Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001021.1 Hibiscus syriacus cultivar Beakdansim tig00002034_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: 72844
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:3971 original size:16 final size:15
Alignment explanation
Indices: 3940--3979 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3930 TTATATATAT
3940 AATATATTTATTTAA
1 AATATATTTATTTAA
* *
3955 AATATTTTTATTTTA
1 AATATATTTATTTAA
3970 AATA-ATTTAT
1 AATATATTTAT
3980 AATTTATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATATATTTATTTAA
Found at i:4196 original size:21 final size:21
Alignment explanation
Indices: 4148--4199 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
4138 TTGGATCGCT
* * *
4148 ACATTAGCAATGTGGACTGCC
1 ACATCAGCATTGTGGACTACC
*
4169 TCATCAGCATTGTGGACTACC
1 ACATCAGCATTGTGGACTACC
*
4190 ACGTCAGCAT
1 ACATCAGCAT
4200 CATAACGGTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (21 bp):
ACATCAGCATTGTGGACTACC
Found at i:4501 original size:15 final size:15
Alignment explanation
Indices: 4483--4517 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
4473 TTTTATGTTT
4483 GTTCATTTATATTCA
1 GTTCATTTATATTCA
4498 GTTCATTTATATTCA
1 GTTCATTTATATTCA
4513 GTTCA
1 GTTCA
4518 ATCTCTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (15 bp):
GTTCATTTATATTCA
Found at i:10171 original size:2 final size:2
Alignment explanation
Indices: 10164--10197 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10154 GTTTTGTGTT
10164 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
10198 GCATTTTCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:12782 original size:16 final size:17
Alignment explanation
Indices: 12763--12808 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
12753 ATGCTGGAAT
12763 ATTTAATTTTCAA-ATA
1 ATTTAATTTTCAACATA
*
12779 ATTTAATTTTTAACATA
1 ATTTAATTTTCAACATA
* *
12796 ATATATTTTTCAA
1 ATTTAATTTTCAA
12809 TTTAAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTAATTTTCAACATA
Found at i:17973 original size:21 final size:21
Alignment explanation
Indices: 17949--18003 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
17939 GTTTCCAGAT
*
17949 TCGCAACGCGAATTTCGACTA
1 TCGCAATGCGAATTTCGACTA
* *
17970 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAATTTCGACTA
17991 TCGCAATGCGAAT
1 TCGCAATGCGAAT
18004 ATGTAAATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAATTTCGACTA
Found at i:18041 original size:21 final size:21
Alignment explanation
Indices: 18017--18083 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
18007 TAAATCGCAA
18017 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
* *
18038 TGCGATAGTTC-AAGTCCGCAT
1 TGCGATAG-TCGAAGTTCGCGT
18059 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
18080 TGCG
1 TGCG
18084 TGGTCGTGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.05
21 36 0.90
22 2 0.05
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.28
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:18235 original size:21 final size:20
Alignment explanation
Indices: 18211--18328 Score: 96
Period size: 21 Copynumber: 5.7 Consensus size: 20
18201 TTTAGAATAA
*
18211 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAA-TTCGACT
* *
18232 ATCGCAATGCGGATAT-GTA-A
1 ATCGCAATGCGAAT-TCG-ACT
* *
18252 ATTGCAATGCGATAGTCGACT
1 ATCGCAATGCGA-ATTCGACT
*
18273 ATCGCAATGCGAATTTAGACT
1 ATCGCAATGCGAA-TTCGACT
* *
18294 ATCACAACGCGAACTTCGACT
1 ATCGCAATGCGAA-TTCGACT
18315 ATCGCAATGCGAAT
1 ATCGCAATGCGAAT
18329 ATTGGAGTAG
Statistics
Matches: 76, Mismatches: 15, Indels: 13
0.73 0.14 0.12
Matches are distributed among these distances:
20 16 0.21
21 60 0.79
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATTCGACT
Found at i:18526 original size:128 final size:128
Alignment explanation
Indices: 18368--18625 Score: 446
Period size: 128 Copynumber: 2.0 Consensus size: 128
18358 TCATCACGTA
*
18368 AGTCTACATGAGTAGTCTCTTTTGTGACAAGTCAAGTTACTATTGAAGTAGAGAATAGACAATC-
1 AGTCTACATGAGTAGTCTCTTTTGTGACAAGTCAAGTTACTATTGAAGTAGAGAAGAGACAA-CA
* *
18432 ACAAAGAAAGAAACAGCACATGAGTTTTCATTTTGTTAGTATTATTGTCATTTCAACTGTTTAT
65 ACAAAGAAAGAAACAGCACATGAGTTTTCATTTTGTCAGTATTATTGTCATTTCAACTATTTAT
18496 AGTCTACATGAGTAGTCTCTTTTGTGACAAGTCAAGTTACTATTGAAGTAGAGAAGAGACAACAA
1 AGTCTACATGAGTAGTCTCTTTTGTGACAAGTCAAGTTACTATTGAAGTAGAGAAGAGACAACAA
* * *
18561 CAAAGAAAGAAACAGCACATGAGTTTTCATTTTGTCGGTGTTCTTGTCATTTCAACTATTTAT
66 CAAAGAAAGAAACAGCACATGAGTTTTCATTTTGTCAGTATTATTGTCATTTCAACTATTTAT
18624 AG
1 AG
18626 ATTATGAGTT
Statistics
Matches: 123, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
127 1 0.01
128 122 0.99
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (128 bp):
AGTCTACATGAGTAGTCTCTTTTGTGACAAGTCAAGTTACTATTGAAGTAGAGAAGAGACAACAA
CAAAGAAAGAAACAGCACATGAGTTTTCATTTTGTCAGTATTATTGTCATTTCAACTATTTAT
Found at i:18676 original size:19 final size:20
Alignment explanation
Indices: 18647--18699 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
18637 GAATTAGAGA
18647 TTAATAAAATTGAA-TTTATT
1 TTAA-AAAATTGAATTTTATT
18667 TTAAAAAATTGAATTTTATT
1 TTAAAAAATTGAATTTTATT
18687 TTAAAAAATTGAA
1 TTAAAAAATTGAA
18700 AAATAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 9 0.28
20 23 0.72
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (20 bp):
TTAAAAAATTGAATTTTATT
Found at i:18708 original size:21 final size:20
Alignment explanation
Indices: 18664--18712 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
18654 AATTGAATTT
** *
18664 ATTTTAAAAAATTGAATTTT
1 ATTTTAAAAAATTGAAAATA
18684 ATTTTAAAAAATTGAAAAATA
1 ATTTTAAAAAATTG-AAAATA
18705 ATTTTAAA
1 ATTTTAAA
18713 TTTATTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (20 bp):
ATTTTAAAAAATTGAAAATA
Found at i:21397 original size:9 final size:9
Alignment explanation
Indices: 21385--21428 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
21375 ATTTTAATTT
21385 TTTTATATA
1 TTTTATATA
21394 TTTTATATA
1 TTTTATATA
*
21403 TTTTAAATA
1 TTTTATATA
* *
21412 TTTTTTATG
1 TTTTATATA
21421 TTTTATAT
1 TTTTATAT
21429 TAAAAATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTATATA
Found at i:21406 original size:27 final size:27
Alignment explanation
Indices: 21375--21428 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
21365 TTATATGATA
*
21375 ATTTT-AATTTTTTTATATATTTTATAT
1 ATTTTAAATATTTTT-TATATTTTATAT
*
21402 ATTTTAAATATTTTTTATGTTTTATAT
1 ATTTTAAATATTTTTTATATTTTATAT
21429 TAAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (27 bp):
ATTTTAAATATTTTTTATATTTTATAT
Found at i:25494 original size:31 final size:31
Alignment explanation
Indices: 25456--25524 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
25446 TTCATGTTTG
25456 AATGGACGCTAAGGAGATATTTACATTTTTC
1 AATGGACGCTAAGGAGATATTTACATTTTTC
25487 AATGGACGCTAAGGAGATATTTACATTTTTC
1 AATGGACGCTAAGGAGATATTTACATTTTTC
25518 AATGGAC
1 AATGGAC
25525 TGTAAATCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (31 bp):
AATGGACGCTAAGGAGATATTTACATTTTTC
Found at i:30442 original size:20 final size:20
Alignment explanation
Indices: 30417--30455 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
30407 CTATTTTTAG
30417 TTGCATGACAACTAATAATT
1 TTGCATGACAACTAATAATT
30437 TTGCATGACAACTAATAAT
1 TTGCATGACAACTAATAAT
30456 CTCTCACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (20 bp):
TTGCATGACAACTAATAATT
Found at i:34115 original size:23 final size:23
Alignment explanation
Indices: 34089--34149 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
34079 CTCATATAAA
*
34089 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* * *
34112 TGCACCGTAGTACCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
34135 TACACCGTAGTGCCA
1 TGCACCGTAGTGCCA
34150 TATAATAATG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:34336 original size:103 final size:103
Alignment explanation
Indices: 34168--34382 Score: 412
Period size: 103 Copynumber: 2.1 Consensus size: 103
34158 TGTCCATAAG
*
34168 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTCACCAGAC
34233 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
34271 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTCACCAGAC
*
34336 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
34374 GACCACATA
1 GACCACATA
34383 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:35338 original size:2 final size:2
Alignment explanation
Indices: 35331--35359 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35321 ATATTTCATT
35331 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35360 CAAAGATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41543 original size:7 final size:7
Alignment explanation
Indices: 41531--41578 Score: 78
Period size: 7 Copynumber: 6.9 Consensus size: 7
41521 TTACAAAATA
41531 TAAATTT
1 TAAATTT
41538 TAAATTT
1 TAAATTT
41545 TAAATTT
1 TAAATTT
41552 TAAATTT
1 TAAATTT
*
41559 TAAATCT
1 TAAATTT
*
41566 TAAATTC
1 TAAATTT
41573 TAAATT
1 TAAATT
41579 ATAATTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:48113 original size:236 final size:235
Alignment explanation
Indices: 47701--48172 Score: 881
Period size: 236 Copynumber: 2.0 Consensus size: 235
47691 ATAGATGAAG
*
47701 ACTTAAATTTCCTACATGAAGCAAAAGCTGGTTGAATTCATGAATAAAAAGAATGCTAGGGAGAG
1 ACTTAAATTTCCTACATGAAGCAAAAGCTGGTTGAATTCATGAATAAAAAGAATGCTAGGGAAAG
* *
47766 AACTGACTGCCCCTAAAGAGATCACCATCAATTCGCCGAACCAATTCCTTCAGCTTGAATACAAG
66 AACTGACTGCCCCTAAAGAGATCACCATCAAATCGCCGAACAAATTCCTTCAGCTTGAATACAAG
47831 CCTCTGGATTCCTGGTTGAGCAAAGGTGTAATGGTCTTGCATGCCATCAAGCAACTGTGACAAGC
131 CCTCTGGATTCCTGGTTGAGCAAAGGTGTAATGGTCTTGCATGCCATCAAGCAACTGTGACAAGC
47896 ACCAATAACAGTCGGCTTCTATGTTGGTGATATTCACCGA
196 ACCAATAACAGTCGGCTTCTATGTTGGTGATATTCACCGA
*
47936 ACTTAAATTTCCTACATGAAGCAAAAGCTGGTTGAATTCATGAATAAAAAAGAATGCTAGTGAAA
1 ACTTAAATTTCCTACATGAAGCAAAAGCTGGTTGAATTCATGAAT-AAAAAGAATGCTAGGGAAA
*
48001 GAACTGACTGCCCCTAAAGAGATTACCATCAAATCGCCGAACAAATTCCTTCAGCTTGAATACAA
65 GAACTGACTGCCCCTAAAGAGATCACCATCAAATCGCCGAACAAATTCCTTCAGCTTGAATACAA
48066 GCCTCTGGATTCCTGGTTGAGCAAAGGTGTAATGGTCTTGCATGCCATCAAGCAACTGTGACAAG
130 GCCTCTGGATTCCTGGTTGAGCAAAGGTGTAATGGTCTTGCATGCCATCAAGCAACTGTGACAAG
*
48131 CACCAATAACAGTTGGCTTCTATGTTGGTGATATTCACCGA
195 CACCAATAACAGTCGGCTTCTATGTTGGTGATATTCACCGA
48172 A
1 A
48173 GATAAATCAG
Statistics
Matches: 230, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
235 45 0.20
236 185 0.80
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.25
Consensus pattern (235 bp):
ACTTAAATTTCCTACATGAAGCAAAAGCTGGTTGAATTCATGAATAAAAAGAATGCTAGGGAAAG
AACTGACTGCCCCTAAAGAGATCACCATCAAATCGCCGAACAAATTCCTTCAGCTTGAATACAAG
CCTCTGGATTCCTGGTTGAGCAAAGGTGTAATGGTCTTGCATGCCATCAAGCAACTGTGACAAGC
ACCAATAACAGTCGGCTTCTATGTTGGTGATATTCACCGA
Found at i:57359 original size:20 final size:20
Alignment explanation
Indices: 57248--57388 Score: 167
Period size: 21 Copynumber: 6.8 Consensus size: 20
57238 AGGGTGTCAA
57248 AGTGCATCCATGCACTCATGC
1 AGTGCATCCATGCAC-CATGC
*
57269 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCATGC
* *
57290 AGTACATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCATGC
*
57311 AGTGTATCCATGCACC-TGCCAC
1 AGTGCATCCATGCACCATG---C
*
57333 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCATGC
57354 AGTGCATCCATGCACCATGC
1 AGTGCATCCATGCACCATGC
57374 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
57389 TCCATTTCGA
Statistics
Matches: 107, Mismatches: 7, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.02
20 36 0.34
21 51 0.48
22 2 0.02
23 14 0.13
24 2 0.02
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.21
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGC
Found at i:60158 original size:21 final size:21
Alignment explanation
Indices: 60096--60173 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
60086 AGGGTGTCAA
* * *
60096 AGTGCATCTATGCACTCATGC
1 AGTGCATCCATGCACCCCTGC
* *
60117 AGTGCGTCTATGCATCCCCTGC
1 AGTGCATCCATGCA-CCCCTGC
*
60139 AGTGCATCCATGCACCCCTGT
1 AGTGCATCCATGCACCCCTGC
60160 AGTGCATCCATGCA
1 AGTGCATCCATGCA
60174 TTTGCCACTA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
21 33 0.66
22 17 0.34
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:60201 original size:30 final size:30
Alignment explanation
Indices: 60162--60235 Score: 130
Period size: 30 Copynumber: 2.4 Consensus size: 30
60152 ACCCCTGTAG
*
60162 TGCATCCATGCATTTGCCACTAGTGCATCGA
1 TGCA-CCATGCAGTTGCCACTAGTGCATCGA
60193 TGCACCATGCAGTTGCCACTAGTGCATCGA
1 TGCACCATGCAGTTGCCACTAGTGCATCGA
60223 TGCACCATGCAGT
1 TGCACCATGCAGT
60236 GCATCCATGC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 38 0.90
31 4 0.10
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.26
Consensus pattern (30 bp):
TGCACCATGCAGTTGCCACTAGTGCATCGA
Found at i:60292 original size:20 final size:20
Alignment explanation
Indices: 60267--60341 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
60257 AATGCAATTA
* *
60267 GTGCATCGATGCACCCTGCT
1 GTGCATCCATGCACCCTACT
* *
60287 GTGCATCCATGCATCATACT
1 GTGCATCCATGCACCCTACT
*
60307 GTGCATCCATGCATCCTACT
1 GTGCATCCATGCACCCTACT
60327 GTGCATCCATGCACC
1 GTGCATCCATGCACC
60342 AAGACTGCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.27
Consensus pattern (20 bp):
GTGCATCCATGCACCCTACT
Found at i:71634 original size:21 final size:21
Alignment explanation
Indices: 71519--71634 Score: 62
Period size: 21 Copynumber: 5.6 Consensus size: 21
71509 GCGAAATAAA
71519 AATCGCAACGCGA-TATCCAG
1 AATCGCAACGCGATTATCCAG
** * *
71539 AATCGCAAATC-AGTT-CCCAT
1 AATCGCAACGCGA-TTATCCAG
* **
71559 AATCACAACGCGATTATGAAG
1 AATCGCAACGCGATTATCCAG
* *
71580 AATCGCAATGCGA-TAGTACA-
1 AATCGCAACGCGATTA-TCCAG
** *
71600 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTATCCAG
71622 AATCGCAACGCGA
1 AATCGCAACGCGA
71635 ACATATAAAT
Statistics
Matches: 68, Mismatches: 20, Indels: 15
0.66 0.19 0.15
Matches are distributed among these distances:
19 1 0.01
20 26 0.38
21 38 0.56
22 3 0.04
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTATCCAG
Found at i:71663 original size:20 final size:20
Alignment explanation
Indices: 71640--71834 Score: 165
Period size: 20 Copynumber: 9.6 Consensus size: 20
71630 CGCGAACATA
71640 TAAATCGCAACGAGTATCCG
1 TAAATCGCAACGAGTATCCG
*
71660 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGAGTATCCG
** *
71681 TAAATCGCAACGACAATACG
1 TAAATCGCAACGAGTATCCG
* * *
71701 TAAAATCACAATGCGTATCCG
1 T-AAATCGCAACGAGTATCCG
* * *
71722 TAAATTGCAACGAGAATACG
1 TAAATCGCAACGAGTATCCG
* * *
71742 TAAACCGCAACGCGTATCTG
1 TAAATCGCAACGAGTATCCG
* * *
71762 TAAATCACAACGAGAATACG
1 TAAATCGCAACGAGTATCCG
* * *
71782 TAAATCGTAATGCGTATCCG
1 TAAATCGCAACGAGTATCCG
** *
71802 TAAATCGCAACGACAATACG
1 TAAATCGCAACGAGTATCCG
71822 TAAAATCGCAACG
1 T-AAATCGCAACG
71835 CGATTTTTAA
Statistics
Matches: 131, Mismatches: 41, Indels: 5
0.74 0.23 0.03
Matches are distributed among these distances:
20 87 0.66
21 44 0.34
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.19
Consensus pattern (20 bp):
TAAATCGCAACGAGTATCCG
Found at i:71773 original size:40 final size:41
Alignment explanation
Indices: 71640--71836 Score: 272
Period size: 40 Copynumber: 4.9 Consensus size: 41
71630 CGCGAACATA
* *
71640 TAAATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCG
1 TAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCG
* * *
71681 TAAATCGCAACGACAATACGTAAAATCACAATGCGTATCCG
1 TAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCG
* * *
71722 TAAATTGCAACGAGAATACGT-AAACCGCAACGCGTATCTG
1 TAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCG
* * *
71762 TAAATCACAACGAGAATACGT-AAATCGTAATGCGTATCCG
1 TAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCG
*
71802 TAAATCGCAACGACAATACGTAAAATCGCAACGCG
1 TAAATCGCAACGAGAATACGTAAAATCGCAACGCG
71837 ATTTTTAAAG
Statistics
Matches: 134, Mismatches: 21, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
40 68 0.51
41 66 0.49
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
TAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCG
Found at i:72450 original size:21 final size:21
Alignment explanation
Indices: 72389--72467 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
72379 TTCTAAACTT
72389 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
72409 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
72429 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
72450 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
72468 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:72471 original size:14 final size:14
Alignment explanation
Indices: 72449--72546 Score: 70
Period size: 14 Copynumber: 6.3 Consensus size: 14
72439 CGAGAGAAAT
72449 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
72463 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
72481 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
*
72496 GATAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
72514 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
72529 GATAATCGCAACGC
1 GAAAATCGCAACGA
72543 GAAA
1 GAAA
72547 TGAAAATCGC
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
14 35 0.52
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.30
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:72485 original size:33 final size:33
Alignment explanation
Indices: 72444--72587 Score: 231
Period size: 33 Copynumber: 4.5 Consensus size: 33
72434 CGCAACGAGA
72444 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
72477 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
72510 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
72543 GAAATGAAAATCGCAAC--GAG-ATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
72573 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
72588 TTGCGATTTT
Statistics
Matches: 107, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
30 23 0.21
31 2 0.02
33 82 0.77
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:72605 original size:19 final size:19
Alignment explanation
Indices: 72583--72712 Score: 112
Period size: 19 Copynumber: 7.1 Consensus size: 19
72573 GAAACCAAAA
*
72583 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
72602 TCGCGTTGCGA-TTTC---
1 TCGCGTTGCGATTTTCATT
*
72617 T--CGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
72634 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
72653 TTGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* **
72672 TC-CGCATGCGATAGTCATT
1 TCGCG-TTGCGATTTTCATT
*
72691 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
72711 TC
1 TC
72713 AACCAAAAGA
Statistics
Matches: 91, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
13 8 0.09
14 3 0.03
15 1 0.01
17 1 0.01
18 6 0.07
19 57 0.63
20 13 0.14
21 2 0.02
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:72647 original size:13 final size:13
Alignment explanation
Indices: 72599--72628 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
72589 TGCGATTTTC
72599 ATTTCGCGTTGCG
1 ATTTCGCGTTGCG
*
72612 ATTTCTCGTTGCG
1 ATTTCGCGTTGCG
72625 ATTT
1 ATTT
72629 TAATTTCGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (13 bp):
ATTTCGCGTTGCG
Done.