Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008382.1 Hibiscus syriacus cultivar Beakdansim tig00111143_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: 67150
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1006 original size:17 final size:16
Alignment explanation
Indices: 984--1018 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
974 CTTCTCAACA
984 TTGTAATTAATGATGTT
1 TTGTAATTAATGAT-TT
1001 TTGTAATTAATGATTT
1 TTGTAATTAATGATTT
1017 TT
1 TT
1019 CGTCTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (16 bp):
TTGTAATTAATGATTT
Found at i:2763 original size:2 final size:2
Alignment explanation
Indices: 2756--2789 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2746 TGACATTTTC
2756 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
2790 TTGTGTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6846 original size:27 final size:29
Alignment explanation
Indices: 6793--6846 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
6783 TAAATTTTAG
*
6793 TAATTATATTATAATAATTTTTGAAAAAA
1 TAATTATATTATAATAATTTCTGAAAAAA
6822 TAATTATTATT-T-ATAATTTCT-AAAA
1 TAATTA-TATTATAATAATTTCTGAAAA
6847 GTAAAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 4 0.17
28 8 0.35
29 7 0.30
30 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (29 bp):
TAATTATATTATAATAATTTCTGAAAAAA
Found at i:8992 original size:16 final size:16
Alignment explanation
Indices: 8971--9012 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
8961 ATTTTTTATC
8971 CGTTTATTTCTACATT
1 CGTTTATTTCTACATT
8987 CGTTTATTTCTACATT
1 CGTTTATTTCTACATT
9003 CGTTTATTTC
1 CGTTTATTTC
9013 ATATCTTCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.07, T:0.57
Consensus pattern (16 bp):
CGTTTATTTCTACATT
Found at i:19943 original size:30 final size:30
Alignment explanation
Indices: 19908--19989 Score: 164
Period size: 30 Copynumber: 2.7 Consensus size: 30
19898 TTTAATATTG
19908 TGTTCGTGTTCGTTTATTTATTTTTGAAAA
1 TGTTCGTGTTCGTTTATTTATTTTTGAAAA
19938 TGTTCGTGTTCGTTTATTTATTTTTGAAAA
1 TGTTCGTGTTCGTTTATTTATTTTTGAAAA
19968 TGTTCGTGTTCGTTTATTTATT
1 TGTTCGTGTTCGTTTATTTATT
19990 GTCCATGAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.59
Consensus pattern (30 bp):
TGTTCGTGTTCGTTTATTTATTTTTGAAAA
Found at i:20310 original size:29 final size:30
Alignment explanation
Indices: 20274--20347 Score: 114
Period size: 29 Copynumber: 2.5 Consensus size: 30
20264 GTAAACACCA
*
20274 TTTTTCAACACCAACACCTACCA-CCCCAT
1 TTTTTCAACACCAACACCCACCATCCCCAT
**
20303 TTTTTCAACACCAACACCCACCATCCCGTT
1 TTTTTCAACACCAACACCCACCATCCCCAT
20333 TTTTTCAACACCAAC
1 TTTTTCAACACCAAC
20348 TCCATCATCC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 22 0.54
30 19 0.46
ACGTcount: A:0.30, C:0.42, G:0.01, T:0.27
Consensus pattern (30 bp):
TTTTTCAACACCAACACCCACCATCCCCAT
Found at i:20356 original size:29 final size:29
Alignment explanation
Indices: 20274--20358 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
20264 GTAAACACCA
20274 TTTTTCAACACCAACACCTACCA-CCCCAT
1 TTTTTCAACACCAACACC-ACCATCCCCAT
**
20303 TTTTTCAACACCAACACCCACCATCCCGTT
1 TTTTTCAACACCAACA-CCACCATCCCCAT
* *
20333 TTTTTCAACACCAACTCCATCATCCC
1 TTTTTCAACACCAACACCACCATCCC
20359 TTGTTCCCTG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 29 0.58
30 21 0.42
ACGTcount: A:0.28, C:0.44, G:0.01, T:0.27
Consensus pattern (29 bp):
TTTTTCAACACCAACACCACCATCCCCAT
Found at i:23178 original size:16 final size:16
Alignment explanation
Indices: 23153--23203 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
23143 CACAAGAAAA
* *
23153 TTTCATCTTTTTATTT
1 TTTCAACTTTTAATTT
23169 TTTCAACTTTTAA-TT
1 TTTCAACTTTTAATTT
*
23184 TTTCATCTTTTCAATTT
1 TTTCAACTTTT-AATTT
23201 TTT
1 TTT
23204 TCACACTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 12 0.40
16 13 0.43
17 5 0.17
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTCAACTTTTAATTT
Found at i:23185 original size:15 final size:15
Alignment explanation
Indices: 23161--23202 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
23151 AATTTCATCT
*
23161 TTTTATTTTTTCAAC
1 TTTTAATTTTTCAAC
*
23176 TTTTAATTTTTCATC
1 TTTTAATTTTTCAAC
23191 TTTTCAATTTTT
1 TTTT-AATTTTT
23203 TTCACACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTAATTTTTCAAC
Found at i:23194 original size:23 final size:22
Alignment explanation
Indices: 23160--23202 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
23150 AAATTTCATC
*
23160 TTTTTATTTTTTCAACTTTTAA
1 TTTTTATCTTTTCAACTTTTAA
*
23182 TTTTTCATCTTTTCAATTTTT
1 TTTTT-ATCTTTTCAACTTTT
23203 TTCACACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTTATCTTTTCAACTTTTAA
Found at i:29111 original size:16 final size:17
Alignment explanation
Indices: 29090--29125 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
29080 TACTATTCAC
29090 GTGAATAG-AAAATTTT
1 GTGAATAGAAAAATTTT
29106 GTGAATAGTAAAAATTTT
1 GTGAATAG-AAAAATTTT
29124 GT
1 GT
29126 CGGTGATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (17 bp):
GTGAATAGAAAAATTTT
Found at i:29890 original size:15 final size:15
Alignment explanation
Indices: 29866--29897 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29856 TGGCAGATCC
*
29866 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
29881 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
29896 AA
1 AA
29898 TAAAGATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:38979 original size:21 final size:20
Alignment explanation
Indices: 38952--39012 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
38942 ATTTTGGTGC
38952 AGAGGGAATCGATTCGCCCCT
1 AGAGGGAATCGATTC-CCCCT
* *
38973 TGAGGGAACCGATTCCCCCT
1 AGAGGGAATCGATTCCCCCT
* *
38993 ACAGGGGAATCGATACCCCC
1 AGA-GGGAATCGATTCCCCC
39013 CTGGGGTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 6 0.18
21 27 0.82
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
AGAGGGAATCGATTCCCCCT
Found at i:44202 original size:13 final size:13
Alignment explanation
Indices: 44184--44209 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44174 AAACCTGGAA
44184 TTAATTACATATT
1 TTAATTACATATT
44197 TTAATTACATATT
1 TTAATTACATATT
44210 AATTAAGAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAATTACATATT
Found at i:44368 original size:10 final size:10
Alignment explanation
Indices: 44353--44383 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
44343 GGGATATACG
*
44353 TGGGTCGGAT
1 TGGGTCAGAT
44363 TGGGTCAGAT
1 TGGGTCAGAT
44373 TGGGTCAGAT
1 TGGGTCAGAT
44383 T
1 T
44384 TTTGATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.16, C:0.10, G:0.42, T:0.32
Consensus pattern (10 bp):
TGGGTCAGAT
Found at i:46468 original size:12 final size:12
Alignment explanation
Indices: 46445--46482 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
46435 ATGAATATTA
46445 AAATTAAA-TTT
1 AAATTAAATTTT
46456 AAATTAAATTTT
1 AAATTAAATTTT
46468 AAA-TATAATTTT
1 AAATTA-AATTTT
46480 AAA
1 AAA
46483 AAATAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AAATTAAATTTT
Found at i:63101 original size:48 final size:48
Alignment explanation
Indices: 63037--64794 Score: 631
Period size: 48 Copynumber: 37.1 Consensus size: 48
63027 TTATAAGTCT
* *
63037 CCACCACCAGTTCACTCCCCACCTCCACCATATGTCTACAAGTCTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * *
63085 CCACCGCCAGTCCACTCCCCACCTCCACCATATGTCTACAAGTCTCCT
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * *
63133 CCACCACCAGTCCACTCCCCACCTCCTCCTTATGTTTACAAGTCACCT
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* *** * * * * * *
63181 CCTCCACCAAAACATTCACCGCCACCTCC-T-T-ACTATAAGTCT---
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * *
63223 CCACCACCAGTTCACTCCCCA---CCACCATATGTCTACAAGTCACCT
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * * * *
63268 CCACCGCCAGTCCACTCCCCGCCTCCTCCTTATGTTTATAAGTCACCTCCT
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGT---CTCCA
** * * * * * *
63319 CCACCAAAATATTCA-TCGCCA-CTCCT-TACAT-T-TATAAGTCTCCA
1 CCACCACCA-GTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* *
63363 CCACCACCAGTTCACT-CCCACCTCCACCATATGTCTACAAGTCTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * * * *
63410 -C-CCGCCAATCCACTCCCCACCTCCT-CTTATGTTTACAAGTCACCT
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * *
63455 CCTCCACCAAG--CA-T--TCA-CTCCTCC---T-TATATAAGTCTCCA
1 CCACCACC-AGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
*
63494 CCACCACCAGTCCACTCCCCACC-CCACCATATGTCTACAAGTCTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * * * *
63541 CCACCGCCAGTCCACTCTCCACCTCCTCCTTATGTTTACAAGTCACCT
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* *** * * * * ** *
63589 CCTCCACCAAAGCATTCACCACCACCTCCTTACATCTATAAGTCTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
** * *
63637 CCACCACCAGTTTATTCCCCACCTCCACCATATGTCTACAAGTCTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * * * * *
63685 CCATCGCCAATCCACTCCCCA-CTCCTCCTTATGTTTACAAGTCACCT
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * * * * * *
63732 CCTCCA-AAG--CATTCACCGCCTTCTCC-T-T-ACTATAAGTCTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
*
63774 CCACCACCAGTCCACTCCCCACCTCCACCATATGTCTACAAGTCTCC-
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * * * *
63821 CCACCGCCAGTCCACTCTCTACCTCCTCCTTATGTTTACAAGTCACTCCT
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGT--CTCCA
* * * * * * * * * *
63871 CCACCA-AAG--CA-TTCACACCACCACCAGT-TTTTTCCCCA-CCTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCA-TATGTCT-ACAAGTCTCCA
* * * * * *
63915 CCATATGTCTACAAGTCTCCAC-CGCCAGTTACTCTCCACCTCCTCCTATGT-TACAAGTCACCT
1 CC--A---CCACCAG--TCCACTC-CC---CAC-CTCC---T-C-CATATGTCTACAAGTCTCCA
* * *** * * * * * ** *
63978 CCTCTACCAAAGCATTCACCGCCACCT-CTTACATCTATAAGTCTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * *
64025 CCACCA-CAGTTCATTCTCCACCTCCACCATATGTCTACAAG--TCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * *
64070 CCACC-GCAGTCCACT--CC-CCTCCT--ATA-GTTTACAAGTCACCT
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* *** * * * * * ** *
64111 CCTCCACCAAAGCATTCACCGCC-ACTCCTTACATCTATAAGTCTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * *
64158 CCACCACCAGTTCATTCCCCACCTCCACCATATGTCTACAAGTCTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * * *
64206 CCACCGCCAGTCCACTCTCCACCTCCT---TATGTTTACAAGTCACCT
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* *** * * * * ** *
64251 CCTCCACCAAAGCATTCACCACCACCTCCTTACATCTATAAGTCTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
** * *
64299 CCACCACCAGTTTATTCCCCACCTCCACCATATGTCTACAAGTCTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * * * * *
64347 CCACCGCCAGTCCA-TTCCCACCTCCTCCACCAAAG-CATTCACGCCACCTCCTTA
1 CCACCACCAGTCCACTCCCCACCTCCTCCA--TATGTC-TACAAG---TCTCC--A
* ** * * * * *
64401 CATTTATAAGTCTCCACACCG-CCAGTTCATCCCCACCTTCTCCATATATCTATAAGTCACCT
1 C---CACCA--C----CA--GTCCA---C-TCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * * * ** *
64463 CCACCACC-GTCCATTCACCACCCCCACCTTACATTTACAAGTCTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* *
64510 CCACCACC-GATTCACTCCCCACCTCCACCATATG-CTTACAAGTCTCCA
1 CCACCACCAG-TCCACTCCCCACCTCCTCCATATGTC-TACAAGTCTCCA
* * *
64558 CCACCACCGGTCCA-TCCCCACCTCCACCATATGTTTACAAG--TCC-
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * *
64602 CCACCACCAGT-CACTCCCCACCTCCACCATATGTCTACAAGTCACCT
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * *
64649 CCACCACCGGTTCA-TCACCACCTCCACCATATGTCTACAAG-CTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * * * * * *
64695 CCACCACCAATACACTCCCCACCTCCTCCCTATATCTATAAGTCACCT
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
* * *
64743 CCACCACCAGTACACTCTCCACCTCCTCC-TATATCTACAAGTCACTCCA
1 CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGT--CTCCA
64792 CCA
1 CCA
64795 TCACATCCTA
Statistics
Matches: 1242, Mismatches: 343, Indels: 249
0.68 0.19 0.14
Matches are distributed among these distances:
38 2 0.00
39 29 0.02
40 7 0.01
41 8 0.01
42 51 0.04
43 23 0.02
44 70 0.06
45 128 0.10
46 66 0.05
47 313 0.25
48 413 0.33
49 24 0.02
50 14 0.01
51 17 0.01
52 10 0.01
53 2 0.00
54 4 0.00
55 1 0.00
56 3 0.00
57 3 0.00
58 7 0.01
59 6 0.00
62 3 0.00
63 10 0.01
64 9 0.01
65 1 0.00
67 4 0.00
68 1 0.00
69 13 0.01
ACGTcount: A:0.24, C:0.45, G:0.07, T:0.24
Consensus pattern (48 bp):
CCACCACCAGTCCACTCCCCACCTCCTCCATATGTCTACAAGTCTCCA
Found at i:63139 original size:27 final size:27
Alignment explanation
Indices: 63055--63141 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
63045 AGTTCACTCC
*
63055 CCACCTCCACCATATGTCTACAAGTCT
1 CCACCACCACCATATGTCTACAAGTCT
* * *
63082 CCACCACCGCC--A-GTC--C-ACTCC
1 CCACCACCACCATATGTCTACAAGTCT
*
63103 CCACCTCCACCATATGTCTACAAGTCT
1 CCACCACCACCATATGTCTACAAGTCT
*
63130 CCTCCACCACCA
1 CCACCACCACCA
63142 GTCCACTCCC
Statistics
Matches: 44, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
21 12 0.27
22 1 0.02
23 1 0.02
24 6 0.14
25 1 0.02
26 1 0.02
27 22 0.50
ACGTcount: A:0.24, C:0.49, G:0.07, T:0.20
Consensus pattern (27 bp):
CCACCACCACCATATGTCTACAAGTCT
Found at i:63157 original size:24 final size:24
Alignment explanation
Indices: 63035--63158 Score: 63
Period size: 24 Copynumber: 5.2 Consensus size: 24
63025 ATTTATAAGT
*
63035 CTCCACCACCAGTTCACTCCCCAC
1 CTCCACCACCAGTCCACTCCCCAC
* * **** *
63059 CTCCACCA-TATGTCTACAAGTCTC
1 CTCCACCACCA-GTCCACTCCCCAC
* *
63083 CACCACCGCCAGTCCACTCCCCAC
1 CTCCACCACCAGTCCACTCCCCAC
* * **** *
63107 CTCCACCA-TATGTCTACAAGTCTC
1 CTCCACCACCA-GTCCACTCCCCAC
63131 CTCCACCACCAGTCCACTCCCCAC
1 CTCCACCACCAGTCCACTCCCCAC
63155 CTCC
1 CTCC
63159 TCCTTATGTT
Statistics
Matches: 63, Mismatches: 33, Indels: 8
0.61 0.32 0.08
Matches are distributed among these distances:
23 2 0.03
24 59 0.94
25 2 0.03
ACGTcount: A:0.22, C:0.52, G:0.06, T:0.19
Consensus pattern (24 bp):
CTCCACCACCAGTCCACTCCCCAC
Found at i:63907 original size:114 final size:110
Alignment explanation
Indices: 63789--63996 Score: 337
Period size: 114 Copynumber: 1.9 Consensus size: 110
63779 ACCAGTCCAC
*
63789 TCCCCACCTCCACCATATGTCTACAAGTCTCCCCACCGCCAGTCCACTCTCTACCTCCTCCTTAT
1 TCCCCACCTCCACCATATGTCTACAAGTCT--CCACCGCCAGT-CACTCTCCACCTCCTCC-TAT
63854 GTTTACAAGTCA-CTCCTCCACCAAAGCATTCACACCACCACCAGTTTTT
62 G-TTACAAGTCACCTCCTCCACCAAAGCATTCACACCACCACCAGTTTTT
*
63903 TCCCCACCTCCACCATATGTCTACAAGTCTCCACCGCCAGTTACTCTCCACCTCCTCCTATGTTA
1 TCCCCACCTCCACCATATGTCTACAAGTCTCCACCGCCAGTCACTCTCCACCTCCTCCTATGTTA
*
63968 CAAGTCACCTCCTCTACCAAAGCATTCAC
66 CAAGTCACCTCCTCCACCAAAGCATTCAC
63997 CGCCACCTCT
Statistics
Matches: 90, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
109 10 0.11
110 24 0.27
111 15 0.17
112 11 0.12
114 30 0.33
ACGTcount: A:0.23, C:0.44, G:0.07, T:0.26
Consensus pattern (110 bp):
TCCCCACCTCCACCATATGTCTACAAGTCTCCACCGCCAGTCACTCTCCACCTCCTCCTATGTTA
CAAGTCACCTCCTCCACCAAAGCATTCACACCACCACCAGTTTTT
Found at i:63943 original size:45 final size:42
Alignment explanation
Indices: 63888--63973 Score: 100
Period size: 44 Copynumber: 2.0 Consensus size: 42
63878 AGCATTCACA
**
63888 CCACCACCAGTTTTTTCCCCACCTCCACCATATGTCTACAAGTCT
1 CCACCACCAG-TTACTCCCCACCTCCACC-TATGT-TACAAGTCT
* * *
63933 CCACCGCCAGTTACTCTCCACCTCCTCCTATGTTACAAGTC
1 CCACCACCAGTTACTCCCCACCTCCACCTATGTTACAAGTC
63974 ACCTCCTCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 8 0.22
43 5 0.14
44 14 0.39
45 9 0.25
ACGTcount: A:0.21, C:0.43, G:0.08, T:0.28
Consensus pattern (42 bp):
CCACCACCAGTTACTCCCCACCTCCACCTATGTTACAAGTCT
Found at i:64324 original size:141 final size:141
Alignment explanation
Indices: 63886--64372 Score: 763
Period size: 141 Copynumber: 3.5 Consensus size: 141
63876 AAAGCATTCA
** *
63886 CACCACCACCAGTTTTTTCCCCACCTCCACCATATGTCTACAAGTCT---CCACCGCCAGT-TAC
1 CACCACCACCAGTTCATTCCCCACCTCCACCATATGTCTACAAGTCTCCACCACCGCCAGTCCAC
*
63947 TCTCCACCTCCTCCTATG-TTACAAGTCACCTCCTCTACCAAAGCATTCACCGCCACCT-CTTAC
66 TCTCCACCTCCT--TATGTTTACAAGTCACCTCCTCCACCAAAGCATTCACCGCCACCTCCTTAC
64010 ATCTATAAGTCTC
129 ATCTATAAGTCTC
*
64023 CACCACCA-CAGTTCATTCTCCACCTCCACCATATGTCTACAAG--TCCACCACCG-CAGTCCA-
1 CACCACCACCAGTTCATTCCCCACCTCCACCATATGTCTACAAGTCTCCACCACCGCCAGTCCAC
64083 -CTCC-CCTCC-TATAGTTTACAAGTCACCTCCTCCACCAAAGCATTCACCGCCA-CTCCTTACA
66 TCTCCACCTCCTTAT-GTTTACAAGTCACCTCCTCCACCAAAGCATTCACCGCCACCTCCTTACA
64144 TCTATAAGTCTC
130 TCTATAAGTCTC
64156 CACCACCACCAGTTCATTCCCCACCTCCACCATATGTCTACAAGTCTCCACCACCGCCAGTCCAC
1 CACCACCACCAGTTCATTCCCCACCTCCACCATATGTCTACAAGTCTCCACCACCGCCAGTCCAC
*
64221 TCTCCACCTCCTTATGTTTACAAGTCACCTCCTCCACCAAAGCATTCACCACCACCTCCTTACAT
66 TCTCCACCTCCTTATGTTTACAAGTCACCTCCTCCACCAAAGCATTCACCGCCACCTCCTTACAT
64286 CTATAAGTCTC
131 CTATAAGTCTC
* *
64297 CACCACCACCAGTTTATTCCCCACCTCCACCATATGTCTACAAGTCTCCACCACCGCCAGTCCAT
1 CACCACCACCAGTTCATTCCCCACCTCCACCATATGTCTACAAGTCTCCACCACCGCCAGTCCAC
64362 TC-CCACCTCCT
66 TCTCCACCTCCT
64373 CCACCAAAGC
Statistics
Matches: 325, Mismatches: 9, Indels: 29
0.90 0.02 0.08
Matches are distributed among these distances:
131 3 0.01
132 3 0.01
133 62 0.19
134 40 0.12
135 4 0.01
136 46 0.14
137 22 0.07
139 4 0.01
140 52 0.16
141 89 0.27
ACGTcount: A:0.24, C:0.44, G:0.07, T:0.25
Consensus pattern (141 bp):
CACCACCACCAGTTCATTCCCCACCTCCACCATATGTCTACAAGTCTCCACCACCGCCAGTCCAC
TCTCCACCTCCTTATGTTTACAAGTCACCTCCTCCACCAAAGCATTCACCGCCACCTCCTTACAT
CTATAAGTCTC
Found at i:64465 original size:119 final size:119
Alignment explanation
Indices: 64246--64484 Score: 342
Period size: 116 Copynumber: 2.0 Consensus size: 119
64236 GTTTACAAGT
64246 CACCTCCTCCACCAAAGCATTCACCACCACCTCCTTACATCTATAAGTCTCCACCACCACCAGTT
1 CACCTCCTCCACCAAAGCATTCACCACCACCTCCTTACATCTATAAGTCTCCACCACCACCAGTT
* *
64311 TATTCCCCACCTCCACCATATGTCTACAAGTCTCCACCACCGCCAGTCCATTCC
66 CATTCCCCACCTCCACCATATATCTACAAGTCTCCACCACCGCCAGTCCATTCC
* * *
64365 CACCTCCTCCACCAAAGCATTCA-CGCCACCTCCTTACATTTATAAGTCTCCA-CACCGCCAGTT
1 CACCTCCTCCACCAAAGCATTCACCACCACCTCCTTACATCTATAAGTCTCCACCACCACCAGTT
* * * * * *
64428 CA-TCCCCACCTTCTCCATATATCTATAAGTCACCTCCACCACC-GTCCATTCAC
66 CATTCCCCACCTCCACCATATATCTACAAGTCTCCACCACCGCCAGTCCATTC-C
64481 CACC
1 CACC
64485 CCCACCTTAC
Statistics
Matches: 108, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
115 8 0.07
116 39 0.36
117 11 0.10
118 27 0.25
119 23 0.21
ACGTcount: A:0.25, C:0.46, G:0.06, T:0.23
Consensus pattern (119 bp):
CACCTCCTCCACCAAAGCATTCACCACCACCTCCTTACATCTATAAGTCTCCACCACCACCAGTT
CATTCCCCACCTCCACCATATATCTACAAGTCTCCACCACCGCCAGTCCATTCC
Found at i:64470 original size:93 final size:95
Alignment explanation
Indices: 64365--64751 Score: 312
Period size: 91 Copynumber: 4.1 Consensus size: 95
64355 AGTCCATTCC
* * * * * *
64365 CACCTCCTCCACCAAAGCATTCA-CGCCACCTCCTTACATTTATAAGTCTCCA-CACCGCC-AGT
1 CACCTCCACCACC-AACCATTCACCACCACCACCTTACATTTACAAGTCTCCACCACCACCGA-T
* *
64427 TCA-TCCCCACCTTCTCCATATATCTATAAGT
64 TCACTCCCCACCTCCACCATATATCTATAAGT
** *
64458 CACCTCCACCACCGTCCATTCACCACCCCCACCTTACATTTACAAGTCTCCACCACCACCGATTC
1 CACCTCCACCACCAACCATTCACCACCACCACCTTACATTTACAAGTCTCCACCACCACCGATTC
* *
64523 ACTCCCCACCTCCACCATAT-GCTTACAAGT
66 ACTCCCCACCTCCACCATATATC-TATAAGT
* * ** * * * ** *
64553 CTCCACCACCACCGGTCCA-TCCCCACCTCCACCATATGTTTACAAG--TCC-CCACCACC-AGT
1 CACCTCCACCACC-AACCATTCACCACCACCACCTTACATTTACAAGTCTCCACCACCACCGATT
* *
64613 CACTCCCCACCTCCACCATATGTCTACAAGT
65 CACTCCCCACCTCCACCATATATCTATAAGT
*** * * ** * * *
64644 CACCTCCACCACCGGTTCA-TCACCACCTCCACCATATGTCTACAAG-CTCCACCACCACCAATA
1 CACCTCCACCACC-AACCATTCACCACCACCACCTTACATTTACAAGTCTCCACCACCACCGATT
* *
64707 CACTCCCCACCTCCTCCCTATATCTATAAGT
65 CACTCCCCACCTCCACCATATATCTATAAGT
64738 CACCTCCACCACCA
1 CACCTCCACCACCA
64752 GTACACTCTC
Statistics
Matches: 250, Mismatches: 34, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
91 71 0.28
92 18 0.07
93 48 0.19
94 52 0.21
95 56 0.22
96 5 0.02
ACGTcount: A:0.26, C:0.47, G:0.06, T:0.22
Consensus pattern (95 bp):
CACCTCCACCACCAACCATTCACCACCACCACCTTACATTTACAAGTCTCCACCACCACCGATTC
ACTCCCCACCTCCACCATATATCTATAAGT
Found at i:64505 original size:47 final size:47
Alignment explanation
Indices: 64428--64787 Score: 284
Period size: 47 Copynumber: 7.7 Consensus size: 47
64418 ACCGCCAGTT
* * * * * *
64428 CATCCCCACCTTCTCCATATATCTATAAGTCACCTCCACCACC-GTC
1 CATCCCCACCTCCACCATATGTTTACAAGTCACCACCACCACCGGTC
* * * ** * * *
64474 CATTCACCACCCCCACCTTACATTTACAAGTCTCCACCACCACCGATT
1 CA-TCCCCACCTCCACCATATGTTTACAAGTCACCACCACCACCGGTC
* *
64522 CACTCCCCACCTCCACCATATGCTTACAAGTCTCCACCACCACCGGTC
1 CA-TCCCCACCTCCACCATATGTTTACAAGTCACCACCACCACCGGTC
*
64570 CATCCCCACCTCCACCATATGTTTACAAGT--CC-CCACCACCAGT-
1 CATCCCCACCTCCACCATATGTTTACAAGTCACCACCACCACCGGTC
* * *
64613 CACTCCCCACCTCCACCATATGTCTACAAGTCACCTCCACCACCGGTT
1 CA-TCCCCACCTCCACCATATGTTTACAAGTCACCACCACCACCGGTC
* * * ** *
64661 CATCACCACCTCCACCATATGTCTACAAG-CTCCACCACCACCAATA
1 CATCCCCACCTCCACCATATGTTTACAAGTCACCACCACCACCGGTC
* * * * * * * *
64707 CACTCCCCACCTCCTCCCTATATCTATAAGTCACCTCCACCACCAGTA
1 CA-TCCCCACCTCCACCATATGTTTACAAGTCACCACCACCACCGGTC
* * * *
64755 CACTCTCCACCTCCTCC-TATATCTACAAGTCAC
1 CA-TCCCCACCTCCACCATATGTTTACAAGTCAC
64788 TCCACCATCA
Statistics
Matches: 264, Mismatches: 41, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
43 2 0.01
44 37 0.14
45 2 0.01
46 18 0.07
47 131 0.50
48 74 0.28
ACGTcount: A:0.26, C:0.47, G:0.06, T:0.22
Consensus pattern (47 bp):
CATCCCCACCTCCACCATATGTTTACAAGTCACCACCACCACCGGTC
Found at i:64565 original size:259 final size:256
Alignment explanation
Indices: 64106--64609 Score: 626
Period size: 259 Copynumber: 1.9 Consensus size: 256
64096 GTTTACAAGT
64106 CACCTCCTCCACCAAAGCATTCACCGCCACTCCTTACATCTATAAGTCTCCACCACCACCAGTTC
1 CACCTCCTCCACCAAAGCATTCACCGCCACTCCTTACATCTATAAGTCTCCACCACCACCAGTTC
* * * *
64171 ATTCCCCACCTCCACCATATGTCTACAAGTCTCCACCACCGCCAGTCCACTCTCCACCTCCTTAT
66 ATTCCCCACCTCCACCATATATCTACAAGTCTCCACCACCGCCAGTCCACTCACCACCACCTTAC
* * ** *
64236 GTTTACAAGTCACCTCCTCCACCAAAGCATTCACCACCACCTCCTTACATCTATAAGTCTCCACC
131 ATTTACAAGT--CCTCCACCACCAAAGCATTCACCACCACCTCCCCACATCTACAAGTCTCCACC
** *
64301 ACCACCAGTTTATTCCCCACCTCCACCATATGTCTACAAGTCTCCACCACCGCCAGTCCATTCC
194 ACCACCAGTCCA-TCCCCACCTCCACCATATGTCTACAAGTCCCCACCACCGCCAGTCCATTCC
* *
64365 CACCTCCTCCACCAAAGCATTCA-CGCCACCTCCTTACATTTATAAGTCTCCA-CACCGCCAGTT
1 CACCTCCTCCACCAAAGCATTCACCGCCA-CTCCTTACATCTATAAGTCTCCACCACCACCAGTT
* * * * *
64428 CA-TCCCCACCTTCTCCATATATCTATAAGTCACCTCCACCACCGTCCA-TTCAC-CACCCCCAC
65 CATTCCCCACCTCCACCATATATCTACAAGT---CTCCACCACCG-CCAGTCCACTCACCACCAC
** * *
64490 CTTACATTTACAAGT-CTCCACCACCACCG-ATTCACTCCCCACCTCCACCATATGCTTACAAGT
126 CTTACATTTACAAGTCCTCCACCACCAAAGCATTCAC-CACCACCTCC-CCACAT-C-TACAAGT
* *
64553 CTCCACCACCACCGGTCCATCCCCACCTCCACCATATGTTTACAAGTCCCCACCACC
187 CTCCACCACCACCAGTCCATCCCCACCTCCACCATATGTCTACAAGTCCCCACCACC
64610 AGTCACTCCC
Statistics
Matches: 211, Mismatches: 25, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
255 6 0.03
256 20 0.09
257 27 0.13
258 54 0.26
259 86 0.41
260 15 0.07
261 3 0.01
ACGTcount: A:0.25, C:0.46, G:0.06, T:0.23
Consensus pattern (256 bp):
CACCTCCTCCACCAAAGCATTCACCGCCACTCCTTACATCTATAAGTCTCCACCACCACCAGTTC
ATTCCCCACCTCCACCATATATCTACAAGTCTCCACCACCGCCAGTCCACTCACCACCACCTTAC
ATTTACAAGTCCTCCACCACCAAAGCATTCACCACCACCTCCCCACATCTACAAGTCTCCACCAC
CACCAGTCCATCCCCACCTCCACCATATGTCTACAAGTCCCCACCACCGCCAGTCCATTCC
Found at i:64655 original size:91 final size:93
Alignment explanation
Indices: 64413--64794 Score: 384
Period size: 94 Copynumber: 4.1 Consensus size: 93
64403 TTTATAAGTC
* * * *
64413 TCCA-CACCGCCAGTTCA-TCCCCACCTTCTCCATATATCTATAAGTCACCTCCACCACC-GTCC
1 TCCACCACCACCAG-TCACTCCCCACCTCCACCATATATCTACAAGTCACCTCCACCACCGGTCC
* * * *
64475 ATTCACCACCCCCACCTTACATTTACAAG
65 ACTCACCACCTCCACCATATATTTACAAG
* * * *
64504 TCTCCACCACCACCGATTCACTCCCCACCTCCACCATAT-GCTTACAAGTCTCCACCACCACCGG
1 --TCCACCACCACC-AGTCACTCCCCACCTCCACCATATATC-TACAAGTCACCTCCACCACCGG
* *
64568 TCCA-TCCCCACCTCCACCATATGTTTACAAG
62 TCCACTCACCACCTCCACCATATATTTACAAG
* *
64599 TCC-CCACCACCAGTCACTCCCCACCTCCACCATATGTCTACAAGTCACCTCCACCACCGGTTCA
1 TCCACCACCACCAGTCACTCCCCACCTCCACCATATATCTACAAGTCACCTCCACCACCGGTCCA
* *
64663 -TCACCACCTCCACCATATGTCTACAAG
66 CTCACCACCTCCACCATATATTTACAAG
* * * * * *
64690 CTCCACCACCACCAATACACTCCCCACCTCCTCCCTATATCTATAAGTCACCTCCACCACCAGTA
1 -TCCACCACCACCAGT-CACTCCCCACCTCCACCATATATCTACAAGTCACCTCCACCACCGGTC
* * *
64755 CACTCTCCACCTCCTCC-TATATCTACAAG
64 CACTCACCACCTCCACCATATATTTACAAG
*
64784 TCACTCCACCA
1 TC-CACCACCA
64795 TCACATCCTA
Statistics
Matches: 247, Mismatches: 31, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
91 71 0.29
92 12 0.05
93 19 0.08
94 72 0.29
95 68 0.28
96 5 0.02
ACGTcount: A:0.25, C:0.47, G:0.06, T:0.22
Consensus pattern (93 bp):
TCCACCACCACCAGTCACTCCCCACCTCCACCATATATCTACAAGTCACCTCCACCACCGGTCCA
CTCACCACCTCCACCATATATTTACAAG
Found at i:64793 original size:94 final size:92
Alignment explanation
Indices: 64430--64794 Score: 387
Period size: 91 Copynumber: 3.9 Consensus size: 92
64420 CGCCAGTTCA
* * * *
64430 TCCCCACCTTCTCCATATATCTATAAGTCACCTCCACCACC-GTCCATTCACCACCCCCACCTTA
1 TCCCCACCTCCTCCATATATCTACAAGTCACCTCCACCACCGGTCCA-TCACCACCTCCACCATA
* * *
64494 CATTTACAAGTCTCCACCACCACCGATTCAC
65 TATCTACAAG--TCCACCACCACC-AATCAC
* * * * *
64525 TCCCCACCTCCACCATAT-GCTTACAAGTCTCCACCACCACCGGTCCATCCCCACCTCCACCATA
1 TCCCCACCTCCTCCATATATC-TACAAGTCACCTCCACCACCGGTCCATCACCACCTCCACCATA
* * *
64589 TGTTTACAAGTCC-CCACCACCAGTCAC
65 TATCTACAAGTCCACCACCACCAATCAC
* * *
64616 TCCCCACCTCCACCATATGTCTACAAGTCACCTCCACCACCGGTTCATCACCACCTCCACCATAT
1 TCCCCACCTCCTCCATATATCTACAAGTCACCTCCACCACCGGTCCATCACCACCTCCACCATAT
*
64681 GTCTACAAGCTCCACCACCACCAATACAC
66 ATCTACAAG-TCCACCACCACCAAT-CAC
* * * * * *
64710 TCCCCACCTCCTCCCTATATCTATAAGTCACCTCCACCACCAGTACACTCTCCACCTCCTCC-TA
1 TCCCCACCTCCTCCATATATCTACAAGTCACCTCCACCACCGGTCCA-TCACCACCTCCACCATA
*
64774 TATCTACAAGTCACTCCACCA
65 TATCTACAAGTC-CACCACCA
64795 TCACATCCTA
Statistics
Matches: 233, Mismatches: 29, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
91 71 0.30
92 12 0.05
93 15 0.06
94 63 0.27
95 67 0.29
96 5 0.02
ACGTcount: A:0.25, C:0.47, G:0.05, T:0.22
Consensus pattern (92 bp):
TCCCCACCTCCTCCATATATCTACAAGTCACCTCCACCACCGGTCCATCACCACCTCCACCATAT
ATCTACAAGTCCACCACCACCAATCAC
Done.