Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000921.1 Hibiscus syriacus cultivar Beakdansim tig00001836_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: 61051
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:297 original size:3 final size:3
Alignment explanation
Indices: 285--346 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
275 GGCTTGCCAC
285 AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
331 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
347 CGGTCCGGGC
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.07
3 53 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:327 original size:29 final size:29
Alignment explanation
Indices: 285--346 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
275 GGCTTGCCAC
285 AATAATATAATAATAATAATAATAATAAT
1 AATAATATAATAATAATAATAATAATAAT
314 AATAATATAATAATAATAATAATAATAAT
1 AATAATATAATAATAATAATAATAATAAT
343 AATA
1 AATA
347 CGGTCCGGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (29 bp):
AATAATATAATAATAATAATAATAATAAT
Found at i:783 original size:134 final size:134
Alignment explanation
Indices: 513--1086 Score: 560
Period size: 134 Copynumber: 4.3 Consensus size: 134
503 AATCTGGAAT
* * * *
513 GTTGATTCCTTCCACTGTT-CTTCAGGGAAGATTGAATCGAGGCAGA-CT-TTCCACTGTTACTC
1 GTTGATTCATTCCACTGTTAC-TCAGGGAAGATTGAATCAAGGCAGATTTGTTCAACTGTTACTC
* ** * * * *
575 AGGGAAGATCAAATCTTGAAAGAGA--GATCTATTTAACTTTTTCTTGAGGGAAAATCAAATCTA
65 AAGGAAGATCAAATCTTGAAAGAGAGGGATCTATTCCACTTCTTCTTAAGGGAAAATCATATAT-
638 GG-GAC
129 GGAGAC
* * * ***
643 GTTGATTCATTCTATTGTTACTCAGGGAATATTGAATCAAGTTTGATTTGTTCAACTGTTACTCA
1 GTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATCAAGGCAGATTTGTTCAACTGTTACTCA
* * *
708 AGGAAGATAAAATCTTGAAAGAGAGGGATCTATTCCACTTCTTCTTAAGGGAAAATCAGATCTGG
66 AGGAAGATCAAATCTTGAAAGAGAGGGATCTATTCCACTTCTTCTTAAGGGAAAATCATATATGG
773 AGAC
131 AGAC
* * *
777 GTTGATTCATTCCACTATT-CTTCAGGGAAGACTGAATCGAGGCAGATTTGTTCCAA-TGTTACT
1 GTTGATTCATTCCACTGTTAC-TCAGGGAAGATTGAATCAAGGCAGATTTGTT-CAACTGTTACT
* * * * * *
840 C-AGGAATATCAAATCTTGAAA-AGAGGGATCTGTT-TATTTCTTCCTGAGGGAAAATCATATAT
64 CAAGGAAGATCAAATCTTGAAAGAGAGGGATCTATTCCACTTCTTCTTAAGGGAAAATCATATAT
*
902 GGGGAC
129 GGAGAC
* * * * *
908 GTTGATTCATTCTATTAATTGTTACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTA
1 GTTGATTCATTC----CACTGTTACTCAGGGAAGATTGAATCAAGGCAGATTTGTTCAACTGTTA
* * * * **
973 CTTAAGGAATATCAAATATTGAAAGAGAGGGATCTGTTCCGTTTCTTCTTAAGGGAAAATCATAT
62 CTCAAGGAAGATCAAATCTTGAAAGAGAGGGATCTATTCCACTTCTTCTTAAGGGAAAATCATAT
* *
1038 AT-AAGGAT
127 ATGGA-GAC
* * * *
1046 GTTGATTTATTCCACCGTTACTCATGGTAGATTGAATCAAG
1 GTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATCAAG
1087 TTTGATTCAC
Statistics
Matches: 368, Mismatches: 58, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
130 36 0.10
131 41 0.11
132 48 0.13
133 21 0.06
134 109 0.30
135 43 0.12
136 20 0.05
137 13 0.04
138 37 0.10
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (134 bp):
GTTGATTCATTCCACTGTTACTCAGGGAAGATTGAATCAAGGCAGATTTGTTCAACTGTTACTCA
AGGAAGATCAAATCTTGAAAGAGAGGGATCTATTCCACTTCTTCTTAAGGGAAAATCATATATGG
AGAC
Found at i:1005 original size:269 final size:263
Alignment explanation
Indices: 492--1034 Score: 723
Period size: 269 Copynumber: 2.0 Consensus size: 263
482 CTATATTTTC
* * * * *
492 AGGGAAGATCAAATCTGGAATGTTGATTCCTTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCA
1 AGGGAAAATCAAATCTGGAACGTTGATTCATTCCACTATTCTTCAGGGAAGACTGAATCGAGGCA
* *
557 GACTTTCCACTGTTACTCAGGGAAGATCAAATCTTGAAAGAGAGATCTATTTAACTTTTTCTTGA
66 GACTTTCCAATGTTACTCAGGGAAGATCAAATCTTGAAAGAGAGATCTATTTAACTTTTTCCTGA
* * ***
622 GGGAAAATCAAATCTAGGGACGTTGATTCATTCTATTGTTACTCAGGGAATATTGAATCAAGTTT
131 GGGAAAATCAAATATAGGGACGTTGATTCATTCTATTGTTACTCAGGGAAGATTGAATCAAGGCA
* *
687 GATTTGTTCAACTGTTACTCAAGGAAGATAAAATCTTGAAAGAGAGGGATCTATTCCACTTCTTC
196 GACTTGTTCAACTGTTACTCAAGGAAGATAAAATATTGAAAGAGAGGGATCTATTCCACTTCTTC
752 TTA
261 TTA
*
755 AGGGAAAATCAGATCTGGAGACGTTGATTCATTCCACTATTCTTCAGGGAAGACTGAATCGAGGC
1 AGGGAAAATCAAATCTGGA-ACGTTGATTCATTCCACTATTCTTCAGGGAAGACTGAATCGAGGC
* * * *
820 AGATTTGTTCCAATGTTACTCA-GGAATATCAAATCTTGAAAAGAGGGATCTGTTT-A-TTTCTT
65 AGA-CT-TTCCAATGTTACTCAGGGAAGATCAAATCTTG-AAAGAGAGATCTATTTAACTTT-TT
* *
882 CCTGAGGGAAAATCATATATGGGGACGTTGATTCATTCTATTAATTGTTACTCAGGGAAGATTGA
126 CCTGAGGGAAAATCAAATATAGGGACGTTGATTCATTC---T-ATTGTTACTCAGGGAAGATTGA
* * * * * *
947 ATCGAGGCAGACTTGTTCCACTGTTACTTAAGGAATATCAAATATTGAAAGAGAGGGATCTGTTC
187 ATCAAGGCAGACTTGTTCAACTGTTACTCAAGGAAGATAAAATATTGAAAGAGAGGGATCTATTC
**
1012 CGTTTCTTCTTA
252 CACTTCTTCTTA
1024 AGGGAAAATCA
1 AGGGAAAATCA
1035 TATATAAGGA
Statistics
Matches: 242, Mismatches: 29, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
263 17 0.07
264 47 0.19
265 53 0.22
266 28 0.12
268 1 0.00
269 96 0.40
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (263 bp):
AGGGAAAATCAAATCTGGAACGTTGATTCATTCCACTATTCTTCAGGGAAGACTGAATCGAGGCA
GACTTTCCAATGTTACTCAGGGAAGATCAAATCTTGAAAGAGAGATCTATTTAACTTTTTCCTGA
GGGAAAATCAAATATAGGGACGTTGATTCATTCTATTGTTACTCAGGGAAGATTGAATCAAGGCA
GACTTGTTCAACTGTTACTCAAGGAAGATAAAATATTGAAAGAGAGGGATCTATTCCACTTCTTC
TTA
Found at i:1415 original size:21 final size:22
Alignment explanation
Indices: 1391--1444 Score: 92
Period size: 21 Copynumber: 2.5 Consensus size: 22
1381 AAAATTTCAA
1391 TTTTCTGATTTAAATGA-AAAC
1 TTTTCTGATTTAAATGAGAAAC
1412 TTTTCTGATTTAAATGAGAAAC
1 TTTTCTGATTTAAATGAGAAAC
*
1434 TTTTCTAATTT
1 TTTTCTGATTT
1445 TTTTGAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (22 bp):
TTTTCTGATTTAAATGAGAAAC
Found at i:1577 original size:42 final size:41
Alignment explanation
Indices: 1476--1586 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 41
1466 ATCCTACCCG
* * * *
1476 AAGTCTTATGGATGGCCCGAAGGACTA-TCATCTTGCTCGA
1 AAGTCTTATAGATGGCCCGAAGGATTACTCATCATGCTCAA
* * *
1516 AAGGCTTATAGATGACCCGAAGGATTTACTCATCATGTTCAA
1 AAGTCTTATAGATGGCCCGAAGGA-TTACTCATCATGCTCAA
1558 AAGTCTTACT-GATGGCCCGAAGGAGTTAC
1 AAGTCTTA-TAGATGGCCCGAAGGA-TTAC
1587 CAATTTTAGA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
40 21 0.36
41 2 0.03
42 34 0.59
43 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (41 bp):
AAGTCTTATAGATGGCCCGAAGGATTACTCATCATGCTCAA
Found at i:1795 original size:190 final size:188
Alignment explanation
Indices: 1516--2151 Score: 772
Period size: 190 Copynumber: 3.4 Consensus size: 188
1506 TCTTGCTCGA
* * ** * * *
1516 AAGG-CTTATAGATGACCCGAAGGATTTACTCATCATGTTCAAAAGTCTTACTGATGGCCCGAAG
1 AAGGTCTTATGGATGGCCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
* * *
1580 GAGTTACCAATTTTAGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTACAAAAATTTCAAA
66 GACTTACCAAATTT-GGAATAGTTTACTAGGTAAGAAA-TTTTCTTACTTTACAAAAA-TTCAAA
*
1645 TTTCTGATTTAAATGAGAAACTTTTTCTCATTTTTC-AAAAACATGTGAAAACATCCT-CCG
128 TTTCTGATTTAAATGAGAAAC-TTTTCTCATTTTTCGAAAAGCATGTGAAAACATCCTGCCG
* * *
1705 AAGGTTTTTATGGGTGGCCCGAAGGATTTAAGCATCAT-CTCGAAAGACTTACTGATGGCCTGAA
1 AAGG-TCTTATGGATGGCCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAA
* * *
1769 GGACTTACCAAATTTGGTAATAGTTTACTAAGTAAGAAAGTTTTCTTACTTTTCAAAAA-TCAAT
65 GGACTTACCAAATTTGG-AATAGTTTACTAGGTAAGAAA-TTTTCTTACTTTACAAAAATTCAAA
* *
1833 TTTCAT-ATTTAAATGAGAAACTTTTCCCATTTTTCGAAAAGCTTGTGAAAACATCCTGCTCG
128 TTTC-TGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAGCATGTGAAAACATCCTGC-CG
* * *
1895 AAGGTCTTATGGATGCCCCGAAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGACCCGAAG
1 AAGGTCTTATGGATGGCCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
* * *
1960 GACTTACCAAATTTTGGAATAGTTTACTAGGTAAGCAAGTTT-TTACTTTTTAAAAAAAATTC-A
66 GACTTACCAAA-TTTGGAATAGTTTACTAGGTAAGAAATTTTCTTAC--TTT-ACAAAAATTCAA
* * * *
2023 ATTTTTAGATCT-AATGAGAAACTTTTCTCA-TTTTCGAAAAGCAAGTGAAAACATCATGCCCG
127 ATTTCT-GATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAGCATGTGAAAACATCCTG-CCG
* * *
2085 AAGGTCTTATGAAT-GCCCGAAGGATTTAAGTATCATGCTCGAAAGACTTACTGATGGCCCAAAG
1 AAGGTCTTATGGATGGCCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
2149 GAC
66 GAC
2152 ATACTAGTTT
Statistics
Matches: 387, Mismatches: 44, Indels: 32
0.84 0.10 0.07
Matches are distributed among these distances:
187 13 0.03
188 46 0.12
189 88 0.23
190 177 0.46
191 58 0.15
192 5 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (188 bp):
AAGGTCTTATGGATGGCCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
GACTTACCAAATTTGGAATAGTTTACTAGGTAAGAAATTTTCTTACTTTACAAAAATTCAAATTT
CTGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAGCATGTGAAAACATCCTGCCG
Found at i:5254 original size:77 final size:79
Alignment explanation
Indices: 5142--5290 Score: 171
Period size: 77 Copynumber: 1.9 Consensus size: 79
5132 TTAATAAATT
* **
5142 TCTTATTTAATTAATTCAAATTAAATATACCTT-AAAGACTTATAATCTGAATTACAATC-TATA
1 TCTTATTTAATTAATTCAAATTAAATATACATTAAAAGACTTATAATCAAAATTACAATCTTATA
5205 ATGTTTATTTAAAA
66 ATGTTTATTTAAAA
* * * * * *
5219 TCTTATTTAATT-ATTCTGAGTTAAATAT-CAATTAAAAGAGTTGTAATCAAAATTACATTCTTT
1 TCTTATTTAATTAATTC-AAATTAAATATAC-ATTAAAAGACTTATAATCAAAATTACAATCTTA
5282 TAATGTTTA
64 TAATGTTTA
5291 CTTACTATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
76 5 0.08
77 23 0.39
78 21 0.36
79 10 0.17
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.44
Consensus pattern (79 bp):
TCTTATTTAATTAATTCAAATTAAATATACATTAAAAGACTTATAATCAAAATTACAATCTTATA
ATGTTTATTTAAAA
Found at i:10822 original size:20 final size:21
Alignment explanation
Indices: 10761--10823 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
10751 ATACAACACT
* *
10761 GATATTATTCTTTATCGATATC
1 GATATTATTCATTATAG-TATC
* * *
10783 GATATTGTTCATCA-AATATC
1 GATATTATTCATTATAGTATC
10803 GATATTATTC-TTATAGTATC
1 GATATTATTCATTATAGTATC
10823 G
1 G
10824 TTAGGAGTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 2 0.06
20 19 0.59
22 11 0.34
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (21 bp):
GATATTATTCATTATAGTATC
Found at i:11103 original size:10 final size:10
Alignment explanation
Indices: 11084--11115 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
11074 CGTGCCAACA
11084 TCAT-TCATT
1 TCATCTCATT
11093 TCATCTCATT
1 TCATCTCATT
11103 TCATCTCATT
1 TCATCTCATT
11113 TCA
1 TCA
11116 ACGAATCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.22, C:0.28, G:0.00, T:0.50
Consensus pattern (10 bp):
TCATCTCATT
Found at i:11302 original size:2 final size:2
Alignment explanation
Indices: 11295--11327 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
11285 TTTGAATTTA
11295 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11328 TTTTAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:11417 original size:24 final size:24
Alignment explanation
Indices: 11377--11434 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
11367 CTACATATAC
11377 ATAT-TTATATAGATAGTATACTTT
1 ATATATTATATAGATAGT-TACTTT
* *
11401 ATATATTATA-AGGTAGTTTCTTT
1 ATATATTATATAGATAGTTACTTT
11424 AGTATA-TATAT
1 A-TATATTATAT
11435 TCATATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 10 0.34
24 14 0.48
25 5 0.17
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.50
Consensus pattern (24 bp):
ATATATTATATAGATAGTTACTTT
Found at i:11543 original size:18 final size:18
Alignment explanation
Indices: 11494--11543 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
11484 ATTGCATACT
* *
11494 TATATATATATATATTTA
1 TATATATATATTTAGTTA
* *
11512 TATATATTTGTTTAGTTA
1 TATATATATATTTAGTTA
*
11530 TATATATACATTTA
1 TATATATATATTTA
11544 TATTTACACT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (18 bp):
TATATATATATTTAGTTA
Found at i:22419 original size:11 final size:10
Alignment explanation
Indices: 22392--22443 Score: 54
Period size: 9 Copynumber: 5.1 Consensus size: 10
22382 ATTTACTTAT
22392 ATAAATAATA
1 ATAAATAATA
22402 A-AAATAATA
1 ATAAATAATA
22411 ATGAAATAATA
1 AT-AAATAATA
*
22422 ATTAAAGCAATA
1 A-TAAA-TAATA
22434 AT-AATAATA
1 ATAAATAATA
22443 A
1 A
22444 AATAATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
9 14 0.39
10 3 0.08
11 13 0.36
12 6 0.17
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (10 bp):
ATAAATAATA
Found at i:23834 original size:3 final size:3
Alignment explanation
Indices: 23826--23881 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
23816 ATTAATTATT
* *
23826 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAA TAT TAA -AA CAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23870 TAA TAA TAA TAA
1 TAA TAA TAA TAA
23882 ATAAAAGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 8 0.17
3 39 0.83
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:23850 original size:19 final size:20
Alignment explanation
Indices: 23826--23882 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
23816 ATTAATTATT
*
23826 TAATAATAATAATA-TAATA
1 TAATAATAATAATATTAAAA
23845 TAATAATAATAATATTAAAA
1 TAATAATAATAATATTAAAA
* *
23865 CAA-AATAATAATAATAAA
1 TAATAATAATAATATTAAA
23883 TAAAAGAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 28 0.82
20 6 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
TAATAATAATAATATTAAAA
Found at i:23851 original size:22 final size:22
Alignment explanation
Indices: 23805--23885 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
23795 GGCCTGTTTG
* *
23805 TAATAATATTAAT-TAAT-TATT
1 TAATAATAATAATATAATATA-A
23826 TAATAATAATAATATAATATAA
1 TAATAATAATAATATAATATAA
* * * *
23848 TAATAATAATATTAAAACAAAA
1 TAATAATAATAATATAATATAA
23870 TAATAATAATAA-ATAA
1 TAATAATAATAATATAA
23886 AAGAAATGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 15 0.30
22 33 0.66
23 2 0.04
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (22 bp):
TAATAATAATAATATAATATAA
Found at i:23892 original size:22 final size:21
Alignment explanation
Indices: 23827--23892 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
23817 TTAATTATTT
* *
23827 AATAATAATAATATAATATAAT
1 AATAATAATAATA-AATAAAAA
* *
23849 AATAATAAT-ATTAA-AACAA
1 AATAATAATAATAAATAAAAA
23868 AATAATAATAATAAATAAAAGA
1 AATAATAATAATAAATAAAA-A
23890 AAT
1 AAT
23893 GAAATGAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 11 0.31
20 6 0.17
21 5 0.14
22 13 0.37
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
AATAATAATAATAAATAAAAA
Found at i:24337 original size:124 final size:122
Alignment explanation
Indices: 24146--24446 Score: 381
Period size: 124 Copynumber: 2.5 Consensus size: 122
24136 TCATTGTGAA
* * * *
24146 CTTCTTCTTCTTCAGATGAGTTCTTCTCATTGTGAACTCCTTCTGGAAATGCTGATGATGATATA
1 CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC-TCTGGAAAAGTTGATGATGATATA
* ** **
24211 TCTCCTTCTGTGATAGAGTCATGCCAAAGGTCAAACAAGCTCTTCTCATTATGAACAT
65 TCTCCTTCTATGATAGAGTCATGAAAAAGGTCAAACAAAATCTTCTCATTATGAACAT
* * * *
24269 CTTCTTCTTTCTTGAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGAT-ACTGGTC
1 CTTCTTC-TTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAGTTGATGA-TGATA
** * *
24333 TATCTCCTTCTATGATAGAGTCATGAAAAAGGTTGAACAAAATTTTCTCATTATGAACTT
63 TATCTCCTTCTATGATAGAGTCATGAAAAAGGTCAAACAAAATCTTCTCATTATGAACAT
* *
24393 CTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTT-TCTGGAAAAGTTGAT
1 CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGTTGAT
24447 CCATCGAATG
Statistics
Matches: 154, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
121 15 0.10
122 2 0.01
123 34 0.22
124 101 0.66
125 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (122 bp):
CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGTTGATGATGATATAT
CTCCTTCTATGATAGAGTCATGAAAAAGGTCAAACAAAATCTTCTCATTATGAACAT
Found at i:24710 original size:113 final size:112
Alignment explanation
Indices: 24359--25446 Score: 1189
Period size: 113 Copynumber: 9.7 Consensus size: 112
24349 AGAGTCATGA
*
24359 AAAAGGTTGAACAAAATT-TTCTCATTATGAACTTCTTCTTCCTCTTCAGATA-AGTTCTTCTCA
1 AAAAGGTTGAAC-AAATTCTTCTCATTATGAAC-TCTTCTTCTTCTTCAGATAGAGTTCTTCTCA
* * *
24422 TTATGAACT-T-TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAAC
64 TTATGAACTCTACCTGGAAAAGTTGATCCATCAAATGATGAATTCATAC
* * *
24469 AAAAAGTTGAACAAATTCTTTTCATTATGAATTTCTTCTTCCTTCTTCAGATA-AGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA-CTCTTCTT-CTTCTTCAGATAGAGTTCTTCTCA
* * *
24533 TTATGAACT-T-TCTGGAAAAGTTGATCCATCGAATGATGGATT--TGAGC
64 TTATGAACTCTACCTGGAAAAGTTGATCCATCAAATGATGAATTCAT-A-C
*
24580 AAAAGGTTGAAAAAATTCTTCTCATTATGAACT-TTCTTCTTCTTCAGATGACGAGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTCTTCTTCTTCTTCAGAT-A-GAGTTCTTCTCA
24644 TTATGAACTCTACCT-GACAATA-TTGATCCATCAAATGATGAATTCATAC
64 TTATGAACTCTACCTGGA-AA-AGTTGATCCATCAAATGATGAATTCATAC
* *
24693 AAAAGGTCGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA-CTCTTCTT-CTTCTTCAGATAGAGTTCTTCTCA
* * * * * *
24757 TTATGAACT-TTCTCTAGAAAAGTTGATCCATCAAGTAATGGATT--TGAGT
64 TTATGAACTCTAC-CTGGAAAAGTTGATCCATCAAATGATGAATTCAT-A-C
24806 AAAAGGTTGAACAAATTCTTCTCATTATGAA-T-TTCTTCTTCTTCAGATGACGAGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTCTTCTTCTTCTTCAGAT-A-GAGTTCTTCTCA
* * *
24869 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
64 TTATGAACTCTACCTGGAAAAGTTGATCCATCAAATGATGAATTCATAC
** * *
24918 AAAAGGTCAAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGAT-GAGTTATTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAAC-TCTTCTT-CTTCTTCAGATAGAGTTCTTCTCA
* * * * *
24982 TTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATT--TGAGT
64 TTATGAACTCTAC-CTGGAAAAGTTGATCCATCAAATGATGAATTCAT-A-C
25031 AAAAGGTTGAACAAATTCTTCTCATTATGAACT-TTCTTCTTCTTCAGATGACGAGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTCTTCTTCTTCTTCAGAT-A-GAGTTCTTCTCA
* *
25095 TTATGAACTCTACCT-GACAATA-TTGATTCATCAAATGATGAATTCAAAC
64 TTATGAACTCTACCTGGA-AA-AGTTGATCCATCAAATGATGAATTCATAC
* *
25144 AAAAGGTCGAACAATTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGAT-GAGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAAC-TCTTCTTC-TTCTTCAGATAGAGTTCTTCTCA
* * * * *
25208 TTATGAACTTTCTA--TGGAAAAGCTAATCCATCAAGTGATGGATT--TGAGT
64 TTATGAAC--TCTACCTGGAAAAGTTGATCCATCAAATGATGAATTCAT-A-C
25257 AAAAGGTTGAACAAATTCTTCTCATTATGAA-T-TTCTTCTTCTTCAGATAACGAGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTCTTCTTCTTCTTCAGAT-A-GAGTTCTTCTCA
* ** *
25320 TTATGAACTCTACCTGGCATTGTTGATCCATCAAATGATGAATTCAAAC
64 TTATGAACTCTACCTGGAAAAGTTGATCCATCAAATGATGAATTCATAC
* *
25369 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCATCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAAC-TCTTCTT-CTTCTTCAGATAGAGTTCTTCTCA
*
25433 TTAAGAACTTCTAC
64 TTATGAAC-TCTAC
25447 TTGTACTGTT
Statistics
Matches: 837, Mismatches: 77, Indels: 124
0.81 0.07 0.12
Matches are distributed among these distances:
108 11 0.01
109 32 0.04
110 58 0.07
111 119 0.14
112 163 0.19
113 367 0.44
114 19 0.02
115 25 0.03
116 43 0.05
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (112 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTCTTCTTCTTCTTCAGATAGAGTTCTTCTCATT
ATGAACTCTACCTGGAAAAGTTGATCCATCAAATGATGAATTCATAC
Found at i:25462 original size:451 final size:448
Alignment explanation
Indices: 24359--25477 Score: 1775
Period size: 451 Copynumber: 2.5 Consensus size: 448
24349 AGAGTCATGA
*
24359 AAAAGGTTGAACAAAATT-TTCTCATTATGAACTTCTTCTTCCTCTTCAGATA--AGTTCTTCTC
1 AAAAGGTTGAAC-AAATTCTTCTCATTATGAA--T-TTCTTCTTCTTCAGATACGAGTTCTTCTC
* * * * *
24421 ATTATGAACT-T-TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAA
62 ATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
* * * *
24484 TTCTTTTCATTATGAATTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTT-TCTGG
127 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCATCTCATTATGAACTTCTCTGG
24548 AAAAGTTGATCCATCGAATGATGGATTTGAGCAAAAGGTTGAAAAAATTCTTCTCATTATGAACT
192 AAAAGTTGATCCATC-AATGATGGATTTGAGCAAAAGGTTGAAAAAATTCTTCTCATTATGAACT
24613 TTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGACAATATTGATCCATCAA
256 TTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGACAATATTGATCCATCAA
* * *
24678 ATGATGAATTCATACAAAAGGTCGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAG
321 ATGATGAATTCAAACAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAG
* * *
24743 ATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCCATCAAGTAATGGATTTGAGT
386 ATGAGTTCTTCTCATTATGAACTTTCTATAGAAAAGCTAATCCATCAAGTAATGGATTTGAGT
24806 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGAT-ACGAGTTCTTCTCATT
**
24871 ATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTCAAACAAATTC
65 ATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTC
*
24936 TTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTT-ATTCTCATTATGAACTTTCTCTGGA
130 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCA-TCTCATTATGAAC-TTCTCTGGA
* * *
25000 AAAGCTGATCCATCAAGTGATGGATTTGAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
193 AAAGTTGATCCATCAA-TGATGGATTTGAGCAAAAGGTTGAAAAAATTCTTCTCATTATGAACTT
*
25065 TCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGACAATATTGATTCATCAAA
257 TCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGACAATATTGATCCATCAAA
*
25130 TGATGAATTCAAACAAAAGGTCGAACAATTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGA
322 TGATGAATTCAAACAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGA
* *
25195 TGAGTTCTTCTCATTATGAACTTTCTATGGAAAAGCTAATCCATCAAGTGATGGATTTGAGT
387 TGAGTTCTTCTCATTATGAACTTTCTATAGAAAAGCTAATCCATCAAGTAATGGATTTGAGT
25257 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATAACGAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGAT-ACGAGTTCTTCTCATT
* *
25322 ATGAACTCTACCTGGCATTGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTTC
65 ATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTC
* * *
25387 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCATCTCATTAAGAACTTCTACTTGTA
130 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCATCTCATTATGAACTTCT-CTGGAA
** *
25452 CTGTTGATCCATTGAATGATGGATTT
194 AAGTTGATCCA-TCAATGATGGATTT
25478 AAATCTTTGC
Statistics
Matches: 620, Mismatches: 39, Indels: 22
0.91 0.06 0.03
Matches are distributed among these distances:
444 15 0.02
445 2 0.00
446 5 0.01
447 45 0.07
448 1 0.00
449 96 0.15
450 8 0.01
451 444 0.72
452 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (448 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATACGAGTTCTTCTCATTA
TGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCT
TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCATCTCATTATGAACTTCTCTGGAAAA
GTTGATCCATCAATGATGGATTTGAGCAAAAGGTTGAAAAAATTCTTCTCATTATGAACTTTCTT
CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGACAATATTGATCCATCAAATGAT
GAATTCAAACAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAG
TTCTTCTCATTATGAACTTTCTATAGAAAAGCTAATCCATCAAGTAATGGATTTGAGT
Found at i:25477 original size:225 final size:226
Alignment explanation
Indices: 24359--25442 Score: 1731
Period size: 225 Copynumber: 4.8 Consensus size: 226
24349 AGAGTCATGA
*
24359 AAAAGGTTGAACAAAATT-TTCTCATTATGAACTTCTTCTTCCTCTTCAGAT-A--AGTTCTTCT
1 AAAAGGTTGAAC-AAATTCTTCTCATTATGAAC-T-TTCTTCTTCTTCAGATGACGAGTTCTTCT
* * * * * *
24420 CATTATGAACT-T-TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAA
63 CATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTCGAACAA
* * *
24483 ATTCTTTTCATTATGAATTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAAC-TT-TCT
128 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
*
24546 GGAAAAGTTGATCCATCGAA-TGATGGATTTGAGC
193 GGAAAAGTTGATCCATC-AAGTGATGGATTTGAGT
*
24580 AAAAGGTTGAAAAAATTCTTCTCATTATGAACTTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
* * *
24645 TATGAACTCTACCTGACAATATTGATCCATCAAATGATGAATTCATACAAAAGGTCGAACAAATT
66 TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTCGAACAAATT
* *
24710 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
*
24775 AAAGTTGATCCATCAAGTAATGGATTTGAGT
196 AAAGTTGATCCATCAAGTGATGGATTTGAGT
24806 AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
*
24870 TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTCAAACAAATT
66 TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTCGAACAAATT
* *
24935 CTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
*
25000 AAAGCTGATCCATCAAGTGATGGATTTGAGT
196 AAAGTTGATCCATCAAGTGATGGATTTGAGT
25031 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
* * * *
25096 TATGAACTCTACCTGACAATATTGATTCATCAAATGATGAATTCAAACAAAAGGTCGAACAATTT
66 TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTCGAACAAATT
* *
25161 CTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTATGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
* *
25226 AAAGCTAATCCATCAAGTGATGGATTTGAGT
196 AAAGTTGATCCATCAAGTGATGGATTTGAGT
*
25257 AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCTTCAGATAACGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
* * *
25321 TATGAACTCTACCTGGCATTGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTT
66 TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTCGAACAAATT
* *
25386 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCATCTCATTAAGAACTT
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
25443 CTACTTGTAC
Statistics
Matches: 806, Mismatches: 47, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
219 15 0.02
220 7 0.01
221 25 0.03
222 20 0.02
223 1 0.00
224 98 0.12
225 364 0.45
226 276 0.34
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (226 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTCGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
AAAGTTGATCCATCAAGTGATGGATTTGAGT
Found at i:25900 original size:22 final size:22
Alignment explanation
Indices: 25875--25927 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
25865 TAAAGCTTTT
* * *
25875 ATCTTTGAAAAGAGAATTTGTC
1 ATCTTTAAAAAGAGAATCTATC
*
25897 ATCTTTAAAAAGGGAATCTATC
1 ATCTTTAAAAAGAGAATCTATC
25919 ATCTTTAAA
1 ATCTTTAAA
25928 GAGTGTAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (22 bp):
ATCTTTAAAAAGAGAATCTATC
Found at i:30849 original size:7 final size:7
Alignment explanation
Indices: 30832--30901 Score: 86
Period size: 7 Copynumber: 9.7 Consensus size: 7
30822 CCTGATTCAA
30832 TTTTTCTT
1 TTTTTC-T
30840 TTTTTCT
1 TTTTTCT
*
30847 TTTTTAT
1 TTTTTCT
*
30854 TTTTTCC
1 TTTTTCT
*
30861 TTTTTCC
1 TTTTTCT
30868 TTTTTCT
1 TTTTTCT
*
30875 TTTTTCC
1 TTTTTCT
30882 TTTTTCT
1 TTTTTCT
30889 TTTTTCCT
1 TTTTT-CT
30897 TTTTT
1 TTTTT
30902 TTATGAGTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
7 42 0.76
8 13 0.24
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:30856 original size:14 final size:14
Alignment explanation
Indices: 30840--30900 Score: 95
Period size: 14 Copynumber: 4.4 Consensus size: 14
30830 AATTTTTCTT
**
30840 TTTTTCTTTTTTAT
1 TTTTTCTTTTTTCC
*
30854 TTTTTCCTTTTTCC
1 TTTTTCTTTTTTCC
30868 TTTTTCTTTTTTCC
1 TTTTTCTTTTTTCC
30882 TTTTTCTTTTTTCC
1 TTTTTCTTTTTTCC
30896 TTTTT
1 TTTTT
30901 TTTATGAGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTTTTTTCC
Found at i:30857 original size:21 final size:20
Alignment explanation
Indices: 30831--30893 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 20
30821 TCCTGATTCA
30831 ATTTTTCTTTTTTTCTTTTTT
1 ATTTTTC-TTTTTTCTTTTTT
*
30852 ATTTTTTCCTTTTTCCTTTTTCT
1 A-TTTTT-CTTTTTTCTTTTT-T
*
30875 -TTTTTCCTTTTTCTTTTTT
1 ATTTTTCTTTTTTCTTTTTT
30894 CCTTTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 6 0.17
22 16 0.44
23 2 0.06
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (20 bp):
ATTTTTCTTTTTTCTTTTTT
Found at i:30894 original size:21 final size:21
Alignment explanation
Indices: 30840--30901 Score: 97
Period size: 21 Copynumber: 2.9 Consensus size: 21
30830 AATTTTTCTT
*
30840 TTTTTCTTTTTTATTTTTTCC
1 TTTTTCTTTTTTCTTTTTTCC
*
30861 TTTTTCCTTTTTCTTTTTTCC
1 TTTTTCTTTTTTCTTTTTTCC
30882 TTTTTCTTTTTTCCTTTTTT
1 TTTTTCTTTTTT-CTTTTTT
30902 TTATGAGTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 30 0.81
22 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTCTTTTTTCTTTTTTCC
Found at i:31200 original size:2 final size:2
Alignment explanation
Indices: 31193--31218 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31183 ACAACAAATG
31193 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
31219 TTAAAAGGAT
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):
AT
Found at i:38075 original size:95 final size:95
Alignment explanation
Indices: 37893--38094 Score: 261
Period size: 95 Copynumber: 2.1 Consensus size: 95
37883 CCATACCATT
*
37893 GTATCGATACTTCTATACTATGGTACCGATACTCCCCTTTCAGTATCGATACCGTTTCGGTATTC
1 GTATCGATACTTCTATACTATGGTACCGATACTCCCCTTTCAGTATCGATACCATTTC-GTATTC
*
37958 TGAAATCCCTGGTATCGATACCTTTCTACTA
65 TGAAATCCATGGTATCGATACCTTTCTACTA
* *
37989 GT-TCTGATACTTCTATACTATGGTATCGATACT-CCCTTTCAGTATTGATACCATTT-GTACAT
1 GTATC-GATACTTCTATACTATGGTACCGATACTCCCCTTTCAGTATCGATACCATTTCGT--AT
* *
38051 TCT-AGATTCCAAT-GTATCGATACCTTTCTCCTA
63 TCTGA-AATCC-ATGGTATCGATACCTTTCTACTA
38084 GTATCGATACT
1 GTATCGATACT
38095 CACATCAGTA
Statistics
Matches: 94, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
93 2 0.02
94 1 0.01
95 59 0.63
96 32 0.34
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (95 bp):
GTATCGATACTTCTATACTATGGTACCGATACTCCCCTTTCAGTATCGATACCATTTCGTATTCT
GAAATCCATGGTATCGATACCTTTCTACTA
Found at i:44441 original size:81 final size:81
Alignment explanation
Indices: 44102--44439 Score: 471
Period size: 81 Copynumber: 4.2 Consensus size: 81
44092 CGCTGTTAAA
* ** * *
44102 CATTTAATCTTTTACTCAAAGGAATTTAGTTTTTCATCTAACTGACATTATTGACACCTTTCTGC
1 CATTTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATTATTGACACCTTTATGC
*
44167 CAAATGCACAGTTAGG
66 CAAATGCACAGCTAGG
* *
44183 CAATTAATCTTTTACTCAAAGGTATTTAGCCTTTCATCTAACTGGCATTATTGACACCTTTATGC
1 CATTTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATTATTGACACCTTTATGC
* *
44248 TAAATGCACAGCTAAG
66 CAAATGCACAGCTAGG
* * *
44264 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATTATTGACACATTTCTGC
1 CATTTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATTATTGACACCTTTATGC
* *
44329 CAAATGCATAACTAGG
66 CAAATGCACAGCTAGG
* * * * *
44345 CAATTAATATTTTATTCAAAGGCATTTAGCCTTTTATCTAACTGGCATTATTGACACCTTTAAGC
1 CATTTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATTATTGACACCTTTATGC
*
44410 CAAATGCACAAG-TATG
66 CAAATGCAC-AGCTAGG
44426 CATTTAATCTTTTA
1 CATTTAATCTTTTA
44440 TTTTAAAACA
Statistics
Matches: 225, Mismatches: 31, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
81 224 1.00
82 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (81 bp):
CATTTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATTATTGACACCTTTATGC
CAAATGCACAGCTAGG
Done.