Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002687.1 Hibiscus syriacus cultivar Beakdansim tig00005551_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: 61170
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4123 original size:860 final size:843
Alignment explanation
Indices: 2285--4580 Score: 3096
Period size: 860 Copynumber: 2.7 Consensus size: 843
2275 AGATGTTGAC
** * * * *
2285 AGATGTAGCTCAAGTAATAACTAAACACATGGTACTGAGCAACGATGGACTCCTTCAAGTGATGG
1 AGATGTAGCTCAAGTAATAACTAAACACATACTACTGAGCAAAGATAGACTCCTTCAAGGGACGG
* * * * * *
2350 ATATTCCTTCCCTATCTTTTATTTTCCAGATATGTAACGGTCTGTACCATCAGATCAAAGGTTGA
66 ATATTCCTTCCCGATCTATTATTTTCCAGATATGTAAAGGTCTCTACCATCAGAGCAAAGGTGGA
** ** * * * *
2415 CACCTGGACCACATCTGGTTAGATTCATGGGAAACGATCTAAATCATATATTATATTTCACAGAT
131 CACCTGGACCACATCTGGTTAGACCCATAAGAAACAATCTAAATCATATATAACACTTCACAGAT
* ** * *
2480 AAACACCAAAAAACTGCATCTACATTCAAATGATATAGAAGCAATGTA-TTCCAAATGCAGTTAT
196 AAACACAAAAAAAAAGCATCTACACTCAAATGATATAGAAACAATGTATTTCCAAATGCAGTTAT
* * * * *
2544 TAAGTGTTATTACCATTTACTTCACCATGTCTAGCCCTTTAACAAAAAATGAAGATTAACATGTG
261 TAAGTGTTACTACCATTTACTTCACCATGTCTAGTCC--T-A-AAAAAAT----ATCAACAAGCG
* * * ** * ** *
2609 TCCCACTATAAATAAAATAAGAATGGCATTCACAC-TTGA-G-TCG-ATAGA--GGTACT----G
318 TCCCACTATATACAAAATAAGAATGGAATTCACACATAAATGTTAGAAT-GACCACTAATAAAAG
* **
2664 GGCAATGTAGTGTCCAGATGTAGCTCAAGTAATAACTAAACGCATAGTACTGGGCAACGATGGAC
382 AGCAATGTAGTGTCCAGATGTAGCTCAAGTAATAACTAAACAAATAGTACTGGGCAACGATGGAC
* * * *
2729 TCCATCAAGGGATGGCTAATAGATAGATTGGAAACTCAAGCCATCAATTGCTTCCCTATCTTTTA
447 TCCATCAAGGGATGGCAAATAGATAGATTGGAAACCCAAACCATCAATTCCTTCCCTATCTTTTA
* * * *
2794 TTTTCTAGATATGTAACAATCCCTACCATTATAGCAAAGGTAGACACCTGACTACATCTGATTA-
512 TTTTCCAGATATGTAACAGTCCCTACCATCATAGCAAAGGTAGACACCTGACTACATCTGGTTAG
* * *
2858 AACTCATGGAAGCAGAAAGGTAAATATTAAATAATATTTCACAGATACACACCAAAAATGAATCA
577 AA-TCATGGAAGCAGACAGCTAAATATTAAATAATATTTCACAGATACACACAAAAAATGAATCA
* *
2923 ATATTCAAAAGATATTGAAGCATGGAAAGTATTGCCAAAATGCACATGTTGTGTTATTATTATTT
641 ATAATCAAAAGATATAGAAGCATGGAAAGTATTGCCAAAATGCACATGTTGTGTTATTATTATTT
* * *
2988 GCTTCACTATGCCTATCACTTTAAGAAAGAGCAGATTCACAACACACATTCCACTGTATCCAAAA
706 GCTTCACTATACCTATCACTTTAAGAAAGAACAAATTCACAACACACATTCCACTGTATCCAAAA
* * * *
3053 TAAGAATGGCTTCTTCATACTTGAATAAATAGAATGACCACTAAATAAAGGGGTGTTGAGAGTTG
771 TAAGAATGGCTTCTTCATACTTGAATAAACAGAATGACCACTAAATAAAGAGGTGCTGAGAGATG
*
3118 TAGCATCC
836 TAGCATCA
* * * *
3126 AGATGTAGCTCAAGTAATAACTTAACACATAGTACTGAGCAAAGATGGACTCCTTCAAGGGATGG
1 AGATGTAGCTCAAGTAATAACTAAACACATACTACTGAGCAAAGATAGACTCCTTCAAGGGACGG
* * * * *
3191 ATATTCCTTCCCTATCTTTTATTTTCCAGATATGTAACGGTCTCTACCATCAGATCAAAGGTTGA
66 ATATTCCTTCCCGATCTATTATTTTCCAGATATGTAAAGGTCTCTACCATCAGAGCAAAGGTGGA
** ** * * *
3256 CACCTGGACCACATCTGGTTAGATTCATGGGAAACGATCTAAATCATATATTACATTTCACAGAT
131 CACCTGGACCACATCTGGTTAGACCCATAAGAAACAATCTAAATCATATATAACACTTCACAGAT
* * * *
3321 AAACACTAAAAAAATGCATCTACATTCAAATGATATAGAAGCAATGTATTTCCAAATGCAGTTAT
196 AAACACAAAAAAAAAGCATCTACACTCAAATGATATAGAAACAATGTATTTCCAAATGCAGTTAT
* * * *
3386 TAAGTGTTATTACCATTTACTTCACCATGTCTAGTCCTTAAAAAAATATCGACACGTGTCCCACT
261 TAAGTGTTACTACCATTTACTTCACCATGTCTAGTCC-TAAAAAAATATCAACAAGCGTCCCACT
** * * *
3451 ATATACAAAATAAGAATGGCCTTCACACTTGAATGTATAGAATGATCACTAATATAAAGATGTAC
325 ATATACAAAATAAGAATGGAATTCACACATAAATGT-TAGAATGACCACT-A-AT--A-A---A-
* * *
3516 TAGAGCAATGTAGTGTCCAGATGTAGCACAAGTAATAACTAAACATAGAGTACTGGGCAACGATG
380 -AGAGCAATGTAGTGTCCAGATGTAGCTCAAGTAATAACTAAACAAATAGTACTGGGCAACGATG
3581 GACTCCATCAAGGGATGGCAAATAGAGATAGATTGGAAACCCAAACCATCAATTCCTTCCCTATC
444 GACTCCATCAAGGGATGGCAAAT--AGATAGATTGGAAACCCAAACCATCAATTCCTTCCCTATC
* *
3646 TTTTATTTTCCAGATATGTAACAGTCCCTACCATCATAGCAAAGGTAGATACCTAACTACATCTG
507 TTTTATTTTCCAGATATGTAACAGTCCCTACCATCATAGCAAAGGTAGACACCTGACTACATCTG
* *
3711 GTTAGAATCATGGAAGCAGACAGCTAAATATTAAATAATATTTCACATATATACACTAAAAAATG
572 GTTAGAATCATGGAAGCAGACAGCTAAATATTAAATAATATTTCACAGATACACAC-AAAAAATG
* * * *
3776 CATCTATAATCAAAAGATATAGAAGCATGGAAAGTATTGCC-AAATGTATATGTTACGTGTTATT
636 AATCAATAATCAAAAGATATAGAAGCATGGAAAGTATTGCCAAAATGCACATGTT--GTGTTATT
* * * *
3840 ATTATTTGCTTCATTGTATCTATCCCTTTAAGAAAGAACAAATTCACAACACACATTCCACTGTA
699 ATTATTTGCTTCACTATACCTATCACTTTAAGAAAGAACAAATTCACAACACACATTCCACTGTA
* *
3905 TCCAAAATAAGAATGGCTTCTTCATACTTGAATGAACAGAATGACCACTAATATAATGAGGTGCT
764 TCCAAAATAAGAATGGCTTCTTCATACTTGAATAAACAGAATGACCACTAA-ATAAAGAGGTGCT
3970 GAGAGATGTAGCATCA
828 GAGAGATGTAGCATCA
*
3986 AGATGTAGCTCAAGTAATAACTAAACACATACTACTGAGCAACGATAGACTCCTTCAAGGGACGG
1 AGATGTAGCTCAAGTAATAACTAAACACATACTACTGAGCAAAGATAGACTCCTTCAAGGGACGG
4051 ATATTCCTTCCCGATCTATTATTTTCCAGATATGTAAAGGTCTCTACCATC-GTAGCAAAGGTGG
66 ATATTCCTTCCCGATCTATTATTTTCCAGATATGTAAAGGTCTCTACCATCAG-AGCAAAGGTGG
** *
4115 ACACCTGGACCACATCTGGTTAGACCCATAAGAAACAATCTAAATGTTATATAATACTTCACAGA
130 ACACCTGGACCACATCTGGTTAGACCCATAAGAAACAATCTAAATCATATATAACACTTCACAGA
*
4180 TAAAGACAAAAAAAAAGCATCTACACTCAAATGATATAGAAACAATGTATTTCCAAATGCAGTTA
195 TAAACACAAAAAAAAAGCATCTACACTCAAATGATATAGAAACAATGTATTTCCAAATGCAGTTA
* *
4245 TTAAGTGTTACTACCTTTTACTTCACCATGTCTAGTCCTCAAAAAATATCAACAAGCGTCCCACT
260 TTAAGTGTTACTACCATTTACTTCACCATGTCTAGTCCTAAAAAAATATCAACAAGCGTCCCACT
4310 ATATACAAAATAAGAATGGAATTCACACATAAATGTTAGAATGACCACTAATAAAAGAGCAATGT
325 ATATACAAAATAAGAATGGAATTCACACATAAATGTTAGAATGACCACTAATAAAAGAGCAATGT
* *
4375 AGTGTCCAGATGTAGCTTAAGTAATAACTAAAAAAATAGTACTGGGCAACGATGGACTCCATCAA
390 AGTGTCCAGATGTAGCTCAAGTAATAACTAAACAAATAGTACTGGGCAACGATGGACTCCATCAA
*
4440 GGGATGG-ATAATAGATAGATT-GAAACCCAAACCATCAATTCCTTCACTATCTTTTATTTTCCA
455 GGGATGGCA-AATAGATAGATTGGAAACCCAAACCATCAATTCCTTCCCTATCTTTTATTTTCCA
* *
4503 GATACGTAACAGTCCCTACCATCA-AGCAAAGGTAGACACCTGACTACATCTGGTTAGACTCATG
519 GATATGTAACAGTCCCTACCATCATAGCAAAGGTAGACACCTGACTACATCTGGTTAGAATCATG
* *
4567 GAAGTAGACGGCTA
584 GAAGCAGACAGCTA
4581 GGATCTGGGT
Statistics
Matches: 1315, Mismatches: 109, Indels: 59
0.89 0.07 0.04
Matches are distributed among these distances:
835 40 0.03
836 2 0.00
837 1 0.00
839 11 0.01
840 3 0.00
841 238 0.18
842 53 0.04
843 1 0.00
844 49 0.04
845 64 0.05
846 9 0.01
847 1 0.00
848 80 0.06
850 1 0.00
853 1 0.00
854 1 0.00
855 80 0.06
856 2 0.00
857 157 0.12
858 58 0.04
859 171 0.13
860 292 0.22
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (843 bp):
AGATGTAGCTCAAGTAATAACTAAACACATACTACTGAGCAAAGATAGACTCCTTCAAGGGACGG
ATATTCCTTCCCGATCTATTATTTTCCAGATATGTAAAGGTCTCTACCATCAGAGCAAAGGTGGA
CACCTGGACCACATCTGGTTAGACCCATAAGAAACAATCTAAATCATATATAACACTTCACAGAT
AAACACAAAAAAAAAGCATCTACACTCAAATGATATAGAAACAATGTATTTCCAAATGCAGTTAT
TAAGTGTTACTACCATTTACTTCACCATGTCTAGTCCTAAAAAAATATCAACAAGCGTCCCACTA
TATACAAAATAAGAATGGAATTCACACATAAATGTTAGAATGACCACTAATAAAAGAGCAATGTA
GTGTCCAGATGTAGCTCAAGTAATAACTAAACAAATAGTACTGGGCAACGATGGACTCCATCAAG
GGATGGCAAATAGATAGATTGGAAACCCAAACCATCAATTCCTTCCCTATCTTTTATTTTCCAGA
TATGTAACAGTCCCTACCATCATAGCAAAGGTAGACACCTGACTACATCTGGTTAGAATCATGGA
AGCAGACAGCTAAATATTAAATAATATTTCACAGATACACACAAAAAATGAATCAATAATCAAAA
GATATAGAAGCATGGAAAGTATTGCCAAAATGCACATGTTGTGTTATTATTATTTGCTTCACTAT
ACCTATCACTTTAAGAAAGAACAAATTCACAACACACATTCCACTGTATCCAAAATAAGAATGGC
TTCTTCATACTTGAATAAACAGAATGACCACTAAATAAAGAGGTGCTGAGAGATGTAGCATCA
Found at i:6148 original size:22 final size:22
Alignment explanation
Indices: 6092--6148 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
6082 TGAAAAAAAT
* *
6092 ATAATTAATATTT-CATTTTAA
1 ATAATTTATATTTAAATTTTAA
**
6113 ATAATTTACCTTTAAATTTTAA
1 ATAATTTATATTTAAATTTTAA
*
6135 CTAATTTATATTTA
1 ATAATTTATATTTA
6149 TACGTTGAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (22 bp):
ATAATTTATATTTAAATTTTAA
Found at i:9391 original size:19 final size:20
Alignment explanation
Indices: 9357--9404 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
9347 TCTAAATCAT
*
9357 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTTCATTTTAG
9377 TTTTCAAAA-TTCATTTTAG
1 TTTTCAAAATTTCATTTTAG
*
9396 CTTTCAAAA
1 TTTTCAAAA
9405 GAAAAGCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTTCATTTTAG
Found at i:11338 original size:21 final size:22
Alignment explanation
Indices: 11314--11367 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
11304 TTCAGTTCGT
*
11314 ATCAAGTTAATTTTA-GTTTGG
1 ATCAAGTTAATTTTAGGTTTGA
*
11335 ATCAATGTT-AGTTTAGGTTTGA
1 ATCAA-GTTAATTTTAGGTTTGA
11357 AT-AAGTTAATT
1 ATCAAGTTAATT
11368 ACCAAGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 3 0.11
21 14 0.52
22 10 0.37
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (22 bp):
ATCAAGTTAATTTTAGGTTTGA
Found at i:12215 original size:2 final size:2
Alignment explanation
Indices: 12173--12199 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12163 AGTATATACC
12173 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 A
12200 AGTATAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14285 original size:13 final size:14
Alignment explanation
Indices: 14267--14296 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
14257 TTATGTTCAG
14267 TAAGTAAATT-ATT
1 TAAGTAAATTAATT
14280 TAAGTAAATTAATT
1 TAAGTAAATTAATT
14294 TAA
1 TAA
14297 TGATTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
TAAGTAAATTAATT
Found at i:14357 original size:20 final size:17
Alignment explanation
Indices: 14311--14357 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
14301 TATAATTAAT
14311 ATTTA-TAATATAAAAA
1 ATTTATTAATATAAAAA
14327 ATTTAATTAATATAATAAGTA
1 ATTT-ATTAATATAA-AA--A
14348 ATTTATTAAT
1 ATTTATTAAT
14358 TGAATTATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.15
17 1 0.04
18 8 0.31
19 2 0.08
20 6 0.23
21 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTTATTAATATAAAAA
Found at i:14718 original size:16 final size:16
Alignment explanation
Indices: 14697--14738 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
14687 GTCTAACTTG
14697 AATTTAGA-TCAATATC
1 AATTTAGACTCAA-ATC
*
14713 AATTTAGACTGAAATC
1 AATTTAGACTCAAATC
14729 AATTTCAGAC
1 AATTT-AGAC
14739 CACCACTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (16 bp):
AATTTAGACTCAAATC
Found at i:15910 original size:14 final size:14
Alignment explanation
Indices: 15891--15918 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15881 AAGTGAAATA
15891 ATAGTTATATAATT
1 ATAGTTATATAATT
15905 ATAGTTATATAATT
1 ATAGTTATATAATT
15919 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:31384 original size:44 final size:43
Alignment explanation
Indices: 31246--31488 Score: 181
Period size: 43 Copynumber: 5.5 Consensus size: 43
31236 TTTTGATTTT
* * * * *
31246 TTTATAATTAAGACCTCTAA-TTTTGT-AATCTCATTTTTTTACA
1 TTTATAATTGAGTCC-CTAATTTTTTTCAATCTCA-CTTTTTACC
* *
31289 TTTATAATTGAAG-CCCTTAATTTTTTTTTTCAATTTCACTTTTTACT
1 TTTATAATTG-AGTCCC-TAA---TTTTTTTCAATCTCACTTTTTACC
** * * *
31336 TTTATAACCGAGGTTCCTAATTTTTTTCAATCTCGCTTTCTACC
1 TTTATAATTGA-GTCCCTAATTTTTTTCAATCTCACTTTTTACC
* * *
31380 TTTATAATTAAAGCCCCTAATTTTTGT-AATCTCACTTTTTACC
1 TTTATAATT-GAGTCCCTAATTTTTTTCAATCTCACTTTTTACC
**
31423 TTTATAATTGAGTCCACTAA-TTTTTTCAATCTCACTTTTTATT
1 TTTATAATTGAGTCC-CTAATTTTTTTCAATCTCACTTTTTACC
* *
31466 TTTACAATTTAGGTCCCTAATTT
1 TTTATAATTGA-GTCCCTAATTT
31489 AATTATTTTT
Statistics
Matches: 159, Mismatches: 27, Indels: 27
0.75 0.13 0.13
Matches are distributed among these distances:
42 10 0.06
43 68 0.43
44 47 0.30
45 1 0.01
46 1 0.01
47 24 0.15
48 8 0.05
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.51
Consensus pattern (43 bp):
TTTATAATTGAGTCCCTAATTTTTTTCAATCTCACTTTTTACC
Found at i:31486 original size:43 final size:43
Alignment explanation
Indices: 31313--31488 Score: 185
Period size: 43 Copynumber: 4.1 Consensus size: 43
31303 CCTTAATTTT
* * ** *
31313 TTTTTTCAATTTCACTTTTTACTTTTATAACCGAGGTTCCTAA
1 TTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGTCCCTAA
* * * * *
31356 TTTTTTTCAATCTCGCTTTCTACCTTTATAATTAAAGCCCCTAA
1 -TTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGTCCCTAA
31400 TTTTTGT-AATCTCACTTTTTACCTTTATAATTGA-GTCCACTAA
1 TTTTT-TCAATCTCACTTTTTACCTTTATAATTGAGGTCC-CTAA
** * *
31443 TTTTTTCAATCTCACTTTTTATTTTTACAATTTAGGTCCCTAA
1 TTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGTCCCTAA
31486 TTT
1 TTT
31489 AATTATTTTT
Statistics
Matches: 110, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
42 4 0.04
43 68 0.62
44 38 0.35
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.51
Consensus pattern (43 bp):
TTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGTCCCTAA
Found at i:32272 original size:16 final size:16
Alignment explanation
Indices: 32221--32277 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
32211 TCATTACATA
32221 ATATAAAATTTTATTAT
1 ATATAAAATTTTA-TAT
* * * *
32238 TTATTAAATTTAATCT
1 ATATAAAATTTTATAT
*
32254 ATATAAAATTTTGTAT
1 ATATAAAATTTTATAT
*
32270 ATACAAAA
1 ATATAAAA
32278 AATCTCATAC
Statistics
Matches: 30, Mismatches: 10, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
16 20 0.67
17 10 0.33
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (16 bp):
ATATAAAATTTTATAT
Found at i:35828 original size:19 final size:20
Alignment explanation
Indices: 35791--35831 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
35781 AAAACAATTA
35791 ATAATATATAATGAATTATT
1 ATAATATATAATGAATTATT
35811 ATAATA-ATAAT-AATTTATT
1 ATAATATATAATGAA-TTATT
35830 AT
1 AT
35832 TTTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 2 0.10
19 12 0.60
20 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
ATAATATATAATGAATTATT
Found at i:35830 original size:22 final size:22
Alignment explanation
Indices: 35789--35853 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
35779 CCAAAACAAT
**
35789 TAATAATATATAATGAATTATTA
1 TAATAATA-ATAATTTATTATTA
*
35812 TAATAATAATAATTTATTATTT
1 TAATAATAATAATTTATTATTA
* *
35834 TTATAAAAATAATATTATTA
1 TAATAATAATAAT-TTATTA
35854 AATTATTAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 22 0.61
23 14 0.39
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TAATAATAATAATTTATTATTA
Found at i:36149 original size:15 final size:15
Alignment explanation
Indices: 36129--36177 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
36119 ATTCTAGTTT
36129 TAATTAATATATTAA
1 TAATTAATATATTAA
*
36144 TAATTAAAAATATTAA
1 TAATT-AATATATTAA
*
36160 AAATATAAT-TATTAA
1 TAAT-TAATATATTAA
36175 TAA
1 TAA
36178 AGTTATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 13 0.46
16 14 0.50
17 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATTAATATATTAA
Found at i:36204 original size:14 final size:15
Alignment explanation
Indices: 36186--36225 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
36176 AAAGTTATAA
**
36186 AAATAATATTTTAAT
1 AAATAATATTGGAAT
36201 -AATAATATTGGAAT
1 AAATAATATTGGAAT
36215 AAATAATATTG
1 AAATAATATTG
36226 ACTAAGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (15 bp):
AAATAATATTGGAAT
Found at i:41390 original size:110 final size:110
Alignment explanation
Indices: 41197--41421 Score: 396
Period size: 110 Copynumber: 2.0 Consensus size: 110
41187 GGAGAGTGAG
*
41197 TTATGTATCTTGATACCAAGCTGTAATAAGAGAATGTTGATGCGGAAGGGTGGAAAGAGGAGAGA
1 TTATGCATCTTGATACCAAGCTGTAATAAGAGAATGTTGATGCGGAAGGGTGGAAAGAGGAGAGA
* * *
41262 GTGAGAATAGAGATAAGAACATGAGGGGAAGTCGAGATACTGATT
66 GAGAGAATAGAGATAAGAACATGAGGGGAAGTCAAGATACTGATC
* *
41307 TTATGCATCTTGATACCAAGCTGTAATAAGATAATGTTGGTGCGGAAGGGTGGAAAGAGGAGAGA
1 TTATGCATCTTGATACCAAGCTGTAATAAGAGAATGTTGATGCGGAAGGGTGGAAAGAGGAGAGA
41372 GAGAGAATAGAGATAAGAACATGAGGGGAAGTCAAGATACTGATC
66 GAGAGAATAGAGATAAGAACATGAGGGGAAGTCAAGATACTGATC
41417 TTATG
1 TTATG
41422 TCAGAAACAA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 109 1.00
ACGTcount: A:0.37, C:0.08, G:0.32, T:0.23
Consensus pattern (110 bp):
TTATGCATCTTGATACCAAGCTGTAATAAGAGAATGTTGATGCGGAAGGGTGGAAAGAGGAGAGA
GAGAGAATAGAGATAAGAACATGAGGGGAAGTCAAGATACTGATC
Found at i:48450 original size:44 final size:44
Alignment explanation
Indices: 48386--48469 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
48376 TCCATCGTTT
* *
48386 AATTCTCTCCAAGTCCAAATCTCTCAATTCTCAACCTTTCTGTA
1 AATTATCTCCAAGTCCAAATCTCCCAATTCTCAACCTTTCTGTA
* *
48430 AATTATCTCTAAGTCCAAATCTCCCTATTCTCAACCTTTC
1 AATTATCTCCAAGTCCAAATCTCCCAATTCTCAACCTTTC
48470 ATTTTCACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.27, C:0.32, G:0.04, T:0.37
Consensus pattern (44 bp):
AATTATCTCCAAGTCCAAATCTCCCAATTCTCAACCTTTCTGTA
Found at i:51415 original size:3 final size:3
Alignment explanation
Indices: 51407--51441 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
51397 GAGGTGATGT
* *
51407 AGA AGA AGA AGA AGA AGA AGA AGG AGA ATA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
51442 GTACAAAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:57697 original size:23 final size:24
Alignment explanation
Indices: 57667--57715 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
57657 AGAAAAGTAG
57667 GACAGTAGAAA-TTGCATGGGATT
1 GACAGTAGAAATTTGCATGGGATT
57690 GACAGTAGAAATTTGCATGGGATT
1 GACAGTAGAAATTTGCATGGGATT
57714 GA
1 GA
57716 AGAAAGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (24 bp):
GACAGTAGAAATTTGCATGGGATT
Done.