Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008717.1 Hibiscus syriacus cultivar Beakdansim tig00111772_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: 3453450
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 16
Found at i:1178150 original size:13 final size:12
Alignment explanation
Indices: 1178133--1178166 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
1178123 GACTTATTAT
1178133 TTATTTATTTTA
1 TTATTTATTTTA
1178145 TATATTTATTTT-
1 T-TATTTATTTTA
1178157 TTATTTATTT
1 TTATTTATTT
1178167 ATTTAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTTATTTTA
Found at i:1178177 original size:11 final size:11
Alignment explanation
Indices: 1178163--1178193 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1178153 TTTTTTATTT
1178163 ATTTATTTAAC
1 ATTTATTTAAC
1178174 ATTTATTTAAC
1 ATTTATTTAAC
1178185 ATTTATTTA
1 ATTTATTTA
1178194 TCTCTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTATTTAAC
Found at i:1178182 original size:4 final size:4
Alignment explanation
Indices: 1178005--1178171 Score: 89
Period size: 4 Copynumber: 41.2 Consensus size: 4
1177995 GTGTTCTTTG
1178005 ATTT ATTT GATTT ATTT ATTT ATTTT ATTT ATTT ATTT ATTT -TTT ATTTT
1 ATTT ATTT -ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT A-TTT
* * * * *
1178055 ATTT TTTT CTTTT GACTTT TTTT CAATTT ATTT AATT -TTT ATTT -GTT
1 ATTT ATTT -ATTT -A-TTT ATTT --ATTT ATTT ATTT ATTT ATTT ATTT
* ** * * *
1178102 ATTTT ATTT -TCT -TTT CCTT -TTG ACTT A-TT ATTT ATTT ATTTT ATAT
1 A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT
1178148 ATTT ATTT -TTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
1178172 ACATTTATTT
Statistics
Matches: 129, Mismatches: 18, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
3 18 0.14
4 82 0.64
5 23 0.18
6 6 0.05
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:1178602 original size:18 final size:18
Alignment explanation
Indices: 1178579--1178618 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1178569 TTTGAAGGTA
1178579 TTCATTTTCGTGTATATG
1 TTCATTTTCGTGTATATG
*
1178597 TTCATTTTTGTGTATATG
1 TTCATTTTCGTGTATATG
1178615 TTCA
1 TTCA
1178619 CAAACATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.10, G:0.15, T:0.57
Consensus pattern (18 bp):
TTCATTTTCGTGTATATG
Found at i:1179496 original size:24 final size:23
Alignment explanation
Indices: 1179452--1179497 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1179442 CGTTTGATTA
**
1179452 TTTATTGTTCACGAATGTGTTCG
1 TTTATTGTTCACGAACATGTTCG
*
1179475 TTTATCTGTTCATGAACATGTTC
1 TTTAT-TGTTCACGAACATGTTC
1179498 ATTTTGAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (23 bp):
TTTATTGTTCACGAACATGTTCG
Found at i:1179671 original size:2 final size:2
Alignment explanation
Indices: 1179664--1179705 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1179654 ATACAAAATA
1179664 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
1179706 GTGTGTAGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1179760 original size:15 final size:15
Alignment explanation
Indices: 1179740--1179779 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1179730 GAACTTAAAA
1179740 AATATTATTAATATT
1 AATATTATTAATATT
1179755 AATATTATT-ATATT
1 AATATTATTAATATT
1179769 --TATTATTAATA
1 AATATTATTAATA
1179780 AAATTATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.29
13 3 0.12
14 5 0.21
15 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATATTATTAATATT
Found at i:1180814 original size:28 final size:28
Alignment explanation
Indices: 1180774--1180829 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1180764 CCGCGTTGAA
*
1180774 CGTGGGTGAGGGAAAGTGAAGAGTAAAG
1 CGTGGGTGAGGGAAAGTGAAGAGAAAAG
*
1180802 CGTGAGGT-AGGGAAAGTGGAGAGAAAAG
1 CGTG-GGTGAGGGAAAGTGAAGAGAAAAG
1180830 TGAGGCAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.38, C:0.04, G:0.46, T:0.12
Consensus pattern (28 bp):
CGTGGGTGAGGGAAAGTGAAGAGAAAAG
Found at i:1180839 original size:26 final size:28
Alignment explanation
Indices: 1180782--1180839 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1180772 AACGTGGGTG
* *
1180782 AGGGAAAGTGAAGAGTAAAGCGTGAGGT
1 AGGGAAAGTGAAGAGTAAAGAGTGAGGC
*
1180810 AGGGAAAGTGGAGAG-AAA-AGTGAGGC
1 AGGGAAAGTGAAGAGTAAAGAGTGAGGC
1180836 AGGG
1 AGGG
1180840 GTACACTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 10 0.37
27 3 0.11
28 14 0.52
ACGTcount: A:0.40, C:0.03, G:0.47, T:0.10
Consensus pattern (28 bp):
AGGGAAAGTGAAGAGTAAAGAGTGAGGC
Found at i:1181965 original size:36 final size:37
Alignment explanation
Indices: 1181922--1181998 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 37
1181912 TTATTATAAT
1181922 TATAATAGGTTTATCTA-TTTTTTTAATATGTAATTA
1 TATAATAGGTTTATCTATTTTTTTTAATATGTAATTA
*
1181958 TATAATAGGTTTATGTATTTTTTTTTAATATGTAATTA
1 TATAATAGGTTTATCTA-TTTTTTTTAATATGTAATTA
1181996 TAT
1 TAT
1181999 GTGCATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 16 0.42
38 22 0.58
ACGTcount: A:0.32, C:0.01, G:0.09, T:0.57
Consensus pattern (37 bp):
TATAATAGGTTTATCTATTTTTTTTAATATGTAATTA
Found at i:1187548 original size:35 final size:35
Alignment explanation
Indices: 1187501--1187571 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1187491 ATAAGTTCAA
1187501 GTGGGGCATCAAAGCACATAATGTAGCATCCGTTT
1 GTGGGGCATCAAAGCACATAATGTAGCATCCGTTT
* *
1187536 GTGGGGCGTCAAAGCACATAATGTTGCATCCGTTT
1 GTGGGGCATCAAAGCACATAATGTAGCATCCGTTT
1187571 G
1 G
1187572 GGTCAGGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (35 bp):
GTGGGGCATCAAAGCACATAATGTAGCATCCGTTT
Found at i:1190974 original size:40 final size:40
Alignment explanation
Indices: 1190927--1191338 Score: 644
Period size: 40 Copynumber: 10.3 Consensus size: 40
1190917 ATTTAATACG
* *
1190927 GAAGATTTTATCTCGCTCAAGATTATTTTTCCTTGAAACA
1 GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
1190967 GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
1 GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
* *
1191007 GAAGATTTTATCTCATTCAAGATTGTTTTTCATTGAAACA
1 GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
*
1191047 GAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAACA
1 GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
* *
1191087 TAAGATTTTATCTCACTCAAGATTGTTTTCCCTTGAAACA
1 GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
* *
1191127 GAAGATTTTATCTCATTCAAGATTTTTTTTCCTTGAAACA
1 GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
* *
1191167 TAAGATTTTATCTCACTCAAGATTTTTTTTCCTTGAAACA
1 GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
* * *
1191207 TAAGATTTTATCTCATTCAATATTGTTTTTCCTTGAAACA
1 GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
*
1191247 AAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
1 GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
* * **
1191287 GAATATTGTATCTCGTTCAAGATTGTTTTTCCTTGAAACA
1 GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
*
1191327 AAAGATTTTATC
1 GAAGATTTTATC
1191339 CCTTGAGATA
Statistics
Matches: 344, Mismatches: 28, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 344 1.00
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (40 bp):
GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
Found at i:1191051 original size:23 final size:23
Alignment explanation
Indices: 1190985--1191053 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
1190975 TATCTCACTC
*
1190985 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCATTGAAACAG
*
1191008 AAGATT-TTATCTCATT----C--
1 AAGATTGTT-TTTCATTGAAACAG
1191025 AAGATTGTTTTTCATTGAAACAG
1 AAGATTGTTTTTCATTGAAACAG
1191048 AAGATT
1 AAGATT
1191054 TTATCTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 16
0.65 0.06 0.30
Matches are distributed among these distances:
17 12 0.34
18 2 0.06
19 1 0.03
21 1 0.03
22 2 0.06
23 17 0.49
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (23 bp):
AAGATTGTTTTTCATTGAAACAG
Found at i:1191062 original size:23 final size:23
Alignment explanation
Indices: 1190999--1191063 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
1190989 TTGTTTTTCC
1190999 TTGAAACAGAAGATTTTATCTCA
1 TTGAAACAGAAGATTTTATCTCA
*
1191022 TT----C--AAGATTGTT-TTTCA
1 TTGAAACAGAAGATT-TTATCTCA
1191039 TTGAAACAGAAGATTTTATCTCA
1 TTGAAACAGAAGATTTTATCTCA
1191062 TT
1 TT
1191064 CAAGATTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 16
0.64 0.04 0.32
Matches are distributed among these distances:
17 12 0.38
18 2 0.06
19 1 0.03
21 1 0.03
22 2 0.06
23 14 0.44
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (23 bp):
TTGAAACAGAAGATTTTATCTCA
Found at i:1191171 original size:23 final size:23
Alignment explanation
Indices: 1191145--1191215 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
1191135 TATCTCATTC
1191145 AAGATTTTTTTTCCTTGAAACAT
1 AAGATTTTTTTTCCTTGAAACAT
* *
1191168 AAGA--TTTTAT-C-T--CAC-T
1 AAGATTTTTTTTCCTTGAAACAT
1191184 CAAGATTTTTTTTCCTTGAAACAT
1 -AAGATTTTTTTTCCTTGAAACAT
1191208 AAGATTTT
1 AAGATTTT
1191216 ATCTCATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
16 1 0.03
17 6 0.17
19 6 0.17
20 2 0.06
21 6 0.17
23 14 0.39
24 1 0.03
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.46
Consensus pattern (23 bp):
AAGATTTTTTTTCCTTGAAACAT
Found at i:1191468 original size:43 final size:43
Alignment explanation
Indices: 1191394--1191626 Score: 285
Period size: 43 Copynumber: 5.4 Consensus size: 43
1191384 CCTGATTTTC
* * * *
1191394 AGGGGTTTCTTGAAGAAAAGCCTG-AGAGACCATCGTGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAAG-GACCATCGTGATATGT
1191437 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
1191480 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
* * *
1191523 A-GGGTTCTTTGATGACAAGCTTG-AGAAATCATCGTGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAAG-GACCATCGTGATATGT
* * * * * *
1191565 AGGGGTTTCTTCATAAAAAGCTTGAGGGACCATCATGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
*
1191608 AGAGGTTCCTT-AGTGACAA
1 AGGGGTTCCTTGA-TGACAA
1191627 TTTAGAAACT
Statistics
Matches: 165, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.01
42 37 0.22
43 123 0.75
44 3 0.02
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (43 bp):
AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
Found at i:1191561 original size:85 final size:85
Alignment explanation
Indices: 1191394--1191626 Score: 301
Period size: 85 Copynumber: 2.7 Consensus size: 85
1191384 CCTGATTTTC
* *
1191394 AGGGGTTTCTTGAAGAAAAGCCTG-AGAGACCATCGTGATATGTAGGGGTTCCTTGATGACAAGC
1 AGGGGTTTCTTGATGAAAAGCTTGAAG-GACCATCGTGATATGTA-GGGTTCCTTGATGACAAGC
*
1191458 TTGAAGGACCATCGTGATATGT
64 TTGAAGAACCATCGTGATATGT
* * *
1191480 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGTAGGGTTCTTTGATGACAAGCTT
1 AGGGGTTTCTTGATGAAAAGCTTGAAGGACCATCGTGATATGTAGGGTTCCTTGATGACAAGCTT
*
1191545 G-AGAAATCATCGTGATATGT
66 GAAG-AACCATCGTGATATGT
* * * *
1191565 AGGGGTTTCTTCATAAAAAGCTTGAGGGACCATCATGATATGTAGAGGTTCCTT-AGTGACAA
1 AGGGGTTTCTTGATGAAAAGCTTGAAGGACCATCGTGATATGTAG-GGTTCCTTGA-TGACAA
1191627 TTTAGAAACT
Statistics
Matches: 129, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
84 2 0.02
85 75 0.58
86 50 0.39
87 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (85 bp):
AGGGGTTTCTTGATGAAAAGCTTGAAGGACCATCGTGATATGTAGGGTTCCTTGATGACAAGCTT
GAAGAACCATCGTGATATGT
Found at i:1191663 original size:128 final size:128
Alignment explanation
Indices: 1191371--1191663 Score: 283
Period size: 128 Copynumber: 2.3 Consensus size: 128
1191361 ACACAATATT
* * * *
1191371 TTTATAAACTAAGCCTGATTTTCAGGGGTTTCTTGAAGAAAAGCCTGAGAGACCATCGTGATATG
1 TTTAGAAACTAAGCCTGATTTTCA-AGGTTTCTTGATGAAAAGCCTGAGAAACCATCGTGATATG
* * * * *
1191436 TAGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAG
65 TAGGGGTTCCTTCATAAAAAGCTTGAAGGACCATCATGATATGTAGAGGTTCCTTGATGACAAG
* * * * * * * * *
1191500 CTT-GAAGGAC-CATCGTGATATGT--AGGGTTCTTTGATGACAAGCTTGAGAAATCATCGTGAT
1 TTTAGAA--ACTAAGCCTGAT-TTTCAAGGTTTC-TTGATGAAAAGCCTGAGAAACCATCGTGAT
* *
1191561 ATGTAGGGGTTTCTTCATAAAAAGCTTGAGGGACCATCATGATATGTAGAGGTTCCTT-AGTGAC
62 ATGTAGGGGTTCCTTCATAAAAAGCTTGAAGGACCATCATGATATGTAGAGGTTCCTTGA-TGAC
1191625 AA-
126 AAG
* *
1191627 TTTAGAAACTGAGCTTGATTTTCAAGAGTTTCTTGAT
1 TTTAGAAACTAAGCCTGATTTTCAAG-GTTTCTTGAT
1191664 TTTTAAGTCC
Statistics
Matches: 128, Mismatches: 26, Indels: 21
0.73 0.15 0.12
Matches are distributed among these distances:
126 4 0.03
127 14 0.11
128 94 0.73
129 12 0.09
130 4 0.03
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (128 bp):
TTTAGAAACTAAGCCTGATTTTCAAGGTTTCTTGATGAAAAGCCTGAGAAACCATCGTGATATGT
AGGGGTTCCTTCATAAAAAGCTTGAAGGACCATCATGATATGTAGAGGTTCCTTGATGACAAG
Found at i:1193087 original size:28 final size:28
Alignment explanation
Indices: 1193047--1193102 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1193037 CCGCGTTGAA
*
1193047 CGTGGGTGAGGGAAAGTGAAGAGTAAAG
1 CGTGGGTGAGGGAAAGTGAAGAGAAAAG
*
1193075 CGTGAGGT-AGGGAAAGTGGAGAGAAAAG
1 CGTG-GGTGAGGGAAAGTGAAGAGAAAAG
1193103 TGAGGCAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.38, C:0.04, G:0.46, T:0.12
Consensus pattern (28 bp):
CGTGGGTGAGGGAAAGTGAAGAGAAAAG
Found at i:1193112 original size:26 final size:28
Alignment explanation
Indices: 1193055--1193112 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1193045 AACGTGGGTG
* *
1193055 AGGGAAAGTGAAGAGTAAAGCGTGAGGT
1 AGGGAAAGTGAAGAGTAAAGAGTGAGGC
*
1193083 AGGGAAAGTGGAGAG-AAA-AGTGAGGC
1 AGGGAAAGTGAAGAGTAAAGAGTGAGGC
1193109 AGGG
1 AGGG
1193113 GTACACTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 10 0.37
27 3 0.11
28 14 0.52
ACGTcount: A:0.40, C:0.03, G:0.47, T:0.10
Consensus pattern (28 bp):
AGGGAAAGTGAAGAGTAAAGAGTGAGGC
Found at i:1194262 original size:36 final size:37
Alignment explanation
Indices: 1194197--1194272 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 37
1194187 TTAATATAAT
1194197 TATAATAGGTTTATCTATTTTTTTTAATATGTAATTA
1 TATAATAGGTTTATCTATTTTTTTTAATATGTAATTA
*
1194234 TATAATATGTTTATCTA-TTTTTTTAATATGTAATTA
1 TATAATAGGTTTATCTATTTTTTTTAATATGTAATTA
1194270 TAT
1 TAT
1194273 GTGCATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 22 0.58
37 16 0.42
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.58
Consensus pattern (37 bp):
TATAATAGGTTTATCTATTTTTTTTAATATGTAATTA
Found at i:1195074 original size:2 final size:2
Alignment explanation
Indices: 1195067--1195101 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1195057 AGTTACGACA
1195067 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1195102 AGAGAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1195672 original size:43 final size:42
Alignment explanation
Indices: 1195625--1195935 Score: 297
Period size: 43 Copynumber: 7.2 Consensus size: 42
1195615 ATTGAGGTTT
* *
1195625 CTAATTTTTATAATCTCATTTTTTACCTTT-TCAATTAAGACCC
1 CTAATTTTT-TAATCTCACTTTTTACCTTTAT-AATTGAGACCC
*
1195668 CTAATTTTTTTCAATC-CAACTTTTTACCTTTATAATTAAG-CCC
1 CTAA-TTTTTT-AATCTC-ACTTTTTACCTTTATAATTGAGACCC
* * * * * *
1195711 TCTAATTTTTTCAATCCCTCCTTTTACCTTTGTAATTGGGACTC
1 -CTAATTTTTT-AATCTCACTTTTTACCTTTATAATTGAGACCC
* * * * *
1195755 ATAATTTTTTCAATCTCACTTTCTACCTTTATAGTCGAGGCCC
1 CTAATTTTTT-AATCTCACTTTTTACCTTTATAATTGAGACCC
* *
1195798 ATAATTTTTTTAATCTCACTTTTCACCTTTATAATTGAGACCC
1 CTAA-TTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCC
* * * *
1195841 TTAATTGTTTCAATCTCACATTTTACCTTTATAATTGAGGCCC
1 CTAATT-TTTTAATCTCACTTTTTACCTTTATAATTGAGACCC
* *
1195884 CTAATTTTTCAATCTCACTTTTTACCTTTATAATTTA-AGCCC
1 CTAATTTTTTAATCTCACTTTTTACCTTTATAATTGAGA-CCC
1195926 CTAATTTTTT
1 CTAATTTTTT
1195936 TCAATTCCAT
Statistics
Matches: 225, Mismatches: 33, Indels: 21
0.81 0.12 0.08
Matches are distributed among these distances:
42 43 0.19
43 140 0.62
44 41 0.18
45 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.47
Consensus pattern (42 bp):
CTAATTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCC
Found at i:1195866 original size:129 final size:129
Alignment explanation
Indices: 1195669--1195940 Score: 345
Period size: 129 Copynumber: 2.1 Consensus size: 129
1195659 TTAAGACCCC
* * * *
1195669 TAATTTTTTTCAATCCAACTTTTTACCTTTATAATTAAGCCCTCTAATTTTTTCAATCCCTCCTT
1 TAATTTTTTTCAATCCAACTTTTCACCTTTATAATTAAGCCCTCTAATTGTTTCAATCCCACATT
* *
1195734 TTACCTTTGTAATTG-GGACTCATAATTTTTTCAATCTCACTTTCTACCTTTATAGTCGAGGCCC
66 TTACCTTTATAATTGAGG-CCCATAA-TTTTTCAATCTCACTTTCTACCTTTATAGTCGAGGCCC
1195798 A
129 A
* *
1195799 TAATTTTTTT-AATCTC-ACTTTTCACCTTTATAATTGAGACCCT-TAATTGTTTCAATCTCACA
1 TAATTTTTTTCAATC-CAACTTTTCACCTTTATAATTAAG-CCCTCTAATTGTTTCAATCCCACA
* * * ** *
1195861 TTTTACCTTTATAATTGAGGCCCCTAATTTTTCAATCTCACTTTTTACCTTTATAATTTAAGCCC
64 TTTTACCTTTATAATTGAGGCCCATAATTTTTCAATCTCACTTTCTACCTTTATAGTCGAGGCCC
*
1195926 C
129 A
1195927 TAATTTTTTTCAAT
1 TAATTTTTTTCAAT
1195941 TCCATAAAAT
Statistics
Matches: 123, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
128 43 0.35
129 63 0.51
130 17 0.14
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (129 bp):
TAATTTTTTTCAATCCAACTTTTCACCTTTATAATTAAGCCCTCTAATTGTTTCAATCCCACATT
TTACCTTTATAATTGAGGCCCATAATTTTTCAATCTCACTTTCTACCTTTATAGTCGAGGCCCA
Found at i:1197145 original size:8 final size:9
Alignment explanation
Indices: 1197123--1197152 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
1197113 TTATGCCTAA
1197123 ATTTTTAAT
1 ATTTTTAAT
1197132 ATTTTTAAT
1 ATTTTTAAT
1197141 ATTTTTAAT
1 ATTTTTAAT
1197150 ATT
1 ATT
1197153 AAAAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:1201224 original size:60 final size:62
Alignment explanation
Indices: 1201119--1201245 Score: 145
Period size: 61 Copynumber: 2.1 Consensus size: 62
1201109 TCTCTTAATT
* * * *
1201119 TAAAT-TTACAAATAACTTAAATAAATTATTAACTAATATTAATAAT-CTTATTTAAAATAC
1 TAAATATTACAAATAACATAAATAAATTATAAACTAATATTAATAATCCTAATATAAAATAC
* * *
1201179 TAAATATTA-AAATTACATAAATTAAATTATAAAGTAA-ATTTATAATCCTAATATAAAATAC
1 TAAATATTACAAATAACATAAA-TAAATTATAAACTAATATTAATAATCCTAATATAAAATAC
*
1201240 TTAATA
1 TAAATA
1201246 CTATAGTAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
60 23 0.41
61 33 0.59
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.39
Consensus pattern (62 bp):
TAAATATTACAAATAACATAAATAAATTATAAACTAATATTAATAATCCTAATATAAAATAC
Found at i:1201415 original size:2 final size:2
Alignment explanation
Indices: 1201408--1201441 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1201398 ATATTTATCC
1201408 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1201442 GTAGTGATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1204275 original size:13 final size:13
Alignment explanation
Indices: 1204254--1204285 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1204244 AGTGAGAGTC
*
1204254 CACACAAACATCT
1 CACAGAAACATCT
1204267 CACAGAAACATCT
1 CACAGAAACATCT
1204280 CACAGA
1 CACAGA
1204286 TTTTCATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.34, G:0.06, T:0.12
Consensus pattern (13 bp):
CACAGAAACATCT
Found at i:1212787 original size:16 final size:17
Alignment explanation
Indices: 1212760--1212793 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1212750 ATTTTCCTAC
1212760 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
1212777 TTTTG-AAAAGTTAATG
1 TTTTGTAAAAGTAAATG
1212793 T
1 T
1212794 GACACTTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Found at i:1213976 original size:20 final size:20
Alignment explanation
Indices: 1213947--1213984 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1213937 TTTCAAAGGG
* *
1213947 ATGCACCGATGCATCAATCT
1 ATGCAACGATGCACCAATCT
1213967 ATGCAACGATGCACCAAT
1 ATGCAACGATGCACCAAT
1213985 GAATTAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCAACGATGCACCAATCT
Found at i:1219519 original size:44 final size:44
Alignment explanation
Indices: 1219469--1219562 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 44
1219459 TTTGTGCTTA
* **
1219469 GTGCATCGATACA-CTTAACAG-TGCATTGATGCATCCCCTTGAAT
1 GTGCATCGATACATCATAA-AGATGCACCGATGCAT-CCCTTGAAT
* *
1219513 GTGCATCGCTACATCATAAAGATGCACCGATGCATGCCTTGAAT
1 GTGCATCGATACATCATAAAGATGCACCGATGCATCCCTTGAAT
1219557 GTGCAT
1 GTGCAT
1219563 TGATGCACAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
44 28 0.65
45 15 0.35
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (44 bp):
GTGCATCGATACATCATAAAGATGCACCGATGCATCCCTTGAAT
Found at i:1220775 original size:17 final size:16
Alignment explanation
Indices: 1220748--1220783 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1220738 TTGTTTTGGA
*
1220748 TTTGGTTGTTTGGATG
1 TTTGGTTGTTTGAATG
1220764 TTTGGATTGTTTGAATG
1 TTTGG-TTGTTTGAATG
1220781 TTT
1 TTT
1220784 ATTTCGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.11, C:0.00, G:0.31, T:0.58
Consensus pattern (16 bp):
TTTGGTTGTTTGAATG
Found at i:1221395 original size:20 final size:20
Alignment explanation
Indices: 1221366--1221403 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1221356 TTTCAAAGGG
*
1221366 ATGCACCGATGCATCAATCC
1 ATGCACCGATGCACCAATCC
*
1221386 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
1221404 GAATTAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:1221485 original size:65 final size:65
Alignment explanation
Indices: 1221416--1221594 Score: 306
Period size: 65 Copynumber: 2.8 Consensus size: 65
1221406 ATTAATTGAC
1221416 CATCGAATGCATTCT-ATGCATCGATGCACTCTCCATGAATCGATGCACTCGGGTTTAAATAAAA
1 CATCGAATGCATT-TGATGCATCGATGCACTCTCCATGAATCGATGCACTCGGGTTTAAATAAAA
1221480 A
65 A
1221481 CATCGAATGCATTTGATGCATCGATGCACTCTCCATGAATCGATGCACTCGGGTTTAAATAAAAA
1 CATCGAATGCATTTGATGCATCGATGCACTCTCCATGAATCGATGCACTCGGGTTTAAATAAAAA
*** *
1221546 CATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACT
1 CATCGAATGCATTTGATGCATCGATGCACTCTCCATGAATCGATGCACT
1221595 TAGGCTATTT
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
64 1 0.01
65 108 0.99
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.27
Consensus pattern (65 bp):
CATCGAATGCATTTGATGCATCGATGCACTCTCCATGAATCGATGCACTCGGGTTTAAATAAAAA
Found at i:1221612 original size:65 final size:64
Alignment explanation
Indices: 1221416--1221639 Score: 236
Period size: 65 Copynumber: 3.5 Consensus size: 64
1221406 ATTAATTGAC
*** * *
1221416 CATCGAATGCATTCT-ATGCATCGATGCACTCTCCATGAATCGATGCACTCGGGTTTAAATAAAA
1 CATCGAATGCATT-TGATGCATCGATGCACAAGCCATGAATCGATGCACTAGGCTTT-AATAAAA
1221480 A
64 A
*** * *
1221481 CATCGAATGCATTTGATGCATCGATGCACTCTCCATGAATCGATGCACTCGGGTTTAAATAAAAA
1 CATCGAATGCATTTGATGCATCGATGCACAAGCCATGAATCGATGCACTAGGCTTT-AATAAAAA
* * **
1221546 CATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTTAGGCTATT-TTTGAA
1 CATCGAATGCATTTGATGCATCGATGCACAAGCCATGAATCGATGCAC-TAGGCT-TTAATAAAA
1221610 A
64 A
* * *
1221611 CATCAAATGCACTTCATGCATCGATGCAC
1 CATCGAATGCATTTGATGCATCGATGCAC
1221640 CCTTAGTGCA
Statistics
Matches: 144, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
64 1 0.01
65 137 0.95
66 4 0.03
67 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (64 bp):
CATCGAATGCATTTGATGCATCGATGCACAAGCCATGAATCGATGCACTAGGCTTTAATAAAAA
Found at i:1225075 original size:9 final size:10
Alignment explanation
Indices: 1225063--1225087 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1225053 AAAAAAACTG
1225063 AAAAAAGAAA
1 AAAAAAGAAA
1225073 AAAAAAGAAA
1 AAAAAAGAAA
1225083 AAAAA
1 AAAAA
1225088 CTGAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1225082 original size:17 final size:17
Alignment explanation
Indices: 1225038--1225085 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1225028 AGTACACTAC
*
1225038 AAAAAACAACAAAAGAAA
1 AAAAAAGAA-AAAAGAAA
**
1225056 AAAACTGAAAAAAGAAA
1 AAAAAAGAAAAAAGAAA
1225073 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
1225086 AACTGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.83, C:0.06, G:0.08, T:0.02
Consensus pattern (17 bp):
AAAAAAGAAAAAAGAAA
Found at i:1225113 original size:6 final size:6
Alignment explanation
Indices: 1225102--1225155 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
1225092 AAAAAGGGCA
*
1225102 TTTATG TTTATG TTTATG TTTATTC TTATATG TTTACT- TTTAT- TTTAT-
1 TTTATG TTTATG TTTATG TTTA-TG TT-TATG TTTA-TG TTTATG TTTATG
1225150 TTTATG
1 TTTATG
1225156 AAGTTATGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 11 0.26
6 22 0.52
7 7 0.17
8 2 0.05
ACGTcount: A:0.19, C:0.04, G:0.09, T:0.69
Consensus pattern (6 bp):
TTTATG
Found at i:1225135 original size:20 final size:19
Alignment explanation
Indices: 1225110--1225149 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1225100 CATTTATGTT
1225110 TATGTTTA-TGTTTATTCTTA
1 TATGTTTACT-TTTATT-TTA
1225130 TATGTTTACTTTTATTTTA
1 TATGTTTACTTTTATTTTA
1225149 T
1 T
1225150 TTTATGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 14 0.74
21 1 0.05
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (19 bp):
TATGTTTACTTTTATTTTA
Found at i:1225137 original size:26 final size:24
Alignment explanation
Indices: 1225104--1225154 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 24
1225094 AAAGGGCATT
1225104 TATGTTTA-TGTTTATGTTTATTCTTA
1 TATGTTTACT-TTTAT-TTTATT-TTA
1225130 TATGTTTACTTTTATTTTATTTTA
1 TATGTTTACTTTTATTTTATTTTA
1225154 T
1 T
1225155 GAAGTTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 4 0.17
25 6 0.25
26 13 0.54
27 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.08, T:0.69
Consensus pattern (24 bp):
TATGTTTACTTTTATTTTATTTTA
Found at i:1231358 original size:30 final size:30
Alignment explanation
Indices: 1231282--1231370 Score: 101
Period size: 32 Copynumber: 2.9 Consensus size: 30
1231272 TTACTCTTAG
* *
1231282 AATTTATTTAATACTTATTATTAAGGGTAC
1 AATTTTTTTAATATTTATTATTAAGGGTAC
* *
1231312 AATTTTTCTCTAATATTTATTATTATGGGCT-T
1 AATTTTT-T-TAATATTTATTATTAAGGG-TAC
1231344 AATTTTTTTAATATTTATTATT-AGGGT
1 AATTTTTTTAATATTTATTATTAAGGGT
1231371 CCTACTCTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.02
29 3 0.06
30 20 0.39
31 2 0.04
32 24 0.47
33 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.10, T:0.54
Consensus pattern (30 bp):
AATTTTTTTAATATTTATTATTAAGGGTAC
Found at i:1232399 original size:22 final size:22
Alignment explanation
Indices: 1232365--1232418 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1232355 ATAATTATTT
* *
1232365 AAAAA-ATTAAATAAAAATACC
1 AAAAACATTTAATAAAAAAACC
*
1232386 AAAAACATTTAATAAAAAAACT
1 AAAAACATTTAATAAAAAAACC
1232408 AAAAACATTTA
1 AAAAACATTTA
1232419 GGTTGAACCG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAAACATTTAATAAAAAAACC
Found at i:1233386 original size:14 final size:14
Alignment explanation
Indices: 1233367--1233398 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1233357 GGGTTCGTTT
1233367 GTTTCACGTAAAAC
1 GTTTCACGTAAAAC
1233381 GTTTCACGTAAAAC
1 GTTTCACGTAAAAC
1233395 GTTT
1 GTTT
1233399 TCCGGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (14 bp):
GTTTCACGTAAAAC
Found at i:1233675 original size:24 final size:22
Alignment explanation
Indices: 1233654--1233700 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1233644 AAAATATATT
1233654 TATTGATATTTCTAATAATATAA
1 TATT-ATATTTCTAATAATATAA
* *
1233677 TATTATATTTTTAATATTATAA
1 TATTATATTTCTAATAATATAA
1233699 TA
1 TA
1233701 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TATTATATTTCTAATAATATAA
Found at i:1233684 original size:32 final size:32
Alignment explanation
Indices: 1233648--1233721 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
1233638 ATTATTAAAA
* *
1233648 TATATTTATTGATATTTCTAATAATATAAT-AT
1 TATATTTATTGATA-TTATAATAAAATAATAAT
*
1233680 TATATTT-TTAATATTATAATAAAATAATCAAT
1 TATATTTATTGATATTATAATAAAATAAT-AAT
1233712 TATA-TTATTG
1 TATATTTATTG
1233722 TTGAAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 13 0.37
31 7 0.20
32 15 0.43
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (32 bp):
TATATTTATTGATATTATAATAAAATAATAAT
Found at i:1234079 original size:65 final size:64
Alignment explanation
Indices: 1233968--1234128 Score: 175
Period size: 66 Copynumber: 2.5 Consensus size: 64
1233958 TTTGTAAAGG
* * *
1233968 CATGCACCGATGCATCAATCCATGCATCGATGCATCATTGAATAAAT-TAAACATCGAATGCATT
1 CATGCACCGATGCA-CAATACATGCATCGATACATCATT-AATAAATAAAAACATCGAATGCATT
1234032 T
64 T
* *
1234033 CATGCACCGATGCACTATACATGCATCGATACACTCTGATT-TTAAATAAAAACATCGAATGCAT
1 CATGCACCGATGCACAATACATGCATCGATACA-TC--ATTAATAAATAAAAACATCGAATGCAT
1234097 TT
63 TT
* * *
1234099 GATGCATCGATGCACACGT-CATGCATCGAT
1 CATGCACCGATGCACA-ATACATGCATCGAT
1234129 GCATTCAGGC
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
64 16 0.20
65 21 0.26
66 41 0.50
67 4 0.05
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACAATACATGCATCGATACATCATTAATAAATAAAAACATCGAATGCATTT
Found at i:1240054 original size:23 final size:22
Alignment explanation
Indices: 1239984--1240064 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
1239974 CACTTGTCAG
*
1239984 TGCATCGATGCATCCCCTTGAATG
1 TGCATCGATGCAT--CCTTGAATA
* *
1240008 TGCATCGATGCAT-CATGAAGA
1 TGCATCGATGCATCCTTGAATA
*
1240029 TGCACCGATGCATGCCTTGAATA
1 TGCATCGATGCAT-CCTTGAATA
1240052 TGCATCGATGCAT
1 TGCATCGATGCAT
1240065 TAAGGTCGTG
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 17 0.35
23 18 0.38
24 13 0.27
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATA
Found at i:1240082 original size:44 final size:44
Alignment explanation
Indices: 1239982--1240087 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 44
1239972 TCCACTTGTC
* * *
1239982 AGTGCATCGATGCATCCCCTTGAATGTGCATCGATGCATCATGA
1 AGTGCATCGATGCATCCCCTTGAATATGCATCGATGCATAAGGA
* * *
1240026 AGATGCACCGATGCAT-GCCTTGAATATGCATCGATGCATTAAGGT
1 AG-TGCATCGATGCATCCCCTTGAATATGCATCGATGCA-TAAGGA
*
1240071 CGTGCATCGATGCATCC
1 AGTGCATCGATGCATCC
1240088 GTCGGGTTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
44 34 0.68
45 16 0.32
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (44 bp):
AGTGCATCGATGCATCCCCTTGAATATGCATCGATGCATAAGGA
Found at i:1240511 original size:13 final size:13
Alignment explanation
Indices: 1240495--1240519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1240485 AAATCAAAAG
1240495 TCTAAATTTAATT
1 TCTAAATTTAATT
1240508 TCTAAATTTAAT
1 TCTAAATTTAAT
1240520 GTTTTTGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
TCTAAATTTAATT
Found at i:1243739 original size:23 final size:23
Alignment explanation
Indices: 1243713--1243757 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1243703 AATAATATTT
1243713 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1243736 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1243758 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1248263 original size:31 final size:31
Alignment explanation
Indices: 1248222--1248375 Score: 206
Period size: 31 Copynumber: 5.0 Consensus size: 31
1248212 GGGGTCAGGG
* *
1248222 TTTACTTATGTTCTTCGGGACATATGGACTT
1 TTTACCTATGTTCTTCGGGACATATGGACTA
*
1248253 TTTACCTATGTTCTTCGGAACATATGGACTA
1 TTTACCTATGTTCTTCGGGACATATGGACTA
1248284 TTTACCTATGTTCTTCGGGACATATGGACTA
1 TTTACCTATGTTCTTCGGGACATATGGACTA
* *
1248315 TTTACCTATGTTCTTCAGAACATATGGACTGA
1 TTTACCTATGTTCTTCGGGACATATGGACT-A
*
1248347 -TTACCTA-GATTCTTCAGGATC-TATGGACT
1 TTTACCTATG-TTCTTCGGGA-CATATGGACT
1248376 GGTCATTCGG
Statistics
Matches: 113, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
30 1 0.01
31 110 0.97
32 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACTA
Found at i:1249048 original size:11 final size:11
Alignment explanation
Indices: 1249032--1249065 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1249022 TTGTCAAAGT
1249032 TACTATAGCAG
1 TACTATAGCAG
*
1249043 TACTATAGCAA
1 TACTATAGCAG
*
1249054 TACTGTAGCAG
1 TACTATAGCAG
1249065 T
1 T
1249066 GCATCGATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (11 bp):
TACTATAGCAG
Found at i:1249118 original size:12 final size:12
Alignment explanation
Indices: 1249101--1249131 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1249091 ATTTTTTCAC
1249101 TGTTCATGGTAT
1 TGTTCATGGTAT
1249113 TGTTCATGGTAT
1 TGTTCATGGTAT
1249125 TGTTCAT
1 TGTTCAT
1249132 CACTGTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.10, G:0.23, T:0.52
Consensus pattern (12 bp):
TGTTCATGGTAT
Found at i:1249135 original size:34 final size:35
Alignment explanation
Indices: 1249097--1249164 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 35
1249087 TTGAATTTTT
* *
1249097 TCACTGTTCATGGTATTGTTC-ATGGTATTGTTCA
1 TCACTGTTCATGGTACTATTCAATGGTATTGTTCA
1249131 TCACTGTTCATGGTACTATTCATATGGTATTGTT
1 TCACTGTTCATGGTACTATTCA-ATGGTATTGTT
1249165 TATACTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 19 0.63
36 11 0.37
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (35 bp):
TCACTGTTCATGGTACTATTCAATGGTATTGTTCA
Found at i:1252944 original size:31 final size:31
Alignment explanation
Indices: 1252906--1253046 Score: 212
Period size: 31 Copynumber: 4.5 Consensus size: 31
1252896 AGGTTCGAGG
*
1252906 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
1252937 GTTTACCTATGTTCTTCGGAACATATAGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
1252968 GTTTACCTATGTTCTTCGGGACATCTGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
1252999 GTTTACCTATGTTCTTCGAAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
1253030 GATTACCTA-GATTCTTC
1 GTTTACCTATG-TTCTTC
1253047 AGGATCTATG
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
30 1 0.01
31 99 0.99
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:1253799 original size:22 final size:22
Alignment explanation
Indices: 1253773--1253817 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1253763 TCGAAAAGTT
*
1253773 TCACTGTTCATGGCATTGTTCA
1 TCACTGTTCACGGCATTGTTCA
*
1253795 TCACTGTTCACGGTATTGTTCA
1 TCACTGTTCACGGCATTGTTCA
1253817 T
1 T
1253818 ATGGTACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (22 bp):
TCACTGTTCACGGCATTGTTCA
Found at i:1259368 original size:22 final size:22
Alignment explanation
Indices: 1259342--1259415 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
1259332 TATGAAATAA
1259342 ACGATCAATAGATTAAATATCG
1 ACGATCAATAGATTAAATATCG
* ** **
1259364 ACGATTAA-ATTTTAATATGAAATAA
1 ACGATCAATAGATTAA-AT---ATCG
1259389 ACGATCAATAGATTAAATATCG
1 ACGATCAATAGATTAAATATCG
1259411 ACGAT
1 ACGAT
1259416 TAAACAGGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
21 5 0.14
22 16 0.43
25 11 0.30
26 5 0.14
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (22 bp):
ACGATCAATAGATTAAATATCG
Found at i:1259376 original size:47 final size:47
Alignment explanation
Indices: 1259322--1259419 Score: 196
Period size: 47 Copynumber: 2.1 Consensus size: 47
1259312 TAAATTTATA
1259322 TAAATTTTAATATGAAATAAACGATCAATAGATTAAATATCGACGAT
1 TAAATTTTAATATGAAATAAACGATCAATAGATTAAATATCGACGAT
1259369 TAAATTTTAATATGAAATAAACGATCAATAGATTAAATATCGACGAT
1 TAAATTTTAATATGAAATAAACGATCAATAGATTAAATATCGACGAT
1259416 TAAA
1 TAAA
1259420 CAGGAAAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (47 bp):
TAAATTTTAATATGAAATAAACGATCAATAGATTAAATATCGACGAT
Found at i:1262461 original size:112 final size:112
Alignment explanation
Indices: 1262259--1262721 Score: 827
Period size: 112 Copynumber: 4.1 Consensus size: 112
1262249 TTGTCGGTTT
* *
1262259 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
1262324 GGTCTATAAATGACAAAACAAGTAAAACGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
1262371 GTGTTGATACTTTATAAAACTATATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1262436 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1262483 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
1262548 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1262595 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1262660 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1262707 GTATCGATACTTTAT
1 GTGTCGATACTTTAT
1262722 TATAAGTATC
Statistics
Matches: 337, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 337 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:1262958 original size:181 final size:181
Alignment explanation
Indices: 1262592--1263039 Score: 734
Period size: 181 Copynumber: 2.5 Consensus size: 181
1262582 AGATATATTG
*
1262592 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* ** * *
1262657 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTATCGATACTTTAT
66 ATCGGTCTCGAAATGAC-AAACAGGTAAAGAGCTACCAGATATATTGAAAGTATCGATACTTTAT
* * *
1262722 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAACGCTAAT
130 TATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACACCAAT
* *
1262774 AAAGTGTCAATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
1262839 ATCGGTCTCGAAATGACAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTATT
66 ATCGGTCTCGAAATGACAAACAGGTAAAGAGCTACCAGATATATTGAAAGTATCGATACTTTATT
*
1262904 ATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
131 ATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACACCAAT
* *
1262955 AAAGTGTCGATATTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1263020 ATCGGTCTCGAAATGACAAA
66 ATCGGTCTCGAAATGACAAA
1263040 ATCGGTAGTA
Statistics
Matches: 247, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
181 171 0.69
182 76 0.31
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (181 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ATCGGTCTCGAAATGACAAACAGGTAAAGAGCTACCAGATATATTGAAAGTATCGATACTTTATT
ATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACACCAAT
Found at i:1264430 original size:19 final size:20
Alignment explanation
Indices: 1264385--1264435 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1264375 TTACATTTTG
1264385 TTAAAATATTAAATGATAAAT
1 TTAAAATATTAAA-GATAAAT
**
1264406 AAAAAATATTAAA-ATAAAT
1 TTAAAATATTAAAGATAAAT
*
1264425 TTAAAAGATTA
1 TTAAAATATTA
1264436 TGAACTATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 14 0.56
21 11 0.44
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
TTAAAATATTAAAGATAAAT
Found at i:1264430 original size:21 final size:20
Alignment explanation
Indices: 1264387--1264424 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1264377 ACATTTTGTT
1264387 AAAATATTAAATGATAAATAA
1 AAAATATTAAA-GATAAATAA
1264408 AAAATATTAAA-ATAAAT
1 AAAATATTAAAGATAAAT
1264425 TTAAAAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAATATTAAAGATAAATAA
Found at i:1267693 original size:60 final size:60
Alignment explanation
Indices: 1267588--1267775 Score: 211
Period size: 60 Copynumber: 3.1 Consensus size: 60
1267578 TATATACGTG
* * *
1267588 TAGTTTGA-GATGAAATTGGAATATTCAAAAAGTTCG-GGACCAATTTAGAATGAATATCA
1 TAGTTTGAGGATGAAATTGAAATATTC-AAAAGTTTGAGGACCAATTTAAAATGAATATCA
** * *
1267647 TAGTTTGAGGATGAAATTGAAATGCTCAAAAGTTTGAGGACTAATTTAAAATG-ATAGTTA
1 TAGTTTGAGGATGAAATTGAAATATTCAAAAGTTTGAGGACCAATTTAAAATGAATA-TCA
* * * * * *
1267707 TAGTTTAAGGATGAAATTAAAATATTTAAAAGTTTAAGGACCAATCTAAAATGAATGTCA
1 TAGTTTGAGGATGAAATTGAAATATTCAAAAGTTTGAGGACCAATTTAAAATGAATATCA
*
1267767 TACTTTGAG
1 TAGTTTGAG
1267776 AACATGTGAT
Statistics
Matches: 106, Mismatches: 19, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
59 19 0.18
60 85 0.80
61 2 0.02
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.32
Consensus pattern (60 bp):
TAGTTTGAGGATGAAATTGAAATATTCAAAAGTTTGAGGACCAATTTAAAATGAATATCA
Found at i:1269480 original size:24 final size:25
Alignment explanation
Indices: 1269448--1269495 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1269438 ATGGCTGAGG
*
1269448 GGATCAATAATGAA-CAAACAACCA
1 GGATCAATAAGGAACCAAACAACCA
* *
1269472 GGATGAATAAGGAACCCAACAACC
1 GGATCAATAAGGAACCAAACAACC
1269496 CATGGGCTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.10
Consensus pattern (25 bp):
GGATCAATAAGGAACCAAACAACCA
Found at i:1271157 original size:66 final size:66
Alignment explanation
Indices: 1271079--1271212 Score: 196
Period size: 66 Copynumber: 2.0 Consensus size: 66
1271069 CCGGCTAGTG
** * *
1271079 TACTCCTCTAGAGTACTTGGGACAAGTCTGGGTCACGAAACATCAGAGTAACGTCTAACTAGCAT
1 TACTCCTCTAGAGTACTTGGGACAAGTCCAGGTCACGAAACATCAAAGTAACGTCCAACTAGCAT
1271144 T
66 T
* * * *
1271145 TACTCCTTTAGAGTACTTGGGACATGTCCAGGTCACGGAGCATCAAAGTAACGTCCAACTAGCAT
1 TACTCCTCTAGAGTACTTGGGACAAGTCCAGGTCACGAAACATCAAAGTAACGTCCAACTAGCAT
1271210 T
66 T
1271211 TA
1 TA
1271213 TGGTGCTCCA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (66 bp):
TACTCCTCTAGAGTACTTGGGACAAGTCCAGGTCACGAAACATCAAAGTAACGTCCAACTAGCAT
T
Found at i:1275164 original size:12 final size:12
Alignment explanation
Indices: 1275147--1275172 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1275137 ACACTACACA
1275147 CCCTTATAGAAG
1 CCCTTATAGAAG
1275159 CCCTTATAGAAG
1 CCCTTATAGAAG
1275171 CC
1 CC
1275173 ACAGAAGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (12 bp):
CCCTTATAGAAG
Found at i:1280386 original size:19 final size:19
Alignment explanation
Indices: 1280362--1280401 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1280352 TCGAAGGCTT
1280362 TTCCTCCTTCCCTTTGCTC
1 TTCCTCCTTCCCTTTGCTC
1280381 TTCCTCCTTCCCTTTGCTC
1 TTCCTCCTTCCCTTTGCTC
1280400 TT
1 TT
1280402 TGCTTTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.00, C:0.45, G:0.05, T:0.50
Consensus pattern (19 bp):
TTCCTCCTTCCCTTTGCTC
Found at i:1282964 original size:19 final size:19
Alignment explanation
Indices: 1282940--1282979 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1282930 TCGAAGGCTT
1282940 TTCCTCCTTCCCTTTGCTC
1 TTCCTCCTTCCCTTTGCTC
1282959 TTCCTCCTTCCCTTTGCTC
1 TTCCTCCTTCCCTTTGCTC
1282978 TT
1 TT
1282980 TGCTTTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.00, C:0.45, G:0.05, T:0.50
Consensus pattern (19 bp):
TTCCTCCTTCCCTTTGCTC
Found at i:1292582 original size:20 final size:20
Alignment explanation
Indices: 1292557--1292599 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1292547 TCTAAGAGTC
1292557 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
1292577 CATTTAGGAGCATATAGTTG
1 CATTTAGAACCATATAGATG
1292597 CAT
1 CAT
1292600 GTGGTAGAAT
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:0.19, T:0.33
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:1295619 original size:174 final size:174
Alignment explanation
Indices: 1295298--1295645 Score: 680
Period size: 173 Copynumber: 2.0 Consensus size: 174
1295288 CAGTGAACGC
1295298 GCCATTGAAAAATTTATCAAACATGAAGGGCAGATTTTGTTGAAGTAAGGTGCATAAGGGCTTGG
1 GCCATTGAAAAATTTATCAAACATGAAGGGCAGATTTTGTTGAAGTAAGGTGCATAAGGGCTTGG
1295363 ATATCATGGAGAAGTCATTGATGAATATTCTATAAAATCCAACATGTCAAGGAAACTCCTAATTC
66 ATATCATGGAGAAGTCATTGATGAATATTCTATAAAATCCAACATGTCAAGGAAACTCCTAATTC
1295428 CCTTGACAGATGTTGTTGGGGGTAGCTTCTCAATCACCTCGATT
131 CCTTGACAGATGTTGTTGGGGGTAGCTTCTCAATCACCTCGATT
1295472 GCCATTG-AAAATTTATCAAACATGAAGGGCAGATTTTGTTGAAGTAAGGTGCATAAGGGCTTGG
1 GCCATTGAAAAATTTATCAAACATGAAGGGCAGATTTTGTTGAAGTAAGGTGCATAAGGGCTTGG
1295536 ATATCATGGAGAAGTCATTGATGAATATTCTATAAAATCCAACATGTTCAAGGAAACTCCTAATT
66 ATATCATGGAGAAGTCATTGATGAATATTCTATAAAATCCAACATG-TCAAGGAAACTCCTAATT
1295601 CCCTTGACAGATGTTGTTGGGGGTAGCTTCTCAATCACCTCGATT
130 CCCTTGACAGATGTTGTTGGGGGTAGCTTCTCAATCACCTCGATT
1295646 TTGACTTTGT
Statistics
Matches: 173, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
173 103 0.60
174 70 0.40
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (174 bp):
GCCATTGAAAAATTTATCAAACATGAAGGGCAGATTTTGTTGAAGTAAGGTGCATAAGGGCTTGG
ATATCATGGAGAAGTCATTGATGAATATTCTATAAAATCCAACATGTCAAGGAAACTCCTAATTC
CCTTGACAGATGTTGTTGGGGGTAGCTTCTCAATCACCTCGATT
Found at i:1300284 original size:189 final size:189
Alignment explanation
Indices: 1299964--1300341 Score: 756
Period size: 189 Copynumber: 2.0 Consensus size: 189
1299954 TTCCAGCCGC
1299964 CTCTCCTCTCTTTTGCTAAAGAATTTAATCTCTAAAGGTCTCCGCATAGATGGATGGCAGTTGAG
1 CTCTCCTCTCTTTTGCTAAAGAATTTAATCTCTAAAGGTCTCCGCATAGATGGATGGCAGTTGAG
1300029 AGCAGATGAAGACAAAGACAGCTGGTTTTTTTATAAAAATATCTTTTTTTGTCTTTTATGCTCCA
66 AGCAGATGAAGACAAAGACAGCTGGTTTTTTTATAAAAATATCTTTTTTTGTCTTTTATGCTCCA
1300094 TAAATGTCGTTTGAGCTTTCGCGACATTCGTATTCTGCTTAGCATTCCCAATTTGTCAT
131 TAAATGTCGTTTGAGCTTTCGCGACATTCGTATTCTGCTTAGCATTCCCAATTTGTCAT
1300153 CTCTCCTCTCTTTTGCTAAAGAATTTAATCTCTAAAGGTCTCCGCATAGATGGATGGCAGTTGAG
1 CTCTCCTCTCTTTTGCTAAAGAATTTAATCTCTAAAGGTCTCCGCATAGATGGATGGCAGTTGAG
1300218 AGCAGATGAAGACAAAGACAGCTGGTTTTTTTATAAAAATATCTTTTTTTGTCTTTTATGCTCCA
66 AGCAGATGAAGACAAAGACAGCTGGTTTTTTTATAAAAATATCTTTTTTTGTCTTTTATGCTCCA
1300283 TAAATGTCGTTTGAGCTTTCGCGACATTCGTATTCTGCTTAGCATTCCCAATTTGTCAT
131 TAAATGTCGTTTGAGCTTTCGCGACATTCGTATTCTGCTTAGCATTCCCAATTTGTCAT
1300342 GACAATTCTC
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
189 189 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (189 bp):
CTCTCCTCTCTTTTGCTAAAGAATTTAATCTCTAAAGGTCTCCGCATAGATGGATGGCAGTTGAG
AGCAGATGAAGACAAAGACAGCTGGTTTTTTTATAAAAATATCTTTTTTTGTCTTTTATGCTCCA
TAAATGTCGTTTGAGCTTTCGCGACATTCGTATTCTGCTTAGCATTCCCAATTTGTCAT
Found at i:1301802 original size:8 final size:8
Alignment explanation
Indices: 1301781--1301809 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1301771 CATTTTTATG
1301781 TCATTTTT
1 TCATTTTT
1301789 TC-TTTTT
1 TCATTTTT
1301796 TCATTTTT
1 TCATTTTT
1301804 TCATTT
1 TCATTT
1301810 AATTATCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (8 bp):
TCATTTTT
Found at i:1301848 original size:30 final size:30
Alignment explanation
Indices: 1301813--1301890 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 30
1301803 TTCATTTAAT
*
1301813 TATCTAAAGTATTTTTTTGGTTAAAATA-A
1 TATCTAAAGTATTTTTTTGGTCAAAATAGA
*
1301842 GTATCTAAAGTTATCTTTTTGGTCAAAATAGA
1 -TATCTAAAG-TATTTTTTTGGTCAAAATAGA
* *
1301874 TACCTAAAATATTTTTT
1 TATCTAAAGTATTTTTT
1301891 CCAAATAGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 16 0.39
31 24 0.59
32 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (30 bp):
TATCTAAAGTATTTTTTTGGTCAAAATAGA
Found at i:1302099 original size:29 final size:29
Alignment explanation
Indices: 1301997--1302096 Score: 139
Period size: 29 Copynumber: 3.5 Consensus size: 29
1301987 AAAAAATTTG
*
1301997 AATACTTTAGGTTCCTATTTTGATCAAAA
1 AATACTTTAGGTACCTATTTTGATCAAAA
* * *
1302026 CATACTTTAGATACCTATTTTGAACAAAA
1 AATACTTTAGGTACCTATTTTGATCAAAA
* *
1302055 AAT-CTTTAGGTACTTACTTTGATCAAAA
1 AATACTTTAGGTACCTATTTTGATCAAAA
1302083 AATACTTTAGGTAC
1 AATACTTTAGGTAC
1302097 TTAAATAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 24 0.39
29 37 0.61
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (29 bp):
AATACTTTAGGTACCTATTTTGATCAAAA
Found at i:1307731 original size:17 final size:17
Alignment explanation
Indices: 1307694--1307736 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1307684 AGTGTTTATT
* * *
1307694 TCTCGAACGAGAGTTTT
1 TCTCGAAAGAGAATTTC
1307711 TCTCGAAAGAGAATTTC
1 TCTCGAAAGAGAATTTC
1307728 TCTC-AAAGA
1 TCTCGAAAGA
1307737 AAGAGAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (17 bp):
TCTCGAAAGAGAATTTC
Found at i:1317809 original size:36 final size:36
Alignment explanation
Indices: 1317769--1317843 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
1317759 TTATGGCTAA
*
1317769 TTTCATATTATATTGTTATACGGGTTTTAACATTAT
1 TTTCATATTATATTGTTATACGGATTTTAACATTAT
* *
1317805 TTTCATATTATATTGTTATATGGATTTTAACATTGT
1 TTTCATATTATATTGTTATACGGATTTTAACATTAT
1317841 TTT
1 TTT
1317844 AAATATGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.56
Consensus pattern (36 bp):
TTTCATATTATATTGTTATACGGATTTTAACATTAT
Found at i:1323505 original size:31 final size:31
Alignment explanation
Indices: 1323442--1323522 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 31
1323432 AAAACACAAG
* *
1323442 TTTTAGTCTTTTACGTTTTCGATTAATTAAA
1 TTTTAGTCTCTTACGTTATCGATTAATTAAA
*
1323473 TTTTAGT-TCTTACGTTATCGATTTATTAAA
1 TTTTAGTCTCTTACGTTATCGATTAATTAAA
* * * *
1323503 ATTTGGTCACTTGCGTTATC
1 TTTTAGTCTCTTACGTTATC
1323523 AATTGTTACA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 25 0.60
31 17 0.40
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.52
Consensus pattern (31 bp):
TTTTAGTCTCTTACGTTATCGATTAATTAAA
Found at i:1323704 original size:32 final size:31
Alignment explanation
Indices: 1323638--1323701 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
1323628 ACTAGGTAGA
* * *
1323638 CCTTAAACTTTAGATGAAGTATCATTTTGAC
1 CCTTAAACTTTAGATAAAATATAATTTTGAC
*
1323669 CCTTAAGCTTTAGATAAAATATTAATTTT-AC
1 CCTTAAACTTTAGATAAAATA-TAATTTTGAC
1323700 CC
1 CC
1323702 CTTGAATTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.39
Consensus pattern (31 bp):
CCTTAAACTTTAGATAAAATATAATTTTGAC
Found at i:1324292 original size:30 final size:30
Alignment explanation
Indices: 1324256--1324355 Score: 143
Period size: 30 Copynumber: 3.4 Consensus size: 30
1324246 GTCAAATTTA
*
1324256 ATGGTCAAATTGATATTTTATCTAAAGTTT
1 ATGGTCAAAATGATATTTTATCTAAAGTTT
*
1324286 ATGGTCAAAATGATATTTTATTTAAAGTTT
1 ATGGTCAAAATGATATTTTATCTAAAGTTT
1324316 A-GGATCAAAATGATATTTTATCTAAAGTCTT
1 ATGG-TCAAAATGATATTTTATCTAAAGT-TT
1324347 A-GGT-AAAAT
1 ATGGTCAAAAT
1324356 AAAAATTAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
29 7 0.11
30 53 0.82
31 5 0.08
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (30 bp):
ATGGTCAAAATGATATTTTATCTAAAGTTT
Found at i:1327604 original size:24 final size:24
Alignment explanation
Indices: 1327574--1327631 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1327564 TTAGTTTAAA
* *
1327574 ATAAAAATAATTATTTATATATTTT
1 ATAAAATTAA-TATTAATATATTTT
*
1327599 ATAAAATTAATATTAATTTATTTT
1 ATAAAATTAATATTAATATATTTT
*
1327623 A-AATATTAA
1 ATAAAATTAA
1327632 GTTTCTGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 7 0.24
24 13 0.45
25 9 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATAAAATTAATATTAATATATTTT
Found at i:1335234 original size:3 final size:3
Alignment explanation
Indices: 1335226--1335286 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
1335216 GATAAGGGAA
1335226 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1335274 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
1335287 TGATAGGAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1335610 original size:24 final size:24
Alignment explanation
Indices: 1335583--1335628 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
1335573 AAAAGATGTG
*
1335583 TTTACAATAGTGTGAGAA-TCCTCC
1 TTTA-AATAGGGTGAGAAGTCCTCC
*
1335607 TTTATATAGGGTGAGAAGTCCT
1 TTTAAATAGGGTGAGAAGTCCT
1335629 TGTTGTAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (24 bp):
TTTAAATAGGGTGAGAAGTCCTCC
Found at i:1337628 original size:6 final size:7
Alignment explanation
Indices: 1337608--1337637 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1337598 TGTCTCTATT
1337608 ATTAAAA
1 ATTAAAA
1337615 ATTAAAA
1 ATTAAAA
1337622 ATTAAAA
1 ATTAAAA
1337629 ATTAAAA
1 ATTAAAA
1337636 AT
1 AT
1337638 ATATTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
ATTAAAA
Found at i:1339614 original size:113 final size:113
Alignment explanation
Indices: 1339411--1340032 Score: 1201
Period size: 113 Copynumber: 5.5 Consensus size: 113
1339401 ATGTTAAACA
*
1339411 AGTTCTTCTCATTATGAACTTCTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1339476 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
*
1339524 AGTTATTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1339589 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
1339637 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1339702 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
1339750 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1339815 GTTGAAC-AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
*
1339862 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGAAGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1339927 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
*
1339975 AGTTCTTCTTATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
1340033 ATCTTTGCTA
Statistics
Matches: 502, Mismatches: 6, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
112 111 0.22
113 391 0.78
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
Found at i:1339979 original size:225 final size:226
Alignment explanation
Indices: 1339411--1340032 Score: 1201
Period size: 225 Copynumber: 2.8 Consensus size: 226
1339401 ATGTTAAACA
*
1339411 AGTTCTTCTCATTATGAACTTCTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
*
1339476 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1339541 ACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
131 ACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
1339606 CATTATGAATTTCTTCTTCCTTCTTCAGATG
196 CATTATGAATTTCTTCTTCCTTCTTCAGATG
1339637 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1339702 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1339767 ACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAAC-AATTCTTCT
131 ACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
1339831 CATTATGAATTTCTTCTTCCTTCTTCAGATG
196 CATTATGAATTTCTTCTTCCTTCTTCAGATG
*
1339862 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGAAGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
*
1339927 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGA
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1339992 ACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
131 ACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
1340033 ATCTTTGCTA
Statistics
Matches: 392, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
225 209 0.53
226 183 0.47
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (226 bp):
AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
CATTATGAATTTCTTCTTCCTTCTTCAGATG
Found at i:1340028 original size:338 final size:339
Alignment explanation
Indices: 1339411--1340032 Score: 1201
Period size: 338 Copynumber: 1.8 Consensus size: 339
1339401 ATGTTAAACA
1339411 AGTTCTTCTCATTATGAACTTCTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTCTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1339476 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGA
*
1339541 ACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
131 ACTTTTTCTGGAAAAGCTGATCCATCAGAAGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
1339606 CATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGC
196 CATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGC
1339671 TGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCT
261 TGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCT
1339736 TCCTTCTTCAGATG
326 TCCTTCTTCAGATG
*
1339750 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTCTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
*
1339815 GTTGAAC-AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGA
1339879 ACTTTTTCTGGAAAAGCTGATCCATCAGAAGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
131 ACTTTTTCTGGAAAAGCTGATCCATCAGAAGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
*
1339944 CATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTTTCTGGAAAAGC
196 CATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGC
1340009 TGATCCATCAGATGATGGATTTGA
261 TGATCCATCAGATGATGGATTTGA
1340033 ATCTTTGCTA
Statistics
Matches: 279, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
338 208 0.75
339 71 0.25
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (339 bp):
AGTTCTTCTCATTATGAACTTCTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAG
GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGA
ACTTTTTCTGGAAAAGCTGATCCATCAGAAGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
CATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGC
TGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCT
TCCTTCTTCAGATG
Found at i:1340460 original size:22 final size:22
Alignment explanation
Indices: 1340432--1340511 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
1340422 CATAAAGTTT
* *
1340432 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTAAAAAGAAAATCTA
* *
1340454 TCATCTTTAAAAAGAAAATTTG
1 TCATCTTTAAAAAGAAAATCTA
* * **
1340476 TCATCTCTGAAGTGAAAATCTA
1 TCATCTTTAAAAAGAAAATCTA
1340498 TCATCTTTAAAAAG
1 TCATCTTTAAAAAG
1340512 TGTAGATGTA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (22 bp):
TCATCTTTAAAAAGAAAATCTA
Found at i:1342255 original size:115 final size:114
Alignment explanation
Indices: 1342054--1342280 Score: 357
Period size: 115 Copynumber: 2.0 Consensus size: 114
1342044 GATCATGCAG
* * *
1342054 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTTCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTTCTACCAAACCAGATCAGATAACTCAAAGA
*
1342119 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* * *
1342168 TTCATCTTTTAAATCCAATGATTGGTTTTTGGGG-TTCATACCAAACCAGATCAGATAACTCAAA
1 TTCATCTTTCAAATCCAATGATCGG-TTCTGGGGTTTC-TACCAAACCAGATCAGATAACTCAAA
*
1342232 GAACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
64 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
1342281 CATGGCACTT
Statistics
Matches: 103, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
114 25 0.24
115 78 0.76
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTTCTACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1344549 original size:19 final size:19
Alignment explanation
Indices: 1344512--1344549 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1344502 ATTCAATTTT
*
1344512 CCTTTTTCTTTTTTTTTTC
1 CCTTTTTCTTTTTTCTTTC
1344531 CCTTTTT-TTTTCTTCTTTC
1 CCTTTTTCTTTT-TTCTTTC
1344550 TTTGCTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
CCTTTTTCTTTTTTCTTTC
Found at i:1344566 original size:13 final size:13
Alignment explanation
Indices: 1344550--1344593 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1344540 TTCTTCTTTC
1344550 TTTGCTGGATTTT
1 TTTGCTGGATTTT
** *
1344563 TTTGCT-TCTTTC
1 TTTGCTGGATTTT
1344575 TTTGCTGGATTTT
1 TTTGCTGGATTTT
1344588 TTTGCT
1 TTTGCT
1344594 TCTTTCTTTG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.05, C:0.14, G:0.18, T:0.64
Consensus pattern (13 bp):
TTTGCTGGATTTT
Found at i:1344570 original size:25 final size:25
Alignment explanation
Indices: 1344534--1344606 Score: 137
Period size: 25 Copynumber: 2.9 Consensus size: 25
1344524 TTTTTTCCCT
*
1344534 TTTTTTTTCTTCTTTCTTTGCTGGA
1 TTTTTTTGCTTCTTTCTTTGCTGGA
1344559 TTTTTTTGCTTCTTTCTTTGCTGGA
1 TTTTTTTGCTTCTTTCTTTGCTGGA
1344584 TTTTTTTGCTTCTTTCTTTGCTG
1 TTTTTTTGCTTCTTTCTTTGCTG
1344607 AATGAGTATA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.03, C:0.16, G:0.14, T:0.67
Consensus pattern (25 bp):
TTTTTTTGCTTCTTTCTTTGCTGGA
Found at i:1344580 original size:12 final size:12
Alignment explanation
Indices: 1344542--1344605 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
1344532 CTTTTTTTTT
1344542 CTTCTTTCTTTG
1 CTTCTTTCTTTG
** *
1344554 CTGGATTTTTTTG
1 CT-TCTTTCTTTG
1344567 CTTCTTTCTTTG
1 CTTCTTTCTTTG
** *
1344579 CTGGATTTTTTTG
1 CT-TCTTTCTTTG
1344592 CTTCTTTCTTTG
1 CTTCTTTCTTTG
1344604 CT
1 CT
1344606 GAATGAGTAT
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
12 20 0.53
13 18 0.47
ACGTcount: A:0.03, C:0.19, G:0.14, T:0.64
Consensus pattern (12 bp):
CTTCTTTCTTTG
Found at i:1347774 original size:14 final size:14
Alignment explanation
Indices: 1347740--1347793 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
1347730 TTGTGCAATA
* *
1347740 CAAATGCAAAGATG
1 CAAATGTAAATATG
1347754 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
1347769 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
1347783 TAAATGTAAAT
1 CAAATGTAAAT
1347794 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:1349444 original size:30 final size:29
Alignment explanation
Indices: 1349399--1349465 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 29
1349389 TGCAAATAAA
*
1349399 ATGAAATATTAATAAGAAAATATATAAATATT
1 ATGAAA-ATTAATAAG--AATATATAAAAATT
*
1349431 ATGAAAA-TAATAAGTATATATAAAAATT
1 ATGAAAATTAATAAGAATATATAAAAATT
*
1349459 TTGAAAA
1 ATGAAAA
1349466 GAAAGAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 18 0.56
30 7 0.22
31 1 0.03
32 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (29 bp):
ATGAAAATTAATAAGAATATATAAAAATT
Found at i:1349455 original size:18 final size:19
Alignment explanation
Indices: 1349414--1349457 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1349404 ATATTAATAA
1349414 GAAAATATATAAATATTAT
1 GAAAATATATAAATATTAT
*
1349433 GAAAATA-ATAAGTATATAT
1 GAAAATATATAAATAT-TAT
*
1349452 AAAAAT
1 GAAAAT
1349458 TTTGAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (19 bp):
GAAAATATATAAATATTAT
Found at i:1350265 original size:15 final size:15
Alignment explanation
Indices: 1350245--1350325 Score: 54
Period size: 15 Copynumber: 4.9 Consensus size: 15
1350235 AATATTAGTG
1350245 AATAAAAATATAAAT
1 AATAAAAATATAAAT
* *
1350260 AATAAATATATGAAT
1 AATAAAAATATAAAT
*
1350275 AAATAAATAAATAAAATACT
1 -AAT-AA-AAATATAA-A-T
*
1350295 AATTTAAACATATAAAT
1 AA--TAAAAATATAAAT
*
1350312 GATAAAAATATAAA
1 AATAAAAATATAAA
1350326 AAATGACCAA
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
15 24 0.48
16 3 0.06
17 4 0.08
18 6 0.12
19 9 0.18
20 3 0.06
21 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
AATAAAAATATAAAT
Found at i:1350277 original size:27 final size:29
Alignment explanation
Indices: 1350232--1350288 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 29
1350222 TGCATTTCAT
1350232 ATAAATATTAGTGAATAAA-AATATAAATA
1 ATAAATATTAGTGAATAAATAA-ATAAATA
1350261 ATAAATA-TA-TGAATAAATAAATAAATA
1 ATAAATATTAGTGAATAAATAAATAAATA
1350288 A
1 A
1350289 AATACTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 16 0.59
28 4 0.15
29 7 0.26
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (29 bp):
ATAAATATTAGTGAATAAATAAATAAATA
Found at i:1353342 original size:23 final size:22
Alignment explanation
Indices: 1353316--1353370 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
1353306 TTTTTAATAA
*
1353316 CTCTGTCTTTATGGCACATTTT
1 CTCTGTCTTTATGACACATTTT
* *
1353338 CCTCT-ACATTTATGACACGTTTT
1 -CTCTGTC-TTTATGACACATTTT
1353361 CTCTGTCTTT
1 CTCTGTCTTT
1353371 TCGTAAGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.15, C:0.25, G:0.11, T:0.49
Consensus pattern (22 bp):
CTCTGTCTTTATGACACATTTT
Found at i:1353985 original size:2 final size:2
Alignment explanation
Indices: 1353978--1354033 Score: 52
Period size: 2 Copynumber: 31.0 Consensus size: 2
1353968 TATAATATGT
* *
1353978 TA TA TA TA TA TA TA TA T- TG TA TA GA -A TA -A TA -A T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1354014 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1354034 AAGTTCATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
1 6 0.13
2 40 0.87
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1354108 original size:3 final size:3
Alignment explanation
Indices: 1354100--1354157 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
1354090 TCTCTAGCAT
1354100 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1354148 ATA ATA ATA A
1 ATA ATA ATA A
1354158 AAGTGTAATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1354321 original size:19 final size:19
Alignment explanation
Indices: 1354282--1354336 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
1354272 AAAATGATTT
1354282 TTTACAAATATTATAAATAATA
1 TTTACAAATA--AT-AATAATA
1354304 TTTACAAATAATAATAATA
1 TTTACAAATAATAATAATA
* *
1354323 ATTACAAATTATAA
1 TTTACAAATAATAA
1354337 GTTAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 19 0.61
20 2 0.06
22 10 0.32
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TTTACAAATAATAATAATA
Found at i:1355918 original size:20 final size:22
Alignment explanation
Indices: 1355893--1355942 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
1355883 GCTGGGGGAT
1355893 TTTTTTAAAAAAT-AT-ATATA
1 TTTTTTAAAAAATAATAATATA
* *
1355913 TTTTTTAAAATATAATAATTTA
1 TTTTTTAAAAAATAATAATATA
1355935 TTTTTTAA
1 TTTTTTAA
1355943 GTCGAGACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 12 0.46
21 2 0.08
22 12 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTTTAAAAAATAATAATATA
Found at i:1356461 original size:51 final size:51
Alignment explanation
Indices: 1356365--1356462 Score: 137
Period size: 51 Copynumber: 1.9 Consensus size: 51
1356355 CCTTTACAGG
* *
1356365 AAGGCGCGCCCCCTGCACCGCGCTATATGCTGATATGGCACCACGTGGGGT
1 AAGGCGCGCCCCCTGCACCGCGCTATATGCTGACATGGCAACACGTGGGGT
*
1356416 AAGGCGCGCCCCCTGCAGCGCGCCT-TATGCTGACATGG-ATACACGTG
1 AAGGCGCGCCCCCTGCACCGCG-CTATATGCTGACATGGCA-ACACGTG
1356463 TGTAAAGCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
50 1 0.02
51 39 0.93
52 2 0.05
ACGTcount: A:0.18, C:0.34, G:0.31, T:0.17
Consensus pattern (51 bp):
AAGGCGCGCCCCCTGCACCGCGCTATATGCTGACATGGCAACACGTGGGGT
Found at i:1356672 original size:10 final size:10
Alignment explanation
Indices: 1356657--1356689 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1356647 TTCATCACAC
1356657 CAAATTCTCT
1 CAAATTCTCT
1356667 CAAATTCTCT
1 CAAATTCTCT
*
1356677 CAACTTCTCT
1 CAAATTCTCT
1356687 CAA
1 CAA
1356690 GGTATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.36
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1358813 original size:3 final size:3
Alignment explanation
Indices: 1358805--1358841 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1358795 ACCTACTCAG
* *
1358805 GAC GAC GAC GAC GAT GAC GAT GAC GAC GAC GAC GAC G
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC G
1358842 GTGATGATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.32, C:0.27, G:0.35, T:0.05
Consensus pattern (3 bp):
GAC
Found at i:1358867 original size:9 final size:9
Alignment explanation
Indices: 1358811--1358867 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
1358801 TCAGGACGAC
*
1358811 GACGACGAT
1 GACGATGAT
*
1358820 GACGATGAC
1 GACGATGAT
* *
1358829 GACGACGAC
1 GACGATGAT
*
1358838 GACGGTGAT
1 GACGATGAT
* *
1358847 GATGATGGT
1 GACGATGAT
1358856 GACGATGAT
1 GACGATGAT
1358865 GAC
1 GAC
1358868 AACGAGGAGT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.30, C:0.18, G:0.37, T:0.16
Consensus pattern (9 bp):
GACGATGAT
Found at i:1364483 original size:3 final size:3
Alignment explanation
Indices: 1364475--1364556 Score: 85
Period size: 3 Copynumber: 27.0 Consensus size: 3
1364465 TATGCTTACA
* * * ** *
1364475 ATT ATT ATT ATT ATT CTT ATA ATT ATT TTT GAAA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
1364521 ATT ATT ATTT ATT ATT ATT ATT A-T ATT ATT ATT ATT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1364557 TGTAATTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
2 2 0.03
3 61 0.92
4 3 0.05
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1365146 original size:37 final size:37
Alignment explanation
Indices: 1365096--1365200 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
1365086 GTGCTTGTGG
* * *
1365096 ATCCTATCTTTAGGAGTTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* * *
1365133 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* *
1365170 ATCCTATTTTTATGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
1365201 GACGAAAAGG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:1366248 original size:106 final size:106
Alignment explanation
Indices: 1365930--1367410 Score: 2201
Period size: 106 Copynumber: 14.0 Consensus size: 106
1365920 ACATTGTTCC
* * * ** *
1365930 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTAGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * * *
1365994 ACCAGCCGTCCTTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1366036 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
1366095 TCAGTC-G-CCCTTTCATCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAG-CGGTCCC-TTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
1366137 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1366201 CCAACGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1366242 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1366307 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*** * * *
1366348 GAGTCCAATATCCTTTATTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGAAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1366413 CCAGCGGTCCCTTCATTGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1366454 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1366519 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1366560 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1366625 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1366666 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1366731 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1366772 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1366837 CCAGCGGTCCCTTCATTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1366878 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1366943 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * **
1366984 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1367049 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1367090 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1367155 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1367196 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1367261 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1367302 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTG-TTGTTGTCAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
1367366 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1367407 GAGT
1 GAGT
1367411 GGAACGATAT
Statistics
Matches: 1259, Mismatches: 103, Indels: 27
0.91 0.07 0.02
Matches are distributed among these distances:
99 2 0.00
100 74 0.06
101 6 0.00
102 4 0.00
104 3 0.00
105 54 0.04
106 1112 0.88
107 4 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1368262 original size:22 final size:22
Alignment explanation
Indices: 1368236--1368290 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1368226 TTGTGTTTGG
1368236 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1368258 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1368280 TCAAAGGTTTG
1 TCAAAGGTTTG
1368291 ATGGGGTAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1368924 original size:14 final size:14
Alignment explanation
Indices: 1368907--1368953 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
1368897 TTCTTTTAGA
1368907 TTTTTGTTCTTTCT
1 TTTTTGTTCTTTCT
*
1368921 TTTTTTTTCTTT-T
1 TTTTTGTTCTTTCT
*
1368934 TTTTT-AT-TTTCT
1 TTTTTGTTCTTTCT
1368946 TTTTTGTT
1 TTTTTGTT
1368954 TTTGCCCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 3 0.11
12 7 0.25
13 7 0.25
14 11 0.39
ACGTcount: A:0.02, C:0.09, G:0.04, T:0.85
Consensus pattern (14 bp):
TTTTTGTTCTTTCT
Found at i:1368931 original size:10 final size:10
Alignment explanation
Indices: 1368916--1368949 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1368906 ATTTTTGTTC
1368916 TTTCTTTTTT
1 TTTCTTTTTT
1368926 TTTCTTTTTT
1 TTTCTTTTTT
*
1368936 TTTATTTTCTT
1 TTTCTTTT-TT
1368947 TTT
1 TTT
1368950 TGTTTTTGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:1368938 original size:15 final size:15
Alignment explanation
Indices: 1368907--1368956 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1368897 TTCTTTTAGA
* *
1368907 TTTTTGTTC-TTTCT
1 TTTTTTTTCTTTTTT
1368921 TTTTTTTTCTTTTTT
1 TTTTTTTTCTTTTTT
*
1368936 TTTATTTTCTTTTTT
1 TTTTTTTTCTTTTTT
1368951 GTTTTT
1 -TTTTT
1368957 GCCCTTTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 8 0.27
15 18 0.60
16 4 0.13
ACGTcount: A:0.02, C:0.08, G:0.04, T:0.86
Consensus pattern (15 bp):
TTTTTTTTCTTTTTT
Found at i:1373640 original size:37 final size:37
Alignment explanation
Indices: 1373599--1373703 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
1373589 GTGCCTGTGG
* * *
1373599 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
1373636 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
1373673 ATCCTATTTTTATGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1373704 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:1374017 original size:28 final size:27
Alignment explanation
Indices: 1373975--1374063 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 27
1373965 AGGACTTCTA
*
1373975 AATTTTATATGTATAATTAGAACTCCC
1 AATTTTATATTTATAATTAGAACTCCC
* * *
1374002 AACTTTTATGTTTATAATTA-AAGTCCTT
1 AA-TTTTATATTTATAATTAGAACTCC-C
* *
1374030 AATTTTTATATTTATAATTGGGACTCCC
1 AA-TTTTATATTTATAATTAGAACTCCC
1374058 AATTTT
1 AATTTT
1374064 GTTCAGTTCT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
27 11 0.22
28 34 0.69
29 4 0.08
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (27 bp):
AATTTTATATTTATAATTAGAACTCCC
Found at i:1378370 original size:117 final size:117
Alignment explanation
Indices: 1378200--1378491 Score: 444
Period size: 117 Copynumber: 2.5 Consensus size: 117
1378190 TTCCCCGAAG
* * **
1378200 CATACACCCACCTGCACACCAATAAGGACTTGCCCTAAGCACGA-AGCTGAGGAGCCTGCAGTAA
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCAC-ACAGCAAAGGAGCCTGCAGTAA
* * **
1378264 TAACGTCTCCATCCAGTCACTTCC-ATAACTACAATGTGTAGGTTCTCCAGTAC
65 TAACGTCCCCATCCAGTCAC-TCCAATAACTACAATGTGTAGGTTCCCCAAAAC
1378317 CATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGCAGTAAT
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGCAGTAAT
* *
1378382 AACTTCCCCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAAAAC
66 AACGTCCCCATCCAGTCACTCCAATAACTACAATGTGTAGGTTCCCCAAAAC
* *
1378434 CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAGCGAAGGAGCCTG
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTG
1378492 AAATACTTCC
Statistics
Matches: 161, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
116 4 0.02
117 157 0.98
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (117 bp):
CATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGCAGTAAT
AACGTCCCCATCCAGTCACTCCAATAACTACAATGTGTAGGTTCCCCAAAAC
Found at i:1379537 original size:29 final size:28
Alignment explanation
Indices: 1379423--1379543 Score: 125
Period size: 30 Copynumber: 4.1 Consensus size: 28
1379413 CATTTTACAG
** * * *
1379423 AAATAGCACCCTTTTTAAAATAATTACAA
1 AAATAGCA-CCTTTTCGAATTAATTCCCA
*
1379452 AAATAGCACCTTTTCGAATTAAATTCCAAA
1 AAATAGCACCTTTTCGAATT-AATTCC-CA
1379482 AAATAGCACCTTTTCGAATTAATTTCCCA
1 AAATAGCACCTTTTCGAATTAA-TTCCCA
* *
1379511 GAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCA-CCTTTTCGAATTAATTCCCA
1379540 AAAT
1 AAAT
1379544 GTCATCCGGT
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
28 9 0.11
29 32 0.40
30 39 0.49
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (28 bp):
AAATAGCACCTTTTCGAATTAATTCCCA
Found at i:1379580 original size:17 final size:18
Alignment explanation
Indices: 1379558--1379598 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1379548 TCCGGTCAAC
1379558 GGTCAAC-GGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1379575 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1379593 GGTCAA
1 GGTCAA
1379599 AACTAGTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.15, C:0.22, G:0.46, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:1385869 original size:117 final size:116
Alignment explanation
Indices: 1385647--1385948 Score: 403
Period size: 117 Copynumber: 2.6 Consensus size: 116
1385637 TTTTATATAT
* **
1385647 TTCCCC-GAAACATACACCCACCTGCACACCAGTAAGGACTTACCCTAAG-CACGAAGCTGAGGA
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGACAC-AA-CAAAGGA
* **
1385710 GCCTGCAGTAATAACGTCTCCATCCAGTTGCTTCCATAACTACAATGTGTAGG
64 GCCTGCAGTAATAACGTCCCCATCCAGTCACTTCCATAACTACAATGTGTAGG
* *
1385763 TTCCCCAGTACCATACACTCACCTGCACACCAGTAAGGACTTACCCTAAGAACACAACAAAGGAG
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAG-ACACAACAAAGGAG
* *
1385828 CCTGCAGTAATAACTTCCCCATCCAGTCAC-TCCAATCACTACAATGTGTAGG
65 CCTGCAGTAATAACGTCCCCATCCAGTCACTTCC-ATAACTACAATGTGTAGG
* * * * *
1385880 TTCCCCAGAACCATACACCCACCTACACACCAGTAAGGACTTACCTTGAGCACTCAGCAAAGGAG
1 TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAG-ACACAACAAAGGAG
1385945 CCTG
65 CCTG
1385949 AAATACTTCC
Statistics
Matches: 164, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
116 9 0.05
117 150 0.91
118 2 0.01
119 3 0.02
ACGTcount: A:0.32, C:0.33, G:0.16, T:0.19
Consensus pattern (116 bp):
TTCCCCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGACACAACAAAGGAGC
CTGCAGTAATAACGTCCCCATCCAGTCACTTCCATAACTACAATGTGTAGG
Found at i:1386973 original size:30 final size:29
Alignment explanation
Indices: 1386889--1386993 Score: 124
Period size: 29 Copynumber: 3.6 Consensus size: 29
1386879 TTTTTAAAAT
*
1386889 AATTACCAAAATAGCA-CAGTTTCGAATTA
1 AATTCCCAAAATAGCACCA-TTTCGAATTA
*
1386918 AATTCCCAAAATAGCACCTTTTCGAATTA
1 AATTCCCAAAATAGCACCATTTCGAATTA
** *
1386947 AATTCTTAGAATAGCACCCATTTCGAATT-
1 AATTCCCAAAATAGCA-CCATTTCGAATTA
*
1386976 AATTCCCAAAATATCACC
1 AATTCCCAAAATAGCACC
1386994 CGGTCAACGG
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.03
29 50 0.78
30 12 0.19
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.30
Consensus pattern (29 bp):
AATTCCCAAAATAGCACCATTTCGAATTA
Done.