Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008717.1 Hibiscus syriacus cultivar Beakdansim tig00111772_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3453450
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 16
Found at i:3231188 original size:22 final size:22
Alignment explanation
Indices: 3231160--3231201 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3231150 CTTTCTTTTC
3231160 TTTTC-TTCTTTTTGAGTGCTGA
1 TTTTCTTTC-TTTTGAGTGCTGA
3231182 TTTTCTTTCTTTTGAGTGCT
1 TTTTCTTTCTTTTGAGTGCT
3231202 TCACTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.07, C:0.14, G:0.17, T:0.62
Consensus pattern (22 bp):
TTTTCTTTCTTTTGAGTGCTGA
Found at i:3232173 original size:19 final size:19
Alignment explanation
Indices: 3232149--3232191 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
3232139 AGTGTCTTAG
3232149 TAGCTAACTAGGTGAGTTA
1 TAGCTAACTAGGTGAGTTA
3232168 TAGCTAACTAGGTGAGTTA
1 TAGCTAACTAGGTGAGTTA
3232187 TAGCT
1 TAGCT
3232192 TGATAAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.33
Consensus pattern (19 bp):
TAGCTAACTAGGTGAGTTA
Found at i:3233944 original size:2 final size:2
Alignment explanation
Indices: 3233937--3233972 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3233927 TTTTATGTAA
3233937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3233973 GAATGAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3234371 original size:118 final size:118
Alignment explanation
Indices: 3234098--3234593 Score: 516
Period size: 119 Copynumber: 4.2 Consensus size: 118
3234088 TCAAAGTTCA
* * * ** * * *
3234098 TCTGTGATGAATTTGAGCAACAAGTTGAATAAGTTCTTCTCATTATGAACTTCTTC-TCTTTCTT
1 TCTGTGATGGATTTGAGTAAAAAGTCAAATAAGTTATTCTCATTATGAACTTCTTCTTC-CTATT
* * *
3234162 TGGGCGAATTCTTCTCATTATGAGCCCCTACATTGGAAATGTTGATCCACCTTC-T
65 TGGACGAATTCTTCTCATTATGA-ACCCTTCATTGGAAATGTTGATCCACC-TCAT
* *
3234217 TCTGTGATGGACTTGAGTAAAAGGTCAAATAAGTTATTCTCATTATGAACTTCTTCTTCCTATTT
1 TCTGTGATGGATTTGAGTAAAAAGTCAAATAAGTTATTCTCATTATGAACTTCTTCTTCCTATTT
* * * ** * * * *
3234282 GGATGAGTTCTTCTCGTTATGAAATCTTTATTGGAAATGTTGAGCTACCTCCT
66 GGACGAATTCTTCTCATTATGAACCCTTCATTGGAAATGTTGATCCACCTCAT
** * *
3234335 TCTGTGATTAATTTGAGTAAAAAGTCAAATACGTTATTCTCATTATGAACTT-TTTTTCCT-TCT
1 TCTGTGATGGATTTGAGTAAAAAGTCAAATAAGTTATTCTCATTATGAACTTCTTCTTCCTAT-T
* * *
3234398 TCGGACGAATTATTCTCATTATGAACCCCTCCACTGGAAATGTTGATCCACCTCAT
65 T-GGACGAATTCTTCTCATTATGAA-CCCTTCATTGGAAATGTTGATCCACCTCAT
* * * * * *
3234454 TCTGTTATGGATTTGAGTAAAAGGTCAAACAAGTTCTTCTCATTATGAACTTATTATTCC-ACTT
1 TCTGTGATGGATTTGAGTAAAAAGTCAAATAAGTTATTCTCATTATGAACTTCTTCTTCCTA-TT
* * * * * *
3234518 TGGATGAGTTTTTCTCGTTATGAACTCTTCATTGGAAATGTTAATCCACCTCAT
65 TGGACGAATTCTTCTCATTATGAACCCTTCATTGGAAATGTTGATCCACCTCAT
*
3234572 TCTGTGATGGATTTGGGTAAAA
1 TCTGTGATGGATTTGAGTAAAA
3234594 TGTCGATGCT
Statistics
Matches: 312, Mismatches: 57, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
116 1 0.00
117 11 0.04
118 133 0.43
119 156 0.50
120 10 0.03
121 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (118 bp):
TCTGTGATGGATTTGAGTAAAAAGTCAAATAAGTTATTCTCATTATGAACTTCTTCTTCCTATTT
GGACGAATTCTTCTCATTATGAACCCTTCATTGGAAATGTTGATCCACCTCAT
Found at i:3234522 original size:237 final size:237
Alignment explanation
Indices: 3234098--3234593 Score: 681
Period size: 237 Copynumber: 2.1 Consensus size: 237
3234088 TCAAAGTTCA
* * ** * * *
3234098 TCTGTGATGAATTTGAGCAACAAGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTCTTTCTTT
1 TCTGTGATGAATTTGAGTAAAAAGTCAAATAAGTTATTCTCATTATGAACTTCTTCTCCTTCTTC
* * * *
3234163 GGGCGAATTCTTCTCATTATGAGCCCCTACATTGGAAATGTTGATCCACCTTCTTCTGTGATGGA
66 GGACGAATTATTCTCATTATGAACCCCTACACTGGAAATGTTGATCCACCTTCTTCTGTGATGGA
* * *
3234228 CTTGAGTAAAAGGTCAAATAAGTTATTCTCATTATGAACTTCTTCTTCCTATTTGGATGAGTTCT
131 CTTGAGTAAAAGGTCAAACAAGTTATTCTCATTATGAACTTATTATTCCTATTTGGATGAGTTCT
* * * *
3234293 TCTCGTTATGAAATCTTTATTGGAAATGTTGAGCTACCTCCT
196 TCTCGTTATGAAATCTTCATTGGAAATGTTAAGCCACCTCAT
* * * *
3234335 TCTGTGATTAATTTGAGTAAAAAGTCAAATACGTTATTCTCATTATGAACTTTTTTTCCTTCTTC
1 TCTGTGATGAATTTGAGTAAAAAGTCAAATAAGTTATTCTCATTATGAACTTCTTCTCCTTCTTC
* *
3234400 GGACGAATTATTCTCATTATGAACCCCTCCACTGGAAATGTTGATCCACC-TCATTCTGTTATGG
66 GGACGAATTATTCTCATTATGAACCCCTACACTGGAAATGTTGATCCACCTTC-TTCTGTGATGG
* *
3234464 ATTTGAGTAAAAGGTCAAACAAGTTCTTCTCATTATGAACTTATTATTCC-ACTTTGGATGAGTT
130 ACTTGAGTAAAAGGTCAAACAAGTTATTCTCATTATGAACTTATTATTCCTA-TTTGGATGAGTT
* * *
3234528 TTTCTCGTTATGAACTCTTCATTGGAAATGTTAATCCACCTCAT
194 CTTCTCGTTATGAAATCTTCATTGGAAATGTTAAGCCACCTCAT
* *
3234572 TCTGTGATGGATTTGGGTAAAA
1 TCTGTGATGAATTTGAGTAAAA
3234594 TGTCGATGCT
Statistics
Matches: 225, Mismatches: 32, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
236 3 0.01
237 222 0.99
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (237 bp):
TCTGTGATGAATTTGAGTAAAAAGTCAAATAAGTTATTCTCATTATGAACTTCTTCTCCTTCTTC
GGACGAATTATTCTCATTATGAACCCCTACACTGGAAATGTTGATCCACCTTCTTCTGTGATGGA
CTTGAGTAAAAGGTCAAACAAGTTATTCTCATTATGAACTTATTATTCCTATTTGGATGAGTTCT
TCTCGTTATGAAATCTTCATTGGAAATGTTAAGCCACCTCAT
Found at i:3234617 original size:118 final size:115
Alignment explanation
Indices: 3234192--3234593 Score: 389
Period size: 118 Copynumber: 3.4 Consensus size: 115
3234182 TGAGCCCCTA
* * * *
3234192 CATTGGAAATGTTGATCCACCTTC-TTCTGTGATGGACTTGAGTAAAAGGTCAAATAAGTTATTC
1 CATTGGAAATGTTGATCCACC-TCATTCTGTGATGGATTTGAGTAAAAAGTC--ATACGCTA-TC
* * *
3234256 TCATTATGAACTTCTTCTTCCTA-TTTGGATGAGTTCTTCTCGTTATGAAATCTT
62 TCATTATGAACTT-TTATTCCTACTTTGGATGAGTTATTCTCGTTATGAACTCTT
* * * * ** *
3234310 TATTGGAAATGTTGAGCTACCTCCTTCTGTGATTAATTTGAGTAAAAAGTCAAATACGTTATTCT
1 CATTGGAAATGTTGATCCACCTCATTCTGTGATGGATTTGAGTAAAAAGTC--ATACGCTA-TCT
* * * * * * * *
3234375 CATTATGAACTTTTTTTCCTTCTTCGGACGAATTATTCTCATTATGAACCCCTC
63 CATTATGAACTTTTATTCCTACTTTGGATGAGTTATTCTCGTTATGAA-CTCTT
* * * *
3234429 CACTGGAAATGTTGATCCACCTCATTCTGTTATGGATTTGAGTAAAAGGTCAAACAAGTTCT-TC
1 CATTGGAAATGTTGATCCACCTCATTCTGTGATGGATTTGAGTAAAAAGTCATAC--G--CTATC
*
3234493 TCATTATGAACTTATTATTCC-ACTTTGGATGAGTTTTTCTCGTTATGAACTCTT
62 TCATTATGAACTT-TTATTCCTACTTTGGATGAGTTATTCTCGTTATGAACTCTT
* *
3234547 CATTGGAAATGTTAATCCACCTCATTCTGTGATGGATTTGGGTAAAA
1 CATTGGAAATGTTGATCCACCTCATTCTGTGATGGATTTGAGTAAAA
3234594 TGTCGATGCT
Statistics
Matches: 234, Mismatches: 42, Indels: 16
0.80 0.14 0.05
Matches are distributed among these distances:
117 12 0.05
118 133 0.57
119 82 0.35
120 6 0.03
121 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (115 bp):
CATTGGAAATGTTGATCCACCTCATTCTGTGATGGATTTGAGTAAAAAGTCATACGCTATCTCAT
TATGAACTTTTATTCCTACTTTGGATGAGTTATTCTCGTTATGAACTCTT
Found at i:3236845 original size:26 final size:28
Alignment explanation
Indices: 3236816--3236872 Score: 91
Period size: 26 Copynumber: 2.1 Consensus size: 28
3236806 TTTAAGGACC
3236816 TTAAGTATAATTTCTCC-TT-TTTGACT
1 TTAAGTATAATTTCTCCTTTCTTTGACT
*
3236842 TTAAGTATAATTTTTCCTTTCTTTGACT
1 TTAAGTATAATTTCTCCTTTCTTTGACT
3236870 TTA
1 TTA
3236873 GAAAGTTCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 16 0.57
27 2 0.07
28 10 0.36
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (28 bp):
TTAAGTATAATTTCTCCTTTCTTTGACT
Found at i:3238844 original size:23 final size:23
Alignment explanation
Indices: 3238817--3238869 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
3238807 TCTTGAAAGA
3238817 CCACATAGGTTTGCACCAAAGTG
1 CCACATAGGTTTGCACCAAAGTG
* *
3238840 TCACATAGGTTTGCACCGAAGTG
1 CCACATAGGTTTGCACCAAAGTG
3238863 CCACATA
1 CCACATA
3238870 TTTGTCCCGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
CCACATAGGTTTGCACCAAAGTG
Found at i:3238887 original size:21 final size:21
Alignment explanation
Indices: 3238855--3238911 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 21
3238845 TAGGTTTGCA
3238855 CCGAAGTG-CCACATATTTGTC
1 CCGAAG-GACCACATATTTGTC
3238876 CCGCAA-GACCACATATTTGTC
1 CCG-AAGGACCACATATTTGTC
3238897 CCGAAGGACCACATA
1 CCGAAGGACCACATA
3238912 AGACCCTCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.09
21 28 0.85
22 2 0.06
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.21
Consensus pattern (21 bp):
CCGAAGGACCACATATTTGTC
Found at i:3239542 original size:54 final size:54
Alignment explanation
Indices: 3239457--3239601 Score: 202
Period size: 54 Copynumber: 2.7 Consensus size: 54
3239447 GATACTACCC
*
3239457 TTCAAGGGTATCGATACCTCCTCATGGTATCGATACCAAAATAACATTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTATCGATACCAAAATAACATTCGATGT
* * ** *
3239511 TTCAAGGGTATCGATACCTCCTCAAGATATCGATACCAATATGGCATTCGGTGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTATCGATACCAAAATAACATTCGATGT
*
3239565 TTTAAGGGTATCGATACCATCCTTC-AGGTATCGATAC
1 TTCAAGGGTATCGATACC-TCC-TCAAGGTATCGATAC
3239602 TACCCTTACG
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
54 65 0.80
55 14 0.17
56 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTCCTCAAGGTATCGATACCAAAATAACATTCGATGT
Found at i:3239596 original size:20 final size:20
Alignment explanation
Indices: 3239571--3239622 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3239561 GTGTTTTAAG
*
3239571 GGTATCGATACCATCCTT-C
1 GGTATCGATACCACCCTTAC
*
3239590 AGGTATCGATACTACCCTTAC
1 -GGTATCGATACCACCCTTAC
3239611 GGTATCGATACC
1 GGTATCGATACC
3239623 TCTATCAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (20 bp):
GGTATCGATACCACCCTTAC
Found at i:3239639 original size:22 final size:22
Alignment explanation
Indices: 3239611--3239666 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
3239601 CTACCCTTAC
* * *
3239611 GGTATCGATACCTCTATCAATA
1 GGTATCGATACATATATCAACA
3239633 GGTATCGATACATATATCAACA
1 GGTATCGATACATATATCAACA
*
3239655 GGTATCAATACA
1 GGTATCGATACA
3239667 ACCCTCTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (22 bp):
GGTATCGATACATATATCAACA
Found at i:3245795 original size:23 final size:23
Alignment explanation
Indices: 3245778--3245874 Score: 176
Period size: 23 Copynumber: 4.2 Consensus size: 23
3245768 CCGAAGGACT
*
3245778 ACATAGGTTTGCACCGAAGTGCC
1 ACATAGGTTTGCACCGAAGTGCA
3245801 ACATAGGTTTGCACCGAAGTGCA
1 ACATAGGTTTGCACCGAAGTGCA
3245824 ACATAGGTTTGCACCGAAGTGCA
1 ACATAGGTTTGCACCGAAGTGCA
*
3245847 ACATAGGTTTGCACCGAAGTGCC
1 ACATAGGTTTGCACCGAAGTGCA
3245870 ACATA
1 ACATA
3245875 TTTGTCCTGG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.22
Consensus pattern (23 bp):
ACATAGGTTTGCACCGAAGTGCA
Found at i:3245834 original size:46 final size:46
Alignment explanation
Indices: 3245741--3245874 Score: 177
Period size: 46 Copynumber: 3.0 Consensus size: 46
3245731 TAACTCGTAA
* * *
3245741 TTTGCATCGAAGTGCCACATA--ATTGTC-CCGAAG-GACTACATAGG
1 TTTGCACCGAAGTGCCACATAGGTTTG-CACCGAAGTG-CAACATAGG
3245785 TTTGCACCGAAGTGCCACATAGGTTTGCACCGAAGTGCAACATAGG
1 TTTGCACCGAAGTGCCACATAGGTTTGCACCGAAGTGCAACATAGG
* *
3245831 TTTGCACCGAAGTGCAACATAGGTTTGCACCGAAGTGCCACATA
1 TTTGCACCGAAGTGCCACATAGGTTTGCACCGAAGTGCAACATA
3245875 TTTGTCCTGG
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
44 20 0.25
45 1 0.01
46 59 0.73
47 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (46 bp):
TTTGCACCGAAGTGCCACATAGGTTTGCACCGAAGTGCAACATAGG
Found at i:3246536 original size:54 final size:54
Alignment explanation
Indices: 3246447--3246570 Score: 155
Period size: 54 Copynumber: 2.3 Consensus size: 54
3246437 GGTACTACCC
* *
3246447 TTCAAGGGTATCGATACCTCCTCATGGTATCGATACCGAA-ATAACATTCGATGT
1 TTCAAGGGTATCGATACCTCCACAAGGTATCGATACC-AATATAACATTCGATGT
* **
3246501 TTCAAGGGTATCGATACCTCCACAAGGTA-CTGATACCAATCTGGCATTCGATGT
1 TTCAAGGGTATCGATACCTCCACAAGGTATC-GATACCAATATAACATTCGATGT
*
3246555 TTTAAGGGTAT-GATAC
1 TTCAAGGGTATCGATAC
3246571 TATCCTTCAG
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
53 8 0.13
54 54 0.87
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTCCACAAGGTATCGATACCAATATAACATTCGATGT
Found at i:3246591 original size:20 final size:20
Alignment explanation
Indices: 3246566--3246610 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3246556 TTAAGGGTAT
*
3246566 GATACTATCCTT-CAGGAATC
1 GATACTACCCTTAC-GGAATC
*
3246586 GATACTACCCTTACGGTATC
1 GATACTACCCTTACGGAATC
3246606 GATAC
1 GATAC
3246611 CTCTATCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (20 bp):
GATACTACCCTTACGGAATC
Found at i:3246699 original size:22 final size:21
Alignment explanation
Indices: 3246661--3246701 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3246651 ATATTTAACC
* *
3246661 CATAAGGTATCGGTACCTGTT
1 CATAAGGTACCGATACCTGTT
3246682 CATAAGGGTACCGATACCTG
1 CATAA-GGTACCGATACCTG
3246702 AAACCCAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (21 bp):
CATAAGGTACCGATACCTGTT
Found at i:3248002 original size:20 final size:20
Alignment explanation
Indices: 3247977--3248018 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3247967 CCTGACTTTT
3247977 TTGGAAGACCTGT-AAATCAG
1 TTGGAAGA-CTGTAAAATCAG
*
3247997 TTGGAAGACTTTAAAATCAG
1 TTGGAAGACTGTAAAATCAG
3248017 TT
1 TT
3248019 ACTAATCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (20 bp):
TTGGAAGACTGTAAAATCAG
Found at i:3249531 original size:32 final size:31
Alignment explanation
Indices: 3249447--3249557 Score: 116
Period size: 32 Copynumber: 3.5 Consensus size: 31
3249437 CCTAAGGTGA
* *
3249447 CCTTGGGTAGGCTCTGAGGCCCCAAGGTATTT
1 CCTTGGGTAGGCTCTTAGGCCCCAAGGTA-CT
3249479 CCTTGGGTAGGCT-TTAAGGCCCCAAGGTACT
1 CCTTGGGTAGGCTCTT-AGGCCCCAAGGTACT
* * * *
3249510 CAGTTTGGTAAGCTCTTAGGCCCTAAGGTACT
1 C-CTTGGGTAGGCTCTTAGGCCCCAAGGTACT
*
3249542 CCTTTGGGCAGGCTCT
1 CC-TTGGGTAGGCTCT
3249558 CAAGATATTA
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
31 3 0.05
32 60 0.92
33 2 0.03
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (31 bp):
CCTTGGGTAGGCTCTTAGGCCCCAAGGTACT
Found at i:3256385 original size:14 final size:15
Alignment explanation
Indices: 3256357--3256396 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
3256347 TGAAATTACT
* *
3256357 GAAAAGTAAAGGACA
1 GAAAATTAAAAGACA
3256372 G-AAATTAAAAGACA
1 GAAAATTAAAAGACA
3256386 GAAAATTAAAA
1 GAAAATTAAAA
3256397 TAAATGGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.65, C:0.05, G:0.17, T:0.12
Consensus pattern (15 bp):
GAAAATTAAAAGACA
Found at i:3256967 original size:20 final size:20
Alignment explanation
Indices: 3256942--3256981 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3256932 ATCTTTAATA
3256942 ATTTTCAAATAATTTGTTGT
1 ATTTTCAAATAATTTGTTGT
3256962 ATTTTCAAATAATTTGTTGT
1 ATTTTCAAATAATTTGTTGT
3256982 TAATGCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (20 bp):
ATTTTCAAATAATTTGTTGT
Found at i:3257405 original size:2 final size:2
Alignment explanation
Indices: 3257398--3257423 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3257388 TTTTGCAGCA
3257398 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3257424 GACAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3263518 original size:6 final size:6
Alignment explanation
Indices: 3263507--3263549 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
3263497 TATATTATAT
* *
3263507 AAATAA ATATAA AAATAAA AAATAAA AAATAA AAATGA AAATA
1 AAATAA AAATAA AAAT-AA AAAT-AA AAATAA AAATAA AAATA
3263550 GTTAAAGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 19 0.59
7 13 0.41
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:3263522 original size:12 final size:12
Alignment explanation
Indices: 3263507--3263549 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
3263497 TATATTATAT
*
3263507 AAATAAATATAA
1 AAATAAAAATAA
3263519 AAATAAAAAATAAA
1 AAAT-AAAAAT-AA
*
3263533 AAATAAAAATGA
1 AAATAAAAATAA
3263545 AAATA
1 AAATA
3263550 GTTAAAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.37
13 11 0.41
14 6 0.22
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (12 bp):
AAATAAAAATAA
Found at i:3263547 original size:7 final size:7
Alignment explanation
Indices: 3263505--3263541 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
3263495 TATATATTAT
3263505 ATAAATAA
1 ATAAA-AA
3263513 ATATAAAA
1 ATA-AAAA
3263521 ATAAAAA
1 ATAAAAA
3263528 ATAAAAA
1 ATAAAAA
3263535 ATAAAAA
1 ATAAAAA
3263542 TGAAAATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 18 0.64
8 8 0.29
9 2 0.07
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (7 bp):
ATAAAAA
Found at i:3263921 original size:135 final size:132
Alignment explanation
Indices: 3263716--3264053 Score: 399
Period size: 135 Copynumber: 2.5 Consensus size: 132
3263706 AATCTGCTCT
* * * * *
3263716 ACTGTTTCTACAGGGTAGATTGAATTGAAAATGATTTGCTTCACTGCCCTTCAGGAAGACCAAAT
1 ACTG-TTCTTCAGGGAAGATTGAATCG-AATTGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
* * * *
3263781 ATGAAATAAGAGGAATCTGCTCC-GCTACTCTTTAGGGGAGAACAGACTCAATAAAAACTTTGAT
64 CTGAAAGAAGAAGAATCTACTCCAG-TACTCTTTA-GGGAGAACAGACTCAA-AAAAACTTTGAT
3263845 CCACTTC
126 CCACTTC
* * * * * *
3263852 GCTGTTCTTCAGGGAAGATTGAATCGAACTTGATTTGCTTCGCTACTCTTTAAGAAGATCAAATC
1 ACTGTTCTTCAGGGAAGATTGAATCGAA-TTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATC
* * ** * *
3263917 TGAAAGAAGAAGAATCTACTCCAGTACTCTTTAGGGAGATCAGACTCGAGGAAATTTTGATTCAC
65 TGAAAGAAGAAGAATCTACTCCAGTACTCTTTAGGGAGAACAGACTCAAAAAAACTTTGATCCAC
3263982 TTC
130 TTC
* *
3263985 ACTGCTCTTCAGGGAAGATTGAATCTGAATTGACTTGCTTCACTGCTCTTCAGGAAGACCAAATC
1 ACTGTTCTTCAGGGAAGATTGAATC-GAATTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATC
3264050 TGAA
65 TGAA
3264054 GGATTGACTC
Statistics
Matches: 170, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
133 72 0.42
134 19 0.11
135 75 0.44
136 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (132 bp):
ACTGTTCTTCAGGGAAGATTGAATCGAATTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCT
GAAAGAAGAAGAATCTACTCCAGTACTCTTTAGGGAGAACAGACTCAAAAAAACTTTGATCCACT
TC
Found at i:3264034 original size:133 final size:135
Alignment explanation
Indices: 3263726--3264053 Score: 405
Period size: 133 Copynumber: 2.4 Consensus size: 135
3263716 ACTGTTTCTA
* * * * *
3263726 CAGGGTAGATTGAAT-TGAAAATGATTTGCTTCACTGCCCTTCAGGAAGACCAAATATGAAATAA
1 CAGGGAAGATTGAATCTG-AATTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAA
* * *
3263790 GAGGAATCTGCTCCGCTACTCTTTAGGGGAGAACAGACTCAATAAAAACTTTGATCCACTTCGCT
65 GAAGAATCTACTCCGCTACTCTTTAGGGGAGAACAGACTCAATAAAAACTTTGATCCACTTCACT
*
3263855 GTTCTT
130 GCTCTT
* * * * *
3263861 CAGGGAAGATTGAATC-GAACTTGATTTGCTTCGCTACTCTTTAAGAAGATCAAATCTGAAAGAA
1 CAGGGAAGATTGAATCTGAA-TTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAA
* * ** * *
3263925 GAAGAATCTACTCCAG-TACTCTTTA-GGGAGATCAGACTCGA-GGAAATTTTGATTCACTTCAC
65 GAAGAATCTACTCC-GCTACTCTTTAGGGGAGAACAGACTCAATAAAAACTTTGATCCACTTCAC
3263987 TGCTCTT
129 TGCTCTT
*
3263994 CAGGGAAGATTGAATCTGAATTGACTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAA
1 CAGGGAAGATTGAATCTGAATTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAA
3264054 GGATTGACTC
Statistics
Matches: 163, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
133 72 0.44
134 19 0.12
135 71 0.44
136 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (135 bp):
CAGGGAAGATTGAATCTGAATTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAG
AAGAATCTACTCCGCTACTCTTTAGGGGAGAACAGACTCAATAAAAACTTTGATCCACTTCACTG
CTCTT
Found at i:3264139 original size:38 final size:38
Alignment explanation
Indices: 3264097--3264737 Score: 631
Period size: 38 Copynumber: 16.8 Consensus size: 38
3264087 AAAAGACTTA
3264097 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
**** *
3264135 AAAGATTGA-TTCCTCTTTGTAAGGGAGTC-AGTAATAAC
1 AAAGATTGACTT-CTCTTCACGAGGAAGTCAAG-AATAAC
* * *
3264173 AAAGATTCACTTCTCTTCATGAGGAAG-CAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *** *
3264210 AAAGATTGACTCCTCTTTGTGAGAAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
3264248 AAAGATTGACTCCTCTTCACGAGGGAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
3264286 AAAGATTGACTTCTCTTCACAAGGAAGTCAAAAATAAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT-AAC
* * *
3264325 AAAGATTGACTTCTCTTCGCGAGAAAGTGAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
3264363 AAATATTGACTCCTCTTCACAAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
** * * * **
3264401 AAAGATTGACACCTTTTCGCGAGGGAGTCGGGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
3264439 AAAGATTGACTTATCTTCACGTGTAAGTCAAGAGTAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * * *
3264477 AAAGATTTACTCCTCTTCGCAAGGGAGTCATGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
3264515 AAAGATTGATTTCTCTTCACGAGAAAGTCAAGAGTAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* ** * *
3264553 AAAGATTGACTCCTCTTCGTGAGGGAGTCAGGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
** *
3264591 AAAGATTGACTTCTCTTCACGAATAAGTCAAGAGTAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * * *
3264629 AAAGATTTACTCCTCTTCGCAAGGGAGTCAGGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
3264667 AAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATGAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
3264705 ATTGGAAGATCGACTCCTCTTCACGAGGGAGTC
1 A----AAGATTGACTTCTCTTCACGAGGAAGTC
3264738 GAATTGAAGC
Statistics
Matches: 479, Mismatches: 114, Indels: 16
0.79 0.19 0.03
Matches are distributed among these distances:
37 32 0.07
38 389 0.81
39 34 0.07
42 24 0.05
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (38 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:3264577 original size:152 final size:152
Alignment explanation
Indices: 3264097--3264737 Score: 721
Period size: 152 Copynumber: 4.2 Consensus size: 152
3264087 AAAAGACTTA
* * * * **** **
3264097 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGA-TTCCTCTTTGTAAGGGA
1 AAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTT-CTCTTCACGAGTAA
* * * *** * *
3264161 GTC-AGTAATAACAAAGATTCACTTCTCTTCATGAGGAAG-CAAGAATAAAAAAGATTGACTCCT
65 GTCAAG-AGTAACAAAGATTTACTCCTCTTCGCAAGGGAGTCAAGAATAACAAAGATTGACTCCT
***
3264224 CTTTGTGAGAAAGTCAAGAATAAC
129 CTTCACGAGAAAGTCAAGAATAAC
* * * *
3264248 AAAGATTGACTCCTCTTCACGAGGGAGTCAAGAATAACAAAGATTGACTTCTCTTCACAAGGAAG
1 AAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGTAAG
* * * * * * ** * *
3264313 TCAAAAATAAAAAAAGATTGACTTCTCTTCGCGAGAAAGTGAAGAATAACAAATATTGACTCCTC
66 TCAAGAGT-AACAAAGATTTACTCCTCTTCGCAAGGGAGTCAAGAATAACAAAGATTGACTCCTC
* *
3264378 TTCACAAGGAAGTCAAGAATAAC
130 TTCACGAGAAAGTCAAGAATAAC
* * * * *
3264401 AAAGATTGACACCTTTTCGCGAGGGAGTCGGGAATAACAAAGATTGACTTATCTTCACGTGTAAG
1 AAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGTAAG
* * *
3264466 TCAAGAGTAACAAAGATTTACTCCTCTTCGCAAGGGAGTCATGAATAACAAAGATTGATTTCTCT
66 TCAAGAGTAACAAAGATTTACTCCTCTTCGCAAGGGAGTCAAGAATAACAAAGATTGACTCCTCT
*
3264531 TCACGAGAAAGTCAAGAGTAAC
131 TCACGAGAAAGTCAAGAATAAC
* *
3264553 AAAGATTGACTCCTCTTCGTGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAATAAG
1 AAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGTAAG
* *
3264618 TCAAGAGTAACAAAGATTTACTCCTCTTCGCAAGGGAGTCAGGAATAACAAAGATTGACTTCTCT
66 TCAAGAGTAACAAAGATTTACTCCTCTTCGCAAGGGAGTCAAGAATAACAAAGATTGACTCCTCT
*
3264683 TCACGAGAAAGTCAAGAATGAC
131 TCACGAGAAAGTCAAGAATAAC
* *
3264705 ATTGGAAGATCGACTCCTCTTCACGAGGGAGTC
1 A----AAGATTGACTCCTCTTCGCGAGGGAGTC
3264738 GAATTGAAGC
Statistics
Matches: 423, Mismatches: 59, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
151 61 0.14
152 235 0.56
153 102 0.24
156 25 0.06
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (152 bp):
AAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGTAAG
TCAAGAGTAACAAAGATTTACTCCTCTTCGCAAGGGAGTCAAGAATAACAAAGATTGACTCCTCT
TCACGAGAAAGTCAAGAATAAC
Found at i:3266023 original size:45 final size:46
Alignment explanation
Indices: 3265900--3266011 Score: 160
Period size: 43 Copynumber: 2.5 Consensus size: 46
3265890 CTTGTATTCA
* *
3265900 TGGATGATATGGGCCTTCAAAAGATGCCCCAACATTTATCATTTCT
1 TGGATAATATGGGCCTTCAAAAAATGCCCCAACATTTATCATTTCT
* *
3265946 T-GCTAATAT--GCCTTCAAAAAATGCCCCAACATTTATTATTT-T
1 TGGATAATATGGGCCTTCAAAAAATGCCCCAACATTTATCATTTCT
3265988 TGGATAATATGGGCCTTCAAAAAA
1 TGGATAATATGGGCCTTCAAAAAA
3266012 AACCCTAACA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
42 2 0.03
43 37 0.64
45 18 0.31
46 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (46 bp):
TGGATAATATGGGCCTTCAAAAAATGCCCCAACATTTATCATTTCT
Found at i:3273358 original size:13 final size:13
Alignment explanation
Indices: 3273340--3273364 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3273330 ATCGGGTTTT
3273340 AAAATAAATAAAA
1 AAAATAAATAAAA
3273353 AAAATAAATAAA
1 AAAATAAATAAA
3273365 TTTGGAGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAAATAAAA
Found at i:3275214 original size:22 final size:22
Alignment explanation
Indices: 3275179--3275249 Score: 83
Period size: 22 Copynumber: 3.1 Consensus size: 22
3275169 AAAATATTAT
*
3275179 ATAAATAAATATAAAAGTAGAAA
1 ATAAATAAAAATAAAA-TAGAAA
3275202 ATAAA-AAAAATAAAATACGAAA
1 ATAAATAAAAATAAAATA-GAAA
3275224 ATAGAATAAAAATGAAAAT-GAAA
1 ATA-AATAAAAAT-AAAATAGAAA
3275247 ATA
1 ATA
3275250 GTTAAATAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
21 2 0.05
22 16 0.37
23 14 0.33
24 6 0.14
25 5 0.12
ACGTcount: A:0.72, C:0.01, G:0.08, T:0.18
Consensus pattern (22 bp):
ATAAATAAAAATAAAATAGAAA
Found at i:3275249 original size:18 final size:18
Alignment explanation
Indices: 3275204--3275249 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3275194 AGTAGAAAAT
3275204 AAAA-AAAATAAAATACG
1 AAAATAAAATAAAATACG
* *
3275221 AAAATAGAATAAAA-ATG
1 AAAATAAAATAAAATACG
3275238 AAAATGAAAATA
1 AAAAT-AAAATA
3275250 GTTAAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (18 bp):
AAAATAAAATAAAATACG
Found at i:3277186 original size:26 final size:25
Alignment explanation
Indices: 3277154--3277204 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
3277144 TTATATTAGG
*
3277154 GACAAATCTCTAAAATTTTAAGAGGA
1 GACAAATCTATAAAATTTT-AGAGGA
*
3277180 GACAAATTTATAAAATTTTAGAGGA
1 GACAAATCTATAAAATTTTAGAGGA
3277205 TGAAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (25 bp):
GACAAATCTATAAAATTTTAGAGGA
Found at i:3277306 original size:13 final size:13
Alignment explanation
Indices: 3277288--3277333 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
3277278 TGTCCTCGCT
3277288 CATCCCCTTAATC
1 CATCCCCTTAATC
*
3277301 CATCCCCTTAATA
1 CATCCCCTTAATC
*
3277314 AATCCCCTTAATC
1 CATCCCCTTAATC
3277327 CATCCCC
1 CATCCCC
3277334 GATTCCATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.26, C:0.46, G:0.00, T:0.28
Consensus pattern (13 bp):
CATCCCCTTAATC
Found at i:3284889 original size:23 final size:23
Alignment explanation
Indices: 3284861--3284915 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
3284851 GCTGGGCGTT
*
3284861 GCTTCAATGACGATTAAAGGATG
1 GCTTCAATGACGATTAAAGGACG
3284884 GCTTCAATGACGATTAAAGGACG
1 GCTTCAATGACGATTAAAGGACG
*
3284907 ACTTCAATG
1 GCTTCAATG
3284916 GTGATGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (23 bp):
GCTTCAATGACGATTAAAGGACG
Found at i:3291807 original size:17 final size:17
Alignment explanation
Indices: 3291785--3291821 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3291775 TTCGAAATAA
3291785 ATTTACCAATCATATCT
1 ATTTACCAATCATATCT
3291802 ATTTACCAATCATATCT
1 ATTTACCAATCATATCT
3291819 ATT
1 ATT
3291822 GACTATACGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTACCAATCATATCT
Found at i:3298013 original size:7 final size:7
Alignment explanation
Indices: 3298001--3298029 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
3297991 AACAGAATTC
3298001 ATATCAT
1 ATATCAT
3298008 ATATCAT
1 ATATCAT
3298015 ATATCAT
1 ATATCAT
3298022 ATATCAT
1 ATATCAT
3298029 A
1 A
3298030 ACAGAATCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (7 bp):
ATATCAT
Found at i:3302651 original size:937 final size:937
Alignment explanation
Indices: 3300838--3302705 Score: 3116
Period size: 937 Copynumber: 2.0 Consensus size: 937
3300828 GCTCGATTCC
*
3300838 AAAACGTCGAAAACTTTGACGGTCTCAACCCTCCACGTGTCGGTGACGACGGAGAAACGGAGAAC
1 AAAACGTCGAAAACTTTGACGGTCTCAACCCTCCACGCGTCGGTGACGACGGAGAAACGGAGAAC
*
3300903 ACCGGTGGACTCGGAACGGCAAAAGGAACATGATGGTGCGAGAGGAGTCGAAAACGGATGGTCGG
66 ACCGGTGGACTCGGAACGGCAAAAGGAACATGATGGTGCGAGAGGAGTCGAAAACGGATGGTCGA
* * *
3300968 ATTGTCGTAAATCGACGAAAAACCAACTCAAATCAAGTTATTACCGATGATACTTATAACTTAAA
131 ATTATCGTAAATCGACGAAAAACCAACTCAAATCAAGTTATTACCAACGATACTTATAACTTAAA
* * *
3301033 TTAACGACGAACAACGATGATTCAAGACGAAAGGTTTGAGGGGTTTTTTTCCTTGGTCGACAACG
196 TTAACGACGAACAACGAAGATTCAAGACGAAAGGTTTAAGGGGTTTTGTTCCTTGGTCGACAACG
** * **
3301098 AACACGATGGTGGTTTCGATTCGTCAATCAGAGGTCAGATGGTGAGTAGATTGGAGTTGAAAGGA
261 AACACGATGGTGGTTTCGATTCGTCAATCAGAGGTCAGACAGCGAGTAGATCAGAGTTGAAAGGA
3301163 GGGTTGAGGAGAAGAGGAAAACAGAGAAATATGCACAGAAAACATACGGGAATGGGTTTATAATT
326 GGGTTGAGGAGAAGAGGAAAACAGAGAAATATGCACAGAAAACATACGGGAATGGGTTTATAATT
3301228 CATTCCAAAAGAAAAATGGGTAAACTATGAGTTTAGCCACTGAACTTCCTACACTTCTTAAAAAG
391 CATTCCAAAAGAAAAATGGGTAAACTATGAGTTTAGCCACTGAACTTCCTACACTTCTTAAAAAG
* *
3301293 GTCTGCCAACTTTACGATTTTATAATTTTATCCTCAATTTTCTTCCAAAATACTAATTAAATCCA
456 GTCTGCCAACTTTACGATTTTATAATTTAATCCTCAATTTTCTTCCAAAATACCAATTAAATCCA
*
3301358 CCACTTTATAATTTCTAAAATTTAGCCCCTAAATTAGGGTGTTACAATTCTCCCCTCCTTAAAAG
521 CCACTTTATAATTTCTAAAATTTAGCCCCTAAATTAGGGTGTTACAATCCTCCCCTCCTTAAAAG
* *
3301423 AATTTCATACTCGAAATTCATTCATGTCATATAATTATAGAAATGAAACCTCCATCAGTTCTTTC
586 AATTTCATACTCGAAATTCATTCATGTCACATAATTACAGAAATGAAACCTCCATCAGTTCTTTC
* * *
3301488 ATATTTTTAAGTAGCTTTTATAAAAGTACGGATCCTCCACTAATCCTTAACTAGCTGAGCATACA
651 ATATTTTTAAGTAGCTTTTACAAAAGTACGGATCCCCCACTAATCCTTAACCAGCTGAGCATACA
3301553 TTCTTAAAAGAACTTTTCCACTTTTCAAAAAAATAATCAAAACAACTTTATCCTTGTGAAATCAA
716 TTCTTAAAAGAACTTTTCCACTTTTCAAAAAAATAATCAAAACAACTTTATCCTTGTGAAATCAA
3301618 TTCAGCCTTGGTTACGTGAATAGGCTCACAGAGCAGCAGCATATCCCAATTTCATTTCTGGAGTC
781 TTCAGCCTTGGTTACGTGAATAGGCTCACAGAGCAGCAGCATATCCCAATTTCATTTCTGGAGTC
* *
3301683 GGGTCAACATTTCTCGGATAATTAACTCTCACACGGCTTGGGGGTACTTTACAGCGTCTAGACAG
846 GGGTCAACATTTCTCGGATAATTAACTCTCACACGGCTCGGGGGTACTTTACAGCATCTAGACAG
3301748 ATGTTACTGGTATTCCTTTTTAACTCG
911 ATGTTACTGGTATTCCTTTTTAACTCG
* *
3301775 AAAACGTC-ATAAACTTTGACGGTCTCACCCCTCCACGCGTCGGTGATGACGGAGAAACGGAGAA
1 AAAACGTCGA-AAACTTTGACGGTCTCAACCCTCCACGCGTCGGTGACGACGGAGAAACGGAGAA
* * *
3301839 CACCGGTGGACTCGGAACGGCACAAGGAACATGATGGTGCGGGAGGTGTCGAAAACGGATGGTCG
65 CACCGGTGGACTCGGAACGGCAAAAGGAACATGATGGTGCGAGAGGAGTCGAAAACGGATGGTCG
* * *
3301904 AATTATCGTGAATCGACGAAAAACCAACTGAAATCGAGTTATTACCAACGATACTT-TCAACTTA
130 AATTATCGTAAATCGACGAAAAACCAACTCAAATCAAGTTATTACCAACGATACTTAT-AACTTA
* **** *
3301968 AATTAATGACGAAGGGTGAAGATTCATA-ATGAAAGGTTTAAGGGGTTTTGTTCCTTGGTCGACA
194 AATTAACGACGAACAACGAAGATTCA-AGACGAAAGGTTTAAGGGGTTTTGTTCCTTGGTCGACA
* *
3302032 ACGAACACGATGGTGGTTTC-AGTTCGTCGATCGGAGGTC-GAACAGCGAGTAGATCAGAGTTGA
258 ACGAACACGATGGTGGTTTCGA-TTCGTCAATCAGAGGTCAG-ACAGCGAGTAGATCAGAGTTGA
* * * *
3302095 AAGGAGGGTTGAGGAGAAGAGGAAAACTGAGAAATATGCGCAGAAAACATATGTGAATGGGTTTA
321 AAGGAGGGTTGAGGAGAAGAGGAAAACAGAGAAATATGCACAGAAAACATACGGGAATGGGTTTA
*
3302160 TAATTCATTCCAAAAGAAAAATGGGTAAACTATGAGTTTAGCCACTGAACTTCCTGCACTTCTTA
386 TAATTCATTCCAAAAGAAAAATGGGTAAACTATGAGTTTAGCCACTGAACTTCCTACACTTCTTA
* * *
3302225 AAATGGTCTGCCAACTTTAGGATTTTATAATTTAATCCTCACTTTTCTTCCAAAATACCAATTAA
451 AAAAGGTCTGCCAACTTTACGATTTTATAATTTAATCCTCAATTTTCTTCCAAAATACCAATTAA
* *
3302290 ATCCACCACTTTATAATTTCTAAAATTTAGCCCCTAAATTGGGGTGTTGCAATCCTCCCCTCCTT
516 ATCCACCACTTTATAATTTCTAAAATTTAGCCCCTAAATTAGGGTGTTACAATCCTCCCCTCCTT
* * * * *
3302355 TAAAGAATTTCATCCTCGAAATTCATTCATGTCACATAATTGCATAAATGAAACTTCCATCAGTT
581 AAAAGAATTTCATACTCGAAATTCATTCATGTCACATAATTACAGAAATGAAACCTCCATCAGTT
*
3302420 CTTTCATATTTTTAAGTAGTTTTTACAAAAGTACGGATCCCCCACTAATCCTTAACCAGCTGAGC
646 CTTTCATATTTTTAAGTAGCTTTTACAAAAGTACGGATCCCCCACTAATCCTTAACCAGCTGAGC
3302485 ATACATTCTTAAAAGAACTTTTCCACTTTTCAAAAAAATAATCAAAACAACTTTATCCTTGTGAA
711 ATACATTCTTAAAAGAACTTTTCCACTTTTCAAAAAAATAATCAAAACAACTTTATCCTTGTGAA
* *
3302550 ATCAATTCAGCCTTGGTTACGTGAATAGGCTCATAGAGCAGTAGCATATCCCAATTTCATTTCTG
776 ATCAATTCAGCCTTGGTTACGTGAATAGGCTCACAGAGCAGCAGCATATCCCAATTTCATTTCTG
* *
3302615 GAGTCGGGTCAGCATTTCTCGGATAATTAACTCTCACATGGCTCGGGGGTACTTTACAGCATCTA
841 GAGTCGGGTCAACATTTCTCGGATAATTAACTCTCACACGGCTCGGGGGTACTTTACAGCATCTA
*
3302680 GACAGATGTTACTGGTATTTCTTTTT
906 GACAGATGTTACTGGTATTCCTTTTT
3302706 GTACAAGTAT
Statistics
Matches: 866, Mismatches: 60, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
936 4 0.00
937 861 0.99
938 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (937 bp):
AAAACGTCGAAAACTTTGACGGTCTCAACCCTCCACGCGTCGGTGACGACGGAGAAACGGAGAAC
ACCGGTGGACTCGGAACGGCAAAAGGAACATGATGGTGCGAGAGGAGTCGAAAACGGATGGTCGA
ATTATCGTAAATCGACGAAAAACCAACTCAAATCAAGTTATTACCAACGATACTTATAACTTAAA
TTAACGACGAACAACGAAGATTCAAGACGAAAGGTTTAAGGGGTTTTGTTCCTTGGTCGACAACG
AACACGATGGTGGTTTCGATTCGTCAATCAGAGGTCAGACAGCGAGTAGATCAGAGTTGAAAGGA
GGGTTGAGGAGAAGAGGAAAACAGAGAAATATGCACAGAAAACATACGGGAATGGGTTTATAATT
CATTCCAAAAGAAAAATGGGTAAACTATGAGTTTAGCCACTGAACTTCCTACACTTCTTAAAAAG
GTCTGCCAACTTTACGATTTTATAATTTAATCCTCAATTTTCTTCCAAAATACCAATTAAATCCA
CCACTTTATAATTTCTAAAATTTAGCCCCTAAATTAGGGTGTTACAATCCTCCCCTCCTTAAAAG
AATTTCATACTCGAAATTCATTCATGTCACATAATTACAGAAATGAAACCTCCATCAGTTCTTTC
ATATTTTTAAGTAGCTTTTACAAAAGTACGGATCCCCCACTAATCCTTAACCAGCTGAGCATACA
TTCTTAAAAGAACTTTTCCACTTTTCAAAAAAATAATCAAAACAACTTTATCCTTGTGAAATCAA
TTCAGCCTTGGTTACGTGAATAGGCTCACAGAGCAGCAGCATATCCCAATTTCATTTCTGGAGTC
GGGTCAACATTTCTCGGATAATTAACTCTCACACGGCTCGGGGGTACTTTACAGCATCTAGACAG
ATGTTACTGGTATTCCTTTTTAACTCG
Found at i:3303484 original size:14 final size:16
Alignment explanation
Indices: 3303451--3303481 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3303441 GTGAAAAGAT
3303451 ACATATATTTTTTAAA
1 ACATATATTTTTTAAA
3303467 ACATA-ATTTTTTAAA
1 ACATATATTTTTTAAA
3303482 CATTCAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
ACATATATTTTTTAAA
Found at i:3303854 original size:14 final size:14
Alignment explanation
Indices: 3303835--3303863 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3303825 AACAGAATTC
3303835 ATATCATATATCAG
1 ATATCATATATCAG
3303849 ATATCATATATCAG
1 ATATCATATATCAG
3303863 A
1 A
3303864 ACATAATCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (14 bp):
ATATCATATATCAG
Found at i:3303905 original size:24 final size:24
Alignment explanation
Indices: 3303858--3303909 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3303848 GATATCATAT
*
3303858 ATCAGAACATAATCCAGATCAGAA
1 ATCAGAACATAATCCAGATAAGAA
*
3303882 ATCAGAACATAATTC-GAATAAGAA
1 ATCAGAACATAATCCAG-ATAAGAA
3303906 ATCA
1 ATCA
3303910 AAATATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (24 bp):
ATCAGAACATAATCCAGATAAGAA
Found at i:3310124 original size:22 final size:20
Alignment explanation
Indices: 3310075--3310124 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
3310065 ACACCATCTC
*
3310075 CATTTCATCATCAACACCAT
1 CATTTCATCATCAAAACCAT
*
3310095 CATCTTCATCCATTAAAACCAT
1 CAT-TTCAT-CATCAAAACCAT
3310117 CAATTTCA
1 C-ATTTCA
3310125 CAACCATCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 15 0.60
23 2 0.08
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (20 bp):
CATTTCATCATCAAAACCAT
Found at i:3310448 original size:22 final size:23
Alignment explanation
Indices: 3310423--3310491 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 23
3310413 AATTGGAGTG
3310423 AAGAAAGAAAAGAAAAGA-CA-AA
1 AAGAAAGAAAAGAAAA-ATCAGAA
3310445 AAG-AAG-AAAGAAAAATTCAGAA
1 AAGAAAGAAAAGAAAAA-TCAGAA
**
3310467 AA-AAAGAAAAGAAAAAGAAGAA
1 AAGAAAGAAAAGAAAAATCAGAA
3310489 AAG
1 AAG
3310492 TTAAAAGGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
19 1 0.03
20 8 0.21
21 5 0.13
22 16 0.41
23 9 0.23
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (23 bp):
AAGAAAGAAAAGAAAAATCAGAA
Found at i:3315700 original size:22 final size:21
Alignment explanation
Indices: 3315663--3315703 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3315653 CCATCTCCAT
*
3315663 TTCATCATCAACACCATCATC
1 TTCATCATCAAAACCATCATC
3315684 TTCATCCATCAAAACCATCA
1 TTCAT-CATCAAAACCATCA
3315704 ATTCCGCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.27
Consensus pattern (21 bp):
TTCATCATCAAAACCATCATC
Found at i:3340246 original size:168 final size:166
Alignment explanation
Indices: 3339968--3340301 Score: 650
Period size: 168 Copynumber: 2.0 Consensus size: 166
3339958 CACACACATG
3339968 AGCCAAGTTTCATCATTCTTTGGCACAAGTAGAACCGGCACGGCACATGGGCTAAGGTTTTCCCT
1 AGCCAAGTTTCATCATTCTTTGGCACAAGTAGAACCGGCACGGCACATGGGCTAAGGTTTTCCCT
3340033 CACGTATCCTTTGGCGATCAACTCAGATACGTGCCTTTGCAATTCCTTAGTTTCTTCGGGGGACC
66 CACGTATCCTTTGGCGATCAACTCAGATACGTGCCTTTGCAATTCCTTAG-TTCTTCGGGGGA-C
3340098 AAATGATATGATCCCGATTATGTGTTTCGAGTCATATA
129 AAATGATATGATCCCGATTATGTGTTTCGAGTCATATA
3340136 AGCCAAGTTTCATCATTCTTTGGCACAAGTAGAACCGGCACGGCACATGGGCTAAGGTTTTCCCT
1 AGCCAAGTTTCATCATTCTTTGGCACAAGTAGAACCGGCACGGCACATGGGCTAAGGTTTTCCCT
3340201 CACGTATCCTTTGGCGATCAACTCAGATACGTGCCTTTGCAATTCCTTAGTTCTTCGGGGGACAA
66 CACGTATCCTTTGGCGATCAACTCAGATACGTGCCTTTGCAATTCCTTAGTTCTTCGGGGGACAA
3340266 ATGATATGATCCCGATTATGTGTTTCGAGTCATATA
131 ATGATATGATCCCGATTATGTGTTTCGAGTCATATA
3340302 TGTGAATGCC
Statistics
Matches: 166, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
166 39 0.23
167 12 0.07
168 115 0.69
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (166 bp):
AGCCAAGTTTCATCATTCTTTGGCACAAGTAGAACCGGCACGGCACATGGGCTAAGGTTTTCCCT
CACGTATCCTTTGGCGATCAACTCAGATACGTGCCTTTGCAATTCCTTAGTTCTTCGGGGGACAA
ATGATATGATCCCGATTATGTGTTTCGAGTCATATA
Found at i:3356621 original size:18 final size:18
Alignment explanation
Indices: 3356598--3356640 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3356588 GACAAGTCAG
**
3356598 TAACATTGAAGGTTGCAC
1 TAACATTGAAAATTGCAC
*
3356616 TAACATTGAAAATTGCAG
1 TAACATTGAAAATTGCAC
3356634 TAACATT
1 TAACATT
3356641 AAACTCACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (18 bp):
TAACATTGAAAATTGCAC
Found at i:3362249 original size:16 final size:17
Alignment explanation
Indices: 3362228--3362261 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3362218 ATAATTAGTA
*
3362228 ATAAAA-AAATAACCTC
1 ATAAAACAAAAAACCTC
3362244 ATAAAACAAAAAACCTC
1 ATAAAACAAAAAACCTC
3362261 A
1 A
3362262 CCAAACACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.65, C:0.21, G:0.00, T:0.15
Consensus pattern (17 bp):
ATAAAACAAAAAACCTC
Found at i:3364425 original size:13 final size:13
Alignment explanation
Indices: 3364393--3364426 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3364383 GTGATGGTCT
* *
3364393 TGATGAAGGTTGT
1 TGATGATGGTTGA
3364406 TGATGATGGTTGA
1 TGATGATGGTTGA
3364419 TGATGATG
1 TGATGATG
3364427 AAATGACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (13 bp):
TGATGATGGTTGA
Found at i:3367105 original size:13 final size:12
Alignment explanation
Indices: 3367086--3367171 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
3367076 ATATAGGCGT
3367086 GATATGGTGATG
1 GATATGGTGATG
3367098 GAATATGGTGAT-
1 G-ATATGGTGATG
*
3367110 GATATAGGCG-T-
1 GATAT-GGTGATG
3367121 GATAATGGTGATG
1 GAT-ATGGTGATG
3367134 GACTATGGTGAT-
1 GA-TATGGTGATG
*
3367146 GATATAGGCG-T-
1 GATAT-GGTGATG
3367157 GATAATGGTGATG
1 GAT-ATGGTGATG
3367170 GA
1 GA
3367172 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:3367141 original size:36 final size:36
Alignment explanation
Indices: 3367068--3367172 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
3367058 ATTTATAAGT
* *
3367068 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
3367103 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
3367139 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
3367173 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:3372811 original size:13 final size:12
Alignment explanation
Indices: 3372792--3372877 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
3372782 ATATAGGCGT
3372792 GATATGGTGATG
1 GATATGGTGATG
3372804 GAATATGGTGAT-
1 G-ATATGGTGATG
*
3372816 GATATAGGCG-T-
1 GATAT-GGTGATG
3372827 GATAATGGTGATG
1 GAT-ATGGTGATG
3372840 GACTATGGTGAT-
1 GA-TATGGTGATG
*
3372852 GATATAGGCG-T-
1 GATAT-GGTGATG
3372863 GATAATGGTGATG
1 GAT-ATGGTGATG
3372876 GA
1 GA
3372878 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:3372847 original size:36 final size:36
Alignment explanation
Indices: 3372774--3372878 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
3372764 ATTTATAAGT
* *
3372774 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
3372809 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
3372845 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
3372879 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:3375638 original size:22 final size:23
Alignment explanation
Indices: 3375613--3375660 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
3375603 CTTGGCTTGC
*
3375613 TTTCTTTT-TGAATTTTTTTCTT
1 TTTCTTTTCTGAATTTTCTTCTT
3375635 TTTCTTTTCTGAATTTTCTTCTT
1 TTTCTTTTCTGAATTTTCTTCTT
3375658 TTT
1 TTT
3375661 TGTACTCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.75
Consensus pattern (23 bp):
TTTCTTTTCTGAATTTTCTTCTT
Found at i:3376048 original size:13 final size:13
Alignment explanation
Indices: 3376016--3376049 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3376006 GTGATGGTCT
* *
3376016 TGATGAAGGTTGT
1 TGATGATGGTTGA
3376029 TGATGATGGTTGA
1 TGATGATGGTTGA
3376042 TGATGATG
1 TGATGATG
3376050 AAATGACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (13 bp):
TGATGATGGTTGA
Found at i:3378601 original size:25 final size:25
Alignment explanation
Indices: 3378567--3378623 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
3378557 GTCATGACAG
* *
3378567 GTAGAAATGAGGCATCTTTTTCGTC
1 GTAGAAATGAGCCATCTTTGTCGTC
3378592 GTAGAAATGAGCCATCTTTGTCGTC
1 GTAGAAATGAGCCATCTTTGTCGTC
3378617 GTAGAAA
1 GTAGAAA
3378624 CAAAGCAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (25 bp):
GTAGAAATGAGCCATCTTTGTCGTC
Found at i:3380315 original size:22 final size:20
Alignment explanation
Indices: 3380289--3380335 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3380279 GTCAACGCTA
*
3380289 GTCAACAACCCGTCAATGATGG
1 GTCAACAA-CCGTCAATG-TCG
*
3380311 GTCAACAACGGTCAATGTCG
1 GTCAACAACCGTCAATGTCG
3380331 GTCAA
1 GTCAA
3380336 TGGTTGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 8 0.35
22 8 0.35
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (20 bp):
GTCAACAACCGTCAATGTCG
Found at i:3380588 original size:25 final size:25
Alignment explanation
Indices: 3380558--3380613 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
3380548 GCATAAAGCC
*
3380558 CACGTGTAGGGGCAATGCATGGGAG
1 CACGTGTAGGGACAATGCATGGGAG
* *
3380583 CACGTGTAGGGACAGTGCATGGGGG
1 CACGTGTAGGGACAATGCATGGGAG
3380608 CACGTG
1 CACGTG
3380614 CGGCATCTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.21, C:0.18, G:0.45, T:0.16
Consensus pattern (25 bp):
CACGTGTAGGGACAATGCATGGGAG
Found at i:3385861 original size:40 final size:39
Alignment explanation
Indices: 3385781--3385878 Score: 144
Period size: 40 Copynumber: 2.5 Consensus size: 39
3385771 AGTCAATAAT
* *
3385781 ATATGCACCGTAGTGCTTACACATAAGGTCGTGGCCACC
1 ATATGCACCGAAGTGCTTACACATAAGGTCATGGCCACC
*
3385820 ATATGCACCGAAGTGCATTACATATAAGGTCAT-GCCAACC
1 ATATGCACCGAAGTGC-TTACACATAAGGTCATGGCC-ACC
3385860 ATATGCACCGAAGTGCTTA
1 ATATGCACCGAAGTGCTTA
3385879 ATCGACATGC
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
39 21 0.39
40 33 0.61
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (39 bp):
ATATGCACCGAAGTGCTTACACATAAGGTCATGGCCACC
Found at i:3387921 original size:17 final size:18
Alignment explanation
Indices: 3387895--3387936 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
3387885 CGAATTTTTA
*
3387895 CCAGACTTTAACAC-TTT
1 CCAGATTTTAACACATTT
3387912 CCAGATTTTAACACAATTT
1 CCAGATTTTAACAC-ATTT
3387931 CCAGAT
1 CCAGAT
3387937 AAAGAATCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.59
19 9 0.41
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (18 bp):
CCAGATTTTAACACATTT
Found at i:3388909 original size:13 final size:13
Alignment explanation
Indices: 3388891--3388916 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3388881 GTAATGAAGA
3388891 AAACTTTAGTTAT
1 AAACTTTAGTTAT
3388904 AAACTTTAGTTAT
1 AAACTTTAGTTAT
3388917 TAAATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
AAACTTTAGTTAT
Found at i:3393540 original size:20 final size:21
Alignment explanation
Indices: 3393490--3393541 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 21
3393480 TACAACCTTC
3393490 TTTTATCATTTTATTTAATTAA
1 TTTTATC-TTTTATTTAATTAA
* * *
3393512 TTATA-CTTTT-TTTTATTAT
1 TTTTATCTTTTATTTAATTAA
3393531 TTTTATCTTTT
1 TTTTATCTTTT
3393542 GAAAATTGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 11 0.44
20 9 0.36
21 1 0.04
22 4 0.16
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTATCTTTTATTTAATTAA
Found at i:3394030 original size:46 final size:46
Alignment explanation
Indices: 3393980--3394111 Score: 156
Period size: 46 Copynumber: 2.9 Consensus size: 46
3393970 TCATTATCGG
* *
3393980 ATGATAAATCCAATTATCAAAATACATGCTGGTGCATCCTCACCGA
1 ATGATAAATCCAATTATCGAATTACATGCTGGTGCATCCTCACCGA
* * * * * *
3394026 ATGATAAATCCGATTATCGATTTACAGGCTGGTGCATCCTTATCGG
1 ATGATAAATCCAATTATCGAATTACATGCTGGTGCATCCTCACCGA
* * * *
3394072 ATGGTAAACCCAATTACCGTATTACATGCTGGTGCATCCT
1 ATGATAAATCCAATTATCGAATTACATGCTGGTGCATCCT
3394112 TACAAGATGG
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (46 bp):
ATGATAAATCCAATTATCGAATTACATGCTGGTGCATCCTCACCGA
Found at i:3394121 original size:46 final size:45
Alignment explanation
Indices: 3394002--3394124 Score: 131
Period size: 46 Copynumber: 2.7 Consensus size: 45
3393992 ATTATCAAAA
* * * * * *
3394002 TACATGCTGGTGCATCCTCACCGAATGATAAATCCGATTATCGATT
1 TACATGCTGGTGCATCCTTACAG-ATGGTAAACCCAATTACCGATT
* *
3394048 TACAGGCTGGTGCATCCTTATCGGATGGTAAACCCAATTACCG-TAT
1 TACATGCTGGTGCATCCTTA-CAGATGGTAAACCCAATTACCGAT-T
3394094 TACATGCTGGTGCATCCTTACAAGATGGTAA
1 TACATGCTGGTGCATCCTTAC-AGATGGTAA
3394125 TGTCCAATCA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
45 2 0.03
46 61 0.94
47 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (45 bp):
TACATGCTGGTGCATCCTTACAGATGGTAAACCCAATTACCGATT
Found at i:3407741 original size:41 final size:41
Alignment explanation
Indices: 3407676--3407753 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
3407666 TATGACTTGA
*
3407676 ATTCTATTTTGATACATTACCTGAATTATGTTCTGATCTGG
1 ATTCTATTATGATACATTACCTGAATTATGTTCTGATCTGG
* * *
3407717 ATTCTATTATGATATC-TTATCTGAATTCTGTTTTGAT
1 ATTCTATTATGATA-CATTACCTGAATTATGTTCTGAT
3407754 TTTTGATATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 31 0.97
42 1 0.03
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.50
Consensus pattern (41 bp):
ATTCTATTATGATACATTACCTGAATTATGTTCTGATCTGG
Found at i:3407923 original size:2 final size:2
Alignment explanation
Indices: 3407916--3407960 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3407906 ATGATGGGGG
3407916 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3407958 TA T
1 TA T
3407961 GTTTTAAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3412542 original size:24 final size:24
Alignment explanation
Indices: 3412515--3412578 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
3412505 ATTTCTGACT
3412515 TGAATTATGTTCTGATACATTACC
1 TGAATTATGTTCTGATACATTACC
* * *
3412539 TGAATTTTATTCCGATACATTACC
1 TGAATTATGTTCTGATACATTACC
*
3412563 TGAATTCTGTTCTGAT
1 TGAATTATGTTCTGAT
3412579 TTCTGGTCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (24 bp):
TGAATTATGTTCTGATACATTACC
Found at i:3412582 original size:12 final size:12
Alignment explanation
Indices: 3412562--3412628 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
3412552 GATACATTAC
*
3412562 CTGAATTCTGTT
1 CTGATTTCTGTT
*
3412574 CTGATTTCTGGT
1 CTGATTTCTGTT
3412586 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* * *
3412598 ATGATATCTGAT
1 CTGATTTCTGTT
*
3412610 CTGAATTCTGTT
1 CTGATTTCTGTT
*
3412622 TTGATTT
1 CTGATTT
3412629 TTGATATCTC
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
11 2 0.05
12 37 0.90
13 2 0.05
ACGTcount: A:0.16, C:0.13, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:3412602 original size:24 final size:24
Alignment explanation
Indices: 3412562--3412633 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
3412552 GATACATTAC
* *
3412562 CTGAATTCTGTTCTGATTTCTGGT
1 CTGAATTCTGTTATGATTTCTGAT
* *
3412586 CTGGATTCTGTTATGATATCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* *
3412610 CTGAATTCTGTTTTGATTTTTGAT
1 CTGAATTCTGTTATGATTTCTGAT
3412634 ATCTCCGTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.51
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:3415405 original size:16 final size:16
Alignment explanation
Indices: 3415384--3415415 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3415374 ATCCTTGTTG
*
3415384 AAATTGTTTCTAGACA
1 AAATTGTATCTAGACA
3415400 AAATTGTATCTAGACA
1 AAATTGTATCTAGACA
3415416 TACTATAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (16 bp):
AAATTGTATCTAGACA
Found at i:3419637 original size:11 final size:10
Alignment explanation
Indices: 3419613--3419651 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
3419603 AACGTAGGAG
3419613 TCTTTTTATTT
1 TCTTTTT-TTT
3419624 TCTCTTTTTTT
1 TCT-TTTTTTT
*
3419635 TCTTTCTTTT
1 TCTTTTTTTT
3419645 TCTTTTT
1 TCTTTTT
3419652 GTTGCAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 12 0.48
11 9 0.36
12 4 0.16
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:3422697 original size:21 final size:21
Alignment explanation
Indices: 3422671--3422716 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
3422661 ACATTGGAAC
3422671 TAACTTTCAATGAAGGATGAG
1 TAACTTTCAATGAAGGATGAG
3422692 TAACTTTCAATGAAGGATGAG
1 TAACTTTCAATGAAGGATGAG
3422713 TAAC
1 TAAC
3422717 CTTTAATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (21 bp):
TAACTTTCAATGAAGGATGAG
Found at i:3423261 original size:15 final size:16
Alignment explanation
Indices: 3423222--3423251 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3423212 TAATTTATAT
3423222 TCATGC-AAATCTAAA
1 TCATGCAAAATCTAAA
3423237 TCATGCAAAATCTAA
1 TCATGCAAAATCTAA
3423252 TTTATGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (16 bp):
TCATGCAAAATCTAAA
Found at i:3425319 original size:21 final size:21
Alignment explanation
Indices: 3425290--3425331 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3425280 TTATTTTAAC
*
3425290 AAAGGTAGTAACGATACTACT
1 AAAGATAGTAACGATACTACT
**
3425311 AAAGATAGTATTGATACTACT
1 AAAGATAGTAACGATACTACT
3425332 TTGCCTAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AAAGATAGTAACGATACTACT
Found at i:3426596 original size:15 final size:15
Alignment explanation
Indices: 3426576--3426629 Score: 63
Period size: 15 Copynumber: 3.3 Consensus size: 15
3426566 ACCATATATC
3426576 ATATAATTACTAATA
1 ATATAATTACTAATA
3426591 ATATAATTACATCAGATA
1 ATATAATTAC-T-A-ATA
*
3426609 GAAATAATTACTAATA
1 -ATATAATTACTAATA
3426625 ATATA
1 ATATA
3426630 GATATACTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 14 0.42
16 4 0.12
17 2 0.06
18 4 0.12
19 9 0.27
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (15 bp):
ATATAATTACTAATA
Found at i:3429980 original size:39 final size:38
Alignment explanation
Indices: 3429768--3430181 Score: 429
Period size: 39 Copynumber: 10.8 Consensus size: 38
3429758 TATTTCGAAA
* *
3429768 AAAAACGTTTTTAAAACCTATATATTATATATA-TTTTC
1 AAAAATGTTTTCAAAA-CTATATATTATATATATTTTTC
* * * *
3429806 AAACATTTTTTCTAAACGATATATTATATATA-TTTTC
1 AAAAATGTTTTCAAAACTATATATTATATATATTTTTC
* **
3429843 AAAAAAAAACGTTTT-AAAACTATATA-T-TATATATTTTAG
1 ----AAAAATGTTTTCAAAACTATATATTATATATATTTTTC
3429882 AAAAATGTTTTCAAAACTATATATTATATATATATATTTTC
1 AAAAATGTTTTCAAAACTATATA-T-TATATATAT-TTTTC
3429923 AAAAATGTTTTCCAAAACTATATATTATATATATTTTTTC
1 AAAAATGTTTT-CAAAACTATATATTATATATA-TTTTTC
* ** *
3429963 AAAATTGTTTTTTAAACTATATATTATATATATTTTGC
1 AAAAATGTTTTCAAAACTATATATTATATATATTTTTC
*
3430001 -AAAATGTTTTTAGAAA-TATATATTATATATA-TTTTC
1 AAAAATGTTTTCA-AAACTATATATTATATATATTTTTC
*
3430037 AAAAACGTTTT-AAGAA-TATATATTATATATA-TTTTC
1 AAAAATGTTTTCAA-AACTATATATTATATATATTTTTC
*
3430073 GAAAATGTTTTCAAAACTATATATTATATATATATTTTC
1 AAAAATGTTTTCAAAACTATATATTATATATAT-TTTTC
* *
3430112 AAAAATGTTTTCAAAACTGTATATTATATATA-CTTTC
1 AAAAATGTTTTCAAAACTATATATTATATATATTTTTC
* *
3430149 GAAAAAATGCTTTCAACACTATATATTATATAT
1 --AAAAATGTTTTCAAAACTATATATTATATAT
3430182 GTTATGTATA
Statistics
Matches: 322, Mismatches: 32, Indels: 43
0.81 0.08 0.11
Matches are distributed among these distances:
35 11 0.03
36 49 0.15
37 75 0.23
38 25 0.08
39 87 0.27
40 39 0.12
41 24 0.07
42 12 0.04
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.45
Consensus pattern (38 bp):
AAAAATGTTTTCAAAACTATATATTATATATATTTTTC
Found at i:3431124 original size:200 final size:201
Alignment explanation
Indices: 3430660--3431132 Score: 553
Period size: 200 Copynumber: 2.4 Consensus size: 201
3430650 ATATATCTTC
* * * * * * * **
3430660 GAGCTGAATGGAATCGAGCTCGAAGGTTTTTGTAGATATATAGCCCTTCTTGCCTTGAGCTATGA
1 GAGCTGAATGGAATCGAACTCGAAAGTTTTTGTTGACAGAAAGCCCTTATCACCTTGAGCTATGA
* *
3430725 TGTAAATTAGGCTGGGAGATAGTTCTTTGTTGCTAAATCGCAGCCAACATAGGTTTTCTTCATGG
66 TGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAATCGCAGCCAACATAGGTTTTCTTCATGA
* *
3430790 TTTAAAGACCTCGGTTTACAATTCAACCGGAAAGTAGTTCCTCGCTACTACCATGCGGATGATAC
131 TTTAAAGACCTCAGTTTACAATTCAACCGGAAAGTAGTTCCTCGCTACTACCATACGGATGATAC
*
3430855 GCCCTT
196 ACCCTT
* * *** * * *
3430861 GAGATGAATGGAATCAAACTCGAAAGTTTTCAATGACAGACAG--CTTATCTCGACTTAAGCTAT
1 GAGCTGAATGGAATCGAACTCGAAAGTTTTTGTTGACAGAAAGCCCTTATCAC--CTTGAGCTAT
* ** * *
3430924 GATGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAGTCGCAGCTGACCTAGG-TTTCTTCTT
64 GATGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAATCGCAGCCAACATAGGTTTTCTTCAT
* * **
3430988 GATTTAAAGACCAT-AGTTTA-AAGTTCAACCGGTAAGTAGTTCCTCGTTGTTACCATACGG-TC
129 GATTTAAAGACC-TCAGTTTACAA-TTCAACCGGAAAGTAGTTCCTCGCTACTACCATACGGAT-
3431050 GATACACCCTT
191 GATACACCCTT
* * *
3431061 GAGCTGAATGGAATCGAACTCAAAAGTTTTTGTTGACAGAAAGCCCTTGTCACCTTGAGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAAGTTTTTGTTGACAGAAAGCCCTTATCACCTTGAGCTATGA
3431126 TGTAAAT
66 TGTAAAT
3431133 GGTTCCTCTA
Statistics
Matches: 225, Mismatches: 40, Indels: 15
0.80 0.14 0.05
Matches are distributed among these distances:
199 8 0.04
200 119 0.53
201 92 0.41
202 6 0.03
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (201 bp):
GAGCTGAATGGAATCGAACTCGAAAGTTTTTGTTGACAGAAAGCCCTTATCACCTTGAGCTATGA
TGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAATCGCAGCCAACATAGGTTTTCTTCATGA
TTTAAAGACCTCAGTTTACAATTCAACCGGAAAGTAGTTCCTCGCTACTACCATACGGATGATAC
ACCCTT
Found at i:3438712 original size:10 final size:9
Alignment explanation
Indices: 3438697--3438762 Score: 64
Period size: 9 Copynumber: 7.3 Consensus size: 9
3438687 CCTAAAAAAT
3438697 AAAAATAGAA
1 AAAAATA-AA
3438707 AAAAATAAA
1 AAAAATAAA
*
3438716 ATAAA-AAA
1 AAAAATAAA
*
3438724 TAAAATAAA
1 AAAAATAAA
3438733 ATAAAATAAA
1 A-AAAATAAA
*
3438743 ATAAAT-AA
1 AAAAATAAA
*
3438751 ATAAATAAA
1 AAAAATAAA
3438760 AAA
1 AAA
3438763 GAAGAAGTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
8 14 0.30
9 17 0.36
10 16 0.34
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.17
Consensus pattern (9 bp):
AAAAATAAA
Found at i:3438716 original size:5 final size:5
Alignment explanation
Indices: 3438692--3438760 Score: 74
Period size: 5 Copynumber: 13.8 Consensus size: 5
3438682 TTGGACCTAA
3438692 AAAAT AAAAAT AGAAA- AAAAT AAAAT AAAAAAT AAAAT AAAAT AAAAT
1 AAAAT -AAAAT A-AAAT AAAAT AAAAT --AAAAT AAAAT AAAAT AAAAT
3438740 AAAAT -AAAT -AAAT -AAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAA
3438761 AAGAAGAAGT
Statistics
Matches: 58, Mismatches: 0, Indels: 11
0.84 0.00 0.16
Matches are distributed among these distances:
4 15 0.26
5 30 0.52
6 8 0.14
7 5 0.09
ACGTcount: A:0.81, C:0.00, G:0.01, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:3438722 original size:22 final size:21
Alignment explanation
Indices: 3438692--3438762 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 21
3438682 TTGGACCTAA
3438692 AAAAT-AAAAATAGAAAAAAAT
1 AAAATAAAAAATA-AAAAAAAT
3438713 AAAATAAAAAATAAAATAAAAT
1 AAAATAAAAAATAAAA-AAAAT
*
3438735 AAAAT--AAAAT-AAATAAAT
1 AAAATAAAAAATAAAAAAAAT
3438753 -AAATAAAAAA
1 AAAATAAAAAA
3438763 GAAGAAGTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
17 4 0.09
18 4 0.09
19 7 0.16
20 5 0.11
21 8 0.18
22 17 0.38
ACGTcount: A:0.82, C:0.00, G:0.01, T:0.17
Consensus pattern (21 bp):
AAAATAAAAAATAAAAAAAAT
Found at i:3438729 original size:27 final size:26
Alignment explanation
Indices: 3438689--3438762 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 26
3438679 TTATTGGACC
3438689 TAAAAAATAAAAATAGAAAAAAATAAAA
1 TAAAAAAT-AAAATA-AAAAAAATAAAA
3438717 TAAAAAATAAAATAAAATAAAATAAAA
1 TAAAAAATAAAATAAAA-AAAATAAAA
3438744 TAAATAAAT-AAATAAAAAA
1 TAAA-AAATAAAATAAAAAA
3438763 GAAGAAGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
26 5 0.11
27 27 0.61
28 12 0.27
ACGTcount: A:0.81, C:0.00, G:0.01, T:0.18
Consensus pattern (26 bp):
TAAAAAATAAAATAAAAAAAATAAAA
Found at i:3438987 original size:48 final size:45
Alignment explanation
Indices: 3438906--3439008 Score: 120
Period size: 46 Copynumber: 2.3 Consensus size: 45
3438896 GTTTTAAAAC
* * * *
3438906 TATATTTTATATATATATTTTTCAAATTGTTTTCCAAAACTATATA
1 TATATTATATATATATATTATTCAAAATATTTTCC-AAACTATATA
*
3438952 TATATTATATATATATATATATTCAAAAATATTTTCCAAATTATATA
1 TATATTATATATATATAT-TATTC-AAAATATTTTCCAAACTATATA
3438999 T-TA-TATATAT
1 TATATTATATAT
3439009 TTTCAAAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
45 7 0.14
46 19 0.38
47 14 0.28
48 10 0.20
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (45 bp):
TATATTATATATATATATTATTCAAAATATTTTCCAAACTATATA
Found at i:3439070 original size:26 final size:27
Alignment explanation
Indices: 3439039--3439104 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
3439029 CTATATATTA
* *
3439039 TATATATTTTCAAAAATGTTTTTAAAAC
1 TATATATTAT-AAAAATGTTTTCAAAAC
* *
3439067 TATATATTATATAAATGTTTTCAAACC
1 TATATATTATAAAAATGTTTTCAAAAC
3439094 TATATATTATA
1 TATATATTATA
3439105 TATATTTTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 25 0.74
28 9 0.26
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (27 bp):
TATATATTATAAAAATGTTTTCAAAAC
Found at i:3439088 original size:39 final size:39
Alignment explanation
Indices: 3438838--3439091 Score: 218
Period size: 37 Copynumber: 6.4 Consensus size: 39
3438828 TTTGAAAACC
* *
3438838 TATACATATTTTCAAACATGTTTTCT-AAACTATATATTA
1 TATAAATATTTTCAAAAATGTTTT-TAAAACTATATATTA
* * *
3438877 TATATAT-TTTTCAAAAAACG-TTTTAAAACTATATTTTA
1 TATAAATATTTTC-AAAAATGTTTTTAAAACTATATATTA
* * *
3438915 TATATATATTTTTC-AAATTGTTTTCCAAAACTATATATATATTA
1 TATAAATA-TTTTCAAAAATGTTTT-TAAAAC----TATATATTA
* ** *
3438959 TATATATATATATATTCAAAAATATTTTCCAAATTATATATTA
1 TATA-A-ATAT-T-TTCAAAAATGTTTTTAAAACTATATATTA
*
3439002 TAT--ATATTTTCAAAAATATTTTTAAAACTATATATTA
1 TATAAATATTTTCAAAAATGTTTTTAAAACTATATATTA
3439039 TAT--ATATTTTCAAAAATGTTTTTAAAACTATATATTA
1 TATAAATATTTTCAAAAATGTTTTTAAAACTATATATTA
*
3439076 TATAAATGTTTTCAAA
1 TATAAATATTTTCAAA
3439092 CCTATATATT
Statistics
Matches: 180, Mismatches: 18, Indels: 34
0.78 0.08 0.15
Matches are distributed among these distances:
37 66 0.37
38 32 0.18
39 28 0.16
40 10 0.06
43 12 0.07
44 12 0.07
45 1 0.01
46 4 0.02
47 7 0.04
48 8 0.04
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.48
Consensus pattern (39 bp):
TATAAATATTTTCAAAAATGTTTTTAAAACTATATATTA
Found at i:3439104 original size:25 final size:27
Alignment explanation
Indices: 3439052--3439106 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
3439042 ATATTTTCAA
*
3439052 AAATGTTTTTAAAACTATATATTATAT
1 AAATGTTTTCAAAACTATATATTATAT
*
3439079 AAATGTTTTCAAACCTATATATTATAT
1 AAATGTTTTCAAAACTATATATTATAT
3439106 A
1 A
3439107 TATTTTCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (27 bp):
AAATGTTTTCAAAACTATATATTATAT
Found at i:3439112 original size:25 final size:26
Alignment explanation
Indices: 3439057--3439118 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
3439047 TTCAAAAATG
* *
3439057 TTTTTAAAACTATATATTATATAAATG
1 TTTTCAAAACTATATATTATAT-AATA
*
3439084 TTTTCAAACCTATATATTATAT-ATA
1 TTTTCAAAACTATATATTATATAATA
3439109 TTTTCGAAAA
1 TTTTC-AAAA
3439119 AATGCTTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 7 0.23
26 3 0.10
27 20 0.67
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (26 bp):
TTTTCAAAACTATATATTATATAATA
Found at i:3439137 original size:64 final size:64
Alignment explanation
Indices: 3439015--3439145 Score: 172
Period size: 64 Copynumber: 2.0 Consensus size: 64
3439005 ATATTTTCAA
* * *
3439015 AAATATTTTTAAAACTATATATTATATATATTTTCAAAAATGTTTTTAAAACTATATATTATAT
1 AAATATTTTCAAAACTATATATTATATATATTTTCAAAAATGCTTTCAAAACTATATATTATAT
* * * * *
3439079 AAATGTTTTCAAACCTATATATTATATATATTTTCGAAAAAATGCTTTCAACATTATATATCATA
1 AAATATTTTCAAAACTATATATTATATATATTTTC--AAAAATGCTTTCAAAACTATATATTATA
3439144 T
64 T
3439145 A
1 A
3439146 TGTTAAACCT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
64 32 0.56
66 25 0.44
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (64 bp):
AAATATTTTCAAAACTATATATTATATATATTTTCAAAAATGCTTTCAAAACTATATATTATAT
Found at i:3445914 original size:17 final size:18
Alignment explanation
Indices: 3445889--3445922 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3445879 TATCAAGAAA
*
3445889 TATATTATT-TTTATTTC
1 TATAATATTATTTATTTC
3445906 TATAATATTATTTATTT
1 TATAATATTATTTATTT
3445923 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TATAATATTATTTATTTC
Found at i:3446064 original size:16 final size:17
Alignment explanation
Indices: 3446043--3446083 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
3446033 TCAAGGAATA
3446043 TATTTATTTTTTAT-TT
1 TATTTATTTTTTATATT
*
3446059 TATTTA-TATTTATATT
1 TATTTATTTTTTATATT
3446075 TATTTATTT
1 TATTTATTT
3446084 ATTCTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 6 0.29
16 14 0.67
17 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTATTTTTTATATT
Found at i:3446097 original size:20 final size:20
Alignment explanation
Indices: 3446041--3446095 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
3446031 TGTCAAGGAA
*
3446041 TATATTTATTTTTTATTTTATT
1 TATATTTA-TATTTA-TTTATT
3446063 TATATTTATATTTATTTATT
1 TATATTTATATTTATTTATT
*
3446083 TATTCTTTATATT
1 TA-TATTTATATT
3446096 ATATATTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 8 0.27
21 14 0.47
22 8 0.27
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TATATTTATATTTATTTATT
Found at i:3446098 original size:32 final size:28
Alignment explanation
Indices: 3446041--3446102 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
3446031 TGTCAAGGAA
3446041 TATATTTATTTTTTATTTTATTTATATT
1 TATATTTATTTTTTATTTTATTTATATT
*
3446069 TATATTTATTTATTTA--TTCTTTATATT
1 TATATTTATTT-TTTATTTTATTTATATT
3446096 ATATATT
1 -TATATT
3446103 AGATAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 10 0.32
28 17 0.55
29 4 0.13
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (28 bp):
TATATTTATTTTTTATTTTATTTATATT
Found at i:3446309 original size:16 final size:16
Alignment explanation
Indices: 3446285--3446319 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3446275 ATATGAGAAA
3446285 AAATCAATTTAAATTT
1 AAATCAATTTAAATTT
* *
3446301 AAATTAATTTAATTTT
1 AAATCAATTTAAATTT
3446317 AAA
1 AAA
3446320 ATAACTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATCAATTTAAATTT
Found at i:3447090 original size:24 final size:24
Alignment explanation
Indices: 3447042--3447142 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
3447032 CGTTAAAATA
* * *
3447042 ATAAACAAACACAAAAGCACAAAC
1 ATAAACGAACACAAAAGAACGAAC
* *
3447066 ATAAATGAACACAAAAGAATGAAC
1 ATAAACGAACACAAAAGAACGAAC
* * * *
3447090 ATAAACGAAAACAAACGAATGAAT
1 ATAAACGAACACAAAAGAACGAAC
* * *
3447114 GTAAACGAACATAAACGAACGAAC
1 ATAAACGAACACAAAAGAACGAAC
3447138 ATAAA
1 ATAAA
3447143 ATTAACTGGT
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.62, C:0.17, G:0.11, T:0.10
Consensus pattern (24 bp):
ATAAACGAACACAAAAGAACGAAC
Found at i:3447255 original size:16 final size:18
Alignment explanation
Indices: 3447234--3447276 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
3447224 TATTTTTTGT
3447234 TTGGGTTTAAAAT-T-AA
1 TTGGGTTTAAAATATCAA
3447250 TTGGGTTTTAAAATATCAA
1 TTGGG-TTTAAAATATCAA
3447269 -TGGGTTTA
1 TTGGGTTTA
3447277 TTGTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.21
17 12 0.50
18 5 0.21
19 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (18 bp):
TTGGGTTTAAAATATCAA
Found at i:3448365 original size:20 final size:18
Alignment explanation
Indices: 3448329--3448365 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 18
3448319 TTGGATGTGT
3448329 TTATATTTATGTTAATGG
1 TTATATTTATGTTAATGG
3448347 TTATATTTTATGTTTAATG
1 TTATA-TTTATG-TTAATG
3448366 TTGATCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (18 bp):
TTATATTTATGTTAATGG
Found at i:3450924 original size:16 final size:16
Alignment explanation
Indices: 3450903--3450936 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3450893 TCAACTAGGC
3450903 ATAATGTATTCATTTA
1 ATAATGTATTCATTTA
3450919 ATAATGTATTCATTTA
1 ATAATGTATTCATTTA
3450935 AT
1 AT
3450937 GATGGTAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (16 bp):
ATAATGTATTCATTTA
Done.