Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006177.1 Hibiscus syriacus cultivar Beakdansim tig00014683_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: 65893
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:115 original size:21 final size:21
Alignment explanation
Indices: 69--109 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
59 TCTATCCGAT
69 AAAAAGAAAGAAATTAGACGA
1 AAAAAGAAAGAAATTAGACGA
90 AAAAAGAAAGAAATTAGACG
1 AAAAAGAAAGAAATTAGACG
110 CTAAAACGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.66, C:0.05, G:0.20, T:0.10
Consensus pattern (21 bp):
AAAAAGAAAGAAATTAGACGA
Found at i:115 original size:22 final size:21
Alignment explanation
Indices: 68--120 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
58 ATCTATCCGA
68 TAAAAAGAAAGAAATTAGACG
1 TAAAAAGAAAGAAATTAGACG
*
89 AAAAAAGAAAGAAATTAGACG
1 TAAAAAGAAAGAAATTAGACG
*
110 CTAAAACGAAA
1 -TAAAAAGAAA
121 AGGAATATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (21 bp):
TAAAAAGAAAGAAATTAGACG
Found at i:3919 original size:28 final size:28
Alignment explanation
Indices: 3876--3932 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
3866 TTGTCGTTGC
* *
3876 TTTCAAACACTGACTCGACGACATAATG
1 TTTCAAACACTAACTCAACGACATAATG
*
3904 TTTCAAACACTAACTCAATGACATAATG
1 TTTCAAACACTAACTCAACGACATAATG
3932 T
1 T
3933 AAATAAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.28
Consensus pattern (28 bp):
TTTCAAACACTAACTCAACGACATAATG
Found at i:4581 original size:3 final size:3
Alignment explanation
Indices: 4573--4607 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4563 ATCCACCGAG
4573 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
4608 CAGTTTCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:13013 original size:184 final size:183
Alignment explanation
Indices: 12688--13052 Score: 639
Period size: 184 Copynumber: 2.0 Consensus size: 183
12678 TTTATTTTGG
12688 ATTAATAATCGAAATGATAAATGTATTTGATGCATATATTCTGATATTTTCATCTGAACTGGAGT
1 ATTAATAATCGAAATGATAAATGTATTTGATGCATATATTCTGATATTTTCATCTGAACTGGAGT
*
12753 AACACATACATGATGAGCACAGCAGAAGATGGTTCATGATGTATGGTAACAAGCATGGGTGATAG
66 AACACATACATGATGAGCACAGCAGAAGATGGTTCATGAAGTATGGTAACAAGCATGGGTGATAG
12818 GAATTGGGGGGGGGGGGGTCTGAAATTGAACCATTGAATAAGAGATTTGCATGA
131 GAA-TGGGGGGGGGGGGGTCTGAAATTGAACCATTGAATAAGAGATTTGCATGA
12872 ATTAATAATCGAAATGATAAATGTATTTGATGCATATATTCTGATA-TTTCATCTGAACTGGAGT
1 ATTAATAATCGAAATGATAAATGTATTTGATGCATATATTCTGATATTTTCATCTGAACTGGAGT
12936 -A-ACATACATGATGAGCACTTATGAGCAGAAGATGGTTCATGAAGTATGGTAACAAGCATGGGT
66 AACACATACATGATGAGCAC-----AGCAGAAGATGGTTCATGAAGTATGGTAACAAGCATGGGT
12999 GATAGGAA-GGGGGGGGGGGGGTCTGAAATTGAACCATTGAATAAGAGATTTGCA
126 GATAGGAATGGGGGGGGGGGGGTCTGAAATTGAACCATTGAATAAGAGATTTGCA
13053 ATCCAACGGT
Statistics
Matches: 175, Mismatches: 1, Indels: 10
0.94 0.01 0.05
Matches are distributed among these distances:
181 17 0.10
182 1 0.01
183 18 0.10
184 92 0.53
186 47 0.27
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (183 bp):
ATTAATAATCGAAATGATAAATGTATTTGATGCATATATTCTGATATTTTCATCTGAACTGGAGT
AACACATACATGATGAGCACAGCAGAAGATGGTTCATGAAGTATGGTAACAAGCATGGGTGATAG
GAATGGGGGGGGGGGGGTCTGAAATTGAACCATTGAATAAGAGATTTGCATGA
Found at i:18492 original size:16 final size:17
Alignment explanation
Indices: 18471--18504 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
18461 ACTATTCATA
18471 TGAATAGT-AAATTTTG
1 TGAATAGTAAAATTTTG
18487 TGAATAGTAAAATTTTG
1 TGAATAGTAAAATTTTG
18504 T
1 T
18505 CGGCGATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (17 bp):
TGAATAGTAAAATTTTG
Found at i:21888 original size:23 final size:23
Alignment explanation
Indices: 21858--21904 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
21848 CGGTGATGAG
21858 TTCGATTACCGGTTTTGGGACTA
1 TTCGATTACCGGTTTTGGGACTA
21881 TTCGATTACCGGTTTTGGGACTA
1 TTCGATTACCGGTTTTGGGACTA
21904 T
1 T
21905 GAAAATCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (23 bp):
TTCGATTACCGGTTTTGGGACTA
Found at i:27493 original size:10 final size:10
Alignment explanation
Indices: 27478--27506 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
27468 TAGATATTGG
27478 AAAATTTCCC
1 AAAATTTCCC
27488 AAAATTTCCC
1 AAAATTTCCC
27498 AAAATTTCC
1 AAAATTTCC
27507 GAGTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTTCCC
Found at i:30581 original size:2 final size:2
Alignment explanation
Indices: 30574--30598 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30564 AATAATAAAT
30574 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 T
30599 TAAGTGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31616 original size:5 final size:5
Alignment explanation
Indices: 31606--31634 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
31596 CTTGCTTATC
31606 TCGTT TCGTT TCGTT TCGTT TCGTT TCGT
1 TCGTT TCGTT TCGTT TCGTT TCGTT TCGT
31635 GTATTCGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.21, T:0.59
Consensus pattern (5 bp):
TCGTT
Found at i:35188 original size:140 final size:140
Alignment explanation
Indices: 34936--35224 Score: 578
Period size: 140 Copynumber: 2.1 Consensus size: 140
34926 TTGGGTTCTT
34936 GATAATTTTCCCTTTTTTATTATTTGTTTCTATTTTGCCTCCTTATTAGATGATATCTTCAAATT
1 GATAATTTTCCCTTTTTTATTATTTGTTTCTATTTTGCCTCCTTATTAGATGATATCTTCAAATT
35001 TTCGAGGACTACCTTAGTGAAGGAAAACCTCCCGCTATGGAACTTTATGCAGTAAGTTTAATCAT
66 TTCGAGGACTACCTTAGTGAAGGAAAACCTCCCGCTATGGAACTTTATGCAGTAAGTTTAATCAT
35066 TACTTGCTAA
131 TACTTGCTAA
35076 GATAATTTTCCCTTTTTTATTATTTGTTTCTATTTTGCCTCCTTATTAGATGATATCTTCAAATT
1 GATAATTTTCCCTTTTTTATTATTTGTTTCTATTTTGCCTCCTTATTAGATGATATCTTCAAATT
35141 TTCGAGGACTACCTTAGTGAAGGAAAACCTCCCGCTATGGAACTTTATGCAGTAAGTTTAATCAT
66 TTCGAGGACTACCTTAGTGAAGGAAAACCTCCCGCTATGGAACTTTATGCAGTAAGTTTAATCAT
35206 TACTTGCTAA
131 TACTTGCTAA
35216 GATAATTTT
1 GATAATTTT
35225 TTTGTTGATC
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 149 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (140 bp):
GATAATTTTCCCTTTTTTATTATTTGTTTCTATTTTGCCTCCTTATTAGATGATATCTTCAAATT
TTCGAGGACTACCTTAGTGAAGGAAAACCTCCCGCTATGGAACTTTATGCAGTAAGTTTAATCAT
TACTTGCTAA
Found at i:39839 original size:40 final size:40
Alignment explanation
Indices: 39765--39872 Score: 94
Period size: 40 Copynumber: 2.7 Consensus size: 40
39755 TTGCACAATC
* *
39765 GCGACATTTA-TAATAAAACGCCACT-AAGGTACATCACTATG
1 GCGACGTTTATTAA-AAAA-GCCACTAAATG-ACATCACTATG
* * *
39806 GCGATGTTTATTAAAAAAGCCACTAAATGACATCTCTATT
1 GCGACGTTTATTAAAAAAGCCACTAAATGACATCACTATG
* * * *
39846 GCGGCGTTTGTTAAAAACGCCAGTAAA
1 GCGACGTTTATTAAAAAAGCCACTAAA
39873 GTACTACTCT
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
40 37 0.67
41 15 0.27
42 3 0.05
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (40 bp):
GCGACGTTTATTAAAAAAGCCACTAAATGACATCACTATG
Found at i:39914 original size:41 final size:41
Alignment explanation
Indices: 39817--40033 Score: 146
Period size: 41 Copynumber: 5.4 Consensus size: 41
39807 CGATGTTTAT
*
39817 TAAAAAAGCCACTAAA-TGAC-ATCTCTATTGCGGCGTTTGT-
1 TAAAAACGCCACTAAAGT-ACTA-CTCTATTGCGGCGTTTGTA
* *
39857 TAAAAACGCCAGTAAAGTACTACTCTGTTGCGGCGTTTGTA
1 TAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTA
* ** * * * * *
39898 TACAAACGCCACTAAAGTAAGAGTATTTTGCAGCATTTG-A
1 TAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTA
* * * *
39938 TCAAAAAATGTCGCT--A--ACAACTCTATTGCGGCGTTTGT-
1 T--AAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTA
* * *
39976 TGAAAAACGCTACTAAAGTACTACTCTGTTGTGGCGTTTGTA
1 T-AAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTA
* *
40018 TACAAATGCCACTAAA
1 TAAAAACGCCACTAAA
40034 ATAAGAGTAT
Statistics
Matches: 132, Mismatches: 34, Indels: 21
0.71 0.18 0.11
Matches are distributed among these distances:
37 8 0.06
38 15 0.11
39 1 0.01
40 36 0.27
41 63 0.48
42 9 0.07
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (41 bp):
TAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTGTA
Found at i:39999 original size:120 final size:117
Alignment explanation
Indices: 39839--40072 Score: 362
Period size: 120 Copynumber: 2.0 Consensus size: 117
39829 TAAATGACAT
*
39839 CTCTATTGCGGCGTTTGTTAAAAACGCCAGTAAAGTACTACTCTGTTGCGGCGTTTGTATACAAA
1 CTCTATTGCGGCGTTTGTTAAAAACGCCACTAAAGTACTACTCTGTTGCGGCGTTTGTATACAAA
* *
39904 CGCCACTAAAGTAAGAGTATTTTGCAGCA-TTTGATCAAAAAATGTCGCTAACAA
66 CGCCACTAAAATAAGAGTATTTTGCAG-AGTTTGAT-AAAAAA-GCCGCTAACAA
* *
39958 CTCTATTGCGGCGTTTGTTGAAAAACGCTACTAAAGTACTACTCTGTTGTGGCGTTTGTATACAA
1 CTCTATTGCGGCGTTTGTT-AAAAACGCCACTAAAGTACTACTCTGTTGCGGCGTTTGTATACAA
* *
40023 ATGCCACTAAAATAAGAGTATTTTGTAGAGTTTGATAAAAAAGCCGCTAA
65 ACGCCACTAAAATAAGAGTATTTTGCAGAGTTTGATAAAAAAGCCGCTAA
40073 AAATAATGCT
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
118 7 0.07
119 26 0.25
120 73 0.69
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (117 bp):
CTCTATTGCGGCGTTTGTTAAAAACGCCACTAAAGTACTACTCTGTTGCGGCGTTTGTATACAAA
CGCCACTAAAATAAGAGTATTTTGCAGAGTTTGATAAAAAAGCCGCTAACAA
Found at i:40186 original size:42 final size:42
Alignment explanation
Indices: 40140--40268 Score: 115
Period size: 41 Copynumber: 3.1 Consensus size: 42
40130 TAACTGTTGT
40140 GGCATTTGTTGTAAAAACGCTACTATATATAAACCCTATTGC
1 GGCATTTGTTGTAAAAACGCTACTATATATAAACCCTATTGC
* * * * * *
40182 GGCATTT-TTATAAAAACGCTGCTA-A-AGTACTA-TCTGTTAC
1 GGCATTTGTTGTAAAAACGCTACTATATA-TA-AACCCTATTGC
* * *
40222 GACGTTTGTTGAAAAAACG-TCACTATATATAAACCCTATTGC
1 GGCATTTGTTGTAAAAACGCT-ACTATATATAAACCCTATTGC
40264 GGCAT
1 GGCAT
40269 ATTGAATGGA
Statistics
Matches: 63, Mismatches: 17, Indels: 14
0.67 0.18 0.15
Matches are distributed among these distances:
39 1 0.02
40 14 0.22
41 29 0.46
42 18 0.29
43 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (42 bp):
GGCATTTGTTGTAAAAACGCTACTATATATAAACCCTATTGC
Found at i:42515 original size:23 final size:23
Alignment explanation
Indices: 42489--42549 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
42479 CTCATATAAA
*
42489 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
42512 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
42535 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
42550 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:42736 original size:103 final size:103
Alignment explanation
Indices: 42565--42885 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
42555 TAATGTCCAT
* * *
42565 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
42630 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
42668 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
42733 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
42771 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
42836 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
42874 AAGGACCACATA
1 AAGGACCACATA
42886 GACCCTCGAC
Statistics
Matches: 213, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 213 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:44095 original size:21 final size:21
Alignment explanation
Indices: 44069--44112 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
44059 ATTTTATTCG
* *
44069 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
44090 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
44111 CT
1 CT
44113 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:49402 original size:30 final size:30
Alignment explanation
Indices: 49352--49408 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
49342 TATTCAAACT
* *
49352 GGTTTTGCCGATTTTTAGCCGGTTCATCCC
1 GGTTTTACCGATTTTCAGCCGGTTCATCCC
*
49382 GGTTTTACCGGTTTTCAGCCGGTTCAT
1 GGTTTTACCGATTTTCAGCCGGTTCAT
49409 TACCAAACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.40
Consensus pattern (30 bp):
GGTTTTACCGATTTTCAGCCGGTTCATCCC
Found at i:54711 original size:29 final size:28
Alignment explanation
Indices: 54679--54746 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
54669 AAGAAGGAGG
*
54679 GAAGAAAAAGGAAGAAAGAAAGTAAAAAT
1 GAAGAAAAAGG-AGAAAGAAAGAAAAAAT
*
54708 GAAGAGAAATGGAGAAAGAAAGAAAAAAT
1 GAAGA-AAAAGGAGAAAGAAAGAAAAAAT
*
54737 CAGAGAAAAA
1 GA-AGAAAAA
54747 ACCCCAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 25 0.76
30 8 0.24
ACGTcount: A:0.68, C:0.01, G:0.25, T:0.06
Consensus pattern (28 bp):
GAAGAAAAAGGAGAAAGAAAGAAAAAAT
Found at i:55042 original size:21 final size:20
Alignment explanation
Indices: 55016--55200 Score: 84
Period size: 21 Copynumber: 8.9 Consensus size: 20
55006 CGCAAATCAG
55016 TTTCCAGATTCGCAATGCGAT
1 TTTCCA-ATTCGCAATGCGAT
* *
55037 TTTCCAATTTCGCATTACGAT
1 TTTCCAA-TTCGCAATGCGAT
*
55058 TTTCCCAATTCGCAATGCGAA
1 TTT-CCAATTCGCAATGCGAT
**** *
55079 TAAGTAAATCGCAATGCGAAT
1 TTTCCAATTCGCAATGCG-AT
*** *
55100 TTGGAAAATCGCAATGCGAT
1 TTTCCAATTCGCAATGCGAT
** * * *
55120 ACT-GACTATCGCAATGCAAT
1 TTTCCAAT-TCGCAATGCGAT
*
55140 TTTCCTAATTCGCATTGCGAT
1 TTTCC-AATTCGCAATGCGAT
* ** **
55161 TTACGTATTCGCGTTGCGAT
1 TTTCCAATTCGCAATGCGAT
*
55181 TTTCATAATTCGCAATGCGA
1 TTTC-CAATTCGCAATGCGA
55201 ATACGTAAAT
Statistics
Matches: 121, Mismatches: 36, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
19 1 0.01
20 43 0.36
21 71 0.59
22 6 0.05
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (20 bp):
TTTCCAATTCGCAATGCGAT
Found at i:55215 original size:20 final size:20
Alignment explanation
Indices: 55190--55301 Score: 127
Period size: 20 Copynumber: 5.5 Consensus size: 20
55180 TTTTCATAAT
55190 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
55210 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
55230 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
55251 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
55271 TTGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
55291 TCGCAATGCGA
1 TCGCAATGCGA
55302 TTTACATAGC
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 56 0.73
21 18 0.23
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:55221 original size:41 final size:41
Alignment explanation
Indices: 55054--55309 Score: 152
Period size: 41 Copynumber: 6.3 Consensus size: 41
55044 TTTCGCATTA
** *
55054 CGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAATG
1 CGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAATG
** * *
55095 CGAATTTGGA-AAATCGCAATGCG-ATAC-TGACTATCGCAATG
1 CG-ATTTTCATAATTCGCAATGCGAATACGT-A-AATCGCAATG
* * * * * **
55136 CAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGTTG
1 CGATTTTCATAATTCGCAATGCGA-ATACGTAAATCGCAATG
*
55177 CGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAACG
1 CGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAATG
* * * *
55218 CGA--TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATG
1 CGATTTTCA-TAATTCGCAATGCGAA-TACGTAAATCGCAATG
* * * * *
55259 CGA-ATACGTAAATT-GCAATGCGAAT-CTTACTATCGCAATG
1 CGATTTTCAT-AATTCGCAATGCGAATACGTA-AATCGCAATG
*
55299 CGATTTACATA
1 CGATTTTCATA
55310 GCGCCATTCG
Statistics
Matches: 161, Mismatches: 40, Indels: 29
0.70 0.17 0.13
Matches are distributed among these distances:
39 5 0.03
40 42 0.26
41 102 0.63
42 8 0.05
43 3 0.02
44 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (41 bp):
CGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAATG
Found at i:55969 original size:20 final size:19
Alignment explanation
Indices: 55880--55992 Score: 101
Period size: 20 Copynumber: 6.1 Consensus size: 19
55870 GAAACCAAAA
*
55880 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
** *
55899 TCGCGTTGCGATAGTCACT
1 TCGCGTTGCGATTTTCATT
55918 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
55932 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
55951 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
55971 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
55991 TC
1 TC
55993 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 2 0.03
19 29 0.38
20 32 0.42
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:59565 original size:14 final size:14
Alignment explanation
Indices: 59546--59581 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
59536 ATTGTTTAAT
59546 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
59560 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
59574 TGATTTGT
1 TGATTTGT
59582 TTAATTGATG
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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:59710 original size:19 final size:19
Alignment explanation
Indices: 59688--59805 Score: 96
Period size: 19 Copynumber: 6.7 Consensus size: 19
59678 AAAAATTACT
59688 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
59707 ATCGCAA--CG--AT-ATA
1 ATCGCAATGCGAAATGAAA
59721 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
59740 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
59754 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
59773 ATCGCAACGTGAAACT-AAA
1 ATCGCAATGCGAAA-TGAAA
*
59792 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
59806 CTAAATTCGC
Statistics
Matches: 80, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
14 19 0.24
15 3 0.04
16 4 0.05
17 4 0.05
18 3 0.04
19 46 0.57
20 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:59730 original size:33 final size:33
Alignment explanation
Indices: 59688--59781 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
59678 AAAAATTACT
* *
59688 ATCGCAATGCGAAATGAAAATCGCAACGATATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
59721 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
59754 ATCGCAATACGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
59782 TGAAACTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:59806 original size:19 final size:19
Alignment explanation
Indices: 59770--59815 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
59760 ATACGAAATG
*
59770 AAAATCGCAACGTGAAACT
1 AAAATCGCAACGCGAAACT
59789 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
*
59808 AAATTCGC
1 AAAATCGC
59816 GTTACGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.46, C:0.24, G:0.15, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACT
Found at i:59862 original size:33 final size:33
Alignment explanation
Indices: 59815--59940 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
59805 ACTAAATTCG
* * *
59815 CGTTACGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
59848 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
59881 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
59914 CGTTGCGATTTTCA-TTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
59941 AGTAATTTCC
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 13 0.15
33 76 0.85
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:59888 original size:14 final size:14
Alignment explanation
Indices: 59836--59923 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
59826 TCATTTCGCT
*
59836 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
59850 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
59867 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
59883 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
59900 CATTGCGATTATCTCG
1 --TTGCGATTCTCTCG
59916 TTGCGATT
1 TTGCGATT
59924 TTCATTCGCA
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 12 0.21
19 12 0.21
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:60006 original size:20 final size:20
Alignment explanation
Indices: 59934--60006 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 20
59924 TTCATTCGCA
* * *
59934 TTGCGATAGTAATTTCCGCG
1 TTGCGATAGTCATTTACGTG
* *
59954 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTACG-TG
*
59974 ATTGCGA-ACGTCATTTTCGTG
1 -TTGCGATA-GTCATTTACGTG
59995 TTGCGATAGTCA
1 TTGCGATAGTCA
60007 AATGATTGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 12 0.30
22 3 0.08
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCATTTACGTG
Found at i:62502 original size:24 final size:24
Alignment explanation
Indices: 62468--62521 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
62458 CTGAAACAAC
*
62468 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
62492 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
62516 ATCAAA
1 ATCAAA
62522 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:63940 original size:20 final size:20
Alignment explanation
Indices: 63892--63950 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
63882 AATAGTTTCT
* *
63892 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
63912 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
63932 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
63951 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:64240 original size:22 final size:22
Alignment explanation
Indices: 64213--64256 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
64203 GATGGAGATA
64213 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
64235 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
64257 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:64473 original size:20 final size:20
Alignment explanation
Indices: 64448--64490 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
64438 GTATTATCTC
* *
64448 GTTGCGAAAGTCAGTATTGA
1 GTTGCGAAAGTAAGTATCGA
*
64468 GTTGCGAAATTAAGTATCGA
1 GTTGCGAAAGTAAGTATCGA
64488 GTT
1 GTT
64491 ACGATTTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (20 bp):
GTTGCGAAAGTAAGTATCGA
Found at i:64527 original size:20 final size:20
Alignment explanation
Indices: 64504--64574 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
64494 ATTTGTATTA
* *
64504 TCGCGTTGCAATTTTCCAAT
1 TCGCATTGCGATTTTCCAAT
*
64524 TCGCATTCCGATTTTCCAAT
1 TCGCATTGCGATTTTCCAAT
* **
64544 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCAAT
64564 TCGCATTGCGA
1 TCGCATTGCGA
64575 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTTCCAAT
Found at i:64674 original size:20 final size:20
Alignment explanation
Indices: 64651--64696 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
64641 GGAAACTGAT
*
64651 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
64671 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
64690 TTGCGAT
1 TTGCGAT
64697 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Done.