Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009149.1 Hibiscus syriacus cultivar Beakdansim tig00112673_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: 1143513
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 5 of 6
Found at i:767690 original size:5 final size:5
Alignment explanation
Indices: 767680--767712 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
767670 ACTGTTCCTC
767680 TCTTT TCTTT TCTTT TCTTT TCTTT TCATTT TC
1 TCTTT TCTTT TCTTT TCTTT TCTTT TC-TTT TC
767713 GTGTTAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (5 bp):
TCTTT
Found at i:772028 original size:2 final size:2
Alignment explanation
Indices: 772021--772092 Score: 74
Period size: 2 Copynumber: 36.5 Consensus size: 2
772011 ATCACATTTT
* * * * ** *
772021 TA TA TA TA TA TA TA TA TA TA TT TA TG TT TA TT TA -A CG TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
772062 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
772093 TCATTATTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (2 bp):
TA
Found at i:773178 original size:2 final size:2
Alignment explanation
Indices: 773171--773238 Score: 56
Period size: 2 Copynumber: 36.5 Consensus size: 2
773161 TTATTGTATG
* * *
773171 TA TA TA TA TA TA TA TA TA TA TA TT TA -A TA T- TT TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
**
773211 TA CC TA T- TA T- TA -A TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
773239 TTAATTATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
1 5 0.10
2 47 0.90
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:779199 original size:14 final size:14
Alignment explanation
Indices: 779180--779216 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
779170 CGTGCAGAGA
779180 CAGCTGTCCAGTGC
1 CAGCTGTCCAGTGC
779194 CAGCTGTCCAGTGC
1 CAGCTGTCCAGTGC
779208 CAGCTGTCC
1 CAGCTGTCC
779217 TTATGGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.14, C:0.38, G:0.27, T:0.22
Consensus pattern (14 bp):
CAGCTGTCCAGTGC
Found at i:782056 original size:26 final size:26
Alignment explanation
Indices: 781966--782056 Score: 84
Period size: 22 Copynumber: 3.6 Consensus size: 26
781956 AGAGAATAAC
* *
781966 AAAAGAAGAAGATGAATAAAGGAAAGAG
1 AAAAGAAAAAG-TTAATAAA-GAAAGAG
* *
781994 AAAAAGTAAAAGTTAA-AATGAAAGAG
1 -AAAAGAAAAAGTTAATAAAGAAAGAG
782020 --AA-AAAAA-TTAATAAAGAAAGAG
1 AAAAGAAAAAGTTAATAAAGAAAGAG
782042 AAAAGAAAAAGTTAA
1 AAAAGAAAAAGTTAA
782057 AAATTTAAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
21 4 0.08
22 13 0.25
23 2 0.04
24 2 0.04
25 5 0.10
26 11 0.22
27 2 0.04
28 3 0.06
29 9 0.18
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.12
Consensus pattern (26 bp):
AAAAGAAAAAGTTAATAAAGAAAGAG
Found at i:796030 original size:23 final size:23
Alignment explanation
Indices: 795976--796032 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
795966 CGTATAAATA
*
795976 CACCGAAGTTCC-CGTAGAATTG
1 CACCGAAGTGCCGCGTAGAATTG
* *
795998 TATCGAAGTGCCGCGTAGAATTG
1 CACCGAAGTGCCGCGTAGAATTG
*
796021 CACCGTAGTGCC
1 CACCGAAGTGCC
796033 ATATAAGATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (23 bp):
CACCGAAGTGCCGCGTAGAATTG
Found at i:796750 original size:19 final size:19
Alignment explanation
Indices: 796722--796771 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
796712 TTTAAGGGGG
796722 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
* *
796741 TGCATTGATGCGCTCCTTA
1 TGCATCGATGCACTCCTTA
796760 TGCATCGATGCA
1 TGCATCGATGCA
796772 TTGATGGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:798214 original size:6 final size:6
Alignment explanation
Indices: 798203--798259 Score: 66
Period size: 6 Copynumber: 9.8 Consensus size: 6
798193 TAAGTCGAAA
* *
798203 AAAAAG AAAAAG AAAAAA AGAAAAG -AACA- AAAAA- AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG
798249 AAAAAG AAAAA
1 AAAAAG AAAAA
798260 TAAGATAGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
5 11 0.25
6 29 0.66
7 4 0.09
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:798219 original size:15 final size:15
Alignment explanation
Indices: 798199--798264 Score: 72
Period size: 15 Copynumber: 4.7 Consensus size: 15
798189 GTCCTAAGTC
798199 GAAAAAAAAGAAAAA
1 GAAAAAAAAGAAAAA
798214 G-AAAAAAAG-AAAA
1 GAAAAAAAAGAAAAA
798227 GAACAAAAAA-AAAAA
1 GAA-AAAAAAGAAAAA
798242 G---AAAAAGAAAAA
1 GAAAAAAAAGAAAAA
*
798254 GAAAAATAAGA
1 GAAAAAAAAGA
798265 TAGGTTCAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
11 5 0.12
12 6 0.14
13 5 0.12
14 9 0.21
15 18 0.42
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.02
Consensus pattern (15 bp):
GAAAAAAAAGAAAAA
Found at i:799308 original size:43 final size:43
Alignment explanation
Indices: 799255--799358 Score: 190
Period size: 43 Copynumber: 2.4 Consensus size: 43
799245 AGAGACAATT
799255 TCAACTTCACAACGAAGGATATTGGGCTCAAGACAACACAAGC
1 TCAACTTCACAACGAAGGATATTGGGCTCAAGACAACACAAGC
*
799298 TCAACTTCACAGCGAAGGATATTGGGCTCAAGACAACACAAGC
1 TCAACTTCACAACGAAGGATATTGGGCTCAAGACAACACAAGC
*
799341 TCAACTTCACAATGAAGG
1 TCAACTTCACAACGAAGG
799359 GGTGACTGAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (43 bp):
TCAACTTCACAACGAAGGATATTGGGCTCAAGACAACACAAGC
Found at i:800292 original size:2 final size:2
Alignment explanation
Indices: 800283--800322 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
800273 TCACATTTTT
800283 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
800323 GTGTGTGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:800327 original size:2 final size:2
Alignment explanation
Indices: 800322--800356 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
800312 TATATATATA
800322 TG TG TG TG 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 TG TG TG TG T
800357 TTATTTAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:801494 original size:6 final size:7
Alignment explanation
Indices: 801481--801508 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
801471 CCTTATATTA
801481 TTATTTT
1 TTATTTT
801488 TTATTTT
1 TTATTTT
801495 TTATTTT
1 TTATTTT
801502 TTATTTT
1 TTATTTT
801509 ATTGTATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTATTTT
Found at i:801528 original size:2 final size:2
Alignment explanation
Indices: 801521--801559 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
801511 TGTATGTATG
801521 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
801560 TTAATTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:801738 original size:4 final size:4
Alignment explanation
Indices: 801729--801753 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
801719 ATATCTATAC
801729 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
801754 TTCTTTGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:801858 original size:15 final size:15
Alignment explanation
Indices: 801840--801886 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
801830 CTTTTGTCTC
801840 TATTTATTTTTATTT
1 TATTTATTTTTATTT
801855 TATTTATTTTGTTTATTT
1 TATTTA--TT-TTTATTT
*
801873 T-TCTATTTTTATTT
1 TATTTATTTTTATTT
801887 ATGTTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 7 0.25
15 8 0.29
17 5 0.18
18 8 0.29
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (15 bp):
TATTTATTTTTATTT
Found at i:801871 original size:18 final size:17
Alignment explanation
Indices: 801848--801906 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
801838 TCTATTTATT
*
801848 TTTATTTTATTTATTTTG
1 TTTATTTT-TTTATTTTA
*
801866 TTTATTTTTCTATTTTTA
1 TTTATTTTTTTA-TTTTA
801884 TTTATGTTTCTTTATTTTCA
1 TTTAT-TTT-TTTATTTT-A
801904 TTT
1 TTT
801907 TGCTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.09
18 17 0.50
19 7 0.21
20 7 0.21
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTATTTTTTTATTTTA
Found at i:801902 original size:27 final size:26
Alignment explanation
Indices: 801842--801907 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
801832 TTTGTCTCTA
*
801842 TTTATTTT-TA-TTTTATTTATTTTG
1 TTTATTTTCTATTTTTATTTATTTTC
801866 TTTATTTTTCTATTTTTATTTATGTTTC
1 TTTA-TTTTCTATTTTTATTTAT-TTTC
801894 TTTATTTTC-ATTTT
1 TTTATTTTCTATTTT
801908 GCTTAATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
24 4 0.11
25 4 0.11
26 7 0.19
27 15 0.41
28 7 0.19
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (26 bp):
TTTATTTTCTATTTTTATTTATTTTC
Found at i:802847 original size:36 final size:37
Alignment explanation
Indices: 802775--802847 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
802765 CATGGTGTAA
*
802775 TGATACCGATGATATGTTATGTGTTTTGACTAACTTT
1 TGATACCGATGATATGTTATGTGTATTGACTAACTTT
802812 TGATACCGATGATATGTTATGTG-ATTGACTAACTTT
1 TGATACCGATGATATGTTATGTGTATTGACTAACTTT
802848 GATTTTTGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 12 0.34
37 23 0.66
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (37 bp):
TGATACCGATGATATGTTATGTGTATTGACTAACTTT
Found at i:803039 original size:22 final size:22
Alignment explanation
Indices: 803013--803057 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
803003 ATGTTTGAAG
803013 AAATTTAT-TATGCTTTTAAATA
1 AAATTTATGTATGC-TTTAAATA
* *
803035 AAATTTTTGTATTCTTTAAATA
1 AAATTTATGTATGCTTTAAATA
803057 A
1 A
803058 CCATGTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (22 bp):
AAATTTATGTATGCTTTAAATA
Found at i:803529 original size:31 final size:31
Alignment explanation
Indices: 803491--803561 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
803481 CTGTTAAAAC
803491 TTGCAATA-CAGTCCCCCAACATTTAGTCAGT
1 TTGCAATATCAG-CCCCCAACATTTAGTCAGT
* *
803522 TTGCAATATGAGCCCCCAACATTTAGTCCGT
1 TTGCAATATCAGCCCCCAACATTTAGTCAGT
*
803553 TTGTAATAT
1 TTGCAATAT
803562 GATCCCCGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (31 bp):
TTGCAATATCAGCCCCCAACATTTAGTCAGT
Found at i:803562 original size:31 final size:31
Alignment explanation
Indices: 803503--803568 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
803493 GCAATACAGT
803503 CCCCCAACATTTAGTCAGTTTGCAATATGAG
1 CCCCCAACATTTAGTCAGTTTGCAATATGAG
* * *
803534 CCCCCAACATTTAGTCCGTTTGTAATATGAT
1 CCCCCAACATTTAGTCAGTTTGCAATATGAG
803565 CCCC
1 CCCC
803569 GACCGTTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (31 bp):
CCCCCAACATTTAGTCAGTTTGCAATATGAG
Found at i:805584 original size:31 final size:30
Alignment explanation
Indices: 805545--805609 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 30
805535 TCAAACGGTC
*
805545 GGGGACCATATTGAAAACGGACTAAATGTT
1 GGGGACCATATTGAAAACAGACTAAATGTT
*
805575 GGGGAACCATATTGCAAACAGACTAAATGTT
1 GGGG-ACCATATTGAAAACAGACTAAATGTT
805606 GGGG
1 GGGG
805610 GACTGTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.35, C:0.14, G:0.29, T:0.22
Consensus pattern (30 bp):
GGGGACCATATTGAAAACAGACTAAATGTT
Found at i:813881 original size:40 final size:40
Alignment explanation
Indices: 813832--813913 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
813822 ATAGGAGTCA
* *
813832 AATATTGCACAATAGTGCTGAGGTCGAGCCCTT-CTCACCT
1 AATAATGCACAATAGTGCTGAGGTC-AGCCCTTGCCCACCT
** *
813872 AATAATGCACCGTAGTGCTGAGGTCAGGCCTTGCCCACCT
1 AATAATGCACAATAGTGCTGAGGTCAGCCCTTGCCCACCT
813912 AA
1 AA
813914 CTTGTACTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
39 6 0.17
40 30 0.83
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
AATAATGCACAATAGTGCTGAGGTCAGCCCTTGCCCACCT
Found at i:814860 original size:30 final size:31
Alignment explanation
Indices: 814801--814860 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
814791 CAATAATTCA
* * *
814801 CAACTTTTCCAAAATTATCGATTTGATCCCT
1 CAACTTTTCAAAAATTATAGATATGATCCCT
*
814832 CAACTTTTTAAAAATTATAGA-ATGATCCC
1 CAACTTTTCAAAAATTATAGATATGATCCC
814861 AAAATTTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
CAACTTTTCAAAAATTATAGATATGATCCCT
Found at i:821066 original size:25 final size:25
Alignment explanation
Indices: 821032--821082 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
821022 AGTACGCCCA
*
821032 ACTGCAAGCTGCCCAGG-AGGAGACC
1 ACTGCAAGCTACCCAGGAAGG-GACC
*
821057 ACTGCCAGCTACCCAGGAAGGGACC
1 ACTGCAAGCTACCCAGGAAGGGACC
821082 A
1 A
821083 TTGATGCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.29, C:0.33, G:0.29, T:0.08
Consensus pattern (25 bp):
ACTGCAAGCTACCCAGGAAGGGACC
Found at i:823354 original size:19 final size:19
Alignment explanation
Indices: 823330--823373 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
823320 TCAAAATAGA
823330 AATTCCAACATTGATTATC
1 AATTCCAACATTGATTATC
823349 AATTCCAACATTGATTATC
1 AATTCCAACATTGATTATC
823368 AATTCC
1 AATTCC
823374 CATCTACGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (19 bp):
AATTCCAACATTGATTATC
Found at i:830679 original size:20 final size:20
Alignment explanation
Indices: 830650--830688 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
830640 AGAGCTCATA
*
830650 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
830670 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
830689 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:832697 original size:57 final size:57
Alignment explanation
Indices: 832609--832724 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
832599 TGGAGGAAAT
* *
832609 GCAAAGCTAAGACGATTGAGTTGGCGCTGAATAACTCGAATCTCATCACCTAAGGAA
1 GCAAAGCTAAGACGATCGAGTTGGAGCTGAATAACTCGAATCTCATCACCTAAGGAA
832666 GCAAAGCTAAGACGATCGAGTTGGAGCTGAATAACTCGAATCTCATCACCTAAGGAA
1 GCAAAGCTAAGACGATCGAGTTGGAGCTGAATAACTCGAATCTCATCACCTAAGGAA
832723 GC
1 GC
832725 TATTTGAGCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (57 bp):
GCAAAGCTAAGACGATCGAGTTGGAGCTGAATAACTCGAATCTCATCACCTAAGGAA
Found at i:840127 original size:33 final size:34
Alignment explanation
Indices: 840064--840136 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 34
840054 CCCGATTATA
*
840064 TATATATATAATATTTTTTATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
840098 TATATATATAATATTTTATA-TTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
840131 TATATA
1 TATATA
840137 AAAAATAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 19 0.50
34 19 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:841289 original size:21 final size:21
Alignment explanation
Indices: 841264--841306 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
841254 GAGTGGAACG
* *
841264 ACGACCTAACTCTTTCCGTTA
1 ACGACCCAACTCTTCCCGTTA
841285 ACGACCCAACTCTTCCCGTTA
1 ACGACCCAACTCTTCCCGTTA
841306 A
1 A
841307 GCTCGTAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.37, G:0.09, T:0.28
Consensus pattern (21 bp):
ACGACCCAACTCTTCCCGTTA
Found at i:842427 original size:2 final size:2
Alignment explanation
Indices: 842420--842451 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
842410 ATAATAAGGA
842420 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
842452 GCTGAATTTA
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:842528 original size:59 final size:59
Alignment explanation
Indices: 842436--842554 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
842426 ATATATATAT
842436 ATATATATATATATATGCTGAATTTATTATCTTAGTGATTGGTTTTCTAAATTTATGGA
1 ATATATATATATATATGCTGAATTTATTATCTTAGTGATTGGTTTTCTAAATTTATGGA
842495 ATATATATATATATATGCTGAATTTATTATCTTAGTGATTGGTTTTCTAAATTTATGGA
1 ATATATATATATATATGCTGAATTTATTATCTTAGTGATTGGTTTTCTAAATTTATGGA
842554 A
1 A
842555 GTTTTCTAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (59 bp):
ATATATATATATATATGCTGAATTTATTATCTTAGTGATTGGTTTTCTAAATTTATGGA
Found at i:842724 original size:11 final size:11
Alignment explanation
Indices: 842708--842738 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
842698 CTAGTTACTT
842708 AAGATCATATA
1 AAGATCATATA
842719 AAGATCATATA
1 AAGATCATATA
*
842730 AAGACCATA
1 AAGATCATA
842739 CAAGGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.55, C:0.13, G:0.10, T:0.23
Consensus pattern (11 bp):
AAGATCATATA
Found at i:844030 original size:3 final size:3
Alignment explanation
Indices: 844022--844067 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
844012 GGTTCTCGTT
*
844022 TTA TTA TTA TTA TTA ATA TTA TTTA TTA TTA TT- TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA TTA
844068 ATTTACATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 1 0.03
3 33 0.87
4 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:844049 original size:19 final size:18
Alignment explanation
Indices: 844022--844067 Score: 74
Period size: 19 Copynumber: 2.5 Consensus size: 18
844012 GGTTCTCGTT
844022 TTATTATTATTATTAATA
1 TTATTATTATTATTAATA
*
844040 TTATTTATTATTATTTATA
1 TTA-TTATTATTATTAATA
844059 TTATTATTA
1 TTATTATTA
844068 ATTTACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTATTATTATTAATA
Found at i:851397 original size:36 final size:36
Alignment explanation
Indices: 851325--851421 Score: 140
Period size: 36 Copynumber: 2.7 Consensus size: 36
851315 ACAAAGTATC
* * *
851325 GTCTCGCTAGAGACGATTTTTCTTAAAAACAAATTTT
1 GTCTCGCTTGAGACAATTTTTC-TCAAAACAAATTTT
851362 GTCTCGCTTGAGACAATTTTTCTCAAAACAAATTTT
1 GTCTCGCTTGAGACAATTTTTCTCAAAACAAATTTT
* *
851398 GTCTCCCTTGAGACAATTTCTCTC
1 GTCTCGCTTGAGACAATTTTTCTC
851422 GGAATACAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 35 0.64
37 20 0.36
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (36 bp):
GTCTCGCTTGAGACAATTTTTCTCAAAACAAATTTT
Found at i:851736 original size:36 final size:36
Alignment explanation
Indices: 851689--851803 Score: 129
Period size: 36 Copynumber: 3.4 Consensus size: 36
851679 TCTTTTAGTC
851689 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACA
* *
851725 GTTTCTCTTGAAAC-AA-----TCATCT-TTGAGTC-
1 GTTTCCCTTGAAACGAATTTTGTC-TCTCTTGAGACA
*
851754 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGACACA
1 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACA
*
851790 GTTTCTCTTGAAAC
1 GTTTCCCTTGAAAC
851804 AATCATCCTT
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
29 13 0.20
30 10 0.16
31 3 0.05
34 3 0.05
35 9 0.14
36 26 0.41
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACA
Found at i:851751 original size:30 final size:30
Alignment explanation
Indices: 851717--851835 Score: 98
Period size: 30 Copynumber: 3.8 Consensus size: 30
851707 TTTGTCTCTC
*
851717 TTGAGACAGTTTCTCTTGAAACAATCATCT
1 TTGAGACAGTTTCCCTTGAAACAATCATCT
*
851747 TTGAGTC-GTTTCCCTTGAAACGAATTTTGTC-TCT
1 TTGAGACAGTTTCCCTTGAAAC-AA-----TCATCT
* * *
851781 CTTGACACAGTTTCTCTTGAAACAATCATCC
1 -TTGAGACAGTTTCCCTTGAAACAATCATCT
* *
851812 TTGAGTCTGTTTCCCTTGAAACAA
1 TTGAGACAGTTTCCCTTGAAACAA
851836 ATCCTTAAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
29 13 0.19
30 30 0.43
31 2 0.03
34 3 0.04
35 9 0.13
36 13 0.19
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (30 bp):
TTGAGACAGTTTCCCTTGAAACAATCATCT
Found at i:851767 original size:65 final size:65
Alignment explanation
Indices: 851663--851833 Score: 281
Period size: 65 Copynumber: 2.6 Consensus size: 65
851653 AAAAATTGTC
* * *
851663 TCTCTTGAAACACA-AATCTTTTAGTCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGT
1 TCTCTTGAAACA-ATCATCTTTGAGTCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGACACAGT
851727 T
65 T
851728 TCTCTTGAAACAATCATCTTTGAGTCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGACACAGTT
1 TCTCTTGAAACAATCATCTTTGAGTCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGACACAGTT
*
851793 TCTCTTGAAACAATCATCCTTGAGTCTGTTTCCCTTGAAAC
1 TCTCTTGAAACAATCATCTTTGAGTC-GTTTCCCTTGAAAC
851834 AAATCCTTAA
Statistics
Matches: 100, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
64 1 0.01
65 85 0.85
66 14 0.14
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.39
Consensus pattern (65 bp):
TCTCTTGAAACAATCATCTTTGAGTCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGACACAGTT
Found at i:851944 original size:43 final size:44
Alignment explanation
Indices: 851889--852093 Score: 124
Period size: 43 Copynumber: 4.7 Consensus size: 44
851879 TCATCCACCG
*
851889 ACCAGACC-TCCTCATCACGTAGGAGCCGTGTCACCCCT-AGATA
1 ACCAG-CCATCCTCATCACGTAGGAACCGTGTCACCCCTAAGATA
* * * * *
851932 ACCAGTCGTCCTCATCATGTAGGAACCATGTTATCATCCCTAAAGATA
1 ACCAGCCATCCTCATCACGTAGGAACC--G-TGTCACCCCT-AAGATA
* * * * *
851980 GCCTA-CCTTCCTCATCATGTAGAAACCGTGTCATCCACT--G---
1 ACC-AGCCATCCTCATCACGTAGGAACCGTGTCA-CCCCTAAGATA
* * * *
852020 ACCAGACC-TCTTCATCACGTAGGAGCCGTGTCA-ACCTCAGATA
1 ACCAG-CCATCCTCATCACGTAGGAACCGTGTCACCCCTAAGATA
*
852063 ACCAACCATCCTCATCACGTAGGAACCGTGT
1 ACCAGCCATCCTCATCACGTAGGAACCGTGT
852094 TATCATCCCT
Statistics
Matches: 124, Mismatches: 22, Indels: 32
0.70 0.12 0.18
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 24 0.19
41 2 0.02
42 3 0.02
43 48 0.39
45 5 0.04
46 12 0.10
48 26 0.21
49 1 0.01
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (44 bp):
ACCAGCCATCCTCATCACGTAGGAACCGTGTCACCCCTAAGATA
Found at i:852075 original size:131 final size:130
Alignment explanation
Indices: 851867--852332 Score: 529
Period size: 131 Copynumber: 3.5 Consensus size: 130
851857 TCTTCATCGC
*
851867 GTAGAAACCATGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATA
1 GTAGAAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATA
* * ** *
851932 ACCAGTCGTCCTCATCATGTAGGAACCATGTTATCATCCCTAAAGATAGCCTACCTTCCTCATCA
66 ACCAGCCGTCCTCATCACGTAGGAACCATGTTATCATCCCTAAAGAT-GCCTGTCATCCTCATCA
851997 T
130 T
* * *
851998 GTAGAAACCGTGTCATCCACTGACCAGACCTCTTCATCACGTAGGAGCCGTGTCA-ACCTCAGAT
1 GTAGAAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCT-AGAT
* * *
852062 AACCAACCATCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGACCTGTCATCCTCATC
65 AACCAGCCGTCCTCATCACGTAGGAACCATGTTATCATCCCTAAAGATG-CCTGTCATCCTCATC
852127 AT
129 AT
* * * * * ** *
852129 TTAGAAACTGTGTTATCCACCGCCCAGATCTCCTCATCACGTAGGAGATGTGTCACCCCTAGTTA
1 GTAGAAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATA
* * * * * * * *
852194 ACCAGCCGTCTTTATCGCGTAGGAATCATATTATCACCCTCTCTAAAGATGGCTTGTCGTCCTCA
66 ACCAGCCGTCCTCATCACGTAGGAACCATGTTATCA---TCCCTAAAGAT-GCCTGTCATCCTCA
**
852259 TCGC
127 TCAT
* ** * * * *
852263 GTAGGAACCGTGTCATCCACCGACCAGATATCCTTATCCCGTAGGAGCCGTGTCACCCTTAGATG
1 GTAGAAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATA
852328 ACCAG
66 ACCAG
852333 AACTCTTCAT
Statistics
Matches: 279, Mismatches: 49, Indels: 11
0.82 0.14 0.03
Matches are distributed among these distances:
130 4 0.01
131 191 0.68
132 3 0.01
134 80 0.29
135 1 0.00
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (130 bp):
GTAGAAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATA
ACCAGCCGTCCTCATCACGTAGGAACCATGTTATCATCCCTAAAGATGCCTGTCATCCTCATCAT
Found at i:852359 original size:265 final size:262
Alignment explanation
Indices: 851881--852359 Score: 611
Period size: 265 Copynumber: 1.8 Consensus size: 262
851871 AAACCATGTC
* *
851881 ATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCA
1 ATCCACCGACCAGACCTCCTCATCACGTAGGAGACGTGTCACCCCTAGATAACCAGCCGTCCTCA
* * * *
851946 TCATGTAGGAACCATGTTATCATCCCTAAAGATAGCCTACCTTCCTCATCATGTAGAAACCGTGT
66 TCACGTAGGAACCATATTATCATCCCTAAAGATAGCCTACCGTCCTCATCACGTAGAAACCGTGT
* * *
852011 CATCCACTGACCAGACCTCTTCATCACGTAGGAGCCGTGTCAACCTCAGATAACCAACCATCCTC
131 CATCCACCGACCAGACATCTTCATCACGTAGGAGCCGTGTCAACCTCAGATAACCAAACATCCTC
852076 ATCACGTAGGAACCGTGTTATCATCCCTAAAGATGACCTGTCATCCTCATCATTTAGAAACTGTG
196 ATCACGTAGGAACCGTGTTATCATCCCTAAAGATGACCTGTCATCCTCATCATTTAGAAACTGTG
852141 TT
261 TT
* * * * * *
852143 ATCCACCGCCCAGATCTCCTCATCACGTAGGAGATGTGTCACCCCTAGTTAACCAGCCGTCTTTA
1 ATCCACCGACCAGACCTCCTCATCACGTAGGAGACGTGTCACCCCTAGATAACCAGCCGTCCTCA
* * * * * ** * *
852208 TCGCGTAGGAATCATATTATCACCCTCTCTAAAGATGGCTTGTCGTCCTCATCGCGTAGGAACCG
66 TCACGTAGGAACCATATTATCA---TCCCTAAAGATAGCCTACCGTCCTCATCACGTAGAAACCG
* * * * *
852273 TGTCATCCACCGACCAGATATCCTT-ATCCCGTAGGAGCCGTGTCACCCTTAGATGACCAGAAC-
128 TGTCATCCACCGACCAGACAT-CTTCATCACGTAGGAGCCGTGTCAACCTCAGATAACCA-AACA
* * *
852336 TCTTCATCACGTATGAGCCGTGTT
191 TCCTCATCACGTAGGAACCGTGTT
852360 GTCCCCTACA
Statistics
Matches: 180, Mismatches: 32, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
262 75 0.42
265 100 0.56
266 5 0.03
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.25
Consensus pattern (262 bp):
ATCCACCGACCAGACCTCCTCATCACGTAGGAGACGTGTCACCCCTAGATAACCAGCCGTCCTCA
TCACGTAGGAACCATATTATCATCCCTAAAGATAGCCTACCGTCCTCATCACGTAGAAACCGTGT
CATCCACCGACCAGACATCTTCATCACGTAGGAGCCGTGTCAACCTCAGATAACCAAACATCCTC
ATCACGTAGGAACCGTGTTATCATCCCTAAAGATGACCTGTCATCCTCATCATTTAGAAACTGTG
TT
Found at i:852517 original size:3 final size:3
Alignment explanation
Indices: 852509--852547 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
852499 GGTTCTCATT
852509 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
852548 ATTTACATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:857683 original size:17 final size:17
Alignment explanation
Indices: 857661--857694 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
857651 TACTAAAAAA
857661 CTTAAACAAATTATTTT
1 CTTAAACAAATTATTTT
*
857678 CTTAAATAAATTATTTT
1 CTTAAACAAATTATTTT
857695 TTCTTTAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
CTTAAACAAATTATTTT
Found at i:858129 original size:25 final size:26
Alignment explanation
Indices: 858101--858240 Score: 81
Period size: 26 Copynumber: 5.3 Consensus size: 26
858091 AAGAAAAAAA
858101 TTCGGTT-AATAATTTTCAAATAAAT
1 TTCGGTTCAATAATTTTCAAATAAAT
* * *
858126 TTCGGTTCGATTAACTGTCAAAT-AAT
1 TTCGGTTC-AATAATTTTCAAATAAAT
* * * * * *
858152 TTCAGTTCGATTAATGGTTAAAGAAAAACA
1 TTCGGTTC-AATAAT-TTTCAA-ATAAA-T
858182 TTCGGTT-AATAATTTTCAAATAAAT
1 TTCGGTTCAATAATTTTCAAATAAAT
* ***
858207 TTCGGTTCGATTAACAGTCAAAT-AAT
1 TTCGGTTC-AATAATTTTCAAATAAAT
858233 TTCGGTTC
1 TTCGGTTC
858241 GATTAATGTT
Statistics
Matches: 87, Mismatches: 20, Indels: 15
0.71 0.16 0.12
Matches are distributed among these distances:
25 14 0.16
26 31 0.36
27 28 0.32
28 6 0.07
29 2 0.02
30 6 0.07
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.39
Consensus pattern (26 bp):
TTCGGTTCAATAATTTTCAAATAAAT
Found at i:858159 original size:26 final size:26
Alignment explanation
Indices: 858116--858246 Score: 106
Period size: 26 Copynumber: 4.9 Consensus size: 26
858106 TTAATAATTT
858116 TCAAATAAATTTCGGTTCGATTAACTG
1 TCAAAT-AATTTCGGTTCGATTAACTG
*
858143 TCAAATAATTTCAGTTCGATTAA-TGG
1 TCAAATAATTTCGGTTCGATTAACT-G
* * * * * *
858169 TTAAAGAAAAACATTCGGTT--AATAATTT
1 -T-CA-AATAA-TTTCGGTTCGATTAACTG
*
858197 TCAAATAAATTTCGGTTCGATTAACAG
1 TCAAAT-AATTTCGGTTCGATTAACTG
858224 TCAAATAATTTCGGTTCGATTAA
1 TCAAATAATTTCGGTTCGATTAA
858247 TGTTAAAGAA
Statistics
Matches: 81, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
25 10 0.12
26 37 0.46
27 18 0.22
28 5 0.06
29 5 0.06
30 6 0.07
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (26 bp):
TCAAATAATTTCGGTTCGATTAACTG
Found at i:858272 original size:81 final size:81
Alignment explanation
Indices: 858037--858261 Score: 371
Period size: 81 Copynumber: 2.8 Consensus size: 81
858027 TAACCGAATA
* * * * *
858037 AAATAAATTTGGGTTCGATTAACGGTAAAATAATTTTGATTCGATTAATGGTTAAAGAAAAAAAT
1 AAATAAATTTCGGTTCGATTAACAGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAAT
858102 TCGGTTAATAATTTTC
66 TCGGTTAATAATTTTC
* * *
858118 AAATAAATTTCGGTTCGATTAACTGTCAAATAATTTCAGTTCGATTAATGGTTAAAGAAAAACAT
1 AAATAAATTTCGGTTCGATTAACAGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAAT
858183 TCGGTTAATAATTTTC
66 TCGGTTAATAATTTTC
858199 AAATAAATTTCGGTTCGATTAACAGTCAAATAATTTCGGTTCGATTAAT-GTTAAAGAAAAAAA
1 AAATAAATTTCGGTTCGATTAACAGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAA
858262 AATCGATTAA
Statistics
Matches: 134, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
80 13 0.10
81 121 0.90
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.36
Consensus pattern (81 bp):
AAATAAATTTCGGTTCGATTAACAGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAAT
TCGGTTAATAATTTTC
Found at i:858355 original size:95 final size:95
Alignment explanation
Indices: 858182--858356 Score: 287
Period size: 95 Copynumber: 1.8 Consensus size: 95
858172 AAGAAAAACA
* *
858182 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACAGTCAAATAATTTCGGTTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCAGTTCGATTAACAGTCAAATAATTTCAGTTCGATTAA
858247 TGTTAAAGAAAAAAAAATCGATTAATTTGG
66 TGTTAAAGAAAAAAAAATCGATTAATTTGG
* * *
858277 TTCGGTTAATAATTTTCAAATAAATTTTAGTTCGATTAACGGTCAAATAATTTCAGTTTGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCAGTTCGATTAACAGTCAAATAATTTCAGTTCGATTAA
*
858342 TGGTTACAGAAAAAA
66 T-GTTAAAGAAAAAA
858357 TTCGGTTAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
95 61 0.84
96 12 0.16
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (95 bp):
TTCGGTTAATAATTTTCAAATAAATTTCAGTTCGATTAACAGTCAAATAATTTCAGTTCGATTAA
TGTTAAAGAAAAAAAAATCGATTAATTTGG
Found at i:861174 original size:2 final size:2
Alignment explanation
Indices: 861163--861210 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
861153 AAAGATAAAA
861163 AT AT -T 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
861204 AT AT AT A
1 AT AT AT A
861211 ATTGTTTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:868161 original size:21 final size:20
Alignment explanation
Indices: 868104--868166 Score: 74
Period size: 19 Copynumber: 3.1 Consensus size: 20
868094 AATTCCTTTG
* *
868104 TTGCATTTACATTTTCAT-T
1 TTGCATTTGCATTTGCATCT
**
868123 TTGCATTCCCATTTGCATCT
1 TTGCATTTGCATTTGCATCT
868143 TTGCATTTGCATGTTGCATCT
1 TTGCATTTGCAT-TTGCATCT
868164 TTG
1 TTG
868167 TATTAGCATC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.41
20 11 0.30
21 11 0.30
ACGTcount: A:0.16, C:0.21, G:0.13, T:0.51
Consensus pattern (20 bp):
TTGCATTTGCATTTGCATCT
Found at i:868175 original size:21 final size:21
Alignment explanation
Indices: 868122--868175 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
868112 ACATTTTCAT
**
868122 TTTGCATTCCCAT-TTGCATC
1 TTTGCATTAGCATGTTGCATC
*
868142 TTTGCATTTGCATGTTGCATC
1 TTTGCATTAGCATGTTGCATC
*
868163 TTTGTATTAGCAT
1 TTTGCATTAGCAT
868176 CTATACATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.48
Consensus pattern (21 bp):
TTTGCATTAGCATGTTGCATC
Found at i:882987 original size:54 final size:53
Alignment explanation
Indices: 882928--883104 Score: 228
Period size: 54 Copynumber: 3.3 Consensus size: 53
882918 CTTGATTTCC
* * *
882928 AGGGGTTTCTTGATGTTTTCAAATGAATTTTGAAAGAAGATAAGCCTAACTTTT
1 AGGGGTTTCTTGATGTCTTCAAATGAATTTTAAAAGAAGCTAAGCCTAA-TTTT
* * *
882982 AGGGGTTTATTGATGTCTTCAAATGGATTTTAAAAGAAGCTAAGCCTGATTTT
1 AGGGGTTTCTTGATGTCTTCAAATGAATTTTAAAAGAAGCTAAGCCTAATTTT
* * * *
883035 CAAGGGTTTCTTGATGTCTTCAAATGAATTTTTAAATAAGCTAAGGCTAATTTTT
1 -AGGGGTTTCTTGATGTCTTCAAATGAATTTTAAAAGAAGCTAAGCCTAA-TTTT
*
883090 TGGGGTTTCTTGATG
1 AGGGGTTTCTTGATG
883105 ATAACTGTAA
Statistics
Matches: 106, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 4 0.04
54 98 0.92
55 4 0.04
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (53 bp):
AGGGGTTTCTTGATGTCTTCAAATGAATTTTAAAAGAAGCTAAGCCTAATTTT
Found at i:884941 original size:200 final size:201
Alignment explanation
Indices: 884535--885311 Score: 1014
Period size: 203 Copynumber: 3.9 Consensus size: 201
884525 GGATAAACCA
* * * *
884535 ATCAACATTTCTAGTGGTGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
* * * * *
884600 ATTGAGAAGAACTTGATCAACCTTAGCTCGATTCCATCACATAAAGAGTTGGAACAGCACCAATA
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCACATAAGGAGTTGGAACAACACCAACA
* * * * *
884665 CTTGGCTCATCCATCATATAC-AAAGTTGGATCAACATCATCAC-TTCATTCGATTCTATCATAG
131 CTTGGCTCATCCATCACAT-CTAGAGTTGGATCAGCATCATCACTTTGA-TCGATTC-ATCAAAG
884728 AATGAGTTGG
193 AATGAG-TGG
* * *
884738 ATCAATATTTCCAATGGAAGGGTTCATAATGAG-A-AA-TCGTCCGATGAGGGAGAA-AAGTTCA
1 ATCAACATTTCCAATGG-AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
* *
884799 TAATGAGAAGAACATGTTCAACCTTAGCTCGATTCCGTCACATAAGGAGTTGGAACAACACCAAC
65 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCACATAAGGAGTTGGAACAACACCAAC
* * *
884864 ACTTTGCTCATCCATTACATCTAGAGTTGGATCAGCATCATCACTTTGATCGATTGCATCACAGA
130 ACTTGGCTCATCCATCACATCTAGAGTTGGATCAGCATCATCACTTTGATCGATT-CATCAAAGA
*
884929 TTGACGTGG
194 ATGA-GTGG
* * * * *
884938 ATCAACATTTCCAGTTGAGAGTTCATAATGAGAAGAACTCGTCCAATGAAGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
* * *
885003 AATGAGAAGAACTTGTTCAACCTTAGTTCGTTTCCATCACATAAGAAGTTGGAACAACA-CAAGC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCACATAAGGAGTTGGAACAACACCAA-C
* * * * * *
885067 ACTTTGCTTATCCATCACATATGGAGTTGGATCAGCATCATCACTTTGTTCAATTCCATCAAAGA
130 ACTTGGCTCATCCATCACATCTAGAGTTGGATCAGCATCATCACTTTGATCGATT-CATCAAAGA
885132 ATGAGGTGG
194 ATGA-GTGG
885141 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
* * *
885206 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCGCATAAGGAGTTGGAACAGCACCGAC-
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCACATAAGGAGTTGGAACAACACCAACA
* *
885270 CTTGGCTTATCCATCACAT-AAGTAGTTGGATCAGCATCATCA
131 CTTGGCTCATCCATCACATCTAG-AGTTGGATCAGCATCATCA
885312 TTTCGCTCGT
Statistics
Matches: 505, Mismatches: 57, Indels: 25
0.86 0.10 0.04
Matches are distributed among these distances:
199 15 0.03
200 136 0.27
201 24 0.05
202 58 0.11
203 257 0.51
204 15 0.03
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (201 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCACATAAGGAGTTGGAACAACACCAACA
CTTGGCTCATCCATCACATCTAGAGTTGGATCAGCATCATCACTTTGATCGATTCATCAAAGAAT
GAGTGG
Found at i:885020 original size:20 final size:19
Alignment explanation
Indices: 884958--885021 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 19
884948 CCAGTTGAGA
884958 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* *
884977 CGTCCAATGAAGGAGAAGAA--
1 -GTTC-AT-AATGAGAAGAACT
884997 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
885017 GTTCA
1 GTTCA
885022 ACCTTAGTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 10 0.29
18 2 0.06
19 3 0.09
20 8 0.23
21 2 0.06
22 10 0.29
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:885344 original size:403 final size:402
Alignment explanation
Indices: 884535--885345 Score: 1080
Period size: 403 Copynumber: 2.0 Consensus size: 402
884525 GGATAAACCA
* * ** *
884535 ATCAACATTTCTAGTGGTGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAGAAGTTCAT
* * *
884600 ATTGAGAAGAACTTGATCAACCTTAGCTCGATTCCATCACATAAAGAGTTGGAACAGCACCAATA
66 AATGAGAAGAACTTGATCAACCTTAGCTCGATTCCATCACATAAAGAGTTGGAACAACACCAACA
* * * *
884665 CTTGGCTCATCCATCATATACAAAGTTGGATCAACATCATCACTTCATTCGATTCTATCATAGAA
131 CTTGGCTCATCCATCACATACAAAGTTGGATCAACATCATCACTTCATTCAATTCCATCAAAGAA
* * * *
884730 TGAGTTGGATCAATATTTCCAATGGAAGGGTTCATAATGAGAAATCGTCCGATGAGGGAGAAAAG
196 TGAGGTGGATCAACATTTCCAATGGAAGAGTTCATAATGAGAAATCATCCGATGAGGGAGAAAAG
*
884795 TTCATAATGAGAAGAACATGTTCAACCTTAGCTCGATTCCGTCACATAAGGAGTTGGAACAACAC
261 TTCATAATGAGAAGAACATGTTCAACCTTAGCTCGATTCCATCACATAAGGAGTTGGAACAACAC
* * * *
884860 CAACACTTTGCTCATCCATTACATCTAGAGTTGGATCAGCATCATCACTTTGATCGATTGCATCA
326 CAACACTTGGCTCATCCATCACATCAAGAGTTGGATCAGCATCATCACTTTGATCGA-TCCATCA
**
884925 CAGATTGACGTGG
390 CAGAAGGACGTGG
* *
884938 ATCAACATTTCCAGTTGAGAGTTCATAATGAGAAGAACTCGTCCAATGAAGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAGAAGTTCAT
* * *
885003 AATGAGAAGAACTTGTTCAACCTTAGTTCGTTTCCATCACAT-AAGAAGTTGGAACAACA-CAAG
66 AATGAGAAGAACTTGATCAACCTTAGCTCGATTCCATCACATAAAG-AGTTGGAACAACACCAA-
* * *** * **
885066 CACTTTGCTTATCCATCACATATGGAGTTGGATCAGCATCATCACTTTGTTCAATTCCATCAAAG
129 CACTTGGCTCATCCATCACATACAAAGTTGGATCAACATCATCACTTCATTCAATTCCATCAAAG
885131 AATGAGGTGGATCAACATTTCCAATGG-AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAG
194 AATGAGGTGGATCAACATTTCCAATGGAAGAGTTCATAATGAG-A-AA-TCATCCGATGAGGGAG
* *
885195 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCGCATAAGGAGTTGGAA
256 AA-AAGTTCATAATGAGAAGAACATGTTCAACCTTAGCTCGATTCCATCACATAAGGAGTTGGAA
* * * *
885260 CAGCACCGAC-CTTGGCTTATCCATCACAT-AAGTAGTTGGATCAGCATCATCA-TTTCGCTCG-
320 CAACACCAACACTTGGCTCATCCATCACATCAAG-AGTTGGATCAGCATCATCACTTT-GATCGA
* *
885321 TCCATCATATAAGGA-GTTGG
383 TCCATCACAGAAGGACG-TGG
885341 ATCAA
1 ATCAA
885346 TATCAACATT
Statistics
Matches: 355, Mismatches: 44, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
402 21 0.06
403 204 0.57
404 7 0.02
405 56 0.16
406 67 0.19
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (402 bp):
ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAGAAGTTCAT
AATGAGAAGAACTTGATCAACCTTAGCTCGATTCCATCACATAAAGAGTTGGAACAACACCAACA
CTTGGCTCATCCATCACATACAAAGTTGGATCAACATCATCACTTCATTCAATTCCATCAAAGAA
TGAGGTGGATCAACATTTCCAATGGAAGAGTTCATAATGAGAAATCATCCGATGAGGGAGAAAAG
TTCATAATGAGAAGAACATGTTCAACCTTAGCTCGATTCCATCACATAAGGAGTTGGAACAACAC
CAACACTTGGCTCATCCATCACATCAAGAGTTGGATCAGCATCATCACTTTGATCGATCCATCAC
AGAAGGACGTGG
Found at i:885417 original size:40 final size:40
Alignment explanation
Indices: 885238--885461 Score: 207
Period size: 42 Copynumber: 5.5 Consensus size: 40
885228 TTAGCTCGAT
* * * **
885238 TCCATCGCATAAGGAGTTGGAACAGCACCGACCTTGGCTTA
1 TCCATCACATAAGGAGTTGGATCAGCATC-ACCTTGGCTCG
* * *
885279 TCCATCACATAAGTAGTTGGATCAGCATCATCATTTCGCTCG
1 TCCATCACATAAGGAGTTGGATCAGCATCA-C-CTTGGCTCG
* ** * ** *
885321 TCCATCATATAAGGAGTTGGATCAATATCAACATTTCCCTTG
1 TCCATCACATAAGGAGTTGGATCAGCATC-AC-CTTGGCTCG
* *
885363 TCCATCATATAAGGAGTTGGATCAGTATCACCTTGGCTCG
1 TCCATCACATAAGGAGTTGGATCAGCATCACCTTGGCTCG
* *
885403 TCCATCACATAAGGAGTTGGATCAGCATCACCTTGGGTCA
1 TCCATCACATAAGGAGTTGGATCAGCATCACCTTGGCTCG
* *
885443 ACCATCGCA-AAGGAGTTGG
1 TCCATCACATAAGGAGTTGG
885462 GTCAACGTTT
Statistics
Matches: 155, Mismatches: 25, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
39 10 0.06
40 49 0.32
41 28 0.18
42 67 0.43
43 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (40 bp):
TCCATCACATAAGGAGTTGGATCAGCATCACCTTGGCTCG
Found at i:885698 original size:3 final size:3
Alignment explanation
Indices: 885692--885728 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
885682 TTTTTACTAT
885692 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
885729 AAAGCAAACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:888306 original size:139 final size:140
Alignment explanation
Indices: 888018--888306 Score: 335
Period size: 139 Copynumber: 2.1 Consensus size: 140
888008 TCCCTAAACT
* *
888018 TTTAATTTAGGAGAATTTTTTATTTGGTCCTCGCTTATGCTCAAGGTTCCGAATTAATTATTCGA
1 TTTAATTTAGGAGAATTCTTAATTTGGTCCTCGCTTATGCTCAAGGTTCCGAATTAATTATTCGA
* * *
888083 TACTTCATAATTAACTAAAATTAATTAGGATTAATATTAGAGCCTTCATCTTAGGCTTAATTTCA
66 TACTTCATAATTAACTAAAATTAATTAAGATTAATATTAGAGCCTCCATCTTAGGATTAATTTCA
*
888148 CCTTTAGTCC
131 CATTTAGTCC
* * *
888158 -TTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTTTGCTCAAGGTTCC-ACTTTAATTATTCG
1 TTTAATTTAGGAGAATTCTTAATTTGGTCCTCGCTTATGCTCAAGGTTCCGA-ATTAATTATTCG
* * *
888221 A-A-TTACA-ATATTGATTAAAATTAATTTAAG-TTAATATTAGATCCTCCA-CTTTA-GATTAG
65 ATACTT-CATA-ATTAACTAAAATTAA-TTAAGATTAATATTAGAGCCTCCATC-TTAGGATTA-
*
888280 ATTTTA-ATTTAGTCCC
125 ATTTCACATTTAGT-CC
888296 TTTAATTTAGG
1 TTTAATTTAGG
888307 GAGTAATATG
Statistics
Matches: 127, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
137 14 0.11
138 43 0.34
139 70 0.55
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (140 bp):
TTTAATTTAGGAGAATTCTTAATTTGGTCCTCGCTTATGCTCAAGGTTCCGAATTAATTATTCGA
TACTTCATAATTAACTAAAATTAATTAAGATTAATATTAGAGCCTCCATCTTAGGATTAATTTCA
CATTTAGTCC
Found at i:890777 original size:14 final size:14
Alignment explanation
Indices: 890760--890788 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
890750 GAACACATTC
890760 TTTTTTAGACATAA
1 TTTTTTAGACATAA
890774 TTTTTTAGACATAA
1 TTTTTTAGACATAA
890788 T
1 T
890789 GACAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTTTTAGACATAA
Found at i:898007 original size:28 final size:28
Alignment explanation
Indices: 897967--898025 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
897957 TCTTGTAATG
897967 TATCATGGTGAACCCGTTTATTACTTCA
1 TATCATGGTGAACCCGTTTATTACTTCA
897995 TATCATGGTGAACCCGTTTATTACTTCA
1 TATCATGGTGAACCCGTTTATTACTTCA
898023 TAT
1 TAT
898026 ACCTATACGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (28 bp):
TATCATGGTGAACCCGTTTATTACTTCA
Found at i:899620 original size:20 final size:20
Alignment explanation
Indices: 899597--899634 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
899587 ATTTTTTTTG
899597 TTCTTTTCAT-TTTTTAATAT
1 TTCTTTT-ATGTTTTTAATAT
899617 TTCTTTTATGTTTTTAAT
1 TTCTTTTATGTTTTTAAT
899635 GTTTTTATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (20 bp):
TTCTTTTATGTTTTTAATAT
Found at i:899631 original size:28 final size:29
Alignment explanation
Indices: 899579--899641 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
899569 AATATCATAA
*
899579 TTTTTAAGATTTTTTTTGTTCTTTTCAT-
1 TTTTTAAGATTTTTTTTGTTCTTTTAATG
*
899607 TTTTTAATATTTCTTTTATG-T-TTTTAATG
1 TTTTTAAGATTT-TTTT-TGTTCTTTTAATG
899636 TTTTTA
1 TTTTTA
899642 TGGATTTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 17 0.57
29 11 0.37
30 2 0.07
ACGTcount: A:0.17, C:0.05, G:0.06, T:0.71
Consensus pattern (29 bp):
TTTTTAAGATTTTTTTTGTTCTTTTAATG
Found at i:900099 original size:21 final size:21
Alignment explanation
Indices: 900070--900109 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
900060 AAATGTAAAA
*
900070 AATTGAAATTTGTT-TTTTAAT
1 AATTAAAATTT-TTATTTTAAT
900091 AATTAAAATTTTTATTTTA
1 AATTAAAATTTTTATTTTA
900110 TTTTTACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
AATTAAAATTTTTATTTTAAT
Found at i:901276 original size:65 final size:65
Alignment explanation
Indices: 901139--901346 Score: 203
Period size: 65 Copynumber: 3.2 Consensus size: 65
901129 TGCACTAAGA
* * *
901139 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGTCTGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACTCTGAGTGCATCAATGCATAGCTG
* * *
901203 GTGTATCGATGCATCAAATGTATTCGATGTTTTCATAAA-ACTCTGAGTGCATCAATGCATAG-T
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATACTCTGAGTGCATCAATGCATAGCT
*
901266 AT
65 -G
* * ** * *
901268 GTGCATCGATGCATGAAATACATTCGATG--TTCAATTTATTCCATG-GTGCATCAATGCATGGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACT-C-TGAGTGCATCAATGCATAG-
*
901330 TTG
63 CTG
901333 GTGCATCGATGCAT
1 GTGCATCGATGCAT
901347 CACTTTGAAA
Statistics
Matches: 120, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 43 0.36
65 66 0.55
66 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACTCTGAGTGCATCAATGCATAGCTG
Found at i:904035 original size:23 final size:23
Alignment explanation
Indices: 904005--904087 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
903995 TGCATGGCCT
904005 TGTGCATCGATGCACACTCAAGG
1 TGTGCATCGATGCACACTCAAGG
* *
904028 TGTGCATCGGTGCAC-CTTCATGG
1 TGTGCATCGATGCACAC-TCAAGG
*
904051 TGT--ATCGATGCACATTCAAAGG
1 TGTGCATCGATGCACACTC-AAGG
*
904073 -GATGTATCGATGCAC
1 TG-TGCATCGATGCAC
904088 TGTTAAGTGT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
21 12 0.24
22 5 0.10
23 22 0.45
24 10 0.20
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (23 bp):
TGTGCATCGATGCACACTCAAGG
Found at i:904062 original size:21 final size:21
Alignment explanation
Indices: 904010--904106 Score: 74
Period size: 23 Copynumber: 4.4 Consensus size: 21
904000 GGCCTTGTGC
904010 ATCGATGCACAC-TCAAGGTGT
1 ATCGATGCAC-CTTCAAGGTGT
* *
904031 GCATCGGTGCACCTTCATGGTGT
1 --ATCGATGCACCTTCAAGGTGT
*
904054 ATCGATGCACATTCAAAGGGATGT
1 ATCGATGCACCTTC-AA-GG-TGT
*
904078 ATCGATGCA-CTGTTAA-GTGT
1 ATCGATGCACCT-TCAAGGTGT
904098 ATCGATGCA
1 ATCGATGCA
904107 TGAAGCACAA
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
20 12 0.19
21 13 0.21
22 2 0.03
23 22 0.35
24 13 0.21
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
ATCGATGCACCTTCAAGGTGT
Found at i:909992 original size:64 final size:62
Alignment explanation
Indices: 909923--910116 Score: 187
Period size: 65 Copynumber: 3.0 Consensus size: 62
909913 AGAGTACAAT
909923 GATGCATAAAATGCATTCGATGTTTCAAAATAGCATGAGTGCATCGATGCATGGCTGGTGCATC
1 GATGCATAAAATGCATTCGATGTTTCAAAATA-CATGAGTGCATCGATGCATGG-TGGTGCATC
* * * * * *
909987 GATGCATCAAATGCATTCGATGTTTTCATAAA-ACTCTGAGTGCATCGATGAATAGTATGTGTAT
1 GATGCATAAAATGCATTCGATG-TTTCA-AAATAC-ATGAGTGCATCGATGCATGGT-GGTGCAT
910051 C
62 C
* * *
910052 GATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGATTGGTGCA
1 GATGCATAAAATGCATTCGATGTTTCAA---AATACATGAGTGCATCGATGCATGG--TGGTGCA
910115 TC
61 TC
910117 ACTTTGAAAA
Statistics
Matches: 106, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
62 1 0.01
63 4 0.04
64 37 0.35
65 59 0.56
66 5 0.05
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (62 bp):
GATGCATAAAATGCATTCGATGTTTCAAAATACATGAGTGCATCGATGCATGGTGGTGCATC
Found at i:910053 original size:65 final size:65
Alignment explanation
Indices: 909923--910075 Score: 188
Period size: 65 Copynumber: 2.4 Consensus size: 65
909913 AGAGTACAAT
* *
909923 GATGCATAAAATGCATTCGATG-TTTCAAAATAGCATGAGTGCATCGATGCATGGCTGGTGCATC
1 GATGCATAAAATGCATTCGATGTTTTCAAAATAGCATGAGTGCATCGATGAATAGCTGGTGCATC
* * * *
909987 GATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGATGAATAG-TATGTGT
1 GATGCATAAAATGCATTCGATGTTTTCA-AAATAGC-ATGAGTGCATCGATGAATAGCT-GGTGC
910049 ATC
63 ATC
*
910052 GATGCATGAAATGCATTCGATGTT
1 GATGCATAAAATGCATTCGATGTT
910076 CAATTTATTC
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
64 23 0.29
65 52 0.67
66 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (65 bp):
GATGCATAAAATGCATTCGATGTTTTCAAAATAGCATGAGTGCATCGATGAATAGCTGGTGCATC
Found at i:911752 original size:2 final size:2
Alignment explanation
Indices: 911747--911796 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
911737 TTTATTTATT
911747 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
911789 TA T- TA TA T
1 TA TA TA TA T
911797 GGTTTGCAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:911830 original size:40 final size:41
Alignment explanation
Indices: 911780--911871 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 41
911770 ATATATATAT
*
911780 ATATATATATATTATATGGTTTGCAAAT-GTTTTT-GAAATAC
1 ATATA-ATATATTATA-GGTTTGAAAATGGTTTTTGGAAATAC
* *
911821 ATATAATATA-TATAGTTTTGAAAATGGTTTTTGGAAATAT
1 ATATAATATATTATAGGTTTGAAAATGGTTTTTGGAAATAC
*
911861 ATATAACATAT
1 ATATAATATAT
911872 AGTTTTGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
38 9 0.20
39 10 0.23
40 20 0.45
41 5 0.11
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (41 bp):
ATATAATATATTATAGGTTTGAAAATGGTTTTTGGAAATAC
Found at i:911863 original size:38 final size:36
Alignment explanation
Indices: 911778--912235 Score: 149
Period size: 38 Copynumber: 12.6 Consensus size: 36
911768 ATATATATAT
* *
911778 ATATATATATATATTATATGGTTTGCAAATGTTTTTGAA
1 ATATATA-ATATA-TATA-GTTTTGAAAATGTTTTTGAA
911817 ATACATATAATATATATAGTTTTGAAAATGGTTTTTGGAA
1 AT--ATATAATATATATAGTTTTGAAAAT-GTTTTT-GAA
* ***
911857 ATATAT-ATAACATATAGTTTTGAAAAACATTTTGAA
1 ATATATAAT-ATATATAGTTTTGAAAATGTTTTTGAA
* **
911893 A-ACT-TATATAATATATAGTTTTG-ATATCATTTTGAAAA
1 ATA-TATA-AT-ATATATAGTTTTGAAAATGTTTTTG--AA
* **
911931 TATATATAATATATATA-TTTTTAAAA-CATTTTGAA
1 -ATATATAATATATATAGTTTTGAAAATGTTTTTGAA
* **
911966 AAACT-TATATAATATATAGTTTTG-AAATCATTTT-AA
1 ATA-TATA-AT-ATATATAGTTTTGAAAATGTTTTTGAA
* ** *
912002 AAATATATATAATATATAGTTTTTTAAATTTTTTTGAA
1 ATATATA-AT-ATATATAGTTTTGAAAATGTTTTTGAA
* * *
912040 AAACT-TATATAATATATAGTTTTAAAAATATTTTTTGAA
1 ATA-TATA-AT-ATATATAGTTTTGAAAAT-GTTTTTGAA
* ** *
912079 A-ACT-TATATAATATATAGTTTTAAAAACATTTTGGAAA
1 ATA-TATA-AT-ATATATAGTTTTGAAAATGTTTTTG-AA
* **
912117 ACTTATATAATAT-T-T--TTTT-TAAATCATTTTGAA
1 A--TATATAATATATATAGTTTTGAAAATGTTTTTGAA
*
912150 A-ACTAT-ATAATATATAGTTTTGAAAACT-TTTTT-TA
1 ATA-TATAAT-ATATATAGTTTTGAAAA-TGTTTTTGAA
* *
912185 A-ATAT-A-ATATATAGTTTAGAAAATATTTTTGAA
1 ATATATAATATATATAGTTTTGAAAATGTTTTTGAA
*
912218 GTATAT-AT-TATATAGTTT
1 ATATATAATATATATAGTTT
912236 ATTTTATAAT
Statistics
Matches: 346, Mismatches: 32, Indels: 87
0.74 0.07 0.19
Matches are distributed among these distances:
30 3 0.01
31 6 0.02
32 22 0.06
33 5 0.01
34 30 0.09
35 19 0.05
36 54 0.16
37 57 0.16
38 97 0.28
39 29 0.08
40 16 0.05
41 8 0.02
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (36 bp):
ATATATAATATATATAGTTTTGAAAATGTTTTTGAA
Found at i:911937 original size:36 final size:36
Alignment explanation
Indices: 911782--912174 Score: 322
Period size: 37 Copynumber: 10.7 Consensus size: 36
911772 ATATATATAT
* * **
911782 ATATATATATTATAT-GGTTTGCAAATGTTTTTG-AA
1 ATATATATAATATATAGTTTTG-AAATCATTTTGAAA
* ** *
911817 ATACATATAATATATATAGTTTTGAAAATGGTTTTTGGAA
1 ATATATAT-A-ATATATAGTTTTG-AAAT-CATTTTGAAA
* *
911857 ATATATATAACATATAGTTTTGAAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTG-AAATCATTTTGAAA
*
911894 ACT-TATATAATATATAGTTTTGATATCATTTTGAAA
1 A-TATATATAATATATAGTTTTGAAATCATTTTGAAA
* * *
911930 ATATATATAATATATATATTTTTAAAACATTTTGAAA
1 ATATATATAATATATA-GTTTTGAAATCATTTTGAAA
*
911967 A-ACTTATATAATATATAGTTTTGAAATCATTTTAAAA
1 ATA--TATATAATATATAGTTTTGAAATCATTTTGAAA
* **
912004 ATATATATAATATATAGTTTTTTAAATTTTTTTGAAA
1 ATATATATAATATATAG-TTTTGAAATCATTTTGAAA
*
912041 A-ACTTATATAATATATAGTTTTAAAAAT-ATTTTTTGAAA
1 ATA--TATATAATATATAGTTTT-GAAATCA--TTTTGAAA
* *
912080 ACT-TATATAATATATAGTTTTAAAAACATTTTGGAAA
1 A-TATATATAATATATAGTTTTGAAATCATTTT-GAAA
* *
912117 ACT-TATATAATAT-T-TTTTTTAAATCATTTTGAAA
1 A-TATATATAATATATAGTTTTGAAATCATTTTGAAA
*
912151 A-CTATATAATATATAGTTTTGAAA
1 ATATATATAATATATAGTTTTGAAA
912175 ACTTTTTTTA
Statistics
Matches: 301, Mismatches: 33, Indels: 48
0.79 0.09 0.13
Matches are distributed among these distances:
33 10 0.03
34 6 0.02
35 28 0.09
36 48 0.16
37 106 0.35
38 77 0.26
39 17 0.06
40 9 0.03
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.46
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTGAAATCATTTTGAAA
Found at i:911999 original size:74 final size:74
Alignment explanation
Indices: 911810--912175 Score: 417
Period size: 74 Copynumber: 5.0 Consensus size: 74
911800 TTGCAAATGT
* * ** * *
911810 TTTTGAAATACATATA-ATATATATAGTTTTGAAAATGGTTTTTGGAAATATATATAACATATAG
1 TTTTGAAAAACTTATATA-ATATATAGTTTTG-AAAT-CATTTTGAAAATATATATAATATATAG
*
911874 TTTTGAAAAACA
63 TTTTTAAAAACA
*
911886 TTTTG-AAAACTTATATAATATATAGTTTTGATATCATTTTGAAAATATATATAATATATA-TAT
1 TTTTGAAAAACTTATATAATATATAGTTTTGAAATCATTTTGAAAATATATATAATATATAGT-T
*
911949 TTTTAAAACA
65 TTTAAAAACA
*
911959 TTTTGAAAAACTTATATAATATATAGTTTTGAAATCATTTTAAAAATATATATAATATATAGTTT
1 TTTTGAAAAACTTATATAATATATAGTTTTGAAATCATTTTGAAAATATATATAATATATAGTTT
* ***
912024 TTTAAATTT
66 TTAAAAACA
*
912033 TTTTGAAAAACTTATATAATATATAGTTTTAAAAAT-ATTTTTTGAAAACT-TATATAATATATA
1 TTTTGAAAAACTTATATAATATATAGTTTT-GAAATCA--TTTTGAAAA-TATATATAATATATA
912096 G-TTTTAAAAACA
62 GTTTTTAAAAACA
* * * *
912108 TTTTGGAAAACTTATATAATAT-T-TTTTTTAAATCATTTTGAAAA-CTATATAATATATAGTTT
1 TTTTGAAAAACTTATATAATATATAGTTTTGAAATCATTTTGAAAATATATATAATATATAGTTT
*
912170 TGAAAA
66 TTAAAA
912176 CTTTTTTTAA
Statistics
Matches: 255, Mismatches: 24, Indels: 27
0.83 0.08 0.09
Matches are distributed among these distances:
70 14 0.05
71 16 0.06
72 5 0.02
73 41 0.16
74 96 0.38
75 54 0.21
76 28 0.11
77 1 0.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (74 bp):
TTTTGAAAAACTTATATAATATATAGTTTTGAAATCATTTTGAAAATATATATAATATATAGTTT
TTAAAAACA
Found at i:912224 original size:34 final size:33
Alignment explanation
Indices: 912153--912236 Score: 109
Period size: 32 Copynumber: 2.5 Consensus size: 33
912143 TTTTGAAAAC
* *
912153 TATATAATATATAGTTTTGAAAACTTTTTTTAA
1 TATATAATATATAGTTTAGAAAACTTTTTTGAA
912186 -ATATAATATATAGTTTAGAAAA-TATTTTTGAA
1 TATATAATATATAGTTTAGAAAACT-TTTTTGAA
*
912218 GTATATATTATATAGTTTA
1 -TATATAATATATAGTTTA
912237 TTTTATAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
31 1 0.02
32 28 0.62
34 16 0.36
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (33 bp):
TATATAATATATAGTTTAGAAAACTTTTTTGAA
Found at i:913519 original size:3 final size:3
Alignment explanation
Indices: 913506--913545 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
913496 CCCCTAATCT
913506 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
913546 TTTTTCTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:913723 original size:26 final size:26
Alignment explanation
Indices: 913694--913744 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
913684 ATTCTTTTTT
913694 ATTTTTTTATT-TTTTAAATTTATTTA
1 ATTTTTTTATTCTTTT-AATTTATTTA
* *
913720 ATTTTTTTCTTCTTTTGATTTATTT
1 ATTTTTTTATTCTTTTAATTTATTT
913745 TTTGATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (26 bp):
ATTTTTTTATTCTTTTAATTTATTTA
Found at i:913749 original size:12 final size:12
Alignment explanation
Indices: 913732--913756 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
913722 TTTTTTCTTC
913732 TTTTGATTTATT
1 TTTTGATTTATT
913744 TTTTGATTTATT
1 TTTTGATTTATT
913756 T
1 T
913757 AATATTGGTT
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTGATTTATT
Found at i:913774 original size:3 final size:3
Alignment explanation
Indices: 913766--913799 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
913756 TAATATTGGT
913766 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
913800 CTAACCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:916761 original size:18 final size:16
Alignment explanation
Indices: 916729--916762 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
916719 ATAATCTTAT
916729 TAAATTTTAATAATAA
1 TAAATTTTAATAATAA
916745 TAAATTTTTACATAATAA
1 TAAA-TTTTA-ATAATAA
916763 ATCTAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTTAATAATAA
Found at i:922474 original size:24 final size:23
Alignment explanation
Indices: 922410--922481 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
922400 ACTACGGTGT
922410 AATTCTACGTGGCACTTCGATGC
1 AATTCTACGTGGCACTTCGATGC
* *
922433 ATTTCTACGCGGTC-CTTCGA-GAC
1 AATTCTACGTGG-CACTTCGATG-C
*
922456 AAATTCTACGTGGCACTTCGGTGC
1 -AATTCTACGTGGCACTTCGATGC
922480 AA
1 AA
922482 ATTTATACGA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
22 1 0.03
23 20 0.51
24 17 0.44
25 1 0.03
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.29
Consensus pattern (23 bp):
AATTCTACGTGGCACTTCGATGC
Found at i:922482 original size:24 final size:24
Alignment explanation
Indices: 922410--922484 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
922400 ACTACGGTGT
*
922410 AATTCTACGTGGCACTTCGATGC-
1 AATTCTACGTGGCACTTCGGTGCA
* * *
922433 ATTTCTACGCGGTC-CTTCGAG-ACA
1 AATTCTACGTGG-CACTTCG-GTGCA
922457 AATTCTACGTGGCACTTCGGTGCA
1 AATTCTACGTGGCACTTCGGTGCA
922481 AATT
1 AATT
922485 TATACGAGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
23 18 0.45
24 22 0.55
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (24 bp):
AATTCTACGTGGCACTTCGGTGCA
Found at i:929379 original size:24 final size:24
Alignment explanation
Indices: 929347--929398 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
929337 ACTACGATGC
929347 AATTCTACGTGGTC-CTTCGG-GACA
1 AATTCTACGTGG-CACTTCGGTG-CA
929371 AATTCTACGTGGCACTTCGGTGCA
1 AATTCTACGTGGCACTTCGGTGCA
929395 AATT
1 AATT
929399 TATACGAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 1 0.04
24 24 0.92
25 1 0.04
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (24 bp):
AATTCTACGTGGCACTTCGGTGCA
Found at i:930048 original size:21 final size:20
Alignment explanation
Indices: 930008--930065 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
929998 TACATCGATG
*
930008 CACTGTAGCAGGTTGATGTAA
1 CACTGTAGCATGTT-ATGTAA
*
930029 CACTGTAGCATGTTACTGTAG
1 CACTGTAGCATGTTA-TGTAA
* *
930050 CACTGCAACATGTTAT
1 CACTGTAGCATGTTAT
930066 TGTTCATTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
CACTGTAGCATGTTATGTAA
Found at i:930971 original size:16 final size:17
Alignment explanation
Indices: 930950--930991 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
930940 ATGTAAAAAT
930950 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
* *
930966 AAATA-TAAAATTTATT
1 AAATATTTAAATTTATA
930982 AAATATTTAA
1 AAATATTTAA
930992 TCAAGTAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 8 0.38
16 10 0.48
17 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:935790 original size:23 final size:23
Alignment explanation
Indices: 935718--935791 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
935708 AAGTGCCACA
* * *
935718 TAGATTTGTCCCGAAGGAGCGCG
1 TAGAATTGTCCCGAAAGACCGCG
* * ***
935741 TAGAATTATCCCGAATGACCATA
1 TAGAATTGTCCCGAAAGACCGCG
*
935764 TAGAATTGTCCCGAAAGATCGCG
1 TAGAATTGTCCCGAAAGACCGCG
935787 TAGAA
1 TAGAA
935792 GCCCTAGACT
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.23
Consensus pattern (23 bp):
TAGAATTGTCCCGAAAGACCGCG
Found at i:936420 original size:15 final size:15
Alignment explanation
Indices: 936400--936454 Score: 101
Period size: 15 Copynumber: 3.7 Consensus size: 15
936390 CCTACTATTG
*
936400 GTATCGATATCCACA
1 GTATCGATACCCACA
936415 GTATCGATACCCACA
1 GTATCGATACCCACA
936430 GTATCGATACCCACA
1 GTATCGATACCCACA
936445 GTATCGATAC
1 GTATCGATAC
936455 TATCCCTTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.24
Consensus pattern (15 bp):
GTATCGATACCCACA
Found at i:939405 original size:18 final size:18
Alignment explanation
Indices: 939379--939422 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
939369 GTGAAGTATG
*
939379 AATGGTGTTGTCGTGGCA
1 AATGTTGTTGTCGTGGCA
*
939397 AATGTTGTTGTCGTGGTA
1 AATGTTGTTGTCGTGGCA
*
939415 AGTGTTGT
1 AATGTTGT
939423 AAGGTTAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.07, G:0.36, T:0.41
Consensus pattern (18 bp):
AATGTTGTTGTCGTGGCA
Found at i:945850 original size:18 final size:18
Alignment explanation
Indices: 945824--945867 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
945814 GTGAAGTATG
*
945824 AATGGTGTTGTCGTGGCA
1 AATGTTGTTGTCGTGGCA
*
945842 AATGTTGTTGTCGTGGTA
1 AATGTTGTTGTCGTGGCA
*
945860 AGTGTTGT
1 AATGTTGT
945868 AAGGTTAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.07, G:0.36, T:0.41
Consensus pattern (18 bp):
AATGTTGTTGTCGTGGCA
Found at i:947841 original size:23 final size:25
Alignment explanation
Indices: 947815--947867 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
947805 AGTTGTAAGA
*
947815 ATGAAAATAAG-AT-AAAACTTGTT
1 ATGAAAATAAGAATCAAAACATGTT
* *
947838 ATGAAACTATGAATCAAAACATGTT
1 ATGAAAATAAGAATCAAAACATGTT
947863 ATGAA
1 ATGAA
947868 TGATAAGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.36
24 2 0.08
25 14 0.56
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (25 bp):
ATGAAAATAAGAATCAAAACATGTT
Found at i:954224 original size:22 final size:20
Alignment explanation
Indices: 954187--954229 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
954177 AAAATATTTA
*
954187 TGATATTTTATTTTAACATT
1 TGATATTTTATTTTAAAATT
*
954207 TGATATTTCTTTTATTAAAATT
1 TGATATTT-TATT-TTAAAATT
954229 T
1 T
954230 CAAGTACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 8 0.42
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (20 bp):
TGATATTTTATTTTAAAATT
Found at i:959357 original size:15 final size:15
Alignment explanation
Indices: 959337--959368 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
959327 TGGTGGCTTT
959337 TTAAAATCCTAGCCG
1 TTAAAATCCTAGCCG
959352 TTAAAATCCTAGCCG
1 TTAAAATCCTAGCCG
959367 TT
1 TT
959369 GGATCCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (15 bp):
TTAAAATCCTAGCCG
Found at i:965400 original size:46 final size:46
Alignment explanation
Indices: 965248--965373 Score: 234
Period size: 46 Copynumber: 2.7 Consensus size: 46
965238 GTGAACTAAT
* *
965248 AGTGCATCGCTTCATAAAATGCATTCGATGTTTTAAACAAGCCTGG
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTAAACAAGCCTGG
965294 AGTGCATCGATGCATAAAATGCATTCGATGTTTTAAACAAGCCTGG
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTAAACAAGCCTGG
965340 AGTGCATCGATGCATAAAATGCATTCGATGTTTT
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTT
965374 CATAAAACCC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (46 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTTAAACAAGCCTGG
Found at i:968139 original size:23 final size:22
Alignment explanation
Indices: 968063--968141 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
968053 CACAGCATAG
* *
968063 TGCATCGATACACATTCAAGGA
1 TGCATCGATGCATATTCAAGGA
* * *
968085 GTGCATCGATTCATCTTC-ATGA
1 -TGCATCGATGCATATTCAAGGA
*
968107 TGTATCGATGCATATTCAAAGGA
1 TGCATCGATGCATATTC-AAGGA
968130 TGCATCGATGCA
1 TGCATCGATGCA
968142 CTAGATAGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
21 14 0.31
22 3 0.07
23 28 0.62
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (22 bp):
TGCATCGATGCATATTCAAGGA
Found at i:974741 original size:44 final size:45
Alignment explanation
Indices: 974618--974742 Score: 189
Period size: 46 Copynumber: 2.8 Consensus size: 45
974608 TATAAAATTT
* *
974618 CTTATCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
974663 CTTACCATTTAATCTCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTC-CATAAGCTCGTAAGCTTATTTTACCAATATA
* *
974709 CTTGCCA-TTATTCCATAAGCTCGTAAGTTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
974743 GCATACTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
44 20 0.27
45 16 0.22
46 37 0.51
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:977608 original size:18 final size:18
Alignment explanation
Indices: 977585--977671 Score: 165
Period size: 18 Copynumber: 4.8 Consensus size: 18
977575 TAAAACCCTG
*
977585 AGTGCATTGATGCATGGC
1 AGTGCATCGATGCATGGC
977603 AGTGCATCGATGCATGGC
1 AGTGCATCGATGCATGGC
977621 AGTGCATCGATGCATGGC
1 AGTGCATCGATGCATGGC
977639 AGTGCATCGATGCATGGC
1 AGTGCATCGATGCATGGC
977657 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
977672 AAAATGCATT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (18 bp):
AGTGCATCGATGCATGGC
Found at i:977627 original size:65 final size:65
Alignment explanation
Indices: 977476--977617 Score: 218
Period size: 65 Copynumber: 2.2 Consensus size: 65
977466 GCACTAATGA
* *
977476 TGCATCGATGCATAAAATGCATTCGATGTTTTAAATAAGCCTGGAGTGCATCGATGCATGGTATG
1 TGCATCGATGCATAAAATGCATTCGATGTTTTAAATAACCCTGGAGTGCATCGATGCATGGCATG
*
977541 TGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AACCCT-GAGTGCATTGATGCATGGCA
1 TGCATCGATGCATAAAATGCATTCGATGTTTT-A-AATAACCCTGGAGTGCATCGATGCATGGCA
977604 -G
64 TG
977605 TGCATCGATGCAT
1 TGCATCGATGCAT
977618 GGCAGTGCAT
Statistics
Matches: 72, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
64 14 0.19
65 50 0.69
66 6 0.08
67 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (65 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTTAAATAACCCTGGAGTGCATCGATGCATGGCATG
Found at i:986612 original size:17 final size:16
Alignment explanation
Indices: 986590--986637 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
986580 ATATTTTGTG
986590 TTTAATTTATTTAAGTA
1 TTTAATTTATTTAA-TA
986607 TTTAATTTATTTAATA
1 TTTAATTTATTTAATA
* *
986623 TTTTATTTAATTAAT
1 TTTAATTTATTTAAT
986638 TTTTTTGTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 15 0.52
17 14 0.48
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTAATTTATTTAATA
Found at i:988413 original size:33 final size:33
Alignment explanation
Indices: 988376--988438 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
988366 CGATGCCGCT
* *
988376 GCCGCCACCATCACCTAGTTTTATGACCCCACC
1 GCCGCCACCATCACATAGTTATATGACCCCACC
*
988409 GCCGCCACCTTCACATAGTTATATGACCCC
1 GCCGCCACCATCACATAGTTATATGACCCC
988439 TCTTGGAGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.22, C:0.43, G:0.13, T:0.22
Consensus pattern (33 bp):
GCCGCCACCATCACATAGTTATATGACCCCACC
Found at i:988896 original size:25 final size:25
Alignment explanation
Indices: 988856--988924 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
988846 AGATTTTGTT
* * *
988856 TTTTTATTATATTTGTATT-TAGTAC
1 TTTTTATTGTAGTTGT-TTATAGGAC
*
988881 TTTTTATTGTAGTTGTTTATTGGAC
1 TTTTTATTGTAGTTGTTTATAGGAC
*
988906 TTTTTATTGTAATT-TTTAT
1 TTTTTATTGTAGTTGTTTAT
988925 TATTATTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
24 7 0.18
25 31 0.82
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (25 bp):
TTTTTATTGTAGTTGTTTATAGGAC
Found at i:988913 original size:12 final size:12
Alignment explanation
Indices: 988877--988925 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
988867 TTTGTATTTA
988877 GTACTTTTTATT
1 GTACTTTTTATT
*
988889 GTAGTTGTTTATT
1 GTACTT-TTTATT
*
988902 GGACTTTTTATT
1 GTACTTTTTATT
*
988914 GTAATTTTTATT
1 GTACTTTTTATT
988926 ATTATTTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 21 0.68
13 10 0.32
ACGTcount: A:0.18, C:0.04, G:0.14, T:0.63
Consensus pattern (12 bp):
GTACTTTTTATT
Found at i:991961 original size:48 final size:45
Alignment explanation
Indices: 991907--991996 Score: 108
Period size: 45 Copynumber: 1.9 Consensus size: 45
991897 GTACCTGCAC
*
991907 CGCGCCTTACATAATTATATAGATAAAGCTAAGGCGCGGCCCCTGTTT
1 CGCGCCTAACATAA-T-TAT-GATAAAGCTAAGGCGCGGCCCCTGTTT
* * * *
991955 CGCGCCTAATATAATTGTGTTAAAGGTAAGGCGCGGCCCCTG
1 CGCGCCTAACATAATTATGATAAAGCTAAGGCGCGGCCCCTG
991997 CCCTGCGCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
45 22 0.59
46 2 0.05
47 1 0.03
48 12 0.32
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (45 bp):
CGCGCCTAACATAATTATGATAAAGCTAAGGCGCGGCCCCTGTTT
Found at i:1003968 original size:75 final size:75
Alignment explanation
Indices: 1003778--1004285 Score: 777
Period size: 75 Copynumber: 6.8 Consensus size: 75
1003768 ATTTCAAGGG
* * * * * *
1003778 AAACTTTCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTCGAGTGAAATAAAATTTATT
1 AAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTT-CT
* *
1003843 ATTTCGAGTAA
65 GTTTCGAGTGA
* *
1003854 AAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCCG
1 AAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTG
*
1003919 TTTTGAGTGA
66 TTTCGAGTGA
* *
1003929 AAACTGTCTCAAGCGAAACGAAGTTTGTTTTAAGAAAAACAATATCAAGTGAGATAAAATTTCTG
1 AAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTG
1003994 TTTCGAGTGA
66 TTTCGAGTGA
*
1004004 AAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTATG
1 AAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTG
* *
1004069 TTTCAAGTAA
66 TTTCGAGTGA
1004079 AAAC-GTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTG
1 AAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTG
*
1004143 TTTCCAGT-A
66 TTTCGAGTGA
* *
1004152 AAACCTATCTCAAGCGAGATGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCT
1 AAA-CTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCT
*
1004217 GTTTCAAGTGA
65 GTTTCGAGTGA
* * *
1004228 AAACTGTCTCAAGCGAGACGAAGATTGTTTTAAGAAAAACTATTTCAAGTGAGATAAA
1 AAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
1004286 TTTTTTGATA
Statistics
Matches: 398, Mismatches: 31, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
73 4 0.01
74 67 0.17
75 267 0.67
76 60 0.15
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.30
Consensus pattern (75 bp):
AAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTG
TTTCGAGTGA
Found at i:1004178 original size:224 final size:226
Alignment explanation
Indices: 1003769--1004285 Score: 817
Period size: 224 Copynumber: 2.3 Consensus size: 226
1003759 AATATTTATA
* * * * * *
1003769 TTTCAAG-GGAAACTTTCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTCGAGTGAAAT
1 TTTCAAGTGAAAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
*
1003833 AAAATTTATTATTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATC
66 AAAATTTATTATTTCAAGTAAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATC
** *
1003898 TCAAGTGAGATAAAATTTCCGTTTTGAGTGAAAACTGTCTCAAGCGAAACGAAGTTTGTTTTAAG
131 TCAAGTGAGATAAAATTTCCGTTTCCAGTGAAAACTATCTCAAGCGAAACGAAGTTTGTTTTAAG
1003963 AAAAACAATATCAAGTGAGATAAAATTTCTG
196 AAAAACAATATCAAGTGAGATAAAATTTCTG
*
1003994 TTTCGAGTGAAAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
1 TTTCAAGTGAAAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
* *
1004059 AAAATTTA-TGTTTCAAGTAAAAAC-GTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATC
66 AAAATTTATTATTTCAAGTAAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATC
* * *
1004122 TCAAGTGAGATAAAATTTCTGTTTCCAGT-AAAACCTATCTCAAGCGAGATGAAGTTTGTTTTAA
131 TCAAGTGAGATAAAATTTCCGTTTCCAGTGAAAA-CTATCTCAAGCGAAACGAAGTTTGTTTTAA
*
1004186 GAAAAACAATCTCAAGTGAGATAAAATTTCTG
195 GAAAAACAATATCAAGTGAGATAAAATTTCTG
* * *
1004218 TTTCAAGTGAAAACTGTCTCAAGCGAGACGAAGATTGTTTTAAGAAAAACTATTTCAAGTGAGAT
1 TTTCAAGTGAAAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
1004283 AAA
66 AAA
1004286 TTTTTTGATA
Statistics
Matches: 269, Mismatches: 21, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
223 4 0.01
224 186 0.69
225 20 0.07
226 59 0.22
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.30
Consensus pattern (226 bp):
TTTCAAGTGAAAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
AAAATTTATTATTTCAAGTAAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATC
TCAAGTGAGATAAAATTTCCGTTTCCAGTGAAAACTATCTCAAGCGAAACGAAGTTTGTTTTAAG
AAAAACAATATCAAGTGAGATAAAATTTCTG
Found at i:1010573 original size:64 final size:64
Alignment explanation
Indices: 1010488--1010648 Score: 177
Period size: 64 Copynumber: 2.5 Consensus size: 64
1010478 TTGTTTAAGG
* * * * *
1010488 TGCATCGATGCACA-TGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGAAGCATAGTGTAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCAAATAGGATTT
1010551 A
64 A
* *
1010552 TGCATCGAAGCATAAG-G-AGTGCATCGATGCATCCCCATTAAATACAAACATCAAATAGGATTT
1 TGCATCGAAGCAT-AGTGTAGTGCATCGATGCAT-CCAATTAAATAAAAACATCAAATAGGATTT
1010615 A
64 A
* *
1010616 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGAAGCATAGTGTAGTGCATCGATGCAT
1010649 ACCTTCATTA
Statistics
Matches: 83, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
63 1 0.01
64 57 0.69
65 24 0.29
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (64 bp):
TGCATCGAAGCATAGTGTAGTGCATCGATGCATCCAATTAAATAAAAACATCAAATAGGATTTA
Found at i:1010648 original size:65 final size:65
Alignment explanation
Indices: 1010524--1010648 Score: 182
Period size: 64 Copynumber: 1.9 Consensus size: 65
1010514 ATGCATGAAT
*
1010524 TTAAATAGAAAACATCGAATAGGATTTATGCATCGAAGCATAAGGAGTGCATCGATGCATCCCCA
1 TTAAATAGAAAACATCAAATAGGATTTATGCATCGAAGCATAAGGAGTGCATCGATGCATCCCCA
* * *
1010589 TTAAATA-CAAACATCAAATAGGATTTATGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TTAAATAGAAAACATCAAATAGGATTTATGCATCGAAGCATAAG-G-AGTGCATCGATGCAT
1010649 ACCTTCATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
63 1 0.02
64 31 0.57
65 22 0.41
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (65 bp):
TTAAATAGAAAACATCAAATAGGATTTATGCATCGAAGCATAAGGAGTGCATCGATGCATCCCCA
Found at i:1012224 original size:149 final size:149
Alignment explanation
Indices: 1012046--1012348 Score: 579
Period size: 149 Copynumber: 2.0 Consensus size: 149
1012036 GAGTCGAGGG
*
1012046 TCTACGCGGTCATTCGGGATATATTTATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCATTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1012111 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
1012176 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
1012195 TCTACGCTGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCATTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1012260 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
1012325 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1012344 TCTAC
1 TCTAC
1012349 ACGGCACTTC
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTCATTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:1015870 original size:65 final size:65
Alignment explanation
Indices: 1015710--1015870 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
1015700 TTGTTTAAGG
* * * **
1015710 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
1015773 A
65 A
*
1015774 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
1015838 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
1015871 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:1017581 original size:149 final size:149
Alignment explanation
Indices: 1017268--1017571 Score: 572
Period size: 149 Copynumber: 2.0 Consensus size: 149
1017258 GAGTCGAGGG
* *
1017268 TCTACGCGGTCCTTCGGGATATATATATATTCTATGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGAGATATATATATATTATATGGAACATGTGTGAAGTCTTGAAAGACACAT
1017333 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
1017398 TATGGCACTACGGTGCAAT
131 TATGGCAATACGGTGCAAT
*
1017417 TCTACGCGGTCCTTCGAGATATATATATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGAGATATATATATATTATATGGAACATGTGTGAAGTCTTGAAAGACACAT
1017482 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
1017547 TATGGCAATACGGTGCAAT
131 TATGGCAATACGGTGCAAT
1017566 TCTACG
1 TCTACG
1017572 TGGCACTTCG
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGAGATATATATATATTATATGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCAATACGGTGCAAT
Found at i:1019125 original size:2 final size:2
Alignment explanation
Indices: 1019118--1019144 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1019108 CTAAATTAGT
1019118 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1019145 CAACATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1020043 original size:18 final size:18
Alignment explanation
Indices: 1020020--1020066 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1020010 CATTTGGGTG
1020020 GGGTTTTGGGTTCTAGTT
1 GGGTTTTGGGTTCTAGTT
** *
1020038 GGGTTTTATGTTCTGGTT
1 GGGTTTTGGGTTCTAGTT
1020056 GGGTTTTGGGT
1 GGGTTTTGGGT
1020067 ATGGGGCTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.04, C:0.04, G:0.40, T:0.51
Consensus pattern (18 bp):
GGGTTTTGGGTTCTAGTT
Found at i:1021096 original size:60 final size:60
Alignment explanation
Indices: 1021032--1021166 Score: 159
Period size: 60 Copynumber: 2.2 Consensus size: 60
1021022 AGTCGACTGG
* * * *
1021032 CCATTTTGTAACTTTTAATAGTTGA-AGAACTCAACAAAGCAACGCCTTATAGT-TGATGGA
1 CCATTTTGTAACTTTTAATAGTCGAGAG-ACTCAACAAAACAACGCCCTATAGTCAGA-GGA
* * *
1021092 CCATTATATAACTTTTAATAGTCGAGAGACTCAACAAAACAACTCCCTATAGTCAGAGGA
1 CCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACGCCCTATAGTCAGAGGA
1021152 CCATTTGTGT-ACTTT
1 CCATTT-TGTAACTTT
1021167 ACCGTAATTT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
60 57 0.90
61 6 0.10
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (60 bp):
CCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACGCCCTATAGTCAGAGGA
Found at i:1022132 original size:16 final size:15
Alignment explanation
Indices: 1022090--1022132 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1022080 TAGTCAATAT
1022090 TTTCAAATTATATTA
1 TTTCAAATTATATTA
* *
1022105 TCTAAAATTTATATTA
1 TTTCAAA-TTATATTA
1022121 TTTCATAATTAT
1 TTTCA-AATTAT
1022133 GTTTAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
15 5 0.23
16 15 0.68
17 2 0.09
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTCAAATTATATTA
Found at i:1028994 original size:2 final size:2
Alignment explanation
Indices: 1028987--1029016 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1028977 TATTCATTTG
*
1028987 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1029017 TATGTACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1035710 original size:3 final size:3
Alignment explanation
Indices: 1035697--1035762 Score: 73
Period size: 3 Copynumber: 22.7 Consensus size: 3
1035687 CGTTATTAAC
* * *
1035697 ATT ACT ATT ATT ATT ATT A-T ATT AAT ATT GTT ATT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
1035743 ATT AAT ATT GTT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
1035763 AAGCTCAATA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
2 4 0.08
3 47 0.92
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1035719 original size:26 final size:26
Alignment explanation
Indices: 1035702--1035762 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
1035692 TTAACATTAC
1035702 TATTATTATTATTATATTAATATTGT
1 TATTATTATTATTATATTAATATTGT
1035728 TATTATTATTATTATATTAATATTGT
1 TATTATTATTATTATATTAATATTGT
1035754 TATTATTAT
1 TATTATTAT
1035763 AAGCTCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (26 bp):
TATTATTATTATTATATTAATATTGT
Found at i:1037318 original size:11 final size:11
Alignment explanation
Indices: 1037304--1037328 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1037294 TTTTGTGTTA
1037304 TTTTAATAAAT
1 TTTTAATAAAT
1037315 TTTTAATAAAT
1 TTTTAATAAAT
1037326 TTT
1 TTT
1037329 ACTAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAATAAAT
Found at i:1039022 original size:23 final size:23
Alignment explanation
Indices: 1038996--1039059 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
1038986 CAGCTCATAT
1038996 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1039019 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1039042 GATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1039060 TATAATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.25, C:0.27, G:0.30, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1039246 original size:103 final size:103
Alignment explanation
Indices: 1039075--1039292 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
1039065 TAATGTCCAT
* * *
1039075 AAGGACCACATATCATTCCTTAAGAATTATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1039140 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
* *
1039178 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1039243 GACTTCATACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
1039281 AAGGACCACATA
1 AAGGACCACATA
1039293 GACCCTCGAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:1040195 original size:64 final size:62
Alignment explanation
Indices: 1040044--1040263 Score: 239
Period size: 64 Copynumber: 3.5 Consensus size: 62
1040034 TAATGAAGGT
* * * * *
1040044 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGTATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTT-TATTATTAATGG
* *
1040107 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTT-ATTATTAAT-GG
* **
1040171 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAAAAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATG--TTTATTATTAATGG
**
1040234 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
1040264 ACACATTCAA
Statistics
Matches: 135, Mismatches: 14, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
62 2 0.01
63 50 0.37
64 77 0.57
65 3 0.02
66 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTATTATTAATGG
Done.