Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014594.1 Kokia drynarioides strain JFW-HI SEQ_129633, 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: 161971
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:8656 original size:162 final size:162
Alignment explanation
Indices: 8382--9934 Score: 2635
Period size: 162 Copynumber: 9.6 Consensus size: 162
8372 GCGTCCAATT
* * *
8382 TGCAAACTCTGAAGATATCGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
1 TGCAAACTCTGACGATATTGGACTGCTCTCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
8447 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
*
8512 CCCAATGTCTATTGCTAAAAGCCCTGGGAGAC
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* *
8544 TGCAAACTCTGAAGATATTGGACTGCT-TCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTTTC
1 TGCAAACTCTGACGATATTGGACTGCTCT-CAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTC
*
8608 AGACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAGCTGCAATAATTTGAGGTATCTCT
65 AGACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCT
8673 TCCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
130 TCCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* *
8706 TGCAAACTTTGACGATATTGGGCTGCTCTCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
1 TGCAAACTCTGACGATATTGGACTGCTCTCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
8771 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
8836 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* *
8868 TGCAAACTCTGACGATATCGGACTGCT-TCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTTTC
1 TGCAAACTCTGACGATATTGGACTGCTCT-CAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTC
* * * *
8932 AGACATAAGCCTCCAAAGTTTAAGGGATGTAGAAGTTCGAAGCTGCAATAATTTGAGGTATCTCT
65 AGACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCT
8997 TCCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
130 TCCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* * * *
9030 TGCAAATTTTGACGATATTGGGCTGCTCTCAATTGGAAGAAATAATCCAAGGCTCAGGAGTGTCA
1 TGCAAACTCTGACGATATTGGACTGCTCTCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
* * *
9095 GACATAAGCCTCCAAAGTTTAAAGGAAGTAGTATTTCAAACCTGCAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
9160 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* * *
9192 TGCAAACTTTGACGATATTGGGCTGCTCTCAATTGGAAGAAATAATCCAAGGCTCAGGAGTGTCA
1 TGCAAACTCTGACGATATTGGACTGCTCTCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
* * * *
9257 GACATAAGCCTCCAAAGTTTAAAGGAAGTAGTATTTCACAACTGCAAAAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
*
9322 CCCAATGTCTATTGCTAAAAGCCTTTGGAGAC
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* * * * * *
9354 TGCAGACTTTGAAGATATCGAACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
1 TGCAAACTCTGACGATATTGGACTGCTCTCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
9419 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
*
9484 CCCAATGTCTATTGCTAAAAGCCCTGGGAGAC
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* *
9516 TGCAAACTCTGAAGATATTGGACTGCT-TCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTTTC
1 TGCAAACTCTGACGATATTGGACTGCTCT-CAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTC
*
9580 AGACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAGCTGCAATAATTTGAGGTATCTCT
65 AGACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCT
9645 TCCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
130 TCCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* *
9678 TGCAAACTTTGACGATATGGGACTGCTCTCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
1 TGCAAACTCTGACGATATTGGACTGCTCTCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
* * *
9743 GACATAAGCCTCCAAAGTTTAAGGGATGTAGAAGTTCTAAACTGCAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
9808 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
*
9840 TGCAAACTCTGACGATATTGGACTGCTCTCAATTGGAAGAAATAATCCAAGGCTCAGGAGTGTCA
1 TGCAAACTCTGACGATATTGGACTGCTCTCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
*
9905 GACATAAGCCTCCAAAGTTTAAAGGAAGTA
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTA
9935 TGTGTTAAAC
Statistics
Matches: 1316, Mismatches: 69, Indels: 12
0.94 0.05 0.01
Matches are distributed among these distances:
161 1 0.00
162 1312 1.00
163 3 0.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (162 bp):
TGCAAACTCTGACGATATTGGACTGCTCTCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
Found at i:11249 original size:23 final size:22
Alignment explanation
Indices: 11223--11271 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
11213 TTTTGAGAAG
*
11223 TTAAAATATAATTTAATTATTT
1 TTAAAATATAATTTAATCATTT
**
11245 ATTAATTTATAATTTAATCATTT
1 -TTAAAATATAATTTAATCATTT
11268 TTAA
1 TTAA
11272 GGAATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAAAATATAATTTAATCATTT
Found at i:24879 original size:24 final size:23
Alignment explanation
Indices: 24852--24897 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
24842 TTGAAAAAAA
24852 ACAT-TTTTCAATTTATTAAAATAT
1 ACATGTTTTCAA-TT-TTAAAATAT
*
24876 ACATGTTTTTAATTTTAAAATA
1 ACATGTTTTCAATTTTAAAATA
24898 GGATGTTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 6 0.30
25 6 0.30
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (23 bp):
ACATGTTTTCAATTTTAAAATAT
Found at i:27694 original size:100 final size:103
Alignment explanation
Indices: 27572--27780 Score: 309
Period size: 100 Copynumber: 2.1 Consensus size: 103
27562 TTTACAACAC
* *
27572 ATAAAAAAAATAAATCTCTACTAAATATGTAATACTACAT-TAATGTAAAAATTAAAATAATGCT
1 ATAAAAAAAATAAATCTATACTAAATATATAATACTAC-TCTAATGTAAAAATTAAAATAATGCT
* * *
27636 AAGATGACTATAT-AAAAATTTTCAATAAATAAAAA-AT
65 AAGATGAATATATAAAAAAATGTCAATAAATAAAAATAT
* * *
27673 GTAAAAAAAA-AAATCTATACTAAATTTATAATACTACTCTAATGTAAACATTAAAATAATGCTA
1 ATAAAAAAAATAAATCTATACTAAATATATAATACTACTCTAATGTAAAAATTAAAATAATGCTA
27737 AGATGAATATATAAAAAAATGTCAATAAATAAAAATAT
66 AGATGAATATATAAAAAAATGTCAATAAATAAAAATAT
27775 ATAAAA
1 ATAAAA
27781 TTATTAAATA
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
99 1 0.01
100 59 0.61
101 29 0.30
102 7 0.07
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (103 bp):
ATAAAAAAAATAAATCTATACTAAATATATAATACTACTCTAATGTAAAAATTAAAATAATGCTA
AGATGAATATATAAAAAAATGTCAATAAATAAAAATAT
Found at i:27798 original size:100 final size:100
Alignment explanation
Indices: 27572--27806 Score: 264
Period size: 100 Copynumber: 2.3 Consensus size: 100
27562 TTTACAACAC
* * *
27572 ATAAAAAAAATAAATCTCTACTAAA-TATGTAATACTACATTAATGTAAAAATTAAAATAATGCT
1 ATAAAAAAAA-AAATATATAC-AAATTATATAATACTACATTAATGTAAAAATTAAAATAATGCT
* * *
27636 AAGATGACTATATAAAAATTTTCAATAAATAAAAAAT
64 AAGATGAATATATAAAAAATGTCAATAAATAAAAAAT
* * *
27673 GTAAAAAAAAAAATCTATACTAAATT-TATAATACTAC-TCTAATGTAAACATTAAAATAATGCT
1 ATAAAAAAAAAAATATATAC-AAATTATATAATACTACAT-TAATGTAAAAATTAAAATAATGCT
27736 AAGATGAATATATAAAAAAATGTCAATAAATAAAAATAT
64 AAGATGAATATAT-AAAAAATGTCAATAAATAAAAA-AT
* **
27775 ATAAAATTATTAAATAT-TA-AAATTATATAATA
1 ATAAAA-AAAAAAATATATACAAATTATATAATA
27807 TAAATTTTTT
Statistics
Matches: 116, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
99 1 0.01
100 63 0.54
101 37 0.32
102 9 0.08
103 6 0.05
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (100 bp):
ATAAAAAAAAAAATATATACAAATTATATAATACTACATTAATGTAAAAATTAAAATAATGCTAA
GATGAATATATAAAAAATGTCAATAAATAAAAAAT
Found at i:27807 original size:16 final size:17
Alignment explanation
Indices: 27769--27800 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
27759 CAATAAATAA
27769 AAATATATAAAATTATT
1 AAATATATAAAATTATT
27786 AAATAT-TAAAATTAT
1 AAATATATAAAATTAT
27801 ATAATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATATAAAATTATT
Found at i:28952 original size:16 final size:18
Alignment explanation
Indices: 28920--28954 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
28910 TGAGTATTTC
28920 AAATATAAAGACTAAAAT
1 AAATATAAAGACTAAAAT
28938 AAATA-AAAGAC-AAAAT
1 AAATATAAAGACTAAAAT
28954 A
1 A
28955 TGTTTGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 6 0.35
18 5 0.29
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (18 bp):
AAATATAAAGACTAAAAT
Found at i:35448 original size:11 final size:11
Alignment explanation
Indices: 35434--35509 Score: 50
Period size: 12 Copynumber: 6.8 Consensus size: 11
35424 GATAATTATT
35434 TTAATATTAAA
1 TTAATATTAAA
35445 TTAATA--AAA
1 TTAATATTAAA
*
35454 -TACTATTAAA
1 TTAATATTAAA
*
35464 ATAAGTATTAAA
1 TTAA-TATTAAA
* *
35476 TTTAATTTTATA
1 -TTAATATTAAA
35488 TTAAATTATTAAA
1 TT-AA-TATTAAA
*
35501 ATAATATTA
1 TTAATATTA
35510 TTTTTGATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 3 0.06
11 15 0.30
12 16 0.32
13 9 0.18
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:36597 original size:19 final size:19
Alignment explanation
Indices: 36573--36611 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
36563 AAACGTTCAC
36573 TTTGATTCTTTTATGGGAT
1 TTTGATTCTTTTATGGGAT
36592 TTTGATTCTTTTATGGGAT
1 TTTGATTCTTTTATGGGAT
36611 T
1 T
36612 ACGAACTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.05, G:0.21, T:0.59
Consensus pattern (19 bp):
TTTGATTCTTTTATGGGAT
Found at i:36777 original size:16 final size:16
Alignment explanation
Indices: 36758--36799 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
36748 GCAAAATCTG
*
36758 AAAGACAAAAAATACA
1 AAAGACAAAAAAGACA
36774 AAAGACAAAAAAGACA
1 AAAGACAAAAAAGACA
36790 AAAGACAAAA
1 AAAGACAAAA
36800 TAGTGAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.76, C:0.12, G:0.10, T:0.02
Consensus pattern (16 bp):
AAAGACAAAAAAGACA
Found at i:39592 original size:25 final size:24
Alignment explanation
Indices: 39550--39619 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 24
39540 TAGCAAACAT
*
39550 TTTTTCTTC-TTTTCTTTTTTTTTC
1 TTTTTC-TCATTTTCTTTTTCTTTC
39574 TTTTTCTCATTTTCGTTTTTCTTTC
1 TTTTTCTCATTTTC-TTTTTCTTTC
39599 TTTTTCTCATTTTCATTTTTC
1 TTTTTCTCATTTTC-TTTTTC
39620 AAGTGACTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
23 2 0.05
24 11 0.26
25 29 0.69
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (24 bp):
TTTTTCTCATTTTCTTTTTCTTTC
Found at i:39615 original size:31 final size:31
Alignment explanation
Indices: 39559--39617 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
39549 TTTTTTCTTC
* *
39559 TTTTCTTTTTTTTTCTTTTTCTCATTTTCGT
1 TTTTCTTTCTTTTTCTATTTCTCATTTTCGT
39590 TTTTCTTTCTTTTTCTCATTT-TCATTTT
1 TTTTCTTTCTTTTTCT-ATTTCTCATTTT
39618 TCAAGTGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (31 bp):
TTTTCTTTCTTTTTCTATTTCTCATTTTCGT
Found at i:55297 original size:30 final size:28
Alignment explanation
Indices: 55265--55321 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
55255 TCATATATAT
55265 ATATATATATTCCAATCTCCCTTACAAA
1 ATATATATATTCCAATCTCCCTTACAAA
55293 ATATATATATTCCAATCTCCCTTACAAA
1 ATATATATATTCCAATCTCCCTTACAAA
55321 A
1 A
55322 ATTCAACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (28 bp):
ATATATATATTCCAATCTCCCTTACAAA
Found at i:55817 original size:21 final size:21
Alignment explanation
Indices: 55793--55836 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
55783 TTTAAACATT
*
55793 AAACCCTAAACCCTAAACCTA
1 AAACCATAAACCCTAAACCTA
* *
55814 AAACCATAAACTCTAAACTTA
1 AAACCATAAACCCTAAACCTA
55835 AA
1 AA
55837 TCATGAACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (21 bp):
AAACCATAAACCCTAAACCTA
Found at i:55875 original size:13 final size:13
Alignment explanation
Indices: 55859--55948 Score: 51
Period size: 13 Copynumber: 6.8 Consensus size: 13
55849 AACTCGAACC
55859 TCAAGTTTAAGGT
1 TCAAGTTTAAGGT
55872 TCAAGGTTT-AGGT
1 TCAA-GTTTAAGGT
* *
55885 TCAAGATT-CGAGT
1 TCAAGTTTAAG-GT
*
55898 TCAAGGTTTAAGAT
1 TCAA-GTTTAAGGT
*
55912 TTAAGATTTAAGGT
1 TCAAG-TTTAAGGT
**
55926 TTGAGTTT-AGGT
1 TCAAGTTTAAGGT
*
55938 TTAAGGTTTAA
1 TCAA-GTTTAA
55949 AGTTTTATGT
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
12 11 0.18
13 26 0.43
14 23 0.38
15 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (13 bp):
TCAAGTTTAAGGT
Found at i:55946 original size:7 final size:7
Alignment explanation
Indices: 55863--56050 Score: 93
Period size: 7 Copynumber: 27.4 Consensus size: 7
55853 CGAACCTCAA
55863 GTTTAAG
1 GTTTAAG
*
55870 GTTCAAG
1 GTTTAAG
55877 GTTT-AG
1 GTTTAAG
*
55883 GTTCAAG
1 GTTTAAG
* **
55890 ATTCGA-
1 GTTTAAG
*
55896 GTTCAAG
1 GTTTAAG
55903 GTTTAAG
1 GTTTAAG
*
55910 ATTTAAG
1 GTTTAAG
*
55917 ATTTAAG
1 GTTTAAG
*
55924 GTTTGA-
1 GTTTAAG
55930 GTTT-AG
1 GTTTAAG
55936 GTTTAAG
1 GTTTAAG
*
55943 GTTTAAA
1 GTTTAAG
* *
55950 GTTTTAT
1 GTTTAAG
**
55957 GTTTGGG
1 GTTTAAG
55964 GTTTAAG
1 GTTTAAG
55971 GTTTAAG
1 GTTTAAG
*
55978 GTTTAAC
1 GTTTAAG
*
55985 ATTT-AG
1 GTTTAAG
* *
55991 CCTTTAAA
1 -GTTTAAG
*
55999 GTTTGAG
1 GTTTAAG
* *
56006 GTTCAAT
1 GTTTAAG
56013 GTTTATA-
1 GTTTA-AG
*
56020 GTTTAGG
1 GTTTAAG
*
56027 GTTT-GG
1 GTTTAAG
56033 GTTTTAAG
1 G-TTTAAG
56041 GTTTAAG
1 GTTTAAG
56048 GTT
1 GTT
56051 CAGGGTTTGG
Statistics
Matches: 138, Mismatches: 33, Indels: 20
0.72 0.17 0.10
Matches are distributed among these distances:
5 1 0.01
6 21 0.15
7 112 0.81
8 4 0.03
ACGTcount: A:0.26, C:0.04, G:0.26, T:0.44
Consensus pattern (7 bp):
GTTTAAG
Found at i:56030 original size:28 final size:27
Alignment explanation
Indices: 55999--56085 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 27
55989 AGCCTTTAAA
* *
55999 GTTTGAGGTTCAATGTTTATA-GTTTAGG
1 GTTTG-GGTTCAAGGTTTA-AGGTTCAGG
*
56027 GTTTGGGTTTTAAGGTTTAAGGTTCAGG
1 GTTTGGG-TTCAAGGTTTAAGGTTCAGG
* * *
56055 GTTTGGGGTTCAGGGTTCAAGATTCAGG
1 GTTT-GGGTTCAAGGTTTAAGGTTCAGG
56083 GTT
1 GTT
56086 CAAGGTTCAG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
27 3 0.06
28 43 0.88
29 3 0.06
ACGTcount: A:0.18, C:0.06, G:0.34, T:0.41
Consensus pattern (27 bp):
GTTTGGGTTCAAGGTTTAAGGTTCAGG
Found at i:56057 original size:7 final size:7
Alignment explanation
Indices: 56047--56099 Score: 61
Period size: 7 Copynumber: 7.6 Consensus size: 7
56037 TAAGGTTTAA
56047 GGTTCAG
1 GGTTCAG
**
56054 GGTTTGG
1 GGTTCAG
56061 GGTTCAG
1 GGTTCAG
*
56068 GGTTCAA
1 GGTTCAG
*
56075 GATTCAG
1 GGTTCAG
*
56082 GGTTCAA
1 GGTTCAG
56089 GGTTCAG
1 GGTTCAG
56096 GGTT
1 GGTT
56100 TAGTGTACCA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.17, C:0.11, G:0.40, T:0.32
Consensus pattern (7 bp):
GGTTCAG
Found at i:56057 original size:14 final size:14
Alignment explanation
Indices: 56040--56101 Score: 79
Period size: 14 Copynumber: 4.4 Consensus size: 14
56030 TGGGTTTTAA
56040 GGTTTAAGGTTCAG
1 GGTTTAAGGTTCAG
**
56054 GGTTTGGGGTTCAG
1 GGTTTAAGGTTCAG
* *
56068 GGTTCAAGATTCAG
1 GGTTTAAGGTTCAG
*
56082 GGTTCAAGGTTCAG
1 GGTTTAAGGTTCAG
56096 GGTTTA
1 GGTTTA
56102 GTGTACCAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.19, C:0.10, G:0.37, T:0.34
Consensus pattern (14 bp):
GGTTTAAGGTTCAG
Found at i:57420 original size:33 final size:34
Alignment explanation
Indices: 57373--57449 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 34
57363 GGCCTTGAAA
* * *
57373 CAAATCCAAACCTAAT-GCCC-AACTCCTTTAACC
1 CAAAACCAAACCTAATAACCCTAAC-CCTATAACC
57406 CAAAACCAAACCTAATAACCCTTAACCCTATAACC
1 CAAAACCAAACCTAATAACCC-TAACCCTATAACC
57441 CAAAACCAA
1 CAAAACCAA
57450 GCAACAACCC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 15 0.39
34 3 0.08
35 17 0.45
36 3 0.08
ACGTcount: A:0.44, C:0.38, G:0.01, T:0.17
Consensus pattern (34 bp):
CAAAACCAAACCTAATAACCCTAACCCTATAACC
Found at i:57652 original size:20 final size:20
Alignment explanation
Indices: 57627--57702 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
57617 ATGAACATTG
*
57627 ACTTTGACCATTAACCGTTA
1 ACTTTGACCATTGACCGTTA
*
57647 ACTTTGACACGTTGACCGTTA
1 ACTTTGAC-CATTGACCGTTA
*
57668 ACTTTGACCATTGACCGTTG
1 ACTTTGACCATTGACCGTTA
57688 ACTTTGACCATTGAC
1 ACTTTGACCATTGAC
57703 TTTTTTGACC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 33 0.65
21 18 0.35
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (20 bp):
ACTTTGACCATTGACCGTTA
Found at i:73599 original size:6 final size:6
Alignment explanation
Indices: 73588--73622 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
73578 AAGCTAACAA
*
73588 AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT GGAAG
1 AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT AGAAG
73623 AGGAGGAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.49, C:0.00, G:0.37, T:0.14
Consensus pattern (6 bp):
AGAAGT
Found at i:74993 original size:17 final size:18
Alignment explanation
Indices: 74960--74993 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
74950 ATTTAATGAT
74960 TTAAATAATTGAAATTTG
1 TTAAATAATTGAAATTTG
*
74978 TTAAAT-ATTTAAATTT
1 TTAAATAATTGAAATTT
74994 AAAAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TTAAATAATTGAAATTTG
Found at i:82375 original size:12 final size:14
Alignment explanation
Indices: 82344--82372 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
82334 TTTCTGTTTA
82344 CTTCTCTCCTTTCC
1 CTTCTCTCCTTTCC
82358 CTTCTCTCC-TTCC
1 CTTCTCTCCTTTCC
82371 CT
1 CT
82373 CTCCTTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (14 bp):
CTTCTCTCCTTTCC
Found at i:90699 original size:37 final size:37
Alignment explanation
Indices: 90658--90731 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
90648 TAGTATTATG
90658 TTAGTTTGTTATTTACATATGTTATTTATAAAAAATC
1 TTAGTTTGTTATTTACATATGTTATTTATAAAAAATC
90695 TTAGTTTGTTATTTACATATGTTATTTATAAAAAATC
1 TTAGTTTGTTATTTACATATGTTATTTATAAAAAATC
90732 AATTAATAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.51
Consensus pattern (37 bp):
TTAGTTTGTTATTTACATATGTTATTTATAAAAAATC
Found at i:95043 original size:23 final size:20
Alignment explanation
Indices: 95017--95062 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 20
95007 TCTCTTTTTT
95017 TAAAATATTTAATTATATCTCTA
1 TAAAATATTT-ATTA-ATCTC-A
95040 TAAAATATTTATTAATCTCA
1 TAAAATATTTATTAATCTCA
95060 TAA
1 TAA
95063 CTCTATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.17
21 5 0.22
22 4 0.17
23 10 0.43
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAAATATTTATTAATCTCA
Found at i:103689 original size:38 final size:38
Alignment explanation
Indices: 103608--103691 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
103598 TGAGTCTATT
* * * *
103608 CAGAATTGCACCCAGAATTGTCACTGCATGATAATATC
1 CAGAATTGCACCCAAAATTGTCAATGCATGAGAATAGC
* *
103646 CAGAATTGCGCCCAAAATTGTCAATGCATGAGCAT-GC
1 CAGAATTGCACCCAAAATTGTCAATGCATGAGAATAGC
103683 CGAGAATTG
1 C-AGAATTG
103692 TCGCTGCAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 2 0.05
38 37 0.95
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (38 bp):
CAGAATTGCACCCAAAATTGTCAATGCATGAGAATAGC
Found at i:103748 original size:26 final size:26
Alignment explanation
Indices: 103719--103770 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
103709 TTAAAATTAA
* * *
103719 CGCTGTGTAAATATGTCCAGAGTTGT
1 CGCTGTATAAACATGTCCAGAATTGT
*
103745 CGCTGTATAAGCATGTCCAGAATTGT
1 CGCTGTATAAACATGTCCAGAATTGT
103771 GCCCAGAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (26 bp):
CGCTGTATAAACATGTCCAGAATTGT
Found at i:106034 original size:20 final size:21
Alignment explanation
Indices: 105996--106037 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
105986 CTCCAAGGAT
*
105996 AAAAAGAGCAGAAAGGAAGAA
1 AAAAAGAGAAGAAAGGAAGAA
*
106017 AAAAAGAGAAGGAA-GAAGAA
1 AAAAAGAGAAGAAAGGAAGAA
106037 A
1 A
106038 GCACCATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (21 bp):
AAAAAGAGAAGAAAGGAAGAA
Found at i:118879 original size:11 final size:11
Alignment explanation
Indices: 118801--118880 Score: 54
Period size: 11 Copynumber: 6.7 Consensus size: 11
118791 ATTATAATAC
118801 AAGTTCAAATTT
1 AAGTT-AAATTT
*
118813 AATTTAAATTT
1 AAGTTAAATTT
118824 AAGTTGAAA-TT
1 AAGTT-AAATTT
*
118835 AAGTTTAATTAAT
1 AAGTTAAATT--T
*
118848 ACAAGTTGAAATTA
1 --AAGTT-AAATTT
*
118862 AATTTAAATTT
1 AAGTTAAATTT
118873 AAGTTAAA
1 AAGTTAAA
118881 ATAAAAATGA
Statistics
Matches: 53, Mismatches: 8, Indels: 15
0.70 0.11 0.20
Matches are distributed among these distances:
10 2 0.04
11 30 0.57
12 11 0.21
13 1 0.02
15 5 0.09
16 4 0.08
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (11 bp):
AAGTTAAATTT
Found at i:118942 original size:88 final size:88
Alignment explanation
Indices: 118816--119053 Score: 318
Period size: 88 Copynumber: 2.7 Consensus size: 88
118806 CAAATTTAAT
* * *
118816 TTAAATTTAAGTTGAAATTAAGTTTAATTAATACAAGTTGAAATTAAATTTAAATTTAAGTTAAA
1 TTAAATTTAAATTGAAATGAAATTTAATTAATACAAGTTGAAATTAAATTTAAATTTAAGTTAAA
118881 ATAAAAATGAATACAAGTTGAAA
66 ATAAAAATGAATACAAGTTGAAA
* * *
118904 TTAAATTTAAATTGAAATGAAATTTACTTAATAGAAGTTGAAATTAAATTTAAATTTACGTTAAA
1 TTAAATTTAAATTGAAATGAAATTTAATTAATACAAGTTGAAATTAAATTTAAATTTAAGTTAAA
*
118969 ATAAAAATTAATACAAGTTGAAA
66 ATAAAAATGAATACAAGTTGAAA
* * * *
118992 TTAAATTTAAATTTAAGTTAAAAATTTAATTTGAA-ATTAAGTTGAAATT-AATTTAAATTTAA
1 TTAAATTTAAATTGAA-AT-GAAATTTAA-TT-AATA-CAAGTTGAAATTAAATTTAAATTTAA
119054 ATGAAGGTGG
Statistics
Matches: 132, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
88 96 0.73
89 1 0.01
90 7 0.05
91 15 0.11
92 13 0.10
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (88 bp):
TTAAATTTAAATTGAAATGAAATTTAATTAATACAAGTTGAAATTAAATTTAAATTTAAGTTAAA
ATAAAAATGAATACAAGTTGAAA
Found at i:119012 original size:11 final size:12
Alignment explanation
Indices: 118983--119053 Score: 60
Period size: 11 Copynumber: 6.2 Consensus size: 12
118973 AAATTAATAC
118983 AAGTTGAAA-TT
1 AAGTTGAAATTT
* *
118994 AAATTTAAATTT
1 AAGTTGAAATTT
*
119006 AAGTTAAAAATTT
1 AAGTT-GAAATTT
*
119019 AATTTGAAA-TT
1 AAGTTGAAATTT
119030 AAGTTGAAA-TT
1 AAGTTGAAATTT
*
119041 AA-TTTAAATTT
1 AAGTTGAAATTT
119052 AA
1 AA
119054 ATGAAGGTGG
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
10 5 0.10
11 25 0.51
12 9 0.18
13 10 0.20
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
AAGTTGAAATTT
Found at i:119066 original size:28 final size:27
Alignment explanation
Indices: 119014--119070 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
119004 TTAAGTTAAA
* *
119014 AATTTAATTTGAAATTAAGTTGAAATT
1 AATTTAATTTGAAATGAAGTGGAAATT
119041 AATTTAAATTT-AAATGAAGGTGGAAATT
1 AATTT-AATTTGAAATGAA-GTGGAAATT
119069 AA
1 AA
119071 AATGAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (27 bp):
AATTTAATTTGAAATGAAGTGGAAATT
Found at i:119423 original size:17 final size:19
Alignment explanation
Indices: 119403--119475 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 19
119393 AAAAGTAATT
119403 AAAAAC-TTTAATTAATAA
1 AAAAACTTTTAATTAATAA
* *
119421 AAAAACTTTTAATTTATTA
1 AAAAACTTTTAATTAATAA
* * *
119440 AATAA-TTTT-TTTAATTTA
1 AAAAACTTTTAATTAA-TAA
*
119458 AAAAACTTTTAAATAATA
1 AAAAACTTTTAATTAATA
119476 TTTATTAAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
17 3 0.07
18 17 0.40
19 19 0.45
20 3 0.07
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAAACTTTTAATTAATAA
Found at i:119467 original size:18 final size:20
Alignment explanation
Indices: 119427--119467 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
119417 ATAAAAAAAC
*
119427 TTTTAATTTATTAAATAATTT
1 TTTTAATTTA-TAAATAACTT
119448 TTTTAATTTA-AAA-AACTT
1 TTTTAATTTATAAATAACTT
119466 TT
1 TT
119468 AAATAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 6 0.32
19 3 0.16
21 10 0.53
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAATTTATAAATAACTT
Found at i:122040 original size:17 final size:17
Alignment explanation
Indices: 122020--122086 Score: 89
Period size: 17 Copynumber: 3.9 Consensus size: 17
122010 GACGAATGGA
*
122020 AATGCAATGACAATGCG
1 AATGCAATGACAATGAG
* * *
122037 AATGCAGTGACAATTAA
1 AATGCAATGACAATGAG
122054 AATGCAATGACAATGAG
1 AATGCAATGACAATGAG
*
122071 AATGTAATGACAATGA
1 AATGCAATGACAATGA
122087 TTACAAACAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (17 bp):
AATGCAATGACAATGAG
Found at i:122062 original size:34 final size:34
Alignment explanation
Indices: 122019--122084 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
122009 AGACGAATGG
* *
122019 AAATGCAATGACAATGCGAATGCAGTGACAATTA
1 AAATGCAATGACAATGAGAATGCAATGACAATTA
*
122053 AAATGCAATGACAATGAGAATGTAATGACAAT
1 AAATGCAATGACAATGAGAATGCAATGACAAT
122085 GATTACAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.21
Consensus pattern (34 bp):
AAATGCAATGACAATGAGAATGCAATGACAATTA
Found at i:122145 original size:13 final size:12
Alignment explanation
Indices: 122127--122159 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
122117 GGTATGCATG
122127 AAAAACTAAAACT
1 AAAAACTAAAA-T
122140 AAAAACTAAAAT
1 AAAAACTAAAAT
122152 -AAAACTAA
1 AAAAACTAA
122160 CTCAACTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.40
12 1 0.05
13 11 0.55
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAACTAAAAT
Found at i:125526 original size:9 final size:9
Alignment explanation
Indices: 125512--125554 Score: 77
Period size: 9 Copynumber: 4.8 Consensus size: 9
125502 CTGAGGGGTT
125512 ACGTGGCTC
1 ACGTGGCTC
125521 ACGTGGCTC
1 ACGTGGCTC
125530 ACGTGGCTC
1 ACGTGGCTC
*
125539 ACGTGGCTA
1 ACGTGGCTC
125548 ACGTGGC
1 ACGTGGC
125555 GATGATGTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.14, C:0.30, G:0.35, T:0.21
Consensus pattern (9 bp):
ACGTGGCTC
Found at i:125612 original size:22 final size:22
Alignment explanation
Indices: 125568--125613 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
125558 GATGTGGTGC
* *
125568 TGACGTGGCGATGACGTGGCGA
1 TGACGTGGCGATGACGCGACGA
125590 TGACGTGGCGATGACGCGACGA
1 TGACGTGGCGATGACGCGACGA
125612 TG
1 TG
125614 TTGACGTGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.43, T:0.17
Consensus pattern (22 bp):
TGACGTGGCGATGACGCGACGA
Found at i:125613 original size:11 final size:11
Alignment explanation
Indices: 125548--125605 Score: 89
Period size: 11 Copynumber: 5.3 Consensus size: 11
125538 CACGTGGCTA
125548 ACGTGGCGATG
1 ACGTGGCGATG
* * *
125559 ATGTGGTGCTG
1 ACGTGGCGATG
125570 ACGTGGCGATG
1 ACGTGGCGATG
125581 ACGTGGCGATG
1 ACGTGGCGATG
125592 ACGTGGCGATG
1 ACGTGGCGATG
125603 ACG
1 ACG
125606 CGACGATGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 41 1.00
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.21
Consensus pattern (11 bp):
ACGTGGCGATG
Found at i:125613 original size:33 final size:33
Alignment explanation
Indices: 125548--125613 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
125538 CACGTGGCTA
* * * * *
125548 ACGTGGCGATGATGTGGTGCTGACGTGGCGATG
1 ACGTGGCGATGACGTGGCGATGACGCGACGATG
125581 ACGTGGCGATGACGTGGCGATGACGCGACGATG
1 ACGTGGCGATGACGTGGCGATGACGCGACGATG
125614 TTGACGTGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.44, T:0.20
Consensus pattern (33 bp):
ACGTGGCGATGACGTGGCGATGACGCGACGATG
Found at i:125833 original size:6 final size:6
Alignment explanation
Indices: 125822--125849 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
125812 AATTTAAAGA
125822 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
125850 GGGTTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:126858 original size:20 final size:20
Alignment explanation
Indices: 126833--126897 Score: 130
Period size: 20 Copynumber: 3.2 Consensus size: 20
126823 TAACAGATTG
126833 TACTATTTTATAGTGGATCC
1 TACTATTTTATAGTGGATCC
126853 TACTATTTTATAGTGGATCC
1 TACTATTTTATAGTGGATCC
126873 TACTATTTTATAGTGGATCC
1 TACTATTTTATAGTGGATCC
126893 TACTA
1 TACTA
126898 GACTGTCTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (20 bp):
TACTATTTTATAGTGGATCC
Found at i:131520 original size:5 final size:5
Alignment explanation
Indices: 131505--131569 Score: 55
Period size: 5 Copynumber: 12.8 Consensus size: 5
131495 ACACGAGTTG
*
131505 AAAAT ACAAT AAAAT AAAAT ACTAAAT -AAAT -AAAT AGGAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT A--AAAT AAAAT AAAAT A--AAAT AAAAT
*
131552 AAAAT AAAGT -AAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
131570 AATAGATTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
4 11 0.22
5 30 0.60
7 9 0.18
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:131580 original size:26 final size:25
Alignment explanation
Indices: 131515--131573 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
131505 AAAATACAAT
*
131515 AAAATAAAATACTAAATAAATAAATAG
1 AAAATAAAATA--AAATAAATAAATAA
*
131542 GAAATAAAATAAAATAAAGTAAATAA
1 AAAATAAAATAAAATAAA-TAAATAA
131568 AAAATA
1 AAAATA
131574 GATTAAAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 7 0.25
26 11 0.39
27 10 0.36
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (25 bp):
AAAATAAAATAAAATAAATAAATAA
Found at i:134330 original size:20 final size:19
Alignment explanation
Indices: 134301--134338 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
134291 AAAAAATCAA
134301 ATAAAAATTTTAGAATTTTT
1 ATAAAAATTTTA-AATTTTT
*
134321 ATAAATATTTTAAATTTT
1 ATAAAAATTTTAAATTTT
134339 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
ATAAAAATTTTAAATTTTT
Found at i:134349 original size:11 final size:11
Alignment explanation
Indices: 134335--134368 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
134325 ATATTTTAAA
134335 TTTTAATTTTT
1 TTTTAATTTTT
134346 TTTTAATTTTT
1 TTTTAATTTTT
*
134357 TGTT-ATTTTT
1 TTTTAATTTTT
134367 TT
1 TT
134369 AAAGAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTAATTTTT
Found at i:134349 original size:18 final size:19
Alignment explanation
Indices: 134328--134371 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
134318 TTTATAAATA
134328 TTTTAAATTTTAATT-TTT
1 TTTTAAATTTTAATTATTT
* **
134346 TTTTAATTTTTTGTTATTT
1 TTTTAAATTTTAATTATTT
134365 TTTTAAA
1 TTTTAAA
134372 GAAAAATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTAAATTTTAATTATTT
Found at i:134544 original size:31 final size:32
Alignment explanation
Indices: 134484--134556 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 32
134474 AATTATATTT
*
134484 ACATTTATT-T-TATTTATTTAATACGATAAA
1 ACATTTATTATATATTTATTTAATACAATAAA
*
134514 ACATTTATTATATATTT-TTTAATATAATAAA
1 ACATTTATTATATATTTATTTAATACAATAAA
*
134545 ATATTTATTATA
1 ACATTTATTATA
134557 CTTACAGTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.24
31 24 0.63
32 5 0.13
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (32 bp):
ACATTTATTATATATTTATTTAATACAATAAA
Found at i:138651 original size:59 final size:58
Alignment explanation
Indices: 138530--138664 Score: 175
Period size: 58 Copynumber: 2.3 Consensus size: 58
138520 TGGGAAATGT
* * *
138530 GGTGTCGGCCATTGGTTACCAAACATCAAAAAAATAATTTTTTTATTCGTGTTTTATG
1 GGTGTCGACCATTGGTTGCCAAACACCAAAAAAATAATTTTTTTATTCGTGTTTTATG
* *
138588 GGTGTCGACCATTGGTTGCCAAACACCCATAAAAAT-ATTTTTTTATTCG-GATTTTTTTG
1 GGTGTCGACCATTGGTTGCCAAACA-CCAAAAAAATAATTTTTTTATTCGTG--TTTTATG
*
138647 GGTGTCGACCATTAGTTG
1 GGTGTCGACCATTGGTTG
138665 AAATAAACCT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
57 1 0.01
58 36 0.53
59 31 0.46
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (58 bp):
GGTGTCGACCATTGGTTGCCAAACACCAAAAAAATAATTTTTTTATTCGTGTTTTATG
Found at i:138680 original size:58 final size:57
Alignment explanation
Indices: 138558--138683 Score: 148
Period size: 59 Copynumber: 2.2 Consensus size: 57
138548 CCAAACATCA
* * *
138558 AAAAAATAATTTTTTTATTCGTGTTTTATGGGTGTCGACCATTGGTTGCCAAACACCC
1 AAAAAAT-ATTTTTTTATTCGTGTTTTATGGGTGTCGACCATTAGTTGCAAAAAACCC
* *
138616 ATAAAAATATTTTTTTATTCG-GATTTTTTTGGGTGTCGACCATTAGTTG-AAATAAACCT
1 A-AAAAATATTTTTTTATTCGTG--TTTTATGGGTGTCGACCATTAGTTGCAAA-AAACCC
138675 AAAAAATAT
1 AAAAAATAT
138684 ATATATTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
57 1 0.02
58 24 0.41
59 34 0.58
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.40
Consensus pattern (57 bp):
AAAAAATATTTTTTTATTCGTGTTTTATGGGTGTCGACCATTAGTTGCAAAAAACCC
Found at i:142680 original size:22 final size:22
Alignment explanation
Indices: 142652--142894 Score: 261
Period size: 22 Copynumber: 10.5 Consensus size: 22
142642 GAACGCTAGC
142652 GTGCTTCTGTTCAGCACTGTGT
1 GTGCTTCTGTTCAGCACTGTGT
142674 GTGCTTCTGTTCAGTACACACTGTGT
1 GTGCTTCTGTTCAG----CACTGTGT
142700 GTGCTTCTGTTCAGCACTGTGT
1 GTGCTTCTGTTCAGCACTGTGT
*
142722 GTGCTTCTGTTTCCCTAGCACTGCGT
1 GTGCTTCTG-TT--C-AGCACTGTGT
* * *
142748 GTGCTTCTGTTTCCCCAACACTATTT
1 GTGCTTCTG-TT---CAGCACTGTGT
142774 GTGCTTCTGTTCAGCACTGTGT
1 GTGCTTCTGTTCAGCACTGTGT
* * *
142796 GTGCTTCTGATCAACACTATGT
1 GTGCTTCTGTTCAGCACTGTGT
*
142818 GTGCTTCTGTTCAGTACTGTGT
1 GTGCTTCTGTTCAGCACTGTGT
* * * *
142840 GTGCTTTTGATCAACACTATGT
1 GTGCTTCTGTTCAGCACTGTGT
*
142862 GTGCTTCTGTTCAACACTGTGT
1 GTGCTTCTGTTCAGCACTGTGT
142884 GTGCTTCTGTT
1 GTGCTTCTGTT
142895 TCCCCAGCAG
Statistics
Matches: 189, Mismatches: 23, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
22 123 0.65
23 2 0.01
25 3 0.02
26 58 0.31
27 3 0.02
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.41
Consensus pattern (22 bp):
GTGCTTCTGTTCAGCACTGTGT
Found at i:143598 original size:13 final size:13
Alignment explanation
Indices: 143580--143604 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
143570 ATGATGATGC
143580 TTATAATTATAAA
1 TTATAATTATAAA
143593 TTATAATTATAA
1 TTATAATTATAA
143605 TATTTTATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTATAATTATAAA
Found at i:145916 original size:25 final size:25
Alignment explanation
Indices: 145877--146002 Score: 99
Period size: 23 Copynumber: 5.4 Consensus size: 25
145867 CACTAGTGCG
145877 CTCTCTGTT-TT-GCAC-GTCTCGTA
1 CTCTCTGTTATTAGCACTGTCT-GTA
*
145900 CTCTCTGTTATTAGCACTGTCTGTG
1 CTCTCTGTTATTAGCACTGTCTGTA
* * *
145925 CTCTCTG--ATTAGCACTTTGTGTG
1 CTCTCTGTTATTAGCACTGTCTGTA
* * *
145948 CTCTCTG--ATTAGTACTTTGTGTA
1 CTCTCTGTTATTAGCACTGTCTGTA
* *
145971 CTCTCTG-T-TTAGCACTGTGTGTG
1 CTCTCTGTTATTAGCACTGTCTGTA
145994 CTCTCTGTT
1 CTCTCTGTT
146003 GCCCTGCACT
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
23 70 0.78
24 3 0.03
25 13 0.14
26 4 0.04
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (25 bp):
CTCTCTGTTATTAGCACTGTCTGTA
Found at i:145999 original size:69 final size:66
Alignment explanation
Indices: 145897--146049 Score: 191
Period size: 69 Copynumber: 2.2 Consensus size: 66
145887 TGCACGTCTC
*
145897 GTACTCTCTGTTATTAGCACTGTCTGTGCTCTCTGATTAGCACT-TTGTGTGCTCTCTGATTAGT
1 GTACTCTCTG-T-TTAGCACTGTCTGTGCTCTCTG-TT-GCACTCTTATGTGCTCTCTG-TTAGT
145961 ACTTTG
61 ACTTTG
* *
145967 TGTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGCCCTGCACTTATGTGCTCTCTGTTAGTA
1 -GTACTCTCTGTTTAGCACTGTCTGTGCTCTCTGTTGCACT---CTTATGTGCTCTCTGTTAGTA
146032 CTTTG
62 CTTTG
146037 GTACTCTCTGTTT
1 GTACTCTCTGTTT
146050 GTTCCGTATA
Statistics
Matches: 75, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
67 4 0.05
68 2 0.03
69 34 0.45
70 12 0.16
71 23 0.31
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (66 bp):
GTACTCTCTGTTTAGCACTGTCTGTGCTCTCTGTTGCACTCTTATGTGCTCTCTGTTAGTACTTT
G
Found at i:147636 original size:6 final size:6
Alignment explanation
Indices: 147618--147673 Score: 67
Period size: 6 Copynumber: 9.0 Consensus size: 6
147608 TAAACCTCTT
* *
147618 AATATA TAATATA AATATA AATATA AACATA AATATGA ATTATA AATATA
1 AATATA -AATATA AATATA AATATA AATATA AATAT-A AATATA AATATA
*
147668 GATATA
1 AATATA
147674 GATTACATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
6 32 0.74
7 11 0.26
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:147678 original size:19 final size:19
Alignment explanation
Indices: 147620--147678 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
147610 AACCTCTTAA
*
147620 TATATAATATAAATATA-AA
1 TATA-AATATAAATATAGAT
*
147639 TATAAACATAAATAT-GAAT
1 TATAAATATAAATATAG-AT
*
147658 TATAAATATAGATATAGAT
1 TATAAATATAAATATAGAT
147677 TA
1 TA
147679 CATAAAAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 10 0.30
19 22 0.67
20 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (19 bp):
TATAAATATAAATATAGAT
Found at i:158332 original size:14 final size:14
Alignment explanation
Indices: 158309--158343 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
158299 TATACTATTC
158309 AAATAATAACAACA
1 AAATAATAACAACA
*
158323 AAATAGTAACAACA
1 AAATAATAACAACA
*
158337 TAATAAT
1 AAATAAT
158344 GAAATTGCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (14 bp):
AAATAATAACAACA
Found at i:158655 original size:20 final size:21
Alignment explanation
Indices: 158621--158659 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
158611 AAACATACAT
158621 ATATAATTATATATTTTAATG
1 ATATAATTATATATTTTAATG
158642 ATATAATT-TATATTTTAA
1 ATATAATTATATATTTTAA
158660 CAAATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (21 bp):
ATATAATTATATATTTTAATG
Found at i:160383 original size:51 final size:51
Alignment explanation
Indices: 160332--160564 Score: 277
Period size: 51 Copynumber: 4.7 Consensus size: 51
160322 TTCTCGCCAT
* * **
160332 GGATTCATTTACTCACGATGACACTTAGTCATCAGACCTTTAATTCA-CCA
1 GGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAA
* * * *
160382 TGATTCATTT-CTCACGATGACACTTAGTCATTGAACCTTTAATCCGTAAA
1 GGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAA
* *
160432 GGAATCATTTACT--C----A-ACTTAGTCATCGGACCTTTAATCCGTAAA
1 GGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAA
* *
160476 GGATTCATTTACTCATGATGACACTTAGTCGTCGGACCTTTAATCCATAAA
1 GGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAA
* *
160527 GGATTCATTTACTTACGATGACACTTAGTCATTGGACC
1 GGATTCATTTACTCACGATGACACTTAGTCATCGGACC
160565 CTTTCGTTTA
Statistics
Matches: 154, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
44 39 0.25
45 1 0.01
49 32 0.21
50 19 0.12
51 63 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (51 bp):
GGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAA
Found at i:160466 original size:44 final size:46
Alignment explanation
Indices: 160401--160539 Score: 174
Period size: 44 Copynumber: 3.0 Consensus size: 46
160391 TCTCACGATG
* * *
160401 ACACTTAGTCATTGAACCTTTAATCCGTAAAGGAATCATTTACTC-
1 ACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCA
160446 A-ACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCATGA
1 ACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTC---A
* *
160494 TGACACTTAGTCGTCGGACCTTTAATCCATAAAGGATTCATTTACT
1 --ACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACT
160540 TACGATGACA
Statistics
Matches: 82, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
44 40 0.49
45 1 0.01
50 1 0.01
51 40 0.49
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (46 bp):
ACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCA
Done.