Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007865.1 Hibiscus syriacus cultivar Beakdansim tig00110237_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: 47753
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:264 original size:65 final size:64
Alignment explanation
Indices: 188--351 Score: 229
Period size: 64 Copynumber: 2.5 Consensus size: 64
178 CGGTGCACCA
*
188 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
253 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
317 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
352 CAATTAATTC
Statistics
Matches: 86, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 53 0.62
65 33 0.38
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:340 original size:17 final size:19
Alignment explanation
Indices: 302--348 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
292 ATATTCAGAG
302 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
321 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
338 TGCATTCGATG
1 TGCA-TCGATG
349 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:362 original size:64 final size:62
Alignment explanation
Indices: 192--397 Score: 209
Period size: 64 Copynumber: 3.2 Consensus size: 62
182 GCACCAAGTG
* * *
192 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGAGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT--TCAGAGTGCATCGATGCATGG--AG
257 -
62 A
*
257 TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAA-ATTCAGAGTGCATCGATGCATGGAG-A
* * * * * * *
321 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGC-TCGATGCATGGTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCA-GAGTGCATCGATGCATGG-AGA
*
385 TGCATCGGTGCAT
1 TGCATCGATGCAT
398 CACCTCAAAT
Statistics
Matches: 123, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.01
64 79 0.64
65 41 0.33
66 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCAGAGTGCATCGATGCATGGAGA
Found at i:8757 original size:64 final size:63
Alignment explanation
Indices: 8689--8897 Score: 235
Period size: 65 Copynumber: 3.2 Consensus size: 63
8679 GTGCACCAAG
*
8689 TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGGCT
1 TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATCCTGAGTGCATCGATGCATGG-T
* * *
8753 TGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG-
1 TGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATATCCTGAGTGCATCGATGCATGGT
* * * * *
8816 AGAATGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAAT-TCACT-AATGCATCGATGCAT
1 TG--TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATATC-CTGAGTGCATCGATGCAT
8879 GGT
61 GGT
*
8882 TGATGCATCGGTGCAT
1 TG-TGCATCGATGCAT
8898 CACCTCAAAT
Statistics
Matches: 125, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
63 1 0.01
64 34 0.27
65 85 0.68
66 5 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (63 bp):
TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATCCTGAGTGCATCGATGCATGGT
Found at i:8839 original size:17 final size:19
Alignment explanation
Indices: 8801--8847 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
8791 ATATTCAGAG
8801 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
8820 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
8837 TGCATTCGATG
1 TGCA-TCGATG
8848 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:10129 original size:11 final size:12
Alignment explanation
Indices: 10075--10134 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 12
10065 TTTTTTTAAA
10075 AAAAATAATAAT
1 AAAAATAATAAT
10087 ATAATAATAATGAAT
1 A-AA-AATAAT-AAT
10102 AAAAATGAAATAAT
1 AAAAAT--AATAAT
10116 AAAAATAAT-AT
1 AAAAATAATAAT
*
10127 AAATATAA
1 AAAAATAA
10135 GGTTATAAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
11 9 0.21
12 4 0.10
13 5 0.12
14 17 0.40
15 7 0.17
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:10349 original size:18 final size:17
Alignment explanation
Indices: 10326--10378 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 17
10316 ATATATATAT
10326 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
10344 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
10361 ATATATAATAAATAAATG
1 ATA-ATAAT-AATAAATG
10379 GACTAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 7 0.23
18 16 0.52
19 8 0.26
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:10753 original size:37 final size:37
Alignment explanation
Indices: 10703--10807 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
10693 GTGCTTGTGG
* * * *
10703 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
10740 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
10777 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
10808 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:12813 original size:23 final size:21
Alignment explanation
Indices: 12761--12822 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
12751 TTTTGGTGCA
*
12761 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
12781 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
12802 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
12823 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:12848 original size:20 final size:20
Alignment explanation
Indices: 12763--12848 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 20
12753 TTGGTGCAGA
* *
12763 GGGAATCGA-TCCCCCCTTG
1 GGGAACCGATTCCCCCCTAG
*
12782 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAACCGATTCCCCC-CT--AG
*
12806 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCC-TAG
* *
12827 GGGAATCGATACCCCCCTAG
1 GGGAACCGATTCCCCCCTAG
12847 GG
1 GG
12849 TTCTGGTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.23
21 23 0.43
22 1 0.02
23 16 0.30
24 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.16
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCTAG
Found at i:17801 original size:40 final size:40
Alignment explanation
Indices: 17750--17834 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 40
17740 CCAGTAGGTT
* * *
17750 GGTGGCTAACTTGTACACATTAGAAAATTCATCTTTGGTA
1 GGTGGCCAACTTGTACACATTAGAAAATTCAACTTTAGTA
* *
17790 GGTGGCCAACTTGTATACATTGGAAAATTCAACTTTAGTA
1 GGTGGCCAACTTGTACACATTAGAAAATTCAACTTTAGTA
17830 GGTGG
1 GGTGG
17835 TCAAACTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (40 bp):
GGTGGCCAACTTGTACACATTAGAAAATTCAACTTTAGTA
Found at i:19218 original size:29 final size:29
Alignment explanation
Indices: 19138--19254 Score: 119
Period size: 29 Copynumber: 3.9 Consensus size: 29
19128 AAAAATAAAT
*
19138 TATATTGTTTAAGTTAAGATAAGTCAAAAATA
1 TATATT-TTTAAGTTAAGATAAG--AATAATA
*
19170 TATA-TTTTAAGTTAAAATAAGAATAATA
1 TATATTTTTAAGTTAAGATAAGAATAATA
* *
19198 TATATTTTTAAGTTAAGATAAAAATAAAA
1 TATATTTTTAAGTTAAGATAAGAATAATA
* *
19227 TATATCTTTTGATAGTTAATATATGAAT
1 TATAT-TTTT-A-AGTTAAGATAAGAAT
19255 TTAAGAATCT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
28 10 0.14
29 26 0.36
30 19 0.26
31 2 0.03
32 16 0.22
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (29 bp):
TATATTTTTAAGTTAAGATAAGAATAATA
Found at i:19227 original size:59 final size:62
Alignment explanation
Indices: 19122--19254 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 62
19112 TTGTAAAAGG
* **
19122 TAAAATAAAAATAAATTATATTGTTTAAGTTAAGATAAGTCAAAAATATATATTTT-A-AGT
1 TAAAATAAGAATAAATTATATTGTTTAAGTTAAGATAAGAAAAAAATATATATTTTGATAGT
*
19182 TAAAATAAGAAT-AATATATATT-TTTAAGTTAAGATAA-AAATAAAATATATCTTTTGATAGT
1 TAAAATAAGAATAAAT-TATATTGTTTAAGTTAAGATAAGAAA-AAAATATATATTTTGATAGT
* *
19243 TAATATATGAAT
1 TAAAATAAGAAT
19255 TTAAGAATCT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
58 1 0.02
59 31 0.49
60 18 0.29
61 13 0.21
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (62 bp):
TAAAATAAGAATAAATTATATTGTTTAAGTTAAGATAAGAAAAAAATATATATTTTGATAGT
Found at i:25074 original size:52 final size:52
Alignment explanation
Indices: 25016--25122 Score: 214
Period size: 52 Copynumber: 2.1 Consensus size: 52
25006 TGTACAAATA
25016 TATGAATGAATTAGTTGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
1 TATGAATGAATTAGTTGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
25068 TATGAATGAATTAGTTGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
1 TATGAATGAATTAGTTGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
25120 TAT
1 TAT
25123 CCTCATGTGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.43
Consensus pattern (52 bp):
TATGAATGAATTAGTTGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
Found at i:27186 original size:21 final size:21
Alignment explanation
Indices: 27160--27204 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27150 GATTTCTGGG
* *
27160 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
27181 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
27202 CAA
1 CAA
27205 ACGACAGAAT
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:27848 original size:23 final size:24
Alignment explanation
Indices: 27805--27851 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
27795 ATATGGCATG
*
27805 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
27829 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
27852 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:28067 original size:31 final size:31
Alignment explanation
Indices: 28029--28184 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
28019 AGGGTCGAGG
*
28029 GTTTACCTATGTTCTTCTGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
28060 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
28091 GATTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
28122 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
28153 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
28184 G
1 G
28185 GTCCTTCGGG
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
31 111 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:28183 original size:62 final size:62
Alignment explanation
Indices: 28031--28184 Score: 249
Period size: 62 Copynumber: 2.5 Consensus size: 62
28021 GGTCGAGGGT
*
28031 TTACCTATGTTCTTCTGG-ACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTC-GGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
28093 TTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
28155 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
28185 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 2 0.02
62 83 0.97
63 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
Found at i:31053 original size:21 final size:21
Alignment explanation
Indices: 31027--31071 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31017 GATTTCTGGG
* *
31027 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
31048 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
31069 CAA
1 CAA
31072 ACGACAGAAT
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:31930 original size:31 final size:31
Alignment explanation
Indices: 31892--32047 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
31882 AGGGTCGAGG
*
31892 GTTTACCTATGTTCTTCTGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
31923 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
31954 GATTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
31985 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
32016 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
32047 G
1 G
32048 GTCCTTCGGG
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
31 111 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:32046 original size:62 final size:62
Alignment explanation
Indices: 31894--32047 Score: 249
Period size: 62 Copynumber: 2.5 Consensus size: 62
31884 GGTCGAGGGT
*
31894 TTACCTATGTTCTTCTGG-ACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTC-GGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
31956 TTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
32018 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
32048 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 2 0.02
62 83 0.97
63 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
Found at i:38938 original size:21 final size:20
Alignment explanation
Indices: 38912--38958 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
38902 GAACGCTGGA
38912 AACCGGTTTTGACCGGTTTTG
1 AACCGGTTTTGACCGG-TTTG
38933 AACCGGTTTTGACCGGTTTG
1 AACCGGTTTTGACCGGTTTG
38953 -ACCGGT
1 AACCGGT
38959 CACGACCCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 6 0.23
20 4 0.15
21 16 0.62
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.34
Consensus pattern (20 bp):
AACCGGTTTTGACCGGTTTG
Found at i:38939 original size:11 final size:10
Alignment explanation
Indices: 38913--38958 Score: 76
Period size: 10 Copynumber: 4.6 Consensus size: 10
38903 AACGCTGGAA
38913 ACCGGTTTTG
1 ACCGGTTTTG
38923 ACCGGTTTTG
1 ACCGGTTTTG
38933 AACCGGTTTTG
1 -ACCGGTTTTG
38944 ACCGG-TTTG
1 ACCGGTTTTG
38953 ACCGGT
1 ACCGGT
38959 CACGACCCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.26
10 15 0.44
11 10 0.29
ACGTcount: A:0.13, C:0.22, G:0.30, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:39012 original size:13 final size:13
Alignment explanation
Indices: 38971--39001 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
38961 CGACCCGTTT
*
38971 ACCCGTTTACCCG
1 ACCCGTTGACCCG
38984 ACCCGTTGACCCG
1 ACCCGTTGACCCG
38997 ACCCG
1 ACCCG
39002 ACCCGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:46155 original size:10 final size:11
Alignment explanation
Indices: 46114--46149 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
46104 GGAAATCGGT
46114 TTTTG-ACC-G
1 TTTTGAACCGG
46123 TTTT-AACCGG
1 TTTTGAACCGG
46133 TTTTGAACCGG
1 TTTTGAACCGG
46144 TTTTGA
1 TTTTGA
46150 CTGGTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 7 0.29
10 5 0.21
11 12 0.50
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (11 bp):
TTTTGAACCGG
Found at i:46300 original size:28 final size:29
Alignment explanation
Indices: 46226--46300 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
46216 ACCGTTGACC
** *
46226 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGGAATG
46255 GGTGCTATTCTGGGAATTAATTC-GAATG
1 GGTGCTATTCTGGGAATTAATTCGGAATG
* *
46283 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
46301 TTTTTAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 18 0.44
29 23 0.56
ACGTcount: A:0.20, C:0.09, G:0.28, T:0.43
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGGAATG
Done.