Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011550.1 Kokia drynarioides strain JFW-HI SEQ_126536, 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: 316084
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 198 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:837 original size:25 final size:24
Alignment explanation
Indices: 774--864 Score: 75
Period size: 25 Copynumber: 3.9 Consensus size: 24
764 AAACACATTA
*
774 TCTTTTTTTCTTTC-TCCTTCTTC
1 TCTTTCTTTCTTTCTTCCTTCTTC
* * *
797 CCCTTCTTCTCCTTCTTCCTTCTTC
1 TCTTTCTT-TCTTTCTTCCTTCTTC
*
822 TTCTTTCTTTCTTTCTTTC-TCTT-
1 -TCTTTCTTTCTTTCTTCCTTCTTC
845 T-TTTCTTTCCTTT-TTCCTTC
1 TCTTTCTTT-CTTTCTTCCTTC
865 AATTTTCGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
21 10 0.19
22 7 0.13
23 5 0.09
24 9 0.17
25 17 0.31
26 6 0.11
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (24 bp):
TCTTTCTTTCTTTCTTCCTTCTTC
Found at i:844 original size:18 final size:17
Alignment explanation
Indices: 774--853 Score: 56
Period size: 18 Copynumber: 4.6 Consensus size: 17
764 AAACACATTA
*
774 TCTTTTTTTCTTTCTCCT
1 TCTTTCTTTC-TTCTCCT
* *
792 TCTTCCCCTTCTTCTCCT
1 TCTT-TCTTTCTTCTCCT
* *
810 TC-TTCCTTCTTCTTCTT
1 TCTTTCTTTCTTC-TCCT
827 TCTTTCTTTCTT-TCTCT
1 TCTTTCTTTCTTCTC-CT
*
844 TTTTTCTTTC
1 TCTTTCTTTC
854 CTTTTTCCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
16 10 0.20
17 16 0.32
18 21 0.42
19 3 0.06
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
TCTTTCTTTCTTCTCCT
Found at i:1682 original size:19 final size:19
Alignment explanation
Indices: 1658--1695 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1648 AAGTTTAGGG
1658 TTAAATTTATTTTTATATC
1 TTAAATTTATTTTTATATC
1677 TTAAATTTATTTTTATATC
1 TTAAATTTATTTTTATATC
1696 GATTTTTTAA
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:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
TTAAATTTATTTTTATATC
Found at i:6962 original size:25 final size:24
Alignment explanation
Indices: 6899--6989 Score: 75
Period size: 25 Copynumber: 3.9 Consensus size: 24
6889 AAACACATTA
*
6899 TCTTTTTTTCTTTC-TCCTTCTTC
1 TCTTTCTTTCTTTCTTCCTTCTTC
* * *
6922 CCCTTCTTCTCCTTCTTCCTTCTTC
1 TCTTTCTT-TCTTTCTTCCTTCTTC
*
6947 TTCTTTCTTTCTTTCTTTC-TCTT-
1 -TCTTTCTTTCTTTCTTCCTTCTTC
6970 T-TTTCTTTCCTTT-TTCCTTC
1 TCTTTCTTT-CTTTCTTCCTTC
6990 AATTTTCGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
21 10 0.19
22 7 0.13
23 5 0.09
24 9 0.17
25 17 0.31
26 6 0.11
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (24 bp):
TCTTTCTTTCTTTCTTCCTTCTTC
Found at i:6969 original size:18 final size:17
Alignment explanation
Indices: 6899--6978 Score: 56
Period size: 18 Copynumber: 4.6 Consensus size: 17
6889 AAACACATTA
*
6899 TCTTTTTTTCTTTCTCCT
1 TCTTTCTTTC-TTCTCCT
* *
6917 TCTTCCCCTTCTTCTCCT
1 TCTT-TCTTTCTTCTCCT
* *
6935 TC-TTCCTTCTTCTTCTT
1 TCTTTCTTTCTTC-TCCT
6952 TCTTTCTTTCTT-TCTCT
1 TCTTTCTTTCTTCTC-CT
*
6969 TTTTTCTTTC
1 TCTTTCTTTC
6979 CTTTTTCCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
16 10 0.20
17 16 0.32
18 21 0.42
19 3 0.06
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
TCTTTCTTTCTTCTCCT
Found at i:7807 original size:19 final size:19
Alignment explanation
Indices: 7783--7820 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
7773 AAGTTTAGGG
7783 TTAAATTTATTTTTATATC
1 TTAAATTTATTTTTATATC
7802 TTAAATTTATTTTTATATC
1 TTAAATTTATTTTTATATC
7821 GATTTTTTAA
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:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
TTAAATTTATTTTTATATC
Found at i:12440 original size:285 final size:286
Alignment explanation
Indices: 11778--12437 Score: 1076
Period size: 285 Copynumber: 2.3 Consensus size: 286
11768 AATTTATTGA
* ** *
11778 GCAATTGAGTGACATAAATATGCTTGTCATCATGGCGGATTAGAGAACTGGCCATTATTAGAACA
1 GCAATTGAGTGGCGGAAATATGCTTGTCATCATGACGGATTAGAGAACTGGCCATTATTAGAACA
11843 CAAATT-TTTTTTTTTGTAAAAAAAATATACAAAAACCGGCTTCCCTCAAGTACGGTTTAATCAA
66 CAAATTATTTTTTTTTGTAAAAAAAATATACAAAAACCGGCTTCCCTCAAGTACGGTTTAATCAA
* * *
11907 CGGTGATGGAGGAGCGGGTAGATTACAAATATAGCATTGAAAAATTTGATCTTCCGCCTATTTAC
131 AGGTGATGGAGGAGCGGGTAGATTACAAATATAGCATTGAAAAATTTGATATTCCGCCCATTTAC
* * * * *
11972 GTAGAAAAATATACAATATTAAGTTAAAATATAAAAATGAAATAAAAAATTAAACAAAATTGAAA
196 GAAAAAAAATACAAAATATTAAGTTAAAATATAAAAATAAAATAAAAAATTAAACAAAATTGAAA
12037 TTTATTGAAAAATATTCTTATCATTT
261 TTTATTGAAAAATATTCTTATCATTT
* * *
12063 GCAATTGAGTGGCGGAAATATGTTTGTCATCATGACAGATTAGAGAACCGGCCATTATTAGAACA
1 GCAATTGAGTGGCGGAAATATGCTTGTCATCATGACGGATTAGAGAACTGGCCATTATTAGAACA
*
12128 CAAATTA-TTTTTTCTGTAAAAAAAATATACAAAAACCGGCTTCCCTCAAGTACGG-TTAGATCA
66 CAAATTATTTTTTTTTGTAAAAAAAATATACAAAAACCGGCTTCCCTCAAGTACGGTTTA-ATCA
* *
12191 AAGGTGATGGAGGAGCGGGTAGATTACGAATATAGCATTGCAAAATTTGATATTCCGCCCATTTA
130 AAGGTGATGGAGGAGCGGGTAGATTACAAATATAGCATTGAAAAATTTGATATTCCGCCCATTTA
12256 CGAAAAAAAATACAAAATATTAAGTTAAAATATAAAAATAAAAT-AAAAATTAAACAAAATTGAA
195 CGAAAAAAAATACAAAATATTAAGTTAAAATATAAAAATAAAATAAAAAATTAAACAAAATTGAA
12320 ATTTATTGAAAAATATTCTTATCATTT
260 ATTTATTGAAAAATATTCTTATCATTT
* * **
12347 GTAATTGAGTGGTGGAAATATGCTTGTCATCATGACGGATTAGAGAACTGATCATTATTAGAACA
1 GCAATTGAGTGGCGGAAATATGCTTGTCATCATGACGGATTAGAGAACTGGCCATTATTAGAACA
12412 CAAATTAATTTTTTTTTGTAAAAAAA
66 CAAATT-ATTTTTTTTTGTAAAAAAA
12438 TATTTTCAAA
Statistics
Matches: 345, Mismatches: 26, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
284 114 0.33
285 215 0.62
286 16 0.05
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.31
Consensus pattern (286 bp):
GCAATTGAGTGGCGGAAATATGCTTGTCATCATGACGGATTAGAGAACTGGCCATTATTAGAACA
CAAATTATTTTTTTTTGTAAAAAAAATATACAAAAACCGGCTTCCCTCAAGTACGGTTTAATCAA
AGGTGATGGAGGAGCGGGTAGATTACAAATATAGCATTGAAAAATTTGATATTCCGCCCATTTAC
GAAAAAAAATACAAAATATTAAGTTAAAATATAAAAATAAAATAAAAAATTAAACAAAATTGAAA
TTTATTGAAAAATATTCTTATCATTT
Found at i:12551 original size:28 final size:28
Alignment explanation
Indices: 12493--12551 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
12483 GAATTTAAAA
* * * **
12493 GAGAATTTGAGAGAATTTTGAGTTATTT
1 GAGAATTTGAGAGAATATGGAGTGAAAT
*
12521 GAGAATTTGAGAGAATATGGTGTGAAAT
1 GAGAATTTGAGAGAATATGGAGTGAAAT
12549 GAG
1 GAG
12552 TAACAAAGGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.34
Consensus pattern (28 bp):
GAGAATTTGAGAGAATATGGAGTGAAAT
Found at i:20077 original size:21 final size:23
Alignment explanation
Indices: 20053--20111 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
20043 AATATCATTT
20053 ATAAATATA-AA-AAAATTAAAA
1 ATAAATATATAATAAAATTAAAA
*
20074 ATAAAAATATATAATAAAATTATAA
1 AT--AAATATATAATAAAATTAAAA
*
20099 ATATATATATAAT
1 ATAAATATATAAT
20112 TGTTTACAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 2 0.06
23 17 0.53
24 2 0.06
25 11 0.34
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
ATAAATATATAATAAAATTAAAA
Found at i:20089 original size:13 final size:12
Alignment explanation
Indices: 20055--20101 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
20045 TATCATTTAT
20055 AAATATAAA-AA
1 AAATATAAATAA
* *
20066 AATTAAAAATAA
1 AAATATAAATAA
20078 AAATATATAATAA
1 AAATATA-AATAA
*
20091 AATTATAAATA
1 AAATATAAATA
20102 TATATATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 7 0.24
12 11 0.38
13 11 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAATATAAATAA
Found at i:20108 original size:25 final size:25
Alignment explanation
Indices: 20052--20109 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
20042 AAATATCATT
*
20052 TATAAATATAAAAAAATTAAAAATA
1 TATATATATAAAAAAATTAAAAATA
* * * *
20077 AAAATATATAATAAAATTATAAATA
1 TATATATATAAAAAAATTAAAAATA
20102 TATATATA
1 TATATATA
20110 ATTGTTTACA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
TATATATATAAAAAAATTAAAAATA
Found at i:20252 original size:29 final size:28
Alignment explanation
Indices: 20187--20252 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
20177 AAAAACCATT
* * *
20187 AAAATATTAGAAATTGAAAATATTGTAA
1 AAAATATTAGAAATCGAAAAGATTATAA
*
20215 AAATTATTAGAAATCGTAAAAGATTATAA
1 AAAATATTAGAAATCG-AAAAGATTATAA
*
20244 AAAAAATTA
1 AAAATATTA
20253 TTTAAAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (28 bp):
AAAATATTAGAAATCGAAAAGATTATAA
Found at i:20688 original size:28 final size:28
Alignment explanation
Indices: 20594--20689 Score: 81
Period size: 28 Copynumber: 3.5 Consensus size: 28
20584 TTTAGTAAAT
* *
20594 TTTTTGTATTTTTATATTATTTTTGTAA
1 TTTTTATAATTTTATATTATTTTTGTAA
* * *
20622 -TCTTATACTTTTCTA-TATTTTT-TAA
1 TTTTTATAATTTTATATTATTTTTGTAA
* * *
20647 TATTTGCATTATTTTATATTTTTTTTGTAA
1 T-TTT-TATAATTTTATATTATTTTTGTAA
20677 TTTTTATAATTTT
1 TTTTTATAATTTT
20690 TAAAAATTTT
Statistics
Matches: 51, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
25 3 0.06
26 7 0.14
27 13 0.25
28 15 0.29
29 9 0.18
30 4 0.08
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (28 bp):
TTTTTATAATTTTATATTATTTTTGTAA
Found at i:20689 original size:19 final size:19
Alignment explanation
Indices: 20591--20690 Score: 57
Period size: 19 Copynumber: 5.4 Consensus size: 19
20581 AATTTTAGTA
20591 AATTTTTTGT-ATTTTTAT
1 AATTTTTTGTAATTTTTAT
* *
20609 ATTATTTTTGTAA-TCTTAT
1 AAT-TTTTTGTAATTTTTAT
* * *
20628 ACTTTTCTAT-ATTTTT-T
1 AATTTTTTGTAATTTTTAT
* * *
20645 AA-TATTTGCATTATTTTAT
1 AATTTTTTGTAAT-TTTTAT
*
20664 ATTTTTTTTGTAATTTTTAT
1 A-ATTTTTTGTAATTTTTAT
20684 AATTTTT
1 AATTTTT
20691 AAAAATTTTC
Statistics
Matches: 57, Mismatches: 17, Indels: 15
0.64 0.19 0.17
Matches are distributed among these distances:
16 3 0.05
17 4 0.07
18 14 0.25
19 21 0.37
20 8 0.14
21 7 0.12
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.68
Consensus pattern (19 bp):
AATTTTTTGTAATTTTTAT
Found at i:21204 original size:29 final size:28
Alignment explanation
Indices: 21156--21234 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 28
21146 TTAAATTAAT
*
21156 AAAA-ATAAAA-TTATACTTTAATCTTTTA
1 AAAATATAAAATTTA-AATTTAAT-TTTTA
21184 AAAATATAAAATTTAAATTTAAATTTTTA
1 AAAATATAAAATTTAAATTT-AATTTTTA
*
21213 AAAATTATAAAATTAAAATTTA
1 AAAA-TATAAAATTTAAATTTA
21235 TTAAAATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 4 0.09
29 20 0.44
30 21 0.47
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (28 bp):
AAAATATAAAATTTAAATTTAATTTTTA
Found at i:21224 original size:8 final size:8
Alignment explanation
Indices: 21182--21253 Score: 53
Period size: 8 Copynumber: 9.2 Consensus size: 8
21172 TTTAATCTTT
*
21182 TAAAAATA
1 TAAAATTA
21190 TAAAATT-
1 TAAAATTA
21197 T-AAATT-
1 TAAAATTA
* *
21203 TAAATTTT
1 TAAAATTA
21211 TAAAAATTA
1 T-AAAATTA
21220 TAAAATTA
1 TAAAATTA
*
21228 -AAATTTA
1 TAAAATTA
*
21235 TTAAAATAA
1 -TAAAATTA
21244 TAAAATTA
1 TAAAATTA
21252 TA
1 TA
21254 TTTTTTATCT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
6 6 0.12
7 11 0.22
8 23 0.45
9 11 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAAAATTA
Found at i:21224 original size:30 final size:29
Alignment explanation
Indices: 21138--21234 Score: 101
Period size: 29 Copynumber: 3.3 Consensus size: 29
21128 TATAATCTTT
**
21138 TTAAAATTTTAAATTAAT-AAAA-ATAAAA
1 TTAAAA-TTTAAATTTTTAAAAATATAAAA
* *
21166 TTATACTTT-AATCTTTTAAAAATATAAAA
1 TTAAAATTTAAAT-TTTTAAAAATATAAAA
*
21195 TTTAAATTTAAATTTTTAAAAATTATAAAA
1 TTAAAATTTAAATTTTTAAAAA-TATAAAA
21225 TTAAAATTTA
1 TTAAAATTTA
21235 TTAAAATAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
26 3 0.05
27 5 0.09
28 8 0.14
29 21 0.38
30 19 0.34
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
TTAAAATTTAAATTTTTAAAAATATAAAA
Found at i:21228 original size:23 final size:22
Alignment explanation
Indices: 21190--21258 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 22
21180 TTTAAAAATA
*
21190 TAAAATT-TAAATTTAAATTTT
1 TAAAATTATAAAATTAAATTTT
21211 TAAAAATTATAAAATTAAAATTTAT
1 T-AAAATTATAAAATT-AAATTT-T
* *
21236 TAAAATAATAAAATTATATTTT
1 TAAAATTATAAAATTAAATTTT
21258 T
1 T
21259 TATCTTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 1 0.02
22 8 0.20
23 11 0.27
24 19 0.46
25 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAAATTATAAAATTAAATTTT
Found at i:31891 original size:15 final size:15
Alignment explanation
Indices: 31867--31896 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31857 CTTCGACTCT
31867 TTGGTCTTAAGAATG
1 TTGGTCTTAAGAATG
*
31882 TTGGTTTTAAGAATG
1 TTGGTCTTAAGAATG
31897 AGTGATTGCC
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:0.27, C:0.03, G:0.27, T:0.43
Consensus pattern (15 bp):
TTGGTCTTAAGAATG
Found at i:47409 original size:12 final size:11
Alignment explanation
Indices: 47365--47413 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
47355 CAGACAATAT
*
47365 AAAAGAAAA-A
1 AAAAGAAAAGG
47375 AAAAGAAAAGG
1 AAAAGAAAAGG
*
47386 ACAAGAAGAAGG
1 AAAAGAA-AAGG
47398 AAAAGGAAAAGG
1 AAAA-GAAAAGG
47410 AAAA
1 AAAA
47414 CCACAAGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 9 0.27
11 6 0.18
12 15 0.45
13 3 0.09
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGG
Found at i:49179 original size:83 final size:82
Alignment explanation
Indices: 49027--49303 Score: 342
Period size: 83 Copynumber: 3.3 Consensus size: 82
49017 AGTTGAGTCA
* * * *
49027 AATCAAGTAAAAAAATTTCGAGTTAGTCGAGTTAGCGAATCCTATTTTAACAACCGAACACAATC
1 AATCGAGTAAAAAAATTTCGAGTTAGTCGAGTTA-CGAATCCTATTTTAGCAACCGAACTCAATT
49092 TGAAATTTTTTCGAATTG
65 TGAAATTTTTTCGAATTG
*
49110 AATCGAGTAAAAAAATTTCGAGTTAGTCGAGTTCACGAATCCTATTTTAGCAACTGAACTCAATT
1 AATCGAGTAAAAAAATTTCGAGTTAGTCGAGTT-ACGAATCCTATTTTAGCAACCGAACTCAATT
**
49175 TGAAATTTTTT-GAATCA
65 TGAAATTTTTTCGAATTG
* * * * *
49192 AATCGAATAAAAAAA-TTCAAGTTAGTCAAGTTGACGAATCCTATTCTAGCAACCAAACTCAATT
1 AATCGAGTAAAAAAATTTCGAGTTAGTCGAGTT-ACGAATCCTATTTTAGCAACCGAACTCAATT
*
49256 TGAAAATTTTTCGAATAGAATCG
65 TGAAATTTTTTCGAAT----T-G
*
49279 AATCGAGTCAAAAAATTTCGAGTTA
1 AATCGAGTAAAAAAATTTCGAGTTA
49304 AGTAAAGTCG
Statistics
Matches: 166, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
81 53 0.32
82 22 0.13
83 69 0.42
84 1 0.01
87 13 0.08
88 8 0.05
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (82 bp):
AATCGAGTAAAAAAATTTCGAGTTAGTCGAGTTACGAATCCTATTTTAGCAACCGAACTCAATTT
GAAATTTTTTCGAATTG
Found at i:50334 original size:6 final size:6
Alignment explanation
Indices: 50311--50345 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
50301 AATTTAACTA
50311 ATAATT ATAAATT A-AATT ATAATT ATAATT ATAAT
1 ATAATT AT-AATT ATAATT ATAATT ATAATT ATAAT
50346 AGTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 17 0.63
7 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATAATT
Found at i:52179 original size:61 final size:58
Alignment explanation
Indices: 52068--52183 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 58
52058 ATCACTTTAA
* * *
52068 TATTAAATTAATATAATACTTATCAATATAAATATTAGATTAAATTTAATATTAAATT
1 TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATT
52126 TATTAAATTAATAGAATACTTATCTACAAGATAAATATTAAATTAAATTTAATATTAA
1 TATTAAATTAATAGAATACTTA--T-CAAGATAAATATTAAATTAAATTTAATATTAA
52184 GATAATTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 21 0.40
60 1 0.02
61 30 0.58
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (58 bp):
TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATT
Found at i:52209 original size:20 final size:18
Alignment explanation
Indices: 52159--52210 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
52149 CTACAAGATA
52159 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
52176 AATATTAAGA-TAATTATTTT
1 AATATTAA-ATTAA-TA-TTT
52196 AATATTAAATTAATA
1 AATATTAAATTAATA
52211 AAGTACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 4 0.13
20 14 0.47
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:53414 original size:43 final size:43
Alignment explanation
Indices: 53361--53446 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
53351 TGGTGAGATC
53361 GACGATGAGGAATGAGAGGGAAGG-GAGAGGTGGTGGGGGTTGG
1 GACGATGAGGAATGAGAGGGAAGGCG-GAGGTGGTGGGGGTTGG
* * * * *
53404 GACGGTGAGGAGTGGGAGGGAAGGCGGCGGTGTTGGGGGTTGG
1 GACGATGAGGAATGAGAGGGAAGGCGGAGGTGGTGGGGGTTGG
53447 ACACAATGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
43 36 0.97
44 1 0.03
ACGTcount: A:0.20, C:0.05, G:0.60, T:0.15
Consensus pattern (43 bp):
GACGATGAGGAATGAGAGGGAAGGCGGAGGTGGTGGGGGTTGG
Found at i:56891 original size:36 final size:36
Alignment explanation
Indices: 56849--56949 Score: 166
Period size: 36 Copynumber: 2.8 Consensus size: 36
56839 TGGTAACAAG
*
56849 CATGACCTTCAGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTCGGGTCAACAGGGAGTAAAATGAGCAT
56885 CATGACCTTCGGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTCGGGTCAACAGGGAGTAAAATGAGCAT
* * *
56921 CATGACCATCGGGTCAATAGGGAATAAAA
1 CATGACCTTCGGGTCAACAGGGAGTAAAA
56950 CGAATAATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.19
Consensus pattern (36 bp):
CATGACCTTCGGGTCAACAGGGAGTAAAATGAGCAT
Found at i:57755 original size:21 final size:22
Alignment explanation
Indices: 57726--57768 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
57716 TACTGATTAT
*
57726 AAATAGGTTTAA-TAAAGGTTAA
1 AAATAGG-TTAATTAAAGCTTAA
57748 AAAT-GGTTAATTAAAGCTTAA
1 AAATAGGTTAATTAAAGCTTAA
57769 TGATAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (22 bp):
AAATAGGTTAATTAAAGCTTAA
Found at i:61558 original size:16 final size:18
Alignment explanation
Indices: 61527--61561 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
61517 TCAAATTAAA
61527 TCCTATTTTTATTTTATT
1 TCCTATTTTTATTTTATT
61545 TCCT-TTTTTA-TTTATT
1 TCCTATTTTTATTTTATT
61561 T
1 T
61562 AATATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 6 0.35
18 4 0.24
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (18 bp):
TCCTATTTTTATTTTATT
Found at i:65769 original size:18 final size:19
Alignment explanation
Indices: 65725--65769 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
65715 TGGAGAAAAA
*
65725 AAGTGCATCCTAACACATT
1 AAGTGTATCCTAACACATT
* *
65744 AGGTGTATCCTGACACA-T
1 AAGTGTATCCTAACACATT
65762 AAGTGTAT
1 AAGTGTAT
65770 AATCTTGTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (19 bp):
AAGTGTATCCTAACACATT
Found at i:68054 original size:2 final size:2
Alignment explanation
Indices: 68047--68090 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
68037 TGATTTATTT
*
68047 AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
68089 AC
1 AC
68091 TTATACATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:68649 original size:3 final size:3
Alignment explanation
Indices: 68641--68674 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
68631 GAAATGAAGA
68641 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
68675 TTTATCATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:84918 original size:30 final size:33
Alignment explanation
Indices: 84862--84922 Score: 92
Period size: 30 Copynumber: 1.9 Consensus size: 33
84852 CCTTAAAAGC
84862 TAAAAAAATAAATTTGGGCTCCTTAAAAGTTGG
1 TAAAAAAATAAATTTGGGCTCCTTAAAAGTTGG
*
84895 TAAAAAAA-AAATTT-GGC-CTTTAAAAGTT
1 TAAAAAAATAAATTTGGGCTCCTTAAAAGTT
84923 TAAAAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.37
31 3 0.11
32 6 0.22
33 8 0.30
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (33 bp):
TAAAAAAATAAATTTGGGCTCCTTAAAAGTTGG
Found at i:85340 original size:21 final size:21
Alignment explanation
Indices: 85316--85359 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
85306 AGTTGGTGTT
*
85316 TTGAGTCAACTAGTCATCAAC
1 TTGAGTCAACTAGCCATCAAC
85337 TTGAGTCAACTAGCCATCAAC
1 TTGAGTCAACTAGCCATCAAC
85358 TT
1 TT
85360 CATTAGGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (21 bp):
TTGAGTCAACTAGCCATCAAC
Found at i:85727 original size:15 final size:16
Alignment explanation
Indices: 85697--85733 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
85687 GAAACTTAGG
85697 TTAATATTTAATAAATA
1 TTAA-ATTTAATAAATA
85714 TTAAATTT-ATAAATA
1 TTAAATTTAATAAATA
85729 -TAAAT
1 TTAAAT
85734 AAACTTAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 7 0.35
16 4 0.20
17 4 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAATTTAATAAATA
Found at i:86842 original size:12 final size:12
Alignment explanation
Indices: 86827--86857 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
86817 TATATATATA
86827 TATATATGAAAT
1 TATATATGAAAT
86839 TATATATGAAAT
1 TATATATGAAAT
*
86851 TAGATAT
1 TATATAT
86858 TATTGTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (12 bp):
TATATATGAAAT
Found at i:86845 original size:2 final size:2
Alignment explanation
Indices: 86797--86833 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
86787 GTTCTCTTTT
86797 TA TA TA TA 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 TA TA TA TA T
86834 GAAATTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:89287 original size:7 final size:6
Alignment explanation
Indices: 89255--89286 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
89245 ATTTGAGTTG
89255 TCTTTGT TCTTTT TCTTTT TCTTTT TCTTTT T
1 TCTTT-T TCTTTT TCTTTT TCTTTT TCTTTT T
89287 TGGGAGGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:94344 original size:18 final size:18
Alignment explanation
Indices: 94321--94356 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
94311 ATCGTATAAT
94321 ATTTAAATATATAATTTA
1 ATTTAAATATATAATTTA
* *
94339 ATTTAAATTTATAGTTTA
1 ATTTAAATATATAATTTA
94357 TTTTTGGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAATTTA
Found at i:98909 original size:37 final size:37
Alignment explanation
Indices: 98836--98923 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 37
98826 TCAAACTTAA
*
98836 GGTTAAAAAAATTGGAGCAAAAAAGAAAAATATTTAG
1 GGTTAAAAAAATTGGAGCAAAAAAGAAAAACATTTAG
* * * * *
98873 GGTTAGAAAGATTTGAGCCAAAAAGAAAAACGTTTAG
1 GGTTAAAAAAATTGGAGCAAAAAAGAAAAACATTTAG
*
98910 AGTTTTAAAAAAAT
1 -G-GTTAAAAAAAT
98924 AAATAATATT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
37 31 0.77
38 1 0.03
39 8 0.20
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.24
Consensus pattern (37 bp):
GGTTAAAAAAATTGGAGCAAAAAAGAAAAACATTTAG
Found at i:100849 original size:27 final size:27
Alignment explanation
Indices: 100818--100957 Score: 183
Period size: 27 Copynumber: 5.2 Consensus size: 27
100808 GCAATAACAT
* * *
100818 AATATCACTCATTTGAGCCAAATACAG
1 AATATCACTCATTCGAGCCAGATACAA
* *
100845 AATATCACTCATTCGAGCCAAATACAG
1 AATATCACTCATTCGAGCCAGATACAA
* *
100872 AATGTCGCTCATTCGAGCCAGATACAA
1 AATATCACTCATTCGAGCCAGATACAA
*
100899 AATATCTCTCATTCGAGCCAGATACAA
1 AATATCACTCATTCGAGCCAGATACAA
* *
100926 AATAT-GCTCATTCGAGCTAGATACAA
1 AATATCACTCATTCGAGCCAGATACAA
100952 AATATC
1 AATATC
100958 GCTTATTGCT
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
26 24 0.23
27 79 0.77
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.25
Consensus pattern (27 bp):
AATATCACTCATTCGAGCCAGATACAA
Found at i:101997 original size:61 final size:61
Alignment explanation
Indices: 101932--102054 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
101922 TACGATTTAG
101932 TCTCTTTTTCTTAATTAATTATCTAAACGATAAACTTTCATTACCAAATTTTAATACGAGA
1 TCTCTTTTTCTTAATTAATTATCTAAACGATAAACTTTCATTACCAAATTTTAATACGAGA
101993 TCTCTTTTTCTTAATTAATTATCTAAACGATAAACTTTCATTACCAAATTTTAATACGAGA
1 TCTCTTTTTCTTAATTAATTATCTAAACGATAAACTTTCATTACCAAATTTTAATACGAGA
102054 T
1 T
102055 TAATGACCTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (61 bp):
TCTCTTTTTCTTAATTAATTATCTAAACGATAAACTTTCATTACCAAATTTTAATACGAGA
Found at i:104897 original size:60 final size:60
Alignment explanation
Indices: 104736--104935 Score: 178
Period size: 59 Copynumber: 3.4 Consensus size: 60
104726 TAAATTTGAT
* * * * * *
104736 AAAGTTGGTGCCAACTATCTAGAGGCCAAAA-ACCTAGGAAAAAAATTTCT--AGT-TTCGAA
1 AAAGGTGGTGCCGACCATCTATAGGCCAAAACA-CTA-GAAAAAAATTTCTCAAGTACT-AAA
* *
104795 AAAGGTGGTGTCGACCATCTATAGGCCAAAACACTAGGAAAAAATTTCTCAAGTACTAAA
1 AAAGGTGGTGCCGACCATCTATAGGCCAAAACACTAGAAAAAAATTTCTCAAGTACTAAA
* ** * **
104855 AAAGGT-GTGCCTACCATCTATAGTTCAAAATACTAGAAAAAAACTTTCTCAAGT-CTTGGA
1 AAAGGTGGTGCCGACCATCTATAGGCCAAAACACTAGAAAAAAA-TTTCTCAAGTAC-TAAA
*
104915 AAAGGTGGTGTCGACCATCTA
1 AAAGGTGGTGCCGACCATCTA
104936 ATGGCCAGCA
Statistics
Matches: 116, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
58 12 0.10
59 61 0.53
60 30 0.26
61 13 0.11
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (60 bp):
AAAGGTGGTGCCGACCATCTATAGGCCAAAACACTAGAAAAAAATTTCTCAAGTACTAAA
Found at i:106485 original size:19 final size:19
Alignment explanation
Indices: 106463--106500 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
106453 TCAATCATTC
*
106463 TTTAAAGTGTTGTAACTTT
1 TTTAAAGTATTGTAACTTT
106482 TTTAAAGTATTGTAACTTT
1 TTTAAAGTATTGTAACTTT
106501 GTGTGAGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (19 bp):
TTTAAAGTATTGTAACTTT
Found at i:112756 original size:33 final size:31
Alignment explanation
Indices: 112679--112757 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
112669 CAGATTAGTA
* **
112679 ATTTTATATACATATTTTTTACAAATTGTAT
1 ATTTTATATATATATTTTTTACAAATAATAT
* *
112710 ATTTTATACATATATTTTTTATAAATAAATATT
1 ATTTTATATATATATTTTTTACAAAT-AATA-T
*
112743 GTTTTATATATATAT
1 ATTTTATATATATAT
112758 ACTTATCTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 23 0.59
32 2 0.05
33 14 0.36
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.56
Consensus pattern (31 bp):
ATTTTATATATATATTTTTTACAAATAATAT
Found at i:112812 original size:55 final size:56
Alignment explanation
Indices: 112714--112851 Score: 161
Period size: 57 Copynumber: 2.4 Consensus size: 56
112704 TTGTATATTT
* *
112714 TATACATATATTTTTTATAAATAAATATTGTTTTATATATATATACTTATCTATTTTA
1 TATACATAT-TTTTTTATAAATAAATACTG-TTTATATATATATACATATCTATTTTA
* * *
112772 TATACATATTTTTTTTTACATATATACTG-TTATATATATATACATATCTATTTTAGA
1 TATACATATTTTTTTATAAATAAATACTGTTTATATATATATACATATCTATTTT--A
* * *
112829 TATATATATTTTATTAAAAATAA
1 TATACATATTTTTTTATAAATAA
112852 TGTATTTACT
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
55 24 0.36
57 34 0.51
58 9 0.13
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (56 bp):
TATACATATTTTTTTATAAATAAATACTGTTTATATATATATACATATCTATTTTA
Found at i:119964 original size:18 final size:18
Alignment explanation
Indices: 119941--119988 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
119931 CTTTTTTAAA
119941 TATAAATTTTGAAAATTT
1 TATAAATTTTGAAAATTT
**
119959 TATAAATATTTTGAATTTTT
1 TAT-AA-ATTTTGAAAATTT
*
119979 TTTAAATTTT
1 TATAAATTTT
119989 TGTGGAGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 8 0.32
19 4 0.16
20 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (18 bp):
TATAAATTTTGAAAATTT
Found at i:121887 original size:3 final size:3
Alignment explanation
Indices: 121879--121917 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
121869 GACACAGATA
121879 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
121918 CCATAAGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:129337 original size:29 final size:29
Alignment explanation
Indices: 129276--129339 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
129266 TTGTTTATAT
*
129276 TTTTATAATTTTTAAAAGATTAAATCAAAA
1 TTTTATAATTTTTAAAAGATAAAAT-AAAA
* *
129306 TTTTATCATTTTTAAAAGAATAAAAT-GAA
1 TTTTATAATTTTTAAAAG-ATAAAATAAAA
129335 TTTTA
1 TTTTA
129340 CTTTTACAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 7 0.23
30 17 0.57
31 6 0.20
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (29 bp):
TTTTATAATTTTTAAAAGATAAAATAAAA
Found at i:131116 original size:19 final size:19
Alignment explanation
Indices: 131088--131129 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
131078 TTCATGATGT
131088 AATGTAAAAA-TCAAATAAA
1 AATGTAAAAACTC-AATAAA
* *
131107 AATGTGAAAACTCATTAAA
1 AATGTAAAAACTCAATAAA
131126 AATG
1 AATG
131130 CATTCCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.24
Consensus pattern (19 bp):
AATGTAAAAACTCAATAAA
Found at i:134557 original size:17 final size:17
Alignment explanation
Indices: 134535--134575 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
134525 TACTCGATTA
134535 GATACTTTTTCGTATTT
1 GATACTTTTTCGTATTT
*
134552 GATACTCTTTCGTATTT
1 GATACTTTTTCGTATTT
*
134569 GACACTT
1 GATACTT
134576 ACTTTTCAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.51
Consensus pattern (17 bp):
GATACTTTTTCGTATTT
Found at i:135516 original size:25 final size:23
Alignment explanation
Indices: 135478--135533 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 23
135468 ATTTAAAATT
135478 TTAAAAATAT--TTTTCTCACAAAA
1 TTAAAAATATAATTTT-T-ACAAAA
135501 -TAAAATATATAATTTTTACAAAA
1 TTAAAA-ATATAATTTTTACAAAA
135524 TTAAAAATAT
1 TTAAAAATAT
135534 TTTTCTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
22 5 0.17
23 14 0.48
24 6 0.21
25 4 0.14
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (23 bp):
TTAAAAATATAATTTTTACAAAA
Found at i:135521 original size:23 final size:20
Alignment explanation
Indices: 135480--135548 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 20
135470 TTAAAATTTT
135480 AAAAATATTTTTCTCACAAAATA
1 AAAAATA-TTTT-T-ACAAAATA
*
135503 AAATATATAATTTTTACAAAATT
1 AAA-A-AT-ATTTTTACAAAATA
135526 AAAAATATTTTT-CTAAAATA
1 AAAAATATTTTTAC-AAAATA
135546 AAA
1 AAA
135549 CTTGAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
19 1 0.03
20 14 0.35
21 2 0.05
22 1 0.03
23 13 0.32
24 2 0.05
25 6 0.15
26 1 0.03
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATATTTTTACAAAATA
Found at i:135663 original size:20 final size:20
Alignment explanation
Indices: 135626--135668 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
135616 GAAAGGGTAA
**
135626 TTTTATATAATTTCATTATAT
1 TTTTATATAATTAAATTAT-T
135647 TTTTAT-TAATTAAATTATT
1 TTTTATATAATTAAATTATT
135666 TTT
1 TTT
135669 AAAATTCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 10 0.50
21 6 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATATAATTAAATTATT
Found at i:144753 original size:23 final size:23
Alignment explanation
Indices: 144727--144786 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
144717 TAAATATGAC
144727 ATATTTTTGGGTATTAATTATAT
1 ATATTTTTGGGTATTAATTATAT
* *
144750 ATATTTTGTGAGTA-TAATTCTAT
1 ATATTTT-TGGGTATTAATTATAT
* *
144773 -TAATTTTGGCTATT
1 ATATTTTTGGGTATT
144787 TGTGATCCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 4 0.13
22 6 0.20
23 15 0.50
24 5 0.17
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.55
Consensus pattern (23 bp):
ATATTTTTGGGTATTAATTATAT
Found at i:158619 original size:67 final size:67
Alignment explanation
Indices: 158536--158670 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
158526 TGATAACGAT
158536 AGTCATAGTCATGCAATTAAATCATACATAATTATGGATATCAAACAAAACCTAATTACATACCT
1 AGTCATAGTCATGCAATTAAATCATACATAATTATGGATATCAAACAAAACCTAATTACATACCT
158601 TA
66 TA
*
158603 AGTCATAGTCATGCAATTAAATCATACATAATTATGGATATCAAACAAAACCTAATTACATACTT
1 AGTCATAGTCATGCAATTAAATCATACATAATTATGGATATCAAACAAAACCTAATTACATACCT
158668 TA
66 TA
158670 A
1 A
158671 CTATCAAGAG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.30
Consensus pattern (67 bp):
AGTCATAGTCATGCAATTAAATCATACATAATTATGGATATCAAACAAAACCTAATTACATACCT
TA
Found at i:158664 original size:32 final size:32
Alignment explanation
Indices: 158560--158664 Score: 88
Period size: 32 Copynumber: 3.2 Consensus size: 32
158550 AATTAAATCA
158560 TACATAATTATGGATATCAAACAAAACCTAAT
1 TACATAATTATGGATATCAAACAAAACCTAAT
* * * ** * *
158592 TACATACCTTAAGTCATAGTCATGCAATTAA-ATCA-
1 TACATA-ATTATG-GATA-TCAAACAA--AACCTAAT
158627 TACATAATTATGGATATCAAACAAAACCTAAT
1 TACATAATTATGGATATCAAACAAAACCTAAT
158659 TACATA
1 TACATA
158665 CTTTAACTAT
Statistics
Matches: 52, Mismatches: 14, Indels: 14
0.65 0.17 0.17
Matches are distributed among these distances:
30 2 0.04
31 2 0.04
32 18 0.35
33 7 0.13
34 7 0.13
35 12 0.23
36 2 0.04
37 2 0.04
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.30
Consensus pattern (32 bp):
TACATAATTATGGATATCAAACAAAACCTAAT
Found at i:168571 original size:9 final size:9
Alignment explanation
Indices: 168557--168583 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
168547 TATTTGCGAA
168557 GTTAATAAG
1 GTTAATAAG
168566 GTTAATAAG
1 GTTAATAAG
168575 GTTAATAAG
1 GTTAATAAG
168584 CTTACCCCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (9 bp):
GTTAATAAG
Found at i:176723 original size:25 final size:25
Alignment explanation
Indices: 176695--176743 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
176685 AAATAATAGG
176695 ATTTGTTGACTCGACTT-GACTCGAA
1 ATTTGTTGACTCGA-TTCGACTCGAA
* *
176720 ATTTTTTGACTTGATTCGACTCGA
1 ATTTGTTGACTCGATTCGACTCGA
176744 TTTGAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (25 bp):
ATTTGTTGACTCGATTCGACTCGAA
Found at i:183706 original size:24 final size:24
Alignment explanation
Indices: 183673--183723 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
183663 ATAAATAATC
*
183673 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
183697 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
183721 TTT
1 TTT
183724 GAGTCAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:183732 original size:24 final size:24
Alignment explanation
Indices: 183681--183735 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
183671 TCTTTCAGTT
*
183681 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTGTTTCAATC
* *
183705 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTGTTTCAATC
183729 AAACTCT
1 AAACTCT
183736 TATTAGTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTCAATC
Found at i:187982 original size:15 final size:16
Alignment explanation
Indices: 187955--187985 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
187945 TGAGTTGTAT
187955 TTAAAAGAATTATTAA
1 TTAAAAGAATTATTAA
187971 TTAAAA-AATTATTAA
1 TTAAAAGAATTATTAA
187986 AAGCAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TTAAAAGAATTATTAA
Found at i:188931 original size:16 final size:18
Alignment explanation
Indices: 188910--188942 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
188900 TTTAAGATTT
188910 AACTAT-GAA-CTTACTA
1 AACTATAGAAGCTTACTA
188926 AACTATAGAAGCTTACT
1 AACTATAGAAGCTTACT
188943 CTGTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (18 bp):
AACTATAGAAGCTTACTA
Found at i:190073 original size:14 final size:14
Alignment explanation
Indices: 190054--190080 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
190044 GATTCACCAG
190054 TTTAATTTTATTTA
1 TTTAATTTTATTTA
190068 TTTAATTTTATTT
1 TTTAATTTTATTT
190081 TGCAATCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTAATTTTATTTA
Found at i:192041 original size:141 final size:141
Alignment explanation
Indices: 191787--192068 Score: 564
Period size: 141 Copynumber: 2.0 Consensus size: 141
191777 AATATACCCG
191787 AACCTATGGAATTTGATTTAAAATTTTTATACATTTTAAAACTACTTATTTAGATTTTTTGCAAT
1 AACCTATGGAATTTGATTTAAAATTTTTATACATTTTAAAACTACTTATTTAGATTTTTTGCAAT
191852 TTCATAATGTTTTATTTAATAGGTTGCATCTGCAAACAATAATTTCTTTTTTATATAAAAAAAAT
66 TTCATAATGTTTTATTTAATAGGTTGCATCTGCAAACAATAATTTCTTTTTTATATAAAAAAAAT
191917 TGCTGAGAGAT
131 TGCTGAGAGAT
191928 AACCTATGGAATTTGATTTAAAATTTTTATACATTTTAAAACTACTTATTTAGATTTTTTGCAAT
1 AACCTATGGAATTTGATTTAAAATTTTTATACATTTTAAAACTACTTATTTAGATTTTTTGCAAT
191993 TTCATAATGTTTTATTTAATAGGTTGCATCTGCAAACAATAATTTCTTTTTTATATAAAAAAAAT
66 TTCATAATGTTTTATTTAATAGGTTGCATCTGCAAACAATAATTTCTTTTTTATATAAAAAAAAT
192058 TGCTGAGAGAT
131 TGCTGAGAGAT
192069 TTCATGTAGA
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 141 1.00
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (141 bp):
AACCTATGGAATTTGATTTAAAATTTTTATACATTTTAAAACTACTTATTTAGATTTTTTGCAAT
TTCATAATGTTTTATTTAATAGGTTGCATCTGCAAACAATAATTTCTTTTTTATATAAAAAAAAT
TGCTGAGAGAT
Found at i:193272 original size:10 final size:10
Alignment explanation
Indices: 193259--193300 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
193249 TTTATACACA
193259 TTTTTATTAT
1 TTTTTATTAT
*
193269 TTTTTTTTAT
1 TTTTTATTAT
**
193279 TTTTTAAAAT
1 TTTTTATTAT
193289 TTTTTATTAT
1 TTTTTATTAT
193299 TT
1 TT
193301 ACCGATGTGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTATTAT
Found at i:197154 original size:40 final size:39
Alignment explanation
Indices: 197050--197403 Score: 251
Period size: 40 Copynumber: 9.0 Consensus size: 39
197040 TTGGACGATG
* * * * *
197050 GTTTT-AATCTGCCCTATGATCGAGGTAAAAAATTAGAC
1 GTTTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGAT
* * * *
197088 GGTTGCGATCTGCTCC-ATGATCGGGGTAAGAGATCGGAT
1 GTTTTCAATCTGC-CCTATGATCGGGGTAAGAGATTGGAT
* *
197127 GATTTTCAATCTGTCCTATGATTGGGGTAAGAGATTGG-T
1 G-TTTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGAT
* ** *
197166 GTGTCTTCAA-CTTGCCCTCTGATTAGGGTAAAAGATTGGAT
1 GT-T-TTCAATC-TGCCCTATGATCGGGGTAAGAGATTGGAT
* * * *
197207 G-CTTCAATCTACGCC-ATGATCGGGATATGAGATT-GACGT
1 GTTTTCAATCTGC-CCTATGATCGGGGTAAGAGATTGGA--T
* * ** *
197246 GTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGAT
1 GTTTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGAT
* * *
197285 G-TTTCAATCTGCCCCATGATCGGGGTATGAGATTGGGT
1 GTTTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGAT
* *
197323 GATTTTCAATCTG-CCTCATGACCGGGGTAACAGATTTGG-T
1 G-TTTTCAATCTGCCCT-ATGATCGGGGTAAGAGA-TTGGAT
* *
197363 GGTTTTCAATCTACCCCATGATCGGGGTAAGAGATTGGAT
1 -GTTTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGAT
197403 G
1 G
197404 GTGATGTAGC
Statistics
Matches: 244, Mismatches: 50, Indels: 43
0.72 0.15 0.13
Matches are distributed among these distances:
37 2 0.01
38 54 0.22
39 46 0.19
40 131 0.54
41 11 0.05
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (39 bp):
GTTTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGAT
Found at i:197226 original size:78 final size:77
Alignment explanation
Indices: 197111--197400 Score: 307
Period size: 78 Copynumber: 3.7 Consensus size: 77
197101 TCCATGATCG
* * ** * *
197111 GGGTAAGAGATCGGATGATTTTCAATCTGTCCTATGATTGGGGTAAGAGATTGGTGTGTCTTCAA
1 GGGTAAAAGATTGGATG--TTTCAATCTACCCCATGATCGGGGTAAGAGATTGG-GTGTCTTCAA
197176 -CTTGCCCTCTGATTA
63 TC-TGCCCTCTGATTA
* * * * *
197191 GGGTAAAAGATTGGATGCTTCAATCTACGCCATGATCGGGATATGAGATTGACGTGTCTTCAATC
1 GGGTAAAAGATTGGATGTTTCAATCTACCCCATGATCGGGGTAAGAGATTG-GGTGTCTTCAATC
197256 TGCCCTCTGATTA
65 TGCCCTCTGATTA
* * *
197269 GGGTAAAAGATTGGATGTTTCAATCTGCCCCATGATCGGGGTATGAGATTGGGTGATTTTCAATC
1 GGGTAAAAGATTGGATGTTTCAATCTACCCCATGATCGGGGTAAGAGATTGGGTG-TCTTCAATC
***
197334 TG-CCTCATGACCG
65 TGCCCTC-TGATTA
*
197347 GGGTAACAGATTTGG-TGGTTTTCAATCTACCCCATGATCGGGGTAAGAGATTGG
1 GGGTAAAAGA-TTGGAT-G-TTTCAATCTACCCCATGATCGGGGTAAGAGATTGG
197401 ATGGTGATGT
Statistics
Matches: 180, Mismatches: 23, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
77 7 0.04
78 119 0.66
79 6 0.03
80 48 0.27
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (77 bp):
GGGTAAAAGATTGGATGTTTCAATCTACCCCATGATCGGGGTAAGAGATTGGGTGTCTTCAATCT
GCCCTCTGATTA
Found at i:197762 original size:98 final size:98
Alignment explanation
Indices: 197629--198019 Score: 482
Period size: 98 Copynumber: 4.0 Consensus size: 98
197619 GATTTGTTCC
** * *
197629 TCATGTTTCTAAGGTACAAGGTTCGTCGTTATGACTTAAATCTTTCCCTCCATATCTTCGTGGTA
1 TCATGTTTCTAAGGTACAAGGTTCACCGTTGTGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
* *
197694 CCAGATTCGTCGTTGTGGCTTTAATCTTTCCTT
66 CCAGATTCGTCGTTGCGGCTTTAATCTTTCCCT
* * * * *
197727 TCATGTTTCTAAGGTACAAGGTTCACCGTTTTGACTTAAACCATTCTCTCCATGT-TTCTGAGGT
1 TCATGTTTCTAAGGTACAAGGTTCACCGTTGTGACTTAAACCTTTCCCTCCATATCTTC-GTGGT
* * *
197791 ACCAGATTCGCCGTCGCGGCTTCAATCTTTCCCT
65 ACCAGATTCGTCGTTGCGGCTTTAATCTTTCCCT
* * * * *
197825 TCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTTGTGGTA
1 TCATGTTTCTAAGGTACAAGGTTCACCGTTGTGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
*
197890 CTAGATTCGTCGTTGCGG-TTTCAATCTTTCCCT
66 CCAGATTCGTCGTTGCGGCTTT-AATCTTTCCCT
* * *
197923 TCATGTTTTTGAGGTACAAGGTTCACCGTTGTGACTTAAACCTTTCCCTCCATATCTTTGTGGTA
1 TCATGTTTCTAAGGTACAAGGTTCACCGTTGTGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
* * * * *
197988 TC-GAGTTCGCCGTTACGGCCTCAATCTTTCCC
66 CCAGA-TTCGTCGTTGCGGCTTTAATCTTTCCC
198020 ATTTCATCTT
Statistics
Matches: 251, Mismatches: 37, Indels: 10
0.84 0.12 0.03
Matches are distributed among these distances:
97 7 0.03
98 241 0.96
99 3 0.01
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (98 bp):
TCATGTTTCTAAGGTACAAGGTTCACCGTTGTGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
CCAGATTCGTCGTTGCGGCTTTAATCTTTCCCT
Found at i:197963 original size:196 final size:196
Alignment explanation
Indices: 197629--198019 Score: 545
Period size: 196 Copynumber: 2.0 Consensus size: 196
197619 GATTTGTTCC
* * *
197629 TCATGTTTCTAAGGTACAAGGTTCGTCGTTATGACTTAAATCTTTCCCTCCATATCTTCGTGGTA
1 TCATGTTTCTAAGGTACAAGGTTCGCCGTTACGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
* * *
197694 CCAGATTCGTCGTTGTGGCTTTAATCTTTCCTTTCATGTTTCTAAGGTACAAGGTTCACCGTTTT
66 CCAGATTCGTCGTTGCGGCTTTAATCTTTCCCTTCATGTTTCTAAGGTACAAGGTTCACCGTTGT
* * * *
197759 GACTTAAACCATTCTCTCCATGT-TTCTGAGGTACC-AGATTCGCCGTCGCGGCTTCAATCTTTC
131 GACTTAAACCATTCCCTCCATATCTT-TGAGGTACCGAG-TTCGCCGTCACGGCCTCAATCTTTC
197822 CCT
194 CCT
* * * *
197825 TCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTTGTGGTA
1 TCATGTTTCTAAGGTACAAGGTTCGCCGTTACGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
* * *
197890 CTAGATTCGTCGTTGCGG-TTTCAATCTTTCCCTTCATGTTTTTGAGGTACAAGGTTCACCGTTG
66 CCAGATTCGTCGTTGCGGCTTT-AATCTTTCCCTTCATGTTTCTAAGGTACAAGGTTCACCGTTG
* * * *
197954 TGACTTAAACCTTTCCCTCCATATCTTTGTGGTATCGAGTTCGCCGTTACGGCCTCAATCTTTCC
130 TGACTTAAACCATTCCCTCCATATCTTTGAGGTACCGAGTTCGCCGTCACGGCCTCAATCTTTCC
198019 C
195 C
198020 ATTTCATCTT
Statistics
Matches: 171, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
195 3 0.02
196 164 0.96
197 4 0.02
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (196 bp):
TCATGTTTCTAAGGTACAAGGTTCGCCGTTACGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
CCAGATTCGTCGTTGCGGCTTTAATCTTTCCCTTCATGTTTCTAAGGTACAAGGTTCACCGTTGT
GACTTAAACCATTCCCTCCATATCTTTGAGGTACCGAGTTCGCCGTCACGGCCTCAATCTTTCCC
T
Found at i:198001 original size:49 final size:47
Alignment explanation
Indices: 197629--198001 Score: 242
Period size: 49 Copynumber: 7.6 Consensus size: 47
197619 GATTTGTTCC
* * *
197629 TCATGTTTCTAAGGTACAAGGTTCGTCGTTATGACTTAAATCTTTCCCT
1 TCATGTTT-TGAGGTACAA-GTTCGCCGTTGTGACTTAAATCTTTCCCT
* * * * * * * * *
197678 CCATATCTTCGTGGTACCAGATTCGTCGTTGTGGCTTTAATCTTTCCTT
1 TCATGT-TTTGAGGTACAAG-TTCGCCGTTGTGACTTAAATCTTTCCCT
* * * * * *
197727 TCATGTTTCTAAGGTACAAGGTTCACCGTTTTGACTTAAACCATTCTCT
1 TCATGTTT-TGAGGTACAA-GTTCGCCGTTGTGACTTAAATCTTTCCCT
* * * * * *
197776 CCATGTTTCTGAGGTACCAGATTCGCCGTCGCGGCTTCAATCTTTCCCT
1 TCATGTTT-TGAGGTACAAG-TTCGCCGTTGTGACTTAAATCTTTCCCT
* *
197825 TCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT
1 TCATGTTT-TGAGGTACAA-GTTCGCCGTTGTGACTTAAATCTTTCCCT
* * * * * ** *
197874 TCATATCTTTGTGGTACTAGATTCGTCGTTGCGGTTTCAATCTTTCCCT
1 TCATGT-TTTGAGGTACAAG-TTCGCCGTTGTGACTTAAATCTTTCCCT
* *
197923 TCATGTTTTTGAGGTACAAGGTTCACCGTTGTGACTTAAACCTTTCCCT
1 TCATG-TTTTGAGGTACAA-GTTCGCCGTTGTGACTTAAATCTTTCCCT
* * * *
197972 CCATATCTTTGTGGTATCGAGTTCGCCGTT
1 TCATGT-TTTGAGGTA-CAAGTTCGCCGTT
198002 ACGGCCTCAA
Statistics
Matches: 246, Mismatches: 66, Indels: 24
0.73 0.20 0.07
Matches are distributed among these distances:
48 6 0.02
49 230 0.93
50 10 0.04
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.39
Consensus pattern (47 bp):
TCATGTTTTGAGGTACAAGTTCGCCGTTGTGACTTAAATCTTTCCCT
Found at i:198029 original size:49 final size:49
Alignment explanation
Indices: 197974--198118 Score: 132
Period size: 49 Copynumber: 2.9 Consensus size: 49
197964 CTTTCCCTCC
* *
197974 ATATCTTTGTGGTATCGAGTTCGCCGTTACGGCCTCAATCTTTCCCAT-
1 ATATCTTTATGGTACCGAGTTCGCCGTTACGGCCTCAATCTTTCCCATA
* * * * * * *
198022 TTCATCTTCATAGAACCG-GATTCGTCATTACGGCCTCAATCCTTCCCATA
1 AT-ATCTTTATGGTACCGAG-TTCGCCGTTACGGCCTCAATCTTTCCCATA
* ** *
198072 ATATCTTCTAAGGTACCGAGTTCGCCGTTACAACCTCAACCTTTCCC
1 ATATCTT-TATGGTACCGAGTTCGCCGTTACGGCCTCAATCTTTCCC
198119 TTTAAATCTC
Statistics
Matches: 72, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
48 2 0.03
49 41 0.57
50 28 0.39
51 1 0.01
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.33
Consensus pattern (49 bp):
ATATCTTTATGGTACCGAGTTCGCCGTTACGGCCTCAATCTTTCCCATA
Found at i:198078 original size:196 final size:196
Alignment explanation
Indices: 197629--198079 Score: 443
Period size: 196 Copynumber: 2.3 Consensus size: 196
197619 GATTTGTTCC
* * * * * * * * *
197629 TCATGTTTCTAAGGTACAAGGTTCGTCGTTATGACTTAAATCTTTCCC-TCCATATCTTCGTGGT
1 TCATGCTTCTGAGGAACAAGGTTCGCCATTACGACTCAAACCTTTCCCAT-AATATCTTCGTGGT
* * *
197693 ACCAGATTCGTCGTTGTGGCTTTAATCTTTCCTTTCATGTTTCTAAGGTACAAGGTTCACCGTTT
65 ACCAGATTCGTCGTTGCGGCTTTAATCTTTCCCTTCATGTTTCTAAGGTACAAGGTTCACCGTTG
* * * *
197758 TGACTTAAACCATTCTCTCCATGTTTCTGAGGTACCAGATTCGCCGTCGCGGCTTCAATCTTTCC
130 TGACTTAAACCATTCCCTCCATATTTCTGAGGTACCAGATTCGCCGTCACGGCCTCAATCTTTCC
197823 CT
195 CT
* * * * * * * *
197825 TCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTTGTGGTA
1 TCATGCTTCTGAGGAACAAGGTTCGCCATTACGACTCAAACCTTTCCCATAATATCTTCGTGGTA
* * *
197890 CTAGATTCGTCGTTGCGG-TTTCAATCTTTCCCTTCATGTTTTTGAGGTACAAGGTTCACCGTTG
66 CCAGATTCGTCGTTGCGGCTTT-AATCTTTCCCTTCATGTTTCTAAGGTACAAGGTTCACCGTTG
* * * *
197954 TGACTTAAACCTTTCCCTCCATATCTT-TGTGGTATC-GAGTTCGCCGTTACGGCCTCAATCTTT
130 TGACTTAAACCATTCCCTCCATAT-TTCTGAGGTACCAGA-TTCGCCGTCACGGCCTCAATCTTT
198017 CCCATT
193 CCC--T
* * * *
198023 TCAT-CTTCAT-A-GAAC-CGGATTCGTCATTACGGCCTCAATCC-TTCCCATAATATCTTC
1 TCATGCTTC-TGAGGAACAAGG-TTCGCCATTAC-GACTCAAACCTTTCCCATAATATCTTC
198080 TAAGGTACCG
Statistics
Matches: 214, Mismatches: 32, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
195 7 0.03
196 187 0.87
197 14 0.07
198 6 0.03
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (196 bp):
TCATGCTTCTGAGGAACAAGGTTCGCCATTACGACTCAAACCTTTCCCATAATATCTTCGTGGTA
CCAGATTCGTCGTTGCGGCTTTAATCTTTCCCTTCATGTTTCTAAGGTACAAGGTTCACCGTTGT
GACTTAAACCATTCCCTCCATATTTCTGAGGTACCAGATTCGCCGTCACGGCCTCAATCTTTCCC
T
Found at i:205985 original size:17 final size:19
Alignment explanation
Indices: 205958--205993 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
205948 TTTCAAATTC
205958 AAATAAATAATTAA-AATA
1 AAATAAATAATTAATAATA
205976 AAAT-AATAATTAATAATA
1 AAATAAATAATTAATAATA
205994 TATAAATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATAAATAATTAATAATA
Found at i:210643 original size:22 final size:22
Alignment explanation
Indices: 210612--210682 Score: 133
Period size: 22 Copynumber: 3.2 Consensus size: 22
210602 CCAGATCTCC
210612 ATGCTTATCTTGACTTTTGTCAA
1 ATGC-TATCTTGACTTTTGTCAA
210635 ATGCTATCTTGACTTTTGTCAA
1 ATGCTATCTTGACTTTTGTCAA
210657 ATGCTATCTTGACTTTTGTCAA
1 ATGCTATCTTGACTTTTGTCAA
210679 ATGC
1 ATGC
210683 ATCAAAATGC
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 44 0.92
23 4 0.08
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (22 bp):
ATGCTATCTTGACTTTTGTCAA
Found at i:224487 original size:21 final size:21
Alignment explanation
Indices: 224463--224502 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
224453 TTTGGAGTTT
224463 GTTCTA-CTGGTAGAAGTCATG
1 GTTCTATC-GGTAGAAGTCATG
224484 GTTCTATCGGTAGAAGTCA
1 GTTCTATCGGTAGAAGTCA
224503 AGCATGTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
GTTCTATCGGTAGAAGTCATG
Found at i:226559 original size:2 final size:2
Alignment explanation
Indices: 226554--226681 Score: 81
Period size: 2 Copynumber: 66.5 Consensus size: 2
226544 TAAGTCAGAA
*
226554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT -T AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * * * * *
226596 AT AT GT AT AA AT AT AG AT AT A- AA AGT -T GT TT AT AT AT A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * *
226636 AA AT -T GT AT A- AC A- AT CT 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 AT AT AT AT AT AT AT
226675 AT AT AT A
1 AT AT AT A
226682 AGTGCAAAAC
Statistics
Matches: 102, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
1 7 0.07
2 93 0.91
3 2 0.02
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:232987 original size:16 final size:16
Alignment explanation
Indices: 232968--233009 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
232958 TCTGGTTTCT
232968 TCTCTCCCTCAGATGC
1 TCTCTCCCTCAGATGC
232984 TCTCTCCCTCAGATGC
1 TCTCTCCCTCAGATGC
233000 TCTCTCCCTC
1 TCTCTCCCTC
233010 TCACTTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.10, C:0.48, G:0.10, T:0.33
Consensus pattern (16 bp):
TCTCTCCCTCAGATGC
Found at i:233763 original size:30 final size:30
Alignment explanation
Indices: 233729--233789 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
233719 TAACTTTTCT
* * * *
233729 TTTTTCTGTTAAATTGATGAAGATGGAACG
1 TTTTTCTGTCAAACTGATCAAGATGAAACG
233759 TTTTTCTGTCAAACTGATCAAGATGAAACG
1 TTTTTCTGTCAAACTGATCAAGATGAAACG
233789 T
1 T
233790 AAACAATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (30 bp):
TTTTTCTGTCAAACTGATCAAGATGAAACG
Found at i:247954 original size:109 final size:110
Alignment explanation
Indices: 247757--247969 Score: 277
Period size: 109 Copynumber: 1.9 Consensus size: 110
247747 ATTTAAAAAA
* * * *
247757 TCGGTTTCAAATAGGATGTTCAATTACTTAGGTTCAAAGAAAAAAAATCATACCCAGCACGTTAG
1 TCGGTTTCAAATAGGATATTCAATTACTTAAGTTCAAAG--AAAAAACCATACCCAACACGTTAG
* *
247822 GGCACAATTTTTCGAGTTCCCTAAAATAAAAGAACATTGAACATTTT
64 AGCACAATTTTTCGAATTCCCTAAAATAAAAGAACATTGAACATTTT
* * * * *
247869 TCGGTTTTAAATAGGATATTTAATTATTTAAGTTCAAAG-AAAAACCATACTCAATACGTTAGAG
1 TCGGTTTCAAATAGGATATTCAATTACTTAAGTTCAAAGAAAAAACCATACCCAACACGTTAGAG
*
247933 CACAATTTCTT-GAATTCCCTAAAATAAAAGAGCATTG
66 CACAATTT-TTCGAATTCCCTAAAATAAAAGAACATTG
247970 CCTTGATTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
109 52 0.59
110 2 0.02
112 34 0.39
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (110 bp):
TCGGTTTCAAATAGGATATTCAATTACTTAAGTTCAAAGAAAAAACCATACCCAACACGTTAGAG
CACAATTTTTCGAATTCCCTAAAATAAAAGAACATTGAACATTTT
Found at i:248230 original size:26 final size:26
Alignment explanation
Indices: 248190--248246 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
248180 TTAAATAATA
248190 AAAAAATAGAAAAAAGAA-TTAATTTT
1 AAAAAATAGAAAAAAGAATTTAA-TTT
248216 AAAAAA-AGAATAAAAGAATTTAATTT
1 AAAAAATAGAA-AAAAGAATTTAATTT
248242 AAAAA
1 AAAAA
248247 GGATAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.14
26 21 0.72
27 4 0.14
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (26 bp):
AAAAAATAGAAAAAAGAATTTAATTT
Found at i:250050 original size:45 final size:45
Alignment explanation
Indices: 249999--250087 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
249989 ATTTGCTTTT
* *
249999 ATAGCTTCAATCTGACTCTCTGGATTTGGGGTATAAGATTGGATA
1 ATAGCTTCAATCTGACGCTCTGGATTTGGGATATAAGATTGGATA
* *
250044 ATAGCTTCAATCTGTCGCTTTGGATTTGGGATATAAGATTGGAT
1 ATAGCTTCAATCTGACGCTCTGGATTTGGGATATAAGATTGGAT
250088 GTGGTGACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (45 bp):
ATAGCTTCAATCTGACGCTCTGGATTTGGGATATAAGATTGGATA
Found at i:250160 original size:45 final size:44
Alignment explanation
Indices: 250022--250311 Score: 156
Period size: 40 Copynumber: 6.8 Consensus size: 44
250012 GACTCTCTGG
** * * * **
250022 ATTTGGGGTATAAGATTGGATAATAGCTTCAATCTGTCGCTTTGG
1 ATTTGGGGTATAAGATTGGATGGTGGCTTCAAT-TTTCCCTTTAA
* * * *
250067 ATTTGGGATATAAGATTGGATGTGGTGACTTCAATCTGCCCTTTTAA
1 ATTTGGGGTATAAGATTGGA--TGGTGGCTTCAATTTTCCC-TTTAA
*
250114 ATTTGGGGTATAAGATTGGATGGTGGCTTCAATTTTCACCTCTAA
1 ATTTGGGGTATAAGATTGGATGGTGGCTTCAATTTTC-CCTTTAA
* * * * * * *
250159 ATTTAGGGTATAATACTGAATGGT--CTTCAATCTGCCCTCT--
1 ATTTGGGGTATAAGATTGGATGGTGGCTTCAATTTTCCCTTTAA
* * * * *
250199 AGTTAGGGTGA-AAAATTGGATGGT--CTTCAATCTGCCCTTT--
1 ATTTGGGGT-ATAAGATTGGATGGTGGCTTCAATTTTCCCTTTAA
** * *
250239 GGTTGGGGTAAAAGATTGGATGAT--CTTCAATTTTCCCTTT--
1 ATTTGGGGTATAAGATTGGATGGTGGCTTCAATTTTCCCTTTAA
* * *
250279 AGTTGGGGTAAAAGATTGGATGGTGTCTTCAAT
1 ATTTGGGGTATAAGATTGGATGGTGGCTTCAAT
250312 CTGCCCTCTA
Statistics
Matches: 202, Mismatches: 35, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
39 1 0.00
40 87 0.43
41 1 0.00
42 12 0.06
43 9 0.04
45 57 0.28
46 4 0.02
47 31 0.15
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (44 bp):
ATTTGGGGTATAAGATTGGATGGTGGCTTCAATTTTCCCTTTAA
Found at i:250207 original size:40 final size:40
Alignment explanation
Indices: 250119--250505 Score: 384
Period size: 40 Copynumber: 9.5 Consensus size: 40
250109 TTTAAATTTG
* * * *
250119 GGGTATAAGATTGGATGGTGGCTTCAATTTTCACCTCTAAATTTA
1 GGGTAAAAGATTGGATGGT--CTTCAATCTGC-CCTCT--AGTTA
* * * *
250164 GGGTATAATACTGAATGGTCTTCAATCTGCCCTCTAGTTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTA
* * *
250204 GGGTGAAAA-ATTGGATGGTCTTCAATCTGCCCTTTGGTTG
1 GGGT-AAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTA
* * * * *
250244 GGGTAAAAGATTGGATGATCTTCAATTTTCCCTTTAGTTG
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTA
*
250284 GGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCTCTAGATA
1 GGGTAAAAGATTGGAT-G-GTCTTCAATCTGCCCTCTAGTTA
* * * * *
250326 AGGTAAAGGATTGAATGGTCTTCAATCTTCCCTCT-GTTTG
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG-TTA
*
250366 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTT-
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTA
* *
250405 GGGTAAAAGATTGGATGGTATCTTCAATTTGTCCTCTAGTTA
1 GGGTAAAAGATTGGATGG--TCTTCAATCTGCCCTCTAGTTA
* * * * *
250447 GGGTAAAAGATTAGATGGTCTTTAGTCTGCCCTCTGGTTG
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTA
250487 GGGTAAAAGATTGGATGGT
1 GGGTAAAAGATTGGATGGT
250506 GGTTTCAATC
Statistics
Matches: 290, Mismatches: 43, Indels: 23
0.81 0.12 0.06
Matches are distributed among these distances:
39 23 0.08
40 166 0.57
41 24 0.08
42 52 0.18
43 9 0.03
45 16 0.06
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (40 bp):
GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTA
Found at i:250386 original size:162 final size:164
Alignment explanation
Indices: 250116--250481 Score: 462
Period size: 162 Copynumber: 2.2 Consensus size: 164
250106 CCTTTTAAAT
* * * * * *
250116 TTGGGGTATAAGATTGGATGGTGGCTTCAATTTTCACCTCTAAATTTAGGGTATAATACTGAATG
1 TTGGGGTAAAAGATTGGATGGTGTCTTCAATCTGC-CCTCTAAA-TTAAGGTATAAGACTGAATG
*
250181 GTCTTCAATCTGCCCTCTAGTTAGGGTGAAAAATTGGATGGTCTTCAATCTGCCCTTTGGTTGGG
64 GTCTTCAATCTGCCCTCTAGTTAGGGTGAAAAATTGGATGGTCTTCAATCTGCCCTCTGGTT-GG
*
250246 GTAAAAGATTGGAT-G-ATCTTCAATTT-TCCCTTTAG
128 GTAAAAGATTGGATGGTATCTTCAATTTGT-CCTCTAG
* *
250281 TTGGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCTCTAGA-TAAGGTA-AAGGATTGAATGG
1 TTGGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCTCTAAATTAAGGTATAA-GACTGAATGG
* *
250344 TCTTCAATCTTCCCTCT-GTTTGGG-GTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTGG
65 TCTTCAATCTGCCCTCTAGTTAGGGTG-AAAA-ATTGGATGGTCTTCAATCTGCCCTCTGGTTGG
250407 GTAAAAGATTGGATGGTATCTTCAATTTGTCCTCTAG
128 GTAAAAGATTGGATGGTATCTTCAATTTGTCCTCTAG
* * * *
250444 TTAGGGTAAAAGATTAGAT-G-GTCTTTAGTCTGCCCTCT
1 TTGGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCTCT
250482 GGTTGGGGTA
Statistics
Matches: 179, Mismatches: 16, Indels: 16
0.85 0.08 0.08
Matches are distributed among these distances:
160 1 0.01
161 44 0.25
162 61 0.34
163 34 0.19
164 8 0.04
165 31 0.17
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.36
Consensus pattern (164 bp):
TTGGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCTCTAAATTAAGGTATAAGACTGAATGGT
CTTCAATCTGCCCTCTAGTTAGGGTGAAAAATTGGATGGTCTTCAATCTGCCCTCTGGTTGGGTA
AAAGATTGGATGGTATCTTCAATTTGTCCTCTAG
Found at i:250468 original size:121 final size:121
Alignment explanation
Indices: 250182--250505 Score: 454
Period size: 121 Copynumber: 2.7 Consensus size: 121
250172 TACTGAATGG
*
250182 TCTTCAATCTGCCCTCTAGTTAGGGTGAAAA-ATTGGATGGTCTTCAATCTGCCCTTTGGTTGGG
1 TCTTCAATCTGCCCTCTAGTTAGGGT-AAAAGATT-GATGGTCTTCAATCTGCCCTCTGGTTGGG
* * * * *
250246 GTAAAAGATTGGATGATCTTCAATTTTCCCTTTAGTTGGGGTAAAAGATTGGATGGTG
64 GTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTGGGGTAAAAGATTGGATGGTA
* * * * *
250304 TCTTCAATCTGCCCTCTAGATAAGGTAAAGGATTGAATGGTCTTCAATCTTCCCTCTGTTTGGGG
1 TCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTG-ATGGTCTTCAATCTGCCCTCTGGTTGGGG
*
250369 TAAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTT-GGGTAAAAGATTGGATGGTA
65 TAAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTGGGGTAAAAGATTGGATGGTA
* * * *
250425 TCTTCAATTTGTCCTCTAGTTAGGGTAAAAGATTAGATGGTCTTTAGTCTGCCCTCTGGTTGGGG
1 TCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATT-GATGGTCTTCAATCTGCCCTCTGGTTGGGG
250490 TAAAAGATTGGATGGT
65 TAAAAGATTGGATGGT
250506 GGTTTCAATC
Statistics
Matches: 178, Mismatches: 21, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
121 93 0.52
122 85 0.48
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.35
Consensus pattern (121 bp):
TCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGATGGTCTTCAATCTGCCCTCTGGTTGGGGT
AAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTGGGGTAAAAGATTGGATGGTA
Found at i:250723 original size:23 final size:23
Alignment explanation
Indices: 250692--250736 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
250682 ACTTCAGGGA
250692 GATAAAGATTTGCTAATGTTAGG
1 GATAAAGATTTGCTAATGTTAGG
*
250715 GATATAGATTTGCTAATGTTAG
1 GATAAAGATTTGCTAATGTTAG
250737 TTTTAATCCG
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:0.33, C:0.04, G:0.24, T:0.38
Consensus pattern (23 bp):
GATAAAGATTTGCTAATGTTAGG
Found at i:250786 original size:50 final size:49
Alignment explanation
Indices: 250712--250826 Score: 176
Period size: 50 Copynumber: 2.3 Consensus size: 49
250702 TGCTAATGTT
*
250712 AGGGATATAGATTTGCTAATGTTAGTTTTAATCCGATCCTTACAACTTC
1 AGGGATATAGATTTGCCAATGTTAGTTTTAATCCGATCCTTACAACTTC
* *
250761 AGGGATATAGGATTTGCCAATGTTAGTTTTAATTCGATCCTTATAACTTC
1 AGGGATATA-GATTTGCCAATGTTAGTTTTAATCCGATCCTTACAACTTC
*
250811 AAGGATATAAGATTTG
1 AGGGATAT-AGATTTG
250827 GTTTTGTAGT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
49 9 0.15
50 50 0.83
51 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (49 bp):
AGGGATATAGATTTGCCAATGTTAGTTTTAATCCGATCCTTACAACTTC
Found at i:251706 original size:21 final size:21
Alignment explanation
Indices: 251681--251726 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
251671 ATCAATGGCC
*
251681 AAAAATTGTAAAAATTGGTAA
1 AAAAATGGTAAAAATTGGTAA
* **
251702 AAAAATGGTCAATGTTGGTAA
1 AAAAATGGTAAAAATTGGTAA
251723 AAAA
1 AAAA
251727 TAGCAAACAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.26
Consensus pattern (21 bp):
AAAAATGGTAAAAATTGGTAA
Found at i:252021 original size:17 final size:16
Alignment explanation
Indices: 251994--252087 Score: 74
Period size: 17 Copynumber: 5.9 Consensus size: 16
251984 CATCTCGACA
251994 TTTCATTTTTCTTTTTC
1 TTTC-TTTTTCTTTTTC
252011 TTTCTTCTTTCTTTTT-
1 TTTCTT-TTTCTTTTTC
*
252027 TCTTCTTTTT-TTTTTT
1 T-TTCTTTTTCTTTTTC
252043 TTTCTTTTTCNTTTCTT-
1 TTTCTTTTTC-TTT-TTC
* *
252060 TTGCATTTTC-TTTTC
1 TTTCTTTTTCTTTTTC
252075 -TTCTTTTT-TTTTT
1 TTTCTTTTTCTTTTT
252088 GGGTAAAATA
Statistics
Matches: 65, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
14 12 0.18
15 15 0.23
16 7 0.11
17 29 0.45
18 2 0.03
ACGTcount: A:0.02, C:0.16, G:0.01, T:0.80
Consensus pattern (16 bp):
TTTCTTTTTCTTTTTC
Found at i:252023 original size:11 final size:10
Alignment explanation
Indices: 252001--252082 Score: 62
Period size: 11 Copynumber: 7.9 Consensus size: 10
251991 ACATTTCATT
252001 TTTCTTTTTC
1 TTTCTTTTTC
252011 TTTCTTCTTTC
1 TTTCTT-TTTC
252022 TTT-TTTCTTC
1 TTTCTTT-TTC
* *
252032 TTTTTTTTTTT
1 -TTTCTTTTTC
252043 TTTCTTTTTC
1 TTTCTTTTTC
*
252053 NTTTCTTTTGC
1 -TTTCTTTTTC
252064 ATTT-TCTTTTC
1 -TTTCT-TTTTC
252075 -TTCTTTTT
1 TTTCTTTTT
252083 TTTTTGGGTA
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
9 7 0.12
10 21 0.36
11 28 0.47
12 3 0.05
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.79
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:252076 original size:43 final size:42
Alignment explanation
Indices: 251999--252087 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 42
251989 CGACATTTCA
* *
251999 TTTTTCTTTTTCTTTCTTCTTTCTTTTTTCTTCTTTTTTTTT
1 TTTTTCTTTTTCTTTCTTCTTGCTTTTTTCTTCTTCTTTTTT
252041 TTTTTCTTTTTCNTTTCTT-TTGCATTTTCTT-TTCTTCTTTTTT
1 TTTTTCTTTTTC-TTTCTTCTTGC-TTTT-TTCTTCTTCTTTTTT
252084 TTTT
1 TTTT
252088 GGGTAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
42 15 0.36
43 25 0.60
44 2 0.05
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.81
Consensus pattern (42 bp):
TTTTTCTTTTTCTTTCTTCTTGCTTTTTTCTTCTTCTTTTTT
Found at i:256216 original size:108 final size:109
Alignment explanation
Indices: 256017--256218 Score: 257
Period size: 108 Copynumber: 1.9 Consensus size: 109
256007 AATTGATTTC
** * *
256017 AAATAAGATGTTCAATTACTTAGGTTCAAAGAAAAAAACCATACCCAACATATTACGGCACAAAT
1 AAATAAGATACTCAATTACTTAGGTTCAAAG-AAAAAACCATACCCAACACATTAAGGCACAAAT
* **
256082 TTCGAGTTTCTTAAAATAAAAGAACATTGAACATTTATCGGTTTT
65 TTCGAGATTCCCAAAATAAAAGAACATTGAACATTTATCGGTTTT
* * * *
256127 AAATAAGATACTCAATTATTTAGGTTCAAAG-AAAAACCATACCCAACACGTTAATGCACAATTT
1 AAATAAGATACTCAATTACTTAGGTTCAAAGAAAAAACCATACCCAACACATTAAGGCACAAATT
256191 CTCGA-ATTCACCAAAA-AAAAGAACATTG
66 -TCGAGATTC-CCAAAATAAAAGAACATTG
256219 CTTTGATTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
108 43 0.54
109 8 0.10
110 28 0.35
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (109 bp):
AAATAAGATACTCAATTACTTAGGTTCAAAGAAAAAACCATACCCAACACATTAAGGCACAAATT
TCGAGATTCCCAAAATAAAAGAACATTGAACATTTATCGGTTTT
Found at i:256493 original size:28 final size:28
Alignment explanation
Indices: 256420--256494 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
256410 CAAATGATTT
*
256420 AAAGGATTAAATAAAAAAAAAGAGAACA
1 AAAGGATTAATTAAAAAAAAAGAGAACA
* *
256448 AAAGGATTAATTAAAAAAAAAAAGAATA
1 AAAGGATTAATTAAAAAAAAAGAGAACA
*
256476 AAAGGATTTAATTTAAAAA
1 AAAGGA-TTAATTAAAAAA
256495 GGAGAAACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 31 0.74
29 11 0.26
ACGTcount: A:0.68, C:0.01, G:0.12, T:0.19
Consensus pattern (28 bp):
AAAGGATTAATTAAAAAAAAAGAGAACA
Found at i:259719 original size:35 final size:36
Alignment explanation
Indices: 259673--259753 Score: 137
Period size: 36 Copynumber: 2.3 Consensus size: 36
259663 TTTCCTGAAA
*
259673 ATATTTCAGAAAA-TTGTTTTCAATAAAACAAACAT
1 ATATTTGAGAAAAGTTGTTTTCAATAAAACAAACAT
*
259708 ATATTTGAGAAAAGTTGTTTTCAATAAAACAAATAT
1 ATATTTGAGAAAAGTTGTTTTCAATAAAACAAACAT
259744 ATATTTGAGA
1 ATATTTGAGA
259754 TTTTCTTGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 12 0.28
36 31 0.72
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (36 bp):
ATATTTGAGAAAAGTTGTTTTCAATAAAACAAACAT
Found at i:261655 original size:66 final size:66
Alignment explanation
Indices: 261533--261786 Score: 323
Period size: 66 Copynumber: 4.0 Consensus size: 66
261523 TTCATTGTCA
* * *
261533 ATTATTTTTCTAAAAATCTCAAGAG-TTTTTGTTTCTCAAAAGAA-GGAATCGAAGAAGAAGAGG
1 ATTATTTCTCTAAAAATCTCTAGAGTTTTTTGTTTCTCAAAA-AATGGAATCGAAGAAGAAGAAG
261596 AG
65 AG
*
261598 ATTATTTCTCTAAAAATCTCTAGAGTTTTTTGTTTCTCAAAAAATGGAATTGAAGAAGAAGAAGA
1 ATTATTTCTCTAAAAATCTCTAGAGTTTTTTGTTTCTCAAAAAATGGAATCGAAGAAGAAGAAGA
261663 G
66 G
*
261664 ATTATTTCTCTAAAAATCTCTAGAGTTTTTTGTTTCTCAAAAAATGGAATC------GAAGAAGT
1 ATTATTTCTCTAAAAATCTCTAGAGTTTTTTGTTTCTCAAAAAATGGAATCGAAGAAGAAGAAGA
261723 G
66 G
* * * * *
261724 ATTAATTCTCTAAAAATCTCCAGA-CTTTTTGTTT-TCAAAAGA-GAGAATCGAAGAAGATGAAG
1 ATTATTTCTCTAAAAATCTCTAGAGTTTTTTGTTTCTCAAAAAATG-GAATCGAAGAAGAAGAAG
261786 A
65 A
261787 AAAAGAGAAA
Statistics
Matches: 168, Mismatches: 12, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
57 1 0.01
58 12 0.07
59 9 0.05
60 30 0.18
64 6 0.04
65 25 0.15
66 85 0.51
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (66 bp):
ATTATTTCTCTAAAAATCTCTAGAGTTTTTTGTTTCTCAAAAAATGGAATCGAAGAAGAAGAAGA
G
Found at i:263052 original size:29 final size:29
Alignment explanation
Indices: 263007--263065 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 29
262997 ACCCAGTAGA
263007 TGCAAGAAAGATGATTTAAAAGCTATTTT
1 TGCAAGAAAGATGATTTAAAAGCTATTTT
263036 TGCAAGAAAGACT-ATTTAAAAGCTATTTT
1 TGCAAGAAAGA-TGATTTAAAAGCTATTTT
263065 T
1 T
263066 TTCTCAGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (29 bp):
TGCAAGAAAGATGATTTAAAAGCTATTTT
Found at i:264450 original size:41 final size:42
Alignment explanation
Indices: 264330--264480 Score: 146
Period size: 43 Copynumber: 3.6 Consensus size: 42
264320 GAATCACTTG
* * *
264330 ATGTATAAAT-GAGAGACTCATGTCTCGGGATGAGCATGAGATT
1 ATGTAT-AATGGA-AGACTCATGTCTCGGAAAGAGCATGAGACT
* * * * *
264373 ATGTGTGAATGGAAGACTCGTGACTCGAAAAAAGCATGAGACT
1 ATGTAT-AATGGAAGACTCATGTCTCGGAAAGAGCATGAGACT
*
264416 ATGT-TAAAGGAAGACTCATGTCTCGGAAAGAGCATGAGAAC-
1 ATGTATAATGGAAGACTCATGTCTCGGAAAGAGCATGAG-ACT
* *
264457 ATGTATAATGGAAAACTTATGTCT
1 ATGTATAATGGAAGACTCATGTCT
264481 TGGTAGAGCA
Statistics
Matches: 88, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
41 32 0.36
42 19 0.22
43 35 0.40
44 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (42 bp):
ATGTATAATGGAAGACTCATGTCTCGGAAAGAGCATGAGACT
Found at i:264491 original size:41 final size:41
Alignment explanation
Indices: 264345--264480 Score: 121
Period size: 41 Copynumber: 3.2 Consensus size: 41
264335 TAAATGAGAG
* * * * *
264345 ACTCATGTCTCGGGATGAGCATGAGATTATGTGTGAATGGAAG
1 ACTCATGTCTCGGAAAGAGCATGAGACTATGT-T-AAAGGAAA
* * * * *
264388 ACTCGTGACTCGAAAAAAGCATGAGACTATGTTAAAGGAAG
1 ACTCATGTCTCGGAAAGAGCATGAGACTATGTTAAAGGAAA
*
264429 ACTCATGTCTCGGAAAGAGCATGAGAAC-ATGTATAATGGAAA
1 ACTCATGTCTCGGAAAGAGCATGAG-ACTATGT-TAAAGGAAA
*
264471 ACTTATGTCT
1 ACTCATGTCT
264481 TGGTAGAGCA
Statistics
Matches: 76, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
41 32 0.42
42 19 0.25
43 25 0.33
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (41 bp):
ACTCATGTCTCGGAAAGAGCATGAGACTATGTTAAAGGAAA
Found at i:268925 original size:14 final size:14
Alignment explanation
Indices: 268883--268925 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
268873 TGTTAAACTA
*
268883 AAAATAAAACAAAAC
1 AAAATAAAAC-AAAT
*
268898 AAAATAAAATAAAT
1 AAAATAAAACAAAT
*
268912 AAAGTAAAACAAAT
1 AAAATAAAACAAAT
268926 CTTGTTGCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (14 bp):
AAAATAAAACAAAT
Found at i:270449 original size:9 final size:9
Alignment explanation
Indices: 270435--270483 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
270425 GCAAATGATT
270435 TTAAAATTA
1 TTAAAATTA
270444 TTAAAATTA
1 TTAAAATTA
*
270453 TTTTTAAAAATA
1 ---TTAAAATTA
270465 -TAAAATTA
1 TTAAAATTA
270473 TTAAAATTA
1 TTAAAATTA
270482 TT
1 TT
270484 TTTTGAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 7 0.21
9 19 0.56
12 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAAAATTA
Found at i:270455 original size:20 final size:20
Alignment explanation
Indices: 270427--270483 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
270417 CCACGTCAGC
*
270427 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
*
270447 AAATTATTTTTAAAAATA-TA
1 AAATTA-TTTTAAAATTATTA
270467 AAATTA--TTAAAATTATT
1 AAATTATTTTAAAATTATT
270484 TTTTGAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 8 0.25
18 1 0.03
20 13 0.41
21 10 0.31
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:270478 original size:29 final size:30
Alignment explanation
Indices: 270436--270507 Score: 119
Period size: 29 Copynumber: 2.4 Consensus size: 30
270426 CAAATGATTT
270436 TAAAATTATTAAAATTATTTTTAAAAAT-A
1 TAAAATTATTAAAATTATTTTTAAAAATAA
**
270465 TAAAATTATTAAAATTATTTTTTGAAATAA
1 TAAAATTATTAAAATTATTTTTAAAAATAA
270495 TAAAATTATTAAA
1 TAAAATTATTAAA
270508 TAATTTTGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 26 0.65
30 14 0.35
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTAAAAATAA
Found at i:271784 original size:19 final size:20
Alignment explanation
Indices: 271752--271790 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
271742 TGATTCAAAA
271752 GTTAGGGTTCAATTT-TTTT
1 GTTAGGGTTCAATTTGTTTT
* *
271771 GTTAGTGTTTAATTTGTTTT
1 GTTAGGGTTCAATTTGTTTT
271791 AATTATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.15, C:0.03, G:0.21, T:0.62
Consensus pattern (20 bp):
GTTAGGGTTCAATTTGTTTT
Found at i:271861 original size:19 final size:19
Alignment explanation
Indices: 271837--271878 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
271827 AAGTTTAAAT
*
271837 TTTTTTAAATTTTAATTAA
1 TTTTTTAAATTTAAATTAA
* *
271856 TTTTTTAAGTTTAAATTCA
1 TTTTTTAAATTTAAATTAA
271875 TTTT
1 TTTT
271879 CTGACGTGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTTAAATTTAAATTAA
Found at i:272343 original size:2 final size:2
Alignment explanation
Indices: 272336--272360 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
272326 CCTAGCTTTT
272336 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
272361 TATATATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:272384 original size:16 final size:16
Alignment explanation
Indices: 272363--272403 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
272353 CACACACATA
*
272363 TATATTCTTTT-TTCTT
1 TATATTATTTTCTT-TT
272379 TATATTATTTTCTTTT
1 TATATTATTTTCTTTT
272395 TATA-TATTT
1 TATATTATTT
272404 CTTGAGACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 16 0.70
17 2 0.09
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (16 bp):
TATATTATTTTCTTTT
Found at i:275392 original size:27 final size:27
Alignment explanation
Indices: 275354--275480 Score: 159
Period size: 27 Copynumber: 4.7 Consensus size: 27
275344 AGGAGTAATA
* *
275354 TGATTCTGGCTCGAAAGAGCGTTATTT
1 TGATTCTGGCTCGAAAGAGCATTATTC
* *
275381 TGATTCTAGCTCG-AA-AGCGTTATTC
1 TGATTCTGGCTCGAAAGAGCATTATTC
*
275406 GGATTCTGGCTCGAAAGAGCATTATTC
1 TGATTCTGGCTCGAAAGAGCATTATTC
**
275433 TGATTCTGAATCGAAAGAGCATTATTC
1 TGATTCTGGCTCGAAAGAGCATTATTC
*
275460 TGATTCTGGGCTCGTAAGAGC
1 TGATTCT-GGCTCGAAAGAGC
275481 TAACCATTCT
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
25 20 0.23
26 4 0.05
27 52 0.60
28 10 0.12
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (27 bp):
TGATTCTGGCTCGAAAGAGCATTATTC
Found at i:275437 original size:52 final size:54
Alignment explanation
Indices: 275355--275480 Score: 159
Period size: 52 Copynumber: 2.4 Consensus size: 54
275345 GGAGTAATAT
* * * *
275355 GATTCTGGCTCGAAAGAGCGTTATTTTGATTCT-AGCTCG-AA-AGCGTTATTCG
1 GATTCTGGCTCGAAAGAGCATTATTCTGATTCTGA-ATCGAAAGAGCATTATTCG
*
275407 GATTCTGGCTCGAAAGAGCATTATTCTGATTCTGAATCGAAAGAGCATTATTCT
1 GATTCTGGCTCGAAAGAGCATTATTCTGATTCTGAATCGAAAGAGCATTATTCG
*
275461 GATTCTGGGCTCGTAAGAGC
1 GATTCT-GGCTCGAAAGAGC
275481 TAACCATTCT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
52 34 0.53
53 3 0.05
54 15 0.23
55 12 0.19
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (54 bp):
GATTCTGGCTCGAAAGAGCATTATTCTGATTCTGAATCGAAAGAGCATTATTCG
Found at i:275495 original size:24 final size:23
Alignment explanation
Indices: 275462--275594 Score: 158
Period size: 24 Copynumber: 5.5 Consensus size: 23
275452 CATTATTCTG
275462 ATTCTGGGCTCGTAAGAGCTAACC
1 ATTCT-GGCTCGTAAGAGCTAACC
275486 ATTCTAGGCTCGTAAGAGCTAACC
1 ATTCT-GGCTCGTAAGAGCTAACC
*
275510 ATTCTGGGCTTGTAAGAGCTAACC
1 ATTCT-GGCTCGTAAGAGCTAACC
* * *
275534 ATTTTGGATTCATAAGAGCTAACC
1 ATTCTGG-CTCGTAAGAGCTAACC
*
275558 ATTCTGAGCTCATAAGAGCTAACC
1 ATTCTG-GCTCGTAAGAGCTAACC
*
275582 GTTCTGCGCTCGT
1 ATTCTG-GCTCGT
275595 GTGGGCTAAG
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
23 2 0.02
24 92 0.97
25 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (23 bp):
ATTCTGGCTCGTAAGAGCTAACC
Found at i:275603 original size:48 final size:47
Alignment explanation
Indices: 275462--275594 Score: 176
Period size: 48 Copynumber: 2.8 Consensus size: 47
275452 CATTATTCTG
275462 ATTCTGGGCTCGTAAGAGCTAACCATTCTAGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACCATTCT-GGCTCGTAAGAGCTAACC
* * * *
275510 ATTCTGGGCTTGTAAGAGCTAACCATTTTGGATTCATAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACCATTCTGG-CTCGTAAGAGCTAACC
* * *
275558 ATTCTGAGCTCATAAGAGCTAACCGTTCTGCGCTCGT
1 ATTCTGGGCTCGTAAGAGCTAACCATTCTG-GCTCGT
275595 GTGGGCTAAG
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
47 2 0.03
48 69 0.96
49 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (47 bp):
ATTCTGGGCTCGTAAGAGCTAACCATTCTGGCTCGTAAGAGCTAACC
Found at i:287574 original size:21 final size:23
Alignment explanation
Indices: 287550--287596 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
287540 TTTAATTATT
287550 TTATTT-A-CTTTTTATTTTTCA
1 TTATTTCACCTTTTTATTTTTCA
*
287571 TTATTTCACTCTTTTTTTTTTTCA
1 TTATTTCAC-CTTTTTATTTTTCA
287595 TT
1 TT
287597 CTTCTTCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 1 0.05
24 15 0.68
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (23 bp):
TTATTTCACCTTTTTATTTTTCA
Found at i:290117 original size:20 final size:19
Alignment explanation
Indices: 290094--290135 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
290084 ATTTATACAA
*
290094 TTTTATTTTTATTTTAATAT
1 TTTTATTTTTAATTTAAT-T
*
290114 TTTTGTTTTTAATTTAATT
1 TTTTATTTTTAATTTAATT
290133 TTT
1 TTT
290136 ACATTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTATTTTTAATTTAATT
Found at i:290844 original size:21 final size:18
Alignment explanation
Indices: 290820--290858 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
290810 GACTAAGTTA
290820 AAAAGTTTTCAAAAAGTAGGG
1 AAAA-TTTT-AAAAA-TAGGG
290841 AAAATTTTAAAAATAGGG
1 AAAATTTTAAAAATAGGG
290859 TCATACGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 4 0.22
21 4 0.22
ACGTcount: A:0.51, C:0.03, G:0.21, T:0.26
Consensus pattern (18 bp):
AAAATTTTAAAAATAGGG
Found at i:296348 original size:15 final size:15
Alignment explanation
Indices: 296328--296356 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
296318 GTATATTTTT
296328 AAATTTTATTTATTG
1 AAATTTTATTTATTG
296343 AAATTTTATTTATT
1 AAATTTTATTTATT
296357 TTTTAACAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
AAATTTTATTTATTG
Found at i:299536 original size:26 final size:26
Alignment explanation
Indices: 299507--299559 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
299497 ACAAAATCTA
299507 GACGATAAGAATCATCATTATCCAAT
1 GACGATAAGAATCATCATTATCCAAT
299533 GACGATAAGAATCATCATTATCCAAT
1 GACGATAAGAATCATCATTATCCAAT
299559 G
1 G
299560 CCTCTTCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (26 bp):
GACGATAAGAATCATCATTATCCAAT
Found at i:300144 original size:43 final size:43
Alignment explanation
Indices: 300049--300149 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 43
300039 AACTGCACAA
* * *
300049 TTAATAACATGTCAATATATTAATAAGAGTCAAATAATATAAT
1 TTAATAACATGTCAACATATTAACAAGAATCAAATAATATAAT
** * *
300092 TTAGGAACATG-CAACCATATTAACACGAATCAAGTAATATAAT
1 TTAATAACATGTCAA-CATATTAACAAGAATCAAATAATATAAT
300135 TTAATAACATGTCAA
1 TTAATAACATGTCAA
300150 TGAATAACAT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
42 3 0.06
43 41 0.87
44 3 0.06
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.31
Consensus pattern (43 bp):
TTAATAACATGTCAACATATTAACAAGAATCAAATAATATAAT
Found at i:301541 original size:34 final size:35
Alignment explanation
Indices: 301493--301566 Score: 132
Period size: 34 Copynumber: 2.1 Consensus size: 35
301483 TTAATTTATA
*
301493 TTACTTACTTACTACTACTAACAAAATAAAA-TAC
1 TTACTTACTAACTACTACTAACAAAATAAAATTAC
301527 TTACTTACTAACTACTACTAACAAAATAAAATTAC
1 TTACTTACTAACTACTACTAACAAAATAAAATTAC
301562 TTACT
1 TTACT
301567 AACAAAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 30 0.79
35 8 0.21
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (35 bp):
TTACTTACTAACTACTACTAACAAAATAAAATTAC
Found at i:301606 original size:25 final size:21
Alignment explanation
Indices: 301542--301593 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
301532 TACTAACTAC
301542 TACTAACAAAATAAAATTACT
1 TACTAACAAAATAAAATTACT
301563 TACTAACAAAATAAAATTACT
1 TACTAACAAAATAAAATTACT
301584 TACTAACAAA
1 TACTAACAAA
301594 TTAATTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (21 bp):
TACTAACAAAATAAAATTACT
Found at i:301970 original size:4 final size:4
Alignment explanation
Indices: 301951--302013 Score: 83
Period size: 4 Copynumber: 15.8 Consensus size: 4
301941 AAAAAAATAC
* *
301951 CTTT CTCT CCTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
*
301999 -TTT CTCT CTTCT CTT
1 CTTT CTTT CTT-T CTT
302014 CTCACCCGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
3 3 0.06
4 44 0.86
5 4 0.08
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:303059 original size:97 final size:97
Alignment explanation
Indices: 302892--303077 Score: 318
Period size: 97 Copynumber: 1.9 Consensus size: 97
302882 AAAAGGATAC
*
302892 TCGATTATTCCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAACCCGA
1 TCGATTATCCCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAACCCGA
* *
302957 GATAAATAAATATTGCCTCGATTTAAGGGTAT
66 AATAAAGAAATATTGCCTCGATTTAAGGGTAT
* *
302989 TCGATTATCCCGATTTGAAGAAAAATCGTGCCTTGTAAGTTAAGGCACAAATTTTCAAAACCCGA
1 TCGATTATCCCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAACCCGA
*
303054 AATAAAGGAATATTGCCTCGATTT
66 AATAAAGAAATATTGCCTCGATTT
303078 TAAATATTTT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 83 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (97 bp):
TCGATTATCCCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAACCCGA
AATAAAGAAATATTGCCTCGATTTAAGGGTAT
Done.