Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002684.1 Hibiscus syriacus cultivar Beakdansim tig00005548_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: 101477
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:11482 original size:18 final size:18
Alignment explanation
Indices: 11455--11490 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11445 GAGATACCTC
*
11455 CTTCCCATCCCGCACATT
1 CTTCCAATCCCGCACATT
*
11473 CTTCCAATCCTGCACATT
1 CTTCCAATCCCGCACATT
11491 ATGATTCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.44, G:0.06, T:0.31
Consensus pattern (18 bp):
CTTCCAATCCCGCACATT
Found at i:13509 original size:26 final size:26
Alignment explanation
Indices: 13480--13529 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
13470 GCTGAGTTGC
*
13480 TTACAACATTAGAATCTTACTAGGAT
1 TTACAACATTAGAATCCTACTAGGAT
*
13506 TTACAACATTAGAGTCCTACTAGG
1 TTACAACATTAGAATCCTACTAGG
13530 TGTTTACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (26 bp):
TTACAACATTAGAATCCTACTAGGAT
Found at i:14699 original size:12 final size:12
Alignment explanation
Indices: 14682--14726 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
14672 GATACGATAT
14682 TGAGAGAGAGTA
1 TGAGAGAGAGTA
*
14694 TGAGAGAGAGTG
1 TGAGAGAGAGTA
*
14706 TTAGAGAGAG-A
1 TGAGAGAGAGTA
14717 -GAGAGAGAGT
1 TGAGAGAGAGT
14727 CGTAAAGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
10 8 0.29
12 20 0.71
ACGTcount: A:0.40, C:0.00, G:0.44, T:0.16
Consensus pattern (12 bp):
TGAGAGAGAGTA
Found at i:31595 original size:24 final size:24
Alignment explanation
Indices: 31568--31646 Score: 149
Period size: 24 Copynumber: 3.3 Consensus size: 24
31558 CTTAAAGATC
31568 ATAAATTTAATTGTTATAAATGAA
1 ATAAATTTAATTGTTATAAATGAA
31592 ATAAATTTAATTGTTATAAATGAA
1 ATAAATTTAATTGTTATAAATGAA
*
31616 GTAAATTTAATTGTTATAAATGAA
1 ATAAATTTAATTGTTATAAATGAA
31640 ATAAATT
1 ATAAATT
31647 ATGTTAGAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (24 bp):
ATAAATTTAATTGTTATAAATGAA
Found at i:46442 original size:16 final size:17
Alignment explanation
Indices: 46411--46443 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46401 GCTGATTCGA
*
46411 GAATTGATGCGTTGGTG
1 GAATTGAAGCGTTGGTG
46428 GAATTGAAG-GTTGGTG
1 GAATTGAAGCGTTGGTG
46444 ACAACTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.03, G:0.42, T:0.33
Consensus pattern (17 bp):
GAATTGAAGCGTTGGTG
Found at i:49600 original size:16 final size:15
Alignment explanation
Indices: 49574--49607 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
49564 GCTACAAGCT
49574 AACAAACTATTCTAG
1 AACAAACTATTCTAG
49589 AACAACACTATTCTAG
1 AACAA-ACTATTCTAG
49605 AAC
1 AAC
49608 TCACAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (15 bp):
AACAAACTATTCTAG
Found at i:55242 original size:16 final size:15
Alignment explanation
Indices: 55216--55249 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
55206 GCTACAAGCT
55216 AACAAACTATTCTAG
1 AACAAACTATTCTAG
55231 AACAACACTATTCTAG
1 AACAA-ACTATTCTAG
55247 AAC
1 AAC
55250 TCACAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (15 bp):
AACAAACTATTCTAG
Found at i:55654 original size:38 final size:36
Alignment explanation
Indices: 55609--55693 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 36
55599 TTGTCCTTAT
* *
55609 TATATATTTTTATAATA-TTACAAGTTGGAAAATATTTA
1 TATATATTTTTATAAAATTTA-AA-TT-CAAAATATTTA
* *
55647 TATATATTTTTTTAAAATTTAAATTCATAATATTTA
1 TATATATTTTTATAAAATTTAAATTCAAAATATTTA
55683 TATATATTTTT
1 TATATATTTTT
55694 TTACAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 20 0.48
37 2 0.05
38 17 0.40
39 3 0.07
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (36 bp):
TATATATTTTTATAAAATTTAAATTCAAAATATTTA
Found at i:56846 original size:14 final size:14
Alignment explanation
Indices: 56827--56855 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56817 ATCACGATCA
56827 TAAATGACGACTTG
1 TAAATGACGACTTG
56841 TAAATGACGACTTG
1 TAAATGACGACTTG
56855 T
1 T
56856 CGCCGTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (14 bp):
TAAATGACGACTTG
Found at i:56912 original size:13 final size:13
Alignment explanation
Indices: 56894--56918 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56884 TTCTATTATA
56894 TTGTTTGAATTTC
1 TTGTTTGAATTTC
56907 TTGTTTGAATTT
1 TTGTTTGAATTT
56919 GTACAACTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TTGTTTGAATTTC
Found at i:57740 original size:56 final size:56
Alignment explanation
Indices: 57680--57797 Score: 218
Period size: 56 Copynumber: 2.1 Consensus size: 56
57670 GCAAAAATTG
57680 AAACGTTGAGAATTAAAGTTTTCCAAAAAAATAGGAGTCAAAATAATTATTCAAAC
1 AAACGTTGAGAATTAAAGTTTTCCAAAAAAATAGGAGTCAAAATAATTATTCAAAC
**
57736 AAACGTTGAGGGTTAAAGTTTTCCAAAAAAATAGGAGTCAAAATAATTATTCAAAC
1 AAACGTTGAGAATTAAAGTTTTCCAAAAAAATAGGAGTCAAAATAATTATTCAAAC
57792 AAACGT
1 AAACGT
57798 CGAGGGTTAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.26
Consensus pattern (56 bp):
AAACGTTGAGAATTAAAGTTTTCCAAAAAAATAGGAGTCAAAATAATTATTCAAAC
Found at i:57803 original size:56 final size:56
Alignment explanation
Indices: 57692--57807 Score: 223
Period size: 56 Copynumber: 2.1 Consensus size: 56
57682 ACGTTGAGAA
*
57692 TTAAAGTTTTCCAAAAAAATAGGAGTCAAAATAATTATTCAAACAAACGTTGAGGG
1 TTAAAGTTTTCCAAAAAAATAGGAGTCAAAATAATTATTCAAACAAACGTCGAGGG
57748 TTAAAGTTTTCCAAAAAAATAGGAGTCAAAATAATTATTCAAACAAACGTCGAGGG
1 TTAAAGTTTTCCAAAAAAATAGGAGTCAAAATAATTATTCAAACAAACGTCGAGGG
57804 TTAA
1 TTAA
57808 TTTTGGTATT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (56 bp):
TTAAAGTTTTCCAAAAAAATAGGAGTCAAAATAATTATTCAAACAAACGTCGAGGG
Found at i:58270 original size:31 final size:31
Alignment explanation
Indices: 58225--58298 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
58215 AAATGACATC
*
58225 TTATATAAAGTTTAGAGGTTAAATTAATATT
1 TTATATAAATTTTAGAGGTTAAATTAATATT
* *
58256 TTATGTAAATTTTAGGGGTTAAATTAATATT
1 TTATATAAATTTTAGAGGTTAAATTAATATT
* *
58287 TTGTCTAAATTT
1 TTATATAAATTT
58299 CGAGATCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.49
Consensus pattern (31 bp):
TTATATAAATTTTAGAGGTTAAATTAATATT
Found at i:64748 original size:3 final size:3
Alignment explanation
Indices: 64740--64793 Score: 90
Period size: 3 Copynumber: 17.7 Consensus size: 3
64730 ATTTTATTTA
*
64740 AAT AAT AAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
64786 AAT AAT AA
1 AAT AAT AA
64794 ATTTTTTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:65698 original size:76 final size:76
Alignment explanation
Indices: 64958--65671 Score: 1257
Period size: 76 Copynumber: 9.4 Consensus size: 76
64948 GTCCTAAAAA
* * * *
64958 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCGCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
65023 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
65034 AAACATCATGCACTGTAGGACTTATAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
65099 AGGCTTTTTGG
66 AGGCTTTTTGG
65110 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
65175 AGGCTTTTTGA
66 AGGCTTTTTGG
*
65186 AAACATCGTGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
65251 AGGCTTTTTGG
66 AGGCTTTTTGG
65262 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
65327 AGGCTTTTTGG
66 AGGCTTTTTGG
*
65338 AAACATCATGCACTGTAGGACTTACAGATGGCCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
65403 AGGCTTTTTGG
66 AGGCTTTTTGG
* * **
65414 AAACATCATGCACTGCAAGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTAA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
65479 AGGCTTTTTGG
66 AGGCTTTTTGG
65490 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
65555 AGGCTTTTTGG
66 AGGCTTTTTGG
* * * *
65566 AAACATTATGCACTGCAGGACTTACAGATGACCCTAAGGCTTCGAAAAAATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
65631 AGGCTTTTTGG
66 AGGCTTTTTGG
*
65642 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
65672 TGGGAAATAG
Statistics
Matches: 611, Mismatches: 27, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 611 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:66366 original size:22 final size:22
Alignment explanation
Indices: 66341--66423 Score: 148
Period size: 22 Copynumber: 3.8 Consensus size: 22
66331 AAATCCAATA
*
66341 AATCTTTCATCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
*
66363 AATCTATCATCTTTAAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
66385 AATCTATCATCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
66407 AATCTATCATCTTTGAA
1 AATCTATCATCTTTGAA
66424 GAGTGTAGAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAGAG
Found at i:70894 original size:26 final size:26
Alignment explanation
Indices: 70830--70897 Score: 88
Period size: 25 Copynumber: 2.7 Consensus size: 26
70820 CTTGATTCAA
*
70830 TTTTCCTT-TTTTTCTTTTTCTTTTT
1 TTTTCCTTCTTTTTCTTTTTCTTCTT
*
70855 TTTTCCCT-TTTTTCTTTTT-TTCTT
1 TTTTCCTTCTTTTTCTTTTTCTTCTT
70879 TTTTCCTTCTTCTTTCTTT
1 TTTTCCTTCTT-TTTCTTT
70898 ACTGGATGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 11 0.29
25 20 0.53
26 7 0.18
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTTCCTTCTTTTTCTTTTTCTTCTT
Found at i:73431 original size:22 final size:22
Alignment explanation
Indices: 73406--73454 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
73396 AAAAAAATGT
*
73406 AATGT-AAATGTAAAAATGCATA
1 AATGTCAAATATAAAAATGCA-A
*
73428 AATGTCAAATATAAGAATGCAA
1 AATGTCAAATATAAAAATGCAA
73450 AATGT
1 AATGT
73455 GCAATTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.27
Consensus pattern (22 bp):
AATGTCAAATATAAAAATGCAA
Found at i:75889 original size:9 final size:7
Alignment explanation
Indices: 75860--75884 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
75850 AAATAAAGTA
75860 AAAATAT
1 AAAATAT
75867 AAAATAT
1 AAAATAT
75874 AAAATAT
1 AAAATAT
75881 AAAA
1 AAAA
75885 AATATTATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATAT
Found at i:78127 original size:3 final size:3
Alignment explanation
Indices: 78119--78160 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
78109 ATTTTATTTA
78119 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
78161 TTTAATGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:79695 original size:60 final size:60
Alignment explanation
Indices: 79615--79753 Score: 183
Period size: 60 Copynumber: 2.3 Consensus size: 60
79605 ATAAATAGTT
* * *
79615 GAGATCATTTTGTAACTTTTAATAGTC-GAGTGACTCAACAAAATAATATCCTATAGTCGA
1 GAGACCATTTTATAATTTTTAATAGTCAGA-TGACTCAACAAAATAATATCCTATAGTCGA
* * * *
79675 GAGACTATTTTATAATTTTTAATAGTCAGATGACTCAATAAAATAGTATCCTATATTCGA
1 GAGACCATTTTATAATTTTTAATAGTCAGATGACTCAACAAAATAATATCCTATAGTCGA
79735 GAGACCATTTGTAT-ATTTT
1 GAGACCATTT-TATAATTTT
79754 ACCAATTAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
60 64 0.93
61 5 0.07
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (60 bp):
GAGACCATTTTATAATTTTTAATAGTCAGATGACTCAACAAAATAATATCCTATAGTCGA
Found at i:88657 original size:29 final size:29
Alignment explanation
Indices: 88624--88690 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
88614 TTTGTAACCG
88624 TTAAATTTTCAAATGTTAT-A-AAATAATAA
1 TTAAATTTTCAAATG--ATCACAAATAATAA
*
88653 TTAAATTTATCGAATGATCACAAATAATAA
1 TTAAATTT-TCAAATGATCACAAATAATAA
88683 -TAAATTTT
1 TTAAATTTT
88691 GATAAACTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
28 3 0.09
29 16 0.47
30 15 0.44
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (29 bp):
TTAAATTTTCAAATGATCACAAATAATAA
Found at i:90322 original size:21 final size:21
Alignment explanation
Indices: 90298--90660 Score: 145
Period size: 21 Copynumber: 16.6 Consensus size: 21
90288 CTGTCGCCTC
90298 CCACCACCACCAGTCTACTCT
1 CCACCACCACCAGTCTACTCT
* * * * *
90319 CCACCTCCTCCAGTATATTCA
1 CCACCACCACCAGTCTACTCT
*
90340 CCACCTA-CACCAGTCTACTCA
1 CCACC-ACCACCAGTCTACTCT
90361 CCACCACCACCTCCAGT-T-CTCT
1 CCACCACCA---CCAGTCTACTCT
* * *
90383 CAGCCCCTCCACCCGTCTACTCT
1 C--CACCACCACCAGTCTACTCT
* * *
90406 CCACCACCACCACCTCCAGTTCT
1 CCACCACCACCA-GTCTA-CTCT
* * *
90429 ATCACCTCCACCAG-CT-GTCT
1 -CCACCACCACCAGTCTACTCT
90449 ACTCACCACCACCAGTCTACTCT
1 -C-CACCACCACCAGTCTACTCT
*
90472 CCACCACCACAACCTCCAGTTCTA-TCA
1 CCACCA-C-C-A---CCAG-TCTACTCT
* * *
90499 CCTCCACTACCTGTCTA--CT
1 CCACCACCACCAGTCTACTCT
90518 -CACCACCACCAGTCTACTCT
1 CCACCACCACCAGTCTACTCT
* * * * *
90538 CCACCTCCTCCAGTATATTCA
1 CCACCACCACCAGTCTACTCT
*
90559 CCACCTA-CACCAGTCTACTCA
1 CCACC-ACCACCAGTCTACTCT
* *
90580 CCTCCACCCCCAGTCTACTCT
1 CCACCACCACCAGTCTACTCT
*
90601 CCACCACCGCCACCTCCAGTTCT-CTCA
1 CCACCA---CCA---CCAG-TCTACTCT
* *
90628 CCCCCACCACCCGTCTACTCT
1 CCACCACCACCAGTCTACTCT
90649 CCACCACCACCA
1 CCACCACCACCA
90661 CCTCCAGTTC
Statistics
Matches: 252, Mismatches: 55, Indels: 70
0.67 0.15 0.19
Matches are distributed among these distances:
18 13 0.05
19 1 0.00
20 15 0.06
21 138 0.55
22 13 0.05
23 13 0.05
24 28 0.11
26 1 0.00
27 23 0.09
28 7 0.03
ACGTcount: A:0.22, C:0.52, G:0.05, T:0.21
Consensus pattern (21 bp):
CCACCACCACCAGTCTACTCT
Found at i:90371 original size:48 final size:46
Alignment explanation
Indices: 90319--90462 Score: 134
Period size: 48 Copynumber: 3.1 Consensus size: 46
90309 AGTCTACTCT
*
90319 CCACCTCCTCCAG-TATATTCACCACCTACACCAGTCTACTCACCACCA
1 CCACC-CCTCCAGTTCTA-TCACC-CCTACACCAGTCTACTCACCACCA
* * * *
90367 CCA--CCTCCAGTTCTCTCAGCCCCTCCACCCGTCTACTCTCCACCA
1 CCACCCCTCCAGTTCTATCA-CCCCTACACCAGTCTACTCACCACCA
* *
90412 CCACCACCTCCAGTTCTATCACCTCC-ACCAGCTGTCTACTCACCACCA
1 CCACC-CCTCCAGTTCTATCACC-CCTA-CACCAGTCTACTCACCACCA
90460 CCA
1 CCA
90463 GTCTACTCTC
Statistics
Matches: 79, Mismatches: 10, Indels: 14
0.77 0.10 0.14
Matches are distributed among these distances:
45 34 0.43
46 4 0.05
47 2 0.03
48 39 0.49
ACGTcount: A:0.22, C:0.51, G:0.06, T:0.21
Consensus pattern (46 bp):
CCACCCCTCCAGTTCTATCACCCCTACACCAGTCTACTCACCACCA
Found at i:90374 original size:45 final size:44
Alignment explanation
Indices: 90298--90587 Score: 123
Period size: 45 Copynumber: 6.6 Consensus size: 44
90288 CTGTCGCCTC
* *
90298 CCACCACCACCAGTCTACT---CTCCACCTCCTCCAGTATATTCA
1 CCACCA-CACCAGTCTACTCACCACCACCACCTCCAGTATATTCA
*
90340 CCACCTACACCAGTCTACTCACCACCACCACCTCCAGT-TCTCTCA
1 CCACC-ACACCAGTCTACTCACCACCACCACCTCCAGTATAT-TCA
* * *
90385 GCC-CCTCCACCCGTCTACTCTCCACCACCACCACCTCCAGT-TCTATCA
1 -CCACC-ACACCAGTCTA--CT-CACCACCACCACCTCCAGTATAT-TCA
* * * * * *
90433 CCTCCACCAGCTGTCTACTCACCACCACCA-GT-C--TACTCTCCA
1 CCACCA-CACCAGTCTACTCACCACCACCACCTCCAGTA-TATTCA
* * * *
90475 CCACCACAACCTCCAGTTCTA-TCACCTCCACTACCT---GTCTACTCA
1 CCACCAC-A---CCAG-TCTACTCACCACCACCACCTCCAGTATATTCA
* *
90520 CCA-C-CACCAGTCTACT---CTCCACCTCCTCCAGTATATTCA
1 CCACCACACCAGTCTACTCACCACCACCACCTCCAGTATATTCA
*
90559 CCACCTACACCAGTCTACTCACCTCCACC
1 CCACC-ACACCAGTCTACTCACCACCACC
90588 CCCAGTCTAC
Statistics
Matches: 193, Mismatches: 25, Indels: 57
0.70 0.09 0.21
Matches are distributed among these distances:
36 9 0.05
38 4 0.02
39 15 0.08
40 1 0.01
41 2 0.01
42 38 0.20
43 6 0.03
44 4 0.02
45 65 0.34
46 10 0.05
47 4 0.02
48 35 0.18
ACGTcount: A:0.23, C:0.50, G:0.05, T:0.22
Consensus pattern (44 bp):
CCACCACACCAGTCTACTCACCACCACCACCTCCAGTATATTCA
Found at i:90442 original size:18 final size:20
Alignment explanation
Indices: 90413--90480 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 20
90403 TCTCCACCAC
*
90413 CACCACCTCCAGT-TCTA-T
1 CACCACCACCAGTGTCTACT
*
90431 CACCTCCACCAGCTGTCTACT
1 CACCACCACCAG-TGTCTACT
90452 CACCACCACCA--GTCTACT
1 CACCACCACCAGTGTCTACT
*
90470 CTCCACCACCA
1 CACCACCACCA
90481 CAACCTCCAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
18 27 0.63
19 1 0.02
20 4 0.09
21 11 0.26
ACGTcount: A:0.24, C:0.50, G:0.06, T:0.21
Consensus pattern (20 bp):
CACCACCACCAGTGTCTACT
Found at i:90467 original size:66 final size:66
Alignment explanation
Indices: 90391--90657 Score: 312
Period size: 66 Copynumber: 4.1 Consensus size: 66
90381 CTCAGCCCCT
* *
90391 CCACCCGTCTACTCTCCACCACCACCACCTCCAGTTCTATCACCTCCACCAGCTGTCTACTCACC
1 CCACCAGTCTACTCTCCACCACCACCACCTCCAGTTCTATCACCTCCACCACCTGTCTACTCACC
90456 A
66 A
* *
90457 CCACCAGTCTACTCTCCACCACCACAACCTCCAGTTCTATCACCTCCACTACCTGTCTACTCACC
1 CCACCAGTCTACTCTCCACCACCACCACCTCCAGTTCTATCACCTCCACCACCTGTCTACTCACC
90522 A
66 A
* * * ** * *
90523 CCACCAGTCTACTCTCCACCTCCTCCA-GTATA-TTC-ACCACCT--A-CACCAGTCTACTCACC
1 CCACCAGTCTACTCTCCACCACCACCACCTCCAGTTCTATCACCTCCACCACCTGTCTACTCA--
90582 TCCA
64 -CCA
* * * * * *
90586 CCCCCAGTCTACTCTCCACCACCGCCACCTCCAGTTCTCTCACCCCCACCACCCGTCTACTCTCC
1 CCACCAGTCTACTCTCCACCACCACCACCTCCAGTTCTATCACCTCCACCACCTGTCTACTCACC
90651 A
66 A
90652 CCACCA
1 CCACCA
90658 CCACCTCCAG
Statistics
Matches: 167, Mismatches: 25, Indels: 18
0.80 0.12 0.09
Matches are distributed among these distances:
60 12 0.07
61 1 0.01
63 33 0.20
64 5 0.03
65 5 0.03
66 98 0.59
68 1 0.01
69 12 0.07
ACGTcount: A:0.22, C:0.52, G:0.05, T:0.21
Consensus pattern (66 bp):
CCACCAGTCTACTCTCCACCACCACCACCTCCAGTTCTATCACCTCCACCACCTGTCTACTCACC
A
Found at i:90586 original size:24 final size:21
Alignment explanation
Indices: 90298--90812 Score: 120
Period size: 21 Copynumber: 23.2 Consensus size: 21
90288 CTGTCGCCTC
* *
90298 CCACCACCACCAGTCTACTCT
1 CCACCACCCCCAGTCTACTCA
* * * *
90319 CCACCTCCTCCAGTATATTCA
1 CCACCACCCCCAGTCTACTCA
*
90340 CCACCTA-CACCAGTCTACTCA
1 CCACC-ACCCCCAGTCTACTCA
90361 CCACCACCACCTCCAGTTCT-CTCA
1 CCACCA-C-CC-CCAG-TCTACTCA
*
90385 GCC-CCTCCACCC-GTCTACTCTCCA
1 -CCACCACC-CCCAGTCTA--CT-CA
90409 CCACCACCACCTCCAGTTCTA-TCA
1 CCACCA-C-CC-CCAG-TCTACTCA
* ** *
90433 CCTCCACCAGCTGTCTACTCA
1 CCACCACCCCCAGTCTACTCA
90454 CCACCA---CCAGTCTACTCTCCA
1 CCACCACCCCCAGTCTA--CT-CA
90475 CCACCACAACCTCCAGTTCTA-TCA
1 CCACCAC--CC-CCAG-TCTACTCA
* ** *
90499 CCTCCACTACCTGTCTACTCA
1 CCACCACCCCCAGTCTACTCA
*
90520 CCACCA---CCAGTCTACTCT
1 CCACCACCCCCAGTCTACTCA
* * * *
90538 CCACCTCCTCCAGTATATTCA
1 CCACCACCCCCAGTCTACTCA
*
90559 CCACCTA-CACCAGTCTACTCA
1 CCACC-ACCCCCAGTCTACTCA
*
90580 CCTCCACCCCCAGTCTACTCTCCA
1 CCACCACCCCCAGTCTA--CT-CA
*
90604 CCACCGCCACCTCCAGTTCT-CTCA
1 CCA---CCACCCCCAG-TCTACTCA
*
90628 CCCCCACCACCC-GTCTACTCTCCA
1 CCACCACC-CCCAGTCTA--CT-CA
90652 CCACCACCACCTCCAGTTCTA-TCA
1 CCACCA-C-CC-CCAG-TCTACTCA
* * *
90676 CCTCCACCACCTGTCTACTCA
1 CCACCACCCCCAGTCTACTCA
90697 CCACAACCACCCCCTCCAGTTCTA-TCA
1 -C-C-ACCA--CCC-CCAG-TCTACTCA
* * *
90724 CCTCCACCACCC-GTCCATTC-
1 CCACCACC-CCCAGTCTACTCA
* *
90744 TCAGCCACCCCCAGT-TGTCTCA
1 CCA-CCACCCCCAGTCT-ACTCA
*
90766 CCACCACCTCCAGTTCT-CTCA
1 CCACCACCCCCAG-TCTACTCA
*
90787 CCACCACCACCC-GTCCACTCA
1 CCACCACC-CCCAGTCTACTCA
90808 CCACC
1 CCACC
90813 TCCACCTAAA
Statistics
Matches: 366, Mismatches: 58, Indels: 140
0.65 0.10 0.25
Matches are distributed among these distances:
18 21 0.06
20 31 0.08
21 160 0.44
22 17 0.05
23 16 0.04
24 57 0.16
25 15 0.04
26 9 0.02
27 21 0.06
28 19 0.05
ACGTcount: A:0.22, C:0.52, G:0.05, T:0.21
Consensus pattern (21 bp):
CCACCACCCCCAGTCTACTCA
Found at i:90608 original size:27 final size:27
Alignment explanation
Indices: 90578--90687 Score: 90
Period size: 27 Copynumber: 4.2 Consensus size: 27
90568 CCAGTCTACT
90578 CACCTCCACCCCCAGTCTACTCTCCAC
1 CACCTCCACCCCCAGTCTACTCTCCAC
* *
90605 CACCGCCACCTCCAGT-T-CTCT-CA-
1 CACCTCCACCCCCAGTCTACTCTCCAC
90628 C-CC-CCACCACCC-GTCTACTCTCCAC
1 CACCTCCACC-CCCAGTCTACTCTCCAC
* * *
90653 CACCACCACCTCCAGTTCTATCACCTCCAC
1 CACCTCCACCCCCAG-TCTA-C-TCTCCAC
90683 CACCT
1 CACCT
90688 GTCTACTCAC
Statistics
Matches: 66, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
21 7 0.11
22 5 0.08
23 5 0.08
24 4 0.06
25 5 0.08
26 5 0.08
27 20 0.30
28 4 0.06
29 1 0.02
30 10 0.15
ACGTcount: A:0.19, C:0.57, G:0.05, T:0.19
Consensus pattern (27 bp):
CACCTCCACCCCCAGTCTACTCTCCAC
Found at i:90635 original size:48 final size:47
Alignment explanation
Indices: 90568--90738 Score: 227
Period size: 48 Copynumber: 3.6 Consensus size: 47
90558 ACCACCTACA
*
90568 CCAG-TCTACTCACCTCCACCCCCAGTCTACTCTCCACCACCGCCACCT
1 CCAGTTCTA-TCACCTCCACCCCC-GTCTACTCTCCACCACCACCACCT
* *
90616 CCAGTTCTCTCACCCCCACCACCCGTCTACTCTCCACCACCACCACCT
1 CCAGTTCTATCACCTCCACC-CCCGTCTACTCTCCACCACCACCACCT
* * * *
90664 CCAGTTCTATCACCTCCACCACCTGTCTACTCACCACAACCACCCCCT
1 CCAGTTCTATCACCTCCACC-CCCGTCTACTCTCCACCACCACCACCT
90712 CCAGTTCTATCACCTCCACCACCCGTC
1 CCAGTTCTATCACCTCCACC-CCCGTC
90739 CATTCTCAGC
Statistics
Matches: 111, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
48 105 0.95
49 6 0.05
ACGTcount: A:0.20, C:0.55, G:0.05, T:0.20
Consensus pattern (47 bp):
CCAGTTCTATCACCTCCACCCCCGTCTACTCTCCACCACCACCACCT
Found at i:90752 original size:96 final size:96
Alignment explanation
Indices: 90568--90745 Score: 250
Period size: 96 Copynumber: 1.9 Consensus size: 96
90558 ACCACCTACA
* * * * *
90568 CCAGTCTACTCACCTCCACCCCCAGTCTACTCTCCACCACCGCCACCTCCAGTTCTCTCACCCCC
1 CCAGTCTACTCACCTCCACCACCAGTCTACTCACCACAACCACCACCTCCAGTTCTATCACCCCC
*
90633 ACCACCCGTCTACTCTCCACCACCACCACCT
66 ACCACCCGTCCACTCTCCACCACCACCACCT
* * *
90664 CCAGTTCTA-TCACCTCCACCACCTGTCTACTCACCACAACCACCCCCTCCAGTTCTATCACCTC
1 CCAG-TCTACTCACCTCCACCACCAGTCTACTCACCACAACCACCACCTCCAGTTCTATCACCCC
*
90728 CACCACCCGTCCATTCTC
65 CACCACCCGTCCACTCTC
90746 AGCCACCCCC
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
96 67 0.94
97 4 0.06
ACGTcount: A:0.20, C:0.54, G:0.05, T:0.21
Consensus pattern (96 bp):
CCAGTCTACTCACCTCCACCACCAGTCTACTCACCACAACCACCACCTCCAGTTCTATCACCCCC
ACCACCCGTCCACTCTCCACCACCACCACCT
Found at i:90807 original size:21 final size:21
Alignment explanation
Indices: 90762--90818 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
90752 CCCCAGTTGT
* * *
90762 CTCACCACCACCTCCAGTTCT
1 CTCACCACCACCACCAGTCCA
*
90783 CTCACCACCACCACCCGTCCA
1 CTCACCACCACCACCAGTCCA
*
90804 CTCACCACCTCCACC
1 CTCACCACCACCACC
90819 TAAACCGGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.60, G:0.04, T:0.16
Consensus pattern (21 bp):
CTCACCACCACCACCAGTCCA
Found at i:91167 original size:31 final size:31
Alignment explanation
Indices: 91132--91199 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
91122 TTGTCAAATT
* * * *
91132 ACTCATTCGTACTAATGAATTATATTTTACA
1 ACTCATTCATACTAATGAATCACACTTTACA
*
91163 ACTCATTCATACTAATTAATCACACTTTACA
1 ACTCATTCATACTAATGAATCACACTTTACA
91194 ACTCAT
1 ACTCAT
91200 AAATGACATC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (31 bp):
ACTCATTCATACTAATGAATCACACTTTACA
Found at i:98945 original size:32 final size:33
Alignment explanation
Indices: 98867--98936 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 33
98857 AAATGTAATA
*
98867 AACAAAATTAAGCAAAATAAATTAACAAAAAGTCC
1 AACAAATTTAA-C-AAATAAATTAACAAAAAGTCC
98902 AACAAATTTAACAAATAAATTAA-AATAAA-TCC
1 AACAAATTTAACAAATAAATTAACAA-AAAGTCC
98934 AAC
1 AAC
98937 CATATTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
32 8 0.24
33 14 0.42
34 1 0.03
35 10 0.30
ACGTcount: A:0.63, C:0.14, G:0.03, T:0.20
Consensus pattern (33 bp):
AACAAATTTAACAAATAAATTAACAAAAAGTCC
Found at i:98992 original size:13 final size:13
Alignment explanation
Indices: 98974--99016 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
98964 ATGATAAATA
*
98974 AAAAAATTACAAT
1 AAAAAACTACAAT
* *
98987 AAAAAAGTCCAAT
1 AAAAAACTACAAT
*
99000 AAACAACTACAAT
1 AAAAAACTACAAT
99013 AAAA
1 AAAA
99017 GTACAAATAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.67, C:0.14, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:99156 original size:15 final size:15
Alignment explanation
Indices: 99136--99167 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
99126 TTTTGACTCC
99136 TCGCTGTCATCGTCG
1 TCGCTGTCATCGTCG
*
99151 TCGCTGTCGTCGTCG
1 TCGCTGTCATCGTCG
99166 TC
1 TC
99168 CTGAGCAGCT
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:0.03, C:0.34, G:0.28, T:0.34
Consensus pattern (15 bp):
TCGCTGTCATCGTCG
Done.