Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004993.1 Hibiscus syriacus cultivar Beakdansim tig00011206_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: 86131
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:6292 original size:25 final size:25
Alignment explanation
Indices: 6258--6307 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
6248 GACATATCTT
6258 GTGATCCTAGTGATTCAAAGGCAAA
1 GTGATCCTAGTGATTCAAAGGCAAA
**
6283 GTGATCCTAGTGATTTGAAGGCAAA
1 GTGATCCTAGTGATTCAAAGGCAAA
6308 TGACAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (25 bp):
GTGATCCTAGTGATTCAAAGGCAAA
Found at i:9942 original size:30 final size:30
Alignment explanation
Indices: 9900--9968 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
9890 ATAAGATCAT
9900 GTTAT-TTGTCATTAAGTTGTTTAGTGGTCA
1 GTTATGTT-TCATTAAGTTGTTTAGTGGTCA
*
9930 GTTATGTTTCATTCAGTTGTTTAGTGGTCA
1 GTTATGTTTCATTAAGTTGTTTAGTGGTCA
*
9960 TTTATGTTT
1 GTTATGTTT
9969 GACACTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 34 0.94
31 2 0.06
ACGTcount: A:0.17, C:0.07, G:0.22, T:0.54
Consensus pattern (30 bp):
GTTATGTTTCATTAAGTTGTTTAGTGGTCA
Found at i:16393 original size:3 final size:3
Alignment explanation
Indices: 16385--16429 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
16375 CTACAAAAAC
16385 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16430 TTGATTACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:16951 original size:14 final size:14
Alignment explanation
Indices: 16934--16965 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
16924 CCAAAAAAAG
16934 GAAAAAAAAAGAAA
1 GAAAAAAAAAGAAA
*
16948 GAAAAGAAAAGAAA
1 GAAAAAAAAAGAAA
16962 GAAA
1 GAAA
16966 GCGAGGAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAAGAAA
Found at i:17299 original size:2 final size:2
Alignment explanation
Indices: 17287--17325 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
17277 GTTTTGGGCT
*
17287 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17326 TTTAAACACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18917 original size:22 final size:26
Alignment explanation
Indices: 18861--18921 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 26
18851 CCTTTTATTT
*
18861 ATTTTTTATTTTTAAGCATATTATGC
1 ATTTTTTATTTTTAAGCATAATATGC
18887 ATTATTTTATTTTTAA-C-TAAT-TG-
1 ATT-TTTTATTTTTAAGCATAATATGC
18910 ATTTTTTATTTT
1 ATTTTTTATTTT
18922 AGTGATTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 9 0.27
23 3 0.09
24 2 0.06
25 3 0.09
26 4 0.12
27 12 0.36
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (26 bp):
ATTTTTTATTTTTAAGCATAATATGC
Found at i:23202 original size:4 final size:4
Alignment explanation
Indices: 23193--25444 Score: 4199
Period size: 4 Copynumber: 568.8 Consensus size: 4
23183 ATTGAGAAAA
23193 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23241 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23289 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23337 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23385 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23433 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23481 ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23527 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
23573 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -CAT ACAT CCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23620 AC-- ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23664 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23712 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23760 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23808 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23856 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23904 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23952 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23998 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24046 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24094 ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24140 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24188 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24236 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24284 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24332 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
24380 ACAT AC-- ACAT CCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24426 ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24472 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24520 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24568 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24616 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24664 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24712 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
24760 ACAT ACAT CCAT ACAT -CAT ACAT CCAT ACAT ACAT --AT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24805 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24853 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
24899 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT CCAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
24947 CCAT -CAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24994 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
25042 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
25090 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
25138 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT CCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
25186 ACAT CCAT ACAT ACAT CCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
25234 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
25282 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
25330 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT CCAT CCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
25378 ACAT CCAT CCAT ACAT GCAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
25426 ACAT ATAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACA
25445 CACACACACA
Statistics
Matches: 2198, Mismatches: 27, Indels: 46
0.97 0.01 0.02
Matches are distributed among these distances:
2 20 0.01
3 9 0.00
4 2169 0.99
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:25449 original size:4 final size:4
Alignment explanation
Indices: 25442--25827 Score: 576
Period size: 4 Copynumber: 96.8 Consensus size: 4
25432 ATACATACAT
*
25442 ACAC ACAC ACAC AAAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
25490 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC A-AC ACAC ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
25537 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
25585 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
25633 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * *
25681 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ATAC AAAC ATAC ATAT
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * * * * * * * *
25729 ATAG ATAC ATAC ATAG ATAC ATAC ATAG ATAC ATAG ATAC ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
*
25777 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC AAAC ACAC ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
25825 ACA
1 ACA
25828 TAAAGACTTT
Statistics
Matches: 364, Mismatches: 17, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
3 3 0.01
4 361 0.99
ACGTcount: A:0.51, C:0.44, G:0.01, T:0.04
Consensus pattern (4 bp):
ACAC
Found at i:26608 original size:66 final size:65
Alignment explanation
Indices: 26462--26611 Score: 169
Period size: 67 Copynumber: 2.3 Consensus size: 65
26452 AATTGCTATA
* * *
26462 TAAAAGTATATCTTTGAGATAGTTTCCCTTGAAACAAAATTTGTCTCCTTTGAGACAGTTTCCCA
1 TAAACGTA-ATCTTTGAGATAGTTTCCCTTAAAACAAAATTTCTCTCCTTTGAGACAGTTTCCCA
26527 T
65 T
* * *
26528 GAATCGTCAATCTTTGAGA-ATGTTTCTCTTAAAAACAAAATTTCTCTCGC-TTGAGACAGTTTC
1 TAAACGT-AATCTTTGAGATA-GTTTCCCTT-AAAACAAAATTTCTCTC-CTTTGAGACAGTTTC
* *
26591 TCTT
62 CCAT
26595 TAAACGTAATCTTTGAG
1 TAAACGTAATCTTTGAG
26612 TCTGTTTCCA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
65 1 0.01
66 32 0.46
67 36 0.51
68 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (65 bp):
TAAACGTAATCTTTGAGATAGTTTCCCTTAAAACAAAATTTCTCTCCTTTGAGACAGTTTCCCAT
Found at i:26877 original size:130 final size:131
Alignment explanation
Indices: 26634--26935 Score: 360
Period size: 130 Copynumber: 2.3 Consensus size: 131
26624 GAAATAAATC
* * *
26634 CCCTAGATAACCAGCCGTCTTCATCACGTAGGAACCGTGTTATCATCCCTAAAAAATGGCATGCC
1 CCCTAGATAACCTGCCGTCCTCATCACGTAGCAACCGTGTTATCATCCCTAAAAAATGGCATGCC
* *
26699 ATCCTCATCACGTAGGAACTGTGTCATCCACCGACCAAACCTCATCATCACATAGGAGCCGTGTC
66 ATCCTCATCACGTAGGAACCGTGTCATCCACCGAACAAACCTCATCATCACATAGGAGCCGTGTC
26764 A
131 A
* ** *
26765 CCCTCAGATAACCTGCCGTCCTCATCACGTA-CATATCGTGTTATC-TCCCT-AACGATGGTATG
1 CCCT-AGATAACCTGCCGTCCTCATCACGTAGCA-ACCGTGTTATCATCCCTAAAAAATGGCATG
** * * * *
26827 TTATCCTCATCACGTAGGAACCGTGTCATCC-CTTGAACAGACCTCCTCATCACATAGGAGTCGT
64 CCATCCTCATCACGTAGGAACCGTGTCATCCAC-CGAACAAACCTCATCATCACATAGGAGCCGT
26891 GTCAA
128 GTC-A
* ** * *
26896 CCTTAGATAACCTTTCGTCCTCATCAAGTAGGAACCGTGT
1 CCCTAGATAACCTGCCGTCCTCATCACGTAGCAACCGTGT
26936 CATCCCTTGA
Statistics
Matches: 145, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
129 1 0.01
130 95 0.66
131 15 0.10
132 34 0.23
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (131 bp):
CCCTAGATAACCTGCCGTCCTCATCACGTAGCAACCGTGTTATCATCCCTAAAAAATGGCATGCC
ATCCTCATCACGTAGGAACCGTGTCATCCACCGAACAAACCTCATCATCACATAGGAGCCGTGTC
A
Found at i:26885 original size:40 final size:40
Alignment explanation
Indices: 26830--26977 Score: 122
Period size: 40 Copynumber: 3.6 Consensus size: 40
26820 TGGTATGTTA
*
26830 TCCTCATCACGTAGGAACCGTGTCATCCCTTGAACAGACC
1 TCCTCATCACATAGGAACCGTGTCATCCCTTGAACAGACC
** * *** *
26870 TCCTCATCACATAGGAGTCGTGTCA-ACCTTAGATAACCTTTCG
1 TCCTCATCACATAGGAACCGTGTCATCCCTT-G--AA-CAGACC
26913 TCCTCATCA-AGTAGGAACCGTGTCATCCCTTG-ACAAGACC
1 TCCTCATCACA-TAGGAACCGTGTCATCCCTTGAAC-AGACC
* * *
26953 TCCTCATCACGTAGGAGCCATGTCA
1 TCCTCATCACATAGGAACCGTGTCA
26978 CCCATATATA
Statistics
Matches: 82, Mismatches: 18, Indels: 16
0.71 0.16 0.14
Matches are distributed among these distances:
39 5 0.06
40 46 0.56
42 3 0.04
43 24 0.29
44 4 0.05
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.25
Consensus pattern (40 bp):
TCCTCATCACATAGGAACCGTGTCATCCCTTGAACAGACC
Found at i:26927 original size:83 final size:83
Alignment explanation
Indices: 26830--27018 Score: 263
Period size: 83 Copynumber: 2.3 Consensus size: 83
26820 TGGTATGTTA
* *
26830 TCCTCATCACGTAGGAACCGTGTCATCCCTTGA-ACAGACCTCCTCATCACATAGGAGTCGTGTC
1 TCCTCATCACGTAGGAACCGTGTCATCCCTTGACA-AGACCTCCTCATCACATAGGAGCCATGTC
* **
26894 AACCTTAGATAACCTTTCG
65 AACCATAGATAACCAGTCG
* *
26913 TCCTCATCAAGTAGGAACCGTGTCATCCCTTGACAAGACCTCCTCATCACGTAGGAGCCATGTCA
1 TCCTCATCACGTAGGAACCGTGTCATCCCTTGACAAGACCTCCTCATCACATAGGAGCCATGTCA
* *
26978 CCCATATATAACCAGTCG
66 ACCATAGATAACCAGTCG
* *
26996 TCCTCATCACGTAAGAACTGTGT
1 TCCTCATCACGTAGGAACCGTGT
27019 TATCAACCTT
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
83 92 0.99
84 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (83 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCTTGACAAGACCTCCTCATCACATAGGAGCCATGTCA
ACCATAGATAACCAGTCG
Found at i:27110 original size:40 final size:42
Alignment explanation
Indices: 27052--27158 Score: 114
Period size: 43 Copynumber: 2.6 Consensus size: 42
27042 AGAACTCTTT
** *
27052 ATCACGTATGAGATGTGTCATCCAC-T-GACG-AGATCTCCTC
1 ATCACGTATGAGCCGTGTCATCC-CTTAGACGAAGACCTCCTC
*
27092 ATCACGTATGAGCCGTGTCA-CCCTTAGACGACTAGACCTCTTC
1 ATCACGTATGAGCCGTGTCATCCCTTAGACGA--AGACCTCCTC
*
27135 ATCACGTATGAGCCGTGTTATCCC
1 ATCACGTATGAGCCGTGTCATCCC
27159 CCATCAACAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
38 1 0.02
39 3 0.05
40 22 0.39
43 27 0.48
44 3 0.05
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (42 bp):
ATCACGTATGAGCCGTGTCATCCCTTAGACGAAGACCTCCTC
Found at i:28817 original size:30 final size:29
Alignment explanation
Indices: 28712--28856 Score: 138
Period size: 30 Copynumber: 5.0 Consensus size: 29
28702 GCCCTTCAAA
28712 TTTCT-TTTTAGCTATTTTAGTCCTTTAAG
1 TTTCTGTTTT-GCTATTTTAGTCCTTTAAG
28741 TTTCTGTTTT-CTA-TTTAGTCCTTTAA-
1 TTTCTGTTTTGCTATTTTAGTCCTTTAAG
* *
28767 ATTCTTGTTGTTGCTGTTTTAG-CCTTTTAAG
1 TTTC-TGTT-TTGCTATTTTAGTCC-TTTAAG
* * *
28798 TTTATGTTTATGCTATTTTAGCCCTATAAG
1 TTTCTGTTT-TGCTATTTTAGTCCTTTAAG
* *
28828 TTTCTATTTTTACTATTTTAGTCCTTTAA
1 TTTCT-GTTTTGCTATTTTAGTCCTTTAA
28857 ATTCTTGTTT
Statistics
Matches: 95, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
26 3 0.03
27 17 0.18
28 5 0.05
29 10 0.11
30 53 0.56
31 7 0.07
ACGTcount: A:0.18, C:0.14, G:0.11, T:0.57
Consensus pattern (29 bp):
TTTCTGTTTTGCTATTTTAGTCCTTTAAG
Found at i:28872 original size:30 final size:30
Alignment explanation
Indices: 28717--28876 Score: 129
Period size: 30 Copynumber: 5.4 Consensus size: 30
28707 TCAAATTTCT
* *
28717 TTTTAGCTATTTTAGTCCTTTAAGTT-TCTG
1 TTTTA-CTATTTTAGTCCTTTAAATTCTATG
28747 TTTT-CTA-TTTAGTCCTTTAAATTCT-TG
1 TTTTACTATTTTAGTCCTTTAAATTCTATG
* * *
28774 TTGTTGCTGTTTTAG-CCTTTTAAGTT-TATG
1 TT-TTACTATTTTAGTCC-TTTAAATTCTATG
* * * *
28804 TTTATGCTATTTTAGCCCTATAAGTTTCTAT-
1 TTT-TACTATTTTAGTCCTTTAA-ATTCTATG
28835 TTTTACTATTTTAGTCCTTTAAATTCT-TG
1 TTTTACTATTTTAGTCCTTTAAATTCTATG
28864 TTTGTACTATTTT
1 TTT-TACTATTTT
28877 TGGTCCTTGT
Statistics
Matches: 108, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
27 19 0.18
28 7 0.06
29 13 0.12
30 59 0.55
31 7 0.06
32 3 0.03
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.57
Consensus pattern (30 bp):
TTTTACTATTTTAGTCCTTTAAATTCTATG
Found at i:30095 original size:29 final size:29
Alignment explanation
Indices: 30060--30130 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
30050 TATTGCTGAG
30060 CTCGACTCAAACTTTAAAAGTAAGCTCAA
1 CTCGACTCAAACTTTAAAAGTAAGCTCAA
30089 CTCGACTCAAACTTTAAAAGTAAGCTCAA
1 CTCGACTCAAACTTTAAAAGTAAGCTCAA
*
30118 CTCAACTCAAACT
1 CTCGACTCAAACT
30131 CACGAACTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (29 bp):
CTCGACTCAAACTTTAAAAGTAAGCTCAA
Found at i:35226 original size:14 final size:14
Alignment explanation
Indices: 35209--35235 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35199 GTTATCACAC
35209 CATTATTATTATAT
1 CATTATTATTATAT
35223 CATTATTATTATA
1 CATTATTATTATA
35236 AGTCTTTCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (14 bp):
CATTATTATTATAT
Found at i:43967 original size:41 final size:42
Alignment explanation
Indices: 43937--44024 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
43927 GGGTGGCCCG
* *
43937 AAGGACTT-ATCATCTTGCTCAAAAGACTTATAGATGACCCA
1 AAGGACTTAAACATCATGCTCAAAAGACTTATAGATGACCCA
* *
43978 AAGGATTTAAACATCATGCTCAAAAGACTTACT-GAT-AGCCA
1 AAGGACTTAAACATCATGCTCAAAAGACTTA-TAGATGACCCA
44019 AAGGAC
1 AAGGAC
44025 GTAGTCAGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 16 0.40
42 23 0.57
43 1 0.03
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (42 bp):
AAGGACTTAAACATCATGCTCAAAAGACTTATAGATGACCCA
Found at i:44428 original size:243 final size:242
Alignment explanation
Indices: 43890--44561 Score: 887
Period size: 243 Copynumber: 2.8 Consensus size: 242
43880 TACTCTTCAG
* * * *
43890 AAAAATCAAT-TGGAAACATCCTGCCCGAAGGTCTTATGGGTGGCCCGAAGGACTTATCATCTTG
1 AAAAATC-ATGTGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTG
* *
43954 CTCAAAAGACTTATAGATGACCCAAAGGATTTAAACATCATGCTCAAAAGACTTACTGATAG-CC
65 CTCAAAAGACTTATAGATGACCCGAAGGATTTAAACATCATGCTCAAAAGACTTACTGATGGCCC
* * * * * * *
44018 AAAGGACGTAGTCAGTAAGAAATTTTGGAAATCATTTTCTTACTCTTCAAG--AAAAACCAATCT
130 GAAGGACTTACTCAGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAAAAAAATCAATCT
* *
44081 TCAGAAAAGGTTTAAATGAGAAACTTTAGAAATCGCTTTCTCATTTTC
195 TCAGAAAAGGTTTAAATGAGAAACTATAGAAATCACTTTCTCATTTTC
* * * * *
44129 AAAAAGT-ATGTGAAAATATCATACCCAAAGGTCTTATGGATTGCCTGAAGGACTTATCATCCTG
1 AAAAA-TCATGTGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTG
* *
44193 CTCGAAAGACTTATAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACTGATGGCCC
65 CTCAAAAGACTTATAGATGACCCGAAGGATTTAAACATCATGCTCAAAAGACTTACTGATGGCCC
* * *
44258 GAAGGACTTACTCAGTAAGAAACTTTAGAAATCACTTTCTTAATTTTCAAGAAAAAAATCATTCT
130 GAAGGACTTACTCAGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAAAAAAATCAATC-
* *
44323 TTCTGAAAA-GTTTCAAATGAGAAACTATGGAAATCACTTTCTCATTTTC
194 TTCAGAAAAGGTTT-AAATGAGAAACTATAGAAATCACTTTCTCATTTTC
* * * *
44372 AAAAATCATGTGAAAACATCTTGCTCGAAGGTTTTATGGATGGCCCGAAGGACTTATCAT-CTCA
1 AAAAATCATGTGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCT-G
* * * *
44436 CTCAAAAGACTTATATATGACCCGAAAG-TTTAAACATCATTCTCAAAAGACTTACT-ATGGCTC
65 CTCAAAAGACTTATAGATGACCCGAAGGATTTAAACATCATGCTCAAAAGACTTACTGATGGCCC
**
44499 GAAGGACTTACTGGGTAAGAAACTTTGGAAAT-AGCTTTCTTACTTTTCAAGAAAAAAATCAAT
130 GAAGGACTTACTCAGTAAGAAACTTTGGAAATCA-CTTTCTTACTTTTCAAGAAAAAAATCAAT
44562 ATTTCTTTCT
Statistics
Matches: 376, Mismatches: 47, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
238 2 0.01
239 108 0.29
240 47 0.12
241 62 0.16
242 42 0.11
243 115 0.31
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (242 bp):
AAAAATCATGTGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGC
TCAAAAGACTTATAGATGACCCGAAGGATTTAAACATCATGCTCAAAAGACTTACTGATGGCCCG
AAGGACTTACTCAGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAAAAAAATCAATCTT
CAGAAAAGGTTTAAATGAGAAACTATAGAAATCACTTTCTCATTTTC
Found at i:44578 original size:33 final size:32
Alignment explanation
Indices: 44533--44598 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
44523 TTGGAAATAG
*
44533 CTTTCTTACTTTTCAAGAAAAAAATCAATATTT
1 CTTTCTTACTTTTCAAAAAAAAAAT-AATATTT
* *
44566 CTTTCTTGCTTTTCAAAAAAAAAATAATCTTT
1 CTTTCTTACTTTTCAAAAAAAAAATAATATTT
44598 C
1 C
44599 AGAAAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 7 0.23
33 23 0.77
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.42
Consensus pattern (32 bp):
CTTTCTTACTTTTCAAAAAAAAAATAATATTT
Found at i:45125 original size:55 final size:58
Alignment explanation
Indices: 44828--45147 Score: 266
Period size: 58 Copynumber: 5.7 Consensus size: 58
44818 TTACATTTAC
* *
44828 AAAT-ATCATTAAGAAA-CCCTAAAAATTAGGCTTGGCTTCTTTAAAAA-TTCATTGG
1 AAATAATCATTAAGAAACCCCTGAAAATTAGGCTTAGCTTCTTTAAAAAGTTCATTGG
* * * * *
44883 AAATAATTATCAAAAAACCCCTGAAAA-TCGGACTTAGCTTCTTTTAAAAGTTCATTGG
1 AAATAATCATTAAGAAACCCCTGAAAATTAGG-CTTAGCTTCTTTAAAAAGTTCATTGG
* * * * * * *
44941 AAATAATCATCAAGAAATCCTTGAAAATCAGACTTAGCTTATTTTAAAAGTTCATTGG
1 AAATAATCATTAAGAAACCCCTGAAAATTAGGCTTAGCTTCTTTAAAAAGTTCATTGG
* * * * * * ** *
44999 AAATAATCATTAAGAAACACTTGGAAATTAGGGTTAGTTTC-TAAAAAACCTC-TT-C
1 AAATAATCATTAAGAAACCCCTGAAAATTAGGCTTAGCTTCTTTAAAAAGTTCATTGG
* * * * * *
45054 TAA-AAGCCTTAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAA-TTCATTTG
1 AAATAATCATTAAGAAACCCCTGAAAATTAGGCTTAGCTTCTTTAAAAAGTTCATTGG
* * *
45110 AAA-AA-AATTAAGAAACCCCTGAAAATCAAGCTTAGCTT
1 AAATAATCATTAAGAAACCCCTGAAAATTAGGCTTAGCTT
45148 TTTTCAAACT
Statistics
Matches: 209, Mismatches: 48, Indels: 16
0.77 0.18 0.06
Matches are distributed among these distances:
54 31 0.15
55 41 0.20
56 18 0.09
57 30 0.14
58 88 0.42
59 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (58 bp):
AAATAATCATTAAGAAACCCCTGAAAATTAGGCTTAGCTTCTTTAAAAAGTTCATTGG
Found at i:53606 original size:24 final size:24
Alignment explanation
Indices: 53579--53624 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
53569 TATAGGAACC
*
53579 TAAAGATAAAATATACAT-TTTATT
1 TAAACATAAAATA-ACATGTTTATT
53603 TAAACATAAAATAACATGTTTA
1 TAAACATAAAATAACATGTTTA
53625 ACTAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (24 bp):
TAAACATAAAATAACATGTTTATT
Found at i:53630 original size:24 final size:24
Alignment explanation
Indices: 53578--53630 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
53568 CTATAGGAAC
* *
53578 CTAAAGATAAAATATACATTTTAT
1 CTAAACATAAAATATACATTTTAA
*
53602 TTAAACATAAAATA-ACATGTTTAA
1 CTAAACATAAAATATACAT-TTTAA
53626 CTAAA
1 CTAAA
53631 AAAGGAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (24 bp):
CTAAACATAAAATATACATTTTAA
Found at i:62227 original size:26 final size:26
Alignment explanation
Indices: 62191--62244 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
62181 ACTAAGTGCA
*
62191 TATGGTGGGCATGACCTTATGTGTAT
1 TATGGTGGGCAAGACCTTATGTGTAT
62217 TATGGTGGGCAAGACCTTATGTGTAT
1 TATGGTGGGCAAGACCTTATGTGTAT
62243 TA
1 TA
62245 GCACTTCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.22, C:0.11, G:0.30, T:0.37
Consensus pattern (26 bp):
TATGGTGGGCAAGACCTTATGTGTAT
Found at i:63484 original size:26 final size:26
Alignment explanation
Indices: 63455--63521 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
63445 ATCATAAATC
*
63455 TATGGCGCGCATTGATGACACACATT
1 TATGACGCGCATTGATGACACACATT
* * * *
63481 TATGACTCACATTTATGACGCACATT
1 TATGACGCGCATTGATGACACACATT
63507 TATGACGCGCATTGA
1 TATGACGCGCATTGA
63522 GCGTAATTGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (26 bp):
TATGACGCGCATTGATGACACACATT
Found at i:63513 original size:13 final size:13
Alignment explanation
Indices: 63464--63519 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
63454 CTATGGCGCG
* *
63464 CATTGATGACACA
1 CATTTATGACGCA
*
63477 CATTTATGACTCA
1 CATTTATGACGCA
63490 CATTTATGACGCA
1 CATTTATGACGCA
*
63503 CATTTATGACGCG
1 CATTTATGACGCA
63516 CATT
1 CATT
63520 GAGCGTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (13 bp):
CATTTATGACGCA
Found at i:70184 original size:17 final size:17
Alignment explanation
Indices: 70158--70220 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
70148 GACCGGTTCT
70158 GACCCAACCCGTTGACC
1 GACCCAACCCGTTGACC
* *
70175 GACCCGACCCATTGACC
1 GACCCAACCCGTTGACC
*
70192 GACCCAACCCGTTTACCC
1 GACCCAACCCGTTGA-CC
*
70210 GACCCGACCCG
1 GACCCAACCCG
70221 ACCTGTTGAC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
17 27 0.69
18 12 0.31
ACGTcount: A:0.22, C:0.49, G:0.17, T:0.11
Consensus pattern (17 bp):
GACCCAACCCGTTGACC
Found at i:70412 original size:29 final size:29
Alignment explanation
Indices: 70258--70405 Score: 183
Period size: 29 Copynumber: 5.2 Consensus size: 29
70248 ATCGGGTGAC
*
70258 ATTTTGGGAATTT-ATTCG-AAATGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
* **
70285 ATTTTGGAAATTTAATTCGAAAAGGTATT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
* *
70314 ATTTTGGGAATTTAATTTGAAAAAGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
* * * *
70343 ATGTTGGGAATTTAATTCAAAAAAGTGTT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
*
70372 ATTTTTGGAATTTAATTCGAAAAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
70401 ATTTT
1 ATTTT
70406 AGTAATTATT
Statistics
Matches: 101, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
27 12 0.12
28 5 0.05
29 84 0.83
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (29 bp):
ATTTTGGGAATTTAATTCGAAAAGGTGCT
Found at i:70433 original size:58 final size:58
Alignment explanation
Indices: 70258--70436 Score: 159
Period size: 58 Copynumber: 3.1 Consensus size: 58
70248 ATCGGGTGAC
* * * * * **
70258 ATTTTGGGAATTT-ATTCG-AAATGTGCTAT-TTTGGAAATTTAATTCGAAAAGGTATT
1 ATTTTTGGAATTTAATTCGAAAAAGTGCTATGTTAGG-AATTTAATTCAAAAAAGTGCT
* * * *
70314 ATTTTGGGAATTTAATTTGAAAAAGTGCTATGTTGGGAATTTAATTCAAAAAAGTGTT
1 ATTTTTGGAATTTAATTCGAAAAAGTGCTATGTTAGGAATTTAATTCAAAAAAGTGCT
* * * * * *
70372 ATTTTTGGAATTTAATTCGAAAAGGTGCTATTTTAGTAA-TTATTTTAAAAAGGGTGCT
1 ATTTTTGGAATTTAATTCGAAAAAGTGCTATGTTAGGAATTTAATTCAAAAA-AGTGCT
70430 ATTTTTG
1 ATTTTTG
70437 TAAAATGGTT
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
56 13 0.13
57 14 0.14
58 72 0.70
59 4 0.04
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (58 bp):
ATTTTTGGAATTTAATTCGAAAAAGTGCTATGTTAGGAATTTAATTCAAAAAAGTGCT
Found at i:77476 original size:24 final size:24
Alignment explanation
Indices: 77440--77496 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
77430 CACCAAAGTG
*
77440 CCACATAG-ATTTGTCTCGAAGGA
1 CCACATAGAATTTGTCCCGAAGGA
* *
77463 TCACGTAGAATTTGTCCCGAAGGA
1 CCACATAGAATTTGTCCCGAAGGA
77487 CCACATAGAA
1 CCACATAGAA
77497 ATATCCTGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (24 bp):
CCACATAGAATTTGTCCCGAAGGA
Found at i:77648 original size:15 final size:15
Alignment explanation
Indices: 77626--77702 Score: 84
Period size: 15 Copynumber: 5.1 Consensus size: 15
77616 TCTTTTATTC
77626 CACATAGAACACTTT
1 CACATAGAACACTTT
* *
77641 CGCATAGAACATTTT
1 CACATAGAACACTTT
* * *
77656 CACGTAGATCACATT
1 CACATAGAACACTTT
77671 CACATA-AAGCACTTT
1 CACATAGAA-CACTTT
*
77686 CACATAGAACACATT
1 CACATAGAACACTTT
77701 CA
1 CA
77703 TATGAAAATA
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
14 1 0.02
15 46 0.94
16 2 0.04
ACGTcount: A:0.39, C:0.26, G:0.09, T:0.26
Consensus pattern (15 bp):
CACATAGAACACTTT
Found at i:77699 original size:30 final size:30
Alignment explanation
Indices: 77626--77702 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
77616 TCTTTTATTC
* * *
77626 CACATAGAACACTTTCGCATAGAACATTTT
1 CACATAGAACACATTCACATAGAACACTTT
* *
77656 CACGTAGATCACATTCACATA-AAGCACTTT
1 CACATAGAACACATTCACATAGAA-CACTTT
77686 CACATAGAACACATTCA
1 CACATAGAACACATTCA
77703 TATGAAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 2 0.05
30 37 0.95
ACGTcount: A:0.39, C:0.26, G:0.09, T:0.26
Consensus pattern (30 bp):
CACATAGAACACATTCACATAGAACACTTT
Found at i:78237 original size:21 final size:20
Alignment explanation
Indices: 78192--78241 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
78182 GTTACCTTTG
78192 GTATCGATACCTTCATATAA
1 GTATCGATACCTTCATATAA
*
78212 GTATCGATACTACTTCA-ATCA
1 GTATCGATAC--CTTCATATAA
78233 GTATCGATA
1 GTATCGATA
78242 ATGCTCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (20 bp):
GTATCGATACCTTCATATAA
Found at i:83827 original size:179 final size:179
Alignment explanation
Indices: 83527--83851 Score: 641
Period size: 179 Copynumber: 1.8 Consensus size: 179
83517 ACGGGGCAGG
83527 CTATTTCCCTCCTGTCCATCTCCTGCTTCACTTCGGGAGCCCTAGTAGTCCGAAATATATTAAGA
1 CTATTTCCCTCCTGTCCATCTCCTGCTTCACTTCGGGAGCCCTAGTAGTCCGAAATATATTAAGA
83592 TACAATCACTAATTATATAAACAATGACAACATACCAATTACCCTATTAGATAAGAGATTTTTAA
66 TACAATCACTAATTATATAAACAATGACAACATACCAATTACCCTATTAGATAAGAGATTTTTAA
83657 CTTTTCATTGACATGTTCATCACCTTTCCTAATCGGGGCAGGTGAATTA
131 CTTTTCATTGACATGTTCATCACCTTTCCTAATCGGGGCAGGTGAATTA
*
83706 CTATTTCCCTCCTGTCCATCTCCTGCTTCACTTCGGGAGCCCTAGTAGTCCGACATATATTAAGA
1 CTATTTCCCTCCTGTCCATCTCCTGCTTCACTTCGGGAGCCCTAGTAGTCCGAAATATATTAAGA
83771 TACAATCACTAATTATATAAACAATGACAACATACCAATTACCCTATTAGATAAGAGATTTTTAA
66 TACAATCACTAATTATATAAACAATGACAACATACCAATTACCCTATTAGATAAGAGATTTTTAA
83836 CTTTTCATTGACATGT
131 CTTTTCATTGACATGT
83852 ACACTTTTTA
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 145 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (179 bp):
CTATTTCCCTCCTGTCCATCTCCTGCTTCACTTCGGGAGCCCTAGTAGTCCGAAATATATTAAGA
TACAATCACTAATTATATAAACAATGACAACATACCAATTACCCTATTAGATAAGAGATTTTTAA
CTTTTCATTGACATGTTCATCACCTTTCCTAATCGGGGCAGGTGAATTA
Found at i:84656 original size:23 final size:23
Alignment explanation
Indices: 84613--84657 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
84603 GTGTTGAATT
*
84613 TGTCCTAAAGGACCACGTAGAAA
1 TGTCCTAAAGGACCACATAGAAA
* *
84636 TGTCCTGAAGGACCGCATAGAA
1 TGTCCTAAAGGACCACATAGAA
84658 CCCTTAGCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (23 bp):
TGTCCTAAAGGACCACATAGAAA
Done.