Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001553.1 Hibiscus syriacus cultivar Beakdansim tig00003055_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: 79532
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:412 original size:34 final size:35
Alignment explanation
Indices: 342--413 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 35
332 ACACATCATA
* **
342 TAAGGCCCTGAGCACAAAGCCGAGGAACTTGTAAG
1 TAAGGCCCTGAGCACAAAGCCGAGGAACCTCCAAG
*
377 TAAGGCCCTGAGCAC-ACGCCGAGGAACCTCCAAG
1 TAAGGCCCTGAGCACAAAGCCGAGGAACCTCCAAG
411 TAA
1 TAA
414 TCTTCCTCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
34 18 0.55
35 15 0.45
ACGTcount: A:0.33, C:0.28, G:0.26, T:0.12
Consensus pattern (35 bp):
TAAGGCCCTGAGCACAAAGCCGAGGAACCTCCAAG
Found at i:522 original size:24 final size:23
Alignment explanation
Indices: 494--580 Score: 93
Period size: 24 Copynumber: 3.7 Consensus size: 23
484 ATTCAAATCA
*
494 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
517 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
* * *
541 AATATTAGATCAGAATCTAGGTC
1 AGTATCAGATCAGAATCCAGGTC
* *
564 AGGTATCATAACAGAAT
1 A-GTATCAGATCAGAAT
581 TCAAATTTGA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
23 20 0.38
24 32 0.62
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:2841 original size:24 final size:24
Alignment explanation
Indices: 2809--2896 Score: 115
Period size: 24 Copynumber: 3.7 Consensus size: 24
2799 CATAAATCAG
* *
2809 GTCAAGTATCATATCAAAATCCAA
1 GTCAAGTATCAGATCAAAATCCAT
*
2833 GTCAAGTATCAGATCAAAATCTAT
1 GTCAAGTATCAGATCAAAATCCAT
*
2857 GTC-AGATATCAGATCATAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAT
*
2881 GTCAAGTATTAGATCA
1 GTCAAGTATCAGATCA
2897 GAATTCAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
23 2 0.04
24 52 0.93
25 2 0.04
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.28
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAT
Found at i:5368 original size:8 final size:8
Alignment explanation
Indices: 5327--5384 Score: 55
Period size: 8 Copynumber: 6.9 Consensus size: 8
5317 TCAAAGTTTT
5327 GGTCAACAG
1 GGTCAAC-G
5336 TGGTCAACG
1 -GGTCAACG
5345 CCGGTCAAC-
1 --GGTCAACG
5354 GGTCAACG
1 GGTCAACG
*
5362 AGTCAACG
1 GGTCAACG
*
5370 GGTAAACG
1 GGTCAACG
5378 GGTCAAC
1 GGTCAAC
5385 AGTGGTCGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
7 7 0.17
8 19 0.46
9 1 0.02
10 14 0.34
ACGTcount: A:0.29, C:0.26, G:0.31, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:7450 original size:24 final size:24
Alignment explanation
Indices: 7423--7498 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
7413 ATATATCAAA
7423 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
7447 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * * *
7471 ATCAGATCAGAATCCAAGACAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
7495 ATCA
1 ATCA
7499 GATCAGAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.09
24 41 0.91
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:7499 original size:24 final size:24
Alignment explanation
Indices: 7440--7554 Score: 144
Period size: 24 Copynumber: 4.8 Consensus size: 24
7430 CATAAATCAG
* * *
7440 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
7464 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
* *
7488 GACAAGTATCAGATCAGAAT-TAT
1 GTCAAGTATCAGATCAGAATCCAT
*
7511 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
7535 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
7555 TCAAATAAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
22 2 0.03
23 16 0.21
24 58 0.74
25 2 0.03
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:9928 original size:13 final size:13
Alignment explanation
Indices: 9907--9936 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
9897 AACAGTCAAT
*
9907 GGGTCAATGGGTC
1 GGGTAAATGGGTC
9920 GGGTAAATGGGTC
1 GGGTAAATGGGTC
9933 GGGT
1 GGGT
9937 TATGACCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.10, G:0.50, T:0.23
Consensus pattern (13 bp):
GGGTAAATGGGTC
Found at i:9974 original size:21 final size:21
Alignment explanation
Indices: 9950--9993 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
9940 GACCGATCAT
9950 ACCGGTCAACTAT-ACACCAAA
1 ACCGGTCAACTATGA-ACCAAA
9971 ACCGGTCAACTATGAACCAAA
1 ACCGGTCAACTATGAACCAAA
9992 AC
1 AC
9994 TGGACAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.43, C:0.32, G:0.11, T:0.14
Consensus pattern (21 bp):
ACCGGTCAACTATGAACCAAA
Found at i:11746 original size:8 final size:8
Alignment explanation
Indices: 11716--11765 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
11706 GGTCAATTGT
11716 GGTCAACG
1 GGTCAACG
11724 TCGGTCAAC-
1 --GGTCAACG
11733 GGTCAACG
1 GGTCAACG
11741 GGTCAACG
1 GGTCAACG
11749 GGTC-A--
1 GGTCAACG
11754 GGTCAACG
1 GGTCAACG
11762 GGTC
1 GGTC
11766 GGGTCGAGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
5 4 0.11
6 1 0.03
7 8 0.22
8 16 0.44
10 7 0.19
ACGTcount: A:0.22, C:0.26, G:0.36, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:11759 original size:13 final size:13
Alignment explanation
Indices: 11741--11770 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11731 ACGGTCAACG
11741 GGTCAACGGGTCA
1 GGTCAACGGGTCA
*
11754 GGTCAACGGGTCG
1 GGTCAACGGGTCA
11767 GGTC
1 GGTC
11771 GAGTCGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:13825 original size:35 final size:35
Alignment explanation
Indices: 13754--13826 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
13744 ATACATCATA
**
13754 TAAGGCCCTGAGCACAAAGCCGAGGAACCGGTAAG
1 TAAGGCCCTGAGCACAAAGCCGAGGAACCGCCAAG
* *
13789 TAAGGCCCTGAGCACACAGCCGAGGAACCTCCAAG
1 TAAGGCCCTGAGCACAAAGCCGAGGAACCGCCAAG
13824 TAA
1 TAA
13827 TCTTCCTCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.34, C:0.29, G:0.27, T:0.10
Consensus pattern (35 bp):
TAAGGCCCTGAGCACAAAGCCGAGGAACCGCCAAG
Found at i:13936 original size:24 final size:23
Alignment explanation
Indices: 13908--13987 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 23
13898 ATTCAAATCA
*
13908 AGTATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAAGTC
*
13931 ATGTATCAGATCAGAAT-CAATGTC
1 A-GTATCATATCAGAATCCAA-GTC
* *
13955 AATATCATATTAGAATCCAAGTC
1 AGTATCATATCAGAATCCAAGTC
13978 AGGTATCATA
1 A-GTATCATA
13988 ACATAATTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
23 19 0.40
24 28 0.60
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (23 bp):
AGTATCATATCAGAATCCAAGTC
Found at i:34556 original size:13 final size:13
Alignment explanation
Indices: 34527--34575 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
34517 TAGTTGACCC
34527 GACCCGA-CCGTT
1 GACCCGACCCGTT
34539 GACCCGACCCGTT
1 GACCCGACCCGTT
*
34552 AACCCGACCCGTT
1 GACCCGACCCGTT
34565 GACCCGACCCG
1 GACCCGACCCG
34576 ACCGTTGACC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
12 7 0.21
13 27 0.79
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:34582 original size:17 final size:17
Alignment explanation
Indices: 34505--34585 Score: 79
Period size: 17 Copynumber: 5.2 Consensus size: 17
34495 GACCGGTCAC
**
34505 GACCCGACCCGATAGTT
1 GACCCGACCCGACCGTT
34522 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
34539 GACCCGA--C--CCGTT
1 GACCCGACCCGACCGTT
*
34552 AACCCGA--C--CCGTT
1 GACCCGACCCGACCGTT
34565 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
34582 GACC
1 GACC
34586 GTTGACCGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
13 23 0.41
15 2 0.04
17 31 0.55
ACGTcount: A:0.20, C:0.44, G:0.22, T:0.14
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:34587 original size:7 final size:7
Alignment explanation
Indices: 34575--34620 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
34565 GACCCGACCC
34575 GACCGTT
1 GACCGTT
34582 GACCGTT
1 GACCGTT
34589 GACCGTT
1 GACCGTT
34596 GACCGTT
1 GACCGTT
34603 GACCG-T
1 GACCGTT
34609 GACCGTT
1 GACCGTT
34616 GACCG
1 GACCG
34621 GTGCTATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.16
7 32 0.84
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:41819 original size:13 final size:13
Alignment explanation
Indices: 41790--41838 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
41780 TAGTTGACCC
41790 GACCCGA-CCGTT
1 GACCCGACCCGTT
41802 GACCCGACCCGTT
1 GACCCGACCCGTT
*
41815 AACCCGACCCGTT
1 GACCCGACCCGTT
41828 GACCCGACCCG
1 GACCCGACCCG
41839 ACCGTTGACC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
12 7 0.21
13 27 0.79
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:41845 original size:17 final size:17
Alignment explanation
Indices: 41768--41848 Score: 79
Period size: 17 Copynumber: 5.2 Consensus size: 17
41758 GACCGGTCAC
**
41768 GACCCGACCCGATAGTT
1 GACCCGACCCGACCGTT
41785 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
41802 GACCCGA--C--CCGTT
1 GACCCGACCCGACCGTT
*
41815 AACCCGA--C--CCGTT
1 GACCCGACCCGACCGTT
41828 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
41845 GACC
1 GACC
41849 GTTGACCGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
13 23 0.41
15 2 0.04
17 31 0.55
ACGTcount: A:0.20, C:0.44, G:0.22, T:0.14
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:41850 original size:7 final size:7
Alignment explanation
Indices: 41838--41875 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
41828 GACCCGACCC
41838 GACCGTT
1 GACCGTT
41845 GACCGTT
1 GACCGTT
41852 GACCGTT
1 GACCGTT
41859 GACCGTT
1 GACCGTT
41866 GACCGTT
1 GACCGTT
41873 GAC
1 GAC
41876 GGTGCTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:50493 original size:24 final size:24
Alignment explanation
Indices: 50394--50481 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 24
50384 AATATAATAA
* *
50394 ATCAAAACAGAATTCATAACAGAT
1 ATCATAACAGAATTCATATCAGAT
* *
50418 ATCATAACATAATCCATATCAGAT
1 ATCATAACAGAATTCATATCAGAT
* * ** * *
50442 ATCAGAATAGAATTCAGGTTAGGT
1 ATCATAACAGAATTCATATCAGAT
50466 ATCATAACAGAATTCA
1 ATCATAACAGAATTCA
50482 AGTCAGAAAT
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (24 bp):
ATCATAACAGAATTCATATCAGAT
Found at i:55095 original size:12 final size:12
Alignment explanation
Indices: 55078--55134 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
55068 CATAAATTAA
55078 AACAGAATTCAG
1 AACAGAATTCAG
55090 AACAG-ATATCAG
1 AACAGAAT-TCAG
*
55102 AACAGAATCCAG
1 AACAGAATTCAG
* * *
55114 ATCAGAAATCAT
1 AACAGAATTCAG
*
55126 AATAGAATT
1 AACAGAATT
55135 TAGGTCATGT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 2 0.06
12 31 0.89
13 2 0.06
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:55114 original size:24 final size:24
Alignment explanation
Indices: 55078--55133 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
55068 CATAAATTAA
* *
55078 AACAGAATTCAGAACAGATATCAG
1 AACAGAATCCAGAACAGAAATCAG
* *
55102 AACAGAATCCAGATCAGAAATCAT
1 AACAGAATCCAGAACAGAAATCAG
*
55126 AATAGAAT
1 AACAGAAT
55134 TTAGGTCATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.52, C:0.16, G:0.14, T:0.18
Consensus pattern (24 bp):
AACAGAATCCAGAACAGAAATCAG
Found at i:59819 original size:24 final size:24
Alignment explanation
Indices: 59790--59855 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
59780 ACGGAAATAT
*
59790 AAATCAAAATAGAATTCAGAAT-AG
1 AAATCAAAACAGAATTCAG-ATCAG
* * *
59814 ATATCATAACAGAATCCAGATCAG
1 AAATCAAAACAGAATTCAGATCAG
*
59838 AAATCAGAACAGAATTCA
1 AAATCAAAACAGAATTCA
59856 TGTCATGTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 2 0.06
24 32 0.94
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.20
Consensus pattern (24 bp):
AAATCAAAACAGAATTCAGATCAG
Found at i:65898 original size:23 final size:24
Alignment explanation
Indices: 65848--65900 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
65838 CTTTATTTCT
* * *
65848 TTTCTTCTTTTTGAGTGATTGACT
1 TTTCTTCTTTTGGAGTGATTCACA
*
65872 TTTCTTCTTTTGGAGTGCTTCA-A
1 TTTCTTCTTTTGGAGTGATTCACA
65895 TTTCTT
1 TTTCTT
65901 TGTTGAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.58
Consensus pattern (24 bp):
TTTCTTCTTTTGGAGTGATTCACA
Found at i:65936 original size:11 final size:11
Alignment explanation
Indices: 65920--65944 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
65910 TTGTTTTTCT
65920 TTCACTTGCAC
1 TTCACTTGCAC
65931 TTCACTTGCAC
1 TTCACTTGCAC
65942 TTC
1 TTC
65945 TTTTGGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:66855 original size:24 final size:24
Alignment explanation
Indices: 66827--66883 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
66817 TCAAGGTAAG
*
66827 CTAGGTGAGTGTCTTGGTAGCTAG
1 CTAGGTGAGTGTCTTGGTAGCTAA
*
66851 TTAGGTGAGTGTCTTGGTAGCTAA
1 CTAGGTGAGTGTCTTGGTAGCTAA
66875 CTAGGTGAG
1 CTAGGTGAG
66884 CTATAGCTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.19, C:0.11, G:0.37, T:0.33
Consensus pattern (24 bp):
CTAGGTGAGTGTCTTGGTAGCTAA
Found at i:69682 original size:6 final size:6
Alignment explanation
Indices: 69671--69696 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
69661 ATTAAGAAAA
69671 GAAATG GAAATG GAAATG GAAATG GA
1 GAAATG GAAATG GAAATG GAAATG GA
69697 TAGAATTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GAAATG
Found at i:78375 original size:29 final size:30
Alignment explanation
Indices: 78342--78402 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
78332 AGAAAAGGTT
*
78342 AAGAAAGAATAAGGTAATGAAA-AATAAGA
1 AAGAAAGAATAAGGAAATGAAATAATAAGA
*
78371 AAGAAAGAATAAGGAAATGAAATAGTAAGA
1 AAGAAAGAATAAGGAAATGAAATAATAAGA
78401 AA
1 AA
78403 ATGAAGATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.13
Consensus pattern (30 bp):
AAGAAAGAATAAGGAAATGAAATAATAAGA
Found at i:78399 original size:16 final size:15
Alignment explanation
Indices: 78344--78407 Score: 60
Period size: 16 Copynumber: 4.2 Consensus size: 15
78334 AAAAGGTTAA
*
78344 GAAAGAATAAGGTAAT
1 GAAA-AATAAGGAAAT
78360 GAAAAATAA-GAAA-
1 GAAAAATAAGGAAAT
78373 GAAAGAATAAGGAAAT
1 GAAA-AATAAGGAAAT
* *
78389 GAAATAGTAAGAAAAT
1 GAAA-AATAAGGAAAT
78405 GAA
1 GAA
78408 GATACTTACA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
13 4 0.10
14 8 0.20
15 9 0.22
16 20 0.49
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.14
Consensus pattern (15 bp):
GAAAAATAAGGAAAT
Found at i:78638 original size:15 final size:14
Alignment explanation
Indices: 78611--78648 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
78601 AAGTCTGTTC
78611 TTTCTTTTTGTTTT
1 TTTCTTTTTGTTTT
78625 TTTCTTTCTTGTTTT
1 TTTCTTT-TTGTTTT
*
78640 CTT-TTTTTG
1 TTTCTTTTTG
78649 CAGCACTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 10 0.45
15 9 0.41
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.82
Consensus pattern (14 bp):
TTTCTTTTTGTTTT
Found at i:78644 original size:18 final size:18
Alignment explanation
Indices: 78608--78645 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
78598 TAGAAGTCTG
*
78608 TTCTTTCTTTTTGTTTTT
1 TTCTTTCTTTTTGTCTTT
78626 TTCTTTCTTGTTT-TCTTT
1 TTCTTTCTT-TTTGTCTTT
78644 TT
1 TT
78646 TTGCAGCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (18 bp):
TTCTTTCTTTTTGTCTTT
Found at i:78886 original size:10 final size:10
Alignment explanation
Indices: 78873--78898 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
78863 TGGAAAGAAT
78873 GAAATGGATA
1 GAAATGGATA
78883 GAAATGGATA
1 GAAATGGATA
78893 GAAATG
1 GAAATG
78899 TTCAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (10 bp):
GAAATGGATA
Done.