Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008345.1 Hibiscus syriacus cultivar Beakdansim tig00111073_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: 297766
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:193437 original size:118 final size:117
Alignment explanation
Indices: 193083--193461 Score: 300
Period size: 116 Copynumber: 3.2 Consensus size: 117
193073 TGGCACTTTG
* * * * * ** * * *
193083 TGTGCTAAAATGATAGGGAAACCATACTGAGTGTATAGATTTTC-GTATGGAGCACTGAGTGTGC
1 TGTGCTAAAAAGGTAAGGAAATCATACTGAGTGTATAGATTTCCAG-ATAAAACACTAAGCGTGC
* * * *** * * * *
193147 TAAATGATAAGGAAATCATATTGAGTGTATAGATTTCCATAT-GGAGCA-CTGA
65 TAAAAGACAAGGAAATCATACTGAAAATATGGATTTCCACATAGG-GCATTTCA
* * * ** ** *
193199 GTGTGCT-AAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGTACTGAGCGTGC
1 -TGTGCTAAAAAGGTAAGGAAATCATACTGAGTGTATAGATTTCCAGATAAAACACTAAGCGTGC
* * * *
193263 TAAATGACAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATTTTA
65 TAAAAGACAAGGAAATCATACTGAAAATATGGATTTCCACATAGGGCATTTCA
* * *
193316 TGTGCTAAAAAGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAACACTAAGGGTGCT
1 TGTGCTAAAAAGGTAAGGAAATCATACTGAGTGTATAGATTTCCAGATAAAACACTAAGCGTGCT
* ** *
193381 ACAAAGATAAGGAAATCATACT-AATGGTATGGATTTTCACATAGGGCATTTCA
66 A-AAAGACAAGGAAATCATACTGAA-AATATGGATTTCCACATAGGGCATTTCA
* **
193434 TGTGCTAAAATGGTAACAAAATCATACT
1 TGTGCTAAAAAGGTAAGGAAATCATACT
193462 AATGGTATGA
Statistics
Matches: 219, Mismatches: 37, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
116 95 0.43
117 60 0.27
118 64 0.29
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (117 bp):
TGTGCTAAAAAGGTAAGGAAATCATACTGAGTGTATAGATTTCCAGATAAAACACTAAGCGTGCT
AAAAGACAAGGAAATCATACTGAAAATATGGATTTCCACATAGGGCATTTCA
Found at i:193548 original size:59 final size:59
Alignment explanation
Indices: 193075--193548 Score: 333
Period size: 59 Copynumber: 8.1 Consensus size: 59
193065 TTACCGAATG
* * * * * *
193075 GCACTTTGTGTGCTAAAATGATAGGGAAACCATACTGAGTGTATAGATTTTC-GTATGGA
1 GCACTTAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATAGATTTCCAG-ATAGA
* * * * *
193134 GCACTGAGTGTGCT-AAATGATAAGGAAATCATATTGAGTGTATAGATTTCCATATGGA
1 GCACTTAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATAGATTTCCAGATAGA
* * * *
193192 GCACTGAGTGTGCT-AAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGA
1 GCACTTAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATAGATTTCCAGATAGA
* * * * * ** * *
193250 GTACTGAGCGTGCT-AAATGACAAGGAAATCATATTGAA-AATATGGATTTCCAGATAGG
1 GCACTTAGTGTGCTAAAATGATAAGGAAATCATACT-AAGTGTATAGATTTCCAGATAGA
* * * * * * *
193308 GCATTTTA-TGTGCTAAAAAGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAAA
1 GCA-CTTAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATAGATTTCCAGATAGA
* * * * * * *
193367 ACACTAAGGGTGCTACAAA-GATAAGGAAATCATACTAA-TGGTATGGATTTTCACATAGG
1 GCACTTAGTGTGCTA-AAATGATAAGGAAATCATACTAAGT-GTATAGATTTCCAGATAGA
* * ** ** * *
193426 GCATTTCA-TGTGCTAAAATGGTAACAAAATCATACTAA-TGGTAT-GAATTTTTAAATAGG
1 GCACTT-AGTGTGCTAAAATGATAAGGAAATCATACTAAGT-GTATAG-ATTTCCAGATAGA
* * * *
193485 GCACTTCGTGTGCTAAAATGAAAAGGGAAGCATACTAAGTGTAT-GATTTTCCAGATAGA
1 GCACTTAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATAGA-TTTCCAGATAGA
193544 GCACT
1 GCACT
193549 GAGAGTACTA
Statistics
Matches: 336, Mismatches: 65, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
58 156 0.46
59 175 0.52
60 5 0.01
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (59 bp):
GCACTTAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATAGATTTCCAGATAGA
Found at i:193693 original size:44 final size:44
Alignment explanation
Indices: 193638--193773 Score: 218
Period size: 44 Copynumber: 3.1 Consensus size: 44
193628 TAAATGAGGT
* *
193638 TAATGGAAAGTATATTAGTAAAATAAGCTTACGAGCTTATGGAA
1 TAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAA
193682 TAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAA
1 TAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAA
* * *
193726 TAAATGATAAGTATGTTGGTAAAATAAGCTTACGAGCTTATGGGA
1 T-AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAA
193771 TAA
1 TAA
193774 ATGGAAAATT
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
44 45 0.52
45 41 0.48
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (44 bp):
TAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAA
Found at i:193752 original size:45 final size:45
Alignment explanation
Indices: 193645--193776 Score: 221
Period size: 45 Copynumber: 3.0 Consensus size: 45
193635 GGTTAATGGA
* *
193645 AAGTATATTAGTAAAATAAGCTTACGAGCTTATGGAAT-AATGGT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGAT
193689 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGAT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGAT
* *
193734 AAGTATGTTGGTAAAATAAGCTTACGAGCTTATGGGATAAATG
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATG
193777 GAAAATTTAT
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
44 37 0.45
45 46 0.55
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (45 bp):
AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGAT
Found at i:195058 original size:19 final size:18
Alignment explanation
Indices: 195031--195075 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
195021 AGCATGTTTA
195031 AAAATAAAACTT-AAAATG
1 AAAATAAAACTTGAAAA-G
195049 AAAATGAAAACTTGAAAAG
1 AAAAT-AAAACTTGAAAAG
195068 AAAATAAA
1 AAAATAAA
195076 GAACTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 13 0.52
20 4 0.16
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.18
Consensus pattern (18 bp):
AAAATAAAACTTGAAAAG
Found at i:195080 original size:20 final size:19
Alignment explanation
Indices: 195031--195081 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
195021 AGCATGTTTA
195031 AAAAT-AAAACTTAAAATG
1 AAAATAAAAACTTAAAATG
*
195049 AAAATGAAAACTTGAAAA-G
1 AAAATAAAAACTT-AAAATG
195068 AAAATAAAGAACTT
1 AAAATAAA-AACTT
195082 TATAAAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.17
19 15 0.52
20 9 0.31
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.20
Consensus pattern (19 bp):
AAAATAAAAACTTAAAATG
Found at i:195876 original size:19 final size:18
Alignment explanation
Indices: 195847--195891 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
195837 CCATGATGTA
195847 ATACCAAAATTCTAATGG
1 ATACCAAAATTCTAATGG
*
195865 ATACCTAAAATTTTAATGG
1 ATACC-AAAATTCTAATGG
*
195884 ATATCAAA
1 ATACCAAA
195892 TTTTTTAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (18 bp):
ATACCAAAATTCTAATGG
Found at i:199023 original size:2 final size:2
Alignment explanation
Indices: 199016--199048 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
199006 TTAATGTAGG
199016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
199049 TACCAACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:204452 original size:21 final size:21
Alignment explanation
Indices: 204426--204507 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
204416 ATTAAAATAA
204426 TATTATTAATTAATAATATTT
1 TATTATTAATTAATAATATTT
* * * *
204447 TATTATTTATTAAAAATAATA
1 TATTATTAATTAATAATATTT
* *
204468 GATTACTTAACTT-ATTAT-TTT
1 TATTA-TTAA-TTAATAATATTT
*
204489 TATTATTTATTAATTAATA
1 TATTATTAATTAA-TAATA
204508 AATAATTATT
Statistics
Matches: 43, Mismatches: 13, Indels: 9
0.66 0.20 0.14
Matches are distributed among these distances:
19 2 0.05
20 4 0.09
21 29 0.67
22 6 0.14
23 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (21 bp):
TATTATTAATTAATAATATTT
Found at i:204458 original size:39 final size:40
Alignment explanation
Indices: 204415--204515 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 40
204405 TTTTCTTTTG
204415 TATTAAAATAAT-ATTA-TTAA-TTAATAATATTTTATTATT
1 TATTAAAATAATAATTACTTAACTT-ATAAT-TTTTATTATT
*
204454 TATTAAAAATAATAGATTACTTAACTTATTATTTTTATTATT
1 TATT-AAAATAATA-ATTACTTAACTTATAATTTTTATTATT
204496 TATTAATTAATAAATAATTA
1 TATTAA--AAT-AATAATTA
204516 TTATTTAAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
39 4 0.08
40 8 0.15
41 2 0.04
42 18 0.34
43 15 0.28
44 6 0.11
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (40 bp):
TATTAAAATAATAATTACTTAACTTATAATTTTTATTATT
Found at i:211329 original size:2 final size:2
Alignment explanation
Indices: 211322--211358 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
211312 CATGGTATTA
211322 AT 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 AT A
211359 ATTTAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:211731 original size:12 final size:12
Alignment explanation
Indices: 211714--211739 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
211704 ATGCATGCCC
211714 TAAAATTTTATT
1 TAAAATTTTATT
211726 TAAAATTTTATT
1 TAAAATTTTATT
211738 TA
1 TA
211740 TGCATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TAAAATTTTATT
Found at i:211749 original size:18 final size:18
Alignment explanation
Indices: 211726--211760 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
211716 AAATTTTATT
211726 TAAAATTTTATTTATGCA
1 TAAAATTTTATTTATGCA
211744 TAAAATTTTATTTATGC
1 TAAAATTTTATTTATGC
211761 GCATATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (18 bp):
TAAAATTTTATTTATGCA
Found at i:222041 original size:32 final size:32
Alignment explanation
Indices: 221994--222073 Score: 133
Period size: 32 Copynumber: 2.5 Consensus size: 32
221984 CGTAACATCT
*
221994 AAACATGGCAGCTCATCTTATGTAATAATATC
1 AAACACGGCAGCTCATCTTATGTAATAATATC
*
222026 AAATACGGCAGCTCATCTTATGTAATAATATC
1 AAACACGGCAGCTCATCTTATGTAATAATATC
*
222058 AAACATGGCAGCTCAT
1 AAACACGGCAGCTCAT
222074 AGAACAAAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (32 bp):
AAACACGGCAGCTCATCTTATGTAATAATATC
Found at i:222498 original size:44 final size:44
Alignment explanation
Indices: 222435--222523 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
222425 AAGTTTGGGG
222435 ATGAATTTATAATATTCTAAAGTTTAGGGATTAAATATAGAATT
1 ATGAATTTATAATATTCTAAAGTTTAGGGATTAAATATAGAATT
222479 ATGAATTTATAATATTCTAAAGTTTAGGGATTAAATATAGAATT
1 ATGAATTTATAATATTCTAAAGTTTAGGGATTAAATATAGAATT
222523 A
1 A
222524 GGGTCATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.44, C:0.02, G:0.13, T:0.40
Consensus pattern (44 bp):
ATGAATTTATAATATTCTAAAGTTTAGGGATTAAATATAGAATT
Found at i:222650 original size:2 final size:2
Alignment explanation
Indices: 222643--222676 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
222633 ATTACTCTAT
222643 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
222677 ATCATATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:224714 original size:39 final size:39
Alignment explanation
Indices: 224659--224756 Score: 137
Period size: 39 Copynumber: 2.5 Consensus size: 39
224649 ATAATTAATT
*
224659 TATATATTTTTAAAAAAAATTAAATTT-ATAAAATTTATA
1 TATATATTTTTTAAAAAAATT-AATTTCATAAAATTTATA
224698 TATATATTTTTTAAAAAAATTAATTTCATAAAATTTATA
1 TATATATTTTTTAAAAAAATTAATTTCATAAAATTTATA
* * *
224737 TA-ATTTTTTTTTACAAAATT
1 TATATATTTTTTAAAAAAATT
224757 GAAAAGATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
38 20 0.37
39 34 0.63
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (39 bp):
TATATATTTTTTAAAAAAATTAATTTCATAAAATTTATA
Found at i:228699 original size:2 final size:2
Alignment explanation
Indices: 228687--228735 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
228677 TTTTATTCCT
* *
228687 TA TA TA CA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
228729 TA TA TA T
1 TA TA TA T
228736 TAGTATATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:236238 original size:3 final size:3
Alignment explanation
Indices: 236230--236258 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
236220 ATTTATTTAT
236230 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
236259 TATGTTACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:242895 original size:27 final size:27
Alignment explanation
Indices: 242865--242964 Score: 148
Period size: 27 Copynumber: 3.7 Consensus size: 27
242855 AGACCCAGCC
*
242865 ACCTCCTCCATCACCTCCTAGAACATT
1 ACCTCCTCCACCACCTCCTAGAACATT
* * *
242892 ACCTCTTCCTCCACCTCCTAGAGCATT
1 ACCTCCTCCACCACCTCCTAGAACATT
242919 ACCTCCTCCACCACCTCCTAGAGA-ATT
1 ACCTCCTCCACCACCTCCTAGA-ACATT
242946 ACCTCCTCCACCACCTCCT
1 ACCTCCTCCACCACCTCCT
242965 CCTCAATCTC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.22, C:0.48, G:0.05, T:0.25
Consensus pattern (27 bp):
ACCTCCTCCACCACCTCCTAGAACATT
Found at i:243193 original size:24 final size:23
Alignment explanation
Indices: 243136--243197 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
243126 TCATACTGCT
*
243136 CCACATCCACTTCCACCCCCACCC
1 CCAC-TCCACTGCCACCCCCACCC
*
243160 CCACTGCCACTGCCACCTCCACCC
1 CCACT-CCACTGCCACCCCCACCC
*
243184 TCCTCTCCACTGCC
1 -CCACTCCACTGCC
243198 TATCCAACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 1 0.03
24 28 0.85
25 4 0.12
ACGTcount: A:0.16, C:0.63, G:0.05, T:0.16
Consensus pattern (23 bp):
CCACTCCACTGCCACCCCCACCC
Found at i:245326 original size:84 final size:84
Alignment explanation
Indices: 245202--245375 Score: 294
Period size: 84 Copynumber: 2.1 Consensus size: 84
245192 GAGAAGCAGG
*
245202 AGCAAGTCTCCCAGAAACCGGAGAAGCAGGAGCAGGTCTCCCAGAAACCGGAGAAGCAGGAGCAG
1 AGCAAGTCTCCCAGAAACCGGAGAAGCAGGAGCAGATCTCCCAGAAACCGGAGAAGCAGGAGCAG
*
245267 GTCTCCCAGAAACCGGAGA
66 ATCTCCCAGAAACCGGAGA
* * * *
245286 AGCAGGTCTCCTAGAAACCGGAGAAGCTGGAGCAGATCTCCCAGAAACTGGAGAAGCAGGAGCAG
1 AGCAAGTCTCCCAGAAACCGGAGAAGCAGGAGCAGATCTCCCAGAAACCGGAGAAGCAGGAGCAG
245351 ATCTCCCAGAAACCGGAGA
66 ATCTCCCAGAAACCGGAGA
245370 AGCAAG
1 AGCAAG
245376 AGTAGATCTC
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.35, C:0.26, G:0.30, T:0.09
Consensus pattern (84 bp):
AGCAAGTCTCCCAGAAACCGGAGAAGCAGGAGCAGATCTCCCAGAAACCGGAGAAGCAGGAGCAG
ATCTCCCAGAAACCGGAGA
Found at i:245383 original size:30 final size:30
Alignment explanation
Indices: 245178--245387 Score: 281
Period size: 30 Copynumber: 7.2 Consensus size: 30
245168 TTTTAGTTCG
**
245178 TCTCCCAGAAACAAGAGAAGCAGGAGCA-A
1 TCTCCCAGAAACCGGAGAAGCAGGAGCAGA
*
245207 GTCTCCCAGAAACCGGAGAAGCAGGAGCAGG
1 -TCTCCCAGAAACCGGAGAAGCAGGAGCAGA
*
245238 TCTCCCAGAAACCGGAGAAGCAGGAGCAGG
1 TCTCCCAGAAACCGGAGAAGCAGGAGCAGA
245268 TCTCCCAGAAACCGGAGAAGC---AG--G-
1 TCTCCCAGAAACCGGAGAAGCAGGAGCAGA
* *
245292 TCTCCTAGAAACCGGAGAAGCTGGAGCAGA
1 TCTCCCAGAAACCGGAGAAGCAGGAGCAGA
*
245322 TCTCCCAGAAACTGGAGAAGCAGGAGCAGA
1 TCTCCCAGAAACCGGAGAAGCAGGAGCAGA
* *
245352 TCTCCCAGAAACCGGAGAAGCAAGAGTAGA
1 TCTCCCAGAAACCGGAGAAGCAGGAGCAGA
245382 TCTCCC
1 TCTCCC
245388 TGTTTTCAGC
Statistics
Matches: 163, Mismatches: 10, Indels: 14
0.87 0.05 0.07
Matches are distributed among these distances:
24 20 0.12
25 1 0.01
27 4 0.02
29 1 0.01
30 137 0.84
ACGTcount: A:0.35, C:0.26, G:0.29, T:0.10
Consensus pattern (30 bp):
TCTCCCAGAAACCGGAGAAGCAGGAGCAGA
Found at i:245386 original size:114 final size:114
Alignment explanation
Indices: 245177--245387 Score: 325
Period size: 114 Copynumber: 1.9 Consensus size: 114
245167 GTTTTAGTTC
*
245177 GTCTCCCAGAAACAAGAGAAGCAGGAGCAAGTCTCCCAGAAACCGGAGAAGCAGGAGCAGGTCTC
1 GTCTCCCAGAAACAAGAGAAGCAGGAGCAAGTCTCCCAGAAACCGGAGAAGCAGGAGCAGATCTC
* *
245242 CCAGAAACCGGAGAAGCAGGAGCAGGTCTCCCAGAAACCGGAGAAGCAG
66 CCAGAAACCGGAGAAGCAAGAGCAGATCTCCCAGAAACCGGAGAAGCAG
* ** * *
245291 GTCTCCTAGAAACCGGAGAAGCTGGAGC-AGATCTCCCAGAAACTGGAGAAGCAGGAGCAGATCT
1 GTCTCCCAGAAACAAGAGAAGCAGGAGCAAG-TCTCCCAGAAACCGGAGAAGCAGGAGCAGATCT
*
245355 CCCAGAAACCGGAGAAGCAAGAGTAGATCTCCC
65 CCCAGAAACCGGAGAAGCAAGAGCAGATCTCCC
245388 TGTTTTCAGC
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
113 2 0.02
114 85 0.98
ACGTcount: A:0.35, C:0.26, G:0.29, T:0.09
Consensus pattern (114 bp):
GTCTCCCAGAAACAAGAGAAGCAGGAGCAAGTCTCCCAGAAACCGGAGAAGCAGGAGCAGATCTC
CCAGAAACCGGAGAAGCAAGAGCAGATCTCCCAGAAACCGGAGAAGCAG
Found at i:249404 original size:4 final size:4
Alignment explanation
Indices: 249395--249424 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
249385 CGAAATTGAT
249395 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
249425 TTAAATATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:249639 original size:42 final size:42
Alignment explanation
Indices: 249580--249673 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 42
249570 AATCACTCAA
*
249580 CGTTAACCTCCGTTAAAATGGGTAACGGAAAGCTTACCTGGC
1 CGTTAACCGCCGTTAAAATGGGTAACGGAAAGCTTACCTGGC
*
249622 CGTTAACCGCCGTTAAAATGGGTGACGGAAAGCTTACCTGGC
1 CGTTAACCGCCGTTAAAATGGGTAACGGAAAGCTTACCTGGC
249664 CGTTAACCGC
1 CGTTAACCGC
249674 TTACCTGACA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.22
Consensus pattern (42 bp):
CGTTAACCGCCGTTAAAATGGGTAACGGAAAGCTTACCTGGC
Found at i:261632 original size:24 final size:24
Alignment explanation
Indices: 261605--261664 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 24
261595 TTAAATCATA
* *
261605 TATATATATATCTACTAAAATT-T
1 TATATATATATATAATAAAATTAT
261628 GTATAT-T-TATATAATAAAATTAT
1 -TATATATATATATAATAAAATTAT
261651 TATATATATATATA
1 TATATATATATATA
261665 TATAGATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 17 0.55
23 3 0.10
24 11 0.35
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (24 bp):
TATATATATATATAATAAAATTAT
Found at i:264413 original size:2 final size:2
Alignment explanation
Indices: 264406--264444 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
264396 TTTAGAAGCA
264406 AT AT 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 AT AT A
264445 AATCCTTGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:265695 original size:6 final size:6
Alignment explanation
Indices: 265684--265723 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
265674 ATTTTCAAAG
*
265684 TATACA TATACA CATACA TATACA TATACA TATACA TATA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATA
265724 TGAAACAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
TATACA
Found at i:268431 original size:22 final size:23
Alignment explanation
Indices: 268386--268432 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
268376 AGTGGAGATA
* *
268386 AAAATGAATACAATAAGAAAAAT
1 AAAATGAAGACAAAAAGAAAAAT
*
268409 AAAATGAAGA-AAAAAGAATAAT
1 AAAATGAAGACAAAAAGAAAAAT
268431 AA
1 AA
268433 TGATAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (23 bp):
AAAATGAAGACAAAAAGAAAAAT
Found at i:268517 original size:30 final size:30
Alignment explanation
Indices: 268461--268526 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
268451 AATAAACGAG
268461 TAAATAAAAAAATAAGAAGAAAAT-AAAAA
1 TAAATAAAAAAATAAGAAGAAAATAAAAAA
* *
268490 TAAATAAAACAAATGTA-AAGAAGATAAAAAA
1 TAAATAAAA-AAAT-AAGAAGAAAATAAAAAA
268521 TAAATA
1 TAAATA
268527 TAAGGAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 9 0.28
30 11 0.34
31 12 0.38
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.17
Consensus pattern (30 bp):
TAAATAAAAAAATAAGAAGAAAATAAAAAA
Found at i:268526 original size:41 final size:42
Alignment explanation
Indices: 268481--268585 Score: 99
Period size: 44 Copynumber: 2.4 Consensus size: 42
268471 AATAAGAAGA
* *
268481 AAATAAAAATAAATAAAACAAATGTAA-AGAAGATAAAAAA-T
1 AAATAAAAATAAATAAAA-AAATGAAATAGAAGAAAAAAAAGT
*
268522 AAATATAAGGAATAAA-AATAAAAATGAAATAGAGGAAAAAAAAGGT
1 AAATA-AA--AATAAATAA-AAAAATGAAATAGAAGAAAAAAAA-GT
*
268568 AAATAGAAATAAATAAAA
1 AAATAAAAATAAATAAAA
268586 TATAATAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
41 5 0.10
42 2 0.04
43 17 0.33
44 21 0.40
45 1 0.02
46 6 0.12
ACGTcount: A:0.71, C:0.01, G:0.11, T:0.16
Consensus pattern (42 bp):
AAATAAAAATAAATAAAAAAATGAAATAGAAGAAAAAAAAGT
Found at i:268557 original size:25 final size:25
Alignment explanation
Indices: 268516--268564 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
268506 AAAGAAGATA
*
268516 AAAAATAAATATAAGGAATAAAAAT
1 AAAAATAAATATAAGGAAAAAAAAT
*
268541 AAAAATGAAATA-GAGGAAAAAAAA
1 AAAAAT-AAATATAAGGAAAAAAAA
268565 GGTAAATAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.14
Consensus pattern (25 bp):
AAAAATAAATATAAGGAAAAAAAAT
Found at i:268854 original size:21 final size:21
Alignment explanation
Indices: 268830--268882 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
268820 GAATATGCAT
*
268830 ATAAATAAAATGTTTTAAAAA
1 ATAAATAAAATATTTTAAAAA
268851 AT-AATAATAA-ATTTTAAAAA
1 ATAAATAA-AATATTTTAAAAA
268871 A-AAGATAAAATA
1 ATAA-ATAAAATA
268883 AAACAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (21 bp):
ATAAATAAAATATTTTAAAAA
Found at i:268909 original size:3 final size:3
Alignment explanation
Indices: 268901--268935 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
268891 CATATAAAAC
268901 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
268936 GAATTATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:269372 original size:37 final size:37
Alignment explanation
Indices: 269322--269429 Score: 198
Period size: 37 Copynumber: 2.9 Consensus size: 37
269312 TTATGGATCC
*
269322 TATTTTTAGGAGTTTGAATCATAGTAAAATTCTATCA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
269359 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
*
269396 TATTTTTAGGAGTTTGAATCATAATAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
269430 ACGTTATGTT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
Found at i:272665 original size:261 final size:261
Alignment explanation
Indices: 272201--272728 Score: 975
Period size: 261 Copynumber: 2.0 Consensus size: 261
272191 AAAATATCAT
272201 TATGGGGTAAAATTACAAAAATACCCTTGTATTGAGAAATAACCAAGACTTTCCCTAGTGGTGAA
1 TATGGGGTAAAATTACAAAAATACCCTTGTATTGAGAAATAACCAAGACTTTCCCTAGTGGTGAA
* *
272266 ATTAACCTCTAGTGAGCAAATGAGCAAAATACTCTGAACTTTAATGGAACTGGAATACTTTCAAG
66 ATTAACCTCCAGTAAGCAAATGAGCAAAATACTCTGAACTTTAATGGAACTGGAATACTTTCAAG
272331 CCTAAGTTACCCGAAGTAATGCTATGGACAAAATTGAATGAAATGATAATAATACCCTTAAAGAG
131 CCTAAGTTACCCGAAGTAATGCTATGGACAAAATTGAATGAAATGATAATAATACCCTTAAAGAG
*
272396 TAAAAGGATTATGGATGAATATGATAATATAGACGACTTGAGAACTTAAATTATGATCCACTTGA
196 TAAAAGGATTATGGATGAATATGATAATAGAGACGACTTGAGAACTTAAATTATGATCCACTTGA
272461 A
261 A
* *
272462 TATGGGGTAAAATTACGAAAATACCCTTGTATTGAGAAATGACCAAGACTTTCCCTAGTGGTGAA
1 TATGGGGTAAAATTACAAAAATACCCTTGTATTGAGAAATAACCAAGACTTTCCCTAGTGGTGAA
* *
272527 ATTAACCTCCAGTAAGCAAATGAGCAAAGTACTCTGAACTTTAATGGAATTGGAATACTTTCAAG
66 ATTAACCTCCAGTAAGCAAATGAGCAAAATACTCTGAACTTTAATGGAACTGGAATACTTTCAAG
* *
272592 CCTAAGTTACCCGAAGTAATGCTATGGACAGAATTGAATGAAATGATGATAATACCCTTAAAGAG
131 CCTAAGTTACCCGAAGTAATGCTATGGACAAAATTGAATGAAATGATAATAATACCCTTAAAGAG
272657 TAAAAGGATTATGGATGAATATGATAATAGAGACGACTTGAGAACTTAAATTATGATCCACTTGA
196 TAAAAGGATTATGGATGAATATGATAATAGAGACGACTTGAGAACTTAAATTATGATCCACTTGA
272722 A
261 A
272723 TATGGG
1 TATGGG
272729 AAATCACCGA
Statistics
Matches: 258, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
261 258 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (261 bp):
TATGGGGTAAAATTACAAAAATACCCTTGTATTGAGAAATAACCAAGACTTTCCCTAGTGGTGAA
ATTAACCTCCAGTAAGCAAATGAGCAAAATACTCTGAACTTTAATGGAACTGGAATACTTTCAAG
CCTAAGTTACCCGAAGTAATGCTATGGACAAAATTGAATGAAATGATAATAATACCCTTAAAGAG
TAAAAGGATTATGGATGAATATGATAATAGAGACGACTTGAGAACTTAAATTATGATCCACTTGA
A
Found at i:273047 original size:2 final size:2
Alignment explanation
Indices: 273040--273074 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
273030 CATCGATGTT
273040 TA TA 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 TA TA T
273075 GTACCGTCCA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:273899 original size:31 final size:31
Alignment explanation
Indices: 273857--273966 Score: 105
Period size: 31 Copynumber: 3.4 Consensus size: 31
273847 TTGGTCGCTG
*
273857 CTGGTAATTCCTTGTATAAGTTCAGCACCGA
1 CTGGTAATTCCTTGTATAGGTTCAGCACCGA
* * * * *
273888 CTGATAATTCCTATCTCTGGCAGGTTCAGTC-GCTA
1 CTGGTAATTCCT-TGTAT---AGGTTCAG-CACCGA
*
273923 CTGGTAATTCCTTGTATAGGTTCAGCATCGA
1 CTGGTAATTCCTTGTATAGGTTCAGCACCGA
273954 CTGGTAATTCCTT
1 CTGGTAATTCCTT
273967 TTAGACCTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
30 1 0.02
31 34 0.55
32 3 0.05
34 3 0.05
35 20 0.32
36 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (31 bp):
CTGGTAATTCCTTGTATAGGTTCAGCACCGA
Found at i:273947 original size:66 final size:66
Alignment explanation
Indices: 273841--273965 Score: 196
Period size: 66 Copynumber: 1.9 Consensus size: 66
273831 GAAGACTTTA
** *
273841 GCAGGTTTGGTCGCTGCTGGTAATTCCTTGTATAAGTTCAGCACCGACTGATAATTCCTATCTCT
1 GCAGGTTCAGTCGCTACTGGTAATTCCTTGTATAAGTTCAGCACCGACTGATAATTCCTATCTCT
273906 G
66 G
* * *
273907 GCAGGTTCAGTCGCTACTGGTAATTCCTTGTATAGGTTCAGCATCGACTGGTAATTCCT
1 GCAGGTTCAGTCGCTACTGGTAATTCCTTGTATAAGTTCAGCACCGACTGATAATTCCT
273966 TTTAGACCTA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.34
Consensus pattern (66 bp):
GCAGGTTCAGTCGCTACTGGTAATTCCTTGTATAAGTTCAGCACCGACTGATAATTCCTATCTCT
G
Found at i:275720 original size:15 final size:15
Alignment explanation
Indices: 275690--275723 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
275680 ATCATTTGTC
**
275690 TTCTTTCTTTTTCTT
1 TTCTTTCTTTACCTT
275705 TTCTTTCTTTACCTT
1 TTCTTTCTTTACCTT
275720 TTCT
1 TTCT
275724 GGTGACGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (15 bp):
TTCTTTCTTTACCTT
Found at i:282602 original size:18 final size:18
Alignment explanation
Indices: 282579--282641 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
282569 TCGAGGGTTA
*
282579 AAAGTGGTCCTACGGGAC
1 AAAGTGGTCCTTCGGGAC
*
282597 AAAGTGGTCCTTTGGGAC
1 AAAGTGGTCCTTCGGGAC
* *
282615 ATAGTTGTCCTTCGGGAC
1 AAAGTGGTCCTTCGGGAC
282633 AAAGTGGTC
1 AAAGTGGTC
282642 TCGTGGGACA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (18 bp):
AAAGTGGTCCTTCGGGAC
Found at i:282649 original size:18 final size:17
Alignment explanation
Indices: 282579--282653 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 17
282569 TCGAGGGTTA
*
282579 AAAGTGGTCCTACGGGAC
1 AAAGTGGTCCT-TGGGAC
282597 AAAGTGGTCCTTTGGGAC
1 AAAGTGGTCC-TTGGGAC
* *
282615 ATAGTTGTCCTTCGGGAC
1 AAAGTGGTCCTT-GGGAC
*
282633 AAAGTGGTCTCGTGGGAC
1 AAAGTGGTC-CTTGGGAC
282651 AAA
1 AAA
282654 ATTCTAAGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
17 2 0.04
18 43 0.90
19 3 0.06
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (17 bp):
AAAGTGGTCCTTGGGAC
Found at i:283113 original size:13 final size:13
Alignment explanation
Indices: 283095--283120 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
283085 GTAATTACAG
283095 TTTAAAGTTATAA
1 TTTAAAGTTATAA
283108 TTTAAAGTTATAA
1 TTTAAAGTTATAA
283121 GTGCTCTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TTTAAAGTTATAA
Found at i:284046 original size:21 final size:20
Alignment explanation
Indices: 284022--284088 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
284012 AGGGGGAACA
284022 GATTCCCCCTGGGGGGTTATC
1 GATTCCCCCTGGGGGG-TATC
*
284043 GATT-CCCC----GGG-AAC
1 GATTCCCCCTGGGGGGTATC
284057 AGATTCCCCCTGGGGGGGTATC
1 -GATTCCCCCT-GGGGGGTATC
284079 GATTCCCCCT
1 GATTCCCCCT
284089 AAATGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 16
0.67 0.04 0.30
Matches are distributed among these distances:
14 2 0.06
15 4 0.11
16 7 0.19
20 4 0.11
21 17 0.47
22 2 0.06
ACGTcount: A:0.13, C:0.33, G:0.30, T:0.24
Consensus pattern (20 bp):
GATTCCCCCTGGGGGGTATC
Found at i:284062 original size:36 final size:36
Alignment explanation
Indices: 284015--284086 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
284005 TATGTGCAGG
*
284015 GGGAACAGATTCCCCCTGGGGGGTTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
284051 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
284087 CTAAATGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.32, T:0.21
Consensus pattern (36 bp):
GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
Found at i:284710 original size:15 final size:15
Alignment explanation
Indices: 284692--284725 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
284682 GAGGGTATTG
284692 TAGTCCTTCGGGACA
1 TAGTCCTTCGGGACA
*
284707 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACA
284722 TAGT
1 TAGT
284726 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (15 bp):
TAGTCCTTCGGGACA
Found at i:290466 original size:36 final size:37
Alignment explanation
Indices: 290401--290472 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 37
290391 ATGTGCAGGA
*
290401 GGAACAGATTCCCCCTCTGGGGGGTATCGATTCCCCG
1 GGAACAGATTCCCCCTCGGGGGGGTATCGATTCCCCG
290438 GGAACAGATTCCCCCT-GGGGGGGTATCGATTCCCC
1 GGAACAGATTCCCCCTCGGGGGGGTATCGATTCCCC
290473 CCTGAATGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 18 0.53
37 16 0.47
ACGTcount: A:0.17, C:0.32, G:0.31, T:0.21
Consensus pattern (37 bp):
GGAACAGATTCCCCCTCGGGGGGGTATCGATTCCCCG
Found at i:291076 original size:15 final size:15
Alignment explanation
Indices: 291058--291092 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
291048 CGAGGGTATT
*
291058 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGAAC
291073 GTAGTCCTTCGGAAC
1 GTAGTCCTTCGGAAC
291088 GTAGT
1 GTAGT
291093 AGTCCTACGG
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:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGAAC
Found at i:297383 original size:21 final size:19
Alignment explanation
Indices: 297337--297383 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
297327 AATTTAAATT
297337 AGGTATCGATACCTAGGGA
1 AGGTATCGATACCTAGGGA
* *
297356 GGGTATCGGTACCTAGAGGAA
1 AGGTATCGATACCTAG-GG-A
297377 AGGTATC
1 AGGTATC
297384 TCAAGTTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 14 0.61
20 2 0.09
21 7 0.30
ACGTcount: A:0.30, C:0.15, G:0.34, T:0.21
Consensus pattern (19 bp):
AGGTATCGATACCTAGGGA
Done.