Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 77 of 230
Found at i:21195827 original size:21 final size:20
Alignment explanation
Indices: 21195798--21195838 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
21195788 CTCTCTCACC
*
21195798 AAAATTTTCAAAAATATTTAT
1 AAAAATTTCAAAAAT-TTTAT
21195819 AAAAATTTCAAAAATTTTAT
1 AAAAATTTCAAAAATTTTAT
21195839 TTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATTTCAAAAATTTTAT
Found at i:21195847 original size:14 final size:14
Alignment explanation
Indices: 21195830--21195859 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21195820 AAAATTTCAA
*
21195830 AAATTTTATTTTTT
1 AAATTATATTTTTT
21195844 AAATTATATTTTTT
1 AAATTATATTTTTT
21195858 AA
1 AA
21195860 GAAAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AAATTATATTTTTT
Found at i:21198013 original size:19 final size:19
Alignment explanation
Indices: 21197978--21198015 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
21197968 AAGTTACAAA
*
21197978 AAATAAAAAATATAAATAT
1 AAATAAAAAATAAAAATAT
21197997 AAATAAAATAA-AAAAATAT
1 AAATAAAA-AATAAAAATAT
21198016 TAATTACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAAAAATAAAAATAT
Found at i:21199918 original size:40 final size:41
Alignment explanation
Indices: 21199840--21199920 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 41
21199830 AGGAAGCGCT
**
21199840 TGTCCACGTGGACAAAAAACGCTTCCTTGAGGGCGCACTTTG
1 TGTCCACGTGGAC-AAAAACGCTTCCTTGAGGAAGCACTTTG
*
21199882 TGTCCACGTGGAC-AAAGCGCTTCCTTGAGGAAGCACTTT
1 TGTCCACGTGGACAAAAACGCTTCCTTGAGGAAGCACTTT
21199921 TTCCGTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 23 0.64
42 13 0.36
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (41 bp):
TGTCCACGTGGACAAAAACGCTTCCTTGAGGAAGCACTTTG
Found at i:21200107 original size:96 final size:96
Alignment explanation
Indices: 21199999--21200309 Score: 423
Period size: 97 Copynumber: 3.2 Consensus size: 96
21199989 ATTTTAGGGG
* * * * * * * *
21199999 TTTAAGGAAAAAATTAAATAAATAAGGGTTTAGGGTTTCTTAATTAAATTAATTATAGATTTTAA
1 TTTAAGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTTAA
21200064 AAAATTAGATTAGGGTTTAGTGTTTATGGTT
66 AAAATTAGATTAGGGTTTAGTGTTTATGGTT
21200095 TTTAAGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAATTATTTT
1 TTTAAGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAA--ATTTT
**
21200160 TTAAAA-TAGATTAGGGTTTAGTG-TT-TGGTT
64 AAAAAATTAGATTAGGGTTTAGTGTTTATGGTT
21200190 TTTAAGGGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTT
1 TTTAA--GAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTT
* * *
21200255 AAAAAAATTAGATTGGGGTTTAGTATTTAGGGTT
64 -AAAAAATTAGATTAGGGTTTAGTGTTTATGGTT
*
21200289 TTTAA-AGAAAAATCAAATAAA
1 TTTAAGAAAAAAATCAAATAAA
21200310 GCTAGTTGTT
Statistics
Matches: 191, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
95 15 0.08
96 71 0.37
97 85 0.45
98 11 0.06
99 9 0.05
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.39
Consensus pattern (96 bp):
TTTAAGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTTAA
AAAATTAGATTAGGGTTTAGTGTTTATGGTT
Found at i:21200862 original size:11 final size:11
Alignment explanation
Indices: 21200846--21200871 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21200836 GTTAGACTTA
21200846 ATAAATAATTT
1 ATAAATAATTT
21200857 ATAAATAATTT
1 ATAAATAATTT
21200868 ATAA
1 ATAA
21200872 TTTTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATAAATAATTT
Found at i:21200871 original size:18 final size:16
Alignment explanation
Indices: 21200850--21200889 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
21200840 GACTTAATAA
21200850 ATAATTTATAAATAATTT
1 ATAATTT-TAAA-AATTT
*
21200868 ATAATTTTTAAAATTT
1 ATAATTTTAAAAATTT
21200884 ATAATT
1 ATAATT
21200890 AATTTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
17 3 0.14
18 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAATTTTAAAAATTT
Found at i:21201039 original size:16 final size:16
Alignment explanation
Indices: 21201018--21201069 Score: 104
Period size: 16 Copynumber: 3.2 Consensus size: 16
21201008 TTTGGTTCGC
21201018 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
21201034 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
21201050 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
21201066 TGTA
1 TGTA
21201070 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.37, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:21201134 original size:44 final size:45
Alignment explanation
Indices: 21201050--21201140 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
21201040 GGATTAGAGG
* * *
21201050 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
21201095 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
21201139 TG
1 TG
21201141 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:21201326 original size:18 final size:17
Alignment explanation
Indices: 21201305--21201339 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21201295 TTATTATTAA
*
21201305 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
21201323 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
21201340 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:21201897 original size:66 final size:65
Alignment explanation
Indices: 21201825--21202022 Score: 161
Period size: 66 Copynumber: 3.2 Consensus size: 65
21201815 GAAATTCTTA
*
21201825 ATAATTAATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAA
1 ATAATTAATATTCTTATATTAATTTACT-AAATCATAATATATAATACTGTAAAATATAAATTAA
21201890 C
65 C
* ** * * *
21201891 ATAATTATTATT-AAATA-TAATTTAAT-AA--A-AATATATAAT-TTAGTAAAAT-T--CTT-A
1 ATAATTAATATTCTTATATTAATTTACTAAATCATAATATATAATACT-GTAAAATATAAATTAA
21201945 -
65 C
* * * *
21201945 AT-ATTAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAATTTA
1 ATAATT-AATATTCTTATATTAATTTACT-AAATCATAATATATAATACTGTAAAATATAAATTA
21202009 AC
64 AC
*
21202011 ATAATTATTATT
1 ATAATTAATATT
21202023 AAATATAATT
Statistics
Matches: 99, Mismatches: 17, Indels: 32
0.67 0.11 0.22
Matches are distributed among these distances:
53 3 0.03
54 7 0.07
55 4 0.04
56 8 0.08
58 4 0.04
59 16 0.16
60 2 0.02
61 16 0.16
62 4 0.04
64 10 0.10
65 4 0.04
66 18 0.18
67 3 0.03
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.43
Consensus pattern (65 bp):
ATAATTAATATTCTTATATTAATTTACTAAATCATAATATATAATACTGTAAAATATAAATTAAC
Found at i:21202108 original size:120 final size:120
Alignment explanation
Indices: 21201288--21202107 Score: 1437
Period size: 120 Copynumber: 6.8 Consensus size: 120
21201278 ATCATATTTA
21201288 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
21201353 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
21201408 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
21201473 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
21201528 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
21201593 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
21201648 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
21201713 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
21201768 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
21201833 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
* * *
21201888 AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAGTAAAATTCTTAAT-ATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT-A
* * * * * *
21201952 ATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAATTT
65 ATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
* *
21202008 AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAT-ATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT-A
* * *
21202072 ATATTCTTATATGAATTTTCTAAAATCATAATATAT
65 ATATTCTTATATTAATTTACTGAAATCATAATATAT
21202108 ATAATACTAC
Statistics
Matches: 680, Mismatches: 19, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
119 3 0.00
120 677 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:21202234 original size:14 final size:15
Alignment explanation
Indices: 21202215--21202247 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
21202205 CATTATTCTT
*
21202215 AAAATTCAAAAA-TA
1 AAAATTAAAAAACTA
21202229 AAAATTAAAAAACTA
1 AAAATTAAAAAACTA
21202244 AAAA
1 AAAA
21202248 ATTTAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATTAAAAAACTA
Found at i:21202717 original size:58 final size:58
Alignment explanation
Indices: 21202594--21202743 Score: 212
Period size: 59 Copynumber: 2.6 Consensus size: 58
21202584 AAAGTTGCTA
* **
21202594 TGTTTTGGCACTAAAAGCAACCGCAAGCCACAACTACCAGCATGTCAAGGATTAAATT
1 TGTTTTGGCACTAAAAGCAACCGCAAGTCACAAGAACCAGCATGTCAAGGATTAAATT
* * * *
21202652 TGTTTTGGCACCAAAAGTAAACCACAAGTCACAAGAACCAGCATGTCAAGGATTGAATT
1 TGTTTTGGCACTAAAAG-CAACCGCAAGTCACAAGAACCAGCATGTCAAGGATTAAATT
*
21202711 TGTTTGGGCACTAAAAGCAACCGCAA-TCACAAG
1 TGTTTTGGCACTAAAAGCAACCGCAAGTCACAAG
21202744 CCACAAGTAC
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
57 7 0.09
58 23 0.29
59 50 0.62
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (58 bp):
TGTTTTGGCACTAAAAGCAACCGCAAGTCACAAGAACCAGCATGTCAAGGATTAAATT
Found at i:21212175 original size:20 final size:21
Alignment explanation
Indices: 21212137--21212176 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
21212127 TACTTTATTT
*
21212137 CATTTTTCTTTATTTTTCTTC
1 CATTTTTCTTTATTATTCTTC
*
21212158 CATTTTT-TTTCTTATTCTT
1 CATTTTTCTTTATTATTCTT
21212177 TCCTTTCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72
Consensus pattern (21 bp):
CATTTTTCTTTATTATTCTTC
Found at i:21212179 original size:21 final size:21
Alignment explanation
Indices: 21212137--21212192 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
21212127 TACTTTATTT
* * *
21212137 CATTTTTCTTTATTTTTCTTC
1 CATTTTTATTTCTTATTCTTC
21212158 CATTTTT-TTTCTTATTCTTTC
1 CATTTTTATTTCTTATTC-TTC
21212179 C-TTTCTTATTTCTT
1 CATTT-TTATTTCTT
21212193 TTCCTTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 11 0.37
21 13 0.43
22 6 0.20
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (21 bp):
CATTTTTATTTCTTATTCTTC
Found at i:21212183 original size:15 final size:17
Alignment explanation
Indices: 21212165--21212198 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
21212155 TTCCATTTTT
21212165 TTTCTTA-TTC-TTTCC
1 TTTCTTATTTCTTTTCC
21212180 TTTCTTATTTCTTTTCC
1 TTTCTTATTTCTTTTCC
21212197 TT
1 TT
21212199 CATTCTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCTTATTTCTTTTCC
Found at i:21212616 original size:6 final size:6
Alignment explanation
Indices: 21212607--21212635 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
21212597 TTATTCTGTC
21212607 GTGGTT GTGGTT GTGGTT GTGGTT G-GGTT
1 GTGGTT GTGGTT GTGGTT GTGGTT GTGGTT
21212636 TCTTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (6 bp):
GTGGTT
Found at i:21214469 original size:18 final size:17
Alignment explanation
Indices: 21214448--21214482 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21214438 TTATTATTAA
*
21214448 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
21214466 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
21214483 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:21214475 original size:55 final size:52
Alignment explanation
Indices: 21214408--21214788 Score: 155
Period size: 55 Copynumber: 7.3 Consensus size: 52
21214398 TATTATCAAT
*
21214408 AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAA
1 AATATATAATTTAATCATATTT-AA-ATAATTATTATTAAATATATTTT-ATTAA
* * * ** * * **
21214463 AATATATAATTTAATAAAATTCTTAATAATTAGCA-TAAATTTGTTTTGGTAA
1 AATATATAATTTAATCATATT-TAAATAATTATTATTAAATATATTTTATTAA
* * * ** * *
21214515 ATTAT-TATTGTTATTGTTATTT--A-AATT-TTAATAAGAT-TATTATTATCAA
1 AATATATAAT-TTAATCATATTTAAATAATTATTATTAA-ATATATT-TTATTAA
*
21214564 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAA
1 -AATATATAATTTAATCATATTT-AA-ATAATTATTATTAAATATATTTT-ATTAA
* * * ** * * **
21214620 AATATATAATTTAATAAAATTCTTAATAATTAGCA-TAAATTTGTTTTGGTAA
1 AATATATAATTTAATCATATT-TAAATAATTATTATTAAATATATTTTATTAA
* * * ** * * *
21214672 ATTAT-TATTGTTATTGTTATTT--A-AATT-TTAATAAGAT-TA--ATATCAA
1 AATATATAAT-TTAATCATATTTAAATAATTATTATTAA-ATATATTTTATTAA
* *
21214718 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAA
1 -AATATATAATTTAATCATATTT-AA-ATAATTATTATTAAATATATT-TTATTAA
21214774 AATATATAATTTAAT
1 AATATATAATTTAAT
21214789 AAAATTCTTA
Statistics
Matches: 231, Mismatches: 64, Indels: 62
0.65 0.18 0.17
Matches are distributed among these distances:
46 3 0.01
47 14 0.06
48 21 0.09
49 10 0.04
50 12 0.05
51 12 0.05
52 34 0.15
53 28 0.12
54 17 0.07
55 60 0.26
56 20 0.09
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (52 bp):
AATATATAATTTAATCATATTTAAATAATTATTATTAAATATATTTTATTAA
Found at i:21214520 original size:75 final size:75
Alignment explanation
Indices: 21214440--21214678 Score: 198
Period size: 78 Copynumber: 3.1 Consensus size: 75
21214430 AAACATAATT
21214440 ATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCATAAATTT
1 ATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCATAAATTT
21214505 GTTTTGGTAA
66 GTTTTGGTAA
* * * * * * * ** * *
21214515 ATTATT-ATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTA-TCAATAATAAATA--ATT
1 ATTATTAAAT-ATATT-TTAATTAAAATAT-ATAA-TTTAATAAAATTC-TTAATAATTAGCA-T
* * * ***
21214576 TAATCATATTTAAACATAA
60 AAAT-TTGTTT--TGGTAA
21214595 TTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCATAAAT
1 --ATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCATAAAT
21214660 TTGTTTTGGTAA
64 TTGTTTTGGTAA
21214672 ATTATTA
1 ATTATTA
21214679 TTGTTATTGT
Statistics
Matches: 115, Mismatches: 34, Indels: 30
0.64 0.19 0.17
Matches are distributed among these distances:
74 2 0.02
75 17 0.15
76 11 0.10
77 13 0.11
78 18 0.16
79 18 0.16
80 13 0.11
81 11 0.10
82 10 0.09
83 2 0.02
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (75 bp):
ATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCATAAATTT
GTTTTGGTAA
Found at i:21214621 original size:157 final size:157
Alignment explanation
Indices: 21214335--21214805 Score: 885
Period size: 157 Copynumber: 3.0 Consensus size: 157
21214325 TAGAATACCC
* *
21214335 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
21214400 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
21214465 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
21214492 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
21214557 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
21214622 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
21214649 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTA--A
1 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
*
21214712 -TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
*
21214776 TATATAATTTAATAAAATTCTTAAAAA
131 TATATAATTTAATAAAATTCTTAATAA
21214803 TTA
1 TTA
21214806 ATATTCTTAT
Statistics
Matches: 310, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
154 92 0.30
155 1 0.00
157 217 0.70
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:21214626 original size:18 final size:17
Alignment explanation
Indices: 21214605--21214639 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21214595 TTATTATTAA
*
21214605 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
21214623 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
21214640 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:21214776 original size:16 final size:16
Alignment explanation
Indices: 21214739--21214780 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
21214729 TTAATCATAT
*
21214739 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
21214755 TT-AAATATATTATAA
1 TTAAAATATATTATAA
21214770 TTAAAATATAT
1 TTAAAATATAT
21214781 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:21214787 original size:14 final size:15
Alignment explanation
Indices: 21214748--21214789 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21214738 TTTAAACATA
*
21214748 ATTATTATTAAATAT
1 ATTATAATTAAATAT
21214763 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
21214777 A-TATAATTTAATA
1 ATTATAATTAAATA
21214790 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:21214876 original size:120 final size:121
Alignment explanation
Indices: 21214737--21215033 Score: 462
Period size: 120 Copynumber: 2.5 Consensus size: 121
21214727 ATTTAATCAT
*
21214737 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAA-A
1 ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
21214801 AATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
66 AA-TAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
21214859 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
21214922 AATAAAATTCTTCTATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 AATAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* *
21214978 ATTTCAA-ATAATTAATATTAAATATGATT-TAATT-AAATATATGATTTAATAAAATT
1 ATTTCAACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAAAATT
21215034 TAAAATTATT
Statistics
Matches: 165, Mismatches: 6, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
119 24 0.15
120 130 0.79
121 10 0.06
122 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (121 bp):
ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
AATAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:21214907 original size:14 final size:15
Alignment explanation
Indices: 21214858--21214909 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
21214848 GTAAAATATA
21214858 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
21214873 TATTAAATATATTAT
1 AATTAAATATATTAT
21214888 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
21214901 AATTTAATA
1 AATTAAATA
21214910 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:21214924 original size:44 final size:43
Alignment explanation
Indices: 21214835--21214925 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
21214825 CTCAAATCAT
* * *
21214835 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
* * *
21214878 AATATATTATAAT-TAAAATATATAATTTAATAAAATTCTTAATA
1 AATATATGATAATGTAAAATATA-AA-TTAACAAAATTATTAATA
21214922 AATA
1 AATA
21214926 AAATTCTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 9 0.22
43 13 0.32
44 18 0.45
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (43 bp):
AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
Found at i:21214960 original size:59 final size:59
Alignment explanation
Indices: 21214777--21214960 Score: 148
Period size: 59 Copynumber: 3.1 Consensus size: 59
21214767 TAATTAAAAT
21214777 ATATAATTTAATAAAATTCTTAA-AAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAAA-TAATATTCTTATATGAATTTACTCAAATCATA
* * * * * * * *
21214836 ATAT-ATGATACTGTAAAA-TATAAATTAACATAATTATTATTAAAT-ATATTATAATTAAA--A
1 ATATAAT-TTA--ATAAAATTCTTAA-TAA-ATAA-TATTCTTATATGA-ATT-TACTCAAATCA
21214896 T-
58 TA
* *
21214897 ATATAATTTAATAAAATTCTTAATAAATAAAATTCTTCTATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAAATAATATTCTTATATGAATTTACTCAAATCATA
21214956 ATATA
1 ATATA
21214961 TGATACTATA
Statistics
Matches: 92, Mismatches: 18, Indels: 30
0.66 0.13 0.21
Matches are distributed among these distances:
56 6 0.07
57 10 0.11
58 9 0.10
59 19 0.21
60 8 0.09
61 11 0.12
62 10 0.11
63 13 0.14
64 6 0.07
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAAATAATATTCTTATATGAATTTACTCAAATCATA
Found at i:21215014 original size:15 final size:15
Alignment explanation
Indices: 21214994--21215032 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
21214984 AATAATTAAT
21214994 ATTAAATATGATTTA
1 ATTAAATATGATTTA
21215009 ATTAAATATATGATTTA
1 ATT-AA-ATATGATTTA
*
21215026 ATAAAAT
1 ATTAAAT
21215033 TTAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 4 0.19
17 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
ATTAAATATGATTTA
Found at i:21215019 original size:17 final size:17
Alignment explanation
Indices: 21214999--21215032 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21214989 TTAATATTAA
*
21214999 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
21215016 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
21215033 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:21215175 original size:93 final size:92
Alignment explanation
Indices: 21215065--21215259 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
21215055 GATTATAGTT
* * *
21215065 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
21215128 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
21215158 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
21215223 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
21215250 TATGAATTTA
1 TATGAATTTA
21215260 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:21218723 original size:9 final size:9
Alignment explanation
Indices: 21218709--21218733 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21218699 TCTGAACTAC
21218709 ATTTATCTT
1 ATTTATCTT
21218718 ATTTATCTT
1 ATTTATCTT
21218727 ATTTATC
1 ATTTATC
21218734 AGCAAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (9 bp):
ATTTATCTT
Found at i:21220545 original size:15 final size:16
Alignment explanation
Indices: 21220525--21220560 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
21220515 TTTAATTTTC
*
21220525 AAATTTTCAAAAA-AA
1 AAATTTTAAAAAATAA
21220540 AAATTTTAAAAAATAA
1 AAATTTTAAAAAATAA
21220556 AAATT
1 AAATT
21220561 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTTTAAAAAATAA
Found at i:21220590 original size:30 final size:31
Alignment explanation
Indices: 21220556--21220657 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
21220546 TAAAAAATAA
*
21220556 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
21220586 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
21220616 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
21220646 AAATTTCATTTT
1 AAATTTCATTTT
21220658 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:21221050 original size:3 final size:3
Alignment explanation
Indices: 21221042--21221088 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
21221032 GCTAGACTTT
* *
21221042 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA AAA GAG GAA GAA GAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
21221089 ATAAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:21221060 original size:10 final size:10
Alignment explanation
Indices: 21221045--21221073 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
21221035 AGACTTTGAA
21221045 GAAGAAGAAG
1 GAAGAAGAAG
21221055 GAAGAAGAAG
1 GAAGAAGAAG
21221065 GAAGAAGAA
1 GAAGAAGAA
21221074 AAAGAGGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:21221204 original size:15 final size:13
Alignment explanation
Indices: 21221182--21221220 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
21221172 GCAGCCCAAG
21221182 AAAAAAACAACAAA
1 AAAAAAACAA-AAA
21221196 AACAAAAACAAAAA
1 AA-AAAAACAAAAA
21221210 AAAAGAAACAA
1 AAAA-AAACAA
21221221 GCCCCCCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 13 0.57
15 8 0.35
ACGTcount: A:0.85, C:0.13, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:21221393 original size:11 final size:11
Alignment explanation
Indices: 21221371--21221438 Score: 56
Period size: 10 Copynumber: 6.5 Consensus size: 11
21221361 GGCCCAGCAG
21221371 AGAAAA-AAAA
1 AGAAAAGAAAA
21221381 AGAAAAGAAAA
1 AGAAAAGAAAA
21221392 AG--AAGAAAA
1 AGAAAAGAAAA
*
21221401 AGAGAAGGAAAA
1 AGA-AAAGAAAA
* *
21221413 A-AGAAGGAAA
1 AGAAAAGAAAA
*
21221423 A-AAAGGAAAA
1 AGAAAAGAAAA
21221433 AGAAAA
1 AGAAAA
21221439 AAGAGGTTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
9 9 0.20
10 19 0.42
11 10 0.22
12 7 0.16
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AGAAAAGAAAA
Found at i:21221397 original size:9 final size:10
Alignment explanation
Indices: 21221377--21221436 Score: 68
Period size: 11 Copynumber: 5.8 Consensus size: 10
21221367 GCAGAGAAAA
*
21221377 AAAAAGAAAAG
1 AAAAAG-AAGG
*
21221388 AAAAAGAAGA
1 AAAAAGAAGG
21221398 AAAAGAGAAGG
1 AAAA-AGAAGG
21221409 AAAAAAGAAGG
1 -AAAAAGAAGG
21221420 AAAAA-AAGG
1 AAAAAGAAGG
21221429 AAAAAGAA
1 AAAAAGAA
21221437 AAAAGAGGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
9 9 0.21
10 13 0.30
11 17 0.40
12 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (10 bp):
AAAAAGAAGG
Found at i:21221415 original size:13 final size:11
Alignment explanation
Indices: 21221388--21221433 Score: 62
Period size: 10 Copynumber: 4.4 Consensus size: 11
21221378 AAAAGAAAAG
21221388 AAAAAGAA-GA
1 AAAAAGAAGGA
21221398 AAAAGAGAAGGA
1 AAAA-AGAAGGA
21221410 AAAAAGAAGG-
1 AAAAAGAAGGA
21221420 AAAAA-AAGGA
1 AAAAAGAAGGA
21221430 AAAA
1 AAAA
21221434 GAAAAAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.12
10 13 0.39
11 10 0.30
12 6 0.18
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAAGAAGGA
Found at i:21221592 original size:14 final size:12
Alignment explanation
Indices: 21221573--21221613 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 12
21221563 CATTTTATGC
21221573 ATTTTTATATTTA
1 ATTTTTA-ATTTA
21221586 TATTTTTAATTTA
1 -ATTTTTAATTTA
21221599 A--TTTAATTTA
1 ATTTTTAATTTA
21221609 ATTTT
1 ATTTT
21221614 ATTTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.40
12 3 0.12
13 5 0.20
14 7 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTTAATTTA
Found at i:21221814 original size:20 final size:22
Alignment explanation
Indices: 21221789--21221831 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
21221779 TCGGGTTTCG
21221789 AAATTT-TCGTG-TCTTCAAAA
1 AAATTTCTCGTGTTCTTCAAAA
*
21221809 AAATTTCTCGTGTTTTTCAAAA
1 AAATTTCTCGTGTTCTTCAAAA
21221831 A
1 A
21221832 TAAGGTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
AAATTTCTCGTGTTCTTCAAAA
Found at i:21221962 original size:18 final size:18
Alignment explanation
Indices: 21221932--21222284 Score: 189
Period size: 17 Copynumber: 19.9 Consensus size: 18
21221922 TAAAAATCGG
*
21221932 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
** *
21221950 AAAAATTCCCGTG-TTGC
1 AAAAATTTTCGTGTTTTC
*
21221967 AAAAATTTTCATGTTTTTC
1 AAAAATTTTCGTG-TTTTC
*
21221986 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
** ***
21222004 AAAAAAATTCCAATTTTC
1 AAAAATTTTCGTGTTTTC
*
21222022 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
21222040 TAAAAA-CTTC-TGTGTTTC
1 -AAAAATTTTCGTGT-TTTC
21222058 AAAAATTTTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* *
21222075 TAAAATTTTCGT-ATTTC
1 AAAAATTTTCGTGTTTTC
*
21222092 AAAAATTTTCTTGTTTTC
1 AAAAATTTTCGTGTTTTC
* * *
21222110 -AAATTTTTCGT-ATTTA
1 AAAAATTTTCGTGTTTTC
**
21222126 AAAAATCCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
21222144 -AAAA-TTCCAGTG-TTTC
1 AAAAATTTTC-GTGTTTTC
*
21222160 AAAATTTTTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
** **
21222177 AAAAAAAAATTCCCGTTTTCC
1 --AAAAATTTTCGTGTTTT-C
* *
21222198 AAAAACTTTCGCGTTTT-
1 AAAAATTTTCGTGTTTTC
**
21222215 AAGAAATTGACCGTG-TTTC
1 AA-AAATT-TTCGTGTTTTC
*
21222234 ATAAATTTTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* *
21222251 AAAGAAATCTCGTG-TTTC
1 AAA-AATTTTCGTGTTTTC
*
21222269 -AAAATTTTCATGTTTT
1 AAAAATTTTCGTGTTTT
21222285 TTTAAAAAAT
Statistics
Matches: 249, Mismatches: 64, Indels: 45
0.70 0.18 0.13
Matches are distributed among these distances:
16 15 0.06
17 101 0.41
18 83 0.33
19 46 0.18
20 3 0.01
21 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:21221985 original size:36 final size:35
Alignment explanation
Indices: 21221932--21222000 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
21221922 TAAAAATCGG
* *
21221932 AAAATTTTTCGTGTTTTCAAAAATTCCCGTGTTGC
1 AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
*
21221967 AAAAATTTTCATGTTTTTCAAAAATTCTCGTGTT
1 AAAAATTTTCATG-TTTTCAAAAATTCCCGTGTT
21222001 TTCAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (35 bp):
AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
Found at i:21222337 original size:15 final size:15
Alignment explanation
Indices: 21222285--21222340 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 15
21222275 TTCATGTTTT
21222285 TTTAAAAAATT-GTG
1 TTTAAAAAATTCGTG
** *
21222299 TTTCTAAAATTCTTGTAT
1 TTTAAAAAATTC--GT-G
21222317 TTTAAAAAATTCGTG
1 TTTAAAAAATTCGTG
21222332 TTTAAAAAA
1 TTTAAAAAA
21222341 AAAGGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
14 9 0.28
15 9 0.28
16 2 0.06
17 2 0.06
18 10 0.31
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (15 bp):
TTTAAAAAATTCGTG
Found at i:21226692 original size:44 final size:44
Alignment explanation
Indices: 21226636--21227218 Score: 282
Period size: 44 Copynumber: 13.2 Consensus size: 44
21226626 TTGGGGAGGT
*
21226636 AAGACCTG-TATCTTCGATCTACTTCA-CACTAGTATGGAAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCATCACTAGTATGG-AAGAC
* * *
21226679 ACGATCTGCTATC-TCTGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTC-GATCTACTTCA--TCACTAGTATGGAAGAC
*** * *
21226723 AAGATCCATTATCTTTGATCTACTTCACCACTAGTATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCATCACTAGTAT-GGAAGAC
* * *
21226768 AAGATCTGCCATCTTCGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAGAC
** * *
21226812 AAGATCCACTATC-TCTGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTC-GATCTACTTCA--TCACTAGTATGGAAGAC
*** * * *
21226856 AAGATCCATTATCTTCGATCTACTTCATGTCAATA-CAT-AAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAGAC
* * * *
21226900 AAGATCCGCTATCTTCGATATACTTCATGTCAATA-AAT-GAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAGAC
** * *
21226944 AAGATCCACTATC-TCTGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTC-GATCTACTTCA--TCACTAGTATGGAAGAC
*** * *
21226988 AAGATCCATTATCTTCGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAGAC
* * *
21227032 AAGATCCGCTATCTTCGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAGAC
** * * *
21227076 AAGATCCACTATCTTTGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAGAC
* *
21227120 AAGATCTGCTATC-TCTGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTC-GATCTACTTCA--TCACTAGTATGGAAGAC
* *** * *
21227164 AATATCCATTATCTTCGATCTACTTCACCACCAGTATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCATCACTAGTAT-GGAAGAC
21227209 AAGATCTGCT
1 AAGATCTGCT
21227219 GCTTTTTCAC
Statistics
Matches: 467, Mismatches: 53, Indels: 38
0.84 0.09 0.07
Matches are distributed among these distances:
42 7 0.01
43 17 0.04
44 383 0.82
45 48 0.10
46 4 0.01
47 8 0.02
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (44 bp):
AAGATCTGCTATCTTCGATCTACTTCATCACTAGTATGGAAGAC
Found at i:21226912 original size:88 final size:88
Alignment explanation
Indices: 21226674--21227190 Score: 740
Period size: 88 Copynumber: 5.9 Consensus size: 88
21226664 CTAGTATGGA
* * *
21226674 AAGACACGATCTGCTATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTT
1 AAGACAAGATCCGCTATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTT
* * * *
21226738 TGATCTACTTCA--CCACTAGTATGGG
65 CGATCTACTTCATGTCAATA-CAT--G
* *
21226763 AAGACAAGATCTGCCATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATC-TC
1 AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTC
21226827 TGATCTACTTCATGTCAATACATG
66 -GATCTACTTCATGTCAATACATG
** * *
21226851 AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATAAAGACAAGATCCGCTATCTTC
1 AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTC
* *
21226916 GATATACTTCATGTCAATAAATG
66 GATCTACTTCATGTCAATACATG
* *
21226939 AAGACAAGATCCACTATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTT
1 AAGACAAGATCCGCTATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTT
21227003 CGATCTACTTCATGTCAATACATG
65 CGATCTACTTCATGTCAATACATG
*
21227027 AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTT
1 AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTC
21227092 GATCTACTTCATGTCAATACATG
66 GATCTACTTCATGTCAATACATG
* * *
21227115 AAGACAAGATCTGCTATC-TCTGATCTACTTCATGTCAATACATGAAGACAATATCCATTATCTT
1 AAGACAAGATCCGCTATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTT
21227179 CGATCTACTTCA
65 CGATCTACTTCA
21227191 CCACCAGTAT
Statistics
Matches: 392, Mismatches: 28, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
87 4 0.01
88 309 0.79
89 71 0.18
90 4 0.01
91 4 0.01
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (88 bp):
AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTC
GATCTACTTCATGTCAATACATG
Found at i:21226962 original size:132 final size:132
Alignment explanation
Indices: 21226687--21227190 Score: 807
Period size: 132 Copynumber: 3.8 Consensus size: 132
21226677 ACACGATCTG
*
21226687 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTTGATCTACTTCA--
1 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
* * * * *
21226750 CCACTAGTATGGGAAGACAAGATCTGCCATCTTCGATCTACTTCATGTCAATACATGAAGACAAG
66 TCAATA-CAT--GAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAG
21226815 ATCCA
128 ATCCA
21226820 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
1 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
* * *
21226885 TCAATACATAAAGACAAGATCCGCTATCTTCGATATACTTCATGTCAATAAATGAAGACAAGATC
66 TCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
21226950 CA
131 CA
21226952 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
1 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
21227017 TCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
66 TCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
21227082 CA
131 CA
* ***
21227084 CTATCTTTGATCTACTTCATGTCAATACATGAAGACAAGATCTGCTATC-TCTGATCTACTTCAT
1 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTC-GATCTACTTCAT
* **
21227148 GTCAATACATGAAGACAATATCCATTATCTTCGATCTACTTCA
65 GTCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCA
21227191 CCACCAGTAT
Statistics
Matches: 349, Mismatches: 19, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
131 2 0.01
132 279 0.80
133 62 0.18
134 2 0.01
135 4 0.01
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (132 bp):
CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
TCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
CA
Found at i:21239201 original size:22 final size:22
Alignment explanation
Indices: 21239184--21239225 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
21239174 TAATAATGAT
21239184 ACAGTAATAATAATATAAATAA
1 ACAGTAATAATAATATAAATAA
* *
21239206 ACAGTATTAATAATAAAAAT
1 ACAGTAATAATAATATAAAT
21239226 TAGAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (22 bp):
ACAGTAATAATAATATAAATAA
Found at i:21243450 original size:19 final size:19
Alignment explanation
Indices: 21243428--21243466 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
21243418 AAGTAGAAAG
*
21243428 AATTTAAATAATGTTGATA
1 AATTTAAATAATGTGGATA
*
21243447 AATTTAAATCATGTGGATA
1 AATTTAAATAATGTGGATA
21243466 A
1 A
21243467 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (19 bp):
AATTTAAATAATGTGGATA
Found at i:21249210 original size:21 final size:22
Alignment explanation
Indices: 21249181--21249230 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
21249171 AATTTTATTT
* *
21249181 ATTCTAAAACCTTAAATCTAAA
1 ATTCTAAAACCCTAAATCCAAA
21249203 ATTC-AAAACCCTAAATCCAAA
1 ATTCTAAAACCCTAAATCCAAA
21249224 ATT-TAAA
1 ATTCTAAA
21249231 TCTCAAATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (22 bp):
ATTCTAAAACCCTAAATCCAAA
Found at i:21249456 original size:118 final size:118
Alignment explanation
Indices: 21249239--21249456 Score: 283
Period size: 118 Copynumber: 1.8 Consensus size: 118
21249229 AATCTCAAAT
* * * *
21249239 CCTAAATCTAAACCCGTAACCCCAAACCATTGAATCTTGAACCCATAACCCCAAACCTTTGAACT
1 CCTAAATCTAAAACCGTAACCCCAAACCATTAAATCTTAAACCCATAACCCCAAACCTTTGAACC
***
21249304 GTAACCCAAACAATTAAACATTGAACATTGAACCCTGAGCCCAAATTATGATC
66 GTAACCCAAACAATTAAACATTGAACACCAAACCCTGAGCCCAAATTATGATC
* * **
21249357 CCTAAATCTAAAATCGTAACCCCAAATCATTAAATCTTAAATTCATAACCCCAAACCTTTGAACC
1 CCTAAATCTAAAACCGTAACCCCAAACCATTAAATCTTAAACCCATAACCCCAAACCTTTGAACC
** * * * *
21249422 GTAACCTGAACTATTGAATATTGAACCCCAAACCC
66 GTAACCCAAACAATTAAACATTGAACACCAAACCC
21249457 AAATCTTGAA
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
118 83 1.00
ACGTcount: A:0.39, C:0.30, G:0.07, T:0.23
Consensus pattern (118 bp):
CCTAAATCTAAAACCGTAACCCCAAACCATTAAATCTTAAACCCATAACCCCAAACCTTTGAACC
GTAACCCAAACAATTAAACATTGAACACCAAACCCTGAGCCCAAATTATGATC
Found at i:21254080 original size:20 final size:21
Alignment explanation
Indices: 21254042--21254080 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
21254032 ACATGATATC
*
21254042 CTTAGAAATTTTTGGTAAAAG
1 CTTAGAAATATTTGGTAAAAG
*
21254063 CTTAGAAA-ATTTGTTAAA
1 CTTAGAAATATTTGGTAAA
21254081 TTTATAGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (21 bp):
CTTAGAAATATTTGGTAAAAG
Found at i:21254317 original size:18 final size:17
Alignment explanation
Indices: 21254283--21254321 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
21254273 TGATCCTTGA
* *
21254283 AAATTTTGATGATATTTT
1 AAATTTTGAT-AAAATTT
21254301 AAATTTTGATAAAATTT
1 AAATTTTGATAAAATTT
21254318 AAAT
1 AAAT
21254322 CTTCTTTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (17 bp):
AAATTTTGATAAAATTT
Found at i:21265512 original size:102 final size:111
Alignment explanation
Indices: 21265382--21265642 Score: 282
Period size: 102 Copynumber: 2.4 Consensus size: 111
21265372 TTCTATCTAT
21265382 TCAATACTGAAACAAGATCCTTA-TTCGATCTACTTCATTCAATAAAGATC-CTATCTCGATATA
1 TCAATACTGAAACAAGAT-CTTATTTCGATCTACTTCATTCAATAAAGATCGCTAT-TCGATATA
21265445 C-TCA-GTCATA-ATGAAGACAAATCCA-TAT-TCTG-TCTACTTCA-G
64 CTTCATGTCATACATG-AGACAAATCCACTATCTCTGATCTACTTCATG
* * *
21265487 TCAA-ACTG-AAC-AGATCTTATTTCGATCTACTT--TAC-ATGAGAGATCGCTATTCGATCTAC
1 TCAATACTGAAACAAGATCTTATTTCGATCTACTTCATTCAAT-AAAGATCGCTATTCGATATAC
*
21265546 TTCATGTCATACATGAGACAAATCCACTATCTTTGATCTACTTCATG
65 TTCATGTCATACATGAGACAAATCCACTATCTCTGATCTACTTCATG
*
21265593 TCAATACATGAAGACAAGATCTGCTATCTCTGATCTACTTCATGTCAATA
1 TCAATAC-TGAA-ACAAGATCT--TATTTC-GATCTACTTCAT-TCAATA
21265643 CATGAAGACA
Statistics
Matches: 128, Mismatches: 6, Indels: 32
0.77 0.04 0.19
Matches are distributed among these distances:
99 2 0.02
100 16 0.12
101 11 0.09
102 33 0.26
103 9 0.07
104 7 0.05
105 13 0.10
106 5 0.04
107 2 0.02
108 2 0.02
109 1 0.01
110 2 0.02
111 6 0.05
113 5 0.04
114 9 0.07
116 1 0.01
117 2 0.02
118 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (111 bp):
TCAATACTGAAACAAGATCTTATTTCGATCTACTTCATTCAATAAAGATCGCTATTCGATATACT
TCATGTCATACATGAGACAAATCCACTATCTCTGATCTACTTCATG
Found at i:21265632 original size:44 final size:43
Alignment explanation
Indices: 21265527--21265678 Score: 183
Period size: 44 Copynumber: 3.6 Consensus size: 43
21265517 TTTACATGAG
21265527 AGATCGCTAT-TC-GATCTACTTCATGTC-ATACATG-AGACA
1 AGATCGCTATCTCTGATCTACTTCATGTCAATACATGAAGACA
* *
21265566 A-ATCCACTATCTTTGATCTACTTCATGTCAATACATGAAGACA
1 AGAT-CGCTATCTCTGATCTACTTCATGTCAATACATGAAGACA
21265609 AGATCTGCTATCTCTGATCTACTTCATGTCAATACATGAAGACA
1 AGATC-GCTATCTCTGATCTACTTCATGTCAATACATGAAGACA
*
21265653 ATATC-CATTATCT-TCGATCTACTTCA
1 AGATCGC--TATCTCT-GATCTACTTCA
21265679 CCACCAGTAT
Statistics
Matches: 98, Mismatches: 5, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
38 2 0.02
39 6 0.06
40 1 0.01
41 15 0.15
42 8 0.08
43 8 0.08
44 58 0.59
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (43 bp):
AGATCGCTATCTCTGATCTACTTCATGTCAATACATGAAGACA
Found at i:21281981 original size:19 final size:20
Alignment explanation
Indices: 21281948--21281987 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
21281938 AAGTAGAAAG
*
21281948 AATTTAAAATAATGTTGATA
1 AATTTAAAATAATGTGGATA
*
21281968 AATTT-AAATCATGTGGATA
1 AATTTAAAATAATGTGGATA
21281987 A
1 A
21281988 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (20 bp):
AATTTAAAATAATGTGGATA
Found at i:21287710 original size:21 final size:21
Alignment explanation
Indices: 21287681--21287745 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
21287671 AATTTTATTT
21287681 ATTCTAAAACCTTAAATCTAAA
1 ATTC-AAAACCTTAAATCTAAA
* *
21287703 ATTCAAAACCCTAAATCCAAA
1 ATTCAAAACCTTAAATCTAAA
* * *
21287724 ATTTAAAATCTCAAATCCTAAA
1 ATTCAAAACCTTAAAT-CTAAA
21287746 TCTAAACCCG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 27 0.77
22 8 0.23
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.28
Consensus pattern (21 bp):
ATTCAAAACCTTAAATCTAAA
Found at i:21287958 original size:119 final size:119
Alignment explanation
Indices: 21287740--21287958 Score: 285
Period size: 119 Copynumber: 1.8 Consensus size: 119
21287730 AATCTCAAAT
* * * *
21287740 CCTAAATCTAAACCCGTAACCCCAAACCATTGAATCTTGAACCCATAACCCCAAACCTTTGAACT
1 CCTAAATCTAAAACCGTAACCCCAAACCATTAAATCTTAAACCCATAACCCCAAACCTTTGAACC
***
21287805 GTAACCCAAACAATTAAACATTGAACATTGAACCCTGAGCCCAAATTATGAATC
66 GTAACCCAAACAATTAAACATTGAACACCAAACCCTGAGCCCAAATTATGAATC
* * **
21287859 CCTAAATCTAAAATCGTAACCCCAAATCATTAAATCTTAAATTCATAACCCCAAACCTTTGAACC
1 CCTAAATCTAAAACCGTAACCCCAAACCATTAAATCTTAAACCCATAACCCCAAACCTTTGAACC
** * * * *
21287924 GTAACCTGAACTATTGAATATTGAACCCCAAACCC
66 GTAACCCAAACAATTAAACATTGAACACCAAACCC
21287959 AAATCTTGAA
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
119 83 1.00
ACGTcount: A:0.40, C:0.30, G:0.07, T:0.23
Consensus pattern (119 bp):
CCTAAATCTAAAACCGTAACCCCAAACCATTAAATCTTAAACCCATAACCCCAAACCTTTGAACC
GTAACCCAAACAATTAAACATTGAACACCAAACCCTGAGCCCAAATTATGAATC
Found at i:21292582 original size:20 final size:20
Alignment explanation
Indices: 21292557--21292625 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
21292547 ACATGATATC
21292557 CTTAGAAATTTTGGTAAAAG
1 CTTAGAAATTTTGGTAAAAG
* * *
21292577 CTTAGAAAATTT-GTTAAAT
1 CTTAGAAATTTTGGTAAAAG
* *
21292596 TTATAGGAATTTTGGTAAATAG
1 CT-TAGAAATTTTGGTAAA-AG
21292618 -TTAGAAAT
1 CTTAGAAAT
21292626 AATTGAAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 6 0.16
20 25 0.68
21 5 0.14
22 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.39
Consensus pattern (20 bp):
CTTAGAAATTTTGGTAAAAG
Found at i:21292738 original size:20 final size:20
Alignment explanation
Indices: 21292715--21292798 Score: 53
Period size: 20 Copynumber: 4.2 Consensus size: 20
21292705 GAAATATTAG
21292715 TAAATTTTTAAAAGTTTTGA
1 TAAATTTTTAAAAGTTTTGA
* ** *
21292735 TAAATTCTTGCAAGTTTTGG
1 TAAATTTTTAAAAGTTTTGA
** * * *
21292755 TAAAAGTGTAGAAGTTCTGA
1 TAAATTTTTAAAAGTTTTGA
* *
21292775 TAAATTATTAGATA-TTTTGA
1 TAAATTTTTA-AAAGTTTTGA
21292795 TAAA
1 TAAA
21292799 CCCTAATGAT
Statistics
Matches: 44, Mismatches: 19, Indels: 2
0.68 0.29 0.03
Matches are distributed among these distances:
20 43 0.98
21 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (20 bp):
TAAATTTTTAAAAGTTTTGA
Found at i:21300264 original size:13 final size:13
Alignment explanation
Indices: 21300219--21300269 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
21300209 ACATTCTCTC
*
21300219 AAAAT-AATAATG
1 AAAATGAATAAAG
21300231 AAAATGTAAATAAA-
1 AAAATG--AATAAAG
*
21300245 TAAATGAATAAAG
1 AAAATGAATAAAG
21300258 AAAATGAATAAA
1 AAAATGAATAAA
21300270 ATTATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 11 0.34
13 11 0.34
14 5 0.16
15 5 0.16
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.22
Consensus pattern (13 bp):
AAAATGAATAAAG
Found at i:21300512 original size:33 final size:32
Alignment explanation
Indices: 21300469--21300558 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 32
21300459 AAAAGTATGT
* *
21300469 ATATATATATAAGTTATAAAAGTATGTACGTGC
1 ATATGTATATAA-TTATAAAAGTATGTACGTAC
* *
21300502 ATATGTATAT-ATTATAAAAATGTATGTATGTAT
1 ATATGTATATAATTAT-AAAA-GTATGTACGTAC
21300535 ATATGTATATAAATTAT-AAAGTAT
1 ATATGTATAT-AATTATAAAAGTAT
21300559 AACAAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
31 4 0.08
32 9 0.18
33 31 0.63
35 5 0.10
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.41
Consensus pattern (32 bp):
ATATGTATATAATTATAAAAGTATGTACGTAC
Found at i:21301740 original size:19 final size:20
Alignment explanation
Indices: 21301707--21301746 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
21301697 AAGTAAAAAG
*
21301707 AATTTAAAATAATGTTGATA
1 AATTTAAAATAATGTGGATA
*
21301727 AATTT-AAATCATGTGGATA
1 AATTTAAAATAATGTGGATA
21301746 A
1 A
21301747 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (20 bp):
AATTTAAAATAATGTGGATA
Found at i:21318343 original size:26 final size:26
Alignment explanation
Indices: 21318314--21318368 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
21318304 TCAACTTATC
21318314 TTTTAAGTT-AATAAATTCTCATTGAG
1 TTTTAAGTTCAATAAATTCTC-TTGAG
* * *
21318340 TTTTCATTTCAATAATTTCTCTTGAG
1 TTTTAAGTTCAATAAATTCTCTTGAG
21318366 TTT
1 TTT
21318369 ATTTTAGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (26 bp):
TTTTAAGTTCAATAAATTCTCTTGAG
Found at i:21319935 original size:96 final size:96
Alignment explanation
Indices: 21319817--21320005 Score: 263
Period size: 96 Copynumber: 2.0 Consensus size: 96
21319807 AAAGGAGGAA
* * * * *
21319817 TACGATTGAGGTATCATCTTTTGTGCGATGTTATTGGTATAGTTCAAAAGATCATAAGGGTTTCC
1 TACGATTGAGATATCATCTTTTGTGCAATGTTATTGGTATAATTCAAAAGATCACAAGAGTTTCC
21319882 AATGTCCAATTAAATATCCAAATAGAGAGAC
66 AATGTCCAATTAAATATCCAAATAGAGAGAC
* * * *
21319913 TACGATTGAGATATCA-CATTTTGTGCAATGTTATTGGTGTAATTCAAAATATTACAAGAGTTTT
1 TACGATTGAGATATCATC-TTTTGTGCAATGTTATTGGTATAATTCAAAAGATCACAAGAGTTTC
* *
21319977 CAATGTCCAGTTAAATATCCAACTAGAGA
65 CAATGTCCAATTAAATATCCAAATAGAGA
21320006 ATAAAGTAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 1 0.01
96 80 0.99
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (96 bp):
TACGATTGAGATATCATCTTTTGTGCAATGTTATTGGTATAATTCAAAAGATCACAAGAGTTTCC
AATGTCCAATTAAATATCCAAATAGAGAGAC
Found at i:21323295 original size:23 final size:22
Alignment explanation
Indices: 21323252--21323296 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
21323242 ATGAGATAAT
*
21323252 TAAAAATAAAAATATTTTTAAA
1 TAAAAATAAAAATATTATTAAA
21323274 TAAAAATATCAAAA-ATTATTAAA
1 TAAAAATA--AAAATATTATTAAA
21323297 AACGAGAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 8 0.40
24 4 0.20
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAAATAAAAATATTATTAAA
Found at i:21329013 original size:26 final size:26
Alignment explanation
Indices: 21328968--21329029 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
21328958 ATGGTAATTA
21328968 AATTAAATT-AAATACTATATAATGT
1 AATTAAATTAAAATACTATATAATGT
* **
21328993 GATTAAATTAAAATGTTATATAATGT
1 AATTAAATTAAAATACTATATAATGT
21329019 AATTAAATTAA
1 AATTAAATTAA
21329030 GTTAATAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 8 0.25
26 24 0.75
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (26 bp):
AATTAAATTAAAATACTATATAATGT
Found at i:21331032 original size:3 final size:3
Alignment explanation
Indices: 21331024--21331051 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
21331014 ACGTGAAAGA
21331024 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
21331052 CAACATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:21333382 original size:172 final size:172
Alignment explanation
Indices: 21333089--21333435 Score: 631
Period size: 172 Copynumber: 2.0 Consensus size: 172
21333079 AATGCAGAGT
*
21333089 ACAAATATCCACAATCTCTAATCAATCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAAT
1 ACAAATATCCACAATATCTAATCAATCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAAT
*
21333154 ATCAGAATAAGTATCATAGTATGCATACAATTATGTTATTCATACGCCCATCACAGAGTATCAGA
66 ATAAGAATAAGTATCATAGTATGCATACAATTATGTTATTCATACGCCCATCACAGAGTATCAGA
21333219 GAGTTCTCGTATAATCAAATTCAAATCATTCATGTATTGGGG
131 GAGTTCTCGTATAATCAAATTCAAATCATTCATGTATTGGGG
* *
21333261 ACAAATGTCCACAATATCTAATCAGTCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAAT
1 ACAAATATCCACAATATCTAATCAATCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAAT
* *
21333326 ATAAGAATAAGTATCATAGTATGTATACAATTATGTTATTCATACGTCCATCACAGAGTATCAGA
66 ATAAGAATAAGTATCATAGTATGCATACAATTATGTTATTCATACGCCCATCACAGAGTATCAGA
*
21333391 GAGTTTTCGTATAATCAAATTCAAATCATTCATGTATTGGGG
131 GAGTTCTCGTATAATCAAATTCAAATCATTCATGTATTGGGG
21333433 ACA
1 ACA
21333436 TCAATATCAG
Statistics
Matches: 168, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
172 168 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (172 bp):
ACAAATATCCACAATATCTAATCAATCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAAT
ATAAGAATAAGTATCATAGTATGCATACAATTATGTTATTCATACGCCCATCACAGAGTATCAGA
GAGTTCTCGTATAATCAAATTCAAATCATTCATGTATTGGGG
Found at i:21336455 original size:21 final size:22
Alignment explanation
Indices: 21336430--21336470 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21336420 AGATATGAAA
* *
21336430 TTAAAT-TATATTTAGGATTCT
1 TTAAATCTAAATTGAGGATTCT
21336451 TTAAATCTAAATTGAGGATT
1 TTAAATCTAAATTGAGGATT
21336471 AGAAACGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (22 bp):
TTAAATCTAAATTGAGGATTCT
Found at i:21341005 original size:13 final size:12
Alignment explanation
Indices: 21340973--21341010 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
21340963 CCTTTCCCCC
21340973 TCCCTTCTCTC-
1 TCCCTTCTCTCT
21340984 TCCCTTCTCTCT
1 TCCCTTCTCTCT
21340996 TCCCTCTCTCTCT
1 TCCCT-TCTCTCT
21341009 TC
1 TC
21341011 TTTTTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.44
12 5 0.20
13 9 0.36
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (12 bp):
TCCCTTCTCTCT
Found at i:21341488 original size:3 final size:3
Alignment explanation
Indices: 21341474--21341542 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
21341464 AATATCCTTG
* * * *
21341474 TTA TTT TTA TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TTA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
21341523 TTA GTA TATA TTT TTA TTA T
1 TTA TTA T-TA TTA TTA TTA T
21341543 GTACGCGTAT
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:21341539 original size:23 final size:22
Alignment explanation
Indices: 21341484--21341545 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
21341474 TTATTTTTAT
*
21341484 TATTAGTATTATTA-GTATTAC
1 TATTATTATTATTATGTATTAC
*
21341505 TATTATTATTATTATGTATTAG
1 TATTATTATTATTATGTATTAC
*
21341527 TATATATTTTTATTATGTA
1 TAT-TATTATTATTATGTA
21341546 CGCGTATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 13 0.36
22 9 0.25
23 14 0.39
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (22 bp):
TATTATTATTATTATGTATTAC
Found at i:21341552 original size:23 final size:23
Alignment explanation
Indices: 21341508--21341553 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
21341498 GTATTACTAT
**
21341508 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTACGAGTATA
* *
21341531 TATTTTTATTATGTACGCGTATA
1 TATTATTATTATGTACGAGTATA
21341554 CATGTATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (23 bp):
TATTATTATTATGTACGAGTATA
Found at i:21351768 original size:21 final size:22
Alignment explanation
Indices: 21351722--21351777 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
21351712 GTGATAGTCC
*
21351722 TACACGATTGTGTGAATGAGAG
1 TACACGATAGTGTGAATGAGAG
* *
21351744 -ACACGCTAGTGTGACTGA-AG
1 TACACGATAGTGTGAATGAGAG
* *
21351764 TACACAATCGTGTG
1 TACACGATAGTGTG
21351778 GGTAGACCGT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (22 bp):
TACACGATAGTGTGAATGAGAG
Found at i:21352285 original size:23 final size:22
Alignment explanation
Indices: 21352238--21352285 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
21352228 CAAACACACT
**
21352238 AACCTATAAGAAAATCAATCTA
1 AACCTATAAGAAAATCAATAGA
21352260 AACCATATATAGAAAATCAA-AGA
1 AACC-TATA-AGAAAATCAATAGA
21352283 AAC
1 AAC
21352286 TGATGTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 8 0.36
24 10 0.45
ACGTcount: A:0.58, C:0.17, G:0.06, T:0.19
Consensus pattern (22 bp):
AACCTATAAGAAAATCAATAGA
Found at i:21352579 original size:3 final size:3
Alignment explanation
Indices: 21352571--21352600 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
21352561 AAAATTAAAT
21352571 ATA ATA ATA A-A ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
21352601 CAACAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:21352593 original size:17 final size:18
Alignment explanation
Indices: 21352558--21352600 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
21352548 TTTTCTTCTC
21352558 AATAAAATTAAATATAAT
1 AATAAAATTAAATATAAT
*
21352576 AATAAAATAATAATAATAAT
1 AATAAAATTA-AAT-ATAAT
21352596 AATAA
1 AATAA
21352601 CAACAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 3 0.14
20 10 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAAAATTAAATATAAT
Found at i:21356527 original size:30 final size:30
Alignment explanation
Indices: 21356481--21356574 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
21356471 TTTTATTATG
*
21356481 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
21356512 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
21356542 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
21356572 CCA
1 CCA
21356575 TAAATATGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
30 51 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:21356536 original size:15 final size:15
Alignment explanation
Indices: 21356491--21356568 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
21356481 CCAATATCTC
21356491 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
21356506 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
21356521 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
21356536 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
21356551 GATACCCATATCTTT
1 GATACCCATATCTTT
21356566 GAT
1 GAT
21356569 TTTCCATAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:21358996 original size:60 final size:60
Alignment explanation
Indices: 21358903--21359015 Score: 181
Period size: 60 Copynumber: 1.9 Consensus size: 60
21358893 CACTATATGA
* *
21358903 TGTGTAGGGATGGGTGAGTGTTTTTAACCCCACATGGTGTGATAAGATGGACGGAGTTGG
1 TGTGTAGGGATAGGTGAGTGTTTTTAACCCCACATGGTATGATAAGATGGACGGAGTTGG
* **
21358963 TGTGTAGGGATAGGTGGGTGTTTTTAACCCCACATGGTATGATGGGATGGACG
1 TGTGTAGGGATAGGTGAGTGTTTTTAACCCCACATGGTATGATAAGATGGACG
21359016 AAGATGGACG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.21, C:0.11, G:0.38, T:0.30
Consensus pattern (60 bp):
TGTGTAGGGATAGGTGAGTGTTTTTAACCCCACATGGTATGATAAGATGGACGGAGTTGG
Found at i:21369032 original size:30 final size:30
Alignment explanation
Indices: 21368942--21369032 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
21368932 AATGTAATGT
* * * *
21368942 TCACACAAGCTGACAGTATTTTAGGGTTGC
1 TCACACAAGCTGACATTATATTAAGGTTTC
* * * *
21368972 TCACACAAGTTGACATTGTAAT-CGGATTTC
1 TCACACAAGCTGACATTATATTAAGG-TTTC
21369002 TCACACAAGCTGACATTATATTAAGGTTTC
1 TCACACAAGCTGACATTATATTAAGGTTTC
21369032 T
1 T
21369033 TGCACGGGCT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
29 2 0.04
30 44 0.92
31 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (30 bp):
TCACACAAGCTGACATTATATTAAGGTTTC
Found at i:21372737 original size:12 final size:12
Alignment explanation
Indices: 21372705--21372759 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
21372695 GTCCATATAC
21372705 ATAT-TATAAA-
1 ATATATATAAAT
21372715 AT-TAT-TAAAT
1 ATATATATAAAT
21372725 ATATATATAAAT
1 ATATATATAAAT
*
21372737 ATATATATGTAAGT
1 ATATATA--TAAAT
21372751 ATATATATA
1 ATATATATA
21372760 TATTTACAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
9 5 0.13
10 5 0.13
11 3 0.08
12 14 0.37
14 11 0.29
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (12 bp):
ATATATATAAAT
Found at i:21372742 original size:14 final size:14
Alignment explanation
Indices: 21372723--21372761 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
21372713 AAATTATTAA
21372723 ATATATATATAAAT
1 ATATATATATAAAT
* *
21372737 ATATATATGTAAGT
1 ATATATATATAAAT
21372751 ATATATATATA
1 ATATATATATA
21372762 TTTACAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (14 bp):
ATATATATATAAAT
Found at i:21372906 original size:3 final size:3
Alignment explanation
Indices: 21372892--21372962 Score: 63
Period size: 3 Copynumber: 22.7 Consensus size: 3
21372882 TAAATGGGTA
* *
21372892 AAT AAA AAT AAT AAT AAGGT AAGT AAT AAT AAT AACT -AC AAT AAT AAT
1 AAT AAT AAT AAT AAT AA--T AA-T AAT AAT AAT AA-T AAT AAT AAT AAT
* *
21372940 GAC AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
21372963 AACTAATTAG
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
3 48 0.86
4 5 0.09
5 3 0.05
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:21374561 original size:50 final size:50
Alignment explanation
Indices: 21374487--21375092 Score: 389
Period size: 50 Copynumber: 12.2 Consensus size: 50
21374477 TAACTCGTAA
** ** * * *
21374487 CTTTAATCTGCTTAACTGTGATGTC-GGAGAAGTAAGATTCGCCATTGTGG
1 CTTTAATCTTTTTAACTGCAATGTCAGG-GAAGCAAGATTCACCGTTGTGG
* * *
21374537 CTTTAATCTTCTTAACTGCAATGTCAGGGAAGCAAGATACACCGTCGTGG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* ** ** ** * *
21374587 GTTTAATCTGCTCCACTGCACCG-CTAGGAAAGCAAGA--CA-CGCTGTGG
1 CTTTAATCTTTTTAACTGCAATGTC-AGGGAAGCAAGATTCACCGTTGTGG
* * * *
21374634 CTTTAGTCTTTTTAACTGCAATGTCGGGGAAGCAAGATACGCCGTTGTGG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
** ** * * * * * * * * *
21374684 CTTTAATCTGCTCCACTGCATTGCCAGGGAAGTAACACTCGCTGCTATGG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* * *
21374734 CTTTAGTCTTTTTAACTGCAATGTCGGGGAAGCAGGATTCACCGTTGTGG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* ** * * * * * * * * *
21374784 CTTTAATCTGTTCCACTGCACTGCCTGGGAGGTAAGATTCGCTGCTGTAG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* *
21374834 CTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAGGATTCACCGTTGTGG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* ** ** * * * *** *
21374884 CTTTAATCTGTTCCACTGCACCGCCTA-AGAAGTAAGATTCACTACTGTAG
1 CTTTAATCTTTTTAACTGCAATGTC-AGGGAAGCAAGATTCACCGTTGTGG
* *
21374934 CTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCATCGTTGTGG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* ** ** * * * * *** *
21374984 CTTTAATCTGTTCCACTGCACCG-CTTGGGAGGTAAGACTCGTTGTTGTAG
1 CTTTAATCTTTTTAACTGCAATGTC-AGGGAAGCAAGATTCACCGTTGTGG
* *
21375034 CTTTAATCTTTTTAACTGCAATGTCAGGGAGGGAAGATTCACCGTTGTGG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
21375084 CTTTAATCT
1 CTTTAATCT
21375093 GTTCCACTGC
Statistics
Matches: 409, Mismatches: 137, Indels: 20
0.72 0.24 0.04
Matches are distributed among these distances:
47 31 0.08
48 3 0.01
49 4 0.01
50 367 0.90
51 4 0.01
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (50 bp):
CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
Found at i:21374779 original size:100 final size:100
Alignment explanation
Indices: 21374536--21375114 Score: 752
Period size: 100 Copynumber: 5.8 Consensus size: 100
21374526 CGCCATTGTG
* * * * *
21374536 GCTTTAATCTTCTTAACTGCAATGTCAGGGAAGCAAGATACACCGTCGTGGGTTTAATCTGCTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* * * *
21374601 ACTGCACCGCTAGGAAAGCAAGACACGCTG-TG--
66 ACTGCACCGCCAGGGAAGTAAGACTCGCTGCTGTA
* * * * *
21374633 GCTTTAGTCTTTTTAACTGCAATGTCGGGGAAGCAAGATACGCCGTTGTGGCTTTAATCTGCTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
** * * *
21374698 ACTGCATTGCCAGGGAAGTAACACTCGCTGCTATG
66 ACTGCACCGCCAGGGAAGTAAGACTCGCTGCTGTA
* * *
21374733 GCTTTAGTCTTTTTAACTGCAATGTCGGGGAAGCAGGATTCACCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* * * *
21374798 ACTGCACTGCCTGGGAGGTAAGATTCGCTGCTGTA
66 ACTGCACCGCCAGGGAAGTAAGACTCGCTGCTGTA
* *
21374833 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAGGATTCACCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* * * *
21374898 ACTGCACCGCCTA-AGAAGTAAGATTCACTACTGTA
66 ACTGCACCGCC-AGGGAAGTAAGACTCGCTGCTGTA
* *
21374933 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCATCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
** * * *
21374998 ACTGCACCGCTTGGGAGGTAAGACTCGTTGTTGTA
66 ACTGCACCGCCAGGGAAGTAAGACTCGCTGCTGTA
* *
21375033 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGGAAGATTCACCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
21375098 ACTGCACCGCCAGGGAA
66 ACTGCACCGCCAGGGAA
21375115 ACTAAGATCT
Statistics
Matches: 427, Mismatches: 50, Indels: 7
0.88 0.10 0.01
Matches are distributed among these distances:
97 82 0.19
98 1 0.00
100 344 0.81
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (100 bp):
GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
ACTGCACCGCCAGGGAAGTAAGACTCGCTGCTGTA
Found at i:21375272 original size:44 final size:44
Alignment explanation
Indices: 21375218--21375835 Score: 438
Period size: 44 Copynumber: 13.8 Consensus size: 44
21375208 CCTTTATTTT
* *
21375218 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* *
21375262 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-GCTTC
* ** * * *
21375308 AGTCTATTCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT--TACTAGCTTC
* *
21375352 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * ** *
21375396 AATCTGCTCCGCTGTAATCTCAGGGAGATAATATCTAAAATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-TACTA-GCTTC
* ** *
21375442 AGTCTATTCCACTGTAATCTCAGGGAGATAA-A--ACCT-GATGT-
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTA-CTAGCT-TC
* * * * * * * *
21375483 GATCTACTCTACTGTAA-CTTCAGAGAGACAAGATCCT-TTA-TTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTC
* * * * *
21375527 AATCCGCTCCACTTTAATCTCAAGGAGATAGGATTACTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
** * *
21375571 AATCTGCTCTGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
21375615 AATCTGCTCTACTGTAATCTCAGGGAGATAAGATTTCTAACTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * * *
21375659 AATCTGATGCGATCTACTCTACTGTAA-CTTCAGAGAGATGAGATCCT-TTA-TTTT
1 AATC---T--G--CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTC
* * *
21375713 AATCCGCTCCACTGTAATCTTAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* *
21375757 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
21375801 AATCTGCTCCACTGTAA-CATCAGGGAGATAAGATT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATT
21375836 CACCATTTCC
Statistics
Matches: 452, Mismatches: 83, Indels: 78
0.74 0.14 0.13
Matches are distributed among these distances:
40 1 0.00
41 24 0.05
42 6 0.01
43 7 0.02
44 296 0.65
45 9 0.02
46 69 0.15
47 5 0.01
49 2 0.00
51 2 0.00
52 1 0.00
53 1 0.00
54 26 0.06
55 2 0.00
56 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:21375364 original size:134 final size:134
Alignment explanation
Indices: 21375198--21375472 Score: 523
Period size: 134 Copynumber: 2.1 Consensus size: 134
21375188 TATAACTTTA
21375198 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCA
1 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCA
*
21375263 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCAGTCTATTCCACTGTAATCT
66 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCAGTCTATTCCACTGTAATCT
21375328 CAGG
131 CAGG
21375332 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCA
1 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCA
* *
21375397 ATCTGCTCCGCTGTAATCTCAGGGAGATAATATCTAAAATTCTTCAGTCTATTCCACTGTAATCT
66 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCAGTCTATTCCACTGTAATCT
21375462 CAGG
131 CAGG
21375466 GAGATAA
1 GAGATAA
21375473 AACCTGATGT
Statistics
Matches: 138, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
134 138 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (134 bp):
GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCA
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCAGTCTATTCCACTGTAATCT
CAGG
Found at i:21375797 original size:186 final size:186
Alignment explanation
Indices: 21375476--21375835 Score: 614
Period size: 186 Copynumber: 1.9 Consensus size: 186
21375466 GAGATAAAAC
* *
21375476 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGACAAGATCCTTTATTTTAATCCGCTCCACTT
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGACAAGATCCTTTATTTTAATCCGCTCCACTG
* **
21375541 TAATCTCAAGGAGATAGGATTACTGGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATT
*
21375606 TCTGGCTTCAATCTGCTCTACTGTAATC-TCAGGGAGATAAGATTTCTAACTTCAAT
131 TCTGGCTTCAATCTGCTCCACTGTAA-CATCAGGGAGATAAGATTTCTAACTTCAAT
**
21375662 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGACAAGATCCTTTATTTTAATCCGCTCCACTG
* *
21375727 TAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATT
21375792 TCTGGCTTCAATCTGCTCCACTGTAACATCAGGGAGATAAGATT
131 TCTGGCTTCAATCTGCTCCACTGTAACATCAGGGAGATAAGATT
21375836 CACCATTTCC
Statistics
Matches: 163, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
185 1 0.01
186 162 0.99
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (186 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGACAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATT
TCTGGCTTCAATCTGCTCCACTGTAACATCAGGGAGATAAGATTTCTAACTTCAAT
Found at i:21377238 original size:19 final size:18
Alignment explanation
Indices: 21377214--21377258 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
21377204 TTAGCCTCTC
21377214 CATTTTTACTTTCATTTTT
1 CATTTTT-CTTTCATTTTT
*
21377233 CATTTTTTTTTCATTTTT
1 CATTTTTCTTTCATTTTT
21377251 CACTTTTT
1 CA-TTTTT
21377259 TTCCTCAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (18 bp):
CATTTTTCTTTCATTTTT
Found at i:21377244 original size:18 final size:19
Alignment explanation
Indices: 21377223--21377260 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
21377213 CCATTTTTAC
21377223 TTTCATTTTTCA-TTTTTT
1 TTTCATTTTTCACTTTTTT
21377241 TTTCATTTTTCACTTTTTT
1 TTTCATTTTTCACTTTTTT
21377260 T
1 T
21377261 CCTCAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTCATTTTTCACTTTTTT
Found at i:21378132 original size:24 final size:25
Alignment explanation
Indices: 21378086--21378132 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
21378076 GACCTTGATA
* * *
21378086 GATTTTTCTTTTTGCTTTTAACTTT
1 GATTTTTCTTTTTGATCTGAACTTT
21378111 GATTTTT-TTTTTGATCTGAACT
1 GATTTTTCTTTTTGATCTGAACT
21378133 CTTGGGATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.15, C:0.11, G:0.11, T:0.64
Consensus pattern (25 bp):
GATTTTTCTTTTTGATCTGAACTTT
Found at i:21382320 original size:24 final size:24
Alignment explanation
Indices: 21382280--21382326 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
21382270 AAAAGGAAAT
*
21382280 AAGAGAAAGTGATGGAAAATGTTG
1 AAGAGAAAGTGAAGGAAAATGTTG
*
21382304 AAGAGAAAG-GAAAGGAAAGTGTT
1 AAGAGAAAGTG-AAGGAAAATGTT
21382327 ATAAATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.49, C:0.00, G:0.34, T:0.17
Consensus pattern (24 bp):
AAGAGAAAGTGAAGGAAAATGTTG
Found at i:21384603 original size:22 final size:22
Alignment explanation
Indices: 21384577--21384621 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
21384567 ATTATGTGTA
21384577 TTAATTCATAATATAA-TTAATT
1 TTAATT-ATAATATAATTTAATT
* *
21384599 TTAATTTTAATCTAATTTAATT
1 TTAATTATAATATAATTTAATT
21384621 T
1 T
21384622 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTATAATATAATTTAATT
Found at i:21386085 original size:3 final size:3
Alignment explanation
Indices: 21386077--21386117 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
21386067 TGAGGATCCT
21386077 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
21386118 TCCCACAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:21392717 original size:21 final size:22
Alignment explanation
Indices: 21392670--21392717 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
21392660 AAACTCCAAA
* * *
21392670 AAAGATTCAAGTACATGAAACT
1 AAAGATTAAAATACATGAAAAT
*
21392692 GAAGATTAAAATA-ATGAAAAT
1 AAAGATTAAAATACATGAAAAT
21392713 AAAGA
1 AAAGA
21392718 AATCTTGATC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.58, C:0.06, G:0.15, T:0.21
Consensus pattern (22 bp):
AAAGATTAAAATACATGAAAAT
Found at i:21397151 original size:14 final size:14
Alignment explanation
Indices: 21397132--21397171 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
21397122 TTGATTGGCA
21397132 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
21397146 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
21397160 GGAAAATGTTTT
1 GTAAAATGTTTT
21397172 ACTTTTCTGT
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:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:21397178 original size:34 final size:35
Alignment explanation
Indices: 21397140--21397206 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
21397130 CAGTAAAATG
* * *
21397140 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACAGGAAAATATTTTAC
*
21397174 TTTTCTGTAAAATGACTTACAGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACAGGAAAATATTTT
21397207 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACAGGAAAATATTTTAC
Found at i:21397193 original size:20 final size:20
Alignment explanation
Indices: 21397155--21397193 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21397145 CGTAAAATGA
**
21397155 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
21397175 TTTCTGTAAAATGACTTAC
1 TTTCTGGAAAATGACTTAC
21397194 AGGAAAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:21398580 original size:27 final size:27
Alignment explanation
Indices: 21398550--21398619 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
21398540 AATAATCAAT
*
21398550 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
21398577 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAAC-AATTCAAAACATATA
*
21398605 TCAAAATCCAACAAT
1 TCAATATCCAACAAT
21398620 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:21402372 original size:24 final size:24
Alignment explanation
Indices: 21402345--21402417 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
21402335 TGCAATCGAT
*
21402345 AGGGTGAATAGAGGAGCTGTGGAA
1 AGGGTGAAGAGAGGAGCTGTGGAA
* *
21402369 AGGGTGAAGAGAGGAACAGTGGAA
1 AGGGTGAAGAGAGGAGCTGTGGAA
*
21402393 AAGGTGAAGAGAGGAGCTGTGGAA
1 AGGGTGAAGAGAGGAGCTGTGGAA
21402417 A
1 A
21402418 ATGTCTTACC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.38, C:0.04, G:0.45, T:0.12
Consensus pattern (24 bp):
AGGGTGAAGAGAGGAGCTGTGGAA
Found at i:21409096 original size:60 final size:61
Alignment explanation
Indices: 21409016--21409131 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 61
21409006 ATTTGGTATC
* *
21409016 TGAACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTTT-GGTCCAATTTGATACT
1 TGAACTTGACACTTTCTCCTAATTTGGTACCTAAACTTTTTTTTAGGTCCAATTTGATACT
* * *
21409076 TGAACTTGGCACTTTCTCCTAATTTGGTACCTAAGCTTTTTTTTAGGTTCAATTTG
1 TGAACTTGACACTTTCTCCTAATTTGGTACCTAAACTTTTTTTTAGGTCCAATTTG
21409132 GTACCTAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 40 0.80
61 10 0.20
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (61 bp):
TGAACTTGACACTTTCTCCTAATTTGGTACCTAAACTTTTTTTTAGGTCCAATTTGATACT
Found at i:21409610 original size:31 final size:31
Alignment explanation
Indices: 21409573--21409651 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
21409563 GGCCCTCAAA
*
21409573 AAGTTTAAGTACCAACTTAAGAAAAAATGTC
1 AAGTTTAAGTACCAAATTAAGAAAAAATGTC
* *
21409604 AAGTTTATGTACCAAATTAAGAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAGAAAAAATGTC
* * *
21409635 AACTTCAAGTATCAAAT
1 AAGTTTAAGTACCAAAT
21409652 GTTATATTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAGAAAAAATGTC
Found at i:21419263 original size:23 final size:23
Alignment explanation
Indices: 21419213--21419267 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
21419203 ATCAGGATCA
* * *
21419213 CACCATAGTGCTAGGAACAGGAG
1 CACCAAAGTGCAAGGAACAGAAG
*
21419236 CACCAAAGTGCAAGTAACAGAAG
1 CACCAAAGTGCAAGGAACAGAAG
*
21419259 TACCAAAGT
1 CACCAAAGT
21419268 ACAAATCAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.13
Consensus pattern (23 bp):
CACCAAAGTGCAAGGAACAGAAG
Found at i:21419573 original size:39 final size:40
Alignment explanation
Indices: 21419530--21419612 Score: 125
Period size: 39 Copynumber: 2.1 Consensus size: 40
21419520 GAAAGGAAAA
**
21419530 AAATTATTTCTAAGGTATTTATAT-TTTCTT-CATTTTGAT
1 AAATTATTTAAAAGGTATTTATATGTTT-TTACATTTTGAT
21419569 AAATTATTTAAAAGGTATTTATATGTTTTTACATTTTGAT
1 AAATTATTTAAAAGGTATTTATATGTTTTTACATTTTGAT
21419609 AAAT
1 AAAT
21419613 ATCTTTTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
39 24 0.60
40 16 0.40
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (40 bp):
AAATTATTTAAAAGGTATTTATATGTTTTTACATTTTGAT
Found at i:21420149 original size:14 final size:15
Alignment explanation
Indices: 21420116--21420149 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
21420106 TTGATAAACA
*
21420116 TTAATATAAAATTGT
1 TTAATATAAAAATGT
21420131 TTAATATAAAAAT-T
1 TTAATATAAAAATGT
21420145 TTAAT
1 TTAAT
21420150 TTTGTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAATATAAAAATGT
Found at i:21423185 original size:6 final size:6
Alignment explanation
Indices: 21423174--21423221 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
21423164 TAAGCTGAGT
21423174 CTATTA CTATTA CTATTA CTATTA CTATTA CTATTA CTATTA CTATTA
1 CTATTA CTATTA CTATTA CTATTA CTATTA CTATTA CTATTA CTATTA
21423222 TTTTGGTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
CTATTA
Found at i:21436014 original size:6 final size:6
Alignment explanation
Indices: 21436003--21436032 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
21435993 AAATAAAAGG
21436003 AATAAA AATAAA AATAAA AAT-AA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA AATAAA A
21436033 TGTGTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:21436020 original size:12 final size:11
Alignment explanation
Indices: 21436003--21436032 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
21435993 AAATAAAAGG
21436003 AATAAAAATAAA
1 AATAAAAAT-AA
21436015 AATAAAAATAA
1 AATAAAAATAA
21436026 AATAAAA
1 AATAAAA
21436033 TGTGTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:21437685 original size:3 final size:3
Alignment explanation
Indices: 21437668--21437749 Score: 80
Period size: 3 Copynumber: 27.7 Consensus size: 3
21437658 TATATATAAA
* * * **
21437668 TAT TA- TAT ATAT TAT TAT AAT TAT TAAC CAT TAT TAT GGT T-T TA-
1 TAT TAT TAT -TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
21437712 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
21437750 AATAAAGTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
2 6 0.09
3 55 0.85
4 4 0.06
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:21438203 original size:14 final size:14
Alignment explanation
Indices: 21438181--21438233 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
21438171 TTATATTATT
*
21438181 ATAACATAAAGTAA
1 ATAAAATAAAGTAA
*
21438195 ATAAAATAAAATGAA
1 ATAAAATAAAGT-AA
* *
21438210 ATAAAACAAAGCAA
1 ATAAAATAAAGTAA
*
21438224 ATGAAATAAA
1 ATAAAATAAA
21438234 AAGAAGGAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.70, C:0.06, G:0.08, T:0.17
Consensus pattern (14 bp):
ATAAAATAAAGTAA
Found at i:21438524 original size:3 final size:3
Alignment explanation
Indices: 21438516--21438571 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
21438506 GTGAGGTAAG
21438516 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21438564 TAT TAT TA
1 TAT TAT TA
21438572 AGATGAGTGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:21443404 original size:26 final size:26
Alignment explanation
Indices: 21443374--21443427 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
21443364 TATTCAAGAA
**
21443374 ATGAAAAATGCTTGATTGAAA-ACTTG
1 ATGAAAAACACTTGA-TGAAAGACTTG
21443400 ATGAAAAACACTTGATGAAAGACTTG
1 ATGAAAAACACTTGATGAAAGACTTG
21443426 AT
1 AT
21443428 TAATGAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (26 bp):
ATGAAAAACACTTGATGAAAGACTTG
Found at i:21445481 original size:27 final size:27
Alignment explanation
Indices: 21445437--21445493 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
21445427 TTTCCTCCGT
* *
21445437 ATTTTTAACTCTAGAAGC-GAGATTAAG
1 ATTTTTAACTCCACAAGCAGA-ATTAAG
21445464 ATTTTTAACTCCACAAGCAGAATTAAG
1 ATTTTTAACTCCACAAGCAGAATTAAG
21445491 ATT
1 ATT
21445494 ATTTTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (27 bp):
ATTTTTAACTCCACAAGCAGAATTAAG
Found at i:21465872 original size:18 final size:19
Alignment explanation
Indices: 21465827--21465875 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
21465817 GAATATTTAC
*
21465827 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
21465847 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
21465865 ATAAAAATAAA
1 ATAAAAATAAA
21465876 ACTTTACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:21468945 original size:37 final size:36
Alignment explanation
Indices: 21468899--21468974 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
21468889 ATTCCAAAAA
21468899 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATTTTAATAGTGTT-ATATT-AATTTAATAT
*
21468935 TAATACTTATTTTAATAGTGTTTTATTAATTTAATAT
1 TAATA-TTATTTTAATAGTGTTATATTAATTTAATAT
21468972 TAA
1 TAA
21468975 AGTGACTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 13 0.36
37 21 0.58
38 2 0.06
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (36 bp):
TAATATTATTTTAATAGTGTTATATTAATTTAATAT
Found at i:21469159 original size:23 final size:25
Alignment explanation
Indices: 21469111--21469158 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
21469101 AGTTGTAGAA
21469111 AGAAAATTCTTTGAAGAGATTATTTT
1 AGAAAATTCTTT-AAGAGATTATTTT
21469137 AGAAAATT-TTT-AGAGA-TATTTT
1 AGAAAATTCTTTAAGAGATTATTTT
21469159 TCTGATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
25 3 0.14
26 8 0.36
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.44
Consensus pattern (25 bp):
AGAAAATTCTTTAAGAGATTATTTT
Done.