Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015205.1 Kokia drynarioides strain JFW-HI SEQ_130249, 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: 458668
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 480 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:245 original size:23 final size:23
Alignment explanation
Indices: 219--291 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
209 TGTGTATGCT
219 TACTGATTTGCGCTATGTGCGCC
1 TACTGATTTGCGCTATGTGCGCC
242 TACTGATTTGCGCTATGTGCGCC
1 TACTGATTTGCGCTATGTGCGCC
* * *
265 TACTGA-TTGCACTTTGTGTGCC
1 TACTGATTTGCGCTATGTGCGCC
287 TACTG
1 TACTG
292 GATTGCACTG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 18 0.38
23 29 0.62
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.37
Consensus pattern (23 bp):
TACTGATTTGCGCTATGTGCGCC
Found at i:299 original size:23 final size:22
Alignment explanation
Indices: 219--314 Score: 102
Period size: 23 Copynumber: 4.2 Consensus size: 22
209 TGTGTATGCT
*
219 TACTGATTTGCGCTATGTGCGCC
1 TACTGA-TTGCACTATGTGCGCC
*
242 TACTGATTTGCGCTATGTGCGCC
1 TACTGA-TTGCACTATGTGCGCC
* *
265 TACTGATTGCACTTTGTGTGCC
1 TACTGATTGCACTATGTGCGCC
* * *
287 TACTGGATTGCACTGTGTGTGCT
1 TACT-GATTGCACTATGTGCGCC
310 TACTG
1 TACTG
315 CTTCCCCAGC
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
22 18 0.27
23 49 0.73
ACGTcount: A:0.14, C:0.23, G:0.26, T:0.38
Consensus pattern (22 bp):
TACTGATTGCACTATGTGCGCC
Found at i:314 original size:45 final size:46
Alignment explanation
Indices: 205--314 Score: 125
Period size: 45 Copynumber: 2.4 Consensus size: 46
195 TTACTGTTCA
* *
205 GCACTGTGTATGCTTACTGATTTGCGCTATGTGCGCCTACTGATTT
1 GCACTGTGTGTGCTTACTGATTTGCACTATGTGCGCCTACTGATTT
* * * * * *
251 GCGCTATGTGCGCCTACTGA-TTGCACTTTGTGTGCCTACTGGA-TT
1 GCACTGTGTGTGCTTACTGATTTGCACTATGTGCGCCTACT-GATTT
296 GCACTGTGTGTGCTTACTG
1 GCACTGTGTGTGCTTACTG
315 CTTCCCCAGC
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
45 34 0.67
46 17 0.33
ACGTcount: A:0.14, C:0.23, G:0.26, T:0.37
Consensus pattern (46 bp):
GCACTGTGTGTGCTTACTGATTTGCACTATGTGCGCCTACTGATTT
Found at i:4702 original size:27 final size:27
Alignment explanation
Indices: 4651--4701 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
4641 TTGGACAAAA
4651 AAACACAAATATCATATTAAAAAAATT
1 AAACACAAATATCATATTAAAAAAATT
*
4678 AAACTCAAATATCA-ATTAAAAAAA
1 AAACACAAATATCATATTAAAAAAA
4702 ACTTTTGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (27 bp):
AAACACAAATATCATATTAAAAAAATT
Found at i:6154 original size:7 final size:7
Alignment explanation
Indices: 6142--6186 Score: 62
Period size: 6 Copynumber: 7.0 Consensus size: 7
6132 ATTATTTGAT
6142 TTAAATA
1 TTAAATA
6149 TT-AA-A
1 TTAAATA
6154 TTAAATA
1 TTAAATA
6161 TTAAA-A
1 TTAAATA
6167 TTAAA-A
1 TTAAATA
6173 TTAAATA
1 TTAAATA
6180 TTAAATA
1 TTAAATA
6187 AAAATAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 3 0.09
6 16 0.46
7 16 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TTAAATA
Found at i:6173 original size:19 final size:19
Alignment explanation
Indices: 6142--6186 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
6132 ATTATTTGAT
6142 TTAAATATTAAATTAAATA
1 TTAAATATTAAATTAAATA
6161 TTAAA-ATTAAAATTAAATA
1 TTAAATATT-AAATTAAATA
6180 TTAAATA
1 TTAAATA
6187 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.12
19 20 0.83
20 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAATATTAAATTAAATA
Found at i:10499 original size:96 final size:96
Alignment explanation
Indices: 10320--10501 Score: 253
Period size: 96 Copynumber: 1.9 Consensus size: 96
10310 AAGGATGTTC
**
10320 GATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGA
* **
10385 TAAGGAAGCATTGTCTCGATTAAGGGTATTT
66 TAAAGAAGCATTACCTCGATTAAGGGTATTT
*
10416 GATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACTCGAA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAG-AA-TCGAA
*
10480 -ATAAAAGAA-TATTACCTCGATT
64 GAT-AAAGAAGCATTACCTCGATT
10502 TTAAAGTTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
95 1 0.01
96 65 0.86
97 10 0.13
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGA
TAAAGAAGCATTACCTCGATTAAGGGTATTT
Found at i:10754 original size:28 final size:28
Alignment explanation
Indices: 10719--10780 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
10709 AAACGAGACT
10719 TTTTGGATACTCG-GAGGCAAAATGGTAA
1 TTTTGGATACTCGAG-GGCAAAATGGTAA
*
10747 TTTTGGATTCTCGAGGGCAAAATGGTAA
1 TTTTGGATACTCGAGGGCAAAATGGTAA
10775 TTTTGG
1 TTTTGG
10781 GAAAATTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.34
Consensus pattern (28 bp):
TTTTGGATACTCGAGGGCAAAATGGTAA
Found at i:10884 original size:29 final size:28
Alignment explanation
Indices: 10852--10957 Score: 88
Period size: 29 Copynumber: 3.6 Consensus size: 28
10842 AATCGAGATA
* *
10852 AAAAATGGAATTTTTGGACATTCGGGGGT
1 AAAAATGGAATTTTTGGA-GTTCAGGGGT
**
10881 AAAAA-GGTAATTTTTGAGAGTTTTGGGGT
1 AAAAATGG-AATTTTTG-GAGTTCAGGGGT
* *
10910 CAAAAATGGAGTTTTTGGAGGTTCAAGGGT
1 -AAAAATGGAATTTTTGGA-GTTCAGGGGT
* *
10940 AAAATTGTAATTTTTGGA
1 AAAAATGGAATTTTTGGA
10958 TAGTTTAGGG
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.03
29 37 0.60
30 21 0.34
31 2 0.03
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAGTTCAGGGGT
Found at i:12050 original size:21 final size:21
Alignment explanation
Indices: 12026--12079 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
12016 AAATATTTAT
*
12026 TTATTATTATTAATAA-ATTCA
1 TTATTATTATTAATAATAAT-A
* *
12047 TTATTACTGTTAATAATAATA
1 TTATTATTATTAATAATAATA
*
12068 ATATTATTATTA
1 TTATTATTATTA
12080 TTATTTATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (21 bp):
TTATTATTATTAATAATAATA
Found at i:12782 original size:6 final size:6
Alignment explanation
Indices: 12773--12829 Score: 57
Period size: 6 Copynumber: 9.7 Consensus size: 6
12763 ACTTGAAGTG
* *
12773 AATTTA AATTTA AA-ATA AATTCA AATTT- -ATTTAAA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT--A AATTTA AATTTA
12820 AATTTA AATT
1 AATTTA AATT
12830 CAATTATAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 4 0.10
5 4 0.10
6 30 0.71
8 4 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:12798 original size:17 final size:17
Alignment explanation
Indices: 12728--12832 Score: 59
Period size: 17 Copynumber: 6.1 Consensus size: 17
12718 AATTTATTTT
* * *
12728 AATTTTAAATACATTTA
1 AATTTAAAATAAATTCA
* *
12745 AATTTAAAGTAAACTCA
1 AATTTAAAATAAATTCA
* * * * *
12762 AACTTGAAGTGAATTTA
1 AATTTAAAATAAATTCA
12779 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTCA
* *
12796 AATTTATTTAA-AAATTTA
1 AATTTA--AAATAAATTCA
*
12814 AATTTAAATTTAAATTCA
1 AATTTAAA-ATAAATTCA
12832 A
1 A
12833 TTATAGTTCA
Statistics
Matches: 64, Mismatches: 20, Indels: 7
0.70 0.22 0.08
Matches are distributed among these distances:
16 1 0.02
17 42 0.66
18 19 0.30
19 2 0.03
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:16102 original size:21 final size:21
Alignment explanation
Indices: 16078--16118 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
16068 AGAGTTTAGA
16078 GGAAG-GAGAAGAGAGGAAAAG
1 GGAAGAGAGAAGA-AGGAAAAG
16099 GGAAGAAGAGAAGAAGGAAA
1 GGAAG-AGAGAAGAAGGAAA
16119 GTGAAGTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (21 bp):
GGAAGAGAGAAGAAGGAAAAG
Found at i:25296 original size:16 final size:16
Alignment explanation
Indices: 25275--25312 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
25265 TATCAAAATA
25275 TAATTTTATTA-TTTAT
1 TAATTTT-TTATTTTAT
25291 TAATTTTTTATTTTAT
1 TAATTTTTTATTTTAT
25307 T-ATTTT
1 TAATTTT
25313 CGAAAGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TAATTTTTTATTTTAT
Found at i:36130 original size:15 final size:17
Alignment explanation
Indices: 36095--36135 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
36085 TAAAAAATAA
*
36095 AAAAATATAAATTATAT
1 AAAAATATAAATTATAC
36112 AAAAATA-AAATT-TAC
1 AAAAATATAAATTATAC
36127 AAAAA-ATAA
1 AAAAATATAA
36136 TTGTAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 9 0.41
16 5 0.23
17 7 0.32
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATATAAATTATAC
Found at i:36131 original size:16 final size:16
Alignment explanation
Indices: 36091--36135 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
36081 ACATTAAAAA
36091 ATAAAAAAATATAAATT
1 ATAAAAAAATA-AAATT
*
36108 ATATAAAAATAAAATT
1 ATAAAAAAATAAAATT
36124 -TACAAAAAATAA
1 ATA-AAAAAATAA
36136 TTGTAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 13 0.52
17 10 0.40
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAAAAATAAAATT
Found at i:36593 original size:15 final size:15
Alignment explanation
Indices: 36573--36643 Score: 51
Period size: 15 Copynumber: 5.0 Consensus size: 15
36563 AAAAGTAATT
36573 TTTAATATTTAAATA
1 TTTAATATTTAAATA
** *
36588 TTTAATATTTTTATT
1 TTTAATATTTAAATA
* * *
36603 TTTTATTTTTTAA-A
1 TTTAATATTTAAATA
36617 TTTAA-ATTT-AATA
1 TTTAATATTTAAATA
*
36630 TTTTAT-TTTAAATA
1 TTTAATATTTAAATA
36644 AACCTAATTA
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
12 2 0.05
13 11 0.26
14 8 0.19
15 22 0.51
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTAATATTTAAATA
Found at i:44002 original size:26 final size:25
Alignment explanation
Indices: 43955--44003 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
43945 AAAAATAGTG
* * *
43955 AAAATATTTTGAAAATTTTATATAA
1 AAAATATTTTCAAAAATATATATAA
43980 AAAATATTTTTCAAAAATATATAT
1 AAAATA-TTTTCAAAAATATATAT
44004 TGTACATTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
AAAATATTTTCAAAAATATATATAA
Found at i:48516 original size:27 final size:24
Alignment explanation
Indices: 48464--48523 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 24
48454 TTTTTTTTTT
*
48464 AAATAT-AAATAATAAAAAATTTA
1 AAATATAAAATAATAAAAAATTAA
*
48487 AAATTTAAAATAATAATGAAAATATAA
1 AAATATAAAATAATAA--AAAAT-TAA
48514 AAATATAAAA
1 AAATATAAAA
48524 ATCTAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 5 0.17
24 9 0.30
26 5 0.17
27 11 0.37
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (24 bp):
AAATATAAAATAATAAAAAATTAA
Found at i:48518 original size:8 final size:8
Alignment explanation
Indices: 48464--48532 Score: 52
Period size: 8 Copynumber: 8.4 Consensus size: 8
48454 TTTTTTTTTT
48464 AAATATAA
1 AAATATAA
48472 ATAATA-AA
1 A-AATATAA
*
48480 AAAT-TTA
1 AAATATAA
*
48487 AAATTTAAA
1 AAATAT-AA
*
48496 ATAATAATGA
1 A-AAT-ATAA
48506 AAATATAA
1 AAATATAA
48514 AAATATAA
1 AAATATAA
*
48522 AAATCTAA
1 AAATATAA
48530 AAA
1 AAA
48533 AATCTATTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
7 8 0.16
8 26 0.53
9 9 0.18
10 5 0.10
11 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (8 bp):
AAATATAA
Found at i:54464 original size:20 final size:21
Alignment explanation
Indices: 54435--54477 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
54425 AAAATAATTT
54435 AAAAAATTTT-AT-ATTTTAA
1 AAAAAATTTTAATAATTTTAA
54454 AAAATAATTTTAATAATTTTAA
1 AAAA-AATTTTAATAATTTTAA
54476 AA
1 AA
54478 TCATTTGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 6 0.29
21 2 0.10
22 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAAAATTTTAATAATTTTAA
Found at i:54471 original size:29 final size:31
Alignment explanation
Indices: 54395--54474 Score: 112
Period size: 29 Copynumber: 2.7 Consensus size: 31
54385 ATTGGAAATT
54395 AAAATAA-TTTAATAATTTTATTATTTCAAA
1 AAAATAATTTTAATAATTTTATTATTTCAAA
* * *
54425 AAAATAATTTAAAAAATTTTA-TATTT-TAA
1 AAAATAATTTTAATAATTTTATTATTTCAAA
54454 AAAATAATTTTAATAATTTTA
1 AAAATAATTTTAATAATTTTA
54475 AAATCATTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 21 0.48
30 12 0.27
31 11 0.25
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (31 bp):
AAAATAATTTTAATAATTTTATTATTTCAAA
Found at i:54478 original size:20 final size:20
Alignment explanation
Indices: 54427--54483 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
54417 ATTTCAAAAA
54427 AATAA-TTTAAAA-AATTTT
1 AATAATTTTAAAATAATTTT
54445 -AT-ATTTTAAAAAATAATTTT
1 AATAATTTT--AAAATAATTTT
*
54465 AATAATTTTAAAATCATTT
1 AATAATTTTAAAATAATTT
54484 GCTGACGTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 1 0.03
17 5 0.16
19 4 0.12
20 15 0.47
21 2 0.06
22 5 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:70256 original size:5 final size:5
Alignment explanation
Indices: 70246--70275 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
70236 GACTATGATG
70246 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
70276 GTTTTGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:71964 original size:17 final size:17
Alignment explanation
Indices: 71931--71999 Score: 77
Period size: 17 Copynumber: 4.0 Consensus size: 17
71921 TTTAAATTAT
*
71931 TTTAGATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
71949 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
71966 TTTCAATTTAGTTTAAA
1 TTTAAATTTATTTTAAA
*
71983 TTTGAAA-TAATTTTAAA
1 TTT-AAATTTATTTTAAA
72000 ACTTAAACTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
17 33 0.75
18 11 0.25
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:73802 original size:29 final size:30
Alignment explanation
Indices: 73720--73862 Score: 118
Period size: 29 Copynumber: 4.8 Consensus size: 30
73710 GGAGGTCCCT
* *
73720 AAATTGTCCAAAAATTATA-TTTTAACCCCC
1 AAATTTTCCAAAAATTATATTTTTGA-CCCC
* **
73750 AAAACTTCTCC-AAAATTCCATTTTTGACCCC
1 -AAA-TTTTCCAAAAATTATATTTTTGACCCC
73781 -AATTTTCCAAAAATTATATTTTT-ACCCTC
1 AAATTTTCCAAAAATTATATTTTTGACCC-C
*
73810 AAA-CTTCCAAAAATTCA-ATTTTTGACCCC
1 AAATTTTCCAAAAATT-ATATTTTTGACCCC
**
73839 AAAACTTCCAAAAATTATCATTTT
1 AAATTTTCCAAAAATTAT-ATTTT
73863 ACCCCCGAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
28 9 0.10
29 37 0.39
30 19 0.20
31 19 0.20
32 10 0.11
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (30 bp):
AAATTTTCCAAAAATTATATTTTTGACCCC
Found at i:73846 original size:30 final size:29
Alignment explanation
Indices: 73746--73854 Score: 123
Period size: 29 Copynumber: 3.7 Consensus size: 29
73736 ATATTTTAAC
* *
73746 CCCCAAAACTTCTCCAAAATTCCATTTTTGA
1 CCCC-AAACTTC-CAAAAATTCAATTTTTGA
**
73777 CCCCAATTTTCCAAAAATT-ATATTTTT-A
1 CCCCAAACTTCCAAAAATTCA-ATTTTTGA
73805 CCCTCAAACTTCCAAAAATTCAATTTTTGA
1 CCC-CAAACTTCCAAAAATTCAATTTTTGA
73835 CCCCAAAACTTCCAAAAATT
1 CCCC-AAACTTCCAAAAATT
73855 ATCATTTTAC
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
28 4 0.06
29 34 0.51
30 25 0.37
31 4 0.06
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (29 bp):
CCCCAAACTTCCAAAAATTCAATTTTTGA
Found at i:73855 original size:59 final size:59
Alignment explanation
Indices: 73726--73927 Score: 207
Period size: 58 Copynumber: 3.4 Consensus size: 59
73716 CCCTAAATTG
* * * **
73726 TCCAAAAATTAT-ATTTTAACCCCCAAAACTTCTCCAAAATTCCATTTTTGACCCCAATTT
1 TCCAAAAATTATCATTTTTACCCCC-AAACTTC-CAAAAATTCAATTTTTGACCCCAAACT
*
73786 TCCAAAAATTAT-ATTTTTACCCTCAAACTTCCAAAAATTCAATTTTTGACCCCAAAACT
1 TCCAAAAATTATCATTTTTACCCCCAAACTTCCAAAAATTCAATTTTTGACCCC-AAACT
* * * * * *
73845 TCCAAAAATTATCA-TTTTACCCCCGAA-TTCTAAAAACTCTATTTTTTATCCCGAAACT
1 TCCAAAAATTATCATTTTTACCCCCAAACTTCCAAAAATTCAATTTTTGA-CCCCAAACT
* *
73903 TTCGAAAATTATCATTTTT-CCCCCA
1 TCCAAAAATTATCATTTTTACCCCCA
73928 GATGTCTAAA
Statistics
Matches: 122, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
58 59 0.48
59 40 0.33
60 23 0.19
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (59 bp):
TCCAAAAATTATCATTTTTACCCCCAAACTTCCAAAAATTCAATTTTTGACCCCAAACT
Found at i:73949 original size:59 final size:59
Alignment explanation
Indices: 73761--74148 Score: 323
Period size: 59 Copynumber: 6.7 Consensus size: 59
73751 AAACTTCTCC
* * ** * ** *
73761 AAAATTCCATTTTTGA-CCCCAATTTTCCAAAAATTAT-ATTTTTACCCTCAAACT-TCCA
1 AAAACTCCATTTTTGATCCCGAAACTTCCAAAAATTATCA-TTTTACCCCCGGA-TGTCTA
* * * * *
73819 AAAATTCAATTTTTGACCCCAAAACTTCCAAAAATTATCATTTTACCCCCGAAT-TCTA
1 AAAACTCCATTTTTGATCCCGAAACTTCCAAAAATTATCATTTTACCCCCGGATGTCTA
* * * * * *
73877 AAAACTCTATTTTTTATCCCGAAACTTTCGAAAATTATCATTTTTCCCCCAGATGTCTA
1 AAAACTCCATTTTTGATCCCGAAACTTCCAAAAATTATCATTTTACCCCCGGATGTCTA
* ** *
73936 AAAACTCCGTTTTTGATCTTGAACCTTCC-AAAATT-T-A---TACCCCCGGATGTCT-
1 AAAACTCCATTTTTGATCCCGAAACTTCCAAAAATTATCATTTTACCCCCGGATGTCTA
** * * *
73988 AAAACTTTATTTTTGATCCTGAATCTTCCAAAAATTACCATTTTACCCCCGGATGTCTA
1 AAAACTCCATTTTTGATCCCGAAACTTCCAAAAATTATCATTTTACCCCCGGATGTCTA
* * * * *
74047 AAAACTCCATTTTTTATCTCGAACCTTCCAAAAATTACCATTTTACCCCCGGATGTCCA
1 AAAACTCCATTTTTGATCCCGAAACTTCCAAAAATTATCATTTTACCCCCGGATGTCTA
** ** *
74106 AAATTTCCATTTTTGA-CCTCGAGCCTTCCAAAAATTACCATTT
1 AAAACTCCATTTTTGATCC-CGAAACTTCCAAAAATTATCATTT
74149 CACCTTGAGA
Statistics
Matches: 275, Mismatches: 44, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
52 24 0.09
53 19 0.07
55 1 0.00
56 1 0.00
57 1 0.00
58 85 0.31
59 143 0.52
60 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (59 bp):
AAAACTCCATTTTTGATCCCGAAACTTCCAAAAATTATCATTTTACCCCCGGATGTCTA
Found at i:74030 original size:111 final size:111
Alignment explanation
Indices: 73858--74148 Score: 311
Period size: 111 Copynumber: 2.6 Consensus size: 111
73848 AAAAATTATC
* * * * * * * *
73858 ATTTTACCCCCGAAT-TCTAAAAACTCTATTTTTTATCCCGAAACTTTCGAAAATTATCATTTTT
1 ATTTTACCCCCGGATGTCT-AAAACTTTATTTTTGATCCTGAAACTTCCAAAAATTACCATTTTA
* *
73922 CCCCCAGATGTCTAAAAACTCCGTTTTTGATCTTGAACCTTCC-AAA
65 CCCCCAGATGTCTAAAAACTCCATTTTTGATCTCGAACCTTCCAAAA
*
73968 ATTTATACCCCCGGATGTCTAAAACTTTATTTTTGATCCTGAATCTTCCAAAAATTACCATTTTA
1 ATTT-TACCCCCGGATGTCTAAAACTTTATTTTTGATCCTGAAACTTCCAAAAATTACCATTTTA
* *
74033 CCCCCGGATGTCTAAAAACTCCATTTTTTATCTCGAACCTTCCAAAAATTA
65 CCCCCAGATGTCTAAAAACTCCATTTTTGATCTCGAACCTTCC--AAA--A
* **
74084 CCATTTTACCCCCGGATGTCCAAAA-TTTCCATTTTTGA-CCTCGAGCCTTCCAAAAATTACCAT
1 --ATTTTACCCCCGGATGTCTAAAACTTT--ATTTTTGATCCT-GAAACTTCCAAAAATTACCAT
74147 TT
61 TT
74149 CACCTTGAGA
Statistics
Matches: 153, Mismatches: 16, Indels: 16
0.83 0.09 0.09
Matches are distributed among these distances:
110 4 0.03
111 86 0.56
112 3 0.02
114 2 0.01
116 4 0.03
117 21 0.14
118 33 0.22
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (111 bp):
ATTTTACCCCCGGATGTCTAAAACTTTATTTTTGATCCTGAAACTTCCAAAAATTACCATTTTAC
CCCCAGATGTCTAAAAACTCCATTTTTGATCTCGAACCTTCCAAAA
Found at i:79856 original size:31 final size:31
Alignment explanation
Indices: 79818--79879 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
79808 TGGGATTGAC
*
79818 TTTGCTTGCTAAAAAATTACTCCCTTTGCCA
1 TTTGCTTGCTAAAAAATTACTCCATTTGCCA
*
79849 TTTGCTTGCTAAAAAATTACTTCATTTGCCA
1 TTTGCTTGCTAAAAAATTACTCCATTTGCCA
79880 CATGTATCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (31 bp):
TTTGCTTGCTAAAAAATTACTCCATTTGCCA
Found at i:80800 original size:305 final size:306
Alignment explanation
Indices: 80209--80932 Score: 891
Period size: 305 Copynumber: 2.3 Consensus size: 306
80199 TATTTTTTCA
*
80209 TTGCAAGATTGGGCTCGTTTAAGCTCGTTAGTGTGATCCGATGCATTCCAACTCCAAGATTTGAT
1 TTGCAAGATTGCGCTCGTTTAAGCTCGTTAGTGTGA--C-ATGCATTCCAACTCCAAGATTTGAT
** * * *
80274 TCCTTGGATCAAGAAGTTCAGGATTTGAAATCTTGATTTCTTTAGATTCTTGAAATATTTACATA
63 TCAATGGACCAAGAAGTTCAAGATTTGAAATCTTGATTTCTTTAGATTATTGAAATATTTACATA
* * * * *
80339 TGGTGAAATTTGATCAAGATTTGATTTCTTGATTTTCTTTAAACCAATAAAGCGAATCTTGATTT
128 TGATGAAATTTGATCAAGATTTGATTTCTTGATTTTCTTTAAACAAAAAAAGCGAATATTGATCT
* * * *
80404 TGTTTTTCTCTTGTATGAGCTTTTAAGGCCTTCGTCACGAACTTTTGGATAGTCAAGCATAATCT
193 CGTTTTTCCCTTGTATGAGCTTGTAAGGCCTTCATCACGAACTTTTGGATAGTCAAGCATAATCT
* *
80469 CTTGAGGAAGTCCCAATGGGCTAATTTTCAATATTTTGAACTTGATTCG
258 CTTGAGGAAGTCCCAATGAGCTAATTTTCAAGATTTTGAACTTGATTCG
* *
80518 TTGCAATATTGCGCTTGTTTAAGCTCGTTAGTGTGA-ATGCATTCCAACTCCAAGATTTGATTCA
1 TTGCAAGATTGCGCTCGTTTAAGCTCGTTAGTGTGACATGCATTCCAACTCCAAGATTTGATTCA
* * *
80582 ATGGGCCAAGAA-TTCCAAGATTT-AGAATCTTGATTT-TTTAGATTATTGGAATCTTTACATAT
66 ATGGACCAAGAAGTT-CAAGATTTGA-AATCTTGATTTCTTTAGATTATTGAAATATTTACATAT
* *
80644 GATGAAATTTGATCAAGATTTGATTTCTTGATTTTCTTTAAATAAAAAAAGTGAATATTGATCTC
129 GATGAAATTTGATCAAGATTTGATTTCTTGATTTTCTTTAAACAAAAAAAGCGAATATTGATCTC
* * **
80709 GTTTTTCCCTTGTATGAGCTTGTAAGGGCCTTCATCATGAACTTTTGGATAGTCACGTTTAATCT
194 GTTTTTCCCTTGTATGAGCTTGTAA-GGCCTTCATCACGAACTTTTGGATAGTCAAGCATAATCT
* * *
80774 CTTGAGGACGTCCCAATGAGCTAATTTTCAAGATTTTGGATTCTTAATTCATTCG
258 CTTGAGGAAGTCCCAATGAGCTAATTTTCAAGATTTT-GA-----ACTTGATTCG
* * * * * * *
80829 TTGCAAGATTGGGCTCGTTTAAGTTTGTCAATGTTATCCAATGCATTCCAACTCCAAGATTTGGT
1 TTGCAAGATTGCGCTCGTTTAAGCTCGTTAGTGTGA--C-ATGCATTCCAACTCCAAGATTT-GA
* * * *
80894 TTC-TTGAACTAAGAATTTCAAGATTTGAAATCTTGATTT
62 TTCAATGGACCAAGAAGTTCAAGATTTGAAATCTTGATTT
80933 TCTTGAAAAT
Statistics
Matches: 355, Mismatches: 44, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
304 106 0.30
305 122 0.34
306 2 0.01
309 33 0.09
311 36 0.10
315 49 0.14
316 7 0.02
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (306 bp):
TTGCAAGATTGCGCTCGTTTAAGCTCGTTAGTGTGACATGCATTCCAACTCCAAGATTTGATTCA
ATGGACCAAGAAGTTCAAGATTTGAAATCTTGATTTCTTTAGATTATTGAAATATTTACATATGA
TGAAATTTGATCAAGATTTGATTTCTTGATTTTCTTTAAACAAAAAAAGCGAATATTGATCTCGT
TTTTCCCTTGTATGAGCTTGTAAGGCCTTCATCACGAACTTTTGGATAGTCAAGCATAATCTCTT
GAGGAAGTCCCAATGAGCTAATTTTCAAGATTTTGAACTTGATTCG
Found at i:84876 original size:28 final size:29
Alignment explanation
Indices: 84843--84897 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
84833 TAACTTTTTG
* *
84843 AATTAATTCATA-TATTATAAAAATATTA
1 AATTAATTAATAGCATTATAAAAATATTA
84871 AATTAATTAATAGCATTATAAAAATAT
1 AATTAATTAATAGCATTATAAAAATAT
84898 AAAAACCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (29 bp):
AATTAATTAATAGCATTATAAAAATATTA
Found at i:95459 original size:14 final size:15
Alignment explanation
Indices: 95404--95460 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
95394 AATTATTGAA
95404 TATAATAAAAAATAT
1 TATAATAAAAAATAT
*
95419 TAATTTATCAATTAAAATAT
1 T-A-TAAT-AA--AAAATAT
95439 TATAATAAAAAATAT
1 TATAATAAAAAATAT
95454 TA-AATAA
1 TATAATAA
95461 TAATTAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
14 5 0.14
15 10 0.29
16 1 0.03
17 5 0.14
18 5 0.14
19 1 0.03
20 8 0.23
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAATAAAAAATAT
Found at i:100690 original size:18 final size:18
Alignment explanation
Indices: 100654--100720 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
100644 CTTATGAAAG
*
100654 AAGAAGAGAA-AAAAAAGA
1 AAGAA-AGAAGAAAAGAGA
*
100672 AAGAAAGAAGAGAAGAGA
1 AAGAAAGAAGAAAAGAGA
*
100690 AGGAAAAGAA-AAAAGAGA
1 AAG-AAAGAAGAAAAGAGA
100708 AAGAAA-AAGAAAA
1 AAGAAAGAAGAAAA
100721 AAAAAATTGC
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
16 2 0.05
17 11 0.27
18 22 0.54
19 6 0.15
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (18 bp):
AAGAAAGAAGAAAAGAGA
Found at i:100690 original size:27 final size:27
Alignment explanation
Indices: 100654--100724 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
100644 CTTATGAAAG
100654 AAGAAGAGAAAAAAAAGAAAGAAAGA-A
1 AAGAAGAGAAAAAAAAGAAA-AAAGAGA
* **
100681 GAGAAGAGAAGGAAAAGAAAAAAGAGA
1 AAGAAGAGAAAAAAAAGAAAAAAGAGA
*
100708 AAGAAAAAGAAAAAAAA
1 AAG-AAGAGAAAAAAAA
100725 AATTGCTTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
26 5 0.14
27 20 0.57
28 10 0.29
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (27 bp):
AAGAAGAGAAAAAAAAGAAAAAAGAGA
Found at i:100705 original size:23 final size:24
Alignment explanation
Indices: 100657--100726 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 24
100647 ATGAAAGAAG
*
100657 AAGAGAAA-AAAAAG-AAAGAAAG
1 AAGAGAAAGAAAAAGAAAAGAAAA
* *
100679 AAGAG-AAGAGAAGGAAAAGAAAA
1 AAGAGAAAGAAAAAGAAAAGAAAA
100702 AAGAGAAAGAAAAAGAAAA-AAAA
1 AAGAGAAAGAAAAAGAAAAGAAAA
100725 AA
1 AA
100727 TTGCTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.05
22 9 0.22
23 18 0.45
24 11 0.28
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (24 bp):
AAGAGAAAGAAAAAGAAAAGAAAA
Found at i:100721 original size:18 final size:19
Alignment explanation
Indices: 100649--100722 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
100639 TTAGACTTAT
*
100649 GAAAGAAGAAGAGAAAAAAAA
1 GAAAGAA-AA-AGAAAAAAGA
*
100670 GAAAG--AAAGAAGAGAAGA
1 GAAAGAAAAAGAA-AAAAGA
*
100688 G-AAGGAAAAGAAAAAAGA
1 GAAAGAAAAAGAAAAAAGA
100706 GAAAGAAAAAGAAAAAA
1 GAAAGAAAAAGAAAAAA
100723 AAAATTGCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
17 7 0.16
18 13 0.29
19 20 0.44
21 5 0.11
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (19 bp):
GAAAGAAAAAGAAAAAAGA
Found at i:100723 original size:9 final size:9
Alignment explanation
Indices: 100660--100724 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
100650 AAAGAAGAAG
100660 AGAAAAAAA
1 AGAAAAAAA
*
100669 AG-AAAGAA
1 AGAAAAAAA
* *
100677 AGAAGAGAAG
1 AGAA-AAAAA
**
100687 AGAAGGAAA
1 AGAAAAAAA
*
100696 AGAAAAAAG
1 AGAAAAAAA
100705 AGAAAGAAAA
1 AGAAA-AAAA
100715 AGAAAAAAA
1 AGAAAAAAA
100724 A
1 A
100725 AATTGCTTAA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
8 7 0.16
9 22 0.51
10 14 0.33
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:102632 original size:19 final size:19
Alignment explanation
Indices: 102608--102648 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
102598 ATCTTTAGAG
102608 ATTCTAATTAAGAGATATT
1 ATTCTAATTAAGAGATATT
102627 ATTCTAATTAAGAGATATT
1 ATTCTAATTAAGAGATATT
102646 ATT
1 ATT
102649 TTCTTAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (19 bp):
ATTCTAATTAAGAGATATT
Found at i:102964 original size:19 final size:19
Alignment explanation
Indices: 102940--102980 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
102930 ATTTTTAGAG
*
102940 ATTCTAATTAGGAGATATT
1 ATTCTAATTAAGAGATATT
102959 ATTCTAATTAAGAGATATT
1 ATTCTAATTAAGAGATATT
102978 ATT
1 ATT
102981 TCCTTAGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (19 bp):
ATTCTAATTAAGAGATATT
Found at i:122514 original size:18 final size:17
Alignment explanation
Indices: 122480--122524 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
122470 ATAATTTTTT
122480 TATAAAAGTACAAAAAATA
1 TATAAAA-TACAAAAAA-A
*
122499 TATAAAATATAAAAAAA
1 TATAAAATACAAAAAAA
122516 TAATAAAAT
1 T-ATAAAAT
122525 TTACTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 15 0.62
19 7 0.29
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (17 bp):
TATAAAATACAAAAAAA
Found at i:128829 original size:17 final size:19
Alignment explanation
Indices: 128796--128830 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
128786 TTCACCATTG
128796 ATTCAACATTCTATGTTTC
1 ATTCAACATTCTATGTTTC
128815 ATTC-ACATT-TATGTTT
1 ATTCAACATTCTATGTTT
128831 ATATCTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (19 bp):
ATTCAACATTCTATGTTTC
Found at i:130546 original size:39 final size:38
Alignment explanation
Indices: 130498--130582 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 38
130488 TTTGTTTACG
*
130498 AAAATGGGTTGGACACAGTACATAAAAAATTAATAAAT
1 AAAATGGGTTGGACACAGTACATAAAAAATAAATAAAT
*
130536 AAAATAGGGTTGGACATAGTACATAAAAAATAAATAAAT
1 AAAAT-GGGTTGGACACAGTACATAAAAAATAAATAAAT
130575 AAAA-GGGT
1 AAAATGGGT
130583 GAACTACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
37 4 0.09
38 5 0.11
39 35 0.80
ACGTcount: A:0.54, C:0.06, G:0.18, T:0.22
Consensus pattern (38 bp):
AAAATGGGTTGGACACAGTACATAAAAAATAAATAAAT
Found at i:133380 original size:1 final size:1
Alignment explanation
Indices: 133374--133410 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
133364 NNNNNNNNNN
133374 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
133411 GGAAAACAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:140906 original size:18 final size:17
Alignment explanation
Indices: 140868--140906 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
140858 TTTACTGTTT
*
140868 TTTTAAAAGAAAAAACG
1 TTTTAAAAGAAAAAACC
*
140885 TTTTAAAATAAAAATACC
1 TTTTAAAAGAAAAA-ACC
140903 TTTT
1 TTTT
140907 TTAGAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (17 bp):
TTTTAAAAGAAAAAACC
Found at i:142638 original size:29 final size:29
Alignment explanation
Indices: 142591--142647 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
142581 TTAACATTAC
* *
142591 AATTTTATTATAATATTTTTAGTAATTTTG
1 AATTTTATAATAATATTTTAAGT-ATTTTG
*
142621 AATTTTA-AATAATCTTTTAAGTATTTT
1 AATTTTATAATAATATTTTAAGTATTTT
142648 ATTGAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.21
29 12 0.50
30 7 0.29
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (29 bp):
AATTTTATAATAATATTTTAAGTATTTTG
Found at i:143892 original size:2 final size:2
Alignment explanation
Indices: 143885--143914 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
143875 AAAATGCCAC
*
143885 GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
143915 ACCTGTCCAT
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:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:150417 original size:17 final size:18
Alignment explanation
Indices: 150380--150424 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
150370 TATAATTTAT
150380 TTATAATTATTTCAATTAAA
1 TTATAATTATTT--ATTAAA
150400 TTATAATTATTT-TTAAA
1 TTATAATTATTTATTAAA
150417 TGTATAAT
1 T-TATAAT
150425 AATTATCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.25
18 6 0.25
20 12 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TTATAATTATTTATTAAA
Found at i:152032 original size:23 final size:20
Alignment explanation
Indices: 152006--152053 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 20
151996 AGACATTTAC
152006 TTGTTAAGTTACACATATTTTCG
1 TTGTTAAGTT--AC-TATTTTCG
**
152029 TTGTTTTGTTACTATTTTCG
1 TTGTTAAGTTACTATTTTCG
152049 TTGTT
1 TTGTT
152054 TCTGGGATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 13 0.57
21 2 0.09
23 8 0.35
ACGTcount: A:0.17, C:0.10, G:0.15, T:0.58
Consensus pattern (20 bp):
TTGTTAAGTTACTATTTTCG
Found at i:153175 original size:23 final size:21
Alignment explanation
Indices: 153133--153180 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
153123 ATTTTCATCA
* *
153133 TTTATTTTTTAAAAAATTAAT
1 TTTATATTTTAAAAAATTAAC
153154 TTTATATTTTAAAAAATTTTAAC
1 TTTATATTTTAAAAAA--TTAAC
153177 TTTA
1 TTTA
153181 AAAAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.65
23 8 0.35
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTATATTTTAAAAAATTAAC
Found at i:153182 original size:16 final size:17
Alignment explanation
Indices: 153151--153185 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
153141 TTAAAAAATT
*
153151 AATTTTATATTTTAAAA
1 AATTTTATACTTTAAAA
153168 AATTTTA-ACTTTAAAA
1 AATTTTATACTTTAAAA
153184 AA
1 AA
153186 ATTAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTTATACTTTAAAA
Found at i:153186 original size:17 final size:17
Alignment explanation
Indices: 153151--153188 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
153141 TTAAAAAATT
*
153151 AATTTTATATTTTAAAA
1 AATTTTATATTTAAAAA
153168 AATTTTA-ACTTTAAAAA
1 AATTTTATA-TTTAAAAA
153185 AATT
1 AATT
153189 AAATTATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTTATATTTAAAAA
Found at i:153373 original size:14 final size:16
Alignment explanation
Indices: 153347--153380 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
153337 TATTGGAATA
153347 AATTTTTTATTTCT-C
1 AATTTTTTATTTCTAC
153362 AATTTTTT-TTTCTAC
1 AATTTTTTATTTCTAC
153377 AATT
1 AATT
153381 AGTTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTTTTTATTTCTAC
Found at i:157102 original size:12 final size:12
Alignment explanation
Indices: 157070--157103 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
157060 GAAGGTTGAA
157070 GAGATGGATGAG
1 GAGATGGATGAG
157082 GATGA-GGATGAG
1 GA-GATGGATGAG
157094 GAGATGGATG
1 GAGATGGATG
157104 TGTAAAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.10
12 16 0.80
13 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.50, T:0.18
Consensus pattern (12 bp):
GAGATGGATGAG
Found at i:157389 original size:27 final size:28
Alignment explanation
Indices: 157358--157423 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
157348 AAACAAATAT
* *
157358 TTTAATTTTTAATTTTAGAAAT-TTAGA
1 TTTAATTTTTAATATTAGAAATGGTAGA
* * *
157385 TTTAATTATTAGTATTATAAATGGGTAGA
1 TTTAATTTTTAATATTAGAAAT-GGTAGA
157414 TTTAATTTTT
1 TTTAATTTTT
157424 TTTGTTTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 18 0.58
29 13 0.42
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.55
Consensus pattern (28 bp):
TTTAATTTTTAATATTAGAAATGGTAGA
Found at i:157776 original size:12 final size:13
Alignment explanation
Indices: 157750--157780 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
157740 TTTTTTAGAT
157750 TTTAATGATTTAA
1 TTTAATGATTTAA
157763 TTTAATGA-TTAA
1 TTTAATGATTTAA
157775 TTTAAT
1 TTTAAT
157781 TAATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (13 bp):
TTTAATGATTTAA
Found at i:163068 original size:2 final size:2
Alignment explanation
Indices: 163061--163088 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
163051 ATTTATTATC
163061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
163089 GAATGATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:169025 original size:20 final size:23
Alignment explanation
Indices: 168982--169028 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
168972 GGCGAATTAA
168982 AAATTATTTATAGAAATTAAAAAT
1 AAATTATTTATAGAAATT-AAAAT
169006 AAATTATTTA-A-AAATT-AAAT
1 AAATTATTTATAGAAATTAAAAT
169026 AAA
1 AAA
169029 AAGTATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.30
22 5 0.22
23 1 0.04
24 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATTATTTATAGAAATTAAAAT
Found at i:169035 original size:22 final size:24
Alignment explanation
Indices: 168979--169035 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
168969 AATGGCGAAT
168979 TAAAAATTATTTATAGAAATTAAA
1 TAAAAATTATTTATAGAAATTAAA
169003 -AATAAATTATTTA-A-AAATTAAA
1 TAA-AAATTATTTATAGAAATTAAA
*
169025 TAAAAAGTATT
1 TAAAAATTATT
169036 AAACTCTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 15 0.50
23 5 0.17
24 10 0.33
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (24 bp):
TAAAAATTATTTATAGAAATTAAA
Found at i:175233 original size:20 final size:19
Alignment explanation
Indices: 175208--175249 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
175198 GGAGGAAAAA
175208 AAAAGAAAAAAAAAAAAGTT
1 AAAAGAAAAAAAAAAAA-TT
* *
175228 AAAAGAACATAAAAAAATT
1 AAAAGAAAAAAAAAAAATT
175247 AAA
1 AAA
175250 TTGCTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAGAAAAAAAAAAAATT
Found at i:177272 original size:27 final size:27
Alignment explanation
Indices: 177214--177266 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
177204 CATTAAAATA
* *
177214 CAAAAACCCTAAAAATAAAAAAGTATT
1 CAAAAACCCTAAAAATAAAAAAATAAT
177241 CAAAAACCCTAAAAA-AGAAAAAATAA
1 CAAAAACCCTAAAAATA-AAAAAATAA
177267 ATAAAATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.68, C:0.15, G:0.04, T:0.13
Consensus pattern (27 bp):
CAAAAACCCTAAAAATAAAAAAATAAT
Found at i:187232 original size:15 final size:15
Alignment explanation
Indices: 187212--187309 Score: 133
Period size: 15 Copynumber: 6.5 Consensus size: 15
187202 GGCAGCATTT
187212 CCGCCATAGCCACCA
1 CCGCCATAGCCACCA
187227 CCGCCATAGCCACCA
1 CCGCCATAGCCACCA
*
187242 CCGCCATAGCCGCCA
1 CCGCCATAGCCACCA
*
187257 CCTCCATAGCCACCA
1 CCGCCATAGCCACCA
*
187272 CCGCCGTAGCCACCA
1 CCGCCATAGCCACCA
* * *
187287 CCTCCATAACCGCCA
1 CCGCCATAGCCACCA
*
187302 CCTCCATA
1 CCGCCATA
187310 ACCGNNNNNN
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 74 1.00
ACGTcount: A:0.24, C:0.53, G:0.12, T:0.10
Consensus pattern (15 bp):
CCGCCATAGCCACCA
Found at i:187310 original size:15 final size:15
Alignment explanation
Indices: 187215--187382 Score: 111
Period size: 15 Copynumber: 11.2 Consensus size: 15
187205 AGCATTTCCG
* *
187215 CCATAGCCACCACCG
1 CCATAGCCGCCACCT
* *
187230 CCATAGCCACCACCG
1 CCATAGCCGCCACCT
187245 CCATAGCCGCCACCT
1 CCATAGCCGCCACCT
* *
187260 CCATAGCCACCACCG
1 CCATAGCCGCCACCT
* *
187275 CCGTAGCCACCACCT
1 CCATAGCCGCCACCT
*
187290 CCATAACCGCCACCT
1 CCATAGCCGCCACCT
* ******
187305 CCATAACCGNNNNNN
1 CCATAGCCGCCACCT
**** *
187320 NNNNAGCCACCACCT
1 CCATAGCCGCCACCT
*
187335 CCATAACCGCCACCT
1 CCATAGCCGCCACCT
* * *
187350 CCATAACCGCCCCCG
1 CCATAGCCGCCACCT
187365 CCATAGCCGCCACCT
1 CCATAGCCGCCACCT
187380 CCA
1 CCA
187383 AAGTTACGAG
Statistics
Matches: 115, Mismatches: 38, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 115 1.00
ACGTcount: A:0.23, C:0.51, G:0.11, T:0.10
Consensus pattern (15 bp):
CCATAGCCGCCACCT
Found at i:187378 original size:45 final size:45
Alignment explanation
Indices: 187215--187382 Score: 165
Period size: 45 Copynumber: 3.7 Consensus size: 45
187205 AGCATTTCCG
* * * *
187215 CCATAGCCACCACCGCCATAGCCACCACCGCCATAGCCGCCACCT
1 CCATAACCGCCACCGCCATAGCCACCACCTCCATAACCGCCACCT
* * *
187260 CCATAGCCACCACCGCCGTAGCCACCACCTCCATAACCGCCACCT
1 CCATAACCGCCACCGCCATAGCCACCACCTCCATAACCGCCACCT
**********
187305 CCATAACCGNNNNNNNNNNAGCCACCACCTCCATAACCGCCACCT
1 CCATAACCGCCACCGCCATAGCCACCACCTCCATAACCGCCACCT
* *
187350 CCATAACCGCCCCCGCCATAGCCGCCACCTCCA
1 CCATAACCGCCACCGCCATAGCCACCACCTCCA
187383 AAGTTACGAG
Statistics
Matches: 97, Mismatches: 26, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
45 97 1.00
ACGTcount: A:0.23, C:0.51, G:0.11, T:0.10
Consensus pattern (45 bp):
CCATAACCGCCACCGCCATAGCCACCACCTCCATAACCGCCACCT
Found at i:195980 original size:17 final size:18
Alignment explanation
Indices: 195958--195993 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
195948 TGATGTCATG
*
195958 ATTTTTTAA-AATGGTAA
1 ATTTTTTAATAATGATAA
195975 ATTTTTTAATAATGATAA
1 ATTTTTTAATAATGATAA
195993 A
1 A
195994 ATTATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (18 bp):
ATTTTTTAATAATGATAA
Found at i:196063 original size:15 final size:16
Alignment explanation
Indices: 196043--196076 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
196033 GATCTTTTAA
196043 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
196058 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
196074 AAA
1 AAA
196077 ATTACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:207553 original size:31 final size:30
Alignment explanation
Indices: 207515--207674 Score: 129
Period size: 31 Copynumber: 5.4 Consensus size: 30
207505 AATTAAAGTA
207515 TAATTTGATACCTGAACTTGACATTTTTTCC
1 TAATTTGATACCTGAACTT-ACATTTTTTCC
*
207546 TAATTTGATACCTAAACTT---TTTTTATCC
1 TAATTTGATACCTGAACTTACATTTTT-TCC
* * *
207574 T-ATTTGGTACCTGAACTTGACACTTTTTCT
1 TAATTTGATACCTGAACTT-ACATTTTTTCC
*
207604 TAATTTGATACCTAAACTT---TTTTTATCC
1 TAATTTGATACCTGAACTTACATTTTT-TCC
* * * *
207632 -AATATGAAACTTGAACTTAACATTTTTTCT
1 TAATTTGATACCTGAACTT-ACATTTTTTCC
*
207662 TAATTTGGTACCT
1 TAATTTGATACCT
207675 AAGCTTTTTT
Statistics
Matches: 99, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
27 38 0.38
28 6 0.06
30 5 0.05
31 50 0.51
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (30 bp):
TAATTTGATACCTGAACTTACATTTTTTCC
Found at i:207587 original size:58 final size:58
Alignment explanation
Indices: 207516--207685 Score: 250
Period size: 58 Copynumber: 2.9 Consensus size: 58
207506 ATTAAAGTAT
*
207516 AATTTGATACCTGAACTTGACATTTTTTCCTAATTTGATACCTAAACTTTTTTTATCC
1 AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTTATCC
* * *
207574 TATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTTATCC
1 AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTTATCC
* * * * * *
207632 AATATGAAACTTGAACTTAACATTTTTTCTTAATTTGGTACCTAAGCTTTTTTT
1 AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTT
207686 TTAGATTCAA
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 99 1.00
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (58 bp):
AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTTATCC
Found at i:211018 original size:31 final size:30
Alignment explanation
Indices: 210975--211046 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
210965 ACAACAAGAG
* * *
210975 GACTATTTTGTCAC-TTTTCGATAATTTTAGT
1 GACTGTTTTGTCACATTTT-GA-AAGTTGAGT
*
211006 GACTGTTTTGTCACATTTTTAAAGTTGAGT
1 GACTGTTTTGTCACATTTTGAAAGTTGAGT
211036 GACTGTTTTGT
1 GACTGTTTTGT
211047 TAAACGTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 18 0.50
31 14 0.39
32 4 0.11
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (30 bp):
GACTGTTTTGTCACATTTTGAAAGTTGAGT
Found at i:214946 original size:13 final size:13
Alignment explanation
Indices: 214920--214953 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
214910 ATCATTAAAG
214920 TTTATTTT-TTTC
1 TTTATTTTCTTTC
*
214932 TTTTTTTTCTTTC
1 TTTATTTTCTTTC
214945 TTTATTTTC
1 TTTATTTTC
214954 ATTTATAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTATTTTCTTTC
Found at i:220448 original size:17 final size:19
Alignment explanation
Indices: 220421--220455 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
220411 AAAAGGAAAA
220421 CAAAAATGAAAC-AAGCTC
1 CAAAAATGAAACTAAGCTC
220439 CAAAAA-GAAACTAAGCT
1 CAAAAATGAAACTAAGCT
220456 TAAGTAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.11
Consensus pattern (19 bp):
CAAAAATGAAACTAAGCTC
Found at i:232644 original size:54 final size:54
Alignment explanation
Indices: 232562--232782 Score: 192
Period size: 54 Copynumber: 4.1 Consensus size: 54
232552 TTCTCTTTAA
* * * ** **
232562 CATTAGTTGTTAGTGTAGCATTGTCTTTTACGACTTCCAAGTTTGAAGGAGAAG
1 CATTAGCTGCTAGTGTAACATTGTCTTTTGTGACAGCCAAGTTTGAAGGAGAAG
* *
232616 CATTAGCTGCTAGTGTAACATTGTCTTTTGTGTCAGCCAAGTTTGAAGGAGAAA
1 CATTAGCTGCTAGTGTAACATTGTCTTTTGTGACAGCCAAGTTTGAAGGAGAAG
* * * * ** * * *
232670 CATTATCTGTTCGTATAACATCATCTTTTGTGACAGACAAGTTCGAAGGA-CAG
1 CATTAGCTGCTAGTGTAACATTGTCTTTTGTGACAGCCAAGTTTGAAGGAGAAG
** ** * **
232723 ACATTAGCTGCTAGTGTAACATCATCTTTTGCAACAGCCAAATTCAAAGGAGAAG
1 -CATTAGCTGCTAGTGTAACATTGTCTTTTGTGACAGCCAAGTTTGAAGGAGAAG
*
232778 GATTA
1 CATTA
232783 ACTTCTTCCA
Statistics
Matches: 134, Mismatches: 31, Indels: 4
0.79 0.18 0.02
Matches are distributed among these distances:
53 1 0.01
54 131 0.98
55 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (54 bp):
CATTAGCTGCTAGTGTAACATTGTCTTTTGTGACAGCCAAGTTTGAAGGAGAAG
Found at i:236418 original size:16 final size:16
Alignment explanation
Indices: 236399--236434 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
236389 TTTAATCAAA
236399 TCGAGTAGTTCGAGTT
1 TCGAGTAGTTCGAGTT
* *
236415 TCGATTTGTTCGAGTT
1 TCGAGTAGTTCGAGTT
236431 TCGA
1 TCGA
236435 TTTATGAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.42
Consensus pattern (16 bp):
TCGAGTAGTTCGAGTT
Found at i:236435 original size:16 final size:16
Alignment explanation
Indices: 236406--236437 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
236396 AAATCGAGTA
236406 GTTCGAGTTTCGATTT
1 GTTCGAGTTTCGATTT
236422 GTTCGAGTTTCGATTT
1 GTTCGAGTTTCGATTT
236438 ATGAATCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
GTTCGAGTTTCGATTT
Found at i:242592 original size:18 final size:17
Alignment explanation
Indices: 242550--242593 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
242540 GCTTTAAGTT
*
242550 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
242567 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
242585 TATAATTTT
1 TATAATTTT
242594 AACCATATTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:242735 original size:17 final size:16
Alignment explanation
Indices: 242715--242748 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
242705 TAAAATTTAT
242715 TAAATATTAAAATAAAA
1 TAAATATTAAAA-AAAA
*
242732 TAAATATTTAAAAAAA
1 TAAATATTAAAAAAAA
242748 T
1 T
242749 CAAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAATATTAAAAAAAA
Found at i:246497 original size:34 final size:34
Alignment explanation
Indices: 246459--246541 Score: 157
Period size: 34 Copynumber: 2.4 Consensus size: 34
246449 TAAATTATAA
246459 ATTCCATTATTTTTTTAATTAATTGGTTCAACCT
1 ATTCCATTATTTTTTTAATTAATTGGTTCAACCT
246493 ATTCCATTATTTTTTTAATTAATTGGTTCAACCT
1 ATTCCATTATTTTTTTAATTAATTGGTTCAACCT
*
246527 ACTCCATTATTTTTT
1 ATTCCATTATTTTTT
246542 CTTCCATTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.54
Consensus pattern (34 bp):
ATTCCATTATTTTTTTAATTAATTGGTTCAACCT
Found at i:249134 original size:22 final size:23
Alignment explanation
Indices: 249106--249164 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 23
249096 TAAATAAGTA
249106 ATTTTTTAAATTAATATTT-ATT
1 ATTTTTTAAATTAATATTTAATT
*
249128 ATTTTTTAATATCAATATTTAATT
1 ATTTTTTAA-ATTAATATTTAATT
*
249152 TTTTATTTAAATT
1 ATTT-TTTAAATT
249165 CAAATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 9 0.29
23 9 0.29
24 8 0.26
25 5 0.16
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTTTTTAAATTAATATTTAATT
Found at i:249156 original size:21 final size:20
Alignment explanation
Indices: 249104--249156 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 20
249094 ATTAAATAAG
*
249104 TAATTTTTTAAATTAATATT
1 TAATTTTTTAAATCAATATT
249124 TATTATTTTTTAATATCAATATT
1 TA--ATTTTTTAA-ATCAATATT
249147 TAATTTTTTA
1 TAATTTTTTA
249157 TTTAAATTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 2 0.07
21 8 0.28
22 9 0.31
23 10 0.34
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATTTTTTAAATCAATATT
Found at i:251147 original size:23 final size:23
Alignment explanation
Indices: 251116--251160 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
251106 TGTAATTTTA
251116 CATACTTGAGTGACAAAAAAAAT
1 CATACTTGAGTGACAAAAAAAAT
*
251139 CATAGTTGAGTGACAAAAAAAA
1 CATACTTGAGTGACAAAAAAAA
251161 AAATCATAAT
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:0.53, C:0.11, G:0.16, T:0.20
Consensus pattern (23 bp):
CATACTTGAGTGACAAAAAAAAT
Found at i:252799 original size:17 final size:17
Alignment explanation
Indices: 252777--252853 Score: 84
Period size: 17 Copynumber: 4.5 Consensus size: 17
252767 CCAACAAGAT
252777 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
**
252794 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
*
252811 TTAAATTTA-CTTAAAA
1 TTAAATTTATTTTAAAA
* *
252827 TTTAAATTTATTATAAAT
1 -TTAAATTTATTTTAAAA
*
252845 TTAAGTTTA
1 TTAAATTTA
252854 AATCTATTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
16 4 0.08
17 41 0.84
18 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:252802 original size:23 final size:23
Alignment explanation
Indices: 252775--252862 Score: 61
Period size: 23 Copynumber: 3.6 Consensus size: 23
252765 GCCCAACAAG
252775 ATTTAAATTTATTTTAAAATTAA
1 ATTTAAATTTATTTTAAAATTAA
* *
252798 ATTT-ATTTTAAGTTTAAATTTACTTAAA
1 ATTTAAATTT-ATTTTAAA---A-TT-AA
* *
252826 ATTTAAATTTATTATAAATTTAA
1 ATTTAAATTTATTTTAAAATTAA
* *
252849 GTTTAAATCTATTT
1 ATTTAAATTTATTT
252863 AAATCAAAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
22 4 0.08
23 24 0.49
24 2 0.04
26 1 0.02
27 2 0.04
28 12 0.24
29 4 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTAAATTTATTTTAAAATTAA
Found at i:252813 original size:6 final size:6
Alignment explanation
Indices: 252775--252856 Score: 57
Period size: 6 Copynumber: 14.3 Consensus size: 6
252765 GCCCAACAAG
* * * *
252775 ATTTAA ATTT-A TTTTAA AATTAA ATTT-A TTTTAA GTTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * *
252820 CTTAAA ATTTAA ATTT-- ATTATAA ATTTAA GTTTAA AT
1 ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA ATTTAA AT
252857 CTATTTAAAT
Statistics
Matches: 57, Mismatches: 13, Indels: 12
0.70 0.16 0.15
Matches are distributed among these distances:
4 3 0.05
5 12 0.21
6 39 0.68
7 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:252819 original size:34 final size:34
Alignment explanation
Indices: 252775--252853 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 34
252765 GCCCAACAAG
* *
252775 ATTTAAATTTATTTTAAAA-TTAAATTTATTTTAA
1 ATTTAAATTTA-CTTAAAATTTAAATTTATTATAA
*
252809 GTTTAAATTTACTTAAAATTTAAATTTATTATAA
1 ATTTAAATTTACTTAAAATTTAAATTTATTATAA
*
252843 ATTTAAGTTTA
1 ATTTAAATTTA
252854 AATCTATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 6 0.15
34 33 0.85
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
ATTTAAATTTACTTAAAATTTAAATTTATTATAA
Found at i:253681 original size:22 final size:21
Alignment explanation
Indices: 253655--253713 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
253645 TGCAAATACA
253655 TATTAAACATATTAAATAATTT
1 TATTAAA-ATATTAAATAATTT
*
253677 TATTAATAATATTGAATAATTT
1 TATTAA-AATATTAAATAATTT
*
253699 TATTAATGATATTAA
1 TATTAA-AATATTAA
253714 TAAGGCTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (21 bp):
TATTAAAATATTAAATAATTT
Found at i:253730 original size:3 final size:3
Alignment explanation
Indices: 253722--253763 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
253712 AATAAGGCTT
*
253722 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
253764 AAAAAAAGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:253758 original size:13 final size:13
Alignment explanation
Indices: 253722--253764 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
253712 AATAAGGCTT
253722 TAAT-AATAAT-A
1 TAATAAATAATAA
253733 TAAT-AATAATAA
1 TAATAAATAATAA
*
253745 TAATAAATAGTAA
1 TAATAAATAATAA
253758 TAATAAA
1 TAATAAA
253765 AAAAAAGCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 10 0.34
12 5 0.17
13 14 0.48
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
TAATAAATAATAA
Found at i:254782 original size:29 final size:28
Alignment explanation
Indices: 254740--255131 Score: 239
Period size: 29 Copynumber: 13.6 Consensus size: 28
254730 AAATTGTTTG
*
254740 AAAATTACATTTTTACCCCTAAACTTCCA
1 AAAATTCCA-TTTTACCCCTAAACTTCCA
* *
254769 AAAATTCCAATTTTACCCCCAAACTTCTA
1 AAAATTCC-ATTTTACCCCTAAACTTCCA
*
254798 AAAATT--A-TTGA-CCCTAAAACTTCCA
1 AAAATTCCATTTTACCCCT-AAACTTCCA
* **
254823 AAAATTTCATTTCGCCCCTAAACTTCCA
1 AAAATTCCATTTTACCCCTAAACTTCCA
*
254851 AAAATTCCATTTTTAACCCCGAAACTTCCA
1 AAAATTCCA-TTTT-ACCCCTAAACTTCCA
* * *
254881 AAAATACCATTTTAACCCTTAAACTTCTA
1 AAAATTCCATTTT-ACCCCTAAACTTCCA
* *
254910 AAAATTCCATTTTAACCTTAAAACTTCCA
1 AAAATTCCATTTTACCCCT-AAACTTCCA
* *
254939 ATAAA-TACATTTTTACCCC-AAACCTCCA
1 A-AAATTCCA-TTTTACCCCTAAACTTCCA
* * * *
254967 AAATTTTCATTTTTGACCCCGAAACTTTCA
1 AAAATTCCA-TTTT-ACCCCTAAACTTCCA
*
254997 AAAATTACCATTTTA-CCCTCGAA-TGTCCA
1 AAAATT-CCATTTTACCCCT-AAACT-TCCA
* * *
255026 AAAACTCCATTTTCAACCTCGAAAC-TCTC-
1 AAAATTCCATTTT--ACCCCTAAACTTC-CA
* ** *
255055 AAAATTACCTTTTTACCCCCGAA-TGTCTA
1 AAAATT-CCATTTTACCCCTAAACT-TCCA
* * *
255084 AAAATTCCATTTTTAACCCCAAAATTTCCC
1 AAAATTCCA-TTTT-ACCCCTAAACTTCCA
255114 AAAATTACCATTTTACCC
1 AAAATT-CCATTTTACCC
255132 TCGAGAATCC
Statistics
Matches: 286, Mismatches: 47, Indels: 60
0.73 0.12 0.15
Matches are distributed among these distances:
24 3 0.01
25 17 0.06
26 1 0.00
27 3 0.01
28 60 0.21
29 117 0.41
30 77 0.27
31 8 0.03
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAATTCCATTTTACCCCTAAACTTCCA
Found at i:254854 original size:53 final size:53
Alignment explanation
Indices: 254756--254856 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
254746 ACATTTTTAC
* *
254756 CCCTAAACTTCCAAAAATTCCAATTTTACCCCCAAACTTCTAAAAATTATTGA
1 CCCTAAACTTCCAAAAATTCCAATTTCACCCCCAAACTTCCAAAAATTATTGA
* * *
254809 CCCTAAAACTTCCAAAAATTTC-ATTTCGCCCCTAAACTTCCAAAAATT
1 CCCT-AAACTTCCAAAAATTCCAATTTCACCCCCAAACTTCCAAAAATT
254857 CCATTTTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 26 0.62
54 16 0.38
ACGTcount: A:0.39, C:0.30, G:0.02, T:0.30
Consensus pattern (53 bp):
CCCTAAACTTCCAAAAATTCCAATTTCACCCCCAAACTTCCAAAAATTATTGA
Found at i:254919 original size:59 final size:58
Alignment explanation
Indices: 254740--255131 Score: 304
Period size: 58 Copynumber: 6.8 Consensus size: 58
254730 AAATTGTTTG
* * * *
254740 AAAATTACATTTTT-ACCCCTAAACTTCCAAAAATTCCAATTTTACCCCCAAACTTCTA
1 AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATACC-ATTTTACCCCCAAACTTCCA
* * ** ** *
254798 AAAATT--A---TTGACCCTAAAACTTCCAAAAATTTCATTTCGCCCCTAAACTTCCA
1 AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATACCATTTTACCCCCAAACTTCCA
* ** *
254851 AAAATTCCATTTTTAACCCCGAAACTTCCAAAAATACCATTTTAACCCTTAAACTTCTA
1 AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATACCATTTT-ACCCCCAAACTTCCA
** *
254910 AAAATTCCA-TTTTAACCTTAAAACTTCCAATAAATA-CATTTTTA-CCCCAAACCTCCA
1 AAAATTCCATTTTTAACCCCAAAACTTCCAA-AAATACCA-TTTTACCCCCAAACTTCCA
* * * * * * *
254967 AAATTTTCATTTTTGACCCCGAAACTTTCAAAAATTACCATTTTACCCTCGAA-TGTCCA
1 AAAATTCCATTTTTAACCCCAAAACTTCCAAAAA-TACCATTTTACCCCCAAACT-TCCA
* * * * * * * *
255026 AAAACTCCATTTTCAACCTCGAAAC-TCTCAAAATTACCTTTTTACCCCCGAA-TGTCTA
1 AAAATTCCATTTTTAACCCCAAAACTTC-CAAAAATACCATTTTACCCCCAAACT-TCCA
* *
255084 AAAATTCCATTTTTAACCCCAAAATTTCCCAAAATTACCATTTTACCC
1 AAAATTCCATTTTTAACCCCAAAACTT-CCAAAAATACCATTTTACCC
255132 TCGAGAATCC
Statistics
Matches: 267, Mismatches: 50, Indels: 33
0.76 0.14 0.09
Matches are distributed among these distances:
53 24 0.09
54 20 0.07
55 1 0.00
56 1 0.00
57 19 0.07
58 117 0.44
59 84 0.31
60 1 0.00
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (58 bp):
AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATACCATTTTACCCCCAAACTTCCA
Found at i:255037 original size:28 final size:29
Alignment explanation
Indices: 254995--255155 Score: 127
Period size: 29 Copynumber: 5.6 Consensus size: 29
254985 CCGAAACTTT
254995 CAAAAATTACCATTTTACCCTCGAATGTC
1 CAAAAATTACCATTTTACCCTCGAATGTC
* * **
255024 CAAAAACT-CCATTTTCAACCTCGAAACTC
1 CAAAAATTACCATTTT-ACCCTCGAATGTC
* *
255053 TC-AAAATTACCTTTTTACCCCCGAATGTC
1 -CAAAAATTACCATTTTACCCTCGAATGTC
* * *
255082 TAAAAATT-CCATTTTTAACCC-CAAAATTTC
1 CAAAAATTACCA-TTTT-ACCCTC-GAATGTC
* *
255112 CCAAAATTACCATTTTACCCTCGAGA-ATC
1 CAAAAATTACCATTTTACCCTCGA-ATGTC
255141 C-AAAATTACCATTTT
1 CAAAAATTACCATTTT
255156 GCCCCCGGGT
Statistics
Matches: 104, Mismatches: 18, Indels: 21
0.73 0.13 0.15
Matches are distributed among these distances:
28 23 0.22
29 50 0.48
30 28 0.27
31 3 0.03
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCTCGAATGTC
Found at i:255169 original size:28 final size:28
Alignment explanation
Indices: 255112--255173 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
255102 CCAAAATTTC
*
255112 CCAAAATTACCATTTTACCCTCGAGAAT
1 CCAAAATTACCATTTTACCCCCGAGAAT
* * *
255140 CCAAAATTACCATTTTGCCCCCGGGTAT
1 CCAAAATTACCATTTTACCCCCGAGAAT
255168 CCAAAA
1 CCAAAA
255174 AGTCTCATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.31, G:0.10, T:0.26
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCCGAGAAT
Found at i:260399 original size:35 final size:35
Alignment explanation
Indices: 260349--260465 Score: 146
Period size: 35 Copynumber: 3.3 Consensus size: 35
260339 ACATTCACAA
* *
260349 GTAAGACCATGGTTGGACCATGACAGTGTATATGC
1 GTAAGACCATGGTTGGACCATGGCAGTGTATATAC
* * * *
260384 GTAAGACCATAGTTGGGCTATGGCAGT-TATTCAAAC
1 GTAAGACCATGGTTGGACCATGGCAGTGTA-T-ATAC
*
260420 GTAAGACCATGGTTGGACCATGGCAATGTATATAC
1 GTAAGACCATGGTTGGACCATGGCAGTGTATATAC
260455 GTAAGACCATG
1 GTAAGACCATG
260466 CTGGGCTATG
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
34 2 0.03
35 38 0.56
36 26 0.38
37 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (35 bp):
GTAAGACCATGGTTGGACCATGGCAGTGTATATAC
Found at i:260458 original size:71 final size:70
Alignment explanation
Indices: 260341--260498 Score: 255
Period size: 71 Copynumber: 2.2 Consensus size: 70
260331 GATAGGTTAC
* * *
260341 ATTCACAA-GTAAGACCATGGTTGGACCATGACAGTGTATATGCGTAAGACCATAGTTGGGCTAT
1 ATTCA-AACGTAAGACCATGGTTGGACCATGACAATGTATATACGTAAGACCAT-GCTGGGCTAT
260405 GGCAGTT
64 GGCAGTT
*
260412 ATTCAAACGTAAGACCATGGTTGGACCATGGCAATGTATATACGTAAGACCATGCTGGGCTATGG
1 ATTCAAACGTAAGACCATGGTTGGACCATGACAATGTATATACGTAAGACCATGCTGGGCTATGG
260477 CAGTT
66 CAGTT
260482 ATTCAAACGTAAGACCA
1 ATTCAAACGTAAGACCA
260499 AAGTGGAGAC
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
70 35 0.43
71 47 0.57
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (70 bp):
ATTCAAACGTAAGACCATGGTTGGACCATGACAATGTATATACGTAAGACCATGCTGGGCTATGG
CAGTT
Found at i:260492 original size:35 final size:36
Alignment explanation
Indices: 260383--260498 Score: 148
Period size: 35 Copynumber: 3.3 Consensus size: 36
260373 AGTGTATATG
260383 CGTAAGACCATAGTTGGGCTATGGCAGTTATTCAAA
1 CGTAAGACCATAGTTGGGCTATGGCAGTTATTCAAA
* * * * *
260419 CGTAAGACCATGGTTGGACCATGGCAATGTA-T-ATA
1 CGTAAGACCATAGTTGGGCTATGGCAGT-TATTCAAA
*
260454 CGTAAGACCAT-GCTGGGCTATGGCAGTTATTCAAA
1 CGTAAGACCATAGTTGGGCTATGGCAGTTATTCAAA
260489 CGTAAGACCA
1 CGTAAGACCA
260499 AAGTGGAGAC
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
33 2 0.03
34 13 0.19
35 25 0.37
36 25 0.37
37 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (36 bp):
CGTAAGACCATAGTTGGGCTATGGCAGTTATTCAAA
Found at i:260545 original size:22 final size:21
Alignment explanation
Indices: 260516--260556 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
260506 GACTTGAACC
* *
260516 TAAAACTTTTACAATATTAAT
1 TAAAACTTTAACAACATTAAT
260537 TAAACACTTTAACAACATTA
1 TAAA-ACTTTAACAACATTA
260557 TCACTCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAACTTTAACAACATTAAT
Found at i:261157 original size:15 final size:16
Alignment explanation
Indices: 261139--261178 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
261129 TATTATTAAT
261139 ATTATTATTGA-TGTC
1 ATTATTATTGATTGTC
261154 ATTATTATT-ATTGTC
1 ATTATTATTGATTGTC
*
261169 ATTAATATTG
1 ATTATTATTG
261179 TTAATGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 21 0.95
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (16 bp):
ATTATTATTGATTGTC
Found at i:261780 original size:6 final size:6
Alignment explanation
Indices: 261761--261851 Score: 57
Period size: 6 Copynumber: 15.5 Consensus size: 6
261751 AAATCCATTC
** **
261761 AAATTT -AA-TT AAATTT AAATTT AAA-GC AAATTT AAATTT AAAAAGAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT --AAATTT
* **
261808 AAATTT AAATTT AACA--T AAATTT AAATTC AAAAAT AAATTT AAA
1 AAATTT AAATTT AA-ATTT AAATTT AAATTT AAATTT AAATTT AAA
261852 CCAATTTAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
4 3 0.05
5 10 0.16
6 45 0.71
7 1 0.02
8 4 0.06
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.37
Consensus pattern (6 bp):
AAATTT
Found at i:261793 original size:17 final size:17
Alignment explanation
Indices: 261761--261851 Score: 87
Period size: 17 Copynumber: 5.2 Consensus size: 17
261751 AAATCCATTC
*
261761 AAATTT-AATTAAATTT
1 AAATTTAAAGTAAATTT
*
261777 AAATTTAAAGCAAATTT
1 AAATTTAAAGTAAATTT
261794 AAATTTAAAAAGATAAATTT
1 AAATTT--AAAG-TAAATTT
261814 AAATTTAACA-TAAATTT
1 AAATTTAA-AGTAAATTT
* *
261831 AAATTCAAAAATAAATTT
1 AAATT-TAAAGTAAATTT
261849 AAA
1 AAA
261852 CCAATTTAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
16 6 0.09
17 27 0.42
18 14 0.22
19 5 0.08
20 12 0.19
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.37
Consensus pattern (17 bp):
AAATTTAAAGTAAATTT
Found at i:261814 original size:37 final size:35
Alignment explanation
Indices: 261770--261851 Score: 112
Period size: 37 Copynumber: 2.3 Consensus size: 35
261760 CAAATTTAAT
261770 TAAATTTAAATTTAA-AGCAAATTTAAATTTAAAAAGA
1 TAAATTTAAATTTAACA-CAAATTTAAA-TTAAAAA-A
* *
261807 TAAATTTAAATTTAACATAAATTTAAATTCAAAAA
1 TAAATTTAAATTTAACACAAATTTAAATTAAAAAA
261842 TAAATTTAAA
1 TAAATTTAAA
261852 CCAATTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 11 0.26
36 6 0.14
37 24 0.57
38 1 0.02
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (35 bp):
TAAATTTAAATTTAACACAAATTTAAATTAAAAAA
Found at i:263042 original size:30 final size:29
Alignment explanation
Indices: 262976--263217 Score: 208
Period size: 30 Copynumber: 8.2 Consensus size: 29
262966 GGAGGTCCCT
* * *
262976 AAACTGTCCAAAAATTACATTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCTCG
*
263006 AAACTTCCAAAAATTCCATTTTTGACCTTG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
* *
263036 AAACTTCCTAAAATTCCATTTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTA-CCTCG
* * *
263066 -AACATCTAAAAATTCAATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
263095 AAACTTCCAAAAATTCCATTTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTTA-CCTCG
* * *
263124 AAACCTCCAAAATTTCCATTTTTTACCTCA
1 AAACTTCCAAAAATTCCA-TTTTTACCTCG
*
263154 AAACATT-CAAAAATTACCATTTTGACCTCG
1 AAAC-TTCCAAAAATT-CCATTTTTACCTCG
* *
263184 -GA-TGTCCAAAAACTT-CATTTTCGACCTCG
1 AAACT-TCCAAAAA-TTCCATTTT-TACCTCG
263213 AAACT
1 AAACT
263218 CTTGAAATTA
Statistics
Matches: 174, Mismatches: 23, Indels: 29
0.77 0.10 0.13
Matches are distributed among these distances:
27 1 0.01
28 7 0.04
29 75 0.43
30 86 0.49
31 5 0.03
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCTCG
Found at i:263078 original size:59 final size:59
Alignment explanation
Indices: 262976--263263 Score: 271
Period size: 59 Copynumber: 4.9 Consensus size: 59
262966 GGAGGTCCCT
* * * *
262976 AAACTGTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTTG
1 AAACT-TCCAAAAATTCCATTTTTACCCTCAAACATCCAAAAATTCCATTTTTGACCTCG
* * * * *
263036 AAACTTCCTAAAATTCCATTTTTACCCCCGAACATCTAAAAATTCAATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACATCCAAAAATTCCATTTTTGACCTCG
* * * *
263095 AAACTTCCAAAAATTCCATTTTTACCCTCAAACCTCCAAAATTTCCATTTTTTACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACATCCAAAAATTCCATTTTTGACCTCG
* ** ** *
263154 AAACATT-CAAAAATTACCATTTTGA-CCTCGGATGTCCAAAAACTT-CATTTTCGACCTCG
1 AAAC-TTCCAAAAATT-CCATTTTTACCCTCAAACATCCAAAAA-TTCCATTTTTGACCTCG
*** * * *
263213 AAAC-TCTTGAAATTACC-TTTTTACCCTCAAATATCTAAAAATTCCCTTTTT
1 AAACTTCCAAAAATT-CCATTTTTACCCTCAAACATCCAAAAATTCCATTTTT
263264 AACCCCAAAT
Statistics
Matches: 187, Mismatches: 35, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
57 8 0.04
58 26 0.14
59 136 0.73
60 17 0.09
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.35
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCAAACATCCAAAAATTCCATTTTTGACCTCG
Found at i:268564 original size:35 final size:35
Alignment explanation
Indices: 268514--268630 Score: 146
Period size: 35 Copynumber: 3.3 Consensus size: 35
268504 ACATTCACAA
* *
268514 GTAAGACCATGGTTGGACCATGACAGTGTATATGC
1 GTAAGACCATGGTTGGACCATGGCAGTGTATATAC
* * * *
268549 GTAAGACCATAGTTGGGCTATGGCAGT-TATTCAAAC
1 GTAAGACCATGGTTGGACCATGGCAGTGTA-T-ATAC
*
268585 GTAAGACCATGGTTGGACCATGGCAATGTATATAC
1 GTAAGACCATGGTTGGACCATGGCAGTGTATATAC
268620 GTAAGACCATG
1 GTAAGACCATG
268631 CTGGGCTATG
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
34 2 0.03
35 38 0.56
36 26 0.38
37 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (35 bp):
GTAAGACCATGGTTGGACCATGGCAGTGTATATAC
Found at i:268623 original size:71 final size:70
Alignment explanation
Indices: 268506--268663 Score: 255
Period size: 71 Copynumber: 2.2 Consensus size: 70
268496 GATAGGTTAC
* * *
268506 ATTCACAA-GTAAGACCATGGTTGGACCATGACAGTGTATATGCGTAAGACCATAGTTGGGCTAT
1 ATTCA-AACGTAAGACCATGGTTGGACCATGACAATGTATATACGTAAGACCAT-GCTGGGCTAT
268570 GGCAGTT
64 GGCAGTT
*
268577 ATTCAAACGTAAGACCATGGTTGGACCATGGCAATGTATATACGTAAGACCATGCTGGGCTATGG
1 ATTCAAACGTAAGACCATGGTTGGACCATGACAATGTATATACGTAAGACCATGCTGGGCTATGG
268642 CAGTT
66 CAGTT
268647 ATTCAAACGTAAGACCA
1 ATTCAAACGTAAGACCA
268664 AAGTGGAGAC
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
70 35 0.43
71 47 0.57
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (70 bp):
ATTCAAACGTAAGACCATGGTTGGACCATGACAATGTATATACGTAAGACCATGCTGGGCTATGG
CAGTT
Found at i:268657 original size:35 final size:36
Alignment explanation
Indices: 268548--268663 Score: 148
Period size: 35 Copynumber: 3.3 Consensus size: 36
268538 AGTGTATATG
268548 CGTAAGACCATAGTTGGGCTATGGCAGTTATTCAAA
1 CGTAAGACCATAGTTGGGCTATGGCAGTTATTCAAA
* * * * *
268584 CGTAAGACCATGGTTGGACCATGGCAATGTA-T-ATA
1 CGTAAGACCATAGTTGGGCTATGGCAGT-TATTCAAA
*
268619 CGTAAGACCAT-GCTGGGCTATGGCAGTTATTCAAA
1 CGTAAGACCATAGTTGGGCTATGGCAGTTATTCAAA
268654 CGTAAGACCA
1 CGTAAGACCA
268664 AAGTGGAGAC
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
33 2 0.03
34 13 0.19
35 25 0.37
36 25 0.37
37 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (36 bp):
CGTAAGACCATAGTTGGGCTATGGCAGTTATTCAAA
Found at i:268710 original size:22 final size:21
Alignment explanation
Indices: 268681--268721 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
268671 GACTTGAACC
* *
268681 TAAAACTTTTACAATATTAAT
1 TAAAACTTTAACAACATTAAT
268702 TAAACACTTTAACAACATTA
1 TAAA-ACTTTAACAACATTA
268722 TCACTCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAACTTTAACAACATTAAT
Found at i:269130 original size:19 final size:19
Alignment explanation
Indices: 269106--269143 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
269096 AACAACGTAG
269106 AAATAA-AATAAGTTAATCA
1 AAATAATAATAA-TTAATCA
*
269125 AAATAATTATAATTAATCA
1 AAATAATAATAATTAATCA
269144 TGAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATAATAATAATTAATCA
Found at i:270100 original size:12 final size:11
Alignment explanation
Indices: 270068--270101 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
270058 CTAAGCCCAC
270068 ACCCAAACCAA
1 ACCCAAACCAA
*
270079 GCCCAAACCAA
1 ACCCAAACCAA
270090 ACCCTAAACCAA
1 ACCC-AAACCAA
270102 TTCAAGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.50, C:0.44, G:0.03, T:0.03
Consensus pattern (11 bp):
ACCCAAACCAA
Found at i:271116 original size:8 final size:8
Alignment explanation
Indices: 271103--271127 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
271093 TAGACTTATT
271103 TTATTTTA
1 TTATTTTA
271111 TTATTTTA
1 TTATTTTA
271119 TTATTTTA
1 TTATTTTA
271127 T
1 T
271128 CTTTAGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTTTA
Found at i:271141 original size:21 final size:21
Alignment explanation
Indices: 271098--271138 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
271088 ATTTTTAGAC
**
271098 TTATTTTATTTTATTATTTTA
1 TTATTTTATTTTAGGATTTTA
271119 TTATTTTATCTTTAGGATTT
1 TTATTTTAT-TTTAGGATTT
271139 ATTTATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (21 bp):
TTATTTTATTTTAGGATTTTA
Found at i:271896 original size:96 final size:96
Alignment explanation
Indices: 271712--271903 Score: 237
Period size: 96 Copynumber: 2.0 Consensus size: 96
271702 TTTTTACAGA
** *
271712 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAATAAGTTAAGGCGCAATTTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAATTTTTCA
*
271777 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* * * * * *
271808 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCGCCTAGTGAGTTAAGGCACAAATTTTTG
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCAC-AATTTTTC
*
271873 A-AACTCGAA-ATAAA-AGAATATTGCCTCGATT
65 AGAA-TCGAAGATAAAGA-AACATTGCCTCGATT
271904 TTTTTAAAGC
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
95 1 0.01
96 68 0.83
97 13 0.16
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAATTTTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:272334 original size:28 final size:29
Alignment explanation
Indices: 272272--272580 Score: 278
Period size: 29 Copynumber: 10.7 Consensus size: 29
272262 GTAAAATGAT
*
272272 AATTTTTGAAAGTTTTGAGGTTAAAAATGG
1 AATTTTTGAAAG-TTTGAGGGTAAAAATGG
* * *
272302 GATTTTTTAAAGTTTG-GGGTAAAATTGG
1 AATTTTTGAAAGTTTGAGGGTAAAAATGG
* *
272330 AATTTTTGGAAGTTTGCGGGTAAAAATGG
1 AATTTTTGAAAGTTTGAGGGTAAAAATGG
* *
272359 ATTTTTTGGAAGTTTTG-GGGTTAAAAATGG
1 AATTTTTGAAAG-TTTGAGGG-TAAAAATGG
* * *
272389 GATTTTTGGAAGTTTGGGGGT-AAAATGG
1 AATTTTTGAAAGTTTGAGGGTAAAAATGG
*
272417 AATTTTTGAAAGTTTGAGGGTAAAATTGG
1 AATTTTTGAAAGTTTGAGGGTAAAAATGG
* *
272446 AATTTTAG-AAGTTTTAGGGTTAAAAAT-G
1 AATTTTTGAAAGTTTGAGGG-TAAAAATGG
* * * *
272474 ACATTTTTGGAAGTTCGAGTGTAAAAAAGG
1 A-ATTTTTGAAAGTTTGAGGGTAAAAATGG
272504 AATTTTT-AGAAGTTTCG-GGGTCAAAAAT-G
1 AATTTTTGA-AAGTTT-GAGGGT-AAAAATGG
* *
272533 AGATTTTTGGAAGTTCGAGGGT-AAAATGG
1 A-ATTTTTGAAAGTTTGAGGGTAAAAATGG
*
272562 AATTTTTGGAAGTTT-AGGG
1 AATTTTTGAAAGTTTGAGGG
272581 ACCTCCGGGG
Statistics
Matches: 233, Mismatches: 30, Indels: 35
0.78 0.10 0.12
Matches are distributed among these distances:
27 4 0.02
28 78 0.33
29 84 0.36
30 67 0.29
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.37
Consensus pattern (29 bp):
AATTTTTGAAAGTTTGAGGGTAAAAATGG
Found at i:272351 original size:29 final size:29
Alignment explanation
Indices: 272272--272580 Score: 312
Period size: 28 Copynumber: 10.7 Consensus size: 29
272262 GTAAAATGAT
* *
272272 AATTTTTGAAAGTTTTGAGGTTAAAAATGG
1 AATTTTTGGAAG-TTTGAGGGTAAAAATGG
* ** *
272302 GATTTTTTAAAGTTTG-GGGTAAAATTGG
1 AATTTTTGGAAGTTTGAGGGTAAAAATGG
*
272330 AATTTTTGGAAGTTTGCGGGTAAAAATGG
1 AATTTTTGGAAGTTTGAGGGTAAAAATGG
*
272359 ATTTTTTGGAAGTTTTG-GGGTTAAAAATGG
1 AATTTTTGGAAG-TTTGAGGG-TAAAAATGG
* *
272389 GATTTTTGGAAGTTTGGGGGT-AAAATGG
1 AATTTTTGGAAGTTTGAGGGTAAAAATGG
* *
272417 AATTTTTGAAAGTTTGAGGGTAAAATTGG
1 AATTTTTGGAAGTTTGAGGGTAAAAATGG
* *
272446 AA-TTTTAGAAGTTTTAGGGTTAAAAAT-G
1 AATTTTTGGAAGTTTGAGGG-TAAAAATGG
* * *
272474 ACATTTTTGGAAGTTCGAGTGTAAAAAAGG
1 A-ATTTTTGGAAGTTTGAGGGTAAAAATGG
*
272504 AATTTTTAGAAGTTTCG-GGGTCAAAAAT-G
1 AATTTTTGGAAGTTT-GAGGGT-AAAAATGG
*
272533 AGATTTTTGGAAGTTCGAGGGT-AAAATGG
1 A-ATTTTTGGAAGTTTGAGGGTAAAAATGG
272562 AATTTTTGGAAGTTT-AGGG
1 AATTTTTGGAAGTTTGAGGG
272581 ACCTCCGGGG
Statistics
Matches: 234, Mismatches: 31, Indels: 31
0.79 0.10 0.10
Matches are distributed among these distances:
27 4 0.02
28 82 0.35
29 75 0.32
30 73 0.31
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.37
Consensus pattern (29 bp):
AATTTTTGGAAGTTTGAGGGTAAAAATGG
Found at i:272372 original size:87 final size:85
Alignment explanation
Indices: 272273--272576 Score: 337
Period size: 87 Copynumber: 3.5 Consensus size: 85
272263 TAAAATGATA
* **
272273 ATTTTTGAAAGTTTTGAGGTTAAAAATGGGATTTTTTAAAGTTTGGGGTAAAATTGGAATTTTTG
1 ATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTGGGGTAAAA-TGGAATTTTTG
272338 GAAGTTTGCGGGTAAAAATGG
65 GAAGTTTGCGGGTAAAAATGG
*
272359 ATTTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGAATTTTT
1 A-TTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTT-GGGGTAAAATGGAATTTTT
* * *
272424 GAAAGTTTGAGGGTAAAATTGG
64 GGAAGTTTGCGGGTAAAAATGG
* * ** * * *
272446 AATTTTAGAAGTTTT-AGGGTTAAAAATGACATTTTTGGAAGTTCGAGTGTAAAAAAGGAATTTT
1 ATTTTTGGAAGTTTTGA-GGTTAAAAATGGGATTTTTGGAAGTTTG-GGGT-AAAATGGAATTTT
*
272510 TAGAAGTTT-CGGGGTCAAAAATGAG
63 TGGAAGTTTGC-GGGT-AAAAATG-G
* * *
272535 ATTTTTGGAAG-TTCGAGGGT-AAAATGGAATTTTTGGAAGTTT
1 ATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTT
272577 AGGGACCTCC
Statistics
Matches: 183, Mismatches: 26, Indels: 17
0.81 0.12 0.08
Matches are distributed among these distances:
85 1 0.01
86 40 0.22
87 111 0.61
88 20 0.11
89 11 0.06
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.38
Consensus pattern (85 bp):
ATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTGGGGTAAAATGGAATTTTTGG
AAGTTTGCGGGTAAAAATGG
Found at i:273355 original size:28 final size:27
Alignment explanation
Indices: 273315--273397 Score: 91
Period size: 26 Copynumber: 3.1 Consensus size: 27
273305 GAGGTAAGAA
* **
273315 AAAACTTCCCTTTTCCCTTTTTTTTTTT
1 AAAACTTCTCTTTTCCC-TTTTTCGTTT
273343 AAAACTTCTCTTTT-CCTTTTTCGTTT
1 AAAACTTCTCTTTTCCCTTTTTCGTTT
* *
273369 -AAACCTCTCTTTTCCCCTTTT-GTTT
1 AAAACTTCTCTTTTCCCTTTTTCGTTT
273394 AAAA
1 AAAA
273398 AAAAATTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
25 16 0.33
26 17 0.35
27 2 0.04
28 13 0.27
ACGTcount: A:0.18, C:0.25, G:0.02, T:0.54
Consensus pattern (27 bp):
AAAACTTCTCTTTTCCCTTTTTCGTTT
Found at i:273372 original size:25 final size:25
Alignment explanation
Indices: 273316--273396 Score: 83
Period size: 25 Copynumber: 3.1 Consensus size: 25
273306 AGGTAAGAAA
* *
273316 AAACTTCCCTTTTCCCTTTTTTTTTTT
1 AAACTTCTCTTTTCCC--TTTTTGTTT
273343 AAAACTTCTCTTTT-CCTTTTTCGTTT
1 -AAACTTCTCTTTTCCCTTTTT-GTTT
* *
273369 AAACCTCTCTTTTCCCCTTTTGTTT
1 AAACTTCTCTTTTCCCTTTTTGTTT
273394 AAA
1 AAA
273397 AAAAAATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
25 24 0.51
26 9 0.19
27 2 0.04
28 12 0.26
ACGTcount: A:0.16, C:0.26, G:0.02, T:0.56
Consensus pattern (25 bp):
AAACTTCTCTTTTCCCTTTTTGTTT
Found at i:273629 original size:13 final size:13
Alignment explanation
Indices: 273606--273644 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
273596 TCTTTTTATT
*
273606 TAATAATTAATAC
1 TAATTATTAATAC
* *
273619 TGATTATTAATAA
1 TAATTATTAATAC
273632 TAATTATTAATAC
1 TAATTATTAATAC
273645 AGTTATCAAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (13 bp):
TAATTATTAATAC
Found at i:274351 original size:17 final size:17
Alignment explanation
Indices: 274331--274373 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
274321 AAATGAATTT
274331 TAAATTTAAATCTATAA
1 TAAATTTAAATCTATAA
*
274348 TAAATTTAAATTTATAA
1 TAAATTTAAATCTATAA
*
274365 TAAACTTAA
1 TAAATTTAA
274374 TTTCAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATCTATAA
Found at i:278282 original size:3 final size:3
Alignment explanation
Indices: 278276--278340 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
278266 TTAAATTGAC
278276 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
278324 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
278341 TTATTATATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.