Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000740.1 Hibiscus syriacus cultivar Beakdansim tig00001430_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: 111648
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2640 original size:29 final size:29
Alignment explanation
Indices: 2608--2663 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
2598 GAATACGGAT
*
2608 GATC-ATTTTGTAACTTTTAATAGTCGAAA
1 GATCAATTTT-TAACTTTTAATAATCGAAA
2637 GATCAATTTTTAACTTTTAATAATCGA
1 GATCAATTTTTAACTTTTAATAATCGA
2664 TGGATTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (29 bp):
GATCAATTTTTAACTTTTAATAATCGAAA
Found at i:9921 original size:24 final size:24
Alignment explanation
Indices: 9901--9984 Score: 116
Period size: 24 Copynumber: 3.5 Consensus size: 24
9891 TAAATTCTAT
* *
9901 TATGATACCTGACCTAGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
* *
9925 TTTGATA-TTGACATGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
*
9948 TATGATACATGACCTGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
9972 TATGATACTTGAC
1 TATGATACTTGAC
9985 TTGAATTATG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 19 0.37
24 32 0.63
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (24 bp):
TATGATACTTGACCTGGATTCTGA
Found at i:14636 original size:24 final size:24
Alignment explanation
Indices: 14609--14695 Score: 140
Period size: 24 Copynumber: 3.7 Consensus size: 24
14599 TGAATTATGT
*
14609 TATGATACCTGACCTGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
*
14633 TATGATA-TTGACATGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
*
14656 TATGATACTTGACCTAGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
14680 TATGATACTTGACCTG
1 TATGATACTTGACCTG
14696 AATTATGTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
23 21 0.37
24 36 0.63
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (24 bp):
TATGATACTTGACCTGGATTCTGA
Found at i:14709 original size:24 final size:24
Alignment explanation
Indices: 14599--14699 Score: 125
Period size: 24 Copynumber: 4.2 Consensus size: 24
14589 ATTTCTGATT
* * *
14599 TGAATTATGTTATGATACCTGACC
1 TGAATTCTGATATGATACTTGACC
* *
14623 TGGATTCTGATATGATA-TTGACA
1 TGAATTCTGATATGATACTTGACC
*
14646 TGGATTCTGATATGATACTTGACC
1 TGAATTCTGATATGATACTTGACC
14670 T-AGATTCTGATATGATACTTGACC
1 TGA-ATTCTGATATGATACTTGACC
14694 TGAATT
1 TGAATT
14700 ATGTTTTGAT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
23 21 0.31
24 45 0.67
25 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.39
Consensus pattern (24 bp):
TGAATTCTGATATGATACTTGACC
Found at i:23046 original size:2 final size:2
Alignment explanation
Indices: 23039--23067 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23029 GTGAATGTTG
23039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23068 CGGTAAAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28322 original size:408 final size:408
Alignment explanation
Indices: 27491--28716 Score: 2402
Period size: 408 Copynumber: 3.0 Consensus size: 408
27481 ACATGTCTGG
27491 CATATATTTGCTTAAAATATACATGTCTGGCACATATTTGAATATGACCCTCCAAATACCCTACA
1 CATATATTTGCTTAAAATATACATGTCTGGCACATATTTGAATATGACCCTCCAAATACCCTACA
27556 GATATATGGAATGAAACTTAGAAAAACATAGAACATACCCGTGTTATACTCATATCAGCCTCTAA
66 GATATATGGAATGAAACTTAGAAAAACATAGAACATACCCGTGTTATACTCATATCAGCCTCTAA
27621 CACTCACACTTGGATCAATAACATGTAAAATCACTTATATATTATGCATATATTCTTTGAGGAAG
131 CACTCACACTTGGATCAATAACATGTAAAATCACTTATATATTATGCATATATTCTTTGAGGAAG
27686 TGTGCATTTCC-AA-ATATATATGCATGGCCTACCAGGTAGAAAAGAACCATATAATGCAAGCTT
196 TGTGCATTTCCAAATATATATATGCATGGCCTACCAGGTAGAAAAGAACCATATAATGCAAGCTT
27749 CAGGTTTCCACTTTCGCTTGAGATCGGGTTGTGAATAGTGATTAACTTCGTCCCGTCAGGAAATG
261 CAGGTTTCCACTTTCGCTTGAGATCGGGTTGTGAATAGTGATTAACTTCGTCCCGTCAGGAAATG
27814 TCCCTTCAACCTTGTATTAAAATAACAGTTGGTTTACTTGCATTGTTGATTTTGACAGAAAAAAA
326 TCCCTTCAACCTTGTATTAAAATAACAGTTGGTTTACTTGCATTGTTGATTTTGACAGAAAAAAA
27879 AGAGTTCACAATATGAGC
391 AGAGTTCACAATATGAGC
27897 CATATATTTGCTTAAAATATACATGTCTGGCACATATTTGAATATGACCCTCCAAATACCCTACA
1 CATATATTTGCTTAAAATATACATGTCTGGCACATATTTGAATATGACCCTCCAAATACCCTACA
27962 GATATATGGAATGAAACTTAGAAAAACATAGAACATACCCGTGTTATACTCATATCAGCCTCTAA
66 GATATATGGAATGAAACTTAGAAAAACATAGAACATACCCGTGTTATACTCATATCAGCCTCTAA
28027 CACTCACACTTGGATCAATAACATGTAAAATCACTTATATATTATGCATATATTCTTTGAGGAAG
131 CACTCACACTTGGATCAATAACATGTAAAATCACTTATATATTATGCATATATTCTTTGAGGAAG
28092 TGTGCATTTCCAAATATATATATGCATGGCCTACCAGGTAGAAAAGAACCATATAATGCAAGCTT
196 TGTGCATTTCCAAATATATATATGCATGGCCTACCAGGTAGAAAAGAACCATATAATGCAAGCTT
28157 CAGGTTTCCACTTTCGCTTGAGATCGGGTTGTGAATAGTGATTAACTTCGTCCCGTCAGGAAATG
261 CAGGTTTCCACTTTCGCTTGAGATCGGGTTGTGAATAGTGATTAACTTCGTCCCGTCAGGAAATG
28222 TCCCTTCAACCTTGTATTAAAATAACAGTTGGTTTACTTGCATTGTTGATTTTGACAGAAAAAAA
326 TCCCTTCAACCTTGTATTAAAATAACAGTTGGTTTACTTGCATTGTTGATTTTGACAGAAAAAAA
28287 AGAGTTCACAATATGAGC
391 AGAGTTCACAATATGAGC
28305 CATATATTTGCTTAAAATATACATGTCTGGCACATATTTGAATATGACCCTCCAAATACCCTACA
1 CATATATTTGCTTAAAATATACATGTCTGGCACATATTTGAATATGACCCTCCAAATACCCTACA
* *
28370 GATATATGGAATTAAACTTAGAAAAACATAGAACATACCCGTGTTAGACTCATATCAGCCTCTAA
66 GATATATGGAATGAAACTTAGAAAAACATAGAACATACCCGTGTTATACTCATATCAGCCTCTAA
28435 CACTCACACTTGGATCAATAACATGTAAAATCACTTATATATTATGCATATATTCTTTGAGGAAG
131 CACTCACACTTGGATCAATAACATGTAAAATCACTTATATATTATGCATATATTCTTTGAGGAAG
28500 TGTGCATTTCCAAATATATATATATGCATGGCCTACCAGGTAGAAAAGAACCATATAATGCAAGC
196 TGTGCATTTCC-AA-ATATATATATGCATGGCCTACCAGGTAGAAAAGAACCATATAATGCAAGC
28565 TTCAGGTTTCCACTTTCGCTTGAGATCGGGTTGTGAATAGTGATTAACTTCGTCCCGTCAGGAAA
259 TTCAGGTTTCCACTTTCGCTTGAGATCGGGTTGTGAATAGTGATTAACTTCGTCCCGTCAGGAAA
28630 TGTCCCTTCAACCTTGTATTAAAATAACAGTTGGTTTACTTGCATTGTTGATTTTGACAGAAAAA
324 TGTCCCTTCAACCTTGTATTAAAATAACAGTTGGTTTACTTGCATTGTTGATTTTGACAGAAAAA
28695 AAAGAGTTCACAATATGAGC
389 AAAGAGTTCACAATATGAGC
28715 CA
1 CA
28717 AGAAAAATCT
Statistics
Matches: 814, Mismatches: 2, Indels: 4
0.99 0.00 0.00
Matches are distributed among these distances:
406 206 0.25
407 2 0.00
408 402 0.49
409 2 0.00
410 202 0.25
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31
Consensus pattern (408 bp):
CATATATTTGCTTAAAATATACATGTCTGGCACATATTTGAATATGACCCTCCAAATACCCTACA
GATATATGGAATGAAACTTAGAAAAACATAGAACATACCCGTGTTATACTCATATCAGCCTCTAA
CACTCACACTTGGATCAATAACATGTAAAATCACTTATATATTATGCATATATTCTTTGAGGAAG
TGTGCATTTCCAAATATATATATGCATGGCCTACCAGGTAGAAAAGAACCATATAATGCAAGCTT
CAGGTTTCCACTTTCGCTTGAGATCGGGTTGTGAATAGTGATTAACTTCGTCCCGTCAGGAAATG
TCCCTTCAACCTTGTATTAAAATAACAGTTGGTTTACTTGCATTGTTGATTTTGACAGAAAAAAA
AGAGTTCACAATATGAGC
Found at i:41184 original size:34 final size:33
Alignment explanation
Indices: 41146--41230 Score: 113
Period size: 32 Copynumber: 2.6 Consensus size: 33
41136 ATTAAAAAAT
*
41146 AATATATAAAGATATATTATT-ATAATTATCTCTA
1 AATATAT-AAGATATA-AATTAATAATTATCTCTA
*
41180 AATATACAAGAT-TAAATTAATAATTATCTCTA
1 AATATATAAGATATAAATTAATAATTATCTCTA
41212 AATATATAAGATA-AAATTA
1 AATATATAAGATATAAATTA
41231 TAAATTCTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
31 3 0.07
32 32 0.70
33 5 0.11
34 6 0.13
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.39
Consensus pattern (33 bp):
AATATATAAGATATAAATTAATAATTATCTCTA
Found at i:44882 original size:42 final size:42
Alignment explanation
Indices: 44833--44915 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
44823 CACATTTGTC
44833 GCCCAATATGAAAATCACTCGT-GTGTGATTGGTCACAATGTT
1 GCCCAATATGAAAATCACTC-TAGTGTGATTGGTCACAATGTT
*
44875 GCCCAATATGAAAATTACTCTAGTGTGATTGGTCACAATGT
1 GCCCAATATGAAAATCACTCTAGTGTGATTGGTCACAATGT
44916 CTCATATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 1 0.03
42 38 0.97
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (42 bp):
GCCCAATATGAAAATCACTCTAGTGTGATTGGTCACAATGTT
Found at i:45652 original size:14 final size:13
Alignment explanation
Indices: 45635--45682 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
45625 AGTTCAAAGC
45635 TGAACGCTCAACAT
1 TGAACGCTCAA-AT
* *
45649 TGAACGTTCAAAGC
1 TGAACGCTCAAA-T
45663 TGAACGCTCAATAT
1 TGAACGCTCAA-AT
45677 TGAACG
1 TGAACG
45683 TTCATACTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.04
14 26 0.93
15 1 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (13 bp):
TGAACGCTCAAAT
Found at i:45658 original size:28 final size:28
Alignment explanation
Indices: 45626--45686 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
45616 CAAAGAGTCA
45626 GTTCAAAGCTGAACGCTCAACATTGAAC
1 GTTCAAAGCTGAACGCTCAACATTGAAC
*
45654 GTTCAAAGCTGAACGCTCAATATTGAAC
1 GTTCAAAGCTGAACGCTCAACATTGAAC
45682 GTTCA
1 GTTCA
45687 TACTCTTGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (28 bp):
GTTCAAAGCTGAACGCTCAACATTGAAC
Found at i:52447 original size:25 final size:24
Alignment explanation
Indices: 52413--52473 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 24
52403 AAAGAAATAA
* * *
52413 TAAAATAATAATAAAAGGTTAAATT
1 TAAAAAAATAATAAAAAG-TAAAAT
*
52438 TAAAAAAATATTTAAAAAGTAAAAT
1 TAAAAAAATA-ATAAAAAGTAAAAT
*
52463 AAAAAAAATAA
1 TAAAAAAATAA
52474 AGATAAAACT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 23 0.79
26 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (24 bp):
TAAAAAAATAATAAAAAGTAAAAT
Found at i:53787 original size:3 final size:3
Alignment explanation
Indices: 53779--53847 Score: 77
Period size: 3 Copynumber: 22.3 Consensus size: 3
53769 TTAACTAAGA
* * *
53779 AAT AAT AAT AAT AAAT AA- AAT AAT TAC AAT AAT AAT AAAT GAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
53825 AAAT AAT AAT AAT AAT AAT AAT A
1 -AAT AAT AAT AAT AAT AAT AAT A
53848 TTTTAAAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
2 2 0.04
3 45 0.80
4 9 0.16
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:53825 original size:10 final size:10
Alignment explanation
Indices: 53782--53845 Score: 76
Period size: 10 Copynumber: 6.1 Consensus size: 10
53772 ACTAAGAAAT
53782 AATAATAATA
1 AATAATAATA
53792 AATAAAATAATTA
1 AAT--AATAA-TA
53805 CAATAATAATA
1 -AATAATAATA
*
53816 AATGATAATA
1 AATAATAATA
53826 AATAATAAT-
1 AATAATAATA
53835 AATAATAATA
1 AATAATAATA
53845 A
1 A
53846 TATTTTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
9 9 0.19
10 21 0.45
11 2 0.04
12 10 0.21
13 2 0.04
14 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (10 bp):
AATAATAATA
Found at i:53957 original size:36 final size:37
Alignment explanation
Indices: 53888--53984 Score: 88
Period size: 36 Copynumber: 2.5 Consensus size: 37
53878 ATGTTTTTTT
*
53888 AAAAATTATATAATATATATATTTTAAAAAAAATGCTTTAA
1 AAAAATTATAT-AT-TATATATTTT--AAAAAATACTTTAA
* * **
53929 AAAAATTATATATTATATATTTT-TAAAATATTTTTT
1 AAAAATTATATATTATATATTTTAAAAAATACTTTAA
* *
53965 AAAAACTATATAATATATAT
1 AAAAATTATATATTATATAT
53985 ATGTTTCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
36 26 0.53
39 10 0.20
40 2 0.04
41 11 0.22
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (37 bp):
AAAAATTATATATTATATATTTTAAAAAATACTTTAA
Found at i:54014 original size:39 final size:38
Alignment explanation
Indices: 53883--54059 Score: 150
Period size: 38 Copynumber: 4.6 Consensus size: 38
53873 CCAAAATGTT
* *
53883 TTTTTAAAAATTATATAATATATATAT-TTTAAAAAAAATG
1 TTTTTAAAAACTATAT-ATATATATATGTTT--CAAAAATG
* * * *
53923 CTTTAAAAAAAT-TATATATTATATAT-TTTTAAAATAT-
1 TTTTTAAAAACTATATATA-TATATATGTTTCAAAA-ATG
53960 TTTTTAAAAACTATATAATATATATATGTTTCAAAAATG
1 TTTTTAAAAACTATAT-ATATATATATGTTTCAAAAATG
* * *
53999 TTTTTCAAAACTATATAT-TATTTACGTTTTCAAAAATG
1 TTTTTAAAAACTATATATATATATATG-TTTCAAAAATG
* *
54037 CTTTTAAATA-TATATATATATAT
1 TTTTTAAAAACTATATATATATAT
54060 GTATATATAT
Statistics
Matches: 114, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
37 26 0.23
38 41 0.36
39 38 0.33
40 9 0.08
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.47
Consensus pattern (38 bp):
TTTTTAAAAACTATATATATATATATGTTTCAAAAATG
Found at i:54042 original size:77 final size:75
Alignment explanation
Indices: 53852--54059 Score: 185
Period size: 77 Copynumber: 2.7 Consensus size: 75
53842 ATAATATTTT
* * * *
53852 AAAAAAC-ATATAATATA-ATTTCCAAAATGTTTTTTTAAAAATTATATAATATATATATTTTAA
1 AAAAAACTATATATTATATATTTTCAAAAT-ATCTTTTAAAAA-TATATAATATATATATTTT-A
53915 AAAAAATGCTTTA
63 AAAAAATGCTTTA
* * * *
53928 AAAAAATTATATATTATATATTTTTAAAATATTTTTTAAAAACTATATAATATATATATGTTT-C
1 AAAAAACTATATATTATATATTTTCAAAATATCTTTTAAAAA-TATATAATATATATAT-TTTAA
*
53992 AAAAATG-TTTT
64 AAAAATGCTTTA
** * *
54003 TCAAAACTATATATTATTTACGTTTTCAAAA-ATGCTTTTAAATATATAT-ATATATAT
1 AAAAAACTATATATTATATA--TTTTCAAAATAT-CTTTTAAAAATATATAATATATAT
54060 GTATATATAT
Statistics
Matches: 111, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
75 27 0.24
76 20 0.18
77 52 0.47
78 12 0.11
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (75 bp):
AAAAAACTATATATTATATATTTTCAAAATATCTTTTAAAAATATATAATATATATATTTTAAAA
AAATGCTTTA
Found at i:54070 original size:53 final size:54
Alignment explanation
Indices: 54010--54113 Score: 142
Period size: 53 Copynumber: 1.9 Consensus size: 54
54000 TTTTCAAAAC
* * *
54010 TATATATTATTTACGTTTTCAAAAATGCTTTT-AAATA-TATATA-TATATATGTA
1 TATATATTATATACATTTTC-AAAATG-TTTTCAAAGACTATATATTATATATGTA
54063 TATATATTATATACATTTTCAAAATGTTTTCAAAGACTATATATTATATAT
1 TATATATTATATACATTTTCAAAATGTTTTCAAAGACTATATATTATATAT
54114 ATTTTTAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
51 4 0.09
52 10 0.22
53 24 0.53
54 7 0.16
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (54 bp):
TATATATTATATACATTTTCAAAATGTTTTCAAAGACTATATATTATATATGTA
Found at i:54146 original size:90 final size:88
Alignment explanation
Indices: 53971--54174 Score: 213
Period size: 90 Copynumber: 2.3 Consensus size: 88
53961 TTTTAAAAAC
* * *
53971 TATATA-ATATATATATGTTTCAAAAATGTTTTTCAAAACTATATATTATTTACGTTTTCAAAAA
1 TATATATATATATACAT-TTTC-AAAATGTTTTTCAAAACTATATATTATATACATTTTCAAAAA
* * *
54035 TGCTTTTAAATATATATATATATATGTA
64 TGCTTTTAAA-A-AAAAACATATAT-TA
* *
54063 TATATAT-TATATACATTTTCAAAATG-TTTTCAAAGACTATATATTATATATATTTT-TAAAAT
1 TATATATATATATACATTTTCAAAATGTTTTTCAAA-ACTATATATTATATACATTTTCAAAAAT
54125 G-TTTTCGAAAAAAAAACATATATTA
65 GCTTTT--AAAAAAAAACATATATTA
54150 TATATCATATATATAC-TTTTCAAAA
1 TATAT-ATATATATACATTTTCAAAA
54175 AGCTATTCTC
Statistics
Matches: 98, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
87 7 0.07
88 24 0.24
89 22 0.22
90 27 0.28
91 4 0.04
92 14 0.14
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (88 bp):
TATATATATATATACATTTTCAAAATGTTTTTCAAAACTATATATTATATACATTTTCAAAAATG
CTTTTAAAAAAAAACATATATTA
Found at i:55380 original size:329 final size:328
Alignment explanation
Indices: 54858--55470 Score: 922
Period size: 329 Copynumber: 1.9 Consensus size: 328
54848 AAGTTGAATA
* * *
54858 TAATCGAACTCAAAGGTCTTTAGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCAAAGGTCTTTAGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTA
* * ** *
54923 CCTTGGAGCTGAGCGTACTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAG
66 CCTTGGAGCTGAGCGTACTCAAACTCAAAGGTCTTTGGCTAACAGATAACCCTTCTAGACTTAAG
* **
54988 TTATGCTGCAAATGATGTGCCCTCGAAGCTGAATGTAATCGAACTTGGGGGTCTTTGGCAGATAG
131 TTATGCTGCAAATGATATGCCCTCGAAGCTGAATGTAATCGAACTTAAGGGTCTTTGGCAGATAG
* * *
55053 CCCTTCTTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
196 CCCTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
*
55118 GTTTTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGCGCCCTCGAAGCT
261 G-TCTTGG-TGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGCGCCCTCGAAGCT
55183 GAGTG
324 GAGTG
* * * * *
55188 TAATCGAACTTAAGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTA
1 TAATCGAACTCAAAGGTCTTTAGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTA
* * * *
55253 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT-GCTAACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTACTCAAACTCAAAGGTCTTTGGCTAACAGATAACCCTTCTAGACTTAAG
* * * *
55317 TTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAG
131 TTATGCTGCAAATGATATGCCCTCGAAGCTGAATGTAATCGAACTTAAGGGTCTTTGGCAGATAG
* *
55382 CTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
196 CCCTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
*
55447 GTCTTGGTGGCAGATAGCCCTTCT
261 GTCTTGGTGGCAGATAACCCTTCT
55471 GGCCTTGAGC
Statistics
Matches: 252, Mismatches: 31, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
327 16 0.06
328 5 0.02
329 141 0.56
330 90 0.36
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (328 bp):
TAATCGAACTCAAAGGTCTTTAGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTA
CCTTGGAGCTGAGCGTACTCAAACTCAAAGGTCTTTGGCTAACAGATAACCCTTCTAGACTTAAG
TTATGCTGCAAATGATATGCCCTCGAAGCTGAATGTAATCGAACTTAAGGGTCTTTGGCAGATAG
CCCTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
GTCTTGGTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGCGCCCTCGAAGCTGA
GTG
Found at i:55383 original size:164 final size:165
Alignment explanation
Indices: 54858--55470 Score: 908
Period size: 165 Copynumber: 3.7 Consensus size: 165
54848 AAGTTGAATA
* * * * * *
54858 TAATCGAACTCAAAGGTCTTTAGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
* * * *
54923 CCTTGGAGCTGAGCGTACTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAG
*
54988 TTATGCTGCAAATGATGTGCCCTCGAAGCTGAATG
131 TTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
** * * *
55023 TAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATG
1 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
* * *
55088 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTGGTTGGCAGATAACCCTTCTTGACTTAAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAG
*
55153 TTATGCTGCAAATGATGCGCCCTCGAAGCTGAGTG
131 TTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
* *
55188 TAATCGAACTTAAGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTA
1 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
* ** * *
55253 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT-GCTAACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAG
* * * *
55317 TTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
131 TTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
*
55352 TAATCGAACTTAAGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
*
55417 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTGG-TGGCAGATAGCCCTTCT
66 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCT
55471 GGCCTTGAGC
Statistics
Matches: 410, Mismatches: 37, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
163 16 0.04
164 150 0.37
165 244 0.60
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (165 bp):
TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAG
TTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
Found at i:58862 original size:18 final size:19
Alignment explanation
Indices: 58821--58865 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
58811 AGTTAATGTG
58821 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
58840 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
58858 AATGCAAA
1 AATGCAAA
58866 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:65840 original size:38 final size:38
Alignment explanation
Indices: 65795--65870 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
65785 TGTTGGGCAC
** * *
65795 AACATAAAATATTATTTTTTTCCTAATATTTTTGGTTG
1 AACATAAAATATTACCTTATTCCTAACATTTTTGGTTG
* *
65833 AACATAAAATTTTACCTTATTCGTAACATTTTTGGTTG
1 AACATAAAATATTACCTTATTCCTAACATTTTTGGTTG
65871 GCAACCGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (38 bp):
AACATAAAATATTACCTTATTCCTAACATTTTTGGTTG
Found at i:69186 original size:19 final size:20
Alignment explanation
Indices: 69162--69212 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
69152 AATGACCAAT
69162 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
69181 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
69201 AAAATCGCAACG
1 AAAATCGCAACG
69213 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:69206 original size:20 final size:20
Alignment explanation
Indices: 69162--69439 Score: 155
Period size: 20 Copynumber: 13.6 Consensus size: 20
69152 AATGACCAAT
* *
69162 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
69181 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
69201 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
***
69221 AAAATCGCAACG-GACAAAAG
1 AAAATCGCAACGCGA-TTTAG
* * **
69241 AAAATCGCAACACGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
69262 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
69285 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
69305 TGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* *
69325 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* * *
69345 AGAGTCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
* * *
69365 AAGAGAATCGCAATGCGACTGAG
1 -A-A-AATCGCAACGCGATTTAG
* * *
69388 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
69408 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
69428 AAAATCGCAACG
1 AAAATCGCAACG
69440 TTAAAAAGAA
Statistics
Matches: 205, Mismatches: 45, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
19 18 0.09
20 143 0.70
21 15 0.07
22 1 0.00
23 28 0.14
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:69373 original size:63 final size:63
Alignment explanation
Indices: 69306--69429 Score: 194
Period size: 63 Copynumber: 2.0 Consensus size: 63
69296 GCGATTGATT
* * * *
69306 GAATCGCAATGCGATTTATAGAATCGCAACGCGATTGAGAGAGTCGCAACGCGATTCAGAAGA
1 GAATCGCAATGCGACTGAGAGAATCGCAACGCGATTGAGAGAATCGCAACGCGATTCAGAAGA
* *
69369 GAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAA
1 GAATCGCAATGCGACTGAGAGAATCGCAACGCGATTGAGAGAATCGCAACGCGATTCAGAA
69430 AATCGCAACG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (63 bp):
GAATCGCAATGCGACTGAGAGAATCGCAACGCGATTGAGAGAATCGCAACGCGATTCAGAAGA
Found at i:69378 original size:83 final size:83
Alignment explanation
Indices: 69266--69439 Score: 258
Period size: 83 Copynumber: 2.1 Consensus size: 83
69256 GCTTCCAAGT
* * ** * *
69266 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTCAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
* *
69331 GCAACGCGATTGAGAGAG
66 GCAACGCGATTGAGAAAA
*
69349 TCGCAACGCGATTCAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
1 TCGCAACGCGATTCAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
*
69414 GCAACGCGATTTAGAAAA
66 GCAACGCGATTGAGAAAA
69432 TCGCAACG
1 TCGCAACG
69440 TTAAAAAGAA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.20
Consensus pattern (83 bp):
TCGCAACGCGATTCAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
GCAACGCGATTGAGAAAA
Found at i:69449 original size:20 final size:20
Alignment explanation
Indices: 69426--69469 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
69416 AACGCGATTT
*
69426 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
69446 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
69466 AGAA
1 AGAA
69470 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:69558 original size:6 final size:6
Alignment explanation
Indices: 69547--69715 Score: 324
Period size: 6 Copynumber: 28.5 Consensus size: 6
69537 GACACGTATT
69547 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
69595 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
69643 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
69691 ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
69716 CGAGACGAGA
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.06
6 153 0.94
ACGTcount: A:0.33, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:70439 original size:6 final size:6
Alignment explanation
Indices: 70403--70478 Score: 117
Period size: 6 Copynumber: 13.5 Consensus size: 6
70393 TCTCGTCTCG
70403 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
70446 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
70479 AATACGTGTC
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 25 0.36
6 45 0.64
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:70734 original size:20 final size:20
Alignment explanation
Indices: 70567--70865 Score: 167
Period size: 20 Copynumber: 14.6 Consensus size: 20
70557 TTCTTTTGAC
*
70567 CGTTGCGATTCTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
*
70587 CGTTGCGATTCTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
70607 CGTTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
*
70627 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
70650 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
70671 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
70689 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
70711 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
70731 CGTTGCGATTTT-GATATACG
1 CGTTGCGATTTTCTAAAT-CG
* **
70751 CGTTGCGATTTATGT-GTTCG
1 CGTTGCGATTT-TCTAAATCG
*
70771 CGTTGCGATTTTC-ATATTCG
1 CGTTGCGATTTTCTA-AATCG
**
70791 CGTTGCGATTTTGGAAAATCG
1 CGTTGCGATTTT-CTAAATCG
** * * *
70812 CAATGCGAATTTGTACTATCG
1 CGTTGCGATTTTCTA-AATCG
* *
70833 CATTGCGATTTTCAAGAATCG
1 CGTTGCGATTTTCTA-AATCG
70854 CGTTGCGATTTT
1 CGTTGCGATTTT
70866 GGAAACTGAT
Statistics
Matches: 219, Mismatches: 44, Indels: 31
0.74 0.15 0.11
Matches are distributed among these distances:
18 2 0.01
19 4 0.02
20 135 0.62
21 58 0.26
22 5 0.02
23 15 0.07
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:70818 original size:21 final size:21
Alignment explanation
Indices: 70788--70870 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
70778 ATTTTCATAT
*
70788 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
70809 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
70830 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
70851 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
70871 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:76008 original size:30 final size:30
Alignment explanation
Indices: 75934--76008 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
75924 TGTATTTCTG
* *
75934 ATCTGCATGGGATTAATTCTCTGTTCTGAC
1 ATCTGCATGGGATTAATTCTCCGTTCTAAC
*** *
75964 ATCTATTTGAGATTAATTC-CCGATTCTAAC
1 ATCTGCATGGGATTAATTCTCCG-TTCTAAC
75994 ATCTGCATGGGATTA
1 ATCTGCATGGGATTA
76009 TAACCCTGTC
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
29 2 0.06
30 32 0.94
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (30 bp):
ATCTGCATGGGATTAATTCTCCGTTCTAAC
Found at i:76318 original size:2 final size:2
Alignment explanation
Indices: 76311--76360 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
76301 TTTATGTTGA
76311 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
76353 AT AT AT AT
1 AT AT AT AT
76361 TGTGTATTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81604 original size:26 final size:28
Alignment explanation
Indices: 81570--81637 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
81560 AAAATATCCA
*
81570 TATCATCACATGCTAAAAATTATTTAAAT
1 TATCACCA-ATGCTAAAAATTATTTAAAT
*
81599 TATCACCATATGTTAAAAATTATTTAAAT
1 TATCACCA-ATGCTAAAAATTATTTAAAT
81628 TCAGTCACCA
1 T-A-TCACCA
81638 CATTGTAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 27 0.79
30 1 0.03
31 6 0.18
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.37
Consensus pattern (28 bp):
TATCACCAATGCTAAAAATTATTTAAAT
Found at i:84070 original size:282 final size:283
Alignment explanation
Indices: 83563--84107 Score: 758
Period size: 282 Copynumber: 1.9 Consensus size: 283
83553 ATAGACAAAC
* * * * *
83563 CCATTGAGGCTTTCACTTTAATTGATGGGGATACAGTTGCCTTGTCACCACCAAATTTTGCTTGC
1 CCATTGAGGCTTTCACTTTAATTGATGGCGATACAGCTGCCTTATCACCACCAAAATTTGCTAGC
* *
83628 TTGGTCTTTATTTCATACTTTTCAAGCTTTTTGGGTTCTCGAAACTGCCGCTGTTCTTGCTTCTC
66 TTGGTCTTTAATTCATAC-TTCCAAGCTTTTTGGGTTCTCGAAAC-GCCGCTGTTCTTGCTTCTC
* * * * * *
83693 GAGTTCTACATCTTTGGAAATACCATCTGGTTTTGGCACACTTTGTGAAAACCTTTTAGATTTTT
129 GAATTCTACATCTTTGGAAACACCATCTGGTTTTGGCACACTTTGAGAAAACCTCTTAGATGTAT
83758 TCTCCCAAAGACCTCTAGGCTCCGTAGGAGTAGAACGCTTAAGTTGCCTTAAAAGGATCTCCCCT
194 TCTCCCAAAGACCTCTAGGCTCCGTAGGAGTAGAACGCTTAAGTTGCCTTAAAAGGATCTCCCCT
83823 GACAAACCCGTTTGGTTCCCTTGAT
259 GACAAACCCGTTTGGTTCCCTTGAT
* *
83848 CCATTGAGGCTTTCCCTTTAATTGATGGCGATACAGCTGCCTTATCACCCCCAAAATTTGCTAGC
1 CCATTGAGGCTTTCACTTTAATTGATGGCGATACAGCTGCCTTATCACCACCAAAATTTGCTAGC
* **
83913 TTGGTCTTTAATTCATA-TTCCGGGAGCTTTTCT-GGTTCTCG-AA-GCTTCTGTTCTTGCTTCT
66 TTGGTCTTTAATTCATACTTCC--AAGCTTTT-TGGGTTCTCGAAACGCCGCTGTTCTTGCTTCT
* * * * * *
83974 CGAATTCTAGATCTTTGGACACACGATCTGGTTTTGGCTCACTTTGAGTATACCTCTTAGATGTA
128 CGAATTCTACATCTTTGGAAACACCATCTGGTTTTGGCACACTTTGAGAAAACCTCTTAGATGTA
* **
84039 TTC-CCTCGAAGACCTCTAGGCTTTGTAGGAGTAGAACGCTTAAGTTGCCTTAAAAGGATCTCCC
193 TTCTCC-CAAAGACCTCTAGGCTCCGTAGGAGTAGAACGCTTAAGTTGCCTTAAAAGGATCTCCC
84103 CTGAC
257 CTGAC
84108 TCTCTCAATC
Statistics
Matches: 229, Mismatches: 27, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
281 2 0.01
282 132 0.58
283 3 0.01
284 2 0.01
285 89 0.39
286 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (283 bp):
CCATTGAGGCTTTCACTTTAATTGATGGCGATACAGCTGCCTTATCACCACCAAAATTTGCTAGC
TTGGTCTTTAATTCATACTTCCAAGCTTTTTGGGTTCTCGAAACGCCGCTGTTCTTGCTTCTCGA
ATTCTACATCTTTGGAAACACCATCTGGTTTTGGCACACTTTGAGAAAACCTCTTAGATGTATTC
TCCCAAAGACCTCTAGGCTCCGTAGGAGTAGAACGCTTAAGTTGCCTTAAAAGGATCTCCCCTGA
CAAACCCGTTTGGTTCCCTTGAT
Found at i:86252 original size:84 final size:83
Alignment explanation
Indices: 86129--86468 Score: 400
Period size: 84 Copynumber: 4.0 Consensus size: 83
86119 AAATCTTTCA
* * * * * ** *
86129 ACTTCGCATCGATCCTCAGATTCCA-AAGATTGACCGCAGTTTACCCCATCCGAGCCATCAATAC
1 ACTTCACATCGATTCTCAGATT-CAGCAGCTTGACCGCA-TTGACCCCATTTGAGCCATCAATAG
86193 CCTCAACTTCCCTCCCCTTT
64 CCTCAACTTCCCTCCCCTTT
* *
86213 ACTTCACATCGATTCTCAGATTCCGCAGCTTGACCGCAGTTTACCCCATTTGAGCCATCAATAGC
1 ACTTCACATCGATTCTCAGATTCAGCAGCTTGACCGCA-TTGACCCCATTTGAGCCATCAATAGC
86278 CTCAACTTCTCC-CCCCTTT
65 CTCAACTTC-CCTCCCCTTT
* * * * *
86297 ACTTCACATCGATTCTCAGATTCAGTATCTTGATCGCCATTGATCCCATTTGAACCATCAATAGC
1 ACTTCACATCGATTCTCAGATTCAGCAGCTTGACCG-CATTGACCCCATTTGAGCCATCAATAGC
*
86362 CTCAACTT-CTTCCCCCTTT
65 CTCAACTTCCCT-CCCCTTT
* * *
86381 ACTTCACATTGATTCTCAGATTCAGCATCTTGATCAC-CATTGATCCCATTTGAGCCATCAATAG
1 ACTTCACATCGATTCTCAGATTCAGCAGCTTGA-C-CGCATTGACCCCATTTGAGCCATCAATAG
*
86445 CCTCAACTTCTCTCCCCTTT
64 CCTCAACTTCCCTCCCCTTT
86465 ACTT
1 ACTT
86469 GGACAACGGT
Statistics
Matches: 226, Mismatches: 22, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
82 1 0.00
83 1 0.00
84 218 0.96
85 5 0.02
86 1 0.00
ACGTcount: A:0.23, C:0.35, G:0.10, T:0.31
Consensus pattern (83 bp):
ACTTCACATCGATTCTCAGATTCAGCAGCTTGACCGCATTGACCCCATTTGAGCCATCAATAGCC
TCAACTTCCCTCCCCTTT
Found at i:88714 original size:35 final size:35
Alignment explanation
Indices: 88675--88745 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
88665 TAAAATATAC
88675 AGTTTAATCTTATAAAACACAATCTCATCTATAAT
1 AGTTTAATCTTATAAAACACAATCTCATCTATAAT
88710 AGTTTAATCTTATAAAACACAATCTCATCTATAAT
1 AGTTTAATCTTATAAAACACAATCTCATCTATAAT
88745 A
1 A
88746 CAAGTGTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.37
Consensus pattern (35 bp):
AGTTTAATCTTATAAAACACAATCTCATCTATAAT
Found at i:89662 original size:16 final size:16
Alignment explanation
Indices: 89641--89671 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
89631 AAGCTACGTC
89641 CAATCTAAAATGTTAT
1 CAATCTAAAATGTTAT
89657 CAATCTAAAATGTTA
1 CAATCTAAAATGTTA
89672 CGAGTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (16 bp):
CAATCTAAAATGTTAT
Found at i:93385 original size:19 final size:19
Alignment explanation
Indices: 93361--93398 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
93351 ATGAAAAAAA
93361 TTAGATGACCAACTGATTC
1 TTAGATGACCAACTGATTC
93380 TTAGATGACCAACTGATTC
1 TTAGATGACCAACTGATTC
93399 CTTAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (19 bp):
TTAGATGACCAACTGATTC
Found at i:96545 original size:51 final size:50
Alignment explanation
Indices: 96482--96611 Score: 127
Period size: 51 Copynumber: 2.5 Consensus size: 50
96472 GTAGCAGTAA
* * * ** *
96482 AGCGCGCTCCCTGCCCCGTGCTATATGCTGATTTGGC-GCCACGTGGGGTAT
1 AGCGCGC-CCCTGCACCGCGCTATACGCTGACATGGCTGACACGT-GGGTAT
* *
96533 AGCGCGTCCCCTGTACCGCGCTATACGCTGACATGGCTTACACGTGGGTAT
1 AGCGCG-CCCCTGCACCGCGCTATACGCTGACATGGCTGACACGTGGGTAT
**
96584 AGCGCGCCCCCTGTTCCGCGCTATACGC
1 AGCGCG-CCCCTGCACCGCGCTATACGC
96612 CACGTAGGGG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
51 61 0.91
52 6 0.09
ACGTcount: A:0.14, C:0.35, G:0.28, T:0.23
Consensus pattern (50 bp):
AGCGCGCCCCTGCACCGCGCTATACGCTGACATGGCTGACACGTGGGTAT
Found at i:96616 original size:39 final size:40
Alignment explanation
Indices: 96573--96650 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
96563 ACATGGCTTA
* *
96573 CACGT-GGGTATAGCG-CGCCCCCTGTTCCGCGCTATACGC
1 CACGTAGGGTATAGCGTCG-CCCCTGCTCAGCGCTATACGC
96612 CACGTAGGGGTATAGCGTCGCCCCTGCTCAGCGCTATAC
1 CACGTA-GGGTATAGCGTCGCCCCTGCTCAGCGCTATAC
96651 CATGGTACGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 5 0.15
41 27 0.79
42 2 0.06
ACGTcount: A:0.15, C:0.36, G:0.28, T:0.21
Consensus pattern (40 bp):
CACGTAGGGTATAGCGTCGCCCCTGCTCAGCGCTATACGC
Found at i:96691 original size:17 final size:17
Alignment explanation
Indices: 96669--96708 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
96659 GAATTATATT
96669 TAGCGCGGACTTACATA
1 TAGCGCGGACTTACATA
*
96686 TAGCGCGGACTTATATA
1 TAGCGCGGACTTACATA
96703 TAGCGC
1 TAGCGC
96709 AGTGCAGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (17 bp):
TAGCGCGGACTTACATA
Found at i:99779 original size:23 final size:23
Alignment explanation
Indices: 99753--99819 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 23
99743 AAAGTCCAAC
*
99753 AAATTTAACAAAATAAAGTTATT
1 AAATTTAACAAAATAAAGTAATT
* *
99776 AAA-TGAGA-AATAATAAA-AAATT
1 AAATTTA-ACAA-AATAAAGTAATT
99798 ACAATTTAACAAAATAAAGTAA
1 A-AATTTAACAAAATAAAGTAA
99820 ATACAAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 11
0.67 0.10 0.22
Matches are distributed among these distances:
22 8 0.24
23 19 0.58
24 6 0.18
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (23 bp):
AAATTTAACAAAATAAAGTAATT
Found at i:111316 original size:15 final size:15
Alignment explanation
Indices: 111296--111326 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
111286 TTAATAATAA
*
111296 ACGAACATAACGAAC
1 ACGAACAAAACGAAC
111311 ACGAACAAAACGAAC
1 ACGAACAAAACGAAC
111326 A
1 A
111327 ATTTTTTTTT
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:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (15 bp):
ACGAACAAAACGAAC
Found at i:111437 original size:15 final size:15
Alignment explanation
Indices: 111395--111452 Score: 66
Period size: 14 Copynumber: 3.9 Consensus size: 15
111385 TAAATAAACG
*
111395 AACATAAACGACCAC
1 AACATAAACGAACAC
111410 GAACAT-AACGAACAC
1 -AACATAAACGAACAC
*
111425 AACATAAATGAACA-
1 AACATAAACGAACAC
*
111439 GACATAAACGAACA
1 AACATAAACGAACA
111453 AAACGTTGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 17 0.46
15 15 0.41
16 5 0.14
ACGTcount: A:0.57, C:0.24, G:0.10, T:0.09
Consensus pattern (15 bp):
AACATAAACGAACAC
Done.