Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015196.1 Kokia drynarioides strain JFW-HI SEQ_130240, 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: 599855
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 661 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:393431 original size:29 final size:29
Alignment explanation
Indices: 393395--393971 Score: 572
Period size: 29 Copynumber: 19.8 Consensus size: 29
393385 GAGGTCCCTA
*
393395 AACTTCCAAAAATTCTATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
*
393424 AACTTCCAAAAATCCCATTTTTAACCC-CG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
*
393453 AAACTTCCAAAAATTCCATTTTTACCCTTG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
*
393483 AACTTCCAAAAATCCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
393512 AAACTTCCAAAAATTCCATTTTTACACC-CG
1 -AACTTCCAAAAATTCCATTTTTAC-CCTCG
* *
393542 AACTTCC-AAAATCCCAATTTTGACCC-CG
1 AACTTCCAAAAATTCC-ATTTTTACCCTCG
* * *
393570 AAATTCCAAAAGTTACATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* *
393599 AAATTCCAAAAA-TCTCATTTTTGA-CCTCT
1 AACTTCCAAAAATTC-CATTTTT-ACCCTCG
* *
393628 TACTTCCAAAAATCCCATTTTTGA-CC-CG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
*
393656 AAACTTCCAAAAATTCCA-TTTTACCCCCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
393685 AACTTCCAAATATCCCATTTTTAACCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* *
393714 AAACTTCCAAAAATTTCATTTTTACCCTTG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
*
393744 AACTTCCAAAAA-TCTCATTTTTGACCC-CAA
1 AACTTCCAAAAATTC-CATTTTT-ACCCTC-G
* * *
393774 AACTTCCAAAAGTTCCATTTTTGCCCTCA
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * * * *
393803 AAATTCAAAAAATCCCAATTTTGACCC-CAA
1 AACTTCCAAAAATTCC-ATTTTTACCCTC-G
*
393833 AACTTCCAAAAATTCCATTTTTACCCTCA
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * **
393862 AACTTCCAAAAATCCCATTTTGACCCTAA
1 AACTTCCAAAAATTCCATTTTTACCCTCG
393891 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* *
393920 AACTTCCAAAAATCCCATTTATGA-CC-CG
1 AACTTCCAAAAATTCCATTT-TTACCCTCG
393948 AAACTTCCAAAAATTCCATTTTTA
1 -AACTTCCAAAAATTCCATTTTTA
393972 TCCCATTTTT
Statistics
Matches: 462, Mismatches: 58, Indels: 57
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.00
28 54 0.12
29 279 0.60
30 124 0.27
31 4 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:393486 original size:59 final size:58
Alignment explanation
Indices: 393394--394060 Score: 578
Period size: 59 Copynumber: 11.3 Consensus size: 58
393384 GGAGGTCCCT
* *
393394 AAACTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT-ACCCCG
* * *
393453 AAACTTCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT-ACCCCG
* *
393512 AAACTTCCAAAAATTCCATTTTTACACC-CGAACTTCC-AAAATCCCAATTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTTAC-CCTCGAACTTCCAAAAATTCC-ATTTTTACCCCG
* * * *
393570 AAA-TTCCAAAAGTTACATTTTTACCCTCGAAATTCCAAAAA-TCTCATTTTTGACCTC-
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTC-CATTTTT-ACCCCG
** *
393627 TTACTTCCAAAAATCCCATTTTTGA-CC-CGAAACTTCCAAAAATTCCA-TTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCG-AACTTCCAAAAATTCCATTTTTA-CCCCG
* * * * *
393685 -AACTTCCAAATATCCCATTTTTAACCTCGAAACTTCCAAAAATTTCATTTTTACCCTTG
1 AAACTTCCAAAAATTCCATTTTTACCCTCG-AACTTCCAAAAATTCCATTTTTACCC-CG
* * *
393744 -AACTTCCAAAAA-TCTCATTTTTGACCC-CAAAACTTCCAAAAGTTCCATTTTTGCCCTC-
1 AAACTTCCAAAAATTC-CATTTTT-ACCCTC-GAACTTCCAAAAATTCCATTTTTACCC-CG
* * * * *
393802 AAAATTCAAAAAATCCCAATTTTGACCC-CAAAACTTCCAAAAATTCCATTTTTACCCTC-
1 AAACTTCCAAAAATTCC-ATTTTTACCCTC-GAACTTCCAAAAATTCCATTTTTACCC-CG
* * **
393861 AAACTTCCAAAAATCCCATTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTACCC-CG
* *
393920 -AACTTCCAAAAATCCCATTTATGA-CC-CGAAACTTCCAAAAATTCCATTTTTATCCCATTTTT
1 AAACTTCCAAAAATTCCATTT-TTACCCTCG-AACTTCCAAAAATTCCATTTTTA---C------
393982 ATCCCG
55 --CCCG
* * * * *
393988 AAACTTTCAAAAATTCCATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTACCCCG
394046 AAACTTCCAAAAATT
1 AAACTTCCAAAAATT
394061 ATCATTTTAC
Statistics
Matches: 518, Mismatches: 50, Indels: 81
0.80 0.08 0.12
Matches are distributed among these distances:
56 4 0.01
57 65 0.13
58 181 0.35
59 207 0.40
60 11 0.02
61 1 0.00
66 1 0.00
68 4 0.01
69 43 0.08
70 1 0.00
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:393611 original size:58 final size:59
Alignment explanation
Indices: 393398--394060 Score: 483
Period size: 58 Copynumber: 11.2 Consensus size: 59
393388 GTCCCTAAAC
* * * *
393398 TTCCAAAAATTCTATTTTTACCCTCG-AACTTCCAAAAATCCCATTTTTAACCCCGAAA
1 TTCCAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCAATTTTGACCCCGAAA
* * * *
393456 CTTCCAAAAATTCCATTTTTACCCTTG-AACTTCCAAAAATCCCATTTTTGACCTCGAAA
1 -TTCCAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCAATTTTGACCCCGAAA
*
393515 CTTCCAAAAATTCCATTTTTACACC-CG-AACTTCC-AAAATCCCAATTTTGACCCCGAAA
1 -TTCCAAAAATTCCATTTTTAC-CCTCGAAACTTCCAAAAATTCCAATTTTGACCCCGAAA
* * * * ** *
393573 TTCCAAAAGTTACATTTTTACCCTCGAAA-TTCCAAAAA-TCTCATTTTTGACCTCTTAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTC-CAATTTTGACCCCGAAA
* *
393631 TTCCAAAAATCCCATTTTTGA-CC-CGAAACTTCCAAAAATTCC-ATTTT-ACCCCCGAAC
1 TTCCAAAAATTCCATTTTT-ACCCTCGAAACTTCCAAAAATTCCAATTTTGA-CCCCGAAA
* * * * * * *
393688 TTCCAAATATCCCATTTTTAACCTCGAAACTTCCAAAAATTTC-ATTTTTACCCTTGAAC
1 TTCCAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCAATTTTGACCC-CGAAA
* * * *
393747 TTCCAAAAA-TCTCATTTTTGACCC-CAAAACTTCCAAAAGTTCCATTTTTG-CCCTCAAAA
1 TTCCAAAAATTC-CATTTTT-ACCCTCGAAACTTCCAAAAATTCCAATTTTGACCC-CGAAA
* * * * *
393806 TTCAAAAAATCCCAATTTTGACCC-CAAAACTTCCAAAAATTCC-ATTTTTACCCTC-AAA
1 TTCCAAAAATTCC-ATTTTTACCCTCGAAACTTCCAAAAATTCCAATTTTGACCC-CGAAA
* * * * *
393864 CTTCCAAAAATCCCATTTTGACCCT-AAAACTTCCAAAAATTCC-ATTTTTACCCTCGAAC
1 -TTCCAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCAATTTTGACCC-CGAAA
* * * *
393923 TTCCAAAAATCCCATTTATGA-CC-CGAAACTTCCAAAAATTCCATTTTTATCCCATTTTTATCC
1 TTCCAAAAATTCCATTT-TTACCCTCGAAACTTCCAAAAATTCC------A----ATTTTGACCC
393986 CGAAA
55 CGAAA
* * * * *
393991 CTTTCAAAAATTCCATTTTTACCC-CCAAACTTTCAAAAA-TCCCATTTTTACCCCGAAA
1 -TTCCAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCAATTTTGACCCCGAAA
394049 CTTCCAAAAATT
1 -TTCCAAAAATT
394061 ATCATTTTAC
Statistics
Matches: 512, Mismatches: 55, Indels: 75
0.80 0.09 0.12
Matches are distributed among these distances:
56 4 0.01
57 60 0.12
58 203 0.40
59 182 0.36
60 15 0.03
68 9 0.02
69 39 0.08
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
TTCCAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCAATTTTGACCCCGAAA
Found at i:393976 original size:40 final size:40
Alignment explanation
Indices: 393931--394011 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
393921 ACTTCCAAAA
393931 ATCCCATTTATGA-CCCGAAACTTCCAAAAATTCCATTTTT
1 ATCCCATTT-TGATCCCGAAACTTCCAAAAATTCCATTTTT
* *
393971 ATCCCATTTTTATCCCGAAACTTTCAAAAATTCCATTTTT
1 ATCCCATTTTGATCCCGAAACTTCCAAAAATTCCATTTTT
394011 A
1 A
394012 CCCCCAAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 2 0.05
40 36 0.95
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (40 bp):
ATCCCATTTTGATCCCGAAACTTCCAAAAATTCCATTTTT
Found at i:394020 original size:29 final size:29
Alignment explanation
Indices: 393974--394074 Score: 132
Period size: 29 Copynumber: 3.5 Consensus size: 29
393964 CATTTTTATC
* *
393974 CCATTTTTATCCCGAAACTTTCAAAAATT
1 CCATTTTTACCCCCAAACTTTCAAAAATT
*
394003 CCATTTTTACCCCCAAACTTTCAAAAATC
1 CCATTTTTACCCCCAAACTTTCAAAAATT
* *
394032 CCATTTTTACCCCGAAACTTCCAAAAATT
1 CCATTTTTACCCCCAAACTTTCAAAAATT
*
394061 ATCA-TTTTACCCCC
1 -CCATTTTTACCCCC
394075 GGATGTTCGA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 61 0.97
30 2 0.03
ACGTcount: A:0.33, C:0.32, G:0.02, T:0.34
Consensus pattern (29 bp):
CCATTTTTACCCCCAAACTTTCAAAAATT
Found at i:394021 original size:69 final size:69
Alignment explanation
Indices: 393905--394040 Score: 177
Period size: 69 Copynumber: 2.0 Consensus size: 69
393895 TCCAAAAATT
* *
393905 CCATTTTTACCCTCGAACTTCCAAAAATCCCATTTATGACCCGAAACTTCCAAAAATTCCATTTT
1 CCATTTTTACCCTCGAACTTCCAAAAATCCCATTTATGACCCCAAACTTCCAAAAATCCCATTTT
393970 TATC
66 TATC
* * * * *
393974 CCATTTTTATCC-CGAAACTTTCAAAAATTCCATTT-TTACCCCCAAACTTTCAAAAATCCCATT
1 CCATTTTTACCCTCG-AACTTCCAAAAATCCCATTTATGA-CCCCAAACTTCCAAAAATCCCATT
394037 TTTA
64 TTTA
394041 CCCCGAAACT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
68 4 0.07
69 54 0.93
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.35
Consensus pattern (69 bp):
CCATTTTTACCCTCGAACTTCCAAAAATCCCATTTATGACCCCAAACTTCCAAAAATCCCATTTT
TATC
Found at i:394069 original size:98 final size:98
Alignment explanation
Indices: 393873--394060 Score: 281
Period size: 98 Copynumber: 1.9 Consensus size: 98
393863 ACTTCCAAAA
* *
393873 ATCCCATTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCAT
1 ATCCCATTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCAT
393938 TTATGACCCGAAACTTCCAAAAATTCCATTTTT
66 TTATGACCCGAAACTTCCAAAAATTCCATTTTT
* * * *
393971 ATCCCATTTTTATCCC-GAAACTTTCAAAAATTCCATTTTTACCCCCAAACTTTCAAAAATCCCA
1 ATCCCATTTTGA-CCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCA
*
394035 TTT-TTACCCCGAAACTTCCAAAAATT
65 TTTATGA-CCCGAAACTTCCAAAAATT
394061 ATCATTTTAC
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
97 2 0.02
98 76 0.94
99 3 0.04
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (98 bp):
ATCCCATTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCAT
TTATGACCCGAAACTTCCAAAAATTCCATTTTT
Found at i:395774 original size:24 final size:23
Alignment explanation
Indices: 395731--395819 Score: 78
Period size: 24 Copynumber: 3.9 Consensus size: 23
395721 AATTTAAATT
395731 AATAAA-AG-TTTAACTT-AAACA
1 AATAAACAGATTTAA-TTGAAACA
395752 AATAAACAGACTTTAATTGAAACA
1 AATAAACAGA-TTTAATTGAAACA
**
395776 AATAAACA-AAGTAATTGAAACA
1 AATAAACAGATTTAATTGAAACA
* * *
395798 ATTAAATAGAGTTTAACTGAAA
1 AATAAACAGA-TTTAATTGAAA
395820 AATTATTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
21 6 0.11
22 19 0.35
23 4 0.07
24 26 0.47
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (23 bp):
AATAAACAGATTTAATTGAAACA
Found at i:395793 original size:22 final size:24
Alignment explanation
Indices: 395747--395803 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 24
395737 AGTTTAACTT
**
395747 AAACAAATAAACAGACTTTAATTG
1 AAACAAATAAACAGACAGTAATTG
395771 AAACAAATAAACA-A-AGTAATTG
1 AAACAAATAAACAGACAGTAATTG
*
395793 AAACAATTAAA
1 AAACAAATAAA
395804 TAGAGTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 16 0.53
23 1 0.03
24 13 0.43
ACGTcount: A:0.61, C:0.11, G:0.07, T:0.21
Consensus pattern (24 bp):
AAACAAATAAACAGACAGTAATTG
Found at i:397740 original size:24 final size:24
Alignment explanation
Indices: 397711--397767 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
397701 GACTAATAAA
*
397711 AGTTTAACTCAAACAAATAAACAT
1 AGTTTAACTCAAACAAATAAACAG
** *
397735 AGTTTATTTGAAACAAATAAACAG
1 AGTTTAACTCAAACAAATAAACAG
397759 AGTTTAACT
1 AGTTTAACT
397768 AAAAGATTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (24 bp):
AGTTTAACTCAAACAAATAAACAG
Found at i:422413 original size:28 final size:27
Alignment explanation
Indices: 422377--422440 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 27
422367 ATCATAGTAG
* *
422377 TTTGTCAATCTCAAAAGCTTTTATAAAT
1 TTTG-CAATCACAAAAGCTTTCATAAAT
422405 TTTGACAATCACAAAAGCTTTCATAAAT
1 TTTG-CAATCACAAAAGCTTTCATAAAT
422433 TTTGCAAT
1 TTTGCAAT
422441 TTGGATTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 4 0.12
28 29 0.88
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.39
Consensus pattern (27 bp):
TTTGCAATCACAAAAGCTTTCATAAAT
Found at i:431048 original size:17 final size:19
Alignment explanation
Indices: 431013--431049 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
431003 AATGTTAGTC
431013 ATATAAATATTAAATAAAA
1 ATATAAATATTAAATAAAA
*
431032 ATATATATATTAAA-AAAA
1 ATATAAATATTAAATAAAA
431050 GTTAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATATAAATATTAAATAAAA
Found at i:431902 original size:104 final size:104
Alignment explanation
Indices: 431716--431930 Score: 272
Period size: 104 Copynumber: 2.1 Consensus size: 104
431706 AAACCCTAAC
** * *
431716 CCTTAAATAAGAAGACAATGCATTTCAACGCACTCAAGCTCATGTCATCCTGCACTGACCATAAT
1 CCTTAAATAAGAAGACAATGCATTTCAACGCACTCAAGCTCACATCATCCTACACTGACCACAAT
* *
431781 ATCAATATCAACCGAACTAAAACTCAATCGGCTCCACAT
66 ATCAATACCAACCGAACTAAAACTCAATCCGCTCCACAT
* * * * *
431820 CCTTAAATAGGATA-ACAATGCGTTTCAACGCACTCGAA-TTCACATCATCCTATACTGACTACA
1 CCTTAAATAAGA-AGACAATGCATTTCAACGCACTC-AAGCTCACATCATCCTACACTGACCACA
* **
431883 ATATCTATACCAATTGAACTAAAACTCAATCCGCTCCACAT
64 ATATCAATACCAACCGAACTAAAACTCAATCCGCTCCACAT
431924 CCTTAAA
1 CCTTAAA
431931 CAATATCGTT
Statistics
Matches: 95, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
104 92 0.97
105 3 0.03
ACGTcount: A:0.37, C:0.28, G:0.09, T:0.25
Consensus pattern (104 bp):
CCTTAAATAAGAAGACAATGCATTTCAACGCACTCAAGCTCACATCATCCTACACTGACCACAAT
ATCAATACCAACCGAACTAAAACTCAATCCGCTCCACAT
Found at i:455816 original size:15 final size:16
Alignment explanation
Indices: 455786--455824 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
455776 TCGTAGAAAT
455786 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
455803 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
455818 ATAATTT
1 ATAATTT
455825 TTAAATGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:467542 original size:31 final size:34
Alignment explanation
Indices: 467470--467548 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 34
467460 TGCTGTTAAA
467470 AAAATATC-AATTTAACTTTTTTTTTTAAAACATTG
1 AAAA-ATCAAATTTAAC-TTTTTTTTTAAAACATTG
*
467505 -ATAATCAAATTTAAC-TTTTTTTT-AAA-ATTG
1 AAAAATCAAATTTAACTTTTTTTTTAAAACATTG
467535 AAAAATCAAATTTA
1 AAAAATCAAATTTA
467549 TATAAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 4 0.10
31 15 0.38
32 8 0.20
33 3 0.08
34 10 0.25
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (34 bp):
AAAAATCAAATTTAACTTTTTTTTTAAAACATTG
Found at i:468524 original size:11 final size:11
Alignment explanation
Indices: 468494--468526 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
468484 TTTTGAGTGA
468494 TTTTATAATAT
1 TTTTATAATAT
*
468505 TTTT-GAATAT
1 TTTTATAATAT
468515 TTTTATAATAT
1 TTTTATAATAT
468526 T
1 T
468527 AAATTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
TTTTATAATAT
Found at i:470478 original size:34 final size:34
Alignment explanation
Indices: 470437--470506 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
470427 TAAAACTATT
*
470437 AAAAATA-TTTTTTAT-ATTTTTAATGATTTTTTAA
1 AAAAATATTTTTTTATGATTTTT--TGAATTTTTAA
470471 AAAAATATTTTTTTATGATTTTTTGAATTTTTAA
1 AAAAATATTTTTTTATGATTTTTTGAATTTTTAA
470505 AA
1 AA
470507 TTTAAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
34 19 0.58
35 8 0.24
36 6 0.18
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (34 bp):
AAAAATATTTTTTTATGATTTTTTGAATTTTTAA
Found at i:471989 original size:23 final size:23
Alignment explanation
Indices: 471955--472015 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 23
471945 TAATCTTTTA
471955 AAAAT-ATAAAAATATAAATTATT
1 AAAATAAT-AAAATATAAATTATT
* *
471978 AAAATAATAAAAT-TATATTTTT
1 AAAATAATAAAATATAAATTATT
* *
472000 ACAATAGTAAAA-ATAA
1 AAAATAATAAAATATAA
472016 CTAATTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 19 0.61
23 10 0.32
24 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
AAAATAATAAAATATAAATTATT
Found at i:488526 original size:20 final size:20
Alignment explanation
Indices: 488501--488551 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
488491 ACATAGACTC
488501 CAAAAAGAAAAGAATTATGT
1 CAAAAAGAAAAGAATTATGT
488521 CAAAAAGAAAAGAATTATGT
1 CAAAAAGAAAAGAATTATGT
488541 CAAAAAGAAAA
1 CAAAAAGAAAA
488552 CATATGTGCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.65, C:0.06, G:0.14, T:0.16
Consensus pattern (20 bp):
CAAAAAGAAAAGAATTATGT
Found at i:494899 original size:13 final size:13
Alignment explanation
Indices: 494881--494906 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
494871 AATTATTCCT
494881 TAGTAACTTCTGG
1 TAGTAACTTCTGG
494894 TAGTAACTTCTGG
1 TAGTAACTTCTGG
494907 AAAGAGCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
TAGTAACTTCTGG
Found at i:496405 original size:21 final size:20
Alignment explanation
Indices: 496361--496405 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
496351 TATTTATATT
*
496361 TATAAAATAAATATTTTTAA
1 TATATAATAAATATTTTTAA
*
496381 -ATATAATAATTAGTTTTTAA
1 TATATAATAAATA-TTTTTAA
496401 TATAT
1 TATAT
496406 GGTGATAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TATATAATAAATATTTTTAA
Found at i:496730 original size:20 final size:22
Alignment explanation
Indices: 496705--496744 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
496695 ATAATAAAAA
496705 TAAAATATTT-TT-TAAATATT
1 TAAAATATTTATTATAAATATT
496725 TAAAATATTTATTATAAATA
1 TAAAATATTTATTATAAATA
496745 AATTTCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAAAATATTTATTATAAATATT
Found at i:498944 original size:31 final size:30
Alignment explanation
Indices: 498824--498980 Score: 185
Period size: 30 Copynumber: 5.3 Consensus size: 30
498814 AAAATCATTT
*
498824 TTTGACCCCCAAAGTTTT-AAAAATTCAAA
1 TTTGACCCCTAAAGTTTTCAAAAATTCAAA
*
498853 TTTGACCCCCAAAG-TTTCTAAAAATTCAAA
1 TTTGACCCCTAAAGTTTTC-AAAAATTCAAA
* ** *
498883 TTTAATACCTAAAGTTTTCAAATATTCAAA
1 TTTGACCCCTAAAGTTTTCAAAAATTCAAA
* *
498913 TTTGACCCCTTAATTTTTCCAAAAATTCAAA
1 TTTGACCCCTAAAGTTTT-CAAAAATTCAAA
*
498944 TTTGA-CCCTAAAGTTTTCAAAAATTAAAA
1 TTTGACCCCTAAAGTTTTCAAAAATTCAAA
*
498973 TTTAACCC
1 TTTGACCC
498981 TGTTTTAATG
Statistics
Matches: 108, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.03
29 29 0.27
30 56 0.52
31 20 0.19
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (30 bp):
TTTGACCCCTAAAGTTTTCAAAAATTCAAA
Found at i:512411 original size:53 final size:53
Alignment explanation
Indices: 512331--512432 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
512321 AAAGAAAGAC
*
512331 TTGGATGATTATGTTACTTCGACTTTTCATTTTGTTTGAAGTATCCATGCGAT
1 TTGGATAATTATGTTACTTCGACTTTTCATTTTGTTTGAAGTATCCATGCGAT
* *
512384 TTGGATAATTATTTTACTTC-AGCTTTTCATTTTGTTTGAAGTATTCATG
1 TTGGATAATTATGTTACTTCGA-CTTTTCATTTTGTTTGAAGTATCCATG
512433 TCCGACACAG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.02
53 44 0.98
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.50
Consensus pattern (53 bp):
TTGGATAATTATGTTACTTCGACTTTTCATTTTGTTTGAAGTATCCATGCGAT
Found at i:519444 original size:15 final size:16
Alignment explanation
Indices: 519419--519452 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
519409 AAAATGTAAT
519419 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
519435 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
519450 TTT
1 TTT
519453 TTTAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:519498 original size:83 final size:81
Alignment explanation
Indices: 519411--519566 Score: 199
Period size: 83 Copynumber: 1.9 Consensus size: 81
519401 TAAAAGTAAA
* * * * *
519411 AATG-TAATTTTATTATTTTAATAATTTATATTTTTATAATTTTTTAAAATAT-TAAATCAATTT
1 AATGATAATTTTACTA--TTAATAATTTAAAATTTTATAA-ATTATAAAATATCTAAAT-AATTT
519474 TTTATTATTTTCGAAAGGTC
62 TTTATTATTTTCGAAAGGTC
519494 AATGTATAATTTTACTATTAATAATTTAAAATTTTATAAATTATAAAATATCTAAATAATTTTTT
1 AATG-ATAATTTTACTATTAATAATTTAAAATTTTATAAATTATAAAATATCTAAATAATTTTTT
*
519559 TTTATTTT
65 ATTATTTT
519567 TAGGAAGACA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
82 25 0.39
83 29 0.45
85 10 0.16
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (81 bp):
AATGATAATTTTACTATTAATAATTTAAAATTTTATAAATTATAAAATATCTAAATAATTTTTTA
TTATTTTCGAAAGGTC
Found at i:532624 original size:19 final size:19
Alignment explanation
Indices: 532602--532640 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
532592 TTAAAAATGT
* *
532602 AAATAAATTATTTTTTAAA
1 AAATAAATAATTTTATAAA
*
532621 AAATGAATAATTTTATAAA
1 AAATAAATAATTTTATAAA
532640 A
1 A
532641 TATACTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
AAATAAATAATTTTATAAA
Found at i:549408 original size:8 final size:8
Alignment explanation
Indices: 549397--549421 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
549387 ATAATTTGAG
549397 TAATAAAT
1 TAATAAAT
549405 TAATAAAT
1 TAATAAAT
549413 TAATAAAT
1 TAATAAAT
549421 T
1 T
549422 TAAAATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAATAAAT
Found at i:567178 original size:30 final size:30
Alignment explanation
Indices: 567142--567204 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
567132 GTTTATACAC
567142 TTAAGTTTTGCTTACATAAGAGTCGTATAT
1 TTAAGTTTTGCTTACATAAGAGTCGTATAT
567172 TTAAGTTTTGCTTACATAAGAGTCGTATAT
1 TTAAGTTTTGCTTACATAAGAGTCGTATAT
567202 TTA
1 TTA
567205 CTTATGTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (30 bp):
TTAAGTTTTGCTTACATAAGAGTCGTATAT
Found at i:570834 original size:55 final size:56
Alignment explanation
Indices: 570768--570879 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 56
570758 GTCATTGAAC
* *
570768 TATTAAAATGGTTGTTATAT-AGCTTTTTTATTCACACCAACCAAAGCTCTCCTTT
1 TATTAAAATGGTTGTTATATAACCTTTTTCATTCACACCAACCAAAGCTCTCCTTT
* * *
570823 TATTAAAATGGTTGTTATATAACCTTTTTCATTCACACTAATCAAAGCTCTTCTTT
1 TATTAAAATGGTTGTTATATAACCTTTTTCATTCACACCAACCAAAGCTCTCCTTT
570879 T
1 T
570880 TCTTTTCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 20 0.39
56 31 0.61
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (56 bp):
TATTAAAATGGTTGTTATATAACCTTTTTCATTCACACCAACCAAAGCTCTCCTTT
Found at i:587031 original size:21 final size:21
Alignment explanation
Indices: 587007--587047 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
586997 CCACTGCAAA
587007 ATTAAAAAAAAAAAAAAAAAG
1 ATTAAAAAAAAAAAAAAAAAG
* * *
587028 ATTAATAATAAATAAAAAAA
1 ATTAAAAAAAAAAAAAAAAA
587048 TCATAAAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (21 bp):
ATTAAAAAAAAAAAAAAAAAG
Found at i:591709 original size:14 final size:15
Alignment explanation
Indices: 591671--591701 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
591661 AGCTGGTTGG
591671 AAATATATTGTATTGA
1 AAATATATTGTATT-A
591687 AAATATATTGTATTA
1 AAATATATTGTATTA
591702 TATATATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 1 0.07
16 14 0.93
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (15 bp):
AAATATATTGTATTA
Done.