Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006332.1 Hibiscus syriacus cultivar Beakdansim tig00015137_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: 82543
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1929 original size:98 final size:99
Alignment explanation
Indices: 1662--1960 Score: 458
Period size: 98 Copynumber: 3.0 Consensus size: 99
1652 ACTTCAACTC
* * *
1662 TTTTTTTAAGCATACTTTAAGGGGAGTTAGCTCGTCACATTATCATCCCACACTCTAAGTGAAAG
1 TTTTTTT-AGCATACTTTAAGGGG-GTCAGCTCATCACACTATCATCCCACACTCTAAGTGAAAG
*
1727 GGAGCATACCTTCCACCCCCGAGCTAGTCAGGTAGAG
64 GGAGCATACCTTCCA-CCCCGAGCTAGTCAGGTAGAA
* *
1764 TTTTTTTAGCATACTTTAATGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTG-AAGG
1 TTTTTTTAGCATACTTTAA-GGGGGTCAGCTCATCACACTATCATCCCACACTCTAAGTGAAAGG
*
1828 GAGCATACCTTCCA-CCCGAGCTAGTCATGTAGAA
65 GAGCATACCTTCCACCCCGAGCTAGTCAGGTAGAA
* *
1862 TTTTTTTAGCATACTTTAAGGGGGTCAACTCATCACACTATCATCCCACACTCTAAGTGAAAAGG
1 TTTTTTTAGCATACTTTAAGGGGGTCAGCTCATCACACTATCATCCCACACTCTAAGTGAAAGGG
1927 AGCATACCTTCCACCCCCGAGCTAGTCAGGTAGA
66 AGCATACCTTCCA-CCCCGAGCTAGTCAGGTAGA
1961 GTCATCTTGT
Statistics
Matches: 181, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
97 37 0.20
98 54 0.30
100 36 0.20
101 44 0.24
102 10 0.06
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.27
Consensus pattern (99 bp):
TTTTTTTAGCATACTTTAAGGGGGTCAGCTCATCACACTATCATCCCACACTCTAAGTGAAAGGG
AGCATACCTTCCACCCCGAGCTAGTCAGGTAGAA
Found at i:2397 original size:25 final size:25
Alignment explanation
Indices: 2366--2418 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
2356 CCATGACAAC
*
2366 AAATATTTCAACCAATTTTTATCAA
1 AAATATTTCAACCAATTATTATCAA
*
2391 AAATATTTCAACCTATTATTATCAA
1 AAATATTTCAACCAATTATTATCAA
2416 AAA
1 AAA
2419 AAAGAACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATATTTCAACCAATTATTATCAA
Found at i:7971 original size:15 final size:15
Alignment explanation
Indices: 7951--7979 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7941 GACGAGGAAC
7951 TGCTAGTACCTCCAT
1 TGCTAGTACCTCCAT
7966 TGCTAGTACCTCCA
1 TGCTAGTACCTCCA
7980 CTGCAACACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.31
Consensus pattern (15 bp):
TGCTAGTACCTCCAT
Found at i:16117 original size:21 final size:21
Alignment explanation
Indices: 16092--16152 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
16082 AACTTTGGAA
16092 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
16113 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
16127 AAATGGTTTTCAAAGTTTGAT
1 AAATGGTTTTCAAAGTTTGGT
16148 AAATG
1 AAATG
16153 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:16198 original size:36 final size:36
Alignment explanation
Indices: 16084--16203 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
16074 TGGCAACCAA
16084 CTTTGGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTT-GAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
16121 CTTTG-AAAATGGTTTTCAAAGTTTGATAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
16156 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
*
16193 -GTTGAAAAATG
1 CTTTGAAAAATG
16204 ATAATGGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 34 0.44
36 18 0.23
37 25 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:19221 original size:23 final size:23
Alignment explanation
Indices: 19195--19269 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
19185 CACCACAGCT
19195 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
** * *
19218 CATATAATTGCGTCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
19241 CGTAGAATTGCACCGTAGTG-CA
1 CATATAATTGCACCGAAGTGCCA
19263 -ATATAAT
1 CATATAAT
19270 AATTTCCATA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
21 5 0.12
22 1 0.03
23 34 0.85
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:19458 original size:103 final size:103
Alignment explanation
Indices: 19279--19496 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
19269 TAATTTCCAT
* *
19279 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
19344 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
*
19382 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
19447 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
19485 AAGGACCACATA
1 AAGGACCACATA
19497 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:25085 original size:23 final size:23
Alignment explanation
Indices: 25059--25133 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
25049 CACCACAGCT
25059 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
** * *
25082 CATATAATTGCGTCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
25105 CGTAGAATTGCACCGTAGTG-CA
1 CATATAATTGCACCGAAGTGCCA
25127 -ATATAAT
1 CATATAAT
25134 AATGTCCATA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
21 5 0.12
22 1 0.03
23 34 0.85
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:25314 original size:103 final size:103
Alignment explanation
Indices: 25143--25360 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
25133 TAATGTCCAT
* *
25143 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
25208 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
*
25246 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
25311 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
25349 AAGGACCACATA
1 AAGGACCACATA
25361 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:26848 original size:2 final size:2
Alignment explanation
Indices: 26841--26865 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26831 GTGTAAATAA
26841 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
26866 CCCATTATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29455 original size:36 final size:37
Alignment explanation
Indices: 29404--29488 Score: 129
Period size: 37 Copynumber: 2.3 Consensus size: 37
29394 TGGCAACCAA
29404 CTTTGAAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
*
29441 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
*
29478 -GTTGAAAAATG
1 CTTTGAAAAATG
29489 ATAATAGGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 18 0.40
37 27 0.60
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (37 bp):
CTTTGAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:32766 original size:22 final size:22
Alignment explanation
Indices: 32741--32782 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
32731 AATTAGTATA
*
32741 TATTTTAAGTTTATTATTTATT
1 TATTTTAAATTTATTATTTATT
32763 TATTTTAAATTTATTATTTA
1 TATTTTAAATTTATTATTTA
32783 ATGATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTTTAAATTTATTATTTATT
Found at i:32938 original size:19 final size:18
Alignment explanation
Indices: 32914--32952 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
32904 CTGATTGCTC
*
32914 AAATTAATTATTCAATTAA
1 AAATTAATTAAT-AATTAA
32933 AAATTAATTAATAATTAA
1 AAATTAATTAATAATTAA
32951 AA
1 AA
32953 TATTCTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATTAATTAATAATTAA
Found at i:34635 original size:14 final size:13
Alignment explanation
Indices: 34618--34690 Score: 69
Period size: 14 Copynumber: 5.4 Consensus size: 13
34608 TTAATAGAAT
34618 TAATTTAATGATTA
1 TAATTTAA-GATTA
34632 TAA-TTAAGATTTA
1 TAATTTAAGA-TTA
*
34645 TAATATAAGGATTA
1 TAATTTAA-GATTA
34659 TAA-TTAAGATTTA
1 TAATTTAAGA-TTA
*
34672 TAATATAAGGATTA
1 TAATTTAA-GATTA
34686 TAATT
1 TAATT
34691 AATATAGAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
12 4 0.08
13 19 0.39
14 22 0.45
15 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.44
Consensus pattern (13 bp):
TAATTTAAGATTA
Found at i:34638 original size:13 final size:12
Alignment explanation
Indices: 34622--34692 Score: 79
Period size: 13 Copynumber: 5.3 Consensus size: 12
34612 TAGAATTAAT
34622 TTAATGATTATAA
1 TTAA-GATTATAA
34635 TTAAGATTTATAA
1 TTAAGA-TTATAA
34648 TATAAGGATTATAA
1 T-TAA-GATTATAA
34662 TTAAGATTTATAA
1 TTAAGA-TTATAA
34675 TATAAGGATTATAA
1 T-TAA-GATTATAA
34689 TTAA
1 TTAA
34693 TATAGAAAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.08
13 24 0.46
14 20 0.38
15 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (12 bp):
TTAAGATTATAA
Found at i:34648 original size:27 final size:27
Alignment explanation
Indices: 34618--34692 Score: 132
Period size: 27 Copynumber: 2.8 Consensus size: 27
34608 TTAATAGAAT
* *
34618 TAATTTAATGATTATAATTAAGATTTA
1 TAATATAAGGATTATAATTAAGATTTA
34645 TAATATAAGGATTATAATTAAGATTTA
1 TAATATAAGGATTATAATTAAGATTTA
34672 TAATATAAGGATTATAATTAA
1 TAATATAAGGATTATAATTAA
34693 TATAGAAAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (27 bp):
TAATATAAGGATTATAATTAAGATTTA
Found at i:34919 original size:101 final size:102
Alignment explanation
Indices: 34742--34942 Score: 314
Period size: 101 Copynumber: 2.0 Consensus size: 102
34732 AGATTTGTTT
*
34742 TAAATTTTAAAAAGTAATCATATTAGTTTAATTATCATAGTTTATTATAAATCCAAAATCTCACA
1 TAAATTTTAAAAAGTAATCATATTA-TTTAATTATCATAGTTTATCATAAATCCAAAATCTCACA
* * *
34807 ACTTCATCAATTGTAATTTATAAGTCAGGTAAATAAAA
65 ACTTCATCAATTGTAACTTATAAGCCAAGTAAATAAAA
* * *
34845 TAAATTTTAAAAATTAATCATATT-TTTAATTATCATAGTTTATCATAAATTCAAAATCTCATAA
1 TAAATTTTAAAAAGTAATCATATTATTTAATTATCATAGTTTATCATAAATCCAAAATCTCACAA
*
34909 CTTTATCAATTGTAACTTATAAGCCAAGTAAATA
66 CTTCATCAATTGTAACTTATAAGCCAAGTAAATA
34943 TCATATTAGT
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 67 0.74
103 23 0.26
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.39
Consensus pattern (102 bp):
TAAATTTTAAAAAGTAATCATATTATTTAATTATCATAGTTTATCATAAATCCAAAATCTCACAA
CTTCATCAATTGTAACTTATAAGCCAAGTAAATAAAA
Found at i:35165 original size:22 final size:22
Alignment explanation
Indices: 35126--35168 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35116 GTTCAATTGA
*
35126 GGTTCAAGTCGTTCTCAAATCG
1 GGTTCAAGTCGGTCTCAAATCG
35148 GGTTCAAGTCGGGT-TCAAATC
1 GGTTCAAGTC-GGTCTCAAATC
35169 CACAATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (22 bp):
GGTTCAAGTCGGTCTCAAATCG
Found at i:37806 original size:20 final size:16
Alignment explanation
Indices: 37757--37796 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
37747 AAAGTAAGGA
37757 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
37773 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
37789 AACCAGAG
1 AACCAGAG
37797 TCTAAAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.30, G:0.15, T:0.05
Consensus pattern (16 bp):
AACCAGAGAAATCCAC
Found at i:41350 original size:21 final size:20
Alignment explanation
Indices: 41326--41480 Score: 177
Period size: 21 Copynumber: 7.5 Consensus size: 20
41316 TCGTACCAAG
*
41326 GACGAGAAGAGCATTCATCAA
1 GACGAGAAG-CCATTCATCAA
*
41347 GACGAGAATGTCATTCATCAA
1 GACGAGAA-GCCATTCATCAA
*
41368 GATGAGAATGCCATTCATCAA
1 GACGAGAA-GCCATTCATCAA
41389 GACGAGAAGGCCATTCATCAA
1 GACGAGAA-GCCATTCATCAA
41410 GACGAGAATGCCATTCATCAA
1 GACGAGAA-GCCATTCATCAA
* *
41431 GACGAGAAGACCCTTCATAAA
1 GACGAGAAG-CCATTCATCAA
* *
41452 GACGAGAAGACC-TTCGTAAA
1 GACGAGAAG-CCATTCATCAA
41472 GACGAGAAG
1 GACGAGAAG
41481 ACCACATCGC
Statistics
Matches: 123, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
20 17 0.14
21 105 0.85
22 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.17
Consensus pattern (20 bp):
GACGAGAAGCCATTCATCAA
Found at i:41406 original size:63 final size:63
Alignment explanation
Indices: 41326--41479 Score: 206
Period size: 63 Copynumber: 2.5 Consensus size: 63
41316 TCGTACCAAG
* * *
41326 GACGAGAAGAG-CATTCATCAAGACGAGAATGTCATTCATCAAGATGAGAATG-CCATTCATCAA
1 GACGAGAAG-GCCATTCATCAAGACGAGAATGCCATTCATCAAGACGAGAA-GACCATTCATAAA
*
41389 GACGAGAAGGCCATTCATCAAGACGAGAATGCCATTCATCAAGACGAGAAGACCCTTCATAAA
1 GACGAGAAGGCCATTCATCAAGACGAGAATGCCATTCATCAAGACGAGAAGACCATTCATAAA
* * *
41452 GACGAGAAGACC-TTCGTAAAGACGAGAA
1 GACGAGAAGGCCATTCATCAAGACGAGAA
41480 GACCACATCG
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
62 16 0.20
63 66 0.80
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.17
Consensus pattern (63 bp):
GACGAGAAGGCCATTCATCAAGACGAGAATGCCATTCATCAAGACGAGAAGACCATTCATAAA
Found at i:45394 original size:2 final size:2
Alignment explanation
Indices: 45387--45474 Score: 167
Period size: 2 Copynumber: 44.0 Consensus size: 2
45377 AGATTCTTCC
*
45387 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45471 AT AT
1 AT AT
45475 CTTCACTTCC
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47905 original size:8 final size:8
Alignment explanation
Indices: 47890--47972 Score: 107
Period size: 8 Copynumber: 10.1 Consensus size: 8
47880 TTGCTTGAAG
47890 ATGAAAAA
1 ATGAAAAA
*
47898 AAGAAAAAA
1 ATG-AAAAA
47907 ATG-AAAA
1 ATGAAAAA
47914 ATG-AAAA
1 ATGAAAAA
47921 ATGAAAAAAA
1 ATG--AAAAA
47931 ATGAAAAA
1 ATGAAAAA
47939 ATGAAGAAA
1 ATGAA-AAA
47948 ATGAAAAA
1 ATGAAAAA
47956 ATGAAAAA
1 ATGAAAAA
47964 ATGAAAAA
1 ATGAAAAA
47972 A
1 A
47973 ATAAAACAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
7 14 0.21
8 32 0.47
9 15 0.22
10 7 0.10
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (8 bp):
ATGAAAAA
Found at i:47973 original size:25 final size:26
Alignment explanation
Indices: 47890--47978 Score: 118
Period size: 25 Copynumber: 3.6 Consensus size: 26
47880 TTGCTTGAAG
47890 ATGAAAAAAA-GAAAAAAATG-AAAA
1 ATGAAAAAAATGAAAAAAATGAAAAA
47914 ATG--AAAAATGAAAAAAAATGAAAAA
1 ATGAAAAAAATG-AAAAAAATGAAAAA
*
47939 ATGAAGAAAATG-AAAAAATGAAAAA
1 ATGAAAAAAATGAAAAAAATGAAAAA
47964 ATGAAAAAAAT-AAAA
1 ATGAAAAAAATGAAAA
47979 CAAAAACAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.09
23 1 0.02
24 12 0.21
25 33 0.58
27 6 0.11
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.11
Consensus pattern (26 bp):
ATGAAAAAAATGAAAAAAATGAAAAA
Found at i:47974 original size:17 final size:17
Alignment explanation
Indices: 47890--47972 Score: 104
Period size: 17 Copynumber: 5.1 Consensus size: 17
47880 TTGCTTGAAG
47890 ATGAAAAAAA-GAAAAAA
1 ATGAAAAAAATG-AAAAA
47907 ATG--AAAAATG-AAAA
1 ATGAAAAAAATGAAAAA
47921 ATGAAAAAAAATGAAAAA
1 ATG-AAAAAAATGAAAAA
*
47939 ATGAAGAAAATGAAAAA
1 ATGAAAAAAATGAAAAA
47956 ATG-AAAAAATGAAAAA
1 ATGAAAAAAATGAAAAA
47972 A
1 A
47973 ATAAAACAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.12
15 5 0.08
16 14 0.24
17 26 0.44
18 7 0.12
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (17 bp):
ATGAAAAAAATGAAAAA
Found at i:47978 original size:8 final size:8
Alignment explanation
Indices: 47893--47993 Score: 64
Period size: 8 Copynumber: 12.5 Consensus size: 8
47883 CTTGAAGATG
*
47893 AAAAAAAG
1 AAAAAAAT
47901 AAAAAAAT
1 AAAAAAAT
*
47909 -GAAAAAT
1 AAAAAAAT
*
47916 -GAAAAAT
1 AAAAAAAT
47923 GAAAAAAAAT
1 --AAAAAAAT
*
47933 GAAAAAAT
1 AAAAAAAT
*
47941 GAAGAAAAT
1 -AAAAAAAT
*
47950 GAAAAAAT
1 AAAAAAAT
*
47958 GAAAAAAT
1 AAAAAAAT
47966 GAAAAAAAT
1 -AAAAAAAT
*
47975 AAAACAA-
1 AAAAAAAT
*
47982 AAACAAAT
1 AAAAAAAT
47990 AAAA
1 AAAA
47994 GGGGGGTTCA
Statistics
Matches: 74, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
7 18 0.24
8 37 0.50
9 13 0.18
10 6 0.08
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:49281 original size:37 final size:37
Alignment explanation
Indices: 49240--49311 Score: 85
Period size: 37 Copynumber: 1.9 Consensus size: 37
49230 CTTCGAAGCG
49240 AATCAAACT-CAAGCCTTCACGAAAGA-GTAGTGAAGTA
1 AATC-AACTACAAGCCTTCAC-AAAGAGGTAGTGAAGTA
* * *
49277 AATCATCTATAAGCCTTCACAAGGAGGTAGTGAAG
1 AATCAACTACAAGCCTTCACAAAGAGGTAGTGAAG
49312 CAACAGAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (37 bp):
AATCAACTACAAGCCTTCACAAAGAGGTAGTGAAGTA
Found at i:49432 original size:54 final size:53
Alignment explanation
Indices: 49321--50098 Score: 1231
Period size: 54 Copynumber: 14.7 Consensus size: 53
49311 GCAACAGAAG
49321 ATTGTTCGAGTTCTACTCCCTGAAGAAAATAG-G-GCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAG-AAATAGAGAGCGGACCCGTAGGAAGATT
49373 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
*
49427 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
49480 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
49534 ATTGTTCGAGTTCTACTCCCTGAAGAAATAG-G-GTGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
49585 ATTGTTCGAGTTCTTACTCCCT-AACGAAATAGAGAGC-GAGCCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAA-GAAATAGAGAGCGGA-CCCGTAGGAAGATT
* *
49639 ATTGTTCGAGTTCTACTCCCCGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
49692 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
49746 ATTGTTCGAGTTCTACTCCCTGAAGAAATAG-G-GTGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
49797 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
* *
49851 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGAAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
49904 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
49958 ATTGTTCGAGTTCTACTCCCTGAAGAAATAG-G-GTGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
50009 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGGAAGAAT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
*
50063 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGGGAGC
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGC
50099 AGACACGATT
Statistics
Matches: 684, Mismatches: 18, Indels: 47
0.91 0.02 0.06
Matches are distributed among these distances:
51 95 0.14
52 73 0.11
53 239 0.35
54 277 0.40
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (53 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:49689 original size:212 final size:212
Alignment explanation
Indices: 49321--50090 Score: 1479
Period size: 212 Copynumber: 3.6 Consensus size: 212
49311 GCAACAGAAG
*
49321 ATTGTTCGAGTTCTACTCCCTGAAGAAAATAGGGCGGACCCGTAGGAAGATTATTGTTCGAGTTC
1 ATTGTTCGAGTTCTACTCCCTGAAG-AAATAGGGTGGACCCGTAGGAAGATTATTGTTCGAGTTC
49386 TTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAA
65 TTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAA
49451 GAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAG
130 GAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAG
49516 CGGACCCGTAGGAAGATT
195 CGGACCCGTAGGAAGATT
49534 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGGGTGGACCCGTAGGAAGATTATTGTTCGAGTTCT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGGGTGGACCCGTAGGAAGATTATTGTTCGAGTTCT
*
49599 TACTCCCT-AACGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCCGAA
66 TACTCCCTGAA-GAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAA
49663 GAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAG
130 GAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAG
49728 CGGACCCGTAGGAAGATT
195 CGGACCCGTAGGAAGATT
49746 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGGGTGGACCCGTAGGAAGATTATTGTTCGAGTTCT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGGGTGGACCCGTAGGAAGATTATTGTTCGAGTTCT
49811 TACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAG
66 TACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAG
*
49876 AAAAAGAGAGCGGACCCGTAGAAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGC
131 AAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGC
49941 GGACCCGTAGGAAGATT
196 GGACCCGTAGGAAGATT
49958 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGGGTGGACCCGTAGGAAGATTATTGTTCGAGTTCT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGGGTGGACCCGTAGGAAGATTATTGTTCGAGTTCT
*
50023 TACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGAATATTGTTCGAGTTCTACTCCCTGAAG
66 TACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAG
50088 AAA
131 AAA
50091 TAGGGAGCAG
Statistics
Matches: 550, Mismatches: 5, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
211 2 0.00
212 521 0.95
213 27 0.05
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (212 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGGGTGGACCCGTAGGAAGATTATTGTTCGAGTTCT
TACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAG
AAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGC
GGACCCGTAGGAAGATT
Found at i:51051 original size:20 final size:16
Alignment explanation
Indices: 51002--51041 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
50992 AAAGTAAGGA
51002 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
51018 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
51034 AACCAGAG
1 AACCAGAG
51042 TCTAAAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.30, G:0.15, T:0.05
Consensus pattern (16 bp):
AACCAGAGAAATCCAC
Found at i:57216 original size:16 final size:17
Alignment explanation
Indices: 57183--57224 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
57173 AATCGATATA
*
57183 CATTATTTTTTGAAAAT
1 CATTATTTATTGAAAAT
57200 CATTATTTATT-AAAAT
1 CATTATTTATTGAAAAT
*
57216 CAATATTTA
1 CATTATTTA
57225 GAATGCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50
Consensus pattern (17 bp):
CATTATTTATTGAAAAT
Found at i:59238 original size:12 final size:12
Alignment explanation
Indices: 59221--59245 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59211 AAAATATTTC
59221 TTATCATCATCA
1 TTATCATCATCA
59233 TTATCATCATCA
1 TTATCATCATCA
59245 T
1 T
59246 CATTTTGTAA
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:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (12 bp):
TTATCATCATCA
Found at i:60961 original size:25 final size:27
Alignment explanation
Indices: 60915--60967 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
60905 TAGAAAAAAA
*
60915 TTAAGGTTTTTTAAATATAATAATATT
1 TTAAGGTTTTTTAAATATAATAAAATT
* *
60942 TTAAGTTTTTTTTAA-A-AATAAAATT
1 TTAAGGTTTTTTAAATATAATAAAATT
60967 T
1 T
60968 CAAAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 9 0.39
26 1 0.04
27 13 0.57
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (27 bp):
TTAAGGTTTTTTAAATATAATAAAATT
Found at i:61211 original size:27 final size:27
Alignment explanation
Indices: 61167--61218 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
61157 GTAGTTATTC
* *
61167 TAAAATTTTATTTGTATTTATTATATA
1 TAAAATTTTATATGTATTTAATATATA
61194 TAAAATTTTTATAT-TATTTAATATA
1 TAAAA-TTTTATATGTATTTAATATA
61219 CGTGTACTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
TAAAATTTTATATGTATTTAATATATA
Found at i:66077 original size:31 final size:31
Alignment explanation
Indices: 66039--66194 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
66029 CCCGAAGGAC
* *
66039 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
66070 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
66101 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
66132 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
66163 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
66194 C
1 C
66195 CCTCGACCCT
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:67089 original size:21 final size:21
Alignment explanation
Indices: 67059--67103 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
67049 ATTCTGTCGT
*
67059 TTGAAGGGGTA-TCGGTTCCCC
1 TTGAAGGGGTACT-GATTCCCC
*
67080 TTGAATGGGTACTGATTCCCC
1 TTGAAGGGGTACTGATTCCCC
67101 TTG
1 TTG
67104 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACTGATTCCCC
Found at i:67878 original size:24 final size:24
Alignment explanation
Indices: 67846--67916 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
67836 TTCATCATTA
67846 TCACCATCATCGTCGTCGTCGTCG
1 TCACCATCATCGTCGTCGTCGTCG
* *
67870 TCACCATCATCGTCATCGTCATCG
1 TCACCATCATCGTCGTCGTCGTCG
** * *
67894 TCGTCATCGTCATCGTCGTCGTC
1 TCACCATCATCGTCGTCGTCGTC
67917 CTGAGCAGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.14, C:0.37, G:0.18, T:0.31
Consensus pattern (24 bp):
TCACCATCATCGTCGTCGTCGTCG
Found at i:67892 original size:15 final size:15
Alignment explanation
Indices: 67852--67913 Score: 79
Period size: 15 Copynumber: 4.1 Consensus size: 15
67842 ATTATCACCA
*
67852 TCATCGTCGTCGTCG
1 TCATCGTCATCGTCG
* ** *
67867 TCGTCACCATCATCG
1 TCATCGTCATCGTCG
67882 TCATCGTCATCGTCG
1 TCATCGTCATCGTCG
67897 TCATCGTCATCGTCG
1 TCATCGTCATCGTCG
67912 TC
1 TC
67914 GTCCTGAGCA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.13, C:0.35, G:0.19, T:0.32
Consensus pattern (15 bp):
TCATCGTCATCGTCG
Found at i:67912 original size:3 final size:3
Alignment explanation
Indices: 67855--67916 Score: 52
Period size: 3 Copynumber: 20.7 Consensus size: 3
67845 ATCACCATCA
* * * * * * *
67855 TCG TCG TCG TCG TCG TCA CCA TCA TCG TCA TCG TCA TCG TCG TCA TCG
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
*
67903 TCA TCG TCG TCG TC
1 TCG TCG TCG TCG TC
67917 CTGAGCAGGT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.11, C:0.35, G:0.21, T:0.32
Consensus pattern (3 bp):
TCG
Found at i:69994 original size:17 final size:18
Alignment explanation
Indices: 69951--69991 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
69941 AACTTATATT
69951 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
69968 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
69986 ATTAAA
1 AGTAAA
69992 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:71201 original size:37 final size:37
Alignment explanation
Indices: 71128--71202 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
71118 GTTGAAAAAT
* *
71128 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* *
71165 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAA
71202 A
1 A
71203 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:72515 original size:22 final size:22
Alignment explanation
Indices: 72475--72518 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
72465 AATTTGAATT
* * *
72475 ATAATATTATTTTTTTTTAAAA
1 ATAATATTAATATTATTTAAAA
72497 ATAATATTAATATTATTTAAAA
1 ATAATATTAATATTATTTAAAA
72519 TTATGTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAATATTAATATTATTTAAAA
Found at i:72527 original size:21 final size:21
Alignment explanation
Indices: 72475--72535 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
72465 AATTTGAATT
** *
72475 ATAATATTATTTTTTTTTAAAA
1 ATAATATTAAATTTATTT-AAA
72497 ATAATATT-AATATTATTTAAA
1 ATAATATTAAAT-TTATTTAAA
* *
72518 ATTATGTTAAATTTATTT
1 ATAATATTAAATTTATTT
72536 TGAATATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATAATATTAAATTTATTTAAA
Found at i:73134 original size:28 final size:28
Alignment explanation
Indices: 73102--73158 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
73092 GTATCTGTAA
*
73102 TGTAATGACTGTTAAATTTGATCGTTAT
1 TGTAATGACTATTAAATTTGATCGTTAT
73130 TGTAATGACTATTAAATTTGATCGTTAT
1 TGTAATGACTATTAAATTTGATCGTTAT
73158 T
1 T
73159 TGACATGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (28 bp):
TGTAATGACTATTAAATTTGATCGTTAT
Found at i:80646 original size:3 final size:3
Alignment explanation
Indices: 80638--80666 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
80628 ATTATAAATT
80638 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
80667 TACAAAGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:81456 original size:60 final size:60
Alignment explanation
Indices: 81332--81456 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
81322 GTTAGGTGAT
* * * * *
81332 CATTTTGTAATTTTTAATAGCCGAGGGACTGAACAAAGCAATTCCCTATAGTCATAAGAT
1 CATTTTGTAACTTTTAAGAGCCGAGAGACTCAACAAAGCAATTCCCTATAGTCATAAGAC
* ** * *
81392 CATTTTGTAACTTTTAAGAGCCGAGAGACTCAATAAAGCTGTAT-CCTATAGTCGTGAGAC
1 CATTTTGTAACTTTTAAGAGCCGAGAGACTCAACAAAGCAAT-TCCCTATAGTCATAAGAC
81452 CATTT
1 CATTT
81457 GTATGGTTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 53 0.98
61 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (60 bp):
CATTTTGTAACTTTTAAGAGCCGAGAGACTCAACAAAGCAATTCCCTATAGTCATAAGAC
Found at i:81571 original size:14 final size:14
Alignment explanation
Indices: 81552--81579 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
81542 AATTCATTCA
81552 AATATTTATAATTT
1 AATATTTATAATTT
81566 AATATTTATAATTT
1 AATATTTATAATTT
81580 GGTAAAATAT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATATTTATAATTT
Done.