Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006522.1 Hibiscus syriacus cultivar Beakdansim tig00015896_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: 204148
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:181385 original size:23 final size:23
Alignment explanation
Indices: 181315--181387 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
181305 ATAGGTAAAC
* **
181315 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
181338 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
181361 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
181384 ATAT
1 ATAT
181388 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:181585 original size:430 final size:431
Alignment explanation
Indices: 179927--183345 Score: 6692
Period size: 430 Copynumber: 7.9 Consensus size: 431
179917 AATTCGCAGT
179927 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
*
179992 AAAAGTATGGACACTTTCAATATAATAGGTAACCATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
180057 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
180122 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
180187 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
180252 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
180317 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
180358 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCC-TTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
180422 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
180487 TAATAGGTATCGTTTATAT-ATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
*
180551 AAAAGTGTCCATACTTTTTTCACTTTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
180616 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
180681 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAA-TTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
180745 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
180786 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTT-AAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
*
180850 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTACCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
*
180915 TAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
180980 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
181045 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
181110 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
181175 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
181216 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
181281 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
181346 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
181411 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
181476 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATAT-TTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
181540 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
181605 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
181646 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
181711 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
*
181776 TAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
181841 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
181906 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
181971 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATAT-AAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
182035 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
182076 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
182141 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
182206 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
182271 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
182336 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
182401 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
182466 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
182507 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
*
182571 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGTCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
182636 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
182701 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
182766 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
182831 ATTAAATT-AAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
182895 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
182936 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAAGTATCGATCCTTTTTAT
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTT-AAAAAAAGTATCGATCCTTTTTAT
183001 AAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAAT
65 AAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAAT
183066 GTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTA
130 GTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTA
183131 TAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTT
195 TAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTT
* *
183196 TAAGATATTAATTTAGTAATTATAGGCGTATAATGATTTATTTTTTACGTTACGATATATATTAT
260 TAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTAT
*
183261 TATTAAATTAAAAATTCTAAATATTATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGC
325 TATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGC
183326 AAATGAAATTATTAAATCAA
390 AAATGAAATTATTAAATCAA
183346 ATAATTCAAA
Statistics
Matches: 2965, Mismatches: 14, Indels: 17
0.99 0.00 0.01
Matches are distributed among these distances:
427 16 0.01
428 180 0.06
429 561 0.19
430 1393 0.47
431 741 0.25
432 74 0.02
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (431 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:181776 original size:23 final size:23
Alignment explanation
Indices: 181745--181808 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
181735 ATAGGTAAAC
*
181745 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* * **
181768 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
181791 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
181809 TGGTTATATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:181815 original size:23 final size:23
Alignment explanation
Indices: 181745--181817 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
181735 ATAGGTAAAC
* **
181745 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
* *
181768 ATATAATGTAATATGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
181791 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
181814 ATAT
1 ATAT
181818 TGTAAAGTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
23 40 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:182006 original size:29 final size:30
Alignment explanation
Indices: 181963--182029 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
181953 GTTACGGTAT
* *
181963 ATATTATTATTAAAT-TAAAA-ATTCTAAATA
1 ATATT-TTATAAAATATAAAACAATC-AAATA
181993 ATATTTTATAAAATATAAAACAATCAAATA
1 ATATTTTATAAAATATAAAACAATCAAATA
*
182023 ATTTTTT
1 ATATTTT
182030 GTGCAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 21 0.66
31 3 0.09
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (30 bp):
ATATTTTATAAAATATAAAACAATCAAATA
Found at i:182206 original size:23 final size:23
Alignment explanation
Indices: 182175--182238 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
182165 ATAGGTAAAC
*
182175 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
182198 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
182221 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
182239 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:182245 original size:23 final size:23
Alignment explanation
Indices: 182175--182247 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
182165 ATAGGTAAAC
* **
182175 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
182198 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
182221 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
182244 ATAT
1 ATAT
182248 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:182636 original size:23 final size:24
Alignment explanation
Indices: 182605--182677 Score: 98
Period size: 23 Copynumber: 3.2 Consensus size: 24
182595 ATAGGTAAAC
*
182605 ATATGATGTAATAGGTAGTC-CTT
1 ATATAATGTAATAGGTAGTCGCTT
*
182628 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGTCGCTT
*
182651 ATATAATGTAATAGGTAGT-GGTT
1 ATATAATGTAATAGGTAGTCGCTT
182674 ATAT
1 ATAT
182678 TGTAAAGTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
22 2 0.04
23 42 0.93
24 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (24 bp):
ATATAATGTAATAGGTAGTCGCTT
Found at i:183067 original size:23 final size:23
Alignment explanation
Indices: 183036--183099 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
183026 ATAGGTAAAC
*
183036 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
183059 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
183082 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
183100 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:183106 original size:23 final size:23
Alignment explanation
Indices: 183036--183108 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
183026 ATAGGTAAAC
* **
183036 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
183059 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
183082 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
183105 ATAT
1 ATAT
183109 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:183411 original size:25 final size:25
Alignment explanation
Indices: 183377--183427 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
183367 ACAACAAATC
*
183377 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
183402 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
183427 A
1 A
183428 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:183697 original size:18 final size:18
Alignment explanation
Indices: 183676--183712 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
183666 GTAATTGGAG
183676 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
183694 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
183712 T
1 T
183713 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:183720 original size:24 final size:24
Alignment explanation
Indices: 183668--183714 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
183658 TTTCATATGT
* *
183668 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
183692 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
183715 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:184056 original size:39 final size:39
Alignment explanation
Indices: 183971--184095 Score: 216
Period size: 39 Copynumber: 3.2 Consensus size: 39
183961 TCCGATGCTC
* * *
183971 ATCAAAATTCAAAGCTCATATGGTGCCAAGC-AAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
184009 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
184048 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
184087 ATCAAAATC
1 ATCAAAATC
184096 TACAACTTGA
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
38 28 0.34
39 55 0.66
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
Found at i:184530 original size:23 final size:23
Alignment explanation
Indices: 184499--184561 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
184489 ATAGGTAAAC
*
184499 ATATGATGTAATAGGTACCCCTT
1 ATATAATGTAATAGGTACCCCTT
* **
184522 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTACCCCTT
184545 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
184562 GTGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTACCCCTT
Found at i:184569 original size:23 final size:23
Alignment explanation
Indices: 184499--184571 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
184489 ATAGGTAAAC
* * **
184499 ATATGATGTAATAGGTACCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
184522 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
184545 ATATAATGTAATAGGTAGT-GGTT
1 ATATAATGTAATAGGTA-TCGGTT
184568 ATAT
1 ATAT
184572 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 43 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:203878 original size:2 final size:2
Alignment explanation
Indices: 203871--203908 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
203861 ATTAATGGAT
203871 TA TA TA TA TA TA TA TA TA TA T- 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
203909 TAATAAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:203893 original size:21 final size:21
Alignment explanation
Indices: 203869--203908 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
203859 AAATTAATGG
203869 ATTATATATATATATATATAT
1 ATTATATATATATATATATAT
203890 ATTATATATATATATATAT
1 ATTATATATATATATATAT
203909 TAATAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTATATATATATATATATAT
Done.