Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002968.1 Hibiscus syriacus cultivar Beakdansim tig00006137_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: 87614
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:16269 original size:55 final size:55
Alignment explanation
Indices: 16162--16274 Score: 156
Period size: 55 Copynumber: 2.1 Consensus size: 55
16152 AGTTTAACAC
* **
16162 TAACTTAAGATTCAATCCATAGTTTAAGAACATCTAATGTAAATAATACGTAGTT
1 TAACTTAAAATTCAATCCATAGTTTAAGAACATCTAATACAAATAATACGTAGTT
* * *
16217 TAACTTAAAATTCGATCCATAGTTTAAGAACATCTGATACAACTAA-ACCGTAGTT
1 TAACTTAAAATTCAATCCATAGTTTAAGAACATCTAATACAAATAATA-CGTAGTT
16272 TAA
1 TAA
16275 GACTAATTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 1 0.02
55 50 0.98
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.33
Consensus pattern (55 bp):
TAACTTAAAATTCAATCCATAGTTTAAGAACATCTAATACAAATAATACGTAGTT
Found at i:18072 original size:60 final size:60
Alignment explanation
Indices: 17988--18171 Score: 163
Period size: 60 Copynumber: 3.1 Consensus size: 60
17978 AAACATATGA
* * * **
17988 ATAGTTGAGTGACCATTTTATAACTTTTAATAGTTGGGGGACTCAACAAAGCAATACCCT
1 ATAGTTAAGAGACCATTTTGTAACTTTTAATAGTTGAAGGACTCAACAAAGCAATACCCT
* * ** * * * *
18048 ATAGTTAAGGGACAATTTTGTAACTTTTAGA-AGCCGAATGATTCAATAAAGCAATGCCCT
1 ATAGTTAAGAGACCATTTTGTAACTTTTA-ATAGTTGAAGGACTCAACAAAGCAATACCCT
** * * * * * *
18108 ATTCTTAAGAGACCATTTTGTAACTTTTAATGGTTGAAGAAATCAATAAAGAAACACCCT
1 ATAGTTAAGAGACCATTTTGTAACTTTTAATAGTTGAAGGACTCAACAAAGCAATACCCT
18168 ATAG
1 ATAG
18172 ACATAACTTT
Statistics
Matches: 95, Mismatches: 27, Indels: 4
0.75 0.21 0.03
Matches are distributed among these distances:
59 1 0.01
60 93 0.98
61 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (60 bp):
ATAGTTAAGAGACCATTTTGTAACTTTTAATAGTTGAAGGACTCAACAAAGCAATACCCT
Found at i:29861 original size:29 final size:29
Alignment explanation
Indices: 29820--29893 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 29
29810 AATATTAATC
** *
29820 ATTAAATGTATATTAGTATTTATT-CATTT
1 ATTAAATAAATATTAATATTT-TTGCATTT
*
29849 ATTAAATAAATA-TAATATTTTTGTATTT
1 ATTAAATAAATATTAATATTTTTGCATTT
*
29877 TTTAAATAAATA-TAATA
1 ATTAAATAAATATTAATA
29894 CAAATAATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 2 0.05
28 27 0.69
29 10 0.26
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (29 bp):
ATTAAATAAATATTAATATTTTTGCATTT
Found at i:29868 original size:28 final size:28
Alignment explanation
Indices: 29836--29893 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
29826 TGTATATTAG
29836 TATTTATT-CATTTATTAAATAAATATAA
1 TATTT-TTGCATTTATTAAATAAATATAA
* *
29864 TATTTTTGTATTTTTTAAATAAATATAA
1 TATTTTTGCATTTATTAAATAAATATAA
29892 TA
1 TA
29894 CAAATAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
TATTTTTGCATTTATTAAATAAATATAA
Found at i:40395 original size:691 final size:691
Alignment explanation
Indices: 39074--40458 Score: 2770
Period size: 691 Copynumber: 2.0 Consensus size: 691
39064 CAGTGGGAGC
39074 TTGATTTGAATTCCTGTTGTTCATCAGATGAAAATATGTTAGATTTATGTGCATGAACGTGACGT
1 TTGATTTGAATTCCTGTTGTTCATCAGATGAAAATATGTTAGATTTATGTGCATGAACGTGACGT
39139 ATTGCATGACTTGATTGCCTTGATTTTTAGGTGGCGGATGCTATTGAGAAAAGCTTTGTCTCCTT
66 ATTGCATGACTTGATTGCCTTGATTTTTAGGTGGCGGATGCTATTGAGAAAAGCTTTGTCTCCTT
39204 CAGAGAAGGCTACTTCTCCGACTCCTACCACTGCTAAAGATGATGATAAAGGGGATGAGAACGAA
131 CAGAGAAGGCTACTTCTCCGACTCCTACCACTGCTAAAGATGATGATAAAGGGGATGAGAACGAA
39269 GATGATAAATTACTCAATGAGATGGAGGAGCTCACATATGCCATGGAGCGTAAGAAGAAAAGAGA
196 GATGATAAATTACTCAATGAGATGGAGGAGCTCACATATGCCATGGAGCGTAAGAAGAAAAGAGA
39334 AAAGAAGCTTCTTGCAAAAAGACGAGCGAAGGCTTATTGCCTTGTTGAAAAAACTATGATCCCTA
261 AAAGAAGCTTCTTGCAAAAAGACGAGCGAAGGCTTATTGCCTTGTTGAAAAAACTATGATCCCTA
39399 TGTTTATGTCTTAGTGCATGTTACCATGCGGCAAATCATGAATGGAGCGAATTTTGTGATTATAC
326 TGTTTATGTCTTAGTGCATGTTACCATGCGGCAAATCATGAATGGAGCGAATTTTGTGATTATAC
39464 CAATGATTATGCATCTACAATATAGTGATTAAGTGATGCCCGGTATTCTTTTTGAAAGAGTTAAG
391 CAATGATTATGCATCTACAATATAGTGATTAAGTGATGCCCGGTATTCTTTTTGAAAGAGTTAAG
39529 CTTCCATCTTATAGGGGTGATAGATATTTATGGTGTTCCACTTTGTTGTAGGATGTTCCCATGCA
456 CTTCCATCTTATAGGGGTGATAGATATTTATGGTGTTCCACTTTGTTGTAGGATGTTCCCATGCA
39594 CACTCATTTTGTTGCTGATTTCTTGCCTCTTTTTGCAGGACAAATCACGGAAGGCAACAGGAATG
521 CACTCATTTTGTTGCTGATTTCTTGCCTCTTTTTGCAGGACAAATCACGGAAGGCAACAGGAATG
39659 CAAATAGATGCCCTGGAAGATGGTTACGTTGATCATGAGTTGTTCTCTCTTTCTTCCATTAAGGT
586 CAAATAGATGCCCTGGAAGATGGTTACGTTGATCATGAGTTGTTCTCTCTTTCTTCCATTAAGGT
39724 TCGTTTTACTAAGGCTGCAAACTGGATAACTCCAATAATGT
651 TCGTTTTACTAAGGCTGCAAACTGGATAACTCCAATAATGT
39765 TTGATTTGAATTCCTGTTGTTCATCAGATGAAAATATGTTAGATTTATGTGCATGAACGTGACGT
1 TTGATTTGAATTCCTGTTGTTCATCAGATGAAAATATGTTAGATTTATGTGCATGAACGTGACGT
39830 ATTGCATGACTTGATTGCCTTGATTTTTAGGTGGCGGATGCTATTGAGAAAAGCTTTGTCTCCTT
66 ATTGCATGACTTGATTGCCTTGATTTTTAGGTGGCGGATGCTATTGAGAAAAGCTTTGTCTCCTT
39895 CAGAGAAGGCTACTTCTCCGACTCCTACCACTGCTAAAGATGATGATAAAGGGGATGAGAACGAA
131 CAGAGAAGGCTACTTCTCCGACTCCTACCACTGCTAAAGATGATGATAAAGGGGATGAGAACGAA
39960 GATGATAAATTACTCAATGAGATGGAGGAGCTCACATATGCCATGGAGCGTAAGAAGAAAAGAGA
196 GATGATAAATTACTCAATGAGATGGAGGAGCTCACATATGCCATGGAGCGTAAGAAGAAAAGAGA
40025 AAAGAAGCTTCTTGCAAAAAGACGAGCGAAGGCTTATTGCCTTGTTGAAAAAACTATGATCCCTA
261 AAAGAAGCTTCTTGCAAAAAGACGAGCGAAGGCTTATTGCCTTGTTGAAAAAACTATGATCCCTA
40090 TGTTTATGTCTTAGTGCATGTTACCATGCGGCAAATCATGAATGGAGCGAATTTTGTGATTATAC
326 TGTTTATGTCTTAGTGCATGTTACCATGCGGCAAATCATGAATGGAGCGAATTTTGTGATTATAC
40155 CAATGATTATGCATCTACAATATAGTGATTAAGTGATGCCCGGTATTCTTTTTGAAAGAGTTAAG
391 CAATGATTATGCATCTACAATATAGTGATTAAGTGATGCCCGGTATTCTTTTTGAAAGAGTTAAG
40220 CTTCCATCTTATAGGGGTGATAGATATTTATGGTGTTCCACTTTGTTGTAGGATGTTCCCATGCA
456 CTTCCATCTTATAGGGGTGATAGATATTTATGGTGTTCCACTTTGTTGTAGGATGTTCCCATGCA
40285 CACTCATTTTGTTGCTGATTTCTTGCCTCTTTTTGCAGGACAAATCACGGAAGGCAACAGGAATG
521 CACTCATTTTGTTGCTGATTTCTTGCCTCTTTTTGCAGGACAAATCACGGAAGGCAACAGGAATG
40350 CAAATAGATGCCCTGGAAGATGGTTACGTTGATCATGAGTTGTTCTCTCTTTCTTCCATTAAGGT
586 CAAATAGATGCCCTGGAAGATGGTTACGTTGATCATGAGTTGTTCTCTCTTTCTTCCATTAAGGT
40415 TCGTTTTACTAAGGCTGCAAACTGGATAACTCCAATAATGT
651 TCGTTTTACTAAGGCTGCAAACTGGATAACTCCAATAATGT
40456 TTG
1 TTG
40459 TAACTAGTAA
Statistics
Matches: 694, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
691 694 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (691 bp):
TTGATTTGAATTCCTGTTGTTCATCAGATGAAAATATGTTAGATTTATGTGCATGAACGTGACGT
ATTGCATGACTTGATTGCCTTGATTTTTAGGTGGCGGATGCTATTGAGAAAAGCTTTGTCTCCTT
CAGAGAAGGCTACTTCTCCGACTCCTACCACTGCTAAAGATGATGATAAAGGGGATGAGAACGAA
GATGATAAATTACTCAATGAGATGGAGGAGCTCACATATGCCATGGAGCGTAAGAAGAAAAGAGA
AAAGAAGCTTCTTGCAAAAAGACGAGCGAAGGCTTATTGCCTTGTTGAAAAAACTATGATCCCTA
TGTTTATGTCTTAGTGCATGTTACCATGCGGCAAATCATGAATGGAGCGAATTTTGTGATTATAC
CAATGATTATGCATCTACAATATAGTGATTAAGTGATGCCCGGTATTCTTTTTGAAAGAGTTAAG
CTTCCATCTTATAGGGGTGATAGATATTTATGGTGTTCCACTTTGTTGTAGGATGTTCCCATGCA
CACTCATTTTGTTGCTGATTTCTTGCCTCTTTTTGCAGGACAAATCACGGAAGGCAACAGGAATG
CAAATAGATGCCCTGGAAGATGGTTACGTTGATCATGAGTTGTTCTCTCTTTCTTCCATTAAGGT
TCGTTTTACTAAGGCTGCAAACTGGATAACTCCAATAATGT
Found at i:40687 original size:132 final size:132
Alignment explanation
Indices: 40450--40717 Score: 439
Period size: 132 Copynumber: 2.0 Consensus size: 132
40440 ATAACTCCAA
*
40450 TAATGTTTGTAACTAGTAAAAATACAATTTATTACTGCAAGTATAAAAGACGACTAAAACGACAC
1 TAATGTTTGTAACTAGTAAAAATACAATTTATTACTGCAAGTATAAAAGACAACTAAAACGACAC
40515 TCAACACAAGGCTGCAGTTATGTCATTTGAACCAGGGGCATAGTTGATGTT-TGATTTTATTGAT
66 TCAACACAAGGCTGCAGTTATGTCATTTGAACCAGGGGCATAGTTGATGTTAT-ATTTTATTGAT
40579 TAT
130 TAT
* * * * *
40582 TAATGTTTGTAACTAGTAAAAATTCAATTTATTACTGCAAGTTTAAAAGGCAACTTAAATGACAC
1 TAATGTTTGTAACTAGTAAAAATACAATTTATTACTGCAAGTATAAAAGACAACTAAAACGACAC
** *
40647 TCGGCACAAGGCTGCAGTTATGTCATTTGAACCAGGGGCATGGTTGATGTTATATTTTATTGATT
66 TCAACACAAGGCTGCAGTTATGTCATTTGAACCAGGGGCATAGTTGATGTTATATTTTATTGATT
40712 AT
131 AT
40714 TAAT
1 TAAT
40718 CTACTTTTTT
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
132 125 0.99
133 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (132 bp):
TAATGTTTGTAACTAGTAAAAATACAATTTATTACTGCAAGTATAAAAGACAACTAAAACGACAC
TCAACACAAGGCTGCAGTTATGTCATTTGAACCAGGGGCATAGTTGATGTTATATTTTATTGATT
AT
Found at i:40955 original size:2 final size:2
Alignment explanation
Indices: 40948--40974 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40938 CTCACAACTG
40948 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 A
40975 ATTTCTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45360 original size:2 final size:2
Alignment explanation
Indices: 45347--45387 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
45337 ATTTGTTTGA
*
45347 AT AT AC AT AT AT 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 AT AT AT AT AT AT A
45388 GGATAATTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:58647 original size:3 final size:3
Alignment explanation
Indices: 58639--58706 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
58629 CCACAAGTTG
*
58639 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
58687 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
58707 AACAATAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:59783 original size:21 final size:19
Alignment explanation
Indices: 59758--59802 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
59748 AGTGAACCGG
59758 CGGTTCAAACCGATTTTCAGC
1 CGGTTCAAACCGATTTT-A-C
**
59779 CGGTTCACCCCGATTTTAC
1 CGGTTCAAACCGATTTTAC
59798 CGGTT
1 CGGTT
59803 TTCAGCTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 1 0.05
21 15 0.68
ACGTcount: A:0.18, C:0.31, G:0.20, T:0.31
Consensus pattern (19 bp):
CGGTTCAAACCGATTTTAC
Found at i:62823 original size:6 final size:6
Alignment explanation
Indices: 62809--62842 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
62799 GGACGGTTAA
*
62809 GATTCC GATTTC GATTCC GATTCC GATTTCC GAT
1 GATTCC GATTCC GATTCC GATTCC GA-TTCC GAT
62843 CTTAATCGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (6 bp):
GATTCC
Found at i:65780 original size:14 final size:15
Alignment explanation
Indices: 65753--65787 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
65743 GAATATATTA
65753 ATATTTTAAAATAAT
1 ATATTTTAAAATAAT
65768 ATATTTT-AAATAAT
1 ATATTTTAAAATAAT
65782 ATATTT
1 ATATTT
65788 ATAATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTTTAAAATAAT
Found at i:66225 original size:15 final size:15
Alignment explanation
Indices: 66189--66234 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
66179 AATTTAAACT
66189 ATAA-AAATATAAAA
1 ATAATAAATATAAAA
*
66203 CA-ATTAAATATAAAA
1 -ATAATAAATATAAAA
*
66218 ATAATAAAAATAAAA
1 ATAATAAATATAAAA
66233 AT
1 AT
66235 TAGATTACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 24 0.92
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAATAAATATAAAA
Found at i:66703 original size:2 final size:2
Alignment explanation
Indices: 66696--66749 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
66686 AACAATACAA
66696 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
66738 AT AT AT AT AT AT
1 AT AT AT AT AT AT
66750 TGTATATGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67667 original size:19 final size:18
Alignment explanation
Indices: 67624--67694 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 18
67614 ATAAAAAGTC
*
67624 AAAATAAAGTTAAATAAT
1 AAAATAAAATTAAATAAT
67642 AAAATAAAATTAAA-AAT
1 AAAATAAAATTAAATAAT
*
67659 ATTAAAT-AAATAAAATAATT
1 A--AAATAAAATTAAATAA-T
*
67679 AAAAGAAAATTCAAAT
1 AAAATAAAATT-AAAT
67695 TAAAAAGGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 4 0.09
18 23 0.53
19 10 0.23
20 6 0.14
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (18 bp):
AAAATAAAATTAAATAAT
Found at i:68590 original size:46 final size:46
Alignment explanation
Indices: 68540--68704 Score: 294
Period size: 46 Copynumber: 3.6 Consensus size: 46
68530 TCCATTTATA
* *
68540 CATTTTAATTATGACATCCTTTCATGTCTTAATTCATCCTTTCATG
1 CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
68586 CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
*
68632 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
*
68678 CATTTTAATTATGGCATCCTTTCATGC
1 CATTTTAATTATGACATCCTTTCATGC
68705 ATTTTACATA
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 116 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (46 bp):
CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
Found at i:68610 original size:26 final size:25
Alignment explanation
Indices: 68540--68710 Score: 174
Period size: 26 Copynumber: 7.3 Consensus size: 25
68530 TCCATTTATA
68540 CATTTTAATTATGACATCCTTTCATG
1 CATTTTAATTATG-CATCCTTTCATG
*
68566 --TCTTAA-T-T-CATCCTTTCATG
1 CATTTTAATTATGCATCCTTTCATG
68586 CATTTTAATTATGACATCCTTTCATG
1 CATTTTAATTATG-CATCCTTTCATG
*
68612 C--CTT-A--ATGCATCCTTTCATG
1 CATTTTAATTATGCATCCTTTCATG
68632 CATTTTAATTATGGCATCCTTTCATG
1 CATTTTAATTAT-GCATCCTTTCATG
*
68658 C--CTT-A--ATGCATCCTTTCATG
1 CATTTTAATTATGCATCCTTTCATG
68678 CATTTTAATTATGGCATCCTTTCATG
1 CATTTTAATTAT-GCATCCTTTCATG
68704 CATTTTA
1 CATTTTA
68711 CATATTCTAA
Statistics
Matches: 121, Mismatches: 6, Indels: 36
0.74 0.04 0.22
Matches are distributed among these distances:
20 39 0.32
21 5 0.04
22 10 0.08
23 6 0.05
24 10 0.08
25 4 0.03
26 47 0.39
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (25 bp):
CATTTTAATTATGCATCCTTTCATG
Found at i:68678 original size:20 final size:20
Alignment explanation
Indices: 68554--68678 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
68544 TTAATTATGA
* *
68554 CATCCTTTCATGTCTTAATT
1 CATCCTTTCATGCCTTAATG
*
68574 CATCCTTTCATGCATTTTAATTATG
1 CATCCTTTCATGC--CTT-A--ATG
68599 ACATCCTTTCATGCCTTAATG
1 -CATCCTTTCATGCCTTAATG
*
68620 CATCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATGC--CTT-A--AT-G
68646 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
68666 CATCCTTTCATGC
1 CATCCTTTCATGC
68679 ATTTTAATTA
Statistics
Matches: 87, Mismatches: 6, Indels: 24
0.74 0.05 0.21
Matches are distributed among these distances:
20 39 0.45
21 5 0.06
22 4 0.05
23 4 0.05
24 4 0.05
25 4 0.05
26 27 0.31
ACGTcount: A:0.22, C:0.26, G:0.09, T:0.44
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:69216 original size:20 final size:19
Alignment explanation
Indices: 69191--69240 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
69181 TGAAATAAGA
69191 AAAATAAAATAAATAAAAT-G
1 AAAATAAAAT-AAT-AAATGG
69211 AAAATAATAATAATAAATGG
1 AAAATAA-AATAATAAATGG
69231 AAAATAAAAT
1 AAAATAAAAT
69241 GCTAATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.25
20 18 0.64
21 3 0.11
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (19 bp):
AAAATAAAATAATAAATGG
Found at i:69312 original size:38 final size:38
Alignment explanation
Indices: 69264--69383 Score: 125
Period size: 38 Copynumber: 3.1 Consensus size: 38
69254 TGTATATATT
* **
69264 AAAAAAACGTTTTTAAAAACTATATGCTATATGTTTTC
1 AAAAAAACGTTTTAAAAAACTATATAATATATGTTTTC
* * *
69302 AAAAATACGTTTTCAAAAACTATATTATATATACGTTTTC
1 AAAAAAACGTTTTAAAAAACTATA-TA-ATATATGTTTTC
* * *
69342 AAAAAGAA-ATTTTAAAAAACTACATATTATATGTTTTC
1 AAAAA-AACGTTTTAAAAAACTATATAATATATGTTTTC
69380 AAAA
1 AAAA
69384 TGTGTTCTTA
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
38 36 0.53
39 3 0.04
40 28 0.41
41 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.38
Consensus pattern (38 bp):
AAAAAAACGTTTTAAAAAACTATATAATATATGTTTTC
Found at i:69395 original size:38 final size:39
Alignment explanation
Indices: 69291--69409 Score: 102
Period size: 38 Copynumber: 3.0 Consensus size: 39
69281 AACTATATGC
* *
69291 TATATGTTTTCAAAAAT-ACGTTTTCAAAAACTATATTATA
1 TATATGTTTTC-AAAATGA-GTTTTAAAAAACTACATTATA
* * *
69331 TATACGTTTTCAAAAAGAAATTTTAAAAAACTACA-TAT-
1 TATATGTTTTCAAAATG-AGTTTTAAAAAACTACATTATA
* *
69369 TATATGTTTTCAAAATGTGTTCTTAAAATTA-TACATTATA
1 TATATGTTTTCAAAATGAGTT-TTAAAA-AACTACATTATA
69409 T
1 T
69410 GTCTTCCAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
37 2 0.03
38 25 0.40
39 11 0.17
40 24 0.38
41 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (39 bp):
TATATGTTTTCAAAATGAGTTTTAAAAAACTACATTATA
Found at i:69509 original size:75 final size:74
Alignment explanation
Indices: 69266--69514 Score: 206
Period size: 75 Copynumber: 3.3 Consensus size: 74
69256 TATATATTAA
* *
69266 AAAAACGT-TTTTAAAAA-C-TATATGCTATATGTTTTCAAAAATACGTTTTCAAAAACTATATT
1 AAAAACGTATTTTAAAAACCATATAT-C-ATATGTTTTTAAAAATATGTTTTC-AAAACTATA-T
69328 ATATATACGTTTTC
62 AT-TATACGTTTTC
* * * * * * * *
69342 AAAAA-GAAATTTTAAAAAACTACATATTATATG-TTTTCAAAATGTGTTCTT-AAAATTATACA
1 AAAAACG-TATTTT-AAAAACCATATATCATATGTTTTTAAAAATATGTT-TTCAAAACTATATA
* *
69404 TTATATGTCTTCC
63 TTATACGT-TTTC
* * *
69417 AAAACCG-ATTTAAAAAACCATATATCATATGTTTTTTTAAAATATGTTTTCAAAACTATATATT
1 AAAAACGTATTTTAAAAACCATATATCATATG-TTTTTAAAAATATGTTTTCAAAACTATATATT
69481 ATACGTTTTC
65 ATACGTTTTC
* *
69491 AAAAACGTGTTTTCAAAACCATAT
1 AAAAACGTATTTTAAAAACCATAT
69515 TATATACATA
Statistics
Matches: 134, Mismatches: 27, Indels: 25
0.72 0.15 0.13
Matches are distributed among these distances:
73 16 0.12
74 21 0.16
75 52 0.39
76 14 0.10
77 15 0.11
78 12 0.09
80 4 0.03
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (74 bp):
AAAAACGTATTTTAAAAACCATATATCATATGTTTTTAAAAATATGTTTTCAAAACTATATATTA
TACGTTTTC
Found at i:69521 original size:37 final size:38
Alignment explanation
Indices: 69461--69535 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 38
69451 TTTTAAAATA
* *
69461 TGTTTTCAAAACTATATATTATAC-GTTTTCAAAAACG
1 TGTTTTCAAAACCATATATTATACAATTTTCAAAAACG
69498 TGTTTTCAAAACCATAT-TATATACATATTTTCAAAAAC
1 TGTTTTCAAAACCATATAT-TATACA-ATTTTCAAAAAC
69536 CGATTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 1 0.03
37 21 0.64
39 11 0.33
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (38 bp):
TGTTTTCAAAACCATATATTATACAATTTTCAAAAACG
Found at i:73471 original size:19 final size:19
Alignment explanation
Indices: 73431--73502 Score: 126
Period size: 19 Copynumber: 3.7 Consensus size: 19
73421 GGCTGCTGGA
*
73431 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG-TTTC
73451 AACCGGTTTGACCGGTTTC
1 AACCGGTTTGACCGGTTTC
73470 AACCGGTTTGACCGGTTTC
1 AACCGGTTTGACCGGTTTC
73489 AACCGGTTTGACCG
1 AACCGGTTTGACCG
73503 ATCTGACCCG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 37 0.73
20 14 0.27
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTTC
Found at i:73476 original size:10 final size:9
Alignment explanation
Indices: 73431--73502 Score: 81
Period size: 9 Copynumber: 7.6 Consensus size: 9
73421 GGCTGCTGGA
73431 AACCGGTTT
1 AACCGGTTT
73440 AACCGGTTTT
1 AACCGG-TTT
73450 CAACCGGTTT
1 -AACCGGTTT
*
73460 GACCGGTTT
1 AACCGGTTT
73469 CAACCGGTTT
1 -AACCGGTTT
*
73479 GACCGGTTT
1 AACCGGTTT
73488 CAACCGGTTT
1 -AACCGGTTT
*
73498 GACCG
1 AACCG
73503 ATCTGACCCG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
9 26 0.48
10 22 0.41
11 6 0.11
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (9 bp):
AACCGGTTT
Found at i:73528 original size:17 final size:17
Alignment explanation
Indices: 73506--73544 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
73496 TTGACCGATC
73506 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
73523 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
73540 TGACC
1 TGACC
73545 GTTGACTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:80740 original size:10 final size:9
Alignment explanation
Indices: 80725--80814 Score: 63
Period size: 10 Copynumber: 9.3 Consensus size: 9
80715 GCTGCTGGAA
80725 ACCGGTTATG
1 ACCGGTT-TG
*
80735 ACCGGTTTTCA
1 ACCGG-TTT-G
*
80746 ACCGGTTCG
1 ACCGGTTTG
80755 AACCGGTTTG
1 -ACCGGTTTG
*
80765 ACCGGTCTG
1 ACCGGTTTG
80774 AACCGGTTTG
1 -ACCGGTTTG
*
80784 ACCGGTCTG
1 ACCGGTTTG
* *
80793 AATCAGTTTG
1 -ACCGGTTTG
*
80803 ACCGGTCTG
1 ACCGGTTTG
80812 ACC
1 ACC
80815 CGACCCGACC
Statistics
Matches: 62, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
9 25 0.40
10 30 0.48
11 7 0.11
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:80770 original size:19 final size:19
Alignment explanation
Indices: 80754--80812 Score: 100
Period size: 19 Copynumber: 3.1 Consensus size: 19
80744 CAACCGGTTC
80754 GAACCGGTTTGACCGGTCT
1 GAACCGGTTTGACCGGTCT
80773 GAACCGGTTTGACCGGTCT
1 GAACCGGTTTGACCGGTCT
* *
80792 GAATCAGTTTGACCGGTCT
1 GAACCGGTTTGACCGGTCT
80811 GA
1 GA
80813 CCCGACCCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.27
Consensus pattern (19 bp):
GAACCGGTTTGACCGGTCT
Found at i:80837 original size:22 final size:22
Alignment explanation
Indices: 80811--80853 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
80801 TGACCGGTCT
80811 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
80833 GACCCGACCCGACTGTTGACC
1 GACCCGACCCGACCGTTGACC
80854 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.47, G:0.23, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:82704 original size:59 final size:59
Alignment explanation
Indices: 82577--82709 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 59
82567 AAAGTATACC
* * * *
82577 ATCATTTTAAATTGATCCTTAAACTTTTAAATATTCTAATTTCATCCCCAAACTATGAAT
1 ATCATTCTAAATTG-TCCTTAAACTTTTAAATATTCTAATTACATACCCAAAATATGAAT
*
82637 ATCATTCTAAATTAGTCCTTAAACTTTTGAACAT-TTC-AATTACA-ACCCAAAATATGACCT
1 ATCATTCTAAATT-GTCCTTAAACTTTT-AA-ATATTCTAATTACATACCCAAAATATGA-AT
82697 -TCATTCTAAATTG
1 ATCATTCTAAATTG
82710 GTCCCCAAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
58 1 0.02
59 23 0.36
60 32 0.50
61 6 0.09
62 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.39
Consensus pattern (59 bp):
ATCATTCTAAATTGTCCTTAAACTTTTAAATATTCTAATTACATACCCAAAATATGAAT
Done.