Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005428.1 Hibiscus syriacus cultivar Beakdansim tig00012445_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: 61271
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6865 original size:3 final size:3
Alignment explanation
Indices: 6857--6896 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
6847 ATATATGAAC
6857 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
6897 AAGTGAAACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:7379 original size:23 final size:22
Alignment explanation
Indices: 7353--7427 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 22
7343 AACTATTTAT
7353 TATATTTTAAAATATTAAATTGA
1 TATATTTTAAAATATTAAATT-A
* *
7376 TATATTTTAATAATATAAAAATA
1 TATATTTTAA-AATATTAAATTA
*
7399 -AAATTCTTAAAATATTAAATATAA
1 TATATT-TTAAAATATTAAAT-T-A
7423 TATAT
1 TATAT
7428 ATAAATTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
22 12 0.29
23 16 0.39
24 10 0.24
25 3 0.07
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (22 bp):
TATATTTTAAAATATTAAATTA
Found at i:8344 original size:6 final size:6
Alignment explanation
Indices: 8333--8359 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
8323 TAGTCCTTCT
8333 CAAACC CAAACC CAAACC CAAACC CAA
1 CAAACC CAAACC CAAACC CAAACC CAA
8360 GGCTTGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAACC
Found at i:13184 original size:2 final size:2
Alignment explanation
Indices: 13177--13222 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
13167 ACATAAAATC
13177 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
13219 AT AT
1 AT AT
13223 GAACAGTGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17804 original size:22 final size:22
Alignment explanation
Indices: 17773--17818 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
17763 TTTCTTAAAA
* *
17773 AATATTAAAATAATACTCGATG
1 AATATAAAAATAATACTCAATG
*
17795 AATATAAAAATAATATTCAATG
1 AATATAAAAATAATACTCAATG
17817 AA
1 AA
17819 ACTCGTCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
AATATAAAAATAATACTCAATG
Found at i:21180 original size:15 final size:15
Alignment explanation
Indices: 21135--21186 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
21125 TTAGTCACTA
*
21135 TTTAATTGCAATTTT
1 TTTAATTTCAATTTT
21150 TTT-A-TT-AATATCTT
1 TTTAATTTCAAT-T-TT
21164 TTTAATTTCAATTTT
1 TTTAATTTCAATTTT
21179 TTTAATTT
1 TTTAATTT
21187 AATACTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
12 3 0.10
13 2 0.06
14 6 0.19
15 14 0.45
16 3 0.10
17 3 0.10
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTAATTTCAATTTT
Found at i:23808 original size:8 final size:7
Alignment explanation
Indices: 23786--23825 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
23776 TTCATACATA
23786 CATTTT-
1 CATTTTG
23792 CATTTTG
1 CATTTTG
23799 CATCTTTG
1 CAT-TTTG
23807 CATTTT-
1 CATTTTG
23813 CATTTTG
1 CATTTTG
23820 C-TTTTG
1 CATTTTG
23826 TATTGCACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 17 0.55
7 7 0.23
8 7 0.23
ACGTcount: A:0.12, C:0.17, G:0.10, T:0.60
Consensus pattern (7 bp):
CATTTTG
Found at i:23936 original size:35 final size:34
Alignment explanation
Indices: 23881--23950 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
23871 CATTCACATA
*
23881 TTTACATTTGCATTTGCATTTTGCATATTTGCATT
1 TTTACATTTGCATTTACATTTT-CATATTTGCATT
* * *
23916 TTTACGTTTGTATTTACATTTTCATTTTTGCATT
1 TTTACATTTGCATTTACATTTTCATATTTGCATT
23950 T
1 T
23951 GCATATTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 12 0.39
35 19 0.61
ACGTcount: A:0.19, C:0.13, G:0.10, T:0.59
Consensus pattern (34 bp):
TTTACATTTGCATTTACATTTTCATATTTGCATT
Found at i:26379 original size:14 final size:14
Alignment explanation
Indices: 26360--26398 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
26350 CATTTATCAG
* *
26360 AAAATAAAAAGGGA
1 AAAATAAAAAAGAA
26374 AAAATAAAAAAGAA
1 AAAATAAAAAAGAA
*
26388 AAAAGAAAAAA
1 AAAATAAAAAA
26399 ATAAGAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (14 bp):
AAAATAAAAAAGAA
Found at i:28649 original size:75 final size:75
Alignment explanation
Indices: 28526--28702 Score: 257
Period size: 75 Copynumber: 2.4 Consensus size: 75
28516 AACAATAAGA
* * * *
28526 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATATGAATGTTGATGCATTTTGAATGT
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATAAGAAATAGGAATGTTGATGCATTTTGAACGC
28591 TTGTATCAGC
66 TTGTATCAGC
* * * *
28601 AAATGCTGGGACATACTGAAAGCTCATTTCAATAAG-AATCAGGAATGTTGATGCATTTTGAACG
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATAAGAAAT-AGGAATGTTGATGCATTTTGAACG
28665 CTTGTATCAGC
65 CTTGTATCAGC
*
28676 AAATGTTGGGGCATGCTGAAGGCCCAT
1 AAATGTTGGGGCATGCTGAAAGCCCAT
28703 ATTATCCTGT
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
74 3 0.03
75 85 0.97
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (75 bp):
AAATGTTGGGGCATGCTGAAAGCCCATTTCAATAAGAAATAGGAATGTTGATGCATTTTGAACGC
TTGTATCAGC
Found at i:29676 original size:53 final size:53
Alignment explanation
Indices: 29572--29727 Score: 215
Period size: 53 Copynumber: 2.9 Consensus size: 53
29562 ATGACCAGAA
* ** * * *
29572 ATCTGTGCAAAAAACACAAGAAATGATGAATGTTTGTCAAATGCTTAACGAAC
1 ATCTGTGCAGAAGCCACAGGAAATGATGAATGTTTGTCAAATGTTTTACGAAC
*
29625 ATCTAG-GTAGAAGCCACAGGAAATGATGAATGTTTGTCAAATGTTTTACGAAC
1 ATCT-GTGCAGAAGCCACAGGAAATGATGAATGTTTGTCAAATGTTTTACGAAC
*
29678 ATCTGTGCAGAAGCCACAGGAAATGATGAATATGTTGTCAAATGTTTTAC
1 ATCTGTGCAGAAGCCACAGGAAATGATGAATGT-TTGTCAAATGTTTTAC
29728 AAACTAGTTA
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
52 1 0.01
53 73 0.80
54 17 0.19
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (53 bp):
ATCTGTGCAGAAGCCACAGGAAATGATGAATGTTTGTCAAATGTTTTACGAAC
Found at i:30126 original size:22 final size:22
Alignment explanation
Indices: 30097--30215 Score: 166
Period size: 22 Copynumber: 5.4 Consensus size: 22
30087 TATATTCTTT
*
30097 AAAGATGATATATTCTCTTTTC
1 AAAGATGATAGATTCTCTTTTC
* *
30119 AATGATGATAGATTCTCTTTTA
1 AAAGATGATAGATTCTCTTTTC
*
30141 AAAAATGATAGATTCTCTTTTC
1 AAAGATGATAGATTCTCTTTTC
*
30163 AAAGATGATATATTCTCTTTTC
1 AAAGATGATAGATTCTCTTTTC
* *
30185 AAAAGATAATAGATTCTCTCTTC
1 -AAAGATGATAGATTCTCTTTTC
30208 AAAGATGA
1 AAAGATGA
30216 AAGCTTTATT
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
22 65 0.77
23 19 0.23
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTTTTC
Found at i:31003 original size:45 final size:45
Alignment explanation
Indices: 30860--31212 Score: 535
Period size: 45 Copynumber: 7.8 Consensus size: 45
30850 CTATTTCCCA
* *
30860 CATCTTTAAAACCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
30906 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* *
30952 TATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
30997 CATCTGTAAGACCTTTAGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
31042 CATCTGTAAGCCCTTTAGTGCATGATATTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
31087 CATCTGTAAGCCCTTCAGTGTATGATGTTTTCAAAACTTTCGGGC
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
31132 CATCTGTAAGACCTTCAGTGCATGATGTTTTAAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
31177 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAA
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAA
31213 AGCCTTTGGG
Statistics
Matches: 282, Mismatches: 25, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
45 208 0.74
46 74 0.26
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (45 bp):
CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:31238 original size:31 final size:31
Alignment explanation
Indices: 31200--31274 Score: 150
Period size: 31 Copynumber: 2.4 Consensus size: 31
31190 TACAGTGCAG
31200 GATGTTTTCAAAAAGCCTTTGGGAGCTTTTT
1 GATGTTTTCAAAAAGCCTTTGGGAGCTTTTT
31231 GATGTTTTCAAAAAGCCTTTGGGAGCTTTTT
1 GATGTTTTCAAAAAGCCTTTGGGAGCTTTTT
31262 GATGTTTTCAAAA
1 GATGTTTTCAAAA
31275 CCTTCGGGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.41
Consensus pattern (31 bp):
GATGTTTTCAAAAAGCCTTTGGGAGCTTTTT
Found at i:31340 original size:106 final size:107
Alignment explanation
Indices: 31154--31349 Score: 358
Period size: 106 Copynumber: 1.8 Consensus size: 107
31144 CTTCAGTGCA
31154 TGATGTTTTAAAAACCTTCGGGTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTAAAAACCTTCGGGTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
*
31219 TGGGAGCTTTTTGATGTTTTCAAAAAGCCTTTGGGAGCTTTT
66 CGGGAGCTTTTTGATGTTTTCAAAAAGCCTTTGGGAGCTTTT
* *
31261 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCT-CAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTAAAAACCTTCGGGTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
31325 CGGGAGCTTTTTGATGTTTTCAAAA
66 CGGGAGCTTTTTGATGTTTTCAAAA
31350 CCTTCGGGTC
Statistics
Matches: 86, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
106 51 0.59
107 35 0.41
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (107 bp):
TGATGTTTTAAAAACCTTCGGGTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAAAGCCTTTGGGAGCTTTT
Found at i:31354 original size:75 final size:76
Alignment explanation
Indices: 31231--31393 Score: 310
Period size: 75 Copynumber: 2.2 Consensus size: 76
31221 GGAGCTTTTT
*
31231 GATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGAC
1 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGAC
31296 C-TCAGTGCAG
66 CTTCAGTGCAG
31306 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGAC
1 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGAC
31371 CTTCAGTGCAG
66 CTTCAGTGCAG
31382 GATGTTTTCAAA
1 GATGTTTTCAAA
31394 TCCTTCGGGT
Statistics
Matches: 86, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
75 65 0.76
76 21 0.24
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (76 bp):
GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGAC
CTTCAGTGCAG
Found at i:31389 original size:45 final size:45
Alignment explanation
Indices: 31336--31494 Score: 264
Period size: 45 Copynumber: 3.5 Consensus size: 45
31326 GGGAGCTTTT
31336 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* *
31381 GGATGTTTTCAAATCCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* *
31426 TGATGTTATCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
31471 TGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
31495 AGCTTTTTGA
Statistics
Matches: 105, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
45 93 0.89
46 4 0.04
47 8 0.08
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
Found at i:31603 original size:115 final size:115
Alignment explanation
Indices: 31398--31693 Score: 398
Period size: 115 Copynumber: 2.5 Consensus size: 115
31388 TTCAAATCCT
* * * *
31398 TCGGGTCATCTGTAAGACCTTCAGTGC-ATGATGTTATCAAAACCTTC-GGGTCATCTGTAAGAC
1 TCGGGTCATCTGTAAGACCTACAGTGCAAT-ATG--AT-AAGACC-TCAGGGCCATCTATAAGAC
* *
31461 CTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACC
61 CTACAATGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACC
* *
31516 TCGGGTCATTTGTAAGACCTACAGTGCAATATGATAAGACCTCAGGGCCATCCATAAGACCTACA
1 TCGGGTCATCTGTAAGACCTACAGTGCAATATGATAAGACCTCAGGGCCATCTATAAGACCTACA
*
31581 ATGTAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACC
66 ATGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACC
* * * * *
31631 TCTGGGTCATCTGTAAGACCTATAATGCAAGATAATAAGACCTCAGGGCCATTTATAAGACCT
1 TC-GGGTCATCTGTAAGACCTACAGTGCAATATGATAAGACCTCAGGGCCATCTATAAGACCT
31694 CTGGGTAGAA
Statistics
Matches: 159, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
114 2 0.01
115 72 0.45
116 55 0.35
118 28 0.18
119 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (115 bp):
TCGGGTCATCTGTAAGACCTACAGTGCAATATGATAAGACCTCAGGGCCATCTATAAGACCTACA
ATGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACC
Found at i:31831 original size:3 final size:3
Alignment explanation
Indices: 31823--31853 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
31813 TAAAATTGTT
31823 TTA TTA TTA TTA TTA TTA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
31854 GATAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:33236 original size:23 final size:23
Alignment explanation
Indices: 33193--33238 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
33183 ATTATCTTTT
* *
33193 TAATTTCAATTTGTTTAATTTAA
1 TAATTTAAATTTATTTAATTTAA
*
33216 TAATTTAAATATTATTTATTTTA
1 TAATTTAAAT-TTATTTAATTTA
33239 TCATATGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TAATTTAAATTTATTTAATTTAA
Found at i:33378 original size:2 final size:2
Alignment explanation
Indices: 33371--33407 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
33361 ATAAAAACAA
33371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33408 GTTAGTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33725 original size:18 final size:18
Alignment explanation
Indices: 33692--33732 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
33682 TTAAGAAAAA
33692 AATA-TTATATTATTATT
1 AATATTTATATTATTATT
33709 AATATTTAT-TTATTTATT
1 AATATTTATATTA-TTATT
33727 AATATT
1 AATATT
33733 AAAGAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATATTTATATTATTATT
Found at i:38342 original size:4 final size:4
Alignment explanation
Indices: 38305--38336 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
38295 ACATAAAAAG
*
38305 ATGT GTGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
38337 GTGTGTAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:49154 original size:14 final size:14
Alignment explanation
Indices: 49135--49162 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49125 CAACATTACA
49135 GGATAACGTCAGTC
1 GGATAACGTCAGTC
49149 GGATAACGTCAGTC
1 GGATAACGTCAGTC
49163 TTCATCCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (14 bp):
GGATAACGTCAGTC
Found at i:57839 original size:21 final size:21
Alignment explanation
Indices: 57815--57870 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
57805 TTTTTTGAAA
57815 TTTTGGCTTTTGTTTT-TGCTT
1 TTTTGGCTTTT-TTTTGTGCTT
57836 TTTTGTG-TTTTTTTTGTGCTT
1 TTTTG-GCTTTTTTTTGTGCTT
*
57857 TTTTTGCTTTTTTT
1 TTTTGGCTTTTTTT
57871 AAAAATAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 5 0.16
21 25 0.81
22 1 0.03
ACGTcount: A:0.00, C:0.07, G:0.16, T:0.77
Consensus pattern (21 bp):
TTTTGGCTTTTTTTTGTGCTT
Found at i:57850 original size:11 final size:11
Alignment explanation
Indices: 57815--57870 Score: 57
Period size: 10 Copynumber: 5.4 Consensus size: 11
57805 TTTTTTGAAA
57815 TTTTG-GCTTT
1 TTTTGTGCTTT
*
57825 TGTTTTTGC-TT
1 T-TTTGTGCTTT
*
57836 TTTTGTGTTTT
1 TTTTGTGCTTT
57847 TTTTGTGC-TT
1 TTTTGTGCTTT
57857 TTTT-TGCTTT
1 TTTTGTGCTTT
57867 TTTT
1 TTTT
57871 AAAAATAGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 3 0.08
10 18 0.47
11 15 0.39
12 2 0.05
ACGTcount: A:0.00, C:0.07, G:0.16, T:0.77
Consensus pattern (11 bp):
TTTTGTGCTTT
Found at i:57869 original size:9 final size:9
Alignment explanation
Indices: 57827--57870 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
57817 TTGGCTTTTG
57827 TTTTTGCTT
1 TTTTTGCTT
*
57836 TTTTGTGTTTT
1 TTTT-TG-CTT
57847 TTTTGTGCTT
1 TTTT-TGCTT
57857 TTTTTGCTT
1 TTTTTGCTT
57866 TTTTT
1 TTTTT
57871 AAAAATAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 14 0.45
10 8 0.26
11 9 0.29
ACGTcount: A:0.00, C:0.07, G:0.14, T:0.80
Consensus pattern (9 bp):
TTTTTGCTT
Done.