Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013849.1 Kokia drynarioides strain JFW-HI SEQ_128877, 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: 46547
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:511 original size:59 final size:59
Alignment explanation
Indices: 354--896 Score: 629
Period size: 59 Copynumber: 9.4 Consensus size: 59
344 GAGGTCCCTA
* * * *
354 AACCTTCCAAAAATTACCAATTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAGCCCCG
** *
413 AATATTCC-AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAGCCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAGCCCCG
* ** * **
471 AACCTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCCGTTTT-GACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAG-CCCCG
*
530 AACCTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAGCCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAGCCCCG
* *
589 AACCTTCCAAAAATTACCATTTTACTCCCGAACTCCCAAAAATCCAATTTTTAGCCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAGCCCCG
* *
648 AACCTT-CTAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTT-GACCCCA
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAG-CCCCG
*
706 AACCTTCCAAAAATTACCATTTT--------AC-CCCAAAAATCCTATTTTTAGCCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAGCCCCG
* *
756 AACCTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTT-GACCCTG
1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAG-CCCCG
* * * * * *
815 AA-CTTCCAAAAAAATCCCATTTTTGA-CCTCGAATCTTCCAAAAATTACCA-TTTTACCCCCG
1 AACCTTCC-AAAAATTACCA-TTTT-ACCCCCGAA-CTCCCAAAAA-TCCCATTTTTAGCCCCG
*
876 AA-CTTCCAAAAA-TCCCATTTT
1 AACCTTCCAAAAATTACCATTTT
897 TGATTTCGAA
Statistics
Matches: 425, Mismatches: 37, Indels: 45
0.84 0.07 0.09
Matches are distributed among these distances:
50 44 0.10
51 3 0.01
57 1 0.00
58 117 0.28
59 214 0.50
60 17 0.04
61 25 0.06
62 4 0.01
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.28
Consensus pattern (59 bp):
AACCTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAGCCCCG
Found at i:747 original size:50 final size:50
Alignment explanation
Indices: 681--782 Score: 170
Period size: 50 Copynumber: 2.0 Consensus size: 50
671 CCCCCGAACT
681 CCCAAAAATCCCATTTTT-GACCCCAAACCTTCCAAAAATTACCATTTTAC
1 CCCAAAAATCCCATTTTTAG-CCCCAAACCTTCCAAAAATTACCATTTTAC
* *
731 CCCAAAAATCCTATTTTTAGCCCCGAACCTTCCAAAAATTACCATTTTAC
1 CCCAAAAATCCCATTTTTAGCCCCAAACCTTCCAAAAATTACCATTTTAC
781 CC
1 CC
783 TCGAACTCCC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 48 0.98
51 1 0.02
ACGTcount: A:0.34, C:0.34, G:0.03, T:0.28
Consensus pattern (50 bp):
CCCAAAAATCCCATTTTTAGCCCCAAACCTTCCAAAAATTACCATTTTAC
Found at i:801 original size:109 final size:107
Alignment explanation
Indices: 623--826 Score: 345
Period size: 109 Copynumber: 1.9 Consensus size: 107
613 CTCCCGAACT
*
623 CCCAAAAATCCAATTTTTAGCCCCGAACCTTCTAAAATTACCATTTTACCCCCGAACTCCCAAAA
1 CCCAAAAATCCAATTTTTAGCCCCGAACCTTCAAAAATTACCATTTTACCCCCGAACTCCCAAAA
688 ATCCCATTTTTGACCCCAAACCTTCCAAAAATTACCATTTTAC
66 ATCCCATTTTTGACCCCAAA-CTTCCAAAAATTACCATTTTAC
* *
731 CCCAAAAATCCTATTTTTAGCCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAA
1 CCCAAAAATCCAATTTTTAGCCCCGAACCTT-CAAAAATTACCATTTTACCCCCGAACTCCCAAA
**
796 AATCCCATTTTTGACCCTGAACTTCCAAAAA
65 AATCCCATTTTTGACCCCAAACTTCCAAAAA
827 AATCCCATTT
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
108 40 0.44
109 50 0.56
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.27
Consensus pattern (107 bp):
CCCAAAAATCCAATTTTTAGCCCCGAACCTTCAAAAATTACCATTTTACCCCCGAACTCCCAAAA
ATCCCATTTTTGACCCCAAACTTCCAAAAATTACCATTTTAC
Found at i:853 original size:90 final size:90
Alignment explanation
Indices: 734--899 Score: 271
Period size: 90 Copynumber: 1.8 Consensus size: 90
724 ATTTTACCCC
* *
734 AAAAATCCTATTTTTAGCCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAAT
1 AAAAATCCCATTTTTAGCCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAAT
799 CCCATTTTTGACCCTGAACTTCCAA
66 CCCATTTTTGACCCTGAACTTCCAA
* * *
824 AAAAATCCCATTTTT-GACCTCGAATCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAA
1 AAAAATCCCATTTTTAG-CCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAA
888 TCCCATTTTTGA
65 TCCCATTTTTGA
900 TTTCGAACCT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
89 1 0.01
90 69 0.99
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.30
Consensus pattern (90 bp):
AAAAATCCCATTTTTAGCCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAAT
CCCATTTTTGACCCTGAACTTCCAA
Found at i:897 original size:29 final size:28
Alignment explanation
Indices: 357--897 Score: 405
Period size: 29 Copynumber: 18.7 Consensus size: 28
347 GTCCCTAAAC
* * *
357 CTTCCAAAAATTACCA-ATTTACCCCCAAA
1 CTTCCAAAAA-TCCCATTTTTA-CCCCGAA
386 CTTCCAAAAATCCCATTTTTAACCCCGAA
1 CTTCCAAAAATCCCATTTTT-ACCCCGAA
* * *
415 TATTCCAAAATTACCA-TTTTACCCCCGAA
1 -CTTCCAAAAATCCCATTTTTA-CCCCGAA
444 CTTCCAAAAATCCCATTTTTAGCCCCGAA
1 CTTCCAAAAATCCCATTTTTA-CCCCGAA
* * *
473 CCTTCTAAAAATTACCA-TTTTACCCCTAAA
1 -CTTCCAAAAA-TCCCATTTTTACCCC-GAA
* *
503 CTTCCAAAAATCCCCGTTTTGACCCCGAA
1 CTTCCAAAAAT-CCCATTTTTACCCCGAA
*
532 CCTTCCAAAAATTACCA-TTTTACCCTCGAA
1 -CTTCCAAAAA-TCCCATTTTTACCC-CGAA
*
562 CTCCCAAAAATCCCATTTTTAGCCCCGAA
1 CTTCCAAAAATCCCATTTTTA-CCCCGAA
*
591 CCTTCCAAAAATTACCA-TTTTACTCCCGAA
1 -CTTCCAAAAA-TCCCATTTTTAC-CCCGAA
* *
621 CTCCCAAAAATCCAATTTTTAGCCCCGAA
1 CTTCCAAAAATCCCATTTTTA-CCCCGAA
* * *
650 CCTTCTAAAATTACCA-TTTTACCCCCGAA
1 -CTTCCAAAAATCCCATTTTTA-CCCCGAA
* *
679 CTCCCAAAAATCCCATTTTTGACCCCAAA
1 CTTCCAAAAATCCCATTTTT-ACCCCGAA
*
708 CCTTCCAAAAATTACCA-TTTTA---C---
1 -CTTCCAAAAA-TCCCATTTTTACCCCGAA
*
731 C--CCAAAAATCCTATTTTTAGCCCCGAA
1 CTTCCAAAAATCCCATTTTTA-CCCCGAA
*
758 CCTTCCAAAAATTACCA-TTTTACCCTCGAA
1 -CTTCCAAAAA-TCCCATTTTTACCC-CGAA
* *
788 CTCCCAAAAATCCCATTTTTGACCCTGAA
1 CTTCCAAAAATCCCATTTTT-ACCCCGAA
*
817 CTTCCAAAAAAATCCCATTTTTGACCTCGAA
1 CTTCC--AAAAATCCCATTTTT-ACCCCGAA
*
848 TCTTCCAAAAATTACCA-TTTTACCCCCGAA
1 -CTTCCAAAAA-TCCCATTTTTA-CCCCGAA
878 CTTCCAAAAATCCCATTTTT
1 CTTCCAAAAATCCCATTTTT
898 GATTTCGAAC
Statistics
Matches: 412, Mismatches: 54, Indels: 92
0.74 0.10 0.16
Matches are distributed among these distances:
19 3 0.01
20 12 0.03
22 1 0.00
24 1 0.00
26 1 0.00
28 45 0.11
29 166 0.40
30 136 0.33
31 42 0.10
32 5 0.01
ACGTcount: A:0.33, C:0.34, G:0.04, T:0.29
Consensus pattern (28 bp):
CTTCCAAAAATCCCATTTTTACCCCGAA
Found at i:914 original size:30 final size:29
Alignment explanation
Indices: 732--926 Score: 159
Period size: 30 Copynumber: 6.6 Consensus size: 29
722 CCATTTTACC
* *
732 CCAAAAATCCTATTTTT-AGCCCCGAACCTT
1 CCAAAAATCCCATTTTTGA-CCTCGAA-CTT
* *
762 CCAAAAATTACCA-TTTT-ACCCTCGAACTC
1 CCAAAAA-TCCCATTTTTGA-CCTCGAACTT
791 CCAAAAATCCCATTTTTGACC-CTGAACTT
1 CCAAAAATCCCATTTTTGACCTC-GAACTT
820 CCAAAAAAATCCCATTTTTGACCTCGAATCTT
1 CC--AAAAATCCCATTTTTGACCTCGAA-CTT
* *
852 CCAAAAATTACCA-TTTT-ACCCCCGAACTT
1 CCAAAAA-TCCCATTTTTGA-CCTCGAACTT
**
881 CCAAAAATCCCATTTTTGATTTCGAACCTT
1 CCAAAAATCCCATTTTTGACCTCGAA-CTT
* *
911 CCAAAACTACCATTTT
1 CCAAAAATCCCATTTT
927 GCCCCCCCGT
Statistics
Matches: 137, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
28 9 0.07
29 41 0.30
30 52 0.38
31 29 0.21
32 6 0.04
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (29 bp):
CCAAAAATCCCATTTTTGACCTCGAACTT
Found at i:933 original size:59 final size:60
Alignment explanation
Indices: 745--932 Score: 183
Period size: 59 Copynumber: 3.2 Consensus size: 60
735 AAAATCCTAT
* * * * *
745 TTTTAGCCCCGAACCTTCCAAAAATTACCA-TTTT-ACCCTCGAA-CTCCCAAAAA-TCCCA
1 TTTTACCCCCGAA-CTTCCAAAAAATCCCATTTTTGA-CCTCGAACCTTCCAAAAACTACCA
* * *
803 TTTTTGA-CCCTGAACTTCCAAAAAAATCCCATTTTTGACCTCGAATCTTCCAAAAATTACCA
1 -TTTT-ACCCCCGAACTTCC-AAAAAATCCCATTTTTGACCTCGAACCTTCCAAAAACTACCA
**
865 TTTTACCCCCGAACTTCC-AAAAATCCCATTTTTGATTTCGAACCTTCC-AAAACTACCA
1 TTTTACCCCCGAACTTCCAAAAAATCCCATTTTTGACCTCGAACCTTCCAAAAACTACCA
*
923 TTTTGCCCCC
1 TTTTACCCCC
933 CCGTGCATCC
Statistics
Matches: 111, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
58 23 0.21
59 46 0.41
60 13 0.12
61 25 0.23
62 4 0.04
ACGTcount: A:0.31, C:0.33, G:0.06, T:0.30
Consensus pattern (60 bp):
TTTTACCCCCGAACTTCCAAAAAATCCCATTTTTGACCTCGAACCTTCCAAAAACTACCA
Found at i:1578 original size:30 final size:30
Alignment explanation
Indices: 1544--1716 Score: 162
Period size: 30 Copynumber: 5.8 Consensus size: 30
1534 NNNNNNNCCC
1544 CGAACCTTCCAAAAATTACCA-TTTT-ACCCT
1 CGAA-CTTCCAAAAA-TACCATTTTTGACCCT
* *
1574 CGAACTCCCAAAAATCCCATTTTTGACCCT
1 CGAACTTCCAAAAATACCATTTTTGACCCT
*
1604 -GAACTTCCAAAAAAATCCCATTTTTGA-CCT
1 CGAACTTCC--AAAAATACCATTTTTGACCCT
*
1634 CGAATCTTCCAAAAATTACCA-TTTT-ACCCC
1 CGAA-CTTCCAAAAA-TACCATTTTTGACCCT
* **
1664 CGAACTTCCAAAAATCCCATTTTTGA-TTT
1 CGAACTTCCAAAAATACCATTTTTGACCCT
*
1693 CGAACCTTCCAAAACTACCATTTT
1 CGAA-CTTCCAAAAATACCATTTT
1717 GCCCCCCCGT
Statistics
Matches: 121, Mismatches: 11, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
28 8 0.07
29 39 0.32
30 45 0.37
31 24 0.20
32 5 0.04
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (30 bp):
CGAACTTCCAAAAATACCATTTTTGACCCT
Found at i:1621 original size:31 final size:30
Alignment explanation
Indices: 1549--1689 Score: 134
Period size: 31 Copynumber: 4.8 Consensus size: 30
1539 NNCCCCGAAC
* *
1549 CTTCCAAAAATTACCA-TTTT-ACCCTCGAA
1 CTTCCAAAAAATCCCATTTTTGACCCT-GAA
*
1578 C-TCCCAAAAATCCCATTTTTGACCCTGAA
1 CTTCCAAAAAATCCCATTTTTGACCCTGAA
1607 CTTCCAAAAAAATCCCATTTTTGA-CCTCGAA
1 CTTCC-AAAAAATCCCATTTTTGACCCT-GAA
* * *
1638 TCTTCCAAAAATTACCA-TTTT-ACCCCCGAA
1 -CTTCCAAAAAATCCCATTTTTGA-CCCTGAA
1668 CTTCC-AAAAATCCCATTTTTGA
1 CTTCCAAAAAATCCCATTTTTGA
1690 TTTCGAACCT
Statistics
Matches: 93, Mismatches: 9, Indels: 19
0.77 0.07 0.16
Matches are distributed among these distances:
28 19 0.20
29 19 0.20
30 19 0.20
31 31 0.33
32 5 0.05
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.30
Consensus pattern (30 bp):
CTTCCAAAAAATCCCATTTTTGACCCTGAA
Found at i:1687 original size:29 final size:29
Alignment explanation
Indices: 1541--1716 Score: 153
Period size: 29 Copynumber: 5.9 Consensus size: 29
1531 NNNNNNNNNN
*
1541 CCCCGAACCTTCCAAAAATTACCA-TTTT-A
1 CCCCGAA-CTTCCAAAAA-TCCCATTTTTGA
*
1570 CCCTCGAACTCCCAAAAATCCCATTTTTGA
1 CCC-CGAACTTCCAAAAATCCCATTTTTGA
*
1600 CCCTGAACTTCCAAAAAAATCCCATTTTTGA
1 CCCCGAACTTCC--AAAAATCCCATTTTTGA
* *
1631 CCTCGAATCTTCCAAAAATTACCA-TTTT-A
1 CCCCGAA-CTTCCAAAAA-TCCCATTTTTGA
1660 CCCCCGAACTTCCAAAAATCCCATTTTTGA
1 -CCCCGAACTTCCAAAAATCCCATTTTTGA
*** * *
1690 TTTCGAACCTTCCAAAACTACCATTTT
1 CCCCGAA-CTTCCAAAAATCCCATTTT
1717 GCCCCCCCGT
Statistics
Matches: 122, Mismatches: 14, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
28 8 0.07
29 42 0.34
30 41 0.34
31 26 0.21
32 5 0.04
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.30
Consensus pattern (29 bp):
CCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:1723 original size:59 final size:60
Alignment explanation
Indices: 1541--1722 Score: 180
Period size: 59 Copynumber: 3.1 Consensus size: 60
1531 NNNNNNNNNN
* * * *
1541 CCCCGAACCTTCCAAAAATTACCA-TTTT-ACCCTCGAA-CTCCCAAAAA-TCCCATTTTTGA-
1 CCCCGAA-CTTCCAAAAAATCCCATTTTTGA-CCTCGAACCTTCCAAAAACTACCA-TTTT-AC
* * *
1600 CCCTGAACTTCCAAAAAAATCCCATTTTTGACCTCGAATCTTCCAAAAATTACCATTTTAC
1 CCCCGAACTTCC-AAAAAATCCCATTTTTGACCTCGAACCTTCCAAAAACTACCATTTTAC
** *
1661 CCCCGAACTTCC-AAAAATCCCATTTTTGATTTCGAACCTTCC-AAAACTACCATTTTGC
1 CCCCGAACTTCCAAAAAATCCCATTTTTGACCTCGAACCTTCCAAAAACTACCATTTTAC
1719 CCCC
1 CCCC
1723 CCGTGCATCC
Statistics
Matches: 106, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
58 23 0.22
59 42 0.40
60 12 0.11
61 25 0.24
62 4 0.04
ACGTcount: A:0.31, C:0.34, G:0.05, T:0.29
Consensus pattern (60 bp):
CCCCGAACTTCCAAAAAATCCCATTTTTGACCTCGAACCTTCCAAAAACTACCATTTTAC
Found at i:2271 original size:791 final size:780
Alignment explanation
Indices: 751--2321 Score: 3025
Period size: 791 Copynumber: 2.0 Consensus size: 780
741 CTATTTTTAG
751 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTGACCCTGA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTGACCCTGA
816 ACTTCCAAAAAAATCCCATTTTTGACCTCGAATCTTCCAAAAATTACCATTTTACCCCCGAACTT
66 ACTTCCAAAAAAATCCCATTTTTGACCTCGAATCTTCCAAAAATTACCATTTTACCCCCGAACTT
881 CCAAAAATCCCATTTTTGATTTCGAACCTTCCAAAACTACCATTTTGCCCCCCCGTGCATCCAAA
131 CCAAAAATCCCATTTTTGATTTCGAACCTTCCAAAACTACCATTTTGCCCCCCCGTGCATCCAAA
* *
946 AAGTCTCGTTTTGAACTCCGATTACATCATTCTTCTCTCTCATTAACTTTTTGCGCTCGTATTTT
196 AAGTCTCGTTTTGAACTCCGATTACATCATTCTTCTCTCTCATTAACTTTTTACGCTCGCATTTT
1011 GTATCTTGGTTTTCTTTCGCGAATAACTTATCCTCTCATTTATTTTGCTTCGTATCCATCATTAA
261 GTATCTTGGTTTTCTTTCGCGAATAACTTATCCTCTCATTTATTTTGCTTCGTATCCATCATTAA
1076 TTGCTTATTCTTGTTAAATTCGCATGCTTGTTTTCGAAATTGTCTTTTTTCATAAAAACTTTAAA
326 TTGCTTATTCTTGTTAAATTCGCATGCTTGTTTTCGAAATTGTCTTTTTTCATAAAAACTTTAAA
1141 ATCGAGGCAATACTCTTTTATTTTGTTGTTTAGAAACTTTGCGCCTTAACTCACTAGGTGTAATT
391 ATCGAGGCAATACTCTTTTATTTTGTTGTTTAGAAACTTTGCGCCTTAACTCACTAGGTGTAATT
1206 TTTCTTCAAATCGAAATAATTGAATGCCCTTAATTGAGGCAATGTTTCCTTGTCTTCGATTCCGA
456 TTTCTTCAAATCGAAATAATTGAATGCCCTTAATTGAGGCAATGTTTCCTTGTCTTCGATTCCGA
1271 AATATTGCGCCTTCACTCACTAGGTGCAATCTTTCTTCAAATAGCGGGATTTTCAAACAAACTCA
521 AATATTGCGCCTTCACTCACTAGGTGCAATCTTTCTTCAAATAGCGGGATTTTCAAACAAACTCA
1336 ATTTCTTTTAAACTTAACACGTGCATTCAAGGATCGTATTTTAAGCTTTATTTGAACTTTTAAAT
586 ATTTCTTTTAAACTTAACACGTGCATTCAAGGATCGTATTTTAAGCTTTATTTGAACTTTTAAAT
1401 GTCACAGATTAAGACCTACATGTTTTCAAAACGGCTTCTAAAACGTTTTGTGGTGATCCAATCAC
651 GTCACAGATTAAGACCTACATGTTTTCAAAACGGCTTCTAAAACGTTTTGTGGTGATCCAATCAC
1466 ACCGAATAAAGGATTGGTGGCGACTCCCATTATTTATCAATTTTAAATGATTTTTCTTCGAGACA
716 ACCGAATAAAGGATTGGTGGCGACTCCCATTATTTATCAATTTTAAATGATTTTTCTTCGAGACA
1531 NNNNNNNNNNCCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTT
1 ----------CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTT
1596 TTGACCCTGAACTTCCAAAAAAATCCCATTTTTGACCTCGAATCTTCCAAAAATTACCATTTTAC
56 TTGACCCTGAACTTCCAAAAAAATCCCATTTTTGACCTCGAATCTTCCAAAAATTACCATTTTAC
1661 CCCCGAACTTCCAAAAATCCCATTTTTGATTTCGAACCTTCCAAAACTACCATTTTGCCCCCCCG
121 CCCCGAACTTCCAAAAATCCCATTTTTGATTTCGAACCTTCCAAAACTACCATTTTGCCCCCCCG
1726 TGCATCCAAAAAGTCTCGTTTTGAACTCCGATTACATCATTCTTCTCTCTCATTAACTTTTTTAC
186 TGCATCCAAAAAGTCTCGTTTTGAACTCCGATTACATCATTCTTCTCTCTCATTAAC-TTTTTAC
1791 GCTCGCATTTTGTATCTTGGTTTTCTTTCGCGAATAACTTATCCTCTCATTTATTTTGCTTCGTA
250 GCTCGCATTTTGTATCTTGGTTTTCTTTCGCGAATAACTTATCCTCTCATTTATTTTGCTTCGTA
1856 TCCATCATTAATTGCTTATTCTTGTTAAATTCGCATGCTTGTTTTCGAAATTGTCTTTTTTCATA
315 TCCATCATTAATTGCTTATTCTTGTTAAATTCGCATGCTTGTTTTCGAAATTGTCTTTTTTCATA
1921 AAAACTTTAAAATCGAGGCAATACTCTTTTATTTTGTTGTTTAGAAACTTTGCGCCTTAACTCAC
380 AAAACTTTAAAATCGAGGCAATACTCTTTTATTTTGTTGTTTAGAAACTTTGCGCCTTAACTCAC
1986 TAGGTGTAATTTTTCTTCAAATCGAAATAATTGAATGCCCTTAATTGAGGCAATGTTTCCTTGTC
445 TAGGTGTAATTTTTCTTCAAATCGAAATAATTGAATGCCCTTAATTGAGGCAATGTTTCCTTGTC
2051 TTCGATTCCGAAATATTGCGCCTTCACTCACTAGGTGCAATCTTTCTTCAAATAGCGGGATTTTC
510 TTCGATTCCGAAATATTGCGCCTTCACTCACTAGGTGCAATCTTTCTTCAAATAGCGGGATTTTC
2116 AAACAAACTCAATTTCTTTTAAACTTAACACGTGCATTCAAGGATCGTATTTTAAGCTTTATTTG
575 AAACAAACTCAATTTCTTTTAAACTTAACACGTGCATTCAAGGATCGTATTTTAAGCTTTATTTG
2181 AACTTTTAAATGTCACAGATTAAGACCTACATGTTTTCAAAACGGCTTCTAAAACGTTTTGTGGT
640 AACTTTTAAATGTCACAGATTAAGACCTACATGTTTTCAAAACGGCTTCTAAAACGTTTTGTGGT
2246 GATCCAATCACACCGAATAAAGGATTGGTGGCGACTCCCATTATTTATCAATTTTAAATGATTTT
705 GATCCAATCACACCGAATAAAGGATTGGTGGCGACTCCCATTATTTATCAATTTTAAATGATTTT
2311 TCTTCGAGACA
770 TCTTCGAGACA
2322 TGTCGTATTT
Statistics
Matches: 778, Mismatches: 2, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
790 242 0.31
791 536 0.69
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (780 bp):
CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTGACCCTGA
ACTTCCAAAAAAATCCCATTTTTGACCTCGAATCTTCCAAAAATTACCATTTTACCCCCGAACTT
CCAAAAATCCCATTTTTGATTTCGAACCTTCCAAAACTACCATTTTGCCCCCCCGTGCATCCAAA
AAGTCTCGTTTTGAACTCCGATTACATCATTCTTCTCTCTCATTAACTTTTTACGCTCGCATTTT
GTATCTTGGTTTTCTTTCGCGAATAACTTATCCTCTCATTTATTTTGCTTCGTATCCATCATTAA
TTGCTTATTCTTGTTAAATTCGCATGCTTGTTTTCGAAATTGTCTTTTTTCATAAAAACTTTAAA
ATCGAGGCAATACTCTTTTATTTTGTTGTTTAGAAACTTTGCGCCTTAACTCACTAGGTGTAATT
TTTCTTCAAATCGAAATAATTGAATGCCCTTAATTGAGGCAATGTTTCCTTGTCTTCGATTCCGA
AATATTGCGCCTTCACTCACTAGGTGCAATCTTTCTTCAAATAGCGGGATTTTCAAACAAACTCA
ATTTCTTTTAAACTTAACACGTGCATTCAAGGATCGTATTTTAAGCTTTATTTGAACTTTTAAAT
GTCACAGATTAAGACCTACATGTTTTCAAAACGGCTTCTAAAACGTTTTGTGGTGATCCAATCAC
ACCGAATAAAGGATTGGTGGCGACTCCCATTATTTATCAATTTTAAATGATTTTTCTTCGAGACA
Found at i:8790 original size:3 final size:3
Alignment explanation
Indices: 8782--8825 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
8772 GGGTTAATAC
8782 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
8826 GGGTGTAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:13351 original size:18 final size:18
Alignment explanation
Indices: 13328--13370 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
13318 GAATAATTTT
13328 TTAATTAAATAAGTTT-AA
1 TTAATTAAA-AAGTTTAAA
* *
13346 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAGTTTAAA
13364 TTAATTA
1 TTAATTA
13371 CAACTGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAGTTTAAA
Found at i:15002 original size:61 final size:60
Alignment explanation
Indices: 14912--15108 Score: 240
Period size: 60 Copynumber: 3.3 Consensus size: 60
14902 CATCCGAGGG
* *
14912 TAAAATAGTAA-TTTT-GAAAAATTAAGGTCAAAGATGGAATTTTTGAAAGTTCGAGGGGT
1 TAAAAT-GTAATTTTTGGAAAAATTAAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGGT
* **
14971 TAAAATGGTAATTTTTGGAAAAAGTAAGGTCAAAAATGGAATTTTGGAGTGTTCG-GGGGT
1 TAAAAT-GTAATTTTTGGAAAAATTAAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGGT
* * *
15031 AAAAATGTAATTTTCTGGAAAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTTGA-GGGT
1 TAAAATGTAATTTT-TGGAAAAATTAAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGGT
* * *
15091 CAAAATATGATTTTTGGA
1 TAAAATGTAATTTTTGGA
15109 CAGTTTAAGG
Statistics
Matches: 119, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
59 22 0.18
60 64 0.54
61 33 0.28
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (60 bp):
TAAAATGTAATTTTTGGAAAAATTAAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGGT
Found at i:15092 original size:30 final size:30
Alignment explanation
Indices: 14937--15119 Score: 115
Period size: 30 Copynumber: 6.1 Consensus size: 30
14927 GAAAAATTAA
* * *
14937 GGTCAAAGATGGAATTTTTGAAAGTTCGAGG
1 GGTCAAAAATGGAATTTTGGAAAGTTTGA-G
* *** *
14968 GGT-TAAAATGGTAATTTTTGGAAAAAGT-AA
1 GGTCAAAAATGG-AA-TTTTGGAAAGTTTGAG
** * *
14998 GGTCAAAAATGGAATTTTGGAGTGTTCGGG
1 GGTCAAAAATGGAATTTTGGAAAGTTTGAG
* **
15028 GGT-AAAAATGTAATTTTCTGGAAAAATT-AG
1 GGTCAAAAATGGAA-TTT-TGGAAAGTTTGAG
15058 GGTCAAAAATGGAATTTTGGAAAGTTTGAG
1 GGTCAAAAATGGAATTTTGGAAAGTTTGAG
* * *
15088 GGTCAAAATAT-GATTTTTGGACAGTTTAAG
1 GGTCAAAA-ATGGAATTTTGGAAAGTTTGAG
15118 GG
1 GG
15120 GCCTCTTGGG
Statistics
Matches: 113, Mismatches: 30, Indels: 19
0.70 0.19 0.12
Matches are distributed among these distances:
29 24 0.21
30 52 0.46
31 29 0.26
32 8 0.07
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (30 bp):
GGTCAAAAATGGAATTTTGGAAAGTTTGAG
Found at i:26927 original size:97 final size:97
Alignment explanation
Indices: 26753--26935 Score: 221
Period size: 97 Copynumber: 1.9 Consensus size: 97
26743 AGGATGTTCA
* * * *
26753 ATTATCTCGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACGAACTTTTAGAATCAGAGAT
1 ATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAAATTTTAGAATCAGAAAT
*
26818 AAAGAAACATTGCCTCGATTTAAGGGTATTCG
66 AAAGAAACATTGCATCGATTTAAGGGTATTCG
* * *
26850 ATTATTTCGATTTGAGGAAAAATTGCACCTAGTAAGTTAAGGCA-AAAATTTTCCA-AACTC-GA
1 ATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAAATTTT--AGAA-TCAGA
*
26912 AATAAA-AGAATATTGCATCGATTT
63 AATAAAGA-AACATTGCATCGATTT
26936 TAAATTTTTC
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
96 7 0.10
97 63 0.86
98 3 0.04
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (97 bp):
ATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAAATTTTAGAATCAGAAAT
AAAGAAACATTGCATCGATTTAAGGGTATTCG
Found at i:27183 original size:28 final size:29
Alignment explanation
Indices: 27152--27212 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
27142 AAAATGTGAT
* *
27152 TTTTCGATACCCGA-GGGTAAAATGGTAA
1 TTTTCGACACCCGAGGGGCAAAATGGTAA
* *
27180 TTTTGGACACTCGAGGGGCAAAATGGTAA
1 TTTTCGACACCCGAGGGGCAAAATGGTAA
27209 TTTT
1 TTTT
27213 GGGAAAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (29 bp):
TTTTCGACACCCGAGGGGCAAAATGGTAA
Found at i:27309 original size:88 final size:89
Alignment explanation
Indices: 27167--27332 Score: 207
Period size: 89 Copynumber: 1.9 Consensus size: 89
27157 GATACCCGAG
* * * *
27167 GGTAAAATGGTAATTTTGGACACTCGAGGGGCAAAATGGTAATTTTGGGAAAG-TTTAGGGTTTA
1 GGTAAAATGGTAATTTTGAAAAATCGAGGGGCAAAATGGTAATTTTGGGAAAGTTTTAGGG-GTA
27231 AAATGG-AATTTTTAAACATCCAAA
65 AAATGGTAATTTTTAAACATCCAAA
* *
27255 GGTAAAATGGTAATTTTGAAAAAAATC-AGGGTCAAAGATGG-AATTTTTGG-AAGTTTTAGGGG
1 GGTAAAATGGTAATTTTG--AAAAATCGAGGGGCAAA-ATGGTAATTTTGGGAAAGTTTTAGGGG
27317 TAAAATGGTAATTTTT
63 TAAAATGGTAATTTTT
27333 GGAAAATCGG
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
88 29 0.43
89 30 0.45
90 8 0.12
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (89 bp):
GGTAAAATGGTAATTTTGAAAAATCGAGGGGCAAAATGGTAATTTTGGGAAAGTTTTAGGGGTAA
AATGGTAATTTTTAAACATCCAAA
Found at i:27419 original size:61 final size:61
Alignment explanation
Indices: 27275--27451 Score: 222
Period size: 61 Copynumber: 2.9 Consensus size: 61
27265 TAATTTTGAA
*
27275 AAAAATCAGGGTCAAAGATGGAATTTTTG-GAAGTTTTAGGGGT-AAAATGGTAA--TTTTTGG
1 AAAAATCAGGGTCAAAAATGGAATTTTTGAG-AG-TTTAGGGGTAAAAAT-GTAATTTTTTTGG
* * *
27335 -AAAATCGGGGTTAAAAATGGAATTTTAGAGAGTTT-GGCGGTAAAAATGTAATTTTTTTGG
1 AAAAATCAGGGTCAAAAATGGAATTTTTGAGAGTTTAGG-GGTAAAAATGTAATTTTTTTGG
* *
27395 AAAAATCAAGGTCAAAAATGGAATTTTTGAAAGTTTAGGGGTAAAAATGTAATTTTT
1 AAAAATCAGGGTCAAAAATGGAATTTTTGAGAGTTTAGGGGTAAAAATGTAATTTTT
27452 AGGAAAGTTC
Statistics
Matches: 101, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
57 2 0.02
58 10 0.10
59 31 0.31
60 8 0.08
61 48 0.48
62 2 0.02
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (61 bp):
AAAAATCAGGGTCAAAAATGGAATTTTTGAGAGTTTAGGGGTAAAAATGTAATTTTTTTGG
Found at i:27440 original size:29 final size:30
Alignment explanation
Indices: 27283--27460 Score: 120
Period size: 29 Copynumber: 5.9 Consensus size: 30
27273 AAAAAAATCA
*
27283 GGGTCAAAGATGGAATTTTTGG-AAGTTTTAG
1 GGGT-AAAAATGGAATTTTTGGAAAG-TTTAG
* *
27314 GGGT-AAAATGGTAATTTTTGGAAA--ATCG
1 GGGTAAAAATGG-AATTTTTGGAAAGTTTAG
* *
27342 GGGTTAAAAATGGAA-TTTTAGAGAGTTT-G
1 GGG-TAAAAATGGAATTTTTGGAAAGTTTAG
* ** *
27371 GCGGTAAAAATGTAATTTTTTTGGAAAAATCA-
1 G-GGTAAAAATGGAA--TTTTTGGAAAGTTTAG
*
27403 AGGTCAAAAATGGAATTTTT-GAAAGTTTAG
1 GGGT-AAAAATGGAATTTTTGGAAAGTTTAG
*
27433 GGGTAAAAATGTAATTTTTAGGAAAGTT
1 GGGTAAAAATGGAATTTTT-GGAAAGTT
27461 CGAGGTCAAA
Statistics
Matches: 113, Mismatches: 19, Indels: 30
0.70 0.12 0.19
Matches are distributed among these distances:
28 12 0.11
29 41 0.36
30 27 0.24
31 16 0.14
32 17 0.15
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (30 bp):
GGGTAAAAATGGAATTTTTGGAAAGTTTAG
Found at i:27457 original size:60 final size:61
Alignment explanation
Indices: 27258--27492 Score: 227
Period size: 60 Copynumber: 3.9 Consensus size: 61
27248 ATCCAAAGGT
* * * * *
27258 AAAATGGTAATTTTGA-AAAAAATCAGGGTCAAAGATGGAATTTTTGGAAGTTTTAGGGGT-
1 AAAATGGTAATTTTTAGGAAAAATCAAGGTCAAAAATGGAATTTTTGAAAG-TTTAGGGGTA
** * * *
27318 AAAATGGTAATTTTT-GG-AAAATCGGGGTTAAAAATGGAATTTTAGAGAGTTT-GGCGGTA
1 AAAATGGTAATTTTTAGGAAAAATCAAGGTCAAAAATGGAATTTTTGAAAGTTTAGG-GGTA
*
27377 AAAAT-GTAATTTTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGAAAGTTTAGGGGTA
1 AAAATGGTAA-TTTTTAGGAAAAATCAAGGTCAAAAATGGAATTTTTGAAAGTTTAGGGGTA
** * *
27438 AAAAT-GTAATTTTTAGGAAAGTTCGAGGTCAAAATAT-G-ATTTTTGGACAGTTTAG
1 AAAATGGTAATTTTTAGGAAAAATCAAGGTCAAAA-ATGGAATTTTT-GAAAGTTTAG
27493 AGGGCCTATA
Statistics
Matches: 148, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
57 2 0.01
58 10 0.07
59 42 0.28
60 47 0.32
61 45 0.30
62 2 0.01
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.34
Consensus pattern (61 bp):
AAAATGGTAATTTTTAGGAAAAATCAAGGTCAAAAATGGAATTTTTGAAAGTTTAGGGGTA
Found at i:28718 original size:19 final size:19
Alignment explanation
Indices: 28694--28735 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
28684 CAAAATTCTT
28694 TTTATTTA-ATATTATAATA
1 TTTATTTATATATTAT-ATA
*
28713 TTTA-TTATTTATTATATA
1 TTTATTTATATATTATATA
28731 TTTAT
1 TTTAT
28736 GGTTAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTTATATATTATATA
Found at i:29454 original size:17 final size:17
Alignment explanation
Indices: 29432--29490 Score: 73
Period size: 17 Copynumber: 3.5 Consensus size: 17
29422 GTTTATATTT
29432 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTCA
* *
29449 AATTTAAATTAAATCCA
1 AATTTAAAATAAATTCA
* *
29466 AATTTAAAGTAAATTTA
1 AATTTAAAATAAATTCA
*
29483 GATTTAAA
1 AATTTAAA
29491 TTTTAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.37
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:29487 original size:6 final size:6
Alignment explanation
Indices: 29418--29493 Score: 52
Period size: 6 Copynumber: 13.2 Consensus size: 6
29408 TTAGACTTTC
* * * *
29418 TAAAGTT TATATT T-AATT TAAA-A TAAATT CAAATT TAAA-T TAAATC
1 TAAA-TT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* * *
29464 CAAATT TAAA-G TAAATT TAGATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT TAAATT T
29494 TAAAAATGAG
Statistics
Matches: 51, Mismatches: 14, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
5 17 0.33
6 31 0.61
7 3 0.06
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:31480 original size:19 final size:18
Alignment explanation
Indices: 31449--31484 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
31439 ATATATATTT
31449 ATAATTTTAGTAATTTTC
1 ATAATTTTAGTAATTTTC
*
31467 ATAATTTTTTGTAATTTT
1 ATAA-TTTTAGTAATTTT
31485 TTAGTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (18 bp):
ATAATTTTAGTAATTTTC
Found at i:31485 original size:11 final size:11
Alignment explanation
Indices: 31453--31493 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
31443 ATATTTATAA
31453 TTTTAGTAA-T
1 TTTTAGTAATT
*
31463 TTTCA-TAATT
1 TTTTAGTAATT
31473 TTTT-GTAATT
1 TTTTAGTAATT
31483 TTTTAGTAATT
1 TTTTAGTAATT
31494 ATCTAAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 3 0.12
10 17 0.65
11 6 0.23
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (11 bp):
TTTTAGTAATT
Found at i:32288 original size:11 final size:11
Alignment explanation
Indices: 32269--32303 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
32259 TATATTCAGT
32269 TTTTATTTTTTA
1 TTTT-TTTTTTA
32281 TTTTTTTTTTA
1 TTTTTTTTTTA
*
32292 GTTTTTTTTTA
1 TTTTTTTTTTA
32303 T
1 T
32304 CTGCATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:33526 original size:18 final size:18
Alignment explanation
Indices: 33500--33538 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
33490 TATTTATATA
* * *
33500 TTTATTATTTTTTTTAAT
1 TTTAATATTGTTTATAAT
33518 TTTAATATTGTTTATAAT
1 TTTAATATTGTTTATAAT
33536 TTT
1 TTT
33539 TATAATTAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTAATATTGTTTATAAT
Found at i:37408 original size:18 final size:18
Alignment explanation
Indices: 37374--37409 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
37364 ATCAGTTCCT
*
37374 CGACTGCAGCTATGGCTG
1 CGACTGCAGCTACGGCTG
*
37392 CGACTGCAGCTGCGGCTG
1 CGACTGCAGCTACGGCTG
37410 GGGCTGCAGT
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:0.14, C:0.31, G:0.36, T:0.19
Consensus pattern (18 bp):
CGACTGCAGCTACGGCTG
Found at i:37659 original size:33 final size:30
Alignment explanation
Indices: 37590--37660 Score: 74
Period size: 33 Copynumber: 2.3 Consensus size: 30
37580 TCTTTATCCT
*
37590 TCTTCTTT-TTCTTTTTCTCTTTTGTCTCG
1 TCTTCTTTCTTCTTTTTCTCTTTTGTCTCA
*
37619 TCATCTTTCTTCTCTTCCTTCTCTTTGTGT-TCA
1 TCTTCTTTCTTCT-TT--TTCTCTTT-TGTCTCA
37652 TCTTCTTTC
1 TCTTCTTTC
37661 GACTCTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 7 0.21
30 4 0.12
31 2 0.06
33 18 0.53
34 3 0.09
ACGTcount: A:0.03, C:0.28, G:0.06, T:0.63
Consensus pattern (30 bp):
TCTTCTTTCTTCTTTTTCTCTTTTGTCTCA
Found at i:37667 original size:33 final size:33
Alignment explanation
Indices: 37604--37667 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
37594 CTTTTTCTTT
* **
37604 TTCTCTTTTGTCTCGTCATCTTTCTTCTCTTCC
1 TTCTCTTTTGTCTCATCATCTTTCGACTCTTCC
*
37637 TTCTCTTTGTGT-TCATCTTCTTTCGACTCTT
1 TTCTCTTT-TGTCTCATCATCTTTCGACTCTT
37668 TATCGTCTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.05, C:0.30, G:0.08, T:0.58
Consensus pattern (33 bp):
TTCTCTTTTGTCTCATCATCTTTCGACTCTTCC
Found at i:37697 original size:6 final size:6
Alignment explanation
Indices: 37682--37724 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
37672 GTCTTCCTTC
*
37682 TCTTTCT TCTTTT TCTTCT TCTCTTT TC-TTT TCTTTT TCTTTT
1 TCTTT-T TCTTTT TCTTTT TCT-TTT TCTTTT TCTTTT TCTTTT
37725 CTGAATCCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 5 0.16
6 18 0.56
7 9 0.28
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TCTTTT
Found at i:37702 original size:12 final size:11
Alignment explanation
Indices: 37688--37726 Score: 60
Period size: 11 Copynumber: 3.4 Consensus size: 11
37678 CTTCTCTTTC
37688 TTCTTTTTCTT
1 TTCTTTTTCTT
37699 CTTCTCTTTTCTT
1 -TTCT-TTTTCTT
37712 TTCTTTTTCTT
1 TTCTTTTTCTT
37723 TTCT
1 TTCT
37727 GAATCCGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.42
12 8 0.31
13 7 0.27
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:37704 original size:21 final size:23
Alignment explanation
Indices: 37673--37726 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
37663 CTCTTTATCG
37673 TCTTCCTTCTC-TTTC-TTCTTTT
1 TCTT-CTTCTCTTTTCTTTCTTTT
37695 TCTTCTTCTCTTTTCTTTTCTTTT
1 TCTTCTTCTCTTTTC-TTTCTTTT
37719 TCTT-TTCT
1 TCTTCTTCT
37727 GAATCCGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.21
22 8 0.28
23 4 0.14
24 11 0.38
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (23 bp):
TCTTCTTCTCTTTTCTTTCTTTT
Found at i:37776 original size:21 final size:21
Alignment explanation
Indices: 37751--37800 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
37741 AGACGACGAA
*
37751 GAAGATGAAGATGATGATGAG
1 GAAGATGAAGATGATGATGAC
*
37772 GAAGAAGAAGATGATGATGAC
1 GAAGATGAAGATGATGATGAC
*
37793 GACGATGA
1 GAAGATGA
37801 GGAAGAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.36, T:0.16
Consensus pattern (21 bp):
GAAGATGAAGATGATGATGAC
Found at i:37788 original size:30 final size:30
Alignment explanation
Indices: 37748--37813 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
37738 AGAAGACGAC
* *
37748 GAAGAAGATGAAGATGATGATGAGGAAGAA
1 GAAGAAGATGAAGACGACGATGAGGAAGAA
* *
37778 GAAGATGATGATGACGACGATGAGGAAGAA
1 GAAGAAGATGAAGACGACGATGAGGAAGAA
37808 GAAGAA
1 GAAGAA
37814 TCTTTATCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.03, G:0.36, T:0.12
Consensus pattern (30 bp):
GAAGAAGATGAAGACGACGATGAGGAAGAA
Found at i:37832 original size:3 final size:3
Alignment explanation
Indices: 37826--37872 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
37816 TTTATCCTTT
* *
37826 TTC TTC TT- TCTC CTC TTC TTC TTC TTC TTC TTC TTC TTT TTC -TC
1 TTC TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
37870 TTC
1 TTC
37873 GGATTTTCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 3 0.08
3 34 0.92
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:37868 original size:15 final size:15
Alignment explanation
Indices: 37826--37979 Score: 63
Period size: 15 Copynumber: 10.3 Consensus size: 15
37816 TTTATCCTTT
* *
37826 TTCTTCTTTCTCCTC
1 TTCTTCTTTTTCTTC
*
37841 TTCTTCTTCTTCTTC
1 TTCTTCTTTTTCTTC
37856 TTCTTCTTTTTC-TC
1 TTCTTCTTTTTCTTC
*** *
37870 TTCGGATTTTCCTTC
1 TTCTTCTTTTTCTTC
** *
37885 TTCACCTTCTTCTAACTC
1 TTCTTCTTTTTCT---TC
37903 TT-TATCCTTTTTCTTC
1 TTCT-T-CTTTTTCTTC
*
37919 TTTTTCTTTTTC-TC
1 TTCTTCTTTTTCTTC
* *
37933 -T-TTCTCTTTC-CC
1 TTCTTCTTTTTCTTC
*
37945 ATCTT-TGTCTTTCTTC
1 TTCTTCT-T-TTTCTTC
37961 TTCTTCTTTTTCTT-
1 TTCTTCTTTTTCTTC
37975 TTCTT
1 TTCTT
37980 TCTCTTTCTC
Statistics
Matches: 105, Mismatches: 21, Indels: 27
0.69 0.14 0.18
Matches are distributed among these distances:
12 9 0.09
13 3 0.03
14 19 0.18
15 50 0.48
16 11 0.10
17 2 0.02
18 4 0.04
19 7 0.07
ACGTcount: A:0.04, C:0.30, G:0.02, T:0.64
Consensus pattern (15 bp):
TTCTTCTTTTTCTTC
Found at i:37927 original size:6 final size:6
Alignment explanation
Indices: 37916--37992 Score: 50
Period size: 6 Copynumber: 13.0 Consensus size: 6
37906 ATCCTTTTTC
* * ** * * *
37916 TTCTTT TTCTTT TTCTCT TTCTCT TTC-CC ATCTTT GTCTTT CTTCTTC
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT -TTCTTT
* *
37964 TTCTTT TTC-TT TTCTTT CTCTTT CTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
37993 GTCTCCCTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
5 8 0.14
6 46 0.79
7 4 0.07
ACGTcount: A:0.01, C:0.27, G:0.01, T:0.70
Consensus pattern (6 bp):
TTCTTT
Found at i:38060 original size:48 final size:48
Alignment explanation
Indices: 37979--38103 Score: 130
Period size: 48 Copynumber: 2.6 Consensus size: 48
37969 TTTCTTTTCT
* * **
37979 TTCTCTTTCTCTT-TGTCTCCCTCAA-CTTCTTTATCCTT-ATCCTTCTCC
1 TTCTCCTTCTCTTCTGT-TTCCTCAACCTT-TTTATCCTTCA-CCACCTCC
* * * *
38027 TTTTCCTTCTCTTCTTTTTCCTCGACCTTTTTATCCTTCACCACCTGC
1 TTCTCCTTCTCTTCTGTTTCCTCAACCTTTTTATCCTTCACCACCTCC
38075 TTCTCCTTCTCTTCTGTTTCCTCAACCTT
1 TTCTCCTTCTCTTCTGTTTCCTCAACCTT
38104 CTTCTCTTCT
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
48 57 0.90
49 6 0.10
ACGTcount: A:0.08, C:0.38, G:0.03, T:0.51
Consensus pattern (48 bp):
TTCTCCTTCTCTTCTGTTTCCTCAACCTTTTTATCCTTCACCACCTCC
Done.