Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005019.1 Hibiscus syriacus cultivar Beakdansim tig00011265_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: 62315
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:774 original size:28 final size:28
Alignment explanation
Indices: 738--815 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
728 AATTTTTATA
* *
738 TAATCTAATATAACTTAAACTAACAAAT
1 TAATATAATATAACTTAAACTAACAAAC
766 TAATATAATATAACTTAAACTAACAAAC
1 TAATATAATATAACTTAAACTAACAAAC
*
794 TAATAATTATATAAC--AAACTAA
1 TAAT-ATAATATAACTTAAACTAA
816 TTAACTAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 7 0.15
28 30 0.65
29 9 0.20
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (28 bp):
TAATATAATATAACTTAAACTAACAAAC
Found at i:1567 original size:29 final size:29
Alignment explanation
Indices: 1473--1599 Score: 101
Period size: 29 Copynumber: 4.2 Consensus size: 29
1463 GCGTGGATGG
* * * *
1473 CGACCTATAAGGTCGCTGGGCGTACATGG
1 CGACCTACAAGGTCGCTGGGAGTGCATGA
* * * *
1502 CGACCTACCATCTTGGTCGCTGGGATTGCTTGG
1 CGACCTA-CA---AGGTCGCTGGGAGTGCATGA
1535 CGACCTACAAGGTCGCTGGGAGTGCATGA
1 CGACCTACAAGGTCGCTGGGAGTGCATGA
*** * *
1564 CGACCTTGTAGGTCGCTTGGAGTGCTTGA
1 CGACCTACAAGGTCGCTGGGAGTGCATGA
1593 CGACCTA
1 CGACCTA
1600 TGGTTGGGTT
Statistics
Matches: 78, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
29 53 0.68
30 1 0.01
32 2 0.03
33 22 0.28
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.24
Consensus pattern (29 bp):
CGACCTACAAGGTCGCTGGGAGTGCATGA
Found at i:4948 original size:104 final size:104
Alignment explanation
Indices: 4768--4980 Score: 417
Period size: 104 Copynumber: 2.0 Consensus size: 104
4758 TCTCTGCCTC
4768 AGTTCAACCCTGGTGGGAAAAGGCTGTTGATGGCTTTTACATATAGGGCTTGGTTTCAACTTGAA
1 AGTTCAACCCTGGTGGGAAAAGGCTGTTGATGGCTTTTACATATAGGGCTTGGTTTCAACTTGAA
4833 ATGATAATAGAAATCTGTTGAAGTACACTAAGTTTCTGA
66 ATGATAATAGAAATCTGTTGAAGTACACTAAGTTTCTGA
4872 AGTTCAACCCTGGTGGGAAAAGGCTGTTGATGGCTTTTACATATAGGGCTTGGTTTCAACTTGAA
1 AGTTCAACCCTGGTGGGAAAAGGCTGTTGATGGCTTTTACATATAGGGCTTGGTTTCAACTTGAA
*
4937 ATGATAATAGAAATCTGTTGAAGTACATTAAGTTTCTGA
66 ATGATAATAGAAATCTGTTGAAGTACACTAAGTTTCTGA
4976 AGTTC
1 AGTTC
4981 TTCTTTCAGT
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 108 1.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (104 bp):
AGTTCAACCCTGGTGGGAAAAGGCTGTTGATGGCTTTTACATATAGGGCTTGGTTTCAACTTGAA
ATGATAATAGAAATCTGTTGAAGTACACTAAGTTTCTGA
Found at i:11845 original size:2 final size:2
Alignment explanation
Indices: 11838--11863 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11828 AAAGATTAAA
11838 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
11864 TATTATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11943 original size:19 final size:20
Alignment explanation
Indices: 11905--11943 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11895 TAAAAGGATT
*
11905 TTTTTAAAAAGATATTTATA
1 TTTTTAAAAAGATATGTATA
*
11925 TTTTTAAAAATA-ATGTATA
1 TTTTTAAAAAGATATGTATA
11944 CTATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTTTAAAAAGATATGTATA
Found at i:25168 original size:54 final size:54
Alignment explanation
Indices: 25083--25206 Score: 185
Period size: 54 Copynumber: 2.3 Consensus size: 54
25073 GTACCCCCTT
* ** *
25083 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGCAAAACTGTTTA
1 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCAAAACCATTCA
* * *
25137 GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGCCAAACCATTCA
1 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCAAAACCATTCA
25191 GGGGGGAATCGGTTCC
1 GGGGGGAATCGGTTCC
25207 TCCTATGGGG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.22, C:0.24, G:0.32, T:0.22
Consensus pattern (54 bp):
GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCAAAACCATTCA
Found at i:25557 original size:10 final size:10
Alignment explanation
Indices: 25542--25566 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25532 AGTTTTGAAA
25542 TTACTCCCCC
1 TTACTCCCCC
25552 TTACTCCCCC
1 TTACTCCCCC
25562 TTACT
1 TTACT
25567 TTAACATACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.52, G:0.00, T:0.36
Consensus pattern (10 bp):
TTACTCCCCC
Found at i:25856 original size:17 final size:17
Alignment explanation
Indices: 25834--25877 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
25824 TTCATAAGTC
25834 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
25851 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
25868 -AAATATCCAA
1 CAAA-ATCCAA
25878 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:27915 original size:21 final size:21
Alignment explanation
Indices: 27837--27923 Score: 77
Period size: 21 Copynumber: 4.0 Consensus size: 21
27827 AACAGAACCC
*
27837 CAGGGGGGGTATCGATTCCC-
1 CAGGGGGGGAATCGATTCCCT
* *
27857 CTGTGGGGGGAATCGGTTCCCCTT
1 CAG-GGGGGGAATCGATT-CCC-T
** *
27881 CAAAGGGGGAATCGGTTCCCT
1 CAGGGGGGGAATCGATTCCCT
*
27902 CAGGGGGGGGATCGATTCCCT
1 CAGGGGGGGAATCGATTCCCT
27923 C
1 C
27924 TGCACCAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.04
21 31 0.58
22 6 0.11
23 13 0.25
24 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.22
Consensus pattern (21 bp):
CAGGGGGGGAATCGATTCCCT
Found at i:33232 original size:54 final size:54
Alignment explanation
Indices: 33147--33270 Score: 176
Period size: 54 Copynumber: 2.3 Consensus size: 54
33137 GTACCCCCTT
* ** *
33147 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCAGAGCAAAACTGTTTA
1 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGAGCAAAACCATTCA
* * * *
33201 GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGCCAAACCATTCA
1 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGAGCAAAACCATTCA
33255 GGGGGGAATCGGTTCC
1 GGGGGGAATCGGTTCC
33271 TCCTATTGGG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.23, C:0.24, G:0.31, T:0.22
Consensus pattern (54 bp):
GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGAGCAAAACCATTCA
Found at i:33650 original size:20 final size:20
Alignment explanation
Indices: 33570--33720 Score: 114
Period size: 20 Copynumber: 7.5 Consensus size: 20
33560 AAATGACCAA
*
33570 CAAATTCGCAACGCG-AACT
1 CAAATTCGCAACGCGAAAGT
* *
33589 CCAATTTCGCAACGCGAATCTGT
1 -CAAATTCGCAACGCGAA--AGT
*
33612 -AAA-TCGCAACAC-ATAAGT
1 CAAATTCGCAACGCGA-AAGT
* *
33630 CAAATTCACAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
* *
33650 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGAAAGT
*
33670 CAAATTCGCAACGCGAAATTT
1 CAAATTCGCAACGCGAAA-GT
* **
33691 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAAAGT
33710 CAAATTCGCAA
1 CAAATTCGCAA
33721 TGCGGAATTT
Statistics
Matches: 105, Mismatches: 18, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
18 2 0.02
19 17 0.16
20 68 0.65
21 17 0.16
23 1 0.01
ACGTcount: A:0.40, C:0.26, G:0.13, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:33710 original size:19 final size:19
Alignment explanation
Indices: 33669--33800 Score: 131
Period size: 19 Copynumber: 6.7 Consensus size: 19
33659 AACACAAAAG
*
33669 TCAAATTCGCAACGCGAAATT
1 TCAAATTCGCAAC-TG-AATT
33690 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
33709 TCAAATTCGCAATGCGGAATT
1 TCAAATTCGCAA--CTGAATT
*
33730 TCAAATTTGCAACTGAATT
1 TCAAATTCGCAACTGAATT
* *
33749 TCAAATTTGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
* *
33769 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
33789 T-AATTTCGCAAC
1 TCAAATTCGCAAC
33801 AGGTTTTAGT
Statistics
Matches: 96, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
19 45 0.47
20 21 0.22
21 30 0.31
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:33713 original size:40 final size:41
Alignment explanation
Indices: 33570--33800 Score: 165
Period size: 40 Copynumber: 5.8 Consensus size: 41
33560 AAATGACCAA
* * * *
33570 CAAATTCGCAACGCGAACTCCAATTTCGCAACGCG-AATCTGT
1 CAAATTCGCAACACGAATTTCAAATTCGCAACGCGAAAT-T-T
** * * *
33612 -AAA-TCGCAACAC-ATAAGTCAAATTCACAACGCGATA-GT
1 CAAATTCGCAACACGA-ATTTCAAATTCGCAACGCGAAATTT
* **
33650 CAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAATTT
1 CAAATTCGCAACACGAATTTCAAATTCGCAACGCGAAATTT
* * *
33691 CAAATTCGCAAC-TGAATTTCAAATTCGCAATGCGGAATTT
1 CAAATTCGCAACACGAATTTCAAATTCGCAACGCGAAATTT
* * * ** *
33731 CAAATTTGCAAC-TGAATTTCAAATTTGCAACTAG-ATTTT
1 CAAATTCGCAACACGAATTTCAAATTCGCAACGCGAAATTT
* *
33770 CGAATTCGCAACACGAATTT-AATTTCGCAAC
1 CAAATTCGCAACACGAATTTCAAATTCGCAAC
33801 AGGTTTTAGT
Statistics
Matches: 154, Mismatches: 28, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
38 1 0.01
39 27 0.18
40 108 0.70
41 18 0.12
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (41 bp):
CAAATTCGCAACACGAATTTCAAATTCGCAACGCGAAATTT
Found at i:33976 original size:14 final size:15
Alignment explanation
Indices: 33957--33994 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
33947 TCCCCATCTC
33957 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
33971 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
33987 TAATTTTT
1 TAATTTTT
33995 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:34609 original size:12 final size:12
Alignment explanation
Indices: 34588--34621 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
34578 ACCACATTTC
*
34588 CAATACCAAACA
1 CAATATCAAACA
34600 CAATATCAAACA
1 CAATATCAAACA
*
34612 CAATCTCAAA
1 CAATATCAAA
34622 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:34774 original size:24 final size:24
Alignment explanation
Indices: 34747--34800 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
34737 GTATTCAAAA
34747 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
34771 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
34795 TTTGAT
1 TTTGAT
34801 GATGTAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:36938 original size:18 final size:18
Alignment explanation
Indices: 36915--36950 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
36905 AAGCAAAAGG
*
36915 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
36933 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
36951 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:37304 original size:20 final size:20
Alignment explanation
Indices: 37260--37308 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
37250 AATTCACAAC
* *
37260 GCGAAATTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCATT
* *
37280 ACGAATTTGACTTTCGTATT
1 GCGAATTTGACTTTCGCATT
37300 GCGAATTTG
1 GCGAATTTG
37309 TACATTCAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.39
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCATT
Found at i:37437 original size:65 final size:65
Alignment explanation
Indices: 37362--37600 Score: 374
Period size: 65 Copynumber: 3.6 Consensus size: 65
37352 AATTTAAAAC
37362 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTA
*
37427 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATAA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTA
* *
37492 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATC-AATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTA
*
37556 AACAAATCGACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAA
37601 AGTGTACCCC
Statistics
Matches: 163, Mismatches: 5, Indels: 8
0.93 0.03 0.05
Matches are distributed among these distances:
64 14 0.09
65 123 0.75
68 4 0.02
69 22 0.13
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTA
Found at i:38868 original size:64 final size:64
Alignment explanation
Indices: 38795--39018 Score: 204
Period size: 64 Copynumber: 3.5 Consensus size: 64
38785 TGTTTGAATG
* * * ** *
38795 TGCACCGATGCATTGGTAGTGCATCAATGCA-CTCTTTTAA-AATAAATACATCGAATGTAATTC
1 TGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
38858 A
64 A
** * **
38859 TGCATCGATGCATAATTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
** ** * ** *
38923 TGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAGCAATAATACTACATCGAATACCTTTTA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
*
38987 TGCACCGATGCATCA-GTAGTGCATCGATGCAT
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCAT
39019 ATCTTCATTA
Statistics
Matches: 131, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
63 1 0.01
64 123 0.94
65 7 0.05
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:39566 original size:31 final size:31
Alignment explanation
Indices: 39528--39718 Score: 337
Period size: 31 Copynumber: 6.2 Consensus size: 31
39518 AGAGTCGAGG
39528 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
39559 GTTTACATATGTTTAAAGGCACATATAAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
39590 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
39621 ATTTACATATGTTTAAAGGCACATATAAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
39652 GTTTATATATGTTTGAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
39683 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
39714 GTTTA
1 GTTTA
39719 TATTGTGACC
Statistics
Matches: 150, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 150 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:42840 original size:64 final size:64
Alignment explanation
Indices: 42772--42996 Score: 240
Period size: 64 Copynumber: 3.5 Consensus size: 64
42762 TTATTTGAAT
** **
42772 ATGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATT
1 ATGCACCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAAT-AATACATCGAATGCAATT
42835 C
64 C
* *
42836 ATGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAA-ACATCGAATGCAATTG
1 ATGCACCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAT-AATACATCGAATGCAATTC
* ** * * * * * ** *
42900 GTGCATTGATGCATAAGGAGTGTATCGATGCATCCCATCAATAATACTACATCGAATACCTTTT
1 ATGCACCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAATACATCGAATGCAATTC
*
42964 ATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 ATGCACCGATGCATAAGTAGTGCATCGATGCAT
42997 ATCTTCATTA
Statistics
Matches: 135, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
63 1 0.01
64 128 0.95
65 6 0.04
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
ATGCACCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAATACATCGAATGCAATTC
Found at i:43530 original size:16 final size:16
Alignment explanation
Indices: 43509--43562 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
43499 TCGAGGGTTT
43509 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
**
43525 ACATATG---AACAGTTT
1 ACATATGTTTAA-AG-GC
43540 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
43556 ACATATG
1 ACATATG
43563 AACATTTTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
13 2 0.07
14 2 0.07
15 7 0.24
16 14 0.48
17 2 0.07
18 2 0.07
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (16 bp):
ACATATGTTTAAAGGC
Found at i:43698 original size:31 final size:31
Alignment explanation
Indices: 43505--43695 Score: 310
Period size: 31 Copynumber: 6.2 Consensus size: 31
43495 AGAGTCGAGG
43505 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
43536 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
43567 TTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* * *
43598 ATTTACATATGTTTAAAGGCACATATAAATA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* * *
43629 GTTTATATATGTTTGAAGGAACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
43660 GTTTATATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
43691 GTTTA
1 GTTTA
43696 TATTGTGACC
Statistics
Matches: 148, Mismatches: 12, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 148 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:45307 original size:21 final size:21
Alignment explanation
Indices: 45283--45358 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
45273 GCGGGCGAGA
* *
45283 CCTCTTGAACGAT-GACAGGGG
1 CCTCTTGAACGATAG-GAGGAG
* *
45304 CCTCTTGAACGGTAGGAGAAG
1 CCTCTTGAACGATAGGAGGAG
*
45325 CCTCTTGAACGATAGGAGGCG
1 CCTCTTGAACGATAGGAGGAG
45346 CCTCTTGAACGAT
1 CCTCTTGAACGAT
45359 GATAGGTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 46 0.98
22 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.30, T:0.21
Consensus pattern (21 bp):
CCTCTTGAACGATAGGAGGAG
Found at i:45658 original size:21 final size:21
Alignment explanation
Indices: 45632--45681 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
45622 ACCATTGTCT
*
45632 TCACGTAAAATACCAACCTCA
1 TCACGTAAAACACCAACCTCA
* * *
45653 TGACGTAAAGCACCGACCTCA
1 TCACGTAAAACACCAACCTCA
45674 TCACGTAA
1 TCACGTAA
45682 CTCCCCTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.32, G:0.12, T:0.18
Consensus pattern (21 bp):
TCACGTAAAACACCAACCTCA
Found at i:47462 original size:20 final size:20
Alignment explanation
Indices: 47423--47462 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
47413 TGCGATTTTG
* * *
47423 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
47443 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
47463 AAAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:48036 original size:41 final size:40
Alignment explanation
Indices: 47983--48086 Score: 127
Period size: 41 Copynumber: 2.6 Consensus size: 40
47973 TGACCATCTC
47983 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTG-AATTCAGT
* * * * * **
48024 GTTGCTAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGAATTCAGT
*
48064 GTTGCGAATTTGACTTCTGTGTT
1 GTTGCGAATTTGACTTTTGTGTT
48087 CCGATTTACA
Statistics
Matches: 51, Mismatches: 12, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
40 23 0.45
41 28 0.55
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.45
Consensus pattern (40 bp):
GTTGCGAATTTGACTTTTGTGTTGCGAATTTGAATTCAGT
Found at i:48058 original size:20 final size:20
Alignment explanation
Indices: 47959--48078 Score: 107
Period size: 20 Copynumber: 6.0 Consensus size: 20
47949 ATATTATGTT
* *
47959 TCGCATTGCGAATTTGACCA
1 TCGCGTTGCGAATTTGACTA
* *
47979 TCTCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
* * *
47999 TTGTGTTGCGAATTTGA-AA
1 TCGCGTTGCGAATTTGACTA
* *
48018 TTCAGTGTTGCTAATTTGACTA
1 -TC-GCGTTGCGAATTTGACTA
*
48040 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
* *
48060 TTGTGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
48079 TCTGTGTTCC
Statistics
Matches: 80, Mismatches: 17, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
20 63 0.79
21 16 0.20
22 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:48079 original size:20 final size:20
Alignment explanation
Indices: 47983--48086 Score: 127
Period size: 20 Copynumber: 5.2 Consensus size: 20
47973 TGACCATCTC
47983 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* **
48003 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTG-ACTTTTGT
* * * *
48024 GTTGCTAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
48044 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
*
48064 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
48084 GTT
1 GTT
48087 CCGATTTACA
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
20 53 0.77
21 16 0.23
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.45
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:48903 original size:7 final size:7
Alignment explanation
Indices: 48891--48915 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
48881 AGAAACCCTA
48891 ATTTCTG
1 ATTTCTG
48898 ATTTCTG
1 ATTTCTG
48905 ATTTCTG
1 ATTTCTG
48912 ATTT
1 ATTT
48916 TTTGTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.60
Consensus pattern (7 bp):
ATTTCTG
Found at i:53845 original size:26 final size:26
Alignment explanation
Indices: 53809--53870 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
53799 GCTTATCACT
*
53809 GGTGACATACTCAAGTTCCTAATAGG
1 GGTGACATACTCAAGTTCCAAATAGG
53835 GGTGACATACTCAAGTTCCAAATAGG
1 GGTGACATACTCAAGTTCCAAATAGG
* *
53861 AGTAACATAC
1 GGTGACATAC
53871 AAATGCATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.24
Consensus pattern (26 bp):
GGTGACATACTCAAGTTCCAAATAGG
Found at i:57916 original size:7 final size:6
Alignment explanation
Indices: 57899--57931 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
57889 TCATTCATTC
57899 ATTTTT ATTTTT ATTTTT ATTTTT ATTTATT AT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTT-TT AT
57932 AAATATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 22 0.85
7 4 0.15
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:57957 original size:19 final size:18
Alignment explanation
Indices: 57901--57957 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
57891 ATTCATTCAT
*
57901 TTTTATTT-TTATTTTTA
1 TTTTATTTATTATTATTA
* *
57918 TTTTTATTTATTATAAATA
1 -TTTTATTTATTATTATTA
57937 TTTTATTATATTATTATTA
1 TTTTATT-TATTATTATTA
57956 TT
1 TT
57958 AAATAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTATTTATTATTATTA
Found at i:59019 original size:14 final size:14
Alignment explanation
Indices: 59002--59031 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
58992 TTCTTTAAAT
59002 TTCAATAAGTTTAA
1 TTCAATAAGTTTAA
59016 TTCAATAAGTTTAA
1 TTCAATAAGTTTAA
59030 TT
1 TT
59032 ATTATTTATT
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:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
TTCAATAAGTTTAA
Found at i:60578 original size:19 final size:20
Alignment explanation
Indices: 60554--60594 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
60544 GTACTAACCA
*
60554 TTTTATTTATA-TTTTTATT
1 TTTTATTTATACATTTTATT
*
60573 TTTTATTTTTACATTTTATT
1 TTTTATTTATACATTTTATT
60593 TT
1 TT
60595 GCTCTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTATTTATACATTTTATT
Done.