Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005447.1 Hibiscus syriacus cultivar Beakdansim tig00012480_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: 78083
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:761 original size:31 final size:30
Alignment explanation
Indices: 726--822 Score: 117
Period size: 29 Copynumber: 3.2 Consensus size: 30
716 GATTTTGATC
*
726 AAATTCAGATGTTAAATTAATATTTTATTTA
1 AAATTTAGA-GTTAAATTAATATTTTATTTA
* *
757 AAATTTAGGGGTTAAAATAATATTTTA-TTA
1 AAATTTA-GAGTTAAATTAATATTTTATTTA
* *
787 AAATTTAGAGATAAATTAGTATTTTATTT-
1 AAATTTAGAGTTAAATTAATATTTTATTTA
816 AAATTTA
1 AAATTTA
823 TAGGTCAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
29 22 0.39
30 12 0.21
31 22 0.39
32 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.46
Consensus pattern (30 bp):
AAATTTAGAGTTAAATTAATATTTTATTTA
Found at i:2891 original size:54 final size:54
Alignment explanation
Indices: 2820--3050 Score: 385
Period size: 54 Copynumber: 4.3 Consensus size: 54
2810 TTTGGGGTGT
* *
2820 ACACGTAGTGCCAATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGC
1 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGC
2874 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGC
1 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGC
* *
2928 ACACTTAGTGTCGATACGGTCGTTCATAAACTTATTAT-AAATTCTGTGGGTTGC
1 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTC-GTGGGTTGC
*
2982 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA-TTCGTGGGTTAC
1 ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGC
*
3035 ACACTTAGTGTCGATA
1 ACACTTAGTGCCGATA
3051 GTACACATAG
Statistics
Matches: 168, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
53 28 0.17
54 138 0.82
55 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (54 bp):
ACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGC
Found at i:5955 original size:103 final size:103
Alignment explanation
Indices: 5784--6104 Score: 570
Period size: 103 Copynumber: 3.1 Consensus size: 103
5774 TAATGTCCAT
5784 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
5849 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
5887 AAGGACCACATATCATTCTTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
5952 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * * *
5990 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTTACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
6055 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
6093 AAAGACCACATA
1 AAGGACCACATA
6105 GACCCTCGAC
Statistics
Matches: 208, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:10976 original size:23 final size:23
Alignment explanation
Indices: 10941--11038 Score: 169
Period size: 23 Copynumber: 4.3 Consensus size: 23
10931 AAATGCACGA
* *
10941 AGTGCCACATAGAATTGCACCGT
1 AGTGCCGCGTAGAATTGCACCGT
10964 AGTGCCGCGTAGAATTGCACCGT
1 AGTGCCGCGTAGAATTGCACCGT
*
10987 AGTGCCGCGTAGAATTACACCGT
1 AGTGCCGCGTAGAATTGCACCGT
11010 AGTGCCGCGTAGAATTGCACCGT
1 AGTGCCGCGTAGAATTGCACCGT
11033 AGTGCC
1 AGTGCC
11039 ATATAATAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.24, C:0.27, G:0.28, T:0.21
Consensus pattern (23 bp):
AGTGCCGCGTAGAATTGCACCGT
Found at i:11264 original size:103 final size:103
Alignment explanation
Indices: 11055--11371 Score: 570
Period size: 103 Copynumber: 3.1 Consensus size: 103
11045 TAATGTCCAT
11055 AAGGACCACATATCATTCCTTAAGAATCATATAC--ATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
11118 GACTT--CACATGTTCAAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
11154 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
11219 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
11257 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
11322 GACTTCACACTTGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
11360 AAGGACCACATA
1 AAGGACCACATA
11372 GACCCTCGAC
Statistics
Matches: 210, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
99 34 0.16
101 34 0.16
103 142 0.68
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:14181 original size:54 final size:54
Alignment explanation
Indices: 14095--14457 Score: 478
Period size: 54 Copynumber: 6.7 Consensus size: 54
14085 TTGTTTTCAA
* * *
14095 TTATTAT-AAGTTCTTTGGGGTGCACACGTAGTGCCGATACGGTCGTTCATAAAC
1 TTATTATGAA-TTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAAC
* * *
14149 TTATTATGAATTCTGTGGGTTGCATACTTAGTGCCAATATGGTCGTTCATAAAC
1 TTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAAC
*
14203 TTATTATGAATT-TCGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAAC
1 TTATTATGAATTCT-GTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAAC
* ** * * *
14257 TTATTATAAATTCTGTGGGTTGCACACTTAGTATCGATACGATCATTCAAAAAC
1 TTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAAC
* * * *
14311 TTATTATGAATTCTGTGGGTTACACACTTAGTGCTGATACGGTAGTTCATAAAT
1 TTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAAC
* * * *
14365 TTATTGTGAATTCTGTGGGTTGCACACTTAGTGCGGATATGGTCATTCATAAAC
1 TTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAAC
** *
14419 TTATTATGAATTCCATGGATTGCACACTTAGTGCCGATA
1 TTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATA
14458 GTACACATAA
Statistics
Matches: 269, Mismatches: 37, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.00
54 265 0.99
55 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (54 bp):
TTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAAC
Found at i:22947 original size:169 final size:169
Alignment explanation
Indices: 22624--22947 Score: 390
Period size: 169 Copynumber: 1.9 Consensus size: 169
22614 GACAATTTTT
* *
22624 CACAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATTGTTTCTATTAAAA
1 CACAAATTTTCAAATTGTTTCACTTGAAACAAAATTAATCTCACTTGAGATTGTTTCTATTAAAA
* * * * * **
22689 ACAAATTTTGTCTCACTTGAGACAGTTTTCCTTAAGACACAAACATTTGAGATTGTTTTTCTTAA
66 ACAAATTTCGTCTCACTGGAGACAGTTTTCCTCAAAACACAAACATTTGAAATTGTTTCACTTAA
***
22754 AAATAAATTTCATTTCACTTGAGATAGTTTCCATCGGAA
131 AAATAAATTTCATAAAACTTGAGATAGTTTCCATCGGAA
* * * *
22793 CACAAA-TTTCAAAGTTGTTTTATTTGAAACAAAATTAATGTCACTTGAGATTGTTTCT-TTCAA
1 CACAAATTTTCAAA-TTGTTTCACTTGAAACAAAATTAATCTCACTTGAGATTGTTTCTATTAAA
*
22856 AACAAA-TTCGTCTCGCTGGAGACAGTTTTTCCTCAAAACACAAA-ATTTGGAAATTGTTTCACT
65 AACAAATTTCGTCTCACTGGAGACAG-TTTTCCTCAAAACACAAACATTT-GAAATTGTTTCACT
*
22919 TGAAACA-AAATTT-ATAAAACCTTTGAGAT
128 T-AAAAATAAATTTCATAAAA-C-TTGAGAT
22948 TATTTCTTTT
Statistics
Matches: 131, Mismatches: 18, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
167 23 0.18
168 51 0.39
169 57 0.44
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (169 bp):
CACAAATTTTCAAATTGTTTCACTTGAAACAAAATTAATCTCACTTGAGATTGTTTCTATTAAAA
ACAAATTTCGTCTCACTGGAGACAGTTTTCCTCAAAACACAAACATTTGAAATTGTTTCACTTAA
AAATAAATTTCATAAAACTTGAGATAGTTTCCATCGGAA
Found at i:23057 original size:67 final size:67
Alignment explanation
Indices: 22932--23066 Score: 155
Period size: 67 Copynumber: 2.0 Consensus size: 67
22922 AACAAAATTT
* * ** * * *
22932 ATAAAACCTTTGAGATTATTTCTTTTGAAATAAATTTTGTCTCTCTTAAGATAGTTTCTCTTGAA
1 ATAAAAACATTGAGATTATTTCCCTTGAAACAAATTTTATCTCTCTTAAGACAGTTTCTCTTGAA
22997 AC
66 AC
* * * *
22999 ATAAAAACATTGAGATTGTTTCCCTTGAAACAAATTTTATCT-TGCTTGAGACATTTTCTCTTGC
1 ATAAAAACATTGAGATTATTTCCCTTGAAACAAATTTTATCTCT-CTTAAGACAGTTTCTCTTGA
23063 AAC
65 AAC
23066 A
1 A
23067 AATTATCCTT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 1 0.02
67 55 0.98
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (67 bp):
ATAAAAACATTGAGATTATTTCCCTTGAAACAAATTTTATCTCTCTTAAGACAGTTTCTCTTGAA
AC
Found at i:23321 original size:140 final size:139
Alignment explanation
Indices: 23065--23497 Score: 604
Period size: 140 Copynumber: 3.1 Consensus size: 139
23055 TCTCTTGCAA
* * *
23065 CAAATTATCCTTAAAGATGGCTAGACATCCTCATCACGTAGGAACAATGTTATCCACCGACAAGA
1 CAAATTATCC-TAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* * *
23130 TCTCATCATCACATAAGAGCA--GTTTCATCCTTAGATAACTAGACTTCCTTATCACGTAGGAAC
65 TCTCCTCATCACGTAAGAGCATCG-TT-ATCCTTAGATAACTAGACTTCCTTATCATGTAGGAAC
*
23193 CGTGTTGTCTCC
128 TGTGTTGTCTCC
*
23205 CAAATTATCTCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATATCATCCACCGACCAGA
1 CAAATTATC-CTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* * * *
23270 TCTCCTCATCACGTAGGAGCATCGTTATCCTTAGATAACCAGACTTTCTTATCATGTAGAAACTG
65 TCTCCTCATCACGTAAGAGCATCGTTATCCTTAGATAACTAGACTTCCTTATCATGTAGGAACTG
*
23335 TGTTGTCCCC
130 TGTTGTCTCC
* * * *
23345 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATTACATAGGAATAATGTCATCCACCGACCAAA
1 CAAATTAT-CCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* * *
23410 TCTCCTCATCACGTAAGAGCATCGTCATCCTTAGATAACTAGACTTCCTGATCATGTAGGAATTG
65 TCTCCTCATCACGTAAGAGCATCGTTATCCTTAGATAACTAGACTTCCTTATCATGTAGGAACTG
23475 TGTTGTCT-C
130 TGTTGTCTCC
23484 CAAATT-TACCTAAA
1 CAAATTAT-CCTAAA
23498 AACGACCAGA
Statistics
Matches: 262, Mismatches: 27, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
138 7 0.03
139 7 0.03
140 243 0.93
141 4 0.02
142 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (139 bp):
CAAATTATCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGAT
CTCCTCATCACGTAAGAGCATCGTTATCCTTAGATAACTAGACTTCCTTATCATGTAGGAACTGT
GTTGTCTCC
Found at i:34077 original size:34 final size:33
Alignment explanation
Indices: 34032--34115 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 33
34022 AAACAACTCC
* *
34032 CTAACTTTTATTTTATTTGTTCATATTAACTTA
1 CTAATTTTTATTTTATTTGTTCATACTAACTTA
* *
34065 CTTACTTTTTATTTT-TATTGTTCTTACTAACTTA
1 C-TAATTTTTATTTTAT-TTGTTCATACTAACTTA
*
34099 CTAATATTTATTTTATT
1 CTAATTTTTATTTTATT
34116 GCACAAACTA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
33 14 0.33
34 28 0.67
ACGTcount: A:0.25, C:0.12, G:0.02, T:0.61
Consensus pattern (33 bp):
CTAATTTTTATTTTATTTGTTCATACTAACTTA
Found at i:34215 original size:201 final size:200
Alignment explanation
Indices: 33871--34242 Score: 570
Period size: 201 Copynumber: 1.9 Consensus size: 200
33861 ACATACTAAC
*
33871 TTTTATTTTTATTATTCTTACTAACTAACTAACATTTTTTTATTGCACAAACTAACCTGCTAATT
1 TTTTATTTTTATTATTCTTACTAACTAACTAACATTTTTTTATTGCACAAACTAACCCGCTAATT
* * *
33936 TTCTAACATTAGAATATTCAACGACCTTGCGGTAACTCACCCTAGGGGATGACTCACATTATTTA
66 TTCTAACATTAGAATATTCAACAACCTTGCGGTAACTCACCCTAGGAGACGACTCACATTATTTA
34001 TGGTCCGGGTTAAACGATTAAAAACAACTCCC-TAACTTTTATTTTATTTGTTCATATTAACTTA
131 TGGTCCGGGTTAAACGATTAAAAACAAC-CCCTTAACTTTTATTTTATTTGTTCATATTAACTTA
34065 CTTACT
195 CTTACT
* * *
34071 TTTTATTTTTATTGTTCTTACTAACTTACTAATATTTATTTTATTGCACAAACTAACCCGCTAAT
1 TTTTATTTTTATTATTCTTACTAACTAACTAACATTT-TTTTATTGCACAAACTAACCCGCTAAT
* * * *
34136 TTTCTAACATTCGAATATTCAACAACCTTGTGGTGACTCGCCCTAGGAGACGA-TC-CGTATTAT
65 TTTCTAACATTAGAATATTCAACAACCTTGCGGTAACTCACCCTAGGAGACGACTCAC--ATTAT
* *
34199 TTATGGTCTGGGTTAAACGATTTAAAACAACCCCTTAACTTTTA
128 TTATGGTCCGGGTTAAACGATTAAAAACAACCCCTTAACTTTTA
34243 AATTTATGCA
Statistics
Matches: 155, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
199 1 0.01
200 39 0.25
201 115 0.74
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (200 bp):
TTTTATTTTTATTATTCTTACTAACTAACTAACATTTTTTTATTGCACAAACTAACCCGCTAATT
TTCTAACATTAGAATATTCAACAACCTTGCGGTAACTCACCCTAGGAGACGACTCACATTATTTA
TGGTCCGGGTTAAACGATTAAAAACAACCCCTTAACTTTTATTTTATTTGTTCATATTAACTTAC
TTACT
Found at i:51676 original size:18 final size:18
Alignment explanation
Indices: 51655--51726 Score: 90
Period size: 18 Copynumber: 3.9 Consensus size: 18
51645 ACTGAAGATT
*
51655 TATCCCGAAGGACCACTT
1 TATCCCGAAGGACCACTA
* *
51673 TATCCTGAAGGACTACTA
1 TATCCCGAAGGACCACTA
*
51691 TGTCCCGAAGGACCACTA
1 TATCCCGAAGGACCACTA
*
51709 TGTCCCCGAAGGACCACT
1 TAT-CCCGAAGGACCACT
51727 GATAACCCTC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
18 33 0.70
19 14 0.30
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (18 bp):
TATCCCGAAGGACCACTA
Found at i:56079 original size:139 final size:140
Alignment explanation
Indices: 55839--56273 Score: 506
Period size: 139 Copynumber: 3.1 Consensus size: 140
55829 CAACCAAATG
* * * * **
55839 TGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCAAGTAGAAACAATGTTGTC-C
1 TGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACTTCCTTAACAAGAAGAAACAATGTCATCTC
* *
55903 ACTGACCAGATCTCCTCAACGGGTAGGAGCAGTGTCATCCTCAAGCAATCACACTTCCTCATCAC
66 ACTGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAAGCAATCAAACTTCCTCATCAC
* *
55968 TTAGGAACCT
131 GTAGGAACCA
* * * *
55978 TGTTGTCTCAAAATTATCCCTAAAAATGGCTAGACTTCCTTAACAAGAAGAAACAATGTCATCTA
1 TGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACTTCCTTAACAAGAAGAAACAATGTCATCTC
* ** * *
56043 AC-GACCAGATCTCCTCAATGCGTAGGAGCAACGTCATCCTCAGGCAATTAAACTTCCTCATCAC
66 ACTGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAAGCAATCAAACTTCCTCATCAC
56107 GTAGGAACCA
131 GTAGGAACCA
* *
56117 TGTTGTCTCCAAATTATCCCTAAAGACGACTAGA-TGTCC-TAATCACGAATG-AACAATGTCAT
1 TGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACT-TCCTTAA-CAAGAA-GAAACAATGTCAT
* * * * * *
56179 -TCACTAACCAGATCTCCTCAACGCGAAAGAGCAGTGTCATCCTC-AGATAACCAGACTTCCTCA
63 CTCACTGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAAG-CAATCAAACTTCCTCA
* * * *
56242 ACGCGAAGGAACCG
127 TCACGTAGGAACCA
56256 TGTTGTCTCCAAATTATC
1 TGTTGTCTCCAAATTATC
56274 TCCAGATTGA
Statistics
Matches: 250, Mismatches: 40, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
138 8 0.03
139 239 0.96
140 3 0.01
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (140 bp):
TGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACTTCCTTAACAAGAAGAAACAATGTCATCTC
ACTGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAAGCAATCAAACTTCCTCATCAC
GTAGGAACCA
Found at i:56574 original size:220 final size:220
Alignment explanation
Indices: 56189--56658 Score: 697
Period size: 220 Copynumber: 2.1 Consensus size: 220
56179 TCACTAACCA
*
56189 GATCTCCTCAACGCGAAAGAGCAGTGTCATCCTCAGATAACCAGACTTCCTCAACGCGAAGGAAC
1 GATCTCCTCAACGAGAAAGAGCAGTGTCATCCTCAGATAACCAGACTTCCTCAACGCGAAGGAAC
* * **
56254 CGTGTTGTCTCCAAATTATCTCCAGATTGATCTTATTTCCTCAACGAGAAGAAACAACATCATCT
66 CGTATTGTCTCCAAATTATCTCCAGATTGACCCGATTTCCTCAACGAGAAGAAACAACATCATCT
* * * *
56319 TCAGCAAATAATTTACATGAAAAAGACCAGATCTCTTCAACATGGATGAGCAGTTTCTTCTTCAA
131 TCAGCAAACAATTTACATGAAAAACACCAGATCTCTTCAACATGGATGAGCAGTGTCGTCTTCAA
56384 CACCAAATTATTTCCAGATTGACCC
196 CACCAAATTATTTCCAGATTGACCC
* * * *
56409 GATCTCCTCAAAGAGAAGGAGCAGTGTCATTCTCAGATAATCAGACTTCCTCAACGCGAAGGAAC
1 GATCTCCTCAACGAGAAAGAGCAGTGTCATCCTCAGATAACCAGACTTCCTCAACGCGAAGGAAC
* * *
56474 CGTATTGTCTCCAAATTATCTCCAGATTGACCCGATTTCCTCAACGAGAGGAAACAACGTTATCT
66 CGTATTGTCTCCAAATTATCTCCAGATTGACCCGATTTCCTCAACGAGAAGAAACAACATCATCT
* * ** *
56539 TCAGCAAACAATTTGCCTGAAAGCCACCTGATCTCTTCAACATGGATGAGCAGTGTCGTCTTCAA
131 TCAGCAAACAATTTACATGAAAAACACCAGATCTCTTCAACATGGATGAGCAGTGTCGTCTTCAA
* *
56604 CATCTAATTATTTCCAGATTGACCC
196 CACCAAATTATTTCCAGATTGACCC
* * * *
56629 GATTTCCTTAACGAGAATGAGCAATGTCAT
1 GATCTCCTCAACGAGAAAGAGCAGTGTCAT
56659 ATTCAACAAA
Statistics
Matches: 222, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
220 222 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (220 bp):
GATCTCCTCAACGAGAAAGAGCAGTGTCATCCTCAGATAACCAGACTTCCTCAACGCGAAGGAAC
CGTATTGTCTCCAAATTATCTCCAGATTGACCCGATTTCCTCAACGAGAAGAAACAACATCATCT
TCAGCAAACAATTTACATGAAAAACACCAGATCTCTTCAACATGGATGAGCAGTGTCGTCTTCAA
CACCAAATTATTTCCAGATTGACCC
Found at i:58027 original size:15 final size:15
Alignment explanation
Indices: 57999--58063 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
57989 TTTATTTATT
* *
57999 TTTCCAGCACTTTAA
1 TTTCCTGCATTTTAA
* *
58014 ATTCCTGCATTTTAT
1 TTTCCTGCATTTTAA
* *
58029 TTTCATGCCTTTTAA
1 TTTCCTGCATTTTAA
*
58044 TTTTCCTGCATTTTTA
1 -TTTCCTGCATTTTAA
58060 TTTC
1 TTTC
58064 AGTCCTTTTA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
15 26 0.68
16 12 0.32
ACGTcount: A:0.18, C:0.22, G:0.06, T:0.54
Consensus pattern (15 bp):
TTTCCTGCATTTTAA
Found at i:58048 original size:16 final size:16
Alignment explanation
Indices: 58023--58077 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
58013 AATTCCTGCA
58023 TTTT-ATTTTCATGCC
1 TTTTAATTTTCATGCC
* *
58038 TTTTAATTTTCCTGCA
1 TTTTAATTTTCATGCC
*
58054 TTTTTA-TTTCA-GTCC
1 TTTTAATTTTCATG-CC
58069 TTTTAATTT
1 TTTTAATTT
58078 CCAACATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
14 1 0.03
15 14 0.45
16 16 0.52
ACGTcount: A:0.16, C:0.16, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTAATTTTCATGCC
Found at i:58050 original size:31 final size:30
Alignment explanation
Indices: 58009--58096 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 30
57999 TTTCCAGCAC
*
58009 TTTAAATTCCTGCATTTTATTTTCA-TGCCT
1 TTTAATTTCCTGCATTTTATTTTCAGT-CCT
58039 TTTAATTTTCCTGCATTTT-TATTTCAGTCCT
1 TTTAA-TTTCCTGCATTTTAT-TTTCAGTCCT
** *
58070 TTTAATTTCCAACATTTAATTTTCAGT
1 TTTAATTTCCTGCATTTTATTTTCAGT
58097 ATTTTGCATT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
30 23 0.46
31 26 0.52
32 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.55
Consensus pattern (30 bp):
TTTAATTTCCTGCATTTTATTTTCAGTCCT
Found at i:58600 original size:16 final size:15
Alignment explanation
Indices: 58581--58614 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
58571 TCTTATTATT
58581 TTTTTATTTCGTTCTA
1 TTTTTATTTCGTT-TA
*
58597 TTTTTATTTTGTTTA
1 TTTTTATTTCGTTTA
58612 TTT
1 TTT
58615 AATTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTTTATTTCGTTTA
Found at i:58603 original size:24 final size:24
Alignment explanation
Indices: 58554--58627 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
58544 AATAGTCTTC
*
58554 TTTGTTTTATTT-TTTTATCTTATTAT
1 TTTG-TTTATTTAATTTAT-TT-TTAT
**
58580 TTT-TTTATTTCGTTCTATTTTTAT
1 TTTGTTTATTTAATT-TATTTTTAT
58604 TTTGTTTATTTAATTTATTTTTAT
1 TTTGTTTATTTAATTTATTTTTAT
58628 CATTGATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
24 23 0.55
25 13 0.31
26 6 0.14
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (24 bp):
TTTGTTTATTTAATTTATTTTTAT
Found at i:59996 original size:23 final size:24
Alignment explanation
Indices: 59941--59996 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
59931 AGGGATTATA
59941 ATTTAGGGTTTTATAGATTTGGTG
1 ATTTAGGGTTTTATAGATTTGGTG
*
59965 -TTTAGGGTTTTA-AG-TTTTGTG
1 ATTTAGGGTTTTATAGATTTGGTG
59986 ATTTAGAGGTT
1 ATTTAG-GGTT
59997 AGGGTTTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.21
22 7 0.24
23 16 0.55
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.52
Consensus pattern (24 bp):
ATTTAGGGTTTTATAGATTTGGTG
Found at i:60010 original size:21 final size:21
Alignment explanation
Indices: 59980--60066 Score: 104
Period size: 21 Copynumber: 4.1 Consensus size: 21
59970 GGTTTTAAGT
* *
59980 TTTGTGATTTAGAGGTTAGGG
1 TTTGAGATTTAGAGGTTAGGA
*
60001 TTTG-GAATTTAAAGGTTAGGA
1 TTTGAG-ATTTAGAGGTTAGGA
* *
60022 TTTGAGATTTAGGGGTTATGA
1 TTTGAGATTTAGAGGTTAGGA
*
60043 TTTGAGATTTAGAGTTTAGGA
1 TTTGAGATTTAGAGGTTAGGA
60064 TTT
1 TTT
60067 ATTTAGGTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.02
21 54 0.96
22 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (21 bp):
TTTGAGATTTAGAGGTTAGGA
Found at i:63482 original size:24 final size:22
Alignment explanation
Indices: 63438--63487 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 22
63428 TTTTCGATTC
63438 TTTTATCTTTTTATTTATCTTG
1 TTTTATCTTTTTATTTATCTTG
*
63460 TTTTAATCTTATTTTTTTATCTTG
1 TTTT-ATCTT-TTTATTTATCTTG
63484 TTTT
1 TTTT
63488 CAGCACAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 4 0.16
23 5 0.20
24 16 0.64
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTATCTTTTTATTTATCTTG
Found at i:71729 original size:17 final size:17
Alignment explanation
Indices: 71697--71730 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
71687 TCATAGATAC
*
71697 TTGGTGATTAGAAAGGT
1 TTGGTGATCAGAAAGGT
*
71714 TTGGTGATCAGGAAGGT
1 TTGGTGATCAGAAAGGT
71731 ATTCATAAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.38, T:0.32
Consensus pattern (17 bp):
TTGGTGATCAGAAAGGT
Found at i:73676 original size:17 final size:17
Alignment explanation
Indices: 73654--73688 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
73644 TGTCGAAAAA
73654 CATAAAATATGACTTTT
1 CATAAAATATGACTTTT
* *
73671 CATAAATTTTGACTTTT
1 CATAAAATATGACTTTT
73688 C
1 C
73689 GATCAAAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (17 bp):
CATAAAATATGACTTTT
Found at i:75942 original size:11 final size:11
Alignment explanation
Indices: 75926--75957 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
75916 TGATTTTTTT
75926 AATATATATAA
1 AATATATATAA
*
75937 AATATATAAAA
1 AATATATATAA
75948 AATATATATA
1 AATATATATA
75958 TATATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATATATATAA
Done.