Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002506.1 Hibiscus syriacus cultivar Beakdansim tig00005104_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: 98700
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4040 original size:20 final size:22
Alignment explanation
Indices: 4015--4067 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
4005 TAATTATGTA
*
4015 TTTGTGACATG-T-TCTCTGTC
1 TTTGTGACATGTTATCTCTGAC
*
4035 TTTGTGATATGTTTATCTCTGAC
1 TTTGTGACATG-TTATCTCTGAC
4058 TTTGTGACAT
1 TTTGTGACAT
4068 ATTTTTCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.37
22 1 0.04
23 16 0.59
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.51
Consensus pattern (22 bp):
TTTGTGACATGTTATCTCTGAC
Found at i:4060 original size:23 final size:23
Alignment explanation
Indices: 4027--4083 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
4017 TGTGACATGT
* * *
4027 TCTCTGTCTTTGTGATATGTTTA
1 TCTCTGACTTTGTGACATATTTA
*
4050 TCTCTGACTTTGTGACATATTTT
1 TCTCTGACTTTGTGACATATTTA
*
4073 TCTCTGCCTTT
1 TCTCTGACTTT
4084 TGGTAGCCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.12, C:0.19, G:0.14, T:0.54
Consensus pattern (23 bp):
TCTCTGACTTTGTGACATATTTA
Found at i:24923 original size:14 final size:14
Alignment explanation
Indices: 24901--24940 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
24891 TTTCTGTTCG
*
24901 TTTAAGTTCATTCA
1 TTTATGTTCATTCA
* *
24915 TTTATGTTCGTTCT
1 TTTATGTTCATTCA
24929 TTTATGTTCATT
1 TTTATGTTCATT
24941 TATGTTTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.60
Consensus pattern (14 bp):
TTTATGTTCATTCA
Found at i:25166 original size:14 final size:14
Alignment explanation
Indices: 25147--25173 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25137 TTATTTGTTT
25147 GTTTACGTTCGTTC
1 GTTTACGTTCGTTC
25161 GTTTACGTTCGTT
1 GTTTACGTTCGTT
25174 TATGTCCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.22, T:0.52
Consensus pattern (14 bp):
GTTTACGTTCGTTC
Found at i:28975 original size:22 final size:21
Alignment explanation
Indices: 28941--28981 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
28931 ATAATTATTT
28941 AAAAAATTAAATAAAAATACA
1 AAAAAATTAAATAAAAATACA
*
28962 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
28982 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACA
Found at i:32361 original size:12 final size:12
Alignment explanation
Indices: 32333--32369 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
32323 TTTGGTAATC
32333 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
32346 CCCGCCCCGATA
1 CCCGCCCCGATA
*
32358 CCCGGCCCGATA
1 CCCGCCCCGATA
32370 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.16, C:0.54, G:0.19, T:0.11
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:33973 original size:31 final size:31
Alignment explanation
Indices: 33938--34006 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
33928 TTAAAAATAC
** *
33938 TTAAGATAT-GATAATTTTTGTTTTTATTTAA
1 TTAAGATATAG-TAATTTTCATTTTCATTTAA
*
33969 TTAAGATATAGTCATTTTCATTTTCATTTAA
1 TTAAGATATAGTAATTTTCATTTTCATTTAA
34000 TTAAGAT
1 TTAAGAT
34007 GTGGTCACCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (31 bp):
TTAAGATATAGTAATTTTCATTTTCATTTAA
Found at i:34510 original size:39 final size:39
Alignment explanation
Indices: 34430--34516 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 39
34420 AACTCTAACA
* * *
34430 TTCTAAAATCTTAATTTCTTAAATTTTGACGCCATTACG
1 TTCTAAATTCTTAAGTTCTTAAATTTTGACGACATTACG
*
34469 TTCTAAATTCTTAAGTTCTTAAATTATT-TC-ACATTATCG
1 TTCTAAATTCTTAAGTTCTTAAATT-TTGACGACATTA-CG
34508 TTCTAAATT
1 TTCTAAATT
34517 ATTTTTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 5 0.12
39 35 0.83
40 2 0.05
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (39 bp):
TTCTAAATTCTTAAGTTCTTAAATTTTGACGACATTACG
Found at i:34837 original size:22 final size:22
Alignment explanation
Indices: 34795--34838 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 22
34785 ATTAACTTAA
34795 ATATTTTATATTAACTTATTAAAT
1 ATATTTTATATTAA--TATTAAAT
34819 ATATTTTACTATTAA-ATTAA
1 ATATTTTA-TATTAATATTAA
34839 TTTAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.26
24 8 0.42
25 6 0.32
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATTTTATATTAATATTAAAT
Found at i:34850 original size:22 final size:21
Alignment explanation
Indices: 34825--34867 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
34815 AAATATATTT
34825 TACTATTAAATTAATTTAAAAA
1 TACT-TTAAATTAATTTAAAAA
** *
34847 TACTTTATTTTTATTTAAAAA
1 TACTTTAAATTAATTTAAAAA
34868 ATATTTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
TACTTTAAATTAATTTAAAAA
Found at i:34876 original size:23 final size:23
Alignment explanation
Indices: 34835--34896 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
34825 TACTATTAAA
34835 TTAATTT-AAAAATA-CTTTATT
1 TTAATTTAAAAAATATCTTTATT
* *
34856 TTTATTTAAAAAATATTTTTATT
1 TTAATTTAAAAAATATCTTTATT
34879 TTAATTTATTAAAAATAT
1 TTAATTTA--AAAAATAT
34897 GATTAAATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.18
22 7 0.21
23 13 0.38
25 8 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAATTTAAAAAATATCTTTATT
Found at i:42998 original size:2 final size:2
Alignment explanation
Indices: 42991--43021 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42981 TTCGAACACA
42991 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 A
43022 GAGTAGGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43371 original size:40 final size:40
Alignment explanation
Indices: 43316--43391 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
43306 AAGGGAGGTA
* *
43316 AGATAGTAGGTTGCCCCTAGCACTAGGTTGAGAACAACTT
1 AGATAGTAAGTTGCCCCCAGCACTAGGTTGAGAACAACTT
43356 AGATAGTAAGTTGCCCCCAGCACTAGGTTGAGAACA
1 AGATAGTAAGTTGCCCCCAGCACTAGGTTGAGAACA
43392 GCTTCCGTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (40 bp):
AGATAGTAAGTTGCCCCCAGCACTAGGTTGAGAACAACTT
Found at i:48546 original size:6 final size:6
Alignment explanation
Indices: 48537--48570 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
48527 CTTTGGTTTT
*
48537 GGCTTC GGCTTC GACTTC GGCTTC GGCTTTC GGC
1 GGCTTC GGCTTC GGCTTC GGCTTC GGC-TTC GGC
48571 CTGGAAAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.03, C:0.32, G:0.32, T:0.32
Consensus pattern (6 bp):
GGCTTC
Found at i:57750 original size:43 final size:43
Alignment explanation
Indices: 57701--57788 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
57691 ACAACACTGC
57701 ACTTGATCATATATAAACCACTTATGGTTTTCAACATTGACCA
1 ACTTGATCATATATAAACCACTTATGGTTTTCAACATTGACCA
57744 ACTTGATCATATATAAACCACTTATGGTTTTCAACATTGACCA
1 ACTTGATCATATATAAACCACTTATGGTTTTCAACATTGACCA
57787 AC
1 AC
57789 AGAAACATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (43 bp):
ACTTGATCATATATAAACCACTTATGGTTTTCAACATTGACCA
Found at i:57798 original size:43 final size:43
Alignment explanation
Indices: 57708--57798 Score: 148
Period size: 43 Copynumber: 2.1 Consensus size: 43
57698 TGCACTTGAT
* *
57708 CATATATAAACCACTTATGGTTTTCAACATTGACCAACTTGAT
1 CATATATAAACCACTTATGGTTTTCAACATTGACCAACTAGAA
57751 CATATATAAACCACTTATGGTTTTCAACATTGACCAAC-AGAAA
1 CATATATAAACCACTTATGGTTTTCAACATTGACCAACTAG-AA
57794 CATAT
1 CATAT
57799 CCAGCCAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 1 0.02
43 44 0.98
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (43 bp):
CATATATAAACCACTTATGGTTTTCAACATTGACCAACTAGAA
Found at i:59494 original size:31 final size:30
Alignment explanation
Indices: 59451--59527 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
59441 GATCATTTTT
* * *
59451 ATTTTTATTTAATTAAGATGCGTTCATGTTC
1 ATTTGTATTTAATTAA-ATGCGGTAATGTTC
*
59482 ATTTGTATTTAATTGAAATGTGGTAATGTTC
1 ATTTGTATTTAATT-AAATGCGGTAATGTTC
*
59513 GTTTGTATTTAATTA
1 ATTTGTATTTAATTA
59528 TTAAGATGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 1 0.03
31 37 0.93
32 2 0.05
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (30 bp):
ATTTGTATTTAATTAAATGCGGTAATGTTC
Found at i:60377 original size:21 final size:23
Alignment explanation
Indices: 60336--60392 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
60326 ATGCCTCTAT
60336 ATATTATTTTT-TTCAATT-AAA
1 ATATTATTTTTATTCAATTAAAA
* *
60357 TTATTATTTTTATTGAA-TAAAA
1 ATATTATTTTTATTCAATTAAAA
*
60379 ATAATATTTTTATT
1 ATATTATTTTTATT
60393 ATTATTTCGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
ATATTATTTTTATTCAATTAAAA
Found at i:62105 original size:222 final size:222
Alignment explanation
Indices: 61716--62163 Score: 697
Period size: 222 Copynumber: 2.0 Consensus size: 222
61706 TATATTCGGG
* * *
61716 TCGGGTCGGGTGAAACTTTATTTTGGTCGAGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTC
1 TCGGGTCGAGTGAAACTTTATTTTGGTCGAGTCGGGTCGGGTTTTTTAAGTGTAATATTCGGGTC
* *
61781 GGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACTCGAAAATATATATAATTTTACCTTATAT
66 GGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCCGACCCGAAAATATATATAATTTTACCTTATAT
* *
61846 ATTTAGGAATAATTATAATAATACTCC-TATATATATATATATATTTCAATTAAGTCACTGTTTT
131 ATTTAGGAATAATTACAATAATACTCCATATATATATA-AT-TATTTCAATTAAGTCAATGTTTT
61910 TATTGAATAAAAAT-ATTTTTTTATTATT
194 TATTGAATAAAAATAATTTTTTTATTATT
* * *
61938 TCGGGTCGAGTGAAATTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTAATATTCGGGTC
1 TCGGGTCGAGTGAAACTTTATTTTGGTCGAGTCGGGTCGGGTTTTTTAAGTGTAATATTCGGGTC
*
62003 GGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGATAAA-ATATATAATTTTACCT
66 GGGTCGAGTTCGGGTTTAGGGTGAAAAAAA-C---CCGACCCGA-AAATATATATAATTTTACCT
*
62067 TATATATTTAGGAATAATTACAATAATACTCC-TATATATATAATTTTTTCAATTAAGTCAATGT
126 TATATATTTAGGAATAATTACAATAATACTCCATATATATATAATTATTTCAATTAAGTCAATGT
62131 TTTTATTGAATAAAAATAATTTTTTTATTATT
191 TTTTATTGAATAAAAATAATTTTTTTATTATT
62163 T
1 T
62164 TGTGTCGTGT
Statistics
Matches: 208, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
222 87 0.42
223 1 0.00
224 35 0.17
225 17 0.08
226 65 0.31
227 3 0.01
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (222 bp):
TCGGGTCGAGTGAAACTTTATTTTGGTCGAGTCGGGTCGGGTTTTTTAAGTGTAATATTCGGGTC
GGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCCGACCCGAAAATATATATAATTTTACCTTATAT
ATTTAGGAATAATTACAATAATACTCCATATATATATAATTATTTCAATTAAGTCAATGTTTTTA
TTGAATAAAAATAATTTTTTTATTATT
Found at i:62614 original size:18 final size:18
Alignment explanation
Indices: 62577--62627 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
62567 TATGAAATTG
* *
62577 GATTCCAATTCC-TGACA
1 GATTCTAATTCCTTCACA
*
62594 GATTCTAATTCTTTCACA
1 GATTCTAATTCCTTCACA
*
62612 GATTTTAATTCCTTCA
1 GATTCTAATTCCTTCA
62628 TAAACATTCC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (18 bp):
GATTCTAATTCCTTCACA
Found at i:65414 original size:24 final size:24
Alignment explanation
Indices: 65382--65436 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
65372 GCTTTCGCTT
*
65382 AGCGCTTCGGCGTCTAAGACCCTA
1 AGCGCTTCGACGTCTAAGACCCTA
* *
65406 AGCGCTTCGACGTTTAGGACCCTA
1 AGCGCTTCGACGTCTAAGACCCTA
*
65430 GGCGCTT
1 AGCGCTT
65437 TACGCTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.18, C:0.31, G:0.27, T:0.24
Consensus pattern (24 bp):
AGCGCTTCGACGTCTAAGACCCTA
Found at i:67255 original size:17 final size:17
Alignment explanation
Indices: 67233--67289 Score: 105
Period size: 17 Copynumber: 3.4 Consensus size: 17
67223 TGGGAACAAG
67233 GAAGCTCATTCAACTGT
1 GAAGCTCATTCAACTGT
67250 GAAGCTCATTCAACTGT
1 GAAGCTCATTCAACTGT
*
67267 GAAGCTTATTCAACTGT
1 GAAGCTCATTCAACTGT
67284 GAAGCT
1 GAAGCT
67290 ATATGGTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (17 bp):
GAAGCTCATTCAACTGT
Found at i:73979 original size:244 final size:242
Alignment explanation
Indices: 73552--74256 Score: 788
Period size: 244 Copynumber: 2.9 Consensus size: 242
73542 AATTAACTAG
* * * * * **
73552 TGTTTATTTTGTG-CAACATTTTATGATTAAATGCTCATCGTTTGTTTATTATTATTGTTGATTT
1 TGTTTATTTTG-GACAATATTTTATGATTAAATACTCCTCGGTTGTTAATTATTATTACTGATTT
** * ** * * * * * *
73616 -TACCTTTTTACAAGATATTAT-TTCAAGGCAATGACTTCT-AGAAATGTGTTTAAAAAGACTAA
65 GGGCCTATTTACGTGAT-TTCTGTGCAGGGCAATGACTTCTGAAAAATGTG-TTAACATGACTAA
* ** * * * ** *
73678 AATTTGTACTTTTTATTCTGGAATCGAGACTGGAACAGTGAGTATGAATTTGGGCATGAAATGTT
128 AAATTACACTTTTTGTTCTCGAATCAAGGTTGGAACAGTG-GCATGAATTTGGGCATGAAATGTT
* * * * *
73743 GATGTGGCAGTGAGTCAGCATCTTCTAGAAGGTTCGCACAGCAGCGTTCAA
192 GATGTGGCAGTGAGTCAACAACTTCTAGAAGCTCCACACAGCAGCGTTCAA
*
73794 TGTTTATTTTGGCCAATATTTTATGATTAAATACTCCTCGGTTGTTAATTATTATTACTGATTTG
1 TGTTTATTTTGGACAATATTTTATGATTAAATACTCCTCGGTTGTTAATTATTATTACTGATTTG
* * *
73859 GGTCTTTTTACGTGATTTCTGTGTAGGGCAATGACTTCTGAAAAATGTGCTTAACATGACTAAAA
66 GGCCTATTTACGTGATTTCTGTGCAGGGCAATGACTTCTGAAAAATGTG-TTAACATGACTAAAA
73924 ATTACACTTTTTGTTCTCGAATCAAGGTTGGAACAGTAGGCATGAATTTGGGCATGAAATGTTGA
130 ATTACACTTTTTGTTCTCGAATCAAGGTTGGAACAGT-GGCATGAATTTGGGCATGAAATGTTGA
* * *
73989 CGTGGCAGTGAGTCAACAACTTCTAGAAGCTCCACTCAGTAGCGTTCAA
194 TGTGGCAGTGAGTCAACAACTTCTAGAAGCTCCACACAGCAGCGTTCAA
* * * * *
74038 TGTTTATTTTGGACAATATTTTATGATTAGATACTCCTCGTTTGTTCATTATTATTGCTGATTTT
1 TGTTTATTTTGGACAATATTTTATGATTAAATACTCCTCGGTTGTTAATTATTATTACTGATTTG
* *
74103 GGCCTATTTATGTGATTTCTGTGCAGGGAAATGACTTCTGAAAAA--TG--AAC-T---T-AAAA
66 GGCCTATTTACGTGATTTCTGTGCAGGGCAATGACTTCTGAAAAATGTGTTAACATGACTAAAAA
* * * *
74159 TGACACTTTTTGTTCTCGAATCAAAGTTGGAACAGTGGACATGAATTTAGGTATGAAATGTTGAT
131 TTACACTTTTTGTTCTCGAATCAAGGTTGGAACAGTGG-CATGAATTTGGGCATGAAATGTTGAT
* *
74224 GTGGCAGTGAGTCAACAACTACTAGAAGATCCA
195 GTGGCAGTGAGTCAACAACTTCTAGAAGCTCCA
74257 GTTAGCAGTG
Statistics
Matches: 402, Mismatches: 55, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
233 2 0.00
234 92 0.23
235 1 0.00
238 1 0.00
239 3 0.01
241 1 0.00
242 60 0.15
243 26 0.06
244 215 0.53
245 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (242 bp):
TGTTTATTTTGGACAATATTTTATGATTAAATACTCCTCGGTTGTTAATTATTATTACTGATTTG
GGCCTATTTACGTGATTTCTGTGCAGGGCAATGACTTCTGAAAAATGTGTTAACATGACTAAAAA
TTACACTTTTTGTTCTCGAATCAAGGTTGGAACAGTGGCATGAATTTGGGCATGAAATGTTGATG
TGGCAGTGAGTCAACAACTTCTAGAAGCTCCACACAGCAGCGTTCAA
Found at i:77954 original size:24 final size:24
Alignment explanation
Indices: 77922--77981 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
77912 GCATAGGTAG
*
77922 TGCATCGATACACACGTTCAGGAA
1 TGCATCGATACACACGTTCAGAAA
77946 TGCATCGATACACACGTTCAGAAA
1 TGCATCGATACACACGTTCAGAAA
77970 TGCATCGATACA
1 TGCATCGATACA
77982 TTATAGTGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (24 bp):
TGCATCGATACACACGTTCAGAAA
Found at i:78779 original size:31 final size:32
Alignment explanation
Indices: 78740--78830 Score: 100
Period size: 31 Copynumber: 2.9 Consensus size: 32
78730 AGAGTCGAGG
*
78740 GTTACCTATGTCTTTCGAGACATATGGACAGT
1 GTTACCTATGTCTTTCGAGACATATGGACAAT
* *
78772 -TTACCTATGTCATTC-AGGACATATGAACAAT
1 GTTACCTATGTCTTTCGA-GACATATGGACAAT
78803 GTTACCTATGT-TCTTCG-GAACATATGGA
1 GTTACCTATGTCT-TTCGAG-ACATATGGA
78831 TAGGTCCTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
30 1 0.02
31 27 0.55
32 21 0.43
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (32 bp):
GTTACCTATGTCTTTCGAGACATATGGACAAT
Found at i:83710 original size:32 final size:32
Alignment explanation
Indices: 83637--83715 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 32
83627 AGTGTCCAGG
* * *
83637 GTTACCGATGTCTTTCGAGACATAAGGACAGT
1 GTTACCTATGTCCTTCAAGACATAAGGACAGT
*
83669 -TTACCTATGTCCTTCAAGACATATGGACAGT
1 GTTACCTATGTCCTTCAAGACATAAGGACAGT
*
83700 GTTACCTATGTTCTTC
1 GTTACCTATGTCCTTC
83716 GGAACATATG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 27 0.66
32 14 0.34
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (32 bp):
GTTACCTATGTCCTTCAAGACATAAGGACAGT
Found at i:86033 original size:11 final size:11
Alignment explanation
Indices: 86019--86045 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
86009 TTAAAAATGT
86019 GATAAAACTAA
1 GATAAAACTAA
86030 GATAAAACTAA
1 GATAAAACTAA
86041 GATAA
1 GATAA
86046 TGTGTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.07, G:0.11, T:0.19
Consensus pattern (11 bp):
GATAAAACTAA
Found at i:86060 original size:21 final size:21
Alignment explanation
Indices: 86034--86078 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
86024 AACTAAGATA
*
86034 AAACTAAGATAATGTGTAAAT
1 AAACTAAGATAATGGGTAAAT
86055 AAACTAAGATAATGGGTAAAT
1 AAACTAAGATAATGGGTAAAT
86076 AAA
1 AAA
86079 AAGATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (21 bp):
AAACTAAGATAATGGGTAAAT
Found at i:86230 original size:24 final size:24
Alignment explanation
Indices: 86197--86257 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
86187 TTTCAAAACT
*
86197 AATAATCAAAAGTAGACAAGACAA
1 AATAAACAAAAGTAGACAAGACAA
* *
86221 AATAAACAAAAATAGAGAAGACAA
1 AATAAACAAAAGTAGACAAGACAA
86245 AATAAACAAAAGT
1 AATAAACAAAAGT
86258 GATCTATCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.67, C:0.10, G:0.11, T:0.11
Consensus pattern (24 bp):
AATAAACAAAAGTAGACAAGACAA
Found at i:87408 original size:6 final size:6
Alignment explanation
Indices: 87397--87425 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
87387 CCCCCACCTT
87397 GGTGAG GGTGAG GGTGAG GGTGAG GGTGA
1 GGTGAG GGTGAG GGTGAG GGTGAG GGTGA
87426 TTATTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.66, T:0.17
Consensus pattern (6 bp):
GGTGAG
Found at i:87475 original size:9 final size:9
Alignment explanation
Indices: 87450--87486 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
87440 TAAAATTTAA
87450 ATTTTATTT
1 ATTTTATTT
*
87459 A-ATTATTT
1 ATTTTATTT
87467 ATTTTATTT
1 ATTTTATTT
87476 ATTTTATTT
1 ATTTTATTT
87485 AT
1 AT
87487 CTTAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
ATTTTATTT
Found at i:88280 original size:244 final size:245
Alignment explanation
Indices: 87842--88362 Score: 764
Period size: 244 Copynumber: 2.1 Consensus size: 245
87832 TGAACAGTGA
* * *
87842 GCATGAAATGCTGACGTGACAGTGAATCAAC-ATCTTCTAGAAGGTTCACACAACTGCGTTAAGT
1 GCATGAAATGCTGACGTGACAGTTAGTCAACAATCTTCTAGAAGGCTCACACAACTGCGTTAAGT
*
87906 GTTTATTTTGGGCAACATTTTATGATTAAATACTCATCGTTTGTTAATTATTATTGTTGATTTGG
66 GTTTATTTTGGACAACATTTTATGATTAAATACTCATCGTTTGTTAATTATTATTGTTGATTTGG
* * * *
87971 GTCTTTTTATGTGATTTGGGTGCAATGTAATGACTTTTGAAAAATGTACTTAAAATAATTAAAAA
131 GTCTTTGTATGTGATTTGGGTGCAACGCAATGACTTTTGAAAAATGTACTTAAAATAACTAAAAA
**
88036 TTACACTTTTTGTTCTCGAATCAAGGCCGGAATAGTAGGCATGAATTTGG
196 TTACACTTTTTGTTCTCGAATCAAGGCCAAAATAGTAGGCATGAATTTGG
* * **
88086 GCATGAAATGCTGACGTGACAGTTAGTCAACAAT-TTCTAGAA-GCTC-CACTTAGTAGCGTTCT
1 GCATGAAATGCTGACGTGACAGTTAGTCAACAATCTTCTAGAAGGCTCACAC-AACT-GCGTTAA
*
88148 GTGTTTATTTTGGACAACATTTTATGATTAAATACTCTTCGTTTGTTAATTATTATTGTTGATTT
64 GTGTTTATTTTGGACAACATTTTATGATTAAATACTCATCGTTTGTTAATTATTATTGTTGATTT
** * * * *
88213 GGGTCTTTGTACT-TGATTTTTGTGCAACGCAATGACTTTTGGAAAATTTGCTTAAAATGACTAA
129 GGGTCTTTGTA-TGTGATTTGGGTGCAACGCAATGACTTTTGAAAAATGTACTTAAAATAACTAA
88277 AAATTACACTTTTTGTTCTCGAATCAAGGCCAAAATAGTAGGCATGAATTTGG
193 AAATTACACTTTTTGTTCTCGAATCAAGGCCAAAATAGTAGGCATGAATTTGG
** *
88330 GCATGAAATGCTGGTGTGGCAGTTAGTCAACAA
1 GCATGAAATGCTGACGTGACAGTTAGTCAACAA
88363 CTTAGCAAAT
Statistics
Matches: 249, Mismatches: 24, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
242 3 0.01
243 5 0.02
244 238 0.96
245 3 0.01
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (245 bp):
GCATGAAATGCTGACGTGACAGTTAGTCAACAATCTTCTAGAAGGCTCACACAACTGCGTTAAGT
GTTTATTTTGGACAACATTTTATGATTAAATACTCATCGTTTGTTAATTATTATTGTTGATTTGG
GTCTTTGTATGTGATTTGGGTGCAACGCAATGACTTTTGAAAAATGTACTTAAAATAACTAAAAA
TTACACTTTTTGTTCTCGAATCAAGGCCAAAATAGTAGGCATGAATTTGG
Found at i:88717 original size:12 final size:11
Alignment explanation
Indices: 88667--88719 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
88657 TTAAATTTAT
88667 TTCTTTTAAATC
1 TTCTTTT-AATC
*
88679 TTCTTCTTAATA
1 TTCTT-TTAATC
* *
88691 TTCTTTTACTT
1 TTCTTTTAATC
88702 TTCTCTTTAATC
1 TTCT-TTTAATC
88714 TTCTTT
1 TTCTTT
88720 ATTTTCTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
11 10 0.29
12 22 0.65
13 2 0.06
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTTTTAATC
Found at i:88730 original size:20 final size:22
Alignment explanation
Indices: 88679--88730 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
88669 CTTTTAAATC
88679 TTCTTCTTAATATTCTTTTACTT
1 TTCTT-TTAATATTCTTTTACTT
*
88702 TTCTCTTTAATCTTC-TTTA-TT
1 TTCT-TTTAATATTCTTTTACTT
88723 TTCTTTTA
1 TTCTTTTA
88731 TTTTACTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.15
21 6 0.22
22 4 0.15
23 12 0.44
24 1 0.04
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (22 bp):
TTCTTTTAATATTCTTTTACTT
Found at i:90507 original size:30 final size:30
Alignment explanation
Indices: 90464--90532 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
90454 GATTTTGAAA
*
90464 AAAAAAAAAAGTTTATGTACCAAACTTAAC
1 AAAAATAAAAGTTTATGTACCAAACTTAAC
* *
90494 AAAAATAATAGTTTATGTACTAAACTTAAC
1 AAAAATAAAAGTTTATGTACCAAACTTAAC
90524 AAAAATAAA
1 AAAAATAAA
90533 CGTATGGTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (30 bp):
AAAAATAAAAGTTTATGTACCAAACTTAAC
Found at i:91163 original size:2 final size:2
Alignment explanation
Indices: 91156--91183 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
91146 AAATAACTTA
91156 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
91184 TTTTATTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91396 original size:55 final size:57
Alignment explanation
Indices: 91293--91506 Score: 197
Period size: 51 Copynumber: 4.0 Consensus size: 57
91283 TGTAAATATG
* * * *
91293 TGTTAAGTGCTACACTTTTTTTATTTTATTTACTTACACCATTATAAGTATGTGTTAAC
1 TGTTAAGTGCTACAC-TTGTTTATTTTATTCACTTACACCAGTGTAAGTATGTGTT-AC
91352 TGTTAAGTGCTACA-TT-TTT-TTTTATTCACTTACACCAGTGTAAGTA-----TA-
1 TGTTAAGTGCTACACTTGTTTATTTTATTCACTTACACCAGTGTAAGTATGTGTTAC
* *** *
91400 TGTTGAGTGCTACACTTGTTTATTTTATTCACTTACATTGGTGTAAGTATATGTT-C
1 TGTTAAGTGCTACACTTGTTTATTTTATTCACTTACACCAGTGTAAGTATGTGTTAC
* * *
91456 TG-T--GT--TATAATTGTTTATTTTATTCACTTACATCAGTGTAAGTATGTGTTA
1 TGTTAAGTGCTACACTTGTTTATTTTATTCACTTACACCAGTGTAAGTATGTGTTA
91507 AGTGCTACAT
Statistics
Matches: 133, Mismatches: 12, Indels: 27
0.77 0.07 0.16
Matches are distributed among these distances:
48 13 0.10
49 3 0.02
50 4 0.03
51 64 0.48
53 2 0.02
55 25 0.19
56 6 0.05
57 2 0.02
59 14 0.11
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (57 bp):
TGTTAAGTGCTACACTTGTTTATTTTATTCACTTACACCAGTGTAAGTATGTGTTAC
Found at i:91444 original size:51 final size:50
Alignment explanation
Indices: 91352--91517 Score: 219
Period size: 51 Copynumber: 3.3 Consensus size: 50
91342 ATGTGTTAAC
*
91352 TGTTAAGTGCTACATT-TTT-TTTTATTCACTTACACCAGTGTAAGTATA
1 TGTTAAGTGCTACATTGTTTATTTTATTCACTTACATCAGTGTAAGTATA
* **
91400 TGTTGAGTGCTACACTTGTTTATTTTATTCACTTACATTGGTGTAAGTATA
1 TGTTAAGTGCTACA-TTGTTTATTTTATTCACTTACATCAGTGTAAGTATA
** * * *
91451 TGTTCTGTGTTATAATTGTTTATTTTATTCACTTACATCAGTGTAAGTATG
1 TGTTAAGTGCTA-CATTGTTTATTTTATTCACTTACATCAGTGTAAGTATA
91502 TGTTAAGTGCTACATT
1 TGTTAAGTGCTACATT
91518 TTTTTGTAGT
Statistics
Matches: 99, Mismatches: 15, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
48 13 0.13
49 2 0.02
50 6 0.06
51 77 0.78
52 1 0.01
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.48
Consensus pattern (50 bp):
TGTTAAGTGCTACATTGTTTATTTTATTCACTTACATCAGTGTAAGTATA
Found at i:91511 original size:102 final size:105
Alignment explanation
Indices: 91272--91515 Score: 275
Period size: 102 Copynumber: 2.3 Consensus size: 105
91262 AGATGTACAT
* * * *
91272 ACTTACATC-GCTGTAAATATGTGTTAAGTGCTACACTTTTTTTATTTTATTTACTTACACCATT
1 ACTTACATCAG-TGTAAGTATGTGTTAAGTGCTACACTTTGTTTATTTTATTCACTTACACCAGT
* *
91336 ATAAGTATGTGTTAACTGTTAAGTGCTACATTTTTTTTTATTC
65 ATAAGTATATGTT-ACTGTT-AGTGATACATTTTTTTTTATTC
* * * *** *
91379 ACTTACACCAGTGTAAGTATATGTTGAGTGCTACAC-TTGTTTATTTTATTCACTTACATTGGTG
1 ACTTACATCAGTGTAAGTATGTGTTAAGTGCTACACTTTGTTTATTTTATTCACTTACACCAGTA
*
91443 TAAGTATATGTT-CTG-T-GTTATA-ATTGTTTATTTTATTC
66 TAAGTATATGTTACTGTTAGTGATACATT-TTT-TTTTATTC
91481 ACTTACATCAGTGTAAGTATGTGTTAAGTGCTACA
1 ACTTACATCAGTGTAAGTATGTGTTAAGTGCTACA
91516 TTTTTTTGTA
Statistics
Matches: 117, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
100 3 0.03
101 7 0.06
102 40 0.34
103 1 0.01
104 3 0.03
106 32 0.27
107 30 0.26
108 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.46
Consensus pattern (105 bp):
ACTTACATCAGTGTAAGTATGTGTTAAGTGCTACACTTTGTTTATTTTATTCACTTACACCAGTA
TAAGTATATGTTACTGTTAGTGATACATTTTTTTTTATTC
Found at i:94217 original size:2 final size:2
Alignment explanation
Indices: 94212--94263 Score: 63
Period size: 2 Copynumber: 26.5 Consensus size: 2
94202 TGTGTGGGTG
*
94212 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TT TA -A TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
*
94253 TA TA TT TA TA T
1 TA TA TA TA TA T
94264 TTAGGTTAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
1 2 0.05
2 39 0.91
3 2 0.05
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:94272 original size:23 final size:23
Alignment explanation
Indices: 94229--94272 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
94219 ATATATATAT
*
94229 ATATATATATATATTATTTAATC
1 ATATATATATATATTAGTTAATC
*
94252 ATATATTTATAT-TTAGGTTAA
1 ATATATATATATATTA-GTTAA
94273 GAAACTTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (23 bp):
ATATATATATATATTAGTTAATC
Found at i:95302 original size:17 final size:17
Alignment explanation
Indices: 95280--95313 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
95270 CCAAAGAAAG
95280 CCCATTATCTACAATCA
1 CCCATTATCTACAATCA
95297 CCCATTATCTACAATCA
1 CCCATTATCTACAATCA
95314 TCACATGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (17 bp):
CCCATTATCTACAATCA
Done.