Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002529.1 Hibiscus syriacus cultivar Beakdansim tig00005142_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: 67149
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:242 original size:17 final size:17
Alignment explanation
Indices: 210--241 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
200 TAAAATATTT
210 TCTCTTTTTAATAAAAC
1 TCTCTTTTTAATAAAAC
227 TCTCTTTTT-ATAAAA
1 TCTCTTTTTAATAAAA
242 AAAGTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (17 bp):
TCTCTTTTTAATAAAAC
Found at i:504 original size:28 final size:28
Alignment explanation
Indices: 473--526 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
463 CAAACGTTTA
* *
473 GGTTTATGGTTTA-TGATATGGGGTTTGT
1 GGTTTAGGGTTTAGTGAT-TGGAGTTTGT
501 GGTTTAGGGTTTAGTGATTGGAGTTT
1 GGTTTAGGGTTTAGTGATTGGAGTTT
527 AAGATTTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (28 bp):
GGTTTAGGGTTTAGTGATTGGAGTTTGT
Found at i:1668 original size:60 final size:60
Alignment explanation
Indices: 1539--1672 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 60
1529 GCACTATACA
* * * * *** * * *
1539 CCTCAAAATATGACTTTTATTCTAAATTAGTCCTTGAACTTTTGAGTATTCTAATTTCAT
1 CCTCAAACTATGACTCTCATCCTAAATTAGTCCCCAAACTTTTAAATATTCTAAATTCAT
*
1599 CCAT-GAACTATGACTCTCATCCTAAATTAGTCCCCAAACTTTTAAATATTCTAAATTCAT
1 CC-TCAAACTATGACTCTCATCCTAAATTAGTCCCCAAACTTTTAAATATTCTAAATTCAT
1659 CCTCAAACTATGAC
1 CCTCAAACTATGAC
1673 CCTAATTCTA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
59 1 0.02
60 58 0.97
61 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (60 bp):
CCTCAAACTATGACTCTCATCCTAAATTAGTCCCCAAACTTTTAAATATTCTAAATTCAT
Found at i:1798 original size:60 final size:59
Alignment explanation
Indices: 1734--1878 Score: 166
Period size: 60 Copynumber: 2.4 Consensus size: 59
1724 TTTGGGGATT
* * * **
1734 AATTTGGGATGAGGGTCATAGTTTGGGGATGATTTTGGAA-TGTTCAAAAGTTTAAGGACC
1 AATTTGGAATGAGGATCATAGTTTGGGG-TGAATTTAAAACT-TTCAAAAGTTTAAGGACC
* * * *
1794 AATTTAGAATGATGATCATAGTTTAAGGGTGAATTTAAAACTTTTAAAAGTTTAAGGACC
1 AATTTGGAATGAGGATCATAGTTT-GGGGTGAATTTAAAACTTTCAAAAGTTTAAGGACC
*
1854 AATTTGGAAGGAGGATCATAGTTTG
1 AATTTGGAATGAGGATCATAGTTTG
1879 AGGACGTACA
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
60 66 0.94
61 4 0.06
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (59 bp):
AATTTGGAATGAGGATCATAGTTTGGGGTGAATTTAAAACTTTCAAAAGTTTAAGGACC
Found at i:1803 original size:29 final size:29
Alignment explanation
Indices: 1771--1858 Score: 72
Period size: 29 Copynumber: 3.0 Consensus size: 29
1761 GATGATTTTG
1771 GAATGTTCAAAAGTTTAAGGACCAATTTA
1 GAATGTTCAAAAGTTTAAGGACCAATTTA
* ***
1800 GAATGATGATC-ATAGTTTAAGGGTGAATTTA
1 GAATG-T--TCAAAAGTTTAAGGACCAATTTA
* *
1831 AAACT-TTTAAAAGTTTAAGGACCAATTT
1 GAA-TGTTCAAAAGTTTAAGGACCAATTT
1859 GGAAGGAGGA
Statistics
Matches: 44, Mismatches: 10, Indels: 10
0.69 0.16 0.16
Matches are distributed among these distances:
28 1 0.02
29 20 0.45
30 2 0.05
31 18 0.41
32 3 0.07
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (29 bp):
GAATGTTCAAAAGTTTAAGGACCAATTTA
Found at i:2411 original size:16 final size:17
Alignment explanation
Indices: 2392--2423 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2382 AATAAATTTC
2392 AATTAAAA-ATATAAAA
1 AATTAAAATATATAAAA
2408 AATTAAAATATATAAA
1 AATTAAAATATATAAA
2424 TATTTAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AATTAAAATATATAAAA
Found at i:4471 original size:24 final size:25
Alignment explanation
Indices: 4411--4495 Score: 72
Period size: 24 Copynumber: 3.5 Consensus size: 25
4401 TCGGGCCGGG
4411 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
4434 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
* * *
4458 T-T-TATTAATATTATATATATATATA
1 TATATATT-ATATTATTTAAAT-TAAA
4483 TATATATATATAT
1 TATATAT-TATAT
4496 ATATATAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
22 4 0.08
23 8 0.16
24 24 0.49
25 4 0.08
26 1 0.02
27 7 0.14
28 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:4476 original size:2 final size:2
Alignment explanation
Indices: 4465--4502 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4455 AAATTTATTA
4465 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4503 ATTATTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4632 original size:24 final size:24
Alignment explanation
Indices: 4600--4655 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
4590 CGTCCCCGTC
4600 CCCGTTTATCATCCCCGAACCCGA
1 CCCGTTTATCATCCCCGAACCCGA
4624 CCCGTTTATCATCCCCGAACCCGA
1 CCCGTTTATCATCCCCGAACCCGA
4648 CCCGTTTA
1 CCCGTTTA
4656 ATTCGGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.20, C:0.45, G:0.12, T:0.23
Consensus pattern (24 bp):
CCCGTTTATCATCCCCGAACCCGA
Found at i:22060 original size:3 final size:3
Alignment explanation
Indices: 22052--22080 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
22042 AAATGAGCAA
22052 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
22081 AAGAGATTGT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:23028 original size:37 final size:36
Alignment explanation
Indices: 22969--23088 Score: 163
Period size: 35 Copynumber: 3.3 Consensus size: 36
22959 ATCTCATTAT
* *
22969 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
23005 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
* *
23041 CA-TTTTCCAGGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
23076 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
23089 TTTGTTACCA
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
35 33 0.45
36 13 0.18
37 27 0.37
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:23044 original size:21 final size:21
Alignment explanation
Indices: 23020--23080 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
23010 TTCAAAGAAA
23020 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
* *
23041 CATTTTCC--A----GGAAA-
1 CATTTACCAAACTTTGAAAAC
23055 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
23076 CATTT
1 CATTT
23081 TTTCAAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 7 0.24
15 4 0.14
16 1 0.03
19 1 0.03
20 4 0.14
21 12 0.41
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:27627 original size:37 final size:36
Alignment explanation
Indices: 27568--27687 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
27558 ATCTCATTAT
* *
27568 CATTTTTC-AACAAACATCTACCAAACTTTGCAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
27604 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
*
27640 CA-TTTTCAAGGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
27675 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
27688 TTGGTTACCA
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
35 34 0.45
36 13 0.17
37 28 0.37
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:27643 original size:21 final size:21
Alignment explanation
Indices: 27619--27679 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
27609 TTCAAAGAAA
27619 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
* *
27640 CATTT-TC-AA----GGAAA-
1 CATTTACCAAACTTTGAAAAC
27654 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
27675 CATTT
1 CATTT
27680 TTTCAAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 5 0.17
15 5 0.17
16 2 0.07
19 2 0.07
20 5 0.17
21 10 0.34
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:32648 original size:18 final size:19
Alignment explanation
Indices: 32608--32649 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
32598 TCAAAAAAAT
32608 TAAAATTAAAATTATTTCA
1 TAAAATTAAAATTATTTCA
32627 -AAAATCTAAAA-TATTT-A
1 TAAAAT-TAAAATTATTTCA
32644 TAAAAT
1 TAAAAT
32650 GTCAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 15 0.71
19 5 0.24
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATTAAAATTATTTCA
Found at i:35566 original size:17 final size:18
Alignment explanation
Indices: 35530--35625 Score: 90
Period size: 18 Copynumber: 5.4 Consensus size: 18
35520 ATGTTTACAA
*
35530 TTATCAAATGATTT-TCAG
1 TTATCAGATGATTTAT-AG
35548 TTATCAGAT-ATTTATAG
1 TTATCAGATGATTTATAG
* *
35565 TTATCAGATGATTTTTAA
1 TTATCAGATGATTTATAG
* *
35583 CTATTAGATG-TTTATAG
1 TTATCAGATGATTTATAG
* * *
35600 TTATAAGATGTTTTACAG
1 TTATCAGATGATTTATAG
35618 TTATCAGA
1 TTATCAGA
35626 CGTAGTTTAA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
17 28 0.44
18 36 0.56
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (18 bp):
TTATCAGATGATTTATAG
Found at i:35569 original size:35 final size:35
Alignment explanation
Indices: 35530--35625 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 35
35520 ATGTTTACAA
35530 TTATCAAATGATTTTCAGTTATCAGATATTTATAG
1 TTATCAAATGATTTTCAGTTATCAGATATTTATAG
* * ** * *
35565 TTATCAGATGATTTTTAACTATTAGATGTTTATAG
1 TTATCAAATGATTTTCAGTTATCAGATATTTATAG
35600 TTAT-AAGATG-TTTTACAGTTATCAGA
1 TTATCAA-ATGATTTT-CAGTTATCAGA
35626 CGTAGTTTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
34 5 0.10
35 43 0.90
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (35 bp):
TTATCAAATGATTTTCAGTTATCAGATATTTATAG
Found at i:38285 original size:10 final size:11
Alignment explanation
Indices: 38257--38297 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
38247 ATTTACTTTA
38257 TATAAATTCTTT
1 TATAAATT-TTT
38269 TATAAATTTTT
1 TATAAATTTTT
*
38280 TA-AAATTTGT
1 TATAAATTTTT
38290 TATAAATT
1 TATAAATT
38298 AGAGAACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.33
11 10 0.37
12 8 0.30
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TATAAATTTTT
Found at i:40431 original size:41 final size:42
Alignment explanation
Indices: 40378--40456 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
40368 CACTACCTTG
*
40378 CGTACTTCAGTGGCCTTT-TATAGAAAACACCGCAATTTCAT
1 CGTACTTCAGTGGCCTTTGTATAAAAAACACCGCAATTTCAT
* * *
40419 CGTACGTT-AGTGGCGTTTGTTTAAAAAACGCCGCAATT
1 CGTAC-TTCAGTGGCCTTTGTATAAAAAACACCGCAATT
40457 GTCCAGTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 14 0.44
42 18 0.56
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (42 bp):
CGTACTTCAGTGGCCTTTGTATAAAAAACACCGCAATTTCAT
Found at i:43690 original size:18 final size:18
Alignment explanation
Indices: 43648--43691 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
43638 TTTTTGCCCT
*
43648 TACTTTTATTAGTTATTA
1 TACTTTTATTAATTATTA
*
43666 TATTTTTATTAATTATTGA
1 TACTTTTATTAATTATT-A
43685 -ACTTTTA
1 TACTTTTA
43692 CTTTTTATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (18 bp):
TACTTTTATTAATTATTA
Found at i:44742 original size:25 final size:24
Alignment explanation
Indices: 44713--44764 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
44703 AAAAATATGT
**
44713 CACAAAAGCAGAGATAAATGTGCAA
1 CACAAAA-CAGAGATAAACATGCAA
*
44738 CAC-AAATAGAGATAAACATGCAA
1 CACAAAACAGAGATAAACATGCAA
44761 CACA
1 CACA
44765 GATAGAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 17 0.74
24 3 0.13
25 3 0.13
ACGTcount: A:0.54, C:0.19, G:0.15, T:0.12
Consensus pattern (24 bp):
CACAAAACAGAGATAAACATGCAA
Found at i:44748 original size:23 final size:23
Alignment explanation
Indices: 44722--44774 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
44712 TCACAAAAGC
**
44722 AGAGATAAATGTGCAACACAAAT
1 AGAGATAAACATGCAACACAAAT
*
44745 AGAGATAAACATGCAACACAGAT
1 AGAGATAAACATGCAACACAAAT
44768 AGA-ATAA
1 AGAGATAA
44775 TTCTTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.55, C:0.13, G:0.17, T:0.15
Consensus pattern (23 bp):
AGAGATAAACATGCAACACAAAT
Found at i:47907 original size:2 final size:2
Alignment explanation
Indices: 47895--47928 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
47885 TTCACACCCT
*
47895 AG AG AG TAG AG AG AG AG AG AG AA AG AG AG AG AG A
1 AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG A
47929 TATGGAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.03
Consensus pattern (2 bp):
AG
Found at i:50948 original size:16 final size:16
Alignment explanation
Indices: 50904--50949 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
50894 AAAAATAATC
*
50904 TCTTATTTTTCTCTTT
1 TCTTATTTTTTTCTTT
* *
50920 TATTATTTCTTTCTTT
1 TCTTATTTTTTTCTTT
*
50936 TCTTTTTTTTTTCT
1 TCTTATTTTTTTCT
50950 CTCCCTCCAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (16 bp):
TCTTATTTTTTTCTTT
Found at i:51522 original size:2 final size:2
Alignment explanation
Indices: 51515--51593 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
51505 TAACAATATC
51515 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
51557 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
51594 ATTTGCTGAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:51875 original size:2 final size:2
Alignment explanation
Indices: 51868--51900 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
51858 ATAAAATCTT
51868 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51901 TGAAGTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52289 original size:29 final size:29
Alignment explanation
Indices: 52245--52319 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
52235 TAACGGAGGT
*
52245 AGGTCGCCATGTACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
52274 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
52303 AGGTCGCCATGCACGCC
1 AGGTCGCCATGCACGCC
52320 ATATACTCAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.20, C:0.43, G:0.28, T:0.09
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:52363 original size:17 final size:18
Alignment explanation
Indices: 52329--52364 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
52319 CATATACTCA
52329 CCATGCAGACGAGCCATAC
1 CCATGCAGAC-AGCCATAC
52348 CCATGCAGAC-GCCATAC
1 CCATGCAGACAGCCATAC
52365 AAGCCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.31, C:0.39, G:0.19, T:0.11
Consensus pattern (18 bp):
CCATGCAGACAGCCATAC
Found at i:52409 original size:28 final size:28
Alignment explanation
Indices: 52378--52433 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
52368 CCATATACTC
52378 ACCATGCAGACGAGCCAGCCAACGGAGA
1 ACCATGCAGACGAGCCAGCCAACGGAGA
52406 ACCATGCAGACGAGCCAGCCAACGGAGA
1 ACCATGCAGACGAGCCAGCCAACGGAGA
52434 GGTCGCCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.32, G:0.29, T:0.04
Consensus pattern (28 bp):
ACCATGCAGACGAGCCAGCCAACGGAGA
Found at i:52447 original size:28 final size:28
Alignment explanation
Indices: 52416--52472 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
52406 ACCATGCAGA
*
52416 CGAGCCAGCCAACGGAGAGGTCGCCATG
1 CGAGCCAGCCAACAGAGAGGTCGCCATG
*
52444 CGAGCCAGCCAATAGAGAGGTCGCCATG
1 CGAGCCAGCCAACAGAGAGGTCGCCATG
52472 C
1 C
52473 AGTCTGGGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.32, G:0.33, T:0.09
Consensus pattern (28 bp):
CGAGCCAGCCAACAGAGAGGTCGCCATG
Found at i:52505 original size:29 final size:29
Alignment explanation
Indices: 52461--52555 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
52451 GCCAATAGAG
* **
52461 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
52490 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
52519 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
52548 AGGTCGCC
1 AGGTCGCC
52556 CCCTGCGAAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:52588 original size:19 final size:19
Alignment explanation
Indices: 52564--52600 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
52554 CCCCCTGCGA
52564 ACCATGCATGCACCAGCCG
1 ACCATGCATGCACCAGCCG
52583 ACCATGCATGCACCAGCC
1 ACCATGCATGCACCAGCC
52601 AAATAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.43, G:0.19, T:0.11
Consensus pattern (19 bp):
ACCATGCATGCACCAGCCG
Found at i:52660 original size:49 final size:48
Alignment explanation
Indices: 52598--52698 Score: 168
Period size: 49 Copynumber: 2.1 Consensus size: 48
52588 GCATGCACCA
*
52598 GCCAAATAACTTCACGTGCTCCTGCT-CCCGCTGCATGCCTGCATGCAT
1 GCCAAATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACA-GCAT
52646 GCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACAGCAT
1 GCCAA-ATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACAGCAT
52695 GCCA
1 GCCA
52699 TGTGATCCTA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
48 5 0.10
49 29 0.58
50 16 0.32
ACGTcount: A:0.20, C:0.39, G:0.19, T:0.23
Consensus pattern (48 bp):
GCCAAATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACAGCAT
Found at i:52930 original size:16 final size:18
Alignment explanation
Indices: 52909--52947 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
52899 GGAGATAAGG
*
52909 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
52925 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
52943 TAAAT
1 TAAAT
52948 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:53091 original size:46 final size:47
Alignment explanation
Indices: 53052--53141 Score: 125
Period size: 45 Copynumber: 2.0 Consensus size: 47
53042 TTATATAGTT
53052 AAAAA-TAATTAATTAGTTTGTT-TT-GTT-AATAGTTAGTTATATAA
1 AAAAATTAATTAATTAGTTT-TTGTTAGTTAAATAGTTAGTTATATAA
*
53096 AAAAATTATTTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTAATTAATTAGTTTTTGTTAGTTAAATAGTT-AGTTATAT
53142 TTGTTTGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
44 7 0.17
45 15 0.38
46 3 0.08
47 7 0.17
48 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (47 bp):
AAAAATTAATTAATTAGTTTTTGTTAGTTAAATAGTTAGTTATATAA
Found at i:53187 original size:12 final size:12
Alignment explanation
Indices: 53170--53222 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
53160 TTATATAAAA
53170 ATTAGTTAGTTT
1 ATTAGTTAGTTT
53182 ATTAGTTAGTTTT
1 ATTAGTTAG-TTT
*
53195 AGTTAGTAAGTTT
1 A-TTAGTTAGTTT
*
53208 ATTAG-TAGTAT
1 ATTAGTTAGTTT
53219 ATTA
1 ATTA
53223 TAATGAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 8 0.22
12 13 0.36
13 8 0.22
14 7 0.19
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (12 bp):
ATTAGTTAGTTT
Found at i:53239 original size:32 final size:32
Alignment explanation
Indices: 53203--53278 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
53193 TTAGTTAGTA
53203 AGTTTATTAGTAG-TATA-TTATAATGAAAAAAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAAAT
*
53235 AGTTTATTAGTTAGTTTTAGTTATATAAAAAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAAAT
*
53268 ATTTTATTAGT
1 AGTTTATTAGT
53279 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.28
33 19 0.49
34 5 0.13
35 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (32 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAAAT
Found at i:55537 original size:17 final size:17
Alignment explanation
Indices: 55515--55547 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
55505 CAATGATGTT
55515 TAGTATCAAATAATTAC
1 TAGTATCAAATAATTAC
55532 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
55548 GTATTAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:55551 original size:14 final size:14
Alignment explanation
Indices: 55514--55564 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
55504 ACAATGATGT
55514 TTAGTATCAAATAA
1 TTAGTATCAAATAA
55528 TTACTAGTATCAAATAA
1 -T--TAGTATCAAATAA
* *
55545 TTAGTATTAAATCA
1 TTAGTATCAAATAA
55559 TTAGTA
1 TTAGTA
55565 ATAATTAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 17 0.53
15 1 0.03
16 1 0.03
17 13 0.41
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (14 bp):
TTAGTATCAAATAA
Found at i:55566 original size:21 final size:21
Alignment explanation
Indices: 55542--55585 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
55532 TAGTATCAAA
* *
55542 TAATTAGTATTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
*
55563 TAATAATTAGTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
55584 TA
1 TA
55586 TCAAATCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (21 bp):
TAATAAGTAGTAAATCATTAG
Found at i:55584 original size:11 final size:11
Alignment explanation
Indices: 55552--55585 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
55542 TAATTAGTAT
55552 TAAATCATTAG
1 TAAATCATTAG
*
55563 T-AATAATTAG
1 TAAATCATTAG
55573 TAAATCATTAG
1 TAAATCATTAG
55584 TA
1 TA
55586 TCAAATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (11 bp):
TAAATCATTAG
Found at i:55593 original size:14 final size:13
Alignment explanation
Indices: 55532--55596 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
55522 AAATAATTAC
*
55532 TAGTATCAAATAAT
1 TAGTAT-AAATCAT
55546 TAGTATTAAATCAT
1 TAGTA-TAAATCAT
*
55560 TAG--T-AATAAT
1 TAGTATAAATCAT
55570 TAG--TAAATCAT
1 TAGTATAAATCAT
55581 TAGTATCAAATCAT
1 TAGTAT-AAATCAT
55595 TA
1 TA
55597 AATATTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
10 9 0.21
11 9 0.21
13 1 0.02
14 23 0.53
15 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TAGTATAAATCAT
Found at i:55715 original size:7 final size:7
Alignment explanation
Indices: 55703--55729 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
55693 TATTACTAAA
55703 TCATTGT
1 TCATTGT
55710 TCATTGT
1 TCATTGT
55717 TCATTGT
1 TCATTGT
55724 TCATTG
1 TCATTG
55730 AACCAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (7 bp):
TCATTGT
Found at i:55821 original size:14 final size:14
Alignment explanation
Indices: 55802--55849 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
55792 TTCAAGTCGT
55802 AAATCATTACTATC
1 AAATCATTACTATC
55816 AAATCATTAC--T-
1 AAATCATTACTATC
*
55827 AAATCATTAATATC
1 AAATCATTACTATC
55841 AAATCATTA
1 AAATCATTA
55850 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:55883 original size:48 final size:48
Alignment explanation
Indices: 55821--55931 Score: 179
Period size: 48 Copynumber: 2.3 Consensus size: 48
55811 CTATCAAATC
55821 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATT
1 ATTACT-AATCATTAATATCAAATCATTAAA-ATTAATAATAAATTCATT
* *
55870 ATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATCATTAAAATTAATAATAAATTCATT
55918 ATTACTAATCATTA
1 ATTACTAATCATTA
55932 CTAAATCATT
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
47 13 0.22
48 40 0.68
49 6 0.10
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (48 bp):
ATTACTAATCATTAATATCAAATCATTAAAATTAATAATAAATTCATT
Found at i:55942 original size:21 final size:21
Alignment explanation
Indices: 55918--56005 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 21
55908 TAATTTCATT
55918 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
* * *
55939 ATTACT-ATCA-AATCATACATA
1 ATTACTAATCATTA-C-TAAATC
* * * *
55960 ATTAATAATAATT--T-CATT
1 ATTACTAATCATTACTAAATC
55978 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
55999 ATTACTA
1 ATTACTA
56006 TCAAATCATT
Statistics
Matches: 49, Mismatches: 11, Indels: 14
0.66 0.15 0.19
Matches are distributed among these distances:
18 14 0.29
19 2 0.04
20 6 0.12
21 24 0.49
22 3 0.06
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:55978 original size:60 final size:59
Alignment explanation
Indices: 55870--56057 Score: 335
Period size: 59 Copynumber: 3.2 Consensus size: 59
55860 ATAAATTATT
55870 ATTACT-AATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATC
55928 ATTACTAAATCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTA-A-AATTAATAATAATTTCATTATTACTAATC
*
55988 ATTACTAAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATCATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATC
56047 ATTACTAAATC
1 ATTACTAAATC
56058 TTATAAATAC
Statistics
Matches: 125, Mismatches: 1, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
58 8 0.06
59 59 0.47
60 56 0.45
61 2 0.02
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (59 bp):
ATTACTAAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATC
Found at i:59172 original size:28 final size:28
Alignment explanation
Indices: 59105--59165 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
59095 AATTTTTATA
* *
59105 TAATCTAATATAACTTAAACTAACAAAT
1 TAATATAATATAACTTAAACTAACAAAC
59133 TAATATAATATAACTTAAACTAACAAAC
1 TAATATAATATAACTTAAACTAACAAAC
59161 TAATA
1 TAATA
59166 ATTTATACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (28 bp):
TAATATAATATAACTTAAACTAACAAAC
Found at i:59175 original size:21 final size:21
Alignment explanation
Indices: 59142--59190 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
59132 TTAATATAAT
59142 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
59163 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
59184 ATTAACT
1 A-TAACT
59191 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:59844 original size:30 final size:30
Alignment explanation
Indices: 59801--59903 Score: 161
Period size: 30 Copynumber: 3.4 Consensus size: 30
59791 TTTGGCGAGC
*
59801 TGGGCGTGTATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
* * *
59831 TGGCCGTGCATGGAGGTCGTTGGACGTGCC
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
*
59861 TGGGCATGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
59891 TGGGCGTGCATGG
1 TGGGCGTGCATGG
59904 GCGTGCATGG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.11, C:0.17, G:0.48, T:0.24
Consensus pattern (30 bp):
TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
Found at i:59874 original size:20 final size:20
Alignment explanation
Indices: 59821--59914 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
59811 TGGAGGTCGT
*
59821 TGGGCGTGCATGGCCGTGCA
1 TGGGCGTGCATGGACGTGCA
* *
59841 TGGAG-GT-CGTTGGACGTGCC
1 TGG-GCGTGC-ATGGACGTGCA
* * *
59861 TGGGCATGCATGGAGGT-CGT
1 TGGGCGTGCATGGACGTGC-A
*
59881 TGGGCGTGCATGGGCGTGCA
1 TGGGCGTGCATGGACGTGCA
59901 TGGGCGTGCATGGA
1 TGGGCGTGCATGGA
59915 GGTCGTGGGG
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
19 3 0.05
20 50 0.89
21 3 0.05
ACGTcount: A:0.12, C:0.19, G:0.47, T:0.22
Consensus pattern (20 bp):
TGGGCGTGCATGGACGTGCA
Found at i:59896 original size:10 final size:10
Alignment explanation
Indices: 59881--59913 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
59871 TGGAGGTCGT
59881 TGGGCGTGCA
1 TGGGCGTGCA
59891 TGGGCGTGCA
1 TGGGCGTGCA
59901 TGGGCGTGCA
1 TGGGCGTGCA
59911 TGG
1 TGG
59914 AGGTCGTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.52, T:0.21
Consensus pattern (10 bp):
TGGGCGTGCA
Found at i:59996 original size:57 final size:58
Alignment explanation
Indices: 59927--60037 Score: 197
Period size: 57 Copynumber: 1.9 Consensus size: 58
59917 TCGTGGGGTA
*
59927 GGTCGCAGGGCGTGCATGGCGACCTGGTTGGTCGCC-GGCGTGCATGGCGACCTGGTT
1 GGTCGCAGGGCGTGCATGGCGACCTGGTTGGTCGCCGGGCGTACATGGCGACCTGGTT
*
59984 GGTCGCCGGGCGTGCATGGCGACCTGGTTGGTCGCCGGGCGTACATGGCGACCT
1 GGTCGCAGGGCGTGCATGGCGACCTGGTTGGTCGCCGGGCGTACATGGCGACCT
60038 ACCTCCGTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
57 35 0.69
58 16 0.31
ACGTcount: A:0.09, C:0.28, G:0.43, T:0.20
Consensus pattern (58 bp):
GGTCGCAGGGCGTGCATGGCGACCTGGTTGGTCGCCGGGCGTACATGGCGACCTGGTT
Found at i:60005 original size:29 final size:29
Alignment explanation
Indices: 59927--60037 Score: 197
Period size: 29 Copynumber: 3.9 Consensus size: 29
59917 TCGTGGGGTA
*
59927 GGTCGCAGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
59956 GGTCGCC-GGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
59984 GGTCGCCGGGCGTGCATGGCGACCTGGTT
1 GGTCGCCGGGCGTGCATGGCGACCTGGTT
*
60013 GGTCGCCGGGCGTACATGGCGACCT
1 GGTCGCCGGGCGTGCATGGCGACCT
60038 ACCTCCGTTA
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
28 28 0.35
29 51 0.65
ACGTcount: A:0.09, C:0.28, G:0.43, T:0.20
Consensus pattern (29 bp):
GGTCGCCGGGCGTGCATGGCGACCTGGTT
Found at i:60298 original size:29 final size:29
Alignment explanation
Indices: 60254--60365 Score: 206
Period size: 29 Copynumber: 3.9 Consensus size: 29
60244 TAACGGAGGT
*
60254 AGGTCGCCATGTACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
60283 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
60312 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
*
60341 AGGTCGCCATGCACGCCCTGCGACC
1 AGGTCGCCATGCACGCCCGGCGACC
60366 TACCCCACGA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.20, C:0.44, G:0.28, T:0.09
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:60394 original size:10 final size:10
Alignment explanation
Indices: 60379--60471 Score: 68
Period size: 10 Copynumber: 9.3 Consensus size: 10
60369 CCCACGACCT
60379 CCATGCACGC
1 CCATGCACGC
60389 CCATGCACGC
1 CCATGCACGC
60399 CCATGCACGC
1 CCATGCACGC
*
60409 CCA-ACGAC-C
1 CCATGC-ACGC
*
60418 TCCATGCATGC
1 -CCATGCACGC
* *
60429 CCAGGCACGT
1 CCATGCACGC
*
60439 CCA-ACGAC-C
1 CCATGC-ACGC
*
60448 TCCATGCACGG
1 -CCATGCACGC
60459 CCATGCACGC
1 CCATGCACGC
60469 CCA
1 CCA
60472 ACGACCTCCA
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
9 3 0.05
10 58 0.91
11 3 0.05
ACGTcount: A:0.23, C:0.47, G:0.19, T:0.11
Consensus pattern (10 bp):
CCATGCACGC
Found at i:60423 original size:30 final size:30
Alignment explanation
Indices: 60389--60491 Score: 161
Period size: 30 Copynumber: 3.4 Consensus size: 30
60379 CCATGCACGC
60389 CCATGCACGCCCATGCACGCCCAACGACCT
1 CCATGCACGCCCATGCACGCCCAACGACCT
* * *
60419 CCATGCATGCCCAGGCACGTCCAACGACCT
1 CCATGCACGCCCATGCACGCCCAACGACCT
*
60449 CCATGCACGGCCATGCACGCCCAACGACCT
1 CCATGCACGCCCATGCACGCCCAACGACCT
*
60479 CCATACACGCCCA
1 CCATGCACGCCCA
60492 GCTCGCCAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.24, C:0.48, G:0.17, T:0.11
Consensus pattern (30 bp):
CCATGCACGCCCATGCACGCCCAACGACCT
Found at i:61133 original size:21 final size:21
Alignment explanation
Indices: 61108--61151 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
61098 AATTTAGTTA
61108 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
61129 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
61150 AT
1 AT
61152 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:61165 original size:28 final size:28
Alignment explanation
Indices: 61128--61181 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
61118 TAGTATAAAT
*
61128 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
61156 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
61182 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:64295 original size:25 final size:25
Alignment explanation
Indices: 64267--64354 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
64257 ATTAATTTTT
64267 ATGATTTGATAGTAATGATTTAGTA
1 ATGATTTGATAGTAATGATTTAGTA
* * *
64292 ATGATTAG-TAATAATGAAATTATTAATTA
1 ATGATTTGATAGTAATG--A-T-TT-AGTA
64321 TGTATGATTTGATAGTAATGATTTAGTA
1 ---ATGATTTGATAGTAATGATTTAGTA
64349 ATGATT
1 ATGATT
64355 AGTAATAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
24 7 0.15
25 13 0.27
26 1 0.02
27 1 0.02
28 5 0.10
29 5 0.10
30 1 0.02
31 1 0.02
32 7 0.15
33 7 0.15
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (25 bp):
ATGATTTGATAGTAATGATTTAGTA
Found at i:64301 original size:10 final size:11
Alignment explanation
Indices: 64276--64360 Score: 50
Period size: 11 Copynumber: 7.6 Consensus size: 11
64266 TATGATTTGA
64276 TAGTAATGATT
1 TAGTAATGATT
64287 TAGTAATGA-T
1 TAGTAATGATT
* *
64297 TAGTAATAATG
1 TAGTAATGATT
* * * * *
64308 AAATTATTAAT
1 TAGTAATGATT
64319 TATGT-ATGATTT
1 TA-GTAATGA-TT
64331 GATAGTAATGATT
1 --TAGTAATGATT
64344 TAGTAATGA-T
1 TAGTAATGATT
64354 TAGTAAT
1 TAGTAAT
64361 AATGAATTAT
Statistics
Matches: 56, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
10 17 0.30
11 27 0.48
12 2 0.04
13 4 0.07
14 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:64348 original size:57 final size:56
Alignment explanation
Indices: 64225--64458 Score: 292
Period size: 57 Copynumber: 4.3 Consensus size: 56
64215 GTATTTATAA
*
64225 GATTTAGTAATGATTAGTAATGATGAATTATTATTAATTTTTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAA--ATTATTAATTTTTATGATTTGATAGTAAT
*
64283 GATTTAGTAATGATTAGTAATAATGAAATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTAATT-TTTATGATTTGATAGTAAT
*
64340 GATTTAGTAATGATTAGTAATAATGAATTATATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAAT-TATTAATTTTT-ATGATTTGATAGTAAT
* *
64398 GA-TTAGTAAT-A--A-TAAT--T--TATTATTAATATTTAATGA-TTGATA-TAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTAAT-TTTTATGATTTGATAGTAAT
64444 GATTTAGTAATGATT
1 GATTTAGTAATGATT
64459 TGATAGTAAT
Statistics
Matches: 161, Mismatches: 7, Indels: 24
0.84 0.04 0.12
Matches are distributed among these distances:
46 6 0.04
47 14 0.09
48 12 0.07
49 4 0.02
51 1 0.01
53 4 0.02
54 1 0.01
56 11 0.07
57 56 0.35
58 52 0.32
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (56 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTAATTTTTATGATTTGATAGTAAT
Found at i:64395 original size:47 final size:47
Alignment explanation
Indices: 64336--64454 Score: 167
Period size: 47 Copynumber: 2.6 Consensus size: 47
64326 GATTTGATAG
*
64336 TAATGATT--TAGTAATGATTAGTAATAATGAA-TTA-TATTAATTTT
1 TAATGATTGATAGTAATGATTAGTAATAAT-AATTTATTATTAATATT
64380 TAATGATTTGATAGTAATGATTAGTAATAATAATTTATTATTAATATT
1 TAATGA-TTGATAGTAATGATTAGTAATAATAATTTATTATTAATATT
64428 TAATGATTGATA-TAATGATTTAGTAAT
1 TAATGATTGATAGTAATGA-TTAGTAAT
64455 GATTTGATAG
Statistics
Matches: 68, Mismatches: 1, Indels: 9
0.87 0.01 0.12
Matches are distributed among these distances:
44 6 0.09
45 2 0.03
46 8 0.12
47 37 0.54
48 15 0.22
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (47 bp):
TAATGATTGATAGTAATGATTAGTAATAATAATTTATTATTAATATT
Found at i:64414 original size:37 final size:36
Alignment explanation
Indices: 64368--64472 Score: 85
Period size: 37 Copynumber: 2.9 Consensus size: 36
64358 AATAATGAAT
*
64368 TATATTAATTTTTAATGATTTGATAGTAATGATT-A
1 TATAATAATTTTTAATGATTTGATAGTAATGATTGA
* * *
64403 GTAATAATAA--TTT-ATTA-TTAATATTTAATGATTGA
1 -T-ATAATAATTTTTAATGATTTGATA-GTAATGATTGA
* *
64438 TATAATGATTTAGTAATGATTTGATAGTAATGATT
1 TATAATAATTT-TTAATGATTTGATAGTAATGATT
64473 TACGACTTGA
Statistics
Matches: 52, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
33 11 0.21
34 12 0.23
35 5 0.10
36 2 0.04
37 17 0.33
38 5 0.10
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (36 bp):
TATAATAATTTTTAATGATTTGATAGTAATGATTGA
Found at i:64452 original size:115 final size:112
Alignment explanation
Indices: 64212--64459 Score: 297
Period size: 115 Copynumber: 2.2 Consensus size: 112
64202 TATGAATTTC
*
64212 TATGTATTTA-TAA-GATTTAGTAATGATTAGTAATGATGAATTATTATTAATTTTTATGATTTG
1 TATG-ATTTAGTAATGATTTAGTAATGATTAGTAATAATGAATTATTATTAATTTTTATGATTTG
* * * *
64275 ATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTAATTATG
65 ATAGTAATGATTTAGTAATAATAAGTAATAATGAAATTAATAATTATA
64323 TATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAATTA-TATTAATTTTTAATGAT
1 TATGA-TT--TAGTAATGATTTAGTAATGATTAGTAATAATGAATTATTATTAATTTTT-ATGAT
* * * * *
64387 TTGATAGTAATGA-TTAGTAATAATAATTTATTATTAATATTTAATGATTGATA
62 TTGATAGTAATGATTTAGTAATAATAAGTAATAATGAA-A-TTAATAATT-ATA
64440 TAATGATTTAGTAATGATTT
1 T-ATGATTTAGTAATGATTT
64460 GATAGTAATG
Statistics
Matches: 117, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
110 1 0.01
111 6 0.05
113 2 0.02
114 32 0.27
115 60 0.51
116 7 0.06
117 5 0.04
118 4 0.03
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (112 bp):
TATGATTTAGTAATGATTTAGTAATGATTAGTAATAATGAATTATTATTAATTTTTATGATTTGA
TAGTAATGATTTAGTAATAATAAGTAATAATGAAATTAATAATTATA
Found at i:64473 original size:14 final size:13
Alignment explanation
Indices: 64428--64472 Score: 60
Period size: 12 Copynumber: 3.6 Consensus size: 13
64418 TATTAATATT
64428 TAATGATTGATA-
1 TAATGATTGATAG
64440 TAATGATT--TAG
1 TAATGATTGATAG
64451 TAATGATTTGATAG
1 TAATGA-TTGATAG
64465 TAATGATT
1 TAATGATT
64473 TACGACTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.07
11 6 0.21
12 10 0.34
13 2 0.07
14 9 0.31
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (13 bp):
TAATGATTGATAG
Found at i:64489 original size:104 final size:104
Alignment explanation
Indices: 64287--64489 Score: 229
Period size: 104 Copynumber: 2.0 Consensus size: 104
64277 AGTAATGATT
64287 TAGTAATGATTAGTAATAATGAAATTATTAATTATGTATGATTTGATAGTAATGATTTAGTAATG
1 TAGTAATGATTAGTAATAATGAAATTATTAATTATGTATGATTTGATAGTAATGATTTAGTAATG
** ***
64352 ATTAGTAATAATGAATTATATTAATTTTTAATGATTTGA
66 ATTAGTAATAATGAATTATACGAATTAACAATGATTTGA
*
64391 TAGTAATGATTAGTAATAAT-AATTTATTATTAA-TATTTAATGA-TTGATA-TAATGATTTAGT
1 TAGTAATGATTAGTAATAATGAA---ATTATTAATTATGT-ATGATTTGATAGTAATGATTTAGT
* * *
64452 AATGATTTGATAGTAATG-ATT-TACGACTTGAACAATGA
62 AATGATTAG-TAATAATGAATTATACGAATT-AACAATGA
64490 ACATGTTTGG
Statistics
Matches: 84, Mismatches: 9, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
103 7 0.08
104 48 0.57
105 17 0.20
106 12 0.14
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.44
Consensus pattern (104 bp):
TAGTAATGATTAGTAATAATGAAATTATTAATTATGTATGATTTGATAGTAATGATTTAGTAATG
ATTAGTAATAATGAATTATACGAATTAACAATGATTTGA
Found at i:64609 original size:11 final size:11
Alignment explanation
Indices: 64577--64615 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
64567 AATGATTTAG
*
64577 TAATAATCATT
1 TAATAATGATT
*
64588 ATAAAAATGATT
1 -TAATAATGATT
64600 TAATAATGATT
1 TAATAATGATT
64611 TAATA
1 TAATA
64616 TTTAATGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (11 bp):
TAATAATGATT
Found at i:64745 original size:17 final size:17
Alignment explanation
Indices: 64723--64755 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
64713 TGATTAATAC
64723 TAATTATTTGATACTAG
1 TAATTATTTGATACTAG
64740 TAATTATTTGATACTA
1 TAATTATTTGATACTA
64756 AACATCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (17 bp):
TAATTATTTGATACTAG
Found at i:66666 original size:26 final size:27
Alignment explanation
Indices: 66623--66678 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
66613 TACTACAATT
* *
66623 AAATATTTCAAAAAATTATCACAATCA
1 AAATAATTCAAAAAATTATAACAATCA
* *
66650 AAATAATTC-AAAGATTATAATAATCA
1 AAATAATTCAAAAAATTATAACAATCA
66676 AAA
1 AAA
66679 AAATATTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.29
Consensus pattern (27 bp):
AAATAATTCAAAAAATTATAACAATCA
Found at i:67130 original size:42 final size:41
Alignment explanation
Indices: 67040--67117 Score: 99
Period size: 39 Copynumber: 1.9 Consensus size: 41
67030 AAACAAAACT
67040 TAACTATTTAACTAACAAAAACGAATAAATAATTTTTTATAA
1 TAACTA-TTAACTAACAAAAACGAATAAATAATTTTTTATAA
* *
67082 TAACTATTAAC-AA-AACAAACTAAT-AATTATTTTTTA
1 TAACTATTAACTAACAA-AAACGAATAAATAATTTTTTA
67118 ACTATATAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
39 13 0.39
40 9 0.27
41 5 0.15
42 6 0.18
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.37
Consensus pattern (41 bp):
TAACTATTAACTAACAAAAACGAATAAATAATTTTTTATAA
Done.