Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 145 of 190
Found at i:42735535 original size:459 final size:454
Alignment explanation
Indices: 42734677--42736069 Score: 1936
Period size: 459 Copynumber: 3.0 Consensus size: 454
42734667 TATTTTTCAA
* *
42734677 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT-CATGCCGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCATGCTGAGGTA--T-TTTTAA
* *
42734741 ATTTCTGTTTTTT--TAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT--CACGCTG
63 ATTTCT-TTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTG
* * **
42734802 AGGTATTTTTTTAATTTCTATTTTTTTCAAAAATCAACTCATAATATGAGAGGTGAGTTGAGCCT
127 AGGTA--TTTTAAATTTCTA-TTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* * *
42734867 CGGGT--CACGCTGAGGTATTTTTCTAATTTCTGTTTTTTCAAAAATCAACTCATAATACGAGAG
189 CGGGTCGCACGCTGAGGTATTTTT-AAATTTC--TTTTTTCAAAAATCAACTCATATTGCGAGAG
* *
42734930 GTGAGTTGAGCCTCGGGT--CACGCTGAGGTATTTTTTTTAAAATTTCTATTTTTTAAAAATCAA
251 GTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTTTTT-AAATTTCT-GTTTTCAAAAATCAA
*
42734993 CTCATAATGCGAGA-AGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTAAATTTCTGTTTT
313 CTCATATTGCGAGAGA-TGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTAAATTTCTGTTTT
42735057 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCGCACGCTGAGGTATTTTAA
377 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-GTCGCACGCTGAGGTATTTTAA
42735122 ATTTCTGTTTTTTC
441 ATTTCTGTTTTTTC
*
42735136 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTTAAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CATGCTGAGGTATTTTTAAAT
* *
42735200 TTCTATTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGTTGAG
65 TTCT-TTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
*
42735265 GTATTTTAAATTTTTATTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
129 GTATTTTAAATTTCTATTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
42735330 CGCACGCTGAGGTATTTTTAAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGT
194 CGCACGCTGAGGTATTTTTAAATTTCT-TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGT
42735395 TGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAATTTCTGTTTTCAAAAATCAACTCATATT
257 TGAGCCTCGGGTCGCACGCTGAGGTATTT-TTTTAAATTTCTGTTTTCAAAAATCAACTCATATT
42735460 GCGAGAGATGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTAAATTTCTG-TTTTTCAAAAAA
321 GCGAGAGATGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTAAATTTCTGTTTTTTC-AAAAA
*
42735524 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCCGGT--CACGCTGAGGTATTTTAAA-TTAT-T
385 TCAACTCATATTGCGAGAGGTGAGTTGAGCCT-CGGTCGCACGCTGAGGTATTTTAAATTTCTGT
42735585 TTTTT-
449 TTTTTC
* * *
42735590 --AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-CGACACATGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CATGCTGAGGTA--T-TTTTA
* * *
42735652 AATTTCTGTTTTTCAAAAATCAACTCATAATGTGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTG
62 AATTTCTTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTG
42735717 AGGTATTTTAAATTTCTATTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
127 AGGTATTTTAAATTTCTATTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
* * * *
42735782 GTCGCACGCTGAGGTATTTTTTTTGAATTTCTGTTTTCAAATATCAACTCATATTGTGAGAGGTG
192 GTCGCACGCTGAGGTA---TTTTTAAATTTCTTTTTTCAAAAATCAACTCATATTGCGAGAGGTG
*
42735847 AGTTGAGCCTCGGGTCGCACGCTGAGGTA---TTTTAAATTTCTGTTTTTCAAAAAATCAACTTA
254 AGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTAAATTTCTG-TTTTC-AAAAATCAACTCA
* * *
42735909 TATTGCGAGAGGTGAGTTGAGGCTCGGGTCGTACGCTGAGGTATTTTTTTTAAATTTCTGCTTTT
317 TATTGCGAGAGATGAGTTGAGCCTCGGGTCGCACGCTGAGGTA----TTTTAAATTTCTG--TTT
42735974 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCT
376 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCGCACGCTGAGGTA----T
42736039 TTTAAATTTCTG--TTTTC
436 TTTAAATTTCTGTTTTTTC
42736056 AAAAATCAACTCAT
1 AAAAATCAACTCAT
42736070 NNNNNNNNNN
Statistics
Matches: 850, Mismatches: 40, Indels: 79
0.88 0.04 0.08
Matches are distributed among these distances:
451 26 0.03
452 40 0.05
453 52 0.06
454 133 0.16
455 72 0.08
456 8 0.01
457 63 0.07
458 59 0.07
459 285 0.34
460 37 0.04
461 49 0.06
465 11 0.01
466 3 0.00
468 12 0.01
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (454 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCATGCTGAGGTATTTTTAAATT
TCTTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGT
ATTTTAAATTTCTATTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCG
CACGCTGAGGTATTTTTAAATTTCTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
CCTCGGGTCGCACGCTGAGGTATTTTTTTAAATTTCTGTTTTCAAAAATCAACTCATATTGCGAG
AGATGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTAAATTTCTGTTTTTTCAAAAATCAACT
CATATTGCGAGAGGTGAGTTGAGCCTCGGTCGCACGCTGAGGTATTTTAAATTTCTGTTTTTTC
Found at i:42736441 original size:77 final size:77
Alignment explanation
Indices: 42736170--42736731 Score: 664
Period size: 78 Copynumber: 7.3 Consensus size: 77
42736160 NNNNNNNNNN
* * * *
42736170 AGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGGTATTTCTTTTAAATTTATGATTTTCCAAAAA
1 AGAGGTGAGTTGAGCCTC-GGAC-CATGCCGAGGTATTTCTTTTAAATTTCTG-TTTTTCAAAAA
42736235 TCAACTCATATTGCG
63 TCAACTCATATTGCG
*
42736250 AGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATTTATGTTTTTCAAAAAAAT
1 AGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATTTCTGTTTTTC--AAAAAT
42736315 CAACTCATATTGCG
64 CAACTCATATTGCG
* *
42736329 AGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATTTCTATTTTTCAAAACTCA
1 AGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCA
*
42736394 ACTTATATTGCG
66 ACTCATATTGCG
* *
42736406 AGAGGTGAGTTGAGCCTTGGACTATGCCGAGGTATTTCTTTTAAA-TTCATGTTTTTCAAAAATC
1 AGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATTTC-TGTTTTTCAAAAATC
42736470 AACTCATATTGCG
65 AACTCATATTGCG
* *
42736483 AGAGGTGAGTTGAGCCTCGGACACATGCCCAAGTATTTCTTTTAAATTTCTGTTTTTCAAAAATC
1 AGAGGTGAGTTGAGCCTCGGAC-CATGCCGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATC
*
42736548 AACTCATAATGCG
65 AACTCATATTGCG
* * * *
42736561 AGAGGTGAGTTGAGCATTGGGTCACAT-CCTGAGGTA--T-TTTTCAATTTCTGTTTTTTCAAAA
1 AGAGGTGAGTTGAGC-CTCGGAC-CATGCC-GAGGTATTTCTTTTAAATTTCTG-TTTTTC-AAA
*
42736622 AATCAACTCATATTTCG
61 AATCAACTCATATTGCG
* * * *
42736639 AGAGGTGAGTTGAGCATCAGGTAACAT-CCTGAGGTA--T-TTTTCAATATCTAG-TTTTCAAAA
1 AGAGGTGAGTTGAGCCTC-GG-ACCATGCC-GAGGTATTTCTTTTAAATTTCT-GTTTTTCAAAA
*
42736699 ATCAA--C-TATTACG
62 ATCAACTCATATTGCG
* *
42736712 ATAGGTGAGTTAAGCCTCGG
1 AGAGGTGAGTTGAGCCTCGG
42736732 GTCGCACGCC
Statistics
Matches: 436, Mismatches: 34, Indels: 32
0.87 0.07 0.06
Matches are distributed among these distances:
72 2 0.00
73 21 0.05
74 1 0.00
76 24 0.06
77 125 0.29
78 151 0.35
79 94 0.22
80 18 0.04
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (77 bp):
AGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCA
ACTCATATTGCG
Found at i:42737032 original size:30 final size:30
Alignment explanation
Indices: 42736944--42737061 Score: 134
Period size: 29 Copynumber: 4.0 Consensus size: 30
42736934 TTTATTTTTG
*
42736944 CATTTTGACCCCTAAACTTTCT-CAAATTA
1 CATTTTGACCCCTAAACTTTCTAAAAATTA
** * *
42736973 CATTTCAACCTCTAAACTTT-TATAAATTA
1 CATTTTGACCCCTAAACTTTCTAAAAATTA
42737002 CATTTTGACCCCTAAACTTTCTAAAAATTA
1 CATTTTGACCCCTAAACTTTCTAAAAATTA
* * *
42737032 CATTTGGACCCTTGAACTTTC-ACAAAATTA
1 CATTTTGACCCCTAAACTTTCTA-AAAATTA
42737062 TGTTTCGGCC
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
28 1 0.01
29 41 0.55
30 33 0.44
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTCTAAAAATTA
Found at i:42737445 original size:10 final size:10
Alignment explanation
Indices: 42737406--42737472 Score: 55
Period size: 10 Copynumber: 6.4 Consensus size: 10
42737396 CCAAGAGGCA
42737406 AAAAAAGAA-
1 AAAAAAGAAG
*
42737415 AAAAAACAAG
1 AAAAAAGAAG
*
42737425 CAAGCAAAAGAGG
1 -AA--AAAAGAAG
42737438 AAAAAAGAAAG
1 AAAAAAG-AAG
**
42737449 AGTAAAGAAG
1 AAAAAAGAAG
42737459 AAAAAAGAAG
1 AAAAAAGAAG
42737469 AAAA
1 AAAA
42737473 GAGAGGAGAG
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
9 8 0.18
10 20 0.44
11 9 0.20
12 2 0.04
13 6 0.13
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.01
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:42737596 original size:4 final size:4
Alignment explanation
Indices: 42737581--42737672 Score: 100
Period size: 4 Copynumber: 22.8 Consensus size: 4
42737571 AAAAGGGAAG
*
42737581 AAGA ATGA AAGA AAGA AAGA AAGA AAGA AAGA AAG- AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
* *
42737628 AAAA GAAGAA AAGGA AAGA AA-A AAGA AA-A AAGAA AAAA AAGA AAG
1 AAGA -AAG-A AA-GA AAGA AAGA AAGA AAGA AAG-A AAGA AAGA AAG
42737673 GAAAAAAATA
Statistics
Matches: 75, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
3 9 0.12
4 54 0.72
5 10 0.13
6 2 0.03
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (4 bp):
AAGA
Found at i:42737619 original size:27 final size:26
Alignment explanation
Indices: 42737588--42737672 Score: 110
Period size: 23 Copynumber: 3.5 Consensus size: 26
42737578 AAGAAGAATG
42737588 AAAGAAAGAAAGAAAGAAAGAAAGAA
1 AAAGAAAGAAAGAAAGAAAGAAAGAA
42737614 AGAAGAAAGAAAG-AA-AAAG-AAGAA
1 A-AAGAAAGAAAGAAAGAAAGAAAGAA
*
42737638 AAGGAAAGAAA-AAAGAAA-AAAGAA
1 AAAGAAAGAAAGAAAGAAAGAAAGAA
42737662 AAA-AAAGAAAG
1 AAAGAAAGAAAG
42737673 GAAAAAAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
23 18 0.35
24 16 0.31
25 4 0.08
26 3 0.06
27 11 0.21
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (26 bp):
AAAGAAAGAAAGAAAGAAAGAAAGAA
Found at i:42737677 original size:27 final size:29
Alignment explanation
Indices: 42737589--42737679 Score: 73
Period size: 30 Copynumber: 3.1 Consensus size: 29
42737579 AGAAGAATGA
*
42737589 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAGA
1 AAGAAAG-AAGAAAGAAAGAAA-AAAGAAAA
42737620 AAGAAAGAA-AAAG-AAGAAAAGGAAAGAAAA
1 AAGAAAGAAGAAAGAAAG-AAA--AAAGAAAA
* *
42737650 AAGAAAAAAGAAA-AAA-AAGAAAGGAAAA
1 AAGAAAGAAGAAAGAAAGAA-AAAAGAAAA
42737678 AA
1 AA
42737680 ATATTCTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
28 12 0.23
29 9 0.17
30 19 0.37
31 12 0.23
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (29 bp):
AAGAAAGAAGAAAGAAAGAAAAAAGAAAA
Found at i:42737720 original size:10 final size:11
Alignment explanation
Indices: 42737705--42737733 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
42737695 TCGGGTTAAA
42737705 CCGACCCGAC-
1 CCGACCCGACT
42737715 CCGACCCGACT
1 CCGACCCGACT
42737726 CCGACCCG
1 CCGACCCG
42737734 TGACCGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.17, C:0.59, G:0.21, T:0.03
Consensus pattern (11 bp):
CCGACCCGACT
Found at i:42738035 original size:15 final size:16
Alignment explanation
Indices: 42738002--42738037 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
42737992 AAATATTCTA
42738002 AAATTCTCGTGATTTTT
1 AAATTCTCGTGA-TTTT
42738019 AAATTCTCGTG-TTTT
1 AAATTCTCGTGATTTT
42738034 AAAT
1 AAAT
42738038 AGAATCACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
17 11 0.58
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (16 bp):
AAATTCTCGTGATTTT
Found at i:42738262 original size:21 final size:21
Alignment explanation
Indices: 42738236--42738336 Score: 76
Period size: 21 Copynumber: 5.1 Consensus size: 21
42738226 TCGTATTTCG
42738236 AAAATTTTCTTGTTTTCAAAA
1 AAAATTTTCTTGTTTTCAAAA
*
42738257 AAAATTTTC-CGTGTTTC---A
1 AAAATTTTCTTGT-TTTCAAAA
*
42738275 TAAA-TTTCTGTGTTTTCAAAA
1 AAAATTTTCT-TGTTTTCAAAA
*
42738296 AAAA-TTTCTCGTCTTTC---A
1 AAAATTTTCTTGT-TTTCAAAA
*
42738314 AAAATTTTCGTGTTTTCAAAA
1 AAAATTTTCTTGTTTTCAAAA
42738335 AA
1 AA
42738337 TTGACCGTGT
Statistics
Matches: 62, Mismatches: 7, Indels: 22
0.68 0.08 0.24
Matches are distributed among these distances:
17 4 0.06
18 17 0.27
19 8 0.13
20 4 0.06
21 29 0.47
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.45
Consensus pattern (21 bp):
AAAATTTTCTTGTTTTCAAAA
Found at i:42738274 original size:56 final size:56
Alignment explanation
Indices: 42738153--42738297 Score: 150
Period size: 56 Copynumber: 2.6 Consensus size: 56
42738143 TAAAAAAAAT
* * *
42738153 CGTGTGTCAAAAATTTTCGTGTTTTAAAAAATTTTCATGTTTTCAAAAAAATTCCC
1 CGTGTTTCAAAAATTCTCGTGATTTAAAAAATTTTCATGTTTTCAAAAAAATTCCC
** * **
42738209 CGTGTTTTCAAAAATTCTCGT-ATTTCGAAAATTTTCTTGTTTTCAAAAAAAATTTTC
1 CGTG-TTTCAAAAATTCTCGTGATTTAAAAAATTTTCATGTTTTC-AAAAAAATTCCC
* *
42738266 CGTGTTTCATAAATT-TCTGTGTTTTCAAAAAA
1 CGTGTTTCAAAAATTCTC-GTGATTT-AAAAAA
42738298 AATTTCTCGT
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
55 2 0.03
56 35 0.49
57 31 0.43
58 4 0.06
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.43
Consensus pattern (56 bp):
CGTGTTTCAAAAATTCTCGTGATTTAAAAAATTTTCATGTTTTCAAAAAAATTCCC
Found at i:42738290 original size:39 final size:39
Alignment explanation
Indices: 42738237--42738458 Score: 181
Period size: 39 Copynumber: 5.6 Consensus size: 39
42738227 CGTATTTCGA
*
42738237 AAATTTTCTTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
1 AAATTTTCGTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
* *
42738276 AAA-TTTCTGTGTTTTCAAAAAAAA-TTTCTCGTCTTTCAA
1 AAATTTTC-GTGTTTTCAAAAAAAATTTTC-CGTGTTTCAT
**
42738315 AAATTTTCGTGTTTTC--AAAAAATTGACCGTGTTTCAT
1 AAATTTTCGTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
* * *
42738352 AAATTTTCGTG-TTTCAAAAAAAATCCTCGTGTTTCGTATTTTAT
1 AAATTTTCGTGTTTTCAAAAAAAA---T--T-TTCCGTGTTTCAT
** * *
42738396 CAATATTTTTATGTTTTCAAAAACAAATTTT--GTGTTTTAA
1 -AA-ATTTTCGTGTTTTCAAAAA-AAATTTTCCGTGTTTCAT
42738436 AAATTTTCGTG-TTTCAAAAAAAA
1 AAATTTTCGTGTTTTCAAAAAAAA
42738459 ATTCGTGTTA
Statistics
Matches: 149, Mismatches: 18, Indels: 35
0.74 0.09 0.17
Matches are distributed among these distances:
36 7 0.05
37 34 0.23
38 23 0.15
39 39 0.26
40 11 0.07
41 1 0.01
42 2 0.01
43 2 0.01
44 8 0.05
45 3 0.02
46 7 0.05
47 9 0.06
48 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (39 bp):
AAATTTTCGTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
Found at i:42738324 original size:17 final size:17
Alignment explanation
Indices: 42738152--42738371 Score: 127
Period size: 18 Copynumber: 11.8 Consensus size: 17
42738142 TTAAAAAAAA
*
42738152 TCGTGTGTCAAAAATTT
1 TCGTGTTTCAAAAATTT
*
42738169 TCGTGTTTTAAAAAATTT
1 TCGTG-TTTCAAAAATTT
* *
42738187 TCATGTTTTCAAAAAAATTCC
1 TCGTG-TTTC--AAAAATT-T
* *
42738208 CCGTGTTTTCAAAAATTC
1 TCGTG-TTTCAAAAATTT
* *
42738226 TCGTATTTCGAAAATTT
1 TCGTGTTTCAAAAATTT
*
42738243 TCTTGTTTTCAAAAAAAATTT
1 TCGTG-TTTC---AAAAATTT
*
42738264 TCCGTGTTTCATAAA-TT
1 T-CGTGTTTCAAAAATTT
42738281 TCTGTGTTTTCAAAAAAAATTT
1 TC-GTG-TTTC---AAAAATTT
*
42738303 CTCGTCTTTCAAAAATTT
1 -TCGTGTTTCAAAAATTT
*
42738321 TCGTGTTTTCAAAAAATTGA
1 TCGTG-TTTC-AAAAATT-T
* *
42738341 CCGTGTTTCATAAATTT
1 TCGTGTTTCAAAAATTT
42738358 TCGTGTTTCAAAAA
1 TCGTGTTTCAAAAA
42738372 AAATCCTCGT
Statistics
Matches: 159, Mismatches: 25, Indels: 38
0.72 0.11 0.17
Matches are distributed among these distances:
16 1 0.01
17 40 0.25
18 52 0.33
19 18 0.11
20 11 0.07
21 28 0.18
22 7 0.04
23 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:42738354 original size:76 final size:76
Alignment explanation
Indices: 42738218--42738375 Score: 223
Period size: 78 Copynumber: 2.1 Consensus size: 76
42738208 CCGTGTTTTC
* * **
42738218 AAAAA-TTCTCGTATTTCGAAAATTTTCTTGTTTTCAAAAAAAATTTTCCGTGTTTCATAAA-TT
1 AAAAATTTCTCGTATTTCAAAAATTTTCGTGTTTTC-AAAAAAATTGACCGTGTTTCATAAATTT
42738281 TCTGTGTTTTCAAA
65 TC-GTG-TTTCAAA
*
42738295 AAAAATTTCTCGTCTTTCAAAAATTTTCGTGTTTTC-AAAAAATTGACCGTGTTTCATAAATTTT
1 AAAAATTTCTCGTATTTCAAAAATTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCATAAATTTT
42738359 CGTGTTTCAAA
66 CGTGTTTCAAA
42738370 AAAAAT
1 AAAAAT
42738376 CCTCGTGTTT
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
75 13 0.18
76 25 0.34
77 9 0.12
78 27 0.36
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (76 bp):
AAAAATTTCTCGTATTTCAAAAATTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCATAAATTTT
CGTGTTTCAAA
Found at i:42738383 original size:37 final size:38
Alignment explanation
Indices: 42738218--42738386 Score: 188
Period size: 39 Copynumber: 4.4 Consensus size: 38
42738208 CCGTGTTTTC
* *
42738218 AAAAATTCTCGTATTTCGA-AAATTTTCTTGTTTTCAAA
1 AAAAATTCTCGTGTTTC-ATAAATTTTCGTGTTTTCAAA
*
42738256 AAAAATTTTCCGTGTTTCATAAA-TTTCTGTGTTTTCAAA
1 AAAAATTCT-CGTGTTTCATAAATTTTC-GTGTTTTCAAA
* *
42738295 AAAAATTTCTCGTCTTTCAAAAATTTTCGTGTTTTC--A
1 AAAAA-TTCTCGTGTTTCATAAATTTTCGTGTTTTCAAA
42738332 AAAAATTGAC-CGTGTTTCATAAATTTTCGTG-TTTCAAA
1 AAAAATT--CTCGTGTTTCATAAATTTTCGTGTTTTCAAA
*
42738370 AAAAATCCTCGTGTTTC
1 AAAAATTCTCGTGTTTC
42738387 GTATTTTATC
Statistics
Matches: 112, Mismatches: 9, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
36 7 0.06
37 33 0.29
38 21 0.19
39 44 0.39
40 7 0.06
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (38 bp):
AAAAATTCTCGTGTTTCATAAATTTTCGTGTTTTCAAA
Found at i:42738441 original size:16 final size:17
Alignment explanation
Indices: 42738420--42738455 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
42738410 TTTCAAAAAC
*
42738420 AAATTTT-GTGTTTTAA
1 AAATTTTCGTGTTTCAA
42738436 AAATTTTCGTGTTTCAA
1 AAATTTTCGTGTTTCAA
42738453 AAA
1 AAA
42738456 AAAATTCGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:42739893 original size:29 final size:29
Alignment explanation
Indices: 42739855--42740190 Score: 473
Period size: 29 Copynumber: 11.7 Consensus size: 29
42739845 TCGGCTATTA
42739855 GGTTTTTAATTAAATTAAATTAGGGTTAG
1 GGTTTTTAATTAAATTAAATTAGGGTTAG
* ***
42739884 GGTTTTTAATTAAAATGGGTTAGGGTTAG
1 GGTTTTTAATTAAATTAAATTAGGGTTAG
* **
42739913 GGTTTTTAATCAAATTAGGTTAGGGTTTAG
1 GGTTTTTAATTAAATTAAATTAGGG-TTAG
42739943 GG-TTTTAATTAAATTAAATTAGGGTTAG
1 GGTTTTTAATTAAATTAAATTAGGGTTAG
* *** *
42739971 GGTTTTTAATTAAAATGGGTCAGGGTTAG
1 GGTTTTTAATTAAATTAAATTAGGGTTAG
42740000 GGTTTTTAATTAAATTAAATTAGGGTTAG
1 GGTTTTTAATTAAATTAAATTAGGGTTAG
42740029 GGTTTTTAATTAAATT-AATTAGGGTTAG
1 GGTTTTTAATTAAATTAAATTAGGGTTAG
* ***
42740057 GGTTTTTAATTAAAATGGGTTAGGGTTAG
1 GGTTTTTAATTAAATTAAATTAGGGTTAG
42740086 GGTTTTTAATTAAATTAAATTAGGGTT-G
1 GGTTTTTAATTAAATTAAATTAGGGTTAG
42740114 GGTTTTTAATTAAATTAAATTAGGGTTAG
1 GGTTTTTAATTAAATTAAATTAGGGTTAG
* *
42740143 GATTTTTAATTAAATTAAATTAGGGTTTG
1 GGTTTTTAATTAAATTAAATTAGGGTTAG
42740172 GGTTTTTAATTAAA-TAAAT
1 GGTTTTTAATTAAATTAAAT
42740191 ANNNNNNNNN
Statistics
Matches: 273, Mismatches: 30, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
28 66 0.24
29 201 0.74
30 6 0.02
ACGTcount: A:0.32, C:0.01, G:0.23, T:0.44
Consensus pattern (29 bp):
GGTTTTTAATTAAATTAAATTAGGGTTAG
Found at i:42740082 original size:86 final size:87
Alignment explanation
Indices: 42739855--42740190 Score: 545
Period size: 86 Copynumber: 3.9 Consensus size: 87
42739845 TCGGCTATTA
42739855 GGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAAATGGGTTAGGGTTAGGGTTTTT
1 GGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAAATGGGTTAGGGTTAGGGTTTTT
* **
42739920 AATCAAATTAGGTTAGGGTTTAG
66 AATTAAATTAAATTAGGG-TTAG
*
42739943 GG-TTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAAATGGGTCAGGGTTAGGGTTTTT
1 GGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAAATGGGTTAGGGTTAGGGTTTTT
42740007 AATTAAATTAAATTAGGGTTAG
66 AATTAAATTAAATTAGGGTTAG
42740029 GGTTTTTAATTAAATT-AATTAGGGTTAGGGTTTTTAATTAAAATGGGTTAGGGTTAGGGTTTTT
1 GGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAAATGGGTTAGGGTTAGGGTTTTT
42740093 AATTAAATTAAATTAGGGTT-G
66 AATTAAATTAAATTAGGGTTAG
* * *** *
42740114 GGTTTTTAATTAAATTAAATTAGGGTTAGGATTTTTAATTAAATTAAATTAGGGTTTGGGTTTTT
1 GGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAAATGGGTTAGGGTTAGGGTTTTT
42740179 AATTAAA-TAAAT
66 AATTAAATTAAAT
42740191 ANNNNNNNNN
Statistics
Matches: 235, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
85 22 0.09
86 122 0.52
87 89 0.38
88 2 0.01
ACGTcount: A:0.32, C:0.01, G:0.23, T:0.44
Consensus pattern (87 bp):
GGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAAATGGGTTAGGGTTAGGGTTTTT
AATTAAATTAAATTAGGGTTAG
Found at i:42740350 original size:28 final size:29
Alignment explanation
Indices: 42740292--42740366 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
42740282 NNNNNNNNNN
42740292 TAGGGTTTTTAATTAAATTAAATTAGGGT
1 TAGGGTTTTTAATTAAATTAAATTAGGGT
42740321 TAGGGTTTTTAATTAAATTAAATTA-GGT
1 TAGGGTTTTTAATTAAATTAAATTAGGGT
*
42740349 TAGGGTTTTTAATCAAAT
1 TAGGGTTTTTAATTAAAT
42740367 AATATCAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 20 0.44
29 25 0.56
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.45
Consensus pattern (29 bp):
TAGGGTTTTTAATTAAATTAAATTAGGGT
Found at i:42740678 original size:24 final size:24
Alignment explanation
Indices: 42740646--42740701 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
42740636 TGTATGTAGA
42740646 GGTGTTTGCATCATGAACGGCGAC
1 GGTGTTTGCATCATGAACGGCGAC
*
42740670 GGTGTTTGCATCATGAACGGCGAG
1 GGTGTTTGCATCATGAACGGCGAC
*
42740694 GGAGTTTG
1 GGTGTTTG
42740702 GAAGCCATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.16, G:0.38, T:0.27
Consensus pattern (24 bp):
GGTGTTTGCATCATGAACGGCGAC
Found at i:42742546 original size:14 final size:15
Alignment explanation
Indices: 42742529--42742562 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
42742519 AATAATTATC
42742529 TAAAAATA-CTTAAA
1 TAAAAATATCTTAAA
42742543 TAAAAATATCTTAAA
1 TAAAAATATCTTAAA
42742558 TAAAA
1 TAAAA
42742563 TTTAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAATATCTTAAA
Found at i:42742698 original size:28 final size:28
Alignment explanation
Indices: 42742660--42742716 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
42742650 TTGAAAATAT
42742660 TAAAAATTTTAAAATTAT-TTTAAAAAA
1 TAAAAATTTTAAAATTATCTTTAAAAAA
*
42742687 TAAAAATATTTAAAATTTTCTTTAAAAAA
1 TAAAAAT-TTTAAAATTATCTTTAAAAAA
42742716 T
1 T
42742717 GAAATTGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 7 0.26
28 10 0.37
29 10 0.37
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAAAATTTTAAAATTATCTTTAAAAAA
Found at i:42742778 original size:22 final size:21
Alignment explanation
Indices: 42742750--42742800 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
42742740 AAATATGGAT
*
42742750 TTGAGAGATTTTTTGAAGGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
*
42742772 TTGAGAGGATTTTGGAAGGAAT
1 TTGAGA-GATTTTGGAAGGAAA
42742794 TTGAGAG
1 TTGAGAG
42742801 TTTAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:42742823 original size:52 final size:52
Alignment explanation
Indices: 42742753--42742852 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
42742743 TATGGATTTG
* * * *
42742753 AGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAAGGAATTTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAGTTTA
42742805 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAG
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAG
42742853 AATATTTGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAGTTTA
Found at i:42742869 original size:24 final size:22
Alignment explanation
Indices: 42742805--42742860 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
42742795 TGAGAGTTTA
42742805 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
42742827 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
42742849 AGAGAATATTTG
1 AGAGAAT-TTTG
42742861 TTTGTGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.29
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:42743617 original size:34 final size:34
Alignment explanation
Indices: 42743574--42743639 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
42743564 AGTAAAATAT
*
42743574 TTTTCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACGGGAAAATATTTTAC
*
42743607 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACGGGAAAATATTTT
42743640 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:42745051 original size:15 final size:15
Alignment explanation
Indices: 42745027--42745062 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
42745017 ATTATAAAGG
42745027 AAGA-AAGAAAAAAA
1 AAGAGAAGAAAAAAA
42745041 AAGAGAAGAAAAAAA
1 AAGAGAAGAAAAAAA
*
42745056 GAGAGAA
1 AAGAGAA
42745063 ATAATGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAGAGAAGAAAAAAA
Found at i:42748701 original size:21 final size:21
Alignment explanation
Indices: 42748672--42748711 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42748662 TAATGTCATA
42748672 TCAGCATTTTCATCTTGAATT
1 TCAGCATTTTCATCTTGAATT
* *
42748693 TCAGTATTTTCATTTTGAA
1 TCAGCATTTTCATCTTGAA
42748712 AAAAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (21 bp):
TCAGCATTTTCATCTTGAATT
Found at i:42752392 original size:3 final size:3
Alignment explanation
Indices: 42752384--42752433 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
42752374 GTAACAACTT
*
42752384 TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42752432 TA
1 TA
42752434 TATTGTTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:42752905 original size:24 final size:24
Alignment explanation
Indices: 42752878--42752929 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
42752868 AATCAAATTC
* *
42752878 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
42752902 AAATATGTTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
42752926 AAAT
1 AAAT
42752930 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:42757287 original size:24 final size:24
Alignment explanation
Indices: 42757260--42757306 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
42757250 AAACCTAATT
42757260 CTAATCAAA-GTAAAATATATTATG
1 CTAAT-AAATGTAAAATATATTATG
*
42757284 CTAATAAATGTTAAATATATTAT
1 CTAATAAATGTAAAATATATTAT
42757307 ATTCATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (24 bp):
CTAATAAATGTAAAATATATTATG
Found at i:42757322 original size:24 final size:24
Alignment explanation
Indices: 42757272--42757323 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
42757262 AATCAAAGTA
* **
42757272 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
* *
42757296 AAATATATTATATTCATAAATACT
1 AAATATATTATACTAATAAATACT
42757320 AAAT
1 AAAT
42757324 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:42769816 original size:25 final size:25
Alignment explanation
Indices: 42769782--42769831 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
42769772 AAATGAACTG
*
42769782 TTGAACAATTTGTTCGATCTTTGCA
1 TTGAACAATTTGTTCGATCTCTGCA
42769807 TTGAACAATTTGTTCGATCTCTGCA
1 TTGAACAATTTGTTCGATCTCTGCA
42769832 CAAACTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (25 bp):
TTGAACAATTTGTTCGATCTCTGCA
Found at i:42771307 original size:4 final size:4
Alignment explanation
Indices: 42771298--42771325 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
42771288 TGAAAGAAGC
42771298 ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA
42771326 GTTTGCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:42774180 original size:8 final size:8
Alignment explanation
Indices: 42774167--42774194 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
42774157 GATTTTTAAA
42774167 TATTATTT
1 TATTATTT
42774175 TATTATTT
1 TATTATTT
42774183 TATTATTT
1 TATTATTT
42774191 TATT
1 TATT
42774195 GTTTAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTATTT
Found at i:42775164 original size:19 final size:19
Alignment explanation
Indices: 42775140--42775177 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
42775130 TCTAGTTTCA
42775140 GATAAAATTTACAGATCTT
1 GATAAAATTTACAGATCTT
*
42775159 GATAAAATTTACGGATCTT
1 GATAAAATTTACAGATCTT
42775178 AATTTGGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (19 bp):
GATAAAATTTACAGATCTT
Found at i:42794385 original size:9 final size:9
Alignment explanation
Indices: 42794371--42794410 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
42794361 GTTAAACAAA
42794371 TCGAGTTAT
1 TCGAGTTAT
42794380 TCGAGTTAT
1 TCGAGTTAT
*
42794389 TCGAGTTAA
1 TCGAGTTAT
42794398 TCGAGTTAT
1 TCGAGTTAT
42794407 TCGA
1 TCGA
42794411 ATCAACTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:42794481 original size:9 final size:9
Alignment explanation
Indices: 42794464--42794500 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42794454 TGAGTTTTCG
42794464 AATTCGAAT
1 AATTCGAAT
*
42794473 AACTCGAAT
1 AATTCGAAT
42794482 AATTCGAAT
1 AATTCGAAT
42794491 AATTCGAAT
1 AATTCGAAT
42794500 A
1 A
42794501 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:42795533 original size:5 final size:5
Alignment explanation
Indices: 42795523--42795548 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42795513 CTCGAAAATT
42795523 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
42795549 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:42800989 original size:3 final size:3
Alignment explanation
Indices: 42800981--42801014 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
42800971 TTAATAACAG
42800981 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
42801015 CAGACCATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:42802788 original size:3 final size:3
Alignment explanation
Indices: 42802754--42802826 Score: 69
Period size: 3 Copynumber: 24.7 Consensus size: 3
42802744 CATCTCCATT
* * *
42802754 TTC TCTC TTC TCC TTC TTA TTC TTC TTT TTC TTC TTC TTC TTC -TC
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * *
42802799 CTC TTC TTT TTC TTC TTT TTC -TC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
42802827 AAACCCTAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:42802811 original size:20 final size:20
Alignment explanation
Indices: 42802754--42802826 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
42802744 CATCTCCATT
* *
42802754 TTCT-CTCTTCTCCTTCTTA
1 TTCTCCTCTTCTTCTTCTTC
* *
42802773 TTCTTCTTTTTCTTCTTCTTC
1 TTC-TCCTCTTCTTCTTCTTC
*
42802794 TTCTCCTCTTCTTTTTCTTC
1 TTCTCCTCTTCTTCTTCTTC
* *
42802814 TTTTTCTCTTCTT
1 TTCTCCTCTTCTT
42802827 AAACCCTAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
19 3 0.07
20 26 0.60
21 14 0.33
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTCCTCTTCTTCTTCTTC
Found at i:42804193 original size:18 final size:16
Alignment explanation
Indices: 42804151--42804193 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
42804141 TGTCGTTCGT
42804151 TTTCAAAATATTATTCA
1 TTTC-AAATATTATTCA
42804168 TTTACAAATCATTATTCAA
1 TTT-CAAAT-ATTATTC-A
42804187 TTTCAAA
1 TTTCAAA
42804194 ACCTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTCAAATATTATTCA
Found at i:42807901 original size:21 final size:22
Alignment explanation
Indices: 42807866--42807913 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
42807856 CAACACACCT
42807866 GTGTGGAAGGAGGCACACGACA
1 GTGTGGAAGGAGGCACACGACA
* *
42807888 GTGTGG-ATGAGGCACACGCCA
1 GTGTGGAAGGAGGCACACGACA
42807909 GTGTG
1 GTGTG
42807914 TGCCAGGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.25, C:0.19, G:0.42, T:0.15
Consensus pattern (22 bp):
GTGTGGAAGGAGGCACACGACA
Found at i:42809693 original size:31 final size:31
Alignment explanation
Indices: 42809658--42809716 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
42809648 ACGTGTATAA
42809658 TTAAATTAAAATTAAAATTTTATATATACAC
1 TTAAATTAAAATTAAAATTTTATATATACAC
* *
42809689 TTAAATTATAATTAAAGTTTTATATATA
1 TTAAATTAAAATTAAAATTTTATATATA
42809717 ATTACACTAA
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:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (31 bp):
TTAAATTAAAATTAAAATTTTATATATACAC
Found at i:42810737 original size:17 final size:17
Alignment explanation
Indices: 42810699--42810736 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
42810689 GTGGGAGTCG
*
42810699 ATTTTAGAATAATTCTT
1 ATTTTAGAATAATTATT
*
42810716 ATTTTAGCATAATTATT
1 ATTTTAGAATAATTATT
42810733 -TTTT
1 ATTTT
42810737 TTCCACTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (17 bp):
ATTTTAGAATAATTATT
Found at i:42829399 original size:3 final size:3
Alignment explanation
Indices: 42829391--42829416 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42829381 TTATGTGAAT
42829391 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
42829417 TTGTTCTACA
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:42831385 original size:2 final size:2
Alignment explanation
Indices: 42831380--42831409 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42831370 CCCCCACCAC
42831380 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
42831410 CCTTTTTAAC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:42837983 original size:30 final size:30
Alignment explanation
Indices: 42837949--42838006 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
42837939 ACAAATCCTA
*
42837949 TCTCAATTTCCTTCCAAAATTCTCTCAAAC
1 TCTCAATTTCCTTCCAAAATCCTCTCAAAC
42837979 TCTCAATTTCCTTCCAAAATCCTCTCAA
1 TCTCAATTTCCTTCCAAAATCCTCTCAA
42838007 TTTCCTTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.36
Consensus pattern (30 bp):
TCTCAATTTCCTTCCAAAATCCTCTCAAAC
Found at i:42838003 original size:22 final size:22
Alignment explanation
Indices: 42837978--42838028 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
42837968 TTCTCTCAAA
42837978 CTCTCAATTTCCTTCC-AAAAT
1 CTCTCAATTTCCTTCCAAAAAT
42837999 CCTCTCAATTTCCTTCCAAAAAT
1 -CTCTCAATTTCCTTCCAAAAAT
42838022 CTCTCAA
1 CTCTCAA
42838029 ATCCATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAAAT
Found at i:42838098 original size:31 final size:31
Alignment explanation
Indices: 42838063--42838127 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
42838053 CTCAATTTCA
*
42838063 TTTTTTAAAATAATTTTAAA-TTTTTTTATAT
1 TTTTTTAAAAT-AGTTTAAATTTTTTTTATAT
42838094 TTTTTTAAAATAGTTTAAATTTTTTTTATAT
1 TTTTTTAAAATAGTTTAAATTTTTTTTATAT
42838125 TTT
1 TTT
42838128 CATCAATGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (31 bp):
TTTTTTAAAATAGTTTAAATTTTTTTTATAT
Found at i:42840498 original size:29 final size:29
Alignment explanation
Indices: 42840439--42841014 Score: 846
Period size: 29 Copynumber: 19.9 Consensus size: 29
42840429 TAATAAAAAT
*
42840439 CCTAATTTAATTAAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
42840469 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
42840498 CTTAATTTAATTAAAAACCCTAACCCTAC
1 CCTAATTTAATTAAAAACCCTAACCCTAA
42840527 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
42840556 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
42840586 CCTAATTTAATTAAAAACCCTAA--C---
1 CCTAATTTAATTAAAAACCCTAACCCTAA
42840610 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
*
42840640 TCTAATTTAATT-AAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
42840669 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
42840698 CCTAATTTAATTAAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
* *
42840728 CCTAATTTAATTAAAAACTCTTACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
42840757 CTTAATTTAATTAAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
*
42840787 CCTAATTTAATTAAAAACCCTTACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
42840816 CTTAATTTAATTAAAAACCCTAACCCTAC
1 CCTAATTTAATTAAAAACCCTAACCCTAA
42840845 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
42840875 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
42840904 CCTAATTTATTTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
* *
42840934 CTTAGTTTAATTAAAAACCCTAA--C-AA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
42840960 CTTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
* *
42840990 CTTAATTTAATTAAAAATCCTAACC
1 CCTAATTTAATTAAAAACCCTAACC
42841015 ATTAACAAAA
Statistics
Matches: 501, Mismatches: 29, Indels: 33
0.89 0.05 0.06
Matches are distributed among these distances:
24 21 0.04
25 2 0.00
26 22 0.04
27 5 0.01
29 253 0.50
30 198 0.40
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.29
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:42840592 original size:88 final size:89
Alignment explanation
Indices: 42840439--42841012 Score: 863
Period size: 88 Copynumber: 6.6 Consensus size: 89
42840429 TAATAAAAAT
* *
42840439 CCTAATTTAATTAAAAACCCTAAACACTAACCTAATTTAATTAAAAACCCT-AACCCTAACTTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAA
*
42840503 TTTAATTAAAAACCCTAACCCTAC
66 TTTAATTAAAAACCCTAACCCTAA
42840527 CCTAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAA
42840591 TTTAATTAAAAACCCTAA--C---
66 TTTAATTAAAAACCCTAACCCTAA
*
42840610 CCTAATTTAATTAAAAACCCTAAACCCTAATCTAATTTAATT-AAAACCCTAAACCCTAACCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAA
42840674 TTTAATTAAAAACCCTAACCCTAA
66 TTTAATTAAAAACCCTAACCCTAA
* * * *
42840698 CCTAATTTAATTAAAAACCCTAAACACTAACCTAATTTAATTAAAAACTCT-TACCCTAACTTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAA
*
42840762 TTTAATTAAAAACCCTAAACACTAA
66 TTTAATTAAAAACCCT-AACCCTAA
* * *
42840787 CCTAATTTAATTAAAAACCCT-TACCCTAACTTAATTTAATTAAAAACCCT-AACCCTACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAA
42840850 TTTAATTAAAAACCCTAAACCCTAA
66 TTTAATTAAAAACCCT-AACCCTAA
* * *
42840875 CCTAATTTAATTAAAAACCCT-AACCCTAACCTAATTTATTTAAAAACCCTAAACCCTAACTTAG
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAA
42840939 TTTAATTAAAAACCCTAA--C-AA
66 TTTAATTAAAAACCCTAACCCTAA
* * *
42840960 CTTAATTTAATTAAAAACCCTAAACCCTAACTTAATTTAATTAAAAATCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAA
42841013 CCATTAACAA
Statistics
Matches: 448, Mismatches: 27, Indels: 24
0.90 0.05 0.05
Matches are distributed among these distances:
83 61 0.14
84 19 0.04
85 23 0.05
86 30 0.07
87 28 0.06
88 226 0.50
89 61 0.14
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.29
Consensus pattern (89 bp):
CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAA
TTTAATTAAAAACCCTAACCCTAA
Found at i:42840611 original size:59 final size:59
Alignment explanation
Indices: 42840439--42841014 Score: 872
Period size: 59 Copynumber: 9.9 Consensus size: 59
42840429 TAATAAAAAT
*
42840439 CCTAATTTAATTAAAAACCCTAAACACTAACCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
* *
42840498 CTTAATTTAATTAAAAACCCT-AACCCTACCCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
42840556 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAA--C---
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
*
42840610 CCTAATTTAATTAAAAACCCTAAACCCTAATCTAATTTAATT-AAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAA
*
42840669 CCTAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAA
* * * *
42840728 CCTAATTTAATTAAAAACTCT-TACCCTAACTTAATTTAATTAAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAA
* * *
42840787 CCTAATTTAATTAAAAACCCT-TACCCTAACTTAATTTAATTAAAAACCCTAACCCTAC
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
42840845 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
* * *
42840904 CCTAATTTATTTAAAAACCCTAAACCCTAACTTAGTTTAATTAAAAACCCTAA--C-AA
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
* * *
42840960 CTTAATTTAATTAAAAACCCTAAACCCTAACTTAATTTAATTAAAAATCCTAACC
1 CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACC
42841015 ATTAACAAAA
Statistics
Matches: 482, Mismatches: 24, Indels: 23
0.91 0.05 0.04
Matches are distributed among these distances:
53 8 0.02
54 43 0.09
56 52 0.11
57 2 0.00
58 101 0.21
59 276 0.57
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.29
Consensus pattern (59 bp):
CCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:42844371 original size:124 final size:123
Alignment explanation
Indices: 42844152--42844430 Score: 497
Period size: 124 Copynumber: 2.3 Consensus size: 123
42844142 CCATGACGGC
42844152 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACCAACTGTAGCGA
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACCAACTGTAGCGA
*
42844217 AATCGCGTCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAGCATCCTAGTAGAA
66 AATCGCGTCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAACATCCTAGTAGAA
42844275 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTTATTTCTTACATGACCAACTGTAGCG
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-TTATTTCTTACATGACCAACTGTAGCG
* * *
42844340 AAATTGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAACATCCTGGTAGAA
65 AAATCGCGTCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAACATCCTAGTAGAA
42844399 GCGATTTTATACTATTTGAC-CAGAAACGTCAA
1 GCGATTTTATACTATTTG-CTCAGAAACGTCAA
42844431 CTCGAAATAA
Statistics
Matches: 150, Mismatches: 4, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
123 37 0.25
124 112 0.75
125 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (123 bp):
GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACCAACTGTAGCGA
AATCGCGTCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAACATCCTAGTAGAA
Found at i:42845675 original size:25 final size:24
Alignment explanation
Indices: 42845639--42845686 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
42845629 AATAAAAATT
*
42845639 AATATTATTTTTATTTATTTTATAA
1 AATATTATTTTTAATT-TTTTATAA
42845664 AATATT-TATTTTAATTTTTTATA
1 AATATTAT-TTTTAATTTTTTATA
42845687 CACCCTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
AATATTATTTTTAATTTTTTATAA
Found at i:42852483 original size:18 final size:20
Alignment explanation
Indices: 42852448--42852485 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42852438 GAAAAATATT
*
42852448 AAATATATATATTATTTTTA
1 AAATATATATAGTATTTTTA
42852468 AAATATA-ATAGT-TTTTTA
1 AAATATATATAGTATTTTTA
42852486 TTTTAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 4 0.24
20 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AAATATATATAGTATTTTTA
Found at i:42852600 original size:9 final size:9
Alignment explanation
Indices: 42852586--42852613 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
42852576 TTTTGTTACA
42852586 ACAATTAAT
1 ACAATTAAT
42852595 ACAATTAAT
1 ACAATTAAT
42852604 ACAATTAAT
1 ACAATTAAT
42852613 A
1 A
42852614 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:42852635 original size:68 final size:66
Alignment explanation
Indices: 42852556--42852697 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 66
42852546 TCAAGTTTGT
*
42852556 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
42852621 AAA
64 AAA
42852624 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
42852689 T
66 A
42852690 TTTACTAA
1 TTTACTAA
42852698 CAATTAATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 44 0.61
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:42852707 original size:16 final size:16
Alignment explanation
Indices: 42852686--42852727 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
42852676 AATAATTTGA
*
42852686 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
42852702 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
42852718 TAGTTTTAAT
1 TAATTTTAAT
42852728 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:42852711 original size:22 final size:23
Alignment explanation
Indices: 42852701--42852762 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
42852691 TTACTAACAA
* * *
42852701 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
42852723 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
42852746 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
42852763 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:42852716 original size:59 final size:66
Alignment explanation
Indices: 42852556--42852719 Score: 216
Period size: 68 Copynumber: 2.5 Consensus size: 66
42852546 TCAAGTTTGT
*
42852556 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTT-ATACAACAATTAATACAATTAATACAATTAATAATTTGAT
42852621 AAA
64 AAA
42852624 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
42852687 AAT
64 AAA
*
42852690 TTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTATACAACAATTA
42852720 GTTTTAATTT
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
59 9 0.10
61 6 0.07
62 3 0.03
64 2 0.02
65 1 0.01
66 27 0.29
67 1 0.01
68 43 0.47
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATACAATTAATAATTTGATAA
A
Found at i:42854153 original size:51 final size:51
Alignment explanation
Indices: 42854094--42854213 Score: 168
Period size: 51 Copynumber: 2.4 Consensus size: 51
42854084 TTTTCTCTAG
**
42854094 TTAATTTAAATTAATTAAAAGATTGATAATAAAAAATTATATCATCACTAA
1 TTAATTTAAATTAATTAAAAGATAAATAATAAAAAATTATATCATCACTAA
* * *
42854145 TTAATTTAAACTGATTAAAAGATAAATAATAAAAAATTATATTATCACTAA
1 TTAATTTAAATTAATTAAAAGATAAATAATAAAAAATTATATCATCACTAA
* * *
42854196 ATAAATTAAATTATTTAA
1 TTAATTTAAATTAATTAA
42854214 GTGATAATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (51 bp):
TTAATTTAAATTAATTAAAAGATAAATAATAAAAAATTATATCATCACTAA
Found at i:42855173 original size:13 final size:12
Alignment explanation
Indices: 42855157--42855190 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
42855147 ATTTAGATTT
42855157 TAAAAATAGAAAA
1 TAAAAATA-AAAA
42855170 TAAAAATAAAAA
1 TAAAAATAAAAA
42855182 TAAAGAATA
1 TAAA-AATA
42855191 TAATTGCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (12 bp):
TAAAAATAAAAA
Found at i:42855180 original size:5 final size:6
Alignment explanation
Indices: 42855157--42855190 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
42855147 ATTTAGATTT
42855157 TAAAAA TAGAAAA TAAAAA TAAAAA TAAAGAA TA
1 TAAAAA TA-AAAA TAAAAA TAAAAA TAAA-AA TA
42855191 TAATTGCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.62
7 10 0.38
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:42859477 original size:3 final size:3
Alignment explanation
Indices: 42859471--42859496 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42859461 CCTTCTTCCC
42859471 CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CT
42859497 ACTCTTCAAG
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:0.35, G:0.31, T:0.35
Consensus pattern (3 bp):
CTG
Found at i:42862416 original size:17 final size:17
Alignment explanation
Indices: 42862370--42862419 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
42862360 TCTCAAATTT
* *
42862370 TGATACCCATATATTTT
1 TGATACCCATATCTTTC
*
42862387 TGATACCTATATCTTTC
1 TGATACCCATATCTTTC
42862404 TGATACCCATATCTTT
1 TGATACCCATATCTTT
42862420 GACTTTCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.06, T:0.46
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:42871526 original size:22 final size:24
Alignment explanation
Indices: 42871482--42871528 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
42871472 AAAAAACTAG
42871482 AAAAACGTGCTATGATGAGAGCAGAC
1 AAAAACGTGCTATGAT--GAGCAGAC
42871508 AAAAACGTGCTA-GAT-AGCAGA
1 AAAAACGTGCTATGATGAGCAGA
42871529 ATCTATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.45, C:0.15, G:0.26, T:0.15
Consensus pattern (24 bp):
AAAAACGTGCTATGATGAGCAGAC
Found at i:42875314 original size:21 final size:21
Alignment explanation
Indices: 42875273--42875315 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
42875263 AATAAAGTAG
*
42875273 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
42875294 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
42875315 A
1 A
42875316 AATTCATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:42880592 original size:17 final size:18
Alignment explanation
Indices: 42880570--42880603 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42880560 ATAATTGTAA
42880570 TTTAAAT-TCTAATTATT
1 TTTAAATGTCTAATTATT
*
42880587 TTTAAATGTGTAATTAT
1 TTTAAATGTCTAATTAT
42880604 CATAACTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAAATGTCTAATTATT
Found at i:42880627 original size:44 final size:44
Alignment explanation
Indices: 42880571--42880660 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
42880561 TAATTGTAAT
* * *
42880571 TTAAATTCTAATTATTTTTAAATGTGTAATTATCATAACTTCTA
1 TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCTA
*
42880615 TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTTTA
1 TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCTA
42880659 TT
1 TT
42880661 TTAATTCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (44 bp):
TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCTA
Found at i:42885073 original size:32 final size:32
Alignment explanation
Indices: 42885035--42885096 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
42885025 CCCGTTTTTT
* *
42885035 AAATAAATATCAAAAAATTATTTTAAAAATTA
1 AAATAAAAATCAAAAAAGTATTTTAAAAATTA
*
42885067 AAATAAAAATTAAAAAAGTATTTTAAAAAT
1 AAATAAAAATCAAAAAAGTATTTTAAAAAT
42885097 ATTTTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (32 bp):
AAATAAAAATCAAAAAAGTATTTTAAAAATTA
Found at i:42889432 original size:21 final size:18
Alignment explanation
Indices: 42889389--42889436 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 18
42889379 TTTAGGCTAG
*
42889389 ATAATTAAATAATTAGGA
1 ATAATTAAATAATTAGAA
42889407 ATAATTAAATAAAATATAGAA
1 ATAATTAAAT--AAT-TAGAA
42889428 ATAATTAAA
1 ATAATTAAA
42889437 ATTAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 10 0.38
20 3 0.12
21 13 0.50
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
ATAATTAAATAATTAGAA
Found at i:42890329 original size:26 final size:25
Alignment explanation
Indices: 42890280--42890360 Score: 62
Period size: 25 Copynumber: 3.3 Consensus size: 25
42890270 TAAAATAAAT
* *
42890280 GAAAGAAAAAGA-ATAGAAAAA-GA
1 GAAAAAAAAAGAGAAAGAAAAAGGA
* * *
42890303 -AAAAACAAAGTAGAACGAAACA-GA
1 GAAAAAAAAAG-AGAAAGAAAAAGGA
*
42890327 GAAGAAAAAGAGAGAAAGAAAAAGGA
1 GAA-AAAAAAAGAGAAAGAAAAAGGA
42890353 GAAAAAAA
1 GAAAAAAA
42890361 TTAGGGTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
22 8 0.18
23 1 0.02
24 8 0.18
25 16 0.36
26 11 0.25
ACGTcount: A:0.72, C:0.04, G:0.22, T:0.02
Consensus pattern (25 bp):
GAAAAAAAAAGAGAAAGAAAAAGGA
Found at i:42890342 original size:13 final size:13
Alignment explanation
Indices: 42890324--42890360 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
42890314 AGAACGAAAC
42890324 AGAGAAGAAAAAG
1 AGAGAAGAAAAAG
42890337 AGAGAAAGAAAAAG
1 AGAG-AAGAAAAAG
42890351 -GAGAA-AAAAA
1 AGAGAAGAAAAA
42890361 TTAGGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.22
12 2 0.09
13 7 0.30
14 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAGAAGAAAAAG
Found at i:42890347 original size:14 final size:14
Alignment explanation
Indices: 42890324--42890360 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
42890314 AGAACGAAAC
42890324 AGAG-AAGAAAAAG
1 AGAGAAAGAAAAAG
42890337 AGAGAAAGAAAAAG
1 AGAGAAAGAAAAAG
42890351 -GAGAAA-AAAA
1 AGAGAAAGAAAA
42890361 TTAGGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 10 0.43
14 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AGAGAAAGAAAAAG
Found at i:42893161 original size:9 final size:9
Alignment explanation
Indices: 42893147--42893182 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
42893137 CTAATTAGGT
*
42893147 GATATTTAG
1 GATATTTTG
42893156 GATATTTTG
1 GATATTTTG
42893165 GATATTTTG
1 GATATTTTG
42893174 GATAATTTT
1 GAT-ATTTT
42893183 ACAATTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (9 bp):
GATATTTTG
Found at i:42893660 original size:13 final size:13
Alignment explanation
Indices: 42893644--42893678 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
42893634 TCAAACTCAT
*
42893644 AAATATTTATTAG
1 AAATATTTATTAA
42893657 AAATATTTATTAA
1 AAATATTTATTAA
42893670 AAATATTTA
1 AAATATTTA
42893679 CGAGACTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (13 bp):
AAATATTTATTAA
Found at i:42894816 original size:16 final size:16
Alignment explanation
Indices: 42894791--42894824 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42894781 ATGAATATAT
* *
42894791 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
42894807 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
42894823 AT
1 AT
42894825 TGGCTATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:42897113 original size:12 final size:13
Alignment explanation
Indices: 42897088--42897118 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
42897078 GACTCACTGA
42897088 TTTTAAAATGATT
1 TTTTAAAATGATT
42897101 TTTTAAAAT-ATT
1 TTTTAAAATGATT
42897113 TTTTAA
1 TTTTAA
42897119 CTTATATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
TTTTAAAATGATT
Found at i:42905830 original size:44 final size:44
Alignment explanation
Indices: 42905703--42905830 Score: 114
Period size: 49 Copynumber: 2.8 Consensus size: 44
42905693 AACAGATCAG
* *
42905703 TGAAGCTACAATTCCTATACCCTTAAAGTTGCAGTAGGTCGAAA
1 TGAAGCTACAATTCTTATACCCTTAAAGTTGCAGTAGATCGAAA
* * * * * *
42905747 TGAAACTACAATGGTGAATTTATATCCC-TAAAATTGCAGTAGATTGGAT
1 TGAAGCTACAAT--T---CTTATA-CCCTTAAAGTTGCAGTAGATCGAAA
*
42905796 TGAAGCTACAATTCTTATACCCTTGAAGTTGCAGT
1 TGAAGCTACAATTCTTATACCCTTAAAGTTGCAGT
42905831 GGGTCAGAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
43 3 0.05
44 26 0.40
46 1 0.02
47 1 0.02
49 31 0.48
50 3 0.05
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (44 bp):
TGAAGCTACAATTCTTATACCCTTAAAGTTGCAGTAGATCGAAA
Found at i:42905917 original size:94 final size:94
Alignment explanation
Indices: 42905703--42906315 Score: 586
Period size: 94 Copynumber: 6.6 Consensus size: 94
42905693 AACAGATCAG
* * *
42905703 TGAAGCTACAATTCCTATACCCTTAAAGTTGCAGTAGGTC-GAAATGAAACTACAATGGTGAAT-
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCAG-AATGAAACTACAATGGTGAATC
* * * * *
42905766 TTATATCCCTAAAATTGCAGTAGATTGGAT
65 CTATATCCCTGAAGTTGCAGTGGATCGGAT
* * * *
42905796 TGAAGCTACAATTCTTATACCCTTGAAGTTGCAGTGGGTCAGAATAAAACTACAACGGTGAATCC
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACAATGGTGAATCC
** *
42905861 TATATCCCTGAAGTTATAGTGGATCAGAT
66 TATATCCCTGAAGTTGCAGTGGATCGGAT
* * * * *
42905890 TAAATCTACAATTCCTATACCCCTGAAGTT-CTAATGGGTC-GAAATAAAACTACAATAGTGAAT
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGC-AGTGGGTCAG-AATGAAACTACAATGGTGAAT
** * *
42905953 ATTATATTCCTAAAGTTGCAGTGGATCGGAT
64 CCTATATCCCTGAAGTTGCAGTGGATCGGAT
* * * * * * *
42905984 TGAAGCTACAATTCCTATACCCCTAAAGTTGTAGTGGGTCGGATTGAAATTACAATGGCGAATCT
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACAATGGTGAATCC
** * * * *
42906049 TACCTCTCTGAAGTTGCAATGGAGCAAGA-
66 TATATCCCTGAAGTTGCAGTGGATC-GGAT
* * * * * * *
42906078 TGAAGTTACGATTCTTATACCCCTGAAGTTGCAGTGGGTCAAAATGAAATTACAAAGGCGAATCC
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACAATGGTGAATCC
* *
42906143 TATATCCCT-AACGTTACAGTGAATCGGAT
66 TATATCCCTGAA-GTTGCAGTGGATCGGAT
* * *
42906172 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAGCTACAA---T---TCC
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACAATGGTGAATCC
* *
42906231 TATA-CCTCTGAAGTTGTAGTGGGTCGGAT
66 TATATCC-CTGAAGTTGCAGTGGATCGGAT
* * * *
42906260 TGAAGCTACAATTCCTATACCCCTGAAGTTACAATGGGTCAGATTGAAGCTACAAT
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACAAT
42906316 TTCTATACCC
Statistics
Matches: 428, Mismatches: 80, Indels: 28
0.80 0.15 0.05
Matches are distributed among these distances:
87 2 0.00
88 74 0.17
89 2 0.00
93 62 0.14
94 285 0.67
95 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (94 bp):
TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACAATGGTGAATCC
TATATCCCTGAAGTTGCAGTGGATCGGAT
Found at i:42906026 original size:44 final size:44
Alignment explanation
Indices: 42905703--42906444 Score: 384
Period size: 44 Copynumber: 16.1 Consensus size: 44
42905693 AACAGATCAG
* * * * *
42905703 TGAAGCTACAATTCCTATACCCTTAAAGTTGCAGTAGGTCGAAA
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCGGAT
* ** * * * * * *
42905747 TGAAACTACAATGGTGAATTTATATCCCTAAAATTGCAGTAGATTGGAT
1 TGAAGCTACAAT--T---CCTATACCCCTGAAGTTGCAGTGGGTCGGAT
* * * *
42905796 TGAAGCTACAATTCTTATACCCTTGAAGTTGCAGTGGGTCAGAA
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCGGAT
* * * ** * *
42905840 TAAAACTACAACGGTGAATCCTATATCCCTGAAGTTATAGTGGATCAGAT
1 TGAAGCTACAA---T---TCCTATACCCCTGAAGTTGCAGTGGGTCGGAT
* * * * *
42905890 TAAATCTACAATTCCTATACCCCTGAAGTT-CTAATGGGTCGAAA
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGC-AGTGGGTCGGAT
* * ** ** * *
42905934 TAAAACTACAATAGTGAATATTATATTCCTAAAGTTGCAGTGGATCGGAT
1 TGAAGCTAC-A-A-T---TCCTATACCCCTGAAGTTGCAGTGGGTCGGAT
* *
42905984 TGAAGCTACAATTCCTATACCCCTAAAGTTGTAGTGGGTCGGAT
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCGGAT
** * * *
42906028 TGAAATTACAATGGCGAATCT-TACCTCTCTGAAGTTGCAATGGAG-CAAGA-
1 TGAAGCTACAAT-TC----CTATACC-C-CTGAAGTTGCAGTGG-GTC-GGAT
* * * ** *
42906078 TGAAGTTACGATTCTTATACCCCTGAAGTTGCAGTGGGTCAAAA
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCGGAT
** * * * **
42906122 TGAAATTACAAAGGCGAATCCTATATCCCT-AACGTTACAGTGAATCGGAT
1 TGAAGCTAC--A----ATTCCTATACCCCTGAA-GTTGCAGTGGGTCGGAT
42906172 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCGGAT
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCGGAT
* *
42906216 TGAAGCTACAATTCCTATACCTCTGAAGTTGTAGTGGGTCGGAT
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCGGAT
* * *
42906260 TGAAGCTACAATTCCTATACCCCTGAAGTTACAATGGGTCAGAT
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCGGAT
* * *
42906304 TGAAGCTACAATTTCTATACCCCTGAAGTTGTAGTGGGTCGAAT
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCGGAT
* * * *
42906348 TGAAGTTACCATAGCAAATCTTAT-CTCCCAGAAGTTGCAGTGGAGT-AGA-
1 TGAAG----C-TA-CAATTCCTATAC-CCCTGAAGTTGCAGTGG-GTCGGAT
* * * *
42906397 TGAAGCTACAAATCTTATACCCTTGAAGTTGTAGTGGGTCGGAT
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCGGAT
42906441 TGAA
1 TGAA
42906445 TTTACATTAG
Statistics
Matches: 537, Mismatches: 111, Indels: 100
0.72 0.15 0.13
Matches are distributed among these distances:
42 2 0.00
43 29 0.05
44 289 0.54
45 7 0.01
46 6 0.01
47 5 0.01
48 7 0.01
49 48 0.09
50 138 0.26
51 6 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCGGAT
Found at i:42906530 original size:94 final size:94
Alignment explanation
Indices: 42906192--42906855 Score: 604
Period size: 94 Copynumber: 7.1 Consensus size: 94
42906182 ATTCCTATAC
** * *
42906192 CCCTGAAGTTGCAGTGG-GTCGGATTGAAGCTACAATTCCTATACCTCTGAAGTTGTAGTGGGTC
1 CCCTGAAGTTGCAGTGGAGTAAGA-TGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTGGGTC
* * *
42906256 GGATTG-A---AGC-TA-CAATTCCTATAC-
65 GGATTGAATCTACCATAGCAAATCTTAT-CT
* * * * *
42906280 CCCTGAAGTTACAATGG-GTCAGATTGAAGCTACAATTTCTATACCCCTGAAGTTGTAGTGGGTC
1 CCCTGAAGTTGCAGTGGAGTAAGA-TGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTGGGTC
*
42906344 GAATTGAAGT-TACCATAGCAAATCTTATCT
65 GGATTGAA-TCTACCATAGCAAATCTTATCT
* * *
42906374 CCCAGAAGTTGCAGTGGAGT-AGATGAAGCTACAAATCTTATACCCTTGAAGTTGTAGTGGGTCG
1 CCCTGAAGTTGCAGTGGAGTAAGATGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTGGGTCG
* *
42906438 GATTGAATTTA-CATTAGCGAATCTTATCT
66 GATTGAATCTACCA-TAGCAAATCTTATCT
* * * * * *
42906467 CCTTGAAGTTGCAGTGGAGAAAGAAGTAGCTACAAATCCTATACCCCTGAAGTTGGAGTGGGTCA
1 CCCTGAAGTTGCAGTGGAGTAAGATGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTGGGTCG
* **
42906532 GATTAAATCTACCATAATAAATCTTATCT
66 GATTGAATCTACCATAGCAAATCTTATCT
* * ** *
42906561 CCCTGAA-TATGCAGTGAAGCAAGATGAAGCTACAAATTTTATACCCCTAAAGTTGCT-GTGGGT
1 CCCTGAAGT-TGCAGTGGAGTAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG-TAGTGGGT
* *
42906624 TGGATTGAATCTACCATAAG-GAATCTTATCT
64 CGGATTGAATCTACCAT-AGCAAATCTTATCT
* * * * * * ** **
42906655 CCTTGACGTTGCAATGGAGTAAGATGAAGCTAAAAATCCTATATCCCTGAAGTTGCAGTAAGTTA
1 CCCTGAAGTTGCAGTGGAGTAAGATGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTGGGTCG
* * *
42906720 GATTGAATATACCATAACGAATCTTATCT
66 GATTGAATCTACCATAGCAAATCTTATCT
* * * * * * *
42906749 CCCTGAAGATGCAGTGAAGTAAGATGAACCTACAAATCATATATCCCTGAAATTGTAGTGGAAT-
1 CCCTGAAGTTGCAGTGGAGTAAGATGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTGG-GTC
* * * *
42906813 GGATTGAAACTACAACATCAAATCTTATCT
65 GGATTGAATCTACCATAGCAAATCTTATCT
*
42906843 CCTTGAAGTTGCA
1 CCCTGAAGTTGCA
42906856 ATTGAACAAG
Statistics
Matches: 473, Mismatches: 84, Indels: 32
0.80 0.14 0.05
Matches are distributed among these distances:
88 64 0.14
89 1 0.00
92 5 0.01
93 81 0.17
94 315 0.67
95 7 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (94 bp):
CCCTGAAGTTGCAGTGGAGTAAGATGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTGGGTCG
GATTGAATCTACCATAGCAAATCTTATCT
Found at i:42908406 original size:12 final size:12
Alignment explanation
Indices: 42908373--42908414 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 12
42908363 TACTTATTTT
42908373 TTTATTTTTATTA
1 TTTA-TTTTATTA
42908386 TCGTTATTTTATTA
1 T--TTATTTTATTA
42908400 TTTATTTTATTA
1 TTTATTTTATTA
42908412 TTT
1 TTT
42908415 CTGGCACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 14 0.52
13 1 0.04
14 9 0.33
15 3 0.11
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTATTTTATTA
Found at i:42908543 original size:25 final size:25
Alignment explanation
Indices: 42908514--42908564 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
42908504 TATGATAATA
*
42908514 TGATTATTGTTATTATTATTACCAT
1 TGATTAATGTTATTATTATTACCAT
*
42908539 TGATTAATGTTATTATTATTATCAT
1 TGATTAATGTTATTATTATTACCAT
42908564 T
1 T
42908565 ATAGTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.57
Consensus pattern (25 bp):
TGATTAATGTTATTATTATTACCAT
Found at i:42914699 original size:13 final size:13
Alignment explanation
Indices: 42914683--42914707 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42914673 TATATATTTT
42914683 TTGATAAATTTAA
1 TTGATAAATTTAA
42914696 TTGATAAATTTA
1 TTGATAAATTTA
42914708 TTTTTTTAAG
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TTGATAAATTTAA
Found at i:42919337 original size:24 final size:24
Alignment explanation
Indices: 42919309--42919360 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
42919299 TTCGTAGGTC
*
42919309 AAATAAATTATGCTAATAAATACT
1 AAATAAATTATACTAATAAATACT
* * * *
42919333 AAATATATTGTACTAGTAAATATT
1 AAATAAATTATACTAATAAATACT
42919357 AAAT
1 AAAT
42919361 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:42921309 original size:24 final size:24
Alignment explanation
Indices: 42921281--42921332 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
42921271 TTCGTATGTC
* *
42921281 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
42921305 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
42921329 AAAT
1 AAAT
42921333 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:42922986 original size:21 final size:20
Alignment explanation
Indices: 42922961--42923016 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 20
42922951 TATTCACTAA
42922961 TTAATTTCCATAATAGATGTT
1 TTAATTTCCATAATAG-TGTT
42922982 TTAA-TTCCTTGATAATAGTGTT
1 TTAATTTCC---ATAATAGTGTT
*
42923004 TT-ATTTCAATAAT
1 TTAATTTCCATAAT
42923017 TTCACTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
19 5 0.17
20 4 0.13
21 5 0.17
22 9 0.30
23 7 0.23
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (20 bp):
TTAATTTCCATAATAGTGTT
Found at i:42924260 original size:17 final size:17
Alignment explanation
Indices: 42924240--42924293 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 17
42924230 TAAAAGAGTT
42924240 ATTAATTAAAAATATGA
1 ATTAATTAAAAATATGA
**
42924257 ATTAA--AAAAATATTT
1 ATTAATTAAAAATATGA
42924272 ATTAATTAAAAATATGA
1 ATTAATTAAAAATATGA
42924289 ATTAA
1 ATTAA
42924294 AAAACATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 13 0.42
17 18 0.58
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (17 bp):
ATTAATTAAAAATATGA
Found at i:42924261 original size:13 final size:13
Alignment explanation
Indices: 42924243--42924312 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 13
42924233 AAGAGTTATT
42924243 AATTAAAAATATG
1 AATTAAAAATATG
*
42924256 AATTAAAAAAATATTTATT
1 AATT---AAAA-A--TATG
42924275 AATTAAAAATATG
1 AATTAAAAATATG
* *
42924288 AATTAAAAAACATT
1 AATT-AAAAATATG
42924302 AATTAAAAATA
1 AATTAAAAATA
42924313 AAAAAAGCTT
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
13 17 0.38
14 11 0.24
15 1 0.02
16 8 0.18
17 1 0.02
19 7 0.16
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (13 bp):
AATTAAAAATATG
Found at i:42924267 original size:15 final size:15
Alignment explanation
Indices: 42924247--42924310 Score: 69
Period size: 15 Copynumber: 4.2 Consensus size: 15
42924237 GTTATTAATT
42924247 AAAAATATGAATTAA
1 AAAAATATGAATTAA
**
42924262 AAAAATATTTATTAA
1 AAAAATATGAATTAA
42924277 TTAAAAATATGAATTAA
1 --AAAAATATGAATTAA
42924294 AAAACAT-T-AATTAA
1 AAAA-ATATGAATTAA
42924308 AAA
1 AAA
42924311 TAAAAAAAGC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
14 9 0.21
15 18 0.43
16 2 0.05
17 13 0.31
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (15 bp):
AAAAATATGAATTAA
Found at i:42924305 original size:14 final size:14
Alignment explanation
Indices: 42924272--42924310 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42924262 AAAAATATTT
*
42924272 ATTAATT-AAAAAT
1 ATTAATTAAAAAAC
*
42924285 ATGAATTAAAAAAC
1 ATTAATTAAAAAAC
42924299 ATTAATTAAAAA
1 ATTAATTAAAAA
42924311 TAAAAAAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (14 bp):
ATTAATTAAAAAAC
Found at i:42925283 original size:27 final size:26
Alignment explanation
Indices: 42925245--42925299 Score: 60
Period size: 27 Copynumber: 2.1 Consensus size: 26
42925235 TTAAGTGTTT
*
42925245 TTCTTTCTTCAA-TTATTTTTCATCTAG
1 TTCTTTCTTCAAGTT-TTTTT-ATCAAG
42925272 TTCTTT-TATCAAGTTTTTTTATCAAG
1 TTCTTTCT-TCAAGTTTTTTTATCAAG
42925298 TT
1 TT
42925300 TTGCAGCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 8 0.32
27 15 0.60
28 2 0.08
ACGTcount: A:0.20, C:0.15, G:0.05, T:0.60
Consensus pattern (26 bp):
TTCTTTCTTCAAGTTTTTTTATCAAG
Found at i:42925291 original size:13 final size:13
Alignment explanation
Indices: 42925260--42925301 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
42925250 TCTTCAATTA
* *
42925260 TTTTTCATCTAGT
1 TTTTTTATCAAGT
*
42925273 TCTTTTATCAAGT
1 TTTTTTATCAAGT
42925286 TTTTTTATCAAGT
1 TTTTTTATCAAGT
42925299 TTT
1 TTT
42925302 GCAGCAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.19, C:0.12, G:0.07, T:0.62
Consensus pattern (13 bp):
TTTTTTATCAAGT
Found at i:42925301 original size:12 final size:12
Alignment explanation
Indices: 42925260--42925362 Score: 73
Period size: 12 Copynumber: 8.3 Consensus size: 12
42925250 TCTTCAATTA
*
42925260 TTTTTCATCTAG
1 TTTTTCATCAAG
*
42925272 TTCTTTTATCAAG
1 TT-TTTCATCAAG
*
42925285 TTTTTTTATCAAG
1 -TTTTTCATCAAG
* *
42925298 TTTTGCAGCAAG
1 TTTTTCATCAAG
* *
42925310 TTCTTT-TTAAAG
1 TT-TTTCATCAAG
42925322 TTTTTCATCAAG
1 TTTTTCATCAAG
* *
42925334 TCTTTTCATAAAA
1 T-TTTTCATCAAG
*
42925347 TTTTCCATCAAG
1 TTTTTCATCAAG
42925359 TTTT
1 TTTT
42925363 GAATCATTTC
Statistics
Matches: 70, Mismatches: 16, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
11 3 0.04
12 35 0.50
13 30 0.43
14 2 0.03
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (12 bp):
TTTTTCATCAAG
Found at i:42925309 original size:25 final size:24
Alignment explanation
Indices: 42925279--42925362 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 24
42925269 TAGTTCTTTT
*
42925279 ATCAAGTTTTTTTATCAAGTTTTGC
1 ATCAAGTTTTTTTAT-AAGTTTTCC
* *
42925304 AGCAAGTTCTTTTTA-AAGTTTTTC
1 ATCAAGTT-TTTTTATAAGTTTTCC
* * *
42925328 ATCAAGTCTTTTCATAAAATTTTCC
1 ATCAAGTTTTTTTAT-AAGTTTTCC
42925353 ATCAAGTTTT
1 ATCAAGTTTT
42925363 GAATCATTTC
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
23 5 0.10
24 14 0.29
25 23 0.48
26 6 0.12
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (24 bp):
ATCAAGTTTTTTTATAAGTTTTCC
Found at i:42940358 original size:12 final size:12
Alignment explanation
Indices: 42940341--42940366 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42940331 CGTGAGTTGA
42940341 TTATAATTTCCT
1 TTATAATTTCCT
42940353 TTATAATTTCCT
1 TTATAATTTCCT
42940365 TT
1 TT
42940367 CTCTAACTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATAATTTCCT
Found at i:42943566 original size:22 final size:24
Alignment explanation
Indices: 42943540--42943583 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
42943530 GAAAAATATT
42943540 AAATAT-ATA-TATTTTATTTTTA
1 AAATATAATAGTATTTTATTTTTA
*
42943562 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTATTTTATTTT
42943584 AAGTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 3 0.16
24 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
AAATATAATAGTATTTTATTTTTA
Found at i:42943694 original size:9 final size:9
Alignment explanation
Indices: 42943680--42943707 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
42943670 TTTTGTTACA
42943680 ACAATTAAT
1 ACAATTAAT
42943689 ACAATTAAT
1 ACAATTAAT
42943698 ACAATTAAT
1 ACAATTAAT
42943707 A
1 A
42943708 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:42943729 original size:68 final size:68
Alignment explanation
Indices: 42943650--42943859 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
42943640 TTAAGTTTGT
*
42943650 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
42943715 AAA
66 AAA
42943718 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
42943783 AAA
66 AAA
42943786 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
42943849 AAT
66 AAA
42943852 TTTACTAA
1 TTTACTAA
42943860 CAATTAATTT
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 27 0.19
67 1 0.01
68 112 0.80
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:42943760 original size:9 final size:9
Alignment explanation
Indices: 42943748--42943775 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
42943738 TTTTATTACA
42943748 ACAATTAAT
1 ACAATTAAT
42943757 ACAATTAAT
1 ACAATTAAT
42943766 ACAATTAAT
1 ACAATTAAT
42943775 A
1 A
42943776 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:42943869 original size:16 final size:15
Alignment explanation
Indices: 42943848--42943887 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
42943838 AATAATTTGA
42943848 TAATTTTACTAACAAT
1 TAATTTTA-TAACAAT
42943864 TAATTTTTATAACAAT
1 TAA-TTTTATAACAAT
*
42943880 TAGTTTTA
1 TAATTTTA
42943888 ATTTTATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 12 0.55
17 5 0.23
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (15 bp):
TAATTTTATAACAAT
Found at i:42943890 original size:22 final size:23
Alignment explanation
Indices: 42943863--42943923 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
42943853 TTACTAACAA
* * *
42943863 TTAATTTTTA-TAACAATTAGTT
1 TTAATTTTTATTAAAAAATAATT
42943885 TTAA-TTTTATTAAAAAATAATT
1 TTAATTTTTATTAAAAAATAATT
* *
42943907 TTAATTTTAATTTAAAA
1 TTAATTTTTATTAAAAA
42943924 CGGGCCGGGC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 5 0.16
22 17 0.53
23 10 0.31
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTTATTAAAAAATAATT
Found at i:42946213 original size:4 final size:4
Alignment explanation
Indices: 42946199--42946258 Score: 50
Period size: 4 Copynumber: 14.0 Consensus size: 4
42946189 TAACCATATG
* *
42946199 TTTA GTTA TTTA TTTA TTTGA TTTGA TTTGA TTTGA TTT- TTTGT TTTA
1 TTTA TTTA TTTA TTTA TTT-A TTT-A TTT-A TTT-A TTTA TTT-A TTTA
42946247 TTTA TTTA TTTA
1 TTTA TTTA TTTA
42946259 CATAATATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.06
4 25 0.50
5 22 0.44
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:42946224 original size:5 final size:5
Alignment explanation
Indices: 42946206--42946237 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
42946196 ATGTTTAGTT
42946206 ATTT- ATTT- ATTTG ATTTG ATTTG ATTTG ATTT
1 ATTTG ATTTG ATTTG ATTTG ATTTG ATTTG ATTT
42946238 TTTGTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.66
Consensus pattern (5 bp):
ATTTG
Found at i:42946234 original size:15 final size:13
Alignment explanation
Indices: 42946206--42946257 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
42946196 ATGTTTAGTT
42946206 ATTTATTTATTTG
1 ATTTATTTATTTG
42946219 ATTTGATTTGATTTG
1 ATTT-ATTT-ATTTG
* *
42946234 ATTT-TTTGTTTT
1 ATTTATTTATTTG
42946246 ATTTATTTATTT
1 ATTTATTTATTT
42946258 ACATAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 7 0.21
13 13 0.39
14 4 0.12
15 9 0.27
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (13 bp):
ATTTATTTATTTG
Found at i:42948195 original size:10 final size:10
Alignment explanation
Indices: 42948180--42948211 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
42948170 TTCATAAGTC
42948180 TCTTACCAAA
1 TCTTACCAAA
42948190 TCTTACCAAA
1 TCTTACCAAA
42948200 TCTTACCAAA
1 TCTTACCAAA
42948210 TC
1 TC
42948212 AGAGAACGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (10 bp):
TCTTACCAAA
Found at i:42948313 original size:42 final size:42
Alignment explanation
Indices: 42948261--42948417 Score: 116
Period size: 42 Copynumber: 3.7 Consensus size: 42
42948251 GCCCGAAGAC
* * **
42948261 TGAATAGAAGCTCATGAGAGTTAAACAGAAACTTATAAGGGT
1 TGAATAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * *
42948303 TGAATGGAAGCTCGTAAGAGCTAAACGGAAACCCATAAGGGT
1 TGAATAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * * * * * ** * *
42948345 TAAACAGAAGCTCAAAAAAGCTGATCAGAAACTTATATGAGT
1 TGAATAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * * * *
42948387 TAAACAGAAGCTCGTGAGAGCTAAACGGAAA
1 TGAATAGAAGCTCATAAGAGCTAAACAGAAA
42948418 GTAAACACAA
Statistics
Matches: 88, Mismatches: 27, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (42 bp):
TGAATAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
Found at i:42955389 original size:37 final size:37
Alignment explanation
Indices: 42955328--42955511 Score: 318
Period size: 37 Copynumber: 5.0 Consensus size: 37
42955318 TACGTATGAT
*
42955328 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
* *
42955363 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
42955400 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
42955437 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
42955474 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
42955511 C
1 C
42955512 GAAGCTATCA
Statistics
Matches: 140, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
35 9 0.06
36 4 0.03
37 127 0.91
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:42955527 original size:46 final size:46
Alignment explanation
Indices: 42955474--42955801 Score: 248
Period size: 52 Copynumber: 6.6 Consensus size: 46
42955464 TAAGTGTAGC
*
42955474 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
42955520 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * * * * *
42955572 CACTTATCACTTTCCACTTTCCACTTG-TCACTTGATCAGAT-AAG-TGTAGCTGAAG
1 CACTTATCAC-TT----TGT-CACTTGATCA---GATAAG-TGTAGCCGAAGCT--AT
** *
42955627 CTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 C-A-CTT--ATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
42955677 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
42955723 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
42955775 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
42955802 AGTACTCAAA
Statistics
Matches: 229, Mismatches: 23, Indels: 60
0.73 0.07 0.19
Matches are distributed among these distances:
46 76 0.33
47 1 0.00
48 2 0.01
49 2 0.01
50 6 0.03
51 12 0.05
52 95 0.41
53 11 0.05
54 12 0.05
55 3 0.01
56 1 0.00
57 1 0.00
58 2 0.01
59 5 0.02
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:42955553 original size:52 final size:52
Alignment explanation
Indices: 42955474--42955795 Score: 389
Period size: 46 Copynumber: 6.2 Consensus size: 52
42955464 TAAGTGTAGC
* *
42955474 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
42955527 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
*
42955579 CACTTTCCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
1 CAC--T----TTT-CACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
*
42955638 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
42955684 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* ** *
42955730 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
42955782 CACTTTGTCACTTG
1 CACTTT-TCACTTG
42955796 ATCAGAAGTA
Statistics
Matches: 242, Mismatches: 13, Indels: 28
0.86 0.05 0.10
Matches are distributed among these distances:
46 88 0.36
50 1 0.00
52 87 0.36
53 15 0.06
54 1 0.00
58 3 0.01
59 47 0.19
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Found at i:42955590 original size:59 final size:58
Alignment explanation
Indices: 42955517--42955643 Score: 218
Period size: 59 Copynumber: 2.2 Consensus size: 58
42955507 TAGCCGAAGC
*
42955517 TATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTT-TCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
*
42955576 TATCACTTTCCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTT-CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
42955635 TATCACTTT
1 TATCACTTT
42955644 GTCACTTGAT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
58 1 0.02
59 64 0.98
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (58 bp):
TATCACTTTCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:42971524 original size:11 final size:11
Alignment explanation
Indices: 42971508--42971532 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42971498 TTCAATTCAA
42971508 ATAATCAATAT
1 ATAATCAATAT
42971519 ATAATCAATAT
1 ATAATCAATAT
42971530 ATA
1 ATA
42971533 TACCAATTCA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATCAATAT
Found at i:42972279 original size:21 final size:21
Alignment explanation
Indices: 42972239--42972285 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
42972229 TAATTTCTCC
* ** *
42972239 TTTCTTTCTTTCCCTTTTTCT
1 TTTCTTTCTCTCCCGGTTTCG
42972260 TTTCTTTCTCTCCCGGTTTCG
1 TTTCTTTCTCTCCCGGTTTCG
42972281 TTTCT
1 TTTCT
42972286 ATTTCTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.00, C:0.30, G:0.06, T:0.64
Consensus pattern (21 bp):
TTTCTTTCTCTCCCGGTTTCG
Found at i:42974109 original size:20 final size:19
Alignment explanation
Indices: 42974072--42974113 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
42974062 GATATCCTCT
*
42974072 TAAATTAAAATGATATATGA
1 TAAATTAAAATGAAATAT-A
42974092 TAAATTAAAAAT-AAATATA
1 TAAATT-AAAATGAAATATA
42974111 TAA
1 TAA
42974114 TCCGATAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 11 0.55
21 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
TAAATTAAAATGAAATATA
Found at i:42975400 original size:17 final size:18
Alignment explanation
Indices: 42975368--42975401 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42975358 ATAAGTATTA
*
42975368 AAAGTAAAATCTAAAAAT
1 AAAGCAAAATCTAAAAAT
42975386 AAAGCAAAA-CTAAAAA
1 AAAGCAAAATCTAAAAA
42975402 AAAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.15
Consensus pattern (18 bp):
AAAGCAAAATCTAAAAAT
Found at i:42980053 original size:34 final size:34
Alignment explanation
Indices: 42980000--42980065 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
42979990 TTTAGTTCTT
42980000 TTATATATTTACATATTTTTCATAAATTTATAAG
1 TTATATATTTACATATTTTTCATAAATTTATAAG
* *
42980034 TTATATA-TTATATATTTTTTTATAAATTTATA
1 TTATATATTTACATA-TTTTTCATAAATTTATA
42980066 TATTTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 6 0.21
34 23 0.79
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (34 bp):
TTATATATTTACATATTTTTCATAAATTTATAAG
Found at i:42981270 original size:48 final size:48
Alignment explanation
Indices: 42981208--42981535 Score: 294
Period size: 48 Copynumber: 7.0 Consensus size: 48
42981198 AAAAGTTGCT
* * * *
42981208 AATATGTTGTGGATGAACCACTAGTCGTGTAGATAAACTGCCGACTAA
1 AATACGTTATGGATGAACCACTGGTCGTGCAGATAAACTGCCGACTAA
* * * * * *
42981256 AGTATGTTATGGATGAACCACTTGTCTTGCATATAAATTGCCGACTAA
1 AATACGTTATGGATGAACCACTGGTCGTGCAGATAAACTGCCGACTAA
* ** * * * * ** *
42981304 AATATGTCCTGGATGAACCACTTGTCATGTAGATAAAAT-TTG--T-T
1 AATACGTTATGGATGAACCACTGGTCGTGCAGATAAACTGCCGACTAA
* * * * *
42981348 AATACATTATGGATAAACCACTTGTCGTGCAGATAAA-AGCTG-CT--
1 AATACGTTATGGATGAACCACTGGTCGTGCAGATAAACTGCCGACTAA
* *
42981392 AATAAGTTATGGATGAACCACTGGTTGTGCAGATAAACTGCCGACTAA
1 AATACGTTATGGATGAACCACTGGTCGTGCAGATAAACTGCCGACTAA
* * * *
42981440 AATACGTTGTGGATGAACCACTGGTCGTGCAGTTAAACTACTGACTAAA
1 AATACGTTATGGATGAACCACTGGTCGTGCAGATAAACTGCCGACT-AA
* *
42981489 AATACGTTGTGGATGAACCACTGGTCGTGCAGACAAACTGCCGACTA
1 AATACGTTATGGATGAACCACTGGTCGTGCAGATAAACTGCCGACTA
42981536 CTCCCTCCCT
Statistics
Matches: 230, Mismatches: 43, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
44 64 0.28
45 5 0.02
46 2 0.01
47 1 0.00
48 114 0.50
49 44 0.19
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (48 bp):
AATACGTTATGGATGAACCACTGGTCGTGCAGATAAACTGCCGACTAA
Done.