Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002625.1 Hibiscus syriacus cultivar Beakdansim tig00005344_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: 63988
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1566 original size:20 final size:20
Alignment explanation
Indices: 1541--1592 Score: 72
Period size: 18 Copynumber: 2.7 Consensus size: 20
1531 GACCAACAAA
1541 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
**
1561 TTCGCAAC-C-CTTTCCAAT
1 TTCGCAACGCGAATTCCAAT
1579 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
1593 GCGAATATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 15 0.58
19 2 0.08
20 9 0.35
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:1672 original size:20 final size:20
Alignment explanation
Indices: 1622--1672 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1612 TGCGATTTTC
*
1622 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
1642 C-AATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
1661 CAAATTCGCAAC
1 CAAATTCGCAAC
1673 TGGATTTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.37, C:0.27, G:0.16, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:1704 original size:18 final size:19
Alignment explanation
Indices: 1660--1709 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
1650 AACGCGAAAG
*
1660 TCAAATTCGCAACTGGATT
1 TCAAATTCGCAACTGGAAT
*
1679 TGAAATTCGCAACT-GAAT
1 TCAAATTCGCAACTGGAAT
*
1697 TCAAATTCTCAAC
1 TCAAATTCGCAAC
1710 ACAAATGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (19 bp):
TCAAATTCGCAACTGGAAT
Found at i:4867 original size:18 final size:17
Alignment explanation
Indices: 4835--4869 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4825 CAAGCAAAGG
*
4835 AAATCAAATCGCAATCA
1 AAATCAAATCCCAATCA
4852 AAATCAAAATCCCAATCA
1 AAATC-AAATCCCAATCA
4870 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (17 bp):
AAATCAAATCCCAATCA
Found at i:6793 original size:21 final size:21
Alignment explanation
Indices: 6769--6824 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
6759 GGCTTCTTCG
6769 ATGATGATATAG-GCCTCTTGA
1 ATGATGATA-AGTGCCTCTTGA
* *
6790 ATGAT-AGGAGGTGCCTCTTGA
1 ATGATGA-TAAGTGCCTCTTGA
*
6811 ATGATGATAGGTGC
1 ATGATGATAAGTGC
6825 ATCGGGCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.30
Consensus pattern (21 bp):
ATGATGATAAGTGCCTCTTGA
Found at i:8434 original size:64 final size:64
Alignment explanation
Indices: 8346--8616 Score: 236
Period size: 64 Copynumber: 4.2 Consensus size: 64
8336 CAATGAAGGT
* * *
8346 ATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTCGATGTT-TCCTTATTAATGA
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATGTTATCATT-TTAATGA
8409 G
64 G
** ** * *
8410 ATGCATCGATGCA-TACCTTATGCATCGATGCACTACTTGCATTTTATGTTCT-ATTATTAATGG
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTTATCATT-TTAATGA
8473 G
64 G
* * * *
8474 ATGCATCGATGCACT-CCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATTTTAA-AAG
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTTATCATTTTAATGA-
8537 G
64 G
* * * * *
8538 ATGCATCGATGCATTAGC-TATGCATCGATGCATCAAAGGCATTCGATGTTCTTC-TTTTAAAG-
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATGTT-ATCATTTTAATGA
8600 G
64 G
8601 AATGCATCGATGCACT
1 -ATGCATCGATGCACT
8617 TATGAATGTG
Statistics
Matches: 171, Mismatches: 25, Indels: 22
0.78 0.11 0.10
Matches are distributed among these distances:
63 4 0.02
64 159 0.93
65 8 0.05
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTTATGCATCGATGCATAAATGCATTCGATGTTATCATTTTAATGAG
Found at i:8580 original size:128 final size:128
Alignment explanation
Indices: 8341--8616 Score: 301
Period size: 128 Copynumber: 2.2 Consensus size: 128
8331 TCTTTCAATG
* * * *
8341 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTCCTTATTAA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTTCATTATTAA
* *** **
8406 TGAGATGCATCGATGCATACCTTATGCATCGATGCACTACTTGCATTTTATGTTCTAT-TATTA
66 AGAGATGCATCGATGCATACCTTATGCATCGATGCACTAAAGGCATTCGATGTTCT-TCTATTA
* * * ** * *
8469 ATGGGATGCATCGATGCACTCCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATT-TTA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTT-TCATTATTA
* *
8533 AA-AGGATGCATCGATGCATTAGC-TATGCATCGATGCA-TCAAAGGCATTCGATGTTCTTCTTT
65 AAGA-GATGCATCGATGCA-TACCTTATGCATCGATGCACT-AAAGGCATTCGATGTTCTTCTAT
8595 TA
127 TA
8597 AAGGAATGCATCGATGCACT
1 AAGGAATGCATCGATGCACT
8617 TATGAATGTG
Statistics
Matches: 123, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
127 3 0.02
128 114 0.93
129 6 0.05
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (128 bp):
AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTTCATTATTAA
AGAGATGCATCGATGCATACCTTATGCATCGATGCACTAAAGGCATTCGATGTTCTTCTATTA
Found at i:12696 original size:64 final size:64
Alignment explanation
Indices: 12608--12878 Score: 209
Period size: 64 Copynumber: 4.2 Consensus size: 64
12598 CAATGAAGGT
* * *
12608 ATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTCGATGTT-TCCTTATTAATGA
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATGTTATCATT-TTAATGA
12671 G
64 G
** ** * *
12672 ATGCATCGATGCA-TACCTTATGCATCGATGCACTACTTGCATTTTATGTTCT-ATTATTAATGG
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTTATCATT-TTAATGA
12735 G
64 G
* * * * *
12736 ATGCATCGATGCACT-CCTTATGCATCGATACATTGATTGCATTCGATGTTATTATTTTAA-AAG
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTTATCATTTTAATGA-
12799 G
64 G
* * * * * * *
12800 ATGCATCGATGCATTAGC-TATGTATCGATGCATCAAAGGCATTTGATGTTCTTC-TTTTAAAG-
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATGTT-ATCATTTTAATGA
12862 G
64 G
12863 AATGCATCGATGCACT
1 -ATGCATCGATGCACT
12879 TATGAATGTG
Statistics
Matches: 167, Mismatches: 29, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
63 4 0.02
64 155 0.93
65 8 0.05
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTTATGCATCGATGCATAAATGCATTCGATGTTATCATTTTAATGAG
Found at i:12842 original size:128 final size:128
Alignment explanation
Indices: 12603--12878 Score: 292
Period size: 128 Copynumber: 2.2 Consensus size: 128
12593 TCTTTCAATG
* * * * *
12603 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTCCTTATTAA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATACATAAAATGCATTCGATGTTTCATTATTAA
* *** *
12668 TGAGATGCATCGATGCATACCTTATGCATCGATGCACTACTTGCATTTTATGTTCTAT-TATTA
66 AGAGATGCATCGATGCATACCTTATGCATCGATGCACTAAAGGCATTTGATGTTCT-TCTATTA
* * * ** * *
12731 ATGGGATGCATCGATGCACTCCTTATGCATCGATACATTGATTGCATTCGATGTTATTATT-TTA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATACATAAAATGCATTCGATGTT-TCATTATTA
* * *
12795 AA-AGGATGCATCGATGCATTAGC-TATGTATCGATGCA-TCAAAGGCATTTGATGTTCTTCTTT
65 AAGA-GATGCATCGATGCA-TACCTTATGCATCGATGCACT-AAAGGCATTTGATGTTCTTCTAT
12857 TA
127 TA
12859 AAGGAATGCATCGATGCACT
1 AAGGAATGCATCGATGCACT
12879 TATGAATGTG
Statistics
Matches: 122, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
127 3 0.02
128 113 0.93
129 6 0.05
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (128 bp):
AAGGAATGCATCGATGCACTACTTATGCATCGATACATAAAATGCATTCGATGTTTCATTATTAA
AGAGATGCATCGATGCATACCTTATGCATCGATGCACTAAAGGCATTTGATGTTCTTCTATTA
Found at i:13726 original size:12 final size:12
Alignment explanation
Indices: 13707--13748 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
13697 GGGCCGCTGA
13707 AAATAAATTAAT
1 AAATAAATTAAT
* *
13719 ATATAAATTAGT
1 AAATAAATTAAT
*
13731 AAATAAATAAAT
1 AAATAAATTAAT
13743 AAATAA
1 AAATAA
13749 TACCGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:14003 original size:13 final size:13
Alignment explanation
Indices: 13985--14011 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13975 CGTAAAGTAC
13985 CGACCTCATGACG
1 CGACCTCATGACG
13998 CGACCTCATGACG
1 CGACCTCATGACG
14011 C
1 C
14012 AAAGCACCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.41, G:0.22, T:0.15
Consensus pattern (13 bp):
CGACCTCATGACG
Found at i:15835 original size:13 final size:13
Alignment explanation
Indices: 15817--15842 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15807 GGGTTTCTTC
15817 AACAAAAAGACAA
1 AACAAAAAGACAA
15830 AACAAAAAGACAA
1 AACAAAAAGACAA
15843 CAAAGACAAA
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:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:16091 original size:22 final size:22
Alignment explanation
Indices: 16060--16110 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
16050 GATGGAGATA
16060 GACGGATTTCGTCAGAAATGGG
1 GACGGATTTCGTCAGAAATGGG
* * *
16082 GATGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCAGAAATGGG
16104 GACGGAT
1 GACGGAT
16111 GTCACCGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.41, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGTCAGAAATGGG
Found at i:16263 original size:20 final size:20
Alignment explanation
Indices: 16238--16322 Score: 134
Period size: 20 Copynumber: 4.2 Consensus size: 20
16228 GCGTAAAAAC
* *
16238 ATTTGACTTTCGCGTTGTGA
1 ATTTGACTATCGCGTTGCGA
16258 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
* *
16278 ATTTGACTTTCGCGTTGAGA
1 ATTTGACTATCGCGTTGCGA
16298 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
16318 ATTTG
1 ATTTG
16323 GAAAATCGCA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:16283 original size:40 final size:40
Alignment explanation
Indices: 16238--16322 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
16228 GCGTAAAAAC
*
16238 ATTTGACTTTCGCGTTGTGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGAGAATTTGACTATCGCGTTGCGA
16278 ATTTGACTTTCGCGTTGAGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGAGAATTTGACTATCGCGTTGCGA
16318 ATTTG
1 ATTTG
16323 GAAAATCGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (40 bp):
ATTTGACTTTCGCGTTGAGAATTTGACTATCGCGTTGCGA
Found at i:19002 original size:18 final size:18
Alignment explanation
Indices: 18932--18994 Score: 99
Period size: 18 Copynumber: 3.5 Consensus size: 18
18922 GCGTAGAATT
*
18932 TGTCCCGAATGACCACTG
1 TGTCCCGAATGACCACTA
*
18950 TGTCCCGAATGATCACTA
1 TGTCCCGAATGACCACTA
*
18968 TGCCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
18986 TGTCCCGAA
1 TGTCCCGAA
18995 AAACCACTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.22
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:25398 original size:22 final size:21
Alignment explanation
Indices: 25365--25412 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
25355 GGGATCGATC
25365 CCCCCTTTA-GGGAACCAATT
1 CCCCCTTTAGGGGAACCAATT
*
25385 CCCCCTTTGAAGGGGAACCGATT
1 CCCCCTTT--AGGGGAACCAATT
25408 CCCCC
1 CCCCC
25413 CCACAGGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
22 1 0.04
23 15 0.62
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
CCCCCTTTAGGGGAACCAATT
Found at i:28554 original size:149 final size:149
Alignment explanation
Indices: 28240--28543 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
28230 GGGTAGAGGG
28240 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
*
28305 ACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
28370 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
28389 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
28454 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
28519 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
28538 TCTACG
1 TCTACG
28544 TGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:28555 original size:23 final size:23
Alignment explanation
Indices: 28521--28566 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
28511 CATTATTATA
*
28521 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
28544 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
28567 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:32987 original size:29 final size:30
Alignment explanation
Indices: 32954--33034 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 30
32944 ACTAATGACT
*
32954 AAAATATAATTTTTG-AAAGTTT-GGTGATC
1 AAAATATAATTTTTGAAAAGTTTAGG-GACC
**
32983 AAAATA-AAACTTTGAAAAGTTTAGGGACC
1 AAAATATAATTTTTGAAAAGTTTAGGGACC
*
33012 AAAAGTATAATTTTTAAAAAGTT
1 AAAA-TATAATTTTTGAAAAGTT
33035 ATATATTTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 6 0.14
29 20 0.48
30 4 0.10
31 12 0.29
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.35
Consensus pattern (30 bp):
AAAATATAATTTTTGAAAAGTTTAGGGACC
Found at i:46743 original size:60 final size:60
Alignment explanation
Indices: 46653--46765 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
46643 GGCTGCGGGC
* * *
46653 GTTCCTCTTGAGGTTGTATCTGCCGAGGCTGTTGGTCTTGATGTCCAAGTGGCTGCAGAT
1 GTTCCTCTTGAGGTTGTATCTGCCGAGGCTGTTGATCTCGAGGTCCAAGTGGCTGCAGAT
* *
46713 GTTCCTCTTGAGGTTGTCTCT-CCTGCGGCTGTTGATCTCGAGGTCCAAGTGGC
1 GTTCCTCTTGAGGTTGTATCTGCC-GAGGCTGTTGATCTCGAGGTCCAAGTGGC
46766 AGGACACGCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.12, C:0.23, G:0.31, T:0.35
Consensus pattern (60 bp):
GTTCCTCTTGAGGTTGTATCTGCCGAGGCTGTTGATCTCGAGGTCCAAGTGGCTGCAGAT
Found at i:46779 original size:60 final size:60
Alignment explanation
Indices: 46655--46791 Score: 159
Period size: 60 Copynumber: 2.3 Consensus size: 60
46645 CTGCGGGCGT
* * * * * * * *
46655 TCCTCTTGAGGTTGTATCTGCCGAGGCTGTTGGTCTTGATGTCCAAGTGGCTGCAGATGT
1 TCCTCTTGAGGTTGTCTCTGCCGAGGCTGTTGATCTCGAGGTCCAAGTGGCAGCACACGC
* *
46715 TCCTCTTGAGGTTGTCTCT-CCTGCGGCTGTTGATCTCGAGGTCCAAGTGGCAGGACACGC
1 TCCTCTTGAGGTTGTCTCTGCC-GAGGCTGTTGATCTCGAGGTCCAAGTGGCAGCACACGC
*
46775 TCCTCTTGGGGTTGTCT
1 TCCTCTTGAGGTTGTCT
46792 TTGCTGTTGG
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 2 0.03
60 63 0.97
ACGTcount: A:0.12, C:0.24, G:0.31, T:0.34
Consensus pattern (60 bp):
TCCTCTTGAGGTTGTCTCTGCCGAGGCTGTTGATCTCGAGGTCCAAGTGGCAGCACACGC
Found at i:47810 original size:11 final size:11
Alignment explanation
Indices: 47794--47856 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
47784 AAAATTACAT
47794 TATTAAAAATA
1 TATTAAAAATA
47805 TATTAAAAATA
1 TATTAAAAATA
* * ***
47816 CACTATTGATA
1 TATTAAAAATA
47827 -ATTATAAAAT-
1 TATTA-AAAATA
47837 T-TTAAAAATA
1 TATTAAAAATA
47847 TATTAAAAAT
1 TATTAAAAAT
47857 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:47936 original size:28 final size:28
Alignment explanation
Indices: 47900--47968 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
47890 GTCCTTGCAG
47900 TAAACCCTAAATTCTAAATCT-TAAACCA
1 TAAACCCTAAATTCTAAA-CTATAAACCA
* * *
47928 TAAATCCTATACTCTAAACTATAAACCA
1 TAAACCCTAAATTCTAAACTATAAACCA
47956 TAAACCCTAAATT
1 TAAACCCTAAATT
47969 ATACTTGCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 2 0.06
28 32 0.94
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (28 bp):
TAAACCCTAAATTCTAAACTATAAACCA
Found at i:54090 original size:31 final size:31
Alignment explanation
Indices: 54052--54154 Score: 81
Period size: 31 Copynumber: 3.4 Consensus size: 31
54042 CCGTTAAAAT
54052 TTTAGGTACTAAAATGAAACAAAAAGTAAAC
1 TTTAGGTACTAAAATGAAACAAAAAGTAAAC
**** * *
54083 TTTAGGTA-TGGTTTTG-AA-AAAATG-AAAG
1 TTTAGGTACT-AAAATGAAACAAAAAGTAAAC
*
54111 TTTAGGTACTAAAATGAAAC-AAAAGTGATAC
1 TTTAGGTACTAAAATGAAACAAAAAGT-AAAC
*
54142 TTTAAGTACTAAA
1 TTTAGGTACTAAA
54155 CATGTAGGAT
Statistics
Matches: 52, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
28 13 0.25
29 12 0.23
30 3 0.06
31 24 0.46
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.29
Consensus pattern (31 bp):
TTTAGGTACTAAAATGAAACAAAAAGTAAAC
Done.