Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007262.1 Kokia drynarioides strain JFW-HI SEQ_121878, 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: 275109
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:806 original size:3 final size:3
Alignment explanation
Indices: 798--845 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
788 ACTGTTGATG
798 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TCAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
844 TA
1 TA
846 AATTGTTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2677 original size:48 final size:48
Alignment explanation
Indices: 2606--2774 Score: 241
Period size: 48 Copynumber: 3.5 Consensus size: 48
2596 GGGGAGGATC
* *
2606 AACGACCGTATTTGGGTCATCAGCACCGACAGGAGAAGGAGCAAGAGA
1 AACGACCGTATTTGGGCCATCAGCACCGACAGGAGAAGGAGCACGAGA
*
2654 AACGACCGTATTTGGGCCATCAGCACCGACAGGAGAAGGAGCACGAGC
1 AACGACCGTATTTGGGCCATCAGCACCGACAGGAGAAGGAGCACGAGA
* * *
2702 AACGACCGT-TTTCGGACCATCAGCACCGACAGGAGGAGGGGCACGAGA
1 AACGACCGTATTT-GGGCCATCAGCACCGACAGGAGAAGGAGCACGAGA
* * *
2750 AACGACCGTAATTGAGCCATTAGCA
1 AACGACCGTATTTGGGCCATCAGCA
2775 GCGAAAGAAA
Statistics
Matches: 108, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
47 3 0.03
48 103 0.95
49 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.30, T:0.12
Consensus pattern (48 bp):
AACGACCGTATTTGGGCCATCAGCACCGACAGGAGAAGGAGCACGAGA
Found at i:13638 original size:42 final size:42
Alignment explanation
Indices: 13579--13660 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
13569 CATAGCGAGC
* *
13579 TGTTCTTGATCCCGAATTTGAAGCCTCTGTAATTCTTGTAGA
1 TGTTCTTGATCCCGAATTTGAAGCCTCTGCAATTCATGTAGA
13621 TGTTCTTGATCCCGAATTTGAAGCCTCTGCAATTCATGTA
1 TGTTCTTGATCCCGAATTTGAAGCCTCTGCAATTCATGTA
13661 TCTGTCTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (42 bp):
TGTTCTTGATCCCGAATTTGAAGCCTCTGCAATTCATGTAGA
Found at i:17319 original size:17 final size:17
Alignment explanation
Indices: 17292--17324 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17282 CATTGATTTG
17292 TTATTTGTGCACATTTAA
1 TTATTTGTGCA-ATTTAA
17310 TTATTT-TGCAATTTA
1 TTATTTGTGCAATTTA
17325 GTCCTTCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (17 bp):
TTATTTGTGCAATTTAA
Found at i:25517 original size:19 final size:19
Alignment explanation
Indices: 25495--25532 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
25485 ATACCATAAT
25495 CAAAATT-AAAGTCCCAAAA
1 CAAAATTAAAAGT-CCAAAA
25514 CAAAATTAAAAGTCCAAAA
1 CAAAATTAAAAGTCCAAAA
25533 GTTCGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.61, C:0.18, G:0.05, T:0.16
Consensus pattern (19 bp):
CAAAATTAAAAGTCCAAAA
Found at i:27422 original size:21 final size:23
Alignment explanation
Indices: 27398--27440 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
27388 TTGTTTAATC
27398 TGAT-AAAAAATC-AATTTTTTG
1 TGATAAAAAAATCAAATTTTTTG
27419 TGATAAAAAAATCAAATTTTTT
1 TGATAAAAAAATCAAATTTTTT
27441 TGTGTTGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 8 0.40
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (23 bp):
TGATAAAAAAATCAAATTTTTTG
Found at i:27554 original size:60 final size:59
Alignment explanation
Indices: 27420--27560 Score: 155
Period size: 61 Copynumber: 2.4 Consensus size: 59
27410 AATTTTTTGT
*
27420 GATAAAAAAATCAAA-TTTTTTTGTGTTGATCATGCAATGGCCGACACTCTCTTTTTCA
1 GATAAAAAAATCAAATTTTTTTTGTGTTGATCATGCAATAGCCGACACTCTCTTTTTCA
* * * *
27478 GATAAAAAAATTTCAAATTTTTTTTGTGTTGGTTATTGC-ATAGTCGACAC-CTCTTTTTATCT
1 GATAAAAAAA--TCAAATTTTTTTTGTGTTGATCA-TGCAATAGCCGACACTCTC-TTTT-TCA
27540 GA-ATAAAAAATCAAATTTTTT
1 GATA-AAAAAATCAAATTTTTT
27561 GGTATGGACA
Statistics
Matches: 71, Mismatches: 5, Indels: 12
0.81 0.06 0.14
Matches are distributed among these distances:
58 10 0.14
60 19 0.27
61 29 0.41
62 13 0.18
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (59 bp):
GATAAAAAAATCAAATTTTTTTTGTGTTGATCATGCAATAGCCGACACTCTCTTTTTCA
Found at i:27594 original size:60 final size:61
Alignment explanation
Indices: 27521--27685 Score: 137
Period size: 61 Copynumber: 2.7 Consensus size: 61
27511 TATTGCATAG
* * * *
27521 TCGACA-CCTCTTTTTATCTGAATAAAAAATCAAATTTTTTGGTATG-GA-CAATGTCATTGC
1 TCGACACCCCCTTTTTATATGAATAAAAAATCAAATTTTTTGGTATGTGATC-ATGCCA-TGA
* * * *
27581 T-GACACCCCCTTTTT-TGTTAAATAAAAAATTCTAATTTTTTTG-ATGTTGATCATGCCATGA
1 TCGACACCCCCTTTTTAT-ATGAATAAAAAA-TCAAATTTTTTGGTATG-TGATCATGCCATGA
* *
27642 TCGACACCCCCTTTTTTATATG-GTAAAAAATCAATTTTTTTGGT
1 TCGACACCCCC-TTTTTATATGAATAAAAAATCAAATTTTTTGGT
27686 GTTTACCATG
Statistics
Matches: 82, Mismatches: 13, Indels: 18
0.73 0.12 0.16
Matches are distributed among these distances:
59 5 0.06
60 22 0.27
61 24 0.29
62 23 0.28
63 7 0.09
64 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (61 bp):
TCGACACCCCCTTTTTATATGAATAAAAAATCAAATTTTTTGGTATGTGATCATGCCATGA
Found at i:27732 original size:18 final size:16
Alignment explanation
Indices: 27703--27754 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
27693 ATGCGATACT
27703 ATAAAATAAATTATAA
1 ATAAAATAAATTATAA
*
27719 ATACAAATTAAATTTACAA
1 ATA-AAA-TAAA-TTATAA
27738 ATAAAATAAATTATAA
1 ATAAAATAAATTATAA
27754 A
1 A
27755 GAATTGTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 9 0.29
17 7 0.23
18 7 0.23
19 8 0.26
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAAATAAATTATAA
Found at i:28699 original size:59 final size:60
Alignment explanation
Indices: 28584--28768 Score: 182
Period size: 59 Copynumber: 3.1 Consensus size: 60
28574 AGATAAAAGG
* * * *
28584 ACACAAAAAAATTCGAAATTTTTTTATTTGAAAAAAGGGAGTGTCGACCATGGCATGGCCA
1 ACACAAAAAAATTTG-AATTTCTTTATCTGAAAAAAAGGAGTGTCGACCATGGCATGGCCA
* *
28645 ACACAAAAAAATTTGAA-TTCTTTATCTGACAAAAAAGG-GTGTCGAGCATTGCATGGCCA
1 ACACAAAAAAATTTGAATTTCTTTATCTGA-AAAAAAGGAGTGTCGACCATGGCATGGCCA
** * * *
28704 ACACCCAAAAATTTGATTTTTTTTATC--AAATTAAAAGGAGGTATCGACCAT-GCAATGGCCA
1 ACACAAAAAAATTTGAATTTCTTTATCTGAAA--AAAAGGA-GTGTCGACCATGGC-ATGGCCA
28765 ACAC
1 ACAC
28769 CAAATTTTTT
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
57 2 0.02
58 1 0.01
59 49 0.47
60 19 0.18
61 34 0.32
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (60 bp):
ACACAAAAAAATTTGAATTTCTTTATCTGAAAAAAAGGAGTGTCGACCATGGCATGGCCA
Found at i:39794 original size:15 final size:17
Alignment explanation
Indices: 39760--39797 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
39750 AATAAAAATG
39760 TAATTTCATCATTTTAA
1 TAATTTCATCATTTTAA
*
39777 TAATTT-AT-ATTTTTA
1 TAATTTCATCATTTTAA
39792 TAATTT
1 TAATTT
39798 TTAAAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATTTCATCATTTTAA
Found at i:40993 original size:9 final size:9
Alignment explanation
Indices: 40979--41019 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
40969 ATTATGAACT
40979 TTTTTTATA
1 TTTTTTATA
40988 TTTTTTA-A
1 TTTTTTATA
* *
40996 ATTTTAAT-
1 TTTTTTATA
41004 TTTTTTATA
1 TTTTTTATA
41013 TTTTTTA
1 TTTTTTA
41020 AAAATTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
8 12 0.46
9 14 0.54
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTTATA
Found at i:45419 original size:180 final size:180
Alignment explanation
Indices: 45112--45472 Score: 677
Period size: 180 Copynumber: 2.0 Consensus size: 180
45102 GATGAAACTT
45112 TAATCATGTTTTAGTGCCATTATCTATGTTATTCGGATTCCACTACTTGCCCCATTTATCTTCGT
1 TAATCATGTTTTAGTGCCATTATCTATGTTATTCGGATTCCACTACTTGCCCCATTTATCTTCGT
45177 ATTTGCATGCATGAAATGATGAAACTTTAATATATAATGTAGTACTTCTATTATCTATGTTATTT
66 ATTTGCATGCATGAAATGATGAAACTTTAATATATAATGTAGTACTTCTATTATCTATGTTATTT
*
45242 GGAATTGAAGAGAATGTTGAATATCGCATGTATATTGGAGAGGGTGTATA
131 GGAATTGAAGAGAATGCTGAATATCGCATGTATATTGGAGAGGGTGTATA
* *
45292 TAATGATGTTTTAGTGCTATTATCTATGTTATTCGGATTCCACTACTTGCCCCATTTATCTTCGT
1 TAATCATGTTTTAGTGCCATTATCTATGTTATTCGGATTCCACTACTTGCCCCATTTATCTTCGT
45357 ATTTGCATGCATGAAATGATGAAACTTTAATATATAATGTAGTACTTCTATTATCTATGTTATTT
66 ATTTGCATGCATGAAATGATGAAACTTTAATATATAATGTAGTACTTCTATTATCTATGTTATTT
* *
45422 GGATTTGAAGAGAATGCTGAATATCGTATGTATATTGGAGAGGGTGTATA
131 GGAATTGAAGAGAATGCTGAATATCGCATGTATATTGGAGAGGGTGTATA
45472 T
1 T
45473 CAGTTTGGTT
Statistics
Matches: 176, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
180 176 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (180 bp):
TAATCATGTTTTAGTGCCATTATCTATGTTATTCGGATTCCACTACTTGCCCCATTTATCTTCGT
ATTTGCATGCATGAAATGATGAAACTTTAATATATAATGTAGTACTTCTATTATCTATGTTATTT
GGAATTGAAGAGAATGCTGAATATCGCATGTATATTGGAGAGGGTGTATA
Found at i:48300 original size:16 final size:17
Alignment explanation
Indices: 48279--48316 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
48269 ATAATTTAAC
48279 CATTTA-TTTAATTTTT
1 CATTTATTTTAATTTTT
48295 CATTTATTTTAATTTTT
1 CATTTATTTTAATTTTT
*
48312 AATTT
1 CATTT
48317 TTGTTGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
CATTTATTTTAATTTTT
Found at i:48470 original size:29 final size:29
Alignment explanation
Indices: 48403--48477 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
48393 AATTTTCATG
**
48403 TAAGCAATTAATTATTTTTTTAAAAATTAA
1 TAAGCAATTAATTA-TTTTAAAAAAATTAA
* **
48433 AAATTAATT-ATTATTTTAAAAAAATTTAA
1 TAAGCAATTAATTATTTTAAAAAAA-TTAA
48462 TAAGCAATTAATTATT
1 TAAGCAATTAATTATT
48478 AATACGATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
28 9 0.26
29 14 0.40
30 12 0.34
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (29 bp):
TAAGCAATTAATTATTTTAAAAAAATTAA
Found at i:50242 original size:27 final size:27
Alignment explanation
Indices: 50204--50258 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
50194 ATTAACTAAG
50204 TTTTTAGTGAGTAATACGTATGAATAA
1 TTTTTAGTGAGTAATACGTATGAATAA
50231 TTTTTAGTGAGTAATACGTATGAATAA
1 TTTTTAGTGAGTAATACGTATGAATAA
50258 T
1 T
50259 AAGCTGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (27 bp):
TTTTTAGTGAGTAATACGTATGAATAA
Found at i:52662 original size:2 final size:2
Alignment explanation
Indices: 52655--52684 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
52645 ATAGAGGTTG
*
52655 CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
52685 AGGTGGTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:86064 original size:12 final size:12
Alignment explanation
Indices: 85978--86064 Score: 51
Period size: 12 Copynumber: 7.8 Consensus size: 12
85968 TAATATTAAG
*
85978 ATAATTATATAA
1 ATAATTAAATAA
* *
85990 AAAATTTAATAA
1 ATAATTAAATAA
*
86002 ATAA--AAATAT
1 ATAATTAAATAA
* *
86012 ATAATTTATTAA
1 ATAATTAAATAA
*
86024 AT-ATTAAATTA
1 ATAATTAAATAA
86035 A-AA-T-AATAA
1 ATAATTAAATAA
* *
86044 AAAAATAAATAA
1 ATAATTAAATAA
86056 ATAATTAAA
1 ATAATTAAA
86065 ATAATTTTAG
Statistics
Matches: 54, Mismatches: 15, Indels: 12
0.67 0.19 0.15
Matches are distributed among these distances:
9 5 0.09
10 11 0.20
11 9 0.17
12 29 0.54
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
ATAATTAAATAA
Found at i:101617 original size:28 final size:28
Alignment explanation
Indices: 101586--101646 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
101576 TAAAAGATAA
101586 AATTATTATATTGT-T-TATGTAGTTAAAT
1 AATTATTATATT-TATCTAT-TAGTTAAAT
*
101614 AATT-TTGTATTTCATCTATTAGTTAAAT
1 AATTATTATATTT-ATCTATTAGTTAAAT
101642 AATTA
1 AATTA
101647 GTTAATGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
26 1 0.04
27 6 0.21
28 18 0.64
29 3 0.11
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.52
Consensus pattern (28 bp):
AATTATTATATTTATCTATTAGTTAAAT
Found at i:107169 original size:19 final size:19
Alignment explanation
Indices: 107145--107182 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
107135 ATTGACTCGT
107145 GATAAGGATACTCTAAACA
1 GATAAGGATACTCTAAACA
107164 GATAAGGATACTCTAAACA
1 GATAAGGATACTCTAAACA
107183 TAATTTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (19 bp):
GATAAGGATACTCTAAACA
Found at i:111399 original size:19 final size:19
Alignment explanation
Indices: 111346--111401 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
111336 ATTTTTATTT
*
111346 TATTAAATATAATAAAATA
1 TATTAAATATAATAATATA
111365 T-TTAATATATAATAATATA
1 TATTAA-ATATAATAATATA
*
111384 TATTAAAAATAATAATAT
1 TATTAAATATAATAATAT
111402 TGTACTTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.12
19 25 0.76
20 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TATTAAATATAATAATATA
Found at i:113846 original size:2 final size:2
Alignment explanation
Indices: 113839--113864 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
113829 ATAACACAAA
113839 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
113865 TGTGTGTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:128907 original size:18 final size:19
Alignment explanation
Indices: 128873--128913 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
128863 AACTTTTTAA
*
128873 TAATTTTCTACAATTTTTT
1 TAATTTTCTACAATTTTTG
*
128892 TAATTTT-TACATTTTTTG
1 TAATTTTCTACAATTTTTG
128910 TAAT
1 TAAT
128914 AATATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.63
Consensus pattern (19 bp):
TAATTTTCTACAATTTTTG
Found at i:129017 original size:23 final size:23
Alignment explanation
Indices: 128982--129029 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
128972 TTTTATAACC
* *
128982 TTTCTATAATTTATTTATTTATT
1 TTTCTAGAATTTATATATTTATT
*
129005 TTTCTAGATTTTATATATTTATT
1 TTTCTAGAATTTATATATTTATT
129028 TT
1 TT
129030 CATTTTTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTCTAGAATTTATATATTTATT
Found at i:132384 original size:9 final size:9
Alignment explanation
Indices: 132372--132397 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
132362 GAAGGAAAAG
132372 GAGAGGGAT
1 GAGAGGGAT
132381 GAGAGGGAT
1 GAGAGGGAT
132390 GAGAGGGA
1 GAGAGGGA
132398 GCGGAGGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.58, T:0.08
Consensus pattern (9 bp):
GAGAGGGAT
Found at i:134798 original size:16 final size:16
Alignment explanation
Indices: 134779--134809 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
134769 GAAGAAAGGA
134779 AAAGAAAAAGAAAAAG
1 AAAGAAAAAGAAAAAG
*
134795 AAAGAAAAGGAAAAA
1 AAAGAAAAAGAAAAA
134810 ATATATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGAAAAAG
Found at i:135083 original size:15 final size:15
Alignment explanation
Indices: 135063--135128 Score: 69
Period size: 15 Copynumber: 4.4 Consensus size: 15
135053 CCAGGATATT
* *
135063 CTCCTCAAGGTTATC
1 CTCCTCAAGGATACC
135078 CTCCTCAAGGATACC
1 CTCCTCAAGGATACC
* * *
135093 CTCCTGAGGGATATC
1 CTCCTCAAGGATACC
* *
135108 CTGCTCAGGGATACC
1 CTCCTCAAGGATACC
135123 CTCCTC
1 CTCCTC
135129 CCTATGCTCC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.20, C:0.36, G:0.18, T:0.26
Consensus pattern (15 bp):
CTCCTCAAGGATACC
Found at i:135097 original size:30 final size:30
Alignment explanation
Indices: 135063--135128 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
135053 CCAGGATATT
*
135063 CTCCTCAAGGTTATCCTCCTCAAGGATACC
1 CTCCTCAAGGATATCCTCCTCAAGGATACC
* * * *
135093 CTCCTGAGGGATATCCTGCTCAGGGATACC
1 CTCCTCAAGGATATCCTCCTCAAGGATACC
135123 CTCCTC
1 CTCCTC
135129 CCTATGCTCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.36, G:0.18, T:0.26
Consensus pattern (30 bp):
CTCCTCAAGGATATCCTCCTCAAGGATACC
Found at i:147248 original size:110 final size:110
Alignment explanation
Indices: 147054--147275 Score: 365
Period size: 110 Copynumber: 2.0 Consensus size: 110
147044 AATATGTGTC
*
147054 ATCATGCATGAAGACCTACTTAGCATATCGCATTTATGAACAATGACCTTATCATATAAATACAC
1 ATCATGCATGAAGACCTACTTAGCATATCGCATTCATGAACAATGACCTTATCATATAAATACAC
**
147119 AAAACTAACTCATGTGAGGAGACATCACATAAAAATACTCAACAA
66 AAAACTAACTCATCCGAGGAGACATCACATAAAAATACTCAACAA
* *
147164 ATCATGCGTGAAGACCTACTTTA-CATATCTCATTCATGAACAATGACCTTATCATATAAATACA
1 ATCATGCATGAAGACCTAC-TTAGCATATCGCATTCATGAACAATGACCTTATCATATAAATACA
* *
147228 CAAAACTAACTCTTCCGAGGAGACATTACATAAAAATACTCAACAA
65 CAAAACTAACTCATCCGAGGAGACATCACATAAAAATACTCAACAA
147274 AT
1 AT
147276 TTCATGAATT
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
110 101 0.97
111 3 0.03
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.26
Consensus pattern (110 bp):
ATCATGCATGAAGACCTACTTAGCATATCGCATTCATGAACAATGACCTTATCATATAAATACAC
AAAACTAACTCATCCGAGGAGACATCACATAAAAATACTCAACAA
Found at i:150443 original size:19 final size:20
Alignment explanation
Indices: 150419--150456 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
150409 TCGGTTTAAT
150419 TAAATAAAT-TATTAAAAAA
1 TAAATAAATATATTAAAAAA
150438 TAAATAAATATATTAAAAA
1 TAAATAAATATATTAAAAA
150457 TAGAGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAATAAATATATTAAAAAA
Found at i:150465 original size:19 final size:19
Alignment explanation
Indices: 150419--150466 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
150409 TCGGTTTAAT
*
150419 TAAATAAATTATTAAAAAA
1 TAAAGAAATTATTAAAAAA
*
150438 TAAATAAATATATT-AAAAA
1 TAAAGAAAT-TATTAAAAAA
*
150457 TAGAGAAATT
1 TAAAGAAATT
150467 GGCAGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 21 0.81
20 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (19 bp):
TAAAGAAATTATTAAAAAA
Found at i:151251 original size:29 final size:29
Alignment explanation
Indices: 151201--151275 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
151191 TTAGAATCAC
* * *
151201 AATCAAAGTTTCACATATAAATTGCAC-AA
1 AATCAAAATTT-ATATATAAATTACACGAA
* *
151230 AATCAGAATTTATATATCAAATTACACGTTA
1 AATCAAAATTTATATAT-AAATTACACG-AA
151261 AATCAAAATTTATAT
1 AATCAAAATTTATAT
151276 GCAATTTTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
28 5 0.14
29 17 0.46
31 15 0.41
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.33
Consensus pattern (29 bp):
AATCAAAATTTATATATAAATTACACGAA
Found at i:152659 original size:24 final size:24
Alignment explanation
Indices: 152615--152660 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
152605 GTAGAGCTCG
* *
152615 AAATTAAATTTTATTTTTTTTATA
1 AAATTAAATGTTATTTATTTTATA
152639 AAATTAAAATGTTA-TTATTTTA
1 AAATT-AAATGTTATTTATTTTA
152661 GTTTTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
AAATTAAATGTTATTTATTTTATA
Found at i:155809 original size:18 final size:19
Alignment explanation
Indices: 155771--155810 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
155761 AAAATCCCAA
*
155771 AAATAAAATGTCATCTCGG
1 AAATAAAATGTCATCTAGG
*
155790 AAATAAATTGTCAT-TAGG
1 AAATAAAATGTCATCTAGG
155808 AAA
1 AAA
155811 CAACACTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (19 bp):
AAATAAAATGTCATCTAGG
Found at i:158518 original size:31 final size:29
Alignment explanation
Indices: 158483--158552 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
158473 ATCTCAAAAT
*
158483 TATACATAAACGATGGTTTAATGTGCAATTG
1 TATACATAAACGATGATTT--TGTGCAATTG
* ** *
158514 TATACATGAACTTTGATTTTGTGCAATTT
1 TATACATAAACGATGATTTTGTGCAATTG
158543 TATACATAAA
1 TATACATAAA
158553 ATTTTGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 18 0.55
31 15 0.45
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (29 bp):
TATACATAAACGATGATTTTGTGCAATTG
Found at i:158563 original size:29 final size:29
Alignment explanation
Indices: 158504--158562 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
158494 GATGGTTTAA
*
158504 TGTGCAATTGTATACATGAACTTTGATTT
1 TGTGCAATTGTATACATAAACTTTGATTT
* *
158533 TGTGCAATTTTATACATAAAATTTTGATTT
1 TGTGCAATTGTATACAT-AAACTTTGATTT
158563 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (29 bp):
TGTGCAATTGTATACATAAACTTTGATTT
Found at i:158771 original size:30 final size:30
Alignment explanation
Indices: 158687--158781 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 30
158677 ATTTCTTTAA
* * * *
158687 ATGTGCATTATTAAATCAAAACTAAAGTTTC
1 ATGTGTATAATTAAATCATAATTAAAG-TTC
* * * *
158718 AAGTATATATTTAAATCATAATTAGAGTTCC
1 ATGTGTATAATTAAATCATAATTAAAGTT-C
*
158749 ATGTGTATAATTACATCA-AATTAAAGTTC
1 ATGTGTATAATTAAATCATAATTAAAGTTC
158778 ATGT
1 ATGT
158782 ATACAATTGC
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
29 5 0.10
30 11 0.22
31 34 0.68
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (30 bp):
ATGTGTATAATTAAATCATAATTAAAGTTC
Found at i:166361 original size:13 final size:14
Alignment explanation
Indices: 166345--166377 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
166335 TTAAATTAAA
166345 TTAAATAATTTT-T
1 TTAAATAATTTTAT
*
166358 TTAAATATTTTTAT
1 TTAAATAATTTTAT
166372 TTAAAT
1 TTAAAT
166378 TTAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTAAATAATTTTAT
Found at i:170212 original size:28 final size:28
Alignment explanation
Indices: 170169--170231 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
170159 AAAATGAGAC
170169 TTTTCGGATACTCGAGGGTAAAATGGTAA
1 TTTT-GGATACTCGAGGGTAAAATGGTAA
*
170198 TTTTGGATTCTCGAGGGTAAAATGGTAA
1 TTTTGGATACTCGAGGGTAAAATGGTAA
170226 TTTTGG
1 TTTTGG
170232 GAAAGTTCAG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 29 0.88
29 4 0.12
ACGTcount: A:0.27, C:0.08, G:0.29, T:0.37
Consensus pattern (28 bp):
TTTTGGATACTCGAGGGTAAAATGGTAA
Found at i:170345 original size:28 final size:27
Alignment explanation
Indices: 170169--170346 Score: 73
Period size: 28 Copynumber: 6.2 Consensus size: 27
170159 AAAATGAGAC
* *
170169 TTTTCGGATACTCGAGGGTAAAATGGTAA
1 TTTT-GGATATTCG-GGGAAAAATGGTAA
*
170198 TTTTGGAT-TCTCGAGGGTAAAATGGTAA
1 TTTTGGATAT-TCG-GGGAAAAATGGTAA
* *
170226 TTTTGGGAAAGTTCAGGGTTAAAAAT-G-AA
1 TTTT-GGATA-TTC-GGG-GAAAAATGGTAA
* *
170255 TTTTTAGACATTCGGGGGAAAAA-GGATAA
1 -TTTTGGATATTC-GGGGAAAAATGG-TAA
*
170284 TTTTGAGAGT-TTCGAGGTCG-AAAATGG-AGT
1 TTTTG-GA-TATTCG-GG--GAAAAATGGTA-A
170314 TTTTGGATATTCGGGGACAAAATGGTAA
1 TTTTGGATATTCGGGGA-AAAATGGTAA
170342 TTTTG
1 TTTTG
170347 AAAGTTTCGC
Statistics
Matches: 116, Mismatches: 12, Indels: 43
0.68 0.07 0.25
Matches are distributed among these distances:
26 1 0.01
27 6 0.05
28 52 0.45
29 29 0.25
30 18 0.16
31 10 0.09
ACGTcount: A:0.31, C:0.07, G:0.29, T:0.33
Consensus pattern (27 bp):
TTTTGGATATTCGGGGAAAAATGGTAA
Found at i:170366 original size:58 final size:57
Alignment explanation
Indices: 170216--170551 Score: 233
Period size: 58 Copynumber: 5.8 Consensus size: 57
170206 TCTCGAGGGT
*
170216 AAAATGGTAATTTTGGGAAAG-TTCAGGGTTAAAAAT-GAATTTTTAGACATTCGGGGGA
1 AAAATGGTAATTTT--GAAAGTTTC-GGGTTAAAAATGGAATTTTTGGACATTCGGGGGA
* ** * *
170274 AAAA-GGATAATTTTGAGAGTTTCGAGGTCGAAAATGGAGTTTTTGGATATTC-GGGGA
1 AAAATGG-TAATTTTGAAAGTTTCG-GGTTAAAAATGGAATTTTTGGACATTCGGGGGA
* ** * *
170331 CAAAATGGTAATTTTGAAAGTTTCGCGATTAAAAATGGAATTTTTGGAGGTTCGAGGGT
1 -AAAATGGTAATTTTGAAAGTTTCG-GGTTAAAAATGGAATTTTTGGACATTCGGGGGA
* * * * *
170390 AAAAT-GTAATTTTTGGAAGTTTTGGGGTCAAAAATTGAATTTTTGGA-AGTTTGGGGGTA
1 AAAATGGTAA-TTTTGAAAG-TTTCGGGTTAAAAATGGAATTTTTGGACA-TTCGGGGG-A
* ** * *
170449 AAAATGG-AATTTTTGGAAGTTTTAAGGTTAAAAATGGAATTTTTGGA-AGTTTGGGGTA
1 AAAATGGTAA-TTTTGAAAG-TTTCGGGTTAAAAATGGAATTTTTGGACA-TTCGGGGGA
* * *
170507 AAATTGG-AATTTTTTAAAGTTTTAGTGG-TAAAAATGGAATTTTTG
1 AAAATGGTAA-TTTTGAAAG-TTTCG-GGTTAAAAATGGAATTTTTG
170552 AAAGTTTTAG
Statistics
Matches: 231, Mismatches: 34, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
56 5 0.02
57 22 0.10
58 142 0.61
59 61 0.26
60 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.36
Consensus pattern (57 bp):
AAAATGGTAATTTTGAAAGTTTCGGGTTAAAAATGGAATTTTTGGACATTCGGGGGA
Found at i:170376 original size:30 final size:29
Alignment explanation
Indices: 170360--170651 Score: 333
Period size: 30 Copynumber: 10.0 Consensus size: 29
170350 GTTTCGCGAT
* *
170360 TAAAAATGGAATTTTTGGAGGTTCGAGGG
1 TAAAAATGGAATTTTTGGAAGTTTGAGGG
*
170389 T-AAAATGTAATTTTTGGAAGTTTTG-GGG
1 TAAAAATGGAATTTTTGGAAG-TTTGAGGG
* *
170417 TCAAAAATTGAATTTTTGGAAGTTTGGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTGAGGG
* *
170447 TAAAAATGGAATTTTTGGAAGTTTTAAGGT
1 TAAAAATGGAATTTTTGGAAG-TTTGAGGG
170477 TAAAAATGGAATTTTTGGAAGTTTG-GGG
1 TAAAAATGGAATTTTTGGAAGTTTGAGGG
* ** *
170505 TAAAATTGGAATTTTTTAAAGTTTTAGTGG
1 TAAAAATGGAATTTTTGGAAGTTTGAG-GG
* *
170535 TAAAAATGGAATTTTTGAAAGTTTTAGTGG
1 TAAAAATGGAATTTTTGGAAGTTTGAG-GG
* *
170565 TAAAAATGGAATTTTTAGAAGTTCGAGGG
1 TAAAAATGGAATTTTTGGAAGTTTGAGGG
*
170594 T-AAAATGGAATTTTTTGAAGTTTGAGGG
1 TAAAAATGGAATTTTTGGAAGTTTGAGGG
*
170622 TCAAAAATGGAATTTTCGGATAGTTT-AGGG
1 T-AAAAATGGAATTTTTGGA-AGTTTGAGGG
170652 ACCTTTAGGG
Statistics
Matches: 228, Mismatches: 25, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
28 70 0.31
29 34 0.15
30 119 0.52
31 5 0.02
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.38
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTGAGGG
Found at i:170557 original size:58 final size:57
Alignment explanation
Indices: 170304--170637 Score: 313
Period size: 58 Copynumber: 5.7 Consensus size: 57
170294 TTCGAGGTCG
* * * *
170304 AAAATGGAGTTTTTGGATA-TTCGGGG-ACAAAATGGTAA-TTTTGAAAG-TTTCGCGATTA
1 AAAATGGAATTTTTGGA-AGTTTGGGGTA-AAAATGG-AATTTTTGAAAGTTTTAG-G-GTA
* * * * *
170362 AAAATGGAATTTTTGGAGGTTCGAGGGT-AAAATGTAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTG-GGGTAAAAATGGAATTTTTGAAAGTTTTAGGGT-A
* * *
170420 AAAATTGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTTAAGGTTA
1 AAAATGGAATTTTTGGAAGTTT-GGGGTAAAAATGGAATTTTTGAAAGTTTT-AGGGTA
* *
170479 AAAATGGAATTTTTGGAAGTTTGGGGTAAAATTGGAATTTTTTAAAGTTTTAGTGGTA
1 AAAATGGAATTTTTGGAAGTTTGGGGTAAAAATGGAATTTTTGAAAGTTTTAG-GGTA
* * **
170537 AAAATGGAATTTTTGAAAGTTTTAGTGGTAAAAATGGAATTTTT-AGAAGTTCGAGGGT-
1 AAAATGGAATTTTTGGAAG-TTT-GGGGTAAAAATGGAATTTTTGA-AAGTTTTAGGGTA
*
170595 AAAATGGAATTTTTTGAAGTTTGAGGGTCAAAAATGGAATTTT
1 AAAATGGAATTTTTGGAAGTTTG-GGGT-AAAAATGGAATTTT
170638 CGGATAGTTT
Statistics
Matches: 236, Mismatches: 25, Indels: 30
0.81 0.09 0.10
Matches are distributed among these distances:
56 1 0.00
57 11 0.05
58 137 0.58
59 59 0.25
60 28 0.12
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (57 bp):
AAAATGGAATTTTTGGAAGTTTGGGGTAAAAATGGAATTTTTGAAAGTTTTAGGGTA
Found at i:170649 original size:88 final size:85
Alignment explanation
Indices: 170360--170651 Score: 354
Period size: 88 Copynumber: 3.3 Consensus size: 85
170350 GTTTCGCGAT
* ** *
170360 TAAAAATGGAATTTTTGGAGGTTCGAGGGT-AAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAA
1 TAAAAATGGAATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGGAAG-TTTGGGGT--AAAA
* * *
170424 TTGAATTTTTGGAAGTTTGGGGG
63 TGGAATTTTTTGAAGTTTGAGGG
*
170447 TAAAAATGGAATTTTTGGAAGTTTTAAGGTTAAAAATGGAATTTTTGGAAGTTTGGGGTAAAATT
1 TAAAAATGGAATTTTTGGAAGTTTT-AGGGTAAAAATGGAATTTTTGGAAGTTTGGGGTAAAA-T
* *
170512 GGAATTTTTTAAAGTTTTAGTGG
64 GGAATTTTTTGAAGTTTGAG-GG
* * *
170535 TAAAAATGGAATTTTTGAAAGTTTTAGTGGTAAAAATGGAATTTTTAGAAGTTCGAGGGTAAAAT
1 TAAAAATGGAATTTTTGGAAGTTTTAG-GGTAAAAATGGAATTTTTGGAAGTTTG-GGGTAAAAT
170600 GGAATTTTTTGAAGTTTGAGGG
64 GGAATTTTTTGAAGTTTGAGGG
*
170622 TCAAAAATGGAATTTTCGGATAG-TTTAGGG
1 T-AAAAATGGAATTTTTGGA-AGTTTTAGGG
170652 ACCTTTAGGG
Statistics
Matches: 179, Mismatches: 18, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
86 4 0.02
87 45 0.25
88 102 0.57
89 28 0.16
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.38
Consensus pattern (85 bp):
TAAAAATGGAATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGGAAGTTTGGGGTAAAATGG
AATTTTTTGAAGTTTGAGGG
Found at i:190973 original size:182 final size:182
Alignment explanation
Indices: 190561--191913 Score: 2249
Period size: 184 Copynumber: 7.4 Consensus size: 182
190551 CTATAACAAA
* * * *
190561 TTACACATCCTGACGTGTTCTAAAATGTATAATTTGCAATATAACTAATTACATAGCTATTATTT
1 TTACACATCCTGACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGCTGTCATTT
* ** *
190626 CCATCTATAAGGACTAAAATGAAAATTAATGAATTTTGGGAGATTTGAGCCTTGCCAGCCTTCTC
66 CCATCTATAAGGACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTC
*
190691 CAGTTTCGCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGC
131 TAGTTT--CCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGC
* *
190745 TTACACATCTTGACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGTTGTCATTT
1 TTACACATCCTGACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGCTGTCATTT
190810 CCATCTATAAGGACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTC
66 CCATCTATAAGGACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTC
* * * *
190875 TAGTTTCCCTTGTTTGTCATGCATCATACTGGATTGGTAGAAAAAGCCATGC
131 TAGTTTCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGC
* * * *
190927 TTACACATCCTGACGAGTTCTAAAATGTATAATTTGCAATATAACAAATTACATAGCTATTATTT
1 TTACACATCCTGACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGCTGTCATTT
* * *
190992 CCATCTATAAGGACTAAAATGAAAATTAACGAATTTTGGGAGATTTGAGCCTTGCCAGCCTTCTC
66 CCATCTATAAGGACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTC
191057 TAGTTTCACCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGC
131 TAGTTT--CCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGC
**
191111 TTACACATCCTGACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAATTGTCATTT
1 TTACACATCCTGACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGCTGTCATTT
191176 CCATCTATAAGGACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTC
66 CCATCTATAAGGACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTC
* *
191241 TAGTTTCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACAAGCCATGC
131 TAGTTTCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGC
* * * *
191293 TTAAACATCCTGACGTGTTCTAAAATGTATAATTTGCAATATAACAAATTACATAGCTATTATTT
1 TTACACATCCTGACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGCTGTCATTT
* * *
191358 CCATCTATAAGGACTAAAATAAAAATTAACGAATTTTGGGAGATTTGAGCCTTGCCAACCTTCTC
66 CCATCTATAAGGACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTC
191423 TAGTTTCGCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGC
131 TAGTTT--CCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGC
* *
191477 TTACACATCCTGACGTGTTCTAAAATATATAATTTGGAATATAACAAATTACATAGTTGTCATTT
1 TTACACATCCTGACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGCTGTCATTT
* *
191542 CCATCTATAAGGACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGTCAACCTTCTC
66 CCATCTATAAGGACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTC
191607 TAGTTTCCCTTGTTTGTCATGCATCATA-TGGATTGGTAGAACACGTCATGC
131 TAGTTTCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGC
*
191658 TTACACATCCTGACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGTTGTCATTT
1 TTACACATCCTGACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGCTGTCATTT
* *
191723 CTATATATAAGGACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTC
66 CCATCTATAAGGACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTC
*
191788 TAGTTTCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGCCATGC
131 TAGTTTCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGC
* * *
191840 TTACACATCCTGACGTGTTCTAAAATGTATAATTTGCAATATAACAAATTATATAGCTGTTATTT
1 TTACACATCCTGACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGCTGTCATTT
191905 CCATCTATA
66 CCATCTATA
191914 CACTCTAGGT
Statistics
Matches: 1093, Mismatches: 71, Indels: 12
0.93 0.06 0.01
Matches are distributed among these distances:
181 176 0.16
182 452 0.41
184 465 0.43
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (182 bp):
TTACACATCCTGACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGCTGTCATTT
CCATCTATAAGGACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTC
TAGTTTCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGC
Found at i:191233 original size:366 final size:365
Alignment explanation
Indices: 190561--191913 Score: 2404
Period size: 366 Copynumber: 3.7 Consensus size: 365
190551 CTATAACAAA
*
190561 TTACACATCCTGACGTGTTCTAAAATGTATAATTTGCAATATAACTAATTACATAGCTATTATTT
1 TTACACATCCTGACGTGTTCTAAAATGTATAATTTGCAATATAACAAATTACATAGCTATTATTT
* *
190626 CCATCTATAAGGACTAAAATGAAAATTAATGAATTTTGGGAGATTTGAGCCTTGCCAGCCTTCTC
66 CCATCTATAAGGACTAAAATAAAAATTAACGAATTTTGGGAGATTTGAGCCTTGCCAGCCTTCTC
* *
190691 CAGTTTCGCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGCTTACACATCTT
131 TAGTTTCGCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGCTTACACATCCT
190756 GACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGTTGTCATTTCCATCTATAAG
196 GACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGTTGTCATTTCCATCTATAAG
190821 GACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTCTAGTTTCCCTT
261 GACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTCTAGTTTCCCTT
*
190886 GTTTGTCATGCATCATACTGGATTGGTAGAAAAAGCCATGC
326 GTTTGTCATGCATCATA-TGGATTGGTAGAACAAGCCATGC
*
190927 TTACACATCCTGACGAGTTCTAAAATGTATAATTTGCAATATAACAAATTACATAGCTATTATTT
1 TTACACATCCTGACGTGTTCTAAAATGTATAATTTGCAATATAACAAATTACATAGCTATTATTT
*
190992 CCATCTATAAGGACTAAAATGAAAATTAACGAATTTTGGGAGATTTGAGCCTTGCCAGCCTTCTC
66 CCATCTATAAGGACTAAAATAAAAATTAACGAATTTTGGGAGATTTGAGCCTTGCCAGCCTTCTC
*
191057 TAGTTTCACCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGCTTACACATCCT
131 TAGTTTCGCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGCTTACACATCCT
*
191122 GACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAATTGTCATTTCCATCTATAAG
196 GACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGTTGTCATTTCCATCTATAAG
191187 GACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTCTAGTTTCCCTT
261 GACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTCTAGTTTCCCTT
191252 GTTTGTCATGCATCATATTGGATTGGTAGAACAAGCCATGC
326 GTTTGTCATGCATCATA-TGGATTGGTAGAACAAGCCATGC
*
191293 TTAAACATCCTGACGTGTTCTAAAATGTATAATTTGCAATATAACAAATTACATAGCTATTATTT
1 TTACACATCCTGACGTGTTCTAAAATGTATAATTTGCAATATAACAAATTACATAGCTATTATTT
*
191358 CCATCTATAAGGACTAAAATAAAAATTAACGAATTTTGGGAGATTTGAGCCTTGCCAACCTTCTC
66 CCATCTATAAGGACTAAAATAAAAATTAACGAATTTTGGGAGATTTGAGCCTTGCCAGCCTTCTC
191423 TAGTTTCGCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGCTTACACATCCT
131 TAGTTTCGCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGCTTACACATCCT
*
191488 GACGTGTTCTAAAATATATAATTTGGAATATAACAAATTACATAGTTGTCATTTCCATCTATAAG
196 GACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGTTGTCATTTCCATCTATAAG
* *
191553 GACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGTCAACCTTCTCTAGTTTCCCTT
261 GACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTCTAGTTTCCCTT
* *
191618 GTTTGTCATGCATCATATGGATTGGTAGAACACGTCATGC
326 GTTTGTCATGCATCATATGGATTGGTAGAACAAGCCATGC
* * * *
191658 TTACACATCCTGACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGTTGTCATTT
1 TTACACATCCTGACGTGTTCTAAAATGTATAATTTGCAATATAACAAATTACATAGCTATTATTT
* * * *
191723 CTATATATAAGGACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTC
66 CCATCTATAAGGACTAAAATAAAAATTAACGAATTTTGGGAGATTTGAGCCTTGCCAGCCTTCTC
*
191788 TAGTTT--CCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGCCATGCTTACACATCCT
131 TAGTTTCGCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGCTTACACATCCT
* * * *
191851 GACGTGTTCTAAAATGTATAATTTGCAATATAACAAATTATATAGCTGTTATTTCCATCTATA
196 GACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGTTGTCATTTCCATCTATA
191914 CACTCTAGGT
Statistics
Matches: 951, Mismatches: 36, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
363 114 0.12
365 147 0.15
366 690 0.73
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (365 bp):
TTACACATCCTGACGTGTTCTAAAATGTATAATTTGCAATATAACAAATTACATAGCTATTATTT
CCATCTATAAGGACTAAAATAAAAATTAACGAATTTTGGGAGATTTGAGCCTTGCCAGCCTTCTC
TAGTTTCGCCCTTGTTTGTCATGCATCATATTGGATTGGTAGAACACGTCATGCTTACACATCCT
GACGTGTTCTAAAATATATAATTTGCAATATAACAAATTACATAGTTGTCATTTCCATCTATAAG
GACTAAAATAAAAATTAACAAATTTTGGGAGATTTGGGCCTTGCCAGCCTTCTCTAGTTTCCCTT
GTTTGTCATGCATCATATGGATTGGTAGAACAAGCCATGC
Found at i:201588 original size:113 final size:113
Alignment explanation
Indices: 201390--201614 Score: 353
Period size: 113 Copynumber: 2.0 Consensus size: 113
201380 TAACTTAAAG
* * ** *
201390 AAACTTAACGGAGAGAAAATATTGAAACTAATGATATTGAATCTTTTGGTTAATGGGTTTTAACG
1 AAACTTAACGGAGAGAAAATATTGAAACCAAAGATATCAAATCTTTTGGTTAATGGGTTTTAAAG
201455 ATTCAAGCTTTGAGACAGATTTGCAACTAAAAATATTGGAATCAAAAT
66 ATTCAAGCTTTGAGACAGATTTGCAACTAAAAATATTGGAATCAAAAT
* *
201503 AAACTTAACGG-GAAGAAGATATTGGAACCAAAGATATCAAATCTTTTGGTTAATGGGTTTTAAA
1 AAACTTAACGGAG-AGAAAATATTGAAACCAAAGATATCAAATCTTTTGGTTAATGGGTTTTAAA
* *
201567 GATTCAAGCTTTGAGACAGATTTGTAACTAAAGATATTGGAATCAAAA
65 GATTCAAGCTTTGAGACAGATTTGCAACTAAAAATATTGGAATCAAAA
201615 GGGAAGAAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
112 1 0.01
113 101 0.99
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.31
Consensus pattern (113 bp):
AAACTTAACGGAGAGAAAATATTGAAACCAAAGATATCAAATCTTTTGGTTAATGGGTTTTAAAG
ATTCAAGCTTTGAGACAGATTTGCAACTAAAAATATTGGAATCAAAAT
Found at i:217413 original size:18 final size:17
Alignment explanation
Indices: 217390--217429 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
217380 TTCTCAACAA
217390 AAAATAGAAAAAAAATTC
1 AAAATA-AAAAAAAATTC
* *
217408 AAAATAATAAAAATTTC
1 AAAATAAAAAAAAATTC
217425 AAAAT
1 AAAAT
217430 TTACAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAATAAAAAAAAATTC
Found at i:221058 original size:14 final size:14
Alignment explanation
Indices: 221025--221058 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
221015 GTTGATGTTG
*
221025 AAAAAATAAAATTT
1 AAAAAATAAAAATT
*
221039 AGAAAATAAAAATT
1 AAAAAATAAAAATT
221053 AAAAAA
1 AAAAAA
221059 GGATATAGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AAAAAATAAAAATT
Found at i:224068 original size:20 final size:21
Alignment explanation
Indices: 224029--224068 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
224019 TAATCTTCTT
* *
224029 TTTTTTTCTTTTTTGCAATTC
1 TTTTTTTCTTTTGTGAAATTC
224050 TTTTTTT-TTTTGTGAAATT
1 TTTTTTTCTTTTGTGAAATT
224069 GAGGGTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.72
Consensus pattern (21 bp):
TTTTTTTCTTTTGTGAAATTC
Found at i:227000 original size:2 final size:2
Alignment explanation
Indices: 226993--227022 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
226983 CAAATCTCAC
226993 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
227023 AGCTATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:227829 original size:22 final size:20
Alignment explanation
Indices: 227804--227851 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
227794 GAACAAAAAC
227804 ATTTTTAAAATAAT-ATAATAT
1 ATTTTT-AAATAATAAT-ATAT
*
227825 AATTTATAAATAATAATATAT
1 -ATTTTTAAATAATAATATAT
227846 ATTTTT
1 ATTTTT
227852 GATAAATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.22
21 11 0.48
22 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTTAAATAATAATATAT
Found at i:227961 original size:2 final size:2
Alignment explanation
Indices: 227954--227980 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
227944 ATAAATAATG
227954 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
227981 GATTCGAAGT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:229655 original size:21 final size:21
Alignment explanation
Indices: 229631--229673 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
229621 AGGTTTAAGG
* *
229631 TCAAGGTTTTGAGTTTTGGAT
1 TCAAGGTTTTAAGTTATGGAT
*
229652 TCAATGTTTTAAGTTATGGAT
1 TCAAGGTTTTAAGTTATGGAT
229673 T
1 T
229674 TGGGCTTCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (21 bp):
TCAAGGTTTTAAGTTATGGAT
Found at i:230362 original size:14 final size:15
Alignment explanation
Indices: 230330--230359 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
230320 TTATCTCTTT
*
230330 ATTTTTATTTTTAAA
1 ATTTTAATTTTTAAA
230345 ATTTTAATTTTTAAA
1 ATTTTAATTTTTAAA
230360 TTTAAGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTAATTTTTAAA
Found at i:233029 original size:23 final size:23
Alignment explanation
Indices: 232990--233036 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
232980 ATTTTTCCTC
*
232990 TAATATTTATATATTTTATAACT
1 TAATATTAATATATTTTATAACT
*
233013 TAATACTTAATAT-TTTTATCACT
1 TAATA-TTAATATATTTTATAACT
233036 T
1 T
233037 CAATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (23 bp):
TAATATTAATATATTTTATAACT
Found at i:233492 original size:2 final size:2
Alignment explanation
Indices: 233485--233513 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
233475 ACAAGATAAC
233485 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
233514 CAACTTTTGC
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:240599 original size:33 final size:33
Alignment explanation
Indices: 240562--240630 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
240552 AAAGATAAAC
*
240562 ATTTATCAAAACGACATAATTTTGTCTTTTCTT
1 ATTTATCAAAACGACACAATTTTGTCTTTTCTT
240595 ATTTATCAAAACGACACAATTTTGTCTTTTCTT
1 ATTTATCAAAACGACACAATTTTGTCTTTTCTT
240628 ATT
1 ATT
240631 CGAATTTTCG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.48
Consensus pattern (33 bp):
ATTTATCAAAACGACACAATTTTGTCTTTTCTT
Found at i:242769 original size:36 final size:36
Alignment explanation
Indices: 242699--242769 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 36
242689 GGACTTAGGC
* * *
242699 TGCGATATTAAATCAACGAGCCTTAATGATATCAGT
1 TGCGATATTAAATCAACGAACCTTAATAAAATCAGT
* * *
242735 TGCGATCTTAAATCAACTAACCTTAGTAAAATCAG
1 TGCGATATTAAATCAACGAACCTTAATAAAATCAG
242770 CTGTGAACAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (36 bp):
TGCGATATTAAATCAACGAACCTTAATAAAATCAGT
Found at i:244256 original size:27 final size:27
Alignment explanation
Indices: 244226--244403 Score: 232
Period size: 27 Copynumber: 6.6 Consensus size: 27
244216 AAATATAAAT
244226 CTACTGAGTCGAGCAAGAAATCTACTG
1 CTACTGAGTCGAGCAAGAAATCTACTG
*
244253 CTACTGAGTCAAGCAAGAAATCTACTG
1 CTACTGAGTCGAGCAAGAAATCTACTG
* * *
244280 CTAGTGAGTCAAACAAGAAATCTACTG
1 CTACTGAGTCGAGCAAGAAATCTACTG
* *
244307 CTTCTGAGTCGACCAAGAAATCTACTG
1 CTACTGAGTCGAGCAAGAAATCTACTG
* * *
244334 CTACTGAGTCAAACAAGAAATCTACAG
1 CTACTGAGTCGAGCAAGAAATCTACTG
* **
244361 CTACTGAGTTGAAG-AAGAAATCTAAAG
1 CTACTGAGTCG-AGCAAGAAATCTACTG
244388 CTACTGAGTCGAGCAA
1 CTACTGAGTCGAGCAA
244404 TAATTTGACC
Statistics
Matches: 133, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
26 2 0.02
27 130 0.98
28 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (27 bp):
CTACTGAGTCGAGCAAGAAATCTACTG
Found at i:244314 original size:81 final size:81
Alignment explanation
Indices: 244214--244403 Score: 272
Period size: 81 Copynumber: 2.3 Consensus size: 81
244204 AAATCACAAG
* * * *
244214 AGAAATATAAATCTACTGAGTCGAGCAAGAAATCTACTGCTACTGAGTCAAGCAAGAAATCTACT
1 AGAAATCTAAAGCTACTGAGTCGAGCAAGAAATCTACTGCTACTGAGTCAAACAAGAAATCTACA
*
244279 GCTAGTGAGTCAAACA
66 GCTACTGAGTCAAACA
** * *
244295 AGAAATCTACTGCTTCTGAGTCGACCAAGAAATCTACTGCTACTGAGTCAAACAAGAAATCTACA
1 AGAAATCTAAAGCTACTGAGTCGAGCAAGAAATCTACTGCTACTGAGTCAAACAAGAAATCTACA
** *
244360 GCTACTGAGTTGAAGA
66 GCTACTGAGTCAAACA
244376 AGAAATCTAAAGCTACTGAGTCGAGCAA
1 AGAAATCTAAAGCTACTGAGTCGAGCAA
244404 TAATTTGACC
Statistics
Matches: 93, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 93 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (81 bp):
AGAAATCTAAAGCTACTGAGTCGAGCAAGAAATCTACTGCTACTGAGTCAAACAAGAAATCTACA
GCTACTGAGTCAAACA
Found at i:246493 original size:51 final size:51
Alignment explanation
Indices: 246416--246560 Score: 202
Period size: 51 Copynumber: 2.8 Consensus size: 51
246406 GTCTCGGTTT
* *
246416 CCAATGGTTTAAAGA-AGAACCCAGGAGAGAAGCGTGCACCTAGGAGAAGTG
1 CCAATGGTTTAAA-ACAGAACCCAGGAGAGAAGCATACACCTAGGAGAAGTG
* *
246467 CCAATGGTTTAAAACAGAACCGAGGAGAGCAGCATACACCTAGGAGAAGTG
1 CCAATGGTTTAAAACAGAACCCAGGAGAGAAGCATACACCTAGGAGAAGTG
* * * *
246518 CCAATGGTTTAAAGCAGAACCCAGAAGAGGATCATACACCTAG
1 CCAATGGTTTAAAACAGAACCCAGGAGAGAAGCATACACCTAG
246561 AAGACGCACT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
50 1 0.01
51 83 0.99
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (51 bp):
CCAATGGTTTAAAACAGAACCCAGGAGAGAAGCATACACCTAGGAGAAGTG
Found at i:253166 original size:21 final size:20
Alignment explanation
Indices: 253120--253167 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
253110 AGGATTTAGA
253120 TATTTTAAAATATTTTTTTC
1 TATTTTAAAATATTTTTTTC
*
253140 GGATTTTAAAATTATATTTTTT-
1 -TATTTTAAAA-TAT-TTTTTTC
253162 TATTTT
1 TATTTT
253168 GAATAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 14 0.61
22 3 0.13
23 6 0.26
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (20 bp):
TATTTTAAAATATTTTTTTC
Found at i:268470 original size:27 final size:27
Alignment explanation
Indices: 268440--268511 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 27
268430 CTAAACATAA
* *
268440 ATAATTTAACAT-ATATTTTTAATATTT
1 ATAATATAACATAATATATTT-ATATTT
* *
268467 ATAATATAATATAATATATTTATTTTT
1 ATAATATAACATAATATATTTATATTT
*
268494 ATAAGATATA-ATAATATA
1 ATAATATA-ACATAATATA
268512 CAAAGGTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
27 30 0.79
28 8 0.21
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (27 bp):
ATAATATAACATAATATATTTATATTT
Found at i:271630 original size:19 final size:19
Alignment explanation
Indices: 271595--271633 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
271585 GAGCAAAAGT
271595 TAAAAATTTTATGTTTTTG
1 TAAAAATTTTATGTTTTTG
*
271614 TAAAACATTTT-TTTTTTTG
1 TAAAA-ATTTTATGTTTTTG
271633 T
1 T
271634 CTCAAAAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (19 bp):
TAAAAATTTTATGTTTTTG
Found at i:273298 original size:6 final size:6
Alignment explanation
Indices: 273287--273334 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
273277 AAGGCCGGCT
* *
273287 TTGTTC TTGTTC TTGTTC TTGATC TTGTTCC ATTGTT- ATGTTC TTGTT
1 TTGTTC TTGTTC TTGTTC TTGTTC TTGTT-C -TTGTTC TTGTTC TTGTT
273335 GTTTACACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 4 0.11
6 25 0.71
7 1 0.03
8 5 0.14
ACGTcount: A:0.06, C:0.15, G:0.17, T:0.62
Consensus pattern (6 bp):
TTGTTC
Found at i:274962 original size:4 final size:4
Alignment explanation
Indices: 274946--274995 Score: 73
Period size: 4 Copynumber: 12.2 Consensus size: 4
274936 ACGAAAAATG
* *
274946 AAGA AAAA AAGA AAGA AAAA AGAGA AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA A-AGA AAGA AAGA AAGA AAGA AAGA AAGA
274995 A
1 A
274996 GGAAGAAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
4 38 0.93
5 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:274964 original size:21 final size:21
Alignment explanation
Indices: 274938--274995 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
274928 GGGGACCAAC
* *
274938 GAAAAATGAAGAAAAAAAGAAA
1 GAAAAAAG-AGAAAGAAAGAAA
274960 GAAAAAAGAGAAAGAAAGAAA
1 GAAAAAAGAGAAAGAAAGAAA
*
274981 GAAAGAA-AGAAAGAA
1 GAAAAAAGAGAAAGAA
274996 GGAAGAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 8 0.24
21 18 0.55
22 7 0.21
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (21 bp):
GAAAAAAGAGAAAGAAAGAAA
Found at i:275011 original size:9 final size:9
Alignment explanation
Indices: 274997--275021 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
274987 AAGAAAGAAG
274997 GAAGAAGGT
1 GAAGAAGGT
275006 GAAGAAGGT
1 GAAGAAGGT
275015 GAAGAAG
1 GAAGAAG
275022 AAGAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (9 bp):
GAAGAAGGT
Done.