Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 117 of 345
Found at i:31150199 original size:14 final size:13
Alignment explanation
Indices: 31150132--31150225 Score: 65
Period size: 13 Copynumber: 7.5 Consensus size: 13
31150122 TATATTTGTG
*
31150132 AAATTAATTTTTT
1 AAATTAATTTTTA
* *
31150145 ATA-T-ATTTTAA
1 AAATTAATTTTTA
* *
31150156 AAATTTATTTTTC
1 AAATTAATTTTTA
*
31150169 AAATTAATTTTTC
1 AAATTAATTTTTA
31150182 AAATTAATTTTT-
1 AAATTAATTTTTA
*
31150194 TAA--AA-TTTTA
1 AAATTAATTTTTA
31150204 AATATTAATTTTTA
1 AA-ATTAATTTTTA
31150218 AATATTAA
1 AA-ATTAA
31150226 CCATATTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
9 4 0.06
10 3 0.05
11 8 0.12
12 4 0.06
13 33 0.51
14 13 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (13 bp):
AAATTAATTTTTA
Found at i:31150232 original size:23 final size:23
Alignment explanation
Indices: 31150184--31150225 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
31150174 AATTTTTCAA
*
31150184 ATTAATTTTTTAAAATTTTAAAT
1 ATTAATTTTTTAAAATATTAAAT
31150207 ATTAA-TTTTT-AAATATTAA
1 ATTAATTTTTTAAAATATTAA
31150226 CCATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 5 0.28
23 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTAATTTTTTAAAATATTAAAT
Found at i:31150315 original size:20 final size:19
Alignment explanation
Indices: 31150277--31150323 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
31150267 TTGTAAATAC
31150277 AATTTCTTTAATTTCTTTTT
1 AATTT-TTTAATTTCTTTTT
31150297 ACATTTTTTAAGTTT-TTTTT
1 A-ATTTTTTAA-TTTCTTTTT
31150317 AATTTTT
1 AATTTTT
31150324 GAAAAGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.24
20 12 0.48
21 7 0.28
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.70
Consensus pattern (19 bp):
AATTTTTTAATTTCTTTTT
Found at i:31150449 original size:22 final size:21
Alignment explanation
Indices: 31150424--31150464 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
31150414 TTTCAAAATT
31150424 AATTTA-AAAAATATATATTTAA
1 AATTTATAAAAA-ATA-ATTTAA
31150446 AATTTATAAAAAATAATTT
1 AATTTATAAAAAATAATTT
31150465 CACAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTTATAAAAAATAATTTAA
Found at i:31150464 original size:36 final size:35
Alignment explanation
Indices: 31150418--31150527 Score: 134
Period size: 34 Copynumber: 3.2 Consensus size: 35
31150408 TAATAATTTC
*
31150418 AAAATTAATTTAAAAAATATATATTTAAAATTTATA
1 AAAAATAATTTAAAAAATATATATTTAAAATTTA-A
* * * *
31150454 AAAAATAATTTCACAAATATATATCT-AAAGTTAA
1 AAAAATAATTTAAAAAATATATATTTAAAATTTAA
* *
31150488 AAAAATAATTTTAAAAATA-ATAATTAAAATTTAA
1 AAAAATAATTTAAAAAATATATATTTAAAATTTAA
31150522 AAAAAT
1 AAAAAT
31150528 TGTAAAACAT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
33 4 0.06
34 31 0.49
35 6 0.10
36 22 0.35
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (35 bp):
AAAAATAATTTAAAAAATATATATTTAAAATTTAA
Found at i:31150609 original size:36 final size:36
Alignment explanation
Indices: 31150569--31150642 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
31150559 TTTTAAAATT
31150569 AATAATAT-AAA-TTAAATAAACAAAATAAAATAAGAA
1 AATAATATAAAACTTAAA-AAACAAAA-AAAATAAGAA
* *
31150605 AATAATATAAAACTTAAAAAAGAAAAAAATTAAGAA
1 AATAATATAAAACTTAAAAAACAAAAAAAATAAGAA
31150641 AA
1 AA
31150643 AGACAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 19 0.56
37 10 0.29
38 5 0.15
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.20
Consensus pattern (36 bp):
AATAATATAAAACTTAAAAAACAAAAAAAATAAGAA
Found at i:31150614 original size:18 final size:18
Alignment explanation
Indices: 31150564--31150616 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
31150554 AAATTTTTTA
* *
31150564 AAATTAATAATATAAATT
1 AAATAAATAATATAAAAT
* *
31150582 AAATAAACAAAATAAAAT
1 AAATAAATAATATAAAAT
31150600 AAGA-AAATAATATAAAA
1 AA-ATAAATAATATAAAA
31150617 CTTAAAAAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (18 bp):
AAATAAATAATATAAAAT
Found at i:31150642 original size:18 final size:19
Alignment explanation
Indices: 31150619--31150671 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
31150609 ATATAAAACT
31150619 TAAAAAAGAAAAAAATTAA
1 TAAAAAAGAAAAAAATTAA
* * *
31150638 -GAAAAAGACAAAATTTAA
1 TAAAAAAGAAAAAAATTAA
31150656 TAAAAAAGTAAAAAAA
1 TAAAAAAG-AAAAAAA
31150672 AAAAATAAGG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 15 0.58
19 6 0.23
20 5 0.19
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (19 bp):
TAAAAAAGAAAAAAATTAA
Found at i:31150873 original size:14 final size:14
Alignment explanation
Indices: 31150854--31150880 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31150844 AAAAATATGG
31150854 TTAATATTTAAAAA
1 TTAATATTTAAAAA
31150868 TTAATATTTAAAA
1 TTAATATTTAAAA
31150881 TTTTTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATATTTAAAAA
Found at i:31150903 original size:23 final size:23
Alignment explanation
Indices: 31150860--31150904 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
31150850 ATGGTTAATA
*
31150860 TTTAAAAATTAATATTTAAAATT
1 TTTAAAAATTAATATTAAAAATT
31150883 TTTAAAAATTAAT-TTGAAAAAT
1 TTTAAAAATTAATATT-AAAAAT
31150905 ACATTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTTAAAAATTAATATTAAAAATT
Found at i:31150904 original size:36 final size:35
Alignment explanation
Indices: 31150859--31150933 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 35
31150849 TATGGTTAAT
* *
31150859 ATTTAAAAATTA-ATATTTAAAAT-TTTTAAAAATTA
1 ATTTAAAAA-TACAT-TTTAAAATATATAAAAAATTA
31150894 ATTTGAAAAATACATTTTAAAATATATAAAAAATTA
1 ATTT-AAAAATACATTTTAAAATATATAAAAAATTA
31150930 ATTT
1 ATTT
31150934 CACAAATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 14 0.40
36 21 0.60
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (35 bp):
ATTTAAAAATACATTTTAAAATATATAAAAAATTA
Found at i:31150961 original size:36 final size:36
Alignment explanation
Indices: 31150886--31150961 Score: 82
Period size: 36 Copynumber: 2.1 Consensus size: 36
31150876 TAAAATTTTT
* * *
31150886 AAAAATTAATTTGAAAAATACATTTTAAAATATATA
1 AAAAATTAATTTCAAAAATACATTCTAAAATATAAA
* * *
31150922 AAAAATTAATTTCACAAATATATATCTAAAGT-TAAA
1 AAAAATTAATTTCAAAAATACAT-TCTAAAATATAAA
31150958 AAAA
1 AAAA
31150962 TATTTTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
36 27 0.82
37 6 0.18
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (36 bp):
AAAAATTAATTTCAAAAATACATTCTAAAATATAAA
Found at i:31151079 original size:31 final size:28
Alignment explanation
Indices: 31151044--31151117 Score: 69
Period size: 31 Copynumber: 2.5 Consensus size: 28
31151034 TAAAGTTAAT
31151044 AATAAAAAATAAAACAAAATAAACAAAATGA
1 AATAAAAAATAAAACAAAA-AAACAAAA--A
* **
31151075 AATAAGAAAA-AAATCAAAAAAGTAAAAA
1 AATAA-AAAATAAAACAAAAAAACAAAAA
31151103 AATAAAAAGATAAAA
1 AATAAAAA-ATAAAA
31151118 TTTATTAAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
27 3 0.08
28 7 0.19
29 3 0.08
30 6 0.17
31 13 0.36
32 4 0.11
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.12
Consensus pattern (28 bp):
AATAAAAAATAAAACAAAAAAACAAAAA
Found at i:31151117 original size:16 final size:17
Alignment explanation
Indices: 31151047--31151110 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 17
31151037 AGTTAATAAT
* *
31151047 AAAAAATAAAACAAAATA
1 AAAAAATCAAA-AAAGTA
* *
31151065 AACAAAATGAAATAAG-A
1 AA-AAAATCAAAAAAGTA
31151082 AAAAAATCAAAAAAGTA
1 AAAAAATCAAAAAAGTA
31151099 AAAAAAT-AAAAA
1 AAAAAATCAAAAA
31151111 GATAAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 16 0.41
17 11 0.28
18 4 0.10
19 8 0.21
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.11
Consensus pattern (17 bp):
AAAAAATCAAAAAAGTA
Found at i:31151158 original size:23 final size:24
Alignment explanation
Indices: 31151132--31151177 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
31151122 TTAAGGAACA
31151132 AAATA-AAAAAGTAAAA-AAAAAAG
1 AAATATAAAAA-TAAAAGAAAAAAG
*
31151155 AAATATGAAAATAAAAGAAAAAA
1 AAATATAAAAATAAAAGAAAAAA
31151178 ATAAAAGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (24 bp):
AAATATAAAAATAAAAGAAAAAAG
Found at i:31151184 original size:30 final size:29
Alignment explanation
Indices: 31151138--31151211 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 29
31151128 AACAAAATAA
*
31151138 AAAAGTAAAAAAAAAAGAAATATGAAAAT
1 AAAAGAAAAAAAAAAAGAAATATGAAAAT
* *
31151167 AAAAGAAAAAAATAAAAGGAATATTAAAAT
1 AAAAGAAAAAAA-AAAAGAAATATGAAAAT
*
31151197 AAAAGAAAAAGAAAA
1 AAAAGAAAAAAAAAA
31151212 CAAAAAGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 14 0.35
30 26 0.65
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.12
Consensus pattern (29 bp):
AAAAGAAAAAAAAAAAGAAATATGAAAAT
Found at i:31151197 original size:17 final size:16
Alignment explanation
Indices: 31151145--31151201 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
31151135 TAAAAAAGTA
* *
31151145 AAAAAAAAAGAAATAT
1 AAAATAAAAGGAATAT
31151161 GAAAATAAAA-GAA-A-
1 -AAAATAAAAGGAATAT
31151175 AAAATAAAAGGAATATT
1 AAAATAAAAGGAATA-T
31151192 AAAATAAAAG
1 AAAATAAAAG
31151202 AAAAAGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 9 0.26
14 3 0.09
15 2 0.06
16 2 0.06
17 18 0.53
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (16 bp):
AAAATAAAAGGAATAT
Found at i:31151843 original size:9 final size:9
Alignment explanation
Indices: 31151829--31151878 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
31151819 ATAAGTATAA
31151829 AATTAACCG
1 AATTAACCG
*
31151838 AATTAATCG
1 AATTAACCG
**
31151847 AATTGCCCG
1 AATTAACCG
*
31151856 AATTACCCG
1 AATTAACCG
31151865 AATTAACCG
1 AATTAACCG
31151874 AATTA
1 AATTA
31151879 TTTGTATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:31158700 original size:23 final size:21
Alignment explanation
Indices: 31158650--31158744 Score: 75
Period size: 23 Copynumber: 4.2 Consensus size: 21
31158640 AGCTTTGTAG
*
31158650 AGCTGAAACGTAAGCCCCTAAGA
1 AGCTGAAACGTAAG-CTCTAA-A
31158673 A-CTGAAACGGTAAGCTCTGAAA
1 AGCTGAAAC-GTAAGCTCT-AAA
* *
31158695 AGCTGAAATGTAAGCTCATAAG
1 AGCTGAAACGTAAGCTC-TAAA
* *
31158717 AGTTGAAACAGTAAGCTCATACA
1 AGCTGAAAC-GTAAGCTC-TAAA
31158740 AGCTG
1 AGCTG
31158745 TGGTGAGTCC
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
22 29 0.49
23 30 0.51
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (21 bp):
AGCTGAAACGTAAGCTCTAAA
Found at i:31158744 original size:45 final size:45
Alignment explanation
Indices: 31158636--31158734 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
31158626 TGAGCTGAAT
* * * *
31158636 AGTAAGCTTTGTAGAGCTGAAACGTAAGCCCCTAAGAACTGAAAC
1 AGTAAGCTCTGAAAAGCTGAAACGTAAGCCCATAAGAACTGAAAC
* * * **
31158681 GGTAAGCTCTGAAAAGCTGAAATGTAAGCTCATAAGAGTTGAAAC
1 AGTAAGCTCTGAAAAGCTGAAACGTAAGCCCATAAGAACTGAAAC
31158726 AGTAAGCTC
1 AGTAAGCTC
31158735 ATACAAGCTG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (45 bp):
AGTAAGCTCTGAAAAGCTGAAACGTAAGCCCATAAGAACTGAAAC
Found at i:31161575 original size:15 final size:16
Alignment explanation
Indices: 31161555--31161584 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31161545 GAACAAATAT
31161555 ATTCGATTC-GATTCA
1 ATTCGATTCAGATTCA
31161570 ATTCGATTCAGATTC
1 ATTCGATTCAGATTC
31161585 CATCTCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (16 bp):
ATTCGATTCAGATTCA
Found at i:31164064 original size:2 final size:2
Alignment explanation
Indices: 31164057--31164082 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31164047 TTTTATCTTA
31164057 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
31164083 TTAACTTTCT
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:31164628 original size:2 final size:2
Alignment explanation
Indices: 31164621--31164654 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
31164611 ACGACTTTTA
*
31164621 AT AT AT AT TT 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
31164655 TAGAATCATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:31164756 original size:64 final size:64
Alignment explanation
Indices: 31164667--31164792 Score: 243
Period size: 64 Copynumber: 2.0 Consensus size: 64
31164657 GAATCATCCA
31164667 TCCCCACTTTATGTTGAATTGATTGAATTGATTATTTATTTATCTTAAATTATAGAATAAAATT
1 TCCCCACTTTATGTTGAATTGATTGAATTGATTATTTATTTATCTTAAATTATAGAATAAAATT
*
31164731 TCCCCACTTTATGTTGAATTGATTGAATTGATTATTTGTTTATCTTAAATTATAGAATAAAA
1 TCCCCACTTTATGTTGAATTGATTGAATTGATTATTTATTTATCTTAAATTATAGAATAAAA
31164793 CTTTAAAGAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (64 bp):
TCCCCACTTTATGTTGAATTGATTGAATTGATTATTTATTTATCTTAAATTATAGAATAAAATT
Found at i:31172355 original size:20 final size:20
Alignment explanation
Indices: 31172332--31172385 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
31172322 CAATTAACCA
31172332 AACCATAGTTAAAATAACTC
1 AACCATAGTTAAAATAACTC
31172352 AACCATAGTTAAAATAACTC
1 AACCATAGTTAAAATAACTC
31172372 AACCATAGTTAAAA
1 AACCATAGTTAAAA
31172386 ATCCTAACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.24
Consensus pattern (20 bp):
AACCATAGTTAAAATAACTC
Found at i:31172355 original size:25 final size:24
Alignment explanation
Indices: 31172326--31172376 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 24
31172316 TTCCAACAAT
31172326 TAACCAAACCATAGTTAAAATAAC
1 TAACCAAACCATAGTTAAAATAAC
31172350 T---C-AACCATAGTTAAAATAAC
1 TAACCAAACCATAGTTAAAATAAC
31172370 TCAACCA
1 T-AACCA
31172377 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 9
0.71 0.00 0.29
Matches are distributed among these distances:
20 19 0.86
21 1 0.05
24 2 0.09
ACGTcount: A:0.51, C:0.24, G:0.04, T:0.22
Consensus pattern (24 bp):
TAACCAAACCATAGTTAAAATAAC
Found at i:31175814 original size:14 final size:14
Alignment explanation
Indices: 31175794--31175827 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
31175784 CAAACAGTAA
*
31175794 AAAAAAAAAACTCTG
1 AAAAAAAAAA-GCTG
31175809 AAAAAAAAAAGCTG
1 AAAAAAAAAAGCTG
31175823 AAAAA
1 AAAAA
31175828 CGAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.74, C:0.09, G:0.09, T:0.09
Consensus pattern (14 bp):
AAAAAAAAAAGCTG
Found at i:31176024 original size:8 final size:8
Alignment explanation
Indices: 31176011--31176049 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
31176001 GAAAAAGAGA
31176011 GAAGAAGG
1 GAAGAAGG
31176019 GAAGAAGG
1 GAAGAAGG
31176027 GAAGAAGG
1 GAAGAAGG
*
31176035 GAAGAAGA
1 GAAGAAGG
31176043 GAAGAAG
1 GAAGAAG
31176050 AAGAAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (8 bp):
GAAGAAGG
Found at i:31176063 original size:16 final size:17
Alignment explanation
Indices: 31175998--31176065 Score: 50
Period size: 19 Copynumber: 3.8 Consensus size: 17
31175988 CATTTTCAGC
31175998 AAAGAA-AAAGAGAGAAG
1 AAAGAAGAAAGA-AGAAG
* *
31176015 AAGGGAAGAAGGGAAGAAGG
1 AA-AGAAGAA-AGAAGAA-G
*
31176035 GAAGAAGAGAAGAAGAAG
1 AAAGAAGA-AAGAAGAAG
31176053 AAAGAA-AAAGAAG
1 AAAGAAGAAAGAAG
31176066 GAGAGGAGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
16 6 0.15
17 3 0.08
18 9 0.22
19 17 0.43
20 5 0.12
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAAGAAGAAG
Found at i:31176151 original size:14 final size:14
Alignment explanation
Indices: 31176102--31176164 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
31176092 TGAGAGAAGA
31176102 AAAAAGAA--AAAG
1 AAAAAGAAGGAAAG
31176114 AAAAAGAGAAGGAGAAG
1 -AAAA-AGAAGGA-AAG
* * *
31176131 AAGAAGAGGGAAGG
1 AAAAAGAAGGAAAG
31176145 AAAAAGAAGGAAAG
1 AAAAAGAAGGAAAG
31176159 AAAAAG
1 AAAAAG
31176165 GTAATTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
13 4 0.10
14 23 0.57
15 6 0.15
16 4 0.10
17 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (14 bp):
AAAAAGAAGGAAAG
Found at i:31176151 original size:17 final size:17
Alignment explanation
Indices: 31176107--31176164 Score: 50
Period size: 19 Copynumber: 3.4 Consensus size: 17
31176097 GAAGAAAAAA
*
31176107 GAAAAAGAAAAAGAGAAG
1 GAAAAAG-AAGAGAGAAG
*
31176125 GAGAAGAAGAAGAGGGAAG
1 GA-AA-AAGAAGAGAGAAG
31176144 GAAAAAGAAG-GA-AA-
1 GAAAAAGAAGAGAGAAG
31176158 GAAAAAG
1 GAAAAAG
31176165 GTAATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 7 0.20
15 2 0.06
16 1 0.03
17 6 0.17
18 4 0.11
19 12 0.34
20 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAGAGAGAAG
Found at i:31176645 original size:25 final size:25
Alignment explanation
Indices: 31176600--31176661 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 25
31176590 GTTTTTTGTT
31176600 AAAATAATATAAAAAATAAAATATG
1 AAAATAATATAAAAAATAAAATATG
*
31176625 AAAATAGTATAATTAAAAAAATAAAATTTG
1 AAAATA--AT-A-T-AAAAAATAAAATATG
31176655 AAAATAA
1 AAAATAA
31176662 AAAAATACGA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 6 0.19
27 2 0.06
28 2 0.06
29 1 0.03
30 20 0.65
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (25 bp):
AAAATAATATAAAAAATAAAATATG
Found at i:31176938 original size:30 final size:28
Alignment explanation
Indices: 31176882--31176941 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 28
31176872 TATGTACTAA
31176882 AATAATATAAAGAAATAAAAACGAAAAT
1 AATAATATAAAGAAATAAAAACGAAAAT
*
31176910 AATATATATTAAA-AAATAATATACGAAAAT
1 AATA-ATA-TAAAGAAATAA-AAACGAAAAT
31176940 AA
1 AA
31176942 AAAAATTACG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 4 0.14
29 9 0.32
30 15 0.54
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.23
Consensus pattern (28 bp):
AATAATATAAAGAAATAAAAACGAAAAT
Found at i:31177094 original size:15 final size:15
Alignment explanation
Indices: 31177047--31177098 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
31177037 AAAATAATAT
*
31177047 AAAAAATAAAATAAG
1 AAAAAATAATATAAG
***
31177062 AAAAAAT-ATATTTT
1 AAAAAATAATATAAG
*
31177076 AAAAAATAATATACG
1 AAAAAATAATATAAG
31177091 AAAAAATA
1 AAAAAATA
31177099 CGAATAAAGT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
14 10 0.34
15 19 0.66
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (15 bp):
AAAAAATAATATAAG
Found at i:31177452 original size:21 final size:22
Alignment explanation
Indices: 31177428--31177469 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
31177418 GGGTTATTTA
31177428 TTAAA-AAAATATTTAAAACAC
1 TTAAATAAAATATTTAAAACAC
*
31177449 TTAAATAATATATTTAAAACA
1 TTAAATAAAATATTTAAAACA
31177470 TTATGTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
TTAAATAAAATATTTAAAACAC
Found at i:31177808 original size:153 final size:148
Alignment explanation
Indices: 31176747--31178546 Score: 1798
Period size: 145 Copynumber: 12.1 Consensus size: 148
31176737 ATTTTATGCT
* * *
31176747 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACAAAAAAAATACGAATAAAGTG-C
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC-AAAAAAATACGAAAAAAGTGTC
** * *
31176811 TAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATAC-T--TA-AATAATACATTTGAAGCAT
65 -AAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAATATAATAATACATTTGAAACAT
31176872 TATGTACTAAAATAATATAA
129 TATGTACTAAAATAATATAA
* * *
31176892 AGAAATAAAA-ACGAAAATAATATATATTAAAAAATAATATACGAAAATAAAAAAATTACGAAGA
1 A-AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC------AAAAAAA-TACGAAAA
* * *
31176956 AAGTATCAAAATCAGGGTTATTTAGTAAAAAACCCTTAATATAAAGAAACAGTT-A-AT--TAAT
58 AAGTGTCAAAATCAGGGTTATTTA-T--TAAA---TTAATATAAA-AAACACTTAATATAATAAT
** * * *
31177017 ACATTTG-AATTTTTTTTGCTAAAATAATATAA
116 ACATTTGAAACATTATGTACTAAAATAATATAA
* * * *
31177049 AAAATAAAATAAGAAAA-AATATATTTTAAAAAATAATATACGAAAAAATACGAATAAAGTG-CT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTC-
* * * *
31177112 AAAATCAGGGATATTTATTGAAA-AAATATAAAAAATA-TT--GA-AATAATACATTTGAAACAT
65 AAAATCAGGGTTATTTATT-AAATTAATATAAAAAACACTTAATATAATAATACATTTGAAACAT
31177172 TATGTACTAAAATAATATGAA
129 TATGTACTAAAATAATAT-AA
*
31177193 GAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCA
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCA
* *
31177258 AAATCAGGATTATTTATTAAATTAGTATAAAAAAACACTTACATAATATACATAATACATTTGAA
66 AAATCAGGGTTATTTATTAAATTAATAT-AAAAAACAC-T---TAATATA-ATAATACATTTGAA
* * *
31177323 ACATTTTTTGCTAAAATAATATAA
125 ACATTATGTACTAAAATAATATAA
* * * * *
31177347 AAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATACGAAAAAATATGAATAAAGTG-CT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTC-
** ** *
31177411 AAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAA-ATAAT-AT--ATTTAAAACATT
65 AAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAATATAATAATACATTTGAAACATT
* *
31177472 ATGTACTAAAATAAGGGTTTTA
130 ATGTACTAAAATAA---TATAA
* * *
31177494 AAATTAAATAATACGAAAGTAATATA-TTTAAAAAA-AAGATACAAAAAAAATATG-AAAAAGTG
1 AAAAT-AA-AATACGAAAATAATATATTTTAAAAAATAAGATAC-AAAAAAATACGAAAAAAGTG
* * *
31177556 TCAAAATCAGTGTTATTTATTAAATTAATATAAAAAATA-TT--GA-AATAATACATTTGAAACA
63 TCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAATATAATAATACATTTGAAACA
31177617 TTATGTACTAAAATAATATGAA
128 TTATGTACTAAAATAATAT-AA
*
31177639 GAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCA
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCA
*
31177704 AAATCAGGGTTATTTATTAAATTAGTATAAAAAACACTTACATAATATACATAATACATTTGAAA
66 AAATCAGGGTTATTTATTAAATTAATATAAAAAACAC-T---TAATATA-ATAATACATTTGAAA
* * *
31177769 CATTTTTTGCTAAAATAATATAA
126 CATTATGTACTAAAATAATATAA
* * * * *
31177792 AAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATACGAAAAAATATGAATAAAGTG-CT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTC-
** ** *
31177856 AAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAA-ATAAT-AT--ATTTAAAACATT
65 AAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAATATAATAATACATTTGAAACATT
* *
31177917 ATGTACTAAAATAAGGGTTTTA
130 ATGTACTAAAATAA---TATAA
* * *
31177939 AAATTAAATAATACGAAAGTAATATA-TTT-AAAAA-AAGATACAAAAAAATATG-AAAAAGTGT
1 AAAAT-AA-AATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGT
* * *
31178000 CAAAATCAGTGTTATTTATTAAATTAATATAAAAAATA-TT--GA-AATAATACATTTGAAACAT
64 CAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAATATAATAATACATTTGAAACAT
31178061 TATGTACTAAAATAATATGAA
129 TATGTACTAAAATAATAT-AA
*
31178082 GAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCA
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCA
*
31178147 AAATCAGGGTTATTTATTAAATTAGTATAAAAAACACTTACATAATATACATAATACATTTGAAA
66 AAATCAGGGTTATTTATTAAATTAATATAAAAAACAC-T---TAATATA-ATAATACATTTGAAA
* * *
31178212 CATTTTTTGCTAAAATAATATAA
126 CATTATGTACTAAAATAATATAA
* * * ** *
31178235 AAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATACGAAAAAATATTAATAAAGTG-CT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTC-
** ** *
31178299 AAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAA-ATAAT-AT--ATTTAAAACATT
65 AAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAATATAATAATACATTTGAAACATT
* *
31178360 ATGTACTAAAATAAGGGTTTTA
130 ATGTACTAAAATAA---TATAA
* * *
31178382 AAATTAAATAATACGAAAGTAATATA-TTTAAAAAA-AAGATACGAAAAAATACG-AAAAAGTGT
1 AAAAT-AA-AATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGT
* * * *
31178444 CAAAATCAGTGTTATTTATTAAATTAATATAAAAAAATACTT-ACATAATAATACATTTAAAACA
64 CAAAATCAGGGTTATTTATTAAATTAATAT-AAAAAACACTTAATATAATAATACATTTGAAACA
* *
31178508 TT-TTTGCTAAAATAATATAA
128 TTATGTACTAAAATAATATAA
*
31178528 AAAATAATATACGAAAATA
1 AAAATAAAATACGAAAATA
31178547 TTTTACTTAT
Statistics
Matches: 1385, Mismatches: 169, Indels: 203
0.79 0.10 0.12
Matches are distributed among these distances:
141 19 0.01
142 25 0.02
143 54 0.04
144 141 0.10
145 260 0.19
146 82 0.06
147 135 0.10
148 52 0.04
149 92 0.07
150 27 0.02
151 29 0.02
152 9 0.01
153 192 0.14
154 153 0.11
155 33 0.02
156 31 0.02
157 34 0.02
158 15 0.01
159 2 0.00
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (148 bp):
AAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCA
AAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAATATAATAATACATTTGAAACATTA
TGTACTAAAATAATATAA
Found at i:31177897 original size:21 final size:22
Alignment explanation
Indices: 31177873--31177914 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
31177863 GGGTTATTTA
31177873 TTAAA-AAAATATTTAAAACAC
1 TTAAATAAAATATTTAAAACAC
*
31177894 TTAAATAATATATTTAAAACA
1 TTAAATAAAATATTTAAAACA
31177915 TTATGTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
TTAAATAAAATATTTAAAACAC
Found at i:31178222 original size:443 final size:444
Alignment explanation
Indices: 31176748--31178546 Score: 2737
Period size: 443 Copynumber: 4.0 Consensus size: 444
31176738 TTTTATGCTA
* * *
31176748 AAATAAAATACCAAAATAATATATTTTAAAAAATAATATACAAAAAAAATACGAATAAAGTG-CT
1 AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC-AAAAAAATACGAAAAAAGTGTC-
** *
31176812 AAAATCAGGGTTATTTATTAAAAAAATAT-AAAAA-A--TAC-T--TA-A-ATAATACATTTGAA
64 AAAATCAGGGTTATTTATTAAATTAGTATAAAAAACACTTACATAATATACATAATACATTTGAA
* * * * * *
31176868 GCATTATGTACTAAAATAATATAAAGAAATAAAA-ACGAAAATAATATATATTAAAAAATAATAT
129 ACATTTTTTGCTAAAATAATATAAA-AAATAAAATAGGAAAATAATATATTTTAAAAAATAATAT
* * * *
31176932 ACGAAAATAAAAAAATTACGAAGAAAGT-ATCAAAATCAGGGTTATTTAGTAAAAAACCCTTAAT
193 ACG------AAAAAA-TATGAATAAAGTGCT-AAAATCAGGGTTATTTA-TTAAAAA-----AAT
** * * * * ** * * * * * *
31176996 ATAAAGAAACAGTTAATTAATACATTT-GAATTTTTTTTGCTAAAATAA---TATAAAAAAT-AA
244 ATTTA-AAACACTTAAATAATATATTTAAAACATTATGTACTAAAATAAGGGTTTTAAAATTAAA
* * * *
31177056 -AATAAGAAA-AAATATATTTTAAAAAATAATATACGAAAAAATACGAATAAAGTG-CTAAAATC
308 TAATACGAAAGTAATATA-TTTAAAAAA-AAGATACAAAAAAATACGAA-AAAGTGTC-AAAATC
* * *
31177118 AGGGATATTTATTGAAA-AAATATAAAAAATATTGAAATAATACATTTGAAACATTATGTACTAA
369 AGTGTTATTTATT-AAATTAATATAAAAAATATTGAAATAATACATTTGAAACATTATGTACTAA
31177182 AATAATATGAAG
433 AATAATATGAAG
31177194 AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCAA
1 AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCAA
*
31177259 AATCAGGATTATTTATTAAATTAGTATAAAAAAACACTTACATAATATACATAATACATTTGAAA
66 AATCAGGGTTATTTATTAAATTAGTAT-AAAAAACACTTACATAATATACATAATACATTTGAAA
31177324 CATTTTTTGCTAAAATAATATAAAAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATAC
130 CATTTTTTGCTAAAATAATATAAAAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATAC
31177389 GAAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAAA
195 GAAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAAA
31177454 TAATATATTTAAAACATTATGTACTAAAATAAGGGTTTTAAAATTAAATAATACGAAAGTAATAT
260 TAATATATTTAAAACATTATGTACTAAAATAAGGGTTTTAAAATTAAATAATACGAAAGTAATAT
*
31177519 ATTTAAAAAAAAGATACAAAAAAAATATGAAAAAGTGTCAAAATCAGTGTTATTTATTAAATTAA
325 ATTTAAAAAAAAGATAC-AAAAAAATACGAAAAAGTGTCAAAATCAGTGTTATTTATTAAATTAA
31177584 TATAAAAAATATTGAAATAATACATTTGAAACATTATGTACTAAAATAATATGAAG
389 TATAAAAAATATTGAAATAATACATTTGAAACATTATGTACTAAAATAATATGAAG
31177640 AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCAA
1 AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCAA
31177705 AATCAGGGTTATTTATTAAATTAGTATAAAAAACACTTACATAATATACATAATACATTTGAAAC
66 AATCAGGGTTATTTATTAAATTAGTATAAAAAACACTTACATAATATACATAATACATTTGAAAC
31177770 ATTTTTTGCTAAAATAATATAAAAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATACG
131 ATTTTTTGCTAAAATAATATAAAAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATACG
31177835 AAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAAAT
196 AAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAAAT
31177900 AATATATTTAAAACATTATGTACTAAAATAAGGGTTTTAAAATTAAATAATACGAAAGTAATATA
261 AATATATTTAAAACATTATGTACTAAAATAAGGGTTTTAAAATTAAATAATACGAAAGTAATATA
*
31177965 TTT-AAAAAAAGATACAAAAAAATATGAAAAAGTGTCAAAATCAGTGTTATTTATTAAATTAATA
326 TTTAAAAAAAAGATACAAAAAAATACGAAAAAGTGTCAAAATCAGTGTTATTTATTAAATTAATA
31178029 TAAAAAATATTGAAATAATACATTTGAAACATTATGTACTAAAATAATATGAAG
391 TAAAAAATATTGAAATAATACATTTGAAACATTATGTACTAAAATAATATGAAG
31178083 AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCAA
1 AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCAA
31178148 AATCAGGGTTATTTATTAAATTAGTATAAAAAACACTTACATAATATACATAATACATTTGAAAC
66 AATCAGGGTTATTTATTAAATTAGTATAAAAAACACTTACATAATATACATAATACATTTGAAAC
31178213 ATTTTTTGCTAAAATAATATAAAAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATACG
131 ATTTTTTGCTAAAATAATATAAAAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATACG
*
31178278 AAAAAATATTAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAAAT
196 AAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAAAT
31178343 AATATATTTAAAACATTATGTACTAAAATAAGGGTTTTAAAATTAAATAATACGAAAGTAATATA
261 AATATATTTAAAACATTATGTACTAAAATAAGGGTTTTAAAATTAAATAATACGAAAGTAATATA
*
31178408 TTTAAAAAAAAGATACGAAAAAATACGAAAAAGTGTCAAAATCAGTGTTATTTATTAAATTAATA
326 TTTAAAAAAAAGATACAAAAAAATACGAAAAAGTGTCAAAATCAGTGTTATTTATTAAATTAATA
* * * * *
31178473 TAAAAAAATACTTACATAATAATACATTTAAAACATT-TTTGCTAAAATAATAT-AAA
391 T-AAAAAATA-TT-GA-AATAATACATTTGAAACATTATGTACTAAAATAATATGAAG
*
31178529 AAATAATATACGAAAATA
1 AAATAAAATACGAAAATA
31178547 TTTTACTTAT
Statistics
Matches: 1276, Mismatches: 49, Indels: 56
0.92 0.04 0.04
Matches are distributed among these distances:
441 18 0.01
442 21 0.02
443 430 0.34
444 72 0.06
445 298 0.23
446 241 0.19
447 55 0.04
448 53 0.04
449 7 0.01
450 3 0.00
451 1 0.00
453 2 0.00
454 9 0.01
455 66 0.05
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (444 bp):
AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCAA
AATCAGGGTTATTTATTAAATTAGTATAAAAAACACTTACATAATATACATAATACATTTGAAAC
ATTTTTTGCTAAAATAATATAAAAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATACG
AAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAAAT
AATATATTTAAAACATTATGTACTAAAATAAGGGTTTTAAAATTAAATAATACGAAAGTAATATA
TTTAAAAAAAAGATACAAAAAAATACGAAAAAGTGTCAAAATCAGTGTTATTTATTAAATTAATA
TAAAAAATATTGAAATAATACATTTGAAACATTATGTACTAAAATAATATGAAG
Found at i:31178340 original size:21 final size:22
Alignment explanation
Indices: 31178316--31178357 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
31178306 GGGTTATTTA
31178316 TTAAA-AAAATATTTAAAACAC
1 TTAAATAAAATATTTAAAACAC
*
31178337 TTAAATAATATATTTAAAACA
1 TTAAATAAAATATTTAAAACA
31178358 TTATGTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
TTAAATAAAATATTTAAAACAC
Found at i:31180512 original size:70 final size:72
Alignment explanation
Indices: 31180412--31180553 Score: 225
Period size: 70 Copynumber: 2.0 Consensus size: 72
31180402 AGTCCGAGCG
*
31180412 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACTATTTC-CGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCTCGG
31180476 GCTCATC
66 GCTCATC
* * * *
31180483 ATCGCATTCACTTTCGGCT-ATACTTCTTATCATCCGGATTTTGCGGGCAATGACAATTTCTCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCTCGG
31180547 GCTCATC
66 GCTCATC
31180554 GGGGGGCGGA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
70 38 0.58
71 27 0.42
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (72 bp):
ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCTCGG
GCTCATC
Found at i:31180644 original size:33 final size:32
Alignment explanation
Indices: 31180598--31180670 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
31180588 GGGTCGTACA
31180598 CACCGCAGCATAGCACCT-CTCCCGGCCCATATC
1 CACCGCAGCATAGCA-CTGC-CCCGGCCCATATC
** *
31180631 CACCGCATTATAGCACTGCCCCGGCCCGTATC
1 CACCGCAGCATAGCACTGCCCCGGCCCATATC
*
31180663 CACTGCAG
1 CACCGCAG
31180671 TACTCCACTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 20 0.59
33 14 0.41
ACGTcount: A:0.21, C:0.45, G:0.18, T:0.16
Consensus pattern (32 bp):
CACCGCAGCATAGCACTGCCCCGGCCCATATC
Found at i:31184707 original size:15 final size:16
Alignment explanation
Indices: 31184688--31184749 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 16
31184678 TACCTTCTTT
31184688 TTTTCTTCTCCTTCT-
1 TTTTCTTCTCCTTCTA
*
31184703 TTTTCTTCCTTCTCTTCTC
1 TTTTCTT-C-TC-CTTCTA
* *
31184722 CTTTCTT-TCCTTTTA
1 TTTTCTTCTCCTTCTA
31184737 TTTTCTTCTCCTT
1 TTTTCTTCTCCTT
31184750 ACTGCTGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
15 17 0.45
16 8 0.21
17 2 0.05
18 5 0.13
19 6 0.16
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTCTTCTCCTTCTA
Found at i:31184860 original size:27 final size:27
Alignment explanation
Indices: 31184830--31184893 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
31184820 CCACACAACT
*
31184830 GGTGCCGCCTCTGCCAGAGGCAACACC
1 GGTGCCGCCTCTGCCAAAGGCAACACC
*
31184857 GGTGCCGCCTCTGCCAAAGGCAACACT
1 GGTGCCGCCTCTGCCAAAGGCAACACC
31184884 GGTGCCGCCT
1 GGTGCCGCCT
31184894 TTGGCACCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.17, C:0.39, G:0.30, T:0.14
Consensus pattern (27 bp):
GGTGCCGCCTCTGCCAAAGGCAACACC
Found at i:31185076 original size:18 final size:18
Alignment explanation
Indices: 31185055--31185092 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
31185045 TTTTTTACTG
31185055 TATTATTTTGA-ATTTTTT
1 TATT-TTTTGATATTTTTT
*
31185073 TATTTTTTTATATTTTTT
1 TATTTTTTGATATTTTTT
31185091 TA
1 TA
31185093 GTAAAAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (18 bp):
TATTTTTTGATATTTTTT
Found at i:31189143 original size:2 final size:2
Alignment explanation
Indices: 31189136--31189166 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31189126 TATCACTTGC
31189136 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31189167 TCTTTCTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31190964 original size:21 final size:20
Alignment explanation
Indices: 31190923--31190966 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
31190913 GCCTAAGACG
* *
31190923 TGAATTGGATTGGATTGAAT
1 TGAATTGAATTGGATTAAAT
*
31190943 TGAATATGAATTGTATTAAAT
1 TGAAT-TGAATTGGATTAAAT
31190964 TGA
1 TGA
31190967 GTTAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (20 bp):
TGAATTGAATTGGATTAAAT
Found at i:31193448 original size:21 final size:20
Alignment explanation
Indices: 31193423--31193487 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
31193413 TAGTCTCCGG
31193423 GCTTCCGTTTAGTACTTATGT
1 GCTTCCGTTTAG-ACTTATGT
* * ** *
31193444 GCTTCAG-TTAG-CCTCCGG
1 GCTTCCGTTTAGACTTATGT
31193462 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAG-ACTTATGT
31193483 GCTTC
1 GCTTC
31193488 AGCTAGATTT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 9 0.29
19 4 0.13
20 4 0.13
21 14 0.45
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (20 bp):
GCTTCCGTTTAGACTTATGT
Found at i:31193451 original size:39 final size:39
Alignment explanation
Indices: 31193405--31193489 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
31193395 GCTTTGATAA
* *
31193405 GCTTCAGTTAGTCTCCGGGCTTCCGTTTAGTACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
31193444 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
31193483 GCTTCAG
1 GCTTCAG
31193490 CTAGATTTCG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.13, C:0.26, G:0.24, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
Found at i:31193502 original size:39 final size:39
Alignment explanation
Indices: 31193405--31193505 Score: 139
Period size: 39 Copynumber: 2.6 Consensus size: 39
31193395 GCTTTGATAA
* * *
31193405 GCTTCAGTTAGTCTCCGGGCTTCCGTTTAGTACTTATGT
1 GCTTCAGCTAGACTCCGGGCTTCCGTTTAGCACTTATGT
* *
31193444 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGCTAGACTCCGGGCTTCCGTTTAGCACTTATGT
* *
31193483 GCTTCAGCTAGATTTCGGGCTTC
1 GCTTCAGCTAGACTCCGGGCTTC
31193506 AGATCACGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.13, C:0.26, G:0.24, T:0.38
Consensus pattern (39 bp):
GCTTCAGCTAGACTCCGGGCTTCCGTTTAGCACTTATGT
Found at i:31194352 original size:26 final size:28
Alignment explanation
Indices: 31194302--31194360 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 28
31194292 CCCGATATAT
31194302 GGCTCT-TCGTGAGCTTCCTACTTAA-A
1 GGCTCTCTCGTGAGCTTCCTACTTAATA
*
31194328 GGCTCTCT-GTGAGCTTCTTGA-TTAATA
1 GGCTCTCTCGTGAGCTTCCT-ACTTAATA
31194355 -GCTCTC
1 GGCTCTC
31194361 CGAAGCTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
26 26 0.90
27 3 0.10
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.37
Consensus pattern (28 bp):
GGCTCTCTCGTGAGCTTCCTACTTAATA
Found at i:31194520 original size:25 final size:25
Alignment explanation
Indices: 31194492--31194547 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
31194482 TGAGCTTCTT
**
31194492 GTTATATAGCCCGGATAAGCTTCCC
1 GTTATATAGCCCACATAAGCTTCCC
* * *
31194517 GTTACATAGCTCACATGAGCTTCCC
1 GTTATATAGCCCACATAAGCTTCCC
31194542 GTTATA
1 GTTATA
31194548 AGGCTTGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (25 bp):
GTTATATAGCCCACATAAGCTTCCC
Found at i:31203139 original size:16 final size:16
Alignment explanation
Indices: 31203118--31203149 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31203108 GATATCACTC
31203118 CATTTTCTAGTATTCG
1 CATTTTCTAGTATTCG
31203134 CATTTTCTAGTATTCG
1 CATTTTCTAGTATTCG
31203150 AATACTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (16 bp):
CATTTTCTAGTATTCG
Found at i:31207139 original size:24 final size:26
Alignment explanation
Indices: 31207092--31207139 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
31207082 AATAAAAAAA
31207092 TTAAAAATATAATAAATCAAATATGT
1 TTAAAAATATAATAAATCAAATATGT
31207118 TTAAAAACT-TAA-AAA-CAAATAT
1 TTAAAAA-TATAATAAATCAAATAT
31207140 TAAAACAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 7 0.33
25 3 0.14
26 10 0.48
27 1 0.05
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (26 bp):
TTAAAAATATAATAAATCAAATATGT
Found at i:31217383 original size:40 final size:40
Alignment explanation
Indices: 31217338--31217504 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
31217328 CGGAATATAA
31217338 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
31217378 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
31217418 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
31217458 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
31217497 CCGGATAT
1 CCGGATAT
31217505 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:31217488 original size:80 final size:79
Alignment explanation
Indices: 31217354--31217504 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
31217344 ATAATCACGT
*
31217354 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
31217419 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
31217434 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
31217497 CCGGATAT
64 CCGGATAT
31217505 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:31218761 original size:56 final size:56
Alignment explanation
Indices: 31218698--31218805 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 56
31218688 CCCCCTTTTC
31218698 CCTTAGTA-ATTTCGGCCAAGAAGAT-GAGAAAGGATGAACAAATTTTTCTTTTCTTT
1 CCTTAGTACA-TTCGGCCAAGAAGATGGAG-AAGGATGAACAAATTTTTCTTTTCTTT
*** **
31218754 CCTTAGTACATTCGGCCAAGCCTATGGAGAAGGATGAACATTTTTTTCTTTT
1 CCTTAGTACATTCGGCCAAGAAGATGGAGAAGGATGAACAAATTTTTCTTTT
31218806 TTTTTTTCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
56 41 0.91
57 4 0.09
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (56 bp):
CCTTAGTACATTCGGCCAAGAAGATGGAGAAGGATGAACAAATTTTTCTTTTCTTT
Found at i:31219790 original size:19 final size:20
Alignment explanation
Indices: 31219766--31219808 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 20
31219756 AATCTTTAAG
31219766 GATATGCAATCTT-AGATAT
1 GATATGCAATCTTAAGATAT
31219785 GATATGCAATCTTAAAGATAT
1 GATATGCAATCTT-AAGATAT
31219806 GAT
1 GAT
31219809 TTTGTAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (20 bp):
GATATGCAATCTTAAGATAT
Found at i:31224496 original size:48 final size:48
Alignment explanation
Indices: 31224399--31224659 Score: 423
Period size: 48 Copynumber: 5.4 Consensus size: 48
31224389 AAGCTATTGC
31224399 TGAAATATGTATGAGATATGTATATGTGTGGTAAAGCCGAATGGCTAGTG
1 TGAAATATGTATGAGATATGTATA--TGTGGTAAAGCCGAATGGCTAGTG
* *
31224449 TGAAATATGTATGAGATATGTATATGTGGTAAAGTCAAATGGCTAGTG
1 TGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTG
31224497 TGAAATATGTATGAGATATGTATATGTGTGGTAAAGCCGAATGGCTAGTG
1 TGAAATATGTATGAGATATGTATA--TGTGGTAAAGCCGAATGGCTAGTG
* *
31224547 TGAAATATGTATAAGATATGTATATGTAGTAAAGCCGAATGGCTAGTG
1 TGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTG
* *
31224595 TGAAATATGTATGAGATATATATATGTGGAAAAGCCGAATGGCTAGTG
1 TGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTG
*
31224643 TGAAATATGTAGGAGAT
1 TGAAATATGTATGAGAT
31224660 GTGTGTATAT
Statistics
Matches: 198, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
48 129 0.65
50 69 0.35
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.31
Consensus pattern (48 bp):
TGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTG
Found at i:31224568 original size:98 final size:98
Alignment explanation
Indices: 31224399--31224653 Score: 442
Period size: 98 Copynumber: 2.6 Consensus size: 98
31224389 AAGCTATTGC
*
31224399 TGAAATATGTATGAGATATGTATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 TGAAATATGTATGAGATATGTATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATAAG
* *
31224464 ATATGTATATGTGGTAAAGTCAAATGGCTAGTG
66 ATATGTATATGTAGTAAAGCCAAATGGCTAGTG
31224497 TGAAATATGTATGAGATATGTATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATAAG
1 TGAAATATGTATGAGATATGTATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATAAG
*
31224562 ATATGTATATGTAGTAAAGCCGAATGGCTAGTG
66 ATATGTATATGTAGTAAAGCCAAATGGCTAGTG
* *
31224595 TGAAATATGTATGAGATA--TATATATGTGGAAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TGAAATATGTATGAGATATGTATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
31224654 GGAGATGTGT
Statistics
Matches: 151, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
96 39 0.26
98 112 0.74
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.32
Consensus pattern (98 bp):
TGAAATATGTATGAGATATGTATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATAAG
ATATGTATATGTAGTAAAGCCAAATGGCTAGTG
Found at i:31224855 original size:37 final size:37
Alignment explanation
Indices: 31224800--31224902 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
31224790 GGAAATATAT
31224800 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
31224837 TCCGAGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
31224874 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
31224903 GGACTATTCG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:31230448 original size:8 final size:7
Alignment explanation
Indices: 31230437--31230494 Score: 53
Period size: 7 Copynumber: 7.4 Consensus size: 7
31230427 CTTCTATTTC
31230437 AAAAGTAA
1 AAAAG-AA
*
31230445 AAAAAAA
1 AAAAGAA
31230452 AAAGAGAA
1 AAA-AGAA
31230460 AAAAGAAAA
1 AAAAG--AA
31230469 AAAGAGAAA
1 AAA-AG-AA
31230478 AAAAGAA
1 AAAAGAA
31230485 AAAAGAA
1 AAAAGAA
31230492 AAA
1 AAA
31230495 TGGAGAGGCC
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
7 19 0.43
8 12 0.27
9 11 0.25
10 2 0.05
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:31230468 original size:17 final size:18
Alignment explanation
Indices: 31230443--31230488 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
31230433 TTTCAAAAGT
31230443 AAAAA-AAAAAAAGAG-A
1 AAAAAGAAAAAAAGAGAA
31230459 AAAAAGAAAAAAAGAGAA
1 AAAAAGAAAAAAAGAGAA
31230477 AAAAAGAAAAAA
1 AAAAAGAAAAAA
31230489 GAAAAATGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 5 0.18
17 10 0.36
18 13 0.46
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAAGAGAA
Found at i:31230489 original size:17 final size:17
Alignment explanation
Indices: 31230443--31230494 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
31230433 TTTCAAAAGT
31230443 AAAAAA-AAAAAAGAG-
1 AAAAAAGAAAAAAGAGA
31230458 AAAAAAGAAAAAAAGAGA
1 AAAAAAG-AAAAAAGAGA
31230476 AAAAAAGAAAAAAGA-A
1 AAAAAAGAAAAAAGAGA
31230492 AAA
1 AAA
31230495 TGGAGAGGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.18
16 4 0.12
17 17 0.50
18 7 0.21
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAGAGA
Found at i:31231584 original size:38 final size:38
Alignment explanation
Indices: 31231450--31231584 Score: 114
Period size: 41 Copynumber: 3.3 Consensus size: 38
31231440 CGCCTTAATC
*
31231450 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGG-----TTCGCAGATCTTATCT
* * *
31231493 CCCTAAGCAGTAGTGG-AGCA-GATCGAAGACTCGCCTTAATC-
1 CCCTAAGCAGTAG-GGTAACAGGTTCGCAGA-T---CTT-ATCT
31231534 CCCTAAGCAGTAGGGTAACAGGTTCGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTTCGCAGATCTTATCT
31231572 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
31231585 CAGAGCAGAT
Statistics
Matches: 76, Mismatches: 7, Indels: 23
0.72 0.07 0.22
Matches are distributed among these distances:
37 8 0.11
38 17 0.22
40 2 0.03
41 20 0.26
42 11 0.14
43 16 0.21
44 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (38 bp):
CCCTAAGCAGTAGGGTAACAGGTTCGCAGATCTTATCT
Found at i:31231721 original size:166 final size:165
Alignment explanation
Indices: 31231444--31231801 Score: 533
Period size: 166 Copynumber: 2.1 Consensus size: 165
31231434 ATTCAGCGCC
31231444 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGG
1 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGG
* * *
31231509 AGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGG-TTCGCAGATCTTATCTC
66 AGCAGATCGAAGACCCGCCTTAATCCCCTAAGCAGTAGGATAACAGGATTCACAGATCTTA--TC
*
31231573 CCTAAGCAGTAGCAGAGCAGATCGATGACGACTCGCT
129 CCTAAGCAGTAGCAGAGCAGATCGAAGACGACTCGCT
*
31231610 TTAATCCCCTAAGTAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGG
1 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGG
* *
31231675 AGCAGATCGAAGACCCGCCTTAATCCTCTAAGCAGTAGGATAACAGGTTAAATTTACAGATCTTA
66 AGCAGATCGAAGACCCGCCTTAATCCCCTAAGCAGTAGGATAACAGG----ATTCACAGATCTTA
* * *
31231740 TCCCTAAGCAGTAGCGGAGCAGATCGAAGACGA-TGCACC
127 TCCCTAAGCAGTAGCAGAGCAGATCGAAGACGACT-CGCT
*
31231779 TTAA-CCCTTAAGCAGTAGGGTAA
1 TTAATCCCCTAAGCAGTAGGGTAA
31231802 TAGACCAAAG
Statistics
Matches: 174, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
166 108 0.62
168 18 0.10
169 37 0.21
171 11 0.06
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (165 bp):
TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGACCCGCCTTAATCCCCTAAGCAGTAGGATAACAGGATTCACAGATCTTATCCC
TAAGCAGTAGCAGAGCAGATCGAAGACGACTCGCT
Found at i:31231739 original size:84 final size:84
Alignment explanation
Indices: 31231440--31231801 Score: 506
Period size: 84 Copynumber: 4.3 Consensus size: 84
31231430 CAAAATTCAG
31231440 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
31231505 GTGGAGCAGATCGAAGACT
66 GCGGAGCAGATCGAAGACT
*
31231524 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGG-----TTCGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
31231584 GCAGAGCAGATCGATGACGACT
66 GCGGAGCAGATCGA--A-GACT
* *
31231606 CGCTTTAATCCCCTAAGTAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
* *
31231671 GTGGAGCAGATCGAAGACC
66 GCGGAGCAGATCGAAGACT
* * *
31231690 CGCCTTAATCCTCTAAGCAGTAGGATAACAGGTTAAATTTACAGATCTTA--TCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
31231753 GCGGAGCAGATCGAAGACGAT
66 GCGGAGCAGATCGAAGAC--T
* *
31231774 GCACCTTAA-CCCTTAAGCAGTAGGGTAA
1 -CGCCTTAATCCCCTAAGCAGTAGGGTAA
31231802 TAGACCAAAG
Statistics
Matches: 247, Mismatches: 20, Indels: 22
0.85 0.07 0.08
Matches are distributed among these distances:
79 39 0.16
81 1 0.00
82 64 0.26
84 96 0.39
85 8 0.03
87 39 0.16
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (84 bp):
CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
GCGGAGCAGATCGAAGACT
Found at i:31232099 original size:175 final size:174
Alignment explanation
Indices: 31231891--31232447 Score: 918
Period size: 175 Copynumber: 3.2 Consensus size: 174
31231881 TTTCGACGGA
* *
31231891 GAGCAAATCGAAGACATAGTAGATCTGACTTTTGGATGTTCTCACATCAAAGCAGATCCAAGATA
1 GAGCAAATCGAAGACATAGCAGATTTGACTTTTGGATGTTCTCACA-CAAAGCAGATCCAAGATA
*
31231956 ACAGATCTAGCATCTCCATTTC-AGCGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATT
65 ACAGATCTGGCATCTCCATTTCGA-CGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATT
*
31232020 TTACTGAAACAGATCCAAGATGATTTGGCATCCTTGTGTGCACAAG
129 TTACTGAAACAGATCCAAGATGATTTGGCATCCTTGTGTTCACAAG
* * * *
31232066 GAGTAAATCGAAGACATAGCCGATTTGACTTTTGGATGTCCTCACACCAAAGTAGATCCAAGATA
1 GAGCAAATCGAAGACATAGCAGATTTGACTTTTGGATGTTCTCACA-CAAAGCAGATCCAAGATA
* *
31232131 ACAGATCTGGCATCTCCATTTTGATGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTT
65 ACAGATCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTT
* *
31232196 TACTGAAACAGATCCAAGATGATTTGGCATCCTTATATTCACAAG
130 TACTGAAACAGATCCAAGATGATTTGGCATCCTTGTGTTCACAAG
*
31232241 GAGCAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTCTCACACAAAAGCAGATCCAAGATA
1 GAGCAAATCGAAGACATAGCAGATTTGACTTTTGGATGTTCTCACAC-AAAGCAGATCCAAGATA
*
31232306 ACAGATCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCGAACCTTCAGATGATTT
65 ACAGATCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTT
* *
31232371 TACTGAAGCAGATCCAAGATGATTTGGCATCTTTGTGTTCACAAG
130 TACTGAAACAGATCCAAGATGATTTGGCATCCTTGTGTTCACAAG
*
31232416 GAGCAAATCGAAGACATAGCAGATTTGGCTTT
1 GAGCAAATCGAAGACATAGCAGATTTGACTTT
31232448 CACGTGTTTA
Statistics
Matches: 354, Mismatches: 26, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
174 1 0.00
175 352 0.99
176 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (174 bp):
GAGCAAATCGAAGACATAGCAGATTTGACTTTTGGATGTTCTCACACAAAGCAGATCCAAGATAA
CAGATCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTTT
ACTGAAACAGATCCAAGATGATTTGGCATCCTTGTGTTCACAAG
Found at i:31232387 original size:86 final size:86
Alignment explanation
Indices: 31231940--31232390 Score: 249
Period size: 86 Copynumber: 5.2 Consensus size: 86
31231930 TCTCACATCA
*
31231940 AAGCAGATCCAAGATAACAGATCTAGCATCTCCATTTC-AGCGGAGAGCAGATACATAGCAGATC
1 AAGCAGATCCAAGATAACAGATCTGGCATCTCCATTTCGA-CGGAGAGCAGATACATAGCAGATC
*
31232004 TAACCTTCAGATGATTTTACTG
65 GAACCTTCAGATGATTTTACTG
* * * * *
31232026 AAACAGATCCAAGAT----GATTTGGCA--TCC-TTGTGTGCACAAGGAGTA-AATCGAAGACAT
1 AAGCAGATCCAAGATAACAGATCTGGCATCTCCATT-T-CG-AC--GGAG-AGCA--G-ATACAT
* * * ** ** **
31232083 AGCCGATTTG-ACTTTTGGATG-TCCTCACACCA
57 AGCAGA-TCGAACCTTCAGATGAT--T-TTACTG
* * * *
31232115 AAGTAGATCCAAGATAACAGATCTGGCATCTCCATTTTGATGGAGAGCAGATACATAGCAGATCT
1 AAGCAGATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCG
31232180 AACCTTCAGATGATTTTACTG
66 AACCTTCAGATGATTTTACTG
* * * * *
31232201 AAACAGATCCAAGAT----GATTTGGCATC-CTTATATTC-ACAAGGAGCA-AATCGAAGACATA
1 AAGCAGATCCAAGATAACAGATCTGGCATCTC-CAT-TTCGAC--GGAG-AGCA--G-ATACATA
* * * * **
31232259 GCAGATTTG-ACTTTCGGATG-TTCTCACACAA
58 GCAGA-TCGAACCTTCAGATGATT-T--TACTG
31232290 AAGCAGATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCG
1 AAGCAGATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCG
31232355 AACCTTCAGATGATTTTACTG
66 AACCTTCAGATGATTTTACTG
31232376 AAGCAGATCCAAGAT
1 AAGCAGATCCAAGAT
31232391 GATTTGGCAT
Statistics
Matches: 262, Mismatches: 58, Indels: 90
0.64 0.14 0.22
Matches are distributed among these distances:
79 2 0.01
80 4 0.02
81 1 0.00
82 21 0.08
83 3 0.01
84 10 0.04
85 2 0.01
86 51 0.19
87 43 0.16
88 42 0.16
89 36 0.14
90 2 0.01
91 10 0.04
92 3 0.01
93 23 0.09
94 3 0.01
95 4 0.02
96 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (86 bp):
AAGCAGATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCG
AACCTTCAGATGATTTTACTG
Found at i:31235929 original size:19 final size:19
Alignment explanation
Indices: 31235905--31235986 Score: 137
Period size: 19 Copynumber: 4.3 Consensus size: 19
31235895 AATCTTTAAG
31235905 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
31235924 GATATGCAATCTTAGATGT
1 GATATGCAATCTTAGATAT
*
31235943 GATATGCAATCTTAGATGT
1 GATATGCAATCTTAGATAT
*
31235962 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
31235981 GATATG
1 GATATG
31235987 ATATGCAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 59 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:31237884 original size:21 final size:21
Alignment explanation
Indices: 31237860--31237911 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
31237850 AACAGCGGTG
*
31237860 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
31237881 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
31237902 GCAGTGAGAT
1 GCGGTGAGAT
31237912 CAGAAACAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.10, G:0.37, T:0.27
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:31238180 original size:32 final size:33
Alignment explanation
Indices: 31238138--31238199 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
31238128 AATGAATTAT
31238138 ATAATCAA-TTTAAATTATTTATTAGATAAAATG
1 ATAATCAATTTTAAATTATTTA-TAGATAAAATG
* *
31238171 ATAAT-AATTTTTAATTTTTTATAGATAAA
1 ATAATCAATTTTAAATTATTTATAGATAAA
31238200 TATTCTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 10 0.38
33 16 0.62
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (33 bp):
ATAATCAATTTTAAATTATTTATAGATAAAATG
Found at i:31238375 original size:14 final size:15
Alignment explanation
Indices: 31238356--31238384 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31238346 TAGGTTATGA
31238356 TACAAA-ATTGATTT
1 TACAAATATTGATTT
31238370 TACAAATATTGATTT
1 TACAAATATTGATTT
31238385 ATTAAACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (15 bp):
TACAAATATTGATTT
Found at i:31239958 original size:32 final size:32
Alignment explanation
Indices: 31239919--31240078 Score: 266
Period size: 32 Copynumber: 5.0 Consensus size: 32
31239909 CATAAAAAAT
*
31239919 ATCATACATTAGGTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
*
31239951 ATCATACATTAGTTTTGCATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
* *
31239983 ATCATACATTAGGTTCACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
* *
31240015 ATCATACATTAGTTTTGCATATGAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
31240047 ATCATACATTAGTTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
31240079 CATAGTTATA
Statistics
Matches: 117, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 117 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (32 bp):
ATCATACATTAGTTTTACATATAAAAAAGTAG
Found at i:31239992 original size:64 final size:64
Alignment explanation
Indices: 31239919--31240078 Score: 293
Period size: 64 Copynumber: 2.5 Consensus size: 64
31239909 CATAAAAAAT
31239919 ATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAG
1 ATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAG
* *
31239983 ATCATACATTAGGTTCACATATAAAAAAGTAGATCATACATTAGTTTTGCATATGAAAAAGTAG
1 ATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAG
*
31240047 ATCATACATTAGTTTTACATATAAAAAAGTAG
1 ATCATACATTAGGTTTACATATAAAAAAGTAG
31240079 CATAGTTATA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 92 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (64 bp):
ATCATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAG
Found at i:31244613 original size:20 final size:20
Alignment explanation
Indices: 31244588--31244625 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31244578 CCAAAGTCTC
31244588 TTTTCTTTTCAATT-TCCATA
1 TTTTC-TTTCAATTATCCATA
31244608 TTTTCTTTCAATTATCCA
1 TTTTCTTTCAATTATCCA
31244626 AATTCAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTCTTTCAATTATCCATA
Found at i:31252065 original size:31 final size:30
Alignment explanation
Indices: 31252006--31252082 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
31251996 CACTGGACTT
* *
31252006 TTTGAAAGTTTTCATTTTAATCACCGAATTA
1 TTTGAAAGTTTTTA-TATAATCACCGAATTA
*
31252037 TTTGAAAGTTTTTATATAAGTCATCGAATTA
1 TTTGAAAGTTTTTATATAA-TCACCGAATTA
*
31252068 TTCGAAAGTTTTTAT
1 TTTGAAAGTTTTTAT
31252083 TTTTTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 4 0.10
31 37 0.90
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (30 bp):
TTTGAAAGTTTTTATATAATCACCGAATTA
Found at i:31262752 original size:4 final size:4
Alignment explanation
Indices: 31262743--31262773 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
31262733 CCATTGATGC
31262743 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
31262774 TTATTTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:31266594 original size:3 final size:3
Alignment explanation
Indices: 31266586--31266875 Score: 130
Period size: 3 Copynumber: 97.7 Consensus size: 3
31266576 ATTTTAAGAG
31266586 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
31266634 AAT AAT AAT AA- AAGT AAT AGA- AAT AAT AAT -GT AAAT AAAT ACA-
1 AAT AAT AAT AAT AA-T AAT A-AT AAT AAT AAT AAT -AAT -AAT A-AT
* * * *
31266677 AA- AAG AA- AAT ATAT AAT -GT GAC AA- AAT CAAT -AT AA- AATT AATT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT AA-T AA-T
* * * * * ** *
31266720 AGT -TT AAT AA- GAT GAT GAT AGC AAT AGT AAT AAT -AT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
31266764 AGT AGAA AAT AAT AAT AAT AAT ACATT AAT AAG AAT AAT AAT AGT -AT
1 AAT A-AT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT AAT AAT
* * * *
31266811 ACT AAT AAT AAC AAT AAT AGA- AAGG AAT GAT AA- AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AA-T AAT AAT AAT AAT AAT -AAT AAT
31266857 AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AA
31266876 AGAATAGTGC
Statistics
Matches: 225, Mismatches: 32, Indels: 60
0.71 0.10 0.19
Matches are distributed among these distances:
2 27 0.12
3 167 0.74
4 29 0.13
5 2 0.01
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:31266820 original size:20 final size:20
Alignment explanation
Indices: 31266771--31266869 Score: 67
Period size: 20 Copynumber: 4.8 Consensus size: 20
31266761 TAAAGTAGAA
31266771 AATAATAATAATAATACATT
1 AATAATAATAATAATACATT
* *
31266791 AATAAGAATAATAATAGTATACT
1 AATAATAATAATAATA-CAT--T
* * **
31266814 AATAATAACAATAATAGAAAGG
1 AATAATAATAATAAT--ACATT
* *
31266836 AATGATAA-AATAATA-AAT
1 AATAATAATAATAATACATT
31266854 AATAATAATAATAATA
1 AATAATAATAATAATA
31266870 AAATAAAGAA
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
18 8 0.13
19 8 0.13
20 15 0.24
21 8 0.13
22 7 0.11
23 14 0.23
24 1 0.02
25 1 0.02
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.28
Consensus pattern (20 bp):
AATAATAATAATAATACATT
Found at i:31266830 original size:23 final size:23
Alignment explanation
Indices: 31266771--31266869 Score: 75
Period size: 23 Copynumber: 4.6 Consensus size: 23
31266761 TAAAGTAGAA
* *
31266771 AATAATAATAATAATACATTAAT
1 AATAATAATAATAGTACACTAAT
* *
31266794 AAGAATAATAATAGTATACTAAT
1 AATAATAATAATAGTACACTAAT
* * **
31266817 AATAACAATAATAG-AAAGGAAT
1 AATAATAATAATAGTACACTAAT
*
31266839 GATAA-AATAATA--A-A-TAAT
1 AATAATAATAATAGTACACTAAT
31266857 AATAATAATAATA
1 AATAATAATAATA
31266870 AAATAAAGAA
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
18 7 0.11
19 8 0.13
20 1 0.02
21 7 0.11
22 9 0.14
23 31 0.49
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.28
Consensus pattern (23 bp):
AATAATAATAATAGTACACTAAT
Found at i:31266952 original size:21 final size:21
Alignment explanation
Indices: 31266896--31266959 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
31266886 CAACAATAAC
* *
31266896 ATAAATAGTAATAG-AAAAACA
1 ATAAA-AGTAATAGTAATAATA
* * *
31266917 ATAATAGAAACAGTAATAATA
1 ATAAAAGTAATAGTAATAATA
31266938 ATAAAAGTAATAGTAATAATA
1 ATAAAAGTAATAGTAATAATA
31266959 A
1 A
31266960 ATGATTAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 6 0.18
21 28 0.82
ACGTcount: A:0.64, C:0.03, G:0.09, T:0.23
Consensus pattern (21 bp):
ATAAAAGTAATAGTAATAATA
Found at i:31267060 original size:18 final size:16
Alignment explanation
Indices: 31267020--31267063 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
31267010 ATGAAGGTAT
*
31267020 AAAAAATAAGTAAAGA
1 AAAAAATAAGCAAAGA
*
31267036 AATAAATAAGCAACGAGA
1 AAAAAATAAGCAA--AGA
31267054 AAAAAATAAG
1 AAAAAATAAG
31267064 AATAATGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 11 0.48
18 12 0.52
ACGTcount: A:0.70, C:0.05, G:0.14, T:0.11
Consensus pattern (16 bp):
AAAAAATAAGCAAAGA
Found at i:31270536 original size:29 final size:29
Alignment explanation
Indices: 31270503--31271000 Score: 271
Period size: 29 Copynumber: 17.1 Consensus size: 29
31270493 GTGGAATCAC
*
31270503 GATGGTCGTCACCATCCCTTTTCATTGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* *
31270532 GATGGTCATCACCATCCAC-TTTCATAATT
1 GATGGTCGTCACCATCC-CTTTTCATAGTT
* * * *
31270561 GATAGCCGAT-GCTATCCCTTTTCATA-TT
1 GATGGTCG-TCACCATCCCTTTTCATAGTT
* *
31270589 CGATGGTCGTTACCATCCCTGTTCATAGTT
1 -GATGGTCGTCACCATCCCTTTTCATAGTT
* * * * *
31270619 GATGGTCGCCACTATCCCCTTTCATAATC
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* *** *
31270648 GATAG-CCAAAGCTATCCCTTTTCATA-TT
1 GATGGTCGTCA-CCATCCCTTTTCATAGTT
* *
31270676 CAATGGTCGTCACCATCCCTTTTCGTAGTT
1 -GATGGTCGTCACCATCCCTTTTCATAGTT
*** * *
31270706 GAAATTCGTTACCATCCCTTTTCACAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
** * *
31270735 GAAAGTCGTTACCATCCCTTTTCATAATT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* * *
31270764 GATAG-C-TGAAGCTATCCCTTTTCATA-TT
1 GATGGTCGT-CA-CCATCCCTTTTCATAGTT
* * *
31270792 CGACGATCGTCACCATACCTTTTCATAGTT
1 -GATGGTCGTCACCATCCCTTTTCATAGTT
* *
31270822 GATGGTCGTCACCATCCCTTTTCATAATC
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* * * * * *
31270851 GATAGCCG-AAGCTATCCCTTTTCATAATC
1 GATGGTCGTCA-CCATCCCTTTTCATAGTT
* * * *** **
31270880 AATAGCCAAAACTGTCCCTTTTTCATA-TT
1 GATGGTCGTCACCATCCC-TTTTCATAGTT
*
31270909 CGATGGTTGTCACCATCCCTTTTCATAGTT
1 -GATGGTCGTCACCATCCCTTTTCATAGTT
* * *
31270939 GATGTTCGTCACCATCCCTTTTCATAATC
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* * * *
31270968 GATAGTCG-AAGCTATCCCTTTCCATAGTT
1 GATGGTCGTCA-CCATCCCTTTTCATAGTT
31270997 GATG
1 GATG
31271001 ATTGTCGTTA
Statistics
Matches: 361, Mismatches: 86, Indels: 44
0.74 0.18 0.09
Matches are distributed among these distances:
27 1 0.00
28 13 0.04
29 313 0.87
30 33 0.09
31 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.36
Consensus pattern (29 bp):
GATGGTCGTCACCATCCCTTTTCATAGTT
Found at i:31270652 original size:87 final size:87
Alignment explanation
Indices: 31270502--31270707 Score: 304
Period size: 87 Copynumber: 2.4 Consensus size: 87
31270492 AGTGGAATCA
* * *
31270502 CGATGGTCGTCACCATCCCTTTTCATTGTTGATGGTCATCACCATCCACTTTCATAATTGATAGC
1 CGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCACCACCATCCACTTTCATAATCGATAGC
* *
31270567 CGATGCTATCCCTTTTCATATT
66 CAAAGCTATCCCTTTTCATATT
* * * * *
31270589 CGATGGTCGTTACCATCCCTGTTCATAGTTGATGGTCGCCACTATCCCCTTTCATAATCGATAGC
1 CGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCACCACCATCCACTTTCATAATCGATAGC
31270654 CAAAGCTATCCCTTTTCATATT
66 CAAAGCTATCCCTTTTCATATT
* *
31270676 CAATGGTCGTCACCATCCCTTTTCGTAGTTGA
1 CGATGGTCGTCACCATCCCTTTTCATAGTTGA
31270708 AATTCGTTAC
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 105 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (87 bp):
CGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCACCACCATCCACTTTCATAATCGATAGC
CAAAGCTATCCCTTTTCATATT
Found at i:31270715 original size:116 final size:115
Alignment explanation
Indices: 31270574--31270993 Score: 491
Period size: 116 Copynumber: 3.6 Consensus size: 115
31270564 AGCCGATGCT
* * * * * *
31270574 ATCCCTTTTCATA-TTCGATGGTCGTTACCATCCCTGTTCATAGTTGATGGTCGCCACTATCCCC
1 ATCCCTTTTCATAGTT-GATGTTCGTCACCATCCCTTTTCATAGTTGATAGTCG-AACTATCCCT
*
31270638 TTTCATAATCGATAGCCAAAGCTATCCCTTTTCATATTCAATGGTCGTCACC
64 TTTCATAATCGATAGCCAAAGCTATCCCTTTTCATATTCGATGGTCGTCACC
* ** * * * * *
31270690 ATCCCTTTTCGTAGTTGAAATTCGTTACCATCCCTTTTCACAGTTGAAAGTCGTTACCATCCCTT
1 ATCCCTTTTCATAGTTGATGTTCGTCACCATCCCTTTTCATAGTTGATAGTCG-AACTATCCCTT
* ** * *
31270755 TTCATAATTGATAGCTGAAGCTATCCCTTTTCATATTCGACGATCGTCACC
65 TTCATAATCGATAGCCAAAGCTATCCCTTTTCATATTCGATGGTCGTCACC
* * * * *
31270806 ATACCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCGAAGCTATCCCTT
1 ATCCCTTTTCATAGTTGATGTTCGTCACCATCCCTTTTCATAGTTGATAGTCGAA-CTATCCCTT
* * * *
31270871 TTCATAATCAATAGCCAAAACTGTCCCTTTTTCATATTCGATGGTTGTCACC
65 TTCATAATCGATAGCCAAAGCTATCCC-TTTTCATATTCGATGGTCGTCACC
* *
31270923 ATCCCTTTTCATAGTTGATGTTCGTCACCATCCCTTTTCATAATCGATAGTCGAAGCTATCCCTT
1 ATCCCTTTTCATAGTTGATGTTCGTCACCATCCCTTTTCATAGTTGATAGTCGAA-CTATCCCTT
*
31270988 TCCATA
65 TTCATA
31270994 GTTGATGATT
Statistics
Matches: 257, Mismatches: 44, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
115 1 0.00
116 166 0.65
117 90 0.35
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (115 bp):
ATCCCTTTTCATAGTTGATGTTCGTCACCATCCCTTTTCATAGTTGATAGTCGAACTATCCCTTT
TCATAATCGATAGCCAAAGCTATCCCTTTTCATATTCGATGGTCGTCACC
Found at i:31272576 original size:42 final size:40
Alignment explanation
Indices: 31272416--31272568 Score: 130
Period size: 42 Copynumber: 3.7 Consensus size: 40
31272406 TGAGTTTACG
* * *
31272416 TGTAAGACCATATCTGGGATATGACTTCGTTATGAGATTTCA
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGA--TCA
* * * * *
31272458 TGT-AGAACCATGTCTGGGACATGGAATCAATATGAGAATCG
1 TGTAAG-ACCATATCTGGGATATGGCATCGATATGAG-ATCA
* *
31272499 TGTAATACCATAGT-TGGGCTATTGGCATCGATATGAGATCCCA
1 TGTAAGACCATA-TCTGGGATA-TGGCATCGATATGAGAT--CA
31272542 TGTAAGACCATATCTGGGATATGGCAT
1 TGTAAGACCATATCTGGGATATGGCAT
31272569 TGGTATGATT
Statistics
Matches: 86, Mismatches: 17, Indels: 16
0.72 0.14 0.13
Matches are distributed among these distances:
41 19 0.22
42 48 0.56
43 19 0.22
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (40 bp):
TGTAAGACCATATCTGGGATATGGCATCGATATGAGATCA
Found at i:31273629 original size:30 final size:30
Alignment explanation
Indices: 31273593--31273653 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
31273583 AAAGTTAAAT
*
31273593 CGCCTACATGGACTAGCACACGGGCATGTA
1 CGCCTACATGGACTAGCACACAGGCATGTA
* *
31273623 CGCCTACATGGCCTAGCACACAGGCGTGTA
1 CGCCTACATGGACTAGCACACAGGCATGTA
31273653 C
1 C
31273654 TTTGGCCGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (30 bp):
CGCCTACATGGACTAGCACACAGGCATGTA
Found at i:31279626 original size:11 final size:11
Alignment explanation
Indices: 31279605--31279642 Score: 58
Period size: 11 Copynumber: 3.3 Consensus size: 11
31279595 AGCTCATTTA
31279605 TATATTATTATT
1 TATA-TATTATT
31279617 TATATATTATT
1 TATATATTATT
31279628 TATATATTTATT
1 TATATA-TTATT
31279640 TAT
1 TAT
31279643 TTCTTTTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 13 0.52
12 12 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATATATTATT
Found at i:31289033 original size:64 final size:64
Alignment explanation
Indices: 31288960--31289170 Score: 151
Period size: 64 Copynumber: 3.2 Consensus size: 64
31288950 CTGGGCCAGA
*
31288960 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
31289024 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
31289086 ACTGGGCCAGA-
54 A-TGGCCCATAG
*
31289097 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
31289161 GCCCATTTCA
1 GCCCATTTCA
31289171 AAATACATGC
Statistics
Matches: 103, Mismatches: 27, Indels: 34
0.63 0.16 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.24
65 5 0.05
66 1 0.01
67 11 0.11
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 16 0.16
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:31289172 original size:137 final size:137
Alignment explanation
Indices: 31288926--31289212 Score: 556
Period size: 137 Copynumber: 2.1 Consensus size: 137
31288916 TATTGGGCCT
**
31288926 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
31288991 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
31289056 CATATGC
131 CATATGC
31289063 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
31289128 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
31289193 CATATGC
131 CATATGC
31289200 AAGCCCATTTGGG
1 AAGCCCATTTGGG
31289213 GAGACTACTC
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 148 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:31289524 original size:26 final size:27
Alignment explanation
Indices: 31289477--31289552 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 27
31289467 TCAATTTAAC
* * * *
31289477 CCTAGGGGTATTTCGGTGATTTTGC-A
1 CCTAGGGGTATTACAGTAATTTTCCAA
*
31289503 CCTAGGGGTATAACAGTAATTTTCCATA
1 CCTAGGGGTATTACAGTAATTTTCCA-A
* *
31289531 CATAGGGGTATTATAGTAATTT
1 CCTAGGGGTATTACAGTAATTT
31289553 AGCTGCTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 20 0.50
28 20 0.50
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (27 bp):
CCTAGGGGTATTACAGTAATTTTCCAA
Found at i:31291030 original size:26 final size:26
Alignment explanation
Indices: 31290994--31291103 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
31290984 CATGTAATTC
31290994 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
31291020 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
31291046 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
31291072 TTGTCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
31291098 TTATCA
1 TTATCA
31291104 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:31295902 original size:12 final size:12
Alignment explanation
Indices: 31295885--31295924 Score: 80
Period size: 12 Copynumber: 3.3 Consensus size: 12
31295875 AGTACTACCT
31295885 CGGCCTCGACCA
1 CGGCCTCGACCA
31295897 CGGCCTCGACCA
1 CGGCCTCGACCA
31295909 CGGCCTCGACCA
1 CGGCCTCGACCA
31295921 CGGC
1 CGGC
31295925 TTCTTCCCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.15, C:0.50, G:0.28, T:0.07
Consensus pattern (12 bp):
CGGCCTCGACCA
Found at i:31297277 original size:64 final size:64
Alignment explanation
Indices: 31297204--31297414 Score: 151
Period size: 64 Copynumber: 3.2 Consensus size: 64
31297194 CTGGGCCAGA
*
31297204 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
31297268 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
31297330 ACTGGGCCAGA-
54 A-TGGCCCATAG
*
31297341 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
31297405 GCCCATTTCA
1 GCCCATTTCA
31297415 AAATACATGC
Statistics
Matches: 103, Mismatches: 27, Indels: 34
0.63 0.16 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.24
65 5 0.05
66 1 0.01
67 11 0.11
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 16 0.16
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:31297416 original size:137 final size:137
Alignment explanation
Indices: 31297170--31297456 Score: 556
Period size: 137 Copynumber: 2.1 Consensus size: 137
31297160 TATTGGGCCT
**
31297170 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
31297235 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
31297300 CATATGC
131 CATATGC
31297307 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
31297372 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
31297437 CATATGC
131 CATATGC
31297444 AAGCCCATTTGGG
1 AAGCCCATTTGGG
31297457 GAGACTACTC
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 148 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:31297768 original size:26 final size:27
Alignment explanation
Indices: 31297721--31297796 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 27
31297711 TCAATTTAAC
* * * *
31297721 CCTAGGGGTATTTCGGTGATTTTGC-A
1 CCTAGGGGTATTACAGTAATTTTCCAA
*
31297747 CCTAGGGGTATAACAGTAATTTTCCATA
1 CCTAGGGGTATTACAGTAATTTTCCA-A
* *
31297775 CATAGGGGTATTATAGTAATTT
1 CCTAGGGGTATTACAGTAATTT
31297797 AGCTGCTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 20 0.50
28 20 0.50
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (27 bp):
CCTAGGGGTATTACAGTAATTTTCCAA
Found at i:31304087 original size:26 final size:26
Alignment explanation
Indices: 31304051--31304160 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
31304041 CATGTAATTC
31304051 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
31304077 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * **
31304103 TTATCATGGAATATTTACCTAATACA
1 TTATCATGAAACATTTACCTAACCCA
* *
31304129 TTGTCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
31304155 TTATCA
1 TTATCA
31304161 ATTTGTATCA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:31305344 original size:10 final size:11
Alignment explanation
Indices: 31305327--31305363 Score: 58
Period size: 10 Copynumber: 3.4 Consensus size: 11
31305317 TTTAAAGCTC
31305327 ATTTATATATT
1 ATTTATATATT
31305338 A-TTATATATT
1 ATTTATATATT
31305348 ATTTATATATTT
1 ATTTATATA-TT
31305360 ATTT
1 ATTT
31305364 CTTTCTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.42
11 8 0.33
12 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTATATATT
Found at i:31305542 original size:17 final size:19
Alignment explanation
Indices: 31305520--31305558 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
31305510 GTTTTTTTGT
*
31305520 TTTTTATATTT-ATTA-TA
1 TTTTTAAATTTCATTAGTA
31305537 TTTTTAAATTTCATTAGTA
1 TTTTTAAATTTCATTAGTA
31305556 TTT
1 TTT
31305559 GATTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 4 0.21
19 5 0.26
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTTAAATTTCATTAGTA
Found at i:31308048 original size:2 final size:2
Alignment explanation
Indices: 31308041--31308068 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31308031 TTCAGAGTAA
31308041 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
31308069 TATTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31315250 original size:2 final size:2
Alignment explanation
Indices: 31315239--31315276 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
31315229 CATGTAAGCC
31315239 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31315277 GGCATTGGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31324110 original size:44 final size:46
Alignment explanation
Indices: 31324062--31324158 Score: 123
Period size: 44 Copynumber: 2.2 Consensus size: 46
31324052 AGCCACCAGC
* *
31324062 CTTATCTCT-CTGAGGTAGCAA-GAGAGCAGGTTGAAGA-TATA-AGT
1 CTTATCTCTCCTGAGGTAGCAAGGA-AGCAGATTGAAAATTATAGA-T
31324106 CTTATCT-TCCTGAGGTAGCAAGGAAGCAGATTGAAAATTATAGAT
1 CTTATCTCTCCTGAGGTAGCAAGGAAGCAGATTGAAAATTATAGAT
31324151 CTTATCTC
1 CTTATCTC
31324159 CTTAAGCAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
43 1 0.02
44 30 0.65
45 14 0.30
46 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (46 bp):
CTTATCTCTCCTGAGGTAGCAAGGAAGCAGATTGAAAATTATAGAT
Found at i:31324197 original size:177 final size:177
Alignment explanation
Indices: 31323834--31324420 Score: 827
Period size: 177 Copynumber: 3.3 Consensus size: 177
31323824 GCGACAACGG
* *
31323834 TGAATCTTATCTCCATGTATCGGTAATGGAGTAGATTTTAGCCACCAGCCTTATCTCTCTAAGGT
1 TGAATCTTATCTCCATGTATCGGTAATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGT
* * * * * *
31323899 AGCAATATAACAGGTTGAATAT-TCACTAGTCTTATCTTCCTGAGGTAGCAATGAAGCAGAATGA
66 AGCAAGAGAGCAGGTTGAAGATAT-A--AGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGA
* ** *
31323963 AAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGACGG
128 AAATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGTAGATCGAAGACGA
* *
31324013 TGAATCTTATCTCCATGTATCGGCAATGGAGTAGATTTTAGCCACCAGCCTTATCTCTCTGAGGT
1 TGAATCTTATCTCCATGTATCGGTAATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGT
31324078 AGCAAGAGAGCAGGTTGAAGATATAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAAAA
66 AGCAAGAGAGCAGGTTGAAGATATAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAAAA
* *
31324143 TTATAGATCTTATCTCCTTAAGCAGTAGTGGAGTAGCTCGAAGACGA
131 TTACAGATCTTATCTCCTTAAGCAGTAGTGGAGTAGATCGAAGACGA
* ** * * *
31324190 CGAATCTTATCTTTATGTATCGAG-AATGGAGCAGATTTTAGCAACCAGCCTTATTTCTCTGATG
1 TGAATCTTATCTCCATGTATCG-GTAATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGG
* * * * *
31324254 TAGCAAGAGAGCAGGCTCAAGATACAAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGATTGAGA
65 TAGCAAGAGAGCAGGTTGAAGATATAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAAA
* *
31324319 ATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGTAGATTGAAGACGT
130 ATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGTAGATCGAAGACGA
* * * *
31324367 TGAATCTTATCTTCATATATCGGTAATGGAGCAGATTTAAGCCACTAGCCTTAT
1 TGAATCTTATCTCCATGTATCGGTAATGGAGCAGATTTTAGCCACCAGCCTTAT
31324421 ATCCCTGAAG
Statistics
Matches: 369, Mismatches: 36, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
176 1 0.00
177 284 0.77
178 1 0.00
179 82 0.22
180 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (177 bp):
TGAATCTTATCTCCATGTATCGGTAATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGT
AGCAAGAGAGCAGGTTGAAGATATAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAAAA
TTACAGATCTTATCTCCTTAAGCAGTAGTGGAGTAGATCGAAGACGA
Found at i:31325879 original size:29 final size:27
Alignment explanation
Indices: 31325816--31325885 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
31325806 TTTTTTGTAG
*
31325816 AATTG-TTTTTATATTATTTATTTTAA
1 AATTGTTTTTTATATAATTTATTTTAA
*
31325842 AATCT-TTTTTTATATAATTTACTTCTTTA
1 AAT-TGTTTTTTATATAATTTA-TT-TTAA
*
31325871 AATTGTTTTATATAT
1 AATTGTTTTTTATAT
31325886 TGTTGATTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
26 3 0.08
27 15 0.42
28 3 0.08
29 15 0.42
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (27 bp):
AATTGTTTTTTATATAATTTATTTTAA
Found at i:31327109 original size:3 final size:3
Alignment explanation
Indices: 31327101--31327142 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
31327091 TTATACTTTC
*
31327101 ATT ATT ATT ACT ATT -TT ATT ATCT ATT ATT ATT ATTT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT A-TT ATT AT
31327143 CATCTATTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 26 0.76
4 6 0.18
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:31327115 original size:24 final size:24
Alignment explanation
Indices: 31327101--31327150 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
31327091 TTATACTTTC
31327101 ATTATTATTACTATTTTATTATCT
1 ATTATTATTACTATTTTATTATCT
*
31327125 ATTATTATTA-T-TTATTATCATCT
1 ATTATTATTACTATT-TTATTATCT
31327148 ATT
1 ATT
31327151 CATCTATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 2 0.08
23 12 0.50
24 10 0.42
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTATTATTACTATTTTATTATCT
Found at i:31327129 original size:21 final size:20
Alignment explanation
Indices: 31327103--31327143 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
31327093 ATACTTTCAT
31327103 TATTATTACTATTTTATTATC
1 TATTATTACTA-TTTATTATC
*
31327124 TATTATTATTATTTATTATC
1 TATTATTACTATTTATTATC
31327144 ATCTATTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTATTACTATTTATTATC
Found at i:31327232 original size:3 final size:3
Alignment explanation
Indices: 31327224--31327303 Score: 153
Period size: 3 Copynumber: 27.0 Consensus size: 3
31327214 TACATATATA
31327224 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31327271 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31327304 ATTTTACTAC
Statistics
Matches: 76, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 74 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:31327506 original size:54 final size:54
Alignment explanation
Indices: 31327448--31327559 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
31327438 TTTAAGTTGG
31327448 TATTGTCCTTTTATGCTCATACTTTGTTATTATTATCATTGTTATTATTCATTT
1 TATTGTCCTTTTATGCTCATACTTTGTTATTATTATCATTGTTATTATTCATTT
31327502 TATTGTCCTTTTATGCTCATACTTTGTTATTATTATCATTGTTATTATTCATTT
1 TATTGTCCTTTTATGCTCATACTTTGTTATTATTATCATTGTTATTATTCATTT
31327556 TATT
1 TATT
31327560 TATCTTTAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.21, C:0.12, G:0.07, T:0.60
Consensus pattern (54 bp):
TATTGTCCTTTTATGCTCATACTTTGTTATTATTATCATTGTTATTATTCATTT
Found at i:31327562 original size:13 final size:13
Alignment explanation
Indices: 31327471--31327559 Score: 51
Period size: 15 Copynumber: 6.6 Consensus size: 13
31327461 TGCTCATACT
31327471 TTGTTATTATTATCA
1 TTGTTATTA-T-TCA
31327486 TTGTTATTATTCA
1 TTGTTATTATTCA
* *
31327499 TT-TTATT-GTCC
1 TTGTTATTATTCA
* *
31327510 TT-TTATGCTCATACT
1 TTGTTAT--T-ATTCA
31327525 TTGTTATTATTATCA
1 TTGTTATTA-T-TCA
31327540 TTGTTATTATTCA
1 TTGTTATTATTCA
31327553 TT-TTATT
1 TTGTTATT
31327560 TATCTTTAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
11 8 0.13
12 10 0.17
13 12 0.20
14 4 0.07
15 22 0.37
16 4 0.07
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (13 bp):
TTGTTATTATTCA
Found at i:31328681 original size:14 final size:14
Alignment explanation
Indices: 31328664--31328697 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31328654 GTGGTTTTGG
31328664 GTTTAGGGTCTCAA
1 GTTTAGGGTCTCAA
* *
31328678 GTTTAAGGTTTCAA
1 GTTTAGGGTCTCAA
31328692 GTTTAG
1 GTTTAG
31328698 AGTATAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (14 bp):
GTTTAGGGTCTCAA
Found at i:31329063 original size:27 final size:24
Alignment explanation
Indices: 31329022--31329074 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 24
31329012 AAGTTTCAAC
31329022 TATAGTTCAGGTTTAAAGTGTAAGTT
1 TATAGTTCAGGTTTAAA-T-TAAGTT
*
31329048 TATAGTTTGAGGTTTAAATTAAGTT
1 TATAG-TTCAGGTTTAAATTAAGTT
31329073 TA
1 TA
31329075 AGGTATATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 8 0.32
26 6 0.24
27 11 0.44
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (24 bp):
TATAGTTCAGGTTTAAATTAAGTT
Found at i:31332622 original size:13 final size:14
Alignment explanation
Indices: 31332606--31332634 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31332596 CTATAAATAT
31332606 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
31332619 TTATAATGGTTTAA
1 TTATAATGGTTTAA
31332633 TT
1 TT
31332635 CGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:31333075 original size:21 final size:21
Alignment explanation
Indices: 31333051--31333091 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
31333041 GCGGATGCAG
31333051 CAGCGAGGGAGGCAGCGACAA
1 CAGCGAGGGAGGCAGCGACAA
*
31333072 CAGCGAGGGAGGTAGCGACA
1 CAGCGAGGGAGGCAGCGACA
31333092 GCAGTGATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.44, T:0.02
Consensus pattern (21 bp):
CAGCGAGGGAGGCAGCGACAA
Found at i:31333553 original size:43 final size:42
Alignment explanation
Indices: 31333460--31333609 Score: 187
Period size: 43 Copynumber: 3.5 Consensus size: 42
31333450 ACAAAAGCGC
* *
31333460 CGCTAAAAGTCATGACTTGTAGCGGCGCTT-CACCACAAACG
1 CGCTAAAAGTCATGACTTTTAGCGGCGCTTCCCCCACAAACG
31333501 TCGCTAAAAG-CAATGACTTTTAGCGGCGCTTCCCCCACAAACG
1 -CGCTAAAAGTC-ATGACTTTTAGCGGCGCTTCCCCCACAAACG
* * * *
31333544 CAGCTAAAAGCCATGACTTTTAGCGGTGCCTCCCCCATAAACG
1 C-GCTAAAAGTCATGACTTTTAGCGGCGCTTCCCCCACAAACG
31333587 CCGCTAAAAGTCATGATCTTTTA
1 -CGCTAAAAGTCATGA-CTTTTA
31333610 TGGCTTTTTT
Statistics
Matches: 96, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
41 1 0.01
42 28 0.29
43 59 0.61
44 8 0.08
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.23
Consensus pattern (42 bp):
CGCTAAAAGTCATGACTTTTAGCGGCGCTTCCCCCACAAACG
Found at i:31336097 original size:31 final size:31
Alignment explanation
Indices: 31336062--31336160 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
31336052 GTTTTAAAAA
31336062 TTAGATTTGTGTTTAATGTTCATGAATATAT
1 TTAGATTTGTGTTTAATGTTCATGAATATAT
* * * * *
31336093 TTAGA-TAGT-TTTAGTAGTGT-ATGATTTTTTT
1 TTAGATTTGTGTTTAAT-GT-TCATGA-ATATAT
*
31336124 TTAGATTTGTGTTTAATGTTCATGGATATAT
1 TTAGATTTGTGTTTAATGTTCATGAATATAT
31336155 TTAGAT
1 TTAGAT
31336161 AGTTTTAGTA
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
29 5 0.10
30 9 0.18
31 24 0.47
32 8 0.16
33 5 0.10
ACGTcount: A:0.26, C:0.02, G:0.18, T:0.54
Consensus pattern (31 bp):
TTAGATTTGTGTTTAATGTTCATGAATATAT
Found at i:31336128 original size:62 final size:62
Alignment explanation
Indices: 31336062--31336186 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
31336052 GTTTTAAAAA
31336062 TTAGATTTGTGTTTAATGTTCATGAATATATTTAGATAGTTTTAGTAGTGTATGATTTTTTT
1 TTAGATTTGTGTTTAATGTTCATGAATATATTTAGATAGTTTTAGTAGTGTATGATTTTTTT
*
31336124 TTAGATTTGTGTTTAATGTTCATGGATATATTTAGATAGTTTTAGTAGTGTATGATTTTTTT
1 TTAGATTTGTGTTTAATGTTCATGAATATATTTAGATAGTTTTAGTAGTGTATGATTTTTTT
31336186 T
1 T
31336187 GTAATAATAG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.25, C:0.02, G:0.18, T:0.55
Consensus pattern (62 bp):
TTAGATTTGTGTTTAATGTTCATGAATATATTTAGATAGTTTTAGTAGTGTATGATTTTTTT
Found at i:31341294 original size:15 final size:15
Alignment explanation
Indices: 31341274--31341304 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31341264 ATATGTAATC
31341274 GCATGGGAGTAATGA
1 GCATGGGAGTAATGA
31341289 GCATGGGAGTAATGA
1 GCATGGGAGTAATGA
31341304 G
1 G
31341305 AAACCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.42, T:0.19
Consensus pattern (15 bp):
GCATGGGAGTAATGA
Found at i:31344506 original size:29 final size:30
Alignment explanation
Indices: 31344448--31344513 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
31344438 TTGGACTTAT
* *
31344448 TTAATTCTTTTTAATAATATAGGAATTAAA
1 TTAATTCTATTTAATAATATAGGAACTAAA
31344478 TTAATT-TATTTAATAATATA-GAGACTAAA
1 TTAATTCTATTTAATAATATAGGA-ACTAAA
*
31344507 TTGATTC
1 TTAATTC
31344514 AATCCCTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 2 0.06
29 23 0.74
30 6 0.19
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (30 bp):
TTAATTCTATTTAATAATATAGGAACTAAA
Found at i:31345377 original size:17 final size:19
Alignment explanation
Indices: 31345341--31345378 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
31345331 TTATCTTTGA
*
31345341 TTTTAAATTGATTCTTAAT
1 TTTTAAAGTGATTCTTAAT
31345360 TTTTAAAGT-ATT-TTAAT
1 TTTTAAAGTGATTCTTAAT
31345377 TT
1 TT
31345379 ACGTTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTAAAGTGATTCTTAAT
Done.