Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011892.1 Corchorus capsularis cultivar CVL-1 contig11913, 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: 119451
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:4373 original size:20 final size:20
Alignment explanation
Indices: 4348--4388 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4338 TCAACAATAC
**
4348 CCATTTCCTAATTCCTAAAG
1 CCATTTCCTAAACCCTAAAG
4368 CCATTTCCTAAACCCTAAAG
1 CCATTTCCTAAACCCTAAAG
4388 C
1 C
4389 TATGACCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (20 bp):
CCATTTCCTAAACCCTAAAG
Found at i:4433 original size:18 final size:18
Alignment explanation
Indices: 4406--4440 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4396 TATAACTAAT
*
4406 CCACTTCCTCAATTTGAA
1 CCACTGCCTCAATTTGAA
4424 CCACTGCCTCAATTTGA
1 CCACTGCCTCAATTTGA
4441 CCCTCTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCACTGCCTCAATTTGAA
Found at i:5208 original size:36 final size:36
Alignment explanation
Indices: 5167--5241 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
5157 AAACATTTAT
* *
5167 ATAAAGCATCCACATTATCAAATATAACAATATTAC
1 ATAAAGCATCCACATTATCAAAGATAACAAGATTAC
* *
5203 ATAAAGCTTCCACATTGTCAAAGATAACAAGATTAC
1 ATAAAGCATCCACATTATCAAAGATAACAAGATTAC
5239 ATA
1 ATA
5242 GATATTACAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.27
Consensus pattern (36 bp):
ATAAAGCATCCACATTATCAAAGATAACAAGATTAC
Found at i:6883 original size:13 final size:13
Alignment explanation
Indices: 6865--6889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6855 TTAGAATTCC
6865 AAATAATATTTAT
1 AAATAATATTTAT
6878 AAATAATATTTA
1 AAATAATATTTA
6890 GAAAATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:7268 original size:13 final size:13
Alignment explanation
Indices: 7250--7274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7240 TTTAATGTTC
7250 TAAATATTATTTA
1 TAAATATTATTTA
7263 TAAATATTATTT
1 TAAATATTATTT
7275 GGAATTCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:7939 original size:2 final size:2
Alignment explanation
Indices: 7932--7963 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
7922 TCAGTGTGAG
7932 TA TA TA TA TA -A 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 T
7964 TAACAGTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8343 original size:203 final size:202
Alignment explanation
Indices: 7994--8375 Score: 543
Period size: 203 Copynumber: 1.9 Consensus size: 202
7984 AATATTATTC
* * * * * * * *
7994 AATACACCGTTAGTGGAGTTTACCATATTATACATGCGGGTCTTGAAGGGTGACATGTGTCCTCT
1 AATACACCGTCAGTGGAGTTTAACAGACTACACAAGCGGGTCATGAAGGGTGACATGTGTCCCCT
* *
8059 AGGGACTAGATTAAAATATTTAAAACTTAATTAATTAAAGAAATTAACATGTGTCAACTCTACAA
66 AGGAACTAGATTAAAATATTTAAAACTTAATTAATTAAAGAAATTAACATGTGTCAACTCCACAA
*
8124 CACGCTTGTGGAGTCCAAAATTTACACCACCGGTGTATCAAATAATTACCATATACATTATGGGT
131 CACGCCTGTGGAGTCCAAAATTTAC-CCACCGGTGTATCAAATAATTACCATATACATTATGGGT
8189 TTATATAT
195 TTATATAT
*
8197 AATACACCGTCAGTGGAGTTTAACAGACTGCACAAGCGGGTCATGAAGGGTGACATGTGTCCCCT
1 AATACACCGTCAGTGGAGTTTAACAGACTACACAAGCGGGTCATGAAGGGTGACATGTGTCCCCT
* * * *
8262 AGGAACTAGATTGAAATATTTAAAATTTAATTAATT-CAGAAAATTGACATGTGTCAACTCCACA
66 AGGAACTAGATTAAAATATTTAAAACTTAATTAATTAAAG-AAATTAACATGTGTCAACTCCACA
* ** *
8326 A-ACTGCCTGTGGAGTCCAAAATTTACGCTTCTGTGTATCAAATAATTACC
130 ACAC-GCCTGTGGAGTCCAAAATTTACCCACCGGTGTATCAAATAATTACC
8376 CATGCATTAT
Statistics
Matches: 157, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
202 24 0.15
203 133 0.85
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (202 bp):
AATACACCGTCAGTGGAGTTTAACAGACTACACAAGCGGGTCATGAAGGGTGACATGTGTCCCCT
AGGAACTAGATTAAAATATTTAAAACTTAATTAATTAAAGAAATTAACATGTGTCAACTCCACAA
CACGCCTGTGGAGTCCAAAATTTACCCACCGGTGTATCAAATAATTACCATATACATTATGGGTT
TATATAT
Found at i:9333 original size:24 final size:24
Alignment explanation
Indices: 9301--9360 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
9291 TTCTTCTTAT
9301 CGTTTTCTTCTTCTTCTTTTGTAC
1 CGTTTTCTTCTTCTTCTTTTGTAC
9325 CGTTTTCTTCTTCTTCTTTTGTAC
1 CGTTTTCTTCTTCTTCTTTTGTAC
*
9349 CG-CTTCTTCTTC
1 CGTTTTCTTCTTC
9361 ATCTCATCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 9 0.26
24 26 0.74
ACGTcount: A:0.03, C:0.28, G:0.08, T:0.60
Consensus pattern (24 bp):
CGTTTTCTTCTTCTTCTTTTGTAC
Found at i:9355 original size:41 final size:41
Alignment explanation
Indices: 9323--9404 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
9313 CTTCTTTTGT
9323 ACCGTTTTCTTCTTCTTCTTTTGTACCGCTTCTTCTTCATCTC
1 ACCGTTTTCTTCTTCTT-TTTT-TACCGCTTCTTCTTCATCTC
* *
9366 ATCTTTTTCTTCTTCTTTTTTTACCGCTTCTTCTTCATC
1 ACCGTTTTCTTCTTCTTTTTTTACCGCTTCTTCTTCATC
9405 ATAATGAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 18 0.49
42 4 0.11
43 15 0.41
ACGTcount: A:0.07, C:0.30, G:0.05, T:0.57
Consensus pattern (41 bp):
ACCGTTTTCTTCTTCTTTTTTTACCGCTTCTTCTTCATCTC
Found at i:16030 original size:15 final size:15
Alignment explanation
Indices: 16006--16035 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15996 AAATTTCTTG
16006 ATGAGCTCATTTGCA
1 ATGAGCTCATTTGCA
*
16021 ATGAGTTCATTTGCA
1 ATGAGCTCATTTGCA
16036 CTATCTGATG
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:0.17, G:0.20, T:0.37
Consensus pattern (15 bp):
ATGAGCTCATTTGCA
Found at i:19655 original size:9 final size:9
Alignment explanation
Indices: 19621--19665 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
19611 GTACTAAGGG
19621 GAAAAAAAA
1 GAAAAAAAA
19630 CGAAAAAACGAA
1 -GAAAAAA--AA
*
19642 AAAAAAAAA
1 GAAAAAAAA
19651 GAAAAAAAA
1 GAAAAAAAA
19660 GAAAAA
1 GAAAAA
19666 CTCAACGGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 16 0.52
10 7 0.23
11 6 0.19
12 2 0.06
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:19658 original size:21 final size:20
Alignment explanation
Indices: 19622--19665 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
19612 TACTAAGGGG
* *
19622 AAAAAAAACGAAAAAACGAA
1 AAAAAAAAAGAAAAAAAGAA
19642 AAAAAAAAAGAAAAAAAAGAA
1 AAAAAAAAAG-AAAAAAAGAA
19663 AAA
1 AAA
19666 CTCAACGGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAAAAAAAGAA
Found at i:26797 original size:31 final size:31
Alignment explanation
Indices: 26759--26847 Score: 142
Period size: 31 Copynumber: 2.9 Consensus size: 31
26749 ATCCGAAATT
26759 AAAGGTTTGGTACTAAGTTGGGATTTTCCTA
1 AAAGGTTTGGTACTAAGTTGGGATTTTCCTA
* *
26790 AAAGGTTTGGTACTAAGTCGAGATTTTCCTA
1 AAAGGTTTGGTACTAAGTTGGGATTTTCCTA
* *
26821 AAAGGTTTGGTACCAAATTGGGATTTT
1 AAAGGTTTGGTACTAAGTTGGGATTTT
26848 AGCCCTTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (31 bp):
AAAGGTTTGGTACTAAGTTGGGATTTTCCTA
Found at i:30632 original size:2 final size:2
Alignment explanation
Indices: 30625--30655 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30615 CATAAAAACT
30625 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
30656 TTTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:36087 original size:27 final size:27
Alignment explanation
Indices: 36055--36132 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 27
36045 AGAATTTCAA
36055 ATAATACATTTGTTGAAGTCTCAAATT
1 ATAATACATTTGTTGAAGTCTCAAATT
*
36082 ATAATACATTTGTTG-AG------ACT
1 ATAATACATTTGTTGAAGTCTCAAATT
36102 -TAATACATTTGTTGAAGTCTCAAATT
1 ATAATACATTTGTTGAAGTCTCAAATT
36128 ATAAT
1 ATAAT
36133 GGACATAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 16
0.69 0.03 0.27
Matches are distributed among these distances:
19 14 0.34
20 4 0.10
26 4 0.10
27 19 0.46
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (27 bp):
ATAATACATTTGTTGAAGTCTCAAATT
Found at i:48434 original size:21 final size:21
Alignment explanation
Indices: 48392--48449 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
48382 TACAAGATAT
* *
48392 AACAATCTAG-GCTAAACTAAA
1 AACAATCT-GCGCTCAACCAAA
* *
48413 AATAATTTGCGCTCAACCAAA
1 AACAATCTGCGCTCAACCAAA
*
48434 AACAATCTGGGCTCAA
1 AACAATCTGCGCTCAA
48450 AAAATAGATG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.21
Consensus pattern (21 bp):
AACAATCTGCGCTCAACCAAA
Found at i:50406 original size:39 final size:38
Alignment explanation
Indices: 50296--50407 Score: 136
Period size: 39 Copynumber: 2.9 Consensus size: 38
50286 GAGAAGAAAA
* * *
50296 TTGCCCTTGTGTTATATGTGTTTAGGAACTTTTGTATAG
1 TTGCCCTTGTGTTATATGTGTTTGGGGAC-TTTGGATAG
* *
50335 ATG-CCTCTGTGTTATATGTGTTTGAGGACTTTGAGATAG
1 TTGCCCT-TGTGTTATATGTGTTTGGGGACTTTG-GATAG
*
50374 TTGCCCTTATGTTATATGTGTTTGGGGACTTTGG
1 TTGCCCTTGTGTTATATGTGTTTGGGGACTTTGG
50408 GGAGAGAGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
38 8 0.13
39 51 0.82
40 3 0.05
ACGTcount: A:0.17, C:0.11, G:0.27, T:0.46
Consensus pattern (38 bp):
TTGCCCTTGTGTTATATGTGTTTGGGGACTTTGGATAG
Found at i:51348 original size:26 final size:28
Alignment explanation
Indices: 51312--51374 Score: 85
Period size: 26 Copynumber: 2.3 Consensus size: 28
51302 CAAGACGTCA
*
51312 TCCCTCTTGATGGAGGA-CGACAATCT-
1 TCCCTCTTGATGGACGATCGACAATCTC
* *
51338 TCCCTCTTGATGGACGATGGACAATTTC
1 TCCCTCTTGATGGACGATCGACAATCTC
51366 TCCCTCTTG
1 TCCCTCTTG
51375 TTATAGTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 16 0.50
27 7 0.22
28 9 0.28
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.32
Consensus pattern (28 bp):
TCCCTCTTGATGGACGATCGACAATCTC
Found at i:51399 original size:256 final size:256
Alignment explanation
Indices: 50932--51445 Score: 875
Period size: 256 Copynumber: 2.0 Consensus size: 256
50922 GCTTGACTTG
* *
50932 CTCAGAAAGGCAAATTCCTCCTCCTTAGGAGATGACAACTTCCAGGAAGGTGAGGTGAACCTTCC
1 CTCAGAAAGGCAAATTCCTCATCCTTAGGAGATGACAACTTCCACGAAGGTGAGGTGAACCTTCC
* * *
50997 TTCTTCTTCTAATAACTTCCAACGGCTGAGAGGGGGGAAGAGAGCACTCCAAGACGTCATTCGTC
66 TTCTTCTTCTAATAACTTCCAACGGCTGAGAGAGGGGAAGAGAGCACTCCAAGACGTCATCCCTC
51062 TTGATGGAGGAAGACAATCTTCCCTCTTGATAGACGATGGACAATTTCTCCCTCTTCTTATAGCA
131 TTGATGGAGGAAGACAATCTTCCCTCTTGATAGACGATGGACAATTTCTCCCTCTTCTTATAGCA
*
51127 ATTCAGCAAGCCTTCGTTGCTTCCTTCGAGCTGAAATCAACTGATTTGCCTAAGAAGTGGC
196 ATTCAGCAAGCCTTCGTTGCTTCCTTCGAGCTGAAATCAACTGATTTGACTAAGAAGTGGC
* * *
51188 CTCAGGAAGGCGAATTCCTCATCCTTAGGAGATGACAACTTCCACGAAGGTGAGGTGAAGCTTCC
1 CTCAGAAAGGCAAATTCCTCATCCTTAGGAGATGACAACTTCCACGAAGGTGAGGTGAACCTTCC
* *
51253 TTCTTCTTCTGATAACTTCCAACGGCTGAGAGAGGGGAGGAGAGCACTCCAAGACGTCATCCCTC
66 TTCTTCTTCTAATAACTTCCAACGGCTGAGAGAGGGGAAGAGAGCACTCCAAGACGTCATCCCTC
* * * *
51318 TTGATGGAGGACGACAATCTTCCCTCTTGATGGACGATGGACAATTTCTCCCTCTTGTTATAGTA
131 TTGATGGAGGAAGACAATCTTCCCTCTTGATAGACGATGGACAATTTCTCCCTCTTCTTATAGCA
* *
51383 ATTCAGCAAGCCTTCGTTGCTTCCTTCGAGTTGAAATCAATTGATTTGACTAAGAAGTGGC
196 ATTCAGCAAGCCTTCGTTGCTTCCTTCGAGCTGAAATCAACTGATTTGACTAAGAAGTGGC
51444 CT
1 CT
51446 TCGAACATCA
Statistics
Matches: 241, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
256 241 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (256 bp):
CTCAGAAAGGCAAATTCCTCATCCTTAGGAGATGACAACTTCCACGAAGGTGAGGTGAACCTTCC
TTCTTCTTCTAATAACTTCCAACGGCTGAGAGAGGGGAAGAGAGCACTCCAAGACGTCATCCCTC
TTGATGGAGGAAGACAATCTTCCCTCTTGATAGACGATGGACAATTTCTCCCTCTTCTTATAGCA
ATTCAGCAAGCCTTCGTTGCTTCCTTCGAGCTGAAATCAACTGATTTGACTAAGAAGTGGC
Found at i:54123 original size:15 final size:17
Alignment explanation
Indices: 54103--54140 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
54093 CGTTCAAATG
54103 TCGGGT-AATT-TGGGT
1 TCGGGTCAATTCTGGGT
54118 TCGGGTCAATTCTGGGT
1 TCGGGTCAATTCTGGGT
54135 T-GGGTC
1 TCGGGTC
54141 GTTTTCGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 9 0.43
17 6 0.29
ACGTcount: A:0.11, C:0.13, G:0.39, T:0.37
Consensus pattern (17 bp):
TCGGGTCAATTCTGGGT
Found at i:54276 original size:101 final size:102
Alignment explanation
Indices: 54043--54295 Score: 377
Period size: 101 Copynumber: 2.5 Consensus size: 102
54033 GTTAAGAAAT
* * * **
54043 TTTCGGGTCATACGAGTTTGGGTAATTTTCGGTTTCG--GGTCGGGTTGGGTCGTTCAAATGTCG
1 TTTCGGGTCATACG-GTTCGGATAATTTTGGGTTT-GAACCTCGGGTTGGGTCGTTCAAATGTCG
54106 GGTAATTTGGGTTCGGGTCAATTCTGGGTTGGGTCGTTTTCGG
64 GGTAATTTGGGTTCGGG---A-TCTGGGTTGGGTCGTTTTCGG
54149 TTTCGGGTCATACGGTTCGGATAATTTTGGGTTTGAACCTCGGGTTGGGTCGTTCAAATGTCGGG
1 TTTCGGGTCATACGGTTCGGATAATTTTGGGTTTGAACCTCGGGTTGGGTCGTTCAAATGTCGGG
54214 TAATTTGGGTTCGGG-TCTGGGTTGGGTCGTTTTCGG
66 TAATTTGGGTTCGGGATCTGGGTTGGGTCGTTTTCGG
*
54250 TTTCGGGTCATACGGTTCGGATAATTTCGGGTTTGAACCTCGGGTT
1 TTTCGGGTCATACGGTTCGGATAATTTTGGGTTTGAACCTCGGGTT
54296 TTCGGGTTTT
Statistics
Matches: 139, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
101 66 0.47
104 1 0.01
105 17 0.12
106 55 0.40
ACGTcount: A:0.12, C:0.14, G:0.36, T:0.38
Consensus pattern (102 bp):
TTTCGGGTCATACGGTTCGGATAATTTTGGGTTTGAACCTCGGGTTGGGTCGTTCAAATGTCGGG
TAATTTGGGTTCGGGATCTGGGTTGGGTCGTTTTCGG
Found at i:55655 original size:15 final size:16
Alignment explanation
Indices: 55622--55656 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
55612 TTTTGGGTTT
55622 GGGTCGTTTCGAGTTC
1 GGGTCGTTTCGAGTTC
*
55638 GGGTCGTTTGGA-TTC
1 GGGTCGTTTCGAGTTC
55653 GGGT
1 GGGT
55657 ACCCAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.06, C:0.14, G:0.43, T:0.37
Consensus pattern (16 bp):
GGGTCGTTTCGAGTTC
Found at i:55857 original size:15 final size:15
Alignment explanation
Indices: 55837--55871 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
55827 TGTATCATAT
55837 AGTATAACTAATTAA
1 AGTATAACTAATTAA
*
55852 AGTATAATTAATTAA
1 AGTATAACTAATTAA
55867 A-TATA
1 AGTATA
55872 TGAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (15 bp):
AGTATAACTAATTAA
Found at i:56895 original size:6 final size:6
Alignment explanation
Indices: 56888--56927 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
56878 ACACAGAAAG
* *
56888 TAAAAG TAAAAA TAAAAA TAAAAC TAAAAA T-AAAA TAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
56928 TTATATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:56937 original size:17 final size:17
Alignment explanation
Indices: 56888--56927 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
56878 ACACAGAAAG
*
56888 TAAAAGTAAAAATAAAAA
1 TAAAACTAAAAAT-AAAA
56906 TAAAACTAAAAATAAAA
1 TAAAACTAAAAATAAAA
56923 TAAAA
1 TAAAA
56928 TTATATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (17 bp):
TAAAACTAAAAATAAAA
Found at i:65697 original size:1 final size:1
Alignment explanation
Indices: 65691--65715 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
65681 AGTAATCTAC
65691 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
65716 GTAAATGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:66513 original size:18 final size:18
Alignment explanation
Indices: 66490--66530 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
66480 CATTTCAGTG
66490 TTTTATTT-TTTATTTTTA
1 TTTTATTTATTT-TTTTTA
*
66508 TTTTATTTATTTTTTTTT
1 TTTTATTTATTTTTTTTA
66526 TTTTA
1 TTTTA
66531 AGTTTCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTATTTATTTTTTTTA
Found at i:67140 original size:15 final size:15
Alignment explanation
Indices: 67120--67148 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
67110 TTGTAAAAGT
67120 AGAAAACGAAATTGC
1 AGAAAACGAAATTGC
67135 AGAAAACGAAATTG
1 AGAAAACGAAATTG
67149 TTAAAGAACT
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:0.55, C:0.10, G:0.21, T:0.14
Consensus pattern (15 bp):
AGAAAACGAAATTGC
Found at i:67332 original size:123 final size:123
Alignment explanation
Indices: 67133--67373 Score: 464
Period size: 123 Copynumber: 2.0 Consensus size: 123
67123 AAACGAAATT
*
67133 GCAGAAAACGAAATTGTTAAAGAACTTGAAATCTTATTGCAAACAATAGGAAGATTACCACCATT
1 GCAGAAAACGAAATTGTTAAAGAACTTGAAATCTTATTGCAAACAAGAGGAAGATTACCACCATT
67198 ATAAACCCAAAATTGCAGCAAACAACTCAGATAGAAACTAAAAGAAAAAGAATTAAAA
66 ATAAACCCAAAATTGCAGCAAACAACTCAGATAGAAACTAAAAGAAAAAGAATTAAAA
67256 GCAGAAAACGAAATTGTTAAAGAACTTGAAATCTTATTGCAAACAAGAGGAAGATTACCACCATT
1 GCAGAAAACGAAATTGTTAAAGAACTTGAAATCTTATTGCAAACAAGAGGAAGATTACCACCATT
*
67321 ATAAACCCAAAATTGCAGCAAACAACTCAGATAGAAACTAAAAGAAGAAGAAT
66 ATAAACCCAAAATTGCAGCAAACAACTCAGATAGAAACTAAAAGAAAAAGAAT
67374 GGCAGCAATT
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 116 1.00
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (123 bp):
GCAGAAAACGAAATTGTTAAAGAACTTGAAATCTTATTGCAAACAAGAGGAAGATTACCACCATT
ATAAACCCAAAATTGCAGCAAACAACTCAGATAGAAACTAAAAGAAAAAGAATTAAAA
Found at i:68794 original size:27 final size:28
Alignment explanation
Indices: 68757--68809 Score: 99
Period size: 27 Copynumber: 1.9 Consensus size: 28
68747 TAATAATTAC
68757 TCCCTCTGTTCCTTTTTAATTGTCCCTT
1 TCCCTCTGTTCCTTTTTAATTGTCCCTT
68785 TCCCT-TGTTCCTTTTTAATTGTCCC
1 TCCCTCTGTTCCTTTTTAATTGTCCC
68810 CCATATTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.08, C:0.32, G:0.08, T:0.53
Consensus pattern (28 bp):
TCCCTCTGTTCCTTTTTAATTGTCCCTT
Found at i:81923 original size:13 final size:13
Alignment explanation
Indices: 81905--81931 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
81895 AGTTTAAACC
81905 TTGAGCTTTCTAA
1 TTGAGCTTTCTAA
81918 TTGAGCTTTCTAA
1 TTGAGCTTTCTAA
81931 T
1 T
81932 GGAACGAGCT
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:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (13 bp):
TTGAGCTTTCTAA
Found at i:83096 original size:11 final size:11
Alignment explanation
Indices: 83076--83105 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
83066 AATTACGATT
83076 TTGTGACAAAG
1 TTGTGACAAAG
*
83087 TTGTGGCAAAG
1 TTGTGACAAAG
83098 TTGTGACA
1 TTGTGACA
83106 TTTCCTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (11 bp):
TTGTGACAAAG
Found at i:84882 original size:18 final size:18
Alignment explanation
Indices: 84854--84901 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
84844 CTTTGAATGT
* * *
84854 TGCTATTGATTGCATTGA
1 TGCTTTTGATTGCAATAA
* *
84872 TGGTTTTGATTACAATAA
1 TGCTTTTGATTGCAATAA
84890 TGCTTTTGATTG
1 TGCTTTTGATTG
84902 TATGCATATT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.23, C:0.08, G:0.21, T:0.48
Consensus pattern (18 bp):
TGCTTTTGATTGCAATAA
Found at i:94715 original size:71 final size:71
Alignment explanation
Indices: 94598--94746 Score: 262
Period size: 71 Copynumber: 2.1 Consensus size: 71
94588 GATTAAAAAG
* *
94598 AATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGGTAATTAAGAAGAATAAAGTCTTAATT
1 AATTAAGAAAAGAAAATACAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGAATAAAGTCTTAATT
94663 CAGGGT
66 CAGGGT
*
94669 AATTAAGAAAAGAAAATACAGTCAAGGTCCTAAGTTGGGCAGTTAAGAAGAATAAAGTCTTAATT
1 AATTAAGAAAAGAAAATACAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGAATAAAGTCTTAATT
*
94734 CTGGGT
66 CAGGGT
94740 AATTAAG
1 AATTAAG
94747 TCTAAATAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.26
Consensus pattern (71 bp):
AATTAAGAAAAGAAAATACAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGAATAAAGTCTTAATT
CAGGGT
Found at i:94863 original size:41 final size:41
Alignment explanation
Indices: 94797--95123 Score: 503
Period size: 41 Copynumber: 8.0 Consensus size: 41
94787 ATTTGGATAA
* *
94797 CAAACATAGTTAAAGTTTTACTCCAGCGTGATTAAGAAAGT
1 CAAACATAGTTAAAGTTTTAATCCAGGGTGATTAAGAAAGT
* *
94838 CAGACATAGTTAAAGTTCTAATCCAGGGTGATTAAGAAAGT
1 CAAACATAGTTAAAGTTTTAATCCAGGGTGATTAAGAAAGT
* *
94879 CAAACATAGTTAAAGTTTTAATCTAGGGCGATTAAGAAAGT
1 CAAACATAGTTAAAGTTTTAATCCAGGGTGATTAAGAAAGT
* *
94920 CAAACATAGTTAAAGTTTTACTCCATGGTGATTAAGAAAGT
1 CAAACATAGTTAAAGTTTTAATCCAGGGTGATTAAGAAAGT
* *
94961 CAAACATAGTT-AAGTTTTTAATCCAAGGTGATTAAGAAAGC
1 CAAACATAGTTAAAG-TTTTAATCCAGGGTGATTAAGAAAGT
* *
95002 CAGACATAGTTAAAGTTCTAATCCAGGGTGATTAAGAAAGT
1 CAAACATAGTTAAAGTTTTAATCCAGGGTGATTAAGAAAGT
*
95043 CAGACATAGTTAAAGTTTTAATCCAGGGTGATTAAGAAAGT
1 CAAACATAGTTAAAGTTTTAATCCAGGGTGATTAAGAAAGT
* *
95084 CAAACGTAGTTGAAGTTTTAATCCAGGGTGATTAAGAAAG
1 CAAACATAGTTAAAGTTTTAATCCAGGGTGATTAAGAAAG
95124 GGAAACACAG
Statistics
Matches: 261, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
40 3 0.01
41 255 0.98
42 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (41 bp):
CAAACATAGTTAAAGTTTTAATCCAGGGTGATTAAGAAAGT
Found at i:95202 original size:37 final size:37
Alignment explanation
Indices: 95131--95352 Score: 363
Period size: 37 Copynumber: 5.9 Consensus size: 37
95121 AAGGGAAACA
95131 CAGTCAAAGAACTTAATTCATGGGAAATTAAGTAAAAG
1 CAGTCAAAGAACTTAATTCA-GGGAAATTAAGTAAAAG
* *
95169 CAGTCAAAAAACTTAATTCCGGGAAATTAAGTAAAAG
1 CAGTCAAAGAACTTAATTCAGGGAAATTAAGTAAAAG
*
95206 CAGTCAAAGAACTTAATTCAGGGTAATTAAGTAAAAG
1 CAGTCAAAGAACTTAATTCAGGGAAATTAAGTAAAAG
95243 ACAGTCAAAGAACTTAATTCAGGGAAATTAAGTAAAAG
1 -CAGTCAAAGAACTTAATTCAGGGAAATTAAGTAAAAG
* *
95281 CAGTCAAAGAACTTAATTCAGGGAAACTAAGCAAAAG
1 CAGTCAAAGAACTTAATTCAGGGAAATTAAGTAAAAG
* *
95318 CAGTCAAAGAACTTAATTCATGGTAATTAAGTAAA
1 CAGTCAAAGAACTTAATTCAGGGAAATTAAGTAAA
95353 GTAAAGCACA
Statistics
Matches: 171, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
37 117 0.68
38 54 0.32
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.23
Consensus pattern (37 bp):
CAGTCAAAGAACTTAATTCAGGGAAATTAAGTAAAAG
Found at i:95248 original size:75 final size:74
Alignment explanation
Indices: 95131--95352 Score: 363
Period size: 75 Copynumber: 3.0 Consensus size: 74
95121 AAGGGAAACA
* *
95131 CAGTCAAAGAACTTAATTCATGGGAAATTAAGTAAAAGCAGTCAAAAAACTTAATTCCGGGAAAT
1 CAGTCAAAGAACTTAATTCA-GGGAAATTAAGTAAAAGCAGTCAAAGAACTTAATTCAGGGAAAT
95196 TAAGTAAAAG
65 TAAGTAAAAG
*
95206 CAGTCAAAGAACTTAATTCAGGGTAATTAAGTAAAAGACAGTCAAAGAACTTAATTCAGGGAAAT
1 CAGTCAAAGAACTTAATTCAGGGAAATTAAGTAAAAG-CAGTCAAAGAACTTAATTCAGGGAAAT
95271 TAAGTAAAAG
65 TAAGTAAAAG
* * * *
95281 CAGTCAAAGAACTTAATTCAGGGAAACTAAGCAAAAGCAGTCAAAGAACTTAATTCATGGTAATT
1 CAGTCAAAGAACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAAGAACTTAATTCAGGGAAATT
95346 AAGTAAA
66 AAGTAAA
95353 GTAAAGCACA
Statistics
Matches: 138, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
74 49 0.36
75 89 0.64
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.23
Consensus pattern (74 bp):
CAGTCAAAGAACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAAGAACTTAATTCAGGGAAATT
AAGTAAAAG
Found at i:95305 original size:112 final size:113
Alignment explanation
Indices: 95130--95352 Score: 394
Period size: 112 Copynumber: 2.0 Consensus size: 113
95120 AAAGGGAAAC
*
95130 ACAGTCAAAGAACTTAATTCATGGGAAATTAAGTAAAAGCAGTCAAAAAACTTAATTCCGGGAAA
1 ACAGTCAAAGAACTTAATTCATGGGAAATTAAGTAAAAGCAGTCAAAAAACTTAATTCAGGGAAA
* *
95195 TTAAGTAAAAGCAGTCAAAGAACTTAATTCAGGGTAATTAAGTAAAAG
66 CTAAGCAAAAGCAGTCAAAGAACTTAATTCAGGGTAATTAAGTAAAAG
*
95243 ACAGTCAAAGAACTTAATTCA-GGGAAATTAAGTAAAAGCAGTCAAAGAACTTAATTCAGGGAAA
1 ACAGTCAAAGAACTTAATTCATGGGAAATTAAGTAAAAGCAGTCAAAAAACTTAATTCAGGGAAA
*
95307 CTAAGCAAAAGCAGTCAAAGAACTTAATTCATGGTAATTAAGTAAA
66 CTAAGCAAAAGCAGTCAAAGAACTTAATTCAGGGTAATTAAGTAAA
95353 GTAAAGCACA
Statistics
Matches: 105, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
112 84 0.80
113 21 0.20
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.22
Consensus pattern (113 bp):
ACAGTCAAAGAACTTAATTCATGGGAAATTAAGTAAAAGCAGTCAAAAAACTTAATTCAGGGAAA
CTAAGCAAAAGCAGTCAAAGAACTTAATTCAGGGTAATTAAGTAAAAG
Found at i:95387 original size:41 final size:41
Alignment explanation
Indices: 95342--95592 Score: 232
Period size: 41 Copynumber: 6.3 Consensus size: 41
95332 AATTCATGGT
*
95342 AATTAAGTAAAGTAAAGCACATACTTAATTTCAAGGAAGGA
1 AATTAAGTAAAGTAAAGCACAGACTTAATTTCAAGGAAGGA
* * *
95383 AATTAGGTGAAGTAAAGCATAGACTTAATTTCAAGGAAGGA
1 AATTAAGTAAAGTAAAGCACAGACTTAATTTCAAGGAAGGA
* * * *
95424 AATT-AGATAAAGCATATCACATACTTAATTTCAAGGAAGGA
1 AATTAAG-TAAAGTAAAGCACAGACTTAATTTCAAGGAAGGA
* * *
95465 AATTAGGTAAAGTAAAGCACAGACTTAATTCCAAGGAAGGG
1 AATTAAGTAAAGTAAAGCACAGACTTAATTTCAAGGAAGGA
* * ** * *
95506 AATTAAGTAGAGTTAAG----GACTTGGTTCCAAGGAAGGG
1 AATTAAGTAAAGTAAAGCACAGACTTAATTTCAAGGAAGGA
** **
95543 AATTAAGTAGGGT----CATGGACTTAATTTCAAGGAAGGA
1 AATTAAGTAAAGTAAAGCACAGACTTAATTTCAAGGAAGGA
*
95580 AATTAAGTCAAGT
1 AATTAAGTAAAGT
95593 CAGGGACTTA
Statistics
Matches: 173, Mismatches: 31, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
37 56 0.32
40 1 0.01
41 115 0.66
42 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.25
Consensus pattern (41 bp):
AATTAAGTAAAGTAAAGCACAGACTTAATTTCAAGGAAGGA
Found at i:95428 original size:82 final size:82
Alignment explanation
Indices: 95342--95514 Score: 267
Period size: 82 Copynumber: 2.1 Consensus size: 82
95332 AATTCATGGT
* * *
95342 AATTAAGTAAAGTAAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTGAAGTAAAGCATAGAC
1 AATTAAGTAAAGCAAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGAC
*
95407 TTAATTTCAAGGAAGGA
66 TTAATTCCAAGGAAGGA
* *
95424 AATT-AGATAAAGCATATCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGA
1 AATTAAG-TAAAGCAAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGA
*
95488 CTTAATTCCAAGGAAGGG
65 CTTAATTCCAAGGAAGGA
95506 AATTAAGTA
1 AATTAAGTA
95515 GAGTTAAGGA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
81 2 0.02
82 78 0.95
83 2 0.02
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (82 bp):
AATTAAGTAAAGCAAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAGTAAAGCACAGAC
TTAATTCCAAGGAAGGA
Found at i:95527 original size:37 final size:37
Alignment explanation
Indices: 95486--95606 Score: 154
Period size: 37 Copynumber: 3.3 Consensus size: 37
95476 GTAAAGCACA
*
95486 GACTTAATTCCAAGGAAGGGAATTAAGTAGAGTTAAG
1 GACTTAATTCCAAGGAAGGGAATTAAGTAGAGTCAAG
** * *
95523 GACTTGGTTCCAAGGAAGGGAATTAAGTAGGGTCATG
1 GACTTAATTCCAAGGAAGGGAATTAAGTAGAGTCAAG
* * *
95560 GACTTAATTTCAAGGAAGGAAATTAAGTCA-AGTCAGG
1 GACTTAATTCCAAGGAAGGGAATTAAGT-AGAGTCAAG
95597 GACTTAATTC
1 GACTTAATTC
95607 AGGGTAATTA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
37 70 0.99
38 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (37 bp):
GACTTAATTCCAAGGAAGGGAATTAAGTAGAGTCAAG
Found at i:95627 original size:37 final size:37
Alignment explanation
Indices: 95594--95705 Score: 165
Period size: 37 Copynumber: 3.1 Consensus size: 37
95584 AAGTCAAGTC
95594 AGGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAA
1 AGGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAA
95631 AGGGACTTAATTC-GGGTTAATTAAGTAGCGTCAATAA
1 AGGGACTTAATTCAGGG-TAATTAAGTAGCGTCAATAA
* ** *
95668 AGGG-CTTAGTTCAGGACAATTAAGTAGAGTCAATAA
1 AGGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAA
95704 AG
1 AG
95706 AAGTTAATCT
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
36 30 0.43
37 39 0.57
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (37 bp):
AGGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAA
Found at i:96091 original size:19 final size:20
Alignment explanation
Indices: 96064--96113 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
96054 CATAGATTCT
* *
96064 GGTTAAGTA-TACTTTATTA
1 GGTTAAGTATTACCTAATTA
*
96083 GGTTTAGTATTACCTAATTA
1 GGTTAAGTATTACCTAATTA
96103 GGTTAA-TATTA
1 GGTTAAGTATTA
96114 GACTTAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (20 bp):
GGTTAAGTATTACCTAATTA
Found at i:97162 original size:6 final size:6
Alignment explanation
Indices: 97147--97187 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
97137 AAAGCAAAGC
*
97147 AAAT-T AAATCT AAATCT AAATCT AAATCT AAATTT AAATCT
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT
97188 GAAGCAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (6 bp):
AAATCT
Found at i:99678 original size:24 final size:24
Alignment explanation
Indices: 99633--99679 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
99623 AAACATTCTT
*
99633 AAAAATTCAAAGCAATCATCAATC
1 AAAAATTCAAAGCAATAATCAATC
99657 AAAAA-TCAAAGCAATAACTCAAT
1 AAAAATTCAAAGCAATAA-TCAAT
99680 ATGTGCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.57, C:0.19, G:0.04, T:0.19
Consensus pattern (24 bp):
AAAAATTCAAAGCAATAATCAATC
Found at i:100366 original size:10 final size:10
Alignment explanation
Indices: 100351--100393 Score: 59
Period size: 10 Copynumber: 4.0 Consensus size: 10
100341 TGGCATTGAG
100351 CGGGCATGGC
1 CGGGCATGGC
100361 CGGGCATGGTGC
1 CGGGCAT-G-GC
100373 GCGGGCATGGC
1 -CGGGCATGGC
100384 CGGGCATGGC
1 CGGGCATGGC
100394 GTGGTGTCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 17 0.57
11 3 0.10
12 3 0.10
13 7 0.23
ACGTcount: A:0.09, C:0.28, G:0.51, T:0.12
Consensus pattern (10 bp):
CGGGCATGGC
Found at i:103840 original size:40 final size:41
Alignment explanation
Indices: 103767--103845 Score: 101
Period size: 39 Copynumber: 2.0 Consensus size: 41
103757 AATAAAAATT
103767 AAAAAGCAGAAACAAAAAATAAAAATATTTTTTT-AAAAGG
1 AAAAAGCAGAAACAAAAAATAAAAATATTTTTTTCAAAAGG
* *
103807 AAAAA-CAGAAA-AGAAAAATTAATATATTTTTTTTCAAAA
1 AAAAAGCAGAAACA-AAAAATAAAAATA-TTTTTTTCAAAA
103846 ATCGGAAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 1 0.03
39 17 0.50
40 12 0.35
41 4 0.12
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.27
Consensus pattern (41 bp):
AAAAAGCAGAAACAAAAAATAAAAATATTTTTTTCAAAAGG
Found at i:104289 original size:6 final size:6
Alignment explanation
Indices: 104274--104350 Score: 129
Period size: 6 Copynumber: 13.0 Consensus size: 6
104264 AAAGCAAAGC
104274 AAAT-T AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT
* *
104321 AAATCT AAACCT AAATCT AAATTT AAATCT
1 AAATCT AAATCT AAATCT AAATCT AAATCT
104351 GAAGCAAAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
5 4 0.06
6 63 0.94
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
AAATCT
Found at i:109091 original size:35 final size:35
Alignment explanation
Indices: 109032--109109 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
109022 TAAGCCATTT
* *
109032 ATTTACTTAGTTACACCAAATTAAGCCAATTACCG
1 ATTTACTTAATTACACCAAATTAAGCCAATTACCA
** * **
109067 ATTTACTTAATTACACTGAGTTAAGTTAATTACCA
1 ATTTACTTAATTACACCAAATTAAGCCAATTACCA
*
109102 AGTTACTT
1 ATTTACTT
109110 GATTTGATAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (35 bp):
ATTTACTTAATTACACCAAATTAAGCCAATTACCA
Found at i:109167 original size:65 final size:64
Alignment explanation
Indices: 109087--109215 Score: 170
Period size: 64 Copynumber: 2.0 Consensus size: 64
109077 TTACACTGAG
* * * * *
109087 TTAAGTTAATTACCAAGTTACTTGATTTGA-TAGTTTACTTAATTGCACCGAATTGAGTTAATTA
1 TTAAGTTAATTACCAAATTACTT-AATT-ACCAATTTACTTAATTGCACCGAATTAAGTTAATTA
109151 C
64 C
* *
109152 TTAATTTAATTACCAAATTACTTAATTACCAATTTTCTTAATTGCACCGAATTAAGTTAATTAC
1 TTAAGTTAATTACCAAATTACTTAATTACCAATTTACTTAATTGCACCGAATTAAGTTAATTAC
109216 CAAGTTACTT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
63 1 0.02
64 34 0.61
65 21 0.38
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (64 bp):
TTAAGTTAATTACCAAATTACTTAATTACCAATTTACTTAATTGCACCGAATTAAGTTAATTAC
Found at i:109178 original size:16 final size:16
Alignment explanation
Indices: 109157--109228 Score: 72
Period size: 16 Copynumber: 4.3 Consensus size: 16
109147 ATTACTTAAT
109157 TTAATTACCAAATTAC
1 TTAATTACCAAATTAC
* *
109173 TTAATTACCAATTTTC
1 TTAATTACCAAATTAC
* *
109189 TTAATTGCACCGAATTAAG
1 TTAATT--ACCAAATT-AC
*
109208 TTAATTACCAAGTTAC
1 TTAATTACCAAATTAC
109224 TTAAT
1 TTAAT
109229 CTAATTATCA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
16 26 0.59
17 6 0.14
18 6 0.14
19 6 0.14
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (16 bp):
TTAATTACCAAATTAC
Found at i:109233 original size:21 final size:21
Alignment explanation
Indices: 109209--109249 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
109199 CGAATTAAGT
*
109209 TAATTACCAAGTTACTTAATC
1 TAATTACCAAATTACTTAATC
* *
109230 TAATTATCAAATTGCTTAAT
1 TAATTACCAAATTACTTAAT
109250 TACACTGAAT
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:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (21 bp):
TAATTACCAAATTACTTAATC
Found at i:109248 original size:56 final size:56
Alignment explanation
Indices: 109152--109279 Score: 149
Period size: 56 Copynumber: 2.4 Consensus size: 56
109142 AGTTAATTAC
* * * *
109152 TTAATTTAATTACCAAATTAC----T-TAATTACCAATTTTCTTAATTGCACCGAA
1 TTAAGTTAATTACCAAATTACTTAATCTAATTACCAAATTGCTTAATTACACCGAA
* * *
109203 TTAAGTTAATTACCAAGTTACTTAATCTAATTATCAAATTGCTTAATTACACTGAA
1 TTAAGTTAATTACCAAATTACTTAATCTAATTACCAAATTGCTTAATTACACCGAA
*
109259 TTAAGTTGATTACCAAATTAC
1 TTAAGTTAATTACCAAATTAC
109280 CAATTTACTT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
51 19 0.30
55 1 0.02
56 43 0.68
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (56 bp):
TTAAGTTAATTACCAAATTACTTAATCTAATTACCAAATTGCTTAATTACACCGAA
Found at i:109278 original size:43 final size:43
Alignment explanation
Indices: 109231--109321 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
109221 TACTTAATCT
* * *
109231 AATTATCAAATTGCTTAATTACACTGAATTAAGTTGATTACCA
1 AATTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCA
* * *
109274 AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCC
1 AATTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCA
109317 AATTA
1 AATTA
109322 GTTAAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.37
Consensus pattern (43 bp):
AATTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCA
Found at i:109383 original size:43 final size:43
Alignment explanation
Indices: 109335--109556 Score: 291
Period size: 43 Copynumber: 5.0 Consensus size: 43
109325 AAATTTTATC
* *
109335 ACCAATTTACTTAATTACATCGAAATAAGTTGTTTACCAAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
*
109378 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAGATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
* *
109421 ACCAATTTACTGAATTACACCGAATTAAGTTGTTTACCAGATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
* *
109464 ACCAATTTACTTAATTACACTGAATTAAGTTGATTACCAAATTACTTAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACC-----A---AATT
* *
109515 ACCAATTTACTTAATTACACCGAATTGAGTTGATTACCAAAT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAAT
109557 GACTTAATTT
Statistics
Matches: 161, Mismatches: 10, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
43 120 0.75
46 1 0.01
48 1 0.01
51 39 0.24
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (43 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
Found at i:109384 original size:100 final size:100
Alignment explanation
Indices: 109175--109556 Score: 351
Period size: 100 Copynumber: 4.0 Consensus size: 100
109165 CAAATTACTT
* * ** * *
109175 AATTACCAATTTTCTTAATTGCACCGAATTAAGTTAATTA-CCAAGTTACTTAATCTAATTATCA
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCCAAGTTACTTAATCTAATCACCA
* *
109239 AATTGCTTAATTACACTGAATTAAGTTGATTACCA
66 AATTACTTAATTACACTGAAATAAGTTGATTACCA
* * *
109274 AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCCAA-TTAGTTAAATTTTATCACC
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCCAAGTTACTT-AATCTAATCACC
* *
109338 AATTTACTTAATTACA-TCGAAATAAGTTGTTTACCA
65 AAATTACTTAATTACACT-GAAATAAGTTGATTACCA
109374 AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTA-CC-AG-------A--T--T-ACCA
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCCAAGTTACTTAATCTAATCACCA
* * * * *
109425 ATTTACTGAATTACACCGAATTAAGTTGTTTACCA
66 AATTACTTAATTACACTGAAATAAGTTGATTACCA
* * * *
109460 GATTACCAATTTACTTAATTACACTGAATTAAGTTGATTA-CCAAATTACTTAA--T--T-ACCA
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCCAAGTTACTTAATCTAATCACCA
* * * *
109519 ATTTACTTAATTACACCGAATTGAGTTGATTACCA
66 AATTACTTAATTACACTGAAATAAGTTGATTACCA
109554 AAT
1 AAT
109557 GACTTAATTT
Statistics
Matches: 246, Mismatches: 24, Indels: 31
0.82 0.08 0.10
Matches are distributed among these distances:
86 74 0.30
87 2 0.01
89 1 0.00
91 1 0.00
94 41 0.17
98 1 0.00
99 44 0.18
100 82 0.33
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (100 bp):
AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCCAAGTTACTTAATCTAATCACCA
AATTACTTAATTACACTGAAATAAGTTGATTACCA
Found at i:109480 original size:16 final size:16
Alignment explanation
Indices: 109461--109532 Score: 81
Period size: 16 Copynumber: 4.3 Consensus size: 16
109451 TGTTTACCAG
109461 ATTACCAATTTACTTA
1 ATTACCAATTTACTTA
* * *
109477 ATTACACTGAATTAAGTTG
1 ATTAC-C--AATTTACTTA
*
109496 ATTACCAAATTACTTA
1 ATTACCAATTTACTTA
109512 ATTACCAATTTACTTA
1 ATTACCAATTTACTTA
109528 ATTAC
1 ATTAC
109533 ACCGAATTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
16 31 0.69
17 1 0.02
18 1 0.02
19 12 0.27
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.40
Consensus pattern (16 bp):
ATTACCAATTTACTTA
Found at i:109832 original size:11 final size:11
Alignment explanation
Indices: 109818--109849 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
109808 GAAGTTCATG
109818 TTTGAAGATTA
1 TTTGAAGATTA
*
109829 TTTGAAGATAA
1 TTTGAAGATTA
109840 TTTGAAGATT
1 TTTGAAGATT
109850 TGAACACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:111173 original size:18 final size:18
Alignment explanation
Indices: 111150--111184 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
111140 AGAAGAAGTA
*
111150 TGCTTTTTAATTACTGTT
1 TGCTTTATAATTACTGTT
*
111168 TGCTTTATAATTGCTGT
1 TGCTTTATAATTACTGT
111185 AGATTTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.11, G:0.14, T:0.57
Consensus pattern (18 bp):
TGCTTTATAATTACTGTT
Found at i:111202 original size:6 final size:6
Alignment explanation
Indices: 111184--111220 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
111174 ATAATTGCTG
*
111184 TAGATT TAAATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA
111221 CTTTGCTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (6 bp):
TAGATT
Found at i:111605 original size:16 final size:17
Alignment explanation
Indices: 111574--111606 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
111564 TTGCGTTATT
*
111574 TAAAAAAAATTGTTTTC
1 TAAAAAAAATTATTTTC
111591 TAAAAAAAA-TATTTTC
1 TAAAAAAAATTATTTTC
111607 CTTTATTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAAAAAAATTATTTTC
Found at i:115581 original size:11 final size:11
Alignment explanation
Indices: 115565--115596 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
115555 GAAGTTCGTG
115565 TTTGAAGATTA
1 TTTGAAGATTA
*
115576 TTTGAAGATAA
1 TTTGAAGATTA
115587 TTTGAAGATT
1 TTTGAAGATT
115597 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:115590 original size:22 final size:22
Alignment explanation
Indices: 115565--115624 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
115555 GAAGTTCGTG
*
115565 TTTGAAGATTATTTGAAGATAA
1 TTTGAAGATTATTTGAAGACAA
115587 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGATTATTTGAAGACAA
*
115606 -TTGAAGAATTATTTCAAGA
1 TTTGAAG-ATTATTTGAAGA
115625 AGTAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (22 bp):
TTTGAAGATTATTTGAAGACAA
Found at i:115599 original size:19 final size:18
Alignment explanation
Indices: 115575--115612 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
115565 TTTGAAGATT
*
115575 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
115594 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
115612 A
1 A
115613 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:117008 original size:15 final size:14
Alignment explanation
Indices: 116974--117004 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
116964 TAGTTTTTAG
*
116974 TTTAATTGCTTTCT
1 TTTAATTGATTTCT
116988 TTTAATTGATTTCT
1 TTTAATTGATTTCT
117002 TTT
1 TTT
117005 TAATCCCCTG
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:0.16, C:0.10, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTAATTGATTTCT
Done.