Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004317.1 Hibiscus syriacus cultivar Beakdansim tig00009468_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: 93855
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:478 original size:9 final size:9
Alignment explanation
Indices: 464--508 Score: 65
Period size: 9 Copynumber: 4.9 Consensus size: 9
454 AGTTTGCTAA
464 AAAATAAAT
1 AAAATAAAT
473 AAAATAAAAT
1 AAAAT-AAAT
483 AAAATAAAT
1 AAAATAAAT
492 -AAATAAAAT
1 AAAAT-AAAT
501 AAAATAAA
1 AAAATAAA
509 AAGAAATGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 4 0.12
9 16 0.48
10 13 0.39
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATAAAT
Found at i:479 original size:5 final size:5
Alignment explanation
Indices: 464--509 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
454 AGTTTGCTAA
464 AAAAT -AAAT AAAAT AAAAT AAAAT -AAAT -AAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
510 AGAAATGGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 12 0.31
5 27 0.69
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:495 original size:23 final size:23
Alignment explanation
Indices: 465--509 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
455 GTTTGCTAAA
465 AAATAAATAAAATAAAATAAAAT
1 AAATAAATAAAATAAAATAAAAT
488 AAATAAATAAAATAAAATAAAA
1 AAATAAATAAAATAAAATAAAA
510 AGAAATGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (23 bp):
AAATAAATAAAATAAAATAAAAT
Found at i:6044 original size:30 final size:31
Alignment explanation
Indices: 6000--6057 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
5990 GGTAAAGTTG
*
6000 AAAAGGTATAAT-AAATAAAATAATAATAAAT
1 AAAAGGGATAATAAAAT-AAATAATAATAAAT
*
6031 AAAAGGGA-AATAAAATAATTAATAATA
1 AAAAGGGATAATAAAATAAATAATAATA
6058 GTAGTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (31 bp):
AAAAGGGATAATAAAATAAATAATAATAAAT
Found at i:6765 original size:76 final size:76
Alignment explanation
Indices: 6685--6875 Score: 348
Period size: 76 Copynumber: 2.5 Consensus size: 76
6675 ACAGTTAACA
*
6685 CTATTTAAACTAAAATACCTAAAACAAAGATAAAAAATAAAAATAATATCCTAAAACTTAATTAA
1 CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATCCTAAAACTTAATTAA
6750 AATACAAAAAC
66 AATACAAAAAC
*
6761 CTATTTAAACTAAAATACCTAAAACAGAGATAAAATATAAAAATAATATCCTAAAACTTAATTAA
1 CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATCCTAAAACTTAATTAA
*
6826 AATACTAAAAC
66 AATACAAAAAC
6837 CTATTTAAACTAAAATACCT-AAACAAAGATAAAATATAA
1 CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
6876 TATTTAAAAT
Statistics
Matches: 111, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
75 18 0.16
76 93 0.84
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.25
Consensus pattern (76 bp):
CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATCCTAAAACTTAATTAA
AATACAAAAAC
Found at i:6783 original size:44 final size:44
Alignment explanation
Indices: 6729--6859 Score: 126
Period size: 44 Copynumber: 3.2 Consensus size: 44
6719 AAATAAAAAT
*
6729 AATATCCTAAAACTTAATTAAAATACAAAAACCTATTTAAACTAA
1 AATA-CCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAA
**
6774 AATACCTAAAACAGAGA-TAAAATA-TAAAA---A--T-AA-T--
1 AATACCTAAAACTTA-ATTAAAATACTAAAACCTATTTAAACTAA
6808 -AT-CCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAA
1 AATACCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAA
6850 AATACCTAAA
1 AATACCTAAA
6860 CAAAGATAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 29
0.66 0.05 0.29
Matches are distributed among these distances:
31 1 0.01
32 16 0.24
33 7 0.10
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
40 2 0.03
43 6 0.09
44 22 0.33
45 5 0.07
ACGTcount: A:0.57, C:0.15, G:0.02, T:0.27
Consensus pattern (44 bp):
AATACCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAA
Found at i:14611 original size:17 final size:17
Alignment explanation
Indices: 14589--14638 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
14579 ATAAAGTAAG
**
14589 AGAAAAGAAAAGGGAAA
1 AGAAAAGAAAAGAAAAA
14606 AGAAAAGAAAAGAAAAA
1 AGAAAAGAAAAGAAAAA
14623 AGAAAAGGAAAA-AAAA
1 AGAAAA-GAAAAGAAAA
14639 TGGGAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 25 0.83
18 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAAAGAAAAGAAAAA
Found at i:14635 original size:13 final size:12
Alignment explanation
Indices: 14589--14636 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
14579 ATAAAGTAAG
*
14589 AGAAAAGAAAAG
1 AGAAAAGAAAAA
*
14601 GGAAAAG--AAA
1 AGAAAAGAAAAA
14611 AGAAAAGAAAAA
1 AGAAAAGAAAAA
14623 AGAAAAGGAAAAA
1 AGAAAA-GAAAAA
14636 A
1 A
14637 AATGGGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 8 0.27
12 15 0.50
13 7 0.23
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AGAAAAGAAAAA
Found at i:27725 original size:20 final size:19
Alignment explanation
Indices: 27711--27757 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
27701 ATTAAGCATC
27711 AAAAATTAAATTTAATGAT
1 AAAAATTAAATTTAATGAT
* * *
27730 AAATATTAAATTTACTTAT
1 AAAAATTAAATTTAATGAT
*
27749 CAAAATTAA
1 AAAAATTAA
27758 TATTATCATG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAAATTAAATTTAATGAT
Found at i:28337 original size:23 final size:23
Alignment explanation
Indices: 28271--28329 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
28261 ATAAATTACT
* *
28271 TAAATTATTTATTATT-T-TTAA
1 TAAATTAATTATAATTCTATTAA
28292 TAAATTAATTATAATTCTATTAA
1 TAAATTAATTATAATTCTATTAA
28315 -AAATTAAATTA-AATT
1 TAAATT-AATTATAATT
28330 TTAATTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 14 0.42
22 10 0.30
23 9 0.27
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TAAATTAATTATAATTCTATTAA
Found at i:42752 original size:65 final size:63
Alignment explanation
Indices: 42633--42842 Score: 221
Period size: 65 Copynumber: 3.3 Consensus size: 63
42623 TTTTTCAGAG
* * *
42633 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CAATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGC
42695 ATT
61 ATT
* * *
42698 TCATGCATCGATGCACATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACAATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
42762 T
63 T
* * * *
42763 TGATGCATCGATGCACCAGCAATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACAATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
42827 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
42843 TCTTAGTGCA
Statistics
Matches: 126, Mismatches: 11, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 48 0.38
65 69 0.55
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACAATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:42842 original size:17 final size:19
Alignment explanation
Indices: 42814--42862 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
42804 TATTTTGAAA
42814 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
42832 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
42851 CACCGATGCACT
1 CATCGATGCACT
42863 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:42858 original size:64 final size:63
Alignment explanation
Indices: 42683--42862 Score: 204
Period size: 65 Copynumber: 2.8 Consensus size: 63
42673 AATTAAATTG
* *
42683 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCATCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCAC-T-CCATGCATCGATGCACTCAGGATTTTATGAA
* *
42748 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCAATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACTC--C-ATGCATCGATGCACTCAGGAT-TTTATG
42811 -A
62 AA
* * *
42812 AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACTC-CA-TGCATCGATGCACT
42863 AAGGGTCCAA
Statistics
Matches: 101, Mismatches: 8, Indels: 13
0.83 0.07 0.11
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 45 0.45
65 51 0.50
66 3 0.03
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCCATGCATCGATGCACTCAGGATTTTATGAA
Found at i:44561 original size:22 final size:22
Alignment explanation
Indices: 44544--44597 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
44534 TATCCCAAAT
44544 GACCTATGAATATGTCCCGAAG
1 GACCTATGAATATGTCCCGAAG
*
44566 GACCTATGAATATGCCCCGAAG
1 GACCTATGAATATGTCCCGAAG
44588 GACCTATGAA
1 GACCTATGAA
44598 ACCCTAGACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (22 bp):
GACCTATGAATATGTCCCGAAG
Found at i:47795 original size:3 final size:3
Alignment explanation
Indices: 47789--47891 Score: 206
Period size: 3 Copynumber: 34.3 Consensus size: 3
47779 TATGTTGTTG
47789 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
47837 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
47885 TTA TTA T
1 TTA TTA T
47892 GGATGATGTT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 100 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:48641 original size:2 final size:2
Alignment explanation
Indices: 48634--48667 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
48624 GAAAGCAAGT
48634 TA TA TA 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
48668 ATTTTAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48762 original size:17 final size:18
Alignment explanation
Indices: 48665--48762 Score: 76
Period size: 17 Copynumber: 5.1 Consensus size: 18
48655 ATATATATAT
48665 ATAATTTTAAGAAAT-AA
1 ATAATTTTAAGAAATAAA
48682 AT-ATTTTAAGAAATTAAA
1 ATAATTTTAAGAAA-TAAA
*
48700 ACTTTTTAAAATTTTAAGAATATATAT
1 A-----T--AATTTTAAGAA-ATA-AA
48727 ATAATTTTAAGAAATAAA
1 ATAATTTTAAGAAATAAA
48745 AT-ATTTTAAGAAATAAA
1 ATAATTTTAAGAAATAAA
48762 A
1 A
48763 CTTTTTAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 24
0.72 0.02 0.26
Matches are distributed among these distances:
16 11 0.16
17 19 0.28
18 6 0.09
19 3 0.04
20 11 0.16
22 1 0.01
23 1 0.01
26 12 0.18
27 3 0.04
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (18 bp):
ATAATTTTAAGAAATAAA
Found at i:48762 original size:62 final size:62
Alignment explanation
Indices: 48657--48780 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
48647 ATATATATAT
48657 ATATATATATAATTTTAAGAAATAAATATTTTAAGAAATTAAAACTTTTTAAAATTTTAAGA
1 ATATATATATAATTTTAAGAAATAAATATTTTAAGAAATTAAAACTTTTTAAAATTTTAAGA
48719 ATATATATATAATTTTAAGAAATAAAATATTTTAAGAAA-TAAAACTTTTTAAAATTTTAAGA
1 ATATATATATAATTTTAAGAAAT-AAATATTTTAAGAAATTAAAACTTTTTAAAATTTTAAGA
48781 GATGAATTCT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 46 0.75
63 15 0.25
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (62 bp):
ATATATATATAATTTTAAGAAATAAATATTTTAAGAAATTAAAACTTTTTAAAATTTTAAGA
Found at i:50078 original size:12 final size:12
Alignment explanation
Indices: 50061--50087 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
50051 GATGAACTTG
50061 TTACAAATAAAA
1 TTACAAATAAAA
50073 TTACAAATAAAA
1 TTACAAATAAAA
50085 TTA
1 TTA
50088 TATTGGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (12 bp):
TTACAAATAAAA
Found at i:61608 original size:2 final size:2
Alignment explanation
Indices: 61601--61635 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
61591 GAAAGCAAGT
61601 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61636 TTTTAAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61706 original size:66 final size:66
Alignment explanation
Indices: 61622--61753 Score: 246
Period size: 66 Copynumber: 2.0 Consensus size: 66
61612 ATATATATAT
* *
61622 ATATATATATATATTTTTAAGAAATAAAATATTTTTAAGAAATTAAAACTTTTTAAAATTTTAAG
1 ATATATATATATAATTTTAAGAAATAAAATATTTTTAAGAAAATAAAACTTTTTAAAATTTTAAG
61687 A
66 A
61688 ATATATATATATAATTTTAAGAAATAAAATATTTTTAAGAAAATAAAACTTTTTAAAATTTTAAG
1 ATATATATATATAATTTTAAGAAATAAAATATTTTTAAGAAAATAAAACTTTTTAAAATTTTAAG
61753 A
66 A
61754 GATGAATTCT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (66 bp):
ATATATATATATAATTTTAAGAAATAAAATATTTTTAAGAAAATAAAACTTTTTAAAATTTTAAG
A
Found at i:61743 original size:18 final size:18
Alignment explanation
Indices: 61632--61735 Score: 73
Period size: 18 Copynumber: 5.1 Consensus size: 18
61622 ATATATATAT
61632 ATATTTTTAAGAAATAAA
1 ATATTTTTAAGAAATAAA
61650 ATATTTTTAAGAAATTAAA
1 ATATTTTTAAGAAA-TAAA
*
61669 ACTTTTTAAAATTTTAAGAATATATATA
1 A-----T--ATTTTTAAGAA-ATA-A-A
*
61697 TATAATTTTAAGAAATAAA
1 -ATATTTTTAAGAAATAAA
61716 ATATTTTTAAGAAAATAAA
1 ATATTTTTAAG-AAATAAA
61735 A
1 A
61736 CTTTTTAAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 25
0.72 0.02 0.26
Matches are distributed among these distances:
18 24 0.34
19 14 0.20
20 1 0.01
21 3 0.04
22 11 0.15
24 2 0.03
26 12 0.17
27 2 0.03
28 1 0.01
29 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (18 bp):
ATATTTTTAAGAAATAAA
Found at i:63053 original size:12 final size:12
Alignment explanation
Indices: 63036--63062 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
63026 GATGAACTTG
63036 TTACAAATAAAA
1 TTACAAATAAAA
63048 TTACAAATAAAA
1 TTACAAATAAAA
63060 TTA
1 TTA
63063 TATTGGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (12 bp):
TTACAAATAAAA
Found at i:70102 original size:40 final size:41
Alignment explanation
Indices: 70027--70109 Score: 114
Period size: 46 Copynumber: 1.9 Consensus size: 41
70017 TCGTCCAATT
70027 TTTTATTTGACTCAACATTTAGATCTTCATATGAGTTCGGGTTTTA
1 TTTTATTTGACTCAACATTTAG----T-ATATGAGTTCGGGTTTTA
70073 TTTTATTTGACTCAACATTTAG-ATATGAGTTCGGGTT
1 TTTTATTTGACTCAACATTTAGTATATGAGTTCGGGTT
70110 GAATTGGGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
40 15 0.41
46 22 0.59
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (41 bp):
TTTTATTTGACTCAACATTTAGTATATGAGTTCGGGTTTTA
Found at i:73917 original size:27 final size:27
Alignment explanation
Indices: 73887--73938 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
73877 GGAGAAAAAT
*
73887 AAAATAACTACAAA-AGTAAAAAAAAGG
1 AAAATAACTA-AAACACTAAAAAAAAGG
*
73914 AAAATAATTAAAACACTAAAAAAAA
1 AAAATAACTAAAACACTAAAAAAAA
73939 TGTTAGTGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.13
Consensus pattern (27 bp):
AAAATAACTAAAACACTAAAAAAAAGG
Found at i:78617 original size:30 final size:30
Alignment explanation
Indices: 78583--78690 Score: 103
Period size: 30 Copynumber: 3.6 Consensus size: 30
78573 AAAATTTTGA
*
78583 TTAGTGACTAAAATATAAAGTTTTGAAAGT
1 TTAGTGACCAAAATATAAAGTTTTGAAAGT
* * *
78613 TTAGTGGCTAAAGTATAAAG-TTTGAAAAGT
1 TTAGTGACCAAAATATAAAGTTTTG-AAAGT
* * * *
78643 TTAGAGACCAAAA-ATTAATTTTTAAAAGT
1 TTAGTGACCAAAATATAAAGTTTTGAAAGT
*
78672 TTAGGGACCAAAAGTATAA
1 TTAGTGACCAAAA-TATAA
78691 TTTTCAAAAG
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
29 25 0.40
30 35 0.56
31 3 0.05
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (30 bp):
TTAGTGACCAAAATATAAAGTTTTGAAAGT
Found at i:78694 original size:30 final size:30
Alignment explanation
Indices: 78622--78702 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
78612 TTTAGTGGCT
* *
78622 AAAGTATAAAGTTTGAAAAGTTTAGAGACCA
1 AAAGTAT-AATTTTCAAAAGTTTAGAGACCA
* * *
78653 AAAAT-TAATTTTTAAAAGTTTAGGGACCA
1 AAAGTATAATTTTCAAAAGTTTAGAGACCA
78682 AAAGTATAATTTTCAAAAGTT
1 AAAGTATAATTTTCAAAAGTT
78703 ATGTATTTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 24 0.56
30 15 0.35
31 4 0.09
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (30 bp):
AAAGTATAATTTTCAAAAGTTTAGAGACCA
Found at i:80801 original size:5 final size:5
Alignment explanation
Indices: 80767--80794 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
80757 TCATTATCTG
80767 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
80795 GTTTTGTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:85331 original size:22 final size:22
Alignment explanation
Indices: 85288--85343 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
85278 GATGCACTGT
*
85288 TCACTATTCACGGGGTATTGTTCA
1 TCACTATTCAC--GGTACTGTTCA
*
85312 TCACTGTTCACGGTACTGTTCA
1 TCACTATTCACGGTACTGTTCA
85334 TCACTATTCA
1 TCACTATTCA
85344 TAAAAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 19 0.66
24 10 0.34
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (22 bp):
TCACTATTCACGGTACTGTTCA
Found at i:86067 original size:24 final size:24
Alignment explanation
Indices: 86040--86099 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
86030 GAGATCAGCG
* *
86040 CCACGAAGAATTTGACCCGAAGGA
1 CCACGTAGAATTTGACCCAAAGGA
** *
86064 CCACGTAGAATTTTTCTCAAAGGA
1 CCACGTAGAATTTGACCCAAAGGA
86088 CCACGTAGAATT
1 CCACGTAGAATT
86100 ATCTCGAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (24 bp):
CCACGTAGAATTTGACCCAAAGGA
Found at i:90883 original size:20 final size:20
Alignment explanation
Indices: 90858--90906 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
90848 TTGAAGAAGT
* * *
90858 ATCGATACTAAGATGTAGGA
1 ATCGATACCAAGAGGAAGGA
*
90878 ATCGATACCAAGAGGAAGGT
1 ATCGATACCAAGAGGAAGGA
90898 ATCGATACC
1 ATCGATACC
90907 GTAATCAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (20 bp):
ATCGATACCAAGAGGAAGGA
Found at i:91433 original size:17 final size:17
Alignment explanation
Indices: 91389--91423 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
91379 TGTGCTAAAC
91389 GAAAGTGA--TATATGT
1 GAAAGTGACCTATATGT
91404 GAAAGTGACCTATATGT
1 GAAAGTGACCTATATGT
91421 GAA
1 GAA
91424 TGTACTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
17 10 0.56
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.29
Consensus pattern (17 bp):
GAAAGTGACCTATATGT
Found at i:91499 original size:2 final size:2
Alignment explanation
Indices: 91492--91540 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
91482 AAGCCCAAGG
91492 TA TA TA TA TA TA TA 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
91534 TA TA TA T
1 TA TA TA T
91541 TAGAGGTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:91607 original size:23 final size:23
Alignment explanation
Indices: 91576--91666 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
91566 GTTGAGGGTT
* **
91576 CTATATGGTCCTTCGGGATGAAC
1 CTATGTGGTCCTTCGGGACAAAC
*
91599 CTATGTGGTCCTTCGGAACAAAC
1 CTATGTGGTCCTTCGGGACAAAC
* *
91622 CTATGTGGTCCTTTGGGACAAAT
1 CTATGTGGTCCTTCGGGACAAAC
91645 CTATGTGGTCCTTCGGGACAAA
1 CTATGTGGTCCTTCGGGACAAA
91667 TATGTGCACT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAC
Done.