Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000101.1 Hibiscus syriacus cultivar Beakdansim tig00000185_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: 67852
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4309 original size:19 final size:20
Alignment explanation
Indices: 4268--4319 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
4258 TGCCAAGCCC
*
4268 TCAGTTTCGATACCGACCCA
1 TCAGTATCGATACCGACCCA
4288 TCAGTATCGATACCGA-CCA
1 TCAGTATCGATACCGACCCA
4307 TCAGTATCGATAC
1 TCAGTATCGATAC
4320 TTTTAAGTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (20 bp):
TCAGTATCGATACCGACCCA
Found at i:14082 original size:18 final size:18
Alignment explanation
Indices: 14043--14084 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
14033 GATTTTTAAG
* *
14043 TAAATTAATTTATAATCA
1 TAAATTAAATTATAATAA
*
14061 -AAATTAAATTATTATAA
1 TAAATTAAATTATAATAA
14078 TAAATTA
1 TAAATTA
14085 TACAAAACGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAATTAAATTATAATAA
Found at i:14183 original size:42 final size:42
Alignment explanation
Indices: 14136--14221 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
14126 ATCAAAATAT
14136 AACTGAAAATAATATAAATATATCATAGATATAGAATAATCC
1 AACTGAAAATAATATAAATATATCATAGATATAGAATAATCC
*
14178 AACTGAAAATAATATAAATATGTCATAGATATAGAATAATCC
1 AACTGAAAATAATATAAATATATCATAGATATAGAATAATCC
14220 AA
1 AA
14222 TATGTACATT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (42 bp):
AACTGAAAATAATATAAATATATCATAGATATAGAATAATCC
Found at i:19048 original size:19 final size:19
Alignment explanation
Indices: 19024--19061 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19014 CATAATTAGC
* *
19024 ATCGACGTTTTGTTTCCTT
1 ATCGACGGTGTGTTTCCTT
19043 ATCGACGGTGTGTTTCCTT
1 ATCGACGGTGTGTTTCCTT
19062 CTTTTGCAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (19 bp):
ATCGACGGTGTGTTTCCTT
Found at i:27915 original size:19 final size:19
Alignment explanation
Indices: 27863--27915 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
27853 TCCGTATACA
27863 ATTATTTAAAATTAAATAGAT
1 ATTATTTAAAA-TAAATA-AT
27884 A-T-TTT--AA-AAATAAT
1 ATTATTTAAAATAAATAAT
27898 ATTATTTAAAATAAATAA
1 ATTATTTAAAATAAATAA
27916 ATAATATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
14 3 0.11
15 6 0.22
16 3 0.11
17 2 0.07
18 2 0.07
19 9 0.33
20 1 0.04
21 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTATTTAAAATAAATAAT
Found at i:27957 original size:22 final size:24
Alignment explanation
Indices: 27891--27958 Score: 88
Period size: 26 Copynumber: 2.9 Consensus size: 24
27881 GATATTTTAA
*
27891 AAATAATATTA-TTTAAAATAAAT
1 AAATAATATGATTTTAAAATAAAT
27914 AAATAATATGATTTTAATAAATAAAT
1 AAATAATATGATTTT-A-AAATAAAT
27940 AAATAA-AT-ATTTTAAAATA
1 AAATAATATGATTTTAAAATA
27959 TTTTCATAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
22 5 0.12
23 11 0.27
24 8 0.20
25 3 0.07
26 14 0.34
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (24 bp):
AAATAATATGATTTTAAAATAAAT
Found at i:28271 original size:21 final size:21
Alignment explanation
Indices: 28245--28293 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
28235 GCGAATATGT
*
28245 AATTCGCGTTGCGATTTTCCA
1 AATTCGCGTTGCGATATTCCA
*
28266 AATTCGCGTTGCGATATTCTA
1 AATTCGCGTTGCGATATTCCA
28287 AATTCGC
1 AATTCGC
28294 AATGCGAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
AATTCGCGTTGCGATATTCCA
Found at i:28299 original size:21 final size:20
Alignment explanation
Indices: 28254--28320 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
28244 TAATTCGCGT
* **
28254 TGCGATTTTCCAAATTCGCGT
1 TGCGATATT-CAAATTCGCAA
28275 TGCGATATTCTAAATTCGCAA
1 TGCGATATTC-AAATTCGCAA
* *
28296 TGCGAAAGTCAAATTCGCAA
1 TGCGATATTCAAATTCGCAA
*
28316 CGCGA
1 TGCGA
28321 AAGTCAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (20 bp):
TGCGATATTCAAATTCGCAA
Found at i:28311 original size:20 final size:20
Alignment explanation
Indices: 28286--28329 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
28276 GCGATATTCT
*
28286 AAATTCGCAATGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
28306 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
28326 AAAT
1 AAAT
28330 GGTTTTACGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:28486 original size:22 final size:22
Alignment explanation
Indices: 28461--28507 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
28451 GGCGACATTT
28461 GTCCCCATCTCCGACGAAATCC
1 GTCCCCATCTCCGACGAAATCC
* *
28483 GTCCCCATTTCCGACGAAATTC
1 GTCCCCATCTCCGACGAAATCC
28505 GTC
1 GTC
28508 TATCTCCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.21, C:0.40, G:0.15, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCC
Found at i:31316 original size:19 final size:19
Alignment explanation
Indices: 31272--31318 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
31262 ATAAGATAGC
*
31272 CTAAATCCACTTAGAGGCT
1 CTAAATTCACTTAGAGGCT
31291 CTAAATTCACTTAGAGGCT
1 CTAAATTCACTTAGAGGCT
31310 CTAAATTCA
1 CTAAATTCA
31319 ATTTCTTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (19 bp):
CTAAATTCACTTAGAGGCT
Found at i:31840 original size:19 final size:20
Alignment explanation
Indices: 31798--31867 Score: 72
Period size: 19 Copynumber: 3.6 Consensus size: 20
31788 ACTAAAACCT
* *
31798 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGA
*
31817 TTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
** *
31836 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTCGA
31856 GTTGCGAATTTG
1 GTTGCGAATTTG
31868 GAAAATCACA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 24 0.57
20 18 0.43
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:31885 original size:21 final size:21
Alignment explanation
Indices: 31859--31904 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
31849 CTTTCGCGTT
31859 GCGAATTTGGAAAATCACAAC
1 GCGAATTTGGAAAATCACAAC
* *
31880 GCGAATTTGGAAAATCGCAAT
1 GCGAATTTGGAAAATCACAAC
31901 GCGA
1 GCGA
31905 TTTACATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (21 bp):
GCGAATTTGGAAAATCACAAC
Found at i:31961 original size:20 final size:20
Alignment explanation
Indices: 31912--31965 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
31902 CGATTTACAT
*
31912 ATTTGCTTTGCGAAATTGGA
1 ATTTGCGTTGCGAAATTGGA
** *
31932 AACTGGGTTGCGAAATTGGA
1 ATTTGCGTTGCGAAATTGGA
31952 ATTTGCGTTGCGAA
1 ATTTGCGTTGCGAA
31966 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.33
Consensus pattern (20 bp):
ATTTGCGTTGCGAAATTGGA
Found at i:33830 original size:35 final size:35
Alignment explanation
Indices: 33784--33859 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
33774 AAAACAATCC
* * *
33784 TCAATTTCATTCTAAACCCCAATTTCTAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
33819 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
33854 TCAATT
1 TCAATT
33860 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:34408 original size:130 final size:130
Alignment explanation
Indices: 34255--34502 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
34245 TATTTATATA
* * **
34255 ATCAATTTGGTTCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
*
34320 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
34385 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
34450 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
34503 CAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:34533 original size:130 final size:129
Alignment explanation
Indices: 34269--34533 Score: 318
Period size: 130 Copynumber: 2.0 Consensus size: 129
34259 ATTTGGTTCT
* **
34269 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
34334 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
34399 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
34464 TGATATATGTTATTGGTGACACATGTCACCACCTAATTACAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
34528 -A
128 CA
34529 AAATT
1 AAATT
34534 TGGGTCTTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 101 0.89
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:34862 original size:28 final size:27
Alignment explanation
Indices: 34831--34893 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
34821 AGTTGATACC
*
34831 ATATTTTAAAAGAATAAATTTAATATTT
1 ATATTTTAAAA-AATAAATTTAATAATT
** *
34859 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAATAATT
34887 ATATTTT
1 ATATTTT
34894 TCATATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 3 0.10
28 22 0.73
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAATAATT
Found at i:35787 original size:20 final size:19
Alignment explanation
Indices: 35748--35789 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
35738 TTTTTAGTAT
*
35748 TTTACGATTTTTGTTATTG
1 TTTACGATTTTTGTCATTG
*
35767 TTTACGATTTTTTGTCGTTG
1 TTTACGA-TTTTTGTCATTG
35787 TTT
1 TTT
35790 TTCTTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.12, C:0.07, G:0.17, T:0.64
Consensus pattern (19 bp):
TTTACGATTTTTGTCATTG
Found at i:36846 original size:17 final size:17
Alignment explanation
Indices: 36820--36853 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
36810 AATTTATTAT
36820 ATCATGAAATTTATAAAA
1 ATCATGAAATTT-TAAAA
36838 ATCAT-AAATTTTAAAA
1 ATCATGAAATTTTAAAA
36854 TATTATATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (17 bp):
ATCATGAAATTTTAAAA
Found at i:38545 original size:42 final size:42
Alignment explanation
Indices: 38486--38570 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
38476 AACAGGGTAC
38486 CTGTAAAGACAATGAGAAAATCCACAGCCTTTGAAACAAATT
1 CTGTAAAGACAATGAGAAAATCCACAGCCTTTGAAACAAATT
38528 CTGTAAAGACAATGAGAAAATCCACAGCCTTTGAAACAAATT
1 CTGTAAAGACAATGAGAAAATCCACAGCCTTTGAAACAAATT
38570 C
1 C
38571 AGTCATATAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (42 bp):
CTGTAAAGACAATGAGAAAATCCACAGCCTTTGAAACAAATT
Found at i:44664 original size:257 final size:257
Alignment explanation
Indices: 43711--44735 Score: 1929
Period size: 257 Copynumber: 4.0 Consensus size: 257
43701 GCGTGTGAAA
*
43711 CAGTCTGATATTAAGATCATGAAGCAGTTCTCAGACTACCTCCAGATAAATAAAGAGGGGGAAAA
1 CAGTCTGATATTAAGATCATGAAGCAGTTCTCAGACTACCTCCAGATAAATAAAAAGGGGGAAAA
43776 GACATGGGAAATTTAAGCTACTTACAAGTGCAGCCTGACTTTTCAAGTCCTCTAAGTTGAAATTC
66 GACATGGGAAATTTAAGCTACTTACAAGTGCAGCCTGACTTTTCAAGTCCTCTAAGTTGAAATTC
*
43841 CAGGCACCGATTCCTCTTATGTACTCTTGCTGCAAGGTGAAAGGAATTTGTATTCAAACTAATGC
131 CAGGCACTGATTCCTCTTATGTACTCTTGCTGCAAGGTGAAAGGAATTTGTATTCAAACTAATGC
43906 TTCAATAAATTATAGGCATTCTTTAGTCAAAGTAAAACTAGGTGCAATTGGATTGGATCATG
196 TTCAATAAATTATAGGCATTCTTTAGTCAAAGTAAAACTAGGTGCAATTGGATTGGATCATG
43968 CAGTCTGATATTAAGATCATGAAGCAGTTCTCAGACTACCTCCAGATAAATAAAAAGGGGGAAAA
1 CAGTCTGATATTAAGATCATGAAGCAGTTCTCAGACTACCTCCAGATAAATAAAAAGGGGGAAAA
44033 GACATGGGAAATTTAAGCTACTTACAAGTGCAGCCTGACTTTTCAAGTCCTCTAAGTTGAAATTC
66 GACATGGGAAATTTAAGCTACTTACAAGTGCAGCCTGACTTTTCAAGTCCTCTAAGTTGAAATTC
44098 CAGGCACTGATTCCTCTTATGTACTCTTGCTGCAAGGTGAAAGGAATTTG---T---ACTAATGC
131 CAGGCACTGATTCCTCTTATGTACTCTTGCTGCAAGGTGAAAGGAATTTGTATTCAAACTAATGC
44157 TTCAATAAATTATAGGCATTCTTTAGTCAAAGTAAAACTAGGTGCAATTGGATTGGATCATG
196 TTCAATAAATTATAGGCATTCTTTAGTCAAAGTAAAACTAGGTGCAATTGGATTGGATCATG
44219 CAGTCTGATATTAAGATCATGAAGCAGTTCTCAGACTACCTCCAGATAAATAAAAA-GGGGAAAA
1 CAGTCTGATATTAAGATCATGAAGCAGTTCTCAGACTACCTCCAGATAAATAAAAAGGGGGAAAA
* *
44283 GACCTGGGAAATTTAAGCTACTTACAAGTGCAACCTGACTTTTCAAGTCCTCTAAGTTGAAATTC
66 GACATGGGAAATTTAAGCTACTTACAAGTGCAGCCTGACTTTTCAAGTCCTCTAAGTTGAAATTC
*
44348 CAGGCACTGATTCGTCTTATGTACTCTTGCTGCAAGGTGAAAGGAATTTGTATTCAAACTAATGC
131 CAGGCACTGATTCCTCTTATGTACTCTTGCTGCAAGGTGAAAGGAATTTGTATTCAAACTAATGC
44413 TTCAATAAATTATAGGCATTCTTTAGTCAAAGTAAAACTAGGTGCAATTGGATTGGATCATG
196 TTCAATAAATTATAGGCATTCTTTAGTCAAAGTAAAACTAGGTGCAATTGGATTGGATCATG
*
44475 CAGTCTGATATTAAGATCATGAAGCTGTTCTCAGACTACCTCCAGATAAATAAAAAGGGGGAAAA
1 CAGTCTGATATTAAGATCATGAAGCAGTTCTCAGACTACCTCCAGATAAATAAAAAGGGGGAAAA
44540 GACATGGGAAATTTAAGCTACTTACAAGTGCAGCCTGACTTTTCAAGTCCTCTAAGTTGAAATTC
66 GACATGGGAAATTTAAGCTACTTACAAGTGCAGCCTGACTTTTCAAGTCCTCTAAGTTGAAATTC
*
44605 CAGGCACTGATTCCTCTTATGTACTCTTGCTGCAAGGTGAAAGTAATTTGTATTCAAACTAATGC
131 CAGGCACTGATTCCTCTTATGTACTCTTGCTGCAAGGTGAAAGGAATTTGTATTCAAACTAATGC
*
44670 TTCAATAAATTATAGGCATTCTTTAGTCAAAGTAAAACTAGGTGAAATTGGATTGGATCATG
196 TTCAATAAATTATAGGCATTCTTTAGTCAAAGTAAAACTAGGTGCAATTGGATTGGATCATG
44732 CAGT
1 CAGT
44736 ATATAAAGCC
Statistics
Matches: 750, Mismatches: 11, Indels: 14
0.97 0.01 0.02
Matches are distributed among these distances:
250 120 0.16
251 126 0.17
253 1 0.00
254 1 0.00
256 125 0.17
257 377 0.50
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (257 bp):
CAGTCTGATATTAAGATCATGAAGCAGTTCTCAGACTACCTCCAGATAAATAAAAAGGGGGAAAA
GACATGGGAAATTTAAGCTACTTACAAGTGCAGCCTGACTTTTCAAGTCCTCTAAGTTGAAATTC
CAGGCACTGATTCCTCTTATGTACTCTTGCTGCAAGGTGAAAGGAATTTGTATTCAAACTAATGC
TTCAATAAATTATAGGCATTCTTTAGTCAAAGTAAAACTAGGTGCAATTGGATTGGATCATG
Found at i:47757 original size:21 final size:21
Alignment explanation
Indices: 47723--47762 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
47713 ATTATTGAAT
* * *
47723 TTTATTTTATCTTTTATTTCA
1 TTTATTGTACCTTTAATTTCA
47744 TTTATTGTACCTTTAATTT
1 TTTATTGTACCTTTAATTT
47763 TTTTAATTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.68
Consensus pattern (21 bp):
TTTATTGTACCTTTAATTTCA
Found at i:48427 original size:21 final size:23
Alignment explanation
Indices: 48375--48434 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
48365 ATTAAACACA
* *
48375 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCACTTAT
48398 ATAACATAATAGGTAGCACTTAT
1 ATAACATAATAGGTAGCACTTAT
* *
48421 ATAATAAAATAGGT
1 ATAACATAATAGGT
48435 TAATTATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAGCACTTAT
Found at i:48536 original size:158 final size:158
Alignment explanation
Indices: 48241--48728 Score: 753
Period size: 158 Copynumber: 3.1 Consensus size: 158
48231 TCAAATACAG
* **
48241 TAACATATTAGGTAGCGCTTATATAATAAAATAATTTAATTAATTAATTTGTTATTACAACATAT
1 TAACATAATAGGTAGCGCTTATATAATAAAATAGGTTAATTAATTAATTTGTTATTACAACATAT
* * * *
48306 TAGGTAAACGCCTAAAATGTTACCAATGATAACATAACCGGTTAATTACTAAAAATATTATTAAA
66 TAGGTAAACGCCTAAAATGTTACCAATGATAACATAACCAGTTAATTACTGAAAATATTATCAAG
*
48371 CACAATAACATATTAGGTAGCGCTTATA
131 CATAATAACATATTAGGTAGCGCTTATA
* *
48399 TAACATAATAGGTAGCACTTATATAATAAAATAGGTTAATTATTTAATTTGTTATTACAACATAT
1 TAACATAATAGGTAGCGCTTATATAATAAAATAGGTTAATTAATTAATTTGTTATTACAACATAT
*
48464 TAGGTAAACGCCTAAAATGTTACCAATGATAACATAACCAGTTAATTACTGAAAACATTATCAAG
66 TAGGTAAACGCCTAAAATGTTACCAATGATAACATAACCAGTTAATTACTGAAAATATTATCAAG
48529 CATAATAACATATTAGGTAGCGCTTATA
131 CATAATAACATATTAGGTAGCGCTTATA
* * *
48557 TAACATAATAGGTAACGCTTATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACACAT
1 TAACATAATAGGTAGCGCTTATATAATAAAATAGGTTAATTAATTAATTTGTTATTACAACATAT
* * * * *
48622 TAGGTAAACACTTAAAATGTTACCAAGGATAACATAA-CTGATTAATTACTGGAAATATTATCAA
66 TAGGTAAACGCCTAAAATGTTACCAATGATAACATAACCAG-TTAATTACTGAAAATATTATCAA
** *
48686 GCATAATAACATATTAAATAGCGCTTATG
130 GCATAATAACATATTAGGTAGCGCTTATA
*
48715 TAACAAAATAGGTA
1 TAACATAATAGGTA
48729 ATTACTTACT
Statistics
Matches: 304, Mismatches: 25, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
157 2 0.01
158 302 0.99
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (158 bp):
TAACATAATAGGTAGCGCTTATATAATAAAATAGGTTAATTAATTAATTTGTTATTACAACATAT
TAGGTAAACGCCTAAAATGTTACCAATGATAACATAACCAGTTAATTACTGAAAATATTATCAAG
CATAATAACATATTAGGTAGCGCTTATA
Found at i:48585 original size:21 final size:23
Alignment explanation
Indices: 48533--48592 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
48523 ATCAAGCATA
* *
48533 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
48556 ATAACATAATAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
* *
48579 ATAATAAAATAGGT
1 ATAACATAATAGGT
48593 TAATTACTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:48893 original size:72 final size:74
Alignment explanation
Indices: 48797--48971 Score: 273
Period size: 72 Copynumber: 2.4 Consensus size: 74
48787 AAAATTTAAA
* * *
48797 CTACTTATTACATTAAAATACCTACCGGTTTTTTTGAAGGTTGCTAATACTATAAACGGT-AAAA
1 CTACCTATTACATTAAAATACCTACCGGGTTTTTTGAAGGTTGCTAATAATATAAACGGTAAAAA
*
48861 AAATA-GTG
66 AAATAGGCG
*
48869 TTACCTATTACATTAAAATACCTACCGGGTTTTTTGAAGGTTGCTAATAATATAAACGGTAAAAA
1 CTACCTATTACATTAAAATACCTACCGGGTTTTTTGAAGGTTGCTAATAATATAAACGGT-AAAA
48934 AAAATAGGCG
65 AAAATAGGCG
*
48944 CTACCTATTACATTAAACTACCTACCGG
1 CTACCTATTACATTAAAATACCTACCGG
48972 ATATGTTGAA
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
72 56 0.60
74 9 0.10
75 28 0.30
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.32
Consensus pattern (74 bp):
CTACCTATTACATTAAAATACCTACCGGGTTTTTTGAAGGTTGCTAATAATATAAACGGTAAAAA
AAATAGGCG
Found at i:49355 original size:118 final size:112
Alignment explanation
Indices: 49051--49526 Score: 590
Period size: 112 Copynumber: 4.3 Consensus size: 112
49041 TAGCTCCTAT
*
49051 AAAGTATCGATATTTTATAAAAATGTATCGATACTTTACAATATTACAGGTAAAAATATGACAAA
1 AAAGTATCGATATTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
*
49116 ACCAGTTTCATTATGATAAAATCGGTAAAGAGCTACCTGATATGTTG
66 ACCAGTTTCATTATGACAAAATCGGTAAAGAGCTACCTGATATGTTG
* *
49163 AAAGTATCGATATTTTATAAAAATGTATTGATACTTTACAATATAACAGGTAAAAATATAACAAA
1 AAAGTATCGATATTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
49228 ACCAGTTTCATTATGACAAAATCGGTAAAGAGCTACCTGATATGTTG
66 ACCAGTTTCATTATGACAAAATCGGTAAAGAGCTACCTGATATGTTG
* *
49275 AAAGTATCGATCTTTTTTATAAAAAAAAATGTATCGATACTTTACAATATAACAAGTAAAAATAT
1 AAAGTATCGA--TATTTTAT----AAAAATGTATCGATACTTTACAATATAACAGGTAAAAATAT
* *
49340 GACAAAAACAGTTTCATTATGACAAAACCGGTAAAGAGCTA-C----A---TG
60 GACAAAACCAGTTTCATTATGACAAAATCGGTAAAGAGCTACCTGATATGTTG
** *
49385 ATCG-ATC-CT-TTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGAC--A
1 AAAGTATCGATATTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
* * * * *
49445 ACTAGTTT-ATTATGACAAAA-CTGGTAAATAACTACCGGATATGTTA
66 ACCAGTTTCATTATGACAAAATC-GGTAAAGAGCTACCTGATATGTTG
* * *
49491 AAAGTATAGATACTTTTGT--ACATGTATCGATACTTT
1 AAAGTATCGATA-TTTTATAAAAATGTATCGATACTTT
49527 GTTGAAAGTT
Statistics
Matches: 320, Mismatches: 25, Indels: 42
0.83 0.06 0.11
Matches are distributed among these distances:
97 1 0.00
98 22 0.07
99 8 0.03
101 43 0.13
103 1 0.00
105 6 0.02
106 4 0.01
107 2 0.01
108 17 0.05
109 3 0.01
110 9 0.03
112 118 0.37
113 1 0.00
114 7 0.02
117 1 0.00
118 77 0.24
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (112 bp):
AAAGTATCGATATTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
ACCAGTTTCATTATGACAAAATCGGTAAAGAGCTACCTGATATGTTG
Found at i:54044 original size:17 final size:16
Alignment explanation
Indices: 54022--54053 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
54012 TATTAAGTAC
54022 TTTAACTATGTATTTTT
1 TTTAACTATGT-TTTTT
54039 TTTAACTATGTTTTT
1 TTTAACTATGTTTTT
54054 AACTTGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (16 bp):
TTTAACTATGTTTTTT
Found at i:54077 original size:28 final size:29
Alignment explanation
Indices: 54022--54080 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
54012 TATTAAGTAC
* * * *
54022 TTTAACTATGTATTTTTTTTAACTATGTT
1 TTTAACTATGTATTATGTTAAACCATGTT
54051 TTTAACT-TGTATTATGTTAAACCATGTT
1 TTTAACTATGTATTATGTTAAACCATGTT
54079 TT
1 TT
54081 GTAATATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.58
Consensus pattern (29 bp):
TTTAACTATGTATTATGTTAAACCATGTT
Found at i:61646 original size:28 final size:28
Alignment explanation
Indices: 61596--61649 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
61586 TAGTAATAAT
**
61596 TAATATTATAAAACTGTTAATAAAAAAA
1 TAATATTATAAAACAATTAATAAAAAAA
* *
61624 TAATATTCTAAAACAATTTATAAAAA
1 TAATATTATAAAACAATTAATAAAAA
61650 TATATTCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (28 bp):
TAATATTATAAAACAATTAATAAAAAAA
Found at i:63440 original size:19 final size:19
Alignment explanation
Indices: 63413--63452 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
63403 ATACCTAAGT
* *
63413 ATTAATATATTATTTTAAA
1 ATTAATATATGAATTTAAA
*
63432 ATTATTATATGAATTTAAA
1 ATTAATATATGAATTTAAA
63451 AT
1 AT
63453 AAATTATTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
ATTAATATATGAATTTAAA
Found at i:66039 original size:15 final size:15
Alignment explanation
Indices: 66008--66050 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
65998 AATTAAAGAC
*
66008 AAAATTTAATTTATTT
1 AAAATTTAA-ATATTT
66024 AAAATTTAAATATTT
1 AAAATTTAAATATTT
*
66039 AAGAATCTAAAT
1 AA-AATTTAAAT
66051 TATTATTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (15 bp):
AAAATTTAAATATTT
Found at i:67553 original size:262 final size:260
Alignment explanation
Indices: 67071--67590 Score: 899
Period size: 258 Copynumber: 2.0 Consensus size: 260
67061 TGGTTTTCAT
67071 AGAAGATTGCTACCCCTTCTCATTTAGTAGGTTATTTCATCAGATTTATCACAATATAATGTACC
1 AGAAGATTGCTACCCCTTCTCATTTAGTAGGTTATTTCATCAGATTTATCACAATATAATGTACC
67136 CAAAGTGAGTTATGAAATAATGAGAGCTTTTACTATAACTCATCCTCACAATAGGCAAGGTGAAT
66 CAAAGTGAGTTATGAAATAATGAGAGCTTTTACTATAAC-CATCCTCACAATAGGCAAGGTGAAT
67201 TTCTTCAAGTTCTTATTAAATGATCCGCCTGAATTTTAGGATTAGAAATCATTAAGAATAAATAT
130 TTCTTCAAGTTCTTATTAAATGATCCGCCTGAATTTTAGGATTAGAAATCATTAAGAATAAATAT
67266 TAACCTCGTTAATCGGTGAATTCAG-TGTATTTCTCGCTAGGATCA-CCAAACTCTTGGGTTTGA
195 TAACCTCGTTAATCGGTGAATTCAGATGTATTTCTCGCTAGGATCACCCAAACTCTTGGGTTTGA
67329 A
260 A
67330 AGAAGATTGCTA-CCCTTCTCATTTACGTAGG-TATTTCATCAGATTTATCACAATATAATGTAC
1 AGAAGATTGCTACCCCTTCTCATTTA-GTAGGTTATTTCATCAGATTTATCACAATATAATGTAC
*
67393 CCAAATTGAGTTATGAAATAATTGAGAGCTTTTACTATAA-CATCCTCACAATAGGCAGGCAAGG
65 CCAAAGTGAGTTATGAAATAA-TGAGAGCTTTTACTATAACCATCCTCACAAT----AGGCAAGG
67457 TGAATTTCTTCAAGTTTCTTATTAAATGATCCGCCTGAATTTTAGGATTAGAAA-CATTAAGAAT
125 TGAATTTCTTCAAG-TTCTTATTAAATGATCCGCCTGAATTTTAGGATTAGAAATCATTAAGAAT
67521 AAATATTTAACCTCGTTAATCGGTGAATTCAGTATGTATTTCTCGCTAGGATCACCCAAACTCTT
189 AAATA-TTAACCTCGTTAATCGGTGAATTCAG-ATGTATTTCTCGCTAGGATCACCCAAACTCTT
67586 GGGTT
252 GGGTT
67591 GAATTCATTA
Statistics
Matches: 249, Mismatches: 1, Indels: 16
0.94 0.00 0.06
Matches are distributed among these distances:
257 12 0.05
258 65 0.26
259 35 0.14
261 37 0.15
262 65 0.26
264 20 0.08
265 15 0.06
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (260 bp):
AGAAGATTGCTACCCCTTCTCATTTAGTAGGTTATTTCATCAGATTTATCACAATATAATGTACC
CAAAGTGAGTTATGAAATAATGAGAGCTTTTACTATAACCATCCTCACAATAGGCAAGGTGAATT
TCTTCAAGTTCTTATTAAATGATCCGCCTGAATTTTAGGATTAGAAATCATTAAGAATAAATATT
AACCTCGTTAATCGGTGAATTCAGATGTATTTCTCGCTAGGATCACCCAAACTCTTGGGTTTGAA
Done.