Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022560.1 Corchorus olitorius cultivar O-4 contig22593, 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: 11855
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Found at i:2444 original size:2 final size:2
Alignment explanation
Indices: 2437--2471 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2427 GATTCCAACA
* *
2437 AG AG AG AG AA AG AG AG AC AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2472 ATTGTTTCTC
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:0.54, C:0.03, G:0.43, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4734 original size:186 final size:184
Alignment explanation
Indices: 4391--6238 Score: 2147
Period size: 186 Copynumber: 10.2 Consensus size: 184
4381 TCTATAAGAG
* * * *** * *
4391 TTTCTTTAAC-AAAGCCGACAACGTTGATTGGTATACATATATTTATCAAACTA-ATTTATGTGG
1 TTTCTTTAACGAAA-CCGACAACGCTCATTGGTGTACATATA-CCGTCAAACTATATGTGTGTGG
* * * *
4454 ATTA-CTTTTTAAGTAGGT--A-C-AT---CTTTAAAGTTACCAAGTTGGGCCAAATGCTAGAGT
64 ATTATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAGCTGGGCCAATTGCTGGAGT
* *
4511 GCTTTACTGATTGATTTAGAATTCGAAAAAACTGATATTTTCTTTAAAT-TCGAGAT
129 GCTTTACTGATTCATTTAGAATTCGAAAAATCTGATATTTTCTTTAAATCT-GAGAT
* * *
4567 TTTCTTTAACGAAACCGATAACGCTCATTGGTGTACATATGCTGTCAAACTAATATGTGTGTGGA
1 TTTCTTTAACGAAACCGACAACGCTCATTGGTGTACATATACCGTCAAACT-ATATGTGTGTGGA
* * *
4632 TTATCTTTCTAAGTGGGTACACCAATGACCTTTGAAGTTACCAAGCTGGACCAATTGTCTGGAGT
65 TTATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAGCTGGGCCAATTG-CTGGAGT
*
4697 GCTGTACTGATTCATTTAGAATTTC-AAAAATCTGATATTTTCTTTAAATCTGAGAT
129 GCTTTACTGATTCATTTAGAA-TTCGAAAAATCTGATATTTTCTTTAAATCTGAGAT
* * * *
4753 TTTCTTTAAAGAAACCGACAACGCTCATTGGTGTATATATGCCAT-AAACTGATATGTGTGTGGA
1 TTTCTTTAACGAAACCGACAACGCTCATTGGTGTACATATACCGTCAAACT-ATATGTGTGTGGA
* * * *
4817 TTATCTTATTAAGTGGGTACACCGATGACCTTTAAAGTTACCAAGCTGGGCCAATTGTTGGATTG
65 TTATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAGCTGGGCCAATTGCTGGAGTG
* * * *
4882 CTTTACTAATTCATTTAGAATTCAAAAAATTTGATATTTTCTTTAAACCTGAGAT
130 CTTTACTGATTCATTTAGAATTCGAAAAATCTGATATTTTCTTTAAATCTGAGAT
* * *
4937 TTTCTTTAGCGAAACCGACAACGCTCATTGGTGTACATATACCGCCAAACTA-ATGTATGTGGAT
1 TTTCTTTAACGAAACCGACAACGCTCATTGGTGTACATATACCGTCAAACTATATGTGTGTGGAT
*
5001 TATCTTTTTGAGTGGGTACACC-ATGACCTTTAAAGTTACCAAGCTGGGCCAATTGCTGGAGTGC
66 TATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAGCTGGGCCAATTGCTGGAGTGC
5065 TTTACTGATTC-TTTCAGAATTCG-AAAATCTGATATTTTCTTTAAATCTGAGAT
131 TTTACTGATTCATTT-AGAATTCGAAAAATCTGATATTTTCTTTAAATCTGAGAT
* * * *
5118 TTTCTTTAACAAAACCGACAACGTTTATTGGTGTACATATACTGTCAAACTA-ATGTGTGTGGAT
1 TTTCTTTAACGAAACCGACAACGCTCATTGGTGTACATATACCGTCAAACTATATGTGTGTGGAT
* *
5182 TATCTTTCTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAGCTGGGCCAATTGTCTAGAGTG
66 TATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAGCTGGGCCAATTG-CTGGAGTG
* * * * *
5247 CTTTACTGAGTCATTTAGAATTTGAAAAATGTGATATTTTCTTAAAATCTGAAAT
130 CTTTACTGATTCATTTAGAATTCGAAAAATCTGATATTTTCTTTAAATCTGAGAT
* * * * *
5302 TTTCTTTAACTAAACCGACAATGCTCATTGGTGTATATATACCATCAAACTAATATGTGTGTAGA
1 TTTCTTTAACGAAACCGACAACGCTCATTGGTGTACATATACCGTCAAACT-ATATGTGTGTGGA
* *
5367 TTATCTTTTTAAGTGGGTACACC---GA---TGAAAGTTACCAAGCTGGGCCAATTGGTGGAGTG
65 TTATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAGCTGGGCCAATTGCTGGAGTG
*
5426 CTTTACTGATTCATTTAGAATTCGAAAAATCTG-----------------G-TAT
130 CTTTACTGATTCATTTAGAATTCGAAAAATCTGATATTTTCTTTAAATCTGAGAT
* *
5463 TTTCTTTAACGAAACCGACAACGCTCATTGGTTTACATATACCGCCAAACTA-ATGTGTGTGGAT
1 TTTCTTTAACGAAACCGACAACGCTCATTGGTGTACATATACCGTCAAACTATATGTGTGTGGAT
* * * *
5527 TATCTTTTTGAGTGGGTACACC-ATGACCTTT---GTTACCAAGTTTGGCCAGTTGCTGGAGTGC
66 TATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAGCTGGGCCAATTGCTGGAGTGC
* * * **
5588 TTTACGGATTCATTCATAATTTTAAAAAAAAAATCTGATATTTTCTTTAAATCTGAGAT
131 TTTACTGATTCATTTAGAA--TT---CGAAAAATCTGATATTTTCTTTAAATCTGAGAT
* * * * ** * *
5647 TTTCTTTAACAAAACAGTCAATGCTCATTGGTGTACATATACTATCAAACTAATAAGTGTGTAGA
1 TTTCTTTAACGAAACCGACAACGCTCATTGGTGTACATATACCGTCAAACT-ATATGTGTGTGGA
* *
5712 TTATCTTTTTAAGTGGGTATACCAATGACCTTTAAAGTTACCAAGCTGGGCCAATTGTCTGGACT
65 TTATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAGCTGGGCCAATTG-CTGGAGT
* *
5777 GTTTTACTGATTCATTTAGAATTTGAAAAATCTGATATTTTCTTTAAATCTGAGAT
129 GCTTTACTGATTCATTTAGAATTCGAAAAATCTGATATTTTCTTTAAATCTGAGAT
* * * * * *
5833 TTTCTTTAACGAAACCGACAATGCTCATTGGTGTATATATATCATCAAGCTTATATGTGTGTGAA
1 TTTCTTTAACGAAACCGACAACGCTCATTGGTGTACATATACCGTCAAAC-TATATGTGTGTGGA
* * * * *
5898 TTATCTTTTTAAGTGGGTACACCGATGACCTTTAAAGTTACCAAGTTAGGCCAGTTGCTAGAGTG
65 TTATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAGCTGGGCCAATTGCTGGAGTG
* *
5963 CTTTACTGATTCATTTAGAATTCGAAAAATATGATATTTTCTTTAAACCTGAGAT
130 CTTTACTGATTCATTTAGAATTCGAAAAATCTGATATTTTCTTTAAATCTGAGAT
* * * * *
6018 TTTCTTTAATGAAACCGATATCGTTCATTGTTGTACATATACCGTCAAA-T-TGATGTGTGTGGA
1 TTTCTTTAACGAAACCGACAACGCTCATTGGTGTACATATACCGTCAAACTAT-ATGTGTGTGGA
* * * * *
6081 TTATCTTTGTAAGTGGGTAAACCAATGACCTTTAAAGGTACCAAGCTAGGCCAATTGCTAGAGTG
65 TTATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAGCTGGGCCAATTGCTGGAGTG
* * * * * * *
6146 CTTTATTAATTCGTTTAGAATTCAAAAAATTTGATATGTTCTTTAAATCTAAGAT
130 CTTTACTGATTCATTTAGAATTCGAAAAATCTGATATTTTCTTTAAATCTGAGAT
* * * * **
6201 TTTCTTCAACGAAAACGATAACACTCATTAATGTACAT
1 TTTCTTTAACGAAACCGACAACGCTCATTGGTGTACAT
6239 TTACAATTGC
Statistics
Matches: 1435, Mismatches: 177, Indels: 113
0.83 0.10 0.07
Matches are distributed among these distances:
159 32 0.02
160 1 0.00
161 91 0.06
162 1 0.00
163 2 0.00
164 1 0.00
166 9 0.01
175 8 0.01
176 33 0.02
177 15 0.01
178 12 0.01
179 36 0.03
180 26 0.02
181 109 0.08
182 93 0.06
183 209 0.15
184 212 0.15
185 197 0.14
186 291 0.20
187 14 0.01
189 2 0.00
190 18 0.01
191 23 0.02
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (184 bp):
TTTCTTTAACGAAACCGACAACGCTCATTGGTGTACATATACCGTCAAACTATATGTGTGTGGAT
TATCTTTTTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAGCTGGGCCAATTGCTGGAGTGC
TTTACTGATTCATTTAGAATTCGAAAAATCTGATATTTTCTTTAAATCTGAGAT
Found at i:4747 original size:18 final size:18
Alignment explanation
Indices: 4724--4762 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
4714 AGAATTTCAA
*
4724 AAATCTGATATTTTCTTT
1 AAATCTGAGATTTTCTTT
4742 AAATCTGAGATTTTCTTT
1 AAATCTGAGATTTTCTTT
4760 AAA
1 AAA
4763 GAAACCGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (18 bp):
AAATCTGAGATTTTCTTT
Found at i:5112 original size:18 final size:18
Alignment explanation
Indices: 5089--5126 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
5079 CAGAATTCGA
*
5089 AAATCTGATATTTTCTTT
1 AAATCTGAGATTTTCTTT
5107 AAATCTGAGATTTTCTTT
1 AAATCTGAGATTTTCTTT
5125 AA
1 AA
5127 CAAAACCGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (18 bp):
AAATCTGAGATTTTCTTT
Found at i:5310 original size:19 final size:18
Alignment explanation
Indices: 5272--5307 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5262 TAGAATTTGA
* *
5272 AAAATGTGATATTTTCTT
1 AAAATCTGAAATTTTCTT
5290 AAAATCTGAAATTTTCTT
1 AAAATCTGAAATTTTCTT
5308 TAACTAAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.47
Consensus pattern (18 bp):
AAAATCTGAAATTTTCTT
Found at i:5564 original size:161 final size:165
Alignment explanation
Indices: 5290--5637 Score: 415
Period size: 161 Copynumber: 2.1 Consensus size: 165
5280 ATATTTTCTT
* * *
5290 AAAATCTGAAATTTTCTTTAACTAAACCGACAATGCTCATTGGTGTATATATACCATCAAACTAA
1 AAAATCTGATATTTTCTTTAACGAAACCGACAATGCTCATTGGTGTACATATACCATCAAACT-A
*
5355 TATGTGTGTAGATTATCTTTTTAAGTGGGTACACCGATGA----AAGTTACCAAGCTGGGCCAAT
65 TATGTGTGTAGATTATCTTTTTAAGTGGGTACACCGATGACCTTTAGTTACCAAGCTGGGCCAAT
*
5416 TGGTGGAGTGCTTTACTGATTCATTTAGAA-TTCGA
130 TGCTGGAGTGCTTTACTGATTCATTTAGAATTTCGA
* * * **
5451 AAAATCTGGTATTTTCTTTAACGAAACCGACAACGCTCATTGGTTTACATATACCGCCAAACTA-
1 AAAATCTGATATTTTCTTTAACGAAACCGACAATGCTCATTGGTGTACATATACCATCAAACTAT
* * * * *
5515 ATGTGTGTGGATTATCTTTTTGAGTGGGTACACC-ATGACCTTT-GTTACCAAGTTTGGCCAGTT
66 ATGTGTGTAGATTATCTTTTTAAGTGGGTACACCGATGACCTTTAGTTACCAAGCTGGGCCAATT
* * * **
5578 GCTGGAGTGCTTTACGGATTCATTCATAATTTTAAAAAA
131 GCTGGAGTGCTTTACTGATTCATTTAGAA-TTT---CGA
5617 AAAATCTGATATTTTCTTTAA
1 AAAATCTGATATTTTCTTTAA
5638 ATCTGAGATT
Statistics
Matches: 157, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
158 4 0.03
159 32 0.20
160 1 0.01
161 97 0.62
163 2 0.01
166 21 0.13
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (165 bp):
AAAATCTGATATTTTCTTTAACGAAACCGACAATGCTCATTGGTGTACATATACCATCAAACTAT
ATGTGTGTAGATTATCTTTTTAAGTGGGTACACCGATGACCTTTAGTTACCAAGCTGGGCCAATT
GCTGGAGTGCTTTACTGATTCATTTAGAATTTCGA
Found at i:5641 original size:18 final size:18
Alignment explanation
Indices: 5618--5655 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
5608 TTTAAAAAAA
*
5618 AAATCTGATATTTTCTTT
1 AAATCTGAGATTTTCTTT
5636 AAATCTGAGATTTTCTTT
1 AAATCTGAGATTTTCTTT
5654 AA
1 AA
5656 CAAAACAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (18 bp):
AAATCTGAGATTTTCTTT
Found at i:5805 original size:531 final size:526
Alignment explanation
Indices: 4482--6216 Score: 2082
Period size: 531 Copynumber: 3.2 Consensus size: 526
4472 ACATCTTTAA
* * * * * *
4482 AGTTACCAAGTTGGGCCAAATGCTAGAGTGCTTTACTGATTGATTTAGAATTCGAAAAAA-CTGA
1 AGTTACCAAGCTGGGCCAATTGCTGGAGTGCTTTACGGATTCATTCAGAATT--AAAAAATCTGA
* *
4546 TATTTTCTTTAAAT-TCGAGATTTTCTTTAACGAAACCGAT-AACGCTCATTGGTGTACATATGC
64 TATTTTCTTTAAATCT-GAGATTTTCTTTAACAAAACCG-TCAACGCTCATTGGTGTACATATAC
*
4609 TGTCAAACTAATATGTGTGTGGATTATCTTTCTAAGTGGGTACACCAATGACCTTTGAAGTTACC
127 TGTCAAACTAATA-GTGTGTGGATTATCTTTCTAAGTGGGTACACCAATGACCTTTAAAGTTACC
* * *
4674 AAGCTGGACCAATTGTCTGGAGTGCTGTACTGATTCATTTAGAATTTCAAAAATCTGATATTTTC
191 AAGCTGGGCCAATTGTCTGGAGTGCTTTACTGATTCATTTAGAATTTGAAAAATCTGATATTTTC
* * *
4739 TTTAAATCTGAGATTTTCTTTAAAGAAACCGACAACGCTCATTGGTGTATATATGCCAT-AAACT
256 TTTAAATCTGAGATTTTCTTTAACGAAACCGACAATGCTCATTGGTGTATATATACCATCAAACT
* *
4803 GATATGTGTGTGGATTATCTTATTAAGTGGGTACACCGATGACCTTTAAAGTTACCAAGCTGGGC
321 AATATGTGTGT-GATTATCTTTTTAAGTGGGTACACCGATG-----TAAAGTTACCAAGCTGGGC
* * * * *
4868 CAATTGTTGGATTGCTTTACTAATTCATTTAGAATTCAAAAAATTTGATATTTTCTTTAAACCTG
380 CAATTGCTGGAGTGCTTTACTGATTCATTTAGAATTCGAAAAATATGATATTTTC-TT-----T-
4933 AGATTTTCTTTAGCGAAACCGACAACGCTCATTGGTGTACATATACCGCCAAACTAATGTATGTG
438 --A--------AGCGAAACCGACAACGCTCATTGGTGTACATATACCGCCAAACTAATGTATGTG
4998 GATTATCTTTTTGAGTGGGTACACCATGACCTTT
493 GATTATCTTTTTGAGTGGGTACACCATGACCTTT
* * **
5032 AAAGTTACCAAGCTGGGCCAATTGCTGGAGTGCTTTACTGATTCTTTCAGAATTCGAAAATCTGA
1 --AGTTACCAAGCTGGGCCAATTGCTGGAGTGCTTTACGGATTCATTCAGAATTAAAAAATCTGA
* * *
5097 TATTTTCTTTAAATCTGAGATTTTCTTTAACAAAACCGACAACGTTTATTGGTGTACATATACTG
64 TATTTTCTTTAAATCTGAGATTTTCTTTAACAAAACCGTCAACGCTCATTGGTGTACATATACTG
5162 TCAAACTAAT-GTGTGTGGATTATCTTTCTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAG
129 TCAAACTAATAGTGTGTGGATTATCTTTCTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAG
* * * *
5226 CTGGGCCAATTGTCTAGAGTGCTTTACTGAGTCATTTAGAATTTGAAAAATGTGATATTTTCTTA
194 CTGGGCCAATTGTCTGGAGTGCTTTACTGATTCATTTAGAATTTGAAAAATCTGATATTTTCTTT
* *
5291 AAATCTGAAATTTTCTTTAACTAAACCGACAATGCTCATTGGTGTATATATACCATCAAACTAAT
259 AAATCTGAGATTTTCTTTAACGAAACCGACAATGCTCATTGGTGTATATATACCATCAAACTAAT
*
5356 ATGTGTGTAGATTATCTTTTTAAGTGGGTACACCGATG-AAAGTTACCAAGCTGGGCCAATTGGT
324 ATGTGTGT-GATTATCTTTTTAAGTGGGTACACCGATGTAAAGTTACCAAGCTGGGCCAATTGCT
* *
5420 GGAGTGCTTTACTGATTCATTTAGAATTCGAAAAATCTGGTATTTTCTTTAA-CGAAACCGACAA
388 GGAGTGCTTTACTGATTCATTTAGAATTCGAAAAATATGATATTTTCTTTAAGCGAAACCGACAA
* *
5484 CGCTCATTGGTTTACATATACCGCCAAACTAATGTGTGTGGATTATCTTTTTGAGTGGGTACACC
453 CGCTCATTGGTGTACATATACCGCCAAACTAATGTATGTGGATTATCTTTTTGAGTGGGTACACC
5549 ATGACCTTT
518 ATGACCTTT
* * * *
5558 -GTTACCAAGTTTGGCCAGTTGCTGGAGTGCTTTACGGATTCATTCATAATTTTAAAAAAAAAAT
1 AGTTACCAAGCTGGGCCAATTGCTGGAGTGCTTTACGGATTCATTCAGAA--TT----AAAAAAT
* *
5622 CTGATATTTTCTTTAAATCTGAGATTTTCTTTAACAAAACAGTCAATGCTCATTGGTGTACATAT
60 CTGATATTTTCTTTAAATCTGAGATTTTCTTTAACAAAACCGTCAACGCTCATTGGTGTACATAT
* * * *
5687 ACTATCAAACTAATAAGTGTGTAGATTATCTTTTTAAGTGGGTATACCAATGACCTTTAAAGTTA
125 ACTGTCAAACTAAT-AGTGTGTGGATTATCTTTCTAAGTGGGTACACCAATGACCTTTAAAGTTA
* *
5752 CCAAGCTGGGCCAATTGTCTGGACTGTTTTACTGATTCATTTAGAATTTGAAAAATCTGATATTT
189 CCAAGCTGGGCCAATTGTCTGGAGTGCTTTACTGATTCATTTAGAATTTGAAAAATCTGATATTT
* *
5817 TCTTTAAATCTGAGATTTTCTTTAACGAAACCGACAATGCTCATTGGTGTATATATATCATCAAG
254 TCTTTAAATCTGAGATTTTCTTTAACGAAACCGACAATGCTCATTGGTGTATATATACCATCAAA
* * *
5882 CTTATATGTGTGTGAATTATCTTTTTAAGTGGGTACACCGATGACCTTTAAAGTTACCAAGTTAG
319 CTAATATGTGTGTG-ATTATCTTTTTAAGTGGGTACACCGATG-----TAAAGTTACCAAGCTGG
* *
5947 GCCAGTTGCTAGAGTGCTTTACTGATTCATTTAGAATTCGAAAAATATGATATTTTCTTTAAACC
378 GCCAATTGCTGGAGTGCTTTACTGATTCATTTAGAATTCGAAAAATATGATATTTTCTTT--A--
* * * * * * * *
6012 TGAGATTTTCTTTAATGAAACCGATATCGTTCATTGTTGTACATATACCGTCAAATTGATGTGTG
439 --AG-----C------GAAACCGACAACGCTCATTGGTGTACATATACCGCCAAACTAATGTATG
* * *
6077 TGGATTATCTTTGTAAGTGGGTAAACCAATGACCTTT
491 TGGATTATCTTTTTGAGTGGGTACACC-ATGACCTTT
* * * *** * * *
6114 AAAGGTACCAAGCTAGGCCAATTGCTAGAGTGCTTTATTAATTCGTTTAGAATTCAAAAAATTTG
1 --AGTTACCAAGCTGGGCCAATTGCTGGAGTGCTTTACGGATTCATTCAGAATT-AAAAAATCTG
* * *
6179 ATATGTTCTTTAAATCTAAGATTTTCTTCAACGAAAAC
63 ATATTTTCTTTAAATCTGAGATTTTCTTTAAC-AAAAC
6217 GATAACACTC
Statistics
Matches: 1042, Mismatches: 99, Indels: 81
0.85 0.08 0.07
Matches are distributed among these distances:
523 43 0.04
525 2 0.00
526 84 0.08
527 1 0.00
529 78 0.07
530 1 0.00
531 206 0.20
535 1 0.00
537 69 0.07
538 1 0.00
539 1 0.00
543 3 0.00
544 67 0.06
549 163 0.16
550 47 0.05
551 71 0.07
552 47 0.05
554 38 0.04
555 70 0.07
556 9 0.01
557 2 0.00
559 38 0.04
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (526 bp):
AGTTACCAAGCTGGGCCAATTGCTGGAGTGCTTTACGGATTCATTCAGAATTAAAAAATCTGATA
TTTTCTTTAAATCTGAGATTTTCTTTAACAAAACCGTCAACGCTCATTGGTGTACATATACTGTC
AAACTAATAGTGTGTGGATTATCTTTCTAAGTGGGTACACCAATGACCTTTAAAGTTACCAAGCT
GGGCCAATTGTCTGGAGTGCTTTACTGATTCATTTAGAATTTGAAAAATCTGATATTTTCTTTAA
ATCTGAGATTTTCTTTAACGAAACCGACAATGCTCATTGGTGTATATATACCATCAAACTAATAT
GTGTGTGATTATCTTTTTAAGTGGGTACACCGATGTAAAGTTACCAAGCTGGGCCAATTGCTGGA
GTGCTTTACTGATTCATTTAGAATTCGAAAAATATGATATTTTCTTTAAGCGAAACCGACAACGC
TCATTGGTGTACATATACCGCCAAACTAATGTATGTGGATTATCTTTTTGAGTGGGTACACCATG
ACCTTT
Found at i:5827 original size:18 final size:18
Alignment explanation
Indices: 5804--5841 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
5794 AGAATTTGAA
*
5804 AAATCTGATATTTTCTTT
1 AAATCTGAGATTTTCTTT
5822 AAATCTGAGATTTTCTTT
1 AAATCTGAGATTTTCTTT
5840 AA
1 AA
5842 CGAAACCGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (18 bp):
AAATCTGAGATTTTCTTT
Found at i:6759 original size:31 final size:31
Alignment explanation
Indices: 6721--6782 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
6711 GAGTTTTGTA
*
6721 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCACCTATTATACCCTTATT
6752 AAACTTTTGAATCACCTATTATACCCTTATT
1 AAACTTTTGAATCACCTATTATACCCTTATT
6783 TTTAGAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCACCTATTATACCCTTATT
Found at i:6889 original size:22 final size:22
Alignment explanation
Indices: 6854--6900 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
6844 TATCCATATA
* *
6854 ACTATTTTATTTTTACCATTTT
1 ACTATTTTACTTTTACAATTTT
* *
6876 ACTATTTTGCTTTTATAATTTT
1 ACTATTTTACTTTTACAATTTT
6898 ACT
1 ACT
6901 CAACTAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.02, T:0.62
Consensus pattern (22 bp):
ACTATTTTACTTTTACAATTTT
Found at i:6898 original size:93 final size:93
Alignment explanation
Indices: 6794--6972 Score: 295
Period size: 93 Copynumber: 1.9 Consensus size: 93
6784 TTAGAATATA
* *
6794 TTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCATATAACTAT
1 TTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCATATAACTAT
*
6859 TTTATTTTTACCATTTTACTATTTTGCT
66 TTTATTTTTACCATATTACTATTTTGCT
* * *
6887 TTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTAT
1 TTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCATATAACTAT
*
6952 TTTATTTTTACGATATTACTA
66 TTTATTTTTACCATATTACTA
6973 ATTTAATTAA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 79 1.00
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (93 bp):
TTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCATATAACTAT
TTTATTTTTACCATATTACTATTTTGCT
Found at i:7644 original size:16 final size:16
Alignment explanation
Indices: 7605--7638 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7595 TTGGCCTCAA
*
7605 GTCACTCGGATTTTGG
1 GTCATTCGGATTTTGG
*
7621 GTCATTCGGGTTTTGG
1 GTCATTCGGATTTTGG
7637 GT
1 GT
7639 TTTTCGACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.15, G:0.35, T:0.41
Consensus pattern (16 bp):
GTCATTCGGATTTTGG
Found at i:10656 original size:1 final size:1
Alignment explanation
Indices: 10650--10681 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
10640 GAGGAGTAGG
10650 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10682 GTTGTTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11029 original size:41 final size:41
Alignment explanation
Indices: 10972--11049 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
10962 CGGCTGTTTT
* *
10972 ATTTTATGAGTTCTTTTAAGAAAATTCAGTTAAGAAATGGA
1 ATTTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAATGGA
*
11013 ATTTTATAAGTGCTTTTAAGAAAATTTAGTTAAGAAA
1 ATTTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAA
11050 AGAAAGTCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.40
Consensus pattern (41 bp):
ATTTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAATGGA
Done.