Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005579.1 Kokia drynarioides strain JFW-HI SEQ_119698, 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: 185887
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 47 characters in sequence are not A, C, G, or T
Found at i:5057 original size:24 final size:23
Alignment explanation
Indices: 5016--5061 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
5006 GGTGAGGAAG
5016 AAATTTCAAAAAAAAAAAAAGAC
1 AAATTTCAAAAAAAAAAAAAGAC
5039 AAATTT-AAAAAAAGGAAAAAAGA
1 AAATTTCAAAAAAA--AAAAAAGA
5062 GAAAAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 6 0.29
24 8 0.38
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATTTCAAAAAAAAAAAAAGAC
Found at i:5074 original size:21 final size:20
Alignment explanation
Indices: 5048--5099 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
5038 CAAATTTAAA
5048 AAAAGGAAAAA-AGAGAAAAAG
1 AAAAGGAAAAATA-AG-AAAAG
5069 AAAAGGAAAAATAAGAAAAG
1 AAAAGGAAAAATAAGAAAAG
*
5089 AAAAAGAAAAA
1 AAAAGGAAAAA
5100 GGGGAGGTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 15 0.52
21 13 0.45
22 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (20 bp):
AAAAGGAAAAATAAGAAAAG
Found at i:5084 original size:15 final size:14
Alignment explanation
Indices: 5056--5093 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
5046 AAAAAAGGAA
*
5056 AAAAGAGAAA-AAG
1 AAAAGAAAAATAAG
5069 AAAAGGAAAAATAAG
1 AAAA-GAAAAATAAG
5084 AAAAGAAAAA
1 AAAAGAAAAA
5094 GAAAAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 11 0.50
15 7 0.32
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAATAAG
Found at i:6091 original size:50 final size:50
Alignment explanation
Indices: 6032--6196 Score: 249
Period size: 50 Copynumber: 3.3 Consensus size: 50
6022 TACAGTTGTG
*
6032 GAGGTGCAGATTGAAACTGTAATGGCAAATCTCATACACCTAAAGCTGTA
1 GAGGTGCAGATTGAAACTGCAATGGCAAATCTCATACACCTAAAGCTGTA
*
6082 GAGGTGCAGATTGAAACCGCAATGGCAAATCTCATACACCTAAAGCTGTA
1 GAGGTGCAGATTGAAACTGCAATGGCAAATCTCATACACCTAAAGCTGTA
* * * * *
6132 GAGGGGCATAATGAAGCTGCAATGGCAAATCTCATTCACCTAAAGCTGTA
1 GAGGTGCAGATTGAAACTGCAATGGCAAATCTCATACACCTAAAGCTGTA
* *
6182 GAGGAGAAGATTGAA
1 GAGGTGCAGATTGAA
6197 GTTACAAGGA
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 103 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.21
Consensus pattern (50 bp):
GAGGTGCAGATTGAAACTGCAATGGCAAATCTCATACACCTAAAGCTGTA
Found at i:6317 original size:47 final size:47
Alignment explanation
Indices: 6259--6401 Score: 198
Period size: 47 Copynumber: 3.0 Consensus size: 47
6249 CCTCCAATCT
*
6259 TTTACCCTAACCAGAAAGCAAGATTGAAGACCATCCGATCTTTTACC
1 TTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCGATCTTTTACC
** * *
6306 TTTACTTTAACCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACC
1 TTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCGATCTTTTACC
* * *
6353 TTTACCCTAACTA-AAGGGCAACATTGAAAACCATCCGATCTTTTACC
1 TTTACCCTAACCAGAA-GGCAAGATTGAAGACCATCCGATCTTTTACC
6400 TT
1 TT
6402 GATCATAGGG
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
46 1 0.01
47 82 0.99
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (47 bp):
TTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCGATCTTTTACC
Found at i:6486 original size:80 final size:81
Alignment explanation
Indices: 6251--6877 Score: 499
Period size: 80 Copynumber: 7.7 Consensus size: 81
6241 AGTTACAACC
* * ** *
6251 TCCAATCTTTTACCCTAACCAGAAAGCAAGATTGAAGACCATCCGATCTTTTACCTTTACTTTAA
1 TCCAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCAATCTTTTACC----C-CGAT
* * *
6316 CCAGAGGGCAAGATTGAAGATCA
61 CTATAGGGC-AGATTGAAGA-AA
* * * * * **
6339 TCCGATCTTTTACCTTTACCCTAACTA-AAGGGCAACATTGAAAACCATCCGATCTTTTACCTTG
1 TCCAATC---T---TTTACCCTAACCAGAA-GGCAAGATTGAAGACCATCCAATCTTTTACCCCG
6403 ATC-ATAGGGCAGATTGAAGAAA
59 ATCTATAGGGCAGATTGAAGAAA
* * * * *
6425 TCCAATCTTTTACCCTAACCAGAAGGTAACATTTAAGACCATCCGATCTTTTACCCCGATC-ATG
1 TCCAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCTATA
*
6489 GGGTAGATTGAAGAAA
66 GGGCAGATTGAAGAAA
* * * * *
6505 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCTAATCTTTTACTCTGATC-ATG
1 TCCAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCTATA
6569 GGGCAGATTGAAGAAA
66 GGGCAGATTGAAGAAA
* * * * * * *
6585 TCCGATCTTTTATCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTA-CCCTAACTAAA
1 TCCAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCTATA
6649 GGGCAAGATTGAAGAAA
66 GGGC-AGATTGAAGAAA
** * * * * *
6666 TCCAATCTTTTACCCCGATCATG-AGGC-AGATTGAAGA-AATCCAATCTTTTA-CCCTAACTAA
1 TCCAATCTTTTACCCTAACCA-GAAGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCTAT
*
6727 AGGGCAAGATTGAAGACCA
65 AGGGC-AGATTGAAGA-AA
** * * ** * *
6746 TCCAATCTTTTACCCCGATCA-TAGGGTAGATTGAAGA-AATCCAATCTTTTACCCCGA-CTATG
1 TCCAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCTATA
* *
6808 GGGTAGATTGAAGCAA
66 GGGCAGATTGAAGAAA
* * * *
6824 TTCAATCTTTTACCCTAACCAGAGGGC-AGATTGAAG-CAATCTAATCTTTTACCC
1 TCCAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCAATCTTTTACCC
6878 TAACCAGAAG
Statistics
Matches: 460, Mismatches: 62, Indels: 44
0.81 0.11 0.08
Matches are distributed among these distances:
78 43 0.09
79 55 0.12
80 248 0.54
81 37 0.08
82 1 0.00
83 1 0.00
86 7 0.02
87 10 0.02
88 12 0.03
89 3 0.01
91 1 0.00
93 2 0.00
94 40 0.09
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (81 bp):
TCCAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCTATA
GGGCAGATTGAAGAAA
Found at i:6519 original size:39 final size:39
Alignment explanation
Indices: 6385--6956 Score: 408
Period size: 39 Copynumber: 14.4 Consensus size: 39
6375 ATTGAAAACC
* * * *
6385 ATCCGATCTTTTACCTTGATCATAGGGCAGATTGAAGAA
1 ATCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGAA
* ** * * *
6424 ATCCAATCTTTTACCCTAACCA-GAAGGTAACATTTAAGACC
1 ATCCAATCTTTTACCCTAATCATG--GGGCAGATTGAAGA-A
* ** *
6465 ATCCGATCTTTTACCCCGATCATGGGGTAGATTGAAGAA
1 ATCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGAA
* *
6504 ATCCAATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGACC
1 ATCCAATCTTTTACCCTAATCATG-GGGC-AGATTGAAGA-A
* * *
6545 ATCTAATCTTTTACTCTGATCATGGGGCAGATTGAAGAA
1 ATCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGAA
* * * *
6584 ATCCGATCTTTTATCCTAACCA-GAGGGCAAGATTGAAGACC
1 ATCCAATCTTTTACCCTAATCATG-GGGC-AGATTGAAGA-A
* **
6625 ATCCGATCTTTTACCCTAA-CTAAAGGGCAAGATTGAAGAA
1 ATCCAATCTTTTACCCTAATC-ATGGGGC-AGATTGAAGAA
** *
6665 ATCCAATCTTTTACCCCGATCATGAGGCAGATTGAAGAA
1 ATCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGAA
** *
6704 ATCCAATCTTTTACCCTAA-CTAAAGGGCAAGATTGAAGACC
1 ATCCAATCTTTTACCCTAATC-ATGGGGC-AGATTGAAGA-A
** * *
6745 ATCCAATCTTTTACCCCGATCATAGGGTAGATTGAAGAA
1 ATCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGAA
** * *
6784 ATCCAATCTTTTACCCCGA-CTATGGGGTAGATTGAAGCA
1 ATCCAATCTTTTACCCTAATC-ATGGGGCAGATTGAAGAA
* * *
6823 ATTCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGCA
1 ATCCAATCTTTTACCCTAATCATG-GGGCAGATTGAAGAA
* * * *
6862 ATCTAATCTTTTACCCTAACCA-GAAGGCAGATTGAAGACC
1 ATCCAATCTTTTACCCTAATCATG-GGGCAGATTGAAGA-A
* ** * * *
6902 AT-CAGATCTCTTACCCCGACCATGGAGTAGATTGAA-ATA
1 ATCCA-ATCTTTTACCCTAATCATGGGGCAGATTGAAGA-A
*
6941 ATTCAATCTTTTACCC
1 ATCCAATCTTTTACCC
6957 CTAAAACTAT
Statistics
Matches: 430, Mismatches: 78, Indels: 50
0.77 0.14 0.09
Matches are distributed among these distances:
38 5 0.01
39 205 0.48
40 119 0.28
41 98 0.23
42 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (39 bp):
ATCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGAA
Found at i:6625 original size:160 final size:157
Alignment explanation
Indices: 6353--6899 Score: 566
Period size: 160 Copynumber: 3.4 Consensus size: 157
6343 ATCTTTTACC
* * * * * *
6353 TTTACCCTAACTAAAGGGCAACATTGAAAACCATCCGATCTTTTACCTTGATCATAGGGCAGATT
1 TTTACCCTAACCAGAGGGC-AGATTGAAGACAATCCAATCTTTTACC-TGATCATAGGGCAGATT
* * *
6418 GAAGAAATCCAATCTTTTACCCTAACCAGAAGGTAACATTTAAGACCATCCGATCTTTTACCCCG
64 GAAGAAATCCAATCTTTTACCCTAACCAG-AGGGAAGATTGAAGACCATCCGATCTTTTACCCCG
6483 ATCATGGGGTAGATTGAAGAAATCCAATCT
128 ATCATGGGGTAGATTGAAGAAATCCAATCT
* * *
6513 TTTACCCTAACCAGAGGGCAAGATTGAAGACCATCTAATCTTTTACTCTGATCATGGGGCAGATT
1 TTTACCCTAACCAGAGGGC-AGATTGAAGACAATCCAATCTTTTAC-CTGATCATAGGGCAGATT
* * **
6578 GAAGAAATCCGATCTTTTATCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCTA
64 GAAGAAATCCAATCTTTTACCCTAACCAGAGGG-AAGATTGAAGACCATCCGATCTTTTACCCCG
* * **
6643 ACTAAAGGGCAAGATTGAAGAAATCCAATCT
128 A-TCATGGGGTAGATTGAAGAAATCCAATCT
** * * *
6674 TTTACCCCGATCATGA-GGCAGATTGAAGA-AATCCAATCTTTTACCCT-AACTAAAGGGCAAGA
1 TTTACCCTAACCA-GAGGGCAGATTGAAGACAATCCAATCTTTTA-CCTGATC-ATAGGGC-AGA
* ** * * * * *
6736 TTGAAGACCATCCAATCTTTTACCCCGATCATAGGGTAGATTGAAGA-AATCCAATCTTTTACCC
62 TTGAAGA-AATCCAATCTTTTACCCTAACCAGAGGGAAGATTGAAGACCATCCGATCTTTTACCC
* *
6800 CGA-CTATGGGGTAGATTGAAGCAATTCAATCT
126 CGATC-ATGGGGTAGATTGAAGAAATCCAATCT
* * * * *
6832 TTTACCCTAACCAGAGGGCAGATTGAAG-CAATCTAATCTTTTACCCTAACCAGAAGGCAGATTG
1 TTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTA-CCTGATCATAGGGCAGATTG
6896 AAGA
65 AAGA
6900 CCATCAGATC
Statistics
Matches: 324, Mismatches: 51, Indels: 27
0.81 0.13 0.07
Matches are distributed among these distances:
157 12 0.04
158 68 0.21
159 40 0.12
160 142 0.44
161 60 0.19
162 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (157 bp):
TTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCTGATCATAGGGCAGATTGA
AGAAATCCAATCTTTTACCCTAACCAGAGGGAAGATTGAAGACCATCCGATCTTTTACCCCGATC
ATGGGGTAGATTGAAGAAATCCAATCT
Found at i:6699 original size:200 final size:198
Alignment explanation
Indices: 6385--6899 Score: 637
Period size: 200 Copynumber: 2.6 Consensus size: 198
6375 ATTGAAAACC
* *
6385 ATCCGATCTTTTACCTTGATCATAGGGCAGATTGAAGA-AATCCAATCTTTTACCCTAACCAGAA
1 ATCCGATCTTTTACC-TGACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCA-AA
* * * * * * *
6449 -GGTAACATTTAAGACCATCCGATCTTTTACCCCGATCATGGGGTAGATTGAAGAAATCCAATCT
64 GGGCAAGATTGAAGA-AATCCAATCTTTTACCCCGATCATGAGGCAGATTGAAGAAATCCAATCT
* * * * *
6513 TTTACCCTAACCAGAGGGCAAGATTGAAGACCATCTAATCTTTTACTCTGATCATGGGGCAGATT
128 TTTACCCTAACCAAAGGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCATAGGGCAGATT
6578 GAAGAA
193 GAAGAA
* * * *
6584 ATCCGATCTTTTATCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCTAACTAAA
1 ATCCGATCTTTTA-CCTGACCAGAGGGC-AGATTGAAGACAATCCAATCTTTTACCCTAACCAAA
6649 GGGCAAGATTGAAGAAATCCAATCTTTTACCCCGATCATGAGGCAGATTGAAGAAATCCAATCTT
64 GGGCAAGATTGAAGAAATCCAATCTTTTACCCCGATCATGAGGCAGATTGAAGAAATCCAATCTT
* *
6714 TTACCCTAACTAAAGGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCATAGGGTAGATTG
129 TTACCCTAACCAAAGGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCATAGGGCAGATTG
6779 AAGAA
194 AAGAA
* * * * * *
6784 ATCCAATCTTTTACCCCGACTATG-GGGTAGATTGAAG-CAATTCAATCTTTTACCCTAACCAGA
1 ATCCGATCTTTTA-CCTGACCA-GAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCAAA
* * ** *
6847 GGGC-AGATTGAAGCAATCTAATCTTTTACCCTAACCA-GAAGGCAGATTGAAGA
64 GGGCAAGATTGAAGAAATCCAATCTTTTACCCCGATCATG-AGGCAGATTGAAGA
6900 CCATCAGATC
Statistics
Matches: 274, Mismatches: 36, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
196 1 0.00
197 42 0.15
198 25 0.09
199 31 0.11
200 143 0.52
201 32 0.12
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (198 bp):
ATCCGATCTTTTACCTGACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCAAAGG
GCAAGATTGAAGAAATCCAATCTTTTACCCCGATCATGAGGCAGATTGAAGAAATCCAATCTTTT
ACCCTAACCAAAGGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCATAGGGCAGATTGAA
GAA
Found at i:22678 original size:6 final size:6
Alignment explanation
Indices: 22667--22699 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
22657 TAATATCTAT
22667 GAAAAA G-AAAA -AAAAA GAAAAA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
22700 GTCTTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 8 0.32
6 17 0.68
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:22688 original size:16 final size:17
Alignment explanation
Indices: 22667--22700 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
22657 TAATATCTAT
22667 GAAAAAGAAAAA-AAAA
1 GAAAAAGAAAAAGAAAA
22683 GAAAAAGAAAAAGAAAA
1 GAAAAAGAAAAAGAAAA
22700 G
1 G
22701 TCTTTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAAAAGAAAA
Found at i:28770 original size:20 final size:19
Alignment explanation
Indices: 28729--28770 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
28719 TTGAGAAAAT
*
28729 AATAATATATATTTTTATA
1 AATAATATATATTTTGATA
28748 AATAACTATGATATTTTGA-A
1 AATAA-TAT-ATATTTTGATA
28768 AAT
1 AAT
28771 GTTTTTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
21 8 0.40
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (19 bp):
AATAATATATATTTTGATA
Found at i:29439 original size:25 final size:25
Alignment explanation
Indices: 29405--29455 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
29395 ATTATCCTCT
29405 TATTTATGGTTAATATCAATATTAA
1 TATTTATGGTTAATATCAATATTAA
29430 TATTTATGGTTAATATCAATATTAA
1 TATTTATGGTTAATATCAATATTAA
29455 T
1 T
29456 TGAACTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (25 bp):
TATTTATGGTTAATATCAATATTAA
Found at i:43485 original size:66 final size:66
Alignment explanation
Indices: 43408--43540 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
43398 TCTAATATGT
*
43408 TTACTAAAATATTTTTTTCTATTTTTTTAATTGTTTTAAGATTGTATAACATTTATTATAATTCT
1 TTACTAAAATATTTTTTTCTATTTTTTTAATTGTTATAAGATTGTATAACATTTATTATAATTCT
43473 A
66 A
43474 TTACTAAAATATTTTTTTCTATTTTTTTAATTGTTATAAGATTGTATAACATTTATTATAATTCT
1 TTACTAAAATATTTTTTTCTATTTTTTTAATTGTTATAAGATTGTATAACATTTATTATAATTCT
43539 A
66 A
43540 T
1 T
43541 AAATATTATA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.57
Consensus pattern (66 bp):
TTACTAAAATATTTTTTTCTATTTTTTTAATTGTTATAAGATTGTATAACATTTATTATAATTCT
A
Found at i:43570 original size:66 final size:66
Alignment explanation
Indices: 43434--43571 Score: 161
Period size: 66 Copynumber: 2.1 Consensus size: 66
43424 TTCTATTTTT
* * * * * ***
43434 TTAATTGTTTTAAGATTGTATAACATTTATTATAATTCTATTACTAAAATATTTTTTTCTATTTT
1 TTAATTGTTATAAGATTGTATAACATTTATTATAATTCTATAAATAAAATATTTATTACTAAAAT
*
43499 T
66 A
**
43500 TTAATTGTTATAAGATTGTATAACATTTATTATAATTCTATAAATATTATATATTATTAC-AAAA
1 TTAATTGTTATAAGATTGTATAACATTTATTATAATTCTATAAATAAAATAT-TTATTACTAAAA
43564 TA
65 TA
43566 TTAATT
1 TTAATT
43572 TTTTATAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
66 55 0.92
67 5 0.08
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (66 bp):
TTAATTGTTATAAGATTGTATAACATTTATTATAATTCTATAAATAAAATATTTATTACTAAAAT
A
Found at i:59231 original size:30 final size:30
Alignment explanation
Indices: 59173--59243 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
59163 TAGTGGTTTA
* * * *
59173 ATTTAAATTAATTTTTAAATTTTTAATA-T
1 ATTTTAATTAATCTTTAAATTATGAATATT
59202 ATTTTAATTATATCTTTAAATTATGAATATT
1 ATTTTAATTA-ATCTTTAAATTATGAATATT
*
59233 ATATTAATTAA
1 ATTTTAATTAA
59244 GTTGTTTTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 9 0.26
30 16 0.46
31 10 0.29
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (30 bp):
ATTTTAATTAATCTTTAAATTATGAATATT
Found at i:59257 original size:95 final size:94
Alignment explanation
Indices: 59080--59330 Score: 342
Period size: 95 Copynumber: 2.7 Consensus size: 94
59070 TAGACATCAT
* * * * *
59080 TTTAAATTAATTTTTAAATTTTGAAATGTTTCAATTATATCTCTAAATCATGAATATTATATTAA
1 TTTAAATTAATTTTTAAATTTTTAAATATTTTAATTATATCTTTAAATTATGAATATTATATTAA
* * * **
59145 CCAAATTTTTTTATTATCTAGTGGTTTAA
66 CCAAATTGTTTTATTATCAAATCATTTAA
59174 TTTAAATTAATTTTTAAATTTTTAATATATTTTAATTATATCTTTAAATTATGAATATTATATTA
1 TTTAAATTAATTTTTAAATTTTTAA-ATATTTTAATTATATCTTTAAATTATGAATATTATATTA
** * *
59239 ATTAAGTTGTTTTGTTATCAAATCATTTAA
65 ACCAAATTGTTTTATTATCAAATCATTTAA
* *
59269 TTTAAATTAGTTTTTAAATTTTAAAATATTTTAATTATATCTTTAAATTATG-ATATTATATT
1 TTTAAATTAATTTTTAAATTTTTAAATATTTTAATTATATCTTTAAATTATGAATATTATATT
59331 TTTTTTGGTA
Statistics
Matches: 140, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
93 10 0.07
94 51 0.36
95 79 0.56
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.53
Consensus pattern (94 bp):
TTTAAATTAATTTTTAAATTTTTAAATATTTTAATTATATCTTTAAATTATGAATATTATATTAA
CCAAATTGTTTTATTATCAAATCATTTAA
Found at i:59456 original size:15 final size:16
Alignment explanation
Indices: 59413--59458 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
59403 TTTGTTAAAA
*
59413 TAGTCATTTTTATTTG
1 TAGTCATTTATATTTG
*
59429 T-CTCATGTTATATTT-
1 TAGTCAT-TTATATTTG
59444 TAGTCATTTATATTT
1 TAGTCATTTATATTT
59459 AAAATGTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.61
Consensus pattern (16 bp):
TAGTCATTTATATTTG
Found at i:60135 original size:231 final size:231
Alignment explanation
Indices: 59732--60194 Score: 890
Period size: 231 Copynumber: 2.0 Consensus size: 231
59722 TCATCTCAAC
59732 TGGACATCCATTTTTAACTGTCATATGGGACTGTCGCTTGAAAGGTAACAGATCTTAACGGTAGA
1 TGGACATCCATTTTTAACTGTCATATGGGACTGTCGCTTGAAAGGTAACAGATCTTAACGGTAGA
59797 GTAATCATTTCGTAACAAAAAATTACGTAAATGACTAAAACGTAATATTTTAAACATAAGTGACT
66 GTAATCATTTCGTAACAAAAAATTACGTAAATGACTAAAACGTAATATTTTAAACATAAGTGACT
*
59862 AAAATGTAATATAAAGCAAATAAATGCGACTATTTTGATAGTTTACCATTTAATTTAAATTAGTT
131 AAAATGTAATATAAAGCAAATAAATACGACTATTTTGATAGTTTACCATTTAATTTAAATTAGTT
*
59927 TTTAAATTTTAAAACATTTTAATTATATATGGATGT
196 TTTAAAATTTAAAACATTTTAATTATATATGGATGT
*
59963 TGGACATCCATTTTTAACTGTCATATGGGACTGTCGCTTGAAAGGTAACAGATTTTAACGGTAGA
1 TGGACATCCATTTTTAACTGTCATATGGGACTGTCGCTTGAAAGGTAACAGATCTTAACGGTAGA
*
60028 GTAATCATTTCGTAACAAAAAATTACGTAAATGACTAAAACGTAATATTTTAAATATAAGTGACT
66 GTAATCATTTCGTAACAAAAAATTACGTAAATGACTAAAACGTAATATTTTAAACATAAGTGACT
60093 AAAATGTAATATAAAGCAAATAAATACGACTATTTTGATAGTTTACCATTTAATTTAAATTAGTT
131 AAAATGTAATATAAAGCAAATAAATACGACTATTTTGATAGTTTACCATTTAATTTAAATTAGTT
60158 TTTAAAATTTAAAACATTTTAATTATATATGGATGT
196 TTTAAAATTTAAAACATTTTAATTATATATGGATGT
60194 T
1 T
60195 ATATTAATTT
Statistics
Matches: 228, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
231 228 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (231 bp):
TGGACATCCATTTTTAACTGTCATATGGGACTGTCGCTTGAAAGGTAACAGATCTTAACGGTAGA
GTAATCATTTCGTAACAAAAAATTACGTAAATGACTAAAACGTAATATTTTAAACATAAGTGACT
AAAATGTAATATAAAGCAAATAAATACGACTATTTTGATAGTTTACCATTTAATTTAAATTAGTT
TTTAAAATTTAAAACATTTTAATTATATATGGATGT
Found at i:72735 original size:2 final size:2
Alignment explanation
Indices: 72728--72754 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
72718 ATGCAGGGAA
72728 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
72755 TGCCCTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:77655 original size:15 final size:17
Alignment explanation
Indices: 77619--77656 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
77609 ATGATAAAAA
77619 TATAATATCATCATTTT
1 TATAATATCATCATTTT
*
77636 AATAATAT-AT-ATTTT
1 TATAATATCATCATTTT
77651 TATAAT
1 TATAAT
77657 TTTTAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 10 0.53
16 2 0.11
17 7 0.37
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (17 bp):
TATAATATCATCATTTT
Found at i:80718 original size:32 final size:34
Alignment explanation
Indices: 80659--80727 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 34
80649 AATAAGCCCG
80659 TTTATAATTAATGGGCTTTCTTAAC-A-AGTCCA
1 TTTATAATTAATGGGCTTTCTTAACAAGAGTCCA
* *
80691 TTTATAGTTCATGGGCTTTC-TATACAAGAGTCCA
1 TTTATAATTAATGGGCTTTCTTA-ACAAGAGTCCA
80725 TTT
1 TTT
80728 CGGCAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 2 0.06
32 20 0.62
33 1 0.03
34 9 0.28
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (34 bp):
TTTATAATTAATGGGCTTTCTTAACAAGAGTCCA
Found at i:90896 original size:16 final size:16
Alignment explanation
Indices: 90877--90910 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
90867 TAATGTGAAT
90877 TTATTG-ATATTTTAAA
1 TTATTGAATA-TTTAAA
90893 TTATTGAATATTTAAA
1 TTATTGAATATTTAAA
90909 TT
1 TT
90911 CGAGTCTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATTGAATATTTAAA
Found at i:92131 original size:57 final size:57
Alignment explanation
Indices: 91974--92236 Score: 226
Period size: 58 Copynumber: 4.5 Consensus size: 57
91964 TTAGACATCC
** * * * *
91974 AGGGATAAAATGATAATTTTTGGAAAAATCGAGGTTGAAAATGGAATTTTTGAAAGTTTG
1 AGGG-TAAAATG-TAATTTTTGGAAAGTTTG-GGGTCAAAATGGAATTTTGGAAAGTTTG
* * *
92034 AGGGTAAAATGATAA-TTTTGGAGAA-ATAGGGGTAAAAAATGGAATTTTGGAAAGTTTG
1 AGGGTAAAATG-TAATTTTTGGA-AAGTTTGGGGT-CAAAATGGAATTTTGGAAAGTTTG
* * *
92092 GGGGTAAAATGTAATTTTTGGAAAGTTTGGGGTCAAAATGGAATTTTGGAAAGATTA
1 AGGGTAAAATGTAATTTTTGGAAAGTTTGGGGTCAAAATGGAATTTTGGAAAGTTTG
* ** ** *
92149 AGGGTAAAAATGTAA-TTTTGAAAAGTTTAAGGTCAAAAATATAATTTTAGAGAAGTTTG
1 AGGGT-AAAATGTAATTTTTGGAAAGTTTGGGGTC-AAAATGGAATTTTGGA-AAGTTTG
* * *
92208 AGGGTCAAAATATAATTTTTTGATAGTTT
1 AGGGT-AAAATGTAATTTTTGGAAAGTTT
92237 AGGGACTTTC
Statistics
Matches: 171, Mismatches: 24, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
57 49 0.29
58 77 0.45
59 31 0.18
60 14 0.08
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.34
Consensus pattern (57 bp):
AGGGTAAAATGTAATTTTTGGAAAGTTTGGGGTCAAAATGGAATTTTGGAAAGTTTG
Found at i:92236 original size:30 final size:29
Alignment explanation
Indices: 91890--92226 Score: 194
Period size: 29 Copynumber: 11.6 Consensus size: 29
91880 GGATATCCGG
* * *
91890 GGGT-AAAATGGTAATTTTGGACA-CTCGA
1 GGGTCAAAAT-GTAATTTTGGAAAGTTTGA
*
91918 GGG-CAAAATAGTAATTTTGGGAAGTTTGA
1 GGGTCAAAAT-GTAATTTTGGAAAGTTTGA
* * * * * **
91947 GGTTAAAAATTGAAATTTTAGACA--TCCA
1 GGGTCAAAA-TGTAATTTTGGAAAGTTTGA
** *
91975 GGGAT-AAAATGATAATTTTTGGAAAAATCGA
1 GGG-TCAAAATG-TAA-TTTTGGAAAGTTTGA
* * * *
92006 GGTTGAAAATGGAATTTTTGAAAGTTTGA
1 GGGTCAAAATGTAATTTTGGAAAGTTTGA
* *
92035 GGGT-AAAATGATAATTTTGGAGAA-ATAG-
1 GGGTCAAAATG-TAATTTTGGA-AAGTTTGA
* * *
92063 GGGTAAAAAATGGAATTTTGGAAAGTTTGG
1 GGGT-CAAAATGTAATTTTGGAAAGTTTGA
92093 GGGT-AAAATGTAATTTTTGGAAAGTTTG-
1 GGGTCAAAATGTAA-TTTTGGAAAGTTTGA
* * *
92121 GGGTCAAAATGGAATTTTGGAAAGATTAA
1 GGGTCAAAATGTAATTTTGGAAAGTTTGA
* *
92150 GGGTAAAAATGTAATTTTGAAAAGTTT-A
1 GGGTCAAAATGTAATTTTGGAAAGTTTGA
* * *
92178 AGGTCAAAAATATAATTTTAGAGAAGTTTGA
1 GGGTC-AAAATGTAATTTTGGA-AAGTTTGA
*
92209 GGGTCAAAATATAATTTT
1 GGGTCAAAATGTAATTTT
92227 TTGATAGTTT
Statistics
Matches: 241, Mismatches: 46, Indels: 42
0.73 0.14 0.13
Matches are distributed among these distances:
27 2 0.01
28 69 0.29
29 106 0.44
30 47 0.20
31 17 0.07
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.32
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTGGAAAGTTTGA
Found at i:94007 original size:6 final size:6
Alignment explanation
Indices: 93981--94074 Score: 72
Period size: 6 Copynumber: 16.0 Consensus size: 6
93971 TTTATTCATT
* * * *
93981 TTTAAA TTTATAA --TAAT TTTAAA TTTAAA TATAAA CTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
94028 -TTAAA TTTAAA TTCTAGAA --TAAA TTTAAA TTTAAA AATAAA TTTAAA
1 TTTAAA TTTAAA TT-TA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
94075 ATGAGTTAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
4 3 0.04
5 9 0.13
6 53 0.75
7 4 0.06
8 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:94014 original size:18 final size:18
Alignment explanation
Indices: 93981--94074 Score: 104
Period size: 18 Copynumber: 5.3 Consensus size: 18
93971 TTTATTCATT
* *
93981 TTTAAATTTATA-ATAAT
1 TTTAAATTTAAATATAAA
93998 TTTAAATTTAAATATAAA
1 TTTAAATTTAAATATAAA
* *
94016 CTTAAACTTAAAT-TAAA
1 TTTAAATTTAAATATAAA
*
94033 TTTAAATTCTAGA-ATAAA
1 TTTAAATT-TAAATATAAA
*
94051 TTTAAATTTAAAAATAAA
1 TTTAAATTTAAATATAAA
94069 TTTAAA
1 TTTAAA
94075 ATGAGTTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
17 24 0.37
18 41 0.63
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (18 bp):
TTTAAATTTAAATATAAA
Found at i:94840 original size:38 final size:39
Alignment explanation
Indices: 94778--94851 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 39
94768 AAAAATTAAT
94778 ATTTTATCAAATAATATTAAAAAATTATAAAACAAAATTC
1 ATTTTATCAAATAATATTAAAAAATT-TAAAACAAAATTC
*
94818 ATTTTATC-AA-AATATCT-AAAAATTTAAAATAAAA
1 ATTTTATCAAATAATAT-TAAAAAATTTAAAACAAAA
94852 AATTACTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
37 9 0.28
38 12 0.38
39 3 0.09
40 8 0.25
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (39 bp):
ATTTTATCAAATAATATTAAAAAATTTAAAACAAAATTC
Found at i:94854 original size:39 final size:40
Alignment explanation
Indices: 94778--94855 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 40
94768 AAAAATTAAT
*
94778 ATTTTATCAAATAATATTAAAAAATTATAAAACAAAATTC
1 ATTTTATCAAATAATATTAAAAAATTATAAAAAAAAATTC
*
94818 ATTTTATC-AA-AATATCTAAAAATTTA-AAATAAAAAATT
1 ATTTTATCAAATAATAT-TAAAAAATTATAAA-AAAAAATT
94856 ACTATGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 8 0.24
39 18 0.53
40 8 0.24
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (40 bp):
ATTTTATCAAATAATATTAAAAAATTATAAAAAAAAATTC
Found at i:99765 original size:21 final size:23
Alignment explanation
Indices: 99715--99767 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
99705 TTAATTTAAT
** *
99715 TAAAATATTAATATATCTTATAA
1 TAAAATATTAATATAGATAATAA
99738 TAAAATATTAATA-AGATAATAA
1 TAAAATATTAATATAGATAATAA
99760 -AAAATATT
1 TAAAATATT
99768 TTGTCAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 8 0.30
22 6 0.22
23 13 0.48
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (23 bp):
TAAAATATTAATATAGATAATAA
Found at i:101333 original size:16 final size:18
Alignment explanation
Indices: 101302--101334 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
101292 TTCACTCTCA
101302 CTCTCACTCTCATTCTTT
1 CTCTCACTCTCATTCTTT
101320 CTCTC-CTCTC-TTCTT
1 CTCTCACTCTCATTCTT
101335 CCTATTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.06, C:0.42, G:0.00, T:0.52
Consensus pattern (18 bp):
CTCTCACTCTCATTCTTT
Found at i:122789 original size:20 final size:20
Alignment explanation
Indices: 122751--122789 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
122741 ACATCTCATG
* * *
122751 CTTTTATTTTTATATATCAA
1 CTTTAATTTTCATAAATCAA
122771 CTTTAATTTTCATAAATCA
1 CTTTAATTTTCATAAATCA
122790 TGAAAAATAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (20 bp):
CTTTAATTTTCATAAATCAA
Found at i:130403 original size:13 final size:13
Alignment explanation
Indices: 130377--130415 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
130367 AATTTTGCAT
130377 TGCTTTTGAGAAAG
1 TGCTTTTGA-AAAG
*
130391 TGCTTTGGAAAAG
1 TGCTTTTGAAAAG
*
130404 TGATTTTGAAAA
1 TGCTTTTGAAAA
130416 ATATTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:141832 original size:23 final size:23
Alignment explanation
Indices: 141806--141850 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
141796 AAATTCAAAT
**
141806 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
141829 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
141851 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:146067 original size:2 final size:2
Alignment explanation
Indices: 146060--146086 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
146050 AACTCCATTT
146060 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 T
146087 TTAAGGTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:147658 original size:28 final size:25
Alignment explanation
Indices: 147626--147689 Score: 65
Period size: 28 Copynumber: 2.4 Consensus size: 25
147616 TTTGAAGTCG
*
147626 AACTCAAATATTTAAGTTGAACAAAAAA
1 AACTCAAATA-TTAAATT-AA-AAAAAA
*
147654 AACTCAAGTATTAAATTAAAAAAAA
1 AACTCAAATATTAAATTAAAAAAAA
*
147679 AATCTCTAATA
1 AA-CTCAAATA
147690 ACAAAATCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 8 0.26
26 8 0.26
27 6 0.19
28 9 0.29
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.27
Consensus pattern (25 bp):
AACTCAAATATTAAATTAAAAAAAA
Found at i:150069 original size:90 final size:90
Alignment explanation
Indices: 149916--150096 Score: 362
Period size: 90 Copynumber: 2.0 Consensus size: 90
149906 GGCCATCAAT
149916 ACCAATAATTGACTCTCAACTTTCAAGTTTAGCATGAATAATGAGATGATTTCTATTAGACAGAT
1 ACCAATAATTGACTCTCAACTTTCAAGTTTAGCATGAATAATGAGATGATTTCTATTAGACAGAT
149981 GAACATAGTCTCTTTTGGATGAGTA
66 GAACATAGTCTCTTTTGGATGAGTA
150006 ACCAATAATTGACTCTCAACTTTCAAGTTTAGCATGAATAATGAGATGATTTCTATTAGACAGAT
1 ACCAATAATTGACTCTCAACTTTCAAGTTTAGCATGAATAATGAGATGATTTCTATTAGACAGAT
150071 GAACATAGTCTCTTTTGGATGAGTA
66 GAACATAGTCTCTTTTGGATGAGTA
150096 A
1 A
150097 TGTATAAATT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (90 bp):
ACCAATAATTGACTCTCAACTTTCAAGTTTAGCATGAATAATGAGATGATTTCTATTAGACAGAT
GAACATAGTCTCTTTTGGATGAGTA
Found at i:152258 original size:9 final size:9
Alignment explanation
Indices: 152230--152268 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
152220 ATTTTTTTTT
152230 TAATTCGAA
1 TAATTCGAA
* *
152239 TAACTCAAA
1 TAATTCGAA
152248 TAATTCGAA
1 TAATTCGAA
*
152257 TAAATCGAA
1 TAATTCGAA
152266 TAA
1 TAA
152269 AACTATTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (9 bp):
TAATTCGAA
Found at i:152267 original size:18 final size:18
Alignment explanation
Indices: 152230--152268 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
152220 ATTTTTTTTT
*
152230 TAATTCGAATAACTCAAA
1 TAATTCGAATAAATCAAA
*
152248 TAATTCGAATAAATCGAA
1 TAATTCGAATAAATCAAA
152266 TAA
1 TAA
152269 AACTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (18 bp):
TAATTCGAATAAATCAAA
Found at i:152449 original size:34 final size:34
Alignment explanation
Indices: 152406--152474 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
152396 CATAAACTAA
* *
152406 ACCCAAATATTTTTAATTTTTTACCTTTTATCTT
1 ACCCAAATATTTTAAATTTTTTACCTTTTACCTT
152440 ACCCAAATATTTTAAATTTTTTACCTTTTACCTT
1 ACCCAAATATTTTAAATTTTTTACCTTTTACCTT
152474 A
1 A
152475 AATGTTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.19, G:0.00, T:0.52
Consensus pattern (34 bp):
ACCCAAATATTTTAAATTTTTTACCTTTTACCTT
Found at i:162467 original size:24 final size:24
Alignment explanation
Indices: 162422--162470 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
162412 AGTTAAATTT
* *
162422 TGTTTAATTGTTTTAATTAAACTC
1 TGTTTAATTGTTTGAATCAAACTC
* *
162446 TGTTTATTTGTTTGAGTCAAACTC
1 TGTTTAATTGTTTGAATCAAACTC
162470 T
1 T
162471 TATTAGTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.53
Consensus pattern (24 bp):
TGTTTAATTGTTTGAATCAAACTC
Found at i:185144 original size:103 final size:104
Alignment explanation
Indices: 184990--185199 Score: 280
Period size: 103 Copynumber: 2.0 Consensus size: 104
184980 TAAACTAAAT
* * * **
184990 AATTTATGCGTGTTTTCTTTGATGCAATAAGGGATTACGGACTTCCAAAAAGAAACCATTTTCAC
1 AATTTATGCATGTTTTCTGTGATGCAATAAGGAATTACACACTTCCAAAAAGAAACCATTTTCAC
*
185055 AAGACCAATATGATTTCTCTC-TTTTACTTTCAAGCCGC
66 AAGACCAATATGATTTCTCTCTTTTTACGTTCAAGCCGC
* * * * * *
185093 AATTTATGCATGTTTTCTGTGATGTAATGAGGAATTGGCACACTTCC-AAAAGGAACTATTTTGA
1 AATTTATGCATGTTTTCTGTGATGCAATAAGGAATT-ACACACTTCCAAAAAGAAACCATTTTCA
*
185157 CAAGACCAATATGATTTGTCTCTTTTTACGTTCAAGCCGC
65 CAAGACCAATATGATTTCTCTCTTTTTACGTTCAAGCCGC
185197 AAT
1 AAT
185200 CTCATCTAAG
Statistics
Matches: 92, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
103 66 0.72
104 26 0.28
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (104 bp):
AATTTATGCATGTTTTCTGTGATGCAATAAGGAATTACACACTTCCAAAAAGAAACCATTTTCAC
AAGACCAATATGATTTCTCTCTTTTTACGTTCAAGCCGC
Done.