Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 75 of 226
Found at i:27851719 original size:21 final size:20
Alignment explanation
Indices: 27851681--27851720 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
27851671 GTTTTCAAAC
*
27851681 AAATTTCGTGTTTAAAAAAG
1 AAATTTCGTGGTTAAAAAAG
*
27851701 AAATTCTCGTGGTTCAAAAA
1 AAATT-TCGTGGTTAAAAAA
27851721 TTTCCGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (20 bp):
AAATTTCGTGGTTAAAAAAG
Found at i:27859848 original size:18 final size:18
Alignment explanation
Indices: 27859813--27859857 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
27859803 GCAATAACTG
*
27859813 ACGTTTTGAAAATTAATA
1 ACGTTTTGAAAATGAATA
27859831 ACGTTTTGAAAGA-GAATA
1 ACGTTTTGAAA-ATGAATA
27859849 AC-TTTTGAA
1 ACGTTTTGAA
27859858 TACGAATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 7 0.28
18 17 0.68
19 1 0.04
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.36
Consensus pattern (18 bp):
ACGTTTTGAAAATGAATA
Found at i:27860914 original size:67 final size:66
Alignment explanation
Indices: 27860686--27860904 Score: 264
Period size: 67 Copynumber: 3.3 Consensus size: 66
27860676 ACCATAGCCT
* * * * * * *
27860686 AGCTATGATCTTACGCATCTT-ACTCTATGTTTAATGTCCTAGCAGACTCTTTATGTTGCCTTAG
1 AGCTATGGTCTTACACATCTTGTC-CCATGTTTAATGTCCTAG-AGACTCTCTATGTTGTCATAG
*
27860750 TCGA
64 T-AA
27860754 A-CTATGGTCTTACACATCTTGTCCCATGTTTAATGTCCTAGCAGACTCTCTATGTTGTCATAGT
1 AGCTATGGTCTTACACATCTTGTCCCATGTTTAATGTCCTAG-AGACTCTCTATGTTGTCATAGT
*
27860818 AG
65 AA
* *
27860820 AGCTATGGTTTTACACATCTTGTCCCATGTTTAATGT-CTTGATGGACTCTCTATGTTGTCATAG
1 AGCTATGGTCTTACACATCTTGTCCCATGTTTAATGTCCTAGA--GACTCTCTATGTTGTCATAG
27860884 TAA
64 TAA
27860887 AGCTATGGTCTTACACAT
1 AGCTATGGTCTTACACAT
27860905 TATACCCCAT
Statistics
Matches: 134, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
65 1 0.01
66 4 0.03
67 127 0.95
68 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (66 bp):
AGCTATGGTCTTACACATCTTGTCCCATGTTTAATGTCCTAGAGACTCTCTATGTTGTCATAGTA
A
Found at i:27864250 original size:2 final size:2
Alignment explanation
Indices: 27864232--27864270 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
27864222 TATATAAGGC
27864232 TA TA TCA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27864271 GCAACGATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:27864378 original size:247 final size:247
Alignment explanation
Indices: 27863861--27864336 Score: 671
Period size: 247 Copynumber: 1.9 Consensus size: 247
27863851 ATATTAGTAG
* *
27863861 AGTAATACATAATATATTAATTATTTTCATATAT-TATTGTTTATTATACTAGTTGAAATATACT
1 AGTAGTACATTATATATTAATTA--TT-ATAT-TGT-TTG-TTATTATACTAGTTGAAATATACT
** * *
27863925 CTAAGTCCCTATACTTTTCATATTTTTGAAAGTTAGCCCTCCTACTATATTATATAATGCTATAT
60 CTAAGTCCCTATACTTTTCATACATTTGAAAGTTAACCCTCCTACTATATTATATAAGGCTATAT
* * *
27863990 CATATTATATGGTATATAATATATTAATAATTCATATATATGCATCAATAATTAAACATTATAAT
125 CATATAATATGATATATAATATATTAATAATTCATATATATGCAACAATAATTAAACATTATAAT
27864055 ATCATGTAATACTATATATTTTATTAGAATCTATAATATAATTATAGTTATATATAAT
190 ATCATGTAATACTATATATTTTATTAGAATCTATAATATAATTATAGTTATATATAAT
* *
27864113 AGTAGTACATTATATATTAATTATTATATTGTTTGTTATTATACTGGTTGAAATATGCTCTAAGT
1 AGTAGTACATTATATATTAATTATTATATTGTTTGTTATTATACTAGTTGAAATATACTCTAAGT
* * *
27864178 CCTTATATTTTTCATACATTTGAAAGTTAATCCTCCTACTATATTATATAAGGCTATATCATATA
66 CCCTATACTTTTCATACATTTGAAAGTTAACCCTCCTACTATATTATATAAGGCTATATCATATA
*
27864243 ATAT-ATATAT-ATATA-T-AT-A-T-ATATATATGCAACGATAATTAAACATTATAATATCATG
131 ATATGATATATAATATATTAATAATTCATATATATGCAACAATAATTAAACATTATAATATCATG
* * * *
27864301 TAATATTATATCTTTTATTATAATCTATATTATAAT
196 TAATACTATATATTTTATTAGAATCTATAATATAAT
27864337 ACTTATGTAT
Statistics
Matches: 204, Mismatches: 19, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
240 68 0.33
241 1 0.00
242 1 0.00
243 2 0.01
244 1 0.00
245 5 0.02
246 5 0.02
247 89 0.44
248 4 0.02
249 5 0.02
250 2 0.01
252 21 0.10
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.45
Consensus pattern (247 bp):
AGTAGTACATTATATATTAATTATTATATTGTTTGTTATTATACTAGTTGAAATATACTCTAAGT
CCCTATACTTTTCATACATTTGAAAGTTAACCCTCCTACTATATTATATAAGGCTATATCATATA
ATATGATATATAATATATTAATAATTCATATATATGCAACAATAATTAAACATTATAATATCATG
TAATACTATATATTTTATTAGAATCTATAATATAATTATAGTTATATATAAT
Found at i:27864578 original size:29 final size:28
Alignment explanation
Indices: 27864541--27864596 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
27864531 TTTATTACAC
27864541 ATATATAATT-ATAGTATTAAAAATATTTT
1 ATATATAATTAATA-TATTAAAAA-ATTTT
* *
27864570 ATATTTAATTAATATTTTAAAAAATTT
1 ATATATAATTAATATATTAAAAAATTT
27864597 ATTTCACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 17 0.71
30 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
ATATATAATTAATATATTAAAAAATTTT
Found at i:27867773 original size:82 final size:82
Alignment explanation
Indices: 27867577--27867873 Score: 274
Period size: 82 Copynumber: 3.6 Consensus size: 82
27867567 ACACCAGCAT
* * * * * ** * *
27867577 AAAGCCTACTAGGCTC-AAGGCTAGATACAACACATCGGCACAAAGCCAGCTAGGTACAAAGCCT
1 AAAGCCTGCTAGGCTCAAAGCCT-GATATAACACACCGGTATGAAGCCTGCTAGGCACAAAGCCT
* *
27867641 GATATAATACACCGATAC
65 GATATAATACAACGGTAC
* * * * * *
27867659 GAAGCCTGCAAAGCTTAAAGCCTAATATAACACACTGGTATGAAGCCTGCTAGGCACAAAGCCTG
1 AAAGCCTGCTAGGCTCAAAGCCTGATATAACACACCGGTATGAAGCCTGCTAGGCACAAAGCCTG
27867724 ATATAATACAACGGTAC
66 ATATAATACAACGGTAC
* * * ** * * * * *
27867741 AAAGCTTGCTAGGCTCAAAACCTGATAAAACACACCGACACGAAGCTTGATAAGCACAAAGCCTA
1 AAAGCCTGCTAGGCTCAAAGCCTGATATAACACACCGGTATGAAGCCTGCTAGGCACAAAGCCTG
* *
27867806 ATGTAATAC-ACTGGCAC
66 ATATAATACAAC-GGTAC
* * *
27867823 AAAACCTGCTAGGCTCAAAGCCTGATATAATACACCGGTATGAAGCTTGCT
1 AAAGCCTGCTAGGCTCAAAGCCTGATATAACACACCGGTATGAAGCCTGCT
27867874 GGACTCAAGG
Statistics
Matches: 169, Mismatches: 44, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
81 2 0.01
82 162 0.96
83 5 0.03
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (82 bp):
AAAGCCTGCTAGGCTCAAAGCCTGATATAACACACCGGTATGAAGCCTGCTAGGCACAAAGCCTG
ATATAATACAACGGTAC
Found at i:27867802 original size:123 final size:123
Alignment explanation
Indices: 27867616--27867881 Score: 313
Period size: 123 Copynumber: 2.2 Consensus size: 123
27867606 ACACATCGGC
** * * * * **
27867616 ACAAAGCCAGCTAGG-TACAAAGCCTGATATAATACACCGATACGAAGCCTGCAAAGCTTAAAGC
1 ACAAAGCTTGCTAGGCT-CAAAACCTGATAAAACACACCGACACGAAGCCTGCAAAGCACAAAGC
* ** *
27867680 CTAATATAACACACTGGTATGAAGCCTGCTAGGCACAAAGCCTGATATAATACAACGGT
65 CTAATATAACACACTGGCACAAAACCTGCTAGGCACAAAGCCTGATATAATACAACGGT
*
27867739 ACAAAGCTTGCTAGGCTCAAAACCTGATAAAACACACCGACACGAAGCTTG-ATAAGCACAAAGC
1 ACAAAGCTTGCTAGGCTCAAAACCTGATAAAACACACCGACACGAAGCCTGCA-AAGCACAAAGC
* * * *
27867803 CTAATGTAATACACTGGCACAAAACCTGCTAGGCTCAAAGCCTGATATAATACACCGGT
65 CTAATATAACACACTGGCACAAAACCTGCTAGGCACAAAGCCTGATATAATACAACGGT
**
27867862 ATGAAGCTTGCT-GGACTCAA
1 ACAAAGCTTGCTAGG-CTCAA
27867882 GGCCCGATAC
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
122 3 0.02
123 117 0.97
124 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (123 bp):
ACAAAGCTTGCTAGGCTCAAAACCTGATAAAACACACCGACACGAAGCCTGCAAAGCACAAAGCC
TAATATAACACACTGGCACAAAACCTGCTAGGCACAAAGCCTGATATAATACAACGGT
Found at i:27867881 original size:41 final size:41
Alignment explanation
Indices: 27867578--27867890 Score: 227
Period size: 41 Copynumber: 7.6 Consensus size: 41
27867568 CACCAGCATA
* * * * * * *
27867578 AAGCCTACTAGGCTC-AAGGCTAGATACAACACATCGGCACA
1 AAGCCTGCTAGGCTCAAAGCCT-GATATAATACACCGGTACG
* *
27867619 AAGCCAGCTAGG-TACAAAGCCTGATATAATACACCGATACG
1 AAGCCTGCTAGGCT-CAAAGCCTGATATAATACACCGGTACG
* * * * * * *
27867660 AAGCCTGCAAAGCTTAAAGCCTAATATAACACACTGGTATG
1 AAGCCTGCTAGGCTCAAAGCCTGATATAATACACCGGTACG
* * *
27867701 AAGCCTGCTAGGCACAAAGCCTGATATAATACAACGGTACA
1 AAGCCTGCTAGGCTCAAAGCCTGATATAATACACCGGTACG
* * * * **
27867742 AAGCTTGCTAGGCTCAAAACCTGATAAAACACACCGACACG
1 AAGCCTGCTAGGCTCAAAGCCTGATATAATACACCGGTACG
* * * * * * * * *
27867783 AAGCTTGATAAGCACAAAGCCTAATGTAATACACTGGCACA
1 AAGCCTGCTAGGCTCAAAGCCTGATATAATACACCGGTACG
* *
27867824 AAACCTGCTAGGCTCAAAGCCTGATATAATACACCGGTATG
1 AAGCCTGCTAGGCTCAAAGCCTGATATAATACACCGGTACG
* * *
27867865 AAGCTTGCT-GGACTCAAGGCCCGATA
1 AAGCCTGCTAGG-CTCAAAGCCTGATA
27867891 CACTATCTCC
Statistics
Matches: 205, Mismatches: 63, Indels: 8
0.74 0.23 0.03
Matches are distributed among these distances:
40 3 0.01
41 196 0.96
42 6 0.03
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.18
Consensus pattern (41 bp):
AAGCCTGCTAGGCTCAAAGCCTGATATAATACACCGGTACG
Found at i:27869179 original size:66 final size:66
Alignment explanation
Indices: 27869073--27869196 Score: 248
Period size: 66 Copynumber: 1.9 Consensus size: 66
27869063 CATTTCAGAG
27869073 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
1 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
27869138 T
66 T
27869139 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCC
1 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCC
27869197 CGTAATATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.27, C:0.38, G:0.18, T:0.18
Consensus pattern (66 bp):
AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
T
Found at i:27871032 original size:23 final size:23
Alignment explanation
Indices: 27871006--27871059 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
27870996 TACTAAATAA
* *
27871006 ATTAATAACAAT-AAAATAATAT
1 ATTAATAAAAATCAAAATAAAAT
*
27871028 CATTAA-AAAAATCAAATTAAAAT
1 -ATTAATAAAAATCAAAATAAAAT
27871051 ATTAATAAA
1 ATTAATAAA
27871060 CTAATATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.30
Consensus pattern (23 bp):
ATTAATAAAAATCAAAATAAAAT
Found at i:27876959 original size:21 final size:21
Alignment explanation
Indices: 27876920--27876959 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27876910 AATTAAGGAC
* **
27876920 AAATTGAGATTGTGCAAATTG
1 AAATTGAAATTGTAAAAATTG
27876941 AAATTGAAATTGTAAAAAT
1 AAATTGAAATTGTAAAAAT
27876960 AAACAGAGTC
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:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (21 bp):
AAATTGAAATTGTAAAAATTG
Found at i:27879275 original size:5 final size:5
Alignment explanation
Indices: 27879258--27879288 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
27879248 AAGAAAATAG
27879258 AAAAT ATAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT
27879289 TGGGTTGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:27879966 original size:38 final size:38
Alignment explanation
Indices: 27879924--27879999 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
27879914 CATTTTTATC
*
27879924 ACATAAAAGCCCGCAGGAAAGATAAGTCCGTTGGCTTT
1 ACATAAAAGCCCACAGGAAAGATAAGTCCGTTGGCTTT
*
27879962 ACATAAAAGTCCACAGGAAAGATAAGTCCGTTGGCTTT
1 ACATAAAAGCCCACAGGAAAGATAAGTCCGTTGGCTTT
27880000 CACTAATACG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (38 bp):
ACATAAAAGCCCACAGGAAAGATAAGTCCGTTGGCTTT
Found at i:27881046 original size:409 final size:410
Alignment explanation
Indices: 27880286--27881115 Score: 1518
Period size: 409 Copynumber: 2.0 Consensus size: 410
27880276 TCCAGTCAAT
27880286 TTTTGCTTGTTGATGCAAAGCTCCTTAAGGAACTTGGCATATCATGAAATTTGTTTGATGGCATC
1 TTTTGCTTGTTGATGCAAAGCTCCTTAAGGAACTTGGCATATCATGAAATTTGTTTGATGGCATC
*
27880351 TAACAATGGTATGTTGATCTCGACATTTATAAATTTTTCGAGGATCTCTTTTTCCCCCTTACCTC
66 CAACAATGGTATGTTGATCTCGACATTTATAAATTTTTCGAGGATCTCTTTTTCCCCCTTACCTC
* *
27880416 TCCGATATTGGCTCAATCGTCCTATAAACGGTGGTTGAATTATGGGCAATGGAGGTTTCGTTCAG
131 ACCGATATTGGCTCAATCGTCCTAGAAACGGTGGTTGAATTATGGGCAATGGAGGTTTCGTTCAG
*
27880481 ACCTGTTCATCGTTCTCTTTCTTTTTCTAGGCAAAATCTTGATCAAGGTTCCTGCCAGGATTCGG
196 ACCTGTTCATCGTTCTCTTTCTTTTTCTAGGCAAAATCTTGATCAAGATTCCTGCCAGGATTCGG
27880546 TTCCAGTACTTTTCCACTTCGTAACGTCACTGCATTTGCGTATTGTCTTGGGTTAGATTCCGTTT
261 TTCCAGTACTTTTCCACTTCGTAACGTCACTGCATTTGCGTATTGTCTTGGGTTAGATTCCGTTT
*
27880611 GTGATGGCAGCTTTCCTTATGAGTTCATTTTCTCAATTGATGTAGTCAACTCTCTTATGGATGCC
326 GTGATGGCAGCTTTCCTTATGAGTTCATTTTCTCAATTGATGTAGTCAACTCTCTTATAGATGCC
27880676 TCAATTTTCTGTTGAAAATC
391 TCAATTTTCTGTTGAAAATC
27880696 TTTTGCTTGTTGATGCAAAGCTCCTTAAGGAACTTGGCATATCATGAAATTTGTTTGATGGCATC
1 TTTTGCTTGTTGATGCAAAGCTCCTTAAGGAACTTGGCATATCATGAAATTTGTTTGATGGCATC
*
27880761 CAACAATGGTATGTTGATCTCGACATTTCTAAATTTTTCGAGGATCTCTTTTT-CCCCTTACCTC
66 CAACAATGGTATGTTGATCTCGACATTTATAAATTTTTCGAGGATCTCTTTTTCCCCCTTACCTC
* * * *
27880825 ACCGATGTTGGCTCAATCGTCCTAGAAACGGTGGTTGAATTATGGGTAATGGATGTTTTGTTCAG
131 ACCGATATTGGCTCAATCGTCCTAGAAACGGTGGTTGAATTATGGGCAATGGAGGTTTCGTTCAG
**
27880890 ACCTGTTCATCGTTCTCTTTCTTTTTCTAGGTGAAATCTTGATCAAGATTCCTGCCAGGATTCGG
196 ACCTGTTCATCGTTCTCTTTCTTTTTCTAGGCAAAATCTTGATCAAGATTCCTGCCAGGATTCGG
27880955 TTCCAGTACTTTTCCACTTCGTAACGTCACTGCATTTGCGTATTGTCTTGGGTTAGATTCCGTTT
261 TTCCAGTACTTTTCCACTTCGTAACGTCACTGCATTTGCGTATTGTCTTGGGTTAGATTCCGTTT
* *
27881020 GTGATGGCAGCTTTCCTTGTGAGTTCATTTTCTCAATTGATGTAGTTAACTCTCTTATAGATGCC
326 GTGATGGCAGCTTTCCTTATGAGTTCATTTTCTCAATTGATGTAGTCAACTCTCTTATAGATGCC
27881085 TCAATTTTCTGTTGAAAATC
391 TCAATTTTCTGTTGAAAATC
*
27881105 TTTTGTTTGTT
1 TTTTGCTTGTT
27881116 TTTGGAGATA
Statistics
Matches: 405, Mismatches: 15, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
409 289 0.71
410 116 0.29
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (410 bp):
TTTTGCTTGTTGATGCAAAGCTCCTTAAGGAACTTGGCATATCATGAAATTTGTTTGATGGCATC
CAACAATGGTATGTTGATCTCGACATTTATAAATTTTTCGAGGATCTCTTTTTCCCCCTTACCTC
ACCGATATTGGCTCAATCGTCCTAGAAACGGTGGTTGAATTATGGGCAATGGAGGTTTCGTTCAG
ACCTGTTCATCGTTCTCTTTCTTTTTCTAGGCAAAATCTTGATCAAGATTCCTGCCAGGATTCGG
TTCCAGTACTTTTCCACTTCGTAACGTCACTGCATTTGCGTATTGTCTTGGGTTAGATTCCGTTT
GTGATGGCAGCTTTCCTTATGAGTTCATTTTCTCAATTGATGTAGTCAACTCTCTTATAGATGCC
TCAATTTTCTGTTGAAAATC
Found at i:27891238 original size:5 final size:5
Alignment explanation
Indices: 27891228--27891269 Score: 75
Period size: 5 Copynumber: 8.2 Consensus size: 5
27891218 TTGCAAGCTA
27891228 GGTTT GGTTT GGTTT GGTTT GGTTT GGTTT GGTTTT GGTTT G
1 GGTTT GGTTT GGTTT GGTTT GGTTT GGTTT GG-TTT GGTTT G
27891270 TTGGGTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 31 0.86
6 5 0.14
ACGTcount: A:0.00, C:0.00, G:0.40, T:0.60
Consensus pattern (5 bp):
GGTTT
Found at i:27891276 original size:15 final size:16
Alignment explanation
Indices: 27891230--27891278 Score: 75
Period size: 15 Copynumber: 3.2 Consensus size: 16
27891220 GCAAGCTAGG
27891230 TTTGGTTTGGTTTGG-
1 TTTGGTTTGGTTTGGT
27891245 TTTGGTTTGGTTTGGT
1 TTTGGTTTGGTTTGGT
*
27891261 TTTGGTTT-GTTGGGT
1 TTTGGTTTGGTTTGGT
27891276 TTT
1 TTT
27891279 TCCATTCACA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 24 0.75
16 8 0.25
ACGTcount: A:0.00, C:0.00, G:0.37, T:0.63
Consensus pattern (16 bp):
TTTGGTTTGGTTTGGT
Found at i:27891796 original size:11 final size:11
Alignment explanation
Indices: 27891780--27891804 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27891770 CCCAATTTCT
27891780 TAGTTAGAAAA
1 TAGTTAGAAAA
27891791 TAGTTAGAAAA
1 TAGTTAGAAAA
27891802 TAG
1 TAG
27891805 AACTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (11 bp):
TAGTTAGAAAA
Found at i:27891907 original size:3 final size:3
Alignment explanation
Indices: 27891899--27891945 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
27891889 GTAGGGAAGC
27891899 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
27891946 CCACTAATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27892492 original size:13 final size:13
Alignment explanation
Indices: 27892474--27892498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27892464 TTTATTAGTG
27892474 AAAGAGTACATAT
1 AAAGAGTACATAT
27892487 AAAGAGTACATA
1 AAAGAGTACATA
27892499 CAAATTTGAT
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:0.16, T:0.20
Consensus pattern (13 bp):
AAAGAGTACATAT
Found at i:27892505 original size:51 final size:52
Alignment explanation
Indices: 27892403--27892509 Score: 144
Period size: 53 Copynumber: 2.1 Consensus size: 52
27892393 CTTTTTACTA
* **
27892403 ATATATAATTTATTAGTGAAAGCGTACATAAAAAAAAAATTGATACAAATTTG
1 ATATATAATTTATTAGTGAAAGAGTACAT-AAAAAAAAATACATACAAATTTG
* * *
27892456 ATATATAATTTATTAGTGAAAGAGTACAT-ATAAAGAGTACATACAAATTTG
1 ATATATAATTTATTAGTGAAAGAGTACATAAAAAAAAATACATACAAATTTG
27892507 ATA
1 ATA
27892510 CTAATAGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
51 20 0.42
53 28 0.58
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.33
Consensus pattern (52 bp):
ATATATAATTTATTAGTGAAAGAGTACATAAAAAAAAATACATACAAATTTG
Found at i:27896084 original size:16 final size:17
Alignment explanation
Indices: 27896065--27896110 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
27896055 TTATTAAATT
*
27896065 ATATATGTT-AATTATA
1 ATATATGTTAAATAATA
27896081 ATATAT-TTAAATAATA
1 ATATATGTTAAATAATA
27896097 AT-TATGTTTAAATA
1 ATATATG-TTAAATA
27896111 TGGATTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 5 0.19
16 14 0.54
17 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (17 bp):
ATATATGTTAAATAATA
Found at i:27896343 original size:15 final size:15
Alignment explanation
Indices: 27896323--27896353 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
27896313 GATTTGCTAT
27896323 TACACCTCTATTCCA
1 TACACCTCTATTCCA
27896338 TACACCTCTATTCCA
1 TACACCTCTATTCCA
27896353 T
1 T
27896354 TACGCCTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.39, G:0.00, T:0.35
Consensus pattern (15 bp):
TACACCTCTATTCCA
Found at i:27897061 original size:31 final size:29
Alignment explanation
Indices: 27897002--27897063 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 29
27896992 TTAACAACCT
*
27897002 AATAACTTAAATAAAAATTTGAATAGTTC
1 AATAACTTAAATAAAAATTTAAATAGTTC
**
27897031 AATAACTTAAATGAATACGTTTAAATAGTTC
1 AATAACTTAAAT-AA-AAATTTAAATAGTTC
27897062 AA
1 AA
27897064 AATCAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 12 0.43
30 2 0.07
31 14 0.50
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (29 bp):
AATAACTTAAATAAAAATTTAAATAGTTC
Found at i:27900048 original size:11 final size:10
Alignment explanation
Indices: 27900033--27900136 Score: 60
Period size: 10 Copynumber: 10.6 Consensus size: 10
27900023 ATTACTAAAA
27900033 ATAATTTAAT
1 ATAATTTAAT
27900043 AATAA-TTAAT
1 -ATAATTTAAT
27900053 -TAA-TTAAT
1 ATAATTTAAT
*
27900061 CATATTTTAAT
1 -ATAATTTAAT
27900072 ATAA-TT-AT
1 ATAATTTAAT
*
27900080 -T-ATTAAAT
1 ATAATTTAAT
27900088 ATAATTTAAT
1 ATAATTTAAT
* * *
27900098 AAAAATAATAT
1 ATAATTTA-AT
27900109 ATAATTTAAT
1 ATAATTTAAT
*
27900119 AATATTTTTAAT
1 -ATA-ATTTAAT
27900131 ATAATT
1 ATAATT
27900137 ATTTTATATT
Statistics
Matches: 71, Mismatches: 12, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
6 1 0.01
7 2 0.03
8 12 0.17
9 3 0.04
10 25 0.35
11 22 0.31
12 6 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTAAT
Found at i:27900084 original size:26 final size:25
Alignment explanation
Indices: 27900037--27900139 Score: 71
Period size: 29 Copynumber: 3.6 Consensus size: 25
27900027 CTAAAAATAA
27900037 TTTAATAATAATTAATTAATTAATCATAT
1 TTTAAT-ATAATT-ATT-ATTAAT-ATAT
27900066 TTTAATATAATTATTATTAAATATAAT
1 TTTAATATAATTATTATT-AATAT-AT
* *
27900093 TTAATAAAAATAATATATAATTTAATAATATT
1 TT--T-AATATAAT-TATTA-TTAAT-ATA-T
27900125 TTTAATATAATTATT
1 TTTAATATAATTATT
27900140 TTATATTAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 19
0.73 0.05 0.23
Matches are distributed among these distances:
26 5 0.08
27 10 0.16
28 9 0.15
29 14 0.23
30 8 0.13
31 8 0.13
32 7 0.11
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTAATATAATTATTATTAATATAT
Found at i:27900099 original size:24 final size:23
Alignment explanation
Indices: 27900072--27900136 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 23
27900062 ATATTTTAAT
27900072 ATAATTATTATTAAATATAATTTA
1 ATAA-TATTATTAAATATAATTTA
*
27900096 ATAA-A--AATAATATATAATTTA
1 ATAATATTATTAA-ATATAATTTA
*
27900117 ATAATATT-TTTAATATAATT
1 ATAATATTATTAAATATAATT
27900137 ATTTTATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
20 4 0.12
21 14 0.41
22 10 0.29
23 2 0.06
24 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAATATTATTAAATATAATTTA
Found at i:27900154 original size:15 final size:15
Alignment explanation
Indices: 27900114--27900204 Score: 78
Period size: 15 Copynumber: 5.9 Consensus size: 15
27900104 AATATATAAT
27900114 TTAATAATATTTT-TA
1 TTAA-AATATTTTATA
* *
27900129 ATATAATTATTTTATA
1 TTA-AAATATTTTATA
*
27900145 TTAAAATATTTTATT
1 TTAAAATATTTTATA
*
27900160 TTAAATTATATTTTGAAA
1 TTAAA--ATATTTT-ATA
27900178 TT-AAATATTTTATA
1 TTAAAATATTTTATA
*
27900192 TTAAATTATTTTA
1 TTAAAATATTTTA
27900205 ATTTTTTTCT
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
14 4 0.07
15 40 0.66
16 5 0.08
17 9 0.15
18 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (15 bp):
TTAAAATATTTTATA
Found at i:27909598 original size:44 final size:44
Alignment explanation
Indices: 27909535--27909869 Score: 244
Period size: 44 Copynumber: 7.5 Consensus size: 44
27909525 CGTTATGGTG
* * * * * * *
27909535 AATCTTATCTCTCTAAAGTTTCAGAGAAGCAGATTAAAGCCACA
1 AATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAGACACA
** *
27909579 AATCTTATCTCTTTGAAGTTACAGTGGAGTAGATTAAAGATACA
1 AATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAGACACA
** * *
27909623 AATCCAATCTCCATGAAGTTACAGTGGATTAGATTGAAA-ACACA
1 AATCTTATCTCCCTGAAGTTACAGTGGAGTAGATT-AAAGACACA
* *
27909667 AATCTTATCTCCCTGAAGTTGCAGTGGAGTATATTGAAA-ACACA
1 AATCTTATCTCCCTGAAGTTACAGTGGAGTAGATT-AAAGACACA
* * * * * * *
27909711 AATCTTATCTCCTTAAAGTTGCAGTCGAGCAGATTAAAGATACG
1 AATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAGACACA
* * ** *
27909755 AATCTTATTTCCCTGAAGTTGCAGTGGAACATATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAG--AC-----ACA
* * ** * *
27909806 AATCTTATCTCCCTGAAGTTGCAGTGAAAAAAATTAAAGTCACA
1 AATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAGACACA
*
27909850 AAT-TTCATCTCCCTAAAGTT
1 AATCTT-ATCTCCCTGAAGTT
27909870 GTAGTGGAAC
Statistics
Matches: 240, Mismatches: 41, Indels: 20
0.80 0.14 0.07
Matches are distributed among these distances:
43 5 0.02
44 193 0.80
45 3 0.01
46 1 0.00
49 1 0.00
51 37 0.15
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAGACACA
Found at i:27909659 original size:233 final size:233
Alignment explanation
Indices: 27909251--27909691 Score: 523
Period size: 233 Copynumber: 1.9 Consensus size: 233
27909241 GTGAAACCAT
* * *
27909251 AAATCCTATACCCCTGAAGTTGCAGTGGAATAGATTGAAGTTATCGTGGCAAATCTTGTCTTCCT
1 AAATCCTATACCCCTGAAGTTGCAGTGGAATAGATTGAAGTCATCATGGCAAATCTTATCTTCCT
* * *
27909316 GAAGTTGCAGTAGAGCAGATTAAAGCCACAAATTCTATCCCCCTGAAGTTATAGTTGAGCAGATT
66 AAAGTTGCAGTAGAGCAGATTAAAGCCACAAATTCTATCCCCCTGAAGTTACAGTGGAGCAGATT
* *** * * ** * * *
27909381 GAAGATACAAAAATTTTCTCCTAGAAGTTGCAGTGGAGCAGATTGAATATGCGAATCTTATTTTC
131 AAAGATACAAAAACAATCTCCTAGAAGTTACAGTGGAGCAGATTGAAAACACAAATCTTATCTCC
27909446 CTGAAGTTGCAGTCGAATAAATTAAATCTACAAATCAC
196 CTGAAGTTGCAGTCGAATAAATTAAATCTACAAATCAC
* * * **
27909484 AAATCCTATACCCCTGAAGTTGCAGTAGG-ATGGATTGAAGTCGTTATGGTGAATCTTATC-TCT
1 AAATCCTATACCCCTGAAGTTGCAGT-GGAATAGATTGAAGTCATCATGGCAAATCTTATCTTC-
* * ** *
27909547 CTAAAGTTTCAG-AGAAGCAGATTAAAGCCACAAA-TCTTATCTCTTTGAAGTTACAGTGGAGTA
64 CTAAAGTTGCAGTAG-AGCAGATTAAAGCCACAAATTC-TATCCCCCTGAAGTTACAGTGGAGCA
** **
27909610 GATTAAAGATACAAATCCAATCTCC-ATGAAGTTACAGTGGATTAGATTGAAAACACAAATCTTA
127 GATTAAAGATACAAAAACAATCTCCTA-GAAGTTACAGTGGAGCAGATTGAAAACACAAATCTTA
27909674 TCTCCCTGAAGTTGCAGT
191 TCTCCCTGAAGTTGCAGT
27909692 GGAGTATATT
Statistics
Matches: 172, Mismatches: 31, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
232 7 0.04
233 163 0.95
234 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (233 bp):
AAATCCTATACCCCTGAAGTTGCAGTGGAATAGATTGAAGTCATCATGGCAAATCTTATCTTCCT
AAAGTTGCAGTAGAGCAGATTAAAGCCACAAATTCTATCCCCCTGAAGTTACAGTGGAGCAGATT
AAAGATACAAAAACAATCTCCTAGAAGTTACAGTGGAGCAGATTGAAAACACAAATCTTATCTCC
CTGAAGTTGCAGTCGAATAAATTAAATCTACAAATCAC
Found at i:27909831 original size:51 final size:50
Alignment explanation
Indices: 27909664--27909972 Score: 227
Period size: 44 Copynumber: 6.6 Consensus size: 50
27909654 GATTGAAAAC
** **
27909664 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTATATT---G--AAA-AC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACATATTAAAGCTAAAGTT
* * * * *
27909708 ACAAATCTTATCTCCTTAAAGTTGCAGTCGAGCAGATTAAAG----A--T
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACATATTAAAGCTAAAGTT
* *
27909752 ACGAATCTTATTTCCCTGAAGTTGCAGTGGAACATATTAAAGCTACAAGTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACATATTAAAGCTA-AAGTT
* *
27909803 ACAAATCTTATCTCCCTGAAGTTGCAGT-GAA-A-A--AAA-TTAAAGTC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACATATTAAAGCTAAAGTT
* * *
27909847 ACAAAT-TTCATCTCCCTAAAGTTGTAGTGGAACAAATTAAAGCT-AA---
1 ACAAATCTT-ATCTCCCTGAAGTTGCAGTGGAACATATTAAAGCTAAAGTT
* * * * *
27909893 A-AAA-CTTATTTCCCTAAAGTTGTAATGGAACATATTGAAGCTACAAGTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACATATTAAAGCTA-AAGTT
27909942 ACAAATCTTATCTCCCTGAAGTTGCAGTGGA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGA
27909973 GCAAATTGAA
Statistics
Matches: 212, Mismatches: 28, Indels: 43
0.75 0.10 0.15
Matches are distributed among these distances:
43 2 0.01
44 126 0.59
45 11 0.05
46 7 0.03
47 2 0.01
48 1 0.00
49 8 0.04
50 7 0.03
51 48 0.23
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (50 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACATATTAAAGCTAAAGTT
Found at i:27909844 original size:95 final size:95
Alignment explanation
Indices: 27909708--27909891 Score: 230
Period size: 95 Copynumber: 1.9 Consensus size: 95
27909698 TATTGAAAAC
* ** * * * *
27909708 ACAAATCTTATCTCCTTAAAGTTGCAGTCGAGCAGATTAAAGAT-ACGAATCTT-ATTTCCCTGA
1 ACAAATCTTATCTCCCTAAAGTTGCAGTCGAAAAAATTAAAG-TCACAAAT-TTCATCTCCCTAA
*
27909771 AGTTGCAGTGGAACATATTAAAGCTACAAGTT
64 AGTTGCAGTGGAACAAATTAAAGCTACAAGTT
*
27909803 ACAAATCTTATCTCCCTGAAGTTGCAGT-GAAAAAAATTAAAGTCACAAATTTCATCTCCCTAAA
1 ACAAATCTTATCTCCCTAAAGTTGCAGTCG-AAAAAATTAAAGTCACAAATTTCATCTCCCTAAA
*
27909867 GTTGTAGTGGAACAAATTAAAGCTA
65 GTTGCAGTGGAACAAATTAAAGCTA
27909892 AAAAACTTAT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
94 4 0.05
95 72 0.95
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (95 bp):
ACAAATCTTATCTCCCTAAAGTTGCAGTCGAAAAAATTAAAGTCACAAATTTCATCTCCCTAAAG
TTGCAGTGGAACAAATTAAAGCTACAAGTT
Found at i:27909915 original size:44 final size:44
Alignment explanation
Indices: 27909809--27910016 Score: 143
Period size: 44 Copynumber: 4.6 Consensus size: 44
27909799 AGTTACAAAT
* * * * * *
27909809 CTTATCTCCCTGAAGTTGCAGTGAAAAAAATTAAAG-TCACAAA
1 CTTATCTCCCTAAAGTTGTAGTGGAACAAATTAAAGCTAAAAAA
*
27909852 TTTCATCTCCCTAAAGTTGTAGTGGAACAAATTAAAGCTAAAAAA
1 CTT-ATCTCCCTAAAGTTGTAGTGGAACAAATTAAAGCTAAAAAA
* * * *
27909897 CTTATTTCCCTAAAGTTGTAATGGAACATATTGAAGCTACAAGTTACAAA
1 CTTATCTCCCTAAAGTTGTAGTGGAACAAATTAAAGCT--AA---A-AAA
* * * ** *
27909947 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAA-CTACTAAT
1 -CTTATCTCCCTAAAGTTGTAGTGGAACAAATT-AAAGCTAAAAAA
*
27909992 CTTATCTCCCCGAAA-TTGTAGTGGA
1 CTTATCT-CCCTAAAGTTGTAGTGGA
27910017 GCAGATTGAA
Statistics
Matches: 129, Mismatches: 25, Indels: 21
0.74 0.14 0.12
Matches are distributed among these distances:
43 2 0.02
44 76 0.59
45 14 0.11
46 2 0.02
49 2 0.02
50 3 0.02
51 28 0.22
52 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTAAAGTTGTAGTGGAACAAATTAAAGCTAAAAAA
Found at i:27910011 original size:95 final size:95
Alignment explanation
Indices: 27909842--27910027 Score: 216
Period size: 95 Copynumber: 2.0 Consensus size: 95
27909832 AAAAAAATTA
* *
27909842 AAGTCACAAATTTCATCTCCCTAAAGTTGTAGTGGAACAAATTAAAGCTAAAAAACTTATTTCCC
1 AAGTCACAAATTTCATCTCCCTAAAGTTGCAGTGGAACAAATTAAAGCTAAAAAACTTATTCCCC
* *
27909907 TAAAGTTGTAATGGAACATATTGAAGCTAC
66 GAAAGTTGTAATGGAACAGATTGAAGCTAC
* * * ** *
27909937 AAGTTACAAATCTT-ATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAA-CTACTAATCTTATCTC
1 AAGTCACAAAT-TTCATCTCCCTAAAGTTGCAGTGGAACAAATT-AAAGCTAAAAAACTTAT-TC
* *
27910000 CCCGAAA-TTGTAGTGGAGCAGATTGAAG
63 CCCGAAAGTTGTAATGGAACAGATTGAAG
27910028 TGACAATTCC
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
95 64 0.84
96 12 0.16
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (95 bp):
AAGTCACAAATTTCATCTCCCTAAAGTTGCAGTGGAACAAATTAAAGCTAAAAAACTTATTCCCC
GAAAGTTGTAATGGAACAGATTGAAGCTAC
Found at i:27910075 original size:139 final size:138
Alignment explanation
Indices: 27909664--27910059 Score: 460
Period size: 139 Copynumber: 2.8 Consensus size: 138
27909654 GATTGAAAAC
* * *
27909664 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTATATTGAAAAC-ACAAATCTTATCTCCTTAAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGAAAATTG-AAACTACAAATCTTATCTCCCTAAA
* * * * *
27909728 GTTGCAGTCGAGCAGATTAAAGATACGAATCTTATTTCCCTGAAGTTGCAGTGGAACATATTAAA
65 GTTGTAGTGGAGCAGATTAAAGATAC-AATCTTATTTCCCTAAAGTTGCAATGGAACATATTGAA
27909793 GCTACAAGTT
129 GCTACAAGTT
* * *
27909803 ACAAATCTTATCTCCCTGAAGTTGCAGTGAAAAAAATT-AAAGTCACAAAT-TTCATCTCCCTAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGAAAATTGAAACT-ACAAATCTT-ATCTCCCTAA
* * * * * *
27909866 AGTTGTAGTGGAACAAATTAAAGCTAAAAAACTTATTTCCCTAAAGTTGTAATGGAACATATTGA
64 AGTTGTAGTGGAGCAGATTAAAGAT-ACAATCTTATTTCCCTAAAGTTGCAATGGAACATATTGA
27909931 AGCTACAAGTT
128 AGCTACAAGTT
* * *
27909942 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAACTACTAATCTTATCTCCCCGAAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGAAAATTGAAACTACAAATCTTATCT-CCCTAAA
* * ** *
27910007 -TTGTAGTGGAGCAGATTGAAG-TGACAATTCCTATAACCCTTAAGTTGCAATGG
65 GTTGTAGTGGAGCAGATTAAAGAT-ACAA-TCTTATTTCCCTAAAGTTGCAATGG
27910060 GTTAGAACGA
Statistics
Matches: 215, Mismatches: 34, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
137 3 0.01
138 6 0.03
139 193 0.90
140 13 0.06
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (138 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGAAAATTGAAACTACAAATCTTATCTCCCTAAAG
TTGTAGTGGAGCAGATTAAAGATACAATCTTATTTCCCTAAAGTTGCAATGGAACATATTGAAGC
TACAAGTT
Found at i:27912645 original size:17 final size:17
Alignment explanation
Indices: 27912623--27912656 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27912613 CGTTTTCATT
*
27912623 TTTAAATAAAAAGTCGA
1 TTTAAAAAAAAAGTCGA
*
27912640 TTTAAAAAAAAATTCGA
1 TTTAAAAAAAAAGTCGA
27912657 CAGGAACCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (17 bp):
TTTAAAAAAAAAGTCGA
Found at i:27913495 original size:3 final size:3
Alignment explanation
Indices: 27913487--27913519 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
27913477 GATGCAGCTC
27913487 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27913520 AAGAAGAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:27922376 original size:14 final size:13
Alignment explanation
Indices: 27922344--27922384 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
27922334 AATCAAGTTT
27922344 TAATA-ATAAAT-
1 TAATATATAAATA
27922355 TAATATATAAATA
1 TAATATATAAATA
*
27922368 TACATATATTAATA
1 TA-ATATATAAATA
27922382 TAA
1 TAA
27922385 ATTTTTGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 5 0.19
12 6 0.23
13 3 0.12
14 12 0.46
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATATATAAATA
Found at i:27923642 original size:25 final size:24
Alignment explanation
Indices: 27923608--27923661 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
27923598 ATTTTATATT
*
27923608 AATATTTATATTAATATTAAATAA
1 AATAATTATATTAATATTAAATAA
**
27923632 ATATAATTATATTCCTATTAAATAA
1 A-ATAATTATATTAATATTAAATAA
27923657 AATAA
1 AATAA
27923662 AAATATTCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
AATAATTATATTAATATTAAATAA
Found at i:27923667 original size:24 final size:25
Alignment explanation
Indices: 27923622--27923670 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
27923612 TTTATATTAA
**
27923622 TATTAAATAAATATAATTATATTCC
1 TATTAAATAAATATAAAAATATTCC
27923647 TATTAAATAAA-ATAAAAATATTCC
1 TATTAAATAAATATAAAAATATTCC
27923671 CACCCCTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (25 bp):
TATTAAATAAATATAAAAATATTCC
Found at i:27923689 original size:6 final size:6
Alignment explanation
Indices: 27923678--27923715 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
27923668 TCCCACCCCT
*
27923678 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CCACCC CC
1 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CC
27923716 GTTCCATCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.03, C:0.84, G:0.00, T:0.13
Consensus pattern (6 bp):
CCTCCC
Found at i:27932867 original size:17 final size:15
Alignment explanation
Indices: 27932827--27932873 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
27932817 CCAGGGCATT
27932827 TTCTTTTTGCTTTGTTG
1 TTCTTTTT-CTTT-TTG
27932844 TTC-TTTTCTTTTCTG
1 TTCTTTTTCTTTT-TG
27932859 CTTCTTTTTCTTTTT
1 -TTCTTTTTCTTTTT
27932874 TTAATCTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 6 0.22
16 8 0.30
17 12 0.44
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (15 bp):
TTCTTTTTCTTTTTG
Found at i:27933931 original size:20 final size:20
Alignment explanation
Indices: 27933903--27933941 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27933893 CATTTTTTTG
*
27933903 TGCTAGTTCCAGAATTGTTT
1 TGCTAGTTCCAGAACTGTTT
*
27933923 TGCTTGTTCCAGAACTGTT
1 TGCTAGTTCCAGAACTGTT
27933942 GCGGTTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.44
Consensus pattern (20 bp):
TGCTAGTTCCAGAACTGTTT
Found at i:27936340 original size:11 final size:11
Alignment explanation
Indices: 27936324--27936350 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
27936314 TAGAAATTAG
27936324 TTTGTGAAACT
1 TTTGTGAAACT
27936335 TTTGTGAAACT
1 TTTGTGAAACT
27936346 TTTGT
1 TTTGT
27936351 ATTGAGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:27938041 original size:721 final size:720
Alignment explanation
Indices: 27936659--27938087 Score: 2777
Period size: 721 Copynumber: 2.0 Consensus size: 720
27936649 TCCTGCATGG
*
27936659 TGGACCTGCACAATGTTGGAACATTTAATGTTGATACCGGGTTCAAAGCCGGTTATTTGAACGAG
1 TGGACCTGCACAATGTTGGAACATTTAATGCTGATACCGGGTTCAAAGCCGGTTATTTGAACGAG
*
27936724 TTGGAAAGAATGCTACAAACGGTTTTGCCAAATGCAATGTTGAAGGCGAAACCTAATATTGAATC
66 TTGGAAAGAATGCTACAAACAGTTTTGCCAAATGCAATGTTGAAGGCGAAACCTAATATTGAATC
27936789 AAGGATTAGGTTACTTAAACGGGAGTGGTCAATCGTCTATGACATGCTTAATGGCCAAAATAATA
131 AAGGATTAGGTTACTTAAACGGGAGTGGTCAATCGTCTATGACATGCTTAATGGCCAAAATAATA
*
27936854 GCGGTTTTGGTTGGGACGAGCATAGGCAGCTCGTTGTTGCTGAAGATGCGGTTTGGGAGTCCTAT
196 GCGGTTTTGGTTGGGACAAGCATAGGCAGCTCGTTGTTGCTGAAGATGCGGTTTGGGAGTCCTAT
* *
27936919 TTAGAGGTAAGATTATTTCAAGTCTTTATTATCTTATTTTTACCAAACTTATTACTAATAAGATT
261 TTAAAGGTAAGATTATTTCAAGTCTTTATTATCTTATTTTTACCAAACTTATGACTAATAAGATT
27936984 TCCTCATTTTTTTAGAGTCACAGAGAAGCCGCTCAATTCAGATATCGCACTTTCCCTTACTACGA
326 TCCTCATTTTTTTAGAGTCACAGAGAAGCCGCTCAATTCAGATATCGCACTTTCCCTTACTACGA
*
27937049 CCAGCTTACTACCATATACGCAAGAGATCGAGCAACTGGGAAAGATGCTCAAACAGCTGCTGATG
391 CCAGCTTACTACCATATACGCAAGAGATCGAGAAACTGGGAAAGATGCTCAAACAGCTGCTGATG
27937114 TTCTTGAAGAAATAAATGCTGATGTTCGTACTACAGCTATGGATGAAGAAAGAAACTCATTCTAT
456 TTCTTGAAGAAATAAATGCTGATGTTCGTACTACAGCTATGGATGAAGAAAGAAACTCATTCTAT
27937179 GACTGCGAAGCTGACATCCCTTTGGATGACATGGATGTTTCTGCTGCGGAGCCGCAACGAGATAG
521 GACTGCGAAGCTGACATCCCTTTGGATGACATGGATGTTTCTGCTGCGGAGCCGCAACGAGATAG
27937244 AGACCAATGGGGTTCCTCATCTTCAAACAAGAGAAAGAAGAAATCTGATGCTCGTGATATGTCTT
586 AGACCAATGGGGTTCCTCATCTTCAAACAAGAGAAAGAAGAAATCTGATGCTCGTGATATGTCTT
27937309 CTTCATTTGATGAGGCTGCCACTTTATTGGCCGAAAACATCAAGGCCGTTGGCGATCAATGTTGG
651 CTTCATTTGATGAGGCTGCCACTTTATTGGCC-AAAACATCAAGGCCGTTGGCGATCAATGTTGG
27937374 ATGACA
715 ATGACA
27937380 TGGACCTGCACAATGTTGGAACATTTAATGCTGATACCGGGTTCAAAGCCGGTTATTTGAACGAG
1 TGGACCTGCACAATGTTGGAACATTTAATGCTGATACCGGGTTCAAAGCCGGTTATTTGAACGAG
27937445 TTGGAAAGAATGCTACAAACAGTTTTGCCAAATGCAATGTTGAAGGCGAAACCTAATATTGAATC
66 TTGGAAAGAATGCTACAAACAGTTTTGCCAAATGCAATGTTGAAGGCGAAACCTAATATTGAATC
27937510 AAGGATTAGGTTACTTAAACGGGAGTGGTCAATCGTCTATGACATGCTTAATGGCCAAAATAATA
131 AAGGATTAGGTTACTTAAACGGGAGTGGTCAATCGTCTATGACATGCTTAATGGCCAAAATAATA
27937575 GCGGTTTTGGTTGGGACAAGCATAGGCAGCTCGTTGTTGCTGAAGATGCGGTTTGGGAGTCCTAT
196 GCGGTTTTGGTTGGGACAAGCATAGGCAGCTCGTTGTTGCTGAAGATGCGGTTTGGGAGTCCTAT
27937640 TTAAAGGTAAGATTATTTCAAGTCTTTATTATCTTATTTTTACCAAACTTATGACTAATAAGATT
261 TTAAAGGTAAGATTATTTCAAGTCTTTATTATCTTATTTTTACCAAACTTATGACTAATAAGATT
* *
27937705 TCCTCATTTTTTTAGAGTCATAGAGAAGCCGCTCAATTTAGATATCGCACTTTCCCTTACTACGA
326 TCCTCATTTTTTTAGAGTCACAGAGAAGCCGCTCAATTCAGATATCGCACTTTCCCTTACTACGA
27937770 CCAGCTTACTACCATATACGCAAGAGATCGAGAAACTGGGAAAGATGCTCAAACAGCTGCTGATG
391 CCAGCTTACTACCATATACGCAAGAGATCGAGAAACTGGGAAAGATGCTCAAACAGCTGCTGATG
27937835 TTCTTGAAGAAATAAATGCTGATGTTCGTACTACAGCTATGGATGAAGAAAGAAACTCATTCTAT
456 TTCTTGAAGAAATAAATGCTGATGTTCGTACTACAGCTATGGATGAAGAAAGAAACTCATTCTAT
27937900 GACTGCGAAGCTGACATCCCTTTGGATGACATGGATGTTTCTGCTGCGGAGCCGCAACGAGATAG
521 GACTGCGAAGCTGACATCCCTTTGGATGACATGGATGTTTCTGCTGCGGAGCCGCAACGAGATAG
27937965 AGACCAATGGGGTTCCTCATCTTCAAACAAGAGAAAGAAGAAATCTGATGCTCGTGATATGTCTT
586 AGACCAATGGGGTTCCTCATCTTCAAACAAGAGAAAGAAGAAATCTGATGCTCGTGATATGTCTT
27938030 CTTCATTTGATGAGGCTGCCACTTTATTGGCCAAAACATCAAGGCCGTTGGCGATCAA
651 CTTCATTTGATGAGGCTGCCACTTTATTGGCCAAAACATCAAGGCCGTTGGCGATCAA
27938088 ATCAGTAGGA
Statistics
Matches: 700, Mismatches: 8, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
720 26 0.04
721 674 0.96
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (720 bp):
TGGACCTGCACAATGTTGGAACATTTAATGCTGATACCGGGTTCAAAGCCGGTTATTTGAACGAG
TTGGAAAGAATGCTACAAACAGTTTTGCCAAATGCAATGTTGAAGGCGAAACCTAATATTGAATC
AAGGATTAGGTTACTTAAACGGGAGTGGTCAATCGTCTATGACATGCTTAATGGCCAAAATAATA
GCGGTTTTGGTTGGGACAAGCATAGGCAGCTCGTTGTTGCTGAAGATGCGGTTTGGGAGTCCTAT
TTAAAGGTAAGATTATTTCAAGTCTTTATTATCTTATTTTTACCAAACTTATGACTAATAAGATT
TCCTCATTTTTTTAGAGTCACAGAGAAGCCGCTCAATTCAGATATCGCACTTTCCCTTACTACGA
CCAGCTTACTACCATATACGCAAGAGATCGAGAAACTGGGAAAGATGCTCAAACAGCTGCTGATG
TTCTTGAAGAAATAAATGCTGATGTTCGTACTACAGCTATGGATGAAGAAAGAAACTCATTCTAT
GACTGCGAAGCTGACATCCCTTTGGATGACATGGATGTTTCTGCTGCGGAGCCGCAACGAGATAG
AGACCAATGGGGTTCCTCATCTTCAAACAAGAGAAAGAAGAAATCTGATGCTCGTGATATGTCTT
CTTCATTTGATGAGGCTGCCACTTTATTGGCCAAAACATCAAGGCCGTTGGCGATCAATGTTGGA
TGACA
Found at i:27938604 original size:91 final size:91
Alignment explanation
Indices: 27938473--27938679 Score: 290
Period size: 91 Copynumber: 2.3 Consensus size: 91
27938463 TTGATTTTAG
* * *
27938473 TAAATTCATATAAGAACATTTTATTATTAAGAGTTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
* *
27938538 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* *
27938565 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
27938630 TGTAATAATTATTATTTTAAATTATA
66 TGTAATAATTATTATTTTAAATTATA
* * * *
27938656 CAAATTCATAAAATATAATTTATT
1 TAAATTCATATAAGAAAATTTATT
27938680 GGTTATAATT
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
91 84 0.82
92 19 0.18
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:27938744 original size:54 final size:54
Alignment explanation
Indices: 27938683--27938878 Score: 130
Period size: 54 Copynumber: 3.4 Consensus size: 54
27938673 ATTTATTGGT
27938683 TATAATTATTTTAAATTT-TATTAAATCATATATTTTAATTAAAATATATTTAA
1 TATAATTATTTTAAATTTATATTAAATCATATATTTTAATTAAAATATATTTAA
* * * * * **
27938736 TATGAATTATTTCAAATTTTCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGA
1 TAT-AATTATTTTAAA-TTTATATTA-A--ATCATATATT-TTAATT-A--AAA-T-ATAT-TTA
27938801 A
54 A
* * *
27938802 TATTAATTA-TTAAGAATTT-TATTAAATTATATATTTTAATTATAATATATTTAA
1 TA-TAATTATTTTA-AATTTATATTAAATCATATATTTTAATTAAAATATATTTAA
*
27938856 TAATAATTATGTT-AATTTATATT
1 T-ATAATTATTTTAAATTTATATT
27938879 TTACAGTATC
Statistics
Matches: 109, Mismatches: 16, Indels: 35
0.68 0.10 0.22
Matches are distributed among these distances:
53 8 0.07
54 24 0.22
55 9 0.08
56 5 0.05
57 3 0.03
59 11 0.10
60 8 0.07
61 10 0.09
63 4 0.04
64 5 0.05
65 10 0.09
66 11 0.10
67 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (54 bp):
TATAATTATTTTAAATTTATATTAAATCATATATTTTAATTAAAATATATTTAA
Found at i:27938820 original size:120 final size:120
Alignment explanation
Indices: 27938696--27938991 Score: 499
Period size: 120 Copynumber: 2.5 Consensus size: 120
27938686 AATTATTTTA
* * *
27938696 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAAT-ATGAATTAT-TTCAAATTT-TCT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAAT-AATTATGTT--AATTTATAT
*
27938758 TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
63 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
27938816 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
27938881 ACAGTATCATATATTATGATTTGAGTTAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
27938936 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAT
27938992 NNNNNNNNNN
Statistics
Matches: 168, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
119 5 0.03
120 159 0.95
121 4 0.02
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:27938856 original size:15 final size:15
Alignment explanation
Indices: 27938821--27938872 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
27938811 TTAAGAATTT
*
27938821 TATTAAATTAT-ATA
1 TATTTAATTATAATA
27938835 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
27938849 TATTTAATAATAAT-
1 TATTTAATTATAATA
27938863 TATGTTAATT
1 TAT-TTAATT
27938873 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:27938937 original size:16 final size:18
Alignment explanation
Indices: 27938906--27938938 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
27938896 ATGATTTGAG
27938906 TTAATTCATATAAGAATA
1 TTAATTCATATAAGAATA
27938924 TTAATT-AT-TAAGAAT
1 TTAATTCATATAAGAAT
27938939 TTTATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (18 bp):
TTAATTCATATAAGAATA
Found at i:27938976 original size:15 final size:15
Alignment explanation
Indices: 27938941--27938991 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
27938931 TTAAGAATTT
*
27938941 TATTAAATTAT-ATA
1 TATTTAATTATAATA
27938955 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
27938969 TATTTAATAATAAT-
1 TATTTAATTATAATA
27938983 TATGTTAAT
1 TAT-TTAAT
27938992 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:27939346 original size:16 final size:16
Alignment explanation
Indices: 27939327--27939378 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
27939317 GATTTGCTAT
* *
27939327 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
27939343 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
27939359 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
27939375 TACA
1 TACA
27939379 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:27943884 original size:6 final size:6
Alignment explanation
Indices: 27943873--27943913 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
27943863 TAAATTATAT
* * *
27943873 TATTAG TATTAG TATTAG TATTAG AATTAT TATTAA TATTA
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTA
27943914 TTGTTATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:27944157 original size:27 final size:28
Alignment explanation
Indices: 27944102--27944173 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 28
27944092 TATTTTACAA
*
27944102 TTTTA-AATATATATATGTGAATA-CAT
1 TTTTATAATATATATACGTGAATATCAT
**
27944128 TTTTATAATATATATACGT-ACATATTTTT
1 TTTTATAATATATATACGTGA-ATA-TCAT
27944157 TTTTATAAATATATATA
1 TTTTAT-AATATATATA
27944174 TGTATACACA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
26 6 0.16
27 15 0.39
29 7 0.18
30 10 0.26
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (28 bp):
TTTTATAATATATATACGTGAATATCAT
Found at i:27945670 original size:12 final size:12
Alignment explanation
Indices: 27945653--27945683 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
27945643 CCTCACACGT
27945653 CCGTGTGCTAGG
1 CCGTGTGCTAGG
27945665 CCGTGTGCTAGG
1 CCGTGTGCTAGG
*
27945677 CTGTGTG
1 CCGTGTG
27945684 AAAACTAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.23, G:0.42, T:0.29
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:27954789 original size:12 final size:12
Alignment explanation
Indices: 27954772--27954801 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
27954762 GACCACACTC
27954772 CCGTGTGCCAGG
1 CCGTGTGCCAGG
27954784 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
27954796 TCGTGT
1 CCGTGT
27954802 AAAAACTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:27963641 original size:27 final size:27
Alignment explanation
Indices: 27963603--27963667 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
27963593 CCTGTCTAGT
27963603 AGGCGCCAATGAAGGAGCATCATGGAG
1 AGGCGCCAATGAAGGAGCATCATGGAG
*
27963630 AGGCGCCAATGAAGGAGCCTCATGGAG
1 AGGCGCCAATGAAGGAGCATCATGGAG
27963657 AGGCGCCAATG
1 AGGCGCCAATG
27963668 GTGCCCTCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.31, C:0.22, G:0.37, T:0.11
Consensus pattern (27 bp):
AGGCGCCAATGAAGGAGCATCATGGAG
Found at i:27963808 original size:3 final size:3
Alignment explanation
Indices: 27963802--27963845 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
27963792 GAGAGAAAGG
*
27963802 AGA AGA AGA A-A AGG AGA AGA AGA AGA AG- AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
27963846 AGAAAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:27963822 original size:17 final size:17
Alignment explanation
Indices: 27963802--27963846 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
27963792 GAGAGAAAGG
*
27963802 AGAAGAAGAAAAGGAGA
1 AGAAGAAGAAAAGAAGA
*
27963819 AGAAGAAGAAGAGAAGA
1 AGAAGAAGAAAAGAAGA
27963836 AGAAGAAGAAA
1 AGAAGAAGAAA
27963847 GAAAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
AGAAGAAGAAAAGAAGA
Found at i:27963840 original size:14 final size:14
Alignment explanation
Indices: 27963801--27963849 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
27963791 AGAGAGAAAG
27963801 GAGAAGAAGAA-AA
1 GAGAAGAAGAAGAA
27963814 GGAGAAGAAGAAGAA
1 -GAGAAGAAGAAGAA
27963829 GAGAAGAAGAAGAA
1 GAGAAGAAGAAGAA
27963843 GA-AAGAA
1 GAGAAGAA
27963850 AAAAAAAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.15
14 27 0.79
15 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (14 bp):
GAGAAGAAGAAGAA
Found at i:27964041 original size:22 final size:21
Alignment explanation
Indices: 27964015--27964301 Score: 223
Period size: 22 Copynumber: 13.1 Consensus size: 21
27964005 TAGATTAGAA
*
27964015 TTTTGTATGAATATTTTAACTT
1 TTTTGTATGAATATTGTAA-TT
*
27964037 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTGTAATT
27964058 TTTT-TAATGAATATTGTAA--
1 TTTTGT-ATGAATATTGTAATT
*
27964077 TGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* *
27964098 ATTTTATAATTAA-ATTTGT-ATT
1 -TTTTGT-ATGAATA-TTGTAATT
* * *
27964120 TATAGTTTTGGAATA--GTAATT
1 TTTTG-TAT-GAATATTGTAATT
27964141 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
27964160 TTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGT-AATT
27964182 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
*
27964207 AGTTTTGTATGAATATTGAAATT
1 --TTTTGTATGAATATTGTAATT
27964230 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
*
27964255 AATTTTGTATGAATATTGCAAATT
1 --TTTTGTATGAATATTG-TAATT
27964279 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
27964300 TT
1 TT
27964302 GTAATTTTGT
Statistics
Matches: 217, Mismatches: 20, Indels: 57
0.74 0.07 0.19
Matches are distributed among these distances:
19 37 0.17
20 8 0.04
21 53 0.24
22 64 0.29
23 12 0.06
24 4 0.02
25 4 0.02
26 2 0.01
27 33 0.15
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.54
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:27964151 original size:83 final size:86
Alignment explanation
Indices: 27964044--27964249 Score: 237
Period size: 83 Copynumber: 2.4 Consensus size: 86
27964034 CTTTTTTGTA
* *
27964044 TGAATATTATAATTTTTT-TAATGAATATTGTAATGTTGTATGAATATTGT-AATTATTTTATAA
1 TGAATA-TGTAATTTTTTGT-ATGAATATTGTAATGTTGTATGAATATTATAAATT-TTTTAT-A
27964107 TTAAAT-TTGT-AT-TTATAGTTTTG
62 -TAAATATTGTAATATTATAGTTTTG
* * *
27964130 -GAATA-GTAATTTTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAA
1 TGAATATGTAATTTTTTGTATGAATATTGTAATGTTGTATGAATATTATAAATTTTTTATATAAA
27964193 TATTGTAATATTATAGTTTTG
66 TATTGTAATATTATAGTTTTG
*
27964214 TATGAATATTGAAATTTTTTGTATGAATATTGTAAT
1 --TGAATA-TGTAATTTTTTGTATGAATATTGTAAT
27964250 ATTATAATTT
Statistics
Matches: 104, Mismatches: 6, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
81 4 0.04
82 5 0.05
83 44 0.42
84 16 0.15
85 5 0.05
87 5 0.05
89 25 0.24
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (86 bp):
TGAATATGTAATTTTTTGTATGAATATTGTAATGTTGTATGAATATTATAAATTTTTTATATAAA
TATTGTAATATTATAGTTTTG
Found at i:27964203 original size:49 final size:49
Alignment explanation
Indices: 27964150--27964371 Score: 301
Period size: 49 Copynumber: 4.6 Consensus size: 49
27964140 TTTTTGTATG
*
27964150 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGT
* *
27964199 AATATTATAGTTTTGTATGAATATTG-AAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGT
* *
27964247 AATATTATAATTTTGTATGAATATTGCAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGT
* * ** *
27964296 AATTTTGTAATTTTGTATGAATATTGT-AA-TGTGGGGAT--ATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGT
27964341 AATATTGTAATTTTTTGTATGAATATTGTAA
1 AATATTGTAA--TTTTGTATGAATATTGTAA
27964372 TTATTTTATA
Statistics
Matches: 157, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
45 16 0.10
47 22 0.14
48 50 0.32
49 69 0.44
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGT
Found at i:27964218 original size:27 final size:25
Alignment explanation
Indices: 27964150--27964325 Score: 183
Period size: 27 Copynumber: 7.1 Consensus size: 25
27964140 TTTTTGTATG
*
27964150 AATATTGTAATTTTGTATGAATATTAT
1 AATATT-T-ATTTTGTATGAATATTGT
27964177 AA-A-TT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
27964199 AATATTATAGTTTTGTATGAATATTG-
1 AATATT-TA-TTTTGTATGAATATTGT
27964225 AA-A-TT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
*
27964247 AATATTATAATTTTGTATGAATATTGC
1 AATATT-T-ATTTTGTATGAATATTGT
27964274 AA-A-TT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
*
27964296 AATTTTGTAATTTTGTATGAATATTGT
1 AATATT-T-ATTTTGTATGAATATTGT
27964323 AAT
1 AAT
27964326 GTGGGGATAT
Statistics
Matches: 129, Mismatches: 4, Indels: 32
0.78 0.02 0.19
Matches are distributed among these distances:
21 16 0.12
22 38 0.29
23 3 0.02
24 6 0.05
25 6 0.05
26 4 0.03
27 56 0.43
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (25 bp):
AATATTTATTTTGTATGAATATTGT
Found at i:27964325 original size:19 final size:19
Alignment explanation
Indices: 27964013--27964304 Score: 124
Period size: 19 Copynumber: 15.5 Consensus size: 19
27964003 TTTAGATTAG
*
27964013 AATTTTGTATGAATATTTT
1 AATTTTGTATGAATATTGT
*
27964032 AACTTTTTTGTATGAATATTAT
1 AA---TTTTGTATGAATATTGT
*
27964054 AATTTTTTTAATGAATATTGT
1 AA-TTTTGT-ATGAATATTGT
*
27964075 AATGTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
27964094 AATTATTTTAT-AATTAAATTTGT
1 AATT-TTGTATGAA-T--A-TTGT
*
27964117 -ATTTATAGTTTTGGAATA--GT
1 AATTT-T-G-TAT-GAATATTGT
27964137 AATTTTTTGTATGAATATTGT
1 AA--TTTTGTATGAATATTGT
*
27964158 AATTTTGTATGAATATTAT
1 AATTTTGTATGAATATTGT
27964177 AAATTTT-T-TG--TA-TG-
1 -AATTTTGTATGAATATTGT
* *
27964191 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
* *
27964207 AGTTTTGTATGAATATTGA
1 AATTTTGTATGAATATTGT
27964226 AATTTT-T-TG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
27964239 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
*
27964255 AATTTTGTATGAATATTGCA
1 AATTTTGTATGAATATTG-T
27964275 AATTTTTTGTATGAATATTGT
1 AA--TTTTGTATGAATATTGT
27964296 AATTTTGTA
1 AATTTTGTA
27964305 ATTTTGTATG
Statistics
Matches: 209, Mismatches: 25, Indels: 78
0.67 0.08 0.25
Matches are distributed among these distances:
13 12 0.06
14 6 0.03
15 5 0.02
16 13 0.06
17 2 0.01
18 5 0.02
19 64 0.31
20 28 0.13
21 21 0.10
22 40 0.19
23 8 0.04
24 2 0.01
25 1 0.00
26 2 0.01
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:27964447 original size:60 final size:60
Alignment explanation
Indices: 27964366--27964487 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
27964356 TGTATGAATA
* * * * * *
27964366 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTGGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
*
27964426 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTTAAAA-TTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
27964486 TT
1 TT
27964488 AGTTTAGTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 6 0.11
60 48 0.89
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:27964571 original size:38 final size:38
Alignment explanation
Indices: 27964521--27964602 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
27964511 CATATAAAGT
27964521 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
* *
27964559 TTATTAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
27964597 TTATAA
1 TTATAA
27964603 CTGACTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:27967758 original size:22 final size:21
Alignment explanation
Indices: 27967723--27967767 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
27967713 TACCTAATTT
*
27967723 TTTTCTTCTTTTCCTTCATTC
1 TTTTCTTCTCTTCCTTCATTC
*
27967744 TTTTCTTCTGCTTCCTTCCTTC
1 TTTTCTTCT-CTTCCTTCATTC
27967766 TT
1 TT
27967768 ATTTCTTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTCTTCTCTTCCTTCATTC
Found at i:27967882 original size:27 final size:27
Alignment explanation
Indices: 27967852--27967908 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
27967842 CTTTCAGAAT
*
27967852 GGCACCACCATTGGCGCCTCCCAGGTA
1 GGCACCACCATTGGCGCCTCCCAGATA
*
27967879 GGCACCACCATTGGCGCCTCCTAGATA
1 GGCACCACCATTGGCGCCTCCCAGATA
27967906 GGC
1 GGC
27967909 GCCAATACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.19, C:0.39, G:0.26, T:0.16
Consensus pattern (27 bp):
GGCACCACCATTGGCGCCTCCCAGATA
Found at i:27974709 original size:25 final size:25
Alignment explanation
Indices: 27974655--27974725 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
27974645 AGATCTCTTT
* *
27974655 CGAGCCATATAACAGGAAGTTTATG
1 CGAGCCATATAACAGGAAGCTTATC
* *
27974680 TGAGCCATGTAACAGGAAGCTTATC
1 CGAGCCATATAACAGGAAGCTTATC
** *
27974705 CGAGCTGTATAATAGGAAGCT
1 CGAGCCATATAACAGGAAGCT
27974726 CATAAGAGCC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (25 bp):
CGAGCCATATAACAGGAAGCTTATC
Found at i:27978764 original size:44 final size:44
Alignment explanation
Indices: 27978701--27978786 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
27978691 GGCTGTTACA
** * *
27978701 GCGGGTATTTGCTGTGTATCCACAACTAGAGGTAGATTCCATTT
1 GCGGGTATTTGCCCTGTATCCACAACCAGAGGCAGATTCCATTT
27978745 GCGGGTATTTGCCCTGTATCCACAACCAGAGGCAGATTCCAT
1 GCGGGTATTTGCCCTGTATCCACAACCAGAGGCAGATTCCAT
27978787 CTGTGGGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.29
Consensus pattern (44 bp):
GCGGGTATTTGCCCTGTATCCACAACCAGAGGCAGATTCCATTT
Found at i:27979744 original size:75 final size:75
Alignment explanation
Indices: 27979621--27979772 Score: 286
Period size: 75 Copynumber: 2.0 Consensus size: 75
27979611 ATCTAAACCG
*
27979621 TTTTTTTTTAACTTGTGAGCTTTTTAGAAAATAGATTAAGTTTTCATTTTAAAATAAATAAATAT
1 TTTTTTTTAAACTTGTGAGCTTTTTAGAAAATAGATTAAGTTTTCATTTTAAAATAAATAAATAT
27979686 TTTAAATTGA
66 TTTAAATTGA
*
27979696 TTTTTTTTAAACTTGTGAGCTTTTTTGAAAATAGATTAAGTTTTCATTTTAAAATAAATAAATAT
1 TTTTTTTTAAACTTGTGAGCTTTTTAGAAAATAGATTAAGTTTTCATTTTAAAATAAATAAATAT
27979761 TTTAAATTGA
66 TTTAAATTGA
27979771 TT
1 TT
27979773 GCTTTATAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (75 bp):
TTTTTTTTAAACTTGTGAGCTTTTTAGAAAATAGATTAAGTTTTCATTTTAAAATAAATAAATAT
TTTAAATTGA
Found at i:27980165 original size:5 final size:5
Alignment explanation
Indices: 27980155--27980185 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
27980145 TGAGCATTCG
27980155 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
27980186 AATTTTCGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:27981225 original size:9 final size:9
Alignment explanation
Indices: 27981211--27981247 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
27981201 TATAGTTTGA
27981211 TATTCGAAT
1 TATTCGAAT
27981220 TATTCGAAT
1 TATTCGAAT
*
27981229 TATTCGAGT
1 TATTCGAAT
27981238 TATTCGAAT
1 TATTCGAAT
27981247 T
1 T
27981248 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:27981323 original size:18 final size:18
Alignment explanation
Indices: 27981300--27981334 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27981290 ATTCGAGTTG
27981300 ATTCGAATAACTCGATTA
1 ATTCGAATAACTCGATTA
*
27981318 ATTCGAATAACTTGATT
1 ATTCGAATAACTCGATT
27981335 CGTTTAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (18 bp):
ATTCGAATAACTCGATTA
Found at i:27981335 original size:32 final size:30
Alignment explanation
Indices: 27981297--27981355 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
27981287 AAAATTCGAG
27981297 TTGATTCGAATAACTCGATTAATTCGAATAAC
1 TTGATTCGAATAACTCGA--AATTCGAATAAC
**
27981329 TTGATTCGTTTAACTCGAAATTCGAAT
1 TTGATTCGAATAACTCGAAATTCGAAT
27981356 TTTTTTTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
32 16 0.64
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (30 bp):
TTGATTCGAATAACTCGAAATTCGAATAAC
Found at i:27986059 original size:17 final size:17
Alignment explanation
Indices: 27986037--27986070 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27986027 AGTTAATTTA
27986037 TTAATATTTTATAAATT
1 TTAATATTTTATAAATT
27986054 TTAATATTTTATAAATT
1 TTAATATTTTATAAATT
27986071 GAAAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAATATTTTATAAATT
Found at i:27988911 original size:12 final size:12
Alignment explanation
Indices: 27988894--27988922 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
27988884 GAAGAAGATT
27988894 AATACGGTAAGG
1 AATACGGTAAGG
27988906 AATACGGTAAGG
1 AATACGGTAAGG
27988918 AATAC
1 AATAC
27988923 ATAGAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.28, T:0.17
Consensus pattern (12 bp):
AATACGGTAAGG
Found at i:27988973 original size:4 final size:4
Alignment explanation
Indices: 27988964--27988988 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27988954 CTTTTCTTTA
27988964 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
27988989 TGCAGATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:27992891 original size:26 final size:26
Alignment explanation
Indices: 27992850--27992907 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
27992840 ATAAGAGCCA
** *
27992850 TAATCAAGAAGTTCACAAAGAACTTT
1 TAATCAAGAAACTCACAAAGAACCTT
* *
27992876 TAATCAAGAAACTCACGAAGAGCCTT
1 TAATCAAGAAACTCACAAAGAACCTT
27992902 TAATCA
1 TAATCA
27992908 GGAGCTCCGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (26 bp):
TAATCAAGAAACTCACAAAGAACCTT
Found at i:27999180 original size:16 final size:16
Alignment explanation
Indices: 27999159--27999190 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
27999149 ATCCTGTTTT
27999159 ATGGTACATTAATATA
1 ATGGTACATTAATATA
27999175 ATGGTACATTAATATA
1 ATGGTACATTAATATA
27999191 GATAATCGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (16 bp):
ATGGTACATTAATATA
Found at i:28000093 original size:14 final size:15
Alignment explanation
Indices: 28000071--28000147 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
28000061 CAATCAAACA
28000071 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
28000085 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
28000100 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
28000120 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
28000134 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
28000148 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:28000112 original size:20 final size:20
Alignment explanation
Indices: 28000087--28000126 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28000077 AATATTTTCC
*
28000087 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
28000107 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
28000127 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:28000132 original size:34 final size:35
Alignment explanation
Indices: 28000075--28000141 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28000065 CAAACACCAG
*
28000075 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
28000110 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
28000142 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28000148 original size:14 final size:14
Alignment explanation
Indices: 28000110--28000149 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
28000100 ACAGAAAAGT
*
28000110 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
28000124 AAATCATTTTACGG
1 AAAACATTTTACAG
28000138 AAAACATTTTAC
1 AAAACATTTTAC
28000150 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:28010119 original size:6 final size:6
Alignment explanation
Indices: 28010087--28010112 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28010077 TTCCATTCTC
28010087 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
28010113 TTAAAATAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:28018637 original size:2 final size:2
Alignment explanation
Indices: 28018630--28018667 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28018620 CAATGATTTG
28018630 AT 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
28018668 TAGTTTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28021955 original size:12 final size:12
Alignment explanation
Indices: 28021940--28021964 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28021930 ATATAAGACA
28021940 ATATAAATTTAT
1 ATATAAATTTAT
28021952 ATATAAATTTAT
1 ATATAAATTTAT
28021964 A
1 A
28021965 ATCCTACAAA
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:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATAAATTTAT
Found at i:28025347 original size:13 final size:13
Alignment explanation
Indices: 28025329--28025356 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28025319 TGCCCCTAAC
28025329 TTACGGGGTATGA
1 TTACGGGGTATGA
28025342 TTACGGGGTATGA
1 TTACGGGGTATGA
28025355 TT
1 TT
28025357 TTTCCTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.36, T:0.36
Consensus pattern (13 bp):
TTACGGGGTATGA
Found at i:28036858 original size:3 final size:3
Alignment explanation
Indices: 28036850--28036881 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28036840 AATCTATCCT
28036850 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28036882 TAACTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28037663 original size:44 final size:44
Alignment explanation
Indices: 28037600--28037888 Score: 373
Period size: 44 Copynumber: 6.6 Consensus size: 44
28037590 GTCACCATAG
* *
28037600 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* **
28037644 CAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGGCTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* *
28037688 CAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * * *
28037732 CAAATCCTATCTCTCTGAAGTTACAGTGGAGCAGACTAAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * *
28037776 CAAATCTTATCTCCCTGAAGTTACAATGAAGCAGATTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * *
28037820 CAAATCTCATCTCCCTGAAGTTGCAGTAGAGCATATCGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
* *
28037864 CAATTCATATAC-CCCTGAAGTTGCA
1 CAAATCTTAT-CTCCCTGAAGTTGCA
28037889 ATGGGTTATA
Statistics
Matches: 215, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
44 214 1.00
45 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
Found at i:28040675 original size:51 final size:51
Alignment explanation
Indices: 28040598--28040701 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
28040588 CCAATTTGTT
*
28040598 ATTTCTCTCCATCAAACTCCCAACTAAATCCACTACTCATATTTTTAGTCC
1 ATTTCTCTCCATCAAACTCCCAACTAAATCCACTACTCAGATTTTTAGTCC
*
28040649 ATTTCTCTCCATCAAACTCCCCACTAAATCCACTACTCAGATTTTTAGTCC
1 ATTTCTCTCCATCAAACTCCCAACTAAATCCACTACTCAGATTTTTAGTCC
28040700 AT
1 AT
28040702 CTCAAACCCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.35
Consensus pattern (51 bp):
ATTTCTCTCCATCAAACTCCCAACTAAATCCACTACTCAGATTTTTAGTCC
Found at i:28042665 original size:23 final size:25
Alignment explanation
Indices: 28042634--28042690 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 25
28042624 TTAAACATCA
*
28042634 TATTAATTAAATCATTATCGTC-A-T
1 TATT-ATTAAATCATCATCGTCAATT
*
28042658 TATTATT--ATTATCATCGTCAATT
1 TATTATTAAATCATCATCGTCAATT
28042681 TATTATTAAA
1 TATTATTAAA
28042691 GCTGTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
21 10 0.37
22 1 0.04
23 11 0.41
24 4 0.15
25 1 0.04
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.49
Consensus pattern (25 bp):
TATTATTAAATCATCATCGTCAATT
Found at i:28042706 original size:180 final size:180
Alignment explanation
Indices: 28042404--28042766 Score: 717
Period size: 180 Copynumber: 2.0 Consensus size: 180
28042394 TTAAACAAAT
28042404 TTTACTTTATCCTTGATTCATTACGACTATCATTTTTTTATTAAACATCATATTAATTAAATCAT
1 TTTACTTTATCCTTGATTCATTACGACTATCATTTTTTTATTAAACATCATATTAATTAAATCAT
*
28042469 TATCGTCATTATTATTATTATCATTGTCAATTTATTATTAAAGCTGTTTCATCACCATTTGATAA
66 TATCGTCATTATTATTATTATCATCGTCAATTTATTATTAAAGCTGTTTCATCACCATTTGATAA
28042534 TGGTATACCTACTATTATTTTGTTCTTATATTATTATTTTACGATAGTCA
131 TGGTATACCTACTATTATTTTGTTCTTATATTATTATTTTACGATAGTCA
28042584 TTTACTTTATCCTTGATTCATTACGACTATCATTTTTTTATTAAACATCATATTAATTAAATCAT
1 TTTACTTTATCCTTGATTCATTACGACTATCATTTTTTTATTAAACATCATATTAATTAAATCAT
28042649 TATCGTCATTATTATTATTATCATCGTCAATTTATTATTAAAGCTGTTTCATCACCATTTGATAA
66 TATCGTCATTATTATTATTATCATCGTCAATTTATTATTAAAGCTGTTTCATCACCATTTGATAA
28042714 TGGTATACCTACTATTATTTTGTTCTTATATTATTATTTTACGATAGTCA
131 TGGTATACCTACTATTATTTTGTTCTTATATTATTATTTTACGATAGTCA
28042764 TTT
1 TTT
28042767 CAAATTTTAT
Statistics
Matches: 182, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 182 1.00
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.50
Consensus pattern (180 bp):
TTTACTTTATCCTTGATTCATTACGACTATCATTTTTTTATTAAACATCATATTAATTAAATCAT
TATCGTCATTATTATTATTATCATCGTCAATTTATTATTAAAGCTGTTTCATCACCATTTGATAA
TGGTATACCTACTATTATTTTGTTCTTATATTATTATTTTACGATAGTCA
Found at i:28052283 original size:14 final size:14
Alignment explanation
Indices: 28052242--28052289 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
28052232 ATGTGCAAAC
28052242 CCCCTGTATGCGAA
1 CCCCTGTATGCGAA
* *
28052256 TCCCCTATAGGCGAA
1 -CCCCTGTATGCGAA
28052271 CCCCTGTATGCGAA
1 CCCCTGTATGCGAA
28052285 CCCCT
1 CCCCT
28052290 ATAGATGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (14 bp):
CCCCTGTATGCGAA
Found at i:28052299 original size:28 final size:29
Alignment explanation
Indices: 28052242--28052300 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
28052232 ATGTGCAAAC
*
28052242 CCCCTGTATGCGAATCCCCTATAGGCGAA
1 CCCCTGTATGCGAATCCCCTATAGACGAA
*
28052271 CCCCTGTATGCGAA-CCCCTATAGATGAA
1 CCCCTGTATGCGAATCCCCTATAGACGAA
28052299 CC
1 CC
28052301 TTTTATATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.20
Consensus pattern (29 bp):
CCCCTGTATGCGAATCCCCTATAGACGAA
Found at i:28052547 original size:23 final size:22
Alignment explanation
Indices: 28052516--28052574 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
28052506 TCTGTTTAAC
28052516 ATGCGAACCCTACATG-TACTATT
1 ATGCGAACCCTACATGTTA-T-TT
* * *
28052539 ATGCAAACCTTATATGTTATTT
1 ATGCGAACCCTACATGTTATTT
28052561 ATGCGAACCCTACA
1 ATGCGAACCCTACA
28052575 CATGGTATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 13 0.45
23 14 0.48
24 2 0.07
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (22 bp):
ATGCGAACCCTACATGTTATTT
Found at i:28052604 original size:16 final size:16
Alignment explanation
Indices: 28052583--28052640 Score: 77
Period size: 15 Copynumber: 3.8 Consensus size: 16
28052573 CACATGGTAT
28052583 ATGCGAACCCT-GATG
1 ATGCGAACCCTAGATG
28052598 CATGCGAACCCTAGATG
1 -ATGCGAACCCTAGATG
*
28052615 -TGCGAACCCTAAATG
1 ATGCGAACCCTAGATG
28052630 -TGCGAACCCTA
1 ATGCGAACCCTA
28052641 TATGTGTGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
15 25 0.62
16 11 0.28
17 4 0.10
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.19
Consensus pattern (16 bp):
ATGCGAACCCTAGATG
Found at i:28052620 original size:15 final size:15
Alignment explanation
Indices: 28052603--28052757 Score: 125
Period size: 15 Copynumber: 10.3 Consensus size: 15
28052593 TGATGCATGC
*
28052603 GAACCCTAGATGTGC
1 GAACCCTAGATGTGT
* *
28052618 GAACCCTAAATGTGC
1 GAACCCTAGATGTGT
*
28052633 GAACCCTATATGTGT
1 GAACCCTAGATGTGT
** *
28052648 GAAATCTATATGTGT
1 GAACCCTAGATGTGT
*
28052663 AAACCCTAGATGTGT
1 GAACCCTAGATGTGT
*
28052678 GAACCCTA-ATGCATGC
1 GAACCCTAGATG--TGT
* * *
28052694 AAACTCTATATGTGT
1 GAACCCTAGATGTGT
28052709 GAACCCT-GTATGTGT
1 GAACCCTAG-ATGTGT
* *
28052724 GAACTCTATATGTGT
1 GAACCCTAGATGTGT
* *
28052739 GAACCCTAAATGTAT
1 GAACCCTAGATGTGT
28052754 GAAC
1 GAAC
28052758 TCTGTATGGG
Statistics
Matches: 113, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
14 3 0.03
15 99 0.88
16 8 0.07
17 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (15 bp):
GAACCCTAGATGTGT
Found at i:28052636 original size:30 final size:30
Alignment explanation
Indices: 28052600--28052842 Score: 157
Period size: 30 Copynumber: 8.1 Consensus size: 30
28052590 CCCTGATGCA
* *
28052600 TGCGAACCCTAGATGTGCGAACCCTAAATG
1 TGCGAACCCTATATGTGTGAACCCTAAATG
** *
28052630 TGCGAACCCTATATGTGTGAAATCTATATG
1 TGCGAACCCTATATGTGTGAACCCTAAATG
** *
28052660 TGTAAACCCTAGATGTGTGAACCCT-AATG
1 TGCGAACCCTATATGTGTGAACCCTAAATG
* * **
28052689 CATGCAAACTCTATATGTGTGAACCCTGTATG
1 --TGCGAACCCTATATGTGTGAACCCTAAATG
* *
28052721 TGTGAACTCTATATGTGTGAACCCTAAATG
1 TGCGAACCCTATATGTGTGAACCCTAAATG
** * * * ** *
28052751 TATGAACTCTGTATGGGCAAACCCTATATG
1 TGCGAACCCTATATGTGTGAACCCTAAATG
* ** * * * *
28052781 GGTAAAACCTATATATATGAACCCTATATG
1 TGCGAACCCTATATGTGTGAACCCTAAATG
* * *
28052811 TGCAAAGCCC-ATATGTGCGAACCCTATATG
1 TGCGAA-CCCTATATGTGTGAACCCTAAATG
28052841 TG
1 TG
28052843 AACCTATTAT
Statistics
Matches: 167, Mismatches: 42, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
29 3 0.02
30 137 0.82
31 24 0.14
32 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (30 bp):
TGCGAACCCTATATGTGTGAACCCTAAATG
Found at i:28052774 original size:91 final size:91
Alignment explanation
Indices: 28052588--28052776 Score: 200
Period size: 91 Copynumber: 2.1 Consensus size: 91
28052578 GGTATATGCG
* * *
28052588 AACCCTGATGCATGCGAACCCTAGATGTGCGAACCCTAAATGTGCGAACCCTATATGTGTGAAAT
1 AACCCTAATGCATGCAAACCCTAGATGTGCGAACCCTAAATGTGCGAACCCTATATGTGTGAAAC
* * * **
28052653 CTATATGTGTAAACCCTAGATGTGTG
66 CTAAATGTATAAACCCTAGATGGGCA
* * * ** * * *
28052679 AACCCTAATGCATGCAAACTCTATATGTGTGAACCCTGTATGTGTGAACTCTATATGTGTGAACC
1 AACCCTAATGCATGCAAACCCTAGATGTGCGAACCCTAAATGTGCGAACCCTATATGTGTGAAAC
* *
28052744 CTAAATGTATGAACTCT-GTATGGGCA
66 CTAAATGTATAAACCCTAG-ATGGGCA
28052770 AACCCTA
1 AACCCTA
28052777 TATGGGTAAA
Statistics
Matches: 79, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
90 1 0.01
91 78 0.99
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (91 bp):
AACCCTAATGCATGCAAACCCTAGATGTGCGAACCCTAAATGTGCGAACCCTATATGTGTGAAAC
CTAAATGTATAAACCCTAGATGGGCA
Found at i:28052778 original size:45 final size:46
Alignment explanation
Indices: 28052729--28052841 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 46
28052719 TGTGTGAACT
* * *
28052729 CTATATGTGTGAACCCTAAATGTATGAACTCTGTATGGGCAAA-CC
1 CTATATGTGTGAACCCTATATGTATGAACCCTATATGGGCAAAGCC
* * * * *
28052774 CTATATGGGTAAAACCTATATATATGAACCCTATATGTGCAAAGCC
1 CTATATGTGTGAACCCTATATGTATGAACCCTATATGGGCAAAGCC
*
28052820 C-ATATGTGCGAACCCTATATGT
1 CTATATGTGTGAACCCTATATGT
28052842 GAACCTATTA
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
45 51 0.94
46 3 0.06
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (46 bp):
CTATATGTGTGAACCCTATATGTATGAACCCTATATGGGCAAAGCC
Found at i:28052782 original size:15 final size:15
Alignment explanation
Indices: 28052604--28052842 Score: 115
Period size: 15 Copynumber: 15.9 Consensus size: 15
28052594 GATGCATGCG
* *
28052604 AACCCTAGATGTGCG
1 AACCCTATATGTGCA
* *
28052619 AACCCTAAATGTGCG
1 AACCCTATATGTGCA
*
28052634 AACCCTATATGTGTGA
1 AACCCTATATGTG-CA
* *
28052650 AA-TCTATATGTGTA
1 AACCCTATATGTGCA
* **
28052664 AACCCTAGATGTGTG
1 AACCCTATATGTGCA
28052679 AACCCTA-ATGCATGCA
1 AACCCTATATG--TGCA
* **
28052695 AACTCTATATGTGTG
1 AACCCTATATGTGCA
* **
28052710 AACCCTGTATGTGTG
1 AACCCTATATGTGCA
* **
28052725 AACTCTATATGTGTG
1 AACCCTATATGTGCA
* ***
28052740 AACCCTAAATGTATG
1 AACCCTATATGTGCA
* * *
28052755 AACTCTGTATGGGCA
1 AACCCTATATGTGCA
* *
28052770 AACCCTATATGGGTA
1 AACCCTATATGTGCA
* * ***
28052785 AAACCTATATATATG
1 AACCCTATATGTGCA
28052800 AACCCTATATGTGCA
1 AACCCTATATGTGCA
*
28052815 AAGCCC-ATATGTGCG
1 AA-CCCTATATGTGCA
28052830 AACCCTATATGTG
1 AACCCTATATGTG
28052843 AACCTATTAT
Statistics
Matches: 175, Mismatches: 42, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
14 9 0.05
15 150 0.86
16 13 0.07
17 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (15 bp):
AACCCTATATGTGCA
Found at i:28053349 original size:18 final size:18
Alignment explanation
Indices: 28053326--28053361 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28053316 TTTGGTGTGT
28053326 CAAGCGATACTCAAGGGC
1 CAAGCGATACTCAAGGGC
28053344 CAAGCGATACTCAAGGGC
1 CAAGCGATACTCAAGGGC
28053362 GAATAGGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.11
Consensus pattern (18 bp):
CAAGCGATACTCAAGGGC
Found at i:28054219 original size:21 final size:23
Alignment explanation
Indices: 28054179--28054226 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
28054169 AGTTAAAAGG
*
28054179 AAAAAGATGAAAAGTAAAGAAAT
1 AAAAACATGAAAAGTAAAGAAAT
28054202 AAAAACAT-AAAA-TAAAGAAAT
1 AAAAACATGAAAAGTAAAGAAAT
28054223 AAAA
1 AAAA
28054227 CGATGGTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 13 0.54
22 4 0.17
23 7 0.29
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.12
Consensus pattern (23 bp):
AAAAACATGAAAAGTAAAGAAAT
Found at i:28060581 original size:13 final size:14
Alignment explanation
Indices: 28060556--28060584 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28060546 AATTAATACT
28060556 AAAAAGAATAAAGA
1 AAAAAGAATAAAGA
28060570 AAAAAGAA-AAAGA
1 AAAAAGAATAAAGA
28060583 AA
1 AA
28060585 TTGTGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (14 bp):
AAAAAGAATAAAGA
Found at i:28066033 original size:11 final size:11
Alignment explanation
Indices: 28066017--28066041 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28066007 ATATTGAAAC
28066017 CTATGCAGTTT
1 CTATGCAGTTT
28066028 CTATGCAGTTT
1 CTATGCAGTTT
28066039 CTA
1 CTA
28066042 AGTTCTCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (11 bp):
CTATGCAGTTT
Found at i:28066527 original size:26 final size:26
Alignment explanation
Indices: 28066491--28066544 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
28066481 TTGGGTATAG
28066491 TCAGATACAGGTAATGTTCAGTTTGT
1 TCAGATACAGGTAATGTTCAGTTTGT
28066517 TCAGATACAGGTAATGTTCAGTTTGT
1 TCAGATACAGGTAATGTTCAGTTTGT
28066543 TC
1 TC
28066545 TAAGCTTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (26 bp):
TCAGATACAGGTAATGTTCAGTTTGT
Found at i:28070227 original size:59 final size:59
Alignment explanation
Indices: 28070123--28070239 Score: 153
Period size: 59 Copynumber: 2.0 Consensus size: 59
28070113 TTACATTTTG
* * * * *
28070123 GTACCTGAACTTGGCTTATGATTCAAATTGGTATCTAATGATTTTTTTTGTCCAATTAA
1 GTACCTGAACTTGGCTTAAGACTCAAATTAGTACCTAACGATTTTTTTTGTCCAATTAA
* * * *
28070182 GTACTTGAACTTGGCTTAAGGCTCAATTTAGTACCTAACGTTTTTTTTTGTCCAATTA
1 GTACCTGAACTTGGCTTAAGACTCAAATTAGTACCTAACGATTTTTTTTGTCCAATTA
28070240 GGGTTACGAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (59 bp):
GTACCTGAACTTGGCTTAAGACTCAAATTAGTACCTAACGATTTTTTTTGTCCAATTAA
Found at i:28071007 original size:29 final size:30
Alignment explanation
Indices: 28070966--28071029 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
28070956 AAAGTTATTA
*
28070966 TTTAGTCCATATAC-TTTGATTTGATCAAT
1 TTTAGTCCATATACTTTTGAATTGATCAAT
* *
28070995 TTTAGTCCCTATACTTTTTGAATTGGTCAAT
1 TTTAGTCCATATAC-TTTTGAATTGATCAAT
28071026 TTTA
1 TTTA
28071030 ATACTTGTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 13 0.43
31 17 0.57
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (30 bp):
TTTAGTCCATATACTTTTGAATTGATCAAT
Found at i:28071453 original size:3 final size:3
Alignment explanation
Indices: 28071445--28071490 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
28071435 ATATACTATC
28071445 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28071491 CCTTTTAGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28081815 original size:5 final size:5
Alignment explanation
Indices: 28081807--28081831 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28081797 TTTTTGTTAA
28081807 TAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT
28081832 AATAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Found at i:28082545 original size:22 final size:20
Alignment explanation
Indices: 28082490--28082536 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
28082480 CTATTTACTT
*
28082490 TTAT-TTTATTAATTTGTTG
1 TTATATTTATTAATATGTTG
28082509 TTATATTT-TTAATATGTTG
1 TTATATTTATTAATATGTTG
28082528 TTATATTTA
1 TTATATTTA
28082537 AATTAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 22 0.88
20 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (20 bp):
TTATATTTATTAATATGTTG
Found at i:28086012 original size:3 final size:3
Alignment explanation
Indices: 28086006--28086051 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
28085996 TTTAAAAGAA
28086006 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
28086052 GGAAAAGATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28094615 original size:44 final size:44
Alignment explanation
Indices: 28094552--28094638 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
28094542 ATAGGTTAAA
*
28094552 TAATATTAAAATAAACTACA-TTAATTAAAGTTTAAGTGGGAAAT
1 TAATATTAAAATAAACTACACTT-ATCAAAGTTTAAGTGGGAAAT
* *
28094596 TAATATTAAAATAACCTACACTTATCAGAGTTTAAGTGGGAAA
1 TAATATTAAAATAAACTACACTTATCAAAGTTTAAGTGGGAAA
28094639 CTAAAAACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 37 0.95
45 2 0.05
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (44 bp):
TAATATTAAAATAAACTACACTTATCAAAGTTTAAGTGGGAAAT
Found at i:28096438 original size:23 final size:22
Alignment explanation
Indices: 28096392--28096438 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
28096382 AGATAAAACT
*
28096392 AAACCCCAAAACCTAAAAATAA
1 AAACCCCAAAACCTAAAAACAA
* *
28096414 AAACCCTCAAAACGTAAACACAA
1 AAACCC-CAAAACCTAAAAACAA
28096437 AA
1 AA
28096439 TTCTCTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.62, C:0.28, G:0.02, T:0.09
Consensus pattern (22 bp):
AAACCCCAAAACCTAAAAACAA
Found at i:28097610 original size:107 final size:107
Alignment explanation
Indices: 28097408--28097697 Score: 476
Period size: 107 Copynumber: 2.7 Consensus size: 107
28097398 TTTAAGAGGG
* * *
28097408 TATTTGG-CTAAACG-AGAAATCGAAACCCAGCGCATTAGGGCACGTTTTCTTGAATTTCCAAAC
1 TATTTGGTC-AAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAAC
* *
28097471 GCAAAATATTGCCTTACTTTGAAATTTTAAAAGTATATTTGGC
65 GCAAAATATTGCCATACTTTGAAATTTTAAAAGGATATTTGGC
28097514 TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
1 TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
*
28097579 CAAAATATTTCCATACTTTGAAATTTTAAAAGGATATTTGGC
66 CAAAATATTGCCATACTTTGAAATTTTAAAAGGATATTTGGC
* * *
28097621 TATTTGGTCAAACAAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTTTCGAATTTTCAAACG
1 TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
28097686 CAAAATATTGCC
66 CAAAATATTGCC
28097698 TTTATTATTT
Statistics
Matches: 172, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
106 12 0.07
107 160 0.93
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (107 bp):
TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
CAAAATATTGCCATACTTTGAAATTTTAAAAGGATATTTGGC
Found at i:28100613 original size:183 final size:183
Alignment explanation
Indices: 28100338--28100754 Score: 692
Period size: 183 Copynumber: 2.3 Consensus size: 183
28100328 ATAGGATTCA
* * * * * * *
28100338 TATCTTCAAACTTGCCCCACT-CAACTTCAGGGGGATAAGGCTTGATATGATAAGATTTAATCCG
1 TATCTTC-AACCTGCTCCACTGCGACCTCAGGGAGATAAGGTTTGATATGATAAGATTTAATCCA
* *
28100402 ACCCTCTGCAACTTCAAAGGTGTAGGATTCATCGTTTTAATCCGCTCCATTGCAACTTTAGGGAG
65 ACCCTCTGCAACTTCAAAGGTATAGGATTCATCGTTTTAATCCGCTCCATTACAACTTTAGGGAG
*
28100467 ATAGGATTAGTAGCTTCAGTCTGTTCCACTGTAACTTCAGGGAGATAAGACTTG
130 ATAGGATTAGTAGCTTCAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTG
*
28100521 TATCTTCAACCTGCTCCATTGCGACCTCAGGGAGATAAGGTTTGATATGATAAGATTTAATCCAA
1 TATCTTCAACCTGCTCCACTGCGACCTCAGGGAGATAAGGTTTGATATGATAAGATTTAATCCAA
* *
28100586 CCCTTTGCAACTTCAAAGGTATAGGATTTATCGTTTTAATCCGCTCCATTACAACTTTAGGGAGA
66 CCCTCTGCAACTTCAAAGGTATAGGATTCATCGTTTTAATCCGCTCCATTACAACTTTAGGGAGA
28100651 TAGGATTAGTAGCTTCAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTG
131 TAGGATTAGTAGCTTCAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTG
*
28100704 TATCTTCAACCTGCTCCACTGCGACCTCAGGAAGATAAGGTTTGATATGAT
1 TATCTTCAACCTGCTCCACTGCGACCTCAGGGAGATAAGGTTTGATATGAT
28100755 CTTCTTTCTA
Statistics
Matches: 218, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
182 10 0.05
183 208 0.95
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (183 bp):
TATCTTCAACCTGCTCCACTGCGACCTCAGGGAGATAAGGTTTGATATGATAAGATTTAATCCAA
CCCTCTGCAACTTCAAAGGTATAGGATTCATCGTTTTAATCCGCTCCATTACAACTTTAGGGAGA
TAGGATTAGTAGCTTCAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTG
Found at i:28100711 original size:44 final size:44
Alignment explanation
Indices: 28100628--28100742 Score: 115
Period size: 44 Copynumber: 2.6 Consensus size: 44
28100618 GTTTTAATCC
* * * * **
28100628 GCTCCATTACAACTTTAGGGAGATAGGATTAGTAGCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAACCT
* *
28100672 GCTCCACTGTAACTTCAGGGAGATAAGACTT-GTATCTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTAGCTTCAACCT
* * *
28100716 GCTCCACTGCGACCTCAGGAAGATAAG
1 GCTCCACTGCAACTTCAGGGAGATAAG
28100743 GTTTGATATG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
44 56 0.97
45 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAACCT
Found at i:28100917 original size:41 final size:45
Alignment explanation
Indices: 28100872--28100976 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
28100862 CGCTCCACTA
* * * *
28100872 CAACTTTAGGGAGATAAGAT-T-C-ATCGT-GGTCTGTTCTACTG
1 CAACTTCAGAGAGATAAGATCTGCTATCGTCAGTCTATTCTACTG
* *
28100913 CAACTTCAGAGAGATAATATCTGCTATCTTCAGTCTATTCTACTG
1 CAACTTCAGAGAGATAAGATCTGCTATCGTCAGTCTATTCTACTG
*
28100958 CAACTTCAGTGAGATAAGA
1 CAACTTCAGAGAGATAAGA
28100977 CTTGTAATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
41 17 0.33
42 1 0.02
43 1 0.02
44 4 0.08
45 29 0.56
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (45 bp):
CAACTTCAGAGAGATAAGATCTGCTATCGTCAGTCTATTCTACTG
Done.