Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000417.1 Hibiscus syriacus cultivar Beakdansim tig00000764_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: 2005044
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1104881 original size:33 final size:31
Alignment explanation
Indices: 1104834--1104911 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 31
1104824 TTAATAATTC
* *
1104834 TAAATAAATAATA-TTATATAAATATTATTTTAA
1 TAAAAAAATAATATTTACATAAATA-TA--TTAA
1104867 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATATTTACATAAATATATTAA
1104898 TATAAAAAATAATA
1 TA-AAAAAATAATA
1104912 ACTATTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
31 6 0.15
32 11 0.27
33 14 0.34
34 10 0.24
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATATTTACATAAATATATTAA
Found at i:1104906 original size:34 final size:33
Alignment explanation
Indices: 1104839--1104944 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
1104829 AATTCTAAAT
*
1104839 AAATAATA-TTATATAAATATTATT-TTA-ATAAAA
1 AAATAATATTTA-ATAAATA-TATTAATATA-AAAA
1104872 AAATAATATTTACATAAATATATTAATATAAAAA
1 AAATAATATTTA-ATAAATATATTAATATAAAAA
* * *
1104906 ATAATAACTATTTAA-AAAAATACTAACATAAAAA
1 A-AATAA-TATTTAATAAATATATTAATATAAAAA
1104940 TAAAT
1 -AAAT
1104945 TTCTTACCAC
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
33 12 0.19
34 36 0.58
35 8 0.13
36 6 0.10
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (33 bp):
AAATAATATTTAATAAATATATTAATATAAAAA
Found at i:1111889 original size:15 final size:15
Alignment explanation
Indices: 1111871--1111926 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
1111861 TAACCGGTTT
1111871 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
1111886 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
* *
1111903 CGGTTATAAAAAAAT
1 CGGTTTTAAAAAAAC
*
1111918 CGATTTTAA
1 CGGTTTTAA
1111927 TATTCCAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 19 0.58
17 14 0.42
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:1111899 original size:17 final size:17
Alignment explanation
Indices: 1111874--1111907 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1111864 CCGGTTTCGG
1111874 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
1111891 TTTTTAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
1111908 ATAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:1112343 original size:13 final size:13
Alignment explanation
Indices: 1112322--1112376 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1112312 AAGTTCGATA
*
1112322 AATTCAAATACTT
1 AATTGAAATACTT
1112335 AATTGAAATACTT
1 AATTGAAATACTT
* *
1112348 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
1112362 AATTGAAATACTT
1 AATTGAAATACTT
1112375 AA
1 AA
1112377 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:1112458 original size:32 final size:33
Alignment explanation
Indices: 1112362--1112460 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1112352 AACTCAACAT
* * *
1112362 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1112395 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1112428 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1112460 A
1 A
1112461 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:1112479 original size:21 final size:21
Alignment explanation
Indices: 1112455--1112494 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1112445 ACTTCAAGTT
1112455 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
1112476 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
1112495 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1114805 original size:11 final size:12
Alignment explanation
Indices: 1114784--1114830 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
1114774 TCCGGATAAA
1114784 AACCGGTTTTTT
1 AACCGGTTTTTT
1114796 AACCGGTTTTTTT
1 AACCGG-TTTTTT
1114809 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
1114823 ATCCGGTT
1 AACCGGTT
1114831 AAAAAACCGG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 13 0.42
13 6 0.19
14 6 0.19
15 6 0.19
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:1114814 original size:15 final size:14
Alignment explanation
Indices: 1114783--1114822 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1114773 TTCCGGATAA
1114783 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
1114796 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
1114809 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
1114823 ATCCGGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:1120749 original size:29 final size:29
Alignment explanation
Indices: 1120707--1120788 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
1120697 AAACTAAATT
*
1120707 GATGTCATTGCTTATATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
1120736 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
1120765 GATGTTATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1120789 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:1121195 original size:13 final size:13
Alignment explanation
Indices: 1121177--1121210 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
1121167 GCCAGAAAAT
1121177 CGAGTTGACTCAC
1 CGAGTTGACTCAC
1121190 CGAGTTGACTCAC
1 CGAGTTGACTCAC
1121203 CGAGTTGA
1 CGAGTTGA
1121211 GCCGAGTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (13 bp):
CGAGTTGACTCAC
Found at i:1125506 original size:29 final size:29
Alignment explanation
Indices: 1125464--1125545 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1125454 AAACTAAATT
1125464 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
1125493 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
1125522 GATGTTATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1125546 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:1131344 original size:16 final size:14
Alignment explanation
Indices: 1131323--1131361 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 14
1131313 CTATTAAATG
1131323 TAACGGTTATACCGGT
1 TAACGGTT-TA-CGGT
1131339 TAACGG-TTACGGT
1 TAACGGTTTACGGT
1131352 TAACGGTTTA
1 TAACGGTTTA
1131362 ATATTAACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 5 0.23
15 1 0.05
16 6 0.27
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (14 bp):
TAACGGTTTACGGT
Found at i:1131750 original size:14 final size:14
Alignment explanation
Indices: 1131731--1131761 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1131721 ATTGATAGAT
1131731 AATGACAATAACTA
1 AATGACAATAACTA
*
1131745 AATGACAATGACTA
1 AATGACAATAACTA
1131759 AAT
1 AAT
1131762 TTATATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.10, T:0.23
Consensus pattern (14 bp):
AATGACAATAACTA
Found at i:1144123 original size:184 final size:176
Alignment explanation
Indices: 1143836--1144215 Score: 532
Period size: 177 Copynumber: 2.1 Consensus size: 176
1143826 ATTAAATTTT
* * * * *
1143836 AAATATTAAATATATTATATATAATATATGGGCTCAGTTCAAATCATTTAAAACTCAATTAAAGA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGTCCAAACCATTTAAAACCCAATTAAAGA
*
1143901 TCCAATAACTTTTAAGCCTAAATCAATATTAATTAATTAAAAAA-TTATAT-ACAATTTTTATTT
66 TCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATGA-AATTTTTATTT
* * *
1143964 TTTAATTATATATTATTTAAATTAATTGTAAATTGTTTTTTTAATTAAA
130 TATAATTATATATTATTTAAATTAATTAT-AATT-TTTTTTGAATTAAA
1144013 AAATATTAAATATATTATATATAACATATGGGCTAAGTCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGTCCAAACCATTTAAAACCCAA-T--T-A
*
1144078 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTT
62 ---AAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATGAAATTT
1144143 TTATTTTATAATTATATATTATTTAAATTAATTATAATTTTTTTTGAATTAAA
124 TTATTTTATAATTATATATTATTTAAATTAATTATAATTTTTTTTGAATTAAA
* * *
1144196 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
1144216 AATTAAAAAA
Statistics
Matches: 181, Mismatches: 13, Indels: 13
0.87 0.06 0.06
Matches are distributed among these distances:
177 53 0.29
178 1 0.01
180 1 0.01
181 1 0.01
182 8 0.04
183 22 0.12
184 51 0.28
185 43 0.24
186 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (176 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGTCCAAACCATTTAAAACCCAATTAAAGA
TCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATGAAATTTTTATTTT
ATAATTATATATTATTTAAATTAATTATAATTTTTTTTGAATTAAA
Found at i:1144230 original size:26 final size:25
Alignment explanation
Indices: 1144172--1144231 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
1144162 TATTTAAATT
* * *
1144172 AATTATAATTTTTTTTGAATTAAAA
1 AATTTTAATTTTTTATAAATTAAAA
*
1144197 AACATTTAATTTTTATATAAATTAAAA
1 AA-TTTTAATTTTT-TATAAATTAAAA
1144224 AATTTTAA
1 AATTTTAA
1144232 AAAAAATTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 2 0.07
26 14 0.50
27 12 0.43
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
AATTTTAATTTTTTATAAATTAAAA
Found at i:1144790 original size:31 final size:31
Alignment explanation
Indices: 1144755--1144818 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
1144745 AATACAGTAA
*
1144755 CCCAATATTTAGTCCATTTGCAATATGGTCC
1 CCCAACATTTAGTCCATTTGCAATATGGTCC
**
1144786 CCCAACATTTAGTCTGTTTGCAATATGGTCC
1 CCCAACATTTAGTCCATTTGCAATATGGTCC
1144817 CC
1 CC
1144819 GAGCGTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.34
Consensus pattern (31 bp):
CCCAACATTTAGTCCATTTGCAATATGGTCC
Found at i:1148076 original size:26 final size:27
Alignment explanation
Indices: 1148046--1148097 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
1148036 TTTTCTTTAA
1148046 CATTAATCGAACCGAAA-TTATTTGAC
1 CATTAATCGAACCGAAATTTATTTGAC
*
1148072 CATTAATCGAACTGAAATTTATTTGA
1 CATTAATCGAACCGAAATTTATTTGA
1148098 AAATTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (27 bp):
CATTAATCGAACCGAAATTTATTTGAC
Found at i:1148103 original size:27 final size:26
Alignment explanation
Indices: 1148047--1148103 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
1148037 TTTCTTTAAC
**
1148047 ATTAATCGAACCGAAATTATTTGACC
1 ATTAATCGAACCGAAATTATTTGAAA
*
1148073 ATTAATCGAACTGAAATTTATTTGAAA
1 ATTAATCGAACCGAAA-TTATTTGAAA
1148100 ATTA
1 ATTA
1148104 TTAACTGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (26 bp):
ATTAATCGAACCGAAATTATTTGAAA
Found at i:1148184 original size:94 final size:96
Alignment explanation
Indices: 1147978--1148202 Score: 393
Period size: 94 Copynumber: 2.4 Consensus size: 96
1147968 TTCTTTAACT
*
1147978 GTTAACCGAACCGAAATTTATTTGAAAATTATTAA-TCGAACCAAATTAACCGAATTTATTTTCT
1 GTTAATCGAACCGAAATTTATTTGAAAATTATTAACTCGAACCAAATTAACCGAATTTATTTTCT
1148042 TTAACATTAATCGAACCGAAATTATTTGACC
66 TTAACATTAATCGAACCGAAATTATTTGACC
* *
1148073 ATTAATCGAACTGAAATTTATTTGAAAATTATTAACT-GAACCAAATTAACCGAATTT-TTTTCT
1 GTTAATCGAACCGAAATTTATTTGAAAATTATTAACTCGAACCAAATTAACCGAATTTATTTTCT
1148136 TTAACATTAATCGAACCGAAATTATTTGACC
66 TTAACATTAATCGAACCGAAATTATTTGACC
*
1148167 GTTAATCGAACCAAAATTTATTTGAAAATTATTAAC
1 GTTAATCGAACCGAAATTTATTTGAAAATTATTAAC
1148203 CGATTTTTTT
Statistics
Matches: 123, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
94 70 0.57
95 52 0.42
96 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (96 bp):
GTTAATCGAACCGAAATTTATTTGAAAATTATTAACTCGAACCAAATTAACCGAATTTATTTTCT
TTAACATTAATCGAACCGAAATTATTTGACC
Found at i:1148452 original size:25 final size:25
Alignment explanation
Indices: 1148423--1148508 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 25
1148413 AAGAAAAAAA
1148423 TCGGTTAATAATTTTCAAATAAATT
1 TCGGTTAATAATTTTCAAATAAATT
* ** * *
1148448 TCGGTTCGATTAATGGTTAAAGAAAAAAAT
1 TCGGTT--AATAAT--TTTCA-AATAAATT
1148478 TCGGTTAATAATTTTCAAATAAATT
1 TCGGTTAATAATTTTCAAATAAATT
*
1148503 CCGGTT
1 TCGGTT
1148509 CGATTAACGG
Statistics
Matches: 45, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
25 17 0.38
26 3 0.07
27 5 0.11
28 5 0.11
29 3 0.07
30 12 0.27
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (25 bp):
TCGGTTAATAATTTTCAAATAAATT
Found at i:1148481 original size:30 final size:30
Alignment explanation
Indices: 1148396--1148483 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 30
1148386 AAATAATTTT
1148396 GGTTCGATTAATGGTTAAAGAAAAAAA-TC
1 GGTTCGATTAATGGTTAAAGAAAAAAATTC
* ** * *
1148425 GGTT--AATAAT--TTTCA-AATAAATTTC
1 GGTTCGATTAATGGTTAAAGAAAAAAATTC
1148450 GGTTCGATTAATGGTTAAAGAAAAAAATTC
1 GGTTCGATTAATGGTTAAAGAAAAAAATTC
1148480 GGTT
1 GGTT
1148484 AATAATTTTC
Statistics
Matches: 43, Mismatches: 10, Indels: 11
0.67 0.16 0.17
Matches are distributed among these distances:
24 5 0.12
25 9 0.21
27 10 0.23
29 7 0.16
30 12 0.28
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (30 bp):
GGTTCGATTAATGGTTAAAGAAAAAAATTC
Found at i:1148500 original size:55 final size:55
Alignment explanation
Indices: 1148384--1148538 Score: 239
Period size: 55 Copynumber: 2.9 Consensus size: 55
1148374 CGATTAACGG
*
1148384 TCAAAT-AATTTTGGTTCGATTAATGGTTAAAGAAAAAAA-TCGGTTAATAATTT
1 TCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATTCGGTTAATAATTT
1148437 TCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATTCGGTTAATAATTT
1 TCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATTCGGTTAATAATTT
* * *
1148492 TCAAATAAATTCCGGTTCGATTAACGG-T-AA-AAAAAAATTTGGTTAAT
1 TCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATTCGGTTAAT
1148539 TTGGTTCGGT
Statistics
Matches: 96, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
52 16 0.17
53 8 0.08
54 33 0.34
55 39 0.41
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (55 bp):
TCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATTCGGTTAATAATTT
Found at i:1153715 original size:21 final size:21
Alignment explanation
Indices: 1153689--1153733 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1153679 ATTTTTGAAA
1153689 AAAATTGAAAATTTAGGTACT
1 AAAATTGAAAATTTAGGTACT
* *
1153710 AAAATTGATACTTTAGGTACT
1 AAAATTGAAAATTTAGGTACT
1153731 AAA
1 AAA
1153734 CACATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (21 bp):
AAAATTGAAAATTTAGGTACT
Found at i:1155103 original size:32 final size:32
Alignment explanation
Indices: 1155058--1155133 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 32
1155048 TGGGCGTAGG
* *
1155058 AGCCAACCTAAGAGAACATCTTGAGGCCTAAA
1 AGCCTACCCAAGAGAACATCTTGAGGCCTAAA
*** * **
1155090 AGCCTACCCAAGAGAGTTTCTTGGGGCCTCGA
1 AGCCTACCCAAGAGAACATCTTGAGGCCTAAA
1155122 AGCCTACCCAAG
1 AGCCTACCCAAG
1155134 GGTCACCTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (32 bp):
AGCCTACCCAAGAGAACATCTTGAGGCCTAAA
Found at i:1157730 original size:23 final size:23
Alignment explanation
Indices: 1157704--1157751 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1157694 ATAAAATACA
*
1157704 ATAACATACTAGATAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
** *
1157727 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
1157750 AT
1 AT
1157752 TGACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGATAGCGCTTAT
Found at i:1158254 original size:23 final size:22
Alignment explanation
Indices: 1158227--1158299 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 22
1158217 ATACTTTACA
* *
1158227 ATATAAGCACTACCTATTATATT
1 ATATAA-CGCTACCTATTACATT
1158250 ATATAAACGCTACCTATTACATT
1 ATAT-AACGCTACCTATTACATT
*
1158273 ATATTAACGCTACCTATTACATC
1 ATA-TAACGCTACCTATTACATT
1158296 ATAT
1 ATAT
1158300 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
22 1 0.02
23 41 0.91
24 3 0.07
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:1158300 original size:23 final size:23
Alignment explanation
Indices: 1158236--1158300 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
1158226 AATATAAGCA
* *
1158236 CTACCTATTATATTATATAAACG
1 CTACCTATTACATTATATTAACG
1158259 CTACCTATTACATTATATTAACG
1 CTACCTATTACATTATATTAACG
*
1158282 CTACCTATTACATCATATT
1 CTACCTATTACATTATATT
1158301 TTTACCTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (23 bp):
CTACCTATTACATTATATTAACG
Found at i:1158753 original size:23 final size:23
Alignment explanation
Indices: 1158718--1158790 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1158708 ATACTTTACA
*
1158718 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1158741 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1158764 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
1158787 ATAT
1 ATAT
1158791 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:1159244 original size:23 final size:23
Alignment explanation
Indices: 1159209--1159281 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1159199 ATACTTTACA
* *
1159209 ATATAAGCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
1159232 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
1159255 ATATTAACGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
1159278 ATAT
1 ATAT
1159282 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:1159282 original size:23 final size:23
Alignment explanation
Indices: 1159218--1159282 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
1159208 AATATAAGCA
*
1159218 CTACCTATTACATTATATAAACG
1 CTACCTATTACATTATATTAACG
1159241 CTACCTATTACATTATATTAACG
1 CTACCTATTACATTATATTAACG
*
1159264 CTACCTATTACATCATATT
1 CTACCTATTACATTATATT
1159283 TTTACCTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.38
Consensus pattern (23 bp):
CTACCTATTACATTATATTAACG
Found at i:1159733 original size:23 final size:23
Alignment explanation
Indices: 1159698--1159770 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1159688 ATACTTTACA
*
1159698 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1159721 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1159744 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
1159767 ATAT
1 ATAT
1159771 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:1159775 original size:489 final size:490
Alignment explanation
Indices: 1157825--1160117 Score: 4301
Period size: 491 Copynumber: 4.7 Consensus size: 490
1157815 TTATAATATG
* * *
1157825 TTGAAAGTGTCTATATTTTTTTATAAAAAAGATCGATACTCTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCTATA-CTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
1157890 TTCAA--TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTTATTTGC
65 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
*
1157953 ACAAAAAATTATTTGATTATTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
1158018 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
195 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
*
1158083 TATCGTAACATAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
260 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
*
1158148 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATG
325 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
*
1158213 ATAGATACTTTACAATATAAGCACTACCTATTATATTATATAAACGCTACCTATTACATTATATT
390 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATT
1158278 AACGCTACCTATTACATCATATTTTTACCTATTATA
455 AACGCTACCTATTACATCATATTTTTACCTATTATA
*
1158314 TTGAAAGTGTCTATAATTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1158379 TCAATTTGTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
66 TCAATTT-TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
1158444 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
*
1158509 TTAACCAAAGATAATAATAATTATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
195 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
1158574 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
260 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
1158639 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
325 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
*
1158704 ATATATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATA-T
390 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATT
1158768 AAGCGCTACCTATTACATCATATTTTTACCTATTATA
455 AA-CGCTACCTATTACATCATATTTTTACCTATTATA
1158805 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1158870 TCAATTTGTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
66 TCAATTT-TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
1158935 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
1159000 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
195 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
*
1159065 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
260 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
* * *
1159130 TTAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATGGACACTTGTATAAAAAGG
325 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
1159195 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATT
390 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATT
1159260 AACGCTACCTATTACATCATATTTTTACCTATTATA
455 AACGCTACCTATTACATCATATTTTTACCTATTATA
* *
1159296 TTGAAAGTGTCTATACTTTTTATAAAAATGATCGATACTTTTTTTTAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1159361 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
1159426 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
*
1159491 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
1159556 ATCGTAACGT-AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
1159620 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGG
326 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAA-GG
1159685 -TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATA-T
390 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATT
1159748 AAGCGCTACCTATTACATCATATTTTTACCTATTATA
455 AA-CGCTACCTATTACATCATATTTTTACCTATTATA
* * *
1159785 TTGAAAGTGTCTATACTTTTTATAAAAATGATCAATACTTTTTTAAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1159850 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
1159915 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
1159980 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
1160045 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
1160110 CAAAAGAT
326 CAAAAGAT
1160118 GTACATACCT
Statistics
Matches: 1768, Mismatches: 28, Indels: 15
0.98 0.02 0.01
Matches are distributed among these distances:
488 54 0.03
489 490 0.28
490 264 0.15
491 957 0.54
492 3 0.00
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (490 bp):
TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATTA
ACGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:1162819 original size:183 final size:183
Alignment explanation
Indices: 1162508--1163693 Score: 2054
Period size: 183 Copynumber: 6.5 Consensus size: 183
1162498 TTTTTCGAAA
* * *
1162508 GTGTAAATGTCAACACTTTTTGACAATGTATCGACACATATTTCTTCCAATCTGGACATAAAGTT
1 GTGTAAATGTCGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTA
* *
1162573 CTGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATT
66 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
1162638 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGAT
131 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGAT
*
1162691 GTGTAAATGTCGACACTTTTTGACAATGTATAGACACATTTTTCTTCCAATCTGGACATAAAGTA
1 GTGTAAATGTCGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTA
*
1162756 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCACTCATAAAACCGGTATATT
66 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
1162821 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGAT
131 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGAT
1162874 GTGTAAATGTCGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTA
1 GTGTAAATGTCGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTA
1162939 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
66 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
*
1163004 TATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGAT
131 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGAT
*
1163057 GTGTAAATGTCGACACTTTTTGACAATGTATCGACATATTTTTCTTCCAATCTGGACATAAAGTA
1 GTGTAAATGTCGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTA
1163122 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
66 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
*
1163187 TATACCGGTTATAATACAAAATTATCTATTACATTATAATTCTGGGTTCCGAT
131 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGAT
* * *
1163240 GTATAAATGTAGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTT
1 GTGTAAATGTCGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTA
*
1163305 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATT
66 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
1163370 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGAT
131 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGAT
* * *
1163423 GTGTAAATGTCGACACTTTTGGACAATGTATCGACACATCTTTCTTCCAATCTGGACATAAAGTT
1 GTGTAAATGTCGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTA
** *
1163488 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTATCTCATAAAATCGGTATATT
66 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
* *
1163553 TATATCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCTGAT
131 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGAT
* * * *
1163606 GTTTTTTCAA--TCGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCATTCTGGACATAA
1 G---TGTAAATGTCGACACTTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAA
* * *
1163668 ATTACAGACACAATATTAAAATGTGT
62 AGTACCGACACAATATTAAAAAGTGT
1163694 GAAAACTTTA
Statistics
Matches: 960, Mismatches: 39, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
183 890 0.93
184 66 0.07
186 4 0.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (183 bp):
GTGTAAATGTCGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTA
CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATT
TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGAT
Found at i:1164909 original size:3 final size:3
Alignment explanation
Indices: 1164901--1164975 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
1164891 ACTTGTTTGG
* * * * * * *
1164901 ATC ATC ATC ATC ATC ATC GTC GTC GTC ATC ATC TTC ATC GTC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
1164949 ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1164976 GTCAGCTTCA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:1164918 original size:12 final size:12
Alignment explanation
Indices: 1164901--1164992 Score: 76
Period size: 12 Copynumber: 7.7 Consensus size: 12
1164891 ACTTGTTTGG
*
1164901 ATCATCATCATC
1 ATCATCATCTTC
* *
1164913 ATCATCGTCGTC
1 ATCATCATCTTC
*
1164925 GTCATCATCTTC
1 ATCATCATCTTC
* *
1164937 ATCGTCAGCTTC
1 ATCATCATCTTC
* *
1164949 ATCGTCATCATC
1 ATCATCATCTTC
*
1164961 ATCGTCATCTTC
1 ATCATCATCTTC
* *
1164973 ATCGTCAGCTTC
1 ATCATCATCTTC
*
1164985 ATCTTCAT
1 ATCATCAT
1164993 TGACCGCTTG
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
12 66 1.00
ACGTcount: A:0.21, C:0.33, G:0.10, T:0.37
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:1164956 original size:24 final size:24
Alignment explanation
Indices: 1164929--1164987 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
1164919 GTCGTCGTCA
1164929 TCATCTTCATCGTCAGCTTCATCG
1 TCATCTTCATCGTCAGCTTCATCG
* *
1164953 TCATCATCATCGTCATCTTCATCG
1 TCATCTTCATCGTCAGCTTCATCG
*
1164977 TCAGCTTCATC
1 TCATCTTCATC
1164988 TTCATTGACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.19, C:0.34, G:0.10, T:0.37
Consensus pattern (24 bp):
TCATCTTCATCGTCAGCTTCATCG
Found at i:1164990 original size:6 final size:6
Alignment explanation
Indices: 1164929--1164992 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
1164919 GTCGTCGTCA
* * * * * *
1164929 TCATCT TCATCG TCAGCT TCATCG TCATCA TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
1164977 TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCAT
1164993 TGACCGCTTG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:1166971 original size:18 final size:18
Alignment explanation
Indices: 1166948--1167008 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1166938 TCTCATTCAT
*
1166948 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
1166966 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
1166985 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
1167004 AATTA
1 AATTA
1167009 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:1166984 original size:19 final size:19
Alignment explanation
Indices: 1166960--1167008 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1166950 TTATATTCAC
1166960 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1166979 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1166998 ATACAAAATTA
1 ATACAAAATTA
1167009 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1168821 original size:33 final size:33
Alignment explanation
Indices: 1168784--1168849 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1168774 CATCTTAATA
*
1168784 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* * *
1168817 TCACCGCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1168850 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1168910 original size:21 final size:21
Alignment explanation
Indices: 1168886--1168926 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1168876 CTTATGCCTC
1168886 TCAAGTGTATCTTCGACTCTA
1 TCAAGTGTATCTTCGACTCTA
* *
1168907 TCAAGTTTCTCTTCGACTCT
1 TCAAGTGTATCTTCGACTCT
1168927 TGATTTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (21 bp):
TCAAGTGTATCTTCGACTCTA
Found at i:1171190 original size:20 final size:20
Alignment explanation
Indices: 1171148--1171195 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1171138 CATTTTACCG
*
1171148 GTTTTATCATTTTGATACCT
1 GTTTTATCATTTTGATACAT
*
1171168 GTTTTATCATATTT-TTACAT
1 GTTTTATCAT-TTTGATACAT
*
1171188 GTTATATC
1 GTTTTATC
1171196 GTTGTGGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.56
Consensus pattern (20 bp):
GTTTTATCATTTTGATACAT
Found at i:1171348 original size:20 final size:20
Alignment explanation
Indices: 1171321--1171367 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1171311 TTCGGTAACG
1171321 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
1171340 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
1171361 TTTTACC
1 TTTTACC
1171368 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:1171549 original size:182 final size:179
Alignment explanation
Indices: 1171107--1171579 Score: 626
Period size: 182 Copynumber: 2.6 Consensus size: 179
1171097 CGTACTTACG
* * * *
1171107 AAAGTAGCGACACTTTCAATATATCTGGTATCATTTTACCGGTTTTATCATTTTGATACCT-GTT
1 AAAGTACCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATA-CTGGTT
* * *
1171171 TTATCATATTTTTACATGTTATATCGTTGTGGATCGATATATATTTTTTAAAATATCGACACATT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCG--ATACATTTTTTAAAATATCGACACATT
*
1171236 ATAGGCGCTAAAATGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
128 ATAGGAGCTAAAATGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* * * *
1171288 AAAGTATCGACACTTTCAATATATTCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTACCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACTGGTTT
* *
1171353 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAA-TATCGACACATTAT
** **
1171418 AGGATTTAAAAACTGCTTCTCTTTTAAATTCATGAAGTGTCGATCCTTATATT
130 AGGAGCT-AAAA-TGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * **
1171471 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGG-TTTATCATTTCAATACTGGTTT
1 AAAGTACCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACTGGTTT
* * *
1171535 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1171580 AATTTGGATC
Statistics
Matches: 256, Mismatches: 31, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
179 14 0.05
180 18 0.07
181 92 0.36
182 95 0.37
183 37 0.14
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (179 bp):
AAAGTACCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACTGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAATATCGACACATTATA
GGAGCTAAAATGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:1172090 original size:30 final size:29
Alignment explanation
Indices: 1172021--1172112 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 29
1172011 TTTAATTACT
* * * *
1172021 TAAA-TATTTTTTTATCAAAATAAGTGCT
1 TAAAGTATTTTTTTATTAAAATAGGTACC
* *
1172049 TTAAGTTTTTTTTTAGTTAAAATAGGTACC
1 TAAAGTATTTTTTTA-TTAAAATAGGTACC
* *
1172079 TAAAGTATTTTTTGATTAAAATAGATACC
1 TAAAGTATTTTTTTATTAAAATAGGTACC
1172108 TAAAG
1 TAAAG
1172113 CATTCAATAT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
28 3 0.06
29 27 0.52
30 22 0.42
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.45
Consensus pattern (29 bp):
TAAAGTATTTTTTTATTAAAATAGGTACC
Found at i:1176814 original size:25 final size:25
Alignment explanation
Indices: 1176786--1176833 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
1176776 ACCAAACATC
1176786 GTAATCTTACATTCCTGCTAAACTT
1 GTAATCTTACATTCCTGCTAAACTT
1176811 GTAATCTTACATTCCTGCTAAAC
1 GTAATCTTACATTCCTGCTAAAC
1176834 GAACAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (25 bp):
GTAATCTTACATTCCTGCTAAACTT
Found at i:1182286 original size:179 final size:183
Alignment explanation
Indices: 1182066--1182441 Score: 681
Period size: 179 Copynumber: 2.1 Consensus size: 183
1182056 TTACTCACAT
1182066 ATACTATATTTTTGTTAAATGAACCTTATGAACAAATATCGGTATAAAAGTTATGTTAATGTCAT
1 ATAC-ATA-TTTTGTTAAATGAACCTTATGAACAAATATCGGTATAAAAGTTATGTTAATGTCAT
1182131 CGATTCAGTATTTTAATTAAGG-TTTA-TACTATTTTTTTTAATAGAAGCTGCTATTA-TATTAT
64 CGATTCAGTATTTTAATTAAGGTTTTATTACTATTTTTTTTAATAGAAGCTGCTATTATTATTAT
1182193 AAAGTGAAAATATTTGAAATTACAATAAGAATTTATAA-TATCATCGT-AACTAA
129 AAAGTGAAAATATTTGAAATTACAATAAGAATTTATAATTATCATCGTAAACTAA
1182246 ATACATATTTTGTTAAATGAACCTTATTGAACAAATATCGGTATAAAAGTTATGTTAATGTCATC
1 ATACATATTTTGTTAAATGAACCTTA-TGAACAAATATCGGTATAAAAGTTATGTTAATGTCATC
1182311 GATTCAGTATTTTAATTAAGGTTTTATTACTATTTTTTTTAATAGAAGCTGCTATTATTATTATA
65 GATTCAGTATTTTAATTAAGGTTTTATTACTATTTTTTTTAATAGAAGCTGCTATTATTATTATA
1182376 AAGTGAAAATATTTGAAATTACAATAAGAATTTATAATTATCATCGTAAACTAA
130 AAGTGAAAATATTTGAAATTACAATAAGAATTTATAATTATCATCGTAAACTAA
*
1182430 ATACATAATTTG
1 ATACATATTTTG
1182442 GACTTTTACA
Statistics
Matches: 189, Mismatches: 1, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
178 19 0.10
179 62 0.33
180 8 0.04
181 30 0.16
182 44 0.23
183 9 0.05
184 17 0.09
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.41
Consensus pattern (183 bp):
ATACATATTTTGTTAAATGAACCTTATGAACAAATATCGGTATAAAAGTTATGTTAATGTCATCG
ATTCAGTATTTTAATTAAGGTTTTATTACTATTTTTTTTAATAGAAGCTGCTATTATTATTATAA
AGTGAAAATATTTGAAATTACAATAAGAATTTATAATTATCATCGTAAACTAA
Found at i:1182828 original size:23 final size:23
Alignment explanation
Indices: 1182797--1182842 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1182787 GAAAAATGTA
1182797 TCACAAAGACAG-AGATAAACGTG
1 TCACAAAGACAGCA-ATAAACGTG
*
1182820 TCACGAAGACAGCAATAAACGTG
1 TCACAAAGACAGCAATAAACGTG
1182843 AAACACAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (23 bp):
TCACAAAGACAGCAATAAACGTG
Found at i:1192387 original size:15 final size:16
Alignment explanation
Indices: 1192346--1192390 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
1192336 TTAATGCAAT
*
1192346 TTAAATTTATTATGAA
1 TTAAATTTTTTATGAA
*
1192362 TTCATATTTTTTATG-A
1 TT-AAATTTTTTATGAA
1192378 TTAAATTTTTTAT
1 TTAAATTTTTTAT
1192391 ATATTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 10 0.40
16 5 0.20
17 10 0.40
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (16 bp):
TTAAATTTTTTATGAA
Found at i:1193271 original size:21 final size:21
Alignment explanation
Indices: 1193242--1193304 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
1193232 TATTTTTCAA
*
1193242 AAAAACATTTACCAAACTTTG
1 AAAACCATTTACCAAACTTTG
*
1193263 AAAACCATTT-TCAAA----G
1 AAAACCATTTACCAAACTTTG
1193279 -AAA-CATTTACCAAACTTTG
1 AAAACCATTTACCAAACTTTG
1193298 AAAACCA
1 AAAACCA
1193305 ATTTTTCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 14
0.65 0.06 0.29
Matches are distributed among these distances:
14 5 0.16
15 7 0.22
16 1 0.03
19 1 0.03
20 7 0.22
21 11 0.34
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.25
Consensus pattern (21 bp):
AAAACCATTTACCAAACTTTG
Found at i:1193330 original size:35 final size:36
Alignment explanation
Indices: 1193199--1193315 Score: 157
Period size: 35 Copynumber: 3.2 Consensus size: 36
1193189 CTCATTATCA
* * **
1193199 TTTTC-AACAAACATCTACCAAACTTTGAAAAATTAT
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCAT
*
1193235 TTTTCAAAAAAACATTTACCAAACTTTGAAAACCA-
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1193270 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAAT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACC-AT
1193307 TTTTCAAAG
1 TTTTCAAAG
1193316 TTGATTGCCA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 33 0.45
36 11 0.15
37 29 0.40
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (36 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
Found at i:1203231 original size:6 final size:6
Alignment explanation
Indices: 1203221--1203932 Score: 1262
Period size: 6 Copynumber: 119.7 Consensus size: 6
1203211 ATTTTAAAAA
*
1203221 TATGTA TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1203269 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1203317 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1203365 TATGTG TA--TG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
*
1203411 --TGTG TATGTG TATGTG TATGTG TATGTG TATGTATG TATGTA TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATG--TG TATGTG TATGTG
1203459 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1203507 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1203555 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1203603 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1203651 TATGTG TATGTG TATGTG TATGTG TA--TG TAGTGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TA-TGTG TATGTG TATGTG
1203698 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1203746 TATGTG TATGTG TA--TG TATGTG TATGTG TATGTG TAT-TG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1203791 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1203839 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * * *
1203887 TATGTG TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATG
1203933 AGAAACCATA
Statistics
Matches: 690, Mismatches: 4, Indels: 24
0.96 0.01 0.03
Matches are distributed among these distances:
4 16 0.02
5 5 0.01
6 659 0.96
7 4 0.01
8 6 0.01
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (6 bp):
TATGTG
Found at i:1204732 original size:11 final size:11
Alignment explanation
Indices: 1204716--1204741 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1204706 ATTAGAAATA
1204716 TTAATATTTTT
1 TTAATATTTTT
1204727 TTAATATTTTT
1 TTAATATTTTT
1204738 TTAA
1 TTAA
1204742 AACGTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTAATATTTTT
Found at i:1204879 original size:15 final size:15
Alignment explanation
Indices: 1204833--1204863 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1204823 GTAAAAAAAA
1204833 TAACATTTTCGATAT
1 TAACATTTTCGATAT
*
1204848 TAATATTTTCGATAT
1 TAACATTTTCGATAT
1204863 T
1 T
1204864 TTCGATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (15 bp):
TAACATTTTCGATAT
Found at i:1206344 original size:21 final size:21
Alignment explanation
Indices: 1206318--1206362 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1206308 GATTTCTGGG
* *
1206318 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1206339 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1206360 CAA
1 CAA
1206363 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1207740 original size:14 final size:14
Alignment explanation
Indices: 1207721--1207748 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1207711 GAAAAGAAGC
1207721 TATGTGATACGTGA
1 TATGTGATACGTGA
1207735 TATGTGATACGTGA
1 TATGTGATACGTGA
1207749 ATTACAAGTT
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:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:1208034 original size:148 final size:149
Alignment explanation
Indices: 1207849--1208153 Score: 567
Period size: 149 Copynumber: 2.1 Consensus size: 149
1207839 GAGTCGAGGG
1207849 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1207914 AC-TGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
1207978 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
1207997 TCTACGCGGTCCTTCGGGATATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACATAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
**
1208062 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTTTTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
1208127 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1208146 TCTACGCG
1 TCTACGCG
1208154 CACTTCGGTG
Statistics
Matches: 152, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
148 65 0.43
149 87 0.57
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1208162 original size:22 final size:22
Alignment explanation
Indices: 1208131--1208173 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1208121 TTTTTATATG
*
1208131 GCACTACGGTGCAATTCTACGC
1 GCACTACGGTGCAATTATACGC
*
1208153 GCACTTCGGTGCAATTATACG
1 GCACTACGGTGCAATTATACG
1208174 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (22 bp):
GCACTACGGTGCAATTATACGC
Found at i:1209992 original size:30 final size:30
Alignment explanation
Indices: 1209934--1210032 Score: 155
Period size: 30 Copynumber: 3.3 Consensus size: 30
1209924 GAAGGACCTA
* *
1209934 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
1209963 TCCAGAGGTCATAAAGATCCTCAGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1209993 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
1210023 TCCATAGGTC
1 TCCAGAGGTC
1210033 CCGAAGAACC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
29 16 0.25
30 48 0.75
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.21
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1210049 original size:30 final size:30
Alignment explanation
Indices: 1209934--1210057 Score: 135
Period size: 30 Copynumber: 4.1 Consensus size: 30
1209924 GAAGGACCTA
* **
1209934 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTAGGTAACTG
1209963 TCCAGAGGTCATAAAGATCCTCA-GTAACTG
1 TCCAGAGGTCATAAAGATCCT-AGGTAACTG
*
1209993 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTAGGTAACTG
* *** *
1210023 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTAGGT-AACTG
1210054 TCCA
1 TCCA
1210058 TATGTCTCAA
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.20
30 56 0.69
31 9 0.11
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTAGGTAACTG
Found at i:1218160 original size:77 final size:78
Alignment explanation
Indices: 1218079--1218233 Score: 179
Period size: 78 Copynumber: 2.0 Consensus size: 78
1218069 ATAAAAATAA
** * * *
1218079 AGGTTCCGCCCAAAAATGTCAT-GATTCACTAAGAAA-TAGGTTGTGATATGTATTGTTAATATT
1 AGGTTCCGCCCAAAAATGTCATAG-TTCACTAAGAAAGTAGGTTGCAATATGAAATCTTAATATT
*
1218142 TTTATTAATAAAAT
65 TTTAATAATAAAAT
** * * * *
1218156 AGGTTGTGTCCAAGAATGTCATAGTTCACTAAGAAAGTATGTTGCAATCTGAAATCTTAATATTT
1 AGGTTCCGCCCAAAAATGTCATAGTTCACTAAGAAAGTAGGTTGCAATATGAAATCTTAATATTT
1218221 TTAATAATAAAAT
66 TTAATAATAAAAT
1218234 GTTATCATAG
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
77 30 0.47
78 34 0.53
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (78 bp):
AGGTTCCGCCCAAAAATGTCATAGTTCACTAAGAAAGTAGGTTGCAATATGAAATCTTAATATTT
TTAATAATAAAAT
Found at i:1223848 original size:21 final size:20
Alignment explanation
Indices: 1223802--1223849 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1223792 GAGTACTACT
* *
1223802 TAAAATGTTATTTTTTTATC
1 TAAAATGTTATTTTGTTACC
1223822 -AGAAATGTTAATTTTGTTACC
1 TA-AAATGTT-ATTTTGTTACC
1223843 TAAAATG
1 TAAAATG
1223850 AATATTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 1 0.04
20 7 0.30
21 14 0.61
22 1 0.04
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (20 bp):
TAAAATGTTATTTTGTTACC
Found at i:1233427 original size:41 final size:41
Alignment explanation
Indices: 1233372--1233459 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
1233362 AAGCAGTCCA
*
1233372 AGAA-CCGTACGCCATCCCTGATGTCACATCTCCATCCACC
1 AGAAGCCGTACGCCATCCCTGATATCACATCTCCATCCACC
* *
1233412 AGAAGCCGTGCGCCATCCCTGATATCACATCTTCATCCACC
1 AGAAGCCGTACGCCATCCCTGATATCACATCTCCATCCACC
1233453 AGAAGCC
1 AGAAGCC
1233460 CCATGTGTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 4 0.09
41 40 0.91
ACGTcount: A:0.26, C:0.40, G:0.15, T:0.19
Consensus pattern (41 bp):
AGAAGCCGTACGCCATCCCTGATATCACATCTCCATCCACC
Found at i:1233919 original size:28 final size:28
Alignment explanation
Indices: 1233876--1233956 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 28
1233866 TTATATATGC
*
1233876 AAAAATAATT-AA-TTAAATAAAATATT
1 AAAAAAAATTAAATTTAAATAAAATATT
* *
1233902 AAAAAAAATTAAATTTAAATAAATTACT
1 AAAAAAAATTAAATTTAAATAAAATATT
* * *
1233930 AACAAAATACTAAATAT-AATAAAATAT
1 AA-AAAAAATTAAATTTAAATAAAATAT
1233957 ACATTAAACA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
26 9 0.20
27 2 0.05
28 22 0.50
29 11 0.25
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (28 bp):
AAAAAAAATTAAATTTAAATAAAATATT
Found at i:1235772 original size:14 final size:15
Alignment explanation
Indices: 1235724--1235776 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
1235714 TTCGAATTCT
1235724 ATGAATTACTGAAAA
1 ATGAATTACTGAAAA
*
1235739 ATGAATTACTGAAAT
1 ATGAATTACTGAAAA
*
1235754 TTGAATT-CTGAAAA
1 ATGAATTACTGAAAA
1235768 ATGAATTAC
1 ATGAATTAC
1235777 ATTTCTGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 12 0.36
15 21 0.64
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (15 bp):
ATGAATTACTGAAAA
Found at i:1236139 original size:90 final size:87
Alignment explanation
Indices: 1235984--1236152 Score: 216
Period size: 90 Copynumber: 1.9 Consensus size: 87
1235974 TTATTATTTT
* * * *
1235984 AAAATATTAAAATAATTTATTTATTATTAAATATTATTTTTATAATTTTATTAATAAAAATATTA
1 AAAATATTAAAATAATTTAATTATTATTAAATAATATTGTTATAATTATATTAATAAAAATATTA
*
1236049 ATATGGTATATTTTAGTGAAATA
66 AT-TAGTATATTTTAGTGAAATA
* *
1236072 AAAATATTATAAATTATATTAATTATTTATTAAAGTAATATTGTTAT-ATTATATT-TTAAAAAT
1 AAAATATTA-AAATAAT-TTAATTA-TTATTAAA-TAATATTGTTATAATTATATTAATAAAAAT
1236135 ATTAATTAGTATATTTTA
62 ATTAATTAGTATATTTTA
1236153 AATATTTGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
88 9 0.13
89 17 0.24
90 19 0.27
91 15 0.21
92 10 0.14
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (87 bp):
AAAATATTAAAATAATTTAATTATTATTAAATAATATTGTTATAATTATATTAATAAAAATATTA
ATTAGTATATTTTAGTGAAATA
Found at i:1236171 original size:23 final size:23
Alignment explanation
Indices: 1236122--1236172 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1236112 TTGTTATATT
**
1236122 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
*
1236145 ATATTTTAAATAT-TTGAATTAAA
1 ATATTTTAAAAATATT-AATTAAA
1236168 ATATT
1 ATATT
1236173 ATTAGATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:1236209 original size:17 final size:17
Alignment explanation
Indices: 1236183--1236343 Score: 50
Period size: 17 Copynumber: 10.3 Consensus size: 17
1236173 ATTAGATTAT
*
1236183 TATATTAATATTATATA
1 TATATAAATATTATATA
1236200 TATATAAATA--ATAT-
1 TATATAAATATTATATA
* * *
1236214 TAT-TCATTATTAAATA
1 TATATAAATATTATATA
*
1236230 TATA-AAAAATTAT-TA
1 TATATAAATATTATATA
* *
1236245 TATATTAAA-ATAAAATA
1 TATA-TAAATATTATATA
**
1236262 TATATGTTATATTATA-A
1 TATAT-AAATATTATATA
* *
1236279 TATAATGATTATT-T-TA
1 TAT-ATAAATATTATATA
1236295 T-TAT-AATATTA-A-A
1 TATATAAATATTATATA
* *
1236308 AATAT-AATATTATTTA
1 TATATAAATATTATATA
1236324 T-TATAAATATT-TATA
1 TATATAAATATTATATA
*
1236339 AATAT
1 TATAT
1236344 TTTAATAATT
Statistics
Matches: 103, Mismatches: 23, Indels: 37
0.63 0.14 0.23
Matches are distributed among these distances:
13 10 0.10
14 15 0.15
15 20 0.19
16 25 0.24
17 27 0.26
18 6 0.06
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (17 bp):
TATATAAATATTATATA
Found at i:1236214 original size:26 final size:26
Alignment explanation
Indices: 1236184--1236332 Score: 74
Period size: 24 Copynumber: 6.0 Consensus size: 26
1236174 TTAGATTATT
1236184 ATATTAATATTATATATATATAAATA
1 ATATTAATATTATATATATATAAATA
* * *
1236210 ATATTATTCATTATTAAATATATAAAAA
1 ATATTAAT-ATTA-TATATATATAAATA
1236238 ATTATTATATATTA-A-A-ATA-AAAT-
1 A-TATTA-ATATTATATATATATAAATA
* *
1236261 ATA-T-ATGTTATAT-TATA-ATATA
1 ATATTAATATTATATATATATAAATA
*
1236283 ATGATT-ATTTTAT-TATAATATTAAA-A
1 AT-ATTAATATTATATAT-ATA-TAAATA
*
1236309 ATA-TAATATTATTTAT-TATAAATA
1 ATATTAATATTATATATATATAAATA
1236333 TTTATAAATA
Statistics
Matches: 96, Mismatches: 10, Indels: 36
0.68 0.07 0.25
Matches are distributed among these distances:
19 5 0.05
20 1 0.01
21 7 0.07
22 4 0.04
23 7 0.07
24 15 0.16
25 13 0.14
26 14 0.15
27 7 0.07
28 13 0.14
29 9 0.09
30 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (26 bp):
ATATTAATATTATATATATATAAATA
Found at i:1236227 original size:20 final size:19
Alignment explanation
Indices: 1236167--1236229 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 19
1236157 TTTGAATTAA
*
1236167 AATATTATTAGATTATTATATT
1 AATATTATT--ATTATTA-AAT
1236189 AATATTA-TATATATATAAAT
1 AATATTATTAT-TAT-TAAAT
1236209 AATATTATTCATTATTAAAT
1 AATATTATT-ATTATTAAAT
1236229 A
1 A
1236230 TATAAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
19 2 0.06
20 18 0.50
21 7 0.19
22 9 0.25
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
AATATTATTATTATTAAAT
Found at i:1236241 original size:19 final size:18
Alignment explanation
Indices: 1236219--1236254 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1236209 AATATTATTC
1236219 ATTATTAAATATATAAAAA
1 ATTATTAAATAT-TAAAAA
*
1236238 ATTATTATATATTAAAA
1 ATTATTAAATATTAAAA
1236255 TAAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTATTAAATATTAAAAA
Found at i:1236280 original size:19 final size:19
Alignment explanation
Indices: 1236258--1236295 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1236248 ATTAAAATAA
1236258 AATATATATG-TTATATTAT
1 AATATA-ATGATTATATTAT
*
1236277 AATATAATGATTATTTTAT
1 AATATAATGATTATATTAT
1236296 TATAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
AATATAATGATTATATTAT
Found at i:1236313 original size:31 final size:31
Alignment explanation
Indices: 1236277--1236343 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1236267 GTTATATTAT
1236277 AATATAATGATTATTTTATTAT-AATA-TTAAA
1 AATATAAT-ATTA-TTTATTATAAATATTTAAA
*
1236308 AATATAATATTATTTATTATAAATATTTATA
1 AATATAATATTATTTATTATAAATATTTAAA
1236339 AATAT
1 AATAT
1236344 TTTAATAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 8 0.24
30 8 0.24
31 17 0.52
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
AATATAATATTATTTATTATAAATATTTAAA
Found at i:1236612 original size:42 final size:42
Alignment explanation
Indices: 1236556--1236650 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
1236546 TTCCTCTAAC
* * * *
1236556 CAAACACTGGAAAACATTTTTCGGAAAACGAATTACGTGAAA
1 CAAACACGGGAAAACATTTTCCGAAAAACGAATTACATGAAA
1236598 CAAACACGGGAAAACATTTTCCGAAAAACGAATTACATGAAA
1 CAAACACGGGAAAACATTTTCCGAAAAACGAATTACATGAAA
1236640 CAAACACGGGA
1 CAAACACGGGA
1236651 TTTCGGGGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.47, C:0.19, G:0.17, T:0.17
Consensus pattern (42 bp):
CAAACACGGGAAAACATTTTCCGAAAAACGAATTACATGAAA
Found at i:1237140 original size:20 final size:19
Alignment explanation
Indices: 1237094--1237141 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
1237084 AGTGTGACTA
* *
1237094 TATATTAAATATCAAATCT
1 TATATTAAAAATCAAATAT
*
1237113 TATGATTAAGAAATGAAATAT
1 TAT-ATTAA-AAATCAAATAT
1237134 TATATTAA
1 TATATTAA
1237142 TATTATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 11 0.46
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (19 bp):
TATATTAAAAATCAAATAT
Found at i:1238535 original size:30 final size:31
Alignment explanation
Indices: 1238476--1238541 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
1238466 GTTAATTTCT
* ** *
1238476 AATTTAATTCTTAAATTTTCAATAAAATATC
1 AATTTAATTCTTAAATGTGAAATAAAATATA
*
1238507 AATTTAA-TCTTAAATGTGAAATATAATATA
1 AATTTAATTCTTAAATGTGAAATAAAATATA
1238537 AATTT
1 AATTT
1238542 GATCCCATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (31 bp):
AATTTAATTCTTAAATGTGAAATAAAATATA
Found at i:1238887 original size:21 final size:21
Alignment explanation
Indices: 1238863--1238902 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1238853 GCAATACAGG
1238863 TTCCAAATTCGCAACGCGATT
1 TTCCAAATTCGCAACGCGATT
1238884 TTCCAAATTCGCAACGCGA
1 TTCCAAATTCGCAACGCGA
1238903 ATATTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (21 bp):
TTCCAAATTCGCAACGCGATT
Found at i:1239051 original size:22 final size:22
Alignment explanation
Indices: 1239026--1239076 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1239016 TCACTCTCTA
* *
1239026 CGGCGACATCCGTCCCCATCTC
1 CGGCGACATCCGTCCACATATC
*
1239048 CGGCGAAATCCGTCCACATATC
1 CGGCGACATCCGTCCACATATC
1239070 CGGCGAC
1 CGGCGAC
1239077 CCCCTCTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.43, G:0.22, T:0.16
Consensus pattern (22 bp):
CGGCGACATCCGTCCACATATC
Found at i:1239478 original size:23 final size:20
Alignment explanation
Indices: 1239417--1239484 Score: 91
Period size: 20 Copynumber: 3.2 Consensus size: 20
1239407 TTTGAAACTT
*
1239417 AAATTCGCAACACGAAAATG
1 AAATTCGCAACGCGAAAATG
*
1239437 AAAATCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATG
1239457 AAATTCGCAACGTTGCGAAAATG
1 AAATTCGCAAC---GCGAAAATG
1239480 AAATT
1 AAATT
1239485 TGCGTTGCGA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.67
23 14 0.33
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATG
Found at i:1239492 original size:20 final size:21
Alignment explanation
Indices: 1239448--1239494 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
1239438 AAATCGCAAC
1239448 GCGAAAATGAAATTCGCAACGTT
1 GCGAAAATGAAATTCG--ACGTT
*
1239471 GCGAAAATGAAATTTG-CGTT
1 GCGAAAATGAAATTCGACGTT
1239491 GCGA
1 GCGA
1239495 TTTTCATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
23 15 0.65
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (21 bp):
GCGAAAATGAAATTCGACGTT
Found at i:1241148 original size:21 final size:21
Alignment explanation
Indices: 1241124--1241173 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1241114 GTTAGGGGAG
* *
1241124 TTACGTGATGAGGTTAATACT
1 TTACGTGAGGAGGTCAATACT
*
1241145 TTACGTGAGGAGGTCAGTACT
1 TTACGTGAGGAGGTCAATACT
1241166 TTACGTGA
1 TTACGTGA
1241174 CGACAATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Found at i:1241296 original size:21 final size:21
Alignment explanation
Indices: 1241251--1241297 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1241241 AATGGTGCTT
* * * *
1241251 TACGTGGTGAGGTATCTACTT
1 TACGTGATGAGGTAGCCACTC
1241272 TACGTGATGAGGTAGCCACTC
1 TACGTGATGAGGTAGCCACTC
1241293 TACGT
1 TACGT
1241298 AAGATTATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (21 bp):
TACGTGATGAGGTAGCCACTC
Found at i:1241627 original size:18 final size:19
Alignment explanation
Indices: 1241584--1241641 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 19
1241574 TTCACCTGTC
*
1241584 ATCATTCAAGAGGTCTCTACT
1 ATCATTCAAGAGG-CCCTA-T
1241605 ATCATTCAAGAGGCCCTTAT
1 ATCATTCAAGAGGCCC-TAT
*
1241625 CATCCTTCAAGAGGCCC
1 -ATCATTCAAGAGGCCC
1241642 CTCCCACCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.09
21 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (19 bp):
ATCATTCAAGAGGCCCTAT
Found at i:1241653 original size:42 final size:42
Alignment explanation
Indices: 1241607--1241700 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
1241597 TCTCTACTAT
*
1241607 CATTCAAGAGGCCCTTATCATCCTTCAAGAGGCCCCTCCCAC
1 CATTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCAC
* * * * * *
1241649 CATTCAAAATGCCCCTGTCATCGTTTAAGAGGTCCCTCCCAC
1 CATTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCAC
**
1241691 TGTTCAAGAG
1 CATTCAAGAG
1241701 CCCGATTCAC
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.24
Consensus pattern (42 bp):
CATTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCAC
Found at i:1241654 original size:21 final size:21
Alignment explanation
Indices: 1241607--1241700 Score: 55
Period size: 21 Copynumber: 4.5 Consensus size: 21
1241597 TCTCTACTAT
* **
1241607 CATTCAAGAGGCCCTTATCATC
1 CATTCAAGAGGCCCCTCCCA-C
1241629 C-TTCAAGAGGCCCCTCCCAC
1 CATTCAAGAGGCCCCTCCCAC
* * ** *
1241649 CATTCAAAATGCCCCTGTCAT
1 CATTCAAGAGGCCCCTCCCAC
* * *
1241670 CGTTTAAGAGGTCCCTCCCAC
1 CATTCAAGAGGCCCCTCCCAC
**
1241691 TGTTCAAGAG
1 CATTCAAGAG
1241701 CCCGATTCAC
Statistics
Matches: 53, Mismatches: 18, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
20 2 0.04
21 50 0.94
22 1 0.02
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.24
Consensus pattern (21 bp):
CATTCAAGAGGCCCCTCCCAC
Found at i:1243643 original size:15 final size:15
Alignment explanation
Indices: 1243619--1243652 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1243609 CTGTTGAACC
*
1243619 GACCCGTTGACCGTT
1 GACCCATTGACCGTT
1243634 GACCCATTGACCGTT
1 GACCCATTGACCGTT
1243649 GACC
1 GACC
1243653 GGCGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (15 bp):
GACCCATTGACCGTT
Found at i:1245996 original size:24 final size:24
Alignment explanation
Indices: 1245969--1246044 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 24
1245959 TGATGATATC
1245969 TGACATGGATTCTGATCTGATACT
1 TGACATGGATTCTGATCTGATACT
* *
1245993 TGACTTGGATTCTGATCTGTTACT
1 TGACATGGATTCTGATCTGATACT
* *
1246017 TGACCT-GATTTCTGATATGATACT
1 TGACATGGA-TTCTGATCTGATACT
1246041 TGAC
1 TGAC
1246045 CTGATTTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 2 0.04
24 44 0.96
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TGACATGGATTCTGATCTGATACT
Found at i:1246045 original size:24 final size:24
Alignment explanation
Indices: 1245978--1246051 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
1245968 CTGACATGGA
*
1245978 TTCTGATCTGATACTTGACTTGGA-
1 TTCTGATCTGATACTTGACCT-GAT
*
1246002 TTCTGATCTGTTACTTGACCTGAT
1 TTCTGATCTGATACTTGACCTGAT
*
1246026 TTCTGATATGATACTTGACCTGAT
1 TTCTGATCTGATACTTGACCTGAT
1246050 TT
1 TT
1246052 ATGCTTTGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 2 0.04
24 43 0.96
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.45
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACCTGAT
Found at i:1249623 original size:21 final size:21
Alignment explanation
Indices: 1249597--1249641 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1249587 GATTTCTGGG
*
1249597 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
*
1249618 CAAGGGGAATCGATACCCCTT
1 CAAGGGGAATCGATACCCATT
1249639 CAA
1 CAA
1249642 ACGAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:1250462 original size:31 final size:31
Alignment explanation
Indices: 1250424--1250565 Score: 257
Period size: 31 Copynumber: 4.6 Consensus size: 31
1250414 AGGGTCGAGG
1250424 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1250455 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1250486 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1250517 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1250548 GATTACCTAGGTTCTTCG
1 GTTTACCTATGTTCTTCG
1250566 AAATCTATGG
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 107 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1251085 original size:21 final size:21
Alignment explanation
Indices: 1251060--1251102 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1251050 AAAGAATATA
1251060 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
1251081 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
1251102 T
1 T
1251103 AAATATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:1252987 original size:24 final size:24
Alignment explanation
Indices: 1252973--1253084 Score: 138
Period size: 24 Copynumber: 4.7 Consensus size: 24
1252963 ATTTGAATTA
1252973 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
*
1252997 TGATCTCATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
*
1253021 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* * *
1253045 TGATCTGTTACTTGACCT-GATTTA
1 TGATCTGATACTTGACATGGA-TTC
*
1253069 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
1253085 CTGATTTATG
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
23 3 0.04
24 73 0.95
25 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:1253085 original size:24 final size:24
Alignment explanation
Indices: 1252970--1253094 Score: 105
Period size: 24 Copynumber: 5.2 Consensus size: 24
1252960 TTGATTTGAA
*
1252970 TTATGATCTGATACTTGACATGGA-
1 TTATGATCTGATACTTGACCT-GAT
* * *
1252994 TTCTGATCTCATA-TCTGACATGGA-
1 TTATGATCTGATACT-TGACCT-GAT
* *
1253018 TTCTGATCTGATACTTGACTTGGA-
1 TTATGATCTGATACTTGACCT-GAT
* *
1253042 TTCTGATCTGTTACTTGACCTGAT
1 TTATGATCTGATACTTGACCTGAT
*
1253066 TTATGATATGATACTTGACCTGAT
1 TTATGATCTGATACTTGACCTGAT
1253090 TTATG
1 TTATG
1253095 TTTTGATTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
23 3 0.03
24 85 0.96
25 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (24 bp):
TTATGATCTGATACTTGACCTGAT
Found at i:1254148 original size:27 final size:26
Alignment explanation
Indices: 1254110--1254167 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 26
1254100 TATTTTTTGC
1254110 TTGTTTAATTGATTTGTAAAAGTTGAT
1 TTGTTTAATTGATTTGTAAAA-TTGAT
**
1254137 TTGTTTAATTGATTTGTTTAATTGAT
1 TTGTTTAATTGATTTGTAAAATTGAT
1254163 TTGTT
1 TTGTT
1254168 GTTTAATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 10 0.34
27 19 0.66
ACGTcount: A:0.24, C:0.00, G:0.17, T:0.59
Consensus pattern (26 bp):
TTGTTTAATTGATTTGTAAAATTGAT
Found at i:1254150 original size:13 final size:13
Alignment explanation
Indices: 1254046--1254167 Score: 92
Period size: 13 Copynumber: 9.4 Consensus size: 13
1254036 TTTTTTTTGC
1254046 TTGTTTAATTGAT
1 TTGTTTAATTGAT
**
1254059 TTGTAAAAGTTGAT
1 TTGTTTAA-TTGAT
1254073 TTGTTTAATTGAT
1 TTGTTTAATTGAT
* * *
1254086 GTGTAAATAATT-CT
1 TTGT--TTAATTGAT
*
1254100 TAT-TTT--TTG-C
1 T-TGTTTAATTGAT
1254110 TTGTTTAATTGAT
1 TTGTTTAATTGAT
**
1254123 TTGTAAAAGTTGAT
1 TTGTTTAA-TTGAT
1254137 TTGTTTAATTGAT
1 TTGTTTAATTGAT
1254150 TTGTTTAATTGAT
1 TTGTTTAATTGAT
1254163 TTGTT
1 TTGTT
1254168 GTTTAATTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 20
0.71 0.13 0.17
Matches are distributed among these distances:
9 1 0.01
10 6 0.07
12 4 0.05
13 43 0.51
14 24 0.29
15 6 0.07
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.57
Consensus pattern (13 bp):
TTGTTTAATTGAT
Found at i:1254409 original size:16 final size:16
Alignment explanation
Indices: 1254380--1254415 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1254370 TGTAAATAAG
* *
1254380 AATTGTTTTTTTGTTT
1 AATTGATTTGTTGTTT
1254396 AATTGATTTGTTGTTT
1 AATTGATTTGTTGTTT
1254412 AATT
1 AATT
1254416 TCACTCTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (16 bp):
AATTGATTTGTTGTTT
Found at i:1254487 original size:20 final size:20
Alignment explanation
Indices: 1254462--1254560 Score: 137
Period size: 20 Copynumber: 5.0 Consensus size: 20
1254452 AGGTACACTT
1254462 TCGCAACGC-AGAAGTCAAAA
1 TCGCAACGCGA-AAGTCAAAA
1254482 TCGCAACGCGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
* * * *
1254502 TCGCAGCACGAAAGTCTACA
1 TCGCAACGCGAAAGTCAAAA
*
1254522 TCGCAACGCGAAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAA
1254542 TCGCAACGCGAAAGTCAAA
1 TCGCAACGCGAAAGTCAAA
1254561 TTCGAGTTGC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 68 0.99
21 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.20, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAA
Found at i:1254603 original size:20 final size:20
Alignment explanation
Indices: 1254574--1254679 Score: 149
Period size: 20 Copynumber: 5.3 Consensus size: 20
1254564 GAGTTGCGAT
*
1254574 TTTCGCATTGTGATTTTGAC
1 TTTCGCATTGCGATTTTGAC
* *
1254594 TTTCGTATTGCGAATTTGAC
1 TTTCGCATTGCGATTTTGAC
* *
1254614 TTTCGCGTTGCGAATTTGAC
1 TTTCGCATTGCGATTTTGAC
* *
1254634 TTTCGCGTTGCGGTTTTGAC
1 TTTCGCATTGCGATTTTGAC
1254654 TTTCGCATTGCGATTTTGAC
1 TTTCGCATTGCGATTTTGAC
1254674 TTTCGC
1 TTTCGC
1254680 GATACGAAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (20 bp):
TTTCGCATTGCGATTTTGAC
Found at i:1255014 original size:18 final size:18
Alignment explanation
Indices: 1254991--1255026 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1254981 AAGACGGTTG
*
1254991 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1255009 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1255027 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1257322 original size:24 final size:24
Alignment explanation
Indices: 1257288--1257341 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1257278 CTGAAACATC
1257288 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
1257312 ATCAAAGTCCGAGTATTGGCCAAT
1 ATCAAAATCCGAGTATTGACCAAG
1257336 ATCAAA
1 ATCAAA
1257342 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1258433 original size:20 final size:20
Alignment explanation
Indices: 1258407--1258518 Score: 115
Period size: 20 Copynumber: 5.6 Consensus size: 20
1258397 TTGGAAAAGC
1258407 GCGTTGCGATTTACATATTA
1 GCGTTGCGATTTACATATTA
* *
1258427 TCGTTGCGATTTACCTATTCA
1 GCGTTGCGATTTACATATT-A
*
1258448 -CGTTGCGATTTTGAC-T-TTC
1 GCGTTGCGA-TTT-ACATATTA
1258467 GCGTTGCGATTTACATATTA
1 GCGTTGCGATTTACATATTA
* *
1258487 TCGTTGCGATTTA-ACTATTC
1 GCGTTGCGATTTACA-TATTA
1258507 GCGTTGCGATTT
1 GCGTTGCGATTT
1258519 TGGAACCTGT
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.03
19 5 0.06
20 64 0.82
21 5 0.06
22 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (20 bp):
GCGTTGCGATTTACATATTA
Found at i:1258455 original size:40 final size:40
Alignment explanation
Indices: 1258408--1258518 Score: 131
Period size: 40 Copynumber: 2.8 Consensus size: 40
1258398 TGGAAAAGCG
** *
1258408 CGTTGCGATTTACATATTATCGTTGCGATTTACCTATTCA-
1 CGTTGCGATTTACATATTCGCGTTGCGATTTACATATT-AT
1258448 CGTTGCGATTTTGAC-T-TTCGCGTTGCGATTTACATATTAT
1 CGTTGCGA-TTT-ACATATTCGCGTTGCGATTTACATATTAT
1258488 CGTTGCGATTTA-ACTATTCGCGTTGCGATTT
1 CGTTGCGATTTACA-TATTCGCGTTGCGATTT
1258519 TGGAACCTGT
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
38 1 0.02
39 5 0.08
40 50 0.81
41 4 0.06
42 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (40 bp):
CGTTGCGATTTACATATTCGCGTTGCGATTTACATATTAT
Found at i:1258484 original size:60 final size:60
Alignment explanation
Indices: 1258406--1258520 Score: 212
Period size: 60 Copynumber: 1.9 Consensus size: 60
1258396 TTTGGAAAAG
*
1258406 CGCGTTGCGATTTACATATTATCGTTGCGATTTACCTATTCACGTTGCGATTTTGACTTT
1 CGCGTTGCGATTTACATATTATCGTTGCGATTTAACTATTCACGTTGCGATTTTGACTTT
*
1258466 CGCGTTGCGATTTACATATTATCGTTGCGATTTAACTATTCGCGTTGCGATTTTG
1 CGCGTTGCGATTTACATATTATCGTTGCGATTTAACTATTCACGTTGCGATTTTG
1258521 GAACCTGTGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (60 bp):
CGCGTTGCGATTTACATATTATCGTTGCGATTTAACTATTCACGTTGCGATTTTGACTTT
Found at i:1258533 original size:60 final size:60
Alignment explanation
Indices: 1258382--1258535 Score: 197
Period size: 60 Copynumber: 2.5 Consensus size: 60
1258372 TGAAAAATAA
* * *
1258382 ATTCGCGCTGCGATTTTGGAAAAGC-GCGTTGCGATTTACATATTATCGTTGCGATTTACCT
1 ATTCGCGTTGCGATTTTGG--AACCTGCGTTGCGATTTACATATTATCGTTGCGATTTAACT
* *
1258443 ATTCACGTTGCGATTTT-G-ACTTTCGCGTTGCGATTTACATATTATCGTTGCGATTTAACT
1 ATTCGCGTTGCGATTTTGGAAC-CT-GCGTTGCGATTTACATATTATCGTTGCGATTTAACT
*
1258503 ATTCGCGTTGCGATTTTGGAACCTGTGTTGCGA
1 ATTCGCGTTGCGATTTTGGAACCTGCGTTGCGA
1258536 AATTGGACTT
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
57 1 0.01
60 60 0.75
61 17 0.21
62 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (60 bp):
ATTCGCGTTGCGATTTTGGAACCTGCGTTGCGATTTACATATTATCGTTGCGATTTAACT
Found at i:1269156 original size:6 final size:6
Alignment explanation
Indices: 1269145--1269170 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1269135 CTTCAACTCC
1269145 TCTCTT TCTCTT TCTCTT TCTCTT TC
1 TCTCTT TCTCTT TCTCTT TCTCTT TC
1269171 ACTTGCATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (6 bp):
TCTCTT
Found at i:1269567 original size:96 final size:96
Alignment explanation
Indices: 1269450--1269642 Score: 386
Period size: 96 Copynumber: 2.0 Consensus size: 96
1269440 CCTCCTAGAA
1269450 ATTTCGTGCATTGTTCATTTCGTTGAAGCCAACAAGAACATGAAAATGAGTTGCTTTAGTCGGGA
1 ATTTCGTGCATTGTTCATTTCGTTGAAGCCAACAAGAACATGAAAATGAGTTGCTTTAGTCGGGA
1269515 TTATGATATGGGGAAATCTTAACCAAATTGT
66 TTATGATATGGGGAAATCTTAACCAAATTGT
1269546 ATTTCGTGCATTGTTCATTTCGTTGAAGCCAACAAGAACATGAAAATGAGTTGCTTTAGTCGGGA
1 ATTTCGTGCATTGTTCATTTCGTTGAAGCCAACAAGAACATGAAAATGAGTTGCTTTAGTCGGGA
1269611 TTATGATATGGGGAAATCTTAACCAAATTGT
66 TTATGATATGGGGAAATCTTAACCAAATTGT
1269642 A
1 A
1269643 CTTTGTTGAA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (96 bp):
ATTTCGTGCATTGTTCATTTCGTTGAAGCCAACAAGAACATGAAAATGAGTTGCTTTAGTCGGGA
TTATGATATGGGGAAATCTTAACCAAATTGT
Found at i:1274134 original size:16 final size:16
Alignment explanation
Indices: 1274096--1274127 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1274086 TTTAAAGTTT
1274096 AAGAATGAATTTAAGA
1 AAGAATGAATTTAAGA
1274112 AAGAATGAATTTAAGA
1 AAGAATGAATTTAAGA
1274128 TGGAATGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (16 bp):
AAGAATGAATTTAAGA
Found at i:1292691 original size:84 final size:84
Alignment explanation
Indices: 1292550--1292709 Score: 250
Period size: 84 Copynumber: 1.9 Consensus size: 84
1292540 ATGTCATAGC
* * *
1292550 TATGTTAACTTATGTACTCATTTTACCTTAATTCATACATAATCATTCTATACTTAGCTCATTTG
1 TATGTTAACTTATGTACTCATTCTAACTCAATTCATACATAATCATTCTATACTTAGCTCATTTG
1292615 CATTCAAACATGGGCTGGT
66 CATTCAAACATGGGCTGGT
* * *
1292634 TATGTTAACTTATGTATTTATTCTAACTCAATTCATACATACA-CATTCTATATTTAGCTCATTT
1 TATGTTAACTTATGTACTCATTCTAACTCAATTCATACATA-ATCATTCTATACTTAGCTCATTT
1292698 GCATTCAAACAT
65 GCATTCAAACAT
1292710 AGGCGGCGAT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
84 68 0.99
85 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (84 bp):
TATGTTAACTTATGTACTCATTCTAACTCAATTCATACATAATCATTCTATACTTAGCTCATTTG
CATTCAAACATGGGCTGGT
Found at i:1293704 original size:21 final size:21
Alignment explanation
Indices: 1293678--1293721 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1293668 ATTGATCAGC
1293678 ATTTCCAACAAGACATTCATA
1 ATTTCCAACAAGACATTCATA
** *
1293699 ATTTCCAATGAGGCATTCATA
1 ATTTCCAACAAGACATTCATA
1293720 AT
1 AT
1293722 AAAAAGAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (21 bp):
ATTTCCAACAAGACATTCATA
Found at i:1295941 original size:22 final size:22
Alignment explanation
Indices: 1295915--1295960 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1295905 ACATTGGTAT
* * *
1295915 TTTTAGAATATAGAATGGTTAG
1 TTTTAAAACATAGAATGGATAG
*
1295937 TTTTAAAACATTGAATGGATAG
1 TTTTAAAACATAGAATGGATAG
1295959 TT
1 TT
1295961 AACCTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (22 bp):
TTTTAAAACATAGAATGGATAG
Found at i:1309862 original size:216 final size:216
Alignment explanation
Indices: 1309495--1309917 Score: 789
Period size: 216 Copynumber: 2.0 Consensus size: 216
1309485 ACCACTAAAC
1309495 CTCCTTTCCAATCACTAGAAGTAGCGCATCCACATTAAGTTTAATAAAACCCTTTGGAGGAGGGG
1 CTCCTTTCCAATCACTAGAAGTAGCGCATCCACATTAAGTTTAATAAAACCCTTTGGAGGAGGGG
1309560 ACCAAGGAAACTTAGTTGAAATTTGATTAGAATGGGACGAGCAAGAATCCATAGGGAAGGGTCAG
66 ACCAAGGAAACTTAGTTGAAATTTGATTAGAATGGGAC-AGCAAGAATCCATAGGGAAGGGTCAG
1309625 CAATAAGAGCATCCTGGAGATAGAAATATGAGTTTCCCTAGCTAGAAACCATGAAGCAAGCCTGC
130 CAATAAGAGCATCCTGGAGATAGAAATATGAGTTTCCCTAGCTAGAAACCATGAAGCAAGCCTGC
1309690 ACCTAGCTAAAAACCTAAACCA
195 ACCTAGCTAAAAACCTAAACCA
1309712 CTCCTCTT-CAATCACTAGAAGTAGCGCATCCACATTAAGTTTAATAAAACCC-TTGGAGGAGGG
1 CTCCT-TTCCAATCACTAGAAGTAGCGCATCCACATTAAGTTTAATAAAACCCTTTGGAGGAGGG
1309775 GACCAAGGAAACTTAGTTGAAATTTGATTAGAATGGGAC-GCAAGAATCCACTAGGGAAGGGTCA
65 GACCAAGGAAACTTAGTTGAAATTTGATTAGAATGGGACAGCAAGAATCCA-TAGGGAAGGGTCA
1309839 GCAATAAGAGCATCCTTGGAGATAGAAATATGAGTTTCCCTAGCTAGAAACCATGAAGCAAGCCT
129 GCAATAAGAGCATCC-TGGAGATAGAAATATGAGTTTCCCTAGCTAGAAACCATGAAGCAAGCCT
1309904 GCACCTAGCTAAAA
193 GCACCTAGCTAAAA
1309918 GAAAATTTCT
Statistics
Matches: 203, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
214 11 0.05
215 28 0.14
216 113 0.56
217 49 0.24
218 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (216 bp):
CTCCTTTCCAATCACTAGAAGTAGCGCATCCACATTAAGTTTAATAAAACCCTTTGGAGGAGGGG
ACCAAGGAAACTTAGTTGAAATTTGATTAGAATGGGACAGCAAGAATCCATAGGGAAGGGTCAGC
AATAAGAGCATCCTGGAGATAGAAATATGAGTTTCCCTAGCTAGAAACCATGAAGCAAGCCTGCA
CCTAGCTAAAAACCTAAACCA
Found at i:1316148 original size:24 final size:23
Alignment explanation
Indices: 1316121--1316168 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
1316111 CTGTGAGTAC
1316121 AAAT-AATTATATTTTTACAATATA
1 AAATAAATT-TATTTTTA-AATATA
1316145 AAATAGAATTTATTTTTAAATATA
1 AAATA-AATTTATTTTTAAATATA
1316169 TAATTTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 10 0.45
25 8 0.36
26 4 0.18
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATAAATTTATTTTTAAATATA
Found at i:1318515 original size:208 final size:208
Alignment explanation
Indices: 1318133--1318550 Score: 786
Period size: 208 Copynumber: 2.0 Consensus size: 208
1318123 TTACTCAAAC
1318133 AACTGGATGTTAGTCCTCTTATATTTGTTGAGCTCAAAGTGCTCAACCTAAAAAAATAAACATAA
1 AACTGGATGTTAGTCCTCTTATATTTGTTGAGCTCAAAGTGCTCAACCTAAAAAAATAAACATAA
1318198 AAAGATGCAATGTGAAACTTCACATACAACACCCGAGAAAAACCTTGTTAACATCAATACCCTTC
66 AAAGATGCAATGTGAAACTTCACA-ACAACACCCGAG-AAAACCTTGTTAACATCAATACCCTTC
1318263 AAATTGAAGTAGCAGCAAGTTTGACAGCTCAAAAACATACACAGTTCCAAGGCCAAGTATAAATT
129 AAATTGAAGTAGCAGCAAGTTTGACAGCTCAAAAACATACACAGTTCCAAGGCCAAGTATAAATT
1318328 CAGTTCAACTGTGGA
194 CAGTTCAACTGTGGA
1318343 AACTGGATGTTAGTCCTCTTATATTTGTTGAGCTCAAAGTGCTCAACCTAAAAAAAATAAACATA
1 AACTGGATGTTAGTCCTCTTATATTTGTTGAGCTCAAAGTGCTCAACCT-AAAAAAATAAACATA
1318408 AAAAGATGCAATGTGAGAACTTCAC-ACAACACCCGAG-AAACCTTGTTAACATCAATACCCTTC
65 AAAAGATGCAATGTGA-AACTTCACAACAACACCCGAGAAAACCTTGTTAACATCAATACCCTTC
1318471 AAATTGAAGTAGCAGCAAGTTTGACAGCTCAAAAACATACACAGTTCCAAGGCCAAGTATAAATT
129 AAATTGAAGTAGCAGCAAGTTTGACAGCTCAAAAACATACACAGTTCCAAGGCCAAGTATAAATT
1318536 CAGTTCAACTGTGGA
194 CAGTTCAACTGTGGA
1318551 TAACGATAGA
Statistics
Matches: 206, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
208 106 0.51
210 61 0.30
211 31 0.15
212 8 0.04
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (208 bp):
AACTGGATGTTAGTCCTCTTATATTTGTTGAGCTCAAAGTGCTCAACCTAAAAAAATAAACATAA
AAAGATGCAATGTGAAACTTCACAACAACACCCGAGAAAACCTTGTTAACATCAATACCCTTCAA
ATTGAAGTAGCAGCAAGTTTGACAGCTCAAAAACATACACAGTTCCAAGGCCAAGTATAAATTCA
GTTCAACTGTGGA
Found at i:1324787 original size:14 final size:14
Alignment explanation
Indices: 1324768--1324796 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1324758 ATCTAAGATC
1324768 TAATCTCCTTTAAA
1 TAATCTCCTTTAAA
1324782 TAATCTCCTTTAAA
1 TAATCTCCTTTAAA
1324796 T
1 T
1324797 CAAATATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATCTCCTTTAAA
Found at i:1325186 original size:22 final size:22
Alignment explanation
Indices: 1325140--1325186 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1325130 TAAATACTTT
* *
1325140 TTATTTGTAATTTGTTTGTTTA
1 TTATTTGTAATATGTTTGTTAA
1325162 TTATTTGATAATATGTTT-TTAA
1 TTATTTG-TAATATGTTTGTTAA
1325184 TTA
1 TTA
1325187 CTTTACTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.64
Consensus pattern (22 bp):
TTATTTGTAATATGTTTGTTAA
Found at i:1326461 original size:14 final size:14
Alignment explanation
Indices: 1326442--1326470 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1326432 TATATTATTC
1326442 TTTATCATTAACAT
1 TTTATCATTAACAT
1326456 TTTATCATTAACAT
1 TTTATCATTAACAT
1326470 T
1 T
1326471 GAAAACACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTATCATTAACAT
Found at i:1332568 original size:24 final size:24
Alignment explanation
Indices: 1332540--1332643 Score: 95
Period size: 24 Copynumber: 4.3 Consensus size: 24
1332530 GAATATTTTA
*
1332540 TCTGATTTCCGACTTGAATTCTGT
1 TCTGATTTCTGACTTGAATTCTGT
* * *
1332564 TCTGA-TACATGACCTGAACTCTGT
1 TCTGATTTC-TGACTTGAATTCTGT
*
1332588 TCTGATTTCTGATCTAG-ATTCTGT
1 TCTGATTTCTGA-CTTGAATTCTGT
* * *
1332612 TCTGATATATGATTTGAATTCTGT
1 TCTGATTTCTGACTTGAATTCTGT
*
1332636 TTTGATTT
1 TCTGATTT
1332644 ATGATATCTC
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
23 4 0.06
24 54 0.87
25 4 0.06
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.47
Consensus pattern (24 bp):
TCTGATTTCTGACTTGAATTCTGT
Found at i:1332593 original size:48 final size:48
Alignment explanation
Indices: 1332540--1332643 Score: 129
Period size: 48 Copynumber: 2.2 Consensus size: 48
1332530 GAATATTTTA
*
1332540 TCTGATTTCCGA-CTTGAATTCTGTTCTGATACATGACCTGAACTCTGT
1 TCTGATTTCCGATCTAG-ATTCTGTTCTGATACATGACCTGAACTCTGT
* * ** *
1332588 TCTGATTTCTGATCTAGATTCTGTTCTGATATATGATTTGAATTCTGT
1 TCTGATTTCCGATCTAGATTCTGTTCTGATACATGACCTGAACTCTGT
*
1332636 TTTGATTT
1 TCTGATTT
1332644 ATGATATCTC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 45 0.94
49 3 0.06
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.47
Consensus pattern (48 bp):
TCTGATTTCCGATCTAGATTCTGTTCTGATACATGACCTGAACTCTGT
Found at i:1332646 original size:24 final size:24
Alignment explanation
Indices: 1332554--1332648 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
1332544 ATTTCCGACT
* *
1332554 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTCTGATATATGATC
* * *
1332578 TGAACTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATATGATC
*
1332602 T-AGATTCTGTTCTGATATATGATT
1 TGA-ATTCTGTTCTGATATATGATC
* *
1332626 TGAATTCTGTTTTGATTTATGAT
1 TGAATTCTGTTCTGATATATGAT
1332649 ATCTCCGTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
23 1 0.02
24 56 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATATGATC
Done.