Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 15 of 136
Found at i:4703078 original size:22 final size:23
Alignment explanation
Indices: 4703053--4703096 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
4703043 TCAGATTTTC
4703053 CTTTTCCTTT-TTT-TTTTTTTGA
1 CTTTT-CTTTCTTTCTTTTTTTGA
4703075 CTTTTCTTTCTTTCTTTTTTTG
1 CTTTTCTTTCTTTCTTTTTTTG
4703097 CTGATTGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 8 0.40
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (23 bp):
CTTTTCTTTCTTTCTTTTTTTGA
Found at i:4705900 original size:6 final size:6
Alignment explanation
Indices: 4705889--4705923 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
4705879 AAAATGTATG
*
4705889 TATTTT TATTTT TATTCT TATTTT TATTTT TATTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTT
4705924 AAAATTTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TATTTT
Found at i:4711612 original size:18 final size:19
Alignment explanation
Indices: 4711577--4711614 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
4711567 AACTAAAGGA
**
4711577 AATTTTATTATTCTATTTT
1 AATTTTATTATTAAATTTT
4711596 AATTTTA-TATTAAATTTT
1 AATTTTATTATTAAATTTT
4711614 A
1 A
4711615 TGACGTTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTTTATTATTAAATTTT
Found at i:4711876 original size:18 final size:17
Alignment explanation
Indices: 4711825--4711879 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
4711815 CTTCGTTTAT
* *
4711825 TATTAATTTTATGTAATA
1 TATTAATTAT-TGTAAAA
*
4711843 TATTAATTATTATAAAA
1 TATTAATTATTGTAAAA
*
4711860 TATTACCTTATTGTAAAA
1 TATTA-ATTATTGTAAAA
4711878 TA
1 TA
4711880 AATTTCAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 10 0.32
18 21 0.68
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (17 bp):
TATTAATTATTGTAAAA
Found at i:4712309 original size:19 final size:21
Alignment explanation
Indices: 4712247--4712303 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
4712237 ATTTTCAATG
4712247 ATATACAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
4712268 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
4712289 ATATACAATCTTAGA
1 ATATACAATCTTAGA
4712304 AGATATGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:4712519 original size:19 final size:21
Alignment explanation
Indices: 4712495--4712533 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
4712485 GGCTTACTGT
*
4712495 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
4712514 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
4712534 TTAAAAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:4715663 original size:15 final size:15
Alignment explanation
Indices: 4715643--4715675 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4715633 ATTTGCATGA
*
4715643 CATGGCATTTCATTT
1 CATGGCATTACATTT
4715658 CATGGCATTACATTT
1 CATGGCATTACATTT
4715673 CAT
1 CAT
4715676 CATAAAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.42
Consensus pattern (15 bp):
CATGGCATTACATTT
Found at i:4724599 original size:44 final size:44
Alignment explanation
Indices: 4724526--4724880 Score: 120
Period size: 44 Copynumber: 8.1 Consensus size: 44
4724516 CCAAGCCTTG
* * * * * *
4724526 TCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCTTA
* * *
4724570 TCTCCCTAAGCAGTAGTGGAGCAGATTGAA-AGCGGCAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-TGGTAGATCTTA
* * * *** * *
4724614 TATTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCA-CCAAG-CCTTG
1 T-CTCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ATGGTAGATCTTA
* * * * * *
4724658 TCTCCTTGAGCAGTAGCGGAGTAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCTTA
* * ** * *
4724702 GCTCTCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCTTA
* * *** * *
4724746 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCA-CCAAG-CCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ATGGTAGATCTTA
* * * * * * *
4724790 TCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATTTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCTTA
** *
4724834 TCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCTTA
4724878 TCT
1 TCT
4724881 TTCCAAGATA
Statistics
Matches: 212, Mismatches: 77, Indels: 44
0.64 0.23 0.13
Matches are distributed among these distances:
42 10 0.05
43 16 0.08
44 166 0.78
45 13 0.06
46 6 0.03
47 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (44 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCTTA
Found at i:4724752 original size:132 final size:132
Alignment explanation
Indices: 4724514--4724931 Score: 696
Period size: 132 Copynumber: 3.2 Consensus size: 132
4724504 ACCGGTGAAA
4724514 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * *
4724579 GCAGTAGTGGAGCAGATTGAAAG-CGGCAAATCTTATATTTCCAAGATAGTGGGAAGCAGATTTA
66 GCAGTAGTGGAGCAGA-TCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
4724643 AGC
130 AGC
* * * *
4724646 CACCAAGCCTTGTCTCCTTGAGCAGTAGCGGAGTAGGTTGAAGATTGTAGATCTTAGCTCTCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
4724711 GCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
4724776 GC
131 GC
*
4724778 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATTTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
4724843 GCAGTAGTGGAGCAGATCAAAGATGGTAAATCTTATCTTTCCAAGATAGT-GGAAGGCAGATTTA
66 GCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAA-GCAGATTTA
4724907 AGC
130 AGC
** *
4724910 CAAAAAGCCTTGTCTCTCTGAG
1 CACCAAGCCTTGTCTCCCTGAG
4724932 AAGTTGCAGT
Statistics
Matches: 268, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
131 9 0.03
132 259 0.97
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:4732345 original size:28 final size:31
Alignment explanation
Indices: 4732292--4732348 Score: 93
Period size: 28 Copynumber: 1.9 Consensus size: 31
4732282 TAGTTAAAAA
4732292 TTAAAATTTTCATAAGAAATTAATTAATTTT
1 TTAAAATTTTCATAAGAAATTAATTAATTTT
4732323 TTAAAATTTT-A-AA-AAATTAATTAATT
1 TTAAAATTTTCATAAGAAATTAATTAATT
4732349 GTTGATGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 13 0.50
29 2 0.08
30 1 0.04
31 10 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (31 bp):
TTAAAATTTTCATAAGAAATTAATTAATTTT
Found at i:4732985 original size:21 final size:21
Alignment explanation
Indices: 4732946--4732985 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4732936 TTTAGCTTTC
* **
4732946 AAAATTCAAAATATTAACAGA
1 AAAATTCAAAAGAAAAACAGA
4732967 AAAATTCAAAAGAAAAACA
1 AAAATTCAAAAGAAAAACA
4732986 ATTTTAGCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.10, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAATTCAAAAGAAAAACAGA
Found at i:4735845 original size:2 final size:2
Alignment explanation
Indices: 4735833--4735874 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
4735823 CACATTGCTA
4735833 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4735874 A
1 A
4735875 CTTTGAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4742138 original size:94 final size:94
Alignment explanation
Indices: 4742011--4742227 Score: 366
Period size: 94 Copynumber: 2.3 Consensus size: 94
4742001 TATAATATGG
* *
4742011 ATTGAAGAATAAATATTACACATATAAAAATTATATTTACTAAAAATAATGGTATTTGTAATAAT
1 ATTGAAGAATAAA-ATTAAAAATATAAAAATTATATTTACTAAAAATAATGGTATTTGTAATAAT
4742076 TATTTGATTTTATAAATAAAATAGTTACTA
65 TATTTGATTTTATAAATAAAATAGTTACTA
*
4742106 ATTGAAGAATAAAAATAAAAATATAAAAATTATATTTACTAAAAATAATGGTATTTGTAATAATT
1 ATTGAAGAATAAAATTAAAAATATAAAAATTATATTTACTAAAAATAATGGTATTTGTAATAATT
4742171 ATTTGATTTTATAAATAAAATAGTTACTA
66 ATTTGATTTTATAAATAAAATAGTTACTA
*
4742200 ATTCAA-AATAAGAATTAAAAATA-AAAAA
1 ATTGAAGAATAA-AATTAAAAATATAAAAA
4742228 GCTTGAAACA
Statistics
Matches: 116, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
93 10 0.09
94 93 0.80
95 13 0.11
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (94 bp):
ATTGAAGAATAAAATTAAAAATATAAAAATTATATTTACTAAAAATAATGGTATTTGTAATAATT
ATTTGATTTTATAAATAAAATAGTTACTA
Found at i:4751613 original size:168 final size:168
Alignment explanation
Indices: 4751335--4751668 Score: 632
Period size: 168 Copynumber: 2.0 Consensus size: 168
4751325 CGAAATTACC
*
4751335 GAATCTTTATTCTGAGTAGACATCAACGCCTCAGCAACGAGTAATCTGATCTACTATCGAACCAA
1 GAATCTTTATTCTGAGTAGACATCAACGCCTCAGCAACGAGTAATCTAATCTACTATCGAACCAA
* *
4751400 GCAGCAATCTATTGTGACTCTGGCCTCTACGTAATCCACCCAGTTGACAATGAACGGAAGGAATC
66 GCAGCAATCTATCGTGACTCCGGCCTCTACGTAATCCACCCAGTTGACAATGAACGGAAGGAATC
4751465 CCCAAAACTATTTTTGGAAAAGACTTTGCTTTGACAGT
131 CCCAAAACTATTTTTGGAAAAGACTTTGCTTTGACAGT
4751503 GAATCTTTATTCTGAGTAGACATCAACGCCTCAGCAACGAGTAATCTAATCTACTATCGAACCAA
1 GAATCTTTATTCTGAGTAGACATCAACGCCTCAGCAACGAGTAATCTAATCTACTATCGAACCAA
*
4751568 GCCGCAATCTATCGTGACTCCGGCCTCTACGTAATCCACCCAGTTGACAATGAACGGAAGGAATC
66 GCAGCAATCTATCGTGACTCCGGCCTCTACGTAATCCACCCAGTTGACAATGAACGGAAGGAATC
4751633 CCCAAAACTATTTTTGGAAAAGACTTTGCTTTGACA
131 CCCAAAACTATTTTTGGAAAAGACTTTGCTTTGACA
4751669 ACTGCTAGAC
Statistics
Matches: 162, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
168 162 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (168 bp):
GAATCTTTATTCTGAGTAGACATCAACGCCTCAGCAACGAGTAATCTAATCTACTATCGAACCAA
GCAGCAATCTATCGTGACTCCGGCCTCTACGTAATCCACCCAGTTGACAATGAACGGAAGGAATC
CCCAAAACTATTTTTGGAAAAGACTTTGCTTTGACAGT
Found at i:4761836 original size:21 final size:21
Alignment explanation
Indices: 4761812--4761851 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4761802 CTTAATGATT
* *
4761812 TAATTGCAATAAATTAAATAA
1 TAATTGAAAGAAATTAAATAA
*
4761833 TAATTTAAAGAAATTAAAT
1 TAATTGAAAGAAATTAAAT
4761852 TTATTTCTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (21 bp):
TAATTGAAAGAAATTAAATAA
Found at i:4766950 original size:30 final size:29
Alignment explanation
Indices: 4766912--4767039 Score: 121
Period size: 29 Copynumber: 4.3 Consensus size: 29
4766902 ACAAAATTAG
* *
4766912 CCACAAAGGCTCACATATAATAGATAACAT
1 CCACAAAGGCTCACATATAACAGAT-ACAA
* * *
4766942 CTACAAAGGCTTCCACATATAACAGATTCAG
1 CCACAAAGGC-T-CACATATAACAGATACAA
* * * * *
4766973 TCACAAAGCCTCGCATATAATAGATTCAA
1 CCACAAAGGCTCACATATAACAGATACAA
*
4767002 CCACAAAGGCTCACATATAACAGAGAACAA
1 CCACAAAGGCTCACATATAACAGA-TACAA
4767032 CCACAAAG
1 CCACAAAG
4767040 ACATCACTTT
Statistics
Matches: 79, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
29 35 0.44
30 21 0.27
31 10 0.13
32 13 0.16
ACGTcount: A:0.45, C:0.26, G:0.12, T:0.18
Consensus pattern (29 bp):
CCACAAAGGCTCACATATAACAGATACAA
Found at i:4766980 original size:61 final size:58
Alignment explanation
Indices: 4766913--4767025 Score: 154
Period size: 61 Copynumber: 1.9 Consensus size: 58
4766903 CAAAATTAGC
* * *
4766913 CACAAAGGCTCACATATAATAGATAACATCTACAAAGGCTTCCACATATAACAGATTCAGT
1 CACAAAGCCTCACATATAATAGAT-ACAACCACAAAGGC-T-CACATATAACAGATTCAGT
* *
4766974 CACAAAGCCTCGCATATAATAGATTCAACCACAAAGGCTCACATATAACAGA
1 CACAAAGCCTCACATATAATAGATACAACCACAAAGGCTCACATATAACAGA
4767026 GAACAACCAC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
58 13 0.28
59 1 0.02
60 11 0.23
61 22 0.47
ACGTcount: A:0.43, C:0.25, G:0.12, T:0.20
Consensus pattern (58 bp):
CACAAAGCCTCACATATAATAGATACAACCACAAAGGCTCACATATAACAGATTCAGT
Found at i:4767225 original size:54 final size:54
Alignment explanation
Indices: 4767156--4767309 Score: 200
Period size: 54 Copynumber: 2.9 Consensus size: 54
4767146 CTTTTCCCAC
* * * * *
4767156 ATGACGCCAAAGTCCCAGACTAGGTCTTGCACTACGTGGTCTTCACATCCTTAT
1 ATGACGCCATAGTCCCAGACTAGGTTTTACACTATGTGGTCTTCACATCCTCAT
* * * * *
4767210 ATGACACCATAGTCCCAAACTAGGTTTTACACAATGTGATTTTCACATCCTCAT
1 ATGACGCCATAGTCCCAGACTAGGTTTTACACTATGTGGTCTTCACATCCTCAT
* *
4767264 ATGACGCCATAGTCCTAGACTAGGTTTTACACTATATGGTCTTCAC
1 ATGACGCCATAGTCCCAGACTAGGTTTTACACTATGTGGTCTTCAC
4767310 TTGTCATGGC
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 83 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (54 bp):
ATGACGCCATAGTCCCAGACTAGGTTTTACACTATGTGGTCTTCACATCCTCAT
Found at i:4771303 original size:31 final size:30
Alignment explanation
Indices: 4771268--4771397 Score: 104
Period size: 29 Copynumber: 4.3 Consensus size: 30
4771258 AGAGAACAAT
4771268 CACAAAGGCTTCAACATATAACAGATTCAGC
1 CACAAAGGCTTC-ACATATAACAGATTCAGC
** * *
4771299 CACAAA-TATTCACATATAATAGATTTAGC
1 CACAAAGGCTTCACATATAACAGATTCAGC
* * * *
4771328 GACAAATGC-TCACATATAACAAAGA-ACAAC
1 CACAAAGGCTTCACATATAAC--AGATTCAGC
* *
4771358 CAAAAAAAGCTTCCACATATAACAGATTCAGC
1 C-ACAAAGGCTT-CACATATAACAGATTCAGC
4771390 CACAAAGG
1 CACAAAGG
4771398 TGTACATATA
Statistics
Matches: 74, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
29 31 0.42
30 5 0.07
31 23 0.31
32 5 0.07
33 10 0.14
ACGTcount: A:0.47, C:0.23, G:0.11, T:0.19
Consensus pattern (30 bp):
CACAAAGGCTTCACATATAACAGATTCAGC
Found at i:4771393 original size:91 final size:90
Alignment explanation
Indices: 4771245--4771412 Score: 239
Period size: 91 Copynumber: 1.9 Consensus size: 90
4771235 ACCACAAAAA
* * * * * *
4771245 GCTCACATATAATAGAGAACAATCACAAAGGCTTCAACATATAACAGATTCAGCCACAAATAT-T
1 GCTCACATATAACAAAGAACAACCAAAAAAGCTTCAACATATAACAGATTCAGCCACAAAGATGT
4771309 CACATATAATAGATTTAGCGACAAAT
66 -ACATATAATAGATTTAGCGACAAAT
* *
4771335 GCTCACATATAACAAAGAACAACCAAAAAAAGCTTCCACATATAACAGATTCAGCCACAAAGGTG
1 GCTCACATATAACAAAGAACAACC-AAAAAAGCTTCAACATATAACAGATTCAGCCACAAAGATG
4771400 TACATATAATAGA
65 TACATATAATAGA
4771413 GAATAATCAC
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
90 21 0.31
91 46 0.68
92 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (90 bp):
GCTCACATATAACAAAGAACAACCAAAAAAGCTTCAACATATAACAGATTCAGCCACAAAGATGT
ACATATAATAGATTTAGCGACAAAT
Found at i:4791648 original size:23 final size:24
Alignment explanation
Indices: 4791620--4791664 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
4791610 AAATTAAATC
4791620 TCTAAGATTACA-AAATCATATTT
1 TCTAAGATTACATAAATCATATTT
*
4791643 TCTAAGATTACATATATCATAT
1 TCTAAGATTACATAAATCATAT
4791665 CTAAGATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATTT
Found at i:4791669 original size:21 final size:22
Alignment explanation
Indices: 4791620--4791678 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
4791610 AAATTAAATC
*
4791620 TCTAAGATTACA-AAATCATATTT
1 TCTAAGATTACATATATCATA--T
4791643 TCTAAGATTACATATATCATA-
1 TCTAAGATTACATATATCATAT
*
4791664 TCTAAGATTGCATAT
1 TCTAAGATTACATAT
4791679 CCTTGAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.42
23 12 0.36
24 7 0.21
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (22 bp):
TCTAAGATTACATATATCATAT
Found at i:4793044 original size:42 final size:42
Alignment explanation
Indices: 4792997--4793304 Score: 580
Period size: 42 Copynumber: 7.3 Consensus size: 42
4792987 CACCAAAACA
*
4792997 GGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
1 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
4793039 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
1 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
4793081 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
1 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
4793123 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
1 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
4793165 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
1 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
4793207 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
1 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
*
4793249 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACAT
1 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
* *
4793291 GTTCTTTAGCGGCG
1 GGTCTTTAGAGGCG
4793305 CTTAGAAAAA
Statistics
Matches: 262, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 262 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (42 bp):
GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
Found at i:4793321 original size:42 final size:42
Alignment explanation
Indices: 4793275--4793388 Score: 192
Period size: 42 Copynumber: 2.7 Consensus size: 42
4793265 TTTTTCTAAG
* *
4793275 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTGAGAAAAAAA
4793317 CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTGAGAAAAAAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTGAGAAAAAAA
**
4793359 CGCAACTAAAGACCATGTTCTTTAGCGGCG
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCG
4793389 TTTATTCTTA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (42 bp):
CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTGAGAAAAAAA
Found at i:4793368 original size:126 final size:126
Alignment explanation
Indices: 4792997--4793417 Score: 331
Period size: 126 Copynumber: 3.3 Consensus size: 126
4792987 CACCAAAACA
* * * ******
4792997 GGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGTGGTCTTTAGAGGCGTTTTTTTCT
1 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGAGGCGCTTAGAAAA
* * * ******* * **
4793062 AAGCGCCGCTAAAGAACGTGGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
66 AAACGCCGCTAAAGAACATGGTCTTTAGAGGCGCTGAGAAAAAAACGCAACTAAAGAACGT
* * ******
4793123 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGTGGTCTTTAGAGGCGTTTTTTTCT
1 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGAGGCGCTTAGAAAA
* * * ******* * **
4793188 AAGCGCCGCTAAAGAACGTGGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACGT
66 AAACGCCGCTAAAGAACATGGTCTTTAGAGGCGCTGAGAAAAAAACGCAACTAAAGAACGT
* *
4793249 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAA
1 GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGAGGCGCTTAGAAAA
* * * * *
4793314 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTGAGAAAAAAACGCAACTAAAGACCAT
66 AAACGCCGCTAAAGAACATGGTCTTTAGAGGCGCTGAGAAAAAAACGCAACTAAAGAACGT
* * * * *
4793375 GTTCTTTAGCGGCG-TTTATTCTTAAGCGCCGTTAAAGAGCATG
1 GGTCTTTAGAGGCGTTTTTTTC-TAAGCGCCGCTAAAGAACATG
4793418 AAAAATAGTG
Statistics
Matches: 260, Mismatches: 34, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
125 6 0.02
126 254 0.98
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (126 bp):
GGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGAGGCGCTTAGAAAA
AAACGCCGCTAAAGAACATGGTCTTTAGAGGCGCTGAGAAAAAAACGCAACTAAAGAACGT
Found at i:4798789 original size:9 final size:9
Alignment explanation
Indices: 4798761--4798825 Score: 67
Period size: 9 Copynumber: 7.2 Consensus size: 9
4798751 GTTATGTATA
*
4798761 ATGTATGTT
1 ATGTAAGTT
**
4798770 ATGCCAGTT
1 ATGTAAGTT
* *
4798779 ATTTAATTT
1 ATGTAAGTT
4798788 ATGTAAGTT
1 ATGTAAGTT
4798797 ATGTAAGTT
1 ATGTAAGTT
* *
4798806 ATTTAATTT
1 ATGTAAGTT
4798815 ATGTAAGTT
1 ATGTAAGTT
4798824 AT
1 AT
4798826 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:4798797 original size:27 final size:27
Alignment explanation
Indices: 4798761--4798825 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
4798751 GTTATGTATA
* *
4798761 ATGTATGTTATGCCAGTTATTTAATTT
1 ATGTAAGTTATGCAAGTTATTTAATTT
*
4798788 ATGTAAGTTATGTAAGTTATTTAATTT
1 ATGTAAGTTATGCAAGTTATTTAATTT
4798815 ATGTAAGTTAT
1 ATGTAAGTTAT
4798826 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (27 bp):
ATGTAAGTTATGCAAGTTATTTAATTT
Found at i:4802639 original size:84 final size:83
Alignment explanation
Indices: 4802490--4802759 Score: 246
Period size: 84 Copynumber: 3.3 Consensus size: 83
4802480 ACTGAACAGA
* * * *
4802490 AAACGGTGCCGCATTGACAAACATTAATTCACACTTGCGGCATTTTCTTAAAAACGCCACTATAA
1 AAACGGCGCCGTATTGGCAAACATTAATTCACACTTGCGGCATTTTCTAAAAAACGCCACTATAA
4802555 GATTTCATTCCAGTAGAG
66 GATTTCATTCCAGTAGAG
* ** *
4802573 AAACGAG-GCCGTATTGGCAAAGATTAATTCACTTTTGCGGCGTTTTTCTAAAAAACGCCACTAT
1 AAACG-GCGCCGTATTGGCAAACATTAATTCACACTTGCGGC-ATTTTCTAAAAAACGCCACTAT
* *
4802637 AAGATTTTATTCCAGTAGAT
64 AAGATTTCATTCCAGTAGAG
** * * * *
4802657 AAACGGCGCCGCT-TTGGCAAATTTTAATACATC-CTTGTGGCGTTTTCATCAAAAACGCCAC-A
1 AAACGGCGCCG-TATTGGCAAACATTAATTCA-CACTTGCGGCATTTTC-TAAAAAACGCCACTA
* * * *
4802719 AAATATTTCTTTCC-TTA-AG
63 TAAGATTTCATTCCAGTAGAG
* *
4802738 AAAACGGCGCCGTTTTGTCAAA
1 -AAACGGCGCCGTATTGGCAAA
4802760 TTTTAAAACA
Statistics
Matches: 156, Mismatches: 23, Indels: 17
0.80 0.12 0.09
Matches are distributed among these distances:
81 2 0.01
82 20 0.13
83 51 0.33
84 81 0.52
85 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (83 bp):
AAACGGCGCCGTATTGGCAAACATTAATTCACACTTGCGGCATTTTCTAAAAAACGCCACTATAA
GATTTCATTCCAGTAGAG
Found at i:4803112 original size:84 final size:84
Alignment explanation
Indices: 4803024--4803179 Score: 233
Period size: 84 Copynumber: 1.9 Consensus size: 84
4803014 CACATTGCCA
* * * *
4803024 AACATTAATTCAC-TCTTGCGGCATTTTCTTAAAAAATGCCACTATAAGATTTCATTCGAGTACA
1 AACATTAATTCACGT-TTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGTAAA
4803088 GAAACGGCACCGTATTGGCC
65 GAAACGGCACCGTATTGGCC
* * *
4803108 AACATTAATTCACGTTTGCGGCATTTTCATACAAAACGCCACTAAAAGATTTTATTCTAGTAAAG
1 AACATTAATTCACGTTTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGTAAAG
4803173 AAACGGC
66 AAACGGC
4803180 GCCACTTTGG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
84 63 0.98
85 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (84 bp):
AACATTAATTCACGTTTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGTAAAG
AAACGGCACCGTATTGGCC
Found at i:4803200 original size:84 final size:84
Alignment explanation
Indices: 4803020--4803196 Score: 216
Period size: 84 Copynumber: 2.1 Consensus size: 84
4803010 GTGTCACATT
* * *
4803020 GCCAAACATTAATTCACTCTTGCGGCATTTTCTTAAAAAATGCCACTATAAGATTTCATTCGAGT
1 GCCAAA-ATTAATTCACTCTTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGT
* *
4803085 ACAGAAACGGCACCGTATTG
65 AAAGAAACGGCACCCTATTG
* * * *
4803105 GCCAACATTAATTCACGT-TTGCGGCATTTTCATACAAAACGCCACTAAAAGATTTTATTCTAGT
1 GCCAAAATTAATTCAC-TCTTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGT
*
4803169 AAAGAAACGGCGCCACT-TTG
65 AAAGAAACGGCACC-CTATTG
4803189 G-CAAAATT
1 GCCAAAATT
4803197 TAATGAATCA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
83 6 0.08
84 66 0.84
85 7 0.09
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (84 bp):
GCCAAAATTAATTCACTCTTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGTA
AAGAAACGGCACCCTATTG
Found at i:4803211 original size:84 final size:84
Alignment explanation
Indices: 4803039--4803233 Score: 189
Period size: 84 Copynumber: 2.3 Consensus size: 84
4803029 TAATTCACTC
* * * * *
4803039 TTGCGGCATTTTCTTAAAAAATGCCACTATAAGATTTCATTCGAGTACAGAAACGGCACCGTATT
1 TTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGTAAAGAAACGGCACCCTATT
* ** *
4803104 GGCCAACATTAATTCACGT
66 GGCCAAAATTAATGAACGA
* * * *
4803123 TTGCGGCATTTTCATACAAAACGCCACTAAAAGATTTTATTCTAGTAAAGAAACGGCGCCACT-T
1 TTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGTAAAGAAACGGCACC-CTAT
4803187 TGG-CAAAATTTAATGAATC-A
65 TGGCCAAAA-TTAATGAA-CGA
* * * *
4803207 TTGCGGCGTTTTTATTAAAATCGCCAC
1 TTGCGGCATTTTCATAAAAAACGCCAC
4803234 AAATTATTTT
Statistics
Matches: 90, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
83 4 0.04
84 84 0.93
85 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (84 bp):
TTGCGGCATTTTCATAAAAAACGCCACTAAAAGATTTCATTCGAGTAAAGAAACGGCACCCTATT
GGCCAAAATTAATGAACGA
Found at i:4803481 original size:82 final size:81
Alignment explanation
Indices: 4803376--4803629 Score: 278
Period size: 90 Copynumber: 3.0 Consensus size: 81
4803366 ACTAATTAAT
* * * *
4803376 CTAAATCTTGTTTAATATATAAATTAA-AAAGTACTAATTAATCTAAATCTTAAACCCTAACCCG
1 CTAAATTTTATTTAATATATAAATTAACAAA-TACTAATTAATCTAAACCCTAAACCCTAACCCG
4803440 ACTCCAAATCCCTAACCC
65 A-TCCAAATCCCTAACCC
*
4803458 CTAAATTTTATTTAATATGTAAATTAACAAACT-CTAATTAATCTAAACCCTAAACCCTAAACCT
1 CTAAATTTTATTTAATATATAAATTAACAAA-TACTAATTAATCTAAACCCTAAA--C----CCT
*
4803522 AACCCCAAATCCCAAATCCCTAACCC
59 AA-CCC-GAT-CCAAATCCCTAACCC
* * * **
4803548 CTAAACTTAATTTAATATATAAATTAACAAACACTAATTAATCTAAACCCTAAACCAAAACCCGA
1 CTAAATTTTATTTAATATATAAATTAACAAATACTAATTAATCTAAACCCTAAACCCTAACCCGA
4803613 TCCTAAATCCCTAACCC
66 TCC-AAATCCCTAACCC
4803630 TTAACCCTTA
Statistics
Matches: 146, Mismatches: 14, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
81 2 0.01
82 58 0.40
83 7 0.05
84 4 0.03
88 6 0.04
89 4 0.03
90 65 0.45
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.28
Consensus pattern (81 bp):
CTAAATTTTATTTAATATATAAATTAACAAATACTAATTAATCTAAACCCTAAACCCTAACCCGA
TCCAAATCCCTAACCC
Found at i:4803512 original size:7 final size:7
Alignment explanation
Indices: 4803500--4803553 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
4803490 TCTAATTAAT
4803500 CTAAACC
1 CTAAACC
4803507 CTAAACC
1 CTAAACC
4803514 CTAAA-C
1 CTAAACC
4803520 CT-AACC
1 CTAAACC
*
4803526 CCAAATCC
1 CTAAA-CC
4803534 C-AAATCC
1 CTAAA-CC
*
4803541 CTAACCC
1 CTAAACC
4803548 CTAAAC
1 CTAAAC
4803554 TTAATTTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 2 0.05
6 5 0.12
7 28 0.70
8 5 0.12
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:4803643 original size:14 final size:14
Alignment explanation
Indices: 4803621--4803660 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
4803611 GATCCTAAAT
4803621 CCCTAACCCTTAAC
1 CCCTAACCCTTAAC
* *
4803635 CCTTAACCCATAAC
1 CCCTAACCCTTAAC
*
4803649 CCCTAAACCTTA
1 CCCTAACCCTTA
4803661 TTTAATATAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.23
Consensus pattern (14 bp):
CCCTAACCCTTAAC
Found at i:4803931 original size:20 final size:21
Alignment explanation
Indices: 4803906--4803949 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4803896 AAAATTAATT
*
4803906 AACCATATATA-TATACCCTA
1 AACCATATATATTAAACCCTA
*
4803926 AACCATATTTATTAAACCCTA
1 AACCATATATATTAAACCCTA
4803947 AAC
1 AAC
4803950 TATAATGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (21 bp):
AACCATATATATTAAACCCTA
Found at i:4804554 original size:115 final size:114
Alignment explanation
Indices: 4804290--4804685 Score: 488
Period size: 115 Copynumber: 3.5 Consensus size: 114
4804280 CTGAAGTAGC
* ** *
4804290 CGTTGGGCTTAGGTCCCTTTGCGGCACTTCT-CCCAAAACGCATCTAAAGCCCTCAGCATTAGCG
1 CGTTGGGCTTAGGTCCCTTTGCGGCGCTT-TACCCAAAACGCCGCTAAAGCCCTAAGCATTAGCG
* * * ** *
4804354 ACGCCTAACCAAAAACGCCACTAAATACTTAAAGGCTAAGAAAACGACGT
65 GCGCTTAACTAAAAACGCCACTAAATACCAAAAGGCTAAGAAAACGGCGT
* * * *
4804404 CGTTGGGCTTAGGTCCGTTTGCGGCGCTTTTCCCAAAACGCTGCTAAAGCCCTAAGCATTAGTGG
1 CGTTGGGCTTAGGTCCCTTTGCGGCGCTTTACCCAAAACGCCGCTAAAGCCCTAAGCATTAGCGG
* * * *
4804469 CGCTTCACTAAAAACGCCACTAAATCCCCAAAAAGCTAATAAAACGGCGT
66 CGCTTAACTAAAAACGCCACTAAAT-ACCAAAAGGCTAAGAAAACGGCGT
*
4804519 CGTCGGGCTTAGGTCCCTTTGCGGCGCTTTACCCAAAACGCCGCTAAAGCCCTAAGCATTAGCGG
1 CGTTGGGCTTAGGTCCCTTTGCGGCGCTTTACCCAAAACGCCGCTAAAGCCCTAAGCATTAGCGG
* * * * *
4804584 CGCTTTACTAAAAACGCCACTAAAGACCGAAAGGCTTAGAAAACGGCAT
66 CGCTTAACTAAAAACGCCACTAAATACCAAAAGGCTAAGAAAACGGCGT
* ** ** *
4804633 CGTTTGGCTTAGGTTTTCTTTGCGGCGCTTTACTGAAAACGCCGCAAAAGCCC
1 CGTTGGGCTTAGG-TCCCTTTGCGGCGCTTTACCCAAAACGCCGCTAAAGCCC
4804686 GGAACATCAG
Statistics
Matches: 243, Mismatches: 36, Indels: 5
0.86 0.13 0.02
Matches are distributed among these distances:
113 1 0.00
114 107 0.44
115 135 0.56
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (114 bp):
CGTTGGGCTTAGGTCCCTTTGCGGCGCTTTACCCAAAACGCCGCTAAAGCCCTAAGCATTAGCGG
CGCTTAACTAAAAACGCCACTAAATACCAAAAGGCTAAGAAAACGGCGT
Found at i:4804809 original size:111 final size:113
Alignment explanation
Indices: 4804324--4804814 Score: 302
Period size: 115 Copynumber: 4.3 Consensus size: 113
4804314 CACTTCTCCC
** * * * * * **
4804324 AAAACGCATCTAAAGCCCTCAGCATTAGCGACGC-CTAACCAAAAACGCCACTAAATACTTAAAG
1 AAAACGCCGCTAAAGCCCT-AACATTAGCG--GCACTTACTAAAAACGCCACGAAAGACCGAAAG
* * * * * * * **
4804388 GCTAAGAAAACGACGTCGTTGGGCTTAGG--TCCGTTTGCGGCGCTTTTCCC
63 GCTTAGAAAACGGCATCGTTGGGATTAGGTTTTC-TTTGCGGCGATTTACTG
* * * * ** * *
4804438 AAAACGCTGCTAAAGCCCTAAGCATTAGTGGCGCTTCACTAAAAACGCCACTAAATCCCCAAAAA
1 AAAACGCCGCTAAAGCCCTAA-CATTAGCGGCACTT-ACTAAAAACGCCACGAAA-GACCGAAAG
* * * * * ** * **
4804503 GCTAATAAAACGGCGTCGTCGGGCTTAGG-TCCCTTTGCGGCGCTTTACCC
63 GCTTAGAAAACGGCATCGTTGGGATTAGGTTTTCTTTGCGGCGATTTACTG
* *
4804553 AAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTTACTAAAAACGCCACTAAAGACCGAAAGG
1 AAAACGCCGCTAAAGCCCTAA-CATTAGCGGCAC-TTACTAAAAACGCCACGAAAGACCGAAAGG
* * *
4804618 CTTAGAAAACGGCATCGTTTGGCTTAGGTTTTCTTTGCGGCGCTTTACTG
64 CTTAGAAAACGGCATCGTTGGGATTAGGTTTTCTTTGCGGCGATTTACTG
* * * * * *
4804668 AAAACGCCGCAAAAGCCCGGAACATCAGCGGCACTTACTTACAAACGCCGCGAAAGCCCCG-AA-
1 AAAACGCCGCTAAAGCCC-TAACATTAGCGGCACTTAC-TAAAAACGCCACGAAAG-ACCGAAAG
* * * * *
4804731 GC-TCGTTAAACGGCGTCGTTGGGATTA-G-TTT-TTTGTGGC-ATTTTCGTG
63 GCTTAG-AAAACGGCATCGTTGGGATTAGGTTTTCTTTGCGGCGATTTAC-TG
4804779 AAAACGCCGCTAAAGCCCTAATCATTAGCGGCACTT
1 AAAACGCCGCTAAAGCCCTAA-CATTAGCGGCACTT
4804815 TATTAAAATC
Statistics
Matches: 314, Mismatches: 50, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
110 6 0.02
111 39 0.12
112 5 0.02
113 6 0.02
114 93 0.30
115 156 0.50
116 9 0.03
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (113 bp):
AAAACGCCGCTAAAGCCCTAACATTAGCGGCACTTACTAAAAACGCCACGAAAGACCGAAAGGCT
TAGAAAACGGCATCGTTGGGATTAGGTTTTCTTTGCGGCGATTTACTG
Found at i:4806745 original size:7 final size:7
Alignment explanation
Indices: 4806719--4806808 Score: 71
Period size: 7 Copynumber: 12.7 Consensus size: 7
4806709 ATACACGACC
*
4806719 CTTTTTC
1 CTTTTTT
4806726 CTTTTTT
1 CTTTTTT
4806733 C-TTTTT
1 CTTTTTT
4806739 CTTTTTTT
1 C-TTTTTT
4806747 CTTCTTTT
1 CTT-TTTT
*
4806755 CTCTTTT
1 CTTTTTT
*
4806762 -TTCTTT
1 CTTTTTT
4806768 CTTTTTCT
1 CTTTTT-T
4806776 CTTTTTCTT
1 C-TTTT-TT
*
4806785 CTCTTTT
1 CTTTTTT
4806792 C-TTTTT
1 CTTTTTT
4806798 CTTTTTT
1 CTTTTTT
4806805 -TTTT
1 CTTTT
4806809 CTGCTGGGCT
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
6 19 0.28
7 25 0.37
8 17 0.25
9 6 0.09
10 1 0.01
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
CTTTTTT
Found at i:4806751 original size:11 final size:11
Alignment explanation
Indices: 4806727--4806810 Score: 56
Period size: 11 Copynumber: 8.0 Consensus size: 11
4806717 CCCTTTTTCC
4806727 TTTTTTCTT-T
1 TTTTTTCTTCT
*
4806737 TTCTTTTTTTCT
1 TT-TTTTCTTCT
*
4806749 TCTTTTC-TC-
1 TTTTTTCTTCT
4806758 TTTTTTCTT-T
1 TTTTTTCTTCT
*
4806768 CTTTTTC-TCT
1 TTTTTTCTTCT
4806778 TTTTCTTC-TCT
1 TTTT-TTCTTCT
4806789 TTTCTTT-TTCT
1 TTT-TTTCTTCT
*
4806800 TTTTTTTTTCT
1 TTTTTTCTTCT
4806811 GCTGGGCTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
9 7 0.12
10 18 0.31
11 31 0.53
12 3 0.05
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTCTTCT
Found at i:4806753 original size:17 final size:17
Alignment explanation
Indices: 4806727--4806810 Score: 93
Period size: 18 Copynumber: 4.9 Consensus size: 17
4806717 CCCTTTTTCC
4806727 TTTT-TTCTTTTTCTTT
1 TTTTCTTCTTTTTCTTT
4806743 TTTTCTTC-TTTTCTCTT
1 TTTTCTTCTTTTTCT-TT
*
4806760 TTTTCTTTCTTTTTCTCT
1 TTTTC-TTCTTTTTCTTT
4806778 TTTTCTTCTCTTTTCTTT
1 TTTTCTTCT-TTTTCTTT
*
4806796 TTCTT-TTTTTTTTCT
1 TT-TTCTTCTTTTTCT
4806811 GCTGGGCTAA
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
16 10 0.17
17 20 0.34
18 21 0.36
19 8 0.14
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCTTCTTTTTCTTT
Found at i:4806759 original size:24 final size:22
Alignment explanation
Indices: 4806728--4806810 Score: 89
Period size: 23 Copynumber: 3.6 Consensus size: 22
4806718 CCTTTTTCCT
4806728 TTTTTCTTTTTCTTTTTTTCTTC
1 TTTTTCTTTTTCTTTTTTT-TTC
4806751 TTTTCTCTTTTTTCTTTCTTTTTCTC
1 TTTT-TC-TTTTTCTTT-TTTTT-TC
*
4806777 TTTTTC-TTCTCTTTTCTTTTTC
1 TTTTTCTTTTTCTTTT-TTTTTC
4806799 TTTTT-TTTTTCT
1 TTTTTCTTTTTCT
4806811 GCTGGGCTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
22 13 0.25
23 15 0.29
24 2 0.04
25 12 0.23
26 10 0.19
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTCTTTTTCTTTTTTTTTC
Found at i:4806781 original size:35 final size:34
Alignment explanation
Indices: 4806730--4806807 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 34
4806720 TTTTTCCTTT
*
4806730 TTTCTTTTTCTTTTTTTCTTCT-TTTCTCTTTTTTC
1 TTTCTTTTTCTCTTTTTCTTCTCTTT-TC-TTTTTC
4806765 TTTCTTTTTCTCTTTTTCTTCTCTTTTCTTTTTC
1 TTTCTTTTTCTCTTTTTCTTCTCTTTTCTTTTTC
*
4806799 TTTTTTTTT
1 TTTCTTTTT
4806808 TCTGCTGGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
34 14 0.35
35 23 0.57
36 3 0.08
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (34 bp):
TTTCTTTTTCTCTTTTTCTTCTCTTTTCTTTTTC
Found at i:4806808 original size:35 final size:35
Alignment explanation
Indices: 4806719--4806810 Score: 109
Period size: 37 Copynumber: 2.5 Consensus size: 35
4806709 ATACACGACC
4806719 CTTTTTCCTTTTTTCTTTT-TCTTTTTTTCTTCTTTT
1 CTTTTT-CTTTTTT-TTTTCTCTTTTTTTCTTCTTTT
4806755 CTCTTTT-TTCTTTCTTTTTCTCTTTTTCTTC-TCTTTT
1 CT-TTTTCTT-TTT-TTTTTCTCTTTTT-TTCTTCTTTT
4806792 CTTTTTCTTTTTTTTTTCT
1 CTTTTTCTTTTTTTTTTCT
4806811 GCTGGGCTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
35 9 0.18
36 16 0.32
37 22 0.44
38 3 0.06
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (35 bp):
CTTTTTCTTTTTTTTTTCTCTTTTTTTCTTCTTTT
Found at i:4806850 original size:26 final size:23
Alignment explanation
Indices: 4806809--4806863 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 23
4806799 TTTTTTTTTT
4806809 CTGCTGGGCTAATGGGCGAACTGGG
1 CTGCTGGGCTAATGGG-G-ACTGGG
**
4806834 CCTGCTGGGCTGCTGGGGACTGGG
1 -CTGCTGGGCTAATGGGGACTGGG
4806858 CTGCTG
1 CTGCTG
4806864 TAGGTTGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 6 0.22
24 6 0.22
25 1 0.04
26 14 0.52
ACGTcount: A:0.09, C:0.24, G:0.45, T:0.22
Consensus pattern (23 bp):
CTGCTGGGCTAATGGGGACTGGG
Found at i:4807083 original size:14 final size:16
Alignment explanation
Indices: 4807066--4807098 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
4807056 ATTTTAAAAG
4807066 TTTTCTTT-T-TTCTT
1 TTTTCTTTCTCTTCTT
4807080 TTTTCTTTCTCTTCTT
1 TTTTCTTTCTCTTCTT
4807096 TTT
1 TTT
4807099 CTTCCTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTTCTCTTCTT
Found at i:4807618 original size:29 final size:29
Alignment explanation
Indices: 4807455--4807620 Score: 120
Period size: 29 Copynumber: 5.6 Consensus size: 29
4807445 CAAAACTTTT
* *
4807455 GGGTCCAAAGTGTAATTTTGAGAAAATTTTA-
1 GGGT-CAAAATGTAATTTT-A-AAAAGTTTAG
* * * *
4807486 GGGTCAAAATGTAATTTCGAGATAGTTCAG
1 GGGTCAAAATGTAATTT-TAAAAAGTTTAG
* * * *
4807516 GGGTTAAAATGTAATTTCAAAAGGTTTAA
1 GGGTCAAAATGTAATTTTAAAAAGTTTAG
* *
4807545 AGGTCATAATGTAATTTTAAAAAGTTTAG
1 GGGTCAAAATGTAATTTTAAAAAGTTTAG
* * *
4807574 TGGTTAAAATGCAATTTTAAAAA-TTTCAG
1 GGGTCAAAATGTAATTTTAAAAAGTTT-AG
* *
4807603 GGGTCAGAATTTAATTTT
1 GGGTCAAAATGTAATTTT
4807621 TATTTTTTGT
Statistics
Matches: 104, Mismatches: 28, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
28 3 0.03
29 68 0.65
30 29 0.28
31 4 0.04
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.36
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTAAAAAGTTTAG
Found at i:4807991 original size:78 final size:78
Alignment explanation
Indices: 4807818--4808483 Score: 848
Period size: 78 Copynumber: 8.7 Consensus size: 78
4807808 GTGTGGCCCA
* ** * *
4807818 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTAAAAAAAAAACAGAAA-TT--GA-AAATTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTT--TTAAAAAACAGAAATTTAAAAGAAATAC
*
4807879 CTCAGC-GTGACCCG
64 CTCGGCAGTGACCCG
* *
4807893 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAAAGAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
4807958 CGGCATGTGA-CCG
66 CGGCA-GTGACCCG
* * *
4807971 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTTAAAAGAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
4808036 CGGCA-TGACCCG
66 CGGCAGTGACCCG
* * * ** * *
4808048 AGGCTCAGCTCACCTCTCGTATTATGAGTTGATTTAAAAAAAACAGAAA-TT--GA-AAATTCCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
* *
4808109 CAGC-GTAACCCG
66 CGGCAGTGACCCG
* *
4808121 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAAAGAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
4808186 CGGCATGTGA-CCG
66 CGGCA-GTGACCCG
* * * *
4808199 AGGCTCAACTCACTTCTCACAATATGAGTTGATTTTTGAAAAACTGAAATTTAAAAGAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
4808264 CGGCA-TGACCCG
66 CGGCAGTGACCCG
* * * *
4808276 AGGCTCAACTCACCTTTCGCATTATGAGTTGA-TTTAAAAAAATAGAAATTTAAAAGAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
4808340 CGGCA-TGACCCG
66 CGGCAGTGACCCG
* *
4808352 AGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTAAAAAATAGAAATTTAAAAGAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
4808415 CGGCATGTGA-CCG
66 CGGCA-GTGACCCG
* *
4808428 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAACAGAAATTGAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAA
4808484 ATATTTCTTG
Statistics
Matches: 520, Mismatches: 52, Indels: 35
0.86 0.09 0.06
Matches are distributed among these distances:
73 70 0.13
74 3 0.01
75 69 0.13
76 115 0.22
77 98 0.19
78 158 0.30
79 7 0.01
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (78 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
CGGCAGTGACCCG
Found at i:4808174 original size:228 final size:228
Alignment explanation
Indices: 4807818--4808483 Score: 1052
Period size: 228 Copynumber: 2.9 Consensus size: 228
4807808 GTGTGGCCCA
* *
4807818 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTAAAAAAAAAACAGAAATTGAAAATTCCTCA
1 AGGCTCAACTCACCTCTCGCATTATGAGTTGATTT--AAAAAAAACAGAAATTGAAAATTCCTCA
4807883 GCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAA
64 GCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAA
4807948 AGAAATACCTCGGCATGTGACCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAA
129 AGAAATACCTCGGCATGTGACCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAA
4808013 ATAGAAATTTAAAAGAAATACCTCGGCATGACCCG
194 ATAGAAATTTAAAAGAAATACCTCGGCATGACCCG
* *
4808048 AGGCTCAGCTCACCTCTCGTATTATGAGTTGATTTAAAAAAAACAGAAATTGAAAATTCCTCAGC
1 AGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAACAGAAATTGAAAATTCCTCAGC
*
4808113 GTAACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAAAG
66 GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAAAG
*
4808178 AAATACCTCGGCATGTGACCGAGGCTCAACTCACTTCTCACAATATGAGTTGATTTTTGAAAAAC
131 AAATACCTCGGCATGTGACCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAA-
4808243 T-GAAATTTAAAAGAAATACCTCGGCATGACCCG
195 TAGAAATTTAAAAGAAATACCTCGGCATGACCCG
* * * *
4808276 AGGCTCAACTCACCTTTCGCATTATGAGTTGATTT-AAAAAAATAGAAATTTAAAAGAAATACCT
1 AGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAACAGAAA-TT--GA-AAATTCCT
* * * * * *
4808340 CGGCATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTAAAAAATAGAAATTTA
62 CAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATA
* **
4808403 AAAGAAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAA
127 AAAGAAATACCTCGGCATGTGACCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAA
* *
4808468 AAACAGAAATTGAAAA
192 AAATAGAAATTTAAAA
4808484 ATATTTCTTG
Statistics
Matches: 405, Mismatches: 25, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
227 12 0.03
228 223 0.55
229 91 0.22
230 32 0.08
231 47 0.12
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (228 bp):
AGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAACAGAAATTGAAAATTCCTCAGC
GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAAAG
AAATACCTCGGCATGTGACCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAAT
AGAAATTTAAAAGAAATACCTCGGCATGACCCG
Found at i:4809648 original size:14 final size:14
Alignment explanation
Indices: 4809629--4809663 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
4809619 TGACAAATTG
4809629 CCTTCAAGCGTTTC
1 CCTTCAAGCGTTTC
4809643 CCTTCAAGCGTTTC
1 CCTTCAAGCGTTTC
*
4809657 CATTCAA
1 CCTTCAA
4809664 TAAGGTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.20, C:0.34, G:0.11, T:0.34
Consensus pattern (14 bp):
CCTTCAAGCGTTTC
Found at i:4820347 original size:27 final size:25
Alignment explanation
Indices: 4820274--4820347 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
4820264 GATCCGATTG
* *
4820274 AAACACAAGAAATTTTTTAAAAAAA
1 AAACACGAGAATTTTTTTAAAAAAA
* *
4820299 AAACACGAGAATTTGTTGAAAATACAA
1 AAACACGAGAATTTTTTTAAAA-A-AA
*
4820326 AAACACGA-AATTTTTTTTAAAA
1 AAACACGAGAATTTTTTTAAAAA
4820348 CGCGAAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 19 0.47
26 11 0.28
27 10 0.25
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.27
Consensus pattern (25 bp):
AAACACGAGAATTTTTTTAAAAAAA
Found at i:4820793 original size:11 final size:10
Alignment explanation
Indices: 4820772--4820826 Score: 51
Period size: 11 Copynumber: 5.4 Consensus size: 10
4820762 ATTTTTCCTA
4820772 TTTTC-TTCT
1 TTTTCTTTCT
4820781 TTTCTCTTTCT
1 TTT-TCTTTCT
*
4820792 TTTT-TCTCT
1 TTTTCTTTCT
4820801 TTTTCTTCTCT
1 TTTTCTT-TCT
*
4820812 TTTCTTTTTCT
1 TTT-TCTTTCT
4820823 TTTT
1 TTTT
4820827 TTTTTCTGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
9 11 0.29
10 5 0.13
11 19 0.50
12 3 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:4820804 original size:29 final size:31
Alignment explanation
Indices: 4820763--4820827 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
4820753 TTTTTTCCTA
4820763 TTTTTCCTATTTTC-T-TCTTTTCTCTTTCT
1 TTTTTCCTATTTTCTTCTCTTTTCTCTTTCT
*
4820792 TTTTTCTCT-TTTTCTTCTCTTTTCTTTTTCT
1 TTTTTC-CTATTTTCTTCTCTTTTCTCTTTCT
4820823 TTTTT
1 TTTTT
4820828 TTTTCTGCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 11 0.34
30 3 0.09
31 18 0.56
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.77
Consensus pattern (31 bp):
TTTTTCCTATTTTCTTCTCTTTTCTCTTTCT
Found at i:4820819 original size:24 final size:24
Alignment explanation
Indices: 4820782--4820833 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
4820772 TTTTCTTCTT
4820782 TTCTCTTTCTTTTTTCTCTTTTTC
1 TTCTCTTTCTTTTTTCTCTTTTTC
* *
4820806 TTCTCTTT-TCTTTTTCTTTTTTTT
1 TTCTCTTTCT-TTTTTCTCTTTTTC
4820830 TTCT
1 TTCT
4820834 GCTGGGCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (24 bp):
TTCTCTTTCTTTTTTCTCTTTTTC
Found at i:4820830 original size:11 final size:11
Alignment explanation
Indices: 4820780--4820833 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
4820770 TATTTTCTTC
*
4820780 TTTTCTCTTTCT
1 TTTTTTCTTT-T
4820792 TTTTTCTCTTTT
1 TTTTT-TCTTTT
* *
4820804 TCTTCTCTTTT
1 TTTTTTCTTTT
*
4820815 CTTTTTCTTTT
1 TTTTTTCTTTT
4820826 TTTTTTCT
1 TTTTTTCT
4820834 GCTGGGCTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
11 21 0.62
12 8 0.24
13 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:4821007 original size:6 final size:6
Alignment explanation
Indices: 4820991--4821035 Score: 54
Period size: 6 Copynumber: 7.0 Consensus size: 6
4820981 TTTTATGCTT
*
4820991 TTTTTC TTTTTTC TTTTTC TTTTTC TTCTTC TTCCTTTC TTTTTC
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TT--TTTC TTTTTC
4821036 AAAACCCTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 23 0.68
7 6 0.18
8 5 0.15
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:4821139 original size:20 final size:20
Alignment explanation
Indices: 4821116--4821165 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
4821106 CTCCTCTACT
*
4821116 TCTC-TTTTCTTCTCTCTTTC
1 TCTCTTTTTCCTCT-TCTTTC
*
4821136 TCTCCTTTTTCCTCTTCTTTT
1 TCT-CTTTTTCCTCTTCTTTC
4821157 TCTCTTTTT
1 TCTCTTTTT
4821166 TGCAAGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 9 0.35
21 9 0.35
22 8 0.31
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (20 bp):
TCTCTTTTTCCTCTTCTTTC
Found at i:4821154 original size:21 final size:22
Alignment explanation
Indices: 4821120--4821166 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
4821110 TCTACTTCTC
*
4821120 TTTTCTTCTCTCTTTCTCTCCT
1 TTTTCCTCTCTCTTTCTCTCCT
* *
4821142 TTTTCCTCT-TCTTTTTCTCTT
1 TTTTCCTCTCTCTTTCTCTCCT
4821163 TTTT
1 TTTT
4821167 GCAAGTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTCCTCTCTCTTTCTCTCCT
Found at i:4821539 original size:58 final size:59
Alignment explanation
Indices: 4821417--4821551 Score: 155
Period size: 58 Copynumber: 2.3 Consensus size: 59
4821407 AGAAAATTTT
* * *
4821417 GGGTCAAAATGTAATTTTGAGATAGTTCAGCGGTCAAAATGAAATTTCAAAAGGTTTAA
1 GGGTCAAAATGTAATTTTGAAAAAGTTCAGCGGTCAAAATGAAATTTCAAAAAGTTTAA
* * * * * * * *
4821476 AGGTCATAATGTAATTTT-AAAAAGTTTAGTGGTTAAAATGCAATTTTAAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGAAAAAGTTCAGCGGTCAAAATGAAATTTCAAAAAGTTTAA
*
4821534 GGGTCAAAATATAATTTT
1 GGGTCAAAATGTAATTTT
4821552 TTATTTTTTG
Statistics
Matches: 62, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
58 46 0.74
59 16 0.26
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (59 bp):
GGGTCAAAATGTAATTTTGAAAAAGTTCAGCGGTCAAAATGAAATTTCAAAAAGTTTAA
Found at i:4821549 original size:29 final size:29
Alignment explanation
Indices: 4821417--4821551 Score: 135
Period size: 29 Copynumber: 4.6 Consensus size: 29
4821407 AGAAAATTTT
* * *
4821417 GGGTCAAAATGTAATTTTGAGATAGTTCAG
1 GGGTCAAAATGTAATTTT-AAAAAGTTTAG
* * * * *
4821447 CGGTCAAAATGAAATTTCAAAAGGTTTAA
1 GGGTCAAAATGTAATTTTAAAAAGTTTAG
* *
4821476 AGGTCATAATGTAATTTTAAAAAGTTTAG
1 GGGTCAAAATGTAATTTTAAAAAGTTTAG
* * *
4821505 TGGTTAAAATGCAATTTTAAAAAGTTTAG
1 GGGTCAAAATGTAATTTTAAAAAGTTTAG
*
4821534 GGGTCAAAATATAATTTT
1 GGGTCAAAATGTAATTTT
4821552 TTATTTTTTG
Statistics
Matches: 83, Mismatches: 22, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
29 68 0.82
30 15 0.18
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTAAAAAGTTTAG
Found at i:4821565 original size:9 final size:8
Alignment explanation
Indices: 4821548--4821581 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
4821538 CAAAATATAA
4821548 TTTTTTAT
1 TTTTTTAT
4821556 TTTTTGTAT
1 TTTTT-TAT
*
4821565 TTTTTGAT
1 TTTTTTAT
4821573 TTTTTTAT
1 TTTTTTAT
4821581 T
1 T
4821582 AAAAAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (8 bp):
TTTTTTAT
Found at i:4823016 original size:29 final size:30
Alignment explanation
Indices: 4822974--4823032 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
4822964 GAATTGAATC
*
4822974 AAATTAAAATTTTAAGTATA-AATTTACATA
1 AAATCAAAATTTTAAGTATACAA-TTACATA
*
4823004 AAATCAAAA-TTTATGTATACAATTACATA
1 AAATCAAAATTTTAAGTATACAATTACATA
4823033 TTAAACCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (30 bp):
AAATCAAAATTTTAAGTATACAATTACATA
Found at i:4823656 original size:14 final size:14
Alignment explanation
Indices: 4823639--4823674 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4823629 CACTCTCAAC
*
4823639 TCTCAATTTATTTT
1 TCTCAATTTATTAT
*
4823653 TCTCAATTTCTTAT
1 TCTCAATTTATTAT
4823667 TCTCAATT
1 TCTCAATT
4823675 GCCAAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.58
Consensus pattern (14 bp):
TCTCAATTTATTAT
Found at i:4826532 original size:34 final size:34
Alignment explanation
Indices: 4826480--4826548 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
4826470 GCCAAGTAAC
* *
4826480 CTTCAAGAACCTGCTTCAAAAGTCGTATAGAAAG
1 CTTCAACAACATGCTTCAAAAGTCGTATAGAAAG
* * *
4826514 CTTCAACAACATGTTTCAAAAGTTGTATGGAAAG
1 CTTCAACAACATGCTTCAAAAGTCGTATAGAAAG
4826548 C
1 C
4826549 CAAATGCTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (34 bp):
CTTCAACAACATGCTTCAAAAGTCGTATAGAAAG
Found at i:4834453 original size:27 final size:27
Alignment explanation
Indices: 4834406--4834462 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
4834396 TTTAATAAAG
4834406 AATGTAATTTTATGCTATTTTGCATTA
1 AATGTAATTTTATGCTATTTTGCATTA
*
4834433 AATGTAATTTTATGCTATTTTGTATTA
1 AATGTAATTTTATGCTATTTTGCATTA
4834460 AAT
1 AAT
4834463 TTGTGTAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (27 bp):
AATGTAATTTTATGCTATTTTGCATTA
Found at i:4849257 original size:44 final size:44
Alignment explanation
Indices: 4849202--4850027 Score: 562
Period size: 45 Copynumber: 18.5 Consensus size: 44
4849192 CAGTATGGGG
* * *
4849202 AGACAAGATCTGTTGTCTTTGATATACTTCACGCCAATACATGA
1 AGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGA
* * * *
4849246 AGACAATATCTGTTTTTTCCTTCGATCTACTTCACCACCAGT-C-TGGGA
1 AGACAAGATCTG--TTAT-CTTTGATCTACTTCA-CGCCAGTACAT--GA
*
4849294 AGACAAGATCTATTATCTTTGATCTACTTCACGCCAGTACATGA
1 AGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGA
* ** * * ***
4849338 AGACAAGATCTGCTT-TCTTCGATCTGTTTCGCCACCAGTATGGGA
1 AGACAAGATCTG-TTATCTTTGATCTACTTC-ACGCCAGTACATGA
*
4849383 AGACAAGATCTGTTACCTTTGATCTACTTCACAAGCCAGTACATGA
1 AGACAAGATCTGTTATCTTTGATCTACTTCAC--GCCAGTACATGA
* * ** * ***
4849429 AGACAAGATCTACTT-TCTTCGATCTGTTTCGC-CATCAGTATGGGA
1 AGACAAGATCT-GTTATCTTTGATCTACTTCACGC--CAGTACATGA
* ** * ***
4849474 AAACAAGATCTGCTT-T-TTTCGATCTGTTTTGC-CACCAGTATGGGA
1 AGACAAGATCTG-TTATCTTT-GATCT-ACTT-CACGCCAGTACATGA
*
4849519 AGACAAGATCTATTATCTTTGATCTACTTCACGCCAGTACATGA
1 AGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGA
* * ** * * ***
4849563 AGACAAGATATGCTT-TCTTCGATCTGTTTCGCCACCAGTATGGGA
1 AGACAAGATCTG-TTATCTTTGATCTACTTC-ACGCCAGTACATGA
*
4849608 AGACAAGATCTGTTATCTTTGATCTACTTCATGCCAGTACATGA
1 AGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGA
* * ** * * ***
4849652 AGACAAGATATGCTT-TCTTCGATCTGTTTCGCCACCAGTATGGGA
1 AGACAAGATCTG-TTATCTTTGATCTACTTC-ACGCCAGTACATGA
4849697 AGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGA
1 AGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGA
* ** * * ***
4849741 AGACAAGATCTGCTT-TCTTCGATCTGTTTCGCCACCAGTATGGGA
1 AGACAAGATCTG-TTATCTTTGATCTACTTC-ACGCCAGTACATGA
* *
4849786 AGACAAGATCTGTTATCTTTGATTTACTTTACGCCAGTACATGA
1 AGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGA
* * * * ***
4849830 AGACAAGATATGCTT-TCTTTGATCTGCTTCGCCACCAGTATGGGA
1 AGACAAGATCTG-TTATCTTTGATCTACTTC-ACGCCAGTACATGA
* * *
4849875 AGGCAAGATCTATTATCTTTGATCTACTCCACGCCAGTACATGA
1 AGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGA
* * * * ***
4849919 AGACAAGATCTACTT-TCTTTGATCTGCTTCGCCACCAGTATGGGA
1 AGACAAGATCT-GTTATCTTTGATCTACTTC-ACGCCAGTACATGA
* * * *
4849964 AGGCAAGATCTGGTATCTCTGATCTACTTCACGTCAGTACATGA
1 AGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGA
*
4850008 AGACAAGATCAGTTATCTTT
1 AGACAAGATCTGTTATCTTT
4850028 CAACCTGCTC
Statistics
Matches: 593, Mismatches: 150, Indels: 78
0.72 0.18 0.10
Matches are distributed among these distances:
43 2 0.00
44 243 0.41
45 267 0.45
46 46 0.08
47 18 0.03
48 17 0.03
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (44 bp):
AGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGA
Found at i:4849313 original size:92 final size:88
Alignment explanation
Indices: 4849153--4849485 Score: 407
Period size: 92 Copynumber: 3.7 Consensus size: 88
4849143 TTTCACGCCA
* * * *
4849153 ATGAAAACAAGGTCTG-TTCTCTTCGATCTACTCTCCCACCAGTATGGGGAGACAAGATCTGTTG
1 ATGAAGACAAGATCTGCTT-TCTTCGATCTACT-TCCCACCAGTATGGGAAGACAAGATCTGTTA
* *
4849217 TCTTTGATATACTTCACGCCAATAC
64 TCTTTGATCTACTTCACGCCAGTAC
* * * *
4849242 ATGAAGACAATATCTGTTTTTTCCTTCGATCTACTTCACCACCAGTCTGGGAAGACAAGATCTAT
1 ATGAAGACAAGATCTG--CTTT-CTTCGATCTACTTC-CCACCAGTATGGGAAGACAAGATCTGT
4849307 TATCTTTGATCTACTTCACGCCAGTAC
62 TATCTTTGATCTACTTCACGCCAGTAC
** *
4849334 ATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTAC
1 ATGAAGACAAGATCTGCTTTCTTCGATCTACTTC-CCACCAGTATGGGAAGACAAGATCTGTTAT
4849399 CTTTGATCTACTTCACAAGCCAGTAC
65 CTTTGATCTACTTCAC--GCCAGTAC
* ** * *
4849425 ATGAAGACAAGATCTACTTTCTTCGATCTGTTTCGCCATCAGTATGGGAAAACAAGATCTG
1 ATGAAGACAAGATCTGCTTTCTTCGATCTACTTC-CCACCAGTATGGGAAGACAAGATCTG
4849486 CTTTTTTCGA
Statistics
Matches: 217, Mismatches: 20, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
89 68 0.31
90 3 0.01
91 69 0.32
92 77 0.35
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (88 bp):
ATGAAGACAAGATCTGCTTTCTTCGATCTACTTCCCACCAGTATGGGAAGACAAGATCTGTTATC
TTTGATCTACTTCACGCCAGTAC
Found at i:4849498 original size:91 final size:89
Alignment explanation
Indices: 4849188--4849485 Score: 407
Period size: 91 Copynumber: 3.3 Consensus size: 89
4849178 ATCTACTCTC
* * * * *
4849188 CCACCAGTATGGGGAGACAAGATCTGTTGTCTTTGATATACTTCACGCCAATACATGAAGACAAT
1 CCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAG
** ** *
4849253 ATCTGTTTTTTCCTTCGATCTACTTCA
66 ATC--TACTTT-CTTCGATCTGTTTCG
* *
4849280 CCACCAGTCTGGGAAGACAAGATCTATTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAG
1 CCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAG
*
4849345 ATCTGCTTTCTTCGATCTGTTTCG
66 ATCTACTTTCTTCGATCTGTTTCG
*
4849369 CCACCAGTATGGGAAGACAAGATCTGTTACCTTTGATCTACTTCACAAGCCAGTACATGAAGACA
1 CCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCAC--GCCAGTACATGAAGACA
4849434 AGATCTACTTTCTTCGATCTGTTTCG
64 AGATCTACTTTCTTCGATCTGTTTCG
* *
4849460 CCATCAGTATGGGAAAACAAGATCTG
1 CCACCAGTATGGGAAGACAAGATCTG
4849486 CTTTTTTCGA
Statistics
Matches: 186, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
89 55 0.30
90 4 0.02
91 66 0.35
92 61 0.33
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (89 bp):
CCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAG
ATCTACTTTCTTCGATCTGTTTCG
Found at i:4850017 original size:89 final size:89
Alignment explanation
Indices: 4849476--4850017 Score: 895
Period size: 89 Copynumber: 6.1 Consensus size: 89
4849466 GTATGGGAAA
* * *
4849476 ACAAGATCTGCTTTTTTCGATCTGTTTTGCCACCAGTATGGGAAGACAAGATCTATTATCTTTGA
1 ACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGA
4849541 TCTACTTCACGCCAGTACATGAAG
66 TCTACTTCACGCCAGTACATGAAG
*
4849565 ACAAGATATGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGA
1 ACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGA
*
4849630 TCTACTTCATGCCAGTACATGAAG
66 TCTACTTCACGCCAGTACATGAAG
*
4849654 ACAAGATATGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGA
1 ACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGA
4849719 TCTACTTCACGCCAGTACATGAAG
66 TCTACTTCACGCCAGTACATGAAG
4849743 ACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGA
1 ACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGA
* *
4849808 TTTACTTTACGCCAGTACATGAAG
66 TCTACTTCACGCCAGTACATGAAG
* * * * *
4849832 ACAAGATATGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTATTATCTTTGA
1 ACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGA
*
4849897 TCTACTCCACGCCAGTACATGAAG
66 TCTACTTCACGCCAGTACATGAAG
* * * * * *
4849921 ACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGA
1 ACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGA
*
4849986 TCTACTTCACGTCAGTACATGAAG
66 TCTACTTCACGCCAGTACATGAAG
4850010 ACAAGATC
1 ACAAGATC
4850018 AGTTATCTTT
Statistics
Matches: 429, Mismatches: 24, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 429 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (89 bp):
ACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGA
TCTACTTCACGCCAGTACATGAAG
Found at i:4850911 original size:13 final size:13
Alignment explanation
Indices: 4850893--4850917 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4850883 AAATTGTCGA
4850893 GGATAACAAAGAT
1 GGATAACAAAGAT
4850906 GGATAACAAAGA
1 GGATAACAAAGA
4850918 AATTGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.24, T:0.12
Consensus pattern (13 bp):
GGATAACAAAGAT
Found at i:4852044 original size:37 final size:37
Alignment explanation
Indices: 4852003--4852074 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
4851993 ATAATATGAT
4852003 TATGAATGAATGAATGAATGGTTTGGCAGAAAAAAAA
1 TATGAATGAATGAATGAATGGTTTGGCAGAAAAAAAA
* *
4852040 TATGAATGAATGAATGAATGTTTTGGTAGAAAAAA
1 TATGAATGAATGAATGAATGGTTTGGCAGAAAAAA
4852075 TCCAAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.47, C:0.01, G:0.24, T:0.28
Consensus pattern (37 bp):
TATGAATGAATGAATGAATGGTTTGGCAGAAAAAAAA
Found at i:4853961 original size:19 final size:19
Alignment explanation
Indices: 4853921--4853962 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
4853911 ATAATCTTTG
* *
4853921 ATGCATATGATGTAATGTA
1 ATGCAAATGATGAAATGTA
4853940 ATGCAAATGCATGAAATG-A
1 ATGCAAATG-ATGAAATGTA
4853959 ATGC
1 ATGC
4853963 GAAAAGAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (19 bp):
ATGCAAATGATGAAATGTA
Found at i:4854010 original size:13 final size:13
Alignment explanation
Indices: 4853992--4854017 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4853982 TGTTCAATTT
4853992 TTTACTAGAAAAC
1 TTTACTAGAAAAC
4854005 TTTACTAGAAAAC
1 TTTACTAGAAAAC
4854018 AAATCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:4859038 original size:89 final size:89
Alignment explanation
Indices: 4858788--4859482 Score: 1086
Period size: 89 Copynumber: 7.8 Consensus size: 89
4858778 TTTCACGCCA
* * * * * * * * *
4858788 ATGAAAACAAGGTCTG-TTCTCTTCGATCTACTCCCCCACTAGTATGGGGAGACAAGATTTGTTG
1 ATGAAGACAAGATCTGCTT-TCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTA
*
4858852 TCTTTGATCTACTTCACGCCAATAC
65 TCTTTGATCTACTTCACGCCAGTAC
* * * * *
4858877 ATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGTCACCAGTCTGGGAAGACAAGATCTAT
1 ATGAAGACAAGATCTG--CTTT-CTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGT
4858942 TATCTTTGATCTACTTCACGCCAGTAC
63 TATCTTTGATCTACTTCACGCCAGTAC
* * *
4858969 ATGAAGACAAGATCTGCTTTCTTCGATCTGTTTTGCCACCAGTATGGGAAAACAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
*
4859034 CTTTGATCTACATCACGCCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
* * * *
4859058 ATGAAGACAAGATCTACTTTTTTCGATCTGTTTCGCCACCAGTATGGGAAGACAGGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
*
4859123 CTTTGATATACTTCACGCCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
* *
4859147 ATGAAGACAAGATCTGCCTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
4859212 CTTTGATCTACTTCACGCCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
*
4859236 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
4859301 CTTTGATCTACTTCACGCCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
*
4859325 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
4859390 CTTTGATCTACTTCACGCCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
*
4859414 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
4859479 CTTT
66 CTTT
4859483 CAACCTGCTC
Statistics
Matches: 566, Mismatches: 36, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
89 485 0.86
90 3 0.01
91 1 0.00
92 77 0.14
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (89 bp):
ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
CTTTGATCTACTTCACGCCAGTAC
Found at i:4864640 original size:20 final size:20
Alignment explanation
Indices: 4864593--4864644 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
4864583 TTTTAAATAA
* *
4864593 ATATAAATATTTTTTTGTAT
1 ATATAATTATTTATTTGTAT
*
4864613 -TA-AATTATTTATTTGTTT
1 ATATAATTATTTATTTGTAT
4864631 ATATAATTATTTAT
1 ATATAATTATTTAT
4864645 ATTTATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 13 0.48
19 4 0.15
20 10 0.37
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
ATATAATTATTTATTTGTAT
Found at i:4869149 original size:18 final size:18
Alignment explanation
Indices: 4869109--4869277 Score: 134
Period size: 18 Copynumber: 9.4 Consensus size: 18
4869099 ACACGCTAAT
*
4869109 AATTTTTTAAAACACGA-
1 AATTTTTTGAAACACGAG
4869126 AA-TTTTTGAAACACGAG
1 AATTTTTTGAAACACGAG
* *
4869143 AACTTTTTGAGAACATGA-
1 AATTTTTTGA-AACACGAG
* ** *
4869161 AATTTTTTTTAAACGTGAA
1 AA-TTTTTTGAAACACGAG
*
4869180 AATTTTTTGAAACACGAA
1 AATTTTTTGAAACACGAG
* *
4869198 AATTTTTTCAAA-ACGCG
1 AATTTTTTGAAACACGAG
* *
4869215 AATTTTTTTATACACGAG
1 AATTTTTTGAAACACGAG
4869233 AATTTTTTTTGAAAACACGAG
1 AA--TTTTTTG-AAACACGAG
*
4869254 AA-TTTTTAAAACACGA-
1 AATTTTTTGAAACACGAG
4869270 AATTTTTT
1 AATTTTTT
4869278 TTGAAAACGC
Statistics
Matches: 125, Mismatches: 17, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
16 15 0.12
17 30 0.24
18 50 0.40
19 14 0.11
20 6 0.05
21 10 0.08
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (18 bp):
AATTTTTTGAAACACGAG
Found at i:4869169 original size:37 final size:36
Alignment explanation
Indices: 4869109--4869283 Score: 160
Period size: 37 Copynumber: 4.8 Consensus size: 36
4869099 ACACGCTAAT
*
4869109 AATTTTTTAAAACACGAAA--TTTTTGAAACACGAG
1 AATTTTTTGAAACACGAAATTTTTTTGAAACACGAG
* * * ** *
4869143 AACTTTTTGAGAACATGAAATTTTTTTTAAACGTGAA
1 AATTTTTTGA-AACACGAAATTTTTTTGAAACACGAG
* * *
4869180 AATTTTTTGAAACACGAAAATTTTTTCAAA-ACGCG
1 AATTTTTTGAAACACGAAATTTTTTTGAAACACGAG
* *
4869215 AATTTTTTTATACACGAGAATTTTTTTTGAAAACACGAG
1 AATTTTTTGAAACACGA-AA-TTTTTTTG-AAACACGAG
*
4869254 AA-TTTTTAAAACACGAAATTTTTTTTGAAA
1 AATTTTTTGAAACACGAAA-TTTTTTTGAAA
4869284 ACGCAAAAAT
Statistics
Matches: 112, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
34 8 0.07
35 24 0.21
36 22 0.20
37 37 0.33
38 15 0.13
39 6 0.05
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.38
Consensus pattern (36 bp):
AATTTTTTGAAACACGAAATTTTTTTGAAACACGAG
Found at i:4869194 original size:55 final size:53
Alignment explanation
Indices: 4869128--4869296 Score: 171
Period size: 55 Copynumber: 3.1 Consensus size: 53
4869118 AAACACGAAA
* * *
4869128 TTTTTGAAACACGAGAACTTTTTGAGAACATGAAATTTTTTTTAAACGTGAAAAT
1 TTTTTGAAACACGAGAA-TTTTT-AAAACACGAAATTTTTTTTAAACGAGAAAAT
* * * **
4869183 TTTTTGAAACACGAAAATTTTTTCAAAACGCG-AATTTTTTTATACACGAGAATTT
1 TTTTTGAAACACGAGAA-TTTTT-AAAACACGAAATTTTTTT-TAAACGAGAAAAT
4869238 TTTTTGAAAACACGAGAATTTTTAAAACACGAAATTTTTTTTGAAAACGCA-AAAAT
1 TTTTTG-AAACACGAGAATTTTTAAAACACGAAATTTTTTTT--AAACG-AGAAAAT
4869294 TTT
1 TTT
4869297 GAAAAGAAGT
Statistics
Matches: 93, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
54 17 0.18
55 55 0.59
56 20 0.22
57 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (53 bp):
TTTTTGAAACACGAGAATTTTTAAAACACGAAATTTTTTTTAAACGAGAAAAT
Found at i:4869250 original size:21 final size:21
Alignment explanation
Indices: 4869226--4869285 Score: 85
Period size: 17 Copynumber: 3.1 Consensus size: 21
4869216 ATTTTTTTAT
4869226 ACACGAGAATTTTTTTTGAAA
1 ACACGAGAATTTTTTTTGAAA
4869247 ACACGAGAA---TTTTT-AAA
1 ACACGAGAATTTTTTTTGAAA
4869264 ACACGA-AATTTTTTTTGAAA
1 ACACGAGAATTTTTTTTGAAA
4869284 AC
1 AC
4869286 GCAAAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.06
17 9 0.26
18 5 0.14
19 5 0.14
20 5 0.14
21 9 0.26
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (21 bp):
ACACGAGAATTTTTTTTGAAA
Found at i:4869970 original size:17 final size:17
Alignment explanation
Indices: 4869947--4869994 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
4869937 TTGGACAGGC
4869947 CTGCTATTTTTTTGCTG
1 CTGCTATTTTTTTGCTG
* * *
4869964 TTGCTATTTTCTTACTG
1 CTGCTATTTTTTTGCTG
*
4869981 CTGCTGTTTTTTTG
1 CTGCTATTTTTTTG
4869995 GGCTGATCTG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.06, C:0.17, G:0.17, T:0.60
Consensus pattern (17 bp):
CTGCTATTTTTTTGCTG
Found at i:4870104 original size:7 final size:7
Alignment explanation
Indices: 4870076--4870150 Score: 52
Period size: 7 Copynumber: 11.1 Consensus size: 7
4870066 TTTTTATTTT
4870076 TTTC-TC
1 TTTCTTC
*
4870082 TTTTTTC
1 TTTCTTC
*
4870089 TTTC-CC
1 TTTCTTC
4870095 TTTCTTC
1 TTTCTTC
*
4870102 TTTCTTT
1 TTTCTTC
4870109 TTTCTTC
1 TTTCTTC
*
4870116 TATCTTTC
1 TTTC-TTC
4870124 TTCTCTT-
1 TT-TCTTC
*
4870131 TTTCTCC
1 TTTCTTC
4870138 TTT-TTC
1 TTTCTTC
4870144 -TTCTTC
1 TTTCTTC
4870150 T
1 T
4870151 CCTTCGACAG
Statistics
Matches: 52, Mismatches: 10, Indels: 13
0.69 0.13 0.17
Matches are distributed among these distances:
5 2 0.04
6 16 0.31
7 26 0.50
8 6 0.12
9 2 0.04
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTCTTC
Found at i:4870134 original size:11 final size:11
Alignment explanation
Indices: 4870072--4870147 Score: 61
Period size: 11 Copynumber: 6.9 Consensus size: 11
4870062 AAAATTTTTA
4870072 TTTTT-TTCTC
1 TTTTTCTTCTC
*
4870082 TTTTTTCTTTCCC
1 -TTTTTC-TTCTC
4870095 TTTCTTCTT-TC
1 TTT-TTCTTCTC
*
4870106 TTTTTTCTTCTA
1 -TTTTTCTTCTC
*
4870118 TCTTTCTTCTC
1 TTTTTCTTCTC
4870129 TTTTTC-TC-C
1 TTTTTCTTCTC
4870138 TTTTTCTTCT
1 TTTTTCTTCT
4870148 TCTCCTTCGA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
9 7 0.13
10 4 0.08
11 25 0.48
12 9 0.17
13 7 0.13
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTTCTTCTC
Found at i:4870798 original size:30 final size:29
Alignment explanation
Indices: 4870669--4870803 Score: 73
Period size: 30 Copynumber: 4.6 Consensus size: 29
4870659 TAAGAAATAT
*
4870669 GGGGCAAAAATGTAATTTTTAGAAAGTTTA
1 GGGGC-AAAATGTAATTTTTACAAAGTTTA
** * *
4870699 GGGGCCCAATTTAA--TTTACAAATTATTA
1 GGGGCAAAATGTAATTTTTACAAAGT-TTA
* * ** *
4870727 GGGG-ATAAGATGTAA-ATTTAGAAAAAATAA
1 GGGGCA-AA-ATGTAATTTTTA-CAAAGTTTA
*
4870757 GGGTCAAAATGTAATTTTTGA-AAAGTTTA
1 GGGGCAAAATGTAATTTTT-ACAAAGTTTA
4870786 GGGGCTAAAATGTAATTT
1 GGGGC-AAAATGTAATTT
4870804 GTATTTTTTC
Statistics
Matches: 78, Mismatches: 18, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
27 8 0.10
28 8 0.10
29 26 0.33
30 31 0.40
31 5 0.06
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (29 bp):
GGGGCAAAATGTAATTTTTACAAAGTTTA
Found at i:4871477 original size:230 final size:228
Alignment explanation
Indices: 4871144--4872167 Score: 1376
Period size: 230 Copynumber: 4.4 Consensus size: 228
4871134 TGAGTTGACC
4871144 TTTGAAAAATAGAAATTGAAAAATACCTCGACGTGTGACCCGAGGCTCAACTCACCTCTCGCATT
1 TTTGAAAAATAGAAATT-AAAAATACCTCG-C--GTGACCCGAGGCTCAACTCACCTCTCGCATT
* * ** * * * *
4871209 ATGTGTTGATTTTTTTTGAAGAGCATAAATTGAAAATACCTCAGCATGACCCGAGACTCAACTCA
62 ATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCA
*
4871274 CCTCTCGCATTATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCT
127 CCTCTCGCATTATGAGTTGA--TTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCC
4871339 GAGGCTCAACTCACCTCTCGCATTATGAGTTGAT-TTTT
190 GAGGCTCAACTCACCTCTCGCATTATGAGTTGATATTTT
*
4871377 TTTGAAAAATAGAAATTAAAAATACCTTCGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATG
1 TTTGAAAAATAGAAATTAAAAATACC-TCGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
* *
4871442 AGTTGATTTTTTTTGAAAAATAGAAGTTAAAAATACCTTAGCGTGACCCGAGGCTCAACTCACCT
65 AGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCT
* *** *
4871507 CTCGCATTATAAGTTGA-TTTTTAAAAAAAATAGAAATTAAAAATACCTCAGTGTGACCCGAGGC
130 CTCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGC
*
4871571 TCAAATCACCTCTCGCATTATGAGTTGATATTTT
195 TCAACTCACCTCTCGCATTATGAGTTGATATTTT
* * *
4871605 TTTGAAAAATAGAAATTAAAAATACCTCAGCATGACCCGAGGTTCAACTCACCTCTCGCATTGTG
1 TTTGAAAAATAGAAATTAAAAATACCTC-GCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
** * * *
4871670 AGCCGATTTTTTTTTGAAAAATAAAAAATAAAAATATCTCAGCGTGACCCGAGGCTCAACTCACC
65 AGTTGA-TTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACC
* * *
4871735 TCTCGCATTATGAGTTAATTTTTTTTGAAAAATAGAAATAAAAAATACCTCAGTGTGACCCGAGG
129 TCTCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGG
4871800 CTCAACTCACCTCTCGCATTATGAGTTGATATTTT
194 CTCAACTCACCTCTCGCATTATGAGTTGATATTTT
4871835 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
1 TTTGAAAAATAGAAATTAAAAATACCTC-GCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
* *
4871900 AGTTGTTTTTTTTTTAAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACC
65 AGTTG-ATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACC
* * * *
4871965 TCTCGCATTATGAGTTGATTTTTTTTGAAAAACATAAATTGAAAATACCTCAGCGTGACCCAAGG
129 TCTCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGG
** * *
4872030 CTCAACTCAGTTCTCGCCA-TCTGAGATGAT-TTTT
194 CTCAACTCACCTCTCG-CATTATGAGTTGATATTTT
**** * * *
4872064 GAAAAAAACATA-AATTTAAAAAAATACCTCGATATGTGACCCGAGGCTCAACTTACCTCTCGCA
1 TTTGAAAA-ATAGAAATT--AAAAATACCTCG---CGTGACCCGAGGCTCAACTCACCTCTCGCA
* * ***
4872128 ATATTAGTTGA-TTTTTGAAAAAAATAGAAATTGAAAAATA
60 TTATGAGTTGATTTTTTTTGAAAAATAGAAATT-AAAAATA
4872168 TTTCTTGAAA
Statistics
Matches: 708, Mismatches: 69, Indels: 29
0.88 0.09 0.04
Matches are distributed among these distances:
227 72 0.10
228 66 0.09
229 81 0.11
230 384 0.54
231 32 0.05
232 17 0.02
233 56 0.08
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (228 bp):
TTTGAAAAATAGAAATTAAAAATACCTCGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGA
GTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTC
TCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCT
CAACTCACCTCTCGCATTATGAGTTGATATTTT
Found at i:4871643 original size:77 final size:76
Alignment explanation
Indices: 4871144--4872167 Score: 1383
Period size: 76 Copynumber: 13.3 Consensus size: 76
4871134 TGAGTTGACC
*
4871144 TTTGAAAAATAGAAATTGAAAAATACCTCGACGTGTGACCCGAGGCTCAACTCACCTCTCGCATT
1 TTTGAAAAATAGAAATT-AAAAATACCTC-A-GCGTGACCCGAGGCTCAACTCACCTCTCGCATT
*
4871209 ATGTGTTGATTTTT
63 ATGAGTTGATTTTT
* ** * * * *
4871223 TTTGAAGAGCATAAATTGAAAATACCTCAGCATGACCCGAGACTCAACTCACCTCTCGCATTATG
1 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
4871288 AGTTGATTTTTTT
66 AGTTGA--TTTTT
*
4871301 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCATTATG
1 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
4871366 AGTTGATTTTT
66 AGTTGATTTTT
*
4871377 TTTGAAAAATAGAAATTAAAAATACCTTC-GCGTGACCCGAGGCTCAACTCACCTCTCGTATTAT
1 TTTGAAAAATAGAAATTAAAAATACC-TCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTAT
4871441 GAGTTGATTTTT
65 GAGTTGATTTTT
* * *
4871453 TTTGAAAAATAGAAGTTAAAAATACCTTAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATA
1 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
4871518 AGTTGA-TTTT
66 AGTTGATTTTT
*** * *
4871528 TAAAAAAAATAGAAATTAAAAATACCTCAGTGTGACCCGAGGCTCAAATCACCTCTCGCATTATG
1 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
4871593 AGTTGATATTTT
66 AGTTGAT-TTTT
* * *
4871605 TTTGAAAAATAGAAATTAAAAATACCTCAGCATGACCCGAGGTTCAACTCACCTCTCGCATTGTG
1 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
**
4871670 AGCCGATTTTTT
66 AGTTGA-TTTTT
* * *
4871682 TTTGAAAAATAAAAAATAAAAATATCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
1 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
*
4871747 AGTTAATTTTT
66 AGTTGATTTTT
* *
4871758 TTTGAAAAATAGAAATAAAAAATACCTCAGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
1 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
4871823 AGTTGATATTTT
66 AGTTGAT-TTTT
4871835 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
1 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
*
4871900 AGTTGTTTTTTT
66 AGTTG-ATTTTT
*
4871912 TTTAAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
1 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
4871977 AGTTGATTTTT
66 AGTTGATTTTT
* * * * ** *
4871988 TTTGAAAAACATAAATTGAAAATACCTCAGCGTGACCCAAGGCTCAACTCAGTTCTCGCCA-TCT
1 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCG-CATTAT
*
4872052 GAGATGATTTTT
65 GAGTTGATTTTT
**** * ** *
4872064 GAAAAAAACATA-AATTTAAAAAAATACCTCGATATGTGACCCGAGGCTCAACTTACCTCTCGCA
1 TTTGAAAA-ATAGAAATT--AAAAATACCTC-A-GCGTGACCCGAGGCTCAACTCACCTCTCGCA
* *
4872128 ATATTAGTTGA-TTTT
61 TTATGAGTTGATTTTT
***
4872143 TGAAAAAAATAGAAATTGAAAAATA
1 TTTGAAAAATAGAAATT-AAAAATA
4872168 TTTCTTGAAA
Statistics
Matches: 838, Mismatches: 90, Indels: 35
0.87 0.09 0.04
Matches are distributed among these distances:
75 68 0.08
76 327 0.39
77 283 0.34
78 100 0.12
79 30 0.04
80 30 0.04
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (76 bp):
TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
AGTTGATTTTT
Found at i:4873023 original size:1 final size:1
Alignment explanation
Indices: 4873017--4873066 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
4873007 TTCATCTTGG
* * * * *
4873017 TTTTTTTCTTTTTTTTGTTTTTGTTTTTTGTTTTTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4873067 AGGCATAATA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:4873030 original size:7 final size:7
Alignment explanation
Indices: 4873027--4873066 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
4873017 TTTTTTTCTT
4873027 TTTTTTG
1 TTTTTTG
4873034 -TTTTTG
1 TTTTTTG
4873040 TTTTTTG
1 TTTTTTG
*
4873047 TTTTTTT
1 TTTTTTG
4873054 TTTTTTG
1 TTTTTTG
4873061 TTTTTT
1 TTTTTT
4873067 AGGCATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (7 bp):
TTTTTTG
Found at i:4873043 original size:21 final size:21
Alignment explanation
Indices: 4873026--4873066 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4873016 GTTTTTTTCT
4873026 TTTTTTTGTTTTTGTTTTTTG
1 TTTTTTTGTTTTTGTTTTTTG
*
4873047 TTTTTTTTTTTTTGTTTTTT
1 TTTTTTTGTTTTTGTTTTTT
4873067 AGGCATAATA
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:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (21 bp):
TTTTTTTGTTTTTGTTTTTTG
Found at i:4878233 original size:4 final size:4
Alignment explanation
Indices: 4878219--4878255 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
4878209 ATGTACATGC
*
4878219 AATG CATG AATG AATG AATG AATG AATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG A
4878256 CAAGTGAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.24
Consensus pattern (4 bp):
AATG
Found at i:4880407 original size:16 final size:17
Alignment explanation
Indices: 4880362--4880576 Score: 113
Period size: 18 Copynumber: 12.1 Consensus size: 17
4880352 CGTGATTCGA
*
4880362 TTGAAACACGAGATTTTTT
1 TTGAAACACGAGA--ATTT
*
4880381 TTAAAAACACGAGAA-TT
1 TT-GAAACACGAGAATTT
* *
4880398 TTGTAACACGGTAATAATTT
1 TTGAAACAC-G--AGAATTT
4880418 TTGAAAACACGA-AATTT
1 TTG-AAACACGAGAATTT
4880435 TTGAAACACGAGAATTTT
1 TTGAAACACGAGAA-TTT
4880453 TTGAAA-AC-ATGAATTTT
1 TTGAAACACGA-GAA-TTT
* * * *
4880470 TTTAAACTCAAAAAATTT
1 TTGAAACAC-GAGAATTT
4880488 TTGAAACACGA-AATTTTT
1 TTGAAACACGAGAA--TTT
* *
4880506 TTGAAAACGCGAAAATTT
1 TTG-AAACACGAGAATTT
4880524 TT-AAACACGAGAATTTTT
1 TTGAAACACGAGAA--TTT
*
4880542 TTGAAAACACGAGAATTC
1 TTG-AAACACGAGAATTT
*
4880560 TTAAAACAC-A-AATTT
1 TTGAAACACGAGAATTT
4880575 TT
1 TT
4880577 TTTTGAAAAC
Statistics
Matches: 158, Mismatches: 18, Indels: 44
0.72 0.08 0.20
Matches are distributed among these distances:
15 6 0.04
16 26 0.16
17 36 0.23
18 41 0.26
19 14 0.09
20 30 0.19
21 5 0.03
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (17 bp):
TTGAAACACGAGAATTT
Found at i:4880461 original size:35 final size:35
Alignment explanation
Indices: 4880362--4880576 Score: 142
Period size: 35 Copynumber: 6.1 Consensus size: 35
4880352 CGTGATTCGA
* *
4880362 TTGAAACACGAGATTTTTTTTAAAAACACGAGAA-TT
1 TTGAAACACGAGA-ATTTTTTGAAAACACGA-AATTT
*
4880398 TTGTAACACG-GTAATAATTTTTGAAAACACGAAATTT
1 TTGAAACACGAG-AAT--TTTTTGAAAACACGAAATTT
* *
4880435 TTGAAACACGAGAATTTTTTGAAAACATGAATTTT
1 TTGAAACACGAGAATTTTTTGAAAACACGAAATTT
* * * * *
4880470 TTTAAACTCAAAAAATTTTTG-AAACACGAAATTTTT
1 TTGAAACACGAGAATTTTTTGAAAACACGAAA--TTT
* *
4880506 TTGAAA-ACGCGAAAATTTTT--AAACACGAGAATTTTT
1 TTGAAACACGAG-AATTTTTTGAAAACACGA-AA--TTT
*
4880542 TTGAAAACACGAGAA-TTCTT-AAAACAC-AAATTT
1 TTG-AAACACGAGAATTTTTTGAAAACACGAAATTT
4880575 TT
1 TT
4880577 TTTTGAAAAC
Statistics
Matches: 147, Mismatches: 20, Indels: 27
0.76 0.10 0.14
Matches are distributed among these distances:
33 5 0.03
34 8 0.05
35 47 0.32
36 43 0.29
37 39 0.27
38 5 0.03
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (35 bp):
TTGAAACACGAGAATTTTTTGAAAACACGAAATTT
Found at i:4880472 original size:53 final size:52
Alignment explanation
Indices: 4880415--4880601 Score: 148
Period size: 53 Copynumber: 3.5 Consensus size: 52
4880405 ACGGTAATAA
* * *
4880415 TTTTTGAAAACACGAAATTTTTGAAACACGAGAATTTTTTGAAAACATGAAT
1 TTTTTTAAAACACAAAATTTTTGAAACACGAGAATTTTTTGAAAACACGAAT
* * * *
4880467 TTTTTTAAACTCAAAAAATTTTTGAAACACGA-AATTTTTTTGAAAACGCGAAA
1 TTTTTTAAA-ACACAAAATTTTTGAAACACGAGAA-TTTTTTGAAAACACGAAT
* * * *
4880520 ATTTTT-AAACACGAGAATTTTTTTGAAAACACGAGAA-TTCTT-AAAACACAAATTT
1 TTTTTTAAAACAC-A-AA-ATTTTTG-AAACACGAGAATTTTTTGAAAACACGAA--T
* *
4880575 TTTTTTGAAAACGCAAAAATTTTGAAA
1 TTTTTT-AAAACACAAAATTTTTGAAA
4880602 AGAAGTATCT
Statistics
Matches: 105, Mismatches: 19, Indels: 21
0.72 0.13 0.14
Matches are distributed among these distances:
51 2 0.02
52 13 0.12
53 52 0.50
54 15 0.14
55 15 0.14
56 3 0.03
57 5 0.05
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (52 bp):
TTTTTTAAAACACAAAATTTTTGAAACACGAGAATTTTTTGAAAACACGAAT
Found at i:4880521 original size:36 final size:36
Alignment explanation
Indices: 4880413--4880601 Score: 162
Period size: 36 Copynumber: 5.3 Consensus size: 36
4880403 ACACGGTAAT
4880413 AATTTTTGAAAACACGAAA--TTTTTG-AAACACGAGA
1 AATTTTTG-AAACACGAAATTTTTTTGAAAACACGA-A
* * * *
4880448 ATTTTTTGAAAACATG-AATTTTTTT--AAACTCAAAA
1 AATTTTTG-AAACACGAAATTTTTTTGAAAACAC-GAA
*
4880483 AATTTTTGAAACACGAAATTTTTTTGAAAACGCGAA
1 AATTTTTGAAACACGAAATTTTTTTGAAAACACGAA
*
4880519 AATTTTT-AAACACGAGAATTTTTTTGAAAACACGAG
1 AATTTTTGAAACACGA-AATTTTTTTGAAAACACGAA
* * *
4880555 AATTCTTAAAACAC-AAATTTTTTTTTGAAAACGC-AA
1 AATTTTTGAAACACGAAA--TTTTTTTGAAAACACGAA
*
4880591 AAATTTTGAAA
1 AATTTTTGAAA
4880602 AGAAGTATCT
Statistics
Matches: 128, Mismatches: 16, Indels: 19
0.79 0.10 0.12
Matches are distributed among these distances:
34 8 0.06
35 46 0.36
36 49 0.38
37 25 0.20
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (36 bp):
AATTTTTGAAACACGAAATTTTTTTGAAAACACGAA
Found at i:4880578 original size:37 final size:36
Alignment explanation
Indices: 4880481--4880602 Score: 124
Period size: 37 Copynumber: 3.3 Consensus size: 36
4880471 TTAAACTCAA
* *
4880481 AAAATTTTTGAAACACGA-AATTTTTTTGAAAACGCG
1 AAAA-TTTTAAAACACGAGAATTTTTTTGAAAACACG
*
4880517 AAAATTTTTAAACACGAGAATTTTTTTGAAAACACG
1 AAAATTTTAAAACACGAGAATTTTTTTGAAAACACG
* * *
4880553 AGAATTCTTAAAACAC-A-AATTTTTTTTTGAAAACGCA
1 AAAATT-TTAAAACACGAGAA--TTTTTTTGAAAACACG
4880590 AAAATTTTGAAAA
1 AAAATTTT-AAAA
4880603 GAAGTATCTT
Statistics
Matches: 74, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
35 14 0.19
36 29 0.39
37 31 0.42
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (36 bp):
AAAATTTTAAAACACGAGAATTTTTTTGAAAACACG
Found at i:4881294 original size:15 final size:15
Alignment explanation
Indices: 4881274--4881321 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
4881264 TTGGACAGGC
4881274 CTGCTATTTTTTTTG
1 CTGCTATTTTTTTTG
*
4881289 CTGCTAATGTTTTTTTA
1 CTGCT-AT-TTTTTTTG
*
4881306 CTGTTACTTTTTTTTG
1 CTGCTA-TTTTTTTTG
4881322 GGGCTGATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 5 0.19
16 10 0.37
17 12 0.44
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.65
Consensus pattern (15 bp):
CTGCTATTTTTTTTG
Found at i:4881417 original size:7 final size:7
Alignment explanation
Indices: 4881402--4881462 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 7
4881392 ATTTTTATTG
*
4881402 TTTTCTC
1 TTTTTTC
4881409 TTTTTTC
1 TTTTTTC
4881416 TTTCCCTTTC
1 TTT---TTTC
*
4881426 TTCTTTC
1 TTTTTTC
4881433 TTTTTTC
1 TTTTTTC
*
4881440 TTCTTTC
1 TTTTTTC
*
4881447 TTTCTTC
1 TTTTTTC
4881454 TATTTTTC
1 T-TTTTTC
4881462 T
1 T
4881463 CCTTTTTCGT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
7 31 0.72
8 6 0.14
10 6 0.14
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTTC
Found at i:4881440 original size:11 final size:11
Alignment explanation
Indices: 4881407--4881462 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
4881397 TATTGTTTTC
4881407 TCTTTTTTCTT
1 TCTTTTTTCTT
*
4881418 TCCCTTTCTTCTT
1 T--CTTTTTTCTT
4881431 TCTTTTTTC-T
1 TCTTTTTTCTT
4881441 TCTTTCTTTC-T
1 TCTTT-TTTCTT
4881452 TCTATTTTTCT
1 TCT-TTTTTCT
4881463 CCTTTTTCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 6 0.16
11 20 0.53
12 2 0.05
13 10 0.26
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (11 bp):
TCTTTTTTCTT
Found at i:4881441 original size:14 final size:14
Alignment explanation
Indices: 4881422--4881454 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
4881412 TTTCTTTCCC
4881422 TTTCTTCTTTCTTT
1 TTTCTTCTTTCTTT
4881436 TTTCTTCTTTCTTT
1 TTTCTTCTTTCTTT
*
4881450 CTTCT
1 TTTCT
4881455 ATTTTTCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCTTCTTTCTTT
Found at i:4881602 original size:13 final size:13
Alignment explanation
Indices: 4881577--4881612 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
4881567 TTTTCTCTTC
4881577 TTTCTTCTTTACTG
1 TTTCTT-TTTACTG
*
4881591 TTTCTTTTTACTT
1 TTTCTTTTTACTG
4881604 TTTCTTTTT
1 TTTCTTTTT
4881613 CTTGCTGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTCTTTTTACTG
Found at i:4888184 original size:72 final size:72
Alignment explanation
Indices: 4888103--4888250 Score: 269
Period size: 72 Copynumber: 2.1 Consensus size: 72
4888093 ATGGGGTGGA
* *
4888103 ACCATTTATTTTATTTTTGTAAAGAGAGAACGATTCCAGTCTGGATAAATTACCCAAAGAGGAAG
1 ACCATTTATTTTATTTTTGTAAAGAAAGAACGATTCCAGGCTGGATAAATTACCCAAAGAGGAAG
4888168 GGATGGG
66 GGATGGG
*
4888175 ACCATTTATTTTATTTTTGTAAAGAAAGAACGATTCCAGGCTGGATAAATTACCCGAAGAGGAAG
1 ACCATTTATTTTATTTTTGTAAAGAAAGAACGATTCCAGGCTGGATAAATTACCCAAAGAGGAAG
4888240 GGATGGG
66 GGATGGG
4888247 ACCA
1 ACCA
4888251 ACAAGCATAT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (72 bp):
ACCATTTATTTTATTTTTGTAAAGAAAGAACGATTCCAGGCTGGATAAATTACCCAAAGAGGAAG
GGATGGG
Found at i:4888436 original size:144 final size:144
Alignment explanation
Indices: 4888239--4888546 Score: 564
Period size: 144 Copynumber: 2.1 Consensus size: 144
4888229 CGAAGAGGAA
* *
4888239 GGGATGGGACCAACAAGCATATTAGACGATAGAGTCAGTGTAATCAAATTCGTTAGCCTCCCAAT
1 GGGATTGGACCAACAAGCATATTAGACCATAGAGTCAGTGTAATCAAATTCGTTAGCCTCCCAAT
*
4888304 TTCCTGTGGAATGGATCCATTAAGCTGGTTGTCCTGAAGGAGCAACGACTCTAGATTGGTTACAT
66 TTCCTGTGGAATGGATCCATTAAGCTGGTTGTCCTGAAGAAGCAACGACTCTAGATTGGTTACAT
4888369 TGCTGATAGAAGAT
131 TGCTGATAGAAGAT
4888383 GGGATTGGACCAACAAGCATATTAGACCATAGA-TACAGTGTAATCAAATTCGTTAGCCTCCCAA
1 GGGATTGGACCAACAAGCATATTAGACCATAGAGT-CAGTGTAATCAAATTCGTTAGCCTCCCAA
*
4888447 TTTCCTGTGGAATGGATCCATTAAGTTGGTTGTCCTGAAGAAGCAACGACTCTAGATTGGTTACA
65 TTTCCTGTGGAATGGATCCATTAAGCTGGTTGTCCTGAAGAAGCAACGACTCTAGATTGGTTACA
4888512 TTGCTGATAGAAGAT
130 TTGCTGATAGAAGAT
4888527 GGGATTGGACCAACAAGCAT
1 GGGATTGGACCAACAAGCAT
4888547 GTTGTTCGAG
Statistics
Matches: 159, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
143 1 0.01
144 158 0.99
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (144 bp):
GGGATTGGACCAACAAGCATATTAGACCATAGAGTCAGTGTAATCAAATTCGTTAGCCTCCCAAT
TTCCTGTGGAATGGATCCATTAAGCTGGTTGTCCTGAAGAAGCAACGACTCTAGATTGGTTACAT
TGCTGATAGAAGAT
Found at i:4889948 original size:37 final size:37
Alignment explanation
Indices: 4889886--4890231 Score: 633
Period size: 37 Copynumber: 9.4 Consensus size: 37
4889876 TACGTATGAT
* *
4889886 CACTTATCAA-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
*
4889921 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
*
4889958 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
4889995 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
4890032 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
4890069 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
4890106 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
4890143 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
4890180 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
*
4890217 CACTTATCACTTTGT
1 CACTTATCAATTTGT
4890232 NNNNNNNNNN
Statistics
Matches: 304, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
35 9 0.03
36 3 0.01
37 292 0.96
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (37 bp):
CACTTATCAATTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:4905853 original size:28 final size:30
Alignment explanation
Indices: 4905816--4905871 Score: 55
Period size: 28 Copynumber: 1.9 Consensus size: 30
4905806 TTCTTTTAAA
* *
4905816 ATTTTAAAAATTTTAAAA-TATA-AAAA-TT
1 ATTTTAAAAAATTAAAAAGTA-ATAAAAATT
*
4905844 ATTTTTAAAAATTAAAAAGTAATAAAAA
1 ATTTTAAAAAATTAAAAAGTAATAAAAA
4905872 ATATAAATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
28 16 0.73
29 6 0.27
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (30 bp):
ATTTTAAAAAATTAAAAAGTAATAAAAATT
Found at i:4906882 original size:7 final size:7
Alignment explanation
Indices: 4906870--4906897 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
4906860 AGTTACTATA
4906870 CTAAATT
1 CTAAATT
4906877 CTAAATT
1 CTAAATT
4906884 CTAAATT
1 CTAAATT
4906891 CTAAATT
1 CTAAATT
4906898 TGTGTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (7 bp):
CTAAATT
Found at i:4910723 original size:21 final size:19
Alignment explanation
Indices: 4910698--4910737 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
4910688 AAATTTATTC
4910698 TATATTAAATCATTATTTAAA
1 TATATTAAAT--TTATTTAAA
*
4910719 TATATTTAATTTATTTAAA
1 TATATTAAATTTATTTAAA
4910738 ATTCAACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATTAAATTTATTTAAA
Found at i:4915277 original size:100 final size:100
Alignment explanation
Indices: 4915079--4915299 Score: 270
Period size: 100 Copynumber: 2.2 Consensus size: 100
4915069 TTGGTCGTAT
* *
4915079 CGCCACATTTGGTGTTGGCACCAAATGAATTTTTTTATTAGATTTTGGTGCCTCCACATGAAGAG
1 CGCCACATTTGGAGTTGGCACCAAAGGAATTTTTTTATTAGATTTTGGTGCCTCCACATGAAGAG
* *
4915144 ACGACATCGAAAAATTCAAAAAAAATTATTGGTGT
66 ACGACATCGAAAAATTCAAAAAAAATTACTGGTGC
* * *
4915179 TGCCACATTTGGAGTTGGCACC-AGGGAATTTTTTT-TATAGATTTTGGTGCCTCCACATGAGGA
1 CGCCACATTTGGAGTTGGCACCAAAGGAATTTTTTTAT-TAGATTTTGGTGCCTCCACATGAAGA
* * *
4915242 GACGATATC-AAAATTTTGTTAAAAAAAA-TACTGGTGC
65 GACGACATCGAAAA--AT-TCAAAAAAAATTACTGGTGC
* *
4915279 CACCACATCTGGAGTTGGCAC
1 CGCCACATTTGGAGTTGGCAC
4915300 TAAGGGAAAC
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
98 5 0.05
99 44 0.42
100 46 0.44
101 9 0.09
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (100 bp):
CGCCACATTTGGAGTTGGCACCAAAGGAATTTTTTTATTAGATTTTGGTGCCTCCACATGAAGAG
ACGACATCGAAAAATTCAAAAAAAATTACTGGTGC
Found at i:4915862 original size:16 final size:15
Alignment explanation
Indices: 4915833--4915861 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4915823 GGATATAGTA
4915833 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
4915848 AAATATTTAAAAAA
1 AAATATTTAAAAAA
4915862 AAGAGACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:4916463 original size:16 final size:15
Alignment explanation
Indices: 4916444--4916485 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
4916434 TAATAAACAA
4916444 ATATTATTTTAAATAT
1 ATATT-TTTTAAATAT
*
4916460 ATA-TTTTTAATTAT
1 ATATTTTTTAAATAT
4916474 ATATTTTATTAA
1 ATATTTT-TTAA
4916486 TGATTTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 12 0.52
15 4 0.17
16 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATTTTTTAAATAT
Found at i:4916467 original size:14 final size:14
Alignment explanation
Indices: 4916442--4916480 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4916432 TATAATAAAC
4916442 AAATAT-TA-TTTT
1 AAATATATATTTTT
4916454 AAATATATATTTTT
1 AAATATATATTTTT
*
4916468 AATTATATATTTT
1 AAATATATATTTT
4916481 ATTAATGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 6 0.25
13 2 0.08
14 16 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AAATATATATTTTT
Found at i:4923074 original size:15 final size:16
Alignment explanation
Indices: 4923046--4923081 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
4923036 TACCTTTTTT
4923046 TTTTTACTTCATTTCC
1 TTTTTACTTCATTTCC
*
4923062 TTTTTCCTT-ATTTCC
1 TTTTTACTTCATTTCC
4923077 TTTTT
1 TTTTT
4923082 TTTCCGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTACTTCATTTCC
Found at i:4923081 original size:16 final size:17
Alignment explanation
Indices: 4923045--4923082 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
4923035 TTACCTTTTT
4923045 TTTTTTACTTCATTTCC
1 TTTTTTACTTCATTTCC
*
4923062 -TTTTTCCTT-ATTTCC
1 TTTTTTACTTCATTTCC
4923077 TTTTTT
1 TTTTTT
4923083 TTCCGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTACTTCATTTCC
Found at i:4934531 original size:41 final size:41
Alignment explanation
Indices: 4934335--4934519 Score: 307
Period size: 41 Copynumber: 4.5 Consensus size: 41
4934325 ACCGGCACTT
* * * *
4934335 AGCCTGCTAGACATAAAGTCTGATATGTTTCACTGGCATCA
1 AGCCTGCTAGACGTAATGTCTGGTATGTTTCACCGGCATCA
*
4934376 AGCCTGTTAGACGTAATGTCTGGTATGTTTCACCGGCATCA
1 AGCCTGCTAGACGTAATGTCTGGTATGTTTCACCGGCATCA
*
4934417 AGCCTGCTAGACGTAATTTCTGGTATGTTTCACCGGCATCA
1 AGCCTGCTAGACGTAATGTCTGGTATGTTTCACCGGCATCA
*
4934458 AGCCTGCTAGATGTAATGTCTGGTATGTTTCACCGGCATCA
1 AGCCTGCTAGACGTAATGTCTGGTATGTTTCACCGGCATCA
4934499 AGCCTGCTAGACGTAATGTCT
1 AGCCTGCTAGACGTAATGTCT
4934520 AGATTACTTC
Statistics
Matches: 134, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 134 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (41 bp):
AGCCTGCTAGACGTAATGTCTGGTATGTTTCACCGGCATCA
Found at i:4934719 original size:12 final size:12
Alignment explanation
Indices: 4934702--4934726 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4934692 AAATTCATAA
4934702 ACATATATATAT
1 ACATATATATAT
4934714 ACATATATATAT
1 ACATATATATAT
4934726 A
1 A
4934727 AAGTCGAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ACATATATATAT
Found at i:4935162 original size:2 final size:2
Alignment explanation
Indices: 4935157--4935194 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
4935147 ATTCGAATCT
*
4935157 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4935195 CTTTGATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4935246 original size:39 final size:40
Alignment explanation
Indices: 4935172--4935247 Score: 95
Period size: 39 Copynumber: 1.9 Consensus size: 40
4935162 ATATATATAT
* *
4935172 ATATATATATATAATATACATATCTTTGATTAAACCTAGA
1 ATATATACATATAATATACATATATTTGATTAAACCTAGA
4935212 ATATATACATAT-ATATAC-TCATATTTG-TTCAAACCT
1 ATATATACATATAATATACAT-ATATTTGATT-AAACCT
4935248 TGTGCACTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
38 3 0.09
39 18 0.56
40 11 0.34
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.41
Consensus pattern (40 bp):
ATATATACATATAATATACATATATTTGATTAAACCTAGA
Found at i:4940144 original size:34 final size:34
Alignment explanation
Indices: 4940101--4940176 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
4940091 CATTTTTTTT
*
4940101 TTTGGTGTGCTAGATGGATCAGCTCATATGAGCA
1 TTTGGTGTGCTAGATGGATCAGCTCATACGAGCA
* * *
4940135 TTTGGTGTGCTGGATGGATTAGCTCTTACGAGCA
1 TTTGGTGTGCTAGATGGATCAGCTCATACGAGCA
*
4940169 TCTGGTGT
1 TTTGGTGT
4940177 AACACCCTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.18, C:0.14, G:0.32, T:0.36
Consensus pattern (34 bp):
TTTGGTGTGCTAGATGGATCAGCTCATACGAGCA
Found at i:4941979 original size:43 final size:43
Alignment explanation
Indices: 4941929--4942033 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 43
4941919 TCCTAGATAT
* * *
4941929 GGTCTTACATGTTATCACATATCGATACCACTACCCCAGACAG
1 GGTCTTACACGTAATCACATATCGATACCAATACCCCAGACAG
* * ** *
4941972 GGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACAT
1 GGTCTTACACGTAATCACATATCGATACCAATACCCCAGACAG
*
4942015 GGTCTTACACGAAATCACA
1 GGTCTTACACGTAATCACA
4942034 CTCCAAGAGT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGTAATCACATATCGATACCAATACCCCAGACAG
Found at i:4946646 original size:60 final size:60
Alignment explanation
Indices: 4946580--4946698 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 60
4946570 AAAAAAAACT
* * *
4946580 AAAATAAATTTTCAAACAATAAATTTTATATATTATGACGAGAT-GACCATACTAGTTGAG
1 AAAATAAATTTTCAAACAATAAATTGTATATATTATCACGAGATCG-CCATACTAATTGAG
** *
4946640 AAAATAAATTTTCAAACAATGTATTGTATATATTATCATGAGATCGCCATACTAATTGA
1 AAAATAAATTTTCAAACAATAAATTGTATATATTATCACGAGATCGCCATACTAATTGA
4946699 TTTATCAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 51 0.98
61 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (60 bp):
AAAATAAATTTTCAAACAATAAATTGTATATATTATCACGAGATCGCCATACTAATTGAG
Found at i:4947163 original size:12 final size:13
Alignment explanation
Indices: 4947146--4947175 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4947136 CTAAGAGACT
4947146 AAAAA-TATATTA
1 AAAAATTATATTA
4947158 AAAAATTATATTA
1 AAAAATTATATTA
4947171 AAAAA
1 AAAAA
4947176 CACTATCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAAATTATATTA
Found at i:4947236 original size:40 final size:42
Alignment explanation
Indices: 4947162--4947242 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 42
4947152 ATATTAAAAA
* * *
4947162 ATTATATTAAAAAACACTATCATAAATTTGATAAATGTTTTT
1 ATTATATTAAAAAACACTATAATAAATATGATAAATATTTTT
*
4947204 ATTATATTAAAAATCAC-A-AATAAATATGATAAATATTTT
1 ATTATATTAAAAAACACTATAATAAATATGATAAATATTTT
4947243 AGGCATAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 18 0.51
41 1 0.03
42 16 0.46
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (42 bp):
ATTATATTAAAAAACACTATAATAAATATGATAAATATTTTT
Found at i:4947519 original size:20 final size:22
Alignment explanation
Indices: 4947484--4947523 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
4947474 CAGTAAATGG
4947484 TTTTAAAATTATTAAAATTATT
1 TTTTAAAATTATTAAAATTATT
4947506 TTTTAAAA-TA-TAAAATTA
1 TTTTAAAATTATTAAAATTA
4947524 CTAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 2 0.11
22 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTAAAATTATTAAAATTATT
Done.