Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 152 of 182
Found at i:46837663 original size:24 final size:24
Alignment explanation
Indices: 46837645--46837719 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
46837635 AGTTTGACTC
46837645 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAATAGAGTTTAATTG
* *
46837669 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAATAGAGTTTAATTG
* *
46837693 AAACAATTAAATAGAGTTTAACTG
1 AAACAAATAAATAGAGTTTAATTG
46837717 AAA
1 AAA
46837720 GATTATTTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.27
Consensus pattern (24 bp):
AAACAAATAAATAGAGTTTAATTG
Found at i:46839696 original size:24 final size:24
Alignment explanation
Indices: 46839641--46839714 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
46839631 AGTTTGACTC
*
46839641 AAAC-AATAAACAGGGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
46839664 AAACAAATAAATATAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* ** *
46839688 ATATGAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
46839712 AAA
1 AAA
46839715 GATTATTTCT
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 4 0.10
24 36 0.90
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.28
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:46846542 original size:23 final size:23
Alignment explanation
Indices: 46846396--46846543 Score: 140
Period size: 23 Copynumber: 6.4 Consensus size: 23
46846386 CACTAGCGCA
*
46846396 CTCTCTGTTTAGCAC-GTCTCGTG
1 CTCTCTGTTTAGCACTGTGT-GTG
* *
46846419 CTCTCTATTTAGCAC-GTCTCGTG
1 CTCTCTGTTTAGCACTGTGT-GTG
* *
46846442 CTCTTTGTTATTAGCACTATGTGTG
1 CTCTCTG-T-TTAGCACTGTGTGTG
*
46846467 CTCTCTGATTAGCACT-TGTGTG
1 CTCTCTGTTTAGCACTGTGTGTG
* * * * *
46846489 CTCTCTGATTAGTACTTTGCGTA
1 CTCTCTGTTTAGCACTGTGTGTG
46846512 CTCTCTGTTTAGCACTGTGTGTG
1 CTCTCTGTTTAGCACTGTGTGTG
46846535 CTCTCTGTT
1 CTCTCTGTT
46846544 GCCCAGCACT
Statistics
Matches: 106, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
22 21 0.20
23 66 0.62
24 1 0.01
25 16 0.15
26 2 0.02
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.43
Consensus pattern (23 bp):
CTCTCTGTTTAGCACTGTGTGTG
Found at i:46856508 original size:16 final size:16
Alignment explanation
Indices: 46856463--46856508 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
46856453 CAAAATTTTA
*
46856463 ATAAA-TAAAAAATAT
1 ATAAATTAATAAATAT
*
46856478 ATAAATTATTAAATAT
1 ATAAATTAATAAATAT
46856494 -TAAATTAATATAATA
1 ATAAATTAATA-AATA
46856509 AAATTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAAATTAATAAATAT
Found at i:46856864 original size:2 final size:2
Alignment explanation
Indices: 46856826--46856850 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46856816 ATATTTATCC
46856826 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
46856851 TAAAGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46859241 original size:89 final size:89
Alignment explanation
Indices: 46859090--46859254 Score: 260
Period size: 89 Copynumber: 1.9 Consensus size: 89
46859080 CCTGCCTCCT
* * * *
46859090 CCATATGTGGAATAAGCAACTCTACAACCCCATTTGATCATTTTCAGTAATTCACTTCAGTTTCT
1 CCATATGTAGAACAAGCAACTCTACAACCCCATTCGATCATATTCAGTAATTCACTTCAGTTTCT
46859155 TAAGCTTCTCTTCTCTTCAAGTCC
66 TAAGCTTCTCTTCTCTTCAAGTCC
*
46859179 CCATATGTAGAACAAGCAACTCTACAACCCCATTCGATCATATTCAGTACCTT-ACTTCAGTTTC
1 CCATATGTAGAACAAGCAACTCTACAACCCCATTCGATCATATTCAGTA-ATTCACTTCAGTTTC
*
46859243 TTCAGCTTCTCT
65 TTAAGCTTCTCT
46859255 CCTTTGAAGT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
89 67 0.97
90 2 0.03
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.35
Consensus pattern (89 bp):
CCATATGTAGAACAAGCAACTCTACAACCCCATTCGATCATATTCAGTAATTCACTTCAGTTTCT
TAAGCTTCTCTTCTCTTCAAGTCC
Found at i:46861846 original size:27 final size:28
Alignment explanation
Indices: 46861808--46861868 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 28
46861798 TTGAACCCCT
*
46861808 AATCTT-GAAATCTGAA-TTTAAATCTCA
1 AATCTTAGAAATC-AAATTTTAAATCTCA
**
46861835 AATCTTAG-AATCAAATTTTAAATCTTG
1 AATCTTAGAAATCAAATTTTAAATCTCA
46861862 AATCTTA
1 AATCTTA
46861869 ACCCAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 2 0.07
27 26 0.90
28 1 0.03
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (28 bp):
AATCTTAGAAATCAAATTTTAAATCTCA
Found at i:46861850 original size:20 final size:19
Alignment explanation
Indices: 46861827--46861865 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
46861817 ATCTGAATTT
46861827 AAATCTCAAATCTTAGAATC
1 AAATCTCAAATCTT-GAATC
* *
46861847 AAATTTTAAATCTTGAATC
1 AAATCTCAAATCTTGAATC
46861866 TTAACCCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (19 bp):
AAATCTCAAATCTTGAATC
Found at i:46866513 original size:22 final size:23
Alignment explanation
Indices: 46866487--46866543 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
46866477 AAACTAGAAT
*
46866487 AAAATTAATATTTATTGTTTAA-
1 AAAATTAATATTTATTATTTAAC
46866509 AAAATT-ATAATTTATTATTTAAC
1 AAAATTAAT-ATTTATTATTTAAC
*
46866532 AAAGTTAATATT
1 AAAATTAATATT
46866544 CTAAATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 2 0.07
22 18 0.60
23 8 0.27
24 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (23 bp):
AAAATTAATATTTATTATTTAAC
Found at i:46867438 original size:7 final size:7
Alignment explanation
Indices: 46867424--46867456 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
46867414 AGCAAATGCC
46867424 AAAA-GG
1 AAAATGG
46867430 AAAATGG
1 AAAATGG
46867437 AAAATGG
1 AAAATGG
46867444 AAAATGG
1 AAAATGG
*
46867451 ATAATG
1 AAAATG
46867457 TAAAGAGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 4 0.16
7 21 0.84
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (7 bp):
AAAATGG
Found at i:46877304 original size:6 final size:6
Alignment explanation
Indices: 46877293--46877317 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
46877283 TAAGCACTTG
46877293 CATATA CATATA CATATA CATATA C
1 CATATA CATATA CATATA CATATA C
46877318 TAAAAAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (6 bp):
CATATA
Found at i:46879135 original size:15 final size:15
Alignment explanation
Indices: 46879105--46879133 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46879095 TAAAATAAAC
46879105 AAAATATAACATTTT
1 AAAATATAACATTTT
46879120 AAAATATAA-ATTTT
1 AAAATATAACATTTT
46879134 TATTGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATATAACATTTT
Found at i:46885327 original size:8 final size:8
Alignment explanation
Indices: 46885314--46885343 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
46885304 GAGGTTTTCA
46885314 TTTTTGTT
1 TTTTTGTT
46885322 TTTTTGTT
1 TTTTTGTT
46885330 TTTTTGTT
1 TTTTTGTT
46885338 TCTTTT
1 T-TTTT
46885344 TTTAATGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (8 bp):
TTTTTGTT
Found at i:46890951 original size:41 final size:39
Alignment explanation
Indices: 46890892--46890979 Score: 117
Period size: 41 Copynumber: 2.3 Consensus size: 39
46890882 GGAAAAAGTT
*
46890892 AAAATAAT--TTTATTATGAATTGATCTGAACATATAACC
1 AAAATAATCCTTTATTATGAATTGATCAGAACATATAA-C
*
46890930 AAAATAATCCTTTAATTATGAATTGATCAGAACATGTAAC
1 AAAATAATCCTTT-ATTATGAATTGATCAGAACATATAAC
*
46890970 AAAACAATCC
1 AAAATAATCC
46890980 AAATTTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
38 8 0.18
40 13 0.30
41 23 0.52
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.32
Consensus pattern (39 bp):
AAAATAATCCTTTATTATGAATTGATCAGAACATATAAC
Found at i:46894317 original size:26 final size:26
Alignment explanation
Indices: 46894267--46894317 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
46894257 ATAAATATCA
* * *
46894267 ATTTCGTATATTTATTTCATGTAAAC
1 ATTTCGTATAATAATTTCATCTAAAC
*
46894293 ATTTCGTATAATAATTTTATCTAAA
1 ATTTCGTATAATAATTTCATCTAAA
46894318 TCTTACATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (26 bp):
ATTTCGTATAATAATTTCATCTAAAC
Found at i:46898558 original size:30 final size:31
Alignment explanation
Indices: 46898507--46898564 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
46898497 ATCTAGTGAC
*
46898507 TTAAATAAAAACTTATGAATAATTTAATAAT
1 TTAAATAAAAACTTATAAATAATTTAATAAT
46898538 TTAAAT-AAAACATT-TAAATAATTTAAT
1 TTAAATAAAAAC-TTATAAATAATTTAAT
46898565 GATCAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (31 bp):
TTAAATAAAAACTTATAAATAATTTAATAAT
Found at i:46905785 original size:14 final size:14
Alignment explanation
Indices: 46905750--46905791 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
46905740 TATATTATTT
*
46905750 TTTTTTTTAAATTTA
1 TTTTTTTT-AATTAA
*
46905765 TTATTTTTAATTAA
1 TTTTTTTTAATTAA
46905779 TTTTTTTT-ATTAA
1 TTTTTTTTAATTAA
46905792 ATCTTTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 5 0.21
14 12 0.50
15 7 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTTTAATTAA
Found at i:46914256 original size:38 final size:38
Alignment explanation
Indices: 46914205--46914283 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
46914195 AATTGATAAT
46914205 GAAAGGCTTGAAACTGAATGAAGTGGATATTGGACATG
1 GAAAGGCTTGAAACTGAATGAAGTGGATATTGGACATG
46914243 GAAAGGCTTGAAACTGAATGAAGTGGATATTGGACATG
1 GAAAGGCTTGAAACTGAATGAAGTGGATATTGGACATG
46914281 GAA
1 GAA
46914284 GTGGGTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.38, C:0.08, G:0.32, T:0.23
Consensus pattern (38 bp):
GAAAGGCTTGAAACTGAATGAAGTGGATATTGGACATG
Found at i:46914286 original size:19 final size:19
Alignment explanation
Indices: 46914224--46914287 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
46914214 GAAACTGAAT
46914224 GAAGTGGATATTGGACATG
1 GAAGTGGATATTGGACATG
* * *
46914243 GAAAGGCTTGAAACT-GA-AT-
1 G-AA-G-TGGATATTGGACATG
46914262 GAAGTGGATATTGGACATG
1 GAAGTGGATATTGGACATG
46914281 GAAGTGG
1 GAAGTGG
46914288 GTTTTTTGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
16 5 0.15
17 3 0.09
18 4 0.12
19 9 0.27
20 4 0.12
21 3 0.09
22 5 0.15
ACGTcount: A:0.34, C:0.06, G:0.36, T:0.23
Consensus pattern (19 bp):
GAAGTGGATATTGGACATG
Found at i:46931162 original size:3 final size:3
Alignment explanation
Indices: 46931154--46931179 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
46931144 TCCCCTTTGT
46931154 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
46931180 ATCTGCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:46933690 original size:223 final size:224
Alignment explanation
Indices: 46933234--46933901 Score: 826
Period size: 228 Copynumber: 3.0 Consensus size: 224
46933224 TTAAGTTTAA
* *
46933234 ATTTTATGAACTTGGGATAATAAATTGTATCAAAGAATAAAAAAAATCGATTTTTTGATTGGTTC
1 ATTTTATGAA-TTGGGCTAATAAATTGTATCAAAGAATAAAAAAAAT-GATTTTTTGATCGGTTC
* *
46933299 AACAAGTTTTGATTCTTGATTCAATGG-AG-GATCCGAATAATTCACTCAAAACCCGTTTCAATG
64 AACAAGTTCTGATTCTTGATTCAATGGCAGTG-T-CGAATAATTCACTCAAAACCCGTTTCAATA
* * *
46933362 CTTTTGTCTAAAACCAATACATCCATCAATTTTTAATCCAATCAATCCGATTCCAACGACATTGA
127 CTTTTGTCT-AAACCAATACATTCATCAATTTTTAATCCAATCGATCCGATTCCAACGACATTAA
* *
46933427 ATTTTACATTCAACTCCGCATCAGTTTGGGTTAG
191 ATTTTACATTCAAGTCAGCATCAGTTTGGGTTAG
* *
46933461 ATTTTATGAATTGGGGCTAATAAATTGTATCAAAGAATAAAAAACA-G-TTTTTTGATCGATTCA
1 ATTTTATGAATT-GGGCTAATAAATTGTATCAAAGAATAAAAAAAATGATTTTTTGATCGGTTCA
* * * * *
46933524 ACAGGTTCCGATTCTTGACTCAATGGCAGTGTCAAATAATTCACTCAAAACCTGTTTCAATACTT
65 ACAAGTTCTGATTCTTGATTCAATGGCAGTGTCGAATAATTCACTCAAAACCCGTTTCAATACTT
46933589 TTGTCTAAACCAATACATTCATCAATTTTTAATCCAATCGATCCGATTCCAACGACATTAAATTT
130 TTGTCTAAACCAATACATTCATCAATTTTTAATCCAATCGATCCGATTCCAACGACATTAAATTT
* * *
46933654 TGCATTCAAGTCAGCATCCGTTTGGGTTAT
195 TACATTCAAGTCAGCATCAGTTTGGGTTAG
* ** *
46933684 ATTTTATGAGCTTGGGCTAATAAATTGTGCCAAAGAATAAAAGAAAAATTGATTTTTT-AACTGG
1 ATTTTATGA-ATTGGGCTAATAAATTGTATCAAAGAAT-AAA-AAAAA-TGATTTTTTGATC-GG
* * * * * * * * *
46933748 TTCAACATGTTGTGATTCTTGATTTAATGACGGTTTCGAACAATTCACTCAAAACCCATGTCAAT
61 TTCAACAAGTTCTGATTCTTGATTCAATGGCAGTGTCGAATAATTCACTCAAAACCCGTTTCAAT
* ** ** * *
46933813 ACTTTTGTTTAGGCCAATACATTTTTCAATTTTCAATCCAATTGATCCGA-TCTCAACGACATTA
126 ACTTTTGTCTAAACCAATACATTCATCAATTTTTAATCCAATCGATCCGATTC-CAACGACATTA
*
46933877 AATTTTACATTCAAGTAAGCATCAG
190 AATTTTACATTCAAGTCAGCATCAG
46933902 CATCAGTAAA
Statistics
Matches: 382, Mismatches: 48, Indels: 21
0.85 0.11 0.05
Matches are distributed among these distances:
223 113 0.30
224 77 0.20
225 8 0.02
226 3 0.01
227 46 0.12
228 135 0.35
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (224 bp):
ATTTTATGAATTGGGCTAATAAATTGTATCAAAGAATAAAAAAAATGATTTTTTGATCGGTTCAA
CAAGTTCTGATTCTTGATTCAATGGCAGTGTCGAATAATTCACTCAAAACCCGTTTCAATACTTT
TGTCTAAACCAATACATTCATCAATTTTTAATCCAATCGATCCGATTCCAACGACATTAAATTTT
ACATTCAAGTCAGCATCAGTTTGGGTTAG
Found at i:46943462 original size:6 final size:6
Alignment explanation
Indices: 46943435--46943482 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
46943425 TGGATCAAGA
* * * * *
46943435 GGAGCC AGAACC GGAGCT GGAGCG GGAGCT GGAGCC GGAGCC GGAGCC
1 GGAGCC GGAGCC GGAGCC GGAGCC GGAGCC GGAGCC GGAGCC GGAGCC
46943483 ACTGCTTCAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.21, C:0.27, G:0.48, T:0.04
Consensus pattern (6 bp):
GGAGCC
Found at i:46943462 original size:12 final size:12
Alignment explanation
Indices: 46943445--46943482 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
46943435 GGAGCCAGAA
46943445 CCGGAGCTGGAG
1 CCGGAGCTGGAG
*
46943457 CGGGAGCTGGAG
1 CCGGAGCTGGAG
*
46943469 CCGGAGCCGGAG
1 CCGGAGCTGGAG
46943481 CC
1 CC
46943483 ACTGCTTCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.16, C:0.29, G:0.50, T:0.05
Consensus pattern (12 bp):
CCGGAGCTGGAG
Found at i:46951652 original size:7 final size:7
Alignment explanation
Indices: 46951636--46951665 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
46951626 TTTGAAGCTT
46951636 AAGATTC
1 AAGATTC
*
46951643 AAGGTTC
1 AAGATTC
46951650 AAGATTC
1 AAGATTC
46951657 AAGATTC
1 AAGATTC
46951664 AA
1 AA
46951666 AGTTTGAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (7 bp):
AAGATTC
Found at i:46952430 original size:18 final size:17
Alignment explanation
Indices: 46952407--46952445 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
46952397 AAAATCTTAT
46952407 TTTTAAAGGTTATATATA
1 TTTTAAAGGTTATAT-TA
**
46952425 TTTTAAATTTTATATTA
1 TTTTAAAGGTTATATTA
46952442 TTTT
1 TTTT
46952446 GAGTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
TTTTAAAGGTTATATTA
Found at i:46961121 original size:13 final size:13
Alignment explanation
Indices: 46961103--46961127 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46961093 TTAATAAAAC
46961103 CAATTGATCAAAT
1 CAATTGATCAAAT
46961116 CAATTGATCAAA
1 CAATTGATCAAA
46961128 CTGATCATTA
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:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (13 bp):
CAATTGATCAAAT
Found at i:46970453 original size:63 final size:63
Alignment explanation
Indices: 46970360--46970478 Score: 166
Period size: 63 Copynumber: 1.9 Consensus size: 63
46970350 CCTCCACGAG
* * * * * *
46970360 AAGCGGTCTGGTACTCGAATCCTTAGCTTTGGCTTCAGAATGCTCAGGTTCTTCCTCTGCAAC
1 AAGCGGTCTGGTACTCAAATCCTCACCTTTGACTTCAGAATGATCAGGTACTTCCTCTGCAAC
* *
46970423 AAGCGGTCTGGTACTCAAATCCTCACCTTTGACTTCAGTATGATCGGGTACTTCCT
1 AAGCGGTCTGGTACTCAAATCCTCACCTTTGACTTCAGAATGATCAGGTACTTCCT
46970479 TCATGTGAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (63 bp):
AAGCGGTCTGGTACTCAAATCCTCACCTTTGACTTCAGAATGATCAGGTACTTCCTCTGCAAC
Found at i:46972156 original size:19 final size:19
Alignment explanation
Indices: 46972132--46972170 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
46972122 TTTAGTTAAA
46972132 CCTATAGGGAGAGGAGGGT
1 CCTATAGGGAGAGGAGGGT
*
46972151 CCTATAGGGAGGGGAGGGT
1 CCTATAGGGAGAGGAGGGT
46972170 C
1 C
46972171 TGGTTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.13, G:0.49, T:0.15
Consensus pattern (19 bp):
CCTATAGGGAGAGGAGGGT
Found at i:46972910 original size:47 final size:47
Alignment explanation
Indices: 46972858--46972961 Score: 192
Period size: 47 Copynumber: 2.2 Consensus size: 47
46972848 TGCATCAGTT
*
46972858 TCAAATGTAATCAATTATTCAATAAATATAAATTTTAATTGAATTAA
1 TCAAATGTAATCAATTATTCAATAAATATAAATTTTAATTCAATTAA
46972905 TCAAATGTAATCAATTATTCAATAAATATAAATTTTAATTCAATTAA
1 TCAAATGTAATCAATTATTCAATAAATATAAATTTTAATTCAATTAA
46972952 TCAAAT-TAAT
1 TCAAATGTAAT
46972962 TGAATAAATA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
46 4 0.07
47 52 0.93
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (47 bp):
TCAAATGTAATCAATTATTCAATAAATATAAATTTTAATTCAATTAA
Found at i:46977600 original size:30 final size:30
Alignment explanation
Indices: 46977564--46977628 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
46977554 GACAATTAAT
46977564 TAATTTTTA-AAAATTTAAAACTATTTTTTA
1 TAATTTTTATAAAATTTAAAA-TATTTTTTA
*** *
46977594 TAATTTTTATACTTTTTAAAATTTTTTTTA
1 TAATTTTTATAAAATTTAAAATATTTTTTA
46977624 TAATT
1 TAATT
46977629 GATGATAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (30 bp):
TAATTTTTATAAAATTTAAAATATTTTTTA
Found at i:46986172 original size:31 final size:31
Alignment explanation
Indices: 46986130--46986196 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
46986120 CCAAATTTAT
*
46986130 TTATTTAAAAAAGTTACAATTGA-TTATTGAA
1 TTATTTAAAAAA-TTACAATTAAGTTATTGAA
* * *
46986161 TTATTTCAAAAATTTCATTTAAGTTATTGAA
1 TTATTTAAAAAATTACAATTAAGTTATTGAA
46986192 TTATT
1 TTATT
46986197 AACATAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.48
Consensus pattern (31 bp):
TTATTTAAAAAATTACAATTAAGTTATTGAA
Found at i:46986513 original size:30 final size:31
Alignment explanation
Indices: 46986456--46986514 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
46986446 AGAATGTCAT
46986456 AATATTCTAGTGATTTATATGAAAATTTTCA
1 AATATTCTAGTGATTTATATGAAAATTTTCA
* * *
46986487 AATATTTTAGTGA-TTATATTATAATTTT
1 AATATTCTAGTGATTTATATGAAAATTTT
46986515 TTGGAGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.51
Consensus pattern (31 bp):
AATATTCTAGTGATTTATATGAAAATTTTCA
Found at i:46987405 original size:19 final size:20
Alignment explanation
Indices: 46987364--46987409 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
46987354 ACAAAACTTT
*
46987364 AATATATAAAAATATTTACA
1 AATATTTAAAAATATTTACA
*
46987384 AATATTTAAAAATCTTTA-A
1 AATATTTAAAAATATTTACA
46987403 AATATTT
1 AATATTT
46987410 TTTATTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATTTAAAAATATTTACA
Found at i:46987439 original size:19 final size:20
Alignment explanation
Indices: 46987403--46987442 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
46987393 AAATCTTTAA
*
46987403 AATATTTTTTATTTAATTTT
1 AATATTTTTTATTAAATTTT
46987423 AATATTTTTT-TTAAATTTT
1 AATATTTTTTATTAAATTTT
46987442 A
1 A
46987443 TTAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
AATATTTTTTATTAAATTTT
Found at i:46988301 original size:2 final size:2
Alignment explanation
Indices: 46988294--46988327 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
46988284 TAATTTATCC
46988294 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
46988328 GTAAATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46994161 original size:18 final size:17
Alignment explanation
Indices: 46994138--46994177 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
46994128 TTACGGCAAA
46994138 TTTTCTAGCAGGGATCG
1 TTTTCTAGCAGGGATCG
46994155 CTTTTCTAGCAGGGATCG
1 -TTTTCTAGCAGGGATCG
46994173 TTTTC
1 TTTTC
46994178 CACGAGGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.40
Consensus pattern (17 bp):
TTTTCTAGCAGGGATCG
Found at i:47001707 original size:6 final size:6
Alignment explanation
Indices: 47001698--47001724 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
47001688 TCATGATGAT
47001698 TATCTC TATCTC TATCTC TATCTC TAT
1 TATCTC TATCTC TATCTC TATCTC TAT
47001725 ACCTATCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.00, T:0.52
Consensus pattern (6 bp):
TATCTC
Found at i:47005013 original size:41 final size:41
Alignment explanation
Indices: 47004951--47005035 Score: 143
Period size: 41 Copynumber: 2.1 Consensus size: 41
47004941 AATAACAATA
*
47004951 AAAGAGAAGTAGGGTCTAATCCTCAGGGACTGGAGAGTCGT
1 AAAGAGAAGTAGGGTCTAATCCTCAGAGACTGGAGAGTCGT
* *
47004992 AAAGGGAAGTAGGGTCTAATCCTCAGAGACTGGGGAGTCGT
1 AAAGAGAAGTAGGGTCTAATCCTCAGAGACTGGAGAGTCGT
47005033 AAA
1 AAA
47005036 AACCATACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.33, C:0.14, G:0.34, T:0.19
Consensus pattern (41 bp):
AAAGAGAAGTAGGGTCTAATCCTCAGAGACTGGAGAGTCGT
Found at i:47005455 original size:32 final size:33
Alignment explanation
Indices: 47005416--47005489 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
47005406 GTCAAAGTTG
* **
47005416 TTTATTTTATTAATTTTGTTTTGATT-AAATT-
1 TTTATTTTACTAATTTCATTTTGATTAAAATTA
*
47005447 TGTTATTTTCCTAATTTCATTTTGATTAAAATTA
1 T-TTATTTTACTAATTTCATTTTGATTAAAATTA
47005481 TTTATTTTA
1 TTTATTTTA
47005490 AGTAAATAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 1 0.03
32 21 0.60
33 12 0.34
34 1 0.03
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (33 bp):
TTTATTTTACTAATTTCATTTTGATTAAAATTA
Found at i:47007294 original size:19 final size:17
Alignment explanation
Indices: 47007266--47007300 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
47007256 AATTGACATT
47007266 AAAATATTAATTCATTAA
1 AAAATATTAATT-ATTAA
47007284 AAAACTATTAATTATTA
1 AAAA-TATTAATTATTA
47007301 TTGGATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATATTAATTATTAA
Found at i:47008023 original size:26 final size:26
Alignment explanation
Indices: 47007994--47008044 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
47007984 TTTAAATAAA
* *
47007994 CAATTAATAGAATCAGTTGGTCAAAT
1 CAATTAAAAGAATCAGTCGGTCAAAT
*
47008020 CAATTAAAAGAATGAGTCGGTCAAA
1 CAATTAAAAGAATCAGTCGGTCAAA
47008045 CTAGCCATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (26 bp):
CAATTAAAAGAATCAGTCGGTCAAAT
Found at i:47012139 original size:15 final size:15
Alignment explanation
Indices: 47012119--47012149 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
47012109 TAATTGCTAC
47012119 TCCTTTATTTTCTAT
1 TCCTTTATTTTCTAT
47012134 TCCTTTATTTTCTAT
1 TCCTTTATTTTCTAT
47012149 T
1 T
47012150 GTAATTTTTT
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:0.13, C:0.19, G:0.00, T:0.68
Consensus pattern (15 bp):
TCCTTTATTTTCTAT
Found at i:47018120 original size:34 final size:32
Alignment explanation
Indices: 47018046--47018120 Score: 102
Period size: 30 Copynumber: 2.4 Consensus size: 32
47018036 TAAAACTTAT
*
47018046 TTTA-TTGTTAATTTTGTTTTTATTTTAGAGA
1 TTTATTTGTTAATTTTGTTATTATTTTAGAGA
47018077 --TATTTGTTAATTTTGTTATTATTTTAGAAGCA
1 TTTATTTGTTAATTTTGTTATTATTTTAG-AG-A
47018109 TTTATTTGTTAA
1 TTTATTTGTTAA
47018121 GCTACATCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 2 0.05
30 23 0.61
31 2 0.05
32 1 0.03
34 10 0.26
ACGTcount: A:0.25, C:0.01, G:0.12, T:0.61
Consensus pattern (32 bp):
TTTATTTGTTAATTTTGTTATTATTTTAGAGA
Found at i:47023281 original size:46 final size:46
Alignment explanation
Indices: 47023214--47023307 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
47023204 AGGAGGGGTT
47023214 ATGAGTAGTTTTAGTTGTTGTGTCAAAAAGGGTATATATGATTAGA
1 ATGAGTAGTTTTAGTTGTTGTGTCAAAAAGGGTATATATGATTAGA
47023260 ATGAGTAGTTTTAGTTGTTGTGTCAAAAAGGGTATATATGATTAGA
1 ATGAGTAGTTTTAGTTGTTGTGTCAAAAAGGGTATATATGATTAGA
47023306 AT
1 AT
47023308 TTCTTATGAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (46 bp):
ATGAGTAGTTTTAGTTGTTGTGTCAAAAAGGGTATATATGATTAGA
Found at i:47027921 original size:23 final size:24
Alignment explanation
Indices: 47027873--47027927 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
47027863 TGCACCTATA
* *
47027873 TTAATGTTATTTAAATAAGATTTT
1 TTAATGTTATTGAAATAAAATTTT
47027897 TTAAT-TTATTGAAA-AAAATTATT
1 TTAATGTTATTGAAATAAAATT-TT
47027920 TTAATGTT
1 TTAATGTT
47027928 TTAATGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 5 0.19
23 15 0.56
24 7 0.26
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (24 bp):
TTAATGTTATTGAAATAAAATTTT
Found at i:47029984 original size:21 final size:20
Alignment explanation
Indices: 47029940--47029983 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
47029930 ATTTGAACTC
47029940 AAAACTCAAGTAAAAAACAA
1 AAAACTCAAGTAAAAAACAA
*
47029960 AAAATTCAAGTAAAAAACAA
1 AAAACTCAAGTAAAAAACAA
47029980 AAAA
1 AAAA
47029984 AATCTCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.73, C:0.11, G:0.05, T:0.11
Consensus pattern (20 bp):
AAAACTCAAGTAAAAAACAA
Found at i:47030315 original size:30 final size:32
Alignment explanation
Indices: 47030259--47030317 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
47030249 ATCATTTTTC
*
47030259 TTTAATTAATATAGAAAATTCAATTAATTAAA
1 TTTAATTAATATAAAAAATTCAATTAATTAAA
*
47030291 TTTATTTAATA-AAAAAATT-AATTAATT
1 TTTAATTAATATAAAAAATTCAATTAATT
47030318 TACTTGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 8 0.32
31 7 0.28
32 10 0.40
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (32 bp):
TTTAATTAATATAAAAAATTCAATTAATTAAA
Found at i:47040552 original size:33 final size:31
Alignment explanation
Indices: 47040496--47040570 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 31
47040486 CAAATAATTT
47040496 TAAAATTATTAAAATTA-TTTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTTTAAAATA
*
47040526 TAACATTATTAAAATTATTATATTTTTTTAAAATA
1 TAAAATTATT-AAA--ATTAT-TTTTTTTAAAATA
47040561 TAAAATTATT
1 TAAAATTATT
47040571 TTGTCTTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
30 9 0.24
31 3 0.08
33 4 0.11
35 22 0.58
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
TAAAATTATTAAAATTATTTTTTTTAAAATA
Found at i:47041132 original size:15 final size:15
Alignment explanation
Indices: 47041112--47041144 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
47041102 TGTGCTTTTA
47041112 TTTCTT-TAATTATGG
1 TTTCTTGTAATT-TGG
47041127 TTTCTTGTAATTTGG
1 TTTCTTGTAATTTGG
47041142 TTT
1 TTT
47041145 GAGAACCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.64
Consensus pattern (15 bp):
TTTCTTGTAATTTGG
Found at i:47047778 original size:40 final size:40
Alignment explanation
Indices: 47047734--47047813 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
47047724 GAACATGATA
47047734 AGAACAACTCAATGCTCAATCAAGTCAGAAGCAAAACTAT
1 AGAACAACTCAATGCTCAATCAAGTCAGAAGCAAAACTAT
*
47047774 AGAACAACTCAATGCTCAATCAAGTCAGAAGCAGAACTAT
1 AGAACAACTCAATGCTCAATCAAGTCAGAAGCAAAACTAT
47047814 GACATAACAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.46, C:0.23, G:0.14, T:0.17
Consensus pattern (40 bp):
AGAACAACTCAATGCTCAATCAAGTCAGAAGCAAAACTAT
Found at i:47052624 original size:27 final size:27
Alignment explanation
Indices: 47052555--47052624 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
47052545 TCAACAAAAA
*
47052555 TTAAAAAA-AAAAAATTCAAAATATTT
1 TTAAAAAATAAAAAAATCAAAATATTT
* * *
47052581 ATAAAAAACTCATAAAAT-AAAATATTT
1 TTAAAAAA-TAAAAAAATCAAAATATTT
47052608 TTAAAAAATTAAAAAAA
1 TTAAAAAA-TAAAAAAA
47052625 AACTAAAGAG
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
26 7 0.21
27 22 0.65
28 5 0.15
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (27 bp):
TTAAAAAATAAAAAAATCAAAATATTT
Found at i:47053854 original size:13 final size:13
Alignment explanation
Indices: 47053836--47053861 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47053826 TATTAAAATA
47053836 AATTCATTATTAT
1 AATTCATTATTAT
47053849 AATTCATTATTAT
1 AATTCATTATTAT
47053862 TGTACATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTCATTATTAT
Found at i:47057837 original size:165 final size:164
Alignment explanation
Indices: 47057542--47057843 Score: 376
Period size: 165 Copynumber: 1.8 Consensus size: 164
47057532 GCTGTTCTAT
* * *
47057542 CTTTGCACTTATGGTGATAATCAAGTATGCTATTGATTATATATGAGGTAATTTTAGCCTGATTG
1 CTTTGCACATATGGTGATAATAAAGTATGCTATTGATTATATATGAGGTAATCTTAGCCTGATTG
* ** *
47057607 GCATCGAGATGGTCCATAGAAGGCTTGCATAGAAATGTTTTCATTATCGAACTGTATGAGGAAGA
66 GCATCGAGATGGTCCACAGAAGGCTTGCATAGAAATGTTTTCATTATCGAAAAGTAAGAGGAAGA
*
47057672 ATGAATCATGGTATACATTTTATTGCTCTCCTCA
131 ATAAATCATGGTATACATTTTATTGCTCTCCTCA
* * * *
47057706 CTTTGCACATATTGTGATGATAAAAGTATGCTATTGATTATATAATGAGTTAATCTTGGCC-GAT
1 CTTTGCACATATGGTGATAAT-AAAGTATGCTATTGATTATAT-ATGAGGTAATCTTAGCCTGAT
* * * * * * *
47057770 TGGCATCTAGCTGGTCCACGGAGGGCTTGCCTAGAAATGTTTTCGTTGT-GAAAAAGTACAG-GG
64 TGGCATCGAGATGGTCCACAGAAGGCTTGCATAGAAATGTTTTCATTATCG-AAAAGTA-AGAGG
47057833 AAGAATAAATC
127 AAGAATAAATC
47057844 GGGGTCAGTG
Statistics
Matches: 115, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
164 19 0.17
165 81 0.70
166 15 0.13
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (164 bp):
CTTTGCACATATGGTGATAATAAAGTATGCTATTGATTATATATGAGGTAATCTTAGCCTGATTG
GCATCGAGATGGTCCACAGAAGGCTTGCATAGAAATGTTTTCATTATCGAAAAGTAAGAGGAAGA
ATAAATCATGGTATACATTTTATTGCTCTCCTCA
Found at i:47059720 original size:21 final size:21
Alignment explanation
Indices: 47059696--47059736 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
47059686 AATTTAATAA
47059696 AAAAATTAAAATAAATAATTT
1 AAAAATTAAAATAAATAATTT
* *
47059717 AAAAATTCAAATAATTAATT
1 AAAAATTAAAATAAATAATT
47059737 ATAATTAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAATTAAAATAAATAATTT
Found at i:47066713 original size:31 final size:31
Alignment explanation
Indices: 47066677--47066806 Score: 103
Period size: 31 Copynumber: 4.3 Consensus size: 31
47066667 CTTTTGGTAC
47066677 AATTTGGTACTTAAACTTGACACTTTTTCTT
1 AATTTGGTACTTAAACTTGACACTTTTTCTT
* * * * *
47066708 AATTTGGTACCTAAAGTTGATATTTTTTCCT
1 AATTTGGTACTTAAACTTGACACTTTTTCTT
*
47066739 AATTTGGTACATAAA-TT-----TTTTGGGGTC-T
1 AATTTGGTACTTAAACTTGACACTTTT----TCTT
* *
47066767 AATTTGGTACTTAAACTTGACCCTTTTTATT
1 AATTTGGTACTTAAACTTGACACTTTTTCTT
47066798 AATTTGGTA
1 AATTTGGTA
47066807 TCTCATTTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
25 4 0.05
28 15 0.19
29 4 0.05
30 3 0.04
31 50 0.62
34 4 0.05
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (31 bp):
AATTTGGTACTTAAACTTGACACTTTTTCTT
Found at i:47066775 original size:90 final size:90
Alignment explanation
Indices: 47066622--47066806 Score: 277
Period size: 90 Copynumber: 2.1 Consensus size: 90
47066612 CTATAACATA
*
47066622 TGGTACATAAACTTGATATTTTTTCCTAATTTGGTATCTAAATTTCTTTTGGTACAATTTGGTAC
1 TGGTACATAAACTTGATATTTTTTCCTAATTTGGTATCTAAATTTCTTTGGGTACAATTTGGTAC
*
47066687 TTAAACTTGACACTTTTTCTTAATT
66 TTAAACTTGACACTTTTTATTAATT
* *
47066712 TGGTACCTAAAGTTGATATTTTTTCCTAATTTGGTA-CATAAATTT-TTTGGGGT-CTAATTTGG
1 TGGTACATAAACTTGATATTTTTTCCTAATTTGGTATC-TAAATTTCTTT-GGGTAC-AATTTGG
*
47066774 TACTTAAACTTGACCCTTTTTATTAATT
63 TACTTAAACTTGACACTTTTTATTAATT
47066802 TGGTA
1 TGGTA
47066807 TCTCATTTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
89 5 0.06
90 82 0.94
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (90 bp):
TGGTACATAAACTTGATATTTTTTCCTAATTTGGTATCTAAATTTCTTTGGGTACAATTTGGTAC
TTAAACTTGACACTTTTTATTAATT
Found at i:47067001 original size:60 final size:60
Alignment explanation
Indices: 47066927--47067057 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 60
47066917 TTAATATAAT
* * * *
47066927 ATTTGGTATCTGAACTTGACATTTTTTCTTAATTTGGTA-TCTAA-ACTTTTTTTGGACCCA
1 ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTGGCACT-TAATA-TTTTTTTAGACCCA
** **
47066987 ATTTGGTACCTGAACTTGGTATTTTTTCCTAATTTGGCACTTAATATTTTTTTAGATTCA
1 ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTGGCACTTAATATTTTTTTAGACCCA
47067047 ATTTGGTACCT
1 ATTTGGTACCT
47067058 AAATTTATTA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
60 59 0.97
61 2 0.03
ACGTcount: A:0.23, C:0.15, G:0.14, T:0.49
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTGGCACTTAATATTTTTTTAGACCCA
Found at i:47067023 original size:31 final size:30
Alignment explanation
Indices: 47066927--47067023 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 30
47066917 TTAATATAAT
* *
47066927 ATTTGGTATCTGAACTTGACATTTTTTCTTA
1 ATTTGGTATCTGAACTTG-TATTTTTTCCTA
* ** *
47066958 ATTTGGTATCTAAACTT-T-TTTTGGACCCA
1 ATTTGGTATCTGAACTTGTATTTT-TTCCTA
*
47066987 ATTTGGTACCTGAACTTGGTATTTTTTCCTA
1 ATTTGGTATCTGAACTT-GTATTTTTTCCTA
47067018 ATTTGG
1 ATTTGG
47067024 CACTTAATAT
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
28 4 0.08
29 17 0.33
31 26 0.51
32 4 0.08
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.48
Consensus pattern (30 bp):
ATTTGGTATCTGAACTTGTATTTTTTCCTA
Found at i:47067320 original size:29 final size:28
Alignment explanation
Indices: 47067284--47067372 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 28
47067274 ACCTTAAAAA
47067284 AAAATGTCAAGTTTAAGTACCAAATTAGG
1 AAAATGTCAAGTTTAAGTACCAAATTA-G
*
47067313 AAAATGTCAAGTTTGAGTACCAAATTAG
1 AAAATGTCAAGTTTAAGTACCAAATTAG
*** *
47067341 ACAAA-AAAAAGTTTAAGTACCAAATTAA
1 A-AAATGTCAAGTTTAAGTACCAAATTAG
47067369 AAAA
1 AAAA
47067373 AAAGTATCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
27 3 0.06
28 21 0.40
29 29 0.55
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (28 bp):
AAAATGTCAAGTTTAAGTACCAAATTAG
Found at i:47068003 original size:6 final size:6
Alignment explanation
Indices: 47067985--47068101 Score: 115
Period size: 6 Copynumber: 20.0 Consensus size: 6
47067975 TTAAATTGAT
47067985 TTTAAA TTT--A TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
47068028 TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAATTA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A TTTAAA TTTAAA
* *
47068077 TTTAAA TTAAAA TACTAAA TTTAAA
1 TTTAAA TTTAAA T-TTAAA TTTAAA
47068102 CATTAAAAAA
Statistics
Matches: 94, Mismatches: 4, Indels: 26
0.76 0.03 0.21
Matches are distributed among these distances:
4 12 0.13
5 4 0.04
6 64 0.68
7 8 0.09
8 6 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:47068003 original size:17 final size:17
Alignment explanation
Indices: 47067985--47068080 Score: 142
Period size: 17 Copynumber: 5.6 Consensus size: 17
47067975 TTAAATTGAT
47067985 TTTAAATTTAT-TTAAA
1 TTTAAATTTATCTTAAA
47068001 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTTAAA
47068018 TTTAAATTTAT-TTAAA
1 TTTAAATTTATCTTAAA
47068034 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTTAAA
*
47068051 TTTAAATTTAATTATTTAAA
1 TTTAAATTT-A-T-CTTAAA
47068071 TTTAAATTTA
1 TTTAAATTTA
47068081 AATTAAAATA
Statistics
Matches: 74, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
16 27 0.36
17 30 0.41
18 1 0.01
19 2 0.03
20 14 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATCTTAAA
Found at i:47068004 original size:33 final size:33
Alignment explanation
Indices: 47067966--47068087 Score: 118
Period size: 33 Copynumber: 3.6 Consensus size: 33
47067956 TTCTTGTTTT
* * *
47067966 AATTTAGAGTTAAATTGATTTTAAATTTATTTA
1 AATTTAAAGTTAAATTAAATTTAAATTTATTTA
* **
47067999 AATTTAAATTTATCTTAAATTTAAATTTATTTA
1 AATTTAAAGTTAAATTAAATTTAAATTTATTTA
* **
47068032 AATTTAAATTTATCTTAAATTTAAATTTAATTATTTA
1 AATTTAAAGTTAAATTAAATTTAAA--T--TTATTTA
*
47068069 AATTTAAATTTAAATTAAA
1 AATTTAAAGTTAAATTAAA
47068088 ATACTAAATT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
33 52 0.68
35 1 0.01
37 24 0.31
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (33 bp):
AATTTAAAGTTAAATTAAATTTAAATTTATTTA
Found at i:47068030 original size:27 final size:27
Alignment explanation
Indices: 47067966--47068087 Score: 96
Period size: 27 Copynumber: 4.5 Consensus size: 27
47067956 TTCTTGTTTT
* *
47067966 AATTTAGAGTTAAATTGATTTTAAATTT-
1 AATTTA-ATTTAAATTTA-TTTAAATTTA
47067994 -ATTTAAATTTAAATTTATCTTAAATTTA
1 AATTT-AATTTAAATTTAT-TTAAATTTA
47068022 AATTT-ATTTAAATTTAAATTT--ATCTTA
1 AATTTAATTTAAATTT--ATTTAAAT-TTA
47068049 AATTTAAATTT-AA-TTATTTAAATTTA
1 AATTT-AATTTAAATTTATTTAAATTTA
*
47068075 AATTTAAATTAAA
1 AATTTAATTTAAA
47068088 ATACTAAATT
Statistics
Matches: 79, Mismatches: 3, Indels: 26
0.73 0.03 0.24
Matches are distributed among these distances:
25 8 0.10
26 13 0.16
27 43 0.54
28 5 0.06
29 10 0.13
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
AATTTAATTTAAATTTATTTAAATTTA
Found at i:47068099 original size:31 final size:29
Alignment explanation
Indices: 47067997--47068101 Score: 95
Period size: 33 Copynumber: 3.3 Consensus size: 29
47067987 TAAATTTATT
*
47067997 TAAATTTAAATTTATCTTAAATTTAAATTTATT
1 TAAATTTAAATTTATCTTAAA-TTAAA---ATC
* *
47068030 TAAATTTAAATTTATCTTAAATTTAAATT
1 TAAATTTAAATTTATCTTAAATTAAAATC
47068059 TAATTATTTAAATTTAAAT-TTAAATTAAAATAC
1 TAA--ATTTAAATTT--ATCTTAAATTAAAAT-C
47068092 TAAATTTAAA
1 TAAATTTAAA
47068102 CATTAAAAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
29 6 0.09
31 17 0.27
32 15 0.23
33 26 0.41
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.50
Consensus pattern (29 bp):
TAAATTTAAATTTATCTTAAATTAAAATC
Found at i:47068792 original size:22 final size:22
Alignment explanation
Indices: 47068765--47068824 Score: 57
Period size: 25 Copynumber: 2.6 Consensus size: 22
47068755 AGAGTTCATC
47068765 ATAATATTTAATAGCAATAATA
1 ATAATATTTAATAGCAATAATA
* *
47068787 ATAATACTAATTAATAGTACTAATA
1 ATAATA-T--TTAATAGCAATAATA
* *
47068812 ATATTAATTAATA
1 ATAATATTTAATA
47068825 TATATATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
22 12 0.39
23 1 0.03
25 18 0.58
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (22 bp):
ATAATATTTAATAGCAATAATA
Found at i:47069972 original size:67 final size:67
Alignment explanation
Indices: 47069861--47070054 Score: 271
Period size: 67 Copynumber: 3.0 Consensus size: 67
47069851 ACTTTCCAAA
*
47069861 ATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCA
1 ATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATT-CA
47069926 TTT
65 TTT
*
47069929 ATTCCATTTTTAACCCCAATTTCACC-AAAATTACCATTTTACCCCCAAACTTTCC--AA---A-
1 ATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCAT
47069987 --
66 TT
* *
47069987 ATTCCATTTTTAACCCCAATTACACCAAAAATTACCATTTTACCCCCGAACCTTCCAAAATTCTA
1 ATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTC-A
47070052 TTT
65 TTT
47070055 TTAATCCCAG
Statistics
Matches: 111, Mismatches: 5, Indels: 20
0.82 0.04 0.15
Matches are distributed among these distances:
58 25 0.23
59 27 0.24
61 3 0.03
65 3 0.03
67 28 0.25
68 25 0.23
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.34
Consensus pattern (67 bp):
ATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCAT
TT
Found at i:47069991 original size:58 final size:59
Alignment explanation
Indices: 47069929--47070202 Score: 347
Period size: 59 Copynumber: 4.7 Consensus size: 59
47069919 AATTCCATTT
*
47069929 ATTCCATTTTTAACCCCAATTTCACC-AAAATTACCATTTTACCCCCAAACTTTCCAAA
1 ATTCTATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAA
* * * *
47069987 ATTCCATTTTTAACCCCAATTACACCAAAAATTACCATTTTACCCCCGAACCTTCCAAA
1 ATTCTATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAA
* * ** * * *
47070046 ATTCTATTTTTAATCCCAGTTTCACTGAAAATTACCATTTTGCCCCTAAACTTTTCAAA
1 ATTCTATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAA
** * * *
47070105 ATTCTATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTATCCCTAAA-TATTTC-AA
1 ATTCTATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCAAACT-TTCCAAA
* *
47070163 ATTCTATTTTTAACCCCGATTCCACCAAAAATTACCATTT
1 ATTCTATTTTTAACCCCAATTTCACCAAAAATTACCATTT
47070203 AAATCCTGAT
Statistics
Matches: 192, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
58 66 0.34
59 126 0.66
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (59 bp):
ATTCTATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAA
Found at i:47077353 original size:38 final size:38
Alignment explanation
Indices: 47077239--47077512 Score: 166
Period size: 38 Copynumber: 7.3 Consensus size: 38
47077229 TACATCCTCT
47077239 TGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
1 TGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
* ** **
47077277 TGAAATTGAAG-AGCA---AGAT--CATTTC-ACATCCTC
1 TGAAATTGAAGTAG-AGTTGGATAACAAGTCTTTAT-CTC
*
47077310 TTGAAACTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
*** ** **
47077349 TGAAATTGAAGTAAGAGCAAGAT--CATTTC-ACATCCTC
1 TGAAATTGAAGT-AGAGTTGGATAACAAGTCTTTAT-CTC
*
47077386 TTGAAATTGAAGTAGAGTTGGATAACAAGTGTTTATCTC
1 -TGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
* * * * *
47077425 TGAAATTGAAATA-AG--AG-TAAGATAGT-TTCCCATCCTTT
1 TGAAATTGAAGTAGAGTTGGATAACA-AGTCTT--TAT-C-TC
47077463 TGAAATTGAAGTAGAGTTGGA-AACAAGTCTTTATCTC
1 TGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
47077500 TGAAATTGAAGTA
1 TGAAATTGAAGTA
47077513 AGAGCAAGAT
Statistics
Matches: 173, Mismatches: 37, Indels: 53
0.66 0.14 0.20
Matches are distributed among these distances:
32 2 0.01
33 7 0.04
34 17 0.10
35 9 0.05
36 4 0.02
37 36 0.21
38 61 0.35
39 24 0.14
40 7 0.04
41 6 0.03
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (38 bp):
TGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
Found at i:47077522 original size:75 final size:76
Alignment explanation
Indices: 47077225--47077575 Score: 527
Period size: 76 Copynumber: 4.7 Consensus size: 76
47077215 GTTTAACGAT
*
47077225 ATTTTACATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT---G-A
1 ATTTCACATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
47077286 AGAGCAAGATC
66 AGAGCAAGATC
*
47077297 ATTTCACATCCTCTTGAAACTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
1 ATTTCACATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
47077362 AGAGCAAGATC
66 AGAGCAAGATC
* *
47077373 ATTTCACATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTGTTTATCTCTGAAATTGAAATA
1 ATTTCACATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
*
47077438 AGAGTAAGAT-
66 AGAGCAAGATC
* *
47077448 AGTTTCCCATCCTTTTGAAATTGAAGTAGAGTTGGA-AACAAGTCTTTATCTCTGAAATTGAAGT
1 A-TTTCACATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGT
47077512 AAGAGCAAGATC
65 AAGAGCAAGATC
* * * * * *
47077524 GTCTCCCATCCTTTTGAAATTGAAGTA-AGTTGGATAGCAAGTCCTTATCTCT
1 ATTTCACATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCT
47077576 CTGAAGAGCA
Statistics
Matches: 257, Mismatches: 15, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
72 57 0.22
74 7 0.03
75 78 0.30
76 115 0.45
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (76 bp):
ATTTCACATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTA
AGAGCAAGATC
Found at i:47077887 original size:27 final size:27
Alignment explanation
Indices: 47077856--47077957 Score: 78
Period size: 31 Copynumber: 3.6 Consensus size: 27
47077846 TCTTGTTTTA
* *
47077856 ATTTAGAGTTAAATTGATTTTAAATTT
1 ATTTAAAGTTAAATTGATCTTAAATTT
* *
47077883 ATTTAAATTTAAATTTATCTTAAATTT
1 ATTTAAAGTTAAATTGATCTTAAATTT
* * *
47077910 AAATTTAATTATTTAAATTTACCTTAAATTT
1 --ATTTAA--AGTTAAATTGATCTTAAATTT
*
47077941 AAATTTAAATTTAAATT
1 --ATTTAAAGTTAAATT
47077958 AAATTTAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.35
29 15 0.23
31 28 0.42
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (27 bp):
ATTTAAAGTTAAATTGATCTTAAATTT
Found at i:47077892 original size:6 final size:6
Alignment explanation
Indices: 47077874--47077980 Score: 100
Period size: 6 Copynumber: 18.0 Consensus size: 6
47077864 TTAAATTGAT
47077874 TTTAAA TTT--A TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A
* *
47077921 TTTAAA TTT-AC CTTAAA TTTAAA TTTAAA TTTAAA -TTAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
*
47077968 TACTAAA TTTAAA
1 T-TTAAA TTTAAA
47077981 CACTAAAAAT
Statistics
Matches: 84, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
4 6 0.07
5 10 0.12
6 51 0.61
7 10 0.12
8 7 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:47077892 original size:17 final size:16
Alignment explanation
Indices: 47077874--47077964 Score: 107
Period size: 17 Copynumber: 5.6 Consensus size: 16
47077864 TTAAATTGAT
47077874 TTTAAATTTATTTAAA
1 TTTAAATTTATTTAAA
47077890 TTTAAATTTATCTTAAA
1 TTTAAATTTAT-TTAAA
*
47077907 TTTAAATTTAATT--A
1 TTTAAATTTATTTAAA
*
47077921 TTTAAATTTACCTTAAA
1 TTTAAATTTA-TTTAAA
47077938 TTTAAATTTAAATTTAAA
1 TTTAAATTT--ATTTAAA
47077956 -TTAAATTTA
1 TTTAAATTTA
47077965 AAATACTAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
14 11 0.17
15 3 0.05
16 13 0.20
17 33 0.50
18 5 0.08
19 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:47077965 original size:11 final size:11
Alignment explanation
Indices: 47077864--47077980 Score: 87
Period size: 11 Copynumber: 10.5 Consensus size: 11
47077854 TAATTTAGAG
* *
47077864 TTAAATTGATT
1 TTAAATTAAAT
*
47077875 TTAAATT-TAT
1 TTAAATTAAAT
47077885 TTAAATTTAAAT
1 TTAAA-TTAAAT
**
47077897 TTATCTTAAAT
1 TTAAATTAAAT
*
47077908 TTAAATTTAA-
1 TTAAATTAAAT
*
47077918 TT-ATTTAAAT
1 TTAAATTAAAT
**
47077928 TTACCTTAAAT
1 TTAAATTAAAT
47077939 TTAAATTTAAAT
1 TTAAA-TTAAAT
47077951 TTAAATTAAAT
1 TTAAATTAAAT
47077962 TTAAAATACTAAAT
1 TT-AAAT--TAAAT
47077976 TTAAA
1 TTAAA
47077981 CACTAAAAAT
Statistics
Matches: 84, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
9 5 0.06
10 10 0.12
11 39 0.46
12 20 0.24
13 3 0.04
14 7 0.08
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:47077975 original size:37 final size:37
Alignment explanation
Indices: 47077902--47077980 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 37
47077892 TAAATTTATC
*
47077902 TTAAATTTAAATTTAATTATTTAAATTTACCTTAAAT
1 TTAAATTTAAATTTAATTATTTAAATATACCTTAAAT
47077939 TTAAATTTAAATTTAAATTAAATTTAAA-ATA-C-TAAAT
1 TTAAATTTAAATTT-AATT--ATTTAAATATACCTTAAAT
47077976 TTAAA
1 TTAAA
47077981 CACTAAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
37 24 0.63
38 5 0.13
39 2 0.05
40 7 0.18
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
TTAAATTTAAATTTAATTATTTAAATATACCTTAAAT
Found at i:47077975 original size:48 final size:47
Alignment explanation
Indices: 47077876--47077978 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 47
47077866 AAATTGATTT
* * *
47077876 TAAATTTATTTAAATTTAAATTTATCTTAAATTTAAATTTAATTATT
1 TAAATTTACTTAAATTTAAATTTATCTTAAATTTAAATTTAAATATC
47077923 TAAATTTACCTTAAATTTAAATTTAAAT-TTAAA-TTAAATTTAAA-ATAC
1 TAAATTTA-CTTAAATTTAAATTT--ATCTTAAATTTAAATTTAAATAT-C
47077971 TAAATTTA
1 TAAATTTA
47077979 AACACTAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
47 10 0.20
48 32 0.65
49 5 0.10
50 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.50
Consensus pattern (47 bp):
TAAATTTACTTAAATTTAAATTTATCTTAAATTTAAATTTAAATATC
Found at i:47079821 original size:59 final size:59
Alignment explanation
Indices: 47079727--47080249 Score: 736
Period size: 59 Copynumber: 8.9 Consensus size: 59
47079717 TATAGGTCCC
*
47079727 CAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCT
1 CAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCT
*
47079786 CAAACTTTCCAAAATTCTATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCT
1 CAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCT
* *
47079845 CAAACTTTCCAAAATTCCATTTTTAACCCCGATTGCACCAAAAATTACCATTTTACCCC
1 CAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCT
* * * *
47079904 CGAACCTTCCAAAATTCCATTTTTAATCCCGATTTCACCAAAAATTACCGTTTTACCCT
1 CAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCT
*
47079963 CAAACTTTCCAAAATTCCA-TTTTAACCCCGTTTTCACCAAAAATTACCATTTTA-CCT
1 CAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCT
* * * * *
47080020 CCGAACTTTCTAAAATTCCATTTTTAACCTCGGTTTTACCAAAAATTACCATTTTTACCC-
1 -CAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCA-TTTTACCCT
* *
47080080 CTAAACTTTCCAAAATTCCATTTTTAACCCTGATTTAACCAAAAATTACCATTTTACTCC-
1 C-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC-CCT
* * * * *
47080140 CGAACTTTCTAAAATTCCATTTTTAATCCCGATTTCACTAAAAATTACCATTTTACCCC
1 CAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCT
* * *
47080199 CAAA-TGTTCC-AATTTTCA-TTTTAACCCCGATTCCACCAAAAATTACCATTT
1 CAAACT-TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTT
47080250 AAACCCCGAT
Statistics
Matches: 416, Mismatches: 40, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
57 33 0.08
58 58 0.14
59 272 0.65
60 51 0.12
61 2 0.00
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (59 bp):
CAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCT
Found at i:47084893 original size:88 final size:88
Alignment explanation
Indices: 47084752--47084979 Score: 241
Period size: 90 Copynumber: 2.6 Consensus size: 88
47084742 TCGAGTAATT
* *
47084752 AATTGAGTGCAAAAAAAAAATTGGGGGCTTAATTG-TTTTTTGAAAAAATTTGAG-GACCTTTTT
1 AATTGAGTGC-AAAAAAAAA-TAGGGGCTTAATTGCTTTTTTGAAAAAAATTGAGAG-CCTTTTT
*
47084815 GATG-A-TTTGAAAGTTCAAGTA-TCC
63 GATGCATTTTGAAAGTTCAAATACT-C
** ** *
47084839 AATTGAGTGCAAAATAAAAGCAGGGGCTTAATTGCTCTTTTTGAAAAAAATTGAGAGTTTTTTTT
1 AATTGAGTGCAAAA-AAAAATAGGGGCTTAATTGCT-TTTTTGAAAAAAATTGAGAGCCTTTTTG
47084904 ATGCATTTTGAAAGTTCAAATACTC
64 ATGCATTTTGAAAGTTCAAATACTC
* * * * *
47084929 AAGTGAATGCAAAAAAAGAATAGAGACTTAATTACTTTTTTGAAAAAAATT
1 AATTGAGTGCAAAAAAA-AATAGGGGCTTAATTGCTTTTTTGAAAAAAATT
47084980 TGAGTGCTTT
Statistics
Matches: 118, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
86 16 0.14
87 15 0.13
88 25 0.21
89 20 0.17
90 41 0.35
91 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (88 bp):
AATTGAGTGCAAAAAAAAATAGGGGCTTAATTGCTTTTTTGAAAAAAATTGAGAGCCTTTTTGAT
GCATTTTGAAAGTTCAAATACTC
Found at i:47086186 original size:16 final size:16
Alignment explanation
Indices: 47086151--47086209 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
47086141 TCTAAAATGA
47086151 TAAA-TTATAA-A-TT
1 TAAATTTATAATATTT
47086164 TACAATTTA-AATATTT
1 TA-AATTTATAATATTT
47086180 TATAATTTATAATATTT
1 TA-AATTTATAATATTT
*
47086197 TAAATTAATAATA
1 TAAATTTATAATA
47086210 ATAAATTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
13 2 0.05
14 4 0.10
15 4 0.10
16 20 0.51
17 9 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATTTATAATATTT
Found at i:47113704 original size:31 final size:31
Alignment explanation
Indices: 47113666--47113728 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
47113656 AATTGTATAA
*
47113666 TTTTTATTCAAGTTAAACCGAAAAACTTAAT
1 TTTTTATTCAAGTTAAACCGAAAAACTCAAT
* * * *
47113697 TTTTTATTCGAGTTGATCCGAATAACTCAAT
1 TTTTTATTCAAGTTAAACCGAAAAACTCAAT
47113728 T
1 T
47113729 AACTCAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (31 bp):
TTTTTATTCAAGTTAAACCGAAAAACTCAAT
Found at i:47123188 original size:13 final size:14
Alignment explanation
Indices: 47123161--47123196 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
47123151 GCCCTTTAAT
47123161 TTTTAATTTTAAAAA
1 TTTT-ATTTTAAAAA
47123176 TTTTATTTT-AAAA
1 TTTTATTTTAAAAA
47123189 TTTTATTT
1 TTTTATTT
47123197 ATATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.57
14 5 0.24
15 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTATTTTAAAAA
Found at i:47130468 original size:3 final size:3
Alignment explanation
Indices: 47130460--47130496 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
47130450 GTCAGTGTCT
*
47130460 CTC CTC CTC CTC CTC C-C CTC CTC CTC CTC CTC TTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
47130497 TTTGAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:47130481 original size:14 final size:14
Alignment explanation
Indices: 47130462--47130489 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47130452 CAGTGTCTCT
47130462 CCTCCTCCTCCTCC
1 CCTCCTCCTCCTCC
47130476 CCTCCTCCTCCTCC
1 CCTCCTCCTCCTCC
47130490 TCTTCCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.71, G:0.00, T:0.29
Consensus pattern (14 bp):
CCTCCTCCTCCTCC
Found at i:47137394 original size:21 final size:21
Alignment explanation
Indices: 47137368--47137420 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
47137358 ATGTCACGTT
*
47137368 AGTATTTTCATCTTAAATTTC
1 AGTATTTTCATCCTAAATTTC
*
47137389 AGTATTTTCATCCTAAATTTT
1 AGTATTTTCATCCTAAATTTC
*
47137410 AGCATTTTCAT
1 AGTATTTTCAT
47137421 ACTGAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (21 bp):
AGTATTTTCATCCTAAATTTC
Found at i:47137915 original size:23 final size:23
Alignment explanation
Indices: 47137864--47137924 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
47137854 TTTTATTTGC
* *
47137864 CTTTGTGACACACTTTTCCTCTG
1 CTTTGTGGCACGCTTTTCCTCTG
*
47137887 -TCTTGTGGCACGCTTTTCTTCTG
1 CT-TTGTGGCACGCTTTTCCTCTG
*
47137910 CTTTGTGGCATGCTT
1 CTTTGTGGCACGCTT
47137925 CTGCCTTATG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 30 0.94
24 1 0.03
ACGTcount: A:0.08, C:0.26, G:0.20, T:0.46
Consensus pattern (23 bp):
CTTTGTGGCACGCTTTTCCTCTG
Found at i:47138464 original size:16 final size:17
Alignment explanation
Indices: 47138440--47138472 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
47138430 ATTGTTATAT
*
47138440 AATTGATATATAAAATA
1 AATTGATATACAAAATA
47138457 AATT-ATATACAAAATA
1 AATTGATATACAAAATA
47138473 TATATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
AATTGATATACAAAATA
Found at i:47148417 original size:3 final size:3
Alignment explanation
Indices: 47148409--47148448 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
47148399 TTTCACTTAG
47148409 ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
47148449 GAAGTTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:47148772 original size:21 final size:21
Alignment explanation
Indices: 47148738--47148788 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
47148728 TTGAATATGT
*
47148738 TTTTTTAT-TTTTAAAAAATA
1 TTTTTTATATATTAAAAAATA
* *
47148758 TTTTTTATATATTAAAAGATG
1 TTTTTTATATATTAAAAAATA
*
47148779 TTTTTAATAT
1 TTTTTTATAT
47148789 TGTTATCTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
TTTTTTATATATTAAAAAATA
Found at i:47149572 original size:20 final size:21
Alignment explanation
Indices: 47149542--47149583 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
47149532 TATTTTGAGT
*
47149542 TTTTGTAATAATATATAAATA
1 TTTTGTAATAATATAAAAATA
47149563 TTTT-TAATAATATAAAAATA
1 TTTTGTAATAATATAAAAATA
47149583 T
1 T
47149584 AAAATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTTGTAATAATATAAAAATA
Found at i:47163357 original size:14 final size:16
Alignment explanation
Indices: 47163338--47163370 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
47163328 AATAGTGAAG
47163338 ATATAAA-A-AAAATT
1 ATATAAATACAAAATT
47163352 ATATAAATACAAAATT
1 ATATAAATACAAAATT
47163368 ATA
1 ATA
47163371 GATCACCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 1 0.06
16 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
ATATAAATACAAAATT
Found at i:47167161 original size:31 final size:31
Alignment explanation
Indices: 47167099--47167162 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
47167089 TAGTATAACT
*** *
47167099 AAGACTTAAAGATAGTAATTTTTTGACAAAA
1 AAGACTTAAAGATAGTAATGAATAGACAAAA
47167130 AAGACTTAAAGATAGTAATGAATAGTA-AAAA
1 AAGACTTAAAGATAGTAATGAATAG-ACAAAA
47167161 AA
1 AA
47167163 CAGGGATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.27
Consensus pattern (31 bp):
AAGACTTAAAGATAGTAATGAATAGACAAAA
Found at i:47171454 original size:16 final size:16
Alignment explanation
Indices: 47171432--47171470 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
47171422 AAGCAAATTA
*
47171432 AAAAATAACAAAAGTT
1 AAAAATAAAAAAAGTT
* *
47171448 AATAATAAAAAAATTT
1 AAAAATAAAAAAAGTT
47171464 AAAAATA
1 AAAAATA
47171471 CAATTAAGAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAAATAAAAAAAGTT
Found at i:47172961 original size:18 final size:20
Alignment explanation
Indices: 47172926--47172967 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 20
47172916 ATATTATGAT
47172926 TTTTTTTTTTCCCTTTTTCTC
1 TTTTTTTTTT-CCTTTTTCTC
47172947 TTTTTTTTTT-C-TTTTCTC
1 TTTTTTTTTTCCTTTTTCTC
47172965 TTT
1 TTT
47172968 CTTCAATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
19 1 0.05
21 10 0.48
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTTTTTCCTTTTTCTC
Found at i:47174599 original size:7 final size:7
Alignment explanation
Indices: 47174591--47174629 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
47174581 AGATGAACAG
*
47174591 ATTACAG
1 ATTACAA
47174598 ATTACAA
1 ATTACAA
47174605 ATTACAA
1 ATTACAA
47174612 ATTACAA
1 ATTACAA
47174619 ATTACAA
1 ATTACAA
47174626 ATTA
1 ATTA
47174630 AAAGAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.31
Consensus pattern (7 bp):
ATTACAA
Found at i:47176258 original size:17 final size:18
Alignment explanation
Indices: 47176225--47176260 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
47176215 TATAATGAGA
47176225 ATGTTAAAAAATAAATAT
1 ATGTTAAAAAATAAATAT
*
47176243 ATGTTTAAAAAT-AATAT
1 ATGTTAAAAAATAAATAT
47176260 A
1 A
47176261 ATAAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (18 bp):
ATGTTAAAAAATAAATAT
Found at i:47176464 original size:18 final size:19
Alignment explanation
Indices: 47176427--47176469 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
47176417 GCATGGAGAT
* *
47176427 AATAAATTATGTATATTAA
1 AATAAATTATATAAATTAA
47176446 AATAAA-TATATAAATTAA
1 AATAAATTATATAAATTAA
*
47176464 ATTAAA
1 AATAAA
47176470 ATGAAGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AATAAATTATATAAATTAA
Found at i:47179073 original size:29 final size:28
Alignment explanation
Indices: 47179009--47179071 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 28
47178999 TTGGTAAAAC
*
47179009 TAAAATTTAGTTCTTATATTTTTATTTT
1 TAAAATTTAGTTCTTATATTTTTAATTT
*
47179037 TAGAAATTTAGTTCTTTTATTTTTCAGATTT
1 TA-AAATTTAGTTCTTATATTTTT-A-ATTT
47179068 TAAA
1 TAAA
47179072 TTAAAGTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.07
29 20 0.67
30 3 0.10
31 5 0.17
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (28 bp):
TAAAATTTAGTTCTTATATTTTTAATTT
Found at i:47185795 original size:1 final size:1
Alignment explanation
Indices: 47185784--47185817 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
47185774 TTAAAAGATG
* *
47185784 TTTTTTCTTTTTTTTTTTTTTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
47185818 AACATTTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:47185798 original size:9 final size:9
Alignment explanation
Indices: 47185784--47185816 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
47185774 TTAAAAGATG
47185784 TTTTTTCTT
1 TTTTTTCTT
*
47185793 TTTTTTTTT
1 TTTTTTCTT
47185802 TTTTTTCTT
1 TTTTTTCTT
47185811 TTTTTT
1 TTTTTT
47185817 TAACATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:47207834 original size:77 final size:78
Alignment explanation
Indices: 47207700--47207855 Score: 271
Period size: 77 Copynumber: 2.0 Consensus size: 78
47207690 TAGACACTAT
47207700 TCCTAATCATTGATGAGGAAAAGTTTGTCACCACATAATTTTATTTTTTTAAAAATATTCTTGTA
1 TCCTAATCATTGATGAGGAAAAGTTTGTCACCACATAATTTTATTTTTTTAAAAATATTCTTGTA
47207765 TGCTTAA-GTGAA
66 TGCTTAAGGTGAA
* *
47207777 TCCTAATCATTGATGATGAAAAGTTTGTCACCACATAATTTTAATTTTTTT-ATAATATTCTTGT
1 TCCTAATCATTGATGAGGAAAAGTTTGTCACCACATAATTTT-ATTTTTTTAAAAATATTCTTGT
47207841 ATGCTTAAGGTGAA
65 ATGCTTAAGGTGAA
47207855 T
1 T
47207856 ATGCTTTTAT
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
77 61 0.81
78 14 0.19
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.43
Consensus pattern (78 bp):
TCCTAATCATTGATGAGGAAAAGTTTGTCACCACATAATTTTATTTTTTTAAAAATATTCTTGTA
TGCTTAAGGTGAA
Found at i:47228711 original size:29 final size:29
Alignment explanation
Indices: 47228678--47228745 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
47228668 ATATTTCTAT
47228678 TATTTTTAA-AAGATTAAAATAAAATTTTA
1 TATTTTTAAGAAGATT-AAATAAAATTTTA
* *
47228707 TATTTTTAAGAAGGTTAAATACAATTTTA
1 TATTTTTAAGAAGATTAAATAAAATTTTA
*
47228736 TCTTTATTAA
1 TATTT-TTAA
47228746 TTTTAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 25 0.74
30 9 0.26
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (29 bp):
TATTTTTAAGAAGATTAAATAAAATTTTA
Found at i:47233070 original size:18 final size:19
Alignment explanation
Indices: 47233033--47233071 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
47233023 CGACCATAAC
47233033 TTTCCAAATACGAATGTTG
1 TTTCCAAATACGAATGTTG
* *
47233052 TTTCCAAGTA-GAGTGTTG
1 TTTCCAAATACGAATGTTG
47233070 TT
1 TT
47233072 AACAAATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (19 bp):
TTTCCAAATACGAATGTTG
Found at i:47234117 original size:34 final size:34
Alignment explanation
Indices: 47234052--47234117 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
47234042 CTCAATCTCA
*
47234052 AACATCAAAATGTCCATAAGCGAAGTCCAAAAGC
1 AACATCAAAATGTCCATAAGCCAAGTCCAAAAGC
*
47234086 AACATCAACAT-TCCATAAGTCCAA-TCTCAAAA
1 AACATCAAAATGTCCATAAG-CCAAGTC-CAAAA
47234118 ATAGTAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.47, C:0.26, G:0.09, T:0.18
Consensus pattern (34 bp):
AACATCAAAATGTCCATAAGCCAAGTCCAAAAGC
Found at i:47237971 original size:20 final size:20
Alignment explanation
Indices: 47237933--47237984 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
47237923 TTTTACTTTC
* *
47237933 CTTCCCTCCAAACACTTTTA
1 CTTCCCTCCAAAAAATTTTA
47237953 CTTTCCC-CCAAAAAATTTTA
1 C-TTCCCTCCAAAAAATTTTA
47237973 CTTCCCTCCAAA
1 CTTCCCTCCAAA
47237985 CTAATAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 5 0.18
20 18 0.64
21 5 0.18
ACGTcount: A:0.29, C:0.38, G:0.00, T:0.33
Consensus pattern (20 bp):
CTTCCCTCCAAAAAATTTTA
Found at i:47238066 original size:91 final size:90
Alignment explanation
Indices: 47237948--47238117 Score: 252
Period size: 91 Copynumber: 1.9 Consensus size: 90
47237938 CTCCAAACAC
* **
47237948 TTTTACTTTCCCCCAAAAAATTTTACTT-CCCTCCAAACTAATAAAACTTTTTTTTTTCTACTTT
1 TTTTACTTTCCCCCAAAAAATTTTACTTCCCCT-CAAACCAATAAAACTTTTTCCTTTCTACTTT
**
47238012 CCCTTTAAAATTTTTACTCTATTTTA
65 CCCTCCAAAATTTTTACTCTATTTTA
*
47238038 TTTTCCTTTCCCCTCAAAAAATTTTACTTCCCCTCAAACCAATAAAACTTTTTCCTTTCTACTTT
1 TTTTACTTTCCCC-CAAAAAATTTTACTTCCCCTCAAACCAATAAAACTTTTTCCTTTCTACTTT
*
47238103 CTCTCCAAAATTTTT
65 CCCTCCAAAATTTTT
47238118 TACTTCTTCA
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
90 12 0.17
91 55 0.77
92 4 0.06
ACGTcount: A:0.27, C:0.26, G:0.00, T:0.46
Consensus pattern (90 bp):
TTTTACTTTCCCCCAAAAAATTTTACTTCCCCTCAAACCAATAAAACTTTTTCCTTTCTACTTTC
CCTCCAAAATTTTTACTCTATTTTA
Found at i:47238838 original size:174 final size:174
Alignment explanation
Indices: 47238544--47238865 Score: 450
Period size: 174 Copynumber: 1.9 Consensus size: 174
47238534 TAAAACAACA
* * *
47238544 ATTAACAATAAAGAAGCAAAACAATTCTCAAGAAAGAATTCACCTAGATTTCATATATCATTATC
1 ATTAACAACAAAGAAGCAAAACAATACCCAAGAAAGAATTCACCTAGATTTCATATATCATTATC
* *
47238609 AATCTGAATTAAACAATTTCTTCACTTAATATCTTGATCCGTAGAAATCCCTAAATTATGATAAT
66 AATCTGAATTAAACAATTTCTTCACTTAATATCTTGATACGTAAAAATCCCTAAATTATGATAAT
*
47238674 ATCTCTTTCGAGAGTAAGCAAAGAACAAATTAAGAAAATAAATG
131 ATATCTTTCGAGAGTAAGCAAAGAACAAATTAAGAAAATAAATG
* ** * * * *
47238718 ATTAACAACCAAGAAGTGAAACAATACCCAAGAAGGAA-TCTACGTAGATTTCATCTGTCATTAT
1 ATTAACAACAAAGAAGCAAAACAATACCCAAGAAAGAATTC-ACCTAGATTTCATATATCATTAT
* * * * *
47238782 CAATCTGAATTAAATAACTTT-TTCACTTAGTATCTTGATATGTAAAAATTCCTAAATTATGCTA
65 CAATCTGAATTAAACAA-TTTCTTCACTTAATATCTTGATACGTAAAAATCCCTAAATTATGATA
47238846 ATATATCTTTCGAGAGTAAG
129 ATATATCTTTCGAGAGTAAG
47238866 AGCAACTGAC
Statistics
Matches: 128, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
173 2 0.02
174 123 0.96
175 3 0.02
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (174 bp):
ATTAACAACAAAGAAGCAAAACAATACCCAAGAAAGAATTCACCTAGATTTCATATATCATTATC
AATCTGAATTAAACAATTTCTTCACTTAATATCTTGATACGTAAAAATCCCTAAATTATGATAAT
ATATCTTTCGAGAGTAAGCAAAGAACAAATTAAGAAAATAAATG
Found at i:47240853 original size:21 final size:24
Alignment explanation
Indices: 47240811--47240855 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 24
47240801 ACTGTAATAA
*
47240811 ATTATTATCACTATTATTGTATTT
1 ATTATTATCACTATTATGGTATTT
47240835 ATTATT-TCA-TATT-TGGTATTT
1 ATTATTATCACTATTATGGTATTT
47240856 TTGTTGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 4 0.20
23 3 0.15
24 6 0.30
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (24 bp):
ATTATTATCACTATTATGGTATTT
Found at i:47245799 original size:15 final size:14
Alignment explanation
Indices: 47245773--47245812 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
47245763 TTTCAATTTT
47245773 ATTTT-AATAATAA
1 ATTTTAAATAATAA
47245786 ATTTTAAGATAAT-A
1 ATTTTAA-ATAATAA
47245800 ATTTTAAATAATA
1 ATTTTAAATAATA
47245813 TTCTTCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 10 0.42
14 9 0.38
15 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTTTAAATAATAA
Found at i:47249945 original size:31 final size:29
Alignment explanation
Indices: 47249881--47249946 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
47249871 ATAACGTAAG
* * *
47249881 TGACTAAAATGTAATATTTCAAACATAAG
1 TGACTAAAATGTAATATTACAAACAAAAA
*
47249910 TGACTAAAATGTAATCTGTGACAAACAAAAA
1 TGACTAAAATGTAATAT-T-ACAAACAAAAA
47249941 TGACTA
1 TGACTA
47249947 TTTTTATAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.52
30 1 0.03
31 14 0.45
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (29 bp):
TGACTAAAATGTAATATTACAAACAAAAA
Found at i:47252827 original size:6 final size:6
Alignment explanation
Indices: 47252816--47252845 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
47252806 AGTGGAGATG
47252816 GGATTA GGATTA GGATTA GGATTA GGATTA
1 GGATTA GGATTA GGATTA GGATTA GGATTA
47252846 AGGGTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
GGATTA
Found at i:47259641 original size:38 final size:38
Alignment explanation
Indices: 47259590--47259664 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
47259580 CAGTGATTTT
*
47259590 GGGACCACAGTCTCGACGAGTAAGTCTATAAATATTAC
1 GGGACCACAGTCTCGACGAGTAAATCTATAAATATTAC
* *
47259628 GGGACCATAGTCTCGACGAGTAAATCTGTAAATATTA
1 GGGACCACAGTCTCGACGAGTAAATCTATAAATATTA
47259665 TTATTTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (38 bp):
GGGACCACAGTCTCGACGAGTAAATCTATAAATATTAC
Found at i:47266285 original size:20 final size:21
Alignment explanation
Indices: 47266243--47266285 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
47266233 ATTGCTCTAT
* *
47266243 TTTTTTAAATATTTTTATTGA
1 TTTTTAAAATATTTTTATAGA
47266264 TTTTTAAAATATTTTT-TAGA
1 TTTTTAAAATATTTTTATAGA
47266284 TT
1 TT
47266286 ATGATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTTTAAAATATTTTTATAGA
Found at i:47272998 original size:22 final size:22
Alignment explanation
Indices: 47272957--47272998 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
47272947 TAGCGAAACG
**
47272957 ATAACAAAATAACAGTAAAATA
1 ATAACAAAATAACAAAAAAATA
*
47272979 ATAATAAAATAACAAAAAAA
1 ATAACAAAATAACAAAAAAA
47272999 ATTAAGCTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.17
Consensus pattern (22 bp):
ATAACAAAATAACAAAAAAATA
Found at i:47278417 original size:2 final size:2
Alignment explanation
Indices: 47278397--47278438 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
47278387 TAACTGCATC
*
47278397 AT AT A- AT AT AT CAT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47278439 GAACAAAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47285903 original size:19 final size:18
Alignment explanation
Indices: 47285879--47285918 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
47285869 AAAAAAATTG
*
47285879 AATTTATAAGTATAAAAAA
1 AATTTATAA-TAGAAAAAA
*
47285898 AATTTATTATAGAAAAAA
1 AATTTATAATAGAAAAAA
47285916 AAT
1 AAT
47285919 AAAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
AATTTATAATAGAAAAAA
Found at i:47288698 original size:21 final size:23
Alignment explanation
Indices: 47288665--47288706 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
47288655 TTTATGTTTA
47288665 AGTTTTGAGAGTTT-TTTTTTCG
1 AGTTTTGAGAGTTTATTTTTTCG
47288687 AGTTTT-AGAGTTTATTTTTT
1 AGTTTTGAGAGTTTATTTTTT
47288707 ATTTCCATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.17, C:0.02, G:0.19, T:0.62
Consensus pattern (23 bp):
AGTTTTGAGAGTTTATTTTTTCG
Found at i:47294305 original size:14 final size:14
Alignment explanation
Indices: 47294286--47294317 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
47294276 ATTATTATTA
*
47294286 ATATATACATACAT
1 ATATATAAATACAT
47294300 ATATATAAATACAT
1 ATATATAAATACAT
47294314 ATAT
1 ATAT
47294318 TTTCCCAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATATAAATACAT
Found at i:47296391 original size:41 final size:41
Alignment explanation
Indices: 47296016--47296393 Score: 514
Period size: 41 Copynumber: 9.3 Consensus size: 41
47296006 GGATGGAAAA
* * * * *
47296016 CGCCGCTAAAAGT-GGAGCAATAGCGGCGTTTATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAGCAAG
* * * * *
47296056 CGCCGCTAAAAGT-GGAGCAATAGCAGCGCTTATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAGCAAG
*
47296096 CGCCGCAAAAGGTCAGAGCAATAGCGGCGCTTATGAGCAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAGCAAG
* *
47296137 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGATCAAA
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAGCAAG
*
47296178 CGCCGCTAAAGGTCAGACCAATAGCGGCGCTTATG-GTCAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAG-CAAG
*
47296219 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATG-GAAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAG-CAAG
* * *
47296260 CGCCACTAAAGGTCAGATCAATAGCGACGCTTATGAGCAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAGCAAG
47296301 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTAT-AGTCAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAG-CAAG
47296342 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAGCAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAGCAAG
* *
47296383 TGCTGCTAAAG
1 CGCCGCTAAAG
47296394 ATTAAAGCAG
Statistics
Matches: 307, Mismatches: 26, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
40 51 0.17
41 253 0.82
42 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.30, T:0.16
Consensus pattern (41 bp):
CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAGCAAG
Found at i:47299702 original size:43 final size:42
Alignment explanation
Indices: 47299475--47299700 Score: 335
Period size: 43 Copynumber: 5.3 Consensus size: 42
47299465 TTTATTAATG
*
47299475 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGTTCT
1 TTAGCGGCGTTTGTGG-AAAAGCGCCGCTAAAGACCATGTTCT
* * *
47299518 TTAGCGGCGTTTTTGGGAAAGCGCCACTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGTTCT
* *
47299560 TTAGCGGCGTTTGTGGGGAAAGCGCCGCTGAAGACCATGTTCT
1 TTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGACCATGTTCT
47299603 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGG-AAAAGCGCCGCTAAAGACCATGTTCT
* *
47299646 TTAGCGGCGTTTTTGTGAAAAGCGCCGCTAAAAACCATGTTCT
1 TTAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAGACCATGTTCT
*
47299689 ATAGCGGCGTTT
1 TTAGCGGCGTTT
47299701 TTTCTAATAA
Statistics
Matches: 168, Mismatches: 12, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
42 38 0.23
43 129 0.77
44 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (42 bp):
TTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:47308057 original size:9 final size:10
Alignment explanation
Indices: 47308032--47308078 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
47308022 CTAAAATATC
47308032 TATTAAATGTA
1 TATTAAATG-A
47308043 TATTAAATG-
1 TATTAAATGA
*
47308052 TATTAATTGA
1 TATTAAATGA
*
47308062 TTTTTAAATGA
1 -TATTAAATGA
47308073 TATTAA
1 TATTAA
47308079 TTAATTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
9 8 0.27
10 5 0.17
11 17 0.57
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (10 bp):
TATTAAATGA
Found at i:47308078 original size:21 final size:21
Alignment explanation
Indices: 47308045--47308101 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
47308035 TAAATGTATA
*
47308045 TTAAATG-TATTAATTGATTT
1 TTAAATGATATTAATTAATTT
47308065 TTAAATGATATTAATTAATTT
1 TTAAATGATATTAATTAATTT
* *
47308086 TAAGAATAATATTAAT
1 TTA-AATGATATTAAT
47308102 AATAAAAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 7 0.22
21 14 0.44
22 11 0.34
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (21 bp):
TTAAATGATATTAATTAATTT
Done.