Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005560.1 Hibiscus syriacus cultivar Beakdansim tig00012896_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: 73746
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1899 original size:21 final size:21
Alignment explanation
Indices: 1857--1899 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1847 TTTATGGGCT
* *
1857 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
1878 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
1899 A
1 A
1900 CGTATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:2622 original size:23 final size:23
Alignment explanation
Indices: 2578--2622 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2568 ATTATTATAT
*
2578 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* * *
2601 GGCACTTCGGTGTATTTATACG
1 GGCACTACGGTGCAATTATACG
2623 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:4032 original size:23 final size:23
Alignment explanation
Indices: 3972--4040 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
3962 CACCACAGCT
* * *
3972 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCATCGGAGTGCCA
*
3995 CGTAGAATTGCATCGGAGTGCCG
1 CGTAGAATTGCATCGGAGTGCCA
* *
4018 CGTAGAATTGTATCGTAGTGCCA
1 CGTAGAATTGCATCGGAGTGCCA
4041 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (23 bp):
CGTAGAATTGCATCGGAGTGCCA
Found at i:4241 original size:103 final size:105
Alignment explanation
Indices: 4056--4274 Score: 343
Period size: 103 Copynumber: 2.1 Consensus size: 105
4046 TAATGTCCAT
*
4056 AAGGACCACATATCATTCCTTAAGAATCATATACATATACATATACTATGGATCAAGTATGTGTC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATAC----ACTAAGGATCAAGTATGTGTC
* *
4121 TCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
62 ACACCAGACTTCACACATGTTCAAAAGAATACATATATGTCCCG
*
4165 AAGGACCACATATCATTCCTTAAGAATCATATACATATGC-C-AAGGATCAAGTATGTGTCACAC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACACTAAGGATCAAGTATGTGTCACAC
4228 CAGACTTCACACATGTTCAAAAGAATACATATATGTCCCG
66 CAGACTTCACACATGTTCAAAAGAATACATATATGTCCCG
*
4268 AATGACC
1 AAGGACC
4275 GCGTAGACCC
Statistics
Matches: 105, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
103 65 0.62
104 1 0.01
109 39 0.37
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (105 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACACTAAGGATCAAGTATGTGTCACAC
CAGACTTCACACATGTTCAAAAGAATACATATATGTCCCG
Found at i:6603 original size:18 final size:18
Alignment explanation
Indices: 6580--6616 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
6570 ACTTTTTTTC
6580 GATTGACGCTTTTACAAA
1 GATTGACGCTTTTACAAA
6598 GATTGACGCTTTTACAAA
1 GATTGACGCTTTTACAAA
6616 G
1 G
6617 CTAAACGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (18 bp):
GATTGACGCTTTTACAAA
Found at i:17918 original size:389 final size:386
Alignment explanation
Indices: 17198--17976 Score: 1186
Period size: 389 Copynumber: 2.0 Consensus size: 386
17188 AACCCTGGTT
* * * *
17198 AGATTGACACATGTGACGATAGCTCATGTACCAGATTTGTCTTTTAAAGTACTGGTACTACTGAA
1 AGATTGACACATGTGACGATAGCTCATGTACAAGATTGGTCTTTTAAAGTACTGGTACCACTAAA
** * * *
17263 AAAGTTTATCATAAGGGGTTCTCAATGAGATTTATCTCTTTGTCAAAATACTGGTATGTTGTAAT
66 AAAGTAAATCATAAGGGGTTCTCAATGAGATTTATCTCTTTGTCAAAATACTGGCATGGTATAAT
* *
17328 TGGAACGTGTGACCTCACAACCAACTTTTGTCTATTTTATTCTAATGAAAACCATTTTTGTATTC
131 TGAAACGTGTGACCTCACAACCAACTTTTGTCTATTTTATTCTAATGAAAAACATTTTTGTATTC
*
17393 TATTTTCTTGGAAATCCATTGTGAATCTTCTGAGAGTGGAACTTTTTGGCATCTAGAGTATACTC
196 TATTTTCTTGGAAATCCATTGTGAATCTTCTGAGAGTAGAACTTTTTGGCATCTAGAGTATACTC
* * *
17458 CAGGATAACTATGCTCTTTTTAAAAGGTGATTAAAATAGTATTATATTTTCTCAATTGCCTCAAT
261 CAGGATAACTATGCTCTGTTTAAAAGGTGATTAAAATAGAATTATATTTTCTCAATTGCCTCAAC
17523 GGGGACTAGGGTTAGCTTTTATGTATTTATATTGCATAGTGACTTTTACCGTCATATGATA
326 GGGGACTAGGGTTAGCTTTTATGTATTTATATTGCATAGTGACTTTTACCGTCATATGATA
17584 AGATTGACACATGTGACTG-TAGCTCATGTACAAGATTGGTCTTTTAAAGTACTGGTACCACTAA
1 AGATTGACACATGTGAC-GATAGCTCATGTACAAGATTGGTCTTTTAAAGTACTGGTACCACT-A
** * * * *
17648 AAAAAGTAAATTGTATGGGGTTCTCTATGAGATTTATCTCTTTGTCGAAATACTGGCATGGTATT
64 AAAAAGTAAATCATAAGGGGTTCTCAATGAGATTTATCTCTTTGTCAAAATACTGGCATGGTATA
* * *
17713 ATTGAAATGTGTGA-C-CACAACCAATTTTTGTCTATTTTACTCTGTAATGTAAAAACATTTTTT
129 ATTGAAACGTGTGACCTCACAACCAACTTTTGTCTATTTTA-T-TCTAATG-AAAAACA-TTTTT
* * * *
17776 GTATTCTATTTTCTTGTAAGTCCATTGTGAATCTTTTGAGATTAGAACTTTTTGGCATCTAGAGT
190 GTATTCTATTTTCTTGGAAATCCATTGTGAATCTTCTGAGAGTAGAACTTTTTGGCATCTAGAGT
** * *
17841 ATACTCCTTGATAACTGTGCTCTGTTTAAAAGGTGATTAAAATAGAATTATATTTTCTTAATTGC
255 ATACTCCAGGATAACTATGCTCTGTTTAAAAGGTGATTAAAATAGAATTATATTTTCTCAATTGC
*
17906 CTCAACGGGGACTAGGGTTAGCTTTTATGTATTTATATTGCATAGTGACTTTTACTGTCATATGA
320 CTCAACGGGGACTAGGGTTAGCTTTTATGTATTTATATTGCATAGTGACTTTTACCGTCATATGA
17971 TA
385 TA
17973 AGAT
1 AGAT
17977 GTCCATTAAG
Statistics
Matches: 354, Mismatches: 33, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
385 23 0.06
386 59 0.17
387 73 0.21
388 6 0.02
389 193 0.55
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (386 bp):
AGATTGACACATGTGACGATAGCTCATGTACAAGATTGGTCTTTTAAAGTACTGGTACCACTAAA
AAAGTAAATCATAAGGGGTTCTCAATGAGATTTATCTCTTTGTCAAAATACTGGCATGGTATAAT
TGAAACGTGTGACCTCACAACCAACTTTTGTCTATTTTATTCTAATGAAAAACATTTTTGTATTC
TATTTTCTTGGAAATCCATTGTGAATCTTCTGAGAGTAGAACTTTTTGGCATCTAGAGTATACTC
CAGGATAACTATGCTCTGTTTAAAAGGTGATTAAAATAGAATTATATTTTCTCAATTGCCTCAAC
GGGGACTAGGGTTAGCTTTTATGTATTTATATTGCATAGTGACTTTTACCGTCATATGATA
Found at i:24656 original size:28 final size:28
Alignment explanation
Indices: 24585--24656 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 28
24575 TTAAAGGCAC
* * *
24585 AAACCCTAAACTTTAAACCCTATATTTA
1 AAACCATAAACTCTAAACCCTAAATTTA
* *
24613 AAACCACAAAGC-CTAAAGCCTAAATTGT-
1 AAACCATAAA-CTCTAAACCCTAAATT-TA
24641 AAACCATAAACTCTAA
1 AAACCATAAACTCTAA
24657 TTCTTAAACT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
27 1 0.03
28 32 0.91
29 2 0.06
ACGTcount: A:0.47, C:0.25, G:0.04, T:0.24
Consensus pattern (28 bp):
AAACCATAAACTCTAAACCCTAAATTTA
Found at i:24700 original size:22 final size:21
Alignment explanation
Indices: 24675--24722 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
24665 CTCAAATATA
24675 AAACTATAAATCATTAAACCTT
1 AAACTATAAATCA-TAAACCTT
* *
24697 AAACCTTTAAATCATAAATCTT
1 AAA-CTATAAATCATAAACCTT
24719 AAAC
1 AAAC
24723 CCTAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.04
22 13 0.57
23 9 0.39
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (21 bp):
AAACTATAAATCATAAACCTT
Found at i:24723 original size:22 final size:23
Alignment explanation
Indices: 24681--24723 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
24671 TATAAAACTA
24681 TAAATCATTAAACCTTAAACCTT
1 TAAATCATTAAACCTTAAACCTT
*
24704 TAAATCA-TAAATCTTAAACC
1 TAAATCATTAAACCTTAAACC
24724 CTAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAATCATTAAACCTTAAACCTT
Found at i:31136 original size:21 final size:20
Alignment explanation
Indices: 31109--31206 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
31099 AATCAGTGTC
31109 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
31130 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
31150 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
31170 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
31191 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
31207 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:31159 original size:41 final size:41
Alignment explanation
Indices: 31050--31206 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
31040 AAATGACCAA
* **
31050 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
31089 CAGAATCGCAAATC-AGTGTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
31130 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
31171 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
31207 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:31216 original size:20 final size:20
Alignment explanation
Indices: 31193--31363 Score: 107
Period size: 20 Copynumber: 8.6 Consensus size: 20
31183 GCGAATATGA
31193 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
31213 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
31233 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
** *
31253 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTAACCAT
* * *
31273 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
31293 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
* **
31313 AAATCGCAACGAG-AATCTGT
1 AAATCGCAACGCGTAA-CCAT
* *
31333 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
31353 AAATCGCAACG
1 AAATCGCAACG
31364 AGAATCTGTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 127 0.97
21 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:31258 original size:60 final size:58
Alignment explanation
Indices: 31173--31382 Score: 208
Period size: 60 Copynumber: 3.5 Consensus size: 58
31163 CGATTTTCCA
* ** * *
31173 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCGAAC-CGTAAATCGCAA-GCGTATCCGT
* ** *
31233 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCG-AACCGTAAATCGCAA-GCGTATCCGT
* *
31293 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGCAA-CGATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGCGAA-CCGTAAATCGCAAGCG-T-ATCCGT
* * *
31353 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGTGAATCCGTAAATCGCAAC
31383 ACTGAAATTT
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 120 0.96
61 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (58 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGCGAACCGTAAATCGCAAGCGTATCCGT
Found at i:31364 original size:20 final size:20
Alignment explanation
Indices: 31227--31382 Score: 174
Period size: 20 Copynumber: 7.8 Consensus size: 20
31217 CGCAATGCGT
*
31227 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
31247 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
31267 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
31287 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
31307 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
31327 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
31347 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
31367 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
31383 ACTGAAATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 119 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:31364 original size:40 final size:40
Alignment explanation
Indices: 31193--31382 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
31183 GCGAATATGA
* *
31193 AAATCGCAACGCGAA-CACATAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAA--CGATAATCCGT
* * * *
31233 AAATCGCAACGTGTATCCGTAAATCGCAACGCGT-TTCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* * *
31273 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
*
31313 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
31353 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
31383 ACTGAAATTT
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 129 0.97
41 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:32103 original size:24 final size:24
Alignment explanation
Indices: 32064--32110 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
32054 AAATTTGGTC
32064 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
32088 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
32111 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:32302 original size:12 final size:12
Alignment explanation
Indices: 32285--32309 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32275 ATATAATCCT
32285 GAAGAAGAAAAA
1 GAAGAAGAAAAA
32297 GAAGAAGAAAAA
1 GAAGAAGAAAAA
32309 G
1 G
32310 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:33423 original size:19 final size:19
Alignment explanation
Indices: 33401--33740 Score: 398
Period size: 19 Copynumber: 19.4 Consensus size: 19
33391 CGGAAATTAC
*
33401 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
33420 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
33434 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
33454 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
33468 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33487 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
33506 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
33520 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33539 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
33558 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
33572 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
33591 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
33605 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
33624 ACTCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33643 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33662 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33681 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
33695 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33714 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33733 AATCGCAA
1 AATCGCAA
33741 CGAGAGAATC
Statistics
Matches: 278, Mismatches: 12, Indels: 62
0.79 0.03 0.18
Matches are distributed among these distances:
14 56 0.20
15 2 0.01
16 21 0.08
17 20 0.07
18 3 0.01
19 163 0.59
20 13 0.05
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:33488 original size:33 final size:34
Alignment explanation
Indices: 33401--33762 Score: 340
Period size: 33 Copynumber: 10.5 Consensus size: 34
33391 CGGAAATTAC
* *
33401 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
33434 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
33468 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
33506 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
* *
33539 AATCGCAATGCGAAATGAAAATCGCAACGA-CAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
* *
33572 AATCGCAATGCGAAATGAAAATCGCAACGA-CAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
33605 AATCGCAATGCGAAATGAAACTCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
33643 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
33681 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
33714 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
33747 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
33763 TATAAACGCA
Statistics
Matches: 294, Mismatches: 13, Indels: 44
0.84 0.04 0.13
Matches are distributed among these distances:
33 160 0.54
34 32 0.11
35 13 0.04
36 12 0.04
37 3 0.01
38 74 0.25
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:33516 original size:52 final size:52
Alignment explanation
Indices: 33429--33721 Score: 381
Period size: 52 Copynumber: 5.6 Consensus size: 52
33419 AAATCCCAAC
33429 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
33482 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
33534 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
33586 ATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATGAAACTCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA-G-AA-TCGCAATGCGAA
*
33638 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
33693 A-G--AATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
33722 TGCGAAATGA
Statistics
Matches: 221, Mismatches: 6, Indels: 27
0.87 0.02 0.11
Matches are distributed among these distances:
47 8 0.04
49 5 0.02
50 5 0.02
51 2 0.01
52 152 0.69
53 16 0.07
54 5 0.02
55 6 0.03
57 18 0.08
58 2 0.01
59 1 0.00
60 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:33577 original size:14 final size:14
Alignment explanation
Indices: 33558--33612 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
33548 GCGAAATGAA
33558 AATCGCAACGACAG
1 AATCGCAACGACAG
*
33572 AATCGCAATGCGAAATG
1 AATCGCAA--CGACA-G
33589 AAAATCGCAACGACAG
1 --AATCGCAACGACAG
33605 AATCGCAA
1 AATCGCAA
33613 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
16 5 0.15
17 5 0.15
19 8 0.24
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (14 bp):
AATCGCAACGACAG
Found at i:33722 original size:52 final size:54
Alignment explanation
Indices: 33401--33762 Score: 346
Period size: 52 Copynumber: 6.9 Consensus size: 54
33391 CGGAAATTAC
*
33401 AATCGCAACGCGAAATGAAAATCCCAA-C---ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAA-GCGAAATGAAAATCGCAAGCGAAATG-AAATCGCAATGC-GAAATGAA
*
33454 AATCGCAA-CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAAGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAATGCGAAATGAA
*
33506 AATCGCAA-CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAAGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAATGCGAAATGAA
* *
33558 AATCGCAA-CGACA-G--AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--
1 AATCGCAAGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAATGCGAAATGAA
*
33605 AATCGCAATGCGAAATGAAACTCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA-GCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAATGCGAAATGAA
33662 AATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-AATCGCAATGCGAAATGAA
1 AATCGCAA-GCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAAATGAA
*
33714 AATCGCAATGCGAAATGAAAATCGCAA-CGAGA-G-AATCGCAATGCGAAAT
1 AATCGCAA-GCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAAAT
33763 TATAAACGCA
Statistics
Matches: 284, Mismatches: 8, Indels: 35
0.87 0.02 0.11
Matches are distributed among these distances:
47 8 0.03
48 9 0.03
49 6 0.02
50 6 0.02
51 2 0.01
52 190 0.67
53 24 0.08
54 7 0.02
55 6 0.02
57 26 0.09
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (54 bp):
AATCGCAAGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAAATGAA
Found at i:33878 original size:19 final size:19
Alignment explanation
Indices: 33769--33870 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
33759 AAATTATAAA
33769 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
33788 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
33808 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
33824 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
33841 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
33860 CGCATTGCGAT
1 CGCATTGCGAT
33871 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:33996 original size:14 final size:14
Alignment explanation
Indices: 33977--34013 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
33967 CATCAATTAC
33977 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
33991 ACAAATCATCTTTT
1 ACAAATCAACTTTT
34005 ACAAATCAA
1 ACAAATCAA
34014 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:36010 original size:14 final size:14
Alignment explanation
Indices: 35991--36047 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
35981 GCGAAATGAA
*
35991 AATCGCAACGACAG
1 AATCGCAACGAAAG
36005 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
36022 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
36038 AATCGCAACG
1 AATCGCAACG
36048 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:36018 original size:33 final size:33
Alignment explanation
Indices: 35972--36064 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
35962 GCGAAACCAA
*
35972 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
36005 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
36038 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
36065 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:36029 original size:19 final size:19
Alignment explanation
Indices: 35935--36069 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
35925 TAGTTTACTT
* *
35935 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
35955 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
35974 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
35993 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
36007 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
36026 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
36040 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
36059 TCGCAATGCGA
1 TCGCAACGCGA
36070 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:36087 original size:19 final size:19
Alignment explanation
Indices: 36065--36177 Score: 111
Period size: 19 Copynumber: 6.5 Consensus size: 19
36055 AAAATCGCAA
36065 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
36084 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
36098 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
36117 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
** *
36131 TGCGATTTTCATTTCGTGT
1 TGCGATTTTGGTTTCGCGT
36150 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
36169 TGCGATTTT
1 TGCGATTTT
36178 AACTTTCGTG
Statistics
Matches: 75, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
14 22 0.29
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 46 0.61
ACGTcount: A:0.07, C:0.17, G:0.28, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:36107 original size:33 final size:33
Alignment explanation
Indices: 36065--36156 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
36055 AAAATCGCAA
36065 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
36098 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
36131 TGCGATTTTCATTTCGTGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
36157 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:36190 original size:20 final size:18
Alignment explanation
Indices: 36129--36193 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 18
36119 CGATTCTGTC
36129 GTTGCGATTTTCATTTCGT
1 GTTGCGATTTT-ATTTCGT
* *
36148 GTTGCGATTTTGGTTTCGC
1 GTTGCGATTTT-ATTTCGT
36167 GTTGCGATTTTAACTTTCGT
1 GTTGCGATTTT-A-TTTCGT
36187 GTTGCGA
1 GTTGCGA
36194 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 27 0.69
20 12 0.31
ACGTcount: A:0.11, C:0.15, G:0.26, T:0.48
Consensus pattern (18 bp):
GTTGCGATTTTATTTCGT
Found at i:36357 original size:93 final size:93
Alignment explanation
Indices: 36241--36709 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
36231 ATGGATTGCA
*
36241 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAAAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
36305 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
36333 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
36398 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
36426 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
36491 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
36519 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
36584 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
36612 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
36677 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
36705 TTACT
1 TTACT
36710 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 370 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:38435 original size:14 final size:14
Alignment explanation
Indices: 38416--38505 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
38406 TTGAAATGAA
38416 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
38430 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
38449 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
38463 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
38482 AATCGCAACGAGAG
1 AATCGCAACGAGAG
38496 AATCGCAACG
1 AATCGCAACG
38506 CGAAATAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:38453 original size:33 final size:33
Alignment explanation
Indices: 38408--38522 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
38398 TCTTTTGGTT
38408 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
38441 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
38474 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
38507 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
38523 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.47, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:38454 original size:19 final size:19
Alignment explanation
Indices: 38430--38527 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
38420 GCAACGAGAG
*
38430 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
38449 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
38463 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
38482 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
38496 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
*
38515 AATCGCAATGCGA
1 AATCGCAACGCGA
38528 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:38558 original size:14 final size:14
Alignment explanation
Indices: 38539--38595 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
38529 TTTGGTTTCG
38539 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
38553 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
38572 CGTTGCGATTATCT
1 CGTTGCGATTCTCT
38586 CGTTGCGATT
1 CGTTGCGATT
38596 GTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 2 0.06
19 10 0.29
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:38577 original size:19 final size:19
Alignment explanation
Indices: 38553--38641 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
38543 GCGATTCTCT
38553 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
38572 CGTTGCGA--TT-A--TCT
1 CGTTGCGATTTTCATTTCG
*
38586 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
38605 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
38625 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
38642 ATCTCGTTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 25 0.45
20 15 0.27
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:38640 original size:39 final size:33
Alignment explanation
Indices: 38523--38641 Score: 148
Period size: 33 Copynumber: 3.4 Consensus size: 33
38513 AAAATCGCAA
**
38523 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
38556 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
38589 TGCGATTGTCATTTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCGT
38628 TGCGATTTTCATTT
1 TGCGATTTTCATTT
38642 ATCTCGTTGC
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
33 49 0.66
35 1 0.01
36 1 0.01
37 1 0.01
39 22 0.30
ACGTcount: A:0.11, C:0.22, G:0.23, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:38774 original size:33 final size:33
Alignment explanation
Indices: 38732--38802 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
38722 AATACTAACT
38732 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
38765 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
38798 TGAAA
1 TGAAA
38803 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:39036 original size:22 final size:22
Alignment explanation
Indices: 38984--39038 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
38974 TGGTTGTGAG
**
38984 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
39006 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
39028 GGATTTCTTCG
1 GGATTTCTTCG
39039 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:39210 original size:20 final size:20
Alignment explanation
Indices: 39185--39378 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
39175 CTTTAAATAT
39185 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
39205 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
39227 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
39246 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
39266 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
39286 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
39306 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
39326 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
39346 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
39366 CGCGTTGCGATTT
1 CGCGTTGCGATTT
39379 TGAAAAATCG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:39372 original size:60 final size:60
Alignment explanation
Indices: 39185--39378 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
39175 CTTTAAATAT
* ** *
39185 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACAGATA
* *** * *
39246 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
* * * * *
39306 CACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
39366 CGCGTTGCGATTT
1 CGCGTTGCGATTT
39379 TGAAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
Found at i:39395 original size:21 final size:21
Alignment explanation
Indices: 39365--39442 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 21
39355 ATTTTCATAT
*
39365 TCGCGTTGCGATTTTGAAAAA
1 TCGCATTGCGATTTTGAAAAA
* * **
39386 TCGCAATGCGAATTTG-ACTA
1 TCGCATTGCGATTTTGAAAAA
* *
39406 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAAAAA
*
39427 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
39443 GAAACTGATT
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGAAAAA
Found at i:39418 original size:61 final size:60
Alignment explanation
Indices: 39345--39501 Score: 167
Period size: 61 Copynumber: 2.6 Consensus size: 60
39335 ATTTATGTGT
*
39345 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGAAAAATCGCA-ATGCGAATT-TGACTA
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGAAAAAT-G-ATATGCG-ATTCTGACGA
* * * * * * **
39406 TCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAACTGATTTGCGATTCTGGGGA
1 TCGCGTTGCGATTTTC-ATATTCGCGTTGCGATTTTGAAAAATGATATGCGATTCTGACGA
*
39467 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTG
39502 TTGGTCATTT
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
59 16 0.20
60 5 0.06
61 37 0.46
62 22 0.28
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (60 bp):
TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGAAAAATGATATGCGATTCTGACGA
Found at i:39437 original size:41 final size:41
Alignment explanation
Indices: 39345--39442 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 41
39335 ATTTATGTGT
* * *
39345 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGAAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTCAAAAA
** * *
39386 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTCAAAAA
39427 TCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTG
39443 GAAACTGATT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTCAAAAA
Found at i:42471 original size:17 final size:17
Alignment explanation
Indices: 42437--42468 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42427 AGAAAGAAAA
42437 TAATATTATTAATTAAT
1 TAATATTATTAATTAAT
42454 TAATATTATT-ATTAA
1 TAATATTATTAATTAA
42469 ATTGGAGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATATTATTAATTAAT
Found at i:45875 original size:31 final size:31
Alignment explanation
Indices: 45837--45900 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
45827 AGGCAGCGAC
*
45837 GGTGAAA-GGAAAACTTGATTGGGTTTTGGTT
1 GGTGAAAGGGAAAA-TTGACTGGGTTTTGGTT
45868 GGTGAAAGGGAAAATTGACTGGGTTTTGGTT
1 GGTGAAAGGGAAAATTGACTGGGTTTTGGTT
45899 GG
1 GG
45901 AAATATGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.25, C:0.03, G:0.39, T:0.33
Consensus pattern (31 bp):
GGTGAAAGGGAAAATTGACTGGGTTTTGGTT
Found at i:55063 original size:193 final size:192
Alignment explanation
Indices: 54718--55102 Score: 679
Period size: 193 Copynumber: 2.0 Consensus size: 192
54708 ATTTCTGACT
54718 TTCAACAAAACCTAGACTATGACAGGTTCTTCTTGACAAGCTTAAGAAATTAGACCCGTACCCAA
1 TTCAACAAAACCTAGACTATGACAGGTTCTTCTTGACAAGCTTAAGAAATTAGACCCGTACCCAA
54783 ATTATAATATTATATGTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCC
66 ATTATAATATTATATGTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCC
*
54848 GGCTTTATGGACATAATTAGCTAGACTAA-AAGGTGATGATATTATATATATACAATAAAGCTG
131 GGCTTTATGGACATAATTAGCTAGACTAATAAAG-G-TGATATTATATATATACAATAAAGCTG
*
54911 TTCAACAACACCTAGACTATGACAGGTTCTTCTTGACAAGCTTAAGAAATTAGACCCGTATACCC
1 TTCAACAAAACCTAGACTATGACAGGTTCTTCTTGACAAGCTTAAGAAATTAGACCCG--TACCC
54976 AAATTATAATA-T-TATGTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGC
64 AAATTATAATATTATATGTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGC
55039 CCGGC-TTATGGACATAATTTAGCTAGACTAATAAAGGTGATATTATATATATACAATAAAGCTG
129 CCGGCTTTATGGACATAA-TTAGCTAGACTAATAAAGGTGATATTATATATATACAATAAAGCTG
55103 AGCTATTCCG
Statistics
Matches: 186, Mismatches: 2, Indels: 9
0.94 0.01 0.05
Matches are distributed among these distances:
192 39 0.21
193 127 0.68
194 4 0.02
195 16 0.09
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (192 bp):
TTCAACAAAACCTAGACTATGACAGGTTCTTCTTGACAAGCTTAAGAAATTAGACCCGTACCCAA
ATTATAATATTATATGTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCC
GGCTTTATGGACATAATTAGCTAGACTAATAAAGGTGATATTATATATATACAATAAAGCTG
Found at i:57081 original size:42 final size:41
Alignment explanation
Indices: 57034--57130 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
57024 ATAATTTAAG
* * *
57034 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGAT-AAA
* * *
57076 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
* *
57117 TCATTCGAGCCATC
1 TCCTTCGGGCCATC
57131 CATAAAGCCT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 13 0.28
42 33 0.72
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
Found at i:57309 original size:42 final size:42
Alignment explanation
Indices: 57250--57381 Score: 237
Period size: 42 Copynumber: 3.1 Consensus size: 42
57240 ACTTAGTAAG
*
57250 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
57292 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
* *
57334 TCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
57376 TCCTTC
1 TCCTTC
57382 GGGTAACTGG
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (42 bp):
TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
Found at i:57441 original size:13 final size:13
Alignment explanation
Indices: 57423--57447 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57413 TGAAGAAAAT
57423 CCATCAGTAAGTG
1 CCATCAGTAAGTG
57436 CCATCAGTAAGT
1 CCATCAGTAAGT
57448 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:57687 original size:80 final size:80
Alignment explanation
Indices: 57437--57717 Score: 458
Period size: 80 Copynumber: 3.5 Consensus size: 80
57427 CAGTAAGTGC
57437 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
57502 GTAGTGAAGCAAATT
66 GTAGTGAAGCAAATT
* * ** *
57517 CATCAGTAAGTCTTTCGAGCATGGTAATTAAATCCTTCGGGTAA-TTTTAAGCCTTCACCGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
**
57581 GTAGTGAAGCAAACC
66 GTAGTGAAGCAAATT
57596 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
57661 GTAGTGAAGCAAATT
66 GTAGTGAAGCAAATT
* *
57676 CATCAGTAAGTCTTTCGAGCAGGATG-TTGAAATCTTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATT-AAATCCTTCGGGT
57718 CATCAGTAAG
Statistics
Matches: 183, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
79 74 0.40
80 109 0.60
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (80 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
GTAGTGAAGCAAATT
Found at i:57722 original size:42 final size:41
Alignment explanation
Indices: 57675--57787 Score: 147
Period size: 42 Copynumber: 2.7 Consensus size: 41
57665 TGAAGCAAAT
*
57675 TCATCAGTAAGTCTTTCGAGCAGGATGTTGAAATCTTTCGGG
1 TCATCAGTAAGTCTTTCGAGCAGGATGTT-AAATCCTTCGGG
*
57717 TCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
1 TCATCAGTAAGTCTTTCGAGCAGGATG-TTAAATCCTTCGGG
* * *
57759 TCATCCA-TAAGTCCTTCGGGTAGGATGTT
1 TCAT-CAGTAAGTCTTTCGAGCAGGATGTT
57788 TTCACACCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
41 2 0.03
42 57 0.90
43 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (41 bp):
TCATCAGTAAGTCTTTCGAGCAGGATGTTAAATCCTTCGGG
Found at i:58262 original size:53 final size:53
Alignment explanation
Indices: 58199--58394 Score: 288
Period size: 53 Copynumber: 3.7 Consensus size: 53
58189 ATCAAACCAT
58199 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
58252 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAGACAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * *
58305 AAGACTGTTTGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCTGCT-GGTC-G
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGG-CAG
*
58358 AAGATTGTTCGAGTTCTACTCCCTGAAGCAATAGGGA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGA
58395 ACAAACCTTT
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
53 125 0.98
54 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
Found at i:66967 original size:14 final size:14
Alignment explanation
Indices: 66929--66970 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
66919 ACCATAACTG
66929 CTTACAACATAACA
1 CTTACAACATAACA
**
66943 CTTATTACATAACA
1 CTTACAACATAACA
66957 CTTA-AACCATAACA
1 CTTACAA-CATAACA
66971 TCCTTCAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 1 0.04
14 23 0.96
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (14 bp):
CTTACAACATAACA
Done.