Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007918.1 Hibiscus syriacus cultivar Beakdansim tig00110321_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: 2302251
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:2228593 original size:23 final size:21
Alignment explanation
Indices: 2228559--2228608 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2228549 ATTATTATAA
2228559 TATTTTA--AAAATAATAATAT
1 TATTTTATTAAAA-AATAATAT
2228579 TATTTTATT-AAAAATAATAT
1 TATTTTATTAAAAAATAATAT
2228599 TATTTTATTA
1 TATTTTATTA
2228609 TATTTGATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTTATTAAAAAATAATAT
Found at i:2228606 original size:20 final size:20
Alignment explanation
Indices: 2228571--2228608 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2228561 TTTTAAAAAT
2228571 AATAATATTATTTTATTAAA
1 AATAATATTATTTTATTAAA
2228591 AATAATATTATTTTATTA
1 AATAATATTATTTTATTA
2228609 TATTTGATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATAATATTATTTTATTAAA
Found at i:2228609 original size:23 final size:24
Alignment explanation
Indices: 2228559--2228609 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
2228549 ATTATTATAA
2228559 TATT-TTAAAAATAATAATATTAT
1 TATTATTAAAAATAATAATATTAT
*
2228582 T-TTATTAAAAATAATATTATT-T
1 TATTATTAAAAATAATAATATTAT
2228604 TATTAT
1 TATTAT
2228610 ATTTGATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTATTAAAAATAATAATATTAT
Found at i:2228685 original size:24 final size:24
Alignment explanation
Indices: 2228635--2228685 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2228625 TTATGTTGTA
** *
2228635 ATTATGATTATTTTTCATCACTTT
1 ATTATGATTATTTTTCAAAACTAT
*
2228659 ATTATGATTATTTTTTAAAACTAT
1 ATTATGATTATTTTTCAAAACTAT
2228683 ATT
1 ATT
2228686 GTAATTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (24 bp):
ATTATGATTATTTTTCAAAACTAT
Found at i:2228698 original size:2 final size:2
Alignment explanation
Indices: 2228691--2228715 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2228681 ATATTGTAAT
2228691 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2228716 TATTTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2228946 original size:21 final size:21
Alignment explanation
Indices: 2228904--2228947 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2228894 TCAGTAAAAA
* *
2228904 TTACCTAAAACATTATTATTT
1 TTACCTAAAACATCAATATTT
*
2228925 TTACCTAAAACATCAATGTTT
1 TTACCTAAAACATCAATATTT
2228946 TT
1 TT
2228948 TAACATTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.02, T:0.45
Consensus pattern (21 bp):
TTACCTAAAACATCAATATTT
Found at i:2229257 original size:31 final size:30
Alignment explanation
Indices: 2229220--2229327 Score: 82
Period size: 30 Copynumber: 3.6 Consensus size: 30
2229210 TAAAAAATAA
*
2229220 AAAATATAATTTATAATAATTTTATT-TTAAT
1 AAAATATAA-TAATAATAATTTT-TTATTAAT
* *
2229251 AAAATATAATAATCATAATTTTTTATTTAT
1 AAAATATAATAATAATAATTTTTTATTAAT
* *
2229281 AAAAT-T-ATAGAT-ATAATATTTTAATAAT
1 AAAATATAATA-ATAATAATTTTTTATTAAT
2229309 AATAAT-TACATACATAATA
1 AA-AATATA-ATA-ATAATA
2229328 TTAAATAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
28 18 0.28
29 9 0.14
30 20 0.31
31 14 0.22
32 3 0.05
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (30 bp):
AAAATATAATAATAATAATTTTTTATTAAT
Found at i:2229325 original size:29 final size:28
Alignment explanation
Indices: 2229242--2229329 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
2229232 ATAATAATTT
*
2229242 TATTTTAATAA-AATATAATAAT-CATAA
1 TATTTTAATAATAATA-ATTAATACATAA
* * * * *
2229269 TTTTTTATTTATAA-AATTATAGATATAA
1 TATTTTAATAATAATAATTA-ATACATAA
2229297 TATTTTAATAATAATAATTACATACATAA
1 TATTTTAATAATAATAATTA-ATACATAA
2229326 TATT
1 TATT
2229330 AAATAAATTA
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
26 3 0.07
27 10 0.22
28 17 0.38
29 15 0.33
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (28 bp):
TATTTTAATAATAATAATTAATACATAA
Found at i:2229397 original size:24 final size:24
Alignment explanation
Indices: 2229346--2229397 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2229336 ATTATTCTAA
2229346 TATT-TTAAAAATAATATTATTAT
1 TATTGTTAAAAATAATATTATTAT
*
2229369 T-TTGTTAATAAATAATATTGTT-T
1 TATTGTTAA-AAATAATATTATTAT
2229392 TATTGT
1 TATTGT
2229398 ATTTGATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 7 0.28
24 16 0.64
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (24 bp):
TATTGTTAAAAATAATATTATTAT
Found at i:2229668 original size:23 final size:23
Alignment explanation
Indices: 2229642--2229692 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
2229632 TAAAAAATTA
**
2229642 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
2229665 ACCTATTACGTTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
2229688 ACCTA
1 ACCTA
2229693 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:2229700 original size:23 final size:23
Alignment explanation
Indices: 2229652--2229701 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2229642 ACCTATTTTA
*
2229652 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
*
2229675 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
2229698 TTAT
1 TTAT
2229702 TGTGCTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:2229793 original size:23 final size:23
Alignment explanation
Indices: 2229729--2229793 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
2229719 CCAGTAATTA
** * *
2229729 ACCTATTTTATTATATAAATGCT
1 ACCTATTACATTATATAAGTACT
*
2229752 ACTTATTACATTATATAAGTACT
1 ACCTATTACATTATATAAGTACT
2229775 ACCTATTACATTATATAAG
1 ACCTATTACATTATATAAG
2229794 CGATACCTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (23 bp):
ACCTATTACATTATATAAGTACT
Found at i:2229800 original size:23 final size:23
Alignment explanation
Indices: 2229750--2229802 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2229740 TATATAAATG
* *
2229750 CTACTTATTACATTATATAAGTA
1 CTACCTATTACATTATATAAGGA
2229773 CTACCTATTACATTATATAAGCGA
1 CTACCTATTACATTATATAAG-GA
2229797 -TACCTA
1 CTACCTA
2229803 ATATGTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (23 bp):
CTACCTATTACATTATATAAGGA
Found at i:2229846 original size:110 final size:110
Alignment explanation
Indices: 2229642--2229912 Score: 434
Period size: 110 Copynumber: 2.5 Consensus size: 110
2229632 TAAAAAATTA
** * *
2229642 ACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGC
1 ACCTATTACATTATATAAGTGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGC
* **
2229707 TTGATAATGTTTCCAGTAATTAACCTATTTTATTATATAAATGCT
66 TTGATAATGTTTCCAGTAATTAACATATTTTATTATATAAACCCT
* * *
2229752 ACTTATTACATTATATAAGTACTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTGC
1 ACCTATTACATTATATAAGTGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGC
* *
2229817 TTGATAATGTTTCTAGTAATTAACATATTTTATTATATAAGCCCT
66 TTGATAATGTTTCCAGTAATTAACATATTTTATTATATAAACCCT
2229862 ACCTATTACATTATATAAGTGCTACCTATTACATTATATAAGCGCTACCTA
1 ACCTATTACATTATATAAGTGCTACCTATTACATTATATAAGCGCTACCTA
2229913 TTACATCATA
Statistics
Matches: 146, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
110 146 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (110 bp):
ACCTATTACATTATATAAGTGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGC
TTGATAATGTTTCCAGTAATTAACATATTTTATTATATAAACCCT
Found at i:2229874 original size:23 final size:23
Alignment explanation
Indices: 2229848--2229923 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
2229838 AACATATTTT
*
2229848 ATTATATAAGCCCTACCTATTAC
1 ATTATATAAGCGCTACCTATTAC
*
2229871 ATTATATAAGTGCTACCTATTAC
1 ATTATATAAGCGCTACCTATTAC
2229894 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTATTAC
*
2229917 ATCATAT
1 ATTATAT
2229924 TTTTACATGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.37
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTATTAC
Found at i:2231758 original size:17 final size:18
Alignment explanation
Indices: 2231721--2231761 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2231711 ATATTATGTA
*
2231721 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
2231739 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
2231756 TTTACT
1 TTTACT
2231762 AATATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:2234358 original size:29 final size:29
Alignment explanation
Indices: 2234312--2234390 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
2234302 TACTGCTACG
*
2234312 GGTGTTAGATCGAGAAATATAATATGACC
1 GGTGTTAGATCGAAAAATATAATATGACC
* *
2234341 GGTGTTAGATCGAAAAATATAATCTGATC
1 GGTGTTAGATCGAAAAATATAATATGACC
*
2234370 GGTGTTAGATCGATAAATATA
1 GGTGTTAGATCGAAAAATATA
2234391 CCGATTACCG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (29 bp):
GGTGTTAGATCGAAAAATATAATATGACC
Found at i:2238048 original size:16 final size:16
Alignment explanation
Indices: 2238023--2238053 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2238013 GTGGGTGTTT
2238023 GATTTCTTTTAATTTC
1 GATTTCTTTTAATTTC
*
2238039 GATTTTTTTTAATTT
1 GATTTCTTTTAATTT
2238054 GTAGTTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.68
Consensus pattern (16 bp):
GATTTCTTTTAATTTC
Found at i:2242735 original size:64 final size:64
Alignment explanation
Indices: 2242659--2242787 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
2242649 TCCGTTTACA
2242659 GAGAAACAACAATCTGGTTGTATATCTGATATCCATGCGTGGCAATCGGCACCTTTACGATTGT
1 GAGAAACAACAATCTGGTTGTATATCTGATATCCATGCGTGGCAATCGGCACCTTTACGATTGT
2242723 GAGAAACAACAATCTGGTTGTATATCTGATATCCATGCGTGGCAATCGGCACCTTTACGATTGT
1 GAGAAACAACAATCTGGTTGTATATCTGATATCCATGCGTGGCAATCGGCACCTTTACGATTGT
2242787 G
1 G
2242788 TAAATTTGAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.29
Consensus pattern (64 bp):
GAGAAACAACAATCTGGTTGTATATCTGATATCCATGCGTGGCAATCGGCACCTTTACGATTGT
Found at i:2246320 original size:26 final size:24
Alignment explanation
Indices: 2246259--2246320 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 24
2246249 CATTTTAATC
2246259 AAATAT-TAATTATTAAAATATTTA
1 AAATATAT-ATTATTAAAATATTTA
*
2246283 AAATATAT-TTATTAATAT-TTCTA
1 AAATATATATTATTAAAATATT-TA
2246306 ATAATATAATATTAT
1 A-AATAT-ATATTAT
2246321 ATTTTTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
22 2 0.06
23 12 0.38
24 11 0.34
25 3 0.09
26 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAATATATATTATTAAAATATTTA
Found at i:2246497 original size:54 final size:50
Alignment explanation
Indices: 2246388--2246487 Score: 121
Period size: 54 Copynumber: 1.9 Consensus size: 50
2246378 TTTTATTTTA
* *
2246388 ATAATATAATAAATTATTAATAAATTATATTATTTATTAATTTCATAGAC
1 ATAATATAATAAATTATTAATAAATAATATTATTTATTAATTTAATAGAC
*
2246438 ATAATATTATTAAATTATTAATAATGAATAATATTATTTA-TATATTTAAT
1 ATAATA-TAATAAATTATTAAT-A--AATAATATTATTTATTA-ATTTAAT
2246488 TAATATAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
50 6 0.14
51 14 0.33
52 1 0.02
53 2 0.05
54 19 0.45
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (50 bp):
ATAATATAATAAATTATTAATAAATAATATTATTTATTAATTTAATAGAC
Found at i:2246522 original size:13 final size:13
Alignment explanation
Indices: 2246477--2246549 Score: 64
Period size: 13 Copynumber: 5.8 Consensus size: 13
2246467 AATATTATTT
2246477 ATATATTTAATTA
1 ATATATTTAATTA
*
2246490 ATATA-ATAATCTA
1 ATATATTTAAT-TA
*
2246503 ATAATATTTAATAA
1 AT-ATATTTAATTA
2246517 ATATATTTAA--A
1 ATATATTTAATTA
*
2246528 ATATA-CTAATTA
1 ATATATTTAATTA
*
2246540 ATATTTTTAA
1 ATATATTTAA
2246550 AATATAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
10 3 0.06
11 6 0.12
12 9 0.19
13 20 0.42
14 6 0.12
15 4 0.08
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATATTTAATTA
Found at i:2246537 original size:23 final size:23
Alignment explanation
Indices: 2246511--2246555 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2246501 TAATAATATT
2246511 TAATAAATATATTTAAAATATAC
1 TAATAAATATATTTAAAATATAC
* *
2246534 TAATTAATATTTTTAAAATATA
1 TAATAAATATATTTAAAATATA
2246556 ATATAACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAC
Found at i:2246631 original size:29 final size:29
Alignment explanation
Indices: 2246595--2246671 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
2246585 AATATAATTT
**
2246595 ATAATATTTTTATTTCAAT-AAA-TATACCA
1 ATAATATTTTTA-TT-AATAAAATTATAAAA
2246624 ATAATATTTTTATTAATAAAATTATAAAA
1 ATAATATTTTTATTAATAAAATTATAAAA
*
2246653 ATAATA-TTTTAATAATAAA
1 ATAATATTTTTATTAATAAA
2246672 TAAATTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 3 0.07
28 17 0.40
29 23 0.53
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (29 bp):
ATAATATTTTTATTAATAAAATTATAAAA
Found at i:2246669 original size:14 final size:14
Alignment explanation
Indices: 2246623--2246670 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2246613 TAAATATACC
*
2246623 AATAATATTTTTATT
1 AATAATA-TTTTAAT
* * *
2246638 AATAAAATTATAAA
1 AATAATATTTTAAT
2246652 AATAATATTTTAAT
1 AATAATATTTTAAT
2246666 AATAA
1 AATAA
2246671 ATAAATTATT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 20 0.77
15 6 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATAATATTTTAAT
Found at i:2246813 original size:24 final size:23
Alignment explanation
Indices: 2246785--2246841 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
2246775 CAATTAGTGA
2246785 AAAAAATATTTAAACACCATTTTT
1 AAAAAATATTTAAA-ACCATTTTT
* * **
2246809 CAAAAAT-TATAAAACGTTTTTT
1 AAAAAATATTTAAAACCATTTTT
2246831 AAAAAATATTT
1 AAAAAATATTT
2246842 TTCAAAACAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
22 13 0.50
23 7 0.27
24 6 0.23
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.39
Consensus pattern (23 bp):
AAAAAATATTTAAAACCATTTTT
Found at i:2252991 original size:13 final size:14
Alignment explanation
Indices: 2252973--2253002 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2252963 TATCATATTC
2252973 CACATA-TTCATGT
1 CACATAGTTCATGT
2252986 CACATAGTTCATGT
1 CACATAGTTCATGT
2253000 CAC
1 CAC
2253003 TTGCATGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (14 bp):
CACATAGTTCATGT
Found at i:2258287 original size:9 final size:9
Alignment explanation
Indices: 2258273--2258309 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
2258263 TTATATGATA
2258273 ATATAATTT
1 ATATAATTT
2258282 ATATAATTT
1 ATATAATTT
*
2258291 A-AAAATTT
1 ATATAATTT
2258299 ATA-AATTT
1 ATATAATTT
2258307 ATA
1 ATA
2258310 AATATGATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 15 0.58
9 11 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
ATATAATTT
Found at i:2258299 original size:8 final size:8
Alignment explanation
Indices: 2258277--2258312 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
2258267 ATGATAATAT
2258277 AATTTATA
1 AATTTATA
*
2258285 TAATTTAAA
1 -AATTTATA
2258294 AATTTATA
1 AATTTATA
2258302 AATTTATA
1 AATTTATA
2258310 AAT
1 AAT
2258313 ATGATGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
AATTTATA
Found at i:2263403 original size:16 final size:17
Alignment explanation
Indices: 2263384--2263416 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2263374 ATTAAATAAA
2263384 AATAAAAAA-AATATTT
1 AATAAAAAATAATATTT
2263400 AATAAAAAATAATATTT
1 AATAAAAAATAATATTT
2263417 TATATCACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAAAAAATAATATTT
Found at i:2265773 original size:19 final size:19
Alignment explanation
Indices: 2265749--2265785 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2265739 ATAACCAATA
*
2265749 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
2265768 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
2265786 CATTATCGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:2265836 original size:20 final size:20
Alignment explanation
Indices: 2265811--2265876 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
2265801 GTTTCCAGAT
*
2265811 TCGCAACTCGATTTTGACTA
1 TCGCAACTCGATTATGACTA
* *
2265831 TCGCAA-TGCGAATATGTA-AA
1 TCGCAACT-CGATTATG-ACTA
* *
2265851 TCGCAACGCGATTCTGACTA
1 TCGCAACTCGATTATGACTA
2265871 TCGCAA
1 TCGCAA
2265877 TGCGATAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 2 0.06
20 32 0.91
21 1 0.03
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (20 bp):
TCGCAACTCGATTATGACTA
Found at i:2265855 original size:40 final size:40
Alignment explanation
Indices: 2265811--2265955 Score: 152
Period size: 40 Copynumber: 3.5 Consensus size: 40
2265801 GTTTCCAGAT
* *
2265811 TCGCAACTCGATTTTGACTATCGCAATGCGAATATGTAAA
1 TCGCAACGCGATTCTGACTATCGCAATGCGAATATGTAAA
**
2265851 TCGCAACGCGATTCTGACTATCGCAATGCG-ATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAATGCGAAT-ATGTA-AA
** *
2265892 TCGCAACGCGATAAT-ACATAATCGCAACGCGATAATATGT-AA
1 TCGCAACGCGATTCTGAC-T-ATCGCAATGCG--AATATGTAAA
2265934 TCGCAACGCGATTCTGACTATC
1 TCGCAACGCGATTCTGACTATC
2265956 TCGTTGCGAT
Statistics
Matches: 86, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
39 2 0.02
40 33 0.38
41 19 0.22
42 26 0.30
43 2 0.02
44 2 0.02
45 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (40 bp):
TCGCAACGCGATTCTGACTATCGCAATGCGAATATGTAAA
Found at i:2265881 original size:20 final size:20
Alignment explanation
Indices: 2265819--2265955 Score: 68
Period size: 21 Copynumber: 6.7 Consensus size: 20
2265809 ATTCGCAACT
*
2265819 CGATTTTGACTATCGCAATG
1 CGATTATGACTATCGCAATG
* * *
2265839 CGAATATGTA-AATCGCAACG
1 CGATTATG-ACTATCGCAATG
*
2265859 CGATTCTGACTATCGCAATG
1 CGATTATGACTATCGCAATG
* *
2265879 CGATAAT-ACATAATCGCAACG
1 CGATTATGAC-T-ATCGCAATG
* *
2265900 CGATAAT-ACATAATCGCAACG
1 CGATTATGAC-T-ATCGCAATG
*
2265921 CGATAATATG--TAATCGCAACG
1 CGAT--TATGACT-ATCGCAATG
*
2265942 CGATTCTGACTATC
1 CGATTATGACTATC
2265956 TCGTTGCGAT
Statistics
Matches: 95, Mismatches: 13, Indels: 18
0.75 0.10 0.14
Matches are distributed among these distances:
19 6 0.06
20 37 0.39
21 50 0.53
23 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (20 bp):
CGATTATGACTATCGCAATG
Found at i:2265896 original size:21 final size:21
Alignment explanation
Indices: 2265849--2265945 Score: 126
Period size: 21 Copynumber: 4.7 Consensus size: 21
2265839 CGAATATGTA
**
2265849 AATCGCAACGCGATTCTGAC-T
1 AATCGCAACGCGATAAT-ACAT
*
2265870 -ATCGCAATGCGATAATACAT
1 AATCGCAACGCGATAATACAT
2265890 AATCGCAACGCGATAATACAT
1 AATCGCAACGCGATAATACAT
**
2265911 AATCGCAACGCGATAATATGT
1 AATCGCAACGCGATAATACAT
2265932 AATCGCAACGCGAT
1 AATCGCAACGCGAT
2265946 TCTGACTATC
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 2 0.03
20 14 0.21
21 52 0.76
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATAATACAT
Found at i:2266166 original size:22 final size:22
Alignment explanation
Indices: 2266136--2266195 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
2266126 GGCGACATCT
*
2266136 GTCCACATCTCTGACGAAATCC
1 GTCCACATCTCCGACGAAATCC
* *
2266158 GTCCCCATCTCCGGCGAAATCC
1 GTCCACATCTCCGACGAAATCC
*
2266180 GT-C-TATCTCCGACGAA
1 GTCCACATCTCCGACGAA
2266196 GTGTGCAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 11 0.33
21 1 0.03
22 21 0.64
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.22
Consensus pattern (22 bp):
GTCCACATCTCCGACGAAATCC
Found at i:2266960 original size:14 final size:14
Alignment explanation
Indices: 2266941--2266977 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2266931 GCTTGTTTAA
2266941 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
2266955 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
2266969 TTGATTTGT
1 TTGATTTGT
2266978 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:2267139 original size:20 final size:20
Alignment explanation
Indices: 2267114--2267209 Score: 156
Period size: 20 Copynumber: 4.8 Consensus size: 20
2267104 GCGATTTTCT
*
2267114 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
*
2267134 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
2267154 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
*
2267174 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
2267194 CGTTGCGATAGTCAAA
1 CGTTGCGATAGTCAAA
2267210 ATCGTAATGC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:2267140 original size:34 final size:36
Alignment explanation
Indices: 2267082--2267209 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 36
2267072 GCAAAAGACT
* * * * *
2267082 TTGCGATAGTCTAATACGCTTTGCGAT-T-TTCTCG
1 TTGCGATAGTCAAATTCCCGTTGCGATATATTCACG
2267116 TTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCACG
1 TTGCGATAGTCAAATTCCCGTTGCGAT-AT---ATTCACG
2267156 TTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCACG
1 TTGCGATAGTCAAATTCCCGTTGCGAT-AT---ATTCACG
2267196 TTGCGATAGTCAAA
1 TTGCGATAGTCAAA
2267210 ATCGTAATGC
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
34 23 0.28
36 1 0.01
40 59 0.71
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (36 bp):
TTGCGATAGTCAAATTCCCGTTGCGATATATTCACG
Found at i:2267169 original size:40 final size:40
Alignment explanation
Indices: 2267114--2267209 Score: 192
Period size: 40 Copynumber: 2.4 Consensus size: 40
2267104 GCGATTTTCT
2267114 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCA
2267154 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCA
2267194 CGTTGCGATAGTCAAA
1 CGTTGCGATAGTCAAA
2267210 ATCGTAATGC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (40 bp):
CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCA
Found at i:2267341 original size:20 final size:20
Alignment explanation
Indices: 2267298--2267343 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2267288 ATTGCGATAA
*
2267298 TCAAATTCACGTTGCGATAG
1 TCAAATTCACGTTGCAATAG
** *
2267318 TCAAATTCGTGTTGCAATAT
1 TCAAATTCACGTTGCAATAG
2267338 TCAAAT
1 TCAAAT
2267344 GAATGTGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (20 bp):
TCAAATTCACGTTGCAATAG
Found at i:2267566 original size:140 final size:140
Alignment explanation
Indices: 2267314--2267596 Score: 494
Period size: 140 Copynumber: 2.0 Consensus size: 140
2267304 TCACGTTGCG
*
2267314 ATAGTCAAATTCGTGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCA
1 ATAGTCAAATTCGTGTTGCAATATTCAAATGAATGTGTAACAAGTGATAACAACTAAACAGATCA
*
2267379 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAAATCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
2267444 AATACACATA
131 AATACACATA
* * * *
2267454 ATAGTTAAATTCGTGTTGCGATATTCAAATGAATGTGTAACAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGTGTTGCAATATTCAAATGAATGTGTAACAAGTGATAACAACTAAACAGATCA
* *
2267519 TAGCAATGTTCAAAATCAAGTTACTAATATATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAAATCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
2267584 AATACACATA
131 AATACACATA
2267594 ATA
1 ATA
2267597 AAACGTTTGC
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
140 135 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGTGTTGCAATATTCAAATGAATGTGTAACAAGTGATAACAACTAAACAGATCA
TAGCAATGTTCAAAATCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:2269734 original size:14 final size:14
Alignment explanation
Indices: 2269715--2269751 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2269705 TCCCGTGGCA
2269715 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
2269729 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
2269743 TTCTTCTTC
1 TT-TTCTTC
2269752 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:2269975 original size:24 final size:24
Alignment explanation
Indices: 2269941--2269993 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
2269931 CTGAAACATC
2269941 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2269965 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2269989 ATCAA
1 ATCAA
2269994 GTTTCGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2270855 original size:21 final size:20
Alignment explanation
Indices: 2270829--2270904 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 20
2270819 GAAAGTCAGA
2270829 ATCGCGTTGCGATTACGTATT
1 ATCGCGTTGCGATTA-GTATT
2270850 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTA-GTATT
*** *
2270871 ATCATATTGCGA-TAGTCATA
1 ATCGCGTTGCGATTAGT-ATT
2270891 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
2270905 TACATATTCG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 13 0.29
21 30 0.67
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (20 bp):
ATCGCGTTGCGATTAGTATT
Found at i:2270910 original size:20 final size:20
Alignment explanation
Indices: 2270887--2270925 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2270877 TTGCGATAGT
*
2270887 CATAATCGCGTTGCGATTTA
1 CATAATCGCATTGCGATTTA
*
2270907 CATATTCGCATTGCGATTT
1 CATAATCGCATTGCGATTT
2270926 TCTAAAATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
CATAATCGCATTGCGATTTA
Found at i:2270985 original size:41 final size:41
Alignment explanation
Indices: 2270878--2270993 Score: 99
Period size: 41 Copynumber: 2.8 Consensus size: 41
2270868 ATTATCATAT
* ** * * *
2270878 TGCGATAGTCATAATCGCGTTGCG-ATTTACATATTCGCAT
1 TGCGATAGTCAAAATCGCGTTGCGAATTTGGAAAATCGCAA
** ****
2270918 TGCGATTTTCTAAAATCGTAACGCGAATTTGGAAAATCGCAA
1 TGCGATAGTC-AAAATCGCGTTGCGAATTTGGAAAATCGCAA
*
2270960 TGCGATAGTCAAAATCGCGTTGCGAATCTGGAAA
1 TGCGATAGTCAAAATCGCGTTGCGAATTTGGAAA
2270994 CTGATTTGCG
Statistics
Matches: 55, Mismatches: 19, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
40 8 0.15
41 28 0.51
42 19 0.35
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (41 bp):
TGCGATAGTCAAAATCGCGTTGCGAATTTGGAAAATCGCAA
Found at i:2271022 original size:20 final size:19
Alignment explanation
Indices: 2270999--2271044 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2270989 GGAAACTGAT
* *
2270999 TTGCGATAATGGAGATCGCG
1 TTGCGAT-ATAGAGATCGCA
*
2271019 TTGCGATTTAGAGATCGCA
1 TTGCGATATAGAGATCGCA
2271038 TTGCGAT
1 TTGCGAT
2271045 TTTATTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATATAGAGATCGCA
Found at i:2271034 original size:19 final size:19
Alignment explanation
Indices: 2271010--2271046 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2271000 TGCGATAATG
*
2271010 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
2271029 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
2271047 TATTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:2271299 original size:2 final size:2
Alignment explanation
Indices: 2271292--2271330 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2271282 AATGGAACTT
2271292 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2271331 CGTGGATGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2275322 original size:15 final size:15
Alignment explanation
Indices: 2275302--2275331 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2275292 ATATCACCGA
2275302 TATTTAAATTTAATT
1 TATTTAAATTTAATT
2275317 TATTTAAATTTAATT
1 TATTTAAATTTAATT
2275332 GTTTGGTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTAAATTTAATT
Found at i:2279055 original size:23 final size:23
Alignment explanation
Indices: 2279029--2279081 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
2279019 AATGCACTGA
2279029 AGTGCCACGTAGAATTGCACCGT
1 AGTGCCACGTAGAATTGCACCGT
*
2279052 AGTGCCGCGTAGAATTGCACCGT
1 AGTGCCACGTAGAATTGCACCGT
2279075 AGTGCCA
1 AGTGCCA
2279082 TATAATAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (23 bp):
AGTGCCACGTAGAATTGCACCGT
Found at i:2281805 original size:49 final size:49
Alignment explanation
Indices: 2281745--2281909 Score: 285
Period size: 49 Copynumber: 3.4 Consensus size: 49
2281735 TACATCTGTA
*
2281745 ACGTCAGACGTGTTAAATCATCATCAATCGTAGCACCACCGTCACAAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCACCGTCACAAAG
*
2281794 ACGTCAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACAAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCACCGTCACAAAG
* **
2281843 ACGTCAGACGTGCTAAATCATCATCAATAGTAGCACCATAGTCACAAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCACCGTCACAAAG
2281892 ACGTCAGACGTGCTAAAT
1 ACGTCAGACGTGCTAAAT
2281910 GCTCCACCTT
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 110 1.00
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.20
Consensus pattern (49 bp):
ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCACCGTCACAAAG
Found at i:2282045 original size:53 final size:53
Alignment explanation
Indices: 2281972--2282078 Score: 137
Period size: 53 Copynumber: 2.0 Consensus size: 53
2281962 TAAATCATTT
* * * *
2281972 ATCATTCACCTATCAGAATCTTTTTCAAATATCATC-AAAATCAAGTATCATAC
1 ATCATTCACCTATCAAAATCTTTTT-AAACATCAACAAAAATCAAGTATAATAC
*
2282025 ATCATTCA-CTCATCAAAATCTTTTTAAACATTAACAAAAATCAAGTATAATAC
1 ATCATTCACCT-ATCAAAATCTTTTTAAACATCAACAAAAATCAAGTATAATAC
2282078 A
1 A
2282079 ATATAAATCT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
52 9 0.19
53 38 0.81
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.33
Consensus pattern (53 bp):
ATCATTCACCTATCAAAATCTTTTTAAACATCAACAAAAATCAAGTATAATAC
Found at i:2289254 original size:49 final size:49
Alignment explanation
Indices: 2289196--2289360 Score: 260
Period size: 49 Copynumber: 3.4 Consensus size: 49
2289186 TACATCTGTA
*
2289196 ACGTCAGACGTGTTAAATCATCATCAATCGTAGCACCACCATCACAAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCACCATCACAAAG
* * *
2289245 ACGTCAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACATAG
1 ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCACCATCACAAAG
* *
2289294 ACGTCAGACATGCTAAATCATCATCAATCGTAGCACCA-TAGTCACAAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCACCA-TCACAAAG
2289343 ACGTCAGACGTGCTAAAT
1 ACGTCAGACGTGCTAAAT
2289361 GCTCCACCTC
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
49 105 1.00
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (49 bp):
ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCACCATCACAAAG
Found at i:2289318 original size:98 final size:100
Alignment explanation
Indices: 2289173--2289360 Score: 292
Period size: 98 Copynumber: 1.9 Consensus size: 100
2289163 ATACACATAA
* * * *
2289173 ATAGCACCACCGTTACATCTGTAACGTCAGACGTGTTAAATCATCATCAATCGTAGCACCACCA-
1 ATAGCACCACCGTCACATCAG-AACGTCAGACATGCTAAATCATCATCAATCGTAGCACCA-CAG
2289237 TCACAAAGACGTCAGACGTGCTAAATCATCATCAATC
64 TCACAAAGACGTCAGACGTGCTAAATCATCATCAATC
*
2289274 ATAGCACCACCGTCACAT-AG-ACGTCAGACATGCTAAATCATCATCAATCGTAGCACCATAGTC
1 ATAGCACCACCGTCACATCAGAACGTCAGACATGCTAAATCATCATCAATCGTAGCACCACAGTC
2289337 ACAAAGACGTCAGACGTGCTAAAT
66 ACAAAGACGTCAGACGTGCTAAAT
2289361 GCTCCACCTC
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
97 1 0.01
98 62 0.77
100 1 0.01
101 17 0.21
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (100 bp):
ATAGCACCACCGTCACATCAGAACGTCAGACATGCTAAATCATCATCAATCGTAGCACCACAGTC
ACAAAGACGTCAGACGTGCTAAATCATCATCAATC
Found at i:2289513 original size:52 final size:53
Alignment explanation
Indices: 2289423--2289528 Score: 128
Period size: 53 Copynumber: 2.0 Consensus size: 53
2289413 TAAATCATTT
* * * *
2289423 ATCATTCACCTATCAGAATTTTTTCAAATATCATC-AAAATCAAGTATCATAC
1 ATCATTCACCTATCAAAATTTTTTAAAATATCAACAAAAATCAAGTATAATAC
*
2289475 ATCATTCA-CTCATCAAAATCTTTTTAAAAT-TTAACAAAAATCAAGTATAATAC
1 ATCATTCACCT-ATCAAAAT-TTTTTAAAATATCAACAAAAATCAAGTATAATAC
2289528 A
1 A
2289529 ATATAAATCT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
51 2 0.04
52 18 0.39
53 26 0.57
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (53 bp):
ATCATTCACCTATCAAAATTTTTTAAAATATCAACAAAAATCAAGTATAATAC
Found at i:2291735 original size:645 final size:645
Alignment explanation
Indices: 2290505--2291796 Score: 2584
Period size: 645 Copynumber: 2.0 Consensus size: 645
2290495 AGTTGACTGA
2290505 CAGAATCTGTTTTGTGCAGAATCTGCTGCCCGTTTTTATAACCTTTTCTCGGTTAAAAATTCATA
1 CAGAATCTGTTTTGTGCAGAATCTGCTGCCCGTTTTTATAACCTTTTCTCGGTTAAAAATTCATA
2290570 TCTTGTTTTATACACCTTGAAACTGATCCCCGTTTGTTTTAAAAGAAACTAGATTGATATACGAA
66 TCTTGTTTTATACACCTTGAAACTGATCCCCGTTTGTTTTAAAAGAAACTAGATTGATATACGAA
2290635 CACAATATATAAAAATCACCTGCTAATCATTTTCATAGAATTTCTGGTGAATTTTCAAACTCACT
131 CACAATATATAAAAATCACCTGCTAATCATTTTCATAGAATTTCTGGTGAATTTTCAAACTCACT
2290700 GCCAAATTCAAAATCTAAACTGTTTTCATTAACTTCATCCTTAAATTCTTCATTAATCCTTACAA
196 GCCAAATTCAAAATCTAAACTGTTTTCATTAACTTCATCCTTAAATTCTTCATTAATCCTTACAA
2290765 CCAACTCTTTAAAATCACTTAACTCTTCATAATCCCTAAAACACAAGAAATCAACATCCCCTTCA
261 CCAACTCTTTAAAATCACTTAACTCTTCATAATCCCTAAAACACAAGAAATCAACATCCCCTTCA
2290830 TCAACTCAAGATAAATTTAAACCTAAACCATAACAATATTTATGTCAAATGAAAGAGAATTTCAT
326 TCAACTCAAGATAAATTTAAACCTAAACCATAACAATATTTATGTCAAATGAAAGAGAATTTCAT
2290895 GTAGGTTATTTATCCTTAATAACCTAACATAAAATTATAGTAAAAATATACCAAAAATAAAACTA
391 GTAGGTTATTTATCCTTAATAACCTAACATAAAATTATAGTAAAAATATACCAAAAATAAAACTA
2290960 GAGTTCTTACCTTTTTGAGCTTAAAGTTTCGGTCACTCTGGAGAAGAAGAAGCTGAGCTTTTCTC
456 GAGTTCTTACCTTTTTGAGCTTAAAGTTTCGGTCACTCTGGAGAAGAAGAAGCTGAGCTTTTCTC
2291025 TTTTCTTCAATTTACTAAACATCATCCCTTATTACACTTGTCACTACATAATAAAATGAATTTAA
521 TTTTCTTCAATTTACTAAACATCATCCCTTATTACACTTGTCACTACATAATAAAATGAATTTAA
2291090 AATTCATTTAATCCACTTTACCATTTTATCCCTAATAAAACTTAATAATTTCATCAATGG
586 AATTCATTTAATCCACTTTACCATTTTATCCCTAATAAAACTTAATAATTTCATCAATGG
2291150 CAGAATCTGTTTTGTGCAGAATCTGCTGCCCGTTTTTATAACCTTTTCTCGGTTAAAAATTCATA
1 CAGAATCTGTTTTGTGCAGAATCTGCTGCCCGTTTTTATAACCTTTTCTCGGTTAAAAATTCATA
2291215 TCTTGTTTTATACACCTTGAAACTGATCCCCGTTTGTTTTAAAAGAAACTAGATTGATATACGAA
66 TCTTGTTTTATACACCTTGAAACTGATCCCCGTTTGTTTTAAAAGAAACTAGATTGATATACGAA
2291280 CACAATATATAAAAATCACCTGCTAATCATTTTCATAGAATTTCTGGTGAATTTTCAAACTCACT
131 CACAATATATAAAAATCACCTGCTAATCATTTTCATAGAATTTCTGGTGAATTTTCAAACTCACT
2291345 GCCAAATTCAAAATCTAAACTGTTTTCATTAACTTCATCCTTAAATTCTTCATTAATCCTTACAA
196 GCCAAATTCAAAATCTAAACTGTTTTCATTAACTTCATCCTTAAATTCTTCATTAATCCTTACAA
2291410 CCAACTCTTTAAAATCACTTAACTCTTCATAATCCCTAAAACACAAGAAATCAACATCCCCTTCA
261 CCAACTCTTTAAAATCACTTAACTCTTCATAATCCCTAAAACACAAGAAATCAACATCCCCTTCA
2291475 TCAACTCAAGATAAATTTAAACCTAAACCATAACAATATTTATGTCAAATGAAAGAGAATTTCAT
326 TCAACTCAAGATAAATTTAAACCTAAACCATAACAATATTTATGTCAAATGAAAGAGAATTTCAT
2291540 GTAGGTTATTTATCCTTAATAACCTAACATAAAATTATAGTAAAAATATACCAAAAATAAAACTA
391 GTAGGTTATTTATCCTTAATAACCTAACATAAAATTATAGTAAAAATATACCAAAAATAAAACTA
2291605 GAGTTCTTACCTTTTTGAGCTTAAAGTTTCGGTCACTCTGGAGAAGAAGAAGCTGAGCTTTTCTC
456 GAGTTCTTACCTTTTTGAGCTTAAAGTTTCGGTCACTCTGGAGAAGAAGAAGCTGAGCTTTTCTC
2291670 TTTTCTTCAATTTACTAAACATCATCCCTTATTACACTTGTCACTACATAATAAAATGAATTTAA
521 TTTTCTTCAATTTACTAAACATCATCCCTTATTACACTTGTCACTACATAATAAAATGAATTTAA
2291735 AATTCATTTAATCCACTTTACCATTTTATCCCTAATAAAACTTAATAATTTCATCAATGG
586 AATTCATTTAATCCACTTTACCATTTTATCCCTAATAAAACTTAATAATTTCATCAATGG
2291795 CA
1 CA
2291797 CTTATGGCAT
Statistics
Matches: 647, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
645 647 1.00
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (645 bp):
CAGAATCTGTTTTGTGCAGAATCTGCTGCCCGTTTTTATAACCTTTTCTCGGTTAAAAATTCATA
TCTTGTTTTATACACCTTGAAACTGATCCCCGTTTGTTTTAAAAGAAACTAGATTGATATACGAA
CACAATATATAAAAATCACCTGCTAATCATTTTCATAGAATTTCTGGTGAATTTTCAAACTCACT
GCCAAATTCAAAATCTAAACTGTTTTCATTAACTTCATCCTTAAATTCTTCATTAATCCTTACAA
CCAACTCTTTAAAATCACTTAACTCTTCATAATCCCTAAAACACAAGAAATCAACATCCCCTTCA
TCAACTCAAGATAAATTTAAACCTAAACCATAACAATATTTATGTCAAATGAAAGAGAATTTCAT
GTAGGTTATTTATCCTTAATAACCTAACATAAAATTATAGTAAAAATATACCAAAAATAAAACTA
GAGTTCTTACCTTTTTGAGCTTAAAGTTTCGGTCACTCTGGAGAAGAAGAAGCTGAGCTTTTCTC
TTTTCTTCAATTTACTAAACATCATCCCTTATTACACTTGTCACTACATAATAAAATGAATTTAA
AATTCATTTAATCCACTTTACCATTTTATCCCTAATAAAACTTAATAATTTCATCAATGG
Found at i:2293087 original size:21 final size:21
Alignment explanation
Indices: 2293063--2293127 Score: 130
Period size: 21 Copynumber: 3.1 Consensus size: 21
2293053 AGCCAATTTA
2293063 TGCATCGATGCACTGCTACAG
1 TGCATCGATGCACTGCTACAG
2293084 TGCATCGATGCACTGCTACAG
1 TGCATCGATGCACTGCTACAG
2293105 TGCATCGATGCACTGCTACAG
1 TGCATCGATGCACTGCTACAG
2293126 TG
1 TG
2293128 ATTTTCGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (21 bp):
TGCATCGATGCACTGCTACAG
Found at i:2293823 original size:25 final size:24
Alignment explanation
Indices: 2293795--2293882 Score: 124
Period size: 24 Copynumber: 3.7 Consensus size: 24
2293785 CTCGTATAAA
*
2293795 TTGCACCGAAGTGCAACGTAGAATT
1 TTGCACCGAAGTGCCACGTAGAA-T
2293820 TTGCACCGAAGTGCCACGTAGAAT
1 TTGCACCGAAGTGCCACGTAGAAT
*
2293844 TTGCACCGAAGTGCCGCGTAGAA-
1 TTGCACCGAAGTGCCACGTAGAAT
* *
2293867 ATGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
2293883 TATAATATTG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
23 13 0.22
24 23 0.40
25 22 0.38
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.20
Consensus pattern (24 bp):
TTGCACCGAAGTGCCACGTAGAAT
Found at i:2297148 original size:96 final size:96
Alignment explanation
Indices: 2297021--2297211 Score: 337
Period size: 96 Copynumber: 2.0 Consensus size: 96
2297011 GCGGTCCTTT
* *
2297021 GGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCA
1 GGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCA
*
2297086 TATATATATGATTCTTAAGGAATGATATGTC
66 TATATATATGATTCTTAAAGAATGATATGTC
*
2297117 GGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGTA
1 GGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCA
*
2297182 TATGTATATGATTCTTAAAGAATGATATGT
66 TATATATATGATTCTTAAAGAATGATATGT
2297212 GGTCCTTATG
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 90 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.36
Consensus pattern (96 bp):
GGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCA
TATATATATGATTCTTAAAGAATGATATGTC
Found at i:2297268 original size:23 final size:23
Alignment explanation
Indices: 2297235--2297297 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2297225 ATTATTATAT
2297235 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
2297258 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
2297281 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
2297298 ATATGAGATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Done.