Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001666.1 Hibiscus syriacus cultivar Beakdansim tig00003335_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: 99387
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:5501 original size:17 final size:17
Alignment explanation
Indices: 5479--5530 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
5469 TTAAGAGTTC
5479 GTTTAATAAATGAACTA
1 GTTTAATAAATGAACTA
* *
5496 GTTTAATTAACGAACTAA
1 GTTTAATAAATGAACT-A
* *
5514 CTTTATTAAATG-ACTA
1 GTTTAATAAATGAACTA
5530 G
1 G
5531 ATGCATGAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
16 1 0.04
17 17 0.63
18 9 0.33
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (17 bp):
GTTTAATAAATGAACTA
Found at i:7843 original size:29 final size:29
Alignment explanation
Indices: 7791--7861 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
7781 GTGATTTATT
*
7791 GACGATGCATTA-ATTTTTTATGGTACAA
1 GACGATGCATTATATGTTTTATGGTACAA
*
7819 GATGATGCATTATATGTTTTATGGTACAA
1 GACGATGCATTATATGTTTTATGGTACAA
7848 GACGATGCATTATA
1 GACGATGCATTATA
7862 GTCGAGACGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 11 0.28
29 28 0.72
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (29 bp):
GACGATGCATTATATGTTTTATGGTACAA
Found at i:9523 original size:23 final size:23
Alignment explanation
Indices: 9497--9570 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
9487 CTTACCTTTT
9497 TTTTCCATAAGCTCGTAAGCTTA
1 TTTTCCATAAGCTCGTAAGCTTA
* *
9520 TTTTACCA-AA-ATACTTAA-CATTTA
1 TTTT-CCATAAGCT-CGTAAGC--TTA
**
9544 AATTCCATAAGCTCGTAAGCTTA
1 TTTTCCATAAGCTCGTAAGCTTA
9567 TTTT
1 TTTT
9571 ATCAATATAC
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 2 0.06
23 18 0.50
24 14 0.39
25 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (23 bp):
TTTTCCATAAGCTCGTAAGCTTA
Found at i:9610 original size:43 final size:46
Alignment explanation
Indices: 9499--9612 Score: 162
Period size: 47 Copynumber: 2.5 Consensus size: 46
9489 TACCTTTTTT
9499 TTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTAACATTTAAA
1 TTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTAACATTT-AA
* * **
9546 TTCCATAAGCTCGTAAGCTTATTTTATCAATATACTTGCCA-TT-A
1 TTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTAACATTTAA
9590 TT-CATAAGCTCGTAAGCTTATTT
1 TTCCATAAGCTCGTAAGCTTATTT
9613 GCATACTTAC
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
43 21 0.33
44 3 0.05
46 2 0.03
47 37 0.59
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.39
Consensus pattern (46 bp):
TTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTAACATTTAA
Found at i:9620 original size:38 final size:41
Alignment explanation
Indices: 9502--9626 Score: 121
Period size: 47 Copynumber: 2.9 Consensus size: 41
9492 CTTTTTTTTC
* *
9502 CATAAGCTCGTAAGCTTATTTTACCAAAATACTTAACATTTAAATT
1 CATAAGCTCGTAAGCTTATTTTAGC--AATACTTACCA-TT--ATT
* *
9548 CCATAAGCTCGTAAGCTTATTTTATCAATATACTTGCCATTATT
1 -CATAAGCTCGTAAGCTTATTTTAGC-A-ATACTTACCATTATT
9592 CATAAGCTCGTAAGCTTA-TTT-GC-ATACTTACCATT
1 CATAAGCTCGTAAGCTTATTTTAGCAATACTTACCATT
9627 TATTAACCAA
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
38 11 0.15
41 1 0.01
42 3 0.04
43 18 0.25
44 3 0.04
46 4 0.06
47 32 0.44
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (41 bp):
CATAAGCTCGTAAGCTTATTTTAGCAATACTTACCATTATT
Found at i:11077 original size:29 final size:29
Alignment explanation
Indices: 11034--11096 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
11024 TCTTCATCAA
* * *
11034 TTTTCCAAAATTTACGAATTTATCCCCAAT
1 TTTTCCAAAACTTACGAAATGAT-CCCAAT
11064 TTTTCC-AAACTTACGAAATGATCCCAAT
1 TTTTCCAAAACTTACGAAATGATCCCAAT
11092 TTTTC
1 TTTTC
11097 TGAGGCTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 11 0.37
29 13 0.43
30 6 0.20
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.40
Consensus pattern (29 bp):
TTTTCCAAAACTTACGAAATGATCCCAAT
Found at i:16109 original size:20 final size:20
Alignment explanation
Indices: 16071--16110 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16061 ATATTTTTTT
* *
16071 ATGAATAGTGAACATTACCC
1 ATGAACAGTGAACAGTACCC
*
16091 ATGAACAGTGAATAGTACCC
1 ATGAACAGTGAACAGTACCC
16111 CATTTACATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (20 bp):
ATGAACAGTGAACAGTACCC
Found at i:16635 original size:47 final size:44
Alignment explanation
Indices: 16566--16677 Score: 145
Period size: 47 Copynumber: 2.5 Consensus size: 44
16556 CCTTTTTTTC
*
16566 CCATAAGCTCTTAAGCTTATTTTACCAAAATACTTAACATTTAAATT
1 CCATAAGCTCATAAGCTTATTTTACCAAAATACTTAACA-TT--ATT
* **
16613 CCATAAGCTCATAAGCTTATTTTACCAATATACTTGCCATTATT
1 CCATAAGCTCATAAGCTTATTTTACCAAAATACTTAACATTATT
*
16657 -CATAAGCTCGTAAGCTTATTT
1 CCATAAGCTCATAAGCTTATTT
16678 GCATACTTAC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
43 20 0.33
44 3 0.05
46 2 0.03
47 35 0.58
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (44 bp):
CCATAAGCTCATAAGCTTATTTTACCAAAATACTTAACATTATT
Found at i:21337 original size:49 final size:49
Alignment explanation
Indices: 21256--21713 Score: 360
Period size: 49 Copynumber: 9.4 Consensus size: 49
21246 GCTTCGTTGT
* * * *
21256 TCTTTAAGGTAGGTCAGAT-AGGAAAAATAAATGAGATATACTCCGCTGC
1 TCTTTAGGGTAGGTTAGATCAGG-AAAAGAAATGAGATATGCTCCGCTGC
* * * * * *
21305 TATTTAGAGTAGGTTGGATCAGGAAAAGAAATGATATCTGCTCCGCTAC
1 TCTTTAGGGTAGGTTAGATCAGGAAAAGAAATGAGATATGCTCCGCTGC
* *
21354 TCTTTAGGGTAGGTTAGATCAGGAAAAGAAATAAGATCTGCAT--GCTGC
1 TCTTTAGGGTAGGTTAGATCAGGAAAAGAAATGAGATATGC-TCCGCTGC
* * * **
21402 TCTTTAGGGTGGGTTAGATCGGGAAAA-AAA-GAGATATGATATGCTGC
1 TCTTTAGGGTAGGTTAGATCAGGAAAAGAAATGAGATATGCTCCGCTGC
* * * * ** *
21449 TCTTCAAGGTA-GTGCAGATC-GAGAAAAGAAAGGAGATATGCTTTGTTGC
1 TCTTTAGGGTAGGT-TAGATCAG-GAAAAGAAATGAGATATGCTCCGCTGC
* * * *
21498 TCTTTAGGGTAGGTCAGATCGGGAAAAGAAAAGAGATATTCTCCGCTGC
1 TCTTTAGGGTAGGTTAGATCAGGAAAAGAAATGAGATATGCTCCGCTGC
* *
21547 TCTTTAGGGTAGGTCAGATCAGGAAAAGGAAA-GAGATATGCTCCGCTTC
1 TCTTTAGGGTAGGTTAGATCAGGAAAA-GAAATGAGATATGCTCCGCTGC
* * * * * * * ** *
21596 TCTCTAGGGTAGGTCATATC-GGAAAAAGAAAGGATATCTACTCTACTAC
1 TCTTTAGGGTAGGTTAGATCAGG-AAAAGAAATGAGATATGCTCCGCTGC
* * * * **
21645 TCTTCAGGGTAGGTCAGATCAAG-AAAGAAAAAGAGATATGCTCTTCTGC
1 TCTTTAGGGTAGGTTAGATCAGGAAAAG-AAATGAGATATGCTCCGCTGC
*
21694 TCTTCAGGGTAGGTTAGATC
1 TCTTTAGGGTAGGTTAGATC
21714 TGGTGTTGAA
Statistics
Matches: 337, Mismatches: 57, Indels: 30
0.79 0.13 0.07
Matches are distributed among these distances:
45 1 0.00
46 9 0.03
47 26 0.08
48 42 0.12
49 247 0.73
50 12 0.04
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (49 bp):
TCTTTAGGGTAGGTTAGATCAGGAAAAGAAATGAGATATGCTCCGCTGC
Found at i:40340 original size:81 final size:81
Alignment explanation
Indices: 40254--40858 Score: 852
Period size: 81 Copynumber: 7.5 Consensus size: 81
40244 CATTTAACCT
* * * * *
40254 TTCATCTACCTTGCATGATTGACA-CTTGTCTACCAAATGCACAGCTAGGTCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACCTT-TCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
* * * *
40318 TCAATGATATTTAACCG
65 TCAACGGTCTTTAATCG
* * *
40335 TTCATCTAACTGTCATAATTGACACCTTTCTGTCAAATGCATAGCTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
40400 CAACGGTCTTTAATCG
66 CAACGGTCTTTAATCG
* **
40416 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATACACAGCTAATCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
*
40481 CAGCGGTCTTTAATCG
66 CAACGGTCTTTAATCG
* ***
40497 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAACTATATCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
40562 CAACGGTCTTTAATCG
66 CAACGGTCTTTAATCG
* * * *
40578 TTCATCTAACTGGCATAATTGACACCTTTCTACGAAATGCATAACTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
*
40643 CAATGGTCTTTAATCG
66 CAACGGTCTTTAATCG
** * * *
40659 TTCATCTAACTGGCATAATTGACACAATTCTGCCAAATGAACAACTAGGCCATTTATTTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
* *
40724 CAACGGTCTTTAACCA
66 CAACGGTCTTTAATCG
* * *
40740 TTCATCTAACTGGCATAATTGACAACTTTTTGCCAAATGCACAGCTAGGCTATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
*
40805 CAATGGTCTTTAATCG
66 CAACGGTCTTTAATCG
* *
40821 TTCATCTAACTAGCATAATTGACACCTTTCTGTCAAAT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAAT
40859 TCATAGTTAG
Statistics
Matches: 466, Mismatches: 57, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
81 463 0.99
82 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (81 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
CAACGGTCTTTAATCG
Found at i:40912 original size:68 final size:68
Alignment explanation
Indices: 40821--41187 Score: 524
Period size: 68 Copynumber: 5.4 Consensus size: 68
40811 TCTTTAATCG
* * *
40821 TTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATTCATAGTTAGACCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGACCTCAAAGGCACTTAG
40886 CCT
66 CCT
* * * * *
40889 TTCATCTAACTAGTATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCTTCAAAGGAACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGACCTCAAAGGCACTTAG
40954 CCT
66 CCT
*
40957 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGA-CTCAAAGGTACTTA
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA-GACCTCAAAGGCACTTA
41021 GCCT
65 GCCT
* * * * *
41025 TTCATCTAACTGGCATAATTGATACATTTATGTCAAATGCACAGTTAGGCCACAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGACCTCAAAGGCACTTAG
*
41090 CTT
66 CCT
* *
41093 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAATTACGTA--TCAAATGCACTT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA-G-ACCTCAAAGGCACTT
*
41156 AACCT
64 AGCCT
41161 TTCATCTAACTGGCATAATTGACACCT
1 TTCATCTAACTGGCATAATTGACACCT
41188 ATAATGCCCA
Statistics
Matches: 268, Mismatches: 27, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
67 1 0.00
68 265 0.99
69 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGACCTCAAAGGCACTTAG
CCT
Found at i:41382 original size:54 final size:55
Alignment explanation
Indices: 41313--41570 Score: 310
Period size: 55 Copynumber: 4.7 Consensus size: 55
41303 TCCTAAACGG
* * *
41313 AAATTAATACACTTAGTATGGATTTCTTAG-TTTGCACACATAGTGTCCATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGTCCATACGA
* * * *
41367 AAATCCATACACTTAGTATGAATTTCTTAGTTTTGCACCCAAAGTGCCCATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGTCCATACGA
* * *
41422 AAATTCATACACCTAGTACGAATTTCTTAGTTTTTCACA-AATAGTG-CCTATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAA-AGTGTCC-ATACGA
* * *
41477 AAATTCATACACATAGTATGAATTTCTTAGTTTTTCACATAAAGTGT-CATATCG-
1 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGTCCATA-CGA
*
41531 AAATTCATACACTTAGTATGGATTTCTTAAGTTTTTGCAC
1 AAATTCATACACTTAGTATGAATTTCTT-AG-TTTTGCAC
41571 GCTTAGTGCC
Statistics
Matches: 178, Mismatches: 18, Indels: 14
0.85 0.09 0.07
Matches are distributed among these distances:
54 60 0.34
55 109 0.61
56 9 0.05
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (55 bp):
AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGTCCATACGA
Found at i:41501 original size:110 final size:109
Alignment explanation
Indices: 41309--41566 Score: 351
Period size: 110 Copynumber: 2.4 Consensus size: 109
41299 TATTTCCTAA
* * *
41309 ACGGAAATTAATACACTTAGTATGGATTTCTTAG-TTTGCACACATAGTGTCCATACGAAAATCC
1 ACGGAAATTCATACACTTAGTATGGATTTCTTAGTTTTTCACAAATAGTGTCCATACGAAAATCC
* *
41373 ATACACTTAGTATGAATTTCTTAGTTTTGCACCCAAAGTGCCCAT
66 ATACACATAGTATGAATTTCTTAGTTTTGCACACAAAGTG-CCAT
* * * *
41418 ACGGAAATTCATACACCTAGTACGAATTTCTTAGTTTTTCACAAATAGTG-CCTATACGAAAATT
1 ACGGAAATTCATACACTTAGTATGGATTTCTTAGTTTTTCACAAATAGTGTCC-ATACGAAAATC
* * *
41482 CATACACATAGTATGAATTTCTTAGTTTTTCACATAAAGTGTCAT
65 CATACACATAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCAT
41527 ATC-GAAATTCATACACTTAGTATGGATTTCTTAAGTTTTT
1 A-CGGAAATTCATACACTTAGTATGGATTTCTT-AGTTTTT
41567 GCACGCTTAG
Statistics
Matches: 130, Mismatches: 15, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
109 62 0.48
110 68 0.52
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (109 bp):
ACGGAAATTCATACACTTAGTATGGATTTCTTAGTTTTTCACAAATAGTGTCCATACGAAAATCC
ATACACATAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCAT
Found at i:46303 original size:23 final size:23
Alignment explanation
Indices: 46273--46317 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
46263 TAACAAAATG
*
46273 ATTTAGTCACAA-TAACAAATTAA
1 ATTTAGTCA-AAGTAAAAAATTAA
46296 ATTTAGTCAAAGTAAAAAATTA
1 ATTTAGTCAAAGTAAAAAATTA
46318 TGTCAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (23 bp):
ATTTAGTCAAAGTAAAAAATTAA
Found at i:47247 original size:21 final size:22
Alignment explanation
Indices: 47210--47250 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
47200 TTAAAAATTA
*
47210 TAAAGGTAGTACTGATACTCAT
1 TAAAGGTAGTACCGATACTCAT
47232 TAAAGG-AGTACCGATACTC
1 TAAAGGTAGTACCGATACTC
47251 CCTGTCCTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (22 bp):
TAAAGGTAGTACCGATACTCAT
Found at i:53112 original size:15 final size:15
Alignment explanation
Indices: 53092--53120 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53082 AATTACCAAT
53092 TTCCATTAAAATATC
1 TTCCATTAAAATATC
53107 TTCCATTAAAATAT
1 TTCCATTAAAATAT
53121 TCCATAGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (15 bp):
TTCCATTAAAATATC
Found at i:53125 original size:13 final size:14
Alignment explanation
Indices: 53092--53125 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
53082 AATTACCAAT
53092 TTCCATTAAAATATC
1 TTCCATTAAAATA-C
53107 TTCCATTAAAATA-
1 TTCCATTAAAATAC
53120 TTCCAT
1 TTCCAT
53126 AGTCAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
15 13 0.68
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (14 bp):
TTCCATTAAAATAC
Found at i:70307 original size:23 final size:23
Alignment explanation
Indices: 70246--70352 Score: 103
Period size: 23 Copynumber: 4.7 Consensus size: 23
70236 GTCGATGGTT
* *
70246 CTATGTGGTCTTTCGGGATAAAC
1 CTATGTGGTCCTTCGGGACAAAC
* *
70269 CTATATGGGTCCTTCGGGACAATC
1 CTATGT-GGTCCTTCGGGACAAAC
* * *
70293 CTATGTGGTCTTTCGAGACAAAA
1 CTATGTGGTCCTTCGGGACAAAC
*
70316 CTATGTAGTCCTTCGGGACAAA-
1 CTATGTGGTCCTTCGGGACAAAC
70338 -TATGTGG-CACTTCGG
1 CTATGTGGTC-CTTCGG
70353 TGCAAATTAT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.01
21 12 0.17
23 37 0.54
24 19 0.28
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAC
Found at i:71740 original size:25 final size:25
Alignment explanation
Indices: 71707--71754 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
71697 GCATAAAAAC
71707 AAAACTTGAAAA-TAAAGAAGAAATA
1 AAAACTTGAAAAGTAAA-AAGAAATA
71732 AAAACTTGAAAAGTAAAAAGAAA
1 AAAACTTGAAAAGTAAAAAGAAA
71755 AAGCTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.69, C:0.04, G:0.12, T:0.15
Consensus pattern (25 bp):
AAAACTTGAAAAGTAAAAAGAAATA
Found at i:72813 original size:16 final size:15
Alignment explanation
Indices: 72792--72821 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
72782 TTTTTATGTC
72792 TTTTTTCTTTCTTTCT
1 TTTTTTCTTT-TTTCT
72808 TTTTTTCTTTTTTC
1 TTTTTTCTTTTTTC
72822 GAACAACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTCTTTTTTCT
Found at i:78068 original size:24 final size:24
Alignment explanation
Indices: 78024--78070 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
78014 GCATAAAAAC
* * *
78024 AAAACTTGAAAATATAGAAGAAAT
1 AAAACTTGAAAAGAAAAAAGAAAT
78048 AAAACTTGAAAAGAAAAAAGAAA
1 AAAACTTGAAAAGAAAAAAGAAA
78071 AAACTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.68, C:0.04, G:0.13, T:0.15
Consensus pattern (24 bp):
AAAACTTGAAAAGAAAAAAGAAAT
Found at i:83343 original size:90 final size:88
Alignment explanation
Indices: 83229--83401 Score: 301
Period size: 89 Copynumber: 1.9 Consensus size: 88
83219 TCCTGAATAT
*
83229 TTAATTTCAATTAATTAAATATAGATTTAATTAACTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAACTTGAAATAATAAAA-CCCTAATATGATTAG
83294 GGTAACTTGGATATAAAAGGATTA
65 GGTAACTTGGATATAAAAGGATTA
*
83318 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAACTTGAAATAATAAAACCCTAATATGATTAG
*
83383 GGTAACTTGGCTATAAAAG
65 GGTAACTTGGATATAAAAG
83402 TGTGTGTTAG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 40 0.50
90 40 0.50
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAACTTGAAATAATAAAACCCTAATATGATTAGG
GTAACTTGGATATAAAAGGATTA
Found at i:84046 original size:2 final size:2
Alignment explanation
Indices: 84039--84090 Score: 95
Period size: 2 Copynumber: 25.5 Consensus size: 2
84029 TGTAACAACG
84039 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
84081 TA TA TGA TA T
1 TA TA T-A TA T
84091 GTTTGTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:93348 original size:40 final size:41
Alignment explanation
Indices: 93283--93474 Score: 181
Period size: 40 Copynumber: 4.7 Consensus size: 41
93273 TTTTTAGCAT
* *
93283 CGTTTTTAGAACAAACGCCACTAAAGACT-GTACTTTAGTGG
1 CGTTTTTA-AACAAACGCCGCTAAAGACTAATACTTTAGTGG
* * *
93324 CGTTTTTATACAAACGTCGCTAAAGACT-ATACTTTAGTTG
1 CGTTTTTAAACAAACGCCGCTAAAGACTAATACTTTAGTGG
* * * * * *
93364 CATTTTTAGACAAACACCGCTATAGATTCATACTTTAGTGG
1 CGTTTTTAAACAAACGCCGCTAAAGACTAATACTTTAGTGG
* * * * * *
93405 CGTTTTCAAAACAAACACCGCTACATACTAGTATTTTAGTGG
1 CGTTTT-TAAACAAACGCCGCTAAAGACTAATACTTTAGTGG
* *
93447 CGTTTTTATACAAACGACGCTAAAGACT
1 CGTTTTTAAACAAACGCCGCTAAAGACT
93475 CGTTTTGTGT
Statistics
Matches: 122, Mismatches: 27, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
40 49 0.40
41 40 0.33
42 33 0.27
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (41 bp):
CGTTTTTAAACAAACGCCGCTAAAGACTAATACTTTAGTGG
Found at i:97470 original size:41 final size:42
Alignment explanation
Indices: 97246--97487 Score: 231
Period size: 42 Copynumber: 5.8 Consensus size: 42
97236 ACATTAATTA
* * * *
97246 GCGGCGTTTGCTCCAAAAACGACACTATAGATCCTACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCCGACCTTTT
** *
97288 GCGGCGTTT-TCTCCAAAAATACCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATC-CGACCTTTT
* * ** *
97331 GCGGCG-TTGTTCCAAAAATGTCATTATAGATCCGACTTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCCGACCTTTT
* ** * *
97372 GCGGTGTTTGTTCCAAAAACGTTGCTTTAGCTCCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCCGACCTTTT
* * * * *
97414 GCAGCATTT-TATCCAAAAACGCCGTTATAGA-GCAACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCCGACCTTTT
97455 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC
97488 TCGATCTATC
Statistics
Matches: 158, Mismatches: 35, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
41 47 0.30
42 97 0.61
43 14 0.09
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCCGACCTTTT
Done.