Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008008.1 Hibiscus syriacus cultivar Beakdansim tig00110470_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: 294377
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:256865 original size:96 final size:96
Alignment explanation
Indices: 256672--257422 Score: 755
Period size: 96 Copynumber: 7.9 Consensus size: 96
256662 CCATTATAAA
* * ** * * * *
256672 TCTCCACCACCGCCCGAACACTCACCACCTCCTCCACATTACATTTACAAATCTCCTCCACCGCC
1 TCTCCACCACCACCAGTCCACTCCCCACCTCCTCC-C--TATATTTACAAGTCTCCTCCACCTCC
* * * * * * * *
256737 GGTTCACTCTCCTCCTCCACCGTAT-TTCTATAAA
63 AGTCCACTCACCACCTCCTCCCTATATT-TACAAG
* * * * * * * *
256771 TCTCCACCACCACCAGTCCATTCTCCACCACCTCCCTATGTCTATAACTCTCCACCACCTCCAGT
1 TCTCCACCACCACCAGTCCACTCCCCACCTCCTCCCTATATTTACAAGTCTCCTCCACCTCCAGT
* * * *
256836 CCACTCTCCACCTCCTCCTTATATCTATAAG
66 CCACTCACCACCTCCTCCCTATATTTACAAG
* * * * * *
256867 TCTCCACCACCTCCAGTCCACTCTCCACCTCC-CCCTTACATTTACAAATCCCCACCACCTCCAG
1 TCTCCACCACCACCAGTCCACTCCCCACCTCCTCCC-TATATTTACAAGTCTCCTCCACCTCCAG
* * *
256931 TCCACTCACCGCCTCCTCCATACATTTACAAG
65 TCCACTCACCACCTCCTCCCTATATTTACAAG
* * * * * * *
256963 TCACCTCCTCCACCAGTCCACTCCCCACCACCTCCTTATATTTATAAGTCTCCACCACCTCCAGT
1 TCTCCACCACCACCAGTCCACTCCCCACCTCCTCCCTATATTTACAAGTCTCCTCCACCTCCAGT
* *
257028 TCACTCACCTCCTCCTCCCTATATTTACAAG
66 CCACTCACCACCTCCTCCCTATATTTACAAG
* * *
257059 TCTCCACCACCTCCAGTCCACTCCCCACCTCCTCCCTACATTTACAAGTCTCCTCCACCACCAGT
1 TCTCCACCACCACCAGTCCACTCCCCACCTCCTCCCTATATTTACAAGTCTCCTCCACCTCCAGT
* *
257124 CCACTCCCCACCTCCTCCCTATGTTTACAAG
66 CCACTCACCACCTCCTCCCTATATTTACAAG
*
257155 TCT---CCACCACCAGTCCACTCCCCACCACCTCCCTATATTTACAAGTCTCCTCCACCTCCAGT
1 TCTCCACCACCACCAGTCCACTCCCCACCTCCTCCCTATATTTACAAGTCTCCTCCACCTCCAGT
* *
257217 GCACTCACCACCTCCTCCCTACATTTACAAG
66 CCACTCACCACCTCCTCCCTATATTTACAAG
* * * * * *
257248 TCTCCTCCACCGCCAGTTCACTCCCCGCCTCCTCCTTATGTTTACAAGTCTCCTCCACCTCCAGT
1 TCTCCACCACCACCAGTCCACTCCCCACCTCCTCCCTATATTTACAAGTCTCCTCCACCTCCAGT
* * *
257313 GCACTCACCACCTCCTCCCTACATTTACAAA
66 CCACTCACCACCTCCTCCCTATATTTACAAG
* * * * * *
257344 TCTCCTCC-CCACCAGTCCACTCTCCGCCTCCTCCCTATGTTTACAAATCTCCTCC-CCACC-GT
1 TCTCCACCACCACCAGTCCACTCCCCACCTCCTCCCTATATTTACAAGTCTCCTCCACCTCCAGT
* *
257406 AC-CTCCCCACCTCCTCC
66 CCACTCACCACCTCCTCC
257423 TTATGCCTAC
Statistics
Matches: 558, Mismatches: 88, Indels: 19
0.84 0.13 0.03
Matches are distributed among these distances:
92 14 0.03
93 88 0.16
94 4 0.01
95 45 0.08
96 375 0.67
97 3 0.01
98 1 0.00
99 28 0.05
ACGTcount: A:0.21, C:0.49, G:0.05, T:0.25
Consensus pattern (96 bp):
TCTCCACCACCACCAGTCCACTCCCCACCTCCTCCCTATATTTACAAGTCTCCTCCACCTCCAGT
CCACTCACCACCTCCTCCCTATATTTACAAG
Found at i:256932 original size:144 final size:144
Alignment explanation
Indices: 256768--257426 Score: 812
Period size: 144 Copynumber: 4.6 Consensus size: 144
256758 GTATTTCTAT
* * * * ** * * * * *
256768 AAATCTCCACCACCACCAGTCCATTCTCCACCACCTCCCTATGTCTATAACTCTCCACCACCTCC
1 AAATCTCCACCACCTCCAGTCCACTCACCACCTCCTCCCTACATTTACAAGTCTCCTCCACCACC
* * * *
256833 AGTCCACTCTCCACCTCCTCCTTATATCTATAAGTCTCCACCACCTCCAGTCCACTCTCCACCTC
66 AGTCCACTCCCCACCTCCTCCTTATATTTACAAGTCTCCACCACCTCCAGTCCACTCACCACCTC
256898 C-CCCTTACATTTAC
131 CTCCC-TACATTTAC
* * * * *
256912 AAATCCCCACCACCTCCAGTCCACTCACCGCCTCCTCCATACATTTACAAGTCACCTCCTCCACC
1 AAATCTCCACCACCTCCAGTCCACTCACCACCTCCTCCCTACATTTACAAGTCTCCTCCACCACC
* * * *
256977 AGTCCACTCCCCACCACCTCCTTATATTTATAAGTCTCCACCACCTCCAGTTCACTCACCTCCTC
66 AGTCCACTCCCCACCTCCTCCTTATATTTACAAGTCTCCACCACCTCCAGTCCACTCACCACCTC
*
257042 CTCCCTATATTTAC
131 CTCCCTACATTTAC
* *
257056 AAGTCTCCACCACCTCCAGTCCACTCCCCACCTCCTCCCTACATTTACAAGTCTCCTCCACCACC
1 AAATCTCCACCACCTCCAGTCCACTCACCACCTCCTCCCTACATTTACAAGTCTCCTCCACCACC
* * * *
257121 AGTCCACTCCCCACCTCCTCCCTATGTTTACAAGTCTCCACCA---CCAGTCCACTCCCCACCAC
66 AGTCCACTCCCCACCTCCTCCTTATATTTACAAGTCTCCACCACCTCCAGTCCACTCACCACCTC
*
257183 CTCCCTATATTTAC
131 CTCCCTACATTTAC
* * * *
257197 AAGTCTCCTCCACCTCCAGTGCACTCACCACCTCCTCCCTACATTTACAAGTCTCCTCCACCGCC
1 AAATCTCCACCACCTCCAGTCCACTCACCACCTCCTCCCTACATTTACAAGTCTCCTCCACCACC
* * * * *
257262 AGTTCACTCCCCGCCTCCTCCTTATGTTTACAAGTCTCCTCCACCTCCAGTGCACTCACCACCTC
66 AGTCCACTCCCCACCTCCTCCTTATATTTACAAGTCTCCACCACCTCCAGTCCACTCACCACCTC
257327 CTCCCTACATTTAC
131 CTCCCTACATTTAC
* * * * ** *
257341 AAATCTCCTCC-CCACCAGTCCACTCTCCGCCTCCTCCCTATGTTTACAAATCTCCTCC-CCACC
1 AAATCTCCACCACCTCCAGTCCACTCACCACCTCCTCCCTACATTTACAAGTCTCCTCCACCACC
*
257404 -GTAC-CTCCCCACCTCCTCCTTAT
66 AGTCCACTCCCCACCTCCTCCTTAT
257427 GCCTACAAGT
Statistics
Matches: 450, Mismatches: 61, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
140 18 0.04
141 132 0.29
142 4 0.01
143 40 0.09
144 253 0.56
145 3 0.01
ACGTcount: A:0.21, C:0.49, G:0.05, T:0.26
Consensus pattern (144 bp):
AAATCTCCACCACCTCCAGTCCACTCACCACCTCCTCCCTACATTTACAAGTCTCCTCCACCACC
AGTCCACTCCCCACCTCCTCCTTATATTTACAAGTCTCCACCACCTCCAGTCCACTCACCACCTC
CTCCCTACATTTAC
Found at i:257071 original size:27 final size:27
Alignment explanation
Indices: 256987--257072 Score: 67
Period size: 27 Copynumber: 3.4 Consensus size: 27
256977 AGTCCACTCC
* *
256987 CCACCACCTCCTTATATTTATAAGTCT
1 CCACCACCTCCCTATATTTACAAGTCT
* * *
257014 CCACCACCT-CC---AGTT-C-ACTCA
1 CCACCACCTCCCTATATTTACAAGTCT
* *
257035 CCTCCTCCTCCCTATATTTACAAGTCT
1 CCACCACCTCCCTATATTTACAAGTCT
257062 CCACCACCTCC
1 CCACCACCTCC
257073 AGTCCACTCC
Statistics
Matches: 41, Mismatches: 12, Indels: 12
0.63 0.18 0.18
Matches are distributed among these distances:
21 10 0.24
22 2 0.05
23 3 0.07
25 3 0.07
26 2 0.05
27 21 0.51
ACGTcount: A:0.22, C:0.45, G:0.03, T:0.29
Consensus pattern (27 bp):
CCACCACCTCCCTATATTTACAAGTCT
Found at i:261544 original size:30 final size:30
Alignment explanation
Indices: 261531--262389 Score: 760
Period size: 30 Copynumber: 28.7 Consensus size: 30
261521 ATTGTACATG
* * * *
261531 TATGGAGGTGGTGGCGGTGACGTGTAAACA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* * * * **
261561 TATGGAGGTGGAGGAGGAGACTTATACATG
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* **
261591 TATGGAGGAGGAGGTGGTGACTCATAAACA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* *
261621 TATGGAGGAGGTGGAGGTGACTTGTAGACA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
261651 TATGGAGGAGGAGGAGGTGACTTGTAAACA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* * *
261681 TATGGAGGAGGAGGAGGTGACTCGTAGACG
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* * **
261711 TATGGAGGAGGTGGTGGTGACTTGTACTCA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* * * *
261741 TATGGAGGGGGAGGAGGAGATTTGTAGACA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* **
261771 TAAGGAGGAGGAGGAGGAGGTGACTTGTACTCA
1 T-A--TGGAGGAGGAGGAGGTGACTTGTAAACA
*
261804 TATGGAGGGGGAGGAGGTGA-TTGTAAACA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* * *
261833 TAAGGAGGAGGTGGAGGTGACTTGTAGACA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
261863 TATGGAGGAGGAGGAGGTGACTTGTAAACA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* *
261893 TATGGAGGAGGAGGAGGTGACTTGTAGACG
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* * * **
261923 TATGGAGGAGGTGGTGGTGACTTATACTCA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* * *
261953 TATGGAGGGGGAGGAGGTGATTTGTAGACA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* **
261983 TAAGGAGGAGGAGGAGGTGACTTGTACTCA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* *
262013 TATGGAGGGGGAGGAGGTGATTTGTAAACA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
**
262043 TA-GGAGGAGGAGGAGGTGACTTGTACTCA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* * * *
262072 TATGGAGGTGGAGGAGGAGACTTGTAGACG
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* *
262102 TATGGAGGGGGAGGAGGTGATTTGTAAACA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* * ***
262132 TACGGAGGAGGTGGAGGTGACTTGTACTTA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* *
262162 TATGGAGGTGGAGGAGGTGATTTGTAAACA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* * * ** *
262192 TAAGGAGGAGGAGGTGGTGACTTATACTCG
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* * * * * * *
262222 TATGGAGGTGGTGGTGGAGAGTTGTACACG
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* * * **
262252 TACGGAGGAGG-TG-GGAGACTTGTACTCA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* * * * *
262280 TATGGAGGCGGAGGCGGAGAGC-TATAAACG
1 TATGGAGGAGGAGGAGGTGA-CTTGTAAACA
* * * * **
262310 TACGGAGGA-GTGGTGGAGACTTGTACTCA
1 TATGGAGGAGGAGGAGGTGACTTGTAAACA
* * *
262339 TATGGCGGAGG-CGATGGTGATTTGTAAACA
1 TATGGAGGAGGAGGA-GGTGACTTGTAAACA
*
262369 TATGGAGGAGGTGGAGGTGAC
1 TATGGAGGAGGAGGAGGTGAC
262390 GCATAATTGT
Statistics
Matches: 662, Mismatches: 155, Indels: 24
0.79 0.18 0.03
Matches are distributed among these distances:
28 22 0.03
29 71 0.11
30 541 0.82
31 4 0.01
32 1 0.00
33 23 0.03
ACGTcount: A:0.28, C:0.08, G:0.42, T:0.22
Consensus pattern (30 bp):
TATGGAGGAGGAGGAGGTGACTTGTAAACA
Found at i:263696 original size:20 final size:20
Alignment explanation
Indices: 263673--263711 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
263663 ACGAACGGAT
*
263673 GTAAACGAACATAAACGAAA
1 GTAAACGAACACAAACGAAA
*
263693 GTAAATGAACACAAACGAA
1 GTAAACGAACACAAACGAA
263712 CGAACGTAAA
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:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (20 bp):
GTAAACGAACACAAACGAAA
Found at i:263947 original size:24 final size:24
Alignment explanation
Indices: 263912--263980 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
263902 AGATTGAGCT
*
263912 AAACATAAATGAA-TACACATAAAC
1 AAACATAAATGAACGA-ACATAAAC
* *
263936 GAGCATAAATGAACGAACATAAAC
1 AAACATAAATGAACGAACATAAAC
263960 AAACATAAATGAACGAACATA
1 AAACATAAATGAACGAACATA
263981 TTACCGAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 38 0.97
25 1 0.03
ACGTcount: A:0.59, C:0.16, G:0.10, T:0.14
Consensus pattern (24 bp):
AAACATAAATGAACGAACATAAAC
Found at i:263980 original size:14 final size:14
Alignment explanation
Indices: 263933--263980 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
263923 AATACACATA
*
263933 AACGAGCATAAATG
1 AACGAACATAAATG
263947 AACGAACAT--A--
1 AACGAACATAAATG
*
263957 AACAAACATAAATG
1 AACGAACATAAATG
263971 AACGAACATA
1 AACGAACATA
263981 TTACCGAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
10 8 0.30
12 2 0.07
14 17 0.63
ACGTcount: A:0.58, C:0.17, G:0.12, T:0.12
Consensus pattern (14 bp):
AACGAACATAAATG
Found at i:269982 original size:21 final size:21
Alignment explanation
Indices: 269957--270004 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
269947 CCTAATATTG
*
269957 CAATGTCAATATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
269978 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
269999 TAATGT
1 CAATGT
270005 TTGAAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:274639 original size:21 final size:21
Alignment explanation
Indices: 274613--274660 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
274603 CCTAATATTG
274613 CAATGTCAAAATTAGGTACAA
1 CAATGTCAAAATTAGGTACAA
*
274634 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTACAA
*
274655 TAATGT
1 CAATGT
274661 TTGAAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTACAA
Found at i:277662 original size:23 final size:24
Alignment explanation
Indices: 277630--277692 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
277620 AACGACTAAA
277630 AATGTATCATAAAGACAG-AGAAT
1 AATGTATCATAAAGACAGAAGAAT
* **
277653 AATGTGTCATAAAGGTAGAAGAAT
1 AATGTATCATAAAGACAGAAGAAT
* *
277677 -ACGTTTCATAAAGACA
1 AATGTATCATAAAGACA
277693 AAATTATTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
23 27 0.84
24 5 0.16
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.24
Consensus pattern (24 bp):
AATGTATCATAAAGACAGAAGAAT
Found at i:280354 original size:20 final size:20
Alignment explanation
Indices: 280314--280354 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
280304 TTAGTTATAT
* * *
280314 TCTATTATTTTTATTATAAA
1 TCTAATATTTTTATAACAAA
280334 TCTAATATTTTTATAACAAA
1 TCTAATATTTTTATAACAAA
280354 T
1 T
280355 AAGATAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (20 bp):
TCTAATATTTTTATAACAAA
Found at i:280603 original size:22 final size:22
Alignment explanation
Indices: 280578--280625 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
280568 CTCGAGTTTC
*
280578 TTTCGATTCGGGTTAATTTCGA
1 TTTCGATTCGGGTTAATTTCAA
** *
280600 TTTCGATTTTGGTTGATTTCAA
1 TTTCGATTCGGGTTAATTTCAA
280622 TTTC
1 TTTC
280626 ACTAAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.52
Consensus pattern (22 bp):
TTTCGATTCGGGTTAATTTCAA
Found at i:290134 original size:82 final size:81
Alignment explanation
Indices: 289894--290163 Score: 355
Period size: 82 Copynumber: 3.3 Consensus size: 81
289884 CTGAATGAAA
* *
289894 TCGAACTCGTCAGGTCTTTAGTTGACAGATAACCCTTCTAGCCTTGAGTTATG-TTGTAATGATG
1 TCGAACTCG-AAGGTCTTT-G-TGGCAGATAACCCTTCTAGCCTTGAGTTATGCTTG-AATGATG
289958 TGCCTTGGAGCTGAGCGTAG
62 TGCCTTGGAGCTGAGCGTAG
** * * * *
289978 TCGAACTCGAAGGTCTTTGTTGGCAGATTGCCCTTCTCGACTTAAGCTATGC-TGCAAATGATGT
1 TCGAACTCGAAGGTCTTTG-TGGCAGATAACCCTTCTAGCCTTGAGTTATGCTTG--AATGATGT
* *
290042 GCCTTTGAGCTGAGCGTGG
63 GCCTTGGAGCTGAGCGTAG
*
290061 TCGAACTCGAAGGTTTTTGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTATGAATGATGTGC
1 TCGAACTCGAAGGTCTTTGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCT-TGAATGATGTGC
290126 CTTGGAGCTGAGCGTAG
65 CTTGGAGCTGAGCGTAG
290143 TCGAACTCGAAGGTCTTTGTG
1 TCGAACTCGAAGGTCTTTGTG
290164 TTTCAAGAGA
Statistics
Matches: 161, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
82 99 0.61
83 51 0.32
84 11 0.07
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (81 bp):
TCGAACTCGAAGGTCTTTGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTTGAATGATGTGCC
TTGGAGCTGAGCGTAG
Found at i:290210 original size:28 final size:28
Alignment explanation
Indices: 290164--290221 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
290154 GGTCTTTGTG
*
290164 TTTCAAGAGAAATATTTTCAAAGGTTTT
1 TTTCAAGAGAAAGATTTTCAAAGGTTTT
290192 TTTCAAGAGAAACGA-TTTCAAAGGTTTT
1 TTTCAAGAGAAA-GATTTTCAAAGGTTTT
290220 TT
1 TT
290222 GTGTTTCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (28 bp):
TTTCAAGAGAAAGATTTTCAAAGGTTTT
Found at i:290256 original size:31 final size:30
Alignment explanation
Indices: 290152--290267 Score: 130
Period size: 31 Copynumber: 3.8 Consensus size: 30
290142 GTCGAACTCG
**
290152 AAGGTCTTTGTGTTTCAAGAGAAATATTTTCA
1 AAGGT-TTTGTGTTTCAAGAGAACGA-TTTCA
290184 AAGG-TTT-T-TTTCAAGAGAAACGATTTCA
1 AAGGTTTTGTGTTTCAAGAG-AACGATTTCA
*
290212 AAGGTTTTTTGTGTTTCAAGAGAACGACTTCA
1 AAGG--TTTTGTGTTTCAAGAGAACGATTTCA
290244 AAGGATTTTGTGTTTCAAGAGAAC
1 AAGG-TTTTGTGTTTCAAGAGAAC
290268 TGTCTCCAGA
Statistics
Matches: 74, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
28 18 0.24
29 4 0.05
30 3 0.04
31 22 0.30
32 18 0.24
33 9 0.12
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (30 bp):
AAGGTTTTGTGTTTCAAGAGAACGATTTCA
Found at i:290372 original size:37 final size:36
Alignment explanation
Indices: 290322--290425 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 36
290312 AAAATTGGTG
290322 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTCA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTCA
* **
290359 TTTCAAGTGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCA
* * *
290395 GTTCAAAAAGAAACTGTCTCAAGGGAGACAA
1 TTTC-AAGAGAAACTGTCTCAAGAGAGACAA
290426 TGGTGAGCAC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 5 0.08
37 54 0.92
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.22
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCA
Found at i:290969 original size:106 final size:106
Alignment explanation
Indices: 290548--291638 Score: 1893
Period size: 106 Copynumber: 10.3 Consensus size: 106
290538 TGTTTCGAGG
* *
290548 CCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
* *
290612 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTTGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
290653 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTG-TGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
* * *
290716 CGGTCCCTTCGCCGTGAAGTTGAACTTACGTTGTCTTGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
290757 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTTATTGACAAC
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA---GTTGTTTGTTGACAAC
290822 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
63 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
290866 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
290931 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
290972 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
291037 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
291078 GCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
291143 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
291184 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
291249 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
291290 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGA-AAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
291354 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
291395 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
291460 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
291501 CCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
*
291566 TGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
291607 CCAATATCCTTCGTTGTGAAGTTGAAATTGGC
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGC
291639 ACTCGAGCAA
Statistics
Matches: 954, Mismatches: 26, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
104 96 0.10
105 154 0.16
106 605 0.63
107 4 0.00
108 2 0.00
109 93 0.10
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (106 bp):
CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:291598 original size:529 final size:528
Alignment explanation
Indices: 290548--291638 Score: 1907
Period size: 529 Copynumber: 2.1 Consensus size: 528
290538 TGTTTCGAGG
* * *
290548 CCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCAGC
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTGTTGACAACCAGC
*
290613 GGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGA
66 GGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGA
* *
290678 AATTGGCTCTGAAATTGGGAAGTTGTTGTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTT
131 AATTGGCTCTGAAATTGAGAAATTGTTGTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTT
* * *
290743 ACGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGT
196 ACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATT-GGAAG-AGT
290808 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
259 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
290873 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTCCC
324 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGGTTATTGACAACCAGCGGTCCC
*
290938 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
389 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGG
291003 CTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
454 CTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
291068 TGTCTGGAGT
519 TGTCTGGAGT
* *
291078 GCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATT-GTTGTTGACAACCAG
*
291143 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
65 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
* *
291208 AAATTGGCTCTGAAATTGAGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
130 AAATTGGCTCTGAAATTGAGAAATT-GTTG-TGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAA
*
291273 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATT-GAA-AG
193 CTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGAAGAG
*
291336 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
258 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* *
291401 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGTTTGTTGACAACCAGCGGTCC
323 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGGTTATTGACAACCAGCGGTCC
291466 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAGTTGAAATTG
388 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAGTTGAAATTG
* * *
291531 GCTCTGATATTGAGAAGTTGTTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCG
453 GCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
291596 TTGTCTGGAGT
518 TTGTCTGGAGT
*
291607 CCAATATCCTTCGTTGTGAAGTTGAAATTGGC
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGC
291639 ACTCGAGCAA
Statistics
Matches: 533, Mismatches: 25, Indels: 7
0.94 0.04 0.01
Matches are distributed among these distances:
529 294 0.55
530 45 0.08
531 103 0.19
532 3 0.01
533 88 0.17
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (528 bp):
CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTGTTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGA
AATTGGCTCTGAAATTGAGAAATTGTTGTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTT
ACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGAAGAGTTG
TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGGTTATTGACAACCAGCGGTCCCTT
CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCT
CTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
TCTGGAGT
Done.