTATATAAGT
* * *
41066 TTTCAAAAACTATTTTTAAAACTATATATTATATAATT
1 TTTCAAAAA-TGTTTTTAAAACTATATACTATATAAGT
* *
41104 TTTCAAAAATGTTTTTAAAACTATTTACTATATAATT
1 TTTCAAAAATGTTTTTAAAACTATATACTATATAAGT
41141 TTTCAAAAATATGTTTTTAAAACTATATA-T-TAT-A--
1 TTTC-AAAA-ATGTTTTTAAAACTATATACTATATAAGT
* *
41175 TTT-AAAAACGTTTTAAAAACTATATACTATATAAGT
1 TTTCAAAAATGTTTTTAAAACTATATACTATATAAGT
* * *
41211 TTTC-AAAATGTTTTAAAAACTATACAGTATATAAATGT
1 TTTCAAAAATGTTTTTAAAACTATATACTATAT-AA-GT
41249 TTTCAAAA
1 TTTCAAAA
41257 CTACATATTA
Statistics
Matches: 215, Mismatches: 14, Indels: 46
0.78 0.05 0.17
Matches are distributed among these distances:
29 5 0.02
30 18 0.08
31 28 0.13
32 17 0.08
33 4 0.02
34 26 0.12
35 1 0.00
36 33 0.15
37 34 0.16
38 28 0.13
39 21 0.10
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTCAAAAATGTTTTTAAAACTATATACTATATAAGT
Found at i:44345 original size:23 final size:23
Alignment explanation
Indices: 44315--44360 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
44305 TCTATGTATT
44315 TTAGAACTATTCATATTTAAATC
1 TTAGAACTATTCATATTTAAATC
44338 TTAGAACTATTCATATTTAAATC
1 TTAGAACTATTCATATTTAAATC
44361 ATCGATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (23 bp):
TTAGAACTATTCATATTTAAATC
Found at i:46560 original size:29 final size:29
Alignment explanation
Indices: 46525--46582 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
46515 ATTTTCACAT
46525 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
46554 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
46583 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Done.