Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022446.1 Corchorus olitorius cultivar O-4 contig22479, 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: 35757
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2049 original size:4 final size:4
Alignment explanation
Indices: 2040--2087 Score: 96
Period size: 4 Copynumber: 12.0 Consensus size: 4
2030 GGTGATGTTT
2040 CTTC CTTC CTTC CTTC CTTC CTTC CTTC CTTC CTTC CTTC CTTC CTTC
1 CTTC CTTC CTTC CTTC CTTC CTTC CTTC CTTC CTTC CTTC CTTC CTTC
2088 TTCTCCTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (4 bp):
CTTC
Found at i:5827 original size:12 final size:12
Alignment explanation
Indices: 5812--5878 Score: 53
Period size: 12 Copynumber: 5.1 Consensus size: 12
5802 TACAAACTAC
5812 CAAATAAACAAA
1 CAAATAAACAAA
5824 CAAATAAACTAAA
1 CAAATAAAC-AAA
* * *
5837 CTAATCTACAAACTAC
1 C-AA---ATAAACAAA
5853 CAAATAAACAAA
1 CAAATAAACAAA
5865 CAAATAAACTAAA
1 CAAATAAAC-AAA
5878 C
1 C
5879 TCACATTCCG
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
12 24 0.56
13 8 0.19
14 2 0.05
15 2 0.05
16 2 0.05
17 5 0.12
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.15
Consensus pattern (12 bp):
CAAATAAACAAA
Found at i:5842 original size:41 final size:41
Alignment explanation
Indices: 5793--5879 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
5783 GAAATTACCT
5793 TAAA-TAATCTACAAACTACCAAATAAACAAACAAATAAAC
1 TAAACTAATCTACAAACTACCAAATAAACAAACAAATAAAC
5833 TAAACTAATCTACAAACTACCAAATAAACAAACAAATAAAC
1 TAAACTAATCTACAAACTACCAAATAAACAAACAAATAAAC
5874 TAAACT
1 TAAACT
5880 CACATTCCGT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 4 0.09
41 42 0.91
ACGTcount: A:0.61, C:0.21, G:0.00, T:0.18
Consensus pattern (41 bp):
TAAACTAATCTACAAACTACCAAATAAACAAACAAATAAAC
Found at i:6649 original size:19 final size:20
Alignment explanation
Indices: 6607--6651 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
6597 AAGAAAAGAA
*
6607 TAAAAAATAAAAAATTAGAG
1 TAAAAAATAAAAAATCAGAG
*
6627 -AAAAAATAATAAATCA-AG
1 TAAAAAATAAAAAATCAGAG
6645 TAAAAAA
1 TAAAAAA
6652 AGTAATTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (20 bp):
TAAAAAATAAAAAATCAGAG
Found at i:15458 original size:19 final size:19
Alignment explanation
Indices: 15426--15472 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
15416 TATTGCTGAT
15426 GTGGCATT-TTGGTCCAAC
1 GTGGCATTGTTGGTCCAAC
15444 GTGGCATTGTTGGTCCAAC
1 GTGGCATTGTTGGTCCAAC
* *
15463 ATAGCATTGT
1 GTGGCATTGT
15473 CACGTCAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (19 bp):
GTGGCATTGTTGGTCCAAC
Found at i:21718 original size:56 final size:56
Alignment explanation
Indices: 21632--21745 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
21622 TACGCAAGGT
21632 CTCGAACCTAAGACCTGCTTAAGCTGGAACAAGCCGCTTACCACTTGATTCAACCC
1 CTCGAACCTAAGACCTGCTTAAGCTGGAACAAGCCGCTTACCACTTGATTCAACCC
21688 CTCGAACCTAAGACCTGCTTAAGCTGGAACAAGCCGCTTACCACTTGATTCAACCC
1 CTCGAACCTAAGACCTGCTTAAGCTGGAACAAGCCGCTTACCACTTGATTCAACCC
21744 CT
1 CT
21746 TGTCGGCATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.22
Consensus pattern (56 bp):
CTCGAACCTAAGACCTGCTTAAGCTGGAACAAGCCGCTTACCACTTGATTCAACCC
Found at i:24794 original size:15 final size:16
Alignment explanation
Indices: 24769--24798 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
24759 AATAATTATT
24769 TTTAGATTATAATATA
1 TTTAGATTATAATATA
24785 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
24799 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:25633 original size:337 final size:329
Alignment explanation
Indices: 25145--27333 Score: 1793
Period size: 337 Copynumber: 6.7 Consensus size: 329
25135 ATACTTTACA
* * **
25145 TCATCTAACCAAATCTCAG-CAACATTGGATTTAAAAATTT-TTTTTACGAGCATCTGAATCTTG
1 TCATCTAATCAAATCTCAGTC-ACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * *
25208 TTTCGATTTAATTAGAAATTAATTTAGAAAAAATAAGAAATACGATATTAAAAGCGTAAAAAACC
65 TTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTAAAA-CGTGAAAAACC
* * *
25273 CTCCAATCTTTTTGGCATTGAATTATATATTTTTATGAGTATATTAGCCAAAAATTGAGGAGAAA
129 CTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATATTAGCTAAAAATTGAGGAGAAA
* *
25338 TCTTTTGTGTCAATTTTTGTAAAATTTTAGCCGAAATCATGTACTAACAAACCATCACATTTTTT
194 T-TTTTGTGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTA-TAA-TAACCATCACA-TTTTT
* *
25403 TGGCTAACAACGCGTTCCGGAGACCCGGC-CTAATTTT-ACATGATTTTTTGGCTCCGAGACTAC
255 TGGCTAAAAACGCGTT-CGGAGCCCCGGCTC-AATTTTGA-ATGA-TTTTTGGCTCCGAGACT-C
*
25466 TTGAAATATCTAAAT
315 TTGAAATATCTATAT
* * * *
25481 TCATTTAATCAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTATGAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGTCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * ***
25546 TTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAGAAACGTCAAAAGTTC
66 TTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTA-AAACGTGAAAAACCC
* * * *
25611 TTCAATTTTTTTGGCGTTGAATTATATATGTTTATGAGTATTTTAGCCAAAAATTGAGGA-AATA
130 TTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATATTAGCTAAAAATTGAGGAGAA-A
* * * *
25675 TTTTTCTAATCAATTTTTACAAAATTTTAGCCGAAATCATG--TAATAACCATCACAGTTTTTGG
194 TTTTTGT-GTCAATTTTTGCAAAATTTTAGCCGAAATCATGTATAATAACCATCACATTTTTTGG
* * * * * * * * *
25738 CTAAAAAAGCGTTCTAGG-GCCCCGGCTCAGTTTTGCATAATTTTTGACGCCAAGACTCCTTTAG
258 CTAAAAACGCGTTC--GGAGCCCCGGCTCAATTTTGAATGATTTTTGGCTCCGAGACT-CTTGAA
*
25802 ATATCCATAT
320 ATATCTATAT
** ** * * *
25812 TCATCTAATCAAATCTCAACCACATTGGTTTTAAGAATTTGTTTTTACAAGTATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGTCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
** *
25877 TTCGATTTAATTA-AAAAAAATTCT-GAAAAAATATGAAAAACGATATTAAAAGCGTAAAAAACC
66 TTCGATTTAATTAGAAATTAATT-TAGAAAAAATATGAAAAACGATATTAAAA-CGTGAAAAACC
* *
25940 CTTCAATCTTTTTGGCGTTGAA-T-TATATTTTTATGAGTATTATGA-CTAAAAATTGAGGAGAT
129 CTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTA-TATTAGCTAAAAATTGAGGAGAA
* * * *
26002 ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC--GTTTAATAATCATCACGA-TTTTT
193 AT-TTTTGTGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTATAATAACCATCAC-ATTTTTT
* * * * *
26064 GGCTAAAAACGCGTTTTAGG-G-CCCAGTTCAATTTTGAATGATTTTTGGCACTGAGACTCTTTG
256 GGCTAAAAACGCG--TTCGGAGCCCCGGCTCAATTTTGAATGATTTTTGGCTCCGAGACTC-TTG
26127 AAATATCTATAT
318 AAATATCTATAT
* * * * *
26139 TCATCTAACCAAATCTCA-T--C----CA-TT---G--TT-TTTATA--AACATTTGAATCATGT
1 TCATCTAATCAAATCTCAGTCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * ** *
26188 TTC-ATTTTAATTAGAAATTAA-TTCG-GAAAA-A--AAAATTGATATTAGAAGA-GTGAAAAGC
66 TTCGA-TTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTA-AA-ACGTGAAAAAC
* * * *
26246 CCTTCAATTTTTTTGGCATTGAATTATATATTTTTTATGAGTAT-TGTGGCTAAAAATTGA-GAC
128 CCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATAT-TAGCTAAAAATTGAGGAG
* * * *
26309 AATATGTTTCTG-GTCATTTTTTTGCAAAATTTTAGCCGAAATC--GTGTAGTAACCATCACTGT
191 AA-AT-TTT-TGTGTCA-ATTTTTGCAAAATTTTAGCCGAAATCATGTATAATAACCATCAC-AT
* * * * * * *
26371 TTTTTTGCTAAAAACGCGAGTCGTGA-CCCCAGCTCAGTTTTGAATGGTTTTTGG-TGTCGACAC
251 TTTTTGGCTAAAAACGCG-TTCG-GAGCCCCGGCTCAATTTTGAATGATTTTTGGCT-CCGAGAC
*
26434 TCTTTGAAATATCTACAT
313 TC-TTGAAATATCTATAT
* * ** *
26452 TCATCTAATAAAATCTTAACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCT-AATTATTG
1 TCATCTAATCAAATCTCAGTCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAA-TCTTG
* *
26516 TTTCGATTTAATTAGGAATTAATTTAGAAAAAATATGAAAAATGATATTAAAAGCGTGAAAAACC
65 TTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTAAAA-CGTGAAAAACC
* *
26581 CTTCAATCTTTTTGGCGTTGAATTATATAGCTTTTTATGAGTATTATGA-CTAAAATTTGAGGAG
129 CTTCAATCTTTTTGGCGTTGAATTATATA--TTTTTATGAGTA-TATTAGCTAAAAATTGAGGAG
* * * * * *
26645 ATATATTTCGGGTCAATTTTTTTTTGCAAAATTTTAGCTGAAATC--GTGTAATAATCATCACGA
191 AAAT-TTTTGTGTCAA----TTTTTGCAAAATTTTAGCCGAAATCATGTATAATAACCATCAC-A
* * * *
26708 -TTTTTGGCTAAAAACGCGTT-TGAGGGCCCGGTTCAATTTTGAATGATTTTTGGCACCGAGACT
250 TTTTTTGGCTAAAAACGCGTTCGGA-GCCCCGGCTCAATTTTGAATGATTTTTGGCTCCGAGACT
26771 CCTTGAAATATCTATAT
314 -CTTGAAATATCTATAT
* * * * * *
26788 TCATCTAACCAAATC-C---CA-A--CCA-TT----A----TTTTTACAAACATTTGAATCATGT
1 TCATCTAATCAAATCTCAGTCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * *
26837 TTCGTTTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAATGATATTAGAAACGTGTAAACCC
66 TTCGATTTAATTAGAAATTAATTTAG-AAAAAATATGAAAAACGATATTA-AAACGTGAAAAACC
* * *
26902 CTTCAATTTTTTTGGCATTGAATTATATATTTTTTATGAGTAT-TGTGGCTAAAAATTGA-GAGA
129 CTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATAT-TAGCTAAAAATTGAGGAGA
* * * * *
26965 ATATTTTTCTGGTCATTTTTTGCAAAATTTTAGTCGAAATCGTGTAT--TAACCATCACTGTTTT
192 A-ATTTTTGT-GTCAATTTTTGCAAAATTTTAGCCGAAATCATGTATAATAACCATCAC-ATTTT
* * ** * * * *
27028 TTTGCTAAAAACGCGTTTCGGGGTTCCGGCTCAGTTTTGCATGATTTTTGGCGT-CGAAACTTTT
254 TTGGCTAAAAACGCG-TTCGGAGCCCCGGCTCAATTTTGAATGATTTTTGGC-TCCGAGACTCTT
27092 CGAAATATC--TA-
317 -GAAATATCTATAT
*
27103 T-A--T--T-AAATCTCAGTCACATTGCATTTAAGGATTTGTTTTTACGAGCATATGAATCTTGT
1 TCATCTAATCAAATCTCAGTCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * **
27162 TTCGATTTAATTAGAAATTAATTCAAAAAAAAT-TGAAAAACGATATTAAAA-GTGAGAAAAGTC
66 TTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTAAAACGTGA-AAAACCC
* * * * * *
27225 TTCCAATCTTTATGGAGTTGAATTATATATATTTTATGCGTATTTTAGAC-AAAAATTTAGGAAA
130 TT-CAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATATTAG-CTAAAAATTGAGGAGA
*
27289 AATATTTCTG-GTCAATTTTTTG-AAAATATTAGCCGAAATCATGTA
192 AAT-TTT-TGTGTCAA-TTTTTGCAAAATTTTAGCCGAAATCATGTA
27334 CGTCAGTCGA
Statistics
Matches: 1503, Mismatches: 235, Indels: 243
0.76 0.12 0.12
Matches are distributed among these distances:
307 39 0.03
308 4 0.00
309 15 0.01
310 39 0.03
311 66 0.04
312 24 0.02
313 67 0.04
314 4 0.00
315 1 0.00
316 37 0.02
317 21 0.01
318 45 0.03
319 11 0.01
320 69 0.05
321 66 0.04
322 13 0.01
323 82 0.05
324 25 0.02
325 45 0.03
326 4 0.00
327 62 0.04
328 94 0.06
329 41 0.03
330 64 0.04
331 102 0.07
332 37 0.02
333 15 0.01
334 54 0.04
335 31 0.02
336 102 0.07
337 183 0.12
338 41 0.03
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (329 bp):
TCATCTAATCAAATCTCAGTCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTAAAACGTGAAAAACCCT
TCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATATTAGCTAAAAATTGAGGAGAAATT
TTTGTGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTATAATAACCATCACATTTTTTGGCTA
AAAACGCGTTCGGAGCCCCGGCTCAATTTTGAATGATTTTTGGCTCCGAGACTCTTGAAATATCT
ATAT
Found at i:27192 original size:971 final size:963
Alignment explanation
Indices: 25155--27334 Score: 2233
Period size: 971 Copynumber: 2.2 Consensus size: 963
25145 TCATCTAACC
* *
25155 AAATCTCAGCAACATTGGATTTAAAAATTT-TTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
1 AAATCTCAGC-ACATTGCATTTAAAAATTTGTTTTTACGAGCATATGAATCTTGTTTCGATTTAA
* * *
25219 TTAGAAATTAATTTAGAAAAAATAAGAAATACGATATTAAAAGCGTAAAAAACCCTCCAATCTTT
65 TTAGAAATTAA-TT----CAAA-AA-AAAT-TGATATTAAAAGAGTAAAAAACCCTCCAATCTTT
*
25284 TTGGCATTGAATTATATATTTTTATGAGTATATTAGCCAAAAATTGAGGAGAAATCTTTTGTGTC
122 TTGGCATTGAATTATATATTTTTATGAGTATATTAGCCAAAAATTGAGGACAAATCTTTTGTGTC
* *
25349 AATTTTTGTAAAATTTTAGCCGAAATCATGTACTAACAAACCATCACATTTTTTTGGCTAACAAC
187 AATTTTTGCAAAATTTTAGCCGAAATCATGTACT---AAACCATCACATTTTTTTGGCTAAAAAC
* * * *
25414 GCGTTCCGGAGACCCGGCCTAATTTTACATGATTTTTTGGCTCCGAGACTACTTGAAATATCTAA
249 GCGGTCCGGAGACCCAGCCTAATTTTACATGAGTTTTTGGCTCCGACACTACTTGAAATATCTAA
* * ** * * *
25479 ATTCATTTAATCAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTATGAGCATCTAAATCTT
314 ATTCATCTAATAAAATCTCAACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATATT
* **
25544 GTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAGAAACGTCAAAAGT
379 GTTTCGATTTAATTAGAAATTAATTTAGAAAAAATAGGAAAAACGATATTAGAAACGTCAAAAAC
* * *
25609 TCTTCAATTTTTTTGGCGTTGAATTATATATGTTTATGAGTATTTTAGCCAAAAATTGAGGAAAT
444 CCTTCAATCTTTTTGGCGTTGAATTATATATGTTTATGAGTATTTGAGCCAAAAATTGAGGAAAT
*
25674 ATTTTTCTAATCAATTTTTACAAAATTTTAGCCGAAATCATGTAATAACCATCACAGTTTTTGGC
509 ATATTTCTAATCAATTTTTACAAAATTTTAGCCGAAATCATGTAATAACCATCACAGTTTTTGGC
* * * * *
25739 TAAAAAAGCGTTCTAGGGCCCCGGCTCAGTTTTGCATAATTTTTGACGCCAAGACTCCTTTAGAT
574 TAAAAAAGCGTTCTAGGGCCCCGGCTCAATTTTGAATAATTTTTGACACCAAGACTCCTTGAAAT
* * **
25804 ATCCATATTCATCTAATCAAATCTCAACCACATTGGTTTTAAGAATTTGTTTTTACAAGTATCTG
639 ATCCATATTCATCTAACCAAATCCCAACCACA-----TTT---AA--T-TTTTTACAAACATCTG
* * *
25869 AATCTTGTTTCGATTTAATTAAAAAAAATTCTGAAAAAATATGAAAAACGATATTAAAAGCGTAA
693 AATCATGTTTCGATTTAATTAAAAAAAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTAA
*
25934 AAAACCCTTCAATCTTTTTGGCGTTGAATTATATTTTTATGAGTATTATGACTAAAAATTGAGGA
758 AAAACCCTTCAATCTTTTTGGCATTGAATTATATTTTTATGAGTATTATGACTAAAAATTGAGGA
* *
25999 GATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTTTAATAATCATCACGATTTTT
823 GATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGATTTTT
* * *
26064 GGCTAAAAACGCGTTTTAGGGCCCAGTTCAATTTTGAATGATTTTTGGCACTGAGACTCTTTGAA
888 GGCTAAAAACGCGTTTCAGGGCCCAGCTCAATTTTGAATGATTTTTGGCACTGAAACTCTTTGAA
26129 ATATCTATATT
953 ATATCTATATT
* * * * ** ** * * *
26140 -CATCTAACCAAATCT-CA--T--CCA-TTGTTTTTATAAACATTTGAATCATGTTTC-ATTTTA
1 AAATCTCAGCACAT-TGCATTTAAAAATTTGTTTTTACGAGCATATGAATCTTGTTTCGA-TTTA
* * * * *
26197 ATTAGAAATTAATTCGGAAAAAAAAATTGATATTAGAAGAGTGAAAAGCCCTTCAATTTTTTTGG
64 ATTAGAAATTAATTC---AAAAAAAATTGATATTAAAAGAGTAAAAAACCCTCCAATCTTTTTGG
* * *
26262 CATTGAATTATATATTTTTTATGAGTAT-TGTGGCTAAAAATTGA-GACAATATGTTTCTG-GTC
126 CATTGAATTATATA-TTTTTATGAGTATAT-TAGCCAAAAATTGAGGACAA-ATCTTT-TGTGTC
* * * *
26324 ATTTTTTTGCAAAATTTTAGCCGAAATCGTGTAGT-AACCATCAC-TGTTTTTTTGCTAAAAACG
187 A-ATTTTTGCAAAATTTTAGCCGAAATCATGTACTAAACCATCACAT-TTTTTTGGCTAAAAACG
* * *
26387 CGAGT-CGTGA-CCCCAG-CTCAGTTTTGA-ATG-GTTTTTGG-TGTCGACACT-CTTTGAAATA
250 CG-GTCCG-GAGACCCAGCCT-AATTTT-ACATGAGTTTTTGGCT-CCGACACTAC-TTGAAATA
* *
26445 TCTACATTCATCTAATAAAATCTTAACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAA
309 TCTAAATTCATCTAATAAAATCTCAACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAA
* * * * *
26510 TTATTGTTTCGATTTAATTAGGAATTAATTTAGAAAAAATATGAAAAATGATATTA-AAAGCGTG
374 ATATTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATAGGAAAAACGATATTAGAAA-CGTC
* * *
26574 AAAAACCCTTCAATCTTTTTGGCGTTGAATTATATAGCTTTTTATGAGTATTATGA-CTAAAATT
438 AAAAACCCTTCAATCTTTTTGGCGTTGAATTATATA--TGTTTATGAGTATT-TGAGCCAAAAAT
* *** * * * *
26638 TGAGGAGATATATTTCGGGTCAATTTTTTTTTGCAAAATTTTAGCTGAAATCGTGTAATAATCAT
500 TGAGGAAATATATTTC---T-AATCAATTTTTACAAAATTTTAGCCGAAATCATGTAATAACCAT
* * * *
26703 CAC-GATTTTTGGCTAAAAACGCGTT-TGAGGG-CCCGGTTCAATTTTGAATGATTTTTGGCACC
561 CACAG-TTTTTGGCTAAAAAAGCGTTCT-AGGGCCCCGGCTCAATTTTGAATAATTTTTGACACC
* *
26765 GAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAA-C-CA-TT-A-TTTTTACAAACA
624 AAGACTCCTTGAAATATCCATATTCATCTAACCAAATCCCAACCACATTTAATTTTTTACAAACA
* * ** *
26825 TTTGAATCATGTTTCGTTTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAATGATATTAGAA
689 TCTGAATCATGTTTCGATTTAATTA-AAAAAAATTCAG-AAAAAATAGGAAAAACGATATTA-AA
** * * * *
26890 A-CGTGTAAACCCCTTCAATTTTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTGGCTAA
751 AGCGTAAAAAACCCTTCAATCTTTTTGGCATTGAA-T-TATA-TTTTTATGAGTATTATGACTAA
* * * * *
26954 AAATTGA-GAGAATATTTTTCTGGTCATTTTTTGCAAAATTTTAGTCGAAATCGTGTATTAACCA
813 AAATTGAGGAG-ATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCA
* * * * * * * *
27018 TCACTGTTTTTTTGCTAAAAACGCGTTTCGGGGTTCCGGCTCAGTTTTGCATGATTTTTGGC-GT
877 TCAC-GATTTTTGGCTAAAAACGCGTTTCAGGG-CCCAGCTCAATTTTGAATGATTTTTGGCACT
27082 CGAAACT-TTTCGAAATATCTATATT
940 -GAAACTCTTT-GAAATATCTATATT
**
27107 AAATCTCAGTCACATTGCATTTAAGGATTTGTTTTTACGAGCATATGAATCTTGTTTCGATTTAA
1 AAATCTCAG-CACATTGCATTTAAAAATTTGTTTTTACGAGCATATGAATCTTGTTTCGATTTAA
* ** *
27172 TTAGAAATTAATTCAAAAAAAATTGAAAAACGATATTAAAAGTG-AGAAAAGTCTTCCAATCTTT
65 TTAGAAATTAATTCAAAAAAAATT-------GATATTAAAAGAGTA-AAAAACCCTCCAATCTTT
* * * * * * *
27236 ATGG-AGTTGAATTATATATATTTTATGCGTATTTTAGACAAAAATTTAGGAAAAATATTTCTG-
122 TTGGCA-TTGAATTATATAT-TTTTATGAGTATATTAGCCAAAAATTGAGGACAAATCTTT-TGT
*
27299 GTCAATTTTTTG-AAAATATTAGCCGAAATCATGTAC
184 GTCAA-TTTTTGCAAAATTTTAGCCGAAATCATGTAC
27335 GTCAGTCGAA
Statistics
Matches: 987, Mismatches: 147, Indels: 130
0.78 0.12 0.10
Matches are distributed among these distances:
960 32 0.03
961 9 0.01
962 49 0.05
963 4 0.00
964 8 0.01
965 77 0.08
966 28 0.03
967 42 0.04
968 8 0.01
969 6 0.01
970 5 0.01
971 177 0.18
972 40 0.04
973 38 0.04
974 98 0.10
975 40 0.04
976 97 0.10
977 89 0.09
978 84 0.09
979 44 0.04
981 1 0.00
983 4 0.00
984 7 0.01
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (963 bp):
AAATCTCAGCACATTGCATTTAAAAATTTGTTTTTACGAGCATATGAATCTTGTTTCGATTTAAT
TAGAAATTAATTCAAAAAAAATTGATATTAAAAGAGTAAAAAACCCTCCAATCTTTTTGGCATTG
AATTATATATTTTTATGAGTATATTAGCCAAAAATTGAGGACAAATCTTTTGTGTCAATTTTTGC
AAAATTTTAGCCGAAATCATGTACTAAACCATCACATTTTTTTGGCTAAAAACGCGGTCCGGAGA
CCCAGCCTAATTTTACATGAGTTTTTGGCTCCGACACTACTTGAAATATCTAAATTCATCTAATA
AAATCTCAACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATATTGTTTCGATTTAA
TTAGAAATTAATTTAGAAAAAATAGGAAAAACGATATTAGAAACGTCAAAAACCCTTCAATCTTT
TTGGCGTTGAATTATATATGTTTATGAGTATTTGAGCCAAAAATTGAGGAAATATATTTCTAATC
AATTTTTACAAAATTTTAGCCGAAATCATGTAATAACCATCACAGTTTTTGGCTAAAAAAGCGTT
CTAGGGCCCCGGCTCAATTTTGAATAATTTTTGACACCAAGACTCCTTGAAATATCCATATTCAT
CTAACCAAATCCCAACCACATTTAATTTTTTACAAACATCTGAATCATGTTTCGATTTAATTAAA
AAAAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTAAAAAACCCTTCAATCTTTTTGGCA
TTGAATTATATTTTTATGAGTATTATGACTAAAAATTGAGGAGATATCTTTCGGGTCAATTTTTG
CAAAATTTTAGCCGAAATCGTGTAATAACCATCACGATTTTTGGCTAAAAACGCGTTTCAGGGCC
CAGCTCAATTTTGAATGATTTTTGGCACTGAAACTCTTTGAAATATCTATATT
Found at i:30455 original size:54 final size:54
Alignment explanation
Indices: 30373--30481 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
30363 TTTAATTTTA
30373 AAAATGGCTTGGAATACTCATTGCTACATGATATGGAAGGAGAGGAATGCTCGG
1 AAAATGGCTTGGAATACTCATTGCTACATGATATGGAAGGAGAGGAATGCTCGG
30427 AAAATGGCTTGGAATACTCATTGCTACATGATATGGAAGGAGAGGAATGCTCGG
1 AAAATGGCTTGGAATACTCATTGCTACATGATATGGAAGGAGAGGAATGCTCGG
30481 A
1 A
30482 TTTACAAAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.24
Consensus pattern (54 bp):
AAAATGGCTTGGAATACTCATTGCTACATGATATGGAAGGAGAGGAATGCTCGG
Found at i:33579 original size:67 final size:66
Alignment explanation
Indices: 33471--33604 Score: 232
Period size: 67 Copynumber: 2.0 Consensus size: 66
33461 GTAAGGAGAA
* *
33471 TTATTTTTAAAAGTATTAATTTTTTTGGCACAAATTGAATAAATGATAATTTAGAATGGTTAAAA
1 TTATTTTTAAAAGTATAAATTTTTTTGGCACAAATTAAATAAATGATAATTTAGAATGGTTAAAA
33536 T
66 T
*
33537 TTATTTTTAAAAGTGATAAATTTTTTTGGCACAAATTAAATAAATGATAATTTAGAATTGTTAAA
1 TTATTTTTAAAAGT-ATAAATTTTTTTGGCACAAATTAAATAAATGATAATTTAGAATGGTTAAA
33602 AT
65 AT
33604 T
1 T
33605 ATAACAACGC
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
66 14 0.22
67 50 0.78
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (66 bp):
TTATTTTTAAAAGTATAAATTTTTTTGGCACAAATTAAATAAATGATAATTTAGAATGGTTAAAA
T
Found at i:35402 original size:29 final size:30
Alignment explanation
Indices: 35342--35416 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
35332 GCTAAATACC
* * *
35342 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATATTTT-CTTTCGGGA
35373 CAAAATAATCCCTTATATTTT-TTTCGGGA
1 CAAAATAATCCCTTATATTTTCTTTCGGGA
*
35402 CAAATTAATCCCTTA
1 CAAAATAATCCCTTA
35417 CGTTTCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 21 0.52
31 19 0.47
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.39
Consensus pattern (30 bp):
CAAAATAATCCCTTATATTTTCTTTCGGGA
Found at i:35599 original size:31 final size:31
Alignment explanation
Indices: 35547--35643 Score: 158
Period size: 31 Copynumber: 3.1 Consensus size: 31
35537 AGGGGACTAA
* *
35547 TTTGTCCTAAAAAAAAAAACATAAGGGATTTT
1 TTTGTCC-CAAAAGAAAAACATAAGGGATTTT
35579 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
*
35610 TTTGTCCCAAAAGAAAAACATTAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
35641 TTT
1 TTT
35644 AGTATTTAGT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
31 55 0.89
32 7 0.11
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.33
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTT
Done.