Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002953.1 Hibiscus syriacus cultivar Beakdansim tig00006097_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: 51835
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:267 original size:17 final size:17
Alignment explanation
Indices: 234--267 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
224 AATTTGTTTA
* *
234 TCTGTTTTTAATCTTTT
1 TCTGTTTTAAATATTTT
251 TCTGTTTTAAATATTTT
1 TCTGTTTTAAATATTTT
268 AGATTTTCGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.68
Consensus pattern (17 bp):
TCTGTTTTAAATATTTT
Found at i:6413 original size:28 final size:28
Alignment explanation
Indices: 6357--6413 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
6347 GGCGTTTGTT
* *
6357 TAAAAAAATGCCGCAATAAGTACTTATA
1 TAAAAAAACGCCGCAATAAGTACTGATA
*
6385 TAAACAAACGCCGCAATAAGTTA-TGATA
1 TAAAAAAACGCCGCAATAAG-TACTGATA
6413 T
1 T
6414 TTAGCGGCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (28 bp):
TAAAAAAACGCCGCAATAAGTACTGATA
Found at i:6480 original size:43 final size:42
Alignment explanation
Indices: 6388--6513 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 42
6378 ACTTATATAA
* * * *
6388 ACAAACGCCGCAATAAGTTATGATATTTAGCGGCGTTTGTCTT
1 ACAAACGCCGCAATAAGTT-TGATATTTAGAGGCGTTTTTATC
* * *
6431 AAAAACGCCGCAATAGGTGTTGAGATTTAGAGGCGTTTTTATC
1 ACAAACGCCGCAATAAGT-TTGATATTTAGAGGCGTTTTTATC
* * *
6474 ACAAACGCCGTAATAAGTTTTGATATTTAGTGGCATTTTT
1 ACAAACGCCGCAATAAG-TTTGATATTTAGAGGCGTTTTT
6514 TTAATGAAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
43 66 0.97
44 2 0.03
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (42 bp):
ACAAACGCCGCAATAAGTTTGATATTTAGAGGCGTTTTTATC
Found at i:13530 original size:2 final size:2
Alignment explanation
Indices: 13523--13607 Score: 138
Period size: 2 Copynumber: 43.5 Consensus size: 2
13513 TATTGGAATT
* *
13523 TA TA TA TA TT TA -A TA T- TT 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
13563 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
13605 TA T
1 TA T
13608 CAATGTTATT
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
1 2 0.03
2 76 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:15200 original size:15 final size:16
Alignment explanation
Indices: 15162--15202 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
15152 AAATGCAGAC
15162 AAATT-TTTGTCTTAA
1 AAATTATTTGTCTTAA
* *
15177 AAATGATTTTTCTT-A
1 AAATTATTTGTCTTAA
15192 AAATTATTTGT
1 AAATTATTTGT
15203 AGACATATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (16 bp):
AAATTATTTGTCTTAA
Found at i:15889 original size:11 final size:11
Alignment explanation
Indices: 15870--15907 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
15860 AATAAATGAC
15870 ATAAAATATAA
1 ATAAAATATAA
* *
15881 ATGAAATATCA
1 ATAAAATATAA
15892 ATAAAATAT-A
1 ATAAAATATAA
15902 ATAAAA
1 ATAAAA
15908 CTAAAAGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 7 0.29
11 17 0.71
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (11 bp):
ATAAAATATAA
Found at i:15926 original size:4 final size:4
Alignment explanation
Indices: 15917--15982 Score: 51
Period size: 4 Copynumber: 15.5 Consensus size: 4
15907 ACTAAAAGGG
** *
15917 AATA AATA AATA AATA AATAA AATA GCTA AACGA AGATA AATA AATA AATA
1 AATA AATA AATA AATA AAT-A AATA AATA AA-TA A-ATA AATA AATA AATA
* *
15968 TATA TATA ATATA AA
1 AATA AATA A-ATA AA
15983 CAAAAAGGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
4 37 0.74
5 12 0.24
6 1 0.02
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:16625 original size:153 final size:153
Alignment explanation
Indices: 16299--16600 Score: 383
Period size: 153 Copynumber: 2.0 Consensus size: 153
16289 ATACCTAAGC
* * * *
16299 ATAAATTGCCGTATGGTATATGGAAGCATTATACATATATGCTAATTACTGAAGTAAAATAGTAA
1 ATAAATTACCATATGATATATGGAAGCATTATAAATATATGCTAATTACTGAAGTAAAATAGTAA
* * * * * *
16364 GGGTAGGTTAAAGCAAGATATGAATATGCTTACCTAACATAACTATTAAATATGGAAGACAAATA
66 GGGTAAGTTAAAGCAAAATATGAATATACTTACCAAAAATAACTATTAAATATAGAAGACAAATA
** * * * *
16429 AATAGCCAGGGCTATATATATAT
131 AATAGAAAGGGCTAAATAAAGAA
* *
16452 ATAAATTACCGTATGATATATGGAAGCATTATAAATATATGCTAATTA-TTAAGGTAAAATAGTA
1 ATAAATTACCATATGATATATGGAAGCATTATAAATATATGCTAATTACTGAA-GTAAAATAGTA
* * *
16516 AGGGTAAGTTGAAGCAAAATATGAATATATTTACCAAAAATAACTATTAAATATAGAAGA-TAAT
65 AGGGTAAGTTAAAGCAAAATATGAATATACTTACCAAAAATAACTATTAAATATAGAAGACAAAT
*
16580 AAATAGAAAGGGTTAAATAAA
130 AAATAGAAAGGGCTAAATAAA
16601 AGGAAATATA
Statistics
Matches: 130, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
152 22 0.17
153 108 0.83
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.29
Consensus pattern (153 bp):
ATAAATTACCATATGATATATGGAAGCATTATAAATATATGCTAATTACTGAAGTAAAATAGTAA
GGGTAAGTTAAAGCAAAATATGAATATACTTACCAAAAATAACTATTAAATATAGAAGACAAATA
AATAGAAAGGGCTAAATAAAGAA
Found at i:18142 original size:22 final size:21
Alignment explanation
Indices: 18064--18142 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 21
18054 CAAGTGATTA
*
18064 TAAATAATTT-AAATATTTTAT
1 TAAA-AATTTAAAATATTGTAT
** * *
18085 TAAAAATTTAAAATAAAGAGAG
1 TAAAAATTTAAAATATTG-TAT
18107 TAAATAATTT-AAATATTGTAT
1 TAAA-AATTTAAAATATTGTAT
18128 TAAAAATGTTAAAAT
1 TAAAAAT-TTAAAAT
18143 CATGATAATA
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
20 8 0.18
21 16 0.36
22 15 0.34
23 5 0.11
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.39
Consensus pattern (21 bp):
TAAAAATTTAAAATATTGTAT
Found at i:19622 original size:16 final size:16
Alignment explanation
Indices: 19601--19631 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
19591 ATACATAGCC
19601 TTTGAATCATTCAGCA
1 TTTGAATCATTCAGCA
19617 TTTGAATCATTCAGC
1 TTTGAATCATTCAGC
19632 GCTTAATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (16 bp):
TTTGAATCATTCAGCA
Found at i:19641 original size:15 final size:16
Alignment explanation
Indices: 19602--19643 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
19592 TACATAGCCT
*
19602 TTGAATCATTCAGCAT
1 TTGAATCATTCAGCAC
*
19618 TTGAATCATTCAGCGC
1 TTGAATCATTCAGCAC
19634 TT-AATCATTC
1 TTGAATCATTC
19644 TGAAGTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (16 bp):
TTGAATCATTCAGCAC
Found at i:23672 original size:21 final size:21
Alignment explanation
Indices: 23648--23689 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23638 TTAAGTGTCG
*
23648 AGGAGCATTATTAAAAAGTCA
1 AGGAGAATTATTAAAAAGTCA
**
23669 AGGAGAATTATTGCAAAGTCA
1 AGGAGAATTATTAAAAAGTCA
23690 TAGTTCGTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (21 bp):
AGGAGAATTATTAAAAAGTCA
Found at i:24271 original size:44 final size:44
Alignment explanation
Indices: 24208--24301 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 44
24198 TACACCAATA
* * *
24208 ACAGTACATAAAACTTAAAAACATCC-CCTGGCATAAAAGCCTTT
1 ACAGTACATAAAACTTAAAAACA-CCACCTGCCATAAAAACCTTC
24252 ACAGTACATAAAACTTAAAAACACCACCTGCCATAAAAACCTTC
1 ACAGTACATAAAACTTAAAAACACCACCTGCCATAAAAACCTTC
24296 ACAGTA
1 ACAGTA
24302 GATTAGAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 2 0.04
44 44 0.96
ACGTcount: A:0.46, C:0.27, G:0.07, T:0.20
Consensus pattern (44 bp):
ACAGTACATAAAACTTAAAAACACCACCTGCCATAAAAACCTTC
Found at i:45428 original size:15 final size:15
Alignment explanation
Indices: 45396--45598 Score: 281
Period size: 15 Copynumber: 13.5 Consensus size: 15
45386 TAATAAGGTT
*
45396 ATTTATT-TTAAA-A
1 ATTTATTATAAAATA
*
45409 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
45424 ATTTATTATAAAATA
1 ATTTATTATAAAATA
45439 ATTTATT-TAAAATA
1 ATTTATTATAAAATA
45453 ATTTATTATAAAATA
1 ATTTATTATAAAATA
45468 ATTTATTATAAAATA
1 ATTTATTATAAAATA
45483 ATTTATTATAAAATA
1 ATTTATTATAAAATA
45498 ATTTATTATAAAATA
1 ATTTATTATAAAATA
45513 ATTTATTATAAAAT-
1 ATTTATTATAAAATA
*
45527 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
45542 ATTTATTATAAAATGGA
1 ATTTATTATAAAAT--A
*
45559 TTGATTTATTTTAAAATA
1 ---ATTTATTATAAAATA
*
45577 ATTTATT-TTAAATA
1 ATTTATTATAAAATA
45591 ATTTATTA
1 ATTTATTA
45599 GTATGAATTG
Statistics
Matches: 174, Mismatches: 6, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
13 7 0.04
14 44 0.25
15 108 0.62
17 1 0.01
18 1 0.01
20 13 0.07
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.50
Consensus pattern (15 bp):
ATTTATTATAAAATA
Found at i:45482 original size:59 final size:58
Alignment explanation
Indices: 45396--45598 Score: 275
Period size: 59 Copynumber: 3.4 Consensus size: 58
45386 TAATAAGGTT
* *
45396 ATTTATTTTAAA-AATTTATTTTAAAATAATTTATTATAAAATAATTTATTTAAAATA
1 ATTTATTTAAAATAATTTATTATAAAATAATTTATTATAAAATAATTTATTTAAAATA
45453 ATTTATTATAAAATAATTTATTATAAAATAATTTATTATAAAATAATTTATTATAAAATA
1 ATTTATT-TAAAATAATTTATTATAAAATAATTTATTATAAAATAATTTATT-TAAAATA
*
45513 ATTTATTATAAAAT-ATTTATTTTAAAATAATTTATTATAAAATGGATTGATTTATTTTAAAATA
1 ATTTATT-TAAAATAATTTATTATAAAATAATTTATTATAAAAT--A---ATTTA-TTTAAAATA
*
45577 ATTTATTTTAAATAATTTATTA
1 ATTTATTTAAAATAATTTATTA
45599 GTATGAATTG
Statistics
Matches: 131, Mismatches: 5, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
57 7 0.05
58 4 0.03
59 65 0.50
60 21 0.16
61 1 0.01
63 5 0.04
64 26 0.20
65 2 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.50
Consensus pattern (58 bp):
ATTTATTTAAAATAATTTATTATAAAATAATTTATTATAAAATAATTTATTTAAAATA
Found at i:45495 original size:74 final size:74
Alignment explanation
Indices: 45396--45598 Score: 288
Period size: 74 Copynumber: 2.7 Consensus size: 74
45386 TAATAAGGTT
*
45396 ATTTATT-TTAAA-AATTTATTTTAAAATAATTTATTATAAAATAATTTATT-TAAAATAATTTA
1 ATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAAT-ATTTA
45458 TTATAAAATA
65 TTATAAAATA
*
45468 ATTTATTATAAAATAATTTATTATAAAATAATTTATTATAAAATAATTTATTATAAAATATTTAT
1 ATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATATTTAT
*
45533 TTTAAAATA
66 TATAAAATA
*
45542 ATTTATTATAAAATGGATTGATTTATTTTAAAATAATTTATT-TTAAATAATTTATTA
1 ATTTATTATAAAAT--A---ATTTATTTTAAAATAATTTATTATAAAATAATTTATTA
45599 GTATGAATTG
Statistics
Matches: 118, Mismatches: 5, Indels: 10
0.89 0.04 0.08
Matches are distributed among these distances:
72 7 0.06
73 4 0.03
74 65 0.55
75 6 0.05
76 1 0.01
78 14 0.12
79 21 0.18
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.50
Consensus pattern (74 bp):
ATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATATTTAT
TATAAAATA
Found at i:45630 original size:22 final size:22
Alignment explanation
Indices: 45605--45694 Score: 81
Period size: 22 Copynumber: 3.7 Consensus size: 22
45595 ATTAGTATGA
45605 ATTGATTTATTTTAAAATATAG
1 ATTGATTTATTTTAAAATATAG
45627 ATTGATTTATTTTAATAATTTATTAG
1 ATTGATTTATTTTAA-AA--TA-TAG
* *
45653 TATGGATTAATTATTTTAAAATATCG
1 -ATTGA-T--TTATTTTAAAATATAG
*
45679 ATTGATTTATCTTAAA
1 ATTGATTTATTTTAAA
45695 TAATTTATTA
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
22 24 0.43
23 2 0.04
24 1 0.02
25 6 0.11
26 5 0.09
27 6 0.11
28 1 0.02
29 2 0.04
30 9 0.16
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
ATTGATTTATTTTAAAATATAG
Found at i:45697 original size:53 final size:52
Alignment explanation
Indices: 45577--45742 Score: 251
Period size: 53 Copynumber: 3.1 Consensus size: 52
45567 TTTTAAAATA
* *
45577 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTG
1 ATTTA-TTTAAATAATTTATTAGTATGGATT-AATTATTTTAAAATATAGATTG
* *
45631 ATTTATTTTAATAATTTATTAGTATGGATTAATTATTTTAAAATATCGATTG
1 ATTTATTTAAATAATTTATTAGTATGGATTAATTATTTTAAAATATAGATTG
* *
45683 ATTTATCTTAAATAATTTATTAGTATGGATTGATTATTTTAAAATATGGATTG
1 ATTTAT-TTAAATAATTTATTAGTATGGATTAATTATTTTAAAATATAGATTG
45736 ATTTATT
1 ATTTATT
45743 ATTGTAGTTA
Statistics
Matches: 104, Mismatches: 7, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
52 27 0.26
53 72 0.69
54 5 0.05
ACGTcount: A:0.37, C:0.01, G:0.10, T:0.52
Consensus pattern (52 bp):
ATTTATTTAAATAATTTATTAGTATGGATTAATTATTTTAAAATATAGATTG
Found at i:45738 original size:25 final size:26
Alignment explanation
Indices: 45710--45764 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
45700 TATTAGTATG
*
45710 GATTGATTATTTTA-AAATATGGATT
1 GATTGATTATTGTAGAAATATGGATT
* **
45735 GATTTATTATTGTAGTTATATGGATT
1 GATTGATTATTGTAGAAATATGGATT
45761 GATT
1 GATT
45765 TATTTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (26 bp):
GATTGATTATTGTAGAAATATGGATT
Found at i:45773 original size:79 final size:80
Alignment explanation
Indices: 45673--45819 Score: 260
Period size: 79 Copynumber: 1.9 Consensus size: 80
45663 TTATTTTAAA
*
45673 ATATCGATTGATTTATCTTAAATAATTTATTAGTATGGATTGA-TTATTTTAAAATATGGATTGA
1 ATATCGATTGATTTATCTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGA
45737 TTTATTATTGTAGTT
66 TTTATTATTGTAGTT
* *
45752 ATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGA
1 ATATCGATTGATTTATCTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGA
45817 TTT
66 TTT
45820 TTTAAATAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
79 41 0.64
80 23 0.36
ACGTcount: A:0.34, C:0.01, G:0.14, T:0.51
Consensus pattern (80 bp):
ATATCGATTGATTTATCTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGA
TTTATTATTGTAGTT
Found at i:45862 original size:19 final size:19
Alignment explanation
Indices: 45838--45877 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
45828 ATTTATTAGT
45838 ATGGATTGATTTATTTAAA
1 ATGGATTGATTTATTTAAA
*
45857 ATGGATTGATTTATTTTAA
1 ATGGATTGATTTATTTAAA
45876 AT
1 AT
45878 AATTTATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (19 bp):
ATGGATTGATTTATTTAAA
Found at i:45898 original size:32 final size:32
Alignment explanation
Indices: 45857--46162 Score: 203
Period size: 32 Copynumber: 9.6 Consensus size: 32
45847 TTTATTTAAA
45857 ATGGATTGATTTATTTTAAATAATTTATTAGT
1 ATGGATTGATTTATTTTAAATAATTTATTAGT
* * *
45889 ATAGATTGATTTATTTTAAATAATTTGTTTGT
1 ATGGATTGATTTATTTTAAATAATTTATTAGT
* * *
45921 ATGGATTGATTGA-TTT--AT--TTTA-AAAT
1 ATGGATTGATTTATTTTAAATAATTTATTAGT
*
45947 ATGGATTGATTTA--TT--AT--TGTAGTT-GT
1 ATGGATTGATTTATTTTAAATAATTTA-TTAGT
45973 ATGGATTGATTTATTTTAAATAATTTATTAGT
1 ATGGATTGATTTATTTTAAATAATTTATTAGT
*
46005 ATGGATTGATTTATTTTAAAATATGGATTGATTA-T
1 ATGGATTGATTTATTTT-AAATA---ATTTATTAGT
* ** * * * * * *
46040 TTTAAATAATTTATTAGTATCGATTGATTTATTTTTAAAAT
1 ATGGATTGATTTATT--T-T-AAATAATTTA---TT--AGT
*
46081 AT-GAATGATTTATTTTAAA-AATTTATTAGT
1 ATGGATTGATTTATTTTAAATAATTTATTAGT
*
46111 ATGGATTGATTTATTTTAAATAATTTATTTGT
1 ATGGATTGATTTATTTTAAATAATTTATTAGT
46143 ATGGATTGATTTATTTTAAA
1 ATGGATTGATTTATTTTAAA
46163 ATATGGATTG
Statistics
Matches: 216, Mismatches: 34, Indels: 48
0.72 0.11 0.16
Matches are distributed among these distances:
25 7 0.03
26 27 0.12
27 3 0.01
28 2 0.01
29 2 0.01
30 6 0.03
31 21 0.10
32 94 0.44
33 5 0.02
35 20 0.09
36 8 0.04
37 2 0.01
38 6 0.03
40 11 0.05
41 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
ATGGATTGATTTATTTTAAATAATTTATTAGT
Found at i:45940 original size:26 final size:27
Alignment explanation
Indices: 45911--46020 Score: 86
Period size: 26 Copynumber: 4.0 Consensus size: 27
45901 ATTTTAAATA
*
45911 ATTTGT-TTGTATGGATTGATTGATTT
1 ATTTGTATTGTATGGATTGATTTATTT
***
45937 ATTT-TAAAATATGGATTGATTTA-TT
1 ATTTGTATTGTATGGATTGATTTATTT
45962 A-TTGTAGTTGTATGGATTGATTTATTTT
1 ATTTGTA-TTGTATGGATTGATTTA-TTT
45990 AAATAATT-TATTAGTATGGATTGATTTATTT
1 --AT--TTGTATT-GTATGGATTGATTTATTT
46021 TAAAATATGG
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
24 2 0.03
25 6 0.09
26 31 0.47
28 2 0.03
30 1 0.02
31 5 0.08
32 17 0.26
33 2 0.03
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (27 bp):
ATTTGTATTGTATGGATTGATTTATTT
Found at i:46041 original size:21 final size:22
Alignment explanation
Indices: 46004--46045 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
45994 AATTTATTAG
46004 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
46026 TATGGATTGA-TTATTTTAAA
1 TATGGATTGATTTATTTTAAA
46046 TAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:46043 original size:26 final size:27
Alignment explanation
Indices: 45920--46043 Score: 66
Period size: 26 Copynumber: 4.7 Consensus size: 27
45910 AATTTGTTTG
45920 TATGGATTGATTGA-TTTATTTTA-AAA
1 TATGGATTGATT-ATTTTATTTTAGAAA
* * ***
45946 TATGGATTGATT-TATTATTGTAGTTG
1 TATGGATTGATTATTTTATTTTAGAAA
** *
45972 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGA-TTATTTT--AT--TTTAGAAA
46004 TATGGATTG---A-TTTATTTTA-AAA
1 TATGGATTGATTATTTTATTTTAGAAA
46026 TATGGATTGATTATTTTA
1 TATGGATTGATTATTTTA
46044 AATAATTTAT
Statistics
Matches: 75, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
22 10 0.13
23 4 0.05
25 10 0.13
26 26 0.35
27 5 0.07
28 4 0.05
30 2 0.03
32 14 0.19
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.52
Consensus pattern (27 bp):
TATGGATTGATTATTTTATTTTAGAAA
Found at i:46211 original size:218 final size:216
Alignment explanation
Indices: 45678--46274 Score: 993
Period size: 219 Copynumber: 2.7 Consensus size: 216
45668 TTAAAATATC
* *
45678 GATTGATTTATCTTAAATAATTTATTAGTATGGATTGA-TTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
*
45742 TATTGTAGTTATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
66 TATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * *
45807 TATAGATTGATT-TTTTAAATAATTTATTAGTATGGATTGATTTATTTAAAATGGATTGATTTAT
131 TATGGATTGATTATTTTAAATAATTTATTAGTATCGATTGATTTATTTAAAATGGAATGATTTAT
45871 TTTAAATAATTTATTAGTATA
196 TTTAAATAATTTATTAGTATA
*
45892 GATTGATTTATTTTAAATAATTTGTTTGTATGGATTGATTGATTTATTTTAAAATATGGATTGAT
1 GATTGATTTATTTTAAATAATTTATTTGTAT-G---GATTGATTTATTTTAAAATATGGATTGAT
45957 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
62 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
*
46022 AAAATATGGATTGATTATTTTAAATAATTTATTAGTATCGATTGATTTATTTTTAAAATATGAAT
127 AAAATATGGATTGATTATTTTAAATAATTTATTAGTATCGATTGATTTA--TTTAAAAT-GGAAT
*
46087 GATTTATTTTAAA-AATTTATTAGTATG
189 GATTTATTTTAAATAATTTATTAGTATA
46114 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
* *
46179 TATTGTAGCTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
66 TATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
46244 TATGGATTGATTTATTTTAAGTAATTTATTA
131 TATGGATTGA-TTATTTTAAATAATTTATTA
46275 TTGTAGTTGT
Statistics
Matches: 360, Mismatches: 13, Indels: 15
0.93 0.03 0.04
Matches are distributed among these distances:
214 28 0.08
215 1 0.00
218 112 0.31
219 120 0.33
220 31 0.09
221 1 0.00
222 51 0.14
223 16 0.04
ACGTcount: A:0.34, C:0.01, G:0.14, T:0.52
Consensus pattern (216 bp):
GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
TATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
TATGGATTGATTATTTTAAATAATTTATTAGTATCGATTGATTTATTTAAAATGGAATGATTTAT
TTTAAATAATTTATTAGTATA
Found at i:46225 original size:80 final size:80
Alignment explanation
Indices: 46026--46259 Score: 323
Period size: 80 Copynumber: 2.9 Consensus size: 80
46016 TATTTTAAAA
* *
46026 TATGGATTGA-TTATTTTAAATAATTTATTAGTATCGATTGATTTATTTTTAAAATAT-GAATGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTTTAAAATATGGATTGA
*
46089 TTTATTTTAAAAATTTATTAG
65 TTTA--TT---AATTTACTAG
*
46110 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
46175 TTATT-ATTGTAGCT-G
66 TTATTAATT-TA-CTAG
*
46190 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
46255 TTATT
66 TTATT
46260 TTAAGTAATT
Statistics
Matches: 140, Mismatches: 6, Indels: 12
0.89 0.04 0.08
Matches are distributed among these distances:
79 3 0.02
80 71 0.51
81 1 0.01
83 2 0.01
84 21 0.15
85 42 0.30
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTAATTTACTAG
Found at i:46247 original size:22 final size:22
Alignment explanation
Indices: 46222--46263 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
46212 AATTTATTAG
46222 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
46244 TATGGATTGATTTATTTTAA
1 TATGAATTGATTTATTTTAA
46264 GTAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:46323 original size:31 final size:31
Alignment explanation
Indices: 46288--46347 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
46278 TAGTTGTATG
* *
46288 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
46319 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
46348 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:51561 original size:52 final size:52
Alignment explanation
Indices: 51478--51593 Score: 189
Period size: 52 Copynumber: 2.2 Consensus size: 52
51468 CAGAGAGAAA
51478 CAATTATGTATTTCATCTGCAGCAAACTCTATCGCCGTGGCTCTTTGATCAT
1 CAATTATGTATTTCATCTGCAGCAAACTCTATCGCCGTGGCTCTTTGATCAT
* *
51530 CAATTATGTATTTCATCTGCAGC-AACTTCTATCGCTGTGGCTCTTTGATCTT
1 CAATTATGTATTTCATCTGCAGCAAAC-TCTATCGCCGTGGCTCTTTGATCAT
*
51582 CAATTATATATT
1 CAATTATGTATT
51594 CAAAATATTA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 3 0.05
52 57 0.95
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (52 bp):
CAATTATGTATTTCATCTGCAGCAAACTCTATCGCCGTGGCTCTTTGATCAT
Done.