Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006690.1 Corchorus capsularis cultivar CVL-1 contig06711, 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: 56124
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Found at i:2471 original size:13 final size:13
Alignment explanation
Indices: 2453--2490 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
2443 GAGGATAATA
2453 ATAATAGGAATTT
1 ATAATAGGAATTT
*
2466 ATAATAGG-A-TA
1 ATAATAGGAATTT
2477 ATAATAGGAATTT
1 ATAATAGGAATTT
2490 A
1 A
2491 CATTTATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (13 bp):
ATAATAGGAATTT
Found at i:5692 original size:48 final size:48
Alignment explanation
Indices: 5503--5973 Score: 612
Period size: 48 Copynumber: 9.9 Consensus size: 48
5493 TCAAATGCTT
* * * *
5503 TTCAGTGTTTCTTTCCTGTTTT-CACCTTCCCGGTCGGAAGGTTCCGTC
1 TTCAGTGTCTATTTCCAGTTTTGC-CCTTCCCGGTCGGAAGGTGCCGTC
*
5551 TTCAGTGTCTATTTCCAGTTTTG-CCTTCCTGGTCGGAAGGTGCCGTC
1 TTCAGTGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCCGTC
*
5598 TTCAGTGTCTATTTCCAGTTTTG-CCTTCCCAGTCGGAAGGTGCCGTC
1 TTCAGTGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCCGTC
*
5645 TTCAGTGACTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCCGTC
1 TTCAGTGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCCGTC
* * *
5693 TTCAGTGTCTATTTCCAGATTTGCCCTTCCTGGTCGGAAGGTGCAGTC
1 TTCAGTGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCCGTC
** * * * * *
5741 TTTGGCGAT-TATTTCCAGTTATGCCCTTCCCGGTCGGAGGGTGCAGTT
1 TTCAGTG-TCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCCGTC
* * * **
5789 TTCGGTGTTTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTACAATC
1 TTCAGTGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCCGTC
* *
5837 TTCAGTGTCTCTTTCCAGTTTTGCCCTTCCCAGTTC-GAAGGTGCCGTC
1 TTCAGTGTCTATTTCCAGTTTTGCCCTTCCC-GGTCGGAAGGTGCCGTC
* * *
5885 TTCAGTGTCTATTTCGAGATTTGCCCTTCCCGGTCGGAAGGTGCAGTC
1 TTCAGTGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCCGTC
*
5933 TTCAGTGTCTCA-TTCCTGTTTTGCCCTTCCCGGTCGGAAGG
1 TTCAGTGTCT-ATTTCCAGTTTTGCCCTTCCCGGTCGGAAGG
5974 CGCTAGATTT
Statistics
Matches: 373, Mismatches: 43, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
47 93 0.25
48 275 0.74
49 5 0.01
ACGTcount: A:0.12, C:0.27, G:0.24, T:0.37
Consensus pattern (48 bp):
TTCAGTGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCCGTC
Found at i:10259 original size:30 final size:29
Alignment explanation
Indices: 10223--10279 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
10213 TCTCCATAGC
10223 CATCTTTAAGTCCATGATAAGACCTTGGCA
1 CATCTTTAAGTCCATGATAAG-CCTTGGCA
***
10253 CATCTTTCCTTCCATGATAAGCCTTGG
1 CATCTTTAAGTCCATGATAAGCCTTGG
10280 GAGCATCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (29 bp):
CATCTTTAAGTCCATGATAAGCCTTGGCA
Found at i:11244 original size:22 final size:22
Alignment explanation
Indices: 11214--11255 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
11204 TTTTCCCGCA
*
11214 ACAACTTCTGTCCCGAAGTTGT
1 ACAACTTCTGACCCGAAGTTGT
* *
11236 ACAAGTTCTGAGCCGAAGTT
1 ACAACTTCTGACCCGAAGTT
11256 ATCCTGCGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (22 bp):
ACAACTTCTGACCCGAAGTTGT
Found at i:11292 original size:52 final size:52
Alignment explanation
Indices: 11210--11313 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
11200 AGGTTTTTCC
* *
11210 CGCAACAACTTCTGTCCCGAAGTTGTACAAGTTCTGAGCCGAAGTTATCCTG
1 CGCAACAACTTCTATCCCGAAGTTGAACAAGTTCTGAGCCGAAGTTATCCTG
* *
11262 CGCAACAACTTCTATCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
1 CGCAACAACTTCTATCCCGAAGTTGAACAAGTTCTGAGCCGAAGTTATCCTG
11314 AAATTCTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (52 bp):
CGCAACAACTTCTATCCCGAAGTTGAACAAGTTCTGAGCCGAAGTTATCCTG
Found at i:11374 original size:22 final size:22
Alignment explanation
Indices: 11339--11384 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
11329 TTTCAACAGG
*
11339 CCAAGTCCTAGGCAGAAGTTGT
1 CCAAGTCCTAGGCAGAACTTGT
* *
11361 CCAAGTTCTGGGCAGAACTTGT
1 CCAAGTCCTAGGCAGAACTTGT
11383 CC
1 CC
11385 TGAATTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (22 bp):
CCAAGTCCTAGGCAGAACTTGT
Found at i:13136 original size:15 final size:16
Alignment explanation
Indices: 13108--13138 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
13098 GAGTGTGAAC
13108 AAAGCAATTTAAATTA
1 AAAGCAATTTAAATTA
13124 AAAGCAA-TTAAATTA
1 AAAGCAATTTAAATTA
13139 TAAAAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAGCAATTTAAATTA
Found at i:14323 original size:17 final size:16
Alignment explanation
Indices: 14275--14325 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
14265 CATGTAATCT
* *
14275 TTGATCACCAATGATC
1 TTGATCACTAGTGATC
14291 TTGCATCACT-GCTGATC
1 TTG-ATCACTAG-TGATC
14308 TTAGATCACTAGTGATC
1 TT-GATCACTAGTGATC
14325 T
1 T
14326 AGGGGGAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 3 0.10
17 24 0.83
18 2 0.07
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (16 bp):
TTGATCACTAGTGATC
Found at i:18770 original size:44 final size:44
Alignment explanation
Indices: 18715--18880 Score: 253
Period size: 44 Copynumber: 3.7 Consensus size: 44
18705 AGAGATTCCA
18715 AGACACAGATTGAAAAACAAAAAACCCTAGCCACTTTTCCATAC
1 AGACACAGATTGAAAAACAAAAAACCCTAGCCACTTTTCCATAC
*
18759 AGACACAGATTGAAAAACAAAAAACCCTAGCCATTTTTCCATAC
1 AGACACAGATTGAAAAACAAAAAACCCTAGCCACTTTTCCATAC
*
18803 AGACACAGATGGAAAAACAAAAAACCCTAGCCACTTTTCCATAC
1 AGACACAGATTGAAAAACAAAAAACCCTAGCCACTTTTCCATAC
*
18847 A-AGCAGAGATTCGAAAAAACGAAAAAAACCCTAG
1 AGA-CACAGATT-G-AAAAAC--AAAAAACCCTAG
18881 TTTACAGTTT
Statistics
Matches: 112, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
43 1 0.01
44 92 0.82
45 1 0.01
46 6 0.05
48 12 0.11
ACGTcount: A:0.48, C:0.25, G:0.11, T:0.16
Consensus pattern (44 bp):
AGACACAGATTGAAAAACAAAAAACCCTAGCCACTTTTCCATAC
Found at i:20845 original size:36 final size:34
Alignment explanation
Indices: 20794--20964 Score: 186
Period size: 36 Copynumber: 4.9 Consensus size: 34
20784 TGAATCAGTA
* *
20794 ATAAGCAACTTAATTCAGGGTGATTAAGTGAGTC
1 ATAATCAACTTAATTCAGGGTAATTAAGTGAGTC
*
20828 GATAATCAACTTTAATTCAGGGTAATTAAGTGAATC
1 -ATAATCAAC-TTAATTCAGGGTAATTAAGTGAGTC
* *
20864 AGTAATCAATTTTAATTCAGGGTAATTAAGTGAGTT
1 A-TAATCAA-CTTAATTCAGGGTAATTAAGTGAGTC
*
20900 AAAGAGT-AACTTAATTCAGGGTAATTAAGT-AGTTC
1 ATA-A-TCAACTTAATTCAGGGTAATTAAGTGAG-TC
20935 AATAAGT-AACTTAATTCAGGGTAATTAAGT
1 -ATAA-TCAACTTAATTCAGGGTAATTAAGT
20965 TTAGTAAGAA
Statistics
Matches: 119, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
34 2 0.02
35 57 0.48
36 59 0.50
37 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (34 bp):
ATAATCAACTTAATTCAGGGTAATTAAGTGAGTC
Found at i:20888 original size:20 final size:19
Alignment explanation
Indices: 20830--20889 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
20820 AGTGAGTCGA
20830 TAATCAACTTTAATTCAGGG
1 TAATCAA-TTTAATTCAGGG
* * *
20850 TAATTAAGTGAA-TCA--G
1 TAATCAATTTAATTCAGGG
20866 TAATCAATTTTAATTCAGGG
1 TAATCAA-TTTAATTCAGGG
20886 TAAT
1 TAAT
20890 TAAGTGAGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
16 7 0.23
17 3 0.10
18 6 0.20
19 3 0.10
20 11 0.37
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
TAATCAATTTAATTCAGGG
Found at i:23902 original size:881 final size:883
Alignment explanation
Indices: 22199--24033 Score: 3404
Period size: 881 Copynumber: 2.1 Consensus size: 883
22189 TATCTGCAAT
22199 AATGGTTGATTCATGGGTAAACTATTGATATTCCAATTCTGTTTTCCTTTCGTCTTCATTACTAT
1 AATGGTTGATTCATGGGTAAACTATTGATATTCCAATTCTGTTTTCCTTTCGTCTTCATTACTAT
* *
22264 TTGGGTGGGTTTCTTCTTCCCTAACATTTCTCTGAATTGGTTTCACATGGACTCCGTTCTGTTTC
66 TTGGGTGGGTTTCTTCTTCCCTAACATTTCTCTGAACTGATTTCACATGGACTCCGTTCTGTTTC
22329 CTAAAATTTCCAGGTGGACGTTGATAAGATCCTTCCATTTAATTTAGCAGCGCCTTAAGATGGCA
131 CTAAAATTTCCAGGTGGACGTTGATAAGATCCTTCCATTTAATTTAGCAGCGCCTTAAGATGGCA
22394 TAACCTAAAGTGGGGAGCTTTCATTTCTTAACTCAACATTTTGAGGTAAATCAGGATTTATTTGT
196 TAACCTAAAGTGGGGAGCTTTCATTTCTTAACTCAACATTTTGAGGTAAATCAGGATTTATTTGT
22459 TGATTATATTATTTGATACTTAAATTTAACATTTCCTTATTTCTCTTTTATTTTACAAAAAAAAA
261 TGATTATATTATTTGATACTTAAATTTAACATTTCCTTATTTCTCTTTTATTTTACAAAAAAAAA
* *
22524 TATTTATCATTTGACTTCCTTTTTATTGAGGTTTCTATTAGTTGCTTATGTTTAGTATATTTCCA
326 TATTTATCATTCGACTTCCTTTTTATTGAGGTTTCTATTAGTTGCTTAGGTTTAGTATATTTCCA
* *
22589 CATTTCCAAAAGCACGGTTAACCAATGCTAAGTATAATCATTTTGTGATGCATTGTGTAAATTAC
391 CATCTCCAAAAGCACGGTTAACCAATGCTAAGTATAATCATTTTGTGATGCATTGCGTAAATTAC
*
22654 ATATGCTCCTGCAAATCCTCTCATCTAATTCAATTTTCATACGACAACTATAAATGCTCCTTGAC
456 ATATGCTCCTGCAAATCCTCTCAACTAATTCAATTTTCATACGACAACTATAAATGCTCCTTGAC
* *
22719 TACAAAAAATTAGGCCTTCCTTATGCAGAAGCCAAATTCTTCCACCTACCCGAGTTCATTAATTT
521 TACAAAAAATTAGGCCTTCCTTATCCAGAAGCCAAATTCTTCCACCTACCCAAGTTCATTAATTT
*
22784 AACAATTGCAATGAAGATTAAAAAATGATCACAGCGTACTATGTTTTTTTAGATAATCAACATAC
586 AACAATTGCAATCAAGATTAAAAAATGATCACAGCGTACTATGTTTTTTTAGATAATCAACATAC
*
22849 ATTTCAAACAACAATTAGTATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGGAGTAGAATA
651 ATTTCAAACAACAATTAATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGGAGTAGAATA
* *
22914 TTAGCTTTATTTTGATGGAATTACCTATAGATGGAGTACAATTTAGGTAATGCACTTTTAAAATG
716 TTAGCTTTATTTTGATGGAATTACCTATAGACGGAGCACAATTTAGGTAATGCACTTTTAAAATG
* *
22979 AAAGAGAGGTCATGAGTTTTTCTTTTATATATGCGAATTATTTGTTTGGATGTATGGGTTTCTCC
781 AAAGAGAGATCATGAGTTTTGCTTTTATATATGCGAATTATTTGTTTGGATGTATGGGTTTCTCC
23044 TAACTGATTAACTT-TAAAATGGTTAACTTGCTTTTAA
846 TAACTGATTAACTTATAAAATGGTTAACTTGCTTTTAA
* *
23081 AATGGTTGATTCATGGGTAAACTATTGGTATTCCAATTCTGTTTTCCTTTCGTCTTCATTTCTAT
1 AATGGTTGATTCATGGGTAAACTATTGATATTCCAATTCTGTTTTCCTTTCGTCTTCATTACTAT
* *
23146 TTGGGTGGGTTTTTTCTTCCCTAACATTTCTCTGAACTGATTTCACATGGACTCTGTTCTGTTTC
66 TTGGGTGGGTTTCTTCTTCCCTAACATTTCTCTGAACTGATTTCACATGGACTCCGTTCTGTTTC
*
23211 CTAAAATTTCCAGGTGGACGTTGATAAGATCCTTCCATTTAATTTAGCAGCGCCTTAGGATGGCA
131 CTAAAATTTCCAGGTGGACGTTGATAAGATCCTTCCATTTAATTTAGCAGCGCCTTAAGATGGCA
* *
23276 TAACCTAAAGTGGGGAGCTTTCATTTCTTAACTCATCATTTTGAGGTAAATCTGGATTTATTTGT
196 TAACCTAAAGTGGGGAGCTTTCATTTCTTAACTCAACATTTTGAGGTAAATCAGGATTTATTTGT
*
23341 TGATTATATTTTTTGATACTTAAATTTAACATTTCCTTATTTCTCTTTTATTTTAC-AAAAAAAA
261 TGATTATATTATTTGATACTTAAATTTAACATTTCCTTATTTCTCTTTTATTTTACAAAAAAAAA
23405 TATTTATCATTCGACTTCCTTTTTATTGAGGTTTCTATTAGTTGCTTAGGTTTAGTATATTTCCA
326 TATTTATCATTCGACTTCCTTTTTATTGAGGTTTCTATTAGTTGCTTAGGTTTAGTATATTTCCA
23470 CATCTCCAAAAGCACGGTTAACCAATGCTAAGTATAATCATTTTGTGATGCATTGCGTAAATTAC
391 CATCTCCAAAAGCACGGTTAACCAATGCTAAGTATAATCATTTTGTGATGCATTGCGTAAATTAC
23535 ATATGCTCCTGCAAATCCTCTCAACTAATTCAATTTTCATACGACAACTATAAATGCTCCTTGAC
456 ATATGCTCCTGCAAATCCTCTCAACTAATTCAATTTTCATACGACAACTATAAATGCTCCTTGAC
23600 TACAAAAAATTAGGCCTTCCTTATCCAGAAGCCAAATTCTTCCACCTACCCAAGTTCATTAATTT
521 TACAAAAAATTAGGCCTTCCTTATCCAGAAGCCAAATTCTTCCACCTACCCAAGTTCATTAATTT
23665 AACAATTGCAATCAAGATTAAAAAATGATCACAGCGTACTATGTTTTTTTAGATAATCAACATAC
586 AACAATTGCAATCAAGATTAAAAAATGATCACAGCGTACTATGTTTTTTTAGATAATCAACATAC
*
23730 ATTTCAAACAACAATTAATATTAGTTTTATTTTGATGAATTATCTAGAGATGGAGGAGTAGAATA
651 ATTTCAAACAACAATTAATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGGAGTAGAATA
* *
23795 TTAGCTTTATTTTGATGGAATTACCTATAGACGGAGCAGAATTTAGGTAATGTACTTTTAAAATG
716 TTAGCTTTATTTTGATGGAATTACCTATAGACGGAGCACAATTTAGGTAATGCACTTTTAAAATG
*
23860 AAAGAGAGATCATGCGTTTTGCTTTTATATATGCGAATTATTTGTTTGGATGTATGGGTTTCTCC
781 AAAGAGAGATCATGAGTTTTGCTTTTATATATGCGAATTATTTGTTTGGATGTATGGGTTTCTCC
23925 TAACTGATTAACTTATAAAATGGTTAACTTGCTTTTAA
846 TAACTGATTAACTTATAAAATGGTTAACTTGCTTTTAA
*
23963 AATGGTTGATTCATGGGTAAACTATTGATATTCCAATTCTGTTTTCCTTTCGTCTTCATTCCTAT
1 AATGGTTGATTCATGGGTAAACTATTGATATTCCAATTCTGTTTTCCTTTCGTCTTCATTACTAT
24028 TTGGGT
66 TTGGGT
24034 TGGTGTAGAC
Statistics
Matches: 923, Mismatches: 29, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
881 525 0.57
882 398 0.43
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (883 bp):
AATGGTTGATTCATGGGTAAACTATTGATATTCCAATTCTGTTTTCCTTTCGTCTTCATTACTAT
TTGGGTGGGTTTCTTCTTCCCTAACATTTCTCTGAACTGATTTCACATGGACTCCGTTCTGTTTC
CTAAAATTTCCAGGTGGACGTTGATAAGATCCTTCCATTTAATTTAGCAGCGCCTTAAGATGGCA
TAACCTAAAGTGGGGAGCTTTCATTTCTTAACTCAACATTTTGAGGTAAATCAGGATTTATTTGT
TGATTATATTATTTGATACTTAAATTTAACATTTCCTTATTTCTCTTTTATTTTACAAAAAAAAA
TATTTATCATTCGACTTCCTTTTTATTGAGGTTTCTATTAGTTGCTTAGGTTTAGTATATTTCCA
CATCTCCAAAAGCACGGTTAACCAATGCTAAGTATAATCATTTTGTGATGCATTGCGTAAATTAC
ATATGCTCCTGCAAATCCTCTCAACTAATTCAATTTTCATACGACAACTATAAATGCTCCTTGAC
TACAAAAAATTAGGCCTTCCTTATCCAGAAGCCAAATTCTTCCACCTACCCAAGTTCATTAATTT
AACAATTGCAATCAAGATTAAAAAATGATCACAGCGTACTATGTTTTTTTAGATAATCAACATAC
ATTTCAAACAACAATTAATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGGAGTAGAATA
TTAGCTTTATTTTGATGGAATTACCTATAGACGGAGCACAATTTAGGTAATGCACTTTTAAAATG
AAAGAGAGATCATGAGTTTTGCTTTTATATATGCGAATTATTTGTTTGGATGTATGGGTTTCTCC
TAACTGATTAACTTATAAAATGGTTAACTTGCTTTTAA
Found at i:26685 original size:23 final size:24
Alignment explanation
Indices: 26649--26701 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
26639 TTTACTCTTC
*
26649 AATAAATTAATAAAAGATAAAA-A
1 AATAAATTAATAAAAAATAAAATA
26672 AATAAA-TAATTAAAAAATAAAATA
1 AATAAATTAA-TAAAAAATAAAATA
26696 AATAAA
1 AATAAA
26702 AAAGAGAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 3 0.11
23 17 0.63
24 7 0.26
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (24 bp):
AATAAATTAATAAAAAATAAAATA
Found at i:26687 original size:16 final size:17
Alignment explanation
Indices: 26665--26704 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
26655 TTAATAAAAG
26665 ATAAAAAAAT-AAAT-A
1 ATAAAAAAATAAAATAA
*
26680 ATTAAAAAATAAAATAA
1 ATAAAAAAATAAAATAA
26697 ATAAAAAA
1 ATAAAAAA
26705 GAGAGGAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 9 0.43
16 4 0.19
17 8 0.38
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (17 bp):
ATAAAAAAATAAAATAA
Found at i:26703 original size:15 final size:15
Alignment explanation
Indices: 26668--26704 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
26658 ATAAAAGATA
*
26668 AAAAAATAAATAATT
1 AAAAAATAAATAAAT
26683 AAAAAATAAAATAAAT
1 AAAAAAT-AAATAAAT
26699 AAAAAA
1 AAAAAA
26705 GAGAGGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAAAATAAATAAAT
Found at i:27338 original size:49 final size:49
Alignment explanation
Indices: 27217--27642 Score: 542
Period size: 49 Copynumber: 8.7 Consensus size: 49
27207 TCAAATCCCA
27217 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTG
1 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTG
*
27266 -TATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCCG
1 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTG
* *
27314 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGAGTTTACTTG
1 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTG
*
27363 TT-TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGCTTTTACCTG
1 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTG
* *
27411 TTATTTCCCAAACTGCCCTTCCCGGACGGAAGGCATTTGCTTTTAGCC-G
1 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTA-CCTG
* * * * *
27460 TTATTTCCCAAAATGCTCTTCCCAGATGAAAGGTATTTGATTTTACCTG
1 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTG
* * *
27509 TT-TTTCCCAAAATGCCCTTCCCGGACGGGAGGCACTT-ATTTTACTTGCTA
1 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTAC---CTG
* * * * ** **
27559 TTTTTTTCAAAAATGCCCTTCCCGGACGGAAGACGCTT-ATTTTTACTCAC
1 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGA-TTTTAC-CTG
*
27609 TT-TTTCCCAAAGTGCCCTTCCCGGACGGAAGGCA
1 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCA
27643 CTAATTTCCA
Statistics
Matches: 332, Mismatches: 36, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
47 7 0.02
48 122 0.37
49 157 0.47
50 9 0.03
51 31 0.09
52 6 0.02
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (49 bp):
TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTG
Found at i:27383 original size:97 final size:97
Alignment explanation
Indices: 27217--27690 Score: 539
Period size: 97 Copynumber: 4.8 Consensus size: 97
27207 TCAAATCCCA
* *
27217 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTATTTCCCAAAATGCC
1 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACTTGTTTTTCCCAAAATGCC
27282 CTTCCCGGACGGAAGGCATTTGATTTTACCCG
66 CTTCCCGGACGGAAGGCATTTGATTTTACCCG
*
27314 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGAGTTTACTTGTTTTTCCCAAAATGCC
1 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACTTGTTTTTCCCAAAATGCC
* *
27379 CTTCCCGGACGGAAGGCATTTGCTTTTACCTG
66 CTTCCCGGACGGAAGGCATTTGATTTTACCCG
* * *
27411 TTATTTCCCAAACTGCCCTTCCCGGACGGAAGGCATTTGCTTTTAGC-CGTTATTTCCCAAAATG
1 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTA-CTTGTT-TTTCCCAAAATG
* * * * * *
27475 CTCTTCCCAGATGAAAGGTATTTGATTTTACCTG
64 CCCTTCCCGGACGGAAGGCATTTGATTTTACCCG
* * * *
27509 TT-TTTCCCAAAATGCCCTTCCCGGACGGGAGGCACTT-ATTTTACTTGCTATTTTTTTCAAAAA
1 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACTTG----TTTTTCCCAAAA
* **
27572 TGCCCTTCCCGGACGGAAGACGCTT-ATTTTTACTCAC-
62 TGCCCTTCCCGGACGGAAGGCATTTGA-TTTTAC-C-CG
* * * * * **
27609 TT-TTTCCCAAAGTGCCCTTCCCGGACGGAAGGCA-CTAATTTCCACTTGCTTTTTCCTAAAACA
1 TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTT-TACTTG-TTTTTCCCAAAATG
*
27672 CCCTTCCCGGATGGAAGGC
64 CCCTTCCCGGACGGAAGGC
27691 GCTAGTTTTA
Statistics
Matches: 323, Mismatches: 42, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
95 1 0.00
96 6 0.02
97 169 0.52
98 71 0.22
99 32 0.10
100 39 0.12
101 5 0.02
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (97 bp):
TTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACTTGTTTTTCCCAAAATGCC
CTTCCCGGACGGAAGGCATTTGATTTTACCCG
Found at i:27661 original size:49 final size:48
Alignment explanation
Indices: 27220--27732 Score: 471
Period size: 49 Copynumber: 10.5 Consensus size: 48
27210 AATCCCATTA
* * *
27220 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCTGTA
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACTTGTT
* **
27268 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACCCGTT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACTTGTT
* *
27316 ATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGAGTTTACTTGTT
1 -TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACTTGTT
* * *
27365 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGCTTTTACCTGTT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACTTGTT
* * * *
27413 ATTTCCCAAACTGCCCTTCCCGGACGGAAGGCATTTGCTTTTAGC-CGTT
1 -TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTA-CTTGTT
* * * * * * *
27462 ATTTCCCAAAATGCTCTTCCCAGATGAAAGGTATTTGATTTTACCTGTT
1 -TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACTTGTT
* *
27511 TTTCCCAAAATGCCCTTCCCGGACGGGAGGCA-CTTATTTTACTTGCTATTT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACTTG----TT
* * * * * **
27562 TTTTCAAAAATGCCCTTCCCGGACGGAAGAC-GCTTATTTTTACTCACTT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGA-TTTTACT-TGTT
* * *
27611 TTTCCCAAAGTGCCCTTCCCGGACGGAAGGCA-CTAATTTCCACTTGCTT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTT-TACTTG-TT
* ** * * *
27660 TTTCCTAAAACACCCTTCCCGGATGGAAGGC-GCT-AGTTTTACTCGCTT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGA-TTTTACTTG-TT
** *
27708 TTTCTTAAAATGCCCTTTCCGGACG
1 TTTCCCAAAATGCCCTTCCCGGACG
27733 AACGACAAGT
Statistics
Matches: 396, Mismatches: 53, Indels: 32
0.82 0.11 0.07
Matches are distributed among these distances:
47 10 0.03
48 149 0.38
49 196 0.49
50 1 0.00
51 33 0.08
52 7 0.02
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (48 bp):
TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATCTGATTTTACTTGTT
Found at i:28791 original size:45 final size:43
Alignment explanation
Indices: 28727--28821 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 43
28717 AACAACAATT
*
28727 AATATTAGCTTTATTTTGAT-GAATTATCTAGAGATTGAGGAGTAG
1 AATATTAGCTTTATTTTGATGGAATTACCTAGAGA-T--GGAGTAG
*
28772 AATATTAGCTTTATTTTGATGGAATTACCTATAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGGAATTACCTAGAGATGGAGTAG
28815 AAT-TTAG
1 AATATTAG
28822 GTAATGAACT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
42 4 0.09
43 10 0.21
45 21 0.45
46 12 0.26
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (43 bp):
AATATTAGCTTTATTTTGATGGAATTACCTAGAGATGGAGTAG
Found at i:32826 original size:110 final size:109
Alignment explanation
Indices: 32627--32837 Score: 354
Period size: 110 Copynumber: 1.9 Consensus size: 109
32617 ATGTAACTTT
32627 TAAAATGATAAGTTAGAATTTTTAAAAACACAACAAATAGATTTCTTTAACTACAAAAACATTTC
1 TAAAATGATAAGTTAGAATTTTTAAAAACACAACAAATAGATTTCTTTAACTACAAAAACATTTC
32692 TCGGTCATATCATTTCTTTATCCAATTTCTCCTCTTTTCATTCC
66 TCGGTCATATCATTTCTTTATCCAATTTCTCCTCTTTTCATTCC
* *
32736 TAAAATGATAAGTTA-AATTTTTTAAAAACGCAACAAATCGATTTCCTTTAACTA-AAAACACAT
1 TAAAATGATAAGTTAGAA-TTTTTAAAAACACAACAAATAGATTT-CTTTAACTACAAAA-ACAT
*
32799 TTCTTGGTCATATCATTTCTTTATCCAATTTCTCCTCTT
63 TTCTCGGTCATATCATTTCTTTATCCAATTTCTCCTCTT
32838 CAAATACAAT
Statistics
Matches: 96, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
108 2 0.02
109 43 0.45
110 51 0.53
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.40
Consensus pattern (109 bp):
TAAAATGATAAGTTAGAATTTTTAAAAACACAACAAATAGATTTCTTTAACTACAAAAACATTTC
TCGGTCATATCATTTCTTTATCCAATTTCTCCTCTTTTCATTCC
Found at i:33671 original size:21 final size:21
Alignment explanation
Indices: 33628--33671 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
33618 ACAAAGGGGG
* * *
33628 TTGCTAAATACTGTCCTAGTT
1 TTGCTAAATACCGCCCCAGTT
*
33649 TTGCTAAATACCGCCCCATTT
1 TTGCTAAATACCGCCCCAGTT
33670 TT
1 TT
33672 TACACTTTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.41
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCAGTT
Found at i:33763 original size:33 final size:33
Alignment explanation
Indices: 33721--33791 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
33711 TACACTGAGG
33721 CTCCCCACTAGGACGG-TTCAGCCACGGCGGAGC
1 CTCCCCACTAGGACGGCTTCA-CCACGGCGGAGC
* * **
33754 CTCCCCACTAGGGCGGCTTCACCATGGTTGAGC
1 CTCCCCACTAGGACGGCTTCACCACGGCGGAGC
33787 CTCCC
1 CTCCC
33792 AAGTGGGGCG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 29 0.88
34 4 0.12
ACGTcount: A:0.15, C:0.41, G:0.27, T:0.17
Consensus pattern (33 bp):
CTCCCCACTAGGACGGCTTCACCACGGCGGAGC
Found at i:35668 original size:15 final size:15
Alignment explanation
Indices: 35650--35679 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35640 TTACTTTTGC
*
35650 TACTTTTATCATTTT
1 TACTTTTACCATTTT
35665 TACTTTTACCATTTT
1 TACTTTTACCATTTT
35680 CCTTACTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:35776 original size:42 final size:42
Alignment explanation
Indices: 35730--35809 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
35720 CTCTTACTGG
*
35730 ATACCATT-TTTGAC-CGTTTTGCTTAACACCATTTTTTAATTA
1 ATACCATTCTTT-ACTC-TTTTACTTAACACCATTTTTTAATTA
*
35772 ATACCATTCTTTACTCTTTTACTTAATACCATTTTTTA
1 ATACCATTCTTTACTCTTTTACTTAACACCATTTTTTA
35810 CTCTACACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
42 30 0.88
43 4 0.12
ACGTcount: A:0.26, C:0.20, G:0.04, T:0.50
Consensus pattern (42 bp):
ATACCATTCTTTACTCTTTTACTTAACACCATTTTTTAATTA
Found at i:35797 original size:25 final size:25
Alignment explanation
Indices: 35763--35813 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
35753 TAACACCATT
35763 TTTTAATTAATACCATTCTTTACTC
1 TTTTAATTAATACCATTCTTTACTC
* *
35788 TTTTACTTAATACCATTTTTTACTC
1 TTTTAATTAATACCATTCTTTACTC
35813 T
1 T
35814 ACACCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTTAATTAATACCATTCTTTACTC
Found at i:35820 original size:42 final size:43
Alignment explanation
Indices: 35738--35847 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 43
35728 GGATACCATT
* * *
35738 TTTGACCGTTTTGCTTAACACCATTTTTTAATTAATACCA-TTC
1 TTTGACC-TTTTACTTAATACCATTTTTTAATTAACACCATTTC
* *
35781 TTT-ACTCTTTTACTTAATACCATTTTTTACTCT-ACACCATTTT
1 TTTGAC-CTTTTACTTAATACCATTTTTTAAT-TAACACCATTTC
*
35824 TTTGACCTTCTTACTCAATACCAT
1 TTTGACCTT-TTACTTAATACCAT
35848 ATTTCACTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
42 28 0.50
43 13 0.23
44 15 0.27
ACGTcount: A:0.25, C:0.24, G:0.04, T:0.48
Consensus pattern (43 bp):
TTTGACCTTTTACTTAATACCATTTTTTAATTAACACCATTTC
Found at i:35864 original size:44 final size:42
Alignment explanation
Indices: 35774--35880 Score: 112
Period size: 44 Copynumber: 2.5 Consensus size: 42
35764 TTTAATTAAT
* * *
35774 ACCATTCTTT-ACTCTT-TTACTTAATACCATTTTTTACTCTAC
1 ACCATT-TTTGAC-CTTCTTACTCAATACCATATTTCACTCTAC
*
35816 ACCATTTTTTTGACCTTCTTACTCAATACCATATTTCACT-TGAT
1 ACCA--TTTTTGACCTTCTTACTCAATACCATATTTCACTCT-AC
35860 ACCATTTTTGACCTTCTTACT
1 ACCATTTTTGACCTTCTTACT
35881 GATTACTTCT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
42 21 0.38
43 7 0.12
44 28 0.50
ACGTcount: A:0.23, C:0.26, G:0.03, T:0.48
Consensus pattern (42 bp):
ACCATTTTTGACCTTCTTACTCAATACCATATTTCACTCTAC
Found at i:35891 original size:14 final size:14
Alignment explanation
Indices: 35872--35908 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
35862 CATTTTTGAC
35872 CTTCTTACTGATTA
1 CTTCTTACTGATTA
35886 CTTCTTACTGATTA
1 CTTCTTACTGATTA
*
35900 CTTTTTACT
1 CTTCTTACT
35909 ACTCTTTGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.19, C:0.22, G:0.05, T:0.54
Consensus pattern (14 bp):
CTTCTTACTGATTA
Found at i:35940 original size:14 final size:14
Alignment explanation
Indices: 35923--35958 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
35913 TTTGCCATTT
*
35923 TTACTTTTTACTTA
1 TTACTTTTTACTGA
*
35937 TTACTCTTTACTGA
1 TTACTTTTTACTGA
35951 TTACTTTT
1 TTACTTTT
35959 ACCTTTTTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.19, C:0.17, G:0.03, T:0.61
Consensus pattern (14 bp):
TTACTTTTTACTGA
Found at i:36257 original size:38 final size:38
Alignment explanation
Indices: 36213--36334 Score: 208
Period size: 38 Copynumber: 3.2 Consensus size: 38
36203 TTTTTAGCTC
*
36213 GACTCTTGATTATCAATTTTACTGATTATTCTTACTTT
1 GACTCTTAATTATCAATTTTACTGATTATTCTTACTTT
* *
36251 GACTCTTAATTATCAATTTTACTGATTACTATTACTTT
1 GACTCTTAATTATCAATTTTACTGATTATTCTTACTTT
36289 GACTCTTAATTATCAATTTTACTGATTATTCTTACTTT
1 GACTCTTAATTATCAATTTTACTGATTATTCTTACTTT
*
36327 GATTCTTA
1 GACTCTTA
36335 CTGTTAATTA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 78 1.00
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.52
Consensus pattern (38 bp):
GACTCTTAATTATCAATTTTACTGATTATTCTTACTTT
Found at i:37184 original size:51 final size:50
Alignment explanation
Indices: 37108--37215 Score: 171
Period size: 51 Copynumber: 2.1 Consensus size: 50
37098 AATATTCAAC
* * *
37108 TTTTATTGTTTAAAATTACTAAACTCAACTCTTACTACATAAAGATTTAAT
1 TTTTA-TGATTAAAATCACTAAACTCAACCCTTACTACATAAAGATTTAAT
37159 TTTTATGATTAAAATCACTAGAACTCAACCCTTACTACATAAAGATTTAAT
1 TTTTATGATTAAAATCACTA-AACTCAACCCTTACTACATAAAGATTTAAT
37210 TTTTAT
1 TTTTAT
37216 TTGCCAAAGA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
50 13 0.25
51 40 0.75
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.42
Consensus pattern (50 bp):
TTTTATGATTAAAATCACTAAACTCAACCCTTACTACATAAAGATTTAAT
Found at i:40349 original size:27 final size:27
Alignment explanation
Indices: 40270--40338 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
40260 GTGAACTTAA
* *
40270 AAAAATGACTAAAATGCCCCTGAGTGC
1 AAAAATGACAAAAATGCCCCTGGGTGC
* *
40297 AATAATGACCAAAATGCCCCTGGGTGC
1 AAAAATGACAAAAATGCCCCTGGGTGC
40324 AAAAATGACAAAAAT
1 AAAAATGACAAAAAT
40339 ATCCTTGGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.17
Consensus pattern (27 bp):
AAAAATGACAAAAATGCCCCTGGGTGC
Found at i:53077 original size:42 final size:42
Alignment explanation
Indices: 53030--53109 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
53020 CTCTTACTGG
*
53030 ATACCATT-TTTGAC-CGTTTTGCTTAACACCAATTTTTAATTA
1 ATACCATTCTTT-ACTC-TTTTACTTAACACCAATTTTTAATTA
* *
53072 ATACCATTCTTTACTCTTTTACTTAATACCATTTTTTA
1 ATACCATTCTTTACTCTTTTACTTAACACCAATTTTTA
53110 CTCTACACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
42 29 0.88
43 4 0.12
ACGTcount: A:0.28, C:0.20, G:0.04, T:0.49
Consensus pattern (42 bp):
ATACCATTCTTTACTCTTTTACTTAACACCAATTTTTAATTA
Found at i:53092 original size:25 final size:25
Alignment explanation
Indices: 53063--53113 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
53053 TAACACCAAT
53063 TTTTAATTAATACCATTCTTTACTC
1 TTTTAATTAATACCATTCTTTACTC
* *
53088 TTTTACTTAATACCATTTTTTACTC
1 TTTTAATTAATACCATTCTTTACTC
53113 T
1 T
53114 ACACCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTTAATTAATACCATTCTTTACTC
Found at i:53146 original size:44 final size:42
Alignment explanation
Indices: 53074--53180 Score: 112
Period size: 44 Copynumber: 2.5 Consensus size: 42
53064 TTTAATTAAT
* * *
53074 ACCATTCTTT-ACTCTT-TTACTTAATACCATTTTTTACTCT-AC
1 ACCATT-TTTGAC-CTTCTTACTCAATACCATATTTCACT-TGAC
*
53116 ACCATTTTTTTGACCTTCTTACTCAATACCATATTTCACTTGAT
1 ACCA--TTTTTGACCTTCTTACTCAATACCATATTTCACTTGAC
53160 ACCATTTTTGACCTTCTTACT
1 ACCATTTTTGACCTTCTTACT
53181 GATTACTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
42 21 0.38
43 7 0.12
44 28 0.50
ACGTcount: A:0.23, C:0.26, G:0.03, T:0.48
Consensus pattern (42 bp):
ACCATTTTTGACCTTCTTACTCAATACCATATTTCACTTGAC
Found at i:53536 original size:38 final size:38
Alignment explanation
Indices: 53416--53601 Score: 211
Period size: 38 Copynumber: 4.9 Consensus size: 38
53406 TACTCTCTCC
* * *
53416 CTTAAGTATCAA-TTTACTGATTAATC---CCTTGACT
1 CTTAATTATCAATTTTACTGATTATTCTTACTTTGACT
** * * *
53450 CTTAATTATTGA-TTTACTGATTACTATTTTTACCTCGACT
1 CTTAATTATCAATTTTACTGA-T--TATTCTTACTTTGACT
*
53490 CTTGATTATCAATTTTACTGATTATTCTTACTTTGACT
1 CTTAATTATCAATTTTACTGATTATTCTTACTTTGACT
* *
53528 CTTAATTATCAATTTTACTGATTACTATTACTTTGACT
1 CTTAATTATCAATTTTACTGATTATTCTTACTTTGACT
53566 CTTAATTATCAATTTTACTGATTATTCTTACTTTGA
1 CTTAATTATCAATTTTACTGATTATTCTTACTTTGA
53602 TTCTAACTGT
Statistics
Matches: 128, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
34 17 0.13
35 1 0.01
37 3 0.02
38 82 0.64
40 17 0.13
41 8 0.06
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (38 bp):
CTTAATTATCAATTTTACTGATTATTCTTACTTTGACT
Found at i:53578 original size:76 final size:76
Alignment explanation
Indices: 53416--53601 Score: 238
Period size: 76 Copynumber: 2.5 Consensus size: 76
53406 TACTCTCTCC
* * * **
53416 CTTAAGTATCAA-TTTACTGATTAATC---CCTTGACTCTTAATTATTGATTTACTGATTACTAT
1 CTTAATTATCAATTTTACTGATTATTCTTACTTTGACTCTTAATTATCAATTTACTGATTACTA-
53477 TTTTACCTCGACT
65 -TTTACCTCGACT
*
53490 CTTGATTATCAATTTTACTGATTATTCTTACTTTGACTCTTAATTATCAATTTTACTGATTACTA
1 CTTAATTATCAATTTTACTGATTATTCTTACTTTGACTCTTAATTATCAA-TTTACTGATTACTA
* *
53555 -TTACTTTGACT
65 TTTACCTCGACT
53566 CTTAATTATCAATTTTACTGATTATTCTTACTTTGA
1 CTTAATTATCAATTTTACTGATTATTCTTACTTTGA
53602 TTCTAACTGT
Statistics
Matches: 98, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
74 10 0.10
75 13 0.13
76 44 0.45
78 17 0.17
79 14 0.14
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (76 bp):
CTTAATTATCAATTTTACTGATTATTCTTACTTTGACTCTTAATTATCAATTTACTGATTACTAT
TTACCTCGACT
Found at i:54487 original size:51 final size:50
Alignment explanation
Indices: 54411--54518 Score: 171
Period size: 51 Copynumber: 2.1 Consensus size: 50
54401 AATATTCAAC
* * *
54411 TTTTATTGTTTAAAATTACTAAACTCAACTCTTACTACATAAAGATTTAAT
1 TTTTA-TGATTAAAATCACTAAACTCAACCCTTACTACATAAAGATTTAAT
54462 TTTTATGATTAAAATCACTAGAACTCAACCCTTACTACATAAAGATTTAAT
1 TTTTATGATTAAAATCACTA-AACTCAACCCTTACTACATAAAGATTTAAT
54513 TTTTAT
1 TTTTAT
54519 TTGCCAAAGA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
50 13 0.25
51 40 0.75
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.42
Consensus pattern (50 bp):
TTTTATGATTAAAATCACTAAACTCAACCCTTACTACATAAAGATTTAAT
Done.