Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005743.1 Hibiscus syriacus cultivar Beakdansim tig00013430_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: 84841
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Found at i:9085 original size:29 final size:29
Alignment explanation
Indices: 9051--9108 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
9041 TTGATCCAAT
*
9051 GTGCAATGT-AATATGAGAACTTTGATTTG
1 GTGCAATGTAAACATGA-AACTTTGATTTG
9080 GTGCAATGTAAACATGAAACTTTGATTTG
1 GTGCAATGTAAACATGAAACTTTGATTTG
9109 TACACTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (29 bp):
GTGCAATGTAAACATGAAACTTTGATTTG
Found at i:23234 original size:15 final size:15
Alignment explanation
Indices: 23216--23246 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
23206 AAATTCTAAA
23216 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
23231 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
23246 T
1 T
23247 CTATCTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:23301 original size:21 final size:21
Alignment explanation
Indices: 23259--23298 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
23249 ATCTGTTGAT
**
23259 AATATATCATTTATGTATTTA
1 AATATATCATACATGTATTTA
23280 AATATATCATACAT-TATTT
1 AATATATCATACATGTATTT
23299 TAATTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (21 bp):
AATATATCATACATGTATTTA
Found at i:24762 original size:31 final size:31
Alignment explanation
Indices: 24727--24786 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
24717 AAACAGTTCA
* **
24727 GATGCATAATTGTTACTATCCCCTAATGCTG
1 GATGCATAACTGAAACTATCCCCTAATGCTG
24758 GATGCATAACTGAAACTATCCCCTAATGC
1 GATGCATAACTGAAACTATCCCCTAATGC
24787 ATAAAGTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (31 bp):
GATGCATAACTGAAACTATCCCCTAATGCTG
Found at i:29621 original size:2 final size:2
Alignment explanation
Indices: 29614--29654 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29604 TTTTACATTC
29614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29655 TAATGACCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30688 original size:26 final size:26
Alignment explanation
Indices: 30658--30721 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
30648 CAGAAATTGC
30658 TGAAACACTTTAACAACAACAAATGT
1 TGAAACACTTTAACAACAACAAATGT
*
30684 TGAAACACTTTAACAACAGCAAATGT
1 TGAAACACTTTAACAACAACAAATGT
30710 TGAAACACTTTA
1 TGAAACACTTTA
30722 TGAAGCATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (26 bp):
TGAAACACTTTAACAACAACAAATGT
Found at i:30745 original size:20 final size:20
Alignment explanation
Indices: 30720--30761 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
30710 TGAAACACTT
30720 TATGAAGCATGTATAA-GCTC
1 TATGAAGCATGT-TAACGCTC
*
30740 TATGAAGTATGTTAACGCTC
1 TATGAAGCATGTTAACGCTC
30760 TA
1 TA
30762 CTCTATGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
TATGAAGCATGTTAACGCTC
Found at i:33237 original size:58 final size:58
Alignment explanation
Indices: 33170--33291 Score: 244
Period size: 58 Copynumber: 2.1 Consensus size: 58
33160 TTCTTCAACA
33170 TTTTTCATATTCTTTTCTGGTTTTATAATTAACCAAGCTAATTTAATCATTTCCCTTT
1 TTTTTCATATTCTTTTCTGGTTTTATAATTAACCAAGCTAATTTAATCATTTCCCTTT
33228 TTTTTCATATTCTTTTCTGGTTTTATAATTAACCAAGCTAATTTAATCATTTCCCTTT
1 TTTTTCATATTCTTTTCTGGTTTTATAATTAACCAAGCTAATTTAATCATTTCCCTTT
33286 TTTTTC
1 TTTTTC
33292 TCTGTATTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 64 1.00
ACGTcount: A:0.23, C:0.17, G:0.05, T:0.55
Consensus pattern (58 bp):
TTTTTCATATTCTTTTCTGGTTTTATAATTAACCAAGCTAATTTAATCATTTCCCTTT
Found at i:36750 original size:37 final size:36
Alignment explanation
Indices: 36675--36750 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
36665 TTTTTATATT
*
36675 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
36711 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
36748 TTT
1 TTT
36751 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:36932 original size:20 final size:20
Alignment explanation
Indices: 36896--36933 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36886 ATCCTATTCC
**
36896 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
36916 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
36934 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:37389 original size:156 final size:155
Alignment explanation
Indices: 37141--37511 Score: 453
Period size: 156 Copynumber: 2.4 Consensus size: 155
37131 CCTGATTTTA
* * * * *
37141 TTATTCCTTCAATTCATCCTTTATTTTAAGTCCGTTATTTTACCAAATTTGAACAACATTCTCCT
1 TTATTTCTTCAATTCATCATTTATTTTAAGT---TTGTTTTACCAAATTTGAACCACATACTCCT
* * *
37206 AAACTACTATAGAATACATATATACTTTCAATTTCTCTTTTTGATTATA-ATTTTT-TATTTTTC
63 AAACCACTATAGAATACATATATACTTTCAATTCCTCTTTTT-AATA-ACATTTTTCTATTTTTC
37269 AATTTAATCCCTCAATTGTTTATAATTTGC
126 AATTTAATCCCTCAATTGTTTATAATTTGC
* *
37299 TTATTTCTTCAATTCATCATTTATTTTAAGTTTGTTTTCCCCAAATTTAAACCACATACTCCTAA
1 TTATTTCTTCAATTCATCATTTATTTTAAGTTTGTTTT-ACCAAATTTGAACCACATACTCCTAA
* * * *
37364 ACCA-TCGTAGAATATATATGA-ACTTTCAATTCCTCTTTTTAATAACATTTTTCTATTTTTTAG
65 ACCACT-ATAGAATACATAT-ATACTTTCAATTCCTCTTTTTAATAACATTTTTCTATTTTTCAA
* * * *
37427 TTTAGTCCCTCATTTTTTTATAATTTTC
128 TTTAATCCCTCAATTGTTTATAATTTGC
* *
37455 TTATTTCTTCACTTCATCATTTATTTTAAGTTTGTTTTTACCAAATTTGAATCACAT
1 TTATTTCTTCAATTCATCATTTATTTTAAGTTTG-TTTTACCAAATTTGAACCACAT
37512 GCTTGTATAC
Statistics
Matches: 185, Mismatches: 22, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
154 1 0.01
155 16 0.09
156 134 0.72
157 5 0.03
158 29 0.16
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.50
Consensus pattern (155 bp):
TTATTTCTTCAATTCATCATTTATTTTAAGTTTGTTTTACCAAATTTGAACCACATACTCCTAAA
CCACTATAGAATACATATATACTTTCAATTCCTCTTTTTAATAACATTTTTCTATTTTTCAATTT
AATCCCTCAATTGTTTATAATTTGC
Found at i:37544 original size:156 final size:154
Alignment explanation
Indices: 37135--37550 Score: 439
Period size: 156 Copynumber: 2.7 Consensus size: 154
37125 TTAGCCCCTG
* * * **
37135 ATTTTATTATTCCTTCAATTCATCCTTTATTTTAAGTCCGTTATTTTACCAAATTTGAACAACAT
1 ATTTTCTTATTTCTTCAATTCATCATTTATTTTAAGTTTG-T-TTTTACCAAATTTGAAC-ACAT
* * * * *
37200 TCTCCTAAACTACTATAGA-ATAC-ATATATACTTTCAATTTCTCTTTTTGATTATAATTTTTTA
63 ACTCCTAAACCAC-ATAGATAT-CTATGTA-ACTTTCAATTCCTCTTTTTGAATATAATTTTTTA
37263 TTTTTCAATTTAATCCCTCAATTGTTTATA
125 TTTTTCAATTTAATCCCTCAATTGTTTATA
* ** *
37293 ATTTGCTTATTTCTTCAATTCATCATTTATTTTAAGTTTGTTTTCCCCAAATTTAAACCACATAC
1 ATTTTCTTATTTCTTCAATTCATCATTTATTTTAAGTTTGTTTTTACCAAATTTGAA-CACATAC
* *
37358 TCCTAAACCATCGTAGAATATATATG-AACTTTCAATTCCTCTTTTT-AATA-ACATTTTTCTAT
65 TCCTAAACCA-CATAG-ATATCTATGTAACTTTCAATTCCTCTTTTTGAATATA-ATTTTT-TAT
* * * * *
37420 TTTTTAGTTTAGTCCCTCATTTTTTTATA
126 TTTTCAATTTAATCCCTCAATTGTTTATA
* *
37449 ATTTTCTTATTTCTTCACTTCATCATTTATTTTAAGTTTGTTTTTACCAAATTTGAATCACATGC
1 ATTTTCTTATTTCTTCAATTCATCATTTATTTTAAGTTTGTTTTTACCAAATTTGAA-CACATAC
** *
37514 TTGTATACCACAATAGATATCTATGTAAC-TTCAATTC
65 TCCTAAACCAC-ATAGATATCTATGTAACTTTCAATTC
37551 TTACTTTTAC
Statistics
Matches: 216, Mismatches: 33, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
154 1 0.00
155 26 0.12
156 146 0.68
157 5 0.02
158 38 0.18
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.49
Consensus pattern (154 bp):
ATTTTCTTATTTCTTCAATTCATCATTTATTTTAAGTTTGTTTTTACCAAATTTGAACACATACT
CCTAAACCACATAGATATCTATGTAACTTTCAATTCCTCTTTTTGAATATAATTTTTTATTTTTC
AATTTAATCCCTCAATTGTTTATA
Found at i:38002 original size:160 final size:160
Alignment explanation
Indices: 37734--38046 Score: 608
Period size: 160 Copynumber: 2.0 Consensus size: 160
37724 AATATTATGA
*
37734 TTATATTTCAGAGTTTTAGATTGTATTTGATATATTAAAAAACATTTAATTTATTATGTGTTGTG
1 TTATATTTCAGAGTTTTAGATTGTATTTAATATATTAAAAAACATTTAATTTATTATGTGTTGTG
*
37799 TTTGTTTGTTAGTTAATCAAAATATTCAAATATAATGCATAATAAACTAAATAAGACATGTATAA
66 TTTGTTTGTTAGTTAATCAAAATATTCAAATATAATACATAATAAACTAAATAAGACATGTATAA
37864 ATTATTCGTATATCATTAAACTTCATGTGT
131 ATTATTCGTATATCATTAAACTTCATGTGT
37894 TTATATTTCAGAGTTTTAGATTGTATTTAATATATTAAAAAACATTTAATTTATTATGTGTTGTG
1 TTATATTTCAGAGTTTTAGATTGTATTTAATATATTAAAAAACATTTAATTTATTATGTGTTGTG
37959 TTTGTTTGTTAGTTAATCAAAATATTCAAATATAATACATAATAAACTAAATAAGACATGTATAA
66 TTTGTTTGTTAGTTAATCAAAATATTCAAATATAATACATAATAAACTAAATAAGACATGTATAA
38024 ATTATTCGTATATCATTAAACTT
131 ATTATTCGTATATCATTAAACTT
38047 TAAATTATAT
Statistics
Matches: 151, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 151 1.00
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (160 bp):
TTATATTTCAGAGTTTTAGATTGTATTTAATATATTAAAAAACATTTAATTTATTATGTGTTGTG
TTTGTTTGTTAGTTAATCAAAATATTCAAATATAATACATAATAAACTAAATAAGACATGTATAA
ATTATTCGTATATCATTAAACTTCATGTGT
Found at i:39318 original size:17 final size:15
Alignment explanation
Indices: 39288--39322 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
39278 TCAGGAATAT
39288 TATAATATAATAAAA
1 TATAATATAATAAAA
39303 TATATATATAACTAAAA
1 TATA-ATATAA-TAAAA
39320 TAT
1 TAT
39323 TAAATGTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 6 0.33
17 8 0.44
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAATATAATAAAA
Found at i:40808 original size:54 final size:54
Alignment explanation
Indices: 40745--40854 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
40735 CGGGAGTGGT
* **
40745 GATGATAGATACGGTGGACGAGATAATTTCCGATCACCGCCGGCAAGGCCATAC
1 GATGATAGATACGGTGGACGAGATAATTTCCGATCACCACCACCAAGGCCATAC
* * *
40799 GATGATAGATATGGTGGACGAGATGATTTCCGATCACCACCACCGAGGCCATAC
1 GATGATAGATACGGTGGACGAGATAATTTCCGATCACCACCACCAAGGCCATAC
40853 GA
1 GA
40855 ATTTGATTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (54 bp):
GATGATAGATACGGTGGACGAGATAATTTCCGATCACCACCACCAAGGCCATAC
Found at i:43654 original size:2 final size:2
Alignment explanation
Indices: 43647--43677 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43637 AATATTCTAT
43647 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43678 TTGGAGAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45834 original size:23 final size:23
Alignment explanation
Indices: 45802--45845 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
45792 GCAATTGCTG
*
45802 CGACATTGGTTTAGGATTACTAC
1 CGACAATGGTTTAGGATTACTAC
45825 CGACAATGGTTTAGGATTACT
1 CGACAATGGTTTAGGATTACT
45846 GCACTATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (23 bp):
CGACAATGGTTTAGGATTACTAC
Found at i:53043 original size:45 final size:46
Alignment explanation
Indices: 52955--53045 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
52945 TTGAAAAAGC
* * *
52955 CTGAGTGCATCAATGCATGGTCTTGTGCATTGATGCATCAAATGCA
1 CTGAGTGCATCAATGCATGGTCATGTGCATCGATGCATAAAATGCA
*
53001 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCAATGCATGGTCATGTGCATCGATGCATAAAATGCA
53046 TTCGATGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (46 bp):
CTGAGTGCATCAATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:53093 original size:20 final size:20
Alignment explanation
Indices: 53065--53103 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53055 CAAGAAATTA
53065 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
53085 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
53104 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:61752 original size:45 final size:46
Alignment explanation
Indices: 61664--61754 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 46
61654 TTGAAAAAGC
* *
61664 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
61710 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
61755 TTCGATGTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:61802 original size:20 final size:20
Alignment explanation
Indices: 61774--61812 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61764 CAAGAAATTA
61774 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
61794 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
61813 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:62834 original size:21 final size:23
Alignment explanation
Indices: 62786--62837 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
62776 GTCGAGGGTT
62786 CTATGTGGTCATTCGGGACAAAA
1 CTATGTGGTCATTCGGGACAAAA
* *
62809 CTATGTGGTCTTTTGGGA-AAAA
1 CTATGTGGTCATTCGGGACAAAA
62831 -TATGTGG
1 CTATGTGG
62838 CACTTCAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 7 0.26
22 4 0.15
23 16 0.59
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.33
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGACAAAA
Found at i:76432 original size:20 final size:20
Alignment explanation
Indices: 76407--76458 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
76397 CGGTTGAATG
*
76407 GGTATCAATACCAGAAGGAT
1 GGTATCGATACCAGAAGGAT
76427 GGTATCGATACCAGAAGGAT
1 GGTATCGATACCAGAAGGAT
76447 GGTATCGATACC
1 GGTATCGATACC
76459 GTTGTTAAGA
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:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (20 bp):
GGTATCGATACCAGAAGGAT
Found at i:77123 original size:21 final size:21
Alignment explanation
Indices: 77082--77191 Score: 78
Period size: 21 Copynumber: 5.0 Consensus size: 21
77072 TCGAAGGTTT
* *
77082 TATGTGGTTCTTCGAG-ACAAA
1 TATGTGGTACTTCG-GTGCAAA
77103 TATGTGGTACTTCGGTGCAAA
1 TATGTGGTACTTCGGTGCAAA
* * *
77124 CCTATGTGGCACTTTGGTGTAAA
1 --TATGTGGTACTTCGGTGCAAA
* ** *
77147 TTTATGTGGTCCTTCGGAACAAT
1 --TATGTGGTACTTCGGTGCAAA
*
77170 TATGTGGCACTTCGGTGCAAA
1 TATGTGGTACTTCGGTGCAAA
77191 T
1 T
77192 TACGAGCTGT
Statistics
Matches: 67, Mismatches: 19, Indels: 6
0.73 0.21 0.07
Matches are distributed among these distances:
20 1 0.01
21 34 0.51
23 32 0.48
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (21 bp):
TATGTGGTACTTCGGTGCAAA
Found at i:77137 original size:23 final size:22
Alignment explanation
Indices: 77099--77193 Score: 88
Period size: 23 Copynumber: 4.3 Consensus size: 22
77089 TTCTTCGAGA
*
77099 CAAA-TATGTGGTACTTCGGTG
1 CAAATTATGTGGCACTTCGGTG
* *
77120 CAAACCTATGTGGCACTTTGGTG
1 CAAA-TTATGTGGCACTTCGGTG
* **
77143 TAAATTTATGTGGTC-CTTCGGAA
1 CAAA-TTATGTGG-CACTTCGGTG
77166 C-AATTATGTGGCACTTCGGTG
1 CAAATTATGTGGCACTTCGGTG
77187 CAAATTA
1 CAAATTA
77194 CGAGCTGTGG
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.02
21 19 0.33
22 7 0.12
23 30 0.52
24 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (22 bp):
CAAATTATGTGGCACTTCGGTG
Found at i:83948 original size:23 final size:23
Alignment explanation
Indices: 83918--83970 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
83908 TTTAGGACAA
83918 TATGTGGCACTTCGATGCAAACC
1 TATGTGGCACTTCGATGCAAACC
* * **
83941 TATGTGGCACTTTGGTGCAAATT
1 TATGTGGCACTTCGATGCAAACC
83964 TATGTGG
1 TATGTGG
83971 TCCTTCGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (23 bp):
TATGTGGCACTTCGATGCAAACC
Found at i:84457 original size:19 final size:19
Alignment explanation
Indices: 84433--84471 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
84423 ACTTTTGGTA
*
84433 TTTATGTAAATTATATGTT
1 TTTATGTAAAATATATGTT
*
84452 TTTATGTAAAATGTATGTT
1 TTTATGTAAAATATATGTT
84471 T
1 T
84472 AATGATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTATGTAAAATATATGTT
Done.