Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006830.1 Hibiscus syriacus cultivar Beakdansim tig00017366_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: 83537
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1886 original size:19 final size:20
Alignment explanation
Indices: 1848--1890 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1838 TAATTTAATT
*
1848 TAATTTAATTTAAGAATTTA
1 TAATATAATTTAAGAATTTA
*
1868 TAATATAATTTTA-AATTTA
1 TAATATAATTTAAGAATTTA
1887 TAAT
1 TAAT
1891 TTAAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TAATATAATTTAAGAATTTA
Found at i:2151 original size:9 final size:9
Alignment explanation
Indices: 2137--2177 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
2127 TAATATATTC
2137 ATAAATTAT
1 ATAAATTAT
2146 ATAAATTA-
1 ATAAATTAT
*
2154 ATTAATTTAT
1 A-TAAATTAT
2164 ATAAATTAT
1 ATAAATTAT
2173 ATAAA
1 ATAAA
2178 ATATTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 1 0.04
9 26 0.93
10 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATAAATTAT
Found at i:4439 original size:49 final size:49
Alignment explanation
Indices: 4367--4464 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
4357 CAAATACATA
4367 GACAAATGATCCACGTTGTTACCTGTATGAAATTCAAAACCAAGAGTAT
1 GACAAATGATCCACGTTGTTACCTGTATGAAATTCAAAACCAAGAGTAT
* *
4416 GACAACTGATCCACGTTGTTACCTGTATGAAATTCAAAACCAATAGTAT
1 GACAAATGATCCACGTTGTTACCTGTATGAAATTCAAAACCAAGAGTAT
4465 AAAGACTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (49 bp):
GACAAATGATCCACGTTGTTACCTGTATGAAATTCAAAACCAAGAGTAT
Found at i:23397 original size:7 final size:7
Alignment explanation
Indices: 23385--23435 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
23375 GTCAAAGGAA
23385 GTCAACG
1 GTCAACG
23392 GTCAACG
1 GTCAACG
*
23399 GTCAATG
1 GTCAACG
23406 GTC-ACG
1 GTCAACG
23412 GTCAACG
1 GTCAACG
*
23419 ATCAACG
1 GTCAACG
*
23426 ATCAACG
1 GTCAACG
23433 GTC
1 GTC
23436 GGGTCGGGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 5 0.13
7 34 0.87
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:23463 original size:9 final size:9
Alignment explanation
Indices: 23451--23490 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
23441 GGGTCAGTCG
*
23451 GGTCAGACC
1 GGTCAAACC
23460 GGTCAAACC
1 GGTCAAACC
*
23469 GGTTCAGACC
1 GG-TCAAACC
23479 GGTCAAACC
1 GGTCAAACC
23488 GGT
1 GGT
23491 TTCCAGCCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:23477 original size:19 final size:19
Alignment explanation
Indices: 23453--23491 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
23443 GTCAGTCGGG
23453 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
23472 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
23491 T
1 T
23492 TCCAGCCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:29216 original size:18 final size:17
Alignment explanation
Indices: 29193--29226 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
29183 AATTAACGTT
29193 TATTCTAGATGAAAAAAA
1 TATTCTAGAT-AAAAAAA
*
29211 TATTCTATATAAAAAA
1 TATTCTAGATAAAAAA
29227 GCATATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (17 bp):
TATTCTAGATAAAAAAA
Found at i:38207 original size:25 final size:26
Alignment explanation
Indices: 38155--38228 Score: 98
Period size: 25 Copynumber: 2.9 Consensus size: 26
38145 GCAATCTTAC
* * *
38155 GAGGCACTTACGAGTGCAACAC-ATT
1 GAGGCACTTTCGAGTGTAATACTATT
38180 GAGGCACTTTCGAGTGTAATACTA-T
1 GAGGCACTTTCGAGTGTAATACTATT
*
38205 GAGACACTTTCGAGTGTAATACTA
1 GAGGCACTTTCGAGTGTAATACTA
38229 GATCTACGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 43 0.98
26 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (26 bp):
GAGGCACTTTCGAGTGTAATACTATT
Found at i:38494 original size:21 final size:22
Alignment explanation
Indices: 38450--38495 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
38440 TTTTATGTGA
*
38450 ATTATTTTTTATGAGTTTTAAT
1 ATTATTTTTGATGAGTTTTAAT
38472 ATTATTTTTGATGAGTTTT-AT
1 ATTATTTTTGATGAGTTTTAAT
38493 ATT
1 ATT
38496 TTTAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (22 bp):
ATTATTTTTGATGAGTTTTAAT
Found at i:44334 original size:30 final size:30
Alignment explanation
Indices: 44298--44371 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
44288 AAAATTGAAT
44298 TAAACGGGGACGAGAAAAAACCGTTTATGC
1 TAAACGGGGACGAGAAAAAACCGTTTATGC
* * * *
44328 TAAACGGTGACGGGAAAAAATCGTTTATGT
1 TAAACGGGGACGAGAAAAAACCGTTTATGC
44358 TAAACGGGGACGAG
1 TAAACGGGGACGAG
44372 TTTAGTAATC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.38, C:0.14, G:0.30, T:0.19
Consensus pattern (30 bp):
TAAACGGGGACGAGAAAAAACCGTTTATGC
Found at i:45863 original size:69 final size:69
Alignment explanation
Indices: 45784--46292 Score: 759
Period size: 69 Copynumber: 7.4 Consensus size: 69
45774 GATGTTGAAC
* * *
45784 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTAGTGATTGAAGTGAAGTAGATAGTGGT
1 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
*
45849 AGAT
66 GGAT
* * *
45853 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGCTTGAAGTGAAGCATATGGTGGT
1 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
45918 GGAT
66 GGAT
* * *
45922 ATAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTGGTGATTGAAGTGAATTAGATGGTGGT
1 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
45987 GGAT
66 GGAT
* * ** * *
45991 GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATAGTGGT
1 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
*
46056 AGAT
66 GGAT
* * *
46060 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGCTTGAAGTGAAGCATATGGTGGT
1 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
46125 -GAT
66 GGAT
* * *
46128 ATAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTGGTGATTGAAGTGAATTAGATGGTGGT
1 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
46193 GGAT
66 GGAT
* * ** *
46197 GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATGGTGGT
1 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
46262 GGAT
66 GGAT
46266 GTAATGGAGATGATAATTGAAGTGGAG
1 GTAATGGAGATGATAATTGAAGTGGAG
46293 GAGATGCCAA
Statistics
Matches: 392, Mismatches: 47, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
68 62 0.16
69 330 0.84
ACGTcount: A:0.33, C:0.01, G:0.38, T:0.28
Consensus pattern (69 bp):
GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGATTGAAGTGAAGTAGATGGTGGT
GGAT
Found at i:46230 original size:206 final size:207
Alignment explanation
Indices: 45784--46292 Score: 948
Period size: 206 Copynumber: 2.5 Consensus size: 207
45774 GATGTTGAAC
* * * * *
45784 GTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTAGTGATTGAAGTGAAGTAGATAGTGGT
1 GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATAGTGGT
45849 AGATGTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGCTTGAAGTGAAGCATATGG
66 AGATGTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGCTTGAAGTGAAGCATATGG
45914 TGGTGGATATAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTGGTGATTGAAGTGAATTAG
131 TGGTGGATATAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTGGTGATTGAAGTGAATTAG
45979 ATGGTGGTGGAT
196 ATGGTGGTGGAT
45991 GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATAGTGGT
1 GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATAGTGGT
46056 AGATGTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGCTTGAAGTGAAGCATATGG
66 AGATGTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGCTTGAAGTGAAGCATATGG
46121 TGGT-GATATAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTGGTGATTGAAGTGAATTAG
131 TGGTGGATATAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTGGTGATTGAAGTGAATTAG
46185 ATGGTGGTGGAT
196 ATGGTGGTGGAT
*
46197 GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATGGTGGT
1 GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATAGTGGT
*
46262 GGATGTAATGGAGATGATAATTGAAGTGGAG
66 AGATGTAATGGAGATGATAATTGAAGTGGAG
46293 GAGATGCCAA
Statistics
Matches: 295, Mismatches: 7, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
206 166 0.56
207 129 0.44
ACGTcount: A:0.33, C:0.01, G:0.38, T:0.28
Consensus pattern (207 bp):
GTAATGGAGATGATAACTGAAATGGAGAAGTGGATGATAATGGTTGAAGTGAAGTAGATAGTGGT
AGATGTAATGGAGATGATAATTGAAGTGGAGAAGTGGATGATGGTGCTTGAAGTGAAGCATATGG
TGGTGGATATAATGGAGATGATAATTGAAGTGGAGAAGTGGATGGTGGTGATTGAAGTGAATTAG
ATGGTGGTGGAT
Found at i:49401 original size:2 final size:2
Alignment explanation
Indices: 49394--49424 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49384 TTATTTGCTT
49394 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
49425 AGAATTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:51369 original size:21 final size:21
Alignment explanation
Indices: 51351--51396 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
51341 TTTAATAAAC
51351 TTTAACAATCATTTTATAATA
1 TTTAACAATCATTTTATAATA
* *
51372 TTTAATAATCATTTTATGAT-
1 TTTAACAATCATTTTATAATA
51392 TTTAA
1 TTTAA
51397 AAGTTTAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTAACAATCATTTTATAATA
Found at i:55611 original size:18 final size:18
Alignment explanation
Indices: 55588--55625 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
55578 AAGAAAAAGC
55588 AAACATGAAATGTGAACT
1 AAACATGAAATGTGAACT
*
55606 AAACATGAGATGTGAACT
1 AAACATGAAATGTGAACT
55624 AA
1 AA
55626 GTACTGCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (18 bp):
AAACATGAAATGTGAACT
Found at i:65356 original size:24 final size:25
Alignment explanation
Indices: 65328--65404 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 25
65318 AAATATTTTA
* *
65328 TCTGATTTC-CGACTTGAATTTTGT
1 TCTGATTTCACGACCTGAATTCTGT
* *
65352 TCTGA-TACATGACCTGAATTCTGT
1 TCTGATTTCACGACCTGAATTCTGT
* * *
65376 TCTGATTTC-TGATCTGGATTCTGT
1 TCTGATTTCACGACCTGAATTCTGT
65400 TCTGA
1 TCTGA
65405 CTTCTGTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
23 2 0.05
24 40 0.91
25 2 0.05
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (25 bp):
TCTGATTTCACGACCTGAATTCTGT
Found at i:65380 original size:12 final size:12
Alignment explanation
Indices: 65365--65422 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
65355 GATACATGAC
65365 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
65377 CTGATTTCTGAT
1 CTGAATTCTGTT
*
65389 CTGGATTCTGTT
1 CTGAATTCTGTT
*
65401 CTGACTTCTGTT
1 CTGAATTCTGTT
* *
65413 TTGATTTCTG
1 CTGAATTCTG
65423 ATATCTCCGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.52
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:68437 original size:9 final size:9
Alignment explanation
Indices: 68425--68475 Score: 54
Period size: 9 Copynumber: 6.0 Consensus size: 9
68415 AATATTTTGC
68425 ATTTAATTT
1 ATTTAATTT
*
68434 ATTTAA-GT
1 ATTTAATTT
68442 ATTTAATTT
1 ATTTAATTT
68451 ATTTAA--T
1 ATTTAATTT
*
68458 ATTTTATTT
1 ATTTAATTT
*
68467 AATTAATTT
1 ATTTAATTT
68476 TTTTGCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.18
8 7 0.21
9 21 0.62
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
ATTTAATTT
Found at i:68447 original size:17 final size:16
Alignment explanation
Indices: 68425--68473 Score: 71
Period size: 16 Copynumber: 3.0 Consensus size: 16
68415 AATATTTTGC
68425 ATTTAATTTATTTAAGT
1 ATTTAATTTATTTAA-T
68442 ATTTAATTTATTTAAT
1 ATTTAATTTATTTAAT
* *
68458 ATTTTATTTAATTAAT
1 ATTTAATTTATTTAAT
68474 TTTTTTGCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 15 0.50
17 15 0.50
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
ATTTAATTTATTTAAT
Found at i:72711 original size:200 final size:200
Alignment explanation
Indices: 72074--72802 Score: 825
Period size: 200 Copynumber: 3.6 Consensus size: 200
72064 AGCGCTTATA
* * *
72074 TTGACATATTTTCTAAGT-AAACCGGTATATTTATACCGGTAACATTGCAAATTTACCTATTACA
1 TTGACCTATTTTCTAA-TAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACA
* ** *
72138 TTATTATTATTATCGGTTTCGATGTTTTTTAGATCGATACAATTT--TAAATGTATCGACACTTT
65 TTA-TA--ATTATTGGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTT
* * * *
72201 ATGCT-TGCACCTCG-TTGGGCATTCATATTTCATTCTGGAAAAAAGTATCGACACAAAGTAAAA
126 AT-ATGTGCACCTCGTTTGGG----C--A-TTCATTCTGGACAAAAGTATCGACACAAATTAAAC
* *
72264 AAGTATCGATACATTATT-
183 AAGTGTCGATATATT-TTG
* * * *
72282 TAGACCTATTTTCTCATAAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATCACAT
1 TTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
* * * * *
72347 TGTAATT-TTCGTTTCGATGTTTTTGGGATCGCTACTTTTAATAAATGTATCGACACTCTATGTG
66 TATAATTATTGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATATG
* * *
72411 TGCACCCCGTTT-GGCATTCATTATGGACAAAATGTATCGACACAAATTTAACAAGTGTCGATAC
131 TGCACCTCGTTTGGGCATTCATTCTGGACAAAA-GTATCGACACAAATTAAACAAGTGTCGATA-
*
72475 T-TTATG
194 TATTTTG
* * * *
72481 CTGACCTATTTTCTCATAAAACCGGTATATTTATATCGGTTACATTATAAATTTACCTATTACAT
1 TTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
*
72546 TATAATTATTGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATTGACACTTTATATG
66 TATAATTATTGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATATG
* * * **
72611 TGCATCTTGTTTGGGCATTCATTCTGGACAATAAGCATCGACACAAATTCCACAAGTGTCGATAT
131 TGCACCTCGTTTGGGCATTCATTCTGGACAA-AAGTATCGACACAAATTAAACAAGTGTCGATAT
72676 ATTTTG
195 ATTTTG
* * * *
72682 TTGACTTATTTTCTAAT-TAACCGGTATATTTATACTGGTTACATTGTTAATTTACCTATTACAT
1 TTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
* *
72746 TATAATTATTGGTTTTGATGTTTTTTGGG-TCGATACTTGTAGA-AAATGTATCGACAC
66 TATAATTATTGGTTTCGATG-TTTTTGGGATCGATACTTTTA-ATAAATGTATCGACAC
72803 ATATTTAGGT
Statistics
Matches: 451, Mismatches: 56, Indels: 36
0.83 0.10 0.07
Matches are distributed among these distances:
198 15 0.03
199 94 0.21
200 147 0.33
201 72 0.16
202 2 0.00
203 3 0.01
204 24 0.05
205 32 0.07
206 2 0.00
207 3 0.01
208 57 0.13
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.40
Consensus pattern (200 bp):
TTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
TATAATTATTGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATATG
TGCACCTCGTTTGGGCATTCATTCTGGACAAAAGTATCGACACAAATTAAACAAGTGTCGATATA
TTTTG
Found at i:74638 original size:19 final size:19
Alignment explanation
Indices: 74614--74685 Score: 144
Period size: 19 Copynumber: 3.8 Consensus size: 19
74604 GAATGTCGTC
74614 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
74633 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
74652 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
74671 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
74686 TTCTAATAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:75518 original size:149 final size:149
Alignment explanation
Indices: 75204--75507 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
75194 GGGTAGAGGG
*
75204 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAATATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
75269 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
75334 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
75353 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
*
75418 ACTTGATCCCTATTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
75483 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
75502 TCTACG
1 TCTACG
75508 TGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:75519 original size:23 final size:23
Alignment explanation
Indices: 75485--75530 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
75475 CATTATTATA
*
75485 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
75508 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
75531 AGCTATGGTG
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:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:77515 original size:200 final size:201
Alignment explanation
Indices: 77164--77822 Score: 1052
Period size: 200 Copynumber: 3.2 Consensus size: 201
77154 GACAGACGCT
* *
77164 TTATGGGTTTCGATGTTTATGGGATCGATACTTTTTATAAATGGATCGACACTTTATGGGTTCAC
1 TTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGGATCGACACTTTATGGGTGCAC
*
77229 CCTTTTTGTGCATTCATTCTGGACAAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTT
66 CCTTTTTGTGCATTCATTCTGGACAAAAAGTATTGACACAAAATTAAAAAGTGTCGATACATGTT
* *
77294 GTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTATA
131 GTAGACCTATTCTTTCATAAAACCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTATA
77359 TTATAC
196 TTATAC
* *
77365 TTATGGATTTCGATGTTTCTGGGATCGATACTTTTTATAAATGGATCGACACTTTATGGGCGCAC
1 TTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGGATCGACACTTTATGGGTGCAC
* *
77430 CCTTTTTG-GCATTCATTCTAGACCAAAAGTATTGACACAAAATTAAAAAGTGTCGATACATGTT
66 CCTTTTTGTGCATTCATTCTGGACAAAAAGTATTGACACAAAATTAAAAAGTGTCGATACATGTT
* *
77494 GTAGACCTATTCTTTCATAAAATCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTACA
131 GTAGACCTATTCTTTCATAAAACCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTATA
77559 TTATAC
196 TTATAC
* * *
77565 TTATGGGTTTCGATGTTTCTGGGATCGATATTTTTTTATAAATGGATCGACACTTTATAGTTGCA
1 TTATGGGTTTCGATGTTTCTGGGATCGATA-CTTTTTATAAATGGATCGACACTTTATGGGTGCA
* *
77630 CCCTTTTTGTGCATTCATTCTGGACAAAAAGTATCAGTATCGACACAAAATAAAAAAGTGTCAAT
65 CCCTTTTTGTGCATTCATTCTGGACAAAAAG--T-A-T-T-GACACAAAATTAAAAAGTGTCGAT
*
77695 ACATGTTGTAGACCTATT-TTCTCATAAAACCGGTATATTTATACCGGTTAGATTGAAAAATTAC
124 ACATGTTGTAGACCTATTCTT-TCATAAAACCGGTATATTTATACCGGTTACATTGAAAAATTAC
77759 CTATTATATTATAC
188 CTATTATATTATAC
* * *
77773 TTATGGGTTTCGATGTTTCTGAGATCGATACTTTTTATATATGGACCGAC
1 TTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGGATCGAC
77823 TCATATGCTT
Statistics
Matches: 422, Mismatches: 27, Indels: 12
0.92 0.06 0.03
Matches are distributed among these distances:
200 149 0.35
201 108 0.26
202 19 0.05
204 1 0.00
205 1 0.00
206 1 0.00
207 20 0.05
208 123 0.29
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (201 bp):
TTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAAATGGATCGACACTTTATGGGTGCAC
CCTTTTTGTGCATTCATTCTGGACAAAAAGTATTGACACAAAATTAAAAAGTGTCGATACATGTT
GTAGACCTATTCTTTCATAAAACCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTATA
TTATAC
Found at i:80082 original size:21 final size:21
Alignment explanation
Indices: 80057--80100 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
80047 CCCCTTATGC
80057 CTCTCAAGTGTCTCTTCAACT
1 CTCTCAAGTGTCTCTTCAACT
* *
80078 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCAACT
80099 CT
1 CT
80101 TAATTGTCTT
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:0.16, C:0.34, G:0.09, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTCTCTTCAACT
Done.