Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007254.1 Hibiscus syriacus cultivar Beakdansim tig00019221_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: 74705
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:803 original size:31 final size:31
Alignment explanation
Indices: 761--821 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
751 TCAATAAAAT
*
761 TTAAAAAATTATAAAA-TACTTATTAAATTTA
1 TTAAAAAATTATAAAATTA-TTAATAAATTTA
*
792 TTAAAAGATTATAAAATTATTAATAAATTT
1 TTAAAAAATTATAAAATTATTAATAAATTT
822 CTAAATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (31 bp):
TTAAAAAATTATAAAATTATTAATAAATTTA
Found at i:1957 original size:15 final size:15
Alignment explanation
Indices: 1933--1963 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1923 TAACAAGACA
1933 ACATTATATAGTCAG
1 ACATTATATAGTCAG
*
1948 ACATTCTATAGTCAG
1 ACATTATATAGTCAG
1963 A
1 A
1964 AGATTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (15 bp):
ACATTATATAGTCAG
Found at i:2328 original size:17 final size:17
Alignment explanation
Indices: 2306--2340 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2296 TGATTAAGCG
*
2306 TTGAATAATTCAATGGC
1 TTGAATAATTCAAAGGC
*
2323 TTGAATGATTCAAAGGC
1 TTGAATAATTCAAAGGC
2340 T
1 T
2341 CTGTATGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (17 bp):
TTGAATAATTCAAAGGC
Found at i:2787 original size:43 final size:43
Alignment explanation
Indices: 2726--2809 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
2716 TATATTATTT
2726 TTCCCTCCTCACCTTCTATCCCATTCAAATCTTAAAAAAAATA
1 TTCCCTCCTCACCTTCTATCCCATTCAAATCTTAAAAAAAATA
2769 TTCCCTCCTCACCTTCTATCCCATTCAAATCTTAAAAAAAA
1 TTCCCTCCTCACCTTCTATCCCATTCAAATCTTAAAAAAAA
2810 AATATTAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.32
Consensus pattern (43 bp):
TTCCCTCCTCACCTTCTATCCCATTCAAATCTTAAAAAAAATA
Found at i:8413 original size:18 final size:18
Alignment explanation
Indices: 8390--8425 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
8380 CCACTAAAAG
*
8390 ATCGTGTGTATATGACTC
1 ATCGTGCGTATATGACTC
8408 ATCGTGCGTATATGACTC
1 ATCGTGCGTATATGACTC
8426 CAGCTAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (18 bp):
ATCGTGCGTATATGACTC
Found at i:10955 original size:33 final size:33
Alignment explanation
Indices: 10913--11276 Score: 416
Period size: 33 Copynumber: 11.1 Consensus size: 33
10903 CCCTCGTCTC
*
10913 CTCAACTTTCCGT-TGTTCTTCCACTTTGGAGTT
1 CTCAACTTTCTGTGT-TTCTTCCACTTTGGAGTT
* *
10946 CTCAACTTTCCGT-TGTTCTTCCACTTCGGAGTT
1 CTCAACTTTCTGTGT-TTCTTCCACTTTGGAGTT
* * *
10979 CTCAGCTTTCTGTGCTTCATCCACTTTGGAG--
1 CTCAACTTTCTGTGTTTCTTCCACTTTGGAGTT
* *
11010 -TCAGCTTTATGTGTTTCTTCCACTTTGGAGTT
1 CTCAACTTTCTGTGTTTCTTCCACTTTGGAGTT
* *
11042 CTCAGCTTTCTGTGTTTCTTCCATTTTGGAGTT
1 CTCAACTTTCTGTGTTTCTTCCACTTTGGAGTT
* * **
11075 CTCAACTTTCTGTGCTTCTTCAACTTTCAAGTT
1 CTCAACTTTCTGTGTTTCTTCCACTTTGGAGTT
* ** *
11108 CTCAACTTGCTGT-TCTTCTTTTACATTGGAGTT
1 CTCAACTTTCTGTGT-TTCTTCCACTTTGGAGTT
*
11141 CTCAACTTTATGTGTTTCTTCCACTTTGGAGTT
1 CTCAACTTTCTGTGTTTCTTCCACTTTGGAGTT
*
11174 CTCAACTTTATGTGTTTCTTCCACTTTGGAGTT
1 CTCAACTTTCTGTGTTTCTTCCACTTTGGAGTT
* * *
11207 CTCAGCTTTCTGTGTTTCTTTCACTTTCGAGTT
1 CTCAACTTTCTGTGTTTCTTCCACTTTGGAGTT
* * **
11240 CTCAACTTTCTGTTTTTCTTCTACAATGGAGTT
1 CTCAACTTTCTGTGTTTCTTCCACTTTGGAGTT
11273 CTCA
1 CTCA
11277 GTCTGCAACA
Statistics
Matches: 285, Mismatches: 40, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
30 27 0.09
33 257 0.90
34 1 0.00
ACGTcount: A:0.14, C:0.24, G:0.15, T:0.47
Consensus pattern (33 bp):
CTCAACTTTCTGTGTTTCTTCCACTTTGGAGTT
Found at i:15864 original size:121 final size:121
Alignment explanation
Indices: 15650--15891 Score: 475
Period size: 121 Copynumber: 2.0 Consensus size: 121
15640 TGATCCTTAA
15650 CTCTCTCGGTTATTCACCCATCCCCTCCCCTATAAATACCCCCGAATGCAAATATCAAACCACAC
1 CTCTCTCGGTTATTCACCCATCCCCTCCCCTATAAATACCCCCGAATGCAAATATCAAACCACAC
15715 CAAAATTACTTTTGCATTTTTCCTTCTATCAACTAAGTAGATTTTGTTATAGTTTT
66 CAAAATTACTTTTGCATTTTTCCTTCTATCAACTAAGTAGATTTTGTTATAGTTTT
*
15771 CTCTCTTGGTTATTCACCCATCCCCTCCCCTATAAATACCCCCGAATGCAAATATCAAACCACAC
1 CTCTCTCGGTTATTCACCCATCCCCTCCCCTATAAATACCCCCGAATGCAAATATCAAACCACAC
15836 CAAAATTACTTTTGCATTTTTCCTTCTATCAACTAAGTAGATTTTGTTATAGTTTT
66 CAAAATTACTTTTGCATTTTTCCTTCTATCAACTAAGTAGATTTTGTTATAGTTTT
15892 TAGAATGAAT
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 120 1.00
ACGTcount: A:0.28, C:0.29, G:0.07, T:0.36
Consensus pattern (121 bp):
CTCTCTCGGTTATTCACCCATCCCCTCCCCTATAAATACCCCCGAATGCAAATATCAAACCACAC
CAAAATTACTTTTGCATTTTTCCTTCTATCAACTAAGTAGATTTTGTTATAGTTTT
Found at i:18689 original size:3 final size:3
Alignment explanation
Indices: 18681--18735 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
18671 TTAATATATT
*
18681 TAA TAA TAA TAA TAA TAA TGA 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
18729 TAA TAA T
1 TAA TAA T
18736 CAATTAATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:19245 original size:112 final size:112
Alignment explanation
Indices: 19060--19475 Score: 640
Period size: 112 Copynumber: 3.7 Consensus size: 112
19050 ATAGAATTAT
* *
19060 GCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* *
19125 CATTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGA
65 CATTATGAACTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGA
*
19173 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGTGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* **
19238 ATTATGAAC-TCTTCTGGAAATGCTGATCCATCGAA-TGATGAATTCAA
66 ATTATGAACTTC-TCTGGAAAAGCTGATCCATC-AAGTGATGAATTTGA
* * *
19285 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
19350 ATTATGAACTTTTTCTGGAAAAGCTGATCCATC-AGATGATGCATTTGA
66 ATTATGAAC-TTCTCTGGAAAAGCTGATCCATCAAG-TGATGAATTTGA
*
19398 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGTGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
19463 ATTATGAACTTCT
66 ATTATGAACTTCT
19476 TCTTCCTCTT
Statistics
Matches: 275, Mismatches: 22, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
111 3 0.01
112 140 0.51
113 131 0.48
114 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGA
Found at i:19438 original size:20 final size:20
Alignment explanation
Indices: 19415--19480 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
19405 GTTGAACAAA
19415 TTCTTCTCATTATGAATTTC
1 TTCTTCTCATTATGAATTTC
* *
19435 TTCTTCCTTC-TTCA-G-ATGTG
1 TTCTT-C-TCATT-ATGAATTTC
*
19455 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAATTTC
19475 TTCTTC
1 TTCTTC
19481 CTCTTCAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
18 3 0.09
19 4 0.11
20 21 0.60
21 4 0.11
22 3 0.09
ACGTcount: A:0.15, C:0.24, G:0.08, T:0.53
Consensus pattern (20 bp):
TTCTTCTCATTATGAATTTC
Found at i:19470 original size:40 final size:39
Alignment explanation
Indices: 19415--19515 Score: 157
Period size: 40 Copynumber: 2.5 Consensus size: 39
19405 GTTGAACAAA
**
19415 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGTG
1 TTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATAAG
*
19455 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAG
1 TTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAG
19494 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAA-TTTCT
19516 CTGGAAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
39 26 0.46
40 30 0.54
ACGTcount: A:0.18, C:0.24, G:0.08, T:0.50
Consensus pattern (39 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAG
Found at i:19496 original size:152 final size:152
Alignment explanation
Indices: 19300--19623 Score: 501
Period size: 152 Copynumber: 2.1 Consensus size: 152
19290 AGGTTGAACA
* * *
19300 AGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTC
** * * *
19365 TGGAAAAGCTGATCCATC-AGATGATGCATT-TGAGCAAAAGGTTGAACAAATTCTTCTCATTAT
66 TGGAAAAAATAATCCATCAAG-TGATGAATTCAG-GCAAAAGGTTGAACAAATTCTTCTCATTAT
19428 GAATTTCTTCTTCCTTCTTCAGATG
129 GAATTTCTTCTTCC-TCTTCAGATG
*
19453 TGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTC
* *
19517 TGGAAAAAATAATTCATCAAGTGATGAATTCAGGGAAAAGGTTGAACAAATTCTTCTCATTATGA
66 TGGAAAAAATAATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGA
19582 ATTTCTTCTTCCTCTTCAGATG
131 ATTTCTTCTTCCTCTTCAGATG
19604 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
19624 CTAACTGGCA
Statistics
Matches: 157, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
151 29 0.18
152 98 0.62
153 30 0.19
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.41
Consensus pattern (152 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAAATAATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGA
ATTTCTTCTTCCTCTTCAGATG
Found at i:19497 original size:39 final size:40
Alignment explanation
Indices: 19415--19512 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 40
19405 GTTGAACAAA
* **
19415 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAG
19455 TTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAG
19494 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
19513 TCTCTGGAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 29 0.53
40 26 0.47
ACGTcount: A:0.18, C:0.23, G:0.08, T:0.50
Consensus pattern (40 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAG
Found at i:19810 original size:489 final size:490
Alignment explanation
Indices: 19062--19967 Score: 1471
Period size: 489 Copynumber: 1.9 Consensus size: 490
19052 AGAATTATGC
*
19062 AAAAAGTTGAACAAATTCTTCTTATTATGAACTTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * **
19127 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATT
66 TTATGAACTTCTCTGGAAAAGCTGATCCACCAAGTGATGAATTTAAGCAAAAAATTGAACAAATT
* * * *
19192 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATTATGAACTCTTCTGGAA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTACTGGAA
* * * *
19257 ATGCTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTC
196 ATGATGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
*
19322 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATC-AGA
261 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCGA-A
19386 TGATGCATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGA
325 TGATGCATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGA
*
19451 TGTGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCT
390 TGAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCT
19516 CTGGAAAAAATAATTCATCAAGTGATGAATTCAGGG
455 CTGGAAAAAATAATTCATCAAGTGATGAATTCAGGG
*
19552 AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCA
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** ** *
19615 TTATGAAC-TCTAACTGGCACTGCTGATCCACCGGGTGATGAATTTAAGCAAAAAATTGAACAAG
66 TTATGAACTTCT--CTGGAAAAGCTGATCCACCAAGTGATGAATTTAAGCAAAAAATTGAACAAA
19679 TTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTG
129 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCT-ACTG
* *
19743 GTAATGATGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
193 GAAATGATGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
*
19808 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCG
258 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCG
*
19873 AATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
323 AATGATGCATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
* *
19938 GATGAGTTCTTCTCTTTATGAACTTTTTCT
388 GATGAGTTCTTCTCATTATGAACTTCTTCT
19968 GGAAAAGCTG
Statistics
Matches: 382, Mismatches: 30, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
487 3 0.01
488 61 0.16
489 288 0.75
490 30 0.08
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (490 bp):
AAAAAGTTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTCTCTGGAAAAGCTGATCCACCAAGTGATGAATTTAAGCAAAAAATTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTACTGGAA
ATGATGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAAT
GATGCATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT
GAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAAATAATTCATCAAGTGATGAATTCAGGG
Found at i:19814 original size:376 final size:377
Alignment explanation
Indices: 19077--19849 Score: 1167
Period size: 376 Copynumber: 2.1 Consensus size: 377
19067 GTTGAACAAA
* *
19077 TTCTTCTTATTATGAACTTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTG
1 TTCTTCTCATTATGAAC-TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTCTCTG
** ** * *
19142 GAAAAGCTGCTCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
65 GAAAAAATAATCCATCAAGTGATGAATTAGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
* * *
19207 TTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATTATGAACTCTTCTGGAAATGCTGATCCATCGA
130 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTGGAAATGCTGATCCACCGA
** * *
19272 ATGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAG
195 ATGATGAATTCAAGCAAAAAATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAA
* ** * * * *
19337 ATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGCATTTGAGCAA
260 ATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGATGATCCATCAAATGATGAATTTAAGCAA
* * *
19402 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGTG
325 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
19455 TTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAAC-TTCTCTG
* *
19519 GAAAAAATAATTCATCAAGTGATGAATTCAG-GGAAAAGGTTGAACAAATTCTTCTCATTATGAA
65 GAAAAAATAATCCATCAAGTGATGAATT-AGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
* *
19583 TTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGCACTGCTGATCCACC
129 TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-ACTGGAAATGCTGATCCACC
** *
19647 GGGTGATGAATTTAAGCAAAAAATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTC
193 GAATGATGAATTCAAGCAAAAAATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* *
19711 AAATGAGTTCTTCTCATTATGAACTCTAACTGGTAATGATGATCCATCAAATGATGAATTTAAGC
258 AAATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGATGATCCATCAAATGATGAATTTAAGC
*
19776 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
323 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
19831 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
19850 TCTCTGGAAA
Statistics
Matches: 357, Mismatches: 35, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
376 191 0.54
377 149 0.42
378 17 0.05
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (377 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTCTCTGG
AAAAAATAATCCATCAAGTGATGAATTAGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATT
TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTGGAAATGCTGATCCACCGAA
TGATGAATTCAAGCAAAAAATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAA
TGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGATGATCCATCAAATGATGAATTTAAGCAAA
AAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
Found at i:19892 original size:113 final size:112
Alignment explanation
Indices: 19455--20225 Score: 1073
Period size: 113 Copynumber: 6.8 Consensus size: 112
19445 TTCAGATGTG
* * *
19455 TTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
** * * * * *
19519 GAAAAAATAATTCATCAAGTGAT-GAATTCAGGGAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAA-TGATGGATTTGA-GCAAAAGGTTGAACAAA
* **
19567 TTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
* ** * ** * * ** *
19631 GCACTGCTGATCCACCGGGTGATGAATTTAAGCAAAAAATTGAACAAG
66 GAAAAGCTGATCCATC-AATGATGGATTTGAGCAAAAGGTTGAACAAA
* * * **
19679 TTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
* * * * * * *
19743 GTAATGATGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAG
66 GAAAAGCTGATCCATC-AATGATGGATTTGAGCAAAAGGTTGAACAAA
* *
19791 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
*
19856 GAAATGCTGATCCATCGAATGATGGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATC-AATGATGGATTTGAGCAAAAGGTTGAACAAA
*
19904 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCTTTATGAACTTTTTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
19969 GAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCA-ATGATGGATTTGAGCAAAAGGTTGAACAAA
*
20017 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATTATGAACTTTTTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
20082 GAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCA-ATGATGGATTTGAGCAAAAGGTTGAACAAA
20130 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
20195 GAAAAGCTGATCCATCATATGATGGATTTGA
66 GAAAAGCTGATCCATCA-ATGATGGATTTGA
20226 ATCTTTGCTA
Statistics
Matches: 603, Mismatches: 51, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
111 1 0.00
112 210 0.35
113 392 0.65
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (112 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
GAAAAGCTGATCCATCAATGATGGATTTGAGCAAAAGGTTGAACAAA
Found at i:20650 original size:22 final size:22
Alignment explanation
Indices: 20625--20679 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
20615 CATAAAGTTT
*
20625 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
20647 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
20669 CCATCTTTGAA
1 TCATCTTTGAA
20680 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:23341 original size:114 final size:113
Alignment explanation
Indices: 23142--23365 Score: 358
Period size: 114 Copynumber: 2.0 Consensus size: 113
23132 ACGATCATGC
* * *
23142 AATTCATCCTTTAATTCCAATGATGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAA
1 AATTCATCCTTTAAATCCAATGATGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAA
23207 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
* * * *
23255 AATTCATCTTTTAAATCTAATGATTGGTTTTGGGGTTCATACCAAATCAGATTAGATAACTCAAA
1 AATTCATCCTTTAAATCCAATGA-TGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
* *
23320 GAACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
65 AAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGA
23366 TCACCTGCAC
Statistics
Matches: 101, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
113 20 0.20
114 81 0.80
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (113 bp):
AATTCATCCTTTAAATCCAATGATGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAA
AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
Found at i:28937 original size:14 final size:14
Alignment explanation
Indices: 28899--28952 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
28889 TTGTGCAATA
* *
28899 CAAATGCAAAGATG
1 CAAATGTAAATATG
28913 CCAAATGTAAATATG
1 -CAAATGTAAATATG
* *
28928 CAAATATAAAAATG
1 CAAATGTAAATATG
*
28942 TAAATGTAAAT
1 CAAATGTAAAT
28953 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:30550 original size:18 final size:18
Alignment explanation
Indices: 30533--30576 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
30523 TAAATAAATA
30533 AAAT-AAAAAATAATAAT
1 AAATAAAAAAATAATAAT
*
30550 ATATAAAAAAATAATAAGT
1 AAATAAAAAAATAATAA-T
30569 -AATAAAAA
1 AAATAAAAA
30577 TTTGAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 19 0.83
19 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
AAATAAAAAAATAATAAT
Found at i:30575 original size:15 final size:15
Alignment explanation
Indices: 30516--30565 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
30506 TTAATTCTTG
*
30516 AATATAATAAATAAAT
1 AATAT-ATAAAAAAAT
*
30532 AAAATA-AAAAATAAT
1 AATATATAAAAA-AAT
30547 AATATATAAAAAAAT
1 AATATATAAAAAAAT
30562 AATA
1 AATA
30566 AGTAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 4 0.14
15 16 0.55
16 9 0.31
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATATATAAAAAAAT
Found at i:32705 original size:3 final size:3
Alignment explanation
Indices: 32697--32760 Score: 83
Period size: 3 Copynumber: 21.3 Consensus size: 3
32687 TCAATATATT
* * * * *
32697 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
32745 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
32761 CAATTAATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:35389 original size:12 final size:12
Alignment explanation
Indices: 35372--35440 Score: 56
Period size: 12 Copynumber: 5.7 Consensus size: 12
35362 TGCTCAAGTG
35372 AAAATTAAATAA
1 AAAATTAAATAA
35384 AAAATT--ATAA
1 AAAATTAAATAA
35394 ACTAAA-T-AATAAA
1 A--AAATTAAAT-AA
35407 AATAATTAAATAA
1 AA-AATTAAATAA
35420 AAACATTAAATAA
1 AAA-ATTAAATAA
*
35433 AATATTAA
1 AAAATTAA
35441 GCAATAAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 16
0.74 0.02 0.25
Matches are distributed among these distances:
10 5 0.10
11 2 0.04
12 19 0.40
13 19 0.40
14 3 0.06
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAATTAAATAA
Found at i:35427 original size:13 final size:14
Alignment explanation
Indices: 35401--35434 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
35391 TAAACTAAAT
35401 AATAAAAATAATTA
1 AATAAAAATAATTA
*
35415 AATAAAAA-CATTA
1 AATAAAAATAATTA
35428 AATAAAA
1 AATAAAA
35435 TATTAAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAAAAATAATTA
Found at i:35473 original size:43 final size:43
Alignment explanation
Indices: 35424--35546 Score: 185
Period size: 43 Copynumber: 2.8 Consensus size: 43
35414 AAATAAAAAC
* *
35424 ATTAAAT-AAAATATTAAGCAATAAAATAGATAAAAAGTCCATA
1 ATTAAATAAAAACATTAAG-AATAAAATAAATAAAAAGTCCATA
*
35467 ATTAAATAAAAACATTAAGAAAAAAATAAATAAAAAGTCCATA
1 ATTAAATAAAAACATTAAGAATAAAATAAATAAAAAGTCCATA
*
35510 ATTAAATAAAAACATTAAAAAATAAAATAAATAAAAA
1 ATTAAATAAAAACATT-AAGAATAAAATAAATAAAAA
35547 TAAGTCTATC
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
43 45 0.62
44 28 0.38
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.23
Consensus pattern (43 bp):
ATTAAATAAAAACATTAAGAATAAAATAAATAAAAAGTCCATA
Found at i:36966 original size:64 final size:66
Alignment explanation
Indices: 36894--37018 Score: 177
Period size: 64 Copynumber: 1.9 Consensus size: 66
36884 AATGCATTTT
*
36894 ATGCATCGATGCATTCAGG-TT-TTATGAAAACATCGAATGCAAT-TTA-TGCATCGATGCACAG
1 ATGCATCGATGCATTCAGGCTTATT-TG-AAACATCGAATGCAATCTTAGTGCACCGATGCACAG
36955 ACC
64 ACC
* *
36958 ATGCATCGATGCATTCGGGCTTATTTGAAACATCGAATGCACTCTTAGTGCACCGATGCAC
1 ATGCATCGATGCATTCAGGCTTATTTGAAACATCGAATGCAATCTTAGTGCACCGATGCAC
37019 TAAGGGTTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
64 33 0.61
65 7 0.13
66 14 0.26
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (66 bp):
ATGCATCGATGCATTCAGGCTTATTTGAAACATCGAATGCAATCTTAGTGCACCGATGCACAGAC
C
Found at i:37244 original size:17 final size:18
Alignment explanation
Indices: 37222--37259 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
37212 TGATCAACAA
37222 CAAGAAATAACA-AGAAT
1 CAAGAAATAACAGAGAAT
* *
37239 CAAGAATTAAGAGAGAAT
1 CAAGAAATAACAGAGAAT
37257 CAA
1 CAA
37260 AGAGAAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.61, C:0.11, G:0.16, T:0.13
Consensus pattern (18 bp):
CAAGAAATAACAGAGAAT
Found at i:39049 original size:15 final size:15
Alignment explanation
Indices: 39029--39066 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
39019 CTTGAAAGTA
39029 AAATCAAAGATTTAC
1 AAATCAAAGATTTAC
39044 AAATCAAAGATTTAC
1 AAATCAAAGATTTAC
39059 AAATCAAA
1 AAATCAAA
39067 CTAGAAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.58, C:0.13, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATCAAAGATTTAC
Found at i:43014 original size:21 final size:21
Alignment explanation
Indices: 42990--43061 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
42980 TGTTCAAAAT
*
42990 GCCTCCTAGAACAAATCCAAA
1 GCCTCCTAGAACAAATCCCAA
*
43011 GCCTTCTAGAACAAATCCCAA
1 GCCTCCTAGAACAAATCCCAA
43032 GCCTCCTAGAACAAATCCCAA
1 GCCTCCTAGAACAAATCCCAA
*
43053 GCGTCCTAG
1 GCCTCCTAG
43062 GACTAGTAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.36, C:0.35, G:0.12, T:0.17
Consensus pattern (21 bp):
GCCTCCTAGAACAAATCCCAA
Found at i:44484 original size:90 final size:90
Alignment explanation
Indices: 44340--44550 Score: 307
Period size: 90 Copynumber: 2.3 Consensus size: 90
44330 AATTTTTAAG
* * * * *
44340 ATTCGATGAATTCATCAAGTCCGTCTCACAATGACCACCCAAATCCTAGGATATGAATTCATCAA
1 ATTCGATGAGTTCATCATGTCCGTCTCACAAGGAACACCCAAATCCTAAGATATGAATTCATCAA
*
44405 GAACATTTAATAGTTCAT-TTTTTCA
66 GAACATTTAATAGTTCATCCTTTT-A
* * *
44430 ATTCGGTGAGTTCATCATGTCCGTCTGACAAGGAACACCCAAATCCTAAGATATGAATTCATCTA
1 ATTCGATGAGTTCATCATGTCCGTCTCACAAGGAACACCCAAATCCTAAGATATGAATTCATCAA
44495 GAACATTTAATAGTTCATCCTTTTA
66 GAACATTTAATAGTTCATCCTTTTA
* *
44520 ATTCGCTGAGTTCATCATGTTCGTCTCACAA
1 ATTCGATGAGTTCATCATGTCCGTCTCACAA
44551 TGACTACTCA
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
90 104 0.96
91 4 0.04
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (90 bp):
ATTCGATGAGTTCATCATGTCCGTCTCACAAGGAACACCCAAATCCTAAGATATGAATTCATCAA
GAACATTTAATAGTTCATCCTTTTA
Found at i:45800 original size:17 final size:17
Alignment explanation
Indices: 45773--45858 Score: 111
Period size: 17 Copynumber: 4.9 Consensus size: 17
45763 AATAAACAAT
45773 CATGCTACTTC-TTTCAAG
1 CATG-TACTTCATTT-AAG
45791 CATGTACTTCATTTAAG
1 CATGTACTTCATTTAAG
* *
45808 CATGTAGTTCATTCAAG
1 CATGTACTTCATTTAAG
45825 CATGTACTTCATTTAAG
1 CATGTACTTCATTTAAG
*
45842 CATGTTATTTCATTTAA
1 CATG-TACTTCATTTAA
45859 TAAAGCATGT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
17 43 0.70
18 18 0.30
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.42
Consensus pattern (17 bp):
CATGTACTTCATTTAAG
Found at i:45828 original size:34 final size:35
Alignment explanation
Indices: 45785--45855 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 35
45775 TGCTACTTCT
45785 TTCAAGCATGTACTTCATTTAAGCATG-TAGTTCA
1 TTCAAGCATGTACTTCATTTAAGCATGTTAGTTCA
*
45819 TTCAAGCATGTACTTCATTTAAGCATGTTATTTCA
1 TTCAAGCATGTACTTCATTTAAGCATGTTAGTTCA
45854 TT
1 TT
45856 TAATAAAGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 27 0.77
35 8 0.23
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (35 bp):
TTCAAGCATGTACTTCATTTAAGCATGTTAGTTCA
Found at i:50494 original size:24 final size:24
Alignment explanation
Indices: 50467--50518 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
50457 AACGGATATA
*
50467 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
50491 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
50515 TCAA
1 TCAA
50519 GTAACATATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:50519 original size:24 final size:24
Alignment explanation
Indices: 50487--50604 Score: 150
Period size: 24 Copynumber: 4.9 Consensus size: 24
50477 AAACATAAAT
*
50487 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
* *
50511 CAGGTCAAGTAACATATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
50535 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
50559 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
50583 CATGTCAAGTATCAGATCAGAA
1 CAGGTCAAGTATCAGATCAGAA
50605 ATCAAATCGA
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
23 5 0.06
24 79 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:50621 original size:48 final size:47
Alignment explanation
Indices: 50490--50621 Score: 142
Period size: 48 Copynumber: 2.7 Consensus size: 47
50480 CATAAATCAG
* * *
50490 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAAGTCAA--AATCAGATCAGAATCCAA
* * *
50538 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAAGTCA-AAATCAGATCAGAATCCAA
*
50586 GTCAAGTATCAGATCAGAAATCAAATCGAAAATCAG
1 GTCAAGTATCAGATCAGAAATCAAGTC-AAAATCAG
50622 GTAAAATATT
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
47 4 0.06
48 62 0.87
49 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAAATCAGATCAGAATCCAA
Found at i:53082 original size:13 final size:13
Alignment explanation
Indices: 53064--53126 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
53054 CAACGGTCAA
53064 CGGGTCAACGGGT
1 CGGGTCAACGGGT
53077 CGGGTCAACGGGT
1 CGGGTCAACGGGT
53090 CGGGTGGGGTCAACGGGT
1 C-----GGGTCAACGGGT
* *
53108 CGGGTAAATGGGT
1 CGGGTCAACGGGT
53121 CGGGTC
1 CGGGTC
53127 GGGTTATGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
13 29 0.69
18 13 0.31
ACGTcount: A:0.14, C:0.19, G:0.49, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:53099 original size:18 final size:18
Alignment explanation
Indices: 53058--53112 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
53048 TCCGGTCAAC
53058 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
*
53079 GGTCAACGGGTCGGGTGG
1 GGTCAACGGGTCGGGTCG
53097 GGTCAACGGGTCGGGT
1 GGTCAACGGGTCGGGT
53113 AAATGGGTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 22 0.67
21 11 0.33
ACGTcount: A:0.15, C:0.20, G:0.49, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:53103 original size:31 final size:31
Alignment explanation
Indices: 53064--53130 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
53054 CAACGGTCAA
*
53064 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
* *
53095 GGGGTCAACGGGTCGGGTAAATGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
53126 CGGGT
1 CGGGT
53131 TATGACCGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.13, C:0.18, G:0.51, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:53108 original size:8 final size:8
Alignment explanation
Indices: 53051--53090 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
53041 GGTCAACTCC
53051 GGTCAAC-
1 GGTCAACG
53058 GGTCAACG
1 GGTCAACG
53066 GGTCAACG
1 GGTCAACG
53074 GGT---CG
1 GGTCAACG
53079 GGTCAACG
1 GGTCAACG
53087 GGTC
1 GGTC
53091 GGGTGGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
5 5 0.17
7 7 0.24
8 17 0.59
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:56007 original size:43 final size:42
Alignment explanation
Indices: 55942--56201 Score: 324
Period size: 43 Copynumber: 6.0 Consensus size: 42
55932 CAAAAATGCT
* *
55942 GCAATAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAATACC
1 GCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACACC
* * * * *
55985 GTAAAAGGTCGATATTTATAGCGACGTTTTTGGAACAAACGCC
1 GCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACACC
* *
56028 GC-AAAGGTTGAGATCTATAGCGGCGTTTTTTGGAACAAACGCC
1 GCAAAAGG-TCAGATCTATAGCGGCG-TTTTTGGAACAAACACC
* *
56071 GCAATAGGTCAGATCTATAGCGGCATTTTTTGGAACAAACACC
1 GCAAAAGGTCAGATCTATAGCGGC-GTTTTTGGAACAAACACC
*
56114 GCAAAAGGTCAGATCTATAGCGGCATTTTTGGATACAAACACC
1 GCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAACACC
* *
56157 GCAAAAGGTCAGATCTATAGTGGCGTTTTTAGATACAAACACC
1 GCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAACACC
56200 GC
1 GC
56202 TAATTTTCTT
Statistics
Matches: 190, Mismatches: 22, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
42 25 0.13
43 161 0.85
44 4 0.02
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (42 bp):
GCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACACC
Found at i:60778 original size:15 final size:15
Alignment explanation
Indices: 60755--60787 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
60745 CGTAGGACTC
60755 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
60770 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
60785 CTA
1 CTA
60788 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:60914 original size:29 final size:29
Alignment explanation
Indices: 60872--60945 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
60862 TTTTGTATGT
60872 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
60900 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
60929 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
60946 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:60986 original size:7 final size:7
Alignment explanation
Indices: 60974--61009 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
60964 TATCACAGGT
60974 CATATCA
1 CATATCA
60981 CATATCA
1 CATATCA
60988 CATATCA
1 CATATCA
60995 CATAT--
1 CATATCA
61000 CATATCA
1 CATATCA
61007 CAT
1 CAT
61010 GAACATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
7 22 0.81
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.31
Consensus pattern (7 bp):
CATATCA
Found at i:61005 original size:12 final size:12
Alignment explanation
Indices: 60961--61009 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
60951 TATCATGTTC
**
60961 TCATATCACAGG
1 TCATATCACATA
60973 TCATATCACATA
1 TCATATCACATA
60985 TCACATATCACATA
1 T--CATATCACATA
60999 TCATATCACAT
1 TCATATCACAT
61010 GAACATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 21 0.64
14 12 0.36
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:61023 original size:19 final size:19
Alignment explanation
Indices: 60981--61024 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
60971 GGTCATATCA
*
60981 CATATCACATATCACATAT
1 CATATCACATAACACATAT
*
61000 CATATCACATGAACATATAT
1 CATATCACAT-AACACATAT
61020 -ATATC
1 CATATC
61025 TTATGCATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.32
Consensus pattern (19 bp):
CATATCACATAACACATAT
Found at i:61515 original size:64 final size:64
Alignment explanation
Indices: 61318--61542 Score: 220
Period size: 64 Copynumber: 3.5 Consensus size: 64
61308 TAATGAAGGT
* * ** ** * ** * *** *
61318 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGTATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTTACTATTAAAGAG
* * * *
61382 ATGCATAGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTTACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTTACTATTAAAGAG
* *
61446 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTTACTATTAAAGAG
**
61509 AGTGCATCGATGCACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
61543 ATTCATACAA
Statistics
Matches: 137, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
63 2 0.01
64 131 0.96
65 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTTACTATTAAAGAG
Found at i:67845 original size:29 final size:29
Alignment explanation
Indices: 67803--67876 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
67793 TTTCATATGT
67803 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
67831 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
67860 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
67877 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:67926 original size:12 final size:12
Alignment explanation
Indices: 67892--67926 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
67882 TATCATGTTC
**
67892 TCATATCACAGG
1 TCATATCACATA
67904 TCATATCACATA
1 TCATATCACATA
67916 TCATATCACAT
1 TCATATCACAT
67927 GAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:68364 original size:64 final size:65
Alignment explanation
Indices: 68296--68461 Score: 221
Period size: 64 Copynumber: 2.6 Consensus size: 65
68286 GTATTATTGT
68296 TGGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGT-TTTACTATTAA
1 TGGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTCTTTACTATTAA
* * * *
68360 TGGGATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTATTTTTAA
1 TGGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTCTTTACTATTAA
** * *
68425 -AAGAGTGCATCGATGCACTACC-AATGCATCAATGCAC
1 TGGGA-TGCATCGATGCACT-CCTTATGCATCGATGCAC
68462 ATTCATACAA
Statistics
Matches: 90, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
64 53 0.59
65 36 0.40
66 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (65 bp):
TGGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTCTTTACTATTAA
Found at i:72595 original size:7 final size:7
Alignment explanation
Indices: 72583--72616 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
72573 CCCGATCACG
72583 GTCAACA
1 GTCAACA
*
72590 GTCAACG
1 GTCAACA
*
72597 GTCAACG
1 GTCAACA
72604 GTCAACA
1 GTCAACA
72611 GTCAAC
1 GTCAAC
72617 GGGTCGGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.15
Consensus pattern (7 bp):
GTCAACA
Found at i:72618 original size:14 final size:14
Alignment explanation
Indices: 72580--72616 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
72570 TCACCCGATC
72580 ACGGTCAACAGTCA
1 ACGGTCAACAGTCA
*
72594 ACGGTCAACGGTCA
1 ACGGTCAACAGTCA
*
72608 ACAGTCAAC
1 ACGGTCAAC
72617 GGGTCGGGTC
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:0.35, C:0.30, G:0.22, T:0.14
Consensus pattern (14 bp):
ACGGTCAACAGTCA
Done.