Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007857.1 Kokia drynarioides strain JFW-HI SEQ_122496, 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: 147065
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:3552 original size:17 final size:18
Alignment explanation
Indices: 3530--3564 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3520 TTGAGAGTGT
3530 TTAAATT-TCGATTAAAA
1 TTAAATTATCGATTAAAA
3547 TTAAATTGATCGATTAAA
1 TTAAATT-ATCGATTAAA
3565 TTTTTAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (18 bp):
TTAAATTATCGATTAAAA
Found at i:3904 original size:20 final size:20
Alignment explanation
Indices: 3879--3925 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
3869 TCAAAAATTG
*
3879 TTATTTTCTTA-TTTTTGTTT
1 TTATTTT-TTATTTTTTATTT
3899 TTATTTTTTATTTTTTATTT
1 TTATTTTTTATTTTTTATTT
3919 TTATTTT
1 TTATTTT
3926 ATAAGTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (20 bp):
TTATTTTTTATTTTTTATTT
Found at i:3905 original size:6 final size:6
Alignment explanation
Indices: 3887--3925 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
3877 TGTTATTTTC
*
3887 TTATTT TTGTTT TTATTTT TTATTTT TTATTT TTATTT T
1 TTATTT TTATTT TTA-TTT TTA-TTT TTATTT TTATTT T
3926 ATAAGTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:3906 original size:7 final size:7
Alignment explanation
Indices: 3879--3925 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
3869 TCAAAAATTG
3879 TTATTTT
1 TTATTTT
3886 CTTA-TTT
1 -TTATTTT
*
3893 TT-GTTT
1 TTATTTT
3899 TTATTTT
1 TTATTTT
3906 TTATTTT
1 TTATTTT
3913 TTA-TTT
1 TTATTTT
3919 TTATTTT
1 TTATTTT
3926 ATAAGTTGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
6 13 0.37
7 19 0.54
8 3 0.09
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (7 bp):
TTATTTT
Found at i:3912 original size:13 final size:13
Alignment explanation
Indices: 3879--3925 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
3869 TCAAAAATTG
3879 TTATTTTCTTATTT
1 TTATTTT-TTATTT
*
3893 TT-GTTTTTATTTT
1 TTATTTTTTA-TTT
3906 TTATTTTTTATTT
1 TTATTTTTTATTT
3919 TTATTTT
1 TTATTTT
3926 ATAAGTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 3 0.10
13 18 0.62
14 8 0.28
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (13 bp):
TTATTTTTTATTT
Found at i:9940 original size:11 final size:11
Alignment explanation
Indices: 9919--9966 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
9909 ATTCAGAGAT
*
9919 AATTAAAAGAG
1 AATTGAAAGAG
* *
9930 GATTGAGAGAG
1 AATTGAAAGAG
9941 AATTGAAAGAG
1 AATTGAAAGAG
*
9952 AAATGAAAGAG
1 AATTGAAAGAG
9963 AATT
1 AATT
9967 TAGAGTAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.19
Consensus pattern (11 bp):
AATTGAAAGAG
Found at i:18527 original size:28 final size:29
Alignment explanation
Indices: 18483--18548 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 29
18473 TAATTTTTAA
*
18483 AAAATT-AAATCAAAATTTAATCATTTTT
1 AAAATTAAAATCAAAATTTAATCATTATT
* *
18511 AAAATTAAAAT-ACAATTTTATCATTATT
1 AAAATTAAAATCAAAATTTAATCATTATT
*
18539 AATA-TAAAAT
1 AAAATTAAAAT
18549 TTTATAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 6 0.18
28 23 0.70
29 4 0.12
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAATTAAAATCAAAATTTAATCATTATT
Found at i:20350 original size:33 final size:33
Alignment explanation
Indices: 20291--20377 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
20281 GGATCAGTAG
* * *
20291 GAGTTTCTTCA-TCCAGGTTAGTGGGAATGCTAT
1 GAGTTTCTTCACTCAAGGTT-GAGGGAATACTAT
* *
20324 GATTTTCTTCACTCGAGGTTGAGGGAATACTAT
1 GAGTTTCTTCACTCAAGGTTGAGGGAATACTAT
* *
20357 GAGTTCCTTCACCCAAGGTTG
1 GAGTTTCTTCACTCAAGGTTG
20378 CAGTAAGGGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
33 38 0.84
34 7 0.16
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (33 bp):
GAGTTTCTTCACTCAAGGTTGAGGGAATACTAT
Found at i:25343 original size:174 final size:174
Alignment explanation
Indices: 25053--25372 Score: 414
Period size: 174 Copynumber: 1.8 Consensus size: 174
25043 AAAACCCTGG
* ** *
25053 CTCCATTTACCTCATTCTGAGCCTTGGCTTCACCACCTGAAACATCATACCTTGAACCCAAATCA
1 CTCCATTTACCTCATTCTGAGCCCTACCTTCACCACCTGAAACATCATACCTTGAACCCAAACCA
** **
25118 CTGGCTGCACCACCTTCACTATCTAAGGTACTCAGATTACCCTCCAAACCAACTTCATCAGG-CT
66 CTCACTGCACCACAGTCACTATCTAAGGTACTCAGATTACCCTCCAAACCAACTTCA-CAGGACT
25182 CATT-ATGACCACAAACTACATCATTAGAACAAGACCGAACCACAC
130 C-TTCATGACCACAAACTACATCATTAGAACAAGACCGAACCACAC
* * **
25227 CTCCATTTACCTCATTCTGAGCCCTACCTTCCCCACCTGAAACCTCATTTCTTGAACCCAAACCA
1 CTCCATTTACCTCATTCTGAGCCCTACCTTCACCACCTGAAACATCATACCTTGAACCCAAACCA
*** * * *
25292 -TCCACTGCATGGCAGTCACTATCTAAGGTTCTCA-AGTTACCCTCCAAACCAACTTTACTGGAC
66 CT-CACTGCACCACAGTCACTATCTAAGGTACTCAGA-TTACCCTCCAAACCAACTTCACAGGAC
25355 TCTTCATGACCACAAACT
129 TCTTCATGACCACAAACT
25373 GCTTCACCAA
Statistics
Matches: 124, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
173 7 0.06
174 117 0.94
ACGTcount: A:0.29, C:0.35, G:0.10, T:0.25
Consensus pattern (174 bp):
CTCCATTTACCTCATTCTGAGCCCTACCTTCACCACCTGAAACATCATACCTTGAACCCAAACCA
CTCACTGCACCACAGTCACTATCTAAGGTACTCAGATTACCCTCCAAACCAACTTCACAGGACTC
TTCATGACCACAAACTACATCATTAGAACAAGACCGAACCACAC
Found at i:29065 original size:4 final size:4
Alignment explanation
Indices: 29049--29078 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
29039 AATTTATCAT
29049 ATAA ATAA CATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA -ATAA ATAA ATAA ATAA ATAA A
29079 ATCCCTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:31084 original size:54 final size:54
Alignment explanation
Indices: 30987--31093 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
30977 AAACCCAATG
* *
30987 TTCCATTTCTTCGGCTTAAAATGTCAGGGTTGAAGGCCAGGTGCCAAATTTATT
1 TTCCATTTCTTCGGCTTAAAATGTCAGGGTTGAAGGACAGGTGCCAAAATTATT
* *
31041 TTCCATTTGTTCGGCTTAAAATAG-CAGGGTTG-AGTGACGGGTGCCAAAATTAT
1 TTCCATTTCTTCGGCTTAAAAT-GTCAGGGTTGAAG-GACAGGTGCCAAAATTAT
31094 GGAGCATAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
53 2 0.04
54 44 0.94
55 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (54 bp):
TTCCATTTCTTCGGCTTAAAATGTCAGGGTTGAAGGACAGGTGCCAAAATTATT
Found at i:31972 original size:63 final size:63
Alignment explanation
Indices: 31868--32010 Score: 259
Period size: 63 Copynumber: 2.3 Consensus size: 63
31858 AGGGAACACC
*
31868 GATATATTGAAGATGAATATATCAACTCCAACCTCATGTAGGTTTCTCTACTTTGAACCAAGA
1 GATACATTGAAGATGAATATATCAACTCCAACCTCATGTAGGTTTCTCTACTTTGAACCAAGA
* *
31931 GATACATTGAGGATGAATATATCAACTCCAACCTCATGTAGGTTTCTCTACTTTGAACCACGA
1 GATACATTGAAGATGAATATATCAACTCCAACCTCATGTAGGTTTCTCTACTTTGAACCAAGA
31994 GATACATTGAAGATGAA
1 GATACATTGAAGATGAA
32011 CATCTAATTT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 76 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (63 bp):
GATACATTGAAGATGAATATATCAACTCCAACCTCATGTAGGTTTCTCTACTTTGAACCAAGA
Found at i:32820 original size:33 final size:33
Alignment explanation
Indices: 32783--32849 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
32773 AGTTCCTTTG
*
32783 CTGAATGACGGAGGAACAGCTGGAGTTTCTTCA
1 CTGAATGACGGAGGAACAGATGGAGTTTCTTCA
** *
32816 CTGAATGTTGGAGGAAGAGATGGAGTTTCTTCA
1 CTGAATGACGGAGGAACAGATGGAGTTTCTTCA
32849 C
1 C
32850 CCAAGGTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (33 bp):
CTGAATGACGGAGGAACAGATGGAGTTTCTTCA
Found at i:32864 original size:33 final size:33
Alignment explanation
Indices: 32794--32864 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
32784 TGAATGACGG
* ** * *
32794 AGGAACAGCTGGAGTTTCTTCACTGAATGTTGG
1 AGGAACAGATGGAGTTTCTTCACCCAAGGTTGC
* *
32827 AGGAAGAGATGGAGTTTCTTCACCCAAGGTTTC
1 AGGAACAGATGGAGTTTCTTCACCCAAGGTTGC
32860 AGGAA
1 AGGAA
32865 TACTGGAGCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (33 bp):
AGGAACAGATGGAGTTTCTTCACCCAAGGTTGC
Found at i:37334 original size:174 final size:174
Alignment explanation
Indices: 37044--37362 Score: 383
Period size: 174 Copynumber: 1.8 Consensus size: 174
37034 AAAACCCTGG
* **
37044 CTCCATTTACCTCATTCAAAGCCTTAGCTTCACCACCTGAAACCTCATACCTTGAACCCAAATCA
1 CTCCATTTACCTCATTCAAAGCCCTAGCTTCACCACCCAAAACCTCATACCTTGAACCCAAATCA
* ** ** * *
37109 CCGGCTGCATCACCTTCACTATCTAAGGTACTCGGATTACCCTCCAAACCAACTTCA-TCGGACT
66 CCGACCACATCACAATCAATATCTAAGGTACTCGGATTAACCTCCAAACCAACTTCACT-GGACT
37173 CATT-ACGACCACAAACTACATCATTAGAACAAGACCGAACCACAC
130 C-TTGACGACCACAAACTACATCATTAGAACAAGACCGAACCACAC
** * * * *
37218 CTCCATTTACCTCATTCTGAGCCCTAGTTTCACCACCCAAAACCTCATTCCTTGAACCTAGATCA
1 CTCCATTTACCTCATTCAAAGCCCTAGCTTCACCACCCAAAACCTCATACCTTGAACCCAAATCA
* ** * * *
37283 CCTACCACATGGCAATCAATATCTAAGGTTCTCATG-TTAACCTCCAAACCAACTTTACTGGACT
66 CCGACCACATCACAATCAATATCTAAGGTACTC-GGATTAACCTCCAAACCAACTTCACTGGACT
*
37347 CTTGATGACCACAAAC
130 CTTGACGACCACAAAC
37363 CGCTTCATCA
Statistics
Matches: 119, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
173 2 0.02
174 115 0.97
175 2 0.02
ACGTcount: A:0.31, C:0.34, G:0.10, T:0.25
Consensus pattern (174 bp):
CTCCATTTACCTCATTCAAAGCCCTAGCTTCACCACCCAAAACCTCATACCTTGAACCCAAATCA
CCGACCACATCACAATCAATATCTAAGGTACTCGGATTAACCTCCAAACCAACTTCACTGGACTC
TTGACGACCACAAACTACATCATTAGAACAAGACCGAACCACAC
Found at i:40091 original size:242 final size:242
Alignment explanation
Indices: 39666--40162 Score: 967
Period size: 242 Copynumber: 2.1 Consensus size: 242
39656 ACAATCCCGT
*
39666 ATATTCTAATTTTATATTTTTTATAATTTAGTCCCAAAAATCCAATTTTTTACTATACTACAATT
1 ATATTCTAATTTTATATTTTTTATAATTTAATCCCAAAAATCCAATTTTTTACTATACTACAATT
39731 TAATTCCTCAAAAACAGATTCTCTTATTCTACAGTTCAGTCTTGAACCTCGTTTTGTACAATATT
66 TAATTCCTCAAAAACAGATTCTCTTATTCTACAGTTCAGTCTTGAACCTCGTTTTGTACAATATT
39796 GTTCAAAACAATCCCTTTTCTAAAATTTTAAAATTTTATAATTTAGTCATTATAACTAAAATCTT
131 GTTCAAAACAATCCCTTTTCTAAAATTTTAAAATTTTATAATTTAGTCATTATAACTAAAATCTT
39861 CAAAATTTCTAAATATAAGTCCTTGATTTTTGAACAGTTAAACTTTC
196 CAAAATTTCTAAATATAAGTCCTTGATTTTTGAACAGTTAAACTTTC
39908 ATATTCTAATTTTATATTTTTTATAATTTAATCCCAAAAATCCAATTTTTTACTATACTACAATT
1 ATATTCTAATTTTATATTTTTTATAATTTAATCCCAAAAATCCAATTTTTTACTATACTACAATT
39973 TAATTCCTCAAAAACAGATTCTCTTATTCTACAGTTCAGTCTTGAACCTCGTTTTGTACAATATT
66 TAATTCCTCAAAAACAGATTCTCTTATTCTACAGTTCAGTCTTGAACCTCGTTTTGTACAATATT
40038 GTTCAAAACAATCCCTTTTCTAAAATTTTAAAATTTTATAATTTAGTCATTATAACTAAAATCTT
131 GTTCAAAACAATCCCTTTTCTAAAATTTTAAAATTTTATAATTTAGTCATTATAACTAAAATCTT
**
40103 CAATTTTTCTAAATATAAGTCCTTGATTTTTGAACAGTTAAACTTTC
196 CAAAATTTCTAAATATAAGTCCTTGATTTTTGAACAGTTAAACTTTC
40150 ATATTCTAATTTT
1 ATATTCTAATTTT
40163 CAAAATTGTA
Statistics
Matches: 252, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
242 252 1.00
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (242 bp):
ATATTCTAATTTTATATTTTTTATAATTTAATCCCAAAAATCCAATTTTTTACTATACTACAATT
TAATTCCTCAAAAACAGATTCTCTTATTCTACAGTTCAGTCTTGAACCTCGTTTTGTACAATATT
GTTCAAAACAATCCCTTTTCTAAAATTTTAAAATTTTATAATTTAGTCATTATAACTAAAATCTT
CAAAATTTCTAAATATAAGTCCTTGATTTTTGAACAGTTAAACTTTC
Found at i:43018 original size:82 final size:81
Alignment explanation
Indices: 42810--43018 Score: 210
Period size: 82 Copynumber: 2.6 Consensus size: 81
42800 GACAGGAGCC
*
42810 TTAATCTCT-TAAAAT-AAAATATTTTTATTTAACCCTTTAAAATTTTTAAAATTTTAAAATAAT
1 TTAAACTCTCTAAAATGAAAA-ATTTTTATTTAACCCTTTAAAATTTTTAAAATTTTAAAATAAT
* *
42873 AAAAATAAAATTATACT
65 AAAAATAAAATTACAAT
* * ** ** * * *
42890 TTAAAC-CGCTAAATTGAAATTTTTTCTATTTAGACATTTTATAATTTTTATAATTTTAAATTAA
1 TTAAACTCTCTAAAATGAAAAATTTT-TATTTA-ACCCTTTAAAATTTTTAAAATTTTAAAATAA
*
42954 TAAAATTAAAATTACAAT
64 TAAAAATAAAATTACAAT
* *
42972 TT-ATCTCTCTAAAAATGATAAAATTTTGATTTAACCCTTTAAAATTT
1 TTAAACTCTCT-AAAATGA-AAAATTTTTATTTAACCCTTTAAAATTT
43019 ACATTTTTAT
Statistics
Matches: 100, Mismatches: 22, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
79 1 0.01
80 14 0.14
81 11 0.11
82 57 0.57
83 11 0.11
84 6 0.06
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (81 bp):
TTAAACTCTCTAAAATGAAAAATTTTTATTTAACCCTTTAAAATTTTTAAAATTTTAAAATAATA
AAAATAAAATTACAAT
Found at i:47255 original size:23 final size:23
Alignment explanation
Indices: 47229--47285 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
47219 TTCATTTAAC
*
47229 TTAATCAAACATGTCCACGAACA
1 TTAAACAAACATGTCCACGAACA
* * *
47252 TTAAACGAACATGTTCTCGAACA
1 TTAAACAAACATGTCCACGAACA
*
47275 TTAAACGAACA
1 TTAAACAAACA
47286 CGTTCATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.23
Consensus pattern (23 bp):
TTAAACAAACATGTCCACGAACA
Found at i:47290 original size:23 final size:23
Alignment explanation
Indices: 47246--47290 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
47236 AACATGTCCA
*
47246 CGAACATTAAACGAACATGTTCT
1 CGAACATTAAACGAACACGTTCT
47269 CGAACATTAAACGAACACGTTC
1 CGAACATTAAACGAACACGTTC
47291 ATGATCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.22
Consensus pattern (23 bp):
CGAACATTAAACGAACACGTTCT
Found at i:49047 original size:16 final size:17
Alignment explanation
Indices: 49014--49048 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
49004 AATATATTTT
*
49014 TTAAAATTTTATAAAAA
1 TTAAAATTTGATAAAAA
49031 TTAAAATTTGA-AAAAA
1 TTAAAATTTGATAAAAA
49047 TT
1 TT
49049 TCTAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
TTAAAATTTGATAAAAA
Found at i:52776 original size:102 final size:102
Alignment explanation
Indices: 52590--52779 Score: 310
Period size: 102 Copynumber: 1.9 Consensus size: 102
52580 TTACCGCATT
* *
52590 GAGGGCACCTTCGAGCTCTCCCCATAAGCTCTTCCTCAAGCATTACAAGGGACACTATTACACTC
1 GAGGGCACCTTCGAACTCTCCCCATAAGCTCTTCCTCAAGCATTACAAGGGACACTACTACACTC
* *
52655 GCCTTTAGCGCGTCTAAACGACCTCAAGGGCTTCGTG
66 GCCTTTAGCACGTCCAAACGACCTCAAGGGCTTCGTG
* *
52692 GAGGGCCCCTTCGAACTCTCCCCATAAGCTCTTCCTCAAGCATTACACA-GGACACTACTCCACT
1 GAGGGCACCTTCGAACTCTCCCCATAAGCTCTTCCTCAAGCATTACA-AGGGACACTACTACACT
52756 CGCCTTTAGCACGTCCAAACGACC
65 CGCCTTTAGCACGTCCAAACGACC
52780 CTTGATGTCC
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
102 80 0.99
103 1 0.01
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (102 bp):
GAGGGCACCTTCGAACTCTCCCCATAAGCTCTTCCTCAAGCATTACAAGGGACACTACTACACTC
GCCTTTAGCACGTCCAAACGACCTCAAGGGCTTCGTG
Found at i:56101 original size:26 final size:28
Alignment explanation
Indices: 56072--56141 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 28
56062 AAAAGAATGG
*
56072 AAAATAAAATAAAAAGAAAA-G-TCAAA
1 AAAATAAAATAAAAACAAAATGTTCAAA
56098 AAAATAAAATAAAAACAAAATTGTTCAAA
1 AAAATAAAATAAAAACAAAA-TGTTCAAA
56127 ACAAA-AAAATAAAAA
1 A-AAATAAAATAAAAA
56142 TCAATTATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 19 0.49
28 1 0.03
29 16 0.41
30 3 0.08
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (28 bp):
AAAATAAAATAAAAACAAAATGTTCAAA
Found at i:57131 original size:117 final size:117
Alignment explanation
Indices: 56921--57154 Score: 450
Period size: 117 Copynumber: 2.0 Consensus size: 117
56911 CTGAATTTGA
56921 ATGGATGTTCTTGACAAACTAGCTTCAAGTTCATTCAGCTCATCCATGTCAAGCTCATCATCAGC
1 ATGGATGTTCTTGACAAACTAGCTTCAAGTTCATTCAGCTCATCCATGTCAAGCTCATCATCAGC
56986 ATCATCATCATCAAGAAGGATATCTTCAGAATCAGCAGCTGCACTAGCTGTG
66 ATCATCATCATCAAGAAGGATATCTTCAGAATCAGCAGCTGCACTAGCTGTG
*
57038 ATGGATGTTCTTGACAAACTAGCTTCAAGTTCATTCAGCTCATCCATGTCAAGCTCATCATCATC
1 ATGGATGTTCTTGACAAACTAGCTTCAAGTTCATTCAGCTCATCCATGTCAAGCTCATCATCAGC
*
57103 ATCATCATCATCAAGAAGGATATTTTCAGAATCAGCAGCTGCACTAGCTGTG
66 ATCATCATCATCAAGAAGGATATCTTCAGAATCAGCAGCTGCACTAGCTGTG
57155 CCACTAGGCC
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 115 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (117 bp):
ATGGATGTTCTTGACAAACTAGCTTCAAGTTCATTCAGCTCATCCATGTCAAGCTCATCATCAGC
ATCATCATCATCAAGAAGGATATCTTCAGAATCAGCAGCTGCACTAGCTGTG
Found at i:62674 original size:17 final size:19
Alignment explanation
Indices: 62644--62680 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
62634 TTTTTTAGAA
62644 TTTAAAAAATTAT-AATTT
1 TTTAAAAAATTATAAATTT
62662 TTTAAAAAA-TATAAATTT
1 TTTAAAAAATTATAAATTT
62680 T
1 T
62681 GGAATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAAAAATTATAAATTT
Found at i:62695 original size:19 final size:19
Alignment explanation
Indices: 62671--62707 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
62661 TTTTAAAAAA
62671 TATAAAT-TTTGGAATTTTT
1 TATAAATATTT-GAATTTTT
62690 TATAAATATTTGAATTTT
1 TATAAATATTTGAATTTT
62708 AAAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGAATTTTT
Found at i:64440 original size:41 final size:41
Alignment explanation
Indices: 64331--64558 Score: 240
Period size: 41 Copynumber: 5.5 Consensus size: 41
64321 GGTGTATAAA
* * * ** *
64331 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTATA
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTG-ATT
* *
64373 AATGGAAGACTCATGTCTCAAAATGAGAATGAGATTTTGATT
1 AA-GGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGATT
* ** *
64415 AAGGAAGACTCATATCTCGAGATGAGAATGAGATTACGAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGATT
* * *
64456 AAGGACGACTCATGTCTCGAAATAAGAATGAGATTTTGATT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGATT
* * * *
64497 GAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGGTT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGATT
* *
64538 AAAGGAAGACTTATGACTCGA
1 -AAGGAAGACTCATGTCTCGA
64559 AAGAGCATAA
Statistics
Matches: 153, Mismatches: 31, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
41 101 0.66
42 23 0.15
43 29 0.19
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.26
Consensus pattern (41 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGATT
Found at i:67515 original size:20 final size:21
Alignment explanation
Indices: 67490--67529 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
67480 TGTGAAGTTT
*
67490 ATTGATGATTA-TTTTATATA
1 ATTGATGAATAGTTTTATATA
*
67510 ATTGATTAATAGTTTTATAT
1 ATTGATGAATAGTTTTATAT
67530 TTAAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (21 bp):
ATTGATGAATAGTTTTATATA
Found at i:74194 original size:21 final size:21
Alignment explanation
Indices: 74168--74208 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
74158 TCAAAATGAC
74168 ATAATTTT-ACCTTTTAACTTA
1 ATAATTTTGA-CTTTTAACTTA
74189 ATAATTTTGACTTTTAACTT
1 ATAATTTTGACTTTTAACTT
74209 TAGAGAGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (21 bp):
ATAATTTTGACTTTTAACTTA
Found at i:78656 original size:2 final size:2
Alignment explanation
Indices: 78649--78677 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
78639 AGATCCCACC
78649 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
78678 CATTTTCTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:80154 original size:22 final size:23
Alignment explanation
Indices: 80102--80154 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
80092 GGGGGAGCGA
* *
80102 AATTAAATTGTAATTTTTACGAT
1 AATTAAATTATAATTTTTAAGAT
*
80125 AATAAAATTATAATTTTTAAGA-
1 AATTAAATTATAATTTTTAAGAT
*
80147 GATTAAAT
1 AATTAAAT
80155 AAAAAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (23 bp):
AATTAAATTATAATTTTTAAGAT
Found at i:80665 original size:16 final size:17
Alignment explanation
Indices: 80634--80669 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
80624 CATACTCCCT
*
80634 TTAAATTTATTTTAAAA
1 TTAAATTTAGTTTAAAA
80651 TTAAATTT-GTTTAAAA
1 TTAAATTTAGTTTAAAA
80667 TTA
1 TTA
80670 TCATTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTAGTTTAAAA
Found at i:80705 original size:29 final size:28
Alignment explanation
Indices: 80673--80824 Score: 132
Period size: 29 Copynumber: 5.2 Consensus size: 28
80663 AAAATTATCA
*
80673 TTTTATCCCCGAATTTCCAAAAATCTCAT
1 TTTTA-CCCCGAACTTCCAAAAATCTCAT
*
80702 TTTTGACCCCAAACCTTCCAAAAAT-TACCA-
1 TTTT-ACCCCGAA-CTTCCAAAAATCT--CAT
*
80732 TTTTACCCCTAAACTTCCAAAAATCTCAT
1 TTTTACCCC-GAACTTCCAAAAATCTCAT
**
80761 TTTTGACCCCGAACCTTCTGAAAAT-TACCA-
1 TTTT-ACCCCGAA-CTTCCAAAAATCT--CAT
80791 TTTTATCCCCGAACTTCCAAAAATCTCAT
1 TTTTA-CCCCGAACTTCCAAAAATCTCAT
80820 TTTTA
1 TTTTA
80825 ACCCTTAACC
Statistics
Matches: 102, Mismatches: 7, Indels: 28
0.74 0.05 0.20
Matches are distributed among these distances:
28 4 0.04
29 49 0.48
30 45 0.44
31 4 0.04
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (28 bp):
TTTTACCCCGAACTTCCAAAAATCTCAT
Found at i:80723 original size:30 final size:29
Alignment explanation
Indices: 80687--80824 Score: 126
Period size: 30 Copynumber: 4.7 Consensus size: 29
80677 ATCCCCGAAT
80687 TTCCAAAAATCTCATTTTTGACCCCAAACC
1 TTCCAAAAATCTCATTTTT-ACCCCAAACC
80717 TTCCAAAAAT-TACCA-TTTTACCCCTAAA-C
1 TTCCAAAAATCT--CATTTTTACCCC-AAACC
*
80746 TTCCAAAAATCTCATTTTTGACCCCGAACC
1 TTCCAAAAATCTCATTTTT-ACCCCAAACC
** *
80776 TTCTGAAAAT-TACCA-TTTTATCCCCGAA-C
1 TTCCAAAAATCT--CATTTTTA-CCCCAAACC
80805 TTCCAAAAATCTCATTTTTA
1 TTCCAAAAATCTCATTTTTA
80825 ACCCTTAACC
Statistics
Matches: 91, Mismatches: 5, Indels: 25
0.75 0.04 0.21
Matches are distributed among these distances:
28 4 0.04
29 39 0.43
30 44 0.48
31 4 0.04
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
TTCCAAAAATCTCATTTTTACCCCAAACC
Found at i:80734 original size:59 final size:58
Alignment explanation
Indices: 80663--80863 Score: 285
Period size: 59 Copynumber: 3.4 Consensus size: 58
80653 AAATTTGTTT
* * **
80663 AAAATTATCATTTTATCCCCGAATTTCCAAAAATCTCATTTTTGACCCCAAACCTTCCA
1 AAAATTACCATTTTA-CCCCGAACTTCCAAAAATCTCATTTTTGACCCCAAACCTTCTG
* *
80722 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCTG
1 AAAATTACCATTTTACCCC-GAACTTCCAAAAATCTCATTTTTGACCCCAAACCTTCTG
* **
80781 AAAATTACCATTTTATCCCCGAACTTCCAAAAATCTCATTTTTAACCCTTAACCTTCTG
1 AAAATTACCATTTTA-CCCCGAACTTCCAAAAATCTCATTTTTGACCCCAAACCTTCTG
80840 AAAATTACCATTTTACCTCCGAAC
1 AAAATTACCATTTTACC-CCGAAC
80864 CTTCTAAATA
Statistics
Matches: 129, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
58 6 0.05
59 119 0.92
60 4 0.03
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCGAACTTCCAAAAATCTCATTTTTGACCCCAAACCTTCTG
Found at i:80854 original size:30 final size:30
Alignment explanation
Indices: 80702--80883 Score: 119
Period size: 30 Copynumber: 6.1 Consensus size: 30
80692 AAAATCTCAT
* * **
80702 TTTTGACCCCAAACCTTCCAAAAATTACCA
1 TTTTAACCCCGAACCTTCTGAAAATTACCA
* * * *
80732 TTTT-ACCCCTAAACTTC-CAAAAAT-CTCA
1 TTTTAACCCCGAACCTTCTGAAAATTAC-CA
*
80760 TTTTTGACCCCGAACCTTCTGAAAATTACCA
1 -TTTTAACCCCGAACCTTCTGAAAATTACCA
* * *
80791 TTTTATCCCCGAA-CTTC-CAAAAAT-CTCA
1 TTTTAACCCCGAACCTTCTGAAAATTAC-CA
**
80819 TTTTTAACCCTTAACCTTCTGAAAATTACCA
1 -TTTTAACCCCGAACCTTCTGAAAATTACCA
*
80850 TTTT-ACCTCCGAACCTTCT-AAATACTACCA
1 TTTTAACC-CCGAACCTTCTGAAA-ATTACCA
80880 TTTT
1 TTTT
80884 GCCCTCGTGC
Statistics
Matches: 120, Mismatches: 20, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
27 2 0.02
28 14 0.12
29 35 0.29
30 53 0.44
31 14 0.12
32 2 0.02
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (30 bp):
TTTTAACCCCGAACCTTCTGAAAATTACCA
Found at i:83443 original size:23 final size:24
Alignment explanation
Indices: 83407--83452 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
83397 TATATTTTAG
* *
83407 AATTTTTATATTTTTTTAAATATA
1 AATTTTGATATTTTTATAAATATA
83431 AATTTTGAT-TTTTTATAAATAT
1 AATTTTGATATTTTTATAAATAT
83453 TTTGAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AATTTTGATATTTTTATAAATATA
Found at i:83461 original size:20 final size:20
Alignment explanation
Indices: 83418--83503 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 20
83408 ATTTTTATAT
*
83418 TTTTTTAAATATAAATTTTG-A
1 TTTTTTAAA-AT-TATTTTGAA
83439 TTTTTTATAAA-TATTTTGAA
1 TTTTTTA-AAATTATTTTGAA
* *
83459 -TTTTAAAAATTATTTTAAA
1 TTTTTTAAAATTATTTTGAA
*
83478 TTTTTGAAAATTATTTTGTAA
1 TTTTTTAAAATTATTTTG-AA
83499 TTTTT
1 TTTTT
83504 GTTGAGAGAG
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.05
19 19 0.35
20 16 0.29
21 15 0.27
22 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTTTAAAATTATTTTGAA
Found at i:84094 original size:32 final size:32
Alignment explanation
Indices: 84058--84123 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
84048 ACATAAACCA
*
84058 TAGCCTTACATGTCTTGTACACTTACCATTAT
1 TAGCCTTACATGTCTTATACACTTACCATTAT
*
84090 TAGCCTTACATGTCTTATTCACTTACCATTAT
1 TAGCCTTACATGTCTTATACACTTACCATTAT
84122 TA
1 TA
84124 ACCCTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (32 bp):
TAGCCTTACATGTCTTATACACTTACCATTAT
Found at i:88742 original size:28 final size:28
Alignment explanation
Indices: 88711--88765 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
88701 AGAAATTATT
* * *
88711 AATAATATTATTTAAATTATAATATATG
1 AATAATAATATTCAAATCATAATATATG
* *
88739 AATATTAATATTCAAATCATGATATAT
1 AATAATAATATTCAAATCATAATATAT
88766 TTTATATTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (28 bp):
AATAATAATATTCAAATCATAATATATG
Found at i:105119 original size:22 final size:22
Alignment explanation
Indices: 105091--105133 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
105081 ACGAATGTAT
105091 TAATTAAAATCTTTG-TTTTGGA
1 TAATTAAAATC-TTGATTTTGGA
105113 TAATTAAAATCTTGATTTTGG
1 TAATTAAAATCTTGATTTTGG
105134 TTACTGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (22 bp):
TAATTAAAATCTTGATTTTGGA
Found at i:110942 original size:35 final size:34
Alignment explanation
Indices: 110873--110942 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 34
110863 CAAACCAACA
110873 TTTTAGCAACTTTTACTCTTTATCTTTCTCCTTT
1 TTTTAGCAACTTTTACTCTTTATCTTTCTCCTTT
*
110907 TTTTAGCAAACTATTTAC-CTTT-TTTTCTCTCCTTT
1 TTTTAGC-AACT-TTTACTCTTTATCTT-TCTCCTTT
110942 T
1 T
110943 AGAGAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
34 10 0.31
35 17 0.53
36 5 0.16
ACGTcount: A:0.16, C:0.23, G:0.03, T:0.59
Consensus pattern (34 bp):
TTTTAGCAACTTTTACTCTTTATCTTTCTCCTTT
Found at i:117301 original size:27 final size:27
Alignment explanation
Indices: 117264--117316 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
117254 TTAGTATAAT
117264 TTTTGGTTTTATTATTATAAATTAAAA
1 TTTTGGTTTTATTATTATAAATTAAAA
117291 TTTTGGTTTTATTATTATAAATTAAA
1 TTTTGGTTTTATTATTATAAATTAAA
117317 TTTACTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.57
Consensus pattern (27 bp):
TTTTGGTTTTATTATTATAAATTAAAA
Found at i:117535 original size:23 final size:23
Alignment explanation
Indices: 117509--117554 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
117499 ATATATTCGT
117509 ATAACATA-AATAAGATAAAAATA
1 ATAA-ATATAATAAGATAAAAATA
* *
117532 ATAATTATAATACGATAAAAATA
1 ATAAATATAATAAGATAAAAATA
117555 TAATAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.26
Consensus pattern (23 bp):
ATAAATATAATAAGATAAAAATA
Found at i:120665 original size:20 final size:20
Alignment explanation
Indices: 120640--120678 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
120630 TTGAATTTAA
*
120640 CTATCAATTTTTTTGAAAGG
1 CTATCAATTTTTTAGAAAGG
120660 CTATCAATTTTTTAGAAAG
1 CTATCAATTTTTTAGAAAG
120679 AGCTGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (20 bp):
CTATCAATTTTTTAGAAAGG
Found at i:120805 original size:18 final size:20
Alignment explanation
Indices: 120784--120820 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
120774 ATATTTTTTT
120784 ATTTTAAA-TATTT-TTAAA
1 ATTTTAAATTATTTATTAAA
120802 ATTTTAAATTATTTATTAA
1 ATTTTAAATTATTTATTAA
120821 TATAACATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTAAATTATTTATTAAA
Found at i:123300 original size:24 final size:23
Alignment explanation
Indices: 123273--123342 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
123263 TCATTAACAT
123273 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* *
123297 TGTTCATGAACATGTTCATTTAA
1 TGTTCGTGAACATGTTCAATTAA
*
123320 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCAATTAA
123343 GTCAAATGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 21 0.51
24 20 0.49
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:123337 original size:12 final size:12
Alignment explanation
Indices: 123262--123336 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
123252 TTGTTTATTA
*
123262 TTCATTAACATTG
1 TTCATGAACA-TG
*
123275 TTCGTGAACATG
1 TTCATGAACATG
* *
123287 TTCAAT-TATATG
1 TTC-ATGAACATG
123299 TTCATGAACATG
1 TTCATGAACATG
**
123311 TTCATTTA-ATG
1 TTCATGAACATG
*
123322 TTCGTGAACATG
1 TTCATGAACATG
123334 TTC
1 TTC
123337 GATTAAGTCA
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
11 10 0.21
12 28 0.60
13 9 0.19
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (12 bp):
TTCATGAACATG
Found at i:127884 original size:43 final size:43
Alignment explanation
Indices: 127836--127919 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
127826 TGCATAACAA
* * *
127836 GGCTTATTGTTTACATCTTATAAAGATAATGCCTAAAATATGT
1 GGCTTATTCTTAACATCTCATAAAGATAATGCCTAAAATATGT
* *
127879 GGCTTATTCTTAACATCTCATAATGATAGTGCCTAAAATAT
1 GGCTTATTCTTAACATCTCATAAAGATAATGCCTAAAATAT
127920 TTACCAAGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (43 bp):
GGCTTATTCTTAACATCTCATAAAGATAATGCCTAAAATATGT
Found at i:130856 original size:54 final size:54
Alignment explanation
Indices: 130792--130899 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
130782 AATTATCGTG
*
130792 TGTTTCATAATGATACTTATGATTTTATAAAATGTCCACTATGATATATGTATC
1 TGTTTCATAATGATACTTATGATTTTATAAAATGTCCAATATGATATATGTATC
130846 TGTTTCATAATGATACTTATGATTTTATAAAATGTCCAATATGATATATGTATC
1 TGTTTCATAATGATACTTATGATTTTATAAAATGTCCAATATGATATATGTATC
130900 CACACCGGTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (54 bp):
TGTTTCATAATGATACTTATGATTTTATAAAATGTCCAATATGATATATGTATC
Found at i:139055 original size:60 final size:58
Alignment explanation
Indices: 138991--139113 Score: 140
Period size: 60 Copynumber: 2.1 Consensus size: 58
138981 CTAATACCTA
* * * *
138991 AACTTGAC-ACTTTTTCTTAAGTTGGTACTTTATCTTTTTTAAGGTCCAATTTGGTACTTG
1 AACTTGACTA-TTTTTCCTAAGTTGGTACATGATATTTTTT--GGTCCAATTTGGTACTTG
* * * *
139051 AACTTGACTATTTTTCCTAATTTGGTGCATGATATTTTTTTGTTCAATTTGGTACTTG
1 AACTTGACTATTTTTCCTAAGTTGGTACATGATATTTTTTGGTCCAATTTGGTACTTG
139109 AACTT
1 AACTT
139114 TTCAAACATT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
58 21 0.39
60 32 0.59
61 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.50
Consensus pattern (58 bp):
AACTTGACTATTTTTCCTAAGTTGGTACATGATATTTTTTGGTCCAATTTGGTACTTG
Found at i:139115 original size:27 final size:26
Alignment explanation
Indices: 139035--139115 Score: 65
Period size: 27 Copynumber: 2.9 Consensus size: 26
139025 TTTTTTAAGG
139035 TCCAATTTGGTACTTGAACTTGACTATTTT
1 TCCAATTTGGTACTTGAACTT---T-TTTT
* *
139065 TCCTAATTTGGTGCATGATA-TTTTTTT
1 TCC-AATTTGGTACTTGA-ACTTTTTTT
*
139092 GTTCAATTTGGTACTTGAACTTTT
1 -TCCAATTTGGTACTTGAACTTTT
139116 CAAACATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
26 1 0.02
27 20 0.48
28 3 0.07
30 3 0.07
31 14 0.33
32 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.51
Consensus pattern (26 bp):
TCCAATTTGGTACTTGAACTTTTTTT
Found at i:140209 original size:16 final size:16
Alignment explanation
Indices: 140178--140212 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
140168 AATATTTAGT
140178 TTTATTGAATATAAAA
1 TTTATTGAATATAAAA
*
140194 TTTATATGAATAAAAAA
1 TTTAT-TGAATATAAAA
140211 TT
1 TT
140213 GAATTGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (16 bp):
TTTATTGAATATAAAA
Found at i:140569 original size:18 final size:17
Alignment explanation
Indices: 140528--140562 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
140518 TTTATAATCC
*
140528 CATAAAAAATATAAAAT
1 CATAAAAAACATAAAAT
140545 CATAAAAAACATTAAAAT
1 CATAAAAAACA-TAAAAT
140563 ATTAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (17 bp):
CATAAAAAACATAAAAT
Found at i:140778 original size:21 final size:21
Alignment explanation
Indices: 140752--140791 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
140742 CAGTAATTAT
140752 AAAACTTATACAAA-ATTCATA
1 AAAACTTATA-AAAGATTCATA
140773 AAAACTTATAAAAGATTCA
1 AAAACTTATAAAAGATTCA
140792 AAACAAGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.57, C:0.12, G:0.03, T:0.28
Consensus pattern (21 bp):
AAAACTTATAAAAGATTCATA
Found at i:140868 original size:8 final size:9
Alignment explanation
Indices: 140590--140874 Score: 72
Period size: 10 Copynumber: 30.2 Consensus size: 9
140580 CTTATGAAAA
*
140590 ATAAAATTT
1 ATAAAAATT
*
140599 ACAAAAATT
1 ATAAAAATT
140608 CATAAAAACTT
1 -ATAAAAA-TT
*
140619 ATAAAATTT
1 ATAAAAATT
*
140628 ATAATAAATA
1 ATAA-AAATT
*
140638 ATAAAAAAT
1 ATAAAAATT
140647 A-AAAACATAT
1 ATAAAA-AT-T
*
140657 TTAAAACATT
1 ATAAAA-ATT
* *
140667 -TACAACTT
1 ATAAAAATT
140675 -TCAATAAATT
1 AT-AA-AAATT
140685 -TACAAAA--
1 ATA-AAAATT
*
140692 A-AAAAATC
1 ATAAAAATT
*
140700 ATAAAAGCTT
1 ATAAAA-ATT
140710 ATGGAAAAATCT
1 AT--AAAAAT-T
*
140722 AGAAAAATT
1 ATAAAAATT
* *
140731 GTAAAAATA
1 ATAAAAATT
**
140740 ATCAGTAATT
1 AT-AAAAATT
*
140750 ATAAAACTT
1 ATAAAAATT
140759 ATACAAAATT
1 ATA-AAAATT
140769 CATAAAAACTT
1 -ATAAAAA-TT
140780 ATAAAAGATT
1 ATAAAA-ATT
140790 CA-AAACAAGTT
1 -ATAAA-AA-TT
*
140801 CTAATAAATT
1 ATAA-AAATT
*
140811 ATAAAAATA
1 ATAAAAATT
***
140820 AT-ATTTTT
1 ATAAAAATT
140828 A-AAAAATT
1 ATAAAAATT
140836 AT-AAAA-T
1 ATAAAAATT
140843 ATTAAAAATAT
1 A-TAAAAAT-T
140854 ATAAAAATT
1 ATAAAAATT
140863 ATAAAAAATT
1 AT-AAAAATT
140873 AT
1 AT
140875 TGATTCCTCA
Statistics
Matches: 203, Mismatches: 39, Indels: 67
0.66 0.13 0.22
Matches are distributed among these distances:
6 4 0.02
7 3 0.01
8 20 0.10
9 59 0.29
10 84 0.41
11 26 0.13
12 7 0.03
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Done.