Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006820.1 Hibiscus syriacus cultivar Beakdansim tig00017331_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: 103749
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:7324 original size:21 final size:21
Alignment explanation
Indices: 7299--7346 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
7289 AGTCGAAGTT
** *
7299 TATATGTGGTCCTTCGGGACA
1 TATATGTAATCCTTCGGAACA
*
7320 TATATGTAATCCTTTGGAACA
1 TATATGTAATCCTTCGGAACA
7341 TATATG
1 TATATG
7347 CGGTACTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.38
Consensus pattern (21 bp):
TATATGTAATCCTTCGGAACA
Found at i:7443 original size:28 final size:28
Alignment explanation
Indices: 7402--7476 Score: 141
Period size: 28 Copynumber: 2.7 Consensus size: 28
7392 TCATTAAGGA
7402 GTGGTCCTTCGGGACATAGATGTGATAT
1 GTGGTCCTTCGGGACATAGATGTGATAT
*
7430 GTGGTCCTTTGGGACATAGATGTGATAT
1 GTGGTCCTTCGGGACATAGATGTGATAT
7458 GTGGTCCTTCGGGACATAG
1 GTGGTCCTTCGGGACATAG
7477 GTTCTTCGGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.32
Consensus pattern (28 bp):
GTGGTCCTTCGGGACATAGATGTGATAT
Found at i:9717 original size:21 final size:21
Alignment explanation
Indices: 9648--9728 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
9638 ACCTCAATTT
* *
9648 TAAATCTTAAACATTAAACCC
1 TAAATCCTAAACCTTAAACCC
* **
9669 CAAAT-CTCAAACCTTAAAAATC
1 TAAATCCT-AAACCTT-AAACCC
*
9691 T-TATCCTAAACCTTAAACCC
1 TAAATCCTAAACCTTAAACCC
*
9711 TAAATCCTAAAACTTAAA
1 TAAATCCTAAACCTTAAA
9729 TCTTAAATTT
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
20 6 0.13
21 33 0.73
22 6 0.13
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAATCCTAAACCTTAAACCC
Found at i:9735 original size:21 final size:21
Alignment explanation
Indices: 9686--9736 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
9676 CAAACCTTAA
*
9686 AAATCTT--ATCCTAAACCTT
1 AAATCTTAAATCCTAAAACTT
* *
9705 AAACCCTAAATCCTAAAACTT
1 AAATCTTAAATCCTAAAACTT
9726 AAATCTTAAAT
1 AAATCTTAAAT
9737 TTTAAACCCT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 5 0.20
21 20 0.80
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATCTTAAATCCTAAAACTT
Found at i:14444 original size:2 final size:2
Alignment explanation
Indices: 14437--14467 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14427 TATTAATTAT
14437 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 T
14468 TGTAGTTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22965 original size:23 final size:23
Alignment explanation
Indices: 22934--22979 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
22924 CACCACAACT
* *
22934 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
*
22957 CGTAGAAATACACCGTAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
22980 TATAAGATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:25322 original size:21 final size:21
Alignment explanation
Indices: 25280--25322 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
25270 AAGTTGATAT
*
25280 AGTGAATTTTCGGGCATGAAC
1 AGTGAATTTTCGGGCATAAAC
* * *
25301 AGTGATTTTTCTGGCTTAAAC
1 AGTGAATTTTCGGGCATAAAC
25322 A
1 A
25323 AAAATTTCAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (21 bp):
AGTGAATTTTCGGGCATAAAC
Found at i:25380 original size:21 final size:22
Alignment explanation
Indices: 25340--25381 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
25330 CAGATTGTGC
25340 AGGGGGTACAGATTCTCCCCTG
1 AGGGGGTACAGATTCTCCCCTG
25362 AGGGGGTATCA-ATTC-CCCCT
1 AGGGGGTA-CAGATTCTCCCCT
25382 AAATGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 12 0.63
23 2 0.11
ACGTcount: A:0.19, C:0.29, G:0.29, T:0.24
Consensus pattern (22 bp):
AGGGGGTACAGATTCTCCCCTG
Found at i:26194 original size:21 final size:21
Alignment explanation
Indices: 26168--26224 Score: 98
Period size: 21 Copynumber: 2.7 Consensus size: 21
26158 GGGTTTCATA
26168 GGTCTTTCGGGACAATACAGT
1 GGTCTTTCGGGACAATACAGT
26189 GGTCTTTCGGGACAATACAGT
1 GGTCTTTCGGGACAATACAGT
26210 GGT-TCTTCGGGACAA
1 GGTCT-TTCGGGACAA
26225 ATTTCATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 1 0.03
21 34 0.97
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (21 bp):
GGTCTTTCGGGACAATACAGT
Found at i:43443 original size:37 final size:36
Alignment explanation
Indices: 43402--43671 Score: 204
Period size: 37 Copynumber: 7.6 Consensus size: 36
43392 GAAAACGTAC
* *
43402 TTTTGAAAATGTATAATATATAGTTTTTTAAAATGGT
1 TTTTGAAAACGTATAATATATAGTTTTTTAAAAT-AT
* * *
43439 TTTTGAAAATGTATAGTATATAG-TTTTAAAAATAT
1 TTTTGAAAACGTATAATATATAGTTTTTTAAAATAT
** *
43474 TTTTTTAAA--TATAATATATAGTTTTTTAAAAAATAA
1 TTTTGAAAACGTATAATATATAGTTTTTT--AAAATAT
* * *
43510 TTTTGAAAACATATAATATATAG-TTTTTAAAACAG
1 TTTTGAAAACGTATAATATATAGTTTTTTAAAATAT
* *
43545 TTTTGAAAACGTATAATATATAATTTTTTTAAAAAAAGTT
1 TTTTGAAAACGTATAATATAT-AGTTTTTT-AAAATA--T
* * *
43585 TTTTTAAAACATAT-ATA-ATA-TTGTTTTGAAAACAT
1 TTTTGAAAACGTATAATATATAGTT-TTTT-AAAATAT
*
43620 ATTTTGAAAA--TGT-ATATATAG-TTTTTAAAATAT
1 -TTTTGAAAACGTATAATATATAGTTTTTTAAAATAT
*
43653 TTTTGAAAACATAT-ATATA
1 TTTTGAAAACGTATAATATA
43672 ATTTTCGAAA
Statistics
Matches: 193, Mismatches: 24, Indels: 35
0.77 0.10 0.14
Matches are distributed among these distances:
32 9 0.05
33 17 0.09
34 20 0.10
35 38 0.20
36 33 0.17
37 42 0.22
38 19 0.10
39 3 0.02
40 12 0.06
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (36 bp):
TTTTGAAAACGTATAATATATAGTTTTTTAAAATAT
Found at i:43477 original size:35 final size:35
Alignment explanation
Indices: 43402--43671 Score: 187
Period size: 35 Copynumber: 7.6 Consensus size: 35
43392 GAAAACGTAC
* * *
43402 TTTTGAAAATGTATAATATATAGTTTTTTAAAATGGT
1 TTTTGAAAACGTATAATATATAG-TTTTAAAAAT-AT
* *
43439 TTTTGAAAATGTATAGTATATAGTTTTAAAAATAT
1 TTTTGAAAACGTATAATATATAGTTTTAAAAATAT
** *
43474 TTTTTTAAA--TATAATATATAGTTTTTTAAAAAATAA
1 TTTTGAAAACGTATAATATATAG--TTTT-AAAAATAT
* * * *
43510 TTTTGAAAACATATAATATATAGTTTTTAAAACAG
1 TTTTGAAAACGTATAATATATAGTTTTAAAAATAT
* *
43545 TTTTGAAAACGTATAATATATAATTTTTTTAAAAAAAGTT
1 TTTTGAAAACGTATAATATAT-A--GTTTTAAAAATA--T
* * *
43585 TTTTTAAAACATAT-ATAATATTGTTTTGAAAACATA-
1 TTTTGAAAACGTATAAT-ATATAGTTTT-AAAA-ATAT
* *
43621 TTTTGAAAA--TGT-ATATATAGTTTTTAAAATAT
1 TTTTGAAAACGTATAATATATAGTTTTAAAAATAT
*
43653 TTTTGAAAACATAT-ATATA
1 TTTTGAAAACGTATAATATA
43672 ATTTTCGAAA
Statistics
Matches: 190, Mismatches: 27, Indels: 35
0.75 0.11 0.14
Matches are distributed among these distances:
31 3 0.02
32 12 0.06
33 20 0.11
34 11 0.06
35 37 0.19
36 36 0.19
37 26 0.14
38 25 0.13
39 4 0.02
40 16 0.08
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (35 bp):
TTTTGAAAACGTATAATATATAGTTTTAAAAATAT
Found at i:43531 original size:108 final size:109
Alignment explanation
Indices: 43366--43671 Score: 294
Period size: 108 Copynumber: 2.8 Consensus size: 109
43356 TCAAACGTAA
* * ** *
43366 TTTTAAAA-GTATATAGTATATGTTTTGAAAACGTACTTTTGAAAATGTATAATATATAGTTTTT
1 TTTTAAAACATATATAATAT-TGTTTTGAAAAAATA-TTTTGAAAA-ATATAATATATAG-TTTT
* * *
43430 TAAAATGGTTTTTGAAAATGTATAGTATAT-A-GTTTTAAAAATA-TTT
62 TAAAAT-GTTTTTGAAAACGTATAATATATAATGTTTTAAAAAAAGTTT
*
43476 TTTT-AAATATA-ATATATAGTT-TTTT-AAAAAATAATTTTGAAAACATATAATATATAGTTTT
1 TTTTAAAACATATATA-ATA-TTGTTTTGAAAAAAT-ATTTTGAAAA-ATATAATATATAGTTTT
* *
43537 TAAAACAG-TTTTGAAAACGTATAATATATAATTTTTTTAAAAAAAGTTT
62 TAAAA-TGTTTTTGAAAACGTATAATATATAA-TGTTTTAAAAAAAGTTT
* *
43586 TTTTAAAACATATATAATATTGTTTTGAAAACATATTTTG-AAAATGT-ATATATAGTTTTTAAA
1 TTTTAAAACATATATAATATTGTTTTGAAAAAATATTTTGAAAAATATAATATATAGTTTTTAAA
* *
43649 ATATTTTTGAAAACATAT-ATATA
66 ATGTTTTTGAAAACGTATAATATA
43672 ATTTTCGAAA
Statistics
Matches: 165, Mismatches: 17, Indels: 31
0.77 0.08 0.15
Matches are distributed among these distances:
106 19 0.12
107 16 0.10
108 56 0.34
109 24 0.15
110 21 0.13
111 20 0.12
112 9 0.05
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (109 bp):
TTTTAAAACATATATAATATTGTTTTGAAAAAATATTTTGAAAAATATAATATATAGTTTTTAAA
ATGTTTTTGAAAACGTATAATATATAATGTTTTAAAAAAAGTTT
Found at i:43708 original size:17 final size:17
Alignment explanation
Indices: 43648--43708 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
43638 TAGTTTTTAA
43648 AATATTTTTGAAAACATAT
1 AATATTTTTG-AAA-ATAT
* *
43667 ATATAATTTTCGAAAACAT
1 A-AT-ATTTTTGAAAATAT
*
43686 ATTATTTTTGAAAATAT
1 AATATTTTTGAAAATAT
43703 AATATT
1 AATATT
43709 ATATAGTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 17 0.50
18 1 0.03
19 5 0.15
20 5 0.15
21 6 0.18
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (17 bp):
AATATTTTTGAAAATAT
Found at i:43734 original size:5 final size:5
Alignment explanation
Indices: 43724--43793 Score: 55
Period size: 5 Copynumber: 15.2 Consensus size: 5
43714 GTTTTTATTA
* * *
43724 TATAT TATAT TATAT TAATAG TATAT TAT-T TTTAT T-T-T TAT-T TTTAT
1 TATAT TATAT TATAT T-ATAT TATAT TATAT TATAT TATAT TATAT TATAT
43771 T-TAT TATA- TAT-T TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT T
43794 TTAATTTCAT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
3 2 0.04
4 18 0.33
5 30 0.56
6 4 0.07
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (5 bp):
TATAT
Found at i:43760 original size:6 final size:6
Alignment explanation
Indices: 43749--43810 Score: 54
Period size: 6 Copynumber: 9.8 Consensus size: 6
43739 TAATAGTATA
* *
43749 TTATTT TTATTT TTATTT TTATTT ATTATATAT TTA-TA TTATATT TTAATT
1 TTATTT TTATTT TTATTT TTATTT -TTAT-T-T TTATTT TTAT-TT TTATTT
*
43800 TCATTT TTATT
1 TTATTT TTATT
43811 AGATCTAGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
5 3 0.07
6 29 0.64
7 8 0.18
8 4 0.09
9 1 0.02
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (6 bp):
TTATTT
Found at i:46308 original size:20 final size:20
Alignment explanation
Indices: 46272--46309 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46262 ATCCTATTCC
**
46272 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
46292 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
46310 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:46964 original size:73 final size:71
Alignment explanation
Indices: 46830--46964 Score: 177
Period size: 70 Copynumber: 1.9 Consensus size: 71
46820 CAACCGCAAT
46830 TTTTTCTTTGTTTCAAAAAATGAAAGGTCGGGGGACGAGGAAGGGAAGGGGGAGTTGAGAGTGAA
1 TTTTTCTTTGTTTCAAAAAATGAAAGGTCGGGGGACGAGGAAGGGAAGGGGGAGTTGAGAGTGAA
46895 AGCATA
66 AGCATA
* * *
46901 TTTTT-TTTGTTTCAGACAATGAAATCGGT-GAGGGGAGGAGGAAAGGG-AGGGGAGAGTTGAGA
1 TTTTTCTTTGTTTCAAAAAATGAAA--GGTCG-GGGGACGAGG-AAGGGAAGGGG-GAGTTGAGA
46963 GT
61 GT
46965 AAAACTGTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
70 17 0.30
71 6 0.11
72 17 0.30
73 16 0.29
ACGTcount: A:0.30, C:0.06, G:0.39, T:0.25
Consensus pattern (71 bp):
TTTTTCTTTGTTTCAAAAAATGAAAGGTCGGGGGACGAGGAAGGGAAGGGGGAGTTGAGAGTGAA
AGCATA
Found at i:47066 original size:12 final size:13
Alignment explanation
Indices: 47049--47081 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
47039 TTTCTTTCAT
47049 TTTTTAAAATA-A
1 TTTTTAAAATATA
47061 TTTTTAAAATATA
1 TTTTTAAAATATA
*
47074 ATTTTAAA
1 TTTTTAAA
47082 TGATATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTTTAAAATATA
Found at i:47195 original size:15 final size:15
Alignment explanation
Indices: 47175--47209 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
47165 ATTTAGTCTT
47175 AATTTCAGTAATATA
1 AATTTCAGTAATATA
* *
47190 AATTTCTGTAATTTA
1 AATTTCAGTAATATA
47205 AATTT
1 AATTT
47210 TACAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (15 bp):
AATTTCAGTAATATA
Found at i:48991 original size:29 final size:29
Alignment explanation
Indices: 48958--49060 Score: 100
Period size: 29 Copynumber: 3.5 Consensus size: 29
48948 GAACATAATA
48958 AATAGTCAAATGACTATTTTATAACTTTT
1 AATAGTCAAATGACTATTTTATAACTTTT
* *** **
48987 AATAGTCAAATGATTTAATAAAATAACTTCC
1 AATAGTCAAATGA-CT-ATTTTATAACTTTT
* *
49018 AATAATCAAATGATTATTTTATAACTTTT
1 AATAGTCAAATGACTATTTTATAACTTTT
*
49047 AATATTCAAA-GACT
1 AATAGTCAAATGACT
49061 TAATAAATAA
Statistics
Matches: 58, Mismatches: 14, Indels: 5
0.75 0.18 0.06
Matches are distributed among these distances:
28 3 0.05
29 31 0.53
30 3 0.05
31 21 0.36
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.40
Consensus pattern (29 bp):
AATAGTCAAATGACTATTTTATAACTTTT
Found at i:49070 original size:29 final size:29
Alignment explanation
Indices: 48978--49070 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 29
48968 TGACTATTTT
*
48978 ATAACTTTTAATAGTCAAATGATTTAATAAA
1 ATAACTTTTAATAATCAAATGA-TTAAT-AA
** * **
49009 ATAACTTCCAATAATCAAATGATTATTTT
1 ATAACTTTTAATAATCAAATGATTAATAA
*
49038 ATAACTTTTAATATTCAAA-GACTTAATAA
1 ATAACTTTTAATAATCAAATGA-TTAATAA
49067 ATAA
1 ATAA
49071 TATCAGATAA
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
28 2 0.04
29 24 0.49
30 4 0.08
31 19 0.39
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (29 bp):
ATAACTTTTAATAATCAAATGATTAATAA
Found at i:49967 original size:87 final size:87
Alignment explanation
Indices: 49821--49983 Score: 283
Period size: 87 Copynumber: 1.9 Consensus size: 87
49811 TATGTTATAT
* *
49821 TATTTAACCGGAAATATTATCAAGTATAATAACATATTAGGTAGTGCTTATATAATGTAATAGGT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGTGCTTACATAATGTAATAGGT
49886 AGCGTTTATATAATAGAATAAG
66 AGCGTTTATATAATAGAATAAG
*
49908 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTA-TCGTTTACATAATGTAATAGG
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGT-GCTTACATAATGTAATAGG
49972 TAGCGTTTATAT
65 TAGCGTTTATAT
49984 TGACCTATTT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
86 1 0.01
87 71 0.99
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGTGCTTACATAATGTAATAGGT
AGCGTTTATATAATAGAATAAG
Found at i:50414 original size:201 final size:200
Alignment explanation
Indices: 50005--50702 Score: 906
Period size: 201 Copynumber: 3.5 Consensus size: 200
49995 CTAACTATAC
* * * * * * * * *
50005 CGGTTTATTTATACTGATAACATTTCAAATTTACCTATTACATTATAATTATCGTTTTCGATGTT
1 CGGTATATTTATACCGGTTACATTACAAAATTACATATTACATTATAATTATGGGTTTCGATGTT
** * *
50070 TTTGGGATCGATACAATTT-TAAATGTATCGACACTTTATGCGTGCACCTCGTTGAGCATTCATT
66 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCTTTGGGCATTCATT
* * * * * *
50134 CTGGA-AAAAAGTATCGACCCATATTTA-AC-AGTGTCGATATATTATGTTGACTTATTCTCACA
131 CTGGACAAAAAGTATCGACACA-AATTACACAAGTGTCAATACATTATGTTGACCTATTCTCTCA
50196 TAAAAT
195 TAAAAT
50202 CGGTATATTTATACCGGTTACATTACAAAATTACATATTACATTATAATTATGTGG-TTCGATGT
1 CGGTATATTTATACCGGTTACATTACAAAATTACATATTACATTATAATTATG-GGTTTCGATGT
* * *
50266 TTTTGGGATAGAGACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTTGGGCATTCA
65 TTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTC-TTTGGGCATTCA
* *
50331 TTCTGGACAAAAATTATCGACACAAATTACACAAGTGTCAATACATTATGTAGACCTATTCTCTC
129 TTCTGGACAAAAAGTATCGACACAAATTACACAAGTGTCAATACATTATGTTGACCTATTCTCTC
50396 ATAAAAT
194 ATAAAAT
* *
50403 CGGTATATTTATACCAGTTACATTAAAAAATTACATATTACATTATAATTATGGGTTTCGATGTT
1 CGGTATATTTATACCGGTTACATTACAAAATTACATATTACATTATAATTATGGGTTTCGATGTT
*
50468 TTTGGGATCGATACTTTTTATAAATGTATTGACACTTTATGCGTGCACCTCGTTTGGGCATTCAT
66 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTC-TTTGGGCATTCAT
* * * * * * * *
50533 TCTGGACAATAAGTATCGACACAAATTCCACAAGTGTCTATACATTATGTTTACCTGTTTTGTAA
130 TCTGGACAAAAAGTATCGACACAAATTACACAAGTGTCAATACATTATGTTGACCTATTCTCTCA
*
50598 T-TAAT
195 TAAAAT
* * ** * * *
50603 CGGTATATTTATACCGGTTATACTATTAATTTACCTATTACATTATAATTATGGGTTTCGATGAT
1 CGGTATATTTATACCGGTTACATTACAAAATTACATATTACATTATAATTATGGGTTTCGATGTT
*
50668 TTTGGGGTCGATAC-TTTTATAAAGTGTATCGACAC
66 TTTGGGATCGATACTTTTTATAAA-TGTATCGACAC
50703 ATATGTTGAC
Statistics
Matches: 441, Mismatches: 52, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
197 69 0.16
198 31 0.07
199 30 0.07
200 101 0.23
201 210 0.48
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (200 bp):
CGGTATATTTATACCGGTTACATTACAAAATTACATATTACATTATAATTATGGGTTTCGATGTT
TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCTTTGGGCATTCATT
CTGGACAAAAAGTATCGACACAAATTACACAAGTGTCAATACATTATGTTGACCTATTCTCTCAT
AAAAT
Found at i:53454 original size:19 final size:19
Alignment explanation
Indices: 53430--53477 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 19
53420 TTACATTCAC
53430 ATACAAAATTAT-AACTCGT
1 ATACAAAATTATGAA-TCGT
53449 ATACAAAATTATGAATCGT
1 ATACAAAATTATGAATCGT
53468 ATACAAAATT
1 ATACAAAATT
53478 TCCCCTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 26 0.93
20 2 0.07
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATGAATCGT
Found at i:55641 original size:22 final size:23
Alignment explanation
Indices: 55613--55667 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
55603 AACCTGCATT
*
55613 TATAATAAAAT-TTATCATTTTA
1 TATAATAAAATACTATCATTTTA
*
55635 TATAATAACTATACTATCATTTTA
1 TATAATAA-AATACTATCATTTTA
55659 TATAA-AAAA
1 TATAATAAAA
55668 CAAAAATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 9 0.32
23 4 0.14
24 15 0.54
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (23 bp):
TATAATAAAATACTATCATTTTA
Found at i:58256 original size:182 final size:182
Alignment explanation
Indices: 57501--58241 Score: 1090
Period size: 182 Copynumber: 4.1 Consensus size: 182
57491 AACCCAAGTG
* * *
57501 TCGATACATTTTTATAAAGTATCTACACTTTATATGCGCTATTACTGATTCTCTTTTAAATTCCA
1 TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCA
* * * *
57566 AAAGTATCGATACTTA-AAGTAAAGTATCGACACTTTTAATATATCTGGTGGCGCTTTACCGGTT
66 AAAGTATCGATACTTATAA-TAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTT
57630 TTGTCATTTTGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
130 TTGTCATTTTGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
* * ** * *
57683 TCGATACATTTTTATAAAATATCGACACTTTATAGACGCTATTACTGCTGGTTTTTTTAATTCCA
1 TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCA
* * *
57748 AAAGTATCGATACTTATAATAAAATATCGATACTTTCAACATATCCGGTAGCTCTTTACCGGTTT
66 AAAGTATCGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTT
*
57813 TGTCATTTTGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGAA
131 TGTCATTTTGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
* * *
57865 TCAATACATTTTTATAAAGTGTCGACACTTTATAGGCGCTATTACTGCTTGTCTTTTAAATTCCA
1 TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCA
* *
57930 AAAGTGTTGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTT
66 AAAGTATCGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTT
* * * *
57995 TGTCATTTAT-AAACCGGTTTTATGATATTTTAACATGTTATATTGTTATGGA
131 TGTCATTT-TGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
* *
58047 TCGATATATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCATTTAAATTCCA
1 TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCA
* * * * * * *
58112 AAAGTGTAGATGCTTATATTAAAGTATCGATACTTTCAACATATCCGATAGCGCTTTGCCGGTTT
66 AAAGTATCGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTT
* * * * *
58177 GGTCATTTTGATACCGATTTTTTCATATTTTTACCTGTTATATTGCTATGGA
131 TGTCATTTTGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
58229 TCGATACATTTTT
1 TCGATACATTTTT
58242 TATTTGTATC
Statistics
Matches: 502, Mismatches: 54, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
181 1 0.00
182 498 0.99
183 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (182 bp):
TCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCA
AAAGTATCGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTT
TGTCATTTTGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
Found at i:59341 original size:21 final size:21
Alignment explanation
Indices: 59291--59344 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
59281 TCGGTGATTG
* * *
59291 CAGCCATAGCAGATGCTATTA
1 CAGCCGTAGCGGACGCTATTA
59312 CAGCCGTAGCGGACGCTATTA
1 CAGCCGTAGCGGACGCTATTA
**
59333 CAGGTGTAGCGG
1 CAGCCGTAGCGG
59345 GTATATCGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (21 bp):
CAGCCGTAGCGGACGCTATTA
Found at i:60432 original size:202 final size:204
Alignment explanation
Indices: 60033--60441 Score: 680
Period size: 202 Copynumber: 2.0 Consensus size: 204
60023 AGGATTAACA
60033 GGTACTTCTAGGTGCCTGATTAGAAATTAGTTACCATTGTAGGGGAGTTCTGCATTTAATACATT
1 GGTACTTCTAGGTGCCTGATTAGAAATTAGTTACCATTGTAGGGGAGTTCTGCATTTAATACATT
* ** * *
60098 ACTTTTACTGAGTTTGAGGGAAAAAATAATGTGTTCATTATTATTTTCCGTTCTATACATATCAC
66 ACTTTTACTGAGTTCGAGAAAAAAAATAATGTGTTCATTATGATTTTCCGTTCTACACATATCAC
60163 TTTAAGCACTTTCAGTTGATTGATATTTTCCTTCTTCAAACTGGGTATATAGAAAAAATATTAAC
131 TTTAAGCACTTTCAGTTGATTGATATTTTCCTTCTTCAAACTGGGTATATAGAAAAAATATTAAC
*
60228 CTCTAAAAG
196 CTCAAAAAG
*
60237 GGTACTTCTAGGTG-CTGATTA-AATATTAGTTACCATTGTAGGGGAGTTTTGCATTTAATACAT
1 GGTACTTCTAGGTGCCTGATTAGAA-ATTAGTTACCATTGTAGGGGAGTTCTGCATTTAATACAT
* *
60300 TACTTTTACTGAGTTCGAGAAAAAAAATACTGTGTTCATTATGA-TTTCCGTTCTACATATATCA
65 TACTTTTACTGAGTTCGAGAAAAAAAATAATGTGTTCATTATGATTTTCCGTTCTACACATATCA
* * *
60364 CTTTAAGCACTTTCAGTTGATTGATATTTTCCTTCTTCAAGCTGTGTATATAGGAAAAATATTAA
130 CTTTAAGCACTTTCAGTTGATTGATATTTTCCTTCTTCAAACTGGGTATATAGAAAAAATATTAA
60429 CCTCAAAAAG
195 CCTCAAAAAG
60439 GGT
1 GGT
60442 GCTTTATAAG
Statistics
Matches: 192, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
202 94 0.49
203 84 0.44
204 14 0.07
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (204 bp):
GGTACTTCTAGGTGCCTGATTAGAAATTAGTTACCATTGTAGGGGAGTTCTGCATTTAATACATT
ACTTTTACTGAGTTCGAGAAAAAAAATAATGTGTTCATTATGATTTTCCGTTCTACACATATCAC
TTTAAGCACTTTCAGTTGATTGATATTTTCCTTCTTCAAACTGGGTATATAGAAAAAATATTAAC
CTCAAAAAG
Found at i:70693 original size:11 final size:12
Alignment explanation
Indices: 70666--70699 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
70656 TTATTATTTA
*
70666 AATAATAAAATT
1 AATAAAAAAATT
70678 AATAAAAAAATT
1 AATAAAAAAATT
70690 -ATAAAAAAAT
1 AATAAAAAAAT
70700 ATTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAAAAAAATT
Found at i:70783 original size:12 final size:12
Alignment explanation
Indices: 70766--70805 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
70756 ATCGAAAAAA
70766 TATTATTAATTT
1 TATTATTAATTT
*
70778 TATTATT--TCT
1 TATTATTAATTT
70788 T-TTATTAATTT
1 TATTATTAATTT
70799 TATTATT
1 TATTATT
70806 GTTAGACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
9 5 0.22
10 3 0.13
11 3 0.13
12 12 0.52
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTATTAATTT
Found at i:70855 original size:21 final size:21
Alignment explanation
Indices: 70829--70873 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
70819 TTAGAAATAT
*
70829 TAAAAATATTAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
70850 TAAAAATAATAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
70871 TAA
1 TAA
70874 TTTTTATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAA
Found at i:72702 original size:32 final size:32
Alignment explanation
Indices: 72658--72727 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
72648 ATAGTATAAA
*
72658 TCATATTCAATCTCTTACAAAACACA-CTCCTT
1 TCATCTTCAATCTCTTACAAAACACACCT-CTT
*
72690 TCATCTTCAATCTCTTACACAACACACCTCTT
1 TCATCTTCAATCTCTTACAAAACACACCTCTT
72722 TCATCT
1 TCATCT
72728 AACCAAATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.30, C:0.34, G:0.00, T:0.36
Consensus pattern (32 bp):
TCATCTTCAATCTCTTACAAAACACACCTCTT
Found at i:74468 original size:21 final size:21
Alignment explanation
Indices: 74442--74486 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
74432 GATTTCTGGG
* *
74442 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
74463 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
74484 CAA
1 CAA
74487 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:75515 original size:2 final size:2
Alignment explanation
Indices: 75508--75591 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
75498 GAACATGTGA
75508 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75592 GTTTAAGAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76262 original size:22 final size:22
Alignment explanation
Indices: 76234--76322 Score: 169
Period size: 22 Copynumber: 4.0 Consensus size: 22
76224 TATGGACATC
76234 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
76256 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
76278 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
76300 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
76323 TTTATACGAG
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
22 51 0.77
23 15 0.23
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:79507 original size:21 final size:21
Alignment explanation
Indices: 79481--79525 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
79471 GATTTCTGGG
* *
79481 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
79502 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
79523 CAA
1 CAA
79526 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:81258 original size:23 final size:22
Alignment explanation
Indices: 81199--81265 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
81189 TATGGACATC
81199 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
81221 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
81243 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
81266 TTTATACGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 29 0.66
23 15 0.34
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:83918 original size:10 final size:10
Alignment explanation
Indices: 83895--83931 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
83885 TTATATATAA
*
83895 TTTTTACAATT
1 TTTTTA-AAAT
83906 TTTTTAAAAT
1 TTTTTAAAAT
83916 TTTTTAAAAT
1 TTTTTAAAAT
83926 TTTTTA
1 TTTTTA
83932 TTAGAACTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 19 0.76
11 6 0.24
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTAAAAT
Found at i:87790 original size:31 final size:33
Alignment explanation
Indices: 87747--87823 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 33
87737 TTTAAATAGT
*
87747 TATTA-TTTTTTATT-AAT-ATATTTATGTAAA
1 TATTATTTTTTTATTAAATAATATTTATATAAA
*
87777 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATT-AAATAATATTTATATAAA
*
87811 TATTATTTATTTA
1 TATTATTTTTTTA
87824 GAATTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
30 5 0.12
31 9 0.22
33 3 0.08
34 23 0.57
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (33 bp):
TATTATTTTTTTATTAAATAATATTTATATAAA
Found at i:87985 original size:17 final size:17
Alignment explanation
Indices: 87963--88016 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
87953 AATGTTAATA
87963 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
87980 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
87997 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
88014 TTT
1 TTT
88017 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:89647 original size:21 final size:21
Alignment explanation
Indices: 89596--89647 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
89586 TATGCCATCT
*
89596 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
89617 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
89638 CCGCAGGGTT
1 CCGCAGGGTT
89648 TTATACCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.17, C:0.35, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:90233 original size:33 final size:33
Alignment explanation
Indices: 90172--90266 Score: 109
Period size: 34 Copynumber: 2.8 Consensus size: 33
90162 ATGTTTTTAT
*
90172 AATACAAATTATATTATTCGAAATTTAAAATAAA
1 AATAAAAATTATATTATTC-AAATTTAAAATAAA
* * *
90206 AATAAAAATAATATTATTCAAATTTAAATTTAA
1 AATAAAAATTATATTATTCAAATTTAAAATAAA
* * *
90239 AATATAAATTATAGTATTTGAAATTTAA
1 AATAAAAATTATATTA-TTCAAATTTAA
90267 CATTAAATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 25 0.48
34 27 0.52
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (33 bp):
AATAAAAATTATATTATTCAAATTTAAAATAAA
Found at i:90240 original size:34 final size:34
Alignment explanation
Indices: 90172--90266 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 34
90162 ATGTTTTTAT
* *
90172 AATACAAATTATATTATTCGAAATTTAAAATAAA
1 AATAAAAATAATATTATTCGAAATTTAAAATAAA
* *
90206 AATAAAAATAATATTATTC-AAATTTAAATTTAA
1 AATAAAAATAATATTATTCGAAATTTAAAATAAA
* * * *
90239 AATATAAATTATAGTATTTGAAATTTAA
1 AATAAAAATAATATTATTCGAAATTTAA
90267 CATTAAATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 27 0.52
34 25 0.48
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (34 bp):
AATAAAAATAATATTATTCGAAATTTAAAATAAA
Found at i:90610 original size:33 final size:32
Alignment explanation
Indices: 90541--90611 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
90531 CACTTCACAT
* *
90541 TTATTCAATTTATCCATAACATTTTATCTAAT
1 TTATTCAAATTATCCATAACATTTTATCTAAG
* *
90573 TTATTCAAATT-TCACATAACGTTTTAATTTAAG
1 TTATTCAAATTATC-CATAACATTTT-ATCTAAG
90606 TTATTC
1 TTATTC
90612 TTAACTTGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 2 0.06
32 20 0.61
33 11 0.33
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.49
Consensus pattern (32 bp):
TTATTCAAATTATCCATAACATTTTATCTAAG
Found at i:91294 original size:128 final size:128
Alignment explanation
Indices: 90666--91294 Score: 1062
Period size: 128 Copynumber: 4.9 Consensus size: 128
90656 TTACCTGATT
* * *
90666 TACTGATATATATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAGTGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
90731 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* *
90794 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGAGCAATGATAACATATTTTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
90859 TGACGAAATAATGGAAGGCGCGCCCTCGGGAACGCGCCTTCATGTGAATAGTGAAATGATATG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
90922 TATTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
90987 TGACGAAATAATGGAAGGCGCGCCCCCGAGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
91050 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
91115 CGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTAAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
91178 TACTGATATATCTAGTGTCCCCAAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
91243 TGACGAAATAATGAAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
91295 ACTCCGATTA
Statistics
Matches: 470, Mismatches: 30, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
127 1 0.00
128 469 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:91378 original size:8 final size:8
Alignment explanation
Indices: 91365--91405 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
91355 TCACAATCTT
91365 TCAAATTC
1 TCAAATTC
91373 TCAAATTC
1 TCAAATTC
* *
91381 CCAAACTC
1 TCAAATTC
91389 T-AAATTC
1 TCAAATTC
91396 TCAAATTC
1 TCAAATTC
91404 TC
1 TC
91406 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:95686 original size:62 final size:63
Alignment explanation
Indices: 95585--95714 Score: 226
Period size: 62 Copynumber: 2.0 Consensus size: 63
95575 TCTAAATACA
95585 ATTAAAAGACCATCACTCAAATGAATATATTTAGAGAAATGTCATCCCAAATAAGATAAAGGCAT
1 ATTAAAAGACCATCACTC--A-GAATATATTTAGAGAAATGTCATCCCAAATAAGATAAAGGCAT
95650 G
63 G
95651 ATTAAAAGACCATCACTC-GAATATATTTAGAGAAATGTCATCCCAAATAAGATAAAGGCATG
1 ATTAAAAGACCATCACTCAGAATATATTTAGAGAAATGTCATCCCAAATAAGATAAAGGCATG
95713 AT
1 AT
95715 CAACTAAGCA
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
62 46 0.72
66 18 0.28
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (63 bp):
ATTAAAAGACCATCACTCAGAATATATTTAGAGAAATGTCATCCCAAATAAGATAAAGGCATG
Found at i:97388 original size:35 final size:35
Alignment explanation
Indices: 97310--97446 Score: 98
Period size: 35 Copynumber: 3.9 Consensus size: 35
97300 ATACTAATAG
* * * * * * *
97310 TGTGTCATGAGTCGCATTCAGACAATGCACAAAAA
1 TGTGTCATGTGTCGTATTCAGATATTGCATAACAC
* **
97345 TGTTTCATGTGTCGTATTCAGATATTGCATAGTAGC
1 TGTGTCATGTGTCGTATTCAGATATTGCATAACA-C
** * **
97381 -GTGTCATGTGTCACATTCAAATAACGCATAACAC
1 TGTGTCATGTGTCGTATTCAGATATTGCATAACAC
*
97415 TGTGTCATGTGTCGTATTTAGAGT-TTGCATAA
1 TGTGTCATGTGTCGTATTCAGA-TATTGCATAA
97447 TAGTCATTCA
Statistics
Matches: 76, Mismatches: 23, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
34 1 0.01
35 74 0.97
36 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (35 bp):
TGTGTCATGTGTCGTATTCAGATATTGCATAACAC
Found at i:99173 original size:25 final size:26
Alignment explanation
Indices: 99145--99221 Score: 70
Period size: 25 Copynumber: 2.9 Consensus size: 26
99135 AATATTTTAT
99145 ATATAAATA-ATATAA-AAATTATAAA
1 ATATAAATATATATAATAAA-TATAAA
* *
99170 ATAT-TATATATATAATTAATATAAA
1 ATATAAATATATATAATAAATATAAA
*
99195 ATATAAAATATTATATATATATATATA
1 ATAT-AAATA-TATATA-ATAAATATA
99222 TATATAATCG
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
24 3 0.07
25 20 0.49
26 2 0.05
27 3 0.07
28 6 0.15
29 7 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
ATATAAATATATATAATAAATATAAA
Found at i:99173 original size:34 final size:33
Alignment explanation
Indices: 99133--99225 Score: 134
Period size: 34 Copynumber: 2.8 Consensus size: 33
99123 CCCGAACCTG
*
99133 AAAATATTTTATATATAAATAATATAAAAATTAT
1 AAAATATTATATATATAAATAATATAAAAA-TAT
*
99167 AAAATATTATATATATAATTAATAT-AAAATAT
1 AAAATATTATATATATAAATAATATAAAAATAT
*
99199 AAAATATTATATATATATATATATATA
1 AAAATATTATATATATAAATA-ATATA
99226 TAATCGGTAC
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
32 22 0.42
33 8 0.15
34 23 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
AAAATATTATATATATAAATAATATAAAAATAT
Found at i:99180 original size:32 final size:31
Alignment explanation
Indices: 99141--99223 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 31
99131 TGAAAATATT
99141 TTATATATAAATAATATAAAAATTATAAAATA
1 TTATATATAAATAATATAAAAA-TATAAAATA
99173 TTATATATATAATTAATAT-AAAATATAAAATA
1 TTATATATA-AA-TAATATAAAAATATAAAATA
*
99205 TTATATATATATATATATA
1 TTATATATAAATA-ATATA
99224 TATAATCGGT
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
30 2 0.04
31 5 0.11
32 27 0.59
33 6 0.13
34 6 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
TTATATATAAATAATATAAAAATATAAAATA
Found at i:101659 original size:2 final size:2
Alignment explanation
Indices: 101652--101688 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
101642 TATTTTCTTC
101652 TA TA TA TA TA TA TA TA T- TA TA TA GTA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
101689 GTTCGCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 28 0.88
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:101674 original size:7 final size:7
Alignment explanation
Indices: 101654--101688 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
101644 TTTTCTTCTA
101654 TATATAT
1 TATATAT
101661 ATATATAT
1 -TATATAT
*
101669 TATATAG
1 TATATAT
101676 TATATAT
1 TATATAT
101683 TATATA
1 TATATA
101689 GTTCGCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (7 bp):
TATATAT
Found at i:101681 original size:14 final size:14
Alignment explanation
Indices: 101652--101690 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
101642 TATTTTCTTC
101652 TATA-TATATA-TA
1 TATATTATATAGTA
101664 TATATTATATAGTA
1 TATATTATATAGTA
101678 TATATTATATAGT
1 TATATTATATAGT
101691 TCGCAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 4 0.16
13 6 0.24
14 15 0.60
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
TATATTATATAGTA
Found at i:101760 original size:38 final size:35
Alignment explanation
Indices: 101717--101822 Score: 110
Period size: 37 Copynumber: 2.9 Consensus size: 35
101707 GAAAAATACG
*
101717 TATATAATATTTTTTAAAAAAAACATTTTGAAAATG
1 TATATAATATTTTTT-AAAAAAACATTTTGAAAATT
* *
101753 TATATATATAGTTTTT--AAAATCATTTTG-AAATT
1 TATATA-ATATTTTTTAAAAAAACATTTTGAAAATT
101786 TATATAATATATAGTTTTAAAAAAACATTTTTGAAAA
1 TATATAATAT-T--TTTTAAAAAAACA-TTTTGAAAA
101823 CATATAATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
32 3 0.05
33 11 0.19
34 11 0.19
35 4 0.07
36 6 0.11
37 14 0.25
38 5 0.09
39 3 0.05
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (35 bp):
TATATAATATTTTTTAAAAAAACATTTTGAAAATT
Found at i:101783 original size:34 final size:32
Alignment explanation
Indices: 101736--101951 Score: 184
Period size: 35 Copynumber: 6.3 Consensus size: 32
101726 TTTTTTAAAA
*
101736 AAAACATTTTGAAAATGTATATATATAGTTTTT
1 AAAACATTTTGAAAATATATATATATAG-TTTT
*
101769 AAAATCATTTTGAAATTTATATAATATATAGTTTT
1 AAAA-CATTTTGAAA-ATATAT-ATATATAGTTTT
*
101804 AAAAAAACATTTTTGAAAACATATA-ATATAGTTTT
1 ---AAAACA-TTTTGAAAATATATATATATAGTTTT
* * *
101839 AAAACGTTTTTGAAAACTATA-ACATATAGTTTG
1 AAAAC-ATTTTGAAAA-TATATATATATAGTTTT
* *
101872 AAAACATTTTTAAAATTATATAATATATGGTTTT
1 AAAACATTTTGAAAA-TATAT-ATATATAGTTTT
* *
101906 GAAAATATCTTTGAAATATATATTATATAAAGTTTT
1 -AAAACAT-TTTGAAA-ATATA-TATATATAGTTTT
101942 AAAACATTTT
1 AAAACATTTT
101952 TTCTTTATAT
Statistics
Matches: 149, Mismatches: 18, Indels: 31
0.75 0.09 0.16
Matches are distributed among these distances:
32 27 0.18
33 21 0.14
34 22 0.15
35 30 0.20
36 29 0.19
37 8 0.05
38 12 0.08
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (32 bp):
AAAACATTTTGAAAATATATATATATAGTTTT
Found at i:101971 original size:103 final size:102
Alignment explanation
Indices: 101753--101952 Score: 226
Period size: 103 Copynumber: 1.9 Consensus size: 102
101743 TTTGAAAATG
* * *
101753 TATAT-ATATAGTTTTTAAAATCATTTTGAAATTTATATAATATATAGTTTTAAAAAAACATTTT
1 TATATCATATAG-TTTGAAAATCATTTTGAAAATTATATAATATATAGTTTT-AAAAAACATCTT
* *
101817 TGAAAACATATAATATAGTTTTAAAACGTTTTTGAAAAC
64 TGAAAACATATAATAAAGTTTTAAAACGTTTTTCAAAAC
* * * * *
101856 TATAACATATAGTTTGAAAA-CATTTTTAAAATTATATAATATATGGTTTT-GAAAATATCTTTG
1 TATATCATATAGTTTGAAAATCATTTTGAAAATTATATAATATATAGTTTTAAAAAACATCTTTG
* *
101919 AAATATATATTATATAAAGTTTTAAAACATTTTT
66 AAA-ACATA-TA-ATAAAGTTTTAAAACGTTTTT
101953 TCTTTATATA
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
100 13 0.16
101 4 0.05
102 29 0.35
103 30 0.37
104 6 0.07
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (102 bp):
TATATCATATAGTTTGAAAATCATTTTGAAAATTATATAATATATAGTTTTAAAAAACATCTTTG
AAAACATATAATAAAGTTTTAAAACGTTTTTCAAAAC
Found at i:101994 original size:16 final size:17
Alignment explanation
Indices: 101973--102007 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
101963 TCATATAGTA
*
101973 TTTTATTCTTT-TTTAT
1 TTTTATTATTTATTTAT
101989 TTTTATTATTTATTTAT
1 TTTTATTATTTATTTAT
102006 TT
1 TT
102008 AATCTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTATTATTTATTTAT
Found at i:103097 original size:17 final size:18
Alignment explanation
Indices: 103061--103098 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
103051 GTTTTCATTC
**
103061 TTTTTTCCTTTTTATTAT
1 TTTTTTCCTTTTTAACAT
103079 TTTTTTCC-TTTTAACAT
1 TTTTTTCCTTTTTAACAT
103096 TTT
1 TTT
103099 ATTATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTCCTTTTTAACAT
Done.