Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007325.1 Hibiscus syriacus cultivar Beakdansim tig00019546_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: 95109
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:20140 original size:28 final size:28
Alignment explanation
Indices: 20100--20155 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
20090 TTATAATATT
*
20100 ATAAACAAGTCTGAAAATCGGTAACATC
1 ATAAACAAGTCTGAAAATCAGTAACATC
20128 ATAAACAAGTCTGAAAATCAGTAACATC
1 ATAAACAAGTCTGAAAATCAGTAACATC
20156 GTTAGCTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.21
Consensus pattern (28 bp):
ATAAACAAGTCTGAAAATCAGTAACATC
Found at i:23281 original size:46 final size:46
Alignment explanation
Indices: 23209--23329 Score: 156
Period size: 46 Copynumber: 2.6 Consensus size: 46
23199 TGTTCTGCAA
* *
23209 TTAGACAATATTATTATATTATTATGGTGT-ACTATTAATTATGTAT
1 TTAGACAATATTATTATTTTAATATGGTGTGA-TATTAATTATGTAT
* * * *
23255 TTAGATAATATTATTGTTTTAGTATGGTGTGATATTATTTATGTAT
1 TTAGACAATATTATTATTTTAATATGGTGTGATATTAATTATGTAT
23301 TT-GAACAATATTATTATTTTAATATGGTG
1 TTAG-ACAATATTATTATTTTAATATGGTG
23330 CGTTACTAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
45 1 0.02
46 63 0.97
47 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.51
Consensus pattern (46 bp):
TTAGACAATATTATTATTTTAATATGGTGTGATATTAATTATGTAT
Found at i:29596 original size:22 final size:22
Alignment explanation
Indices: 29571--29614 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29561 GAAAATATTG
* *
29571 TTTTTATAAAACTAAAAAATAA
1 TTTTTAGAAAAATAAAAAATAA
*
29593 TTTTTAGAAAAATAGAAAATAA
1 TTTTTAGAAAAATAAAAAATAA
29615 ATGAAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (22 bp):
TTTTTAGAAAAATAAAAAATAA
Found at i:32933 original size:19 final size:19
Alignment explanation
Indices: 32901--32937 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
32891 AAATGAAAAC
32901 AAAAATAAATGAAAATATG
1 AAAAATAAATGAAAATATG
32920 AAAACATAAA-GAAAATAT
1 AAAA-ATAAATGAAAATAT
32938 TTTCAGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.70, C:0.03, G:0.08, T:0.19
Consensus pattern (19 bp):
AAAAATAAATGAAAATATG
Found at i:33908 original size:26 final size:26
Alignment explanation
Indices: 33879--33940 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
33869 ATGTTTTCTA
* *
33879 ATTTTTAAAAATTTAAAATGAAAAC-T
1 ATTTTTAAAAAATAAAAAT-AAAACAT
** *
33905 ATTTAAAAAAAATAAAAATAGAACAT
1 ATTTTTAAAAAATAAAAATAAAACAT
33931 ATTTTTAAAA
1 ATTTTTAAAA
33941 CTAAAAGTAG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (26 bp):
ATTTTTAAAAAATAAAAATAAAACAT
Found at i:37759 original size:14 final size:15
Alignment explanation
Indices: 37735--37767 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
37725 TAGCTTTTGT
37735 GAATGCAAGTAAAGA
1 GAATGCAAGTAAAGA
37750 GAAT-CAAGTAAAGA
1 GAATGCAAGTAAAGA
37764 GAAT
1 GAAT
37768 ATGATTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.55, C:0.06, G:0.24, T:0.15
Consensus pattern (15 bp):
GAATGCAAGTAAAGA
Found at i:47719 original size:2 final size:2
Alignment explanation
Indices: 47712--47754 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
47702 CAGGGCTAAC
47712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47754 A
1 A
47755 AAAGAAGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52834 original size:6 final size:6
Alignment explanation
Indices: 52823--52860 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
52813 AAGTTTATCT
52823 TTTGGG TTTGGG TTTGGG TTTGGG TTTAGGG TTATGGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTT-GGG TT-TGGG
52861 GGTGGTCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 21 0.70
7 8 0.27
8 1 0.03
ACGTcount: A:0.05, C:0.00, G:0.47, T:0.47
Consensus pattern (6 bp):
TTTGGG
Found at i:58470 original size:168 final size:170
Alignment explanation
Indices: 58153--58719 Score: 667
Period size: 171 Copynumber: 3.3 Consensus size: 170
58143 TTTTAATAGT
* * ** * * *
58153 ATAAATTGTAACGAGTTTATCAACCTACAAGTGTTTCATTATATATATAATTGAATAAGGTAGCG
1 ATAAATTGTAATGAGTTTATCGATTTACAAGTGTTTCA-T-TATATATGATTGAATAAGGTAACA
* * *
58218 TTTATTCTATTTATGAATCTTTAGGAGTATCTTGTAACGAGTTTATCGACTCATACGTGTTCTAT
64 TTTATTCTATTTATGAATCTTAAGAAATATCTTGTAACGAGTTTATCGACTCATACGTGTTCTAT
*
58283 TATATAATTAAACTAATTTGTCGTTTCTTGTATATATGAA-C
129 TATATAATTAAATTAATTTGTCGTTTCTTGTATATATGAACC
* * * * *
58324 ATAAATTGTAATGAGTTTATTGATTTACATGTGTTTCATTGTATATGATTGAATGAGGTAATATT
1 ATAAATTGTAATGAGTTTATCGATTTACAAGTGTTTCATTATATATGATTGAATAAGGTAACATT
** * *
58389 TATTCTATTTATGAATCTTAAGAAATATCTACTAACAAGTTTAT-TACTCATACGTGTTCTATTA
66 TATTCTATTTATGAATCTTAAGAAATATCTTGTAACGAGTTTATCGACTCATACGTGTTCTATTA
* *
58453 TATAACTAAATTAATTTGTCGTTTCTTGTATAAATGAACACC
131 TATAATTAAATTAATTTGTCGTTTCTTGTATATATG-A-ACC
* * *
58495 ATAAGTCGTAATGAGTTTATCGATTTACACGTGTTTCATTATATATGATTGAATAAGGTAACATT
1 ATAAATTGTAATGAGTTTATCGATTTACAAGTGTTTCATTATATATGATTGAATAAGGTAACATT
* *
58560 TATTCTATTTATGAATCTTAA-AAATTATCTTGTAACGAGTTTATCGACTCATATGTGTTCCATT
66 TATTCTATTTATGAATCTTAAGAAA-TATCTTGTAACGAGTTTATCGACTCATACGTGTTCTATT
* * ** * *
58624 ATATAATTAAGTTAATTTATAATTTCTTGTACATATGAATAAC
130 ATATAATTAAATTAATTTGTCGTTTCTTGTATATATG-A-ACC
* * * ** * *
58667 ATAAACTATAATGAGTCTATCGACCTACACA-TGTTTCATTCTA-ATTATTGAAT
1 ATAAATTGTAATGAGTTTATCGATTTACA-AGTGTTTCATTATATATGATTGAAT
58720 TAATTTATAG
Statistics
Matches: 336, Mismatches: 54, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
168 52 0.15
169 59 0.18
170 5 0.01
171 137 0.41
172 83 0.25
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (170 bp):
ATAAATTGTAATGAGTTTATCGATTTACAAGTGTTTCATTATATATGATTGAATAAGGTAACATT
TATTCTATTTATGAATCTTAAGAAATATCTTGTAACGAGTTTATCGACTCATACGTGTTCTATTA
TATAATTAAATTAATTTGTCGTTTCTTGTATATATGAACC
Found at i:61577 original size:27 final size:27
Alignment explanation
Indices: 61547--61628 Score: 86
Period size: 27 Copynumber: 3.3 Consensus size: 27
61537 GGTCAGCATC
61547 TTCTTCAACTTTAGGTCAAAAATCCCT
1 TTCTTCAACTTTAGGTCAAAAATCCCT
* * **
61574 TTCTTCATC-GT-GGTC-AGCAT--C-
1 TTCTTCAACTTTAGGTCAAAAATCCCT
61595 TTCTTCAACTTTAGGTCAAAAATCCCT
1 TTCTTCAACTTTAGGTCAAAAATCCCT
61622 TTCTTCA
1 TTCTTCA
61629 TGGGAATGCA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
21 8 0.20
22 2 0.05
23 4 0.10
24 6 0.15
25 4 0.10
26 2 0.05
27 15 0.37
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (27 bp):
TTCTTCAACTTTAGGTCAAAAATCCCT
Found at i:61604 original size:48 final size:48
Alignment explanation
Indices: 61533--61629 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
61523 TTTTGAACTC
61533 TCGTGGTCAGCATCTTCTTCAACTTTAGGTCAAAAATCCCTTTCTTCA
1 TCGTGGTCAGCATCTTCTTCAACTTTAGGTCAAAAATCCCTTTCTTCA
61581 TCGTGGTCAGCATCTTCTTCAACTTTAGGTCAAAAATCCCTTTCTTCA
1 TCGTGGTCAGCATCTTCTTCAACTTTAGGTCAAAAATCCCTTTCTTCA
61629 T
1 T
61630 GGGAATGCAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (48 bp):
TCGTGGTCAGCATCTTCTTCAACTTTAGGTCAAAAATCCCTTTCTTCA
Found at i:63786 original size:29 final size:29
Alignment explanation
Indices: 63744--63801 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
63734 TTCTTATTAT
63744 TTTTATACAGTATTAAATACCGTACAATC
1 TTTTATACAGTATTAAATACCGTACAATC
* * *
63773 TTTTATACAGTATTGATTACCGTGCAATC
1 TTTTATACAGTATTAAATACCGTACAATC
63802 CTAATCATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (29 bp):
TTTTATACAGTATTAAATACCGTACAATC
Found at i:69019 original size:12 final size:12
Alignment explanation
Indices: 69002--69026 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
68992 TGAAAAGAAA
69002 TTCACCCACAAT
1 TTCACCCACAAT
69014 TTCACCCACAAT
1 TTCACCCACAAT
69026 T
1 T
69027 GTTGAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.40, G:0.00, T:0.28
Consensus pattern (12 bp):
TTCACCCACAAT
Found at i:72859 original size:20 final size:20
Alignment explanation
Indices: 72830--72867 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
72820 GAAACAGGTT
* *
72830 CGAGTTAACTCGGATCGAAC
1 CGAGTCAACTCGAATCGAAC
72850 CGAGTCAACTCGAATCGA
1 CGAGTCAACTCGAATCGA
72868 TCTGACCCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (20 bp):
CGAGTCAACTCGAATCGAAC
Found at i:74930 original size:32 final size:32
Alignment explanation
Indices: 74888--75030 Score: 137
Period size: 32 Copynumber: 4.5 Consensus size: 32
74878 CCTAAGGTGA
* *
74888 CCTTGGGTAGGCTCTGAGGCCCCAAGGCATTT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGCACTT
* *
74920 CCTTGAGTAGGCTCTAAGGCCCCAAGGTACTT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGCACTT
* * ** *
74952 CATTGGGTAGGCTCTTAGGCCTTAAGGTAC-T
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGCACTT
* * * *
74983 CCTTTAGGTAGGCTCTTAGGCCCTAAGGTAC-T
1 CC-TTGGGTAGGCTCTAAGGCCCCAAGGCACTT
75015 CCATTGGGTAGGCTCT
1 CC-TTGGGTAGGCTCT
75031 CAGGGTAAGT
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
31 2 0.02
32 94 0.98
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.29
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAGGCACTT
Found at i:74994 original size:64 final size:64
Alignment explanation
Indices: 74890--75030 Score: 185
Period size: 64 Copynumber: 2.2 Consensus size: 64
74880 TAAGGTGACC
* *
74890 TTGGGTAGGCTCTGAGGCCCCAAGGCATTTCCTTGAGTAGGCTCTAAGGCCCCAAGGTACTTCA
1 TTGGGTAGGCTCTGAGGCCCCAAGGCATCTCCTTGAGTAGGCTCTAAGGCCCCAAGGTACTCCA
* ** * * * *
74954 TTGGGTAGGCTCTTAGGCCTTAAGGTA-CTCCTTTAGGTAGGCTCTTAGGCCCTAAGGTACTCCA
1 TTGGGTAGGCTCTGAGGCCCCAAGGCATCTCCTTGA-GTAGGCTCTAAGGCCCCAAGGTACTCCA
75018 TTGGGTAGGCTCT
1 TTGGGTAGGCTCT
75031 CAGGGTAAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
63 6 0.09
64 61 0.91
ACGTcount: A:0.18, C:0.24, G:0.28, T:0.29
Consensus pattern (64 bp):
TTGGGTAGGCTCTGAGGCCCCAAGGCATCTCCTTGAGTAGGCTCTAAGGCCCCAAGGTACTCCA
Found at i:85427 original size:19 final size:19
Alignment explanation
Indices: 85403--85470 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
85393 TCCAAGTTCG
85403 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
** *
85422 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATTTTCCAAATT
85441 CGCGTTGCGATTTTCCAAATT
1 --CGTTGCGATTTTCCAAATT
85462 CGTTGCGAT
1 CGTTGCGAT
85471 ATTCGACGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 25 0.61
21 16 0.39
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:85432 original size:40 final size:40
Alignment explanation
Indices: 85384--85554 Score: 220
Period size: 40 Copynumber: 4.5 Consensus size: 40
85374 CATATTCGCA
85384 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
85424 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
*
85464 TTGCG--A-T---A-TT--CG--ACGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
*
85493 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
*
85535 TTGCGATAGTCGAAGTTCGC
1 TTGCGATAGTCCAAGTTCGC
85555 AACGACTGGT
Statistics
Matches: 116, Mismatches: 2, Indels: 24
0.82 0.01 0.17
Matches are distributed among these distances:
29 21 0.18
31 3 0.03
32 1 0.01
33 2 0.02
34 1 0.01
35 1 0.01
36 2 0.02
37 1 0.01
38 3 0.03
40 48 0.41
41 2 0.02
42 31 0.27
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (40 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
Found at i:85457 original size:21 final size:21
Alignment explanation
Indices: 85377--85471 Score: 99
Period size: 21 Copynumber: 4.7 Consensus size: 21
85367 CGATTTACAT
*
85377 ATTCGCATTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
* **
85398 GTTCGCGTTGCGATTTTCCAA
1 ATTCGCGTTGCGATAGTCCAA
85419 ATT--CGTTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
* **
85438 GTTCGCGTTGCGATTTTCCAA
1 ATTCGCGTTGCGATAGTCCAA
85459 ATT--CGTTGCGATA
1 ATTCGCGTTGCGATA
85472 TTCGACGATT
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
19 25 0.42
21 35 0.58
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (21 bp):
ATTCGCGTTGCGATAGTCCAA
Found at i:85490 original size:29 final size:29
Alignment explanation
Indices: 85448--85505 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
85438 GTTCGCGTTG
*
85448 CGATTTTCCAAATTCGTTGCGATATTCGA
1 CGATTTTCCAAATTCGTTGCGATAGTCGA
85477 CGATTTTCCAAATTCGTTGCGATAGTCGA
1 CGATTTTCCAAATTCGTTGCGATAGTCGA
85506 AGTTCGCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (29 bp):
CGATTTTCCAAATTCGTTGCGATAGTCGA
Found at i:85517 original size:21 final size:21
Alignment explanation
Indices: 85491--85554 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
85481 TTTCCAAATT
85491 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTTCG
* * *
85512 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCGAAGTTCG
85533 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTTCG
85554 C
1 C
85555 AACGACTGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 8 0.24
21 17 0.52
23 8 0.24
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (21 bp):
CGTTGCGATAGTCGAAGTTCG
Found at i:85519 original size:69 final size:71
Alignment explanation
Indices: 85408--85547 Score: 248
Period size: 69 Copynumber: 2.0 Consensus size: 71
85398 GTTCGCGTTG
85408 CGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGAT
1 CGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGAT
*
85471 ATTCGA
66 AGTCGA
*
85477 CGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGAT
1 CGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGAT
85542 AGTCGA
66 AGTCGA
85548 AGTTCGCAAC
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
69 42 0.63
70 2 0.03
71 23 0.34
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (71 bp):
CGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGAT
AGTCGA
Found at i:85646 original size:6 final size:6
Alignment explanation
Indices: 85635--85659 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
85625 AAAGACACGT
85635 ATTACC ATTACC ATTACC ATTACC A
1 ATTACC ATTACC ATTACC ATTACC A
85660 CGACCACGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTACC
Found at i:86179 original size:6 final size:6
Alignment explanation
Indices: 86168--86192 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
86158 TCTCGTCTCG
86168 GGTCGT GGTCGT GGTCGT GGTCGT G
1 GGTCGT GGTCGT GGTCGT GGTCGT G
86193 ATAATACGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:86341 original size:21 final size:21
Alignment explanation
Indices: 86317--86425 Score: 109
Period size: 21 Copynumber: 5.2 Consensus size: 21
86307 AATAAATTGT
*
86317 AACGCGAACTTCGACTATCGC
1 AACGCGAACTTGGACTATCGC
*
86338 AA--CGAACTTGGAATAAATCGC
1 AACGCGAACTTGGACT--ATCGC
86359 AACGCGAACTTGGACTATCGC
1 AACGCGAACTTGGACTATCGC
* *
86380 AA--CGAATTTGGAATAAATCGC
1 AACGCGAACTTGGACT--ATCGC
*
86401 AACGCGAACTTCGACTATCGC
1 AACGCGAACTTGGACTATCGC
86422 AACG
1 AACG
86426 AATTTGGAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
19 20 0.28
21 32 0.44
23 20 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (21 bp):
AACGCGAACTTGGACTATCGC
Found at i:86349 original size:42 final size:42
Alignment explanation
Indices: 86287--86448 Score: 265
Period size: 42 Copynumber: 3.9 Consensus size: 42
86277 TGCGATTTTG
* *
86287 GACTATCGCAACGAATTTGGAATAAATTGTAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
86329 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
86371 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
86413 GACTATCGCAACGAATTTGG-A-AAATCGCAATGCGAA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAA
86449 TATGTAAATC
Statistics
Matches: 113, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
40 14 0.12
41 1 0.01
42 98 0.87
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:89967 original size:16 final size:16
Alignment explanation
Indices: 89943--89981 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
89933 AAATGATTCA
*
89943 TGTTCATTGTACAATT
1 TGTTGATTGTACAATT
89959 TGTTGATTGTACAATT
1 TGTTGATTGTACAATT
89975 TGTTGAT
1 TGTTGAT
89982 GATAAGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (16 bp):
TGTTGATTGTACAATT
Found at i:94199 original size:20 final size:21
Alignment explanation
Indices: 94174--94266 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
94164 TTTTCCCAAT
*
94174 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
94194 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
* *
94215 TCGCAATGC-AAATAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
94235 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
94256 TCGCAATGCGA
1 TCGCAATGCGA
94267 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:94219 original size:41 final size:41
Alignment explanation
Indices: 94174--94266 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
94164 TTTTCCCAAT
94174 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
94215 TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
94256 TCGCAATGCGA
1 TCGCAATGCGA
94267 TACTGACTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:94279 original size:41 final size:41
Alignment explanation
Indices: 94193--94327 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
94183 GAATAAGTAA
* * *
94193 ATCGCAACGCGAATTGGGAAAATCGCAATGCAAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGC-GATACTG-ACT
94234 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
94275 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
94316 TTCGCAACGCGA
1 ATCGCAACGCGA
94328 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:94280 original size:20 final size:20
Alignment explanation
Indices: 94255--94345 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
94245 AATTGGGAAA
*
94255 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
94275 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
94296 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
94316 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
94336 TTCGCAACGC
1 ATCGCAACGC
94346 AATAATACAT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 43 0.75
21 14 0.25
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:94565 original size:22 final size:22
Alignment explanation
Indices: 94537--94580 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
94527 CACTCTCTCA
94537 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
94559 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
94581 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:94880 original size:20 final size:20
Alignment explanation
Indices: 94857--94899 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
94847 GATAGTCGAA
94857 TTCGCATTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
**
94877 TTCGTGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
94897 TTC
1 TTC
94900 AGAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.12, C:0.19, G:0.16, T:0.53
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Done.