Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000095.1 Hibiscus syriacus cultivar Beakdansim tig00000178_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: 65776
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:772 original size:17 final size:17
Alignment explanation
Indices: 746--783 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
736 ATTATCGGCA
746 TGAAAGGATCTCATAGT
1 TGAAAGGATCTCATAGT
*
763 TGAAATGATCTCATAGT
1 TGAAAGGATCTCATAGT
780 TGAA
1 TGAA
784 TGTATAGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (17 bp):
TGAAAGGATCTCATAGT
Found at i:852 original size:42 final size:43
Alignment explanation
Indices: 791--1047 Score: 196
Period size: 42 Copynumber: 6.0 Consensus size: 43
781 GAATGTATAG
*
791 GGGTACATTATC-AC-AGAAAAATATACTATAGTTGAAATGCAT
1 GGGTGCATTATCAACGAG-AAAATATACTATAGTTGAAATGCAT
833 GGGTGCATTATCAACGA-AAAAGTATACTATAGTTGAAATGCATAT
1 GGGTGCATTATCAACGAGAAAA-TATACTATAGTTGAAATGC--AT
* *
878 GGGTGCATTATCAA-TAGAAAA-ATA-TATAGTTGAAATGTATAT
1 GGGTGCATTATCAACGAGAAAATATACTATAGTTGAAATG--CAT
* * * *
920 GGGTGCATTATCAAC-AGAAAGTAT-TTATAGCTGAAATGTAT
1 GGGTGCATTATCAACGAGAAAATATACTATAGTTGAAATGCAT
** * * * *
961 ATGTACATTAT-TAC-ATAAAAGCATACTATAGTTGAAATGCATAT
1 GGGTGCATTATCAACGAGAAAA-TATACTATAGTTGAAATGC--AT
* *
1005 GGGTGCATTATCAAC-AGAAAAGTATGCCATAGTT-AAAGTGCAT
1 GGGTGCATTATCAACGAGAAAA-TATACTATAGTTGAAA-TGCAT
1048 AATGGTGTAT
Statistics
Matches: 175, Mismatches: 23, Indels: 33
0.76 0.10 0.14
Matches are distributed among these distances:
40 6 0.03
41 13 0.07
42 61 0.35
43 40 0.23
44 15 0.09
45 40 0.23
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (43 bp):
GGGTGCATTATCAACGAGAAAATATACTATAGTTGAAATGCAT
Found at i:957 original size:85 final size:86
Alignment explanation
Indices: 782--1029 Score: 285
Period size: 85 Copynumber: 2.9 Consensus size: 86
772 CTCATAGTTG
* * *
782 AATGTATAGGGGTACATTATC-ACAGAAAAATATACTATAGTTGAAATG-CATGGGTGCATTATC
1 AATGTATATGGGTACATTATCAATAG-AAAA-ATACTATAGTTGAAATGATATGGGTGCATTATC
* *
845 AACGAAAAAGTATACTATAGTTGA
64 AAC-AGAAAGTATACTATAGCTGA
* *
869 AATGCATATGGGTGCATTATCAATAGAAAAATA-TATAGTTGAAATGTATATGGGTGCATTATCA
1 AATGTATATGGGTACATTATCAATAGAAAAATACTATAGTTGAAATG-ATATGGGTGCATTATCA
*
933 ACAGAAAGTAT-TTATAGCTGA
65 ACAGAAAGTATACTATAGCTGA
* *
954 AATGTATAT--GTACATTATTACATA-AAAGCATACTATAGTTGAAATGCATATGGGTGCATTAT
1 AATGTATATGGGTACATTATCA-ATAGAAA-AATACTATAGTTGAAATG-ATATGGGTGCATTAT
1016 CAACAGAAAAGTAT
63 CAACAG-AAAGTAT
1030 GCCATAGTTA
Statistics
Matches: 141, Mismatches: 13, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
83 12 0.09
84 6 0.04
85 63 0.45
86 18 0.13
87 39 0.28
88 3 0.02
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.31
Consensus pattern (86 bp):
AATGTATATGGGTACATTATCAATAGAAAAATACTATAGTTGAAATGATATGGGTGCATTATCAA
CAGAAAGTATACTATAGCTGA
Found at i:3972 original size:18 final size:18
Alignment explanation
Indices: 3949--3993 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3939 ATCAATACAT
*
3949 TAATATCCAACCAACACA
1 TAATATCCAACAAACACA
**
3967 TAATATCCAACAAACATG
1 TAATATCCAACAAACACA
3985 TAATATCCA
1 TAATATCCA
3994 CCACATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.02, T:0.22
Consensus pattern (18 bp):
TAATATCCAACAAACACA
Found at i:7979 original size:25 final size:25
Alignment explanation
Indices: 7951--7998 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
7941 AAGATTAAAC
*
7951 CCCTCAACTCATATAAACCCTATAA
1 CCCTCAACTCATAGAAACCCTATAA
* * *
7976 CCCTTAATTTATAGAAACCCTAT
1 CCCTCAACTCATAGAAACCCTAT
7999 CACAAAATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.38, C:0.31, G:0.02, T:0.29
Consensus pattern (25 bp):
CCCTCAACTCATAGAAACCCTATAA
Found at i:23098 original size:15 final size:15
Alignment explanation
Indices: 23078--23107 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
23068 GAAAGAGAGG
23078 ATGAAGATGTCTCGA
1 ATGAAGATGTCTCGA
23093 ATGAAGATGTCTCGA
1 ATGAAGATGTCTCGA
23108 GTACCGTATG
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:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (15 bp):
ATGAAGATGTCTCGA
Found at i:23473 original size:25 final size:25
Alignment explanation
Indices: 23439--23488 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
23429 ATCCACAACA
23439 GAGGCAGAATATGTAACAGCTACAC
1 GAGGCAGAATATGTAACAGCTACAC
*
23464 GAGGCAGAATATGTAGCAGCTACAC
1 GAGGCAGAATATGTAACAGCTACAC
23489 AAGCCAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (25 bp):
GAGGCAGAATATGTAACAGCTACAC
Found at i:27125 original size:3 final size:3
Alignment explanation
Indices: 27117--27225 Score: 193
Period size: 3 Copynumber: 36.7 Consensus size: 3
27107 AATATATATT
*
27117 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
27164 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27212 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
27226 TGGATAAAAA
Statistics
Matches: 101, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
2 2 0.02
3 99 0.98
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27795 original size:113 final size:113
Alignment explanation
Indices: 27543--28305 Score: 1375
Period size: 113 Copynumber: 6.8 Consensus size: 113
27533 AGAATTATGC
* * * *
27543 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
27608 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
*
27655 AAAAGGTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
27720 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
27768 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
27833 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
27881 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
27946 TATGAACTTTCTCTGGAAAAGCTGATCTCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
27994 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
28059 TATGAACTTTCTCTGGAAAAGCTGATCTCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
28107 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
28172 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
28220 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
28285 TATGAACTTTCTCTGGAAAAG
66 TATGAACTTTCTCTGGAAAAG
28306 CTAATCTTTC
Statistics
Matches: 636, Mismatches: 14, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
112 68 0.11
113 568 0.89
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
Found at i:29108 original size:83 final size:83
Alignment explanation
Indices: 28956--29424 Score: 784
Period size: 83 Copynumber: 5.7 Consensus size: 83
28946 CCTACTGAAT
* * * ** *
28956 CAGATCAGATAACTCGAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATGTTCCGAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCTAAACTCA
29020 ATGATTGGTTCTGCCAAAC
65 ATGATTGGTTCTGCCAAAC
* *
29039 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
29104 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
29122 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
29187 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
* *
29205 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACACATTCATCTT-TCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCT-AAACTCA
29269 ATGATTGGTTCTGCCAAAC
65 ATGATTGGTTCTGCCAAAC
29288 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
*
29353 TGATT-ATTCTGTCC-AAC
66 TGATTGGTTCTG-CCAAAC
29370 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTT
29425 TCATTTAATT
Statistics
Matches: 367, Mismatches: 15, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
82 64 0.17
83 300 0.82
84 3 0.01
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
TGATTGGTTCTGCCAAAC
Found at i:30590 original size:9 final size:8
Alignment explanation
Indices: 30561--30636 Score: 50
Period size: 8 Copynumber: 9.2 Consensus size: 8
30551 CTTGACCCCC
30561 TTTCTTTT
1 TTTCTTTT
30569 TCTTCTCTTT
1 T-TTCT-TTT
30579 TTT-TTTCAT
1 TTTCTTT--T
*
30588 TTTC-TAT
1 TTTCTTTT
30595 TTT-TTTT
1 TTTCTTTT
** *
30602 TTAGTTTC
1 TTTCTTTT
30610 TTTCTTTT
1 TTTCTTTT
30618 CTTTCTTTT
1 -TTTCTTTT
30627 TTTCTTTT
1 TTTCTTTT
30635 TT
1 TT
30637 CTTCAAGCAT
Statistics
Matches: 53, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
7 10 0.19
8 20 0.38
9 19 0.36
10 4 0.08
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.80
Consensus pattern (8 bp):
TTTCTTTT
Found at i:30609 original size:18 final size:18
Alignment explanation
Indices: 30571--30610 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
30561 TTTCTTTTTC
* *
30571 TTCTCTTTTTTTTTCATT
1 TTCTATTTTTTTTTCAGT
*
30589 TTCTATTTTTTTTTTAGT
1 TTCTATTTTTTTTTCAGT
30607 TTCT
1 TTCT
30611 TTCTTTTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (18 bp):
TTCTATTTTTTTTTCAGT
Found at i:30617 original size:18 final size:18
Alignment explanation
Indices: 30567--30636 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 18
30557 CCCCTTTCTT
*
30567 TTTCTTCTCTTTTTTTTTCAT
1 TTTCTT-TC-TTTTTTTT-AC
*
30588 TTTCTATT-TTTTTTTTAG
1 TTTCT-TTCTTTTTTTTAC
*
30606 TTTCTTTCTTTTCTTT-C
1 TTTCTTTCTTTTTTTTAC
*
30623 TTTTTTTCTTTTTT
1 TTTCTTTCTTTTTT
30637 CTTCAAGCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
17 14 0.33
18 13 0.31
19 8 0.19
21 6 0.14
22 1 0.02
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.80
Consensus pattern (18 bp):
TTTCTTTCTTTTTTTTAC
Found at i:30631 original size:12 final size:12
Alignment explanation
Indices: 30565--30633 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
30555 ACCCCCTTTC
30565 TTTTTC-TTCTCT
1 TTTTTCTTTCT-T
*
30577 TTTTT-TTTCAT
1 TTTTTCTTTCTT
* *
30588 TTTCTATTT-TT
1 TTTTTCTTTCTT
*
30599 TTTTTAGTTTCTT
1 TTTTT-CTTTCTT
30612 TCTTTTCTTTCTT
1 T-TTTTCTTTCTT
30625 TTTTTCTTT
1 TTTTTCTTT
30634 TTTCTTCAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
11 10 0.22
12 22 0.48
13 10 0.22
14 4 0.09
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.80
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:37976 original size:15 final size:15
Alignment explanation
Indices: 37956--37986 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
37946 GAAATGAATT
37956 ATGAATGTATGCAAA
1 ATGAATGTATGCAAA
*
37971 ATGAATGTATGTAAA
1 ATGAATGTATGCAAA
37986 A
1 A
37987 AACATTGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.29
Consensus pattern (15 bp):
ATGAATGTATGCAAA
Found at i:43446 original size:3 final size:3
Alignment explanation
Indices: 43428--43544 Score: 189
Period size: 3 Copynumber: 38.7 Consensus size: 3
43418 TATATATGTT
* *
43428 TAA TATA TAT TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
43474 TAA TAA TAA TAA TAA TAG TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43522 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
43545 TGGATAAAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
3 102 0.97
4 3 0.03
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:58976 original size:21 final size:21
Alignment explanation
Indices: 58952--59012 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
58942 ACTTTGAAAA
58952 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
58973 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
58987 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
59008 AAATG
1 AAATG
59013 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:59059 original size:36 final size:36
Alignment explanation
Indices: 58950--59052 Score: 181
Period size: 35 Copynumber: 2.9 Consensus size: 36
58940 CAACTTTGAA
58950 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
58986 -AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
*
59021 AAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 AAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
59053 GTTGAAATAT
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
35 35 0.55
36 7 0.11
37 22 0.34
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (36 bp):
AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:60276 original size:15 final size:15
Alignment explanation
Indices: 60252--60283 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
60242 AGGCAGATCG
*
60252 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
60267 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
60282 AA
1 AA
60284 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:62876 original size:25 final size:25
Alignment explanation
Indices: 62842--62890 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
62832 ATCGAACCCA
62842 TTTTCTTATCCTTAATCCATCCCGG
1 TTTTCTTATCCTTAATCCATCCCGG
62867 TTTTCTTATCCTTAATCCATCCCG
1 TTTTCTTATCCTTAATCCATCCCG
62891 CTCTCGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.16, C:0.33, G:0.06, T:0.45
Consensus pattern (25 bp):
TTTTCTTATCCTTAATCCATCCCGG
Found at i:64417 original size:19 final size:20
Alignment explanation
Indices: 64366--64426 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 20
64356 ATTCCCTGTG
64366 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
64389 GGGGGAATCGGTTCCCTCAA
1 GGGGGAATCGGTTCCCTCAA
*
64409 GGGGG-ATCGATTCCCTCA
1 GGGGGAATCGGTTCCCTCA
64427 CCAAAATGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 12 0.32
20 7 0.19
21 2 0.05
22 3 0.08
23 13 0.35
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Done.