Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004794.1 Hibiscus syriacus cultivar Beakdansim tig00010804_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: 57139
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:2686 original size:74 final size:74
Alignment explanation
Indices: 2507--2704 Score: 260
Period size: 74 Copynumber: 2.7 Consensus size: 74
2497 GTTGTACAAG
* * * *
2507 GGGGGAATCGGTACCCCCT-TGGGGG-ATCGGTTCCCTCCGAGCATAC-GGAATTCTCGGAACAA
1 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAACAA
** *
2569 AACTGTTTA
66 AACCATTCA
* *
2578 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCA
1 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAACAA
2643 AACCATTCA
66 AACCATTCA
* *
2652 -GGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAA
2705 TTTTTGGCTT
Statistics
Matches: 112, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
71 17 0.15
72 6 0.05
73 40 0.36
74 49 0.44
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.23
Consensus pattern (74 bp):
GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAACAA
AACCATTCA
Found at i:4154 original size:21 final size:21
Alignment explanation
Indices: 4128--4167 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4118 CAGAACCCCA
*
4128 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
4149 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
4168 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:4202 original size:20 final size:21
Alignment explanation
Indices: 4148--4210 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
4138 GATTCCCCTG
4148 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
4172 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
4192 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
4211 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:10524 original size:21 final size:22
Alignment explanation
Indices: 10470--10525 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
10460 TTTTTCTCGG
*
10470 TTTTGTCTCTTGTTTCTCTGTAT
1 TTTTGTCTC-TGTTCCTCTGTAT
* * *
10493 CTTTCTCTCTGTTCCTCT-TTT
1 TTTTGTCTCTGTTCCTCTGTAT
10514 TTTTGTCTCTGT
1 TTTTGTCTCTGT
10526 CTCTGGTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 12 0.44
22 8 0.30
23 7 0.26
ACGTcount: A:0.02, C:0.23, G:0.11, T:0.64
Consensus pattern (22 bp):
TTTTGTCTCTGTTCCTCTGTAT
Found at i:10990 original size:3 final size:3
Alignment explanation
Indices: 10982--11034 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
10972 AATATATATT
*
10982 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11030 TAA TA
1 TAA TA
11035 TGGGTAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:11939 original size:113 final size:113
Alignment explanation
Indices: 11289--11922 Score: 1128
Period size: 113 Copynumber: 5.6 Consensus size: 113
11279 TTTTGATGAG
* *
11289 TTCTTCTCATTATGAACTT-TCTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCT
** * * * *
11353 GAAAAAAAAATAACCCATCAAGTAATAGATTTGAG-CAAAAAGGTTGAACAAA
65 G--GCAAAAATAATCCATCAAGTGAT-GAATTCAGAC-AAAAGGTTGAACAAA
*
11405 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
11470 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
66 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
11518 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
11583 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
66 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
11631 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
11696 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
66 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
11744 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
11809 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
66 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
11857 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
11922 G
66 G
11923 AAATGTCAAT
Statistics
Matches: 508, Mismatches: 8, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
113 425 0.84
114 20 0.04
116 62 0.12
117 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
Found at i:13231 original size:83 final size:83
Alignment explanation
Indices: 12677--13219 Score: 908
Period size: 83 Copynumber: 6.5 Consensus size: 83
12667 TAGTTCTTAC
*
12677 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
1 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATTTTCCAAA
*
12742 TTCAATGATTGGTTCTGT
66 TTCAATGATTTGTTCTGT
* * * *
12760 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATTCTATGAGA-ACATTCATCTTCCAA
1 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGA-ACACATTCATTTTCCAA
*
12824 ATTCAATGATTGGTTCTGT
65 ATTCAATGATTTGTTCTGT
* * *
12843 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATTTTCGAAA
1 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATTTTCCAAA
12908 TTCAATGATTTGTTCTGT
66 TTCAATGATTTGTTCTGT
* * *
12926 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATAAACACATTCATCTTCCTAA
1 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATTTTCCAAA
12991 TTCAATGATTTGTTCTGT
66 TTCAATGATTTGTTCTGT
*
13009 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATTTTCTAAA
1 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATTTTCCAAA
13074 TTCAATGATTTGTTCTGT
66 TTCAATGATTTGTTCTGT
*
13092 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATTTTCGAAA
1 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATTTTCCAAA
*
13157 TCCAATGATTTGTTCTGT
66 TTCAATGATTTGTTCTGT
* *
13175 CAAACCAGATCAGATAATTCAAAGAACACTTCCAGAAGATGCTAT
1 CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTAT
13220 TGGCAAATTC
Statistics
Matches: 437, Mismatches: 21, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
82 1 0.00
83 435 1.00
84 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (83 bp):
CAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATTTTCCAAA
TTCAATGATTTGTTCTGT
Found at i:24922 original size:18 final size:17
Alignment explanation
Indices: 24884--24932 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
24874 AAATACTTGC
*
24884 AAATAAAATAAACAT-AT
1 AAAT-AAATAAAAATAAT
*
24901 AAATATTATAAAAATAAT
1 AAATA-AATAAAAATAAT
24919 AAATAAATAAAAAT
1 AAATAAATAAAAAT
24933 TTGACAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 19 0.70
18 7 0.26
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAAATAAAAATAAT
Found at i:26974 original size:3 final size:3
Alignment explanation
Indices: 26960--26991 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
26950 TTATATATAT
*
26960 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
26992 TGGGTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27403 original size:292 final size:296
Alignment explanation
Indices: 26892--27432 Score: 986
Period size: 292 Copynumber: 1.8 Consensus size: 296
26882 CGGTTGGTTT
*
26892 GTTTGTAACTGGGCCGATCCAGTTGTAATTGGGTCTGTAATTATTATTATATATGTATTTATATA
1 GTTTGTAACTGGGCCGATCCAGTTGTAATTGGGTCTGTAATTATTATTATATATGTATTAATATA
*
26957 TATTAATAATGATAATAATAATAATAATAATAATATGGGTAAAAAAATTAGTATCTTCAGAAGAG
66 TATTAATAATAATAATAATAATAATAATAATAATATGGGTAAAAAAATTAGTATCTTCAGAAGAG
27022 GTATTACTTATTGTACCTATACCTTCAATGTAACCTTTTGAATTATCACTAAAAATCATTTCTCC
131 GTATTACTTATTGTACCTATACCTTCAATGTAACCTTTTGAATTATCACTAAAAATCATTTCTCC
27087 TCTATTTTTGGCATTAAGCTCCATGAATCGGCTTTTGTCTCCGGTCATGTATCTAGGGTTTAGGA
196 TCTATTTTTGGCATTAAGCTCCATGAATCGGCTTTTGTCTCCGGTCATGTATCTAGGGTTTAGGA
27152 AACCCTAACTGAAACCCCCAAATATTTAGGGTTCTA
261 AACCCTAACTGAAACCCCCAAATATTTAGGGTTCTA
27188 GTTTGTAACT-GGCCGATCCAGTTGTAATTGGGTCTGTAATTAATTATTTATATATGTATTAATA
1 GTTTGTAACTGGGCCGATCCAGTTGTAATTGGGTCTGTAATT-ATTA-TTATATATGTATTAATA
* *
27252 TAT-TTAATAATAATGATAATAATAATAATAAT-ATATGGGTAAACAAA-TAGTATCTTCAGAAG
64 TATATTAATAATAATAATAATAATAATAATAATAATATGGGTAAAAAAATTAGTATCTTCAGAAG
27314 AGGT-TTACTTATTGTACCTATACCTTCAATGTAACC-TTTGAATTATCACTAAAAATCATTTCT
129 AGGTATTACTTATTGTACCTATACCTTCAATGTAACCTTTTGAATTATCACTAAAAATCATTTCT
27377 CCTCTATTTTTGGCATTAAGCTCCATGAATCGGCTTTTGTCTCCGGTCATGTATCT
194 CCTCTATTTTTGGCATTAAGCTCCATGAATCGGCTTTTGTCTCCGGTCATGTATCT
27433 TGAGCATCCA
Statistics
Matches: 239, Mismatches: 4, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
292 83 0.35
293 32 0.13
294 19 0.08
295 45 0.19
296 41 0.17
297 19 0.08
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (296 bp):
GTTTGTAACTGGGCCGATCCAGTTGTAATTGGGTCTGTAATTATTATTATATATGTATTAATATA
TATTAATAATAATAATAATAATAATAATAATAATATGGGTAAAAAAATTAGTATCTTCAGAAGAG
GTATTACTTATTGTACCTATACCTTCAATGTAACCTTTTGAATTATCACTAAAAATCATTTCTCC
TCTATTTTTGGCATTAAGCTCCATGAATCGGCTTTTGTCTCCGGTCATGTATCTAGGGTTTAGGA
AACCCTAACTGAAACCCCCAAATATTTAGGGTTCTA
Found at i:31823 original size:22 final size:22
Alignment explanation
Indices: 31797--31841 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
31787 TTTGACCGGT
*
31797 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACAGTTGAC
31819 CCGACCCGACCCGACAGTTGAC
1 CCGACCCGACCCGACAGTTGAC
31841 C
1 C
31842 GTTGACCGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.09
Consensus pattern (22 bp):
CCGACCCGACCCGACAGTTGAC
Found at i:31910 original size:29 final size:29
Alignment explanation
Indices: 31849--32005 Score: 138
Period size: 29 Copynumber: 5.4 Consensus size: 29
31839 ACCGTTGACC
* * ** *
31849 GGTGATATTCTGGGAATTAATTCGATTTT
1 GGTGCTATTTTGGGAATTAATTCGAAATG
*
31878 GGTGTTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
** ** *
31907 GGTGCTATTTTGATAATTTTTTCGAAAAAG
1 GGTGCTATTTTGGGAATTAATTCG-AAATG
* *
31937 GGTGATATTCTGGGAATTAATTCGAAAT-
1 GGTGCTATTTTGGGAATTAATTCGAAATG
* * * *
31965 -ATGCTATTTTGGTAATTAATTTGAAAAG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
31993 GGTGCTATTTTGG
1 GGTGCTATTTTGG
32006 TTATTATTTT
Statistics
Matches: 100, Mismatches: 25, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
27 21 0.21
29 57 0.57
30 22 0.22
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAATG
Found at i:32006 original size:29 final size:29
Alignment explanation
Indices: 31878--32032 Score: 129
Period size: 29 Copynumber: 5.3 Consensus size: 29
31868 ATTCGATTTT
* * * *
31878 GGTGTTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGTAATTAATTTGAAAAG
* *
31907 GGTGCTATTTTGATAATT-TTTTCGAAAAAG
1 GGTGCTATTTTGGTAATTAATTT-G-AAAAG
* * * *
31937 GGTGATATTCTGGGAATTAATTCGAAATA-
1 GGTGCTATTTTGGTAATTAATTTGAAA-AG
31966 --TGCTATTTTGGTAATTAATTTGAAAAG
1 GGTGCTATTTTGGTAATTAATTTGAAAAG
* * *
31993 GGTGCTATTTTGGTTATTATTTTAAAAAG
1 GGTGCTATTTTGGTAATTAATTTGAAAAG
32022 TGGTGCTATTT
1 -GGTGCTATTT
32033 ATGTAAAATG
Statistics
Matches: 99, Mismatches: 19, Indels: 15
0.74 0.14 0.11
Matches are distributed among these distances:
26 1 0.01
27 21 0.21
28 2 0.02
29 43 0.43
30 30 0.30
31 2 0.02
ACGTcount: A:0.29, C:0.05, G:0.23, T:0.43
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTAATTTGAAAAG
Found at i:32784 original size:14 final size:14
Alignment explanation
Indices: 32767--32804 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
32757 ACATGATACG
32767 TGATTTCTGA-ATA
1 TGATTTCTGATATA
32780 TTGATTTCCTGATATA
1 -TGATTT-CTGATATA
32796 TGATTTCTG
1 TGATTTCTG
32805 TATTTCGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.41
15 10 0.45
16 3 0.14
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (14 bp):
TGATTTCTGATATA
Found at i:33298 original size:19 final size:18
Alignment explanation
Indices: 33259--33292 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33249 ATTTGCTGTC
33259 GTTTTGGATATATATTTT
1 GTTTTGGATATATATTTT
*
33277 GTTTTGTAT-TATATTT
1 GTTTTGGATATATATTT
33293 AATGTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.65
Consensus pattern (18 bp):
GTTTTGGATATATATTTT
Found at i:33548 original size:20 final size:20
Alignment explanation
Indices: 33523--33562 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
33513 CGCTTACTTT
33523 GCAGGTTGTTTGCCTCCTTC
1 GCAGGTTGTTTGCCTCCTTC
33543 GCAGGTTGTTTGCCTCCTTC
1 GCAGGTTGTTTGCCTCCTTC
33563 CTAGATCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.30, G:0.25, T:0.40
Consensus pattern (20 bp):
GCAGGTTGTTTGCCTCCTTC
Found at i:36375 original size:19 final size:18
Alignment explanation
Indices: 36337--36384 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
36327 GTTGTTTTAA
*
36337 AAATAAAAAATAAGAATT
1 AAATAAAAAAAAAGAATT
*
36355 AAATAAAAGAAAAATAATT
1 AAATAAAA-AAAAAGAATT
36374 AAATAAAAAAA
1 AAATAAAAAAA
36385 TTAAAGAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (18 bp):
AAATAAAAAAAAAGAATT
Found at i:37178 original size:76 final size:75
Alignment explanation
Indices: 37016--37190 Score: 181
Period size: 76 Copynumber: 2.3 Consensus size: 75
37006 CTAAAATACC
* * * * * * * **
37016 TAAAAAATAATATAATATTCTAAATCCTAATTAAAACACTAAAACCTGTTTCAACTAAAATACCT
1 TAAAATATAAAATAATATCCTAAAACCTAATTAAAACACAAAAACCTATTTAAACTAAAATACAA
37081 AATACAAAGA
66 AATACAAAGA
* *
37091 TAAAATATAAAAATAATATCCTAAAACTTAATTAAAATACAAAAACCTATTTAAACTAAAATACA
1 TAAAATAT-AAAATAATATCCTAAAACCTAATTAAAACACAAAAACCTATTTAAACTAAAATACA
*
37156 AAGATA-AAATA
65 AA-ATACAAAGA
** * *
37167 TAATGTTTAAAATATTATCCTAAA
1 TAAAATATAAAATAATATCCTAAA
37191 CTTGAGTTTA
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
75 22 0.27
76 57 0.70
77 3 0.04
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.29
Consensus pattern (75 bp):
TAAAATATAAAATAATATCCTAAAACCTAATTAAAACACAAAAACCTATTTAAACTAAAATACAA
AATACAAAGA
Found at i:38852 original size:9 final size:10
Alignment explanation
Indices: 38829--38871 Score: 54
Period size: 9 Copynumber: 4.4 Consensus size: 10
38819 GCATTTGATA
*
38829 AAATAAAAATA
1 AAAT-AAAATG
38840 AAAT-AAATG
1 AAATAAAATG
38849 AAATAAAAT-
1 AAATAAAATG
38858 AAATAAAATG
1 AAATAAAATG
38868 AAAT
1 AAAT
38872 GGGTTGTCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 17 0.59
10 8 0.28
11 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (10 bp):
AAATAAAATG
Found at i:38854 original size:14 final size:14
Alignment explanation
Indices: 38829--38871 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
38819 GCATTTGATA
38829 AAATAAAAATAAAAT
1 AAAT-AAAATAAAAT
*
38844 AAATGAAATAAAAT
1 AAATAAAATAAAAT
*
38858 AAATAAAATGAAAT
1 AAATAAAATAAAAT
38872 GGGTTGTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:38858 original size:19 final size:20
Alignment explanation
Indices: 38829--38871 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
38819 GCATTTGATA
38829 AAATAAAAATAAA-ATAAATG
1 AAATAAAAATAAATA-AAATG
38849 AAAT-AAAATAAATAAAATG
1 AAATAAAAATAAATAAAATG
38868 AAAT
1 AAAT
38872 GGGTTGTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (20 bp):
AAATAAAAATAAATAAAATG
Found at i:38872 original size:5 final size:5
Alignment explanation
Indices: 38826--38871 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
38816 TAAGCATTTG
* *
38826 ATAAA ATAAAA ATAAA AT-AA ATGAA ATAAA AT-AA ATAAA ATGAA AT
1 ATAAA AT-AAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
38872 GGGTTGTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 8 0.22
5 23 0.64
6 5 0.14
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:43487 original size:29 final size:29
Alignment explanation
Indices: 43448--43562 Score: 149
Period size: 29 Copynumber: 4.0 Consensus size: 29
43438 AAATTGTCAT
* *
43448 TTTTTCACAAAAATTCCCATAATGTCACC
1 TTTTTCACAAAAAATCCCAGAATGTCACC
* *
43477 TTTTCCACAAAAAATCCTAGAATGTCACC
1 TTTTTCACAAAAAATCCCAGAATGTCACC
* **
43506 TTTTTCATAAAAAATCTTAGAATGTCACC
1 TTTTTCACAAAAAATCCCAGAATGTCACC
* *
43535 TTTTTCACAAAAATTCTCAGAATGTCAC
1 TTTTTCACAAAAAATCCCAGAATGTCAC
43563 TGGGTCGGGT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (29 bp):
TTTTTCACAAAAAATCCCAGAATGTCACC
Found at i:43647 original size:19 final size:20
Alignment explanation
Indices: 43598--43648 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
43588 GGTCGGGTCA
43598 GACCGGTC-AACCAGGTTCG
1 GACCGGTCAAACCAGGTTCG
*
43617 GACCGGTTAAACCA-GTTCG
1 GACCGGTCAAACCAGGTTCG
43636 GACCGGTCAAACC
1 GACCGGTCAAACC
43649 GGTCATAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 24 0.83
20 5 0.17
ACGTcount: A:0.25, C:0.31, G:0.27, T:0.16
Consensus pattern (20 bp):
GACCGGTCAAACCAGGTTCG
Found at i:50636 original size:29 final size:29
Alignment explanation
Indices: 50575--50679 Score: 142
Period size: 29 Copynumber: 3.7 Consensus size: 29
50565 TCCACATTCG
*
50575 AAAATTCCCA-AATTGTCA-TTTTTTCACA
1 AAAATTCCCAGAA-TGTCACATTTTTCACA
*
50603 AAAATTCCCAGAATGTCACATTTTCCACA
1 AAAATTCCCAGAATGTCACATTTTTCACA
* *
50632 AAAATTCACAGAATGTCACCTTTTTCACA
1 AAAATTCCCAGAATGTCACATTTTTCACA
*
50661 AATATTCCCAGAATGTCAC
1 AAAATTCCCAGAATGTCAC
50680 TGGGTCGGGT
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
28 15 0.22
29 53 0.78
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.31
Consensus pattern (29 bp):
AAAATTCCCAGAATGTCACATTTTTCACA
Found at i:50709 original size:17 final size:17
Alignment explanation
Indices: 50681--50722 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
50671 GAATGTCACT
*
50681 GGGTCGGGTCAACTGGTC
1 GGGTC-GGTCAACGGGTC
50699 GGGTCGGTCAACGGGTC
1 GGGTCGGTCAACGGGTC
50716 GGGTCGG
1 GGGTCGG
50723 GTTAGACCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.10, C:0.21, G:0.50, T:0.19
Consensus pattern (17 bp):
GGGTCGGTCAACGGGTC
Found at i:50749 original size:19 final size:19
Alignment explanation
Indices: 50727--50793 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
50717 GGTCGGGTTA
50727 GACCGGTCAACCTGGTTTG
1 GACCGGTCAACCTGGTTTG
*
50746 GACCGGTCAACCTGGTTCG
1 GACCGGTCAACCTGGTTTG
* *
50765 GACCTGTCAAGCC-GGTTTA
1 GACCGGTCAA-CCTGGTTTG
50784 GACCGGTCAA
1 GACCGGTCAA
50794 ACCGGTCATA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 40 0.95
20 2 0.05
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.22
Consensus pattern (19 bp):
GACCGGTCAACCTGGTTTG
Found at i:51584 original size:19 final size:18
Alignment explanation
Indices: 51565--51613 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
51555 GTTGTTTTTA
51565 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
51583 AAATAAAAGAAAAATAATT
1 AAATAAAA-AATAAGAATT
51602 AAATAAACAAAT
1 AAATAAA-AAAT
51614 TAAAGAGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:51879 original size:12 final size:12
Alignment explanation
Indices: 51862--51900 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
51852 ACGTTTTGAA
51862 TTTAGCCTTCGC
1 TTTAGCCTTCGC
51874 TTTAGCCTTCGC
1 TTTAGCCTTCGC
51886 TTTAGCCTTCAGC
1 TTTAGCCTTC-GC
51899 TT
1 TT
51901 GAAGAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.10, C:0.31, G:0.15, T:0.44
Consensus pattern (12 bp):
TTTAGCCTTCGC
Found at i:52150 original size:65 final size:63
Alignment explanation
Indices: 52081--52264 Score: 291
Period size: 65 Copynumber: 2.9 Consensus size: 63
52071 CCAAAACATC
52081 TTAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCTAAAAAAATAATACAATATT
1 TTAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCTAAAAAAATAATAC-A-ATT
52146 TTAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCT-AAAAAATAATACAATT
1 TTAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCTAAAAAAATAATACAATT
* * *
52208 CTAAATCCTAATTAAAACAC-TAAAACCTATTTCAACTAAAATACCTAAAAAAGATAA
1 TTAAATCCTAATTAAAACACTTAAAA-CTATCTAAACTAAAATACCTAAAAAA-ATAA
52265 AATATAAAAA
Statistics
Matches: 113, Mismatches: 3, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
61 5 0.04
62 40 0.35
63 6 0.05
64 16 0.14
65 46 0.41
ACGTcount: A:0.55, C:0.17, G:0.01, T:0.28
Consensus pattern (63 bp):
TTAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCTAAAAAAATAATACAATT
Found at i:52245 original size:62 final size:64
Alignment explanation
Indices: 52082--52259 Score: 290
Period size: 62 Copynumber: 2.8 Consensus size: 64
52072 CAAAACATCT
*
52082 TAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCTAAAAAAATAATACAATATTT
1 TAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCT-AAAAAATAATACAATATTC
52147 TAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCTAAAAAATAATAC-A-ATTC
1 TAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCTAAAAAATAATACAATATTC
* *
52209 TAAATCCTAATTAAAACAC-TAAAACCTATTTCAACTAAAATACCTAAAAAA
1 TAAATCCTAATTAAAACACTTAAAA-CTATCTAAACTAAAATACCTAAAAAA
52260 GATAAAATAT
Statistics
Matches: 109, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
61 5 0.05
62 46 0.42
63 1 0.01
64 12 0.11
65 45 0.41
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (64 bp):
TAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCTAAAAAATAATACAATATTC
Found at i:52315 original size:18 final size:19
Alignment explanation
Indices: 52284--52322 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
52274 ATAATATCCT
52284 AAAAACTTAATTAAAATAA
1 AAAAACTTAATTAAAATAA
* *
52303 AAAAAC-TATTTAAACTAA
1 AAAAACTTAATTAAAATAA
52321 AA
1 AA
52323 TACAAAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAACTTAATTAAAATAA
Done.