Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004857.1 Hibiscus syriacus cultivar Beakdansim tig00010949_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: 110801
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:63 original size:2 final size:2
Alignment explanation
Indices: 56--91 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
46 TTTATTCTTT
*
56 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
92 AGTAATAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:8977 original size:4 final size:4
Alignment explanation
Indices: 8968--9019 Score: 104
Period size: 4 Copynumber: 13.0 Consensus size: 4
8958 ATACTGTCAA
8968 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9016 TATG
1 TATG
9020 CATAACCATC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:18323 original size:3 final size:3
Alignment explanation
Indices: 18315--18407 Score: 134
Period size: 3 Copynumber: 30.7 Consensus size: 3
18305 CTCCGTTAAC
* * *
18315 CTT CTT CTT CTT -TCT CTT CAT CTT CCTA CTT CCT CTT CTT CTT CTT
1 CTT CTT CTT CTT CT-T CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT
18361 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
18408 AAGGAGCTTC
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
2 1 0.01
3 77 0.95
4 3 0.04
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:19273 original size:31 final size:31
Alignment explanation
Indices: 19235--19330 Score: 138
Period size: 31 Copynumber: 3.1 Consensus size: 31
19225 CTTTTTAGGT
*
19235 TTATAAATCGATAATATTAGTGATTAATTTG
1 TTATAAATCGATAATATTAGTGACTAATTTG
* * *
19266 TTATAAATCAATAATGTTAGTGACTAGTTTG
1 TTATAAATCGATAATATTAGTGACTAATTTG
* *
19297 TTATAAATCGATAACATTAGTGACCAATTTG
1 TTATAAATCGATAATATTAGTGACTAATTTG
19328 TTA
1 TTA
19331 CTTTCGAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.42
Consensus pattern (31 bp):
TTATAAATCGATAATATTAGTGACTAATTTG
Found at i:19984 original size:20 final size:22
Alignment explanation
Indices: 19944--20000 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
19934 ATTTTATCAT
19944 AATATTATAAAATTAATTATTA
1 AATATTATAAAATTAATTATTA
19966 AATA-TATAAAATT-ATTATTA
1 AATATTATAAAATTAATTATTA
*
19986 AATGATTATTAAATT
1 AAT-ATTATAAAATT
20001 TATCAAAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 10 0.31
21 10 0.31
22 12 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
AATATTATAAAATTAATTATTA
Found at i:19993 original size:11 final size:10
Alignment explanation
Indices: 19929--20003 Score: 55
Period size: 11 Copynumber: 7.2 Consensus size: 10
19919 TAAAATAATC
*
19929 ATTAAATTTT
1 ATTAAATATT
*
19939 ATCATAATATT
1 ATTA-AATATT
*
19950 ATAAAATTAATT
1 ATTAAA-T-ATT
19962 ATTAAATA-T
1 ATTAAATATT
*
19971 ATAAAATTATT
1 ATTAAA-TATT
19982 ATTAAATGATT
1 ATTAAAT-ATT
19993 ATTAAAT-TT
1 ATTAAATATT
20002 AT
1 AT
20004 CAAAATGTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
9 10 0.19
10 9 0.17
11 26 0.49
12 8 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (10 bp):
ATTAAATATT
Found at i:21707 original size:15 final size:15
Alignment explanation
Indices: 21687--21716 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21677 CAGCATTTGT
21687 AAATTTAATTAAAGC
1 AAATTTAATTAAAGC
21702 AAATTTAATTAAAGC
1 AAATTTAATTAAAGC
21717 TTAGATCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (15 bp):
AAATTTAATTAAAGC
Found at i:22306 original size:14 final size:14
Alignment explanation
Indices: 22287--22313 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22277 TTTTATTGAT
22287 AAAAATTATATTTA
1 AAAAATTATATTTA
22301 AAAAATTATATTT
1 AAAAATTATATTT
22314 CTTATAAATC
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAAATTATATTTA
Found at i:28933 original size:20 final size:20
Alignment explanation
Indices: 28905--28942 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28895 ATAGTATGAC
*
28905 TAATAAAATTTAAAAAATAG
1 TAATAAAATTAAAAAAATAG
*
28925 TAATCAAATTAAAAAAAT
1 TAATAAAATTAAAAAAAT
28943 TCATAGTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
TAATAAAATTAAAAAAATAG
Found at i:31260 original size:45 final size:45
Alignment explanation
Indices: 31135--31267 Score: 216
Period size: 47 Copynumber: 3.0 Consensus size: 45
31125 AGGTGTTTCT
* *
31135 GGGT-TTTCTATATATTATGTTCTAAC-TATCAAAGTTCAGTTCA
1 GGGTGTTTCTTTATATTATGTTCTAACACATCAAAGTTCAGTTCA
31178 GGGTGTTTCTTTATATTATATGTTCTAACACATCAAAGTTCAGTTCA
1 GGGTGTTTCTTTATA-T-TATGTTCTAACACATCAAAGTTCAGTTCA
31225 GGGTGTTTCTTTATATTATGTTCTAACACATCAAAGTTCAGTT
1 GGGTGTTTCTTTATATTATGTTCTAACACATCAAAGTTCAGTT
31268 ACTTGTCTTA
Statistics
Matches: 84, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
43 4 0.05
44 9 0.11
45 28 0.33
46 12 0.14
47 31 0.37
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (45 bp):
GGGTGTTTCTTTATATTATGTTCTAACACATCAAAGTTCAGTTCA
Found at i:41472 original size:6 final size:6
Alignment explanation
Indices: 41461--41530 Score: 54
Period size: 6 Copynumber: 12.0 Consensus size: 6
41451 ATCACCTATA
* * * * * * *
41461 TATATG TATATG --TATG CATTTA TATATG TGTGTG TTTATG TTTATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
*
41507 TATATG TATATG TATATG TTTATG
1 TATATG TATATG TATATG TATATG
41531 CAAATGTATG
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
4 4 0.08
6 47 0.92
ACGTcount: A:0.26, C:0.01, G:0.19, T:0.54
Consensus pattern (6 bp):
TATATG
Found at i:41524 original size:24 final size:24
Alignment explanation
Indices: 41461--41539 Score: 72
Period size: 24 Copynumber: 3.4 Consensus size: 24
41451 ATCACCTATA
***
41461 TATATGTATATGTATGCATTTA--
1 TATATGTATATGTATATGTTTATG
* * *
41483 TATATGTGTGTGTTTATGTTTATG
1 TATATGTATATGTATATGTTTATG
41507 TATATGTATATGTATATGTTTATG
1 TATATGTATATGTATATGTTTATG
* *
41531 CAAATGTAT
1 TATATGTAT
41540 GCATTTATAT
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 16 0.36
24 28 0.64
ACGTcount: A:0.28, C:0.03, G:0.18, T:0.52
Consensus pattern (24 bp):
TATATGTATATGTATATGTTTATG
Found at i:41537 original size:12 final size:12
Alignment explanation
Indices: 41483--41530 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
41473 TATGCATTTA
* *
41483 TATATGTGTGTG
1 TATATGTTTATG
*
41495 TTTATGTTTATG
1 TATATGTTTATG
*
41507 TATATGTATATG
1 TATATGTTTATG
41519 TATATGTTTATG
1 TATATGTTTATG
41531 CAAATGTATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.56
Consensus pattern (12 bp):
TATATGTTTATG
Found at i:52959 original size:130 final size:130
Alignment explanation
Indices: 52813--53060 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
52803 TATTTATATA
* ** *
52813 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTG
* * * *
52878 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACTTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTAGTGACACATGTCACCACCTAATTATTTATATATGCT
52943 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTG
* * *
53008 TTAACACATGATCATGATATATGTTATTAGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTAGTGACACATGTCACCACCTAATTA
53061 GAAGAAAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTAGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:53091 original size:130 final size:129
Alignment explanation
Indices: 52827--53091 Score: 282
Period size: 130 Copynumber: 2.0 Consensus size: 129
52817 ATTTGGTCCT
* ** * *
52827 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTGTTAACACATGATCA
* * * *** * * **** *
52892 TGACACGTGTCATTGGTGACACATGTCACCACTTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTAGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
52957 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTGTTAACACATGATCA
* * * *
53022 TGATATATGTTATTAGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTAGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
53086 -A
128 CA
53087 AAATT
1 AAATT
53092 TGGGTCTTGG
Statistics
Matches: 110, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
130 97 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAAGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTAGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:53420 original size:28 final size:27
Alignment explanation
Indices: 53389--53451 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
53379 AGTTGATACA
*
53389 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
53417 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
53445 ATATTTT
1 ATATTTT
53452 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:53552 original size:16 final size:18
Alignment explanation
Indices: 53531--53564 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
53521 ATTTCTTATT
53531 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
53547 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
53565 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:54088 original size:21 final size:21
Alignment explanation
Indices: 54058--54108 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
54048 CTCAAACTCC
* * *
54058 AAACCCTAAATCATATACTCT
1 AAACCTTAAATCATAAACCCT
* *
54079 AAATCTTAAATCTTAAACCCT
1 AAACCTTAAATCATAAACCCT
54100 AAACCTTAA
1 AAACCTTAA
54109 CTCTAAAAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.29
Consensus pattern (21 bp):
AAACCTTAAATCATAAACCCT
Found at i:57484 original size:30 final size:29
Alignment explanation
Indices: 57450--57509 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
57440 AATTGGTTTT
*
57450 CTGGAATTTGAATTATTAGAAAATGAATTA
1 CTGGAATTTGAATT-CTAGAAAATGAATTA
*
57480 CTGGAATTTGAATTCTGGAAAATGAATTA
1 CTGGAATTTGAATTCTAGAAAATGAATTA
57509 C
1 C
57510 ATTTTTGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (29 bp):
CTGGAATTTGAATTCTAGAAAATGAATTA
Found at i:57505 original size:14 final size:15
Alignment explanation
Indices: 57458--57509 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
57448 TTCTGGAATT
* *
57458 TGAATTATTAGAAAA
1 TGAATTACTGGAAAA
**
57473 TGAATTACTGGAATT
1 TGAATTACTGGAAAA
57488 TGAATT-CTGGAAAA
1 TGAATTACTGGAAAA
57502 TGAATTAC
1 TGAATTAC
57510 ATTTTTGGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAAAA
Found at i:57896 original size:25 final size:24
Alignment explanation
Indices: 57847--57897 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
57837 TTATTAAATA
*
57847 TAAAAAAAATTATTATATATTTAT
1 TAAAAAAAAATATTATATATTTAT
*
57871 TAAAATAAAAATA-TATATCTTATAT
1 TAAAA-AAAAATATTATATATT-TAT
57896 TA
1 TA
57898 TTATAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAAAAAAAATATTATATATTTAT
Found at i:57972 original size:25 final size:25
Alignment explanation
Indices: 57927--57974 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
57917 TTTATTATAA
*
57927 TATTAAAAATATAATATTATATTAT
1 TATTAAAAATATAATAATATATTAT
*
57952 TATTAAATAT-TAATAAATATATT
1 TATTAAAAATATAAT-AATATATT
57975 TTAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TATTAAAAATATAATAATATATTAT
Found at i:57982 original size:53 final size:54
Alignment explanation
Indices: 57861--57983 Score: 125
Period size: 53 Copynumber: 2.3 Consensus size: 54
57851 AAAAATTATT
* *
57861 ATATATTTATTA-AA-A-TAAAAATATATATCTTATATTATTATAATATAATTGA
1 ATATA-TTATTATAATATTAAAAATATATATATTATATTATTATAATATAATTAA
* *
57913 TTATTTTATTATAATATTAAAAATATA-ATATTATATTATTATTAAATATTAA-TAA
1 ATATATTATTATAATATTAAAAATATATATATTATATTATTA-T-AATA-TAATTAA
57968 ATATATT-TTA-AATATT
1 ATATATTATTATAATATT
57984 TTAATAATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
51 6 0.10
52 5 0.08
53 20 0.34
54 14 0.24
55 11 0.19
56 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (54 bp):
ATATATTATTATAATATTAAAAATATATATATTATATTATTATAATATAATTAA
Found at i:57987 original size:23 final size:22
Alignment explanation
Indices: 57923--57999 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 22
57913 TTATTTTATT
** *
57923 ATAATATTAAAAATA-TAATATT
1 ATAATATTTTAAATATTAATA-A
*
57945 ATATTATTATTAAATATTAATAA
1 ATAATATT-TTAAATATTAATAA
57968 AT-ATATTTTAAATATTTTAATAA
1 ATAATATTTTAAATA--TTAATAA
*
57991 TTAATATTT
1 ATAATATTT
58000 CGATGAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
21 7 0.16
22 11 0.25
23 15 0.34
24 11 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATATTTTAAATATTAATAA
Found at i:57989 original size:84 final size:81
Alignment explanation
Indices: 57837--57989 Score: 181
Period size: 84 Copynumber: 1.9 Consensus size: 81
57827 ATATTATTCA
*
57837 TTATTAAATATAAAAAAAATTATTATATATTTATTAAAATAAAAATATATATCTTATATTATTAT
1 TTATTAAATATAAAAAAAATTATTATATATTTATTAAAATAAAAATATATATCTTATAATATTAT
57902 AATATAATTGATTATT
66 AATATAATTGATTATT
57918 TTATTATAATATTAAAAATATAA-TATTATAT-TATTATTAAATATTAATAAATATAT-T-TTA-
1 TTATTA-AATA-TAAAAA-A-AATTATTATATAT-TTATTAAA-A-TAA-AAATATATATCTTAT
*
57978 AATATTTTAATA
58 AATATTATAATA
57990 ATTAATATTT
Statistics
Matches: 62, Mismatches: 2, Indels: 13
0.81 0.03 0.17
Matches are distributed among these distances:
81 6 0.10
82 4 0.06
83 7 0.11
84 27 0.44
85 6 0.10
86 4 0.06
87 8 0.13
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (81 bp):
TTATTAAATATAAAAAAAATTATTATATATTTATTAAAATAAAAATATATATCTTATAATATTAT
AATATAATTGATTATT
Found at i:58229 original size:42 final size:42
Alignment explanation
Indices: 58183--58262 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
58173 ACCAAACACT
*
58183 GGAAAACATTTTTCAG-AAAACGAATTACGTGAAACAAAAACA
1 GGAAAACA-TTTTCAGAAAAACGAATTACATGAAACAAAAACA
*
58225 GGAAAACATTTTCCGAAAAACGAATTACATGAAACAAA
1 GGAAAACATTTTCAGAAAAACGAATTACATGAAACAAA
58263 CACGAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 6 0.17
42 29 0.83
ACGTcount: A:0.53, C:0.15, G:0.14, T:0.19
Consensus pattern (42 bp):
GGAAAACATTTTCAGAAAAACGAATTACATGAAACAAAAACA
Found at i:65422 original size:18 final size:18
Alignment explanation
Indices: 65399--65437 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
65389 TTTTTTTTCC
*
65399 TTTATATGTACATACATA
1 TTTATATATACATACATA
*
65417 TTTATATATATATACATA
1 TTTATATATACATACATA
65435 TTT
1 TTT
65438 TGAAACTACG
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:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTATATATACATACATA
Found at i:65550 original size:39 final size:38
Alignment explanation
Indices: 65503--65647 Score: 122
Period size: 41 Copynumber: 3.8 Consensus size: 38
65493 TAGTTTAAAA
* *
65503 AAAACATTTTAGAAAATATATGTAGTATATA-A-TTTTTT
1 AAAACATTTT-GAAAATATATATA-TATATATAGTTTTTG
65541 AAAATCATTTTGAAAACTTATATATATATATATAGTTTTTG
1 AAAA-CATTTTGAAAA--TATATATATATATATAGTTTTTG
*
65582 AAAACATTTTTG-AAA-ACATATATAT-TATAG-TTTTG
1 AAAACA-TTTTGAAAATATATATATATATATAGTTTTTG
* * * * *
65617 AAAATATTTTAAAAACATTTATATATTTATA
1 AAAACATTTTGAAAATATATATATATATATA
65648 TATTATATGT
Statistics
Matches: 91, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
34 4 0.04
35 13 0.14
36 13 0.14
37 13 0.14
38 9 0.10
39 12 0.13
40 13 0.14
41 14 0.15
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (38 bp):
AAAACATTTTGAAAATATATATATATATATAGTTTTTG
Found at i:65591 original size:12 final size:12
Alignment explanation
Indices: 65576--65600 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
65566 ATATATATAG
65576 TTTTTGAAAACA
1 TTTTTGAAAACA
65588 TTTTTGAAAACA
1 TTTTTGAAAACA
65600 T
1 T
65601 ATATATTATA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:65597 original size:79 final size:76
Alignment explanation
Indices: 65503--65650 Score: 181
Period size: 79 Copynumber: 1.9 Consensus size: 76
65493 TAGTTTAAAA
* * * * *
65503 AAAACATTTTAGAAAATATATGTAGTATATAATTTTTTAAAATCATTTTGAAAAC-TTATATATA
1 AAAACATTTTAGAAAACATATATA-T-TAT-AGTTTTGAAAAT-ATTTTAAAAACATTATATATA
65567 TATATATAGTTTTTG
62 TATATATAGTTTTTG
* *
65582 AAAACATTTTTGAAAACATATATATTATAGTTTTGAAAATATTTTAAAAACATTTATATATTTAT
1 AAAACATTTTAGAAAACATATATATTATAGTTTTGAAAATATTTTAAAAACA-TTATATATATAT
65647 ATAT
65 ATAT
65651 TATATGTTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 10 0.17
76 10 0.17
77 18 0.30
78 1 0.02
79 21 0.35
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (76 bp):
AAAACATTTTAGAAAACATATATATTATAGTTTTGAAAATATTTTAAAAACATTATATATATATA
TATAGTTTTTG
Found at i:65616 original size:35 final size:36
Alignment explanation
Indices: 65448--65642 Score: 130
Period size: 34 Copynumber: 5.2 Consensus size: 36
65438 TGAAACTACG
* * *
65448 TATATAATATATAGTTTTT-AATA-GTTTTTAAAAC-
1 TATAT-ATATATAGTTTTTGAAAACATTTTAAAAACA
*** *
65482 TATATAATATATAGTTTAAAAAAAACATTTTAGAAAATA
1 TATAT-ATATATAGTTT-TTGAAAACATTTTA-AAAACA
* * * *
65521 TATGTAGTATATAATTTTTTAAAATCATTTTGAAAACTTATA
1 TATATA-TATATAGTTTTTGAAAA-CATTTT-AAAA---ACA
*
65563 TATATATATATAGTTTTTGAAAACATTTTTGAAAACA
1 TATATATATATAGTTTTTGAAAACA-TTTTAAAAACA
*
65600 TATATAT-TATAG-TTTTGAAAATATTTTAAAAACA
1 TATATATATATAGTTTTTGAAAACATTTTAAAAACA
*
65634 TTTATATAT
1 TATATATAT
65643 TTATATATTA
Statistics
Matches: 129, Mismatches: 19, Indels: 25
0.75 0.11 0.14
Matches are distributed among these distances:
34 33 0.26
35 11 0.09
36 8 0.06
37 13 0.10
38 9 0.07
39 22 0.17
40 6 0.05
41 19 0.15
42 8 0.06
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
TATATATATATAGTTTTTGAAAACATTTTAAAAACA
Found at i:65685 original size:53 final size:53
Alignment explanation
Indices: 65600--65753 Score: 160
Period size: 52 Copynumber: 3.0 Consensus size: 53
65590 TTTGAAAACA
* * * *
65600 TATATATTATA-G-TTTTGAAAATATTTTAAAAACATTTATATATTTATATA-T
1 TATAT-TTATATGTTTTTGAAAACATGTTGAAAACATTTGTATATTTATATACT
* *
65651 TATATGTTATATGTTTTTGAAAACATGTTGAAAACATTTGTATATTTTTGAAAACT
1 TATAT-TTATATGTTTTTGAAAACATGTTGAAAACATTTGTATATTTAT--ATACT
*
65707 TATA--TA-ATATTTTTGAAAACATGTTGAAAACATTTGTATA-TTATATA
1 TATATTTATATGTTTTTGAAAACATGTTGAAAACATTTGTATATTTATATA
65754 GTTTAAAAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
49 2 0.02
51 13 0.15
52 34 0.39
53 32 0.36
55 2 0.02
56 5 0.06
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.47
Consensus pattern (53 bp):
TATATTTATATGTTTTTGAAAACATGTTGAAAACATTTGTATATTTATATACT
Found at i:65703 original size:20 final size:22
Alignment explanation
Indices: 65678--65728 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
65668 TGAAAACATG
*
65678 TTGAAAACATT-TGT-ATATTT
1 TTGAAAACATTATATAATATTT
65698 TTGAAAAC-TTATATAATATTT
1 TTGAAAACATTATATAATATTT
65719 TTGAAAACAT
1 TTGAAAACAT
65729 GTTGAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 2 0.07
20 10 0.37
21 14 0.52
22 1 0.04
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (22 bp):
TTGAAAACATTATATAATATTT
Found at i:65785 original size:36 final size:34
Alignment explanation
Indices: 65696--65791 Score: 97
Period size: 36 Copynumber: 2.8 Consensus size: 34
65686 ATTTGTATAT
* * *
65696 TTTTGAAAACTTATATA--ATATTTTTGAAAACA
1 TTTTGAAAATTTATATATTATATGTTTAAAAACA
* *
65728 TGTTGAAAACATTTGTATATTATATAGTTTAAAAATCA
1 TTTTG-AAA-ATTTATATATTATAT-GTTTAAAAA-CA
65766 TTTTGAAAATTTATATATTATATGTT
1 TTTTGAAAATTTATATATTATATGTT
65792 ATATGTTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
32 4 0.08
33 3 0.06
34 7 0.14
35 3 0.06
36 18 0.35
37 10 0.20
38 6 0.12
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (34 bp):
TTTTGAAAATTTATATATTATATGTTTAAAAACA
Found at i:65851 original size:20 final size:19
Alignment explanation
Indices: 65828--65881 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
65818 ATATATTATC
65828 TATTATTATTTATTTTAATT
1 TATT-TTATTTATTTTAATT
*
65848 TATTTTAATTTATTTTATTT
1 TATTTT-ATTTATTTTAATT
*
65868 TAATTTATTT-TTTT
1 TATTTTATTTATTTT
65882 GGTCTTTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.13
19 6 0.19
20 21 0.68
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTATTTATTTTAATT
Found at i:65875 original size:15 final size:15
Alignment explanation
Indices: 65836--65878 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
65826 TCTATTATTA
* *
65836 TTTATTTTAATTTAT
1 TTTAATTTATTTTAT
65851 TTTAATTTATTTTAT
1 TTTAATTTATTTTAT
65866 TTTAATTTATTTT
1 TTTAATTTATTTT
65879 TTTGGTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTAATTTATTTTAT
Found at i:65878 original size:10 final size:10
Alignment explanation
Indices: 65835--65874 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
65825 ATCTATTATT
65835 ATTTATTTTA
1 ATTTATTTTA
65845 ATTTATTTTA
1 ATTTATTTTA
65855 ATTTATTTTA
1 ATTTATTTTA
* *
65865 TTTTAATTTA
1 ATTTATTTTA
65875 TTTTTTTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTTATTTTA
Found at i:67388 original size:6 final size:6
Alignment explanation
Indices: 67354--67380 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
67344 GAATCGAATT
67354 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
67381 TTAATTTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:67971 original size:17 final size:17
Alignment explanation
Indices: 67949--67993 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
67939 TACATAATGT
67949 GAAATTTGAGCGTGAAA
1 GAAATTTGAGCGTGAAA
*
67966 GAAATTTGATCGTGAAA
1 GAAATTTGAGCGTGAAA
*
67983 GAATTTTGAGC
1 GAAATTTGAGC
67994 AAGTTTCACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.29
Consensus pattern (17 bp):
GAAATTTGAGCGTGAAA
Found at i:76395 original size:2 final size:2
Alignment explanation
Indices: 76388--76416 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
76378 AGAAATTGTT
76388 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 T
76417 GTTTATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:77681 original size:228 final size:222
Alignment explanation
Indices: 77285--77727 Score: 737
Period size: 228 Copynumber: 2.0 Consensus size: 222
77275 GTAAATTATC
* *
77285 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTAGTT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATCTTAGTT
*
77350 AATATTGTTAAATTTAAAATCTAAATAATATTTTATAATATCAAACAATCAATAATTTTTTGTGT
66 AATATTGTTAAATTTAAAATCTAAATAATATTTTATAATATCAAACAATCAATAATATTTTGTGT
77415 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA-AAATTGAAACA
131 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTGAAACA
77479 TAAATTACATAACTTTCAAAAAAGTATA
196 TAAATTACATAACTTT-AAAAAAGTATA
* *
77507 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTAT-CTTAG
*
77572 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA-ATATAAT
64 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTAT--AATATC-AAACAATCAATA-AT-AT
*
77636 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
124 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
77701 TGAAACATAAATTACATAACTTTAAAA
189 TGAAACATAAATTACATAACTTTAAAA
77728 GCAGTTTTAA
Statistics
Matches: 206, Mismatches: 7, Indels: 10
0.92 0.03 0.04
Matches are distributed among these distances:
222 36 0.17
223 20 0.10
224 40 0.19
226 7 0.03
227 12 0.06
228 64 0.31
229 27 0.13
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (222 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATCTTAGTT
AATATTGTTAAATTTAAAATCTAAATAATATTTTATAATATCAAACAATCAATAATATTTTGTGT
AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTGAAACA
TAAATTACATAACTTTAAAAAAGTATA
Found at i:77816 original size:20 final size:19
Alignment explanation
Indices: 77793--77838 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
77783 CGATATACCA
77793 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
77813 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
77833 GGTAAA
1 GGTAAA
77839 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:78005 original size:17 final size:18
Alignment explanation
Indices: 77969--78008 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
77959 GTAAAATTAT
77969 ATAAAACCGGTAACAAAATG
1 ATAAAACCGGT-A-AAAATG
77989 ATAAAACCGGT-AAAATG
1 ATAAAACCGGTAAAAATG
78006 ATA
1 ATA
78009 CCGGATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
20 11 0.55
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.17
Consensus pattern (18 bp):
ATAAAACCGGTAAAAATG
Found at i:80358 original size:32 final size:33
Alignment explanation
Indices: 80317--80381 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
80307 AAATAGATGG
*
80317 AGTGGTGAAAGAAG-TAGAGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTAGAGTGTTAAGGGGTGA
* *
80349 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTTAGAGTGTTAAGGGGTGA
80382 TATTAAGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTAGAGTGTTAAGGGGTGA
Found at i:82174 original size:18 final size:18
Alignment explanation
Indices: 82154--82192 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
82144 GTCGAGTTAA
82154 TTTGTATAAGATTTATAAT
1 TTTG-ATAAGATTTATAAT
*
82173 TTTGATACGATTTAT-AT
1 TTTGATAAGATTTATAAT
82190 TTT
1 TTT
82193 TATGTGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (18 bp):
TTTGATAAGATTTATAAT
Found at i:82680 original size:194 final size:197
Alignment explanation
Indices: 82312--83264 Score: 1704
Period size: 194 Copynumber: 4.9 Consensus size: 197
82302 CAATATGGCC
* *
82312 AACAGGGTGCACCCATAAAGTGTCGATCC-TATATAAAAAAGTGTCAATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
82376 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATGAGA
65 CC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
82440 GAATATGTCTAAATAATGTGTCG--AC-AATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
129 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
82502 TGGA
194 TGGA
*
82506 AACAAGGTGCACCCCTAAAGTGTCGATCC-TATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
82570 CAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGA
66 CAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
82634 ATATGTCT-AATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
131 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
82698 GA
196 GA
82700 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
82765 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 C-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
82830 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATG-AT
130 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
82894 GGA
195 GGA
82897 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
82962 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAGTATAATGTAATATGTAATTTTTCAATCTAA-CCGGTACAATTATACCGGTTTTATGAGAG
*
83027 AAT-TGTCTAAATAATGTGTCG-CACT-ATATAG-TTGTGTCGATACTTTTTTCCCATAATGAAT
130 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
83088 GGA
195 GGA
*
83091 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCCAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
83156 CAAAGTATAATGTAATA-GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
66 CAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
83220 ATATGTCTAAATAA--TGTCGACACTAATATAGTTTGTGTCGATACT
131 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
83265 AATTTAAATA
Statistics
Matches: 737, Mismatches: 8, Indels: 28
0.95 0.01 0.04
Matches are distributed among these distances:
191 17 0.02
192 91 0.12
193 107 0.15
194 205 0.28
195 40 0.05
196 104 0.14
197 121 0.16
198 52 0.07
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (197 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
GA
Found at i:83140 original size:391 final size:392
Alignment explanation
Indices: 82312--83264 Score: 1709
Period size: 391 Copynumber: 2.5 Consensus size: 392
82302 CAATATGGCC
* *
82312 AACAGGGTGCACCCATAAAGTGTCGATCC-TATATAAAAAAGTGTCAATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
82376 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
82440 GAATATGTCTAAATAATGTGTCG--AC-AATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
*
82502 TGGAAACAAGGTGCACCCCTAAAGTGTCGATCCTATATAAAAAGTGTCGATCCCAAAATCATCGA
195 TGGAAACAAGGTGCACCCATAAAGTGTCGATCCTATATAAAAAGTGTCGATCCCAAAATCATCGA
*
82567 ACCCAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGA
260 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGA
82632 GAATATGTCTAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
325 GAATATGTCTAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
82697 GGA
390 GGA
82700 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
82765 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
82830 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATG-AT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
82894 GGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
196 GGAAACAAGGTGCACCCATAAAGTGTCGATCC-TATATAAAAAGTGTCGATCCCAAAATCATCGA
82959 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCCGGTACAATTATACCGGTTTTATGA
260 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA-CCGGTACAATTATACCGG-TTTATGA
*
83024 GAGAAT-TGTCTAAATAATGTGTCG-CACT-ATATAG-TTGTGTCGATACTTTTTTCCCATAATG
323 GAGAATATGTCT-AATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATG
83085 AATGGA
387 AATGGA
*
83091 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCCAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
83156 C-AAAGTATAATGTAATA-GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
83219 AATATGTCTAAATAA--TGTCGACACTAATATAGTTTGTGTCGATACT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
83265 AATTTAAATA
Statistics
Matches: 550, Mismatches: 6, Indels: 19
0.96 0.01 0.03
Matches are distributed among these distances:
387 31 0.06
388 95 0.17
389 114 0.21
390 16 0.03
391 132 0.24
392 110 0.20
393 27 0.05
394 25 0.05
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (392 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGAAACAAGGTGCACCCATAAAGTGTCGATCCTATATAAAAAGTGTCGATCCCAAAATCATCGAA
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGAG
AATATGTCTAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
GA
Found at i:84683 original size:3 final size:3
Alignment explanation
Indices: 84675--84764 Score: 99
Period size: 3 Copynumber: 30.0 Consensus size: 3
84665 TCTTTTAACA
* * * ** * *
84675 GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
84723 GAT GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
84765 CCAAACAAGT
Statistics
Matches: 70, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.34, C:0.06, G:0.34, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:86468 original size:182 final size:183
Alignment explanation
Indices: 85840--86527 Score: 1192
Period size: 183 Copynumber: 3.8 Consensus size: 183
85830 CAAAGTTTTC
* * *
85840 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAAT-GAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* *
85904 AAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
66 AAAAAAGTGTCGACATT---TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
* *
85967 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
86023 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAG-AAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
86087 AAAAAAGTGTCGACATTTACACATCGGAACCCATATTTATAATGTAATAGATAATTTTGTAATA-
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
86151 AACCGGTAT-AAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
*
86203 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
86268 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
86333 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
* *
86386 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAG-AAAATGTGTCGATATCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
86450 AAAAAAGTGTCGACATTTACACATCGGAACCCAAATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
86515 AACCGGTATAAAA
131 AACCGGTATAAAA
86528 TGTGTCGATA
Statistics
Matches: 487, Mismatches: 12, Indels: 13
0.95 0.02 0.03
Matches are distributed among these distances:
180 84 0.17
181 92 0.19
182 149 0.31
183 155 0.32
184 4 0.01
185 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (183 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
Found at i:86505 original size:363 final size:362
Alignment explanation
Indices: 85840--86528 Score: 1220
Period size: 363 Copynumber: 1.9 Consensus size: 362
85830 CAAAGTTTTC
* *
85840 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGAAGAAAAATGTGTCGATACCATTTA
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGAATGAAGAAAAATGTGTCGATACCATTTA
85905 AAAAAGTGTCGATTGAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAGTGTCGATT--AAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
*
85970 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAAT
129 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAAT
86035 ATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAATGTGTCGATACCATTTAAAAAAGTGTCGA
194 ATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAATGTGTCGATACCATTTAAAAAAGTGTCGA
*
86100 CATTTACACATCGGAACCCATATTTATAATGTAATAGATAATTTTGTAATA-AACCGGTATAAAA
259 CATTTACACATCGGAACCCAAATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAAA
86164 TACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
324 TACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
* *
86203 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGAAT-GAAGAAAAATGTGTCGATACCATTT
* *
86268 AAAAAAGTGTCGACATT-TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATA
65 AAAAAAGTGTCG--ATTAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATA
*
86332 TAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCGACACTTTCTAA
128 TAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAA
* *
86397 TATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAATGTGTCGATATCATTTAAAAAAGTGTCG
193 TATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAATGTGTCGATACCATTTAAAAAAGTGTCG
86462 ACATTTACACATCGGAACCCAAATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAA
258 ACATTTACACATCGGAACCCAAATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAA
86527 AT
323 AT
86529 GTGTCGATAC
Statistics
Matches: 311, Mismatches: 11, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
363 257 0.83
364 51 0.16
366 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (362 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGAATGAAGAAAAATGTGTCGATACCATTTA
AAAAAGTGTCGATTAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAA
CCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATAT
TGTGTCGGTACTTTATGTCCAGATTGGAAGAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
TTTACACATCGGAACCCAAATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAAATA
CCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
Found at i:86566 original size:23 final size:23
Alignment explanation
Indices: 86521--86566 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
86511 ATATAACCGG
86521 TATAAAATGTGTCGATACCTTTT
1 TATAAAATGTGTCGATACCTTTT
*
86544 TATAAAA-GTGTCGATACTTTTT
1 TATAAAATGTGTCGATACCTTTT
86566 T
1 T
86567 CACTGTGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (23 bp):
TATAAAATGTGTCGATACCTTTT
Found at i:89701 original size:23 final size:23
Alignment explanation
Indices: 89670--89732 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
89660 ATAGGTAAAC
*
89670 ATATGATGTAATAGGTACCCCTT
1 ATATAATGTAATAGGTACCCCTT
* **
89693 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTACCCCTT
89716 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
89733 GTGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTACCCCTT
Found at i:89740 original size:23 final size:23
Alignment explanation
Indices: 89670--89742 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
89660 ATAGGTAAAC
* * **
89670 ATATGATGTAATAGGTACCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
89693 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
89716 ATATAATGTAATAGGTAGT-GGTT
1 ATATAATGTAATAGGTA-TCGGTT
89739 ATAT
1 ATAT
89743 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 43 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:89770 original size:20 final size:20
Alignment explanation
Indices: 89745--89783 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
89735 GGTTATATTG
* *
89745 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
89765 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
89784 TCACTGTGGA
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:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:89950 original size:28 final size:28
Alignment explanation
Indices: 89887--89951 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
89877 GTTACGATAT
*
89887 ATATTATTATAAATTAAAAATTCTAAATA
1 ATATT-TTATAAATTAAAAAATCTAAATA
89916 ATATTTTATAAATATAAAAACATC-AAATA
1 ATATTTTATAAAT-TAAAAA-ATCTAAATA
*
89945 ATTTTTT
1 ATATTTT
89952 GTGCAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 8 0.25
29 22 0.69
30 2 0.06
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (28 bp):
ATATTTTATAAATTAAAAAATCTAAATA
Found at i:90126 original size:23 final size:23
Alignment explanation
Indices: 90095--90158 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
90085 ATAGGTAAAC
*
90095 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
90118 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
90141 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
90159 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:90165 original size:23 final size:23
Alignment explanation
Indices: 90095--90167 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
90085 ATAGGTAAAC
* **
90095 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
90118 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
90141 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
90164 ATAT
1 ATAT
90168 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:90195 original size:20 final size:20
Alignment explanation
Indices: 90170--90208 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
90160 GGTTATATTG
* *
90170 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
90190 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
90209 TCACTGTGGA
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:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:90556 original size:22 final size:23
Alignment explanation
Indices: 90523--90585 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
90513 ATAGGTAAAC
*
90523 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
90546 ATAT-ATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
*
90568 ATATAATGTAATATGTAG
1 ATATAATGTAATAGGTAG
90586 TGGTTATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 19 0.56
23 15 0.44
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:90592 original size:23 final size:22
Alignment explanation
Indices: 90523--90599 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 22
90513 ATAGGTAAAC
* **
90523 ATATGATGTAATAGGTAGCCCTT
1 ATAT-ATGTAATAGGTATCGGTT
*
90546 ATATATGTAATAGGTATCGTTT
1 ATATATGTAATAGGTATCGGTT
*
90568 ATATAATGTAATATGTAGT-GGTT
1 ATAT-ATGTAATAGGTA-TCGGTT
90591 ATAT-TGTAA
1 ATATATGTAA
90600 AGTGTCTATC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
21 5 0.11
22 19 0.40
23 22 0.47
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (22 bp):
ATATATGTAATAGGTATCGGTT
Found at i:90856 original size:426 final size:430
Alignment explanation
Indices: 89571--91258 Score: 3141
Period size: 426 Copynumber: 3.9 Consensus size: 430
89561 AATTCGCAGT
89571 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
*
89636 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTACCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
89701 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
*
89766 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCCTTTGAGTGAGTTTTA
196 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
*
89831 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTCTTACGTTACGATATATATTATTA
261 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
89896 -TAAATTAAAAATTCTAAATAATATTTTAT-AAATATAAAAAC-ATCAAATAATTTTTTGTGCAA
326 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAA
89958 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
*
89998 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCATTTTTAT-
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
90061 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
90126 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
90191 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
196 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
*
90256 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTA
261 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
90321 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAA
326 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAA
*
90386 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATAAA
391 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
90426 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
90490 AAAAGTATGGACACTTTC-ATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATAT-ATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
*
90553 TAATAGGTATCGTTTATATAATGTAATATGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
*
90618 AAAAGTGTTCATAC-TTTTTCACTGTGGAAAACATTAATTTAAGGTTATC-TTTGAGTGAGTTTT
196 -AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
*
90681 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
260 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATT
90746 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
325 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
90811 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
390 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
90852 ACACTGTTAAAAAAATTGAAACATAAATTACAT-AGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
*
90916 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAACCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
90981 TAATAGGTATCG-TTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
91045 AAAAGTGTCCATACTTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTT
196 -AAAGTGTCCATAC-TTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTT
*
91110 TAAGATATTAATTTAGTAATTATAGGCGTATAATGA-TTATTTTTTACGTTACGATATATATTAT
259 TAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTAT
* *
91174 TATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGC
324 TATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGC
91239 AAATGAAATTATTAAATCAA
389 AAATGAAATTATTAAATCAA
91259 ATAATTCAAA
Statistics
Matches: 1233, Mismatches: 17, Indels: 20
0.97 0.01 0.02
Matches are distributed among these distances:
425 256 0.21
426 324 0.26
427 251 0.20
428 191 0.15
429 163 0.13
430 48 0.04
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (430 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
TTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAA
ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:90981 original size:23 final size:23
Alignment explanation
Indices: 90950--91011 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
90940 ATAGGTAAAC
*
90950 ATATGATGTAATAGGTAACCCTT
1 ATATAATGTAATAGGTAACCCTT
* *
90973 ATATAATGTAATAGGT-ATCGTT
1 ATATAATGTAATAGGTAACCCTT
90995 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
91012 GTGGTTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAACCCTT
Found at i:90999 original size:22 final size:22
Alignment explanation
Indices: 90950--91021 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
90940 ATAGGTAAAC
* * *
90950 ATATGATGTAATAGGTAACCCTT
1 ATATAATGTAATAGGT-ATCGTT
90973 ATATAATGTAATAGGTATCGTT
1 ATATAATGTAATAGGTATCGTT
*
90995 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTA-TCGTT
91018 ATAT
1 ATAT
91022 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 21 0.48
23 23 0.52
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (22 bp):
ATATAATGTAATAGGTATCGTT
Found at i:91324 original size:25 final size:25
Alignment explanation
Indices: 91290--91340 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
91280 ACAACAAATC
*
91290 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
91315 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
91340 A
1 A
91341 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:91609 original size:18 final size:18
Alignment explanation
Indices: 91588--91624 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
91578 GTAATTGGAG
91588 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
91606 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
91624 T
1 T
91625 ATATTTCGGC
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:91956 original size:39 final size:39
Alignment explanation
Indices: 91880--92003 Score: 216
Period size: 38 Copynumber: 3.2 Consensus size: 39
91870 TCCGATGCTC
*
91880 ATCAAAATCCAAAGCTCATATG-TGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
*
91918 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGG-A
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
91956 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
91995 ATCAAAATC
1 ATCAAAATC
92004 TACAACTTGA
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
38 57 0.70
39 24 0.30
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.19
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
Found at i:92438 original size:23 final size:23
Alignment explanation
Indices: 92407--92470 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
92397 ATAGGTAAAC
*
92407 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
92430 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
92453 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
92471 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:92477 original size:23 final size:23
Alignment explanation
Indices: 92407--92479 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
92397 ATAGGTAAAC
* **
92407 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
92430 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
92453 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
92476 ATAT
1 ATAT
92480 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:94388 original size:14 final size:14
Alignment explanation
Indices: 94369--94396 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
94359 ATCATAACAA
94369 AATTATATAACTAT
1 AATTATATAACTAT
94383 AATTATATAACTAT
1 AATTATATAACTAT
94397 TATTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:97491 original size:18 final size:19
Alignment explanation
Indices: 97462--97497 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
97452 ATTAATGTTG
97462 ATGATAAATCAATTATCTA
1 ATGATAAATCAATTATCTA
97481 ATGAT-AATCAATTATCT
1 ATGATAAATCAATTATCT
97498 GTTCACTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (19 bp):
ATGATAAATCAATTATCTA
Done.