Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009079.1 Hibiscus syriacus cultivar Beakdansim tig00112518_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: 283420
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:214507 original size:3 final size:3
Alignment explanation
Indices: 214493--214527 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
214483 AGAGATATTA
*
214493 TCT TCA TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
214528 ATGTACGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:215136 original size:64 final size:63
Alignment explanation
Indices: 215063--215286 Score: 252
Period size: 64 Copynumber: 3.5 Consensus size: 63
215053 TGTTTGAATG
** * *
215063 TGCACCGATGCATTGGTAGTGCATCGATGAACTCTTTTAA-AATAAAGACATCGAATGCAATTCA
1 TGCACCGATGCATAAGTAGTGCATCGATGCA-TCTATTAATAATAAA-ACATCGAATGCAATTCA
* * * **
215127 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGT
1 TGCACCGATGCATAAGTAGTGCATCGATGCAT-CTATTAATAATAAAACATCGAATGCAATTCA
* * * * * * *
215191 TGCATCGATGCATAAGGAGTGCATCGATGCATCTCAATAATAATACAACATCGAATACATTTTA
1 TGCACCGATGCATAAGTAGTGCATCGATGCATCT-ATTAATAATAAAACATCGAATGCAATTCA
*
215255 TGCACCGATGCATCAGTAGTGCATCGATGCAT
1 TGCACCGATGCATAAGTAGTGCATCGATGCAT
215287 ACCTTCATTA
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
63 2 0.01
64 129 0.95
65 5 0.04
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (63 bp):
TGCACCGATGCATAAGTAGTGCATCGATGCATCTATTAATAATAAAACATCGAATGCAATTCA
Found at i:215980 original size:31 final size:31
Alignment explanation
Indices: 215942--216083 Score: 221
Period size: 31 Copynumber: 4.6 Consensus size: 31
215932 AGGGTCGAGG
*
215942 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
215973 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
216004 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
216035 GTTTACCTATATTCTTCTGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
216066 ATTTACCTAGGTTCTTCG
1 GTTTACCTATGTTCTTCG
216084 AAATCTATGG
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 100 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:219278 original size:64 final size:64
Alignment explanation
Indices: 219205--219428 Score: 215
Period size: 64 Copynumber: 3.5 Consensus size: 64
219195 TATTTGAATG
* * **
219205 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGAAATTC
1 TGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGAAATTC
219268 A
64 A
* * * **
219269 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGAAATTCA
* ** * * *
219333 TGCATCGATGCATAAGG-AGTGCATCGATGCATCTCAACAATAATACAACATCGAAT-ACATTTT
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGA-AATTC
219396 A
64 A
* *
219397 TGCACCGATGCATCA-GTAGTGCATCGGTGCAT
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCAT
219429 ACCTTCATTA
Statistics
Matches: 133, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
63 1 0.01
64 124 0.93
65 8 0.06
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGAAATTCA
Found at i:220122 original size:31 final size:31
Alignment explanation
Indices: 220084--220270 Score: 331
Period size: 31 Copynumber: 6.0 Consensus size: 31
220074 AGCGTCGAGG
220084 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
220115 GTTTACCTATGTTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
220146 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
220177 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
220208 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
220239 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
220270 G
1 G
220271 GTCCTTCGGG
Statistics
Matches: 151, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
31 150 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:221268 original size:60 final size:60
Alignment explanation
Indices: 221129--221284 Score: 145
Period size: 60 Copynumber: 2.6 Consensus size: 60
221119 CCCTCATTTC
* * * * * *
221129 AAATTAGTCCCTAAACTTTTAAACATTTCAATTTCATCCTTAAACTATGAATATTATTCT
1 AAATTGGTCCCCAAACTTTTGAACATTTCATTTTCATCCCTAAACTATGAATATTATCCT
* ** ** *
221189 AAATTGGTCCTCATGCTTTTGAACATTTCATTTTCATCCCCT-AGTTATG-ATCTTCATCCT
1 AAATTGGTCCCCAAACTTTTGAACATTTCATTTTCAT-CCCTAAACTATGAATATT-ATCCT
*
221249 AAATTGGTCCCCAAACTTTTTGAATATTTCAATTTT
1 AAATTGGTCCCCAAAC-TTTTGAACATTTC-ATTTT
221285 ATACTAAATG
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
59 4 0.05
60 52 0.68
61 15 0.20
62 5 0.07
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (60 bp):
AAATTGGTCCCCAAACTTTTGAACATTTCATTTTCATCCCTAAACTATGAATATTATCCT
Found at i:221576 original size:60 final size:60
Alignment explanation
Indices: 221418--221578 Score: 189
Period size: 60 Copynumber: 2.7 Consensus size: 60
221408 GATGAATTTG
* * * *
221418 AGGATGAAATTGAAATATCTAAAAGTTTAGGGACCAATTTATAATGAGATTAATAGTTCT
1 AGGATGAAATTGAAATATTTAAAAGTTTAAGGACTAATTTATAATGAGAGTAATAGTTCT
* * * * * *
221478 GGGATGAAATTCAAATGTTCAAAAGTTTAAGGACTAATTTGTAATGAGAGTCATAGTT-T
1 AGGATGAAATTGAAATATTTAAAAGTTTAAGGACTAATTTATAATGAGAGTAATAGTTCT
* * *
221537 AAGGATGAAATTGGAATATTTAAAAGTTTAAAGATTAATTTA
1 -AGGATGAAATTGAAATATTTAAAAGTTTAAGGACTAATTTA
221579 AAATAAATCA
Statistics
Matches: 82, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 1 0.01
60 81 0.99
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (60 bp):
AGGATGAAATTGAAATATTTAAAAGTTTAAGGACTAATTTATAATGAGAGTAATAGTTCT
Found at i:232726 original size:30 final size:30
Alignment explanation
Indices: 232602--232750 Score: 84
Period size: 30 Copynumber: 5.0 Consensus size: 30
232592 CATGAAACAG
* * * *
232602 GACGGGGAACGAGGTCCTATGCAGAATCAC
1 GACGGGAAACGAAGTCCCATGCAGAATCAT
* * * * * * *
232632 AATGGGGAACGAGGTCCCATACAAAATCAA
1 GACGGGAAACGAAGTCCCATGCAGAATCAT
* * ** * *
232662 AACGGGACACGAAGTCTAATGCA-ATGTCAG
1 GACGGGAAACGAAGTCCCATGCAGA-ATCAT
* *
232692 GACGGGAAATGAAGTCCTATGCAGAATCAT
1 GACGGGAAACGAAGTCCCATGCAGAATCAT
* * *
232722 GACGGGGAACGGAGTCCCATGCAGGATCA
1 GACGGGAAACGAAGTCCCATGCAGAATCA
232751 GAACTATATC
Statistics
Matches: 90, Mismatches: 27, Indels: 4
0.74 0.22 0.03
Matches are distributed among these distances:
29 1 0.01
30 88 0.98
31 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.30, T:0.15
Consensus pattern (30 bp):
GACGGGAAACGAAGTCCCATGCAGAATCAT
Found at i:235539 original size:3 final size:3
Alignment explanation
Indices: 235531--235584 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
235521 ATATATATAT
235531 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
235579 ATA ATA
1 ATA ATA
235585 TATAGTCTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:236010 original size:20 final size:20
Alignment explanation
Indices: 235966--236010 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
235956 AAACATCCTA
* *
235966 TTTTACAGATGACCCGGAGG
1 TTTTACAAATGACCCGGAAG
* *
235986 ATTTACAAATTACCCGGAAG
1 TTTTACAAATGACCCGGAAG
236006 TTTTA
1 TTTTA
236011 ATATTCTAGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (20 bp):
TTTTACAAATGACCCGGAAG
Found at i:236177 original size:119 final size:119
Alignment explanation
Indices: 235966--236472 Score: 879
Period size: 119 Copynumber: 4.3 Consensus size: 119
235956 AAACATCCTA
* *
235966 TTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAAGTTTTAATATTCTAGAACATTAAATG
1 TTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATG
*
236031 AGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCTACCCTAAGG
66 AGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGG
* * *
236085 TTTTACAGAAGACCCGGAGGATTTACAAATTACCTGGAGGTTTTAATTTTCTAGAACATTAAATA
1 TTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATG
* * *
236150 AGAAACTTTGGTAGTCGCTTTCTCATTTTCTTGCGAAAACATCCTACCCTGAGG
66 AGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGG
* *
236204 TTTTACAGATGACCCAGAGAATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATG
1 TTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATG
236269 AGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGG
66 AGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGG
* *
236323 TTTTACAGATGACCCGGAGGATTTAAAAATTACCCGAAGGTTTTAATTTTCTAGAACATTAAATG
1 TTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATG
236388 AGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGG
66 AGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGG
* *
236442 TTTTACAGATGACCCGAAGGATTTAAAAATT
1 TTTTACAGATGACCCGGAGGATTTACAAATT
236473 TGTGAGAAAT
Statistics
Matches: 366, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
119 366 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (119 bp):
TTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATG
AGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGG
Found at i:236248 original size:20 final size:20
Alignment explanation
Indices: 236194--236248 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
236184 GAAAACATCC
* *
236194 TACCCTGAGGTTTTACAGAT
1 TACCCAGAGGTTTTACAAAT
* **
236214 GACCCAGAGAATTTACAAAT
1 TACCCAGAGGTTTTACAAAT
*
236234 TACCCGGAGGTTTTA
1 TACCCAGAGGTTTTA
236249 ATTTTCTAGA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
TACCCAGAGGTTTTACAAAT
Found at i:236283 original size:238 final size:238
Alignment explanation
Indices: 235718--236472 Score: 1163
Period size: 238 Copynumber: 3.2 Consensus size: 238
235708 AATTAAAGTA
* * * * *
235718 AAAACATCATACTCTGAGGTTTTATAGATGACCCAGAGGATTTACAAATTATCCGGAGGATTTAA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCAGAGGATTTACAAATTACCCGGAGGTTTTAA
* * * *
235783 TTTTCTTGAACATTAAATGAGAAACTTTGGTAACCGCTTTCTCATTTTCATGTGAAAACATCCTA
66 TTTTCTAGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCTA
* * * *
235848 CCCTGAGGTTTTATAGATGACCC-AAGGATTTACAAATTA-CTCGGAGGATTTAATTTTCTTGAA
131 CCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCT-GGAGGTTTTAATTTTCTAGAA
*
235911 CATTAAATGAGAAACTTTGGTAATCACTTTCGCATTTTCATGCG
195 CATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGCG
* *
235955 AAAACA---T--CCT-A--TTTTACAGATGACCCGGAGGATTTACAAATTACCCGGAAGTTTTAA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCAGAGGATTTACAAATTACCCGGAGGTTTTAA
*
236012 TATTCTAGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCTA
66 TTTTCTAGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCTA
* *
236077 CCCTAAGGTTTTACAGAAGACCCGGAGGATTTACAAATTACCTGGAGGTTTTAATTTTCTAGAAC
131 CCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCTGGAGGTTTTAATTTTCTAGAAC
* * * *
236142 ATTAAATAAGAAACTTTGGTAGTCGCTTTCTCATTTTCTTGCG
196 ATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGCG
*
236185 AAAACATCCTACCCTGAGGTTTTACAGATGACCCAGAGAATTTACAAATTACCCGGAGGTTTTAA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCAGAGGATTTACAAATTACCCGGAGGTTTTAA
236250 TTTTCTAGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCTA
66 TTTTCTAGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCTA
* * *
236315 CCCTGAGGTTTTACAGATGACCCGGAGGATTTAAAAATTACCCGAAGGTTTTAATTTTCTAGAAC
131 CCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCTGGAGGTTTTAATTTTCTAGAAC
236380 ATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGCG
196 ATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGCG
*
236423 AAAACATCCTACCCTGAGGTTTTACAGATGACCC-GAAGGATTTAAAAATT
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCAG-AGGATTTACAAATT
236473 TGTGAGAAAT
Statistics
Matches: 470, Mismatches: 37, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
229 121 0.26
230 79 0.17
231 3 0.01
232 2 0.00
233 1 0.00
234 1 0.00
235 3 0.01
236 1 0.00
237 7 0.01
238 252 0.54
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (238 bp):
AAAACATCCTACCCTGAGGTTTTACAGATGACCCAGAGGATTTACAAATTACCCGGAGGTTTTAA
TTTTCTAGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGCGAAAACATCCTA
CCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATTACCTGGAGGTTTTAATTTTCTAGAAC
ATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGCG
Found at i:236342 original size:20 final size:20
Alignment explanation
Indices: 236314--236368 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
236304 AAAACATCCT
* * *
236314 ACCCTGAGGTTTTACAGATG
1 ACCCGGAGGTTTTAAAAATG
* *
236334 ACCCGGAGGATTTAAAAATT
1 ACCCGGAGGTTTTAAAAATG
*
236354 ACCCGAAGGTTTTAA
1 ACCCGGAGGTTTTAA
236369 TTTTCTAGAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (20 bp):
ACCCGGAGGTTTTAAAAATG
Found at i:237978 original size:52 final size:50
Alignment explanation
Indices: 237898--238033 Score: 182
Period size: 51 Copynumber: 2.7 Consensus size: 50
237888 ATATCCCAAC
* * * *
237898 CTTTTTATGCTGGTGTGAGCCTTCAAGATGCCTCATATGGATTACTTCTGT
1 CTTTTTATGCTGATGTGAGCCTTCAAGATGCC-CACATGGATAACTTATGT
* * *
237949 CTTTTTCATGTTGATGTGAGCCTTTAAGATACCCACATGGATAACTTATGT
1 CTTTTT-ATGCTGATGTGAGCCTTCAAGATGCCCACATGGATAACTTATGT
238000 CTTTTTTATGCTGATGTGAGCCTTCAAGATGCCC
1 C-TTTTTATGCTGATGTGAGCCTTCAAGATGCCC
238034 CAGATAGATA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
51 46 0.63
52 27 0.37
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (50 bp):
CTTTTTATGCTGATGTGAGCCTTCAAGATGCCCACATGGATAACTTATGT
Found at i:238415 original size:28 final size:28
Alignment explanation
Indices: 238375--238441 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
238365 GTCGCATTCT
238375 TGCCCTTTTTGCTATGCACT-GGAATATA
1 TGCCCTTTTTGCTATGCACTAGG-ATATA
238403 TGCCCTTTTTGCTATGCACTAGGATATA
1 TGCCCTTTTTGCTATGCACTAGGATATA
238431 TGCCCTTTTTG
1 TGCCCTTTTTG
238442 AATAGGGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 36 0.95
29 2 0.05
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (28 bp):
TGCCCTTTTTGCTATGCACTAGGATATA
Found at i:239380 original size:10 final size:10
Alignment explanation
Indices: 239365--239425 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 10
239355 ATTCAATTTC
239365 TTTTTCTTTT
1 TTTTTCTTTT
239375 TTTTTCTCTTT
1 TTTTTCT-TTT
*
239386 TTTTCCTTTT
1 TTTTTCTTTT
*
239396 TCCTTTTTTTTGT
1 T--TTTTCTTT-T
*
239409 TCTTTTCTCTT
1 T-TTTTCTTTT
239420 TTTTTC
1 TTTTTC
239426 CTGATGGATG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 16 0.38
11 11 0.26
12 13 0.31
13 2 0.05
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:239386 original size:18 final size:17
Alignment explanation
Indices: 239363--239424 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 17
239353 TGATTCAATT
239363 TCTTTTTCTTTTTTTTTC
1 TCTTTTT-TTTTTTTTTC
**
239381 TCTTTTTTTCCTTTTTC
1 TCTTTTTTTTTTTTTTC
239398 -CTTTTTTTTGTTCTTTTC
1 TCTTTTTTTT-TT-TTTTC
239416 TCTTTTTTT
1 TCTTTTTTT
239425 CCTGATGGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 8 0.22
17 9 0.24
18 12 0.32
19 8 0.22
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.81
Consensus pattern (17 bp):
TCTTTTTTTTTTTTTTC
Found at i:239414 original size:27 final size:27
Alignment explanation
Indices: 239364--239423 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
239354 GATTCAATTT
*
239364 CTTTTTCTTTTTTTTTCTCTTTTTTTC
1 CTTTTTCTTTTTTTTTCTCTTTTTCTC
239391 CTTTTTCCTTTTTTTTGT-TC-TTTTCTC
1 CTTTTT-CTTTTTTTT-TCTCTTTTTCTC
*
239418 TTTTTT
1 CTTTTT
239424 TCCTGATGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 17 0.59
28 11 0.38
29 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (27 bp):
CTTTTTCTTTTTTTTTCTCTTTTTCTC
Found at i:242702 original size:20 final size:20
Alignment explanation
Indices: 242680--242724 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
242670 ATGGTTTTCA
242680 TTTCTGCGCTCAATTTATCAT
1 TTTC-GCGCTCAATTTATCAT
242701 TTTCGCGCTCAATTTATCAT
1 TTTCGCGCTCAATTTATCAT
242721 TTTC
1 TTTC
242725 AATTTTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.18, C:0.24, G:0.09, T:0.49
Consensus pattern (20 bp):
TTTCGCGCTCAATTTATCAT
Found at i:245723 original size:37 final size:37
Alignment explanation
Indices: 245674--245749 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
245664 ACATAAAAGG
245674 TAATAATAAAATAAAATTACAATTACATATATTTAAA
1 TAATAATAAAATAAAATTACAATTACATATATTTAAA
* *
245711 TAATAATAAAATAAAATTGCAATTATATATATTTAAA
1 TAATAATAAAATAAAATTACAATTACATATATTTAAA
245748 TA
1 TA
245750 GTCAGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (37 bp):
TAATAATAAAATAAAATTACAATTACATATATTTAAA
Found at i:250377 original size:10 final size:10
Alignment explanation
Indices: 250362--250448 Score: 51
Period size: 10 Copynumber: 8.8 Consensus size: 10
250352 CGCTTGAAGA
250362 AGAAAAAAAG
1 AGAAAAAAAG
250372 AGAAAAAAATG
1 AGAAAAAAA-G
250383 A-AAAAAAATG
1 AGAAAAAAA-G
250393 A-AAAAAATA-
1 AGAAAAAA-AG
*
250402 ATAATAAAAATG
1 AGAA-AAAAA-G
*
250414 AG--AAGAAG
1 AGAAAAAAAG
*
250422 A-AAAAGAAG
1 AGAAAAAAAG
*
250431 GGAAAAAAAG
1 AGAAAAAAAG
250441 AGAAAAAA
1 AGAAAAAA
250449 GGGAAAAGGG
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
8 2 0.03
9 11 0.17
10 42 0.67
11 7 0.11
12 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:250387 original size:19 final size:19
Alignment explanation
Indices: 250363--250510 Score: 68
Period size: 19 Copynumber: 7.9 Consensus size: 19
250353 GCTTGAAGAA
250363 GAAAAAAAGAGAAAAAAAT
1 GAAAAAAAGAGAAAAAAAT
250382 GAAAAAAA-ATGAAAAAAAT
1 GAAAAAAAGA-GAAAAAAAT
* * *
250401 -AATAATAAAAATGAGAAGAA-
1 GAA-AA-AAAGA-GAAAAAAAT
*
250421 GAAAAAGAAGGGAAAAAAA-
1 GAAAAA-AAGAGAAAAAAAT
* *
250440 GAGAAAAAAGGGAAAAGGGAA-
1 GA-AAAAAAGAGAAAA--AAAT
*
250461 G-AAAAAA-TG--AAAAAT
1 GAAAAAAAGAGAAAAAAAT
250476 G-AAAAAAGAG--AAAAAT
1 GAAAAAAAGAGAAAAAAAT
250492 GAAAAAAAGAGAAATAAAA
1 GAAAAAAAGAGAAA-AAAA
250511 GGAGGGTTCA
Statistics
Matches: 104, Mismatches: 10, Indels: 29
0.73 0.07 0.20
Matches are distributed among these distances:
14 2 0.02
15 7 0.07
16 10 0.10
17 9 0.09
18 4 0.04
19 44 0.42
20 15 0.14
21 13 0.12
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.07
Consensus pattern (19 bp):
GAAAAAAAGAGAAAAAAAT
Found at i:250390 original size:21 final size:21
Alignment explanation
Indices: 250364--250417 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
250354 CTTGAAGAAG
250364 AAAAAAA-GAGAAAAA-AATGA
1 AAAAAAATGAGAAAAATAAT-A
*
250384 AAAAAAATGAAAAAAATAATA
1 AAAAAAATGAGAAAAATAATA
*
250405 ATAAAAATGAGAA
1 AAAAAAATGAGAA
250418 GAAGAAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.24
21 19 0.66
22 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (21 bp):
AAAAAAATGAGAAAAATAATA
Found at i:250467 original size:69 final size:70
Alignment explanation
Indices: 250362--250511 Score: 164
Period size: 69 Copynumber: 2.1 Consensus size: 70
250352 CGCTTGAAGA
* * * *
250362 AGAAAAAAAGAGAAAAAAATGAAAAAAAATGAAAAAAAT-AATAAT-AAAAATGAGAAGAA-GAA
1 AGAAAAAAAGAGAAAAAAAGGAAAAAAAATG-AAAAAATGAAAAATGAAAAAAGAGAAAAATGAA
250424 AAAGAAG
65 AAA-AAG
* * **
250431 GGAAAAAAAGAGAAAAAAGGGAAAAGGGAA-GAAAAAATGAAAAATGAAAAAAGAGAAAAATGAA
1 AGAAAAAAAGAGAAAAAAAGGAAAA-AAAATGAAAAAATGAAAAATGAAAAAAGAGAAAAATGAA
250495 AAAAAG
65 AAAAAG
250501 AGAAATAAAAG
1 AGAAA-AAAAG
250512 GAGGGTTCAA
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
68 7 0.10
69 28 0.42
70 21 0.31
71 11 0.16
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (70 bp):
AGAAAAAAAGAGAAAAAAAGGAAAAAAAATGAAAAAATGAAAAATGAAAAAAGAGAAAAATGAAA
AAAAG
Found at i:250488 original size:16 final size:17
Alignment explanation
Indices: 250363--250505 Score: 76
Period size: 18 Copynumber: 7.8 Consensus size: 17
250353 GCTTGAAGAA
250363 GAAAAAAAGAGAAAAAAAT
1 GAAAAAAAGAG--AAAAAT
*
250382 GAAAAAAAATGAAAAAAAT
1 G-AAAAAAA-GAGAAAAAT
* *
250401 AATAATAAAAATGAGAAGAA-
1 --GAA-AAAAA-GAGAAAAAT
* *
250421 GAAAAAGAAGGGAAAAAAA
1 GAAAAA-AAGAG-AAAAAT
* **
250440 GAGAAAAAAGGGAAAAGG
1 GA-AAAAAAGAGAAAAAT
250458 GAAGAAAAA-ATGAAAAAT
1 GAA-AAAAAGA-GAAAAAT
250476 G-AAAAAAGAGAAAAAT
1 GAAAAAAAGAGAAAAAT
250492 GAAAAAAAGAGAAA
1 GAAAAAAAGAGAAA
250506 TAAAAGGAGG
Statistics
Matches: 99, Mismatches: 12, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
16 13 0.13
17 20 0.20
18 25 0.25
19 14 0.14
20 13 0.13
21 14 0.14
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.06
Consensus pattern (17 bp):
GAAAAAAAGAGAAAAAT
Found at i:250506 original size:15 final size:15
Alignment explanation
Indices: 250461--250510 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
250451 GAAAAGGGAA
*
250461 GAAAAAATGAAAAAT
1 GAAAAAAAGAAAAAT
250476 GAAAAAAGAGAAAAAT
1 GAAAAAA-AGAAAAAT
*
250492 GAAAAAAAGAGAAAT
1 GAAAAAAAGAAAAAT
250507 -AAAA
1 GAAAA
250511 GGAGGGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
14 4 0.12
15 14 0.44
16 14 0.44
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (15 bp):
GAAAAAAAGAAAAAT
Found at i:251871 original size:36 final size:37
Alignment explanation
Indices: 251783--251891 Score: 157
Period size: 36 Copynumber: 3.0 Consensus size: 37
251773 CAAAACAGGC
* * * *
251783 CAATCTTAAGCCTTCATGAAAGAGCAGTGAAGCAATT
1 CAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAT
* *
251820 CAAACTTAATCCTTCACGGAAGAGTAGTGAAGCAAAT
1 CAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAT
251857 C-ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1 CAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
251892 CTCGTTTGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
36 32 0.50
37 32 0.50
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (37 bp):
CAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAT
Found at i:251977 original size:55 final size:55
Alignment explanation
Indices: 251894--252376 Score: 535
Period size: 55 Copynumber: 8.9 Consensus size: 55
251884 GAAGCAAACT
* *
251894 CGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* * * *
251945 AGTTCGTTGAAGATTGTTCGAGTTCTATACTCTTTGAAGGAATAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
** * *
252000 CGTTTCATGAAGATTATTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
*
252055 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
** * *
252110 CGTTT-TATGAAGATTACTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACA
1 CGTTTGT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* * * *
252165 CGTTTGTTAAAGA---TT-GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGAC-
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* *
252215 CTGTTTATTGAAGATT-TTCCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 C-GTTTGTTGAAGATTGTT-CGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* * * * *
252271 CGCTTTATTAAAGATTGTTCAAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 CG-TTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACA
* * * *
252327 CATTT-TATGAAGATTGCTCGAGTTTTATACT-TCCTGAAGGAATAGGGAGC
1 CGTTTGT-TGAAGATTGTTCGAGTTCTATACTCT-CTGAAGGAATAGAGAGC
252377 AGACTCGTCA
Statistics
Matches: 368, Mismatches: 46, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
50 1 0.00
51 53 0.14
52 1 0.00
53 2 0.01
54 5 0.01
55 258 0.70
56 46 0.12
57 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (55 bp):
CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
Found at i:252107 original size:110 final size:110
Alignment explanation
Indices: 251909--252376 Score: 601
Period size: 110 Copynumber: 4.3 Consensus size: 110
251899 GTTGAAGATT
* * * * *
251909 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTAAAGATTGTTCGAGTTCTATA
* * *
251974 CTCTTTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTATTC
66 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTACTC
* *
252019 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACACGTTTGTTGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTAAAGATTGTTCGAGTTCTATA
252084 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTACTC
66 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTACTC
*
252129 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTAAAGA---TT-GAGTCCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTAAAGATTGTTCGAGTTCTATA
* * * *
252190 CTCTCTGAAAGAATAGGGAGCGGACCTG-TTTATTGAAGATT-TTCC
66 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTA-TGAAGATTACT-C
* * * * *
252235 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGCTTTATTAAAGATTGTTCAAG-TCTTA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACG-TTTGTTAAAGATTGTTCGAGTTC-TA
* * * * *
252299 TACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGCTC
64 TACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTACTC
*
252346 GAGTTTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTTCTATACTCT-CTGAAGGAATAGGGAGC
252377 AGACTCGTCA
Statistics
Matches: 317, Mismatches: 30, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
105 5 0.02
106 78 0.25
107 12 0.04
110 153 0.48
111 64 0.20
112 5 0.02
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (110 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTAAAGATTGTTCGAGTTCTATA
CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTACTC
Found at i:252264 original size:161 final size:165
Alignment explanation
Indices: 251909--252340 Score: 522
Period size: 161 Copynumber: 2.6 Consensus size: 165
251899 GTTGAAGATT
* * ** *
251909 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT-TGAAGATTGTTCGAGTTCTAT
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTT-TTATGAAGATTGTTCGAGTTCTAT
* * * * *
251973 ACTCTTTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTATTCGAGTTCTATACTCTCTGAA
65 ACTCTCTGAAGGAATAGAGAGCGAACACGTTTCATGAAGATGATTCGAGTCCTATACTCTCTGAA
* *
252038 GGAATAGAGAGCGAACACGTTTGTTGAAGATTGTTC
130 AGAATAGAGAGCGAACACGTTTATTGAAGATTGTTC
**
252074 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTACTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATA
* * *
252139 CTCTCTGAAGGAATAGGGAGCGAACACGTTT-GTTAA-A-GATT-GAGTCCTATACTCTCTGAAA
66 CTCTCTGAAGGAATAGAGAGCGAACACGTTTCATGAAGATGATTCGAGTCCTATACTCTCTGAAA
* *
252200 GAATAGGGAGCGGAC-CTGTTTATTGAAGATT-TTCC
131 GAATAGAGAGCGAACAC-GTTTATTGAAGATTGTT-C
* * *
252235 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGCTTTATTAAAGATTGTTCAAG-TCTTA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTA-TGAAGATTGTTCGAGTTC-TA
* * *
252299 TACTCTCTGAATGAATAGAGAGC-AGACACATTTTATGAAGAT
64 TACTCTCTGAAGGAATAGAGAGCGA-ACACGTTTCATGAAGAT
252341 TGCTCGAGTT
Statistics
Matches: 229, Mismatches: 29, Indels: 18
0.83 0.11 0.07
Matches are distributed among these distances:
160 3 0.01
161 90 0.39
162 44 0.19
163 4 0.02
164 5 0.02
165 83 0.36
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (165 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATA
CTCTCTGAAGGAATAGAGAGCGAACACGTTTCATGAAGATGATTCGAGTCCTATACTCTCTGAAA
GAATAGAGAGCGAACACGTTTATTGAAGATTGTTC
Found at i:253559 original size:16 final size:16
Alignment explanation
Indices: 253538--253580 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
253528 GTTAGATTAG
253538 TTTAGGTTTTAGCTTA
1 TTTAGGTTTTAGCTTA
253554 TTTAGGTTTTAGCTTA
1 TTTAGGTTTTAGCTTA
253570 TTTAGGTTTTA
1 TTTAGGTTTTA
253581 TATTAATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.58
Consensus pattern (16 bp):
TTTAGGTTTTAGCTTA
Found at i:255442 original size:25 final size:25
Alignment explanation
Indices: 255408--255458 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
255398 TGCAGAAGAC
255408 AAAAACGACATGGGAAGCCGATCAG
1 AAAAACGACATGGGAAGCCGATCAG
255433 AAAAACGACATGGGAAGCCGATCAG
1 AAAAACGACATGGGAAGCCGATCAG
255458 A
1 A
255459 TACAGAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.27, T:0.08
Consensus pattern (25 bp):
AAAAACGACATGGGAAGCCGATCAG
Found at i:256489 original size:21 final size:20
Alignment explanation
Indices: 256463--256505 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
256453 TTATTAAAAA
*
256463 TTTATCGATAATATTATTATT
1 TTTATCGAAAATATTATT-TT
*
256484 TTTATCTAAAATATTATTTT
1 TTTATCGAAAATATTATTTT
256504 TT
1 TT
256506 AATAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTATCGAAAATATTATTTT
Found at i:257872 original size:16 final size:16
Alignment explanation
Indices: 257853--257902 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
257843 AATTAAAAAC
257853 ATTTTTCATTAGATAG
1 ATTTTTCATTAGATAG
* * * *
257869 A--TTTAATTAAAAAC
1 ATTTTTCATTAGATAG
257883 ATTTTTCATTAGATAG
1 ATTTTTCATTAGATAG
257899 ATTT
1 ATTT
257903 AATTCAAAAG
Statistics
Matches: 24, Mismatches: 8, Indels: 4
0.67 0.22 0.11
Matches are distributed among these distances:
14 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (16 bp):
ATTTTTCATTAGATAG
Found at i:257874 original size:30 final size:30
Alignment explanation
Indices: 257838--257911 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
257828 ATTGACGAAG
257838 GATTTAATTAAAAACATTTTTCATTAGATA
1 GATTTAATTAAAAACATTTTTCATTAGATA
257868 GATTTAATTAAAAACATTTTTCATTAGATA
1 GATTTAATTAAAAACATTTTTCATTAGATA
*
257898 GATTTAATTCAAAA
1 GATTTAATTAAAAA
257912 GACAATCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (30 bp):
GATTTAATTAAAAACATTTTTCATTAGATA
Found at i:262833 original size:41 final size:41
Alignment explanation
Indices: 262775--262954 Score: 342
Period size: 41 Copynumber: 4.4 Consensus size: 41
262765 ATTCGCGTTG
* *
262775 CATTTCGCGTTGTGATAGTTGAAAATCGAGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
262816 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
262857 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
262898 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
262939 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
262955 TTTCCATTTC
Statistics
Matches: 137, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 137 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:262947 original size:102 final size:102
Alignment explanation
Indices: 262841--263056 Score: 389
Period size: 102 Copynumber: 2.1 Consensus size: 102
262831 TAGTTGAAAA
262841 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCATTTCG
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-AAAATCGCGTTGCGATTTTCCATTTCG
262905 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
65 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
* *
262943 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATTTCGC
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTAAAATCGCGTTGCGATTTTCCATTTCGC
*
263008 GTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATT
66 GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
263045 TCGCGTTGCGAT
1 TCGCGTTGCGAT
263057 AGTCTACAGT
Statistics
Matches: 110, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
102 109 0.99
103 1 0.01
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (102 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTAAAATCGCGTTGCGATTTTCCATTTCGC
GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
Found at i:262988 original size:41 final size:41
Alignment explanation
Indices: 262943--263084 Score: 232
Period size: 41 Copynumber: 3.4 Consensus size: 41
262933 ATTTTCCATT
262943 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG
* *
262984 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAG
263025 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG
*
263066 TTGTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
263085 AATTCGTTGT
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
40 1 0.01
41 76 0.82
42 16 0.17
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG
Found at i:262988 original size:82 final size:82
Alignment explanation
Indices: 262820--263078 Score: 299
Period size: 82 Copynumber: 3.1 Consensus size: 82
262810 ATTTTCCATT
* ** **
262820 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT-TTTCCATTTCG
* * *
262885 CGTTGCGAT--TTTCCATT
65 CGTTGCGATAGTCTACA-G
262902 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCATTTCGC
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCATTTCGC
262967 GTTGCGATAGTCTACAG
66 GTTGCGATAGTCTACAG
* ** ** * ** *
262984 TCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCG
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTCCATTTCG
263048 CGTTGCGATAGTCTACAG
65 CGTTGCGATAGTCTACAG
*
263066 TTGTCGTTGCGAT
1 TCG-CGTTGCGAT
263079 TTTCCAAATT
Statistics
Matches: 155, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
81 30 0.19
82 112 0.72
83 13 0.08
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (82 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCATTTCGC
GTTGCGATAGTCTACAG
Found at i:263093 original size:82 final size:81
Alignment explanation
Indices: 262942--263101 Score: 259
Period size: 82 Copynumber: 2.0 Consensus size: 81
262932 GATTTTCCAT
*
262942 TTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATTTCG
1 TTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCAATTC-
263007 CGTTGCGATAGTTGAAA
65 CGTTGCGATAGTTGAAA
*
263024 TTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 TTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCG-CGTTGCGATTTTCC-AATT
*
263089 -CGTTGTGATAGTT
64 CCGTTGCGATAGTT
263102 AAAAAAAAAG
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
82 56 0.77
83 14 0.19
84 3 0.04
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.40
Consensus pattern (81 bp):
TTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCAATTCC
GTTGCGATAGTTGAAA
Found at i:263188 original size:6 final size:6
Alignment explanation
Indices: 263177--263225 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
263167 AGACACGTAT
263177 GACCAC GACCAC GACCAC GACCAC GACCAC GACC-C GACC-C GACC-C
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
263222 GACC
1 GACC
263226 CGAGACGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.35
6 28 0.65
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:263735 original size:6 final size:6
Alignment explanation
Indices: 263724--263774 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
263714 TCTCGTCTCG
263724 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
263772 GGT
1 GGT
263775 AATGGTAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:263780 original size:6 final size:6
Alignment explanation
Indices: 263771--263807 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
263761 GTCGTGGTCG
263771 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
263808 ACGTGTCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:263780 original size:12 final size:12
Alignment explanation
Indices: 263729--263804 Score: 62
Period size: 12 Copynumber: 6.3 Consensus size: 12
263719 TCTCGGGTCG
**
263729 TGGTCGTGGTCG
1 TGGTCGTGGTAA
**
263741 TGGTCGTGGTCG
1 TGGTCGTGGTAA
**
263753 TGGTCGTGGTCG
1 TGGTCGTGGTAA
263765 TGGTCGTGGTAA
1 TGGTCGTGGTAA
**
263777 TGGTAATGGTAA
1 TGGTCGTGGTAA
**
263789 TGGTAATGGTAA
1 TGGTCGTGGTAA
263801 TGGT
1 TGGT
263805 AATACGTGTC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 60 1.00
ACGTcount: A:0.13, C:0.09, G:0.43, T:0.34
Consensus pattern (12 bp):
TGGTCGTGGTAA
Found at i:264087 original size:21 final size:21
Alignment explanation
Indices: 264001--264087 Score: 68
Period size: 21 Copynumber: 4.2 Consensus size: 21
263991 GTTGCGATTT
** *
264001 CAACTATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
*
264022 CAACTATCGAAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
264043 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
264063 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
264084 CAAC
1 CAAC
264088 GTGAATTTGC
Statistics
Matches: 47, Mismatches: 18, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
20 13 0.28
21 34 0.72
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:264531 original size:2 final size:2
Alignment explanation
Indices: 264516--264551 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
264506 CTTTGATGCA
* *
264516 AT AT AT AG AC 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
264552 TGATGTGAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:266193 original size:14 final size:14
Alignment explanation
Indices: 266176--266287 Score: 93
Period size: 14 Copynumber: 8.0 Consensus size: 14
266166 AATTATGTGA
266176 TAGGATTTATGGTT
1 TAGGATTTATGGTT
* *
266190 TAGGTTTTAGGGTT
1 TAGGATTTATGGTT
* *
266204 TATGATTTATAGTT
1 TAGGATTTATGGTT
*
266218 TAGGTTTTA-GGTTT
1 TAGGATTTATGG-TT
* *
266232 TAGGGTTTATGATT
1 TAGGATTTATGGTT
*
266246 TA-GAGTTTATAGTT
1 TAGGA-TTTATGGTT
*
266260 TAGGATTTAAGGTT
1 TAGGATTTATGGTT
**
266274 TATAATTTATGGTT
1 TAGGATTTATGGTT
266288 AATGGTTTAA
Statistics
Matches: 75, Mismatches: 19, Indels: 8
0.74 0.19 0.08
Matches are distributed among these distances:
13 2 0.03
14 70 0.93
15 3 0.04
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (14 bp):
TAGGATTTATGGTT
Found at i:266296 original size:35 final size:35
Alignment explanation
Indices: 266181--266296 Score: 146
Period size: 35 Copynumber: 3.3 Consensus size: 35
266171 TGTGATAGGA
*
266181 TTTATGGTTTAGGTTTTAGGGTTTATGATTTATAG
1 TTTATGGTTTAGGTTTTAGGGTTTATGATTTATGG
266216 TTTA-GGTTTTAGGTTTTAGGGTTTATGATTTA-GAG
1 TTTATGG-TTTAGGTTTTAGGGTTTATGATTTATG-G
* * * *
266251 TTTATAGTTTAGGATTTAAGGTTTATAATTTATGG
1 TTTATGGTTTAGGTTTTAGGGTTTATGATTTATGG
*
266286 TTAATGGTTTA
1 TTTATGGTTTA
266297 ATTTATACAC
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
34 2 0.03
35 66 0.94
36 2 0.03
ACGTcount: A:0.23, C:0.00, G:0.24, T:0.53
Consensus pattern (35 bp):
TTTATGGTTTAGGTTTTAGGGTTTATGATTTATGG
Found at i:266615 original size:17 final size:18
Alignment explanation
Indices: 266576--266612 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
266566 AATGTCAAAT
266576 AATTAAAATTACAAGACAC
1 AATTAAAA-TACAAGACAC
266595 AATTAAAA-ACAAG-CAC
1 AATTAAAATACAAGACAC
266611 AA
1 AA
266613 ATTGGAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
19 8 0.44
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.16
Consensus pattern (18 bp):
AATTAAAATACAAGACAC
Found at i:268883 original size:17 final size:17
Alignment explanation
Indices: 268861--268899 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
268851 AAATTCGAGT
268861 TCGAGTTTGAGCTTGAA
1 TCGAGTTTGAGCTTGAA
268878 TCGAGTTTGAGCTTGAA
1 TCGAGTTTGAGCTTGAA
*
268895 CCGAG
1 TCGAG
268900 CTCAAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (17 bp):
TCGAGTTTGAGCTTGAA
Found at i:269060 original size:31 final size:31
Alignment explanation
Indices: 269000--269060 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
268990 TTTCGAGCCT
* *
269000 TTTCGAGTTCGAGTCGAGTTTCAATATTTTC
1 TTTCGAGTTCGAGTCGAGCTTCAAAATTTTC
*
269031 TTTCGAGTTCGAGTCGAGCTTGAAAATTTT
1 TTTCGAGTTCGAGTCGAGCTTCAAAATTTT
269061 AGGCTCGCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.43
Consensus pattern (31 bp):
TTTCGAGTTCGAGTCGAGCTTCAAAATTTTC
Found at i:270672 original size:17 final size:19
Alignment explanation
Indices: 270640--270674 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
270630 TCCTTTTTAA
270640 TATATGTTTAAATAAAAAG
1 TATATGTTTAAATAAAAAG
270659 TATAT-TTT-AATAAAAA
1 TATATGTTTAAATAAAAA
270675 TTATTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (19 bp):
TATATGTTTAAATAAAAAG
Found at i:270688 original size:15 final size:15
Alignment explanation
Indices: 270650--270695 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
270640 TATATGTTTA
270650 AATAAAAAGTATATTTT
1 AATAAAAA-T-TATTTT
270667 AATAAAAATTATTATT
1 AATAAAAATTATT-TT
270683 AA-AAAAATTATTT
1 AATAAAAATTATTT
270696 CACAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.04
15 14 0.50
16 5 0.18
17 8 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
AATAAAAATTATTTT
Found at i:274271 original size:2 final size:2
Alignment explanation
Indices: 274264--274298 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
274254 AAATAAATAA
* *
274264 AT AT AT AT AT AT AT AT AT AG AT AT AT AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
274299 ATTTACAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (2 bp):
AT
Found at i:274700 original size:43 final size:43
Alignment explanation
Indices: 274672--274764 Score: 132
Period size: 43 Copynumber: 2.2 Consensus size: 43
274662 CAAACGTTGT
274672 AATAGGTGTTGATATTTAACGACATTTGTCAGAAAAACACCGC
1 AATAGGTGTTGATATTTAACGACATTTGTCAGAAAAACACCGC
** * * * *
274715 AATAGGTGTTGATATTTAACGGTATTTTTTAGACAAACGCCGC
1 AATAGGTGTTGATATTTAACGACATTTGTCAGAAAAACACCGC
274758 AATAGGT
1 AATAGGT
274765 TATGATGTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (43 bp):
AATAGGTGTTGATATTTAACGACATTTGTCAGAAAAACACCGC
Found at i:274888 original size:42 final size:42
Alignment explanation
Indices: 274801--274991 Score: 242
Period size: 42 Copynumber: 4.5 Consensus size: 42
274791 AAAACGCCCT
* * *
274801 AGTAGGTGTTGATGTTTTGTGGCAT-TTTTCTCACAAAC-ACAGC
1 AGTAGGTGTTGATGTTTTGCGG--TGTTTTCCCACAAACGTC-GC
*
274844 AGTAGATGTTGATGTTTTGCGGTGTTTTCCCACAAACGTCGC
1 AGTAGGTGTTGATGTTTTGCGGTGTTTTCCCACAAACGTCGC
*
274886 AGTAGGTGTTAATGTTTTGCGGTGTTTTCCCACAAACGTCGC
1 AGTAGGTGTTGATGTTTTGCGGTGTTTTCCCACAAACGTCGC
* * * * *
274928 AGTATGTGTTGATGTTTTGTGGCGTTTTTCCCACAAACGCCGT
1 AGTAGGTGTTGATGTTTTGCGGTG-TTTTCCCACAAACGTCGC
274971 AGTAGGTGTTGATGTTTTGCG
1 AGTAGGTGTTGATGTTTTGCG
274992 ACATTTTTAG
Statistics
Matches: 131, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.01
42 74 0.56
43 56 0.43
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.38
Consensus pattern (42 bp):
AGTAGGTGTTGATGTTTTGCGGTGTTTTCCCACAAACGTCGC
Found at i:274901 original size:85 final size:86
Alignment explanation
Indices: 274767--274999 Score: 264
Period size: 85 Copynumber: 2.7 Consensus size: 86
274757 CAATAGGTTA
* * * *
274767 TGATGTTTAGCGGCGATTTTCTCTA-AAACGCC-CTAGTAGGTGTTGATGTTTTGTGGCATTTTT
1 TGATGTTTTGCGGCGTTTTTC-CCACAAACGCCGC-AGTAGGTGTTGATGTTTTGCGGCATTTTT
*
274830 CTCACAAAC-ACAGCAGTA-GATGT
64 CCCACAAACGAC-GCAGTATG-TGT
* * *
274853 TGATGTTTTGCGGTG-TTTTCCCACAAACGTCGCAGTAGGTGTTAATGTTTTGCGG--TGTTTTC
1 TGATGTTTTGCGGCGTTTTTCCCACAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCAT-TTTTC
*
274915 CCACAAACGTCGCAGTATGTGT
65 CCACAAACGACGCAGTATGTGT
* * *
274937 TGATGTTTTGTGGCGTTTTTCCCACAAACGCCGTAGTAGGTGTTGATGTTTTGCGACATTTTT
1 TGATGTTTTGCGGCGTTTTTCCCACAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCATTTTT
275000 AGCAAAAACG
Statistics
Matches: 125, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
83 1 0.01
84 36 0.29
85 69 0.55
86 18 0.14
87 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (86 bp):
TGATGTTTTGCGGCGTTTTTCCCACAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCATTTTTCC
CACAAACGACGCAGTATGTGT
Found at i:275010 original size:43 final size:42
Alignment explanation
Indices: 274747--274991 Score: 239
Period size: 43 Copynumber: 5.8 Consensus size: 42
274737 TATTTTTTAG
* * * *
274747 ACAAACGCCGCAATAGGT-TATGATGTTTAGCGGCGATTTTCTCT
1 ACAAACGCCGCAGTAGGTGT-TGATGTTTTGC-GCGTTTTTC-CC
* * *
274791 A-AAACGCC-CTAGTAGGTGTTGATGTTTTGTGGCATTTTTCTC
1 ACAAACGCCGC-AGTAGGTGTTGATGTTTTG-CGCGTTTTTCCC
* * *
274833 ACAAACACAGCAGTAGATGTTGATGTTTTGCG-GTGTTTTCCC
1 ACAAACGCCGCAGTAGGTGTTGATGTTTTGCGCGT-TTTTCCC
* *
274875 ACAAACGTCGCAGTAGGTGTTAATGTTTTGCG-GTGTTTTCCC
1 ACAAACGCCGCAGTAGGTGTTGATGTTTTGCGCGT-TTTTCCC
* * *
274917 ACAAACGTCGCAGTATGTGTTGATGTTTTGTGGCGTTTTTCCC
1 ACAAACGCCGCAGTAGGTGTTGATGTTTTG-CGCGTTTTTCCC
*
274960 ACAAACGCCGTAGTAGGTGTTGATGTTTTGCG
1 ACAAACGCCGCAGTAGGTGTTGATGTTTTGCG
274992 ACATTTTTAG
Statistics
Matches: 168, Mismatches: 25, Indels: 18
0.80 0.12 0.09
Matches are distributed among these distances:
41 1 0.01
42 75 0.45
43 87 0.52
44 5 0.03
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (42 bp):
ACAAACGCCGCAGTAGGTGTTGATGTTTTGCGCGTTTTTCCC
Found at i:275472 original size:21 final size:21
Alignment explanation
Indices: 275418--275477 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
275408 CTTCTCTCTG
*
275418 TGCTGCCGCTGCTTCTCTAGC
1 TGCTTCCGCTGCTTCTCTAGC
* * *
275439 TGTTTCCGTTGCTTCTCTGGC
1 TGCTTCCGCTGCTTCTCTAGC
* *
275460 TGCTTCTGCTGCTGCTCT
1 TGCTTCCGCTGCTTCTCT
275478 CTCTCTTCCT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.33, G:0.23, T:0.42
Consensus pattern (21 bp):
TGCTTCCGCTGCTTCTCTAGC
Done.