Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002931.1 Hibiscus syriacus cultivar Beakdansim tig00006056_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: 74123
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4480 original size:30 final size:30
Alignment explanation
Indices: 4446--4503 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
4436 CTTTCGTAAT
*
4446 TATCTTTTTTAAATATGTAGGATCGAGAGG
1 TATCTTTTTTAAATATGTAAGATCGAGAGG
4476 TATCTTTTTTAAATATGTAAGATCGAGA
1 TATCTTTTTTAAATATGTAAGATCGAGA
4504 AGTAAGGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (30 bp):
TATCTTTTTTAAATATGTAAGATCGAGAGG
Found at i:10614 original size:36 final size:36
Alignment explanation
Indices: 10569--10966 Score: 171
Period size: 36 Copynumber: 11.0 Consensus size: 36
10559 AAAATATAAT
*
10569 TTTTAGAAAACAGTTTTCTAAA-ATATATATTATATAG
1 TTTT-GAAAACA-TTTTCAAAACATATATATTATATAG
* * *
10606 TTTCGAAAACA-TTTCGAAAATATATATATTATATAA
1 TTTTGAAAACATTTTC-AAAACATATATATTATATAG
* *
10642 TTTTGAAAA-ATTTTGAAAACATATATAATATATAG
1 TTTTGAAAACATTTTCAAAACATATATATTATATAG
* * * ** *
10677 TTTTTGAAAATACTTTTAAAAATATATATAACATAAAG
1 -TTTTGAAAACA-TTTTCAAAACATATATATTATATAG
* * *
10715 TTTTGAAATCATTTTGAAAATATATATATAATATATAG
1 TTTTGAAAACATTTTCAAAACATATATAT--TATATAG
* * * * * *
10753 TTTTTAAAATATTTTTGAAAAAAAACTTCTATAATATATAG
1 TTTTGAAAACA-TTTT----CAAAACATATATATTATATAG
* * *
10794 TTTT-AAAATATTTTTGAAAA-ATTATATAATATATAG
1 TTTTGAAAACA-TTTTCAAAACA-TATATATTATATAG
* *
10830 TTTTAAAAACATTTTTTGAAAAC-T-TATA-TA-ATA-
1 TTTTGAAAACA--TTTTCAAAACATATATATTATATAG
* * * * *
10863 TTTTTAAATCATTTTTGAAAA-TTATATAATATATAG
1 TTTTGAAAACA-TTTTCAAAACATATATATTATATAG
* *
10899 TTTTGAAAAAAATATT-AAAA-ATATA-A-TATATAG
1 TTTTG-AAAACATTTTCAAAACATATATATTATATAG
* * ** *
10932 -TTTAAAAATATTTTTGAAATATATATATATATATA
1 TTTTGAAAACATTTTCAAAACATATATAT-TATATA
10967 TATATTATAG
Statistics
Matches: 292, Mismatches: 41, Indels: 57
0.75 0.11 0.15
Matches are distributed among these distances:
31 8 0.03
32 17 0.06
33 25 0.09
34 11 0.04
35 34 0.12
36 95 0.33
37 23 0.08
38 44 0.15
39 4 0.01
40 11 0.04
41 11 0.04
43 9 0.03
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (36 bp):
TTTTGAAAACATTTTCAAAACATATATATTATATAG
Found at i:10633 original size:38 final size:37
Alignment explanation
Indices: 10561--10968 Score: 286
Period size: 38 Copynumber: 11.2 Consensus size: 37
10551 TTTTTAAAAA
* **
10561 AATATA-ATTTTTAGAAAACAGTTTTCTAAAATATATAT
1 AATATATAGTTTT-GAAAACA-TTTTGAAAAATATATAT
* *
10599 --TATATAGTTTCGAAAACATTTCG-AAAATATATAT
1 AATATATAGTTTTGAAAACATTTTGAAAAATATATAT
* * *
10633 ATTATATAATTTTGAAAA-ATTTTG-AAAACATATAT
1 AATATATAGTTTTGAAAACATTTTGAAAAATATATAT
*
10668 AATATATAGTTTTTGAAAATACTTTT-AAAAATATATAT
1 AATATATAG-TTTTGAAAACA-TTTTGAAAAATATATAT
* * *
10706 AACATAAAGTTTTGAAATCATTTTGAAAATATATATAT
1 AATATATAGTTTTGAAAACATTTTGAAAA-ATATATAT
* * * *
10744 AATATATAGTTTTTAAAATATTTTTGAAAAAAAACTTCTAT
1 AATATATAGTTTTGAAAACA-TTTTG-AAAAATA--TATAT
*
10785 AATATATAGTTTT-AAAATATTTTTGAAAAAT-TATAT
1 AATATATAGTTTTGAAAACA-TTTTGAAAAATATATAT
* *
10821 AATATATAGTTTTAAAAACATTTTTTGAAAACT-TATAT
1 AATATATAGTTTTGAAAACA--TTTTGAAAAATATATAT
*
10859 -A-ATAT--TTTT-AAATCATTTTTG-AAAAT-TATAT
1 AATATATAGTTTTGAAAACA-TTTTGAAAAATATATAT
* *
10890 AATATATAGTTTTGAAAAAAATATT---AAA-A-ATAT
1 AATATATAGTTTTG-AAAACATTTTGAAAAATATATAT
* * *
10923 AATATATAG-TTTAAAAATATTTTTGAAATATATATAT
1 AATATATAGTTTTGAAAACA-TTTTGAAAAATATATAT
10960 ATATATATA
1 A-ATATATA
10969 TATTATAGTT
Statistics
Matches: 306, Mismatches: 35, Indels: 58
0.77 0.09 0.15
Matches are distributed among these distances:
31 14 0.05
32 13 0.04
33 22 0.07
34 18 0.06
35 31 0.10
36 63 0.21
37 33 0.11
38 67 0.22
39 12 0.04
40 16 0.05
41 17 0.06
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (37 bp):
AATATATAGTTTTGAAAACATTTTGAAAAATATATAT
Found at i:10858 original size:31 final size:30
Alignment explanation
Indices: 10822--10890 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 30
10812 AAATTATATA
10822 ATATATAGTTTTAAAAACATTTTTTGAAAACTT
1 ATATATA-TTTTAAAAACA-TTTTTGAAAA-TT
* *
10855 ATATAATATTTTTAAATCATTTTTGAAAATT
1 ATAT-ATATTTTAAAAACATTTTTGAAAATT
10886 ATATA
1 ATATA
10891 ATATATAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 1 0.03
31 6 0.18
32 10 0.30
33 13 0.39
34 3 0.09
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (30 bp):
ATATATATTTTAAAAACATTTTTGAAAATT
Found at i:12241 original size:3 final size:3
Alignment explanation
Indices: 12148--12223 Score: 50
Period size: 3 Copynumber: 25.3 Consensus size: 3
12138 TTTTGTTTTC
* * * *
12148 TAT TAT TAT TAT TTT TAT TAA TCT TGATT TAT TAT T-T TAT TAT T-C
1 TAT TAT TAT TAT TAT TAT TAT TAT T-A-T TAT TAT TAT TAT TAT TAT
* *
12193 TAT TGT T-T TGTT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT T
12224 TTAATGCTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
2 5 0.09
3 47 0.82
4 3 0.05
5 2 0.04
ACGTcount: A:0.25, C:0.03, G:0.04, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:14961 original size:99 final size:99
Alignment explanation
Indices: 14785--14972 Score: 331
Period size: 99 Copynumber: 1.9 Consensus size: 99
14775 TTATAATATT
* * *
14785 ATATATATACAATAAAGCTTGAGATGTCCCTCTAAGGCAATTTGTTAAACGCCTCGGCTTTATGG
1 ATATATATACAATAAAGCTTGAGATGTCCCTCTAAGGCAATTGGTTAAACGCCCCGACTTTATGG
14850 ATAAGATTCAACTAACCTGATAAAGGTGATTATA
66 ATAAGATTCAACTAACCTGATAAAGGTGATTATA
* *
14884 ATATCTATACAATAAAGCTTGAGTTGTCCCTCTAAGGCAATTGGTTAAACGCCCCGACTTTATGG
1 ATATATATACAATAAAGCTTGAGATGTCCCTCTAAGGCAATTGGTTAAACGCCCCGACTTTATGG
14949 ATAAGATTCAACTAACCTGATAAA
66 ATAAGATTCAACTAACCTGATAAA
14973 TGTGTTTGTA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 84 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAGATGTCCCTCTAAGGCAATTGGTTAAACGCCCCGACTTTATGG
ATAAGATTCAACTAACCTGATAAAGGTGATTATA
Found at i:16329 original size:84 final size:83
Alignment explanation
Indices: 16188--16505 Score: 385
Period size: 84 Copynumber: 3.8 Consensus size: 83
16178 CAACATAGCC
* * *
16188 CAAGGCAATAAGGGTTATCTGCCACCAAAAGACATTCGAGTTCGATTACACTCAGCTCAAAGGCA
1 CAAGGCAAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
*
16253 CATCATTTTCATCATAACT
65 CATCATTTACATCATAACT
*
16272 CAAGGCTAA-AAGGGTTATCTGCCAACACAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGC
1 CAAGGC-AAGAAGGGTTATCTGCCAACA-AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGC
*
16336 ACATCATTTACAGT-ATAACC
64 ACATCATTTACA-TCATAACT
* * * * * *
16356 CAAGGCTAGAATGGTTATTTGTCAACAAATACCTTCGAGTTCGATTACGCTCAGCTCAAAGGCAC
1 CAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAC
* * *
16421 ATCATTTGCAACATAGCT
66 ATCATTTACATCATAACT
* * * * *
16439 TAAGGCAAGAAGGGCTATCT-TC--CAAAGACCTTCGAGTTCGATTACACTTAGCTCAAAGACAC
1 CAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAC
16501 ATCAT
66 ATCAT
16506 GTAACACCCC
Statistics
Matches: 204, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
80 41 0.20
82 2 0.01
83 65 0.32
84 93 0.46
85 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (83 bp):
CAAGGCAAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAC
ATCATTTACATCATAACT
Found at i:17099 original size:23 final size:23
Alignment explanation
Indices: 17073--17139 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 23
17063 CACCACAGCT
*
17073 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
*
17096 CGTAGAATTGCACCGAAGTG-CC
1 CGTAGAAATGCACCGAAGTGCCC
* * *
17118 CGTAGAATTACACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
17140 ATATAATGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 20 0.51
23 19 0.49
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:17122 original size:22 final size:22
Alignment explanation
Indices: 17081--17139 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 22
17071 CTCGTATAAA
17081 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
17104 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
* *
17126 TACACCGTAGTGCC
1 TGCACCGAAGTGCC
17140 ATATAATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 22 0.65
23 12 0.35
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:17922 original size:65 final size:65
Alignment explanation
Indices: 17750--17897 Score: 244
Period size: 65 Copynumber: 2.3 Consensus size: 65
17740 TTTTTTTCAT
* *
17750 GGGGGAATCGGTTCCCCCCCT-GGGGTATCGATTCCCCACTAGCATTCTGGAATTCATATTCGTT
1 GGGGGTATCGGTT--CCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTT
17814 GA
64 GA
*
17816 GGGGGTATCGGTTCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTGA
1 GGGGGTATCGGTTCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTTGA
17881 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
17898 TTGAATGGGT
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
64 6 0.08
65 60 0.77
66 12 0.15
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.29
Consensus pattern (65 bp):
GGGGGTATCGGTTCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTTGA
Found at i:23978 original size:23 final size:23
Alignment explanation
Indices: 23960--24018 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
23950 CTCGTATAAA
23960 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
23983 TGCACCGAAGTG-CCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
24005 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
24019 ATATAATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:24739 original size:66 final size:65
Alignment explanation
Indices: 24630--24779 Score: 246
Period size: 66 Copynumber: 2.3 Consensus size: 65
24620 TTTTTTTCAT
* *
24630 GGGGGAATCGGTTCCCCCCCCTGGGGTATCGATTCCCCACTAGCATTCTGGAATTCATATTCGTT
1 GGGGGTATCGGTT--CCCCCCTGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTT
24695 GA
64 GA
*
24697 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTG
1 GGGGGTATCGGTTCCCCCCT-GGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTTG
24762 A
65 A
24763 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
24780 TTGAATGGGT
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
65 7 0.09
66 60 0.76
67 12 0.15
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (65 bp):
GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATTCGTTGA
Found at i:25841 original size:161 final size:160
Alignment explanation
Indices: 25517--26163 Score: 710
Period size: 161 Copynumber: 4.0 Consensus size: 160
25507 GAGGATGTTA
* * *
25517 CACATCATTTACAGCATAACTCAAGGCTAAAAGGGTTATCTATCAACAAATACCTTCAAGTTCGA
1 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTAT-AACAAAAACCTTCGAGTTCGA
* * * * *
25582 TTACACTCAGCTCAAGGCACATCATCTGCAGCATAACTTAGGTTATAAGGGTTATCTGCCAAAGA
65 TTACACTCAGCTCAAGGCACATCATTTGCAACATAACTAAGGCTAGAAGGGTTATCTGCCAAAGA
25647 CCTTCGAGTTCGATTACACTCAGCTCAAAGG
130 CCTTCGAGTTCGATTACACTCAGCTCAAAGG
* * *
25678 CACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTAAAAAAAAACCTTCGAGTTCGA
1 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTAT-AACAAAAACCTTCGAGTTCGA
*
25743 TTACACTCAGCTCAAGGCATATCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAAAG
65 TTACACTCAGCTCAAGGCACATCATTTGCAACATAACT-AAGGCTAGAAGGGTTATCTGCCAAAG
* *
25808 ACCTTTGAGTTCGATTACACTCAGCT-TAAGG
129 ACCTTCGAGTTCGATTACACTCAGCTCAAAGG
* * * * * *
25839 CACATCATTTGCAGTATACCTCAATGCTAGAAGGGTTA--TATACCAAAGACCTTCGAGTTCGAT
1 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATAACAAAAACCTTCGAGTTCGAT
* ** * * *
25902 TACACTTAGCTCAAGGCACATCATTTATAACATAGCTTAAGGCAAGAAGGGTTATCTGTCAAAGA
66 TACACTCAGCTCAAGGCACATCATTTGCAACATAAC-TAAGGCTAGAAGGGTTATCTGCCAAAGA
* *
25967 CCTTCGAGTTTGATTACATTCAGCTCAAAGG
130 CCTTCGAGTTCGATTACACTCAGCTCAAAGG
* * ** ** * * ** ** *
25998 CACATCATTTGCAGCTTAGTTCAAGGAAATAAGGGCTATC--TGCCAAAGTCCTTCGAGTTTGAT
1 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATAACAAAAACCTTCGAGTTCGAT
* * * * * * * *
26061 TACACACAGCTCAAAGGCGCATCATTTGCAGCATAGCTCAAGACGAGAAGGGATGTCTGCTAACA
66 TACACTCAGCTC-AAGGCACATCATTTGCAACATAACT-AAGGCTAGAAGGGTTATCTGC---C-
* *
26126 AAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGG
125 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG
26162 CA
1 CA
26164 TATTAAATTT
Statistics
Matches: 415, Mismatches: 60, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
158 97 0.23
159 67 0.16
160 36 0.09
161 130 0.31
162 48 0.12
163 1 0.00
164 36 0.09
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (160 bp):
CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATAACAAAAACCTTCGAGTTCGAT
TACACTCAGCTCAAGGCACATCATTTGCAACATAACTAAGGCTAGAAGGGTTATCTGCCAAAGAC
CTTCGAGTTCGATTACACTCAGCTCAAAGG
Found at i:26045 original size:80 final size:80
Alignment explanation
Indices: 25517--26163 Score: 701
Period size: 79 Copynumber: 8.0 Consensus size: 80
25507 GAGGATGTTA
* * * * * *
25517 CACATCATTTACAGCATAACTCAAGGCTAAAAGGGTTATCTATCAACAAATACCTTCAAGTTCGA
1 CACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCT-GC--CAAAGACCTTCGAGTTCGA
25582 TTACACTCAGCTC-AAGG
63 TTACACTCAGCTCAAAGG
* * * * *
25599 CACATCATCTGCAGCATAACT-TAGGTTATAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTA
1 CACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTA
25663 CACTCAGCTCAAAGG
66 CACTCAGCTCAAAGG
* * * ** *
25678 CACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTAAAAAAAAACCTTCGAGTTCGA
1 CACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTG---CCAAAGACCTTCGAGTTCGA
25743 TTACACTCAGCTC-AAGG
63 TTACACTCAGCTCAAAGG
* * * *
25760 CATATCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAAAGACCTTTGAGTTCGATTA
1 CACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTA
*
25825 CACTCAGCT-TAAGG
66 CACTCAGCTCAAAGG
* * * * *
25839 CACATCATTTGCAGTATACCTCAATGCTAGAAGGGTTATATACCAAAGACCTTCGAGTTCGATTA
1 CACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTA
*
25904 CACTTAGCTC-AAGG
66 CACTCAGCTCAAAGG
** * * * * *
25918 CACATCATTTATAACATAGCTTAAGGCAAGAAGGGTTATCTGTCAAAGACCTTCGAGTTTGATTA
1 CACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTA
*
25983 CATTCAGCTCAAAGG
66 CACTCAGCTCAAAGG
* * ** * * * *
25998 CACATCATTTGCAGCTTAGTTCAAGGAAATAAGGGCTATCTGCCAAAGTCCTTCGAGTTTGATTA
1 CACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTA
*
26063 CACACAGCTCAAAGG
66 CACTCAGCTCAAAGG
* * * * * *
26078 CGCATCATTTGCAGCATAGCTCAAGACGAGAAGGGATGTCTGCTAACAAAAGACCTTCAAGTTCG
1 CACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGC---C-AAAGACCTTCGAGTTCG
*
26143 ATTACATTCAGCTCAAAGG
62 ATTACACTCAGCTCAAAGG
26162 CA
1 CA
26164 TATTAAATTT
Statistics
Matches: 479, Mismatches: 74, Indels: 22
0.83 0.13 0.04
Matches are distributed among these distances:
78 30 0.06
79 184 0.38
80 123 0.26
81 16 0.03
82 63 0.13
83 31 0.06
84 32 0.07
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (80 bp):
CACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTA
CACTCAGCTCAAAGG
Found at i:26792 original size:30 final size:31
Alignment explanation
Indices: 26758--26824 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
26748 TTAGTAATAT
* * *
26758 AATATAATTTTT-GAAAATGTTTTTTTAAAA
1 AATATAATTTTTAGAAAACGGTTTTCTAAAA
26788 AATATAATTTTTAGAAAACGGTTTTCTAAAA
1 AATATAATTTTTAGAAAACGGTTTTCTAAAA
*
26819 TATATA
1 AATATA
26825 TATACCATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (31 bp):
AATATAATTTTTAGAAAACGGTTTTCTAAAA
Found at i:26933 original size:38 final size:37
Alignment explanation
Indices: 26881--27125 Score: 245
Period size: 37 Copynumber: 6.7 Consensus size: 37
26871 TTTTGAATTT
* * *
26881 TTTTGAAAACATATATAATGTATAGTTTTTTAAAATAC
1 TTTTGAAAATATATATAATATATAG-TTTTTAAAACAC
* * *
26919 TTTTGAAAATATATATAATATATGGTTTTGAAATCA-
1 TTTTGAAAATATATATAATATATAGTTTTTAAAACAC
* *
26955 TTTTGAATATATATATAATATATAGTTTTTAAAACAT
1 TTTTGAAAATATATATAATATATAGTTTTTAAAACAC
* * * *
26992 TTTTCAAAAAACTTATATAATATATAGTTTTAAAAACAT
1 TTTTGAAAATA--TATATAATATATAGTTTTTAAAACAC
*
27031 TTTTGAAAA-ATTATATAATATATAGTTTTAAAAACAC
1 TTTTGAAAATA-TATATAATATATAGTTTTTAAAACAC
* * *
27068 TTTTTGAAAA-CT-TAT-ATA-ATA-TTTTTAAATCAT
1 -TTTTGAAAATATATATAATATATAGTTTTTAAAACAC
27101 TTTTGAAAA-ATATATAATATATAGT
1 TTTTGAAAATATATATAATATATAGT
27126 AAACCAAGAC
Statistics
Matches: 178, Mismatches: 21, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
32 10 0.06
33 12 0.07
34 6 0.03
35 6 0.03
36 36 0.20
37 43 0.24
38 32 0.18
39 33 0.19
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAACAC
Found at i:26959 original size:36 final size:37
Alignment explanation
Indices: 26815--27125 Score: 267
Period size: 38 Copynumber: 8.6 Consensus size: 37
26805 ACGGTTTTCT
* * * * *
26815 AAAATATATATATACCATCTAGTTTCAAAAACA-TTTCG
1 AAAATATATATA-A-TATATAGTTTTAAAATCATTTTTG
* *
26853 AAAATATATAT--TATATAGTTTT-GAAT-TTTTTTG
1 AAAATATATATAATATATAGTTTTAAAATCATTTTTG
* * *
26886 AAAACATATATAATGTATAGTTTTTTAAAAT-ACTTTTG
1 AAAATATATATAATATATAG--TTTTAAAATCATTTTTG
* *
26924 AAAATATATATAATATATGGTTTTGAAATCA-TTTTG
1 AAAATATATATAATATATAGTTTTAAAATCATTTTTG
* *
26960 AATATATATATAATATATAGTTTTTAAAA-CATTTTTC
1 AAAATATATATAATATATAG-TTTTAAAATCATTTTTG
* *
26997 AAAAAACTTATATAATATATAGTTTTAAAAACATTTTTG
1 AAAATA--TATATAATATATAGTTTTAAAATCATTTTTG
*
27036 AAAA-ATTATATAATATATAGTTTTAAAAACACTTTTTG
1 AAAATA-TATATAATATATAGTTTTAAAATCA-TTTTTG
27074 AAAACT-TATAT-A-ATAT--TTTT-AAATCATTTTTG
1 AAAA-TATATATAATATATAGTTTTAAAATCATTTTTG
27106 AAAA-ATATATAATATATAGT
1 AAAATATATATAATATATAGT
27126 AAACCAAGAC
Statistics
Matches: 229, Mismatches: 24, Indels: 43
0.77 0.08 0.15
Matches are distributed among these distances:
31 5 0.02
32 11 0.05
33 25 0.11
34 12 0.05
35 7 0.03
36 37 0.16
37 47 0.21
38 60 0.26
39 25 0.11
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (37 bp):
AAAATATATATAATATATAGTTTTAAAATCATTTTTG
Found at i:27949 original size:24 final size:25
Alignment explanation
Indices: 27905--27966 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
27895 TTTTCTATTA
*
27905 TTATTATTTT-TTATTTGTCTTGAT
1 TTATTATTTTATTATTTCTCTTGAT
**
27929 TTATTATTTTATTA-TTCTCTTTTT
1 TTATTATTTTATTATTTCTCTTGAT
27953 TTATTATTATTATT
1 TTATTATT-TTATT
27967 TTTAATGCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 25 0.76
25 8 0.24
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (25 bp):
TTATTATTTTATTATTTCTCTTGAT
Found at i:30721 original size:227 final size:227
Alignment explanation
Indices: 30290--30736 Score: 767
Period size: 227 Copynumber: 2.0 Consensus size: 227
30280 GTAAATTATC
* *
30290 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATCATTAGT
**
30355 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
30420 TGTGTAAATGAAATTATTAAATTAATATTGTAAGTGGAAAACATGAAACACTATTAAAAAATTTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAAGTGGAAAACATGAAACACTATTAAAAAATTTG
30485 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
30518 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTAT-ATTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATCATTAG
30582 TTAATATTGTTAAATTT-AAATGCTAAATAATATTTTATAAAATATC-AAACAATCAAATAAAAT
65 TTAATATTGTTAAATTTAAAAT-CTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
* *
30645 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAA-
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAAGTGGAAAACATGAAACACTATTAAA-AAAT
30709 TTGAAACATAAATTACATAACTTTAAAA
193 TTGAAACATAAATTACATAACTTTAAAA
30737 GCAGTTTTAA
Statistics
Matches: 209, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
226 4 0.02
227 101 0.48
228 84 0.40
229 20 0.10
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATCATTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAAGTGGAAAACATGAAACACTATTAAAAAATTTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:30825 original size:20 final size:19
Alignment explanation
Indices: 30802--30847 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
30792 CGATATACCA
30802 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
30822 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
30842 GGTAAA
1 GGTAAA
30848 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:30992 original size:20 final size:19
Alignment explanation
Indices: 30969--31015 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
30959 CGATATAACA
*
30969 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
30989 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
31009 GGTAAAA
1 GGTAAAA
31016 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:33137 original size:184 final size:184
Alignment explanation
Indices: 32828--33499 Score: 1236
Period size: 184 Copynumber: 3.7 Consensus size: 184
32818 CTTTCAACAT
** *
32828 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
32893 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
32958 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
33012 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCCAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
33077 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* **
33142 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATTAGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
33196 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
33261 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
33326 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTATACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
33380 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
*
33445 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
33500 CCATTTAAAA
Statistics
Matches: 470, Mismatches: 18, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
184 470 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:36089 original size:23 final size:23
Alignment explanation
Indices: 36058--36121 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
36048 ATAGGTAAAC
*
36058 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
36081 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
36104 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
36122 TGGTTATATT
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:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:36128 original size:23 final size:23
Alignment explanation
Indices: 36058--36130 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
36048 ATAGGTAAAC
* **
36058 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
36081 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
36104 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
36127 ATAT
1 ATAT
36131 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:36517 original size:23 final size:23
Alignment explanation
Indices: 36486--36549 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
36476 ATAGGTAAAC
*
36486 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
36509 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
36532 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
36550 TGGTTATATT
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:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:36556 original size:23 final size:23
Alignment explanation
Indices: 36486--36558 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
36476 ATAGGTAAAC
* **
36486 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
36509 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
36532 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
36555 ATAT
1 ATAT
36559 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:36978 original size:23 final size:23
Alignment explanation
Indices: 36915--36979 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
36905 ATAGGTAAAC
* *
36915 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
36938 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
36961 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
36980 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:37204 original size:18 final size:18
Alignment explanation
Indices: 37183--37219 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
37173 GTAATTGGAG
37183 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
37201 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
37219 T
1 T
37220 ATATATTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:38561 original size:4 final size:5
Alignment explanation
Indices: 38533--38558 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
38523 TTAATCCGAT
38533 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
38559 TAATTAATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:38609 original size:37 final size:38
Alignment explanation
Indices: 38562--38726 Score: 158
Period size: 37 Copynumber: 4.4 Consensus size: 38
38552 AAATAAATAA
* * * *
38562 TTAATCGAATATAAATTTGT-AATAGTATATTTATATT
1 TTAATTGAATATAAATTTATAAATAATATATTTACATT
*
38599 TTAATTGAATATAAATTCATAAATAATATATTTACA-T
1 TTAATTGAATATAAATTTATAAATAATATATTTACATT
* * *
38636 TTAATTAAATATAAATTTATAAATAATACATTCT-TATT
1 TTAATTGAATATAAATTTATAAATAATATATT-TACATT
* * * * * *
38674 TAAATCGAGTATAAATTTGT-AGTAATATATTCACATT
1 TTAATTGAATATAAATTTATAAATAATATATTTACATT
*
38711 TTAATTAAATATAAAT
1 TTAATTGAATATAAAT
38727 CCTTAAATAA
Statistics
Matches: 102, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
37 72 0.71
38 30 0.29
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (38 bp):
TTAATTGAATATAAATTTATAAATAATATATTTACATT
Found at i:39356 original size:189 final size:189
Alignment explanation
Indices: 39029--39404 Score: 646
Period size: 189 Copynumber: 2.0 Consensus size: 189
39019 TAAAATCACG
* * * *
39029 AACATCGTCTAATTTTGCAAGAGTTTAAAAGAACTATGCTCAATGGTCTCCTTAAAGCAGTCTCA
1 AACATCGTCTAATTTTGCAACAGTTTAAAAGAAATATCCTCAATGGTCTCCTTAAAGCAGCCTCA
*
39094 CTTCACTCTCACATAGGTGGCTTACGTTGCCCGACTCATCAAAGCACATAAAAGTCATTAAAAGT
66 CTTCACTCTCACATAGGTGGCTTACGTTGCCCGACTCATCAAAACACATAAAAGTCATTAAAAGT
*
39159 TGTGCTTAACCCTATACCACTTTAATCATTATTTACATCTTATGAACAAACTTGGGACA
131 TGTGCTTAACCCTATACCACTTTAATCATTATTTACATCATATGAACAAACTTGGGACA
* *
39218 AACATCGTCTAATTTTGTAACAGTTTAAAATAAATATCCTCAATGGTCTCCTTAAAGCAGCCTCA
1 AACATCGTCTAATTTTGCAACAGTTTAAAAGAAATATCCTCAATGGTCTCCTTAAAGCAGCCTCA
* *
39283 CTTCACTCTCACATAGGTGGCTTATGTTGCTCGACTCATCAAAACACATAAAAGTCATTAAAAG-
66 CTTCACTCTCACATAGGTGGCTTACGTTGCCCGACTCATCAAAACACATAAAAGTCATTAAAAGT
39347 TGTTGCTTAACCCTATACCACTTTAATCATTATTTACATCATATGAACAAACTTGGGA
131 TG-TGCTTAACCCTATACCACTTTAATCATTATTTACATCATATGAACAAACTTGGGA
39405 TAAAAGACCC
Statistics
Matches: 176, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
188 2 0.01
189 174 0.99
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (189 bp):
AACATCGTCTAATTTTGCAACAGTTTAAAAGAAATATCCTCAATGGTCTCCTTAAAGCAGCCTCA
CTTCACTCTCACATAGGTGGCTTACGTTGCCCGACTCATCAAAACACATAAAAGTCATTAAAAGT
TGTGCTTAACCCTATACCACTTTAATCATTATTTACATCATATGAACAAACTTGGGACA
Found at i:40964 original size:19 final size:20
Alignment explanation
Indices: 40942--40979 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40932 AAAACAAAAA
40942 ATTAAAAT-TAATAAAAATT
1 ATTAAAATATAATAAAAATT
*
40961 ATTAAAATATACTAAAAAT
1 ATTAAAATATAATAAAAAT
40980 AAATTATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
ATTAAAATATAATAAAAATT
Found at i:42064 original size:32 final size:36
Alignment explanation
Indices: 41988--42091 Score: 106
Period size: 36 Copynumber: 2.9 Consensus size: 36
41978 ATTTTAATTG
* *
41988 AATATAAATTCATAAATAATATATTTTATTTTATCA
1 AATATAAATTCATAAATAATACATTTTATATTATCA
* *
42024 AATATAAATTTATAAATAATACATTTT-TATTTCAATTA
1 AATATAAATTCATAAATAATACATTTTATA-TT--ATCA
* *
42062 AATATAAATTTAT-AATAATATATTTT-TATT
1 AATATAAATTCATAAATAATACATTTTATATT
42092 TTAATTGAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
35 1 0.02
36 29 0.48
37 14 0.23
38 16 0.27
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (36 bp):
AATATAAATTCATAAATAATACATTTTATATTATCA
Found at i:42125 original size:43 final size:37
Alignment explanation
Indices: 41940--42107 Score: 171
Period size: 37 Copynumber: 4.5 Consensus size: 37
41930 TACAATATTA
* * * **
41940 TATTTCAAATGAATATAAATTCT-TAATAATATACTCA
1 TATTTCAATTAAATATAAATT-TATAATAATATATTTT
* * *
41977 TATTTTAATTGAATATAAATTCATAAATAATATA-TTT
1 TATTTCAATTAAATATAAATTTAT-AATAATATATTTT
* * *
42014 TATTT-TATCAAATATAAATTTATAAATAATACATTTT
1 TATTTCAATTAAATATAAATTTAT-AATAATATATTTT
42051 TATTTCAATTAAATATAAATTTATAATAATATATTTT
1 TATTTCAATTAAATATAAATTTATAATAATATATTTT
* *
42088 TATTTTAATTGAATATAAAT
1 TATTTCAATTAAATATAAAT
42108 CCTTAGATAA
Statistics
Matches: 112, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
36 23 0.21
37 64 0.57
38 25 0.22
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (37 bp):
TATTTCAATTAAATATAAATTTATAATAATATATTTT
Found at i:42666 original size:11 final size:11
Alignment explanation
Indices: 42650--42676 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
42640 TTACTACTGA
42650 CCATATATTAG
1 CCATATATTAG
42661 CCATATATTAG
1 CCATATATTAG
42672 CCATA
1 CCATA
42677 CACCTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (11 bp):
CCATATATTAG
Found at i:47538 original size:31 final size:31
Alignment explanation
Indices: 47503--47562 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
47493 ACCGGTCATA
* *
47503 ACCCGACCCGTTTATCCGACCCGTTGACCCT
1 ACCCGACCCGTTGACCCGACCCGTTGACCCT
*
47534 ACCCGACCTGTTGACCCGACCCGTTGACC
1 ACCCGACCCGTTGACCCGACCCGTTGACC
47563 GGCGTTGACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.17, C:0.45, G:0.18, T:0.20
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCCGTTGACCCT
Found at i:47539 original size:18 final size:18
Alignment explanation
Indices: 47518--47556 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
47508 ACCCGTTTAT
*
47518 CCGACCCGTTGACCCTAC
1 CCGACCCGTTGACCCGAC
*
47536 CCGACCTGTTGACCCGAC
1 CCGACCCGTTGACCCGAC
47554 CCG
1 CCG
47557 TTGACCGGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.49, G:0.21, T:0.15
Consensus pattern (18 bp):
CCGACCCGTTGACCCGAC
Found at i:50215 original size:24 final size:24
Alignment explanation
Indices: 50083--50201 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
50073 TTTGATTTGA
* *
50083 ATTCTGATCTGATACTTGACATAG
1 ATTCTGATATGATACTTGACATGG
*
50107 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
*
50131 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
50155 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
*
50179 ATTTTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
50202 AATTATGTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 85 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:55194 original size:72 final size:72
Alignment explanation
Indices: 55067--55210 Score: 200
Period size: 72 Copynumber: 2.0 Consensus size: 72
55057 TGAATATTTT
** * * *
55067 ATCTGATTTTTGATTTGAATTCTGATCTGATACTTGACATGGATTCTGATCTGATA-TCTGACAT
1 ATCTGATACTTGACTTGAATTCTGATATGATACTTGACATGGATTCTGATATGATACT-TGACAT
55131 GGATTATG
65 GGATTATG
* * *
55139 ATCTGATACTTGACTTGGATTCTGATATGATACTTGACTTGGATTTTGATATGATACTTGACATG
1 ATCTGATACTTGACTTGAATTCTGATATGATACTTGACATGGATTCTGATATGATACTTGACATG
55204 GATTATG
66 GATTATG
55211 TTTTGATTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 62 0.98
73 1 0.02
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (72 bp):
ATCTGATACTTGACTTGAATTCTGATATGATACTTGACATGGATTCTGATATGATACTTGACATG
GATTATG
Found at i:55205 original size:24 final size:24
Alignment explanation
Indices: 55085--55207 Score: 176
Period size: 24 Copynumber: 5.1 Consensus size: 24
55075 TTTGATTTGA
55085 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
55109 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
* *
55133 ATTATGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
55157 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
55181 ATTTTGATATGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
55205 ATT
1 ATT
55208 ATGTTTTGAT
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 89 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:55379 original size:43 final size:43
Alignment explanation
Indices: 55318--55412 Score: 147
Period size: 43 Copynumber: 2.2 Consensus size: 43
55308 GGGCCTTACT
* *
55318 TGGTGTGTTGGTGGGTGTATGGTTTTGGGGAA-CCTACACATTA
1 TGGTGTGTTAGTGGGTGTATGGTTCT-GGGAATCCTACACATTA
*
55361 TGGTGTGTTAGTGGGTGTATGGTTCTGGGAATCTTACACATTA
1 TGGTGTGTTAGTGGGTGTATGGTTCTGGGAATCCTACACATTA
55404 TGGTGTGTT
1 TGGTGTGTT
55413 CGGTTGGAGG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
42 5 0.10
43 43 0.90
ACGTcount: A:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (43 bp):
TGGTGTGTTAGTGGGTGTATGGTTCTGGGAATCCTACACATTA
Found at i:59339 original size:22 final size:22
Alignment explanation
Indices: 59311--59354 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
59301 ACTGTGTAAT
59311 TGACTATCAACCAGAGAAAGCA
1 TGACTATCAACCAGAGAAAGCA
59333 TGACTATCAACCAGAGAAAGCA
1 TGACTATCAACCAGAGAAAGCA
59355 AATGTTGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.14
Consensus pattern (22 bp):
TGACTATCAACCAGAGAAAGCA
Found at i:67941 original size:2 final size:2
Alignment explanation
Indices: 67934--67960 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
67924 AAACACTACA
67934 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
67961 AGGTACACGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70722 original size:60 final size:60
Alignment explanation
Indices: 70562--70726 Score: 156
Period size: 60 Copynumber: 2.8 Consensus size: 60
70552 CTCATTTTTG
* ** * * *
70562 AATTGGTCCTTAACCTTTTGAATATTCTAATTTTTTCCCCAAACTATGAATCTCATTCTA
1 AATTGGTCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAATTATGAACCTCATTCTA
* * * * * *
70622 AA-TGATTCCTTAAACTTTTGAAAATTCCAA-TCCAAACCCTAAATTAT-AACCCTCTTTCTA
1 AATTG-GTCCTTAAACTTTTGAATATTCTAATTTC-ATCCCTAAATTATGAA-CCTCATTCTA
* *
70682 AATTGGTCCCTAAACTTTTGAATGTTCTAATTTCATCCCTAAATT
1 AATTGGTCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAATT
70727 CATCCAATTA
Statistics
Matches: 81, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
59 5 0.06
60 72 0.89
61 4 0.05
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
AATTGGTCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAATTATGAACCTCATTCTA
Found at i:73583 original size:21 final size:20
Alignment explanation
Indices: 73558--73604 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
73548 GTTTGTATCT
73558 TCTCTGTTTTTTTTTTCTGTC
1 TCTCTGTTTTTTTTTT-TGTC
*
73579 TCTCT-CTTTTTTTTTTGTC
1 TCTCTGTTTTTTTTTTTGTC
73598 TCTCTGT
1 TCTCTGT
73605 CCCGTTCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 9 0.39
20 9 0.39
21 5 0.22
ACGTcount: A:0.00, C:0.21, G:0.09, T:0.70
Consensus pattern (20 bp):
TCTCTGTTTTTTTTTTTGTC
Found at i:74055 original size:11 final size:11
Alignment explanation
Indices: 74039--74063 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
74029 TTATTTATAT
74039 ATATATATTTA
1 ATATATATTTA
74050 ATATATATTTA
1 ATATATATTTA
74061 ATA
1 ATA
74064 ATAATAATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATATATTTA
Found at i:74067 original size:3 final size:3
Alignment explanation
Indices: 74059--74123 Score: 96
Period size: 3 Copynumber: 22.0 Consensus size: 3
74049 AATATATATT
* * *
74059 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA T-A TAG TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
74106 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Done.