Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004400.1 Hibiscus syriacus cultivar Beakdansim tig00009648_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: 91538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6900 original size:45 final size:45
Alignment explanation
Indices: 6830--7081 Score: 288
Period size: 45 Copynumber: 5.6 Consensus size: 45
6820 TGCAAGTTAG
* * *
6830 ATAAATGAAAATGTATAACAATGCATAATCAGCACGAAAGGATGCC
1 ATAAATG-AAATGCATAACAATGCATAATCGGCATGAAAGGATGCC
** * * * *
6876 ATAAATGAAATGTTTAACAGTGCATAATCGACATGAAATGATGTC
1 ATAAATGAAATGCATAACAATGCATAATCGGCATGAAAGGATGCC
* ** *
6921 AGAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACAATGCATAATCGGCATGAAAGGATGCC
* *
6966 ATAAATGAAATGCATAACAATGCATTATCGGCATAAAAGGATGCC
1 ATAAATGAAATGCATAACAATGCATAATCGGCATGAAAGGATGCC
** * * **
7011 ATAAATGAAATGCATAATGATGCATTATCGGCATGAAATGATATC
1 ATAAATGAAATGCATAACAATGCATAATCGGCATGAAAGGATGCC
*
7056 ATAAATGAAAATGCATAACGATGCAT
1 ATAAATG-AAATGCATAACAATGCAT
7082 TATAAGCATG
Statistics
Matches: 179, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
45 155 0.87
46 24 0.13
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (45 bp):
ATAAATGAAATGCATAACAATGCATAATCGGCATGAAAGGATGCC
Found at i:26656 original size:27 final size:27
Alignment explanation
Indices: 26601--26656 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
26591 CCGCCATCAC
*
26601 CACTTTGAACTTGAAACTCCATAGCAT
1 CACTTTGAACTTGAAACTCCACAGCAT
* *
26628 CACTTTGAACTTGAAAGTCCACAGTAT
1 CACTTTGAACTTGAAACTCCACAGCAT
26655 CA
1 CA
26657 AGATCTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCACAGCAT
Found at i:27362 original size:60 final size:60
Alignment explanation
Indices: 27269--27398 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 60
27259 CGATTTTTAC
**
27269 TTTCAATTTCATCCTTAAAATATCACTATTATTCTAAATTAGTCC-CTAAACTTTCAAACA
1 TTTCAATTTTTTCCTTAAAATATCACTATTATTCTAAATTAGTCCTC-AAACTTTCAAACA
* * **
27329 TTTCAATTTTTTCCTTAAACTATCATTATTATTCTAAATTAGTCCTCAAACTTTTGAACA
1 TTTCAATTTTTTCCTTAAAATATCACTATTATTCTAAATTAGTCCTCAAACTTTCAAACA
27389 TTTC-ATTTTT
1 TTTCAATTTTT
27399 ATTCCCAAAC
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
59 6 0.10
60 56 0.89
61 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.02, T:0.46
Consensus pattern (60 bp):
TTTCAATTTTTTCCTTAAAATATCACTATTATTCTAAATTAGTCCTCAAACTTTCAAACA
Found at i:27409 original size:60 final size:60
Alignment explanation
Indices: 27269--27444 Score: 178
Period size: 60 Copynumber: 2.9 Consensus size: 60
27259 CGATTTTTAC
** * * * *
27269 TTTCAATTTCATCCTTAAAATATCACTATTATTCTAAATTAGTCC-CTAAACTTTCAAACA
1 TTTCAATTTTTTCCTCAAACTATCATTATTATTCTAAATTAGTCCTC-AAACTTTTAAACA
* *
27329 TTTCAATTTTTTCCTTAAACTATCATTATTATTCTAAATTAGTCCTCAAACTTTTGAACA
1 TTTCAATTTTTTCCTCAAACTATCATTATTATTCTAAATTAGTCCTCAAACTTTTAAACA
* * * * *
27389 TTTCATTTTTATTCC-CAAACTATGATCT-TCATCCTAAATTGGTCCTCAAACCTTTT
1 TTTCAATTTT-TTCCTCAAACTATCAT-TATTATTCTAAATTAGTCCTCAAA-CTTTT
27445 TAATAGTTCA
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
60 89 0.89
61 11 0.11
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (60 bp):
TTTCAATTTTTTCCTCAAACTATCATTATTATTCTAAATTAGTCCTCAAACTTTTAAACA
Found at i:27714 original size:60 final size:60
Alignment explanation
Indices: 27592--27714 Score: 153
Period size: 60 Copynumber: 2.0 Consensus size: 60
27582 TTTGGATGAA
* *
27592 TTTGAGGATGAAATTGAAGGATCTAAAAGTTTAAGGACCAATTTAGAATAAGAGTCATAG
1 TTTGAGGATGAAATTGAAAGATCTAAAAGTTTAAGGACCAATTTAGAATAAGAGTCAAAG
* * *
27652 TTTGAGGATGAAATTGGAATAG-T-TAAAAGTTTAAGGACTAATTTA-AATTGAGAGTTAAAG
1 TTTGAGGATGAAATT-GAA-AGATCTAAAAGTTTAAGGACCAATTTAGAA-TAAGAGTCAAAG
27712 TTT
1 TTT
27715 AGGGACATGT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
59 2 0.04
60 48 0.87
61 4 0.07
62 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.33
Consensus pattern (60 bp):
TTTGAGGATGAAATTGAAAGATCTAAAAGTTTAAGGACCAATTTAGAATAAGAGTCAAAG
Found at i:28584 original size:50 final size:51
Alignment explanation
Indices: 28469--28613 Score: 193
Period size: 51 Copynumber: 2.9 Consensus size: 51
28459 AATCGATGTA
* * * * *
28469 AGTATGTATTAAGTACTACATTTTTTTATTTTATTTACTTACACAGTTGTG
1 AGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACAGGTGTG
* * *
28520 AGTACGTGTTAAGTGCTGCACTTTTTTATTTTATTCACTTACACTGGTGT-
1 AGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACAGGTGTG
* *
28570 AGTATGTGTTAAGTGTTACACTTTTTTGTTTTATTCACTTACAC
1 AGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACAC
28614 CTGTGTAAGG
Statistics
Matches: 82, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 40 0.49
51 42 0.51
ACGTcount: A:0.23, C:0.13, G:0.14, T:0.49
Consensus pattern (51 bp):
AGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACAGGTGTG
Found at i:28620 original size:50 final size:49
Alignment explanation
Indices: 28469--28620 Score: 187
Period size: 50 Copynumber: 3.0 Consensus size: 49
28459 AATCGATGTA
* * * * *
28469 AGTATGTATTAAGTACTACATTTTTTTATTTTATTTACTTACACAGTTGT
1 AGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACTG-TGT
* *
28519 GAGTACGTGTTAAGTGCTGCACTTTTTTATTTTATTCACTTACACTGGTGT
1 -AGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACT-GTGT
* *
28570 AGTATGTGTTAAGTGTTACACTTTTTTGTTTTATTCACTTACACCTGTGT
1 AGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACA-CTGTGT
28620 A
1 A
28621 AGGAGCGGTT
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
50 44 0.50
51 43 0.49
52 1 0.01
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (49 bp):
AGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACTGTGT
Found at i:29262 original size:19 final size:19
Alignment explanation
Indices: 29182--29263 Score: 62
Period size: 20 Copynumber: 4.2 Consensus size: 19
29172 CTTTTAAATT
29182 TAATAAAATTGTTATATTTA
1 TAATAAAATT-TTATATTTA
*
29202 TAATTAAAATTTAAGTATTTA
1 TAA-TAAAATTTTA-TATTTA
* **
29223 -ATTTAAAATTTTA-ATAGA
1 TA-ATAAAATTTTATATTTA
29241 TAATAAAA-TTTATAATTTA
1 TAATAAAATTTTAT-ATTTA
29260 TAAT
1 TAAT
29264 TTTGATTTTC
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
17 4 0.08
18 8 0.17
19 8 0.17
20 15 0.31
21 13 0.27
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.48
Consensus pattern (19 bp):
TAATAAAATTTTATATTTA
Found at i:29826 original size:31 final size:31
Alignment explanation
Indices: 29791--30086 Score: 140
Period size: 31 Copynumber: 9.8 Consensus size: 31
29781 TGATATTTTA
*
29791 AAAATATATTTTTAAAATTTAAGATAAGAAT
1 AAAATATATTTTTAAAAGTTAAGATAAGAAT
*
29822 AAAATATATTTTT--AAGTGAAGATAAGAAT
1 AAAATATATTTTTAAAAGTTAAGATAAGAAT
* * **
29851 AAAATATATATTTGT-ATA-TTAAAATAATTAT
1 AAAATATAT-TTT-TAAAAGTTAAGATAAGAAT
** * ** *
29882 AAAATAT-TTAAATATATTTTAAGTTAAG-AT
1 AAAATATATT-TTTAAAAGTTAAGATAAGAAT
* * * *
29912 AAAAAAATATTGTTAAAAATTAAGATAATAAT
1 -AAAATATATTTTTAAAAGTTAAGATAAGAAT
** * *
29944 AAAATATATTTTT--AAGCGAATATAA-AGGT
1 AAAATATATTTTTAAAAGTTAAGATAAGA-AT
* * * * *
29973 AAAATACATGTTTTTATA-TTAAAATAAAAAT
1 AAAATATAT-TTTTAAAAGTTAAGATAAGAAT
* *
30004 AAAA-ATATATTTAATAAATTAAGA-AA-AAT
1 AAAATATATTTTTAA-AAGTTAAGATAAGAAT
*
30033 AAAATATATTTATT--AAGTTAA-AT-AGAAA
1 AAAATATATTT-TTAAAAGTTAAGATAAGAAT
*
30061 AAAATATATTTTTAAAATTTAAGATA
1 AAAATATATTTTTAAAAGTTAAGATA
30087 TATAAAATAT
Statistics
Matches: 196, Mismatches: 45, Indels: 48
0.68 0.16 0.17
Matches are distributed among these distances:
27 4 0.02
28 20 0.10
29 59 0.30
30 23 0.12
31 83 0.42
32 7 0.04
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.38
Consensus pattern (31 bp):
AAAATATATTTTTAAAAGTTAAGATAAGAAT
Found at i:29844 original size:29 final size:30
Alignment explanation
Indices: 29791--29859 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
29781 TGATATTTTA
* *
29791 AAAATATATTTTTAAAATTTAAGATAAGAAT
1 AAAATATATTTTT-AAAGTGAAGATAAGAAT
29822 AAAATATATTTTT-AAGTGAAGATAAGAAT
1 AAAATATATTTTTAAAGTGAAGATAAGAAT
29851 AAAATATAT
1 AAAATATAT
29860 ATTTGTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 23 0.64
31 13 0.36
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (30 bp):
AAAATATATTTTTAAAGTGAAGATAAGAAT
Found at i:30030 original size:28 final size:26
Alignment explanation
Indices: 29992--30071 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 26
29982 GTTTTTATAT
* *
29992 TAAAATAAAAATAAAAATATATTTAA
1 TAAATTAAAAAAAAAAATATATTTAA
*
30018 TAAATTAAGAAAAATAAAATATATTTAT
1 TAAATTAA-AAAAA-AAAATATATTTAA
*
30046 TAAGTTAAATAGAAAAAAATATATTT
1 TAAATTAAA-A-AAAAAAATATATTT
30072 TTAAAATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 7 0.15
27 5 0.11
28 31 0.67
29 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (26 bp):
TAAATTAAAAAAAAAAATATATTTAA
Found at i:30094 original size:29 final size:29
Alignment explanation
Indices: 29905--30096 Score: 89
Period size: 29 Copynumber: 6.6 Consensus size: 29
29895 ATATTTTAAG
*
29905 TTAAGAT-AA-AAAA-ATATTGTTAAAAA
1 TTAAGATAAATAAAATATATTTTTAAAAA
*
29931 TTAAGATAATAATAAAATATATTTTT--AAG
1 TTAAGAT-A-AATAAAATATATTTTTAAAAA
** * * * *
29960 CGAATATAAAGGTAAAATACATGTTTT-TATA
1 TTAAGATAAA--TAAAATATAT-TTTTAAAAA
* *
29991 TTAAAATAAAAATAAAA-ATATATTTAATAAA
1 TTAAGAT--AAATAAAATATATTTTTAA-AAA
* *
30022 TTAAGAAAAATAAAATATATTTATT--AAG
1 TTAAGATAAATAAAATATATTT-TTAAAAA
* *
30050 TTAA-ATAGAAAAAAATATATTTTTAAAAT
1 TTAAGATA-AATAAAATATATTTTTAAAAA
*
30079 TTAAGATATATAAAATAT
1 TTAAGATAAATAAAATAT
30097 TATTAATTTT
Statistics
Matches: 123, Mismatches: 24, Indels: 35
0.68 0.13 0.19
Matches are distributed among these distances:
26 7 0.06
27 6 0.05
28 20 0.16
29 42 0.34
30 19 0.15
31 26 0.21
33 3 0.02
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (29 bp):
TTAAGATAAATAAAATATATTTTTAAAAA
Found at i:31088 original size:12 final size:11
Alignment explanation
Indices: 31062--31093 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
31052 ATGACTACAT
31062 AATAATAATAA
1 AATAATAATAA
31073 AATAATAATGAA
1 AATAATAAT-AA
31085 AATAATAAT
1 AATAATAAT
31094 TTAAACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
AATAATAATAA
Found at i:31144 original size:21 final size:21
Alignment explanation
Indices: 31120--31163 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31110 AAAAAAGGAC
31120 AATAATAAAATGAAAA-TAAAT
1 AATAATAAAAT-AAAATTAAAT
*
31141 AATAATTAAATAAAATTAAAT
1 AATAATAAAATAAAATTAAAT
31162 AA
1 AA
31164 CAAGATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
AATAATAAAATAAAATTAAAT
Found at i:32490 original size:3 final size:3
Alignment explanation
Indices: 32482--32525 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
32472 AATTATTTAT
*
32482 TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
32526 AATTGAGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:32506 original size:20 final size:20
Alignment explanation
Indices: 32483--32522 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
32473 ATTATTTATT
*
32483 AATAATAATAATAATAATAA
1 AATAATAATAATAAAAATAA
32503 AATAATAATAATAAAAATAA
1 AATAATAATAATAAAAATAA
32523 TAAAATTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AATAATAATAATAAAAATAA
Found at i:32508 original size:23 final size:23
Alignment explanation
Indices: 32482--32528 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
32472 AATTATTTAT
*
32482 TAATAATAATAATAATAATAAAA
1 TAATAATAATAAAAATAATAAAA
32505 TAATAATAATAAAAATAATAAAA
1 TAATAATAATAAAAATAATAAAA
32528 T
1 T
32529 TGAGATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
TAATAATAATAAAAATAATAAAA
Found at i:33076 original size:122 final size:123
Alignment explanation
Indices: 32824--33389 Score: 664
Period size: 122 Copynumber: 4.7 Consensus size: 123
32814 TGATGAATTA
* * *
32824 ATGC-AAGGTTTGAACAAGTTCTTCTCATTATGAACTTATT-ATCCTTCTTCAGATGAGTTATTC
1 ATGCAAAGG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTATTC
* *
32887 TCATTATGAACTCTTC-C-AGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTC
65 TCATTATGAACT-TTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTC
* * * * *
32945 ACGCAAAGGTTTAACAAGTTCTTCTCGTTATGAACTTCTTCTTTC-TCTTCAGATAAGTTCTTCT
1 ATGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTATTCT
* *
33009 CATTATGAACTTTCTCTGGAAAAGTTGATGTTAATCTATCTCCTTCTGTGATAGAGTC
66 CATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTC
* *
33067 ATGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCC-TCTTCAGATAAGTTCTTCT
1 ATGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTATTCT
*
33131 CATTATGAACTTTCTCTGGAAAAGTTGATGCTGATTTATCTCCTTCTGTGATAGAGTC
66 CATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTC
* *
33189 ATGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTATTCT
1 ATGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTATTCT
* * * * *** ** * *
33254 CATTATGAGCTCTAC-CTGG-CAA--TGA---TGATCCATCGAGTGATG-AATTTGAG-C
66 CATTATGAACT-TTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGA-TAGAGTC
* * * *
33305 A---AAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCT
1 ATGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTATTCT
* *
33367 TATTATGAACTTTCTTTGGAAAA
66 CATTATGAACTTTCTCTGGAAAA
33390 TTTCATCCAT
Statistics
Matches: 391, Mismatches: 45, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
112 2 0.01
113 69 0.18
114 2 0.01
116 3 0.01
117 14 0.04
120 6 0.02
121 60 0.15
122 203 0.52
123 30 0.08
124 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (123 bp):
ATGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTATTCT
CATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTC
Found at i:33805 original size:22 final size:22
Alignment explanation
Indices: 33766--33821 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
33756 AATAAAGCTT
*
33766 TCATCTTT-AAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
33787 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
33809 TCATCTTTGAAGA
1 TCATCTTTGAAGA
33822 ATATAGATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 8 0.24
22 25 0.76
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:38484 original size:2 final size:2
Alignment explanation
Indices: 38477--38515 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
38467 GACAACAAAG
*
38477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38516 TTGAAAGGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:42338 original size:15 final size:14
Alignment explanation
Indices: 42318--42351 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
42308 ATAAAATGTA
42318 AAAATAATAAAAAAT
1 AAAATAA-AAAAAAT
*
42333 AAAATAAGAAAAAT
1 AAAATAAAAAAAAT
42347 AAAAT
1 AAAAT
42352 GGTTAGTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (14 bp):
AAAATAAAAAAAAT
Found at i:42985 original size:13 final size:13
Alignment explanation
Indices: 42955--42990 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
42945 AAATAAAATA
*
42955 AAAAACATTA-AT
1 AAAAATATTATAT
42967 AAAAATATTATAT
1 AAAAATATTATAT
42980 AAAAATATTAT
1 AAAAATATTAT
42991 GAAAATAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAAATATTATAT
Found at i:42995 original size:24 final size:24
Alignment explanation
Indices: 42942--42998 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
42932 ATTTTATACT
42942 TGAAAATAAAATAAAAAACATTAA
1 TGAAAATAAAATAAAAAACATTAA
* ** *
42966 TAAAAATATTATATAAAAATATT-A
1 TGAAAATAAAATA-AAAAACATTAA
42990 TGAAAATAA
1 TGAAAATAA
42999 TGAGTATATA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (24 bp):
TGAAAATAAAATAAAAAACATTAA
Found at i:43530 original size:2 final size:2
Alignment explanation
Indices: 43525--43585 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
43515 TATATTAATT
43525 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43567 TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA
43586 AATAAGATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43901 original size:12 final size:11
Alignment explanation
Indices: 43875--43906 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
43865 TTTTATAAAT
43875 AATAATAATAA
1 AATAATAATAA
43886 AATAATAATGAA
1 AATAATAAT-AA
43898 AATAATAAT
1 AATAATAAT
43907 TTAAACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
AATAATAATAA
Found at i:45352 original size:3 final size:3
Alignment explanation
Indices: 45346--45383 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
45336 TTATTATTAT
*
45346 TAA TAA TAA TAA -AG TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
45384 AACCGGGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:52333 original size:42 final size:42
Alignment explanation
Indices: 52274--52353 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
52264 ACCGATGATG
* * *
52274 ATGCCCAGCCCTCCAGTTCATATGCCATCTCCTCAGGGGTAT
1 ATGCCAAGCCCACCAGTTCATATGCCATCTCCGCAGGGGTAT
* *
52316 ATGCCAAGCCCACCAGTTTATATGTCATCTCCGCAGGG
1 ATGCCAAGCCCACCAGTTCATATGCCATCTCCGCAGGG
52354 TTACATTCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (42 bp):
ATGCCAAGCCCACCAGTTCATATGCCATCTCCGCAGGGGTAT
Found at i:52368 original size:42 final size:42
Alignment explanation
Indices: 52274--52373 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
52264 ACCGATGATG
* * * *
52274 ATGCCCAGCCCTCCAGTTCATATGCCATCTCCTCAGGGGTAT
1 ATGCCAAGCCCACCAGTTCATATGCCATCTCCGCAGGGGTAC
* * *
52316 ATGCCAAGCCCACCAGTTTATATGTCATCTCCGCAGGGTTAC
1 ATGCCAAGCCCACCAGTTCATATGCCATCTCCGCAGGGGTAC
* * *
52358 ATTCCTAGCCCGCCAG
1 ATGCCAAGCCCACCAG
52374 GTTACATGCC
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (42 bp):
ATGCCAAGCCCACCAGTTCATATGCCATCTCCGCAGGGGTAC
Found at i:52376 original size:21 final size:21
Alignment explanation
Indices: 52352--52391 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
52342 ATCTCCGCAG
*
52352 GGTTACATTCCTAGCCCGCCA
1 GGTTACATGCCTAGCCCGCCA
52373 GGTTACATGCCTAGCCCGC
1 GGTTACATGCCTAGCCCGC
52392 ATGGTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.23
Consensus pattern (21 bp):
GGTTACATGCCTAGCCCGCCA
Found at i:52397 original size:21 final size:20
Alignment explanation
Indices: 52346--52397 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
52336 TATGTCATCT
*
52346 CCGCAGGGTTACATTCCTAGC
1 CCGCA-GGTTACATGCCTAGC
52367 CCGCCAGGTTACATGCCTAGC
1 CCG-CAGGTTACATGCCTAGC
52388 CCGCATGGTT
1 CCGCA-GGTT
52398 TTATGACACC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.17, C:0.35, G:0.25, T:0.23
Consensus pattern (20 bp):
CCGCAGGTTACATGCCTAGC
Found at i:52978 original size:34 final size:34
Alignment explanation
Indices: 52905--52971 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
52895 ATTAAATATT
* **
52905 TTTAATATACAAATTATAGTATTTGAAATTTAAA
1 TTTAAAATACAAATTATAGTATTCAAAATTTAAA
52939 TTTAAAATACAAATTAT-GATATTCAAAATTTAA
1 TTTAAAATACAAATTATAG-TATTCAAAATTTAA
52972 CATTAAATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 1 0.03
34 28 0.97
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (34 bp):
TTTAAAATACAAATTATAGTATTCAAAATTTAAA
Found at i:53610 original size:138 final size:138
Alignment explanation
Indices: 53374--53878 Score: 832
Period size: 138 Copynumber: 3.7 Consensus size: 138
53364 AGTTCCCCGA
53374 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCG-AGC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCA-C
** ** *
53438 CCATGGGAACGCATTTTCACCACTTTGCCAAGTCCCCTTAGAAATAATAGGTACTGACATGAATA
65 CCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTAAGAAATAATAGGTACTGACATGAATA
53503 GTTCTCCAG
130 GTTCTCCAG
*
53512 GGGACATGAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCACC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCACC
* *
53577 CCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTAAAAAATAATAGGTACTAACATGAATAG
66 CCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTAAGAAATAATAGGTACTGACATGAATAG
53642 TTCTCCAG
131 TTCTCCAG
*
53650 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCACC
* *
53715 CCCGGGAACGTGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGACATGAATAG
66 CCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTAAGAAATAATAGGTACTGACATGAATAG
53780 TTCTCCAG
131 TTCTCCAG
* * * *
53788 GGGACATGAGTGACATAATAGAGCAATGATAACATATTCTCTGACAAAATAATGGAACGTGCGCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCACC
* * *
53853 TCCAGGAACGCGTTTTCACCACTTTG
66 CCCGGGAACGCGCTTTCACCACTTTG
53879 GGTACTGATA
Statistics
Matches: 345, Mismatches: 21, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
138 344 1.00
139 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (138 bp):
GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCACC
CCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTAAGAAATAATAGGTACTGACATGAATAG
TTCTCCAG
Found at i:53968 original size:116 final size:116
Alignment explanation
Indices: 53763--53987 Score: 317
Period size: 116 Copynumber: 1.9 Consensus size: 116
53753 AGAAATAATA
* * *
53763 GGTACTGACATGAATAGTTCTCCAGGGGACATGAGTGACATAATAGAGCAATGATAACATATTCT
1 GGTACTGACATGAATAGTGCCCCAGGGGACATGAGTGACATAATAGAGCAATGATAACATATTAT
* * * *
53828 CTGACAAAATAATGGAACGTGCGCCTCCAGGAACGCGTTTTCACCACTTTG
66 CTAACAAAATAATGGAACGCGCGCCCCCAGGAACGCGTCTTCACCACTTTG
* * * *
53879 GGTACTGATATGAATAGTGCCCCTGAGGGATATGAGTGA-ATAATAGAGCAATTATAACATATTA
1 GGTACTGACATGAATAGTGCCCCAG-GGGACATGAGTGACATAATAGAGCAATGATAACATATTA
* *
53943 TCTAACAACATAATGGAAGGCGCGCCCCCAGGAACGCGTCTTCAC
65 TCTAACAAAATAATGGAACGCGCGCCCCCAGGAACGCGTCTTCAC
53988 ATGAATAGTA
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
116 83 0.87
117 12 0.13
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (116 bp):
GGTACTGACATGAATAGTGCCCCAGGGGACATGAGTGACATAATAGAGCAATGATAACATATTAT
CTAACAAAATAATGGAACGCGCGCCCCCAGGAACGCGTCTTCACCACTTTG
Found at i:57150 original size:21 final size:21
Alignment explanation
Indices: 57124--57173 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
57114 AATAATTAAT
*
57124 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
57145 ATTATTAATTTTAAAATATT-
1 ATTATTAATTATAAAAAATTA
*
57165 ATAATTAAT
1 ATTATTAAT
57174 ATCGCGTGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:63663 original size:17 final size:17
Alignment explanation
Indices: 63641--63692 Score: 104
Period size: 17 Copynumber: 3.1 Consensus size: 17
63631 AGAACTGGAA
63641 GGCATACACATGCTTCG
1 GGCATACACATGCTTCG
63658 GGCATACACATGCTTCG
1 GGCATACACATGCTTCG
63675 GGCATACACATGCTTCG
1 GGCATACACATGCTTCG
63692 G
1 G
63693 CCCTATGATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (17 bp):
GGCATACACATGCTTCG
Found at i:71808 original size:14 final size:14
Alignment explanation
Indices: 71789--71815 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
71779 AACAGACTAT
71789 TCTGTTTTCTACAG
1 TCTGTTTTCTACAG
71803 TCTGTTTTCTACA
1 TCTGTTTTCTACA
71816 TGGTATCAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.11, T:0.52
Consensus pattern (14 bp):
TCTGTTTTCTACAG
Found at i:76540 original size:14 final size:14
Alignment explanation
Indices: 76521--76547 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
76511 AACAGACTAT
76521 TCTGTTTTCTACAG
1 TCTGTTTTCTACAG
76535 TCTGTTTTCTACA
1 TCTGTTTTCTACA
76548 CTTACCTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.11, T:0.52
Consensus pattern (14 bp):
TCTGTTTTCTACAG
Found at i:81025 original size:29 final size:29
Alignment explanation
Indices: 80983--81051 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
80973 ATAAGTAAAA
*
80983 GTGCAATAAAATAAAAGTTAGTGGTTAAT
1 GTGCAATAAAATAAAAGTTAGTAGTTAAT
81012 GTGCAATAAAATAAAAGTTAGTAGTTAAT
1 GTGCAATAAAATAAAAGTTAGTAGTTAAT
*
81041 ATGCAATAAAA
1 GTGCAATAAAA
81052 ATATATACAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.49, C:0.04, G:0.17, T:0.29
Consensus pattern (29 bp):
GTGCAATAAAATAAAAGTTAGTAGTTAAT
Done.