Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002061.1 Hibiscus syriacus cultivar Beakdansim tig00004198_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: 345124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:271096 original size:49 final size:50
Alignment explanation
Indices: 271034--271212 Score: 207
Period size: 49 Copynumber: 3.6 Consensus size: 50
271024 TACATCAGTA
*
271034 TAAGTATGTGTTAAGTGTTATATTTTTTATTTTATTCACTTACACCGGTG
1 TAAGTATGTGTTAAGTGTTACATTTTTTATTTTATTCACTTACACCGGTG
* * * *
271084 T-AGTATGTGTTAACTGTTACACTTTTTGTTTTATTCACTTACACTGGTG
1 TAAGTATGTGTTAAGTGTTACATTTTTTATTTTATTCACTTACACCGGTG
* * ** * *
271133 TAAGTATGTATTATGTACTACATTTGTTTATTTTATTCACTTACATCGATG
1 TAAGTATGTGTTAAGTGTTACATTT-TTTATTTTATTCACTTACACCGGTG
* * *
271184 TAAGTATGTATTTAGTGCTACAATTTTTT
1 TAAGTATGTGTTAAGTGTTAC-ATTTTTT
271213 GTAGTATGAA
Statistics
Matches: 108, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
49 44 0.41
50 18 0.17
51 42 0.39
52 4 0.04
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.50
Consensus pattern (50 bp):
TAAGTATGTGTTAAGTGTTACATTTTTTATTTTATTCACTTACACCGGTG
Found at i:274469 original size:18 final size:19
Alignment explanation
Indices: 274448--274485 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
274438 TCACTTTCTC
274448 TTGTTA-TTACATAAGTCA
1 TTGTTATTTACATAAGTCA
*
274466 TTGTTATTTACATAATTCA
1 TTGTTATTTACATAAGTCA
274485 T
1 T
274486 AATCATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (19 bp):
TTGTTATTTACATAAGTCA
Found at i:274529 original size:17 final size:16
Alignment explanation
Indices: 274501--274534 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
274491 TATAACTTAT
274501 ATCACAAAATCACATC
1 ATCACAAAATCACATC
*
274517 ATCACATAAATCATATC
1 ATCACA-AAATCACATC
274534 A
1 A
274535 CATAGCAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (16 bp):
ATCACAAAATCACATC
Found at i:276743 original size:19 final size:20
Alignment explanation
Indices: 276706--276744 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
276696 AATTTTAGTT
276706 TTTTTAAATATATTATTTTA
1 TTTTTAAATATATTATTTTA
*
276726 TTTTTAAATA-ATTTTTTTA
1 TTTTTAAATATATTATTTTA
276745 AAATTACCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTAAATATATTATTTTA
Found at i:277464 original size:36 final size:34
Alignment explanation
Indices: 277385--277467 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 34
277375 CGACTTTTAT
*
277385 TATTTAAAATTTATTATTAATATTACAAAATATA
1 TATTTAAAATTTATAATTAATATTACAAAATATA
*
277419 T-TTTAAAAATATT-TAATTAATTAGTTTCAAAATATA
1 TATTT-AAAAT-TTATAATTAA-TA-TTACAAAATATA
277455 TATTTAAAATTTA
1 TATTTAAAATTTA
277468 CTTTTTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
33 3 0.07
34 12 0.29
35 6 0.15
36 17 0.41
37 3 0.07
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (34 bp):
TATTTAAAATTTATAATTAATATTACAAAATATA
Found at i:278229 original size:24 final size:23
Alignment explanation
Indices: 278194--278259 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
278184 CTGACGTTTT
278194 TTTTA-AGATTTTTTTGAAATAC
1 TTTTAGAGATTTTTTTGAAATAC
*
278216 TTTTAGAGATTTTTCTGAAATAC
1 TTTTAGAGATTTTTTTGAAATAC
* *
278239 TTTTAGGGTTTTTTTATGAAA
1 TTTTAGAGATTTTTT-TGAAA
278260 ACACTTTATC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.13
23 28 0.74
24 5 0.13
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.53
Consensus pattern (23 bp):
TTTTAGAGATTTTTTTGAAATAC
Found at i:280803 original size:16 final size:15
Alignment explanation
Indices: 280776--280811 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
280766 AATGAATAAA
280776 ATTAT-TTAAATATG
1 ATTATATTAAATATG
280790 ATTATATTATAATATG
1 ATTATATTA-AATATG
280806 ATTATA
1 ATTATA
280812 AGCCATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.25
15 3 0.15
16 12 0.60
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
ATTATATTAAATATG
Found at i:281859 original size:18 final size:18
Alignment explanation
Indices: 281836--281876 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
281826 AGGATTACAC
281836 CATCATCA-AAGGCTGCAA
1 CATCATCACAA-GCTGCAA
*
281854 CATCATCACAAGCTGTAA
1 CATCATCACAAGCTGCAA
281872 CATCA
1 CATCA
281877 CAACCACCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (18 bp):
CATCATCACAAGCTGCAA
Found at i:289246 original size:69 final size:69
Alignment explanation
Indices: 289134--289272 Score: 226
Period size: 69 Copynumber: 2.0 Consensus size: 69
289124 AACCGTCGTA
* *
289134 AGCAAGGCAATGTTTTCATCAGGAGATATTACAGGGCACGTAAATGCTCAAAATGGTAATCAACA
1 AGCAAGGCAATGTTCTCATCAGGAGATAATACAGGGCACGTAAATGCTCAAAATGGTAATCAACA
289199 TCTC
66 TCTC
* *
289203 AGCAAGGCAATGTTCTCATCCGGAGATAGAT-CAGGGCATGTAAATGCTCAAAATGGTAATCAAC
1 AGCAAGGCAATGTTCTCATCAGGAGATA-ATACAGGGCACGTAAATGCTCAAAATGGTAATCAAC
289267 ATCTC
65 ATCTC
289272 A
1 A
289273 ACTCCCATCT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
69 64 0.98
70 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (69 bp):
AGCAAGGCAATGTTCTCATCAGGAGATAATACAGGGCACGTAAATGCTCAAAATGGTAATCAACA
TCTC
Found at i:291846 original size:26 final size:26
Alignment explanation
Indices: 291817--291870 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
291807 TAAAGAATTC
** *
291817 GATTTCAAAAATCTAAATTTATTAAA
1 GATTTCAAAAAAATAAATTTATAAAA
*
291843 GATTTTAAAAAAATAAATTTATAAAA
1 GATTTCAAAAAAATAAATTTATAAAA
291869 GA
1 GA
291871 GTGATATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (26 bp):
GATTTCAAAAAAATAAATTTATAAAA
Found at i:292580 original size:17 final size:18
Alignment explanation
Indices: 292539--292582 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
292529 CTTGACTTGA
*
292539 TAAAAAATAATAATTTAAT
1 TAAATAATAATAATTT-AT
292558 TAAAATAATAATAATTT-T
1 T-AAATAATAATAATTTAT
292576 TAAATAA
1 TAAATAA
292583 ATTACATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 2 0.09
19 1 0.04
20 14 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAATAATAATAATTTAT
Found at i:293507 original size:25 final size:26
Alignment explanation
Indices: 293449--293509 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
293439 TTTGTGTATG
293449 TTTT-TTTTATATAAAACTATTTTGA
1 TTTTATTTTATATAAAACTATTTTGA
* *
293474 TTTACATTTTATATAACA-TAGTTTT-A
1 TTT-TATTTTATATAAAACTA-TTTTGA
293500 TTTTATTTTA
1 TTTTATTTTA
293510 AATTAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 9 0.30
26 6 0.20
27 15 0.50
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (26 bp):
TTTTATTTTATATAAAACTATTTTGA
Found at i:296837 original size:3 final size:3
Alignment explanation
Indices: 296829--296857 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
296819 TGTAAATATA
296829 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
296858 TTCAAGACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:297280 original size:81 final size:80
Alignment explanation
Indices: 297138--297346 Score: 250
Period size: 81 Copynumber: 2.6 Consensus size: 80
297128 GATAACACGA
* *
297138 TTCCAACGTGATGAGG-ATGATGGTTATCTA-GGG-G-CACACTCCAACGTGATGAGGATATCTG
1 TTCCTACGTGATGAGGAAT--TGGTTATCTAGGGGTGACACACTCCAACGTGATGAGGAGATCTG
297199 GTCGGTGGATGAAACGG
64 GTCGGTGGATGAAACGG
* * *
297216 TTCCTACGTGATGAGGAATTGGTTATCTAGGGGTGACACGGCTCCAATGTGATGAGGAGGTCTGG
1 TTCCTACGTGATGAGGAATTGGTTATCTAGGGGTGACAC-ACTCCAACGTGATGAGGAGATCTGG
* *
297281 TCGGTGGATGACATGG
65 TCGGTGGATGAAACGG
* *
297297 TT-CTAC-TGATGAGGACGTTGGTTATCTAGGGGTGACACATCTCCTACGTG
1 TTCCTACGTGATGAGGA-ATTGGTTATCTAGGGGTGACACA-CTCCAACGTG
297347 GAGGAGGCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
77 10 0.09
78 18 0.16
79 12 0.11
80 36 0.32
81 37 0.33
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.27
Consensus pattern (80 bp):
TTCCTACGTGATGAGGAATTGGTTATCTAGGGGTGACACACTCCAACGTGATGAGGAGATCTGGT
CGGTGGATGAAACGG
Found at i:297402 original size:80 final size:79
Alignment explanation
Indices: 297238--297410 Score: 197
Period size: 80 Copynumber: 2.2 Consensus size: 79
297228 GAGGAATTGG
* * * * * *
297238 TTATCTAGGGGTGACACGGCTCCAATGTGATGAGGAGGTCTGGTCGGTGGATGACATGGTTCTAC
1 TTATCTAGGGGTGACACAGCTCCAACGTGA-GAGGAGGCCTGATCAGTGGATGACATGATTCTAC
* *
297303 TGATGAGGACGTTGG
65 TGATGAGGACGCTGA
* *
297318 TTATCTAGGGGTGACACATCTCCTACGTG-GAGGAGGCCTGATCAGTGGATGACATGATTCATA-
1 TTATCTAGGGGTGACACAGCTCCAACGTGAGAGGAGGCCTGATCAGTGGATGACATGATTC-TAC
297381 TGTATGAGGACGACTGA
65 TG-ATGAGGACG-CTGA
*
297398 TTATCTAAGGGTG
1 TTATCTAGGGGTG
297411 CATGGCTCCT
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
78 29 0.37
79 11 0.14
80 39 0.49
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.28
Consensus pattern (79 bp):
TTATCTAGGGGTGACACAGCTCCAACGTGAGAGGAGGCCTGATCAGTGGATGACATGATTCTACT
GATGAGGACGCTGA
Found at i:297578 original size:65 final size:67
Alignment explanation
Indices: 297502--297671 Score: 210
Period size: 64 Copynumber: 2.6 Consensus size: 67
297492 TTATTTCAAG
**
297502 AACTGTCTCAAGGGAGACAAAACTTTG-TTCAA-GGAAACAAACTCAAAGATTTGTGTTTCAAGA
1 AACTGTCTCAAGGGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATGGGTGTTTCAAGA
297565 GA
66 GA
* * ** * * *
297567 AATTGTCTCAAGGGA-A-AAAA-TTCGTTTCAAGGGAAATGATCTCAAATATGGGTGTTTCAGGA
1 AACTGTCTCAAGGGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATGGGTGTTTCAAGA
297629 GA
66 GA
297631 AACTGTCT-AAGGGAGACAAAAC-TTGTTTCAAGGGAAACAAA
1 AACTGTCTCAAGGGAGACAAAACTTTGTTTCAAGGGAAACAAA
297672 ACTTGTTCAA
Statistics
Matches: 86, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
62 3 0.03
63 15 0.17
64 35 0.41
65 33 0.38
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (67 bp):
AACTGTCTCAAGGGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATGGGTGTTTCAAGA
GA
Found at i:297682 original size:20 final size:21
Alignment explanation
Indices: 297639--297691 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
297629 GAAACTGTCT
*
297639 AAGGGAGACAAAACTTGTTTC
1 AAGGGAAACAAAACTTGTTTC
297660 AAGGGAAACAAAACTTG-TTC
1 AAGGGAAACAAAACTTGTTTC
297680 AAGGGAAACAAA
1 AAGGGAAACAAA
297692 TTAAAAGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.47, C:0.13, G:0.23, T:0.17
Consensus pattern (21 bp):
AAGGGAAACAAAACTTGTTTC
Found at i:298638 original size:260 final size:264
Alignment explanation
Indices: 298144--298667 Score: 961
Period size: 260 Copynumber: 2.0 Consensus size: 264
298134 GATGTTGAAT
*
298144 CCAAAGGTGCCCCACCATTCACTATTTCTTGCTTCAACACTGATTCTAAGCATGAACTTTGTGTC
1 CCAAAGGTGCCCCACCATTCACCATTTCTTGCTTCAACACTGATTCTAAGCATGAACTTTGTGTC
*
298209 TGAGAGCCACATGCCATCTACCAAGATCTAGTCCAGAGAGATTGTCTTGTTTGAAAATCATTTTC
66 TGAGAGCCACATGCCATATACCAAGATCTAGTCCAGAGAGATTGTCTTGTTTGAAAATCATTTTC
298274 TTCTTCTTTATTTTCAAACTCTGAAAATATCAATTAAAAGGATGTTGAAAAATGTTTAATCAAAG
131 TTCTTCTTTATTTTCAAACTCTGAAAATATCAATTAAAAGGATGTTGAAAAATGTTTAATCAAAG
298339 TTTGAAAATATTGCCCCTTTCTAGGTTTTACAATTGAGGTAAATCATAAAATAAGAGTTCATTGG
196 TTTGAAAATATTGCCCCTTTCTAGGTTTTACAATTGAGGTAAATCAT-AAATAAGAGTTCATTGG
298404 ATATC
260 ATATC
298409 CCAAAGGTGCCCCACCATTCACCATTTCTTGCTTCAACACTGATTCTAAGCATG-AC-TT-TGTC
1 CCAAAGGTGCCCCACCATTCACCATTTCTTGCTTCAACACTGATTCTAAGCATGAACTTTGTGTC
298471 TGAGAGCCACATGCCATATACCAAGATCTAGTCCAGAGAGATTGTCTTGTTTGAAAATCATTTT-
66 TGAGAGCCACATGCCATATACCAAGATCTAGTCCAGAGAGATTGTCTTGTTTGAAAATCATTTTC
*
298535 TTCTTCTTTTTTTTCAAACTCTGAAAATATCAATT-AAAGGATGTTGAAAAATGTTTAATCAAAG
131 TTCTTCTTTATTTTCAAACTCTGAAAATATCAATTAAAAGGATGTTGAAAAATGTTTAATCAAAG
298599 TTTTG-AAATATTGCCCCTTTCTAGGTTTTACAATTGAGGTAAATCATAAATAAGAGTTCATTGG
196 -TTTGAAAATATTGCCCCTTTCTAGGTTTTACAATTGAGGTAAATCATAAATAAGAGTTCATTGG
298663 ATATC
260 ATATC
298668 AAAGAATTAA
Statistics
Matches: 255, Mismatches: 3, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
259 22 0.09
260 71 0.28
261 38 0.15
262 67 0.26
263 2 0.01
264 2 0.01
265 53 0.21
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Consensus pattern (264 bp):
CCAAAGGTGCCCCACCATTCACCATTTCTTGCTTCAACACTGATTCTAAGCATGAACTTTGTGTC
TGAGAGCCACATGCCATATACCAAGATCTAGTCCAGAGAGATTGTCTTGTTTGAAAATCATTTTC
TTCTTCTTTATTTTCAAACTCTGAAAATATCAATTAAAAGGATGTTGAAAAATGTTTAATCAAAG
TTTGAAAATATTGCCCCTTTCTAGGTTTTACAATTGAGGTAAATCATAAATAAGAGTTCATTGGA
TATC
Found at i:299332 original size:10 final size:10
Alignment explanation
Indices: 299309--299353 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
299299 GCTTCTTGTC
299309 TTTTTC-TT-
1 TTTTTCTTTG
299317 TTTTTCTTTG
1 TTTTTCTTTG
* *
299327 TTTTTCTCTC
1 TTTTTCTTTG
299337 TTTTTCTTTG
1 TTTTTCTTTG
299347 TTTTTCT
1 TTTTTCT
299354 CTCTGCTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 23 0.74
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (10 bp):
TTTTTCTTTG
Found at i:299340 original size:20 final size:20
Alignment explanation
Indices: 299309--299357 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
299299 GCTTCTTGTC
299309 TTTTTCT-T-TTTTTCTTTG
1 TTTTTCTCTCTTTTTCTTTG
299327 TTTTTCTCTCTTTTTCTTTG
1 TTTTTCTCTCTTTTTCTTTG
299347 TTTTTCTCTCT
1 TTTTTCTCTCT
299358 GCTTTGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.24
19 1 0.03
20 21 0.72
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTTCTCTCTTTTTCTTTG
Found at i:299368 original size:22 final size:20
Alignment explanation
Indices: 299323--299368 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
299313 TCTTTTTTTC
**
299323 TTTGTTTTTCTCTCTTTTTC
1 TTTGTTTTTCTCTCTTTTGA
299343 TTTGTTTTTCTCTCTGCTTTGA
1 TTTGTTTTTCTCTCT--TTTGA
299365 TTTG
1 TTTG
299369 ATCTTTGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.68
22 7 0.32
ACGTcount: A:0.02, C:0.17, G:0.11, T:0.70
Consensus pattern (20 bp):
TTTGTTTTTCTCTCTTTTGA
Found at i:303270 original size:2 final size:2
Alignment explanation
Indices: 303263--303293 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
303253 AGCATATTTC
303263 TA 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 TA T
303294 TCCCTATTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:304502 original size:19 final size:19
Alignment explanation
Indices: 304478--304524 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
304468 CTTTAACATG
304478 TGCATCGATGTACTACCCA
1 TGCATCGATGTACTACCCA
304497 TGCATCGATGTACTACCCA
1 TGCATCGATGTACTACCCA
304516 TGCATCGAT
1 TGCATCGAT
304525 ACACCAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (19 bp):
TGCATCGATGTACTACCCA
Found at i:310355 original size:27 final size:27
Alignment explanation
Indices: 310325--310386 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
310315 TTATGGAAAT
*
310325 AATACACATTTTAA-ATTTATTT-AGATA
1 AATA-ACATTTTAATAATTATTTAAGA-A
310352 AATAACATTTTAATAATTATTTAAGAA
1 AATAACATTTTAATAATTATTTAAGAA
310379 AATAACAT
1 AATAACAT
310387 CAAAAAGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 9 0.28
27 20 0.62
28 3 0.09
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (27 bp):
AATAACATTTTAATAATTATTTAAGAA
Found at i:314826 original size:22 final size:23
Alignment explanation
Indices: 314800--314846 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
314790 TCTGATTTCT
314800 TAAAAAATATATTTATTA-ATTA
1 TAAAAAATATATTTATTATATTA
** *
314822 TAAAACTTGTATTTATTATATTA
1 TAAAAAATATATTTATTATATTA
314845 TA
1 TA
314847 TTTTTTAGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAAAATATATTTATTATATTA
Found at i:320773 original size:20 final size:21
Alignment explanation
Indices: 320733--320773 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
320723 TAATGTTATT
320733 GTCATAAGATTTTAAAACAAAA
1 GTCATAAGATTTT-AAACAAAA
320755 GTCATAAGATTTT-AACAAA
1 GTCATAAGATTTTAAACAAA
320774 TCGTCACGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
22 13 0.68
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (21 bp):
GTCATAAGATTTTAAACAAAA
Found at i:321920 original size:47 final size:47
Alignment explanation
Indices: 321813--321905 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
321803 AACCCGAAGG
321813 GTATGTAGTGC-TTTTTAATTCTAATAACGAAATTGAGTCATCGCTT
1 GTATGTAGTGCTTTTTTAATTCTAATAACGAAATTGAGTCATCGCTT
321859 GTATGTAGTGCTTTTTTAATTCTAATAACGAAATTGAGTCATCGCTT
1 GTATGTAGTGCTTTTTTAATTCTAATAACGAAATTGAGTCATCGCTT
321906 TATCATTCGG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 11 0.24
47 35 0.76
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (47 bp):
GTATGTAGTGCTTTTTTAATTCTAATAACGAAATTGAGTCATCGCTT
Found at i:324263 original size:2 final size:2
Alignment explanation
Indices: 324256--324360 Score: 210
Period size: 2 Copynumber: 52.5 Consensus size: 2
324246 CCACAATGAC
324256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
324298 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
324340 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
324361 ATCAATATAA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 103 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:324585 original size:30 final size:30
Alignment explanation
Indices: 324550--324606 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
324540 GAAGGACCTA
**
324550 TCCATATGTTTCGAA-GAACATAGGTAACTG
1 TCCATATGTCCCGAATG-ACATAGGTAACTG
324580 TCCATATGTCCCGAATGACATAGGTAA
1 TCCATATGTCCCGAATGACATAGGTAA
324607 TTCTCGACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (30 bp):
TCCATATGTCCCGAATGACATAGGTAACTG
Found at i:325182 original size:20 final size:20
Alignment explanation
Indices: 325157--325195 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
325147 TTTTCAAAGG
325157 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
325177 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
325196 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:328683 original size:13 final size:13
Alignment explanation
Indices: 328665--328689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
328655 AGAACCATGC
328665 TTTGTGAAAATAA
1 TTTGTGAAAATAA
328678 TTTGTGAAAATA
1 TTTGTGAAAATA
328690 TTTTTGGGCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
TTTGTGAAAATAA
Found at i:331093 original size:24 final size:24
Alignment explanation
Indices: 331065--331144 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
331055 CACTTAACAA
331065 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCCTTTGAATG
* *
331089 TGCATCGATTCAT-CATGTTG-A--
1 TGCATCGATGCATCCCT-TTGAATG
*
331110 TGCACCGATGCA-CGCC-TTGAATG
1 TGCATCGATGCATC-CCTTTGAATG
331133 TGCATCGATGCA
1 TGCATCGATGCA
331145 CAGGGTCATG
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
20 3 0.07
21 11 0.25
22 1 0.02
23 14 0.32
24 15 0.34
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTTGAATG
Found at i:332712 original size:18 final size:16
Alignment explanation
Indices: 332691--332729 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
332681 CCTCACGAGC
332691 TGCTCCTACCTCCTCTCG
1 TGCTCCT-CCTCCT-TCG
332709 TGCTCCTCCTCCTTCG
1 TGCTCCTCCTCCTTCG
332725 -GCTCC
1 TGCTCC
332730 GACTGATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.24
16 3 0.14
17 6 0.29
18 7 0.33
ACGTcount: A:0.03, C:0.51, G:0.13, T:0.33
Consensus pattern (16 bp):
TGCTCCTCCTCCTTCG
Found at i:333854 original size:20 final size:20
Alignment explanation
Indices: 333829--333867 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
333819 TTTTCAAAGG
333829 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
333849 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
333868 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:333936 original size:45 final size:46
Alignment explanation
Indices: 333887--333977 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
333877 GAACATCGAA
* *
333887 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
333932 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
333978 GCTTTTTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 21 0.49
46 22 0.51
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:338534 original size:8 final size:8
Alignment explanation
Indices: 338521--338556 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
338511 TTCTCTCCCT
*
338521 AAAAATTA
1 AAAAATGA
338529 AAAAATG-
1 AAAAATGA
338536 AAAAATGA
1 AAAAATGA
338544 AAAAATGA
1 AAAAATGA
338552 AAAAA
1 AAAAA
338557 AGGAAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (8 bp):
AAAAATGA
Found at i:338541 original size:15 final size:15
Alignment explanation
Indices: 338521--338555 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
338511 TTCTCTCCCT
*
338521 AAAAATTAAAAAATG
1 AAAAATGAAAAAATG
338536 AAAAATGAAAAAATG
1 AAAAATGAAAAAATG
338551 AAAAA
1 AAAAA
338556 AAGGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (15 bp):
AAAAATGAAAAAATG
Found at i:339085 original size:28 final size:27
Alignment explanation
Indices: 339017--339083 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
339007 AATTTATTTA
* *
339017 TTTATTTATTTTGATTTGGCCATGCAAT
1 TTTATTTATTTTAATTTAGCCA-GCAAT
*
339045 TTTATTAATTTTAATTTAGCCA-CACAT
1 TTTATTTATTTTAATTTAGCCAGCA-AT
339072 TTTATTTATTTT
1 TTTATTTATTTT
339084 TATATTTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.06
27 13 0.38
28 19 0.56
ACGTcount: A:0.25, C:0.10, G:0.07, T:0.57
Consensus pattern (27 bp):
TTTATTTATTTTAATTTAGCCAGCAAT
Found at i:341875 original size:30 final size:30
Alignment explanation
Indices: 341836--341916 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
341826 GAAATAAACG
341836 AAATCCCAAAAGAAAAATGAAGCTGGCACA
1 AAATCCCAAAAGAAAAATGAAGCTGGCACA
* *** *
341866 AATTCCC-AAAGATATGGTGAAGTTGGCACA
1 AAATCCCAAAAGA-AAAATGAAGCTGGCACA
*
341896 AAATCCTAAAAGAAAAATGAA
1 AAATCCCAAAAGAAAAATGAA
341917 AGTCGAGTTG
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
29 5 0.13
30 29 0.74
31 5 0.13
ACGTcount: A:0.51, C:0.16, G:0.17, T:0.16
Consensus pattern (30 bp):
AAATCCCAAAAGAAAAATGAAGCTGGCACA
Found at i:344685 original size:2 final size:2
Alignment explanation
Indices: 344678--344712 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
344668 CCTATATGAA
344678 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 A
344713 ATTCTGGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.