Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006209.1 Hibiscus syriacus cultivar Beakdansim tig00014789_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: 80570
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2209 original size:30 final size:30
Alignment explanation
Indices: 2175--2231 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
2165 AACTTCTCTT
2175 TATGTATGTAAATGACTAACTATATGTATG
1 TATGTATGTAAATGACTAACTATATGTATG
* *
2205 TATGTATGTAAATGACTTATTATATGT
1 TATGTATGTAAATGACTAACTATATGT
2232 GTATAGGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (30 bp):
TATGTATGTAAATGACTAACTATATGTATG
Found at i:11145 original size:21 final size:21
Alignment explanation
Indices: 11096--11174 Score: 110
Period size: 21 Copynumber: 3.9 Consensus size: 21
11086 GAGTCGAGGG
* *
11096 TCTACGCGGTCCTTCGGGACA
1 TCTACGTGGTCATTCGGGACA
11117 --TA-GTGGTCATTCGGGACA
1 TCTACGTGGTCATTCGGGACA
11135 TCTACGTGGTCATTCGGGACA
1 TCTACGTGGTCATTCGGGACA
*
11156 TCTACGTGGTCCTTCGGGA
1 TCTACGTGGTCATTCGGGA
11175 TAAATTCTAC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
18 14 0.27
19 2 0.04
20 2 0.04
21 34 0.65
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.28
Consensus pattern (21 bp):
TCTACGTGGTCATTCGGGACA
Found at i:11151 original size:39 final size:41
Alignment explanation
Indices: 11096--11174 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 41
11086 GAGTCGAGGG
*
11096 TCTACGCGGTCCTTCGGGACA-TA-GTGGTCATTCGGGACA
1 TCTACGCGGTCATTCGGGACACTACGTGGTCATTCGGGACA
* *
11135 TCTACGTGGTCATTCGGGACATCTACGTGGTCCTTCGGGA
1 TCTACGCGGTCATTCGGGACA-CTACGTGGTCATTCGGGA
11175 TAAATTCTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 19 0.56
41 2 0.06
42 13 0.38
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.28
Consensus pattern (41 bp):
TCTACGCGGTCATTCGGGACACTACGTGGTCATTCGGGACA
Found at i:12987 original size:190 final size:189
Alignment explanation
Indices: 12660--13041 Score: 755
Period size: 190 Copynumber: 2.0 Consensus size: 189
12650 GTAAAAAAGG
12660 ATGAATACATGGTAAGTTTGTCCAAAATGCATCAAATGAGGAAATTCACAAGCTTAGGAATGATC
1 ATGAATACATGGTAAGTTTGTCCAAAATGCATCAAATGAGGAAATTCACAAGCTTAGGAATGATC
12725 TAAAAAAGAATTGAGAGAGAACAAGGAATTCCACAGAAAAAAGATGAAAGCACGTGTACCATCCT
66 TAAAAAAGAATTGAGAGAGAACAAGGAATTCCACAGAAAAAAGATGAAAGCACGTGTACCATCCT
12790 TTGACTTTACTATTGACGCAATTATAAAAATTACCACCAAATTTTTAGAACTATTGGTA
131 TTGACTTTACTATTGACGCAATTATAAAAATTACCACCAAATTTTTAGAACTATTGGTA
12849 ATGAATACATGGTAAGTTTGTCCAAAATGCATCAAATGAGGAAATTCACAAGCTTAGGAATGATC
1 ATGAATACATGGTAAGTTTGTCCAAAATGCATCAAATGAGGAAATTCACAAGCTTAGGAATGATC
12914 TAAAAAAAGAATTGAGAGAGAACAAGGAATTCCACAGAAAAAAGATGAAAGCACGTGTACCATCC
66 T-AAAAAAGAATTGAGAGAGAACAAGGAATTCCACAGAAAAAAGATGAAAGCACGTGTACCATCC
12979 TTTGACTTTACTATTGACGCAATTATAAAAATTACCACCAAATTTTTAGAACTATTGGTA
130 TTTGACTTTACTATTGACGCAATTATAAAAATTACCACCAAATTTTTAGAACTATTGGTA
13039 ATG
1 ATG
13042 TTGCATGTCC
Statistics
Matches: 192, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
189 66 0.34
190 126 0.66
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (189 bp):
ATGAATACATGGTAAGTTTGTCCAAAATGCATCAAATGAGGAAATTCACAAGCTTAGGAATGATC
TAAAAAAGAATTGAGAGAGAACAAGGAATTCCACAGAAAAAAGATGAAAGCACGTGTACCATCCT
TTGACTTTACTATTGACGCAATTATAAAAATTACCACCAAATTTTTAGAACTATTGGTA
Found at i:17923 original size:15 final size:15
Alignment explanation
Indices: 17903--17934 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
17893 CCATTTACCC
17903 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
17918 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
17933 GA
1 GA
17935 TCGGAGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.31, G:0.28, T:0.25
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:19275 original size:18 final size:18
Alignment explanation
Indices: 19249--19284 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19239 TCGAAAGGAC
*
19249 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
19267 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
19285 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:21339 original size:18 final size:18
Alignment explanation
Indices: 21313--21348 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21303 TTCGAAGGAC
*
21313 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
21331 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
21349 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:22576 original size:24 final size:24
Alignment explanation
Indices: 22480--22588 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
22470 GAATATTTTA
* *
22480 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
22504 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * * *
22528 TCTGAT-TCCTAACCCGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
22552 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
22576 TTTGATTTCTGAT
1 TCTGATATCTGAT
22589 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 61 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:24743 original size:13 final size:12
Alignment explanation
Indices: 24725--24798 Score: 57
Period size: 13 Copynumber: 6.0 Consensus size: 12
24715 TCACAACCCG
24725 ACCCGACCCGTTT
1 ACCCGACCCG-TT
24738 ACCCGACCCGTT
1 ACCCGACCCGTT
*
24750 GACCTGACCCG--
1 -ACCCGACCCGTT
24761 ACCCGTTGACCCG--
1 ACCC---GACCCGTT
24774 ACCCGACCCGTTT
1 ACCCGACCCG-TT
24787 ACCCGACCCGTT
1 ACCCGACCCGTT
24799 GACCGTTGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
10 9 0.17
12 4 0.08
13 39 0.75
ACGTcount: A:0.16, C:0.47, G:0.19, T:0.18
Consensus pattern (12 bp):
ACCCGACCCGTT
Found at i:24743 original size:18 final size:18
Alignment explanation
Indices: 24738--24796 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
24728 CGACCCGTTT
*
24738 ACCCGACCCGTTGACCTG
1 ACCCGACCCGTTGACCCG
24756 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
24774 ACCCGACCCGTTTACCCG
1 ACCCGACCCGTTGACCCG
24792 ACCCG
1 ACCCG
24797 TTGACCGTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.17, C:0.49, G:0.20, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:26154 original size:18 final size:18
Alignment explanation
Indices: 26128--26163 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
26118 TCGAAAGGAC
*
26128 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
26146 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
26164 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:27377 original size:24 final size:24
Alignment explanation
Indices: 27281--27389 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
27271 GAATATTTTA
* *
27281 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
27305 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * * *
27329 TCTGAT-TCCTAACCCGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
27353 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
27377 TTTGATTTCTGAT
1 TCTGATATCTGAT
27390 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 61 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:28182 original size:2 final size:2
Alignment explanation
Indices: 28175--28209 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28165 TGACTAAAAT
28175 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 T
28210 GAAAATAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31649 original size:20 final size:19
Alignment explanation
Indices: 31624--31679 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
31614 TAAAAATTAA
31624 TATAATATAAATTTTTTAGT
1 TATAATATAAATTTTTTA-T
* *
31644 TATAAT-TAAAATTATTAT
1 TATAATATAAATTTTTTAT
*
31662 TA-ATTATATAATTTTTTA
1 TATAATATA-AATTTTTTA
31680 AAATAAACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 2 0.07
18 5 0.17
19 16 0.55
20 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TATAATATAAATTTTTTAT
Found at i:31803 original size:2 final size:2
Alignment explanation
Indices: 31796--31821 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31786 TATTTTGTAG
31796 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
31822 GGAAATATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45129 original size:125 final size:124
Alignment explanation
Indices: 44809--45112 Score: 466
Period size: 124 Copynumber: 2.4 Consensus size: 124
44799 AAGTTGTGAT
* *
44809 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGAAGACAAGATTCAGACCAAGGAGGTATTAA
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGTATTAA
* * *
44874 GAATGAGCCTTACAATTTGAGGTGTTGGGGCATTTTGATGCCCGTACCAGTATAAGATA
66 GAATGAGCCTCACAATTTGAGGTGATGGGGCATTTTGAGGCCCGTACCAGTATAAGATA
* * *
44933 ATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCATAAA
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGTATTAA
* *
44998 GAATGAGCCTCACAATTTGAGGTGATGGGGCATTTTGAAGGCCCTTACCAGTGTAAGATA
66 GAATGAGCCTCACAATTTGAGGTGATGGGGCATTTTG-AGGCCCGTACCAGTATAAGATA
** *
45058 ATGTTGGGGCGA-GACCAAACCCACGTCATGTTGAGATGAAAAGATTCAGACCAAG
1 ATGTTGGGGC-ACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAG
45113 AAATTATTGA
Statistics
Matches: 165, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
124 95 0.58
125 69 0.42
126 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (124 bp):
ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGTATTAA
GAATGAGCCTCACAATTTGAGGTGATGGGGCATTTTGAGGCCCGTACCAGTATAAGATA
Found at i:45959 original size:36 final size:36
Alignment explanation
Indices: 45839--45992 Score: 166
Period size: 36 Copynumber: 4.2 Consensus size: 36
45829 AAGTCAATCC
* * *
45839 TAAGCCTTCACCGGAGAATAGTGAAGCAATCAATCT
1 TAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCT
* * *
45875 GAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCA
1 TAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCT
* *
45911 TAAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCT
1 TAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCT
* * * * *
45947 TAAGTCTTCACCA-AAAAGTAGTGAAGCAGATCCCTTT
1 TAAGCCTTCACCAGAGAA-TAGTGAAGCA-AACCATCT
45984 TAAGCCTTC
1 TAAGCCTTC
45993 TCAGAAGAAT
Statistics
Matches: 101, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
35 2 0.02
36 86 0.85
37 13 0.13
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (36 bp):
TAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCT
Found at i:46438 original size:51 final size:50
Alignment explanation
Indices: 46374--46777 Score: 511
Period size: 51 Copynumber: 7.8 Consensus size: 50
46364 AAGATTATTT
* * *
46374 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTATGAAGATATCC
1 GAGTTCCATACTCCTTA-AGAAAGAAGGAGCGAACCCGTTTGAAGATATCC
* *
46425 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCTT-AAGAAAGAAGGAGCGAACCCGTTTGAAGATATCC
* * *
46476 GAGTTTCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
1 GAGTTCCATACTCCTT-AAGAAAGAAGGAGCGAACCCGTTTG-A-AGATATCC
* * * *
46529 GAGTTCCCTACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCC
1 GAGTTCCATACTCCTTA-AGAAAGAAGGAGCGAACCCGTTTGAAGATATCC
46580 GAGTTCCATACTCCTTAATGAAAGAAGGAGCGAACCCGTTTGAAGATATCC
1 GAGTTCCATACTCCTTAA-GAAAGAAGGAGCGAACCCGTTTGAAGATATCC
46631 GAGTTCCATACTCCTTAATGAAAGAAGGAGCGAACCCGTTTGAAGATATCC
1 GAGTTCCATACTCCTTAA-GAAAGAAGGAGCGAACCCGTTTGAAGATATCC
** *
46682 GAGTTCCATACTCCTTAATGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTCT
1 GAGTTCCATACTCCTTAA-GAAAGAAGGAGCGAACCCGTTTGAAG-ATA--TCC
* * * * *
46736 GAGTTCCATACTCCCTAGAGAAATAGGGAGTGAACCCATTTG
1 GAGTTCCATACTCCTTA-AGAAAGAAGGAGCGAACCCGTTTG
46778 TTGAAGATTG
Statistics
Matches: 317, Mismatches: 27, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
50 1 0.00
51 230 0.73
52 7 0.02
53 41 0.13
54 37 0.12
55 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (50 bp):
GAGTTCCATACTCCTTAAGAAAGAAGGAGCGAACCCGTTTGAAGATATCC
Found at i:46655 original size:155 final size:153
Alignment explanation
Indices: 46362--46777 Score: 582
Period size: 155 Copynumber: 2.7 Consensus size: 153
46352 GTGAAGCAAA
*
46362 TGAAGATTATTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTATGAAGATATCCGA
1 TGAAGA-TATCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTATGAAGATATCCGA
* * *
46427 GTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTTCATACTCCTT
65 GTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATATCCGAGTTCCATACTCCTT
46492 AAAGAAAGAAGGAGCGAACCCGTT
130 AAAGAAAGAAGGAGCGAACCCGTT
* * *
46516 TGAAGAGATGTCTGAGTTCCCTACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCG
1 TG-A-AGATATCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTATGAAGATATCCG
*
46581 AGTTCCATACTCCTTAATGAAAGAAGGAGCGAACCCGTTTGAAGATATCCGAGTTCCATACTCCT
64 AGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATATCCGAGTTCCATACTCCT
*
46646 TAATGAAAGAAGGAGCGAACCCGTT
129 TAAAGAAAGAAGGAGCGAACCCGTT
* * * *
46671 TGAAGATATCCGAGTTCCATACTCCTTA-ATGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTC
1 TGAAGATATCTGAGTTCCATACTCCCTAGA-GAAAGAGGGAGCGAACCCGTATGAAG-ATA--TC
* * * * * * *
46735 TGAGTTCCATACTCCCTAGAGAAATAGGGAGTGAACCCATTTG
62 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG
46778 TTGAAGATTG
Statistics
Matches: 233, Mismatches: 23, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
152 1 0.00
153 45 0.19
154 6 0.03
155 141 0.61
156 40 0.17
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.23
Consensus pattern (153 bp):
TGAAGATATCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTATGAAGATATCCGAG
TTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATATCCGAGTTCCATACTCCTTA
AAGAAAGAAGGAGCGAACCCGTT
Found at i:46813 original size:55 final size:55
Alignment explanation
Indices: 46775--47101 Score: 434
Period size: 55 Copynumber: 6.0 Consensus size: 55
46765 GTGAACCCAT
46775 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
* * * * *
46830 TCGTTGAAGATATATT-GAGTCTTATACTCTCTGAA-AGAATAGGGAGCTGACACGA
1 TTGTTGAAGAT-TGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGGGCAGACGCGA
* * * * *
46885 TTGTTGAAGATTATTCGAGTCTCATACTCTCTGAA-AGAATAGGGAGTAGACACGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGGGCAGACGCGA
46940 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
* *
46995 TTGATGAAGATTG-TAG-GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
* * * *
47048 TTGATGAAGATTG-TAG-GTCTTATACTCTCTGAAGATATAGGGGGCAGACACGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
47101 T
1 T
47102 CGTGGAAGCA
Statistics
Matches: 250, Mismatches: 18, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
53 89 0.36
54 7 0.03
55 150 0.60
56 4 0.02
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (55 bp):
TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
Found at i:54059 original size:17 final size:17
Alignment explanation
Indices: 54016--54057 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
54006 TTTATTATAT
*
54016 ATATATTTTAAATATTT
1 ATATATTTTAAATATTA
*
54033 GTATATTTTAAATATTA
1 ATATATTTTAAATATTA
54050 A-ATATTTT
1 ATATATTTT
54058 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
ATATATTTTAAATATTA
Found at i:74929 original size:28 final size:28
Alignment explanation
Indices: 74890--74952 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
74880 GTTCGGGTCA
74890 GGTCGGG-TTTTTTAAGTGTGATATTCG
1 GGTCGGGTTTTTTTAAGTGTGATATTCG
74917 GGTCGGGTTTTTTTAAGTGTGATATTCG
1 GGTCGGGTTTTTTTAAGTGTGATATTCG
*
74945 GGTTGGGT
1 GGTCGGGT
74953 CGGGTTCGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 7 0.21
28 27 0.79
ACGTcount: A:0.13, C:0.06, G:0.37, T:0.44
Consensus pattern (28 bp):
GGTCGGGTTTTTTTAAGTGTGATATTCG
Done.