Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015218.1 Kokia drynarioides strain JFW-HI SEQ_130262, 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: 183870
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 262 characters in sequence are not A, C, G, or T
Found at i:671 original size:29 final size:29
Alignment explanation
Indices: 623--886 Score: 277
Period size: 29 Copynumber: 9.0 Consensus size: 29
613 AGAGGTCCTT
*
623 AAACTATCCAAAAATTCCATTTTTACCCCC
1 AAACT-TCCAAAAATCCCATTTTTACCCCC
*
653 TAACTTCCAAAAATCCCA-TTTTACCCCCC
1 AAACTTCCAAAAATCCCATTTTTA-CCCCC
682 AAACTTCCAAAAATCCCATTTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTACCCCC
* *
711 AAACTTCCAAAATTACCC--TTCTACCCCC
1 AAACTTCCAAAAAT-CCCATTTTTACCCCC
** *
739 GAAACTTCCAAAAATTTCATTTTTACCACCG
1 -AAACTTCCAAAAATCCCATTTTTACC-CCC
* *
770 AGA-TTCCAAAAATCCCATTTTTCACCCCG
1 AAACTTCCAAAAATCCCATTTTT-ACCCCC
* *
799 AAACTTCCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATCCCATTTTTACCCCC
* * * *
828 GAGCTTCCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCC
*
858 AAACTTCCAAAAATTACCA-TTTTACCCCC
1 AAACTTCCAAAAA-TCCCATTTTTACCCCC
887 GGATGTCTAA
Statistics
Matches: 198, Mismatches: 25, Indels: 23
0.80 0.10 0.09
Matches are distributed among these distances:
28 15 0.08
29 117 0.59
30 60 0.30
31 6 0.03
ACGTcount: A:0.34, C:0.34, G:0.03, T:0.29
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTACCCCC
Found at i:719 original size:58 final size:58
Alignment explanation
Indices: 623--886 Score: 311
Period size: 59 Copynumber: 4.5 Consensus size: 58
613 AGAGGTCCTT
* *
623 AAACTATCCAAAAATTCCATTTTTACCCCCTAACTTCCAAAAATCCCATTTTACCCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTACCCCCG
* * *
682 AAACTTCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAATTACCC-TTCTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAAT-CCCATTTTACCCCCG
* * * *
740 AAACTTCCAAAAATTTCATTTTTACCACCGAGA-TTCCAAAAATCCCATTTTTCACCCCG
1 AAACTTCCAAAAATTCCATTTTTACC-CCCAAACTTCCAAAAATCCCATTTTAC-CCCCG
* * * * *
799 AAACTTCCAAAAATTCCATTTTTACCCTCGAGCTTCCAAAAATTCCATTTTTGA-CCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCA-TTTT-ACCCCCG
858 AAACTTCCAAAAATTACCA-TTTTACCCCC
1 AAACTTCCAAAAATT-CCATTTTTACCCCC
887 GGATGTCTAA
Statistics
Matches: 175, Mismatches: 22, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
57 3 0.02
58 82 0.47
59 83 0.47
60 7 0.04
ACGTcount: A:0.34, C:0.34, G:0.03, T:0.29
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTACCCCCG
Found at i:811 original size:59 final size:58
Alignment explanation
Indices: 623--944 Score: 304
Period size: 59 Copynumber: 5.5 Consensus size: 58
613 AGAGGTCCTT
* *
623 AAACTATCCAAAAATTCCATTTTTACCCCCTA-ACTTCCAAAAATCCCATTTTACCCCCC
1 AAACT-TCCAAAAATTCCATTTTTA-CCCCGAGACTTCCAAAAATCCCATTTTACCCCCG
* * * * *
682 AAACTTCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAATTACCC-TTCTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCCGAGACTTCCAAAAAT-CCCATTTTACCCCCG
* *
740 AAACTTCCAAAAATTTCATTTTTACCACCGAGA-TTCCAAAAATCCCATTTTTCACCCCG
1 AAACTTCCAAAAATTCCATTTTTACC-CCGAGACTTCCAAAAATCCCATTTTAC-CCCCG
* *
799 AAACTTCCAAAAATTCCATTTTTACCCTCGAG-CTTCCAAAAATTCCATTTTTGA-CCCCA
1 AAACTTCCAAAAATTCCATTTTTACCC-CGAGACTTCCAAAAATCCCA-TTTT-ACCCCCG
* * * *
858 AAACTTCCAAAAATTACCA-TTTTACCCCCG-GA-TGTCTAAAGATTCCATTCTTAACCCCG
1 AAACTTCCAAAAATT-CCATTTTTA-CCCCGAGACT-TCCAAAAATCCCATT-TTACCCCCG
*
917 -AACTTTCCTAAAATTACCA-TTTTACCCC
1 AAAC-TTCCAAAAATT-CCATTTTTACCCC
945 CGAGTATACG
Statistics
Matches: 227, Mismatches: 20, Indels: 33
0.81 0.07 0.12
Matches are distributed among these distances:
57 8 0.04
58 88 0.39
59 121 0.53
60 10 0.04
ACGTcount: A:0.33, C:0.34, G:0.04, T:0.30
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCGAGACTTCCAAAAATCCCATTTTACCCCCG
Found at i:943 original size:29 final size:28
Alignment explanation
Indices: 624--944 Score: 260
Period size: 29 Copynumber: 11.0 Consensus size: 28
614 GAGGTCCTTA
*
624 AACTATCCAAAAATTCCATTTTTACCCCCT
1 AACT-TCCAAAAATTCCATTTTTA-CCCCG
* *
654 AACTTCCAAAAATCCCA-TTTTACCCCCCA
1 AACTTCCAAAAATTCCATTTTTA--CCCCG
* *
683 AACTTCCAAAAATCCCATTTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTA-CCCCG
* *
712 AACTTCC-AAAATTACC-CTTCTACCCCCG
1 AACTTCCAAAAATT-CCATTTTTA-CCCCG
*
740 AAACTTCCAAAAATTTCATTTTTACCACCG
1 -AACTTCCAAAAATTCCATTTTTACC-CCG
*
770 AGA-TTCCAAAAATCCCATTTTTCACCCCG
1 A-ACTTCCAAAAATTCCATTTTT-ACCCCG
799 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCC-CG
* *
829 AGCTTCCAAAAATTCCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCC-G
859 AACTTCCAAAAATTACCA-TTTTACCCCCG
1 AACTTCCAAAAATT-CCATTTTTA-CCCCG
* * * *
888 GA-TGTCTAAAGATTCCATTCTTAACCCCG
1 AACT-TCCAAAAATTCCATT-TTTACCCCG
*
917 AACTTTCCTAAAATTACCA-TTTTACCCC
1 AAC-TTCCAAAAATT-CCATTTTTACCCC
945 CGAGTATACG
Statistics
Matches: 244, Mismatches: 25, Indels: 45
0.78 0.08 0.14
Matches are distributed among these distances:
28 23 0.09
29 131 0.54
30 83 0.34
31 7 0.03
ACGTcount: A:0.33, C:0.34, G:0.04, T:0.30
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTTACCCCG
Found at i:4199 original size:18 final size:18
Alignment explanation
Indices: 4158--4210 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
4148 ACAAATAACT
4158 TAAAAATTATAAAAAAAA
1 TAAAAATTATAAAAAAAA
* *
4176 TCAAAATTA-AAAAATATA
1 TAAAAATTATAAAAA-AAA
4194 TAAAAAGTTCATAAAAA
1 TAAAAA-TT-ATAAAAA
4211 TCTTAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 5 0.18
18 15 0.54
19 2 0.07
20 1 0.04
21 5 0.18
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (18 bp):
TAAAAATTATAAAAAAAA
Found at i:8335 original size:18 final size:18
Alignment explanation
Indices: 8312--8346 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
8302 TGGTGGTGCT
8312 CCAGTTGCTGCGGCTGCA
1 CCAGTTGCTGCGGCTGCA
*
8330 CCAGTTGCTGCTGCTGC
1 CCAGTTGCTGCGGCTGC
8347 TGGTGGTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.34, G:0.31, T:0.26
Consensus pattern (18 bp):
CCAGTTGCTGCGGCTGCA
Found at i:11811 original size:18 final size:16
Alignment explanation
Indices: 11788--11835 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 16
11778 TTTTTTTTAC
11788 ATTTTATAAAATTTGAAA
1 ATTTTATAAAATTTG--A
11806 ATTTTATAAATATATTGA
1 ATTTTATAAA-AT-TTGA
11824 ATTTTA-AAAATT
1 ATTTTATAAAATT
11836 ATTTTGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
16 2 0.07
17 3 0.11
18 17 0.61
19 2 0.07
20 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (16 bp):
ATTTTATAAAATTTGA
Found at i:11953 original size:18 final size:18
Alignment explanation
Indices: 11916--11954 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
11906 GACCAATATG
* *
11916 TTATTTGAGTTATTCCAA
1 TTATTCGAGTTAGTCCAA
*
11934 TTATTCGAGTTAGTCGAA
1 TTATTCGAGTTAGTCCAA
11952 TTA
1 TTA
11955 AAAAATTTAA
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:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (18 bp):
TTATTCGAGTTAGTCCAA
Found at i:12145 original size:31 final size:28
Alignment explanation
Indices: 12079--12147 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 28
12069 CCGTACATCT
*
12079 AAAATTTAACTCTTTTACTTTTATTTTC
1 AAAATTTAACTCTTTTACTTTTAATTTC
*
12107 AAGAATTTAATCTCTTTGTATTTTTAAATTTC
1 AA-AATTTAA-CTCTTT-TACTTTT-AATTTC
12139 AAAATTTAA
1 AAAATTTAA
12148 ATTTAATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 2 0.06
29 7 0.20
30 6 0.17
31 13 0.37
32 7 0.20
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.52
Consensus pattern (28 bp):
AAAATTTAACTCTTTTACTTTTAATTTC
Found at i:16249 original size:7 final size:7
Alignment explanation
Indices: 16237--16273 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
16227 TCTTGATGAA
16237 AGTGGTG
1 AGTGGTG
16244 AGTGGTG
1 AGTGGTG
16251 AGTGGTG
1 AGTGGTG
16258 AGTGGTG
1 AGTGGTG
16265 AGTGGTG
1 AGTGGTG
16272 AG
1 AG
16274 AGACAGACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.16, C:0.00, G:0.57, T:0.27
Consensus pattern (7 bp):
AGTGGTG
Found at i:17392 original size:2 final size:2
Alignment explanation
Indices: 17385--17414 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17375 AAGTTGAAGA
17385 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17415 TAAAGCTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18823 original size:15 final size:15
Alignment explanation
Indices: 18786--18824 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
18776 TATTCTTATT
18786 ATTTCTTTTTTCTTC
1 ATTTCTTTTTTCTTC
* *
18801 ATTCCTTTTTTTTTC
1 ATTTCTTTTTTCTTC
*
18816 TTTTCTTTT
1 ATTTCTTTT
18825 ATTAACAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (15 bp):
ATTTCTTTTTTCTTC
Found at i:19632 original size:14 final size:15
Alignment explanation
Indices: 19599--19640 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
19589 ATAAAAATAT
*
19599 TATAAAAAGAAAAAA
1 TATAAAATGAAAAAA
*
19614 TATAAAATGAAATAA
1 TATAAAATGAAAAAA
*
19629 -ATAAAGTGAAAA
1 TATAAAATGAAAA
19641 CGAAATTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (15 bp):
TATAAAATGAAAAAA
Found at i:25826 original size:31 final size:31
Alignment explanation
Indices: 25791--25865 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
25781 TTTTAAAGCA
*
25791 AAACTAAAATT-ACAAAATTTGAAAAGTACAT
1 AAACTAAAATTGAC-AAATTTAAAAAGTACAT
*
25822 AAACTAAAATTGACCAATTTAAAAAGTACA-
1 AAACTAAAATTGACAAATTTAAAAAGTACAT
*
25852 AAAGTTAAAATTGA
1 AAA-CTAAAATTGA
25866 TCACATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 3 0.08
31 34 0.87
32 2 0.05
ACGTcount: A:0.57, C:0.09, G:0.08, T:0.25
Consensus pattern (31 bp):
AAACTAAAATTGACAAATTTAAAAAGTACAT
Found at i:40000 original size:21 final size:24
Alignment explanation
Indices: 39956--40001 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
39946 TCAATATAAC
39956 AATAAATAATGATATATAACTATT
1 AATAAATAATGATATATAACTATT
*
39980 AATATATAATG-TAT-T-ACTATT
1 AATAAATAATGATATATAACTATT
40001 A
1 A
40002 TATGTTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 1 0.05
23 3 0.14
24 10 0.48
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (24 bp):
AATAAATAATGATATATAACTATT
Found at i:44830 original size:37 final size:37
Alignment explanation
Indices: 44774--44888 Score: 153
Period size: 37 Copynumber: 3.1 Consensus size: 37
44764 CATTCATTCT
* *
44774 TGAAT-CACCGGCACAAAACCTGCTAGGCACATAA-CC
1 TGAATACACCGGCACGAAACCTACTAGGCACA-AAGCC
* *
44810 TGATTACACCGGCACGAAACCTACTAGGCACAAAGCT
1 TGAATACACCGGCACGAAACCTACTAGGCACAAAGCC
* *
44847 TGAATGCACCGGCACGAAACCTACTTGGCACAAAGCC
1 TGAATACACCGGCACGAAACCTACTAGGCACAAAGCC
44884 TGAAT
1 TGAAT
44889 TTATAGAAGC
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 6 0.09
37 63 0.91
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.16
Consensus pattern (37 bp):
TGAATACACCGGCACGAAACCTACTAGGCACAAAGCC
Found at i:47023 original size:30 final size:30
Alignment explanation
Indices: 46989--47046 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
46979 TAAAAGTACA
*
46989 ATTTTTAAAGGATTAAATTAAAATTTTATC
1 ATTTTTAAAGGATTAAAGTAAAATTTTATC
* * *
47019 ATTTTTAAGGGGTTAAAGTATAATTTTA
1 ATTTTTAAAGGATTAAAGTAAAATTTTA
47047 GTTTTATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (30 bp):
ATTTTTAAAGGATTAAAGTAAAATTTTATC
Found at i:47867 original size:7 final size:7
Alignment explanation
Indices: 47855--47889 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
47845 ACATGCATTC
47855 ATGCCAG
1 ATGCCAG
47862 ATGCCAG
1 ATGCCAG
47869 ATGCCAG
1 ATGCCAG
47876 ATGCCAG
1 ATGCCAG
47883 ATGCCAG
1 ATGCCAG
47890 TGAATTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (7 bp):
ATGCCAG
Found at i:53637 original size:2 final size:2
Alignment explanation
Indices: 53632--53657 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53622 AAAAAAAACA
53632 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
53658 TAAGACCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56759 original size:127 final size:127
Alignment explanation
Indices: 56533--56782 Score: 491
Period size: 127 Copynumber: 2.0 Consensus size: 127
56523 AGTGAATATT
56533 AGCATTGCTTCCAATTTGTAACAGAACTGGTTTTAATGCCTGTGTTTGAGCTTATTGGAACTGAT
1 AGCATTGCTTCCAATTTGTAACAGAACTGGTTTTAATGCCTGTGTTTGAGCTTATTGGAACTGAT
56598 GGCAGTGGAACTTATAATATAAATTAGAAGGAAAATTTCTACCAAATTTTTAATATGGTCGC
66 GGCAGTGGAACTTATAATATAAATTAGAAGGAAAATTTCTACCAAATTTTTAATATGGTCGC
56660 AGCATTGCTTCCAATTTGTAACAGAACTGGTTTTAATGCCTGTGTTTGAGCTTATTGGAACTGAT
1 AGCATTGCTTCCAATTTGTAACAGAACTGGTTTTAATGCCTGTGTTTGAGCTTATTGGAACTGAT
*
56725 GGCAGTGGAACTTATAATATAAATTAGAAGGAAAATTTCTACCAAGTTTTTAATATGG
66 GGCAGTGGAACTTATAATATAAATTAGAAGGAAAATTTCTACCAAATTTTTAATATGG
56783 AAGTTTCTAT
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 122 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.36
Consensus pattern (127 bp):
AGCATTGCTTCCAATTTGTAACAGAACTGGTTTTAATGCCTGTGTTTGAGCTTATTGGAACTGAT
GGCAGTGGAACTTATAATATAAATTAGAAGGAAAATTTCTACCAAATTTTTAATATGGTCGC
Found at i:70225 original size:22 final size:22
Alignment explanation
Indices: 70200--70242 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
70190 AAAGTTACAA
* *
70200 TAAAAAATATTTTTTTAAATAT
1 TAAAAAATAATTTTTAAAATAT
*
70222 TAAAATATAATTTTTAAAATA
1 TAAAAAATAATTTTTAAAATA
70243 AACAAATCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAAAAATAATTTTTAAAATAT
Found at i:72516 original size:12 final size:12
Alignment explanation
Indices: 72467--72572 Score: 58
Period size: 12 Copynumber: 8.9 Consensus size: 12
72457 TTGTTTATTA
*
72467 TTCATTAACATTG
1 TTCATGAACA-TG
*
72480 TTCGTGAACATG
1 TTCATGAACATG
* *
72492 TTCAAT-TATATG
1 TTC-ATGAACATG
72504 TTCATGAACATG
1 TTCATGAACATG
** **
72516 TTTGTTTA-ATG
1 TTCATGAACATG
72527 TTCATGAACATG
1 TTCATGAACATG
*
72539 TTCGATTAA-AT-
1 TTC-ATGAACATG
**
72550 TAAATGAACATG
1 TTCATGAACATG
72562 TTCATGAACAT
1 TTCATGAACAT
72573 TAAACAAACG
Statistics
Matches: 66, Mismatches: 21, Indels: 13
0.66 0.21 0.13
Matches are distributed among these distances:
10 4 0.06
11 12 0.18
12 37 0.56
13 13 0.20
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (12 bp):
TTCATGAACATG
Found at i:72531 original size:23 final size:24
Alignment explanation
Indices: 72478--72565 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 24
72468 TCATTAACAT
*
72478 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTATA
***
72502 TGTTCATGAACATGTTTGTTTA-A
1 TGTTCATGAACATGTTCAATTATA
* *
72525 TGTTCATGAACATGTTCGATTAAA
1 TGTTCATGAACATGTTCAATTATA
**
72549 T-TAAATGAACATGTTCA
1 TGTTCATGAACATGTTCA
72566 TGAACATTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
23 34 0.63
24 20 0.37
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (24 bp):
TGTTCATGAACATGTTCAATTATA
Found at i:72574 original size:23 final size:23
Alignment explanation
Indices: 72530--72576 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
72520 TTTAATGTTC
*
72530 ATGAACATGTTCGATTAAATTAA
1 ATGAACATGTTCGATGAAATTAA
72553 ATGAACATGTTC-ATGAACATTAA
1 ATGAACATGTTCGATGAA-ATTAA
72576 A
1 A
72577 CAAACGAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (23 bp):
ATGAACATGTTCGATGAAATTAA
Found at i:73924 original size:23 final size:23
Alignment explanation
Indices: 73904--73948 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
73894 ATGTTATTTT
*
73904 TTATGCGTTTTTACTATTATTTCG
1 TTAT-CGTTTTTAATATTATTTCG
*
73928 TTATCTTTTTTAATATTATTT
1 TTATCGTTTTTAATATTATTT
73949 AAATATTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.64
Consensus pattern (23 bp):
TTATCGTTTTTAATATTATTTCG
Found at i:77523 original size:19 final size:20
Alignment explanation
Indices: 77499--77549 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
77489 AAGTTTTAAC
77499 TTTAATAATAATGTA-TTA-T
1 TTTAATAATAAT-TAGTTAGT
77518 TTTAATAA-AATTAGTTAGT
1 TTTAATAATAATTAGTTAGT
77537 TTTAATAATAATT
1 TTTAATAATAATT
77550 TAAAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.07
18 6 0.21
19 17 0.59
20 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (20 bp):
TTTAATAATAATTAGTTAGT
Found at i:88919 original size:18 final size:17
Alignment explanation
Indices: 88898--88931 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
88888 TTAACAAATA
*
88898 TAAACATATTAGACTATG
1 TAAACAT-TTACACTATG
88916 TAAACATTTACACTAT
1 TAAACATTTACACTAT
88932 TATTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (17 bp):
TAAACATTTACACTATG
Found at i:89855 original size:17 final size:16
Alignment explanation
Indices: 89833--89872 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
89823 TTATTTAATC
89833 ACATATTAACAATATAA
1 ACATATTAA-AATATAA
*
89850 ACATATTAAACTATAA
1 ACATATTAAAATATAA
*
89866 AAATATT
1 ACATATT
89873 TACATTATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
ACATATTAAAATATAA
Found at i:94071 original size:14 final size:14
Alignment explanation
Indices: 94052--94078 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
94042 AATAACCCTA
94052 AACCAAAATATGTT
1 AACCAAAATATGTT
94066 AACCAAAATATGT
1 AACCAAAATATGT
94079 GAGTAACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (14 bp):
AACCAAAATATGTT
Found at i:94150 original size:6 final size:6
Alignment explanation
Indices: 94141--94200 Score: 63
Period size: 6 Copynumber: 10.2 Consensus size: 6
94131 ATCAGAATCT
* *
94141 AATCAA AATCAA AAT-AA AAT-TA AATCGAA AATGAA AATCAA AATTC-A
1 AATCAA AATCAA AATCAA AATCAA AATC-AA AATCAA AATCAA AA-TCAA
94188 AATCAA AATCAA A
1 AATCAA AATCAA A
94201 TAAACCCTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 11 0.24
6 29 0.63
7 6 0.13
ACGTcount: A:0.65, C:0.12, G:0.03, T:0.20
Consensus pattern (6 bp):
AATCAA
Found at i:94625 original size:30 final size:31
Alignment explanation
Indices: 94558--94628 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
94548 ATCTAATTTC
*
94558 AGTGACTGTTTTGTCACTTTTCGATAATGTT
1 AGTGACTGTTTTGTAACTTTTCGATAATGTT
94589 AGTGACTGTTTTGTAACATTTTC-A-AA-GTT
1 AGTGACTGTTTTGTAAC-TTTTCGATAATGTT
94618 GAGTGACTGTT
1 -AGTGACTGTT
94629 GTGTTAAATG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 3 0.08
30 12 0.32
31 17 0.46
32 5 0.14
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.45
Consensus pattern (31 bp):
AGTGACTGTTTTGTAACTTTTCGATAATGTT
Found at i:95287 original size:15 final size:16
Alignment explanation
Indices: 95269--95301 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
95259 TCCTTCATAT
95269 TTTCT-CTTCCCTTTC
1 TTTCTCCTTCCCTTTC
95284 TTTCTCCTTCCCTTTC
1 TTTCTCCTTCCCTTTC
95300 TT
1 TT
95302 GCTGTCCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTCTCCTTCCCTTTC
Found at i:96605 original size:72 final size:72
Alignment explanation
Indices: 96484--96830 Score: 297
Period size: 72 Copynumber: 4.7 Consensus size: 72
96474 AGGTGGGCGT
* * * * * * *
96484 TGAATTGCTACCAAAACTTTTAGATGGTTCTACAATTGCCAACAG-GATGGGTATGAATATGGAG
1 TGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAA-AGAGATGGGTATGAATATGGAG
96548 -GTGAACA
65 AGTGAACA
* * * * * * *
96555 CTGGATTGCTACCATATCCTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTAAGACTATGGAG
1 -TGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTATGAATATGGAG
96620 AG-GAACA
65 AGTGAACA
* * * *
96627 TTGAATTGTTACCAAAGCTTGTAGAAGATTCTACAAGTCCTAAAGAGATGGGTCAT-AATACGGA
1 -TGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGT-ATGAATATGGA
*
96691 GGAGTGGAGCA
64 -GAGT-GAACA
* * * * *
96702 TCGAATTGATATCAAAGCTTATGGAAGATTCTCCAAGTGCTAAAGAGATGGATATGAAAATGGAG
1 T-GAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTATGAATATGGA-
*
96767 GAGGTGAACGT
64 GA-GTGAAC-A
* * ** * *
96778 TCAATCGATGTCAAAGCTTATAGAAGATTCTTCAAATGCTAAAGAGATGGGTA
1 TGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTA
96831 AGGATGTGGC
Statistics
Matches: 224, Mismatches: 41, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
71 2 0.01
72 106 0.47
73 5 0.02
74 3 0.01
75 105 0.47
76 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (72 bp):
TGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTATGAATATGGAGA
GTGAACA
Found at i:96739 original size:75 final size:73
Alignment explanation
Indices: 96574--96830 Score: 279
Period size: 75 Copynumber: 3.5 Consensus size: 73
96564 TACCATATCC
* *
96574 TATAGAAGATTCTACAAGTGCTAAAGAGATGGGTA-AGACTATGGA-GA-GGAACATTGAATTGT
1 TATAGAAGATTCTACAAGTGCTAAAGAGATGGGTATA-A-TATGGAGGAGGGAACATCGAATTGA
*
96636 TACCAAAGCT
64 TATCAAAGCT
* * * *
96646 TGTAGAAGATTCTACAAGTCCTAAAGAGATGGGTCATAATACGGAGGAGTGGAGCATCGAATTGA
1 TATAGAAGATTCTACAAGTGCTAAAGAGATGGGT-ATAATATGGAGGAG-GGAACATCGAATTGA
96711 TATCAAAGCT
64 TATCAAAGCT
* * * * * *
96721 TATGGAAGATTCTCCAAGTGCTAAAGAGATGGATATGAAAATGGAGGAGGTGAACGTTC-AATCG
1 TATAGAAGATTCTACAAGTGCTAAAGAGATGGGTAT-AATATGGAGGAGG-GAAC-ATCGAATTG
*
96785 ATGTCAAAGCT
63 ATATCAAAGCT
* *
96796 TATAGAAGATTCTTCAAATGCTAAAGAGATGGGTA
1 TATAGAAGATTCTACAAGTGCTAAAGAGATGGGTA
96831 AGGATGTGGC
Statistics
Matches: 155, Mismatches: 22, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
72 37 0.24
73 4 0.03
74 4 0.03
75 108 0.70
76 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (73 bp):
TATAGAAGATTCTACAAGTGCTAAAGAGATGGGTATAATATGGAGGAGGGAACATCGAATTGATA
TCAAAGCT
Found at i:104142 original size:4 final size:4
Alignment explanation
Indices: 104127--104177 Score: 68
Period size: 4 Copynumber: 12.8 Consensus size: 4
104117 CTTCTTCTCC
* *
104127 TTCT TCCT TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT
104175 TTC
1 TTC
104178 CTTCATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 3 0.07
4 35 0.85
5 3 0.07
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTCT
Found at i:104142 original size:12 final size:11
Alignment explanation
Indices: 104127--104187 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 11
104117 CTTCTTCTCC
104127 TTCTTCCTTTCT
1 TTCTTCCTTT-T
*
104139 TTCTTTCTTTCT
1 TTCTTCCTTT-T
104151 TTCTTTCTCTTTT
1 TTC-TTC-CTTTT
*
104164 TTCTTTCTTTT
1 TTCTTCCTTTT
*
104175 TTCCTTCATTTT
1 TT-CTTCCTTTT
104187 T
1 T
104188 CGTTGGTCCC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
11 7 0.17
12 24 0.59
13 6 0.15
14 4 0.10
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (11 bp):
TTCTTCCTTTT
Found at i:105075 original size:21 final size:21
Alignment explanation
Indices: 105051--105193 Score: 196
Period size: 21 Copynumber: 6.8 Consensus size: 21
105041 CTTCTATGGC
*
105051 AATGAACCTGACCCAGGCAGA
1 AATGAACCCGACCCAGGCAGA
* *
105072 AATGAACCCGACCCTGGCAGG
1 AATGAACCCGACCCAGGCAGA
* * *
105093 AATGAACCCGATCCTGGCAGG
1 AATGAACCCGACCCAGGCAGA
*
105114 AATGAACCCGACCCTGGCAGA
1 AATGAACCCGACCCAGGCAGA
* *
105135 AATGAACCCGACCCGGGAAGA
1 AATGAACCCGACCCAGGCAGA
105156 AATGAACCCGACCCAGGCAGA
1 AATGAACCCGACCCAGGCAGA
*
105177 AATGAACCTGACCCAGG
1 AATGAACCCGACCCAGG
105194 ACGCAAAATT
Statistics
Matches: 111, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 111 1.00
ACGTcount: A:0.34, C:0.31, G:0.26, T:0.09
Consensus pattern (21 bp):
AATGAACCCGACCCAGGCAGA
Found at i:114842 original size:29 final size:28
Alignment explanation
Indices: 114810--114989 Score: 148
Period size: 29 Copynumber: 6.1 Consensus size: 28
114800 TAGTAATCTC
* * *
114810 TGGATGTTTCGGAGTCAAAATGGGATTTT
1 TGGAAGTTTCGGGGT-AAAATGGTATTTT
*
114839 TGGAAG-TTCGAGGGTAAAATGGTAATTT
1 TGGAAGTTTCG-GGGTAAAATGGTATTTT
*
114867 TGAGAAGTTTCGGGGTTAAAAATGATATTTT
1 TG-GAAGTTTCGGGG-T-AAAATGGTATTTT
* *
114898 TGGGAGTTTAGGGGTAAAATGGTATTTTT
1 TGGAAGTTTCGGGGTAAAATGGTA-TTTT
* ** *
114927 TAGAAGTTTTAGGGTCAAAAATGGGATTTT
1 TGGAAGTTTCGGGGT--AAAATGGTATTTT
*
114957 TGGAAG-TTCGGGGGTAAAATGGTAAATTT
1 TGGAAGTTTC-GGGGTAAAATGGT-ATTTT
114986 TGGA
1 TGGA
114990 CAATTTAGGG
Statistics
Matches: 122, Mismatches: 19, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
28 32 0.26
29 41 0.34
30 28 0.23
31 21 0.17
ACGTcount: A:0.29, C:0.03, G:0.31, T:0.36
Consensus pattern (28 bp):
TGGAAGTTTCGGGGTAAAATGGTATTTT
Found at i:114913 original size:59 final size:59
Alignment explanation
Indices: 114826--114987 Score: 200
Period size: 59 Copynumber: 2.7 Consensus size: 59
114816 TTTCGGAGTC
* * *
114826 AAAATGGGATTTTTGGAAGTTC-GAGGGTAAAATGGTAATTTTGAGAAGTTTCGGGGTTA
1 AAAATGAGATTTTTGGAAGTTCAG-GGGTAAAATGGTAATTTTGAGAAGTTTCAGGGTCA
* * * * * *
114885 AAAATGATATTTTTGGGAGTTTAGGGGTAAAATGGTATTTTTTAGAAGTTTTAGGGTCA
1 AAAATGAGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTGAGAAGTTTCAGGGTCA
* *
114944 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAAATTTTG
1 AAAATGAGATTTTTGGAAGTTCAGGGGTAAAATGGT-AATTTTG
114988 GACAATTTAG
Statistics
Matches: 85, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 79 0.93
60 6 0.07
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.36
Consensus pattern (59 bp):
AAAATGAGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTGAGAAGTTTCAGGGTCA
Found at i:116069 original size:13 final size:13
Alignment explanation
Indices: 116051--116077 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
116041 TATTATTAAA
116051 TATTACATTTGTC
1 TATTACATTTGTC
116064 TATTACATTTGTC
1 TATTACATTTGTC
116077 T
1 T
116078 TTTTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (13 bp):
TATTACATTTGTC
Found at i:117480 original size:20 final size:20
Alignment explanation
Indices: 117432--117473 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
117422 TTTCTTATCC
117432 GAAGCGAGCCCACACTCGCA
1 GAAGCGAGCCCACACTCGCA
117452 GAAGCGAGCCCACACTCGCA
1 GAAGCGAGCCCACACTCGCA
117472 GA
1 GA
117474 CGTGAGCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.38, G:0.26, T:0.05
Consensus pattern (20 bp):
GAAGCGAGCCCACACTCGCA
Found at i:118905 original size:6 final size:6
Alignment explanation
Indices: 118890--118926 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
118880 ATGGAATTGG
118890 CCCT-C CCCTGC CCCTGC CCCTGC CCCTGC CCCTGC CC
1 CCCTGC CCCTGC CCCTGC CCCTGC CCCTGC CCCTGC CC
118927 TGCTCTGCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.00, C:0.70, G:0.14, T:0.16
Consensus pattern (6 bp):
CCCTGC
Found at i:125279 original size:18 final size:18
Alignment explanation
Indices: 125255--125337 Score: 84
Period size: 17 Copynumber: 4.8 Consensus size: 18
125245 TTAAGTTTAT
125255 TTTAAAAA-TTAAATTTG
1 TTTAAAAATTTAAATTTG
*
125272 TTTAAAAATTTAAATTTA
1 TTTAAAAATTTAAATTTG
*
125290 TTT-TAAATTTAAATTTG
1 TTTAAAAATTTAAATTTG
*
125307 ATTT--AAGTTTAAATTTG
1 -TTTAAAAATTTAAATTTG
**
125324 TTTTCAAATTTAAA
1 TTTAAAAATTTAAA
125338 ATTATTATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.05
17 32 0.56
18 22 0.39
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (18 bp):
TTTAAAAATTTAAATTTG
Found at i:125284 original size:36 final size:36
Alignment explanation
Indices: 125244--125333 Score: 105
Period size: 34 Copynumber: 2.6 Consensus size: 36
125234 CCAAACTCCC
*
125244 TTTAAGTTTATTTTAAAAATTAAATTTG-TTTAAAAA
1 TTTAAATTTATTTT-AAAATTAAATTTGATTTAAAAA
* *
125280 TTTAAATTTATTTTAAATTTAAATTTGATTT--AAG
1 TTTAAATTTATTTTAAAATTAAATTTGATTTAAAAA
* *
125314 TTTAAATTTGTTTTCAAATT
1 TTTAAATTTATTTTAAAATT
125334 TAAAATTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 19 0.40
35 12 0.26
36 16 0.34
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (36 bp):
TTTAAATTTATTTTAAAATTAAATTTGATTTAAAAA
Found at i:125288 original size:6 final size:6
Alignment explanation
Indices: 125277--125322 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
125267 ATTTGTTTAA
* * *
125277 AAATTT AAATTT -ATTTT AAATTT AAATTT -GATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
125323 GTTTTCAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
5 8 0.25
6 24 0.75
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (6 bp):
AAATTT
Found at i:125333 original size:35 final size:34
Alignment explanation
Indices: 125244--125337 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 34
125234 CCAAACTCCC
* *
125244 TTTAAGTTTATTTTAAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTATTTT-AAATTTAAATTTGTTT-AAAA
*
125280 TTTAAATTTATTTTAAATTTAAATTTGATTT-AAG
1 TTTAAATTTATTTTAAATTTAAATTTG-TTTAAAA
*
125314 TTTAAATTTGTTTTCAAATTTAAA
1 TTTAAATTTATTTT-AAATTTAAA
125338 ATTATTATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
34 15 0.29
35 21 0.40
36 16 0.31
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTGTTTAAAA
Found at i:125351 original size:17 final size:17
Alignment explanation
Indices: 125244--125353 Score: 105
Period size: 18 Copynumber: 6.3 Consensus size: 17
125234 CCAAACTCCC
*
125244 TTTAAGTTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* * *
125262 ATTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
125280 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
125297 TTTAAATTTGA-TTTAAG
1 TTTAAATTT-ATTTTAAA
*
125314 TTTAAATTTGTTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
125332 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
125349 TTTAA
1 TTTAA
125354 TATAAGTAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
17 37 0.49
18 38 0.51
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:127263 original size:30 final size:30
Alignment explanation
Indices: 127203--127551 Score: 345
Period size: 30 Copynumber: 11.7 Consensus size: 30
127193 CTAAAATGTT
* *
127203 CAAAAATTCCATTTTTACCCTCG-GACTTC
1 CAAAAATCCCATTTTTACCCTCGAAACTTC
*
127232 CAAAAATCCCATTTTTAACCTCGAAACTTC
1 CAAAAATCCCATTTTTACCCTCGAAACTTC
*
127262 CAAAAATCCCATTTTTACCCCCG-AACTTC
1 CAAAAATCCCATTTTTACCCTCGAAACTTC
* ** * *
127291 TAAAAATCTTATTTTTGACCCT-AAAACTTT
1 CAAAAATCCCATTTTT-ACCCTCGAAACTTC
* *
127321 CAAAAATCCCATTTTTACCCCCTAAACTTC
1 CAAAAATCCCATTTTTACCCTCGAAACTTC
*
127351 TAAAAATCCCATTTTTGACCCTCGAAACTTC
1 CAAAAATCCCATTTTT-ACCCTCGAAACTTC
127382 CAAAAATCCCATTTTTACCCTC-AAACTTC
1 CAAAAATCCCATTTTTACCCTCGAAACTTC
* * * * *
127411 TAAAATTCCCATTTTTAACCTCAAAACTTT
1 CAAAAATCCCATTTTTACCCTCGAAACTTC
* **
127441 TAAAAATCCCATTTTTGA-CCTCGAAACCAC
1 CAAAAATCCCATTTTT-ACCCTCGAAACTTC
* * *
127471 CAAAAATCTCATTTTTAACCC-CAAAACTTT
1 CAAAAATCCCATTTTT-ACCCTCGAAACTTC
* *
127501 CAAAAGGT-CCATTTTTACCCCCG-AACTTC
1 CAAAA-ATCCCATTTTTACCCTCGAAACTTC
* *
127530 TAAAAATCTCATTTTTGACCCT
1 CAAAAATCCCATTTTT-ACCCT
127552 GAATTTTCCC
Statistics
Matches: 263, Mismatches: 45, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
28 1 0.00
29 90 0.34
30 141 0.54
31 31 0.12
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (30 bp):
CAAAAATCCCATTTTTACCCTCGAAACTTC
Found at i:127408 original size:60 final size:60
Alignment explanation
Indices: 127201--127551 Score: 397
Period size: 59 Copynumber: 5.9 Consensus size: 60
127191 TCCTAAAATG
* * ** * * *
127201 TTCAAAAATTCCATTTTTACCCTCGGACTTCCAAAAATCCCATTTTT-AACCTCGAAACT
1 TTCAAAAATCCCATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTGACCCTCAAAACT
* * **
127260 TCCAAAAATCCCATTTTTACCCCCGAACTTCTAAAAATCTTATTTTTGACCCT-AAAACT
1 TTCAAAAATCCCATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTGACCCTCAAAACT
*
127319 TTCAAAAATCCCATTTTTACCCCCTAAACTTCTAAAAATCCCATTTTTGACCCTCGAAACT
1 TTCAAAAATCCCATTTTTACCCCC-AAACTTCTAAAAATCCCATTTTTGACCCTCAAAACT
* * * *
127380 TCCAAAAATCCCATTTTTACCCTCAAACTTCTAAAATTCCCATTTTT-AACCTCAAAACT
1 TTCAAAAATCCCATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTGACCCTCAAAACT
* * * ** * * *
127439 TTTAAAAATCCCATTTTTGACCTCGAAACCACCAAAAATCTCATTTTTAACCC-CAAAACT
1 TTCAAAAATCCCATTTTT-ACCCCCAAACTTCTAAAAATCCCATTTTTGACCCTCAAAACT
* * *
127499 TTCAAAAGGT-CCATTTTTACCCCCGAACTTCTAAAAATCTCATTTTTGACCCT
1 TTCAAAA-ATCCCATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTGACCCT
127552 GAATTTTCCC
Statistics
Matches: 246, Mismatches: 39, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
59 121 0.49
60 94 0.38
61 31 0.13
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (60 bp):
TTCAAAAATCCCATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTGACCCTCAAAACT
Found at i:140358 original size:15 final size:14
Alignment explanation
Indices: 140324--140360 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
140314 TTGTTTTTTT
140324 TTTTTTAAAAATTA
1 TTTTTTAAAAATTA
*
140338 TATTTTAAAAATATA
1 TTTTTTAAAAAT-TA
140353 TTTTTTAA
1 TTTTTTAA
140361 TTGTAAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTTTAAAAATTA
Found at i:141021 original size:2 final size:2
Alignment explanation
Indices: 141014--141041 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
141004 TTAAATAACA
141014 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
141042 GATTGAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:142350 original size:6 final size:6
Alignment explanation
Indices: 142339--142394 Score: 85
Period size: 6 Copynumber: 9.3 Consensus size: 6
142329 TGCTTTGGCA
* * *
142339 GGTGCC GGTGCC GGTGCC GGTGCT GGTGCT GGTGCT GGTGCT GGTGCT
1 GGTGCT GGTGCT GGTGCT GGTGCT GGTGCT GGTGCT GGTGCT GGTGCT
142387 GGTGCT GG
1 GGTGCT GG
142395 GTTTTCCATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.00, C:0.21, G:0.52, T:0.27
Consensus pattern (6 bp):
GGTGCT
Found at i:146783 original size:32 final size:32
Alignment explanation
Indices: 146747--146808 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
146737 AGCTTTTGGT
146747 TTTTTCATGTCATCAAAGAGTTGAACAATGGA
1 TTTTTCATGTCATCAAAGAGTTGAACAATGGA
* ** *
146779 TTTTTCGTGTTGTCAAAGAGTTTAACAATG
1 TTTTTCATGTCATCAAAGAGTTGAACAATG
146809 AAAATAGATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTCATCAAAGAGTTGAACAATGGA
Found at i:160717 original size:55 final size:55
Alignment explanation
Indices: 160649--160756 Score: 144
Period size: 55 Copynumber: 2.0 Consensus size: 55
160639 AATTTTCTAA
** * * * *
160649 AAATATTGTTTCTTTTGGATCGATTGTTTTTATGTTTAAATCGATTGTCATGTTG
1 AAATATTACTTCTTTTGAATCAATCGTTTATATGTTTAAATCGATTGTCATGTTG
* *
160704 AAATATTACTTCTTTTGAATCAATCGTTTATATGTTTAAATTGATTGTTATGT
1 AAATATTACTTCTTTTGAATCAATCGTTTATATGTTTAAATCGATTGTCATGT
160757 AGAACGTCTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (55 bp):
AAATATTACTTCTTTTGAATCAATCGTTTATATGTTTAAATCGATTGTCATGTTG
Found at i:163023 original size:32 final size:32
Alignment explanation
Indices: 162983--163045 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
162973 ATTGAGCAAA
*
162983 AAAAAAAACAATCTGAATTAATATGAAAGAAC
1 AAAAAAAACAATCTGAATTAATACGAAAGAAC
163015 AAAAAAAACAATCTGAATTAATACGAAAGAA
1 AAAAAAAACAATCTGAATTAATACGAAAGAA
163046 ACTTGAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.17
Consensus pattern (32 bp):
AAAAAAAACAATCTGAATTAATACGAAAGAAC
Found at i:163132 original size:19 final size:20
Alignment explanation
Indices: 163098--163137 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
163088 AGTTTATTTT
**
163098 ATCAAAATAACTTTAA-AAA
1 ATCAAAATAAAATTAATAAA
163117 ATCAAAATAAAATTAATAAA
1 ATCAAAATAAAATTAATAAA
163137 A
1 A
163138 AAAAACCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (20 bp):
ATCAAAATAAAATTAATAAA
Found at i:168282 original size:22 final size:23
Alignment explanation
Indices: 168256--168298 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
168246 ACCTAAAATT
*
168256 TTAAATTC-GAAAAATAAAAGGA
1 TTAAATCCTGAAAAATAAAAGGA
*
168278 TTAAATCCTTAAAAATAAAAG
1 TTAAATCCTGAAAAATAAAAG
168299 TATGAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.26
Consensus pattern (23 bp):
TTAAATCCTGAAAAATAAAAGGA
Found at i:176503 original size:2 final size:2
Alignment explanation
Indices: 176498--176523 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
176488 AAATAAATAA
176498 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
176524 CACTAACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:176886 original size:29 final size:27
Alignment explanation
Indices: 176827--176888 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 27
176817 ATGTCAACAC
*
176827 TTAAATAATTTTTAAAAAATTAAAAAT
1 TTAAAAAATTTTTAAAAAATTAAAAAT
*
176854 TTAAAAAATTATTTTAAAAA-TAAAAAGT
1 TTAAAAAATT-TTTAAAAAATTAAAAA-T
176882 ATTAAAA
1 -TTAAAA
176889 CTGTTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 15 0.50
28 9 0.30
29 6 0.20
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
TTAAAAAATTTTTAAAAAATTAAAAAT
Found at i:176984 original size:36 final size:37
Alignment explanation
Indices: 176943--177020 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 37
176933 TTTTTTTTTT
*
176943 TTTATAGTTGT-CACAGAA-TTTTTTGCATATTTACAA
1 TTTATACTTGTCCACAGAACTTTTTT-CATATTTACAA
*
176979 TTTATACTTGTGCCACAGAACTTTTTTTATATTTACAA
1 TTTATACTTGT-CCACAGAACTTTTTTCATATTTACAA
177017 TTTA
1 TTTA
177021 ATCCCTTCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 10 0.27
38 21 0.57
39 6 0.16
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (37 bp):
TTTATACTTGTCCACAGAACTTTTTTCATATTTACAA
Found at i:179041 original size:27 final size:27
Alignment explanation
Indices: 179010--179063 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
179000 CTGAAATTGA
179010 TTTATTTTGCTAAATTAAATCAATAAG
1 TTTATTTTGCTAAATTAAATCAATAAG
179037 TTTATTTTGCTAAATTAAATCAATAAG
1 TTTATTTTGCTAAATTAAATCAATAAG
179064 GAAATTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (27 bp):
TTTATTTTGCTAAATTAAATCAATAAG
Found at i:179070 original size:27 final size:27
Alignment explanation
Indices: 179013--179071 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
179003 AAATTGATTT
***
179013 ATTTTGCTAAATTAAATCAATAAGTTT
1 ATTTTGCTAAATTAAATCAATAAGGAA
179040 ATTTTGCTAAATTAAATCAATAAGGAA
1 ATTTTGCTAAATTAAATCAATAAGGAA
179067 ATTTT
1 ATTTT
179072 TCATTGGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (27 bp):
ATTTTGCTAAATTAAATCAATAAGGAA
Done.