Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001203.1 Hibiscus syriacus cultivar Beakdansim tig00002378_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: 59998
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:17513 original size:34 final size:33
Alignment explanation
Indices: 17471--17558 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 33
17461 AATGGTAATA
*
17471 AACAAAATTAACCAAAATACATTAACAA-AAAGTCC
1 AACAAAATTAA-CAAAATAAATTAA-AATAAA-TCC
*
17506 AACAAATTTAACAAAATAAATTAAAATAAATCC
1 AACAAAATTAACAAAATAAATTAAAATAAATCC
**
17539 AACAAAATTAATGAAATAAA
1 AACAAAATTAACAAAATAAA
17559 GTAAGTATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 22 0.47
34 15 0.32
35 10 0.21
ACGTcount: A:0.64, C:0.14, G:0.02, T:0.20
Consensus pattern (33 bp):
AACAAAATTAACAAAATAAATTAAAATAAATCC
Found at i:18081 original size:33 final size:33
Alignment explanation
Indices: 18014--18081 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
18004 TCCTCCAGGA
* **
18014 GGGGTCATAAAACTCTGTGACGGTGACGGTGGC
1 GGGGTCATAAAACTCGGTGACGGTGACGACGGC
*
18047 GGGGTCATAAAA-TCAGGTGACGGTGGCGACGGC
1 GGGGTCATAAAACTC-GGTGACGGTGACGACGGC
18080 GG
1 GG
18082 CATCGGGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.22, C:0.18, G:0.43, T:0.18
Consensus pattern (33 bp):
GGGGTCATAAAACTCGGTGACGGTGACGACGGC
Found at i:19865 original size:17 final size:18
Alignment explanation
Indices: 19836--19883 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
19826 TGCAAAAAAA
*
19836 TTAATTAAA-TAAAATA-
1 TTAAATAAATTAAAATAC
*
19852 TTAAA-AAATTTAAATAC
1 TTAAATAAATTAAAATAC
19869 TTAAATAAATTAAAA
1 TTAAATAAATTAAAA
19884 CAAAATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 5 0.19
18 8 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAATAAATTAAAATAC
Found at i:19897 original size:22 final size:23
Alignment explanation
Indices: 19863--19905 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
19853 TAAAAAATTT
19863 AAATACTTAAATA-AATTAAAACA
1 AAATACTTAAATATAA-TAAAACA
19886 AAATA-TTAAATATAATAAAA
1 AAATACTTAAATATAATAAAA
19906 TATACTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (23 bp):
AAATACTTAAATATAATAAAACA
Found at i:20345 original size:2 final size:2
Alignment explanation
Indices: 20283--20330 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
20273 AAAACGCTTA
20283 AT AT AT 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 AT AT AT
20325 AT AT AT
1 AT AT AT
20331 GAATTATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20430 original size:17 final size:18
Alignment explanation
Indices: 20402--20436 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
20392 ATTTGCTGCT
20402 CTGTATTTTTTTTTCTCA
1 CTGTATTTTTTTTTCTCA
20420 CTGTA-TTTTTTTTCTCA
1 CTGTATTTTTTTTTCTCA
20437 AATAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.11, C:0.17, G:0.06, T:0.66
Consensus pattern (18 bp):
CTGTATTTTTTTTTCTCA
Found at i:29184 original size:31 final size:31
Alignment explanation
Indices: 29148--29207 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
29138 ATTAAATATA
*
29148 TTTTATT-TTAATGTAAAAATATATATTTTAT
1 TTTTATTCTTAAT-TAAAAAAATATATTTTAT
*
29179 TTTTATTCTTACTTAAAAAAATATATTTT
1 TTTTATTCTTAATTAAAAAAATATATTTT
29208 TTAAATATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (31 bp):
TTTTATTCTTAATTAAAAAAATATATTTTAT
Found at i:29328 original size:29 final size:28
Alignment explanation
Indices: 29296--29388 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 28
29286 AAATATATAC
*
29296 TATTTTATTCTTATCTTTACTTAAAAATA
1 TATTTTATTATTAT-TTTACTTAAAAATA
* * *
29325 TATTTTATTATTATTGTAAATTAAAAACA
1 TATTTTATTATTATT-TTACTTAAAAATA
*
29354 TGTTTTATTATTATTTTAACTTTTAAAAATA
1 TATTTTATTATTATTTT-AC--TTAAAAATA
29385 TATT
1 TATT
29389 AAAATATTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.04
29 38 0.75
31 11 0.22
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (28 bp):
TATTTTATTATTATTTTACTTAAAAATA
Found at i:29545 original size:29 final size:29
Alignment explanation
Indices: 29513--29569 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
29503 ACATTGAAAT
*
29513 ATATTTAATAAATTAAGACAAAAATAAAA
1 ATATTTAATAAATTAAAACAAAAATAAAA
*
29542 ATATTTAATAAGTTAAAACAAAAATAAA
1 ATATTTAATAAATTAAAACAAAAATAAA
29570 GATAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (29 bp):
ATATTTAATAAATTAAAACAAAAATAAAA
Found at i:30699 original size:30 final size:31
Alignment explanation
Indices: 30659--30720 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
30649 AATTTTTTAG
* *
30659 TCAAAGAAAATAA-TAATCAAATGCTTAACA
1 TCAAACAAAATAACTAATCAAATGATTAACA
* *
30689 TCAAACAAAATAACTAATTAAATTATTAACA
1 TCAAACAAAATAACTAATCAAATGATTAACA
30720 T
1 T
30721 ATCAACATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.56, C:0.13, G:0.03, T:0.27
Consensus pattern (31 bp):
TCAAACAAAATAACTAATCAAATGATTAACA
Found at i:30905 original size:23 final size:23
Alignment explanation
Indices: 30879--30926 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
30869 ATAAAGTACA
*
30879 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
30902 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
30925 AT
1 AT
30927 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:31368 original size:23 final size:23
Alignment explanation
Indices: 31315--31377 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
31305 ATATAACCAT
31315 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* ** *
31338 TACTTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
31361 TACCTATTACATCATAT
1 TACCTATTACATTATAT
31378 GTTTACCTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:31760 original size:21 final size:20
Alignment explanation
Indices: 31730--31783 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
31720 GATAGACACT
*
31730 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
31751 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
31774 TTACATTATA
1 TTACATTATA
31784 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:31771 original size:23 final size:23
Alignment explanation
Indices: 31745--31807 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
31735 ATATAACCAT
31745 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
31768 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
31791 TACCTATTACATCATAT
1 TACCTATTACATTATAT
31808 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:31835 original size:430 final size:427
Alignment explanation
Indices: 31038--31905 Score: 1684
Period size: 430 Copynumber: 2.0 Consensus size: 427
31028 GGATCGATAC
31038 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
31103 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATACCGT
66 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATACCGT
31168 AACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAG
131 AACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAG
31233 ATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACA
196 ATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACA
*
31298 CTTTACAATATAACCATTACCTATTACATTATATAAACGATACTTATTACATTATATAAGGGCTA
261 CTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTA
31363 CCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGAT
326 CCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGAT
31428 ACTTTTTTTAAAACTTATGTAATTTATGTTTCAA-TTT
390 ACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
31465 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
31530 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
66 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAAT-A-ATATACC
31595 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
129 GTAACGT-AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
31660 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
193 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
31725 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
258 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
31790 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAGGATCG
323 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAGGATCG
31855 ATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
388 ATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
31895 TTTAACAGTGT
1 TTTAACAGTGT
31906 ACTGCGAATT
Statistics
Matches: 436, Mismatches: 1, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
427 120 0.28
428 1 0.00
429 60 0.14
430 255 0.58
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (427 bp):
TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATACCGT
AACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAG
ATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACA
CTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTA
CCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAGGATCGATA
CTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
Found at i:34124 original size:184 final size:184
Alignment explanation
Indices: 33581--34313 Score: 1423
Period size: 184 Copynumber: 4.0 Consensus size: 184
33571 GAGACATTCG
33581 TGGGTTCCGATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATAT
1 TGGGTTCCGATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATAT
33646 GGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAA
66 GGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAA
33711 GACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTA
131 GACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTA
33765 TGGGTTCCGATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACA-TTTTCTTCCAATAT
1 TGGGTTCCGATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATAT
33829 GGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAA
66 GGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAA
33894 GACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTA
131 GACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTA
33948 TGGGTTCCGATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATAT
1 TGGGTTCCGATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATAT
34013 GGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAA
66 GGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAA
34078 GACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTA
131 GACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTA
* *
34132 TGGGTTCCGATGTGTAAAATGTCGACACTTTTTGAAATCGTATCGACACATTTTTCTTCCAATAT
1 TGGGTTCCGATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATAT
34197 GGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAA
66 GGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAA
**
34262 GACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
131 GACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
34314 ATGTTGAAAG
Statistics
Matches: 544, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
183 183 0.34
184 361 0.66
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TGGGTTCCGATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATAT
GGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAA
GACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTA
Found at i:52261 original size:22 final size:22
Alignment explanation
Indices: 52218--52261 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
52208 ACCAAATCCC
** *
52218 CATAAATCTATAAATTCTTAAA
1 CATAAATCTATAAAACCCTAAA
*
52240 CATAAATCTTTAAAACCCTAAA
1 CATAAATCTATAAAACCCTAAA
52262 ACAAAATTTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (22 bp):
CATAAATCTATAAAACCCTAAA
Found at i:54174 original size:29 final size:28
Alignment explanation
Indices: 54136--54193 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
54126 ATAGTATTTT
*
54136 AATATATTAACTTACATA-AAAAATATTAA
1 AATATATTAA-TTA-ATATAAAAAAATTAA
*
54165 AATATTTTAATTAATATAAAAAAATTAA
1 AATATATTAATTAATATAAAAAAATTAA
54193 A
1 A
54194 TGACCCCCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 3 0.12
28 14 0.54
29 9 0.35
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (28 bp):
AATATATTAATTAATATAAAAAAATTAA
Found at i:56767 original size:105 final size:107
Alignment explanation
Indices: 56638--56888 Score: 310
Period size: 108 Copynumber: 2.4 Consensus size: 107
56628 AAATATGAAA
* * *
56638 ATAACTAAAT-AGTTTAATTACTTATTTTATTATTAATATTATCAACATATT-GTAACGCCTAAA
1 ATAACAAAATAAG-TTAATTACTTATTTTGTTATAAATATTATCAACATATTAGTAACGCCTAAA
* * * * *
56701 ATGTTACTAAA-TTTAAGTTGATAGGGCCTTAGAAATCTCACT
65 ATGCTACCAAACTTTAAGCTGATAGGGCATTAGAAATCTCACG
*** * *
56743 ATAACAAAATAAGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAGGTTGTGCTTAAT
1 ATAACAAAATAAGTTAATTACTTATTTTGTTATAAATATTATCAACATATTA-GTAACGCCTAAA
*
56808 ATGCTACCAAACTTTAAGCTGATAGGGCATTCGAAATCTCACG
65 ATGCTACCAAACTTTAAGCTGATAGGGCATTAGAAATCTCACG
* * *
56851 ACAACAAAATATGTTAAATACTTATTTTGTTATAAATA
1 ATAACAAAATAAGTTAATTACTTATTTTGTTATAAATA
56889 ATAACATACT
Statistics
Matches: 125, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
105 45 0.36
106 2 0.02
107 16 0.13
108 62 0.50
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.38
Consensus pattern (107 bp):
ATAACAAAATAAGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAGTAACGCCTAAAA
TGCTACCAAACTTTAAGCTGATAGGGCATTAGAAATCTCACG
Found at i:57809 original size:99 final size:99
Alignment explanation
Indices: 57614--57805 Score: 244
Period size: 99 Copynumber: 1.9 Consensus size: 99
57604 ATTTCAAACA
* * * ** *
57614 GTTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAAGTAGTT
1 GTTAAATTGTAAATATTTTACCGTTCACATTAATATTATACAATTAAACAAACCGATAAGTAGTT
*
57679 TAGCGTAATAGGTAACAGTTATTTTATTTAACCG
66 TACCGTAATAGGTAACAGTTATTTTATTTAACCG
* * * * *
57713 GTTAAATTGTAAATATTTTACTGTTCACATTAATATTGTACAATTAAATAAA-TGATAGGTAGTT
1 GTTAAATTGTAAATATTTTACCGTTCACATTAATATTATACAATTAAACAAACCGATAAGTAGTT
*
57777 TACCGTAATAGGTAGC-GCTTATTTTATTT
66 TACCGTAATAGGTAACAG-TTATTTTATTT
57806 TAACGTGTTA
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
97 1 0.01
98 34 0.43
99 44 0.56
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (99 bp):
GTTAAATTGTAAATATTTTACCGTTCACATTAATATTATACAATTAAACAAACCGATAAGTAGTT
TACCGTAATAGGTAACAGTTATTTTATTTAACCG
Found at i:57861 original size:77 final size:74
Alignment explanation
Indices: 57768--57959 Score: 262
Period size: 73 Copynumber: 2.6 Consensus size: 74
57758 AAATAAATGA
* *
57768 TAGGTAGTTTACCGTAATAGGTAGCGCTTATTTTATTTTAAC-GTGTTACATTATTATTATACCT
1 TAGGTAGTTTAACGTAATAGGTAGCGCCTATTTTATTTTAACAGT-TTAC---ATTATTATACCT
57832 TTAAACAAACCAG
62 TTAAACAAACCAG
* *
57845 TGGGTAGTTTAACGTAATAGGTAGCGCCTATTTTA-TTTCACAGTTTACATTATTATACCTTTAA
1 TAGGTAGTTTAACGTAATAGGTAGCGCCTATTTTATTTTAACAGTTTACATTATTATACCTTTAA
* *
57909 ACGAACCGG
66 ACAAACCAG
* *
57918 TAGGTAGTTTAACGTAATAGGTATCACCTATTTTATTTTAAC
1 TAGGTAGTTTAACGTAATAGGTAGCGCCTATTTTATTTTAAC
57960 CGGTTAAGTA
Statistics
Matches: 103, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
73 55 0.53
74 5 0.05
76 9 0.09
77 34 0.33
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.40
Consensus pattern (74 bp):
TAGGTAGTTTAACGTAATAGGTAGCGCCTATTTTATTTTAACAGTTTACATTATTATACCTTTAA
ACAAACCAG
Found at i:58002 original size:100 final size:99
Alignment explanation
Indices: 57895--58165 Score: 393
Period size: 100 Copynumber: 2.7 Consensus size: 99
57885 CAGTTTACAT
* **
57895 TATTATACCTTTAAACGAACCGGTAGGTAGTTTAACGTAATAGGTATCACCTATTTTATTTTAAC
1 TATTATACCTTTAAAC-AACCGGTAGGTAGTTTAACGTAATAGGTAGCGTCTATTTTATTTTAAC
*
57960 CGGTTAAGTAGT-AGATATTTTACCGGTTACATTAA
65 CGGTTAAGTAGTGA-ATATTTCACCGGTTACATTAA
* * *
57995 TATTATACCTTTAAACAAACCGGTAGGTAGTTTAACATAATATGTAGCGTTTATTTTATTTTAAC
1 TATTATACCTTTAAAC-AACCGGTAGGTAGTTTAACGTAATAGGTAGCGTCTATTTTATTTTAAC
*
58060 CGGTTAAGTTGTGAATATTTCACCGGTTACATTAA
65 CGGTTAAGTAGTGAATATTTCACCGGTTACATTAA
* *
58095 TATTATACATTT-CACAACCGGATAGGTAGTTTAACGTAATATGGTAGCGTCTATTTTATTTTAA
1 TATTATACCTTTAAACAACCGG-TAGGTAGTTTAACGTAATA-GGTAGCGTCTATTTTATTTTAA
58159 CCGGTTA
64 CCGGTTA
58166 CATTATTATT
Statistics
Matches: 154, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
98 6 0.04
99 20 0.13
100 127 0.82
101 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (99 bp):
TATTATACCTTTAAACAACCGGTAGGTAGTTTAACGTAATAGGTAGCGTCTATTTTATTTTAACC
GGTTAAGTAGTGAATATTTCACCGGTTACATTAA
Found at i:58444 original size:73 final size:72
Alignment explanation
Indices: 58330--58557 Score: 255
Period size: 72 Copynumber: 3.1 Consensus size: 72
58320 AAATTGTAAA
* **
58330 TATTTTAACGTTTACA-TATTATATACCTTTAAACAAACGGTAACTAGTTTAACGTAATAGATAT
1 TATTTTACCGTTTACATTA-T-TATACCTTTAAACAAACGGTAGTTAGTTTAACGTAATAGAT-T
* *
58394 -CGTCTATTT
63 GAGCCTATTT
*
58403 TATTTTACCGTTTACATTATTATACCTTTAAACAAATCGGTAGTTAGTTT-ACGTAATAGGTTGA
1 TATTTTACCGTTTACATTATTATACCTTTAAACAAA-CGGTAGTTAGTTTAACGTAATAGATTGA
58467 GCCTATTT
65 GCCTATTT
* * *
58475 TATTTCACCGTTTACATTATTATTATACCTTTAAACAAACTAGTAGTTAGTTTAACGTAATAGGT
1 TATTTTACCGTTTAC---ATTATTATACCTTTAAACAAAC-GGTAGTTAGTTTAACGTAATAGAT
* *
58540 TGCGCTTATTT
62 TGAGCCTATTT
*
58551 TAATTTA
1 TATTTTA
58558 ACAGGTTATG
Statistics
Matches: 135, Mismatches: 12, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
71 1 0.01
72 47 0.35
73 27 0.20
74 3 0.02
75 32 0.24
76 25 0.19
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (72 bp):
TATTTTACCGTTTACATTATTATACCTTTAAACAAACGGTAGTTAGTTTAACGTAATAGATTGAG
CCTATTT
Found at i:58528 original size:245 final size:254
Alignment explanation
Indices: 57975--58565 Score: 711
Period size: 245 Copynumber: 2.4 Consensus size: 254
57965 AAGTAGTAGA
* * * ** * * *
57975 TATTTTACCGGTTACATTAATATTATACCTTTAAACAAACCGGTAGGTAGTTTAACATAATATGT
1 TATTTCACCGTTTACATTATTATTATACCTTTAAACAAACTAGTAGCTAGTTTAACGTAATAAGT
* * * * *
58040 AGCGTTTATTTTATTTTAACCGGTTAAGTTGTGAATATTTCACCGGTTACATTAATATTATACAT
66 TGCGCTTATTTTATTTTAACCGGTTAAATTGTAAATATTTCAACGGTTACATTAATATTATACAT
* * ** *
58105 TTCACAACCGGATAGGTAGTTTAACGTAATATGGTAGCGTCTATTTTATTTTAACCGGTTACATT
131 TTAACAAACGGATAACTAGTTTAACGTAATATGATAGCGTCTATTTTATTTTAACCGGTT--ATT
* * * * *
58170 ATTATTATTATACATTTAAACAAACAGGTAGCTAGTTTAACTTAATATGTTGCGCTTATTT
194 ATCATTATTATACATTTAAACAAACAGGTAGCTAGTTTAACGTAATAGGTTGAGCCTATTT
* * * * *
58231 TATTTCACCGTTTACA-TATAATTATAACTTTAAATAAATTAATAGCTAGTTTAACGTAATAAGT
1 TATTTCACCGTTTACATTATTATTATACCTTTAAACAAACTAGTAGCTAGTTTAACGTAATAAGT
* * * *
58295 TGCGCTTATTTTATTTTAACCGGTTAAATTGTAAATATTTTAACGTTTACA-TATTA-TATACCT
66 TGCGCTTATTTTATTTTAACCGGTTAAATTGTAAATATTTCAACGGTTACATTAATATTATACAT
*
58358 TTAAACAAACGG-TAACTAGTTTAACGTAATA-GATATCGTCTATTTTATTTT-ACC-G-T-TTA
131 TT-AACAAACGGATAACTAGTTTAACGTAATATGATAGCGTCTATTTTATTTTAACCGGTTATTA
* *
58417 -CATTATTATACCTTTAAACAAATC-GGTAGTTAGTTT-ACGTAATAGGTTGAGCCTATTT
195 TCATTATTATACATTTAAACAAA-CAGGTAGCTAGTTTAACGTAATAGGTTGAGCCTATTT
* *
58475 TATTTCACCGTTTACATTATTATTATACCTTTAAACAAACTAGTAGTTAGTTTAACGTAATAGGT
1 TATTTCACCGTTTACATTATTATTATACCTTTAAACAAACTAGTAGCTAGTTTAACGTAATAAGT
* *
58540 TGCGCTTATTTTAATTTAACAGGTTA
66 TGCGCTTATTTTATTTTAACCGGTTA
58566 TGTTGTAATT
Statistics
Matches: 288, Mismatches: 44, Indels: 17
0.83 0.13 0.05
Matches are distributed among these distances:
244 34 0.12
245 96 0.33
246 4 0.01
249 1 0.00
250 1 0.00
251 3 0.01
252 18 0.06
253 25 0.09
254 11 0.04
255 81 0.28
256 14 0.05
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (254 bp):
TATTTCACCGTTTACATTATTATTATACCTTTAAACAAACTAGTAGCTAGTTTAACGTAATAAGT
TGCGCTTATTTTATTTTAACCGGTTAAATTGTAAATATTTCAACGGTTACATTAATATTATACAT
TTAACAAACGGATAACTAGTTTAACGTAATATGATAGCGTCTATTTTATTTTAACCGGTTATTAT
CATTATTATACATTTAAACAAACAGGTAGCTAGTTTAACGTAATAGGTTGAGCCTATTT
Done.