Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005608.1 Hibiscus syriacus cultivar Beakdansim tig00013042_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: 106494
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:8185 original size:35 final size:35
Alignment explanation
Indices: 8139--8214 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
8129 AAAACAGTCC
* *
8139 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
**
8174 TCAATTTCATTCTAAACCTTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
8209 TCAATT
1 TCAATT
8215 ATGTCAGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:8746 original size:130 final size:129
Alignment explanation
Indices: 8600--8846 Score: 395
Period size: 130 Copynumber: 1.9 Consensus size: 129
8590 TATTTATATA
* **
8600 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATATGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATATGACATGTG
*
8665 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCA-CACCTAATTATTTATATATGCT
* *
8730 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATTATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATATGACATGTG
* * * *
8795 TTAACCCATGATCATGATATATGTTATTGGTGACACATGTCACACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACACCTAATTA
8847 GAAGAAAATT
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
129 10 0.09
130 97 0.91
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (129 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATATGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACACCTAATTATTTATATATGCT
Found at i:9203 original size:28 final size:26
Alignment explanation
Indices: 9171--9231 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
9161 AGTTGATACA
*
9171 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTT-AAA-AATAAATTTAAGAATT
* * *
9199 ATATTTTTAAACTAAATTTAATAATT
1 ATATTTTAAAAATAAATTTAAGAATT
9225 ATATTTT
1 ATATTTT
9232 TCATATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 20 0.69
27 2 0.07
28 7 0.24
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (26 bp):
ATATTTTAAAAATAAATTTAAGAATT
Found at i:9330 original size:16 final size:18
Alignment explanation
Indices: 9309--9342 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
9299 ATTTCTTATT
9309 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
9325 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
9343 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:12513 original size:14 final size:14
Alignment explanation
Indices: 12494--12523 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12484 TTCGTGAACA
*
12494 TTCGGTTATGTTCG
1 TTCGGTTATATTCG
12508 TTCGGTTATATTCG
1 TTCGGTTATATTCG
12522 TT
1 TT
12524 TACGTTCGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.53
Consensus pattern (14 bp):
TTCGGTTATATTCG
Found at i:12540 original size:24 final size:24
Alignment explanation
Indices: 12493--12540 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12483 GTTCGTGAAC
* *
12493 ATTCGGTTATGTTCGTTCGGTTAT
1 ATTCGGTTACGTTCGTTCAGTTAT
* *
12517 ATTCGTTTACGTTCGTTCATTTAT
1 ATTCGGTTACGTTCGTTCAGTTAT
12541 GTTTAACCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.52
Consensus pattern (24 bp):
ATTCGGTTACGTTCGTTCAGTTAT
Found at i:13626 original size:16 final size:16
Alignment explanation
Indices: 13605--13658 Score: 99
Period size: 16 Copynumber: 3.4 Consensus size: 16
13595 CTCCAACGTT
13605 TATGTTCGTGTTCGTC
1 TATGTTCGTGTTCGTC
13621 TATGTTCGTGTTCGTC
1 TATGTTCGTGTTCGTC
*
13637 TATGTTCGTGTTCGTT
1 TATGTTCGTGTTCGTC
13653 TATGTT
1 TATGTT
13659 TGTTTATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.07, C:0.15, G:0.24, T:0.54
Consensus pattern (16 bp):
TATGTTCGTGTTCGTC
Found at i:15797 original size:13 final size:15
Alignment explanation
Indices: 15763--15796 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
15753 ATACCTAAAT
15763 CTAAAATATTAAACC
1 CTAAAATATTAAACC
*
15778 CTAAAATA-TAACCC
1 CTAAAATATTAAACC
15792 CTAAA
1 CTAAA
15797 TCTTAAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (15 bp):
CTAAAATATTAAACC
Found at i:17351 original size:54 final size:54
Alignment explanation
Indices: 17256--17427 Score: 224
Period size: 54 Copynumber: 3.2 Consensus size: 54
17246 TGAATAAGTT
* * * *
17256 CCCACGCCTTAAGT-AGAGA-TTCTTTTGCAG-TAGCTCGGGATGGATAAGCCGTG
1 CCCACGCCTTAACTGA-AGACTTCTTATGC-GTTAGCTCCGGATGAATAAGCCGTG
*
17309 CCCACGCCTTAACTGAAGACTTCTTATGCGTTAGCTCCGGATGAATAAGTCGTG
1 CCCACGCCTTAACTGAAGACTTCTTATGCGTTAGCTCCGGATGAATAAGCCGTG
* * *
17363 CCCAAGCCTTAACTGAAGACTTCTTCTGCGTTAGCTCTGGATGAATAAGCCGTG
1 CCCACGCCTTAACTGAAGACTTCTTATGCGTTAGCTCCGGATGAATAAGCCGTG
*
17417 CCCATGCCTTA
1 CCCACGCCTTA
17428 TGCGAACGCC
Statistics
Matches: 106, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
53 17 0.16
54 89 0.84
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (54 bp):
CCCACGCCTTAACTGAAGACTTCTTATGCGTTAGCTCCGGATGAATAAGCCGTG
Found at i:20010 original size:16 final size:16
Alignment explanation
Indices: 19989--20021 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19979 AATAAAAAAA
19989 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
20005 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
20021 A
1 A
20022 ATTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:20115 original size:16 final size:16
Alignment explanation
Indices: 20082--20122 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
20072 CGTTCATTTA
*
20082 ATAAAT-AA-ACGAAT
1 ATAAATGAACACGAAC
20096 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
20112 ATAAACGAACA
1 ATAAATGAACA
20123 TAAACGTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 6 0.26
15 2 0.09
16 15 0.65
ACGTcount: A:0.61, C:0.15, G:0.10, T:0.15
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:21243 original size:14 final size:14
Alignment explanation
Indices: 21226--21264 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
21216 GAACATAAGT
21226 GAACATAACCGAAC
1 GAACATAACCGAAC
21240 GAACAT-A---AAC
1 GAACATAACCGAAC
21250 GAACATAACCGAAC
1 GAACATAACCGAAC
21264 G
1 G
21265 TTCACGAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 8
0.72 0.00 0.28
Matches are distributed among these distances:
10 9 0.43
11 1 0.05
13 1 0.05
14 10 0.48
ACGTcount: A:0.51, C:0.26, G:0.15, T:0.08
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:21243 original size:24 final size:24
Alignment explanation
Indices: 21216--21264 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
21206 ATAAATGAAT
**
21216 GAACATAAGTGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
21240 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
21264 G
1 G
21265 TTCACGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.22, G:0.16, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:25811 original size:19 final size:19
Alignment explanation
Indices: 25787--25828 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
25777 TTTTAAAATC
*
25787 AAAATCAGGTTCTCAACCT
1 AAAATCAGATTCTCAACCT
*
25806 AAAATCAGATTTTCAACCT
1 AAAATCAGATTCTCAACCT
25825 AAAA
1 AAAA
25829 CCTGTTTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.26
Consensus pattern (19 bp):
AAAATCAGATTCTCAACCT
Found at i:25863 original size:38 final size:38
Alignment explanation
Indices: 25807--25906 Score: 155
Period size: 38 Copynumber: 2.6 Consensus size: 38
25797 TCTCAACCTA
* *
25807 AAATCAGATTTTCAACCTAAAACCTGTTTTCCAAACAT
1 AAATAAGATTTTCAACCTAAAACCTATTTTCCAAACAT
*
25845 AAATTAGATTTTCAACCTAAAACCTATTTTCCAAACAT
1 AAATAAGATTTTCAACCTAAAACCTATTTTCCAAACAT
* *
25883 AAATAAGGTTTCCAACCTAAAACC
1 AAATAAGATTTTCAACCTAAAACC
25907 AGATTTCTAC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (38 bp):
AAATAAGATTTTCAACCTAAAACCTATTTTCCAAACAT
Found at i:25873 original size:18 final size:18
Alignment explanation
Indices: 25799--25912 Score: 61
Period size: 18 Copynumber: 6.0 Consensus size: 18
25789 AATCAGGTTC
25799 TCAACCTAAAATCAGATTT
1 TCAACCTAAAA-CAGATTT
*
25818 TCAACCTAAAACCTG-TTT
1 TCAACCTAAAA-CAGATTT
* **
25836 TCCAAACATAAATTAGATTT
1 T-C-AACCTAAAACAGATTT
**
25856 TCAACCTAAAACCTATTT
1 TCAACCTAAAACAGATTT
* *
25874 TCCAAACATAAATA-AGGTTT
1 T-C-AACCTAAA-ACAGATTT
*
25894 CCAACCTAAAACCAGATTT
1 TCAACCTAAAA-CAGATTT
25913 CTACGTTAAC
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
17 1 0.01
18 23 0.33
19 23 0.33
20 21 0.30
21 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31
Consensus pattern (18 bp):
TCAACCTAAAACAGATTT
Found at i:25913 original size:19 final size:19
Alignment explanation
Indices: 25800--25913 Score: 65
Period size: 19 Copynumber: 6.0 Consensus size: 19
25790 ATCAGGTTCT
* *
25800 CAACCTAAAATCAGATTTT
1 CAACCTAAAACCAGATTTC
* *
25819 CAACCTAAAACCTGTTTTC
1 CAACCTAAAACCAGATTTC
* ** *
25838 CAAAC-ATAAATTAGATTTT
1 CAACCTA-AAACCAGATTTC
*
25857 CAACCTAAAACCTA-TTTTC
1 CAACCTAAAACC-AGATTTC
* *
25876 CAAACATAAATA--AGGTTTC
1 C-AACCTAAA-ACCAGATTTC
25895 CAACCTAAAACCAGATTTC
1 CAACCTAAAACCAGATTTC
25914 TACGTTAACT
Statistics
Matches: 68, Mismatches: 19, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
17 1 0.01
18 9 0.13
19 48 0.71
20 9 0.13
21 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (19 bp):
CAACCTAAAACCAGATTTC
Found at i:28020 original size:29 final size:25
Alignment explanation
Indices: 27953--28000 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
27943 CATGGCAACC
27953 CTACGAGGCACTTTCGAGTGCAATT
1 CTACGAGGCACTTTCGAGTGCAATT
27978 CTACGAGGCACTTTCGAGTGCAA
1 CTACGAGGCACTTTCGAGTGCAA
28001 ATATATCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (25 bp):
CTACGAGGCACTTTCGAGTGCAATT
Found at i:29389 original size:21 final size:21
Alignment explanation
Indices: 29345--29390 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
29335 GTACAGCTTT
*
29345 CCCCCCAAGGGGAACAGATTC
1 CCCCCCAAGGGGAACAGATGC
* * *
29366 CCCCCCAGGGGGTACCGATGC
1 CCCCCCAAGGGGAACAGATGC
29387 CCCC
1 CCCC
29391 TGTCTAACGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.46, G:0.26, T:0.09
Consensus pattern (21 bp):
CCCCCCAAGGGGAACAGATGC
Found at i:31377 original size:27 final size:27
Alignment explanation
Indices: 31343--31397 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
31333 TTTTCAAATG
*
31343 TTTTGATTTTATAAATTTTAAATTTTT
1 TTTTGATTTTATAAATTTTAAAATTTT
31370 TTTTGATTTTATAAATTTTAAAATTTT
1 TTTTGATTTTATAAATTTTAAAATTTT
31397 T
1 T
31398 GACCTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (27 bp):
TTTTGATTTTATAAATTTTAAAATTTT
Found at i:32198 original size:21 final size:21
Alignment explanation
Indices: 32149--32211 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
32139 CAGATTGTCT
* *
32149 AGGGGGTACAGATTCCCCCTGC
1 AGGGGGTACCGATTCCCCC-CC
**
32171 AACGGGTACCGATTCCCCCCC
1 AGGGGGTACCGATTCCCCCCC
32192 AGGGGGTACCGATTCCCCCC
1 AGGGGGTACCGATTCCCCCC
32212 TGTCTAACGA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.17, C:0.40, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGGTACCGATTCCCCCCC
Found at i:34139 original size:23 final size:24
Alignment explanation
Indices: 34099--34144 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
34089 ATCGGTCTAA
34099 AATTTTATAAATTCTATTTTTTTT
1 AATTTTATAAATTCTATTTTTTTT
* *
34123 AATTTT-TTAATTTTATTTTTTT
1 AATTTTATAAATTCTATTTTTTT
34145 AATATGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (24 bp):
AATTTTATAAATTCTATTTTTTTT
Found at i:35726 original size:31 final size:31
Alignment explanation
Indices: 35683--35745 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
35673 AGCATAGCTG
* *
35683 AGGGACTAAAATCGAATGGACTGATAACGTT
1 AGGGACTAAAATCGAACGGACCGATAACGTT
* * *
35714 AGGGACTGAAATCGGACGGACCGATAATGTT
1 AGGGACTAAAATCGAACGGACCGATAACGTT
35745 A
1 A
35746 AAGACTGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.21
Consensus pattern (31 bp):
AGGGACTAAAATCGAACGGACCGATAACGTT
Found at i:37968 original size:15 final size:15
Alignment explanation
Indices: 37948--37994 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
37938 ATGCATAGGC
37948 TTGGAGAATGAGCTT
1 TTGGAGAATGAGCTT
*
37963 TTGGAGGA-G-GC--
1 TTGGAGAATGAGCTT
37974 TTGGAGAATGAGCTT
1 TTGGAGAATGAGCTT
37989 TTGGAG
1 TTGGAG
37995 GAGCCTTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
11 7 0.27
12 1 0.04
13 4 0.15
14 1 0.04
15 13 0.50
ACGTcount: A:0.23, C:0.06, G:0.40, T:0.30
Consensus pattern (15 bp):
TTGGAGAATGAGCTT
Found at i:37973 original size:26 final size:26
Alignment explanation
Indices: 37944--37997 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
37934 TTCCATGCAT
37944 AGGCTTGGAGAATGAGCTTTTGGAGG
1 AGGCTTGGAGAATGAGCTTTTGGAGG
37970 AGGCTTGGAGAATGAGCTTTTGGAGG
1 AGGCTTGGAGAATGAGCTTTTGGAGG
37996 AG
1 AG
37998 CCTTTGCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.24, C:0.07, G:0.43, T:0.26
Consensus pattern (26 bp):
AGGCTTGGAGAATGAGCTTTTGGAGG
Found at i:47836 original size:44 final size:43
Alignment explanation
Indices: 47741--47844 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 43
47731 CAAATTATCC
* * *** *
47741 TGTCATTAGTGGCATTTTTTGCCACAAACGTTGCTAATTCTCT
1 TGTCTTTAGTGGCGTTTTTTGCCACAAACGCCACTAATTCTAT
47784 TGTCTTTAGTGGCGTTTTTTAGCCACAAAACGCCACTAATT-TAT
1 TGTCTTTAGTGGCGTTTTTT-GCCAC-AAACGCCACTAATTCTAT
* *
47828 TGTTTTTAGTGGTGTTT
1 TGTCTTTAGTGGCGTTT
47845 GTAATACAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 18 0.35
44 22 0.43
45 11 0.22
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.44
Consensus pattern (43 bp):
TGTCTTTAGTGGCGTTTTTTGCCACAAACGCCACTAATTCTAT
Found at i:50128 original size:39 final size:38
Alignment explanation
Indices: 50056--50160 Score: 115
Period size: 39 Copynumber: 2.7 Consensus size: 38
50046 AAGTACTACT
*
50056 CTGTTGCGGCGTTTGTTGAAAAACGCCACTATAGATGA
1 CTGTTACGGCGTTTGTTGAAAAACGCCACTATAGATGA
* *
50094 CTGTTACGGCGTTTGTTGAAAAAATGTCACTATAGAT-A
1 CTGTTACGGCGTTTGTTG-AAAAACGCCACTATAGATGA
* *
50132 CTCTATTACGTCGTTTGTAT-AAAAACGCC
1 --CTGTTACGGCGTTTGT-TGAAAAACGCC
50161 GCTAAAGTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
38 18 0.32
39 23 0.41
40 14 0.25
41 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (38 bp):
CTGTTACGGCGTTTGTTGAAAAACGCCACTATAGATGA
Found at i:50341 original size:82 final size:83
Alignment explanation
Indices: 50103--50387 Score: 319
Period size: 83 Copynumber: 3.5 Consensus size: 83
50093 ACTGTTACGG
* * * * *
50103 CGTTTGTTGAAAAAATGTCACTATAGAT--ACTCTATTACGTCGTTTGTATAAAAACGCCGCTAA
1 CGTTTGTTGAAAAAATGCCACTATAGATGAACCCTATTGCGGCTTTTGTATAAAAACGCCGCTAA
* * * *
50166 AGTATTACTCTTTTGTGA
66 AGTACTACTATGTTGCGA
** ** * * *
50184 TATTTGTTGAAAAAACACCACTATAGATGAACCCTATTGAGGCATTTT-TATACAATCGCCGCTA
1 CGTTTGTTGAAAAAATGCCACTATAGATGAACCCTATTGCGGC-TTTTGTATAAAAACGCCGCTA
* **
50248 AAGGACTACTATGTCACGA
65 AAGTACTACTATGTTGCGA
* *
50267 CGTTTGTTGAAAAAAGGCCACTATAGATGAA-CCTATTGCGGCTTTTGTATAAAAACACCGCTAA
1 CGTTTGTTGAAAAAATGCCACTATAGATGAACCCTATTGCGGCTTTTGTATAAAAACGCCGCTAA
*
50331 AGTACTACTATGTTGCGG
66 AGTACTACTATGTTGCGA
*
50349 CGTTTGTTG-AAAAATGTCACTATAGATGAACCCTATTGC
1 CGTTTGTTGAAAAAATGCCACTATAGATGAACCCTATTGC
50388 ATCATTTTTA
Statistics
Matches: 166, Mismatches: 33, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
81 46 0.28
82 55 0.33
83 62 0.37
84 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (83 bp):
CGTTTGTTGAAAAAATGCCACTATAGATGAACCCTATTGCGGCTTTTGTATAAAAACGCCGCTAA
AGTACTACTATGTTGCGA
Found at i:50412 original size:82 final size:83
Alignment explanation
Indices: 50095--50420 Score: 306
Period size: 82 Copynumber: 4.0 Consensus size: 83
50085 TATAGATGAC
* * * * * *
50095 TGTTACGGCGTTTGTTGAAAAAATGTCACTATAGAT--ACTCTATTAC-GTCGTTTGTATAAAAA
1 TGTTACGACGTTTGTTGAAAAAATGCCACTATAGATGAACCCTATTGCAG-CATTTTTATAAAAA
* *
50157 CGCCGCTAAAGTATTACTC
65 CGCCGCTAAAGTACTACTA
* ** ** ** * *
50176 TTTTGTGATATTTGTTGAAAAAACACCACTATAGATGAACCCTATTG-AGGCATTTTTATACAAT
1 TGTTACGACGTTTGTTGAAAAAATGCCACTATAGATGAACCCTATTGCA-GCATTTTTATAAAAA
*
50240 CGCCGCTAAAGGACTACTA
65 CGCCGCTAAAGTACTACTA
* * *
50259 TGTCACGACGTTTGTTGAAAAAAGGCCACTATAGATGAA-CCTATTGCGGC-TTTTGTATAAAAA
1 TGTTACGACGTTTGTTGAAAAAATGCCACTATAGATGAACCCTATTGCAGCATTTT-TATAAAAA
*
50322 CACCGCTAAAGTACTACTA
65 CGCCGCTAAAGTACTACTA
* * * * * *
50341 TGTTGCGGCGTTTGTTG-AAAAATGTCACTATAGATGAACCCTATTGCATCATTTTTATACAAAT
1 TGTTACGACGTTTGTTGAAAAAATGCCACTATAGATGAACCCTATTGCAGCATTTTTATAAAAAC
**
50405 GTTGCTAAAGTACTAC
66 GCCGCTAAAGTACTAC
50421 CTTGTCAAGG
Statistics
Matches: 194, Mismatches: 43, Indels: 15
0.77 0.17 0.06
Matches are distributed among these distances:
81 50 0.26
82 75 0.39
83 68 0.35
84 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (83 bp):
TGTTACGACGTTTGTTGAAAAAATGCCACTATAGATGAACCCTATTGCAGCATTTTTATAAAAAC
GCCGCTAAAGTACTACTA
Found at i:50414 original size:164 final size:164
Alignment explanation
Indices: 50103--50402 Score: 399
Period size: 164 Copynumber: 1.8 Consensus size: 164
50093 ACTGTTACGG
* * * *
50103 CGTTTGTTGAAAAAATGTCACTATAGATACTCTATTACGTCGTTTGTATAAAAACGCCGCTAAAG
1 CGTTTGTTGAAAAAAGGCCACTATAGATACTCTATTACGGCGTTTGTATAAAAACACCGCTAAAG
* * * * *
50168 TATTACTCTTTTGTGATATTTGTTGAAAAAACACCACTATAGATGAACCCTATTGAGGCATTTTT
66 TACTACTATGTTGCGACATTTGTTGAAAAAACACCACTATAGATGAACCCTATTGAGGCATTTTT
50233 ATACAATCGCCGCTAAAGGACTACTATGTCACGA
131 ATACAATCGCCGCTAAAGGACTACTATGTCACGA
* *
50267 CGTTTGTTGAAAAAAGGCCACTATAGATGAAC-CTATTGCGGCTTTTGTATAAAAACACCGCTAA
1 CGTTTGTTGAAAAAAGGCCACTATAGAT--ACTCTATTACGGCGTTTGTATAAAAACACCGCTAA
* * *** *
50331 AGTACTACTATGTTGCGGCGTTTGTTG-AAAAATGTCACTATAGATGAACCCTATTGCA-TCATT
64 AGTACTACTATGTTGCGACATTTGTTGAAAAAACACCACTATAGATGAACCCTATTG-AGGCATT
50394 TTTATACAA
128 TTTATACAA
50403 ATGTTGCTAA
Statistics
Matches: 116, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
164 65 0.56
165 49 0.42
166 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (164 bp):
CGTTTGTTGAAAAAAGGCCACTATAGATACTCTATTACGGCGTTTGTATAAAAACACCGCTAAAG
TACTACTATGTTGCGACATTTGTTGAAAAAACACCACTATAGATGAACCCTATTGAGGCATTTTT
ATACAATCGCCGCTAAAGGACTACTATGTCACGA
Found at i:51176 original size:26 final size:26
Alignment explanation
Indices: 51147--51237 Score: 71
Period size: 26 Copynumber: 3.5 Consensus size: 26
51137 TATATTTTTG
51147 TTATAATTTAAATTGATATAATTCAT
1 TTATAATTTAAATTGATATAATTCAT
* * * *
51173 TTATAA-TAATAATT-TTCTGAATTTA-
1 TTATAATTTA-AATTGATAT-AATTCAT
* *
51198 TTATAGTTTAAATTGATATGATTCAT
1 TTATAATTTAAATTGATATAATTCAT
*
51224 ATATAATTGTAAAT
1 TTATAATT-TAAAT
51238 ATAATTTAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 11
0.67 0.17 0.16
Matches are distributed among these distances:
25 17 0.36
26 25 0.53
27 5 0.11
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (26 bp):
TTATAATTTAAATTGATATAATTCAT
Found at i:58045 original size:21 final size:21
Alignment explanation
Indices: 58021--58065 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
58011 TTAATATAAT
58021 TTCTTTAATTTTATCAGTTTA
1 TTCTTTAATTTTATCAGTTTA
58042 TTCTTTAATTTTATCAGTTTA
1 TTCTTTAATTTTATCAGTTTA
58063 TTC
1 TTC
58066 CAAAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.62
Consensus pattern (21 bp):
TTCTTTAATTTTATCAGTTTA
Found at i:58072 original size:21 final size:21
Alignment explanation
Indices: 58027--58072 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
58017 TAATTTCTTT
***
58027 AATTTTATCAGTTTATTCTTT
1 AATTTTATCAGTTTATTCCAA
58048 AATTTTATCAGTTTATTCCAA
1 AATTTTATCAGTTTATTCCAA
58069 AATT
1 AATT
58073 AATTGTACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.54
Consensus pattern (21 bp):
AATTTTATCAGTTTATTCCAA
Found at i:59071 original size:23 final size:23
Alignment explanation
Indices: 59041--59084 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
59031 CTCAAGACTC
*
59041 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTCAAGCTCGATTTT
59064 GAGCTCGATTCAAGCTCGATT
1 GAGCTCGATTCAAGCTCGATT
59085 CAAGCTCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (23 bp):
GAGCTCGATTCAAGCTCGATTTT
Found at i:59100 original size:17 final size:17
Alignment explanation
Indices: 59078--59114 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
59068 TCGATTCAAG
59078 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
59095 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
59112 CTC
1 CTC
59115 AAACTCGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:59110 original size:11 final size:11
Alignment explanation
Indices: 59042--59093 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
59032 TCAAGACTCG
*
59042 AGCTCGATTGA
1 AGCTCGATTCA
**
59053 AGCTCGATTTTG
1 AGCTCGA-TTCA
59065 AGCTCGATTCA
1 AGCTCGATTCA
59076 AGCTCGATTCA
1 AGCTCGATTCA
59087 AGCTCGA
1 AGCTCGA
59094 ACTCGATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
11 27 0.75
12 9 0.25
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:59931 original size:33 final size:33
Alignment explanation
Indices: 59894--59981 Score: 149
Period size: 33 Copynumber: 2.7 Consensus size: 33
59884 CCAATTAAGC
*
59894 TTACTTACAAAAGATGGCAACAATATGTCAATT
1 TTACTTACAAAAGATGGCAACAACATGTCAATT
*
59927 TTACTTACAAAAGATGGCAGCAACATGTCAATT
1 TTACTTACAAAAGATGGCAACAACATGTCAATT
*
59960 TTACTTACAAAAGATTGCAACA
1 TTACTTACAAAAGATGGCAACA
59982 TGTCCAAGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (33 bp):
TTACTTACAAAAGATGGCAACAACATGTCAATT
Found at i:59982 original size:30 final size:30
Alignment explanation
Indices: 59894--59994 Score: 112
Period size: 33 Copynumber: 3.1 Consensus size: 30
59884 CCAATTAAGC
*
59894 TTACTTACAAAAGATGGCAACAATATGTCAATT
1 TTACTTACAAAAGATAGCAAC---ATGTCAATT
59927 TTACTTACAAAAGATGGCAGCAACATGTCAATT
1 TTACTTACAAAAGAT---AGCAACATGTCAATT
* *
59960 TTACTTACAAAAGATTGCAACATGTCCAAGT
1 TTACTTACAAAAGATAGCAACATGT-CAATT
59991 TTAC
1 TTAC
59995 AAAAGATGGG
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
30 9 0.15
31 8 0.13
33 39 0.64
36 5 0.08
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.30
Consensus pattern (30 bp):
TTACTTACAAAAGATAGCAACATGTCAATT
Found at i:61867 original size:69 final size:69
Alignment explanation
Indices: 61776--61920 Score: 290
Period size: 69 Copynumber: 2.1 Consensus size: 69
61766 TTATCTTTAA
61776 TTCATTTTCAATTCATCACTTCTTTAAATCATACTTAAATCCTTATGTTTTATTATAATCTTAAT
1 TTCATTTTCAATTCATCACTTCTTTAAATCATACTTAAATCCTTATGTTTTATTATAATCTTAAT
61841 TTTC
66 TTTC
61845 TTCATTTTCAATTCATCACTTCTTTAAATCATACTTAAATCCTTATGTTTTATTATAATCTTAAT
1 TTCATTTTCAATTCATCACTTCTTTAAATCATACTTAAATCCTTATGTTTTATTATAATCTTAAT
61910 TTTC
66 TTTC
61914 TTCATTT
1 TTCATTT
61921 AAATTTCATT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 76 1.00
ACGTcount: A:0.28, C:0.17, G:0.01, T:0.53
Consensus pattern (69 bp):
TTCATTTTCAATTCATCACTTCTTTAAATCATACTTAAATCCTTATGTTTTATTATAATCTTAAT
TTTC
Found at i:62048 original size:16 final size:17
Alignment explanation
Indices: 62027--62065 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
62017 TAGAAACTAA
62027 TTAATAT-AATAAAAAT
1 TTAATATAAATAAAAAT
62043 TTAATATAAATAAAAAT
1 TTAATATAAATAAAAAT
62060 TTAATA
1 TTAATA
62066 ATATTAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAATATAAATAAAAAT
Found at i:62476 original size:11 final size:11
Alignment explanation
Indices: 62460--62522 Score: 69
Period size: 11 Copynumber: 5.9 Consensus size: 11
62450 GTATTATAGA
62460 ATTTTTAATAT
1 ATTTTTAATAT
62471 ATTTTTAA-A-
1 ATTTTTAATAT
62480 ATTTTATAAT-T
1 ATTTT-TAATAT
***
62491 ATCAATAATAT
1 ATTTTTAATAT
62502 ATTTTTAATAT
1 ATTTTTAATAT
62513 ATTTTTAATA
1 ATTTTTAATA
62523 ATGTAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.19
11 29 0.69
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:65140 original size:24 final size:26
Alignment explanation
Indices: 65108--65155 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
65098 TTATTCTTTC
65108 GCTTCAATCAAGC-TC-AAATTTTAG
1 GCTTCAATCAAGCTTCTAAATTTTAG
*
65132 GCTTCAATCGAGCTTCTAAATTTT
1 GCTTCAATCAAGCTTCTAAATTTT
65156 TTTTAGTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.57
25 2 0.10
26 7 0.33
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (26 bp):
GCTTCAATCAAGCTTCTAAATTTTAG
Found at i:69189 original size:3 final size:3
Alignment explanation
Indices: 69181--69231 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
69171 ATCAATGAAA
69181 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
69229 AAT
1 AAT
69232 GAAGGATCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:73404 original size:6 final size:6
Alignment explanation
Indices: 73393--73471 Score: 158
Period size: 6 Copynumber: 13.2 Consensus size: 6
73383 GACACGTATT
73393 ACCAAG ACCAAG ACCAAG ACCAAG ACCAAG ACCAAG ACCAAG ACCAAG
1 ACCAAG ACCAAG ACCAAG ACCAAG ACCAAG ACCAAG ACCAAG ACCAAG
73441 ACCAAG ACCAAG ACCAAG ACCAAG ACCAAG A
1 ACCAAG ACCAAG ACCAAG ACCAAG ACCAAG A
73472 GCCGAGACGG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.51, C:0.33, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCAAG
Found at i:79185 original size:112 final size:111
Alignment explanation
Indices: 79056--79824 Score: 877
Period size: 112 Copynumber: 6.9 Consensus size: 111
79046 ATAGAGTCAT
* *
79056 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCGTCAGATGATAAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAT-AGTTCTTCTCA
** *
79121 TTATGAACTTTCTCTGGAAAAATTGATCCATCGAGTGATGAATTCAA
65 TTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAA
* *
79168 GCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATCTTCATATG--AGTTCTTCT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-T--TCTTCAGATGATAGTTCTTCT
* * * *
79231 CATTATGAACTCTAC-CTGGCAATGTTGATCCATCGAGTGATGAATTCGA
63 CATTATGAACT-TTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAA
79280 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATG--AGTTCTTCT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC-T-T-CTTCTTCAGATGATAGTTCTTCT
* * * * *
79343 CATTATGAACTTCCTCTGGAAAAGTTAATCGATCAAGTGATGAATTCAG
63 CATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAA
* * *
79392 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTATTCTTCCTCTTCAGAT-A-AGTTCTTCT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAA---CTTCTTCTTCTTCAGATGATAGTTCTTCT
*
79455 CATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCGA
63 CATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAA
*
79504 GCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATG--AGTTCTTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC---TT-CTTCTTCAGATGATAGTTCTTC
** * **
79567 TCATTATGAACACT-TCTGGAAATGTTGATCCATCAAGTGATGGATTTGA
62 TCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAA
* *
79616 GCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGACG--AGTTCTTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC-T--TCTT-CTTCTTCAGATGATAGTTCTTC
* * * ** *
79679 TCATTATGAACTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATTAAA
62 TCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAA
*
79729 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG--AGTTCTTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGATAGTTCTTC
* *
79792 TCATTATGAACTCTAC-CTGG-CATGTTGATCCAT
62 TCATTATGAACT-TTCTCTGGAAATGTTGATCCAT
79825 TGAGTATTGG
Statistics
Matches: 578, Mismatches: 54, Indels: 50
0.85 0.08 0.07
Matches are distributed among these distances:
109 3 0.01
111 2 0.00
112 418 0.72
113 134 0.23
114 5 0.01
115 15 0.03
116 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (111 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCAGATGATAGTTCTTCTCAT
TATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAA
Found at i:79351 original size:224 final size:224
Alignment explanation
Indices: 79056--79803 Score: 1074
Period size: 224 Copynumber: 3.3 Consensus size: 224
79046 ATAGAGTCAT
* *
79056 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTC-T-T-CTTCGTCAGATGATAAGTTCTTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATG---AGTTCTTC
* * *
79118 TCATTATGAACTTTCTCTGGAAAAATTGATCCATCGAGTGATGAATTCAAGCAAAAGATTGAACA
63 TCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
* *
79183 AGTTCTTCTCATTATGAACTTCTTCTTCATCTTCATATGAGTTCTTCTCATTATGAACTCTAC-C
128 AGTTCTTCTCATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTC
79247 TGGCAATGTTGATCCATCGAGTGATGAATTCGA
192 TGGCAATGTTGATCCATCGAGTGATGAATTCGA
79280 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
79345 TTATGAACTTCCTCTGGAAAAGTTAATCGATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGT
* * * * *
79410 TCTTCTCATTATGAATTTATTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGA
131 TCTTCTCATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
*
79475 AATGTTGATCCATCAAGTGATGAATTCGA
196 AATGTTGATCCATCGAGTGATGAATTCGA
* *
79504 GCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT-CTCCTTCTTCAGATGAGTTCTTCTC
** * * ** *
79569 ATTATGAACACT-TCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTAAACAAG
65 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAG
* * *
79633 TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAACTTTCTCTG
130 TTCTTCTCATTATGAACTTCTTCTT-CATCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * **
79698 GCAATGCTAATCCATCGGGTGATGAATTAAA
194 GCAATGTTGATCCATCGAGTGATGAATTCGA
*
79729 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTC
79794 ATTATGAACT
65 ATTATGAACT
79804 CTACCTGGCA
Statistics
Matches: 468, Mismatches: 49, Indels: 13
0.88 0.09 0.02
Matches are distributed among these distances:
223 2 0.00
224 290 0.62
225 164 0.35
226 1 0.00
227 11 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (224 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGT
TCTTCTCATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
AATGTTGATCCATCGAGTGATGAATTCGA
Found at i:79485 original size:336 final size:336
Alignment explanation
Indices: 78938--79829 Score: 1150
Period size: 336 Copynumber: 2.6 Consensus size: 336
78928 GAATTAAGGC
* * * *
78938 AAGGTTGAATAAATTCTTCTCATTATGAATTTCTTCTCCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * * * *
79003 GAAC-TCTTCCGGAAATGTTGATGCTGAT-ATATCTTCTTCTGTGAT-AGAGTCATGCAAAAGGT
66 GAACTTCCTCTGGAAATGTTAAT-C-GATCA-A---------GTGATGA-ATTCAAGCAAAAGGT
* * * **
79065 TGAACAAGTTCTTCTTATTATGAACTTCTTCTTCGTC-AGATGATAAGTTCTTCTCATTATGAAC
118 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCA-GATAAGTTCTTCTCATTATGAAC
** *
79129 TTTCTCTGGAAAAATTGATCCATCGAGTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCA
182 TTTCTCTGGAAATGTTGATCCATCGAGTGATGAATTCAAGCAAAAGATTAAACAAGTTCTTCTCA
* * * *
79194 TTATGAACTTCTTCTT-CATCTTCATATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTG
247 TTATGAACTTCTTATTCCATCTTCAGATGAGTTCTTCTCATTATGAACACT-CCTGGAAATGTTG
*
79258 ATCCATCGAGTGATGAATTCGAGCAA
311 ATCCATCAAGTGATGAATTCGAGCAA
79284 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
* *
79349 GAACTTCCTCTGGAAAAGTTAATCGATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTT
66 GAACTTCCTCTGGAAATGTTAATCGATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATTCTT
* *
79414 CTCATTATGAATTTATTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATG
131 CTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATG
* * *
79479 TTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTA
196 TTGATCCATCGAGTGATGAATTCAAGCAAAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTA
* *
79544 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATCCATCAAGTGATG
261 TTCCATCTTCAGATGAGTTCTTCTCATTATGAACACTCCTGGAAATGTTGATCCATCAAGTGATG
* *
79609 GATTTGAGCAA
326 AATTCGAGCAA
* * *
79620 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGACGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * ** *
79685 TGAACTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATTAAAGCAAAAGGTTGAACAAATTCT
65 TGAACTTCCTCTGGAAATGTTAATCGATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATTCT
* * *
79750 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGG-C
130 TCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACT-TTCTCTGGAA
*
79813 ATGTTGATCCATTGAGT
193 ATGTTGATCCATCGAGT
79830 ATTGGATTCA
Statistics
Matches: 487, Mismatches: 51, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
336 215 0.44
337 152 0.31
338 33 0.07
339 2 0.00
345 4 0.01
346 67 0.14
347 14 0.03
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (336 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTCCTCTGGAAATGTTAATCGATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATTCTT
CTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATG
TTGATCCATCGAGTGATGAATTCAAGCAAAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTA
TTCCATCTTCAGATGAGTTCTTCTCATTATGAACACTCCTGGAAATGTTGATCCATCAAGTGATG
AATTCGAGCAA
Found at i:83637 original size:12 final size:12
Alignment explanation
Indices: 83618--83667 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
83608 GTAAAAATGA
83618 AAATGTAAATAC
1 AAATGTAAATAC
*
83630 AAACGTAAAAAATAC
1 AAATGT---AAATAC
*
83645 AAATGTAAATGC
1 AAATGTAAATAC
83657 AAATGTAAATA
1 AAATGTAAATA
83668 TATGAATGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
12 20 0.65
15 11 0.35
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.22
Consensus pattern (12 bp):
AAATGTAAATAC
Found at i:83640 original size:27 final size:27
Alignment explanation
Indices: 83610--83665 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
83600 GTAATTATGT
83610 AAAAATGA-AAATGTAAATACAAACGTA
1 AAAAAT-ACAAATGTAAATACAAACGTA
* *
83637 AAAAATACAAATGTAAATGCAAATGTA
1 AAAAATACAAATGTAAATACAAACGTA
83664 AA
1 AA
83666 TATATGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.20
Consensus pattern (27 bp):
AAAAATACAAATGTAAATACAAACGTA
Found at i:83644 original size:15 final size:15
Alignment explanation
Indices: 83624--83653 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
83614 ATGAAAATGT
83624 AAATACAAACGTAAA
1 AAATACAAACGTAAA
*
83639 AAATACAAATGTAAA
1 AAATACAAACGTAAA
83654 TGCAAATGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (15 bp):
AAATACAAACGTAAA
Found at i:83754 original size:8 final size:7
Alignment explanation
Indices: 83725--83766 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
83715 ATAAAAGTAT
83725 AAATGCA
1 AAATGCA
* *
83732 CAATGAA
1 AAATGCA
83739 AAATGCA
1 AAATGCA
83746 AAGATGCA
1 AA-ATGCA
83754 AAATG-A
1 AAATGCA
83760 AAATGCA
1 AAATGCA
83767 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.57, C:0.12, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:85290 original size:26 final size:28
Alignment explanation
Indices: 85259--85316 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
85249 ACTTGAAAAT
*
85259 AAAATAAT-A-TACATATAAATATTATG
1 AAAATAATAAGTACATATAAAAATTATG
* *
85285 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAATAAGTACATATAAAAATTATG
85313 AAAA
1 AAAA
85317 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAATAATAAGTACATATAAAAATTATG
Found at i:85800 original size:2 final size:2
Alignment explanation
Indices: 85787--85822 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
85777 AAATTTAAAA
85787 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
85823 AATAAGATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:87069 original size:44 final size:43
Alignment explanation
Indices: 86998--87121 Score: 139
Period size: 44 Copynumber: 2.9 Consensus size: 43
86988 AGTTGATGCT
* * *
86998 TGCTGGAAGCTGTTTGAATGA-GGACGTGGAAGGGCTGCTGGCA
1 TGCTGGAAGCTGTTGGAAT-ATGCACGTGGAGGGGCTGCTGGCA
* * *
87041 GTGCTGGAAGTTGTTGGAATTTGCACGTGGAGGGGATGCTGGCA
1 -TGCTGGAAGCTGTTGGAATATGCACGTGGAGGGGCTGCTGGCA
*
87085 --CTGGAAGCTGCTGGAA-ATGCACGTGGAGGGGCTGCTG
1 TGCTGGAAGCTGTTGGAATATGCACGTGGAGGGGCTGCTG
87122 TCGTTGGTTG
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 19 0.28
41 14 0.20
44 36 0.52
ACGTcount: A:0.19, C:0.15, G:0.43, T:0.23
Consensus pattern (43 bp):
TGCTGGAAGCTGTTGGAATATGCACGTGGAGGGGCTGCTGGCA
Found at i:91229 original size:21 final size:21
Alignment explanation
Indices: 91203--91244 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
91193 AAACTCTAAT
91203 ATTAAAT-TCTAAATCCTAAAC
1 ATTAAATCTC-AAATCCTAAAC
91224 ATTAAATCTCAAATCCTAAAC
1 ATTAAATCTCAAATCCTAAAC
91245 TTCATACCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (21 bp):
ATTAAATCTCAAATCCTAAAC
Found at i:95342 original size:35 final size:38
Alignment explanation
Indices: 95273--95343 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
95263 CAACAAACTT
*
95273 ATAATAAGTATTAAATGGTAAATGATAACCAAATTACA
1 ATAATAAGTATTAAATGGTAAATGATAACAAAATTACA
95311 ATAACTAA-TATTAAATGGT-AAT-A-AACAAAATTA
1 ATAA-TAAGTATTAAATGGTAAATGATAACAAAATTA
95344 ACTGAAATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
35 9 0.29
36 1 0.03
37 3 0.10
38 15 0.48
39 3 0.10
ACGTcount: A:0.55, C:0.07, G:0.08, T:0.30
Consensus pattern (38 bp):
ATAATAAGTATTAAATGGTAAATGATAACAAAATTACA
Found at i:98290 original size:19 final size:20
Alignment explanation
Indices: 98253--98295 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
98243 GGGTGCTAAC
98253 TTAAAAATAATATTATTTT-
1 TTAAAAATAATATTATTTTA
*
98272 TTAAAAA-AATTATTTTTTTA
1 TTAAAAATAA-TATTATTTTA
98292 TTAA
1 TTAA
98296 TGCTCAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 15 0.71
20 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAAAATAATATTATTTTA
Found at i:102054 original size:9 final size:10
Alignment explanation
Indices: 102036--102065 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
102026 AATTAATAGT
102036 TTATTTTAAA
1 TTATTTTAAA
102046 TTA-TTTAAA
1 TTATTTTAAA
102055 TTATTTTAAA
1 TTATTTTAAA
102065 T
1 T
102066 GAGTGATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTATTTTAAA
Found at i:103100 original size:3 final size:3
Alignment explanation
Indices: 103092--103133 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
103082 ACATGACATC
103092 TAA TAA TAA TAA T-A TAA TAA TAA TAA T-A TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
103134 TACATTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:103110 original size:11 final size:11
Alignment explanation
Indices: 103094--103133 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
103084 ATGACATCTA
103094 ATAATAATAAT
1 ATAATAATAAT
103105 ATAATAATAAT
1 ATAATAATAAT
103116 A-ATATAATAAT
1 ATA-ATAATAAT
103127 AATAATA
1 -ATAATA
103134 TACATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 1 0.04
11 20 0.77
12 4 0.15
13 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:103111 original size:14 final size:14
Alignment explanation
Indices: 103092--103135 Score: 88
Period size: 14 Copynumber: 3.1 Consensus size: 14
103082 ACATGACATC
103092 TAATAATAATAATA
1 TAATAATAATAATA
103106 TAATAATAATAATA
1 TAATAATAATAATA
103120 TAATAATAATAATA
1 TAATAATAATAATA
103134 TA
1 TA
103136 CATTATTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:103114 original size:17 final size:17
Alignment explanation
Indices: 103092--103133 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
103082 ACATGACATC
103092 TAATAATAATA-ATATAA
1 TAATAATAATATA-ATAA
103109 TAATAATAATATAATAA
1 TAATAATAATATAATAA
103126 TAATAATA
1 TAATAATA
103134 TACATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 23 0.96
18 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATAATAATATAATAA
Done.