Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014996.1 Corchorus capsularis cultivar CVL-1 contig15017, 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: 76295
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:4202 original size:28 final size:28
Alignment explanation
Indices: 4168--4223 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
4158 TTTTAAAAAA
4168 TTAAAAACTACCCATTTGAAAATAAACC
1 TTAAAAACTACCCATTTGAAAATAAACC
4196 TTAAAAACTACCCATTTGAAAATAAACC
1 TTAAAAACTACCCATTTGAAAATAAACC
4224 ACCAATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.21, G:0.04, T:0.25
Consensus pattern (28 bp):
TTAAAAACTACCCATTTGAAAATAAACC
Found at i:12979 original size:3 final size:3
Alignment explanation
Indices: 12971--13006 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
12961 TCCACTTGCT
12971 GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC
1 GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC
13007 TACATGTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.67, G:0.33, T:0.00
Consensus pattern (3 bp):
GCC
Found at i:15580 original size:11 final size:11
Alignment explanation
Indices: 15564--15588 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15554 CTTATTGTGA
15564 TTTTTTCCCTT
1 TTTTTTCCCTT
15575 TTTTTTCCCTT
1 TTTTTTCCCTT
15586 TTT
1 TTT
15589 CACTACAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTCCCTT
Found at i:24573 original size:19 final size:19
Alignment explanation
Indices: 24549--24589 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
24539 AATGGATTTT
*
24549 TTTTGGAGCGTTCTACCGC
1 TTTTGGAGCGTACTACCGC
*
24568 TTTTGGAGCGTACTATCGC
1 TTTTGGAGCGTACTACCGC
24587 TTT
1 TTT
24590 GTGGTCATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.41
Consensus pattern (19 bp):
TTTTGGAGCGTACTACCGC
Found at i:24609 original size:28 final size:28
Alignment explanation
Indices: 24572--24679 Score: 117
Period size: 28 Copynumber: 4.2 Consensus size: 28
24562 TACCGCTTTT
* *
24572 GGAGCGTACTATCGCTTTGTGGTCATTG
1 GGAGCGTACTACCGCTTCGTGGTCATTG
*
24600 GGAGCGTACTACCGCTTCGTGGTCGTTG
1 GGAGCGTACTACCGCTTCGTGGTCATTG
24628 GGAGCGTACTACCG---C----T-ATT-
1 GGAGCGTACTACCGCTTCGTGGTCATTG
*
24647 GGAGCGTACTACCGCTTCGCGGTCATTG
1 GGAGCGTACTACCGCTTCGTGGTCATTG
24675 GGAGC
1 GGAGC
24680 ACTCCATCTT
Statistics
Matches: 67, Mismatches: 4, Indels: 18
0.75 0.04 0.20
Matches are distributed among these distances:
19 14 0.21
20 2 0.03
21 1 0.01
22 1 0.01
25 1 0.01
26 1 0.01
27 3 0.04
28 44 0.66
ACGTcount: A:0.15, C:0.24, G:0.33, T:0.28
Consensus pattern (28 bp):
GGAGCGTACTACCGCTTCGTGGTCATTG
Found at i:24986 original size:26 final size:26
Alignment explanation
Indices: 24815--25444 Score: 664
Period size: 26 Copynumber: 24.3 Consensus size: 26
24805 GTTGGCGAAT
* * * *
24815 GGCGCCCTCTTCTAAGATTGATGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
*
24841 GTCGCTCTCTTCCAAGATGGTGGATGTAC
1 GGCGCTCTCTTCCAAGATGGT---TGTAC
* * *
24870 AGCGCTCTCGTCCAAAATGGTGGATGTAC
1 GGCGCTCTCTTCCAAGATGGT---TGTAC
* *
24899 GGCGCTCAT-GTCCAAAATGGTGGATGTAC
1 GGCGCTC-TCTTCCAAGATGGT---TGTAC
* *
24928 GGCG--CTCGTCCAAAATGGTGGATGTAC
1 GGCGCTCTCTTCCAAGATGGT---TGTAC
*
24955 GGCGCTCTCTTTCAAGATGGTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
* *
24981 GGCG--CTCGTCCAAAATGGTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
*
25005 GACGCTCTCTTCCAAGATGGTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
* * * *
25031 -G-GCACTCGTCCAAAATGGTTGTAT
1 GGCGCTCTCTTCCAAGATGGTTGTAC
*
25055 GGCGCTCTCTTCCAAGATGTTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
25081 GGCGCTCTCTTCCAAGATGGTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
* *
25107 GGCG--CTCGTCCAAAATGGTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
*
25131 GACGCTCTCTTCCAAGATGGTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
* *
25157 GGCG--CTCGTCCAAAATGGTGGATGTAC
1 GGCGCTCTCTTCCAAGATGGT---TGTAC
25184 GGCGCTCTCTTCCAAGATGGTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
* *
25210 GGCG--CTCGTCCAAAATGGTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
25234 GGCGCTCTCTTCCAAGATGGTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
* * *
25260 GGCGCTCTCATCCAAGATGGATATAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
* *
25286 GGCG--CTCGTCCAAAATGGTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
*
25310 GGCGCTCTCTTCCAAGATGGTTCTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
* * *
25336 GGCG--CTCGTCCAAAATGTTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
25360 GGCGCTCTCTTCCAAGATGGTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
25386 GGCGCTCTCTTCCAAGATGGTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
25412 GGCGCTCTCTTCCAAGATGGTTGTAC
1 GGCGCTCTCTTCCAAGATGGTTGTAC
25438 GGCGCTC
1 GGCGCTC
25445 GTCCAAAATG
Statistics
Matches: 519, Mismatches: 61, Indels: 48
0.83 0.10 0.08
Matches are distributed among these distances:
24 135 0.26
25 1 0.00
26 263 0.51
27 34 0.07
29 85 0.16
30 1 0.00
ACGTcount: A:0.19, C:0.26, G:0.27, T:0.28
Consensus pattern (26 bp):
GGCGCTCTCTTCCAAGATGGTTGTAC
Found at i:25025 original size:50 final size:50
Alignment explanation
Indices: 24836--25456 Score: 662
Period size: 50 Copynumber: 12.0 Consensus size: 50
24826 CTAAGATTGA
* *
24836 TGTACGTCGCTCTCTTCCAAGATGGTGGATGTACAGCGCTCTCGTCCAAAATGGT
1 TGTACGGCGCTCTCTTCCAAGATGGT---TGTAC-G-GCGCTCGTCCAAAATGGT
* *
24891 GGATGTACGGCGCTCAT-GTCCAAAATGGTGGATGTACGGCGCTCGTCCAAAATGGT
1 ---TGTACGGCGCTC-TCTTCCAAGATGGT---TGTACGGCGCTCGTCCAAAATGGT
*
24947 GGATGTACGGCGCTCTCTTTCAAGATGGTTGTACGGCGCTCGTCCAAAATGGT
1 ---TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCGTCCAAAATGGT
* *
25000 TGTACGACGCTCTCTTCCAAGATGGTTGTACGGCACTCGTCCAAAATGGT
1 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCGTCCAAAATGGT
* * * *
25050 TGTATGGCGCTCTCTTCCAAGATGTTTGTACGGCGCTCTCTTCCAAGATGGT
1 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCG--CTCGTCCAAAATGGT
* * * * *
25102 TGTACGGCG--CTCGTCCAAAATGGTTGTACGACGCTCTCTTCCAAGATGGT
1 TGTACGGCGCTCTCTTCCAAGATGGTTGTACG--GCGCTCGTCCAAAATGGT
* * * *
25152 TGTACGGCG--CTCGTCCAAAATGGTGGATGTACGGCGCTCTCTTCCAAGATGGT
1 TGTACGGCGCTCTCTTCCAAGATGGT---TGTACGGCG--CTCGTCCAAAATGGT
* * * *
25205 TGTACGGCG--CTCGTCCAAAATGGTTGTACGGCGCTCTCTTCCAAGATGGT
1 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCG--CTCGTCCAAAATGGT
* * *
25255 TGTACGGCGCTCTCATCCAAGATGGATATACGGCGCTCGTCCAAAATGGT
1 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCGTCCAAAATGGT
* *
25305 TGTACGGCGCTCTCTTCCAAGATGGTTCTACGGCGCTCGTCCAAAATGTT
1 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCGTCCAAAATGGT
* *
25355 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCTCTTCCAAGATGGT
1 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCG--CTCGTCCAAAATGGT
25407 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCGTCCAAAATGGT
1 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCGTCCAAAATGGT
25457 GGATGTACAG
Statistics
Matches: 510, Mismatches: 38, Indels: 38
0.87 0.06 0.06
Matches are distributed among these distances:
50 276 0.54
51 2 0.00
52 90 0.18
53 69 0.14
55 1 0.00
56 41 0.08
57 1 0.00
58 29 0.06
59 1 0.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.28
Consensus pattern (50 bp):
TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCGTCCAAAATGGT
Found at i:25079 original size:76 final size:78
Alignment explanation
Indices: 24836--25456 Score: 695
Period size: 76 Copynumber: 8.0 Consensus size: 78
24826 CTAAGATTGA
* *
24836 TGTACGTCGCTCTCTTCCAAGATGGTGGATGTACAGCGCTCTCGTCCAAAATGGTGGATGTACGG
1 TGTACGGCGCTCTCTTCCAAGATGGT---TGTACGGCGCTCTCGTCCAAAATGGT---TGTACGG
24901 CGCTCAT-GTCCAAAATGGT
60 CGCTC-TCGTCCAAAATGGT
* * * * *
24920 GGATGTACGGCG--CTCGTCCAAAATGGTGGATGTACGGCGCTCTCTTTCAAGATGGTTGTACGG
1 ---TGTACGGCGCTCTCTTCCAAGATGGT---TGTACGGCGCTCTCGTCCAAAATGGTTGTACGG
24983 CG--CTCGTCCAAAATGGT
60 CGCTCTCGTCCAAAATGGT
* * *
25000 TGTACGACGCTCTCTTCCAAGATGGTTGTAC-G-GCACTCGTCCAAAATGGTTGTATGGCGCTCT
1 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCTCGTCCAAAATGGTTGTACGGCGCTCT
* * *
25063 CTTCCAAGATGTT
66 CGTCCAAAATGGT
*
25076 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCG--CTCGTCCAAAATGGTTGTACGACGCTCT
1 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCTCGTCCAAAATGGTTGTACGGCGCTCT
* *
25139 CTTCCAAGATGGT
66 CGTCCAAAATGGT
* * * *
25152 TGTACGGCG--CTCGTCCAAAATGGTGGATGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCG-
1 TGTACGGCGCTCTCTTCCAAGATGGT---TGTACGGCGCTCTCGTCCAAAATGGTTGTACGGCGC
25214 -CTCGTCCAAAATGGT
63 TCTCGTCCAAAATGGT
* * * *
25229 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCTCATCCAAGATGGATATACGGCG--CT
1 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCTCGTCCAAAATGGTTGTACGGCGCTCT
25292 CGTCCAAAATGGT
66 CGTCCAAAATGGT
* *
25305 TGTACGGCGCTCTCTTCCAAGATGGTTCTACGGCG--CTCGTCCAAAATGTTTGTACGGCGCTCT
1 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCTCGTCCAAAATGGTTGTACGGCGCTCT
* *
25368 CTTCCAAGATGGT
66 CGTCCAAAATGGT
* *
25381 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCG--CT
1 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCTCGTCCAAAATGGTTGTACGGCGCTCT
25444 CGTCCAAAATGGT
66 CGTCCAAAATGGT
25457 GGATGTACAG
Statistics
Matches: 468, Mismatches: 48, Indels: 47
0.83 0.09 0.08
Matches are distributed among these distances:
74 54 0.12
75 1 0.00
76 235 0.50
77 40 0.09
78 22 0.05
79 48 0.10
80 13 0.03
82 9 0.02
85 38 0.08
87 8 0.02
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.28
Consensus pattern (78 bp):
TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCTCGTCCAAAATGGTTGTACGGCGCTCT
CGTCCAAAATGGT
Found at i:25503 original size:54 final size:54
Alignment explanation
Indices: 24851--25677 Score: 387
Period size: 50 Copynumber: 16.0 Consensus size: 54
24841 GTCGCTCTCT
* *
24851 TCCAAGATGGTGGATGTACAGCGCTCTCGTCCAAAATGGTGGATGTACGGCGCTCATG
1 TCCAAAATGGTGGATGTACAGCG--CTCGTCCAAAATGGTGGATGTACAGCGCTC--G
* *
24909 TCCAAAATGGTGGATGTACGGCGCTCGTCCAAAATGGTGGATGTACGGCGCTC-
1 TCCAAAATGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTACAGCGCTCG
* * * *
24962 TCTTTCAAGATGGT---TGTACGGCGCTCGTCCAAAATGGT---TGTACGACGCTCTCT
1 TC---CAAAATGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTAC-A-GCGCTCG
* * * * * * *
25015 TCCAAGATGGT---TGTACGGCACTCGTCCAAAATGGTTGTATG-GC-GCTCTCT
1 TCCAAAATGGTGGATGTACAGCGCTCGTCCAAAATGG-TGGATGTACAGCGCTCG
* * * * * *
25065 TCCAAGAT-GT--TTGTACGGCGCTCTCTTCCAAGATGGT---TGTACGGCGCTCG
1 TCCAAAATGGTGGATGTACAGCG--CTCGTCCAAAATGGTGGATGTACAGCGCTCG
* * * *
25115 TCCAAAATGGT---TGTACGACGCTCTCTTCCAAGATGGT---TGTACGGCGCTCG
1 TCCAAAATGGTGGATGTAC-A-GCGCTCGTCCAAAATGGTGGATGTACAGCGCTCG
* * * *
25165 TCCAAAATGGTGGATGTACGGCGCTCTCTTCCAAGATGGT---TGTACGGCGCTCG
1 TCCAAAATGGTGGATGTACAGCG--CTCGTCCAAAATGGTGGATGTACAGCGCTCG
* * * *
25218 TCCAAAATGGT---TGTACGGCGCTCTCTTCCAAGATGGT---TGTACGGCGCTC-
1 TCCAAAATGGTGGATGTACAGCG--CTCGTCCAAAATGGTGGATGTACAGCGCTCG
* * * * * *
25267 T-CATCCAA-GATGGATATACGGCGCTCGTCCAAAATGGT---TGTACGGCGCTCTCT
1 TCCA--AAATGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTACAGCG--CTCG
* * * * * *
25320 TCCAAGATGGT---TCTACGGCGCTCGTCCAAAAT-GT--TTGTACGGCGCTCTCT
1 TCCAAAATGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTACAGCG--CTCG
* * * * * *
25370 TCCAAGATGGT---TGTACGGCGCTCTCTTCCAAGATGGT---TGTACGGCGCTCTCT
1 TCCAAAATGGTGGATGTACAGCG--CTCGTCCAAAATGGTGGATGTACAGCG--CTCG
* *
25422 TCCAAGATGGT---TGTACGGCGCTCGTCCAAAATGGTGGATGTACAGCGCTCG
1 TCCAAAATGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTACAGCGCTCG
* * *
25473 TCAAAAATGGTGGACGTATAGCGCTCGTCCAAAATGGTGGATGTACAGCGCTCG
1 TCCAAAATGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTACAGCGCTCG
*
25527 TCCAAAATGGTGGATGTACAACGCTCGTCCAAAA---TGG--G--CA---CTCG
1 TCCAAAATGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTACAGCGCTCG
* ** *
25571 TCCAAGATGGTGGATGTATGGCGCTCGTCCAAAATGGTGGATGTACGGCGCTCG
1 TCCAAAATGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTACAGCGCTCG
* *
25625 TCCAAAATGGTGGATGTACAACGCTCGTCCAAAATGGTGGATGTACGGCGCTC
1 TCCAAAATGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTACAGCGCTC
25678 ACTCTTTTGA
Statistics
Matches: 664, Mismatches: 52, Indels: 110
0.80 0.06 0.13
Matches are distributed among these distances:
44 34 0.05
47 5 0.01
48 4 0.01
49 10 0.02
50 244 0.37
51 22 0.03
52 76 0.11
53 86 0.13
54 124 0.19
56 38 0.06
58 21 0.03
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.26
Consensus pattern (54 bp):
TCCAAAATGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTACAGCGCTCG
Found at i:25595 original size:98 final size:98
Alignment explanation
Indices: 25469--25661 Score: 341
Period size: 98 Copynumber: 2.0 Consensus size: 98
25459 ATGTACAGCG
25469 CTCGTCAAAAATGGTGGACGTATAGCGCTCGTCCAAAATGGTGGATGTACAGCGCTCGTCCAAAA
1 CTCGTCAAAAATGGTGGACGTATAGCGCTCGTCCAAAATGGTGGATGTACAGCGCTCGTCCAAAA
25534 TGGTGGATGTACAACGCTCGTCCAAAATGGGCA
66 TGGTGGATGTACAACGCTCGTCCAAAATGGGCA
* * * * *
25567 CTCGTCCAAGATGGTGGATGTATGGCGCTCGTCCAAAATGGTGGATGTACGGCGCTCGTCCAAAA
1 CTCGTCAAAAATGGTGGACGTATAGCGCTCGTCCAAAATGGTGGATGTACAGCGCTCGTCCAAAA
25632 TGGTGGATGTACAACGCTCGTCCAAAATGG
66 TGGTGGATGTACAACGCTCGTCCAAAATGG
25662 TGGATGTACG
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.22
Consensus pattern (98 bp):
CTCGTCAAAAATGGTGGACGTATAGCGCTCGTCCAAAATGGTGGATGTACAGCGCTCGTCCAAAA
TGGTGGATGTACAACGCTCGTCCAAAATGGGCA
Found at i:25599 original size:27 final size:27
Alignment explanation
Indices: 25567--25677 Score: 186
Period size: 27 Copynumber: 4.1 Consensus size: 27
25557 AAAATGGGCA
* *
25567 CTCGTCCAAGATGGTGGATGTATGGCG
1 CTCGTCCAAAATGGTGGATGTACGGCG
25594 CTCGTCCAAAATGGTGGATGTACGGCG
1 CTCGTCCAAAATGGTGGATGTACGGCG
**
25621 CTCGTCCAAAATGGTGGATGTACAACG
1 CTCGTCCAAAATGGTGGATGTACGGCG
25648 CTCGTCCAAAATGGTGGATGTACGGCG
1 CTCGTCCAAAATGGTGGATGTACGGCG
25675 CTC
1 CTC
25678 ACTCTTTTGA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 78 1.00
ACGTcount: A:0.23, C:0.23, G:0.32, T:0.23
Consensus pattern (27 bp):
CTCGTCCAAAATGGTGGATGTACGGCG
Found at i:25612 original size:71 final size:71
Alignment explanation
Indices: 25496--25634 Score: 233
Period size: 71 Copynumber: 2.0 Consensus size: 71
25486 ACGTATAGCG
25496 CTCGTCCAAAATGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTACAACGCTCGTCCAAAA
1 CTCGTCCAAAATGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTACAACGCTCGTCCAAAA
25561 TGGGCA
66 TGGGCA
* ** **
25567 CTCGTCCAAGATGGTGGATGTATGGCGCTCGTCCAAAATGGTGGATGTACGGCGCTCGTCCAAAA
1 CTCGTCCAAAATGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTACAACGCTCGTCCAAAA
25632 TGG
66 TGG
25635 TGGATGTACA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.22
Consensus pattern (71 bp):
CTCGTCCAAAATGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTACAACGCTCGTCCAAAA
TGGGCA
Found at i:25677 original size:125 final size:125
Alignment explanation
Indices: 25442--25670 Score: 386
Period size: 125 Copynumber: 1.8 Consensus size: 125
25432 TTGTACGGCG
*
25442 CTCGTCCAAAATGGTGGATGTACAGCGCTCGTCAAAAATGGTGGACGTATAGCGCTCGTCCAAAA
1 CTCGTCCAAAATGGTGGATGTACAGCGCTCGTCAAAAATGGTGGACGTACAGCGCTCGTCCAAAA
*
25507 TGGTGGATGTACAGCGCTCGTCCAAAATGGTGGATGTACAACGCTCGTCCAAAATGGGCA
66 TGGTGGATGTACAACGCTCGTCCAAAATGGTGGATGTACAACGCTCGTCCAAAATGGGCA
* ** * * *
25567 CTCGTCCAAGATGGTGGATGTATGGCGCTCGTCCAAAATGGTGGATGTACGGCGCTCGTCCAAAA
1 CTCGTCCAAAATGGTGGATGTACAGCGCTCGTCAAAAATGGTGGACGTACAGCGCTCGTCCAAAA
25632 TGGTGGATGTACAACGCTCGTCCAAAATGGTGGATGTAC
66 TGGTGGATGTACAACGCTCGTCCAAAATGGTGGATGTAC
25671 GGCGCTCACT
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 96 1.00
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (125 bp):
CTCGTCCAAAATGGTGGATGTACAGCGCTCGTCAAAAATGGTGGACGTACAGCGCTCGTCCAAAA
TGGTGGATGTACAACGCTCGTCCAAAATGGTGGATGTACAACGCTCGTCCAAAATGGGCA
Found at i:25868 original size:29 final size:29
Alignment explanation
Indices: 25807--25930 Score: 171
Period size: 29 Copynumber: 4.3 Consensus size: 29
25797 TCTAGGGGGT
25807 GTACTACCACTTCGTGAGC-TTGGAGGGC
1 GTACTACCACTTCGTGAGCTTTGGAGGGC
*
25835 ATACTACCACTTCGTGAGCTTTGGAGGGC
1 GTACTACCACTTCGTGAGCTTTGGAGGGC
* * * *
25864 GTACTACCCCTTCTTGAGTTTTGGAGGGA
1 GTACTACCACTTCGTGAGCTTTGGAGGGC
* *
25893 GTACTACCACTTCGTGAGCCTAGG-GGGC
1 GTACTACCACTTCGTGAGCTTTGGAGGGC
25921 GTACTACCAC
1 GTACTACCAC
25931 CATTGTTTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
28 31 0.37
29 52 0.63
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.27
Consensus pattern (29 bp):
GTACTACCACTTCGTGAGCTTTGGAGGGC
Found at i:26081 original size:30 final size:29
Alignment explanation
Indices: 25975--26069 Score: 154
Period size: 29 Copynumber: 3.3 Consensus size: 29
25965 ATTTTTTTGC
25975 CTTTGGAGGGAGTACTACCACTTTGTGAA
1 CTTTGGAGGGAGTACTACCACTTTGTGAA
* *
26004 CTTTGGAGGGAGTACTACCAATTTGTGAG
1 CTTTGGAGGGAGTACTACCACTTTGTGAA
**
26033 CTTTGGAGGGAGTACTACCACTGCGTGAA
1 CTTTGGAGGGAGTACTACCACTTTGTGAA
26062 CTTTGGAG
1 CTTTGGAG
26070 AGCCGTACTA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (29 bp):
CTTTGGAGGGAGTACTACCACTTTGTGAA
Found at i:26107 original size:59 final size:56
Alignment explanation
Indices: 25969--26112 Score: 162
Period size: 58 Copynumber: 2.5 Consensus size: 56
25959 CTTGGTATTT
** *
25969 TTTTGCCTTTGGAGGGAGTACTACCACTTTGTGAACTTTGGAGGGAGTACTACCAA
1 TTTTGCCTTTGGAGGGAGTACTACCACTGCGTGAACTTTGGAGGCAGTACTACCAA
* * **
26025 TTTGTGAGCTTTGGAGGGAGTACTACCACTGCGTGAACTTTGGAGAGCCGTACTACCGC
1 TTT-TG-CCTTTGGAGGGAGTACTACCACTGCGTGAACTTTGGAG-GCAGTACTACCAA
* *
26084 TTCTTGCTCTTTGGGGGGCGTACTACCAC
1 TT-TTGC-CTTTGGAGGGAGTACTACCAC
26113 CATTTTTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
56 3 0.04
57 2 0.03
58 35 0.48
59 32 0.44
60 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (56 bp):
TTTTGCCTTTGGAGGGAGTACTACCACTGCGTGAACTTTGGAGGCAGTACTACCAA
Found at i:26624 original size:28 final size:29
Alignment explanation
Indices: 26552--26631 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 29
26542 ATTTGGACTC
*
26552 TATCTTGGCTGTATGCCTTTGGAAAATCTT
1 TATCTAGGCTGTATGCCTTTGG-AAATCTT
* * *
26582 TGTATAGGCAGTATGCCTTTAGG-AAT-TT
1 TATCTAGGCTGTATGCCTTT-GGAAATCTT
26610 TATCTAGGCTGTATGCCTTTGG
1 TATCTAGGCTGTATGCCTTTGG
26632 GGTAGGTTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
27 2 0.05
28 19 0.45
29 3 0.07
30 16 0.38
31 2 0.05
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (29 bp):
TATCTAGGCTGTATGCCTTTGGAAATCTT
Found at i:26642 original size:20 final size:20
Alignment explanation
Indices: 26614--26651 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
26604 GAATTTTATC
26614 TAGGCTGTATGCCTTTGGGG
1 TAGGCTGTATGCCTTTGGGG
*
26634 TAGGTTGTATGCCTTTGG
1 TAGGCTGTATGCCTTTGG
26652 AAATTTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.13, G:0.37, T:0.39
Consensus pattern (20 bp):
TAGGCTGTATGCCTTTGGGG
Found at i:26649 original size:48 final size:48
Alignment explanation
Indices: 26586--26729 Score: 245
Period size: 48 Copynumber: 3.0 Consensus size: 48
26576 AATCTTTGTA
*
26586 TAGGCAGTATGCCTTTAGG-AATTTTATCTAGGCTGTATGCCTTTGGGG
1 TAGGCTGTATGCCTTT-GGAAATTTTATCTAGGCTGTATGCCTTTGGGG
* *
26634 TAGGTTGTATGCCTTTGGAAATTTTATCTAGGCTTTATGCCTTTGGGG
1 TAGGCTGTATGCCTTTGGAAATTTTATCTAGGCTGTATGCCTTTGGGG
26682 TAGGCTGTATGCCTTTGGAAATTTTATCTAGGCTGTATGCCTTTGGGG
1 TAGGCTGTATGCCTTTGGAAATTTTATCTAGGCTGTATGCCTTTGGGG
26730 GGTGCCCATT
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
47 2 0.02
48 88 0.98
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.40
Consensus pattern (48 bp):
TAGGCTGTATGCCTTTGGAAATTTTATCTAGGCTGTATGCCTTTGGGG
Found at i:26674 original size:28 final size:28
Alignment explanation
Indices: 26634--26727 Score: 96
Period size: 28 Copynumber: 3.6 Consensus size: 28
26624 GCCTTTGGGG
*
26634 TAGGTTGTATGCCTTTGGAAATTTTATC
1 TAGGCTGTATGCCTTTGGAAATTTTATC
* **
26662 TAGGCTTTATGCCTTTGG--------GG
1 TAGGCTGTATGCCTTTGGAAATTTTATC
26682 TAGGCTGTATGCCTTTGGAAATTTTATC
1 TAGGCTGTATGCCTTTGGAAATTTTATC
26710 TAGGCTGTATGCCTTTGG
1 TAGGCTGTATGCCTTTGG
26728 GGGGTGCCCA
Statistics
Matches: 51, Mismatches: 7, Indels: 16
0.69 0.09 0.22
Matches are distributed among these distances:
20 17 0.33
28 34 0.67
ACGTcount: A:0.17, C:0.14, G:0.27, T:0.43
Consensus pattern (28 bp):
TAGGCTGTATGCCTTTGGAAATTTTATC
Found at i:26685 original size:20 final size:20
Alignment explanation
Indices: 26662--26699 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
26652 AAATTTTATC
*
26662 TAGGCTTTATGCCTTTGGGG
1 TAGGCTGTATGCCTTTGGGG
26682 TAGGCTGTATGCCTTTGG
1 TAGGCTGTATGCCTTTGG
26700 AAATTTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.16, G:0.34, T:0.39
Consensus pattern (20 bp):
TAGGCTGTATGCCTTTGGGG
Found at i:26846 original size:58 final size:57
Alignment explanation
Indices: 26747--27116 Score: 429
Period size: 58 Copynumber: 6.4 Consensus size: 57
26737 ATTTTAGGTT
* * * * * * *
26747 GTGCGACCAAGGGATGCTTGTTTTTCTTCTTGCACGTGTGGGGGATGCCCA-TTGGGCC
1 GTGCGACCGAGGGATGCTCGATTTT-TTATTACATGAGTGGGGGATGCCCACTT-GGCC
* * * *
26805 ATGTGACCGAGGGATGCTTGATTTATTTATCACATGAGTGGGGGATGCCCACTTGGCC
1 GTGCGACCGAGGGATGCTCGATTT-TTTATTACATGAGTGGGGGATGCCCACTTGGCC
* * * * * *
26863 GTGTGATCGAGGGATGCTCCG-TTTTCTTATTGCGTGAGTAGGGGATGCCCACTTGGTC
1 GTGCGACCGAGGGATGCT-CGATTTT-TTATTACATGAGTGGGGGATGCCCACTTGGCC
*
26921 GTGTGACCGAGGGATGCTCGATTTATTTATTACATGAGTGGGGGATGCCCACTTGGCC
1 GTGCGACCGAGGGATGCTCGATTT-TTTATTACATGAGTGGGGGATGCCCACTTGGCC
* * *
26979 GTGCGACCGAGGGATGCTCGATCGTCTTATTACATGAGTGCGGGATGCCCACTTGGCC
1 GTGCGACCGAGGGATGCTCGAT-TTTTTATTACATGAGTGGGGGATGCCCACTTGGCC
* * * *
27037 GTGCGACCGAGGGATGCTCAATCGTCTTATTACATGAGTGGGGGATGCCCACTTGGTC
1 GTGCGACCGAGGGATGCTCGAT-TTTTTATTACATGAGTGGGGGATGCCCACTTGGCC
27095 GTGCGACCGAGGGATGCTCGAT
1 GTGCGACCGAGGGATGCTCGAT
27117 CGATATTGCT
Statistics
Matches: 275, Mismatches: 30, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
57 3 0.01
58 266 0.97
59 6 0.02
ACGTcount: A:0.17, C:0.21, G:0.34, T:0.28
Consensus pattern (57 bp):
GTGCGACCGAGGGATGCTCGATTTTTTATTACATGAGTGGGGGATGCCCACTTGGCC
Found at i:26888 original size:116 final size:117
Alignment explanation
Indices: 26747--27113 Score: 474
Period size: 116 Copynumber: 3.2 Consensus size: 117
26737 ATTTTAGGTT
* * * * * * *
26747 GTGCGACCAAGGGATGCT-TGTTTTTCTTCTTGCACGTGTGGGGGATGCCCA-TTGGGCCATGTG
1 GTGCGACCGAGGGATGCTCCGATTTTCTTATTGCATGAGTGGGGGATGCCCACTT-GGCCGTGTG
* *
26810 ACCGAGGGATGCTTGATTTATTTATCACATGAGTGGGGGATGCCCACTTGGCC
65 ACCGAGGGATGCTCGATTTATTTATTACATGAGTGGGGGATGCCCACTTGGCC
* * * * *
26863 GTGTGATCGAGGGATGCTCCG-TTTTCTTATTGCGTGAGTAGGGGATGCCCACTTGGTCGTGTGA
1 GTGCGACCGAGGGATGCTCCGATTTTCTTATTGCATGAGTGGGGGATGCCCACTTGGCCGTGTGA
26927 CCGAGGGATGCTCGATTTATTTATTACATGAGTGGGGGATGCCCACTTGGCC
66 CCGAGGGATGCTCGATTTATTTATTACATGAGTGGGGGATGCCCACTTGGCC
** * * *
26979 GTGCGACCGAGGGATGCT-CGATCGTCTTATTACATGAGTGCGGGATGCCCACTTGGCCGTGCGA
1 GTGCGACCGAGGGATGCTCCGATTTTCTTATTGCATGAGTGGGGGATGCCCACTTGGCCGTGTGA
* * * *
27043 CCGAGGGATGCTCAATCGT-CTTATTACATGAGTGGGGGATGCCCACTTGGTC
66 CCGAGGGATGCTCGAT-TTATTTATTACATGAGTGGGGGATGCCCACTTGGCC
27095 GTGCGACCGAGGGATGCTC
1 GTGCGACCGAGGGATGCTC
27114 GATCGATATT
Statistics
Matches: 219, Mismatches: 27, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
115 2 0.01
116 213 0.97
117 4 0.02
ACGTcount: A:0.17, C:0.22, G:0.34, T:0.28
Consensus pattern (117 bp):
GTGCGACCGAGGGATGCTCCGATTTTCTTATTGCATGAGTGGGGGATGCCCACTTGGCCGTGTGA
CCGAGGGATGCTCGATTTATTTATTACATGAGTGGGGGATGCCCACTTGGCC
Found at i:27050 original size:174 final size:174
Alignment explanation
Indices: 26784--27116 Score: 481
Period size: 174 Copynumber: 1.9 Consensus size: 174
26774 TCTTGCACGT
* * * * *
26784 GTGGGGGATGCCCATTGGGCCATGTGACCGAGGGATGCTTGATTTATTTATCACATGAGTGGGGG
1 GTGGGGGATGCCCATTGGGCCATGCGACCGAGGGATGCTCGATGTACTTATCACATGAGTGCGGG
* * ** ** * *
26849 ATGCCCACTTGGCCGTGTGATCGAGGGATGCTCCGTTTTCTTATTGCGTGAGTAGGGGATGCCCA
66 ATGCCCACTTGGCCGTGCGACCGAGGGATGCTCAATCGTCTTATTACATGAGTAGGGGATGCCCA
*
26914 CTTGGTCGTGTGACCGAGGGATGCTCGATTTATTTATTACATGA
131 CTTGGTCGTGCGACCGAGGGATGCTCGATTTATTTATTACATGA
* *
26958 GTGGGGGATGCCCACTT-GGCCGTGCGACCGAGGGATGCTCGATCGT-CTTATTACATGAGTGCG
1 GTGGGGGATGCCCA-TTGGGCCATGCGACCGAGGGATGCTCGAT-GTACTTATCACATGAGTGCG
*
27021 GGATGCCCACTTGGCCGTGCGACCGAGGGATGCTCAATCGTCTTATTACATGAGTGGGGGATGCC
64 GGATGCCCACTTGGCCGTGCGACCGAGGGATGCTCAATCGTCTTATTACATGAGTAGGGGATGCC
27086 CACTTGGTCGTGCGACCGAGGGATGCTCGAT
129 CACTTGGTCGTGCGACCGAGGGATGCTCGAT
27117 CGATATTGCT
Statistics
Matches: 140, Mismatches: 17, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
174 137 0.98
175 3 0.02
ACGTcount: A:0.17, C:0.21, G:0.34, T:0.27
Consensus pattern (174 bp):
GTGGGGGATGCCCATTGGGCCATGCGACCGAGGGATGCTCGATGTACTTATCACATGAGTGCGGG
ATGCCCACTTGGCCGTGCGACCGAGGGATGCTCAATCGTCTTATTACATGAGTAGGGGATGCCCA
CTTGGTCGTGCGACCGAGGGATGCTCGATTTATTTATTACATGA
Found at i:30266 original size:58 final size:58
Alignment explanation
Indices: 30184--30430 Score: 271
Period size: 58 Copynumber: 4.3 Consensus size: 58
30174 AATAACGATT
* * ** *
30184 GAGCATCCCTTGGTCGCATAGCCAAGTGGGCATCCCCCACTCATGTAATAAGAAAACC
1 GAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGCAATAAGAAAACC
* * *
30242 GAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGTAAATC
1 GAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGCAATAAGAAAACC
*** * * * *
30300 GAGCATCCCTCGGTCACGTTGCCCAGTGGACATCCCCCACTCATGCAATAATAAGACC
1 GAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGCAATAAGAAAACC
* * * * * *
30358 GAGCAACCCTCGGTCACACGACCCAA-TGGGCATCCCCCACACGTGCAAGAAGAAAAAC
1 GAGCATCCCTCGGTCACACG-GCCAAGTGGGCATCCCCCACTCATGCAATAAGAAAACC
* *
30416 AAGCATCCCTTGGTC
1 GAGCATCCCTCGGTC
30431 GCACAAGCTA
Statistics
Matches: 156, Mismatches: 32, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
58 153 0.98
59 3 0.02
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (58 bp):
GAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGCAATAAGAAAACC
Found at i:30421 original size:116 final size:116
Alignment explanation
Indices: 30185--30430 Score: 314
Period size: 116 Copynumber: 2.1 Consensus size: 116
30175 ATAACGATTG
* * * *
30185 AGCATCCCTTGGTCGCATAGCCAAGTGGGCATCCCCCACTCATGTAATAAGAAAACCGAGCATCC
1 AGCATCCCTTGGTCACATAGCCAAGTGGACATCCCCCACTCATGCAATAAGAAAACCGAGCAACC
* * * * * * *
30250 CTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGTAAATCG
66 CTCGGTCACACGCCCAAGTGGGCATCCCCCACACATGCAAGAAGAAAAACA
* * * * * *
30301 AGCATCCCTCGGTCACGTTGCCCAGTGGACATCCCCCACTCATGCAATAATAAGACCGAGCAACC
1 AGCATCCCTTGGTCACATAGCCAAGTGGACATCCCCCACTCATGCAATAAGAAAACCGAGCAACC
*
30366 CTCGGTCACACGACCCAA-TGGGCATCCCCCACACGTGCAAGAAGAAAAACA
66 CTCGGTCACACG-CCCAAGTGGGCATCCCCCACACATGCAAGAAGAAAAACA
30417 AGCATCCCTTGGTC
1 AGCATCCCTTGGTC
30431 GCACAAGCTA
Statistics
Matches: 110, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
116 106 0.96
117 4 0.04
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (116 bp):
AGCATCCCTTGGTCACATAGCCAAGTGGACATCCCCCACTCATGCAATAAGAAAACCGAGCAACC
CTCGGTCACACGCCCAAGTGGGCATCCCCCACACATGCAAGAAGAAAAACA
Found at i:30521 original size:46 final size:47
Alignment explanation
Indices: 30452--30542 Score: 148
Period size: 46 Copynumber: 1.9 Consensus size: 47
30442 AATGGGCACC
30452 CCCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCATACAGCCTA
1 CCCCAAAGGCATA-AGCCTAGATAAAATTTCCAAAGGCATACAGCCTA
* *
30500 CCCCAAAGGCGT-AGCCTAGATAAAATTTCCAAAGGCATGCAGC
1 CCCCAAAGGCATAAGCCTAGATAAAATTTCCAAAGGCATACAGC
30543 AGATAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 30 0.73
48 11 0.27
ACGTcount: A:0.37, C:0.29, G:0.18, T:0.16
Consensus pattern (47 bp):
CCCCAAAGGCATAAGCCTAGATAAAATTTCCAAAGGCATACAGCCTA
Found at i:30585 original size:28 final size:28
Alignment explanation
Indices: 30512--30632 Score: 133
Period size: 28 Copynumber: 4.4 Consensus size: 28
30502 CCAAAGGCGT
*
30512 AGCCTAGATAAAATTTCCAAAGGCATGC
1 AGCCTAGATAAAATTTCCAAAGGCATAC
* *
30540 AG-C-AGATAAAATATCTAAAGGCATAC
1 AGCCTAGATAAAATTTCCAAAGGCATAC
30566 AGCCTAGATAAAA-TTCCTAAAGGCATAC
1 AGCCTAGATAAAATTTCC-AAAGGCATAC
* *
30594 TA-CCTATACAAAAATTTCCAAAGGCATAC
1 -AGCCTAGA-TAAAATTTCCAAAGGCATAC
*
30623 AGCCAAGATA
1 AGCCTAGATA
30633 GAGTCCAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
26 22 0.29
27 4 0.05
28 27 0.36
29 19 0.25
30 4 0.05
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.21
Consensus pattern (28 bp):
AGCCTAGATAAAATTTCCAAAGGCATAC
Found at i:31025 original size:29 final size:29
Alignment explanation
Indices: 30972--31361 Score: 396
Period size: 29 Copynumber: 13.3 Consensus size: 29
30962 AAAAAAAAAG
* *
30972 GTGGTAGTACGCCC-CCAAGGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
31000 GTGGTAGTACTCCCTCCAAAGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
* **
31029 GTGGTAGTACTCCCTCCAAAGTTCAATAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
* *
31058 GTGGTAGTA-TGCCCTCCAAAGTTCCCGAA
1 GTGGTAGTACT-CCCTCCAAAGCTCACGAA
* *
31087 GTGGTAGTACTCCCTCCAAAGTTCAAGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
*
31116 GTGGTAGTACTACCTCCAAAGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
*
31145 GTGGTAGTACTCCCTCCAAAGTTC-CTGAA
1 GTGGTAGTACTCCCTCCAAAGCTCAC-GAA
*
31174 GTGGTAGTACTCCCTCCAAAGGCAAAAAT-ACCAA
1 GTGGTAGTACTCCCTCCAAA-GC-----TCACGAA
** * * ** * ** ** *
31208 GTCATGGGA-AACTTAAAAAG-AAAAGAAA
1 GTGGTAGTACTCCCTCCAAAGCTCACG-AA
*
31236 GTGGTAGTACTACCTCCAAAGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
* *
31265 GTGGTAGTACTCCCTCCAAAGTTCAAGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
*
31294 GTGGTAGTACTACCTCCAAAGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
*
31323 GTGGTAGTACTCCCTCCAAAGTTCACGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
31352 GTGGTAGTAC
1 GTGGTAGTAC
31362 AGCCCCTAGA
Statistics
Matches: 299, Mismatches: 48, Indels: 29
0.80 0.13 0.08
Matches are distributed among these distances:
27 1 0.00
28 22 0.07
29 257 0.86
30 4 0.01
32 1 0.00
33 5 0.02
34 7 0.02
35 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (29 bp):
GTGGTAGTACTCCCTCCAAAGCTCACGAA
Found at i:31065 original size:58 final size:58
Alignment explanation
Indices: 30972--31361 Score: 448
Period size: 58 Copynumber: 6.7 Consensus size: 58
30962 AAAAAAAAAG
* * * * *
30972 GTGGTAGTACGCCC-CCAAGGCTCACGAAGTGGTAGTACTCCCTCCAAAGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGTTCAAGAAGTGGTAGTACTACCTCCAAAGCTCACGAA
* * * *
31029 GTGGTAGTACTCCCTCCAAAGTTCAATAAGTGGTAGTA-TGCCCTCCAAAGTTCCCGAA
1 GTGGTAGTACTCCCTCCAAAGTTCAAGAAGTGGTAGTACT-ACCTCCAAAGCTCACGAA
31087 GTGGTAGTACTCCCTCCAAAGTTCAAGAAGTGGTAGTACTACCTCCAAAGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGTTCAAGAAGTGGTAGTACTACCTCCAAAGCTCACGAA
** * *
31145 GTGGTAGTACTCCCTCCAAAGTTCCTGAAGTGGTAGTACTCCCTCCAAAGGCAAAAAT-ACCAA
1 GTGGTAGTACTCCCTCCAAAGTTCAAGAAGTGGTAGTACTACCTCCAAA-GC-----TCACGAA
** * * ** * ** **
31208 GTCATGGGA-AACTTAAAAAG-AAAAGAAAGTGGTAGTACTACCTCCAAAGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGTTCAAG-AAGTGGTAGTACTACCTCCAAAGCTCACGAA
31265 GTGGTAGTACTCCCTCCAAAGTTCAAGAAGTGGTAGTACTACCTCCAAAGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGTTCAAGAAGTGGTAGTACTACCTCCAAAGCTCACGAA
*
31323 GTGGTAGTACTCCCTCCAAAGTTCACGAAGTGGTAGTAC
1 GTGGTAGTACTCCCTCCAAAGTTCAAGAAGTGGTAGTAC
31362 AGCCCCTAGA
Statistics
Matches: 278, Mismatches: 42, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
56 1 0.00
57 23 0.08
58 208 0.75
59 6 0.02
61 3 0.01
62 27 0.10
63 9 0.03
64 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (58 bp):
GTGGTAGTACTCCCTCCAAAGTTCAAGAAGTGGTAGTACTACCTCCAAAGCTCACGAA
Found at i:31558 original size:27 final size:27
Alignment explanation
Indices: 31492--31867 Score: 455
Period size: 27 Copynumber: 13.6 Consensus size: 27
31482 CAAATGAGAA
* *
31492 AGCGCCATACATCCACCATCTTGGACAAG
1 AGCGCCGTACATCCACCATTTTGGAC--G
31521 AGCGCCGTACATCCACCATTTTGGACG
1 AGCGCCGTACATCCACCATTTTGGACG
*
31548 AGCGCTGTACATCCACCATTTTGGACG
1 AGCGCCGTACATCCACCATTTTGGACG
*
31575 AGCGCCGTACATCCACCATTTTGGACA
1 AGCGCCGTACATCCACCATTTTGGACG
* * *
31602 AGCGTCGTACATCCACTATCTTGGACAAG
1 AGCGCCGTACATCCACCATTTTGGAC--G
31631 AGCGCCGTACATCCACCATTTTGGACG
1 AGCGCCGTACATCCACCATTTTGGACG
* *
31658 AGCACTGTACATCCACCATTTTGGACG
1 AGCGCCGTACATCCACCATTTTGGACG
31685 AGCGCCGTACATCCACCATTTTGGACG
1 AGCGCCGTACATCCACCATTTTGGACG
* * *
31712 AGCGTCGTACATCCACTATCTTGGACAAG
1 AGCGCCGTACATCCACCATTTTGGAC--G
31741 AGCGCCGTACATCCACCATTTTGGACG
1 AGCGCCGTACATCCACCATTTTGGACG
** *
31768 AGCGTTGTACATCCACTATTTTGGACG
1 AGCGCCGTACATCCACCATTTTGGACG
** * * *
31795 AGCATCGTGCATCCACCATCTTGGAAGAG
1 AGCGCCGTACATCCACCATTTTGG-A-CG
* * *
31824 AGCGCCATACATCCACCATCTTGGATGAG
1 AGCGCCGTACATCCACCATTTTGGA--CG
31853 AGCGCCGTACATCCA
1 AGCGCCGTACATCCA
31868 TATTGGAAAA
Statistics
Matches: 304, Mismatches: 36, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
27 193 0.63
28 2 0.01
29 109 0.36
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (27 bp):
AGCGCCGTACATCCACCATTTTGGACG
Found at i:31634 original size:83 final size:82
Alignment explanation
Indices: 31492--31867 Score: 445
Period size: 83 Copynumber: 4.5 Consensus size: 82
31482 CAAATGAGAA
* *
31492 AGCGCCATACATCCACCATCTTGGACAAGAGCGCCGTACATCCACCATTTTGGACGAGCGCT-GT
1 AGCGCCGTACATCCACCATTTTGGAC-A-AGCGCCGTACATCCACCATTTTGGACGAGCGCTCGT
*
31556 ACATCCACCATTTTGGACG
64 ACATCCACCATCTTGGACG
* * *
31575 AGCGCCGTACATCCACCATTTTGGACAAGCGTCGTACATCCACTATCTTGGACAAGAGCGC-CGT
1 AGCGCCGTACATCCACCATTTTGGACAAGCGCCGTACATCCACCATTTTGGAC--GAGCGCTCGT
*
31639 ACATCCACCATTTTGGACG
64 ACATCCACCATCTTGGACG
* * *
31658 AGCACTGTACATCCACCATTTTGGACGAGCGCCGTACATCCACCATTTTGGACGAGCG-TCGTAC
1 AGCGCCGTACATCCACCATTTTGGACAAGCGCCGTACATCCACCATTTTGGACGAGCGCTCGTAC
*
31722 ATCCACTATCTTGGACAAG
66 ATCCACCATCTTGGAC--G
* ** * * *
31741 AGCGCCGTACATCCACCATTTTGGACGAGCGTTGTACATCCACTATTTTGGACGAGC-ATCGTGC
1 AGCGCCGTACATCCACCATTTTGGACAAGCGCCGTACATCCACCATTTTGGACGAGCGCTCGTAC
*
31805 ATCCACCATCTTGGAAGAG
66 ATCCACCATCTTGG-A-CG
* * *
31824 AGCGCCATACATCCACCATCTTGGATGAGAGCGCCGTACATCCA
1 AGCGCCGTACATCCACCATTTTGGA-CA-AGCGCCGTACATCCA
31868 TATTGGAAAA
Statistics
Matches: 255, Mismatches: 27, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
81 47 0.18
82 1 0.00
83 193 0.76
84 1 0.00
85 13 0.05
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (82 bp):
AGCGCCGTACATCCACCATTTTGGACAAGCGCCGTACATCCACCATTTTGGACGAGCGCTCGTAC
ATCCACCATCTTGGACG
Found at i:31684 original size:110 final size:110
Alignment explanation
Indices: 31499--31867 Score: 585
Period size: 110 Copynumber: 3.3 Consensus size: 110
31489 GAAAGCGCCA
31499 TACATCCACCATCTTGGACAAGAGCGCCGTACATCCACCATTTTGGACGAGCGCTGTACATCCAC
1 TACATCCACCATCTTGGACAAGAGCGCCGTACATCCACCATTTTGGACGAGCGCTGTACATCCAC
31564 CATTTTGGACGAGCGCCGTACATCCACCATTTTGGACAAGCGTCG
66 CATTTTGGACGAGCGCCGTACATCCACCATTTTGGACAAGCGTCG
* *
31609 TACATCCACTATCTTGGACAAGAGCGCCGTACATCCACCATTTTGGACGAGCACTGTACATCCAC
1 TACATCCACCATCTTGGACAAGAGCGCCGTACATCCACCATTTTGGACGAGCGCTGTACATCCAC
*
31674 CATTTTGGACGAGCGCCGTACATCCACCATTTTGGACGAGCGTCG
66 CATTTTGGACGAGCGCCGTACATCCACCATTTTGGACAAGCGTCG
* *
31719 TACATCCACTATCTTGGACAAGAGCGCCGTACATCCACCATTTTGGACGAGCGTTGTACATCCAC
1 TACATCCACCATCTTGGACAAGAGCGCCGTACATCCACCATTTTGGACGAGCGCTGTACATCCAC
* ** * * * * *
31784 TATTTTGGACGAGCATCGTGCATCCACCATCTTGGAAGAGAGCGCCA
66 CATTTTGGACGAGCGCCGTACATCCACCATTTTGG-ACA-AGCGTCG
**
31831 TACATCCACCATCTTGGATGAGAGCGCCGTACATCCA
1 TACATCCACCATCTTGGACAAGAGCGCCGTACATCCA
31868 TATTGGAAAA
Statistics
Matches: 240, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
110 200 0.83
111 1 0.00
112 39 0.16
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (110 bp):
TACATCCACCATCTTGGACAAGAGCGCCGTACATCCACCATTTTGGACGAGCGCTGTACATCCAC
CATTTTGGACGAGCGCCGTACATCCACCATTTTGGACAAGCGTCG
Found at i:31937 original size:27 final size:27
Alignment explanation
Indices: 31877--31988 Score: 80
Period size: 27 Copynumber: 4.1 Consensus size: 27
31867 ATATTGGAAA
* **
31877 AGGGCGCCGCATGCCCACCATAACAAG
1 AGGGCGCCGCACGCCCACCATCGCAAG
** *
31904 AAAGCGCCGCGCGCCCACCATCGCAAG
1 AGGGCGCCGCACGCCCACCATCGCAAG
* * *** **
31931 AGGGCGCCGTAAGCCCATTGTCGGGAG
1 AGGGCGCCGCACGCCCACCATCGCAAG
* * *
31958 AGGACGCCGCGCGCCCACCATCGGAAG
1 AGGGCGCCGCACGCCCACCATCGCAAG
31985 AGGG
1 AGGG
31989 AGTGCGCTCA
Statistics
Matches: 60, Mismatches: 25, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.24, C:0.36, G:0.33, T:0.07
Consensus pattern (27 bp):
AGGGCGCCGCACGCCCACCATCGCAAG
Found at i:32032 original size:19 final size:19
Alignment explanation
Indices: 32008--32065 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 19
31998 AATGACCGCG
*
32008 AAACGGTAGTATGCTCCCA
1 AAACGGTAGTACGCTCCCA
32027 AAACGGTAGTACGCTCCCA
1 AAACGGTAGTACGCTCCCA
* *
32046 AAGCGGTAGTACACTCCCA
1 AAACGGTAGTACGCTCCCA
32065 A
1 A
32066 TGACCGCGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.33, C:0.29, G:0.21, T:0.17
Consensus pattern (19 bp):
AAACGGTAGTACGCTCCCA
Found at i:32341 original size:24 final size:24
Alignment explanation
Indices: 32313--32365 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
32303 GAAGATGAGC
32313 CACCATAAAACATG-GG-AGAATGCT
1 CACCAT-AAA-ATGAGGTAGAATGCT
*
32337 CACCATCAAATGAGGTAGAATGCT
1 CACCATAAAATGAGGTAGAATGCT
32361 CACCA
1 CACCA
32366 CGGAAGGCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 3 0.12
23 4 0.15
24 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.17
Consensus pattern (24 bp):
CACCATAAAATGAGGTAGAATGCT
Found at i:45181 original size:73 final size:73
Alignment explanation
Indices: 45089--45235 Score: 258
Period size: 73 Copynumber: 2.0 Consensus size: 73
45079 GTAAAACAAA
* *
45089 TGTTTATACTAGATGTATAAGTTGATGCCTACTCTATTATATTAACTAATCAAAGTCTCTTTGTT
1 TGTTTATACTAGATATATAAGTTGATACCTACTCTATTATATTAACTAATCAAAGTCTCTTTGTT
45154 GTAAAGTT
66 GTAAAGTT
* *
45162 TGTTTATACTGGATATATAAGTTGATACCTACTCTATTATATTAACTAATCCAAGTCTCTTTGTT
1 TGTTTATACTAGATATATAAGTTGATACCTACTCTATTATATTAACTAATCAAAGTCTCTTTGTT
45227 GTAAAGTT
66 GTAAAGTT
45235 T
1 T
45236 TATACTGTTG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (73 bp):
TGTTTATACTAGATATATAAGTTGATACCTACTCTATTATATTAACTAATCAAAGTCTCTTTGTT
GTAAAGTT
Found at i:48064 original size:35 final size:35
Alignment explanation
Indices: 47994--48681 Score: 829
Period size: 35 Copynumber: 19.7 Consensus size: 35
47984 TTCTTACTAA
*
47994 ACTTAATTACCCTGAATTAAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATT-AAGTTGATTACTGACTT
* * * *
48030 ACTTAATTATCCTAAATTAAGTTGATTACCGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
48065 ACTTAATTACCCTAAATTAAAATTGATTACT-A---
1 ACTTAATTACCCTGAATT-AAGTTGATTACTGACTT
*
48097 ACTTAATTACCCTGAATTAAGTT-ATTCACTGACCT
1 ACTTAATTACCCTGAATTAAGTTGATT-ACTGACTT
* *
48132 ACTTGATTGCCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
48167 ACTTAATTACCCTGAATTAAGTTTG-TTACTAACTT
1 ACTTAATTACCCTGAATTAAG-TTGATTACTGACTT
48202 ACTTAATTACCCTGAATTAAGTTGATTACTATTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTAC---TGACTT
*
48240 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
48275 ACTTAATTATCCTGAATTAAGTTTATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
48310 ACTTAATTACCCTGAATTAAGTTGATTACTGATTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
48345 ACTTAATTACCCTGAATTAAGTTGATTACTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGA-T--TACTGACTT
*
48383 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
48418 ACTTAATTACCCTGAATTAAGTTGATTAATGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
48453 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
48488 ACTTAATTACCCTGAATTAAGTTTG-TTACTAACTTGCTTT
1 ACTTAATTACCCTGAATTAAG-TTGATTACTGA----C-TT
*
48528 ACTTAATTACCCTGAATTAAGCT-ACTTACTG----
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
* *
48559 ACTTAATTACCCTGAATTAAGTT-ACCTA-TTACTT
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
* *
48593 ACTTAATTACCCTGAATTAAGTTG----CTAATTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * *
48624 GCTTAATTACCCTGAATTAAATT-ATCCACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGAT-TACTGACTT
48659 ACTTAATTACCCTGAATTAAGTT
1 ACTTAATTACCCTGAATTAAGTT
48682 ACTTATTACT
Statistics
Matches: 575, Mismatches: 43, Indels: 69
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.01
31 58 0.10
32 18 0.03
34 26 0.05
35 336 0.58
36 36 0.06
37 1 0.00
38 67 0.12
39 2 0.00
40 27 0.05
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
Found at i:48303 original size:143 final size:141
Alignment explanation
Indices: 47994--48682 Score: 873
Period size: 143 Copynumber: 4.9 Consensus size: 141
47984 TTCTTACTAA
* * *
47994 ACTTAATTACCCTGAATTAAAGTTGATTACTGACTCACTTAATTATCCTAAATTAAGTTGATTAC
1 ACTTAATTACCCTGAATT-AAGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTAC
* * * *
48059 CGACTCACTTAATTACCCTAAATTAAAATTGA-T--TACT-A---ACTTAATTACCCTGAATTAA
65 TGACTTACTTAATTACCCTGAATT-AAGTTGATTACTACTGACTTACTTAATTACCCTGAATTAA
48117 GTTATTCACTGACC
129 GTTATT-ACTGACC
* *
48131 TACTTGATTGCCCTGAATTAAGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTTG-TTA
1 -ACTTAATTACCCTGAATTAAGTTGATTACTGACTTACTTAATTACCCTGAATTAAG-TTGATTA
* *
48195 CTAACTTACTTAATTACCCTGAATTAAGTTGATTACTATTGACTTACTTAATTACCCTGAATTAA
64 CTGACTTACTTAATTACCCTGAATTAAGTTGATTACTACTGACTTACTTAATTACCCTGAATTAA
48260 GTTGATTACTGACTC
129 GTT-ATTACTGAC-C
* *
48275 ACTTAATTATCCTGAATTAAGTTTATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTACT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTACT
*
48340 GATTTACTTAATTACCCTGAATTAAGTTGATTACTACTGACTTACTTAATTACCCTGAATTAAGT
66 GACTTACTTAATTACCCTGAATTAAGTTGATTACTACTGACTTACTTAATTACCCTGAATTAAGT
48405 TGATTACTGACTC
131 T-ATTACTGAC-C
*
48418 ACTTAATTACCCTGAATTAAGTTGATTAATGACTTACTTAATTACCCTGAATTAAGTTGATTACT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTACT
*
48483 GACTCACTTAATTACCCTGAATTAAGTTTG-TTACTAACTTG-CTTTACTTAATTACCCTGAATT
66 GACTTACTTAATTACCCTGAATTAAG-TTGATTACT-AC-TGAC-TTACTTAATTACCCTGAATT
*
48546 AAGCTACTTACTG---
127 AAGTTA-TTACTGACC
* *
48559 ACTTAATTACCCTGAATTAAGTT-ACCTA-TTACTTACTTAATTACCCTGAATTAAGTTG----C
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTTACTTAATTACCCTGAATTAAGTTGATTAC
* * * * *
48618 TAATTTGCTTAATTACCCTGAATTAAATT-A-T-CCACTGACTTACTTAATTACCCTGAATTAAG
65 TGACTTACTTAATTACCCTGAATTAAGTTGATTACTACTGACTTACTTAATTACCCTGAATTAAG
48680 TTA
130 TTA
48683 CTTATTACTG
Statistics
Matches: 499, Mismatches: 33, Indels: 45
0.86 0.06 0.08
Matches are distributed among these distances:
131 27 0.05
132 3 0.01
133 1 0.00
134 1 0.00
135 2 0.00
136 29 0.06
137 60 0.12
138 19 0.04
139 3 0.01
140 31 0.06
141 25 0.05
142 3 0.01
143 252 0.51
144 11 0.02
145 32 0.06
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (141 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTACT
GACTTACTTAATTACCCTGAATTAAGTTGATTACTACTGACTTACTTAATTACCCTGAATTAAGT
TATTACTGACC
Found at i:48563 original size:31 final size:31
Alignment explanation
Indices: 48528--48686 Score: 167
Period size: 31 Copynumber: 4.9 Consensus size: 31
48518 AACTTGCTTT
*
48528 ACTTAATTACCCTGAATTAAGCTACTTACTG
1 ACTTAATTACCCTGAATTAAGTTACTTACTG
*
48559 ACTTAATTACCCTGAATTAAGTTACCTATTACTT
1 ACTTAATTACCCTGAATTAAGTTA-C--TTACTG
* * *
48593 ACTTAATTACCCTGAATTAAGTTGCTAATTTG
1 ACTTAATTACCCTGAATTAAGTTACTTA-CTG
* * *
48625 -CTTAATTACCCTGAATTAAATTATCCACTGACTT
1 ACTTAATTACCCTGAATT-AAGT-T--ACTTACTG
48659 ACTTAATTACCCTGAATTAAGTTACTTA
1 ACTTAATTACCCTGAATTAAGTTACTTA
48687 TTACTGATTC
Statistics
Matches: 106, Mismatches: 13, Indels: 18
0.77 0.09 0.13
Matches are distributed among these distances:
31 46 0.43
32 5 0.05
33 3 0.03
34 32 0.30
35 20 0.19
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (31 bp):
ACTTAATTACCCTGAATTAAGTTACTTACTG
Found at i:48578 original size:14 final size:15
Alignment explanation
Indices: 48530--48584 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
48520 CTTGCTTTAC
48530 TTAA-TTACCCTGAA
1 TTAAGTTACCCTGAA
* * *
48544 TTAAGCTACTTACTGAC
1 TTAAGTTAC--CCTGAA
48561 TTAA-TTACCCTGAA
1 TTAAGTTACCCTGAA
48575 TTAAGTTACC
1 TTAAGTTACC
48585 TATTACTTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
14 12 0.39
15 8 0.26
16 3 0.10
17 8 0.26
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (15 bp):
TTAAGTTACCCTGAA
Found at i:62459 original size:21 final size:22
Alignment explanation
Indices: 62430--62480 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
62420 ACTTTTTTTG
* *
62430 TTTTGTTTTGTT-TTTGTCTCT
1 TTTTTTTTTGTTCTTTGTCCCT
*
62451 TTTTTTTTTGTTCTTTTTCCCT
1 TTTTTTTTTGTTCTTTGTCCCT
62473 TTTTTTTT
1 TTTTTTTT
62481 CTTTTTGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (22 bp):
TTTTTTTTTGTTCTTTGTCCCT
Found at i:62827 original size:26 final size:26
Alignment explanation
Indices: 62761--62828 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
62751 ATTTCTGGAA
* *
62761 AACAAGGGAAAGGGACAATTAAAAAGG
1 AACAAAGG-AAGGGACAATTAAAAAAG
* *
62788 AATAAGGGAAAGGGACAATTAAAAAAG
1 AACAAAGG-AAGGGACAATTAAAAAAG
62815 AACAGAAGG-AGGGA
1 AACA-AAGGAAGGGA
62829 GTAGTTTAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 5 0.14
27 28 0.78
28 3 0.08
ACGTcount: A:0.56, C:0.06, G:0.31, T:0.07
Consensus pattern (26 bp):
AACAAAGGAAGGGACAATTAAAAAAG
Found at i:66741 original size:12 final size:12
Alignment explanation
Indices: 66724--66766 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
66714 TAGTACATTC
66724 TTTATTTTCTTA
1 TTTATTTTCTTA
*
66736 TTTATTTTCTCA
1 TTTATTTTCTTA
* *
66748 TGTAATTTCTTA
1 TTTATTTTCTTA
66760 TTTATTT
1 TTTATTT
66767 AAGATTTTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (12 bp):
TTTATTTTCTTA
Found at i:67163 original size:20 final size:20
Alignment explanation
Indices: 67119--67173 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
67109 AATTTTTTTA
*
67119 AAAAAAAAATCTACCCATTTG
1 AAAAGAAAA-CTACCCATTTG
67140 -AAAGAAAACTACCCATTTG
1 AAAAGAAAACTACCCATTTG
*
67159 AAAAGAAAACCACCC
1 AAAAGAAAACTACCC
67174 CCACATAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 11 0.35
20 20 0.65
ACGTcount: A:0.53, C:0.24, G:0.07, T:0.16
Consensus pattern (20 bp):
AAAAGAAAACTACCCATTTG
Found at i:67468 original size:29 final size:29
Alignment explanation
Indices: 67430--67487 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
67420 TATTAATGAA
*
67430 TGGACAATTTGCACCATAAACTTTAATTT
1 TGGACAATTTGCACCATAAACTATAATTT
*
67459 TGGACAATTTGCACCCTAAACTATAATTT
1 TGGACAATTTGCACCATAAACTATAATTT
67488 ACAGATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.36
Consensus pattern (29 bp):
TGGACAATTTGCACCATAAACTATAATTT
Found at i:67818 original size:31 final size:31
Alignment explanation
Indices: 67776--67852 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 31
67766 ACACTGTCTA
* *
67776 ATTTAGGCTCAAATTGGTTG-ATTTCGATAA-C
1 ATTTAGACTCAAATTGGATGCATTTC-A-AAGC
*
67807 ATTTAGACTC-AATTTGATGCATTTCAAAGC
1 ATTTAGACTCAAATTGGATGCATTTCAAAGC
*
67837 GTTTAGACTCAAATTG
1 ATTTAGACTCAAATTG
67853 AGCAAGTTCG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 2 0.05
30 18 0.47
31 18 0.47
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (31 bp):
ATTTAGACTCAAATTGGATGCATTTCAAAGC
Found at i:68798 original size:7 final size:7
Alignment explanation
Indices: 68788--68814 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
68778 TTAATCATCT
68788 TTTTTTA
1 TTTTTTA
68795 TTTTTTA
1 TTTTTTA
68802 TTTTTTA
1 TTTTTTA
68809 TTTTTT
1 TTTTTT
68815 TTTGCTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:73835 original size:15 final size:15
Alignment explanation
Indices: 73815--73843 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
73805 TTCAAACTTC
73815 AAAAAAAAACAAAAA
1 AAAAAAAAACAAAAA
73830 AAAAAAAAACAAAA
1 AAAAAAAAACAAAA
73844 CCCAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAACAAAAA
Done.