Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004954.1 Hibiscus syriacus cultivar Beakdansim tig00011140_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: 86023
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1043 original size:17 final size:17
Alignment explanation
Indices: 1023--1055 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1013 AATTTAAGGA
1023 AATAAAAAATATATATT
1 AATAAAAAATATATATT
*
1040 AATAGAAAATATATAT
1 AATAAAAAATATATAT
1056 GATATATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AATAAAAAATATATATT
Found at i:5639 original size:31 final size:31
Alignment explanation
Indices: 5564--5655 Score: 130
Period size: 31 Copynumber: 3.0 Consensus size: 31
5554 TTACATGGTA
* * ** *
5564 GAAAATATTAATAAAATATACCATGTCATTG
1 GAAAATATTAATACAGTATGTCATATCATTG
5595 GAAAATATTAATACAGTATGTCATATCATTG
1 GAAAATATTAATACAGTATGTCATATCATTG
*
5626 GAAAATATTAATACGGTATGTCATATCATT
1 GAAAATATTAATACAGTATGTCATATCATT
5656 TTAGAGTGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (31 bp):
GAAAATATTAATACAGTATGTCATATCATTG
Found at i:9028 original size:2 final size:2
Alignment explanation
Indices: 9021--9053 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9011 ATTAAATAAT
9021 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
9054 GGATTTTGTG
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:15426 original size:15 final size:14
Alignment explanation
Indices: 15405--15450 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
15395 ATTTGAGTAT
15405 TTATTTTTAAAATA
1 TTATTTTTAAAATA
* **
15419 TTATTTTTTGAAGGA
1 TTA-TTTTTAAAATA
15434 TTATTTTTAAAATA
1 TTATTTTTAAAATA
15448 TTA
1 TTA
15451 AAAAGAAGAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TTATTTTTAAAATA
Found at i:20044 original size:6 final size:6
Alignment explanation
Indices: 20035--20084 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
20025 TTGCGAAAAT
20035 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
20083 GA
1 GA
20085 GACGAGACGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.34, C:0.48, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:20091 original size:5 final size:5
Alignment explanation
Indices: 20081--20112 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
20071 GACCACGACC
20081 ACGAG ACGAG ACGAG ACGAG ACGAG ACG-G ACG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACG
20113 GCGGCGGCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.38, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:20736 original size:22 final size:22
Alignment explanation
Indices: 20709--20761 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
20699 AATTTGGAAA
20709 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
20731 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
20753 ATCGCAACG
1 ATCGCAACG
20762 CGAAATGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:20799 original size:41 final size:41
Alignment explanation
Indices: 20750--20928 Score: 295
Period size: 41 Copynumber: 4.4 Consensus size: 41
20740 ACAACTGTAG
20750 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
20791 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *** * *
20832 ACTATCGCAACGCGAAATGGACAATCGCGTTGCGCTTTTCG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
20873 ACTATAGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
20914 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
20929 TTTTCAACTA
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 124 1.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:20924 original size:103 final size:103
Alignment explanation
Indices: 20814--21003 Score: 308
Period size: 103 Copynumber: 1.8 Consensus size: 103
20804 GAAATGGAAA
* *** * *
20814 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGACAATCGCGTTGCGCTTTTCGACTATA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATA
20879 GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
66 GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
* *
20917 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAATTATC
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATA
20982 GCAACGCGAAATGGAAAATCGC
66 GCAACGCGAAATGGAAAATCGC
21004 GTTCTATCTC
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 79 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (103 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATA
GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
Found at i:20962 original size:41 final size:41
Alignment explanation
Indices: 20917--21003 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 41
20907 ATTTTCAACT
20917 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
*
20958 ATCGCAACGCGATTTTCAATTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
20999 ATCGC
1 ATCGC
21004 GTTCTATCTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:20965 original size:82 final size:82
Alignment explanation
Indices: 20750--20969 Score: 205
Period size: 82 Copynumber: 2.7 Consensus size: 82
20740 ACAACTGTAG
* ** *
20750 ACTATCGCAACGCGAAATGGAA-AATCGCAACGCG-ATTTTC-AACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAAT-CAACAATCGCAACGCGCA-AATCGAA-AATCGCAACGCGAAATGGA
20812 AAATCGCAACGCGATTTTCA
63 AAATCGCAACGCGATTTTCA
** *** *** ** *
20832 ACTATCGCAACGCGAAATGGACAATCGCGTTGCGCTTTTCGACTATAGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATCAACAATCGCAACGCGCAAATCGAAAATCGCAACGCGAAATGGAAAA
20897 TCGCAACGCGATTTTCA
66 TCGCAACGCGATTTTCA
** * *
20914 ACTATCGCAACGCGATTTTCAACTATCGCAACGCG-AAATGGAAAATCGCAACGCGA
1 ACTATCGCAACGCGA-AATCAACAATCGCAACGCGCAAATCGAAAATCGCAACGCGA
20970 TTTTCAATTA
Statistics
Matches: 112, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
81 2 0.02
82 98 0.88
83 12 0.11
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (82 bp):
ACTATCGCAACGCGAAATCAACAATCGCAACGCGCAAATCGAAAATCGCAACGCGAAATGGAAAA
TCGCAACGCGATTTTCA
Found at i:20990 original size:62 final size:62
Alignment explanation
Indices: 20750--20990 Score: 261
Period size: 62 Copynumber: 3.9 Consensus size: 62
20740 ACAACTGTAG
** **
20750 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
* ** ** * ** ** * *** * *
20812 A-AATCGCAACGCGATTTTCAACTATCGCAACGCGA-AATGGACAATCGCGTTGCGCTTTTCG
1 ACTATCGCAACGCGAAATGGAA-AATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
*
20873 ACTATAGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
*
20935 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAATTATCGCAACGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGA
20991 AATGGAAAAT
Statistics
Matches: 137, Mismatches: 39, Indels: 6
0.75 0.21 0.03
Matches are distributed among these distances:
61 40 0.29
62 97 0.71
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (62 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
Found at i:22073 original size:25 final size:25
Alignment explanation
Indices: 22040--22094 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
22030 CTCTACTCGT
*
22040 AATG-TATATAATT-TTTCATATATA
1 AATGATATATAATTATAT-ATATATA
22064 AATGATATATAATTATATATATATA
1 AATGATATATAATTATATATATATA
*
22089 TATGAT
1 AATGAT
22095 GTTTTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 4 0.15
25 21 0.78
26 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (25 bp):
AATGATATATAATTATATATATATA
Found at i:22915 original size:2 final size:2
Alignment explanation
Indices: 22908--22932 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22898 TTTAAATAAA
22908 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
22933 AATTGAATCT
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:23261 original size:3 final size:3
Alignment explanation
Indices: 23253--23280 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
23243 AATTAGTAGC
23253 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
23281 TTGATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:26589 original size:46 final size:48
Alignment explanation
Indices: 26518--26621 Score: 149
Period size: 47 Copynumber: 2.2 Consensus size: 48
26508 TAGAATATAG
* *
26518 AATATAATAAATAATATTATTTAATACAAAAAATAC-TTTTATTTTTAA
1 AATATTAT-AATAATATTAGTTAATACAAAAAATACTTTTTATTTTTAA
**
26566 AATATTATAATAAT-TTAGTTAATATTAAAAATACTTTTTATTTTTAA
1 AATATTATAATAATATTAGTTAATACAAAAAATACTTTTTATTTTTAA
26613 AATATTATA
1 AATATTATA
26622 GATATTAAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
46 17 0.33
47 27 0.53
48 7 0.14
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (48 bp):
AATATTATAATAATATTAGTTAATACAAAAAATACTTTTTATTTTTAA
Found at i:31710 original size:41 final size:44
Alignment explanation
Indices: 31626--31721 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 44
31616 TGTTCATGAT
* *
31626 TTAAAAAATATATAATATATTAAGTTATAATCCTATTTTAATTA
1 TTAAAAAATATATAATATATTAAATTATAATCCTATTTAAATTA
*
31670 TTAAAAAAT-TATTATAT-TTAAATTATAAT-C-ATCTTAAATTA
1 TTAAAAAATATATAATATATTAAATTATAATCCTAT-TTAAATTA
31711 TTAAAAGAATA
1 TTAAAA-AATA
31722 GGATTAAGCC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
40 2 0.04
41 14 0.30
42 14 0.30
43 7 0.15
44 9 0.20
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (44 bp):
TTAAAAAATATATAATATATTAAATTATAATCCTATTTAAATTA
Found at i:32367 original size:16 final size:16
Alignment explanation
Indices: 32346--32377 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
32336 GTCCGAATGT
32346 ACTTACTCTTTTTAAA
1 ACTTACTCTTTTTAAA
32362 ACTTACTCTTTTTAAA
1 ACTTACTCTTTTTAAA
32378 GAATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (16 bp):
ACTTACTCTTTTTAAA
Found at i:33410 original size:25 final size:25
Alignment explanation
Indices: 33345--33411 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
33335 TATCCGACCT
* * *
33345 AAAT-AAATATATTTTTATAAAGTA
1 AAATAAAATATATATTTAAAAAATA
33369 AAATAAGGAAT-TA-ATTTAAAAAATA
1 AAATAA--AATATATATTTAAAAAATA
33394 AAATAAAATATATATTTA
1 AAATAAAATATATATTTA
33412 TTATAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
23 3 0.09
24 6 0.17
25 21 0.60
26 2 0.06
27 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (25 bp):
AAATAAAATATATATTTAAAAAATA
Found at i:35311 original size:21 final size:21
Alignment explanation
Indices: 35285--35330 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
35275 ATTAATAACA
* *
35285 CTAAACCTTAACCCATAACTT
1 CTAAACCCTAAACCATAACTT
* *
35306 CTAAACCCTAAACCTTAATTT
1 CTAAACCCTAAACCATAACTT
35327 CTAA
1 CTAA
35331 CTTAAAACTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.30
Consensus pattern (21 bp):
CTAAACCCTAAACCATAACTT
Found at i:38009 original size:15 final size:14
Alignment explanation
Indices: 37982--38011 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
37972 TCTGGCTTTG
37982 GTTTCAGTATTTTT
1 GTTTCAGTATTTTT
37996 GTTTCAGTATTTTT
1 GTTTCAGTATTTTT
38010 GT
1 GT
38012 CCTTTCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.07, G:0.17, T:0.63
Consensus pattern (14 bp):
GTTTCAGTATTTTT
Found at i:51735 original size:20 final size:20
Alignment explanation
Indices: 51710--51749 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
51700 ATCGATTGAA
*
51710 ATTTTTGAATATCTCTTGTT
1 ATTTTTGAATATCTATTGTT
51730 ATTTTTGAATATCTATTGTT
1 ATTTTTGAATATCTATTGTT
51750 TGTGATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.07, G:0.10, T:0.60
Consensus pattern (20 bp):
ATTTTTGAATATCTATTGTT
Found at i:53240 original size:42 final size:42
Alignment explanation
Indices: 53189--53328 Score: 133
Period size: 42 Copynumber: 3.4 Consensus size: 42
53179 AAAATCATAC
*
53189 TTTAGCAGCGTTTTTTAAACAAACGCCGTAATAGAGTGGTAA
1 TTTAGCAGCGTTTTTTAAACAAACGCCGAAATAGAGTGGTAA
** * * *
53231 TTTAGCAGCG-TTTTTAGCTCAAACGCCGCAATTGAGTTGT--
1 TTTAGCAGCGTTTTTTA-AACAAACGCCGAAATAGAGTGGTAA
** * *
53271 TTATAGTGGCGTTTTTTCAACAAACACCGAAATAGAGTGGTAA
1 TT-TAGCAGCGTTTTTTAAACAAACGCCGAAATAGAGTGGTAA
* *
53314 TGTAGCGGCGTTTTT
1 TTTAGCAGCGTTTTT
53329 GTACAAACGC
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
40 2 0.03
41 29 0.38
42 45 0.58
43 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34
Consensus pattern (42 bp):
TTTAGCAGCGTTTTTTAAACAAACGCCGAAATAGAGTGGTAA
Found at i:53295 original size:41 final size:41
Alignment explanation
Indices: 53250--53378 Score: 93
Period size: 41 Copynumber: 3.1 Consensus size: 41
53240 GTTTTTAGCT
53250 CAAACGCCGCAATTGAGTTGTTTATAGTGGCGTTTTTTCAA
1 CAAACGCCGCAATTGAGTTGTTTATAGTGGCGTTTTTTCAA
* * * * * * *
53291 CAAACACCGAAATAGAGTGGTAATGTAGCGGCGTTTTTGT--A
1 CAAACGCCGCAATTGAGTTGT-TTATAGTGGCGTTTTT-TCAA
* * * * *
53332 CAAACGCCACGA-TAATGTTATTTATAGTGGCGTTTGTTCAA
1 CAAACGCCGCAATTGA-GTTGTTTATAGTGGCGTTTTTTCAA
*
53373 AAAACG
1 CAAACG
53379 ACGGTATAGA
Statistics
Matches: 63, Mismatches: 20, Indels: 10
0.68 0.22 0.11
Matches are distributed among these distances:
39 1 0.02
40 13 0.21
41 35 0.56
42 13 0.21
43 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (41 bp):
CAAACGCCGCAATTGAGTTGTTTATAGTGGCGTTTTTTCAA
Found at i:53295 original size:83 final size:82
Alignment explanation
Indices: 53196--53492 Score: 282
Period size: 83 Copynumber: 3.6 Consensus size: 82
53186 TACTTTAGCA
* * *
53196 GCGTTT-TTTAAACAAACGCCGTAATAGAGTGGTAATTTAGCAGCGTTTTTAGCTCAAACGCCGC
1 GCGTTTGTTCAAA-AAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTTTAG-TCAAACGCCGC
53260 AATTGAGTTGTTTATAGTG
64 AATTGAGTTGTTTATAGTG
* * * * * * * *
53279 GCGTTTTTTCAACAAACACCGAAATAGAGTGGTAATGTAGCGGCGTTTTT-GTACAAACGCCACG
1 GCGTTTGTTCAAAAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTTTAGT-CAAACGCCGCA
* *
53343 A-TAATGTTATTTATAGTG
65 ATTGA-GTTGTTTATAGTG
* * * *
53361 GCGTTTGTTCAAAAAACGACGGT-ATAGATTAGTAATTTAGCTGCGTTTATTAAAT-AAACGCCG
1 GCGTTTGTTCAAAAAACG-CCGTAATAGAGTAGTAATTTAGCGGCGTTT-TT-AGTCAAACGCCG
*
53424 CAATAGTA-TTGTTTATAGTG
63 CAATTG-AGTTGTTTATAGTG
* * * *
53444 GCGTTTGTGCAAAAAATGCCGTAATAGAGTAATAATTTAGTGGCGTTTT
1 GCGTTTGTTCAAAAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTT
53493 ACAAGAAACG
Statistics
Matches: 172, Mismatches: 32, Indels: 21
0.76 0.14 0.09
Matches are distributed among these distances:
81 3 0.02
82 63 0.37
83 100 0.58
84 4 0.02
85 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (82 bp):
GCGTTTGTTCAAAAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTTTAGTCAAACGCCGCAA
TTGAGTTGTTTATAGTG
Found at i:54503 original size:14 final size:14
Alignment explanation
Indices: 54484--54510 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54474 TTTATTATTT
54484 CTAGATATATTATA
1 CTAGATATATTATA
54498 CTAGATATATTAT
1 CTAGATATATTAT
54511 GCCATTTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (14 bp):
CTAGATATATTATA
Found at i:60797 original size:12 final size:12
Alignment explanation
Indices: 60773--60810 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
60763 AAGCAAGGGA
60773 AGCAG-AGAGAGC
1 AGCAGCAGA-AGC
60785 AGCAGCAGAAGC
1 AGCAGCAGAAGC
*
60797 AGCAGCGGAAGC
1 AGCAGCAGAAGC
60809 AG
1 AG
60811 AGAGAGAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 21 0.88
13 3 0.12
ACGTcount: A:0.39, C:0.21, G:0.39, T:0.00
Consensus pattern (12 bp):
AGCAGCAGAAGC
Found at i:60821 original size:21 final size:21
Alignment explanation
Indices: 60783--60861 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
60773 AGCAGAGAGA
*
60783 GCAGCAGCAGA-AGCAGCAGCG
1 GCAGCA-CAGAGAGAAGCAGCG
* * *
60804 GAAGCAGAGAGAGAAGCAGTG
1 GCAGCACAGAGAGAAGCAGCG
*
60825 GCAGCACAGAGAGAGGCAGCG
1 GCAGCACAGAGAGAAGCAGCG
*
60846 GCAGAACAGAGAGAAG
1 GCAGCACAGAGAGAAG
60862 TAATATATCA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 3 0.06
21 44 0.94
ACGTcount: A:0.39, C:0.19, G:0.41, T:0.01
Consensus pattern (21 bp):
GCAGCACAGAGAGAAGCAGCG
Found at i:61366 original size:43 final size:43
Alignment explanation
Indices: 61288--61425 Score: 163
Period size: 43 Copynumber: 3.2 Consensus size: 43
61278 ACATATTTTT
* * *
61288 CGGCGTTTGTAGG-AAAACGCCGCTAAATATCAACATCTTCTG
1 CGGCGTTTGTAGGAAAAACGCCGCTAAAAATAAACATCTACTG
*
61330 CGGCGTTTGTAGGAAAAACGCCGGTAAAAATAAACATCTACTG
1 CGGCGTTTGTAGGAAAAACGCCGCTAAAAATAAACATCTACTG
* * * ** *
61373 CGGCGTTTGT-GAAGAAAACGCCGCTAAACATCAACGCCTATTG
1 CGGCGTTTGTAGGA-AAAACGCCGCTAAAAATAAACATCTACTG
61416 CGGCGTTTGT
1 CGGCGTTTGT
61426 CTGCCAAATG
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
42 15 0.18
43 68 0.82
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (43 bp):
CGGCGTTTGTAGGAAAAACGCCGCTAAAAATAAACATCTACTG
Found at i:61449 original size:43 final size:43
Alignment explanation
Indices: 61302--61552 Score: 211
Period size: 43 Copynumber: 5.8 Consensus size: 43
61292 GTTTGTAGGA
* ** **
61302 AAACGCCGCTAAATATCAACATCT-TCTGCGGCGTTTGTAGGAA
1 AAACGCCGCTAAATATCAACACCTAT-TGCGGCGTTTGTCTGCC
* * * * * ** *
61345 AAACGCCGGTAAAAATAAACATCTACTGCGGCGTTTGTGAAG-A
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT-CTGCC
* *
61388 AAACGCCGCTAAACATCAACGCCTATTGCGGCGTTTGTCTGCC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTGCC
* * *
61431 AAATGCCGTTAAATATCAACACCTATTGCGGCGTTTTTCTGCC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTGCC
* * *
61474 AAACGCCGCTAAATATCAATACCTTTTGCGGCGTTTGT-TGAAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTG-CC
* * * ***
61517 AATCGCCGCTATATGTTGTCACCTATTGCGGCGTTT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
61553 TTTTGTTGAA
Statistics
Matches: 171, Mismatches: 33, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
42 3 0.02
43 166 0.97
44 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTGCC
Found at i:66339 original size:21 final size:20
Alignment explanation
Indices: 66253--66410 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
66243 AAATGACCAA
**
66253 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
66272 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
66292 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
66312 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
66333 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* ** *
66354 CAAATTCGCATTGTGATTTT
1 CAAAATCGCAACGCGATTTT
* *
66374 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
66395 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
66411 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 41 0.40
21 45 0.44
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:66439 original size:20 final size:20
Alignment explanation
Indices: 66377--66606 Score: 223
Period size: 20 Copynumber: 11.5 Consensus size: 20
66367 TGATTTTCCA
* ** *
66377 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
66397 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
66417 AAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
66437 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
66457 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
66477 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
66497 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
66517 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
66537 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
66557 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
66577 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
66597 AAATCACAAC
1 AAATCGCAAC
66607 ACTGAAATTT
Statistics
Matches: 174, Mismatches: 30, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 170 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:67527 original size:12 final size:12
Alignment explanation
Indices: 67510--67534 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
67500 ATATAATCCT
67510 GAAGAAGAAAAA
1 GAAGAAGAAAAA
67522 GAAGAAGAAAAA
1 GAAGAAGAAAAA
67534 G
1 G
67535 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:69840 original size:19 final size:19
Alignment explanation
Indices: 69818--70086 Score: 291
Period size: 19 Copynumber: 15.4 Consensus size: 19
69808 CGGAAATTAC
*
69818 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
69837 AATCACAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
69851 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
69871 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
69885 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
69904 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
69923 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
69937 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
69956 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
69975 AATCGCAA--C--AA-GAG
1 AATCGCAATGCGAAATGAA
69989 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
70008 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
70027 AATCGCAA----AGA-GAG
1 AATCGCAATGCGAAATGAA
70041 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
70060 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
70079 AATCGCAA
1 AATCGCAA
70087 CGAGAGAATC
Statistics
Matches: 212, Mismatches: 12, Indels: 52
0.77 0.04 0.19
Matches are distributed among these distances:
14 52 0.25
15 6 0.03
16 6 0.03
17 5 0.02
18 7 0.03
19 123 0.58
20 13 0.06
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:69905 original size:33 final size:33
Alignment explanation
Indices: 69818--70108 Score: 233
Period size: 33 Copynumber: 8.5 Consensus size: 33
69808 CGGAAATTAC
* *
69818 AATCGCAACGCGAAATGAAAATCACAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
69851 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
69885 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
69923 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
69956 AATCGCAATGCGAAATGAAAATCGCAACAAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
* *
69989 AATCGCAATGCGAAATGAAAATCGCAATGCG-A
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
*
70021 AAT-GAAAAT-CGCAAA-GAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCG-AAATGA-A-AATCGCAA--CG--A-GAA
*
70060 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
70093 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
70109 TATAAACGCA
Statistics
Matches: 216, Mismatches: 17, Indels: 50
0.76 0.06 0.18
Matches are distributed among these distances:
31 5 0.02
32 10 0.05
33 111 0.51
34 32 0.15
35 6 0.03
36 5 0.02
37 2 0.01
38 29 0.13
39 11 0.05
40 5 0.02
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:70124 original size:52 final size:52
Alignment explanation
Indices: 69846--70108 Score: 499
Period size: 52 Copynumber: 5.0 Consensus size: 52
69836 AAATCACAAC
69846 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
69899 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
69951 ATGAAAATCGCAATGCGAAATGAAAATCGCAACAAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
70003 ATGAAAATCGCAATGCGAAATGAAAATCGCAAAGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
70055 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
70107 AT
1 AT
70109 TATAAACGCA
Statistics
Matches: 206, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
52 190 0.92
53 16 0.08
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:70157 original size:19 final size:19
Alignment explanation
Indices: 70133--70177 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
70123 GATTCTCTCG
70133 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
70152 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
70171 TTGCGAT
1 TTGCGAT
70178 AGTCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:70183 original size:19 final size:19
Alignment explanation
Indices: 70142--70185 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
70132 GTTGCGATTT
**
70142 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
70161 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
70180 TCATTT
1 TCATTT
70186 TTGCCTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:70303 original size:14 final size:14
Alignment explanation
Indices: 70284--70320 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
70274 CATCAATTAC
70284 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
70298 ACAAATCATCTTTT
1 ACAAATCAACTTTT
70312 ACAAATCAA
1 ACAAATCAA
70321 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:72318 original size:14 final size:14
Alignment explanation
Indices: 72299--72355 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
72289 GCGAAATGAA
*
72299 AATCGCAACGACAG
1 AATCGCAACGAAAG
72313 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
72330 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
72346 AATCGCAACG
1 AATCGCAACG
72356 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:72326 original size:33 final size:33
Alignment explanation
Indices: 72280--72372 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
72270 GCGAAACCAA
*
72280 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
72313 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
72346 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
72373 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:72337 original size:19 final size:19
Alignment explanation
Indices: 72243--72377 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
72233 TAGTTTACTT
* *
72243 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
72263 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
72282 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
72301 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
72315 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
72334 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
72348 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
72367 TCGCAATGCGA
1 TCGCAACGCGA
72378 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:72415 original size:33 final size:33
Alignment explanation
Indices: 72373--72464 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
72363 AAAATCGCAA
*
72373 TGCGATTTTGGTTTCGCGTTGTGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
72406 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
72439 TGCGATTTTTATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
72465 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.16, G:0.28, T:0.48
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:72427 original size:19 final size:19
Alignment explanation
Indices: 72373--72501 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
72363 AAAATCGCAA
72373 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
72392 TGTGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
72406 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
72425 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
72439 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
72458 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
72477 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
72497 TGCGA
1 TGCGA
72502 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 13 0.15
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:72665 original size:93 final size:93
Alignment explanation
Indices: 72549--73017 Score: 922
Period size: 93 Copynumber: 5.1 Consensus size: 93
72539 ATGGATTGCA
72549 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
72613 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
72641 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
72706 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
72734 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
72799 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
72827 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
72892 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
72920 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
72985 TAGCAGAATTGGCAGCAACCAAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
73013 TTACT
1 TTACT
73018 AAGCAATCTA
Statistics
Matches: 375, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 4 0.01
93 371 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:74741 original size:14 final size:14
Alignment explanation
Indices: 74722--74811 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
74712 TTGAAATGAA
74722 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
74736 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
74755 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
74769 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
74788 AATCGCAACGAGAG
1 AATCGCAACGAGAG
74802 AATCGCAACG
1 AATCGCAACG
74812 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:74759 original size:33 final size:33
Alignment explanation
Indices: 74714--74828 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
74704 TCTTTTGGTT
74714 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
74747 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
74780 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
74813 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
74829 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:74760 original size:19 final size:19
Alignment explanation
Indices: 74736--74833 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
74726 GCAACGAGAG
*
74736 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
74755 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
74769 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
74788 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
74802 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
74821 AATCGCAATGCGA
1 AATCGCAACGCGA
74834 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 32 0.50
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:74864 original size:14 final size:14
Alignment explanation
Indices: 74845--74901 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
74835 TTTGGTTTCG
74845 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
74859 CGTTGCGATTTTCATATCG
1 CGTTGCGA--TTC---TCT
74878 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
74892 CGTTGCGATT
1 CGTTGCGATT
74902 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:74879 original size:33 final size:33
Alignment explanation
Indices: 74842--74906 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
74832 GATTTTGGTT
74842 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
74875 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
74907 TTCTCTCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.43
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
Found at i:74912 original size:21 final size:21
Alignment explanation
Indices: 74886--74961 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
74876 CGCGTTGCGA
74886 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
74907 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
*
74927 TTCTCTCGTTACGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
74948 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
74962 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.13, C:0.25, G:0.16, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:74942 original size:41 final size:41
Alignment explanation
Indices: 74885--74962 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
74875 TCGCGTTGCG
* *
74885 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGACAGTC
74926 ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGAC
74963 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.14, C:0.26, G:0.15, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:75083 original size:33 final size:33
Alignment explanation
Indices: 75041--75111 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
75031 AATACTAACT
*
75041 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
75074 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
75107 TGAAA
1 TGAAA
75112 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:75517 original size:20 final size:20
Alignment explanation
Indices: 75492--75681 Score: 199
Period size: 20 Copynumber: 9.7 Consensus size: 20
75482 CTTTAAATAT
75492 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
75512 CGCGTTGCGATTT-TGTATTA
1 CGCGTTGCGATTTACGGA-TA
*
75532 -TCGTTGCGA-TTACGGATA
1 CGCGTTGCGATTTACGGATA
*
75550 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
75570 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
75590 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
75610 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * * *
75630 CGAGTTGCGATTTA-TGTTT
1 CGCGTTGCGATTTACGGATA
* ** *
75649 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
75669 CGCGTTGCGATTT
1 CGCGTTGCGATTT
75682 GGAAAATCGC
Statistics
Matches: 140, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
18 4 0.03
19 34 0.24
20 102 0.73
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:75691 original size:20 final size:20
Alignment explanation
Indices: 75648--75743 Score: 75
Period size: 21 Copynumber: 4.7 Consensus size: 20
75638 GATTTATGTT
* * *
75648 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTGCAAAA
*
75668 TCGCGTTGCGATTTGGAAAA
1 TCGCGTTGCGATTTGCAAAA
** * **
75688 TCGCAATGCGAATTTGTACTA
1 TCGCGTTGCG-ATTTGCAAAA
* *
75709 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTGCAA-AA
75730 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
75744 TGGAAACTGA
Statistics
Matches: 59, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 29 0.49
21 30 0.51
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGATTTGCAAAA
Found at i:78671 original size:37 final size:37
Alignment explanation
Indices: 78629--78704 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
78619 GTCCCGTACG
78629 TGACGGTATATAACGAGAGCCTTCTGCATCGCCTTTT
1 TGACGGTATATAACGAGAGCCTTCTGCATCGCCTTTT
* *
78666 TGACGGTATATGACGAGAGCCTTCTGCATTGCCTTTT
1 TGACGGTATATAACGAGAGCCTTCTGCATCGCCTTTT
78703 TG
1 TG
78705 TTTTGGTTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (37 bp):
TGACGGTATATAACGAGAGCCTTCTGCATCGCCTTTT
Found at i:78994 original size:21 final size:21
Alignment explanation
Indices: 78968--79018 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
78958 ACGTTCGTGA
* ** *
78968 ATTTTTTTTCTAAAGTAGTTG
1 ATTTTTTTTATAAAAAAATTG
*
78989 ATTTTTTATATAAAAAAATTG
1 ATTTTTTTTATAAAAAAATTG
79010 ATTTTTTTT
1 ATTTTTTTT
79019 TTCAAAATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (21 bp):
ATTTTTTTTATAAAAAAATTG
Found at i:85614 original size:31 final size:31
Alignment explanation
Indices: 85573--85645 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
85563 ACATTGATCT
* *
85573 ATTCGATTTAGTCCCTCAGCCATTGACTCCC
1 ATTCGTTTTAGTCCCTCAACCATTGACTCCC
*
85604 ATTCGTTTTAGTCCCTCAACCGTTGACTCCC
1 ATTCGTTTTAGTCCCTCAACCATTGACTCCC
85635 ATTCGATTTTA
1 ATTCG-TTTTA
85646 TCCTTAGCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
31 33 0.87
32 5 0.13
ACGTcount: A:0.19, C:0.32, G:0.12, T:0.37
Consensus pattern (31 bp):
ATTCGTTTTAGTCCCTCAACCATTGACTCCC
Done.