Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003138.1 Hibiscus syriacus cultivar Beakdansim tig00006584_pilon, 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: 108414
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2718 original size:29 final size:29
Alignment explanation
Indices: 2641--2763 Score: 122
Period size: 29 Copynumber: 4.2 Consensus size: 29
2631 TATGATAGTT
* * *
2641 AAGGTACCATATTTGACATTTTGACAAACTA
1 AAGGTACCACATTCGACATTTT-A-AAAGTA
* *
2672 TAGGTACCGCA-TCAGACATTTTAAAAGTA
1 AAGGTACCACATTC-GACATTTTAAAAGTA
* *
2701 AAGGTACCACATTCGACATGTTGAAAGTA
1 AAGGTACCACATTCGACATTTTAAAAGTA
* * *
2730 TAGGTACCATATTGGACATTTTAAAAGTA
1 AAGGTACCACATTCGACATTTTAAAAGTA
2759 AAGGT
1 AAGGT
2764 GTCACGTTGG
Statistics
Matches: 75, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
29 55 0.73
30 4 0.05
31 16 0.21
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (29 bp):
AAGGTACCACATTCGACATTTTAAAAGTA
Found at i:2751 original size:58 final size:59
Alignment explanation
Indices: 2641--2763 Score: 158
Period size: 58 Copynumber: 2.1 Consensus size: 59
2631 TATGATAGTT
* * * *
2641 AAGGTACCATATTTGACATTTTGACAAACTATAGGTACCGCATCAGACATTTTAAAAGTA
1 AAGGTACCACATTCGACATGTTGA-AAACTATAGGTACCACATCAGACATTTTAAAAGTA
* * **
2701 AAGGTACCACATTCGACATGTTG-AAAGTATAGGTACCATATTGGACATTTTAAAAGTA
1 AAGGTACCACATTCGACATGTTGAAAACTATAGGTACCACATCAGACATTTTAAAAGTA
2759 AAGGT
1 AAGGT
2764 GTCACGTTGG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 35 0.64
60 20 0.36
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (59 bp):
AAGGTACCACATTCGACATGTTGAAAACTATAGGTACCACATCAGACATTTTAAAAGTA
Found at i:8161 original size:16 final size:16
Alignment explanation
Indices: 8142--8186 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
8132 CCATTTTCTT
8142 AGTTTGAGAGTTT-CAA
1 AGTTTGAGAGTTTAC-A
*
8158 AGTTTGAAAGTTTACA
1 AGTTTGAGAGTTTACA
*
8174 CGTTTGAGAGTTT
1 AGTTTGAGAGTTT
8187 GAGATTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (16 bp):
AGTTTGAGAGTTTACA
Found at i:8439 original size:83 final size:82
Alignment explanation
Indices: 8300--8586 Score: 376
Period size: 83 Copynumber: 3.5 Consensus size: 82
8290 ATAGAACATG
* * **
8300 CACCTTTCATTTCTGATGGAATGGAACACTATGACATGATAGAGATTCTATGAATAATAATGGAA
1 CACCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTATGAATAATAATGGAA
*
8365 AACGCTTCCATTGGAACA
66 AACGCTTCC-CTGGAACA
*
8383 CACCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAA
1 CACCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTATGAATAATAATGGAA
*
8448 AACGCTTCCCCTAGAACA
66 AACGCTT-CCCTGGAACA
* * * * * *
8466 CATCTTTCATTTCAGATGGGATGTAACAATATGACATGGCAGAGATTATATGAATAATAGTGGAA
1 CACCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTATGAATAATAATGGAA
* **
8531 AACGCTTCCCCGGAATG
66 AACGCTTCCCTGGAACA
** * *
8548 TGCCTTTCATTTTGGATGGGATGAAACACTATGACATGG
1 CACCTTTCATTTCGGATGGGATGGAACACTATGACATGG
8587 TGGAGATTAT
Statistics
Matches: 178, Mismatches: 25, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
82 38 0.21
83 138 0.78
84 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (82 bp):
CACCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTATGAATAATAATGGAA
AACGCTTCCCTGGAACA
Found at i:9480 original size:31 final size:32
Alignment explanation
Indices: 9436--9495 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 32
9426 CCTTAAACAA
9436 TAAATAAAAGCATACACATACACCTAAAATAG
1 TAAATAAAAGCATACACATACACCTAAAATAG
9468 TAAAT-AAAGCATACACATACACCTAAAA
1 TAAATAAAAGCATACACATACACCTAAAA
9496 CAAAATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.57, C:0.20, G:0.05, T:0.18
Consensus pattern (32 bp):
TAAATAAAAGCATACACATACACCTAAAATAG
Found at i:12102 original size:17 final size:16
Alignment explanation
Indices: 12068--12110 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
12058 AGACCTCGAG
12068 AAAAAGAACGAGACAA
1 AAAAAGAACGAGACAA
12084 AAAAAGAGACGGAGA-AA
1 AAAAAGA-AC-GAGACAA
*
12101 AAGAAGAACG
1 AAAAAGAACG
12111 TTGGAGTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 1 0.04
16 9 0.38
17 10 0.42
18 4 0.17
ACGTcount: A:0.65, C:0.09, G:0.26, T:0.00
Consensus pattern (16 bp):
AAAAAGAACGAGACAA
Found at i:12634 original size:24 final size:24
Alignment explanation
Indices: 12602--12657 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
12592 AAAAAACAAA
12602 AATGATCTCATATCCAAGACCAAC
1 AATGATCTCATATCCAAGACCAAC
*
12626 AATGATCTCATATCTAAGACCAAC
1 AATGATCTCATATCCAAGACCAAC
12650 AATGATCT
1 AATGATCT
12658 TGAAGGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (24 bp):
AATGATCTCATATCCAAGACCAAC
Found at i:14974 original size:14 final size:14
Alignment explanation
Indices: 14955--14983 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
14945 GTTTCAATGA
14955 ATTTAAATTATATC
1 ATTTAAATTATATC
14969 ATTTAAATTATATC
1 ATTTAAATTATATC
14983 A
1 A
14984 AATGGATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTAAATTATATC
Found at i:16527 original size:44 final size:44
Alignment explanation
Indices: 16450--16536 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
16440 TTTGTACAAA
* * *
16450 GTGCATCGATACACTTTGAAGGTGTACCAATGCATTCCTTGAAG
1 GTGCATCGATACACTATGAAAGTGCACCAATGCATTCCTTGAAG
**
16494 GTGCATCGATACACTATGAAAGTGCACTGATGCATTCCTTGAA
1 GTGCATCGATACACTATGAAAGTGCACCAATGCATTCCTTGAA
16537 TGTGTATCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (44 bp):
GTGCATCGATACACTATGAAAGTGCACCAATGCATTCCTTGAAG
Found at i:20040 original size:24 final size:24
Alignment explanation
Indices: 20013--20058 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
20003 GTTGTCCCTA
* *
20013 TCATCGTCATCCTCATCCTCCTTG
1 TCATCATCATCCTCATCATCCTTG
* *
20037 TCATTATCGTCCTCATCATCCT
1 TCATCATCATCCTCATCATCCT
20059 CTTTCTCCTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.15, C:0.39, G:0.07, T:0.39
Consensus pattern (24 bp):
TCATCATCATCCTCATCATCCTTG
Found at i:20072 original size:27 final size:27
Alignment explanation
Indices: 20012--20079 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
20002 CGTTGTCCCT
* *
20012 ATCATCGTCATCCTCATCCTCCTTGTC
1 ATCATCGTCATCATCATCCTCCTTCTC
* * *
20039 ATTATCGTCCTCATCATCCTCTTTCTC
1 ATCATCGTCATCATCATCCTCCTTCTC
* *
20066 CTCATCGTTATCAT
1 ATCATCGTCATCAT
20080 AACTCTCAAC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.16, C:0.37, G:0.06, T:0.41
Consensus pattern (27 bp):
ATCATCGTCATCATCATCCTCCTTCTC
Found at i:22067 original size:14 final size:14
Alignment explanation
Indices: 22048--22078 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
22038 CAAAATTATT
22048 TAAATAAATTCAAA
1 TAAATAAATTCAAA
*
22062 TAAATAAATTCTAA
1 TAAATAAATTCAAA
22076 TAA
1 TAA
22079 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATAAATTCAAA
Found at i:22584 original size:16 final size:16
Alignment explanation
Indices: 22563--22593 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
22553 GGCTAAGGCG
22563 CTTTCTACTAACAGCA
1 CTTTCTACTAACAGCA
22579 CTTTCTACTAACAGC
1 CTTTCTACTAACAGC
22594 GCCTTACTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.32, G:0.06, T:0.32
Consensus pattern (16 bp):
CTTTCTACTAACAGCA
Found at i:23527 original size:40 final size:40
Alignment explanation
Indices: 23472--23551 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
23462 GGTAAAAAAA
* *
23472 AAAAGCATTCCAAAGATTAAGAAAACCAGCAATAACACTG
1 AAAAGCATTCCAAAGATCAAGAAAACCAACAATAACACTG
23512 AAAAGCATTCCAAAGATCAAGAAAACCAACAATAACACTG
1 AAAAGCATTCCAAAGATCAAGAAAACCAACAATAACACTG
23552 CATTTAGCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.54, C:0.21, G:0.11, T:0.14
Consensus pattern (40 bp):
AAAAGCATTCCAAAGATCAAGAAAACCAACAATAACACTG
Found at i:24874 original size:18 final size:18
Alignment explanation
Indices: 24847--24901 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
24837 AAACCTTAAG
*
24847 CAAATGTAATTGCCACAT
1 CAAATATAATTGCCACAT
24865 CAAATATAATTGCCA-AT
1 CAAATATAATTGCCACAT
* *
24882 TAAAGATGAATTGCCACAT
1 CAAATAT-AATTGCCACAT
24901 C
1 C
24902 TTTTCGATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 7 0.23
18 22 0.71
19 2 0.06
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (18 bp):
CAAATATAATTGCCACAT
Found at i:25208 original size:25 final size:25
Alignment explanation
Indices: 25171--25248 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
25161 CTGACTAAGC
25171 CACTAA-GCAATATACAAAAAATGAA
1 CACTAAGGC-ATATACAAAAAATGAA
25196 CACTAAGGCATATACAAAAAAT--A
1 CACTAAGGCATATACAAAAAATGAA
* * *
25219 C-C-AAGCCATATGCAAAAAATGAC
1 CACTAAGGCATATACAAAAAATGAA
25242 CACTAAG
1 CACTAAG
25249 CTTTAACATC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
21 16 0.36
22 1 0.02
23 3 0.07
24 1 0.02
25 22 0.49
26 2 0.04
ACGTcount: A:0.54, C:0.21, G:0.10, T:0.15
Consensus pattern (25 bp):
CACTAAGGCATATACAAAAAATGAA
Found at i:25229 original size:21 final size:22
Alignment explanation
Indices: 25175--25243 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 22
25165 CTAAGCCACT
*
25175 AAGCAATATACAAAAAATGAACAC
1 AAGCCATATACAAAAAATG-AC-C
*
25199 TAAGGCATATACAAAAAAT-ACC
1 -AAGCCATATACAAAAAATGACC
*
25221 AAGCCATATGCAAAAAATGACC
1 AAGCCATATACAAAAAATGACC
25243 A
1 A
25244 CTAAGCTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
21 16 0.41
22 5 0.13
23 2 0.05
25 16 0.41
ACGTcount: A:0.57, C:0.19, G:0.10, T:0.14
Consensus pattern (22 bp):
AAGCCATATACAAAAAATGACC
Found at i:27287 original size:48 final size:48
Alignment explanation
Indices: 27219--27326 Score: 162
Period size: 48 Copynumber: 2.2 Consensus size: 48
27209 TTTTCATATT
* *
27219 CCACAGCAGCCATTGCTATGGGATAAATGCATTCATTTACATCAATTC
1 CCACAACAACCATTGCTATGGGATAAATGCATTCATTTACATCAATTC
* * * *
27267 CCATAACAACCATTGTTATGGGATAAATGCATTCATTTACGTCGATTC
1 CCACAACAACCATTGCTATGGGATAAATGCATTCATTTACATCAATTC
27315 CCACAACAACCA
1 CCACAACAACCA
27327 ATATGCACTC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (48 bp):
CCACAACAACCATTGCTATGGGATAAATGCATTCATTTACATCAATTC
Found at i:28424 original size:21 final size:21
Alignment explanation
Indices: 28395--28435 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28385 CAACAAAGTT
*
28395 CCAATAACCAATATCTATATC
1 CCAACAACCAATATCTATATC
* *
28416 CCAACAACCACTATTTATAT
1 CCAACAACCAATATCTATAT
28436 AACATCAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.29, G:0.00, T:0.29
Consensus pattern (21 bp):
CCAACAACCAATATCTATATC
Found at i:29971 original size:3 final size:3
Alignment explanation
Indices: 29963--29992 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
29953 AACTCTCCCC
29963 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
29993 TGGTCAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:30358 original size:24 final size:24
Alignment explanation
Indices: 30330--30397 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
30320 TGTTAAAATG
*
30330 ATAAAAAAACACAAATGAATGAAC
1 ATAAAAAAACACAAATGAACGAAC
** * *
30354 ATAAATGAACACAAACGAACGGAC
1 ATAAAAAAACACAAATGAACGAAC
* * *
30378 ATAAACAAATATAAATGAAC
1 ATAAAAAAACACAAATGAAC
30398 ATAAACGAAA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.62, C:0.15, G:0.10, T:0.13
Consensus pattern (24 bp):
ATAAAAAAACACAAATGAACGAAC
Found at i:30630 original size:14 final size:14
Alignment explanation
Indices: 30614--30665 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
30604 ATAAACGAAC
30614 ATAAACGAACA-AA
1 ATAAACGAACATAA
30627 CATAAACGAACATAA
1 -ATAAACGAACATAA
*
30642 ATAAACAAACATAA
1 ATAAACGAACATAA
*
30656 ATGAACGAAC
1 ATAAACGAAC
30666 GGATTACTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
14 32 0.94
15 2 0.06
ACGTcount: A:0.63, C:0.17, G:0.08, T:0.12
Consensus pattern (14 bp):
ATAAACGAACATAA
Found at i:30636 original size:24 final size:24
Alignment explanation
Indices: 30604--30661 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
30594 TGGGTTAAAT
*
30604 ATAAACGAACATAAACGAACAAAC
1 ATAAACGAACATAAACAAACAAAC
*
30628 ATAAACGAACATAAATAAACAAAC
1 ATAAACGAACATAAACAAACAAAC
*
30652 ATAAATGAAC
1 ATAAACGAAC
30662 GAACGGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.64, C:0.17, G:0.07, T:0.12
Consensus pattern (24 bp):
ATAAACGAACATAAACAAACAAAC
Found at i:31240 original size:40 final size:40
Alignment explanation
Indices: 31196--31274 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
31186 ACTTGTTAGA
*
31196 TAAAAAAAAGGAAATAAAAATAAATAAGAT-A-ATAAAAAAT
1 TAAAAAAAAGAAAAT-AAAATAAA-AAGATAAGATAAAAAAT
*
31236 TAAAATAAAGAAAATAAAATAAAAAGATAAGATAAAAAA
1 TAAAAAAAAGAAAATAAAATAAAAAGATAAGATAAAAAA
31275 AGAGTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 5 0.14
39 9 0.26
40 21 0.60
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (40 bp):
TAAAAAAAAGAAAATAAAATAAAAAGATAAGATAAAAAAT
Found at i:31244 original size:13 final size:12
Alignment explanation
Indices: 31207--31322 Score: 56
Period size: 13 Copynumber: 8.9 Consensus size: 12
31197 AAAAAAAAGG
31207 AAATAAAAATAAA
1 AAAT-AAAATAAA
* * *
31220 TAAGATAATAAA
1 AAATAAAATAAA
31232 AAATTAAAATAAAGA
1 AAA-TAAAAT-AA-A
31247 AAATAAAATAAA
1 AAATAAAATAAA
*
31259 AAGATAAGATAAA
1 AA-ATAAAATAAA
* *
31272 AAA-AGAGTAAA
1 AAATAAAATAAA
31283 AATGATAAAGATAAA
1 AA--ATAAA-ATAAA
*
31298 AAAGTAAGTAA-AAT
1 AAA-TAA--AATAAA
31312 AAATAAAATAA
1 AAATAAAATAA
31323 TGATAAAAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 25
0.67 0.11 0.22
Matches are distributed among these distances:
11 9 0.12
12 15 0.19
13 24 0.31
14 18 0.23
15 11 0.14
16 1 0.01
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:31273 original size:70 final size:69
Alignment explanation
Indices: 31193--31362 Score: 159
Period size: 70 Copynumber: 2.4 Consensus size: 69
31183 GAAACTTGTT
*
31193 AGATAAAAAAAAGGAAATAAAAATAA-ATAAGATAATAAAA-AATTAAAATAAAGAAAATAA-AA
1 AGAT-AAAAAAA-G-AATAAAAATAATA-AAGATAA-AAAAGAAGTAAAATAAAGAAAATAATAA
31255 TAAAAAGATA
61 TAAAAA-ATA
* * * *
31265 AGATAAAAAAAGAGTAAAAATGATAAAGATAAAAAAGTAAGTAAAATAAATAAAATAATGATAAA
1 AGATAAAAAAAGAATAAAAATAATAAAGATAAAAAAG-AAGTAAAATAAAGAAAATAATAATAAA
31330 AAATA
65 AAATA
* *
31335 ATGACAAACAAAATAAATAAAAA-AATAA
1 A-GATAAA-AAAA-GAATAAAAATAATAA
31363 TAGTAAGAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
68 4 0.05
69 16 0.20
70 24 0.29
71 19 0.23
72 12 0.15
73 7 0.09
ACGTcount: A:0.73, C:0.01, G:0.09, T:0.17
Consensus pattern (69 bp):
AGATAAAAAAAGAATAAAAATAATAAAGATAAAAAAGAAGTAAAATAAAGAAAATAATAATAAAA
AATA
Found at i:31274 original size:25 final size:26
Alignment explanation
Indices: 31246--31300 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
31236 TAAAATAAAG
*
31246 AAAATAAAATAAAAA-GAT-AAGATA
1 AAAAAAAAATAAAAATGATAAAGATA
* *
31270 AAAAAAGAGTAAAAATGATAAAGATA
1 AAAAAAAAATAAAAATGATAAAGATA
31296 AAAAA
1 AAAAA
31301 GTAAGTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 12 0.46
25 3 0.12
26 11 0.42
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.15
Consensus pattern (26 bp):
AAAAAAAAATAAAAATGATAAAGATA
Found at i:31275 original size:26 final size:26
Alignment explanation
Indices: 31246--31358 Score: 54
Period size: 26 Copynumber: 4.2 Consensus size: 26
31236 TAAAATAAAG
*
31246 AAAATAAAATAAA-AAGATAAGATAA
1 AAAATAAAATAAACAAAATAAGATAA
* * *
31271 AAAA-AGAGTAAA-AATGATAAAGATAA
1 AAAATAAAATAAACAA-AAT-AAGATAA
*
31297 AAAAGTAAGTAAAATAAATAAAATAATGATAA
1 AAAA-T----AAAATAAACAAAATAA-GATAA
* *
31329 AAAATAATGACAAACAAAATAA-ATAA
1 AAAATAA-AATAAACAAAATAAGATAA
31355 AAAA
1 AAAA
31359 ATAATAGTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 21
0.70 0.08 0.21
Matches are distributed among these distances:
24 8 0.12
25 7 0.10
26 19 0.28
27 2 0.03
28 11 0.16
31 3 0.04
32 17 0.25
33 2 0.03
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.17
Consensus pattern (26 bp):
AAAATAAAATAAACAAAATAAGATAA
Found at i:31301 original size:25 final size:24
Alignment explanation
Indices: 31240--31310 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 24
31230 AAAAATTAAA
31240 ATAAAGA-AAATAAA-A-TAAAAAG
1 ATAAAGATAAA-AAAGAGTAAAAAG
31262 AT-AAGATAAAAAAAGAGTAAAAATG
1 ATAAAGAT-AAAAAAGAGTAAAAA-G
31287 ATAAAGATAAAAAAGTAAGTAAAA
1 ATAAAGATAAAAAAG--AGTAAAA
31311 TAAATAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
21 4 0.10
22 5 0.12
23 4 0.10
24 6 0.15
25 10 0.24
26 5 0.12
27 7 0.17
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (24 bp):
ATAAAGATAAAAAAGAGTAAAAAG
Found at i:31433 original size:14 final size:15
Alignment explanation
Indices: 31392--31434 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
31382 ATATATAATA
*
31392 AAGAAATAAATAAAC
1 AAGAAGTAAATAAAC
*
31407 AAGAAGAAAATAAA-
1 AAGAAGTAAATAAAC
*
31421 AATAAGTAAATAAA
1 AAGAAGTAAATAAA
31435 TAAAATCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.14
Consensus pattern (15 bp):
AAGAAGTAAATAAAC
Found at i:31437 original size:63 final size:61
Alignment explanation
Indices: 31370--31572 Score: 140
Period size: 63 Copynumber: 3.3 Consensus size: 61
31360 TAATAGTAAG
31370 AATAATATATATATATATAATAAAGAAATAAATAAACAAGAAGAAAATAAAAATAAGTAAATA
1 AATAATATATATATATATAATAAAGAAATAAATAAA-AAGAAGAAAATAAAAA-AAGTAAATA
* * *
31433 AATAA-A-AT-CA-ATAT-A-AAAGAAATAAA-AAAAATGAA-ATAAATGTAAAAAAATTAAAAA
1 AATAATATATATATATATAATAAAGAAATAAATAAAAA-GAAGA-AAA--TAAAAAAAGTAAATA
* * * * *
31490 AAT-ATATATAAAAATA-AGATAAAGGAAA-AAATAAAAAAAAGAAACAAAAAGAAAAAGGAAAT
1 AATAATATATATATATATA-ATAAA-GAAATAAATAAAAAGAAG-AA-AATAA-AAAAAGTAAAT
31552 A
61 A
*
31553 TATATATATATATATATATA
1 AATA-ATATATATATATATA
31573 TGATAATATT
Statistics
Matches: 108, Mismatches: 12, Indels: 37
0.69 0.08 0.24
Matches are distributed among these distances:
55 3 0.03
56 10 0.09
57 22 0.20
58 9 0.08
59 5 0.05
60 4 0.04
61 3 0.03
62 11 0.10
63 26 0.24
64 3 0.03
65 11 0.10
66 1 0.01
ACGTcount: A:0.70, C:0.01, G:0.07, T:0.22
Consensus pattern (61 bp):
AATAATATATATATATATAATAAAGAAATAAATAAAAAGAAGAAAATAAAAAAAGTAAATA
Found at i:31463 original size:24 final size:23
Alignment explanation
Indices: 31428--31472 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
31418 AAAAATAAGT
*
31428 AAATAAATAAAATCAATATAAAAG
1 AAATAAAAAAAATCAA-ATAAAAG
*
31452 AAATAAAAAAAATGAAATAAA
1 AAATAAAAAAAATCAAATAAA
31473 TGTAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (23 bp):
AAATAAAAAAAATCAAATAAAAG
Found at i:31464 original size:29 final size:28
Alignment explanation
Indices: 31418--31493 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
31408 AGAAGAAAAT
*
31418 AAAAATAAGTAAATAAATAAAATCAATATAA
1 AAAAATAA--AAA-AAATAAAATAAATATAA
* *
31449 AAGAAATAAAAAAAATGAAATAAATGTAA
1 AA-AAATAAAAAAAATAAAATAAATATAA
*
31478 AAAAATTAAAAAAATA
1 AAAAATAAAAAAAATA
31494 TATATAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 12 0.31
29 16 0.41
30 3 0.08
31 2 0.05
32 6 0.15
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (28 bp):
AAAAATAAAAAAAATAAAATAAATATAA
Found at i:31470 original size:14 final size:13
Alignment explanation
Indices: 31399--31539 Score: 51
Period size: 14 Copynumber: 10.7 Consensus size: 13
31389 ATAAAGAAAT
*
31399 AAATAAACAAGAAG
1 AAATAAA-AAAAAG
*
31413 AAAATAAAAATAAG
1 -AAATAAAAAAAAG
* *
31427 TAAATAAATAAAAT
1 -AAATAAAAAAAAG
* *
31441 CAAT--ATAAAAG
1 AAATAAAAAAAAG
31452 AAATAAAAAAAATG
1 AAATAAAAAAAA-G
31466 AAATAAATGTAAAAA-
1 AAATAAA---AAAAAG
* *
31481 AATTAAAAAAATAT
1 AAATAAAAAAA-AG
* *
31495 ATATAAAAATAAG
1 AAATAAAAAAAAG
**
31508 --ATAAAGGAAA-
1 AAATAAAAAAAAG
31518 AAATAAAAAAAAG
1 AAATAAAAAAAAG
*
31531 AAACAAAAA
1 AAATAAAAA
31540 GAAAAAGGAA
Statistics
Matches: 95, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
11 16 0.17
12 12 0.13
13 18 0.19
14 31 0.33
15 13 0.14
17 5 0.05
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (13 bp):
AAATAAAAAAAAG
Found at i:31474 original size:9 final size:9
Alignment explanation
Indices: 31207--31473 Score: 76
Period size: 9 Copynumber: 29.4 Consensus size: 9
31197 AAAAAAAAGG
31207 AAATAAAAAT
1 AAAT-AAAAT
*
31217 AAATAAGAT
1 AAATAAAAT
31226 -AATAAAA-
1 AAATAAAAT
*
31233 AATTAAAAT
1 AAATAAAAT
*
31242 AAAGAAAAT
1 AAATAAAAT
31251 AAAATAAAA-
1 -AAATAAAAT
* *
31260 AGATAAGAT
1 AAATAAAAT
31269 AAA-AAAA-
1 AAATAAAAT
* *
31276 GAGTAAAA-
1 AAATAAAAT
*
31284 ATGATAAAGAT
1 A-AATAAA-AT
*
31295 AAA-AAAGT
1 AAATAAAAT
*
31303 AAGTAAAAT
1 AAATAAAAT
31312 AAATAAAAT
1 AAATAAAAT
31321 -AATGATAAA-
1 AAAT-A-AAAT
* *
31330 AAATAATGAC
1 AAATAA-AAT
*
31340 AAACAAAAT
1 AAATAAAAT
31349 AAATAAAA-
1 AAATAAAAT
*
31357 AAATAATAGT
1 AAATAA-AAT
*
31367 AAGA-ATAAT
1 AA-ATAAAAT
* *
31376 ATATATATAT
1 AAATA-AAAT
*
31386 ATAAT-AAAG
1 A-AATAAAAT
31395 AAAT-AAAT
1 AAATAAAAT
* *
31403 AAACAAGAAGA
1 AAATAA-AA-T
31414 AAATAAAAAT
1 AAAT-AAAAT
*
31424 AAGT-AAAT
1 AAATAAAAT
31432 AAATAAAAT
1 AAATAAAAT
*
31441 CAATATAAAAG
1 -AA-ATAAAAT
*
31452 AAATAAAAA
1 AAATAAAAT
*
31461 AAATGAAAT
1 AAATAAAAT
31470 AAAT
1 AAAT
31474 GTAAAAAAAT
Statistics
Matches: 185, Mismatches: 45, Indels: 55
0.65 0.16 0.19
Matches are distributed among these distances:
7 1 0.01
8 55 0.30
9 73 0.39
10 39 0.21
11 15 0.08
12 2 0.01
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:31521 original size:17 final size:17
Alignment explanation
Indices: 31499--31550 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
31489 AAATATATAT
*
31499 AAAAATAAGATAAAGGA
1 AAAAATAAGAAAAAGGA
*
31516 AAAAATAA-AAAAAAGA
1 AAAAATAAGAAAAAGGA
31532 AACAAA-AAGAAAAAGGA
1 AA-AAATAAGAAAAAGGA
31549 AA
1 AA
31551 TATATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 10 0.33
17 20 0.67
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06
Consensus pattern (17 bp):
AAAAATAAGAAAAAGGA
Found at i:31529 original size:9 final size:9
Alignment explanation
Indices: 31413--31545 Score: 54
Period size: 9 Copynumber: 14.1 Consensus size: 9
31403 AAACAAGAAG
31413 AAAATAAAA
1 AAAATAAAA
*
31422 ATAAGT-AAA
1 A-AAATAAAA
*
31431 TAAATAAAA
1 AAAATAAAA
*
31440 TCAATATAAAA
1 --AAAATAAAA
*
31451 GAAATAAAA
1 AAAATAAAA
31460 AAAATGAAATA
1 AAAAT-AAA-A
**
31471 AATGTAAAA
1 AAAATAAAA
*
31480 AAATTAAAA
1 AAAATAAAA
*
31489 AAATATATATA
1 AAA-ATA-AAA
*
31500 AAAATAAGA
1 AAAATAAAA
* **
31509 TAAA-GGAA
1 AAAATAAAA
31517 AAAATAAAA
1 AAAATAAAA
*
31526 AAAAGAAACA
1 AAAATAAA-A
*
31536 AAAAGAAAA
1 AAAATAAAA
31545 A
1 A
31546 GGAAATATAT
Statistics
Matches: 91, Mismatches: 23, Indels: 20
0.68 0.17 0.15
Matches are distributed among these distances:
8 7 0.08
9 45 0.49
10 23 0.25
11 16 0.18
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.17
Consensus pattern (9 bp):
AAAATAAAA
Found at i:31604 original size:38 final size:38
Alignment explanation
Indices: 31564--31637 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 38
31554 ATATATATAT
* *
31564 ATATATATATGATAATATTAA-AAAAGA-ATAAATAAA
1 ATATATATATTAGAATATTAATAAAAGATATAAATAAA
* *
31600 ATATATGTATTAGAATATTAATAAAATATATAAATAAA
1 ATATATATATTAGAATATTAATAAAAGATATAAATAAA
31638 TAAAAATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 18 0.56
37 5 0.16
38 9 0.28
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (38 bp):
ATATATATATTAGAATATTAATAAAAGATATAAATAAA
Found at i:31639 original size:23 final size:24
Alignment explanation
Indices: 31593--31654 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
31583 AAAAAAGAAT
* * *
31593 AAATAAAATATATGTATTAGAATAT
1 AAATAAAATATAT-AAATAGAATAA
*
31618 TAATAAAATATATAAATA-AATAA
1 AAATAAAATATATAAATAGAATAA
*
31641 AAATAATATATATA
1 AAATAAAATATATA
31655 TATATACATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 16 0.52
24 3 0.10
25 12 0.39
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (24 bp):
AAATAAAATATATAAATAGAATAA
Found at i:33579 original size:85 final size:85
Alignment explanation
Indices: 33453--34786 Score: 1398
Period size: 85 Copynumber: 15.8 Consensus size: 85
33443 ATATGTCATC
* * * ** * *
33453 GAGCTGAATGGAATCGAACTCGACA-GTTTTTGTTGATAGATAGA-TTTTCTCGACTTAAGCTAT
1 GAGCTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATA-ACCCTTCTCGCCTTGAGCTAT
* *
33516 GCTATAAATTTGACATGCCCTT
64 GCTATAAATTTGATATGCCTTT
* * * * * * *
33538 GAGCTGAATGGAATCGAACTTGAAGGTATTTTTTGACAGATAACCCTTCTTGCCTTGAGCTGTGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
33603 TGTAAATTTGATATGCCTTT
66 TATAAATTTGATATGCCTTT
* * * ** *
33623 GAGCTGAATGTATTTGAACTCGAAGGTCTTGGTTGACAGATTGCCCTTCTCGCCTTGAGCTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
33688 TGTAAATTTGATATGCCTTT
66 TATAAATTTGATATGCCTTT
* * * * *
33708 GAGCTTG-ATGTAATTGAACTCGAAGGTCTTGGTTGACAGCTAGCCCTTCTCGCCTTGAGCTATA
1 GAGC-TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
33772 CTATAAATTTGATATGCCTTT
65 CTATAAATTTGATATGCCTTT
* * * * * * *
33793 GAGCTGACTTTAATCGAACTCGAAGGTCTTTGCTGACAGATAACACTTCTCGTCTTTAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
* *
33858 TGTAAATTGGATATGCCTTT
66 TATAAATTTGATATGCCTTT
* *
33878 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAACTCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* *
33943 TTATAAATTTGATGTGCCTTT
65 CTATAAATTTGATATGCCTTT
* * * *
33964 GAGTTGACTGTAATCGAACTTC-AAGGT-TTTGGTTGACATATAACCCTTCTCGCCTTGAGTTAT
1 GAGCTGAATGTAATCGAAC-TCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGCCTTGAGCTAT
* *
34027 GCTGTAAATGTGATATGCCTTT
64 GCTATAAATTTGATATGCCTTT
* * *
34049 GAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGACACATAACCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* *
34114 CTATAAATTTGATGTTCCTTT
65 CTATAAATTTGATATGCCTTT
* * * * * *
34135 GAGCTGAATGTAATCTAACTCGAAGGTCTTGGTAGAAAGATAACCCTTCTCACCTTGAGTTATG-
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
* *
34199 --T---TGT-AAATGCCTTT
66 TATAAATTTGATATGCCTTT
* * * * *
34213 GAGCTGAATATAATCGAACTCGAAGGCCTTTGTTGATAGATAGCCCTTCTCGGCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
* *
34278 TATAAATTTGATGTACCTTT
66 TATAAATTTGATATGCCTTT
* * * * *
34298 GAGCTGAATGTAATCGAACTCGAAGGACTTGGTAGACAGATAACCCTTCTCACCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
* * *
34363 TGTAAATGCTTTTGATGTACCTTT
66 TATAAA----TTTGATATGCCTTT
* * * ** * *
34387 GAGCTGAGTGTAATCGTACTCGAAGGTCCTTTATTGACAGATAGTCATTCTTGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGT-CTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* * *
34452 CTGTAAATTTAATGTGCCTTT
65 CTATAAATTTGATATGCCTTT
* * ** * *
34473 GAGCTGAGTGTAATCGAACTTGAAGGTCTTCATTGACAGATAGA-CATTCTCGCCTTGAGTTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATA-ACCCTTCTCGCCTTGAGCTATG
** *
34537 CTGCAAATTTGATATG-ATTAT
65 CTATAAATTTGATATGCCTT-T
* * * *
34558 GAGCTAAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCCATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
34623 -A-ACA----A-ATGCCTTT
66 TATAAATTTGATATGCCTTT
* * *
34636 GAGATGAATGTAATCGAACTCGAAGGTCTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
34701 -AGTAAATTTGATATGGCTTT
66 TA-TAAATTTGATATGCCTTT
* * * * *
34721 GAGTTGAATGTAATCAAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCCATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
34786 T
66 T
34787 GCCAATAGTT
Statistics
Matches: 1054, Mismatches: 161, Indels: 67
0.82 0.13 0.05
Matches are distributed among these distances:
78 126 0.12
79 5 0.00
80 2 0.00
81 1 0.00
82 1 0.00
83 2 0.00
84 13 0.01
85 645 0.61
86 181 0.17
87 5 0.00
89 38 0.04
90 35 0.03
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
TATAAATTTGATATGCCTTT
Found at i:34015 original size:171 final size:170
Alignment explanation
Indices: 33453--34786 Score: 1486
Period size: 171 Copynumber: 7.9 Consensus size: 170
33443 ATATGTCATC
* * * * ** * * *
33453 GAGCTGAATGGAATCGAACTCGACA-GTTTTTGTTGATAGATAGA-TTTTCTCGACTTAAGCTAT
1 GAGCTGAATGTAATCGAACTCGA-AGGTCTTGGTTGACAGATA-ACCCTTCTCGCCTTGAGTTAT
* * * * * * *
33516 GCTATAAATTTGACATGCCCTTGAGCTGAATGGAATCGAACTTGAAGGTATTTTTTGACAGATAA
64 GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAA
* * * * *
33581 CCCTTCTTGCCTTGAGCTGTGTTGTAAATTTGATATGCCTTT
129 CCCTTCTCGCCTTGAGCTATGCTATAAATTTGATGTGCCTTT
* * ** * *
33623 GAGCTGAATGTATTTGAACTCGAAGGTCTTGGTTGACAGATTGCCCTTCTCGCCTTGAGCTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
* * * *
33688 TGTAAATTTGATATGCCTTTGAGCTTG-ATGTAATTGAACTCGAAGGTCTTGGTTGACAGCTAGC
66 TGTAAATTTGATATGCCTTTGAGC-TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAAC
* *
33752 CCTTCTCGCCTTGAGCTATACTATAAATTTGATATGCCTTT
130 CCTTCTCGCCTTGAGCTATGCTATAAATTTGATGTGCCTTT
* * * * * * *
33793 GAGCTGACTTTAATCGAACTCGAAGGTCTTTGCTGACAGATAACACTTCTCGTCTTTAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
* *
33858 TGTAAATTGGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAAC
66 TGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAAC
* *
33923 TCTTCTCGCCTTGAGCTATGTTATAAATTTGATGTGCCTTT
130 CCTTCTCGCCTTGAGCTATGCTATAAATTTGATGTGCCTTT
* * * *
33964 GAGTTGACTGTAATCGAACTTC-AAGGTTTTGGTTGACATATAACCCTTCTCGCCTTGAGTTATG
1 GAGCTGAATGTAATCGAAC-TCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
* * * *
34028 CTGTAAATGTGATATGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGACACATAA
65 CTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAA
*
34093 CCCTTCTCGCCTTGAGCTATGCTATAAATTTGATGTTCCTTT
129 CCCTTCTCGCCTTGAGCTATGCTATAAATTTGATGTGCCTTT
* * * * *
34135 GAGCTGAATGTAATCTAACTCGAAGGTCTTGGTAGAAAGATAACCCTTCTCACCTTGAGTTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
* * * *
34200 TGT--A----A-ATGCCTTTGAGCTGAATATAATCGAACTCGAAGGCCTTTGTTGATAGATAGCC
66 TGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACC
* *
34258 CTTCTCGGCTTGAGCTATGCTATAAATTTGATGTACCTTT
131 CTTCTCGCCTTGAGCTATGCTATAAATTTGATGTGCCTTT
* * *
34298 GAGCTGAATGTAATCGAACTCGAAGGACTTGGTAGACAGATAACCCTTCTCACCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
* * * * *
34363 TGTAAATGCTTTTGATGTACCTTTGAGCTGAGTGTAATCGTACTCGAAGGTCCTTTATTGACAGA
66 TGTAAA----TTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGT-CTTTGTTGACAGA
** * * * *
34428 TAGTCATTCTTGCCTTGAGCTATGCTGTAAATTTAATGTGCCTTT
126 TAACCCTTCTCGCCTTGAGCTATGCTATAAATTTGATGTGCCTTT
* * ** *
34473 GAGCTGAGTGTAATCGAACTTGAAGGTCTTCATTGACAGATAGA-CATTCTCGCCTTGAGTTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATA-ACCCTTCTCGCCTTGAGTTATG
* * * * *
34537 CTGCAAATTTGATATG-ATTATGAGCTAAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAG
65 CTGTAAATTTGATATGCCTT-TGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAA
*
34601 CCCTTCTCGCCTTGAGCCATGC-A-ACAA----A--TGCCTTT
129 CCCTTCTCGCCTTGAGCTATGCTATA-AATTTGATGTGCCTTT
* * * * *
34636 GAGATGAATGTAATCGAACTCGAAGGTCTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
* * * * * *
34701 AGTAAATTTGATATGGCTTTGAGTTGAATGTAATCAAACTCGAAGGTCTTGGTTGACAGATAGCC
66 TGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACC
*
34766 CTTCTCGCCTTGAGCCATGCT
131 CTTCTCGCCTTGAGCTATGCT
34787 GCCAATAGTT
Statistics
Matches: 995, Mismatches: 144, Indels: 56
0.83 0.12 0.05
Matches are distributed among these distances:
163 254 0.26
164 34 0.03
165 3 0.00
168 1 0.00
169 6 0.01
170 266 0.27
171 289 0.29
172 2 0.00
173 1 0.00
174 29 0.03
175 109 0.11
176 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (170 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
TGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACC
CTTCTCGCCTTGAGCTATGCTATAAATTTGATGTGCCTTT
Found at i:34587 original size:423 final size:416
Alignment explanation
Indices: 33453--34786 Score: 1508
Period size: 423 Copynumber: 3.2 Consensus size: 416
33443 ATATGTCATC
* * * * ** * *
33453 GAGCTGAATGGAATCGAACTCGACA-GTTTTTGTTGATAGATAGA-TTTTCTCGACTTAAGCTAT
1 GAGCTGAATGTAATCGAACTCGA-AGGTCTTGGTTGACAGATA-ACCCTTCTCGCCTTGAGCTAT
** * * * * *
33516 GCTATAAATTTGACATGCCCTTGAGCTGAATGGAATCGAACTTGAAGGTATTTTTTGACAGATAA
64 GCTATAAATTTGATGTACCTTTGAGCTGAATGTAATCGAACTCGAAGGT-TTTATTGACAGATAA
* * * * * *
33581 CCCTTCTTGCCTTGAGCTGTGTTGTAAATTTGATATGCCTTTGAGCTGAATGTATTTGAACTCGA
128 CCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTTGA
* * * *
33646 AGGTCTTGGTTGACAGATTGCCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGCCTTTGAG
193 AGGTCTTCGTTGACAGATAGACCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATG-CTTTGAG
** * * *
33711 CTTGATGTAATTGAACTCGAAGGTCTTGGTTGACAGCTAGCCCTTCTCGCCTTGAGCTATACTAT
257 CTAAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAG-T-TA-TGT
* * * * * * * *
33776 AAATTTGATATGCCTTTGAGCTGACTTTAATCGAACTCGAAGGTCTTTGCTGACAGATAACACTT
319 ---TAT-AAATGCCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGTTGATAGATAGCCCTT
* * * * *
33841 CTCGTCTTTAGTTATGCTGTAAATTGGATATGCCTTT
380 CTCGCCTTGAGCTATGCTATAAATTTGATATGCCTTT
* * *
33878 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAACTCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* * * * * *
33943 TTATAAATTTGATGTGCCTTTGAGTTGACTGTAATCGAACTTC-AAGGTTTTGGTTGACATATAA
65 CTATAAATTTGATGTACCTTTGAGCTGAATGTAATCGAAC-TCGAAGGTTTT-ATTGACAGATAA
* * *
34007 CCCTTCTCGCCTTGAGTTATGCTGTAAATGTGATATGCCTTTGAGCTGAGTGTAATCGAACTTGA
128 CCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTTGA
* * * * *
34072 AGGTCTTTTGTTGACACATA-ACCCTTCTCGCCTTGAGCTATGCTATAAATTTGATGTTCCTTTG
193 AGGTC-TTCGTTGACAGATAGA-CCTTCTCGCCTTGAGCTATGCTGTAAATTTGAT-ATGCTTTG
* * * * * *
34136 AGCTGAATGTAATCTAACTCGAAGGTCTTGGTAGAAAGATAACCCTTCTCACCTTGAGTTATGTT
255 AGCTAAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGTT
* * *
34201 GTAAATGCCTTTGAGCTGAATATAATCGAACTCGAAGGCCTTTGTTGATAGATAGCCCTTCTCGG
320 ATAAATGCCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGTTGATAGATAGCCCTTCTCGC
* *
34266 CTTGAGCTATGCTATAAATTTGATGTACCTTT
385 CTTGAGCTATGCTATAAATTTGATATGCCTTT
* * * *
34298 GAGCTGAATGTAATCGAACTCGAAGGACTTGGTAGACAGATAACCCTTCTCACCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
* * *
34363 TGTAAATGCTTTTGATGTACCTTTGAGCTGAGTGTAATCGTACTCGAAGGTCCTTTATTGACAGA
66 TATAAA----TTTGATGTACCTTTGAGCTGAATGTAATCGAACTCGAAGGT--TTTATTGACAGA
** * * *
34428 TAGTCATTCTTGCCTTGAGCTATGCTGTAAATTTAATGTGCCTTTGAGCTGAGTGTAATCGAACT
125 TAACCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACT
* * * * *
34493 TGAAGGTCTTCATTGACAGATAGACATTCTCGCCTTGAGTTATGCTGCAAATTTGATATGATTAT
190 TGAAGGTCTTCGTTGACAGATAGACCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCTT-T
** *
34558 GAGCTAAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCCATGC
254 GAGCTAAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGT
* * * *
34623 AACAAATGCCTTTGAGATGAATGTAATCGAACTCGAAGGTCTTTGTTGATAGATAGCCCTTCTCG
319 TATAAATGCCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGTTGATAGATAGCCCTTCTCG
*
34688 CCTTGAGCTATGC-AGTAAATTTGATATGGCTTT
384 CCTTGAGCTATGCTA-TAAATTTGATATGCCTTT
* * * *
34721 GAGTTGAATGTAATCAAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCCATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
34786 T
66 T
34787 GCCAATAGTT
Statistics
Matches: 773, Mismatches: 118, Indels: 38
0.83 0.13 0.04
Matches are distributed among these distances:
419 35 0.05
420 107 0.14
421 2 0.00
422 6 0.01
423 275 0.36
424 76 0.10
425 33 0.04
426 141 0.18
427 97 0.13
428 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (416 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
TATAAATTTGATGTACCTTTGAGCTGAATGTAATCGAACTCGAAGGTTTTATTGACAGATAACCC
TTCTTGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTTGAAGG
TCTTCGTTGACAGATAGACCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCTTTGAGCTAA
ATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGTTATAAAT
GCCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGTTGATAGATAGCCCTTCTCGCCTTGAG
CTATGCTATAAATTTGATATGCCTTT
Found at i:35628 original size:14 final size:14
Alignment explanation
Indices: 35609--35635 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35599 CAGAGTTATA
35609 ATTCTTTGACAAAT
1 ATTCTTTGACAAAT
35623 ATTCTTTGACAAA
1 ATTCTTTGACAAA
35636 CATGCATTTT
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:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (14 bp):
ATTCTTTGACAAAT
Found at i:36106 original size:95 final size:95
Alignment explanation
Indices: 35913--36170 Score: 378
Period size: 95 Copynumber: 2.7 Consensus size: 95
35903 AGTTGGATCA
* * *
35913 ATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCGATATCATTGTATAG-ATATTA
1 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTC-A-AGC-TT-TATTGTATATTA
35977 TAATCATCTTTATCAGGCTAGCTGAATATTATCC
62 TAATCATCTTTATCAGGCTAGCTGAATATTATCC
36011 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACTA-CTCAAGCTTTATTGTATATTATAA
1 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGAC-AGCTCAAGCTTTATTGTATATTATAA
* *
36075 TC-GCTTTTATCAGGCTAGCTGAATCTTATCC
65 TCATC-TTTATCAGGCTAGCTGAATATTATCC
* *
36106 ATAAAGCCAGGGCGTTTAACCAATTTCTCTAGAGGGACAGCTCAAGCTTTATTGTATATTATAAT
1 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTGTATATTATAAT
36171 ATTATAATTT
Statistics
Matches: 149, Mismatches: 7, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
94 6 0.04
95 99 0.66
96 2 0.01
97 1 0.01
98 40 0.27
99 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (95 bp):
ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTGTATATTATAAT
CATCTTTATCAGGCTAGCTGAATATTATCC
Found at i:37720 original size:39 final size:39
Alignment explanation
Indices: 37677--37757 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
37667 AAATAAAAAG
37677 AATTAGTGAGGTAAAGATAAAAATCAAAACAATGATGAA
1 AATTAGTGAGGTAAAGATAAAAATCAAAACAATGATGAA
*
37716 AATTAGTGAGGTAAGGATAAAAATCAAAACAATGATGAA
1 AATTAGTGAGGTAAAGATAAAAATCAAAACAATGATGAA
37755 AAT
1 AAT
37758 AAAAGTCCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.56, C:0.05, G:0.19, T:0.21
Consensus pattern (39 bp):
AATTAGTGAGGTAAAGATAAAAATCAAAACAATGATGAA
Found at i:38805 original size:25 final size:25
Alignment explanation
Indices: 38773--38870 Score: 87
Period size: 25 Copynumber: 3.9 Consensus size: 25
38763 GAAAAAAAGG
*
38773 AAAATTAAAATAAATAAGATAATAA
1 AAAATTAAAATAAAAAAGATAATAA
38798 AAAATTAAAATAAAGAAA-ATAA-AA
1 AAAATTAAAATAAA-AAAGATAATAA
* *
38822 AACAAATGAAATAAAAAAGATAAGATAA
1 AA-AATTAAAATAAAAAAGAT-A-ATAA
*
38850 AAAA--AAGAGTAAAAAAGATAA
1 AAAATTAA-AATAAAAAAGATAA
38871 AGTAAAGATA
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
24 8 0.13
25 32 0.52
26 14 0.23
27 3 0.05
28 4 0.07
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.16
Consensus pattern (25 bp):
AAAATTAAAATAAAAAAGATAATAA
Found at i:38818 original size:22 final size:24
Alignment explanation
Indices: 38773--38823 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
38763 GAAAAAAAGG
*
38773 AAAATTAAAATAAATAAGATAATAA
1 AAAATTAAAAT-AATAAGAAAATAA
38798 AAAATTAAAAT-A-AAGAAAATAA
1 AAAATTAAAATAATAAGAAAATAA
38820 AAAA
1 AAAA
38824 CAAATGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 13 0.52
23 1 0.04
25 11 0.44
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (24 bp):
AAAATTAAAATAATAAGAAAATAA
Found at i:38862 original size:12 final size:11
Alignment explanation
Indices: 38843--38918 Score: 54
Period size: 11 Copynumber: 7.1 Consensus size: 11
38833 TAAAAAAGAT
38843 AAGATAAAAAA
1 AAGATAAAAAA
38854 AAGAGT--AAAA
1 AAGA-TAAAAAA
**
38864 AAGATAAAGTA
1 AAGATAAAAAA
38875 AAGATAAAAAA
1 AAGATAAAAAA
*
38886 GTAAG-T-AAAAT
1 --AAGATAAAAAA
*
38897 AA-ATAAAATA
1 AAGATAAAAAA
38907 AAGATAAAAAA
1 AAGATAAAAAA
38918 A
1 A
38919 TAATGACAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
9 4 0.08
10 13 0.27
11 27 0.55
12 2 0.04
13 3 0.06
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (11 bp):
AAGATAAAAAA
Found at i:38867 original size:21 final size:20
Alignment explanation
Indices: 38843--38918 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 20
38833 TAAAAAAGAT
38843 AAGATAAAAAAAAGAGTAAAA
1 AAGATAAAAAAAAGA-TAAAA
**
38864 AAGATAAAGTAAAGATAAAA
1 AAGATAAAAAAAAGATAAAA
38884 AAG-TAAGTAAAATAA-ATAAAATA
1 AAGATAA--AAAA-AAGAT-AAA-A
38907 AAGATAAAAAAA
1 AAGATAAAAAAA
38919 TAATGACAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
19 3 0.07
20 8 0.18
21 18 0.40
22 9 0.20
23 4 0.09
24 3 0.07
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (20 bp):
AAGATAAAAAAAAGATAAAA
Found at i:38879 original size:32 final size:31
Alignment explanation
Indices: 38816--38918 Score: 106
Period size: 32 Copynumber: 3.3 Consensus size: 31
38806 AATAAAGAAA
*
38816 ATAAAAAACAAA-TGAAATAAA-AAAGAT-AAG
1 ATAAAAAA-AAAGTAAAATAAATAAA-ATAAAG
*
38846 ATAAAAAAAAGAGTAAAA-AAGATAAAGTAAAG
1 ATAAAAAAAA-AGTAAAATAA-ATAAAATAAAG
*
38878 ATAAAAAAGTAAGTAAAATAAATAAAATAAAG
1 ATAAAAAA-AAAGTAAAATAAATAAAATAAAG
38910 ATAAAAAAA
1 ATAAAAAAA
38919 TAATGACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
29 2 0.03
30 11 0.18
31 6 0.10
32 39 0.64
33 3 0.05
ACGTcount: A:0.74, C:0.01, G:0.11, T:0.15
Consensus pattern (31 bp):
ATAAAAAAAAAGTAAAATAAATAAAATAAAG
Found at i:38905 original size:5 final size:5
Alignment explanation
Indices: 38773--38915 Score: 57
Period size: 5 Copynumber: 27.8 Consensus size: 5
38763 GAAAAAAAGG
* *
38773 AAAATT AAAAT -AAAT AAGAT AATAA- AAAATT AAAAT -AAAG AAAAT
1 AAAA-T AAAAT AAAAT AAAAT AA-AAT AAAA-T AAAAT AAAAT AAAAT
* * * * *
38818 AAAAA ACAAAT GAAAT AAAA- AAGAT AAGAT AAAAA AAAGAGT AAAA-
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-A-T AAAAT
* *
38864 AAGAT AAAGT AAAGAT AAAA- AAGTAAGT AAAAT -AAAT AAAAT AAAGAT
1 AAAAT AAAAT AAA-AT AAAAT AA--AA-T AAAAT AAAAT AAAAT AAA-AT
38912 AAAA
1 AAAA
38916 AAATAATGAC
Statistics
Matches: 104, Mismatches: 16, Indels: 35
0.67 0.10 0.23
Matches are distributed among these distances:
4 21 0.20
5 51 0.49
6 27 0.26
7 3 0.03
8 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.09, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:39193 original size:12 final size:12
Alignment explanation
Indices: 39178--39202 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39168 ATAATATTAA
39178 AAAAGAATAAAT
1 AAAAGAATAAAT
39190 AAAAGAATAAAT
1 AAAAGAATAAAT
39202 A
1 A
39203 TATATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAAGAATAAAT
Found at i:39265 original size:2 final size:2
Alignment explanation
Indices: 39258--39287 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39248 AATAAAAATA
39258 AT 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 AT
39288 CTAAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42670 original size:21 final size:21
Alignment explanation
Indices: 42644--42691 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
42634 GTTTCCAGAT
42644 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
42665 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
42686 TCGCAA
1 TCGCAA
42692 TGCAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:42775 original size:42 final size:40
Alignment explanation
Indices: 42706--43185 Score: 382
Period size: 42 Copynumber: 11.4 Consensus size: 40
42696 ATTTTTCAAA
* *
42706 TTCGTTGCGATAGTCCAAGTTCGCGTTGTGATTTATTCCAAA
1 TTCGTTGCGATAGTCCAAGTT--CGTTGCGATTTATTCCAAG
* *
42748 TTCGCGTTGCGATAGTCCAAGTTCGTTGCGA--TAGTCGAAG
1 TT--CGTTGCGATAGTCCAAGTTCGTTGCGATTTATTCCAAG
* * *
42788 TTCACGTTGCGATTTATTCCAAGTTCGTTGCGA--TAGTCGAAG
1 TT--CGTTGCGA--TAGTCCAAGTTCGTTGCGATTTATTCCAAG
* * *
42830 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGA--TAGTCGAAG
1 TT--CGTTGCGA--TAGTCCAAGTTCGTTGCGATTTATTCCAAG
* * * * *
42872 TCCGCGTTGCGATTTATTCCAAATTCGTTGC-A-ATAGTCCAAG
1 T--TCGTTGCGA--TAGTCCAAGTTCGTTGCGATTTATTCCAAG
*
42914 TTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAG
1 TT--CGTTGCGATAGTCCAAGTT--CGTTGCGATTTATTCCAAG
* ** * *
42958 TTCGTTGAGATAGTTGAAGTTCGCGTTGGGATTTATTCAAAG
1 TTCGTTGCGATAGTCCAAGTT--CGTTGCGATTTATTCCAAG
* *
43000 TTCGTTGCGATAGTCGAAGTTCGTGTTGTGATTTATTCCAAG
1 TTCGTTGCGATAGTCCAAGTTC--GTTGCGATTTATTCCAAG
*
43042 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAG
1 TTCGTTGCGATAGTCCAAGTT--CGTTGCGATTTATTCCAAG
* * *
43084 TTCATTGAGATAGTCGAAGTTCGCTTTGCGATTTATTCCAAG
1 TTCGTTGCGATAGTCCAAGTTCG--TTGCGATTTATTCCAAG
*
43126 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAG
1 TTCGTTGCGATAGTCCAAGTT--CGTTGCGATTTATTCCAAG
43168 TTCGTTGCGATAGTCCAA
1 TTCGTTGCGATAGTCCAA
43186 AATCGCAACG
Statistics
Matches: 387, Mismatches: 30, Indels: 42
0.84 0.07 0.09
Matches are distributed among these distances:
40 28 0.07
41 1 0.00
42 325 0.84
43 1 0.00
44 32 0.08
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (40 bp):
TTCGTTGCGATAGTCCAAGTTCGTTGCGATTTATTCCAAG
Found at i:42977 original size:147 final size:147
Alignment explanation
Indices: 42696--43073 Score: 602
Period size: 147 Copynumber: 2.6 Consensus size: 147
42686 TCGCAATGCA
*
42696 ATTT-TTCAAA-TTCGTTGCGATAGTCCAAGTTCGCGTTGTGATTTATTCCAAATTCGCGTTGCG
1 ATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATT--CGTTGCG
*
42759 ATAGTCCAAGTT--CGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAGTTCGTTGCGAT
64 ATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAGTTCGTTGAGAT
42822 AGTCGAAGTTCGCGTTGCG
129 AGTCGAAGTTCGCGTTGCG
* * * *
42841 ATTTATTCCAAGTTCGTTGCGATAGTCGAAGTCCGCGTTGCGATTTATTCCAAATTCGTTGCAAT
1 ATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGAT
*
42906 AGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGAGATAG
66 AGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAGTTCGTTGAGATAG
* *
42971 TTGAAGTTCGCGTTGGG
131 TCGAAGTTCGCGTTGCG
* *
42988 ATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGTGTTGTGATTTATTCCAAGTTCGTTGCGAT
1 ATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGAT
*
43053 AGTCGAAGTTCGCGTTGCGAT
66 AGTCCAAGTTCGCGTTGCGAT
43074 TTATTCCAAG
Statistics
Matches: 213, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
145 22 0.10
146 5 0.02
147 186 0.87
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (147 bp):
ATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGAT
AGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAGTTCGTTGAGATAG
TCGAAGTTCGCGTTGCG
Found at i:43117 original size:126 final size:126
Alignment explanation
Indices: 42908--43182 Score: 469
Period size: 126 Copynumber: 2.2 Consensus size: 126
42898 GTTGCAATAG
* *
42908 TCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGAGATAGTT
1 TCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCATTGAGATAGTC
* * *
42973 GAAGTTCGCGTTGGGATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGTGTTGTGATTTAT
64 GAAGTTCGCGTTGCGATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
43036 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCATTGAGATAGTCGA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCATTGAGATAGTCGA
* *
43101 AGTTCGCTTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
66 AGTTCGCGTTGCGATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
43162 TCCAAGTTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
43183 CAAAATCGCA
Statistics
Matches: 140, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
126 132 0.94
128 8 0.06
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (126 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCATTGAGATAGTCGA
AGTTCGCGTTGCGATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:43132 original size:147 final size:143
Alignment explanation
Indices: 42696--43136 Score: 518
Period size: 147 Copynumber: 3.0 Consensus size: 143
42686 TCGCAATGCA
*
42696 ATTT-TTCAAA-TTCGTTGCGATAGTCCAAGTTCGCGTTGTGATTTATTCCAAATTCGCGTTGCG
1 ATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATT--CGTTGCG
42759 ATAGTCCAAGTT--CGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAGTTCGTTGCGAT
64 ATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCA--TTGCGA-TTATTCCAAGTTCGTTGCGAT
*
42822 AGTCGAAGTTCGCGTTGCG
126 ATTCGAAGTTC-CGTTGCG
* * * *
42841 ATTTATTCCAAGTTCGTTGCGATAGTCGAAGTCCGCGTTGCGATTTATTCCAAATTCGTTGCAAT
1 ATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGAT
* *
42906 AGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGAGATAG
66 AGTCCAAGTTCGCGTTGCGATAGTCGAAGTT--CATTGCGA-TTATTCCAAGTTCGTTGCGATA-
*
42971 TT-GAAGTTCGCGTTGGG
127 TTCGAAGTTC-CGTTGCG
* *
42988 ATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGTGTTGTGATTTATTCCAAGTTCGTTGCGAT
1 ATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGAT
* * * * * *
43053 AGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCATTGAGA-TAGTCGAAGTTCGCTTTGCGATT
66 AGTCCAAGTTCGCGTTGCGA--TAGTCGAAGTTCATTGCGATTATTCCAAGTTCG--TTGCGA--
*
43117 TATTCCAAGTT-CGTTGCG
125 TATTCGAAGTTCCGTTGCG
43135 AT
1 AT
43137 AGTCGAAGTT
Statistics
Matches: 257, Mismatches: 25, Indels: 26
0.83 0.08 0.08
Matches are distributed among these distances:
145 33 0.13
146 5 0.02
147 199 0.77
148 3 0.01
149 17 0.07
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (143 bp):
ATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGAT
AGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCATTGCGATTATTCCAAGTTCGTTGCGATATTCG
AAGTTCCGTTGCG
Found at i:43283 original size:6 final size:6
Alignment explanation
Indices: 43272--43320 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
43262 GAAGACACGT
43272 ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC
1 ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC
43320 A
1 A
43321 CGACCACGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
ATTACC
Found at i:43994 original size:6 final size:6
Alignment explanation
Indices: 43983--44019 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
43973 TCGTCTCATC
* *
43983 TCGTGG TCGTGG TCGTGG TCGTGG TAGTGG TAGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
44020 AATACATGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.05, C:0.11, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:44142 original size:21 final size:21
Alignment explanation
Indices: 44116--44249 Score: 123
Period size: 21 Copynumber: 6.4 Consensus size: 21
44106 ATTTTGGATT
*
44116 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
44137 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
44158 ATCGCAATGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* * *
44179 ATCACAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
44200 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
44221 ATCGCAACGAATTTGGAACAA
1 ATCGCAACGAACTTGGAATAA
44242 ATCGCAAC
1 ATCGCAAC
44250 ACGAACTTCG
Statistics
Matches: 90, Mismatches: 15, Indels: 16
0.74 0.12 0.13
Matches are distributed among these distances:
19 19 0.21
21 53 0.59
23 18 0.20
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:44174 original size:42 final size:42
Alignment explanation
Indices: 44115--44229 Score: 203
Period size: 42 Copynumber: 2.7 Consensus size: 42
44105 GATTTTGGAT
*
44115 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAC
1 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGAC
* *
44157 TATCGCAATGAACTTGGAATAAATCACAACGCGAACTTCGAC
1 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGAC
44199 TATCGCAACGAACTTGGAATAAATCGCAACG
1 TATCGCAACGAACTTGGAATAAATCGCAACG
44230 AATTTGGAAC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (42 bp):
TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGAC
Found at i:44246 original size:42 final size:41
Alignment explanation
Indices: 44115--44290 Score: 187
Period size: 42 Copynumber: 4.2 Consensus size: 41
44105 GATTTTGGAT
*
44115 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAC
1 TATCGCAACGAACTTGGAATAAATCGCAAC-CGAACTTCGAC
* *
44157 TATCGCAATGAACTTGGAATAAATCACAACGCGAACTTCGAC
1 TATCGCAACGAACTTGGAATAAATCGCAAC-CGAACTTCGAC
* *
44199 TATCGCAACGAACTTGGAATAAATCGCAA-CGAATTTGGAAC
1 TATCGCAACGAACTTGGAATAAATCGCAACCGAACTTCG-AC
* * * *
44240 AAATCGCAACACGAACTTCGACT--ATCGCAACTCGAACTTGGAC
1 -TATCGC-A-ACGAACTTGGAATAAATCGCAAC-CGAACTTCGAC
44283 TATCGCAA
1 TATCGCAA
44291 TGCGAATATG
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
40 8 0.07
41 3 0.03
42 83 0.72
43 3 0.03
44 19 0.16
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (41 bp):
TATCGCAACGAACTTGGAATAAATCGCAACCGAACTTCGAC
Found at i:44288 original size:63 final size:62
Alignment explanation
Indices: 44137--44290 Score: 202
Period size: 63 Copynumber: 2.4 Consensus size: 62
44127 TTTGGAATAA
* * * *
44137 ATCGCAACGCGAACTTCGACTATCGCAATGAACTTGGAATAAATCACAACGCGAACTTCGACT
1 ATCGCAAC-CGAACTTGGACTATCGCAACGAACTTGGAACAAATCACAACACGAACTTCGACT
* * *
44200 ATCGCAA-CGAACTTGGAATAAATCGCAACGAATTTGGAACAAATCGCAACACGAACTTCGACT
1 ATCGCAACCGAACTTGGACT--ATCGCAACGAACTTGGAACAAATCACAACACGAACTTCGACT
44263 ATCGCAACTCGAACTTGGACTATCGCAA
1 ATCGCAAC-CGAACTTGGACTATCGCAA
44291 TGCGAATATG
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
61 10 0.13
63 58 0.73
65 11 0.14
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (62 bp):
ATCGCAACCGAACTTGGACTATCGCAACGAACTTGGAACAAATCACAACACGAACTTCGACT
Found at i:44296 original size:21 final size:20
Alignment explanation
Indices: 44109--44290 Score: 120
Period size: 21 Copynumber: 8.7 Consensus size: 20
44099 CGTTGCGATT
* *
44109 TTGGATTATCGCAA-CGAAT
1 TTGGACTATCGCAACCGAAC
*
44128 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAAC-CGAAC
* *
44151 TTCGACTATCGCAA-TGAAC
1 TTGGACTATCGCAACCGAAC
* *
44170 TTGGAATAAATCACAACGCGAAC
1 TTGGACT--ATCGCAAC-CGAAC
*
44193 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAACCGAAC
* *
44212 TTGGAATAAATCGCAA-CGAAT
1 TTGGACT--ATCGCAACCGAAC
*
44233 TTGGAACAAATCGCAACACGAAC
1 TTGG-AC-TATCGCAAC-CGAAC
*
44256 TTCGACTATCGCAACTCGAAC
1 TTGGACTATCGCAAC-CGAAC
44277 TTGGACTATCGCAA
1 TTGGACTATCGCAA
44291 TGCGAATATG
Statistics
Matches: 127, Mismatches: 22, Indels: 26
0.73 0.13 0.15
Matches are distributed among these distances:
19 25 0.20
21 74 0.58
22 3 0.02
23 25 0.20
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (20 bp):
TTGGACTATCGCAACCGAAC
Found at i:47769 original size:17 final size:17
Alignment explanation
Indices: 47749--47781 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
47739 ATATTTATTT
47749 ATAT-AAAATATAATATA
1 ATATGAAAA-ATAATATA
47766 ATATGAAAAATAATAT
1 ATATGAAAAATAATAT
47782 TGTAATATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATGAAAAATAATATA
Found at i:54481 original size:17 final size:17
Alignment explanation
Indices: 54459--54501 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
54449 CTCATTGAAG
54459 TTTATTTTTTCTT-CTAT
1 TTTATTTTTTCTTACT-T
54476 TTTA-TTTTTCTTACTT
1 TTTATTTTTTCTTACTT
*
54492 TTAATTTTTT
1 TTTATTTTTT
54502 TTAATTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTATTTTTTCTTACTT
Found at i:54847 original size:14 final size:15
Alignment explanation
Indices: 54828--54862 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
54818 AACACTTTGT
54828 AAAACA-AGTAAATA
1 AAAACATAGTAAATA
*
54842 AAAACATTGTAAATA
1 AAAACATAGTAAATA
54857 AAAACA
1 AAAACA
54863 CTAAATTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.17
Consensus pattern (15 bp):
AAAACATAGTAAATA
Found at i:55303 original size:21 final size:21
Alignment explanation
Indices: 55277--55318 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
55267 ATCCATGTCA
55277 TAACATTGTTAGAAGGTTAAC
1 TAACATTGTTAGAAGGTTAAC
55298 TAACATTGTTAGAAGGTTAAC
1 TAACATTGTTAGAAGGTTAAC
55319 GGTGTTGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (21 bp):
TAACATTGTTAGAAGGTTAAC
Found at i:55788 original size:24 final size:25
Alignment explanation
Indices: 55734--55789 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
55724 AAAAATATAT
55734 AAATATTTCAAAATTGTGTACAAAA
1 AAATATTTCAAAATTGTGTACAAAA
55759 AAATATTTCAAAATTGTGTAC-AAA
1 AAATATTTCAAAATTGTGTACAAAA
55783 AAATATT
1 AAATATT
55790 ACATATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 10 0.32
25 21 0.68
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (25 bp):
AAATATTTCAAAATTGTGTACAAAA
Found at i:63247 original size:23 final size:21
Alignment explanation
Indices: 63193--63275 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
63183 TTTTGGTGCA
63193 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAATCGATTCCCCCCAT
* **
63213 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCAT
63234 GAAGGGGAATCGATTCCCCCCA-
1 G-A-GGGAATCGATTCCCCCCAT
* *
63256 CAGGGGAATCGATACCCCCC
1 GA-GGGAATCGATTCCCCCC
63276 TGGGGTTCTG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 10 0.19
21 26 0.50
22 1 0.02
23 15 0.29
ACGTcount: A:0.24, C:0.35, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCAT
Found at i:72385 original size:20 final size:20
Alignment explanation
Indices: 72360--72397 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
72350 TTTGGTTCAA
72360 GGAATGTAAGATTACCAGCG
1 GGAATGTAAGATTACCAGCG
72380 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
72398 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.21
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGCG
Found at i:72402 original size:18 final size:19
Alignment explanation
Indices: 72360--72402 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
72350 TTTGGTTCAA
72360 GGAATGTAAGATTACCAGCG
1 GGAATGTAAGATTACCA-CG
72380 GGAATGTAAGATTACCA-G
1 GGAATGTAAGATTACCACG
72398 GGAAT
1 GGAAT
72403 AGGATTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.26
20 17 0.74
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (19 bp):
GGAATGTAAGATTACCACG
Found at i:72625 original size:36 final size:37
Alignment explanation
Indices: 72553--72626 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
72543 GTTGGAAAAT
* * *
72553 ATTTATATATTTTCTTTTAAAAATTTAAATTCATAAA
1 ATTTATATAATTTCTTTTAAAAATTAAAAATCATAAA
72590 ATTTATATAATTT-TTTTACAAAATTAAAAAT-ATAAA
1 ATTTATATAATTTCTTTTA-AAAATTAAAAATCATAAA
72626 A
1 A
72627 AGGTTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 11 0.33
37 22 0.67
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATAATTTCTTTTAAAAATTAAAAATCATAAA
Found at i:75691 original size:16 final size:16
Alignment explanation
Indices: 75665--75705 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
75655 TATTATTTTA
75665 GTTAAAA-ATTAAAAT
1 GTTAAAAGATTAAAAT
75680 GTTAAAAGATTAAAAT
1 GTTAAAAGATTAAAAT
75696 GTTAAAAGAT
1 GTTAAAAGAT
75706 AAAGAATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (16 bp):
GTTAAAAGATTAAAAT
Found at i:86348 original size:21 final size:22
Alignment explanation
Indices: 86307--86346 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
86297 TACCCCTAAT
86307 TATGAATAGTGCCTTATAAAGA
1 TATGAATAGTGCCTTATAAAGA
*
86329 TATGAA-AGTGTCTT-TAAA
1 TATGAATAGTGCCTTATAAA
86347 AGCGTAAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.35
Consensus pattern (22 bp):
TATGAATAGTGCCTTATAAAGA
Found at i:89329 original size:21 final size:21
Alignment explanation
Indices: 89305--89344 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
89295 TGGTGTCTAG
*
89305 GATTTAAGGTTTAGAGTTTAA
1 GATTTAAGGTTTAAAGTTTAA
*
89326 GATTTAGGGTTTAAAGTTT
1 GATTTAAGGTTTAAAGTTT
89345 GATATAGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (21 bp):
GATTTAAGGTTTAAAGTTTAA
Found at i:89539 original size:2 final size:2
Alignment explanation
Indices: 89532--89560 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
89522 GTAAGCGGAT
89532 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
89561 TGAGGTACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92757 original size:21 final size:21
Alignment explanation
Indices: 92731--92770 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
92721 TGGTTAATAA
* *
92731 ATCGCAATGCGATTTTGGACT
1 ATCGCAACGCGAATTTGGACT
92752 ATCGCAACGCGAATTTGGA
1 ATCGCAACGCGAATTTGGA
92771 AACTGAGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (21 bp):
ATCGCAACGCGAATTTGGACT
Found at i:92865 original size:21 final size:21
Alignment explanation
Indices: 92805--92865 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
92795 CGTTGCGATT
* * **
92805 TCGCAATGCGAATTTAGACTA
1 TCGCAACGCGAATTTGGAAAA
*
92826 TCGCAACGCGAA-ATGGAAAA
1 TCGCAACGCGAATTTGGAAAA
92846 TCGCAACGCGAATTTGGAAA
1 TCGCAACGCGAATTTGGAAA
92866 CTGAGTTGCG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (21 bp):
TCGCAACGCGAATTTGGAAAA
Found at i:94644 original size:130 final size:130
Alignment explanation
Indices: 94411--94669 Score: 500
Period size: 130 Copynumber: 2.0 Consensus size: 130
94401 TAAGATTAGT
*
94411 GTCGACTCCCGATCAAACCCCCGTTGACCTTTCACCATAAGCTGCCACCATTTGTCGTGGAGAAG
1 GTCGACTCCCGATCAAACCCCCATTGACCTTTCACCATAAGCTGCCACCATTTGTCGTGGAGAAG
94476 CATTCGAAGGTTCGTCAGATTTTAAGCCACAGTCGTTGTTTCTCATTGATTCCAACCGATACTGC
66 CATTCGAAGGTTCGTCAGATTTTAAGCCACAGTCGTTGTTTCTCATTGATTCCAACCGATACTGC
94541 GTCGACTCCCGATCAAACCCCCATTGACCTTTCACCATAAGCTGCCACCATTTGTCGTGGAGAAG
1 GTCGACTCCCGATCAAACCCCCATTGACCTTTCACCATAAGCTGCCACCATTTGTCGTGGAGAAG
*
94606 CATTCGAAGGTTCGTCGGATTTTAAGCCACAGTCGTTGTTTCTCATTGATTCCAACCGATACTG
66 CATTCGAAGGTTCGTCAGATTTTAAGCCACAGTCGTTGTTTCTCATTGATTCCAACCGATACTG
94670 ACATCCATAT
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 127 1.00
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (130 bp):
GTCGACTCCCGATCAAACCCCCATTGACCTTTCACCATAAGCTGCCACCATTTGTCGTGGAGAAG
CATTCGAAGGTTCGTCAGATTTTAAGCCACAGTCGTTGTTTCTCATTGATTCCAACCGATACTGC
Found at i:101751 original size:29 final size:25
Alignment explanation
Indices: 101691--101751 Score: 59
Period size: 29 Copynumber: 2.3 Consensus size: 25
101681 ATTTAAGAAT
* *
101691 AAATAAATTATTTTTTAAAAGTTAC
1 AAATAAATTATTTTTTAAAAATTAA
*
101716 AACTAAATTATTTTATTATTAAAAATTAA
1 AAATAAATTA--TT-TT-TTAAAAATTAA
101745 AAATAAA
1 AAATAAA
101752 ATAAATAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 9 0.32
27 2 0.07
28 2 0.07
29 15 0.54
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (25 bp):
AAATAAATTATTTTTTAAAAATTAA
Found at i:102012 original size:27 final size:28
Alignment explanation
Indices: 101967--102019 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
101957 AATAATTCAA
*
101967 GATAAAAATTAAAATTAAAAT-TAAAAT
1 GATAAAAATTAAAAGTAAAATATAAAAT
**
101994 GATAAAAATTTTAAGTAAAATATAAA
1 GATAAAAATTAAAAGTAAAATATAAA
102020 TTTATGAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (28 bp):
GATAAAAATTAAAAGTAAAATATAAAAT
Found at i:102173 original size:60 final size:60
Alignment explanation
Indices: 102061--102207 Score: 159
Period size: 60 Copynumber: 2.5 Consensus size: 60
102051 ATTATAATTT
* ** * * * *
102061 TCATTTTAAATTAGTCCTTATGCTTTTTAATATTTTAATTTCATCCTCAAACTACGACTC
1 TCATTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCATCCTCAAACTACGACTA
* ** * *
102121 TCATTCTAAACTAGTCCTTAAACTTTTAAACATTCTAATTTCATTTTTAAACTATGACTA
1 TCATTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCATCCTCAAACTACGACTA
* * *
102181 TCTTTCTAAATTGGTCCCTAAACTTTT
1 TCATTCTAAATTAGTCCTTAAACTTTT
102208 GAATCTTCCA
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.46
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCATCCTCAAACTACGACTA
Found at i:102223 original size:60 final size:60
Alignment explanation
Indices: 102109--102224 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
102099 TTTCATCCTC
* * *
102109 AAACTACGACTCTCATTCTAAACTAGTCCTTAAACTTTTAAACATTCTAATTTCATTTTT
1 AAACTACGACTATCATTCTAAACTAGTCCCTAAACTTTTAAACATTCCAATTTCATTTTT
* * * * * *
102169 AAACTATGACTATCTTTCTAAATTGGTCCCTAAACTTTTGAATC-TTCCACTTTCAT
1 AAACTACGACTATCATTCTAAACTAGTCCCTAAACTTTT-AAACATTCCAATTTCAT
102225 CTAAATATGT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
60 43 0.93
61 3 0.07
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.41
Consensus pattern (60 bp):
AAACTACGACTATCATTCTAAACTAGTCCCTAAACTTTTAAACATTCCAATTTCATTTTT
Found at i:106715 original size:13 final size:13
Alignment explanation
Indices: 106697--106723 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
106687 TTACAGACGC
106697 GCATATGAAGACT
1 GCATATGAAGACT
106710 GCATATGAAGACT
1 GCATATGAAGACT
106723 G
1 G
106724 TTTAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Done.