Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001689.1 Hibiscus syriacus cultivar Beakdansim tig00003374_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: 71972
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:5985 original size:22 final size:22
Alignment explanation
Indices: 5960--6004 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5950 AATATTTTAA
*
5960 ATAAGATATTCCTTATTTTTTT
1 ATAACATATTCCTTATTTTTTT
* **
5982 ATAACATGTTTTTTATTTTTTT
1 ATAACATATTCCTTATTTTTTT
6004 A
1 A
6005 ATTTCTAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (22 bp):
ATAACATATTCCTTATTTTTTT
Found at i:7081 original size:3 final size:3
Alignment explanation
Indices: 7073--7098 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7063 ATTCATAAAT
7073 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
7099 TTTTGGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16009 original size:21 final size:21
Alignment explanation
Indices: 15985--16043 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
15975 CTCACCTGAT
15985 GATCGATACTATAGAAGACAA
1 GATCGATACTATAGAAGACAA
* * ** * * *
16006 GATCGTTCCTATTCACGAGAT
1 GATCGATACTATAGAAGACAA
16027 GATCGATACTATAGAAG
1 GATCGATACTATAGAAG
16044 GTGGGATCGT
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (21 bp):
GATCGATACTATAGAAGACAA
Found at i:16099 original size:126 final size:126
Alignment explanation
Indices: 15969--16211 Score: 290
Period size: 126 Copynumber: 1.9 Consensus size: 126
15959 GGCAAGACCG
* * * * *
15969 TTCCTACTCACCTGATGATCGATACTATAGAA-GACAAGATCGTTCCTATTCACGAGATGATCGA
1 TTCCTACTCACCAGAAGATCGATACTATAGAAGGA-AAGATCGTTCCTACTCACCAGAAGATCGA
* * * * * *
16033 TACTATAGAAGGTGGGATCGTTCCTACTCACCTGATGATTGGTACTACAGGAGGAGGGATCT
65 TACTACAGAAGGTGGGATCGTTCATACTCACCAGAAGATCGGTACAACAGGAGGAGGGATCT
* * ** * * *
16095 TTCCTACTCACCAGAAGATTGGTACTATAGAAGGAGGGATTGTTCCTGCTCACCAGAAGATCGGT
1 TTCCTACTCACCAGAAGATCGATACTATAGAAGGAAAGATCGTTCCTACTCACCAGAAGATCGAT
* *
16160 ACTACAGAAGGTGGGATTGTTCATGCTCACCAGAAGATCGGTACAACAGGAG
66 ACTACAGAAGGTGGGATCGTTCATACTCACCAGAAGATCGGTACAACAGGAG
16212 ACAGTACAAG
Statistics
Matches: 96, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
126 94 0.98
127 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (126 bp):
TTCCTACTCACCAGAAGATCGATACTATAGAAGGAAAGATCGTTCCTACTCACCAGAAGATCGAT
ACTACAGAAGGTGGGATCGTTCATACTCACCAGAAGATCGGTACAACAGGAGGAGGGATCT
Found at i:16176 original size:42 final size:42
Alignment explanation
Indices: 15968--16208 Score: 225
Period size: 42 Copynumber: 5.7 Consensus size: 42
15958 AGGCAAGACC
* * * * ** *
15968 GTTCCTACTCACCTGATGATCGATACTATAGAA-GACAAGATC
1 GTTCCTACTCACCAGAAGATCGGTACTACAGAAGGA-GGGATT
* * * * * * *
16010 GTTCCTATTCACGAGATGATCGATACTATAGAAGGTGGGATC
1 GTTCCTACTCACCAGAAGATCGGTACTACAGAAGGAGGGATT
* * * *
16052 GTTCCTACTCACCTGATGATTGGTACTACAGGAGGAGGGATCT
1 GTTCCTACTCACCAGAAGATCGGTACTACAGAAGGAGGGAT-T
* *
16095 -TTCCTACTCACCAGAAGATTGGTACTATAGAAGGAGGGATT
1 GTTCCTACTCACCAGAAGATCGGTACTACAGAAGGAGGGATT
* *
16136 GTTCCTGCTCACCAGAAGATCGGTACTACAGAAGGTGGGATT
1 GTTCCTACTCACCAGAAGATCGGTACTACAGAAGGAGGGATT
* * *
16178 GTTCATGCTCACCAGAAGATCGGTACAACAG
1 GTTCCTACTCACCAGAAGATCGGTACTACAG
16209 GAGACAGTAC
Statistics
Matches: 171, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
41 1 0.01
42 169 0.99
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (42 bp):
GTTCCTACTCACCAGAAGATCGGTACTACAGAAGGAGGGATT
Found at i:18619 original size:9 final size:9
Alignment explanation
Indices: 18607--18663 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
18597 TAATATTTTG
18607 TATTTAATT
1 TATTTAATT
*
18616 TATTTAA-G
1 TATTTAATT
18624 TATTTAATT
1 TATTTAATT
18633 TATTTAA--
1 TATTTAATT
* *
18640 TATTTTACT
1 TATTTAATT
18649 TATTTAATT
1 TATTTAATT
*
18658 TTTTTA
1 TATTTA
18664 CAGATATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 6 0.15
8 7 0.18
9 26 0.67
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TATTTAATT
Found at i:18628 original size:17 final size:17
Alignment explanation
Indices: 18606--18655 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
18596 TTAATATTTT
18606 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
18623 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
18640 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
18656 TTTTTTTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:18651 original size:16 final size:16
Alignment explanation
Indices: 18615--18660 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
18605 TGTATTTAAT
* *
18615 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
18632 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
18648 TTATTTAAT-TTTT
1 TTATTTAATATTTT
18661 TTACAGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:26485 original size:50 final size:50
Alignment explanation
Indices: 26431--26531 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
26421 ACATAATTAT
26431 AGTTTTAAAACAAGGAAATAATTAAAATTATAAT-GAGGAGTTACAACTAG
1 AGTTTTAAAACAAGGAAATAATTAAAATTATAATGGA-GAGTTACAACTAG
* * *
26481 AGTTTTAAAATAAGTAAATAATTAAAATTATAATGGAGAGTTACTACTAG
1 AGTTTTAAAACAAGGAAATAATTAAAATTATAATGGAGAGTTACAACTAG
26531 A
1 A
26532 ATTATAAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 45 0.96
51 2 0.04
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.31
Consensus pattern (50 bp):
AGTTTTAAAACAAGGAAATAATTAAAATTATAATGGAGAGTTACAACTAG
Found at i:28598 original size:76 final size:76
Alignment explanation
Indices: 28471--28636 Score: 235
Period size: 76 Copynumber: 2.2 Consensus size: 76
28461 TAAACTCAAA
* * *
28471 TTTTAGGATAATATTTTAAACATTATATTTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 TTTTAGGATATTATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAAG-TTTTAGT
28536 ATTTTAATTAAG
65 ATTTTAATTAAG
* * *
28548 TTTTAGGATATTATTTT-TATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAAGTTTTAGTA
1 TTTTAGGATATTATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAAGTTTTAGTA
*
28612 TTTTAATTAGG
66 TTTTAATTAAG
* *
28623 ATTTAGAATATTAT
1 TTTTAGGATATTAT
28637 ATTATTTTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
75 30 0.38
76 34 0.43
77 16 0.20
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.57
Consensus pattern (76 bp):
TTTTAGGATATTATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAAGTTTTAGTA
TTTTAATTAAG
Found at i:29301 original size:21 final size:22
Alignment explanation
Indices: 29276--29316 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
29266 CTTTAATTTG
29276 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
29297 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
29317 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:29648 original size:24 final size:24
Alignment explanation
Indices: 29616--29661 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
29606 AACATTCCCC
29616 TTGCAAACTTCAA-TCTCAAAAACT
1 TTGCAAACTTCAACT-TCAAAAACT
29640 TTGCAAACTTCAACTTCAAAAA
1 TTGCAAACTTCAACTTCAAAAA
29662 ACTACTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.28
Consensus pattern (24 bp):
TTGCAAACTTCAACTTCAAAAACT
Found at i:34947 original size:21 final size:21
Alignment explanation
Indices: 34921--34960 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
34911 AGTGCCCAAC
*
34921 AATAACAAAATCGATAAAAAA
1 AATAACAAAACCGATAAAAAA
34942 AATAACAAAACCGATAAAA
1 AATAACAAAACCGATAAAA
34961 CATCCAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.70, C:0.12, G:0.05, T:0.12
Consensus pattern (21 bp):
AATAACAAAACCGATAAAAAA
Found at i:37964 original size:68 final size:69
Alignment explanation
Indices: 37889--38020 Score: 180
Period size: 70 Copynumber: 1.9 Consensus size: 69
37879 TAAAAGATAT
* *
37889 TATTTAATTTGAATATTAGTAGGATAATTAT-TA-TTTAAATATATCAAATTAAAA-AGATATTT
1 TATTTAATTTGAATATTA-AAAGATAATTATATACTTTAAATATATCAAATTAAAATA-ATATTT
37951 TTCATC
64 TTCATC
* *
37957 TATTTAATTTGAATATTAAAAGATAATTATATACTTTTGAATATTTCAAATTAAAATAATATTT
1 TATTTAATTTGAATATTAAAAGATAATTATATAC-TTTAAATATATCAAATTAAAATAATATTT
38021 GTTTAAGTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
67 10 0.18
68 20 0.36
70 25 0.45
71 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (69 bp):
TATTTAATTTGAATATTAAAAGATAATTATATACTTTAAATATATCAAATTAAAATAATATTTTT
CATC
Found at i:38279 original size:21 final size:21
Alignment explanation
Indices: 38164--38279 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
38154 GCGAAATAAA
**
38164 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
38184 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
38204 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
38225 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
38245 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
38267 AATCGCAACGCGA
1 AATCGCAACGCGA
38280 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:38328 original size:20 final size:20
Alignment explanation
Indices: 38267--38495 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
38257 GATTTTCCAG
* ** *
38267 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
38287 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
38307 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
38327 AATCACAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
38347 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
38367 AATCGCAATGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
38387 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
38407 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
38427 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
38447 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
38467 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
38487 AATCACAAC
1 AATCGCAAC
38496 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:39226 original size:24 final size:24
Alignment explanation
Indices: 39187--39233 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
39177 AAATTTGGTC
39187 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
39211 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
39234 GATATTTCAG
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:39425 original size:12 final size:12
Alignment explanation
Indices: 39408--39432 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39398 ATATAATCCT
39408 GAAGAAGAAAAA
1 GAAGAAGAAAAA
39420 GAAGAAGAAAAA
1 GAAGAAGAAAAA
39432 G
1 G
39433 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:41763 original size:33 final size:33
Alignment explanation
Indices: 41712--41995 Score: 268
Period size: 33 Copynumber: 8.2 Consensus size: 33
41702 CGGAAATTAC
* * *
41712 AATCGCAACGAGAGAATCGCAATGCGAAATAAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
*
41745 AATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
*
41779 AATCGCAATGCGAAATGAAAATCACAATGCGAAATGAA
1 AATCGCAA--C--AA-GAAAATCGCAATGCGAAATGAA
* *
41817 AATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
* * *
41851 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
*
41890 AAT-GCGAA-ATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACAAGAAAATCGCAATGCGAAATGAA
* * *
41922 AATCGCAACGAGAGAATCGCAATACGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
* *
41955 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
41988 AATCGCAA
1 AATCGCAA
41996 TGCGAAATGA
Statistics
Matches: 210, Mismatches: 23, Indels: 36
0.78 0.09 0.13
Matches are distributed among these distances:
31 1 0.00
32 8 0.04
33 110 0.52
34 32 0.15
36 3 0.01
38 23 0.11
39 32 0.15
40 1 0.00
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:41795 original size:19 final size:19
Alignment explanation
Indices: 41726--42019 Score: 314
Period size: 19 Copynumber: 16.7 Consensus size: 19
41716 GCAACGAGAG
*
41726 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
*
41745 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
41759 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
41779 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
41798 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
41817 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
41831 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
41851 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
41870 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
41884 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
41903 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
41922 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
41936 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
*
41955 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
41969 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
41988 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
42007 AATCGCATTGCGA
1 AATCGCAATGCGA
42020 TTCTCTCGTT
Statistics
Matches: 234, Mismatches: 14, Indels: 54
0.77 0.05 0.18
Matches are distributed among these distances:
14 49 0.21
15 6 0.03
16 8 0.03
17 10 0.04
18 3 0.01
19 131 0.56
20 27 0.12
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:41921 original size:52 final size:52
Alignment explanation
Indices: 41712--42019 Score: 371
Period size: 52 Copynumber: 5.9 Consensus size: 52
41702 CGGAAATTAC
* *
41712 AATCGCAACGAGAGAATCGCAATGCGAAATAAAAATCCCAA--C--AA-GAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
41759 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCACAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
41817 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
41870 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* * * *
41922 AATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAA
* * *
41975 AATGCGAAATGA-A-AATCGCAATGCGAAATGAAAATCGCATTGCGA
1 AAT-CGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
42020 TTCTCTCGTT
Statistics
Matches: 231, Mismatches: 15, Indels: 25
0.85 0.06 0.09
Matches are distributed among these distances:
47 8 0.03
49 1 0.00
50 1 0.00
52 112 0.48
53 86 0.37
54 7 0.03
55 2 0.01
56 1 0.00
57 2 0.01
58 11 0.05
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:41941 original size:14 final size:14
Alignment explanation
Indices: 41922--41976 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
41912 GCGAAATGAA
41922 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
41936 AATCGCAATACGAAATGAA
1 AATCGC-A-ACG--A-GAG
41955 AATCGCAACGAGAG
1 AATCGCAACGAGAG
41969 AATCGCAA
1 AATCGCAA
41977 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 8 0.24
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:42068 original size:19 final size:19
Alignment explanation
Indices: 42032--42115 Score: 115
Period size: 19 Copynumber: 4.6 Consensus size: 19
42022 CTCTCGTTGT
42032 GATTTTCATTTCCGCATTGC
1 GATTTTCATTT-CGCATTGC
42052 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
42071 GA--TTC-TCTCG--TTGC
1 GATTTTCATTTCGCATTGC
42085 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
42104 GATTTTCATTTC
1 GATTTTCATTTC
42116 AACATAATGC
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 26 0.46
20 11 0.19
ACGTcount: A:0.14, C:0.23, G:0.15, T:0.48
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:42076 original size:53 final size:52
Alignment explanation
Indices: 42009--42115 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 52
41999 GAAATGAAAA
*
42009 TCGCATTGCGATTCTCTCGTTGTGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
42062 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
42114 TC
1 TC
42116 AACATAATGC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 20 0.38
53 33 0.62
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:42225 original size:14 final size:14
Alignment explanation
Indices: 42206--42242 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
42196 CATCAATTAC
42206 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
42220 ACAAATCATCTTTT
1 ACAAATCAACTTTT
42234 ACAAATCAA
1 ACAAATCAA
42243 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:44211 original size:19 final size:19
Alignment explanation
Indices: 44169--44321 Score: 112
Period size: 19 Copynumber: 8.6 Consensus size: 19
44159 TAGTTTACTT
* *
44169 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
44189 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
44208 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
44227 TCGCAACGCGAAA-CCAAA
1 TCGCAACGCGAAATGAAAA
*
44245 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
44259 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
44278 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
44292 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
44311 TCGCAATGCGA
1 TCGCAACGCGA
44322 TTTTGGTTTC
Statistics
Matches: 108, Mismatches: 15, Indels: 21
0.75 0.10 0.15
Matches are distributed among these distances:
14 18 0.17
15 1 0.01
16 10 0.09
17 3 0.03
18 11 0.10
19 53 0.49
20 12 0.11
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:44262 original size:14 final size:14
Alignment explanation
Indices: 44243--44299 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
44233 CGCGAAACCA
*
44243 AATCGCAACGACAG
1 AATCGCAACGAAAG
44257 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
44274 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
44290 AATCGCAACG
1 AATCGCAACG
44300 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:44284 original size:33 final size:33
Alignment explanation
Indices: 44187--44316 Score: 154
Period size: 33 Copynumber: 3.8 Consensus size: 33
44177 CGAAACTTAA
* *
44187 AATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAATGAAAATCGCAAC--G--A-CAG
**
44225 AATCGCAACGCGAAA-CCAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
44257 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
44290 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
44317 TGCGATTTTG
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
32 16 0.20
33 41 0.50
35 1 0.01
37 9 0.11
38 15 0.18
ACGTcount: A:0.46, C:0.24, G:0.21, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:44352 original size:14 final size:14
Alignment explanation
Indices: 44333--44391 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
44323 TTTGGTTTCG
44333 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
44347 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
44364 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
44380 CGTTGCGATTTT
1 CGTTGCGATTTT
44392 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:44359 original size:33 final size:33
Alignment explanation
Indices: 44317--44440 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
44307 AAAATCGCAA
*
44317 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
44350 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
44383 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
44416 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
44441 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:44371 original size:19 final size:18
Alignment explanation
Indices: 44317--44408 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
44307 AAAATCGCAA
44317 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
44336 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
44350 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
44369 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
44383 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
44402 TGCGATT
1 TGCGATT
44409 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:44418 original size:14 final size:14
Alignment explanation
Indices: 44366--44422 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
44356 TTTGGTTTCG
*
44366 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
44380 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
44399 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
44413 CGTTGCGATT
1 CGTTGCGATT
44423 TTAAGTTTCG
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 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:44661 original size:93 final size:93
Alignment explanation
Indices: 44539--44945 Score: 787
Period size: 93 Copynumber: 4.4 Consensus size: 93
44529 AGGGTATTAG
44539 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
1 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
44604 CTATTTCACAGTGTTAAAGAATACACAA
66 CTATTTCACAGTGTTAAAGAATACACAA
44632 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
1 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
44697 CTATTTCACAGTGTTAAAGAATACACAA
66 CTATTTCACAGTGTTAAAGAATACACAA
44725 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
1 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
*
44790 CTATTTCACAGTGTTAAAGAATACACAG
66 CTATTTCACAGTGTTAAAGAATACACAA
44818 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
1 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
*
44883 CTATTTCACAGTGTTAAAGAATACACAG
66 CTATTTCACAGTGTTAAAGAATACACAA
*
44911 TTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
44946 AAGCAATCTA
Statistics
Matches: 312, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 312 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
CTATTTCACAGTGTTAAAGAATACACAA
Found at i:46659 original size:20 final size:20
Alignment explanation
Indices: 46628--46691 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
46618 TTTTGGTTGA
46628 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
46648 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
46668 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
46689 AAT
1 AAT
46692 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:46680 original size:21 final size:21
Alignment explanation
Indices: 46626--46690 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
46616 TCTTTTGGTT
46626 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
46647 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
46667 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
46688 GAA
1 GAA
46691 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:46768 original size:33 final size:33
Alignment explanation
Indices: 46716--46795 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
46706 AAAATCGCAA
** *
46716 TGCGATTTTGGTTTTGCGTTGCGATTCTCTCAT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCAT
*
46749 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCAT
46782 TGCGATTTTCATTT
1 TGCGATTTTCATTT
46796 TTCTCATTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.10, C:0.20, G:0.21, T:0.49
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCAT
Found at i:46784 original size:14 final size:14
Alignment explanation
Indices: 46732--46788 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
46722 TTTGGTTTTG
46732 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
46746 CATTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
46765 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
46779 CGTTGCGATT
1 CGTTGCGATT
46789 TTCATTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:46805 original size:21 final size:21
Alignment explanation
Indices: 46776--46849 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
46766 GTTGCGATTC
46776 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
* **
46797 TCTCATTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
46818 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
46839 TCTCGTTGCGA
1 TCTCGTTGCGA
46850 CTCTTCTGCA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
20 6 0.14
21 30 0.71
22 6 0.14
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:46971 original size:33 final size:33
Alignment explanation
Indices: 46929--46999 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
46919 AATACTAACT
46929 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
46962 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
46995 TGAAA
1 TGAAA
47000 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:47403 original size:20 final size:20
Alignment explanation
Indices: 47378--47570 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
47368 CTTTAAAAAT
47378 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
47398 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
47418 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
47439 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
47459 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
47479 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
47499 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
47519 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
47539 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
47559 CGCGTTGCGATT
1 CGCGTTGCGATT
47571 CTGGAAAATC
Statistics
Matches: 152, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
20 134 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:51156 original size:18 final size:18
Alignment explanation
Indices: 51133--51213 Score: 103
Period size: 18 Copynumber: 4.6 Consensus size: 18
51123 AAATGTTTAT
51133 AGTTATCAGATGATTTTC
1 AGTTATCAGATGATTTTC
*
51151 AGTTATCAGAT-ATTTAC
1 AGTTATCAGATGATTTTC
* *
51168 AGTTATCGGACGATTTTC
1 AGTTATCAGATGATTTTC
*
51186 AGTTATTAGATG-TTTTAC
1 AGTTATCAGATGATTTT-C
51204 AGTTATCAGA
1 AGTTATCAGA
51214 CGTAGATTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
17 18 0.34
18 35 0.66
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (18 bp):
AGTTATCAGATGATTTTC
Found at i:51173 original size:35 final size:36
Alignment explanation
Indices: 51128--51215 Score: 124
Period size: 35 Copynumber: 2.5 Consensus size: 36
51118 ATTCTAAATG
* *
51128 TTTATAGTTATCAGATGATTTTCAGTTATCAGAT-A
1 TTTACAGTTATCAGACGATTTTCAGTTATCAGATGA
* * *
51163 TTTACAGTTATCGGACGATTTTCAGTTATTAGATGT
1 TTTACAGTTATCAGACGATTTTCAGTTATCAGATGA
51199 TTTACAGTTATCAGACG
1 TTTACAGTTATCAGACG
51216 TAGATTAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 30 0.65
36 16 0.35
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (36 bp):
TTTACAGTTATCAGACGATTTTCAGTTATCAGATGA
Found at i:51325 original size:7 final size:7
Alignment explanation
Indices: 51310--51339 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
51300 AAGTGAGTGC
51310 TTATCAG
1 TTATCAG
*
51317 TTATTAG
1 TTATCAG
51324 TTATCAG
1 TTATCAG
51331 TTATCAG
1 TTATCAG
51338 TT
1 TT
51340 CAATTTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50
Consensus pattern (7 bp):
TTATCAG
Found at i:52227 original size:18 final size:18
Alignment explanation
Indices: 52206--52240 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52196 ATTAAAGTTA
*
52206 AAAAGAAAATTATTAAAT
1 AAAACAAAATTATTAAAT
*
52224 AAAACAAAATTTTTAAA
1 AAAACAAAATTATTAAA
52241 CATTTAAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAACAAAATTATTAAAT
Found at i:55318 original size:19 final size:19
Alignment explanation
Indices: 55269--55320 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
55259 TTATGATTAA
*
55269 ATTAAA-TAAAAATTAAAG
1 ATTAAATTATAAATTAAAG
* * * *
55287 TTTACATTTTAAATTAAGG
1 ATTAAATTATAAATTAAAG
55306 ATTAAATTATAAATT
1 ATTAAATTATAAATT
55321 TTAAATAGAG
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (19 bp):
ATTAAATTATAAATTAAAG
Found at i:55418 original size:30 final size:30
Alignment explanation
Indices: 55384--55442 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
55374 TATTAACATG
* *
55384 AATTATTTTATTATCAAGTATTTAAACACT
1 AATTATTTAAATATCAAGTATTTAAACACT
*
55414 AATTATTTAAATATCAATTATTTAAACAC
1 AATTATTTAAATATCAAGTATTTAAACAC
55443 GACTCATGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (30 bp):
AATTATTTAAATATCAAGTATTTAAACACT
Found at i:55420 original size:15 final size:16
Alignment explanation
Indices: 55397--55442 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
55387 TATTTTATTA
*
55397 TCAAGTATTTAAACAC
1 TCAATTATTTAAACAC
*
55413 T-AATTATTTAAATA-
1 TCAATTATTTAAACAC
55427 TCAATTATTTAAACAC
1 TCAATTATTTAAACAC
55443 GACTCATGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.39
Consensus pattern (16 bp):
TCAATTATTTAAACAC
Found at i:55596 original size:2 final size:2
Alignment explanation
Indices: 55589--55622 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55579 ATATTTTGTC
55589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55623 TTCCGTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70343 original size:3 final size:3
Alignment explanation
Indices: 70328--70357 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
70318 ACTCTTCTCC
*
70328 CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
70358 TTCCTCCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
CTT
Found at i:71829 original size:26 final size:27
Alignment explanation
Indices: 71787--71840 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
71777 TACATGCCCC
71787 CTAATCACATGTACCGTACTTTGCAAA
1 CTAATCACATGTACCGTACTTTGCAAA
71814 CTAATCAC-TGTACCGTACTTTGCAAA
1 CTAATCACATGTACCGTACTTTGCAAA
71840 C
1 C
71841 AACGCCGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (27 bp):
CTAATCACATGTACCGTACTTTGCAAA
Done.