Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007149.1 Hibiscus syriacus cultivar Beakdansim tig00018699_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: 59303
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:497 original size:19 final size:18
Alignment explanation
Indices: 456--497 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
446 TGATGAATTA
**
456 GTATCGATACATAGGTGG
1 GTATCGATACATAGGAAG
474 GTATCGATACATGAGGAAG
1 GTATCGATACAT-AGGAAG
493 GTATC
1 GTATC
498 ATATCTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.26
Consensus pattern (18 bp):
GTATCGATACATAGGAAG
Found at i:677 original size:22 final size:22
Alignment explanation
Indices: 635--677 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
625 ATACTGAAAG
*
635 GAAGTATCAATATCATAGTATA
1 GAAGTATCAATACCATAGTATA
* *
657 GAAGTATCGATACCATGGTAT
1 GAAGTATCAATACCATAGTAT
678 GGGTACCGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (22 bp):
GAAGTATCAATACCATAGTATA
Found at i:1130 original size:45 final size:45
Alignment explanation
Indices: 1024--1253 Score: 321
Period size: 45 Copynumber: 5.3 Consensus size: 45
1014 TTTTTGATCA
*
1024 CATAAATGAAATGCATAACGGTACA-TAAAGGCATGAAAGGATG-
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
1067 CATAAATGAAATGTATAACGGTGCATTAAAGGTATGAAAGGATAC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
1112 CATAAATGAAATGCATAACAGTGTATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
1157 CATAAATAAAATGCATAACGGTGCATTAAAGGCATAAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
*
1202 CAT-AA--AAATGCATAACGGTGC-TTACAGGCATGAAA-GATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
*
1242 CATGAATGAAAT
1 CATAAATGAAAT
1254 AATAAATAAT
Statistics
Matches: 167, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
40 8 0.05
41 14 0.08
42 16 0.10
43 27 0.16
44 18 0.11
45 84 0.50
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
Found at i:10133 original size:3 final size:3
Alignment explanation
Indices: 10125--10184 Score: 63
Period size: 3 Copynumber: 19.7 Consensus size: 3
10115 TAAACAAATA
10125 AAT AAT AAT AAT AAT AAT AAT -AT AACCT AAT -AT AAT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA--T AAT AAT AAT -AAT AAT AAT
10171 -AT AAAT AAT AAT AA
1 AAT -AAT AAT AAT AA
10185 AAACTATATA
Statistics
Matches: 50, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
2 6 0.12
3 36 0.72
4 5 0.10
5 3 0.06
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:10142 original size:12 final size:13
Alignment explanation
Indices: 10121--10184 Score: 82
Period size: 12 Copynumber: 5.2 Consensus size: 13
10111 AAATTAAACA
10121 AATAAATAATAAT
1 AATAAATAATAAT
10134 AAT-AATAATAAT
1 AATAAATAATAAT
*
10146 -ATAACCTAAT-AT
1 AATAA-ATAATAAT
10158 AATAAATAATAAT
1 AATAAATAATAAT
10171 -ATAAATAATAAT
1 AATAAATAATAAT
10183 AA
1 AA
10185 AAACTATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
11 2 0.05
12 28 0.64
13 14 0.32
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAAATAATAAT
Found at i:10165 original size:25 final size:25
Alignment explanation
Indices: 10127--10184 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
10117 AACAAATAAA
10127 TAATAATAATAATAATAATATAACC
1 TAATAATAATAATAATAATATAACC
*
10152 TAAT-ATAATAAATAATAATATAA-A
1 TAATAATAAT-AATAATAATATAACC
10176 TAATAATAA
1 TAATAATAA
10185 AAACTATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (25 bp):
TAATAATAATAATAATAATATAACC
Found at i:10331 original size:96 final size:97
Alignment explanation
Indices: 10231--10410 Score: 260
Period size: 97 Copynumber: 1.9 Consensus size: 97
10221 ATATAATATA
*
10231 TATATATTATATATGTTTTCAAAAAT-CGTTTT-AAAAACCATATA-TATATATATTCAAAACTA
1 TATATA-T-TATATGTTTTCAAAAATGCGTTTTCAAAAACCATATATTATATATATTCAAAACCA
*
10293 TAT-TATATACGTTTTTAAAAACCGTTTTTTTAAC
64 TATAT-TATACGTTTTCAAAAACCGTTTTTTTAAC
* * *
10327 TATATATTATATGTTTTCAAAAATGTGTTTTCAAAAACCATATATTATATGTTTTCAAAACCATA
1 TATATATTATATGTTTTCAAAAATGCGTTTTCAAAAACCATATATTATATATATTCAAAACCATA
10392 TATTATACGTTTTCAAAAA
66 TATTATACGTTTTCAAAAA
10411 TATTTTTAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
94 17 0.23
95 6 0.08
96 18 0.24
97 33 0.44
98 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.44
Consensus pattern (97 bp):
TATATATTATATGTTTTCAAAAATGCGTTTTCAAAAACCATATATTATATATATTCAAAACCATA
TATTATACGTTTTCAAAAACCGTTTTTTTAAC
Found at i:10332 original size:58 final size:59
Alignment explanation
Indices: 10233--10348 Score: 144
Period size: 58 Copynumber: 2.0 Consensus size: 59
10223 ATAATATATA
* *
10233 TATATTATATATGTTTTCAAAAATCGTTTTAAAAACCATATA-TATATATATTCAAAAC
1 TATATTATATACGTTTTCAAAAACCGTTTTAAAAACCATATATTATATATATTCAAAAC
* *** * * *
10291 TATATTATATACGTTTTTAAAAACCGTTTTTTTAACTATATATTATATGTTTTCAAAA
1 TATATTATATACGTTTTCAAAAACCGTTTTAAAAACCATATATTATATATATTCAAAA
10349 ATGTGTTTTC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
58 35 0.73
59 13 0.27
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (59 bp):
TATATTATATACGTTTTCAAAAACCGTTTTAAAAACCATATATTATATATATTCAAAAC
Found at i:10383 original size:24 final size:24
Alignment explanation
Indices: 10352--10410 Score: 102
Period size: 23 Copynumber: 2.5 Consensus size: 24
10342 TTCAAAAATG
10352 TGTTTTCAAAAACCATATATTATA
1 TGTTTTCAAAAACCATATATTATA
10376 TGTTTTC-AAAACCATATATTATA
1 TGTTTTCAAAAACCATATATTATA
*
10399 CGTTTTCAAAAA
1 TGTTTTCAAAAA
10411 TATTTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 22 0.67
24 11 0.33
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (24 bp):
TGTTTTCAAAAACCATATATTATA
Found at i:10434 original size:35 final size:37
Alignment explanation
Indices: 10373--10444 Score: 114
Period size: 35 Copynumber: 2.0 Consensus size: 37
10363 ACCATATATT
10373 ATATGTTTTCAAAACCATATATTATACGTTTTCAAAA
1 ATATGTTTTCAAAACCATATATTATACGTTTTCAAAA
10410 ATAT-TTTT-AAAACCATAT-TATATACGTTTTCAAAA
1 ATATGTTTTCAAAACCATATAT-TATACGTTTTCAAAA
10445 CCATATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
34 1 0.03
35 25 0.74
36 4 0.12
37 4 0.12
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (37 bp):
ATATGTTTTCAAAACCATATATTATACGTTTTCAAAA
Found at i:10444 original size:96 final size:94
Alignment explanation
Indices: 10234--10444 Score: 257
Period size: 96 Copynumber: 2.2 Consensus size: 94
10224 TAATATATAT
*
10234 ATATTATATATGTTTTCAAAAATCGTTTTAAAAACCATATATATATATATTCAAAACTATATTAT
1 ATATTATATATGTTTTCAAAAATCGTTTTAAAAACCATATATATATATATTCAAAACCATATTAT
* * ** *
10299 ATACGTTTTTAAAAACCGTTTTTTTAACT
66 ATACGTTTTCAAAAACCATTTTTAAAACC
* * *
10328 ATA-TATTATATGTTTTCAAAAATGTGTTTTCAAAAACCATATATTATATGTTTTCAAAACCATA
1 ATATTA-TATATGTTTTCAAAAAT-CGTTTT-AAAAACCATATA-TATATATATTCAAAACCATA
*
10392 -TATTATACGTTTTCAAAAA-TATTTTTAAAACC
62 TTA-TATACGTTTTCAAAAACCATTTTTAAAACC
*
10424 ATATTATATACGTTTTCAAAA
1 ATATTATATATGTTTTCAAAA
10445 CCATATTATA
Statistics
Matches: 100, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
93 2 0.02
94 20 0.20
95 5 0.05
96 39 0.39
97 34 0.34
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.44
Consensus pattern (94 bp):
ATATTATATATGTTTTCAAAAATCGTTTTAAAAACCATATATATATATATTCAAAACCATATTAT
ATACGTTTTCAAAAACCATTTTTAAAACC
Found at i:10454 original size:56 final size:57
Alignment explanation
Indices: 10330--10500 Score: 238
Period size: 56 Copynumber: 2.9 Consensus size: 57
10320 TTTTAACTAT
10330 ATATTATATGTTTTCAAAAATGTGTTTTCAAAAACCATA-TATTATATGTTTTCAAAACCA
1 ATATTATATGTTTTCAAAAATGT-TTTT--AAAACCATATTA-TATATGTTTTCAAAACCA
* * *
10390 TATATTATACGTTTTCAAAAATATTTTTAAAACCATATTATATACGTTTTCAAAACC-
1 -ATATTATATGTTTTCAAAAATGTTTTTAAAACCATATTATATATGTTTTCAAAACCA
* *
10447 ATATTATATATTTTCAAAAATGTTTTCAAAACCATATTATATATGTTTTCAAAA
1 ATATTATATGTTTTCAAAAATGTTTTTAAAACCATATTATATATGTTTTCAAAA
10501 GTATATTAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
56 49 0.49
58 25 0.25
59 2 0.02
60 4 0.04
61 21 0.21
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.43
Consensus pattern (57 bp):
ATATTATATGTTTTCAAAAATGTTTTTAAAACCATATTATATATGTTTTCAAAACCA
Found at i:10460 original size:21 final size:21
Alignment explanation
Indices: 10410--10465 Score: 85
Period size: 23 Copynumber: 2.6 Consensus size: 21
10400 GTTTTCAAAA
*
10410 ATATTTTTAAAACCATATTAT
1 ATATTTTCAAAACCATATTAT
10431 ATACGTTTTCAAAACCATATTAT
1 ATA--TTTTCAAAACCATATTAT
10454 ATATTTTCAAAA
1 ATATTTTCAAAA
10466 ATGTTTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 12 0.38
23 20 0.62
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATTTTCAAAACCATATTAT
Found at i:10477 original size:33 final size:34
Alignment explanation
Indices: 10435--10523 Score: 117
Period size: 35 Copynumber: 2.6 Consensus size: 34
10425 TATTATATAC
10435 GTTTTCAAAACCATATTATATA-TTTTCAAAAAT
1 GTTTTCAAAACCATATTATATAGTTTTCAAAAAT
*
10468 GTTTTCAAAACCATATTATATATGTTTTCAAAAGT
1 GTTTTCAAAACCATATTATATA-GTTTTCAAAAAT
* * * *
10503 ATATTAAAAACTATATTATAT
1 GTTTTCAAAACCATATTATAT
10524 GATTATGTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
33 22 0.45
35 27 0.55
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (34 bp):
GTTTTCAAAACCATATTATATAGTTTTCAAAAAT
Found at i:11295 original size:21 final size:19
Alignment explanation
Indices: 11263--11302 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
11253 TCGAAAATAT
*
11263 TAAAAATTTAATGTTTTAAA
1 TAAAAATATAAT-TTTTAAA
11283 TAAAAATAATAATTTTTAAA
1 TAAAAAT-ATAATTTTTAAA
11303 GTAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAAAATATAATTTTTAAA
Found at i:19935 original size:36 final size:36
Alignment explanation
Indices: 19888--19960 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
19878 CTTTCTCATT
19888 TCATCTTGTATTAAACAATAATTTGCTTCAACTTTC
1 TCATCTTGTATTAAACAATAATTTGCTTCAACTTTC
19924 TCATCTTGTATTAAACAATAATTTGCTTCAACTTTC
1 TCATCTTGTATTAAACAATAATTTGCTTCAACTTTC
19960 T
1 T
19961 TGCAACCGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.45
Consensus pattern (36 bp):
TCATCTTGTATTAAACAATAATTTGCTTCAACTTTC
Found at i:21128 original size:19 final size:19
Alignment explanation
Indices: 21069--21135 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
21059 GTTCGAATTG
21069 CGAATTTAAAAACTGTATTA
1 CGAATTT-AAAACTGTATTA
* * ** *
21089 CGAAATTAGAGTTCGTGTTA
1 CGAATTTAAAACT-GTATTA
*
21109 CGAATTTAAAACTGTTTTA
1 CGAATTTAAAACTGTATTA
*
21128 CGATTTTA
1 CGAATTTA
21136 TTGGTTATTT
Statistics
Matches: 35, Mismatches: 11, Indels: 3
0.71 0.22 0.06
Matches are distributed among these distances:
19 15 0.43
20 20 0.57
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (19 bp):
CGAATTTAAAACTGTATTA
Found at i:21316 original size:33 final size:34
Alignment explanation
Indices: 21274--21338 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
21264 ATGAGGAAAT
21274 GATT-AAAAAAATGTATTATCAGTTTTAATATAC
1 GATTAAAAAAAATGTATTATCAGTTTTAATATAC
21307 GATTAAAAAAAATGTATTATCAGTTTTAATAT
1 GATTAAAAAAAATGTATTATCAGTTTTAATAT
21339 TTAAATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 4 0.13
34 27 0.87
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (34 bp):
GATTAAAAAAAATGTATTATCAGTTTTAATATAC
Found at i:30265 original size:23 final size:23
Alignment explanation
Indices: 30247--30327 Score: 117
Period size: 23 Copynumber: 3.5 Consensus size: 23
30237 CTCGTATAAC
* *
30247 TGCACCGAAGTACCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAA
*
30270 TGCACCGAAGTGCCATGTAGAAA
1 TGCACCGAAGTGCCACGTAGAAA
*
30293 TGCACCGAAGTGCCATGTAGAAA
1 TGCACCGAAGTGCCACGTAGAAA
*
30316 TGCACCGTAGTG
1 TGCACCGAAGTG
30328 TCATATAAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAA
Found at i:31027 original size:14 final size:14
Alignment explanation
Indices: 31008--31034 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30998 CATGCCTGTG
31008 TGTATCGATACACA
1 TGTATCGATACACA
31022 TGTATCGATACAC
1 TGTATCGATACAC
31035 CCCTGAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
TGTATCGATACACA
Found at i:31109 original size:21 final size:21
Alignment explanation
Indices: 31083--31131 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
31073 AATTTAGTCT
31083 TAGTGTATCGGTACCCATTTA
1 TAGTGTATCGGTACCCATTTA
*
31104 TAGTGTATCGGTACCTATTTA
1 TAGTGTATCGGTACCCATTTA
31125 TAGTGTA
1 TAGTGTA
31132 CCGATATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (21 bp):
TAGTGTATCGGTACCCATTTA
Found at i:37201 original size:23 final size:23
Alignment explanation
Indices: 37152--37207 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
37142 CGTATAACTG
* * *
37152 CACCGAAGTACCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAAATA
**
37175 CACCGAAGTGCCGTGTAGAAATA
1 CACCGAAGTGCCACGTAGAAATA
*
37198 CACCGTAGTG
1 CACCGAAGTG
37208 TCATATAAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAAATA
Found at i:41206 original size:91 final size:91
Alignment explanation
Indices: 41038--41217 Score: 269
Period size: 91 Copynumber: 2.0 Consensus size: 91
41028 TTTGTCAATT
* * * * * *
41038 TAATGTTGGTTTTGTTGTCAAACTCTTGAGTGAATTAATGTTCAAGTCTTTTTACAAGACAGAGG
1 TAATGTTAGTATTGTTGTCAAACCCTTGAGTGAATTAATGTTCAAGTCTTATCACAAGACAGAAG
41103 TAGTTTTTTTAATTAATCTGGCCAAG
66 TAGTTTTTTTAATTAATCTGGCCAAG
41129 TAATGTTAGTATTGTTGTCAAACCCTTGAGTGAATTAATGTTCAAGTCTTATCACAAG--AGAA-
1 TAATGTTAGTATTGTTGTCAAACCCTTGAGTGAATTAATGTTCAAGTCTTATCACAAGACAGAAG
*
41191 -AGTTTTTTTTATTAATCTGGCCAAG
66 TAGTTTTTTTAATTAATCTGGCCAAG
41216 TA
1 TA
41218 TAAGACAATA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
87 26 0.32
89 3 0.04
91 53 0.65
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (91 bp):
TAATGTTAGTATTGTTGTCAAACCCTTGAGTGAATTAATGTTCAAGTCTTATCACAAGACAGAAG
TAGTTTTTTTAATTAATCTGGCCAAG
Found at i:43464 original size:2 final size:2
Alignment explanation
Indices: 43459--43483 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43449 AAACACACAC
43459 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
43484 CCAAGAACAC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:54909 original size:350 final size:346
Alignment explanation
Indices: 54233--54931 Score: 1209
Period size: 350 Copynumber: 2.0 Consensus size: 346
54223 GTGGTAGAAA
* **
54233 TAAAAGATAGATTAGAAAAAGATTTATAGTAGTTCAACTTTCTCAATCAAAGTCTACATTCACTA
1 TAAAAGATAGATTAGAAAAAGATCTATAGTAGTTCAACTTTCTCAATCAAAGTCTACAACCACTA
54298 CCTTAGCTCCACACTAAGGATTTCAACAAATTCACTATTTTTTCTTTCTTTTTCTAGGCTCAAGA
66 CCTTAGCTCCACACTAAGGATTTCAACAAATTCACTATTTTTTCTTTCTTTTTCTAGGCTCAAGA
* *
54363 GTAACCTTTACAACTCTCTAGTTTTCAAGGATAAACTATAATCACTCCCCTTTTACAAATGATAA
131 GTAACCTTTACAACTCTCTAGTTTTCAAGGATAAACTATAACCACTCCCCTTTTACAAAGGATAA
**
54428 GAAATGTAAACAAGAAACCTCACAAGGTAGGTGTTTACAAAGATTTAAGCTCACAAGAATAAAAA
196 GAAATGTAAACAAGAAACCTCACAAGGTAAATGTTTACAAAGATTTAAGCTCACAAGAATAAAAA
* *
54493 CAAAAGATATTCAATTAAACTCTGTACACTTATGTGCAAGATAAAAATGAAGGAAATATGAATAA
261 CAAAAGATATTCAATTAAACTATGTACACTTATGTGCAAGATAAAAATGAAGGAAATAGGAATAA
54558 AAACTCTTTTCTCTTGATCTC
326 AAACTCTTTTCTCTTGATCTC
* *
54579 TAAAAGATAAGAATTAGAAACAAGATCTATAGTGGTTCGACTTTCTCAATCAAAGTCTACAACCA
1 TAAAAGAT-AG-ATTAGAAA-AAGATCTATAGTAGTTCAACTTTCTCAATCAAAGTCTACAACCA
* *
54644 CTATCTTAGCTCCATACTAAGGATTTCAACAAATTCACTAATTTTTTCTTTCTTTTTCTAGGCTC
63 CTACCTTAGCTCCACACTAAGGATTTCAACAAATTCACT-ATTTTTTCTTTCTTTTTCTAGGCTC
*
54709 AAGAGTAACCTTTACAACTCTTTAGTTTTCAAGGATAAACTATAACCACTCCCCTTTTACAAAGG
127 AAGAGTAACCTTTACAACTCTCTAGTTTTCAAGGATAAACTATAACCACTCCCCTTTTACAAAGG
*
54774 ATAAGAAATGTAAACAAGAAACCTCACAAGGTAAATGTTTCCAAAGATTTAAGCTCACAAGAATA
192 ATAAGAAATGTAAACAAGAAACCTCACAAGGTAAATGTTTACAAAGATTTAAGCTCACAAGAATA
* *
54839 AAAACCAAAGATATTCAATTAAACTATGTACACTTCTGTGCAAGATAAAAATGAAGGAAATAGGA
257 AAAACAAAAGATATTCAATTAAACTATGTACACTTATGTGCAAGATAAAAATGAAGGAAATAGGA
54904 ATAAAAACTCTTTTCTCTTGATCTC
322 ATAAAAACTCTTTTCTCTTGATCTC
54929 TAA
1 TAA
54932 GCTTAGAAAG
Statistics
Matches: 332, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
346 8 0.02
347 2 0.01
348 8 0.02
349 76 0.23
350 238 0.72
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31
Consensus pattern (346 bp):
TAAAAGATAGATTAGAAAAAGATCTATAGTAGTTCAACTTTCTCAATCAAAGTCTACAACCACTA
CCTTAGCTCCACACTAAGGATTTCAACAAATTCACTATTTTTTCTTTCTTTTTCTAGGCTCAAGA
GTAACCTTTACAACTCTCTAGTTTTCAAGGATAAACTATAACCACTCCCCTTTTACAAAGGATAA
GAAATGTAAACAAGAAACCTCACAAGGTAAATGTTTACAAAGATTTAAGCTCACAAGAATAAAAA
CAAAAGATATTCAATTAAACTATGTACACTTATGTGCAAGATAAAAATGAAGGAAATAGGAATAA
AAACTCTTTTCTCTTGATCTC
Found at i:55103 original size:20 final size:20
Alignment explanation
Indices: 55078--55150 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
55068 CTGCACATGC
55078 AGTTTCAAAACTTTGAAGAA
1 AGTTTCAAAACTTTGAAGAA
*
55098 AGTTTCGAAACTTTTG-AGAA
1 AGTTTCAAAAC-TTTGAAGAA
*
55118 AGTTTCGAAAC-TT-AATGAA
1 AGTTTCAAAACTTTGAA-GAA
*
55137 AGTATCAAAACTTT
1 AGTTTCAAAACTTT
55151 TAAACACATT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.07
19 12 0.26
20 27 0.59
21 4 0.09
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (20 bp):
AGTTTCAAAACTTTGAAGAA
Found at i:55304 original size:20 final size:20
Alignment explanation
Indices: 55261--55317 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
55251 TTATGGGTGC
* **
55261 AAAGTTTTGAAACT-TTTGT
1 AAAGTTTCGAAACTCTTAAT
55280 AAAGTTTCGAAACTCTTAAT
1 AAAGTTTCGAAACTCTTAAT
*
55300 AAAGTTTCAAAACTCTTA
1 AAAGTTTCGAAACTCTTA
55318 CAAAGTTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 13 0.39
20 20 0.61
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (20 bp):
AAAGTTTCGAAACTCTTAAT
Found at i:55327 original size:20 final size:20
Alignment explanation
Indices: 55280--55330 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
55270 AAACTTTTGT
* *
55280 AAAGTTTCGAAACTCTTAAT
1 AAAGTTTCAAAACTCTTAAC
55300 AAAGTTTCAAAACTCTT-AC
1 AAAGTTTCAAAACTCTTAAC
55319 AAAGTTTTCAAA
1 AAAG-TTTCAAA
55331 CTATGAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAGTTTCAAAACTCTTAAC
Found at i:55425 original size:11 final size:11
Alignment explanation
Indices: 55409--55445 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
55399 ATTTAAAAAG
55409 TTTTAAACACA
1 TTTTAAACACA
55420 TTTTAAACAC-
1 TTTTAAACACA
*
55430 -TTTAAACATA
1 TTTTAAACACA
55440 TTTTAA
1 TTTTAA
55446 TTAACTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 8 0.35
11 15 0.65
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (11 bp):
TTTTAAACACA
Found at i:57213 original size:23 final size:22
Alignment explanation
Indices: 57146--57201 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
57136 GTGGAATTCA
*
57146 AAGGGTGGTACCAGTACTAGTTG
1 AAGGG-GGTATCAGTACTAGTTG
57169 AAGGGGGTATCAGTACTAGTTG
1 AAGGGGGTATCAGTACTAGTTG
57191 AAGGGGGTATC
1 AAGGGGGTATC
57202 GATATTGAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 27 0.84
23 5 0.16
ACGTcount: A:0.27, C:0.11, G:0.38, T:0.25
Consensus pattern (22 bp):
AAGGGGGTATCAGTACTAGTTG
Found at i:57900 original size:23 final size:21
Alignment explanation
Indices: 57867--57973 Score: 89
Period size: 23 Copynumber: 5.0 Consensus size: 21
57857 GTGGTCCTTA
57867 GGGACAATTATGTGGCACTTC
1 GGGACAATTATGTGGCACTTC
57888 GGTG-CAAACTTATGTGGTCA-TTC
1 GG-GAC-AA-TTATGTGG-CACTTC
*
57911 GGGACAA-TATGTGGTACTTC
1 GGGACAATTATGTGGCACTTC
*
57931 GGCG-CAAACCTATGTGGTCA-TTC
1 GG-GAC-AA-TTATGTGG-CACTTC
57954 GGGACAATTATGTGGCACTT
1 GGGACAATTATGTGGCACTT
57974 AAGTACAAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 26
0.71 0.03 0.26
Matches are distributed among these distances:
19 1 0.01
20 15 0.21
21 15 0.21
22 9 0.13
23 27 0.39
24 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (21 bp):
GGGACAATTATGTGGCACTTC
Found at i:57938 original size:43 final size:44
Alignment explanation
Indices: 57856--57973 Score: 184
Period size: 43 Copynumber: 2.7 Consensus size: 44
57846 GAGGGTCTTG
* * * *
57856 TGTGGTCCTTAGGGACAATTATGTGGCACTTCGGTGCAAACTTA
1 TGTGGTCATTCGGGACAATTATGTGGCACTTCGGCGCAAACCTA
*
57900 TGTGGTCATTCGGGACAA-TATGTGGTACTTCGGCGCAAACCTA
1 TGTGGTCATTCGGGACAATTATGTGGCACTTCGGCGCAAACCTA
57943 TGTGGTCATTCGGGACAATTATGTGGCACTT
1 TGTGGTCATTCGGGACAATTATGTGGCACTT
57974 AAGTACAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 40 0.60
44 27 0.40
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (44 bp):
TGTGGTCATTCGGGACAATTATGTGGCACTTCGGCGCAAACCTA
Done.