Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006619.1 Hibiscus syriacus cultivar Beakdansim tig00016259_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: 141007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:822 original size:54 final size:54
Alignment explanation
Indices: 478--822 Score: 323
Period size: 52 Copynumber: 6.6 Consensus size: 54
468 TGTTAAAGGA
* * * * *
478 ATATGTTGATGAATGACCGTTATCG---GTAAGTGTGTAACCCATAGAATTCATC
1 ATATGTTGATGAACGACCG-TATCGACACTAAGTGTGCAACCCACAAAATTCATC
*
530 ATATGTTGATGAACGACCGTATCGACACAAAGTGT--AACCCACAAAATTCATC
1 ATATGTTGATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATC
* *
582 ATATGTTGACGAACGACCGTATCGACACAAAGTGTGCAA-CCACAAAATT-ATC
1 ATATGTTGATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATC
* * * *
634 ATATG-TAATGAATGACCATATCGGCACTAAGTGTGCAACCC-CAAAATTCATC
1 ATATGTTGATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATC
* * * * * * *
686 ATATGTT-ATGAATGACCGTATTGGCACTAGGTGTGCAAACCAAAAAATTCATT
1 ATATGTTGATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATC
* ** ** * * ** *
739 ATATATTGATGAATAATTGTATAGGCACTAAGTGTGCAACCCACGTAATTCATA
1 ATATGTTGATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATC
* * *
793 ATATGTTTATGAACGACCGCATCAACACTA
1 ATATGTTGATGAACGACCGTATCGACACTA
823 CTTGCGCATC
Statistics
Matches: 244, Mismatches: 39, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
51 39 0.16
52 115 0.47
53 26 0.11
54 64 0.26
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (54 bp):
ATATGTTGATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATC
Found at i:6183 original size:21 final size:21
Alignment explanation
Indices: 6157--6218 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
6147 ATCACTGTAA
6157 GATTTTATGGCTTCGACAAAT
1 GATTTTATGGCTTCGACAAAT
*
6178 GATTTTATGGCTTCGAAAAAT
1 GATTTTATGGCTTCGACAAAT
*
6199 GATTTTATGGCTTCAACAAA
1 GATTTTATGGCTTCGACAAA
6219 GGCCTTGATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (21 bp):
GATTTTATGGCTTCGACAAAT
Found at i:9937 original size:132 final size:132
Alignment explanation
Indices: 9743--10075 Score: 425
Period size: 132 Copynumber: 2.5 Consensus size: 132
9733 GTCTTTGCTT
* * * *
9743 CTCTTCAGGGTAGATCAGATCTAGAAATGTTGATTCACTTCAGTTCTCTTTAGGGAAGATTGAAT
1 CTCTTCAGGGTAGATCAGATCTGGAAACGTTGATTCACTTCACTACTCTTTAGGGAAGATTGAAT
* * * * ** * *
9808 CGAGGTAGATTTATTCCACTGCTCCTTAGGGAAGATTAAATCTAGAGAAAGGGGATATGCTTCGC
66 CGAGGAAGATTTATTCCACTGCTCCTCAGGGAAGATCAAATCTAGAAAAAGGAAATATGCTCCAC
9873 TG
131 TG
* * * *
9875 CTCTTCAGGGTAGATCAGATTTGGAAACGTTGATTCACTTCACTACACTTTAGAGAAAATTGAAT
1 CTCTTCAGGGTAGATCAGATCTGGAAACGTTGATTCACTTCACTACTCTTTAGGGAAGATTGAAT
* * * * *
9940 CTAGGAAGATTTATTCCATTGCTCCTCAGGGAATATCAAATCTGGAAAAAGTAAATATGCTCCAC
66 CGAGGAAGATTTATTCCACTGCTCCTCAGGGAAGATCAAATCTAGAAAAAGGAAATATGCTCCAC
*
10005 TT
131 TG
* * *
10007 CTCTTCAGGGTAGATCAGATCTGGAAACTTTGATTAAC-TCAACTATTCTTTAGGGAAGATTGAA
1 CTCTTCAGGGTAGATCAGATCTGGAAACGTTGATTCACTTC-ACTACTCTTTAGGGAAGATTGAA
10071 TCGAG
65 TCGAG
10076 TTTTATATTT
Statistics
Matches: 170, Mismatches: 30, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
131 2 0.01
132 168 0.99
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (132 bp):
CTCTTCAGGGTAGATCAGATCTGGAAACGTTGATTCACTTCACTACTCTTTAGGGAAGATTGAAT
CGAGGAAGATTTATTCCACTGCTCCTCAGGGAAGATCAAATCTAGAAAAAGGAAATATGCTCCAC
TG
Found at i:21125 original size:33 final size:34
Alignment explanation
Indices: 21088--21151 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
21078 AAATGAAAAT
*
21088 GGATTTTGAA-AATC-AAAATGAAATCTTGAAGAA
1 GGATTTAGAACAATCAAAAATGAAAT-TTGAAGAA
*
21121 GGATTTAGAACTATCAAAAATGAAATTTGAA
1 GGATTTAGAACAATCAAAAATGAAATTTGAA
21152 AGTATCGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 9 0.33
34 8 0.30
35 10 0.37
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.28
Consensus pattern (34 bp):
GGATTTAGAACAATCAAAAATGAAATTTGAAGAA
Found at i:25078 original size:23 final size:22
Alignment explanation
Indices: 25036--25116 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 22
25026 GTAGGGCGGA
*
25036 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATTCCCCCTTGAAG
*
25058 GGGAATCGATTCCCCCTTTGAAT
1 GGGAATCGATTCCCCC-TTGAAG
* *
25081 GGGAATTGATT-CCCCAT--AG
1 GGGAATCGATTCCCCCTTGAAG
*
25100 GGGAATCGATACCCCCT
1 GGGAATCGATTCCCCCT
25117 GGGGTTCTGG
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
19 10 0.20
20 4 0.08
21 1 0.02
22 19 0.39
23 15 0.31
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (22 bp):
GGGAATCGATTCCCCCTTGAAG
Found at i:27098 original size:165 final size:165
Alignment explanation
Indices: 26827--27159 Score: 607
Period size: 165 Copynumber: 2.0 Consensus size: 165
26817 AAAGGGGGAG
*
26827 AAATGTTTGTGTTTTTAAAAGAGGAGTAGTGTTAAAGTAAGGGGGAGTAGTATTTTTCAAAATCA
1 AAATGTTTGTGTTTTTAAAAGAGGAGTAGTGTTAAAGTAAGGGGGAGTAGTACTTTTCAAAATCA
*
26892 AAATTCATTTTGAAATTAGAAAGTCTTAAAACGTTTTGTTATATCAAAAAGGGGGAGATTGTTGA
66 AAATTCATTTTGAAATTAGAAAATCTTAAAACGTTTTGTTATATCAAAAAGGGGGAGATTGTTGA
26957 AAACATTTTGTTGTTTCGATATAACAAATTAAATTTA
131 AAACATTTTGTTG-TTCGATATAACAAATTAAA-TTA
26994 AAATGTTTGTGTTTTTAAAAGAGGAGTAGTGTTAAAGTAA-GGGG-GTAGTACTTTTCAAAATCA
1 AAATGTTTGTGTTTTTAAAAGAGGAGTAGTGTTAAAGTAAGGGGGAGTAGTACTTTTCAAAATCA
*
27057 AAATTCATTTTGAAATTAGAAAATCTTAAAATGTTTTGTTATATCAAAAAGGGGGAGATTGTTGA
66 AAATTCATTTTGAAATTAGAAAATCTTAAAACGTTTTGTTATATCAAAAAGGGGGAGATTGTTGA
27122 AAACATTTTGTTGTTCGATATAACAAATTAAATTA
131 AAACATTTTGTTGTTCGATATAACAAATTAAATTA
27157 AAA
1 AAA
27160 GAATTTTAAT
Statistics
Matches: 163, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
163 6 0.04
164 19 0.12
165 94 0.58
166 4 0.02
167 40 0.25
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (165 bp):
AAATGTTTGTGTTTTTAAAAGAGGAGTAGTGTTAAAGTAAGGGGGAGTAGTACTTTTCAAAATCA
AAATTCATTTTGAAATTAGAAAATCTTAAAACGTTTTGTTATATCAAAAAGGGGGAGATTGTTGA
AAACATTTTGTTGTTCGATATAACAAATTAAATTA
Found at i:29664 original size:17 final size:18
Alignment explanation
Indices: 29629--29666 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29619 ATATTTGTCA
*
29629 TTTAATAAAAATATTCAT
1 TTTAATAAAAATATACAT
*
29647 TTTAATTAAAATA-ACAT
1 TTTAATAAAAATATACAT
29664 TTT
1 TTT
29667 TATAGTATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAATAAAAATATACAT
Found at i:30007 original size:5 final size:5
Alignment explanation
Indices: 29989--30018 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
29979 ATTCAAATGT
29989 ATAAA ATAATA ATAAA ATAAA ATAAA ATAA
1 ATAAA ATAA-A ATAAA ATAAA ATAAA ATAA
30019 TTAAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:31758 original size:7 final size:7
Alignment explanation
Indices: 31741--31784 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
31731 AATTTTGACT
31741 AAATAAAA
1 AAAT-AAA
31749 AAATAAA
1 AAATAAA
31756 AAATAAA
1 AAATAAA
*
31763 ATAA-AAT
1 A-AATAAA
31770 AAATAAA
1 AAATAAA
31777 AAATAAA
1 AAATAAA
31784 A
1 A
31785 GATTCAGGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 2 0.06
7 24 0.75
8 6 0.19
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:31775 original size:21 final size:20
Alignment explanation
Indices: 31741--31784 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 20
31731 AATTTTGACT
31741 AAATAAAAAAATAAAAAATA
1 AAATAAAAAAATAAAAAATA
31761 AAATAAAATAAATAAAAAATA
1 AAATAAAA-AAATAAAAAATA
31782 AAA
1 AAA
31785 GATTCAGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (20 bp):
AAATAAAAAAATAAAAAATA
Found at i:46745 original size:10 final size:10
Alignment explanation
Indices: 46730--46758 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
46720 CCTTACATGC
46730 CAAAAATAAA
1 CAAAAATAAA
46740 CAAAAAT-AA
1 CAAAAATAAA
46749 CAAAAATAAA
1 CAAAAATAAA
46759 GTGAAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (10 bp):
CAAAAATAAA
Found at i:55277 original size:19 final size:21
Alignment explanation
Indices: 55234--55285 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
55224 GAAACCCCTT
55234 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
55255 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
55274 TGAAGATACATG
1 TGAAAATACATG
55286 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:58620 original size:23 final size:23
Alignment explanation
Indices: 58588--58649 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 23
58578 CCTTGGCTTG
58588 CTTTTCTCTTTT-TGAAATCTTT-TT
1 CTTTT-TCTTTTCTG-AAT-TTTCTT
58612 CTTTTTCTTTTCTGAATTTTCTT
1 CTTTTTCTTTTCTGAATTTTCTT
58635 CTTTTTGTCTTTTCT
1 C-TTTT-TCTTTTCT
58650 TTCTTTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.09
23 12 0.35
24 11 0.32
25 8 0.24
ACGTcount: A:0.08, C:0.18, G:0.05, T:0.69
Consensus pattern (23 bp):
CTTTTTCTTTTCTGAATTTTCTT
Found at i:58649 original size:16 final size:17
Alignment explanation
Indices: 58628--58659 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
58618 CTTTTCTGAA
58628 TTTTC-TTCTTTTTGTC
1 TTTTCTTTCTTTTTGTC
58644 TTTTCTTTCTTTTTGT
1 TTTTCTTTCTTTTTGT
58660 ACTCCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGTC
Found at i:59422 original size:19 final size:21
Alignment explanation
Indices: 59379--59430 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
59369 GAAACCCCTT
59379 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
59400 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
59419 TGAAGATACATG
1 TGAAAATACATG
59431 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:62269 original size:105 final size:103
Alignment explanation
Indices: 62085--62273 Score: 263
Period size: 105 Copynumber: 1.8 Consensus size: 103
62075 GAGTTACTGT
* ****
62085 TAATAGTGTTGAACATTTGGTCACTAAAAACACTTACTGTGACAACTTTGGTGGTCACAAAATAT
1 TAATAGTATTGAACATTTGGTCACTAAAAACACTTACTGTGACAACTTTAACAGTCACAAAATAT
62150 ACTTTCAGTGTAAAATAAATTTATAACATTTTCTATTGA
66 ACTTTCAGTGTAAAA-AAATTTATAACATTTTCTATTGA
*
62189 TAATAGTATTGAACATTTGGTCACTAAGAAATACTTACTGTGACAA-TATTAACAGTCACAAAAT
1 TAATAGTATTGAACATTTGGTCACTAA-AAACACTTACTGTGACAACT-TTAACAGTCACAAAAT
* * *
62253 ATATTTTTAGTTTAAAAAAAT
64 ATACTTTCAGTGTAAAAAAAT
62274 CACCACAAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
104 31 0.42
105 43 0.58
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (103 bp):
TAATAGTATTGAACATTTGGTCACTAAAAACACTTACTGTGACAACTTTAACAGTCACAAAATAT
ACTTTCAGTGTAAAAAAATTTATAACATTTTCTATTGA
Found at i:63718 original size:7 final size:7
Alignment explanation
Indices: 63706--63744 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
63696 CGTGGTGTAT
63706 TATAATA
1 TATAATA
63713 TATAATA
1 TATAATA
63720 TATAATA
1 TATAATA
*
63727 TATAGTA
1 TATAATA
63734 TATAATA
1 TATAATA
63741 TATA
1 TATA
63745 TAGTTTAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (7 bp):
TATAATA
Found at i:63870 original size:13 final size:13
Alignment explanation
Indices: 63852--63876 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63842 CATATTTTAA
63852 TTCATATTACATT
1 TTCATATTACATT
63865 TTCATATTACAT
1 TTCATATTACAT
63877 GCCATGTTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (13 bp):
TTCATATTACATT
Found at i:70699 original size:46 final size:46
Alignment explanation
Indices: 70649--70940 Score: 446
Period size: 46 Copynumber: 6.3 Consensus size: 46
70639 ATATCAATTT
* *
70649 ATGCATTTAAATTATGGAATCCTTTCATGCCTTAATGTATCCTTTC
1 ATGCATTTTAATTATGGAATCCTTTCATGCCTTAATGCATCCTTTC
* *
70695 ATGCATTTTAGTTTAT-GACATTCTTTCATGCCTTAATGCATCCTTTC
1 ATGCATTTTA-ATTATGGA-ATCCTTTCATGCCTTAATGCATCCTTTC
*
70742 ATGCATTTTAATTATGGAATCCTTTCATGCCTTAAGGCATCCTTTC
1 ATGCATTTTAATTATGGAATCCTTTCATGCCTTAATGCATCCTTTC
*
70788 ATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTC
1 ATGCATTTTAATTATGGAATCCTTTCATGCCTTAATGCATCCTTTC
*
70834 ATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTC
1 ATGCATTTTAATTATGGAATCCTTTCATGCCTTAATGCATCCTTTC
* * *
70880 ATTCATTTTAATTAT-GACAT-CTTTCATGCCTTAATGCCTCCATTC
1 ATGCATTTTAATTATGGA-ATCCTTTCATGCCTTAATGCATCCTTTC
70925 ATGCATTTTAATTATG
1 ATGCATTTTAATTATG
70941 TATTCAATTT
Statistics
Matches: 227, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
45 38 0.17
46 147 0.65
47 42 0.19
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.44
Consensus pattern (46 bp):
ATGCATTTTAATTATGGAATCCTTTCATGCCTTAATGCATCCTTTC
Found at i:70770 original size:26 final size:26
Alignment explanation
Indices: 70687--70908 Score: 170
Period size: 20 Copynumber: 9.5 Consensus size: 26
70677 GCCTTAATGT
* *
70687 ATCCTTTCATGCATTTTAGTTTATGAC
1 ATCCTTTCATGCATTTTA-ATTATGGC
* *
70714 ATTCTTTCATGC--CTT-A--AT-GC
1 ATCCTTTCATGCATTTTAATTATGGC
*
70734 ATCCTTTCATGCATTTTAATTATGGA
1 ATCCTTTCATGCATTTTAATTATGGC
*
70760 ATCCTTTCATGC--CTT-A--A-GGC
1 ATCCTTTCATGCATTTTAATTATGGC
70780 ATCCTTTCATGCATTTTAATTATGGC
1 ATCCTTTCATGCATTTTAATTATGGC
*
70806 ATCCTTTCATGC--CTT-A--AT-GC
1 ATCCTTTCATGCATTTTAATTATGGC
70826 ATCCTTTCATGCATTTTAATTATGGC
1 ATCCTTTCATGCATTTTAATTATGGC
*
70852 ATCCTTTCATGC--CTT-A--AT-GC
1 ATCCTTTCATGCATTTTAATTATGGC
* *
70872 ATCCTTTCATTCATTTTAATTATGAC
1 ATCCTTTCATGCATTTTAATTATGGC
70898 AT-CTTTCATGC
1 ATCCTTTCATGC
70909 CTTAATGCCT
Statistics
Matches: 154, Mismatches: 17, Indels: 50
0.70 0.08 0.23
Matches are distributed among these distances:
20 53 0.34
21 7 0.05
22 8 0.05
23 7 0.05
24 6 0.04
25 17 0.11
26 45 0.29
27 11 0.07
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (26 bp):
ATCCTTTCATGCATTTTAATTATGGC
Found at i:71342 original size:20 final size:21
Alignment explanation
Indices: 71314--71365 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
71304 AAGCTCAGTA
71314 GTATCGATACTAC-TACTATG
1 GTATCGATACTACATACTATG
* *
71334 GTATTGATACTTCTATACTATG
1 GTATCGATACTAC-ATACTATG
71356 GTATCGATAC
1 GTATCGATAC
71366 CCCCTTCTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 11 0.41
22 16 0.59
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
GTATCGATACTACATACTATG
Found at i:71477 original size:95 final size:95
Alignment explanation
Indices: 71313--71553 Score: 274
Period size: 95 Copynumber: 2.6 Consensus size: 95
71303 CAAGCTCAGT
* * * * * * **
71313 AGTATCGATACTAC-TACTATGGTATTGATACTTCTATACTATGGTATCGATACCCCCTTCTGGT
1 AGTATCGATAC-CCTTACCATGGTATCGGTACTACCATACTATGGTATCGATACCCCCTTCCAGT
*
71377 ATCGATACCAATTTTAGATTCGATGTTTCCC
65 ATCGATACCAATTTTAGATTCGATGTTACCC
* * **
71408 GGTATCGATACCCTTTCCATGGTATCGGTACTACCATACTATGGTA-CTGATATTCCCTTCCAGT
1 AGTATCGATACCCTTACCATGGTATCGGTACTACCATACTATGGTATC-GATACCCCCTTCCAGT
* *
71472 ATCGATACTAATTTTAGATTCGATGTTACCT
65 ATCGATACCAATTTTAGATTCGATGTTACCC
* * *
71503 AGTATCGATACCCTTACCATGGTATCGATATTACCTTA-T-TGGTATCGATAC
1 AGTATCGATACCCTTACCATGGTATCGGTACTACCATACTATGGTATCGATAC
71554 TGATTGAATC
Statistics
Matches: 122, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
93 9 0.07
94 4 0.03
95 109 0.89
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (95 bp):
AGTATCGATACCCTTACCATGGTATCGGTACTACCATACTATGGTATCGATACCCCCTTCCAGTA
TCGATACCAATTTTAGATTCGATGTTACCC
Found at i:79319 original size:18 final size:18
Alignment explanation
Indices: 79298--79336 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
79288 GGAAAAGAAT
79298 AGAAAA-AAAAGACAAAAA
1 AGAAAAGAAAA-ACAAAAA
*
79316 AGAAAAGAAAAATAAAAA
1 AGAAAAGAAAAACAAAAA
79334 AGA
1 AGA
79337 GAAATGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (18 bp):
AGAAAAGAAAAACAAAAA
Found at i:80054 original size:12 final size:10
Alignment explanation
Indices: 80022--80078 Score: 60
Period size: 10 Copynumber: 5.4 Consensus size: 10
80012 TTTTGAAAAG
80022 AAAAAAGAATA
1 AAAAAAGAA-A
80033 ACAAAAAGAAA
1 A-AAAAAGAAA
*
80044 GAAAAAGAGAA
1 AAAAAAGA-AA
*
80055 AAAAAACAAA
1 AAAAAAGAAA
*
80065 AAAAAACAAA
1 AAAAAAGAAA
80075 AAAA
1 AAAA
80079 GGGAAAATAG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
10 23 0.56
11 10 0.24
12 8 0.20
ACGTcount: A:0.84, C:0.05, G:0.09, T:0.02
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:81467 original size:16 final size:15
Alignment explanation
Indices: 81431--81469 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
81421 ACACATGGTG
*
81431 TATTATAATATATAA
1 TATTATAGTATATAA
81446 TA-TATAGTATATAA
1 TATTATAGTATATAA
81460 TATTTATAGT
1 TA-TTATAGT
81470 TTCTATACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 13 0.62
15 2 0.10
16 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
TATTATAGTATATAA
Found at i:81598 original size:20 final size:20
Alignment explanation
Indices: 81575--81612 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
81565 GTATTAAATA
81575 ATTGCATGGCATATTTTAGT
1 ATTGCATGGCATATTTTAGT
81595 ATTGCATGGCATATTTTA
1 ATTGCATGGCATATTTTA
81613 ATTCATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (20 bp):
ATTGCATGGCATATTTTAGT
Found at i:81683 original size:16 final size:16
Alignment explanation
Indices: 81662--81692 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
81652 GTGTGTGTTA
81662 CATATTATATAGTTTG
1 CATATTATATAGTTTG
81678 CATATTATATAGTTT
1 CATATTATATAGTTT
81693 ATAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (16 bp):
CATATTATATAGTTTG
Found at i:83752 original size:22 final size:22
Alignment explanation
Indices: 83723--83771 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
83713 AAAATCATTT
*
83723 AAAATATA-TATATATGTTTTC
1 AAAATATATTATATACGTTTTC
83744 AAAACTATATTATATACGTTTTC
1 AAAA-TATATTATATACGTTTTC
83767 AAAAT
1 AAAAT
83772 GTTTTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 5 0.20
23 16 0.64
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (22 bp):
AAAATATATTATATACGTTTTC
Found at i:83796 original size:36 final size:36
Alignment explanation
Indices: 83736--83877 Score: 202
Period size: 36 Copynumber: 4.0 Consensus size: 36
83726 ATATATATAT
83736 ATGTTTTCAAAAC--TATATTATATACGTTTTCAAA
1 ATGTTTTCAAAACTATATATTATATACGTTTTCAAA
*
83770 ATGTTTTCAAAACTATATATTATATACGTTTTTAAA
1 ATGTTTTCAAAACTATATATTATATACGTTTTCAAA
* * *
83806 ACGCTTTCAAAACCATATATTATAT--GTTTTCAAAA
1 ATGTTTTCAAAACTATATATTATATACGTTTTC-AAA
*
83841 ATGTTTTCAAAACTATATATTATATACGTTTTTAAA
1 ATGTTTTCAAAACTATATATTATATACGTTTTCAAA
83877 A
1 A
83878 CTAGACATTA
Statistics
Matches: 94, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
34 18 0.19
35 25 0.27
36 46 0.49
37 5 0.05
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (36 bp):
ATGTTTTCAAAACTATATATTATATACGTTTTCAAA
Found at i:83856 original size:71 final size:69
Alignment explanation
Indices: 83740--83878 Score: 235
Period size: 71 Copynumber: 2.0 Consensus size: 69
83730 ATATATATGT
83740 TTTCAAAACTATATTATATACGTTTTCAAAATGTTTTCAAAACTATATATTATATACGTTTTTAA
1 TTTCAAAACTATATTATATA-GTTTTCAAAATGTTTTCAAAACTATATATTATATACGTTTTTAA
83805 AACGC
65 AACGC
83810 TTTCAAAACCATATATTATAT-GTTTTCAAAAATGTTTTCAAAACTATATATTATATACGTTTTT
1 TTTCAAAA-C-TATATTATATAGTTTTC-AAAATGTTTTCAAAACTATATATTATATACGTTTTT
83874 AAAAC
63 AAAAC
83879 TAGACATTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
70 14 0.21
71 42 0.64
72 10 0.15
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (69 bp):
TTTCAAAACTATATTATATAGTTTTCAAAATGTTTTCAAAACTATATATTATATACGTTTTTAAA
ACGC
Found at i:87988 original size:65 final size:65
Alignment explanation
Indices: 87839--87995 Score: 190
Period size: 65 Copynumber: 2.4 Consensus size: 65
87829 TACACTAGGG
** * * * * *
87839 GTGCATCGGTACACTAATTACATTCGATGTTTCAAAAGAGCCAGGAGTGCATTGATGCATGGTCT
1 GTGCATCGGTACAAAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTACATCGATGCATGGTCT
* * **
87904 GTGCATCGGTACAAAAAATGCATTTGATGTTTCAAAATATTCAAGAGTACATCGATGCATGG-CT
1 GTGCATCGGTACAAAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTACATCGATGCATGGTC-
87968 T
65 T
*
87969 GTGCATCGGTACAAAAAATGTATTCGA
1 GTGCATCGGTACAAAAAATGCATTCGA
87996 AATGGGTGTG
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 1 0.01
65 77 0.99
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACAAAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTACATCGATGCATGGTCT
Found at i:88014 original size:34 final size:34
Alignment explanation
Indices: 87976--88040 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
87966 CTTGTGCATC
*
87976 GGTACAAAAAATGTATTCGAAATGGGTGTGCCTT
1 GGTACAAAAAATGCATTCGAAATGGGTGTGCCTT
*
88010 GGTACACAAAATGCATTCGAAATGGGTGTGC
1 GGTACAAAAAATGCATTCGAAATGGGTGTGC
88041 ATCAATGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (34 bp):
GGTACAAAAAATGCATTCGAAATGGGTGTGCCTT
Found at i:88435 original size:22 final size:22
Alignment explanation
Indices: 88407--88450 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
88397 AAAAAGTAAA
*
88407 AATTACTCTCACTTACTATATT
1 AATTACTCCCACTTACTATATT
*
88429 AATTACTCCCCCTTACTATATT
1 AATTACTCCCACTTACTATATT
88451 CTCCCCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTACTCCCACTTACTATATT
Found at i:90645 original size:23 final size:22
Alignment explanation
Indices: 90614--90690 Score: 93
Period size: 23 Copynumber: 3.5 Consensus size: 22
90604 AGCATTGTGC
90614 ATCGATGCACATTCAAGGAGTGT
1 ATCGATGCACATTCAAGG-GTGT
* * *
90637 ATCGGTGCACCTT-AATGGTGT
1 ATCGATGCACATTCAAGGGTGT
*
90658 ATCGATGCACATTCAAGGGATGC
1 ATCGATGCACATTCAAGGG-TGT
90681 ATCGATGCAC
1 ATCGATGCAC
90691 TGTCTAGTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
21 15 0.33
22 7 0.16
23 23 0.51
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (22 bp):
ATCGATGCACATTCAAGGGTGT
Found at i:98727 original size:65 final size:65
Alignment explanation
Indices: 98646--98776 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
98636 ACAAACAATC
98646 TCTTCCCCTCTTCTTTTTCTCTCCTAAATCTCTTAACTTTGTTCATTAAGTACAATTACAATTTT
1 TCTTCCCCTCTTCTTTTTCTCTCCTAAATCTCTTAACTTTGTTCATTAAGTACAATTACAATTTT
*
98711 TCTTCCCCTCTTCTTTTTCTCTCCTAAATCTCTTAACTTTGTTCATTAAGTGCAATTACAATTTT
1 TCTTCCCCTCTTCTTTTTCTCTCCTAAATCTCTTAACTTTGTTCATTAAGTACAATTACAATTTT
98776 T
1 T
98777 TTGCTACAGA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.21, C:0.26, G:0.04, T:0.50
Consensus pattern (65 bp):
TCTTCCCCTCTTCTTTTTCTCTCCTAAATCTCTTAACTTTGTTCATTAAGTACAATTACAATTTT
Found at i:99770 original size:56 final size:56
Alignment explanation
Indices: 99703--99814 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
99693 GGGTTTTCAA
99703 AGTGTGTTTTACACAAGTAATCTGCAACCAAGAATGAAAGGGAAAACAACAATTAG
1 AGTGTGTTTTACACAAGTAATCTGCAACCAAGAATGAAAGGGAAAACAACAATTAG
* * *
99759 AGTGTGTTTTACATAAGTAATCTGCAACTAAGAATGAAAGGGGAAACAACAATTAG
1 AGTGTGTTTTACACAAGTAATCTGCAACCAAGAATGAAAGGGAAAACAACAATTAG
99815 TGGCAAATGT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (56 bp):
AGTGTGTTTTACACAAGTAATCTGCAACCAAGAATGAAAGGGAAAACAACAATTAG
Found at i:123089 original size:63 final size:63
Alignment explanation
Indices: 122985--123151 Score: 246
Period size: 63 Copynumber: 2.7 Consensus size: 63
122975 TAATCGCACC
* * *
122985 TTTCTTTTAATTCCATAATCGTTCGTCTACCACATTGATTATCACTCGTCTCTACTATGCGCT
1 TTTCCTTTAATTCCATAATCGTCCGTCTCCCACATTGATTATCACTCGTCTCTACTATGCGCT
* *
123048 TTTCCTTTAATTCCATAATCGTCCGTCTCCCACATTGATTATCATTCGTCTCTACTATGCGTT
1 TTTCCTTTAATTCCATAATCGTCCGTCTCCCACATTGATTATCACTCGTCTCTACTATGCGCT
* * *
123111 TTTCCTTTAATTCTACAA-CTGTCCGTCTCCCACATTAATTA
1 TTTCCTTTAATTCCATAATC-GTCCGTCTCCCACATTGATTA
123152 CCACACATCT
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
62 1 0.01
63 94 0.99
ACGTcount: A:0.21, C:0.28, G:0.08, T:0.43
Consensus pattern (63 bp):
TTTCCTTTAATTCCATAATCGTCCGTCTCCCACATTGATTATCACTCGTCTCTACTATGCGCT
Found at i:125084 original size:21 final size:21
Alignment explanation
Indices: 125060--125099 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
125050 TGCAGTCGTA
*
125060 TCAGATGGCACCATAGCCATT
1 TCAGATGCCACCATAGCCATT
*
125081 TCAGATGCCACCGTAGCCA
1 TCAGATGCCACCATAGCCA
125100 GGTCAGACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.20
Consensus pattern (21 bp):
TCAGATGCCACCATAGCCATT
Found at i:125105 original size:21 final size:21
Alignment explanation
Indices: 125060--125114 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
125050 TGCAGTCGTA
* * **
125060 TCAGATGGCACCATAGCCATT
1 TCAGATGCCACCGTAGCCAGG
125081 TCAGATGCCACCGTAGCCAGG
1 TCAGATGCCACCGTAGCCAGG
125102 TCAGACT-CCACCG
1 TCAGA-TGCCACCG
125115 CTTCCATATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.25, C:0.35, G:0.22, T:0.18
Consensus pattern (21 bp):
TCAGATGCCACCGTAGCCAGG
Found at i:135592 original size:20 final size:20
Alignment explanation
Indices: 135564--135601 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
135554 ACATGTACTT
135564 TCATATTTCAGATTCATAAC
1 TCATATTTCAGATTCATAAC
*
135584 TCATGTTTCAGATTCATA
1 TCATATTTCAGATTCATA
135602 GCCCAACGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (20 bp):
TCATATTTCAGATTCATAAC
Found at i:136112 original size:16 final size:16
Alignment explanation
Indices: 136091--136132 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
136081 TCTTCACTAG
*
136091 AACCTTTTATGGTGAT
1 AACCTTTTATGATGAT
136107 AACCTTTTATGATGAT
1 AACCTTTTATGATGAT
136123 AACCTTTTAT
1 AACCTTTTAT
136133 TCTCTTACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (16 bp):
AACCTTTTATGATGAT
Done.