Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005803.1 Hibiscus syriacus cultivar Beakdansim tig00013609_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: 79336
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4202 original size:21 final size:20
Alignment explanation
Indices: 4146--4204 Score: 100
Period size: 20 Copynumber: 2.9 Consensus size: 20
4136 TTTTGCCCTA
4146 GTTCATCCAGTATCGATATT
1 GTTCATCCAGTATCGATATT
4166 GTTCATCCAGTATCGATATT
1 GTTCATCCAGTATCGATATT
*
4186 GTTCATCCCAATATCGATA
1 GTTCAT-CCAGTATCGATA
4205 CTCAAACCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 26 0.70
21 11 0.30
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (20 bp):
GTTCATCCAGTATCGATATT
Found at i:5504 original size:22 final size:22
Alignment explanation
Indices: 5479--5520 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5469 AATATATATA
*
5479 ATAAGTTA-TAAAATAATTAATT
1 ATAAATTATTAAAA-AATTAATT
5501 ATAAATTATTAAAAAATTAA
1 ATAAATTATTAAAAAATTAA
5521 AAATTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
ATAAATTATTAAAAAATTAATT
Found at i:10715 original size:20 final size:20
Alignment explanation
Indices: 10690--10737 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
10680 TCAAAATCGT
*
10690 TTTTCAAAATTTC-ATTTTGC
1 TTTTCAAAA-TCCAATTTTGC
10710 TTTTCAAAATCCAATTTTGC
1 TTTTCAAAATCCAATTTTGC
10730 -TTTCAAAA
1 TTTTCAAAA
10738 GAAAATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (20 bp):
TTTTCAAAATCCAATTTTGC
Found at i:11269 original size:8 final size:8
Alignment explanation
Indices: 11256--11284 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
11246 GTCATTGAGC
11256 AATAAAAG
1 AATAAAAG
11264 AATAAAAG
1 AATAAAAG
11272 AATAAAAG
1 AATAAAAG
11280 AATAA
1 AATAA
11285 TTGGGTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (8 bp):
AATAAAAG
Found at i:12621 original size:25 final size:25
Alignment explanation
Indices: 12572--12692 Score: 135
Period size: 25 Copynumber: 5.0 Consensus size: 25
12562 AATCTTATAT
*
12572 GGCACTACGGTGC-AA-TTCTACGC
1 GGCACTTCGGTGCAAATTTCTACGC
12595 GGCACTTCGGTGCAAATTTCTACGC
1 GGCACTTCGGTGCAAATTTCTACGC
12620 GGCACTTCGGTGCAAATTTCTACGC
1 GGCACTTCGGTGCAAATTTCTACGC
*
12645 GGTC-CTTCGG-GACAAA-TTCTACGT
1 GG-CACTTCGGTG-CAAATTTCTACGC
* * * *
12669 GACATTTCGGTGAAAATTTATACG
1 GGCACTTCGGTGCAAATTTCTACG
12693 AGATGTGGTG
Statistics
Matches: 85, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
23 13 0.15
24 19 0.22
25 52 0.61
26 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (25 bp):
GGCACTTCGGTGCAAATTTCTACGC
Found at i:12686 original size:49 final size:50
Alignment explanation
Indices: 12587--12692 Score: 128
Period size: 49 Copynumber: 2.1 Consensus size: 50
12577 TACGGTGCAA
* *
12587 TTCTACGCGGCACTTCGGTGCAAATTTCTACGCGGCACTTCGGTGCAAAT
1 TTCTACGCGGCACTTCGGTGCAAATTTCTACGCGACACTTCGGTGAAAAT
* *
12637 TTCTACGCGGTC-CTTCGG-GACAAA-TTCTACGTGACATTTCGGTGAAAAT
1 TTCTACGCGG-CACTTCGGTG-CAAATTTCTACGCGACACTTCGGTGAAAAT
*
12686 TTATACG
1 TTCTACG
12693 AGATGTGGTG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
49 28 0.57
50 20 0.41
51 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (50 bp):
TTCTACGCGGCACTTCGGTGCAAATTTCTACGCGACACTTCGGTGAAAAT
Found at i:13248 original size:21 final size:21
Alignment explanation
Indices: 13224--13272 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
13214 ACGAAAGTTT
*
13224 CTGTAGCAGTGCATCGATGCA
1 CTGTAGCAGTGCATCGATACA
13245 CTGTAGCAGTGCATCGATACA
1 CTGTAGCAGTGCATCGATACA
*
13266 TTGTAGC
1 CTGTAGC
13273 CCTGTTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
CTGTAGCAGTGCATCGATACA
Found at i:15755 original size:22 final size:22
Alignment explanation
Indices: 15730--15776 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
15720 ATATTTAATT
*
15730 TTTAAATTTTTAAATAATTTTA
1 TTTAAATTTTAAAATAATTTTA
15752 TTTAAATTTTAAAATAATTTTA
1 TTTAAATTTTAAAATAATTTTA
15774 TTT
1 TTT
15777 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTAAATTTTAAAATAATTTTA
Found at i:32877 original size:14 final size:14
Alignment explanation
Indices: 32858--32893 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
32848 ATACACAATC
32858 GAATAAGTAATATA
1 GAATAAGTAATATA
32872 GAATAAGTAATATA
1 GAATAAGTAATATA
*
32886 GAGTAAGT
1 GAATAAGT
32894 GAGTATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (14 bp):
GAATAAGTAATATA
Found at i:39476 original size:10 final size:10
Alignment explanation
Indices: 39461--39486 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
39451 TTATTATTAT
39461 ATTTAAATAC
1 ATTTAAATAC
39471 ATTTAAATAC
1 ATTTAAATAC
39481 ATTTAA
1 ATTTAA
39487 GTACCTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (10 bp):
ATTTAAATAC
Found at i:39909 original size:22 final size:22
Alignment explanation
Indices: 39822--39910 Score: 81
Period size: 22 Copynumber: 3.8 Consensus size: 22
39812 TAAAAATCAT
*
39822 TTAATTTGATTAAATTTAAAGG
1 TTAATTTGATTAAATTTAGAGG
* *
39844 TTATTTTAATTAAATTT-GAAGG
1 TTAATTTGATTAAATTTAG-AGG
*
39866 TTAATTTGATTGAATAAGATTTAGATG
1 TTAATTTGA-T---TAA-ATTTAGAGG
39893 TTAATTTGATTAAATTTA
1 TTAATTTGATTAAATTTA
39911 TCAAGTTTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
22 30 0.56
23 4 0.07
26 4 0.07
27 15 0.28
28 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.48
Consensus pattern (22 bp):
TTAATTTGATTAAATTTAGAGG
Found at i:44854 original size:19 final size:19
Alignment explanation
Indices: 44830--44890 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
44820 AAACCGAAAC
44830 CGGTTTTTTCGGTTCGGTT
1 CGGTTTTTTCGGTTCGGTT
*
44849 CGGTTTTTT---TAACGGTT
1 CGGTTTTTTCGGT-TCGGTT
* *
44866 CGGGTTTTTCGGTTCGTTT
1 CGGTTTTTTCGGTTCGGTT
44885 CGGTTT
1 CGGTTT
44891 ATCGGTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.39
19 18 0.55
20 1 0.03
ACGTcount: A:0.03, C:0.15, G:0.30, T:0.52
Consensus pattern (19 bp):
CGGTTTTTTCGGTTCGGTT
Found at i:44889 original size:18 final size:18
Alignment explanation
Indices: 44834--44897 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
44824 CGAAACCGGT
44834 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
44852 TTTTT---TTAACGGTTCGGG
1 TTTTTCGGTT--CGGTTC-GG
*
44870 TTTTTCGGTTCGTTTCGG
1 TTTTTCGGTTCGGTTCGG
*
44888 TTTATCGGTT
1 TTTTTCGGTT
44898 TTTCAATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
15 2 0.05
17 6 0.16
18 23 0.61
19 5 0.13
21 2 0.05
ACGTcount: A:0.05, C:0.14, G:0.28, T:0.53
Consensus pattern (18 bp):
TTTTTCGGTTCGGTTCGG
Found at i:45464 original size:5 final size:5
Alignment explanation
Indices: 45452--45481 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
45442 TTTTTTTTAA
45452 ACCC- ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG A
45482 ACAGTGCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.23, C:0.60, G:0.17, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:51824 original size:25 final size:25
Alignment explanation
Indices: 51796--51848 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
51786 TTTTTTTTTC
51796 AAAACTATATAATATACATTTTCAA
1 AAAACTATATAATATACATTTTCAA
* * *
51821 AAAACTATATATTATACGTTTTTAA
1 AAAACTATATAATATACATTTTCAA
51846 AAA
1 AAA
51849 TATTTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (25 bp):
AAAACTATATAATATACATTTTCAA
Found at i:51854 original size:37 final size:36
Alignment explanation
Indices: 51813--51947 Score: 130
Period size: 39 Copynumber: 3.6 Consensus size: 36
51803 TATAATATAC
51813 ATTTTCAAAAAACTATATATTATACGTTTTTAAAAAT
1 ATTTTCAAAAAAC-ATATATTATACGTTTTTAAAAAT
* * *
51850 ATTTTTTTAAAAATATATATATTATACGTTTTCTTAGAAAT
1 A--TTTTCAAAAA-ACATATATTATACG-TTT-TTAAAAAT
* * * *
51891 GTTTTC-AAAATCATATATTATACATTTTTAAAAGT
1 ATTTTCAAAAAACATATATTATACGTTTTTAAAAAT
*
51926 ATTTT-AAAAAACATATACTATA
1 ATTTTCAAAAAACATATATTATA
51948 TACTTTCAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
35 24 0.30
36 3 0.04
37 12 0.15
38 4 0.05
39 25 0.32
40 4 0.05
41 7 0.09
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
ATTTTCAAAAAACATATATTATACGTTTTTAAAAAT
Found at i:51858 original size:14 final size:14
Alignment explanation
Indices: 51839--51865 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51829 ATATTATACG
51839 TTTTTAAAAATATT
1 TTTTTAAAAATATT
51853 TTTTTAAAAATAT
1 TTTTTAAAAATAT
51866 ATATATTATA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTTAAAAATATT
Found at i:52233 original size:18 final size:19
Alignment explanation
Indices: 52205--52251 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
52195 TAGAAACATA
**
52205 TATTTTA-AAATTTTATTT
1 TATTTTATAAATTGCATTT
52223 TA-TTTATAAA-TGCATTT
1 TATTTTATAAATTGCATTT
52240 TATTTTATAAAT
1 TATTTTATAAAT
52252 ATATATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTTTATAAATTGCATTT
Found at i:58687 original size:28 final size:29
Alignment explanation
Indices: 58647--58715 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
58637 ACTAATGGCT
*
58647 ACTGTATAGATGTGTTG-AAAAATAATCA
1 ACTGCATAGATGTGTTGAAAAAATAATCA
58675 ACTGCATAGATGTGTTGAAAAAATAATCA
1 ACTGCATAGATGTGTTGAAAAAATAATCA
58704 ACTGCATAGATG
1 ACTGCATAGATG
58716 ATGGTCCCAC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 16 0.41
29 23 0.59
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (29 bp):
ACTGCATAGATGTGTTGAAAAAATAATCA
Found at i:60669 original size:21 final size:21
Alignment explanation
Indices: 60645--60684 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
60635 AAGACTTTAT
60645 TTTCAAAATAT-AAAAATGATA
1 TTTCAAAAT-TGAAAAATGATA
60666 TTTCAAAATTGAAAAATGA
1 TTTCAAAATTGAAAAATGA
60685 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTGAAAAATGATA
Found at i:61824 original size:332 final size:331
Alignment explanation
Indices: 61216--61876 Score: 1223
Period size: 332 Copynumber: 2.0 Consensus size: 331
61206 GACAAGAACC
* *
61216 GGTTCATAGAGCTTAACGCCAAAAATGGAGGAGAAGTGACTTTTGGTGATAATTCAAAAGGTCAC
1 GGTTCATAGAGCTTAACGCAAAAAATAGAGGAGAAGTGACTTTTGGTGATAATTCAAAAGGTCAC
* *
61281 ATTGAAGGAATAGGTACTAAGGTAATACCTCTTCCATAAAAATTCAAAATGTTTTATATGTGAAT
66 ATTGAAGGAATAGGCACTAAAGTAATACCTCTTCCATAAAAATTCAAAATGTTTTATATGTGAAT
61346 GGGTTAAAGCATAATCTATTAAGTATTAGTCAATTTTGTGATAAGGGATTCAATGTCACGTTTGA
131 GGGTTAAAGCATAATCTATTAAGTATTAGTCAATTTTGTGATAAGGGATTCAATGTCACGTTTGA
*
61411 AACTAATGGTTGTAAAGTCATTGACATTGCATCTAATCGGATTATGCTTGTTGGTCATAGAATAG
196 AACTAATGGTTGTAAAGTCATTGACATTGCATCTAATCGGATTATACTTGTTGGTCATAGAATAG
*
61476 GAAACATATGCATGGTGCATTTAGATTCTATAGATATGACTAATTTATGTCTAGTTGCTAAGGAT
261 GAAACATATACATGGTGCATTTAGATTCTATAGATATGACTAATTTATGTCTAGTTGCTAAGGAT
61541 GAGCCT
326 GAGCCT
* *
61547 GGTTCATAGAGCTTAATGCAAAAAATAGTGGAGAAGTGACTTTTGGTGATAATTCAAAAGGTCAC
1 GGTTCATAGAGCTTAACGCAAAAAATAGAGGAGAAGTGACTTTTGGTGATAATTCAAAAGGTCAC
*
61612 ATTGAAGGAATAGGCACTATAAGTAATACCTCTTCCATACAAATTCAAAATGTTTTATATGTGAA
66 ATTGAAGGAATAGGCACTA-AAGTAATACCTCTTCCATAAAAATTCAAAATGTTTTATATGTGAA
*
61677 TGGGTTAAAGCATAATCTATTAAGTATTAGTCAATTTTGTGATAAGGGATTCAATGTCATGTTTG
130 TGGGTTAAAGCATAATCTATTAAGTATTAGTCAATTTTGTGATAAGGGATTCAATGTCACGTTTG
61742 AAACTAATGGTTGTAAAGTCATTGACATTGCATCTAATCGGATTATACTTGTTGGTCATAGAATA
195 AAACTAATGGTTGTAAAGTCATTGACATTGCATCTAATCGGATTATACTTGTTGGTCATAGAATA
61807 GGAAACATATACATGGTGCATTTAGATTCTATAGATATGACTAATTTATGTCTAGTTGCTAAGGA
260 GGAAACATATACATGGTGCATTTAGATTCTATAGATATGACTAATTTATGTCTAGTTGCTAAGGA
61872 TGAGC
325 TGAGC
61877 ATGATAGTTG
Statistics
Matches: 319, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
331 79 0.25
332 240 0.75
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (331 bp):
GGTTCATAGAGCTTAACGCAAAAAATAGAGGAGAAGTGACTTTTGGTGATAATTCAAAAGGTCAC
ATTGAAGGAATAGGCACTAAAGTAATACCTCTTCCATAAAAATTCAAAATGTTTTATATGTGAAT
GGGTTAAAGCATAATCTATTAAGTATTAGTCAATTTTGTGATAAGGGATTCAATGTCACGTTTGA
AACTAATGGTTGTAAAGTCATTGACATTGCATCTAATCGGATTATACTTGTTGGTCATAGAATAG
GAAACATATACATGGTGCATTTAGATTCTATAGATATGACTAATTTATGTCTAGTTGCTAAGGAT
GAGCCT
Found at i:64965 original size:20 final size:22
Alignment explanation
Indices: 64864--64995 Score: 135
Period size: 23 Copynumber: 6.0 Consensus size: 22
64854 GATTTATCCT
* *
64864 TTGAATATGCATCGATACAC-C
1 TTGAATGTGCATCGATGCACTC
* * *
64885 TTGAAGGTACACCGATGCACTCC
1 TTGAATGTGCATCGATGCACT-C
*
64908 TTGAATGTGCATCGATGAACTCC
1 TTGAATGTGCATCGATGCACT-C
*
64931 TTGAATGTACATCGATGCACTC
1 TTGAATGTGCATCGATGCACTC
*
64953 -TG-TTGTGCATCGATGCACTCC
1 TTGAATGTGCATCGATGCACT-C
*
64974 TTGAATGTGCATCGATACACTC
1 TTGAATGTGCATCGATGCACTC
64996 ATCGGGTTTT
Statistics
Matches: 91, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
20 15 0.16
21 18 0.20
22 4 0.04
23 54 0.59
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (22 bp):
TTGAATGTGCATCGATGCACTC
Found at i:64974 original size:43 final size:44
Alignment explanation
Indices: 64864--64995 Score: 153
Period size: 43 Copynumber: 3.0 Consensus size: 44
64854 GATTTATCCT
* * * *
64864 TTGAATATGCATCGAT-ACACCTTGAAGGTACACCGATGCACTCC
1 TTGAATGTGCATCGATGACTCCTTGAATGTACATCGATGCACT-C
64908 TTGAATGTGCATCGATGAACTCCTTGAATGTACATCGATGCACTC
1 TTGAATGTGCATCGATG-ACTCCTTGAATGTACATCGATGCACTC
* * *
64953 -TG-TTGTGCATCGATGCACTCCTTGAATGTGCATCGATACACTC
1 TTGAATGTGCATCGATG-ACTCCTTGAATGTACATCGATGCACTC
64996 ATCGGGTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
43 37 0.47
44 17 0.22
45 1 0.01
46 23 0.29
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (44 bp):
TTGAATGTGCATCGATGACTCCTTGAATGTACATCGATGCACTC
Found at i:67780 original size:64 final size:64
Alignment explanation
Indices: 67633--67789 Score: 210
Period size: 65 Copynumber: 2.4 Consensus size: 64
67623 AAATTGAATT
67633 TCGAATGCATTTAGTGCACCGATGCACAAGCCATGCATCGATGCACCCCTGAAAATTTTGAAACA
1 TCGAATGCATTT-GTGCACCGATGCACAAGCCATGCATCGATGCACCCCTGAAAATTTTGAAACA
* * ***
67698 TCGAATGCATTAAGTGCACCGATGCACAAGGCATGCATCGATGCA-CCCTGGCTATTTTGAAACA
1 TCGAATGCATT-TGTGCACCGATGCACAAGCCATGCATCGATGCACCCCTGAAAATTTTGAAACA
*
67762 TTGAA-GCAGATTTGTGCACCGATGCACA
1 TCGAATGC--ATTTGTGCACCGATGCACA
67790 CCCTAGTGTA
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
63 2 0.02
64 35 0.43
65 45 0.55
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (64 bp):
TCGAATGCATTTGTGCACCGATGCACAAGCCATGCATCGATGCACCCCTGAAAATTTTGAAACA
Found at i:71147 original size:83 final size:82
Alignment explanation
Indices: 70960--71351 Score: 494
Period size: 83 Copynumber: 4.8 Consensus size: 82
70950 GAAATAAAAG
* *
70960 TTTAATATT-TAAATTTAAACA-ATATTATTATCTATTTAAGTTTAGATATTAAAAGAGTTTTGG
1 TTTAATATTATAAATTTAAA-AGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
*
71023 -T-AGTAAAACTCTCAGA
65 TTGAATAAAACTCTCAGA
* *
71039 TTTAATATTATAAATTTAAAAGATATTATAATCTTTTTAAACTTAGATATTAAAAGAGTTTTGGT
1 TTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGGT
* * *
71104 TGGAATAAAACTTTAAGG
66 T-GAATAAAACTCTCAGA
* *
71122 TTTAATATTATAAATTTAAAAGATATTATAATCTCTTTAAATTTAGATATTAAAAGAGTTTTGTT
1 TTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGGT
*
71187 TAGAGTAAAACTCTCAGA
66 T-GAATAAAACTCTCAGA
* * * * *
71205 TTTAATATTTTAAATTTGAAAGATATTATAATTTGTTTAAATTTAGATATCAAAAGAGTTTTGGT
1 TTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGGT
*
71270 TAAATTAAAACTCTCAGA
66 TGAA-TAAAACTCTCAGA
* * * *
71288 TTTAATATTTTAAATTTAAAAAGATATTATTATATA-TT---TTTAGATATTAAAAGAGTTTTAG
1 TTTAATATTATAAATTT-AAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
71349 TTG
65 TTG
71352 GAGAAAAACT
Statistics
Matches: 275, Mismatches: 31, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
79 10 0.04
80 71 0.26
81 1 0.00
82 1 0.00
83 178 0.65
84 14 0.05
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.44
Consensus pattern (82 bp):
TTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGGT
TGAATAAAACTCTCAGA
Found at i:71173 original size:42 final size:41
Alignment explanation
Indices: 71038--71173 Score: 98
Period size: 42 Copynumber: 3.3 Consensus size: 41
71028 AAACTCTCAG
*
71038 ATTTAATATTATAAATTTAAAAGATATTATAATCTTTTTAA
1 ATTTAATATTATAAATTTAAAAGATATTATAATCTCTTTAA
* * ** * *** **
71079 ACTTAGATATTAAAAGAGTTT--TGGTTGGAATAA-AACTTTAA
1 ATTTA-ATATTATAA-A-TTTAAAAGATATTATAATCTCTTTAA
*
71120 GGTTTAATATTATAAATTTAAAAGATATTATAATCTCTTTAA
1 -ATTTAATATTATAAATTTAAAAGATATTATAATCTCTTTAA
71162 ATTTAGATATTA
1 ATTTA-ATATTA
71174 AAAGAGTTTT
Statistics
Matches: 64, Mismatches: 23, Indels: 15
0.63 0.23 0.15
Matches are distributed among these distances:
39 3 0.05
40 1 0.02
41 27 0.42
42 29 0.45
43 1 0.02
44 3 0.05
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (41 bp):
ATTTAATATTATAAATTTAAAAGATATTATAATCTCTTTAA
Found at i:74772 original size:35 final size:34
Alignment explanation
Indices: 74725--74837 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 34
74715 AAAACAATCC
* *
74725 TCAATTTTATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
*
74760 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * *
74795 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
74830 TCAATTTC
1 TCAATTTC
74838 TGTCTTTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
34 1 0.01
35 61 0.90
36 6 0.09
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:75927 original size:35 final size:34
Alignment explanation
Indices: 75879--75990 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 34
75869 ATTCCTCCTT
* *
75879 AAATTGAAATATTTTAGAATTTGGATTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGG-TTTTAGAATG
* *
75914 TAATTGAATTATTTTGGAATTTAGTGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGT-TTTAGAATG
** *
75949 AAATTGAATTGCTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGTTTTAGAATG
75984 AAATTGA
1 AAATTGA
75991 GGAATGTTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
34 1 0.02
35 64 0.97
36 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGTTTTAGAATG
Found at i:76256 original size:23 final size:20
Alignment explanation
Indices: 76205--76256 Score: 50
Period size: 23 Copynumber: 2.4 Consensus size: 20
76195 TTTACCCTAA
76205 ATTTTATTATATTTTAATTAT
1 ATTTT-TTATATTTTAATTAT
*
76226 TTTATTTTATATTGTTTAATTAGT
1 ATT-TTTTATA-T-TTTAATTA-T
76250 ATTTTTT
1 ATTTTTT
76257 TTACATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 7 0.28
22 3 0.12
23 12 0.48
24 3 0.12
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
ATTTTTTATATTTTAATTAT
Done.