Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005051.1 Hibiscus syriacus cultivar Beakdansim tig00011340_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: 74553
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2624 original size:47 final size:48
Alignment explanation
Indices: 2555--2651 Score: 187
Period size: 47 Copynumber: 2.0 Consensus size: 48
2545 CATTCTAATT
2555 TCATCCCAAACTATATGTATACACTAATCACATCCC-TGTTGATAAAA
1 TCATCCCAAACTATATGTATACACTAATCACATCCCTTGTTGATAAAA
2602 TCATCCCAAACTATATGTATACACTAATCACATCCCTTGTTGATAAAA
1 TCATCCCAAACTATATGTATACACTAATCACATCCCTTGTTGATAAAA
2650 TC
1 TC
2652 GTTAGGCAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 36 0.73
48 13 0.27
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (48 bp):
TCATCCCAAACTATATGTATACACTAATCACATCCCTTGTTGATAAAA
Found at i:2831 original size:60 final size:58
Alignment explanation
Indices: 2750--2915 Score: 165
Period size: 58 Copynumber: 2.8 Consensus size: 58
2740 ATAGAATTGG
**
2750 AATATTCAAAAGTTTGGGGACTAATTTAGAAAGAGGGTTATAGTTTAGAGATGAAATTAA
1 AATATTCAAAAGTTTAAGGACTAATTTAGAAAGA--GTTATAGTTTAGAGATGAAATTAA
* * * * * * **
2810 AATGTTCAAAAGTTTAAGGACTAGTTAAGAATA-AGTCATAGTTTAGGGATGATATTGG
1 AATATTCAAAAGTTTAAGGACTAATTTAGAA-AGAGTTATAGTTTAGAGATGAAATTAA
*
2868 AATATTCAAAAGTTTAAGGACCAATTTA-AAATGAAAGTTATAGTTTAG
1 AATATTCAAAAGTTTAAGGACTAATTTAGAAA-G--AGTTATAGTTTAG
2916 GGATATATGA
Statistics
Matches: 86, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
56 1 0.01
57 2 0.02
58 43 0.50
60 39 0.45
61 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.33
Consensus pattern (58 bp):
AATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGTTATAGTTTAGAGATGAAATTAA
Found at i:2876 original size:58 final size:58
Alignment explanation
Indices: 2745--2923 Score: 184
Period size: 60 Copynumber: 3.0 Consensus size: 58
2735 TGGGTATAGA
** * * *
2745 ATTGGAATATTCAAAAGTTTGGGGACTAATTTAGAA-AGAGGGTTATAGTTTAGAGATGAA
1 ATTGGAATATTCAAAAGTTTAAGGACTAATTAAGAATA-A--GTTATAGTTTAGGGATGAT
** * * *
2805 ATTAAAATGTTCAAAAGTTTAAGGACTAGTTAAGAATAAGTCATAGTTTAGGGATGAT
1 ATTGGAATATTCAAAAGTTTAAGGACTAATTAAGAATAAGTTATAGTTTAGGGATGAT
*
2863 ATTGGAATATTCAAAAGTTTAAGGACCAATTTAA-AATGAAAGTTATAGTTTAGGGAT-AT
1 ATTGGAATATTCAAAAGTTTAAGGACTAA-TTAAGAAT--AAGTTATAGTTTAGGGATGAT
2922 AT
1 AT
2924 GATACAGTTA
Statistics
Matches: 99, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
58 43 0.43
59 8 0.08
60 47 0.47
61 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (58 bp):
ATTGGAATATTCAAAAGTTTAAGGACTAATTAAGAATAAGTTATAGTTTAGGGATGAT
Found at i:5713 original size:25 final size:25
Alignment explanation
Indices: 5665--5713 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5655 AGTTGGACAA
* *
5665 CAAGAATGACGTGTTAGTTCGATAG
1 CAAGAATCACGTGTTAGGTCGATAG
*
5690 CAAGAATCACGTGTTAGGTGGATA
1 CAAGAATCACGTGTTAGGTCGATA
5714 CTGCGACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.27
Consensus pattern (25 bp):
CAAGAATCACGTGTTAGGTCGATAG
Found at i:10902 original size:65 final size:65
Alignment explanation
Indices: 10833--10994 Score: 195
Period size: 65 Copynumber: 2.5 Consensus size: 65
10823 AATTAAATTG
* * * * *
10833 AACATTGAATGCATTTCATGCATCAATGCACTTA-CCATGCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTT-TG
10896 AA
65 -A
* * * *
10898 AACATCGAATGCATTTGATGCATCGATGCAC-CAGTCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTTTGA
*
10962 AACATCGAATGCAGTTGATGCATCGATGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
10995 TTAGTGCACC
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 32 0.38
65 49 0.58
66 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTTTGA
Found at i:19312 original size:65 final size:65
Alignment explanation
Indices: 19243--19404 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 65
19233 AATTAAATTG
* * *
19243 AACATCGAATGCATTTCATGCATCGATGCACTTA-CCATGCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTT-TG
19306 AA
65 -A
* * * *
19308 AACATCGAATGCATTTGATACATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTTTGA
* *
19372 AACATCGAATGCACTTGATGCATCGTTGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
19405 TTAGTGCACC
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 30 0.36
65 51 0.61
66 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTTTGA
Found at i:21149 original size:22 final size:23
Alignment explanation
Indices: 21110--21155 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
21100 GTTTTGACCT
21110 GACCCGACCCGTTCACCCAACCC
1 GACCCGACCCGTTCACCCAACCC
* *
21133 GACCCGA-CCGTTGACCCGACCC
1 GACCCGACCCGTTCACCCAACCC
21155 G
1 G
21156 TTGACCGACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.20, C:0.52, G:0.20, T:0.09
Consensus pattern (23 bp):
GACCCGACCCGTTCACCCAACCC
Found at i:21150 original size:12 final size:13
Alignment explanation
Indices: 21109--21172 Score: 75
Period size: 12 Copynumber: 5.3 Consensus size: 13
21099 AGTTTTGACC
21109 TGACCCGACCCGT
1 TGACCCGACCCGT
* *
21122 TCACCCAACCC--
1 TGACCCGACCCGT
21133 -GACCCGA-CCGT
1 TGACCCGACCCGT
21144 TGACCCGACCCGT
1 TGACCCGACCCGT
21157 TGA-CCGACCCGT
1 TGACCCGACCCGT
21169 TGAC
1 TGAC
21173 TGTTGATCGT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 2 0.05
10 5 0.12
12 19 0.45
13 16 0.38
ACGTcount: A:0.19, C:0.47, G:0.20, T:0.14
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:21185 original size:14 final size:14
Alignment explanation
Indices: 21166--21195 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21156 TTGACCGACC
*
21166 CGTTGACTGTTGAT
1 CGTTGACCGTTGAT
21180 CGTTGACCGTTGAT
1 CGTTGACCGTTGAT
21194 CG
1 CG
21196 GGTGGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.30, T:0.37
Consensus pattern (14 bp):
CGTTGACCGTTGAT
Found at i:21252 original size:29 final size:29
Alignment explanation
Indices: 21195--21275 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 29
21185 ACCGTTGATC
*
21195 GGGTGGTATTTTGGTAATTATTTTAAAAA
1 GGGTGGTATTTTGGTAATTATCTTAAAAA
* * *
21224 TGGTGGTATTCTGGTAATTATCTTGAAAA
1 GGGTGGTATTTTGGTAATTATCTTAAAAA
** *
21253 GGGTTCTATTTTCGTAATTATCT
1 GGGTGGTATTTTGGTAATTATCT
21276 ATTGATCTCC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (29 bp):
GGGTGGTATTTTGGTAATTATCTTAAAAA
Found at i:22003 original size:24 final size:24
Alignment explanation
Indices: 21969--22040 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
21959 TTTTTGACAA
21969 GATTTTGATATGATACTTGACCTG
1 GATTTTGATATGATACTTGACCTG
* * *
21993 GATTTTTATATGATACATGACATG
1 GATTTTGATATGATACTTGACCTG
* * *
22017 GATTCTGATCTGCTACTTGACCTG
1 GATTTTGATATGATACTTGACCTG
22041 AATTATGTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (24 bp):
GATTTTGATATGATACTTGACCTG
Found at i:23946 original size:82 final size:80
Alignment explanation
Indices: 23842--24004 Score: 290
Period size: 82 Copynumber: 2.0 Consensus size: 80
23832 CATACTACTA
*
23842 AAACTAATTTATAAGCAACAAACATATATTTAATATACATGCCAACTAGATAGGTTAAAAGCAGT
1 AAACTAATTTAAAAGCAACAAACATATATTTAATATACATGCCAACTAGATAGGTTAAAAGCAGT
*
23907 AAATGTCGTATTGAT
66 AAATGTCGTACTGAT
23922 AAACTAATTTACCAAAGCAACAAACATATATTTAATATACATGCCAACTAGATAGGTTAAAAGCA
1 AAACTAATTTA--AAAGCAACAAACATATATTTAATATACATGCCAACTAGATAGGTTAAAAGCA
23987 GTAAATGTCGTACTGAT
64 GTAAATGTCGTACTGAT
24004 A
1 A
24005 CTAGAATAGG
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
80 11 0.14
82 68 0.86
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.28
Consensus pattern (80 bp):
AAACTAATTTAAAAGCAACAAACATATATTTAATATACATGCCAACTAGATAGGTTAAAAGCAGT
AAATGTCGTACTGAT
Found at i:24172 original size:2 final size:2
Alignment explanation
Indices: 24165--24195 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24155 AATTGACTTT
24165 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24196 TTCTTACAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27604 original size:44 final size:43
Alignment explanation
Indices: 27553--27672 Score: 136
Period size: 44 Copynumber: 2.7 Consensus size: 43
27543 TTGAGAATTA
27553 GCGGCGTTTCTAGTGCAAAAACGCCGCTAAATGCATGGTATATT
1 GCGGCGTTTCTAGTGC-AAAACGCCGCTAAATGCATGGTATATT
* * **
27597 GCGGCGTTTGTA-TACTACAAACGCCGCTAAATGTTTGGTATATT
1 GCGGCGTTTCTAGTGC-A-AAACGCCGCTAAATGCATGGTATATT
*
27641 GCGGCATTTCTAGTTTGC-AAACGCCGCTAAAT
1 GCGGCGTTTCTAG--TGCAAAACGCCGCTAAAT
27673 AACACAGGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
43 3 0.05
44 59 0.92
47 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (43 bp):
GCGGCGTTTCTAGTGCAAAACGCCGCTAAATGCATGGTATATT
Found at i:28052 original size:21 final size:21
Alignment explanation
Indices: 27994--28062 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
27984 GCTGATATGT
* * *
27994 TGCTTCTCTCTGTGCTGCCGC
1 TGCTTCTCTCTCTGCTTCCAC
*
28015 TGCTTCTTTCTCTGCTTCCAC
1 TGCTTCTCTCTCTGCTTCCAC
*
28036 TGCTGCTCTCTCTGCTTCC-C
1 TGCTTCTCTCTCTGCTTCCAC
28056 TTGCTTC
1 -TGCTTC
28063 ATTTTCCGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 1 0.03
21 39 0.98
ACGTcount: A:0.01, C:0.39, G:0.16, T:0.43
Consensus pattern (21 bp):
TGCTTCTCTCTCTGCTTCCAC
Found at i:34156 original size:52 final size:52
Alignment explanation
Indices: 34088--34246 Score: 291
Period size: 52 Copynumber: 3.1 Consensus size: 52
34078 TAACAGCAAA
*
34088 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAATCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
* *
34140 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAATAGTCTTCAAC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
34192 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
34244 ATA
1 ATA
34247 TTGTTCAGTA
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 102 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (52 bp):
ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
Found at i:35369 original size:42 final size:42
Alignment explanation
Indices: 35316--35450 Score: 157
Period size: 42 Copynumber: 3.2 Consensus size: 42
35306 TTATACAAAA
* * *
35316 AAACGCTGCTAATTTACCACTCTATTGCGGCGTTTTTGGTAT
1 AAACGCCGCTAATTTACCACTATATTGCGGCGTTTTTGCTAT
* * * *
35358 AAACGCCGCTAAATTAACACTATATTGCGGTGTTTTAGCTA-
1 AAACGCCGCTAATTTACCACTATATTGCGGCGTTTTTGCTAT
* * *
35399 AAACGCCGCTACATGT-CTACTATATTGCGGCGTTTTTACTAT
1 AAACGCCGCTA-ATTTACCACTATATTGCGGCGTTTTTGCTAT
35441 AAACGCCGCT
1 AAACGCCGCT
35451 GTTGTTTAAC
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
41 31 0.40
42 46 0.60
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (42 bp):
AAACGCCGCTAATTTACCACTATATTGCGGCGTTTTTGCTAT
Found at i:36459 original size:37 final size:37
Alignment explanation
Indices: 36415--36519 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
36405 CATTTTTGTC
36415 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
36452 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
36489 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
36520 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:41748 original size:183 final size:183
Alignment explanation
Indices: 41440--41972 Score: 996
Period size: 183 Copynumber: 2.9 Consensus size: 183
41430 ATTAAATCCG
41440 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
41505 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
41570 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
*
41623 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGTCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
41688 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
41753 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
41806 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
41871 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
41935 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTT
41973 TAGTTAAACC
Statistics
Matches: 341, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
182 1 0.00
183 340 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:43157 original size:36 final size:34
Alignment explanation
Indices: 43117--43230 Score: 93
Period size: 36 Copynumber: 3.2 Consensus size: 34
43107 CACTCAAATT
43117 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-A-TTTGTCTCACTTGAGAC
* * * * ** *
43153 TGTTTTTCTCGAAAAAAGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAAACA-ATTTGTCTCACTTGAGAC
*
43189 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGAC
*
43225 CGTTTT
1 TGTTTT
43231 CACTCGAAAG
Statistics
Matches: 59, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
35 4 0.07
36 49 0.83
37 6 0.10
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (34 bp):
TGTTTTTCTTAAAACAATTTGTCTCACTTGAGAC
Found at i:43193 original size:72 final size:75
Alignment explanation
Indices: 43101--43275 Score: 200
Period size: 72 Copynumber: 2.4 Consensus size: 75
43091 ATGCAGATGA
* * * *
43101 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
43163 GAAA-AAAG-AT
64 GAAAGAAAGCAT
*
43173 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
*
43238 AAGAAGGCAT
66 AAGAAAGCAT
* **
43248 TTCATTTCACCCAAGGCTGTTTTT-TTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
43276 GAAGATTTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
71 1 0.01
72 50 0.57
73 8 0.09
74 3 0.03
75 8 0.09
76 18 0.20
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAAGCAT
Found at i:43552 original size:108 final size:104
Alignment explanation
Indices: 43346--43665 Score: 443
Period size: 108 Copynumber: 3.1 Consensus size: 104
43336 ATAGTTTCTC
* * *
43346 TTGAAAACATTTCCCTTGGAATTAATTTTTTCTCTCC-TGAGATAGTTTCCCTCGAAACAGAAAT
1 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAAT
* *
43410 TTTATCT-CCTTGAGACAGTTTCTCTTGGAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
43448 TTGAAAACATTTCCCTTAAAATGATTTTTTTTTCTCTCTCTTGAGATAGTTTCCCTCGAAACAGA
1 TTGAAAACATTTCCCTTGAAATGA--TTTTTTTCTCTC-CTTGAGATAGTTTCCCTCGAAACAG-
43513 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
62 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * * * *
43556 TTGAAAACATTTCTCTTGAAATGAATTTTATCTC-GCTTGAGATAGTTTCCCTTGAAAC-G-AAT
1 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAAT
** *
43618 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
43657 TTGAAAACA
1 TTGAAAACA
43666 ATTTAACGAA
Statistics
Matches: 197, Mismatches: 15, Indels: 13
0.88 0.07 0.06
Matches are distributed among these distances:
101 48 0.24
102 21 0.11
103 1 0.01
104 33 0.17
105 1 0.01
106 31 0.16
107 10 0.05
108 52 0.26
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:43618 original size:36 final size:36
Alignment explanation
Indices: 43565--43640 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
43555 ATTGAAAACA
* * * *
43565 TTTCTCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
43601 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
43637 TTTC
1 TTTC
43641 TCTCCAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:44043 original size:105 final size:105
Alignment explanation
Indices: 43809--44470 Score: 902
Period size: 105 Copynumber: 6.3 Consensus size: 105
43799 AACATCCGAG
* * * * * * *
43809 ATTTCAACTCCACGACGAAGGATATCGTGACACTCGAGACAACACAAGTTCAACTTCACAAAGAA
1 ATTTCAACTTCACAACGAAGGATAT--TG-GACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
43874 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
43918 ATTTCAACTTCACAATGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
43983 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
44023 ATTTCAACTTCACAACGAAGGATATTGGACTTCAAACAACGCAAGTTCAACTTCACGACAAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
44088 ACCGCTGCTTGTCAAAAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
44128 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
44193 ACCGCTGCTTGTCAACAACAACTTCCCAATATCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
44233 ATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
44298 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGAGTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
** * * *
44333 ATTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** *
44398 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* * *
44439 ATTTCAACTTCACGACGGATGATATTGGACTC
1 ATTTCAACTTCACAACGAAGGATATTGGACTC
44471 GGAACAATGC
Statistics
Matches: 499, Mismatches: 48, Indels: 15
0.89 0.09 0.03
Matches are distributed among these distances:
100 80 0.16
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 300 0.60
106 82 0.16
107 2 0.00
109 22 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:45066 original size:37 final size:37
Alignment explanation
Indices: 45013--45117 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
45003 CATTTTCGTC
45013 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
45050 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
45087 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
45118 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:45513 original size:18 final size:17
Alignment explanation
Indices: 45474--45516 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
45464 ATTATATGGA
45474 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
45490 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
45508 TATTATTAT
1 TATTATTAT
45517 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:47449 original size:18 final size:18
Alignment explanation
Indices: 47422--47456 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47412 ACCCAAAATA
47422 TAACTGTTTGGAAAATGT
1 TAACTGTTTGGAAAATGT
* *
47440 TAACTTTTTGGATAATG
1 TAACTGTTTGGAAAATG
47457 CCGGTCATAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (18 bp):
TAACTGTTTGGAAAATGT
Found at i:47590 original size:23 final size:23
Alignment explanation
Indices: 47564--47612 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
47554 TTTGGCTCAA
47564 TGGCTCGACTCAGCCCAGCTTCT
1 TGGCTCGACTCAGCCCAGCTTCT
*
47587 TGGCTCGACTCATCCCAGCTTCT
1 TGGCTCGACTCAGCCCAGCTTCT
47610 TGG
1 TGG
47613 TTCAATCGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.37, G:0.22, T:0.29
Consensus pattern (23 bp):
TGGCTCGACTCAGCCCAGCTTCT
Found at i:48302 original size:30 final size:32
Alignment explanation
Indices: 48266--48326 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
48256 AATAAAAATA
48266 TTCATAAT-TAA-AATATATTTATTAATATTT
1 TTCATAATATAATAATATATTTATTAATATTT
* *
48296 TTCATAATATAATATTATATTTTTTAATATT
1 TTCATAATATAATAATATATTTATTAATATT
48327 ATAATAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 8 0.30
31 3 0.11
32 16 0.59
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (32 bp):
TTCATAATATAATAATATATTTATTAATATTT
Found at i:48319 original size:23 final size:23
Alignment explanation
Indices: 48285--48339 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
48275 AAAATATATT
*
48285 TATTA-ATATTTTTCATAATATAA
1 TATTATAT-TTTTTAATAATATAA
*
48308 TATTATATTTTTTAATATTATAA
1 TATTATATTTTTTAATAATATAA
*
48331 TAATATATT
1 TATTATATT
48340 CAATTATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTATATTTTTTAATAATATAA
Found at i:48325 original size:20 final size:22
Alignment explanation
Indices: 48285--48336 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
48275 AAAATATATT
48285 TATTAATATTTTTCATAATATAA
1 TATTAATATTTTT-ATAATATAA
*
48308 TATT-ATATTTTT-TAATATTA
1 TATTAATATTTTTATAATATAA
*
48328 TAATAATAT
1 TATTAATAT
48337 ATTCAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 10 0.38
21 4 0.15
22 8 0.31
23 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTAATATTTTTATAATATAA
Found at i:65818 original size:26 final size:26
Alignment explanation
Indices: 65781--65892 Score: 143
Period size: 26 Copynumber: 4.3 Consensus size: 26
65771 AATCTTTGGT
65781 ATAAATGAAACCTTCGAGTGCAATTG
1 ATAAATGAAACCTTCGAGTGCAATTG
* *
65807 ATAAATGGAACCTTTGAGTGCAATTG
1 ATAAATGAAACCTTCGAGTGCAATTG
* * * **
65833 ATAAATGACACTTTCGAGTGTAATAA
1 ATAAATGAAACCTTCGAGTGCAATTG
* *
65859 ATAAATGAAACCTTTGAGTGCAAGTG
1 ATAAATGAAACCTTCGAGTGCAATTG
65885 ATAAATGA
1 ATAAATGA
65893 CACTATGTGT
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 70 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.29
Consensus pattern (26 bp):
ATAAATGAAACCTTCGAGTGCAATTG
Found at i:65849 original size:52 final size:52
Alignment explanation
Indices: 65781--65896 Score: 169
Period size: 52 Copynumber: 2.2 Consensus size: 52
65771 AATCTTTGGT
* * ** * *
65781 ATAAATGAAACCTTCGAGTGCAATTGATAAATGGAACCTTTGAGTGCAATTG
1 ATAAATGACACTTTCGAGTGCAATAAATAAATGAAACCTTTGAGTGCAAGTG
*
65833 ATAAATGACACTTTCGAGTGTAATAAATAAATGAAACCTTTGAGTGCAAGTG
1 ATAAATGACACTTTCGAGTGCAATAAATAAATGAAACCTTTGAGTGCAAGTG
65885 ATAAATGACACT
1 ATAAATGACACT
65897 ATGTGTGCAA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (52 bp):
ATAAATGACACTTTCGAGTGCAATAAATAAATGAAACCTTTGAGTGCAAGTG
Found at i:67113 original size:166 final size:165
Alignment explanation
Indices: 66904--67594 Score: 455
Period size: 166 Copynumber: 4.1 Consensus size: 165
66894 TCCTTCGGGA
* * * *
66904 AACTATTCATCACAACAACTCCTCTATC-GGTGGGGTGCAACACTATGACATGATGGAGATTTCC
1 AACTATTCATCACAACAACTCCTCTATCTGAT-GGATCCAACACTATGACATGA-AGAGATTTCC
* * **
66968 TACAAATGGTGAAAGTGTTTCTTGTGAAAATAGTCTTCCCTTTTATAGAGAATCCCTACATTTTT
64 TACAAAAGGTGAAAGTGTTTCTTGTGAAAATAGACTTCCCTTTTATAGAGAATCTATACATTTTT
*
67033 AGTTAATTTTATCTTCAGATAATATTCCTATTAGGT-
129 AGTTAATTTTATCTTCAGATAATATTCCCATTAGGTG
* * * * * *
67069 AACTATTCATCCCAACAACTCCCCTATCTAATAGGATTCAACACTATGACATGGCAGAGATTCCC
1 AACTATTCATCACAACAACTCCTCTATCTGAT-GGATCCAACACTATGACAT-GAAGAGATTTCC
* *** * * * * * * *
67134 TGCAAAAGGTGAAAACAATTT-TTCTGATAATGGCCTTCCC-TTTAAAGAGAATGTATGCATTTT
64 TACAAAAGGTG-AAAGTGTTTCTTGTGAAAATAGACTTCCCTTTTATAGAGAATCTATACATTTT
* * * * * *
67197 CAATTCAAATTTATCTTCAGATAATGTTCCCCTTCGGTG
128 TAGTT-AATTTTATCTTCAGATAATATTCCCATTAGGTG
* * * ** *
67236 AACTATTCATCACAAAAACTTCTTTATCTGATGGATCCAATGCTATGACATGGAAGAGATTTTCT
1 AACTATTCATCACAACAACTCCTCTATCTGATGGATCCAACACTATGACAT-GAAGAGATTTCCT
* * * * * * *
67301 ACAAAAGGTGAAAGTGATTCATGTGAAAATA-ACTTCCTTTTTTTAGAGAATCTTTTCATTTACT
65 ACAAAAGGTGAAAGTGTTTCTTGTGAAAATAGACTTCCCTTTTATAGAGAATCTATACATTT-TT
* * * * *
67365 AGTCAATTTTATCTTAAGATAATGTCCCCCTTTAGG-G
129 AGTTAATTTTATCTTCAGATAATAT-TCCCATTAGGTG
* * * * * *** * ** *
67402 AATTATTCATCACAATAATTCCCCTTTCTGATAGGAAATAACACAATGACATGGCGAGATTTCTT
1 AACTATTCATCACAACAACTCCTCTATCTGAT-GGATCCAACACTATGACATGAAGAGATTTCCT
* * * * ** * * *
67467 GCAAAAGGTTAAAACT-TTTCTTGTGTAAATATCCTTCCCTTTTTTTTTTAGAGAATCTCTTCAT
65 ACAAAAGG-TGAAAGTGTTTCTTGTGAAAATAGACTTCCC----TTTTATAGAGAATCTATACAT
* * * *
67531 TTTCCAGTCAATTTTATCTTGAGATAATTTTCTCC-TTCAGG-G
125 TTT-TAGTTAATTTTATCTTCAGATAATATTC-CCATT-AGGTG
* * *
67573 AAGTATTCATGACTACAACTCC
1 AACTATTCATCACAACAACTCC
67595 CATGTCTATA
Statistics
Matches: 403, Mismatches: 104, Indels: 32
0.75 0.19 0.06
Matches are distributed among these distances:
165 57 0.14
166 210 0.52
167 65 0.16
170 3 0.01
171 68 0.17
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (165 bp):
AACTATTCATCACAACAACTCCTCTATCTGATGGATCCAACACTATGACATGAAGAGATTTCCTA
CAAAAGGTGAAAGTGTTTCTTGTGAAAATAGACTTCCCTTTTATAGAGAATCTATACATTTTTAG
TTAATTTTATCTTCAGATAATATTCCCATTAGGTG
Found at i:67508 original size:332 final size:332
Alignment explanation
Indices: 66869--67481 Score: 745
Period size: 332 Copynumber: 1.8 Consensus size: 332
66859 TCTTCGCCAG
* * * *
66869 TCAATTTTATATTCAGATAATGTTATCCTTCGGGAAACTATTCATCACAACAACTCCTCTATCGG
1 TCAAATTTATATTCAGATAATGTTACCCTTCGGGAAACTATTCATCACAAAAACTCCTCTATCGA
* * * * * *
66934 TGGGGTGCAACACTATGACATGATGGAGATTTCCTACAAATGGTGAAAGTGTTTCTTGTGAAAAT
66 TGGGATCCAACACTATGACATGATAGAGATTTCCTACAAAAGGTGAAAGTGATTCATGTGAAAAT
* * * * *
66999 AGTCTTCCCTTTTATAGAGAATCCCTACATTTTTAGTTAATTTTATCTTCAGATAATATTCCTAT
131 AGACTTCCCTTTTATAGAGAATCCCTACATTTCTAGTCAATTTTATCTTAAGATAATATCCCTAT
* * * *
67064 TAGGTAACTATTCATCCCAACAACTCCCCTATCTAATAGGATTCAACACTATGACATGGCAGAGA
196 TAGGGAACTATTCATCACAACAACTCCCCTATCTAATAGGAATCAACACAATGACATGGCAGAGA
*
67129 TTCCCTGCAAAAGGTGAAAACAATTTTTCTGATAATGGCCTTCCCTTTAAAGAGAATGTATGCAT
261 TTCCCTGCAAAAGGTGAAAACAATTTTTCTGATAATAGCCTTCCCTTTAAAGAGAATGTATGCAT
67194 TTTCAAT
326 TTTCAAT
* * * *
67201 TCAAATTTATCTTCAGATAATGTTCCCCTTCGGTG-AACTATTCATCACAAAAACTTCTTTATCT
1 TCAAATTTATATTCAGATAATGTTACCCTTCGG-GAAACTATTCATCACAAAAACTCCTCTATC-
** *
67265 GAT-GGATCCAATGCTATGACATGGA-AGAGATTTTCTACAAAAGGTGAAAGTGATTCATGTGAA
64 GATGGGATCCAACACTATGACAT-GATAGAGATTTCCTACAAAAGGTGAAAGTGATTCATGTGAA
* * ** * *
67328 AATA-ACTTCCTTTTTTTAGAGAATCTTTTCATTTACTAGTCAATTTTATCTTAAGATAATGTCC
128 AATAGACTTCCCTTTTATAGAGAATCCCTACATTT-CTAGTCAATTTTATCTTAAGATAATAT--
* * * * *
67392 CCCT-TTAGGGAATTATTCATCACAATAATTCCCCTTTCTGATAGGAAAT-AACACAATGACATG
190 CCCTATTAGGGAACTATTCATCACAACAACTCCCCTATCTAATAGG-AATCAACACAATGACATG
* * *
67455 GC-GAGATTTCTTGCAAAAGGTTAAAAC
254 GCAGAGATTCCCTGCAAAAGGTGAAAAC
67482 TTTTCTTGTG
Statistics
Matches: 234, Mismatches: 40, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
331 24 0.10
332 151 0.65
333 54 0.23
334 5 0.02
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Consensus pattern (332 bp):
TCAAATTTATATTCAGATAATGTTACCCTTCGGGAAACTATTCATCACAAAAACTCCTCTATCGA
TGGGATCCAACACTATGACATGATAGAGATTTCCTACAAAAGGTGAAAGTGATTCATGTGAAAAT
AGACTTCCCTTTTATAGAGAATCCCTACATTTCTAGTCAATTTTATCTTAAGATAATATCCCTAT
TAGGGAACTATTCATCACAACAACTCCCCTATCTAATAGGAATCAACACAATGACATGGCAGAGA
TTCCCTGCAAAAGGTGAAAACAATTTTTCTGATAATAGCCTTCCCTTTAAAGAGAATGTATGCAT
TTTCAAT
Found at i:69085 original size:21 final size:21
Alignment explanation
Indices: 69047--69093 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
69037 TAAATAATAT
*
69047 AGAAACAAAGGTAAATGAGGG
1 AGAAACAAAGATAAATGAGGG
* * *
69068 AGAAACAGAGATAGATGATGG
1 AGAAACAAAGATAAATGAGGG
69089 A-AAAC
1 AGAAAC
69094 CTAAAGCATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.53, C:0.06, G:0.30, T:0.11
Consensus pattern (21 bp):
AGAAACAAAGATAAATGAGGG
Found at i:70629 original size:166 final size:167
Alignment explanation
Indices: 70105--71063 Score: 749
Period size: 166 Copynumber: 5.7 Consensus size: 167
70095 ATATAAAAAT
* * * * *
70105 GGGAGTTGTGGTGATAAATAGTTCCCCGAAGGGAAACATTATATGAAGATAACATTGACTGGAAA
1 GGGAGTTGTTGTGATGAATAGTTCCCTGAAGGGGAACATTATATGAAGATAAAATTGACTGGAAA
* * * * * * *
70170 AGGCATAGATTCTCT-AAAAAAAGGAA--TTCCATTTTCAC---AAGTGCTTTCACCTTTTGCAT
66 ATGCAAAGATTCTCTGAAAAAAGGGAAGGTT--ATTTTCACAAGAAGCGCTTTCACTTTTTGTAG
* ** * *
70229 AGAATCTCTTCCATGTCATAGTGCTGCATCCCATTAAACAG
129 GGAATCTC-TCCATGTCATAGTATTGCATCCCATCAGAC-G
* ** * *
70270 GGGAGTTGTTATGATGAATAGTTCCCTGAAAGGATAATATTATCTGAAGATAAAATTGACTGGAA
1 GGGAGTTGTTGTGATGAATAGTTCCCTG-AAGGGGAACATTATATGAAGATAAAATTGACTGGAA
* * * *
70335 AATGCAAAAATTCTCTGAAAAAAGGGAAGATAATTTTCACAAGAAGCACTTTCACCTTTTT-TAG
65 AATGCAAAGATTCTCTGAAAAAAGGGAAGGTTATTTTCACAAGAAGCGCTTTCA-CTTTTTGTAG
* * ** *
70399 GGAATCTCTACTATGCCATAG-AGTTATATCCCATCAGATAG
129 GGAATCTCT-CCATGTCATAGTA-TTGCATCCCATCAGA-CG
* * * * *
70440 GGGAGTTGTTATAATTAATAGTTCCCTGAAGGGGAACATCATATGAAGA-AACAATTAACTGGAA
1 GGGAGTTGTTGTGATGAATAGTTCCCTGAAGGGGAACATTATATGAAGATAA-AATTGACTGGAA
* * * * * *
70504 AATACAGAGATTCTCT-AAAAAATGGAAGGTTTTTTTCACAAGAACCGTTTTCACTTTTTGTA-G
65 AATGCAAAGATTCTCTGAAAAAAGGGAAGGTTATTTTCACAAGAAGCGCTTTCACTTTTTGTAGG
* *
70567 GAATCTCTGTCATGTCATAGTATTGCATCGCATCAGACG
130 GAATCTCT-CCATGTCATAGTATTGCATCCCATCAGACG
* ** * * *
70606 GGGAGTTGATGTGATGAATAGTTCCCCAAAAGTGAACATTATCTG-AGATAAAATTGACTGGAAA
1 GGGAGTTGTTGTGATGAATAGTTCCCTGAAGGGGAACATTATATGAAGATAAAATTGACTGGAAA
* * * * * * ** *
70670 ATGCATAGATTCTATGGAAAGAAGAAGAAGGCTATTTTCACAAGATGCATTTTCA-TCTTTCGTA
66 ATGCAAAGATTCTCT-GAAAAAAG-GGAAGGTTATTTTCACAAGAAGCGCTTTCACT-TTTTGTA
* * **
70734 GGGAATCTCTACCATATCATAGT-TTCGCATCTCATCAGATA
128 GGGAATCTCT-CCATGTCATAGTATT-GCATCCCATCAGACG
* * * *** *
70775 GGGAGTTCTTGTGAAGAATATTTTTTTGAAGGGGAACATTATTTGAAGATAAAATTGACT-G---
1 GGGAGTTGTTGTGATGAATAGTTCCCTGAAGGGGAACATTATATGAAGATAAAATTGACTGGAAA
* * * * *
70836 ATGTAGAGATTCTCTGGAAAAAAGGGGAAGGCTATTTTCACAAGATGCGCTTTCACCTTTTGTAG
66 ATGCAAAGATTCTCT-GAAAAAA-GGGAAGGTTATTTTCACAAGAAGCGCTTTCACTTTTTGTAG
* * * * *
70901 GGAATCTTTGCCATGCCATAGTGTTGCATCCTATCAGTCG
129 GGAATCTCT-CCATGTCATAGTATTGCATCCCATCAGACG
* * **
70941 AGGGAGTTGTTGTGATGAATAGTT-CCTAAAGGGGAACA-TA-AT-AATGATAAAATTAACTACA
1 -GGGAGTTGTTGTGATGAATAGTTCCCTGAAGGGGAACATTATATGAA-GATAAAATTGACT-GG
* * * * * *
71002 AAAATGCAAAAATGCCCTG-AAAAATGGAAGGTTATTTTCATAAGAAGCGTTTTCACTTTTTG
63 AAAATGCAAAGATTCTCTGAAAAAAGGGAAGGTTATTTTCACAAGAAGCGCTTTCACTTTTTG
71064 CGAAGCTCGG
Statistics
Matches: 628, Mismatches: 134, Indels: 63
0.76 0.16 0.08
Matches are distributed among these distances:
163 2 0.00
164 13 0.02
165 53 0.08
166 206 0.33
167 87 0.14
168 68 0.11
169 117 0.19
170 77 0.12
171 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.31
Consensus pattern (167 bp):
GGGAGTTGTTGTGATGAATAGTTCCCTGAAGGGGAACATTATATGAAGATAAAATTGACTGGAAA
ATGCAAAGATTCTCTGAAAAAAGGGAAGGTTATTTTCACAAGAAGCGCTTTCACTTTTTGTAGGG
AATCTCTCCATGTCATAGTATTGCATCCCATCAGACG
Found at i:70649 original size:335 final size:333
Alignment explanation
Indices: 70121--70966 Score: 855
Period size: 335 Copynumber: 2.5 Consensus size: 333
70111 TGTGGTGATA
* * * *
70121 AATAGTTCCCCGAAGGGAAACATTATATGAAGATAAC-ATTGACTGGAAAAGGCATAGATTCTCT
1 AATAGTTCCCTGAAGGGGAACATTATATGAAGATAACAATTGACTGGAAAATGCAGAGATTCTCT
*
70185 AAAAAAAGGAA--TTCCATTTTCACAAG-TGCTTTCACCTTTTGCATA-GAATCTCT-TCCATGT
66 AAAAAAAGGAAGGTT--ATTTTCACAAGACGCTTTCACCTTTTG--TAGGAATCTCTGT-CATGT
* * * * ** *
70245 CATAGTGCTGCATCCCATTAAACAGGGGAGTTGTTATGATGAATAGTTCCCTGAAAGGATAATAT
126 CATAGTGTTGCAT-CCATCAGAC-GGGGAGTTGTTGTGATGAATAGTTCCCCAAAAGGA-AACAT
* *
70310 TATCTGAAGATAAAATTGACTGGAAAATGCAAAAATTCTCT-GAAAAAAG-GGAA-GATAATTTT
188 TATCTG-AGATAAAATTGACTGGAAAATGCAAAAATTCTATGGAAAAAAGAAGAAGGAT-ATTTT
** * * *
70372 CACAAGAAGCACTTTCACCTTTTTTAGGGAATCTCTACTATGCCATAGAGTT-ATATCCCATCAG
251 CACAAGAAGCACTTTCACCTTTCGTAGGGAATCTCTACCATACCATAG-GTTCACATCCCATCAG
* *
70436 ATAGGGGAGTTGTTAT-AATT
315 ATA-GGGAGTTCTTATGAA-G
* * *
70456 AATAGTTCCCTGAAGGGGAACATCATATGAAGA-AACAATTAACTGGAAAATACAGAGATTCTCT
1 AATAGTTCCCTGAAGGGGAACATTATATGAAGATAACAATTGACTGGAAAATGCAGAGATTCTCT
* * * *
70520 AAAAAATGGAAGGTTTTTTTCACAAGAACCGTTTTCACTTTTTGTAGGAATCTCTGTCATGTCAT
66 AAAAAAAGGAAGGTTATTTTCACAAG-A-CGCTTTCACCTTTTGTAGGAATCTCTGTCATGTCAT
* *
70585 AGTATTGCATCGCATCAGACGGGGAGTTGATGTGATGAATAGTTCCCCAAAAGTG-AACATTATC
129 AGTGTTGCATC-CATCAGACGGGGAGTTGTTGTGATGAATAGTTCCCCAAAAG-GAAACATTATC
* * * *
70649 TGAGATAAAATTGACTGGAAAATGCATAGATTCTATGGAAAGAAGAAGAAGGCTATTTTCACAAG
192 TGAGATAAAATTGACTGGAAAATGCAAAAATTCTATGGAAAAAAGAAGAAGGATATTTTCACAAG
* * * * * * *
70714 ATGCATTTTCATCTTTCGTAGGGAATCTCTACCATATCATAGTTTCGCATCTCATCAGATAGGGA
257 AAGCACTTTCACCTTTCGTAGGGAATCTCTACCATACCATAGGTTCACATCCCATCAGATAGGGA
*
70779 GTTCTTGTGAAG
322 GTTCTTATGAAG
* *** * *
70791 AATATTTTTTTGAAGGGGAACATTATTTGAAGATAA-AATTGACT-G---ATGTAGAGATTCTCT
1 AATAGTTCCCTGAAGGGGAACATTATATGAAGATAACAATTGACTGGAAAATGCAGAGATTCTCT
* * * *
70851 GGAAAAAAGGGGAAGGCTATTTTCACAAGATGCGCTTTCACCTTTTGTAGGGAATCTTTGCCATG
66 --AAAAAA-AGGAAGGTTATTTTCACAAGA--CGCTTTCACCTTTTGTA-GGAATCTCTGTCATG
* *
70916 CCATAGTGTTGCATCCTATCAGTCGAGGGAGTTGTTGTGATGAATAGTTCC
125 TCATAGTGTTGCATCC-ATCAGACG-GGGAGTTGTTGTGATGAATAGTTCC
70967 TAAAGGGGAA
Statistics
Matches: 425, Mismatches: 63, Indels: 45
0.80 0.12 0.08
Matches are distributed among these distances:
331 13 0.03
333 7 0.02
334 68 0.16
335 169 0.40
336 120 0.28
337 35 0.08
338 13 0.03
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (333 bp):
AATAGTTCCCTGAAGGGGAACATTATATGAAGATAACAATTGACTGGAAAATGCAGAGATTCTCT
AAAAAAAGGAAGGTTATTTTCACAAGACGCTTTCACCTTTTGTAGGAATCTCTGTCATGTCATAG
TGTTGCATCCATCAGACGGGGAGTTGTTGTGATGAATAGTTCCCCAAAAGGAAACATTATCTGAG
ATAAAATTGACTGGAAAATGCAAAAATTCTATGGAAAAAAGAAGAAGGATATTTTCACAAGAAGC
ACTTTCACCTTTCGTAGGGAATCTCTACCATACCATAGGTTCACATCCCATCAGATAGGGAGTTC
TTATGAAG
Found at i:71687 original size:15 final size:15
Alignment explanation
Indices: 71647--71687 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
71637 TAATTATGTA
71647 ATTGTATTTTCTGAT
1 ATTGTATTTTCTGAT
*
71662 ATTAG-AATTTCTGAT
1 ATT-GTATTTTCTGAT
71677 ATTGTATTTTC
1 ATTGTATTTTC
71688 CTGTCTTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.24, C:0.07, G:0.12, T:0.56
Consensus pattern (15 bp):
ATTGTATTTTCTGAT
Done.