Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003019.1 Hibiscus syriacus cultivar Beakdansim tig00006266_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: 63225
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:3762 original size:10 final size:11
Alignment explanation
Indices: 3734--3760 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3724 TTTTGATTTG
3734 CATTTTAAAAA
1 CATTTTAAAAA
3745 CATTTTAAAAA
1 CATTTTAAAAA
3756 CATTT
1 CATTT
3761 AATGTTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (11 bp):
CATTTTAAAAA
Found at i:4278 original size:21 final size:21
Alignment explanation
Indices: 4249--4326 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
4239 GGTGTCATCA
* * *
4249 AACCCTGCGGGCTGGGCATAT
1 AACCCTGCGGGATGGGAATGT
* *
4270 AACCTTGCGGGATGGGTATGT
1 AACCCTGCGGGATGGGAATGT
* *
4291 AACCTTACGGGATGGGAATGT
1 AACCCTGCGGGATGGGAATGT
4312 AACCCTGCGGAGATG
1 AACCCTGCGG-GATG
4327 ACATATAAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
21 44 0.92
22 4 0.08
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.22
Consensus pattern (21 bp):
AACCCTGCGGGATGGGAATGT
Found at i:6120 original size:24 final size:24
Alignment explanation
Indices: 6093--6146 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
6083 ACAAACAAAT
*
6093 TTAATTAGCATAAATAATAATTA-A
1 TTAATTA-AATAAATAATAATTATA
6117 TTAATTTAAATAAATAATAATTATA
1 TTAA-TTAAATAAATAATAATTATA
6142 TTAAT
1 TTAAT
6147 ATTATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
TTAATTAAATAAATAATAATTATA
Found at i:6168 original size:11 final size:12
Alignment explanation
Indices: 6131--6172 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
6121 TTTAAATAAA
*
6131 TAATAATTATAT
1 TAATAATAATAT
*
6143 TAAT-ATTATAT
1 TAATAATAATAT
6154 TAATAATAATA-
1 TAATAATAATAT
6165 TAATAATA
1 TAATAATA
6173 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:6179 original size:23 final size:25
Alignment explanation
Indices: 6105--6174 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
6095 AATTAGCATA
* *
6105 AATAATAAT-TAATTAAT-TTAAATA
1 AATAATAATATAA-TAATATTATATT
*
6129 AATAATAATTATATTAATATTATATT
1 AATAATAA-TATAATAATATTATATT
6155 AATAATAATATAATAATATT
1 AATAATAATATAATAATATT
6175 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
24 8 0.21
25 16 0.41
26 15 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AATAATAATATAATAATATTATATT
Found at i:6189 original size:15 final size:15
Alignment explanation
Indices: 6169--6198 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6159 ATAATATAAT
*
6169 AATATTTTTAAAAAA
1 AATATTTATAAAAAA
6184 AATATTTATAAAAAA
1 AATATTTATAAAAAA
6199 TATAACAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATTTATAAAAAA
Found at i:9040 original size:4 final size:4
Alignment explanation
Indices: 9020--9057 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
9010 CTGGTAATAT
*
9020 TTTC -TTC TTTC TCTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
9058 GTGTTTTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:10501 original size:20 final size:21
Alignment explanation
Indices: 10463--10501 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
10453 ATATTTCCGT
10463 AGGCAGAGTGCGAAGAGCTAC
1 AGGCAGAGTGCGAAGAGCTAC
10484 AGGCGAGAGTG-G-AGAGCT
1 AGGC-AGAGTGCGAAGAGCT
10502 TGGCGAACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.31, C:0.15, G:0.44, T:0.10
Consensus pattern (21 bp):
AGGCAGAGTGCGAAGAGCTAC
Found at i:16086 original size:15 final size:19
Alignment explanation
Indices: 16048--16087 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
16038 CTCTCGATGA
16048 ACTCATCGGTTCTCTCCTC
1 ACTCATCGGTTCTCTCCTC
16067 ACTCATCGGTTCTCTCCTC
1 ACTCATCGGTTCTCTCCTC
16086 AC
1 AC
16088 ACAAGAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.12, C:0.42, G:0.10, T:0.35
Consensus pattern (19 bp):
ACTCATCGGTTCTCTCCTC
Found at i:27157 original size:23 final size:23
Alignment explanation
Indices: 27127--27187 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
27117 AGCTCATATA
27127 AATT-CACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
27149 AATTGCACCGTAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
27172 AAATGCACCGAAGTGC
1 AATTGCACCGAAGTGC
27188 TATATAAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 4 0.12
23 30 0.88
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:32177 original size:23 final size:23
Alignment explanation
Indices: 32135--32201 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
32125 CACCACAGCT
* *
32135 CATATAAATACACCGAAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
* * * *
32158 CGTAGAATTGCACCGTAGTGCCG
1 CATAGAAATGCACCGAAGTGCCA
32181 CATAGAAATGCACCGAAGTGC
1 CATAGAAATGCACCGAAGTGC
32202 TATATAAAGT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.18
Consensus pattern (23 bp):
CATAGAAATGCACCGAAGTGCCA
Found at i:32996 original size:2 final size:2
Alignment explanation
Indices: 32989--33073 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
32979 TCATACAGTC
32989 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33031 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33073 T
1 T
33074 CATAACTCCA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39334 original size:20 final size:20
Alignment explanation
Indices: 39309--39348 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39299 AATTTGTAAA
39309 TCGCAACAC-AGAAGTCAAAT
1 TCGCAACACGA-AAGTCAAAT
*
39329 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACGAAAGTCAAAT
39349 GTTTTTACGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAGTCAAAT
Found at i:39501 original size:22 final size:22
Alignment explanation
Indices: 39476--39523 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
39466 CTACAGCGAC
*
39476 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACAAA
*
39498 ATCCGTCCCCATTTCCGACAAA
1 ATCCGTCCCCATCTCCGACAAA
39520 ATCC
1 ATCC
39524 ATCTATCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.44, G:0.10, T:0.21
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACAAA
Found at i:39760 original size:13 final size:13
Alignment explanation
Indices: 39742--39766 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39732 TATTTGTTGT
39742 TTTGTCTTTTTGA
1 TTTGTCTTTTTGA
39755 TTTGTCTTTTTG
1 TTTGTCTTTTTG
39767 TTGAAGAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.08, G:0.16, T:0.72
Consensus pattern (13 bp):
TTTGTCTTTTTGA
Found at i:41723 original size:20 final size:20
Alignment explanation
Indices: 41698--41751 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
41688 GACCAACAAA
41698 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
41718 TTCGCAAC-CTAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
41738 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
41752 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:41852 original size:20 final size:20
Alignment explanation
Indices: 41827--41866 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41817 AATTTGTAAA
41827 TCGCAACAC-AGAAGTCAAAT
1 TCGCAACACGA-AAGTCAAAT
*
41847 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACGAAAGTCAAAT
41867 GTTTTTACGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAGTCAAAT
Found at i:42014 original size:22 final size:22
Alignment explanation
Indices: 41989--42044 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
41979 ACTCTCTACA
* *
41989 ACGACATCCGTCCCCATCTCCG
1 ACGAAATCCATCCCCATCTCCG
*
42011 ACGAAATCCATCCCCATTTCCG
1 ACGAAATCCATCCCCATCTCCG
*
42033 ACAAAATCCATC
1 ACGAAATCCATC
42045 TATCTCCATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.29, C:0.43, G:0.09, T:0.20
Consensus pattern (22 bp):
ACGAAATCCATCCCCATCTCCG
Found at i:42340 original size:19 final size:20
Alignment explanation
Indices: 42302--42344 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
42292 AACACCAAAT
42302 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
42322 TCGCAACGC-AAAACT-AAAA
1 TCGCAACGCGAAAA-TGAAAA
42341 TCGC
1 TCGC
42345 GAATTTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.47, C:0.26, G:0.16, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:44256 original size:42 final size:42
Alignment explanation
Indices: 44233--44326 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
44223 CGCCTTCTAT
44233 CGTTCAAGAGGCCCCTATCATCA-TCGAAGTAGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCATTC-AAGTAGCCCCTCCCAC
* * * * *
44275 CGTTCAAGAGGCCCCTGTCATCATTCAAGTGGTCCTTCCCGC
1 CGTTCAAGAGGCCCCTATCATCATTCAAGTAGCCCCTCCCAC
44317 CGTTCAAGAG
1 CGTTCAAGAG
44327 CCCGATTCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 44 0.96
43 2 0.04
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATCATTCAAGTAGCCCCTCCCAC
Found at i:44288 original size:21 final size:21
Alignment explanation
Indices: 44264--44326 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
44254 CATCGAAGTA
44264 GCCCCTCCCACCGTTCAAGAG
1 GCCCCTCCCACCGTTCAAGAG
** * * *
44285 GCCCCTGTCATCATTCAAGTG
1 GCCCCTCCCACCGTTCAAGAG
* * *
44306 GTCCTTCCCGCCGTTCAAGAG
1 GCCCCTCCCACCGTTCAAGAG
44327 CCCGATTCAT
Statistics
Matches: 29, Mismatches: 13, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.40, G:0.21, T:0.22
Consensus pattern (21 bp):
GCCCCTCCCACCGTTCAAGAG
Found at i:45737 original size:14 final size:14
Alignment explanation
Indices: 45718--45757 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
45708 TTTTGATTAA
45718 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
45732 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
45746 TTGATTTGTAAA
1 TTGATTTGTAAA
45758 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:45750 original size:61 final size:66
Alignment explanation
Indices: 45667--45807 Score: 177
Period size: 66 Copynumber: 2.2 Consensus size: 66
45657 TTTTACATTG
45667 AAAGTTGATTTG-TTACAATTGATGAGGAAATAAG-A-T-TTATTTT-TTGATTAATTGATTTGT
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
45727 A
66 A
* ** * * *
45728 AAAGTTGATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTT-CTTGATTAATTGATTTG
45792 TA
65 TA
45794 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
45808 GTTTCTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
61 26 0.38
62 4 0.06
63 1 0.01
64 6 0.09
66 31 0.46
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.50
Consensus pattern (66 bp):
AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
A
Found at i:46160 original size:39 final size:39
Alignment explanation
Indices: 46106--46192 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
46096 TCAAGTTGTA
46106 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
* *
46145 GATTTTGTTTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
46184 GATTTTGAT
1 GATTTTGAT
46193 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.16, C:0.15, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:46549 original size:24 final size:24
Alignment explanation
Indices: 46486--46538 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
46476 AGTGGAGCCG
*
46486 AAATTTATATTGAAATTCAAACTC
1 AAATTTAAATTGAAATTCAAACTC
*
46510 AAATTTAAATTTAAATTCAAACTC
1 AAATTTAAATTGAAATTCAAACTC
*
46534 CAATT
1 AAATT
46539 ACATATGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATTTAAATTGAAATTCAAACTC
Found at i:46950 original size:25 final size:25
Alignment explanation
Indices: 46916--46965 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
46906 ATTATTTTTC
*
46916 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
46941 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
46966 TAATGATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:47073 original size:34 final size:33
Alignment explanation
Indices: 47030--47108 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 33
47020 TATTGAAGGT
*
47030 AAATTCGCAACGCGAAATAAACGT-TGCGATAGTC
1 AAATTCGCAACGCAAAAT-AAC-TATGCGATAGTC
* **
47064 AAATTCGCAA-TCAAAATTGCTATGCGATAGTC
1 AAATTCGCAACGCAAAATAACTATGCGATAGTC
47096 AAATTCGCAACGC
1 AAATTCGCAACGC
47109 TTATTTCGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
31 1 0.03
32 21 0.55
33 6 0.16
34 10 0.26
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.23
Consensus pattern (33 bp):
AAATTCGCAACGCAAAATAACTATGCGATAGTC
Found at i:47182 original size:54 final size:54
Alignment explanation
Indices: 47100--47249 Score: 248
Period size: 54 Copynumber: 2.8 Consensus size: 54
47090 ATAGTCAAAT
* *
47100 TCGCAACGCTTATTTCGCATTGCGAATTTGACTTTCGTGTT-TCGAATTTGACTA
1 TCGCAACGCTTATTTCGCGTTGCGAATTTGACTTTCGCGTTGT-GAATTTGACTA
47154 TCGCAACGCTTATTTCGCGTTGCGAATTTGACTTTCGCGTTGTGAATTTGACTA
1 TCGCAACGCTTATTTCGCGTTGCGAATTTGACTTTCGCGTTGTGAATTTGACTA
* *
47208 CCACAACGCTTATTTCGCGTTGCGAATTTGACTTTCGCGTTG
1 TCGCAACGCTTATTTCGCGTTGCGAATTTGACTTTCGCGTTG
47250 ATCGCAACAA
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
54 90 0.99
55 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.39
Consensus pattern (54 bp):
TCGCAACGCTTATTTCGCGTTGCGAATTTGACTTTCGCGTTGTGAATTTGACTA
Found at i:47191 original size:20 final size:20
Alignment explanation
Indices: 47166--47206 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
47156 GCAACGCTTA
47166 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
47186 TTTCGCGTTGTGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
47206 T
1 T
47207 ACCACAACGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.17, G:0.24, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:49851 original size:24 final size:24
Alignment explanation
Indices: 49822--49868 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
49812 AAAAATCCGA
49822 GTATTGACCAAGATCAAAGTTCGT
1 GTATTGACCAAGATCAAAGTTCGT
*
49846 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
49869 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGT
Found at i:49877 original size:24 final size:24
Alignment explanation
Indices: 49826--49877 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
49816 ATCCGAGTAT
** *
49826 TGACCAAGATCAAAGTTCGTGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
49850 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
49874 TGAC
1 TGAC
49878 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:50774 original size:20 final size:20
Alignment explanation
Indices: 50738--50969 Score: 154
Period size: 20 Copynumber: 11.6 Consensus size: 20
50728 ACTAAAACCT
*
50738 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
50757 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
**
50776 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTCGC
*
50796 GTTGCGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGC
** *
50816 GTTGCGAATTTGACTTTTGC
1 GTTGCGAATTTGAAATTCGC
* *
50836 GTTGAGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGC
* *
50856 GTTGAGAATTTTGAAAATCGC
1 GTTGCGAA-TTTGAAATTCGC
*** *
50877 AACGCGAATTTGGAAAATCGC
1 GTTGCGAATTT-GAAATTCGC
**
50898 AATGCG-ATTT-ACATATTCGC
1 GTTGCGAATTTGA-A-ATTCGC
* *
50918 GTTGCGAAATTGGAAATT-GG
1 GTTGCG-AATTTGAAATTCGC
* *
50938 GTTGCGAAATTGGAATTCGC
1 GTTGCGAATTTGAAATTCGC
50958 GTTGCGAATTTG
1 GTTGCGAATTTG
50970 TTGGTCATTT
Statistics
Matches: 168, Mismatches: 31, Indels: 27
0.74 0.14 0.12
Matches are distributed among these distances:
18 1 0.01
19 37 0.22
20 94 0.56
21 30 0.18
22 5 0.03
23 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:50885 original size:21 final size:21
Alignment explanation
Indices: 50861--50904 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
50851 ATCGCGTTGA
*
50861 GAATTTTGAAAATCGCAACGC
1 GAATTTGGAAAATCGCAACGC
*
50882 GAATTTGGAAAATCGCAATGC
1 GAATTTGGAAAATCGCAACGC
50903 GA
1 GA
50905 TTTACATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (21 bp):
GAATTTGGAAAATCGCAACGC
Found at i:52417 original size:24 final size:23
Alignment explanation
Indices: 52390--52436 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
52380 GATGGAAATA
52390 AATTAGTAATAAA-AATAAAAATTT
1 AATTA-TAA-AAAGAATAAAAATTT
*
52414 AATTATAAAAAGACTAAAAATTT
1 AATTATAAAAAGAATAAAAATTT
52437 TCAAAAGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 13 0.62
24 5 0.24
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (23 bp):
AATTATAAAAAGAATAAAAATTT
Found at i:61792 original size:54 final size:55
Alignment explanation
Indices: 61709--61821 Score: 219
Period size: 54 Copynumber: 2.1 Consensus size: 55
61699 AATGGAAACG
61709 AAATATGGGTAATTGTAATTTGTAAGAATCTCAATGCGAGAAATATAATTCATAA
1 AAATATGGGTAATTGTAATTTGTAAGAATCTCAATGCGAGAAATATAATTCATAA
61764 AAATAT-GGTAATTGTAATTTGTAAGAATCTCAATGCGAGAAATATAATTCATAA
1 AAATATGGGTAATTGTAATTTGTAAGAATCTCAATGCGAGAAATATAATTCATAA
61818 AAAT
1 AAAT
61822 TGAAACTTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 52 0.90
55 6 0.10
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (55 bp):
AAATATGGGTAATTGTAATTTGTAAGAATCTCAATGCGAGAAATATAATTCATAA
Found at i:62526 original size:17 final size:18
Alignment explanation
Indices: 62504--62553 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
62494 TTTTCCGACT
*
62504 ATCGCAATACGATGTAA-
1 ATCGCAATACGATATAAC
*
62521 ATCGCAATGCGATTATAAC
1 ATCGCAATACGA-TATAAC
62540 TATCGCAATACGAT
1 -ATCGCAATACGAT
62554 TCTGACTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 11 0.41
18 4 0.15
19 1 0.04
20 11 0.41
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (18 bp):
ATCGCAATACGATATAAC
Found at i:62546 original size:20 final size:20
Alignment explanation
Indices: 62501--62593 Score: 86
Period size: 20 Copynumber: 4.8 Consensus size: 20
62491 GATTTTTCCG
* *
62501 ACTATCGCAATACGA-TGTA
1 ACTATCGCAATGCGATTCTA
*
62520 A--ATCGCAATGCGATTATA
1 ACTATCGCAATGCGATTCTA
* *
62538 ACTATCGCAATACGATTCTG
1 ACTATCGCAATGCGATTCTA
* *
62558 ACTATCGCAACGCGATTCTG
1 ACTATCGCAATGCGATTCTA
*
62578 ACTGTCGC-ATGCGATT
1 ACTATCGCAATGCGATT
62594 TTCAAATTCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
17 11 0.18
18 4 0.06
19 8 0.13
20 39 0.63
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (20 bp):
ACTATCGCAATGCGATTCTA
Done.