Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007979.1 Hibiscus syriacus cultivar Beakdansim tig00110418_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: 2767453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 13
Found at i:1816755 original size:14 final size:13
Alignment explanation
Indices: 1816720--1816764 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1816710 TAAAATAATA
1816720 ATAATAATTAAAAT
1 ATAA-AATTAAAAT
**
1816734 ATTGAATTAAACAT
1 ATAAAATTAAA-AT
1816748 ATAAAATTAAAAT
1 ATAAAATTAAAAT
1816761 ATAA
1 ATAA
1816765 CTAAACAGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (13 bp):
ATAAAATTAAAAT
Found at i:1816769 original size:25 final size:28
Alignment explanation
Indices: 1816720--1816771 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
1816710 TAAAATAATA
*
1816720 ATAATAATTAAAATATTGAATTAAACAT
1 ATAATAATTAAAATATTGAACTAAACAT
1816748 ATAA-AATTAAAATA-T-AACTAAACA
1 ATAATAATTAAAATATTGAACTAAACA
1816772 GTGACTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 1 0.04
27 10 0.43
28 4 0.17
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (28 bp):
ATAATAATTAAAATATTGAACTAAACAT
Found at i:1816871 original size:32 final size:30
Alignment explanation
Indices: 1816778--1816872 Score: 88
Period size: 32 Copynumber: 3.1 Consensus size: 30
1816768 AACAGTGACT
1816778 AAAATAAATAAA--ATTAAAACTATAGTATTA
1 AAAATAAATAAAGTATTAAAA-T-TAGTATTA
* * *
1816808 AAATATAAA-AAAGTAATAAATTTTGTAATTA
1 AAA-ATAAATAAAGTATTAAAATTAGT-ATTA
1816839 AAAATAAATGAAAGTATTAAAATTAGTGATTA
1 AAAATAAAT-AAAGTATTAAAATTAGT-ATTA
1816871 AA
1 AA
1816873 CTATAACATA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
30 14 0.27
31 13 0.25
32 25 0.48
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.32
Consensus pattern (30 bp):
AAAATAAATAAAGTATTAAAATTAGTATTA
Found at i:1817086 original size:2 final size:2
Alignment explanation
Indices: 1817079--1817145 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
1817069 TTATTTTCCT
1817079 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
1817121 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1817146 TATGCTAGGG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1818149 original size:3 final size:3
Alignment explanation
Indices: 1818141--1818248 Score: 150
Period size: 3 Copynumber: 36.7 Consensus size: 3
1818131 TTTGGGCCTG
1818141 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1818189 TAA TAA T-A TAA TAG TAA TAA -AA TAA TAA TAG TAA TAAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
* *
1818232 TAA TAA AAA TAA AAA TA
1 TAA TAA TAA TAA TAA TA
1818249 TAAAACCCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
2 6 0.06
3 84 0.90
4 3 0.03
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1822200 original size:2 final size:2
Alignment explanation
Indices: 1822193--1822224 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1822183 GTATTCACCC
1822193 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
1822225 CCGTATATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1827373 original size:41 final size:42
Alignment explanation
Indices: 1827316--1827396 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
1827306 GGTCTTATGG
* * * *
1827316 ATGACCCGAAGGATTT-ATCTTCTTGCTCGAGAGACTCACAA
1 ATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTCACAA
1827357 ATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTCAC
1 ATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTCAC
1827397 TGATAGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 15 0.43
42 20 0.57
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (42 bp):
ATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTCACAA
Found at i:1829663 original size:14 final size:14
Alignment explanation
Indices: 1829644--1829697 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
1829634 TTAATAAGAA
1829644 AATGCAAAAATAAG
1 AATGCAAAAATAAG
*
1829658 AATGCAAATATAGATG
1 AATGCAAAAATA-A-G
1829674 CAAATGCAAAAATAAG
1 --AATGCAAAAATAAG
1829690 AATGCAAA
1 AATGCAAA
1829698 TGTAGATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 11 0.32
ACGTcount: A:0.59, C:0.09, G:0.15, T:0.17
Consensus pattern (14 bp):
AATGCAAAAATAAG
Found at i:1829674 original size:12 final size:14
Alignment explanation
Indices: 1829644--1829711 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 14
1829634 TTAATAAGAA
*
1829644 AATGCAAAAATAAG
1 AATGCAAATATAAG
1829658 AATGCAAATATAGATG
1 AATGCAAATATA-A-G
*
1829674 CAAATGCAAAAATAAG
1 --AATGCAAATATAAG
*
1829690 AATGCAAATGT-AG
1 AATGCAAATATAAG
1829703 -ATGCAAATA
1 AATGCAAATA
1829712 CAAATGCACG
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
12 8 0.18
13 2 0.04
14 20 0.44
15 1 0.02
16 2 0.04
17 1 0.02
18 11 0.24
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.19
Consensus pattern (14 bp):
AATGCAAATATAAG
Found at i:1829684 original size:32 final size:32
Alignment explanation
Indices: 1829643--1829715 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
1829633 ATTAATAAGA
1829643 AAATGCAAAAATAAGAATGCAAATATAGATGC
1 AAATGCAAAAATAAGAATGCAAATATAGATGC
*
1829675 AAATGCAAAAATAAGAATGCAAATGTAGATGC
1 AAATGCAAAAATAAGAATGCAAATATAGATGC
*
1829707 AAATACAAA
1 AAATGCAAA
1829716 TGCACGAGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.58, C:0.10, G:0.15, T:0.18
Consensus pattern (32 bp):
AAATGCAAAAATAAGAATGCAAATATAGATGC
Found at i:1832040 original size:2 final size:2
Alignment explanation
Indices: 1832035--1832062 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1832025 ACATTATACC
1832035 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
1832063 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1832067 original size:2 final size:2
Alignment explanation
Indices: 1832062--1832088 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1832052 TATATATATA
1832062 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1832089 TAATATACAA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1834283 original size:32 final size:32
Alignment explanation
Indices: 1834247--1834314 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
1834237 ATTAATAAGA
1834247 AAATGAAAAAATAAGAATGCAAATATAGATGC
1 AAATGAAAAAATAAGAATGCAAATATAGATGC
* *
1834279 AAATGCAAAAATAAGAATGCAAATGTAGATGC
1 AAATGAAAAAATAAGAATGCAAATATAGATGC
1834311 AAAT
1 AAAT
1834315 ACAAATGCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.57, C:0.07, G:0.16, T:0.19
Consensus pattern (32 bp):
AAATGAAAAAATAAGAATGCAAATATAGATGC
Found at i:1834299 original size:14 final size:14
Alignment explanation
Indices: 1834248--1834301 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1834238 TTAATAAGAA
*
1834248 AATGAAAAAATAAG
1 AATGCAAAAATAAG
*
1834262 AATGCAAATATAGATG
1 AATGCAAAAATA-A-G
1834278 CAAATGCAAAAATAAG
1 --AATGCAAAAATAAG
1834294 AATGCAAA
1 AATGCAAA
1834302 TGTAGATGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 18 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 11 0.33
ACGTcount: A:0.61, C:0.07, G:0.15, T:0.17
Consensus pattern (14 bp):
AATGCAAAAATAAG
Found at i:1839848 original size:18 final size:19
Alignment explanation
Indices: 1839810--1839858 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
1839800 TTTATTTTTA
*
1839810 TTTTATGTTTTTTACTGTT
1 TTTTATGTTTTTTACTATT
*
1839829 TTTTAT-TTTTTTAGTATT
1 TTTTATGTTTTTTACTATT
1839847 TTAATTATGTTT
1 TT--TTATGTTT
1839859 ATTAATTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 12 0.48
19 6 0.24
20 4 0.16
21 3 0.12
ACGTcount: A:0.16, C:0.02, G:0.08, T:0.73
Consensus pattern (19 bp):
TTTTATGTTTTTTACTATT
Found at i:1841709 original size:22 final size:22
Alignment explanation
Indices: 1841684--1841740 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
1841674 CCTAAACTTA
*
1841684 TTTCAATTCATATATGTATGGT
1 TTTCTATTCATATATGTATGGT
1841706 TTTCTATTCATATATGTATGGT
1 TTTCTATTCATATATGTATGGT
1841728 TTTCTATTCATAT
1 TTTCTATTCATAT
1841741 TATTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.54
Consensus pattern (22 bp):
TTTCTATTCATATATGTATGGT
Found at i:1847284 original size:18 final size:18
Alignment explanation
Indices: 1847244--1847284 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1847234 TTTTTGCGTT
*
1847244 CACCATTTCCTCGACCTC
1 CACCATTTCCTCGACCAC
1847262 CACCATTTCCTCGACCAC
1 CACCATTTCCTCGACCAC
*
1847280 GACCA
1 CACCA
1847285 CGTCCTCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.49, G:0.07, T:0.22
Consensus pattern (18 bp):
CACCATTTCCTCGACCAC
Found at i:1854130 original size:34 final size:34
Alignment explanation
Indices: 1854067--1854137 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 34
1854057 TAAAATCTAA
1854067 TTTTAAGTTTTACATTTCGATATTTAATTTTATTT
1 TTTTAAGTTTTACATTTCGATATTTAATTTT-TTT
* *
1854102 TTTTGAGTTTTATATTTACG-TA-TTAATTTTTTT
1 TTTTAAGTTTTACATTT-CGATATTTAATTTTTTT
1854135 TTT
1 TTT
1854138 CAAAAGTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 6 0.18
34 8 0.24
35 17 0.52
36 2 0.06
ACGTcount: A:0.23, C:0.04, G:0.07, T:0.66
Consensus pattern (34 bp):
TTTTAAGTTTTACATTTCGATATTTAATTTTTTT
Found at i:1855697 original size:18 final size:20
Alignment explanation
Indices: 1855671--1855717 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1855661 TTTTTATTTA
1855671 TTAATTTA-TTTTAAAAATT
1 TTAATTTATTTTTAAAAATT
1855690 TTAA-TTATTTTTAAAAA-T
1 TTAATTTATTTTTAAAAATT
1855708 TT-ATTTATTT
1 TTAATTTATTT
1855718 CTTTAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 1 0.04
18 12 0.46
19 13 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAATTTATTTTTAAAAATT
Found at i:1855746 original size:4 final size:4
Alignment explanation
Indices: 1855737--1855826 Score: 60
Period size: 4 Copynumber: 22.8 Consensus size: 4
1855727 TTTTGTTCGG
* * * **
1855737 TTTA TTTA TTTCAA ATTA TTTA TTCA TTTC TTT- TGAA TTTA TTTA TTTA
1 TTTA TTTA TTT--A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * **
1855786 TATA TTTA TTTA ATTA TTTA -GAA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1855827 GTTTGTTTCG
Statistics
Matches: 64, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
3 5 0.08
4 56 0.88
6 3 0.05
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:1857432 original size:23 final size:23
Alignment explanation
Indices: 1857379--1857445 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
1857369 GTGCCATATA
*
1857379 TTTGTCCCAAAGAACCACGT-AGT
1 TTTGTCCC-AAGAACCACATAAGT
* *
1857402 TTTATCCCAACGGACCACATAAG-
1 TTTGTCCCAA-GAACCACATAAGT
1857425 TTTGTCCCGAAGAACCACATA
1 TTTGTCCC-AAGAACCACATA
1857446 TAACCCTCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
22 2 0.06
23 30 0.83
24 4 0.11
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (23 bp):
TTTGTCCCAAGAACCACATAAGT
Found at i:1864025 original size:20 final size:20
Alignment explanation
Indices: 1863990--1864030 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1863980 AGACCAGTCA
* *
1863990 ACCTGTTGACCTGACCGTTG
1 ACCTGTTGACCCGACCATTG
*
1864010 ACCTGTTGTCCCGACCATTG
1 ACCTGTTGACCCGACCATTG
1864030 A
1 A
1864031 ACGTATGCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.32, G:0.22, T:0.29
Consensus pattern (20 bp):
ACCTGTTGACCCGACCATTG
Found at i:1864796 original size:31 final size:31
Alignment explanation
Indices: 1864761--1864857 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 31
1864751 ATGCATGTTC
1864761 TGATCTTCCATATTGGACTTCTAGATCTTAG
1 TGATCTTCCATATTGGACTTCTAGATCTTAG
* * * ** *
1864792 TGATCTACGATA-AGTCCTTATAGATTCTT-G
1 TGATCTTCCATATTGGACTTCTAGA-TCTTAG
* *
1864822 T-ATCTTTCATATTGGACTCCTAGATCTTAG
1 TGATCTTCCATATTGGACTTCTAGATCTTAG
1864852 TGATCT
1 TGATCT
1864858 ACGGTAAGTC
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
29 11 0.23
30 19 0.40
31 18 0.38
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (31 bp):
TGATCTTCCATATTGGACTTCTAGATCTTAG
Found at i:1864837 original size:60 final size:60
Alignment explanation
Indices: 1864763--1864996 Score: 281
Period size: 60 Copynumber: 3.9 Consensus size: 60
1864753 GCATGTTCTG
* * * * *
1864763 ATCTTCCATATTGGACTTCTAGATCTTAGTGATCTACGATAAGTCCTTATAGATTCTTGT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGATCTACGGTAAGTCCTTATGGATACATGT
* *
1864823 ATCTTTCATATTGGACTCCTAGATCTTAGTGATCTACGGTAAGTCCTTATGGATGCATGT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGATCTACGGTAAGTCCTTATGGATACATGT
* * * ** *
1864883 ATCTTCCATACTAGG-CTCCTAGATCTTAGTGGTCTATGGTAAGTTATTATGGATACCTGT
1 ATCTTCCATA-TTGGACTCCTAGATCTTAGTGATCTACGGTAAGTCCTTATGGATACATGT
* * * * **
1864943 ATTTTCTATAATGGACTCCTAGATCTTAATGATCTATTGTAAGTCCTTATGGAT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGATCTACGGTAAGTCCTTATGGAT
1864997 GTCTGTTTTG
Statistics
Matches: 149, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
59 2 0.01
60 144 0.97
61 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (60 bp):
ATCTTCCATATTGGACTCCTAGATCTTAGTGATCTACGGTAAGTCCTTATGGATACATGT
Found at i:1864976 original size:120 final size:120
Alignment explanation
Indices: 1864763--1864997 Score: 312
Period size: 120 Copynumber: 2.0 Consensus size: 120
1864753 GCATGTTCTG
* * * * *
1864763 ATCTTCCATATTGGACTTCTAGATCTTAGTGATCTACGATAAGTCCTTATAGATTCTTGTATCTT
1 ATCTTCCATATAGGACTCCTAGATCTTAGTGATCTACGATAAGTCATTATAGATACCTGTATCTT
* *
1864828 TCATATTGGACTCCTAGATCTTAGTGATCTACGGTAAGTCCTTATGGATGCATGT
66 TCATAATGGACTCCTAGATCTTAATGATCTACGGTAAGTCCTTATGGATGCATGT
* * * * *
1864883 ATCTTCCATACTAGG-CTCCTAGATCTTAGTGGTCTATGGTAAGTTATTATGGATACCTGTAT-T
1 ATCTTCCATA-TAGGACTCCTAGATCTTAGTGATCTACGATAAGTCATTATAGATACCTGTATCT
**
1864946 TTCTATAATGGACTCCTAGATCTTAATGATCTATTGTAAGTCCTTATGGATG
65 TTC-ATAATGGACTCCTAGATCTTAATGATCTACGGTAAGTCCTTATGGATG
1864998 TCTGTTTTGG
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
119 4 0.04
120 92 0.93
121 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (120 bp):
ATCTTCCATATAGGACTCCTAGATCTTAGTGATCTACGATAAGTCATTATAGATACCTGTATCTT
TCATAATGGACTCCTAGATCTTAATGATCTACGGTAAGTCCTTATGGATGCATGT
Found at i:1867368 original size:18 final size:18
Alignment explanation
Indices: 1867344--1867392 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1867334 AATATTGCTT
*
1867344 CCACGTCAGGAATCTCTT
1 CCACGTCAGGAATCTCTA
* *
1867362 TCACGTCAGAAATCTCTA
1 CCACGTCAGGAATCTCTA
*
1867380 CCACGTCAAGAAT
1 CCACGTCAGGAAT
1867393 TCCTAAGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (18 bp):
CCACGTCAGGAATCTCTA
Found at i:1874981 original size:20 final size:20
Alignment explanation
Indices: 1874937--1875009 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
1874927 ATGACCAACA
* * *
1874937 AAATCACAATGCGAA-ATAA
1 AAATCGCAACGCGAACATAT
1874956 AAATCGCAACGCGAACATAT
1 AAATCGCAACGCGAACATAT
1874976 AAATCGCAACGCGAACATAT
1 AAATCGCAACGCGAACATAT
1874996 AAATCGCAACGCGA
1 AAATCGCAACGCGA
1875010 TTCTGACTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
19 13 0.26
20 37 0.74
ACGTcount: A:0.48, C:0.23, G:0.15, T:0.14
Consensus pattern (20 bp):
AAATCGCAACGCGAACATAT
Found at i:1875062 original size:20 final size:21
Alignment explanation
Indices: 1875018--1875069 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1875008 GATTCTGACT
*
1875018 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGTAAA
1875039 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
*
1875059 ATCGTAACGCG
1 ATCGCAACGCG
1875070 ATTTTTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGTATCCGTAAA
Found at i:1875652 original size:20 final size:20
Alignment explanation
Indices: 1875627--1875723 Score: 110
Period size: 20 Copynumber: 4.8 Consensus size: 20
1875617 TTCTAAACTT
*
1875627 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
1875647 AAAATCGCAACACGAAAAT-
1 AAAATCGCAACACGAAAATG
*
1875666 AACTATCGCAACGAGCG-AAATG
1 AA-AATCGCAAC-A-CGAAAATG
*
1875688 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
1875707 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
1875724 CCAAAATCGC
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
19 23 0.34
20 28 0.41
21 13 0.19
22 4 0.06
ACGTcount: A:0.51, C:0.21, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1875704 original size:19 final size:19
Alignment explanation
Indices: 1875627--1875734 Score: 110
Period size: 19 Copynumber: 5.5 Consensus size: 19
1875617 TTCTAAACTT
**
1875627 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCG-AAATG
*
1875647 AAAATCGCAACACGAAAAT-
1 AAAATCGCAACGCG-AAATG
*
1875666 AACTATCGCAACGAGCGAAATG
1 AA-AATCGCAAC--GCGAAATG
1875688 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
**
1875707 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
1875726 AAAATCGCA
1 AAAATCGCA
1875735 TTGCGATTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
19 36 0.46
20 26 0.33
21 12 0.15
22 4 0.05
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1875783 original size:33 final size:33
Alignment explanation
Indices: 1875738--1875807 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
1875728 AATCGCATTG
*
1875738 CGATTTTTATTTCGCGTTGCGATTCTCTCGTTC
1 CGATTTTAATTTCGCGTTGCGATTCTCTCGTTC
* *
1875771 CGATTTTAATTTCGCGTTGCGATTCTTTCGTTG
1 CGATTTTAATTTCGCGTTGCGATTCTCTCGTTC
1875804 CGAT
1 CGAT
1875808 AGTCATTTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.47
Consensus pattern (33 bp):
CGATTTTAATTTCGCGTTGCGATTCTCTCGTTC
Found at i:1875816 original size:33 final size:33
Alignment explanation
Indices: 1875746--1875868 Score: 111
Period size: 33 Copynumber: 3.5 Consensus size: 33
1875736 TGCGATTTTT
* * ** *
1875746 ATTTCGCGTTGCGATTCTCTCGTTCCGATTTTA
1 ATTTCGCGTTGCGATTCTTTCGTTGCGATAGTC
1875779 ATTTCGCGTTGCGATTCTTTCGTTGCGATAGTC
1 ATTTCGCGTTGCGATTCTTTCGTTGCGATAGTC
*
1875812 ATTTCCGCGTTACGATAGTCATTCTCTCGTTGCGATAGTC
1 ATTT-CGCGTTGCGAT--TC--T-T-TCGTTGCGATAGTC
*
1875852 ATTCTCTCGTTGCGATT
1 ATT-TCGCGTTGCGATT
1875869 TTCATTTCAA
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
33 32 0.43
34 10 0.14
36 2 0.03
38 2 0.03
39 1 0.01
40 26 0.35
41 1 0.01
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTTTCGTTGCGATAGTC
Found at i:1875827 original size:20 final size:21
Alignment explanation
Indices: 1875799--1875876 Score: 90
Period size: 20 Copynumber: 3.9 Consensus size: 21
1875789 GCGATTCTTT
1875799 CGTTGCGATAGTCATTTC-CG
1 CGTTGCGATAGTCATTTCTCG
* *
1875819 CGTTACGATAGTCA-TTCTCT
1 CGTTGCGATAGTCATTTCTCG
*
1875839 CGTTGCGATAGTCA-TTCTCT
1 CGTTGCGATAGTCATTTCTCG
**
1875859 CGTTGCGATTTTCATTTC
1 CGTTGCGATAGTCATTTC
1875877 AACCAAAAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
19 3 0.06
20 45 0.88
21 3 0.06
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.41
Consensus pattern (21 bp):
CGTTGCGATAGTCATTTCTCG
Found at i:1877732 original size:94 final size:94
Alignment explanation
Indices: 1877571--1877893 Score: 549
Period size: 94 Copynumber: 3.4 Consensus size: 94
1877561 TAGATTGCCT
* *
1877571 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
1877636 ATTTGTCTTTTTTTTTGTCCTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
1877665 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1877730 ATTTGTCTTTGTTTTGTCTTTTAGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1877759 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1877824 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
1877853 AGTAAATTTGTTTGATTGCTGCCAATTCTGCTAAACTGTGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGT
1877894 TGTCATTGAA
Statistics
Matches: 219, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
93 17 0.08
94 202 0.92
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1878335 original size:21 final size:20
Alignment explanation
Indices: 1878240--1878347 Score: 67
Period size: 21 Copynumber: 5.2 Consensus size: 20
1878230 GCCCGACTCA
1878240 CCTGTCATCGTTCAAGAGG-
1 CCTGTCATCGTTCAAGAGGC
**
1878259 CCTCCCCTATCGTTCAAGAGGCC
1 CCT-GTC-ATCGTTCAAGAGG-C
* ** *
1878282 CCTATCATCCCTCAAGAGTC
1 CCTGTCATCGTTCAAGAGGC
*
1878302 CC-GTCCCACCGTTCAAGAGGC
1 CCTGT--CATCGTTCAAGAGGC
*
1878323 CACTGTCATCGTTGAAGAGGTC
1 C-CTGTCATCGTTCAAGAGG-C
1878345 CCT
1 CCT
1878348 CCCAACATTC
Statistics
Matches: 66, Mismatches: 14, Indels: 16
0.69 0.15 0.17
Matches are distributed among these distances:
19 4 0.06
20 4 0.06
21 49 0.74
22 4 0.06
23 5 0.08
ACGTcount: A:0.20, C:0.36, G:0.20, T:0.23
Consensus pattern (20 bp):
CCTGTCATCGTTCAAGAGGC
Found at i:1878341 original size:42 final size:42
Alignment explanation
Indices: 1878269--1878351 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
1878259 CCTCCCCTAT
*
1878269 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCGTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCC-TCCCAC
* ** *
1878311 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
1878352 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 30 0.86
43 5 0.14
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:1879724 original size:14 final size:14
Alignment explanation
Indices: 1879705--1879740 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1879695 ATTGTTTAAT
1879705 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1879719 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1879733 TGATTTGT
1 TGATTTGT
1879741 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1879905 original size:19 final size:19
Alignment explanation
Indices: 1879875--1880027 Score: 102
Period size: 19 Copynumber: 8.8 Consensus size: 19
1879865 ACAACGAGAG
*
1879875 AATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1879894 AATTGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1879913 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
* *
1879927 AATCGCAATGTGAAATGAC
1 AATCGCAATGCGAAATGAA
* *
1879946 TATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1879960 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
*
1879979 AATCGCAAT--G-AGTG--
1 AATCGCAATGCGAAATGAA
1879993 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
1880013 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
1880028 CTAATTTCAC
Statistics
Matches: 102, Mismatches: 16, Indels: 32
0.68 0.11 0.21
Matches are distributed among these distances:
14 28 0.27
15 2 0.02
16 6 0.06
17 4 0.04
18 5 0.05
19 46 0.45
20 11 0.11
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1879942 original size:33 final size:33
Alignment explanation
Indices: 1879898--1880022 Score: 187
Period size: 33 Copynumber: 3.8 Consensus size: 33
1879888 AATGAAAATT
1879898 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
* **
1879931 GCAATGTGAAATGACTATCGCAACGAGAGAATC
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
* * *
1879964 GCAATGCGAAATAAAAATCGCAATGAGTGAATC
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
1879997 GCAATGCGAAAATGAAAATCGCAACG
1 GCAATGCG-AAATGAAAATCGCAACG
1880023 CGAAACTAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 65 0.81
34 15 0.19
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (33 bp):
GCAATGCGAAATGAAAATCGCAACGAGAGAATC
Found at i:1880062 original size:20 final size:18
Alignment explanation
Indices: 1880039--1880119 Score: 71
Period size: 20 Copynumber: 4.4 Consensus size: 18
1880029 TAATTTCACG
1880039 TTGCGATTTTCATTTTCGAA
1 TTGCGATTTTCA-TTTCG-A
*
1880059 TTGCGA--TTCA-CTCG-
1 TTGCGATTTTCATTTCGA
1880073 TTGCGATTTTCATTTTCGTA
1 TTGCGATTTTCA-TTTCG-A
*
1880093 TTACGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCG-A
1880112 TTGCGATT
1 TTGCGATT
1880120 CTCTCGTTGC
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
14 6 0.12
16 7 0.14
18 7 0.14
19 13 0.26
20 17 0.34
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.48
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGA
Found at i:1880847 original size:20 final size:20
Alignment explanation
Indices: 1880785--1880990 Score: 215
Period size: 20 Copynumber: 10.4 Consensus size: 20
1880775 GATGGAATGA
**
1880785 GTTGCGATTTA-GG-TAATC
1 GTTGCGATTTACGGATACGC
**
1880803 GTTGCGATTTAC-G-TAATC
1 GTTGCGATTTACGGATACGC
1880821 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * * *
1880841 ATTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGC
*
1880861 GTTGCGATTTACAGATACGC
1 GTTGCGATTTACGGATACGC
* * *
1880881 GTTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGC
1880901 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1880921 GTTGCGATTTTACGTAT-TGTC
1 GTTGCGA-TTTACGGATACG-C
1880942 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1880962 GTTGCGATTTTACGGATACTC
1 GTTGCGA-TTTACGGATACGC
1880983 GTTGCGAT
1 GTTGCGAT
1880991 AGTCAGAATC
Statistics
Matches: 158, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
18 29 0.18
19 1 0.01
20 92 0.58
21 36 0.23
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1880945 original size:41 final size:40
Alignment explanation
Indices: 1880785--1881051 Score: 294
Period size: 40 Copynumber: 6.7 Consensus size: 40
1880775 GATGGAATGA
** *
1880785 GTTGCGATTTA-GG-TAATCGTTGCGATTTACGTA--ATC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTC
*
1880821 GTTGCGATTTACGGATACGCATTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTC
*
1880861 GTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTC
*
1880901 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTC
1 GTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCTC
* *
1880942 GTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTC
1 GTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCTC
* * ** * *
1880983 GTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTCGC
1 GTTGCGAT-TTACGGATA-CGCGTTGCGATTTACGTATTCTC
* ** *
1881023 GTTGCGATTTTCATATTCGCGTTGCGATT
1 GTTGCGATTTACGGATACGCGTTGCGATT
1881052 CTGGAAAATC
Statistics
Matches: 200, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
36 11 0.05
37 2 0.01
38 17 0.09
39 1 0.00
40 97 0.49
41 71 0.35
42 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (40 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTC
Found at i:1881022 original size:20 final size:20
Alignment explanation
Indices: 1880999--1881051 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1880989 ATAGTCAGAA
*
1880999 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
1881019 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
1881039 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1881052 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:1881112 original size:42 final size:42
Alignment explanation
Indices: 1881019--1881112 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 42
1881009 ATTTATATGT
* *
1881019 TCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
** * *
1881060 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTCTGCAAAA
1881102 TCGCGTTGCGA
1 TCGCGTTGCGA
1881113 TTCTGGGAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 8 0.19
42 31 0.74
43 3 0.07
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
Found at i:1887101 original size:14 final size:14
Alignment explanation
Indices: 1887076--1887104 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1887066 GTGTTTAGTC
1887076 TTTTGTATTTAAGA
1 TTTTGTATTTAAGA
1887090 TTTTGTATTTAAGA
1 TTTTGTATTTAAGA
1887104 T
1 T
1887105 ATATCTAGAT
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:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (14 bp):
TTTTGTATTTAAGA
Found at i:1887124 original size:16 final size:15
Alignment explanation
Indices: 1887103--1887138 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1887093 TGTATTTAAG
1887103 ATATATCTAGATAAAA
1 ATATATCTAGA-AAAA
*
1887119 ATATATCTATAAAAA
1 ATATATCTAGAAAAA
1887134 ATATA
1 ATATA
1887139 GACAAGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (15 bp):
ATATATCTAGAAAAA
Found at i:1891893 original size:12 final size:12
Alignment explanation
Indices: 1891876--1891900 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1891866 CTCATTTTTC
1891876 TTTAATTTCATT
1 TTTAATTTCATT
1891888 TTTAATTTCATT
1 TTTAATTTCATT
1891900 T
1 T
1891901 GATTTGAAAA
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAATTTCATT
Found at i:1894821 original size:18 final size:19
Alignment explanation
Indices: 1894798--1894850 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1894788 ATAATGCTAA
*
1894798 TTATAATAT-TAGTATATT
1 TTATAATATATAATATATT
*
1894816 TTATAACTTTATAATATATT
1 TTATAA-TATATAATATATT
1894836 TT-TAATATATTAATA
1 TTATAATATA-TAATA
1894851 GGACTAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 9 0.31
19 10 0.34
20 10 0.34
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TTATAATATATAATATATT
Found at i:1898064 original size:20 final size:20
Alignment explanation
Indices: 1898039--1898082 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1898029 AGTTAGGAGA
*
1898039 AGCTGCTTAGATGTATTTGT
1 AGCTGCTTAGATGTATATGT
1898059 AGCTGCTTAGATGTATATGT
1 AGCTGCTTAGATGTATATGT
1898079 AGCT
1 AGCT
1898083 TGTACTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.41
Consensus pattern (20 bp):
AGCTGCTTAGATGTATATGT
Found at i:1907347 original size:19 final size:19
Alignment explanation
Indices: 1907323--1907359 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1907313 AAATTCACAC
1907323 AGGGTTTAATTATACGCGT
1 AGGGTTTAATTATACGCGT
*
1907342 AGGGTTTAATTGTACGCG
1 AGGGTTTAATTATACGCG
1907360 CAGTCACTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.30, T:0.35
Consensus pattern (19 bp):
AGGGTTTAATTATACGCGT
Found at i:1907667 original size:18 final size:19
Alignment explanation
Indices: 1907644--1907696 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1907634 ATAATGCTAA
*
1907644 TTATAATAT-TAGTATATT
1 TTATAATATATAATATATT
*
1907662 TTATAACTTTATAATATATT
1 TTATAA-TATATAATATATT
1907682 TT-TAATATATTAATA
1 TTATAATATA-TAATA
1907697 GGACTAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 9 0.31
19 10 0.34
20 10 0.34
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TTATAATATATAATATATT
Found at i:1908375 original size:37 final size:37
Alignment explanation
Indices: 1908302--1908382 Score: 128
Period size: 39 Copynumber: 2.2 Consensus size: 37
1908292 AATCATACCT
1908302 AAAATTTAGTTTTTGTTTCATTTTAGTACCTGTCGTTA
1 AAAATTTAGTTTTTGTTTCATTTTAGTACC-GTCGTTA
*
1908340 AAAATATTAGTTTTTGTTTCATTTTAGTACC-TCGTTC
1 AAAAT-TTAGTTTTTGTTTCATTTTAGTACCGTCGTTA
1908377 AAAATT
1 AAAATT
1908383 AAATGTTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 1 0.02
37 10 0.24
38 5 0.12
39 25 0.61
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (37 bp):
AAAATTTAGTTTTTGTTTCATTTTAGTACCGTCGTTA
Found at i:1909963 original size:18 final size:18
Alignment explanation
Indices: 1909940--1909982 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1909930 TTGAAAAGTT
1909940 GATATCAAATGTTAGAGA
1 GATATCAAATGTTAGAGA
1909958 GATATCAAATGTTAGAGA
1 GATATCAAATGTTAGAGA
1909976 GATATCA
1 GATATCA
1909983 TTTGCATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (18 bp):
GATATCAAATGTTAGAGA
Found at i:1910606 original size:19 final size:20
Alignment explanation
Indices: 1910571--1910608 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1910561 CTCTAAATCC
1910571 GTTTTCAAAATTTCATTTTG
1 GTTTTCAAAATTTCATTTTG
1910591 GTTTTCAAAA-TTCATTTT
1 GTTTTCAAAATTTCATTTT
1910609 ACCTTTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (20 bp):
GTTTTCAAAATTTCATTTTG
Found at i:1910615 original size:19 final size:20
Alignment explanation
Indices: 1910573--1910618 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1910563 CTAAATCCGT
***
1910573 TTTCAAAATTTCATTTTGGT
1 TTTCAAAATTTCATTTTACC
1910593 TTTCAAAA-TTCATTTTACC
1 TTTCAAAATTTCATTTTACC
1910612 TTTCAAA
1 TTTCAAA
1910619 CGAAAATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.50
Consensus pattern (20 bp):
TTTCAAAATTTCATTTTACC
Found at i:1912030 original size:19 final size:19
Alignment explanation
Indices: 1912006--1912078 Score: 110
Period size: 19 Copynumber: 3.8 Consensus size: 19
1911996 GAGCCTTATG
1912006 GTAGTATCGATACTACCTA
1 GTAGTATCGATACTACCTA
1912025 GTAGTATCGATACTACCTA
1 GTAGTATCGATACTACCTA
* *
1912044 GTGGTATCGGTACTACCTA
1 GTAGTATCGATACTACCTA
* *
1912063 GTGGTATCGGTACTAC
1 GTAGTATCGATACTAC
1912079 TCTTACTTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (19 bp):
GTAGTATCGATACTACCTA
Found at i:1917168 original size:9 final size:9
Alignment explanation
Indices: 1917156--1917202 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
1917146 CATTCGGAGC
1917156 ATGAGAAGT
1 ATGAGAAGT
*
1917165 ATGAGGAGT
1 ATGAGAAGT
1917174 ATGAGAAGT
1 ATGAGAAGT
** *
1917183 ATTCGGAGT
1 ATGAGAAGT
1917192 ATGAGAAGT
1 ATGAGAAGT
1917201 AT
1 AT
1917203 TCGGAGCATG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.38, C:0.02, G:0.34, T:0.26
Consensus pattern (9 bp):
ATGAGAAGT
Found at i:1917172 original size:18 final size:18
Alignment explanation
Indices: 1917134--1917214 Score: 101
Period size: 18 Copynumber: 4.5 Consensus size: 18
1917124 GCTGAAGAAT
*
1917134 GAGCATGA-AAGGCATTCG
1 GAGCATGAGAA-GTATTCG
**
1917152 GAGCATGAGAAGTATGAG
1 GAGCATGAGAAGTATTCG
*
1917170 GAGTATGAGAAGTATTCG
1 GAGCATGAGAAGTATTCG
*
1917188 GAGTATGAGAAGTATTCG
1 GAGCATGAGAAGTATTCG
1917206 GAGCATGAG
1 GAGCATGAG
1917215 GAGCTTGGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
18 53 0.96
19 2 0.04
ACGTcount: A:0.35, C:0.09, G:0.36, T:0.21
Consensus pattern (18 bp):
GAGCATGAGAAGTATTCG
Found at i:1925012 original size:2 final size:2
Alignment explanation
Indices: 1925007--1925064 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1924997 GCGAATTACC
1925007 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
1925049 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
1925065 AACCATCGAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1928915 original size:16 final size:17
Alignment explanation
Indices: 1928879--1928923 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
1928869 TTTATGAGGA
1928879 AATTGGAATCTGTGAAGG
1 AATTGGAATCTGT-AAGG
*
1928897 AATTGAAATCTGT-AGG
1 AATTGGAATCTGTAAGG
1928913 AATTGGAATCT
1 AATTGGAATCT
1928924 AAATCTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 13 0.52
18 12 0.48
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.31
Consensus pattern (17 bp):
AATTGGAATCTGTAAGG
Found at i:1930928 original size:14 final size:14
Alignment explanation
Indices: 1930872--1930945 Score: 60
Period size: 14 Copynumber: 5.0 Consensus size: 14
1930862 AAACAATCTA
1930872 ATTATATATATATAT
1 ATTATATATATA-AT
* *
1930887 ATTAAATATTTTAAAAT
1 ATT--ATA-TATATAAT
1930904 AATTATA-ATATAAT
1 -ATTATATATATAAT
*
1930918 ATTATTTATATAAT
1 ATTATATATATAAT
*
1930932 ATTGTATATATAAT
1 ATTATATATATAAT
1930946 CTCATTAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
13 5 0.11
14 24 0.51
15 3 0.06
16 3 0.06
17 5 0.11
18 7 0.15
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (14 bp):
ATTATATATATAAT
Found at i:1932795 original size:137 final size:138
Alignment explanation
Indices: 1932506--1932852 Score: 337
Period size: 137 Copynumber: 2.5 Consensus size: 138
1932496 AGTAATTTAG
* * * * ** * * *
1932506 TGAATCAAATAGTTAAAATGGAACCTTGGGCATAAAAG-AAGGACCAAACTAAAAAAATCTCCAA
1 TGAATCAAAGAATTAAGATTGAACCTCAGGCATAAAAGCAAGGACCAAA-TTAAAAATTCTCCTA
* * * * * * *
1932570 AAGTAAAGGATTATAGTGAAATTGAACCCTAGATGAAGGCTCTAATATTAAACTTAATCAATTTT
65 AATTAAAAGACTATAGTGAAATTAAACCCTAGATGAAGGCTCTAAAATTAAACCTAATCAATTAT
* *
1932635 GCAATTTAT
130 ACAAATTAT
* * *
1932644 TGAATCAAATAATT-AG-TGTGGAACCTCAGTCATAAAAGCAAGAACCAAATTAAAAATTCTCCT
1 TGAATCAAAGAATTAAGAT-T-GAACCTCAGGCATAAAAGCAAGGACCAAATTAAAAATTCTCCT
* * *
1932707 AAATTAAAAGACTA-AGGTG-AATTAAACCTTAGGTGAATGCTCTAAAATTAAACCTAATCAATT
64 AAATTAAAAGACTATA-GTGAAATTAAACCCTAGATGAAGGCTCTAAAATTAAACCTAATCAATT
1932770 ATACAAATTAT
128 ATACAAATTAT
* * * * * *
1932781 T-AGGTCAAAGAATTAAGATTGAACCTCGGGCATAGAAGCGAGGACCAAATTAAAATTTCACCTA
1 TGA-ATCAAAGAATTAAGATTGAACCTCAGGCATAAAAGCAAGGACCAAATTAAAAATTCTCCTA
1932845 AATTAAAA
65 AATTAAAA
1932853 AGTTTAGGAA
Statistics
Matches: 171, Mismatches: 31, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
136 2 0.01
137 103 0.60
138 56 0.33
139 10 0.06
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.26
Consensus pattern (138 bp):
TGAATCAAAGAATTAAGATTGAACCTCAGGCATAAAAGCAAGGACCAAATTAAAAATTCTCCTAA
ATTAAAAGACTATAGTGAAATTAAACCCTAGATGAAGGCTCTAAAATTAAACCTAATCAATTATA
CAAATTAT
Found at i:1933403 original size:3 final size:3
Alignment explanation
Indices: 1933397--1933422 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1933387 ATATAAATAA
1933397 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1933423 AAAAATAATG
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1945925 original size:30 final size:31
Alignment explanation
Indices: 1945863--1945925 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
1945853 ATGAAAATTT
*
1945863 TAAATTAAAAATACTTAAAATGATATTTTTAA
1 TAAATTAAAAATACTT-AAATGATAGTTTTAA
*
1945895 TAAATTAAAAATTC-T-AATGAATAGTTTTAA
1 TAAATTAAAAATACTTAAATG-ATAGTTTTAA
1945925 T
1 T
1945926 TTTAAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.14
30 10 0.36
31 1 0.04
32 13 0.46
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (31 bp):
TAAATTAAAAATACTTAAATGATAGTTTTAA
Found at i:1949106 original size:27 final size:28
Alignment explanation
Indices: 1949051--1949130 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
1949041 AAAAAGTTTG
1949051 AATAATTTAGATATCTATTTTGACATAA
1 AATAATTTAGATATCTATTTTGACATAA
* * *
1949079 AATATTTTAGGTATCTATTTTGACTAAAA
1 AATAATTTAGATATCTATTTTGAC-ATAA
*
1949108 ATATAATATTAGATATTTATTTT
1 A-ATAAT-TTAGATATCTATTTT
1949131 TACCAAAAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
28 22 0.51
29 4 0.09
30 4 0.09
31 13 0.30
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (28 bp):
AATAATTTAGATATCTATTTTGACATAA
Found at i:1949701 original size:20 final size:20
Alignment explanation
Indices: 1949676--1949875 Score: 124
Period size: 20 Copynumber: 9.8 Consensus size: 20
1949666 CGATATTCCA
*
1949676 AGAATCGCAATGCGATTAAG
1 AGAATCGCAACGCGATTAAG
*
1949696 AGAATCGCAACGCGATTTAG
1 AGAATCGCAACGCGATTAAG
* * *
1949716 AAAATGGCAACG-G-TCAAACG
1 AGAATCGCAACGCGAT-TAA-G
* * *
1949736 AAAATGGCAACGCGATATTCCA-
1 AGAATCGCAACGCG--ATT-AAG
*
1949758 AGAATCGCAATGCGATTAAG
1 AGAATCGCAACGCGATTAAG
*
1949778 AGAATCGCAACGCGATTTAG
1 AGAATCGCAACGCGATTAAG
* *
1949798 AAAATCGCAACG-G-TCAAACG
1 AGAATCGCAACGCGAT-TAA-G
* *
1949818 AAAATCGCAACGCGAAATTCCA-
1 AGAATCGCAACGCG--ATT-AAG
* *
1949840 AGAACCGCAATGCGATTAAG
1 AGAATCGCAACGCGATTAAG
1949860 AGAATCGCAACGCGAT
1 AGAATCGCAACGCGAT
1949876 CGCAAAACTG
Statistics
Matches: 139, Mismatches: 25, Indels: 32
0.71 0.13 0.16
Matches are distributed among these distances:
18 2 0.01
19 6 0.04
20 103 0.74
21 2 0.01
22 22 0.16
24 4 0.03
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AGAATCGCAACGCGATTAAG
Found at i:1949753 original size:82 final size:82
Alignment explanation
Indices: 1949617--1949875 Score: 421
Period size: 82 Copynumber: 3.2 Consensus size: 82
1949607 TGACCAACAA
* * * * * *
1949617 AATCGCAACGCGATAT-CAAAATCTCAACGTTGAAAAGAAAATCGCAACGCGATATTCCAAGAAT
1 AATCGCAACGCGATTTAGAAAATCGCAACGGTCAAACGAAAATCGCAACGCGATATTCCAAGAAT
1949681 CGCAATGCGATTAAGAG
66 CGCAATGCGATTAAGAG
* *
1949698 AATCGCAACGCGATTTAGAAAATGGCAACGGTCAAACGAAAATGGCAACGCGATATTCCAAGAAT
1 AATCGCAACGCGATTTAGAAAATCGCAACGGTCAAACGAAAATCGCAACGCGATATTCCAAGAAT
1949763 CGCAATGCGATTAAGAG
66 CGCAATGCGATTAAGAG
* *
1949780 AATCGCAACGCGATTTAGAAAATCGCAACGGTCAAACGAAAATCGCAACGCGAAATTCCAAGAAC
1 AATCGCAACGCGATTTAGAAAATCGCAACGGTCAAACGAAAATCGCAACGCGATATTCCAAGAAT
1949845 CGCAATGCGATTAAGAG
66 CGCAATGCGATTAAGAG
1949862 AATCGCAACGCGAT
1 AATCGCAACGCGAT
1949876 CGCAAAACTG
Statistics
Matches: 165, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
81 15 0.09
82 150 0.91
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.17
Consensus pattern (82 bp):
AATCGCAACGCGATTTAGAAAATCGCAACGGTCAAACGAAAATCGCAACGCGATATTCCAAGAAT
CGCAATGCGATTAAGAG
Found at i:1949995 original size:6 final size:6
Alignment explanation
Indices: 1949986--1950012 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1949976 CATTACTATT
1949986 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
1950013 CGAGATGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1950519 original size:6 final size:6
Alignment explanation
Indices: 1950508--1950537 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1950498 TCTCGTCTCG
1950508 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1950538 ACGTGTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1950696 original size:20 final size:20
Alignment explanation
Indices: 1950668--1950845 Score: 197
Period size: 20 Copynumber: 9.0 Consensus size: 20
1950658 ATATAATAAG
1950668 CGCATTGCGATTCTTGGAAT
1 CGCATTGCGATTCTTGGAAT
*
1950688 CGCAATGCGACTT-TCTGG-AT
1 CGCATTGCGA-TTCT-TGGAAT
*
1950708 CGCATTGCGCTTCTTGGAAT
1 CGCATTGCGATTCTTGGAAT
** *
1950728 CGTGTTGCGATT-TTCTGAAT
1 CGCATTGCGATTCTT-GGAAT
1950748 CGCATTGCGATTCTTGGAAT
1 CGCATTGCGATTCTTGGAAT
*
1950768 CGCGTTGCGATTC-T-GAAT
1 CGCATTGCGATTCTTGGAAT
*
1950786 CGCGTTGCGATTCTTGGAAT
1 CGCATTGCGATTCTTGGAAT
* *
1950806 CGCGTTGCGATT-TTCTGAAT
1 CGCATTGCGATTCTT-GGAAT
1950826 CGCATTGCGATTCTTGGAAT
1 CGCATTGCGATTCTTGGAAT
1950846 ATTGCGTTGC
Statistics
Matches: 134, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
18 17 0.13
19 11 0.08
20 97 0.72
21 9 0.07
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCATTGCGATTCTTGGAAT
Found at i:1950723 original size:40 final size:40
Alignment explanation
Indices: 1950668--1950863 Score: 288
Period size: 40 Copynumber: 4.9 Consensus size: 40
1950658 ATATAATAAG
** * *
1950668 CGCATTGCGATTCTTGGAATCGCAATGCGACTTTCTGGAT
1 CGCATTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAAT
* *
1950708 CGCATTGCGCTTCTTGGAATCGTGTTGCGATTTTCTGAAT
1 CGCATTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAAT
1950748 CGCATTGCGATTCTTGGAATCGCGTTGCGA--TTCTGAAT
1 CGCATTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAAT
*
1950786 CGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAAT
1 CGCATTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAAT
*
1950826 CGCATTGCGATTCTTGGAATATTGCGTTGCGATTTTCT
1 CGCATTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCT
1950864 TTTCAACGTT
Statistics
Matches: 141, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
38 37 0.26
40 86 0.61
41 1 0.01
42 17 0.12
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (40 bp):
CGCATTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAAT
Found at i:1950813 original size:78 final size:78
Alignment explanation
Indices: 1950668--1950859 Score: 285
Period size: 78 Copynumber: 2.4 Consensus size: 78
1950658 ATATAATAAG
** * * *
1950668 CGCATTGCGATTCTTGGAATCGCAATGCGACTTTCTGGATCGCATTGCGCTTCTTGGAATCGTGT
1 CGCATTGCGATTCTTGGAATCGCGTTGCGA--TTCTGAATCGCATTGCGATTCTTGGAATCGCGT
1950733 TGCGATTTTCTGAAT
64 TGCGATTTTCTGAAT
*
1950748 CGCATTGCGATTCTTGGAATCGCGTTGCGATTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTG
1 CGCATTGCGATTCTTGGAATCGCGTTGCGATTCTGAATCGCATTGCGATTCTTGGAATCGCGTTG
1950813 CGATTTTCTGAAT
66 CGATTTTCTGAAT
*
1950826 CGCATTGCGATTCTTGGAATATTGCGTTGCGATT
1 CGCATTGCGATTCTTGG-A-ATCGCGTTGCGATT
1950860 TTCTTTTCAA
Statistics
Matches: 103, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
78 61 0.59
79 1 0.01
80 41 0.40
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36
Consensus pattern (78 bp):
CGCATTGCGATTCTTGGAATCGCGTTGCGATTCTGAATCGCATTGCGATTCTTGGAATCGCGTTG
CGATTTTCTGAAT
Found at i:1950901 original size:20 final size:20
Alignment explanation
Indices: 1950693--1950901 Score: 144
Period size: 20 Copynumber: 10.4 Consensus size: 20
1950683 GGAATCGCAA
* * *
1950693 TGCGACTTTCTGGATCGCAT
1 TGCGATTTTCTGAATCGCGT
* * *
1950713 TGCGCTTCTT-GGAATCGTGT
1 TGCGATT-TTCTGAATCGCGT
*
1950733 TGCGATTTTCTGAATCGCAT
1 TGCGATTTTCTGAATCGCGT
*
1950753 TGCGATTCTT-GGAATCGCGT
1 TGCGATT-TTCTGAATCGCGT
1950773 TGCGA--TTCTGAATCGCGT
1 TGCGATTTTCTGAATCGCGT
*
1950791 TGCGATTCTT-GGAATCGCGT
1 TGCGATT-TTCTGAATCGCGT
*
1950811 TGCGATTTTCTGAATCGCAT
1 TGCGATTTTCTGAATCGCGT
* *
1950831 TGCGATTCTT-GGAATATTGCGT
1 TGCGATT-TTCTG-A-ATCGCGT
** *
1950853 TGCGATTTTCT-TTTCAACGT
1 TGCGATTTTCTGAATC-GCGT
* * *
1950873 TGTGCTTTTCTAAATCGCGT
1 TGCGATTTTCTGAATCGCGT
1950893 TGCGATTTT
1 TGCGATTTT
1950902 GTTGGTCATT
Statistics
Matches: 144, Mismatches: 31, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
17 2 0.01
18 14 0.10
19 5 0.03
20 98 0.68
21 13 0.09
22 12 0.08
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (20 bp):
TGCGATTTTCTGAATCGCGT
Found at i:1952818 original size:13 final size:13
Alignment explanation
Indices: 1952800--1952846 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
1952790 AGCACTGTGA
1952800 AAAGAAAATAATG
1 AAAGAAAATAATG
1952813 AAAGAAAATAATG
1 AAAGAAAATAATG
*
1952826 AAAGAAAATAAAG
1 AAAGAAAATAATG
*
1952839 AAACAAAA
1 AAAGAAAA
1952847 GTGGAGATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.74, C:0.02, G:0.13, T:0.11
Consensus pattern (13 bp):
AAAGAAAATAATG
Found at i:1954260 original size:17 final size:17
Alignment explanation
Indices: 1954238--1954273 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1954228 AAATTAGGAT
1954238 TATATATAAA-ACTAAAA
1 TATATATAAACA-TAAAA
1954255 TATATATAAACATAAAA
1 TATATATAAACATAAAA
1954272 TA
1 TA
1954274 AAATAGGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TATATATAAACATAAAA
Found at i:1962755 original size:31 final size:31
Alignment explanation
Indices: 1962717--1962794 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
1962707 TCAACTTATC
**
1962717 TCATTATTTGTTTTCTTTTTATCCCTCTGCT
1 TCATTATTTGACTTCTTTTTATCCCTCTGCT
1962748 TCATTATTTGACTTCTTTTTATCCCTCTGCT
1 TCATTATTTGACTTCTTTTTATCCCTCTGCT
1962779 TCATTATTTGACTTCT
1 TCATTATTTGACTTCT
1962795 ATCTGTTGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.13, C:0.23, G:0.06, T:0.58
Consensus pattern (31 bp):
TCATTATTTGACTTCTTTTTATCCCTCTGCT
Found at i:1970061 original size:29 final size:29
Alignment explanation
Indices: 1970029--1970089 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
1970019 GTTCTTGATT
1970029 TTCAAAGTCCTATGCAAATTCTAACAAAA
1 TTCAAAGTCCTATGCAAATTCTAACAAAA
1970058 TTCAAAGTCCTATGCAAATTCTAACAAAA
1 TTCAAAGTCCTATGCAAATTCTAACAAAA
1970087 TTC
1 TTC
1970090 TTTCCTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.30
Consensus pattern (29 bp):
TTCAAAGTCCTATGCAAATTCTAACAAAA
Found at i:1970940 original size:21 final size:21
Alignment explanation
Indices: 1970914--1971013 Score: 105
Period size: 21 Copynumber: 4.7 Consensus size: 21
1970904 AGGGTGTCAA
*
1970914 AGTGCATTCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
1970935 AGTGCATCCATGCACCTCTGC
1 AGTGCATCCATGCACCCCTGC
*
1970956 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTGC
* * *
1970978 TAGTGCATCGATGCA-CCATGT
1 -AGTGCATCCATGCACCCCTGC
1970999 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1971014 TCCATTTCGA
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
20 14 0.22
21 35 0.54
22 2 0.03
23 14 0.22
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1971058 original size:20 final size:20
Alignment explanation
Indices: 1971033--1971125 Score: 159
Period size: 20 Copynumber: 4.7 Consensus size: 20
1971023 AATGTAATTA
1971033 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
1971053 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
1971073 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
* *
1971093 GTGCATCGATGCATCATGTT
1 GTGCATCGATGCATCCTGCT
*
1971113 GTGCATCCATGCA
1 GTGCATCGATGCA
1971126 CCAAGGCTGC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.17, C:0.28, G:0.25, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:1971556 original size:31 final size:31
Alignment explanation
Indices: 1971493--1971556 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1971483 TTTGTAAAAG
* * *
1971493 GGAAAGGTTCTAGTTTATCCCGTAAAAGCTA
1 GGAAAGGTTCTAGTTTAGCCCGAAAAAACTA
* *
1971524 GGAAAGGTTCTATTTTAGCCTGAAAAAACTA
1 GGAAAGGTTCTAGTTTAGCCCGAAAAAACTA
1971555 GG
1 GG
1971557 GAGTTGTAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (31 bp):
GGAAAGGTTCTAGTTTAGCCCGAAAAAACTA
Found at i:1974196 original size:21 final size:21
Alignment explanation
Indices: 1974172--1974211 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1974162 AAACAATTGG
*
1974172 TAACATTTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
1974193 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
1974212 CATTAAACAT
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:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:1974485 original size:23 final size:21
Alignment explanation
Indices: 1974434--1974493 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 21
1974424 AGGGTGTCAA
*
1974434 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTAC
1974455 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTAC
*
1974477 TAGTGCATCGATGCACC
1 -AGTGCATCCATGCACC
1974494 AAGTAGTGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.47
22 1 0.03
23 17 0.50
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:1975738 original size:18 final size:18
Alignment explanation
Indices: 1975715--1975757 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1975705 TTGTTTTTTA
1975715 AAATAAAAGATAAA-AATT
1 AAATAAAAGA-AAACAATT
*
1975733 AAATAATAGAAAACAATT
1 AAATAAAAGAAAACAATT
*
1975751 AATTAAA
1 AAATAAA
1975758 TAATTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAACAATT
Found at i:1976509 original size:18 final size:18
Alignment explanation
Indices: 1976487--1976530 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
1976477 AAAAGTAAGG
1976487 AAAATATAATTCCT-ATA
1 AAAATATAATTCCTAATA
1976504 ATAAATAGATAATTCCTAATA
1 A-AAAT--ATAATTCCTAATA
1976525 AAAATA
1 AAAATA
1976531 CTTAAACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 1 0.04
18 5 0.22
20 13 0.57
21 4 0.17
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAATATAATTCCTAATA
Found at i:1976517 original size:20 final size:20
Alignment explanation
Indices: 1976492--1976530 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1976482 TAAGGAAAAT
1976492 ATAATTCCT-ATAATAAATAG
1 ATAATTCCTAATAA-AAATAG
1976512 ATAATTCCTAATAAAAATA
1 ATAATTCCTAATAAAAATA
1976531 CTTAAACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (20 bp):
ATAATTCCTAATAAAAATAG
Found at i:1978486 original size:14 final size:13
Alignment explanation
Indices: 1978454--1978496 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1978444 TTAAGTACCT
*
1978454 AAAAATTAAAAGG
1 AAAAATTAAAAGA
*
1978467 AAAAATTATAAGA
1 AAAAATTAAAAGA
*
1978480 AATAAATTAAACGA
1 AA-AAATTAAAAGA
1978494 AAA
1 AAA
1978497 TGATAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (13 bp):
AAAAATTAAAAGA
Found at i:1978511 original size:24 final size:25
Alignment explanation
Indices: 1978468--1978514 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1978458 ATTAAAAGGA
*
1978468 AAAATTATAAGAAATAAATTAAACG
1 AAAATGATAAGAAATAAATTAAACG
1978493 AAAATGATAA-AAATAAATTAAA
1 AAAATGATAAGAAATAAATTAAA
1978515 GAAGTAGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.23
Consensus pattern (25 bp):
AAAATGATAAGAAATAAATTAAACG
Found at i:1984921 original size:20 final size:21
Alignment explanation
Indices: 1984896--1984935 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1984886 CTCTACATAG
1984896 TAGTATCAATACCAT-AGGCA
1 TAGTATCAATACCATCAGGCA
*
1984916 TAGTATCTATACCATCAGGC
1 TAGTATCAATACCATCAGGC
1984936 CCCAACGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (21 bp):
TAGTATCAATACCATCAGGCA
Found at i:1987009 original size:27 final size:26
Alignment explanation
Indices: 1986965--1987015 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1986955 CTAGAAGGTG
*
1986965 CTGACTAGATCTTATAGAAAACTGCTA
1 CTGACTAGACCTTATAG-AAACTGCTA
* *
1986992 CTGACTGGACCTTCTAGAAACTGC
1 CTGACTAGACCTTATAGAAACTGC
1987016 CACGTTAGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (26 bp):
CTGACTAGACCTTATAGAAACTGCTA
Found at i:1999650 original size:24 final size:24
Alignment explanation
Indices: 1999606--1999655 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1999596 ATAAATAACC
*
1999606 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1999630 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
1999654 AA
1 AA
1999656 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:2005926 original size:31 final size:32
Alignment explanation
Indices: 2005869--2005928 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
2005859 ATAGGGTAAA
*
2005869 TTATATATTTGGTCACCAACCTATTATTTAGT
1 TTATATATTTGATCACCAACCTATTATTTAGT
2005901 TTATAT-TTTGATCACTCAA-CTATTATTT
1 TTATATATTTGATCAC-CAACCTATTATTT
2005929 TTTTAAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (32 bp):
TTATATATTTGATCACCAACCTATTATTTAGT
Found at i:2009036 original size:21 final size:21
Alignment explanation
Indices: 2009012--2009053 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2009002 TCGACATTTC
2009012 GAAAGATGGTTCTAACAAGAT
1 GAAAGATGGTTCTAACAAGAT
2009033 GAAAGATGGTTCTAACAAGAT
1 GAAAGATGGTTCTAACAAGAT
2009054 CGGTTATCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.24
Consensus pattern (21 bp):
GAAAGATGGTTCTAACAAGAT
Found at i:2017432 original size:3 final size:3
Alignment explanation
Indices: 2017424--2017450 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2017414 ACACTGTTTA
2017424 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2017451 TTCTTTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2017697 original size:7 final size:7
Alignment explanation
Indices: 2017685--2017719 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
2017675 AAACTTTGAA
2017685 TATTTGC
1 TATTTGC
2017692 TATTTGC
1 TATTTGC
2017699 TATTTGC
1 TATTTGC
2017706 TATTTGC
1 TATTTGC
2017713 TATTTGC
1 TATTTGC
2017720 CAAGACCAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (7 bp):
TATTTGC
Found at i:2020126 original size:26 final size:27
Alignment explanation
Indices: 2020076--2020130 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
2020066 ATGAAGATCT
* *
2020076 TGATGCTGTGGACTTTCAAGTTCAAAG
1 TGATGCTATGGACGTTCAAGTTCAAAG
2020103 TGATGCTATGGA-GTTCAAGTTCAAAG
1 TGATGCTATGGACGTTCAAGTTCAAAG
2020129 TG
1 TG
2020131 GTGATGGCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (27 bp):
TGATGCTATGGACGTTCAAGTTCAAAG
Found at i:2020597 original size:21 final size:21
Alignment explanation
Indices: 2020571--2020707 Score: 165
Period size: 21 Copynumber: 6.6 Consensus size: 21
2020561 GTTTCCAGAT
*
2020571 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
2020592 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
2020613 TCGCAATACGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
2020634 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
2020655 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
2020675 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
2020696 TCGAAATGCGAA
1 TCGCAATGCGAA
2020708 TATGTAAATC
Statistics
Matches: 103, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
20 17 0.17
21 86 0.83
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:2020679 original size:20 final size:20
Alignment explanation
Indices: 2020654--2020726 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
2020644 AACTTGGACT
2020654 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
2020674 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
*
2020695 ATCGAAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
2020715 ATCGCAATGCGA
1 ATCGCAATGCGA
2020727 TAGTCGAAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.05
19 3 0.07
20 23 0.52
21 11 0.25
22 3 0.07
23 2 0.05
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:2020695 original size:41 final size:41
Alignment explanation
Indices: 2020591--2020726 Score: 161
Period size: 41 Copynumber: 3.3 Consensus size: 41
2020581 AACTTCGACT
* * *
2020591 ATCGCAATGCGAACTTCGACTATCGCAATACGAACT-TCG-ACT
1 ATCGCAATGCGAACGTCGACTATCGCAATGCGAA-TAT-GTA-A
* *
2020633 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACGTCGACTATCGCAATGCGAATATGTAA
*
2020674 ATCGCAATGCGATA-GTCGACTATCGAAATGCGAATATGTAA
1 ATCGCAATGCGA-ACGTCGACTATCGCAATGCGAATATGTAA
2020715 ATCGCAATGCGA
1 ATCGCAATGCGA
2020727 TAGTCGAAGT
Statistics
Matches: 85, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
41 50 0.59
42 35 0.41
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.24
Consensus pattern (41 bp):
ATCGCAATGCGAACGTCGACTATCGCAATGCGAATATGTAA
Found at i:2020706 original size:62 final size:62
Alignment explanation
Indices: 2020578--2020760 Score: 164
Period size: 62 Copynumber: 2.9 Consensus size: 62
2020568 GATTCGCAAC
* * * * *
2020578 GCGAACTTCGACTATCGCAATGCGAACT-TCG-ACTATCGCAATACGA-ACTTCGACTATCGCAA
1 GCGAACTTGGACTATCGCAATGCGAA-TAT-GTA-AATCGCAATGCGATA-GTCGACTATCGAAA
2020640 T
62 T
2020641 GCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGAAAT
1 GCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGAAAT
* * * *
2020703 GCGAA-TATGTA-AATCGCAATGCG-ATA-GTCGAAGTTCGCATTGCGATAGTCGACTATCG
1 GCGAACT-TGGACTATCGCAATGCGAATATGT--AA-ATCGCAATGCGATAGTCGACTATCG
2020761 CATTGCGATT
Statistics
Matches: 104, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
59 2 0.02
60 3 0.03
61 14 0.13
62 57 0.55
63 28 0.27
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (62 bp):
GCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGAAAT
Found at i:2020746 original size:21 final size:21
Alignment explanation
Indices: 2020716--2020810 Score: 90
Period size: 21 Copynumber: 4.6 Consensus size: 21
2020706 AATATGTAAA
*
2020716 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
2020737 TCGCATTGCGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
*
2020757 ATCGCATTGCGAT-TTAC-ATA-T
1 -TCGCATTGCGATAGT-CGA-AGT
*
2020778 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
*
2020799 TCGCGTTGCGAT
1 TCGCATTGCGAT
2020811 TTATTCCAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
20 17 0.27
21 44 0.71
22 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:2020768 original size:62 final size:62
Alignment explanation
Indices: 2020675--2020810 Score: 170
Period size: 62 Copynumber: 2.2 Consensus size: 62
2020665 AATATGTAAA
* *
2020675 TCGCAATGCGATAGTCGACTATCGAAATGCGAATATGTA-A-A-TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGACTATCGAAATGCG-AT-T-TACATATTCGCAATGCGATAGTCCAAGT
* * *
2020737 TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGACTATCGAAATGCGATTTACATATTCGCAATGCGATAGTCCAAGT
*
2020799 TCGCGTTGCGAT
1 TCGCATTGCGAT
2020811 TTATTCCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
59 2 0.03
60 2 0.03
61 3 0.05
62 58 0.89
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.29
Consensus pattern (62 bp):
TCGCATTGCGATAGTCGACTATCGAAATGCGATTTACATATTCGCAATGCGATAGTCCAAGT
Found at i:2020808 original size:41 final size:41
Alignment explanation
Indices: 2020736--2020813 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
2020726 ATAGTCGAAG
*
2020736 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCAACTATCGCATTGCGATTTACATA
* *
2020777 TTCGCATTGCGATAGTCCAAGT-TCGCGTTGCGATTTA
1 TTCGCATTGCGATAGT-CAACTATCGCATTGCGATTTA
2020814 TTCCAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 30 0.91
42 3 0.09
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (41 bp):
TTCGCATTGCGATAGTCAACTATCGCATTGCGATTTACATA
Found at i:2020824 original size:23 final size:21
Alignment explanation
Indices: 2020716--2020826 Score: 82
Period size: 21 Copynumber: 5.2 Consensus size: 21
2020706 AATATGTAAA
* * *
2020716 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAAT
* *
2020737 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAAT
* * *
2020757 ATCGCATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGTCCAAAT
*
2020778 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAAT
* *
2020799 TCGCGTTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAAT
2020822 TCGCA
1 TCGCA
2020827 ACGACTGGTG
Statistics
Matches: 69, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
20 15 0.22
21 42 0.61
23 12 0.17
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAT
Found at i:2021616 original size:21 final size:20
Alignment explanation
Indices: 2021592--2021676 Score: 72
Period size: 21 Copynumber: 4.3 Consensus size: 20
2021582 ACTATCATTT
2021592 TGCGAACTTGGACTATCGCAA
1 TGCGAA-TTGGACTATCGCAA
2021613 TGCGAA-T--A-TATCGCAA
1 TGCGAATTGGACTATCGCAA
* *
2021629 TGCGAATATGTA-AATCGCAA
1 TGCGAAT-TGGACTATCGCAA
* *
2021649 TGCGATAGTCGACTATCGCAA
1 TGCGA-ATTGGACTATCGCAA
2021670 TGCGAAT
1 TGCGAAT
2021677 ATTAAATACA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
16 14 0.27
17 1 0.02
18 1 0.02
19 1 0.02
20 16 0.31
21 19 0.37
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (20 bp):
TGCGAATTGGACTATCGCAA
Found at i:2021626 original size:16 final size:17
Alignment explanation
Indices: 2021603--2021677 Score: 71
Period size: 16 Copynumber: 4.1 Consensus size: 17
2021593 GCGAACTTGG
2021603 ACTATCGCAATGCGAAT
1 ACTATCGCAATGCGAAT
2021620 A-TATCGCAATGCGAAT
1 ACTATCGCAATGCGAAT
*
2021636 ATGTAAATCGCAATGCGATAGT
1 A-CT--ATCGCAATGCGA-A-T
2021658 CGACTATCGCAATGCGAAT
1 --ACTATCGCAATGCGAAT
2021677 A
1 A
2021678 TTAAATACAA
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
16 16 0.33
17 2 0.04
18 1 0.02
19 1 0.02
20 13 0.27
21 13 0.27
22 1 0.02
23 1 0.02
24 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (17 bp):
ACTATCGCAATGCGAAT
Found at i:2021713 original size:39 final size:41
Alignment explanation
Indices: 2021621--2021699 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
2021611 AATGCGAATA
*
2021621 TATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAC
1 TATCGCAATGCGAATATGTAAATCACAATGCGATAGTCGAC
2021662 TATCGCAATGCGAATAT-TAAAT-ACAATGCGATAGTCGA
1 TATCGCAATGCGAATATGTAAATCACAATGCGATAGTCGA
2021700 AGTTCGCGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
39 15 0.41
40 5 0.14
41 17 0.46
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (41 bp):
TATCGCAATGCGAATATGTAAATCACAATGCGATAGTCGAC
Found at i:2021714 original size:21 final size:21
Alignment explanation
Indices: 2021688--2021838 Score: 184
Period size: 21 Copynumber: 7.2 Consensus size: 21
2021678 TTAAATACAA
*
2021688 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCAT
*
2021709 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCGAAGTTCGCAT
*
2021730 TGCGATAGTCG-ACTATCGCAT
1 TGCGATAGTCGAAGT-TCGCAT
*
2021751 TGCGAT-TTAC-ATA-TTCGCAT
1 TGCGATAGT-CGA-AGTTCGCAT
*
2021771 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCGAAGTTCGCAT
*
2021792 TGCGATAGTCGAAGTTCACAT
1 TGCGATAGTCGAAGTTCGCAT
*
2021813 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCAT
2021834 TGCGA
1 TGCGA
2021839 ATCTGGAAAC
Statistics
Matches: 113, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
20 17 0.15
21 95 0.84
22 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCAT
Found at i:2021807 original size:83 final size:81
Alignment explanation
Indices: 2021643--2021824 Score: 242
Period size: 83 Copynumber: 2.2 Consensus size: 81
2021633 AATATGTAAA
* * *
2021643 TCGCAATGCGATAGTCGACTATCGCAATGCGAATATTAAATACAATGCGATAGTCGAAGTTCGCG
1 TCGCATTGCGATAGTCGACTATCGCAATGCGAATATTAAATACAATGCGATAGTCCAAGTTCGCA
2021708 TTGCGATAGTCCAAGT
66 TTGCGATAGTCCAAGT
* * *
2021724 TCGCATTGCGATAGTCGACTATCGCATTGCG-AT-TTACATATTCGCATTGCGATAGTCCAAGTT
1 TCGCATTGCGATAGTCGACTATCGCAATGCGAATATTA-A-A-T-ACAATGCGATAGTCCAAGTT
*
2021787 CGCATTGCGATAGTCGAAGT
62 CGCATTGCGATAGTCCAAGT
*
2021807 TCACATTGCGATAGTCGA
1 TCGCATTGCGATAGTCGA
2021825 AGTTCGCGTT
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
79 3 0.03
80 3 0.03
81 30 0.34
82 1 0.01
83 52 0.58
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (81 bp):
TCGCATTGCGATAGTCGACTATCGCAATGCGAATATTAAATACAATGCGATAGTCCAAGTTCGCA
TTGCGATAGTCCAAGT
Found at i:2021814 original size:62 final size:62
Alignment explanation
Indices: 2021702--2021818 Score: 191
Period size: 62 Copynumber: 1.9 Consensus size: 62
2021692 ATAGTCGAAG
* *
2021702 TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCACATTGCGATTTACATA
*
2021764 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGT-TCACATTGCGAT
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCG-ACTATCACATTGCGAT
2021819 AGTCGAAGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
62 49 0.96
63 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (62 bp):
TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCACATTGCGATTTACATA
Found at i:2024267 original size:18 final size:20
Alignment explanation
Indices: 2024246--2024288 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
2024236 GTTTAATAAT
2024246 TAATATAA-TATTTTTT-AA
1 TAATATAAGTATTTTTTAAA
*
2024264 TAATATAAGTTTTTTTTAAA
1 TAATATAAGTATTTTTTAAA
2024284 TAATA
1 TAATA
2024289 ATTAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
19 7 0.32
20 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TAATATAAGTATTTTTTAAA
Found at i:2025196 original size:2 final size:2
Alignment explanation
Indices: 2025189--2025245 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2025179 CAATCACATA
2025189 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2025231 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
2025246 GTTTGCTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2027203 original size:2 final size:2
Alignment explanation
Indices: 2027156--2027184 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2027146 AATGAAGTAC
2027156 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2027185 CTTTTGAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2035582 original size:41 final size:41
Alignment explanation
Indices: 2035523--2035611 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 41
2035513 GCGGTTTTTA
* * *
2035523 AAAAAAGCTACTATAGAACGATTC-TTTTGCGGTGTTTGTTT
1 AAAAAAGCCACTAAAGAACGA-TCATTTTGCAGTGTTTGTTT
*
2035564 AAAAACGCCACTAAAGAACGATCATTTTGCAGTGTTTGTTT
1 AAAAAAGCCACTAAAGAACGATCATTTTGCAGTGTTTGTTT
*
2035605 AGAAAAG
1 AAAAAAG
2035612 TACTAGGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 2 0.05
41 39 0.95
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (41 bp):
AAAAAAGCCACTAAAGAACGATCATTTTGCAGTGTTTGTTT
Found at i:2036578 original size:17 final size:17
Alignment explanation
Indices: 2036548--2036625 Score: 72
Period size: 17 Copynumber: 4.6 Consensus size: 17
2036538 AATTTAATCT
2036548 TTTAAAAATT-ATATTA
1 TTTAAAAATTAATATTA
2036564 TTTAAAAATTAATATTA
1 TTTAAAAATTAATATTA
* *
2036581 ATTAGAAATTAATTATTA
1 TTTAAAAATTAA-TATTA
* *
2036599 ATAAGAAAATTTAATA-T-
1 TTTA-AAAA-TTAATATTA
2036616 TTTAAAAATT
1 TTTAAAAATT
2036626 TTAAAATTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
15 2 0.04
16 14 0.27
17 18 0.35
18 9 0.17
19 5 0.10
20 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTAAAAATTAATATTA
Found at i:2036599 original size:18 final size:17
Alignment explanation
Indices: 2036553--2036669 Score: 69
Period size: 17 Copynumber: 6.5 Consensus size: 17
2036543 AATCTTTTAA
* *
2036553 AAATT-ATATTATTTAA
1 AAATTAATATTAATTAG
2036569 AAATTAATATTAATTAG
1 AAATTAATATTAATTAG
*
2036586 AAATTAATTATTAATAAG
1 AAATTAA-TATTAATTAG
*
2036604 AAAATTTAATATT--TTAA
1 -AAA-TTAATATTAATTAG
* *
2036621 AAATTTTAAAATTATATTCTTAAA
1 AAA--TTAATATTA-A---TT-AG
2036645 AAATTAATATTAATTAG
1 AAATTAATATTAATTAG
2036662 AAATTAAT
1 AAATTAAT
2036670 GTCACGAGTT
Statistics
Matches: 81, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
16 8 0.10
17 35 0.43
18 11 0.14
19 7 0.09
20 4 0.05
21 1 0.01
22 8 0.10
23 2 0.02
24 5 0.06
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (17 bp):
AAATTAATATTAATTAG
Found at i:2036625 original size:16 final size:16
Alignment explanation
Indices: 2036536--2036626 Score: 62
Period size: 16 Copynumber: 5.4 Consensus size: 16
2036526 AGATTGATTG
*
2036536 AAAATTTAATCTTTTA
1 AAAATTTAATATTTTA
*
2036552 AAAATTATATTA-TTTA
1 AAAATT-TAATATTTTA
2036568 AAAA-TTAATATTAATTA
1 AAAATTTAATATT--TTA
* *
2036585 GAAA-TTAATTATTAATAA
1 AAAATTTAA-TATT--TTA
2036603 GAAAATTTAATATTTTA
1 -AAAATTTAATATTTTA
2036620 AAAATTT
1 AAAATTT
2036627 TAAAATTATA
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
14 4 0.07
15 2 0.03
16 21 0.34
17 15 0.25
18 8 0.13
19 7 0.11
20 4 0.07
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (16 bp):
AAAATTTAATATTTTA
Found at i:2036651 original size:22 final size:22
Alignment explanation
Indices: 2036612--2036656 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2036602 AGAAAATTTA
*
2036612 ATATTTTAAAAATTTTAAAATT
1 ATATTTTAAAAATATTAAAATT
*
2036634 ATATTCTTAAAAA-ATTAATATT
1 ATATT-TTAAAAATATTAAAATT
2036656 A
1 A
2036657 ATTAGAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTTTAAAAATATTAAAATT
Found at i:2040746 original size:20 final size:20
Alignment explanation
Indices: 2040721--2040761 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2040711 TCATGGATGT
2040721 TTTCTCTAATTATAAAAACA
1 TTTCTCTAATTATAAAAACA
*
2040741 TTTCTCTAATTTTAAAAACA
1 TTTCTCTAATTATAAAAACA
2040761 T
1 T
2040762 GTCTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTCTCTAATTATAAAAACA
Found at i:2040834 original size:19 final size:19
Alignment explanation
Indices: 2040786--2040853 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
2040776 AAATATAGGT
*
2040786 TGATCTCCGATTTCTGTTA
1 TGATCTCTGATTTCTGTTA
* * *
2040805 TGAACTTTGATATCTGTTA
1 TGATCTCTGATTTCTGTTA
* *
2040824 TGATCTCTGATTTCCGATA
1 TGATCTCTGATTTCTGTTA
*
2040843 TGATTTCTGAT
1 TGATCTCTGAT
2040854 CTCTATTTTC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (19 bp):
TGATCTCTGATTTCTGTTA
Found at i:2041801 original size:25 final size:27
Alignment explanation
Indices: 2041763--2041812 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
2041753 TTTACCGTTG
*
2041763 TGTTTAT-AATTTTTTTTTATTTTACA
1 TGTTTATAAATTTTTTTTAATTTTACA
2041789 TGTTT-TAAATTTTTTTTAATTTTA
1 TGTTTATAAATTTTTTTTAATTTTA
2041813 TGGGATTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (27 bp):
TGTTTATAAATTTTTTTTAATTTTACA
Done.