Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005251.1 Hibiscus syriacus cultivar Beakdansim tig00011875_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: 69827
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:16459 original size:30 final size:29
Alignment explanation
Indices: 16425--16487 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
16415 ATCATTATCA
16425 TTAACCCATTT-AAAGCATGTCATCTTGTAC
1 TTAACCC-TTTGAAA-CATGTCATCTTGTAC
* *
16455 TTAA-CCTTTGTAATATGTCATCTTGTAC
1 TTAACCCTTTGAAACATGTCATCTTGTAC
16483 TTAAC
1 TTAAC
16488 ATTTGTAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 21 0.72
29 4 0.14
30 4 0.14
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.41
Consensus pattern (29 bp):
TTAACCCTTTGAAACATGTCATCTTGTAC
Found at i:16472 original size:28 final size:28
Alignment explanation
Indices: 16441--16495 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
16431 CATTTAAAGC
*
16441 ATGTCATCTTGTACTTAACCTTTGTAAT
1 ATGTCATCTTGTACTTAACATTTGTAAT
16469 ATGTCATCTTGTACTTAACATTTGTAA
1 ATGTCATCTTGTACTTAACATTTGTAA
16496 CATATCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (28 bp):
ATGTCATCTTGTACTTAACATTTGTAAT
Found at i:16503 original size:28 final size:28
Alignment explanation
Indices: 16444--16503 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
16434 TTAAAGCATG
* * *
16444 TCATCTTGTACTTAACCTTTGTAATATG
1 TCATCTTGTACTTAACATTTGTAACATA
16472 TCATCTTGTACTTAACATTTGTAACATA
1 TCATCTTGTACTTAACATTTGTAACATA
16500 TCAT
1 TCAT
16504 ATAATACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.45
Consensus pattern (28 bp):
TCATCTTGTACTTAACATTTGTAACATA
Found at i:16600 original size:30 final size:29
Alignment explanation
Indices: 16566--16628 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
16556 ATCATTATCA
16566 TTAACCCATTTAAAACATGTCATCTTGTAC
1 TTAACCC-TTTAAAACATGTCATCTTGTAC
** *
16596 TTAA-CCTTTGTAATATGTCATCTTGTAC
1 TTAACCCTTTAAAACATGTCATCTTGTAC
16624 TTAAC
1 TTAAC
16629 ATTTGTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 23 0.79
29 2 0.07
30 4 0.14
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (29 bp):
TTAACCCTTTAAAACATGTCATCTTGTAC
Found at i:16644 original size:28 final size:28
Alignment explanation
Indices: 16579--16644 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
16569 ACCCATTTAA
*
16579 AACATGTCATCTTGTACTTAACCTTTGT
1 AACATGTCATCTTGTACTTAACATTTGT
*
16607 AATATGTCATCTTGTACTTAACATTTGT
1 AACATGTCATCTTGTACTTAACATTTGT
*
16635 AACATATCAT
1 AACATGTCAT
16645 ATAATACATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (28 bp):
AACATGTCATCTTGTACTTAACATTTGT
Found at i:16646 original size:141 final size:141
Alignment explanation
Indices: 16392--16672 Score: 553
Period size: 141 Copynumber: 2.0 Consensus size: 141
16382 ATTATGAACA
*
16392 TCAACATCATTATCATGATCTCTATCATTATCATTAACCCATTTAAAGCATGTCATCTTGTACTT
1 TCAACATCATTATCATGATCTCTATCATTATCATTAACCCATTTAAAACATGTCATCTTGTACTT
16457 AACCTTTGTAATATGTCATCTTGTACTTAACATTTGTAACATATCATATAATACATTTCACCAAG
66 AACCTTTGTAATATGTCATCTTGTACTTAACATTTGTAACATATCATATAATACATTTCACCAAG
16522 CAATATACACT
131 CAATATACACT
16533 TCAACATCATTATCATGATCTCTATCATTATCATTAACCCATTTAAAACATGTCATCTTGTACTT
1 TCAACATCATTATCATGATCTCTATCATTATCATTAACCCATTTAAAACATGTCATCTTGTACTT
16598 AACCTTTGTAATATGTCATCTTGTACTTAACATTTGTAACATATCATATAATACATTTCACCAAG
66 AACCTTTGTAATATGTCATCTTGTACTTAACATTTGTAACATATCATATAATACATTTCACCAAG
16663 CAATATACAC
131 CAATATACAC
16673 AGTATCACAT
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 139 1.00
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (141 bp):
TCAACATCATTATCATGATCTCTATCATTATCATTAACCCATTTAAAACATGTCATCTTGTACTT
AACCTTTGTAATATGTCATCTTGTACTTAACATTTGTAACATATCATATAATACATTTCACCAAG
CAATATACACT
Found at i:16934 original size:42 final size:42
Alignment explanation
Indices: 16875--16988 Score: 151
Period size: 42 Copynumber: 2.7 Consensus size: 42
16865 TATAAAATTA
*
16875 TCCCGAATGACCTCGTATATGTCCTGAAAGACAACT-TATATG
1 TCCCGAATGACCTCGTATATGTCCCGAAAGACAA-TATATATG
* * *
16917 TCCCGAA-GAACCTCGTATATGTCCCGAAGGACGATATGTATG
1 TCCCGAATG-ACCTCGTATATGTCCCGAAAGACAATATATATG
*
16959 TCCCGAATGACCTCGTATATGTCCCAAAAG
1 TCCCGAATGACCTCGTATATGTCCCGAAAG
16989 GCTACTCCTT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
41 2 0.03
42 60 0.95
43 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
TCCCGAATGACCTCGTATATGTCCCGAAAGACAATATATATG
Found at i:16935 original size:21 final size:20
Alignment explanation
Indices: 16875--16983 Score: 94
Period size: 21 Copynumber: 5.2 Consensus size: 20
16865 TATAAAATTA
16875 TCCCGAATGACCTCGTATATG
1 TCCCGAA-GACCTCGTATATG
* ** *
16896 TCCTGAAAGACAACTTATATG
1 TCCCG-AAGACCTCGTATATG
16917 TCCCGAAGAACCTCGTATATG
1 TCCCGAAG-ACCTCGTATATG
* * *
16938 TCCCGAAGGACGAT-ATGTATG
1 TCCCGAA-GAC-CTCGTATATG
16959 TCCCGAATGACCTCGTATATG
1 TCCCGAA-GACCTCGTATATG
16980 TCCC
1 TCCC
16984 AAAAGGCTAC
Statistics
Matches: 68, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
20 4 0.06
21 60 0.88
22 4 0.06
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (20 bp):
TCCCGAAGACCTCGTATATG
Found at i:17093 original size:21 final size:21
Alignment explanation
Indices: 17005--17094 Score: 63
Period size: 21 Copynumber: 4.3 Consensus size: 21
16995 CCTTAATGAT
*
17005 CACATATATATTCCAAAGGAC
1 CACATATATATCCCAAAGGAC
* * * ** *
17026 CAAATATGTGTCCTGAAGAAC
1 CACATATATATCCCAAAGGAC
* * * *
17047 CTCATATATGTTCCAAAGGAT
1 CACATATATATCCCAAAGGAC
* *
17068 TACATATATATCCCGAAGGAC
1 CACATATATATCCCAAAGGAC
17089 CACATA
1 CACATA
17095 GAACCCTTGA
Statistics
Matches: 47, Mismatches: 22, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (21 bp):
CACATATATATCCCAAAGGAC
Found at i:18582 original size:21 final size:21
Alignment explanation
Indices: 18528--18590 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
18518 TCTCCTAAAG
18528 GACCTCGTATATGTCCCGAAA
1 GACCTCGTATATGTCCCGAAA
** * * *
18549 GACGACATGTATGTCTCGAAA
1 GACCTCGTATATGTCCCGAAA
18570 GACCTCGTATATGTCCC-AAA
1 GACCTCGTATATGTCCCGAAA
18590 G
1 G
18591 GACCACTCCT
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (21 bp):
GACCTCGTATATGTCCCGAAA
Found at i:18594 original size:21 final size:20
Alignment explanation
Indices: 18514--18590 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 20
18504 AATGACAACT
* *
18514 TATATCTCCTAAAGGACCTCG
1 TATATGTCCCAAA-GACCTCG
** *
18535 TATATGTCCCGAAAGACGACA
1 TATATGTCCC-AAAGACCTCG
* *
18556 TGTATGTCTCGAAAGACCTCG
1 TATATGTC-CCAAAGACCTCG
18577 TATATGTCCCAAAG
1 TATATGTCCCAAAG
18591 GACCACTCCT
Statistics
Matches: 42, Mismatches: 12, Indels: 5
0.71 0.20 0.08
Matches are distributed among these distances:
20 5 0.12
21 33 0.79
22 4 0.10
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (20 bp):
TATATGTCCCAAAGACCTCG
Found at i:18689 original size:21 final size:21
Alignment explanation
Indices: 18616--18690 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
18606 ATCACTTCCA
* *
18616 AAGGACCAAATATGTGTCCCG
1 AAGGACCACATATATGTCCCG
* * * *
18637 AAGAACCGCATATATGTTCCA
1 AAGGACCACATATATGTCCCG
** *
18658 AAGGATTACATATATATCCCG
1 AAGGACCACATATATGTCCCG
18679 AAGGACCACATA
1 AAGGACCACATA
18691 GAACCATCGA
Statistics
Matches: 39, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (21 bp):
AAGGACCACATATATGTCCCG
Found at i:18905 original size:20 final size:20
Alignment explanation
Indices: 18868--18906 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18858 GTCATATAAC
* *
18868 TCATATCACATAGGTTCATA
1 TCATATAACATAGATTCATA
*
18888 TCATATAACATATATTCAT
1 TCATATAACATAGATTCAT
18907 GTAGTTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (20 bp):
TCATATAACATAGATTCATA
Found at i:21665 original size:2 final size:2
Alignment explanation
Indices: 21658--21696 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
21648 TATGGAGTTA
21658 AT AT AT 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
21697 GACTATATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25481 original size:23 final size:22
Alignment explanation
Indices: 25451--25532 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
25441 GCATGGCCTT
25451 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
25473 AGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
25495 GTGTATCGATACACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
*
25518 GATACATCGATGCAC
1 G-TGCATCGATGCAC
25533 TGTTAAGTGT
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
21 14 0.31
22 2 0.04
23 19 0.42
24 10 0.22
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:31446 original size:463 final size:461
Alignment explanation
Indices: 30596--31512 Score: 1334
Period size: 463 Copynumber: 2.0 Consensus size: 461
30586 ATACCAATTA
*
30596 TTGAGTTAATCGATCGACGAATATAGCCAAGAGGGGGGTGAATTAGTAATTAAAATTTTGGTGGA
1 TTGAGTTAAACGATCGACGAATATAGCCAAGAGGGGGGTGAATTAGTAATTAAAATTTTGGTGGA
*
30661 AGCTTTTGCAGAAAATTGAAAGTAATTACACAGCGATTTTGAGTGGTTCGACTTTCTCAACCAAA
66 AGCTTTTGCAGAAAATTGAAAGTAATTACACAGCGATTTAGAGTGGTTCGACTTTCTCAACCAAA
*
30726 GTCTACGTACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTT
131 GTCTACGCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTT
*
30791 TTGAGGAAAAATAGTAACCTTATAAATCCCTCAAGAATTATACCCCAAATTCTTGAGAACACTCT
196 TTGAGGAAAAATAGTAACCTTACAAATCCCTCAAGAATTATACCCCAAATTCTTGAGAACACTCT
30856 CTCCCAAAGAGAACAATACAAATTTTGCAAACTTACAAGAAAATCCTCACAAGGCAAGATGTTTG
261 CTCCCAAAGAGAACAATACAAATTTTGCAAACTTACAAGAAAATCCTCACAAGGCAAGATGTTTG
* * *
30921 CACAATTCTAGAACAAAGAAATAACACTCAAGAATGAATATAATTGAGTACAAGTAGTGTTCTTG
326 CACAATTCTAGAACAAAGAAAGAACACTCAAGAATGAATATAATTGAGCACAAATAGTGTTCTTG
* * *
30986 AAAGCAAAATGAATATTGAATGAAAAATAGGCTTGAAGTGCTCAAACAATGA-GTTTGATGCTTT
391 AAAGCAAAATGAATATTGAAAGAAAAATAGGCTTGAACTGCACAAA-AATGATGTTTGATGCTTT
31050 CTCTTTG
455 CTCTTTG
* * *
31057 TTGAGTTAAACGATCGATGGAATA-GGCCAAGAGGGGGGGTGAATTGGTAATTAAAATTTTGGTG
1 TTGAGTTAAACGATCGA-CGAATATAGCCAAGA-GGGGGGTGAATTAGTAATTAAAATTTTGGTG
* * ** * *
31121 GAATCTTTTGCAGAAAATTGAAAAG-ATTTGTACATCGATTTAGAGTGGTTCGACTTTTTCAACC
64 GAAGCTTTTGCAGAAAATTG-AAAGTAATTACACAGCGATTTAGAGTGGTTCGACTTTCTCAACC
*
31185 AAAGTCTATGCCACTACCTTAGCTATCCACACTAAGGATTTTCCAACAAATTCACTAATTTGATC
128 AAAGTCTACG-CACTACCTTAGCTATCCACACTAAGGATTTTCC-ACAAATTCACTAATTTG-TC
* *
31250 TTTCTTTTGAGGCCAAAAT-GATAACCTTACAACTCCCTCAAGAA-TATACCCC-AATTCTTGAG
190 TTTCTTTTGAGG-AAAAATAG-TAACCTTACAAATCCCTCAAGAATTATACCCCAAATTCTTGAG
* * * * * *
31312 AACACTCTTTCTCAAAGAGAAGATTACAAA-TTTGCAAACTTACAAGGAAATCCTCACAAGG-TA
253 AACACTCTCTCCCAAAGAGAACAATACAAATTTTGCAAACTTACAAGAAAATCCTCACAAGGCAA
*
31375 GATTGTTTGCACAATTCTATAAC-AAGATAAGAACACTCAA-AGAT-AATTATAATTGAGCACAA
318 GA-TGTTTGCACAATTCTAGAACAAAGA-AAGAACACTCAAGA-ATGAA-TATAATTGAGCACAA
* * * * *
31437 ATTGTGTTCTTGAAAGCAAAATGAATATTGAAAGGAAATTTGGCTTGAACTGCACAAAATTGATG
379 ATAGTGTTCTTGAAAGCAAAATGAATATTGAAAGAAAAATAGGCTTGAACTGCACAAAAATGATG
31502 TTTGATGCTTT
444 TTTGATGCTTT
31513 TTCTCTTATT
Statistics
Matches: 409, Mismatches: 34, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
461 23 0.06
462 110 0.27
463 174 0.43
464 53 0.13
465 23 0.06
466 26 0.06
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (461 bp):
TTGAGTTAAACGATCGACGAATATAGCCAAGAGGGGGGTGAATTAGTAATTAAAATTTTGGTGGA
AGCTTTTGCAGAAAATTGAAAGTAATTACACAGCGATTTAGAGTGGTTCGACTTTCTCAACCAAA
GTCTACGCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCTT
TTGAGGAAAAATAGTAACCTTACAAATCCCTCAAGAATTATACCCCAAATTCTTGAGAACACTCT
CTCCCAAAGAGAACAATACAAATTTTGCAAACTTACAAGAAAATCCTCACAAGGCAAGATGTTTG
CACAATTCTAGAACAAAGAAAGAACACTCAAGAATGAATATAATTGAGCACAAATAGTGTTCTTG
AAAGCAAAATGAATATTGAAAGAAAAATAGGCTTGAACTGCACAAAAATGATGTTTGATGCTTTC
TCTTTG
Found at i:31836 original size:19 final size:19
Alignment explanation
Indices: 31812--31889 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
31802 ATTAGCCAGA
31812 GTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGGCTT
*
31831 GTGCATCGATGCATCAAATGCATT
1 GTGCATCGATGCAT----GGC-TT
31855 GAGTGCATCGATGCATGG-TAT
1 --GTGCATCGATGCATGGCT-T
31876 GTGCATCGATGCAT
1 GTGCATCGATGCAT
31890 AAAATGCATT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
19 28 0.57
20 1 0.02
21 1 0.02
22 1 0.02
23 2 0.04
24 2 0.04
26 14 0.29
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.29
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTT
Found at i:31859 original size:45 final size:45
Alignment explanation
Indices: 31810--31899 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
31800 AAATTAGCCA
*
31810 GAGTGCATCGATGCATGGCT-TGTGCATCGATGCATCAAATGCATT
1 GAGTGCATCGATGCATGG-TATGTGCATCGATGCATAAAATGCATT
31855 GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCATT
1 GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCATT
31900 CGATGTTCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 1 0.02
45 42 0.98
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (45 bp):
GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCATT
Found at i:32152 original size:19 final size:21
Alignment explanation
Indices: 32113--32153 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
32103 AATCAAATAT
32113 TCTTAGAAAATCATTTGAAAA
1 TCTTAGAAAATCATTTGAAAA
*
32134 TCTTA-AAATTCATTT-AAAA
1 TCTTAGAAAATCATTTGAAAA
32153 T
1 T
32154 TAATTTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 9 0.47
21 5 0.26
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTTAGAAAATCATTTGAAAA
Found at i:32977 original size:21 final size:21
Alignment explanation
Indices: 32953--32996 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
32943 CCGAAGGAGG
*
32953 AGGAGGAGCACGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
* *
32974 AGGAGCAGCTCGTGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
32995 AG
1 AG
32997 CTCCCGGAGT
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:0.39, C:0.16, G:0.36, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:34558 original size:23 final size:22
Alignment explanation
Indices: 34528--34630 Score: 136
Period size: 23 Copynumber: 4.6 Consensus size: 22
34518 GCATGGCCTT
34528 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
34550 CGTGCATCGATGCACATTCAAGG
1 -GTGCATCGATGCACATTCAAGG
* * *
34573 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
34595 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
34617 ATGCATCGATGCAC
1 GTGCATCGATGCAC
34631 TGTTAGGTGT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
21 15 0.21
22 16 0.23
23 39 0.56
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:34611 original size:44 final size:42
Alignment explanation
Indices: 34528--34649 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 42
34518 GCATGGCCTT
* *
34528 GTGCATCGATGCACATTCAAGGCGTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACCTTC-A-G-GTGTATCGATGCACATTCAAGG
*
34573 CGTGCATCGGTGCACCTTCATGGTGTATCGATGCACATTCAAGG
1 -GTGCATCGATGCACCTTCA-GGTGTATCGATGCACATTCAAGG
* *
34617 ATGCATCGATGCA-CTGTTAGGTGTATCGATGCA
1 GTGCATCGATGCACCT-TCAGGTGTATCGATGCA
34650 TTAAGCACAA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
42 16 0.24
43 13 0.19
44 21 0.31
45 2 0.03
46 16 0.24
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (42 bp):
GTGCATCGATGCACCTTCAGGTGTATCGATGCACATTCAAGG
Found at i:34646 original size:20 final size:21
Alignment explanation
Indices: 34532--34649 Score: 105
Period size: 23 Copynumber: 5.4 Consensus size: 21
34522 GGCCTTGTGC
*
34532 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
*
34555 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* * *
34578 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
*
34599 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
34621 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
34641 ATCGATGCA
1 ATCGATGCA
34650 TTAAGCACAA
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.13
21 22 0.27
22 14 0.17
23 36 0.43
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:35883 original size:21 final size:22
Alignment explanation
Indices: 35864--35926 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
35854 CATATTATAT
35864 GGAACTACGGTGCAATTATAAGC
1 GGAACTACGGTGCAATTAT-AGC
* *
35887 GGCACTTCGGTGCAATTATAAGC
1 GGAACTACGGTGCAATTAT-AGC
* *
35910 GGCACTTCGGTGCAATT
1 GGAACTACGGTGCAATT
35927 CTACGTGGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (22 bp):
GGAACTACGGTGCAATTATAGC
Found at i:35954 original size:23 final size:23
Alignment explanation
Indices: 35871--35952 Score: 119
Period size: 23 Copynumber: 3.6 Consensus size: 23
35861 TATGGAACTA
35871 CGGTGCAATTATAAGCGGCACTT
1 CGGTGCAATTATAAGCGGCACTT
35894 CGGTGCAATTATAAGCGGCACTT
1 CGGTGCAATTATAAGCGGCACTT
* * *
35917 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTATAAGCGGCACTT
* *
35940 TGGTGCATTTATA
1 CGGTGCAATTATA
35953 CGAGCTATGG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
CGGTGCAATTATAAGCGGCACTT
Found at i:36311 original size:28 final size:27
Alignment explanation
Indices: 36255--36311 Score: 62
Period size: 28 Copynumber: 2.0 Consensus size: 27
36245 AATCATATGT
*
36255 TGATTAAAAGAATAGATATAAGAGGATA
1 TGATTAAAAGAATAAATATAAGA-GATA
*
36283 TGATTATAAGATATAAATGATAAGA-ATA
1 TGATTAAAAGA-ATAAAT-ATAAGAGATA
36311 T
1 T
36312 TGATAGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 14 0.56
29 5 0.20
30 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.30
Consensus pattern (27 bp):
TGATTAAAAGAATAAATATAAGAGATA
Found at i:37903 original size:31 final size:30
Alignment explanation
Indices: 37829--37956 Score: 136
Period size: 31 Copynumber: 4.2 Consensus size: 30
37819 AACTTATTAA
* *
37829 ATATATTTTATT-TTAATTTTAATTTTAAAAT
1 ATATATCTTATTCTT-ATTTTAA-TTAAAAAT
* *
37860 ATAGATCTTTATTCTTATCTTCAATTAAAAAT
1 ATATATC-TTATTCTTAT-TTTAATTAAAAAT
37892 ATATATCTTATTCTTATTTTTAATTAAAAAT
1 ATATATCTTATTCTTA-TTTTAATTAAAAAT
* *
37923 ATAT-T-TTATTCTTATTTTAACTAGAAAT
1 ATATATCTTATTCTTATTTTAATTAAAAAT
37951 ATATAT
1 ATATAT
37957 TATTATTAAC
Statistics
Matches: 84, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
28 16 0.19
29 10 0.12
30 1 0.01
31 30 0.36
32 21 0.25
33 6 0.07
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (30 bp):
ATATATCTTATTCTTATTTTAATTAAAAAT
Found at i:37924 original size:63 final size:59
Alignment explanation
Indices: 37829--37956 Score: 150
Period size: 59 Copynumber: 2.1 Consensus size: 59
37819 AACTTATTAA
* * *
37829 ATATATTTTATTTTAATTTTAATTTTAAAATATAGATCTTTATTCTTATCTTCAATTAAAAAT
1 ATATATCTTATTTTAATTTTAA-TTTAAAA-ATATAT-TTTATTCTTAT-TTCAACTAAAAAT
* * *
37892 ATATATCTTATTCTTATTTTTAA-TTAAAAATATATTTTATTCTTATTTTAACTAGAAAT
1 ATATATCTTATT-TTAATTTTAATTTAAAAATATATTTTATTCTTATTTCAACTAAAAAT
37951 ATATAT
1 ATATAT
37957 TATTATTAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
59 16 0.28
60 11 0.19
61 5 0.09
62 6 0.10
63 11 0.19
64 9 0.16
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (59 bp):
ATATATCTTATTTTAATTTTAATTTAAAAATATATTTTATTCTTATTTCAACTAAAAAT
Found at i:37942 original size:24 final size:25
Alignment explanation
Indices: 37884--38018 Score: 98
Period size: 28 Copynumber: 5.2 Consensus size: 25
37874 TTATCTTCAA
37884 TTAAAAATATATATCTTATTCTTATTT
1 TTAAAAATATATAT-TTATTCTTA-TT
*
37911 TTAATTAAAAATATATTTTATTCTTATT
1 TTAA--AAATATATA-TTTATTCTTATT
* **
37939 TTAACTAGAA-ATATATATTATTATTAAC
1 TTAA--A-AATATATAT-TTATTCTTATT
*
37967 TTAAAATGTATATATTT-TT-TTATT
1 TTAAAA-ATATATATTTATTCTTATT
*
37991 TT-AAAGTATATATTTATTCTTATT
1 TTAAAAATATATATTTATTCTTATT
38015 TTAA
1 TTAA
38019 TATAAAATAT
Statistics
Matches: 90, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
22 10 0.11
23 5 0.06
24 12 0.13
25 4 0.04
26 3 0.03
27 11 0.12
28 25 0.28
29 19 0.21
30 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (25 bp):
TTAAAAATATATATTTATTCTTATT
Found at i:37973 original size:23 final size:22
Alignment explanation
Indices: 37934--37984 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
37924 TATTTTATTC
37934 TTATTTTAACTAGAAATATATA
1 TTATTTTAACTAGAAATATATA
*
37956 TTATTATTAACTTA-AAATGTATA
1 TTATT-TTAAC-TAGAAATATATA
37979 -TATTTT
1 TTATTTT
37985 TTTATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 2 0.08
22 9 0.35
23 13 0.50
24 2 0.08
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (22 bp):
TTATTTTAACTAGAAATATATA
Found at i:38022 original size:22 final size:22
Alignment explanation
Indices: 37974--38018 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
37964 AACTTAAAAT
37974 GTATATATTTTTTTATTTTAAA
1 GTATATATTTTTTTATTTTAAA
37996 GTATATATTTATTCTTATTTTAA
1 GTATATATTT-TT-TTATTTTAA
38019 TATAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.48
23 2 0.10
24 9 0.43
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (22 bp):
GTATATATTTTTTTATTTTAAA
Found at i:44333 original size:22 final size:21
Alignment explanation
Indices: 44276--44321 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
44266 TCTTGCAATC
44276 TGAATAAAAAAGAAAGACAGG
1 TGAATAAAAAAGAAAGACAGG
44297 TGAATAAAAAAGAAAGACAGG
1 TGAATAAAAAAGAAAGACAGG
44318 TGAA
1 TGAA
44322 ATCAAAAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.61, C:0.04, G:0.24, T:0.11
Consensus pattern (21 bp):
TGAATAAAAAAGAAAGACAGG
Found at i:44933 original size:104 final size:104
Alignment explanation
Indices: 44808--45016 Score: 364
Period size: 104 Copynumber: 2.0 Consensus size: 104
44798 ATTTTAAATT
* *
44808 TTTGTGTACTCTCTTACCAAAAACAATTTTATAATATTACAAGTACTACAAGTTTGAAAGGATGT
1 TTTGTGTACTCTCTTACCAAAAACAATTTCATAATATTACAAGTACTAAAAGTTTGAAAGGATGT
**
44873 TTGTTTACTTCAGAATGATTAAGTATTGAATGATTTAAA
66 TTGTTTACTTCAGAATGATTAAACATTGAATGATTTAAA
*
44912 TTTGTGTACTCTCTTACCAAAAACAATTTCATAATATTACATGTACTAAAAGTTTGAAAGGATGT
1 TTTGTGTACTCTCTTACCAAAAACAATTTCATAATATTACAAGTACTAAAAGTTTGAAAGGATGT
*
44977 TTGTTTACTTCAGAATGATTAAACGTTGAATGATTTAAA
66 TTGTTTACTTCAGAATGATTAAACATTGAATGATTTAAA
45016 T
1 T
45017 GTTGAATGAT
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 99 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.39
Consensus pattern (104 bp):
TTTGTGTACTCTCTTACCAAAAACAATTTCATAATATTACAAGTACTAAAAGTTTGAAAGGATGT
TTGTTTACTTCAGAATGATTAAACATTGAATGATTTAAA
Found at i:45020 original size:16 final size:16
Alignment explanation
Indices: 44989--45027 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
44979 GTTTACTTCA
44989 GAATGA-TTAAACGTT
1 GAATGATTTAAACGTT
*
45004 GAATGATTTAAATGTT
1 GAATGATTTAAACGTT
45020 GAATGATT
1 GAATGATT
45028 CAGAAGCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (16 bp):
GAATGATTTAAACGTT
Found at i:46998 original size:3 final size:3
Alignment explanation
Indices: 46992--47048 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
46982 TTTTTATAAA
* * *
46992 TAT TAT TAT TAT TAT TAT TAT TAA TA- TAA TAT ATAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
47037 TATT TAT TAT TA
1 TA-T TAT TAT TA
47049 AATAAATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:47020 original size:30 final size:31
Alignment explanation
Indices: 46986--47063 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 31
46976 TAATTTTTTT
46986 TATAAATATTATTATTATTA-TTATTATTAA
1 TATAAATATTATTATTATTATTTATTATTAA
*
47016 TATAATATATATTACTATTATTATTTATTATTAA
1 TAT-A-A-ATATTATTATTATTATTTATTATTAA
47050 -ATAAATATATATTA
1 TATAAATAT-TATTA
47064 CAAATTACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
30 7 0.17
31 6 0.15
32 2 0.05
33 16 0.39
34 10 0.24
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (31 bp):
TATAAATATTATTATTATTATTTATTATTAA
Found at i:47049 original size:34 final size:33
Alignment explanation
Indices: 46991--47064 Score: 114
Period size: 34 Copynumber: 2.2 Consensus size: 33
46981 TTTTTTATAA
*
46991 ATATTATTATTATTATTATTATT-AATATAATAT
1 ATATTACTATTATTATTATTATTAAATA-AATAT
47024 ATATTACTATTATTATTTATTATTAAATAAATAT
1 ATATTACTATTATTA-TTATTATTAAATAAATAT
47058 ATATTAC
1 ATATTAC
47065 AAATTACATC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
33 14 0.37
34 20 0.53
35 4 0.11
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (33 bp):
ATATTACTATTATTATTATTATTAAATAAATAT
Found at i:48338 original size:17 final size:17
Alignment explanation
Indices: 48306--48353 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
48296 TAACAGTTGG
*
48306 ATATTTTTCA-TTTAAT
1 ATATTTTGCATTTTAAT
48322 ATATTTTGCATTTTAAT
1 ATATTTTGCATTTTAAT
*
48339 AT-TATTGC-TTTTAAT
1 ATATTTTGCATTTTAAT
48354 TTCTTTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.24
16 14 0.48
17 8 0.28
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.60
Consensus pattern (17 bp):
ATATTTTGCATTTTAAT
Found at i:48379 original size:15 final size:14
Alignment explanation
Indices: 48371--48427 Score: 55
Period size: 15 Copynumber: 4.0 Consensus size: 14
48361 ATTTTGATTA
48371 TTATTATT-TTATT
1 TTATTATTATTATT
*
48384 TTGTTATTATATATGT
1 TTATTATTAT-TAT-T
*
48400 TTA-AATTATTATT
1 TTATTATTATTATT
48413 TTCATTATTATTATT
1 TT-ATTATTATTATT
48428 ATCTTAAGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 10 0.29
14 5 0.14
15 17 0.49
16 3 0.09
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATT
Found at i:48532 original size:13 final size:14
Alignment explanation
Indices: 48503--48544 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
48493 TAAAATTCTA
48503 TTTATAAATTTAAT
1 TTTATAAATTTAAT
*
48517 TTTATAAA-TTACT
1 TTTATAAATTTAAT
*
48530 TTTATCATATTTAAT
1 TTTAT-AAATTTAAT
48545 ATATATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 9 0.39
14 10 0.43
15 4 0.17
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATAAATTTAAT
Found at i:48721 original size:136 final size:134
Alignment explanation
Indices: 48541--48895 Score: 391
Period size: 136 Copynumber: 2.6 Consensus size: 134
48531 TTATCATATT
* * ** *
48541 TAATATATATTTATTTTTCAATATTAAGAAATGGCAAACATAAAGTAACTAGATGTTCATTTTCT
1 TAATATATATTTATTTTTTAATATTAAGAAAGGGCATTCTTAAAGTAACTAGATG-TCATTTTCT
*
48606 GATATTTTTAAATAAATAATTTATTTTTATAAATTATATATATTAATC-TATTT-TTAGATAAAT
65 GATATTTTTAAATAAATAATTTACTTTTATAAATTATA-ATATTAATCATATTTATTAGATAAAT
48669 GTTTTA
129 GTTTTA
* *
48675 TCAATATATATTTATTTTTTAAATATTAGGAAAGGGCATTCTTAAAGCAACT-GTATGTCAATTT
1 T-AATATATATTTATTTTTT-AATATTAAGAAAGGGCATTCTTAAAGTAACTAG-ATGTC-ATTT
* * *
48739 TCTGATATTTTTTAATAAATATTTTACTTTTATAAATTATAATATTAATCAAAATTTTTATTAGA
62 TCTGATATTTTTAAATAAATAATTTACTTTTATAAATTATAATATTAATC---ATATTTATTAGA
48804 TAAATGTTTTA
124 TAAATGTTTTA
** * * * * *
48815 T--TA-ATATTTATTTTTTAATATTAAGAAATGATC-TGTTTTAAAGTACCTAGAAGCCCTTTTC
1 TAATATATATTTATTTTTTAATATTAAGAAA-GGGCAT-TCTTAAAGTAACTAGATGTCATTTTC
*
48876 TGATATTTCTAAATAAATAA
64 TGATATTTTTAAATAAATAA
48896 ATATCTTATT
Statistics
Matches: 186, Mismatches: 23, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
134 1 0.01
135 63 0.34
136 98 0.53
137 3 0.02
139 4 0.02
140 17 0.09
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.47
Consensus pattern (134 bp):
TAATATATATTTATTTTTTAATATTAAGAAAGGGCATTCTTAAAGTAACTAGATGTCATTTTCTG
ATATTTTTAAATAAATAATTTACTTTTATAAATTATAATATTAATCATATTTATTAGATAAATGT
TTTA
Found at i:48916 original size:21 final size:20
Alignment explanation
Indices: 48892--48939 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
48882 TTCTAAATAA
48892 ATAAATATCTTAT-TTAAAAAT
1 ATAAATAT-TT-TCTTAAAAAT
*
48913 ATAATATATTTTCTTAAAATT
1 ATAA-ATATTTTCTTAAAAAT
48934 ATAAAT
1 ATAAAT
48940 TTGAAATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAAATATTTTCTTAAAAAT
Found at i:60922 original size:2 final size:2
Alignment explanation
Indices: 60915--60945 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
60905 TAAATAATAA
60915 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 A
60946 CATTTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61141 original size:59 final size:59
Alignment explanation
Indices: 61074--61220 Score: 165
Period size: 57 Copynumber: 2.5 Consensus size: 59
61064 TAAGGTTTTA
*
61074 CTTTGTTGAGTCCCTGACTATTAAAAGTTACAAAATGAT-TCTTCAACTATATGAAACTG
1 CTTTGTTGAGTCCCTGACTATTAAAAGTTACAAAATGATCTC-TCAACTATAGGAAACTG
** * * * ** *
61133 CTTTGTTGAGT-ATTGACTATT-AAAGTTACAAAATGATCTCTCGAGTGTAGGGTATTG
1 CTTTGTTGAGTCCCTGACTATTAAAAGTTACAAAATGATCTCTCAACTATAGGAAACTG
*
61190 TTTTGTTGAGTCCCTTGACTATTAAAAGTTA
1 CTTTGTTGAGTCCC-TGACTATTAAAAGTTA
61221 TAGAATGACC
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
57 36 0.50
58 10 0.14
59 19 0.26
60 7 0.10
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (59 bp):
CTTTGTTGAGTCCCTGACTATTAAAAGTTACAAAATGATCTCTCAACTATAGGAAACTG
Found at i:62204 original size:87 final size:87
Alignment explanation
Indices: 61965--62206 Score: 367
Period size: 87 Copynumber: 2.8 Consensus size: 87
61955 ATCATTTAAT
* * * *
61965 TGGAAATATTATCAAGTAAAATAACAAATTAGGTAACGCTTATATAATGTAATAGATAGCGTTTA
1 TGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGATAGCGCTTA
62030 TATAATAAAATAGGGTAATTAC
66 TATAATAAAATAGGGTAATTAC
* * * * *
62052 TGGAAACATTATCAAGCACAATAACATATTAGGTAGCGTTTATATAATGTAATAGATAACACTTA
1 TGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGATAGCGCTTA
* *
62117 TATAATAAAATATGTTAATTAC
66 TATAATAAAATAGGGTAATTAC
* *
62139 TGTAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTA
1 TGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGATAGCGCTTA
62204 TAT
66 TAT
62207 TGACATATTA
Statistics
Matches: 137, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 137 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.33
Consensus pattern (87 bp):
TGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGATAGCGCTTA
TATAATAAAATAGGGTAATTAC
Found at i:62856 original size:200 final size:198
Alignment explanation
Indices: 62219--62888 Score: 924
Period size: 198 Copynumber: 3.4 Consensus size: 198
62209 ACATATTATA
* * * *
62219 TCATAAAACAGATATATTTATACCGGTAACATTACAAATTTATCTATTACATTATAATTATCGGT
1 TCATAAAACCGATATATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGT
62284 TTCGATATTTTTGAGATCGATA-TAATTT--TAAATGTATCGACACTTTATGCGTGCACCTCGTT
66 TTCGATATTTTTG-GATCGATACT--TTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTT
* * * *
62346 GGGCATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAACGTGTCGATACATTATGTATAACT
128 TGGCATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCT
62411 ATTTTC
193 ATTTTC
* * * * * * *
62417 TCATAAAACCGGTATATTTCTACCGGATACATTGTAAATTTACTTATTACATTGTAATTATCAGT
1 TCATAAAACCGATATATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGT
* *
62482 TTGGAT-TTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTGCACCTCG-TTG
66 TTCGATATTTTT-GGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTG
62545 GACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTA
130 G-CATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTA
62610 TTTTC
194 TTTTC
* * * *
62615 TCATAAAACCGATAAAATTTCTACCGAG-TACATTGTAAATTTACCTATTACATTGTAATTATCG
1 TCATAAAACCGAT-ATATTTATACCG-GTTACATTATAAATTTACCTATTACATTATAATTATCG
*
62679 GTTTCGATATTTTTAGGATCGATACTTTTAATAAATGTATCAACACTTTATGCGTGCACCTCGTT
64 GTTTCGATATTTTT-GGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTT
* *** *
62744 TGGCATTCATTCTGGACAAAATGTATCGACAC-TTTTTAAATTTGTGTCGATACATTATGTAGAC
128 TGGCATTCATTCTGGA-AAAAAGTATCGACACAAACTTAAA-ATGTGTCGATACATTATGTAGAC
62808 CTATTCTT-
191 CTATT-TTC
* *
62816 TCATAAAACCGGTATATTTATACTGGTTACATTATAAATTTACCTATTACATTATAATTATCGGT
1 TCATAAAACCGATATATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGT
62881 TTCGATAT
66 TTCGATAT
62889 AACATATGTG
Statistics
Matches: 423, Mismatches: 36, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
196 3 0.01
197 16 0.04
198 169 0.40
199 53 0.13
200 123 0.29
201 57 0.13
202 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (198 bp):
TCATAAAACCGATATATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGT
TTCGATATTTTTGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGG
CATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTATT
TTC
Found at i:63005 original size:26 final size:31
Alignment explanation
Indices: 62947--63011 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 31
62937 CTATTCTCTC
*
62947 ATTATAATATAATTAATAATATATTACTCTT
1 ATTATAATATAATTAATAATATATTAATCTT
62978 ATTATAATA-AA-TAATAA-ATA-TAAT-TT
1 ATTATAATATAATTAATAATATATTAATCTT
*
63004 ATAATAAT
1 ATTATAAT
63012 TTTATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 9 0.28
27 3 0.09
28 3 0.09
29 6 0.19
30 2 0.06
31 9 0.28
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (31 bp):
ATTATAATATAATTAATAATATATTAATCTT
Found at i:63030 original size:31 final size:30
Alignment explanation
Indices: 62989--63082 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
62979 TTATAATAAA
*
62989 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAA-TAATAATAATTTT-TTAT
*
63019 TAATAAAATATAATAATCATAATTTTTTAT
1 TAATAAAATATAATAATAATAATTTTTTAT
* * *
63049 TTATAAAAT-T-ATAGAT-ATAATATTTTAA
1 TAATAAAATATAATA-ATAATAATTTTTTAT
63077 TAATAA
1 TAATAA
63083 TATAGACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
28 18 0.33
29 5 0.09
30 24 0.44
31 8 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TAATAAAATATAATAATAATAATTTTTTAT
Found at i:63082 original size:14 final size:14
Alignment explanation
Indices: 63000--63085 Score: 50
Period size: 14 Copynumber: 6.1 Consensus size: 14
62990 AATAAATATA
**
63000 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
63015 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
63028 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * * *
63042 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
63056 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
63070 ATTTTAATAATAAT
1 ATTTTAATAATAAT
63084 AT
1 AT
63086 AGACATAAAT
Statistics
Matches: 52, Mismatches: 16, Indels: 7
0.69 0.21 0.09
Matches are distributed among these distances:
13 10 0.19
14 37 0.71
15 5 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:63082 original size:28 final size:28
Alignment explanation
Indices: 63014--63082 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
63004 ATAATAATTT
*
63014 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
63041 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
63069 TATTTTAATAATAA
1 TATTTTAATAATAA
63083 TATAGACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:63253 original size:30 final size:29
Alignment explanation
Indices: 63178--63253 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 29
63168 GTATTTGATG
*
63178 TTTATAATTATATTGTAATTATGATTATTT
1 TTTA-AATTATATTCTAATTATGATTATTT
* *
63208 TTT--ATCA-CTTC--ATTATGATTATTT
1 TTTAAATTATATTCTAATTATGATTATTT
63232 TTTAAAATTATATTCTAATTAT
1 TTT-AAATTATATTCTAATTAT
63254 ATATATATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
24 16 0.46
26 2 0.06
27 6 0.17
28 3 0.09
30 8 0.23
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (29 bp):
TTTAAATTATATTCTAATTATGATTATTT
Found at i:63494 original size:21 final size:21
Alignment explanation
Indices: 63455--63495 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
63445 CGGTAAAAAT
* *
63455 TACCTAAAACATTATTATTTC
1 TACCTAAAACATCAATATTTC
63476 TACCTAAAACATCAATATTT
1 TACCTAAAACATCAATATTT
63496 TTTAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (21 bp):
TACCTAAAACATCAATATTTC
Found at i:63799 original size:31 final size:28
Alignment explanation
Indices: 63764--63844 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 28
63754 ATAAAAAATA
*
63764 AAAATATAATTTATAATAATTTTATTTTAAT
1 AAAATATAA-TAATAATAATTTT-TTTT-AT
*
63795 AAAATATAATAATCATAATTTTTTTTAT
1 AAAATATAATAATAATAATTTTTTTTAT
63823 AAAATTATAGAT-ATAAT-ATTTT
1 AAAA-TATA-ATAATAATAATTTT
63845 AATAATAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
28 11 0.24
29 12 0.27
30 13 0.29
31 9 0.20
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
AAAATATAATAATAATAATTTTTTTTAT
Found at i:63817 original size:26 final size:27
Alignment explanation
Indices: 63785--63855 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
63775 TATAATAATT
63785 TTATTTTAATAAAATATAATA-ATCATAA
1 TTATTTTAATAAAATAT-ATAGAT-ATAA
* *
63813 TTTTTTTTATAAAAT-TATAGATATAA
1 TTATTTTAATAAAATATATAGATATAA
63839 -TATTTTAATAATAATAT
1 TTATTTTAATAA-AATAT
63856 TTACATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
25 9 0.25
26 10 0.28
27 4 0.11
28 13 0.36
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
TTATTTTAATAAAATATATAGATATAA
Found at i:63831 original size:29 final size:31
Alignment explanation
Indices: 63764--63827 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
63754 ATAAAAAATA
*
63764 AAAATATAATTTATAATAATTTTATTTTAAT
1 AAAATATAATTAATAATAATTTTATTTTAAT
*
63795 AAAATATAA-TAATCATAATTTT-TTTT-AT
1 AAAATATAATTAATAATAATTTTATTTTAAT
63823 AAAAT
1 AAAAT
63828 TATAGATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 7 0.23
29 4 0.13
30 11 0.35
31 9 0.29
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (31 bp):
AAAATATAATTAATAATAATTTTATTTTAAT
Found at i:63877 original size:14 final size:15
Alignment explanation
Indices: 63835--63879 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
63825 AATTATAGAT
*
63835 ATAATATTTTAAT-A
1 ATAATATTTAAATAA
*
63849 ATAATATTTACATAA
1 ATAATATTTAAATAA
63864 ATAATA-TTAAATAA
1 ATAATATTTAAATAA
63878 AT
1 AT
63880 TAGTATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATATTTAAATAA
Found at i:64220 original size:23 final size:23
Alignment explanation
Indices: 64185--64235 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
64175 TAAATAATTA
**
64185 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
64208 ACCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGCT
64231 ACCTA
1 ACCTA
64236 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:64307 original size:23 final size:23
Alignment explanation
Indices: 64272--64319 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
64262 TCAGTAATTA
**
64272 ACCTATTTTATTATATAAGAGCT
1 ACCTATTACATTATATAAGAGCT
*
64295 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGAGCT
64318 AC
1 AC
64320 ATAATATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (23 bp):
ACCTATTACATTATATAAGAGCT
Found at i:64312 original size:87 final size:87
Alignment explanation
Indices: 64179--64409 Score: 408
Period size: 87 Copynumber: 2.7 Consensus size: 87
64169 ATAAATTAAA
*
64179 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTA
64244 TTGTGCTTGATAATGTTTTCAG
66 TTGTGCTTGATAATGTTTTCAG
* * *
64266 TAATTAACCTATTTTATTATATAAGAGCTACCTATTACATTATATAAGCGCTACATAATATGTTG
1 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTA
*
64331 TTGTGTTTGATAATGTTTTCAG
66 TTGTGCTTGATAATGTTTTCAG
*
64353 TAATTAACCTATTTTATTATATAAGCGTTACCTATTACATTATATAAGCGCTACCTA
1 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTA
64410 TTACATTATA
Statistics
Matches: 136, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 136 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.42
Consensus pattern (87 bp):
TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTA
TTGTGCTTGATAATGTTTTCAG
Found at i:64443 original size:23 final size:23
Alignment explanation
Indices: 64359--64436 Score: 129
Period size: 23 Copynumber: 3.4 Consensus size: 23
64349 TCAGTAATTA
** *
64359 ACCTATTTTATTATATAAGCGTT
1 ACCTATTACATTATATAAGCGCT
64382 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
64405 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
64428 ACCTATTAC
1 ACCTATTAC
64437 TTCATATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:66189 original size:2 final size:2
Alignment explanation
Indices: 66182--66209 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
66172 TCAACCTGAA
66182 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
66210 TATTAGGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68512 original size:2 final size:2
Alignment explanation
Indices: 68505--68531 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
68495 ATTTTATAAT
68505 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
68532 TGGACTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:69412 original size:15 final size:15
Alignment explanation
Indices: 69392--69424 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
69382 GTTGTCAGGC
69392 ACAAGACTAATAAGT
1 ACAAGACTAATAAGT
69407 ACAAGACTAATAAGT
1 ACAAGACTAATAAGT
69422 ACA
1 ACA
69425 TATGATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.15, G:0.12, T:0.18
Consensus pattern (15 bp):
ACAAGACTAATAAGT
Done.