Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003902.1 Hibiscus syriacus cultivar Beakdansim tig00008433_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: 230710
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:162183 original size:84 final size:84
Alignment explanation
Indices: 162059--162827 Score: 937
Period size: 84 Copynumber: 9.1 Consensus size: 84
162049 ACTCAAGTTG
** * * *
162059 AGAAGGGTTATCTATCAACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATT
*
162124 TGCAGCATAGCTCAAGGAA
66 TGCAGCATAGCTCAAGGCA
* * * *
162143 AGAATGGTTATTTTCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATT
* *
162208 TGCAGCATAACTCAAGGCT
66 TGCAGCATAGCTCAAGGCA
* * *
162227 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTTGACTACGCTCAGCTCAAAGGCACCATCAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCA-CATCAT
* * *
162292 TTGCAGCATAGCTTAAGTCG
65 TTGCAGCATAGCTCAAGGCA
** * * * * *
162312 AGAAAAGCTATCTGCCACCAAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATT
* *
162377 TGCAGCATAACTCAAGGCT
66 TGCAGCATAGCTCAAGGCA
* * ** * *
162396 AGAAGGGTTATCTGCCCACCAAAGACCTTCGAGTTCTTCTACACTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATT
*
162461 TGCAACATAGCTCAAGGCA
66 TGCAGCATAGCTCAAGGCA
* * * *
162480 AGAAGGGTTATTTGCCCACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGACATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATT
* * *
162545 TGCAGCATAACTCAATGCT
66 TGCAGCATAGCTCAAGGCA
* * * * * *
162564 AGAAGGGTTATATGCTAACCAAAGACCTTCGAGTTCGATTACGCTTAACTCAAAGGCACCATCAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCA-CATCAT
*
162629 TTGCAACATAGCTCAAGGCA
65 TTGCAGCATAGCTCAAGGCA
* * * * **
162649 AGAAGGGCTATTTGCCAACAAAAGACCTTCAAGTTCGACTACTCTCAGCTCCGAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATT
*
162714 TGCAGCAT-GACTCAAGGCT
66 TGCAGCATAG-CTCAAGGCA
* * * * * *
162733 AGAAGGGTTATCTGCCAACAAAAGACCTTCTAGTTCGATTACACTCAACTCGAAGACACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATT
* *
162798 TACAGCATAACTCAAGGCA
66 TGCAGCATAGCTCAAGGCA
162817 AGAAGGGTTAT
1 AGAAGGGTTAT
162828 ATGTCAATAA
Statistics
Matches: 581, Mismatches: 100, Indels: 8
0.84 0.15 0.01
Matches are distributed among these distances:
83 1 0.00
84 442 0.76
85 138 0.24
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (84 bp):
AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATT
TGCAGCATAGCTCAAGGCA
Found at i:162686 original size:337 final size:337
Alignment explanation
Indices: 162042--162827 Score: 1155
Period size: 337 Copynumber: 2.3 Consensus size: 337
162032 AAACTATCGA
* ** *
162042 CAGCATAACTCAA-GTTGAGAAGGGTTATCTATCAACCAAAGACCTTCGAGTTCGA-CTACGCTC
1 CAGCATAACTCAAGGCT-AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTC-ATCTACACTC
* * *
162105 AACTCCAAGGCACATCATTTGCAGCATAGCTCAAGGAAAGAATGGTTATTTTCCAACAAAAGACC
64 AACTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACC
*
162170 TTCGAGTTCGACTACGCTCAGCTCAAAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGT
129 TTCGAGTTCGACTACGCTCAGCTCAAAGACATATCATTTGCAGCATAACTCAAGGCTAGAAGGGT
* * * * *
162235 TATCTGCCAACCAAAGACCTTTGAGTTTGACTACGCTCAGCTCAAAGGCACCATCATTTGCAGCA
194 TATATGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAACTCAAAGGCACCATCATTTGCAACA
* * * * * *
162300 TAGCTTAAGTCGAGAAAAGCTATCTGCCACCAAAATACCTTCGAGTTCGACTACGCTCAGCTCCA
259 TAGCTCAAGGCAAGAAAAGCTATCTGCCAACAAAAGACCTTCAAGTTCGACTACGCTCAGCTCCA
*
162365 AGGCATATCATTTG
324 AGGCACATCATTTG
* * *
162379 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCCACCAAAGACCTTCGAGTTCTTCTACACTCAG
1 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCATCTACACTCAA
* *
162444 CTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCCACAAAAGACCTT
66 CTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTT
*
162509 CGAGTTCGACTACGCTCAGCTCAAAGACATATCATTTGCAGCATAACTCAATGCTAGAAGGGTTA
131 CGAGTTCGACTACGCTCAGCTCAAAGACATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTA
* * *
162574 TATGCTAACCAAAGACCTTCGAGTTCGATTACGCTTAACTCAAAGGCACCATCATTTGCAACATA
196 TATGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAACTCAAAGGCACCATCATTTGCAACATA
** * * *
162639 GCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCAAGTTCGACTACTCTCAGCTCCGAG
261 GCTCAAGGCAAGAAAAGCTATCTGCCAACAAAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAG
162704 GCACATCATTTG
326 GCACATCATTTG
* * *
162716 CAGCATGACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCTAGTTCGAT-TACACTCA
1 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTC-ATCTACACTCA
* * * *
162780 ACTCGAAGACACATCATTTACAGCATAACTCAAGGCAAGAAGGGTTAT
65 ACTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTAT
162828 ATGTCAATAA
Statistics
Matches: 401, Mismatches: 45, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
337 398 0.99
338 3 0.01
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (337 bp):
CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCATCTACACTCAA
CTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTT
CGAGTTCGACTACGCTCAGCTCAAAGACATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTA
TATGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAACTCAAAGGCACCATCATTTGCAACATA
GCTCAAGGCAAGAAAAGCTATCTGCCAACAAAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAG
GCACATCATTTG
Found at i:162823 original size:253 final size:250
Alignment explanation
Indices: 162041--162830 Score: 1008
Period size: 253 Copynumber: 3.1 Consensus size: 250
162031 GAAACTATCG
**
162041 ACAGCATAACTCAAGTTGAGAAGGGTTATCTAT-CAACCAAAGACCTTCGAGTTCGACTACGCTC
1 ACAGCATAACTCAAGGCGAGAAGGGTTA--TATGCAACCAAAGACCTTCGAGTTCGACTACGCTC
* * *
162105 AACTCCAAGGCACATCATTTGCAGCATAGCTCAAGGAAAGAATGGTTATTTTCCAACAAAAGACC
64 AACTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACC
* * *
162170 TTCGAGTTCGACTACGCTCAGCTCAAAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGT
129 TTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCAT-ACTCAAGGCTAGAAGGGT
* * *
162235 TATCTGCCAACCAAAGACCTT-TGAGTTTGACTACGCTCAGCTCAAAGGCACCATCATTT
193 TATCTGCCAACAAAAGACCTTCT-AGTTCGACTACGCTCAGCTCAAAGACA-CATCATTT
* * * * ** * * * *
162294 GCAGCATAGCTTAAGTCGAGAAAAGCTATCTGCCACCAAAATACCTTCGAGTTCGACTACGCTCA
1 ACAGCATAACTCAAGGCGAGAAGGGTTATATGCAACC-AAAGACCTTCGAGTTCGACTACGCTCA
* * * * * * *
162359 GCTCCAAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCCACCAAAGACCT
65 ACTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCT
** * *
162424 TCGAGTTCTTCTACACTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTT
130 TCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATA-CTCAAGGCTAGAAGGGTT
* * * *
162489 ATTTGCCCACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGACATATCATTT
194 ATCTGCCAACAAAAGACCTTCTAGTTCGACTACGCTCAGCTCAAAGACACATCATTT
* * * * *
162546 GCAGCATAACTCAATGCTAGAAGGGTTATATGCTAACCAAAGACCTTCGAGTTCGATTACGCTTA
1 ACAGCATAACTCAAGGCGAGAAGGGTTATATGC-AACCAAAGACCTTCGAGTTCGACTACGCTCA
* * *
162611 ACTCAAAGGCACCATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACC
65 ACTCCAAGGCA-CATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACC
* * *
162676 TTCAAGTTCGACTACTCTCAGCTCCGAGGCACATCATTTGCAGCATGACTCAAGGCTAGAAGGGT
129 TTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCAT-ACTCAAGGCTAGAAGGGT
* * * *
162741 TATCTGCCAACAAAAGACCTTCTAGTTCGATTACACTCAACTCGAAGACACATCATTT
193 TATCTGCCAACAAAAGACCTTCTAGTTCGACTACGCTCAGCTCAAAGACACATCATTT
*
162799 ACAGCATAACTCAAGGCAAGAAGGGTTATATG
1 ACAGCATAACTCAAGGCGAGAAGGGTTATATG
162831 TCAATAAAAT
Statistics
Matches: 455, Mismatches: 75, Indels: 14
0.84 0.14 0.03
Matches are distributed among these distances:
251 2 0.00
252 69 0.15
253 383 0.84
254 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (250 bp):
ACAGCATAACTCAAGGCGAGAAGGGTTATATGCAACCAAAGACCTTCGAGTTCGACTACGCTCAA
CTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTT
CGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATACTCAAGGCTAGAAGGGTTAT
CTGCCAACAAAAGACCTTCTAGTTCGACTACGCTCAGCTCAAAGACACATCATTT
Found at i:163512 original size:31 final size:31
Alignment explanation
Indices: 163452--163518 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
163442 TGCATATATA
**
163452 ATATAGTTTTTGAAAATATTTTTTTAAAAAT
1 ATATAGTTTTTGAAAATATTTTTGAAAAAAT
* *
163483 TTATAGTTTTTGAAAATGTTTTTGAAAAAAT
1 ATATAGTTTTTGAAAATATTTTTGAAAAAAT
163514 ATATA
1 ATATA
163519 TAATATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (31 bp):
ATATAGTTTTTGAAAATATTTTTGAAAAAAT
Found at i:163603 original size:36 final size:36
Alignment explanation
Indices: 163514--163824 Score: 173
Period size: 36 Copynumber: 8.4 Consensus size: 36
163504 TTGAAAAAAT
163514 ATATATAATATATATAG-TTTTAAAAAAACATTTTGAAAA
1 ATATAT-ATA-ATATAGTTTTTAAAAAAACATTTTG--AA
*
163553 CATATATATTATATAGTTTTTAAAAAAACATTTTGAA
1 -ATATATATAATATAGTTTTTAAAAAAACATTTTGAA
* *
163590 ATATATATAATATAGTTTTT--GAAAACATTTTAAA
1 ATATATATAATATAGTTTTTAAAAAAACATTTTGAA
*
163624 ATATATATATTATATGATTTTT--AAAAACATTTTGAAAAAA
1 ATATATATAATATA-G-TTTTTAAAAAAACATTTTG----AA
163664 TATATATATAATATATAGTTTTT---AAAACATTTTGAA
1 -ATATATAT-A-ATATAGTTTTTAAAAAAACATTTTGAA
* * * * *
163700 A-ACTATATAATATATGATTTTGAAAAGA-TTTTTAAAAA
1 ATA-TATATAATATA-GTTTTTAAAAAAACATTTT--GAA
* **
163738 ATATATATAATATA-TAATTTTAAAATATGA-TTTGAA
1 ATATATATAATATAGT--TTTTAAAAAAACATTTTGAA
* * * ** *
163774 A-ATATATATTATATGATTTTAAAAATATTTTTTAAA
1 ATATATATAATATA-GTTTTTAAAAAAACATTTTGAA
163810 ATATATAT-ATATAGT
1 ATATATATAATATAGT
163825 ATATAATTTT
Statistics
Matches: 217, Mismatches: 29, Indels: 55
0.72 0.10 0.18
Matches are distributed among these distances:
33 5 0.02
34 32 0.15
35 27 0.12
36 53 0.24
37 11 0.05
38 30 0.14
39 21 0.10
40 19 0.09
41 13 0.06
42 2 0.01
43 4 0.02
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (36 bp):
ATATATATAATATAGTTTTTAAAAAAACATTTTGAA
Found at i:163739 original size:75 final size:74
Alignment explanation
Indices: 163501--163835 Score: 307
Period size: 73 Copynumber: 4.5 Consensus size: 74
163491 TTTGAAAATG
* *
163501 TTTTTGAAAAAATATATATA-ATATATATAGTTTTAAAAAAACATTTTGAAAACATATATATTAT
1 TTTTT-AAAAAATATATATATA-ATATATAGTTTT--TAAAACATTTTG-AAA-ATATATAATAT
*
163565 ATAGTTTTTAAAAAAACA
60 AT-GATTTT--AAAAACA
*
163583 -TTTT---GAA-ATATATAT-A-ATATAGTTTTTGAAAACATTTT-AAAATATATATATTATATG
1 TTTTTAAAAAATATATATATAATATATAGTTTTT-AAAACATTTTGAAAATATATA-A-TATATG
163640 ATTTTTAAAAACA
63 A-TTTTAAAAACA
*
163653 TTTTGAAAAAATATATATATAATATATAGTTTTTAAAACATTTTGAAAACTATATAATATATGAT
1 TTTTTAAAAAATATATATATAATATATAGTTTTTAAAACATTTTGAAAA-TATATAATATATGAT
* *
163718 TTTGAAAAGA
65 TTTAAAAACA
* * *
163728 TTTTT-AAAAA-ATATATATAATATATA-ATTTTAAAATATGATTTGAAAATATATATTATATGA
1 TTTTTAAAAAATATATATATAATATATAGTTTTTAAAACAT--TTTGAAAATATATAATATATGA
*
163790 TTTTAAAAATA
64 TTTTAAAAACA
* * *
163801 TTTTTTAAAATATATATATATAGTATATAATTTTT
1 -TTTTTAAAAAATATATATATAATATATAGTTTTT
163836 TAAATGATCT
Statistics
Matches: 216, Mismatches: 17, Indels: 45
0.78 0.06 0.16
Matches are distributed among these distances:
70 14 0.06
71 7 0.03
72 19 0.09
73 48 0.22
74 30 0.14
75 26 0.12
76 40 0.19
77 22 0.10
78 6 0.03
81 4 0.02
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.44
Consensus pattern (74 bp):
TTTTTAAAAAATATATATATAATATATAGTTTTTAAAACATTTTGAAAATATATAATATATGATT
TTAAAAACA
Found at i:163770 original size:13 final size:13
Alignment explanation
Indices: 163711--163813 Score: 51
Period size: 13 Copynumber: 8.3 Consensus size: 13
163701 ACTATATAAT
*
163711 ATATGATTTTGAA
1 ATATGATTTTAAA
163724 A-A-GATTTTTAAA
1 ATATGA-TTTTAAA
* * *
163736 AAAT-ATATATAAT
1 ATATGAT-TTTAAA
*
163749 ATATAATTTTAAA
1 ATATGATTTTAAA
*
163762 ATATGATTTGAAA
1 ATATGATTTTAAA
*
163775 ATAT-ATATT---
1 ATATGATTTTAAA
163784 ATATGATTTTAAAA
1 ATATGATTTT-AAA
*
163798 ATAT-TTTTTAAA
1 ATATGATTTTAAA
163810 ATAT
1 ATAT
163814 ATATATATAG
Statistics
Matches: 68, Mismatches: 12, Indels: 21
0.67 0.12 0.21
Matches are distributed among these distances:
9 4 0.06
10 4 0.06
11 2 0.03
12 19 0.28
13 33 0.49
14 6 0.09
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (13 bp):
ATATGATTTTAAA
Found at i:163788 original size:149 final size:149
Alignment explanation
Indices: 163445--163835 Score: 403
Period size: 149 Copynumber: 2.6 Consensus size: 149
163435 TTAAAAATGC
* ** * * **
163445 ATATATAATATAGTTTTTGAAAATATTTTTTTAA-A-A-AT-TTATA-GTTTTTGAAAATGTTTT
1 ATATATAATATAGTTTTTGAAAACA-TTTTAAAATATATATATTATATGATTTTAAAAACATTTT
* *
163505 TGAAAAAATATATATA-ATATATATAGTTTTAAAAAAACATTTTGAAAACATATATATTATATAG
65 TGAAAAAATATATATATA-ATATATAGTTTT--TAAAACATTTTGAAAACATATATAATATATAG
* *
163569 TTTTTAAAAAAACATTTTGAAAT
127 ATTTTAAAAAAACATTTTAAAAT
163592 ATATATAATATAGTTTTTGAAAACATTTTAAAATATATATATTATATGATTTTTAAAAACA-TTT
1 ATATATAATATAGTTTTTGAAAACATTTTAAAATATATATATTATATGA-TTTTAAAAACATTTT
163656 TGAAAAAATATATATATAATATATAGTTTTTAAAACATTTTGAAAAC-TATATAATATAT-GATT
65 TGAAAAAATATATATATAATATATAGTTTTTAAAACATTTTGAAAACATATATAATATATAGATT
* * *
163719 TTGAAAAGA-TTTTTAAAAAAT
130 TTAAAAAAACATTTT--AAAAT
* * *
163740 ATATATAATATA-TAATTTT-AAAATATGATTTGAAA-ATATATATTATATGATTTTAAAAATAT
1 ATATATAATATAGT--TTTTGAAAACAT--TTTAAAATATATATATTATATGATTTTAAAAACAT
* * * *
163802 TTTTTAAAATATATATATATAGTATATAATTTTT
62 TTTTGAAAAAATATATATATAATATATAGTTTTT
163836 TAAATGATCT
Statistics
Matches: 209, Mismatches: 21, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
146 10 0.05
147 36 0.17
148 44 0.21
149 67 0.32
150 11 0.05
151 32 0.15
152 9 0.04
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (149 bp):
ATATATAATATAGTTTTTGAAAACATTTTAAAATATATATATTATATGATTTTAAAAACATTTTT
GAAAAAATATATATATAATATATAGTTTTTAAAACATTTTGAAAACATATATAATATATAGATTT
TAAAAAAACATTTTAAAAT
Found at i:163855 original size:4 final size:4
Alignment explanation
Indices: 163846--163887 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
163836 TAAATGATCT
163846 TTTA TTTA TTTA TTTA TTTA -TTA -TTA -TTA TTTA -TTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
163888 ATTGTTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 12 0.33
4 24 0.67
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:163877 original size:17 final size:18
Alignment explanation
Indices: 163846--163902 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 18
163836 TAAATGATCT
163846 TTTATTTA-T-TTATTTA
1 TTTATTTATTATTATTTA
163862 TTTA-TTATTATTATTTA
1 TTTATTTATTATTATTTA
*
163879 -TTATTTATTATTGTTTA
1 TTTATTTATTATTATTTA
*
163896 TTCATTT
1 TTTATTT
163903 TTTTCATTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 3 0.09
16 8 0.23
17 19 0.54
18 5 0.14
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTATTTATTATTATTTA
Found at i:163879 original size:7 final size:7
Alignment explanation
Indices: 163846--163890 Score: 65
Period size: 7 Copynumber: 6.3 Consensus size: 7
163836 TAAATGATCT
163846 TTTATTTA
1 TTTA-TTA
163854 TTTATTTA
1 TTTA-TTA
163862 TTTATTA
1 TTTATTA
163869 -TTATTA
1 TTTATTA
163875 TTTATTA
1 TTTATTA
163882 TTTATTA
1 TTTATTA
163889 TT
1 TT
163891 GTTTATTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.17
7 18 0.50
8 12 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTATTA
Found at i:165021 original size:31 final size:31
Alignment explanation
Indices: 164985--165050 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
164975 AGCATGTATG
* *
164985 TTTATTTTATTTTATTTTGG-TCCTTTA-ACCT
1 TTTATTTT-TATTATTTGGGATCCTTTACA-CT
165016 TTTATTTTTATTATTTGGGATCCTTTACACT
1 TTTATTTTTATTATTTGGGATCCTTTACACT
165047 TTTA
1 TTTA
165051 ATCATTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 9 0.29
31 21 0.68
32 1 0.03
ACGTcount: A:0.18, C:0.12, G:0.08, T:0.62
Consensus pattern (31 bp):
TTTATTTTTATTATTTGGGATCCTTTACACT
Found at i:165063 original size:4 final size:4
Alignment explanation
Indices: 165054--165090 Score: 65
Period size: 4 Copynumber: 9.0 Consensus size: 4
165044 ACTTTTAATC
165054 ATTT ATTT ATTT ATTT ATTT ATTAT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATT-T ATTT ATTT ATTT
165091 TATCTTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:181775 original size:32 final size:31
Alignment explanation
Indices: 181726--181817 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 31
181716 AAAATTTGAT
**
181726 AAAT-TTAATAACCATTTTATAATAATTCTA
1 AAATATTAATAATAATTTTATAATAATTCTA
181756 CAAATATTAATAATAATTTTATAGA-AATT-TA
1 -AAATATTAATAATAATTTTATA-ATAATTCTA
* *
181787 ATAAAATTCAATAATTATTTTATAATAATTC
1 A-AATATT-AATAATAATTTTATAATAATTC
181818 CATAATTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
30 1 0.02
31 12 0.24
32 37 0.73
33 1 0.02
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (31 bp):
AAATATTAATAATAATTTTATAATAATTCTA
Found at i:181808 original size:22 final size:22
Alignment explanation
Indices: 181739--181824 Score: 61
Period size: 21 Copynumber: 4.0 Consensus size: 22
181729 TTTAATAACC
* * *
181739 ATTTTATAATAATTCTACAAAT
1 ATTTTATAATAATTCAATAATT
* ** *
181761 A-TTAATAATAATTTTATAGA-A
1 ATTTTATAATAATTCAATA-ATT
*
181782 ATTTAATAA-AATTCAATAATT
1 ATTTTATAATAATTCAATAATT
*
181803 ATTTTATAATAATTCCATAATT
1 ATTTTATAATAATTCAATAATT
181825 TTAATGATCG
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
20 1 0.02
21 30 0.59
22 20 0.39
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (22 bp):
ATTTTATAATAATTCAATAATT
Found at i:182367 original size:61 final size:60
Alignment explanation
Indices: 182300--182428 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
182290 ATAGTCTGGT
* * * * *
182300 GACCATTTTATAAATTTTTAATAGTCGA-TGGACTGAATAAAGTAATAATCTATAGTCAAAG
1 GACCATTTTAT-AACTTTCAATAGTCAAGT-GACTGAACAAAGTAATAACCTATAGTCAAAG
* * * * *
182361 GACCATTTTGTAACTTTCAATAGTCAAGTGACTTAACAAAGTAGTACCCTATAGTCAAGG
1 GACCATTTTATAACTTTCAATAGTCAAGTGACTGAACAAAGTAATAACCTATAGTCAAAG
182421 GACCATTT
1 GACCATTT
182429 ATGTTATTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
60 46 0.81
61 11 0.19
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (60 bp):
GACCATTTTATAACTTTCAATAGTCAAGTGACTGAACAAAGTAATAACCTATAGTCAAAG
Found at i:187394 original size:23 final size:23
Alignment explanation
Indices: 187363--187407 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
187353 CGGTTCCCCT
* *
187363 AGGGGGAATCGGTTCCTCTTCAA
1 AGGGAGAATCGGTTCCCCTTCAA
187386 AGGGAGAATCGGTTCCCCTTCA
1 AGGGAGAATCGGTTCCCCTTCA
187408 CGGGGGTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.24
Consensus pattern (23 bp):
AGGGAGAATCGGTTCCCCTTCAA
Found at i:193800 original size:20 final size:19
Alignment explanation
Indices: 193759--193811 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
193749 AAAAAGCTTG
193759 TTGTCTTCAGTTTGCCATA
1 TTGTCTTCAGTTTGCCATA
193778 TTGTCTTCAGTGTTGCCCA-A
1 TTGTCTTCAGT-TTG-CCATA
*
193798 TTGTCTTTAGTTTG
1 TTGTCTTCAGTTTG
193812 ACAATATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 14 0.45
20 14 0.45
21 3 0.10
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.49
Consensus pattern (19 bp):
TTGTCTTCAGTTTGCCATA
Found at i:198421 original size:20 final size:22
Alignment explanation
Indices: 198396--198440 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
198386 AAAATATATT
*
198396 AATATAATA-ATAATAAA-ATA
1 AATATAATAGATAACAAAGATA
198416 AATATAATAGATAACAAAGATA
1 AATATAATAGATAACAAAGATA
198438 AAT
1 AAT
198441 GAAAGTTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
21 7 0.32
22 6 0.27
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (22 bp):
AATATAATAGATAACAAAGATA
Found at i:198480 original size:12 final size:12
Alignment explanation
Indices: 198451--198492 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
198441 GAAAGTTAGA
* *
198451 AAAAAAAGAAAA
1 AAAAAAATAAAT
198463 ATAAAAAATAAAT
1 A-AAAAAATAAAT
198476 AAAAAAATAAAT
1 AAAAAAATAAAT
198488 AAAAA
1 AAAAA
198493 GGACCAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.86, C:0.00, G:0.02, T:0.12
Consensus pattern (12 bp):
AAAAAAATAAAT
Found at i:200856 original size:28 final size:28
Alignment explanation
Indices: 200810--200900 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 28
200800 GGTCTTTGTG
*
200810 TTTCAAGAGAAA-TATTTTCAAAGGTTTT
1 TTTCAAGAGAAACGA-TTTCAAAGGTTTT
200838 TTTCAAGAGAAACGATTTCAAAGGTTTTTTGT
1 TTTCAAGAGAAACGATTTCAAAGG---TTT-T
* *
200870 GTTTCAAGAGAAACGACTTCAAAGGATTT
1 -TTTCAAGAGAAACGATTTCAAAGGTTTT
200899 TT
1 TT
200901 GTGTTTCAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
28 23 0.43
29 2 0.04
30 2 0.04
31 3 0.06
32 1 0.02
33 23 0.43
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (28 bp):
TTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:200879 original size:33 final size:32
Alignment explanation
Indices: 200798--200916 Score: 149
Period size: 33 Copynumber: 3.8 Consensus size: 32
200788 GTCAAACTCG
* *
200798 AAGGTCTTTGTGTTTCAAGAGAAA-TATTTTCA
1 AAGGTTTTTGTGTTTCAAGAGAAACGA-TTTCA
200830 AAGG--TTT-T-TTTCAAGAGAAACGATTTCA
1 AAGGTTTTTGTGTTTCAAGAGAAACGATTTCA
*
200858 AAGGTTTTTTGTGTTTCAAGAGAAACGACTTCA
1 AAGG-TTTTTGTGTTTCAAGAGAAACGATTTCA
200891 AAGGATTTTTGTGTTTCAAGAGAAAC
1 AAGG-TTTTTGTGTTTCAAGAGAAAC
200917 TGTCTCCAGA
Statistics
Matches: 78, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
28 21 0.27
29 2 0.03
30 3 0.04
31 3 0.04
32 5 0.06
33 44 0.56
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (32 bp):
AAGGTTTTTGTGTTTCAAGAGAAACGATTTCA
Found at i:201062 original size:37 final size:37
Alignment explanation
Indices: 200972--201074 Score: 118
Period size: 37 Copynumber: 2.8 Consensus size: 37
200962 AGATTGGTGT
* *
200972 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTCGT
1 TTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTCGG
** * * *
201009 TTCAAGTGGAATTGTCTCAAGAGAGACAAAA-TTTGG
1 TTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTCGG
*
201045 TTCAAAAAGAAACTGTCTCAAGGGAGACAA
1 TTC-AAAAGAAACTGTCTCAAGAGAGACAA
201075 TGGTGAGCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 6 0.11
37 49 0.89
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (37 bp):
TTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTCGG
Found at i:201770 original size:315 final size:316
Alignment explanation
Indices: 201197--202558 Score: 2437
Period size: 315 Copynumber: 4.3 Consensus size: 316
201187 TGTTTCGAGG
* * * *
201197 CCAATATCCTTCGCTGTGAAGTTGAACTTAGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAG
*
201262 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
201327 AAATTGGCTCTGAAATTGA-AA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
130 AAATTGGCTCTGAAATTGAGAAGATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
* *
201390 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGT
195 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-A
201455 TGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
259 TGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
201513 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGAAAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
201578 GGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
*
201643 AATTGGCTCTGAAATTGA-AA-ATGTTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAAC
131 AATTGGCTCTGAAATTGAGAAGATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* *
201706 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTT
196 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-AT
201771 GTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
260 GTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
201828 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
201893 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
* * *
201958 AATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAAC
131 AATTGGCTCTGAAATTGAGAAGATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
202023 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
196 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
* *
202088 TTTGTTGAAAACCAGCGGTCCCTTCGTTGTAAAGTTGAACTTGCGTTGTCTGGAGT
261 TTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
202144 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-AAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
202208 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
* * *
202273 AATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAAC
131 AATTGGCTCTGAAATTGAGAAGATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
202338 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
196 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
*
202403 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
261 TTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * * *
202459 CCAATATCCTTCGTGGTGAAGTTGAAATCGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
202524 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
202559 TGAGCGACCC
Statistics
Matches: 1020, Mismatches: 23, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
315 720 0.71
316 199 0.20
317 101 0.10
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (316 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
AATTGGCTCTGAAATTGAGAAGATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
TTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:201972 original size:211 final size:210
Alignment explanation
Indices: 201197--202558 Score: 2424
Period size: 211 Copynumber: 6.5 Consensus size: 210
201187 TGTTTCGAGG
* * * *
201197 CCAATATCCTTCGCTGTGAAGTTGAACTTAGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAG
201262 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
65 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
201327 AAATTGGCTCTGAAATTGA-AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
130 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
201391 TTGCGTTGTCTGGAGT
195 TTGCGTTGTCTGGAGT
* *
201407 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAG
201472 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
65 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
* *
201537 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGAAAACCAGCGGTCCCTTCGTTGTGAAGTTGAAC
130 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
201602 TTGCGTTGTCTGGAGT
195 TTGCGTTGTCTGGAGT
*
201618 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-AAATGTTTGTTGACAACCAGT
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
201682 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
66 GGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
* * *
201747 AATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAAC
131 AATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
201812 TTGCGTTGTCTGGAGT
195 TTGCGTTGTCTGGAGT
201828 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
201893 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
66 GGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
* * *
201958 AATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAAC
131 AATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
202023 TTGCGTTGTCTGGAGT
195 TTGCGTTGTCTGGAGT
*
202039 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGAAAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
202104 GGTCCCTTCGTTGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
66 GGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
202169 AATTGGCTCTGAAATTGA-AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
131 AATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
202233 TGCGTTGTCTGGAGT
196 TGCGTTGTCTGGAGT
* *
202248 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAG
202313 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
65 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
202378 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
130 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
202443 TTGCGTTGTCTGGAGT
195 TTGCGTTGTCTGGAGT
* * * *
202459 CCAATATCCTTCGTGGTGAAGTTGAAATCGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
202524 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 GGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
202559 TGAGCGACCC
Statistics
Matches: 1116, Mismatches: 31, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
209 203 0.18
210 399 0.36
211 514 0.46
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (210 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
GGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
AATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
TGCGTTGTCTGGAGT
Found at i:202188 original size:526 final size:526
Alignment explanation
Indices: 201197--202558 Score: 2593
Period size: 526 Copynumber: 2.6 Consensus size: 526
201187 TGTTTCGAGG
* * * *
201197 CCAATATCCTTCGCTGTGAAGTTGAACTTAGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAG
201262 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
201327 AAATTGGCTCTGAAATTGA-AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
201391 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTT
196 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTT
201456 GTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
261 GTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
201521 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGAAAACCAGCGGTCCCTT
326 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGAAAACCAGCGGTCCCTT
*
201586 CGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
391 CGTTGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
201651 CTGAAATTGAAAATGTTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
456 CTGAAATTGAAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
201716 TGGAGT
521 TGGAGT
201722 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAG
201787 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
201852 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
201917 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTT
196 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTT
201982 GTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
261 GTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
202047 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGAAAACCAGCGGTCCCTT
326 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGAAAACCAGCGGTCCCTT
202112 CGTTGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
391 CGTTGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
202177 CTGAAATTGAAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
456 CTGAAATTGAAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
202242 TGGAGT
521 TGGAGT
202248 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAG
202313 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
202378 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* * * * *
202443 TTGCGTTGTCTGGAGTCCAATATCCTTCGTGGTGAAGTTGAAATCGGCTCTGAAATTGGGAA-AT
196 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTT
* *
202507 GTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
261 GTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
202559 TGAGCGACCC
Statistics
Matches: 823, Mismatches: 13, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
525 196 0.24
526 627 0.76
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (526 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAG
CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTT
GTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGAAAACCAGCGGTCCCTT
CGTTGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
CTGAAATTGAAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGT
Found at i:206319 original size:20 final size:22
Alignment explanation
Indices: 206294--206338 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
206284 AAAATATATT
*
206294 AATATAATA-ATAATAAA-ATA
1 AATATAATAGATAACAAAGATA
206314 AATATAATAGATAACAAAGATA
1 AATATAATAGATAACAAAGATA
206336 AAT
1 AAT
206339 GAAAGTTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
21 7 0.32
22 6 0.27
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (22 bp):
AATATAATAGATAACAAAGATA
Found at i:206368 original size:17 final size:17
Alignment explanation
Indices: 206348--206382 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
206338 TGAAAGTTAG
206348 AAAAAAAAGAAAAATAA
1 AAAAAAAAGAAAAATAA
* *
206365 AAAATAAATAAAAATAA
1 AAAAAAAAGAAAAATAA
206382 A
1 A
206383 TAAATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (17 bp):
AAAAAAAAGAAAAATAA
Found at i:206383 original size:14 final size:14
Alignment explanation
Indices: 206366--206392 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
206356 GAAAAATAAA
206366 AAATAAATAAAAAT
1 AAATAAATAAAAAT
206380 AAATAAATAAAAA
1 AAATAAATAAAAA
206393 GGACCAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:209367 original size:2 final size:2
Alignment explanation
Indices: 209352--209388 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
209342 ATATTGGTAG
209352 TA TA -A TA T- 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
209389 TAGTTTATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:213312 original size:12 final size:12
Alignment explanation
Indices: 213295--213320 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
213285 GTCGGTAGAA
213295 TAAATAATATTT
1 TAAATAATATTT
213307 TAAATAATATTT
1 TAAATAATATTT
213319 TA
1 TA
213321 TTAAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATAATATTT
Found at i:215661 original size:14 final size:15
Alignment explanation
Indices: 215633--215662 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
215623 TCTTGTTAGA
215633 GACTTAAATAAAAGG
1 GACTTAAATAAAAGG
215648 GACTTAAA-AAAAGG
1 GACTTAAATAAAAGG
215662 G
1 G
215663 TTAGCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.07, G:0.23, T:0.17
Consensus pattern (15 bp):
GACTTAAATAAAAGG
Found at i:223935 original size:94 final size:93
Alignment explanation
Indices: 223771--223960 Score: 280
Period size: 94 Copynumber: 2.0 Consensus size: 93
223761 GAGTCGAAGG
223771 TTACCTATGTTCTTCGGGACATATGGACAAGATTACCTATGTCTTTCGGGACATATGGACATTAT
1 TTACCTATGTTCTTCGGGACATATGGACAAGATTACCTATGTCTTTCGGGACATATGGACATTAT
* *
223836 TCTATG-TCTTTTGGGACATATGGACAGTA
66 CCTATGTTC-TTCGGGACATATGGACAG-A
*
223865 TTACCTATGTTCTTCGGGACATATGGACAA-TTTACCTATGT-TCTTCGGGACATATGGACAGTT
1 TTACCTATGTTCTTCGGGACATATGGACAAGATTACCTATGTCT-TTCGGGACATATGGACA-TT
223928 -TACCTATGTTCTTCGGGACATATGGACAGA
64 AT-CCTATGTTCTTCGGGACATATGGACAGA
223958 TTA
1 TTA
223961 TTATACGAGC
Statistics
Matches: 89, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
92 1 0.01
93 32 0.36
94 54 0.61
95 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (93 bp):
TTACCTATGTTCTTCGGGACATATGGACAAGATTACCTATGTCTTTCGGGACATATGGACATTAT
CCTATGTTCTTCGGGACATATGGACAGA
Found at i:223956 original size:31 final size:31
Alignment explanation
Indices: 223771--223956 Score: 263
Period size: 31 Copynumber: 6.0 Consensus size: 31
223761 GAGTCGAAGG
*
223771 TTACCTATGTTCTTCGGGACATATGGACAAGA
1 TTACCTATGTTCTTCGGGACATATGGAC-AGT
223803 TTACCTATG-TCTTTCGGGACATATGGACA--
1 TTACCTATGTTC-TTCGGGACATATGGACAGT
* *
223832 TTATTCTATG-TCTTTTGGGACATATGGACAGT
1 TTA-CCTATGTTC-TTCGGGACATATGGACAGT
*
223864 ATTACCTATGTTCTTCGGGACATATGGACAAT
1 -TTACCTATGTTCTTCGGGACATATGGACAGT
223896 TTACCTATGTTCTTCGGGACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
223927 TTACCTATGTTCTTCGGGACATATGGACAG
1 TTACCTATGTTCTTCGGGACATATGGACAG
223957 ATTATTATAC
Statistics
Matches: 142, Mismatches: 6, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
29 3 0.02
30 24 0.17
31 63 0.44
32 47 0.33
33 5 0.04
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGT
Found at i:224731 original size:19 final size:19
Alignment explanation
Indices: 224686--224732 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
224676 ACACTGTAGC
224686 ATTGTTCATACAATATAGT
1 ATTGTTCATACAATATAGT
* * *
224705 ACTATTCATACCATATAGT
1 ATTGTTCATACAATATAGT
224724 ATTGTTCAT
1 ATTGTTCAT
224733 GAAAACATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (19 bp):
ATTGTTCATACAATATAGT
Done.