Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 34 of 171
Found at i:15502729 original size:4 final size:4
Alignment explanation
Indices: 15502720--15502746 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
15502710 CCCAGTCTTA
15502720 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
15502747 AGAGAGCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:15503438 original size:3 final size:3
Alignment explanation
Indices: 15503430--15503464 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
15503420 AAACGAATGT
15503430 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
15503465 TTTCGACGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:15504414 original size:13 final size:13
Alignment explanation
Indices: 15504396--15504423 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15504386 CACCTCAGTA
15504396 AGTGACTGCTCGT
1 AGTGACTGCTCGT
15504409 AGTGACTGCTCGT
1 AGTGACTGCTCGT
15504422 AG
1 AG
15504424 ATGTAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (13 bp):
AGTGACTGCTCGT
Found at i:15509011 original size:2 final size:2
Alignment explanation
Indices: 15509004--15509029 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15508994 AAGTGCTGCT
15509004 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
15509030 GTTCATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15510041 original size:42 final size:42
Alignment explanation
Indices: 15509982--15510066 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
15509972 CTAATCTAAT
15509982 TAATATAAAATTAGTATTACACATTTACTATTACTATATAGG
1 TAATATAAAATTAGTATTACACATTTACTATTACTATATAGG
15510024 TAATATAAAATTAGTATTACACATTTACTATTACTATATAGG
1 TAATATAAAATTAGTATTACACATTTACTATTACTATATAGG
15510066 T
1 T
15510067 GAGATTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.41
Consensus pattern (42 bp):
TAATATAAAATTAGTATTACACATTTACTATTACTATATAGG
Found at i:15522796 original size:22 final size:22
Alignment explanation
Indices: 15522765--15522806 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
15522755 ACAGTATATT
15522765 ATTTCACTAATAAATAAAATGC
1 ATTTCACTAATAAATAAAATGC
* *
15522787 ATTTCTCTAATAAATTAAAT
1 ATTTCACTAATAAATAAAAT
15522807 TTATGTCTCC
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:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTTCACTAATAAATAAAATGC
Found at i:15522815 original size:22 final size:22
Alignment explanation
Indices: 15522771--15522815 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
15522761 TATTATTTCA
*
15522771 CTAATAAATAAAATGCATTTCT
1 CTAATAAATAAAATGCATGTCT
* **
15522793 CTAATAAATTAAATTTATGTCT
1 CTAATAAATAAAATGCATGTCT
15522815 C
1 C
15522816 CTTTCTCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (22 bp):
CTAATAAATAAAATGCATGTCT
Found at i:15529783 original size:55 final size:55
Alignment explanation
Indices: 15529699--15529853 Score: 192
Period size: 55 Copynumber: 2.9 Consensus size: 55
15529689 TGAGAATTTG
**
15529699 AAAAAAAAAATTGGTGTTGGCCATTGCATGACCGACACTCCTTTTTTTATCTGAC
1 AAAAAAAATTTTGGTGTTGGCCATTGCATGACCGACACTCCTTTTTTTATCTGAC
* *
15529754 AAAAAAAATTTTGGTGTTGGCTATTGCATGTCCGACACCTCC-TTTTTTATCTGAC
1 AAAAAAAATTTTGGTGTTGGCCATTGCATGACCGACA-CTCCTTTTTTTATCTGAC
*** *
15529809 --AAATTTTTTTTGTGTTGGCCATTGCATGACCGACA-TCTCTTTTTT
1 AAAAAAAATTTTGGTGTTGGCCATTGCATGACCGACACTC-CTTTTTT
15529854 GTCAAATAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
51 2 0.02
52 1 0.01
53 34 0.39
55 46 0.53
56 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39
Consensus pattern (55 bp):
AAAAAAAATTTTGGTGTTGGCCATTGCATGACCGACACTCCTTTTTTTATCTGAC
Found at i:15529932 original size:59 final size:57
Alignment explanation
Indices: 15529808--15530383 Score: 352
Period size: 59 Copynumber: 9.6 Consensus size: 57
15529798 TTTTATCTGA
* * * * *
15529808 CAAATTTTTTTTGTGTTGGCCATTGCATGACCGACATCTCTTTTTTGTCAAATAAAAAATT
1 CAAA-TTTTTTGGTGTTGGCCA-TGCATGGCTGACA-CCCCTTTTTGTC-AATAAAAAATT
* *
15529869 CAAATTTTTTGGTGTTGACTATGCCATGGCCT-ACATCCCCTTTTTGTCACAT-AAAAATT
1 CAAATTTTTTGGTGTTGGCCATG-CATGG-CTGACA-CCCCTTTTTGTCA-ATAAAAAATT
* * * *
15529928 CAAATATTTTGATGTTGGCCATTGCATGGTTGACACCCCTTTTTATCTGAATAAAAAATT
1 CAAATTTTTTGGTGTTGGCCA-TGCATGGCTGACACCCCTTTTTGTC--AATAAAAAATT
* * *
15529988 -AAATTTTTTTGTGTTGGCCATTACATGGCTGACACCTCTTTTTGTCAGATAAAAAATT
1 CAAATTTTTTGGTGTTGGCCA-TGCATGGCTGACACCCCTTTTTGTCA-ATAAAAAATT
* * * * *
15530046 CAAATTTTTTGGTGTTGGCCATGCTATGACCGACACCACTTTTTATCTGAATAAAAAAAAT
1 CAAATTTTTTGGTGTTGGCCATGC-ATGGCTGACACCCCTTTTTGTC--AAT-AAAAAATT
* * * *
15530107 CAAA-TTTTT-ATGTTGACCATTGCATGGCCT-ACACTCCTTTTT-TTATTTGATAAAAAAATT
1 CAAATTTTTTGGTGTTGGCCA-TGCATGG-CTGACACCCCTTTTTGTCA----AT-AAAAAATT
* * * *
15530167 CAAATTTTTTTGGTGTTGGCTATGCATTGGCCGACACTACCTTTTTATCAGATAAAAAAAATT
1 CAAA-TTTTTTGGTGTTGGCCATGCA-TGGCTGACAC-CCCTTTTTGTCA-AT--AAAAAATT
* ** *
15530230 -AATTTTTTTGGTGTTGATCATTGCATGGCCGACACCCC-TTTT-T-AGATAAAAAAATT
1 CAAATTTTTTGGTGTTGGCCA-TGCATGGCTGACACCCCTTTTTGTCA-AT-AAAAAATT
* * * *
15530286 CAAATTTTTTAAGTGTTAGCCATGCATTGGCCGAC-CCCAATATTGGTTGTCAGATAAAAAA--
1 CAAATTTTTT-GGTGTTGGCCATGCA-TGGCTGACACCC-CT-TT--TTGTCA-ATAAAAAATT
* *
15530347 CAAATTTTTTTGTGTTGACCATGCATTGGCTGACACC
1 CAAATTTTTTGGTGTTGGCCATGCA-TGGCTGACACC
15530384 AACTTTCCAT
Statistics
Matches: 419, Mismatches: 56, Indels: 80
0.75 0.10 0.14
Matches are distributed among these distances:
56 10 0.02
57 20 0.05
58 41 0.10
59 138 0.33
60 93 0.22
61 53 0.13
62 21 0.05
63 30 0.07
64 11 0.03
65 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (57 bp):
CAAATTTTTTGGTGTTGGCCATGCATGGCTGACACCCCTTTTTGTCAATAAAAAATT
Found at i:15530043 original size:118 final size:119
Alignment explanation
Indices: 15529814--15530372 Score: 463
Period size: 118 Copynumber: 4.7 Consensus size: 119
15529804 CTGACAAATT
* * * * *
15529814 TTTTTTG-TGTTGGCCATTGCATGACCGACATCTCTTTTT-TGTCAAATAAAAAATTCAAATTTT
1 TTTTTTGATGTTGGCCA-TGCATGGCCGACACCCCTTTTTATCT-GAATAAAAAATT-AAATTTT
* * * *
15529877 TTGGTGTTGACTA-TGCCATGGCCTACATCCCCTTTTTGTCACAT--AAAAATTCAAA
63 TTTGTGTTGACCATTG-CATGGCCTACATCCTCTTTTTGTCAGATAAAAAAATTCAAA
* **
15529932 TATTTTGATGTTGGCCATTGCATGGTTGACACCCCTTTTTATCTGAATAAAAAATTAAATTTTTT
1 TTTTTTGATGTTGGCCA-TGCATGGCCGACACCCCTTTTTATCTGAATAAAAAATTAAATTTTTT
* *
15529997 TGTGTTGGCCATTACATGG-CTGACA-CCTCTTTTTGTCAGAT-AAAAAATTCAAA
65 TGTGTTGACCATTGCATGGCCT-ACATCCTCTTTTTGTCAGATAAAAAAATTCAAA
* * * *
15530050 TTTTTTGGTGTTGGCCATGCTATGACCGACACCACTTTTTATCTGAATAAAAAAAATCAAA--TT
1 TTTTTTGATGTTGGCCATGC-ATGGCCGACACCCCTTTTTATCTGAAT--AAAAAATTAAATTTT
* * * **
15530113 TTTATGTTGACCATTGCATGGCCTACACTCCTTTTTTTATTTGATAAAAAAATTCAAA
63 TTTGTGTTGACCATTGCATGGCCTACA-TCCTCTTTTTGTCAGATAAAAAAATTCAAA
* * * * *
15530171 TTTTTTTGGTGTTGGCTATGCATTGGCCGACACTACCTTTTTATCAGATAAAAAAAATT-AATTT
1 -TTTTTTGATGTTGGCCATGCA-TGGCCGACAC-CCCTTTTTATCTGA-ATAAAAAATTAAATTT
* * *
15530235 TTTTGGTGTTGATCATTGCATGGCCGACA-CC-CCTTTT-T-AGATAAAAAAATTCAAA
62 TTTT-GTGTTGACCATTGCATGGCCTACATCCTCTTTTTGTCAGATAAAAAAATTCAAA
* * * * * *
15530290 TTTTTTAAGTGTTAGCCATGCATTGGCCGAC-CCCAATATTGGTTGTCAG-ATAAAAAA-CAAAT
1 TTTTTTGA-TGTTGGCCATGCA-TGGCCGACACCC-CT-TT--TTATCTGAATAAAAAATTAAAT
15530352 TTTTTTGTGTTGACCA-TGCAT
60 TTTTTTGTGTTGACCATTGCAT
15530373 TGGCTGACAC
Statistics
Matches: 365, Mismatches: 51, Indels: 51
0.78 0.11 0.11
Matches are distributed among these distances:
117 25 0.07
118 120 0.33
119 95 0.26
120 25 0.07
121 25 0.07
122 37 0.10
123 16 0.04
124 22 0.06
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (119 bp):
TTTTTTGATGTTGGCCATGCATGGCCGACACCCCTTTTTATCTGAATAAAAAATTAAATTTTTTT
GTGTTGACCATTGCATGGCCTACATCCTCTTTTTGTCAGATAAAAAAATTCAAA
Found at i:15530883 original size:60 final size:60
Alignment explanation
Indices: 15530807--15530929 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 60
15530797 GATGACTGCA
* * * * * *
15530807 ATGATCAACACAAAAAAATTTGATTTTTTTAT-TCAGATAGAAAGGGGTGTCGGTCATGGC
1 ATGATCAACACAAAAAAATTTAAATTTTTTATCTAACA-AAAAAGGGGTGTCGATCATGGC
* *
15530867 ATGATCAACACCAAAAAATTTAAATTTTTTATCTAACAAAAAAGGGGTGTCGATTATGGC
1 ATGATCAACACAAAAAAATTTAAATTTTTTATCTAACAAAAAAGGGGTGTCGATCATGGC
15530927 ATG
1 ATG
15530930 GTCTGTAACA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
60 51 0.94
61 3 0.06
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (60 bp):
ATGATCAACACAAAAAAATTTAAATTTTTTATCTAACAAAAAAGGGGTGTCGATCATGGC
Found at i:15531273 original size:26 final size:24
Alignment explanation
Indices: 15531243--15531309 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
15531233 TGTTTTTAAC
15531243 TAATATATTAATTAATAATATTATTA
1 TAATATATTAA-TAAT-ATATTATTA
*
15531269 TAATA-AATAATAATATATTATTA
1 TAATATATTAATAATATATTATTA
*
15531292 T-TTATATTATATAATATA
1 TAATATATTA-ATAATATA
15531310 AAGAAAGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
22 2 0.06
23 13 0.36
24 12 0.33
25 4 0.11
26 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATATATTAATAATATATTATTA
Found at i:15531309 original size:12 final size:12
Alignment explanation
Indices: 15531243--15531309 Score: 52
Period size: 12 Copynumber: 5.6 Consensus size: 12
15531233 TGTTTTTAAC
15531243 TAATATATTA-A
1 TAATATATTATA
15531254 TTAATAATATTATTA
1 -TAAT-ATATTA-TA
*
15531269 TAATA-AATA-A
1 TAATATATTATA
15531279 TAATATATTAT-
1 TAATATATTATA
*
15531290 TATTTATATTATA
1 TA-ATATATTATA
15531303 TAATATA
1 TAATATA
15531310 AAGAAAGGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
10 6 0.14
11 5 0.11
12 19 0.43
13 9 0.20
14 4 0.09
15 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TAATATATTATA
Found at i:15532328 original size:18 final size:19
Alignment explanation
Indices: 15532305--15532348 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
15532295 GATATGAAAC
*
15532305 AAAAATGAGAA-TGATGTG
1 AAAAATGAGAATTGAAGTG
15532323 AAAAAT-AGAATTGAAGTG
1 AAAAATGAGAATTGAAGTG
*
15532341 AAATATGA
1 AAAAATGA
15532349 TTTTTACCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 17 0.77
19 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (19 bp):
AAAAATGAGAATTGAAGTG
Found at i:15532782 original size:25 final size:24
Alignment explanation
Indices: 15532737--15532788 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
15532727 TATTGTTATT
*
15532737 TATTTACTTTTATTAATTAATCTA
1 TATTTAATTTTATTAATTAATCTA
*
15532761 TATTTAATATTTATGTAA-TAATTTA
1 TATTTAAT-TTTAT-TAATTAATCTA
15532786 TAT
1 TAT
15532789 GATATTAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 14 0.58
26 3 0.12
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (24 bp):
TATTTAATTTTATTAATTAATCTA
Found at i:15538409 original size:32 final size:32
Alignment explanation
Indices: 15538307--15538415 Score: 84
Period size: 31 Copynumber: 3.5 Consensus size: 32
15538297 ATTTTTTTGA
* * *
15538307 CTTAATTTGATACTTGAACTTGATATTTTTT-
1 CTTAATTTGGTACCTAAACTTGATATTTTTTC
* * * **
15538338 TTTAATTTAGTACCTAAGCTT--T-TTTTGAAC
1 CTTAATTTGGTACCTAAACTTGATATTTT-TTC
*
15538368 C-CAATTTGGTACCTAAACTTGATATTTTTTC
1 CTTAATTTGGTACCTAAACTTGATATTTTTTC
*
15538399 CTTAATTTGGTATCTAA
1 CTTAATTTGGTACCTAA
15538416 GCTTTTTTTT
Statistics
Matches: 56, Mismatches: 16, Indels: 11
0.67 0.19 0.13
Matches are distributed among these distances:
28 4 0.07
29 17 0.30
31 18 0.32
32 17 0.30
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.50
Consensus pattern (32 bp):
CTTAATTTGGTACCTAAACTTGATATTTTTTC
Found at i:15538416 original size:61 final size:59
Alignment explanation
Indices: 15538264--15538446 Score: 215
Period size: 59 Copynumber: 3.0 Consensus size: 59
15538254 TTAATATTTG
* ** ** * *
15538264 AACTTGATACTTTTTTTTAATTTGATATCTAAAATTTTTTTG-ACTTAATTTGATACTTG
1 AACTTGATA-TTTTTTTTAATTTGGTATCTAAGCTTTTTTTGAACCCAATTTGATACCTA
* * *
15538323 AACTTGATATTTTTTTTTAATTTAGTACCTAAGCTTTTTTTGAACCCAATTTGGTACCTA
1 AACTTGATA-TTTTTTTTAATTTGGTATCTAAGCTTTTTTTGAACCCAATTTGATACCTA
*
15538383 AACTTGATATTTTTTCCTTAATTTGGTATCTAAGCTTTTTTTTTAACCCAATTTGATACCTA
1 AACTTGATATTTTTT--TTAATTTGGTATCTAAGC-TTTTTTTGAACCCAATTTGATACCTA
15538445 AA
1 AA
15538447 TTTATTAAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
59 42 0.40
60 21 0.20
61 16 0.15
62 26 0.25
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (59 bp):
AACTTGATATTTTTTTTAATTTGGTATCTAAGCTTTTTTTGAACCCAATTTGATACCTA
Found at i:15538647 original size:32 final size:32
Alignment explanation
Indices: 15538587--15538673 Score: 115
Period size: 32 Copynumber: 2.7 Consensus size: 32
15538577 TTAAAAAAGA
15538587 TTAGGTA-CTAAATTAG-AAAAAAGAGTCAAGT
1 TTAGGTATC-AAATTAGAAAAAAAGAGTCAAGT
*
15538618 TTAGGTATCAAATTAGAAAAAAAGTGTCAAGT
1 TTAGGTATCAAATTAGAAAAAAAGAGTCAAGT
* *
15538650 TTAAGTATCAAATTGGACAAAAAA
1 TTAGGTATCAAATTAGA-AAAAAA
15538674 AATTTAAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 14 0.28
32 30 0.60
33 6 0.12
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.26
Consensus pattern (32 bp):
TTAGGTATCAAATTAGAAAAAAAGAGTCAAGT
Found at i:15540430 original size:25 final size:25
Alignment explanation
Indices: 15540336--15540445 Score: 75
Period size: 25 Copynumber: 4.3 Consensus size: 25
15540326 TATTAATAAT
* *
15540336 TTAAATTAAATAAT-TTTTTATCTA
1 TTAAATTAAATACTATTTTTATTTA
* * *
15540360 TTAAATTTTATTACCTATTTTCTGTTTAA
1 TTAAA-TTAAATA-CTATTTT-TATTT-A
15540389 TTTAAATTAAATA--ATTTTTATTTA
1 -TTAAATTAAATACTATTTTTATTTA
* *
15540413 TTAAATTATATACTATTTATA-TTA
1 TTAAATTAAATACTATTTTTATTTA
15540437 TATAAATTA
1 T-TAAATTA
15540446 GTATTTATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
23 11 0.16
24 10 0.15
25 22 0.33
26 6 0.09
27 4 0.06
28 3 0.04
29 6 0.09
30 5 0.07
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (25 bp):
TTAAATTAAATACTATTTTTATTTA
Found at i:15540455 original size:25 final size:23
Alignment explanation
Indices: 15540390--15540445 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
15540380 TCTGTTTAAT
* * *
15540390 TTAAATTAAATAATTTTTATTTA
1 TTAAATTATATACTATTTATTTA
15540413 TTAAATTATATACTATTTATATTA
1 TTAAATTATATACTATTTAT-TTA
15540437 TATAAATTA
1 T-TAAATTA
15540446 GTATTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 17 0.61
24 4 0.14
25 7 0.25
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAAATTATATACTATTTATTTA
Found at i:15540461 original size:25 final size:24
Alignment explanation
Indices: 15540390--15540464 Score: 66
Period size: 23 Copynumber: 3.1 Consensus size: 24
15540380 TCTGTTTAAT
* * *
15540390 TTAAATTAAATAAT-TTTTATTTA
1 TTAAATTATATACTATTTTAATTA
15540413 TTAAATTATATACTA-TTTATATTA
1 TTAAATTATATACTATTTTA-ATTA
*
15540437 TATAAATTAGTAT-TTATTTTAATTA
1 T-TAAATTA-TATACTATTTTAATTA
15540462 TTA
1 TTA
15540465 GCATATACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
23 16 0.37
24 6 0.14
25 14 0.33
26 7 0.16
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (24 bp):
TTAAATTATATACTATTTTAATTA
Found at i:15560245 original size:15 final size:15
Alignment explanation
Indices: 15560211--15560244 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
15560201 TTATTTGTGA
*
15560211 TTTTTCCCATAAAAT
1 TTTTTCACATAAAAT
15560226 TTTTTCACAT-AAAT
1 TTTTTCACATAAAAT
15560240 TTTTT
1 TTTTT
15560245 TTATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTTCACATAAAAT
Found at i:15562874 original size:29 final size:29
Alignment explanation
Indices: 15562843--15562898 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
15562833 AACAATACTA
15562843 AAAAAT-AATTAAATATAAAAATAGAATG
1 AAAAATAAATTAAATATAAAAATAGAATG
*
15562871 AAAAATAAATTAATTATAAAAATAGAAT
1 AAAAATAAATTAAATATAAAAATAGAAT
15562899 TTTTTTGGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (29 bp):
AAAAATAAATTAAATATAAAAATAGAATG
Found at i:15564900 original size:22 final size:22
Alignment explanation
Indices: 15564841--15564906 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
15564831 ATTTAATTAT
* *
15564841 TATATTTTTTGAACTTATAAAA
1 TATATTTTTTTAAATTATAAAA
*
15564863 TATATTATTTAATAAATTA-AAAA
1 TATATT-TTT-TTAAATTATAAAA
15564886 TAATATTTTTTTAAATATATA
1 T-ATATTTTTTTAAAT-TATA
15564907 GGATGTGACG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
22 11 0.31
23 13 0.37
24 11 0.31
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TATATTTTTTTAAATTATAAAA
Found at i:15568982 original size:16 final size:16
Alignment explanation
Indices: 15568963--15568999 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
15568953 ATTATGTTAA
15568963 GGGTTTAATTAATTTG
1 GGGTTTAATTAATTTG
15568979 GGGTTTAATTAATTTG
1 GGGTTTAATTAATTTG
15568995 GGGTT
1 GGGTT
15569000 GCAAGGACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.49
Consensus pattern (16 bp):
GGGTTTAATTAATTTG
Found at i:15579328 original size:17 final size:17
Alignment explanation
Indices: 15579303--15579335 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
15579293 TTTTAATTTG
15579303 AATTCTAAAAAATAATA
1 AATTCTAAAAAATAATA
*
15579320 AATTTTAAAAAATAAT
1 AATTCTAAAAAATAAT
15579336 GATTAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTCTAAAAAATAATA
Found at i:15581574 original size:14 final size:15
Alignment explanation
Indices: 15581555--15581587 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
15581545 ATATTATAAC
15581555 AATTTTATCTTTCA-
1 AATTTTATCTTTCAT
*
15581569 AATTTTATTTTTCAT
1 AATTTTATCTTTCAT
15581584 AATT
1 AATT
15581588 AAAACATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (15 bp):
AATTTTATCTTTCAT
Found at i:15581678 original size:2 final size:2
Alignment explanation
Indices: 15581671--15581702 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
15581661 AAAAATATTA
*
15581671 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15581703 CTTTTGTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:15600001 original size:103 final size:103
Alignment explanation
Indices: 15599822--15600027 Score: 308
Period size: 103 Copynumber: 2.0 Consensus size: 103
15599812 TTTTGGAAGT
* * *
15599822 TCTAGAATACTCCACAATCGAATAGCATTTAATGAGTTAGGTGGAAAAGTTTTAGAATTAGATCT
1 TCTAGAATACTCCACAATCGAATAACATTTAATGAGTTAGGTGGAAAAGTTCTAGAATTAAATCT
*
15599887 TGACCGTCCATTAAGATTAATTGTAACCATTAGATCGA
66 TGACCGTCCATTAAGATTAATAGTAACCATTAGATCGA
*
15599925 TCTAGAATACTTCACCAAT-GAATAACATTTAATGAGTTAGGT-GAAAATGTTCTAGAATTAAAT
1 TCTAGAATACTCCA-CAATCGAATAACATTTAATGAGTTAGGTGGAAAA-GTTCTAGAATTAAAT
* * *
15599988 CTTGACTGTCCATTAGGATTAATAGTAACTATTAGATCGA
64 CTTGACCGTCCATTAAGATTAATAGTAACCATTAGATCGA
15600028 AAGGGGTTTG
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
102 5 0.05
103 84 0.90
104 4 0.04
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (103 bp):
TCTAGAATACTCCACAATCGAATAACATTTAATGAGTTAGGTGGAAAAGTTCTAGAATTAAATCT
TGACCGTCCATTAAGATTAATAGTAACCATTAGATCGA
Found at i:15601533 original size:23 final size:23
Alignment explanation
Indices: 15601460--15601633 Score: 167
Period size: 23 Copynumber: 7.5 Consensus size: 23
15601450 TATACGGAAC
* *
15601460 AAACAGAGAGCAC-CAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
*
15601482 -AACAGAGAGCACATA-AGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
15601503 GGGTAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACACAGTGCT
* * *
15601529 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
*
15601552 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
15601575 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
* *
15601598 AATAACAGAGAGCATGAGAC-GTGCT
1 -A-AACAGAGAGCA-CACACAGTGCT
15601623 AAACAGAGAGC
1 AAACAGAGAGC
15601634 GCGCTAGTGT
Statistics
Matches: 129, Mismatches: 14, Indels: 17
0.81 0.09 0.11
Matches are distributed among these distances:
21 17 0.13
22 1 0.01
23 71 0.55
24 2 0.02
25 29 0.22
26 9 0.07
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:15601582 original size:69 final size:67
Alignment explanation
Indices: 15601460--15601611 Score: 200
Period size: 69 Copynumber: 2.2 Consensus size: 67
15601450 TATACGGAAC
*
15601460 AAACAGAGAGCACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGTAACAGAGAGCACACACAG
1 AAACAGAGAGCACCAAAGTACTAACAGAGAGCACACAAGTGC---GTAACAGAGAGCACACACAG
15601525 TGCT-
63 TGCTA
*
15601529 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACACAGTGC-TAATCAGAGAGCACACACA
1 AAACAGAGAGCAC-CAAAGTACTAA-CAGAGAGCACACA-AGTGCGTAA-CAGAGAGCACACACA
15601593 GTGCTA
62 GTGCTA
15601599 ATAACAGAGAGCA
1 A-AACAGAGAGCA
15601612 TGAGACGTGC
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
68 3 0.04
69 32 0.43
70 12 0.16
71 22 0.30
72 5 0.07
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (67 bp):
AAACAGAGAGCACCAAAGTACTAACAGAGAGCACACAAGTGCGTAACAGAGAGCACACACAGTGC
TA
Found at i:15601633 original size:48 final size:47
Alignment explanation
Indices: 15601461--15601633 Score: 185
Period size: 46 Copynumber: 3.7 Consensus size: 47
15601451 ATACGGAACA
* * * **
15601461 AACAGAGAGCAC-CAAAGTACT-AACAGAGAGCACATAAGTGCTGGGT
1 AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAGTGCT-AAT
* *
15601507 AACAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
1 AACAGAGAGCACACACAGTGCTAAACAGAGAGCACAC-AAGTGCTAAT
*
15601555 --CAGAGAGCACACACAGTGCTAATCAGAGAGCACACACAGTGCTAAT
1 AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACA-AGTGCTAAT
* *
15601601 AACAGAGAGCATGAGAC-GTGCTAAACAGAGAGC
1 AACAGAGAGCA-CACACAGTGCTAAACAGAGAGC
15601634 GCGCTAGTGT
Statistics
Matches: 107, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
45 1 0.01
46 53 0.50
47 7 0.07
48 37 0.35
49 9 0.08
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (47 bp):
AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAGTGCTAAT
Found at i:15601884 original size:31 final size:31
Alignment explanation
Indices: 15601849--15601914 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
15601839 TTATAATCAG
15601849 TTTAGCCAATATGTACAGTAAATTCTTTTAA
1 TTTAGCCAATATGTACAGTAAATTCTTTTAA
15601880 TTTAGCCAATATGTACAGTAAATTCTTTTAA
1 TTTAGCCAATATGTACAGTAAATTCTTTTAA
15601911 TTTA
1 TTTA
15601915 CCCCTTCTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (31 bp):
TTTAGCCAATATGTACAGTAAATTCTTTTAA
Found at i:15604314 original size:18 final size:18
Alignment explanation
Indices: 15604291--15604327 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15604281 TATTTTTGAG
*
15604291 AAATTTTTCAAAATTTAA
1 AAATTTTTCAAAATATAA
*
15604309 AAATTTTTTAAAATATAA
1 AAATTTTTCAAAATATAA
15604327 A
1 A
15604328 TTTTGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTTTCAAAATATAA
Found at i:15604343 original size:18 final size:19
Alignment explanation
Indices: 15604322--15604357 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15604312 TTTTTTAAAA
15604322 TATAAAT-TTTGAAATTTT
1 TATAAATATTTGAAATTTT
*
15604340 TATAAATATTTTAAATTT
1 TATAAATATTTGAAATTT
15604358 AAAAACTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TATAAATATTTGAAATTTT
Found at i:15608111 original size:9 final size:9
Alignment explanation
Indices: 15608097--15608138 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
15608087 TACTTTCTTT
15608097 CAATGAATA
1 CAATGAATA
15608106 CAATGAATA
1 CAATGAATA
*
15608115 CAATGAATG
1 CAATGAATA
*
15608124 GAATGGAATA
1 CAAT-GAATA
15608134 CAATG
1 CAATG
15608139 GAATGAGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.50, C:0.10, G:0.19, T:0.21
Consensus pattern (9 bp):
CAATGAATA
Found at i:15609923 original size:29 final size:30
Alignment explanation
Indices: 15609860--15609924 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
15609850 ATAATTTAAA
* * *
15609860 AAAATTTGATCAAATTAAAATTTCATTTAT
1 AAAATTTGATAAAATCAAAATTTCATATAT
*
15609890 AAAATTTTATAAAATCAAAA-TTCATATAT
1 AAAATTTGATAAAATCAAAATTTCATATAT
15609919 AAAATT
1 AAAATT
15609925 GCACGTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (30 bp):
AAAATTTGATAAAATCAAAATTTCATATAT
Found at i:15610014 original size:19 final size:19
Alignment explanation
Indices: 15609992--15610035 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
15609982 CATACATACG
15609992 TCGGTGCACAATACTCCGA
1 TCGGTGCACAATACTCCGA
15610011 TCGGTGCACAATACTCCGA
1 TCGGTGCACAATACTCCGA
15610030 TCGGTG
1 TCGGTG
15610036 TAGCTGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.23
Consensus pattern (19 bp):
TCGGTGCACAATACTCCGA
Found at i:15611041 original size:35 final size:34
Alignment explanation
Indices: 15610993--15611062 Score: 81
Period size: 36 Copynumber: 2.0 Consensus size: 34
15610983 TAAAATTTTA
* *
15610993 AAATTTAAGGTTAA-TACTAATAATTTTGTTTTTATT
1 AAATTCAAGGTTAATTAC-AAT-ATTTT-TTTTAATT
15611029 AAATTCAA-GTTAATTACAATATTTTTTTTAATT
1 AAATTCAAGGTTAATTACAATATTTTTTTTAATT
15611062 A
1 A
15611063 TAAGACTACC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
33 8 0.26
34 5 0.16
35 8 0.26
36 10 0.32
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (34 bp):
AAATTCAAGGTTAATTACAATATTTTTTTTAATT
Found at i:15625430 original size:4 final size:4
Alignment explanation
Indices: 15625421--15625476 Score: 69
Period size: 4 Copynumber: 13.8 Consensus size: 4
15625411 AAATAAACGG
* *
15625421 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GAAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
15625471 -AAA GAA
1 GAAA GAA
15625477 GGAGAGAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 3 0.06
4 36 0.77
5 8 0.17
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:15625443 original size:17 final size:17
Alignment explanation
Indices: 15625421--15625471 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
15625411 AAATAAACGG
15625421 GAAAGAAAGAAAGAAAA
1 GAAAGAAAGAAAGAAAA
15625438 GAAAGAAAGAAAG-AAA
1 GAAAGAAAGAAAGAAAA
* *
15625454 GAAGGAGAGGAAAGAAAA
1 GAAAGA-AAGAAAGAAAA
15625472 AAGAAGGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 8 0.27
17 19 0.63
18 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGAAAA
Found at i:15625466 original size:21 final size:21
Alignment explanation
Indices: 15625420--15625482 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
15625410 CAAATAAACG
*
15625420 GGAAAGAAAGAAAGAA-AAGAA
1 GGAAAGAAAGAAAGAAGGAG-A
*
15625441 AGAAAGAAAGAAAGAAGGAGA
1 GGAAAGAAAGAAAGAAGGAGA
15625462 GGAAAGAAA-AAAGAAGGAGA
1 GGAAAGAAAGAAAGAAGGAGA
15625482 G
1 G
15625483 AAATGTAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.32
21 24 0.63
22 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (21 bp):
GGAAAGAAAGAAAGAAGGAGA
Found at i:15630366 original size:20 final size:21
Alignment explanation
Indices: 15630341--15630382 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
15630331 CTTACTACTA
15630341 ACTAAC-AACAAAATAAAATT
1 ACTAACTAACAAAATAAAATT
*
15630361 ACTAACTAACAAAATTAAATT
1 ACTAACTAACAAAATAAAATT
15630382 A
1 A
15630383 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (21 bp):
ACTAACTAACAAAATAAAATT
Found at i:15630624 original size:4 final size:4
Alignment explanation
Indices: 15630617--15630646 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
15630607 TCATTCTTCC
15630617 TTCT TTCT TTCT TTCT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
15630647 CTTCAAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:15637528 original size:2 final size:2
Alignment explanation
Indices: 15637521--15637553 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15637511 ACTATTTGTA
15637521 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15637554 CTGCCATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15638352 original size:2 final size:2
Alignment explanation
Indices: 15638345--15638378 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15638335 AATTCACTTA
15638345 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
15638379 GAAACAACAA
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:15640096 original size:24 final size:24
Alignment explanation
Indices: 15640043--15640097 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
15640033 ATTGCTAGGT
**
15640043 TCAATAAATAACAATCAAAACAATA
1 TCAA-AAATAACAAGAAAAACAATA
*
15640068 GCAAAAATAACAAGAAAAACAGA-A
1 TCAAAAATAACAAGAAAAACA-ATA
15640092 TCAAAA
1 TCAAAA
15640098 CAGTAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.67, C:0.15, G:0.05, T:0.13
Consensus pattern (24 bp):
TCAAAAATAACAAGAAAAACAATA
Found at i:15640145 original size:43 final size:42
Alignment explanation
Indices: 15640071--15640165 Score: 131
Period size: 43 Copynumber: 2.2 Consensus size: 42
15640061 AACAATAGCA
*
15640071 AAAATAACAAGAAAAACAGAATCAAAACAGTAAAAAAA-ACAC
1 AAAATAACAAGAAAAACAGAACCAAAACAGTAAAAAAATAC-C
*
15640113 TAAAATAACAA-AAAAACAGCAACCAAAGCAGTAAAAAAATACC
1 -AAAATAACAAGAAAAACAG-AACCAAAACAGTAAAAAAATACC
15640156 AAAATAACAA
1 AAAATAACAA
15640166 TATAATTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
42 18 0.38
43 28 0.58
44 2 0.04
ACGTcount: A:0.69, C:0.16, G:0.06, T:0.08
Consensus pattern (42 bp):
AAAATAACAAGAAAAACAGAACCAAAACAGTAAAAAAATACC
Found at i:15640149 original size:42 final size:43
Alignment explanation
Indices: 15640071--15640165 Score: 131
Period size: 42 Copynumber: 2.2 Consensus size: 43
15640061 AACAATAGCA
* *
15640071 AAAATAACAAGAAAAACAGAATCAAAACAGTAAAAAAAACACT
1 AAAATAACAAGAAAAACAGAACCAAAACAGTAAAAAAAACACC
* *
15640114 AAAATAACAA-AAAAACAGCAACCAAAGCAGT-AAAAAAATACC
1 AAAATAACAAGAAAAACAG-AACCAAAACAGTAAAAAAAACACC
15640156 AAAATAACAA
1 AAAATAACAA
15640166 TATAATTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
42 27 0.57
43 20 0.43
ACGTcount: A:0.69, C:0.16, G:0.06, T:0.08
Consensus pattern (43 bp):
AAAATAACAAGAAAAACAGAACCAAAACAGTAAAAAAAACACC
Found at i:15640394 original size:29 final size:29
Alignment explanation
Indices: 15640361--15640424 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
15640351 GATCAGGTCT
* * *
15640361 AATTTTATATATGGACTTTGATTTTATGC
1 AATTTTATATATGAAATTTGATTTAATGC
*
15640390 AATTTTATATATGAAATTTGATTTAATGT
1 AATTTTATATATGAAATTTGATTTAATGC
15640419 AATTTT
1 AATTTT
15640425 CACAAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.53
Consensus pattern (29 bp):
AATTTTATATATGAAATTTGATTTAATGC
Found at i:15641010 original size:23 final size:24
Alignment explanation
Indices: 15640966--15641010 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
15640956 ACTCAAATTT
* **
15640966 AATTTTAAAAATTATTTTTATACA
1 AATTATAAAAATTATTAGTATACA
15640990 AATTATAAAAATTA-TAGTATA
1 AATTATAAAAATTATTAGTATA
15641011 ATCATGAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
AATTATAAAAATTATTAGTATACA
Found at i:15646180 original size:20 final size:20
Alignment explanation
Indices: 15646153--15646191 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
15646143 AAGGTCTCAA
15646153 GTTTAGATTATAAT-TTTGG
1 GTTTAGATTATAATATTTGG
*
15646172 GTTTAAGATTTTAATATTTG
1 GTTT-AGATTATAATATTTG
15646192 TTTATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (20 bp):
GTTTAGATTATAATATTTGG
Found at i:15648592 original size:3 final size:3
Alignment explanation
Indices: 15648584--15648611 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
15648574 AAGGAAAATC
15648584 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
15648612 CAAAGTCCTA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:15652424 original size:15 final size:15
Alignment explanation
Indices: 15652390--15652438 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
15652380 AAATCTTTTT
15652390 ATATTATTAAC-TT-
1 ATATTATTAACTTTA
* *
15652403 GTATTATTAGCTTTA
1 ATATTATTAACTTTA
*
15652418 ATATTATTAATTTTA
1 ATATTATTAACTTTA
15652433 ATATTA
1 ATATTA
15652439 ATTATTGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
13 9 0.31
14 2 0.07
15 18 0.62
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (15 bp):
ATATTATTAACTTTA
Found at i:15663109 original size:2 final size:2
Alignment explanation
Indices: 15663102--15663128 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15663092 AAACACTTAG
15663102 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
15663129 TCCTGCTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15679777 original size:24 final size:24
Alignment explanation
Indices: 15679746--15679796 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
15679736 AGAAATAATC
* *
15679746 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
15679770 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
15679794 TTT
1 TTT
15679797 GATTCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.59
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:15680430 original size:29 final size:28
Alignment explanation
Indices: 15680384--15680449 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
15680374 TTAACATAAT
15680384 ATTTGGTATTTAATTTTGATATTTTGT-TA
1 ATTTGGTATTTAATTTTG-T-TTTTGTCTA
*
15680413 ATTTAGTATTTACA-TTTGTTTTTGTCTA
1 ATTTGGTATTTA-ATTTTGTTTTTGTCTA
15680441 ATTTGGTAT
1 ATTTGGTAT
15680450 CTGAACTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 6 0.18
28 11 0.33
29 15 0.45
30 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.14, T:0.61
Consensus pattern (28 bp):
ATTTGGTATTTAATTTTGTTTTTGTCTA
Found at i:15684986 original size:6 final size:6
Alignment explanation
Indices: 15684976--15685022 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
15684966 AGACAATGTG
*
15684976 AGAGAT GGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGA
1 AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGA
15685023 GATACTGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.36, T:0.15
Consensus pattern (6 bp):
AGAGAT
Found at i:15696664 original size:3 final size:3
Alignment explanation
Indices: 15696656--15696684 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
15696646 GCCACGTCAT
15696656 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
15696685 TTCTGGATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:15711531 original size:11 final size:11
Alignment explanation
Indices: 15711515--15711539 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15711505 AATATTTCTT
15711515 AATAAATTAAA
1 AATAAATTAAA
15711526 AATAAATTAAA
1 AATAAATTAAA
15711537 AAT
1 AAT
15711540 TTTATTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAATTAAA
Found at i:15720354 original size:1 final size:1
Alignment explanation
Indices: 15720350--15720384 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
15720340 TTTTTTTTTT
*
15720350 GGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
15720385 CAGTCGTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:15729748 original size:2 final size:2
Alignment explanation
Indices: 15729741--15729770 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15729731 TTAAATTTAG
15729741 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
15729771 GTAATTTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15734489 original size:16 final size:16
Alignment explanation
Indices: 15734421--15734492 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 16
15734411 TAACAAGATT
15734421 ATTATTAAATATAAT-
1 ATTATTAAATATAATA
* *
15734436 -TTAATAAAAATAATA
1 ATTATTAAATATAATA
15734451 A--A-TAAAT-TAATCA
1 ATTATTAAATATAAT-A
15734464 TATT-TT-AATATAATA
1 -ATTATTAAATATAATA
15734479 ATTATTAAATATAA
1 ATTATTAAATATAA
15734493 CTTAATAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 19
0.67 0.05 0.29
Matches are distributed among these distances:
12 4 0.09
13 5 0.11
14 17 0.39
15 6 0.14
16 12 0.27
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTATTAAATATAATA
Found at i:15734510 original size:31 final size:30
Alignment explanation
Indices: 15734421--15734512 Score: 77
Period size: 31 Copynumber: 3.1 Consensus size: 30
15734411 TAACAAGATT
15734421 ATTATTAAATATAATTTAATAAAAAT-AATA
1 ATTATTAAATATAA-TTAATAAAAATAAATA
* ***
15734451 A--A-TAAAT-TAATCATATTTTAATATAATA
1 ATTATTAAATATAATTA-ATAAAAATA-AATA
15734479 ATTATTAAATATAACTTAATAAAAATAAATA
1 ATTATTAAATATAA-TTAATAAAAATAAATA
15734510 ATT
1 ATT
15734513 TGATATCACT
Statistics
Matches: 46, Mismatches: 8, Indels: 15
0.67 0.12 0.22
Matches are distributed among these distances:
25 2 0.04
26 8 0.17
27 5 0.11
28 6 0.13
30 2 0.04
31 12 0.26
32 9 0.20
33 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (30 bp):
ATTATTAAATATAATTAATAAAAATAAATA
Found at i:15746078 original size:13 final size:13
Alignment explanation
Indices: 15746042--15746079 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
15746032 ATTTGAAGAA
*
15746042 TATTATTTAAAAT
1 TATTATTTTAAAT
15746055 TATTATTTTAAAT
1 TATTATTTTAAAT
15746068 T-TTATTATTAAA
1 TATTATT-TTAAA
15746080 ATAAAGTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATTTTAAAT
Found at i:15747334 original size:11 final size:11
Alignment explanation
Indices: 15747318--15747345 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
15747308 TATTTTTTTT
15747318 TGTTTTGGTAC
1 TGTTTTGGTAC
15747329 TGTTTTGGTAC
1 TGTTTTGGTAC
15747340 TGTTTT
1 TGTTTT
15747346 TGTTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.25, T:0.61
Consensus pattern (11 bp):
TGTTTTGGTAC
Found at i:15747361 original size:12 final size:12
Alignment explanation
Indices: 15747346--15747390 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
15747336 GTACTGTTTT
15747346 TGTTATTTTTAC
1 TGTTATTTTTAC
**
15747358 TGTTATTTTTGT
1 TGTTATTTTTAC
*
15747370 TGTT-GTTTTAC
1 TGTTATTTTTAC
15747381 TGTTATTTTT
1 TGTTATTTTT
15747391 GTTACTGTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.11, C:0.04, G:0.13, T:0.71
Consensus pattern (12 bp):
TGTTATTTTTAC
Found at i:15747382 original size:23 final size:24
Alignment explanation
Indices: 15747345--15747420 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
15747335 GGTACTGTTT
*
15747345 TTGTTATTTTTACTGTTATTTTTG
1 TTGTTGTTTTTACTGTTATTTTTG
15747369 TTGTTG-TTTTACTGTTATTTTTG
1 TTGTTGTTTTTACTGTTATTTTTG
** ** *
15747392 TTACTGTTTTTGTTGTAATTTTTG
1 TTGTTGTTTTTACTGTTATTTTTG
15747416 TTGTT
1 TTGTT
15747421 TGAGTGTTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 21 0.49
24 22 0.51
ACGTcount: A:0.11, C:0.04, G:0.16, T:0.70
Consensus pattern (24 bp):
TTGTTGTTTTTACTGTTATTTTTG
Found at i:15747407 original size:15 final size:15
Alignment explanation
Indices: 15747367--15747407 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
15747357 CTGTTATTTT
*
15747367 TGTTGTTGTT-TTAC
1 TGTTTTTGTTGTTAC
15747381 TGTTATTT-TTGTTAC
1 TGTT-TTTGTTGTTAC
15747396 TGTTTTTGTTGT
1 TGTTTTTGTTGT
15747408 AATTTTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.07, C:0.05, G:0.20, T:0.68
Consensus pattern (15 bp):
TGTTTTTGTTGTTAC
Found at i:15753432 original size:224 final size:226
Alignment explanation
Indices: 15753038--15753473 Score: 619
Period size: 224 Copynumber: 1.9 Consensus size: 226
15753028 AATAATAATT
* * **
15753038 TAACATTTAGTTGACACGAATTCAAACATTATCATCTTTTTTCTCTTTCAATATTGTAATAATAA
1 TAACATTTAGTTGACACGAATTCAAACATTACCATCTCTTTTCTCTCCCAATATTGTAATAATAA
* * * *
15753103 TAAAATTTAAAACATTAAATTATTATCAATCCACTGCTCTTTTAGTCAACTTTATTTGTTTTACG
66 TAAAAATTAAAACATTAAATTATTATCAATCCACTGCGCTTTTAGTCAACTTTAGTTGTTTCACG
* * * *
15753168 TTCCACAGGCCTAAAACTCTAATGAAACTATTAGAAAGGGTTTTTTGATTATCCTACTTTCATTC
131 CTCCACAGGCCTAAAACTCTAATGAAACTAATAAAAAGGGTTTTATGATTATCCTACTTTCATTC
15753233 GACTAAAAATCTATTATTGAATAATATTATC
196 GACTAAAAATCTATTATTGAATAATATTATC
* * * *
15753264 TAACATTTAGTTGATATGAATTTAAACATTGCCATCTCTTTTCTCTCCCAATATTGTAATAA-AA
1 TAACATTTAGTTGACACGAATTCAAACATTACCATCTCTTTTCTCTCCCAATATTGTAATAATAA
*
15753328 -AAAAATTAAAACATTAAATTATTATCAATCCAC-GACGCTTTTAGTCAACTTTAGTTGTTTCAT
66 TAAAAATTAAAACATTAAATTATTATCAATCCACTG-CGCTTTTAGTCAACTTTAGTTGTTTCAC
* * * *
15753391 GCTCGATAGGCCTAAAACTCTATTGAGAA-TAATAAAAAGGGTTTTATGATTATCCTATTTTCAT
130 GCTCCACAGGCCTAAAACTCTAATGA-AACTAATAAAAAGGGTTTTATGATTATCCTACTTTCAT
* *
15753455 TCGATTAAAAATTTATTAT
194 TCGACTAAAAATCTATTAT
15753474 AGCAGAATAT
Statistics
Matches: 185, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
223 1 0.01
224 126 0.68
225 4 0.02
226 54 0.29
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (226 bp):
TAACATTTAGTTGACACGAATTCAAACATTACCATCTCTTTTCTCTCCCAATATTGTAATAATAA
TAAAAATTAAAACATTAAATTATTATCAATCCACTGCGCTTTTAGTCAACTTTAGTTGTTTCACG
CTCCACAGGCCTAAAACTCTAATGAAACTAATAAAAAGGGTTTTATGATTATCCTACTTTCATTC
GACTAAAAATCTATTATTGAATAATATTATC
Found at i:15754279 original size:6 final size:6
Alignment explanation
Indices: 15754270--15754298 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
15754260 TCTTTTAAAT
15754270 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
15754299 TCAGTTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:15755540 original size:30 final size:31
Alignment explanation
Indices: 15755506--15755576 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
15755496 CATTTAACAC
15755506 AACAGTCACTCAAC-TT-T-GAAAATGTGACAA
1 AACAGTCACT-AACGTTATCGAAAA-GTGACAA
15755536 AACAGTCACTAACGTTATCGAAAAGTGACAA
1 AACAGTCACTAACGTTATCGAAAAGTGACAA
*
15755567 AATAGTCACT
1 AACAGTCACT
15755577 GAAATTATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 3 0.08
30 12 0.32
31 17 0.46
32 5 0.14
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.23
Consensus pattern (31 bp):
AACAGTCACTAACGTTATCGAAAAGTGACAA
Found at i:15757256 original size:29 final size:30
Alignment explanation
Indices: 15757210--15757279 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
15757200 ATTAATAATT
* *
15757210 TATA-AAAATTAAATC-AAATCAAATTTTTA
1 TATATAAAATTAAATCAAAACCAAA-ATTTA
*
15757239 TATATAAAATTATA-CAAAACCAAAATTTA
1 TATATAAAATTAAATCAAAACCAAAATTTA
*
15757268 TGTATAAAATTA
1 TATATAAAATTA
15757280 CACATACCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.36
Consensus pattern (30 bp):
TATATAAAATTAAATCAAAACCAAAATTTA
Found at i:15772248 original size:29 final size:30
Alignment explanation
Indices: 15772215--15772278 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
15772205 GAATTCCAAA
* *
15772215 TATATAATTGTAC-CAAATTAAAGTTCATG
1 TATATAATTGCACACAAATCAAAGTTCATG
*
15772244 TATATAATTGCACATTAAATCAAAGTTCATG
1 TATATAATTGCACA-CAAATCAAAGTTCATG
15772275 TATA
1 TATA
15772279 ATTTTGAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 12 0.40
31 18 0.60
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (30 bp):
TATATAATTGCACACAAATCAAAGTTCATG
Found at i:15777136 original size:10 final size:10
Alignment explanation
Indices: 15777123--15777163 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
15777113 ATTATTTTGG
15777123 TTGTTGTTTT
1 TTGTTGTTTT
15777133 TTGTTGTTTT
1 TTGTTGTTTT
*
15777143 TATGTTATTTT
1 T-TGTTGTTTT
*
15777154 TTATTGTTTT
1 TTGTTGTTTT
15777164 GATTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.07, C:0.00, G:0.15, T:0.78
Consensus pattern (10 bp):
TTGTTGTTTT
Found at i:15777173 original size:18 final size:18
Alignment explanation
Indices: 15777150--15777185 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
15777140 TTTTATGTTA
* *
15777150 TTTTTTATTGTTTTGATT
1 TTTTTTACTATTTTGATT
15777168 TTTTTTACTATTTTGATT
1 TTTTTTACTATTTTGATT
15777186 GTTATTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.75
Consensus pattern (18 bp):
TTTTTTACTATTTTGATT
Found at i:15777203 original size:22 final size:22
Alignment explanation
Indices: 15777178--15777221 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
15777168 TTTTTTACTA
**
15777178 TTTTGATTGTTATTTTGATGCT
1 TTTTGATTACTATTTTGATGCT
**
15777200 TTTTTTTTACTATTTTGATGCT
1 TTTTGATTACTATTTTGATGCT
15777222 ATTATTTTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.66
Consensus pattern (22 bp):
TTTTGATTACTATTTTGATGCT
Found at i:15777229 original size:22 final size:22
Alignment explanation
Indices: 15777188--15777229 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
15777178 TTTTGATTGT
* *
15777188 TATTTTGATGCTTTTTTTTTAC
1 TATTTTGATGCTATTATTTTAC
15777210 TATTTTGATGCTATTATTTT
1 TATTTTGATGCTATTATTTT
15777230 TATTGCTGTT
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:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (22 bp):
TATTTTGATGCTATTATTTTAC
Found at i:15777253 original size:12 final size:12
Alignment explanation
Indices: 15777223--15777316 Score: 79
Period size: 12 Copynumber: 8.2 Consensus size: 12
15777213 TTTGATGCTA
*
15777223 TTATTTTTATTG
1 TTATTTTTGTTG
* *
15777235 CTGTTTTTGTTG
1 TTATTTTTGTTG
15777247 TTATTTTTGTTG
1 TTATTTTTGTTG
*
15777259 CTATTTTTGTTG
1 TTATTTTTGTTG
*
15777271 ----TTTTGTTA
1 TTATTTTTGTTG
*
15777279 TTATTTTTGTTA
1 TTATTTTTGTTG
* *
15777291 CTGTTTTTGTTG
1 TTATTTTTGTTG
*
15777303 TTATTTTGGTTG
1 TTATTTTTGTTG
15777315 TT
1 TT
15777317 TGAATGTTAT
Statistics
Matches: 65, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
8 7 0.11
12 58 0.89
ACGTcount: A:0.09, C:0.03, G:0.17, T:0.71
Consensus pattern (12 bp):
TTATTTTTGTTG
Found at i:15777889 original size:22 final size:22
Alignment explanation
Indices: 15777864--15777905 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
15777854 TTTTTTTGTC
* *
15777864 AAATTACTTTAAAATAGATGAA
1 AAATTAATTAAAAATAGATGAA
*
15777886 AAATTAATTAAAAATTGATG
1 AAATTAATTAAAAATAGATG
15777906 TACCATCTAT
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:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (22 bp):
AAATTAATTAAAAATAGATGAA
Found at i:15800778 original size:16 final size:16
Alignment explanation
Indices: 15800759--15800792 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
15800749 AGATAATCTT
15800759 ACCTTCCATCAATCAA
1 ACCTTCCATCAATCAA
15800775 ACCTTCCATCAATCAA
1 ACCTTCCATCAATCAA
15800791 AC
1 AC
15800793 ACTTGAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (16 bp):
ACCTTCCATCAATCAA
Found at i:15801062 original size:4 final size:4
Alignment explanation
Indices: 15801053--15801091 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
15801043 ACACTTGTTA
* *
15801053 TTAT TTAT TTAT GTAT TTAT TTAT TTCAT TTAT TCAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT-AT TTAT TTAT TT
15801092 GTTAATTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:15801951 original size:31 final size:31
Alignment explanation
Indices: 15801905--15801963 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
15801895 AAATAATCAT
*
15801905 TAAAATATTTGAAAGTTTTCATTTAAGTCAC
1 TAAAATATTTAAAAGTTTTCATTTAAGTCAC
*
15801936 TAAACTATTTAAAAGTTTTCATTTAAGT
1 TAAAATATTTAAAAGTTTTCATTTAAGT
15801964 TATTGGGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (31 bp):
TAAAATATTTAAAAGTTTTCATTTAAGTCAC
Found at i:15804186 original size:31 final size:31
Alignment explanation
Indices: 15804151--15804209 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
15804141 AGTCTAATGT
15804151 CTTAAATAAAAACTTTTGAATAGTTCAAAGA
1 CTTAAATAAAAACTTTTGAATAGTTCAAAGA
15804182 CTTAAATAAAAACTTTTGAATAGTTCAA
1 CTTAAATAAAAACTTTTGAATAGTTCAA
15804210 TGGCAGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.34
Consensus pattern (31 bp):
CTTAAATAAAAACTTTTGAATAGTTCAAAGA
Found at i:15804546 original size:35 final size:36
Alignment explanation
Indices: 15804507--15804578 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
15804497 TATTGTGTTT
*
15804507 AAATTTTGTTTAAATTAATTAAA-TTGTCAACAATA
1 AAATTTTGTTTAAATAAATTAAATTTGTCAACAATA
* *
15804542 AAATTTTGTTTATATAAATTAAATTTGTTAACAATA
1 AAATTTTGTTTAAATAAATTAAATTTGTCAACAATA
15804578 A
1 A
15804579 TATAATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 21 0.64
36 12 0.36
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
AAATTTTGTTTAAATAAATTAAATTTGTCAACAATA
Found at i:15813298 original size:21 final size:20
Alignment explanation
Indices: 15813270--15813312 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
15813260 CACTAACAAG
15813270 TTAACAAAT-TCCGCTAGGAC
1 TTAACAAATCTCC-CTAGGAC
15813290 TTAATCAAATCTCCCTAGGAC
1 TTAA-CAAATCTCCCTAGGAC
15813311 TT
1 TT
15813313 TGTCATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 14 0.67
22 3 0.14
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.30
Consensus pattern (20 bp):
TTAACAAATCTCCCTAGGAC
Found at i:15827113 original size:18 final size:18
Alignment explanation
Indices: 15827092--15827126 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
15827082 AAAATGAGCC
15827092 AAAAAGAGAAAA-AAAAGA
1 AAAAAGA-AAAAGAAAAGA
15827110 AAAAAGAAAAAGAAAAG
1 AAAAAGAAAAAGAAAAG
15827127 GGGAGGGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAAGA
Found at i:15833165 original size:2 final size:2
Alignment explanation
Indices: 15833158--15833189 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15833148 ACATTTCTTC
15833158 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15833190 GCTCTTCCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15847044 original size:30 final size:30
Alignment explanation
Indices: 15847010--15847075 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
15847000 CTAACACATC
15847010 CAGAAAAGAGAAC-ATTACTTCAGGATACCT
1 CAGAAAAGA-AACAATTACTTCAGGATACCT
* * *
15847040 CAGAAAGGAAACTAATTATTTCAGGTTACCT
1 CAGAAAAGAAAC-AATTACTTCAGGATACCT
15847071 -AGAAA
1 CAGAAA
15847076 TGGATTCATC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 3 0.10
30 13 0.42
31 15 0.48
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (30 bp):
CAGAAAAGAAACAATTACTTCAGGATACCT
Found at i:15850635 original size:55 final size:55
Alignment explanation
Indices: 15850568--15850677 Score: 161
Period size: 55 Copynumber: 2.0 Consensus size: 55
15850558 TACCATAATA
15850568 CTTAATTAAAC-AAC-CATCAAATGTTATTACCATAAACAAACTTCTCTTTCAAACT
1 CTTAATTAAACAAACGCAT-AAA-GTTATTACCATAAACAAACTTCTCTTTCAAACT
* * *
15850623 CTTAATTCAACAAACGTATAAAGTTATTACTATAAACAAACTTCTCTTTCAAACT
1 CTTAATTAAACAAACGCATAAAGTTATTACCATAAACAAACTTCTCTTTCAAACT
15850678 ACTTTTTAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
55 42 0.84
56 6 0.12
57 2 0.04
ACGTcount: A:0.42, C:0.22, G:0.03, T:0.34
Consensus pattern (55 bp):
CTTAATTAAACAAACGCATAAAGTTATTACCATAAACAAACTTCTCTTTCAAACT
Found at i:15863108 original size:30 final size:29
Alignment explanation
Indices: 15863062--15863138 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
15863052 GGGATCCAAA
** ** *
15863062 TTTTTTTTCAGTTTTTAAGGGGTTTAAAT
1 TTTTTTTTCAACTTTTAAGAAGCTTAAAT
*
15863091 TTTTTTTATTAACTTTTAAGAAGCTTAAAT
1 TTTTTTT-TCAACTTTTAAGAAGCTTAAAT
15863121 TTTTTTTTCAACTTTTAA
1 TTTTTTTTCAACTTTTAA
15863139 AGGGCTCAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 17 0.43
30 23 0.57
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.58
Consensus pattern (29 bp):
TTTTTTTTCAACTTTTAAGAAGCTTAAAT
Found at i:15871667 original size:20 final size:21
Alignment explanation
Indices: 15871638--15871691 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
15871628 AAAATTTGAT
* *
15871638 AAATACATAAATA-TTTTAAA
1 AAATATATAAATACATTTAAA
15871658 AAATATAT-AATACATTTAAA
1 AAATATATAAATACATTTAAA
* *
15871678 ATATATAAAAATAC
1 AAATATATAAATAC
15871692 CCCACCTCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 19 0.68
21 5 0.18
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATATATAAATACATTTAAA
Found at i:15872722 original size:93 final size:94
Alignment explanation
Indices: 15872612--15872801 Score: 280
Period size: 93 Copynumber: 2.0 Consensus size: 94
15872602 AAGTGTGTGA
15872612 AAATGGGTTTAGATTTTTTTCAATT-AAGATTTAAGG-TTTAAAAATTTTAATTAATTAAATCTA
1 AAATGGGTTTAGATTTTTTTCAATTAAAG-TTT-AGGATTTAAAAATTTTAATTAATTAAATCTA
*
15872675 TTTAATTA-AAATTTTATTTTCATTACA-TTG
64 TTTAATTACAAA-TTTATTCTCATTACATTTG
* *
15872705 AAATGGGTTTAGGTTTTTTTCAATTAAAGTTTAGGATTTAAAAATTTTAATTAATTAAATTTATT
1 AAATGGGTTTAGATTTTTTTCAATTAAAGTTTAGGATTTAAAAATTTTAATTAATTAAATCTATT
* *
15872770 TAATTACAGATTTATTCTCATTCCATTTG
66 TAATTACAAATTTATTCTCATTACATTTG
15872799 AAA
1 AAA
15872802 ATCTAAGTTG
Statistics
Matches: 88, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
92 3 0.03
93 74 0.84
94 11 0.12
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.48
Consensus pattern (94 bp):
AAATGGGTTTAGATTTTTTTCAATTAAAGTTTAGGATTTAAAAATTTTAATTAATTAAATCTATT
TAATTACAAATTTATTCTCATTACATTTG
Found at i:15873062 original size:15 final size:16
Alignment explanation
Indices: 15873006--15873062 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
15872996 TTTTTATTTG
15873006 TATATATTTTTAGATT
1 TATATATTTTTAGATT
* **
15873022 TATTATATTTTTTGAAAA
1 TA-TATATTTTTAG-ATT
15873040 TATATATTTTTAGATT
1 TATATATTTTTAGATT
15873056 TAT-TATT
1 TATATATT
15873063 ATACTGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
15 4 0.12
16 6 0.18
17 20 0.61
18 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (16 bp):
TATATATTTTTAGATT
Found at i:15885866 original size:12 final size:11
Alignment explanation
Indices: 15885849--15885882 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
15885839 GGGTGAAATA
15885849 TTTTTTATAAGT
1 TTTTTTATAA-T
15885861 TTTTTTATATAT
1 TTTTTTATA-AT
15885873 TTTTTTATAA
1 TTTTTTATAA
15885883 AATTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 19 0.90
13 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (11 bp):
TTTTTTATAAT
Found at i:15886488 original size:1 final size:1
Alignment explanation
Indices: 15886482--15886510 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
15886472 ACAAATGGCG
15886482 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
15886511 AATCTTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:15897094 original size:2 final size:2
Alignment explanation
Indices: 15897087--15897129 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
15897077 TGCTCCTGTG
15897087 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
15897129 T
1 T
15897130 TTGAGAACCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:15902264 original size:23 final size:26
Alignment explanation
Indices: 15902219--15902270 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 26
15902209 TATAGGAGCC
* *
15902219 TTTAATATTTTATTAGTTCTAAATAA
1 TTTAATATTATATTAGTTCTAAAAAA
15902245 TTTAA-ATTATATTA-TT-TAAAAAA
1 TTTAATATTATATTAGTTCTAAAAAA
15902268 TTT
1 TTT
15902271 TCTTATGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
24 2 0.08
25 8 0.33
26 5 0.21
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
TTTAATATTATATTAGTTCTAAAAAA
Found at i:15906044 original size:139 final size:139
Alignment explanation
Indices: 15905773--15906193 Score: 763
Period size: 139 Copynumber: 3.0 Consensus size: 139
15905763 GTCATCATCC
* *
15905773 ATTGCCATTCTGTTAGGATACTTTGTTGATTCTGTTTTTTTGTTCTAGGAGGTTCAATGTGTTGC
1 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
* * *
15905838 T-GTTGTACAAATATTATGTTGCTTCCGATTTTGCACAACCATGTTTGTAGAAACTGTGTTTTGA
66 TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
15905902 GACCCAAAT
131 GACCCAAAT
*
15905911 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGGGGTTCAATGTGTTGC
1 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
15905976 TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
66 TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
15906041 GACCCAAAT
131 GACCCAAAT
* *
15906050 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTATTCTAAGAGGTTCAATGTGTTGC
1 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
15906115 TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
66 TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
15906180 GACCCAAAT
131 GACCCAAAT
15906189 ATTGA
1 ATTGA
15906194 GTGTTGCTTA
Statistics
Matches: 273, Mismatches: 9, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
138 63 0.23
139 210 0.77
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.42
Consensus pattern (139 bp):
ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
GACCCAAAT
Found at i:15907050 original size:25 final size:25
Alignment explanation
Indices: 15907016--15907064 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
15907006 AAAGTATATT
15907016 AGTTTAGGATTAAGAAATAAGACTC
1 AGTTTAGGATTAAGAAATAAGACTC
15907041 AGTTTAGGATTAAGAAATAAGACT
1 AGTTTAGGATTAAGAAATAAGACT
15907065 ACAAGTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.29
Consensus pattern (25 bp):
AGTTTAGGATTAAGAAATAAGACTC
Found at i:15911155 original size:57 final size:56
Alignment explanation
Indices: 15911018--15911162 Score: 170
Period size: 57 Copynumber: 2.5 Consensus size: 56
15911008 ATATATTATA
* *
15911018 ATTTTTACT-AATTCATATTTTAATAATAATTATATTACAAATATTATTAAATTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTACAAATATTAATAAATTACAT
* *
15911075 ATTATTTTATTAAATTGTATTTAATAATAATTATGTTA-AATATAATTAAATAAATTA-AT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTACAA-AT-ATT-AATAAATTACAT
15911134 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
15911163 CATTAAAATT
Statistics
Matches: 77, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
57 29 0.38
58 22 0.29
59 14 0.18
60 12 0.16
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (56 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTACAAATATTAATAAATTACAT
Found at i:15911158 original size:31 final size:31
Alignment explanation
Indices: 15911065--15911158 Score: 74
Period size: 31 Copynumber: 3.1 Consensus size: 31
15911055 CAAATATTAT
*
15911065 TAAATTACATATTATTTTATTAAATTGTATTTAA
1 TAAATTA-ATA-T-TTTTATTAAATTATATTTAA
* * *
15911099 T-AA-T-A-A-TTATGTTAAA-TATAATTAAA
1 TAAATTAATATTTTTATTAAATTAT-ATTTAA
15911125 TAAATTAATATTTTTATTAAATTATATTTAA
1 TAAATTAATATTTTTATTAAATTATATTTAA
15911156 TAA
1 TAA
15911159 TAATCATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 17
0.66 0.10 0.24
Matches are distributed among these distances:
25 2 0.04
26 14 0.30
27 2 0.04
28 1 0.02
29 2 0.04
30 2 0.04
31 16 0.35
32 4 0.09
33 2 0.04
34 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (31 bp):
TAAATTAATATTTTTATTAAATTATATTTAA
Found at i:15911159 original size:26 final size:26
Alignment explanation
Indices: 15911079--15911160 Score: 67
Period size: 26 Copynumber: 3.0 Consensus size: 26
15911069 TTACATATTA
*
15911079 TTTTATTAAATTGTATTTAATAATAAT
1 TTTTATTAAATTATATTTAATAAT-AT
* * *
15911106 TATGTTAAATATAATTA-AATAAATTAATAT
1 T-T-TT-ATTA-AATTATATTTAA-TAATAT
15911136 TTTTATTAAATTATATTTAATAATA
1 TTTTATTAAATTATATTTAATAATA
15911161 ATCATTAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
26 10 0.24
27 8 0.19
28 3 0.07
29 3 0.07
30 10 0.24
31 8 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTTATTAAATTATATTTAATAATAT
Found at i:15911184 original size:57 final size:60
Alignment explanation
Indices: 15911065--15911184 Score: 158
Period size: 57 Copynumber: 2.0 Consensus size: 60
15911055 CAAATATTAT
* * * *
15911065 TAAATTACATATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAATATAATTAAA
1 TAAATTACATATTATTTTATTAAATTATATTTAATAATAATCATGTAAAATATAATAAAA
*
15911125 TAAATTA-ATA-T-TTTTATTAAATTATATTTAATAATAATCAT-TAAAATTTAATAACAA
1 TAAATTACATATTATTTTATTAAATTATATTTAATAATAATCATGTAAAATATAATAA-AA
15911182 TAA
1 TAA
15911185 TCATCTAACT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
56 10 0.19
57 33 0.61
58 1 0.02
59 3 0.06
60 7 0.13
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.47
Consensus pattern (60 bp):
TAAATTACATATTATTTTATTAAATTATATTTAATAATAATCATGTAAAATATAATAAAA
Found at i:15911353 original size:16 final size:16
Alignment explanation
Indices: 15911332--15911371 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
15911322 TGAATTACTG
15911332 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
15911348 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
15911364 ATTACAGC
1 ATTACAGC
15911372 GAACCAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:15926585 original size:13 final size:13
Alignment explanation
Indices: 15926567--15926622 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
15926557 TATTTAATAG
15926567 TTTTATACAATTT
1 TTTTATACAATTT
**
15926580 TTTTATTGAATTT
1 TTTTATACAATTT
* *
15926593 TTTTATATAGTTT
1 TTTTATACAATTT
*
15926606 ATCTTA-ACAATTT
1 -TTTTATACAATTT
15926619 TTTT
1 TTTT
15926623 TAATGTTTAC
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
12 3 0.09
13 26 0.79
14 4 0.12
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTATACAATTT
Found at i:15928705 original size:17 final size:17
Alignment explanation
Indices: 15928673--15928706 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15928663 TTTATTTTTC
* *
15928673 TAGAAAGATATTTTCCT
1 TAGAAAGAAATGTTCCT
15928690 TAGAAAGAAATGTTCCT
1 TAGAAAGAAATGTTCCT
15928707 GATTTGATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (17 bp):
TAGAAAGAAATGTTCCT
Found at i:15937479 original size:4 final size:4
Alignment explanation
Indices: 15937470--15937495 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
15937460 TTTTATTGCA
15937470 AGGC AGGC AGGC AGGC AGGC AGGC AG
1 AGGC AGGC AGGC AGGC AGGC AGGC AG
15937496 TCAGTCGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.50, T:0.00
Consensus pattern (4 bp):
AGGC
Found at i:15959718 original size:67 final size:67
Alignment explanation
Indices: 15959610--15959747 Score: 276
Period size: 67 Copynumber: 2.1 Consensus size: 67
15959600 GTTTATAATG
15959610 TAAAAAAAGAAGAGATAGCACTGGACAGGTGTCAAAAGAAGGAAGGGTTATAGATAATAAAAAAG
1 TAAAAAAAGAAGAGATAGCACTGGACAGGTGTCAAAAGAAGGAAGGGTTATAGATAATAAAAAAG
15959675 AT
66 AT
15959677 TAAAAAAAGAAGAGATAGCACTGGACAGGTGTCAAAAGAAGGAAGGGTTATAGATAATAAAAAAG
1 TAAAAAAAGAAGAGATAGCACTGGACAGGTGTCAAAAGAAGGAAGGGTTATAGATAATAAAAAAG
15959742 AT
66 AT
15959744 TAAA
1 TAAA
15959748 CTACATAAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 71 1.00
ACGTcount: A:0.53, C:0.06, G:0.25, T:0.17
Consensus pattern (67 bp):
TAAAAAAAGAAGAGATAGCACTGGACAGGTGTCAAAAGAAGGAAGGGTTATAGATAATAAAAAAG
AT
Found at i:15960092 original size:24 final size:24
Alignment explanation
Indices: 15960046--15960095 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
15960036 ATACATAAAT
***
15960046 ATTTAAAAATATATATCGTAATAA
1 ATTTAAAAATATATATAAAAATAA
*
15960070 ATTTAAAAATATATGTAAAAATAA
1 ATTTAAAAATATATATAAAAATAA
15960094 AT
1 AT
15960096 AAATAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (24 bp):
ATTTAAAAATATATATAAAAATAA
Found at i:15960690 original size:19 final size:19
Alignment explanation
Indices: 15960668--15960704 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15960658 TATTTTAAAA
*
15960668 ATATTTATGTATTTTTTAT
1 ATATTTATGAATTTTTTAT
*
15960687 ATATTTTTGAATTTTTTA
1 ATATTTATGAATTTTTTA
15960705 AAATTAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
ATATTTATGAATTTTTTAT
Found at i:15960789 original size:51 final size:50
Alignment explanation
Indices: 15960696--15960798 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
15960686 TATATTTTTG
* * *
15960696 AATTTTTTAAAATTAAGATAAATTGAAATTATTTGTAAATTTTGAGGTTT
1 AATTTTTTAAAATTAAGATAAATTGAAATAATATGTAAATTTTGAGGGTT
* * *
15960746 AATTTTTTAAAATTATGACTACATT-AATATAATATGTAAATTTTTAGGGTT
1 AATTTTTTAAAATTAAGA-TAAATTGAA-ATAATATGTAAATTTTGAGGGTT
15960797 AA
1 AA
15960799 AGGTGTTACT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
50 19 0.42
51 26 0.58
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.47
Consensus pattern (50 bp):
AATTTTTTAAAATTAAGATAAATTGAAATAATATGTAAATTTTGAGGGTT
Found at i:15965638 original size:32 final size:31
Alignment explanation
Indices: 15965602--15965664 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
15965592 ATGATAGAGC
*
15965602 ATAAAAAAATTGATGGTTCAGTCTTTATCATT
1 ATAAAAAAATTAATGGTTCAGTC-TTATCATT
**
15965634 ATAAAAATGTTAATGGTTCAGTCTTATCATT
1 ATAAAAAAATTAATGGTTCAGTCTTATCATT
15965665 GTAATTCATC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 8 0.29
32 20 0.71
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.41
Consensus pattern (31 bp):
ATAAAAAAATTAATGGTTCAGTCTTATCATT
Found at i:15976273 original size:12 final size:12
Alignment explanation
Indices: 15976256--15976282 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
15976246 AAAAAATTAT
15976256 TTTAATTTTTCA
1 TTTAATTTTTCA
15976268 TTTAATTTTTCA
1 TTTAATTTTTCA
15976280 TTT
1 TTT
15976283 CTTTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTAATTTTTCA
Found at i:15977856 original size:18 final size:18
Alignment explanation
Indices: 15977818--15977856 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
15977808 GGTACTTGAA
*
15977818 TTTGATATTTTTTTTTAT
1 TTTGATATTTATTTTTAT
15977836 TTTGATATTTAATTTTT-T
1 TTTGATATTT-ATTTTTAT
15977854 TTT
1 TTT
15977857 CAATTTGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTGATATTTATTTTTAT
Found at i:15977871 original size:24 final size:23
Alignment explanation
Indices: 15977824--15977871 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
15977814 TGAATTTGAT
* *
15977824 ATTTTTTTTTATTTTGATATTTA
1 ATTTTTTTTTAATTTGATACTTA
*
15977847 ATTTTTTTTTCAATTTGGTACTTA
1 ATTTTTTTTT-AATTTGATACTTA
15977871 A
1 A
15977872 ACTTGACACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.67
Consensus pattern (23 bp):
ATTTTTTTTTAATTTGATACTTA
Found at i:15977895 original size:31 final size:28
Alignment explanation
Indices: 15977851--15977934 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 28
15977841 TATTTAATTT
15977851 TTTTTTCAATTTGGTACTTAAACTTGACA
1 TTTTTT-AATTTGGTACTTAAACTTGACA
* *
15977880 CTTTCTCTTATTTTGGTA-TCTAAGCTTGACA
1 -TTT-T-TTAATTTGGTACT-TAAACTTGACA
*
15977911 TTTTTTAAGTTGGTACTTAAACTT
1 TTTTTTAATTTGGTACTTAAACTT
15977935 TTTGGGTCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
28 15 0.33
29 2 0.04
30 7 0.16
31 19 0.42
32 2 0.04
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (28 bp):
TTTTTTAATTTGGTACTTAAACTTGACA
Found at i:15980392 original size:2 final size:2
Alignment explanation
Indices: 15980385--15980454 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
15980375 CTCATCTCAA
15980385 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
15980427 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
15980455 AGTATATATA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:15991713 original size:23 final size:22
Alignment explanation
Indices: 15991687--15991810 Score: 102
Period size: 23 Copynumber: 5.8 Consensus size: 22
15991677 CTTATAAAAA
15991687 TAATTAAAAATAAAAAAACACAT
1 TAATTAAAAATAAAAAAA-ACAT
*
15991710 TAATTAAAAATAAAAATAAC--
1 TAATTAAAAATAAAAAAAACAT
*
15991730 TAA--AAAAATATAATCAAAACAT
1 TAATTAAAAATA-AA-AAAAACAT
*
15991752 TAATTAAAAATAAAAATAAC--
1 TAATTAAAAATAAAAAAAACAT
* *
15991772 TAA--AAAAATATAATCAAAATAT
1 TAATTAAAAATA-AA-AAAAACAT
15991794 TAATTAAAAATAAAAAA
1 TAATTAAAAATAAAAAA
15991811 GTTTGAAACA
Statistics
Matches: 80, Mismatches: 9, Indels: 25
0.70 0.08 0.22
Matches are distributed among these distances:
18 14 0.17
19 4 0.05
20 13 0.16
22 14 0.17
23 21 0.26
24 14 0.17
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (22 bp):
TAATTAAAAATAAAAAAAACAT
Found at i:15991824 original size:42 final size:42
Alignment explanation
Indices: 15991706--15991809 Score: 199
Period size: 42 Copynumber: 2.5 Consensus size: 42
15991696 ATAAAAAAAC
15991706 ACATTAATTAAAAATAAAAATAACTAAAAAAATATAATCAAA
1 ACATTAATTAAAAATAAAAATAACTAAAAAAATATAATCAAA
15991748 ACATTAATTAAAAATAAAAATAACTAAAAAAATATAATCAAA
1 ACATTAATTAAAAATAAAAATAACTAAAAAAATATAATCAAA
*
15991790 ATATTAATTAAAAATAAAAA
1 ACATTAATTAAAAATAAAAA
15991810 AGTTTGAAAC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (42 bp):
ACATTAATTAAAAATAAAAATAACTAAAAAAATATAATCAAA
Done.