Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014842.1 Corchorus capsularis cultivar CVL-1 contig14863, 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: 113744
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:5493 original size:17 final size:17
Alignment explanation
Indices: 5467--5503 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5457 CCCTCCTCAT
5467 GGTACCAGGTAGCATAA
1 GGTACCAGGTAGCATAA
* *
5484 GGTACTAGGTAGCATGA
1 GGTACCAGGTAGCATAA
5501 GGT
1 GGT
5504 GCTGGATAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.22
Consensus pattern (17 bp):
GGTACCAGGTAGCATAA
Found at i:7515 original size:22 final size:22
Alignment explanation
Indices: 7446--7519 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
7436 AAGCACTTGA
*
7446 CCGGCCACACCGGCTACATGAC
1 CCGGCCACACCGGCCACATGAC
* * *** *
7468 CCGACCATGACAATCGCACA-GGC
1 CCGGCCA-CACCGGC-CACATGAC
7491 CCGGCCACACCGGCCACATGAC
1 CCGGCCACACCGGCCACATGAC
7513 CCGGCCA
1 CCGGCCA
7520 TGCCCATGCA
Statistics
Matches: 36, Mismatches: 13, Indels: 6
0.65 0.24 0.11
Matches are distributed among these distances:
21 4 0.11
22 18 0.50
23 11 0.31
24 3 0.08
ACGTcount: A:0.24, C:0.46, G:0.23, T:0.07
Consensus pattern (22 bp):
CCGGCCACACCGGCCACATGAC
Found at i:11165 original size:486 final size:486
Alignment explanation
Indices: 10254--11225 Score: 1854
Period size: 486 Copynumber: 2.0 Consensus size: 486
10244 CATCAAGTTC
* *
10254 ATCTTCTAAGAATCATGTTAAGTGCTTCAAGTGTCAAGTATTTGGGCACTATGCTAAGGATTGTG
1 ATCTTCTAAGAATCATGTTAAGTGCTTCAAATGTCAAGGATTTGGGCACTATGCTAAGGATTGTG
10319 TTAACAAGAAGGTTATGTTCATCAATGAACATGGGGAAGTCGAAAGTGAAGATGAAGAGTTTACT
66 TTAACAAGAAGGTTATGTTCATCAATGAACATGGGGAAGTCGAAAGTGAAGATGAAGAGTTTACT
*
10384 CTAGGATCTAGTGGTGATGGAGATAATGAAGGAGATGCGCATAGTGATAGTGACGATGGTGATGG
131 CTAGGATCTAGTGGTGATGGAGATAATGAAGGAGATGCGCATAGTGATAGTAACGATGGTGATGG
*
10449 ATTCGCACTTAAGAGTTTGGTTGCTAGGAGAACTTTGAGTGCTTATGTGAAAGAAGATGTGAATA
196 ATTCACACTTAAGAGTTTGGTTGCTAGGAGAACTTTGAGTGCTTATGTGAAAGAAGATGTGAATA
*
10514 ATCAAAGAGAGAACTTGTTTCATACTAGGATGTATGCGAGTGGGAAGCCTAGTAGTGTGATTATC
261 ATCAAAGAGAGAACTTGTTCCATACTAGGATGTATGCGAGTGGGAAGCCTAGTAGTGTGATTATC
*
10579 GATGGTGGGAGTTGTACAAACATAGTTAGTGTTTATTTGGTGAAGGAGATGCAATTACCCACTAC
326 GATGGTGGGAGTTGTACAAACATAGCTAGTGTTTATTTGGTGAAGGAGATGCAATTACCCACTAC
*
10644 CAAACACCCTAAATCCTATAGCTTAGGTTGGATCAACGATAAAGAGGAGATTAGGGTTAACAAAC
391 CAAACACCCTAAACCCTATAGCTTAGGTTGGATCAACGATAAAGAGGAGATTAGGGTTAACAAAC
10709 AAGTTTTAGTTTCTCTTTCTTTGGGCAGGTA
456 AAGTTTTAGTTTCTCTTTCTTTGGGCAGGTA
10740 ATCTTCTAAGAATCATGTTAAGTGCTTCAAATGTCAAGGATTTGGGCACTATGCTAAGGATTGTG
1 ATCTTCTAAGAATCATGTTAAGTGCTTCAAATGTCAAGGATTTGGGCACTATGCTAAGGATTGTG
10805 TTAACAAGAAGGTTATGTTCATCAATGAACATGGGGAAGTCGAAAGTGAAGATGAAGAGTTTACT
66 TTAACAAGAAGGTTATGTTCATCAATGAACATGGGGAAGTCGAAAGTGAAGATGAAGAGTTTACT
* * *
10870 CTAGGATCTAGTGGTGATGGAGATGATGAAGGAGATGTGCATAGTGATAGTAATGATGGTGATGG
131 CTAGGATCTAGTGGTGATGGAGATAATGAAGGAGATGCGCATAGTGATAGTAACGATGGTGATGG
10935 ATTCACACTTAAGAGTTTGGTTGCTAGGAGAACTTTGAGTGCTTATGTGAAAGAAGATGTGAATA
196 ATTCACACTTAAGAGTTTGGTTGCTAGGAGAACTTTGAGTGCTTATGTGAAAGAAGATGTGAATA
11000 ATCAAAGAGAGAACTTGTTCCATACTAGGATGTATGCGAGTGGGAAGCCTAGTAGTGTGATTATC
261 ATCAAAGAGAGAACTTGTTCCATACTAGGATGTATGCGAGTGGGAAGCCTAGTAGTGTGATTATC
11065 GATGGTGGGAGTTGTACAAACATAGCTAGTGTTTATTTGGTGAAGGAGATGCAATTACCCACTAC
326 GATGGTGGGAGTTGTACAAACATAGCTAGTGTTTATTTGGTGAAGGAGATGCAATTACCCACTAC
11130 CAAACACCCTAAACCCTATAGCTTAGGTTGGATCAACGATAAAGAGGAGATTAGGGTTAACAAAC
391 CAAACACCCTAAACCCTATAGCTTAGGTTGGATCAACGATAAAGAGGAGATTAGGGTTAACAAAC
11195 AAGTTTTAGTTTCTCTTTCTTTGGGCAGGTA
456 AAGTTTTAGTTTCTCTTTCTTTGGGCAGGTA
11226 CAAAGGAGAT
Statistics
Matches: 476, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
486 476 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (486 bp):
ATCTTCTAAGAATCATGTTAAGTGCTTCAAATGTCAAGGATTTGGGCACTATGCTAAGGATTGTG
TTAACAAGAAGGTTATGTTCATCAATGAACATGGGGAAGTCGAAAGTGAAGATGAAGAGTTTACT
CTAGGATCTAGTGGTGATGGAGATAATGAAGGAGATGCGCATAGTGATAGTAACGATGGTGATGG
ATTCACACTTAAGAGTTTGGTTGCTAGGAGAACTTTGAGTGCTTATGTGAAAGAAGATGTGAATA
ATCAAAGAGAGAACTTGTTCCATACTAGGATGTATGCGAGTGGGAAGCCTAGTAGTGTGATTATC
GATGGTGGGAGTTGTACAAACATAGCTAGTGTTTATTTGGTGAAGGAGATGCAATTACCCACTAC
CAAACACCCTAAACCCTATAGCTTAGGTTGGATCAACGATAAAGAGGAGATTAGGGTTAACAAAC
AAGTTTTAGTTTCTCTTTCTTTGGGCAGGTA
Found at i:14208 original size:22 final size:22
Alignment explanation
Indices: 14182--14244 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
14172 ATCATTACTA
* *
14182 TTACTGATTTCTATTTTACCCT
1 TTACTGATTACCATTTTACCCT
14204 TTACTGATTACCATTTTACCCT
1 TTACTGATTACCATTTTACCCT
*
14226 TTACCGATTACCATTTTAC
1 TTACTGATTACCATTTTAC
14245 TGATTACCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.22, C:0.25, G:0.05, T:0.48
Consensus pattern (22 bp):
TTACTGATTACCATTTTACCCT
Found at i:14243 original size:15 final size:15
Alignment explanation
Indices: 14225--14260 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
14215 CATTTTACCC
14225 TTTACCGATTACCAT
1 TTTACCGATTACCAT
*
14240 TTTACTGATTACCAT
1 TTTACCGATTACCAT
14255 TTTACC
1 TTTACC
14261 CTTTATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (15 bp):
TTTACCGATTACCAT
Found at i:14330 original size:22 final size:22
Alignment explanation
Indices: 14300--14366 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
14290 CTTCCTTTTT
14300 CTTTCTTACTGATTACCACTTTA
1 CTTT-TTACTGATTACCACTTTA
14323 CTTTTTACTGATTACC-CTTTTA
1 CTTTTTACTGATTACCAC-TTTA
* *
14345 C-TTTTACTGGTTACTA-TTTA
1 CTTTTTACTGATTACCACTTTA
14365 CT
1 CT
14367 CATTACCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 5 0.13
21 13 0.33
22 17 0.44
23 4 0.10
ACGTcount: A:0.19, C:0.22, G:0.06, T:0.52
Consensus pattern (22 bp):
CTTTTTACTGATTACCACTTTA
Found at i:14391 original size:32 final size:32
Alignment explanation
Indices: 14346--14410 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
14336 ACCCTTTTAC
**
14346 TTTTACTGGTTACTATTTACTCATT-ACCATTT
1 TTTTACTAATTACTATTTAC-CATTCACCATTT
* *
14378 TTTTACTAATTACTCTTTACCCTTCACCATTT
1 TTTTACTAATTACTATTTACCATTCACCATTT
14410 T
1 T
14411 ACTCTTCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 3 0.11
32 25 0.89
ACGTcount: A:0.22, C:0.23, G:0.03, T:0.52
Consensus pattern (32 bp):
TTTTACTAATTACTATTTACCATTCACCATTT
Found at i:14477 original size:14 final size:14
Alignment explanation
Indices: 14428--14477 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
14418 GATGGTTATC
14428 CTTTACTATTTTACT
1 CTTTACT-TTTTACT
14443 CTTTTACTTTTTACT
1 C-TTTACTTTTTACT
** *
14458 GATTACTTTTGACT
1 CTTTACTTTTTACT
14472 CTTTAC
1 CTTTAC
14478 CATTATACCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 15 0.52
15 8 0.28
16 6 0.21
ACGTcount: A:0.18, C:0.20, G:0.04, T:0.58
Consensus pattern (14 bp):
CTTTACTTTTTACT
Found at i:14536 original size:40 final size:37
Alignment explanation
Indices: 14449--14536 Score: 90
Period size: 40 Copynumber: 2.3 Consensus size: 37
14439 TACTCTTTTA
*
14449 CTTTTTACTGATTACTTTTGACTCTTTACCATTATAC
1 CTTTTTACTGATTACTTTTGACTATTTACCATTATAC
* * *
14486 CTTTTT-CTGATTACAATTTTGATTATGATTACCATTCT-T
1 CTTTTTACTGATTAC--TTTTGACTAT--TTACCATTATAC
14525 CTTTTTACTGAT
1 CTTTTTACTGAT
14537 CATTTTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
36 8 0.19
37 6 0.14
38 8 0.19
39 6 0.14
40 14 0.33
ACGTcount: A:0.22, C:0.18, G:0.07, T:0.53
Consensus pattern (37 bp):
CTTTTTACTGATTACTTTTGACTATTTACCATTATAC
Found at i:14807 original size:22 final size:22
Alignment explanation
Indices: 14782--14842 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
14772 CCCTTTACCA
*
14782 ATTATCCTTTTACTTTTTACTG
1 ATTATCCTTCTACTTTTTACTG
**
14804 ATTATTGTTCTA-TTTTTACTG
1 ATTATCCTTCTACTTTTTACTG
*
14825 GTTA-CCATTCTACTTTTT
1 ATTATCC-TTCTACTTTTT
14843 TTTTACTTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.18, C:0.16, G:0.07, T:0.59
Consensus pattern (22 bp):
ATTATCCTTCTACTTTTTACTG
Found at i:14881 original size:22 final size:22
Alignment explanation
Indices: 14856--14908 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
14846 TACTTACTAT
*
14856 CATTTGACTCGTTTCTAATTAC
1 CATTTGACTCCTTTCTAATTAC
* *
14878 CATTTTACCCCTTTCTAATTAC
1 CATTTGACTCCTTTCTAATTAC
*
14900 CACTTGACT
1 CATTTGACT
14909 TTAATAATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.28, G:0.06, T:0.43
Consensus pattern (22 bp):
CATTTGACTCCTTTCTAATTAC
Found at i:14929 original size:20 final size:20
Alignment explanation
Indices: 14893--14930 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
14883 TACCCCTTTC
**
14893 TAATTACCACTTGACTTTAA
1 TAATTACCACTCCACTTTAA
14913 TAATTACCACTCCACTTT
1 TAATTACCACTCCACTTT
14931 TACTGATCAT
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:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (20 bp):
TAATTACCACTCCACTTTAA
Found at i:14955 original size:20 final size:20
Alignment explanation
Indices: 14930--15009 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
14920 CACTCCACTT
*
14930 TTACTGATCATCTTGTACTC
1 TTACTGATCATCTTTTACTC
* * *
14950 TTACTGGTTATCTTTTACTTT
1 TTACTGATCATCTTTTAC-TC
*
14971 TTACTAATCATCTTTTACTC
1 TTACTGATCATCTTTTACTC
* * *
14991 TTACAGATTATTTTTTACT
1 TTACTGATCATCTTTTACT
15010 ATTCACCTTT
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 31 0.66
21 16 0.34
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.54
Consensus pattern (20 bp):
TTACTGATCATCTTTTACTC
Found at i:14982 original size:41 final size:41
Alignment explanation
Indices: 14928--15009 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
14918 ACCACTCCAC
* * *
14928 TTTTACTGATCATCTTGTACTCTTACTGGTTATCTTTTACT
1 TTTTACTAATCATCTTGTACTCTTACAGATTATCTTTTACT
* *
14969 TTTTACTAATCATCTTTTACTCTTACAGATTATTTTTTACT
1 TTTTACTAATCATCTTGTACTCTTACAGATTATCTTTTACT
15010 ATTCACCTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.21, C:0.18, G:0.06, T:0.55
Consensus pattern (41 bp):
TTTTACTAATCATCTTGTACTCTTACAGATTATCTTTTACT
Found at i:14983 original size:21 final size:21
Alignment explanation
Indices: 14928--14989 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
14918 ACCACTCCAC
*
14928 TTTTACTGATCATCTTGTAC-
1 TTTTACTGATCATCTTTTACT
* * *
14948 TCTTACTGGTTATCTTTTACT
1 TTTTACTGATCATCTTTTACT
*
14969 TTTTACTAATCATCTTTTACT
1 TTTTACTGATCATCTTTTACT
14990 CTTACAGATT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.55
Consensus pattern (21 bp):
TTTTACTGATCATCTTTTACT
Found at i:15006 original size:34 final size:32
Alignment explanation
Indices: 14968--15043 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 32
14958 TATCTTTTAC
* *
14968 TTTTTACTAATCATCTTTTACTCTTACAGATTAT
1 TTTTTACTAATCACCTTTTACCCTTA-A-ATTAT
* *
15002 TTTTTACTATTCACCTTTTACCCTTAACTTAT
1 TTTTTACTAATCACCTTTTACCCTTAAATTAT
*
15034 TTATTACTAA
1 TTTTTACTAA
15044 CTTATTAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
32 12 0.33
33 1 0.03
34 23 0.64
ACGTcount: A:0.26, C:0.20, G:0.01, T:0.53
Consensus pattern (32 bp):
TTTTTACTAATCACCTTTTACCCTTAAATTAT
Found at i:18501 original size:34 final size:34
Alignment explanation
Indices: 18458--18523 Score: 116
Period size: 34 Copynumber: 1.9 Consensus size: 34
18448 ATCCAACTTG
18458 TGCATGTCTAATTAATTGA-TAAATTGAGAATTTA
1 TGCATGTCTAATTAATT-ACTAAATTGAGAATTTA
18492 TGCATGTCTAATTAATTACTAAATTGAGAATT
1 TGCATGTCTAATTAATTACTAAATTGAGAATT
18524 AGTTAATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 1 0.03
34 30 0.97
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (34 bp):
TGCATGTCTAATTAATTACTAAATTGAGAATTTA
Found at i:22536 original size:24 final size:24
Alignment explanation
Indices: 22509--22555 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
22499 TAGGAGGGTT
* *
22509 AGGGGCTATTTCAGTGTTTGAGGC
1 AGGGGCTATTGCAATGTTTGAGGC
* *
22533 AGGGGTTGTTGCAATGTTTGAGG
1 AGGGGCTATTGCAATGTTTGAGG
22556 GAGGAGGTGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.09, G:0.40, T:0.34
Consensus pattern (24 bp):
AGGGGCTATTGCAATGTTTGAGGC
Found at i:24568 original size:12 final size:12
Alignment explanation
Indices: 24553--24595 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
24543 CTACAGCAAC
24553 TTCAACTACATT
1 TTCAACTACATT
24565 TTCAAC-ATCATT
1 TTCAACTA-CATT
*
24577 TTCAACTCCATT
1 TTCAACTACATT
*
24589 CTCAACT
1 TTCAACT
24596 TCTAAACCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 26 0.96
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (12 bp):
TTCAACTACATT
Found at i:26739 original size:14 final size:14
Alignment explanation
Indices: 26720--26746 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
26710 ACATATTCAA
26720 ATAGACTATATAAC
1 ATAGACTATATAAC
26734 ATAGACTATATAA
1 ATAGACTATATAA
26747 TAATATTATC
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:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (14 bp):
ATAGACTATATAAC
Found at i:27282 original size:32 final size:32
Alignment explanation
Indices: 27246--27311 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
27236 AAACTTGATT
27246 TTAAATAGCATTAAGATGGAAATTGAACAATC
1 TTAAATAGCATTAAGATGGAAATTGAACAATC
27278 TTAAATAGCATTAAGATGGAAATTGAACAATC
1 TTAAATAGCATTAAGATGGAAATTGAACAATC
27310 TT
1 TT
27312 TATGTCTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.30
Consensus pattern (32 bp):
TTAAATAGCATTAAGATGGAAATTGAACAATC
Found at i:28592 original size:31 final size:31
Alignment explanation
Indices: 28557--28635 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
28547 ACGGTATTCG
*
28557 ACGTGGCATGCCACGTGGATCAAAAAGTAAC
1 ACGTGGCACGCCACGTGGATCAAAAAGTAAC
* * *
28588 ACGTGGAACACCACGTGGATCAAAAAGTGAC
1 ACGTGGCACGCCACGTGGATCAAAAAGTAAC
*
28619 ACGTGGCACGCCGCGTG
1 ACGTGGCACGCCACGTG
28636 TGCCAAAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.32, C:0.25, G:0.29, T:0.14
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGGATCAAAAAGTAAC
Found at i:28643 original size:31 final size:31
Alignment explanation
Indices: 28567--28653 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
28557 ACGTGGCATG
* *
28567 CCACGTGGATCAAAAAGTAACACGTGGAACA
1 CCACGTGGACCAAAAAGTGACACGTGGAACA
* * *
28598 CCACGTGGATCAAAAAGTGACACGTGGCACG
1 CCACGTGGACCAAAAAGTGACACGTGGAACA
* *
28629 CCGCGTGTG-CCAAAAAGTGGCACGT
1 CCACGTG-GACCAAAAAGTGACACGT
28654 CACATGTACC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
31 48 0.98
32 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.28, T:0.14
Consensus pattern (31 bp):
CCACGTGGACCAAAAAGTGACACGTGGAACA
Found at i:28680 original size:31 final size:31
Alignment explanation
Indices: 28645--28703 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
28635 GTGCCAAAAA
*
28645 GTGGCACGTCACATGTACC-AAAGAGTGATAC
1 GTGGCACGCCACATGTACCGAAA-AGTGATAC
*
28676 GTGGCACGCCACGTGTACCGAAAAGTGA
1 GTGGCACGCCACATGTACCGAAAAGTGA
28704 GGTGACACGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.31, C:0.24, G:0.29, T:0.17
Consensus pattern (31 bp):
GTGGCACGCCACATGTACCGAAAAGTGATAC
Found at i:33731 original size:11 final size:11
Alignment explanation
Indices: 33715--33746 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
33705 GAAGTTCGTG
33715 TTTGAAGATTA
1 TTTGAAGATTA
*
33726 TTTGAAGATAA
1 TTTGAAGATTA
33737 TTTGAAGATT
1 TTTGAAGATT
33747 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:33741 original size:22 final size:22
Alignment explanation
Indices: 33715--33774 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
33705 GAAGTTCGTG
*
33715 TTTGAAGATTATTTGAAGATAA
1 TTTGAAGATTATTTGAAGACAA
33737 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGATTATTTGAAGACAA
*
33756 -TTGAAGAATTATTTCAAGA
1 TTTGAAG-ATTATTTGAAGA
33775 AGTAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (22 bp):
TTTGAAGATTATTTGAAGACAA
Found at i:33749 original size:19 final size:18
Alignment explanation
Indices: 33725--33762 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
33715 TTTGAAGATT
*
33725 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
33744 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
33762 A
1 A
33763 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:35109 original size:6 final size:6
Alignment explanation
Indices: 35098--35128 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
35088 ATAATTGCTA
35098 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
35129 CTTTGCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:43077 original size:63 final size:65
Alignment explanation
Indices: 42973--43098 Score: 211
Period size: 63 Copynumber: 2.0 Consensus size: 65
42963 GTGAAAAGGG
*
42973 GTTATTGCCGAAAAACAAACGGTGAAATGGGGTAGTCAGATGGAGCTTTTTTAAT-TTGATTTTT
1 GTTATTGCCGAAAAACAAACGGTGAAAAGGGGTAGTCAGATGGAGCTTTTTTAATCTTGATTTTT
* *
43037 GTTATTGCC-AAAAACAAACGGTGAAAAGGGGTAGTTAGATGGAGTTTTTTTAATCTTGATTT
1 GTTATTGCCGAAAAACAAACGGTGAAAAGGGGTAGTCAGATGGAGCTTTTTTAATCTTGATTT
43099 ATCAGATTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 42 0.72
64 16 0.28
ACGTcount: A:0.31, C:0.09, G:0.25, T:0.36
Consensus pattern (65 bp):
GTTATTGCCGAAAAACAAACGGTGAAAAGGGGTAGTCAGATGGAGCTTTTTTAATCTTGATTTTT
Found at i:49043 original size:6 final size:6
Alignment explanation
Indices: 49032--49067 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
49022 TTATTTCCTA
49032 CAAGAG CAAGAG CAAGAG CAAGAG CAAGAG CAAGAG
1 CAAGAG CAAGAG CAAGAG CAAGAG CAAGAG CAAGAG
49068 TTTGAGCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.17, G:0.33, T:0.00
Consensus pattern (6 bp):
CAAGAG
Found at i:52528 original size:33 final size:33
Alignment explanation
Indices: 52475--52619 Score: 170
Period size: 33 Copynumber: 4.5 Consensus size: 33
52465 TACCCTCTGG
* *
52475 GGATGGCACAACCATTGGCATGCCGCCCTGTGA
1 GGATGGCACGACCATGGGCATGCCGCCCTGTGA
*
52508 GGATGGCACGACTATGGGCATGCCGCCC--TGA
1 GGATGGCACGACCATGGGCATGCCGCCCTGTGA
* * **
52539 GGATGGCACGACTATGTGTGTGCCGCCCTGTGA
1 GGATGGCACGACCATGGGCATGCCGCCCTGTGA
* *
52572 GGATGACACGACCATGGGCAT-CTCGCCCTCTGA
1 GGATGGCACGACCATGGGCATGC-CGCCCTGTGA
*
52605 GGATGGCGCGACCAT
1 GGATGGCACGACCAT
52620 TGTCGTGCCA
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
31 28 0.29
32 1 0.01
33 66 0.69
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (33 bp):
GGATGGCACGACCATGGGCATGCCGCCCTGTGA
Found at i:52565 original size:64 final size:66
Alignment explanation
Indices: 52467--52654 Score: 222
Period size: 64 Copynumber: 2.9 Consensus size: 66
52457 ATCTATGCTA
* * * * * *
52467 CCCTCTGGGGATGGCACAACCATTGGCATGCCGCCCTGTGAGGATGGCACGACTATGGGCATGC-
1 CCCTCTGAGGATGGCACGACCATTGTCGTGCCGCCCTGTGAGGATGACACGACCATGGGCAT-CT
52531 CG
65 CG
*
52533 -CC-CTGAGGATGGCACGACTATGTGT-GTGCCGCCCTGTGAGGATGACACGACCATGGGCATCT
1 CCCTCTGAGGATGGCACGACCAT-TGTCGTGCCGCCCTGTGAGGATGACACGACCATGGGCATCT
52595 CG
65 CG
* * ** *
52597 CCCTCTGAGGATGGCGCGACCATTGTCGTGCCACCCCCTGAGGATGACACGCCCATGG
1 CCCTCTGAGGATGGCACGACCATTGTCGTGCCGCCCTGTGAGGATGACACGACCATGG
52655 TCGTGCCGTC
Statistics
Matches: 104, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
63 1 0.01
64 50 0.48
65 9 0.09
66 44 0.42
ACGTcount: A:0.18, C:0.31, G:0.32, T:0.19
Consensus pattern (66 bp):
CCCTCTGAGGATGGCACGACCATTGTCGTGCCGCCCTGTGAGGATGACACGACCATGGGCATCTC
G
Found at i:52673 original size:33 final size:33
Alignment explanation
Indices: 52616--52678 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
52606 GATGGCGCGA
* * *
52616 CCATTGTCGTGCCACCCCCTGAGGATGACACGC
1 CCATGGTCGTGCCACCCCCGGAGGACGACACGC
**
52649 CCATGGTCGTGCCGTCCCCGGAGGACGACA
1 CCATGGTCGTGCCACCCCCGGAGGACGACA
52679 TAGATCAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.17, C:0.38, G:0.29, T:0.16
Consensus pattern (33 bp):
CCATGGTCGTGCCACCCCCGGAGGACGACACGC
Found at i:52673 original size:66 final size:66
Alignment explanation
Indices: 52505--52654 Score: 173
Period size: 66 Copynumber: 2.3 Consensus size: 66
52495 TGCCGCCCTG
* * * *
52505 TGAGGATGGCACGACTATGGGCATGC-CGCCCT--GAGGATGGCACGACTATGTGTGTGCCGCCC
1 TGAGGATGACACGACCATGGGCAT-CTCGCCCTCGGAGGATGGCACGACCATGTGTGTGCCACCC
**
52567 TG
65 CC
* *
52569 TGAGGATGACACGACCATGGGCATCTCGCCCTCTGAGGATGGCGCGACCAT-TGTCGTGCCACCC
1 TGAGGATGACACGACCATGGGCATCTCGCCCTCGGAGGATGGCACGACCATGTGT-GTGCCACCC
52633 CC
65 CC
*
52635 TGAGGATGACACGCCCATGG
1 TGAGGATGACACGACCATGG
52655 TCGTGCCGTC
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 28 0.38
65 3 0.04
66 42 0.57
ACGTcount: A:0.19, C:0.30, G:0.33, T:0.19
Consensus pattern (66 bp):
TGAGGATGACACGACCATGGGCATCTCGCCCTCGGAGGATGGCACGACCATGTGTGTGCCACCCC
C
Found at i:52710 original size:13 final size:13
Alignment explanation
Indices: 52689--52718 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
52679 TAGATCAATT
*
52689 TTTTTAAAAATAA
1 TTTTAAAAAATAA
52702 TTTTAAAAAATAA
1 TTTTAAAAAATAA
52715 TTTT
1 TTTT
52719 TTATGTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAAAAAATAA
Found at i:55019 original size:21 final size:21
Alignment explanation
Indices: 54993--55037 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
54983 AGACAAATAA
54993 AATTTTTAGAAGGAGACTTAT
1 AATTTTTAGAAGGAGACTTAT
* *
55014 AATTTTTAGAAGGGGACTTTT
1 AATTTTTAGAAGGAGACTTAT
55035 AAT
1 AAT
55038 ATTAGAGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (21 bp):
AATTTTTAGAAGGAGACTTAT
Found at i:59156 original size:39 final size:40
Alignment explanation
Indices: 59111--59221 Score: 136
Period size: 39 Copynumber: 2.8 Consensus size: 40
59101 TCTCTCTCCC
*
59111 CAAAGTCCCCAAACACATATAACACAGGGGCAACTCT-CT
1 CAAAGTCCCCAAACACATATAACACAGGGGCAACTATACT
* ** *
59150 CAAAGTCCTCAAACACATATAACACAGATGCATCTATACT
1 CAAAGTCCCCAAACACATATAACACAGGGGCAACTATACT
* * *
59190 -AAAGTCCCTAAACACATATAACATAAGGGCAA
1 CAAAGTCCCCAAACACATATAACACAGGGGCAA
59222 TTTTCTTCTC
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
39 57 0.97
40 2 0.03
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.18
Consensus pattern (40 bp):
CAAAGTCCCCAAACACATATAACACAGGGGCAACTATACT
Found at i:63070 original size:35 final size:34
Alignment explanation
Indices: 63031--63115 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 34
63021 ATTTCATCAG
*
63031 ATTCAACACTTGGGGACTCCAACAACCCCTTCATC
1 ATTCAACACTTGGGG-CTCCAACAACCCATTCATC
* * *
63066 ATTCAACAATTGGGTGCTCCAACAACTCATTCTTC
1 ATTCAACACTTGGG-GCTCCAACAACCCATTCATC
63101 ATTC-ACTACTTGGGG
1 ATTCAAC-ACTTGGGG
63116 GCTTCAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
34 3 0.07
35 39 0.91
36 1 0.02
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.28
Consensus pattern (34 bp):
ATTCAACACTTGGGGCTCCAACAACCCATTCATC
Found at i:63571 original size:72 final size:72
Alignment explanation
Indices: 63483--63830 Score: 470
Period size: 72 Copynumber: 4.8 Consensus size: 72
63473 CCCATGGTCT
* * * *
63483 TCTTCTTCATTGCGATTGTAGCCGAGGTAGTTCCCACATTTGGCAGCCCTTCACATAATCCTTAC
1 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCATAATCCTTAC
63548 ATGATAA
66 ATGATAA
* * * * *
63555 TC-ACCTTCATTACGATTGTAGCCGTGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTC
1 TCTTCC-TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCATAATCCTTA
63619 CATGATAA
65 CATGATAA
* *
63627 TCTTCCAT-ATTGCGGTTGTAGCCGAGGCAATTCCCACATTTGGCTA-TCCTTCGCATAATCCTT
1 TCTTCC-TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGC-AGTCCTTCGCATAATCCTT
* *
63690 ACGTGATTA
64 ACATGATAA
* * *
63699 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCAAATTTGCCAGTCCTTCGCATAATCCTTAT
1 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCATAATCCTTAC
* *
63764 GTGATTA
66 ATGATAA
*
63771 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCC
1 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCATAATCC
63831 ATGCTACTAC
Statistics
Matches: 244, Mismatches: 27, Indels: 11
0.87 0.10 0.04
Matches are distributed among these distances:
71 23 0.09
72 217 0.89
73 4 0.02
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.32
Consensus pattern (72 bp):
TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCATAATCCTTAC
ATGATAA
Found at i:64626 original size:19 final size:19
Alignment explanation
Indices: 64602--64638 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
64592 GCAACAAAGC
*
64602 TCGAAGCAGACTATCACAT
1 TCGAAGCACACTATCACAT
*
64621 TCGAAGCTCACTATCACA
1 TCGAAGCACACTATCACA
64639 AAATGGAGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
TCGAAGCACACTATCACAT
Found at i:75037 original size:26 final size:26
Alignment explanation
Indices: 75003--75052 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
74993 ATCCCTCTTG
* *
75003 AAAAAAAAATGAGTGTTAGTAACCTC
1 AAAAAAAAAAGAGAGTTAGTAACCTC
* *
75029 AAAAGAAAAAGGGAGTTAGTAACC
1 AAAAAAAAAAGAGAGTTAGTAACC
75053 CCTAAATCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.52, C:0.10, G:0.20, T:0.18
Consensus pattern (26 bp):
AAAAAAAAAAGAGAGTTAGTAACCTC
Found at i:77759 original size:39 final size:39
Alignment explanation
Indices: 77715--77817 Score: 138
Period size: 39 Copynumber: 2.6 Consensus size: 39
77705 CCCAAAGTCC
* *
77715 CCAAACACATATAACACAGGGGCAACTCT-CTCAAAGTT
1 CCAAACACATATAACACAAGGGCAACTATACTCAAAGTT
* *
77753 CTCAAACACATATAACACAAAGGCATCTATACT-AAAGTT
1 C-CAAACACATATAACACAAGGGCAACTATACTCAAAGTT
77792 CCTAAACACATATAACACAAGGGCAA
1 CC-AAACACATATAACACAAGGGCAA
77818 TTTTCTTCTC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.04
39 52 0.93
40 2 0.04
ACGTcount: A:0.45, C:0.26, G:0.11, T:0.18
Consensus pattern (39 bp):
CCAAACACATATAACACAAGGGCAACTATACTCAAAGTT
Found at i:79775 original size:31 final size:31
Alignment explanation
Indices: 79736--79807 Score: 119
Period size: 31 Copynumber: 2.3 Consensus size: 31
79726 CTTGCAACAT
*
79736 GGCTTATTTGGCTTTTTTTTAAGAGTTCAG-
1 GGCTTATTTGGCATTTTTTTAAGAGTTCAGA
79766 GAGCTTATTTGGCATTTTTTTAAGAGTTCAGA
1 G-GCTTATTTGGCATTTTTTTAAGAGTTCAGA
79798 GGCTTATTTG
1 GGCTTATTTG
79808 ACGGTTCGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 1 0.03
31 37 0.95
32 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.47
Consensus pattern (31 bp):
GGCTTATTTGGCATTTTTTTAAGAGTTCAGA
Found at i:89338 original size:14 final size:14
Alignment explanation
Indices: 89311--89349 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
89301 GAACTCACTG
* *
89311 ATGAGTTTAGCTCA
1 ATGAGCTTAACTCA
89325 ATGAGCTTAACTCA
1 ATGAGCTTAACTCA
89339 ATGAGCTTAAC
1 ATGAGCTTAAC
89350 GACTGTATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (14 bp):
ATGAGCTTAACTCA
Found at i:90194 original size:13 final size:12
Alignment explanation
Indices: 90164--90206 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
90154 CATCGATACC
90164 TCGATATATCCG
1 TCGATATATCCG
90176 TCGATATATCCG
1 TCGATATATCCG
90188 TTCGATATATCCG
1 -TCGATATATCCG
*
90201 ACGATA
1 TCGATA
90207 CCTGTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:90584 original size:25 final size:25
Alignment explanation
Indices: 90539--90587 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
90529 TTTTAAACTC
*
90539 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
90564 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
90588 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:90587 original size:21 final size:21
Alignment explanation
Indices: 90506--90589 Score: 66
Period size: 22 Copynumber: 3.9 Consensus size: 21
90496 CCGTTTAGTA
* *
90506 ATTTAATATGTATTATTTATTT
1 ATTTAAAATATATTA-TTATTT
* *
90528 ATTTTAAACT-CATTATT-TATT
1 A-TTTAAAATATATTATTAT-TT
90549 ATTTAAAATATATTTATTATTT
1 ATTTAAAATATA-TTATTATTT
90571 ATTTAATAATATA-TATTAT
1 ATTTAA-AATATATTATTAT
90590 ATCTAAGATA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
20 8 0.16
21 12 0.24
22 18 0.35
23 13 0.25
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (21 bp):
ATTTAAAATATATTATTATTT
Found at i:94261 original size:110 final size:110
Alignment explanation
Indices: 94020--94247 Score: 399
Period size: 109 Copynumber: 2.1 Consensus size: 110
94010 CTAATATCTT
94020 TATCTTTATAATTACTTTATTTTTACCAAAAAAATTTGGATATACTAAAATTTTTTCTAATATAC
1 TATCTTTATAATTACTTTATTTTTACCAAAAAAATTTGGATATACTAAAATTTTTTCTAATATAC
94085 AATTTTATTCTACTAAAAACTCAATTTTCATTTAATTAAATCTAA
66 AATTTTATTCTACTAAAAACTCAATTTTCATTTAATTAAATCTAA
*
94130 TATCTTTATAATTACTTTATTTTTACCAAAAAAA-TTGGATATATTAAAATTTTTTCTAATATAC
1 TATCTTTATAATTACTTTATTTTTACCAAAAAAATTTGGATATACTAAAATTTTTTCTAATATAC
* *
94194 AATTTTATTTTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAA
66 AATTTTATTCTACTAAAAACTCAATTTTCATTTAATTAAATCT-AA
94239 TAT-TTTATA
1 TATCTTTATA
94248 TTTTTTTTAT
Statistics
Matches: 114, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
108 7 0.06
109 73 0.64
110 34 0.30
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (110 bp):
TATCTTTATAATTACTTTATTTTTACCAAAAAAATTTGGATATACTAAAATTTTTTCTAATATAC
AATTTTATTCTACTAAAAACTCAATTTTCATTTAATTAAATCTAA
Found at i:96296 original size:86 final size:85
Alignment explanation
Indices: 96151--96318 Score: 293
Period size: 86 Copynumber: 2.0 Consensus size: 85
96141 TCTATTTTTA
*
96151 TTTAACTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTA-AAA
1 TTTAACTAAATCCAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTACAAA
96215 AATCTTAGATATATTAGAAGTG
66 AA--TTAGATATATTAGAAGTG
*
96237 TTTAATTAAATCCAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTACAAA
1 TTTAACTAAATCCAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTACAAA
96302 AATTAGATATATTAGAA
66 AATTAGATATATTAGAA
96319 TATTTTAAAT
Statistics
Matches: 79, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
85 15 0.19
86 59 0.75
87 5 0.06
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.49
Consensus pattern (85 bp):
TTTAACTAAATCCAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTACAAA
AATTAGATATATTAGAAGTG
Found at i:96929 original size:33 final size:33
Alignment explanation
Indices: 96892--96955 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
96882 AATTATTTTA
*
96892 TTTTTACCA-TTTTACTATTTTATTTAAAAAAAC
1 TTTTTA-CATTTTTACTATTTTAATTAAAAAAAC
96925 TTTTTACATTTTTACTATTTTAATTAAAAAA
1 TTTTTACATTTTTACTATTTTAATTAAAAAA
96956 TTAGATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.07
33 27 0.93
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (33 bp):
TTTTTACATTTTTACTATTTTAATTAAAAAAAC
Found at i:99353 original size:14 final size:13
Alignment explanation
Indices: 99319--99363 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
99309 CTTCCTCAGT
99319 TCCTTTTTAATTG
1 TCCTTTTTAATTG
*
99332 T-CTCTTTTCATTG
1 TCCT-TTTTAATTG
99345 TTCCTTTTTAATTG
1 -TCCTTTTTAATTG
99359 TCCTT
1 TCCTT
99364 CATATTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 2 0.07
13 14 0.52
14 9 0.33
15 2 0.07
ACGTcount: A:0.11, C:0.20, G:0.07, T:0.62
Consensus pattern (13 bp):
TCCTTTTTAATTG
Found at i:108309 original size:20 final size:20
Alignment explanation
Indices: 108272--108310 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
108262 TTACTATTAT
108272 TTTTGAATTTAATGTTTTAC
1 TTTTGAATTTAATGTTTTAC
*
108292 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATGTTTTA
108311 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATGTTTTAC
Found at i:108510 original size:22 final size:22
Alignment explanation
Indices: 108482--108710 Score: 205
Period size: 22 Copynumber: 10.3 Consensus size: 22
108472 TGTCTCTGTG
*
108482 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
108504 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
108527 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
108548 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
*
108571 -AGTTATCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
*
108592 AGGTTATCAAAATTTCATAGCG-
1 TGGTTATCAAAATTTCATAG-GA
*
108614 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * *
108636 TCAAGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAGGA
* ** *
108660 AGGTTATTGAAATTTCATAGTA
1 TGGTTATCAAAATTTCATAGGA
* * *
108682 TGGTTATCACAATTTTATAGAA
1 TGGTTATCAAAATTTCATAGGA
*
108704 AGGTTAT
1 TGGTTAT
108711 TAAAGAGATT
Statistics
Matches: 168, Mismatches: 29, Indels: 20
0.77 0.13 0.09
Matches are distributed among these distances:
21 6 0.04
22 140 0.83
23 5 0.03
24 17 0.10
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:108552 original size:44 final size:42
Alignment explanation
Indices: 108483--109112 Score: 252
Period size: 44 Copynumber: 14.4 Consensus size: 42
108473 GTCTCTGTGT
* * *
108483 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTTCAT-AGGTGGTTATCAAAATTTCAT-AGGA
* *
108527 GGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAG-GTGGTTATCAAAATTTCATA-GGA
* * *
108571 AGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGCGT
1 GGTTATCAAAATTTCATAGG-TGGTTATCAAAATTTCATAG-GA
* * * *
108615 GGTTACCAAAATTTCATAGGATCAAGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAGG-T--GGTTATCAAAATTTCATAGG-A
** * * * *
108661 GGTTATTGAAATTTCATAGTATGGTTATCACAATTTTATAGAAA
1 GGTTATCAAAATTTCATAG-GTGGTTATCAAAATTTCATAG-GA
* * * **
108705 GG-T-T----A-TT-A-AAGAGATTATCAAAATGCCATAGCGA
1 GGTTATCAAAATTTCATAGGTGGTTATCAAAATTTCATAG-GA
* *
108739 GGTTAT-AAGAATTTCATAGTGGGGTTAACAAAATTTCATAAGGA
1 GGTTATCAA-AATTTCATAG-GTGGTTATCAAAATTTCAT-AGGA
* * *
108783 GGTTA-CTAATATTTCATGGGGGAGGTTATCAAAATTTCATAGTGTA
1 GGTTATC-AAAATTTCAT--AGGTGGTTATCAAAATTTCATAG-G-A
* * *
108829 -TTTATCAAAAATTT-TTAGTGTGGTTATCAAAATTTCATATGAA
1 GGTTATC-AAAATTTCATAG-GTGGTTATCAAAATTTCATA-GGA
* * * * *
108872 GGTTATAAAAGTCTCAATTTCATAAGG-AG-TACCAAAATTTGATAGAA
1 GGTTAT-CAA-----AATTTCAT-AGGTGGTTATCAAAATTTCATAGGA
* * ** *
108919 GGTTATC-AAATCTCATAGAGTGATTATTGAAATTTCCTAGAGA
1 GGTTATCAAAATTTCATAG-GTGGTTATCAAAATTTCATAG-GA
* * * *
108962 TCGGATTATCAAAATTT-ATAGGAAGATTATCAAAATTTCATACTGT
1 --GG-TTATCAAAATTTCATAGG-TGGTTATCAAAATTTCATA-GGA
* * * * * * *
109008 TGTTATCAAAATTTCAAAATGAGGTTATCAAAATTACATAATGT
1 GGTTATCAAAATTTC-ATAGGTGGTTATCAAAATTTCAT-AGGA
* * * *
109052 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTT-ATAGAGA
1 GGTTATCAAAATTTCATAG-GTGGTTATCAAAATTTCATAG-GA
109095 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
109113 AAGAGGTAAT
Statistics
Matches: 440, Mismatches: 93, Indels: 107
0.69 0.15 0.17
Matches are distributed among these distances:
34 17 0.04
35 2 0.00
36 2 0.00
37 2 0.00
38 1 0.00
39 2 0.00
40 9 0.02
41 2 0.00
42 14 0.03
43 44 0.10
44 205 0.47
45 36 0.08
46 67 0.15
47 14 0.03
48 13 0.03
49 6 0.01
50 2 0.00
51 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (42 bp):
GGTTATCAAAATTTCATAGGTGGTTATCAAAATTTCATAGGA
Found at i:108585 original size:66 final size:65
Alignment explanation
Indices: 108479--108714 Score: 267
Period size: 66 Copynumber: 3.5 Consensus size: 65
108469 TCTTGTCTCT
* * * * *
108479 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATAGGA-AGTTATTAAAATTTCAT-AGGAAGGTTATCAAAATTTCA
108543 TA
64 TA
*
108545 GTGTGGTTACCAAAATTTCATATGGAAGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT
1 GTGTGGTTACCAAAATTTCATA-GGAAGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTCAT
108610 A
65 A
* * **
108611 GCGTGGTTACCAAAATTTCATAGGATCAAGTTATTAAAATTTCTTAGGAAGGTTATTGAAATTTC
1 GTGTGGTTACCAAAATTTCATAGG---AAGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTC
108676 ATA
63 ATA
* * * * *
108679 GTATGGTTATCACAATTTTATAGAAAGGTTATTAAA
1 GTGTGGTTACCAAAATTTCATAGGAA-GTTATTAAA
108715 GAGATTATCA
Statistics
Matches: 147, Mismatches: 17, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
65 7 0.05
66 83 0.56
67 2 0.01
68 55 0.37
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.37
Consensus pattern (65 bp):
GTGTGGTTACCAAAATTTCATAGGAAGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTCATA
Found at i:108819 original size:23 final size:22
Alignment explanation
Indices: 108719--109132 Score: 98
Period size: 22 Copynumber: 18.6 Consensus size: 22
108709 ATTAAAGAGA
**
108719 TTATCAAAATGCCAT-AGCGAGG
1 TTATCAAAATTTCATGAG-GAGG
*
108741 TTAT-AAGAATTTCAT-AGTGGGG
1 TTATCAA-AATTTCATGAG-GAGG
* *
108763 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCATGAGGAGG
* *
108785 TTA-CTAATATTTCATGGGGGAGG
1 TTATC-AAAATTTCAT-GAGGAGG
*
108808 TTATCAAAATTTCAT-AGTGTA-T
1 TTATCAAAATTTCATGAG-G-AGG
* *
108830 TTATCAAAAATTT--TTAGTGTGG
1 TTATC-AAAATTTCATGAG-GAGG
*
108852 TTATCAAAATTTCAT-ATGAAGG
1 TTATCAAAATTTCATGA-GGAGG
* *
108874 TTATAAAAGTCTCAATTTCATAAGGA-G
1 TTAT-CAA-----AATTTCATGAGGAGG
* * *
108901 -TACCAAAATTTGAT-AGAAGG
1 TTATCAAAATTTCATGAGGAGG
*
108921 TTATC-AAATCTCAT-A-GAGTG
1 TTATCAAAATTTCATGAGGAG-G
** *
108941 ATTATTGAAATTTCCT-AGAGATCGG
1 -TTATCAAAATTTCATGAG-GA--GG
*
108966 ATTATCAAAATTT-AT-AGGAAGA
1 -TTATCAAAATTTCATGAGG-AGG
* **
108988 TTATCAAAATTTCAT-ACTGTTG
1 TTATCAAAATTTCATGA-GGAGG
** *
109010 TTATCAAAATTTCAAAATGAGG
1 TTATCAAAATTTCATGAGGAGG
* * * * *
109032 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATGAGGAGG
109054 TTATCAAAATTTCATAGAGG-GG
1 TTATCAAAATTTCAT-GAGGAGG
* *
109076 TCAACAAAATTT-AT-AGAGAGG
1 TTATCAAAATTTCATGAG-GAGG
* *
109097 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATGAGGAGG
* *
109119 TAATCAAATTTTCA
1 TTATCAAAATTTCA
109133 AAATTTGATT
Statistics
Matches: 298, Mismatches: 55, Indels: 78
0.69 0.13 0.18
Matches are distributed among these distances:
19 7 0.02
20 18 0.06
21 45 0.15
22 153 0.51
23 39 0.13
24 7 0.02
25 14 0.05
26 3 0.01
27 1 0.00
28 10 0.03
29 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATGAGGAGG
Found at i:108842 original size:146 final size:144
Alignment explanation
Indices: 108573--108843 Score: 305
Period size: 146 Copynumber: 1.9 Consensus size: 144
108563 CATATGGAAG
** * *
108573 TTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGCGTGGTTACCAAAATTTCATAGGATC
1 TTATCAAAATGCCATAGGAAGGTTATCAAAATTTCATAGCGGGGTTAACAAAATTTCATAGGA--
* * ** * *
108638 AAGTTATTAAAATTTCTTAGGAAGGTTATTGAAATTTCATAGTATGGTTATCACAATTTTATAGA
64 AAGTTACTAAAATTTCTGAGGAAGGTTATCAAAATTTCATAGTATAGTTATCAAAATTTTATAGA
108703 AAGGTTATTAAAGAGA
129 AAGGTTATTAAAGAGA
*
108719 TTATCAAAATGCCATAGCG-AGGTTAT-AAGAATTTCATAGTGGGGTTAACAAAATTTCATAAGG
1 TTATCAAAATGCCATAG-GAAGGTTATCAA-AATTTCATAGCGGGGTTAACAAAATTTCAT-AGG
* * * * * *
108782 -AGGTTACTAATATTTCATGGGGGAGGTTATCAAAATTTCATAGTGTATTTATCAAAAATTTT
63 AAAGTTACTAAAATTTC-TGAGGAAGGTTATCAAAATTTCATAGTATAGTTATC-AAAATTTT
108844 TAGTGTGGTT
Statistics
Matches: 103, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
144 13 0.13
145 30 0.29
146 56 0.54
147 4 0.04
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (144 bp):
TTATCAAAATGCCATAGGAAGGTTATCAAAATTTCATAGCGGGGTTAACAAAATTTCATAGGAAA
GTTACTAAAATTTCTGAGGAAGGTTATCAAAATTTCATAGTATAGTTATCAAAATTTTATAGAAA
GGTTATTAAAGAGA
Found at i:109084 original size:66 final size:65
Alignment explanation
Indices: 108986--109113 Score: 159
Period size: 66 Copynumber: 2.0 Consensus size: 65
108976 TTTATAGGAA
* ** * *
108986 GATTATCAAAATTTCATACTGTTGTTATCAAAATTTCA-AAATGAGGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATACAGGGGTCAACAAAATTT-ATAAA-GAGGTTATCAAAATTACATAAT
109050 GT
64 GT
* * *
109052 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTATAGAGAGGTTATCAAAATTTCATAA
1 GATTATCAAAATTTCATACAGGGGTCAACAAAATTTATAAAGAGGTTATCAAAATTACATAA
109114 AGAGGTAATC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
65 21 0.40
66 32 0.60
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (65 bp):
GATTATCAAAATTTCATACAGGGGTCAACAAAATTTATAAAGAGGTTATCAAAATTACATAATGT
Found at i:109124 original size:22 final size:22
Alignment explanation
Indices: 108967--109132 Score: 135
Period size: 22 Copynumber: 7.6 Consensus size: 22
108957 AGAGATCGGA
108967 TTATCAAAATTT-ATAGGAAGA--
1 TTATCAAAATTTCATA--AAGAGG
** **
108988 TTATCAAAATTTCATACTGTTG
1 TTATCAAAATTTCATAAAGAGG
109010 TTATCAAAATTTCA-AAATGAGG
1 TTATCAAAATTTCATAAA-GAGG
* * * *
109032 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAAGAGG
* *
109054 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAAAGAGG
* * *
109076 TCAACAAAATTT-ATAGAGAGG
1 TTATCAAAATTTCATAAAGAGG
109097 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
* *
109119 TAATCAAATTTTCA
1 TTATCAAAATTTCA
109133 AAATTTGATT
Statistics
Matches: 115, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
20 1 0.01
21 31 0.27
22 81 0.70
23 2 0.02
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:109333 original size:44 final size:44
Alignment explanation
Indices: 109275--109380 Score: 130
Period size: 44 Copynumber: 2.4 Consensus size: 44
109265 TTTCATATTA
*
109275 AGATTAT-AAAATTTCATAGT-T-TAGTTTTCAAAATTCCATAA-G
1 AGATTATCAAAATTTCATAGTATGTAG--ATCAAAATTCCATAAGG
*
109317 AGAGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAAGG
1 AGA-TTATCAAAATTTCATAGTATGTAGATCAAAATTCCATAAGG
*
109362 AGATTAACAAAATTTCATA
1 AGATTATCAAAATTTCATA
109381 ATAAGGTTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
42 3 0.05
43 4 0.07
44 41 0.73
45 5 0.09
46 3 0.05
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (44 bp):
AGATTATCAAAATTTCATAGTATGTAGATCAAAATTCCATAAGG
Found at i:109395 original size:22 final size:22
Alignment explanation
Indices: 109257--109549 Score: 106
Period size: 22 Copynumber: 13.6 Consensus size: 22
109247 TCAGGGAGGA
* *
109257 TATCAAAATTTCATATTAAGAT
1 TATCAAAATTTCATAATAAGGT
* *
109279 TAT-AAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-ATAAGGT
* * *
109300 TTTCAAAATTCCATAA-GAGAGT
1 TATCAAAATTTCATAATAAG-GT
* *
109322 TATCAAAATTTCATAGT-ATGT
1 TATCAAAATTTCATAATAAGGT
* ** *
109343 AGATCAAAATTTCATAAGGAGAT
1 -TATCAAAATTTCATAATAAGGT
*
109366 TAACAAAATTTCATAATAAGGT
1 TATCAAAATTTCATAATAAGGT
* ** ***
109388 TATGAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAATAAGGT
*
109410 TATCAAAA-TT--T-GT-A-GT
1 TATCAAAATTTCATAATAAGGT
* * **
109426 TATCAAGATTTCTTAAGGAGGT
1 TATCAAAATTTCATAATAAGGT
* ** *
109448 TATCAAAATTTTA-AAGGGAGATT
1 TATCAAAATTTCATAA-TAAG-GT
* * **
109471 TATTAAAATTTTATAGGAAGGTT
1 TATCAAAATTTCATAATAAGG-T
109494 TATC-AAATTTCATAATAAGGT
1 TATCAAAATTTCATAATAAGGT
* * ** *
109515 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAATAAGGT
109537 TATCAAAATTTCA
1 TATCAAAATTTCA
109550 GATTGTGATT
Statistics
Matches: 202, Mismatches: 51, Indels: 36
0.70 0.18 0.12
Matches are distributed among these distances:
16 9 0.04
17 3 0.01
18 1 0.00
19 2 0.01
20 1 0.00
21 25 0.12
22 138 0.68
23 22 0.11
24 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATAATAAGGT
Found at i:109495 original size:23 final size:23
Alignment explanation
Indices: 109447--109500 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
109437 CTTAAGGAGG
*
109447 TTATCAAAATTTTAAAGGGAGAT
1 TTATCAAAATTTTAAAGGAAGAT
* * *
109470 TTATTAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTAAAGGAAGAT
109493 TTATCAAA
1 TTATCAAA
109501 TTTCATAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTAAAGGAAGAT
Found at i:109556 original size:22 final size:22
Alignment explanation
Indices: 109514--109560 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
109504 CATAATAAGG
* *
109514 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
*
109536 TTATCAAAATTTCAGATTGTGA
1 TTATCAAAATTTCAGAGTGTGA
109558 TTA
1 TTA
109561 CTAACAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:109616 original size:22 final size:22
Alignment explanation
Indices: 109591--109653 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
109581 TTTTAAATTT
*
109591 TCATAACGTGGTTATCAATATA
1 TCATAACGTGGTTATCAACATA
** * *
109613 TCATATGGAGGTTATCAACATC
1 TCATAACGTGGTTATCAACATA
**
109635 TCATAGTGTTGGTTATCAA
1 TCATAACG-TGGTTATCAA
109654 AATTTCATTG
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 23 0.72
23 9 0.28
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (22 bp):
TCATAACGTGGTTATCAACATA
Found at i:109672 original size:45 final size:45
Alignment explanation
Indices: 109599--109687 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
109589 TTTCATAACG
* * *
109599 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
109644 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATAGTG
109688 AGGTCTTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:109701 original size:22 final size:22
Alignment explanation
Indices: 109601--109685 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 22
109591 TCATAACGTG
* * * *
109601 GTTATCAATATATCATATGGAG
1 GTTATCAAAATTTCATAGGGAA
* * ***
109623 GTTATCAACATCTCATAGTGTTG
1 GTTATCAAAATTTCATAG-GGAA
*
109646 GTTATCAAAATTTCATTGGGAA
1 GTTATCAAAATTTCATAGGGAA
109668 GTTATCAAAATTTCATAG
1 GTTATCAAAATTTCATAG
109686 TGAGGTCTTC
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 33 0.66
23 17 0.34
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGGAA
Found at i:110014 original size:2 final size:2
Alignment explanation
Indices: 110007--110040 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
109997 TTAAAACTAT
110007 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
110041 AAACTAAACA
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):
TA
Found at i:112480 original size:13 final size:13
Alignment explanation
Indices: 112462--112494 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
112452 TTACTCACGG
112462 AAGTCAACGGTCA
1 AAGTCAACGGTCA
112475 AAGTCAACGGTCA
1 AAGTCAACGGTCA
*
112488 AGGTCAA
1 AAGTCAA
112495 AGTCAGCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.15
Consensus pattern (13 bp):
AAGTCAACGGTCA
Found at i:113527 original size:12 final size:12
Alignment explanation
Indices: 113510--113552 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
113500 TAAATACAGG
*
113510 TATCGATGGATA
1 TATCGACGGATA
113522 TATCGAACGGATA
1 TATCG-ACGGATA
*
113535 TATCGACAGATA
1 TATCGACGGATA
113547 TATCGA
1 TATCGA
113553 GGTATCAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:113726 original size:11 final size:11
Alignment explanation
Indices: 113712--113740 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
113702 ATATGTAGAC
113712 TATTTTTTTTT
1 TATTTTTTTTT
113723 TA-TTTTTTTT
1 TATTTTTTTTT
113733 TATTTTTT
1 TATTTTTT
113741 GTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (11 bp):
TATTTTTTTTT
Found at i:113730 original size:10 final size:10
Alignment explanation
Indices: 113715--113740 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
113705 TGTAGACTAT
113715 TTTTTTTTTA
1 TTTTTTTTTA
113725 TTTTTTTTTA
1 TTTTTTTTTA
113735 TTTTTT
1 TTTTTT
113741 GTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTA
Done.