Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007898.1 Hibiscus syriacus cultivar Beakdansim tig00110287_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: 546391
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:14747 original size:24 final size:24
Alignment explanation
Indices: 14715--14776 Score: 124
Period size: 24 Copynumber: 2.6 Consensus size: 24
14705 ACAAGAATAT
14715 ATAAAGAAGTTATAACTAATGTAC
1 ATAAAGAAGTTATAACTAATGTAC
14739 ATAAAGAAGTTATAACTAATGTAC
1 ATAAAGAAGTTATAACTAATGTAC
14763 ATAAAGAAGTTATA
1 ATAAAGAAGTTATA
14777 TAAAAAATCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (24 bp):
ATAAAGAAGTTATAACTAATGTAC
Found at i:15192 original size:23 final size:22
Alignment explanation
Indices: 15133--15196 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
15123 ACTTGGACCC
*
15133 CTATAAATATATATAAAATTTA
1 CTATATATATATATAAAATTTA
* *
15155 CTA-ATGTTCTAATATAAAATTTA
1 CTATAT-ATAT-ATATAAAATTTA
15178 TCTATATATATATATAAAA
1 -CTATATATATATATAAAA
15197 GATGCAGTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
21 1 0.03
22 5 0.15
23 20 0.61
24 5 0.15
25 2 0.06
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
CTATATATATATATAAAATTTA
Found at i:16409 original size:25 final size:26
Alignment explanation
Indices: 16360--16409 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
16350 AATTTTTTCC
* *
16360 TAAATTTGATATTTTTTATAGAATTT
1 TAAATTTAATATTTTTAATAGAATTT
*
16386 TAAATTTAATA-TTTTAATATAATT
1 TAAATTTAATATTTTTAATAGAATT
16410 GATCATCAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (26 bp):
TAAATTTAATATTTTTAATAGAATTT
Found at i:17428 original size:24 final size:24
Alignment explanation
Indices: 17379--17425 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
17369 TGTTAAAATA
**
17379 AAAAAGAATATCAAACTTTTGTTT
1 AAAAAGAATATCAAACTTCAGTTT
17403 AAAAA-AATATCAAACTTCAGTTT
1 AAAAAGAATATCAAACTTCAGTTT
17426 TAATCTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (24 bp):
AAAAAGAATATCAAACTTCAGTTT
Found at i:20611 original size:23 final size:23
Alignment explanation
Indices: 20585--20633 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
20575 ATAACTTAAA
* * *
20585 AAATAATTTTAAAATTTAAGATG
1 AAATAATTTGAAAATTAAAAATG
20608 AAATAATTTGAAAATTAAAAATG
1 AAATAATTTGAAAATTAAAAATG
20631 AAA
1 AAA
20634 GTCTTAGTTT
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:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (23 bp):
AAATAATTTGAAAATTAAAAATG
Found at i:21470 original size:16 final size:16
Alignment explanation
Indices: 21447--21484 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
21437 ACCATATACT
21447 ATTAAAAAA-ATTAAA
1 ATTAAAAAATATTAAA
*
21462 ATCTAAAAAATATTTAA
1 AT-TAAAAAATATTAAA
21479 ATTAAA
1 ATTAAA
21485 GCATGAACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 11 0.55
17 7 0.35
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTAAAAAATATTAAA
Found at i:21912 original size:60 final size:59
Alignment explanation
Indices: 21842--21989 Score: 144
Period size: 59 Copynumber: 2.5 Consensus size: 59
21832 AAAAGTTTTG
* * *
21842 GGACCAATTTAGAATGAGGA-TCATAGTGTTG-GGATGAAATTGGAATGTTAAAAAATTGAA
1 GGACTAATTTAGAATGA-GATTCATAGT-TTGTGG-TGAAATTAGAATATTAAAAAATTGAA
* * * *
21902 GGACTAATTTAAAATGAGATTCATAGTTTGTGGTGAAATTAGAATATTCAAAATTTTAA
1 GGACTAATTTAGAATGAGATTCATAGTTTGTGGTGAAATTAGAATATTAAAAAATTGAA
*
21961 GGA-TCAATTT-GAATGA-AGTTGATAGTTTG
1 GGACT-AATTTAGAATGAGA-TTCATAGTTTG
21990 GGGACATATG
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
57 1 0.01
58 16 0.21
59 34 0.45
60 24 0.32
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.34
Consensus pattern (59 bp):
GGACTAATTTAGAATGAGATTCATAGTTTGTGGTGAAATTAGAATATTAAAAAATTGAA
Found at i:24232 original size:16 final size:17
Alignment explanation
Indices: 24200--24232 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
24190 CAAAAACGTC
24200 TTTTAAAAACAATTTTT
1 TTTTAAAAACAATTTTT
*
24217 TTTTAAAAATAATTTT
1 TTTTAAAAACAATTTT
24233 ATAAGACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAAAAACAATTTTT
Found at i:26953 original size:26 final size:25
Alignment explanation
Indices: 26865--26966 Score: 195
Period size: 25 Copynumber: 4.0 Consensus size: 25
26855 TGCAGTTGGG
26865 GATTTAGGGTTTGAAACCCTAAACT
1 GATTTAGGGTTTGAAACCCTAAACT
26890 GATTTAGGGTTTGAAACCCTAAACT
1 GATTTAGGGTTTGAAACCCTAAACT
26915 GATTTAGGGTTTGAAACCCTAAACT
1 GATTTAGGGTTTGAAACCCTAAACT
26940 GATTTTAGGGTTTGAAACCCTAAACT
1 GA-TTTAGGGTTTGAAACCCTAAACT
26966 G
1 G
26967 GTGGGTTGTT
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
25 52 0.68
26 24 0.32
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (25 bp):
GATTTAGGGTTTGAAACCCTAAACT
Found at i:27048 original size:3 final size:3
Alignment explanation
Indices: 27040--27100 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
27030 GCAAAAATTG
*
27040 TAA TAA TAAA TAA TAA TAA -AA TAA TAA T-A TAA TGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27084 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
27101 CGGAAAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 6 0.12
3 43 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:27463 original size:90 final size:89
Alignment explanation
Indices: 27348--27517 Score: 288
Period size: 90 Copynumber: 1.9 Consensus size: 89
27338 TTTTAGGAAG
* *
27348 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAAT-GTTGACACGGCTCTTAC
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAT-CT-ATGGTTGACACGGCTCATAC
27412 ATGATGAAGAGATCTGGCCATCTAAA
64 ATGATGAAGAGATCTGGCCATCTAAA
*
27438 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGT
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACAT
27503 GATGAAGAGATCTGG
66 GATGAAGAGATCTGG
27518 TCTGGGGATG
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
88 2 0.03
89 34 0.45
90 40 0.53
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (89 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACAT
GATGAAGAGATCTGGCCATCTAAA
Found at i:27481 original size:46 final size:46
Alignment explanation
Indices: 27348--27481 Score: 132
Period size: 46 Copynumber: 3.0 Consensus size: 46
27338 TTTTAGGAAG
*
27348 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCT-AA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAT-CTAAA
* * * * * * * **
27394 --TGTTGACACGGCTCTTACATGATGAAGA-GATCTGGCCATCTAAA
1 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAAA
27438 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
27482 TGGTTGACAC
Statistics
Matches: 64, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
43 3 0.05
44 29 0.45
46 31 0.48
47 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (46 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAA
Found at i:27502 original size:43 final size:44
Alignment explanation
Indices: 27365--27507 Score: 139
Period size: 46 Copynumber: 3.2 Consensus size: 44
27355 ACTCGGTTCC
*
27365 TACGTGATGAGGACGGCTGGTTATCCTAAT-GTTGACACGGCTCT
1 TACGTGATGAGGACGGCTGGTTAT-CTAATGGTTGACACGGCTCA
* * * ** * * * *
27409 TACATGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAGGACG-GCTGGTTATCTAATGGT--TGACACGGCTCA
27455 TACGTGATGAGGACGGCTGGTTATCT-ATGGTTGACACGGCTCA
1 TACGTGATGAGGACGGCTGGTTATCTAATGGTTGACACGGCTCA
27498 TACGTGATGA
1 TACGTGATGA
27508 AGAGATCTGG
Statistics
Matches: 76, Mismatches: 18, Indels: 11
0.72 0.17 0.10
Matches are distributed among these distances:
43 24 0.32
44 19 0.25
45 4 0.05
46 28 0.37
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (44 bp):
TACGTGATGAGGACGGCTGGTTATCTAATGGTTGACACGGCTCA
Found at i:27518 original size:43 final size:44
Alignment explanation
Indices: 27381--27518 Score: 129
Period size: 43 Copynumber: 3.1 Consensus size: 44
27371 ATGAGGACGG
* *
27381 CTGGTTATCCTAAT-GTTGACACGGCTCTTACATGATGAAGAGAT
1 CTGGTTAT-CTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
** * * * * * *
27425 CTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-G
1 CTGGTTATCTAATGGT--TGACACGGCTCATACGTGATGAAGA-GAT
27471 CTGGTTATCT-ATGGTTGACACGGCTCATACGTGATGAAGAGAT
1 CTGGTTATCTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
27514 CTGGT
1 CTGGT
27519 CTGGGGATGA
Statistics
Matches: 72, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
42 1 0.01
43 30 0.42
44 8 0.11
45 4 0.06
46 28 0.39
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (44 bp):
CTGGTTATCTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
Found at i:40784 original size:30 final size:31
Alignment explanation
Indices: 40706--40790 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 31
40696 AAACATACAT
* *
40706 GATTAAAATAATAAAAATAGCAA-TAAAAGG
1 GATTAAAATAGTAAAAATAGAAACTAAAAGG
* * * *
40736 GATCAAAAT-GGATGAAATAAAAACT-AAAGG
1 GATTAAAATAGTA-AAAATAGAAACTAAAAGG
40766 GATTAAAATAGTAAAAATAGAAACT
1 GATTAAAATAGTAAAAATAGAAACT
40791 TATGAGTCTA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
29 1 0.02
30 38 0.90
31 3 0.07
ACGTcount: A:0.60, C:0.05, G:0.15, T:0.20
Consensus pattern (31 bp):
GATTAAAATAGTAAAAATAGAAACTAAAAGG
Found at i:42301 original size:26 final size:25
Alignment explanation
Indices: 42213--42386 Score: 330
Period size: 25 Copynumber: 6.9 Consensus size: 25
42203 TGCAGTTGGG
42213 GATTTAGGGTTTGAAACCCTAAACT
1 GATTTAGGGTTTGAAACCCTAAACT
42238 GATTTAGGGTTTGAAACCCTAAACT
1 GATTTAGGGTTTGAAACCCTAAACT
42263 GATTTAGGGTTTGAAACCCTAAACT
1 GATTTAGGGTTTGAAACCCTAAACT
42288 GATTTTAGGGTTTGAAACCCTAAACT
1 GA-TTTAGGGTTTGAAACCCTAAACT
42314 GATTTTAGGGTTTGAAACCCTAAACT
1 GA-TTTAGGGTTTGAAACCCTAAACT
42340 GATTTAGGGTTTGAAACCCTAAACT
1 GATTTAGGGTTTGAAACCCTAAACT
42365 GATTTAGGGTTTGAAACCCTAA
1 GATTTAGGGTTTGAAACCCTAA
42387 TCTGGTGGGT
Statistics
Matches: 148, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
25 97 0.66
26 51 0.34
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (25 bp):
GATTTAGGGTTTGAAACCCTAAACT
Found at i:42472 original size:3 final size:3
Alignment explanation
Indices: 42464--42524 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
42454 GCAAAAATTG
*
42464 TAA TAA TAAA TAA TAA TAA -AA TAA TAA T-A TAA TGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42508 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
42525 CGGAAAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 6 0.12
3 43 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:50500 original size:23 final size:23
Alignment explanation
Indices: 50470--50538 Score: 138
Period size: 23 Copynumber: 3.0 Consensus size: 23
50460 TGCATCCGTA
50470 TCCTTGGCCTACACCTGATGGTG
1 TCCTTGGCCTACACCTGATGGTG
50493 TCCTTGGCCTACACCTGATGGTG
1 TCCTTGGCCTACACCTGATGGTG
50516 TCCTTGGCCTACACCTGATGGTG
1 TCCTTGGCCTACACCTGATGGTG
50539 GTCTTACATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.13, C:0.30, G:0.26, T:0.30
Consensus pattern (23 bp):
TCCTTGGCCTACACCTGATGGTG
Found at i:53480 original size:10 final size:11
Alignment explanation
Indices: 53461--53491 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
53451 TGAGTTTTGT
53461 TTATTTATTTA
1 TTATTTATTTA
53472 TTA-TTATTTA
1 TTATTTATTTA
53482 TTATTTATTT
1 TTATTTATTT
53492 TTGTTGCAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:53941 original size:12 final size:12
Alignment explanation
Indices: 53924--53978 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
53914 GACAAGCACA
53924 AGGTGGTAGAGG
1 AGGTGGTAGAGG
53936 AGGTGGTAGAGG
1 AGGTGGTAGAGG
* *
53948 AGGAGGCAGAGG
1 AGGTGGTAGAGG
*
53960 TGGTGGTAGAGG
1 AGGTGGTAGAGG
*
53972 TGGTGGT
1 AGGTGGT
53979 GGATTTCGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.22, C:0.02, G:0.58, T:0.18
Consensus pattern (12 bp):
AGGTGGTAGAGG
Found at i:57625 original size:29 final size:29
Alignment explanation
Indices: 57582--57647 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
57572 TGAATTCTAC
57582 AGCGACCTTGGAGGTCGCCATGGCATCCG
1 AGCGACCTTGGAGGTCGCCATGGCATCCG
*
57611 GGCGACCTTGGAGGTCGCCATGGCATCCG
1 AGCGACCTTGGAGGTCGCCATGGCATCCG
57640 AGCGACCT
1 AGCGACCT
57648 GTGTGGTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.17, C:0.32, G:0.35, T:0.17
Consensus pattern (29 bp):
AGCGACCTTGGAGGTCGCCATGGCATCCG
Found at i:57743 original size:20 final size:20
Alignment explanation
Indices: 57718--57755 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57708 GTATTGGAGC
*
57718 ATGCATGGGGGAGTTGTGGG
1 ATGCATGGGGGAGCTGTGGG
*
57738 ATGCATGTGGGAGCTGTG
1 ATGCATGGGGGAGCTGTG
57756 CATGGGACGT
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:0.16, C:0.08, G:0.50, T:0.26
Consensus pattern (20 bp):
ATGCATGGGGGAGCTGTGGG
Found at i:57767 original size:20 final size:20
Alignment explanation
Indices: 57744--57781 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57734 TGGGATGCAT
* *
57744 GTGGGAGCTGTGCATGGGAC
1 GTGGGAACTATGCATGGGAC
57764 GTGGGAACTATGCATGGG
1 GTGGGAACTATGCATGGG
57782 CCATGCACGT
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:0.18, C:0.13, G:0.47, T:0.21
Consensus pattern (20 bp):
GTGGGAACTATGCATGGGAC
Found at i:58335 original size:21 final size:21
Alignment explanation
Indices: 58310--58353 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
58300 AATCTAGTTA
58310 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
58331 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
58352 AT
1 AT
58354 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:58363 original size:28 final size:30
Alignment explanation
Indices: 58330--58392 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
58320 TAGTATAAAT
*
58330 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
58358 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
58388 TATTA
1 TATTA
58393 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:58902 original size:16 final size:16
Alignment explanation
Indices: 58881--58937 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
58871 TAATTTCCGT
58881 TTTAAAAAATATTGTG
1 TTTAAAAAATATTGTG
*
58897 TTTAAAAATATTTAATGTTG
1 TTTAAAAA-A--TATTG-TG
* *
58917 TTTTAAAAATATTTTG
1 TTTAAAAAATATTGTG
58933 TTTAA
1 TTTAA
58938 TTTACATTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
16 14 0.44
17 4 0.12
19 5 0.16
20 9 0.28
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (16 bp):
TTTAAAAAATATTGTG
Found at i:58941 original size:20 final size:20
Alignment explanation
Indices: 58892--58934 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
58882 TTAAAAAATA
58892 TTGTGTTTAAAAATATTTAATG
1 TTGT-TTTAAAAATATTT-ATG
58914 TTGTTTTAAAAATATTT-TG
1 TTGTTTTAAAAATATTTATG
58933 TT
1 TT
58935 TAATTTACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
21 13 0.62
22 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (20 bp):
TTGTTTTAAAAATATTTATG
Found at i:59231 original size:26 final size:25
Alignment explanation
Indices: 59202--59260 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
59192 AAATCATATT
*
59202 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
59228 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
59254 ATTATTA
1 ATTATTA
59261 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:62170 original size:26 final size:25
Alignment explanation
Indices: 62141--62631 Score: 301
Period size: 26 Copynumber: 19.7 Consensus size: 25
62131 ATTGATGATT
62141 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTT-ATAATAATCATTA
62167 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTT-ATAATAATCATTA
62193 TAGTAATGATTTAGTAATAATCATTA
1 TAGTAATGATTTA-TAATAATCATTA
** *
62219 TAAAAATGA-TT-TAATAATGATT-
1 TAGTAATGATTTATAATAATCATTA
* * *
62241 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTT-AT-A-ATAATCATTA
62265 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTT-ATAATAATCATTA
62291 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTT-ATAATAATCATTA
* *
62317 TAATAATGATTTAGTAATATTCATTA
1 TAGTAATGATTTA-TAATAATCATTA
** *
62343 TAAAAATGA-TT-TAATAATGATT-
1 TAGTAATGATTTATAATAATCATTA
* * *
62365 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTT-AT-A-ATAATCATTA
62389 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTT-ATAATAATCATTA
62415 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTT-ATAATAATCATTA
*
62441 TAATAATGATTTAGTAATAATCATTA
1 TAGTAATGATTTA-TAATAATCATTA
** * *
62467 TAAAAATGA--TCTAATAATGATT-
1 TAGTAATGATTTATAATAATCATTA
* * *
62489 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTT-AT-A-ATAATCATTA
62513 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTT-ATAATAATCATTA
* * * *
62539 TAATAATCA-TTATAATAATGATTT
1 TAGTAATGATTTATAATAATCATTA
* * * * *
62563 TA-TAATAATTATTTAGTTATTATT-
1 TAGTAATGATT-TATAATAATCATTA
* *
62587 TAGTAATTATTTATAATAATGATTTAA
1 TAGTAATGATTTATAATAATCA-TT-A
*
62614 TACTAATGATTTAATAAT
1 TAGTAATGATTT-ATAAT
62632 TATTACTAAT
Statistics
Matches: 381, Mismatches: 47, Indels: 72
0.76 0.09 0.14
Matches are distributed among these distances:
19 3 0.01
20 13 0.03
21 1 0.00
22 9 0.02
23 37 0.10
24 51 0.13
25 45 0.12
26 189 0.50
27 28 0.07
28 5 0.01
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.45
Consensus pattern (25 bp):
TAGTAATGATTTATAATAATCATTA
Found at i:62306 original size:124 final size:124
Alignment explanation
Indices: 62087--62579 Score: 884
Period size: 124 Copynumber: 4.0 Consensus size: 124
62077 ATGTATTTAT
62087 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGA-TTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
*
62151 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAGTAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
62210 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
62275 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
62334 TATTCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
62399 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
62458 TAATCATTATAAAAATGATCTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * *
62523 TTGATAATAATCATTATAATAATCA-TT-ATAATAATGATTTTATAATAATTATTTAGT
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCA--TTATAATAATGATTTAGT
62580 TATTATTTAG
Statistics
Matches: 359, Mismatches: 8, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
122 9 0.03
123 47 0.13
124 303 0.84
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:62609 original size:98 final size:99
Alignment explanation
Indices: 62291--62631 Score: 331
Period size: 98 Copynumber: 3.4 Consensus size: 99
62281 ATAATCATTA
* * *
62291 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-AGTAATATTCATTATAAAAATGATT-
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGA-TAATAATCATTATAATAATGATTA
* * * *
62354 TAATAATGATTTA-AATATTTAATGATTTGATGATT
65 TAATAATGATTTATAATAATTATTTAATT-ATGATT
62389 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGA-TTA
* * * * *
62454 GTAATAATCA-TTATAAAAATGATCTAATAATGATT
65 -TAATAATGATTTATAATAATTATTTAATTATGATT
* * * * *
62489 TA--AAT-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAATAATCATTATAATAATCATT
1 TAGTAATGATTTGAT-A-ATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATT
* *
62550 ATAATAATGATTTTATAATAATTATTTAGTTATTATT
64 ATAATAATGA-TTTATAATAATTATTTAATTATGATT
* * * *
62587 TAGTAATTATTT-ATAATAATGATTTAATACTAATGATTTAATAAT
1 TAGTAATGATTTGATAATAATCA-TT-ATAGTAATGATTTGATAAT
62632 TATTACTAAT
Statistics
Matches: 200, Mismatches: 28, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
96 8 0.04
97 9 0.05
98 120 0.60
99 12 0.06
100 16 0.08
101 35 0.17
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (99 bp):
TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTAT
AATAATGATTTATAATAATTATTTAATTATGATT
Found at i:62622 original size:14 final size:14
Alignment explanation
Indices: 62144--62631 Score: 143
Period size: 12 Copynumber: 36.1 Consensus size: 14
62134 GATGATTTAG
*
62144 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
62158 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
62170 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
62184 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
62196 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
62210 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
62222 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
62233 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
62249 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
62268 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
62282 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
62294 TAATGATTTGATAA
1 TAATGATTTAATAA
*
62308 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
62320 TAATGATTTAGTAA
1 TAATGATTTAATAA
* *
62334 TATTCA-TT-ATAA
1 TAATGATTTAATAA
*
62346 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
62357 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
62373 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
62392 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
62406 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
62418 TAATGATTTGATAA
1 TAATGATTTAATAA
*
62432 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
62444 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
62458 TAATCA-TT-ATAA
1 TAATGATTTAATAA
* *
62470 AAATGA--T-CTAA
1 TAATGATTTAATAA
*
62481 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
62497 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
62516 TAATGATTTGATAA
1 TAATGATTTAATAA
*
62530 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
62542 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
62554 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
62568 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
62580 T-ATTATTTAGTAA
1 TAATGATTTAATAA
62593 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
62603 TAATGATTTAATAC
1 TAATGATTTAATAA
62617 TAATGATTTAATAA
1 TAATGATTTAATAA
62631 T
1 T
62632 TATTACTAAT
Statistics
Matches: 362, Mismatches: 65, Indels: 94
0.69 0.12 0.18
Matches are distributed among these distances:
10 4 0.01
11 39 0.11
12 102 0.28
13 40 0.11
14 102 0.28
15 6 0.02
16 33 0.09
18 3 0.01
19 27 0.07
20 6 0.02
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.45
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:62626 original size:38 final size:37
Alignment explanation
Indices: 62223--62644 Score: 114
Period size: 38 Copynumber: 10.7 Consensus size: 37
62213 TCATTATAAA
* * * * *
62223 AATGATTTAATAATGATTTA-AATATTTA-ATGATTT
1 AATGATTTAATAATGATTTATAATAATCATTTAATAT
* *
62258 GATGATTTAGTAATGATTTGATAATAATCA-TT-ATAGT
1 AATGATTTAATAATGATTT-ATAATAATCATTTAATA-T
* * * *
62295 AATGATTTGATAATAATCATTATAATAATGATTTAGTAAT
1 AATGATTTAATAATGAT--TTATAATAATCATTTAAT-AT
* * *
62335 ATTCATTATAAAAATGATTTAATAATGATTTAAAT-ATTTAATGATTT
1 AATGATT-TAATAATGATTT-AT-A--A--T-AATCATTTAAT-A--T
* *
62382 GATGATTTAGTAATGATTTGATAATAATCA-TT-ATAGT
1 AATGATTTAATAATGATTT-ATAATAATCATTTAATA-T
* * * *
62419 AATGATTTGATAATAATCATTATAATAATGATTTAGTAAT
1 AATGATTTAATAATGAT--TTATAATAATCATTTAAT-AT
* * *
62459 AATCATTATAAAAATGATCTAATAATGATTTAAAT-ATTTAATGATTT
1 AATGATT-TAATAATGAT-T--T-AT-A-AT-AATCATTTAAT-A--T
* *
62506 GATGATTTAGTAATGATTTGATAATAATCA-TT-ATAAT
1 AATGATTTAATAATGATTT-ATAATAATCATTTAAT-AT
* * *
62543 AATCATTATAATAATGATTTTATAATAATTATTTAGT-T
1 AATGATT-TAATAATGA-TTTATAATAATCATTTAATAT
* * * *
62581 -ATTATTTAGTAATTATTTATAATAATGATTTAATACT
1 AATGATTTAATAATGATTTATAATAATCATTTAATA-T
*
62618 AATGATTTAATAATTA-TTACTAATAAT
1 AATGATTTAATAATGATTTA-TAATAAT
62645 TATAGAATAC
Statistics
Matches: 286, Mismatches: 59, Indels: 81
0.67 0.14 0.19
Matches are distributed among these distances:
35 34 0.12
36 10 0.03
37 50 0.17
38 57 0.20
39 20 0.07
40 29 0.10
41 21 0.07
42 2 0.01
43 7 0.02
44 1 0.00
45 18 0.06
46 26 0.09
47 11 0.04
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (37 bp):
AATGATTTAATAATGATTTATAATAATCATTTAATAT
Found at i:62654 original size:38 final size:38
Alignment explanation
Indices: 62584--62657 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
62574 TTTAGTTATT
* **
62584 ATTTAGTAATTATTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATGATAGAATACTAATG
*
62622 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATGATAGAATACTAA
62658 CAAATGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATGATAGAATACTAATG
Found at i:62864 original size:17 final size:17
Alignment explanation
Indices: 62839--62871 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
62829 ACTAAATATT
*
62839 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
62856 TAATGATTTGATACTA
1 TAATGATTTGATACTA
62872 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:62864 original size:25 final size:23
Alignment explanation
Indices: 62785--62864 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
62775 GATTTATTGT
62785 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
62806 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
62833 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
62855 GTAATGATTT
1 -TAAT-ATTT
62865 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:65053 original size:15 final size:14
Alignment explanation
Indices: 65030--65060 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
65020 TACAACATTA
65030 AACTTTAATATAAT
1 AACTTTAATATAAT
65044 AACTTATAATATAAT
1 AACTT-TAATATAAT
65059 AA
1 AA
65061 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:65068 original size:16 final size:16
Alignment explanation
Indices: 65035--65081 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
65025 CATTAAACTT
*
65035 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
65050 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
65066 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
65082 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:65202 original size:32 final size:34
Alignment explanation
Indices: 65122--65202 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 34
65112 CTAAACCCTT
*
65122 AAAC-AACTAATAAAATATTCTTTTATATAACTA
1 AAACTAACTAATAAACTATTCTTTTATATAACTA
65155 AAACTAACTAA-AAACTATT-TTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTCTTTT-A-TATAACTA
*
65187 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
65203 TACTAACTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
31 5 0.12
32 13 0.31
33 13 0.31
34 11 0.26
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTCTTTTATATAACTA
Found at i:65343 original size:47 final size:48
Alignment explanation
Indices: 65241--65345 Score: 124
Period size: 46 Copynumber: 2.2 Consensus size: 48
65231 CAACAAACAA
* **
65241 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTGTT
1 ATATAAC-TAACTATTTAACTAAAACAAACTAATTAAATAATTTTTACT
* * *
65290 ATATAACTAACTA-TTAAC-AAAATAAACTAATTAATTATTTTTTAACT
1 ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTT-ACT
65337 ATATAACTA
1 ATATAACTA
65346 TCAAACATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
46 21 0.43
47 15 0.31
48 6 0.12
49 7 0.14
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (48 bp):
ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTTACT
Found at i:65401 original size:41 final size:40
Alignment explanation
Indices: 65311--65401 Score: 94
Period size: 41 Copynumber: 2.2 Consensus size: 40
65301 TATTAACAAA
* *
65311 ATAAACTAATTAATTATTTTTTAACTATATAACTATCAAAC
1 ATAAACTAATTAAATAATTTTTAACTATATAACTAT-AAAC
* * *
65352 ATATACTAATTAAATAATTTTTAATTTATGTATACTAT-AAC
1 ATAAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAAC
*
65393 TTAAACTAA
1 ATAAACTAA
65402 CAATCATATA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
41 31 0.76
42 5 0.12
43 5 0.12
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
ATAAACTAATTAAATAATTTTTAACTATATAACTATAAAC
Found at i:65566 original size:21 final size:19
Alignment explanation
Indices: 65527--65567 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
65517 ACCTTATCTC
65527 CCTTTCTTCTTCTTACTTT
1 CCTTTCTTCTTCTTACTTT
*
65546 CCTTTCTCTCTTTCTTTCTTT
1 CCTTTCT-TC-TTCTTACTTT
65567 C
1 C
65568 TCGGCTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 2 0.11
21 10 0.53
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.63
Consensus pattern (19 bp):
CCTTTCTTCTTCTTACTTT
Found at i:65597 original size:26 final size:26
Alignment explanation
Indices: 65552--65607 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
65542 CTTTCCTTTC
* *
65552 TCTCTTTCTTTCTTTCTCGGCTGTAA
1 TCTCTTTCTCTCTTTCTCGGCTGCAA
65578 TCTC-TTCTCTCTTTCTTCGGCTGCAA
1 TCTCTTTCTCTCTTTC-TCGGCTGCAA
65604 TCTC
1 TCTC
65608 GACGACCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.07, C:0.32, G:0.11, T:0.50
Consensus pattern (26 bp):
TCTCTTTCTCTCTTTCTCGGCTGCAA
Found at i:65934 original size:29 final size:29
Alignment explanation
Indices: 65901--66033 Score: 185
Period size: 29 Copynumber: 4.6 Consensus size: 29
65891 TCGTGAGCTA
**
65901 GGACTACATGGCGACCTACTTGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
**
65930 GGACTACATGGCGACCTACTTGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
65959 GGACTACATGGCGACCTACAAGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
* *
65988 GGACTACATGGTGACCTACAAGGTCGCCC
1 GGACTACATGGCGACCTACAAGGTCGCCG
* * *
66017 AGACTGCATAGCGACCT
1 GGACTACATGGCGACCT
66034 CTCCATTGGC
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 96 1.00
ACGTcount: A:0.22, C:0.31, G:0.29, T:0.18
Consensus pattern (29 bp):
GGACTACATGGCGACCTACAAGGTCGCCG
Found at i:74324 original size:10 final size:10
Alignment explanation
Indices: 74309--74348 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
74299 TTTATCACAC
74309 CAAATTCTCT
1 CAAATTCTCT
74319 CAAATTCTCT
1 CAAATTCTCT
74329 -AAATTTCTCT
1 CAAA-TTCTCT
*
74339 CAAATACTCT
1 CAAATTCTCT
74349 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:74669 original size:110 final size:111
Alignment explanation
Indices: 74475--74806 Score: 594
Period size: 111 Copynumber: 3.0 Consensus size: 111
74465 TGGAAATCAT
*
74475 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
74540 TATTTAGTTGATTTATTTAATGCATGATTATTATATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
74586 ATATCTCGACACTTTGCTGATACGGTAACATTTT-ACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
74650 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* * *
74696 ATATCTCGACACTTTACTGATACGATAACATTTTAATGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
74761 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
74807 TTTTTGTAAT
Statistics
Matches: 213, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
110 106 0.50
111 107 0.50
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:76705 original size:9 final size:9
Alignment explanation
Indices: 76693--76754 Score: 88
Period size: 9 Copynumber: 6.9 Consensus size: 9
76683 ACCTGCTCAG
76693 GACGATGAC
1 GACGATGAC
*
76702 GACGACGAC
1 GACGATGAC
76711 GACGATGAC
1 GACGATGAC
76720 GACGATGAC
1 GACGATGAC
* *
76729 GATGGTGAC
1 GACGATGAC
*
76738 GACGACGAC
1 GACGATGAC
76747 GACGATGA
1 GACGATGA
76755 TGACAGCGAG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.32, C:0.23, G:0.35, T:0.10
Consensus pattern (9 bp):
GACGATGAC
Found at i:76707 original size:3 final size:3
Alignment explanation
Indices: 76693--76751 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
76683 ACCTGCTCAG
* * * * **
76693 GAC GAT GAC GAC GAC GAC GAC GAT GAC GAC GAT GAC GAT GGT GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
76741 GAC GAC GAC GA
1 GAC GAC GAC GA
76752 TGATGACAGC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.32, C:0.24, G:0.36, T:0.08
Consensus pattern (3 bp):
GAC
Found at i:79333 original size:19 final size:19
Alignment explanation
Indices: 79309--79347 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
79299 TCGAATACAT
79309 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
79328 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
79347 T
1 T
79348 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:79449 original size:64 final size:65
Alignment explanation
Indices: 79295--79455 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
79285 GAATTAATTG
* * * *** *
79295 AACATCGAATACATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
79360 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
79423 A
65 A
*
79424 AACATCGAATGCATTTTATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
79456 CTTGGTACAC
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 36 0.43
65 48 0.57
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:80783 original size:121 final size:121
Alignment explanation
Indices: 80569--80815 Score: 485
Period size: 121 Copynumber: 2.0 Consensus size: 121
80559 TGAGACAAGC
80569 TTCAAGTCACACATGAAGGTACAGATGAGGTAAAGAAATCAAAAATTAGTATTCTAACGCATAGC
1 TTCAAGTCACACATGAAGGTACAGATGAGGTAAAGAAATCAAAAATTAGTATTCTAACGCATAGC
80634 TATGAAAATTTCAGGATGAAACCAAATGAAGACATCAAAGCTATGACGGATAGATT
66 TATGAAAATTTCAGGATGAAACCAAATGAAGACATCAAAGCTATGACGGATAGATT
80690 TTCAAGTCACACATGAAGGTACAGATGAGGTAAAGAAATCAAAAATTAGTATTCTAACGCATAGC
1 TTCAAGTCACACATGAAGGTACAGATGAGGTAAAGAAATCAAAAATTAGTATTCTAACGCATAGC
*
80755 TATGAAAATTTCAGGATGAAACCAAATGAAGACATCAAAGCTATGATGGATAGATT
66 TATGAAAATTTCAGGATGAAACCAAATGAAGACATCAAAGCTATGACGGATAGATT
80811 TTCAA
1 TTCAA
80816 CGATTGTCAA
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 125 1.00
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.24
Consensus pattern (121 bp):
TTCAAGTCACACATGAAGGTACAGATGAGGTAAAGAAATCAAAAATTAGTATTCTAACGCATAGC
TATGAAAATTTCAGGATGAAACCAAATGAAGACATCAAAGCTATGACGGATAGATT
Found at i:85376 original size:24 final size:24
Alignment explanation
Indices: 85349--85428 Score: 105
Period size: 24 Copynumber: 3.5 Consensus size: 24
85339 TTAACAATGC
85349 ATCGATGCATCCCTTTGAATGTGT
1 ATCGATGCATCCCTTTGAATGTGT
* *
85373 ATCGATGCATCACC-ATG-A--TGC
1 ATCGATGCATC-CCTTTGAATGTGT
85394 ATCGATGCATCCCTTTGAATGTGT
1 ATCGATGCATCCCTTTGAATGTGT
85418 ATCGATGCATC
1 ATCGATGCATC
85429 ACCATGATGC
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
20 2 0.04
21 15 0.32
22 1 0.02
23 1 0.02
24 26 0.55
25 2 0.04
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (24 bp):
ATCGATGCATCCCTTTGAATGTGT
Found at i:85397 original size:45 final size:45
Alignment explanation
Indices: 85345--85471 Score: 211
Period size: 45 Copynumber: 2.8 Consensus size: 45
85335 GCATTTAACA
85345 ATGCATCGATGCATCCCTTTGAATGTGTATCGATGCATCACCATG
1 ATGCATCGATGCATCCCTTTGAATGTGTATCGATGCATCACCATG
85390 ATGCATCGATGCATCCCTTTGAATGTGTATCGATGCATCACCATG
1 ATGCATCGATGCATCCCTTTGAATGTGTATCGATGCATCACCATG
* * * *
85435 ATGCACCGATGCATACC-TTGAATATGCATCGATGCAT
1 ATGCATCGATGCATCCCTTTGAATGTGTATCGATGCAT
85472 GAGGCCATGC
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
44 18 0.23
45 60 0.77
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (45 bp):
ATGCATCGATGCATCCCTTTGAATGTGTATCGATGCATCACCATG
Found at i:85399 original size:21 final size:22
Alignment explanation
Indices: 85344--85471 Score: 95
Period size: 24 Copynumber: 5.7 Consensus size: 22
85334 TGCATTTAAC
*
85344 AATGCATCGATGCATC-CCTTTG
1 AATGCATCGATGCATCACC-ATG
*
85366 AATGTGTATCGATGCATCACCATG
1 AA--TGCATCGATGCATCACCATG
*
85390 -ATGCATCGATGCATC-CCTTTG
1 AATGCATCGATGCATCACC-ATG
*
85411 AATGTGTATCGATGCATCACCATG
1 AA--TGCATCGATGCATCACCATG
* *
85435 -ATGCACCGATGCAT-ACCTTG
1 AATGCATCGATGCATCACCATG
85455 AATATGCATCGATGCAT
1 -A-ATGCATCGATGCAT
85472 GAGGCCATGC
Statistics
Matches: 85, Mismatches: 10, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
20 7 0.08
21 26 0.31
22 3 0.04
23 15 0.18
24 30 0.35
25 4 0.05
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (22 bp):
AATGCATCGATGCATCACCATG
Found at i:87009 original size:19 final size:19
Alignment explanation
Indices: 86985--87023 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
86975 TCGAATGCAT
86985 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
87004 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
87023 T
1 T
87024 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:87148 original size:64 final size:65
Alignment explanation
Indices: 86971--87133 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 65
86961 GAATTAATTG
* * * *
86971 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* * ** **
87036 AACATCGAATGCTTTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
87099 A
65 A
87100 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
87134 TGGTGCACCG
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 35 0.42
65 48 0.58
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:88916 original size:20 final size:21
Alignment explanation
Indices: 88888--88934 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
88878 GGATTATGAG
*
88888 AAATTATTTTT-AAAATAT-AA
1 AAATGATTTTTCAAAAT-TGAA
88908 AAATGATTTTTCAAAATTGAA
1 AAATGATTTTTCAAAATTGAA
88929 AAATGA
1 AAATGA
88935 AAACAAACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.38
Consensus pattern (21 bp):
AAATGATTTTTCAAAATTGAA
Found at i:92629 original size:21 final size:23
Alignment explanation
Indices: 92605--92656 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
92595 AGTGAATCGA
92605 TCCCCCCATG-AGGG-AACCGAT
1 TCCCCCCATGAAGGGTAACCGAT
**
92626 TCCCCCTTTGAAGGGTAACCGAT
1 TCCCCCCATGAAGGGTAACCGAT
92649 TCCCCCCA
1 TCCCCCCA
92657 CAGGGGAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 4 0.16
23 13 0.52
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.19
Consensus pattern (23 bp):
TCCCCCCATGAAGGGTAACCGAT
Found at i:93388 original size:21 final size:21
Alignment explanation
Indices: 93364--93403 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
93354 ACCGTCAACC
*
93364 AAATCCACTTCCAAATCCTCA
1 AAATCCAATTCCAAATCCTCA
*
93385 AAATCCAATTCCTAATCCT
1 AAATCCAATTCCAAATCCT
93404 AATCCCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATCCAATTCCAAATCCTCA
Found at i:97663 original size:29 final size:29
Alignment explanation
Indices: 97618--97687 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
97608 TACTGCTACG
*
97618 GGTGTTAGATCGGGAAATATAATCTGACC
1 GGTGTTAGATCGAGAAATATAATCTGACC
*
97647 GGTGTTAGATCGAGAAATATAATCTGATC
1 GGTGTTAGATCGAGAAATATAATCTGACC
97676 GGTGTTAGATCG
1 GGTGTTAGATCG
97688 GTATATATAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.30, C:0.11, G:0.29, T:0.30
Consensus pattern (29 bp):
GGTGTTAGATCGAGAAATATAATCTGACC
Found at i:98623 original size:2 final size:2
Alignment explanation
Indices: 98616--98649 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
98606 CCAACTAAGC
98616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98650 TATTTTAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:105045 original size:28 final size:28
Alignment explanation
Indices: 105013--105067 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
105003 GATATTATTG
105013 CATAAAGCATGCAAGACAGTTATGGAAT
1 CATAAAGCATGCAAGACAGTTATGGAAT
**
105041 CATAAAGCATGCAAGATGGTTATGGAA
1 CATAAAGCATGCAAGACAGTTATGGAA
105068 ACAAAGTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.22
Consensus pattern (28 bp):
CATAAAGCATGCAAGACAGTTATGGAAT
Found at i:116909 original size:37 final size:41
Alignment explanation
Indices: 116863--116952 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 41
116853 TTGAAAGAAT
116863 ATAAAATAA-T-AAGATATTTT-AC-TATTAAA-ATATAAGA
1 ATAAAATAAGTAAAGATATTTTAACTTATTAAATA-ATAAGA
*
116900 ATAAAATAATAGTAAATATATTTTAACTTATTAAATAATAAGA
1 ATAAAAT-A-AGTAAAGATATTTTAACTTATTAAATAATAAGA
116943 ATAAAATAAG
1 ATAAAATAAG
116953 ATACAATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
37 7 0.16
38 1 0.02
39 1 0.02
40 1 0.02
41 11 0.24
42 3 0.07
43 20 0.44
44 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (41 bp):
ATAAAATAAGTAAAGATATTTTAACTTATTAAATAATAAGA
Found at i:116941 original size:43 final size:42
Alignment explanation
Indices: 116876--117000 Score: 138
Period size: 43 Copynumber: 3.0 Consensus size: 42
116866 AAATAATAAG
*
116876 ATATTTTAC-TATTAAAATATAAGAATAAAATAATAGTA-AAT
1 ATATTTTACTTATTAAAATATAAGAATAAAATAAGA-TACAAT
116917 ATATTTTAACTTATT-AAATAATAAGAATAAAATAAGATACAAT
1 ATATTTT-ACTTATTAAAAT-ATAAGAATAAAATAAGATACAAT
*
116960 ATATATTTACTTA--AAAGT-TAAG-ATAATAATAAGATACAAT
1 ATAT-TTTACTTATTAAAATATAAGAATAA-AATAAGATACAAT
117000 A
1 A
117001 ATATATTTTA
Statistics
Matches: 75, Mismatches: 2, Indels: 15
0.82 0.02 0.16
Matches are distributed among these distances:
39 4 0.05
40 18 0.24
41 7 0.09
42 11 0.15
43 32 0.43
44 3 0.04
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (42 bp):
ATATTTTACTTATTAAAATATAAGAATAAAATAAGATACAAT
Found at i:117555 original size:14 final size:14
Alignment explanation
Indices: 117536--117562 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
117526 GTGCAACCAT
117536 TTGATTTTATTGGG
1 TTGATTTTATTGGG
117550 TTGATTTTATTGG
1 TTGATTTTATTGG
117563 TGAAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (14 bp):
TTGATTTTATTGGG
Found at i:123335 original size:2 final size:2
Alignment explanation
Indices: 123280--123322 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
123270 AGATATATTC
123280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
123322 A
1 A
123323 CACTCTCATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:126574 original size:35 final size:35
Alignment explanation
Indices: 126529--126597 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
126519 TACGTTTAGT
126529 ACCTAAATTATTGTTTTTGTTAGATTTTGGTGTCA
1 ACCTAAATTATTGTTTTTGTTAGATTTTGGTGTCA
*
126564 ACCTAAATTATTGTTTTTGTTATATTTTGGTGTC
1 ACCTAAATTATTGTTTTTGTTAGATTTTGGTGTC
126598 TACATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.22, C:0.09, G:0.16, T:0.54
Consensus pattern (35 bp):
ACCTAAATTATTGTTTTTGTTAGATTTTGGTGTCA
Found at i:126641 original size:3 final size:3
Alignment explanation
Indices: 126633--126659 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
126623 AATGTTTAGT
126633 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
126660 AAGAAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:127350 original size:60 final size:59
Alignment explanation
Indices: 127278--127460 Score: 183
Period size: 60 Copynumber: 3.1 Consensus size: 59
127268 ATCCTCAAAG
* * * * * *
127278 TATGACCTTCATTTTAAATTGGTCCAT-AAATTTTTTAATATTCCAAATTT-ATCTCTAAAC
1 TATGA-CTTCATTATAAATTAGTCC-TCAAACTTTTAAACATTCC-AATTTCATCCCTAAAC
* *
127338 TATGACTATCATTCTAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCATCCCTAAAC
1 TATGACT-TCATTATAAATTAGTCCTCAAACTTTTAAACATTCCAATTTCATCCCTAAAC
* * * *
127398 TATGACTTTCATTATAAATTTGTCCCCAAACTTTTTGAACATTCTAATTTCATCCC-AAAC
1 TATGAC-TTCATTATAAATTAGTCCTCAAAC-TTTTAAACATTCCAATTTCATCCCTAAAC
127458 TAT
1 TAT
127461 ATGTATACAC
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
59 8 0.08
60 75 0.71
61 22 0.21
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (59 bp):
TATGACTTCATTATAAATTAGTCCTCAAACTTTTAAACATTCCAATTTCATCCCTAAAC
Found at i:127635 original size:60 final size:60
Alignment explanation
Indices: 127538--127694 Score: 190
Period size: 60 Copynumber: 2.6 Consensus size: 60
127528 AATTTGGGGG
* * * * *
127538 TGAAATTAGAATATTCAAAAGTTTAAAGACTAGTTTAGAAAGGGGGTCATGGCTTAG-GGA
1 TGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAGAAAGAGAGTCATAG-TTAGAAGA
* * * *
127598 TGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTGAAGA
1 TGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAGAAAGAGAGTCATAGTTAGAAGA
* * *
127658 TGAAATTAGAATATTTAAAAGTTTAATGACCAATTTA
1 TGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTA
127695 AAATGAAAAT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
59 3 0.04
60 80 0.96
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (60 bp):
TGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAGAAAGAGAGTCATAGTTAGAAGA
Found at i:131240 original size:25 final size:27
Alignment explanation
Indices: 131181--131240 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
131171 ACATGTAACT
131181 TATAAAAT-GATTTATCAGTACACATA
1 TATAAAATAGATTTATCAGTACACATA
* * *
131207 AATAAAATAGATTT-TCAG-ACTCGTA
1 TATAAAATAGATTTATCAGTACACATA
131232 TATAAAATA
1 TATAAAATA
131241 AAATACAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 13 0.45
26 11 0.38
27 5 0.17
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.33
Consensus pattern (27 bp):
TATAAAATAGATTTATCAGTACACATA
Found at i:131633 original size:2 final size:2
Alignment explanation
Indices: 131626--131668 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
131616 TCTTTTTAAA
131626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
131668 A
1 A
131669 CCCCCATCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:131853 original size:24 final size:24
Alignment explanation
Indices: 131826--131934 Score: 114
Period size: 24 Copynumber: 4.5 Consensus size: 24
131816 AAACGAAGAT
*
131826 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
131850 ATCAGATATCAGAACATAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
131874 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
131898 GTAATG-TATCAGAACAGAATTCA-
1 ATCA-GAAATCAGAACAGAATTCAG
*
131921 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
131935 TAAAATATTT
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
23 1 0.01
24 66 0.97
25 1 0.01
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:131855 original size:12 final size:12
Alignment explanation
Indices: 131828--131897 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
131818 ACGAAGATAT
* *
131828 CAGAAATCAAAA
1 CAGAATTCAGAA
*
131840 CAGAATTCAGAT
1 CAGAATTCAGAA
131852 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
131864 CATAATCCAGAT
1 CAGAATTCAGAA
*
131876 CAGAAATCAGAA
1 CAGAATTCAGAA
131888 CAGAATTCAG
1 CAGAATTCAG
131898 GTAATGTATC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:131930 original size:48 final size:48
Alignment explanation
Indices: 131826--131934 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 48
131816 AAACGAAGAT
* * * *
131826 ATCAGAAATCAAAACAGAATTCAGATCAGATATCAGAACATAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCAAG
*
131874 ATCAGAAATCAGAACAGAATTCAGGTAATG-TATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGATAA-GATATCAGAACAGAA-TCAAG
*
131923 -TCGGAAATCAGA
1 ATCAGAAATCAGA
131935 TAAAATATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 48 0.91
49 5 0.09
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCAAG
Found at i:132762 original size:21 final size:21
Alignment explanation
Indices: 132736--132780 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
132726 GATTTCTGGG
* *
132736 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
132757 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
132778 CAA
1 CAA
132781 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:134555 original size:22 final size:22
Alignment explanation
Indices: 134480--134547 Score: 136
Period size: 22 Copynumber: 3.1 Consensus size: 22
134470 TCCTTATGGA
134480 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
134502 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
134524 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
134546 CA
1 CA
134548 TTTATACGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (22 bp):
CAATTCTACGGGCACTTCGGTG
Found at i:137713 original size:21 final size:21
Alignment explanation
Indices: 137687--137731 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
137677 GATTTCTGGG
* *
137687 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
137708 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
137729 CAA
1 CAA
137732 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:139499 original size:22 final size:22
Alignment explanation
Indices: 139424--139491 Score: 136
Period size: 22 Copynumber: 3.1 Consensus size: 22
139414 TCCTTATGGA
139424 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
139446 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
139468 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
139490 CA
1 CA
139492 TTTATACGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (22 bp):
CAATTCTACGGGCACTTCGGTG
Found at i:146790 original size:29 final size:29
Alignment explanation
Indices: 146732--146792 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
146722 GAGAGTCAAA
* * *
146732 TTATAATTTTATATAAATTAATATCTATT
1 TTATAATTTTAAAAAAATTAAAATCTATT
*
146761 TTATCATTTTAAAAAAATTAAAAATC-ATT
1 TTATAATTTTAAAAAAATT-AAAATCTATT
146790 TTA
1 TTA
146793 GCATATAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (29 bp):
TTATAATTTTAAAAAAATTAAAATCTATT
Found at i:150816 original size:15 final size:15
Alignment explanation
Indices: 150796--150828 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
150786 GTGATGAGTT
150796 TGATGATGGGTTTGA
1 TGATGATGGGTTTGA
150811 TGATGATGGGTTTGA
1 TGATGATGGGTTTGA
150826 TGA
1 TGA
150829 AGGGGGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.39
Consensus pattern (15 bp):
TGATGATGGGTTTGA
Found at i:150828 original size:12 final size:12
Alignment explanation
Indices: 150775--150816 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
150765 AAAGTGATTG
*
150775 TGATGAGTTTGG
1 TGATGAGTTTGA
150787 TGATGAGTTTGA
1 TGATGAGTTTGA
*
150799 TGATGGGTTTGA
1 TGATGAGTTTGA
150811 TGATGA
1 TGATGA
150817 TGGGTTTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.40
Consensus pattern (12 bp):
TGATGAGTTTGA
Found at i:156551 original size:72 final size:72
Alignment explanation
Indices: 156434--156570 Score: 247
Period size: 72 Copynumber: 1.9 Consensus size: 72
156424 CGTAATCTCA
* *
156434 GCTTAATTTAGATAGGATTTCTCTGCTTTAAACTCTTAGGTAGCAGAAACCTTAAATTTGACCAT
1 GCTTAATTTAGATAGAATTTCTCTGCTTGAAACTCTTAGGTAGCAGAAACCTTAAATTTGACCAT
156499 TATTTAT
66 TATTTAT
*
156506 GCTTAATTTAGATAGAATTTCTCTTCTTGAAACTCTTAGGTAGCAGAAACCTTAAATTTGACCAT
1 GCTTAATTTAGATAGAATTTCTCTGCTTGAAACTCTTAGGTAGCAGAAACCTTAAATTTGACCAT
156571 CTTTTGGTCA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (72 bp):
GCTTAATTTAGATAGAATTTCTCTGCTTGAAACTCTTAGGTAGCAGAAACCTTAAATTTGACCAT
TATTTAT
Found at i:158629 original size:16 final size:16
Alignment explanation
Indices: 158610--158641 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
158600 TGCCTTGGTT
158610 ATCTTATTACCTTTTC
1 ATCTTATTACCTTTTC
158626 ATCTTATTACCTTTTC
1 ATCTTATTACCTTTTC
158642 TTTCTCTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (16 bp):
ATCTTATTACCTTTTC
Found at i:164502 original size:32 final size:32
Alignment explanation
Indices: 164441--164525 Score: 127
Period size: 32 Copynumber: 2.7 Consensus size: 32
164431 AAATACTATA
* *
164441 TATTCAATTGGTAATCCACT-AATGATCAACG
1 TATTCCATTGTTAATCCACTAAATGATCAACG
*
164472 TATTCCATTTTTAATCCACTAAATGATCAACG
1 TATTCCATTGTTAATCCACTAAATGATCAACG
*
164504 TATTTCATTGTTAATCCACTAA
1 TATTCCATTGTTAATCCACTAA
164526 TAATCGATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 17 0.35
32 31 0.65
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (32 bp):
TATTCCATTGTTAATCCACTAAATGATCAACG
Found at i:183075 original size:19 final size:19
Alignment explanation
Indices: 183017--183082 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
183007 ACCCGACCCG
183017 AAATAATATATTT-ATTAAA
1 AAAT-ATATATTTAATTAAA
*
183036 AAATATTATTTTTCAA-T-AA
1 AAATA-TATATTT-AATTAAA
183055 AAATATATATTTAATTAAA
1 AAATATATATTTAATTAAA
183074 AAATATATA
1 AAATATATA
183083 GAGAGATGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
17 2 0.05
18 8 0.20
19 28 0.70
20 1 0.03
21 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATATATATTTAATTAAA
Found at i:183079 original size:17 final size:17
Alignment explanation
Indices: 183021--183081 Score: 63
Period size: 17 Copynumber: 3.4 Consensus size: 17
183011 GACCCGAAAT
183021 AATATATTT-ATTAAAA
1 AATATATTTAATTAAAA
183037 AATATTATTTTTCAA-TAAAA
1 AATA-TA--TTT-AATTAAAA
183057 ATATATATTTAATTAAAA
1 A-ATATATTTAATTAAAA
183075 AATATAT
1 AATATAT
183082 AGAGAGATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 9 0.24
19 3 0.08
20 8 0.21
21 4 0.11
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATATTTAATTAAAA
Found at i:185528 original size:16 final size:18
Alignment explanation
Indices: 185507--185548 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
185497 GTTTTTTTAT
185507 TATTAATATAGAG-TAA-
1 TATTAATATAGAGATAAG
185523 TATTAATAT-GAGATAAG
1 TATTAATATAGAGATAAG
185540 TA-TAATATA
1 TATTAATATA
185549 ATATATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.13
16 18 0.78
17 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (18 bp):
TATTAATATAGAGATAAG
Found at i:193309 original size:124 final size:124
Alignment explanation
Indices: 193089--193337 Score: 498
Period size: 124 Copynumber: 2.0 Consensus size: 124
193079 TAAGAGTTTG
193089 GAATACTCGTTTGTAGTTGACTTTTTGTTAAAGGCAAATTGTCCTTGATATGGATAGATTTAGAA
1 GAATACTCGTTTGTAGTTGACTTTTTGTTAAAGGCAAATTGTCCTTGATATGGATAGATTTAGAA
193154 AGAAGTGCCCTTTAATTATCCTTAAATGTTAATATCTGTGACGTTGAAAGATTTGTCAA
66 AGAAGTGCCCTTTAATTATCCTTAAATGTTAATATCTGTGACGTTGAAAGATTTGTCAA
193213 GAATACTCGTTTGTAGTTGACTTTTTGTTAAAGGCAAATTGTCCTTGATATGGATAGATTTAGAA
1 GAATACTCGTTTGTAGTTGACTTTTTGTTAAAGGCAAATTGTCCTTGATATGGATAGATTTAGAA
193278 AGAAGTGCCCTTTAATTATCCTTAAATGTTAATATCTGTGACGTTGAAAGATTTGTCAA
66 AGAAGTGCCCTTTAATTATCCTTAAATGTTAATATCTGTGACGTTGAAAGATTTGTCAA
193337 G
1 G
193338 GGAGACAATA
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 125 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.39
Consensus pattern (124 bp):
GAATACTCGTTTGTAGTTGACTTTTTGTTAAAGGCAAATTGTCCTTGATATGGATAGATTTAGAA
AGAAGTGCCCTTTAATTATCCTTAAATGTTAATATCTGTGACGTTGAAAGATTTGTCAA
Found at i:197566 original size:17 final size:17
Alignment explanation
Indices: 197544--197576 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
197534 CAATTGTAGT
197544 TAAAATATC-AAATTAAA
1 TAAAATA-CAAAATTAAA
197561 TAAAATACAAAATTAA
1 TAAAATACAAAATTAA
197577 GGGATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAATACAAAATTAAA
Found at i:199786 original size:21 final size:21
Alignment explanation
Indices: 199750--199799 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 21
199740 TTGGGATGGA
199750 TGGGTGTTGGAATTTAAGGATT
1 TGGGT-TTGGAATTTAAGGATT
199772 TAGGGTTTGG-ATTTAAGGATT
1 T-GGGTTTGGAATTTAAGGATT
199793 TGGGTTT
1 TGGGTTT
199800 AGAGATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.22
21 12 0.44
22 5 0.19
23 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (21 bp):
TGGGTTTGGAATTTAAGGATT
Found at i:201551 original size:6 final size:6
Alignment explanation
Indices: 201540--201602 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
201530 TCTTTATGGC
* * * *
201540 CTTATT CTTATT CTTATG CTTATG CTTATT CTTGTT CTT-TT GCTTCTT
1 CTTATT CTTATT CTTATT CTTATT CTTATT CTTATT CTTATT -CTTATT
* *
201588 CATATC CTTATT CTT
1 CTTATT CTTATT CTT
201603 CTTTTTCTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
5 2 0.04
6 43 0.91
7 2 0.04
ACGTcount: A:0.13, C:0.21, G:0.06, T:0.60
Consensus pattern (6 bp):
CTTATT
Found at i:201569 original size:24 final size:24
Alignment explanation
Indices: 201540--201602 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
201530 TCTTTATGGC
201540 CTTATTCTTATTCTTATGCTTATG
1 CTTATTCTTATTCTTATGCTTATG
* * * *
201564 CTTATTCTTGTTCTTTTGCTTCTT
1 CTTATTCTTATTCTTATGCTTATG
* *
201588 CATATCCTTATTCTT
1 CTTATTCTTATTCTT
201603 CTTTTTCTCC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.13, C:0.21, G:0.06, T:0.60
Consensus pattern (24 bp):
CTTATTCTTATTCTTATGCTTATG
Found at i:202968 original size:90 final size:90
Alignment explanation
Indices: 202829--203355 Score: 770
Period size: 90 Copynumber: 5.9 Consensus size: 90
202819 AAGTAGCAGG
* *
202829 CGACGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCAGAATGTCCGAGAACAGGAAG
1 CGACGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCGGAATGTCCGAGAACCGGAAG
* * *
202894 TCCATCTTCATCTTGGAGTAATCGA
66 TCTATCATCATCTTGGAGTAACCGA
* *
202919 CGGCGATTCCATGCTTCATTCTTTTCTCTAAACGAAGTCCAATCGGAATGTCCGAGAACCGGAAG
1 CGACGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCGGAATGTCCGAGAACCGGAAG
* *
202984 TCCATCATCATCTTGTAGTAACCGA
66 TCTATCATCATCTTGGAGTAACCGA
*
203009 CGACGATTCCATGCTTCATTCTTTTCTCTAAATGACGTCCAATCGGAATGTCCGAGAACCGGAAG
1 CGACGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCGGAATGTCCGAGAACCGGAAG
*
203074 TCTATCATCATCTTGTAGTAACCGA
66 TCTATCATCATCTTGGAGTAACCGA
*
203099 CGACGATTCCATGC-TCTATTCTTTTCTCTAAAGGAAGTCCAATCGGAATGTCCGAGAACCGGAA
1 CGACGATTCCATGCTTC-ATTCTTTTCTCTAAATGAAGTCCAATCGGAATGTCCGAGAACCGGAA
* ** * *
203163 GTTTATCATCATCTTGGAACAATCGG
65 GTCTATCATCATCTTGGAGTAACCGA
* * * *
203189 CGGCGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCGGAATGACCTAGAACGGGAAG
1 CGACGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCGGAATGTCCGAGAACCGGAAG
* *
203254 -CATATCCTCATCTTGCAGTAACCGA
66 TC-TATCATCATCTTGGAGTAACCGA
* * * * *
203279 CGACGATTCCATGCTTCATTCTTCTCTCTAAAAGAAGTCCAATCAGAATGGCCTAGAACCGGAAG
1 CGACGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCGGAATGTCCGAGAACCGGAAG
203344 TCTATCATCATC
66 TCTATCATCATC
203356 ATCTTGAAGT
Statistics
Matches: 395, Mismatches: 38, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
89 2 0.01
90 390 0.99
91 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (90 bp):
CGACGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCGGAATGTCCGAGAACCGGAAG
TCTATCATCATCTTGGAGTAACCGA
Found at i:211050 original size:300 final size:302
Alignment explanation
Indices: 210368--211874 Score: 2952
Period size: 300 Copynumber: 5.0 Consensus size: 302
210358 TTTTGTTCTG
210368 CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
1 CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
210433 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
66 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
210498 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
131 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
210563 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
196 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
210628 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCA
261 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCA
*
210670 CTCCATTTATCTCACAAAACAAAACTTTACCTTGGAATGTTTTGTTTTTCCATGAAAGACAGGGT
1 CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
210735 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
66 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
210800 ATTCAAC-TTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
131 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
210864 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGT-AA
196 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
210928 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCA
261 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCA
210970 CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
1 CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
211035 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
66 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
211100 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGC-AATATTCTGCTTCTAC
131 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
211164 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
196 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
211229 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCA
261 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCA
211271 CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
1 CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
*
211336 TCTTTGCAATTGCAACAGCAGATTAGTTATCAC--GATATCCTTTGCTGCTTCCTCTTAGATCAG
66 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
211399 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
131 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
211464 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
196 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
211529 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCA
261 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCA
*
211571 CTCCATTTATCTCACAAAACAAAACTTTACCTTGGAATGTTTTGTTTTTCCATGAAAGACAGGGT
1 CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
211636 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
66 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
211701 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
131 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
211766 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
196 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
211831 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCA
261 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCA
211873 CT
1 CT
211875 GTCTGTATAC
Statistics
Matches: 1195, Mismatches: 5, Indels: 10
0.99 0.00 0.01
Matches are distributed among these distances:
299 77 0.06
300 478 0.40
301 301 0.25
302 339 0.28
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (302 bp):
CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCA
Found at i:211533 original size:601 final size:601
Alignment explanation
Indices: 210368--211874 Score: 2946
Period size: 601 Copynumber: 2.5 Consensus size: 601
210358 TTTTGTTCTG
210368 CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
1 CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
210433 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
66 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
210498 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
131 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
210563 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
196 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
210628 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCACTCCATTTATCTCACAAAACAAA
261 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCACTCCATTTATCTCACAAAACAAA
*
210693 ACTTTACCTTGGAATGTTTTGTTTTTCCATGAAAGACAGGGTTCTTTGCAATTGCAACAGCAGAT
326 ACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGTTCTTTGCAATTGCAACAGCAGAT
*
210758 TAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAGATTCAACTTCTTAGCCAAATGGC
391 TAGTTATCAC-AGATATCCTTTGCTGCTTCCTCTTAGATCAGATTCAACTTCTTAGCCAAATGGC
210823 TTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTACTGTTGATTGGACAATTGTTTCTTG
455 TTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTACTGTTGATTGGACAATTGTTTCTTG
210888 CTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAAAAGTATCCAAAAGTGCTTTTCATA
520 CTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAAAAGTATCCAAAAGTGCTTTTCATA
210953 TTGAATCACTCCAATCA
585 TTGAATCACTCCAATCA
210970 CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
1 CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
211035 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
66 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
211100 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGC-AATATTCTGCTTCTAC
131 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
211164 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
196 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
211229 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCACTCCATTTATCTCACAAAACAAA
261 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCACTCCATTTATCTCACAAAACAAA
211294 ACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGTTCTTTGCAATTGCAACAGCAGAT
326 ACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGTTCTTTGCAATTGCAACAGCAGAT
211359 TAGTTATCAC-GATATCCTTTGCTGCTTCCTCTTAGATCAGATTCAACTTTCTTAGCCAAATGGC
391 TAGTTATCACAGATATCCTTTGCTGCTTCCTCTTAGATCAGATTCAAC-TTCTTAGCCAAATGGC
211423 TTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTACTGTTGATTGGACAATTGTTTCTTG
455 TTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTACTGTTGATTGGACAATTGTTTCTTG
211488 CTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAAAAAGTATCCAAAAGTGCTTTTCAT
520 CTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGT-AAAAAGTATCCAAAAGTGCTTTTCAT
211553 ATTGAATCACTCCAATCA
584 ATTGAATCACTCCAATCA
*
211571 CTCCATTTATCTCACAAAACAAAACTTTACCTTGGAATGTTTTGTTTTTCCATGAAAGACAGGGT
1 CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
211636 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
66 TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
211701 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
131 ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
211766 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
196 TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
211831 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCACT
261 AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCACT
211875 GTCTGTATAC
Statistics
Matches: 899, Mismatches: 3, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
599 36 0.04
600 119 0.13
601 441 0.49
602 303 0.34
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (601 bp):
CTCCATTTATCTCACAAAACAAAACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGT
TCTTTGCAATTGCAACAGCAGATTAGTTATCACAATATATCCTTTGCTGCTTCCTCTTAGATCAG
ATTCAACTTTCTTAGCCAAATGGCTTGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTAC
TGTTGATTGGACAATTGTTTCTTGCTTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAA
AAAGTATCCAAAAGTGCTTTTCATATTGAATCACTCCAATCACTCCATTTATCTCACAAAACAAA
ACTTTACCTTGAAATGTTTTGTTTTTCCATGAAAGACAGGGTTCTTTGCAATTGCAACAGCAGAT
TAGTTATCACAGATATCCTTTGCTGCTTCCTCTTAGATCAGATTCAACTTCTTAGCCAAATGGCT
TGGTTAACAACAATAGTTGTAGCAAATATTCTGCTTCTACTGTTGATTGGACAATTGTTTCTTGC
TTTCTTGAGTTCCATGAAAAACACCAGAATCAAGTGTAAAAAGTATCCAAAAGTGCTTTTCATAT
TGAATCACTCCAATCA
Found at i:221403 original size:133 final size:129
Alignment explanation
Indices: 221160--221537 Score: 404
Period size: 133 Copynumber: 2.9 Consensus size: 129
221150 ACTCTTCTCT
* * *
221160 TTGCGAGTCAAGTCT-AGTTTTACATGACTTCTATTCGTGGGTTAAGTCAAGTTGAAATTAGCTC
1 TTGCGAGTTAAGT-TGAGTTTTAGATGACTTC-ATT-GTTGGTTAAGTCAAGTTGAAATTAGCTC
* ** * ** * * *
221224 CTTTTTGCGAGTTGAGCTAGTTGAGATTGGTGTCTCCTTGCAAGTTGAGTCGAGTTGTGGACTCC
63 C-TTTTGCAAGTTGAGCTAGTTGAGATTGACGCCTCCTTGTGAGTTGAGCCAAGTTGTGAACTCC
221289 TCCTC
127 T-C-C
221294 ATTGCGAGTTAAGTTGAGTTTTAGATGACTTCATTGTTGGTTAAGTCAAGTTGAAATTAGCTCCT
1 -TTGCGAGTTAAGTTGAGTTTTAGATGACTTCATTGTTGGTTAAGTCAAGTTGAAATTAGCTCCT
* *
221359 CTTTGCAAGTTGAGCTAGTTGAAATTGACGCCTCCTTGTGAGTTGGGCCAAGTTGTGAACTCCTC
65 -TTTGCAAGTTGAGCTAGTTGAGATTGACGCCTCCTTGTGAGTTGAGCCAAGTTGTGAACTCCTC
221424 C
129 C
* * * *
221425 TTGCGAGTTAAGTCGAGTTTTGGATGACTCCCCTT-TGTGGTTTAAGTCAAG-TGAGAATTAGCT
1 TTGCGAGTTAAGTTGAGTTTTAGATGACT-TCATTGT-TGG-TTAAGTCAAGTTGA-AATTAGCT
* * * *
221488 CCTTAT-CACGAGTTAAGCTAGTTGAGATTGACTCCTCTTTGTGAGTTGAG
62 CCTTTTGCA--AGTTGAGCTAGTTGAGATTGACGCCTCCTTGTGAGTTGAG
221538 ACATGCCGTG
Statistics
Matches: 211, Mismatches: 24, Indels: 19
0.83 0.09 0.07
Matches are distributed among these distances:
130 30 0.14
131 12 0.06
132 58 0.27
133 80 0.38
134 4 0.02
135 27 0.13
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (129 bp):
TTGCGAGTTAAGTTGAGTTTTAGATGACTTCATTGTTGGTTAAGTCAAGTTGAAATTAGCTCCTT
TTGCAAGTTGAGCTAGTTGAGATTGACGCCTCCTTGTGAGTTGAGCCAAGTTGTGAACTCCTCC
Found at i:222545 original size:10 final size:10
Alignment explanation
Indices: 222526--222592 Score: 50
Period size: 10 Copynumber: 6.9 Consensus size: 10
222516 TAAAATGTTA
222526 TCTTTCTTCT
1 TCTTTCTTCT
*
222536 TCTTTTTTCT
1 TCTTTCTTCT
* *
222546 TATTT-ATCT
1 TCTTTCTTCT
**
222555 TCCTCCCTTCT
1 T-CTTTCTTCT
*
222566 TTTTTCTTCT
1 TCTTTCTTCT
222576 TC-TTCTTCT
1 TCTTTCTTCT
222585 TC-TTCTTC
1 TCTTTCTTC
222593 CCCTCCCATT
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
9 19 0.43
10 21 0.48
11 4 0.09
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (10 bp):
TCTTTCTTCT
Found at i:222577 original size:3 final size:3
Alignment explanation
Indices: 222561--222592 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
222551 ATCTTCCTCC
222561 CTT CTT -TT -TT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
222593 CCCTCCCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:223767 original size:15 final size:15
Alignment explanation
Indices: 223747--223789 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
223737 TTTTAAAATA
223747 AATATTAATTTATCT
1 AATATTAATTTATCT
223762 AATATTAATTTATCT
1 AATATTAATTTATCT
223777 AATATTAATTTAT
1 AATATTAATTTAT
223790 AGAGATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (15 bp):
AATATTAATTTATCT
Found at i:231301 original size:16 final size:16
Alignment explanation
Indices: 231282--231319 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
231272 TTTAATGGTT
*
231282 CTCATCGTTAACGGTG
1 CTCATCGATAACGGTG
231298 CTCATCGATAACGGTG
1 CTCATCGATAACGGTG
231314 CTCATC
1 CTCATC
231320 TATACTATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (16 bp):
CTCATCGATAACGGTG
Found at i:232573 original size:18 final size:18
Alignment explanation
Indices: 232546--232586 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
232536 AATTGATAGA
232546 ATTT-TTAAA-TATTATTG
1 ATTTATTAAATTATT-TTG
232563 ATTTATTAAATTATTTTG
1 ATTTATTAAATTATTTTG
*
232581 AATTAT
1 ATTTAT
232587 GACAAATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 13 0.62
19 4 0.19
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
ATTTATTAAATTATTTTG
Found at i:239616 original size:48 final size:48
Alignment explanation
Indices: 239539--239635 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
239529 CATAGTTTGT
239539 GTATGATGACTATCGATCGATTTTATTTAATGCATAAGTTGCATTTTC
1 GTATGATGACTATCGATCGATTTTATTTAATGCATAAGTTGCATTTTC
* * * *
239587 GTATGATGATTATCGATCGCTTTTGTTTAATGCATATGTTGCATTTTC
1 GTATGATGACTATCGATCGATTTTATTTAATGCATAAGTTGCATTTTC
239635 G
1 G
239636 CATCAGTACT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.45
Consensus pattern (48 bp):
GTATGATGACTATCGATCGATTTTATTTAATGCATAAGTTGCATTTTC
Found at i:241642 original size:26 final size:24
Alignment explanation
Indices: 241613--241660 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
241603 ACCATTGTTC
241613 ATTTATAAATCTAAATAAATAAGATT
1 ATTT-TAAATCTAAA-AAATAAGATT
* *
241639 ATTTTACATCTAAAATATAAGA
1 ATTTTAAATCTAAAAAATAAGA
241661 AATATGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 9 0.45
26 4 0.20
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
ATTTTAAATCTAAAAAATAAGATT
Found at i:243402 original size:2 final size:2
Alignment explanation
Indices: 243395--243427 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
243385 AAACGTAAAA
*
243395 AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
243428 CCTAGAGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:244371 original size:20 final size:20
Alignment explanation
Indices: 244346--244386 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
244336 GGCCCTTATA
244346 TAGAAGAAAATTATTATTTT
1 TAGAAGAAAATTATTATTTT
244366 TAGAAGAAAATTATTATTTT
1 TAGAAGAAAATTATTATTTT
244386 T
1 T
244387 TAATAGTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (20 bp):
TAGAAGAAAATTATTATTTT
Found at i:245731 original size:22 final size:22
Alignment explanation
Indices: 245706--245747 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
245696 TCCTCGGCAA
245706 CAATTCCTTAATATTTTATTTT
1 CAATTCCTTAATATTTTATTTT
245728 CAATTCCTTAATATTTTATT
1 CAATTCCTTAATATTTTATT
245748 AGAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (22 bp):
CAATTCCTTAATATTTTATTTT
Found at i:247214 original size:2 final size:2
Alignment explanation
Indices: 247209--247240 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
247199 ACACACACAC
247209 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
247241 CAATAAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:255638 original size:60 final size:59
Alignment explanation
Indices: 255574--255703 Score: 161
Period size: 60 Copynumber: 2.2 Consensus size: 59
255564 TTCTAATTTT
* * * *
255574 ATCCTAAACTATGACTCTCATTTTAAATTGGTCCGTCAAACTTTTTAATGCTCCAAATTC
1 ATCCTAAACTATGACTCTCATTATAAATTGGT-CATCAAACTTTTAAATACTCCAAATTC
* * * *
255634 ATCCTCAAACTATGACTCTCATTATAATTTGGTCATTAAACTTTTAAATATTCCAATTTC
1 ATCCT-AAACTATGACTCTCATTATAAATTGGTCATCAAACTTTTAAATACTCCAAATTC
*
255694 ACCCTAAACT
1 ATCCTAAACT
255704 TTTGAATGAT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
59 5 0.08
60 30 0.50
61 25 0.42
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.38
Consensus pattern (59 bp):
ATCCTAAACTATGACTCTCATTATAAATTGGTCATCAAACTTTTAAATACTCCAAATTC
Found at i:257741 original size:39 final size:40
Alignment explanation
Indices: 257669--257746 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
257659 ATTTATGTTG
* * *
257669 TGATCTCTTAGTAGCATGACAGGGTCATACATCAATGAAA
1 TGATCTCTTAGCAGCACGACAGAGTCATACATCAATGAAA
257709 TGATCTCTTAGCAGCACGACA-AGTCATACATCAATGAA
1 TGATCTCTTAGCAGCACGACAGAGTCATACATCAATGAA
257747 TCATCTGCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 16 0.46
40 19 0.54
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (40 bp):
TGATCTCTTAGCAGCACGACAGAGTCATACATCAATGAAA
Found at i:258873 original size:29 final size:29
Alignment explanation
Indices: 258822--258909 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
258812 CTTCCCAGCA
* *
258822 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACGCCGGGCGACCTTG
* * *
258851 TAGGTCGCCATGCACGCCAGGCGACATAG
1 TAGGTCGCCATGCACGCCGGGCGACCTTG
*
258880 TAGGTCGCCATGCACGCTGGGCGACCTTG
1 TAGGTCGCCATGCACGCCGGGCGACCTTG
258909 T
1 T
258910 CCTACGCCTT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.16, C:0.33, G:0.32, T:0.19
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCGGGCGACCTTG
Found at i:258945 original size:22 final size:23
Alignment explanation
Indices: 258914--258957 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
258904 CCTTGTCCTA
**
258914 CGCCTTGCTCCCCGTTGCATGCT
1 CGCCTTGCTCCCCACTGCATGCT
258937 CGCC-TGCTCCCCACTGCATGC
1 CGCCTTGCTCCCCACTGCATGC
258958 AGGCGACCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.07, C:0.48, G:0.20, T:0.25
Consensus pattern (23 bp):
CGCCTTGCTCCCCACTGCATGCT
Found at i:258986 original size:22 final size:22
Alignment explanation
Indices: 258955--259005 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
258945 CCCCACTGCA
*
258955 TGCA-GGCGACCTCTTCTGACG
1 TGCATGGCGACCTCTTCCGACG
258976 TGCATGGCGACCTCTTCCGACG
1 TGCATGGCGACCTCTTCCGACG
258998 TGCATGGC
1 TGCATGGC
259006 ACATGCAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.14, C:0.33, G:0.29, T:0.24
Consensus pattern (22 bp):
TGCATGGCGACCTCTTCCGACG
Found at i:259045 original size:31 final size:31
Alignment explanation
Indices: 259010--259071 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
259000 CATGGCACAT
259010 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
259041 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
259072 TAGAACACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.39, G:0.13, T:0.23
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCACCACAGCTCGTA
Found at i:260654 original size:31 final size:30
Alignment explanation
Indices: 260619--260714 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 30
260609 AAAATTTAGA
260619 AGTTTAGGGACTAATTTAGAATGAGGATCAT
1 AGTTTAGGGACTAATTTAGAATG-GGATCAT
* * *
260650 AGTTTAGGGA-TGAAATTAGAAT--GTTCAAA
1 AGTTTAGGGACT-AATTTAGAATGGGATC-AT
* *
260679 AGTTTAAGGACTAATTTAGAATGGGAGTTAT
1 AGTTTAGGGACTAATTTAGAATGGGA-TCAT
260710 AGTTT
1 AGTTT
260715 GAGGATGAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
28 3 0.06
29 19 0.37
30 2 0.04
31 26 0.51
32 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.34
Consensus pattern (30 bp):
AGTTTAGGGACTAATTTAGAATGGGATCAT
Found at i:260691 original size:60 final size:61
Alignment explanation
Indices: 260618--260763 Score: 208
Period size: 60 Copynumber: 2.4 Consensus size: 61
260608 GAAAATTTAG
* * *
260618 AAGTTTAGGGACTAATTTAGAATGAGGA-TCATAGTTT-AGGGATGAAATTAGAATGTTCAA
1 AAGTTTAAGGACTAATTTAGAATGAGGAGTCATAGTTTGA-GGATGAAATTAAAATATTCAA
*
260678 AAGTTTAAGGACTAATTTAGAATG-GGAGTTATAGTTTGAGGATGAAATTAAAATATTCAA
1 AAGTTTAAGGACTAATTTAGAATGAGGAGTCATAGTTTGAGGATGAAATTAAAATATTCAA
* *
260738 AAGTTTAAGGACCAATTTAAAATGAG
1 AAGTTTAAGGACTAATTTAGAATGAG
260764 ACTTACAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
59 3 0.04
60 72 0.94
61 2 0.03
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.32
Consensus pattern (61 bp):
AAGTTTAAGGACTAATTTAGAATGAGGAGTCATAGTTTGAGGATGAAATTAAAATATTCAA
Found at i:269562 original size:59 final size:59
Alignment explanation
Indices: 269442--269604 Score: 181
Period size: 59 Copynumber: 2.7 Consensus size: 59
269432 GAGGAAGTTG
* * * *
269442 GGGATGAAATTGGAATATTCAAAAGTTTAGGGA-TAAATTTAGAAAGAATGTCATAGTTTA
1 GGGATGAAATTAGAATATTTAAAAGTTTAAGGACT-AATTTA-AAAGAATGTCATAATTTA
*
269502 GGGATGAAATTAGAATGTTTAAAAG-TTAAGGACTAATTTAAAATGTAA-GTCATAATTTA
1 GGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAAAA-G-AATGTCATAATTTA
* * *
269561 GGGATGTAATTCA-AATAATTAAAAGTTTAAGGACAAATTTAAAA
1 GGGATGAAATT-AGAATATTTAAAAGTTTAAGGACTAATTTAAAA
269605 AAATAAAATG
Statistics
Matches: 89, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
58 3 0.03
59 43 0.48
60 43 0.48
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.32
Consensus pattern (59 bp):
GGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAAAAGAATGTCATAATTTA
Found at i:272580 original size:20 final size:20
Alignment explanation
Indices: 272551--272606 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
272541 TTTCAGAGTG
*
272551 ATGCACCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
272571 ATGCATCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
*
272591 ATGCATCAATGCACCA
1 ATGCATCGATGCACCA
272607 TGAATTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.32, C:0.36, G:0.14, T:0.18
Consensus pattern (20 bp):
ATGCATCGATGCACCAATCC
Found at i:272646 original size:65 final size:64
Alignment explanation
Indices: 272570--272778 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
272560 TGCACCAATC
*
272570 CATGCATCGATGCACCAATCCATGCATCAATGCACCATGAATTAAATTG-AACATCGAATGCATT
1 CATGCATCGATGCACC-ATCCATGCATCAATGCACC-TGAATTATATTGAAACATCGAATGCATT
272634 T
64 T
* * *
272635 CATGCATCGATGCA-CATACCATGCACCAATGCA-CTGAGGATTTTA-TGAAAATATCGAATGCA
1 CATGCATCGATGCACCAT-CCATGCATCAATGCACCTGA--ATTATATTG-AAACATCGAATGCA
272697 TTT
62 TTT
* * * ** * *
272700 GATGCATCGATGCACCAGCCATGCATCGATGCACTCTG-GCTATTTTGAAACATCGAATGCACTT
1 CATGCATCGATGCACCATCCATGCATCAATGCAC-CTGAATTATATTGAAACATCGAATGCATTT
*
272764 GATGCATCGATGCAC
1 CATGCATCGATGCAC
272779 TCTTAGTGCA
Statistics
Matches: 121, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
62 3 0.02
63 5 0.04
64 51 0.42
65 57 0.47
66 2 0.02
67 3 0.02
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (64 bp):
CATGCATCGATGCACCATCCATGCATCAATGCACCTGAATTATATTGAAACATCGAATGCATTT
Found at i:272778 original size:17 final size:19
Alignment explanation
Indices: 272750--272798 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
272740 TATTTTGAAA
272750 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
272768 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
272787 CATCGATGCACT
1 CATCGATGCACT
272799 GAGAGTCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.25
18 7 0.25
19 14 0.50
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Done.