Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009289.1 Hibiscus syriacus cultivar Beakdansim tig00112988_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: 1661737
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1304271 original size:12 final size:12
Alignment explanation
Indices: 1304249--1304293 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1304239 GAATAAAAGG
1304249 AAAATATAATAGT
1 AAAA-ATAATAGT
*
1304262 AAAAATAATAAT
1 AAAAATAATAGT
*
1304274 AAATATAATAGT
1 AAAAATAATAGT
*
1304286 AATAATAA
1 AAAAATAA
1304294 AAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:1304314 original size:2 final size:2
Alignment explanation
Indices: 1304307--1304356 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1304297 TGCAAAGAAA
1304307 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
1304349 AT AT AT AT
1 AT AT AT AT
1304357 GTGTGGGTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1304935 original size:37 final size:37
Alignment explanation
Indices: 1304889--1304985 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
1304879 GGATCCTATC
* *
1304889 TTTAAGAGTTTAAATCATAGTAGAACTCTATCATATT
1 TTTAAGAGTTTGAATCCTAGTAGAACTCTATCATATT
* * * *
1304926 TTTATGAGTTTGAATCCTAGCAAAATTCTATCATATT
1 TTTAAGAGTTTGAATCCTAGTAGAACTCTATCATATT
*
1304963 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAAGAGTTTGAATCCTAGTAG
1304986 GACAAAAAGG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (37 bp):
TTTAAGAGTTTGAATCCTAGTAGAACTCTATCATATT
Found at i:1305241 original size:22 final size:22
Alignment explanation
Indices: 1305215--1305265 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1305205 CAGCACGTGG
1305215 CTTCTCGTTGCACTTCGGTCTT
1 CTTCTCGTTGCACTTCGGTCTT
*
1305237 CTTCTCGTTGCCCTTCGGTCTT
1 CTTCTCGTTGCACTTCGGTCTT
1305259 CTTCTCG
1 CTTCTCG
1305266 GTTTAAAGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.02, C:0.35, G:0.18, T:0.45
Consensus pattern (22 bp):
CTTCTCGTTGCACTTCGGTCTT
Found at i:1306026 original size:106 final size:106
Alignment explanation
Indices: 1305735--1307215 Score: 2181
Period size: 106 Copynumber: 14.0 Consensus size: 106
1305725 GCATTGTTCT
* * * ** *
1305735 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
1305800 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * * *
1305841 TAGTTCAATATCATTCGCTGTGAAGTTGAAATTGACTTTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * *
1305900 TCAGTC-GCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGCCTTG
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
** * * * *
1305942 G-GTTTAAGATCCTTCGTTGAGAATTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1306006 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1306047 GAGTCCAATAT-CTTATGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 GAGTCCAATATCCTT-CGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1306111 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* **
1306153 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTAAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1306218 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1306259 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1306324 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1306365 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1306430 CCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
1306471 GAGTCCAATATCCTTTATTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1306536 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1306577 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1306642 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1306683 GAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1306748 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1306789 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGGCAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1306854 CCAACGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
1306895 GAGTCCAATATCCTTTATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1306960 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1307001 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1307066 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1307107 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
1307171 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1307212 GAGT
1 GAGT
1307216 GGCACGATAT
Statistics
Matches: 1246, Mismatches: 117, Indels: 25
0.90 0.08 0.02
Matches are distributed among these distances:
100 73 0.06
101 5 0.00
102 4 0.00
104 3 0.00
105 59 0.05
106 1099 0.88
107 3 0.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1308068 original size:22 final size:22
Alignment explanation
Indices: 1308042--1308118 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
1308032 TTATGTTTGG
1308042 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1308064 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1308086 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1308108 TCAACGGTTTG
1 TCAAAGGTTTG
1308119 ATGGGGTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1308748 original size:22 final size:21
Alignment explanation
Indices: 1308723--1308805 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 21
1308713 TTTTTTGTCC
*
1308723 CTTTTTCTTTTGATTTTTGCTT
1 CTTTTTTTTTTG-TTTTTGCTT
* *
1308745 CTTTTCTTTTTTGTTCTTGATT
1 CTTTT-TTTTTTGTTTTTGCTT
1308767 CTCTTTTTTATTTGTTTTTTGCTT
1 CT-TTTTTT-TTTG-TTTTTGCTT
*
1308791 CTTTGCTTTTTTGTT
1 CTTT-TTTTTTTGTT
1308806 CTTGATTGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
22 19 0.38
23 19 0.38
24 12 0.24
ACGTcount: A:0.04, C:0.13, G:0.10, T:0.73
Consensus pattern (21 bp):
CTTTTTTTTTTGTTTTTGCTT
Found at i:1308761 original size:15 final size:15
Alignment explanation
Indices: 1308736--1308808 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 15
1308726 TTTCTTTTGA
1308736 TTTTTGCTTCTTTTCT
1 TTTTTG-TTCTTTTCT
1308752 TTTTTGTTCTTGATTCT
1 TTTTTGTTCTT--TTCT
* * *
1308769 CTTTT-TT-ATTTGT
1 TTTTTGTTCTTTTCT
*
1308782 TTTTTGCTTCTTTGCT
1 TTTTTG-TTCTTTTCT
1308798 TTTTTGTTCTT
1 TTTTTGTTCTT
1308809 GATTGGATCT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
13 7 0.16
15 13 0.29
16 17 0.38
17 8 0.18
ACGTcount: A:0.03, C:0.14, G:0.10, T:0.74
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Found at i:1308786 original size:46 final size:46
Alignment explanation
Indices: 1308723--1308812 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
1308713 TTTTTTGTCC
*
1308723 CTTTTTCTTTTGATTTTTGCTTCTTTTCTTTTTTGTTCTTGATTCT
1 CTTTTTCTTTTGATTTTTGCTTCTTTGCTTTTTTGTTCTTGATTCT
*
1308769 CTTTTT-TATTTGTTTTTTGCTTCTTTGCTTTTTTGTTCTTGATT
1 CTTTTTCT-TTTGATTTTTGCTTCTTTGCTTTTTTGTTCTTGATT
1308813 GGATCTTTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 1 0.02
46 40 0.98
ACGTcount: A:0.04, C:0.13, G:0.10, T:0.72
Consensus pattern (46 bp):
CTTTTTCTTTTGATTTTTGCTTCTTTGCTTTTTTGTTCTTGATTCT
Found at i:1308804 original size:23 final size:22
Alignment explanation
Indices: 1308730--1308805 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 22
1308720 TCCCTTTTTC
*
1308730 TTTTGATTTTTGCTTCTTTTCTT
1 TTTTGTTTTTTGCTTC-TTTCTT
* * *
1308753 TTTTG-TTCTTGATTCTCTTTTT
1 TTTTGTTTTTTGCTTCT-TTCTT
1308775 TATTTGTTTTTTGCTTCTTTGCTT
1 T-TTTGTTTTTTGCTTCTTT-CTT
1308799 TTTTGTT
1 TTTTGTT
1308806 CTTGATTGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
21 1 0.02
22 13 0.30
23 17 0.40
24 12 0.28
ACGTcount: A:0.04, C:0.12, G:0.11, T:0.74
Consensus pattern (22 bp):
TTTTGTTTTTTGCTTCTTTCTT
Found at i:1311824 original size:8 final size:8
Alignment explanation
Indices: 1311811--1311880 Score: 70
Period size: 9 Copynumber: 8.4 Consensus size: 8
1311801 AAATAGTAAG
1311811 TAAAAAAA
1 TAAAAAAA
1311819 T-AAAAAA
1 TAAAAAAA
* * *
1311826 TATATATA
1 TAAAAAAA
1311834 TATAAAAAA
1 TA-AAAAAA
1311843 TAAAAAAA
1 TAAAAAAA
1311851 TAAAATAAA
1 TAAAA-AAA
1311860 TAAAACAAA
1 TAAAA-AAA
1311869 TAAACAAAA
1 TAAA-AAAA
1311878 TAA
1 TAA
1311881 TAATAACAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
7 7 0.14
8 17 0.33
9 26 0.51
10 1 0.02
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (8 bp):
TAAAAAAA
Found at i:1311857 original size:13 final size:14
Alignment explanation
Indices: 1311839--1311890 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 14
1311829 ATATATATAA
1311839 AAAATAAA-AAAAT
1 AAAATAAACAAAAT
*
1311852 AAAATAAATAAAA-
1 AAAATAAACAAAAT
*
1311865 CAAATAAACAAAAT
1 AAAATAAACAAAAT
1311879 AATAAT-AACAAA
1 AA-AATAAACAAA
1311891 GTACGAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 19 0.58
14 11 0.33
15 3 0.09
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAATAAACAAAAT
Found at i:1311948 original size:23 final size:23
Alignment explanation
Indices: 1311816--1311953 Score: 75
Period size: 23 Copynumber: 5.7 Consensus size: 23
1311806 GTAAGTAAAA
* *
1311816 AAATAAAAAATATATATATATAAA
1 AAATAAAAAAT-TAAATATATAAT
*
1311840 AAATAAAAAAATAAA-ATA-AAT
1 AAATAAAAAATTAAATATATAAT
* ** *
1311861 AAAACAAATAAACAAAATAATAATAAC
1 -AAATAAA-AAATTAAAT-AT-ATAAT
* *
1311888 AAAGTACGAATAATATATATATATAAT
1 AAA-TA--AAAAAT-TAAATATATAAT
1311915 AAATAAAAAATTAAATATAT-AT
1 AAATAAAAAATTAAATATATAAT
*
1311937 AAATTAATAAATTAAAT
1 AAA-TAAAAAATTAAAT
1311954 GACGAAAAGA
Statistics
Matches: 87, Mismatches: 16, Indels: 23
0.69 0.13 0.18
Matches are distributed among these distances:
21 2 0.02
22 14 0.16
23 29 0.33
24 15 0.17
25 2 0.02
26 6 0.07
27 10 0.11
28 4 0.05
29 5 0.06
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (23 bp):
AAATAAAAAATTAAATATATAAT
Found at i:1312449 original size:12 final size:11
Alignment explanation
Indices: 1312421--1312461 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
1312411 TAACAAAATA
* *
1312421 AATAATATAAA
1 AATAATACAAG
1312432 AATAATACAAG
1 AATAATACAAG
1312443 TAATAATACAAG
1 -AATAATACAAG
1312455 AATAATA
1 AATAATA
1312462 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:1312489 original size:3 final size:3
Alignment explanation
Indices: 1312483--1312588 Score: 68
Period size: 3 Copynumber: 37.0 Consensus size: 3
1312473 AAAGTAAAAA
*
1312483 AAT AAT AAT AAT AA- AAT -AT AAA AAT -AT ATAT AAT -AT AAAT AAGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT -AAT AA-T
* * * *
1312527 -AG AAT AA- AAGG AA- AAT -AT AAT AGT AAA AAT AAT AAT -AT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1312568 AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
1312589 GCAAAGAAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
2 16 0.20
3 58 0.71
4 8 0.10
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1319165 original size:21 final size:21
Alignment explanation
Indices: 1319139--1319178 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1319129 CCTCCTTTGA
*
1319139 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1319160 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1319179 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1322731 original size:37 final size:37
Alignment explanation
Indices: 1322690--1322794 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
1322680 GTGCTTGTGG
* * *
1322690 ATCCTATATTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
1322727 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
1322764 ATCCTATTTTTAAGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1322795 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:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:1327892 original size:21 final size:20
Alignment explanation
Indices: 1327867--1327928 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
1327857 CGCAAATTCG
*
1327867 TGTTGCATTTCGCGTTGCGA
1 TGTTGAATTTCGCGTTGCGA
**
1327887 TAGTTGAAAATCGCGTTGCGA
1 T-GTTGAATTTCGCGTTGCGA
* **
1327908 TTTTTTATTTCGCGTTGCGA
1 TGTTGAATTTCGCGTTGCGA
1327928 T
1 T
1327929 TTTCCAAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (20 bp):
TGTTGAATTTCGCGTTGCGA
Found at i:1328056 original size:11 final size:11
Alignment explanation
Indices: 1328026--1328060 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1328016 GACACGTATT
1328026 ACCACGACCACG
1 ACCACGACC-CG
1328038 ACCACGACCCG
1 ACCACGACCCG
*
1328049 ACCTCGACCCG
1 ACCACGACCCG
1328060 A
1 A
1328061 GACGAGACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.29, C:0.51, G:0.17, T:0.03
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:1328771 original size:22 final size:22
Alignment explanation
Indices: 1328700--1328771 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
1328690 TTTTAACAAA
* *
1328700 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAAACT
* *
1328722 ATCGCAAC-A-AATTTGGAAA--
1 ATCGCAACGACAA-CTGTAAACT
1328741 ATCGCAACGACAACTGTAAACT
1 ATCGCAACGACAACTGTAAACT
1328763 ATCGCAACG
1 ATCGCAACG
1328772 CGATTTTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
19 8 0.20
20 8 0.20
21 7 0.17
22 17 0.43
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAAACT
Found at i:1328845 original size:19 final size:20
Alignment explanation
Indices: 1328811--1328855 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1328801 AACACGAATT
*
1328811 TGCGATATTGGAGATCGCAA
1 TGCGATATTAGAGATCGCAA
*
1328831 TGCGA-ATTAGAGATCGCAT
1 TGCGATATTAGAGATCGCAA
1328850 TGCGAT
1 TGCGAT
1328856 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (20 bp):
TGCGATATTAGAGATCGCAA
Found at i:1331121 original size:2 final size:2
Alignment explanation
Indices: 1331114--1331138 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1331104 AGACTTTCCC
1331114 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 A
1331139 GAAATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1335186 original size:29 final size:29
Alignment explanation
Indices: 1335147--1335232 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 29
1335137 GTTTAAATCG
* *
1335147 ATTCTTAAACTTTTGAATATTCTAATTTT
1 ATTCTCAAACTTTTGAATATTCTAATTTA
* * *
1335176 A-TCATCAAAC-TATGACTCATTCTAAATTA
1 ATTC-TCAAACTTTTGAAT-ATTCTAATTTA
* *
1335205 ATTCTTAAACTTTTGAATATTCCAATTT
1 ATTCTCAAACTTTTGAATATTCTAATTT
1335233 CATCCCTAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
28 7 0.16
29 29 0.67
30 7 0.16
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (29 bp):
ATTCTCAAACTTTTGAATATTCTAATTTA
Found at i:1335242 original size:29 final size:29
Alignment explanation
Indices: 1335210--1335302 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 29
1335200 AATTAATTCT
1335210 TAAACTTTTGAATATTCCAATTTCATCCC
1 TAAACTTTTGAATATTCCAATTTCATCCC
* ** * *
1335239 TAAACTATTGCCCTCA-TCTTAAATT-AGTCCC
1 TAAACTTTTG-AAT-ATTC-CAATTTCA-TCCC
* *
1335270 CAAACTTTTAAATATTCCAATTTCATCCC
1 TAAACTTTTGAATATTCCAATTTCATCCC
1335299 TAAA
1 TAAA
1335303 TTCATTCAAA
Statistics
Matches: 45, Mismatches: 13, Indels: 12
0.64 0.19 0.17
Matches are distributed among these distances:
29 21 0.47
30 8 0.18
31 16 0.36
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (29 bp):
TAAACTTTTGAATATTCCAATTTCATCCC
Found at i:1335244 original size:58 final size:60
Alignment explanation
Indices: 1335147--1335302 Score: 185
Period size: 60 Copynumber: 2.6 Consensus size: 60
1335137 GTTTAAATCG
* * *
1335147 ATTCTTAAACTTTTGAATATTCTAATTTTAT-CATCAAACTA-TG-ACTCAT-TCTAAATTA
1 ATTCTTAAACTTTTGAATATTCCAATTTCATCCCT-AAACTATTGCACTCATCT-TAAATTA
*
1335205 ATTCTTAAACTTTTGAATATTCCAATTTCATCCCTAAACTATTGCCCTCATCTTAAATTA
1 ATTCTTAAACTTTTGAATATTCCAATTTCATCCCTAAACTATTGCACTCATCTTAAATTA
* * ** *
1335265 GTCCCCAAACTTTTAAATATTCCAATTTCATCCCTAAA
1 ATTCTTAAACTTTTGAATATTCCAATTTCATCCCTAAA
1335303 TTCATTCAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
58 35 0.41
59 4 0.05
60 45 0.53
61 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41
Consensus pattern (60 bp):
ATTCTTAAACTTTTGAATATTCCAATTTCATCCCTAAACTATTGCACTCATCTTAAATTA
Found at i:1335619 original size:60 final size:60
Alignment explanation
Indices: 1335487--1335619 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 60
1335477 GAATGGCATA
* * * *
1335487 ATAATTTGAGGATGTAATTGAAATATTTAAAAGTTTGAGGATTAATTTAGAATAAAAATC
1 ATAATTTGAGGATGAAACTGAAATATTTAAAACTTTGAGGATTAATTTAGAATAAAAACC
* * * * *
1335547 ATAGTTTAAGGATGAAACT-ATAATGTTTAAAACTTT-AGGATCTAATTTAGAATGAAGACC
1 ATAATTTGAGGATGAAACTGA-AATATTTAAAACTTTGAGGAT-TAATTTAGAATAAAAACC
1335607 ATAATTTGAGGAT
1 ATAATTTGAGGAT
1335620 ATGTGAGGCA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 6 0.10
60 54 0.90
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (60 bp):
ATAATTTGAGGATGAAACTGAAATATTTAAAACTTTGAGGATTAATTTAGAATAAAAACC
Found at i:1336547 original size:14 final size:15
Alignment explanation
Indices: 1336527--1336565 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1336517 ATTAGTACCA
1336527 CATTTAAATATTTTT
1 CATTTAAATATTTTT
1336542 -ATTT-AAT-TTTTT
1 CATTTAAATATTTTT
1336554 CATTTAAA-ATTT
1 CATTTAAATATTT
1336566 GAATCTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
12 5 0.24
13 7 0.33
14 9 0.43
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (15 bp):
CATTTAAATATTTTT
Found at i:1338588 original size:12 final size:12
Alignment explanation
Indices: 1338571--1338605 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1338561 TAATTAATAT
1338571 ATGTATATATGC
1 ATGTATATATGC
*
1338583 ATGTATATATGT
1 ATGTATATATGC
*
1338595 ATGTATGTATG
1 ATGTATATATG
1338606 GATATTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (12 bp):
ATGTATATATGC
Found at i:1345787 original size:32 final size:33
Alignment explanation
Indices: 1345716--1345788 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 33
1345706 ATTTTATGTC
1345716 AGGAGTACGGACTTAGGAAGTTATATTAAAAATTT
1 AGGAGTACGGACTTAGGAAGTTATATT--AAATTT
1345751 AGGAGTACGGACTTAGGAAGTTATATT-AATTT
1 AGGAGTACGGACTTAGGAAGTTATATTAAATTT
1345783 AGGAGT
1 AGGAGT
1345789 TCGAAATTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
32 11 0.29
35 27 0.71
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (33 bp):
AGGAGTACGGACTTAGGAAGTTATATTAAATTT
Found at i:1348790 original size:21 final size:21
Alignment explanation
Indices: 1348748--1348790 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1348738 TTTCTGGGTT
* * *
1348748 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1348769 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1348790 A
1 A
1348791 TGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1348851 original size:66 final size:67
Alignment explanation
Indices: 1348748--1348921 Score: 210
Period size: 67 Copynumber: 2.6 Consensus size: 67
1348738 TTTCTGGGTT
* * *
1348748 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCCTCAAT-G-AAATGAATTTCCAGAAT
1 AGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTC-ATCGTAAATGAAATTCCAGAAT
1348810 GCTAG
63 GCTAG
* *
1348815 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCT
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCT
*
1348880 TG
66 AG
* *
1348882 AGGGGAATCGATACCCCCAGGGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCA--GGGGGGAACCGATACCCCC
1348922 ATGAGAAAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
65 4 0.04
66 20 0.21
67 52 0.55
69 18 0.19
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.18
Consensus pattern (67 bp):
AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCT
AG
Found at i:1349258 original size:29 final size:29
Alignment explanation
Indices: 1349224--1349295 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
1349214 CATATTATGA
**
1349224 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
1349253 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
1349282 TACATGACATGAAT
1 TACATGACATGAAT
1349296 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:1349352 original size:30 final size:31
Alignment explanation
Indices: 1349310--1349369 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1349300 AGAAAAAGTT
*
1349310 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
1349341 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
1349370 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:1349617 original size:22 final size:22
Alignment explanation
Indices: 1349589--1349633 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1349579 TTATGGACAT
1349589 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1349611 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1349633 A
1 A
1349634 TTTATACGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:1349641 original size:22 final size:22
Alignment explanation
Indices: 1349589--1349641 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1349579 TTATGGACAT
*
1349589 AATTCTACGGGCACTTCGGTGC
1 AATTATACGGGCACTTCGGTGC
*
1349611 AATTCTACGGGCACTTCGGTGC
1 AATTATACGGGCACTTCGGTGC
*
1349633 ATTTATACG
1 AATTATACG
1349642 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (22 bp):
AATTATACGGGCACTTCGGTGC
Found at i:1355716 original size:21 final size:21
Alignment explanation
Indices: 1355674--1355716 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1355664 TTTCTGGGTT
* * *
1355674 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1355695 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1355716 A
1 A
1355717 TGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1355782 original size:67 final size:69
Alignment explanation
Indices: 1355696--1355848 Score: 222
Period size: 68 Copynumber: 2.2 Consensus size: 69
1355686 ACCCATTCAA
* *
1355696 GGGGAACCGATACCCCCTCAAT-G-AAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCC
1 GGGGAACCGATACCCCCTC-ATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCC
1355759 A-GGG
65 AGGGG
* * *
1355763 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1355828 GGGG
66 GGGG
*
1355832 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1355849 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
66 2 0.03
67 20 0.26
68 36 0.47
69 19 0.25
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGGG
Found at i:1356185 original size:29 final size:29
Alignment explanation
Indices: 1356151--1356222 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
1356141 CATATTATGA
**
1356151 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
1356180 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
1356209 TACATGACATGAAT
1 TACATGACATGAAT
1356223 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:1356279 original size:30 final size:31
Alignment explanation
Indices: 1356237--1356296 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1356227 AGAAAAAGTT
*
1356237 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
1356268 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
1356297 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:1356590 original size:22 final size:22
Alignment explanation
Indices: 1356516--1356582 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
1356506 TTATGGACAT
1356516 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1356538 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1356560 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1356582 A
1 A
1356583 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:1367201 original size:75 final size:75
Alignment explanation
Indices: 1367116--1367256 Score: 212
Period size: 75 Copynumber: 1.9 Consensus size: 75
1367106 TTTGATGTTT
* *
1367116 GGACTCTGTTTCTTATTGAAACCTGAATTAGGGTTTTGGTTCCGTGGCTTGTTGGG-TGTTTGGA
1 GGACTCTGTTTCTTATTGAAACCTGAATCAGGGTTTTGGTTCCATGGCTTG-TGGGATGTTTGGA
1367180 TTTTTGTTTAA
65 TTTTTGTTTAA
* * * *
1367191 GGACTCTGTTTCTTCTTGAAATCTGAATCAGGGTTTTGGTTTCATGTCTTGTGGGATGTTTGGAT
1 GGACTCTGTTTCTTATTGAAACCTGAATCAGGGTTTTGGTTCCATGGCTTGTGGGATGTTTGGAT
1367256 T
66 T
1367257 AATGAATTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 4 0.07
75 55 0.93
ACGTcount: A:0.15, C:0.11, G:0.28, T:0.46
Consensus pattern (75 bp):
GGACTCTGTTTCTTATTGAAACCTGAATCAGGGTTTTGGTTCCATGGCTTGTGGGATGTTTGGAT
TTTTGTTTAA
Found at i:1371949 original size:25 final size:25
Alignment explanation
Indices: 1371914--1371966 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
1371904 TTGCCAAATT
1371914 GGTTGACGAATGCTATGTTAACGCA
1 GGTTGACGAATGCTATGTTAACGCA
* *
1371939 GGTTGAGGAATGCTATGTTAACGTA
1 GGTTGACGAATGCTATGTTAACGCA
1371964 GGT
1 GGT
1371967 CTATCCCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.30
Consensus pattern (25 bp):
GGTTGACGAATGCTATGTTAACGCA
Found at i:1372229 original size:25 final size:27
Alignment explanation
Indices: 1372201--1372260 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
1372191 ATCTCATTTG
1372201 AGGGCAAGAG-A-ATACCTGGAGAGCA
1 AGGGCAAGAGAATATACCTGGAGAGCA
1372226 AGGGCAAGAGAATATACCTGGAGAGCA
1 AGGGCAAGAGAATATACCTGGAGAGCA
1372253 AGGGCAAG
1 AGGGCAAG
1372261 GGTTGCTGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 10 0.30
26 1 0.03
27 22 0.67
ACGTcount: A:0.40, C:0.15, G:0.37, T:0.08
Consensus pattern (27 bp):
AGGGCAAGAGAATATACCTGGAGAGCA
Found at i:1378341 original size:21 final size:21
Alignment explanation
Indices: 1378317--1378361 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1378307 GTTTTGAAAA
*
1378317 AAAATTGAAAGTTT-AGATACT
1 AAAACTGAAAGTTTAAG-TACT
*
1378338 AAAACTGATAGTTTAAGTACT
1 AAAACTGAAAGTTTAAGTACT
1378359 AAA
1 AAA
1378362 TGCGTAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (21 bp):
AAAACTGAAAGTTTAAGTACT
Found at i:1394385 original size:319 final size:319
Alignment explanation
Indices: 1393806--1394444 Score: 1179
Period size: 319 Copynumber: 2.0 Consensus size: 319
1393796 TATTCACATT
*
1393806 GATCTCTTTGTTCAATTCATCGGATTAGGTTCCCGATAAACCCTCTTAAAAGTTATGAAATCACC
1 GATCTCTTTGTTCAATTCATCGGATTAGGTTCCCGAGAAACCCTCTTAAAAGTTATGAAATCACC
* *
1393871 TCAAAACTATTAAACTTTGTTCTTCATCGTTTACCTTCAAATGGACTCTATCTAGGGATGTATTC
66 TCAAAACCATTAAACTTTGTTCTGCATCGTTTACCTTCAAATGGACTCTATCTAGGGATGTATTC
*
1393936 TTCATCTCACAGACATCTCTCAAACGTTTCGATTTTCGAATGAAGTTCTCGATCTTTGAGAAGAT
131 TTCAGCTCACAGACATCTCTCAAACGTTTCGATTTTCGAATGAAGTTCTCGATCTTTGAGAAGAT
*
1394001 CAAAACCCAGAATATTATTTTTAATTTTCTTTACCGATTAATTGAATGACTCGTCAGTGACTTTT
196 CAAAACCCAGAATATTATTTTTAATTTTCTTTACCGATTAATTAAATGACTCGTCAGTGACTTTT
*
1394066 TGAAATGGGTGACCTGTTTATAATATTACTAATGATTGAATGAGTTATGGTGTAACTTG
261 TGAAATGGGTGACCCGTTTATAATATTACTAATGATTGAATGAGTTATGGTGTAACTTG
* *
1394125 GATCTCTTTGTTCAATTCATCGGATTAGGTTCCCGAGGAACCCTCTTTAAAGTTATGAAATCACC
1 GATCTCTTTGTTCAATTCATCGGATTAGGTTCCCGAGAAACCCTCTTAAAAGTTATGAAATCACC
*
1394190 TCAGAACCATTAAACTTTGTTCTGCATCGTTTACCTTCAAATGGACTCTATCTAGGGATGTATTC
66 TCAAAACCATTAAACTTTGTTCTGCATCGTTTACCTTCAAATGGACTCTATCTAGGGATGTATTC
1394255 TTCAGCTCACAGACATCTCTCAAACGTTTCGATTTTCGAATGAAGTTCTCGATCTTTGAGAAGAT
131 TTCAGCTCACAGACATCTCTCAAACGTTTCGATTTTCGAATGAAGTTCTCGATCTTTGAGAAGAT
* *
1394320 CAAAACCTATAATATTATTTTTAATTTTCTTTACCGATTAATTAAATGACTCGTCAGTGACTTTT
196 CAAAACCCAGAATATTATTTTTAATTTTCTTTACCGATTAATTAAATGACTCGTCAGTGACTTTT
1394385 TGAAATGGGTGACCCGTTTATAATATTACTAATGATTGAATGAGTTATGGTGTAACTTG
261 TGAAATGGGTGACCCGTTTATAATATTACTAATGATTGAATGAGTTATGGTGTAACTTG
1394444 G
1 G
1394445 CCAATAAAAA
Statistics
Matches: 309, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
319 309 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (319 bp):
GATCTCTTTGTTCAATTCATCGGATTAGGTTCCCGAGAAACCCTCTTAAAAGTTATGAAATCACC
TCAAAACCATTAAACTTTGTTCTGCATCGTTTACCTTCAAATGGACTCTATCTAGGGATGTATTC
TTCAGCTCACAGACATCTCTCAAACGTTTCGATTTTCGAATGAAGTTCTCGATCTTTGAGAAGAT
CAAAACCCAGAATATTATTTTTAATTTTCTTTACCGATTAATTAAATGACTCGTCAGTGACTTTT
TGAAATGGGTGACCCGTTTATAATATTACTAATGATTGAATGAGTTATGGTGTAACTTG
Found at i:1395820 original size:4 final size:4
Alignment explanation
Indices: 1395811--1395862 Score: 90
Period size: 4 Copynumber: 13.5 Consensus size: 4
1395801 TGATATGTAC
1395811 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- AT-T
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1395857 ATGT AT
1 ATGT AT
1395863 TTGTTTCTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 4 0.09
4 42 0.91
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:1399047 original size:72 final size:72
Alignment explanation
Indices: 1398912--1399047 Score: 175
Period size: 73 Copynumber: 1.9 Consensus size: 72
1398902 ATAGTGACGT
* * *
1398912 TTTATTAATAAACGCCACTATAGATGGACCTATTGCGACGTATTTTTAAAAAAACGCCACTATTA
1 TTTATTAATAAACGCCACTATAGATGGACCTATTACGACGTATTGTCAAAAAAACGCCACTATTA
1398977 TTGCGGA
66 TTGCGGA
* * * * * *
1398984 TTTATTGATAAAACGCCATTATAGATTGATCTATTACGACGT-TTGTCCAGAAAACGCCACTATT
1 TTTATTAAT-AAACGCCACTATAGATGGACCTATTACGACGTATTGTCAAAAAAACGCCACTATT
1399048 GTTGTCCCGA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
72 26 0.48
73 28 0.52
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (72 bp):
TTTATTAATAAACGCCACTATAGATGGACCTATTACGACGTATTGTCAAAAAAACGCCACTATTA
TTGCGGA
Found at i:1399767 original size:13 final size:13
Alignment explanation
Indices: 1399749--1399775 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1399739 TTACAGACGC
1399749 GCATATGAAGACT
1 GCATATGAAGACT
1399762 GCATATGAAGACT
1 GCATATGAAGACT
1399775 G
1 G
1399776 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:1401237 original size:21 final size:20
Alignment explanation
Indices: 1401213--1401255 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
1401203 TACTAAAAAT
* *
1401213 TTCAAGTTTTTTGAGTTACTA
1 TTCAAGTTATTTAAGTTA-TA
1401234 TTCAAGTTATTTAAGTTATA
1 TTCAAGTTATTTAAGTTATA
1401254 TT
1 TT
1401256 TTACAACTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (20 bp):
TTCAAGTTATTTAAGTTATA
Found at i:1401369 original size:59 final size:59
Alignment explanation
Indices: 1401302--1401420 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
1401292 GAGTCAAGTT
*
1401302 AAATTTAACCAAAATTTAACCGTAGATTGTAAGAAATGAGTTGGCTTGTATAATAAATA
1 AAATTTAACCAAAATTTAACCGTAGATTGTAAGAAATGAGTTGGCTTATATAATAAATA
1401361 AAATTTAACCAAAATTTAACCGTAGATTGTAAGAAATGAGTTGGCTTATATAATAAATA
1 AAATTTAACCAAAATTTAACCGTAGATTGTAAGAAATGAGTTGGCTTATATAATAAATA
1401420 A
1 A
1401421 GTAATTAAAG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.32
Consensus pattern (59 bp):
AAATTTAACCAAAATTTAACCGTAGATTGTAAGAAATGAGTTGGCTTATATAATAAATA
Found at i:1401507 original size:31 final size:30
Alignment explanation
Indices: 1401464--1401554 Score: 89
Period size: 29 Copynumber: 3.0 Consensus size: 30
1401454 ATCAAACGTA
**
1401464 TTTTTTGATCAAAATAAG-TATGTAAAGTTAT
1 TTTTTTG-TCAAAATAAGTTACCTAAAG-TAT
1401495 CTTTTTTGTCAAAAT-AGTTACCTAAAGTAT
1 -TTTTTTGTCAAAATAAGTTACCTAAAGTAT
* * *
1401525 TTTTTAGTCAAAATATG-TACTTAAAGTAT
1 TTTTTTGTCAAAATAAGTTACCTAAAGTAT
1401554 T
1 T
1401555 CAATTATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 25 0.48
30 6 0.12
31 14 0.27
32 7 0.13
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (30 bp):
TTTTTTGTCAAAATAAGTTACCTAAAGTAT
Found at i:1402963 original size:17 final size:17
Alignment explanation
Indices: 1402936--1402974 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1402926 AATTTACAAT
1402936 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
1402952 TAATTATAAATAATATC
1 TAATTATAAATAATATC
1402969 TAATTA
1 TAATTA
1402975 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:1403103 original size:9 final size:9
Alignment explanation
Indices: 1403089--1403114 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1403079 TATATTTAAA
1403089 GGTTAATTC
1 GGTTAATTC
1403098 GGTTAATTC
1 GGTTAATTC
1403107 GGTTAATT
1 GGTTAATT
1403115 AACCGATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (9 bp):
GGTTAATTC
Found at i:1406727 original size:14 final size:14
Alignment explanation
Indices: 1406708--1406743 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1406698 CCATACATAC
*
1406708 TACTACAATTAAGT
1 TACTACAACTAAGT
1406722 TACTACAACTAAGT
1 TACTACAACTAAGT
1406736 TACTACAA
1 TACTACAA
1406744 GAGTTACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (14 bp):
TACTACAACTAAGT
Found at i:1411226 original size:3 final size:3
Alignment explanation
Indices: 1411220--1411245 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1411210 GCTATCTTCT
1411220 TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TC
1411246 ATCTTCCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
TCC
Found at i:1411270 original size:27 final size:26
Alignment explanation
Indices: 1411240--1411303 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
1411230 CCTCCTCCTC
*
1411240 CTCCTCATCTTCCTCTACTTCTTTCTG
1 CTCCTC-TCTTCCTCCACTTCTTTCTG
1411267 CT-C-CTCTTCCTCCACTTCTTTCTG
1 CTCCTCTCTTCCTCCACTTCTTTCTG
*
1411291 TTCCTCTTCTTCC
1 CTCCTC-TCTTCC
1411304 ACTTCCTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 20 0.62
25 2 0.06
26 2 0.06
27 8 0.25
ACGTcount: A:0.05, C:0.44, G:0.03, T:0.48
Consensus pattern (26 bp):
CTCCTCTCTTCCTCCACTTCTTTCTG
Found at i:1411274 original size:24 final size:24
Alignment explanation
Indices: 1411247--1411313 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
1411237 CTCCTCCTCA
*
1411247 TCTTCCTCTACTTCTTTCTGCTCC
1 TCTTCCTCCACTTCTTTCTGCTCC
*
1411271 TCTTCCTCCACTTCTTTCTGTTCC
1 TCTTCCTCCACTTCTTTCTGCTCC
* *
1411295 TCTTCTTCCACTTCCTTCT
1 TCTTCCTCCACTTCTTTCT
1411314 CTTTTTCTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.04, C:0.42, G:0.03, T:0.51
Consensus pattern (24 bp):
TCTTCCTCCACTTCTTTCTGCTCC
Found at i:1415329 original size:75 final size:75
Alignment explanation
Indices: 1415205--1415413 Score: 260
Period size: 75 Copynumber: 2.8 Consensus size: 75
1415195 AAAGCCAAAA
* * **
1415205 ATTT-CAGATTGCTCAGAGGGAACCGATTTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 ATTTCCAGAATGCTCGGAGGGAACCGA-TT-CCCCCATAGGAGGAACCGATTCCCCCCTGAACAG
1415269 TTTGGCTCCGAG
64 TTTGGCTCCGAG
* *
1415281 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACATTT
1 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTGAACAGTT
* *
1415346 TTGTTCCGAG
66 TGGCTCCGAG
* * * * *
1415356 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCTG
1 ATTTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCTG
1415414 TTCAACGGTC
Statistics
Matches: 117, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
75 85 0.73
76 12 0.10
77 20 0.17
ACGTcount: A:0.23, C:0.31, G:0.24, T:0.22
Consensus pattern (75 bp):
ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTGAACAGTT
TGGCTCCGAG
Found at i:1421205 original size:21 final size:21
Alignment explanation
Indices: 1421179--1421241 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
1421169 TTTTGGTGCA
*
1421179 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
1421200 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
1421221 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
1421242 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:1421249 original size:21 final size:21
Alignment explanation
Indices: 1421223--1421262 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1421213 CCCCCTTTGA
*
1421223 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1421244 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1421263 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1424028 original size:75 final size:75
Alignment explanation
Indices: 1423853--1424048 Score: 243
Period size: 74 Copynumber: 2.6 Consensus size: 75
1423843 AATTTTAGAT
* * * **
1423853 TGCTCAGAGGGAACCGATTCCCCCCAATAGGAGGAACCGATTCCCCCCTGAATGGTTTGGCTCCG
1 TGCTCGGAGGGAACCGA-TCCCCCCCATAGGAGGAACCGATT-CCCCCTAAACAGTTTGGCTCCG
*
1423918 AGATTTCCAGAA
64 AGAATTCCAGAA
* * * *
1423930 TGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCTAAACATTTTTGTTCCGAG
1 TGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTGGCTCCGAG
*
1423994 AATTCCAGTA
66 AATTCCAGAA
* *
1424004 TGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 TGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCC
1424049 CTGTTCAACG
Statistics
Matches: 104, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
74 61 0.59
75 26 0.25
76 1 0.01
77 16 0.15
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.20
Consensus pattern (75 bp):
TGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTGGCTCCGAG
AATTCCAGAA
Found at i:1430420 original size:23 final size:24
Alignment explanation
Indices: 1430386--1430455 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 24
1430376 ACTAACCGAG
* *
1430386 CGTTAAACGAACATGTTCGTGAA-
1 CGTTAAATGAACATGTTCGCGAAT
*
1430409 CGTTAAATGAACACGTTCGCGAAT
1 CGTTAAATGAACATGTTCGCGAAT
** * *
1430433 ATTTAAATGAACTTGTTCACGAA
1 CGTTAAATGAACATGTTCGCGAA
1430456 CATTAAACGG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (24 bp):
CGTTAAATGAACATGTTCGCGAAT
Found at i:1433470 original size:58 final size:59
Alignment explanation
Indices: 1433364--1433479 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 59
1433354 TTTTGGTTGT
1433364 CATTAGCCAAGATAGTTGTTATTTTTTTAGCATCTAATTGCAGTGAGTAATAACATTGA
1 CATTAGCCAAGATAGTTGTTATTTTTTTAGCATCTAATTGCAGTGAGTAATAACATTGA
* *
1433423 CATTAGCCACGATAGTTGTTA-TTTTTTAGCATCTAATTGCTGTGAGTAATAACATTG
1 CATTAGCCAAGATAGTTGTTATTTTTTTAGCATCTAATTGCAGTGAGTAATAACATTG
1433480 TCATCAATGA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 35 0.64
59 20 0.36
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (59 bp):
CATTAGCCAAGATAGTTGTTATTTTTTTAGCATCTAATTGCAGTGAGTAATAACATTGA
Found at i:1447552 original size:19 final size:19
Alignment explanation
Indices: 1447530--1447597 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
1447520 TTAATTAATA
*
1447530 AAATATAATAAATCATTAT
1 AAATATAATAAATAATTAT
* *
1447549 AAATATATTATTTTAATAATTTT
1 AAATATA--A--TAAATAATTAT
* *
1447572 AAAAATAATAAATGATTAT
1 AAATATAATAAATAATTAT
1447591 AAATATA
1 AAATATA
1447598 TTATTATAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 21 0.57
21 2 0.05
23 14 0.38
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (19 bp):
AAATATAATAAATAATTAT
Found at i:1447590 original size:42 final size:41
Alignment explanation
Indices: 1447505--1447602 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 41
1447495 TATTTTTATA
1447505 TATAAGATATATT-TTTTAATTAATAAAATATAATAAATCAT
1 TATAA-ATATATTATTTTAATTAATAAAATATAATAAATCAT
*
1447546 TATAAATATATTATTTTAA-TAATTTTAAAA-ATAATAAATGAT
1 TATAAATATATTATTTTAATTAA---TAAAATATAATAAATCAT
1447588 TATAAATATATTATT
1 TATAAATATATTATT
1447603 ATAAAATATA
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
40 10 0.19
41 11 0.21
42 26 0.50
43 5 0.10
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (41 bp):
TATAAATATATTATTTTAATTAATAAAATATAATAAATCAT
Found at i:1447611 original size:15 final size:14
Alignment explanation
Indices: 1447544--1447617 Score: 64
Period size: 15 Copynumber: 5.2 Consensus size: 14
1447534 ATAATAAATC
1447544 ATTATAAATATATT
1 ATTATAAATATATT
*
1447558 ATT-TTAATA-ATT
1 ATTATAAATATATT
* *
1447570 -TTAAAAATAATAAATG
1 ATTATAAAT-AT--ATT
1447586 ATTATAAATATATT
1 ATTATAAATATATT
1447600 ATTATAAAATATATT
1 ATTAT-AAATATATT
1447615 ATT
1 ATT
1447618 TTAATTATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
11 2 0.04
12 6 0.13
13 6 0.13
14 10 0.21
15 12 0.26
16 4 0.09
17 7 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (14 bp):
ATTATAAATATATT
Found at i:1453511 original size:20 final size:20
Alignment explanation
Indices: 1453469--1453513 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1453459 TCTACCTTCT
* *
1453469 TCCCTTACTCTCTCTATACC
1 TCCCTTACCCTCTCTACACC
1453489 TCCCTTACCCTCTC-ACACTC
1 TCCCTTACCCTCTCTACAC-C
1453509 TCCCT
1 TCCCT
1453514 CTCCTCCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.13, C:0.51, G:0.00, T:0.36
Consensus pattern (20 bp):
TCCCTTACCCTCTCTACACC
Found at i:1453560 original size:8 final size:9
Alignment explanation
Indices: 1453508--1453646 Score: 58
Period size: 8 Copynumber: 14.8 Consensus size: 9
1453498 CTCTCACACT
1453508 CTCCCTCTC
1 CTCCCTCTC
1453517 CTCCCTCTC
1 CTCCCTCTC
*
1453526 TCTCCTTCTGCCC
1 -CTCC--CT-CTC
1453539 CTCCCTCTC
1 CTCCCTCTC
1453548 C-CCCT-TC
1 CTCCCTCTC
*
1453555 CTCCCTAT-
1 CTCCCTCTC
1453563 CTCCCTCT-
1 CTCCCTCTC
** *
1453571 CTCTTTTTC
1 CTCCCTCTC
*
1453580 TCTCTCTCTAC
1 -CTCCCTCT-C
1453591 C-CCTCTCTC
1 CTCC-CTCTC
1453600 TCTACCTCTCTC
1 -CT-CC-CTCTC
1453612 TCTCACTCTCTC
1 -CTC-C-CTCTC
1453624 CTCCCTCTC
1 CTCCCTCTC
1453633 C-CCCTC-C
1 CTCCCTCTC
1453640 CTCCCTC
1 CTCCCTC
1453647 CTCCCCTCCC
Statistics
Matches: 106, Mismatches: 9, Indels: 31
0.73 0.06 0.21
Matches are distributed among these distances:
7 5 0.05
8 30 0.28
9 21 0.20
10 19 0.18
11 5 0.05
12 24 0.23
13 2 0.02
ACGTcount: A:0.03, C:0.59, G:0.01, T:0.37
Consensus pattern (9 bp):
CTCCCTCTC
Found at i:1453620 original size:12 final size:14
Alignment explanation
Indices: 1453578--1453623 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
1453568 TCTCTCTTTT
1453578 TCTCTCTCTCTACC
1 TCTCTCTCTCTACC
*
1453592 CCTCTCTCTCTACC
1 TCTCTCTCTCTACC
1453606 TCTCTCTCTC-A-C
1 TCTCTCTCTCTACC
1453618 TCTCTC
1 TCTCTC
1453624 CTCCCTCTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 7 0.23
13 1 0.03
14 22 0.73
ACGTcount: A:0.07, C:0.52, G:0.00, T:0.41
Consensus pattern (14 bp):
TCTCTCTCTCTACC
Found at i:1453622 original size:14 final size:13
Alignment explanation
Indices: 1453578--1453632 Score: 62
Period size: 14 Copynumber: 4.3 Consensus size: 13
1453568 TCTCTCTTTT
1453578 TCTCTCTCTCTACC
1 TCTCTCTCTC-ACC
*
1453592 CCTCTCTCTCTACC
1 TCTCTCTCTC-ACC
1453606 TCTCTCTCTCA-C
1 TCTCTCTCTCACC
1453618 TCTCTC-CTC-CC
1 TCTCTCTCTCACC
1453629 TCTC
1 TCTC
1453633 CCCCTCCCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
11 8 0.21
12 7 0.18
13 1 0.03
14 22 0.58
ACGTcount: A:0.05, C:0.55, G:0.00, T:0.40
Consensus pattern (13 bp):
TCTCTCTCTCACC
Found at i:1453644 original size:16 final size:16
Alignment explanation
Indices: 1453623--1453660 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1453613 CTCACTCTCT
1453623 CCTCCCT-CTCCCCCTC
1 CCTCCCTCCT-CCCCTC
1453639 CCTCCCTCCTCCCCTC
1 CCTCCCTCCTCCCCTC
1453655 CCTCCC
1 CCTCCC
1453661 CATCCAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 19 0.90
17 2 0.10
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (16 bp):
CCTCCCTCCTCCCCTC
Found at i:1453657 original size:12 final size:12
Alignment explanation
Indices: 1453621--1453659 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1453611 CTCTCACTCT
1453621 CTCCTCCCTCTCC
1 CTCCTCCC-CTCC
1453634 C-CCT-CCCTCC
1 CTCCTCCCCTCC
1453644 CTCCTCCCCTCC
1 CTCCTCCCCTCC
1453656 CTCC
1 CTCC
1453660 CCATCCAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.21
11 5 0.21
12 13 0.54
13 1 0.04
ACGTcount: A:0.00, C:0.74, G:0.00, T:0.26
Consensus pattern (12 bp):
CTCCTCCCCTCC
Found at i:1461603 original size:60 final size:59
Alignment explanation
Indices: 1461515--1461667 Score: 164
Period size: 60 Copynumber: 2.5 Consensus size: 59
1461505 ATGAAATTGG
* * * *
1461515 AATGTTCAAAAAGTTTGGGGACCAATTTAAAATGA-ATGTCATAGTTTGGGGATAAAATTAA
1 AATGTT-AAAAAGTTT-GAGACCAATTTAAAATGATA-GTCATAGGTTAGGGAAAAAATTAA
* * * *
1461576 AATGTTAAAAAATTTGACGACTAATTTAGAATGATAGTTATAGGTTAGGGAAAAAATTAA
1 AATGTTAAAAAGTTTGA-GACCAATTTAAAATGATAGTCATAGGTTAGGGAAAAAATTAA
* *
1461636 AATATTTAAAAGTTTAGAGACCAATTTAAAAT
1 AATGTTAAAAAGTTT-GAGACCAATTTAAAAT
1461668 AAGGTATATA
Statistics
Matches: 76, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
59 1 0.01
60 66 0.87
61 9 0.12
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (59 bp):
AATGTTAAAAAGTTTGAGACCAATTTAAAATGATAGTCATAGGTTAGGGAAAAAATTAA
Found at i:1461928 original size:18 final size:19
Alignment explanation
Indices: 1461893--1461929 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1461883 CACGGAATGT
1461893 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1461913 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1461930 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1463407 original size:152 final size:152
Alignment explanation
Indices: 1463131--1463432 Score: 568
Period size: 152 Copynumber: 2.0 Consensus size: 152
1463121 ACTATTTATC
* *
1463131 GACTATGCATTTGGAATTGGCCTAGCCGGATAGGGTTCGAGGCGTTTTTGTTGCTTGTGCTACAA
1 GACTATGCATTTGGAATTGGCCTAGCCGGAAAGGGTTCGAGGCATTTTTGTTGCTTGTGCTACAA
1463196 GGCAGAAGGCATTACACCCTGTACATGCTGAGGAGCACCGGCCGTCGGATCCCATCGAGATATCC
66 GGCAGAAGGCATTACACCCTGTACATGCTGAGGAGCACCGGCCGTCGGATCCCATCGAGATATCC
1463261 CCTTGATTGGCTTCATAATCGA
131 CCTTGATTGGCTTCATAATCGA
1463283 GACTATGCATTTGGAATTGGCCTAGCCGGAAAGGGTTCGAGGCATTTTTGTTGCTTGTGCTACAA
1 GACTATGCATTTGGAATTGGCCTAGCCGGAAAGGGTTCGAGGCATTTTTGTTGCTTGTGCTACAA
* *
1463348 GGCAGAAGGCATTACACCCTGTACATGCTGAGGAGTACCGGCCGTCGGATCCTATCGAGATATCC
66 GGCAGAAGGCATTACACCCTGTACATGCTGAGGAGCACCGGCCGTCGGATCCCATCGAGATATCC
1463413 CCTTGATTGGCTTCATAATC
131 CCTTGATTGGCTTCATAATC
1463433 CGATGCAAGA
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
152 146 1.00
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.27
Consensus pattern (152 bp):
GACTATGCATTTGGAATTGGCCTAGCCGGAAAGGGTTCGAGGCATTTTTGTTGCTTGTGCTACAA
GGCAGAAGGCATTACACCCTGTACATGCTGAGGAGCACCGGCCGTCGGATCCCATCGAGATATCC
CCTTGATTGGCTTCATAATCGA
Found at i:1463570 original size:107 final size:105
Alignment explanation
Indices: 1463384--1463642 Score: 430
Period size: 107 Copynumber: 2.5 Consensus size: 105
1463374 GCTGAGGAGT
* *
1463384 ACCGGCCGTCGGATCCTATCGAGATATCCCCTTGATTGGCTTCATAATCCGATGCAAGATTGCTT
1 ACCGGCCGTCGGATCCAATCGAGATATCCCCTTAATTGGCTTCATAATCCGATGCAAGATTGCTT
1463449 CTTAAACTATTGACTCTTTCTTCGTGTCTAAAATTCCGGCGC
66 CTTAAACTATTGACTCTTTCTTCGTGTC--AAATTCCGGCGC
* *
1463491 ACCGGCCGTCGGATCCCATCGAGATATCCCCTTAATTGGCTTCATCATCCGATGCAAGATTGCTT
1 ACCGGCCGTCGGATCCAATCGAGATATCCCCTTAATTGGCTTCATAATCCGATGCAAGATTGCTT
*
1463556 CTTAAACTATTGACTCTTTCTTCGTGTCGAATTCCGGCGC
66 CTTAAACTATTGACTCTTTCTTCGTGTCAAATTCCGGCGC
**
1463596 ACCGGCCGTCGGATCCAATCGAGATATCCCC-TAATCAGCTTCATAAT
1 ACCGGCCGTCGGATCCAATCGAGATATCCCCTTAATTGGCTTCATAAT
1463643 ATTATGGATA
Statistics
Matches: 144, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
104 13 0.09
105 41 0.28
107 90 0.62
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.31
Consensus pattern (105 bp):
ACCGGCCGTCGGATCCAATCGAGATATCCCCTTAATTGGCTTCATAATCCGATGCAAGATTGCTT
CTTAAACTATTGACTCTTTCTTCGTGTCAAATTCCGGCGC
Found at i:1463794 original size:12 final size:12
Alignment explanation
Indices: 1463777--1463801 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1463767 ATTATTGTGA
1463777 AATTTAAAATTT
1 AATTTAAAATTT
1463789 AATTTAAAATTT
1 AATTTAAAATTT
1463801 A
1 A
1463802 TCTCATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTTAAAATTT
Found at i:1464029 original size:2 final size:2
Alignment explanation
Indices: 1464022--1464048 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1464012 TTGATGACAC
1464022 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 A
1464049 AAGTAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1464669 original size:3 final size:3
Alignment explanation
Indices: 1464661--1464741 Score: 162
Period size: 3 Copynumber: 27.0 Consensus size: 3
1464651 ATTTAAATAC
1464661 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1464709 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1464742 GTTGTTGTTG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1465059 original size:24 final size:23
Alignment explanation
Indices: 1465030--1465075 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
1465020 AAATTCCAGG
*
1465030 AGCTCGATTGAAGCTCGAGACTCT
1 AGCTCGATTCAAGCTCGA-ACTCT
1465054 AGCTCGATTCAAGCTCGAACTC
1 AGCTCGATTCAAGCTCGAACTC
1465076 GATTCAAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (23 bp):
AGCTCGATTCAAGCTCGAACTCT
Found at i:1465078 original size:17 final size:17
Alignment explanation
Indices: 1465056--1465109 Score: 90
Period size: 17 Copynumber: 3.2 Consensus size: 17
1465046 GAGACTCTAG
1465056 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
1465073 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
**
1465090 CTCGATAAAAGCTCGAA
1 CTCGATTCAAGCTCGAA
1465107 CTC
1 CTC
1465110 AAACTCGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:1472026 original size:27 final size:28
Alignment explanation
Indices: 1471965--1472026 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
1471955 CACTTAAATT
*
1471965 ATAATAAAAATATAAAATAAATTATTAA
1 ATAATAAAAATATAAAATAAATAATTAA
*
1471993 GTAATAAATAAT-TAAAAT-AATAATTAA
1 ATAATAAA-AATATAAAATAAATAATTAA
1472020 ATAATAA
1 ATAATAA
1472027 TTTTTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 14 0.47
28 13 0.43
29 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (28 bp):
ATAATAAAAATATAAAATAAATAATTAA
Found at i:1472028 original size:11 final size:12
Alignment explanation
Indices: 1471961--1472028 Score: 57
Period size: 15 Copynumber: 5.3 Consensus size: 12
1471951 ATATCACTTA
* *
1471961 AATTATAATAAA
1 AATTAAAATAAT
1471973 AATATAAAATAAAT
1 AAT-TAAAAT-AAT
*
1471987 TATTAAGTAATAAAT
1 AATTAA--AAT-AAT
1472002 AATTAAAATAAT
1 AATTAAAATAAT
1472014 AATT-AAATAAT
1 AATTAAAATAAT
1472025 AATT
1 AATT
1472029 TTTTTAATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
11 11 0.23
12 10 0.21
13 11 0.23
14 4 0.08
15 12 0.25
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (12 bp):
AATTAAAATAAT
Found at i:1472096 original size:12 final size:12
Alignment explanation
Indices: 1472063--1472099 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1472053 CATTAAGTAA
1472063 TAAATTAT-A-T
1 TAAATTATAATT
1472073 TAAATATATAATT
1 TAAAT-TATAATT
1472086 TAAATTATAATT
1 TAAATTATAATT
1472098 TA
1 TA
1472100 CTTTTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.21
11 3 0.12
12 10 0.42
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TAAATTATAATT
Found at i:1472121 original size:69 final size:65
Alignment explanation
Indices: 1471969--1472132 Score: 183
Period size: 69 Copynumber: 2.5 Consensus size: 65
1471959 TAAATTATAA
*
1471969 TAAA-AATATAAAATAAATTATTAAGTAATAAATAATTAAAATAATAATTAAATAATAATTTTTT
1 TAAATAATGTAAAATAAATTATTAAGTAATAAATAATTAAAATAATAATTAAATAATAATTTTTT
* * * *
1472033 T-AATGATGGTAATATTAAATCATTAAGTAATAAATTATATT-AAATATATAATTTAAATTATAA
1 TAAATAAT-GTAA-AATAAATTATTAAGTAATAAA-TA-ATTAAAATA-ATAA-TTAAATAATAA
1472096 TTTACTTT
60 TTT--TTT
1472104 TAAATAAT-TAAAATAAATTATTAAGTAAT
1 TAAATAATGTAAAATAAATTATTAAGTAAT
1472133 GTTTTTTAAG
Statistics
Matches: 82, Mismatches: 8, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
63 2 0.02
64 3 0.04
65 3 0.04
66 19 0.23
67 7 0.09
68 7 0.09
69 29 0.35
70 3 0.04
71 4 0.05
72 5 0.06
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (65 bp):
TAAATAATGTAAAATAAATTATTAAGTAATAAATAATTAAAATAATAATTAAATAATAATTTTTT
Found at i:1474697 original size:5 final size:6
Alignment explanation
Indices: 1474682--1474706 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1474672 GTATTGACAA
1474682 TTTTTG TTTTTG TTTTTG TTTTTG T
1 TTTTTG TTTTTG TTTTTG TTTTTG T
1474707 AGTATGTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:1474869 original size:13 final size:13
Alignment explanation
Indices: 1474851--1474877 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1474841 TCAGACTTTA
1474851 TACTGATAGACCT
1 TACTGATAGACCT
1474864 TACTGATAGACCT
1 TACTGATAGACCT
1474877 T
1 T
1474878 TGTAATAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (13 bp):
TACTGATAGACCT
Found at i:1478329 original size:20 final size:22
Alignment explanation
Indices: 1478304--1478343 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1478294 AGTAGTATCT
1478304 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1478324 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1478344 TTTGCAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1478418 original size:20 final size:21
Alignment explanation
Indices: 1478371--1478431 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
1478361 CCATAATAGG
1478371 GGGTATCGGTACCCCTTCATA
1 GGGTATCGGTACCCCTTCATA
1478392 GGGTATCGGTACCCCTTCATA
1 GGGTATCGGTACCCCTTCATA
* *
1478413 -GGTATCGATACACCTTCAT
1 GGGTATCGGTACCCCTTCAT
1478432 TAAATTCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 17 0.45
21 21 0.55
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (21 bp):
GGGTATCGGTACCCCTTCATA
Found at i:1478605 original size:14 final size:14
Alignment explanation
Indices: 1478586--1478612 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1478576 ACCTGCAGGG
1478586 GGTATCGGTACACA
1 GGTATCGGTACACA
1478600 GGTATCGGTACAC
1 GGTATCGGTACAC
1478613 CAGTGTATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (14 bp):
GGTATCGGTACACA
Found at i:1481726 original size:2 final size:2
Alignment explanation
Indices: 1481719--1481760 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1481709 CTAAGTCGTC
1481719 TA TA TA TA 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 TA TA TA TA
1481761 AGTGATATAA
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):
TA
Found at i:1482748 original size:20 final size:20
Alignment explanation
Indices: 1482712--1482749 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1482702 ATCCTATTCC
**
1482712 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1482732 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1482750 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1491287 original size:31 final size:31
Alignment explanation
Indices: 1491252--1491321 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
1491242 TCAAAAAACA
* *
1491252 TAATATTTCATCACT-TTCGTTTTTATTTCAT
1 TAATATGTCATCA-TATTCGTTTTTATTTAAT
**
1491283 TAATATGTGGTCATATTCGTTTTTATTTAAT
1 TAATATGTCATCATATTCGTTTTTATTTAAT
*
1491314 TAAGATGT
1 TAATATGT
1491322 AGTCACTTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (31 bp):
TAATATGTCATCATATTCGTTTTTATTTAAT
Found at i:1492596 original size:26 final size:26
Alignment explanation
Indices: 1492552--1492602 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1492542 TTTAAGACAG
*
1492552 ACAAAAATATATTATCAATTGAAAAT
1 ACAAAAATATATGATCAATTGAAAAT
*
1492578 ACAAAAATTATATGA-CAATTTAAAA
1 ACAAAAA-TATATGATCAATTGAAAA
1492603 ATTTTACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.59, C:0.08, G:0.04, T:0.29
Consensus pattern (26 bp):
ACAAAAATATATGATCAATTGAAAAT
Found at i:1492603 original size:27 final size:26
Alignment explanation
Indices: 1492552--1492604 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
1492542 TTTAAGACAG
* *
1492552 ACAAAAATATATTATCAATTGAAAAT
1 ACAAAAATATATGATCAATTAAAAAT
1492578 ACAAAAATTATATGA-CAATTTAAAAAT
1 ACAAAAA-TATATGATCAA-TTAAAAAT
1492605 TTTACATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.30
Consensus pattern (26 bp):
ACAAAAATATATGATCAATTAAAAAT
Found at i:1494623 original size:21 final size:21
Alignment explanation
Indices: 1494589--1494630 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1494579 TAAGTTTTGA
* *
1494589 AAAAATTGAAAGTTTATGTAC
1 AAAAACTGAAAGTTTAGGTAC
*
1494610 AAAAACTGATAGTTTAGGTAC
1 AAAAACTGAAAGTTTAGGTAC
1494631 TAAACGTGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (21 bp):
AAAAACTGAAAGTTTAGGTAC
Found at i:1495283 original size:2 final size:2
Alignment explanation
Indices: 1495278--1495355 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
1495268 CCCCCACCAC
*
1495278 CT CT CT CT CA CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1495320 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1495356 ATATATATAT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.01, C:0.50, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1495360 original size:2 final size:2
Alignment explanation
Indices: 1495355--1495408 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1495345 TCTCTCTCTC
1495355 TA TA TA TA 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 TA TA TA TA
1495397 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1495409 AAGAACTTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1498039 original size:45 final size:45
Alignment explanation
Indices: 1497978--1498082 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 45
1497968 ATTAGTAGAA
*
1497978 AAAAATAATATTTTAGGTAGCGC-CTAATATTAACATTTTC-GATAG
1 AAAAATAATATTTTAGGTAGCGCTC-AATATTAACATTTCCTG-TAG
* * *
1498023 AAAAATAATATTTTAGGTATCGCTCGATATTAAGATTTCCTGTAG
1 AAAAATAATATTTTAGGTAGCGCTCAATATTAACATTTCCTGTAG
*
1498068 AAAAATAATGTTTTA
1 AAAAATAATATTTTA
1498083 AGTAACGTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
45 51 0.96
46 2 0.04
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (45 bp):
AAAAATAATATTTTAGGTAGCGCTCAATATTAACATTTCCTGTAG
Found at i:1503791 original size:4 final size:4
Alignment explanation
Indices: 1503782--1503820 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
1503772 CATATATACA
* * *
1503782 TATG TATG TATG TATG TATA TATA TATA TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1503821 ATAAGTTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:1503808 original size:24 final size:24
Alignment explanation
Indices: 1503774--1503820 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1503764 AATTTGTCCA
*
1503774 TATATACATATGTATGTATGTATG
1 TATATACATATATATGTATGTATG
*
1503798 TATATATATATATATGTATGTAT
1 TATATACATATATATGTATGTAT
1503821 ATAAGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (24 bp):
TATATACATATATATGTATGTATG
Found at i:1521321 original size:28 final size:27
Alignment explanation
Indices: 1521285--1521384 Score: 92
Period size: 29 Copynumber: 3.5 Consensus size: 27
1521275 AAAAACTTTG
* *
1521285 AATAGTTTAGGTACCTATCTTGACATAA
1 AATACTTTAGGTACCTATTTTGACA-AA
* *
1521313 AATACTTTATGTACCTATTTTGATAAA
1 AATACTTTAGGTACCTATTTTGACAAA
* *
1521340 TAATAACTTTAGATACTTATTTTGACCAAAA
1 -AAT-ACTTTAGGTACCTATTTTGA-C-AAA
*
1521371 AATATTTTAGGTAC
1 AATACTTTAGGTAC
1521385 TTAAATGAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
27 2 0.03
28 24 0.41
29 26 0.45
30 3 0.05
31 3 0.05
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (27 bp):
AATACTTTAGGTACCTATTTTGACAAA
Found at i:1525980 original size:20 final size:20
Alignment explanation
Indices: 1525951--1525993 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1525941 TTAATAATAT
1525951 ATAAAATAT-ATAATTTTAAA
1 ATAAAATATAAT-ATTTTAAA
* *
1525971 ATAAATTATAATTTTTTAAA
1 ATAAAATATAATATTTTAAA
1525991 ATA
1 ATA
1525994 TTGCTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAAATATAATATTTTAAA
Found at i:1527741 original size:421 final size:423
Alignment explanation
Indices: 1526952--1528228 Score: 2089
Period size: 421 Copynumber: 3.0 Consensus size: 423
1526942 AAGTTATAAA
* * * *
1526952 ATGAATAATCATGTGACCATTTTGTAACTTTTAATAGTCGGGGGACTTAATAAAACATCATTCTA
1 ATGAATAGTCAGGTGACCATTTTGTAACTTTTAATAGTC-GAGGACTTAATAAAACATCATTATA
* *
1527017 TAGTCCCTCGACTATTAGGTAAAATATATAAATAGTCCCTTGACCATATGATACTATTTTATTAA
65 TAGTCCCTCGACTATTAGGTAAAATATACAAATAGTCCCTTGACTATATGATACTATTTTATTAA
* * * **
1527082 GTCTCTCGACTGTTAAAAATTACAAAATGATCATTTAACTATAGAATGACACTTTATAAAGTCTA
130 GTCCCTTGACTGTTAAAAATTACAAAATGATCCTTTAACTATAGAATGACACTTTATAAAGTCCC
* *
1527147 TTGACTATTAAAAGTTATAAAATGGTCATCCCACTATTCATTATGTTTCAGACCCGTCATTTTCT
195 TTGGCTATTAAAAGTTATAAAATGGTCATCCCACTATTCATTATGTTTCAGACCCGTCTTTTTCT
*
1527212 ATTAAAAAAATTGGTCGTTGTCTAAGTTGGACGTTAACATAATGACTGAAATATGATAGTCGTTT
260 ATTAAAAAAATCGGTCGTTGTCTAAGTTGGACGTTAACATAATGACTGAAATATGATAGTCGTTT
* * *
1527277 AAGACTTTAGGATCAGATTTTATCATATCACATTT-TGCAGGTTAACGTTTAGCTCAAAATACTG
325 AAGACTCTAGGATCAAATTTTATCATATCACATTTAT-CAGGTTAACGTTTAGCTCATAATACTG
1527341 CCAATTTTTAACGGAAAATGACGAGTTTGCAACAT
389 CCAATTTTTAACGGAAAATGACGAGTTTGCAACAT
1527376 ATGAATAGTCAGGTGACCATTTTGTAACTTTTAATAGTCGATGGACTTAATAAAACATCA-T-TA
1 ATGAATAGTCAGGTGACCATTTTGTAACTTTTAATAGTCGA-GGACTTAATAAAACATCATTATA
*
1527439 TAGTCCCTCGACTATTAGGTAAAATATACAAATAGTCCCTTGACTATATGATACTACTTTATTAA
65 TAGTCCCTCGACTATTAGGTAAAATATACAAATAGTCCCTTGACTATATGATACTATTTTATTAA
* *
1527504 GTCCCTTGACTGTTAAAAATTACAAAATGCTCCTTTAAATATAGAATGACACTTTATAAAGTCCC
130 GTCCCTTGACTGTTAAAAATTACAAAATGATCCTTTAACTATAGAATGACACTTTATAAAGTCCC
* *
1527569 TTGGCTATTAAAAGTTA-AAAATGATCATCCCACTATTCGTTATGTTTCAGACCCGTCTTTTTCT
195 TTGGCTATTAAAAGTTATAAAATGGTCATCCCACTATTCATTATGTTTCAGACCCGTCTTTTTCT
1527633 ATTAAAAAAATCGGTCGTTGTCTAAGTTGGACGTTAACATAATGACTGAAATATGATAGTCGTTT
260 ATTAAAAAAATCGGTCGTTGTCTAAGTTGGACGTTAACATAATGACTGAAATATGATAGTCGTTT
*
1527698 AAGACTCTAGGATCAAATTTTATCATATCACATTTATCAGGTTAACGTTTAGCTCATAATATTGC
325 AAGACTCTAGGATCAAATTTTATCATATCACATTTATCAGGTTAACGTTTAGCTCATAATACTGC
* *
1527763 CAATTTTTAATGGAAAATGACGAGTTTACAACAT
390 CAATTTTTAACGGAAAATGACGAGTTTGCAACAT
*
1527797 ATGAATAGTCAGGTGACCATTTTATAACTTTTAATAGTCGAGAGACTTAATAAAACATCATTATA
1 ATGAATAGTCAGGTGACCATTTTGTAACTTTTAATAGTCGAG-GACTTAATAAAACATCATTATA
* * *
1527862 TAGTCCCTCGACTATTAGGTAAAATATACAAATAGTCCATTGACTACATTATACTATTTTATTAA
65 TAGTCCCTCGACTATTAGGTAAAATATACAAATAGTCCCTTGACTATATGATACTATTTTATTAA
* * *
1527927 GTCCCTTGACTGTTAAAATTTACAAAATGATCCTTTAACTATAAAATGACGCTTTATAAAGTCCC
130 GTCCCTTGACTGTTAAAAATTACAAAATGATCCTTTAACTATAGAATGACACTTTATAAAGTCCC
*
1527992 TTGGCTATTAAAAGTTATAAAATGGTCATCCCACTATTTATTATGTTTCAGACCCGTCTTTTTCT
195 TTGGCTATTAAAAGTTATAAAATGGTCATCCCACTATTCATTATGTTTCAGACCCGTCTTTTTCT
* *
1528057 ATTTAAAAAATCGGTCATTGTCTAAGTTGGACGTTAACATAATGACTGAAATATGATAGTCGTTT
260 ATTAAAAAAATCGGTCGTTGTCTAAGTTGGACGTTAACATAATGACTGAAATATGATAGTCGTTT
* * * * * *
1528122 AAGATTCTAGGATCATATTTTATCATATCACATTTAGCAGGTTAACGTTCAACTCATAATACTGT
325 AAGACTCTAGGATCAAATTTTATCATATCACATTTATCAGGTTAACGTTTAGCTCATAATACTGC
*
1528187 CAA-TTTTAACGGAAAAAT-ATGAGTTTGCAACAT
390 CAATTTTTAACGG-AAAATGACGAGTTTGCAACAT
1528220 ATGAATAGT
1 ATGAATAGT
1528229 TAGGGTGTCA
Statistics
Matches: 797, Mismatches: 49, Indels: 15
0.93 0.06 0.02
Matches are distributed among these distances:
420 1 0.00
421 256 0.32
422 140 0.18
423 172 0.22
424 228 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Consensus pattern (423 bp):
ATGAATAGTCAGGTGACCATTTTGTAACTTTTAATAGTCGAGGACTTAATAAAACATCATTATAT
AGTCCCTCGACTATTAGGTAAAATATACAAATAGTCCCTTGACTATATGATACTATTTTATTAAG
TCCCTTGACTGTTAAAAATTACAAAATGATCCTTTAACTATAGAATGACACTTTATAAAGTCCCT
TGGCTATTAAAAGTTATAAAATGGTCATCCCACTATTCATTATGTTTCAGACCCGTCTTTTTCTA
TTAAAAAAATCGGTCGTTGTCTAAGTTGGACGTTAACATAATGACTGAAATATGATAGTCGTTTA
AGACTCTAGGATCAAATTTTATCATATCACATTTATCAGGTTAACGTTTAGCTCATAATACTGCC
AATTTTTAACGGAAAATGACGAGTTTGCAACAT
Found at i:1528466 original size:22 final size:22
Alignment explanation
Indices: 1528440--1528491 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
1528430 TAAACGAACT
*
1528440 AACATAAACGAATGAGTTACTG
1 AACATAAACGAATGAATTACTG
1528462 AACATAAACGAATGAATTACTG
1 AACATAAACGAATGAATTACTG
*
1528484 AACGTAAA
1 AACATAAA
1528492 TGAACATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.21
Consensus pattern (22 bp):
AACATAAACGAATGAATTACTG
Found at i:1528863 original size:12 final size:13
Alignment explanation
Indices: 1528844--1528881 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1528834 TACCAATTTA
1528844 GTTAATCTATCAT
1 GTTAATCTATCAT
* *
1528857 G-TCATCTATCAC
1 GTTAATCTATCAT
1528869 GTTAATCTATCAT
1 GTTAATCTATCAT
1528882 TATGGGCTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (13 bp):
GTTAATCTATCAT
Found at i:1529558 original size:31 final size:31
Alignment explanation
Indices: 1529520--1529588 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1529510 ATTTACCAGG
* *
1529520 AAGAAAAAACTGAAACATCGACGGTCAATAA
1 AAGAAAAAACCGAAACATCGACGGTCAAGAA
* *
1529551 AAGAAAAACCCGAAACATCGACGGTCGAGAA
1 AAGAAAAAACCGAAACATCGACGGTCAAGAA
1529582 AAGAAAA
1 AAGAAAA
1529589 TACAACTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.55, C:0.17, G:0.19, T:0.09
Consensus pattern (31 bp):
AAGAAAAAACCGAAACATCGACGGTCAAGAA
Found at i:1531393 original size:29 final size:29
Alignment explanation
Indices: 1531351--1531409 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1531341 TTCTGTTAAA
*
1531351 GATATAGCAAATCACCATAGCATCCAAAT
1 GATATAACAAATCACCATAGCATCCAAAT
1531380 GATATAACAAATCACCATAGCATCCAAAT
1 GATATAACAAATCACCATAGCATCCAAAT
1531409 G
1 G
1531410 CAGTGCTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.46, C:0.24, G:0.10, T:0.20
Consensus pattern (29 bp):
GATATAACAAATCACCATAGCATCCAAAT
Found at i:1534404 original size:32 final size:34
Alignment explanation
Indices: 1534365--1534440 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
1534355 TGAAAAAAAT
1534365 AATATATAGAGGGGTATTATTGTAATTATTCCTA
1 AATATATAGAGGGGTATTATTGTAATTATTCCTA
* *
1534399 AATATATAGAGGGGTGTTATTGTAATTATTTCTA
1 AATATATAGAGGGGTATTATTGTAATTATTCCTA
1534433 AATATATA
1 AATATATA
1534441 AAGTAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.42
Consensus pattern (34 bp):
AATATATAGAGGGGTATTATTGTAATTATTCCTA
Found at i:1535163 original size:39 final size:39
Alignment explanation
Indices: 1535115--1535199 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
1535105 AAACGTACGA
*
1535115 TTTAGGGTTTATAATTTGAGGTTTAAGTAC-GATTTAGGG
1 TTTAAGGTTTATAATTTGAGGTTTAAGT-CTGATTTAGGG
1535154 TTTAAGGTTTATAATTTGAGGTTTAAGTCTGATTTAGGG
1 TTTAAGGTTTATAATTTGAGGTTTAAGTCTGATTTAGGG
1535193 TTTAAGG
1 TTTAAGG
1535200 GTTAGTGTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 1 0.02
39 43 0.98
ACGTcount: A:0.26, C:0.02, G:0.27, T:0.45
Consensus pattern (39 bp):
TTTAAGGTTTATAATTTGAGGTTTAAGTCTGATTTAGGG
Found at i:1559414 original size:174 final size:174
Alignment explanation
Indices: 1558922--1559618 Score: 921
Period size: 174 Copynumber: 4.0 Consensus size: 174
1558912 CTTTTGAATT
* * ** * * **
1558922 TTGCATGTTGTTTTTGCTTGTTCTGTTTGTTCTACCTGCGGGAAACTTTAGAAGAATTTATTAGA
1 TTGCATGTTGTTTTCGCTTGTTCCGTTTGCCCTACCTGCGGGAAACTTTAGTAGAATTTCTTCTA
* * * *
1558987 TATTGCGTTTTGTATTCGGCTTCTGTTGTT-GATATTTCGTCTAGCATATCTTCTGATATATTTT
66 TTTTGCGTTCTGTATTCGGCCTCTGTTGTTGGATATTTCGTCTTGCATATCTTCTGATATATTTT
1559051 CCACTA-TGCCATTTTAGTTCAAAGTTGTTTCGGTTCCATATGCA
131 CCACTATTG-CATTTTAGTTCAAAGTTGTTTCGGTTCCATATGCA
* * *
1559095 TTGCATGTTGTTTTCACTTGTTCCGTTTGTCCTACGGTCCTACCTGCTGGAAACTTTACTAGAAT
1 TTGCATGTTGTTTTCGCTTGTTCCGTTTG-----C---CCTACCTGCGGGAAACTTTAGTAGAAT
*
1559160 TTCTTCTATTTTGTGTTCTGTATTCGGCCTCTGTTGTTGGATATTTCGTCTTGCATATCTTCTGA
58 TTCTTCTATTTTGCGTTCTGTATTCGGCCTCTGTTGTTGGATATTTCGTCTTGCATATCTTCTGA
* * *
1559225 TATATTTTCCACTATTGCATTTTTGTTCAAAGTTGTTTTGGTTCCATATCCA
123 TATATTTTCCACTATTGCATTTTAGTTCAAAGTTGTTTCGGTTCCATATGCA
* *
1559277 TTGCATGCTGTTTTCGCTTGTTCCGTTTGCCCTACATGCGGGAAACTTTAGTAGAATTTCTTCTA
1 TTGCATGTTGTTTTCGCTTGTTCCGTTTGCCCTACCTGCGGGAAACTTTAGTAGAATTTCTTCTA
* *
1559342 TTTTGCGTTCTGGATTCGGCCTCTGCTGTTGGATATTTCGTCTTGCATATCTTCTGATATATTTT
66 TTTTGCGTTCTGTATTCGGCCTCTGTTGTTGGATATTTCGTCTTGCATATCTTCTGATATATTTT
* * * *
1559407 TCACTATTGCGTTTTACTTCCAAGTTGTTTCGGTTCCATATGCA
131 CCACTATTGCATTTTAGTTCAAAGTTGTTTCGGTTCCATATGCA
** * * * * *
1559451 TTTTATGTTGTTTTCGCTTGTTCCGTTTGTCCTACCTTCGGGATACTTTTGTAGAATTTCTTCTG
1 TTGCATGTTGTTTTCGCTTGTTCCGTTTGCCCTACCTGCGGGAAACTTTAGTAGAATTTCTTCTA
* * * * *
1559516 TTTTTCTTTCTGTATTCGGCCTCTATTGTTGGATATTTCATCTTGCATATCTTCTGAGATATTTT
66 TTTTGCGTTCTGTATTCGGCCTCTGTTGTTGGATATTTCGTCTTGCATATCTTCTGATATATTTT
* * *
1559581 TCACTATTGCATTTTAGTTCCAAGTTGTTTCAGTTCCA
131 CCACTATTGCATTTTAGTTCAAAGTTGTTTCGGTTCCA
1559619 CACGCAGTTT
Statistics
Matches: 461, Mismatches: 53, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
173 26 0.06
174 280 0.61
177 1 0.00
181 54 0.12
182 98 0.21
183 2 0.00
ACGTcount: A:0.16, C:0.19, G:0.17, T:0.48
Consensus pattern (174 bp):
TTGCATGTTGTTTTCGCTTGTTCCGTTTGCCCTACCTGCGGGAAACTTTAGTAGAATTTCTTCTA
TTTTGCGTTCTGTATTCGGCCTCTGTTGTTGGATATTTCGTCTTGCATATCTTCTGATATATTTT
CCACTATTGCATTTTAGTTCAAAGTTGTTTCGGTTCCATATGCA
Found at i:1562407 original size:17 final size:17
Alignment explanation
Indices: 1562380--1562418 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1562370 AATTTATAAT
1562380 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
1562396 TAATTATAAATAATATC
1 TAATTATAAATAATATC
1562413 TAATTA
1 TAATTA
1562419 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:1569539 original size:129 final size:128
Alignment explanation
Indices: 1569405--1569817 Score: 514
Period size: 129 Copynumber: 3.2 Consensus size: 128
1569395 TCGATATTAA
* * *
1569405 AAAAAATAGGGACCTCAATTATAAAGGTATAATTGAGTTTGAAAAAACTTAGGGGTCTCAATTAG
1 AAAAATTAGGGACCTCAATTATAAAGGTATAATTGAGATTGAAAAAACTTAGGGGCCTCAATTAG
* * *
1569470 AAAGTTAGAAAGTAAGATTAAAAAAAACTTAAGGGCCTCAATTTTAAAGTTAGAAAAGTGGAATT
66 AAAGTTAGAAAGTGAGATT-AAAAAAACTTAAAGGCCTCAATTATAAAGTTA-AAAAGTGGAATT
* * * *
1569535 AAAAATTAAGG-CCTCAATTATAAAGGCATAATTGAGATCGAAAAAACTTAGAGGCCTCAATTAG
1 AAAAATTAGGGACCTCAATTATAAAGGTATAATTGAGATTGAAAAAACTTAGGGGCCTCAATTAG
*
1569599 AAAGTTAGAAAGTGATATTAAAAAAACTTAAAGGCCTCAATTATAAAGTTAAAAAAGTAGG-ATT
66 AAAGTTAGAAAGTGAGATTAAAAAAACTTAAAGGCCTCAATTATAAAGTT-AAAAAGT-GGAATT
* * *
1569663 AAAAAATTA-GGAGCTTCAGTTATAAAGGTAGAGATTGAGATTGAAAAAACTTAGGGGCCTCAAT
1 -AAAAATTAGGGA-CCTCAATTATAAAGGTATA-ATTGAGATTGAAAAAACTTAGGGGCCTCAAT
* * * * * *
1569727 T-GAAAATGTAGAAAGTGAGATT-GAAAAATTTAAAAGCCTCAATTAAAAAGTTAAAAAG-AGAG
63 TAGAAAGT-TAGAAAGTGAGATTAAAAAAACTTAAAGGCCTCAATTATAAAGTTAAAAAGTGGA-
1569789 ATT
126 ATT
1569792 ATAAAATTAGGGACCTCAATTATAAA
1 A-AAAATTAGGGACCTCAATTATAAA
1569818 AGTAAAAAAG
Statistics
Matches: 246, Mismatches: 26, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
127 1 0.00
128 41 0.17
129 103 0.42
130 58 0.24
131 43 0.17
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.26
Consensus pattern (128 bp):
AAAAATTAGGGACCTCAATTATAAAGGTATAATTGAGATTGAAAAAACTTAGGGGCCTCAATTAG
AAAGTTAGAAAGTGAGATTAAAAAAACTTAAAGGCCTCAATTATAAAGTTAAAAAGTGGAATT
Found at i:1569637 original size:44 final size:43
Alignment explanation
Indices: 1569417--1569817 Score: 261
Period size: 43 Copynumber: 9.3 Consensus size: 43
1569407 AAAATAGGGA
* * * * **
1569417 CCTCAATTATAAAGGTA-TAATTGAGTTTGAAAAAACTTAGGGG
1 CCTCAATTATAAAGTTAGAAAGTGAGATT-AAAAAACTTAAAGG
* * * *
1569460 TCTCAATTAGAAAGTTAGAAAGTAAGATTAAAAAAAACTTAAGGG
1 CCTCAATTATAAAGTTAGAAAGTGAGATT--AAAAAACTTAAAGG
*
1569505 CCTCAATTTTAAAGTTAGAAAAGTG-GAATT-AAAAA-TT-AAGG
1 CCTCAATTATAAAGTTAG-AAAGTGAG-ATTAAAAAACTTAAAGG
** * * * *
1569546 CCTCAATTATAAAGGCA-TAATTGAGATCGAAAAAACTTAGAGG
1 CCTCAATTATAAAGTTAGAAAGTGAGAT-TAAAAAACTTAAAGG
* *
1569589 CCTCAATTAGAAAGTTAGAAAGTGATATTAAAAAAACTTAAAGG
1 CCTCAATTATAAAGTTAGAAAGTGAGATT-AAAAAACTTAAAGG
* *
1569633 CCTCAATTATAAAGTTAAAAAAGT-AGGATTAAAAAA-TT-AGGAG
1 CCTCAATTATAAAGTT-AGAAAGTGA-GATTAAAAAACTTAAAG-G
* * * * * **
1569676 CTTCAGTTATAAAGGTAGAGATTGAGATTGAAAAAACTTAGGGG
1 CCTCAATTATAAAGTTAGAAAGTGAGATT-AAAAAACTTAAAGG
* * *
1569720 CCTCAATTGA-AAA-TGTAGAAAGTGAGATTGAAAAATTTAAAAG
1 CCTCAATT-ATAAAGT-TAGAAAGTGAGATTAAAAAACTTAAAGG
* * * * *
1569763 CCTCAATTAAAAAGTTAAAAAGAGAGATTATAAAA-TT-AGGG
1 CCTCAATTATAAAGTTAGAAAGTGAGATTAAAAAACTTAAAGG
1569804 ACCTCAATTATAAA
1 -CCTCAATTATAAA
1569818 AGTAAAAAAG
Statistics
Matches: 278, Mismatches: 57, Indels: 47
0.73 0.15 0.12
Matches are distributed among these distances:
39 6 0.02
40 1 0.00
41 24 0.09
42 29 0.10
43 95 0.34
44 74 0.27
45 41 0.15
46 8 0.03
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (43 bp):
CCTCAATTATAAAGTTAGAAAGTGAGATTAAAAAACTTAAAGG
Found at i:1569819 original size:43 final size:43
Alignment explanation
Indices: 1569763--1569944 Score: 142
Period size: 43 Copynumber: 4.3 Consensus size: 43
1569753 AATTTAAAAG
* *
1569763 CCTCAATTA-AAAAGTTAAAAAGAGAGATT-ATAAAATTAGGGA
1 CCTCAATTATAAAAGTTAAAAAGA-AAATTAAAAAAATTAGGGA
* * *
1569805 CCTCAATTATAAAAGTAAAAAAGAAATTTAAAAAAATTAGAGA
1 CCTCAATTATAAAAGTTAAAAAGAAAATTAAAAAAATTAGGGA
* * * * * *
1569848 CTTCAATTAT-AAAGATAAAAAGTAAGATTGAATAATATTA-TGA
1 CCTCAATTATAAAAGTTAAAAAG-AAAATT-AAAAAAATTAGGGA
* * * * *
1569891 CATCAATTATAAAGGTAAAAAATAAAATT-AAAAAATTAAGGA
1 CCTCAATTATAAAAGTTAAAAAGAAAATTAAAAAAATTAGGGA
*
1569933 CCT-AACTATAAA
1 CCTCAATTATAAA
1569945 GATGAAAAAA
Statistics
Matches: 110, Mismatches: 24, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
41 15 0.14
42 26 0.24
43 53 0.48
44 16 0.15
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.26
Consensus pattern (43 bp):
CCTCAATTATAAAAGTTAAAAAGAAAATTAAAAAAATTAGGGA
Found at i:1569839 original size:85 final size:85
Alignment explanation
Indices: 1569750--1569953 Score: 202
Period size: 85 Copynumber: 2.4 Consensus size: 85
1569740 AGTGAGATTG
* *
1569750 AAAAATTTAAA-AGCCTCAATTAAAAAGTTAAAAAG-AGAGATT-ATAAAATTAGGGACCTCAAT
1 AAAAATTTAAAGA-CCTCAATTAAAAAGATAAAAAGTA-AGATTAATAAAATTA-GGACATCAAT
*
1569812 TATAAAAGTAAAAAAGAAATTTA
63 TATAAAAGTAAAAAAGAAAATTA
* * * * * *
1569835 AAAAAATTAGAGACTTCAATTATAAAGATAAAAAGTAAGATTGAATAATATTATGACATCAATTA
1 AAAAATTTAAAGACCTCAATTAAAAAGATAAAAAGTAAGATT-AATAAAATTAGGACATCAATTA
* *
1569900 TAAAGGTAAAAAATAAAATTA
65 TAAAAGTAAAAAAGAAAATTA
* * *
1569921 AAAAA-TTAAGGACCT-AACTATAAAGATGAAAAA
1 AAAAATTTAAAGACCTCAATTAAAAAGAT-AAAAA
1569954 ATTGAGGCTC
Statistics
Matches: 99, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
84 11 0.11
85 45 0.45
86 35 0.35
87 8 0.08
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.25
Consensus pattern (85 bp):
AAAAATTTAAAGACCTCAATTAAAAAGATAAAAAGTAAGATTAATAAAATTAGGACATCAATTAT
AAAAGTAAAAAAGAAAATTA
Found at i:1569910 original size:86 final size:85
Alignment explanation
Indices: 1569765--1569925 Score: 209
Period size: 86 Copynumber: 1.9 Consensus size: 85
1569755 TTTAAAAGCC
* *
1569765 TCAATTAAAAAGTTAAAAAGAGAGATTATAAAATTAGGGACCTCAATTATAAAAGTAAAAAAGAA
1 TCAATTAAAAAGATAAAAAGAGAGATTATAAAATTAGGGACATCAATTATAAAAGTAAAAAAGAA
*
1569830 ATTTAAAAAAATTAGAGACT
66 AATTAAAAAAATTAGAGACT
* * * *
1569850 TCAATTATAAAGATAAAAAGTA-AGATTGAATAATATTA-TGACATCAATTATAAAGGTAAAAAA
1 TCAATTAAAAAGATAAAAAG-AGAGATT--ATAAAATTAGGGACATCAATTATAAAAGTAAAAAA
*
1569913 TAAAATTAAAAAA
63 GAAAATTAAAAAA
1569926 TTAAGGACCT
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
85 23 0.35
86 34 0.52
87 8 0.12
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.26
Consensus pattern (85 bp):
TCAATTAAAAAGATAAAAAGAGAGATTATAAAATTAGGGACATCAATTATAAAAGTAAAAAAGAA
AATTAAAAAAATTAGAGACT
Found at i:1582924 original size:31 final size:33
Alignment explanation
Indices: 1582844--1582948 Score: 151
Period size: 33 Copynumber: 3.2 Consensus size: 33
1582834 ACCTAACCCT
* *
1582844 ACCCGATCCGACCCGTATATCAAACTTAAAAAA
1 ACCCGACCCGACCCGAATATCAAACTTAAAAAA
* **
1582877 ACCCGACCCGATCCGAATATCATGCTT-AAAAA
1 ACCCGACCCGACCCGAATATCAAACTTAAAAAA
1582909 ACCCGA-CCGACCCGAATATCAAACTTAAAAAA
1 ACCCGACCCGACCCGAATATCAAACTTAAAAAA
1582941 ACCCGACC
1 ACCCGACC
1582949 TGAATACCAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
31 17 0.27
32 22 0.35
33 23 0.37
ACGTcount: A:0.41, C:0.33, G:0.10, T:0.15
Consensus pattern (33 bp):
ACCCGACCCGACCCGAATATCAAACTTAAAAAA
Found at i:1585997 original size:28 final size:28
Alignment explanation
Indices: 1585941--1586006 Score: 69
Period size: 33 Copynumber: 2.2 Consensus size: 28
1585931 AGGTGACGAA
*
1585941 ACACATACACGTCATCATTTTAGACATG
1 ACACATACACGTCATCACTTTAGACATG
*
1585969 ACACATATCATGTCTATCACTTTGAATGACATG
1 ACACATA-CACGTC-ATCACTTT--A-GACATG
1586002 ACACA
1 ACACA
1586007 CGCCACGTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 7 0.23
29 5 0.16
30 7 0.23
32 1 0.03
33 11 0.35
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (28 bp):
ACACATACACGTCATCACTTTAGACATG
Found at i:1590721 original size:31 final size:31
Alignment explanation
Indices: 1590686--1590771 Score: 102
Period size: 33 Copynumber: 2.7 Consensus size: 31
1590676 AATAATAATA
1590686 AATTTGAT-AATCTTAATGATCATTTTATAAC
1 AATTTGATAAAT-TTAATGATCATTTTATAAC
* *
1590717 AATTTGATAAAATTTAACTAATCGTTTTATAAC
1 AATTTGAT-AAATTTAA-TGATCATTTTATAAC
* *
1590750 AACTCGATAAATTTAATGATCA
1 AATTTGATAAATTTAATGATCA
1590772 AAACAACTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
31 12 0.26
32 12 0.26
33 22 0.48
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
AATTTGATAAATTTAATGATCATTTTATAAC
Done.