Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001394.1 Hibiscus syriacus cultivar Beakdansim tig00002724_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: 65260
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Found at i:5575 original size:54 final size:53
Alignment explanation
Indices: 5510--5881 Score: 496
Period size: 54 Copynumber: 6.9 Consensus size: 53
5500 TACCAAATAA
* * *
5510 GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAATCATTTC
1 GCACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTC
* * *
5563 AGCACTATGTGTGCAATTCACGAAATTCATCATATGTTGATGAACAATCGTTTC
1 -GCACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTC
* * *
5617 GACACTATGTGT--AACTCACGGAATTCATCATATGTTGGTGAACAACCGTTTC
1 G-CACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTC
* * *
5669 AACACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
1 -GCACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTC
*
5723 GACACTATGTGTGCAATTCACAGAATTCATCATATGTTGATGAACAACCATTTC
1 G-CACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTC
* * * * *
5777 GGCATTATGTGTGTAACTCACAGAATTCATCATATATTGATGAACAACCATTTC
1 -GCACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTC
* *
5831 GACACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACGACCAT
1 G-CACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCAT
5882 ATAGGCACTA
Statistics
Matches: 284, Mismatches: 27, Indels: 14
0.87 0.08 0.04
Matches are distributed among these distances:
52 45 0.16
53 2 0.01
54 236 0.83
55 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (53 bp):
GCACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTC
Found at i:5788 original size:160 final size:161
Alignment explanation
Indices: 5511--5881 Score: 577
Period size: 160 Copynumber: 2.3 Consensus size: 161
5501 ACCAAATAAG
* *
5511 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAATCATTTCAGCACTATGTGTG
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCAGCACTATGTGTG
* * *
5576 CAATTCACGAAATTCATCATATGTTGATGAACAATCGTTTCGACACTA-TGTGTAACTCACGGAA
66 CAATTCACGAAATTCATCATATGTTGATGAACAACCATTTCGACACTAGTGTGTAACTCACAGAA
* * *
5640 TTCATCATATGTTGGTGAACAACCGTTTCAA
131 TTCATCATATATTGATGAACAACCATTTCAA
*
5671 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC-GACACTATGTGT
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCAG-CACTATGTGT
* *
5735 GCAATTCAC-AGAATTCATCATATGTTGATGAACAACCATTTCGGCATTATGTGTGTAACTCACA
65 GCAATTCACGA-AATTCATCATATGTTGATGAACAACCATTTCGACACTA-GTGTGTAACTCACA
*
5799 GAATTCATCATATATTGATGAACAACCATTTCGA
128 GAATTCATCATATATTGATGAACAACCATTTCAA
*
5833 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACGACCAT
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCAT
5882 ATAGGCACTA
Statistics
Matches: 193, Mismatches: 14, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
159 2 0.01
160 102 0.53
162 89 0.46
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (161 bp):
CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCAGCACTATGTGTG
CAATTCACGAAATTCATCATATGTTGATGAACAACCATTTCGACACTAGTGTGTAACTCACAGAA
TTCATCATATATTGATGAACAACCATTTCAA
Found at i:8049 original size:2 final size:2
Alignment explanation
Indices: 8042--8066 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8032 TGTCAGAAAG
8042 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
8067 GCTTTTGTGG
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:10082 original size:22 final size:22
Alignment explanation
Indices: 10031--10091 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
10021 TTCAAAAATG
*
10031 GTATCGATACCATA-T-T-ATA
1 GTATCGATACCATAGTATGGTA
*
10050 GTATTGATACCATAGTATGGTA
1 GTATCGATACCATAGTATGGTA
* *
10072 GTATCGCTACCATGGTATGG
1 GTATCGATACCATAGTATGG
10092 GTACCGATAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 13 0.38
20 1 0.03
21 1 0.03
22 19 0.56
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (22 bp):
GTATCGATACCATAGTATGGTA
Found at i:10579 original size:45 final size:45
Alignment explanation
Indices: 10515--10971 Score: 774
Period size: 45 Copynumber: 10.2 Consensus size: 45
10505 TGAAAATAAT
* * * *
10515 AATGCATATGGGTGCATTATCAACAGAAAAATATACCATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
*
10560 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
*
10605 AATGCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
*
10650 AATGCATATGGGTGCATTATCAACA-AAAAATATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
*
10694 AATGCATATGGGTGCATTATCAATATAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* *
10739 AATGCATATGGGTGCATTATCAACAGAAAATTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
*
10784 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* *
10829 AATGCATATGGGTGCATTATCAACATAAAAGTATGCAATAGTTAA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
10874 AATG-ATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
10918 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTG-A
10964 AATGCATA
1 AATGCATA
10972 ATGGTTCATT
Statistics
Matches: 391, Mismatches: 18, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
44 83 0.21
45 299 0.76
46 9 0.02
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
Found at i:10736 original size:134 final size:135
Alignment explanation
Indices: 10515--10971 Score: 783
Period size: 134 Copynumber: 3.4 Consensus size: 135
10505 TGAAAATAAT
* *
10515 AATGCATATGGGTGCATTATCAACAGAAAAATATACCATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAATATGCTATAGTTGAAATGCATATGGGTGCATTAT
* *
10580 CAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCCATA
66 CAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCTATA
10645 GTTGA
131 GTTGA
10650 AATGCATATGGGTGCATTATCAACA-AAAAATATGCTATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAATATGCTATAGTTGAAATGCATATGGGTGCATTAT
* * *
10714 CAATATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAATTATGCTATA
66 CAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCTATA
10779 GTTGA
131 GTTGA
*
10784 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAATATGCTATAGTTGAAATGCATATGGGTGCATTAT
* *
10849 CAACATAAAAGTATGCAATAGTTAAAATG-ATATGGGTGCATTATCAACATAAAAGTATGCTATA
66 CAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCTATA
10913 GTTGA
131 GTTGA
* *
10918 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAAATGCATA
1 AATGCATATGGGTGCATTATCAACAGAAAAATATGCTATAGTTG-AAATGCATA
10972 ATGGTTCATT
Statistics
Matches: 306, Mismatches: 14, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
134 208 0.68
135 98 0.32
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (135 bp):
AATGCATATGGGTGCATTATCAACAGAAAAATATGCTATAGTTGAAATGCATATGGGTGCATTAT
CAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCTATA
GTTGA
Found at i:10816 original size:179 final size:180
Alignment explanation
Indices: 10515--10971 Score: 783
Period size: 179 Copynumber: 2.5 Consensus size: 180
10505 TGAAAATAAT
* * * *
10515 AATGCATATGGGTGCATTATCAACAGAAAAATATACCATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTAT
*
10580 CAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCCATA
66 CAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCCATA
* *
10645 GTTGAAATGCATATGGGTGCATTATCAACA-AAAAATATGCTATAGTTGA
131 GTTGAAATGCATATGGGTGCATTATCAACATAAAAATATGCAATAGTTAA
*
10694 AATGCATATGGGTGCATTATCAATATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTAT
* *
10759 CAACAGAAAATTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATA
66 CAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCCATA
*
10824 GTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCAATAGTTAA
131 GTTGAAATGCATATGGGTGCATTATCAACATAAAAATATGCAATAGTTAA
10874 AATG-ATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTAT
*
10938 CAACATAAAAGTATGCTATAGTTGAAAATGCATA
66 CAACAGAAAAGTATGCTATAGTTG-AAATGCATA
10972 ATGGTTCATT
Statistics
Matches: 262, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
179 233 0.89
180 29 0.11
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (180 bp):
AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTAT
CAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCCATA
GTTGAAATGCATATGGGTGCATTATCAACATAAAAATATGCAATAGTTAA
Found at i:12913 original size:17 final size:17
Alignment explanation
Indices: 12893--12951 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
12883 TTTAGGGAAG
12893 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
12910 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
12926 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
12943 TAGTTCATT
1 TAGTTCATT
12952 GAATAAAATT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:21218 original size:20 final size:20
Alignment explanation
Indices: 21192--21243 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
21182 TGATTCAATT
21192 GGTATCGATACCGAAGGG-A
1 GGTATCGATACCGAAGGGAA
*
21211 GAGTATCGATACTGAAGGGAA
1 G-GTATCGATACCGAAGGGAA
21232 GGTATCGATACC
1 GGTATCGATACC
21244 ATTTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 26 0.90
21 2 0.07
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.19
Consensus pattern (20 bp):
GGTATCGATACCGAAGGGAA
Found at i:21295 original size:19 final size:19
Alignment explanation
Indices: 21268--21326 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 19
21258 TGCAAAAATG
21268 GTATCGATACCATAGTATA
1 GTATCGATACCATAGTATA
*
21287 GTATTGATACCATAGTATGGTA
1 GTATCGATACCATAGTA---TA
*
21309 GTATCGATACCATGGTAT
1 GTATCGATACCATAGTAT
21327 GGGTATCGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 17 0.50
22 17 0.50
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (19 bp):
GTATCGATACCATAGTATA
Found at i:21317 original size:22 final size:22
Alignment explanation
Indices: 21268--21328 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
21258 TGCAAAAATG
21268 GTATCGATACCATAGTA---TA
1 GTATCGATACCATAGTATGGTA
*
21287 GTATTGATACCATAGTATGGTA
1 GTATCGATACCATAGTATGGTA
*
21309 GTATCGATACCATGGTATGG
1 GTATCGATACCATAGTATGG
21329 GTATCGTACT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 16 0.44
22 20 0.56
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (22 bp):
GTATCGATACCATAGTATGGTA
Found at i:25303 original size:34 final size:34
Alignment explanation
Indices: 25260--25328 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
25250 CGTTCCATAC
* *
25260 AGCATCCGTTGATAAGGGCTGAATAAGTAAAACT
1 AGCATCCGTTAATAAGGGCTGAATAAGAAAAACT
25294 AGCATCCGTTAATAAGGGCTGAATAAGAAAAACT
1 AGCATCCGTTAATAAGGGCTGAATAAGAAAAACT
25328 A
1 A
25329 TATGGTGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (34 bp):
AGCATCCGTTAATAAGGGCTGAATAAGAAAAACT
Found at i:27328 original size:7 final size:7
Alignment explanation
Indices: 27316--27542 Score: 454
Period size: 7 Copynumber: 32.4 Consensus size: 7
27306 AGGAAGGAAG
27316 GAATTTA
1 GAATTTA
27323 GAATTTA
1 GAATTTA
27330 GAATTTA
1 GAATTTA
27337 GAATTTA
1 GAATTTA
27344 GAATTTA
1 GAATTTA
27351 GAATTTA
1 GAATTTA
27358 GAATTTA
1 GAATTTA
27365 GAATTTA
1 GAATTTA
27372 GAATTTA
1 GAATTTA
27379 GAATTTA
1 GAATTTA
27386 GAATTTA
1 GAATTTA
27393 GAATTTA
1 GAATTTA
27400 GAATTTA
1 GAATTTA
27407 GAATTTA
1 GAATTTA
27414 GAATTTA
1 GAATTTA
27421 GAATTTA
1 GAATTTA
27428 GAATTTA
1 GAATTTA
27435 GAATTTA
1 GAATTTA
27442 GAATTTA
1 GAATTTA
27449 GAATTTA
1 GAATTTA
27456 GAATTTA
1 GAATTTA
27463 GAATTTA
1 GAATTTA
27470 GAATTTA
1 GAATTTA
27477 GAATTTA
1 GAATTTA
27484 GAATTTA
1 GAATTTA
27491 GAATTTA
1 GAATTTA
27498 GAATTTA
1 GAATTTA
27505 GAATTTA
1 GAATTTA
27512 GAATTTA
1 GAATTTA
27519 GAATTTA
1 GAATTTA
27526 GAATTTA
1 GAATTTA
27533 GAATTTA
1 GAATTTA
27540 GAA
1 GAA
27543 CACATACTGA
Statistics
Matches: 220, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 220 1.00
ACGTcount: A:0.43, C:0.00, G:0.15, T:0.42
Consensus pattern (7 bp):
GAATTTA
Found at i:28437 original size:34 final size:30
Alignment explanation
Indices: 28399--28467 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
28389 TTGATATGAC
*
28399 AATTTAAGGCAAAATGGTTTTTGTACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
28433 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
28462 AATTTA
1 AATTTA
28468 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:28478 original size:29 final size:30
Alignment explanation
Indices: 28408--28467 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
28398 CAATTTAAGG
*
28408 CAAAATGGTTTTTGTACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
28439 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
28468 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:28573 original size:21 final size:21
Alignment explanation
Indices: 28547--28607 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
28537 AGGGTGTCAA
28547 AGTGCATCCATGCACCCTTGC
1 AGTGCATCCATGCACCCTTGC
28568 AGTGCATCCATGCACCCTTGC
1 AGTGCATCCATGCACCCTTGC
28589 AGTGCATCCATGCATCCCT
1 AGTGCATCCATGCA-CCCT
28608 GTACCTGCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
21 35 0.90
22 4 0.10
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCACCCTTGC
Found at i:28806 original size:21 final size:21
Alignment explanation
Indices: 28773--28812 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
28763 TTTGAGTAGA
*
28773 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
28795 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
28813 ATATACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:29980 original size:19 final size:20
Alignment explanation
Indices: 29956--30003 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
29946 AACGATTTTC
*
29956 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
29975 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
29995 TTTTGAAAA
1 TTTTGAAAA
30004 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:31316 original size:34 final size:30
Alignment explanation
Indices: 31278--31346 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
31268 TTGATATAAC
31278 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
31312 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
31341 AATTTA
1 AATTTA
31347 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:31357 original size:29 final size:30
Alignment explanation
Indices: 31287--31346 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
31277 CAATTTAAGG
31287 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
31318 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
31347 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:31452 original size:21 final size:21
Alignment explanation
Indices: 31426--31486 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
31416 AGGGTGTCAA
31426 AGTGCATCCATGCACCCTTGC
1 AGTGCATCCATGCACCCTTGC
31447 AGTGCATCCATGCACCCTTGC
1 AGTGCATCCATGCACCCTTGC
31468 AGTGCATCCATGCATCCCT
1 AGTGCATCCATGCA-CCCT
31487 GTACCTGCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
21 35 0.90
22 4 0.10
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCACCCTTGC
Found at i:31685 original size:21 final size:21
Alignment explanation
Indices: 31652--31691 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
31642 TTTGAGTAGA
*
31652 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
31674 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
31692 ATATACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:32859 original size:19 final size:20
Alignment explanation
Indices: 32835--32882 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
32825 AACGATTTTC
*
32835 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
32854 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
32874 TTTTGAAAA
1 TTTTGAAAA
32883 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:34195 original size:34 final size:30
Alignment explanation
Indices: 34157--34225 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
34147 TTGATATAAC
34157 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
34191 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
34220 AATTTA
1 AATTTA
34226 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:34236 original size:29 final size:30
Alignment explanation
Indices: 34166--34225 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
34156 CAATTTAAGG
34166 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
34197 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
34226 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:34331 original size:21 final size:21
Alignment explanation
Indices: 34305--34362 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
34295 AGGGTGTCAA
34305 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
34326 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
34347 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
34363 TGCACTAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:34608 original size:20 final size:22
Alignment explanation
Indices: 34570--34609 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
34560 TTGAGTAGAA
34570 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
34592 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
34610 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:37892 original size:3 final size:3
Alignment explanation
Indices: 37884--37964 Score: 65
Period size: 3 Copynumber: 27.0 Consensus size: 3
37874 TTTTTATTTT
* * * * * *
37884 TTA TTA TTA TAA TAA TAA TTA TAA TTA TTA TT- TTA TTA TAA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
37931 TTA TTA TTA CCA TTA CTA TTAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
37965 ATAAATAATT
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
2 2 0.03
3 57 0.92
4 3 0.05
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:45358 original size:46 final size:47
Alignment explanation
Indices: 45303--45433 Score: 138
Period size: 54 Copynumber: 2.7 Consensus size: 47
45293 AAATCTGGGT
* * * *
45303 AGAAGCCACAGGAAATGATGAATGTGTTGTC-TGCGAACATCTGTGC
1 AGAAACCACAAGAAATGATGAATGTGTTGTCTTACGAACATCTGTAC
* *
45349 AGAAACCACATGAAAGGATGAATGTGTTGTCAATTATTTTACGAACATCTGTAC
1 AGAAACCACAAGAAATGATGAATGTGTTGTC-------TTACGAACATCTGTAC
45403 AGAAACCACAAGAAATGATGAATGTGTTGTC
1 AGAAACCACAAGAAATGATGAATGTGTTGTC
45434 AAATATTTTA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
46 28 0.40
54 42 0.60
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (47 bp):
AGAAACCACAAGAAATGATGAATGTGTTGTCTTACGAACATCTGTAC
Found at i:45400 original size:54 final size:54
Alignment explanation
Indices: 45336--45448 Score: 181
Period size: 54 Copynumber: 2.1 Consensus size: 54
45326 GTGTTGTCTG
* * *
45336 CGAACATCTGTGCAGAAACCACATGAAAGGATGAATGTGTTGTCAATTATTTTA
1 CGAACATCTGTACAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATATTTTA
*
45390 CGAACATCTGTACAGAAACCACAAGAAATGATGAATGTGTTGTCAAATATTTTA
1 CGAACATCTGTACAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATATTTTA
*
45444 TGAAC
1 CGAAC
45449 CAGTGGTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (54 bp):
CGAACATCTGTACAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATATTTTA
Found at i:47157 original size:215 final size:218
Alignment explanation
Indices: 46497--47403 Score: 1313
Period size: 219 Copynumber: 4.2 Consensus size: 218
46487 CTATTTCCCT
* * *
46497 AGATGATAAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT
1 AGATGATAAAG-CCTTCGGGTCATCCATAAGACCTTCAATGCTGGATGTTTTCAAATGAGATTTT
* *
46562 AGAAACTAAGCCTTCGAGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAA
65 AGAAACTAAGCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAA
* * * * * *
46627 CAAAGGGGTTCCTTTACAACTAATAAACTAAGCCTTCGGAAGTTTCTTGATTTGTAAATCCTTCG
130 CAAAGGGGTTCATTGACAACTAAGAAACTAAGCCTTCGGGAGTTTCTTAATTTTTAAATCCTTCG
* *
46692 GGTCATATGTAAGCCTTTCGAGTA
195 GGTCATCTGTAAGCCTTTCGAGCA
* * *
46716 TGAAAGATAAAGCCTTCGGGTCATCCATATGACCTTCAATGCTGGATGTTTTCAAATGAGATTTT
1 AG-ATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAATGCTGGATGTTTTCAAATGAGATTTT
46781 AGAAACTAAGCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAA
65 AGAAACTAAGCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAA
* * *
46846 CAAAGGGGTTCATTTACAACTAATAAACTAAGCCTTCGGGAGTTTCTTAATTTATAAATCCTTCG
130 CAAAGGGGTTCATTGACAACTAAGAAACTAAGCCTTCGGGAGTTTCTTAATTTTTAAATCCTTCG
*
46911 AGTCATCTGTAAGCCTTTCGAGCA
195 GGTCATCTGTAAGCCTTTCGAGCA
* *
46935 GGATGATAAAGCCTTCGGGTTATCCATAAGACCTTCAATGCTGGATGTTTTCAAATGAGATTTTA
1 AGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAATGCTGGATGTTTTCAAATGAGATTTTA
*
47000 GAAACTAAGCTTTCGGGGGTTTGCT-ATTATCTC-AAA-AGTTGTTAAAGGAAGCTAAGCCTAAC
66 GAAACTAAGCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAAC
* * *
47062 AAAGGGGTTCATTGACAACTTAGAAACTAAGCCTTCGGGGGTTTCTTAATTTTTAAATTCTTCGG
131 AAAGGGGTTCATTGACAACTAAGAAACTAAGCCTTCGGGAGTTTCTTAATTTTTAAATCCTTCGG
* * * *
47127 GTTATCTGTAAGCTTTTGGAACA
196 GTCATCTGTAAGCCTTTCGAGCA
* * * *
47150 AGATGATAAAGCCTTTGGGTCATCCATAAGACCTTCAGTGATGAATGTTTTCAAATGAGATTTTA
1 AGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAATGCTGGATGTTTTCAAATGAGATTTTA
* ** * *
47215 GAAACTAAGCCTTT-GGGGGTTTCTTAATTATCTTGAAAGAGTTGCTAAA-GAATGCTAGGCCTA
66 GAAACTAAG-CTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAA-GCTAAGCCTA
* * * * *
47278 ACAAAGGTGTTCCTTGACAATTAAGAAACTAAGCCTTTAGGG-GTTTCTTGATTTTTAAATCCTT
129 ACAAAGGGGTTCATTGACAACTAAGAAACTAAGCC-TTCGGGAGTTTCTTAATTTTTAAATCCTT
*
47342 CGGGGTCATCTGTAAACCTTTCGAGCA
193 C-GGGTCATCTGTAAGCCTTTCGAGCA
47369 AGATGATAAAGCCTTCGGGTCATCCATAAGACCTT
1 AGATGATAAAGCCTTCGGGTCATCCATAAGACCTT
47404 GATAACTAAG
Statistics
Matches: 625, Mismatches: 55, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
215 180 0.29
216 14 0.02
217 14 0.02
218 154 0.25
219 255 0.41
220 8 0.01
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (218 bp):
AGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAATGCTGGATGTTTTCAAATGAGATTTTA
GAAACTAAGCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAAC
AAAGGGGTTCATTGACAACTAAGAAACTAAGCCTTCGGGAGTTTCTTAATTTTTAAATCCTTCGG
GTCATCTGTAAGCCTTTCGAGCA
Found at i:47832 original size:3 final size:3
Alignment explanation
Indices: 47826--47902 Score: 70
Period size: 3 Copynumber: 26.3 Consensus size: 3
47816 TTTTCTTTTT
* * * *
47826 TTA TTA TTA TTA TAA TAA TTA TTA TTT TTA TTA TTA -TA TTA TTA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
47873 TTA TTA TTA -AA TAA TT- TTA TTTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA T
47903 AGGCCCGAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
2 5 0.08
3 54 0.87
4 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:47867 original size:17 final size:17
Alignment explanation
Indices: 47826--47902 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 17
47816 TTTTCTTTTT
* *
47826 TTATTATTATTATAATAA
1 TTATTATTTTTATTAT-A
47844 TTATTATTTTTATTATTATA
1 TTATTA--TTT-TTATTATA
47864 TTATTATTTTTATTAT-
1 TTATTATTTTTATTATA
* * *
47880 TAAATAATTTTATT-TA
1 TTATTATTTTTATTATA
47896 TTATTAT
1 TTATTAT
47903 AGGCCCGAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
15 1 0.02
16 15 0.32
17 7 0.15
18 9 0.19
20 9 0.19
21 6 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTTATTATA
Found at i:47868 original size:20 final size:20
Alignment explanation
Indices: 47826--47903 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
47816 TTTTCTTTTT
* *
47826 TTATTATTATTATAATAATTA
1 TTATTTTTATTATTAT-ATTA
47847 TTATTTTTATTATTATATTA
1 TTATTTTTATTATTATATTA
* *
47867 TTATTTTTATTATTAAATAA
1 TTATTTTTATTATTATATTA
47887 TT-TTATTTATTATTATA
1 TTATT-TTTATTATTATA
47904 GGCCCGAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
19 2 0.04
20 35 0.69
21 14 0.27
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTTTTATTATTATATTA
Found at i:50610 original size:54 final size:54
Alignment explanation
Indices: 50480--50843 Score: 437
Period size: 54 Copynumber: 6.8 Consensus size: 54
50470 CCAAATAGGA
* * * * *
50480 ACTAAGTGTGCAATTCATGGAATTCTTCATATGTTGATGAAAAACCATTTC-AG
1 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGAC
*
50533 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAATCATTTCGAC
1 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGAC
* * *
50587 AATATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCGGC
1 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGAC
* * * *
50641 ACTAAGTTTTCAATTCACAGAATTCATCATATGTTGATGAACAACCATTTCGAC
1 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGAC
* * * * *
50695 ACTATGTGTGCTACTCACGAAATTCATCATTTGTTGATGAACAATCA-TTC-AGC
1 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGA-C
* * * * ** *
50748 AATATATGTGCAACTCACGAAATTCATCATATGTTGATGAACAACTGTTTCGGC
1 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGAC
* * * *
50802 ACTAAGTGTGCAATTCATGAAATTCATCATATTTTGATGAAC
1 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAAC
50844 GATCGCATAG
Statistics
Matches: 267, Mismatches: 40, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
52 1 0.00
53 90 0.34
54 176 0.66
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (54 bp):
ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGAC
Found at i:50760 original size:161 final size:160
Alignment explanation
Indices: 50480--50843 Score: 525
Period size: 161 Copynumber: 2.3 Consensus size: 160
50470 CCAAATAGGA
* * * *
50480 ACTAAGTGTGCAATTCATGGAATTCTTCATATGTTGATGAAAAACCATTTCAGACTATGTGTGCA
1 ACTAAGTGTGCAATTCA-AGAATTCATCATATGTTGATGAACAACCATTTCACACTATGTGTGCA
* * * *
50545 ATTCACGGAATTCATCATATGTTGATGAACAATCATTTCGACAATATGTGTGCAACTCACGGAAT
65 ACTCACGAAATTCATCATATGTTGATGAACAATCATTTCGACAATATATGTGCAACTCACGAAAT
50610 TCATCATATGTTGATGAACAACCATTTCGGC
130 TCATCATATGTTGATGAACAACCATTTCGGC
* *
50641 ACTAAGTTTTCAATTCACAGAATTCATCATATGTTGATGAACAACCATTTCGACACTATGTGTGC
1 ACTAAGTGTGCAATTCA-AGAATTCATCATATGTTGATGAACAACCATTTC-ACACTATGTGTGC
* *
50706 TACTCACGAAATTCATCATTTGTTGATGAACAATCA-TTC-AGCAATATATGTGCAACTCACGAA
64 AACTCACGAAATTCATCATATGTTGATGAACAATCATTTCGA-CAATATATGTGCAACTCACGAA
**
50769 ATTCATCATATGTTGATGAACAACTGTTTCGGC
128 ATTCATCATATGTTGATGAACAACCATTTCGGC
* *
50802 ACTAAGTGTGCAATTCATGAAATTCATCATATTTTGATGAAC
1 ACTAAGTGTGCAATTCAAG-AATTCATCATATGTTGATGAAC
50844 GATCGCATAG
Statistics
Matches: 181, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
160 2 0.01
161 135 0.75
162 44 0.24
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (160 bp):
ACTAAGTGTGCAATTCAAGAATTCATCATATGTTGATGAACAACCATTTCACACTATGTGTGCAA
CTCACGAAATTCATCATATGTTGATGAACAATCATTTCGACAATATATGTGCAACTCACGAAATT
CATCATATGTTGATGAACAACCATTTCGGC
Found at i:50811 original size:107 final size:108
Alignment explanation
Indices: 50480--50843 Score: 441
Period size: 107 Copynumber: 3.4 Consensus size: 108
50470 CCAAATAGGA
* * * * * *
50480 ACTAAGTGTGCAATTCATGGAATTCTTCATATGTTGATGAAAAACCATTTCAG-ACTATGTGTGC
1 ACTAAGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCATTTCAGCACTATATGTGC
*
50544 AATTCACGGAATTCATCATATGTTGATGAACAA-TCATTTCGAC
66 AATTCACGAAATTCATCATATGTTGATGAACAACT-ATTTCGAC
* * * * * *
50587 AATATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCGGCACTA-AGTTTT
1 ACTAAGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCATTTCAGCACTATA-TGTG
*
50651 CAATTCAC-AGAATTCATCATATGTTGATGAACAACCATTTCGAC
65 CAATTCACGA-AATTCATCATATGTTGATGAACAACTATTTCGAC
* * * * *
50695 ACTATGTGTGCTACTCACGAAATTCATCATTTGTTGATGAACAATCA-TTCAGCAATATATGTGC
1 ACTAAGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCATTTCAGCACTATATGTGC
* * *
50759 AACTCACGAAATTCATCATATGTTGATGAACAACTGTTTCGGC
66 AATTCACGAAATTCATCATATGTTGATGAACAACTATTTCGAC
* * *
50802 ACTAAGTGTGCAATTCATGAAATTCATCATATTTTGATGAAC
1 ACTAAGTGTGCAACTCACGAAATTCATCATATGTTGATGAAC
50844 GATCGCATAG
Statistics
Matches: 220, Mismatches: 31, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
107 130 0.59
108 90 0.41
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (108 bp):
ACTAAGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCATTTCAGCACTATATGTGC
AATTCACGAAATTCATCATATGTTGATGAACAACTATTTCGAC
Found at i:55031 original size:22 final size:22
Alignment explanation
Indices: 55004--55045 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
54994 TGCAAAAATG
55004 GTATCGATACCATAGTATGGTA
1 GTATCGATACCATAGTATGGTA
*
55026 GTATCGATACCATGGTATGG
1 GTATCGATACCATAGTATGG
55046 GAATCGATAC
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:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (22 bp):
GTATCGATACCATAGTATGGTA
Found at i:55598 original size:45 final size:45
Alignment explanation
Indices: 55469--55949 Score: 682
Period size: 45 Copynumber: 11.0 Consensus size: 45
55459 AATAATAATA
* * *
55469 CATATGGGTGCATTATTAACAAAAAAGTA--CCATAGTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
*
55512 AATATGGGTGCATTAT-AA-ATAGAAAGTATGCTATAGTTGAAATG
1 CATATGGGTGCATTATCAACATA-AAAGTATGCTATAGTTGAAATG
*
55556 CATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
* * *
55601 CATATGGGTGCAATATCAACAGAAAAGTATGCTATAGTTGAATTG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
* *
55646 CATATGGGTACATTATCAACATAAGAG--TGCTATAGTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
*
55689 CACAT-GGTGCATTATCAACATAAAAGTATGCT-TAGTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
* **
55732 CATATGGGTGCATTATCAACAGAAAAGTATATTATAGTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
*
55777 CATATGGGTGCATTATCAACAT-AAAGTATGATATAGTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
* *
55821 CATATGGGTGCATTATCAACATAAAAGTATGCAATATTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
* *
55866 CTTAT-GGTGCATTCTCAACATAAAAGTATGCTATAGTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
*
55910 CATATAGGTGCATTATCAACAT-AAA--ATGCTATAGTTGAAA
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAA
55950 AATAGTGGTA
Statistics
Matches: 394, Mismatches: 33, Indels: 23
0.88 0.07 0.05
Matches are distributed among these distances:
41 2 0.01
42 42 0.11
43 49 0.12
44 141 0.36
45 157 0.40
46 3 0.01
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.31
Consensus pattern (45 bp):
CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
Found at i:55625 original size:89 final size:89
Alignment explanation
Indices: 55469--55935 Score: 651
Period size: 89 Copynumber: 5.3 Consensus size: 89
55459 AATAATAATA
* * * * *
55469 CATATGGGTGCATTATTAACAAAAAAGTA--CCATAGTTGAAATGAATATGGGTGCATTATAAAT
1 CATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATGCATATGGGTGCATTATCAAC
*
55532 AGAAAGTATGCTATAGTTGAAATG
66 AAAAAGTATGCTATAGTTGAAATG
*
55556 CATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATGCATATGGGTGCAATATCAAC
1 CATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATGCATATGGGTGCATTATCAAC
*
55621 AGAAAAGTATGCTATAGTTGAATTG
66 A-AAAAGTATGCTATAGTTGAAATG
* * * *
55646 CATATGGGTACATTATCAACATAAGAG--TGCTATAGTTGAAATGCACAT-GGTGCATTATCAAC
1 CATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATGCATATGGGTGCATTATCAAC
55708 ATAAAAGTATGCT-TAGTTGAAATG
66 A-AAAAGTATGCTATAGTTGAAATG
* ***
55732 CATATGGGTGCATTATCAACAGAAAAGTATATTATAGTTGAAATGCATATGGGTGCATTATCAAC
1 CATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATGCATATGGGTGCATTATCAAC
* *
55797 ATAAAGTATGATATAGTTGAAATG
66 AAAAAGTATGCTATAGTTGAAATG
* * * *
55821 CATATGGGTGCATTATCAACATAAAAGTATGCAATATTTGAAATGCTTAT-GGTGCATTCTCAAC
1 CATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATGCATATGGGTGCATTATCAAC
55885 ATAAAAGTATGCTATAGTTGAAATG
66 A-AAAAGTATGCTATAGTTGAAATG
*
55910 CATATAGGTGCATTATCAACATAAAA
1 CATATGGGTGCATTATCAACATAAAA
55936 TGCTATAGTT
Statistics
Matches: 339, Mismatches: 33, Indels: 14
0.88 0.09 0.04
Matches are distributed among these distances:
86 34 0.10
87 52 0.15
88 60 0.18
89 147 0.43
90 46 0.14
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.30
Consensus pattern (89 bp):
CATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATGCATATGGGTGCATTATCAAC
AAAAAGTATGCTATAGTTGAAATG
Found at i:62383 original size:44 final size:45
Alignment explanation
Indices: 62283--62424 Score: 225
Period size: 45 Copynumber: 3.2 Consensus size: 45
62273 TGAAAATAAT
*
62283 AATGCATATGGGTACATTATCAACAGAAACGTATGCCATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCCATAGTTGA
* *
62328 AAAGCATATGGGTACATTATCAACAGAAAAGTA-GCTATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCCATAGTTGA
* *
62372 AATGCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCCATAGTTGA
62417 AATG-ATAT
1 AATGCATAT
62425 AATTGAATTG
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
44 44 0.49
45 45 0.51
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (45 bp):
AATGCATATGGGTACATTATCAACAGAAAAGTATGCCATAGTTGA
Found at i:62460 original size:59 final size:60
Alignment explanation
Indices: 62363--62484 Score: 210
Period size: 59 Copynumber: 2.0 Consensus size: 60
62353 GAAAAGTAGC
*
62363 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATG-A
1 TATAATTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATGCA
* *
62422 TATAATTGAATTGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATGCA
1 TATAATTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATGCA
62482 TAT
1 TAT
62485 GGGTGCATTA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
59 55 0.93
60 4 0.07
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.33
Consensus pattern (60 bp):
TATAATTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATGCA
Found at i:62482 original size:45 final size:45
Alignment explanation
Indices: 62422--62771 Score: 551
Period size: 45 Copynumber: 7.8 Consensus size: 45
62412 GTTGAAATGA
* *
62422 TATAATTGAATTGCATATGGGTGCATTATCAACATAAAAGTATGC
1 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
*
62467 TATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGC
1 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
*
62512 TATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGC
1 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
*
62557 TATAGTTGAAATGCATATGGGTGCATTATCAACATCAAAGTATGC
1 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
*
62602 TATAGTTGAAATGCATAT-GGTTCATTATCAACATAAAAGTATGC
1 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
* * *
62646 AATAGTTGAAATTCATATGAGTGCATTATCAACATAAAAGTATGC
1 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
* *
62691 TATAGTTAAAATGCATATGGTTGCATTATCAACATAAAAGTATGC
1 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
* *
62736 TATAGTTAAAAATGCATAAT-GGTGCATTATAAACAT
1 TATAGTT-GAAATGCAT-ATGGGTGCATTATCAACAT
62772 GAATGGAGGT
Statistics
Matches: 284, Mismatches: 18, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
44 40 0.14
45 219 0.77
46 23 0.08
47 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (45 bp):
TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
Found at i:62506 original size:104 final size:104
Alignment explanation
Indices: 62331--62529 Score: 346
Period size: 104 Copynumber: 1.9 Consensus size: 104
62321 TAGTTGAAAA
62331 GCATATGGGTACATTATCAACAGAAAAGTAGCTATAGTTGAAATGCATATGGGTGCATTATCAAC
1 GCATATGGGTACATTATCAACAGAAAAGTAGCTATAGTTGAAATGCATATGGGTGCATTATCAAC
*
62396 ATAAAAGTATGCCATAGTTGAAATG-ATATAATTGAATT
66 AGAAAAGTATGCCATAGTTGAAATGCATATAATTGAATT
* *
62434 GCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAA
1 GCATATGGGTACATTATCAACAGAAAAGTA-GCTATAGTTGAAATGCATATGGGTGCATTATCAA
*
62499 CAGAAAAGTATGCTATAGTTGAAATGCATAT
65 CAGAAAAGTATGCCATAGTTGAAATGCATAT
62530 GGGTGCATTA
Statistics
Matches: 90, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 28 0.31
104 58 0.64
105 4 0.04
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (104 bp):
GCATATGGGTACATTATCAACAGAAAAGTAGCTATAGTTGAAATGCATATGGGTGCATTATCAAC
AGAAAAGTATGCCATAGTTGAAATGCATATAATTGAATT
Found at i:64744 original size:22 final size:22
Alignment explanation
Indices: 64676--64745 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
64666 TACTGAAAGG
* * * *
64676 AGTATCAGTACCATAGTGTAGT
1 AGTATCGGTACTATAGTATAGA
* *
64698 AGTATCGATACTAGAG-A-A-A
1 AGTATCGGTACTATAGTATAGA
*
64717 GGTATCGGTACTATAGTATAGA
1 AGTATCGGTACTATAGTATAGA
64739 AGTATCG
1 AGTATCG
64746 ATGCCATGGT
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
19 13 0.37
20 2 0.06
21 1 0.03
22 19 0.54
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (22 bp):
AGTATCGGTACTATAGTATAGA
Found at i:65166 original size:53 final size:53
Alignment explanation
Indices: 65087--65243 Score: 199
Period size: 53 Copynumber: 3.0 Consensus size: 53
65077 ACCAAAATAG
* * * * *
65087 GCACTAAGTATACAATTCACGGAATTCATCATATGTGATGAACAACTGTTTCA
1 GCACTATGTGTACAACTCACAGAATTCATCATATGTGATGAACAACCGTTTCA
* * *
65140 GTACTATGTGTACAACTTACAGAATTC-TCATATGTTGATGAACAACCGTTTCG
1 GCACTATGTGTACAACTCACAGAATTCATCATATG-TGATGAACAACCGTTTCA
* * *
65193 GCACTATGTGTGCAACTCACGGAATTCATCATATTTGATGAACAACCGTTT
1 GCACTATGTGTACAACTCACAGAATTCATCATATGTGATGAACAACCGTTT
65244 TCGACACTAA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 7 0.08
53 76 0.85
54 6 0.07
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (53 bp):
GCACTATGTGTACAACTCACAGAATTCATCATATGTGATGAACAACCGTTTCA
Done.