Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008560.1 Hibiscus syriacus cultivar Beakdansim tig00111467_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: 753118
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:2596 original size:19 final size:19
Alignment explanation
Indices: 2572--2608 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2562 ACGAGAGTTG
*
2572 TCGTCTCTTGAAAATTTTC
1 TCGTCTCTTAAAAATTTTC
2591 TCGTCTCTTAAAAATTTT
1 TCGTCTCTTAAAAATTTT
2609 AAATTTTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (19 bp):
TCGTCTCTTAAAAATTTTC
Found at i:5466 original size:21 final size:21
Alignment explanation
Indices: 5436--5483 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
5426 GCAGGGGTAC
* *
5436 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
*
5457 ATGCCAAGCCCACCAGTTCAT
1 ATGCCAAGCCCACCACTTCAT
5478 ATGCCA
1 ATGCCA
5484 TCTCCGCAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.42, G:0.12, T:0.21
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:5513 original size:21 final size:21
Alignment explanation
Indices: 5487--5601 Score: 144
Period size: 21 Copynumber: 5.5 Consensus size: 21
5477 TATGCCATCT
*
5487 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
5508 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
5529 CCGCCA-GGTTACATTCCGAGC
1 CCG-CAGGGTTACATTCCTAGC
* *
5550 TCGTAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
5571 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
*
5592 CCGCATGGTT
1 CCGCAGGGTT
5602 TTATACCATA
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.04
21 76 0.93
22 3 0.04
ACGTcount: A:0.18, C:0.33, G:0.25, T:0.23
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:5540 original size:42 final size:42
Alignment explanation
Indices: 5493--5601 Score: 173
Period size: 42 Copynumber: 2.6 Consensus size: 42
5483 ATCTCCGCAG
5493 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCA
1 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCA
* *
5535 GGTTACATTCCGAGCTCGTAGGGTTACATTCCTAGCCCGCCA
1 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCA
* * *
5577 GGTTACATGCCTAGCCCGCATGGTT
1 GGTTACATTCCGAGCCCGCAGGGTT
5602 TTATACCATA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.18, C:0.32, G:0.25, T:0.25
Consensus pattern (42 bp):
GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCA
Found at i:6218 original size:34 final size:34
Alignment explanation
Indices: 6116--6219 Score: 154
Period size: 34 Copynumber: 3.1 Consensus size: 34
6106 AATGTTTTTC
*
6116 AAATACAAATTATATTATTCGAAATTTAAAATAA
1 AAATACAAATTATATTATTCGAAATTTAAAATTA
* *
6150 AAATAAAAATAATATTATTCGAAATTTAAAATTA
1 AAATACAAATTATATTATTCGAAATTTAAAATTA
* * *
6184 AAATACAAATTATAGTATTCAAAATTTAACATTA
1 AAATACAAATTATATTATTCGAAATTTAAAATTA
6218 AA
1 AA
6220 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 62 1.00
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.35
Consensus pattern (34 bp):
AAATACAAATTATATTATTCGAAATTTAAAATTA
Found at i:6844 original size:128 final size:128
Alignment explanation
Indices: 6616--7349 Score: 1362
Period size: 128 Copynumber: 5.7 Consensus size: 128
6606 ACAATCCATC
6616 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
6681 GGAAGGCGCGCCCCCGAGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
6744 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
6809 GGAAGGCGCCCCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
6872 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
6937 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
7000 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
7065 GGAAGGCGC-CCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* *
7127 TAGTGTCCCCGAAGGACATGTGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
7192 GGAAGGCGCGCCCCTGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
7255 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * * *
7320 GGAATGCGCGTCCCTGGGAACACGCCTTCA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
7350 TGTGAATAGT
Statistics
Matches: 590, Mismatches: 15, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
127 125 0.21
128 465 0.79
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:7213 original size:255 final size:255
Alignment explanation
Indices: 6616--7349 Score: 1360
Period size: 255 Copynumber: 2.9 Consensus size: 255
6606 ACAATCCATC
6616 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
6681 GGAAGGCGCGCCCCCGAGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
*
6746 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTTGACAAAATAATGG
131 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
*
6811 AAGGCGCCCCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
196 AAGGCG-CCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
6872 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
6937 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
7002 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
131 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
7067 AAGGCGCCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
196 AAGGCGCCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* *
7127 TAGTGTCCCCGAAGGACATGTGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
7192 GGAAGGCGCGCCCCTGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
7257 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
131 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
* * * *
7322 AATGCGCGTCCCTGGGAACACGCCTTCA
196 AAGGCGC-CCCCCGGGAACGCGCCTTCA
7350 TGTGAATAGT
Statistics
Matches: 467, Mismatches: 10, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
255 251 0.54
256 216 0.46
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (255 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
AAGGCGCCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:7348 original size:383 final size:384
Alignment explanation
Indices: 6616--7349 Score: 1362
Period size: 383 Copynumber: 1.9 Consensus size: 384
6606 ACAATCCATC
6616 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
6681 GGAAGGCGCGCCCCCGAGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
66 GGAAGGCGCGCCCCCGAGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
* *
6746 GTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTTGACAAAATAATGG
131 GTGTCCCCGAAGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
6811 AAGGCGCCCCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATAGT
196 AAGGCGCCCCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATAGT
6876 GTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAA
261 GTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAA
*
6941 GGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
326 GGCGCGCCCCCGGGAACACGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
7000 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
7065 GGAAGGCGC-CCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
66 GGAAGGCGCGCCCCCGAGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
*
7129 GTGTCCCCGAAGGACATGTGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
131 GTGTCCCCGAAGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
* * *
7194 AAGGCGCGCCCCTGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATAGT
196 AAGGCGCCCCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATAGT
7259 GTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAA
261 GTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAA
* * *
7324 TGCGCGTCCCTGGGAACACGCCTTCA
326 GGCGCGCCCCCGGGAACACGCCTTCA
7350 TGTGAATAGT
Statistics
Matches: 339, Mismatches: 11, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
383 265 0.78
384 74 0.22
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (384 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGAGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
GTGTCCCCGAAGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
AAGGCGCCCCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATAGT
GTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAA
GGCGCGCCCCCGGGAACACGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:12337 original size:6 final size:6
Alignment explanation
Indices: 12327--12384 Score: 80
Period size: 6 Copynumber: 9.7 Consensus size: 6
12317 CCTGATGATT
* * * *
12327 CAAAAT CAAAAC CAAAAC CAATAC CAAAAT CAAAAC CAAAAC CAAAAT
1 CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC
12375 CAAAAC CAAA
1 CAAAAC CAAA
12385 TGAATCATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.66, C:0.28, G:0.00, T:0.07
Consensus pattern (6 bp):
CAAAAC
Found at i:12360 original size:18 final size:18
Alignment explanation
Indices: 12327--12384 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
12317 CCTGATGATT
* *
12327 CAAAATCAAAACCAAAAC
1 CAAAACCAAAATCAAAAC
*
12345 CAATACCAAAATCAAAAC
1 CAAAACCAAAATCAAAAC
12363 CAAAACCAAAATCAAAAC
1 CAAAACCAAAATCAAAAC
12381 CAAA
1 CAAA
12385 TGAATCATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.66, C:0.28, G:0.00, T:0.07
Consensus pattern (18 bp):
CAAAACCAAAATCAAAAC
Found at i:13991 original size:24 final size:25
Alignment explanation
Indices: 13958--14008 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
13948 ATTTTTACCA
*
13958 TTTTTAAAATTTTATAAATATTT-TC
1 TTTTTAAAATTTTA-AAAAATTTATC
13983 TTTTT-AAATTTTAAAAAATTTATC
1 TTTTTAAAATTTTAAAAAATTTATC
14007 TT
1 TT
14009 CTAATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
24 12 0.50
25 5 0.21
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTTAAAATTTTAAAAAATTTATC
Found at i:15242 original size:32 final size:32
Alignment explanation
Indices: 15201--15280 Score: 124
Period size: 32 Copynumber: 2.5 Consensus size: 32
15191 TTGAGTCAGA
*
15201 TCGAGTCAGATCAATATACAATTGATCAATTT
1 TCGAATCAGATCAATATACAATTGATCAATTT
** *
15233 TTTAATCAGATCAATATAGAATTGATCAATTT
1 TCGAATCAGATCAATATACAATTGATCAATTT
15265 TCGAATCAGATCAATA
1 TCGAATCAGATCAATA
15281 CTAGATAGAC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (32 bp):
TCGAATCAGATCAATATACAATTGATCAATTT
Found at i:15278 original size:17 final size:17
Alignment explanation
Indices: 15224--15279 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
15214 ATATACAATT
**
15224 GATCAATTTTTTAATCA
1 GATCAATTTTAGAATCA
* *
15241 GATCAA-TATAGAAT-T
1 GATCAATTTTAGAATCA
*
15256 GATCAATTTTCGAATCA
1 GATCAATTTTAGAATCA
15273 GATCAAT
1 GATCAAT
15280 ACTAGATAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 6 0.20
16 11 0.37
17 13 0.43
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (17 bp):
GATCAATTTTAGAATCA
Found at i:15295 original size:32 final size:31
Alignment explanation
Indices: 15201--15297 Score: 113
Period size: 32 Copynumber: 3.0 Consensus size: 31
15191 TTGAGTCAGA
* *
15201 TCGAGTCAGATCAATATACAATTGATCAATTT
1 TCGAATCAGATCAATATA-GATTGATCAATTT
**
15233 TTTAATCAGATCAATATAGAATTGATCAATTT
1 TCGAATCAGATCAATATAG-ATTGATCAATTT
* *
15265 TCGAATCAGATCAATACTAGATAGACCAATTT
1 TCGAATCAGATCAATA-TAGATTGATCAATTT
15297 T
1 T
15298 TAGTTTGGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
32 52 0.95
33 3 0.05
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.35
Consensus pattern (31 bp):
TCGAATCAGATCAATATAGATTGATCAATTT
Found at i:17907 original size:14 final size:14
Alignment explanation
Indices: 17888--17929 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
17878 TTAAAAGTTT
17888 TAATTTTTTTTATA
1 TAATTTTTTTTATA
17902 TAATTTTTTGTTA-A
1 TAATTTTTT-TTATA
17916 TAATTTGTTTTTAT
1 TAATTT-TTTTTAT
17930 CTCTAGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (14 bp):
TAATTTTTTTTATA
Found at i:18249 original size:2 final size:2
Alignment explanation
Indices: 18242--18274 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
18232 TTGCAGGAAC
18242 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18275 TGGTGTGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19649 original size:108 final size:108
Alignment explanation
Indices: 19458--20081 Score: 380
Period size: 108 Copynumber: 5.6 Consensus size: 108
19448 CGTCTTTTTA
* * * ***
19458 AAGCTGATGGGGCCTTAGAAA-TCTGACGATAACAAAATAGGTTAAATACTTAATTTGTTATCAA
1 AAGCTGATGGAGCCTTAGAAATTC-GACGATAACAAAATAGGTTAATTACTGAATACATTATCAA
* *
19522 TATTATCAACATATTAGGTAACACCTAAAATGTTACCAAAGCTT
65 TATAATCAACATATTAGGTAACGCCTAAAATGTTACCAAAGCTT
** *
19566 AAGCTGACAGAGCCTTAGAAATTCGACGATAACAAAATAGGTTAATTACTGGAA-ACAATATCAA
1 AAGCTGATGGAGCCTTAGAAATTCGACGATAACAAAATAGGTTAATTACT-GAATACATTATCAA
* * * * ** **
19630 TCATAAT-AACATGA-CAGGTAACGCTTATTTAACGTAATAGGTAGTGTCTTTTT
65 T-ATAATCAACAT-ATTAGGTAACGCCTA--AAATGT--TA-CCAAAG-C---TT
* * * * ** * ***
19683 AAAGCTGGTGGGGTCTTAGAAATCCGGTGATAACAAAATAGGTTAATTACTTAATTTGTTATCAA
1 -AAGCTGATGGAGCCTTAGAAATTCGACGATAACAAAATAGGTTAATTACTGAATACATTATCAA
* * *
19748 TATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTT
65 TATAATCAACATATTAGGTAACGCCTAAAATGTTACCAAAGCTT
*
19792 AAGCTGATGGAGCTTTAGAAATTCGACGATAACAAAATAGGTTAATTACTGGAA-ACATTATCAA
1 AAGCTGATGGAGCCTTAGAAATTCGACGATAACAAAATAGGTTAATTACT-GAATACATTATCAA
* ** * * ** * ** * *
19856 CCATAAT-AACATAGCAAGTAGCGTTTATTTAATGTAATAGGTAGATTCTGTTT
65 -TATAATCAACATATTAGGTAACGCCTA--AAATGT--TA-CCA-A---AGCTT
* * * * * * ***
19909 AAAGTTGATGGGGCCTTAGAAATTCGACGATAACAAAATATGTTAAATGCTTAATTTGTTATCAA
1 -AAGCTGATGGAGCCTTAGAAATTCGACGATAACAAAATAGGTTAATTACTGAATACATTATCAA
* * * *
19974 TATTATCAACATATTAGGTAACACCTAATATGTTACCAAAGTTT
65 TATAATCAACATATTAGGTAACGCCTAAAATGTTACCAAAGCTT
* * * * * *
20018 AAGCTAATCGAGCCTTAGAAATACGACGATAATAAAATAAGTTAATTATTGGAA-ACATTATCAA
1 AAGCTGATGGAGCCTTAGAAATTCGACGATAACAAAATAGGTTAATTACT-GAATACATTATCAA
20082 CCAGAATAAC
Statistics
Matches: 381, Mismatches: 103, Indels: 64
0.70 0.19 0.12
Matches are distributed among these distances:
108 177 0.46
109 23 0.06
110 9 0.02
112 5 0.01
113 6 0.02
114 6 0.02
116 8 0.02
117 19 0.05
118 128 0.34
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.31
Consensus pattern (108 bp):
AAGCTGATGGAGCCTTAGAAATTCGACGATAACAAAATAGGTTAATTACTGAATACATTATCAAT
ATAATCAACATATTAGGTAACGCCTAAAATGTTACCAAAGCTT
Found at i:19763 original size:226 final size:225
Alignment explanation
Indices: 19369--20199 Score: 1151
Period size: 226 Copynumber: 3.7 Consensus size: 225
19359 TTTTTAACTT
* * * * *
19369 TAACAAAATCGGTTAATTACTGGAAAC-ATCATCAACCATAATTACATAACAGGTAGCGTTTATT
1 TAACAAAATAGGTTAATTACTGGAAACAAT-ATCAACCATAATAACATAACAAGTAACGCTTATT
* *
19433 TAACGTAATAGGTAGCGTCTTTTTAAAGCTGATGGGGCCTTAGAAATCTGACGATAACAAAATAG
65 TAACGTAATAGGTAGCGTCTGTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAAATAG
19498 GTTAAATACTTAATTTGTTATCAATATTATCAACATATTAGGTAACACCTAAAATGTTACCAAAG
130 GTTAAATACTTAATTTGTTATCAATATTATCAACATATTAGGTAACACCTAAAATGTTACCAAAG
*
19563 CTTAAGCTGACAGAGCCTTAGAAATTCGACGA
195 TTTAAGCTGAC-GAGCCTTAGAAATTCGACGA
* * *
19595 TAACAAAATAGGTTAATTACTGGAAACAATATCAATCATAATAACATGACAGGTAACGCTTATTT
1 TAACAAAATAGGTTAATTACTGGAAACAATATCAACCATAATAACATAACAAGTAACGCTTATTT
* * * * **
19660 AACGTAATAGGTAGTGTCTTTTTAAAGCTGGTGGGGTCTTAGAAATCCGGTGATAACAAAATAGG
66 AACGTAATAGGTAGCGTCTGTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAAATAGG
* * *
19725 TTAATTACTTAATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGT
131 TTAAATACTTAATTTGTTATCAATATTATCAACATATTAGGTAACACCTAAAATGTTACCAAAGT
* *
19790 TTAAGCTGATGGAGCTTTAGAAATTCGACGA
196 TTAAGCTGA-CGAGCCTTAGAAATTCGACGA
* * * *
19821 TAACAAAATAGGTTAATTACTGGAAACATTATCAACCATAATAACATAGCAAGTAGCGTTTATTT
1 TAACAAAATAGGTTAATTACTGGAAACAATATCAACCATAATAACATAACAAGTAACGCTTATTT
* ** * * *
19886 AATGTAATAGGTAGATTCTGTTTAAAGTTGATGGGGCCTTAGAAATTCGACGATAACAAAATATG
66 AACGTAATAGGTAGCGTCTGTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAAATAGG
* *
19951 TTAAATGCTTAATTTGTTATCAATATTATCAACATATTAGGTAACACCTAATATGTTACCAAAGT
131 TTAAATACTTAATTTGTTATCAATATTATCAACATATTAGGTAACACCTAAAATGTTACCAAAGT
* *
20016 TTAAGCTAATCGAGCCTTAGAAATACGACGA
196 TTAAGCTGA-CGAGCCTTAGAAATTCGACGA
* * * * * *
20047 TAATAAAATAAGTTAATTATTGGAAACATTATCAACCAGAATAACATAACAAGTAACGCTCATTT
1 TAACAAAATAGGTTAATTACTGGAAACAATATCAACCATAATAACATAACAAGTAACGCTTATTT
* * * * * * * *
20112 AATGTAATAGGTGGCATCTGTTTAAAGCTTATAGGGCCTTAAAAATCTGACGATAACAAAATAAG
66 AACGTAATAGGTAGCGTCTGTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAAATAGG
* *
20177 TTAATTACTTAATTTGTTTTCAA
131 TTAAATACTTAATTTGTTATCAA
20200 AGAAATCAAT
Statistics
Matches: 537, Mismatches: 66, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
226 535 1.00
227 2 0.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (225 bp):
TAACAAAATAGGTTAATTACTGGAAACAATATCAACCATAATAACATAACAAGTAACGCTTATTT
AACGTAATAGGTAGCGTCTGTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAAATAGG
TTAAATACTTAATTTGTTATCAATATTATCAACATATTAGGTAACACCTAAAATGTTACCAAAGT
TTAAGCTGACGAGCCTTAGAAATTCGACGA
Found at i:20295 original size:19 final size:18
Alignment explanation
Indices: 20267--20305 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
20257 GTTTCAAAAT
*
20267 TATAAGTATCAGTACTTG
1 TATAAGTATCAATACTTG
20285 TATACAGTATCAATACTTG
1 TATA-AGTATCAATACTTG
20304 TA
1 TA
20306 CATTTACGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (18 bp):
TATAAGTATCAATACTTG
Found at i:20546 original size:14 final size:14
Alignment explanation
Indices: 20527--20557 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
20517 ATTATCATTA
20527 TACCGATAAAATTT
1 TACCGATAAAATTT
20541 TACCGATAAAATTT
1 TACCGATAAAATTT
20555 TAC
1 TAC
20558 TGTTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (14 bp):
TACCGATAAAATTT
Found at i:22251 original size:54 final size:54
Alignment explanation
Indices: 22178--22302 Score: 155
Period size: 54 Copynumber: 2.4 Consensus size: 54
22168 CCTGAATGAT
* * * *
22178 GGTATCGATA-CATTAAAACATCGAATGCCAGATTGGTATCGATACCTTGAGGA
1 GGTATCGATACCCTTGAAACATCGAATACCAGATTGGTATCGATACCATGAGGA
** ** *
22231 GGTATCGATACCCTTGAAACATCGAATATTATTTTGGTATCGGTACCATGAGGA
1 GGTATCGATACCCTTGAAACATCGAATACCAGATTGGTATCGATACCATGAGGA
22285 GGTATCGATACCC-TGAAA
1 GGTATCGATACCCTTGAAA
22303 GGGAAGTATC
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
53 15 0.24
54 47 0.76
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (54 bp):
GGTATCGATACCCTTGAAACATCGAATACCAGATTGGTATCGATACCATGAGGA
Found at i:22927 original size:44 final size:44
Alignment explanation
Indices: 22864--22962 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
22854 GTTTTATTTA
* *
22864 ACACTTCAGTGCAAACTTATGTAGTCTTTCAGGACAAATATGTG
1 ACACTTCGGTGCAAACTTATGTAGTCCTTCAGGACAAATATGTG
* * * *
22908 ACACTTCGGTGCAAACTTATGTGGTCCTTCGGGATAATTATGTG
1 ACACTTCGGTGCAAACTTATGTAGTCCTTCAGGACAAATATGTG
*
22952 GCACTTCGGTG
1 ACACTTCGGTG
22963 AAAATTACGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (44 bp):
ACACTTCGGTGCAAACTTATGTAGTCCTTCAGGACAAATATGTG
Found at i:22950 original size:21 final size:22
Alignment explanation
Indices: 22902--22969 Score: 77
Period size: 21 Copynumber: 3.1 Consensus size: 22
22892 TCAGGACAAA
* *
22902 TATGTGACACTTCGGTGCAAACT
1 TATGTGGCACTTCGGTG-AAAAT
*
22925 TATGTGGTC-CTTCGG-GATAAT
1 TATGTGG-CACTTCGGTGAAAAT
22946 TATGTGGCACTTCGGTGAAAAT
1 TATGTGGCACTTCGGTGAAAAT
22968 TA
1 TA
22970 CGAGCTGTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.03
21 16 0.42
22 8 0.21
23 12 0.32
24 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGAAAAT
Found at i:37604 original size:20 final size:20
Alignment explanation
Indices: 37575--37612 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37565 GATACCCTTA
*
37575 AAGGGAAGTATCGATACTAT
1 AAGGGAAGTACCGATACTAT
*
37595 AAGGGTAGTACCGATACT
1 AAGGGAAGTACCGATACT
37613 TCTAAACATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (20 bp):
AAGGGAAGTACCGATACTAT
Found at i:47408 original size:21 final size:21
Alignment explanation
Indices: 47365--47408 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
47355 GGATGAACTG
* *
47365 TGGCTTTGTAAAAGTATTGCT
1 TGGCTTTGTAAAAATATTCCT
47386 TGGCTTTGTAACAAAT-TTCCT
1 TGGCTTTGTAA-AAATATTCCT
47407 TG
1 TG
47409 ATTTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (21 bp):
TGGCTTTGTAAAAATATTCCT
Found at i:48941 original size:14 final size:14
Alignment explanation
Indices: 48922--48956 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
48912 TTATATGTTA
*
48922 AGGCAAGCAAATTT
1 AGGCAAGCAAATCT
48936 AGGCAAGCAAATCT
1 AGGCAAGCAAATCT
48950 AGGCAAG
1 AGGCAAG
48957 TATACACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.26, T:0.14
Consensus pattern (14 bp):
AGGCAAGCAAATCT
Found at i:55295 original size:21 final size:21
Alignment explanation
Indices: 55271--55325 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
55261 CAAGGTAATT
*
55271 TGTTGTAAAGCCAAGCTACAC
1 TGTTGCAAAGCCAAGCTACAC
55292 TGTTGCAAAGCCAAGCTACAC
1 TGTTGCAAAGCCAAGCTACAC
55313 TGTTGCAAAGCCA
1 TGTTGCAAAGCCA
55326 TAGTTCATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (21 bp):
TGTTGCAAAGCCAAGCTACAC
Found at i:67630 original size:199 final size:199
Alignment explanation
Indices: 67285--67646 Score: 490
Period size: 199 Copynumber: 1.8 Consensus size: 199
67275 TGGTACTTAT
* * * *
67285 GCCTATTATCATTAAATCGGTAGACATTTATCGTTTACATGGTTAATTTACCTATTACTTTATAG
1 GCCTATTATCATTAAACCGGTAGACATTTATCGTTTACATGATTAATTAACCTATTACTTTAAAG
* * ** * * * * *
67350 TAATTGGTTTTGAACTTAAAAGTATTGATACTCTATATATGTGTATCAATACATTTGGTGTGCAA
66 TAATAGGCTTCAAAATTAAAAGTATTGATACTCTACATATATATATCAATACATTTGGTGTACAA
*
67415 ATTCTTTGATAAGCATACTGGAATAAAAGTATCCATACCTATTTAAAAAGTATTGATACTTTTAT
131 ATTCTTTGAGAAGCATACTGGAATAAAAGTATCCATACCTATTTAAAAAGTATTGATACTTTTAT
67480 ATAG
196 ATAG
* * * *
67484 GCCTATTGTCATTATACCGGTAGACTTTTATCGTTTACATTATTAATTAACCTATTACTTTAAAG
1 GCCTATTATCATTAAACCGGTAGACATTTATCGTTTACATGATTAATTAACCTATTACTTTAAAG
** * * * *
67549 TAATAGGCTTCAAAATTCCAAGTATTGATACTTTCCATATATATATCCATACATTTTGTGTACAA
66 TAATAGGCTTCAAAATTAAAAGTATTGATACTCTACATATATATATCAATACATTTGGTGTACAA
* *
67614 ATTGTTTGGGAAGCATACTGGAATAAAAGTATC
131 ATTCTTTGAGAAGCATACTGGAATAAAAGTATC
67647 GGTACGGGCA
Statistics
Matches: 137, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
199 137 1.00
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (199 bp):
GCCTATTATCATTAAACCGGTAGACATTTATCGTTTACATGATTAATTAACCTATTACTTTAAAG
TAATAGGCTTCAAAATTAAAAGTATTGATACTCTACATATATATATCAATACATTTGGTGTACAA
ATTCTTTGAGAAGCATACTGGAATAAAAGTATCCATACCTATTTAAAAAGTATTGATACTTTTAT
ATAG
Found at i:67790 original size:61 final size:60
Alignment explanation
Indices: 67695--67816 Score: 201
Period size: 61 Copynumber: 2.0 Consensus size: 60
67685 GTCTGTTTTA
* *
67695 TTTTACCGTTTATATTATTAGTAACCTTTAAACAAATTGGTAGGT-ATTTTAACGTAATAGG
1 TTTTACCGTTTACATTATTAGTAACCTTTAAACAAATCGGTAGGTGA--TTAACGTAATAGG
67756 TTTTACCGTTTACATTATTAGTAACCTTTAAACAAATCGGTAGGTGATTAACGTAATAGG
1 TTTTACCGTTTACATTATTAGTAACCTTTAAACAAATCGGTAGGTGATTAACGTAATAGG
67816 T
1 T
67817 AACACCTATT
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
60 14 0.24
61 43 0.74
62 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (60 bp):
TTTTACCGTTTACATTATTAGTAACCTTTAAACAAATCGGTAGGTGATTAACGTAATAGG
Found at i:68074 original size:6 final size:6
Alignment explanation
Indices: 68063--68088 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
68053 AGTGGAGCTC
68063 AAATTG AAATTG AAATTG AAATTG AA
1 AAATTG AAATTG AAATTG AAATTG AA
68089 CATGTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (6 bp):
AAATTG
Found at i:70065 original size:57 final size:57
Alignment explanation
Indices: 70003--70111 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 57
69993 CCATTATATG
* * **
70003 AGTATATGTTTTATGTGA-ATAAATAATAATTTGAATAATTTTATGTGAAATACTATA
1 AGTATATGTTATATGTGAGA-AAATAATAAATTGAATAATGCTATGTGAAATACTATA
* *
70060 AGTATATGTTATATGTGAGAAAATGATAAATTGCATAATGCTATGTGAAATA
1 AGTATATGTTATATGTGAGAAAATAATAAATTGAATAATGCTATGTGAAATA
70112 TTCAGTAGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 44 0.98
58 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (57 bp):
AGTATATGTTATATGTGAGAAAATAATAAATTGAATAATGCTATGTGAAATACTATA
Found at i:71788 original size:47 final size:45
Alignment explanation
Indices: 71718--71842 Score: 175
Period size: 47 Copynumber: 2.8 Consensus size: 45
71708 TATAAAATCT
*
71718 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAA-ACTA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATA-TA
*
71763 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
71810 CTTGCCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
71843 GCATACTTAC
Statistics
Matches: 74, Mismatches: 3, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
43 21 0.28
44 3 0.04
45 10 0.14
46 2 0.03
47 37 0.50
48 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:71850 original size:38 final size:41
Alignment explanation
Indices: 71718--71856 Score: 131
Period size: 47 Copynumber: 3.2 Consensus size: 41
71708 TATAAAATCT
* *
71718 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAACTA
1 CTTACCA-TTAT-TCATAAGCTCGTAAGCTTATTTTAGC-AA-TA
*
71763 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCA-TT--ATT-CATAAGCTCGTAAGCTTATTTTAGC-A-ATA
*
71810 CTTGCCATTATTCATAAGCTCGTAAGCTTA-TTT-GC-ATA
1 CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAATA
71848 CTTACCATT
1 CTTACCATT
71857 TATTAACCAT
Statistics
Matches: 85, Mismatches: 5, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
38 11 0.13
41 1 0.01
42 3 0.04
43 18 0.21
44 3 0.04
45 10 0.12
46 2 0.02
47 36 0.42
48 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (41 bp):
CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAATA
Found at i:75799 original size:6 final size:6
Alignment explanation
Indices: 75781--75837 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
75771 TCTCTTTCTC
*
75781 TTTTC- TTTCTCA TTTTCA TTTT-- TTTTC- TTCTTCA TTTTCA TTTTCT
1 TTTTCA TTT-TCA TTTTCA TTTTCA TTTTCA TT-TTCA TTTTCA TTTTCA
75827 TTTTCTA TTTT
1 TTTTC-A TTTT
75838 TTTTTTCTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 4 0.09
5 5 0.11
6 26 0.59
7 9 0.20
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTCA
Found at i:75805 original size:34 final size:35
Alignment explanation
Indices: 75764--75847 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 35
75754 TTCATCTCTA
75764 ATTTTTTTCTCTT-TCTC-TTTTC-TTTCTCATTTTC-
1 ATTTTTTT-TCTTCT-TCATTTTCATTT-TCATTTTCT
*
75798 ATTTTTTTTCTTCTTCATTTTCATTTTCTTTTTCT
1 ATTTTTTTTCTTCTTCATTTTCATTTTCATTTTCT
75833 ATTTTTTTT-TTCTTC
1 ATTTTTTTTCTTCTTC
75848 TTCTATTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
33 6 0.13
34 27 0.60
35 12 0.27
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (35 bp):
ATTTTTTTTCTTCTTCATTTTCATTTTCATTTTCT
Found at i:75807 original size:35 final size:35
Alignment explanation
Indices: 75752--75846 Score: 90
Period size: 35 Copynumber: 2.7 Consensus size: 35
75742 GAAATATTTT
* * *
75752 TTTTCA-TCTCTAATTTTTTTCTCTTTCTCTTTTC-
1 TTTTCATTTTCTATTTTTTTTCTCTTTC-ATTTTCA
75786 TTTCTCATTTTC-ATTTTTTTTCT-TCTTCATTTTCA
1 TTT-TCATTTTCTATTTTTTTTCTCT-TTCATTTTCA
* *
75821 TTTTCTTTTTCTATTTTTTTTTTCTT
1 TTTTCATTTTCTATTTTTTTTCTCTT
75847 CTTCTATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
34 16 0.32
35 30 0.60
36 4 0.08
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (35 bp):
TTTTCATTTTCTATTTTTTTTCTCTTTCATTTTCA
Found at i:75809 original size:22 final size:23
Alignment explanation
Indices: 75779--75829 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
75769 TTTCTCTTTC
75779 TCTTTTCTT-TCTCATTTTCATTT
1 TCTTTTCTTCT-TCATTTTCATTT
75802 T-TTTTCTTCTTCATTTTCATTT
1 TCTTTTCTTCTTCATTTTCATTT
75824 TCTTTT
1 TCTTTT
75830 TCTATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.73
Consensus pattern (23 bp):
TCTTTTCTTCTTCATTTTCATTT
Found at i:75851 original size:19 final size:19
Alignment explanation
Indices: 75799--75861 Score: 92
Period size: 19 Copynumber: 3.4 Consensus size: 19
75789 CTCATTTTCA
75799 TTTTTTTTCTTCTTC-ATT
1 TTTTTTTTCTTCTTCTATT
** *
75817 TTCATTTTCTTTTTCTATT
1 TTTTTTTTCTTCTTCTATT
75836 TTTTTTTTCTTCTTCTATT
1 TTTTTTTTCTTCTTCTATT
75855 TTTTTTT
1 TTTTTTT
75862 ATTCTTATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
18 12 0.32
19 26 0.68
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTTTCTTCTTCTATT
Found at i:75861 original size:18 final size:18
Alignment explanation
Indices: 75799--75867 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
75789 CTCATTTTCA
75799 TTTTTTTTCTTCTTC-AT
1 TTTTTTTTCTTCTTCTAT
* *
75816 TTTCATTTTCTTTTTCTATT
1 TTT-TTTTTCTTCTTCTA-T
75836 TTTTTTTTCTTCTTCTAT
1 TTTTTTTTCTTCTTCTAT
*
75854 TTTTTTTTATTCTT
1 TTTTTTTTCTTCTT
75868 ATAATATATA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.07
18 24 0.55
19 13 0.30
20 4 0.09
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTTTCTTCTTCTAT
Found at i:77515 original size:17 final size:17
Alignment explanation
Indices: 77493--77577 Score: 97
Period size: 17 Copynumber: 5.1 Consensus size: 17
77483 CTGGAGAACA
77493 ATTTGATTCACATAATC
1 ATTTGATTCACATAATC
*
77510 ATTTGATTCAC--AAGC
1 ATTTGATTCACATAATC
*
77525 AAGGTTTGA-ACACATAATC
1 -A--TTTGATTCACATAATC
77544 ATTTGATTCACATAATC
1 ATTTGATTCACATAATC
77561 ATTTGATTCAC-TAATC
1 ATTTGATTCACATAATC
77577 A
1 A
77578 ACAATGATTC
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
15 3 0.05
16 12 0.21
17 34 0.59
18 6 0.10
19 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (17 bp):
ATTTGATTCACATAATC
Found at i:78871 original size:47 final size:45
Alignment explanation
Indices: 78801--78925 Score: 166
Period size: 47 Copynumber: 2.8 Consensus size: 45
78791 TATAAAATCC
*
78801 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAA-ACTA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATA-TA
*
78846 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
**
78893 CTTGTCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
78926 GCATACTTAC
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
43 21 0.29
44 3 0.04
45 10 0.14
46 2 0.03
47 36 0.49
48 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:85147 original size:57 final size:57
Alignment explanation
Indices: 85085--85194 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
85075 ACGCCCATTA
* *
85085 TATGAGTATATGTTTTATGTGA-ATAAATGATAATTTGAATAATGCTATGTGAAATAC
1 TATGAGTATATGTTTTATGTGAGA-AAATGATAAATTGAATAATCCTATGTGAAATAC
*
85142 TATGAGTATATGTTTTATGTGAGAAAATGATAAATTGCATAATCCTATGTGAA
1 TATGAGTATATGTTTTATGTGAGAAAATGATAAATTGAATAATCCTATGTGAA
85195 CTATTTATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
57 48 0.98
58 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (57 bp):
TATGAGTATATGTTTTATGTGAGAAAATGATAAATTGAATAATCCTATGTGAAATAC
Found at i:85335 original size:24 final size:24
Alignment explanation
Indices: 85308--85369 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
85298 GTGAACTTTG
85308 GTGCATATTCTACGTGGTACTTCA
1 GTGCATATTCTACGTGGTACTTCA
*
85332 GTGCATATTCTACGTGGTACTTCG
1 GTGCATATTCTACGTGGTACTTCA
*
85356 GTGCAAATTCTACG
1 GTGCATATTCTACG
85370 CGATAGTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (24 bp):
GTGCATATTCTACGTGGTACTTCA
Found at i:88349 original size:31 final size:32
Alignment explanation
Indices: 88314--88383 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
88304 ATAAATTACT
*
88314 AATTTGACCTCT-AAACTTTAGATAAAATATC
1 AATTTGACCTCTGAAACTTTAAATAAAATATC
* *
88345 AATTTGA-TTTTGAAACTTTAAATAAAATATC
1 AATTTGACCTCTGAAACTTTAAATAAAATATC
*
88376 AAATTGAC
1 AATTTGAC
88384 TCGTGAATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (32 bp):
AATTTGACCTCTGAAACTTTAAATAAAATATC
Found at i:93608 original size:10 final size:9
Alignment explanation
Indices: 93533--93633 Score: 55
Period size: 10 Copynumber: 10.6 Consensus size: 9
93523 TGAAAAGAAA
93533 AAAAACTAA-
1 AAAAA-TAAT
*
93542 AAAAATAGT
1 AAAAATAAT
93551 AACAAATAAT
1 AA-AAATAAT
*
93561 -AAAATAGT
1 AAAAATAAT
* *
93569 AAGAATAAC
1 AAAAATAAT
93578 AAGAAATGGAA-
1 AA-AAAT--AAT
*
93589 AATAATAAT
1 AAAAATAAT
93598 AAAAGATAAT
1 AAAA-ATAAT
93608 AAAATAATAAT
1 -AAA-AATAAT
93619 AACAAATAAT
1 AA-AAATAAT
93629 AAAAA
1 AAAAA
93634 GGTATAATTA
Statistics
Matches: 72, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
8 10 0.14
9 21 0.29
10 27 0.38
11 11 0.15
12 3 0.04
ACGTcount: A:0.70, C:0.04, G:0.07, T:0.19
Consensus pattern (9 bp):
AAAAATAAT
Found at i:93612 original size:21 final size:21
Alignment explanation
Indices: 93539--93632 Score: 84
Period size: 21 Copynumber: 4.2 Consensus size: 21
93529 GAAAAAAAAC
* *
93539 TAAAAAAATAGTAACAAATAA
1 TAAAATAATAATAACAAATAA
*
93560 TAAAATAGTAAGAATAACAAGA-AA
1 T-AAA-A-TAATAATAACAA-ATAA
93584 TGGAAAATAATAATAA-AAGATAA
1 T--AAAATAATAATAACAA-ATAA
93607 TAAAATAATAATAACAAATAA
1 TAAAATAATAATAACAAATAA
93628 TAAAA
1 TAAAA
93633 AGGTATAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
21 23 0.38
22 9 0.15
23 12 0.20
24 13 0.21
25 4 0.07
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.20
Consensus pattern (21 bp):
TAAAATAATAATAACAAATAA
Found at i:95351 original size:34 final size:35
Alignment explanation
Indices: 95279--95379 Score: 125
Period size: 34 Copynumber: 2.9 Consensus size: 35
95269 GAACTCGGAG
*
95279 GTGTTTCAAGAGAAACAATCTCGAAGGTTTTTTTTT
1 GTGTTTCAAGAGAAACAATCTCAAAGG-TTTTTTTT
* * *
95315 GTGTTTCAAGGGAAATAATTTCAAAGG-TTTTTTT
1 GTGTTTCAAGAGAAACAATCTCAAAGGTTTTTTTT
*
95349 GTGTTTCAAGAGAAACAGAT-TCAAAGATTTT
1 GTGTTTCAAGAGAAACA-ATCTCAAAGGTTTT
95380 GTTTCAAGGG
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
34 28 0.50
35 5 0.09
36 23 0.41
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (35 bp):
GTGTTTCAAGAGAAACAATCTCAAAGGTTTTTTTT
Found at i:95438 original size:36 final size:36
Alignment explanation
Indices: 95398--95492 Score: 127
Period size: 36 Copynumber: 2.6 Consensus size: 36
95388 GGAAACTAAC
*
95398 TCAAGAGAGACAGAACTTGTTTTAAGAGAAAATGAA
1 TCAAGAGAGACAAAACTTGTTTTAAGAGAAAATGAA
* * * **
95434 TCAAGAGAGACAAAATTTGTTTTAAGATAAACTGTC
1 TCAAGAGAGACAAAACTTGTTTTAAGAGAAAATGAA
95470 TCAAGAGAGACAAAACTTTGTTT
1 TCAAGAGAGACAAAAC-TTGTTT
95493 CAAGTTGGGT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 45 0.88
37 6 0.12
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (36 bp):
TCAAGAGAGACAAAACTTGTTTTAAGAGAAAATGAA
Found at i:96037 original size:99 final size:99
Alignment explanation
Indices: 95855--96091 Score: 323
Period size: 99 Copynumber: 2.3 Consensus size: 99
95845 ATTGCTCTGA
* *
95855 GTCCAATATCCTTCG-TCGTGAAGTTGAAATTGGTTCTGGAACTGGAAAATTGTTTGTTGACAGT
1 GTCCAATATCCTTCGAT-GTGAAGTTGAAATT-G-ACT----CT-GAAAATTGTTTGTTGACAAT
*
95919 CAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTTGG
58 CAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTATTGG
* * * *
95961 GTCCAATATTCTTTGCTGTGAAGTTGAAATTGACTCTGAAAGTTGTTTGTTGACAATCAGCCGCC
1 GTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAAATTGTTTGTTGACAATCAGCCGCC
*
96026 CCTTCGTCGTGAAGTTGAGCTTGTGTTGTATTGG
66 CCTTCGCCGTGAAGTTGAGCTTGTGTTGTATTGG
96060 GTCCAATATCCTTCGATGTGAAGTTGAAATTG
1 GTCCAATATCCTTCGATGTGAAGTTGAAATTG
96092 GTTATGAAAT
Statistics
Matches: 120, Mismatches: 10, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
99 87 0.73
100 2 0.02
104 2 0.02
105 1 0.01
106 27 0.22
107 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (99 bp):
GTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAAATTGTTTGTTGACAATCAGCCGCC
CCTTCGCCGTGAAGTTGAGCTTGTGTTGTATTGG
Found at i:97181 original size:25 final size:30
Alignment explanation
Indices: 97143--97216 Score: 86
Period size: 25 Copynumber: 2.6 Consensus size: 30
97133 TTTAAATATG
97143 TAATTATATAATATTTTTAA-TT-TTTTTA
1 TAATTATATAATATTTTTAATTTATTTTTA
**
97171 -AA-TATAT-ATATTCATAATTTATTTTTA
1 TAATTATATAATATTTTTAATTTATTTTTA
*
97198 TAATTATATGATATTTTTA
1 TAATTATATAATATTTTTA
97217 GAAAATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
25 8 0.22
26 7 0.19
27 8 0.22
28 2 0.05
29 5 0.14
30 7 0.19
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (30 bp):
TAATTATATAATATTTTTAATTTATTTTTA
Found at i:97188 original size:34 final size:35
Alignment explanation
Indices: 97128--97197 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 35
97118 AAATTATATG
* *
97128 ATTTTTTTAAATATGTAATTATATAA-TATTTTTA
1 ATTTTTTTAAATATATAATTACATAATTATTTTTA
97162 ATTTTTTTAAATATATATATT-CATAATTTATTTTTA
1 ATTTTTTTAAATATATA-ATTACATAA-TTATTTTTA
97198 TAATTATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 20 0.65
35 3 0.10
36 8 0.26
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (35 bp):
ATTTTTTTAAATATATAATTACATAATTATTTTTA
Found at i:97510 original size:20 final size:20
Alignment explanation
Indices: 97462--97523 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
97452 AACTTAAATC
*
97462 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
97482 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
97500 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
97519 AAAAT
1 AAAAT
97524 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:97624 original size:12 final size:12
Alignment explanation
Indices: 97570--97628 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
97560 TAATTTTTTT
* *
97570 TTAAAAATAATA
1 TTAAATATAAAA
97582 TTAAA-ATTAAAA
1 TTAAATA-TAAAA
* *
97594 TCAAATATAATA
1 TTAAATATAAAA
97606 -T-AATATAAAA
1 TTAAATATAAAA
97616 TTAAATATAAAA
1 TTAAATATAAAA
97628 T
1 T
97629 CTTTTTGAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
10 8 0.21
11 2 0.05
12 27 0.71
13 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
TTAAATATAAAA
Found at i:98148 original size:44 final size:44
Alignment explanation
Indices: 98015--98335 Score: 250
Period size: 43 Copynumber: 7.3 Consensus size: 44
98005 GGGTCTAAAC
* * * *
98015 TATAAAAGTAAAAAGT-GATATTG-AAGAATTA-GAGAACTCAAT
1 TATAAATGTAAAAAGTAGAGATTGAAAAAATTAGGAG-CCTCAAT
* * ** *
98057 TATAAATGTACAAAA-T-GAGATTGAAAAAATTGGGGGAATCGAT
1 TATAAATGTA-AAAAGTAGAGATTGAAAAAATTAGGAGCCTCAAT
*
98100 TATAAATATAAAAAGTAG-GATTGAAAAAATTAGGAGCCTCAAAT
1 TATAAATGTAAAAAGTAGAGATTGAAAAAATTAGGAGCCTC-AAT
* * * *
98144 TATAAATGT-AAAAGTTGAGATTGAAAAAAAAACTAGGGGCCTCGAT
1 TATAAATGTAAAAAGTAGAGATTG---AAAAAATTAGGAGCCTCAAT
* * ** *
98190 TATAAATGTACAAAA-T-GAGATTGAAAAAATTGGGGGAATCGAT
1 TATAAATGTA-AAAAGTAGAGATTGAAAAAATTAGGAGCCTCAAT
* * **
98233 TATAAATATAAAAAGTA-TGATTGAAAAAATTAGGAGTATCAAAT
1 TATAAATGTAAAAAGTAGAGATTGAAAAAATTAGGAGCCTC-AAT
*
98277 TATAAATGT-AAAAGTTGAGATTGAAAAAAATATTAGGAGCCTCAAT
1 TATAAATGTAAAAAGTAGAGATTG--AAAAA-ATTAGGAGCCTCAAT
98323 TATAAATGTAAAA
1 TATAAATGTAAAA
98336 GGCATGATTA
Statistics
Matches: 226, Mismatches: 33, Indels: 35
0.77 0.11 0.12
Matches are distributed among these distances:
42 24 0.11
43 101 0.45
44 33 0.15
46 35 0.15
47 29 0.13
48 4 0.02
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.26
Consensus pattern (44 bp):
TATAAATGTAAAAAGTAGAGATTGAAAAAATTAGGAGCCTCAAT
Found at i:98216 original size:90 final size:84
Alignment explanation
Indices: 98015--98358 Score: 275
Period size: 90 Copynumber: 3.9 Consensus size: 84
98005 GGGTCTAAAC
* * * * *
98015 TATAAAAGTAAAAAGTGATATTG-AAGAATTA-GAGAACTCAATTATAAATGTACAAAATGAGAT
1 TATAAATGTAAAAA-TGAGATTGAAAAAATTAGGAG-CCTCAATTATAAATGTA-AAAGTGAGAT
*
98078 TGAAAAAATTGGGGGAATCGAT
63 TGAAAAAATTAGGGGAATCGAT
*
98100 TATAAATATAAAAA-GTAGGATTGAAAAAATTAGGAGCCTCAAATTATAAATGTAAAAGTTGAGA
1 TATAAATGTAAAAATG-A-GATTGAAAAAATTAGGAGCCTC-AATTATAAATGTAAAAG-TGAGA
* **
98164 TTGAAAAAAAAACTAGGGGCCTCGAT
62 TTG---AAAAAATTAGGGGAATCGAT
* * ** * *
98190 TATAAATGTACAAAATGAGATTGAAAAAATTGGGGGAATCGATTATAAATATAAAAAGT-ATGAT
1 TATAAATGTA-AAAATGAGATTGAAAAAATTAGGAGCCTCAATTATAAATGT-AAAAGTGA-GAT
* * *
98254 TGAAAAAATTAGGAGTATCAAAT
63 TGAAAAAATTAGGGGAATC-GAT
*
98277 TATAAATGTAAAAGTTGAGATTGAAAAAAATATTAGGAGCCTCAATTATAAATGTAAAAG-GCAT
1 TATAAATGTAAAA-ATGAGATTG--AAAAA-ATTAGGAGCCTCAATTATAAATGTAAAAGTG-A-
*
98341 GATTAAAAAAATTTAGGG
60 GATTGAAAAAA-TTAGGG
98359 CCGTCAAATA
Statistics
Matches: 207, Mismatches: 31, Indels: 36
0.76 0.11 0.13
Matches are distributed among these distances:
83 1 0.00
84 1 0.00
85 16 0.08
86 29 0.14
87 44 0.21
88 1 0.00
89 26 0.13
90 78 0.38
91 10 0.05
92 1 0.00
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.26
Consensus pattern (84 bp):
TATAAATGTAAAAATGAGATTGAAAAAATTAGGAGCCTCAATTATAAATGTAAAAGTGAGATTGA
AAAAATTAGGGGAATCGAT
Found at i:98228 original size:133 final size:133
Alignment explanation
Indices: 98051--98332 Score: 501
Period size: 133 Copynumber: 2.1 Consensus size: 133
98041 AATTAGAGAA
98051 CTCAATTATAAATGTACAAAATGAGATTGAAAAAATTGGGGGAATCGATTATAAATATAAAAAGT
1 CTCAATTATAAATGTACAAAATGAGATTGAAAAAATTGGGGGAATCGATTATAAATATAAAAAGT
*
98116 AGGATTGAAAAAATTAGGAGCCTCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAACTAGG
66 AGGATTGAAAAAATTAGGAGCATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAACTAGG
*
98181 GGC
131 AGC
*
98184 CTCGATTATAAATGTACAAAATGAGATTGAAAAAATTGGGGGAATCGATTATAAATATAAAAAGT
1 CTCAATTATAAATGTACAAAATGAGATTGAAAAAATTGGGGGAATCGATTATAAATATAAAAAGT
* * * *
98249 ATGATTGAAAAAATTAGGAGTATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAATATTAGG
66 AGGATTGAAAAAATTAGGAGCATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAACTAGG
98314 AGC
131 AGC
98317 CTCAATTATAAATGTA
1 CTCAATTATAAATGTA
98333 AAAGGCATGA
Statistics
Matches: 141, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 141 1.00
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (133 bp):
CTCAATTATAAATGTACAAAATGAGATTGAAAAAATTGGGGGAATCGATTATAAATATAAAAAGT
AGGATTGAAAAAATTAGGAGCATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAACTAGG
AGC
Found at i:98350 original size:46 final size:42
Alignment explanation
Indices: 98051--98373 Score: 179
Period size: 43 Copynumber: 7.3 Consensus size: 42
98041 AATTAGAGAA
* * * * *
98051 CTCAATTATAAATGTACAAAATGAGATT-GAAAAAATTGGGGGA
1 CTCAATTATAAATGT--AAAAGGAGATTAAAAAAAATTAGGAGC
* * * * *
98094 ATCGATTATAAATATAAAAAGTAGGATT-GAAAAAATTAGGAGC
1 CTCAATTATAAATGT-AAAAGGA-GATTAAAAAAAATTAGGAGC
* *
98137 CTCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAACTAGGGGC
1 CTC-AATTATAAATGTAAAAG--GAGATT--AAAAAAAATTAGGAGC
* * * * * *
98184 CTCGATTATAAATGTACAAAATGAGATT-GAAAAAATTGGGGGA
1 CTCAATTATAAATGT--AAAAGGAGATTAAAAAAAATTAGGAGC
* * * * * *
98227 ATCGATTATAAATATAAAAAGTATGATT-GAAAAAATTAGGAGT
1 CTCAATTATAAATGT-AAAAGGA-GATTAAAAAAAATTAGGAGC
*
98270 ATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAATATTAGGAGC
1 CTC-AATTATAAATGTAAAAG--GAGATT-AAAAAAA-ATTAGGAGC
*
98317 CTCAATTATAAATGTAAAAGGCATGATTAAAAAAATTTAGG-GC
1 CTCAATTATAAATGTAAAAGG-A-GATTAAAAAAAATTAGGAGC
*
98360 CGTCAAATATAAAT
1 C-TCAATTATAAAT
98374 AAAAAAATAA
Statistics
Matches: 223, Mismatches: 38, Indels: 37
0.75 0.13 0.12
Matches are distributed among these distances:
42 10 0.04
43 86 0.39
44 45 0.20
45 10 0.04
46 43 0.19
47 25 0.11
48 4 0.02
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.27
Consensus pattern (42 bp):
CTCAATTATAAATGTAAAAGGAGATTAAAAAAAATTAGGAGC
Found at i:98371 original size:44 final size:45
Alignment explanation
Indices: 98123--98373 Score: 184
Period size: 43 Copynumber: 5.6 Consensus size: 45
98113 AGTAGGATTG
98123 AAAAA-ATTAGGAGCCTCAAATTATAAATGTAAAAGTTGAGATTGAA
1 AAAAATATTAGGAGCCTCAAA-TATAAATGTAAAAG-TGAGATTGAA
* * * * * *
98169 AAAAAAACTAGGGGCCTCGATTATAAATGTACAAAATGAGATTG--
1 AAAAATATTAGGAGCCTCAAATATAAATGTA-AAAGTGAGATTGAA
* * ** * * *
98213 AAAAA-ATTGGGGGAATCGATTATAAATATAAAAAGT-ATGATTG--
1 AAAAATATTAGGAGCCTCAAATATAAATGT-AAAAGTGA-GATTGAA
**
98256 AAAAA-ATTAGGAGTATCAAATTATAAATGTAAAAGTTGAGATTGAA
1 AAAAATATTAGGAGCCTCAAA-TATAAATGTAAAAG-TGAGATTGAA
*
98302 AAAAATATTAGGAGCCTCAATTATAAATGTAAAAG-GCATGATT-AA
1 AAAAATATTAGGAGCCTCAAATATAAATGTAAAAGTG-A-GATTGAA
98347 AAAAAT-TTAGG-GCCGTCAAATATAAAT
1 AAAAATATTAGGAGCC-TCAAATATAAAT
98374 AAAAAAATAA
Statistics
Matches: 171, Mismatches: 21, Indels: 28
0.78 0.10 0.13
Matches are distributed among these distances:
42 1 0.01
43 51 0.30
44 37 0.22
45 10 0.06
46 46 0.27
47 26 0.15
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (45 bp):
AAAAATATTAGGAGCCTCAAATATAAATGTAAAAGTGAGATTGAA
Found at i:98379 original size:133 final size:132
Alignment explanation
Indices: 98051--98380 Score: 410
Period size: 133 Copynumber: 2.5 Consensus size: 132
98041 AATTAGAGAA
* * * * * *
98051 CTCAATTATAAATGTACAAAATGAGATTGAAAAAATTGGGGGAATCGATTATAAATATAAAAAGT
1 CTCAATTATAAATGTA-AAAAGGAGATTAAAAAAATTAGGGCAATCAAATATAAATATAAAAAGT
*
98116 AGGATTGAAAAAATTAGGAGCCTCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAACTAGG
65 AGGATTGAAAAAATTAGGAGCATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAACTAGG
*
98181 GGC
130 AGC
* * * * * * *
98184 CTCGATTATAAATGTACAAAATGAGATTGAAAAAATTGGGGGAATCGATTATAAATATAAAAAGT
1 CTCAATTATAAATGTA-AAAAGGAGATTAAAAAAATTAGGGCAATCAAATATAAATATAAAAAGT
* * * *
98249 ATGATTGAAAAAATTAGGAGTATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAATATTAGG
65 AGGATTGAAAAAATTAGGAGCATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAACTAGG
98314 AGC
130 AGC
** *
98317 CTCAATTATAAATGT-AAAAGGCATGATTAAAAAAATTTAGGGCCGTCAAATATAAATAAAAAAA
1 CTCAATTATAAATGTAAAAAGG-A-GATTAAAAAAA-TTAGGGCAATCAAATATAAATATAAAAA
98381 TAAAAAAATA
Statistics
Matches: 177, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
131 5 0.03
132 1 0.01
133 150 0.85
134 21 0.12
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (132 bp):
CTCAATTATAAATGTAAAAAGGAGATTAAAAAAATTAGGGCAATCAAATATAAATATAAAAAGTA
GGATTGAAAAAATTAGGAGCATCAAATTATAAATGTAAAAGTTGAGATTGAAAAAAAAACTAGGA
GC
Found at i:101042 original size:14 final size:15
Alignment explanation
Indices: 101013--101045 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
101003 ATTCATAAAC
101013 CGTTCATATAACGTT
1 CGTTCATATAACGTT
*
101028 CGTTCATGT-ACGTT
1 CGTTCATATAACGTT
101042 CGTT
1 CGTT
101046 AAGCTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (15 bp):
CGTTCATATAACGTT
Found at i:101409 original size:22 final size:22
Alignment explanation
Indices: 101392--101438 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
101382 AAATTAAACT
101392 AACGCTAAATGAACATTAAAAG
1 AACGCTAAATGAACATTAAAAG
* *
101414 AACGCTTAATGAACATTAAATG
1 AACGCTAAATGAACATTAAAAG
101436 AAC
1 AAC
101439 ATGTTCACGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (22 bp):
AACGCTAAATGAACATTAAAAG
Found at i:101411 original size:11 final size:11
Alignment explanation
Indices: 101397--101440 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
101387 AAACTAACGC
101397 TAAATGAACAT
1 TAAATGAACAT
* *
101408 TAAAAGAACGCT
1 TAAATGAAC-AT
101420 T-AATGAACAT
1 TAAATGAACAT
101430 TAAATGAACAT
1 TAAATGAACAT
101441 GTTCACGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
10 2 0.07
11 23 0.85
12 2 0.07
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.25
Consensus pattern (11 bp):
TAAATGAACAT
Found at i:101570 original size:80 final size:79
Alignment explanation
Indices: 101424--101576 Score: 243
Period size: 80 Copynumber: 1.9 Consensus size: 79
101414 AACGCTTAAT
* * *
101424 GAACATTAAATGAACATGTTCACGAATAATAAATAATGAACATGAACACCTTCAAAAATAAATAA
1 GAACATTAAACGAACATGTTCACGAACAATAAATAACGAACATGAACACCTTCAAAAATAAATAA
101489 ATGAACACGTTTGC
66 ATGAACACGTTTGC
** *
101503 GAACATTAAACGAACATGTTCGTGAACAATAAATAAACGAACATGAATACCTTCAAAAATAAATA
1 GAACATTAAACGAACATGTTCACGAACAATAAAT-AACGAACATGAACACCTTCAAAAATAAATA
101568 AATGAACAC
65 AATGAACAC
101577 AAACATGATA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 30 0.45
80 37 0.55
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.22
Consensus pattern (79 bp):
GAACATTAAACGAACATGTTCACGAACAATAAATAACGAACATGAACACCTTCAAAAATAAATAA
ATGAACACGTTTGC
Found at i:102284 original size:76 final size:76
Alignment explanation
Indices: 102148--102292 Score: 218
Period size: 76 Copynumber: 1.9 Consensus size: 76
102138 AAGTAACTTC
* * * * *
102148 GGAATAAAAAGGTCCTCCGAAAGATATCTTCTATCGATCAGAGACTATGGAGTCCCATGTTTTAC
1 GGAATAAAAAGATCCTCCGAAAGATATCCTCTATCGATCAGAGACTATGAAATCCCATGTTCTAC
102213 TACAAGACTCT
66 TACAAGACTCT
* * *
102224 GGAATAAAAATATCCTCCGAAAGATATCCTCTATCGATCAGAGACTCTGAAATCCTATGTTCTAC
1 GGAATAAAAAGATCCTCCGAAAGATATCCTCTATCGATCAGAGACTATGAAATCCCATGTTCTAC
102289 TACA
66 TACA
102293 CATCATCTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 61 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (76 bp):
GGAATAAAAAGATCCTCCGAAAGATATCCTCTATCGATCAGAGACTATGAAATCCCATGTTCTAC
TACAAGACTCT
Found at i:102888 original size:26 final size:25
Alignment explanation
Indices: 102832--102889 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
102822 TAAAATGTTC
* * * *
102832 TATTAAAAGTTATTTTTTACAACAC
1 TATTAAAAATTATTTTTAAAAACAA
*
102857 TTTTAAAAATTATTTTTCAAAAACAA
1 TATTAAAAATTATTTTT-AAAAACAA
102883 TATTAAA
1 TATTAAA
102890 TTGACCCTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (25 bp):
TATTAAAAATTATTTTTAAAAACAA
Found at i:110824 original size:60 final size:60
Alignment explanation
Indices: 110751--110885 Score: 136
Period size: 59 Copynumber: 2.3 Consensus size: 60
110741 GATTAAGGAT
* * *
110751 AAAG-TACACAAATGATTC-CTTGATAATAA-AATATTATTTTATTGAGT-CATCCTATTATTA
1 AAAGTTACA-AAATGATTCTC-TAATAATAAGAA-ATTATTTTATTGAGTCCAT-CGACTATTA
* * * *
110811 AAAGTTACAAAATGA-TCTCTAATTATAAGGAGTTATTTTGTTGAGTCCATCGACTATTA
1 AAAGTTACAAAATGATTCTCTAATAATAAGAAATTATTTTATTGAGTCCATCGACTATTA
110870 AAAGTTACAAAATGAT
1 AAAGTTACAAAATGAT
110886 CATAATCTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
59 44 0.70
60 15 0.24
61 4 0.06
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (60 bp):
AAAGTTACAAAATGATTCTCTAATAATAAGAAATTATTTTATTGAGTCCATCGACTATTA
Found at i:111143 original size:31 final size:31
Alignment explanation
Indices: 111071--111157 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
111061 ATTTTATAAC
* *
111071 TTTTAATAATCGAATGACTCAACAAAAGAATA
1 TTTT-ATAATTGAAAGACTCAACAAAAGAATA
**
111103 TTTTATAATTGAAAGACTCAACAAATTAATA
1 TTTTATAATTGAAAGACTCAACAAAAGAATA
*
111134 TTTTATAATT-AAA-ACTCAATAAAA
1 TTTTATAATTGAAAGACTCAACAAAA
111158 CGATATCTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
29 9 0.18
30 3 0.06
31 33 0.67
32 4 0.08
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (31 bp):
TTTTATAATTGAAAGACTCAACAAAAGAATA
Found at i:114658 original size:19 final size:20
Alignment explanation
Indices: 114620--114658 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
114610 GTCCTTTAGC
*
114620 ATAAAATTTATGCGTGTGTA
1 ATAAAATTTATGCGTCTGTA
*
114640 ATAAAA-TTATGTGTCTGTA
1 ATAAAATTTATGCGTCTGTA
114659 TGTAGGAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATAAAATTTATGCGTCTGTA
Found at i:119446 original size:31 final size:31
Alignment explanation
Indices: 119410--119468 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
119400 AACTTAAAAG
*
119410 AGTTTTGCAATACTGAGA-TTTAAATAATTTT
1 AGTTTTACAATACTGA-ACTTTAAATAATTTT
*
119441 AGTTTTATAATACTGAACTTTAAATAAT
1 AGTTTTACAATACTGAACTTTAAATAAT
119469 CCATACAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAACTTTAAATAATTTT
Found at i:119518 original size:22 final size:22
Alignment explanation
Indices: 119492--119534 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
119482 TAATAAATTA
*
119492 TTTAAAATAACTCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
119514 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
119535 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:119543 original size:22 final size:22
Alignment explanation
Indices: 119494--119542 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
119484 ATAAATTATT
* **
119494 TAAAATAACTCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
119516 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
119539 TAAA
1 TAAA
119543 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:119552 original size:32 final size:31
Alignment explanation
Indices: 119514--119979 Score: 198
Period size: 32 Copynumber: 17.4 Consensus size: 31
119504 CAATCCATAT
119514 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
119546 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
119576 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
119594 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
119626 TTTAAAATAAAT-AA---AT-CT-AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
119648 TTTAAAATAAATCAATCCATATTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
119680 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
119702 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
119734 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
119756 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
119786 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
119804 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
119836 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
119866 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
119884 TTTAAAATAAATCAATCCATACTGATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
119916 TTTAAAATAAAT--A---AT-C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
119936 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
119968 TTTAAAATAAAT
1 TTTAAAATAAAT
119980 TATTTAAAAA
Statistics
Matches: 340, Mismatches: 6, Indels: 176
0.65 0.01 0.34
Matches are distributed among these distances:
20 15 0.04
21 1 0.00
22 87 0.26
23 10 0.03
24 11 0.03
25 5 0.01
26 57 0.17
27 6 0.02
28 13 0.04
30 7 0.02
31 11 0.03
32 117 0.34
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAAATA
Found at i:119623 original size:22 final size:23
Alignment explanation
Indices: 119548--119622 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
119538 ATAAATTATT
119548 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
119570 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
119596 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
119619 TAAA
1 TAAA
119623 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:119652 original size:22 final size:22
Alignment explanation
Indices: 119626--119670 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
119616 TAATAAATTA
*
119626 TTTAAAATAAATAAATCTATAT
1 TTTAAAATAAATAAATCCATAT
*
119648 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATAAATCCATAT
119670 T
1 T
119671 AATAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATAAATCCATAT
Found at i:119659 original size:54 final size:54
Alignment explanation
Indices: 119577--119856 Score: 457
Period size: 54 Copynumber: 5.3 Consensus size: 54
119567 CAACTACAAT
119577 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * *
119631 AATAAATAAATCTATATTTTAAAATAAATCAATCCATATTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
119685 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
119739 AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC-AACTACA--A--T--
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAA-TAAATTATTTAA
*
119787 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
119841 AATAAATCAATCCATA
1 AATAAATCAATCCATA
119857 CAACTACAAT
Statistics
Matches: 209, Mismatches: 9, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
48 41 0.20
49 2 0.01
50 2 0.01
52 2 0.01
53 2 0.01
54 160 0.77
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:119677 original size:22 final size:22
Alignment explanation
Indices: 119624--119676 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
119614 ACTAATAAAT
*
119624 TATT-TAAAATAAATAAATCTA
1 TATTATAAAATAAATAAATCCA
* *
119645 TATTTTAAAATAAATCAATCCA
1 TATTATAAAATAAATAAATCCA
119667 TATTAATAAA
1 TATT-ATAAA
119677 TTATTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 4 0.15
22 19 0.70
23 4 0.15
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (22 bp):
TATTATAAAATAAATAAATCCA
Found at i:119706 original size:22 final size:22
Alignment explanation
Indices: 119680--119722 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
119670 TAATAAATTA
119680 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
119702 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
119723 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:119715 original size:108 final size:102
Alignment explanation
Indices: 119546--119856 Score: 498
Period size: 102 Copynumber: 3.0 Consensus size: 102
119536 TAATAAATTA
*
119546 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCCATATTTTAAAATAAATCAATC
* *
119611 CATACTAATAAATTATTTAAAATAAATAAATCTATAT
66 CATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
119648 TTTAAAATAAATCAATCCATATTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
1 TTTAAAATAAATCAATCCATA-CAACTAAA--A--T--AATAAATCAATCCATATTTTAAAATAA
119712 ATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
59 ATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
119756 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCCATATTTTAAAATAAATCAATC
*
119821 TATACTAATAAATTATTTAAAATAAATCAATCCATA
66 CATACTAATAAATTATTTAAAATAAATCAATCCATA
119857 CAACTACAAT
Statistics
Matches: 194, Mismatches: 7, Indels: 16
0.89 0.03 0.07
Matches are distributed among these distances:
102 93 0.48
103 2 0.01
104 2 0.01
106 2 0.01
107 2 0.01
108 93 0.48
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (102 bp):
TTTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCCATATTTTAAAATAAATCAATC
CATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:119731 original size:22 final size:22
Alignment explanation
Indices: 119682--119730 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
119672 ATAAATTATT
**
119682 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
119704 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
119727 TAAA
1 TAAA
119731 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:119760 original size:22 final size:22
Alignment explanation
Indices: 119734--119820 Score: 111
Period size: 22 Copynumber: 3.8 Consensus size: 22
119724 TAATAAATTA
119734 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
119756 TTTAAAATAAATCAATCCATACAAC
1 TTTAAAATAAATCAATCCAT---AT
**
119781 TACAATAATAAATCAATCCATAT
1 TTTAA-AATAAATCAATCCATAT
119804 TTTAAAATAAATCAATC
1 TTTAAAATAAATCAATC
119821 TATACTAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
22 32 0.58
23 4 0.07
25 4 0.07
26 15 0.27
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:119842 original size:80 final size:80
Alignment explanation
Indices: 119631--119931 Score: 357
Period size: 80 Copynumber: 3.8 Consensus size: 80
119621 AATTATTTAA
* * *
119631 AATAAATAAATCTATATTTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* **
119696 CCAT---ATTTTAA-
66 CCATACAACTACAAT
** * ** * ** **
119707 AATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATCCA-TATTTTAAAATAAATC
1 AATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATACTAATAAATTA-TTTAAAATAAATC
119769 AATCCATACAACTACAAT
63 AATCCATACAACTACAAT
*
119787 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
119852 CCATACAACTACAAT
66 CCATACAACTACAAT
*
119867 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTGATAAATTATTTAAAATAAAT-AAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
119931 C
66 C
119932 ATATTTTAAA
Statistics
Matches: 187, Mismatches: 28, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
75 2 0.01
76 38 0.20
77 8 0.04
78 10 0.05
79 17 0.09
80 110 0.59
81 2 0.01
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:119913 original size:22 final size:22
Alignment explanation
Indices: 119838--119912 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
119828 ATAAATTATT
**
119838 TAAAATAAATCAATCCATACAA
1 TAAAATAAATCAATCCATATGA
**
119860 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATGA
119886 TAAAATAAATCAATCCATACTGA
1 TAAAATAAATCAATCCATA-TGA
119909 TAAA
1 TAAA
119913 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.53, C:0.17, G:0.01, T:0.28
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATGA
Found at i:119952 original size:52 final size:52
Alignment explanation
Indices: 119867--120029 Score: 194
Period size: 52 Copynumber: 3.1 Consensus size: 52
119857 CAACTACAAT
*
119867 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTGATAAATTATTTAA
1 AATAAAT-AAT-CATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
119921 AATAAATAATCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATAATCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
119973 AAT--A-AAT--TATTTAAAAATAAATCAATCCATTTTA-TAATAATTTATTTTAA
1 AATAAATAATCATATTTTAAAATAAATCAATCCA---TACTAATAAATTA-TTTAA
120023 AATAAAT
1 AATAAAT
120030 TATTTTATAA
Statistics
Matches: 97, Mismatches: 5, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
47 20 0.21
49 12 0.12
50 11 0.11
52 44 0.45
53 3 0.03
54 7 0.07
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.39
Consensus pattern (52 bp):
AATAAATAATCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:119969 original size:132 final size:128
Alignment explanation
Indices: 119739--119979 Score: 380
Period size: 132 Copynumber: 1.9 Consensus size: 128
119729 AATTATTTAA
119739 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATAT
119804 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
66 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
* *
119867 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTGA-TAAATTATTTAAAATAAAT-AA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAA
119930 T-CATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT
59 TCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT
119980 TATTTAAAAA
Statistics
Matches: 104, Mismatches: 2, Indels: 10
0.90 0.02 0.09
Matches are distributed among these distances:
128 42 0.40
129 1 0.01
130 1 0.01
132 50 0.48
133 3 0.03
134 7 0.07
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (128 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATAT
TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
Found at i:119991 original size:15 final size:15
Alignment explanation
Indices: 119959--120104 Score: 195
Period size: 15 Copynumber: 9.5 Consensus size: 15
119949 AATCTATACT
119959 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
*
119973 AATAAATTATTTAAA
1 AATAAATTATTTTAA
*
119988 AATAAATCAATCCATTTTAT
1 AATAAAT---T--ATTTTAA
*
120008 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
120023 AATAAATTATTTTAT
1 AATAAATTATTTTAA
120038 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
120053 AATAAATTATTTTAT
1 AATAAATTATTTTAA
120068 AATAAATTATTTTAA
1 AATAAATTATTTTAA
120083 AATAAATTATTTTAA
1 AATAAATTATTTTAA
120098 AATAAAT
1 AATAAAT
120105 AACCTTATTA
Statistics
Matches: 116, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
14 9 0.08
15 94 0.81
17 1 0.01
18 1 0.01
20 11 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:121962 original size:28 final size:27
Alignment explanation
Indices: 121923--121980 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 27
121913 TACTGAGGTT
*
121923 TAAGGAAAGTTCAAGGATTATTAAAAC
1 TAAGGAAAGTTCAAGGATGATTAAAAC
121950 TAAGTGAAAGTTCAAGGATGATTAAAAC
1 TAAG-GAAAGTTCAAGGATGATTAAAAC
121978 TAA
1 TAA
121981 ATGATTAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (27 bp):
TAAGGAAAGTTCAAGGATGATTAAAAC
Found at i:123031 original size:49 final size:49
Alignment explanation
Indices: 122959--123133 Score: 278
Period size: 49 Copynumber: 3.6 Consensus size: 49
122949 GGTTATCGAG
*
122959 GGTGCATTTCAGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAT
1 GGTGCATTTCAGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAC
*
123008 GGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAC
1 GGTGCATTTCAGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAC
* * *
123057 GGTGCATTTAAGTATAAAAGGTGCCACTAACGAAAGTTAAATGCATAAC
1 GGTGCATTTCAGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAC
* * *
123106 GGTACATTTCGGCTTAAAAGGTGCCACT
1 GGTGCATTTCAGCATAAAAGGTGCCACT
123134 CATGGTATCC
Statistics
Matches: 115, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 115 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (49 bp):
GGTGCATTTCAGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAC
Found at i:124054 original size:37 final size:37
Alignment explanation
Indices: 123997--124101 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
123987 CCTTTTCGTC
*
123997 CTACTAGGATTCAAATTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
124034 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
124071 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
124102 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:124979 original size:4 final size:4
Alignment explanation
Indices: 124964--125049 Score: 52
Period size: 4 Copynumber: 21.2 Consensus size: 4
124954 TATTTTTTAA
*
124964 TATT TCATT TATT TATT TATT TATT T-TT CCT-TT TATT TTTT TACTT
1 TATT T-ATT TATT TATT TATT TATT TATT --TATT TATT TATT TA-TT
* * * * * *
125010 TTTT TA-T TCTT CATT TATT CATT TATT CATT TATT CATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT T
125050 TTTCCCTCTA
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
3 5 0.08
4 47 0.76
5 10 0.16
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:126119 original size:15 final size:15
Alignment explanation
Indices: 126099--126127 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
126089 ACCTCACAAA
126099 ATTTTTTATTTTGTC
1 ATTTTTTATTTTGTC
126114 ATTTTTTATTTTGT
1 ATTTTTTATTTTGT
126128 TTTTATCATT
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:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (15 bp):
ATTTTTTATTTTGTC
Found at i:129474 original size:9 final size:8
Alignment explanation
Indices: 129449--129517 Score: 51
Period size: 7 Copynumber: 9.1 Consensus size: 8
129439 AGATCCAATC
129449 AAGAA-AA
1 AAGAAGAA
*
129456 AAAAAGAA
1 AAGAAGAA
129464 AAGAAGCAA
1 AAGAAG-AA
129473 AAGAAG-A
1 AAGAAGAA
129480 AA-AA-AA
1 AAGAAGAA
129486 AAGAA-AA
1 AAGAAGAA
129493 AAG-AGAA
1 AAGAAGAA
*
129500 ACAAAAGAA
1 A-AGAAGAA
*
129509 AAAAAGAA
1 AAGAAGAA
129517 A
1 A
129518 GAACAAAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
6 6 0.12
7 17 0.33
8 16 0.31
9 13 0.25
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (8 bp):
AAGAAGAA
Found at i:129480 original size:27 final size:27
Alignment explanation
Indices: 129448--129525 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 27
129438 AAGATCCAAT
129448 CAAGAAAAAAAAAGAAAAGAAGCAAAA
1 CAAGAAAAAAAAAGAAAAGAAGCAAAA
*
129475 GAAGAAAAAAAAAGAAAA-AAG-AGAAA
1 CAAGAAAAAAAAAGAAAAGAAGCA-AAA
129501 CAA-AAGAAAAAAAG-AAAGAA-CAAAA
1 CAAGAA-AAAAAAAGAAAAGAAGCAAAA
129526 ATCAAAAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
25 9 0.20
26 19 0.42
27 17 0.38
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.00
Consensus pattern (27 bp):
CAAGAAAAAAAAAGAAAAGAAGCAAAA
Found at i:129482 original size:26 final size:27
Alignment explanation
Indices: 129453--129539 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
129443 CCAATCAAGA
* *
129453 AAAAAAAAGAAAAGAAGCAAAAGAAGA
1 AAAAAAAAGAAAAGAAGCAAAACAAAA
129480 AAAAAAAAGAAAA-AAG-AGAAACAAAA
1 AAAAAAAAGAAAAGAAGCA-AAACAAAA
*
129506 GAAAAAAAG-AAAGAA-CAAAAATCAAAA
1 AAAAAAAAGAAAAGAAGC-AAAA-CAAAA
*
129533 AGAAAAA
1 AAAAAAA
129540 GGGACAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
25 4 0.08
26 22 0.44
27 24 0.48
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.01
Consensus pattern (27 bp):
AAAAAAAAGAAAAGAAGCAAAACAAAA
Found at i:129484 original size:19 final size:16
Alignment explanation
Indices: 129449--129517 Score: 57
Period size: 19 Copynumber: 3.8 Consensus size: 16
129439 AGATCCAATC
*
129449 AAGAAAAAAAAAGAAAA
1 AAGAAAAAAGAA-AAAA
129466 GAAGCAAAAGAAGAAAAAAA
1 -AAG-AAAA-AAG-AAAAAA
129486 AAGAAAAAAGAGAAACAA
1 AAGAAAAAAGA-AAA-AA
129504 AAGAAAAAAAGAAA
1 AAG-AAAAAAGAAA
129518 GAACAAAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
16 1 0.02
17 6 0.14
18 14 0.32
19 15 0.34
20 6 0.14
21 2 0.05
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAGAAAAAA
Found at i:129505 original size:31 final size:30
Alignment explanation
Indices: 129449--129526 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
129439 AGATCCAATC
*
129449 AAGAAAAAAAAAG---AAAAGAAGCAAAAG
1 AAGAAAAAAAAAGAAAAAAAGAAACAAAAG
129476 AAGAAAAAAAAAGAAAAAAGAGAAACAAAAG
1 AAGAAAAAAAAAGAAAAAA-AGAAACAAAAG
*
129507 AA-AAAAAGAAAGAACAAAAA
1 AAGAAAAAAAAAGAA-AAAAA
129527 TCAAAAAGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 13 0.30
30 15 0.34
31 16 0.36
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (30 bp):
AAGAAAAAAAAAGAAAAAAAGAAACAAAAG
Found at i:129517 original size:17 final size:16
Alignment explanation
Indices: 129454--129517 Score: 65
Period size: 18 Copynumber: 3.7 Consensus size: 16
129444 CAATCAAGAA
*
129454 AAAAAAAGAAAAGAAG
1 AAAAAAAGAAAAAAAG
*
129470 CAAAAGAAGAAAAAAAAAG
1 -AAAA-AA-AGAAAAAAAG
129489 AAAAAAGAGAAACAAAAG
1 AAAAAA-AGAAA-AAAAG
129507 AAAAAAAGAAA
1 AAAAAAAGAAA
129518 GAACAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 16 0.39
18 17 0.41
19 8 0.20
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAAAAG
Found at i:129533 original size:40 final size:39
Alignment explanation
Indices: 129445--129539 Score: 93
Period size: 40 Copynumber: 2.4 Consensus size: 39
129435 GCGAAGATCC
* *
129445 AATCAAGAAAAAAAAAGAAAAGAAGCAAAAGAAGAAAAAA
1 AATCAA-AAAAAAAAACAAAAGAAGAAAAAGAAGAAAAAA
** * *
129485 AAAGAAAAAAGAGAAACAAAAGAA-AAAAAGAAAGAACAAA
1 AATCAAAAAA-AAAAACAAAAGAAGAAAAAG-AAGAAAAAA
*
129525 AATCAAAAAGAAAAA
1 AATCAAAAAAAAAAA
129540 GGGACAAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
39 13 0.30
40 30 0.70
ACGTcount: A:0.79, C:0.05, G:0.14, T:0.02
Consensus pattern (39 bp):
AATCAAAAAAAAAAACAAAAGAAGAAAAAGAAGAAAAAA
Found at i:129540 original size:26 final size:25
Alignment explanation
Indices: 129452--129540 Score: 81
Period size: 26 Copynumber: 3.4 Consensus size: 25
129442 TCCAATCAAG
*
129452 AAAAAAAAAGAAAAGAAGCAAAAGA-AG
1 AAAAAAAAAG-AAAGAA-CAAAA-ACAA
* * *
129479 AAAAAAAAAGAAAAAAGAGAAACAA
1 AAAAAAAAAGAAAGAACAAAAACAA
129504 AAGAAAAAAAGAAAGAACAAAAATCAA
1 AA-AAAAAAAGAAAGAACAAAAA-CAA
*
129531 AAAGAAAAAG
1 AAAAAAAAAG
129541 GGACAAAAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
24 1 0.02
25 6 0.12
26 29 0.57
27 15 0.29
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.01
Consensus pattern (25 bp):
AAAAAAAAAGAAAGAACAAAAACAA
Found at i:130218 original size:22 final size:22
Alignment explanation
Indices: 130144--130220 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
130134 GCTACCCCAT
* *
130144 CAAACCGTTGAGCATCAAATAC
1 CAAACCTTTGAGCATCAAATGC
*
130166 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
130188 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
130210 CAAACCTTTGA
1 CAAACCTTTGA
130221 CCAAACATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:131226 original size:106 final size:106
Alignment explanation
Indices: 131026--132327 Score: 2001
Period size: 106 Copynumber: 12.3 Consensus size: 106
131016 ATATCGTGCC
* * * * * * * * *
131026 ACTCAAGACAACACAAGTTCAACTTCACAATGAAAGGACGGCTGGTTGTCAA-CAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
131090 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
131131 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
131196 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
131237 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
131302 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
131343 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGAGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
131408 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
131449 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
131514 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
131555 ACTCCAGACAACGCATGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * * *
131620 AGTTTCAGAGCCAATTTCAACTTCACATCGAAGAATTTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
131661 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
**
131726 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
131767 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTAGTCAACAAA-TACTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC-TTCC
*
131831 CTATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
131873 ACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
131938 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
131979 ACTCCAGACAACGCAAGTTCAACTTTACGATGAAGGGACCGCTGGTTGTCAACAAACACCTT--C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
132042 AATTTTAGAGCCAATTTCAACTTCACA-CGAAGGATA-TGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
132081 ACT-CAGACAACGCAAGTTCAAC-TCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
132144 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
132185 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAATTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * * * *
132250 AATTTCAGAGCTAATTTCAACTTCTCAGCGAAGTATCTTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
132291 AC-CCAAGGCAACACAAGCTCAACTTCACGACGAAGGG
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGG
132328 GCCACCCGCG
Statistics
Matches: 1103, Mismatches: 84, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
100 34 0.03
101 19 0.02
102 33 0.03
103 17 0.02
104 33 0.03
105 66 0.06
106 899 0.82
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:133025 original size:37 final size:37
Alignment explanation
Indices: 132923--133027 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
132913 CCTTTTCGTC
* *
132923 CTACTAGGACTCAAACTCCTAAAAATAAGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
132960 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
132997 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
133028 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:133892 original size:4 final size:4
Alignment explanation
Indices: 133879--133911 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
133869 TATATATTAA
133879 TATT TCATT TATT TATT TATT TATT TATT TATT
1 TATT T-ATT TATT TATT TATT TATT TATT TATT
133912 CTTTCCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:136316 original size:55 final size:55
Alignment explanation
Indices: 136230--136606 Score: 619
Period size: 55 Copynumber: 6.9 Consensus size: 55
136220 TTCACAAATG
* * * **
136230 CATTATGAATTCCATGGGGTTGCACACATAGTGTCAATACAAAAATTCATAAACT
1 CATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAACT
* * *
136285 CATTATGAATTTCGTGGGGTTGCACATATAGTGTCGATACGGAAATTCATAAACT
1 CATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAACT
* * ** *
136340 CATTATGAATTTTGTGGGGTTGCACATATAGTGCCAATACTAAAATTCATAAACA
1 CATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAACT
136395 CATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAACT
1 CATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAACT
*
136450 CATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACAGAAATTCATAAACT
1 CATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAACT
*
136505 CATTATGAATTTCGTGGGGTTGCATACATAGTGCCAATACGGAAATTCATAAACT
1 CATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAACT
136560 CATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATT
1 CATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATT
136607 GCAACATATA
Statistics
Matches: 301, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 301 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (55 bp):
CATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAACT
Found at i:139699 original size:21 final size:19
Alignment explanation
Indices: 139671--139716 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
139661 TCATTGAATC
139671 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
139691 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
139710 ACTTAGT
1 A-TTAGT
139717 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:149231 original size:36 final size:36
Alignment explanation
Indices: 149191--149293 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
149181 ACGGTGCTGG
* *
149191 ACATTAATACACAAATGTACCAAAGATGATATGATA
1 ACATTAATACACGAATGTACCAAAGCTGATATGATA
149227 ACATTAATACACGAATGTACCAAAGCTGATATGATA
1 ACATTAATACACGAATGTACCAAAGCTGATATGATA
*
149263 ACATTGATACACGAATGTACCAAAGCTGATA
1 ACATTAATACACGAATGTACCAAAGCTGATA
149294 ATGGATAAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.24
Consensus pattern (36 bp):
ACATTAATACACGAATGTACCAAAGCTGATATGATA
Found at i:151629 original size:21 final size:20
Alignment explanation
Indices: 151597--151635 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
151587 TTCTACGTGG
*
151597 TTCTTGGGACATATATGTAA
1 TTCTTGGAACATATATGTAA
151617 TTCTGTGGAACATATATGT
1 TTCT-TGGAACATATATGT
151636 GGTACTTCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (20 bp):
TTCTTGGAACATATATGTAA
Found at i:151712 original size:18 final size:18
Alignment explanation
Indices: 151689--151723 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
151679 GTTTTTAAGG
151689 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
151707 AGTGGTTCTTCGGGACA
1 AGTGGTCCTTCGGGACA
151724 AACATACAGT
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:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:154684 original size:29 final size:30
Alignment explanation
Indices: 154632--154692 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
154622 ATTTCGGGAC
** *
154632 CTAAACTTTTCAAAGTTTATATTTTAGCCA
1 CTAAACTTTTCAAAACTTACATTTTAGCCA
*
154662 CTAAAC-TTTCAAAACTTACATTTTAGTCA
1 CTAAACTTTTCAAAACTTACATTTTAGCCA
154691 CT
1 CT
154693 GGTCAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (30 bp):
CTAAACTTTTCAAAACTTACATTTTAGCCA
Found at i:154766 original size:2 final size:2
Alignment explanation
Indices: 154759--154794 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
154749 TTTCTATACG
154759 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
154795 GATGAAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:155029 original size:17 final size:17
Alignment explanation
Indices: 155007--155044 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
154997 GATATAATTG
155007 ATACTTTAGAAGAATCA
1 ATACTTTAGAAGAATCA
*
155024 ATACTTTAGAAGAATCG
1 ATACTTTAGAAGAATCA
155041 ATAC
1 ATAC
155045 ATGAAATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (17 bp):
ATACTTTAGAAGAATCA
Found at i:170220 original size:29 final size:30
Alignment explanation
Indices: 170164--170224 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
170154 CATTTTGAGT
**
170164 AACGAAATGAAACGTTAGGCACCTAACTGA
1 AACGAAATGAAACGTTAGGCAAATAACTGA
170194 AACGAAAT-AAACGTTAGG-AAATAAACTGA
1 AACGAAATGAAACGTTAGGCAAAT-AACTGA
170223 AA
1 AA
170225 AAAGGGCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 18 0.64
30 8 0.29
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.16
Consensus pattern (30 bp):
AACGAAATGAAACGTTAGGCAAATAACTGA
Found at i:172458 original size:57 final size:57
Alignment explanation
Indices: 172369--172476 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 57
172359 TATGACATTA
*
172369 TTTTATTGATTTCTTAGATTATTAAAAATTATAAAATAATTTCGT-GATTATAAGATG
1 TTTTATTGATTTCTTAAATTATTAAAAATTATAAAATAATTTC-TCGATTATAAGATG
* *
172426 TTTTATTGA-TTCTCTAAATTATTAAAAGTTATAAAATAGTTTCTCGATTAT
1 TTTTATTGATTTCT-TAAATTATTAAAAATTATAAAATAATTTCTCGATTAT
172477 TCATATGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
56 5 0.11
57 41 0.89
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (57 bp):
TTTTATTGATTTCTTAAATTATTAAAAATTATAAAATAATTTCTCGATTATAAGATG
Found at i:172711 original size:20 final size:20
Alignment explanation
Indices: 172674--172711 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
172664 TTAAAACATA
*
172674 TTAATAGTTAAGTGACTATT
1 TTAATAGTTAAGTAACTATT
172694 TTAATAGTTGAA-TAACTA
1 TTAATAGTT-AAGTAACTA
172712 AATAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (20 bp):
TTAATAGTTAAGTAACTATT
Found at i:179096 original size:23 final size:23
Alignment explanation
Indices: 179061--179120 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
179051 ATCAAGCAAA
* *
179061 ATAACATATTAGGTATCGTTTAT
1 ATAACATAATAGGTAGCGTTTAT
* *
179084 ATAATATAATAGGTAGCGTTTCT
1 ATAACATAATAGGTAGCGTTTAT
*
179107 ATAACAAAATAGGT
1 ATAACATAATAGGT
179121 TAATTACTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGTTTAT
Found at i:179219 original size:109 final size:110
Alignment explanation
Indices: 179061--179316 Score: 372
Period size: 109 Copynumber: 2.3 Consensus size: 110
179051 ATCAAGCAAA
* * * * ** *
179061 ATAACATATTAGGTATCGTTTATATAATATAATAGGTAGCGTTTCTATAACAAAATAGGTTAATT
1 ATAACGTAATAGGTAGCGTTTATATAATATAATAGGTAACACTTATATAACAAAATAGGTTAATT
179126 ACTAGAAACATTATTAAGCACAATAACATATTAGGTACCGCTTAT
66 ACTAGAAACATTATTAAGCACAATAACATATTAGGTACCGCTTAT
* *
179171 ATAATGTAATA-GTAGCGTTTATATAA-ACTAATAGGTAACACTTATATAATAAAATAGGTTAAT
1 ATAACGTAATAGGTAGCGTTTATATAATA-TAATAGGTAACACTTATATAACAAAATAGGTTAAT
* *
179234 TACTGGAAACATTATTAAGCACAATAACATATTAGGTAGCGCTTAT
65 TACTAGAAACATTATTAAGCACAATAACATATTAGGTACCGCTTAT
* *
179280 ATAACGTAATAGGTAGCGTTTATATATTAAAATAGGT
1 ATAACGTAATAGGTAGCGTTTATATAATATAATAGGT
179317 TAATTATTAA
Statistics
Matches: 129, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
108 1 0.01
109 98 0.76
110 29 0.22
111 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (110 bp):
ATAACGTAATAGGTAGCGTTTATATAATATAATAGGTAACACTTATATAACAAAATAGGTTAATT
ACTAGAAACATTATTAAGCACAATAACATATTAGGTACCGCTTAT
Found at i:179283 original size:23 final size:23
Alignment explanation
Indices: 179257--179305 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
179247 ATTAAGCACA
*
179257 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
179280 ATAACGTAATAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGCTTAT
179303 ATA
1 ATA
179306 TTAAAATAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:179920 original size:110 final size:111
Alignment explanation
Indices: 179727--180285 Score: 763
Period size: 111 Copynumber: 5.1 Consensus size: 111
179717 AAAATGTATT
* * * *
179727 GATACTTTACAATATAACAGGTAAAAATATGAC--AACTATTTTCATTATGACAAAAACAGT-AA
1 GATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAA
* *
179789 ATTTACCTGATATGTTGAAAGTATCGATCCTTTTATAAAAA-AATC
66 ATTTACCTGATATGTTGAAAGTATAGATCCTTTTATAAAAAGGATC
* * *
179834 GATACTTTACAATATAACAGGTAAAAATATGACAAAACCAATTTTATTATGACAAAAACGGTAAA
1 GATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAA
*
179899 ATTTACCTGATATGTTGAAAGTATCGATCCTTTTATAAAAAGGATC
66 ATTTACCTGATATGTTGAAAGTATAGATCCTTTTATAAAAAGGATC
* * * *
179945 GATACTTTACAATATAACAAGTATAAATATAACAAAACTAGTTTCATTATGACAAAACCGGTAAA
1 GATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAA
* * * *
180010 ATTTACCTAATATGTTGAAAGTATAGATCGTTTTATAGAAAGGATA
66 ATTTACCTGATATGTTGAAAGTATAGATCCTTTTATAAAAAGGATC
* * * *
180056 GATATTTTACAATATAACAAATAAAAATATGACAAAATCAGTTTCATTATGACAAAACCGGTAAA
1 GATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAA
* **
180121 ATTTACTTGATATGTTGAAAGTATAGAT-CTTTTATAAAAAGGAGA
66 ATTTACCTGATATGTTGAAAGTATAGATCCTTTTATAAAAAGGATC
* *
180166 GAGACTTTACAATATAACATGTAAAAATATGACAAAACCAGTTTCATTATGAC-AAAACTGGTAA
1 GATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAAC-GGTAA
* * * *
180230 AATTTTA-CTGATATGTTTAAAGTATAAATACTTTTTATAAAAATGATC
65 AA-TTTACCTGATATGTTGAAAGTATAGAT-CCTTTTATAAAAAGGATC
180278 GATACTTT
1 GATACTTT
180286 TTTTAAAGTT
Statistics
Matches: 402, Mismatches: 42, Indels: 11
0.88 0.09 0.02
Matches are distributed among these distances:
107 33 0.08
109 27 0.07
110 131 0.33
111 191 0.48
112 20 0.05
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (111 bp):
GATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAA
ATTTACCTGATATGTTGAAAGTATAGATCCTTTTATAAAAAGGATC
Found at i:180203 original size:221 final size:221
Alignment explanation
Indices: 179730--180272 Score: 754
Period size: 221 Copynumber: 2.5 Consensus size: 221
179720 ATGTATTGAT
* * * *
179730 ACTTTACAATATAACAGGTAAAAATATGAC--AACTATTTTCATTATGACAAAAACAGT-AAATT
1 ACTTTACAATATAACAAGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACCGGTAAAATT
* * **
179792 TACCTGATATGTTGAAAGTATCGATCCTTTTATAAAAAAATCGATACTTTACAATATAACAGGTA
66 TACCTGATATGTTGAAAGTATAGATCCTTTTATAAAAAAATAGATACTTTACAATATAACAAATA
*
179857 AAAATATGACAAAACCAATTTTATTATGACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTA
131 AAAATATGACAAAACCAATTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTA
* ** *
179922 TCGATCCTTTTATAAAAAGGATCGAT
196 TAGATCCTTTTATAAAAAGGAGAGAG
* *
179948 ACTTTACAATATAACAAGTATAAATATAACAAAACTAGTTTCATTATGACAAAACCGGTAAAATT
1 ACTTTACAATATAACAAGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACCGGTAAAATT
* * ** *
180013 TACCTAATATGTTGAAAGTATAGATCGTTTTATAGAAAGGATAGATATTTTACAATATAACAAAT
66 TACCTGATATGTTGAAAGTATAGATCCTTTTATA-AAAAAATAGATACTTTACAATATAACAAAT
* * * *
180078 AAAAATATGACAAAATCAGTTTCATTATGACAAAACCGGTAAAATTTACTTGATATGTTGAAAGT
130 AAAAATATGACAAAACCAATTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTGAAAGT
180143 ATAGAT-CTTTTATAAAAAGGAGAGAG
195 ATAGATCCTTTTATAAAAAGGAGAGAG
* * *
180169 ACTTTACAATATAACATGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACTGGTAAAATT
1 ACTTTACAATATAACAAGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACCGGTAAAA-T
* * *
180234 TTA-CTGATATGTTTAAAGTATAAATACTTTTTATAAAAA
65 TTACCTGATATGTTGAAAGTATAGAT-CCTTTTATAAAAA
180273 TGATCGATAC
Statistics
Matches: 285, Mismatches: 34, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
218 27 0.09
220 24 0.08
221 133 0.47
222 101 0.35
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (221 bp):
ACTTTACAATATAACAAGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACCGGTAAAATT
TACCTGATATGTTGAAAGTATAGATCCTTTTATAAAAAAATAGATACTTTACAATATAACAAATA
AAAATATGACAAAACCAATTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTA
TAGATCCTTTTATAAAAAGGAGAGAG
Found at i:181093 original size:111 final size:111
Alignment explanation
Indices: 180750--181639 Score: 1340
Period size: 111 Copynumber: 8.0 Consensus size: 111
180740 GTATCAATAT
* * * *
180750 TTTACAATATAACATGTAAAAATATGACAAAACCAGTTTCATTATGAAAAAAACAGTAAACA-TT
1 TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAA-ATTT
* * * *
180814 ATCTGATATGTTAAAAGTATCGATCC-TTTATAAAAAAGATCGATAC
65 ACCTGATATGTTGAAAGTATAGATCCTTTTATAAAAAAGATAGATAC
*
180860 TTTACAATATAACATGTAAAAATATGACAAAACCAGTTTCATTATGACAAAA-CGGTAAAATTTA
1 TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTA
* * *
180924 CCTGATATGTTGAAAGTATCGATCCTTTTATAAAAAGGATCGATAC
66 CCTGATATGTTGAAAGTATAGATCCTTTTATAAAAAAGATAGATAC
* * *
180970 TTTACAATATAACAGGTATAAATATGACAAAACCAGTTTTATTATGATAAAACCGGTAAAATTTA
1 TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTA
* *
181035 CCTGATATGTTGAAAATATATATCCTTTTATAAAAAAGATAGATAC
66 CCTGATATGTTGAAAGTATAGATCCTTTTATAAAAAAGATAGATAC
* *
181081 TTTACAAAATAACAGGTAAAAATATGACAAAACCA-TTTCATTATGACAAAAACGGTAAAATTTA
1 TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTA
* * * * *
181145 CCTAATATGTTGAAAGTATAAATCTTTTTTATTAAAAAGATAGATAT
66 CCTGATATGTTGAAAGTATAGATC-CTTTTATAAAAAAGATAGATAC
* *
181192 TTTACAATATAACAGATAAAAATATGACAAAATCAGTTTCATTATGACAAAACCGGTAAAATTTA
1 TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTA
*
181257 CCTAATATGTTGAAAGTATAGATCCTTTTATAAAAAAAGATAGATAC
66 CCTGATATGTTGAAAGTATAGATCCTTTTAT-AAAAAAGATAGATAC
*
181304 TTTACAATATAACAGGTAAAAATATGACAAAACC-GTTTCATTATGACAAAAACGGTAAAATTTA
1 TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTA
* * * *
181368 CCTGATATGTTGAAAATATTGACCCTTTTATAAAAATGATAGATAC
66 CCTGATATGTTGAAAGTATAGATCCTTTTATAAAAAAGATAGATAC
*
181414 TTTATAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTA
1 TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTA
*
181479 CCTGATATGTTGAAAGTATAGATCCTTTTATAAAAAGGATAGATAC
66 CCTGATATGTTGAAAGTATAGATCCTTTTATAAAAAAGATAGATAC
* * *
181525 TTTATAATATAACAGGTAAAAATATGATAAAATCAGTTTCATTATGACAAAACCGGTAAAATTTA
1 TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTA
* * * *
181590 CATGATATGTTGAAAGTATAGATACTTTTTATAAAAAGGATCGATAC
66 CCTGATATGTTGAAAGTATAGAT-CCTTTTATAAAAAAGATAGATAC
181637 TTT
1 TTT
181640 TTTTAAAGTT
Statistics
Matches: 720, Mismatches: 52, Indels: 14
0.92 0.07 0.02
Matches are distributed among these distances:
108 1 0.00
109 32 0.04
110 212 0.29
111 355 0.49
112 120 0.17
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (111 bp):
TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAATTTA
CCTGATATGTTGAAAGTATAGATCCTTTTATAAAAAAGATAGATAC
Found at i:181530 original size:20 final size:21
Alignment explanation
Indices: 181491--181531 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
181481 TGATATGTTG
* *
181491 AAAGTATAGATCCTTTTATAA
1 AAAGGATAGATACTTTTATAA
181512 AAAGGATAGATAC-TTTATAA
1 AAAGGATAGATACTTTTATAA
181532 TATAACAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (21 bp):
AAAGGATAGATACTTTTATAA
Done.