Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000450.1 Kokia drynarioides strain JFW-HI SEQ_111303, 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: 58704
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Found at i:34 original size:11 final size:11
Alignment explanation
Indices: 14--48 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
4 GAAAATAATT
*
14 TTAAACTTAAA
1 TTAAATTTAAA
25 TTAAATTTAAA
1 TTAAATTTAAA
*
36 ATAAATTTAAA
1 TTAAATTTAAA
47 TT
1 TT
49 TTTAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:35 original size:17 final size:17
Alignment explanation
Indices: 21--80 Score: 79
Period size: 16 Copynumber: 3.6 Consensus size: 17
11 ATTTTAAACT
21 TAAA-TTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
37 TAAATTTAAATTTTTAAA
1 TAAATTTAAA-TTTAAAA
*
55 CAAATTT-AATTTAAAA
1 TAAATTTAAATTTAAAA
71 TAAATTTAAA
1 TAAATTTAAA
81 GGGAATATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 16 0.43
17 9 0.24
18 12 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:66 original size:34 final size:35
Alignment explanation
Indices: 12--80 Score: 113
Period size: 34 Copynumber: 2.0 Consensus size: 35
2 TTGAAAATAA
12 TTTTAAACTTAAATTAAATTTAAAATAAATTTAAAT
1 TTTTAAAC-TAAATTAAATTTAAAATAAATTTAAAT
*
48 TTTTAAAC-AAATTTAATTTAAAATAAATTTAAA
1 TTTTAAACTAAATTAAATTTAAAATAAATTTAAA
81 GGGAATATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 24 0.75
36 8 0.25
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (35 bp):
TTTTAAACTAAATTAAATTTAAAATAAATTTAAAT
Found at i:1001 original size:20 final size:18
Alignment explanation
Indices: 955--1001 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 18
945 AAAAATACTA
*
955 AAAATATTTAATTAATTT
1 AAAATAATTAATTAATTT
973 AAAATTAATTATATTAATATT
1 AAAA-TAATTA-ATTAAT-TT
994 AAAATAAT
1 AAAATAAT
1002 ATAAAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 4 0.16
19 5 0.20
20 10 0.40
21 6 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATAATTAATTAATTT
Found at i:5783 original size:43 final size:42
Alignment explanation
Indices: 5645--5909 Score: 248
Period size: 41 Copynumber: 6.3 Consensus size: 42
5635 AGGGTGATAG
* * * * * *
5645 TTTATTTGCAAATATGCTATGCATCCACAGCCTAGTGGTAG-
1 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGGCAGT
* * * * *
5686 TTTATCTTCAAATATGTTATGCATCCACAGCCTAGTGGCA-A
1 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGGCAGT
* * * * *
5727 TTTATTTGCAAATATGGTGTGCATCCACAGCCCAATGGTAGTT
1 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGGCAG-T
* *
5770 TTTATCTGCAAATATGTTGTGCATACACAATCCAGTGGCAGTT
1 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGGCAG-T
* * *
5813 TTTATTTTCAAATATGTTGTGCATCCACAACCCAATGGCAG-
1 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGGCAGT
* * **
5854 TTTATCTGTAAATATGTTGTGCATCTACAACCCAGTGATAGTT
1 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGGCAG-T
*
5897 TTTATCTACAAAT
1 TTTATCTGCAAAT
5910 CAATGGTGGT
Statistics
Matches: 186, Mismatches: 33, Indels: 8
0.82 0.15 0.04
Matches are distributed among these distances:
41 103 0.55
43 83 0.45
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (42 bp):
TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGGCAGT
Found at i:5858 original size:84 final size:83
Alignment explanation
Indices: 5645--5901 Score: 302
Period size: 84 Copynumber: 3.1 Consensus size: 83
5635 AGGGTGATAG
* * * * *
5645 TTTATTTGCAAATATGCTATGCATCCACAGCCTAGTGGTAGTTTATCTTCAAATATGTTATGCAT
1 TTTATTTGCAAATATGCTGTGCATCCACAGCCCAATGGTAGTTTATCTGCAAATATGTTGTGCAT
* * *
5710 CCACAGCCTAGTGGCA--A
66 -CACAACCCAGTGGCAGTT
*
5727 TTTATTTGCAAATATGGTGTGCATCCACAGCCCAATGGTAGTTTTTATCTGCAAATATGTTGTGC
1 TTTATTTGCAAATATGCTGTGCATCCACAGCCCAATGGTAG--TTTATCTGCAAATATGTTGTGC
*
5792 ATACACAATCCAGTGGCAGTT
64 AT-CACAACCCAGTGGCAGTT
* * * * *
5813 TTTATTTTCAAATATGTTGTGCATCCACAACCCAATGGCAGTTTATCTGTAAATATGTTGTGCAT
1 TTTATTTGCAAATATGCTGTGCATCCACAGCCCAATGGTAGTTTATCTGCAAATATGTTGTGCAT
**
5878 CTACAACCCAGTGATAGTT
66 C-ACAACCCAGTGGCAGTT
5897 TTTAT
1 TTTAT
5902 CTACAAATCA
Statistics
Matches: 151, Mismatches: 19, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
82 37 0.25
83 1 0.01
84 76 0.50
86 37 0.25
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (83 bp):
TTTATTTGCAAATATGCTGTGCATCCACAGCCCAATGGTAGTTTATCTGCAAATATGTTGTGCAT
CACAACCCAGTGGCAGTT
Found at i:7736 original size:21 final size:20
Alignment explanation
Indices: 7691--7742 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
7681 TGTACTAGTT
*
7691 CTACCGATACAAGTATGATTT
1 CTACCGATACAAGTATGA-TA
7712 CTACCGATACAAGTCATGCA-A
1 CTACCGATACAAGT-ATG-ATA
7733 CTACCGATAC
1 CTACCGATAC
7743 CAAAAACACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 24 0.86
22 3 0.11
23 1 0.04
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (20 bp):
CTACCGATACAAGTATGATA
Found at i:17121 original size:45 final size:45
Alignment explanation
Indices: 17054--17159 Score: 140
Period size: 45 Copynumber: 2.4 Consensus size: 45
17044 CTATTTGGCT
* * * *
17054 TTTGTGGCATTGTGTTCGCCATTATGACGTATTTTTTATGTTCCC
1 TTTGTGGCATTCTGTTCACCATTATGACGTATTCTATATGTTCCC
* * * *
17099 TTTGTGGCATTTTGTTCACCATTGTGGCGTATTCTATATGTTGCC
1 TTTGTGGCATTCTGTTCACCATTATGACGTATTCTATATGTTCCC
17144 TTTGTGGCATTCTGTT
1 TTTGTGGCATTCTGTT
17160 GGGCCTTTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (45 bp):
TTTGTGGCATTCTGTTCACCATTATGACGTATTCTATATGTTCCC
Found at i:17166 original size:21 final size:21
Alignment explanation
Indices: 17141--17180 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17131 TCTATATGTT
*
17141 GCCTTTGT-GGCATTCTGTTGG
1 GCCTTT-TCGGCATTATGTTGG
17162 GCCTTTTCGGCATTATGTT
1 GCCTTTTCGGCATTATGTT
17181 TACCATTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.07, C:0.20, G:0.28, T:0.45
Consensus pattern (21 bp):
GCCTTTTCGGCATTATGTTGG
Found at i:19289 original size:29 final size:29
Alignment explanation
Indices: 19257--19616 Score: 162
Period size: 29 Copynumber: 12.5 Consensus size: 29
19247 ACCTGGGAGC
*
19257 AAAATGATAACTTTTGGATGTTCGAGGGT
1 AAAATGATAATTTTTGGATGTTCGAGGGT
** * *
19286 AAAAT-AGTAATTTTTGGATACTCGGGGGC
1 AAAATGA-TAATTTTTGGATGTTCGAGGGT
* *
19315 AAAAAGATAA-TTTTGGATGTTCGGGGGT
1 AAAATGATAATTTTTGGATGTTCGAGGGT
* * ***
19343 --AATGGTAAATTTTGGACACTC-AGGGGT
1 AAAATGATAATTTTTGGATGTTCGA-GGGT
19370 AAAAT-AGTAATTTTTGGATGTTC-AGGGCT
1 AAAATGA-TAATTTTTGGATGTTCGAGGG-T
* * * * *
19399 AAAAATGGTAATTTTTGAAAAGTTTGGGGGTT
1 -AAAATGATAATTTTTG-GATGTTCGAGGG-T
* *
19431 GAAAATG-TAA-TTTTGGATATTCAAGGGT
1 -AAAATGATAATTTTTGGATGTTCGAGGGT
* * * *
19459 AAAAGGGT-ACTTTTGGATGTGTAG-GGGT
1 AAAATGATAATTTTTGGATGT-TCGAGGGT
* *
19487 AAAAT-AGTAA-TTTTGTAAAGTTCG-GGGT
1 AAAATGA-TAATTTTTG-GATGTTCGAGGGT
* *
19515 CAAAAGGGTAA-TTTTGGATGTTCGAGGGT
1 -AAAATGATAATTTTTGGATGTTCGAGGGT
* *
19544 AAAATGATAATTTTTAGAAAGTTC-AGGGTT
1 AAAATGATAATTTTT-GGATGTTCGAGGG-T
* * *
19574 AAAAATG-TGATTTTTGGAAGTTTGAGGGT
1 -AAAATGATAATTTTTGGATGTTCGAGGGT
19603 AAAAATG-TAATTTT
1 -AAAATGATAATTTT
19617 AGAGAAGTTA
Statistics
Matches: 251, Mismatches: 54, Indels: 52
0.70 0.15 0.15
Matches are distributed among these distances:
26 6 0.02
27 19 0.08
28 64 0.25
29 101 0.40
30 38 0.15
31 13 0.05
32 10 0.04
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAATGATAATTTTTGGATGTTCGAGGGT
Found at i:19475 original size:28 final size:28
Alignment explanation
Indices: 19437--19557 Score: 93
Period size: 28 Copynumber: 4.3 Consensus size: 28
19427 GGTTGAAAAT
19437 GTAATTTTGGATATTCAAGGGTAAAAGG
1 GTAATTTTGGATATTCAAGGGTAAAAGG
* * * **
19465 GTACTTTTGGATGTGT-AGGGGTAAAATA
1 GTAATTTTGGATAT-TCAAGGGTAAAAGG
* * *
19493 GTAATTTTGTAAAGTTC-GGGGTCAAAAGG
1 GTAATTTTGGATA-TTCAAGGGT-AAAAGG
* * *
19522 GTAATTTTGGATGTTCGAGGGTAAAATG
1 GTAATTTTGGATATTCAAGGGTAAAAGG
*
19550 ATAATTTT
1 GTAATTTT
19558 TAGAAAGTTC
Statistics
Matches: 71, Mismatches: 17, Indels: 10
0.72 0.17 0.10
Matches are distributed among these distances:
28 51 0.72
29 20 0.28
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (28 bp):
GTAATTTTGGATATTCAAGGGTAAAAGG
Found at i:19605 original size:59 final size:59
Alignment explanation
Indices: 19483--19645 Score: 169
Period size: 59 Copynumber: 2.8 Consensus size: 59
19473 GGATGTGTAG
* ** * *
19483 GGGT-AAAATAGTAATTTT-GTA-AAGTTCGGGGTCAAAAGGGT-AATTTTGGATGTTCGA
1 GGGTAAAAAT-GTAATTTTAG-AGAAGTTAGGGGTCAAAAATGTGATTTTTGGAAGTTCGA
* *
19540 GGGT-AAAATGATAATTTTTAGA-AAGTTCA-GGGTTAAAAATGTGATTTTTGGAAGTTTGA
1 GGGTAAAAATG-TAA-TTTTAGAGAAGTT-AGGGGTCAAAAATGTGATTTTTGGAAGTTCGA
19599 GGGTAAAAATGTAATTTTAGAGAAGTTAGGGGTCAAAAATGTGATTT
1 GGGTAAAAATGTAATTTTAGAGAAGTTAGGGGTCAAAAATGTGATTT
19646 CTGAACAGTT
Statistics
Matches: 90, Mismatches: 8, Indels: 14
0.80 0.07 0.12
Matches are distributed among these distances:
56 1 0.01
57 12 0.13
58 28 0.31
59 43 0.48
60 6 0.07
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (59 bp):
GGGTAAAAATGTAATTTTAGAGAAGTTAGGGGTCAAAAATGTGATTTTTGGAAGTTCGA
Found at i:19624 original size:30 final size:29
Alignment explanation
Indices: 19522--19645 Score: 103
Period size: 29 Copynumber: 4.2 Consensus size: 29
19512 GGTCAAAAGG
* *
19522 GTAATTTT-GGATGTTCGAGGGT-AAAAT
1 GTAATTTTAGGAAGTTTGAGGGTAAAAAT
* *
19549 GATAATTTTTAGAAAG-TTCAGGGTTAAAAAT
1 G-TAA-TTTTAGGAAGTTTGAGGG-TAAAAAT
* *
19580 GTGATTTTTGGAAGTTTGAGGGTAAAAAT
1 GTAATTTTAGGAAGTTTGAGGGTAAAAAT
*
19609 GTAATTTTAGAGAAGTTAG-GGGTCAAAAAT
1 GTAATTTTAG-GAAGTTTGAGGGT-AAAAAT
*
19639 GTGATTT
1 GTAATTT
19646 CTGAACAGTT
Statistics
Matches: 77, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
27 1 0.01
28 3 0.04
29 36 0.47
30 31 0.40
31 6 0.08
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (29 bp):
GTAATTTTAGGAAGTTTGAGGGTAAAAAT
Found at i:21459 original size:18 final size:17
Alignment explanation
Indices: 21436--21478 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
21426 TGGACATTTT
*
21436 AATTTAAATTTAAGAATA
1 AATTTAAACTTAA-AATA
21454 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
*
21471 AATCTAAA
1 AATTTAAA
21479 ATAAAATGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (17 bp):
AATTTAAACTTAAAATA
Found at i:22244 original size:210 final size:209
Alignment explanation
Indices: 21843--23136 Score: 1378
Period size: 209 Copynumber: 6.2 Consensus size: 209
21833 TCTTGATCTT
* * * * * *
21843 CTTCTCTGTATCTCATCAAGAAGATGACTAGTTTATTGTTTCGACCTGCTTCTCAATATCTCATC
1 CTTCTCTGTATCTCATCAGGAAGATGACCATTTTATTGCTTCGACCTGCTTCTCAGTACCTCATC
* * * *
21908 GAGAAGCTAGGGTTC-AACGTTTCCCTCACATCAAGCTTTGTTTCATTGATTTGGTCTACTT-TT
66 AAGAAGCTGGGGTTCGAA-GTTTCGCTCACATCGAGCTTTGTTTCATTGATTTGGTCTACTTCTT
* ** * * * *
21971 CAGTATCTCATCAGGAAGATGGCTACATCGCTTGTTTTGATCCGCTTTTCTGTATCTCATCAGGA
130 -AGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAGGA
*
22036 AGACAAATTTGGTCCA
194 AGACGAATTTGGTCCA
*** *
22052 CTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGCTCCGACCTGCTTCTCAGTACCTCATC
1 CTTCTCTGTATCTCATCAGGAAGATGACCATTTTATTGCTTCGACCTGCTTCTCAGTACCTCATC
*
22117 AAGAAGTTGGGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTTTCATTGATTTGGTCTACTTCTT
66 AAGAAGCTGGGGTTCGAAGTTTCGCTCACATCGAGCTTT-GTTTCATTGATTTGGTCTACTTCTT
* * * *
22182 AATATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCACTTCTCTATATCTCATCAGGAA
130 AGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAGGAA
22247 GACGAATTTGGTCCA
195 GACGAATTTGGTCCA
* * *
22262 CTTCTCTGTATCTCATCAGGAAGCTGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCTGTATCTCATCAGGAAGATGACCATTTTATTGCTTCGACCTGCTTCTCAGTACCTCATC
* * ** ** * * *
22327 -AGAAAGTTGTGG-TCAGAAGTTTCGCTGGCATTAAGCTTTGTTTCATTGAGTTGGTATAGTT-T
66 AAG-AAGCTGGGGTTC-GAAGTTTCGCTCACATCGAGCTTTGTTTCATTGATTTGGTCTACTTCT
** * * **
22389 GCT-GTATCTCATCAGGAAGATGACATCCTCACTTGTTTCAATCTGCTTCTCTGTATCTCATCAG
129 --TAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAG
22453 GAAGACGAATTTGGTCCA
192 GAAGACGAATTTGGTCCA
* * * *
22471 CTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATTGTTTCGACCTGCTTCTTAGTACCTCATC
1 CTTCTCTGTATCTCATCAGGAAGATGACCATTTTATTGCTTCGACCTGCTTCTCAGTACCTCATC
* * * * *
22536 AAGAAGTTGGGGTTCGAAGTTTCGCTCGCATTGAGCTTTGTTTCATTGAGTTGGTATACTTCTCT
66 AAGAAGCTGGGGTTCGAAGTTTCGCTCACATCGAGCTTTGTTTCATTGATTTGGTCTACTTCT-T
* * * ** * * * *
22601 -GTATCTCATTAGGAATATGACCGCCTCACTTGTTTTAATCTGCTTCTCTCTATTTCATTAAGAA
130 AGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAGGAA
*
22665 GACGAACTTGGTCCA
195 GACGAATTTGGTCCA
* * *
22680 CTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCGACCATGCTTCTCAGTACCTTAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCATTTTATTGCTTCGACC-TGCTTCTCAGTACCTCAT
* * * * *
22745 CAGGAAGCTGAGGTTCGAAGTTTCACCCACATCGAGCTTTGGCTTCATTGATTTGGTCTACTTCT
65 CAAGAAGCTGGGGTTCGAAGTTTCGCTCACATCGAGCTTT-GTTTCATTGATTTGGTCTACTTCT
* * * * * * *
22810 CAATATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTTTTCTGTGTCTCATCAAGA
129 TAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAGGA
* *
22875 AGACCG-ATCTGGTTCA
194 AGA-CGAATTTGGTCCA
* * * * * ** *
22891 CTTCTCTCTATCTCATAAGGGAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCTGTATCTCATCAGGAAGATGACCATTTTATTGCTTCGACCTGCTTCTCAGTACCTCATC
* ** * * * * *
22956 AGGAAGCTAAGATTCGAAGATTT-GCTCAC-T-----TTGGTTTCATGGATTTGGTTTACTTCTC
66 AAGAAGCTGGGGTTCGAAG-TTTCGCTCACATCGAGCTTTGTTTCATTGATTTGGTCTACTTCTT
* * * * * * *
23014 AGTATCTCATCAAGAAGATGATCGTATTACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGCA
130 AGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAGGAA
* * *
23079 GACGGATCTGGTTCA
195 GACGAATTTGGTCCA
* *
23094 CTTCT-TAGTATCTCATCAGGAAGTTGACCATTTTATTTCTTCG
1 CTTCTCT-GTATCTCATCAGGAAGATGACCATTTTATTGCTTCG
23137 GATAATTGTA
Statistics
Matches: 940, Mismatches: 128, Indels: 40
0.85 0.12 0.04
Matches are distributed among these distances:
202 3 0.00
203 125 0.13
204 2 0.00
208 1 0.00
209 410 0.44
210 273 0.29
211 124 0.13
212 2 0.00
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (209 bp):
CTTCTCTGTATCTCATCAGGAAGATGACCATTTTATTGCTTCGACCTGCTTCTCAGTACCTCATC
AAGAAGCTGGGGTTCGAAGTTTCGCTCACATCGAGCTTTGTTTCATTGATTTGGTCTACTTCTTA
GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAGGAAG
ACGAATTTGGTCCA
Found at i:22733 original size:419 final size:414
Alignment explanation
Indices: 21843--23136 Score: 1471
Period size: 419 Copynumber: 3.1 Consensus size: 414
21833 TCTTGATCTT
* * * * * * *
21843 CTTCTCTGTATCTCATCAAGAAGATGACTAGTTTATTGTTTCGACCTGCTTCTCAATATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
* * *
21908 -GAGAAGCTAGGGTTCA-ACGTTTCCCTCACATCAAGCTTTGTTTCATTGATTTGGTCTACTTTT
66 AGA-AAG-TTGGGTTCAGAAGTTTCACTCACATCAAGCTTTGTTTCATTGATTTGGTCTAC-TTT
* *
21971 CAGTATCTCATCAGGAAGATGGCTACATCGCTTGTTTTGATCCGCTTTTCTGTATCTCATCAGGA
128 CAGTATCTCATCAGGAAGATGACT-CATCACTTGTTTTGATCCGCTTTTCTGTATCTCATCAGGA
* * *
22036 AGACAAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGCTCCGACCTGC
192 AGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGACCTGC
22101 TTCTCAGTACCTCATCAAGAAGTTGGGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTTTCATTG
257 TTCTCAGTACCTCATCAAGAAGTTGGGGTTCGAAGTTTCGCTC-CAT-GAGCTTTGGTTTCATTG
* * * *
22166 ATTTGGTCTACTTCT-TAATATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCACTTCT
320 ATTTGGTATACTTCTCT-GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCT
22230 CTATATCTCATCAGGAAGACGAATTTGGTCCA
384 CTATATCTCATCAGGAAGACGAA-TTGGTCCA
* * *
22262 CTTCTCTGTATCTCATCAGGAAGCTGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
* ** * * * *
22327 AGAAAGTTGTGG-TCAGAAGTTTCGCTGGCATTAAGCTTTGTTTCATTGAGTTGGTATAGTTTGC
66 AGAAAGTTG-GGTTCAGAAGTTTCACTCACATCAAGCTTTGTTTCATTGATTTGGTCTACTTT-C
* * ** * *
22391 TGTATCTCATCAGGAAGATGACATCCTCACTTGTTTCAATCTGCTTCTCTGTATCTCATCAGGAA
129 AGTATCTCATCAGGAAGATGAC-TCATCACTTGTTTTGATCCGCTTTTCTGTATCTCATCAGGAA
* * ** *
22456 GACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATTGTTTCGACCTGCT
193 GACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGACCTGCT
*
22521 TCTTAGTACCTCATCAAGAAGTTGGGGTTCGAAGTTTCGCTCGCATTGAGCTTT-GTTTCATTGA
258 TCTCAGTACCTCATCAAGAAGTTGGGGTTCGAAGTTTCGCTC-CA-TGAGCTTTGGTTTCATTGA
* * * * **
22585 GTTGGTATACTTCTCTGTATCTCATTAGGAATATGACCGCCTCACTTGTTTTAATCTGCTTCTCT
321 TTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCT
* * * *
22650 CTATTTCATTAAGAAGACGAACTTGGTCCA
386 ATATCTCATCAGGAAGACGAA-TTGGTCCA
* *
22680 CTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCGACCATGCTTCTCAGTACCTTAT
1 CTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCGACC-TGCTTCTCAGTATCTCAT
* * * * *
22745 CAGGAAGCTGAGGTTC-GAAGTTTCACCCACATCGAGCTTTGGCTTCATTGATTTGGTCTACTTC
65 CAGAAAGTTG-GGTTCAGAAGTTTCACTCACATCAAGCTTT-GTTTCATTGATTTGGTCTACTT-
* * * * * *
22809 TCAATATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTTTTCTGTGTCTCATCAAG
127 TCAGTATCTCATCAGGAAGATGA-CTCATCACTTGTTTTGATCCGCTTTTCTGTATCTCATCAGG
* * * * * * *
22874 AAGACCG-ATCTGGTTCACTTCTCTCTATCTCATAAGGGAGGTAACCGCTTTATTGCTTCGACCT
191 AAGA-CGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGACCT
* * * ** * *
22938 GCTTCTCAGTATCTCATCAGGAAGCTAAGATTCGAAGATTT-GCT-C---A-CTTTGGTTTCATG
255 GCTTCTCAGTACCTCATCAAGAAGTTGGGGTTCGAAG-TTTCGCTCCATGAGCTTTGGTTTCATT
* * * * * * *
22997 GATTTGGTTTACTTCTCAGTATCTCATCAAGAAGATGATCGTATTACTTGTTTTGATCCACTTCT
319 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCT
* * * * *
23062 CTGTGTCTCATCAGGCAGACGGATCTGGTTCA
384 CTATATCTCATCAGGAAGACGAAT-TGGTCCA
* *
23094 CTTCTTAGTATCTCATCAGGAAGTTGACCATTTTATTTCTTCG
1 CTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCG
23137 GATAATTGTA
Statistics
Matches: 738, Mismatches: 121, Indels: 37
0.82 0.14 0.04
Matches are distributed among these distances:
413 5 0.01
414 123 0.17
418 140 0.19
419 306 0.41
420 157 0.21
421 7 0.01
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (414 bp):
CTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
AGAAAGTTGGGTTCAGAAGTTTCACTCACATCAAGCTTTGTTTCATTGATTTGGTCTACTTTCAG
TATCTCATCAGGAAGATGACTCATCACTTGTTTTGATCCGCTTTTCTGTATCTCATCAGGAAGAC
GAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGACCTGCTTCT
CAGTACCTCATCAAGAAGTTGGGGTTCGAAGTTTCGCTCCATGAGCTTTGGTTTCATTGATTTGG
TATACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTATATC
TCATCAGGAAGACGAATTGGTCCA
Found at i:23331 original size:41 final size:41
Alignment explanation
Indices: 23212--23331 Score: 195
Period size: 41 Copynumber: 2.9 Consensus size: 41
23202 GTAAGAGATC
* *
23212 AGAATCTTCATTCTGCCCTTCTTGATTAAGGGTAAAAAACT
1 AGAATCTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGACT
* * *
23253 GGAATCTTCAATCTACCCTTCTTAATTAAGGGTAAAAGACT
1 AGAATCTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGACT
23294 AGAATCTTCAATCTGCCCTTCTTGATTAAGGGTAAAAG
1 AGAATCTTCAATCTGCCCTTCTTGATTAAGGGTAAAAG
23332 TTTGAATGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (41 bp):
AGAATCTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGACT
Found at i:23645 original size:50 final size:51
Alignment explanation
Indices: 23591--23758 Score: 159
Period size: 50 Copynumber: 3.4 Consensus size: 51
23581 TCGGGTTCGC
* * *
23591 CGTCGCGACCTCAA-CCTTTCCCATCACATATTCTTAGGAACTGAATTCAG
1 CGTCGCGGCCTCAATCCTTTCCCATCACATCTTCTTAGGAACTGGATTCAG
* ** * * * * *
23641 CGTCGCGGCTTCAATCC-TTCCTTTCATC-TCTTCATA-GTACCGGGTTCAC
1 CGTCGCGGCCTCAATCCTTTCCCATCA-CATCTTCTTAGGAACTGGATTCAG
* *
23690 CGTTGCTGCCTCAA-CCTTTCCCATCACATCTTCTTAGGAACTGGATTC-G
1 CGTCGCGGCCTCAATCCTTTCCCATCACATCTTCTTAGGAACTGGATTCAG
23739 TCGTCGCGGCCTCAATCCTT
1 -CGTCGCGGCCTCAATCCTT
23759 CCCTTCGTCT
Statistics
Matches: 88, Mismatches: 23, Indels: 13
0.71 0.19 0.10
Matches are distributed among these distances:
48 3 0.03
49 33 0.38
50 45 0.51
51 7 0.08
ACGTcount: A:0.18, C:0.34, G:0.16, T:0.32
Consensus pattern (51 bp):
CGTCGCGGCCTCAATCCTTTCCCATCACATCTTCTTAGGAACTGGATTCAG
Found at i:23754 original size:99 final size:98
Alignment explanation
Indices: 23577--23909 Score: 407
Period size: 99 Copynumber: 3.4 Consensus size: 98
23567 TGTTTTTTAA
* * * * *
23577 GGTATCGGGTTCGCCGTCGCGACCTCAACCTTTCCCATCACATATTCTTAGGAACTGAATTCAGC
1 GGTACCGGGTTCACCATTGCGACCTCAACCTTTCCCATCACATCTTCTTAGGAACTGAATTC-GC
* * *
23642 GTCGCGGCTTCAATCCTTCCTTTCATCTCTTCAT
65 GTCGCGGCCTCAATCCTTCCCTTCGTCTCTTCAT
* * *
23676 AGTACCGGGTTCACCGTTGCTG-CCTCAACCTTTCCCATCACATCTTCTTAGGAACTGGATTCGT
1 GGTACCGGGTTCACCATTGC-GACCTCAACCTTTCCCATCACATCTTCTTAGGAACTGAATTCG-
23740 CGTCGCGGCCTCAATCCTTCCCTTCGTCTCTTCAT
64 CGTCGCGGCCTCAATCCTTCCCTTCGTCTCTTCAT
* * * * * * * *
23775 GGTGCCGGGTTCACCATTACGAGCTCAACCTTTCCTATCACATCTTTTTAAGAACCGAATTCACC
1 GGTACCGGGTTCACCATTGCGACCTCAACCTTTCCCATCACATCTTCTTAGGAACTGAATTC-GC
23840 GTCGCGGCCTCAATCCTTCCCTTCGTCTCTTCAT
65 GTCGCGGCCTCAATCCTTCCCTTCGTCTCTTCAT
* * ** *
23874 GGTACTGCGTTCGTCATTGCGGCCTCAACCTTTCCC
1 GGTACCGGGTTCACCATTGCGACCTCAACCTTTCCC
23910 TGTCAAACTT
Statistics
Matches: 201, Mismatches: 29, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
98 2 0.01
99 198 0.99
100 1 0.00
ACGTcount: A:0.17, C:0.34, G:0.17, T:0.32
Consensus pattern (98 bp):
GGTACCGGGTTCACCATTGCGACCTCAACCTTTCCCATCACATCTTCTTAGGAACTGAATTCGCG
TCGCGGCCTCAATCCTTCCCTTCGTCTCTTCAT
Found at i:30572 original size:7 final size:8
Alignment explanation
Indices: 30550--30677 Score: 85
Period size: 8 Copynumber: 14.4 Consensus size: 8
30540 ATAATTTCTC
30550 ATTAAAAA
1 ATTAAAAA
30558 ATTAAAAA
1 ATTAAAAA
30566 ATTAAAAA
1 ATTAAAAA
30574 ATTAAAAA
1 ATTAAAAA
* *
30582 ATCATTAAA
1 ATTA-AAAA
*
30591 ATGACTAAAA
1 ATTA--AAAA
30601 ATCATAAAAA
1 AT--TAAAAA
30611 ATTAAAAA
1 ATTAAAAA
*
30619 ATATTAAAA
1 AT-TAAAAA
*
30628 TTTAAATAA
1 ATTAAA-AA
30637 TATTATAAAA
1 -ATTA-AAAA
30647 ATTATAAAA
1 ATTA-AAAA
*
30656 ACTTATAAAT
1 A-TTA-AAAA
30666 ATTATAAAA
1 ATTA-AAAA
30675 ATT
1 ATT
30678 CTAATAAATT
Statistics
Matches: 100, Mismatches: 11, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
8 38 0.38
9 34 0.34
10 25 0.25
11 2 0.02
12 1 0.01
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (8 bp):
ATTAAAAA
Found at i:30573 original size:9 final size:9
Alignment explanation
Indices: 30553--30677 Score: 55
Period size: 9 Copynumber: 13.9 Consensus size: 9
30543 ATTTCTCATT
30553 AAAAAATT-
1 AAAAAATTA
30561 AAAAAATT-
1 AAAAAATTA
30569 AAAAAATTA
1 AAAAAATTA
30578 AAAAATCATTA
1 AAAAA--ATTA
** *
30589 AAATGACT-
1 AAAAAATTA
*
30597 -AAAAATCA
1 AAAAAATTA
30605 TAAAAAATTA
1 -AAAAAATTA
30615 AAAAATATT-
1 AAAAA-ATTA
*
30624 -AAAATTTA
1 AAAAAATTA
*
30632 AATAATATTA
1 AA-AAAATTA
*
30642 TAAAAATTA
1 AAAAAATTA
*
30651 TAAAAACTTA
1 -AAAAAATTA
* *
30661 TAAATATTA
1 AAAAAATTA
*
30670 TAAAAATT
1 AAAAAATT
30678 CTAATAAATT
Statistics
Matches: 87, Mismatches: 19, Indels: 21
0.69 0.15 0.17
Matches are distributed among these distances:
7 5 0.06
8 20 0.23
9 32 0.37
10 23 0.26
11 7 0.08
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (9 bp):
AAAAAATTA
Found at i:30646 original size:28 final size:27
Alignment explanation
Indices: 30615--30676 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
30605 TAAAAAATTA
* *
30615 AAAAATATTAAAATTTAAATAATATTAT
1 AAAAATATAAAAACTTAAA-AATATTAT
*
30643 AAAAATTATAAAAACTTATAAATATTAT
1 AAAAA-TATAAAAACTTAAAAATATTAT
30671 AAAAAT
1 AAAAAT
30677 TCTAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 18 0.60
29 11 0.37
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (27 bp):
AAAAATATAAAAACTTAAAAATATTAT
Found at i:30661 original size:19 final size:18
Alignment explanation
Indices: 30550--30792 Score: 130
Period size: 19 Copynumber: 13.1 Consensus size: 18
30540 ATAATTTCTC
30550 ATTA-AAAAATTA-AAAA
1 ATTATAAAAATTATAAAA
30566 ATTA-AAAAATTA-AAAA
1 ATTATAAAAATTATAAAA
* * *
30582 ATCATTAAAATGACTAAAA
1 ATTATAAAAATTA-TAAAA
*
30601 ATCATAAAAAATTA-AAAA
1 ATTAT-AAAAATTATAAAA
*
30619 A-TATTAAAATT-TAAATAA
1 ATTATAAAAATTAT-AA-AA
30637 TATTATAAAAATTATAAAA
1 -ATTATAAAAATTATAAAA
*
30656 ACTTATAAATATTATAAAA
1 A-TTATAAAAATTATAAAA
* *
30675 ATTCTAATAAATTAT-AAT
1 ATTATAA-AAATTATAAAA
* *
30693 TTTTTATAAAATTAATAGAATA
1 ATTATA-AAAATT-ATA-AA-A
*
30715 TATT-T-AAAATTTTAAAATA
1 -ATTATAAAAATTAT-AAA-A
30734 ACTTATAAAAATTCATAAATA
1 A-TTATAAAAATT-ATAAA-A
30755 ATTATAAATAA-TATAAAA
1 ATTATAAA-AATTATAAAA
*
30773 ATTAGAAAAATATATAAAA
1 ATTATAAAAAT-TATAAAA
30792 A
1 A
30793 ATCATTTAAA
Statistics
Matches: 182, Mismatches: 19, Indels: 49
0.73 0.08 0.20
Matches are distributed among these distances:
16 25 0.14
17 12 0.07
18 33 0.18
19 58 0.32
20 33 0.18
21 17 0.09
22 2 0.01
23 2 0.01
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (18 bp):
ATTATAAAAATTATAAAA
Found at i:30677 original size:28 final size:27
Alignment explanation
Indices: 30562--30790 Score: 70
Period size: 28 Copynumber: 8.4 Consensus size: 27
30552 TAAAAAATTA
* *
30562 AAAAATTA-AAAAATTA-AAAAATCAT
1 AAAAATTATAAATATTATAAAAATTAT
* * * * *
30587 TAAAATGACTAAAAATCATAAAAAATTAA
1 AAAAATTA-TAAATATTAT-AAAAATTAT
30616 AAAATATTA-AAAT-TTA-AATAATATTAT
1 AAAA-ATTATAAATATTATAA-AA-ATTAT
* *
30643 AAAAATTATAAAAACTTATAAATATTAT
1 AAAAATTATAAATA-TTATAAAAATTAT
* * ** *
30671 AAAAATTCTAATAAATTAT-AATTTTTT
1 AAAAATTATAA-ATATTATAAAAATTAT
*
30698 ATAAAATTAATAGAATA-TATTTAAAATT-T
1 A-AAAATT-ATA-AATATTA-TAAAAATTAT
* *
30727 -TAAA--AT-AA-CTTATAAAAATTCAT
1 AAAAATTATAAATATTATAAAAATT-AT
* *
30750 AAATAATTATAAATAATATAAAAATTAG
1 AAA-AATTATAAATATTATAAAAATTAT
30778 AAAAATATATAAA
1 AAAAAT-TATAAA
30791 AAATCATTTA
Statistics
Matches: 151, Mismatches: 26, Indels: 51
0.66 0.11 0.22
Matches are distributed among these distances:
21 7 0.05
22 4 0.03
23 1 0.01
24 3 0.02
25 10 0.07
26 6 0.04
27 35 0.23
28 42 0.28
29 33 0.22
30 10 0.07
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.34
Consensus pattern (27 bp):
AAAAATTATAAATATTATAAAAATTAT
Found at i:30761 original size:10 final size:9
Alignment explanation
Indices: 30736--30792 Score: 62
Period size: 10 Copynumber: 6.0 Consensus size: 9
30726 TTAAAATAAC
30736 TTATAAAAA
1 TTATAAAAA
30745 TTCATAAATAA
1 TT-ATAAA-AA
30756 TTATAAATAA
1 TTATAAA-AA
30766 -TATAAAAA
1 TTATAAAAA
*
30774 TTAGAAAAA
1 TTATAAAAA
30783 TATATAAAAA
1 T-TATAAAAA
30793 ATCATTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
8 2 0.05
9 16 0.38
10 20 0.48
11 4 0.10
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:30771 original size:9 final size:10
Alignment explanation
Indices: 30638--30790 Score: 73
Period size: 9 Copynumber: 15.8 Consensus size: 10
30628 TTTAAATAAT
30638 ATTATAAA-A
1 ATTATAAATA
30647 ATTATAAA-A
1 ATTATAAATA
30656 ACTTATAAAT-
1 A-TTATAAATA
30666 ATTATAAA-A
1 ATTATAAATA
*
30675 ATTCT-AATAA
1 ATTATAAAT-A
* *
30685 ATTATAATTT
1 ATTATAAATA
*
30695 TTTAT-AA-A
1 ATTATAAATA
30703 ATTAATAGAATA
1 ATT-ATA-AATA
30715 TATT-T-AA-A
1 -ATTATAAATA
*
30723 ATTTTAAAATA
1 ATTAT-AAATA
30734 ACTTATAAA-A
1 A-TTATAAATA
30744 ATTCATAAATA
1 ATT-ATAAATA
30755 ATTATAAATA
1 ATTATAAATA
30765 A-TATAAA-A
1 ATTATAAATA
*
30773 ATTAGAAA-A
1 ATTATAAATA
30782 ATATATAAA
1 AT-TATAAA
30791 AAATCATTTA
Statistics
Matches: 113, Mismatches: 11, Indels: 39
0.69 0.07 0.24
Matches are distributed among these distances:
7 3 0.03
8 8 0.07
9 42 0.37
10 39 0.35
11 14 0.12
12 4 0.04
13 3 0.03
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (10 bp):
ATTATAAATA
Found at i:31509 original size:11 final size:10
Alignment explanation
Indices: 31483--31514 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
31473 GATTCAATAA
31483 ATATTTTTAT
1 ATATTTTTAT
31493 A-ATTTTTAT
1 ATATTTTTAT
31502 ATATTTTTA-
1 ATATTTTTAT
31511 ATAT
1 ATAT
31515 CTTATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
ATATTTTTAT
Found at i:31512 original size:17 final size:19
Alignment explanation
Indices: 31483--31527 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
31473 GATTCAATAA
*
31483 ATAT-TTTTATAAT-TTTT
1 ATATATTTTATAATATCTT
31500 ATATATTTT-TAATATCTT
1 ATATATTTTATAATATCTT
31518 ATA-ATTTTAT
1 ATATATTTTAT
31528 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
ATATATTTTATAATATCTT
Found at i:31649 original size:19 final size:19
Alignment explanation
Indices: 31572--31698 Score: 89
Period size: 19 Copynumber: 6.5 Consensus size: 19
31562 TTAGTATGAT
* *
31572 TTTTTATAAATTTTATACC
1 TTTTTATAATTTTTATAAC
* *
31591 TATTGATAATTTTTATAA-
1 TTTTTATAATTTTTATAAC
31609 TTTGTATGATAATTTATTATAAC
1 TTT-T-T-ATAATTT-TTATAAC
*
31632 TTTTTAGAATTTTTATAAGC
1 TTTTTATAATTTTTATAA-C
* *
31652 -TTTTATAATATTTATAAG
1 TTTTTATAATTTTTATAAC
* *
31670 TTTTGATGAATCCTTTATAA-
1 TTTTTAT-AAT-TTTTATAAC
31690 TTTTTATAA
1 TTTTTATAA
31699 GTTTATAGAA
Statistics
Matches: 86, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
18 2 0.02
19 43 0.50
20 16 0.19
21 15 0.17
22 7 0.08
23 3 0.03
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (19 bp):
TTTTTATAATTTTTATAAC
Found at i:35361 original size:50 final size:50
Alignment explanation
Indices: 35290--35439 Score: 273
Period size: 50 Copynumber: 3.0 Consensus size: 50
35280 GGAGCTGATA
* *
35290 ACTGCAATGTCCATGGAGACATGCAAAGCAAGCTTAGAATTCTGATTTTT
1 ACTGCAATATCCATGGTGACATGCAAAGCAAGCTTAGAATTCTGATTTTT
35340 ACTGCAATATCCATGGTGACATGCAAAGCAAGCTTAGAATTCTGATTTTT
1 ACTGCAATATCCATGGTGACATGCAAAGCAAGCTTAGAATTCTGATTTTT
*
35390 ACTGCAATATCCATGGTGCCATGCAAAGCAAGCTTAGAATTCTGATTTTT
1 ACTGCAATATCCATGGTGACATGCAAAGCAAGCTTAGAATTCTGATTTTT
35440 GATGGTGCAT
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 97 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (50 bp):
ACTGCAATATCCATGGTGACATGCAAAGCAAGCTTAGAATTCTGATTTTT
Found at i:40844 original size:18 final size:17
Alignment explanation
Indices: 40789--40849 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
40779 TCTCTATTTT
*
40789 TTTAATAAAAAATTATTA
1 TTTAATATAAAA-TATTA
* * *
40807 CTTAATATAACATAAT-
1 TTTAATATAAAATATTA
40823 TTTAATATATAAATATTA
1 TTTAATATA-AAATATTA
*
40841 TTTAGTATA
1 TTTAATATA
40850 CATCTATTAC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
16 8 0.24
17 8 0.24
18 17 0.52
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (17 bp):
TTTAATATAAAATATTA
Found at i:42178 original size:12 final size:12
Alignment explanation
Indices: 42157--42214 Score: 64
Period size: 12 Copynumber: 4.7 Consensus size: 12
42147 CTACCTCATC
42157 CTTT-TTCTTTT
1 CTTTCTTCTTTT
42168 CTTTCTTCTTTT
1 CTTTCTTCTTTT
* *
42180 CCTTCGCCTCTTTGT
1 -CTT-TCTTCTTT-T
42195 CTTTCTTCTTTT
1 CTTTCTTCTTTT
42207 CTTTCTTC
1 CTTTCTTC
42215 CCCTTTTCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 4 0.10
12 16 0.41
13 9 0.23
14 9 0.23
15 1 0.03
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.67
Consensus pattern (12 bp):
CTTTCTTCTTTT
Found at i:42254 original size:99 final size:98
Alignment explanation
Indices: 42144--42582 Score: 579
Period size: 96 Copynumber: 4.6 Consensus size: 98
42134 TTCTCTTCAC
* *
42144 CTTCTACCTCATCCTTTTTCTTTTCTTTCTTCTTTTCCTTCGCCTCTTTGTCTTTCTTCTTTTCT
1 CTTCTACCTCATCC-TTTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCT
* *
42209 TTCTTCCCCTTTTCTATTTCTGCATCTTCATCTT
65 TTCTTTCCCTCTTCTATTTCTGCATCTTCATCTT
*
42243 CTTCTACCTCATCCTTCTTCTTTTCCTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCT
1 CTTCTACCTCATCCTT-TTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCT
*
42308 CTCTTTCCCTCTTCTATTTCTGCATCTTCATCTT
65 TTCTTTCCCTCTTCTATTTCTGCATCTTCATCTT
* *
42342 C-T-T--CT-A-CCTTATC----C-TTCTTCTTCTCCTTTGCCTCTTTGTCTTTGTTCTTTTCTT
1 CTTCTACCTCATCCTTTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTT
* *
42396 TCTTTCCCTCTTCTATTTCTTCATCTTCTTCTT
66 TCTTTCCCTCTTCTATTTCTGCATCTTCATCTT
* *
42429 CTTCTACCTTATCC--TTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCTT
1 CTTCTACCTCATCCTTTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTT
* *
42492 TCTTTCCCTCTTCTATTTCTTCATCTTCATCTA
66 TCTTTCCCTCTTCTATTTCTGCATCTTCATCTT
* *
42525 CCT-TATCCT--T-CTTCTTTTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT
1 CTTCTA-CCTCATCCTT-TTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT
42583 CTCTGTCTCT
Statistics
Matches: 305, Mismatches: 19, Indels: 35
0.85 0.05 0.10
Matches are distributed among these distances:
87 70 0.23
88 2 0.01
89 1 0.00
91 4 0.01
92 3 0.01
93 7 0.02
94 2 0.01
95 5 0.02
96 116 0.38
97 1 0.00
98 3 0.01
99 91 0.30
ACGTcount: A:0.05, C:0.33, G:0.03, T:0.59
Consensus pattern (98 bp):
CTTCTACCTCATCCTTTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTT
TCTTTCCCTCTTCTATTTCTGCATCTTCATCTT
Found at i:42271 original size:12 final size:12
Alignment explanation
Indices: 42254--42306 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
42244 TTCTACCTCA
42254 TCCTTCTTCTTT
1 TCCTTCTTCTTT
*
42266 TCCTTCTTCTTC
1 TCCTTCTTCTTT
*
42278 TCCTTTGCCTCTTT
1 TCC-TT-CTTCTTT
*
42292 GTCTTTCTTCTTT
1 -TCCTTCTTCTTT
42305 TC
1 TC
42307 TCTCTTTCCC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
12 16 0.48
13 8 0.24
14 7 0.21
15 2 0.06
ACGTcount: A:0.00, C:0.34, G:0.04, T:0.62
Consensus pattern (12 bp):
TCCTTCTTCTTT
Found at i:42300 original size:39 final size:40
Alignment explanation
Indices: 42257--42399 Score: 112
Period size: 43 Copynumber: 3.5 Consensus size: 40
42247 TACCTCATCC
42257 TTCTTCTTT-TCCTTCTTCTTCTCCTTTGCCTCTTTGTCT
1 TTCTTCTTTATCCTTCTTCTTCTCCTTTGCCTCTTTGTCT
* * ** * **
42296 TTCTTCTTTTCTCTCTTTCCCTCTTCTATTTCTGCATCTTCATC-
1 TTCTTC-TTTATC-C-TT-CTTCTTCTCCTT-TGCCTCTTTGTCT
42340 TTCTTCTACCTTATCCTTCTTCTTCTCCTTTGCCTCTTTGTCT
1 TTCTTCT---TTATCCTTCTTCTTCTCCTTTGCCTCTTTGTCT
* *
42383 TTGTTCTTT-TCTTTCTT
1 TTCTTCTTTATCCTTCTT
42400 TCCCTCTTCT
Statistics
Matches: 79, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
39 13 0.16
40 5 0.06
41 2 0.03
42 10 0.13
43 18 0.23
44 17 0.22
45 10 0.13
46 4 0.05
ACGTcount: A:0.03, C:0.32, G:0.04, T:0.60
Consensus pattern (40 bp):
TTCTTCTTTATCCTTCTTCTTCTCCTTTGCCTCTTTGTCT
Found at i:42357 original size:87 final size:87
Alignment explanation
Indices: 42266--42523 Score: 399
Period size: 87 Copynumber: 2.9 Consensus size: 87
42256 CTTCTTCTTT
* *
42266 TCCTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTCTCTTTCCCTCTTCTATTTCTGC
1 TCCTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTATTTCTTC
42331 ATCTTCATCTTCTTCTACCTTA
66 ATCTTCATCTTCTTCTACCTTA
*
42353 TCCTTCTTCTTCTCCTTTGCCTCTTTGTCTTTGTTCTTTTCTTTCTTTCCCTCTTCTATTTCTTC
1 TCCTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTATTTCTTC
*
42418 ATCTTCTTCTTCTTCTACCTTA
66 ATCTTCATCTTCTTCTACCTTA
42440 TCCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTC
1 TCCTTC--TTC-TTC-TC--CT--TT-GCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTC
42505 TATTTCTTCATCTTCATCT
57 TATTTCTTCATCTTCATCT
42524 ACCTTATCCT
Statistics
Matches: 156, Mismatches: 6, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
87 89 0.57
89 3 0.02
90 3 0.02
91 2 0.01
93 2 0.01
95 2 0.01
96 55 0.35
ACGTcount: A:0.05, C:0.33, G:0.03, T:0.59
Consensus pattern (87 bp):
TCCTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTATTTCTTC
ATCTTCATCTTCTTCTACCTTA
Found at i:42459 original size:12 final size:12
Alignment explanation
Indices: 42442--42495 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
42432 CTACCTTATC
42442 CTTCTTTTCTTT
1 CTTCTTTTCTTT
* *
42454 CTTCTTCTCCTTCG
1 CTTCTT-TTCTT-T
*
42468 CCTCTTTGTCTTT
1 CTTCTTT-TCTTT
42481 CTTCTTTTCTTT
1 CTTCTTTTCTTT
42493 CTT
1 CTT
42496 TCCCTCTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
12 14 0.42
13 11 0.33
14 8 0.24
ACGTcount: A:0.00, C:0.31, G:0.04, T:0.65
Consensus pattern (12 bp):
CTTCTTTTCTTT
Found at i:42465 original size:27 final size:28
Alignment explanation
Indices: 42424--42486 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
42414 CTTCATCTTC
*
42424 TTCTTCTTCTACCTTATCCTTCTTT-TCT
1 TTCTTCTTCTACCTTAGCC-TCTTTGTCT
*
42452 TTCTTCTTCT-CCTTCGCCTCTTTGTCT
1 TTCTTCTTCTACCTTAGCCTCTTTGTCT
42479 TTCTTCTT
1 TTCTTCTT
42487 TTCTTTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 5 0.16
27 17 0.53
28 10 0.31
ACGTcount: A:0.03, C:0.33, G:0.03, T:0.60
Consensus pattern (28 bp):
TTCTTCTTCTACCTTAGCCTCTTTGTCT
Found at i:42638 original size:96 final size:96
Alignment explanation
Indices: 42356--42615 Score: 238
Period size: 96 Copynumber: 2.7 Consensus size: 96
42346 TACCTTATCC
* * * * * ** *
42356 TTCTTCTTCTCCTTTGCCTCTTTGTCTTTGTTCTTTTCTTTCTTTCCCTCTTCTATTTCTTCATC
1 TTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTCTCTTTCTATCACTCTTCTACCTCTCCATC
* * * ** * * *
42421 TTCTTCT-TCTTCTACCTTATCCTTCTTTTCT
66 TTCATCTACCTTAT-CAGTCTTCTTTTTTTCT
* * * ** *
42452 TTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTATTTCTTCATC
1 TTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTCTCTTTCTATCACTCTTCTACCTCTCCATC
**
42517 TTCATCTACCTTATCCTTCTTCTTTTTTTCT
66 TTCATCTACCTTATCAGTCTTCTTTTTTTCT
* *
42548 TTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTCTCTGTCTCTATCACT-TTCT-CCTCTCCC
1 TTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTCTCT-T-TCTATCACTCTTCTACCTCTCCA
42611 TCTTC
64 TCTTC
42616 CTCTTCATCT
Statistics
Matches: 145, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
96 129 0.89
97 9 0.06
98 7 0.05
ACGTcount: A:0.04, C:0.33, G:0.03, T:0.59
Consensus pattern (96 bp):
TTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTCTCTTTCTATCACTCTTCTACCTCTCCATC
TTCATCTACCTTATCAGTCTTCTTTTTTTCT
Found at i:42815 original size:66 final size:64
Alignment explanation
Indices: 42743--42901 Score: 162
Period size: 66 Copynumber: 2.4 Consensus size: 64
42733 ACTTTTCCCC
*
42743 TTCTCCTTGTCTTTTTTCTTCTTT-TTCTTATCATC-TCTCTCTTCATCTTCTTTCTCCTCAACC
1 TTCTCCTTGTCTTTTTTCTTCTTTCTTCTTATCATCTTCTC-CTTCATCTTC-TTCT-ATC-ACC
42806 TCT
62 TCT
* * * * *
42809 TTCTCCTTATGCTTCTTTTCTTTTTTCTTCTTCTCTTCTTTTCCTTCATCTTCTTCTATCACCTC
1 TTCTCCTTGT-CTT-TTTTCTTCTTTCTTCTTATCATCTTCTCCTTCATCTTCTTCTATCACCTC
42874 T
64 T
* * *
42875 TTATCCTTGT-GTTTTCCTTCTTTCTTC
1 TTCTCCTTGTCTTTTTTCTTCTTTCTTC
42902 ATCTTCACCT
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
63 13 0.17
64 1 0.01
66 23 0.29
67 5 0.06
68 14 0.18
69 19 0.24
70 3 0.04
ACGTcount: A:0.06, C:0.31, G:0.03, T:0.60
Consensus pattern (64 bp):
TTCTCCTTGTCTTTTTTCTTCTTTCTTCTTATCATCTTCTCCTTCATCTTCTTCTATCACCTCT
Found at i:42847 original size:23 final size:23
Alignment explanation
Indices: 42820--42865 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42810 TCTCCTTATG
* **
42820 CTTCTTTTCTTTTTTCTTCTTCT
1 CTTCTTTTCCTTCATCTTCTTCT
42843 CTTCTTTTCCTTCATCTTCTTCT
1 CTTCTTTTCCTTCATCTTCTTCT
42866 ATCACCTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (23 bp):
CTTCTTTTCCTTCATCTTCTTCT
Found at i:46394 original size:14 final size:15
Alignment explanation
Indices: 46373--46411 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
46363 AAAAAAAAAA
46373 AAACTAAATTTATAG
1 AAACTAAATTTATAG
*
46388 AAA-TAAAATTATAG
1 AAACTAAATTTATAG
46402 AAACTAAATT
1 AAACTAAATT
46412 CAAAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (15 bp):
AAACTAAATTTATAG
Found at i:48779 original size:29 final size:28
Alignment explanation
Indices: 48660--49263 Score: 454
Period size: 29 Copynumber: 20.6 Consensus size: 28
48650 ATTTGGGGTC
* *
48660 AAAAATGGAATTTTTAGAAATTCAGAGGT
1 AAAAATGGAATTTTTGGAATTTC-GAGGT
* *
48689 -AAAAGGGTAA-TTTTGAGAGTTTCGAGGT
1 AAAAATGG-AATTTTTG-GAATTTCGAGGT
* * *
48717 CGAAAAT--AATGTCTTTGGATATTT-GGGGG
1 -AAAAATGGAAT-T-TTTGGA-ATTTCGAGGT
* *
48746 CAAAATGGTAATTTTTGAAATTTTCGAGGT
1 AAAAATGG-AATTTTTGGAA-TTTCGAGGT
* *
48776 AAAAATGGAAATTTTGGAAGTTTTGAGGT
1 AAAAATGGAATTTTTGGAA-TTTCGAGGT
*
48805 CAAAAATGGAATTTTTGGAAGTTCGAGGGT
1 -AAAAATGGAATTTTTGGAATTTCGA-GGT
* * *
48835 AAAAATAGAATTTTTGGAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGAA-TTTCGAGG-T
* * *
48865 AAAAAATAGAA-TTTTGGAAGTTTGGGGGT
1 -AAAAATGGAATTTTTGGAA-TTTCGAGGT
*
48894 AAAAATGGAATTTTTGGAAGTTTCAAGGT
1 AAAAATGGAATTTTTGGAA-TTTCGAGGT
*
48923 CAAAAAT-GAGATTTTTGGAAGTTCGAGGGT
1 -AAAAATGGA-ATTTTTGGAATTTCGA-GGT
*
48953 AAAAATGGAATTTTT-AAAGTTTCGAGGT
1 AAAAATGGAATTTTTGGAA-TTTCGAGGT
*
48981 CAAAAATGGAATTTTTGGAAGTTCGAGGGT
1 -AAAAATGGAATTTTTGGAATTTCGA-GGT
* *
49011 AAAATTGGAATTTTTGGAAGTTTCAAGGT
1 AAAAATGGAATTTTTGGAA-TTTCGAGGT
* *
49040 CAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 -AAAAATGGAATTTTTGGAATTTCGA-GGT
* * *
49070 CAAAATAGAA-TTTTGGAAGTTTCAAGGT
1 AAAAATGGAATTTTTGGAA-TTTCGAGGT
* *
49098 CAAAAATGGGATTTTTGG-ATGTTTGAAGGT
1 -AAAAATGGAATTTTTGGAAT-TTCG-AGGT
**
49128 AAAAATGGAATTTTTGGAAGTTTTAAGGGT
1 AAAAATGGAATTTTTGGAA-TTTCGA-GGT
*
49158 CAAAAATGGAATTTTTGGAAATTCGAGGGT
1 -AAAAATGGAATTTTTGGAATTTCGA-GGT
* * *
49188 AAAATTGGAATTTTTGGAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAA-TTTCGAGGT
* *
49217 TAAAATGGAATTTTTGGAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAATTTCGA-GGT
*
49246 CAAAATGGAATTTTTGGA
1 AAAAATGGAATTTTTGGA
49264 CAGTTTAGGG
Statistics
Matches: 467, Mismatches: 67, Indels: 82
0.76 0.11 0.13
Matches are distributed among these distances:
27 2 0.00
28 50 0.11
29 242 0.52
30 140 0.30
31 33 0.07
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAATTTCGAGGT
Found at i:48809 original size:59 final size:59
Alignment explanation
Indices: 48747--49269 Score: 671
Period size: 59 Copynumber: 8.9 Consensus size: 59
48737 ATTTGGGGGC
* * * **
48747 AAAATGGTAATTTTTGAAATTTTCGA-GGTAAAAATGGAAATTTTGGAAGTTTTGAGGTCA
1 AAAATGG-AATTTTTGGAA-GTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCA
* *** *
48807 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATAGAATTTTTGGAAGTTTTGGGGTTAA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGG-TCA
* * *
48867 AAAATAGAA-TTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCA
* *
48925 AAAAT-GAGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTT-AAAGTTTCGAGGTCA
1 AAAATGGA-ATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCA
*
48983 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAATTGGAATTTTTGGAAGTTTCAAGGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCA
* * *
49042 AAAATGGGATTTTTGGAAGTTCGAGGGTCAAAATAGAA-TTTTGGAAGTTTCAAGGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCA
* * * * *
49100 AAAATGGGATTTTTGGATGTTTGAAGGTAAAAATGGAATTTTTGGAAGTTTTAAGGGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAA-GGTCA
* * *** *
49160 AAAATGGAATTTTTGGAAATTCGAGGGTAAAATTGGAATTTTTGGAAGTTTTGGGGT-T
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCA
*
49218 AAAATGGAATTTTTGGAAGTTCGAGGGTCAAAATGGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGA-AGTTT
49270 AGGGACCTCC
Statistics
Matches: 411, Mismatches: 43, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
57 2 0.00
58 161 0.39
59 180 0.44
60 68 0.17
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCA
Found at i:50241 original size:20 final size:20
Alignment explanation
Indices: 50216--50253 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
50206 ATATTACCAT
50216 TTATTATTATTATTATTAAA
1 TTATTATTATTATTATTAAA
50236 TTATTATTATTATTATTA
1 TTATTATTATTATTATTA
50254 TTATTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTATTATTATTATTAAA
Found at i:50272 original size:3 final size:3
Alignment explanation
Indices: 50216--50259 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
50206 ATATTACCAT
*
50216 TTA TTA TTA TTA TTA TTA -AA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
50260 AAAACAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 37 0.97
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:51047 original size:24 final size:23
Alignment explanation
Indices: 51010--51056 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
51000 TGGACTTTTG
*
51010 ATTTAAATAGATTTAAACTTTAA
1 ATTTAAATAAATTTAAACTTTAA
*
51033 ATTTATAATAAATTTAAATTTTAA
1 ATTTA-AATAAATTTAAACTTTAA
51057 GTAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTAAATAAATTTAAACTTTAA
Found at i:51048 original size:17 final size:17
Alignment explanation
Indices: 51023--51102 Score: 97
Period size: 17 Copynumber: 4.6 Consensus size: 17
51013 TAAATAGATT
*
51023 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
* *
51041 TAAATTTAAATTTTAAG
1 TAAATTTAAATTTAAAA
*
51058 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
51075 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
51092 GAAATTTAAAT
1 TAAATTTAAAT
51103 CCTATTGGGC
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
17 48 0.92
18 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:51102 original size:6 final size:6
Alignment explanation
Indices: 51020--51090 Score: 51
Period size: 6 Copynumber: 12.2 Consensus size: 6
51010 ATTTAAATAG
* *
51020 ATTTAA ACTTTAA ATTTATA A--TAA ATTTAA ATTTTA A-GTAA ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * *
51067 ACTTAA A-ATAA ATTTAA TTTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA A
51091 AGAAATTTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
4 2 0.04
5 9 0.18
6 31 0.62
7 8 0.16
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:51782 original size:206 final size:201
Alignment explanation
Indices: 51418--51909 Score: 536
Period size: 206 Copynumber: 2.4 Consensus size: 201
51408 TCTGGTTTCA
* * * * * * **
51418 TTGACTTGGCCTTCTTCTCAGTATCTCATTAGGAAGACGACCATATCACTTATTTTGATCCACTT
1 TTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATTACTTGTTTCAATCCACTT
* * * * ** * * * **
51483 CTCAGTGTTTCATCAGGAAGATGGTTTTGGTTCACTTCCCCGTATTTCGTCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTACCAGTATCTAATCAGGAAGCTAACCAT
*
51548 TTTATTACTTCAACTTGCTTCTCAGTATCTTATCAAGAAGCTG-GGGTTCAAGGATTTGCTCACA
131 TTTATTACTTCAACTTGCTTCTCAGTATCTCATCAAGAAGCTGAGGGTTCAA-GATTTGCTCACA
*
51612 TCGAGCGTGGGT
195 TCGA--GT---C
* * *
51624 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTACATTGCTTGTTTCAATCCACTT
1 TTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATTACTTGTTTCAATCCACTT
*
51689 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTATCAGTATCTAATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTACCAGTATCTAATCAGGAAGCTAACCAT
* * * * * * * *
51754 TTTATTGCTTCGACTTGCTTCTCAGTATCTCATTAGGAGGCTGAGGTTTGAAGATTTTCTCACAT
131 TTTATTACTTCAACTTGCTTCTCAGTATCTCATCAAGAAGCTGAGGGTTCAAGATTTGCTCACAT
51819 CGAGTC
196 CGAGTC
* * * * * * ***
51825 CTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTTACTTGTTTCAATTTGCTT
1 TTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATTACTTGTTTCAATCCACTT
*
51890 CTCTGTATCTCATCTGGAAG
66 CTCTGTATCTCATCAGGAAG
51910 CTGGGATTCG
Statistics
Matches: 240, Mismatches: 45, Indels: 7
0.82 0.15 0.02
Matches are distributed among these distances:
201 73 0.30
204 2 0.01
206 159 0.66
207 6 0.03
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (201 bp):
TTGACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATTACTTGTTTCAATCCACTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTACCAGTATCTAATCAGGAAGCTAACCAT
TTTATTACTTCAACTTGCTTCTCAGTATCTCATCAAGAAGCTGAGGGTTCAAGATTTGCTCACAT
CGAGTC
Found at i:52055 original size:115 final size:114
Alignment explanation
Indices: 51730--52045 Score: 389
Period size: 116 Copynumber: 2.7 Consensus size: 114
51720 TCACTTATCA
* * *
51730 GTATCTAATCAGGAAGCTAACCATTTTATTGCTTCGACTTGCTTCTCAGTATCTCATTAGGAGGC
1 GTATCTAATCAGGAAGCTAACCATTTTATTGTTTCGACTTGCTTCTCAGTATCTCATCAGGAAGC
* * * *
51795 TGAGGTTTGAAGATTTTCTCACATCGAGTCCTGAGTTGGTATTCTTCTCT
66 TG-GGTTCGAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCT
* * * *** * * * *
51845 GTATCTCATCAGGAAGATGACCGCCTTACTTGTTTCAATTTGCTTCTCTGTATCTCATCTGGAAG
1 GTATCTAATCAGGAAGCTAACCATTTTA-TTGTTTCGACTTGCTTCTCAGTATCTCATCAGGAAG
* *
51910 CTGGGATTCGAAGATCTGATCACATCGAGCCCTGAGTTGGTATACTTCTCT
65 CTGGG-TTCGAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCT
* * * *
51961 GTATCTTATCAGGAAGCTAACCATTTTATTATTTCGACCTACTTCTCAGTATCTCATCAGGAAGC
1 GTATCTAATCAGGAAGCTAACCATTTTATTGTTTCGACTTGCTTCTCAGTATCTCATCAGGAAGC
52026 TTGGGTTCGAAGATTTGCTC
66 -TGGGTTCGAAGATTTGCTC
52046 GCTTTGAGCC
Statistics
Matches: 164, Mismatches: 34, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
115 67 0.41
116 97 0.59
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (114 bp):
GTATCTAATCAGGAAGCTAACCATTTTATTGTTTCGACTTGCTTCTCAGTATCTCATCAGGAAGC
TGGGTTCGAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCT
Done.