Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007746.1 Hibiscus syriacus cultivar Beakdansim tig00110009_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: 3674400
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 15
Found at i:3640019 original size:39 final size:39
Alignment explanation
Indices: 3639937--3640022 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 39
3639927 AGTGCACGAT
* * * ** *
3639937 GTCTTCAGGTAAAATAGGAAGACTCCAAGCTTATTTGAT
1 GTCTTCAGGCAAAATAAGAAGACTCCAAGATTACATGAC
*
3639976 GTCTTCAGGCAAAATAAGAAGACTCCAAGATTACATGGC
1 GTCTTCAGGCAAAATAAGAAGACTCCAAGATTACATGAC
3640015 GTCTTCAG
1 GTCTTCAG
3640023 TCTAGGGTGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (39 bp):
GTCTTCAGGCAAAATAAGAAGACTCCAAGATTACATGAC
Found at i:3640672 original size:22 final size:21
Alignment explanation
Indices: 3640629--3640672 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
3640619 AGAAATGTTA
*
3640629 AAAAATATAATTATAATGACG
1 AAAAATATAATTATAATAACG
* *
3640650 AAAAATAATATTTATTATAACG
1 AAAAAT-ATAATTATAATAACG
3640672 A
1 A
3640673 TGAAAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (21 bp):
AAAAATATAATTATAATAACG
Found at i:3641705 original size:27 final size:27
Alignment explanation
Indices: 3641666--3641728 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
3641656 ATATTTTAAT
* *
3641666 GAATGTAATTAATATCAATAGTTGAAT
1 GAATGTGATTAATATCAATAGTTGAAG
* * *
3641693 TAATGTGATTAATATTAATATTTGAAG
1 GAATGTGATTAATATCAATAGTTGAAG
3641720 GAATGTGAT
1 GAATGTGAT
3641729 GGATATTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.40
Consensus pattern (27 bp):
GAATGTGATTAATATCAATAGTTGAAG
Found at i:3643995 original size:102 final size:104
Alignment explanation
Indices: 3643775--3644359 Score: 396
Period size: 102 Copynumber: 5.5 Consensus size: 104
3643765 TTAAACAAAA
* *
3643775 AATATGTTAAATCAAAATAAATAGTCTAATTAAATTATATTTACAATAAAAACAAAAAAAAGCAA
1 AATATGTAAAATCAAAATAAATAGTCTAA-TAATTTATATTTACAAT-AAAACAAAAAAAA-CAA
* *
3643840 TAAAATTTAAACTAAACTTACCAAACCACTCAAATACGATTT
63 TAAAATTTAAACTAAACTTACCAAACCACTCAAATACAACTT
*
3643882 AATATGTAAAATCAAAATAAATAGATC-AATAATTTATA-TTACTCAAT-AAA-AAATAAAA-AA
1 AATATGTAAAATCAAAATAAATAG-TCTAATAATTTATATTTA--CAATAAAACAAAAAAAACAA
* * ** *
3643942 TATAGTTTAAACTAAACTTATGAAACTACTCAAATACAACTT
63 TAAAATTTAAACTAAACTTACCAAACCACTCAAATACAACTT
3643984 AATATGTAAAATCAAAAATAAATAGTCTAATAA-TTATAATTTA-AATTAAAAACAAAAATTATA
1 AATATGTAAAATC-AAAATAAATAGTCTAATAATTTAT-ATTTACAA-T-AAAAC-AAAA--A-A
* * * * ***
3644047 CTAAAAATTACACGAAAATTTAAATTAAACTTATCAAACCACTCGAATACGGTTT
58 --AACAA-T-----AAAATTTAAACTAAACTTACCAAACCACTCAAATACAACTT
* * * **
3644102 AATATTTAAAATAAAAATAAATAGTGTAATTAATTTATTATTTA-AATGAAAACCCTAAACCCTA
1 AATATGTAAAATCAAAATAAATAGTCTAA-TAATTTA-TATTTACAAT-AAAA--C-AAA--AAA
* * * * *
3644166 AATAATTAATTTTAAACTAAACTTACCAAACCACTCAAATACGATTT
58 AACAATAAAATTTAAACTAAACTTACCAAACCACTCAAATACAACTT
* * * * * * ** *
3644213 AATCTGTAAAATAAAAATAATTAGTTTAATAA-TT-TATCT-CAATAAAATATAATTTAAACTA-
1 AATATGTAAAATCAAAATAAATAGTCTAATAATTTATATTTACAATAAAACA-AA-AAAAACAAT
* *
3644274 AAAATTT----T-AACTGACCAAACTACTCAAATACAACTT
64 AAAATTTAAACTAAACTTACCAAACCACTCAAATACAACTT
*
3644310 AATATGTAAAATCAAAATAAATAGTCTAATAA-TTATTATTTAAAATAAAA
1 AATATGTAAAATCAAAATAAATAGTCTAATAATTTA-TATTTACAATAAAA
3644360 ATAAAAATTA
Statistics
Matches: 386, Mismatches: 56, Indels: 79
0.74 0.11 0.15
Matches are distributed among these distances:
97 54 0.14
98 1 0.00
99 4 0.01
100 7 0.02
101 2 0.01
102 62 0.16
103 23 0.06
104 15 0.04
105 6 0.02
106 15 0.04
107 36 0.09
108 3 0.01
109 3 0.01
110 3 0.01
111 62 0.16
112 2 0.01
113 1 0.00
116 1 0.00
117 19 0.05
118 51 0.13
119 11 0.03
120 5 0.01
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (104 bp):
AATATGTAAAATCAAAATAAATAGTCTAATAATTTATATTTACAATAAAACAAAAAAAACAATAA
AATTTAAACTAAACTTACCAAACCACTCAAATACAACTT
Found at i:3644391 original size:11 final size:12
Alignment explanation
Indices: 3644361--3644389 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3644351 AAAATAAAAA
3644361 TAAAAATTACAC
1 TAAAAATTACAC
3644373 TAAAAATTACAC
1 TAAAAATTACAC
3644385 TAAAA
1 TAAAA
3644390 TTTAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAAAATTACAC
Found at i:3644392 original size:325 final size:329
Alignment explanation
Indices: 3643845--3644471 Score: 908
Period size: 325 Copynumber: 1.9 Consensus size: 329
3643835 AGCAATAAAA
*
3643845 TTTAAACTAAACTTACCAAACCACTCAAATACGATTTAATATGTAAAATCAAAATAAATAGATCA
1 TTTAAACTAAACTTACCAAACCACTCAAATACGATTTAATATGTAAAATAAAAATAAATAGATCA
* * ** * **
3643910 ATAATTTATATTACTCAATAAAAAATAAAAAATATAGTTTAAACTAAACTTATGAAACTACTCAA
66 ATAATTTATATTACTCAAT-AAAAATAAAAAATAAACTAAAAACTAAACTGACCAAACTACTCAA
*
3643975 ATACAACTTAATATGTAAAATCAAAAATAAATAGTCTAATAATTATAATTTAAATTAAAAACAAA
130 ATACAACTTAATATGTAAAATCAAAAATAAATAGTCTAATAATTATAATTTAAAATAAAAACAAA
* *
3644040 AATTATACTAAAAATTACACGAAAATTTAAATTAAACTTATCAAACCACT-CGAATACGGTTTAA
195 AATTACACTAAAAATTACACGAAAATTTAAATTAAACTTATCAAA-CACTGCGAATACAGTTTAA
* *
3644104 TATTTAAAATAAAAATAAATAGTGTAATTAATTTATTATTTAAATGAAAACCCTAAACCCTAAAT
259 TATGTAAAATAAAAATAAATAATGTAATTAATTTA-TATTTAAATGAAAACCCTAAACCCTAAAT
3644169 AATTAAT
323 AATTAAT
* * * *
3644176 TTTAAACTAAACTTACCAAACCACTCAAATACGATTTAATCTGTAAAATAAAAATAATTAGTTTA
1 TTTAAACTAAACTTACCAAACCACTCAAATACGATTTAATATGTAAAATAAAAATAAATAGATCA
* ** * *
3644241 ATAA-TT-TA-T-CTCAAT-AAAATATAATTTAAACTAAAAATTTTAACTGACCAAACTACTCAA
66 ATAATTTATATTACTCAATAAAAATAAAAAATAAACTAAAAA-CTAAACTGACCAAACTACTCAA
* *
3644301 ATACAACTTAATATGTAAAATC-AAAATAAATAGTCTAATAATTATTATTTAAAATAAAAATAAA
130 ATACAACTTAATATGTAAAATCAAAAATAAATAGTCTAATAATTATAATTTAAAATAAAAACAAA
* * **
3644365 AATTACACTAAAAATTACACTAAAATTTAAATTAAACTTATTAAACTGTGCGAATACAGTTTAAT
195 AATTACACTAAAAATTACACGAAAATTTAAATTAAACTTATCAAACACTGCGAATACAGTTTAAT
*
3644430 ATGTAAAATTAAAATAAATAATGTAATTAATTTATATTTAAA
260 ATGTAAAATAAAAATAAATAATGTAATTAATTTATATTTAAA
3644472 ATAAAAAAAC
Statistics
Matches: 265, Mismatches: 29, Indels: 11
0.87 0.10 0.04
Matches are distributed among these distances:
324 10 0.04
325 141 0.53
326 39 0.15
327 6 0.02
328 1 0.00
329 2 0.01
330 2 0.01
331 64 0.24
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.33
Consensus pattern (329 bp):
TTTAAACTAAACTTACCAAACCACTCAAATACGATTTAATATGTAAAATAAAAATAAATAGATCA
ATAATTTATATTACTCAATAAAAATAAAAAATAAACTAAAAACTAAACTGACCAAACTACTCAAA
TACAACTTAATATGTAAAATCAAAAATAAATAGTCTAATAATTATAATTTAAAATAAAAACAAAA
ATTACACTAAAAATTACACGAAAATTTAAATTAAACTTATCAAACACTGCGAATACAGTTTAATA
TGTAAAATAAAAATAAATAATGTAATTAATTTATATTTAAATGAAAACCCTAAACCCTAAATAAT
TAAT
Found at i:3644711 original size:24 final size:25
Alignment explanation
Indices: 3644681--3644735 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
3644671 CCGTTAGATG
**
3644681 CATTATTGGTGCAC-ATAATGGCAC
1 CATTATTAATGCACAATAATGGCAC
*
3644705 CATTATTAATGCCCAATAATGGCAC
1 CATTATTAATGCACAATAATGGCAC
3644730 CATTAT
1 CATTAT
3644736 GCCTATTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (25 bp):
CATTATTAATGCACAATAATGGCAC
Found at i:3646433 original size:44 final size:44
Alignment explanation
Indices: 3646363--3646455 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
3646353 GCATATCCAA
* * *
3646363 TATTTTACCATATACTTGCCATTTATTTCATAAGCTTGTAAGCT
1 TATTTTACCATATACTTACCATTTATTCCATAAGCTCGTAAGCT
*
3646407 TATTTTACCAATATACTTACTA-TTATTCCATAAGCTCGTAAGCT
1 TATTTTACC-ATATACTTACCATTTATTCCATAAGCTCGTAAGCT
3646451 TATTT
1 TATTT
3646456 GCATGGTTAC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 34 0.77
45 10 0.23
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (44 bp):
TATTTTACCATATACTTACCATTTATTCCATAAGCTCGTAAGCT
Found at i:3648567 original size:30 final size:30
Alignment explanation
Indices: 3648520--3648577 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
3648510 TTTGGTCCCT
* *
3648520 AAACTTTTCAAAGTTTATACTTTAGTCATC
1 AAACTTTCCAAAGTTTATAATTTAGTCATC
*
3648550 AAACTTTACCAAA-TTTATAATTTGGTCA
1 AAACTTT-CCAAAGTTTATAATTTAGTCA
3648578 CTAAATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (30 bp):
AAACTTTCCAAAGTTTATAATTTAGTCATC
Found at i:3649371 original size:55 final size:55
Alignment explanation
Indices: 3649312--3650362 Score: 750
Period size: 55 Copynumber: 18.9 Consensus size: 55
3649302 CTATACGGTA
** * * * * * *
3649312 ATTCATCAACTCATGATGAATTATGTGGTTTTACATATATAGTGTCGGTACGGTT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCTGTACGGCT
*
3649367 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCGGTACGGCT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCTGTACGGCT
** *
3649422 ATTCATCAACTCATGATGAATTATGTGGATTTGCACACATAGTGT-TGGTACGTCT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCT-GTACGGCT
3649477 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTG-CATGTACGGGCT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTC-TGTAC-GGCT
3649533 ATTCATCAACTCATGATGAATTCCGT-GAGTTTGCACACATAGT-TCCTGTACGGCT
1 ATTCATCAACTCATGATGAATTCCGTGGA-TTTGCACACATAGTGT-CTGTACGGCT
* ** ** *
3649588 ATTCATCAACTCATGATAAATTTTGTTAATTTGCACACATAGTG-CATGCACGGCT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTC-TGTACGGCT
* * * *
3649643 ATTCATCAACTCATGATGAATTCCGTGGATATGCACACATAGTGCCTATACGACT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCTGTACGGCT
* * *
3649698 ATTCATCAACTAATGATGAATTCTGTGGATTTGCACACATAGTG-CTGTACGACT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCTGTACGGCT
* * *
3649752 ATTCATCAACTCATGATGAATT-C-T--ATTCAT-CAACTCAT-GATGAATTCCGT--GGAT
1 ATTCATCAACTCATGATGAATTCCGTGGATT--TGC-ACACATAG-TG---TCTGTACGGCT
* * * *
3649806 -TTGCACACAGAGCATC-TG-TAGTACACTT-AGTACTGATACCATTGCAC-CATTAGTG-CTAA
1 ATT-CA-TCA-A-C-TCATGAT-G-A-A-TTCCGT--GGAT----TTGCACACA-TAGTGTCT-G
*
3649865 TATGG-T
49 TACGGCT
* ** * * ** * *
3649871 AATTTAAAAACTTTC-T-ATTCATATT-CATTTATTAGAATGCACA-AGTAGTGCCTATACGG-T
1 -ATTCATCAAC--TCATGA-TGA-ATTCCGTGGATT----TGCACACA-TAGTGTCTGTACGGCT
*** * * *
3649931 AATT--T-AACTCATGATGAATTATATGGTTTTGCATACATAGTG-CTGGTACGACT
1 -ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCT-GTACGGCT
* * * **
3649984 A-TCATCAACTCATGATAAATTCTGTGAATTTGCACACATAGTG-CTGGTACAACT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCT-GTACGGCT
* * ** * * * *
3650038 ATTAATAAACTCATGATGAATTTTGTGGATTTACACACATAGTGCCTATACGACT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCTGTACGGCT
* * * * * *
3650093 ATTCATCAACTCATGATGAATTCCGTGAATTTGTAAATATAGTGCCTGTACAGCT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCTGTACGGCT
*
3650148 ATTCATTAACTCATGATGAATTCCGT-GAGTTTGCACACATAGTGTCTGTACGGCT
1 ATTCATCAACTCATGATGAATTCCGTGGA-TTTGCACACATAGTGTCTGTACGGCT
* * *
3650203 ATTCAACAACTCATGATGAATTTCGTTGATTTGCACACATAGT-TCCTGTACGGCT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGT-CTGTACGGCT
* * *
3650258 ATTCATCAACTCATGATGAATTCCGTGAATTTGCAAATATAGTG-CATGTACGGCT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTC-TGTACGGCT
* * *
3650313 AGTCATCAACTCATGATGAATTCCGTGGATTTGCACATAGAGTGTCTGTA
1 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCTGTA
3650363 GTACACTTAG
Statistics
Matches: 817, Mismatches: 108, Indels: 142
0.77 0.10 0.13
Matches are distributed among these distances:
50 3 0.00
51 5 0.01
52 24 0.03
53 5 0.01
54 80 0.10
55 555 0.68
56 69 0.08
57 9 0.01
58 3 0.00
59 1 0.00
60 26 0.03
61 3 0.00
62 3 0.00
63 4 0.00
64 5 0.01
65 6 0.01
66 5 0.01
67 8 0.01
68 2 0.00
69 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCTGTACGGCT
Found at i:3649782 original size:24 final size:24
Alignment explanation
Indices: 3649750--3649798 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3649740 TGCTGTACGA
3649750 CTATTCATCAACTCATGATGAATT
1 CTATTCATCAACTCATGATGAATT
3649774 CTATTCATCAACTCATGATGAATT
1 CTATTCATCAACTCATGATGAATT
3649798 C
1 C
3649799 CGTGGATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (24 bp):
CTATTCATCAACTCATGATGAATT
Found at i:3650826 original size:20 final size:21
Alignment explanation
Indices: 3650775--3650826 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
3650765 GTTTCGAAAT
*
3650775 GGTATCGATAC-CTTCCCTTC
1 GGTATCGATACTCTTCCCTAC
*
3650795 GGCATCGATACTC-TCCCTAC
1 GGTATCGATACTCTTCCCTAC
3650815 GGTATCGATACT
1 GGTATCGATACT
3650827 GATTGAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.19, C:0.33, G:0.17, T:0.31
Consensus pattern (21 bp):
GGTATCGATACTCTTCCCTAC
Found at i:3651786 original size:18 final size:18
Alignment explanation
Indices: 3651763--3651799 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3651753 AAGCACTTTA
3651763 ACATAATCCTTTTGTTAC
1 ACATAATCCTTTTGTTAC
3651781 ACATAATCCTTTTGTTAC
1 ACATAATCCTTTTGTTAC
3651799 A
1 A
3651800 ATTCCTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (18 bp):
ACATAATCCTTTTGTTAC
Found at i:3656878 original size:55 final size:55
Alignment explanation
Indices: 3656817--3657896 Score: 922
Period size: 55 Copynumber: 19.9 Consensus size: 55
3656807 CTATACGATA
* * * * * *
3656817 ATTCATCACCTCATGATGAATACTCTGGTTTTGTACACATAGTGTCGGTACGGCT
1 ATTCATCAACTCATGATGAATTCTCTGGATTTGCACACATAGTGCCTGTACGGCT
* * *
3656872 ATTCATCAACTCATGATGAATTCTGTGGATTTGCACACATAGTGTCGGTACGGCT
1 ATTCATCAACTCATGATGAATTCTCTGGATTTGCACACATAGTGCCTGTACGGCT
* **
3656927 ATTCATCAACTCATGATGAATTC-CGTGGATTTGCATACATAGTGCCAATACGGCT
1 ATTCATCAACTCATGATGAATTCTC-TGGATTTGCACACATAGTGCCTGTACGGCT
3656982 ATTCATCAACTCATGATGAATTC-CGTGGATTTGCACACATAGTGCCTGTACGGGCT
1 ATTCATCAACTCATGATGAATTCTC-TGGATTTGCACACATAGTGCCTGTAC-GGCT
* * * * * *
3657038 ATTCAT---GTCATGATGAATTCTGTGAATTTGCACACATAGTGCATGTATGACT
1 ATTCATCAACTCATGATGAATTCTCTGGATTTGCACACATAGTGCCTGTACGGCT
* * * * * *
3657090 ATTCATCAACTCATGATGAATTTTGTGAATTTGCATACATAATGCCTGTATGGCT
1 ATTCATCAACTCATGATGAATTCTCTGGATTTGCACACATAGTGCCTGTACGGCT
*
3657145 ATTCATCAACTCATGATGAATT-TCGTGGATTTGCACACATAGTGCCTATACGGCT
1 ATTCATCAACTCATGATGAATTCTC-TGGATTTGCACACATAGTGCCTGTACGGCT
*
3657200 ATTCATCAACTCATGATGAATTC-CGTGGATTTGCACACATAGTGCATGTACGGCT
1 ATTCATCAACTCATGATGAATTCTC-TGGATTTGCACACATAGTGCCTGTACGGCT
* * * * * *
3657255 ATTTATCAACTCATGACGAATTCTATGAATTTACACACATAGTGTCTGTACGGCT
1 ATTCATCAACTCATGATGAATTCTCTGGATTTGCACACATAGTGCCTGTACGGCT
* * * * *
3657310 ATTCATTAACTCATGATGAATT-TCGTGGATTTACACACATAGTGTCTGTA-GTACA
1 ATTCATCAACTCATGATGAATTCTC-TGGATTTGCACACATAGTGCCTGTACG-GCT
* * * *** * **
3657365 ATT-AT-TA--C-TGAT--ATAC-C--G--TTGCATCA-TTAGTGCTAATATGGTA
1 ATTCATCAACTCATGATGAATTCTCTGGATTTGCA-CACATAGTGCCTGTACGGCT
* * * * * * *
3657408 ATTTAACAACTTTC-T-ATTCATATTCAT-T-TATTAATGCACA-GTAGTACCTATACGG-T
1 ATTCATCAAC--TCATGA-TGA-ATTC-TCTGGATT--TGCACACATAGTGCCTGTACGGCT
* * * * * *
3657464 AAT--TCAA-TGCATGATGAATTCTATGGTTTTGCATACATAGTG-ATGGTACGACT
1 ATTCATCAACT-CATGATGAATTCTCTGGATTTGCACACATAGTGCCT-GTACGGCT
* * ***
3657517 ATTCATCAACTCATGATGAATTC-CGTGGATTTGCACACATAGTTCCGGTACAATT
1 ATTCATCAACTCATGATGAATTCTC-TGGATTTGCACACATAGTGCCTGTACGGCT
* * ** * *
3657572 ATTCATCAACTCATGATGAATTTTGTGGATTTATACACATAGTGCATGTACGACT
1 ATTCATCAACTCATGATGAATTCTCTGGATTTGCACACATAGTGCCTGTACGGCT
* * *
3657627 ATTCATCAACTCATGATGAATT-TCGTGAATTTGCATATATAGTGCCTGTACGGCT
1 ATTCATCAACTCATGATGAATTCTC-TGGATTTGCACACATAGTGCCTGTACGGCT
*
3657682 ATTCATTAACTCATGATGAATT-TC-GTGAGTTTGCACACATAGTGCCTGTACGGCT
1 ATTCATCAACTCATGATGAATTCTCTG-GA-TTTGCACACATAGTGCCTGTACGGCT
* * * * *
3657737 ATTCATCAACTCATGATGAATTTTGTTGAATTGCACACATAGTGCATGTACGGCT
1 ATTCATCAACTCATGATGAATTCTCTGGATTTGCACACATAGTGCCTGTACGGCT
* * * *
3657792 ATTCATCAACTCATGATGAATTC-CGTGAATTTACAAACATAGTGCATGTACGGCT
1 ATTCATCAACTCATGATGAATTCTC-TGGATTTGCACACATAGTGCCTGTACGGCT
* *
3657847 AGTCATCAACTCGTGATGAATTC-CATGGATTTGCACACATAGTGCCTGTA
1 ATTCATCAACTCATGATGAATTCTC-TGGATTTGCACACATAGTGCCTGTA
3657897 GTACACTTAG
Statistics
Matches: 847, Mismatches: 127, Indels: 102
0.79 0.12 0.09
Matches are distributed among these distances:
43 15 0.02
44 4 0.00
45 2 0.00
48 4 0.00
49 3 0.00
50 4 0.00
51 9 0.01
52 26 0.03
53 46 0.05
54 11 0.01
55 690 0.81
56 17 0.02
57 12 0.01
58 4 0.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCTCTGGATTTGCACACATAGTGCCTGTACGGCT
Found at i:3657312 original size:165 final size:165
Alignment explanation
Indices: 3656817--3657896 Score: 1027
Period size: 165 Copynumber: 6.6 Consensus size: 165
3656807 CTATACGATA
* * * * * *
3656817 ATTCATCACCTCATGATGAATACTC-TGGTTTTGTACACATAGTGTCGGTACGGCTATTCATCAA
1 ATTCATCAACTCATGATGAAT-TTCGTGGATTTGCACACATAGTGCCTGTACGGCTATTCATCAA
* * *
3656881 CTCATGATGAATTCTGTGGATTTGCACACATAGTGTCGGTACGGCTATTCATCAACTCATGATGA
65 CTCATGATGAATTCCGTGGATTTGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGA
* * * * **
3656946 ATTCCGTGGATTTGCATACATAGTGCCAATACGGCT
130 ATTCTGTGAATTTACACACATAGTGCCTGTACGGCT
*
3656982 ATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCCTGTACGGGCTATTCAT---
1 ATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCCTGTAC-GGCTATTCATCAA
* * * * * *
3657044 GTCATGATGAATTCTGTGAATTTGCACACATAGTGCATGTATGACTATTCATCAACTCATGATGA
65 CTCATGATGAATTCCGTGGATTTGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGA
* * * * *
3657109 ATTTTGTGAATTTGCATACATAATGCCTGTATGGCT
130 ATTCTGTGAATTTACACACATAGTGCCTGTACGGCT
*
3657145 ATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCCTATACGGCTATTCATCAAC
1 ATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCCTGTACGGCTATTCATCAAC
* * *
3657210 TCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGCTATTTATCAACTCATGACGAA
66 TCATGATGAATTCCGTGGATTTGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAA
* *
3657275 TTCTATGAATTTACACACATAGTGTCTGTACGGCT
131 TTCTGTGAATTTACACACATAGTGCCTGTACGGCT
* * * * * *
3657310 ATTCATTAACTCATGATGAATTTCGTGGATTTACACACATAGTGTCTGTA-GTACAATT-AT-TA
1 ATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCCTGTACG-GCTATTCATCAA
* * * * * *
3657372 --C-TGAT--ATACC---G--TTGCATCA-TTAGTG-CTAATATGG-TAATTTAACAACTTTC-T
65 CTCATGATGAATTCCGTGGATTTGCA-CACATAGTGCCT-GTACGGCT-ATTCATCAAC--TCAT
* * * ** * *
3657423 -ATTCATATTCAT-T-TATTAATGCACAGTAGTACCTATACGG-T
125 GA-TGA-ATTC-TGTGAATTTACACACA-TAGTGCCTGTACGGCT
* * * * * *
3657464 AAT--TCAA-TGCATGATGAA-TTCTATGGTTTTGCATACATAGTG-ATGGTACGACTATTCATC
1 ATTCATCAACT-CATGATGAATTTC-GTGGATTTGCACACATAGTGCCT-GTACGGCTATTCATC
* * ***
3657524 AACTCATGATGAATTCCGTGGATTTGCACACATAGTTCCGGTACAATTATTCATCAACTCATGAT
63 AACTCATGATGAATTCCGTGGATTTGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGAT
* * * * *
3657589 GAATTTTGTGGATTTATACACATAGTGCATGTACGACT
128 GAATTCTGTGAATTTACACACATAGTGCCTGTACGGCT
* * * *
3657627 ATTCATCAACTCATGATGAATTTCGTGAATTTGCATATATAGTGCCTGTACGGCTATTCATTAAC
1 ATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCCTGTACGGCTATTCATCAAC
*
3657692 TCATGATGAATTTCGT-GAGTTTGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGA
66 TCATGATGAATTCCGTGGA-TTTGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGA
* * *
3657756 ATTTTGTTGAA-TTGCACACATAGTGCATGTACGGCT
130 ATTCTG-TGAATTTACACACATAGTGCCTGTACGGCT
* * * * * *
3657792 ATTCATCAACTCATGATGAATTCCGTGAATTTACAAACATAGTGCATGTACGGCTAGTCATCAAC
1 ATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCCTGTACGGCTATTCATCAAC
* *
3657857 TCGTGATGAATTCCATGGATTTGCACACATAGTGCCTGTA
66 TCATGATGAATTCCGTGGATTTGCACACATAGTGCCTGTA
3657897 GTACACTTAG
Statistics
Matches: 753, Mismatches: 115, Indels: 94
0.78 0.12 0.10
Matches are distributed among these distances:
151 5 0.01
152 38 0.05
153 27 0.04
154 16 0.02
155 19 0.03
156 2 0.00
157 4 0.01
158 4 0.01
159 4 0.01
160 4 0.01
161 2 0.00
162 27 0.04
163 154 0.20
164 26 0.03
165 401 0.53
166 20 0.03
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (165 bp):
ATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCCTGTACGGCTATTCATCAAC
TCATGATGAATTCCGTGGATTTGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAA
TTCTGTGAATTTACACACATAGTGCCTGTACGGCT
Found at i:3658347 original size:20 final size:20
Alignment explanation
Indices: 3658311--3658362 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3658301 ATTTCGAAAT
* *
3658311 GGTATCGACAC-CTTCCCTTT
1 GGTATCGATACTC-TCCCTTC
*
3658331 GTTATCGATACTCTCCCTTC
1 GGTATCGATACTCTCCCTTC
3658351 GGTATCGATACT
1 GGTATCGATACT
3658363 GATTGAATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.17, C:0.31, G:0.15, T:0.37
Consensus pattern (20 bp):
GGTATCGATACTCTCCCTTC
Found at i:3658839 original size:32 final size:33
Alignment explanation
Indices: 3658777--3658861 Score: 120
Period size: 33 Copynumber: 2.5 Consensus size: 33
3658767 AACCTTATAC
*
3658777 TTTCTCTTTATAATTTTTATAATAATATTTTATT
1 TTTCT-TTTTTAATTTTTATAATAATATTTTATT
3658811 TTTCTTTTTTAATTTTTCATAAT-A-ATTTTATT
1 TTTCTTTTTTAATTTTT-ATAATAATATTTTATT
3658843 TTTCTTTTTATAATTTTTA
1 TTTCTTTTT-TAATTTTTA
3658862 ATTACATATA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
32 18 0.38
33 20 0.42
34 10 0.21
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (33 bp):
TTTCTTTTTTAATTTTTATAATAATATTTTATT
Found at i:3658851 original size:31 final size:32
Alignment explanation
Indices: 3658781--3658861 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 32
3658771 TTATACTTTC
*
3658781 TCTTTATAATTTTTATAATAATATTTTATTTT
1 TCTTTTTAATTTTTATAATAATATTTTATTTT
3658813 TCTTTTTTAATTTTTCATAAT-A-ATTTTATTTT
1 TC-TTTTTAATTTTT-ATAATAATATTTTATTTT
3658845 TCTTTTTATAATTTTTA
1 TC-TTTT-TAATTTTTA
3658862 ATTACATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
32 20 0.44
33 20 0.44
34 5 0.11
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (32 bp):
TCTTTTTAATTTTTATAATAATATTTTATTTT
Found at i:3662852 original size:16 final size:18
Alignment explanation
Indices: 3662820--3662857 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3662810 AGAACTTTGA
*
3662820 AAAATATGTAAACAAAT-
1 AAAATATGTAAAAAAATG
3662837 AAAATAT-TAAAAAAATG
1 AAAATATGTAAAAAAATG
3662854 AAAA
1 AAAA
3662858 ATCTTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAATATGTAAAAAAATG
Found at i:3665007 original size:29 final size:27
Alignment explanation
Indices: 3664953--3665007 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
3664943 AAGAGATTGA
*
3664953 AGATGAAAGGAGTGTGTTGTGTGTAAG
1 AGATGAAAGGAGTGTGTTGTATGTAAG
3664980 AGATGAAAGGAGTGTGTTATGTATGTAA
1 AGATGAAAGGAGTGTG-T-TGTATGTAA
3665008 ATTTTTTAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 16 0.64
28 1 0.04
29 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.31
Consensus pattern (27 bp):
AGATGAAAGGAGTGTGTTGTATGTAAG
Done.