Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008783.1 Hibiscus syriacus cultivar Beakdansim tig00111914_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: 61965
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:758 original size:95 final size:95
Alignment explanation
Indices: 633--854 Score: 288
Period size: 95 Copynumber: 2.3 Consensus size: 95
623 TACCAGCGAT
* *
633 GTAGTATCAATACCATGGTAAGGGTATCGATACAAGGAAACATCGAACCTAATTTTGGTATCGAT
1 GTAGTATCGATACCATGGTAAGGGTATCGATACAAGGAAACATCGAACATAATTTTGGTATCGAT
* * *
698 AC-CGAATGGAGGTATCGGTACCATA-TCATA
66 ACAAGAA-GGAGGTATCGATACCATAGT-AGA
* ** *
728 GTAGTATCGATACCATGGTAAGGGTATCGATACCAGGCTACATCGAAGATAATTTTGGTATCGAT
1 GTAGTATCGATACCATGGTAAGGGTATCGATACAAGGAAACATCGAACATAATTTTGGTATCGAT
* *
793 ACAAGAAGGGGGTATCGATACCATAGTAGG
66 ACAAGAAGGAGGTATCGATACCATAGTAGA
* *
823 GTAGTATCGATACGATAGT-AGGGTATCGATAC
1 GTAGTATCGATACCATGGTAAGGGTATCGATAC
855 TGAAGAGCCA
Statistics
Matches: 112, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
94 13 0.12
95 95 0.85
96 4 0.04
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.26
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTAAGGGTATCGATACAAGGAAACATCGAACATAATTTTGGTATCGAT
ACAAGAAGGAGGTATCGATACCATAGTAGA
Found at i:824 original size:19 final size:20
Alignment explanation
Indices: 784--854 Score: 76
Period size: 19 Copynumber: 3.5 Consensus size: 20
774 AGATAATTTT
*
784 GGTATCGATA-CA-AGAAGGG
1 GGTATCGATACCATAGTA-GG
803 GGTATCGATACCATAGTAGG
1 GGTATCGATACCATAGTAGG
*
823 GTAGTATCGATACGATAGTA-G
1 G--GTATCGATACCATAGTAGG
844 GGTATCGATAC
1 GGTATCGATAC
855 TGAAGAGCCA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
19 20 0.43
20 5 0.11
21 5 0.11
22 16 0.35
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.24
Consensus pattern (20 bp):
GGTATCGATACCATAGTAGG
Found at i:832 original size:22 final size:22
Alignment explanation
Indices: 804--847 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
794 CAAGAAGGGG
804 GTATCGATACCATAGTAGGGTA
1 GTATCGATACCATAGTAGGGTA
*
826 GTATCGATACGATAGTAGGGTA
1 GTATCGATACCATAGTAGGGTA
848 TCGATACTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (22 bp):
GTATCGATACCATAGTAGGGTA
Found at i:1345 original size:44 final size:45
Alignment explanation
Indices: 1275--1565 Score: 291
Period size: 44 Copynumber: 6.7 Consensus size: 45
1265 AGGATGCCAT
* *
1275 AGTTGAAATGCATATAGGTGCATTATCAACAGAAAAGTATGCTGG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAG
* *
1320 AGTTGAAATGCGTAT-GGTGCATTATCAACAGAAAAGTAAGCTAG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAG
* * * *
1364 AGTTGAAATGCATATGGGTACATTATCAAC--AAATGTATGTTAT
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAG
*
1407 AGTTGAAATGCATATGGGTGCATTATC-ACAG--AA-CATGCTAG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAG
** * * *
1448 AGTTGAAATATATATGGGTACATTATCAACAG--AA-TATACTAT
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAG
** * *
1490 AGTTGAAATGCATATGGGTGTGTTATCAACAGAAAAG-ATGTTAT
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAG
* * *
1534 AGTTTAAAGTGCATAAT-GGTGTATTATAAACA
1 AGTTGAAA-TGCAT-ATGGGTGCATTATCAACA
1566 TAAATGGAGG
Statistics
Matches: 207, Mismatches: 30, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
41 29 0.14
42 41 0.20
43 35 0.17
44 55 0.27
45 45 0.22
46 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (45 bp):
AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAG
Found at i:1471 original size:84 final size:86
Alignment explanation
Indices: 1275--1526 Score: 307
Period size: 84 Copynumber: 2.9 Consensus size: 86
1265 AGGATGCCAT
* * ** *
1275 AGTTGAAATGCATATAGGTGCATTATCAACAGAAAAGTATGCTGGAGTTGAAATGCGTAT-GGTG
1 AGTTGAAATGCATATGGGTACATTATCAAC---AAAGTATGCTATAGTTGAAATGCATATGGGTG
1339 CATTATCAACAGAAAAGTAAGCTAG
63 CATTATCAACAGAAAAGT-AGCTAG
*
1364 AGTTGAAATGCATATGGGTACATTATCAACAAATGTATGTTATAGTTGAAATGCATATGGGTGCA
1 AGTTGAAATGCATATGGGTACATTATCAACAAA-GTATGCTATAGTTGAAATGCATATGGGTGCA
*
1429 TTATC-ACAGAACA-T-GCTAG
65 TTATCAACAGAAAAGTAGCTAG
** * **
1448 AGTTGAAATATATATGGGTACATTATCAACAGAA-TATACTATAGTTGAAATGCATATGGGTGTG
1 AGTTGAAATGCATATGGGTACATTATCAACA-AAGTATGCTATAGTTGAAATGCATATGGGTGCA
1512 TTATCAACAGAAAAG
65 TTATCAACAGAAAAG
1527 ATGTTATAGT
Statistics
Matches: 144, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
83 31 0.22
84 41 0.28
85 2 0.01
86 4 0.03
87 27 0.19
88 11 0.08
89 28 0.19
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (86 bp):
AGTTGAAATGCATATGGGTACATTATCAACAAAGTATGCTATAGTTGAAATGCATATGGGTGCAT
TATCAACAGAAAAGTAGCTAG
Found at i:1494 original size:42 final size:42
Alignment explanation
Indices: 1275--1523 Score: 234
Period size: 42 Copynumber: 5.8 Consensus size: 42
1265 AGGATGCCAT
* * * *
1275 AGTTGAAATGCATATAGGTGCATTATCAACAGAAAAGTATGCTGG
1 AGTTGAAATGCATATGGGTACATTATCAACAG--AA-TATACTAG
* * *
1320 AGTTGAAATGCGTAT-GGTGCATTATCAACAGAAAAGTAAGCTAG
1 AGTTGAAATGCATATGGGTACATTATCAACAGAATA-T-A-CTAG
** *
1364 AGTTGAAATGCATATGGGTACATTATCAACA-AATGTATGTTAT
1 AGTTGAAATGCATATGGGTACATTATCAACAGAA--TATACTAG
* * *
1407 AGTTGAAATGCATATGGGTGCATTATC-ACAGAACATGCTAG
1 AGTTGAAATGCATATGGGTACATTATCAACAGAATATACTAG
** *
1448 AGTTGAAATATATATGGGTACATTATCAACAGAATATACTAT
1 AGTTGAAATGCATATGGGTACATTATCAACAGAATATACTAG
***
1490 AGTTGAAATGCATATGGGTGTGTTATCAACAGAA
1 AGTTGAAATGCATATGGGTACATTATCAACAGAA
1524 AAGATGTTAT
Statistics
Matches: 171, Mismatches: 25, Indels: 19
0.80 0.12 0.09
Matches are distributed among these distances:
41 30 0.18
42 46 0.27
43 30 0.18
44 35 0.20
45 29 0.17
46 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (42 bp):
AGTTGAAATGCATATGGGTACATTATCAACAGAATATACTAG
Found at i:1560 original size:128 final size:128
Alignment explanation
Indices: 1273--1548 Score: 326
Period size: 126 Copynumber: 2.1 Consensus size: 128
1263 AAAGGATGCC
* * * * *
1273 ATAGTTGAAATGCATATAGGTGCATTATCAACAGAAAAGTATGCTGGAGTTGAAATGCGTATGGT
1 ATAGTTGAAATGCATATGGGTGCATTATC-ACAG--AA-CATGCTAGAGTTGAAATACATATGGT
* *
1338 GCATTATCAACAGAAAAGTAAGCTAGAGTTGAAATGCATATGGGTACATTATCAACAAATGTATG
62 ACATTATCAACAGAAAAGTAAGCTAGAGTTGAAATGCATATGGGTACATTATCAACAAAAGTATG
1403 TT
127 TT
*
1405 ATAGTTGAAATGCATATGGGTGCATTATCACAGAACATGCTAGAGTTGAAATATATATGGGTACA
1 ATAGTTGAAATGCATATGGGTGCATTATCACAGAACATGCTAGAGTTGAAATACATAT-GGTACA
* * ***
1470 TTATCAACAGAATA-T-A-CTATAGTTGAAATGCATATGGGTGTGTTATCAACAGAAAAG-ATGT
65 TTATCAACAGAAAAGTAAGCTAGAGTTGAAATGCATATGGGTACATTATCAAC--AAAAGTATGT
1531 T
128 T
*
1532 ATAGTTTAAAGTGCATA
1 ATAGTTGAAA-TGCATA
1549 ATGGTGTATT
Statistics
Matches: 126, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
126 30 0.24
127 15 0.12
128 29 0.23
129 20 0.16
131 4 0.03
132 28 0.22
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (128 bp):
ATAGTTGAAATGCATATGGGTGCATTATCACAGAACATGCTAGAGTTGAAATACATATGGTACAT
TATCAACAGAAAAGTAAGCTAGAGTTGAAATGCATATGGGTACATTATCAACAAAAGTATGTT
Found at i:7819 original size:95 final size:93
Alignment explanation
Indices: 7565--7822 Score: 327
Period size: 95 Copynumber: 2.7 Consensus size: 93
7555 AAGCGATGTA
* * *
7565 GTATCGATACCAGTAAACATCGAACCTAATTTTGGTATCGATGCCGAAGGGAGGTATGGGTACCA
1 GTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGATACCGAAGGG-GGTATCGGTACC-
* *
7630 AAAGATTGTAGTATCGATACCATGGTAAGG
64 ATAGATAGTAGTATCGATACCATGGTAAGG
* * * * *
7660 GTATCGATACTAGGAAACATCGAACCTAATTTTTGTATCAAAACCGAAGGTGGGTATTGGTACCA
1 GTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGATACCGAAGG-GGGTATCGGTACCA
*
7725 TAGCATAGTAGTATTGATACCATGGTAAGG
65 TAG-ATAGTAGTATCGATACCATGGTAAGG
** * * *
7755 GTATCGATACCAGGCTACATCGAAGCTAATTTTGGTATCGATACTAGAAGGGGGTATCGATACCA
1 GTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGATAC-CGAAGGGGGTATCGGTACCA
7820 TAG
65 TAG
7823 TATGGGTATC
Statistics
Matches: 140, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
94 3 0.02
95 131 0.94
96 6 0.04
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (93 bp):
GTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGATACCGAAGGGGGTATCGGTACCAT
AGATAGTAGTATCGATACCATGGTAAGG
Found at i:8326 original size:45 final size:45
Alignment explanation
Indices: 8226--8526 Score: 324
Period size: 45 Copynumber: 6.7 Consensus size: 45
8216 TATGAAAATA
*** * * *
8226 GAAATGCATATGGGTGCATTATTGGCATG-AAAGGATGCCATAGTT
1 GAAATGCATATGGGTGCATTATCAACA-GAAAAGTATGCTAGAGTT
* * *
8271 GAAATACATATGGGTTCATTACCAACAGAAAAGTATGCTAGAGTT
1 GAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTT
* *
8316 AAAATGCATATGGGTGCATTATCAATAGAAAAGTATGCTAGAGTT
1 GAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTT
* * * * *
8361 GAATTGTATATGGGTGCATTATCAACATACATGTATGCTAGAGTT
1 GAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTT
* * *
8406 GAAATGCATATGGGTGCATTATCAACAGAAGAGCATGCTATAGTTT
1 GAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAG-TT
* * *
8452 GAAAT--ATATGGGGTACATTATCAACAGAAAA-T-TACTATAGTT
1 GAAATGCATAT-GGGTGCATTATCAACAGAAAAGTATGCTAGAGTT
* *
8494 GAAATGCATATGAGTGCATTATCAACATAAAAG
1 GAAATGCATATGGGTGCATTATCAACAGAAAAG
8527 ATGTTAGTTT
Statistics
Matches: 214, Mismatches: 36, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
42 7 0.03
43 25 0.12
44 9 0.04
45 166 0.78
46 7 0.03
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (45 bp):
GAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTT
Found at i:13065 original size:6 final size:6
Alignment explanation
Indices: 13037--13074 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
13027 GTTCTACAAC
*
13037 AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAAAG AA
1 AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AA
13075 CTCCTACATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 5 0.18
6 17 0.61
7 6 0.21
ACGTcount: A:0.82, C:0.03, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:13108 original size:5 final size:5
Alignment explanation
Indices: 13098--13140 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
13088 TTTGGAGTAC
13098 AAAAG AAAAG AAAAG AAAAG --AAG AAAAG AAAA- AAGAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG
13141 TTGAAGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 3 0.09
4 2 0.06
5 27 0.79
6 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:13352 original size:14 final size:15
Alignment explanation
Indices: 13317--13352 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
13307 TGTTATCTCT
13317 TCTTACC-TCTTACC
1 TCTTACCATCTTACC
13331 TCTT-CCATCTTACC
1 TCTTACCATCTTACC
13345 T-TTACCAT
1 TCTTACCAT
13353 ATTCATTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.17, C:0.39, G:0.00, T:0.44
Consensus pattern (15 bp):
TCTTACCATCTTACC
Found at i:17739 original size:44 final size:44
Alignment explanation
Indices: 17689--18030 Score: 490
Period size: 44 Copynumber: 7.7 Consensus size: 44
17679 GTAAGTATGC
* * **
17689 AAATAAGCTTACGATCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATA-TGGTA
17733 AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATGGTA
1 AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATGGTA
17777 AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATGGTA
1 AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATGGTA
* * * *
17821 AAATAAGCTTACGAGTTTATGGGATAAATGGTAAGTATATTGGCA
1 AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATA-TGGTA
* *
17866 AAATAAACTTACGAGCCTATGGTATAAATGATAAGTATATGGTA
1 AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATGGTA
*
17910 AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATGATA
1 AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATGGTA
* * *
17954 AAATAAGCTTATGAGCTTATGGGATAAATTG-TAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGTATAAA-TGATAAGTA-TATGGTA
17999 AAATAAGCTTACGAGCTTATGGTTAATAAATG
1 AAATAAGCTTACGAGCTTATGG-T-ATAAATG
18031 GTAAAATATT
Statistics
Matches: 269, Mismatches: 23, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
44 185 0.69
45 77 0.29
46 2 0.01
47 5 0.02
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.32
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATGGTA
Found at i:17775 original size:20 final size:19
Alignment explanation
Indices: 17750--17824 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 19
17740 CTTACGAGCT
17750 TATGGTATAAATGATAAGTA
1 TATGGTA-AAATGATAAGTA
*
17770 TATGGTAAAATAAGCTTACGAGCT-
1 TATGGTAAAAT--G-ATA--AG-TA
17794 TATGGTATAAATGATAAGTA
1 TATGGTA-AAATGATAAGTA
17814 TATGGTAAAAT
1 TATGGTAAAAT
17825 AAGCTTACGA
Statistics
Matches: 45, Mismatches: 2, Indels: 17
0.70 0.03 0.27
Matches are distributed among these distances:
19 9 0.20
20 16 0.36
21 1 0.02
22 4 0.09
23 1 0.02
24 9 0.20
25 5 0.11
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (19 bp):
TATGGTAAAATGATAAGTA
Found at i:17877 original size:133 final size:133
Alignment explanation
Indices: 17689--18030 Score: 553
Period size: 133 Copynumber: 2.6 Consensus size: 133
17679 GTAAGTATGC
* *
17689 AAATAAGCTTACGA-TCTTATGGAAT-AATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGT-TTATGGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
17752 TGGTATAAATGATAAGTATATGGTAAAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATAT
65 TGGTATAAATGATAAGTATATGGTAAAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATAT
*
17817 GGTA
130 GATA
* * *
17821 AAATAAGCTTACGAGTTTATGGGATAAATGGTAAGTATATTGGCAAAATAAACTTACGAGCCTAT
1 AAATAAGCTTACGAGTTTATGGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
17886 GGTATAAATGATAAGTATATGGTAAAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATG
66 GGTATAAATGATAAGTATATGGTAAAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATG
17951 ATA
131 ATA
* * * *
17954 AAATAAGCTTATGAGCTTATGGGATAAATTGTAAGTATTTTGGTAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTACGAGTTTATGGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
18019 GGTTAATAAATG
66 GG-T-ATAAATG
18031 GTAAAATATT
Statistics
Matches: 193, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
132 22 0.11
133 163 0.84
134 1 0.01
135 7 0.04
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.32
Consensus pattern (133 bp):
AAATAAGCTTACGAGTTTATGGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
GGTATAAATGATAAGTATATGGTAAAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATG
ATA
Found at i:17891 original size:89 final size:88
Alignment explanation
Indices: 17689--18030 Score: 490
Period size: 89 Copynumber: 3.8 Consensus size: 88
17679 GTAAGTATGC
* * **
17689 AAATAAGCTTACGATCTTATGGAAT-AATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATA-TGGTAAAATAAGCTTACGAGCTTAT
17753 GGTATAAATGATAAGTATATGGTA
65 GGTATAAATGATAAGTATATGGTA
*
17777 AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATGGTAAAATAAGCTTACGAGTTTATG
1 AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATGGTAAAATAAGCTTACGAGCTTATG
* * *
17842 GGATAAATGGTAAGTATATTGGCA
66 GTATAAATGATAAGTATA-TGGTA
* *
17866 AAATAAACTTACGAGCCTATGGTATAAATGATAAGTATATGGTAAAATAAGCTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATGGTAAAATAAGCTTACGAGCTTATG
*
17931 GTATAAATGATAAGTATATGATA
66 GTATAAATGATAAGTATATGGTA
* * *
17954 AAATAAGCTTATGAGCTTATGGGATAAATTG-TAAGTATTTTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGTATAAA-TGATAAGTA-TATGGTAAAATAAGCTTACGAGCTTA
18018 TGGTTAATAAATG
64 TGG-T-ATAAATG
18031 GTAAAATATT
Statistics
Matches: 228, Mismatches: 20, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
88 97 0.43
89 123 0.54
90 1 0.00
91 7 0.03
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.32
Consensus pattern (88 bp):
AAATAAGCTTACGAGCTTATGGTATAAATGATAAGTATATGGTAAAATAAGCTTACGAGCTTATG
GTATAAATGATAAGTATATGGTA
Found at i:17908 original size:20 final size:20
Alignment explanation
Indices: 17883--17950 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 20
17873 CTTACGAGCC
17883 TATGGTATAAATGATAAGTA
1 TATGGTATAAATGATAAGTA
*
17903 TATGGTA-AAATAAGCTTACGAGCT-
1 TATGGTATAAAT--G-ATA--AG-TA
17927 TATGGTATAAATGATAAGTA
1 TATGGTATAAATGATAAGTA
17947 TATG
1 TATG
17951 ATAAAATAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 16
0.68 0.04 0.29
Matches are distributed among these distances:
19 5 0.13
20 13 0.34
21 1 0.03
22 4 0.11
23 1 0.03
24 9 0.24
25 5 0.13
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (20 bp):
TATGGTATAAATGATAAGTA
Found at i:18471 original size:26 final size:26
Alignment explanation
Indices: 18442--18493 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
18432 GATTCCCCCC
18442 ACTGTTCACGGGTACTATTCACTATT
1 ACTGTTCACGGGTACTATTCACTATT
* *
18468 ACTGTTCATGGGTACTGTTCACTATT
1 ACTGTTCACGGGTACTATTCACTATT
18494 CATAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (26 bp):
ACTGTTCACGGGTACTATTCACTATT
Found at i:20842 original size:47 final size:47
Alignment explanation
Indices: 20774--20922 Score: 239
Period size: 47 Copynumber: 3.2 Consensus size: 47
20764 ATAAAATATT
* * *
20774 TTACCATTT--ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
20819 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
* *
20866 TTACCATTTAAATTTCAGAAGCTCGTAAGCTTATTTTATCAATATAC
1 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
20913 TTACCATTTA
1 TTACCATTTA
20923 TTAACCAATA
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 9 0.09
47 88 0.91
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.40
Consensus pattern (47 bp):
TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
Found at i:23391 original size:12 final size:12
Alignment explanation
Indices: 23374--23411 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
23364 TCTTCTCAGT
23374 TCTCTGTTTCTG
1 TCTCTGTTTCTG
*
23386 TCTCTG--TCTC
1 TCTCTGTTTCTG
23396 TCTCTGTTTCTG
1 TCTCTGTTTCTG
23408 TCTC
1 TCTC
23412 CCTTTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.00, C:0.32, G:0.13, T:0.55
Consensus pattern (12 bp):
TCTCTGTTTCTG
Found at i:23899 original size:3 final size:3
Alignment explanation
Indices: 23891--23945 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
23881 AATATATATT
23891 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23938 TAA TAA TA
1 TAA TAA TA
23946 TGGATAAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:24481 original size:113 final size:113
Alignment explanation
Indices: 24265--24940 Score: 1104
Period size: 113 Copynumber: 6.0 Consensus size: 113
24255 AGAATTATGC
* * * *
24265 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCT
* * * * * *
24330 CATTATGAAC--TCTACATGGCAATGTTGATCCATCAAATGATGAATTCAAGC
63 CATTATGAACTTTCT-C-TGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
*
24381 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
24446 TATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
24494 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
24559 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGAATCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
24607 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
24672 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
*
24720 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
24785 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
* * *
24833 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAATTCCTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
24898 TATGAACCTTCTCTGGAAAAGATAATCCATCAAATGATAGATT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATT
24941 GAATCTTTGC
Statistics
Matches: 535, Mismatches: 23, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
113 484 0.90
114 1 0.00
115 3 0.01
116 47 0.09
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
Found at i:26615 original size:16 final size:17
Alignment explanation
Indices: 26577--26621 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
26567 AATAGAAAAG
*
26577 AATAAATTGAATTTCAAA
1 AATAAATTGAATCTC-AA
26595 AATAAATTGAATCTC-A
1 AATAAATTGAATCTCAA
26611 AATAAATTGAA
1 AATAAATTGAA
26622 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (17 bp):
AATAAATTGAATCTCAA
Found at i:26957 original size:1 final size:1
Alignment explanation
Indices: 26953--27010 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
26943 GACCCCCCCC
* * * * * * *
26953 TTTTTCTTTTTTTTTCTTTCTTTTTTTTTCTTTTCTTTTTCTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27011 CTTCAAGCAT
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:26968 original size:10 final size:10
Alignment explanation
Indices: 26952--27010 Score: 68
Period size: 10 Copynumber: 5.8 Consensus size: 10
26942 TGACCCCCCC
26952 CTTTTTCTTTT
1 CTTTTT-TTTT
*
26963 -TTTTTCTTT
1 CTTTTTTTTT
26972 CTTTTTTTTT
1 CTTTTTTTTT
26982 CTTTTCTTTTT
1 CTTTT-TTTTT
26993 CTTTTTTCTTT
1 CTTTTTT-TTT
27004 -TTTTTTT
1 CTTTTTTT
27011 CTTCAAGCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 4 0.09
10 26 0.60
11 13 0.30
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:26974 original size:14 final size:14
Alignment explanation
Indices: 26955--27009 Score: 85
Period size: 14 Copynumber: 3.9 Consensus size: 14
26945 CCCCCCCCTT
26955 TTTCTTTTTTTTTC
1 TTTCTTTTTTTTTC
26969 TTTCTTTTTTTTTC
1 TTTCTTTTTTTTTC
*
26983 TTTTCTTTTTCTTT-
1 -TTTCTTTTTTTTTC
26997 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
27010 TCTTCAAGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 12 0.32
14 14 0.37
15 12 0.32
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTCTTTTTTTTTC
Found at i:27011 original size:24 final size:25
Alignment explanation
Indices: 26952--27013 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
26942 TGACCCCCCC
*
26952 CTTTTTCTTTT-TTTTTCTTTCTTT
1 CTTTTTTTTTTCTTTTTCTTTCTTT
26976 -TTTTTTCTTTTCTTTTTCTTT-TTT
1 CTTTTTT-TTTTCTTTTTCTTTCTTT
27000 CTTTTTTTTTTCTT
1 CTTTTTTTTTTCTT
27014 CAAGCATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
23 5 0.15
24 14 0.41
25 15 0.44
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (25 bp):
CTTTTTTTTTTCTTTTTCTTTCTTT
Found at i:27013 original size:29 final size:29
Alignment explanation
Indices: 26954--27009 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
26944 ACCCCCCCCT
*
26954 TTTTCTTTTTTTTTCTTTCTTTTTTTTTC
1 TTTTCTTTTTCTTTCTTTCTTTTTTTTTC
26983 TTTTCTTTTTCTTT-TTTCTTTTTTTTT
1 TTTTCTTTTTCTTTCTTTCTTTTTTTTT
27010 TCTTCAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (29 bp):
TTTTCTTTTTCTTTCTTTCTTTTTTTTTC
Found at i:39305 original size:16 final size:17
Alignment explanation
Indices: 39284--39316 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
39274 TTGGTATATT
39284 TGTTTTTTTTT-TTCTC
1 TGTTTTTTTTTCTTCTC
39300 TGTTTTTTTTTCTTCTC
1 TGTTTTTTTTTCTTCTC
39317 AGTTCTCTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (17 bp):
TGTTTTTTTTTCTTCTC
Found at i:39820 original size:11 final size:12
Alignment explanation
Indices: 39798--39826 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
39788 TGTAATTAAT
39798 TATTTATATATA
1 TATTTATATATA
39810 TATTT-TATATA
1 TATTTATATATA
39821 TATTTA
1 TATTTA
39827 ATAATGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTTATATATA
Found at i:39839 original size:3 final size:3
Alignment explanation
Indices: 39825--39871 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
39815 TATATATATT
*
39825 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
39872 TGGATAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:40930 original size:29 final size:28
Alignment explanation
Indices: 40898--40962 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
40888 AAAATTACAT
* * *
40898 TTTGGTC-CCTAAACTTTTCAAAGTTATAC
1 TTTGGTCACC-AAACTTTACAAA-TGATAA
*
40927 TTTGATCACCAAACTTTACAAATGATAA
1 TTTGGTCACCAAACTTTACAAATGATAA
40955 TTTGGTCA
1 TTTGGTCA
40963 TTAAATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 11 0.37
29 17 0.57
30 2 0.07
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.38
Consensus pattern (28 bp):
TTTGGTCACCAAACTTTACAAATGATAA
Found at i:41699 original size:22 final size:23
Alignment explanation
Indices: 41654--41699 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
41644 GATTAAAAGA
* *
41654 TAGATATAAGAGGATATGATTAT
1 TAGATATAAGAGGATAAGAATAT
*
41677 TAGATATAA-ATGATAAGAATAT
1 TAGATATAAGAGGATAAGAATAT
41699 T
1 T
41700 GTTGGTGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (23 bp):
TAGATATAAGAGGATAAGAATAT
Found at i:43449 original size:27 final size:29
Alignment explanation
Indices: 43418--43487 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 29
43408 GTTCTGGAGA
*
43418 ACATAGGTAACCGTCC-AT-TCCTGAAGG
1 ACATAGGTAACCGTCCAATGTCCTGAAAG
* *
43445 ACATAGGTAAACTGTCCATATGTCTTGAAAG
1 ACATAGGT-AACCGTCCA-ATGTCCTGAAAG
43476 ACATAGGTAACC
1 ACATAGGTAACC
43488 CTCGACTTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 8 0.23
28 7 0.20
30 5 0.14
31 15 0.43
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (29 bp):
ACATAGGTAACCGTCCAATGTCCTGAAAG
Found at i:43752 original size:2 final size:2
Alignment explanation
Indices: 43745--43809 Score: 107
Period size: 2 Copynumber: 33.5 Consensus size: 2
43735 CATATAATCT
43745 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
43786 -A TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
43810 TCATGTACAT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43778 original size:29 final size:29
Alignment explanation
Indices: 43745--43809 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
43735 CATATAATCT
43745 TATATATATATAATATATATATATATATA
1 TATATATATATAATATATATATATATATA
*
43774 TATATATATATAATATATATATATATATT
1 TATATATATATAATATATATATATATATA
43803 TATATAT
1 TATATAT
43810 TCATGTACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TATATATATATAATATATATATATATATA
Found at i:44545 original size:20 final size:20
Alignment explanation
Indices: 44520--44574 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 20
44510 ATTTAAAGTA
44520 GGTATCGGTACCCTCTATAG
1 GGTATCGGTACCCTCTATAG
44540 GGTATCGGTACACCCCTCTATAG
1 GGTATCGGT--A-CCCTCTATAG
44563 GGTATCGGTACC
1 GGTATCGGTACC
44575 ATACCTAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.34
21 1 0.03
22 1 0.03
23 19 0.59
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.27
Consensus pattern (20 bp):
GGTATCGGTACCCTCTATAG
Found at i:44560 original size:23 final size:23
Alignment explanation
Indices: 44530--44573 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
44520 GGTATCGGTA
44530 CCCTCTATAGGGTATCGGTACAC
1 CCCTCTATAGGGTATCGGTACAC
44553 CCCTCTATAGGGTATCGGTAC
1 CCCTCTATAGGGTATCGGTAC
44574 CATACCTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (23 bp):
CCCTCTATAGGGTATCGGTACAC
Found at i:46253 original size:19 final size:21
Alignment explanation
Indices: 46210--46261 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
46200 GAAACCCCTT
46210 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
46231 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
46250 TGAAGATACATG
1 TGAAAATACATG
46262 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:49506 original size:24 final size:25
Alignment explanation
Indices: 49479--49530 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
49469 CTTGGCTTGC
*
49479 TTTCTTCTT-TGAATTT-CTTTTTCT
1 TTTCTT-TTCTGAATTTTCTTCTTCT
49503 TTTCTTTTCTGAATTTTCTTCTTCT
1 TTTCTTTTCTGAATTTTCTTCTTCT
49528 TTT
1 TTT
49531 TGTCTTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 2 0.08
24 13 0.52
25 10 0.40
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTCTTTTCTGAATTTTCTTCTTCT
Found at i:49519 original size:19 final size:18
Alignment explanation
Indices: 49497--49549 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
49487 TTGAATTTCT
49497 TTTTCTTTTCTTTTCTGAA
1 TTTTCTTTTCTTTT-TGAA
**
49516 TTTTCTTCTTCTTTTTGTC
1 TTTTCTT-TTCTTTTTGAA
49535 TTTTC-TTTCTTTTTG
1 TTTTCTTTTCTTTTTG
49550 TACTCCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 9 0.29
18 1 0.03
19 14 0.45
20 7 0.23
ACGTcount: A:0.04, C:0.17, G:0.06, T:0.74
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTGAA
Found at i:49527 original size:25 final size:24
Alignment explanation
Indices: 49479--49530 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
49469 CTTGGCTTGC
*
49479 TTTCTTCTTTGAATTTCTTTTTCT
1 TTTCTTCTTTGAATTTCTTCTTCT
49503 TTTCTT-TTCTGAATTTTCTTCTTCT
1 TTTCTTCTT-TGAA-TTTCTTCTTCT
49528 TTT
1 TTT
49531 TGTCTTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 2 0.08
24 10 0.40
25 13 0.52
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (24 bp):
TTTCTTCTTTGAATTTCTTCTTCT
Found at i:50284 original size:16 final size:17
Alignment explanation
Indices: 50258--50291 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
50248 AATACATGAC
50258 TTTTAAATGAAAATACA
1 TTTTAAATGAAAATACA
*
50275 TTTT-AATGAAGATACA
1 TTTTAAATGAAAATACA
50291 T
1 T
50292 GCTCTTGGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (17 bp):
TTTTAAATGAAAATACA
Found at i:53786 original size:15 final size:15
Alignment explanation
Indices: 53766--53816 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
53756 AGATAAGGTA
53766 ATGAAATAAGAAAGG
1 ATGAAATAAGAAAGG
*
53781 ATGAAA-GA-AAAGG
1 ATGAAATAAGAAAGG
53794 TAATGAAATAAGAAAGG
1 --ATGAAATAAGAAAGG
53811 ATGAAA
1 ATGAAA
53817 GAAAATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 5 0.17
14 1 0.03
15 18 0.60
16 1 0.03
17 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (15 bp):
ATGAAATAAGAAAGG
Found at i:53794 original size:30 final size:30
Alignment explanation
Indices: 53754--53833 Score: 133
Period size: 30 Copynumber: 2.7 Consensus size: 30
53744 ATGGTTAAGA
*
53754 AAAGATAAGGTAATGAAATAAGAAAGGATG
1 AAAGAAAAGGTAATGAAATAAGAAAGGATG
53784 AAAGAAAAGGTAATGAAATAAGAAAGGATG
1 AAAGAAAAGGTAATGAAATAAGAAAGGATG
* *
53814 AAAGAAAATGAAATGAAATA
1 AAAGAAAAGGTAATGAAATA
53834 GAGAGAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (30 bp):
AAAGAAAAGGTAATGAAATAAGAAAGGATG
Found at i:53808 original size:18 final size:18
Alignment explanation
Indices: 53755--53808 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
53745 TGGTTAAGAA
*
53755 AAGATAAGGTAATGAAAT
1 AAGAAAAGGTAATGAAAT
53773 AAG-AAAGG--ATG--A-
1 AAGAAAAGGTAATGAAAT
53785 AAGAAAAGGTAATGAAAT
1 AAGAAAAGGTAATGAAAT
53803 AAGAAA
1 AAGAAA
53809 GGATGAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 12
0.69 0.02 0.29
Matches are distributed among these distances:
12 3 0.10
13 6 0.21
15 6 0.21
17 5 0.17
18 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (18 bp):
AAGAAAAGGTAATGAAAT
Done.