Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009418.1 Hibiscus syriacus cultivar Beakdansim tig00113376_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: 52919
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:215 original size:14 final size:14
Alignment explanation
Indices: 198--233 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
188 GTTAAAAAAA
198 TATTATTAAATTAT
1 TATTATTAAATTAT
212 TATTATTAAATTAT
1 TATTATTAAATTAT
226 TATT-TTAA
1 TATTATTAA
234 TTTTAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTATTAAATTAT
Found at i:2673 original size:96 final size:97
Alignment explanation
Indices: 2508--2700 Score: 361
Period size: 96 Copynumber: 2.0 Consensus size: 97
2498 TCACTTTTAT
* *
2508 TTTCGTTATACTTAAGGGTATTTTTTCATTTTAGCCAATTAGAAGTATTTTAGTAACTTATCCTA
1 TTTCGTTATACTTAAGGGTATTTTTTAATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTA
2573 AATCTTTTATTATTAGACATCCCTTAATCCAC
66 AATCTTTTATTATTAGACATCCCTTAATCCAC
2605 TTTCGTTATACTTAAGGGTA-TTTTTAATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTA
1 TTTCGTTATACTTAAGGGTATTTTTTAATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTA
2669 AATCTTTTATTATTAGACATCCCTTAATCCAC
66 AATCTTTTATTATTAGACATCCCTTAATCCAC
2701 AAACATTTTA
Statistics
Matches: 94, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
96 74 0.79
97 20 0.21
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.45
Consensus pattern (97 bp):
TTTCGTTATACTTAAGGGTATTTTTTAATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTA
AATCTTTTATTATTAGACATCCCTTAATCCAC
Found at i:2732 original size:96 final size:95
Alignment explanation
Indices: 2535--2730 Score: 259
Period size: 96 Copynumber: 2.1 Consensus size: 95
2525 GTATTTTTTC
*
2535 ATTTTAGCCAATTAGAAGTATTTTAGTAACTTATCCTAAATCTTTTATTATTAGACATCCCTTAA
1 ATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTAAATCTTTTATTATTAGACATCCCTTAA
*** * * ** * *
2600 TCCACTTTCGTTATACTTAAGGGTATTTTTA
66 TCCACAAACATTATAC-GAAGGAAAGTTTGA
2631 ATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTAAATCTTTTATTATTAGACATCCCTTAA
1 ATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTAAATCTTTTATTATTAGACATCCCTTAA
*
2696 TCCACAAACATTTTA-GAAGTGAAAGTTTGA
66 TCCACAAACATTATACGAAG-GAAAGTTTGA
*
2726 CTTTT
1 ATTTT
2731 TAAGTAGGGA
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 3 0.03
95 10 0.11
96 74 0.85
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (95 bp):
ATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTAAATCTTTTATTATTAGACATCCCTTAA
TCCACAAACATTATACGAAGGAAAGTTTGA
Found at i:2894 original size:20 final size:20
Alignment explanation
Indices: 2866--2916 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2856 TCTACCTTCG
* *
2866 ATATGGATACTTGATGAACA
1 ATATCGATACTTCATGAACA
*
2886 ATATCGATACTTCTTGAACA
1 ATATCGATACTTCATGAACA
*
2906 ATATTGATACT
1 ATATCGATACT
2917 CTTAGTCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (20 bp):
ATATCGATACTTCATGAACA
Found at i:3891 original size:2 final size:2
Alignment explanation
Indices: 3884--3920 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3874 CATGACCTCA
3884 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3921 GCTTGATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6476 original size:32 final size:32
Alignment explanation
Indices: 6440--6583 Score: 105
Period size: 32 Copynumber: 4.5 Consensus size: 32
6430 ACTGACGAAA
*
6440 TGATATGTATCACATCACTCAAAGTGATGATG
1 TGATATGTATCACATCACTCAAAATGATGATG
* * **
6472 TGATATTTGTCATGTCACTCAAAATGATGATG
1 TGATATGTATCACATCACTCAAAATGATGATG
* * * *
6504 TTCATATG--TCAAATCATTTAAAATGATGATG
1 -TGATATGTATCACATCACTCAAAATGATGATG
* * * * * *
6535 TAACATATATCACATCACTTAAAGTAATGATG
1 TGATATGTATCACATCACTCAAAATGATGATG
*
6567 T-AGTATGTATCATATCA
1 TGA-TATGTATCACATCA
6584 ATAATTAGAT
Statistics
Matches: 87, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
30 4 0.05
31 20 0.23
32 58 0.67
33 5 0.06
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (32 bp):
TGATATGTATCACATCACTCAAAATGATGATG
Found at i:10521 original size:19 final size:18
Alignment explanation
Indices: 10476--10525 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
10466 GTTTGATTAA
*
10476 TTTAATTATTTTTTAATC
1 TTTAAATATTTTTTAATC
10494 TTTATAATATTTTTTAAAAT-
1 TTTA-AATATTTTTT--AATC
10514 TTTAAATATTTT
1 TTTAAATATTTT
10526 AGATGATGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 4 0.14
19 17 0.61
20 4 0.14
21 3 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAAATATTTTTTAATC
Found at i:10674 original size:15 final size:16
Alignment explanation
Indices: 10656--10688 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10646 GAAATTTTTT
10656 TAACTTT-ATATATAA
1 TAACTTTGATATATAA
*
10671 TAACTTTGATATTTAA
1 TAACTTTGATATATAA
10687 TA
1 TA
10689 TTTACAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (16 bp):
TAACTTTGATATATAA
Found at i:12918 original size:29 final size:29
Alignment explanation
Indices: 12886--12943 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
12876 TATTTTATTG
*
12886 TTATAATTAT-ATTATTATAATATATAATA
1 TTATAATTATAATT-TAATAATATATAATA
*
12915 TTATAATTTTAATTTAATAATATATAATA
1 TTATAATTATAATTTAATAATATATAATA
12944 AATTATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTATAATTATAATTTAATAATATATAATA
Found at i:12920 original size:8 final size:8
Alignment explanation
Indices: 12891--12943 Score: 53
Period size: 8 Copynumber: 7.1 Consensus size: 8
12881 TATTGTTATA
*
12891 ATTATATT
1 ATTATAAT
12899 ATTATAAT
1 ATTATAAT
12907 A-TATAAT
1 ATTATAAT
12914 ATTATAAT
1 ATTATAAT
12922 -TT-TAAT
1 ATTATAAT
12928 -TTAATAAT
1 ATT-ATAAT
12936 A-TATAAT
1 ATTATAAT
12943 A
1 A
12944 AATTATTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
6 6 0.15
7 15 0.38
8 19 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
ATTATAAT
Found at i:12927 original size:21 final size:22
Alignment explanation
Indices: 12857--12967 Score: 59
Period size: 21 Copynumber: 4.9 Consensus size: 22
12847 TTGTTGATAT
*
12857 TTTTAATAATATAGTATTAT-A
1 TTTTAATAATATAATATTATAA
* ** *
12878 TTTTATTGTTATAAT-TATATTA
1 TTTTAATAATATAATAT-TATAA
*
12900 TTATAAT-ATATAATATTATAA
1 TTTTAATAATATAATATTATAA
*
12921 TTTTAATTTAATA-ATATATAATAAA
1 TTTTAA--TAATATA-ATATTAT-AA
*
12946 TTATTAATAAAATTAATATTAT
1 TT-TTAATAATA-TAATATTAT
12968 TTATTAATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
20 1 0.01
21 29 0.43
22 7 0.10
23 2 0.03
24 13 0.19
25 10 0.15
26 5 0.07
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTAATAATATAATATTATAA
Found at i:13047 original size:14 final size:14
Alignment explanation
Indices: 13028--13062 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
13018 AAATATAATA
13028 TAATATTCTTATTT
1 TAATATTCTTATTT
13042 TAATATTCTTATTT
1 TAATATTCTTATTT
13056 TAATATT
1 TAATATT
13063 TTAGTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (14 bp):
TAATATTCTTATTT
Found at i:13201 original size:28 final size:29
Alignment explanation
Indices: 13129--13225 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 29
13119 TAATATAATT
13129 TATAATACTTTTATTTTAATAAAA-TATAATAA
1 TATAATACTTTTA-TTT-ATAAAATTAT-AT-A
* *
13161 TCGTAATATTTTTATTTATAAAATTATATA
1 T-ATAATACTTTTATTTATAAAATTATATA
* * * *
13191 TATAATA-TTTTAATAATAATATTACATA
1 TATAATACTTTTATTTATAAAATTATATA
*
13219 AATAATA
1 TATAATA
13226 TTAAATAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
28 23 0.42
29 5 0.09
30 2 0.04
31 8 0.15
32 7 0.13
33 10 0.18
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (29 bp):
TATAATACTTTTATTTATAAAATTATATA
Found at i:13222 original size:14 final size:14
Alignment explanation
Indices: 13178--13235 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
13168 ATTTTTATTT
* * *
13178 ATAAAATTATATAT
1 ATAATATTAAATAA
*
13192 ATAATATTTTAAT-A
1 ATAATA-TTAAATAA
*
13206 ATAATATTACATAA
1 ATAATATTAAATAA
13220 ATAATATTAAATAA
1 ATAATATTAAATAA
13234 AT
1 AT
13236 TATTCTAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
13 4 0.11
14 27 0.77
15 4 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATATTAAATAA
Found at i:22671 original size:31 final size:31
Alignment explanation
Indices: 22633--22774 Score: 230
Period size: 31 Copynumber: 4.6 Consensus size: 31
22623 AGGGTCGAGG
* *
22633 GTTTACCTATGTTCTTCGGGACATATAGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
22664 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
22695 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
22726 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
22757 GATTACCTAGGTTCTTCG
1 GTTTACCTATGTTCTTCG
22775 AAATCTATGG
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 105 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:23276 original size:21 final size:21
Alignment explanation
Indices: 23251--23293 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
23241 AAAGAATATA
23251 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
23272 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
23293 T
1 T
23294 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:27605 original size:20 final size:20
Alignment explanation
Indices: 27580--27623 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
27570 ACAATAACTA
27580 GGAATGAACAATTTTCATAC
1 GGAATGAACAATTTTCATAC
27600 GGAATGAACAATTTTCATAC
1 GGAATGAACAATTTTCATAC
27620 GGAA
1 GGAA
27624 CAAACATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (20 bp):
GGAATGAACAATTTTCATAC
Found at i:27629 original size:20 final size:20
Alignment explanation
Indices: 27586--27629 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
27576 ACTAGGAATG
**
27586 AACAATTTTCATACGGAATG
1 AACAATTTTCATACGGAACA
27606 AACAATTTTCATACGGAACA
1 AACAATTTTCATACGGAACA
27626 AACA
1 AACA
27630 TAGATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.25
Consensus pattern (20 bp):
AACAATTTTCATACGGAACA
Found at i:28755 original size:23 final size:23
Alignment explanation
Indices: 28729--28774 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
28719 TTGTCCCCCA
*
28729 AAATTAATATAGTATTCCAAACC
1 AAATTAACATAGTATTCCAAACC
*
28752 AAATTAACGTAGTATTCCAAACC
1 AAATTAACATAGTATTCCAAACC
28775 TCGTACACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.28
Consensus pattern (23 bp):
AAATTAACATAGTATTCCAAACC
Found at i:35205 original size:18 final size:18
Alignment explanation
Indices: 35182--35222 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
35172 AATTACTAGA
35182 AACATTATCAACCATAAT
1 AACATTATCAACCATAAT
35200 AACATTATCAACCATAAT
1 AACATTATCAACCATAAT
35218 AACAT
1 AACAT
35223 AACAAATAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (18 bp):
AACATTATCAACCATAAT
Found at i:35899 original size:128 final size:129
Alignment explanation
Indices: 35572--35914 Score: 316
Period size: 128 Copynumber: 2.7 Consensus size: 129
35562 AATATATTAT
* ** * * *
35572 CGTGTACATTGCT-AATTTACCTATTATTTTAAAGT-ATCAGGCTTCGAAATTATAAGAATCGAT
1 CGTGTACATTG-TAAATTAACCTATTACGTTAAAGTAAT-AGGTTTCGAAATTACAAGTATCGAT
* *** * ** * * *
35635 A-TTTATATAAAAGTATCTATACTTGTACATTTACTCCTATTTTCATTATACAAGTAGAAATGTT
64 ACTTTATACATGTGTATCGATACTTG-ATGTTTACGCTTATTATCATTATACAAGTAG-AATGTT
35699 TAC
127 TAC
* * * * * * * *
35702 CGTGTACATTGTTAATTTACCTATTACTTTACAGTAATAGGTTTCGAAATTCCACGTATTGATAT
1 CGTGTACATTGTAAATTAACCTATTACGTTAAAGTAATAGGTTTCGAAATTACAAGTATCGATAC
* * * * *
35767 TTTATGCATGTGTATTGATACTTGATGTTTACGCTTATTATCATTATACTAGTAG-ATTTTTAT
66 TTTATACATGTGTATCGATACTTGATGTTTACGCTTATTATCATTATACAAGTAGAATGTTTAC
* * * *
35830 CGTTTTCATTGTAAATTAACCTATTACGTTAAAGTAATATGTTTCGAAATTATAAGTATCGATAC
1 CGTGTACATTGTAAATTAACCTATTACGTTAAAGTAATAGGTTTCGAAATTACAAGTATCGATAC
*
35895 TTTATATATGTGTATCGATA
66 TTTATACATGTGTATCGATA
35915 TATTTTGCGT
Statistics
Matches: 172, Mismatches: 38, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
128 76 0.44
129 1 0.01
130 76 0.44
131 19 0.11
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (129 bp):
CGTGTACATTGTAAATTAACCTATTACGTTAAAGTAATAGGTTTCGAAATTACAAGTATCGATAC
TTTATACATGTGTATCGATACTTGATGTTTACGCTTATTATCATTATACAAGTAGAATGTTTAC
Found at i:36384 original size:200 final size:199
Alignment explanation
Indices: 35778--36528 Score: 979
Period size: 200 Copynumber: 3.8 Consensus size: 199
35768 TTATGCATGT
* * * * * * * *
35778 GTATTGATACTTGATGTTTACGCTTATTATCATTATACTAGTAGATTTTTATCGTTTTCATTGTA
1 GTATCGATACTTGGTATTTACGCCTATTATCATTATACTGGTAGA-TTTTACCATTTACATTGTA
* * * **
35843 AATTAACCTATTACGTTAAAGTAATATGTTTCGAAATTATAAGTATCGATACTTTATATATGTGT
65 AATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGT
* * *
35908 ATCGATA-TATTTTGCGTGCAATTTGTTTGAGAAGCATACTGGAATAAAAGTATTGATACCTATA
130 ATCGATACT-TTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCGATACATATA
*
35972 TAGACAA
194 TA-AAAA
* *
35979 -TATCGATACTTGGTATTTACGCCTATTATCAATATAATGGTAGATTTGTACCATTTACATTGTA
1 GTATCGATACTTGGTATTTACGCCTATTATCATTATACTGGTAGATTT-TACCATTTACATTGTA
* ** * * * *
36043 AATTTACCTATTACTTTAAAGTAATCGGTTTCGAAATT-TGAGTATCAATATTTTGTACATGTGT
65 AATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGT
* *
36107 ATCGATACATTTTGCGTGCAAATTG-TTGAGAAGCATACTGGACTAAAAGTATCGATACATATAT
130 ATCGATACTTTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCGATACATATAT
*
36171 ATAAA
195 AAAAA
* * * * * * * * *
36176 GTATCGATACTTGGTATATACACTTAGTATCATTATACCGGTAAACTTTTACCCTTTATATTGTT
1 GTATCGATACTTGGTATTTACGCCTATTATCATTATACTGGTAGA-TTTTACCATTTACATTGTA
* * *
36241 AATTTACCTATTACTTTATAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTGTAAATGTGT
65 AATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGT
* *
36306 ATCGATACTTTTTACGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCGATACATGTAT
130 ATCGATACTTTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCGATACATATAT
36371 AAAAA
195 AAAAA
* * * * *
36376 GTATCGATACTTTGTGTTTACGCCTATTATCATTAAACTGATAGATTTTTACCGTTTACATTGTA
1 GTATCGATACTTGGTATTTACGCCTATTATCATTATACTGGTAGA-TTTTACCATTTACATTGTA
*
36441 AATTTACATATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGT
65 AATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGT
36506 ATCGATACTTTTTGCGTGCAAAT
130 ATCGATACTTTTTGCGTGCAAAT
36529 AACCGGGTAG
Statistics
Matches: 476, Mismatches: 68, Indels: 13
0.85 0.12 0.02
Matches are distributed among these distances:
197 2 0.00
198 122 0.26
199 93 0.20
200 259 0.54
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.40
Consensus pattern (199 bp):
GTATCGATACTTGGTATTTACGCCTATTATCATTATACTGGTAGATTTTACCATTTACATTGTAA
ATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGTA
TCGATACTTTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCGATACATATATA
AAAA
Found at i:39307 original size:21 final size:19
Alignment explanation
Indices: 39283--39338 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
39273 TCGATCGCAA
*
39283 TGCGATAGTCCAAGTTCGCGT
1 TGCGATAGTCCAAATT--CGT
*
39304 TGCGATTTATTCCAAATTCGT
1 TGCGA--TAGTCCAAATTCGT
39325 TGCGATAGTCCAAA
1 TGCGATAGTCCAAA
39339 ATCGCAACGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 8 0.27
21 13 0.43
23 9 0.30
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (19 bp):
TGCGATAGTCCAAATTCGT
Found at i:40114 original size:21 final size:21
Alignment explanation
Indices: 40090--40205 Score: 130
Period size: 21 Copynumber: 5.6 Consensus size: 21
40080 TTTGGAATAA
*
40090 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
40111 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
40132 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
*
40152 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
* *
40173 ATCGCAACGCGAACTTCCACT
1 ATCGCAATGCGAACTTCGACT
*
40194 ATCGCATTGCGA
1 ATCGCAATGCGA
40206 TTTACATATT
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
20 17 0.21
21 64 0.79
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:40173 original size:62 final size:64
Alignment explanation
Indices: 40062--40205 Score: 188
Period size: 62 Copynumber: 2.3 Consensus size: 64
40052 CGTTGCGATT
* *
40062 TTGGACTATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAATATGG-ATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
* *
40125 TTGGACTATCGCAATGCGAATAT-G-TAAATCGCAATGCGAACTTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAATGCGAATATGGATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
** *
40187 TTCCACTATCGCATTGCGA
1 TTGGACTATCGCAATGCGA
40206 TTTACATATT
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
62 51 0.71
63 14 0.19
64 1 0.01
65 6 0.08
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (64 bp):
TTGGACTATCGCAATGCGAATATGGATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
Found at i:40243 original size:21 final size:21
Alignment explanation
Indices: 40214--40372 Score: 200
Period size: 21 Copynumber: 7.6 Consensus size: 21
40204 GATTTACATA
*
40214 TTCGCATTGCAATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
40235 TTCGAATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
40256 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
*
40277 TTCGCATTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAG
*
40297 TATCGCATTGCGAT-TTAC-ATA-
1 T-TCGCATTGCGATAGT-CGA-AG
*
40318 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
40339 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
40360 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
40373 TTATTCCAAA
Statistics
Matches: 121, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
20 17 0.14
21 103 0.85
22 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:40261 original size:104 final size:104
Alignment explanation
Indices: 40174--40364 Score: 276
Period size: 104 Copynumber: 1.8 Consensus size: 104
40164 ACTTGGACTA
* *
40174 TCGCAACGCGA-ACTTCCACTATCGCATTGCGATTTACATATTCGCATTGCAATAGTCGAAGTTC
1 TCGCAACGCGATA-GTCCACTATCGCATTGCGATTTACATATTCGCATTGCAATAGTCCAAGTTC
* * *
40238 GAATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGT
65 GAATTGCGATAGTCGAAGTTCGCAATGCGATACTCCAACT
** * *
40278 TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
1 TCGCAACGCGATAGTCCACTATCGCATTGCGATTTACATATTCGCATTGCAATAGTCCAAGTTCG
*
40343 CATTGCGATAGTCGAAGTTCGC
66 AATTGCGATAGTCGAAGTTCGC
40365 GTTGCGATTT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
104 78 0.99
105 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (104 bp):
TCGCAACGCGATAGTCCACTATCGCATTGCGATTTACATATTCGCATTGCAATAGTCCAAGTTCG
AATTGCGATAGTCGAAGTTCGCAATGCGATACTCCAACT
Found at i:40373 original size:62 final size:63
Alignment explanation
Indices: 40214--40375 Score: 224
Period size: 62 Copynumber: 2.6 Consensus size: 63
40204 GATTTACATA
* * *
40214 TTCGCATTGCAATAGTCGAAGTTCGAATTGCGATAGT-CGAAGTTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAGTTCGCATTGCGAT-TTACGAAGTTCGCATTGCGATAGTCCAAG
*
40277 TTCGCATTGCGATAGTCG-ACTATCGCATTGCGATTTAC-ATA-TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAGT-TCGCATTGCGATTTACGA-AGTTCGCATTGCGATAGTCCAAG
*
40339 TTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTA
1 TTCGCATTGCGATAGTCGAAGTTCGCATTGCGATTTA
40376 TTCCAAATTC
Statistics
Matches: 89, Mismatches: 6, Indels: 9
0.86 0.06 0.09
Matches are distributed among these distances:
62 57 0.64
63 32 0.36
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (63 bp):
TTCGCATTGCGATAGTCGAAGTTCGCATTGCGATTTACGAAGTTCGCATTGCGATAGTCCAAG
Found at i:40641 original size:17 final size:17
Alignment explanation
Indices: 40619--40654 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40609 TAGTCGGTTT
* *
40619 AATTTGATCAAATGGTA
1 AATTTGATAAAATGATA
40636 AATTTGATAAAATGATA
1 AATTTGATAAAATGATA
40653 AA
1 AA
40655 AATTGAGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.14, T:0.33
Consensus pattern (17 bp):
AATTTGATAAAATGATA
Found at i:48124 original size:27 final size:29
Alignment explanation
Indices: 48071--48128 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 29
48061 CAAACAGAAC
48071 AAAAGCAAGAGGGAGGGGGGAAGAAGATG
1 AAAAGCAAGAGGGAGGGGGGAAGAAGATG
48100 AAAA-CAAGAGGGA-GGGGGAAGAAGATG
1 AAAAGCAAGAGGGAGGGGGGAAGAAGATG
48127 AA
1 AA
48129 CAAGTGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 16 0.55
28 9 0.31
29 4 0.14
ACGTcount: A:0.48, C:0.03, G:0.45, T:0.03
Consensus pattern (29 bp):
AAAAGCAAGAGGGAGGGGGGAAGAAGATG
Found at i:49108 original size:30 final size:30
Alignment explanation
Indices: 49072--49171 Score: 128
Period size: 30 Copynumber: 3.3 Consensus size: 30
49062 TAATATATGT
* * * * *
49072 AAATGAATTATCTAAAAATTATTTTACGTA
1 AAATGAATTACCTGAAAACTGTTTTACATA
* *
49102 AAATGAATTACCCGAAAACTGTTTTACTTA
1 AAATGAATTACCTGAAAACTGTTTTACATA
49132 AAATGAATTACCTGAAAACTGTTTTACATA
1 AAATGAATTACCTGAAAACTGTTTTACATA
*
49162 CAATGAATTA
1 AAATGAATTA
49172 TATCTTCTCG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (30 bp):
AAATGAATTACCTGAAAACTGTTTTACATA
Found at i:49334 original size:30 final size:30
Alignment explanation
Indices: 49277--49332 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
49267 ATGAAAAATA
* *
49277 ATTTACATAAATTGAATTACTTTAAAATTG
1 ATTTACATAAAATGAATTACTTAAAAATTG
*
49307 ATTTACGTAAAATGAATTA-TTAAAAA
1 ATTTACATAAAATGAATTACTTAAAAA
49333 ATAATTTCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
29 6 0.26
30 17 0.74
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.39
Consensus pattern (30 bp):
ATTTACATAAAATGAATTACTTAAAAATTG
Done.