Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008675.1 Hibiscus syriacus cultivar Beakdansim tig00111691_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: 97836
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:241 original size:22 final size:23
Alignment explanation
Indices: 213--269 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
203 AATATACCAT
213 TACCTATTACATTATA-AAACGA
1 TACCTATTACATTATATAAACGA
** *
235 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
258 TACCTATTACAT
1 TACCTATTACAT
270 CTATGTTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:647 original size:21 final size:20
Alignment explanation
Indices: 622--673 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
612 GATAGACACT
*
622 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
643 TTACATTATAAACGATACCTA
1 TTACATTAT-AACCATACCTA
664 TTACATTATA
1 TTACATTATA
674 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:684 original size:23 final size:22
Alignment explanation
Indices: 627--697 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 22
617 ACACTTTACA
*
627 ATATAACCATTACCTATTACATT
1 ATATAACGA-TACCTATTACATT
650 ATA-AACGATACCTATTACATT
1 ATATAACGATACCTATTACATT
* * *
671 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGATACCTATTACATT
694 ATAT
1 ATAT
698 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.38
22 6 0.14
23 20 0.48
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (22 bp):
ATATAACGATACCTATTACATT
Found at i:1042 original size:20 final size:20
Alignment explanation
Indices: 1009--1047 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
999 TCCACAGTGA
* * *
1009 AAAAAGTATGGACATTTTAT
1 AAAAAGGATAGACACTTTAT
1029 AAAAAGGATAGACACTTTA
1 AAAAAGGATAGACACTTTA
1048 CAATATAACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (20 bp):
AAAAAGGATAGACACTTTAT
Found at i:1112 original size:23 final size:22
Alignment explanation
Indices: 1050--1121 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
1040 ACACTTTACA
*
1050 ATATAACCATTACCTATTACATT
1 ATATAACGA-TACCTATTACATT
1073 ATATAACGATACCTATTACATT
1 ATATAACGATACCTATTACATT
* * *
1095 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGATACCTATTACATT
1118 ATAT
1 ATAT
1122 GTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 19 0.43
23 25 0.57
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (22 bp):
ATATAACGATACCTATTACATT
Found at i:1499 original size:21 final size:20
Alignment explanation
Indices: 1469--1520 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
1459 GATAGACACT
*
1469 TTACAATATAACAATTACCTA
1 TTACATTATAACAA-TACCTA
*
1490 TTACATTATAAACGATACCTA
1 TTACATTAT-AACAATACCTA
1511 TTACATTATA
1 TTACATTATA
1521 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACAATACCTA
Found at i:1531 original size:23 final size:22
Alignment explanation
Indices: 1474--1544 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 22
1464 ACACTTTACA
*
1474 ATATAACAATTACCTATTACATT
1 ATATAACGA-TACCTATTACATT
1497 ATA-AACGATACCTATTACATT
1 ATATAACGATACCTATTACATT
* * *
1518 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGATACCTATTACATT
1541 ATAT
1 ATAT
1545 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.38
22 6 0.14
23 20 0.48
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (22 bp):
ATATAACGATACCTATTACATT
Found at i:1961 original size:23 final size:22
Alignment explanation
Indices: 1899--1970 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
1889 ACACTTTACA
*
1899 ATATAACCATTACCTATTACATT
1 ATATAACGA-TACCTATTACATT
1922 ATATAACGATACCTATTACATT
1 ATATAACGATACCTATTACATT
* * *
1944 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGATACCTATTACATT
1967 ATAT
1 ATAT
1971 GTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 19 0.43
23 25 0.57
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (22 bp):
ATATAACGATACCTATTACATT
Found at i:2009 original size:425 final size:430
Alignment explanation
Indices: 3--3340 Score: 6235
Period size: 424 Copynumber: 7.9 Consensus size: 430
1 AC
*
3 TTATTTGATTGTTTTGATATTTTAT-AAATATTATTTAGATTTTTTAATTT-A-AAT-A-ATATA
1 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATA
63 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
66 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
128 AAAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAGTATGGACACTTTTATAAAAAGGAT
131 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
*
192 AGACACTTTACAATAT-ACCATTACCTATTACATTATAAAACGATACCTATTACATTATATAAGG
196 AGACACTTTACAATATAACCATTACCTATTACATTATATAACGATACCTATTACATTATATAAGG
256 GCTACCTATTACATC-TATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGAT
261 GCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGAT
320 CGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCC
326 CGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCC
385 ACCTACAATATTGATTTAATAATTTCATTTGCAC-AAAAA
391 ACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAA
424 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAAT-A-ATATA
1 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATA
487 CCGTAACGT-AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
66 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
551 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTAT-AAAAGGAT
131 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
615 AGACACTTTACAATATAACCATTACCTATTACATTATA-AACGATACCTATTACATTATATAAGG
196 AGACACTTTACAATATAACCATTACCTATTACATTATATAACGATACCTATTACATTATATAAGG
679 GCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGAT
261 GCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGAT
744 CGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCC
326 CGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCC
809 ACCTACAATATTGATTTAATAATTTCATTTGCAC-AAAAA
391 ACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAA
848 TTATTTGATTG-TTTGATA-TTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATA
1 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATA
911 CCGTAACGT-AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
66 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
975 AAAAGATAACCTTAAATT-ATGTTTTCCACAGTGAAAAAAGTATGGACA-TTTTATAAAAAGGAT
131 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
1038 AGACACTTTACAATATAACCATTACCTATTACATTATATAACGATACCTATTACATTATATAAGG
196 AGACACTTTACAATATAACCATTACCTATTACATTATATAACGATACCTATTACATTATATAAGG
1103 GCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGAT
261 GCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGAT
1168 CGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAA-TTTTTTAACAGTGTTTCATGTTTTCC
326 CGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCC
1232 -CCTACAATATTGATTTAATAATTTCATTTGCACAAAAAA
391 ACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAA
1271 TTATTTGATTGTTTTGATATTTTAT-AAATATTATTTAGAATTTTTAATTTAATAAT-A-ATATA
1 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATA
1333 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
66 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
1398 -AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
131 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
*
1462 AGACACTTTACAATATAACAATTACCTATTACATTATA-AACGATACCTATTACATTATATAAGG
196 AGACACTTTACAATATAACCATTACCTATTACATTATATAACGATACCTATTACATTATATAAGG
1526 GCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGAT
261 GCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGAT
1591 CGATAC-TTTTTTAAAACTTATGT-ATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCC
326 CGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCC
1654 ACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAA
391 ACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAA
1694 TTATTTGA-TGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATA
1 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATA
1758 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTT-AAACTCACTC
66 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
1822 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
131 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
1887 AGACACTTTACAATATAACCATTACCTATTACATTATATAACGATACCTATTACATTATATAAGG
196 AGACACTTTACAATATAACCATTACCTATTACATTATATAACGATACCTATTACATTATATAAGG
1952 GCTACCTATTACATCATATGTTTACCTATTATA-TGAAAGTGTCCATACTTTTTATAAAAAGGAT
261 GCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGAT
2016 CGATAC-TTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAAACAGTGTTTCATGTTTTC
326 CGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTT-AACAGTGTTTCATGTTTTC
2080 CACCTACAATATTGATTTAATAATTTCATTTGCAC-AAAAA
390 CACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAA
2120 TTA-TTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATA
1 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATA
2184 CCGTAACGT-AAAAATAAATCATTAGACGCCTATAATTACT-AATTAATATCTTAAAACTCACTC
66 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
2247 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
131 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
2312 AGACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAG
196 AGACACTTTACAATATAACCATTACCTATTACATTATAT-AACGATACCTATTACATTATATAAG
2377 GGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
260 GGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
2442 TCGATACTTTTTTTAAAAC-TATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTC-TGTTTTC
325 TCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTC
2505 CACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAA
390 CACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAA
2546 TTATTTGA-TGTTTTGATATTTTAT-AAATATTATTTAGAATTTTTAATTTAATAATAATATATA
1 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATA
2609 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT-AATTAATATCTTAAAACTCACTC
66 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
2673 -AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
131 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
2737 AGACACTTTACAATA-AACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAG
196 AGACACTTTACAATATAACCATTACCTATTACATTATAT-AACGATACCTATTACATTATATAAG
2801 GGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTAT-AAAAGGA
260 GGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
2865 TCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTC
325 TCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTC
2930 CACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAA
390 CACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAA
2971 TTA-TTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAAT-ATAATATATA
1 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATA
3034 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
66 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
3099 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
131 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
3164 AGACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACA-T-TATAAG
196 AGACACTTTACAATATAACCATTACCTATTACATTATAT-AACGATACCTATTACATTATATAAG
3227 GGCTACCTATTA-ATCATATGTTTACCTA-T-TATTGAAAGTGTCCATACTTTTTAT-AAAAGGA
260 GGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
3288 TCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAA-TTTTTTAACAGTGT
325 TCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGT
3341 ACTGCGAATT
Statistics
Matches: 2874, Mismatches: 3, Indels: 79
0.97 0.00 0.03
Matches are distributed among these distances:
421 38 0.01
422 204 0.07
423 639 0.22
424 701 0.24
425 671 0.23
426 369 0.13
427 201 0.07
428 51 0.02
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (430 bp):
TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATA
CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
AGACACTTTACAATATAACCATTACCTATTACATTATATAACGATACCTATTACATTATATAAGG
GCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGAT
CGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCC
ACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAA
Found at i:2349 original size:21 final size:20
Alignment explanation
Indices: 2319--2372 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
2309 GATAGACACT
*
2319 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
2340 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
2363 TTACATTATA
1 TTACATTATA
2373 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:2360 original size:23 final size:23
Alignment explanation
Indices: 2334--2396 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2324 ATATAACCAT
2334 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
2357 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
2380 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2397 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2786 original size:23 final size:23
Alignment explanation
Indices: 2749--2820 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
2739 ACACTTTACA
*
2749 ATAAACCATTACCTATTACATTAT
1 ATAAACGA-TACCTATTACATTAT
2773 ATAAACGATACCTATTACATTAT
1 ATAAACGATACCTATTACATTAT
** * *
2796 ATAAGGGCTACCTATTACATCAT
1 ATAAACGATACCTATTACATTAT
2819 AT
1 AT
2821 GTTTACCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 36 0.84
24 7 0.16
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (23 bp):
ATAAACGATACCTATTACATTAT
Found at i:3201 original size:21 final size:20
Alignment explanation
Indices: 3171--3225 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 20
3161 GATAGACACT
*
3171 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
3192 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
3215 TTACATTATAA
1 TTACATTATAA
3226 GGGCTACCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
20 2 0.07
21 8 0.28
22 1 0.03
23 14 0.48
24 4 0.14
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:6319 original size:183 final size:183
Alignment explanation
Indices: 5791--6454 Score: 1223
Period size: 183 Copynumber: 3.7 Consensus size: 183
5781 TTTTAAATGG
*
5791 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
5856 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTT-C
65 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
5920 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
130 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
5974 TATGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT
1 TATGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT
6039 AAGACCGG--TA--TATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCG
66 AAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCG
6100 ATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 ATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
6153 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
6218 TAAGACC-GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
65 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
6282 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
130 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
6336 TATGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT
1 TATGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT
**
6401 AAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 AAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
6455 ATGTTGAAAG
Statistics
Matches: 469, Mismatches: 5, Indels: 14
0.96 0.01 0.03
Matches are distributed among these distances:
178 48 0.10
179 84 0.18
180 45 0.10
181 2 0.00
182 86 0.18
183 204 0.43
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (183 bp):
TATGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT
AAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCG
ATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
Found at i:7825 original size:3 final size:3
Alignment explanation
Indices: 7817--7867 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
7807 ACTTGTTTGG
* * * *
7817 ATC ATC ATC TTC ATC ATC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
7865 ATC
1 ATC
7868 GTCAGCTTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:7834 original size:12 final size:12
Alignment explanation
Indices: 7817--7879 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
7807 ACTTGTTTGG
7817 ATCATCATCTTC
1 ATCATCATCTTC
*
7829 ATCATCATCGTC
1 ATCATCATCTTC
*
7841 ATCATCATCATC
1 ATCATCATCTTC
*
7853 ATCGTCATCTTC
1 ATCATCATCTTC
* *
7865 ATCGTCAGCTTC
1 ATCATCATCTTC
7877 ATC
1 ATC
7880 TTCTGCGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.37
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:7878 original size:18 final size:18
Alignment explanation
Indices: 7821--7882 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
7811 GTTTGGATCA
7821 TCATCTTCATCATCATCG
1 TCATCTTCATCATCATCG
*
7839 TCATCATCATCATCATCG
1 TCATCTTCATCATCATCG
* * *
7857 TCATCTTCATCGTCAGCT
1 TCATCTTCATCATCATCG
7875 TCATCTTC
1 TCATCTTC
7883 TGCGACCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCATCATCG
Found at i:7882 original size:6 final size:6
Alignment explanation
Indices: 7821--7882 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
7811 GTTTGGATCA
* * * * * *
7821 TCATCT TCATCA TCATCG TCATCA TCATCA TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
7869 TCAGCT TCATCT TC
1 TCATCT TCATCT TC
7883 TGCGACCGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:10025 original size:200 final size:199
Alignment explanation
Indices: 9345--10562 Score: 2137
Period size: 200 Copynumber: 6.1 Consensus size: 199
9335 TTTAAATTAG
* *
9345 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
9410 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
9474 CGACAC-TTTTTATATATGGATCGACACTTTATTGATTCACCTTG-TAAAATTCATTCT-GGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTAAAATTCATTCTGGGAAA
9536 AAAA
196 AAAA
9540 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
9605 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * * *
9670 CGACAC-TTTTTATATATGGATCGACACTTTATTGATTCACCTCGTAAAAATTCATTCT-GGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTAAAATTCATTCTGGGAAA
9733 AAAA
196 AAAA
9737 TATCGACACAAACTATATTAGTGTCGACACA-TATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
9801 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* **
9866 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTG-TTAAAATTCATTCTGGGAA
9931 AAAAA
195 AAAAA
9936 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
10001 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* **
10066 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGG-A
131 CGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTG-TTAAAATTCATTCTGGGAA
10130 AAAAA
195 AAAAA
10135 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
10200 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* **
10265 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTG-TTAAAATTCATTCTGGGAA
10330 AAAAA
195 AAAAA
10335 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
10400 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *
10465 CGACACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTAAAATTCATTCTGGGAAA
10530 AAAA
196 AAAA
*
10534 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
10563 TGACCCTTAA
Statistics
Matches: 996, Mismatches: 20, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
195 119 0.12
196 154 0.15
197 86 0.09
198 11 0.01
199 287 0.29
200 339 0.34
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTAAAATTCATTCTGGGAAA
AAAA
Found at i:10307 original size:399 final size:398
Alignment explanation
Indices: 9345--10562 Score: 2207
Period size: 399 Copynumber: 3.1 Consensus size: 398
9335 TTTAAATTAG
* *
9345 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
9410 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * * **
9474 CGACAC-TTTTTATATATGGATCGACACTTTATTGATTCACCTTG--TAAAATTCATTCT-GGAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
9535 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
196 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
9600 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
261 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
* *
9665 GGGATCGACAC-TTTTTATATATGGATCGACACTTTATTGATTCACCTCGTAAAAATTCATTCTG
326 GGGATCGACACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTG
9729 GAAAAAAA
391 GAAAAAAA
9737 TATCGACACAAACTATATTAGTGTCGACACA-TATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
9801 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
9866 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
9931 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
196 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
*
9996 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
261 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
* * ***
10061 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
326 GGGATCGACACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCT
*
10126 GGGAAAAAA
390 GGAAAAAAA
10135 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
10200 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
10265 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
10330 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
196 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
10395 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
261 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
10460 GGGATCGACACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTG
326 GGGATCGACACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTG
10525 GAAAAAAAA
391 G-AAAAAAA
*
10534 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
10563 TGACCCTTAA
Statistics
Matches: 792, Mismatches: 25, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
391 87 0.11
392 44 0.06
393 35 0.04
395 11 0.01
396 144 0.18
397 34 0.04
398 63 0.08
399 374 0.47
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (398 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
GGGATCGACACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTG
GAAAAAAA
Found at i:10669 original size:37 final size:38
Alignment explanation
Indices: 10628--10707 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
10618 TCTCATTCAT
*
10628 AATTAT-ATTCACATAAAAAAATATAAATCGTATACAA
1 AATTATAAATCACATAAAAAAATATAAATCGTATACAA
** * * *
10665 AATTATAAATCGTATACAAAATTATAAATCTTATACAA
1 AATTATAAATCACATAAAAAAATATAAATCGTATACAA
10703 AATTA
1 AATTA
10708 ACTCGACATT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 6 0.17
38 30 0.83
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (38 bp):
AATTATAAATCACATAAAAAAATATAAATCGTATACAA
Found at i:10671 original size:19 final size:19
Alignment explanation
Indices: 10644--10707 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
10634 ATTCACATAA
*
10644 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
10663 AAAATTATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
10682 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
10701 AAAATTA
1 AAAATTA
10708 ACTCGACATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:12537 original size:33 final size:33
Alignment explanation
Indices: 12500--12565 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
12490 CATCTTAATA
*
12500 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
12533 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
12566 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:14712 original size:24 final size:24
Alignment explanation
Indices: 14675--14727 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
14665 CCGTTCTATC
14675 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
14699 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
14723 TATTT
1 TATTT
14728 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:14918 original size:20 final size:19
Alignment explanation
Indices: 14872--14918 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
14862 TCCGGTATCA
*
14872 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
14891 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
14912 TTTTACC
1 TTTTACC
14919 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:15082 original size:20 final size:20
Alignment explanation
Indices: 15034--15083 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
15024 TCGACACTTT
15034 TAATTTTACCGGTTTTATCA
1 TAATTTTACCGGTTTTATCA
*
15054 T-TTTGTTACCGGTTTTATCA
1 TAATT-TTACCGGTTTTATCA
15074 TAATTTTACC
1 TAATTTTACC
15084 TGGTATATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52
Consensus pattern (20 bp):
TAATTTTACCGGTTTTATCA
Found at i:24208 original size:16 final size:17
Alignment explanation
Indices: 24182--24224 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
24172 ATAGATTATC
24182 AATTGAAAATATA-AAAA
1 AATT-AAAATATATAAAA
*
24199 AATTAAAATATATAATA
1 AATTAAAATATATAAAA
*
24216 ATTTAAAAT
1 AATTAAAAT
24225 TTTCAGGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AATTAAAATATATAAAA
Found at i:24221 original size:17 final size:16
Alignment explanation
Indices: 24182--24224 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
24172 ATAGATTATC
*
24182 AATTGAAAATATAAAA
1 AATTTAAAATATAAAA
* *
24198 AAATTAAAATATATAAT
1 AATTTAAAATATA-AAA
24215 AATTTAAAAT
1 AATTTAAAAT
24225 TTTCAGGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AATTTAAAATATAAAA
Found at i:27176 original size:23 final size:23
Alignment explanation
Indices: 27150--27197 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
27140 ATAAAGTACA
*
27150 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
27173 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
27196 AT
1 AT
27198 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:27479 original size:25 final size:25
Alignment explanation
Indices: 27451--27501 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
27441 TTAATCCAAA
*
27451 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
27476 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
27501 T
1 T
27502 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:27795 original size:21 final size:22
Alignment explanation
Indices: 27770--27821 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
27760 ACACTTTACA
*
27770 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
27793 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
27816 ATATAA
1 ATATAA
27822 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:27806 original size:23 final size:23
Alignment explanation
Indices: 27780--27842 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
27770 ATATAACCAC
27780 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
27803 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
27826 TACCTATTACATCATAT
1 TACCTATTACATTATAT
27843 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:28226 original size:21 final size:22
Alignment explanation
Indices: 28201--28252 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
28191 ACACTTTACA
*
28201 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
28224 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
28247 ATATAA
1 ATATAA
28253 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:28237 original size:23 final size:23
Alignment explanation
Indices: 28211--28273 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
28201 ATATAACCAC
28211 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
28234 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
28257 TACCTATTACATCATAT
1 TACCTATTACATTATAT
28274 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:28658 original size:23 final size:22
Alignment explanation
Indices: 28631--28682 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
28621 ACACTTTACA
*
28631 ATATAACCACTACCTATTATATT
1 ATATAACCA-TACCTATTACATT
*
28654 ATATAAACGATACCTATTACATT
1 ATAT-AACCATACCTATTACATT
28677 ATATAA
1 ATATAA
28683 GGGGTACCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.08
23 20 0.77
24 4 0.15
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (22 bp):
ATATAACCATACCTATTACATT
Found at i:28690 original size:23 final size:23
Alignment explanation
Indices: 28641--28703 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
28631 ATATAACCAC
*
28641 TACCTATTATATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
28664 TACCTATTACATTATATAAGGGG
1 TACCTATTACATTATATAAACGA
*
28687 TACCTATTACATCATAT
1 TACCTATTACATTATAT
28704 GTTTACCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:28794 original size:430 final size:431
Alignment explanation
Indices: 27533--28802 Score: 2434
Period size: 431 Copynumber: 2.9 Consensus size: 431
27523 TTTGAATTAT
* *
27533 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
1 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTAT
*
27598 TTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTATACGCCTATA
66 TTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATA
*
27663 ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAATCTTAAATTAATGTTTTCCACAGTGA
131 ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
27728 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATT
196 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATT
27793 ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
261 ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
27858 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTT
326 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTT
27923 TCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA
391 TCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA
27964 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTAT
1 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTAT
*
28029 TTAGAATTTTTAATTTAATAATAATATATAACGTAACGTAAAAAATAAATCATTAGACGCCTATA
66 TTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATA
*
28094 ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATATTTTCCACAGTGA
131 ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
28159 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATT
196 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATT
28224 ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
261 ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
28289 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTT
326 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTT
28354 TCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA
391 TCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA
*
28395 TTGATTTAATAATTTTATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTAT
1 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTAT
*
28460 TTAGAA-TTTTAATTTAATAATAATATATATCGTAACGTAAGAAATAAATCATTAGACGCCTATA
66 TTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATA
*
28524 ATTACTAAATTAATATCTTAAAACTCACTCAAAGGATAACCTTAAATTAATGTTTTCCACAGTGA
131 ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
*
28589 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTATATT
196 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATT
*
28654 ATATAAACGATACCTATTACATTATATAAGGGGTACCTATTACATCATATGTTTACCTATTATAT
261 ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
28719 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTT
326 TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTT
28784 TCAATTTTTTTAACAGTGT
391 TCAATTTTTTTAACAGTGT
28803 ACTGTGAATT
Statistics
Matches: 826, Mismatches: 13, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
430 331 0.40
431 495 0.60
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.40
Consensus pattern (431 bp):
TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTAT
TTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATA
ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
AAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATT
ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTT
TCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA
Found at i:31858 original size:22 final size:23
Alignment explanation
Indices: 31827--31869 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
31817 TTCCACAGTG
31827 AAAAAAGTATCGACAC-TTTTAT
1 AAAAAAGTATCGACACATTTTAT
*
31849 AAAAAGGTATCGACACATTTT
1 AAAAAAGTATCGACACATTTT
31870 TATACCGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (23 bp):
AAAAAAGTATCGACACATTTTAT
Found at i:32439 original size:183 final size:183
Alignment explanation
Indices: 31865--32557 Score: 1223
Period size: 183 Copynumber: 3.8 Consensus size: 183
31855 GTATCGACAC
31865 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
31930 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
31995 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
32048 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
32113 TGTCGACACTTTTTTAAATGGTATCGACACA-TTTTCTTCCAATCTGAACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
*
32177 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAATCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
*
32230 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
*
32295 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
*
32360 AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
* *
32413 ATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTTTTTT
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATG---TGT
* * * * *
32478 CAA--TCGACAC-TTTTTAAATGGTATCGACACATTTTTCTTTCATTCTGGACATAAAGTACAGA
63 AAATGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGA
*
32540 CACAATATTAAAAAGTGT
128 CACAATATTAGAAAGTGT
32558 GAAAACTTTG
Statistics
Matches: 493, Mismatches: 13, Indels: 8
0.96 0.03 0.02
Matches are distributed among these distances:
182 180 0.37
183 302 0.61
184 7 0.01
186 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
Found at i:33764 original size:3 final size:3
Alignment explanation
Indices: 33756--33827 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
33746 ACTTGTTTGG
* * * **
33756 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
33804 AGC TTC ATC GTC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC
33828 TGTTAAAAGA
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.25, C:0.35, G:0.06, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:35598 original size:198 final size:198
Alignment explanation
Indices: 35260--36231 Score: 1881
Period size: 198 Copynumber: 4.9 Consensus size: 198
35250 TATTTAAATT
35260 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
*
35325 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTGGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
35390 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
35455 AAA
196 AAA
35458 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
*
35523 TAATTGTACTGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
35588 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
35653 AAA
196 AAA
*
35656 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTG
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
35721 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
35786 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
35851 AAA
196 AAA
35854 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
35919 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
35984 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTCTGGGA
36049 AAAA
195 AAAA
36053 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
36118 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
* *
36183 ATTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
131 ATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
36232 GGCCATATTG
Statistics
Matches: 765, Mismatches: 7, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
198 567 0.74
199 161 0.21
200 37 0.05
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (198 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
AAA
Found at i:36396 original size:19 final size:19
Alignment explanation
Indices: 36350--36398 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
36340 TTATATTCAC
*
36350 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
36369 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
36388 ATACAAAATTA
1 ATACAAAATTA
36399 ACTCGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:38228 original size:33 final size:33
Alignment explanation
Indices: 38191--38256 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
38181 CATCTTAATA
*
38191 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
38224 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
38257 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:38330 original size:21 final size:21
Alignment explanation
Indices: 38290--38354 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
38280 CCCCTTATTC
* *
38290 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
38311 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
38332 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
38353 CT
1 CT
38355 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:40643 original size:20 final size:19
Alignment explanation
Indices: 40587--40634 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
40577 ATCTGGTATC
40587 ATTTTACCGGTTTTATCAT
1 ATTTTACCGGTTTTATCAT
*
40606 TTTGTTACCGGTTTTATCAT
1 ATT-TTACCGGTTTTATCAT
40626 AATTTTACC
1 -ATTTTACC
40635 TGTTATATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.84
21 2 0.08
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (19 bp):
ATTTTACCGGTTTTATCAT
Found at i:40781 original size:20 final size:20
Alignment explanation
Indices: 40755--40800 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
40745 CACTTTTAAA
40755 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
40774 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
40795 TTTACC
1 TTTACC
40801 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:42552 original size:18 final size:19
Alignment explanation
Indices: 42517--42553 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
42507 CACGGAATGT
42517 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GGGAATAA
42537 AAGATTATCA-GGGAATA
1 AAGATTATCAGGGGAATA
42554 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGGGAATAA
Found at i:42732 original size:37 final size:37
Alignment explanation
Indices: 42698--42767 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
42688 TACAAATTGT
42698 AAAATATTTATAT-ATTTTCTT-TAAAAAATTAAATTC
1 AAAATATTTATATAATTTT-TTCTAAAAAATTAAATTC
* *
42734 ATAATATTTATATAATTTTTTCTACAAAATTAAA
1 AAAATATTTATATAATTTTTTCTAAAAAATTAAA
42768 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 14 0.47
37 16 0.53
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (37 bp):
AAAATATTTATATAATTTTTTCTAAAAAATTAAATTC
Found at i:43916 original size:20 final size:20
Alignment explanation
Indices: 43886--43923 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
43876 CCGTCCCCGA
43886 ACCCGACCCG-AAATATTAT
1 ACCCGACCCGAAAATATTAT
43905 ACCCGAACCCGAAAATATT
1 ACCCG-ACCCGAAAATATT
43924 TTATATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.39, C:0.32, G:0.11, T:0.18
Consensus pattern (20 bp):
ACCCGACCCGAAAATATTAT
Found at i:43956 original size:25 final size:25
Alignment explanation
Indices: 43928--43982 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
43918 AATATTTTAT
43928 ATATAAT-TAACATAAAAAATATAAA
1 ATATAATAT-ACATAAAAAATATAAA
* * **
43953 ATATTATATATATAATTAATATAAA
1 ATATAATATACATAAAAAATATAAA
43978 ATATA
1 ATATA
43983 TAAAATATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATAATATACATAAAAAATATAAA
Found at i:43963 original size:34 final size:34
Alignment explanation
Indices: 43916--44000 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 34
43906 CCCGAACCCG
*
43916 AAAATATTTTATATATAATTAACATAAAAAATAT
1 AAAATATTATATATATAATTAACATAAAAAATAT
* *
43950 AAAATATTATATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAACATAAAAAATAT
43984 AAAATATTATATATATA
1 AAAATATTATATATATA
44001 TAATCGGGGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAACATAAAAAATAT
Found at i:43999 original size:18 final size:18
Alignment explanation
Indices: 43946--44003 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
43936 AACATAAAAA
43946 ATATAAAATATTATATAT
1 ATATAAAATATTATATAT
* *
43964 ATA-ATTAATA-TA-AAAT
1 ATATA-AAATATTATATAT
43980 ATATAAAATATTATATAT
1 ATATAAAATATTATATAT
43998 ATATAA
1 ATATAA
44004 TCGGGGCGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 10 0.31
17 6 0.19
18 16 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAAAATATTATATAT
Found at i:53847 original size:38 final size:41
Alignment explanation
Indices: 53790--53885 Score: 128
Period size: 38 Copynumber: 2.4 Consensus size: 41
53780 TTAACGGAAT
* *
53790 TCTGAGTTGTCAATTAAAAA-A-TATAAAAAATTGAGA-AA-
1 TCTGAGTTATCAATAAAAAATATTATAAAAAATTG-GATAAG
*
53828 TCTGAGTTATTAATAAAAAATATTATAAAAAATTGGATAAG
1 TCTGAGTTATCAATAAAAAATATTATAAAAAATTGGATAAG
53869 TCTGAGTTATCAATAAA
1 TCTGAGTTATCAATAAA
53886 TTTTTTAACA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
38 17 0.34
39 3 0.06
40 14 0.28
41 16 0.32
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.32
Consensus pattern (41 bp):
TCTGAGTTATCAATAAAAAATATTATAAAAAATTGGATAAG
Found at i:57378 original size:15 final size:15
Alignment explanation
Indices: 57358--57392 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
57348 AGCAAGGCTC
*
57358 TTCGAGTGATGCTTG
1 TTCGAGTGAAGCTTG
*
57373 TTCGAGTGAAGTTTG
1 TTCGAGTGAAGCTTG
57388 TTCGA
1 TTCGA
57393 ATGGTGAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.40
Consensus pattern (15 bp):
TTCGAGTGAAGCTTG
Found at i:77546 original size:16 final size:16
Alignment explanation
Indices: 77525--77558 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
77515 TTACTATTCA
*
77525 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
77541 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
77557 CG
1 CG
77559 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:83327 original size:15 final size:15
Alignment explanation
Indices: 83307--83343 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
83297 ATATTTAGCT
* *
83307 GGGCGGGCGGATGTG
1 GGGCGGGCGAATGCG
83322 GGGCGGGCGAATGCG
1 GGGCGGGCGAATGCG
83337 GGGCGGG
1 GGGCGGG
83344 TAAGGTCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.16, G:0.68, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGAATGCG
Found at i:95201 original size:17 final size:18
Alignment explanation
Indices: 95179--95215 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
95169 TCTTATGCAC
95179 ATCAATA-GT-TTTATCAG
1 ATCAATATGTCTTT-TCAG
95196 ATCAATATGTCTTTTCAG
1 ATCAATATGTCTTTTCAG
95214 AT
1 AT
95216 TTATTAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (18 bp):
ATCAATATGTCTTTTCAG
Found at i:97048 original size:15 final size:16
Alignment explanation
Indices: 96999--97053 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 16
96989 AATTTAAAAT
96999 TAAAATAAATTAATTGTA
1 TAAAAT-AATTAATT-TA
* *
97017 T-AAATAATTTATGTA
1 TAAAATAATTAATTTA
97032 TAAAATAA-TAATTTA
1 TAAAATAATTAATTTA
*
97047 TATAATA
1 TAAAATA
97054 TTTAGCCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 14 0.45
16 12 0.39
17 4 0.13
18 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
TAAAATAATTAATTTA
Found at i:97542 original size:20 final size:21
Alignment explanation
Indices: 97496--97542 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
97486 TAGGGTTCAT
*
97496 GAGTTTAGGGTTTATAATGTA
1 GAGTTTAGGGTTTAAAATGTA
*
97517 -AGGTTTA-GGTTTAAAATTTA
1 GA-GTTTAGGGTTTAAAATGTA
97537 GAGTTT
1 GAGTTT
97543 GAAGTGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.45
Consensus pattern (21 bp):
GAGTTTAGGGTTTAAAATGTA
Done.