Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004102.1 Hibiscus syriacus cultivar Beakdansim tig00008970_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: 59397
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1799 original size:78 final size:75
Alignment explanation
Indices: 1638--1818 Score: 202
Period size: 78 Copynumber: 2.4 Consensus size: 75
1628 AGGTTCCTTG
* * * * * *
1638 GCTTTGTGCTCAGGGTAAGTCCTTACTGTAGCTCATTTGTTTTTTGCTCAGGGTAAGTCCTTACT
1 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGCTCATCTGCTTTGTGCTCAGGATAAGACCTTACT
1703 AGGCTCCTCA
66 AGGCTCCTCA
* * *
1713 ACTTTGTGCTTAGGGTAAGTCCTTACTGCAGACTCATCTGCTTTGTG-TACTGGATAAGACCTTA
1 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAG-CTCATCTGCTTTGTGCT-CAGGATAAGACCTTA
*
1777 CTGCAGGCTCCTCT
64 CT--AGGCTCCTCA
* * *
1791 GCTTTGTGCACATGGTAAGTCTTTACTG
1 GCTTTGTGCTCAGGGTAAGTCCTTACTG
1819 GGTATACAGG
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
75 29 0.33
76 26 0.30
78 32 0.37
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (75 bp):
GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGCTCATCTGCTTTGTGCTCAGGATAAGACCTTACT
AGGCTCCTCA
Found at i:1817 original size:39 final size:39
Alignment explanation
Indices: 1638--1818 Score: 181
Period size: 39 Copynumber: 4.7 Consensus size: 39
1628 AGGTTCCTTG
* *
1638 GCTTTGTGCTCAGGGTAAGTCCTTACTGTA-GCTCATTT
1 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCATCT
* * * *
1676 GTTTTTTGCTCAGGGTAAGTCCTTACT--AGGCTCCTCA
1 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCATCT
* * *
1713 ACTTTGTGCTTAGGGTAAGTCCTTACTGCAGACTCATCT
1 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCATCT
* * * *
1752 GCTTTGTG-TACTGGATAAGACCTTACTGCAGGCTCCTCT
1 GCTTTGTGCT-CAGGGTAAGTCCTTACTGCAGGCTCATCT
* * *
1791 GCTTTGTGCACATGGTAAGTCTTTACTG
1 GCTTTGTGCTCAGGGTAAGTCCTTACTG
1819 GGTATACAGG
Statistics
Matches: 113, Mismatches: 25, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
36 1 0.01
37 28 0.25
38 26 0.23
39 58 0.51
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (39 bp):
GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCATCT
Found at i:7768 original size:39 final size:39
Alignment explanation
Indices: 7714--7905 Score: 276
Period size: 39 Copynumber: 4.9 Consensus size: 39
7704 GATTTCCGCA
* * * *
7714 GCTCCTCGGTTTTGTGCTCAGGTTAAGTCCTTACTGCAG
1 GCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
*
7753 GCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGCAG
1 GCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
* * *
7792 GCTCCTCAGCTTTATGCACAAGGTAAGTCCTTACTGCAG
1 GCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
** *
7831 GCTCCTCTGCTTTGTGCACAGTATAAGACCTTACTGCAG
1 GCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
*
7870 GCTCATCTGCTTTGTGCACAGGGTAAGTCCTTACTG
1 GCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTG
7906 GGTGTACAGG
Statistics
Matches: 136, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 136 1.00
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.32
Consensus pattern (39 bp):
GCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
Found at i:8284 original size:2 final size:2
Alignment explanation
Indices: 8277--8308 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8267 AGGTATTTTG
8277 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
8309 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12633 original size:40 final size:40
Alignment explanation
Indices: 12578--12657 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
12568 TAAGGATATG
12578 TGAGGATTGCCATTTATTTCTCAAGGGCGTCAGTAAGTTT
1 TGAGGATTGCCATTTATTTCTCAAGGGCGTCAGTAAGTTT
12618 TGAGGATTGCCATTTATTTCTCAAGGGCGTCAGTAAGTTT
1 TGAGGATTGCCATTTATTTCTCAAGGGCGTCAGTAAGTTT
12658 GTGGATCGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.38
Consensus pattern (40 bp):
TGAGGATTGCCATTTATTTCTCAAGGGCGTCAGTAAGTTT
Found at i:22430 original size:12 final size:13
Alignment explanation
Indices: 22409--22471 Score: 51
Period size: 14 Copynumber: 4.9 Consensus size: 13
22399 TAATATATAG
22409 TTTTGAAAATATT
1 TTTTGAAAATATT
22422 TTTTG-AAATA-T
1 TTTTGAAAATATT
* * * *
22433 ATAT-AATATATAG
1 TTTTGAAAATAT-T
22446 TTTTGAAAATACTT
1 TTTTGAAAATA-TT
22460 TTTTGAAAATAT
1 TTTTGAAAATAT
22472 ATATAATATA
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
11 7 0.19
12 5 0.14
13 8 0.22
14 16 0.43
15 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (13 bp):
TTTTGAAAATATT
Found at i:22440 original size:37 final size:38
Alignment explanation
Indices: 22363--22631 Score: 300
Period size: 37 Copynumber: 7.1 Consensus size: 38
22353 GTCTGGAGTT
22363 TATAGTTTT-AAAATATTTTTTTCTTGAAAATATATATAATA
1 TATAGTTTTGAAAATA---TTTT-TTGAAAATATATATAATA
22404 TATAGTTTTGAAAATATTTTTTG-AAATATATATAATA
1 TATAGTTTTGAAAATATTTTTTGAAAATATATATAATA
22441 TATAGTTTTGAAAATACTTTTTTGAAAATATATATAATA
1 TATAGTTTTGAAAATA-TTTTTTGAAAATATATATAATA
* *
22480 TATAGTTTTGAAAAATATTTTTCGAAAACATATATAATA
1 TATAGTTTTG-AAAATATTTTTTGAAAATATATATAATA
* * *
22519 TATAGTTTTAAAAACA-TTTTTGAAACA-GTATATAATA
1 TATAGTTTTGAAAATATTTTTTGAAA-ATATATATAATA
* * *
22556 TATAGTTTTTAAAAAATATTTTTG-AAA-ACATATAATA
1 TATAGTTTTGAAAATAT-TTTTTGAAAATATATATAATA
* * * **
22593 TATAATTTTGAAAACA-TTTGTGAAAACGTATATAATA
1 TATAGTTTTGAAAATATTTTTTGAAAATATATATAATA
22630 TA
1 TA
22632 GTTTTTAAAA
Statistics
Matches: 203, Mismatches: 16, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
35 5 0.02
36 3 0.01
37 93 0.46
38 18 0.09
39 63 0.31
40 6 0.03
41 9 0.04
42 6 0.03
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.44
Consensus pattern (38 bp):
TATAGTTTTGAAAATATTTTTTGAAAATATATATAATA
Found at i:22491 original size:76 final size:73
Alignment explanation
Indices: 22386--22631 Score: 314
Period size: 76 Copynumber: 3.3 Consensus size: 73
22376 TATTTTTTTC
22386 TTGAAAATATATATAATATATAGTTTTGAAAATATTTTTTGAAATATATATAATATATAGTTTTG
1 TTGAAAATATATATAATATATAGTTTTGAAAATATTTTTTGAAA-ATATATAATATATAGTTTT-
*
22451 AAAATACTTTT
64 AAAA-ACATTT
*
22462 TTGAAAATATATATAATATATAGTTTTGAAAAATATTTTTCGAAAACATATATAATATATAGTTT
1 TTGAAAATATATATAATATATAGTTTTG-AAAATATTTTTTG-AAA-ATATATAATATATAGTTT
22527 TAAAAACATTT
63 TAAAAACATTT
* * * * *
22538 TTGAAACA-GTATATAATATATAGTTTTTAAAAAATATTTTTGAAAACATATAATATATAATTTT
1 TTGAAA-ATATATATAATATATAGTTTTGAAAATAT-TTTTTGAAAATATATAATATATAGTTTT
*
22602 GAAAACATTT
64 AAAAACATTT
* **
22612 GTGAAAACGTATATAATATA
1 TTGAAAATATATATAATATA
22632 GTTTTTAAAA
Statistics
Matches: 154, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
73 1 0.01
74 43 0.28
75 9 0.06
76 62 0.40
77 17 0.11
78 22 0.14
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (73 bp):
TTGAAAATATATATAATATATAGTTTTGAAAATATTTTTTGAAAATATATAATATATAGTTTTAA
AAACATTT
Found at i:25232 original size:7 final size:7
Alignment explanation
Indices: 25224--25255 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
25214 TGGTATATAA
*
25224 TTCATAA
1 TTCATAT
25231 TTCATAT
1 TTCATAT
25238 TTCATAT
1 TTCATAT
25245 TTCATAT
1 TTCATAT
25252 TTCA
1 TTCA
25256 GTCACATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (7 bp):
TTCATAT
Found at i:30373 original size:15 final size:15
Alignment explanation
Indices: 30353--30386 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30343 CAGATTATGC
* *
30353 AGAGTGATGGGGAAG
1 AGAGTGAAGGAGAAG
30368 AGAGTGAAGGAGAAG
1 AGAGTGAAGGAGAAG
30383 AGAG
1 AGAG
30387 GGAAAGGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.50, T:0.09
Consensus pattern (15 bp):
AGAGTGAAGGAGAAG
Found at i:31331 original size:43 final size:43
Alignment explanation
Indices: 31279--31420 Score: 137
Period size: 43 Copynumber: 3.3 Consensus size: 43
31269 GCCAAAGTTG
* * * *
31279 TTGATATTTAGCGGCATTTTCTTC-ACAAACGCTGCAATATGTC
1 TTGAGATTTAGCGGCATTTT-TGCTAAAAACGCCGCAATATGTC
* * *
31322 TTGAGATTTAGCGGCGTTTTTGCTAAAAACGCCGTAATATGTG
1 TTGAGATTTAGCGGCATTTTTGCTAAAAACGCCGCAATATGTC
* * *
31365 TTGAGATTTAGCGACGTTTTTAGCT-AAAACGCCGCAATA-GGC
1 TTGAGATTTAGCGGCATTTTT-GCTAAAAACGCCGCAATATGTC
*
31407 GTTGAGGTTTAGCG
1 -TTGAGATTTAGCG
31421 ACGTTTTTAA
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
42 3 0.04
43 78 0.93
44 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (43 bp):
TTGAGATTTAGCGGCATTTTTGCTAAAAACGCCGCAATATGTC
Found at i:31421 original size:43 final size:44
Alignment explanation
Indices: 31305--31429 Score: 157
Period size: 43 Copynumber: 2.9 Consensus size: 44
31295 TTTTCTTCAC
* * *
31305 AAACGCTGCAATATGTC-TTGAGATTTAGCGGCGTTTTT-GCTAA
1 AAACGCCGCAATA-GGCGTTGAGATTTAGCGACGTTTTTAGCTAA
* * *
31348 AAACGCCGTAATATGTGTTGAGATTTAGCGACGTTTTTAGCT-A
1 AAACGCCGCAATAGGCGTTGAGATTTAGCGACGTTTTTAGCTAA
*
31391 AAACGCCGCAATAGGCGTTGAGGTTTAGCGACGTTTTTA
1 AAACGCCGCAATAGGCGTTGAGATTTAGCGACGTTTTTA
31430 ATGCAAACGC
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
43 67 0.96
44 3 0.04
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (44 bp):
AAACGCCGCAATAGGCGTTGAGATTTAGCGACGTTTTTAGCTAA
Found at i:31438 original size:43 final size:42
Alignment explanation
Indices: 31304--31442 Score: 129
Period size: 43 Copynumber: 3.2 Consensus size: 42
31294 ATTTTCTTCA
* * * * *
31304 CAAACGCTGCAATATGTC-TTGAGATTTAGCGGCGTTTTTGCTA
1 CAAACGCCGCAATA-GGCGTTGAGATTTAGCGACGTTTTT-ATG
* * * *
31347 AAAACGCCGTAATATGTGTTGAGATTTAGCGACGTTTTTA-G
1 CAAACGCCGCAATAGGCGTTGAGATTTAGCGACGTTTTTATG
*
31388 CTAAAACGCCGCAATAGGCGTTGAGGTTTAGCGACGTTTTTAATG
1 C--AAACGCCGCAATAGGCGTTGAGATTTAGCGACGTTTTT-ATG
31433 CAAACGCCGC
1 CAAACGCCGC
31443 TAAAAATTGG
Statistics
Matches: 77, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
43 74 0.96
44 1 0.01
45 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (42 bp):
CAAACGCCGCAATAGGCGTTGAGATTTAGCGACGTTTTTATG
Found at i:31893 original size:21 final size:21
Alignment explanation
Indices: 31869--31908 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31859 TGTGCTGCCA
* *
31869 CTGCTTCTCTCTCTGCTTCTG
1 CTGCTGCTCTCTCGGCTTCTG
31890 CTGCTGCTCTCTCGGCTTC
1 CTGCTGCTCTCTCGGCTTC
31909 CCTTGCTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.00, C:0.40, G:0.17, T:0.42
Consensus pattern (21 bp):
CTGCTGCTCTCTCGGCTTCTG
Found at i:34486 original size:42 final size:41
Alignment explanation
Indices: 34412--34518 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 41
34402 AGGACAATTG
* * *
34412 CGGCGTTTATATTAAAAACGCC-GTAAAAGAACTACTCTATTA
1 CGGCGTTTAT-TAAAAAACGCCACT-AAGGAACTACTCTATTA
* * * * *
34454 CTGCGTTTTTTACGAAAACGCCACTAAGGAACTATTCTATTG
1 CGGCGTTTATTA-AAAAACGCCACTAAGGAACTACTCTATTA
34496 CGGCGTTTATTAAAAAACGCCAC
1 CGGCGTTTATTAAAAAACGCCAC
34519 CTAATATCAA
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
41 11 0.21
42 40 0.77
43 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (41 bp):
CGGCGTTTATTAAAAAACGCCACTAAGGAACTACTCTATTA
Found at i:35764 original size:41 final size:41
Alignment explanation
Indices: 35716--35941 Score: 196
Period size: 41 Copynumber: 5.5 Consensus size: 41
35706 GACTATATAT
* *
35716 TTAACA-TTTTGCGGCGTTTATACAAAAAAACGCCACTTTTGA
1 TTAACACTATTGCGGCGTTT-TAC-AAAAAACGCCACTATTGA
* * * * *
35758 TT-ACATTATTGTGGCG-TTTGCTAATAAACGCCACTATTGT
1 TTAACACTATTGCGGCGTTTTAC-AAAAAACGCCACTATTGA
* * *
35798 TTAACACTATTGCGACGTTTGT-CTAAAAACGCCACTTTTGA
1 TTAACACTATTGCGGCGTTT-TACAAAAAACGCCACTATTGA
* *
35839 TTAACACTATTACGGCGTTTGTAC-AAAAATGCCACTATTGA
1 TTAACACTATTGCGGCGTTT-TACAAAAAACGCCACTATTGA
* *
35880 TTAACACTATTGCGGCGTTTTAGGAACAAACGCCACTATATG-
1 TTAACACTATTGCGGCGTTTTA-CAAAAAACGCCACTAT-TGA
*
35922 TGTAATA-TATTGCGGCGTTT
1 T-TAACACTATTGCGGCGTTT
35942 GTGGTAAAAA
Statistics
Matches: 152, Mismatches: 23, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
40 21 0.14
41 84 0.55
42 40 0.26
43 7 0.05
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (41 bp):
TTAACACTATTGCGGCGTTTTACAAAAAACGCCACTATTGA
Found at i:35918 original size:124 final size:124
Alignment explanation
Indices: 35727--35955 Score: 286
Period size: 124 Copynumber: 1.8 Consensus size: 124
35717 TAACATTTTG
* * * * *
35727 CGGCGTTTATACAAAAAAACGCCACTTTTGATTACATTATTGTGGCGTTTGCTAATAAACGCCAC
1 CGGCGTTTATAC-AAAAAACGCCACTATTGATTACACTATTGCGGCGTTTGCGAACAAACGCCAC
*
35792 TAT-TGTTTAACACTATTGCGACGTTTGT-CTAAAAACGCCACTTTTGATTAACACTATTA
65 TATATGTGTAACA-TATTGCGACGTTTGTGCTAAAAACGCCACTTTTGATTAACACTATTA
* *
35851 CGGCGTTTGTAC-AAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTAG-GAACAAACGCC
1 CGGCGTTTATACAAAAAACGCCACTATTGATT-ACACTATTGCGGCG-TTT-GCGAACAAACGCC
* * *
35914 ACTATATGTGTAATATATTGCGGCGTTTGTGGTAAAAACGCC
63 ACTATATGTGTAACATATTGCGACGTTTGTGCTAAAAACGCC
35956 GCTAATTTAC
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
122 17 0.19
123 12 0.13
124 42 0.47
125 18 0.20
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (124 bp):
CGGCGTTTATACAAAAAACGCCACTATTGATTACACTATTGCGGCGTTTGCGAACAAACGCCACT
ATATGTGTAACATATTGCGACGTTTGTGCTAAAAACGCCACTTTTGATTAACACTATTA
Found at i:35953 original size:42 final size:41
Alignment explanation
Indices: 35741--35955 Score: 215
Period size: 41 Copynumber: 5.2 Consensus size: 41
35731 GTTTATACAA
* * * *
35741 AAAAACGCCACTTTTGATT-ACATTATTGTGGCGTTTG-CT
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTGT
* * *
35780 AATAAACGCCACTATTGTTTAACACTATTGCGACGTTTGTCT
1 AA-AAACGCCACTATTGATTAACACTATTGCGGCGTTTGTGT
* * **
35822 AAAAACGCCACTTTTGATTAACACTATTACGGCGTTTGTAC
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTGT
* *
35863 AAAAATGCCACTATTGATTAACACTATTGCGGCGTTT-TAGG
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGT-GT
*
35904 AACAAACGCCACTATATG-TGTAATA-TATTGCGGCGTTTGTGGT
1 AA-AAACGCCACTAT-TGAT-TAACACTATTGCGGCGTTTGT-GT
35947 AAAAACGCC
1 AAAAACGCC
35956 GCTAATTTAC
Statistics
Matches: 148, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.01
40 16 0.11
41 84 0.57
42 36 0.24
43 10 0.07
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (41 bp):
AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTGT
Found at i:35975 original size:42 final size:41
Alignment explanation
Indices: 35929--36042 Score: 126
Period size: 41 Copynumber: 2.8 Consensus size: 41
35919 ATGTGTAATA
35929 TATTGCGGCGTTTGTGGTAAAAACGCCGCTAATTTACCACTC
1 TATTGCGGCGTTTGTGGTAAAAACGCCGCTAATTTA-CACTC
* * * * *
35971 TATTGTGGCGTTT-TGGCT-AAATCGTCGCAAAATTTATACTC
1 TATTGCGGCGTTTGTGG-TAAAAACGCCGC-TAATTTACACTC
*
36012 TATTGCGGCGTTTGTGG-AAAAACACCGCTAA
1 TATTGCGGCGTTTGTGGTAAAAACGCCGCTAA
36043 AGTATCAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
40 2 0.03
41 34 0.59
42 22 0.38
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (41 bp):
TATTGCGGCGTTTGTGGTAAAAACGCCGCTAATTTACACTC
Found at i:36557 original size:9 final size:9
Alignment explanation
Indices: 36538--36571 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
36528 TAGAGTATGA
36538 TTTTTATTTT
1 TTTTTA-TTT
36548 TTTTTATTT
1 TTTTTATTT
36557 TTTTTATTT
1 TTTTTATTT
36566 TCTTTT
1 T-TTTT
36572 GTTATTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.57
10 10 0.43
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTATTT
Found at i:36571 original size:13 final size:13
Alignment explanation
Indices: 36555--36587 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
36545 TTTTTTTTAT
36555 TTTTTTTATTTTC
1 TTTTTTTATTTTC
*
36568 TTTTGTTATTTTC
1 TTTTTTTATTTTC
36581 TTTTTTT
1 TTTTTTT
36588 GTTAATTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.03, T:0.85
Consensus pattern (13 bp):
TTTTTTTATTTTC
Found at i:36579 original size:19 final size:19
Alignment explanation
Indices: 36537--36579 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
36527 GTAGAGTATG
*
36537 ATTTTTATTTTTTTTTATT
1 ATTTTTATTTTCTTTTATT
* *
36556 TTTTTTATTTTCTTTTGTT
1 ATTTTTATTTTCTTTTATT
36575 ATTTT
1 ATTTT
36580 CTTTTTTTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.84
Consensus pattern (19 bp):
ATTTTTATTTTCTTTTATT
Found at i:45881 original size:64 final size:63
Alignment explanation
Indices: 45809--45929 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 63
45799 ATGGTTCAAG
* *
45809 GTGTATCGATGCACATA-AAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACA-AGAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATGCCATCA
* * * *
45873 GTGTATCGATGCACAAGTAGTGCATTGATGGACCCCCTTAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATG
45930 AGATTTATGC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 18 0.36
64 32 0.64
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATGCCATCA
Found at i:50879 original size:60 final size:61
Alignment explanation
Indices: 50794--50915 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 61
50784 AATTCTTATA
* * *
50794 ATATTTTAAAATTGAGATAAAAATAAAATATATTTTTAC-AGTTAATA-TAAGAATAAAATAT
1 ATATTTTAAAATTAAAATAAAAATAAAATATA-TTTAACAAGTTAA-AGTAAGAATAAAATAT
* * *
50855 ATATTTT-AAATTAAAATAATAATAAATTATATTTAACAATTTAAAGTAAGAATAAAATAT
1 ATATTTTAAAATTAAAATAAAAATAAAATATATTTAACAAGTTAAAGTAAGAATAAAATAT
50915 A
1 A
50916 ATAAGAAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
59 6 0.11
60 40 0.75
61 7 0.13
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (61 bp):
ATATTTTAAAATTAAAATAAAAATAAAATATATTTAACAAGTTAAAGTAAGAATAAAATAT
Found at i:50889 original size:27 final size:30
Alignment explanation
Indices: 50794--50915 Score: 115
Period size: 30 Copynumber: 4.0 Consensus size: 30
50784 AATTCTTATA
* * *
50794 ATATTTTAAAATTGAGATAAAAATAAAATAT
1 ATATTTT-AAATTAAAATAAGAATAAAATAT
* *
50825 AT-TTTTACAGTTAATATAAGAATAAAATAT
1 ATATTTTA-AATTAAAATAAGAATAAAATAT
*
50855 ATATTTTAAATTAAAATAATAAT-AAAT-T
1 ATATTTTAAATTAAAATAAGAATAAAATAT
* *
50883 ATATTTAACAATTTAAAGTAAGAATAAAATAT
1 ATATTTTA-AA-TTAAAATAAGAATAAAATAT
50915 A
1 A
50916 ATAAGAAAAG
Statistics
Matches: 75, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
28 8 0.11
29 7 0.09
30 47 0.63
31 11 0.15
32 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (30 bp):
ATATTTTAAATTAAAATAAGAATAAAATAT
Found at i:51897 original size:18 final size:19
Alignment explanation
Indices: 51874--51919 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
51864 ATAAAAATTT
51874 TTTAATGTTAATATGT-AA
1 TTTAATGTTAATATGTGAA
51892 TTTAAT-TTAATATGTGAA
1 TTTAATGTTAATATGTGAA
51910 TTTAA-GTTAA
1 TTTAATGTTAA
51920 CATATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (19 bp):
TTTAATGTTAATATGTGAA
Found at i:54446 original size:2 final size:2
Alignment explanation
Indices: 54439--54498 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
54429 CATCACTAAC
54439 AT AT AT AT AT AT AT AT -T 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
54480 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
54499 ATCACACCGA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55115 original size:19 final size:20
Alignment explanation
Indices: 55093--55160 Score: 68
Period size: 19 Copynumber: 3.4 Consensus size: 20
55083 TAGCATACAC
*
55093 ATTATATTA-TACATTATAT
1 ATTATATTATTACAATATAT
* *
55112 ATTACACTATTCACAATATAT
1 ATTATATTATT-ACAATATAT
*
55133 A-TATATTATTACACTATAT
1 ATTATATTATTACAATATAT
55152 ATATATATT
1 AT-TATATT
55161 TTTTACAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 16 0.41
20 8 0.21
21 15 0.38
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTATATTATTACAATATAT
Found at i:55151 original size:21 final size:21
Alignment explanation
Indices: 55095--55160 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
55085 GCATACACAT
*
55095 TATATTA-TACATTATATAT-
1 TATATTATTACACTATATATA
* * *
55114 TACACTATT-CACAATATATA
1 TATATTATTACACTATATATA
55134 TATATTATTACACTATATATA
1 TATATTATTACACTATATATA
55155 TATATT
1 TATATT
55161 TTTTACAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 13 0.35
20 8 0.22
21 16 0.43
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (21 bp):
TATATTATTACACTATATATA
Found at i:56528 original size:24 final size:24
Alignment explanation
Indices: 56480--56528 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
56470 TTTATAACCA
** * *
56480 TTTATTTTATTTTTTTTTTTTTTT
1 TTTATTTTATTACTTTCTTTCTTT
56504 TTTATTTTATTACTTTCTTTCTTT
1 TTTATTTTATTACTTTCTTTCTTT
56528 T
1 T
56529 ATCGTTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (24 bp):
TTTATTTTATTACTTTCTTTCTTT
Found at i:56545 original size:25 final size:25
Alignment explanation
Indices: 56508--56555 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
56498 TTTTTTTTTA
* *
56508 TTTTATTACTTTCTTTCTTTTATCG
1 TTTTATTACTTTCATTATTTTATCG
56533 TTTTATTTA-TTTCATTATTTTAT
1 TTTTA-TTACTTTCATTATTTTAT
56556 TTATTTAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTTATTACTTTCATTATTTTATCG
Found at i:56795 original size:18 final size:19
Alignment explanation
Indices: 56760--56795 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
56750 CAAGGAATGT
56760 AAGATTACCAGTGGAATAA
1 AAGATTACCAGTGGAATAA
*
56779 AAGATTATCAG-GGAATA
1 AAGATTACCAGTGGAATA
56796 GGATTACTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.22
Consensus pattern (19 bp):
AAGATTACCAGTGGAATAA
Found at i:57003 original size:31 final size:33
Alignment explanation
Indices: 56941--57004 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 33
56931 TTGAAAATAT
**
56941 TTATATATTTTCTTTAATAAATTAATCATAAAA
1 TTATATATTTTCTTTAATAAATTAAAAATAAAA
56974 TTATA-ATTTT-TTTACA-AAATTAAAAATAAAA
1 TTATATATTTTCTTTA-ATAAATTAAAAATAAAA
57005 AAGGTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 17 0.61
32 6 0.21
33 5 0.18
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (33 bp):
TTATATATTTTCTTTAATAAATTAAAAATAAAA
Found at i:58992 original size:46 final size:44
Alignment explanation
Indices: 58871--59012 Score: 241
Period size: 45 Copynumber: 3.2 Consensus size: 44
58861 ATCAATAAAT
*
58871 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAA-ATAC
58916 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAA-ATAC
58961 TTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACC-AATAC
1 TTACCATTT-ATTCCATAAGCTCGTAAGCTTATTTTACCAAATAC
59005 TTACCATT
1 TTACCATT
59013 AGTATGATTT
Statistics
Matches: 94, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
44 12 0.13
45 53 0.56
46 29 0.31
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (44 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAATAC
Found at i:59276 original size:30 final size:30
Alignment explanation
Indices: 59240--59337 Score: 80
Period size: 30 Copynumber: 3.3 Consensus size: 30
59230 GGAAATCTAT
59240 ACACTCAGTATGATTTCCTTATCATTTAGC
1 ACACTCAGTATGATTTCCTTATCATTTAGC
* * * * *
59270 ACACTCAG--TG--CTCCATATGGAAATCTA-T
1 ACACTCAGTATGATTTCCTTAT---CATTTAGC
59298 ACACTCAGTATGATTTTCCTTATCATTTAGC
1 ACACTCAGTATGA-TTTCCTTATCATTTAGC
59329 ACACTCAGT
1 ACACTCAGT
59338 GTTTCATATG
Statistics
Matches: 49, Mismatches: 10, Indels: 17
0.64 0.13 0.22
Matches are distributed among these distances:
26 6 0.12
28 10 0.20
29 4 0.08
30 14 0.29
31 9 0.18
33 6 0.12
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (30 bp):
ACACTCAGTATGATTTCCTTATCATTTAGC
Found at i:59346 original size:59 final size:58
Alignment explanation
Indices: 59072--59390 Score: 351
Period size: 58 Copynumber: 5.5 Consensus size: 58
59062 CCATACCATT
* * ** * * *
59072 AGTATGATTTCCTTATCTTTGTAGCACCCT-AGTGCTTTATCTGAAAATCCATACACTC
1 AGTATGATTTCCTTATCATT-TAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
* * * * * * ***
59130 AGTATGA-TTCTCTTACCTTTTTAGCACA-TAAATGC-CCTATCTGGAAATCCATATTTTC
1 AGTATGATTTC-CTTATC-ATTTAGCACACTCAGTGCTCC-ATATGGAAATCTATACACTC
* * *
59188 AATATGATTTTCTTATCATTTAGCACACTCAGTGCCCCATATGGAAATCTATACACTC
1 AGTATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
59246 AGTATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
1 AGTATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
* *
59304 AGTATGATTTTCCTTATCATTTAGCACACTCAGTGTTTCATATGGAAATCTATACACTC
1 AGTATGA-TTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
*
59363 AGT-TGATTTCCTTATTATTTTAGCACAC
1 AGTATGATTTCCTTATCA-TTTAGCACAC
59391 AAAGTGC
Statistics
Matches: 226, Mismatches: 26, Indels: 18
0.84 0.10 0.07
Matches are distributed among these distances:
57 23 0.10
58 144 0.64
59 59 0.26
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (58 bp):
AGTATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
Found at i:59397 original size:117 final size:118
Alignment explanation
Indices: 59030--59397 Score: 373
Period size: 116 Copynumber: 3.2 Consensus size: 118
59020 TTTTGTTACC
* * * * * *
59030 ATTTTAGCACATGAAA-TACCCTATGTGAAAATCCATAC-CATTAGTATGA-TTTCCTTATCTTT
1 ATTTTAGCACA-CAAAGTGCCCTATATGGAAATCCATACAC-TCAGTATGATTTTCCTTATCATT
* * * * *
59092 GTAGCACCCT-AGTGCTTT-ATCTGAAAATCCATACACTCAGTATGA-TTCTCTTACCT
64 -TAGCACACTCAGTG-TTTCATATGGAAATCTATACACTCAGTATGATTTC-CTTA-TT
* * *** *
59148 -TTTTAGCACATAAA-TGCCCTATCTGGAAATCCATATTTTCAATATGATTTT-CTTATCATTTA
1 ATTTTAGCACACAAAGTGCCCTATATGGAAATCCATACACTCAGTATGATTTTCCTTATCATTTA
*** *
59210 GCACACTCAGTGCCCCATATGGAAATCTATACACTCAGTATGATTTCCTTATC
66 GCACACTCAGTGTTTCATATGGAAATCTATACACTCAGTATGATTTCCTTATT
** *
59263 A-TTTAGCACACTCAGTGCTCC-ATATGGAAATCTATACACTCAGTATGATTTTCCTTATCATTT
1 ATTTTAGCACACAAAGTGC-CCTATATGGAAATCCATACACTCAGTATGATTTTCCTTATCATTT
59326 AGCACACTCAGTGTTTCATATGGAAATCTATACACTCAGT-TGATTTCCTTATT
65 AGCACACTCAGTGTTTCATATGGAAATCTATACACTCAGTATGATTTCCTTATT
59379 ATTTTAGCACACAAAGTGC
1 ATTTTAGCACACAAAGTGC
Statistics
Matches: 207, Mismatches: 33, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
115 18 0.09
116 109 0.53
117 80 0.39
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (118 bp):
ATTTTAGCACACAAAGTGCCCTATATGGAAATCCATACACTCAGTATGATTTTCCTTATCATTTA
GCACACTCAGTGTTTCATATGGAAATCTATACACTCAGTATGATTTCCTTATT
Done.