Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006045.1 Hibiscus syriacus cultivar Beakdansim tig00014296_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: 81532
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:10888 original size:64 final size:63
Alignment explanation
Indices: 10813--10933 Score: 188
Period size: 64 Copynumber: 1.9 Consensus size: 63
10803 ATTGTTCAAG
* * *
10813 GTGTATCGATGCACAAGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATACCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATACCATCA
* *
10877 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAATA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATA
10934 GAATTTATGC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
63 17 0.33
64 35 0.67
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATACCATCA
Found at i:10952 original size:63 final size:64
Alignment explanation
Indices: 10821--10952 Score: 142
Period size: 64 Copynumber: 2.1 Consensus size: 64
10811 AGGTGTATCG
* * * * * * *
10821 ATGCACAAGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATACCATCAGTGTATCG
1 ATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACAATCAGTGCACCA
* * * *
10885 ATGCACAAGTAGTGCATCGATGCACCCCCTT-AAATACAAACATCGAATAGAATTTA-TGCACCA
1 ATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACAA-TCAGTGCACCA
10948 ATGCA
1 ATGCA
10953 TGAATAGAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
63 27 0.48
64 29 0.52
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (64 bp):
ATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACAATCAGTGCACCA
Found at i:10963 original size:25 final size:25
Alignment explanation
Indices: 10929--10984 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
10919 TACAAACATC
10929 GAATAGAATTTATGCACCAATGCAT
1 GAATAGAATTTATGCACCAATGCAT
10954 GAATAGAATTTATGCACCAATGCAT
1 GAATAGAATTTATGCACCAATGCAT
*
10979 AAATAG
1 GAATAG
10985 TGCATCGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (25 bp):
GAATAGAATTTATGCACCAATGCAT
Found at i:12598 original size:23 final size:23
Alignment explanation
Indices: 12558--12616 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
12548 ATCTTATATC
* *
12558 GCACTTCGGAGCATTTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
* * *
12581 GCACTACGGTGCAATTCTATGTG
1 GCACTTCGGTGCAATTCTACGCG
12604 GCACTTCGGTGCA
1 GCACTTCGGTGCA
12617 TTTATACGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Found at i:17240 original size:182 final size:184
Alignment explanation
Indices: 16934--17319 Score: 618
Period size: 182 Copynumber: 2.1 Consensus size: 184
16924 TTTTATAATT
* *
16934 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAA
16998 TTATAAAATAAAAAATTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 TTATAAAATAAAAAATTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
* * *
17063 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTTATCCCATATGTTA
131 TGAATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGGCTGA-CCCATATGTTA
*
17118 TATATAATATATTTAATATTTTTTAATT-AAAAAATAGTTTATAATTAATTTAAATAATATAT-A
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAA
* * * *
17181 TTAT-AAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 TTATAAAATAAAAAATTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
*
17245 TGAATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGGCTGAGCCATATGTTA
131 TGAATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGGCTGACCCATATGTTA
* *
17299 CATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
17320 AATTTCGGTT
Statistics
Matches: 188, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
181 29 0.15
182 96 0.51
183 5 0.03
184 40 0.21
185 18 0.10
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAA
TTATAAAATAAAAAATTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
TGAATCTTAAATTATTAATTAAGTTTTAAATGGTTTGGGCTGACCCATATGTTA
Found at i:24333 original size:27 final size:26
Alignment explanation
Indices: 24295--24382 Score: 108
Period size: 27 Copynumber: 3.4 Consensus size: 26
24285 TCCTACAGTG
* *
24295 GATGCTCCAGAAGGGACAACTGCAGCA
1 GATGCTCCAGAAGGAAAAACT-CAGCA
*
24322 GATGCTCTAGAAGGAAAAACT--GCA
1 GATGCTCCAGAAGGAAAAACTCAGCA
*
24346 GATGCTCCAGAAGGAAAAACTACAACA
1 GATGCTCCAGAAGGAAAAACT-CAGCA
24373 GATGCTCCAG
1 GATGCTCCAG
24383 GGGAGACGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
24 23 0.43
27 30 0.57
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.14
Consensus pattern (26 bp):
GATGCTCCAGAAGGAAAAACTCAGCA
Found at i:24351 original size:24 final size:24
Alignment explanation
Indices: 24295--24366 Score: 90
Period size: 24 Copynumber: 2.9 Consensus size: 24
24285 TCCTACAGTG
* *
24295 GATGCTCCAGAAGGGACAACTGCAGCA
1 GATGCTCCAGAAGGAAAAACT---GCA
*
24322 GATGCTCTAGAAGGAAAAACTGCA
1 GATGCTCCAGAAGGAAAAACTGCA
24346 GATGCTCCAGAAGGAAAAACT
1 GATGCTCCAGAAGGAAAAACT
24367 ACAACAGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
24 23 0.56
27 18 0.44
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14
Consensus pattern (24 bp):
GATGCTCCAGAAGGAAAAACTGCA
Found at i:26535 original size:32 final size:31
Alignment explanation
Indices: 26465--26572 Score: 117
Period size: 32 Copynumber: 3.4 Consensus size: 31
26455 TTATGGTCAC
* * *
26465 CCTTGGGTAGGCTCTTAGGCCCCGAGATGCT
1 CCTTGGGTAGGCTCTTAGGCCCCAAGGTACT
**
26496 CCATTGGGTAGATTCTTAGGCCCCAAGGTACT
1 CC-TTGGGTAGGCTCTTAGGCCCCAAGGTACT
* *
26528 CACTTGGGTAGGCTCTAAGGCCCCAAGGTATT
1 C-CTTGGGTAGGCTCTTAGGCCCCAAGGTACT
* *
26560 CTTTAGGTAGGCT
1 CCTTGGGTAGGCT
26573 TTAAGACCGC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
31 12 0.19
32 51 0.80
33 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.28
Consensus pattern (31 bp):
CCTTGGGTAGGCTCTTAGGCCCCAAGGTACT
Found at i:26572 original size:31 final size:32
Alignment explanation
Indices: 26513--26596 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 32
26503 GTAGATTCTT
* *
26513 AGGCCCCAAGGTACTCACTTGGGTAGGCTCTA
1 AGGCCCCAAGGTATTCACTTAGGTAGGCTCTA
* *
26545 AGGCCCCAAGGTATTC-TTTAGGTAGGCTTTA
1 AGGCCCCAAGGTATTCACTTAGGTAGGCTCTA
* * *
26576 AGACCGCAAGGTATTCCCTTA
1 AGGCCCCAAGGTATTCACTTA
26597 TGTTGGCTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 26 0.59
32 18 0.41
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (32 bp):
AGGCCCCAAGGTATTCACTTAGGTAGGCTCTA
Found at i:30517 original size:51 final size:50
Alignment explanation
Indices: 30407--30712 Score: 264
Period size: 51 Copynumber: 6.3 Consensus size: 50
30397 CTTTCCTCTT
* *** *
30407 TGATGAAGGAGCAT-ACTACTTTCTGTTGAAGAAGATTCTTTTATCGCTCC-C
1 TGATGAAGGAGCATCGCTAC-TTCCCATGAAGAAGATTC-TTTACCGC-CCTC
* * *
30458 TGACGAAGGAGCATCGTTACTTCCTCATGAAGAAGATTATTTACCGCCCTC
1 TGATGAAGGAGCATCGCTACTTCC-CATGAAGAAGATTCTTTACCGCCCTC
* * * *
30509 CGATGAAGGAGC-T-G---------ATGAAGAAGATTCTTCATCACCCTC
1 TGATGAAGGAGCATCGCTACTTCCCATGAAGAAGATTCTTTACCGCCCTC
* * * *
30548 CGCTGAGGGAGCATCGCTACTTCCCGATGAAGAAGATTTTTTACCGCCCTC
1 TGATGAAGGAGCATCGCTACTTCCC-ATGAAGAAGATTCTTTACCGCCCTC
*
30599 TGATGAAGGAGCATCGCTACTTCCCGATGAAGAAGATTCTTTACCTCCCTC
1 TGATGAAGGAGCATCGCTACTTCCC-ATGAAGAAGATTCTTTACCGCCCTC
* * *
30650 TGATGAAGGGGCATCGCTACTT-TC-TGATGAAGATTCTTTACCGCCCTC
1 TGATGAAGGAGCATCGCTACTTCCCATGAAGAAGATTCTTTACCGCCCTC
*
30698 TGATGATGGAGCATC
1 TGATGAAGGAGCATC
30713 ACCGCCCTCT
Statistics
Matches: 209, Mismatches: 31, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
39 31 0.15
40 1 0.00
41 1 0.00
48 35 0.17
49 1 0.00
50 4 0.02
51 122 0.58
52 14 0.07
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (50 bp):
TGATGAAGGAGCATCGCTACTTCCCATGAAGAAGATTCTTTACCGCCCTC
Found at i:30547 original size:39 final size:39
Alignment explanation
Indices: 30484--30559 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
30474 TTACTTCCTC
* *
30484 ATGAAGAAGATTATTTACCGCCCTCCGATGAAGGAGCTG
1 ATGAAGAAGATTATTCACCACCCTCCGATGAAGGAGCTG
* * * *
30523 ATGAAGAAGATTCTTCATCACCCTCCGCTGAGGGAGC
1 ATGAAGAAGATTATTCACCACCCTCCGATGAAGGAGC
30560 ATCGCTACTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (39 bp):
ATGAAGAAGATTATTCACCACCCTCCGATGAAGGAGCTG
Found at i:30647 original size:24 final size:24
Alignment explanation
Indices: 30569--30647 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
30559 CATCGCTACT
*
30569 TCCCGATGAAGAAGATTTTTTACC
1 TCCCGATGAAGAAGATTCTTTACC
* * ** *
30593 GCCCTCTGATGAAGGAGCA-TCGCTACT
1 -TCC-C-GATGAAGAAG-ATTCTTTACC
30620 TCCCGATGAAGAAGATTCTTTACC
1 TCCCGATGAAGAAGATTCTTTACC
30644 TCCC
1 TCCC
30648 TCTGATGAAG
Statistics
Matches: 39, Mismatches: 11, Indels: 9
0.66 0.19 0.15
Matches are distributed among these distances:
23 1 0.03
24 18 0.46
25 3 0.08
26 3 0.08
27 13 0.33
28 1 0.03
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (24 bp):
TCCCGATGAAGAAGATTCTTTACC
Found at i:30654 original size:27 final size:27
Alignment explanation
Indices: 30573--30657 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 27
30563 GCTACTTCCC
* *
30573 GATGAAGAAGATTTTTTACCGCCCTCT
1 GATGAAGAAGATTCTTTACCTCCCTCT
* ** *
30600 GATGAAGGAGCA-TCGCTA-CTTCC-C-
1 GATGAAGAAG-ATTCTTTACCTCCCTCT
30624 GATGAAGAAGATTCTTTACCTCCCTCT
1 GATGAAGAAGATTCTTTACCTCCCTCT
30651 GATGAAG
1 GATGAAG
30658 GGGCATCGCT
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
23 1 0.02
24 13 0.30
25 5 0.12
26 4 0.09
27 19 0.44
28 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (27 bp):
GATGAAGAAGATTCTTTACCTCCCTCT
Found at i:30728 original size:48 final size:48
Alignment explanation
Indices: 30579--30730 Score: 146
Period size: 48 Copynumber: 3.1 Consensus size: 48
30569 TCCCGATGAA
* *
30579 GAAGATTTTTTACCGCCCTCTGATGAAGGAGCATCGCTACTTCC-CGATGAA-
1 GAAGATTCTTTACCGCCCTCTGATGAAGGAGCATCACTAC--CCTC--T-AAT
* * * ** *
30630 GAAGATTCTTTACCTCCCTCTGATGAAGGGGCATCGCTACTTTCTGAT
1 GAAGATTCTTTACCGCCCTCTGATGAAGGAGCATCACTACCCTCTAAT
* **
30678 GAAGATTCTTTACCGCCCTCTGATGATGGAGCATCACCGCCCTCTAAT
1 GAAGATTCTTTACCGCCCTCTGATGAAGGAGCATCACTACCCTCTAAT
30726 GAAGA
1 GAAGA
30731 AGATTCTTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
47 1 0.01
48 45 0.54
50 1 0.01
51 37 0.44
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.28
Consensus pattern (48 bp):
GAAGATTCTTTACCGCCCTCTGATGAAGGAGCATCACTACCCTCTAAT
Found at i:30728 original size:99 final size:101
Alignment explanation
Indices: 30523--30758 Score: 250
Period size: 99 Copynumber: 2.3 Consensus size: 101
30513 GAAGGAGCTG
* * * * * *
30523 ATGAAGAAGATTCTTCATCACCCTCCGCTG-AGGGAGCATCGCTACTTCCCGATGAAGAAGATTT
1 ATGAAGAAGATTCTTTACCTCCCTCTGATGAAGGGAGCATCGCTACTTCCC-ATGAAGAAGATTC
* ** *
30587 TTTACCGCCCTCTGATGAAGGAGCATCGCTACTTCCCG
65 TTTACCGCCCTCTGATGAAGGAGCATCAC-ACGCCCCA
* *
30625 ATGAAGAAGATTCTTTACCTCCCTCTGATGAAGGG-GCATCGCTACTT-TC-TGATGAAGATTCT
1 ATGAAGAAGATTCTTTACCTCCCTCTGATGAAGGGAGCATCGCTACTTCCCATGAAGAAGATTCT
*
30687 TTACCGCCCTCTGATGATGGAGCATCAC-CGCCCTCTA
66 TTACCGCCCTCTGATGAAGGAGCATCACACGCCC-C-A
* *
30724 ATGAAGAAGATTCTTTCCCAT-CATCTGATGAAGGG
1 ATGAAGAAGATTCTTTACC-TCCCTCTGATGAAGGG
30759 CCCTCACCAT
Statistics
Matches: 115, Mismatches: 15, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
97 3 0.03
98 1 0.01
99 68 0.59
100 1 0.01
101 1 0.01
102 37 0.32
103 4 0.03
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (101 bp):
ATGAAGAAGATTCTTTACCTCCCTCTGATGAAGGGAGCATCGCTACTTCCCATGAAGAAGATTCT
TTACCGCCCTCTGATGAAGGAGCATCACACGCCCCA
Found at i:30738 original size:51 final size:50
Alignment explanation
Indices: 30574--30757 Score: 158
Period size: 51 Copynumber: 3.7 Consensus size: 50
30564 CTACTTCCCG
* * ** * **
30574 ATGAAGAAGATTTTTTACCGCCCTCTGATGAAGGAGCATCGCTACTTCCCG
1 ATGAAGAAGATTCTTTACCGCCCTCTGATGAAGGAGCATCCCGCCCT-CTA
* * * *
30625 ATGAAGAAGATTCTTTACCTCCCTCTGATGAAGGGGCAT--CGCTACT-TT
1 ATGAAGAAGATTCTTTACCGCCCTCTGATGAAGGAGCATCCCGC-CCTCTA
* * *
30673 CTGATGAAGATTCTTTACCGCCCTCTGATGATGGAGCATCACCGCCCTCTA
1 ATGAAGAAGATTCTTTACCGCCCTCTGATGAAGGAGCATC-CCGCCCTCTA
* ** *
30724 ATGAAGAAGATTCTTTCCCATCATCTGATGAAGG
1 ATGAAGAAGATTCTTTACCGCCCTCTGATGAAGG
30758 GCCCTCACCA
Statistics
Matches: 105, Mismatches: 23, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
48 34 0.32
49 1 0.01
50 3 0.03
51 67 0.64
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (50 bp):
ATGAAGAAGATTCTTTACCGCCCTCTGATGAAGGAGCATCCCGCCCTCTA
Found at i:35111 original size:23 final size:23
Alignment explanation
Indices: 35085--35153 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
35075 TACCACAGCT
* *
35085 CGTATAATTGTATCGAAGTGCCA
1 CGTAGAATTGCATCGAAGTGCCA
* *
35108 CGTAGAATTGCATCGGAGTGCCG
1 CGTAGAATTGCATCGAAGTGCCA
* *
35131 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCATCGAAGTGCCA
35154 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCATCGAAGTGCCA
Found at i:36357 original size:15 final size:14
Alignment explanation
Indices: 36334--36381 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
36324 CCTATAATAC
*
36334 ATAAATCATTTTCAT
1 ATAAATCA-TATCAT
*
36349 ATAACTCATATCAT
1 ATAAATCATATCAT
*
36363 ATAAATTCATACCAT
1 ATAAA-TCATATCAT
36378 ATAA
1 ATAA
36382 CATATAATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 9 0.32
15 19 0.68
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAAATCATATCAT
Found at i:36803 original size:21 final size:21
Alignment explanation
Indices: 36779--36821 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
36769 TCTGGTTCGT
*
36779 TTGAGGGGGTATC-AGTTCCCC
1 TTGAAGGGGTATCGA-TTCCCC
*
36800 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
36821 T
1 T
36822 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:37346 original size:285 final size:285
Alignment explanation
Indices: 36836--37405 Score: 1041
Period size: 285 Copynumber: 2.0 Consensus size: 285
36826 CAGAAATCAC
* * *
36836 ATTTTGAGCTTGAAAATCACTTCATTTTCAGTTTCACACTTCCTATTTCACTTCTTTTAATATTC
1 ATTTTGAGCTCGAAAATCACTTCATTTTCAGTTCCACACTTCCTATTTCACTTCCTTTAATATTC
* *
36901 TTAACTCAAATATACATACTTAAACTAATAAATTTTCATTCAAAATATCTTTAACTTAAAATTCC
66 TTAACTCAAAGATACATACTTAAACTAATAAATTTTCATTCAAAATATCTTTAACTTAAAAATCC
*
36966 ACTCCTCCACATAGCATTCAAGAATCATACCAATTTTTCCATGTTACTCAAACTTAATTCTAACA
131 ACTCCTCCACATAGCATTCAAGAATCATACCAATTTTTCCATGTTACCCAAACTTAATTCTAACA
*
37031 CTTCTAGCTTCTTATTCTCATAGATGACAAGTCAAATTCAACTTCTAATTTGAGTAATGAACTCT
196 CTTCTAGCTTCTTATTCTCATAGATGACAAGTCAAATTCAACTTCCAATTTGAGTAATGAACTCT
37096 TAATCTTTAATCTCTCCTAATTCCA
261 TAATCTTTAATCTCTCCTAATTCCA
37121 ATTTTGAGCTCGAAAATCACTTCATTTTCAGTTCCACACTTCCTATTTCACTTCCTTTAATATTC
1 ATTTTGAGCTCGAAAATCACTTCATTTTCAGTTCCACACTTCCTATTTCACTTCCTTTAATATTC
* * *
37186 TTAACTCAAAGATACGTACTTAAACTAATAAATTTTCATTCAATATCTCTTTAACTTAAAAATCC
66 TTAACTCAAAGATACATACTTAAACTAATAAATTTTCATTCAAAATATCTTTAACTTAAAAATCC
37251 ACTCCTCCACATAGCATTCAAGAATCATACCAATTTTTCCATGTTACCCAAACTTAATTCTAACA
131 ACTCCTCCACATAGCATTCAAGAATCATACCAATTTTTCCATGTTACCCAAACTTAATTCTAACA
*
37316 CTTCTAGCTTCTTATTCTTATAGATGACAAGTCAAATTCAACTTCCAATTTGAGTAATGAACTCT
196 CTTCTAGCTTCTTATTCTCATAGATGACAAGTCAAATTCAACTTCCAATTTGAGTAATGAACTCT
37381 TAATCTTTAATCTCTCCTAATTCCA
261 TAATCTTTAATCTCTCCTAATTCCA
37406 CCATCCTTTG
Statistics
Matches: 274, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
285 274 1.00
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (285 bp):
ATTTTGAGCTCGAAAATCACTTCATTTTCAGTTCCACACTTCCTATTTCACTTCCTTTAATATTC
TTAACTCAAAGATACATACTTAAACTAATAAATTTTCATTCAAAATATCTTTAACTTAAAAATCC
ACTCCTCCACATAGCATTCAAGAATCATACCAATTTTTCCATGTTACCCAAACTTAATTCTAACA
CTTCTAGCTTCTTATTCTCATAGATGACAAGTCAAATTCAACTTCCAATTTGAGTAATGAACTCT
TAATCTTTAATCTCTCCTAATTCCA
Found at i:40412 original size:23 final size:23
Alignment explanation
Indices: 40386--40454 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
40376 CACCACAGCT
*
40386 CGTATAATTGCACCGAAGTTCCA
1 CGTATAATTGCACCGAAGTGCCA
* *
40409 CGTAGT-ATTGCACCGGAGTGCCG
1 CGTA-TAATTGCACCGAAGTGCCA
* *
40432 CATAGAATTGCACCGTAA-TGCCA
1 CGTATAATTGCACCG-AAGTGCCA
40455 TATAATAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
23 34 0.94
24 2 0.06
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
CGTATAATTGCACCGAAGTGCCA
Found at i:41400 original size:2 final size:2
Alignment explanation
Indices: 41393--41428 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
41383 ATATCTCCTA
41393 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
41429 CTATTAATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54524 original size:13 final size:13
Alignment explanation
Indices: 54502--54531 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
54492 ACTAAACACC
54502 TTTC-ACATACCT
1 TTTCAACATACCT
54514 TTTCAACATACCT
1 TTTCAACATACCT
54527 TTTCA
1 TTTCA
54532 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:59873 original size:18 final size:19
Alignment explanation
Indices: 59850--59888 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
59840 TTTTTAATTA
*
59850 ATTTTT-ATTATATAAAAT
1 ATTTTTAATTATAAAAAAT
59868 ATTTTTACATTATAAAAAAT
1 ATTTTTA-ATTATAAAAAAT
59888 A
1 A
59889 AAAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTTAATTATAAAAAAT
Found at i:69771 original size:16 final size:17
Alignment explanation
Indices: 69750--69789 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
69740 ATTTACCGAT
*
69750 GATTTATATATTTATC-
1 GATTTATATATTGATCA
69766 GATTTA-ATATTGATCA
1 GATTTATATATTGATCA
69782 GA-TTATAT
1 GATTTATAT
69790 TTTTTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (17 bp):
GATTTATATATTGATCA
Found at i:71740 original size:23 final size:23
Alignment explanation
Indices: 71708--71792 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
71698 TTATCTTCGC
71708 GAACATGTTCGTTTAATGTTCAT
1 GAACATGTTCGTTTAATGTTCAT
* *
71731 GAGCATGTTCGTTTATATGTTCAA
1 GAACATGTTCGTTTA-ATGTTCAT
** **
71755 GAACATGTTTATTTAGCGTTCAT
1 GAACATGTTCGTTTAATGTTCAT
*
71778 GAACGTGTTCGTTTA
1 GAACATGTTCGTTTA
71793 TCGTCCTTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
23 31 0.62
24 19 0.38
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (23 bp):
GAACATGTTCGTTTAATGTTCAT
Found at i:73714 original size:30 final size:30
Alignment explanation
Indices: 73670--73739 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
73660 ACTTTAGATG
73670 CAAATA-TT-TATAATTATTTTATAATAAT
1 CAAATATTTATATAATTATTTTATAATAAT
73698 CAAATATTTATATAATTATTTTATAATAAT
1 CAAATATTTATATAATTATTTTATAATAAT
73728 CAAATATTTATA
1 CAAATATTTATA
73740 CAAATATGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 6 0.15
29 2 0.05
30 32 0.80
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
CAAATATTTATATAATTATTTTATAATAAT
Found at i:77582 original size:28 final size:30
Alignment explanation
Indices: 77541--77603 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
77531 TTAGTCCTTA
77541 AGCTTCAACTATAAATACCC-AACCCATTT
1 AGCTTCAACTATAAATACCCTAACCCATTT
*
77570 AGCTT-AACTATAAATACCCTAACTCATTT
1 AGCTTCAACTATAAATACCCTAACCCATTT
77599 AGCTT
1 AGCTT
77604 TAAAACCATC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 14 0.44
29 18 0.56
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.32
Consensus pattern (30 bp):
AGCTTCAACTATAAATACCCTAACCCATTT
Found at i:80904 original size:20 final size:20
Alignment explanation
Indices: 80879--80945 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
80869 TTCGTGGATG
80879 GATGCACAGCAGGATGCATC
1 GATGCACAGCAGGATGCATC
* * **
80899 GATGCAAACCTTGATGCATC
1 GATGCACAGCAGGATGCATC
*
80919 GATGCACAGAAGGATGCATC
1 GATGCACAGCAGGATGCATC
80939 GATGCAC
1 GATGCAC
80946 TAATTGCATT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (20 bp):
GATGCACAGCAGGATGCATC
Found at i:81048 original size:20 final size:20
Alignment explanation
Indices: 80967--81047 Score: 76
Period size: 20 Copynumber: 4.0 Consensus size: 20
80957 GGTATTTGAG
* *
80967 TGCATGGATGCACTGCATGA
1 TGCATAGATGCACTGCAGGA
*
80987 TGCATCGATGCACTAGTGCAGG-
1 TGCATAGATGCAC---TGCAGGA
*
81009 TGCATAGATGCACTGTAGGGA
1 TGCATAGATGCACTGCA-GGA
81030 TGCAT-GATGCACTGCAGG
1 TGCATAGATGCACTGCAGG
81048 GGGTGCATGG
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
19 5 0.10
20 24 0.47
21 5 0.10
22 12 0.24
23 5 0.10
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (20 bp):
TGCATAGATGCACTGCAGGA
Found at i:81054 original size:21 final size:20
Alignment explanation
Indices: 81007--81056 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
80997 CACTAGTGCA
*
81007 GGTGCATAGATGCACTGTAGG
1 GGTGCAT-GATGCACTGCAGG
*
81028 GATGCATGATGCACTGCAGGG
1 GGTGCATGATGCACTGCA-GG
81049 GGTGCATG
1 GGTGCATG
81057 GATACACTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.22, C:0.16, G:0.40, T:0.22
Consensus pattern (20 bp):
GGTGCATGATGCACTGCAGG
Done.