Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005757.1 Hibiscus syriacus cultivar Beakdansim tig00013477_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: 74531
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:1774 original size:28 final size:28
Alignment explanation
Indices: 1742--1799 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1732 GAAAAGGGAG
*
1742 TAAAATGTAAGAAATATTAGAAAAC-ATA
1 TAAAAAGTAAGAAATATTA-AAAACTATA
* *
1770 TAAAAAGTAAGAAGTGTTAAAAACTATA
1 TAAAAAGTAAGAAATATTAAAAACTATA
1798 TA
1 TA
1800 TATAAATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.59, C:0.03, G:0.12, T:0.26
Consensus pattern (28 bp):
TAAAAAGTAAGAAATATTAAAAACTATA
Found at i:2737 original size:9 final size:9
Alignment explanation
Indices: 2725--2823 Score: 52
Period size: 9 Copynumber: 11.7 Consensus size: 9
2715 AAAATTGTTT
2725 AAATATTAA
1 AAATATTAA
2734 AAATA-T--
1 AAATATTAA
2740 AAATA-TAA
1 AAATATTAA
*
2748 AAATTTTAA
1 AAATATTAA
2757 AAA-A-T-A
1 AAATATTAA
* *
2763 AATTACTAA
1 AAATATTAA
* *
2772 AAATAATAT
1 AAATATTAA
*
2781 ACATATTAA
1 AAATATTAA
*
2790 AAATAATAA
1 AAATATTAA
*
2799 AATTATTATA
1 AAATATTA-A
2809 AGAAT-TTAA
1 A-AATATTAA
2818 AAATAT
1 AAATAT
2824 ATATATATAC
Statistics
Matches: 67, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
6 9 0.13
7 2 0.03
8 9 0.13
9 40 0.60
10 5 0.07
11 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (9 bp):
AAATATTAA
Found at i:2751 original size:23 final size:24
Alignment explanation
Indices: 2725--2776 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
2715 AAAATTGTTT
2725 AAATATTAAAAATATAAA-TA-TAA
1 AAATATTAAAAA-ATAAATTACTAA
*
2748 AAATTTTAAAAAATAAATTACTAA
1 AAATATTAAAAAATAAATTACTAA
2772 AAATA
1 AAATA
2777 ATATACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.20
23 13 0.52
24 7 0.28
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
AAATATTAAAAAATAAATTACTAA
Found at i:2805 original size:18 final size:18
Alignment explanation
Indices: 2747--2806 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
2737 TATAAATATA
2747 AAAATT-TT-AAAA-AAT
1 AAAATTATTAAAAATAAT
*
2762 -AAATTACTAAAAATAAT
1 AAAATTATTAAAAATAAT
*
2779 ATACA-TATTAAAAATAAT
1 A-AAATTATTAAAAATAAT
2797 AAAATTATTA
1 AAAATTATTA
2807 TAAGAATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
14 5 0.14
15 1 0.03
16 4 0.11
17 5 0.14
18 18 0.51
19 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTATTAAAAATAAT
Found at i:11295 original size:24 final size:24
Alignment explanation
Indices: 11268--11321 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
11258 ATATCGATGG
* *
11268 AGATGGATTTTGTGATAGAAGTGA
1 AGATGAATGTTGTGATAGAAGTGA
* *
11292 AGATGAATGTTGTGATGGAATTGA
1 AGATGAATGTTGTGATAGAAGTGA
11316 AGATGA
1 AGATGA
11322 TGAAGATGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.31
Consensus pattern (24 bp):
AGATGAATGTTGTGATAGAAGTGA
Found at i:20573 original size:29 final size:29
Alignment explanation
Indices: 20531--20634 Score: 109
Period size: 29 Copynumber: 3.6 Consensus size: 29
20521 AACCCAACCA
**
20531 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
20560 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* *** *
20589 GAGGTCGCCATGCACTCGGGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
20618 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
20635 GGGGCGACCA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.19, C:0.38, G:0.30, T:0.13
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:20613 original size:58 final size:58
Alignment explanation
Indices: 20532--20648 Score: 144
Period size: 58 Copynumber: 2.0 Consensus size: 58
20522 ACCCAACCAT
** *
20532 AGGTCGCCATGCACTCCCAGCGACCTCCTAGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACTCCCAGCGACCAACGAGGTCGCCATGCACGCCCGGCGACCAAGG
*** * * **
20590 AGGTCGCCATGCACTCGGGGCGACCAAGGAGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACTCCCAGCGACCAACGAGGTCGCCATGCACGCCCGGCGACCAAGG
20648 A
1 A
20649 TTCATGCATG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.21, C:0.36, G:0.32, T:0.11
Consensus pattern (58 bp):
AGGTCGCCATGCACTCCCAGCGACCAACGAGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:20658 original size:29 final size:29
Alignment explanation
Indices: 20561--20648 Score: 149
Period size: 29 Copynumber: 3.0 Consensus size: 29
20551 GCGACCTCCT
* **
20561 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACTCGGGGCGACCAAGG
20590 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACTCGGGGCGACCAAGG
20619 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACTCGGGGCGACCAAGG
20648 A
1 A
20649 TTCATGCATG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.22, C:0.33, G:0.36, T:0.09
Consensus pattern (29 bp):
AGGTCGCCATGCACTCGGGGCGACCAAGG
Found at i:20725 original size:15 final size:15
Alignment explanation
Indices: 20705--20734 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20695 CATGGGGCAC
20705 TCGAGGCGACCAAGG
1 TCGAGGCGACCAAGG
20720 TCGAGGCGACCAAGG
1 TCGAGGCGACCAAGG
20735 ATGACCAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.40, T:0.07
Consensus pattern (15 bp):
TCGAGGCGACCAAGG
Found at i:20911 original size:29 final size:29
Alignment explanation
Indices: 20878--20962 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
20868 AGCAGGGGAT
* * **
20878 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
* *
20907 GTCGCCGGGCGTGCATGGCGACCTAGGAG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
*
20936 GTCGCTGGGAGTGCATGGCGACCTACG
1 GTCGCCGGGAGTGCATGGCGACCTACG
20963 GCCACTGTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.18
Consensus pattern (29 bp):
GTCGCCGGGAGTGCATGGCGACCTACGAG
Found at i:21299 original size:13 final size:12
Alignment explanation
Indices: 21266--21295 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21256 TTAAGATAAT
*
21266 AAAATATCTTAA
1 AAAATATTTTAA
21278 AAAATATTTTAA
1 AAAATATTTTAA
21290 AAAATA
1 AAAATA
21296 ATTTGATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATATTTTAA
Found at i:23315 original size:50 final size:50
Alignment explanation
Indices: 23240--23335 Score: 165
Period size: 50 Copynumber: 1.9 Consensus size: 50
23230 GTATCTCCAA
* *
23240 AACAAGACGACATTCACCTCTATAATTCCACTACAAACAATCAATTATAG
1 AACAAGACGACATTCACCTCCATAATTCCACCACAAACAATCAATTATAG
*
23290 AACAAGACGACATTCACCTCCATAATTCCACCACGAACAATCAATT
1 AACAAGACGACATTCACCTCCATAATTCCACCACAAACAATCAATT
23336 GTAATTCTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.43, C:0.29, G:0.06, T:0.22
Consensus pattern (50 bp):
AACAAGACGACATTCACCTCCATAATTCCACCACAAACAATCAATTATAG
Found at i:23749 original size:15 final size:15
Alignment explanation
Indices: 23731--23864 Score: 106
Period size: 15 Copynumber: 8.5 Consensus size: 15
23721 CTCCTCTTCC
23731 TCTTTCTTGGGTTCT
1 TCTTTCTTGGGTTCT
* *
23746 TCTTTCTTCGGCTCT
1 TCTTTCTTGGGTTCT
* * *
23761 TCCTTCTTAGGCTCT
1 TCTTTCTTGGGTTCT
*
23776 TCTTTCTTTGGTTTCTCT
1 TCTTTC-TTGG-GT-TCT
*
23794 TCCTTCTTGGGTTCT
1 TCTTTCTTGGGTTCT
*
23809 TCTTTCTTTGGTTCCT
1 TCTTTCTTGGGTT-CT
23825 CCTCTTTCTTGGGTTCT
1 --TCTTTCTTGGGTTCT
* * * *
23842 TCCTTCTTTGGCTCC
1 TCTTTCTTGGGTTCT
23857 TCTTTCTT
1 TCTTTCTT
23865 CTCTGGTTTC
Statistics
Matches: 95, Mismatches: 18, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
15 63 0.66
16 6 0.06
17 6 0.06
18 20 0.21
ACGTcount: A:0.01, C:0.28, G:0.14, T:0.57
Consensus pattern (15 bp):
TCTTTCTTGGGTTCT
Found at i:23857 original size:30 final size:31
Alignment explanation
Indices: 23728--23864 Score: 152
Period size: 33 Copynumber: 4.4 Consensus size: 31
23718 CTTCTCCTCT
*
23728 TCCTCTTTCTTGGGTTCTTCTTTCTTCGG-C
1 TCCTCTTTCTTGGGTTCTTCTTTCTTTGGTC
* * * *
23758 TCTTCCTTCTTAGGCTCTTCTTTCTTTGGTTTC
1 TCCTCTTTCTTGGGTTCTTCTTTCTTTGG--TC
* *
23791 TCTTCCTTCTTGGGTTCTTCTTTCTTTGGTTCC
1 TCCTCTTTCTTGGGTTCTTCTTTCTTTGG-T-C
*
23824 TCCTCTTTCTTGGGTTCTTCCTTCTTTGG-C
1 TCCTCTTTCTTGGGTTCTTCTTTCTTTGGTC
23854 TCCTCTTTCTT
1 TCCTCTTTCTT
23865 CTCTGGTTTC
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
30 36 0.39
32 2 0.02
33 55 0.59
ACGTcount: A:0.01, C:0.29, G:0.14, T:0.56
Consensus pattern (31 bp):
TCCTCTTTCTTGGGTTCTTCTTTCTTTGGTC
Found at i:29246 original size:186 final size:185
Alignment explanation
Indices: 28931--29321 Score: 642
Period size: 186 Copynumber: 2.1 Consensus size: 185
28921 ATAAAATTTT
* * *
28931 AAATATTAAATATATTATATATAACGTATGAGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTCAGCACAAACCATTTAAAACCCAATTAATAA
*
28996 TTTAAGATCCAATAACTTTGAAACCTAAATCAATATTAATTAATTAAAAATTTTATATAAAATTT
66 TTTAAGATCCAATAACTTTGAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAA-TT
* *
29061 TTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTATGAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAACTATAAACTGTTTTT-TGAATTAAA
*
29118 AAATATTAAATATATTATATATAACATATGGGCTCAGCACAAACCATTT-AAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTCAGCACAAACCATTTAAAACCCAATTAATAA
*
29182 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAGATCCAATAACTTTGAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
* *
29247 TTATTTTATAATTATATATTATTTAAATTAACTATAAACTGTTTTTTTAATTATA
131 TTATTTTATAATTATATATTATTTAAATTAACTATAAACTGTTTTTTGAATTAAA
* *
29302 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
29322 AATTAGAAAA
Statistics
Matches: 192, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
183 8 0.04
184 17 0.09
185 47 0.24
186 74 0.39
187 46 0.24
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATGAGCTCAGCACAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTGAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAACTATAAACTGTTTTTTGAATTAAA
Found at i:48736 original size:17 final size:18
Alignment explanation
Indices: 48716--48753 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
48706 TGTAGTTTAA
48716 AAAAATAA-ATAAATCAT
1 AAAAATAAGATAAATCAT
*
48733 AAAATTAAGATAAATCAT
1 AAAAATAAGATAAATCAT
48751 AAA
1 AAA
48754 TTTAGTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (18 bp):
AAAAATAAGATAAATCAT
Found at i:52788 original size:12 final size:12
Alignment explanation
Indices: 52771--52796 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52761 ATTAATTAAT
52771 ACTAATCAAGTA
1 ACTAATCAAGTA
52783 ACTAATCAAGTA
1 ACTAATCAAGTA
52795 AC
1 AC
52797 AATATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (12 bp):
ACTAATCAAGTA
Found at i:52861 original size:43 final size:45
Alignment explanation
Indices: 52786--52876 Score: 159
Period size: 43 Copynumber: 2.1 Consensus size: 45
52776 TCAAGTAACT
*
52786 AATCAAGTAACAATATATATATAATATTATTAACAAACAATACCA
1 AATCAAGTAACAATATATATATAATATTATTAACAAACAAGACCA
52831 AATCAAGTAAC-A-ATATATATAATATTATTAACAAACAAGACCA
1 AATCAAGTAACAATATATATATAATATTATTAACAAACAAGACCA
52874 AAT
1 AAT
52877 GATAATTCGG
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
43 33 0.73
44 1 0.02
45 11 0.24
ACGTcount: A:0.56, C:0.13, G:0.03, T:0.27
Consensus pattern (45 bp):
AATCAAGTAACAATATATATATAATATTATTAACAAACAAGACCA
Found at i:53771 original size:17 final size:17
Alignment explanation
Indices: 53749--53790 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
53739 AGAAGATGAG
53749 TCTTTTT-TTTTTGTATT
1 TCTTTTTATTTTTG-ATT
53766 TCTTTTTCATTTTTGATT
1 TCTTTTT-ATTTTTGATT
53784 T-TTTTTA
1 TCTTTTTA
53791 CTTATGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 12 0.52
18 4 0.17
19 6 0.26
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.79
Consensus pattern (17 bp):
TCTTTTTATTTTTGATT
Found at i:61512 original size:30 final size:30
Alignment explanation
Indices: 61440--61513 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
61430 TGCTTGTTTT
* * * *
61440 CATTTCGATTATATGGATATACTATGTTGC
1 CATTTCGACTATATGAACATACTAGGTTGC
* *
61470 CATTT-TAGCTATATGAACCTACTAGGTTGC
1 CATTTCGA-CTATATGAACATACTAGGTTGC
61500 CATTTCGACTATAT
1 CATTTCGACTATAT
61514 AAATGTATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
29 1 0.03
30 33 0.94
31 1 0.03
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (30 bp):
CATTTCGACTATATGAACATACTAGGTTGC
Found at i:61928 original size:93 final size:92
Alignment explanation
Indices: 61749--62303 Score: 515
Period size: 93 Copynumber: 6.0 Consensus size: 92
61739 AACTCCGTCT
* * * * * *
61749 ATTAATGGATGAAAGCTTGAATAACGTTGACATGTTTTAACTAAACACTTTGATGTTTATGGAC-
1 ATTAATGGATG-AAGTTTGAATAGCGTTGAAATATCTTAACTAAACACTTTGATGTTTATAGACT
* **
61813 ATAAGATGTTATGTTATCCAAGTTGTTAC
65 A-AAGAGGTTAACTTATCCAAGTTGTTAC
* * *
61842 ATTAATGGATGTAAGTTTAAATAGCGTTGAAATATCTTAATTAAACATTTTGATGTTTATAGACT
1 ATTAATGGATG-AAGTTTGAATAGCGTTGAAATATCTTAACTAAACACTTTGATGTTTATAGACT
* *
61907 AAAGAGGTAAACTTATGCAAGTTGTTAC
65 AAAGAGGTTAACTTATCCAAGTTGTTAC
* * * * *
61935 GTTAATAGATAGAAATTTGAATAGCGTTGAAATATCTTAACTAAACACTTTAATGTTTATGGACT
1 ATTAATGGAT-GAAGTTTGAATAGCGTTGAAATATCTTAACTAAACACTTTGATGTTTATAGACT
*
62000 AAAGAGGTTAATTTATCCAAGTTGTTAC
65 AAAGAGGTTAACTTATCCAAGTTGTTAC
* * * * * * * * *
62028 ATTAATGGATGAAACTTTGAATTGTGTTGAATTTTTTTTTAACTAAATACTTTGATTTTTACAGA
1 ATTAATGGATG-AAGTTTGAATAGCGTTGAA--ATATCTTAACTAAACACTTTGATGTTTATAGA
* * ** *
62093 CTAAAGAGGCTAATTTATTTAAGTAGTTAC
63 CTAAAGAGGTTAACTTATCCAAGTTGTTAC
* * ** *
62123 ATTAATGGATGAGAGTTTGAATAGCGTTGAAATGTCTTAATTAAGTACTTTGATGTTTACAGACT
1 ATTAATGGATGA-AGTTTGAATAGCGTTGAAATATCTTAACTAAACACTTTGATGTTTATAGACT
* * *
62188 GGAA-ATGTTTACTTATCCAAGTTGTTAC
65 -AAAGAGGTTAACTTATCCAAGTTGTTAC
* ** * * * * * *
62216 ATTAATGGATG--GATTGAATAATGTTAAAATGTCTTAACTAAATAATTTGATGTTTACAAACTA
1 ATTAATGGATGAAGTTTGAATAGCGTTGAAATATCTTAACTAAACACTTTGATGTTTATAGACTA
* * *
62279 AAAAGGTTAACTCATCCAAATTGTT
66 AAGAGGTTAACTTATCCAAGTTGTT
62304 GATGGAAGTT
Statistics
Matches: 381, Mismatches: 73, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
89 2 0.01
90 61 0.16
92 1 0.00
93 236 0.62
94 5 0.01
95 76 0.20
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.39
Consensus pattern (92 bp):
ATTAATGGATGAAGTTTGAATAGCGTTGAAATATCTTAACTAAACACTTTGATGTTTATAGACTA
AAGAGGTTAACTTATCCAAGTTGTTAC
Found at i:62206 original size:188 final size:185
Alignment explanation
Indices: 61749--62290 Score: 531
Period size: 188 Copynumber: 2.9 Consensus size: 185
61739 AACTCCGTCT
* * * * *
61749 ATTAATGGATGAAAGCTTGAATAACGTTGACATGTTTTAACTAAACACTTTGATGTTTATGGACA
1 ATTAATGGATGAGAGTTTGAATAGCGTTGAAATGTCTTAACTAAACACTTTGATGTTTATGGAC-
* * *
61814 TAAGATG-TTATGTTATCCAAGTTGTTACATTAATGGATGTAAGTTTAAATAGCGTTGAAATATC
65 TAAGATGTTTA-CTTATCCAAGTTGTTACATTAATGGATGAAACTTTAAATAGCGTTGAAATATC
* * * *
61878 TTAATTAAACATTTTGATGTTTATAGACTAAAGAGGTAAACTTATGCAAGTTGTTAC
129 TTAACTAAACACTTTGATGTTTACAGACTAAAGAGGTAAACTTATGCAAGTAGTTAC
* * * * *
61935 GTTAATAGAT-AGAAATTTGAATAGCGTTGAAATATCTTAACTAAACACTTTAATGTTTATGGAC
1 ATTAATGGATGAG-AGTTTGAATAGCGTTGAAATGTCTTAACTAAACACTTTGATGTTTATGGAC
* * * * * * * *
61999 TAAAGAGGTTAATTTATCCAAGTTGTTACATTAATGGATGAAACTTTGAATTGTGTTGAATTTTT
65 T-AAGATGTTTACTTATCCAAGTTGTTACATTAATGGATGAAACTTTAAATAGCGTTGAA--ATA
* * * * **
62064 TTTTAACTAAATACTTTGATTTTTACAGACTAAAGAGGCT-AATTTATTTAAGTAGTTAC
127 TCTTAACTAAACACTTTGATGTTTACAGACTAAAGAGG-TAAACTTATGCAAGTAGTTAC
* ** **
62123 ATTAATGGATGAGAGTTTGAATAGCGTTGAAATGTCTTAATTAAGTACTTTGATGTTTACAGACT
1 ATTAATGGATGAGAGTTTGAATAGCGTTGAAATGTCTTAACTAAACACTTTGATGTTTATGGACT
* * ** * *
62188 GGAA-ATGTTTACTTATCCAAGTTGTTACATTAATGGATG-GA--TTGAATAATGTTAAAATGTC
66 --AAGATGTTTACTTATCCAAGTTGTTACATTAATGGATGAAACTTTAAATAGCGTTGAAATATC
* * * * *
62249 TTAACTAAATAATTTGATGTTTACAAACTAAAAAGGTTAACT
129 TTAACTAAACACTTTGATGTTTACAGACTAAAGAGGTAAACT
62291 CATCCAAATT
Statistics
Matches: 291, Mismatches: 56, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
182 1 0.00
183 37 0.13
185 14 0.05
186 99 0.34
187 3 0.01
188 132 0.45
189 5 0.02
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.39
Consensus pattern (185 bp):
ATTAATGGATGAGAGTTTGAATAGCGTTGAAATGTCTTAACTAAACACTTTGATGTTTATGGACT
AAGATGTTTACTTATCCAAGTTGTTACATTAATGGATGAAACTTTAAATAGCGTTGAAATATCTT
AACTAAACACTTTGATGTTTACAGACTAAAGAGGTAAACTTATGCAAGTAGTTAC
Found at i:63776 original size:16 final size:17
Alignment explanation
Indices: 63755--63789 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
63745 AACCTACTTA
63755 CAAAGAAAATCAAA-AT
1 CAAAGAAAATCAAAGAT
63771 CAAAGAAAATCAAAGAT
1 CAAAGAAAATCAAAGAT
63788 CA
1 CA
63790 CATATTTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.66, C:0.14, G:0.09, T:0.11
Consensus pattern (17 bp):
CAAAGAAAATCAAAGAT
Found at i:65347 original size:29 final size:29
Alignment explanation
Indices: 65298--65486 Score: 181
Period size: 29 Copynumber: 6.6 Consensus size: 29
65288 TAGAGGATCC
*
65298 CATGCAGAATCAGGACTAGGATATAATCT
1 CATGCAGAATCAGGACGAGGATATAATCT
* * *
65327 CATGTAGAATCAGAACGAGGATATATTCT
1 CATGCAGAATCAGGACGAGGATATAATCT
* * * *
65356 CATGCAAAATTAGGTCGGGGATATAAT-T
1 CATGCAGAATCAGGACGAGGATATAATCT
*
65384 CTATGCAGAATCAGGATGA-GAGTATAATCT
1 C-ATGCAGAATCAGGACGAGGA-TATAATCT
* *
65414 CATGCAGAATCTA-GATGAGAATATAATAC-
1 CATGCAGAATC-AGGACGAGGATATAAT-CT
* *
65443 CATTCAGAATCAGGATG-GGATATAATCT
1 CATGCAGAATCAGGACGAGGATATAATCT
*
65471 CATGCAGAATTAGGAC
1 CATGCAGAATCAGGAC
65487 ATAGATTATG
Statistics
Matches: 130, Mismatches: 22, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
27 1 0.01
28 26 0.20
29 98 0.75
30 5 0.04
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (29 bp):
CATGCAGAATCAGGACGAGGATATAATCT
Done.