Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013490.1 Kokia drynarioides strain JFW-HI SEQ_128516, 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: 66140
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:721 original size:59 final size:59
Alignment explanation
Indices: 649--1080 Score: 593
Period size: 59 Copynumber: 7.3 Consensus size: 59
639 GTCCCTAAAG
*
649 CTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCATAAATCACCATTTTACCCCCAAA
1 CTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCCCCAAA
* * *
708 CTTCCAAAAATCCCAATTTTAACCCTAAACCTTCAAAAAATCACCATTTTACCCCCTAAA
1 CTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCCCC-AAA
* *
768 CTTCCAAAAAT-CCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCCTCGAA
1 CTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCCCCAAA
*
826 CTTCCAAAAATCCCATTTTTAACCTCAAACCTTCCAAAAATCACCATTTTACCCCCCAAA
1 CTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTA-CCCCCAAA
* * * * *
886 CTTTCAAAAATCCCATTTTAAACCCCAAACCTTCTAAAAATTACCATTTTACCCTCGAAA
1 CTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCC-CCAAA
* * * *
946 C-TCAAAAAATCCCA-TTTTAACCCCAAACCTTCCAAAAATTACCATTTTACCCTCGAA
1 CTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCCCCAAA
* * ** * * * *
1003 CTTCCAAAAATCCAATTTTTGACCCTGAACCTTCCAAAAATTACCATTCTACCTCCGAA
1 CTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCCCCAAA
1062 CTTCCAAAAATCCC-TTTTT
1 CTTCCAAAAATCCCATTTTT
1081 CGACCTCGAA
Statistics
Matches: 333, Mismatches: 34, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
57 3 0.01
58 65 0.20
59 194 0.58
60 71 0.21
ACGTcount: A:0.37, C:0.34, G:0.01, T:0.28
Consensus pattern (59 bp):
CTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCCCCAAA
Found at i:1090 original size:29 final size:27
Alignment explanation
Indices: 649--1119 Score: 250
Period size: 30 Copynumber: 16.0 Consensus size: 27
639 GTCCCTAAAG
* *
649 CTTCCAAAAATCCCATTTTTAACCCCAAA
1 CTTCCAAAAATCCCA-TTTT-ACCTCGAA
* * *
678 CCTTCCATAAATCACCATTTTACCCCCAAA
1 -CTTCCAAAAATC-CCATTTTA-CCTCGAA
*
708 CTTCCAAAAATCCCAATTTTAACC-CTAAA
1 CTTCCAAAAATCCC-ATTTT-ACCTC-GAA
* * *
737 CCTTCAAAAAATCACCATTTTACCCCCTAAA
1 -CTTCCAAAAATC-CCATTTTA-CCTC-GAA
* *
768 CTTCCAAAAAT-CCATTTTTAACCCCAAA
1 CTTCCAAAAATCCCA-TTTT-ACCTCGAA
796 CCTTCCAAAAATCACCATTTTACCCTCGAA
1 -CTTCCAAAAATC-CCATTTTA-CCTCGAA
*
826 CTTCCAAAAATCCCATTTTTAACCTCAAA
1 CTTCCAAAAATCCCA-TTTT-ACCTCGAA
* *
855 CCTTCCAAAAATCACCATTTTACCCCCCAAA
1 -CTTCCAAAAATC-CCATTTTA--CCTCGAA
* * *
886 CTTTCAAAAATCCCATTTTAAACCCCAAA
1 CTTCCAAAAATCCCATTTT--ACCTCGAA
* *
915 CCTTCTAAAAATTACCATTTTACCCTCGAAA
1 -CTTCCAAAAA-TCCCATTTTA-CCTCG-AA
* * *
946 C-TCAAAAAATCCCATTTTAACCCCAAA
1 CTTCCAAAAATCCCATTTT-ACCTCGAA
*
973 CCTTCCAAAAATTACCATTTTACCCTCGAA
1 -CTTCCAAAAA-TCCCATTTTA-CCTCGAA
*
1003 CTTCCAAAAATCCAATTTTTGACC-CTGAA
1 CTTCCAAAAATCCCA-TTTT-ACCTC-GAA
* *
1032 CCTTCCAAAAATTACCATTCTACCTCCGAA
1 -CTTCCAAAAA-TCCCATTTTACCT-CGAA
*
1062 CTTCCAAAAATCCCTTTTTCGACCTCGAAA
1 CTTCCAAAAATCCCATTTT--ACCTCG-AA
* *
1092 C-TCTCAAAATTGCCATTTTACCCTCGAA
1 CTTC-CAAAAATCCCATTTTA-CCTCGAA
1120 AAATTTTCCC
Statistics
Matches: 364, Mismatches: 33, Indels: 90
0.75 0.07 0.18
Matches are distributed among these distances:
27 2 0.01
28 37 0.10
29 138 0.38
30 150 0.41
31 37 0.10
ACGTcount: A:0.36, C:0.34, G:0.02, T:0.28
Consensus pattern (27 bp):
CTTCCAAAAATCCCATTTTACCTCGAA
Found at i:1120 original size:29 final size:30
Alignment explanation
Indices: 651--1120 Score: 229
Period size: 29 Copynumber: 15.9 Consensus size: 30
641 CCCTAAAGCT
*
651 TCCAAAAATCCCATTTTTAACCC-C-AAAC-C
1 TCCAAAAATACCA-TTTT-ACCCTCGAAACTC
* *
680 TTCCATAAATCACCATTTTACCC-CCAAACT-
1 -TCCAAAAAT-ACCATTTTACCCTCGAAACTC
*
710 TCCAAAAATCCCAATTTTAACCCT--AAAC-C
1 TCCAAAAATACC-ATTTT-ACCCTCGAAACTC
* * *
739 TTCAAAAAATCACCATTTTACCCCCTAAACT-
1 -TCCAAAAAT-ACCATTTTACCCTCGAAACTC
770 TCCAAAAAT-CCATTTTTAACCC-C-AAAC-C
1 TCCAAAAATACCA-TTTT-ACCCTCGAAACTC
798 TTCCAAAAATCACCATTTTACCCTCG-AACT-
1 -TCCAAAAAT-ACCATTTTACCCTCGAAACTC
* *
828 TCCAAAAATCCCATTTTTAACCTC-AAAC-C
1 TCCAAAAATACCA-TTTTACCCTCGAAACTC
* *
857 TTCCAAAAATCACCATTTTACCCCCCAAACT-
1 -TCCAAAAAT-ACCATTTTACCCTCGAAACTC
* *
888 TTCAAAAATCCCATTTTAAACCC-C-AAAC-C
1 TCCAAAAATACCATTTT--ACCCTCGAAACTC
*
917 TTCTAAAAATTACCATTTTACCCTCGAAA--C
1 -TCCAAAAA-TACCATTTTACCCTCGAAACTC
* *
947 TCAAAAAATCCCATTTTAACCC-C-AAAC-C
1 TCCAAAAATACCATTTT-ACCCTCGAAACTC
975 TTCCAAAAATTACCATTTTACCCTCG-AACT-
1 -TCCAAAAA-TACCATTTTACCCTCGAAACTC
*
1005 TCCAAAAAT-CCAATTTTTGACCCT-GAACCT-
1 TCCAAAAATACC-A-TTTT-ACCCTCGAAACTC
*
1035 TCCAAAAATTACCATTCTA-CCTCCG-AACT-
1 TCCAAAAA-TACCATTTTACCCT-CGAAACTC
* *
1064 TCCAAAAAT-CCCTTTTTCGACCTCGAAACTC
1 TCCAAAAATACCATTTTAC--CCTCGAAACTC
* *
1095 T-CAAAATTGCCATTTTACCCTCGAAA
1 TCCAAAAATACCATTTTACCCTCGAAA
1121 AATTTTCCCG
Statistics
Matches: 353, Mismatches: 31, Indels: 113
0.71 0.06 0.23
Matches are distributed among these distances:
27 10 0.03
28 28 0.08
29 137 0.39
30 132 0.37
31 44 0.12
32 2 0.01
ACGTcount: A:0.36, C:0.34, G:0.02, T:0.28
Consensus pattern (30 bp):
TCCAAAAATACCATTTTACCCTCGAAACTC
Found at i:2756 original size:17 final size:17
Alignment explanation
Indices: 2734--2767 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2724 AAAATTTATT
2734 TTTTAA-AAGAATAAACA
1 TTTTAACAA-AATAAACA
2751 TTTTAACAAAATAAACA
1 TTTTAACAAAATAAACA
2768 AATTATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (17 bp):
TTTTAACAAAATAAACA
Found at i:4827 original size:18 final size:19
Alignment explanation
Indices: 4806--4847 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
4796 TATTTATTTT
4806 AAATATAATAT-TATAAAA
1 AAATATAATATGTATAAAA
*
4824 AAATA-AATATGTATTAAA
1 AAATATAATATGTATAAAA
*
4842 TAATAT
1 AAATAT
4848 TTAAATTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAATATAATATGTATAAAA
Found at i:4845 original size:31 final size:31
Alignment explanation
Indices: 4765--4852 Score: 81
Period size: 36 Copynumber: 2.7 Consensus size: 31
4755 TTTTTAGTAT
* *
4765 TATG-ATTAAAAAATATTTTTAAAAAATAAAA
1 TATGTATTAAATAATA-TTTAAAAAAATAAAA
*
4796 TATTTATTTTAAATATAATATTATAAAAAAAT-AAA
1 TATGTA--TT-AA-ATAATATT-TAAAAAAATAAAA
4831 TATGTATTAAATAATATTTAAA
1 TATGTATTAAATAATATTTAAA
4853 TTAGTTAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
30 4 0.09
31 11 0.23
32 3 0.06
33 2 0.04
34 2 0.04
35 12 0.26
36 13 0.28
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (31 bp):
TATGTATTAAATAATATTTAAAAAAATAAAA
Found at i:4847 original size:36 final size:36
Alignment explanation
Indices: 4776--4847 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
4766 ATGATTAAAA
* * * **
4776 AATATTTTTAAAAAATAAAATATTTATTTTAAATAT
1 AATATTATAAAAAAATAAAATATGTATTAAAAATAT
4812 AATATTATAAAAAAAT-AAATATGTATTAAATAATAT
1 AATATTATAAAAAAATAAAATATGTATTAAA-AATAT
4848 TTAAATTAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (36 bp):
AATATTATAAAAAAATAAAATATGTATTAAAAATAT
Found at i:9988 original size:21 final size:21
Alignment explanation
Indices: 9962--10003 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
9952 GATTGATCTC
*
9962 TCTCAATGGAAACTATTACCA
1 TCTCAATGAAAACTATTACCA
9983 TCTCAATGAAAACTATTACCA
1 TCTCAATGAAAACTATTACCA
10004 ACTACCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (21 bp):
TCTCAATGAAAACTATTACCA
Found at i:10429 original size:141 final size:141
Alignment explanation
Indices: 10257--10538 Score: 564
Period size: 141 Copynumber: 2.0 Consensus size: 141
10247 TTAGTTAAAC
10257 TAGCAAGGTAAACATTTGCTTGTCATTGGCTTTTGAATGAAATTTACACAATTTTCTATTTATTC
1 TAGCAAGGTAAACATTTGCTTGTCATTGGCTTTTGAATGAAATTTACACAATTTTCTATTTATTC
10322 AAATGTTATGGTAGATATTTGAGAAATGTGAAAGTTATATTGATAAAATTCAAAGTATTGATATA
66 AAATGTTATGGTAGATATTTGAGAAATGTGAAAGTTATATTGATAAAATTCAAAGTATTGATATA
10387 ATTAAAAATAA
131 ATTAAAAATAA
10398 TAGCAAGGTAAACATTTGCTTGTCATTGGCTTTTGAATGAAATTTACACAATTTTCTATTTATTC
1 TAGCAAGGTAAACATTTGCTTGTCATTGGCTTTTGAATGAAATTTACACAATTTTCTATTTATTC
10463 AAATGTTATGGTAGATATTTGAGAAATGTGAAAGTTATATTGATAAAATTCAAAGTATTGATATA
66 AAATGTTATGGTAGATATTTGAGAAATGTGAAAGTTATATTGATAAAATTCAAAGTATTGATATA
10528 ATTAAAAATAA
131 ATTAAAAATAA
10539 ACACCAGTTT
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 141 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (141 bp):
TAGCAAGGTAAACATTTGCTTGTCATTGGCTTTTGAATGAAATTTACACAATTTTCTATTTATTC
AAATGTTATGGTAGATATTTGAGAAATGTGAAAGTTATATTGATAAAATTCAAAGTATTGATATA
ATTAAAAATAA
Found at i:11907 original size:27 final size:27
Alignment explanation
Indices: 11853--11965 Score: 106
Period size: 27 Copynumber: 4.0 Consensus size: 27
11843 AATACTTTAT
*
11853 AATTAAT-TAATATAAATTATTTGT-AA
1 AATTAATATAACATAAATTATTT-TAAA
11879 AATTAATGAT-ACATAAATTATTTTAAA
1 AATTAAT-ATAACATAAATTATTTTAAA
*
11906 AACTTAATATAATAATAAATTATTTTAAA
1 AA-TTAATATAA-CATAAATTATTTTAAA
*
11935 TAATATAATATAACGATAAATGATATTTAAA
1 -AAT-TAATATAAC-ATAAATTAT-TTTAAA
11966 TGATTTAATA
Statistics
Matches: 73, Mismatches: 4, Indels: 15
0.79 0.04 0.16
Matches are distributed among these distances:
26 8 0.11
27 18 0.25
28 7 0.10
29 16 0.22
30 18 0.25
31 6 0.08
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (27 bp):
AATTAATATAACATAAATTATTTTAAA
Found at i:11975 original size:31 final size:30
Alignment explanation
Indices: 11891--12015 Score: 103
Period size: 31 Copynumber: 4.1 Consensus size: 30
11881 TTAATGATAC
* * *
11891 ATAAATTATTTTAAA-AACTTAATATAATA
1 ATAAATGATTTTAAATAATTTAATATAACA
* * *
11920 ATAAATTATTTTAAATAATATAATATAACG
1 ATAAATGATTTTAAATAATTTAATATAACA
* *
11950 ATAAATGATATTTAAATGATTTAATATAATA
1 ATAAATGAT-TTTAAATAATTTAATATAACA
*
11981 TTACAA-GAAATATTTAAATAATTTAA-ATAACA
1 ATA-AATG--AT-TTTAAATAATTTAATATAACA
12013 ATA
1 ATA
12016 CATAATATAT
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
29 15 0.19
30 18 0.23
31 20 0.26
32 9 0.12
33 16 0.21
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (30 bp):
ATAAATGATTTTAAATAATTTAATATAACA
Found at i:11980 original size:61 final size:56
Alignment explanation
Indices: 11855--11980 Score: 134
Period size: 56 Copynumber: 2.2 Consensus size: 56
11845 TACTTTATAA
*
11855 TTAAT-TAAT-ATAAATTATTTGTAAAATTAATGATACATAAATTATTTTAAAAAC
1 TTAATATAATAATAAATTATTTGTAAAATTAATGATACATAAATGATTTTAAAAAC
* *
11909 TTAATATAATAATAAATTATTT-TAAATAATATAAT-ATAACGATAAATGATATTTAAATGAT
1 TTAATATAATAATAAATTATTTGT-AA-AAT-TAATGAT-AC-ATAAATGAT-TTTAAA-AAC
11970 TTAATATAATA
1 TTAATATAATA
11981 TTACAAGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
54 5 0.08
55 5 0.08
56 13 0.22
57 5 0.08
58 6 0.10
59 8 0.13
60 6 0.10
61 12 0.20
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (56 bp):
TTAATATAATAATAAATTATTTGTAAAATTAATGATACATAAATGATTTTAAAAAC
Found at i:18066 original size:42 final size:42
Alignment explanation
Indices: 17930--18079 Score: 157
Period size: 42 Copynumber: 3.6 Consensus size: 42
17920 ATGCTCCAAC
* *
17930 CGAGTCATAAGTCTTCCTTTTCAAAC--ACT-T-ATGCTC-TAT
1 CGAGTCATAAGTCTTCC-TTT-AAACATAATATCATGCTCATCT
*
17969 CGAGTCATAAGTCTTCCTTTAAACATAATATCATGATCATCT
1 CGAGTCATAAGTCTTCCTTTAAACATAATATCATGCTCATCT
* * *
18011 CGAGCCACAAGTCTTCCTTTAAACATAATCTCATGCTCATCT
1 CGAGTCATAAGTCTTCCTTTAAACATAATATCATGCTCATCT
* * *
18053 CGAGTCGTGAGTCTTCCATTTATACAT
1 CGAGTCATAAGTCTTCC-TTTAAACAT
18080 CAAGTGATTC
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
37 4 0.04
38 3 0.03
39 19 0.20
40 1 0.01
41 5 0.05
42 53 0.57
43 8 0.09
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.35
Consensus pattern (42 bp):
CGAGTCATAAGTCTTCCTTTAAACATAATATCATGCTCATCT
Found at i:19362 original size:16 final size:16
Alignment explanation
Indices: 19338--19376 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
19328 ACCCACCCAT
*
19338 ACCCAATCTGATATAA
1 ACCCAATCTAATATAA
*
19354 ACTCAATCTAATATAA
1 ACCCAATCTAATATAA
19370 ACCCAAT
1 ACCCAAT
19377 ATAAACCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.03, T:0.26
Consensus pattern (16 bp):
ACCCAATCTAATATAA
Found at i:21225 original size:24 final size:24
Alignment explanation
Indices: 21189--21263 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
21179 GTATACTAGT
* *
21189 TAACTATTTTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
21213 TAACCATTCTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
* * *
21237 TAACCATCCTCGGCTCGTGAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
21261 TAA
1 TAA
21264 TGTTGTTTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (24 bp):
TAACCATTCTGGGCTCGTAAGAGC
Found at i:22002 original size:21 final size:21
Alignment explanation
Indices: 21954--22005 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
21944 GGAGTTTTTA
*
21954 GTATCGGTAGAAGCATGACAT
1 GTATCGGTAGAAGCATCACAT
* *
21975 GTTTCGGTAGAAGTC-TCACTT
1 GTATCGGTAGAAG-CATCACAT
21996 GTATCGGTAG
1 GTATCGGTAG
22006 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGCATCACAT
Found at i:25644 original size:18 final size:18
Alignment explanation
Indices: 25621--25670 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
25611 CAAAGGGAAT
25621 AGCATACTGGCTCATTAG
1 AGCATACTGGCTCATTAG
* * *
25639 AGCATATTAGCTCATTTG
1 AGCATACTGGCTCATTAG
25657 AGCAATACTGGCTC
1 AGC-ATACTGGCTC
25671 GTAAGAGCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (18 bp):
AGCATACTGGCTCATTAG
Found at i:26425 original size:21 final size:21
Alignment explanation
Indices: 26401--26440 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
26391 CTTGTTTTGT
*
26401 TAGAAGAGTCACTTGTATCTG
1 TAGAACAGTCACTTGTATCTG
* *
26422 TAGAACTGTTACTTGTATC
1 TAGAACAGTCACTTGTATC
26441 AATAAAAATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (21 bp):
TAGAACAGTCACTTGTATCTG
Found at i:30633 original size:17 final size:17
Alignment explanation
Indices: 30590--30624 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
30580 TGCCGGGGAA
*
30590 TGGCGTTTGTTTGATGT
1 TGGCATTTGTTTGATGT
30607 TGGCATTTGTTTGATGT
1 TGGCATTTGTTTGATGT
30624 T
1 T
30625 TGCTTTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.09, C:0.06, G:0.31, T:0.54
Consensus pattern (17 bp):
TGGCATTTGTTTGATGT
Found at i:36156 original size:39 final size:39
Alignment explanation
Indices: 36113--36606 Score: 314
Period size: 39 Copynumber: 12.7 Consensus size: 39
36103 GAAGATTCTA
* *
36113 ATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCG
36152 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT---TCG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATCAGTCG
** * ** * *
36191 ATCTCTTACCCTAAGCTTGGGGCAGAT-TGCAACCGTCTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTC-G
* * * * * *
36230 ATATTTTACCCCGAGCTTGGGGCAGATCAACATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCG
* * *** * *
36269 ATCTCTTACCCCGAG-CTGGGGTAAAT-TGTAGCCGTACG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGT-CG
* * *
36307 ATCTTTTACCCCAAGCCTGAGGCAGATCACCATCA-TCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGT-CG
* *
36346 ATCTCTTACCTCGAGCCTAGGGCAGATCACCATCA-TCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGT-CG
* ** * *
36385 ATCTCTTACCTCGAGCCTGGAACAGATCACCATCA-ACTA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTC-G
* ** *
36424 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCG
* * * * **
36463 ATCTCTTACCCCAAGCCTAGAGCAAAT-TGCAGTC-GTCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCAGT-CG
* * *
36502 ATCTTTTACCTCGAGCCTAGGGCAGATTGCAACCATC---CG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-C-ACCATCAGTCG
* * * *
36541 ATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCG
* *
36580 ATCTCTTACCCCAAGCTTGGGGCAGAT
1 ATCTCTTACCCCGAGCCTGGGGCAGAT
36607 TGCAACCATA
Statistics
Matches: 354, Mismatches: 79, Indels: 44
0.74 0.17 0.09
Matches are distributed among these distances:
35 2 0.01
36 6 0.02
37 4 0.01
38 29 0.08
39 293 0.83
40 10 0.03
41 2 0.01
42 6 0.02
43 2 0.01
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCG
Found at i:36273 original size:78 final size:78
Alignment explanation
Indices: 36112--36615 Score: 371
Period size: 78 Copynumber: 6.5 Consensus size: 78
36102 TGAAGATTCT
* * * *
36112 AATCTCTTACCCCGAGCCTAGGGCAGA-T-C-ACCATCAGTCAATCTCTTACCCCGAGCCTGGGG
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATC---CGATCTTTTACCCCGAGCCTGGGG
36174 CAGATTGCAGCCATTC-G--
63 CAGA-T-CA-CCA-TCAGCC
** * * * *
36191 -ATCTCTTACCCTAAGCTTGGGGCAGATTGCAACCGTCTGATATTTTACCCCGAGCTTGGGGCAG
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAG
*
36255 ATCAACATCAGCC
66 ATCACCATCAGCC
* * * * * * * *
36268 AATCTCTTACCCCGAGC-TGGGGTAAATTGTAGCCGTACGATCTTTTACCCCAAGCCTGAGGCAG
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAG
*
36332 ATCACCATCATCC
66 ATCACCATCAGCC
* * * * ** * * * * **
36345 GATCTCTTACCTCGAGCCTAGGGCAGATCACCATCATCCGATCTCTTACCTCGAGCCTGGAACAG
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAG
* *
36410 ATCACCATCAACT
66 ATCACCATCAGCC
** * * * * * * * * *
36423 AATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAACCAATCTCTTACCCCAAGCCTAGAGCAA
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAG
**
36488 AT-TGCAGTC-GTCC
66 ATCACCA-TCAG-CC
* * * * * *
36501 GATCTTTTACCTCGAGCCTAGGGCAGATTGCAACCATCCGATCTTTTACCCCGAGCCTAGGGCAG
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAG
36566 ATCACCATCAGCC
66 ATCACCATCAGCC
*
36579 AATCTCTTACCCCAAGCTTGGGGCAGATTGCAACCAT
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCAT
36616 AAAAAAAAAC
Statistics
Matches: 329, Mismatches: 84, Indels: 25
0.75 0.19 0.06
Matches are distributed among these distances:
74 2 0.01
75 3 0.01
76 2 0.01
77 66 0.20
78 246 0.75
79 4 0.01
80 1 0.00
81 5 0.02
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (78 bp):
AATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAG
ATCACCATCAGCC
Found at i:36369 original size:116 final size:116
Alignment explanation
Indices: 36113--36606 Score: 352
Period size: 117 Copynumber: 4.2 Consensus size: 116
36103 GAAGATTCTA
* *
36113 ATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGTCAATCTCTTACCCCGAGCCTGGGGCAGA
1 ATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAG-CTGGGGCAAA
* * * * ** * *
36178 TTGCAGCCATTCGATCTCTTACCCTAAGCTTGGGGCAGATTGCAACCGTCTG
65 TTGCAGCCATACGATCTCTTACCCCAAGCCTGAGGCAGATCACAACCATCCG
* * * * * *
36230 ATATTTTACCCCGAGCTTGGGGCAGATCAACATCAGCCAATCTCTTACCCCGAGCTGGGGTAAAT
1 ATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTGGGGCAAAT
* * * * *
36295 TGTAGCCGTACGATCTTTTACCCCAAGCCTGAGGCAGATCACCATCATCCG
66 TGCAGCCATACGATCTCTTACCCCAAGCCTGAGGCAGATCACAACCATCCG
* * * * ** *
36346 ATCTCTTACCTCGAGCCTAGGGCAGATCACCATCATCCGATCTCTTACCTCGAGCCTGGAACAGA
1 ATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAG-CTGGGGCAAA
* * * * * * * *
36411 -T-CA-CCATCAACTAATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAACCA
65 TTGCAGCCAT--AC-GATCTCTTACCCCAAGCCTGAGGCAGATCACAACCATCCG
* * * ** * * * *
36463 ATCTCTTACCCCAAGCCTAGAGCAAAT-TGCAGTC-GTCCGATCTTTTACCTCGAGCCTAGGGCA
1 ATCTCTTACCCCGAGCCTAGGGCAGATCACCA-TCAG-CCAATCTCTTACCCCGAG-CTGGGGCA
* * * * * * * * *
36526 GATTGCAACCATCCGATCTTTTACCCCGAGCCT-AGGGCAGATCACCATCAGCCA
63 AATTGCAGCCATACGATCTCTTACCCCAAGCCTGA-GGCAGATCACAACCATCCG
* * *
36580 ATCTCTTACCCCAAGCTTGGGGCAGAT
1 ATCTCTTACCCCGAGCCTAGGGCAGAT
36607 TGCAACCATA
Statistics
Matches: 303, Mismatches: 64, Indels: 20
0.78 0.17 0.05
Matches are distributed among these distances:
114 3 0.01
115 1 0.00
116 97 0.32
117 194 0.64
118 2 0.01
119 2 0.01
120 4 0.01
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (116 bp):
ATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTGGGGCAAAT
TGCAGCCATACGATCTCTTACCCCAAGCCTGAGGCAGATCACAACCATCCG
Found at i:37198 original size:17 final size:17
Alignment explanation
Indices: 37178--37221 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
37168 TGAATCCAAA
*
37178 TTTAAATTTAAATTTCT
1 TTTAAATTTAAATTTAT
*
37195 TTTAAGA-ATAAATTTAT
1 TTTAA-ATTTAAATTTAT
37212 TTTAAATTTA
1 TTTAAATTTA
37222 CCTAAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:37545 original size:40 final size:40
Alignment explanation
Indices: 37499--37579 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
37489 GAAATGTCAG
37499 TAGGGTTTAAATGACAAACAACAAAAGAACATGATTGTAA
1 TAGGGTTTAAATGACAAACAACAAAAGAACATGATTGTAA
* * *
37539 TAGGGTTTAAGTGGCAAACAACAAAAGAATATGATTGTAA
1 TAGGGTTTAAATGACAAACAACAAAAGAACATGATTGTAA
37579 T
1 T
37580 TCAGGCTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.47, C:0.09, G:0.20, T:0.25
Consensus pattern (40 bp):
TAGGGTTTAAATGACAAACAACAAAAGAACATGATTGTAA
Found at i:38206 original size:3 final size:3
Alignment explanation
Indices: 38198--38232 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
38188 GCAACCATGA
38198 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
38233 CAGTTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39124 original size:29 final size:29
Alignment explanation
Indices: 39042--39352 Score: 267
Period size: 30 Copynumber: 10.6 Consensus size: 29
39032 CCCAAAAGGT
* * *
39042 CCCTAAAC-TTTCCAAAAATCATATTTTGA
1 CCCTAAACTTTTCC-AAAATTACATTTTAA
* *
39071 CCCTCGAACTTCTCCAAAATTACATTTTAA
1 CCCT-AAACTTTTCCAAAATTACATTTTAA
* * * *
39101 CCTTAAATTTTTCCAAAATAACATTTTGAC
1 CCCTAAACTTTTCCAAAATTACATTTT-AA
* * *
39131 CCCTAAACTTTTCTAAAATAACATTATAA
1 CCCTAAACTTTTCCAAAATTACATTTTAA
*
39160 CCCTAAACTTTTTCAAAATTACATTTTAA
1 CCCTAAACTTTTCCAAAATTACATTTTAA
*
39189 CCCTAACCTTTTCCAAAATTACATTTTAA
1 CCCTAAACTTTTCCAAAATTACATTTTAA
* *
39218 CCCATAAACTTTTCTAAAATTACATTTTGA
1 CCC-TAAACTTTTCCAAAATTACATTTTAA
* * *
39248 CCATTAAACTTTTCCAAAATTATATTTT-G
1 CC-CTAAACTTTTCCAAAATTACATTTTAA
* * *
39277 CCCCAAA-ATTTCCAAAAATCACATTTTCAA
1 CCCTAAACTTTTCC-AAAATTACATTTT-AA
*
39307 -CCTCAAA-ATTTCCAAAAGTT-CGATTTTAA
1 CCCT-AAACTTTTCCAAAA-TTAC-ATTTTAA
*
39336 TCCTAAA-TTTTCCAAAA
1 CCCTAAACTTTTCCAAAA
39353 ATTTGAATTT
Statistics
Matches: 232, Mismatches: 38, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
27 5 0.02
28 14 0.06
29 102 0.44
30 107 0.46
31 4 0.02
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTTTCCAAAATTACATTTTAA
Found at i:39127 original size:59 final size:59
Alignment explanation
Indices: 39050--39352 Score: 248
Period size: 59 Copynumber: 5.2 Consensus size: 59
39040 GTCCCTAAAC
* * * * *
39050 TTTCCAAAAATCATATTTTGACCCTCGAACTTCTCCAAAATTACATTTTAACCTTAAATT
1 TTTCC-AAAATTACATTTTGACCCTCAAACTTTTCCAAAATTACATTTTAACCATAAATT
* * * * *
39110 TTTCCAAAATAACATTTTGACCC-CTAAACTTTTCTAAAATAACATTATAACCCTAAACTT
1 TTTCCAAAATTACATTTTGACCCTC-AAACTTTTCCAAAATTACATTTTAACCATAAA-TT
* * *
39170 TTT-CAAAATTACATTTTAACCCT-AACCTTTTCCAAAATTACATTTTAACCCATAAACT
1 TTTCCAAAATTACATTTTGACCCTCAAACTTTTCCAAAATTACATTTTAA-CCATAAATT
* * * * **
39228 TTTCTAAAATTACATTTTGACCATTAAACTTTTCCAAAATTATATTTTGCCCCA-AAA--
1 TTTCCAAAATTACATTTTGACCCTCAAACTTTTCCAAAATTACATTTT-AACCATAAATT
* * * *
39285 TTTCCAAAAATCACATTTTCAACCTCAAA-ATTTCCAAAAGTT-CGATTTTAATCC-TAAA-T
1 TTTCC-AAAATTACATTTTGACCCTCAAACTTTTCCAAAA-TTAC-ATTTTAA-CCATAAATT
39344 TTTCCAAAA
1 TTTCCAAAA
39353 ATTTGAATTT
Statistics
Matches: 197, Mismatches: 33, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
57 13 0.07
58 60 0.30
59 90 0.46
60 34 0.17
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.37
Consensus pattern (59 bp):
TTTCCAAAATTACATTTTGACCCTCAAACTTTTCCAAAATTACATTTTAACCATAAATT
Found at i:39201 original size:88 final size:89
Alignment explanation
Indices: 39077--39275 Score: 274
Period size: 88 Copynumber: 2.2 Consensus size: 89
39067 TTGACCCTCG
* * * * *
39077 AACTTCTCCAAAATTACATTTTAACCTTAAATTTTTCCAAAATAACATTTTGACCCCTAAACTTT
1 AACTTTTCCAAAATTACATTTTAACCCTAAACTTTTCCAAAATAACATTTTAACCCATAAACTTT
39142 TCTAAAATAACATTATAACC-CTA
66 TCTAAAATAACATTATAACCACTA
* * *
39165 AACTTTTTCAAAATTACATTTTAACCCTAACCTTTTCCAAAATTACATTTTAACCCATAAACTTT
1 AACTTTTCCAAAATTACATTTTAACCCTAAACTTTTCCAAAATAACATTTTAACCCATAAACTTT
* * * *
39230 TCTAAAATTACATTTTGACCATTA
66 TCTAAAATAACATTATAACCACTA
*
39254 AACTTTTCCAAAATTATATTTT
1 AACTTTTCCAAAATTACATTTT
39276 GCCCCAAAAT
Statistics
Matches: 96, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
88 74 0.77
89 22 0.23
ACGTcount: A:0.38, C:0.21, G:0.01, T:0.40
Consensus pattern (89 bp):
AACTTTTCCAAAATTACATTTTAACCCTAAACTTTTCCAAAATAACATTTTAACCCATAAACTTT
TCTAAAATAACATTATAACCACTA
Found at i:39295 original size:88 final size:88
Alignment explanation
Indices: 39077--39308 Score: 245
Period size: 88 Copynumber: 2.6 Consensus size: 88
39067 TTGACCCTCG
* ** * * *
39077 AACTTCTCCAAAATTACATTTTAACCTTAA-ATTTTTCCAAAATAACATTTTGACCCCTAAACTT
1 AACTTTTCCAAAATTACATTTTAACCCCAACA-ATTTCCAAAATAACATTTTAACCCATAAACTT
39141 TTCTAAAATAACATTATAACCCTA
65 TTCTAAAATAACATTATAACCCTA
* * ** *
39165 AACTTTTTCAAAATTACATTTTAACCCTAACCTTTTCCAAAATTACATTTTAACCCATAAACTTT
1 AACTTTTCCAAAATTACATTTTAACCCCAACAATTTCCAAAATAACATTTTAACCCATAAACTTT
* * * *
39230 TCTAAAATTACATTTTGACCATTA
66 TCTAAAATAACATTATAACC-CTA
* * *
39254 AACTTTTCCAAAATTATATTTT-GCCCCAA-AATTTCCAAAAATCACATTTTCAACC
1 AACTTTTCCAAAATTACATTTTAACCCCAACAATTTCC-AAAATAACATTTT-AACC
39309 TCAAAATTTC
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
87 5 0.04
88 91 0.75
89 26 0.21
ACGTcount: A:0.38, C:0.23, G:0.01, T:0.38
Consensus pattern (88 bp):
AACTTTTCCAAAATTACATTTTAACCCCAACAATTTCCAAAATAACATTTTAACCCATAAACTTT
TCTAAAATAACATTATAACCCTA
Found at i:39364 original size:30 final size:29
Alignment explanation
Indices: 39277--39374 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 29
39267 TTATATTTTG
* *
39277 CCCCAAAATTTCCAAAAA-TCACATTTTCAA
1 CCCCAAATTTTCCAAAAATTC-GATTTT-AA
* * *
39307 CCTCAAAATTTCCAAAAGTTCGATTTTAA
1 CCCCAAATTTTCCAAAAATTCGATTTTAA
* * *
39336 TCCTAAATTTTCCAAAAATTTGAATTTTAA
1 CCCCAAATTTTCCAAAAATTCG-ATTTTAA
39366 CCCCAAATT
1 CCCCAAATT
39375 CCTCAAAAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
29 18 0.33
30 35 0.64
31 2 0.04
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.34
Consensus pattern (29 bp):
CCCCAAATTTTCCAAAAATTCGATTTTAA
Found at i:42314 original size:20 final size:21
Alignment explanation
Indices: 42276--42314 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42266 ATGAATTTGC
*
42276 ATTTTTTTCTCTTCCAATTCA
1 ATTTTTTTCTCTTCAAATTCA
42297 ATTTTTTTCT-TTCAAATT
1 ATTTTTTTCTCTTCAAATT
42315 TTGAGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTTTCTCTTCAAATTCA
Done.