Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007860.1 Hibiscus syriacus cultivar Beakdansim tig00110223_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: 2941097
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 16
Found at i:157124 original size:107 final size:107
Alignment explanation
Indices: 156938--157199 Score: 407
Period size: 107 Copynumber: 2.4 Consensus size: 107
156928 AAAAGATGAA
*
156938 CACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGATTTGAATCGGAAGTGTCAATGCTTCCT
1 CACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGATTTGAATCGGAAGTGCCAATGCTTCCT
* *
157003 TCCGTTCGATTTGAATCGGAAGTGCCGATGCTTCCTTCCGTT
66 TCCGTTCGATTTGAATAGGAAGTGCCGATGCTTCCCTCCGTT
* *
157045 CACTTGAATCGGAAGTGCCGGTGCTTCCTTCCGTTCGATTTGAATCGGAAGTGCCGATGCTTCCT
1 CACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGATTTGAATCGGAAGTGCCAATGCTTCCT
*
157110 TCCGTTCGATTTGAATAGGAAGTTCCGATGCTTCCCTCCGTT
66 TCCGTTCGATTTGAATAGGAAGTGCCGATGCTTCCCTCCGTT
* * * * * *
157152 CGATTTGAATCGGAAGTGCCAATGGTTCCCTCTGTTCGACTTGAATCG
1 C-ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGATTTGAATCG
157200 ATGCAAACTT
Statistics
Matches: 141, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
107 102 0.72
108 39 0.28
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (107 bp):
CACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGATTTGAATCGGAAGTGCCAATGCTTCCT
TCCGTTCGATTTGAATAGGAAGTGCCGATGCTTCCCTCCGTT
Found at i:161529 original size:21 final size:21
Alignment explanation
Indices: 161503--161551 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
161493 ACCGTGATTA
*
161503 CGGCCGTCGCGAGCGCTATTG
1 CGGCCGTCACGAGCGCTATTG
*
161524 CGGCCGTCACGAGTGCTATTG
1 CGGCCGTCACGAGCGCTATTG
161545 CGGCCGT
1 CGGCCGT
161552 TGCAGGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.10, C:0.33, G:0.37, T:0.20
Consensus pattern (21 bp):
CGGCCGTCACGAGCGCTATTG
Found at i:168833 original size:8 final size:8
Alignment explanation
Indices: 168824--168886 Score: 117
Period size: 8 Copynumber: 7.9 Consensus size: 8
168814 AAATAAATGT
*
168824 ATGTATGT
1 ATGTATGC
168832 ATGTATGC
1 ATGTATGC
168840 ATGTATGC
1 ATGTATGC
168848 ATGTATGC
1 ATGTATGC
168856 ATGTATGC
1 ATGTATGC
168864 ATGTATGC
1 ATGTATGC
168872 ATGTATGC
1 ATGTATGC
168880 ATGTATG
1 ATGTATG
168887 TATGAGGCTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 54 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (8 bp):
ATGTATGC
Found at i:169855 original size:6 final size:6
Alignment explanation
Indices: 169820--169865 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
169810 TAATACTAGG
*
169820 ATCAAT A-CAAGT ATCAAT ACTC-AC ATCAAT ATCAAT ATCAAT ATCA
1 ATCAAT ATCAA-T ATCAAT A-TCAAT ATCAAT ATCAAT ATCAAT ATCA
169866 TAATGTCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
5 5 0.15
6 24 0.71
7 5 0.15
ACGTcount: A:0.48, C:0.22, G:0.02, T:0.28
Consensus pattern (6 bp):
ATCAAT
Found at i:182679 original size:21 final size:20
Alignment explanation
Indices: 182642--182683 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
182632 TAGGTCCTTA
182642 TATTTAATGTTTATTTTCATT
1 TATTTAATGTTTATTTT-ATT
*
182663 TATTTTATGTTGT-TTTTATT
1 TATTTAATGTT-TATTTTATT
182683 T
1 T
182684 TACTGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 14 0.74
22 1 0.05
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.71
Consensus pattern (20 bp):
TATTTAATGTTTATTTTATT
Found at i:182820 original size:43 final size:43
Alignment explanation
Indices: 182772--182877 Score: 194
Period size: 43 Copynumber: 2.5 Consensus size: 43
182762 TTTAGTTTTA
*
182772 AATCTTTTGCAGGTTTGAAACACAATTATTACTGACACATGAT
1 AATCTTTTGCAGGTTTGAAACACAATTATTACTAACACATGAT
*
182815 AATCTTTTGCAGTTTTGAAACACAATTATTACTAACACATGAT
1 AATCTTTTGCAGGTTTGAAACACAATTATTACTAACACATGAT
182858 AATCTTTTGCAGGTTTGAAA
1 AATCTTTTGCAGGTTTGAAA
182878 ATCTTCAAAG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (43 bp):
AATCTTTTGCAGGTTTGAAACACAATTATTACTAACACATGAT
Found at i:183214 original size:119 final size:118
Alignment explanation
Indices: 182993--183429 Score: 601
Period size: 119 Copynumber: 3.7 Consensus size: 118
182983 CAACCTTGCC
* * *
182993 TCAAAATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCC-A-ATGAGGGAGAAGAAGTTCA
1 TCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACA-GAGGGAGAAGAAGTTCA
* * * **
183056 TAATAAGAAGAACTTGTTCAACCTTGGTTCGATCCCATCACAGAAAGAAATGGA
65 TAATGAGAAGAACTTGTTCAACCTTGGTTCAATTCCATCACAGAAAGAGGTGGA
* *
183110 TCAACATATTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGCGAAGAAGTTCA
1 TCAACATTTTC-AGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCA
* * *
183175 TAATGAGAAGAACTTGTTCAACTTTGGTTCAATTCCATCAAAGAATGAGGTGGA
65 TAATGAGAAGAACTTGTTCAACCTTGGTTCAATTCCATCACAGAAAGAGGTGGA
* * *
183229 TCAACATTTTACAGTAGAGAGTTCATAATGAGAAGAACTCATCCGACAGTGGGAGAAGAACTTCA
1 TCAACATTTT-CAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCA
* * *
183294 TAATGAGAAGAACTTGTTTAACCTTGGTTCAATTCTATCACAGAAGGAGGTGGA
65 TAATGAGAAGAACTTGTTCAACCTTGGTTCAATTCCATCACAGAAAGAGGTGGA
* * *
183348 TCAACATTTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGAACAGAAGAGTGAA-AAGTT
1 TCAACATTTT-CAGTGGAGAGTTCATAATGAGAAGAACTCATCCG-ACAG-AGGGAGAAGAAGTT
183412 CATAATGAGAAGAACTTG
63 CATAATGAGAAGAACTTG
183430 GAACTCAAAT
Statistics
Matches: 284, Mismatches: 30, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
117 8 0.03
118 31 0.11
119 212 0.75
120 28 0.10
121 5 0.02
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (118 bp):
TCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTGGTTCAATTCCATCACAGAAAGAGGTGGA
Found at i:183660 original size:11 final size:11
Alignment explanation
Indices: 183646--183679 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
183636 AAACATTTTT
183646 TAAGAAAAAAA
1 TAAGAAAAAAA
183657 TAAGAAAAAAGA
1 TAAGAAAAAA-A
*
183669 GAAGAAAAAAA
1 TAAGAAAAAAA
183680 AGTGAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (11 bp):
TAAGAAAAAAA
Found at i:184410 original size:20 final size:20
Alignment explanation
Indices: 184358--184410 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
184348 CTGTTTTATT
*
184358 TTATTTTAATTTAGTCATCG
1 TTATTTTAATTTAGTCAACG
*
184378 TTAGTTCTAATTTAG-CAACTG
1 TTA-TTTTAATTTAGTCAAC-G
184399 TTATTTTAATTT
1 TTATTTTAATTT
184411 TTGCATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.55
Consensus pattern (20 bp):
TTATTTTAATTTAGTCAACG
Found at i:184634 original size:21 final size:20
Alignment explanation
Indices: 184597--184638 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
184587 TAGGTCCTTA
184597 TATTTAATGTTTATTTTCATT
1 TATTTAATGTTTATTTT-ATT
*
184618 TATTTTATGTTGT-TTTTATT
1 TATTTAATGTT-TATTTTATT
184638 T
1 T
184639 TACTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 14 0.74
22 1 0.05
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.71
Consensus pattern (20 bp):
TATTTAATGTTTATTTTATT
Found at i:189491 original size:36 final size:36
Alignment explanation
Indices: 189395--189491 Score: 88
Period size: 38 Copynumber: 2.6 Consensus size: 36
189385 CAATATAAAT
** *
189395 TTTGTCTCGCTTGAGACAGTCTCATTTAATACAGAGGA
1 TTTGTCTCGCTTGAGACAGT-TTTTTTAAAACAGA-GA
* * ** *
189433 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAGA-C
1 TTTGTCTCGCTTGAGACAGTTTTT-TTAAAACAGAGA
189469 TTTGTCTCGCTTGAGACAGTTTT
1 TTTGTCTCGCTTGAGACAGTTTT
189492 ACTCGAAAGA
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
36 19 0.41
37 2 0.04
38 25 0.54
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (36 bp):
TTTGTCTCGCTTGAGACAGTTTTTTTAAAACAGAGA
Found at i:189606 original size:77 final size:75
Alignment explanation
Indices: 189446--189757 Score: 436
Period size: 75 Copynumber: 4.1 Consensus size: 75
189436 ATCTCACTTG
* *
189446 AGATTGTTTTTCTTAAAACAGACTTTGTCTCGCTTGAGACAGTTTTACTCGAAAGAAGACGTTTC
1 AGATTGTTTTTCTTAAAACAGACTTTGTCTCGCTTAAGACAGTTTTACTCGAAAGAAGACATTTC
*
189511 ATTTGACTCA
66 ATTTCACTCA
* * *
189521 AGATTGTTTTTCTTAAAACATTA-TTTGTCTCGCTTAAGACACTTTTTTACTCGAAAGAATACAT
1 AGATTGTTTTTCTTAAAACA-GACTTTGTCTCGCTTAAGACA--GTTTTACTCGAAAGAAGACAT
189585 TTCATTTCACTCA
63 TTCATTTCACTCA
*
189598 AGATTGTTTTTATTAAAACAGACTTTGTCTCGCTTAAGACAGTTTTACTCGAAAGAAGACATTTC
1 AGATTGTTTTTCTTAAAACAGACTTTGTCTCGCTTAAGACAGTTTTACTCGAAAGAAGACATTTC
*
189663 ATTTGACTCA
66 ATTTCACTCA
*
189673 AGA-TCTTTTTCTTAAAACAAGA-TTTGTCTCGCTTAAGA-AGGTTTTTACTCGAAA-AAGACAT
1 AGATTGTTTTTCTTAAAAC-AGACTTTGTCTCGCTTAAGACA-G-TTTTACTCGAAAGAAGACAT
*
189734 TTCATTTCACTTA
63 TTCATTTCACTCA
*
189747 AGATTATTTTT
1 AGATTGTTTTT
189758 AAAGAAGATT
Statistics
Matches: 213, Mismatches: 16, Indels: 16
0.87 0.07 0.07
Matches are distributed among these distances:
73 1 0.00
74 51 0.24
75 92 0.43
76 2 0.01
77 67 0.31
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (75 bp):
AGATTGTTTTTCTTAAAACAGACTTTGTCTCGCTTAAGACAGTTTTACTCGAAAGAAGACATTTC
ATTTCACTCA
Found at i:189625 original size:152 final size:149
Alignment explanation
Indices: 189446--189758 Score: 500
Period size: 152 Copynumber: 2.1 Consensus size: 149
189436 ATCTCACTTG
* * *
189446 AGATTGTTTTTCTTAAAACAGACTTTGTCTCGCTTGAGACAGTTTTACTCGAAAGAAGACGTTTC
1 AGATTGTTTTTATTAAAACAGACTTTGTCTCGCTTAAGACAGTTTTACTCGAAAGAAGACATTTC
* ** *
189511 ATTTGACTCAAGATTGTTTTTCTTAAAACATTATTTGTCTCGCTTAAGACACTTTTTTACTCGAA
66 ATTTGACTCAAGA-TCTTTTTCTTAAAACAAGATTTGTCTCGCTTAAGA-ACGTTTTTACTCGAA
*
189576 AGAATACATTTCATTTCACTCA
129 A-AAGACATTTCATTTCACTCA
189598 AGATTGTTTTTATTAAAACAGACTTTGTCTCGCTTAAGACAGTTTTACTCGAAAGAAGACATTTC
1 AGATTGTTTTTATTAAAACAGACTTTGTCTCGCTTAAGACAGTTTTACTCGAAAGAAGACATTTC
*
189663 ATTTGACTCAAGATCTTTTTCTTAAAACAAGATTTGTCTCGCTTAAGAAGGTTTTTACTCGAAAA
66 ATTTGACTCAAGATCTTTTTCTTAAAACAAGATTTGTCTCGCTTAAGAACGTTTTTACTCGAAAA
*
189728 AGACATTTCATTTCACTTA
131 AGACATTTCATTTCACTCA
*
189747 AGATTATTTTTA
1 AGATTGTTTTTA
189759 AAGAAGATTT
Statistics
Matches: 150, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
149 29 0.19
150 14 0.09
151 32 0.21
152 75 0.50
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (149 bp):
AGATTGTTTTTATTAAAACAGACTTTGTCTCGCTTAAGACAGTTTTACTCGAAAGAAGACATTTC
ATTTGACTCAAGATCTTTTTCTTAAAACAAGATTTGTCTCGCTTAAGAACGTTTTTACTCGAAAA
AGACATTTCATTTCACTCA
Found at i:190026 original size:116 final size:117
Alignment explanation
Indices: 189762--190663 Score: 999
Period size: 116 Copynumber: 7.6 Consensus size: 117
189752 ATTTTTAAAG
* * * *
189762 AAGATTTCATCTCTCTTGAGATAGTTTCCCTTGGAACAGAAGATTTTATCTCGCTTGAGATAGTT
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
* * *
189827 TCCCTTGAAACAGGAGATTTTATCTCGCTTGCGATAGTTTCCCTCGAAACAGA
66 TCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACA-A
*
189880 AA-ATTTTATCTCGCTTGAGATAGTTT-CCTCGAAACAGAAGATTTTATCTCGCTTGAGACAGTT
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
* *
189943 TCCCTCGAAACAGAAGA-TTTATCTCGCTTGAGTTAGTTTCCCTTGAAACAA
66 TCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
* * * *
189994 AAGATTTTATCTTGCTTCAGATAGTTTCCCTCGAAATAGAAAATTTTATCTCGCTTGAGATAGTT
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
** * * * *
190059 TCCCTTAAAATAGAAGATTTTGTCTTGCTTGAGATAGTTTCCCTCGAAACAG
66 TCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
* * *
190111 AAGA-TTTATCTTGCTTGAG-TCAATTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGT
1 AAGATTTTATCTCGCTTGAGAT-AGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGT
* *
190174 TTACCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
65 TTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
* * * **
190227 AATA-TTTATCACGCTTGAG-TCAGTTTTCCTTAAAACAGAAGATTTTATCTCGCTTGAGATAGT
1 AAGATTTTATCTCGCTTGAGAT-AGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGT
* *
190290 TTCCCTCGAAACAGAAAAATTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
65 TTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
* * *
190343 AAGATTTTATCTCGCTTGAGACAGTTTCCCTCGAAACAGAAGA-TTTATCTCGATTGAG-TCAGC
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGAT-AGT
* * *
190406 TTCTCTTGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC-A
65 TTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
** *** * * *
190458 AA-A---TCCCTCGAAACAAAAGAT-TTTATCTCACTTGAGATAGTTTCCCTCGAAACAGAATAT
1 AAGATTTTATCTCG---CTTGAGATAGTT-TC-C-CTCGA-A-A--------C-AGA-AG-AT-T
* * * * *
190518 TTGTCTCGCTTGAGATAGTTTCCCTCGAAATAGAAGA-TTTGTCTCGCTTGAGACAGTTTTCCTC
46 TTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTC
*
190582 GAAACAG
111 GAAACAA
*
190589 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAACAGAAGATTTTATCTCGCTTGAGATAGTT
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
190654 TCCCTCGAAA
66 TCCCTCGAAA
190664 TCTTACTTGA
Statistics
Matches: 662, Mismatches: 87, Indels: 72
0.81 0.11 0.09
Matches are distributed among these distances:
111 5 0.01
113 2 0.00
114 10 0.02
115 58 0.09
116 401 0.61
117 90 0.14
118 5 0.01
119 2 0.00
120 1 0.00
126 1 0.00
127 2 0.00
128 3 0.00
129 2 0.00
130 32 0.05
131 32 0.05
132 9 0.01
133 2 0.00
135 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (117 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
TCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
Found at i:190201 original size:20 final size:20
Alignment explanation
Indices: 190142--190201 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
190132 AATTTCCCTT
190142 GAAACAGAAGATTTTATCTC
1 GAAACAGAAGATTTTATCTC
**** *
190162 GCTTGAGATAG--TTTACCTC
1 GAAACAGA-AGATTTTATCTC
190181 GAAACAGAAGATTTTATCTC
1 GAAACAGAAGATTTTATCTC
190201 G
1 G
190202 CTTGAGATAG
Statistics
Matches: 27, Mismatches: 10, Indels: 6
0.63 0.23 0.14
Matches are distributed among these distances:
18 2 0.07
19 11 0.41
20 12 0.44
21 2 0.07
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (20 bp):
GAAACAGAAGATTTTATCTC
Found at i:190460 original size:39 final size:39
Alignment explanation
Indices: 189760--190457 Score: 962
Period size: 39 Copynumber: 18.0 Consensus size: 39
189750 TTATTTTTAA
* * * *
189760 AGAAGATTTCATCTCTCTTGAGATAGTTTCCCTTGGAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
189799 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
189838 AGGAGATTTTATCTCGCTTGCGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
189877 AGAAAATTTTATCTCGCTTGAGATAGTTT-CCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
189915 AGAAGATTTTATCTCGCTTGAGACAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
189954 AGAAGA-TTTATCTCGCTTGAGTTAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
189992 AAAAGATTTTATCTTGCTTCAGATAGTTTCCCTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* ** *
190031 AGAAAATTTTATCTCGCTTGAGATAGTTTCCCTTAAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
190070 AGAAGATTTTGTCTTGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
190109 AGAAGA-TTTATCTTGCTTGAG-TCAATTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGAT-AGTTTCCCTCGAAAC
*
190147 AGAAGATTTTATCTCGCTTGAGATAGTTTACCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
190186 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * **
190225 AGAATA-TTTATCACGCTTGAG-TCAGTTTTCCTTAAAAC
1 AGAAGATTTTATCTCGCTTGAGAT-AGTTTCCCTCGAAAC
190263 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
190302 AGAAAAATTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
190341 AAAAGATTTTATCTCGCTTGAGACAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
190380 AGAAGA-TTTATCTCGATTGAG-TCAGCTTCTCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGAT-AGTTTCCCTCGAAAC
*
190418 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
190457 A
1 A
190458 AAATCCCTCG
Statistics
Matches: 581, Mismatches: 67, Indels: 22
0.87 0.10 0.03
Matches are distributed among these distances:
37 2 0.00
38 165 0.28
39 411 0.71
40 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:190466 original size:15 final size:15
Alignment explanation
Indices: 190446--190475 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
190436 TGAGATAGTT
190446 TCCCTCGAAACAAAA
1 TCCCTCGAAACAAAA
190461 TCCCTCGAAACAAAA
1 TCCCTCGAAACAAAA
190476 GATTTTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.33, G:0.07, T:0.13
Consensus pattern (15 bp):
TCCCTCGAAACAAAA
Found at i:190513 original size:131 final size:130
Alignment explanation
Indices: 190330--190587 Score: 374
Period size: 131 Copynumber: 2.0 Consensus size: 130
190320 TGAGATAGTT
*
190330 TCCCTCGAAACAAAAGATTTTATCTCGCTTGAGACAGTTTCCCTCGAAACAGAAGATTTATCTCG
1 TCCCTCGAAACAAAAGATTTTATCTCACTTGAGACAGTTTCCCTCGAAACAGAAGATTTATCTCG
* * *
190395 ATTGAG-TCAGCTTCTCTTGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
66 ATTGAGAT-AGCTTCCCTCGAAACAAAAGA-TTTATCTCGCTTGAGACAGTTTCCCTCGAAACAA
190459 AA
129 AA
* * *
190461 TCCCTCGAAACAAAAGATTTTATCTCACTTGAGATAGTTTCCCTCGAAACAGAATATTTGTCTCG
1 TCCCTCGAAACAAAAGATTTTATCTCACTTGAGACAGTTTCCCTCGAAACAGAAGATTTATCTCG
* * * * * *
190526 CTTGAGATAGTTTCCCTCGAAATAGAAGATTTGTCTCGCTTGAGACAGTTTTCCTCGAAACA
66 ATTGAGATAGCTTCCCTCGAAACAAAAGATTTATCTCGCTTGAGACAGTTTCCCTCGAAACA
190588 GAAGATTTTA
Statistics
Matches: 113, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
130 30 0.27
131 82 0.73
132 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (130 bp):
TCCCTCGAAACAAAAGATTTTATCTCACTTGAGACAGTTTCCCTCGAAACAGAAGATTTATCTCG
ATTGAGATAGCTTCCCTCGAAACAAAAGATTTATCTCGCTTGAGACAGTTTCCCTCGAAACAAAA
Found at i:190526 original size:92 final size:92
Alignment explanation
Indices: 190369--190547 Score: 247
Period size: 92 Copynumber: 1.9 Consensus size: 92
190359 TGAGACAGTT
* * *
190369 TCCCTCGAAACAGAAGATTTATCTCGATTGAGTCAGCTTCTCTTGAAACAAAAGATTTTATCTCG
1 TCCCTCGAAACAAAAGATTTATCTCGATTGAGTCAGCTTCCCTCGAAACAAAAGATTTTATCTCG
190434 CTTGAGATAGTTTCCCTCGAAACAAAA
66 CTTGAGATAGTTTCCCTCGAAACAAAA
* * * *
190461 TCCCTCGAAACAAAAGATTTTATCTC-ACTTGAGAT-AGTTTCCCTCGAAACAGAATA-TTTGTC
1 TCCCTCGAAACAAAAGA-TTTATCTCGA-TTGAG-TCAGCTTCCCTCGAAACAAAAGATTTTATC
190523 TCGCTTGAGATAGTTTCCCTCGAAA
63 TCGCTTGAGATAGTTTCCCTCGAAA
190548 TAGAAGATTT
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
92 47 0.61
93 29 0.38
94 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (92 bp):
TCCCTCGAAACAAAAGATTTATCTCGATTGAGTCAGCTTCCCTCGAAACAAAAGATTTTATCTCG
CTTGAGATAGTTTCCCTCGAAACAAAA
Found at i:190602 original size:39 final size:39
Alignment explanation
Indices: 190461--190663 Score: 311
Period size: 39 Copynumber: 5.3 Consensus size: 39
190451 CGAAACAAAA
* *
190461 TCCCTCGAAACAAAAGATTTTATCTCACTTGAGATAGTT
1 TCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
* *
190500 TCCCTCGAAACAGAATA-TTTGTCTCGCTTGAGATAGTT
1 TCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
* * *
190538 TCCCTCGAAATAGAAGA-TTTGTCTCGCTTGAGACAGTT
1 TCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
*
190576 TTCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
1 TCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
*
190615 TCCCTCAAAACAGAAGATTTTATCTCGCTTGAGATAGTT
1 TCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
190654 TCCCTCGAAA
1 TCCCTCGAAA
190664 TCTTACTTGA
Statistics
Matches: 149, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
38 69 0.46
39 80 0.54
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (39 bp):
TCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
Found at i:190602 original size:77 final size:77
Alignment explanation
Indices: 190461--190663 Score: 309
Period size: 77 Copynumber: 2.6 Consensus size: 77
190451 CGAAACAAAA
* * * *
190461 TCCCTCGAAACAAAAGATTTTATCTCACTTGAGATAGTTTCCCTCGAAACAGAATATTTGTCTCG
1 TCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTATCTCG
190526 CTTGAGATAGTT
66 CTTGAGATAGTT
* * * *
190538 TCCCTCGAAATAGAAGA-TTTGTCTCGCTTGAGACAGTTTTCCTCGAAACAGAAGATTTTATCTC
1 TCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGA-TTTATCTC
190602 GCTTGAGATAGTT
65 GCTTGAGATAGTT
*
190615 TCCCTCAAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAA
1 TCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAA
190664 TCTTACTTGA
Statistics
Matches: 111, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
76 33 0.30
77 50 0.45
78 28 0.25
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (77 bp):
TCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTATCTCG
CTTGAGATAGTT
Found at i:191182 original size:91 final size:91
Alignment explanation
Indices: 191027--191207 Score: 267
Period size: 91 Copynumber: 2.0 Consensus size: 91
191017 AGATAAACCG
* * *
191027 ATCAACATTTCCGATGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGAAGAAGACGTTCAT
1 ATCAACATTTCCGATGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGAAGAAGAAGTTCAT
**
191092 AATGGGAAG-AGCTTGTTCAACCTTGC
66 AATAAGAAGAAG-TTGTTCAACCTTGC
* *
191118 ATCAACATTTCC-AGTGGAGAGTTCATAATGAGAAAAACTCATCCAATGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCGA-TGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGAAGAAGAAGTTCA
191182 TAATAAGAAGAAGTTGTTCAACCTTG
65 TAATAAGAAGAAGTTGTTCAACCTTG
191208 GTTCGATCCC
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
90 1 0.01
91 78 0.96
92 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.24
Consensus pattern (91 bp):
ATCAACATTTCCGATGGAGAGTTCATAATGAGAAAAACTCATCCAACGAGGAAGAAGAAGTTCAT
AATAAGAAGAAGTTGTTCAACCTTGC
Found at i:191351 original size:119 final size:119
Alignment explanation
Indices: 191118--191555 Score: 623
Period size: 119 Copynumber: 3.7 Consensus size: 119
191108 TCAACCTTGC
*
191118 ATCAACA-TTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCC-A-ATGAGGGAGAAGAAGTT
1 ATCAACATTTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACA-GAGGGAGAAGAAGTT
* * * * *
191180 CATAATAAGAAGAAGTTGTTCAACCTTGGTTCGATCCCATCACAGAAGGAGGTGG
65 CATAATGAGAAGAACTTGTTCAACCTTGGTTCAATTCCATCAAAGAAGGAGGTGG
* * * *
191235 ATCAATATTTTCTATTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGCGAAGAAGTTC
1 ATCAACATTTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTC
* *
191300 ATAATGAGAAGAACTTGTTCAACTTTGGTTCAATTCCATCAAAGAATGAGGTGG
66 ATAATGAGAAGAACTTGTTCAACCTTGGTTCAATTCCATCAAAGAAGGAGGTGG
* * * *
191354 ATCAACATTTTCCAGTAGAGAGTTCATAATTAGAAGAACTCATCCGACAGTGGGAGAAGAACTTC
1 ATCAACATTTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTC
* * *
191419 ATAATGAGAAGAACTTGTTTAACCTTGGTTCAATTCTATCATAGAAGGAGGTGG
66 ATAATGAGAAGAACTTGTTCAACCTTGGTTCAATTCCATCAAAGAAGGAGGTGG
* * *
191473 ATCAACATTTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGAACAGAAGAGTGAA-AAGT
1 ATCAACATTTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCG-ACAG-AGGGAGAAGAAGT
191537 TCATAATGAGAAGAACTTG
64 TCATAATGAGAAGAACTTG
191556 GAACTCAAAA
Statistics
Matches: 284, Mismatches: 32, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
117 6 0.02
118 34 0.12
119 212 0.75
120 27 0.10
121 5 0.02
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.26
Consensus pattern (119 bp):
ATCAACATTTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTGGTTCAATTCCATCAAAGAAGGAGGTGG
Found at i:192764 original size:21 final size:20
Alignment explanation
Indices: 192727--192768 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
192717 TATGTCCTTA
192727 TATTTAATGTTTATTTTCATT
1 TATTTAATGTTTATTTT-ATT
*
192748 TATTTTATGTTGT-TTTTATT
1 TATTTAATGTT-TATTTTATT
192768 T
1 T
192769 TACTGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 14 0.74
22 1 0.05
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.71
Consensus pattern (20 bp):
TATTTAATGTTTATTTTATT
Found at i:192802 original size:17 final size:16
Alignment explanation
Indices: 192746--192802 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 16
192736 TTTATTTTCA
192746 TTTATTTTATGTTG-TT
1 TTTATTTTAT-TTGATT
*
192762 TTTATTTTA-CTGATT
1 TTTATTTTATTTGATT
192777 TTTATTTTTATTTGATAT
1 TTTA-TTTTATTTGAT-T
192795 TTTATTTT
1 TTTATTTT
192803 TTTAATTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
14 2 0.06
15 6 0.17
16 14 0.40
17 8 0.23
18 5 0.14
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.74
Consensus pattern (16 bp):
TTTATTTTATTTGATT
Found at i:196046 original size:3 final size:3
Alignment explanation
Indices: 196038--196091 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
196028 ATGCTCCTGT
* * *
196038 TGA TGA TGA TGA TGA TGG TGG TGA TGA TGA TGA CGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
196086 TGA TGA
1 TGA TGA
196092 GAGTGAAGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:198559 original size:22 final size:22
Alignment explanation
Indices: 198534--198605 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
198524 CGCCACAACT
198534 CATAATTTGCACCAAAGTGTCA
1 CATAATTTGCACCAAAGTGTCA
* * *
198556 CATAATTAT-C-CTAGAG-GACCA
1 CATAATT-TGCACCAAAGTG-TCA
*
198577 CATAGTTTGCACCAAAGTGTCA
1 CATAATTTGCACCAAAGTGTCA
*
198599 GATAATT
1 CATAATT
198606 ATCCTATAGG
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
20 2 0.06
21 13 0.36
22 19 0.53
23 2 0.06
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (22 bp):
CATAATTTGCACCAAAGTGTCA
Found at i:198604 original size:43 final size:43
Alignment explanation
Indices: 198534--198666 Score: 212
Period size: 43 Copynumber: 3.1 Consensus size: 43
198524 CGCCACAACT
*
198534 CATAATTTGCACCAAAGTGTCACATAATTATCCTAGAGGACCA
1 CATAGTTTGCACCAAAGTGTCACATAATTATCCTAGAGGACCA
* *
198577 CATAGTTTGCACCAAAGTGTCAGATAATTATCCTATAGGACCA
1 CATAGTTTGCACCAAAGTGTCACATAATTATCCTAGAGGACCA
* * *
198620 CATAGTTTGCACCAAAGTGCCATATAATTGTCCTAGAGGACCA
1 CATAGTTTGCACCAAAGTGTCACATAATTATCCTAGAGGACCA
198663 CATA
1 CATA
198667 ATTGTCCCGA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (43 bp):
CATAGTTTGCACCAAAGTGTCACATAATTATCCTAGAGGACCA
Found at i:198668 original size:21 final size:21
Alignment explanation
Indices: 198643--198687 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
198633 AAAGTGCCAT
198643 ATAATTGTCCTAG-AGGACCAC
1 ATAATTGTCC-AGAAGGACCAC
*
198664 ATAATTGTCCCGAAGGACCAC
1 ATAATTGTCCAGAAGGACCAC
198685 ATA
1 ATA
198688 GACCCTCGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (21 bp):
ATAATTGTCCAGAAGGACCAC
Found at i:199453 original size:19 final size:20
Alignment explanation
Indices: 199429--199488 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
199419 GTATCGGTAC
199429 CACCCT-AAGGGTACCGATA
1 CACCCTCAAGGGTACCGATA
*
199448 CACCCTTCAAGGGTATCGATA
1 CACCC-TCAAGGGTACCGATA
*
199469 C-CTCTGC-AGGGTACCGATA
1 CACCCT-CAAGGGTACCGATA
199488 C
1 C
199489 TGAATTTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 18 0.51
20 4 0.11
21 13 0.37
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.20
Consensus pattern (20 bp):
CACCCTCAAGGGTACCGATA
Found at i:199461 original size:21 final size:20
Alignment explanation
Indices: 199435--199488 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
199425 GTACCACCCT
*
199435 AAGGGTACCGATACACCCTTC
1 AAGGGTACCGATAC-CCCTGC
* *
199456 AAGGGTATCGATACCTCTGC
1 AAGGGTACCGATACCCCTGC
199476 -AGGGTACCGATAC
1 AAGGGTACCGATAC
199489 TGAATTTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (20 bp):
AAGGGTACCGATACCCCTGC
Found at i:202144 original size:18 final size:21
Alignment explanation
Indices: 202106--202144 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
202096 TTTCTTTCAA
202106 ATAATCATATATAAAATAAAT
1 ATAATCATATATAAAATAAAT
202127 ATAAT-ATA-ATAAAA-AAAT
1 ATAATCATATATAAAATAAAT
202145 TTACCTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 3 0.17
21 5 0.28
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAATCATATATAAAATAAAT
Found at i:205248 original size:15 final size:15
Alignment explanation
Indices: 205230--205267 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
205220 GAACAAATAA
205230 CAGTAGACCTTATAC
1 CAGTAGACCTTATAC
205245 CAGTAGACCTTATAC
1 CAGTAGACCTTATAC
205260 CAGTAGAC
1 CAGTAGAC
205268 TTGATAGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (15 bp):
CAGTAGACCTTATAC
Found at i:207822 original size:20 final size:19
Alignment explanation
Indices: 207785--207827 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
207775 TGAATGACAT
207785 ATAAATATATAAACAAATTA
1 ATAAATATATAAACAAA-TA
*
207805 ATAAATAT-TAAATGAAATA
1 ATAAATATATAAA-CAAATA
207824 ATAA
1 ATAA
207828 GATACATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
ATAAATATATAAACAAATA
Found at i:208814 original size:12 final size:12
Alignment explanation
Indices: 208797--208835 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
208787 GATCATTAAC
208797 ATATAATATAAA
1 ATATAATATAAA
208809 ATATAAATAATAAA
1 ATAT-AAT-ATAAA
*
208823 ATATATTATAAA
1 ATATAATATAAA
208835 A
1 A
208836 ATATGCTACG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 10 0.42
13 5 0.21
14 9 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:209088 original size:6 final size:6
Alignment explanation
Indices: 209079--209110 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
209069 TGACAAGCTC
*
209079 ACATGA ACATGA ACATAA ACATGA ACATGA AC
1 ACATGA ACATGA ACATGA ACATGA ACATGA AC
209111 CGAACCAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.53, C:0.19, G:0.12, T:0.16
Consensus pattern (6 bp):
ACATGA
Found at i:211992 original size:144 final size:146
Alignment explanation
Indices: 211822--212092 Score: 528
Period size: 146 Copynumber: 1.9 Consensus size: 146
211812 AACTGAGCTA
211822 TCTATCTGATGTAATCCGACTC-TTTTTTTTTC-TTTTTTTTTGCTCTCTTTTGTTTTTACTTGG
1 TCTATCTGATGTAATCCGACTCTTTTTTTTTTCTTTTTTTTTTGCTCTCTTTTGTTTTTACTTGG
211885 TTGGGTTGTTGTTCTTGTCACTGCTTCGTTGGGCACGCCCGCAGGTTTTGCAGAGAAACTTATTA
66 TTGGGTTGTTGTTCTTGTCACTGCTTCGTTGGGCACGCCCGCAGGTTTTGCAGAGAAACTTATTA
211950 GCAGGGGTTGTTGCTC
131 GCAGGGGTTGTTGCTC
211966 TCTATCTGATGTAATCCGACTCTTTTTTTTTTCTTTTTTTTTTGCTCTCTTTTGTTTTTACTTGG
1 TCTATCTGATGTAATCCGACTCTTTTTTTTTTCTTTTTTTTTTGCTCTCTTTTGTTTTTACTTGG
212031 TTGGGTTGTTGTTCTTGTCACTGCTTCGTTGGGCACGCCCGCAGGTTTTGCAGAGAAACTTA
66 TTGGGTTGTTGTTCTTGTCACTGCTTCGTTGGGCACGCCCGCAGGTTTTGCAGAGAAACTTA
212093 GCAGGGGGCT
Statistics
Matches: 125, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
144 22 0.18
145 10 0.08
146 93 0.74
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (146 bp):
TCTATCTGATGTAATCCGACTCTTTTTTTTTTCTTTTTTTTTTGCTCTCTTTTGTTTTTACTTGG
TTGGGTTGTTGTTCTTGTCACTGCTTCGTTGGGCACGCCCGCAGGTTTTGCAGAGAAACTTATTA
GCAGGGGTTGTTGCTC
Found at i:215982 original size:16 final size:16
Alignment explanation
Indices: 215955--216000 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
215945 GATATGAGAA
215955 AAATTCAATTTAAATTT
1 AAATT-AATTTAAATTT
*
215972 AAATTAATTTAATTTT
1 AAATTAATTTAAATTT
*
215988 AAAATAATGTTAA
1 AAATTAAT-TTAA
216001 TAAGTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
AAATTAATTTAAATTT
Found at i:218188 original size:173 final size:173
Alignment explanation
Indices: 217899--218246 Score: 687
Period size: 173 Copynumber: 2.0 Consensus size: 173
217889 GTAGTTATCG
217899 GAATATATAATATGAAACTTGTACAATTTGATCGGATTCCAGGAACGAGGTCCTATTCAAGAGAA
1 GAATATATAATATGAAACTTGTACAATTTGATCGGATTCCAGGAACGAGGTCCTATTCAAGAGAA
*
217964 TTGATTACTAAACAATCTAATTAGGCATTTAAGGTTGATACTATAGAATCCCATTATGTTTCATG
66 TTGATTACTAAACAATCTAATCAGGCATTTAAGGTTGATACTATAGAATCCCATTATGTTTCATG
218029 TACATCATGAAAGCATTCAGGAATGATCGGAGTAATTTGAGCT
131 TACATCATGAAAGCATTCAGGAATGATCGGAGTAATTTGAGCT
218072 GAATATATAATATGAAACTTGTACAATTTGATCGGATTCCAGGAACGAGGTCCTATTCAAGAGAA
1 GAATATATAATATGAAACTTGTACAATTTGATCGGATTCCAGGAACGAGGTCCTATTCAAGAGAA
218137 TTGATTACTAAACAATCTAATCAGGCATTTAAGGTTGATACTATAGAATCCCATTATGTTTCATG
66 TTGATTACTAAACAATCTAATCAGGCATTTAAGGTTGATACTATAGAATCCCATTATGTTTCATG
218202 TACATCATGAAAGCATTCAGGAATGATCGGAGTAATTTGAGCT
131 TACATCATGAAAGCATTCAGGAATGATCGGAGTAATTTGAGCT
218245 GA
1 GA
218247 TAAAGGAGAA
Statistics
Matches: 174, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
173 174 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (173 bp):
GAATATATAATATGAAACTTGTACAATTTGATCGGATTCCAGGAACGAGGTCCTATTCAAGAGAA
TTGATTACTAAACAATCTAATCAGGCATTTAAGGTTGATACTATAGAATCCCATTATGTTTCATG
TACATCATGAAAGCATTCAGGAATGATCGGAGTAATTTGAGCT
Found at i:218992 original size:18 final size:18
Alignment explanation
Indices: 218969--219004 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
218959 TTTGAATTTC
218969 TTAATTAATCTAAGACAT
1 TTAATTAATCTAAGACAT
* *
218987 TTAATTAGTCTAGGACAT
1 TTAATTAATCTAAGACAT
219005 AAGGGTATTT
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:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (18 bp):
TTAATTAATCTAAGACAT
Found at i:224514 original size:21 final size:21
Alignment explanation
Indices: 224483--224539 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
224473 ATGAACTGGA
* *
224483 TGAACAGTATCGATACTGGT-
1 TGAAGAGTATCGATACTGATG
224503 TGAAGAAGTATCGATACTGATG
1 TGAAG-AGTATCGATACTGATG
224525 TGAAG-GTATCGATAC
1 TGAAGAGTATCGATAC
224540 CAAGGATACG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.42
21 14 0.42
22 5 0.15
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.28
Consensus pattern (21 bp):
TGAAGAGTATCGATACTGATG
Found at i:224638 original size:22 final size:23
Alignment explanation
Indices: 224613--224655 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
224603 ACTGAAGTAG
224613 GTATCAATACCATA-GAAGAGAA
1 GTATCAATACCATAGGAAGAGAA
* *
224635 GTATCGATACTATAGGAAGAG
1 GTATCAATACCATAGGAAGAG
224656 TATCGATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (23 bp):
GTATCAATACCATAGGAAGAGAA
Found at i:225234 original size:15 final size:15
Alignment explanation
Indices: 225216--225268 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
225206 ATATGATATA
*
225216 TGAATAAATGCTATG
1 TGAATAAATACTATG
225231 TGAAATGAAATACTATG
1 TG-AAT-AAATACTATG
* * *
225248 AGAATAAGTTCTATG
1 TGAATAAATACTATG
225263 TGAATA
1 TGAATA
225269 TGTGATAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 15 0.48
16 6 0.19
17 10 0.32
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (15 bp):
TGAATAAATACTATG
Found at i:225450 original size:23 final size:23
Alignment explanation
Indices: 225420--225517 Score: 96
Period size: 23 Copynumber: 4.3 Consensus size: 23
225410 TTGAGGGTTA
* *
225420 TATGTGGTCATTCGAGATAAATC
1 TATGTGGTCATTCGGGACAAATC
*
225443 TATGTGGTCCATT-GGGACAAACC
1 TATGTGGT-CATTCGGGACAAATC
*
225466 TATGTGGTCATCCGGGACAAATTC
1 TATGTGGTCATTCGGGACAAA-TC
225490 TATGTGG-CACTTCGGTG-CAAAT-
1 TATGTGGTCA-TTCGG-GACAAATC
225512 TATGTG
1 TATGTG
225518 AGCAGTGGTG
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
22 9 0.14
23 34 0.53
24 20 0.31
25 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (23 bp):
TATGTGGTCATTCGGGACAAATC
Found at i:230444 original size:20 final size:20
Alignment explanation
Indices: 230396--230467 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
230386 GGATGAACAA
*
230396 TATCGATACTGGT-TGAAGAAG
1 TATCGATACTGATATGAAG--G
*
230417 TATGGATACTGATATGAAGG
1 TATCGATACTGATATGAAGG
** *
230437 TATCGATACCAAGGAT-AAGG
1 TATCGATACTGA-TATGAAGG
230457 TATCGATACTG
1 TATCGATACTG
230468 TAAGTAAAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
20 23 0.56
21 13 0.32
22 5 0.12
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (20 bp):
TATCGATACTGATATGAAGG
Found at i:231311 original size:23 final size:23
Alignment explanation
Indices: 231281--231357 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
231271 TCGAGGGTTT
* *
231281 TATGTGGTCAATCGGGACAAATC
1 TATGTGGTCATTCGGGAAAAATC
*
231304 TATGTGGTCCTTCGGGAAAAATC
1 TATGTGGTCATTCGGGAAAAATC
*
231327 TATGTGGTCATTCGGGATAAATTC
1 TATGTGGTCATTCGGGA-AAAATC
231351 TATGTGG
1 TATGTGG
231358 CACTTCGATG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 36 0.75
24 12 0.25
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.32
Consensus pattern (23 bp):
TATGTGGTCATTCGGGAAAAATC
Found at i:231938 original size:11 final size:11
Alignment explanation
Indices: 231924--231956 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
231914 TCCAAATGAA
231924 AGTCAAATTTT
1 AGTCAAATTTT
231935 AGTCAAATTTT
1 AGTCAAATTTT
231946 AGTCAAATTTT
1 AGTCAAATTTT
231957 CAAAGAGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (11 bp):
AGTCAAATTTT
Found at i:234305 original size:26 final size:26
Alignment explanation
Indices: 234246--234305 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
234236 GATTTTATGT
*
234246 TAGGGGAT--CAAATTTATGAAATTG
1 TAGGGGATGACAAATTTATAAAATTG
* *
234270 TAAGGAATGACAAATTTATAAAATTG
1 TAGGGGATGACAAATTTATAAAATTG
234296 TAGGGGATGA
1 TAGGGGATGA
234306 AAACAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 6 0.21
26 23 0.79
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.30
Consensus pattern (26 bp):
TAGGGGATGACAAATTTATAAAATTG
Found at i:237111 original size:31 final size:31
Alignment explanation
Indices: 237059--237129 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
237049 ATTCAGGTAT
* *
237059 GATTTTTTTTAAAAAAATTGGGATCTGGTTG
1 GATTTTTTTTAAAAAAATTGGGATCGGGTCG
** *
237090 GATTTTTTTTAAAAATTTTGGGTTCGGGTCG
1 GATTTTTTTTAAAAAAATTGGGATCGGGTCG
*
237121 GGTTTTTTT
1 GATTTTTTT
237130 AAGTGTGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.21, C:0.04, G:0.24, T:0.51
Consensus pattern (31 bp):
GATTTTTTTTAAAAAAATTGGGATCGGGTCG
Found at i:240610 original size:9 final size:9
Alignment explanation
Indices: 240583--240628 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
240573 TAAAATTATG
240583 ATAAT-TTA
1 ATAATATTA
* *
240591 ATAAAAGTA
1 ATAATATTA
240600 ATAATATTA
1 ATAATATTA
240609 ATAATATT-
1 ATAATATTA
240617 ATAATA-TA
1 ATAATATTA
240625 ATAA
1 ATAA
240629 AATATACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 1 0.03
8 14 0.44
9 17 0.53
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (9 bp):
ATAATATTA
Found at i:245718 original size:20 final size:20
Alignment explanation
Indices: 245693--245735 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
245683 TCTAAAGGCC
245693 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
245713 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
245733 CAT
1 CAT
245736 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:253467 original size:21 final size:21
Alignment explanation
Indices: 253443--253483 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
253433 ACGTTTTCAC
*
253443 CTTTCACTTCCTATCTTTTTA
1 CTTTCACTTCCTATCATTTTA
* *
253464 CTTTTACTTTCTATCATTTT
1 CTTTCACTTCCTATCATTTT
253484 CTTCTCCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (21 bp):
CTTTCACTTCCTATCATTTTA
Found at i:256136 original size:20 final size:20
Alignment explanation
Indices: 256111--256153 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
256101 TCTAAAAGCC
256111 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
256131 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
256151 CAT
1 CAT
256154 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:266540 original size:25 final size:25
Alignment explanation
Indices: 266506--266565 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
266496 ATTTATAGTA
*
266506 GAAAACTAATATTTATTATAATGAC
1 GAAAAATAATATTTATTATAATGAC
*
266531 TAAAAATAATATTTATTATAATGAC
1 GAAAAATAATATTTATTATAATGAC
266556 GAAAAATAAT
1 GAAAAATAAT
266566 GGCATGATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (25 bp):
GAAAAATAATATTTATTATAATGAC
Found at i:266622 original size:44 final size:42
Alignment explanation
Indices: 266572--266696 Score: 152
Period size: 37 Copynumber: 3.0 Consensus size: 42
266562 TAATGGCATG
266572 ATTAATTATCCATTAATAAATCAGGTAGGTTGGTGGTGGTGGTT
1 ATTAATTATCCATTAAT-AA-CAGGTAGGTTGGTGGTGGTGGTT
* *
266616 ATTAATTATCCATTAATAAC---TGGGTAGGT--TGGTGGTT
1 ATTAATTATCCATTAATAACAGGTAGGTTGGTGGTGGTGGTT
*
266653 ATTAATTATCCATTAATAACAGGGTAGGTTGTTGGTTGGTGGTT
1 ATTAATTATCCATTAATAACA-GGTAGGTTGGTGG-TGGTGGTT
266697 GAACGAGAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
37 28 0.41
39 7 0.10
41 6 0.09
42 1 0.01
43 2 0.03
44 25 0.36
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.40
Consensus pattern (42 bp):
ATTAATTATCCATTAATAACAGGTAGGTTGGTGGTGGTGGTT
Found at i:266862 original size:34 final size:33
Alignment explanation
Indices: 266816--266895 Score: 117
Period size: 34 Copynumber: 2.4 Consensus size: 33
266806 TTTAAGCATT
*
266816 ATTTTTATAAAAAAATATTGTTAATATATTTAA
1 ATTTTAATAAAAAAATATTGTTAATATATTTAA
* *
266849 ATTTATAATAAAAAATTATTGTTAATATATTTAC
1 ATTT-TAATAAAAAAATATTGTTAATATATTTAA
266883 ATTTTAA-AAAAAA
1 ATTTTAATAAAAAA
266896 TTAATAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 6 0.14
33 7 0.16
34 30 0.70
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (33 bp):
ATTTTAATAAAAAAATATTGTTAATATATTTAA
Found at i:269333 original size:27 final size:27
Alignment explanation
Indices: 269295--269468 Score: 127
Period size: 27 Copynumber: 6.2 Consensus size: 27
269285 TTTAATGAAC
269295 GTGATTAATATCAATAGTTGAATTAAT
1 GTGATTAATATCAATAGTTGAATTAAT
* *
269322 GTGATTAATATCAATATTTGGATTAATAT
1 GTGATTAATATCAATAGTTGAATT-A-AT
** * * * *
269351 GATGGATATTTGTTGATGCTATACTTTAATGAAT
1 G-T-G--A-TTAAT-AT-CAATAGTTGAATTAAT
*
269385 GTGATTAATATCAATAGTTGAATGAAT
1 GTGATTAATATCAATAGTTGAATTAAT
** *
269412 GTGAAAAATATCAATAGTTAAATTAA-
1 GTGATTAATATCAATAGTTGAATTAAT
*
269438 -TGATTAATATCAATATTTGAATTAAT
1 GTGATTAATATCAATAGTTGAATTAAT
*
269464 ATGAT
1 GTGAT
269469 GGATATTTGT
Statistics
Matches: 114, Mismatches: 22, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
25 21 0.18
27 61 0.54
28 3 0.03
29 6 0.05
30 2 0.02
31 1 0.01
32 1 0.01
33 2 0.02
34 6 0.05
35 3 0.03
36 8 0.07
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.41
Consensus pattern (27 bp):
GTGATTAATATCAATAGTTGAATTAAT
Found at i:269406 original size:90 final size:90
Alignment explanation
Indices: 269248--269438 Score: 283
Period size: 90 Copynumber: 2.1 Consensus size: 90
269238 TATATATTTT
* *
269248 TTTGAATTAATTTGATGGATATTTGTTGACACTATATTTTAATGAACGTGATTAATATCAATAGT
1 TTTGAATTAATATGATGGATATTTGTTGACACTATACTTTAATGAACGTGATTAATATCAATAGT
* **
269313 TGAATTAATGTGATTAATATCAATA
66 TGAATGAATGTGAAAAATATCAATA
* ** *
269338 TTTGGATTAATATGATGGATATTTGTTGATGCTATACTTTAATGAATGTGATTAATATCAATAGT
1 TTTGAATTAATATGATGGATATTTGTTGACACTATACTTTAATGAACGTGATTAATATCAATAGT
269403 TGAATGAATGTGAAAAATATCAATA
66 TGAATGAATGTGAAAAATATCAATA
* *
269428 GTTAAATTAAT
1 TTTGAATTAAT
269439 GATTAATATC
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.42
Consensus pattern (90 bp):
TTTGAATTAATATGATGGATATTTGTTGACACTATACTTTAATGAACGTGATTAATATCAATAGT
TGAATGAATGTGAAAAATATCAATA
Found at i:269452 original size:25 final size:25
Alignment explanation
Indices: 269386--269463 Score: 93
Period size: 25 Copynumber: 3.0 Consensus size: 25
269376 TTAATGAATG
*
269386 TGATTAATATCAATAGTTGAATGAA
1 TGATTAATATCAATAGTTGAATTAA
** *
269411 TGTGAAAAATATCAATAGTTAAATTAA
1 --TGATTAATATCAATAGTTGAATTAA
*
269438 TGATTAATATCAATATTTGAATTAA
1 TGATTAATATCAATAGTTGAATTAA
269463 T
1 T
269464 ATGATGGATA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 22 0.51
27 21 0.49
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (25 bp):
TGATTAATATCAATAGTTGAATTAA
Found at i:269462 original size:115 final size:116
Alignment explanation
Indices: 269301--269542 Score: 360
Period size: 115 Copynumber: 2.1 Consensus size: 116
269291 GAACGTGATT
* * *
269301 AATATCAATAGTTGAATTAATGTGATTAATATCAATATTTGGATTAATATGATGGATATTTGTTG
1 AATATCAATAGTTAAATTAA-GTGATTAATATCAATATTTGAATTAATATGATGGATATTTGTTA
* * * *
269366 ATGCTATACTTTAATGAATGTGATTAATATCAATAGTTGAATGAATGTGAAA
65 ATGCTATACTTTAACGAACGTGAATAATATCAATACTTGAATGAATGTGAAA
269418 AATATCAATAGTTAAATTAA-TGATTAATATCAATATTTGAATTAATATGATGGATATTTGTTAA
1 AATATCAATAGTTAAATTAAGTGATTAATATCAATATTTGAATTAATATGATGGATATTTGTTAA
* * * **
269482 TGTTATATTTTAACGAACGTGAATAATATCAATACTTGAATTAATGTGATT
66 TGCTATACTTTAACGAACGTGAATAATATCAATACTTGAATGAATGTGAAA
269533 AATATCAATA
1 AATATCAATA
269543 TTTGAATGAT
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
115 94 0.83
117 19 0.17
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.40
Consensus pattern (116 bp):
AATATCAATAGTTAAATTAAGTGATTAATATCAATATTTGAATTAATATGATGGATATTTGTTAA
TGCTATACTTTAACGAACGTGAATAATATCAATACTTGAATGAATGTGAAA
Found at i:271121 original size:84 final size:84
Alignment explanation
Indices: 271017--271266 Score: 285
Period size: 83 Copynumber: 3.0 Consensus size: 84
271007 AACTCGACAA
** *
271017 TTTTGTTGATAGATAGCCCTTCTTGCCTCGAGCTATAGTGTAAATGATGTGCCCTTGAGCTGAGT
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATAGTGTAAATGATGTGCCCTTGAGCTGAGT
271082 GTAATCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * * * * *
271101 TTTTGTTGGCAGATAGCCCTTCTCGACTTAATCTAT-GTTGCAAATGACGTG-TCTTG-GACATG
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATAG-TGTAAATGATGTGCCCTTGAG-C-TG
* *
271163 CGAT-TAGTCGAACTCGAAGGTC
63 AG-TGTAATCGAACTCGAAGGTC
* * *
271185 -TTGGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATATTGTAAATGATGTGCCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATAGTGTAAATGATGTGCCCTTGAGCTGAGT
*
271249 GTAACCGAACTCGAAGGT
66 GTAATCGAACTCGAAGGT
271267 TTTGTATTTC
Statistics
Matches: 133, Mismatches: 25, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
82 2 0.02
83 65 0.49
84 64 0.48
85 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (84 bp):
TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATAGTGTAAATGATGTGCCCTTGAGCTGAGT
GTAATCGAACTCGAAGGTC
Found at i:271307 original size:28 final size:28
Alignment explanation
Indices: 271273--271330 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
271263 AGGTTTTGTA
* *
271273 TTTCAAGAGAAA-TATTTTCAAGGGTTTT
1 TTTCAAGAGAAACGA-TTTCAAAGGTTTT
271301 TTTCAAGAGAAACGATTTCAAAGGTTTT
1 TTTCAAGAGAAACGATTTCAAAGGTTTT
271329 TT
1 TT
271331 GTGTTTCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (28 bp):
TTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:271417 original size:67 final size:69
Alignment explanation
Indices: 271297--271450 Score: 181
Period size: 67 Copynumber: 2.3 Consensus size: 69
271287 TTTTCAAGGG
* * * *
271297 TTTT-TTTCAAGAGAAACGATTTCAAAGGTTTTTTGTGTTTCAAGAGAAACTGTCTAAAGGGAGG
1 TTTTGTTTCAAGAGAAACGATTTCAAAGG-TATTGGTGTTTCAAGAGAAACTGTCTAAAGAGAGA
271361 CAAAA
65 CAAAA
*
271366 TTTTGTTTCAAGAGAAAC-ATATTCAAA-G-ATTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 TTTTGTTTCAAGAGAAACGAT-TTCAAAGGTATTGGTGTTTCAAGAGAAACTGTCTAAAGAGAGA
271428 CAAAA
65 CAAAA
* * * *
271433 CTTAGTTCCAAAAGAAAC
1 TTTTGTTTCAAGAGAAAC
271451 TGTCTTAAGG
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
67 48 0.65
69 7 0.09
70 19 0.26
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (69 bp):
TTTTGTTTCAAGAGAAACGATTTCAAAGGTATTGGTGTTTCAAGAGAAACTGTCTAAAGAGAGAC
AAAA
Found at i:271581 original size:21 final size:20
Alignment explanation
Indices: 271519--271583 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
271509 GGAAACTATC
271519 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGAC-AAATTTGTT
* *
271540 TCAAG-G-G--AAA-CTGTC
1 TCAAGAGAGACAAATTTGTT
271555 TCAAGAGAGACAAAGTTTGTT
1 TCAAGAGAGACAAA-TTTGTT
271576 TCAAGAGA
1 TCAAGAGA
271584 AACTGTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 1 0.03
19 4 0.12
20 1 0.03
21 16 0.47
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (20 bp):
TCAAGAGAGACAAATTTGTT
Found at i:271605 original size:36 final size:36
Alignment explanation
Indices: 271499--271605 Score: 171
Period size: 36 Copynumber: 3.0 Consensus size: 36
271489 ATTCAAAGAT
* *
271499 TTTGTTTC-AGGGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAG
271534 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAG
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAG
* *
271570 TTTGTTTCAAGAGAAACTGTCTCAAGATAGACAAAG
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAG
271606 AAAAAATTTG
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 8 0.12
36 59 0.88
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAG
Found at i:275448 original size:24 final size:24
Alignment explanation
Indices: 275420--275480 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
275410 AAATAACAAA
*
275420 ATGCAAAAAATGTCTAAATGCA-TG
1 ATGCAAAAAATGTCT-AAGGCATTG
** *
275444 ATGCATGAAATGTCTGAGGCATTG
1 ATGCAAAAAATGTCTAAGGCATTG
*
275468 ATCCAAAAAATGT
1 ATGCAAAAAATGT
275481 GCATGTTATT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (24 bp):
ATGCAAAAAATGTCTAAGGCATTG
Found at i:277040 original size:13 final size:13
Alignment explanation
Indices: 277022--277051 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
277012 TTAATTGCGA
277022 AAAATTAAAAATT
1 AAAATTAAAAATT
*
277035 AAAATTAAAATTT
1 AAAATTAAAAATT
277048 AAAA
1 AAAA
277052 ACTCAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:277927 original size:21 final size:21
Alignment explanation
Indices: 277903--278027 Score: 83
Period size: 21 Copynumber: 6.0 Consensus size: 21
277893 GATTCGCGTT
277903 GCGATAGTCCAAAATCGCAAC
1 GCGATAGTCCAAAATCGCAAC
* * * * ***
277924 GCGAT-TTTCAGATTCGCGTT
1 GCGATAGTCCAAAATCGCAAC
**
277944 GCGATAGTCCAAAATCGCATT
1 GCGATAGTCCAAAATCGCAAC
* *
277965 GCGATCGTCCAAAATCACAAC
1 GCGATAGTCCAAAATCGCAAC
* * * * **
277986 GCGAT-TTTCATATTCGCATT
1 GCGATAGTCCAAAATCGCAAC
278006 GCGATAGTCCAAAATCGCAAC
1 GCGATAGTCCAAAATCGCAAC
278027 G
1 G
278028 GTAAAGCGAC
Statistics
Matches: 73, Mismatches: 29, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
20 26 0.36
21 47 0.64
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (21 bp):
GCGATAGTCCAAAATCGCAAC
Found at i:277947 original size:20 final size:20
Alignment explanation
Indices: 277883--277948 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
277873 AAATCTCAAC
*
277883 GCGATTTTTAGATTCGCGTT
1 GCGATTTTCAGATTCGCGTT
* * * * ***
277903 GCGATAGTCCAAAATCGCAAC
1 GCGAT-TTTCAGATTCGCGTT
277924 GCGATTTTCAGATTCGCGTT
1 GCGATTTTCAGATTCGCGTT
277944 GCGAT
1 GCGAT
277949 AGTCCAAAAT
Statistics
Matches: 30, Mismatches: 15, Indels: 2
0.64 0.32 0.04
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (20 bp):
GCGATTTTCAGATTCGCGTT
Found at i:277969 original size:41 final size:41
Alignment explanation
Indices: 277844--277962 Score: 211
Period size: 41 Copynumber: 2.9 Consensus size: 41
277834 TTCGCATTGA
* *
277844 GATTTTCAGATTTGCGTTGCGATAGTCCAAAATCTCAACGC
1 GATTTTCAGATTCGCGTTGCGATAGTCCAAAATCGCAACGC
*
277885 GATTTTTAGATTCGCGTTGCGATAGTCCAAAATCGCAACGC
1 GATTTTCAGATTCGCGTTGCGATAGTCCAAAATCGCAACGC
277926 GATTTTCAGATTCGCGTTGCGATAGTCCAAAATCGCA
1 GATTTTCAGATTCGCGTTGCGATAGTCCAAAATCGCA
277963 TTGCGATCGT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (41 bp):
GATTTTCAGATTCGCGTTGCGATAGTCCAAAATCGCAACGC
Found at i:277975 original size:62 final size:62
Alignment explanation
Indices: 277896--278024 Score: 213
Period size: 62 Copynumber: 2.1 Consensus size: 62
277886 ATTTTTAGAT
* * *
277896 TCGCGTTGCGATAGTCCAAAATCGCAACGCGATTTTCAGATTCGCGTTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAATCACAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAAA
* *
277958 TCGCATTGCGATCGTCCAAAATCACAACGCGATTTTCATATTCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAATCACAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAAA
278020 TCGCA
1 TCGCA
278025 ACGGTAAAGC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (62 bp):
TCGCATTGCGATAGTCCAAAATCACAACGCGATTTTCAGATTCGCATTGCGATAGTCCAAAA
Found at i:279224 original size:21 final size:21
Alignment explanation
Indices: 279160--279224 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
279150 TTTACCGTTA
*
279160 CGATTTTGGACTATCGCAACT
1 CGATTTTGGACTATCGCAACG
* * ** ***
279181 CGAATCT-GAAAATCGCGTTG
1 CGATTTTGGACTATCGCAACG
279201 CGATTTTGGACTATCGCAACG
1 CGATTTTGGACTATCGCAACG
279222 CGA
1 CGA
279225 ATCTGAAAAT
Statistics
Matches: 28, Mismatches: 15, Indels: 2
0.62 0.33 0.04
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (21 bp):
CGATTTTGGACTATCGCAACG
Found at i:279244 original size:20 final size:20
Alignment explanation
Indices: 279181--279244 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
279171 TATCGCAACT
279181 CGAATCTGAAAATCGCGTTG
1 CGAATCTGAAAATCGCGTTG
* * ** ***
279201 CGATTTTGGACTATCGCAACG
1 CGAATCT-GAAAATCGCGTTG
279222 CGAATCTGAAAATCGCGTTG
1 CGAATCTGAAAATCGCGTTG
279242 CGA
1 CGA
279245 TAAATTTTGG
Statistics
Matches: 29, Mismatches: 14, Indels: 2
0.64 0.31 0.04
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (20 bp):
CGAATCTGAAAATCGCGTTG
Found at i:279267 original size:45 final size:41
Alignment explanation
Indices: 279155--279323 Score: 275
Period size: 41 Copynumber: 4.0 Consensus size: 41
279145 GTCGCTTTAC
* *
279155 CGTTACGATTTTGGACTATCGCAACTCGAATCTGAAAATCG
1 CGTTGCGATTTTGGACTATCGCAACGCGAATCTGAAAATCG
279196 CGTTGCGATTTTGGACTATCGCAACGCGAATCTGAAAATCG
1 CGTTGCGATTTTGGACTATCGCAACGCGAATCTGAAAATCG
279237 CGTTGCGATAAATTTTGGACTATCGCAACGCGAATCTGAAAATCG
1 CGTTGCG----ATTTTGGACTATCGCAACGCGAATCTGAAAATCG
*
279282 CGTTGCGATTTTGGACTATCGCAACGCAAATCTGAAAATCG
1 CGTTGCGATTTTGGACTATCGCAACGCGAATCTGAAAATCG
279323 C
1 C
279324 AACGCAAATT
Statistics
Matches: 121, Mismatches: 3, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
41 80 0.66
45 41 0.34
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (41 bp):
CGTTGCGATTTTGGACTATCGCAACGCGAATCTGAAAATCG
Found at i:279307 original size:86 final size:86
Alignment explanation
Indices: 279162--279323 Score: 306
Period size: 86 Copynumber: 1.9 Consensus size: 86
279152 TACCGTTACG
* *
279162 ATTTTGGACTATCGCAACTCGAATCTGAAAATCGCGTTGCGATTTTGGACTATCGCAACGCGAAT
1 ATTTTGGACTATCGCAACGCGAATCTGAAAATCGCGTTGCGATTTTGGACTATCGCAACGCAAAT
279227 CTGAAAATCGCGTTGCGATAA
66 CTGAAAATCGCGTTGCGATAA
279248 ATTTTGGACTATCGCAACGCGAATCTGAAAATCGCGTTGCGATTTTGGACTATCGCAACGCAAAT
1 ATTTTGGACTATCGCAACGCGAATCTGAAAATCGCGTTGCGATTTTGGACTATCGCAACGCAAAT
279313 CTGAAAATCGC
66 CTGAAAATCGC
279324 AACGCAAATT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 74 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (86 bp):
ATTTTGGACTATCGCAACGCGAATCTGAAAATCGCGTTGCGATTTTGGACTATCGCAACGCAAAT
CTGAAAATCGCGTTGCGATAA
Found at i:281988 original size:104 final size:95
Alignment explanation
Indices: 281862--282123 Score: 256
Period size: 95 Copynumber: 2.7 Consensus size: 95
281852 CACGAAAATA
* *
281862 TAAATTAAACTTACCAAACCACTCGAATACAGTTTAATCTGTAAAATAAAAATAAATAGTCTAAT
1 TAAACTAAACTTACCAAACCACTCAAATACAGTTTAATCTGTAAAATAAAAATAAATAGTCTAA-
* * *
281927 TACTTTATATTTACAATAAAAACCCTAAACAATATATTT
65 TAATTTATA-TTAC--T--AAA---TAAAAAATATAATT
* * ** * *
281966 TACACTAAACTTACCAAACCACTCCAATAC-GATTTAATCCCTAAAATAAAAATAATTAGTCTCA
1 TAAACTAAACTTACCAAACCACTCAAATACAG-TTTAATCTGTAAAATAAAAATAAATAGTCTAA
*
282030 TAATTTATATTACTCAATAAAAAATATAATT
65 TAATTTATATTACTAAATAAAAAATATAATT
* * ** * **
282061 TAAACTAAACTTATCAAACTACTCAAATACAACTTAATATGTAAAATCGAAATAAATAGTCTA
1 TAAACTAAACTTACCAAACCACTCAAATACAGTTTAATCTGTAAAATAAAAATAAATAGTCTA
282124 GCTAATAAAT
Statistics
Matches: 132, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
95 61 0.46
98 2 0.02
100 1 0.01
102 4 0.03
103 9 0.07
104 55 0.42
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.31
Consensus pattern (95 bp):
TAAACTAAACTTACCAAACCACTCAAATACAGTTTAATCTGTAAAATAAAAATAAATAGTCTAAT
AATTTATATTACTAAATAAAAAATATAATT
Found at i:282462 original size:100 final size:100
Alignment explanation
Indices: 282344--282536 Score: 234
Period size: 100 Copynumber: 1.9 Consensus size: 100
282334 TACTAAATAA
* * *
282344 AAAATATAATTTAAACTTACCAAACTACT-CAAATACAACTT-AATATGTAAAATTAAAATAAA-
1 AAAATATAAATTAAACTTACCAAAC-AATGCAAATA-AACTTCAATATGTAAAATCAAAATAAAT
282406 CAATCTAA-TAA-TTATTATTTAAAAATAAAAATTACACG
64 CAA-CTAATTAATTTA-TATTT-AAAATAAAAATTACACG
* * * * *
282444 AAAATTTAAATTAAACTTACCAAACAATGCAAATATAGTTCAATCTGTAAAATCAAAATAAATTA
1 AAAATATAAATTAAACTTACCAAACAATGCAAATAAACTTCAATATGTAAAATCAAAATAAATCA
282509 ACTAATTAATTTATATTTAAAATAAAAA
66 ACTAATTAATTTATATTTAAAATAAAAA
282537 AATGAAACAA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
99 5 0.06
100 62 0.77
101 10 0.12
102 3 0.04
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (100 bp):
AAAATATAAATTAAACTTACCAAACAATGCAAATAAACTTCAATATGTAAAATCAAAATAAATCA
ACTAATTAATTTATATTTAAAATAAAAATTACACG
Found at i:304751 original size:29 final size:29
Alignment explanation
Indices: 304716--304796 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
304706 AGATTACCTC
*
304716 AAAATTGTATTACGTAAAATGAATTATAT
1 AAAATTGTTTTACGTAAAATGAATTATAT
* * * *
304745 GAAATTGTTTTACATAAAATAAATTATCT
1 AAAATTGTTTTACGTAAAATGAATTATAT
*
304774 AAAATTATTTTACGTAAAATGAA
1 AAAATTGTTTTACGTAAAATGAA
304797 GATGTTATTG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (29 bp):
AAAATTGTTTTACGTAAAATGAATTATAT
Found at i:305053 original size:19 final size:19
Alignment explanation
Indices: 305031--305073 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
305021 TTTATTAGCA
*
305031 TAATACTAAAT-TATTATAT
1 TAATACTAAATATA-TAAAT
*
305050 TAATATTAAATATATAAAT
1 TAATACTAAATATATAAAT
305069 TAATA
1 TAATA
305074 TTACTCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATACTAAATATATAAAT
Found at i:305516 original size:30 final size:30
Alignment explanation
Indices: 305482--305562 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
305472 TAGAAAATAA
305482 TTTACGTAAAATGAATTAGC-TGAAAACTGT
1 TTTACGTAAAATGAATTA-CATGAAAACTGT
* * * *
305512 TTTACATAAAACGAATTACATGAATATTGT
1 TTTACGTAAAATGAATTACATGAAAACTGT
305542 TTTACGTAAAATTG-ATTACAT
1 TTTACGTAAAA-TGAATTACAT
305563 TTTTTGGGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
29 1 0.02
30 41 0.95
31 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (30 bp):
TTTACGTAAAATGAATTACATGAAAACTGT
Found at i:305885 original size:17 final size:17
Alignment explanation
Indices: 305865--305907 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
305855 ATATTATAAA
305865 AATAATATATAAATATT
1 AATAATATATAAATATT
* **
305882 AATAATTTATTTATATT
1 AATAATATATAAATATT
*
305899 AAAAATATA
1 AATAATATA
305908 ATATTACTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATAATATATAAATATT
Found at i:305936 original size:39 final size:38
Alignment explanation
Indices: 305850--305940 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 38
305840 TAATACTAAA
305850 TTAT-TATATTATAAAAATAATATATAAATATTAATAAT
1 TTATGTATATTA-AAAAATAATATATAAATATTAATAAT
*
305888 TTATTTATATTAAAAATATAATATTACTAAA-ATT-AT-AT
1 TTATGTATATTAAAAA-ATAATA-TA-TAAATATTAATAAT
305926 TATATGTATATTAAA
1 T-TATGTATATTAAA
305941 TATTTTAATA
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
38 11 0.23
39 27 0.57
40 5 0.11
41 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (38 bp):
TTATGTATATTAAAAAATAATATATAAATATTAATAAT
Found at i:305984 original size:18 final size:18
Alignment explanation
Indices: 305963--306012 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
305953 TAATATTTTT
*
305963 TATTAAAATGATATTAAA
1 TATTAAAATAATATTAAA
**
305981 TATTAATTTAATATTAAA
1 TATTAAAATAATATTAAA
*
305999 TATATGAAATAATA
1 TAT-TAAAATAATA
306013 AATTTTTGAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (18 bp):
TATTAAAATAATATTAAA
Found at i:306227 original size:14 final size:14
Alignment explanation
Indices: 306208--306234 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
306198 GAAAATGAAG
306208 AAAATATTTTTCAA
1 AAAATATTTTTCAA
306222 AAAATATTTTTCA
1 AAAATATTTTTCA
306235 GTTATCAAAC
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:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATATTTTTCAA
Found at i:307849 original size:2 final size:2
Alignment explanation
Indices: 307842--307868 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
307832 TTGGTGACGT
307842 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 T
307869 GGCTCCGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:311284 original size:37 final size:36
Alignment explanation
Indices: 311240--311611 Score: 238
Period size: 37 Copynumber: 9.8 Consensus size: 36
311230 AATAATATAG
311240 TATAGTTTTTGAAAATATTTTTGAAAAACATATAATA
1 TATAGTTTTTGAAAATATTTTTG-AAAACATATAATA
* *
311277 TATAGTTTTTTTTAAAATCAGTTTTTGAAAATATAT-ATA
1 TATAG--TTTTTGAAAAT-A-TTTTTGAAAACATATAATA
* * * *
311316 GTAT-GGTTTCGAAAACACGTTTTTGAAAACGTATAATA
1 -TATAGTTTTTGAAAATA--TTTTTGAAAACATATAATA
*
311354 TATAG-TTTTGAAAACATATTTTTGAAAACATATATAATT
1 TATAGTTTTTG-AAA-ATATTTTTGAAAAC--ATATAATA
*
311393 TATAGGTTTTATGAAAAAATCGGTTTTGGAAAACATATAATA
1 TATA-GTTTT-TGAAAATAT---TTTT-GAAAACATATAATA
* *
311435 TATAG-TTTTGAAAACACATTTTTGAAAGCATATAATA
1 TATAGTTTTTG-AAA-ATATTTTTGAAAACATATAATA
* * *
311472 TATAATTTTT--ATATATTTTTGAAAACGTATATATAA
1 TATAGTTTTTGAAAATATTTTTGAAAACATATA-AT-A
* *
311508 TATAATTTTTTGAAAGAGTATTTTTAAAAACATAT-ATAA
1 TAT-AGTTTTTGAAA-A-TATTTTTGAAAACATATAAT-A
* * *** *
311547 TATAGTTTTTTTTAAAAAAAAATTGAAAACATATAGTA
1 TATAG--TTTTTGAAAATATTTTTGAAAACATATAATA
311585 TATAGTTTTT-AAAATGATTTTTGAAAA
1 TATAGTTTTTGAAAAT-ATTTTTGAAAA
311612 TATAATGTAT
Statistics
Matches: 265, Mismatches: 37, Indels: 67
0.72 0.10 0.18
Matches are distributed among these distances:
34 16 0.06
35 7 0.03
36 18 0.07
37 67 0.25
38 34 0.13
39 38 0.14
40 31 0.12
41 31 0.12
42 13 0.05
43 4 0.02
44 6 0.02
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.42
Consensus pattern (36 bp):
TATAGTTTTTGAAAATATTTTTGAAAACATATAATA
Found at i:311315 original size:42 final size:43
Alignment explanation
Indices: 311221--311315 Score: 117
Period size: 42 Copynumber: 2.2 Consensus size: 43
311211 GGGCTTATTT
311221 AATATATATAATAATATAGTATAGTTTTTGAAAATATTTTTGAA
1 AATATATATAATAATATAGTATA-TTTTTGAAAATATTTTTGAA
* *
311265 AA-ACATATAAT-ATATAGT-T-TTTTTTAAAATCAGTTTTTGAA
1 AATATATATAATAATATAGTATATTTTTGAAAAT-A-TTTTTGAA
311306 AATATATATA
1 AATATATATA
311316 GTATGGTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
39 10 0.22
40 1 0.02
41 11 0.24
42 13 0.29
43 8 0.18
44 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (43 bp):
AATATATATAATAATATAGTATATTTTTGAAAATATTTTTGAA
Found at i:311378 original size:14 final size:14
Alignment explanation
Indices: 311359--311386 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
311349 TAATATATAG
311359 TTTTGAAAACATAT
1 TTTTGAAAACATAT
311373 TTTTGAAAACATAT
1 TTTTGAAAACATAT
311387 ATAATTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TTTTGAAAACATAT
Found at i:311448 original size:118 final size:114
Alignment explanation
Indices: 311240--311611 Score: 319
Period size: 118 Copynumber: 3.2 Consensus size: 114
311230 AATAATATAG
* *** *
311240 TATAGTTTTTGAAAATATTTTTGAAAA-ACATATAATATATAGTTTTTTTTAAAATCAGTTTTTG
1 TATAG-TTTTGAAAATATTTTTGAAAACATATATAATATATAGTTTTTGAAAAAATCAGTTTTGG
* * * *
311304 AAAATATATATAGTATGGTTTCGAAAACACGTTTTTGAAAACGTATAATA
65 AAAACATATATAGTATAGTTTCGAAAACACATTTTTGAAAACATATAATA
* *
311354 TATAGTTTTGAAAACATATTTTTGAAAACATATATAATTTATAGGTTTTATGAAAAAATCGGTTT
1 TATAGTTTTG-AAA-ATATTTTTGAAAACATATATAATATATA-GTTTT-TGAAAAAATCAGTTT
* *
311419 TGGAAAACATATAATA-TATAGTTTTGAAAACACATTTTTGAAAGCATATAATA
62 TGGAAAACATAT-ATAGTATAGTTTCGAAAACACATTTTTGAAAACATATAATA
* * * * * * *
311472 TATAATTTT-TATATATTTTTGAAAACGTATATATAATATA-ATTTTTTGAAAGAGT-A-TTTTT
1 TATAGTTTTGAAAATATTTTTGAAAAC--ATATATAATATATAGTTTTTGAAAAAATCAGTTTTG
* * ** *** *
311533 AAAAACATATATAATATAGTTTTTTTTAAAA-A-AAAATTGAAAACATATAGTA
64 GAAAACATATATAGTATAG---TTTCGAAAACACATTTTTGAAAACATATAATA
*
311585 TATAGTTTTTAAAATGATTTTTGAAAA
1 TATAGTTTTGAAAAT-ATTTTTGAAAA
311612 TATAATGTAT
Statistics
Matches: 212, Mismatches: 32, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
111 3 0.01
112 18 0.08
113 28 0.13
114 19 0.09
115 50 0.24
116 14 0.07
117 16 0.08
118 61 0.29
119 3 0.01
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.42
Consensus pattern (114 bp):
TATAGTTTTGAAAATATTTTTGAAAACATATATAATATATAGTTTTTGAAAAAATCAGTTTTGGA
AAACATATATAGTATAGTTTCGAAAACACATTTTTGAAAACATATAATA
Found at i:311687 original size:29 final size:28
Alignment explanation
Indices: 311654--311717 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
311644 CATAGTATAC
*
311654 ATATTATTTTTATA-TATATTGTTTATTA
1 ATATTATTATTATATTATATTG-TTATTA
*
311682 TTTATTA-TATTATATTATATTGTTATTA
1 -ATATTATTATTATATTATATTGTTATTA
311710 ATATTATT
1 ATATTATT
311718 GTTCATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 5 0.17
28 13 0.43
29 12 0.40
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (28 bp):
ATATTATTATTATATTATATTGTTATTA
Found at i:311689 original size:10 final size:11
Alignment explanation
Indices: 311654--311717 Score: 60
Period size: 12 Copynumber: 5.7 Consensus size: 11
311644 CATAGTATAC
*
311654 ATATTATTTTT
1 ATATTATTATT
*
311665 ATATATATTGTT
1 ATAT-TATTATT
311677 -TATTATTTATT
1 ATATTA-TTATT
311688 ATATTA-TATT
1 ATATTATTATT
*
311698 ATATTGTTATT
1 ATATTATTATT
311709 AATATTATT
1 -ATATTATT
311718 GTTCATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
10 11 0.25
11 15 0.34
12 18 0.41
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
ATATTATTATT
Found at i:311702 original size:22 final size:24
Alignment explanation
Indices: 311654--311697 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
311644 CATAGTATAC
311654 ATATTATTT-TTATA-TATATTGT
1 ATATTATTTATTATATTATATTGT
*
311676 TTATTATTTATTATATTATATT
1 ATATTATTTATTATATTATATT
311698 ATATTGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 5 0.26
24 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
ATATTATTTATTATATTATATTGT
Found at i:313137 original size:29 final size:26
Alignment explanation
Indices: 313097--313149 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
313087 ATTTTTATTT
*
313097 TATTTTTTATTTTCTTTTAATTTTTAA
1 TATTTTTTATTTTATTTT-ATTTTTAA
313124 TATTTTCTTCATTTTATTTTATTTTT
1 TATTTT-TT-ATTTTATTTTATTTTT
313150 CTCTTTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.26
28 8 0.35
29 9 0.39
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (26 bp):
TATTTTTTATTTTATTTTATTTTTAA
Found at i:325297 original size:37 final size:36
Alignment explanation
Indices: 325249--325596 Score: 239
Period size: 38 Copynumber: 9.6 Consensus size: 36
325239 AGTATATATA
325249 ATAATAGTATAGTTTTTGAAAATATTTTTGAAAAACAT
1 ATAATA-TATAGTTTTTGAAAATATTTTTG-AAAACAT
* * * *
325287 ATAATATATAGTTATT-AAAAAATCGGTTTTTAAAATAT
1 ATAATATATAGTTTTTGAAAATAT---TTTTGAAAACAT
* *
325325 AT-ATA-ATATGGTTTTGAAAACACGTTTTTGAAAACAT
1 ATAATATATA-GTTTTTGAAAATA--TTTTTGAAAACAT
*
325362 ATAATATATAG-TTTTGAAAACA----T------AT
1 ATAATATATAGTTTTTGAAAATATTTTTGAAAACAT
*
325387 ATAATATATAGTTTTTTTAAAA-ATTGGTTTTGGAAAACAT
1 ATAATATATAG-TTTTTGAAAATA-T--TTTT-GAAAACAT
*
325427 ATAATATATAG-TTTTGAAAACACATTTTTGAAAACAT
1 ATAATATATAGTTTTTG-AAA-ATATTTTTGAAAACAT
*
325464 ATAATATATAGTTTTT--AAATATTTTTGAAAACGT
1 ATAATATATAGTTTTTGAAAATATTTTTGAAAACAT
* *
325498 ATATATAATATAGTTTTTAAAAGAGTATTTTTAAAAACAT
1 ATA-AT-ATATAGTTTTTGAAA-A-TATTTTTGAAAACAT
* *
325538 ATAATATATAGTTTTTTAAAAAATATTTTTGAAAAAAT
1 ATAATATATAG-TTTTT-GAAAATATTTTTGAAAACAT
*
325576 ATAGTATATAGTTTTT-AAAAT
1 ATAATATATAGTTTTTGAAAAT
325597 GGTTTTTCAA
Statistics
Matches: 255, Mismatches: 18, Indels: 77
0.73 0.05 0.22
Matches are distributed among these distances:
25 13 0.05
26 1 0.00
27 8 0.03
31 1 0.00
33 1 0.00
34 17 0.07
35 9 0.04
36 20 0.08
37 63 0.25
38 66 0.26
39 19 0.07
40 36 0.14
41 1 0.00
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (36 bp):
ATAATATATAGTTTTTGAAAATATTTTTGAAAACAT
Found at i:325309 original size:38 final size:36
Alignment explanation
Indices: 325249--325595 Score: 243
Period size: 37 Copynumber: 9.6 Consensus size: 36
325239 AGTATATATA
**
325249 ATAATAGTATAGTTTTTGAAAATATTTTTGAAAAACAT
1 ATAATA-TATAGTTTTAAAAAATATTTTTG-AAAACAT
* *
325287 ATAATATATAGTTATTAAAAAATCGGTTTTT-AAAATAT
1 ATAATATATAGTT-TTAAAAAAT--ATTTTTGAAAACAT
* * **
325325 AT-ATAATATGGTTTTGAAAACACGTTTTTGAAAACAT
1 ATAAT-ATATAGTTTT-AAAAAATATTTTTGAAAACAT
* * *
325362 ATAATATATAGTTTTGAAAACATA----T-ATAATAT
1 ATAATATATAGTTTT-AAAAAATATTTTTGAAAACAT
* * * *
325394 ATAGT-T-T--TTTTAAAAATTGGTTTTGGAAAACAT
1 ATAATATATAGTTTTAAAAAAT-ATTTTTGAAAACAT
* *
325427 ATAATATATAGTTTTGAAAACACATTTTTGAAAACAT
1 ATAATATATAGTTTT-AAAAAATATTTTTGAAAACAT
* *
325464 ATAATATATAGTTTT--TAAATATTTTTGAAAACGT
1 ATAATATATAGTTTTAAAAAATATTTTTGAAAACAT
* *
325498 ATATATAATATAGTTTTTAAAAGAGTATTTTTAAAAACAT
1 ATA-AT-ATATAG-TTTTAAAA-AATATTTTTGAAAACAT
*
325538 ATAATATATAGTTTTTTAAAAAATATTTTTGAAAAAAT
1 ATAATATATAG--TTTTAAAAAATATTTTTGAAAACAT
* *
325576 ATAGTATATAGTTTTTAAAA
1 ATAATATATAGTTTTAAAAA
325596 TGGTTTTTCA
Statistics
Matches: 245, Mismatches: 39, Indels: 52
0.73 0.12 0.15
Matches are distributed among these distances:
27 5 0.02
28 4 0.02
30 1 0.00
31 1 0.00
32 9 0.04
33 10 0.04
34 19 0.08
35 3 0.01
36 20 0.08
37 70 0.29
38 69 0.28
39 12 0.05
40 22 0.09
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (36 bp):
ATAATATATAGTTTTAAAAAATATTTTTGAAAACAT
Found at i:325379 original size:23 final size:24
Alignment explanation
Indices: 325350--325401 Score: 88
Period size: 25 Copynumber: 2.2 Consensus size: 24
325340 GAAAACACGT
325350 TTTTGAAAAC-ATATAATATATAG
1 TTTTGAAAACAATATAATATATAG
325373 TTTTGAAAACATATATAATATATAG
1 TTTTGAAAACA-ATATAATATATAG
325398 TTTT
1 TTTT
325402 TTTAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 10 0.37
25 17 0.63
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (24 bp):
TTTTGAAAACAATATAATATATAG
Found at i:325443 original size:102 final size:99
Alignment explanation
Indices: 325274--325478 Score: 295
Period size: 102 Copynumber: 2.0 Consensus size: 99
325264 TTGAAAATAT
* * *
325274 TTTTGAAAAACATATAATATATAGTTATTAAAAAATCGGTTTTTAAAATATATATAATATGGTTT
1 TTTTGAAAAACATATAATATATAGTTATTAAAAAATCGGTTTTGAAAACATATATAATATAGTTT
*
325339 TGAAAACACGTTTTTGAAAACATATAATATATAG
66 TGAAAACACATTTTTGAAAACATATAATATATAG
* * * *
325373 TTTTGAAAACATATATAATATATAGTTTTTTTAAAAATTGGTTTTGGAAAACATATA-ATATATA
1 TTTTGAAAA-ACATATAATATATAG-TTATTAAAAAATCGGTTTT-GAAAACATATATA-ATATA
325437 GTTTTGAAAACACATTTTTGAAAACATATAATATATAG
62 GTTTTGAAAACACATTTTTGAAAACATATAATATATAG
325475 TTTT
1 TTTT
325479 TAAATATTTT
Statistics
Matches: 94, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
99 9 0.10
100 14 0.15
101 17 0.18
102 54 0.57
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (99 bp):
TTTTGAAAAACATATAATATATAGTTATTAAAAAATCGGTTTTGAAAACATATATAATATAGTTT
TGAAAACACATTTTTGAAAACATATAATATATAG
Found at i:325892 original size:14 final size:14
Alignment explanation
Indices: 325875--325907 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
325865 ATTTCTATGT
*
325875 AGGGAATTATTTGC
1 AGGGAATTATTTAC
325889 AGGGAATTATTTAC
1 AGGGAATTATTTAC
325903 AGGGA
1 AGGGA
325908 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:326321 original size:65 final size:64
Alignment explanation
Indices: 326248--326369 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 64
326238 TTAATTGAAA
* *
326248 CATCGATGCACTCTGAATA-TTTTCAAAACATCGAATGCATTTGATGCATCGATGCACAAGCCAT
1 CATCGATGCAC-CAGAATATTTTTC-AAACATCGAATGCATTTCATGCATCGATGCACAAGCCAT
326312 G
64 G
** *
326313 CATCGATGCACCAGGCTATTTTTCAAACATTGAATGCATTTCATGCATCGATGCACA
1 CATCGATGCACCAGAATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACA
326370 CTTGGTGCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
64 35 0.69
65 16 0.31
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
CATCGATGCACCAGAATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACAAGCCATG
Found at i:332970 original size:21 final size:21
Alignment explanation
Indices: 332930--332984 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
332920 AAAACCGTCC
*
332930 TCCCGTTCCTCAACATCCTAG
1 TCCCGTTCCTCAACAACCTAG
** *
332951 TCCCGTTCCTCCTCAACCTAA
1 TCCCGTTCCTCAACAACCTAG
* *
332972 TCCTGATCCTCAA
1 TCCCGTTCCTCAA
332985 GCTCCTAATG
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.44, G:0.07, T:0.29
Consensus pattern (21 bp):
TCCCGTTCCTCAACAACCTAG
Found at i:334902 original size:19 final size:17
Alignment explanation
Indices: 334858--334904 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
334848 TTAATTGAAA
334858 CATCGAATGCATTCCATG
1 CATCG-ATGCATTCCATG
334876 CA-CTGATGCATTCTCCATG
1 CATC-GATGCA-T-TCCATG
334895 CATCGATGCA
1 CATCGATGCA
334905 CTCTGAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 6 0.24
18 4 0.16
19 14 0.56
20 1 0.04
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (17 bp):
CATCGATGCATTCCATG
Found at i:334924 original size:65 final size:64
Alignment explanation
Indices: 334806--335016 Score: 205
Period size: 65 Copynumber: 3.2 Consensus size: 64
334796 TATTCAAAGG
* * ** *
334806 CATGCACCGATGCATC-AGTCCATGCATCGATGCATCGATGAAT-TAATTGAAACATCGAATGCA
1 CATGCATCGATGCA-CAAG-CCATGCATCGATGCA-CCA-GAATATTTTTCAAACATCGAATGCA
*
334869 TTC
62 TTT
**** *
334872 CATGCA-CTGATGCATTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAAACATCGAATGCAT
1 CATGCATC-GATGCACAAGCCATGCATCGATGCAC-CAGAATATTTTTC-AAACATCGAATGCAT
334935 TT
63 TT
* **
334937 GATGCATCGATGCACAAGCCATGCATCGATGCACCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCATCGATGCACAAGCCATGCATCGATGCACCAGAATATTTTTCAAACATCGAATGCATTT
335001 CATGCATCGATGCACA
1 CATGCATCGATGCACA
335017 CTTGGTGCAC
Statistics
Matches: 120, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
64 43 0.36
65 64 0.53
66 13 0.11
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACAAGCCATGCATCGATGCACCAGAATATTTTTCAAACATCGAATGCATTT
Found at i:337277 original size:44 final size:46
Alignment explanation
Indices: 337212--337325 Score: 117
Period size: 45 Copynumber: 2.5 Consensus size: 46
337202 ATTTTCTTTA
* *
337212 TTTTTATTTTTCTATTATTTCTCTTGAAA-TTTAACA-TTTATACAT
1 TTTTTTTTTTTTTATT-TTTCTCTTGAAATTTTAACATTTTATACAT
* * * *
337257 TTTTTTTTTTTTTATTTTTCT-TTTAAATTTTAATATTTTCTTCAT
1 TTTTTTTTTTTTTATTTTTCTCTTGAAATTTTAACATTTTATACAT
* * *
337302 CTTATTTTATTTTATTTTTCTCTT
1 TTTTTTTTTTTTTATTTTTCTCTT
337326 TTAACCTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
43 5 0.09
44 11 0.19
45 39 0.68
46 2 0.04
ACGTcount: A:0.20, C:0.10, G:0.01, T:0.69
Consensus pattern (46 bp):
TTTTTTTTTTTTTATTTTTCTCTTGAAATTTTAACATTTTATACAT
Found at i:338147 original size:19 final size:19
Alignment explanation
Indices: 338120--338156 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
338110 TTGATCCTAA
*
338120 TTTTAAATTTTAAATTTAT
1 TTTTAAATTTCAAATTTAT
*
338139 TTTTTAATTTCAAATTTA
1 TTTTAAATTTCAAATTTA
338157 AAATAAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAATTTCAAATTTAT
Found at i:344528 original size:20 final size:20
Alignment explanation
Indices: 344503--344576 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
344493 TTTTCCCAAT
*
344503 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
344523 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
344544 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
344564 TCGCAACGCGAAT
1 TCGCAACGCGAAT
344577 TGGGAAAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:344546 original size:21 final size:21
Alignment explanation
Indices: 344520--344586 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
344510 GCGAATAAGT
344520 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
344541 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
344561 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
344582 AAATC
1 AAATC
344587 ACAATGTGAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 16 0.43
21 21 0.57
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:344548 original size:41 final size:41
Alignment explanation
Indices: 344503--344592 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
344493 TTTTCCCAAT
344503 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
344544 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
344585 TCACAATG
1 TCGCAATG
344593 TGATACTGAC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:344651 original size:20 final size:20
Alignment explanation
Indices: 344626--344678 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
344616 TAATAAAAAA
* *
344626 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
344646 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
344666 TCGCAACGCGATA
1 TCGCAACGCGATA
344679 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:344894 original size:22 final size:22
Alignment explanation
Indices: 344866--344909 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
344856 CACTCTCTCA
344866 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
344888 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
344910 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:345211 original size:20 final size:20
Alignment explanation
Indices: 345188--345230 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
345178 GATAGTCGAA
345188 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
345208 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
345228 TTC
1 TTC
345231 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:346571 original size:18 final size:18
Alignment explanation
Indices: 346550--346594 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
346540 TCCACTTCGG
*
346550 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
346568 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
346586 GAGCCATCA
1 GAGCCATCA
346595 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:347130 original size:19 final size:20
Alignment explanation
Indices: 347087--347131 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
347077 CGCAACACGA
*
347087 AAATGACTATCGTAATGCGG
1 AAATGACTATCGCAATGCGG
*
347107 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
347126 AAATGA
1 AAATGA
347132 AAATCGCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:347150 original size:14 final size:14
Alignment explanation
Indices: 347131--347220 Score: 81
Period size: 14 Copynumber: 5.9 Consensus size: 14
347121 ATGCGAAATG
347131 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
347145 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
347161 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
347177 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
347193 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
347209 AAAATCACAACG
1 AAAATCGCAACG
347221 CGAAATGAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
14 29 0.46
16 16 0.25
18 18 0.29
ACGTcount: A:0.49, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:347173 original size:32 final size:33
Alignment explanation
Indices: 347115--347237 Score: 214
Period size: 32 Copynumber: 3.8 Consensus size: 33
347105 GGAAATGGCT
*
347115 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
347148 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
347180 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
347212 ATCACAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
347238 TGCGATTTGT
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
32 63 0.72
33 24 0.28
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:347273 original size:14 final size:14
Alignment explanation
Indices: 347254--347311 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
347244 TTGTGTTTCG
347254 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
347268 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
347284 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
347300 CGTTGCGATTTT
1 CGTTGCGATTTT
347312 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:347288 original size:32 final size:33
Alignment explanation
Indices: 347249--347327 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
347239 GCGATTTGTG
347249 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
347281 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
347314 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
347328 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:347326 original size:19 final size:19
Alignment explanation
Indices: 347268--347385 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
347258 GCGATTTTGT
347268 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
347286 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
347300 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
347319 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
347339 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
347358 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
347378 TGTTGCGA
1 CGTTGCGA
347386 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:349254 original size:14 final size:14
Alignment explanation
Indices: 349235--349270 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
349225 ATTGTTTAAT
349235 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
349249 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
349263 TGATTTGT
1 TGATTTGT
349271 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:349403 original size:33 final size:36
Alignment explanation
Indices: 349358--349473 Score: 139
Period size: 38 Copynumber: 3.2 Consensus size: 36
349348 AAAACAGACT
* ***
349358 ATCGCAACGCGAAATGGCTATCGCAA-CG-A-GAAA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
349391 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
349429 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
349467 ATCGCAA
1 ATCGCAA
349474 CGAGAAAATC
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
33 22 0.30
35 2 0.03
37 1 0.01
38 49 0.66
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.15
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:349409 original size:19 final size:19
Alignment explanation
Indices: 349387--349492 Score: 177
Period size: 19 Copynumber: 5.8 Consensus size: 19
349377 ATCGCAACGA
349387 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
349406 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
349425 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
349444 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
349463 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
349477 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
349493 TTTTCATTTC
Statistics
Matches: 84, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.13
15 1 0.01
16 2 0.02
17 2 0.02
19 68 0.81
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Done.