Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 133 of 208
Found at i:40745379 original size:27 final size:27
Alignment explanation
Indices: 40745349--40745432 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
40745339 ATGTCGAGAG
40745349 TTAAAAATATGATCCTTAGTAGAAAAT
1 TTAAAAATATGATCCTTAGTAGAAAAT
* *
40745376 TT-AAAA-ATGCATTACTTA-T-G---AG
1 TTAAAAATATG-A-TCCTTAGTAGAAAAT
40745398 TTAAAAATATGATCCTTAGTAGAAAAT
1 TTAAAAATATGATCCTTAGTAGAAAAT
40745425 TTAAAAAT
1 TTAAAAAT
40745433 GCATTACTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 18
0.67 0.06 0.27
Matches are distributed among these distances:
22 8 0.18
23 6 0.14
24 4 0.09
25 4 0.09
26 6 0.14
27 16 0.36
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (27 bp):
TTAAAAATATGATCCTTAGTAGAAAAT
Found at i:40745402 original size:49 final size:49
Alignment explanation
Indices: 40745346--40745443 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
40745336 TTAATGTCGA
40745346 GAGTTAAAAATATGATCCTTAGTAGAAAATTTAAAAATGCATTACTTAT
1 GAGTTAAAAATATGATCCTTAGTAGAAAATTTAAAAATGCATTACTTAT
40745395 GAGTTAAAAATATGATCCTTAGTAGAAAATTTAAAAATGCATTACTTAT
1 GAGTTAAAAATATGATCCTTAGTAGAAAATTTAAAAATGCATTACTTAT
40745444 TTAGACTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (49 bp):
GAGTTAAAAATATGATCCTTAGTAGAAAATTTAAAAATGCATTACTTAT
Found at i:40745415 original size:22 final size:24
Alignment explanation
Indices: 40745345--40745420 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 24
40745335 CTTAATGTCG
40745345 AGAGTTAAAAATATGATCCTTAGT
1 AGAGTTAAAAATATGATCCTTAGT
* * *
40745369 AGAAAATTTAAAA-ATGCATTACTTA-T
1 AG--AGTTAAAAATATG-A-TCCTTAGT
40745395 -GAGTTAAAAATATGATCCTTAGT
1 AGAGTTAAAAATATGATCCTTAGT
40745418 AGA
1 AGA
40745421 AAATTTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
22 5 0.13
23 9 0.23
24 7 0.18
25 4 0.10
26 9 0.23
27 5 0.13
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (24 bp):
AGAGTTAAAAATATGATCCTTAGT
Found at i:40745442 original size:27 final size:27
Alignment explanation
Indices: 40745363--40745442 Score: 82
Period size: 23 Copynumber: 3.1 Consensus size: 27
40745353 AAATATGATC
40745363 CTTAGTAGAAAATTTAAAAATGCATTA
1 CTTAGTAGAAAATTTAAAAATGCATTA
* * *
40745390 CTTA-T-G--AGTTAAAAATATG-A-TC
1 CTTAGTAGAAAATTTAAAA-ATGCATTA
40745412 CTTAGTAGAAAATTTAAAAATGCATTA
1 CTTAGTAGAAAATTTAAAAATGCATTA
40745439 CTTA
1 CTTA
40745443 TTTAGACTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 5 0.12
23 9 0.22
24 4 0.10
25 4 0.10
26 9 0.22
27 9 0.22
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (27 bp):
CTTAGTAGAAAATTTAAAAATGCATTA
Found at i:40746522 original size:24 final size:23
Alignment explanation
Indices: 40746486--40746531 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
40746476 TATTAGTTAA
40746486 AAAAATATAAATATGTACATATATT
1 AAAAATATAAATA--TACATATATT
*
40746511 AAAAA-ATCAATATACATATAT
1 AAAAATATAAATATACATATAT
40746532 ATATATATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
24 6 0.30
25 5 0.25
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAATATAAATATACATATATT
Found at i:40746530 original size:36 final size:34
Alignment explanation
Indices: 40746490--40746563 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 34
40746480 AGTTAAAAAA
* *
40746490 ATATAAATATGTACATATATTAAAAAATCAATATAC
1 ATATAAATATATACAGATATTAAAAAAT-AAT-TAC
* * *
40746526 ATATATATATATATAGATTTTAAAAAATAATTAC
1 ATATAAATATATACAGATATTAAAAAATAATTAC
40746560 ATAT
1 ATAT
40746564 GAAAATTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 7 0.21
35 3 0.09
36 23 0.70
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (34 bp):
ATATAAATATATACAGATATTAAAAAATAATTAC
Found at i:40750701 original size:28 final size:28
Alignment explanation
Indices: 40750661--40750732 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
40750651 AAACCAAAAG
* * * *
40750661 TGCAAGCTAAAGTGGCGGACAGTCTAAA
1 TGCAAGCCAAAGTGGCAGACAATCCAAA
40750689 TGCAAGCCAAAGTGGCAGACAATCCAAA
1 TGCAAGCCAAAGTGGCAGACAATCCAAA
40750717 TGCAAGCCAAAAGTGG
1 TGCAAGCC-AAAGTGG
40750733 GTGCTAGCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 32 0.82
29 7 0.18
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14
Consensus pattern (28 bp):
TGCAAGCCAAAGTGGCAGACAATCCAAA
Found at i:40750819 original size:88 final size:89
Alignment explanation
Indices: 40750689--40750862 Score: 262
Period size: 88 Copynumber: 2.0 Consensus size: 89
40750679 ACAGTCTAAA
* * *
40750689 TGCAAGCCAAAGTGGCAGACAATCCAAATGCAAGCCAAAAGTGGGTGCTAGCCTAATTGGT-GAC
1 TGCAAGCCAAAGTGGCAGACAATCCAAATGCAAGCCAAAAGTGGGTGCAAGCCAAAGTGGTGGAC
*
40750753 AGTTTAAGTGAAAGCCAAAGTTGG
66 AGTCTAAGTGAAAGCCAAAGTTGG
* *
40750777 TGCAAGCCACAA-TGGCAGACAGTCTAAATGCAAGCCAAAAGTGGGTGCAAGCCAAAGTGGTGGA
1 TGCAAGCCA-AAGTGGCAGACAATCCAAATGCAAGCCAAAAGTGGGTGCAAGCCAAAGTGGTGGA
*
40750841 CAGTCTAAGTGCAAGCCAAAGT
65 CAGTCTAAGTGAAAGCCAAAGT
40750863 GGCAGACAGT
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
88 53 0.69
89 24 0.31
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.17
Consensus pattern (89 bp):
TGCAAGCCAAAGTGGCAGACAATCCAAATGCAAGCCAAAAGTGGGTGCAAGCCAAAGTGGTGGAC
AGTCTAAGTGAAAGCCAAAGTTGG
Found at i:40750828 original size:45 final size:44
Alignment explanation
Indices: 40750689--40750864 Score: 194
Period size: 45 Copynumber: 4.0 Consensus size: 44
40750679 ACAGTCTAAA
* *
40750689 TGCAAGCCAAAGTGGCAGACAATCCAAATGCAAGCCAAAAGTGGG
1 TGCAAGCCAAAGTGGCAGACAGTCTAAATGCAAGCC-AAAGTGGG
* * * * * * * *
40750734 TGCTAGCCTAATTGG-TGACAGTTTAAGTGAAAGCCAAAGTTGG
1 TGCAAGCCAAAGTGGCAGACAGTCTAAATGCAAGCCAAAGTGGG
40750777 TGCAAGCCACAA-TGGCAGACAGTCTAAATGCAAGCCAAAAGTGGG
1 TGCAAGCCA-AAGTGGCAGACAGTCTAAATGCAAGCC-AAAGTGGG
** *
40750822 TGCAAGCCAAAGTGGTGGACAGTCTAAGTGCAAGCCAAAGTGG
1 TGCAAGCCAAAGTGGCAGACAGTCTAAATGCAAGCCAAAGTGG
40750865 CAGACAGTCT
Statistics
Matches: 107, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
43 17 0.16
44 41 0.38
45 49 0.46
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.17
Consensus pattern (44 bp):
TGCAAGCCAAAGTGGCAGACAGTCTAAATGCAAGCCAAAGTGGG
Found at i:40750835 original size:16 final size:17
Alignment explanation
Indices: 40750805--40750836 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40750795 ACAGTCTAAA
40750805 TGCAAGCCAAAAGTGGG
1 TGCAAGCCAAAAGTGGG
40750822 TGCAAGCC-AAAGTGG
1 TGCAAGCCAAAAGTGG
40750837 TGGACAGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.19, G:0.34, T:0.12
Consensus pattern (17 bp):
TGCAAGCCAAAAGTGGG
Found at i:40750861 original size:28 final size:28
Alignment explanation
Indices: 40750821--40750972 Score: 175
Period size: 28 Copynumber: 5.4 Consensus size: 28
40750811 CCAAAAGTGG
40750821 GTGCAAGCCAAAGTGGTGGACAGTCTAA
1 GTGCAAGCCAAAGTGGTGGACAGTCTAA
**
40750849 GTGCAAGCCAAAGTGGCAGACAGTCTAA
1 GTGCAAGCCAAAGTGGTGGACAGTCTAA
*
40750877 GTGCAAACCAAAGTAGCG-GGA-AGTCTAA
1 GTGCAAGCCAAAGT-G-GTGGACAGTCTAA
* * *
40750905 ATCCAAGCCAAAGTGGTGGATAGTCTAA
1 GTGCAAGCCAAAGTGGTGGACAGTCTAA
*
40750933 GTGCAAGCCAAAGTGGCAGG-CAGTCTAA
1 GTGCAAGCCAAAGTGG-TGGACAGTCTAA
* *
40750961 ATGCAAGTCAAA
1 GTGCAAGCCAAA
40750973 AGTAGCGGCA
Statistics
Matches: 106, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.01
27 4 0.04
28 95 0.90
29 5 0.05
30 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.16
Consensus pattern (28 bp):
GTGCAAGCCAAAGTGGTGGACAGTCTAA
Found at i:40750930 original size:84 final size:85
Alignment explanation
Indices: 40750824--40750980 Score: 262
Period size: 84 Copynumber: 1.9 Consensus size: 85
40750814 AAAGTGGGTG
* *
40750824 CAAGCCAAAGTGGTGGACAGTCTAAGTGCAAGCCAAAGTGGCAGACAGTCTAAGTGCAA-ACCAA
1 CAAGCCAAAGTGGTGGACAGTCTAAGTGCAAGCCAAAGTGGCAGACAGTCTAAATGCAAGACAAA
40750888 AGTAGCGGGAAGTCTAAATC
66 AGTAGCGGGAAGTCTAAATC
* * *
40750908 CAAGCCAAAGTGGTGGATAGTCTAAGTGCAAGCCAAAGTGGCAGGCAGTCTAAATGCAAGTCAAA
1 CAAGCCAAAGTGGTGGACAGTCTAAGTGCAAGCCAAAGTGGCAGACAGTCTAAATGCAAGACAAA
40750973 AGTAGCGG
66 AGTAGCGG
40750981 CAAGCCAAAG
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 56 0.84
85 11 0.16
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.16
Consensus pattern (85 bp):
CAAGCCAAAGTGGTGGACAGTCTAAGTGCAAGCCAAAGTGGCAGACAGTCTAAATGCAAGACAAA
AGTAGCGGGAAGTCTAAATC
Found at i:40759381 original size:45 final size:44
Alignment explanation
Indices: 40759314--40759417 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 44
40759304 CCAAAAAAAG
* * *
40759314 TGCAAGCCAAAGTTGGTGCAAGCCAAAGCGACAAACAGTCTAAA
1 TGCAAGCCAAAGTGGGGGCAAGCCAAAGCGACAAACAATCTAAA
* * * *
40759358 TGCAAGCCAAAAGTGGGGGCAAGCCAAAGTGGCAGACAATCTAAG
1 TGCAAGCC-AAAGTGGGGGCAAGCCAAAGCGACAAACAATCTAAA
*
40759403 TGTAAGCCAAAGTGG
1 TGCAAGCCAAAGTGG
40759418 AAGACAATCT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 15 0.29
45 36 0.71
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.13
Consensus pattern (44 bp):
TGCAAGCCAAAGTGGGGGCAAGCCAAAGCGACAAACAATCTAAA
Found at i:40759422 original size:28 final size:28
Alignment explanation
Indices: 40759378--40759470 Score: 141
Period size: 28 Copynumber: 3.3 Consensus size: 28
40759368 AAGTGGGGGC
*
40759378 AAGCCAAAGTGGCAGACAATCTAAGTGT
1 AAGCCAAAGTGGCAGACAATCTAAATGT
* **
40759406 AAGCCAAAGTGGAAGACAATCTAAATAC
1 AAGCCAAAGTGGCAGACAATCTAAATGT
*
40759434 AAGCCAAAGTGGCATACAATCTAAATGT
1 AAGCCAAAGTGGCAGACAATCTAAATGT
40759462 AAGCCAAAG
1 AAGCCAAAG
40759471 ATGGTGCAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.16
Consensus pattern (28 bp):
AAGCCAAAGTGGCAGACAATCTAAATGT
Found at i:40759483 original size:44 final size:43
Alignment explanation
Indices: 40759433--40759564 Score: 156
Period size: 44 Copynumber: 3.0 Consensus size: 43
40759423 AATCTAAATA
* *
40759433 CAAGCCAAAGTGGCATACAATCTAAATGTAAGCCAAAGATGGTG
1 CAAGCCAAAGTGGCAGACAATCTAAATGCAAGCCAAA-ATGGTG
* * * * * *
40759477 CAAGCCAAAGTGGTAGATAGTCTAAGTGCAAGTCAAACTTGGTG
1 CAAGCCAAAGTGGCAGACAATCTAAATGCAAGCCAAA-ATGGTG
* *
40759521 CAAGACAAAGTGGCAGAGAATCTAAATGCAAGCCAAAATGGTG
1 CAAGCCAAAGTGGCAGACAATCTAAATGCAAGCCAAAATGGTG
40759564 C
1 C
40759565 GCAATATAAA
Statistics
Matches: 72, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
43 6 0.08
44 66 0.92
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.18
Consensus pattern (43 bp):
CAAGCCAAAGTGGCAGACAATCTAAATGCAAGCCAAAATGGTG
Found at i:40762022 original size:15 final size:15
Alignment explanation
Indices: 40762002--40762030 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40761992 GGCTACTCGG
40762002 TTTTGGAAAATTTTA
1 TTTTGGAAAATTTTA
40762017 TTTTGGAAAATTTT
1 TTTTGGAAAATTTT
40762031 TAAAGCTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (15 bp):
TTTTGGAAAATTTTA
Found at i:40768229 original size:18 final size:19
Alignment explanation
Indices: 40768202--40768240 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
40768192 ATTAATTTTG
*
40768202 ATCAAGTAAATT-AAATTA
1 ATCAAATAAATTAAAATTA
40768220 ATCAAATAAATTAAAATTA
1 ATCAAATAAATTAAAATTA
40768239 AT
1 AT
40768241 ATGATACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:40770523 original size:16 final size:17
Alignment explanation
Indices: 40770493--40770524 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40770483 ACAATCTAAA
40770493 TGCAAGCCGAAAGTGGG
1 TGCAAGCCGAAAGTGGG
40770510 TGCAAGCC-AAAGTGG
1 TGCAAGCCGAAAGTGG
40770525 TGGACGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.31, C:0.19, G:0.38, T:0.12
Consensus pattern (17 bp):
TGCAAGCCGAAAGTGGG
Found at i:40770646 original size:28 final size:28
Alignment explanation
Indices: 40770509--40770652 Score: 144
Period size: 28 Copynumber: 5.1 Consensus size: 28
40770499 CCGAAAGTGG
* * **
40770509 GTGCAAGCCAAAGTGGTGGACGGTTTAA
1 GTGCAAGCCAAAGTGGCGGACAGTCCAA
* * * *
40770537 ATGCAAGCCAAAAGTGGTGGATAGTCTAA
1 GTGCAAGCC-AAAGTGGCGGACAGTCCAA
* * *
40770566 GTGCAAGCCAAAGTGGCGGGCAATCAAA
1 GTGCAAGCCAAAGTGGCGGACAGTCCAA
* * *
40770594 ATGCAAGCCAAAGTGGCGAATAGTCCAA
1 GTGCAAGCCAAAGTGGCGGACAGTCCAA
*
40770622 GTGCAAGCCAAAGTGGCAGACAGTCCAA
1 GTGCAAGCCAAAGTGGCGGACAGTCCAA
40770650 GTG
1 GTG
40770653 GGAGACAAAA
Statistics
Matches: 95, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
28 71 0.75
29 24 0.25
ACGTcount: A:0.35, C:0.19, G:0.31, T:0.16
Consensus pattern (28 bp):
GTGCAAGCCAAAGTGGCGGACAGTCCAA
Found at i:40770661 original size:28 final size:28
Alignment explanation
Indices: 40770559--40770687 Score: 98
Period size: 28 Copynumber: 4.6 Consensus size: 28
40770549 AGTGGTGGAT
* * * *
40770559 AGTCTAAGTGCAAGCCAAAGTGGCGGGC
1 AGTCCAAGTGCAAGACAAAGTGGCAGAC
* * * * *
40770587 AATCAAAATGCAAGCCAAAGTGGC-GAAT
1 AGTCCAAGTGCAAGACAAAGTGGCAG-AC
*
40770615 AGTCCAAGTGCAAGCCAAAGTGGCAGAC
1 AGTCCAAGTGCAAGACAAAGTGGCAGAC
** * *
40770643 AGTCCAAGTGGGAGACAAAATGACAGAC
1 AGTCCAAGTGCAAGACAAAGTGGCAGAC
* *
40770671 AATCCAAGTGTAAGACA
1 AGTCCAAGTGCAAGACA
40770688 CTCCATAACA
Statistics
Matches: 82, Mismatches: 17, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
27 1 0.01
28 80 0.98
29 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.13
Consensus pattern (28 bp):
AGTCCAAGTGCAAGACAAAGTGGCAGAC
Found at i:40771650 original size:31 final size:31
Alignment explanation
Indices: 40771615--40771673 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
40771605 GTTATCATAG
* *
40771615 AAACTACAATGTAAAATTTTATTTTTTATAT
1 AAACTACAATGTAAAATTCTATATTTTATAT
** *
40771646 AAACTTTAGTGTAAAATTCTATATTTTA
1 AAACTACAATGTAAAATTCTATATTTTA
40771674 AATTTATTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (31 bp):
AAACTACAATGTAAAATTCTATATTTTATAT
Found at i:40776174 original size:2 final size:2
Alignment explanation
Indices: 40776157--40776192 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
40776147 TGTAGTACTG
* *
40776157 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40776193 TATTGAGAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:40781898 original size:29 final size:29
Alignment explanation
Indices: 40781820--40781958 Score: 203
Period size: 28 Copynumber: 4.9 Consensus size: 29
40781810 CAGTCTGCCT
* *
40781820 TTTTGGCTTGCA-TTTGGACTATCTATCA
1 TTTTGGCTTGCACTTTGGACTGTCTGTCA
* *
40781848 TTTTGGCTTGCA-TTTGGACTGTCCGCCA
1 TTTTGGCTTGCACTTTGGACTGTCTGTCA
* *
40781876 CTTTGGATTGCACTTTGGACTGTCTGTCA
1 TTTTGGCTTGCACTTTGGACTGTCTGTCA
40781905 TTTTGGCTTGCAC-TTGGACTGTCTGTCA
1 TTTTGGCTTGCACTTTGGACTGTCTGTCA
40781933 TTTTGGCTTGCACTTTGGACTGTCTG
1 TTTTGGCTTGCACTTTGGACTGTCTG
40781959 CATGATCTTC
Statistics
Matches: 99, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 62 0.63
29 37 0.37
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.43
Consensus pattern (29 bp):
TTTTGGCTTGCACTTTGGACTGTCTGTCA
Found at i:40781909 original size:57 final size:57
Alignment explanation
Indices: 40781821--40781958 Score: 206
Period size: 57 Copynumber: 2.4 Consensus size: 57
40781811 AGTCTGCCTT
* * *
40781821 TTTGGCTTGCA-TTTGGACTATCTATCATTTTGGCTTGCATTTGGACTGTCCGCCAC
1 TTTGGCTTGCACTTTGGACTGTCTGTCATTTTGGCTTGCACTTGGACTGTCCGCCAC
* * * *
40781877 TTTGGATTGCACTTTGGACTGTCTGTCATTTTGGCTTGCACTTGGACTGTCTGTCAT
1 TTTGGCTTGCACTTTGGACTGTCTGTCATTTTGGCTTGCACTTGGACTGTCCGCCAC
40781934 TTTGGCTTGCACTTTGGACTGTCTG
1 TTTGGCTTGCACTTTGGACTGTCTG
40781959 CATGATCTTC
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
56 10 0.14
57 63 0.86
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.43
Consensus pattern (57 bp):
TTTGGCTTGCACTTTGGACTGTCTGTCATTTTGGCTTGCACTTGGACTGTCCGCCAC
Found at i:40782828 original size:109 final size:109
Alignment explanation
Indices: 40782715--40782911 Score: 288
Period size: 109 Copynumber: 1.8 Consensus size: 109
40782705 TTCTGACAAT
* * * *
40782715 GCTATAACGTCGCATACATGTGTCTCCACTAACTAGAGGTATAGACACAATGGATGCGTCTCCAC
1 GCTATAACGTCGCACACATGTGTCTCCACTAACTAGAAGTAGAGACACAATGGATGCATCTCCAC
40782780 TGAC-ACACCTATAGAGATGCATGCCTCGTGTCTTCATAGACTGA
66 TGACTA-ACCTATAGAGATGCATGCCTCGTGTCTTCATAGACTGA
* * * *
40782824 GCTATAGCGTCGCGCACATGTGTCTCCACTAACTAGAAGTAGAGACACAATGGATGTATCTCTAC
1 GCTATAACGTCGCACACATGTGTCTCCACTAACTAGAAGTAGAGACACAATGGATGCATCTCCAC
* *
40782889 TGACTAAGCTATGGAGATGCATG
66 TGACTAACCTATAGAGATGCATG
40782912 AGTTTTTGCA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
109 76 0.99
110 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (109 bp):
GCTATAACGTCGCACACATGTGTCTCCACTAACTAGAAGTAGAGACACAATGGATGCATCTCCAC
TGACTAACCTATAGAGATGCATGCCTCGTGTCTTCATAGACTGA
Found at i:40786457 original size:51 final size:51
Alignment explanation
Indices: 40786398--40786501 Score: 156
Period size: 51 Copynumber: 2.0 Consensus size: 51
40786388 AACCATCACA
* *
40786398 AATTTTGTTCTTTCG-AATATTGATATATTAGCTCTTCTGGAGCTTTTAACT
1 AATTTTGTTC-TACGAAATATTGATATATTAGCTCTTCTGGAGCTTTCAACT
* *
40786449 AATTTTGTTCTACGAAATATTGATATATTTGCTCTTTTGGAGCTTTCAACT
1 AATTTTGTTCTACGAAATATTGATATATTAGCTCTTCTGGAGCTTTCAACT
40786500 AA
1 AA
40786502 GTTTCATATC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
50 3 0.06
51 45 0.94
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.47
Consensus pattern (51 bp):
AATTTTGTTCTACGAAATATTGATATATTAGCTCTTCTGGAGCTTTCAACT
Found at i:40787228 original size:21 final size:21
Alignment explanation
Indices: 40787197--40787249 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
40787187 AAAATAAGTT
* *
40787197 AATAAAATAATT-ATAACTAAT
1 AATAAATTAATTAATAA-TAAA
*
40787218 AATGAATTAATTAATAATAAA
1 AATAAATTAATTAATAATAAA
40787239 AATAAATTAAT
1 AATAAATTAAT
40787250 CAAATATGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
AATAAATTAATTAATAATAAA
Found at i:40795159 original size:24 final size:24
Alignment explanation
Indices: 40795034--40795160 Score: 119
Period size: 24 Copynumber: 5.3 Consensus size: 24
40795024 GAGTCTTGGT
* * *
40795034 GATTTGTTCAAATATTGTTCTAGC
1 GATTTGTTCACATATTATTCTGGC
* *
40795058 GATTTTTTCGCATATTATTCTGGC
1 GATTTGTTCACATATTATTCTGGC
* * *
40795082 GATCTGTTCACAAATTATTCTTGC
1 GATTTGTTCACATATTATTCTGGC
* ** * * *
40795106 GACTTGTTCGTATATTGTGCTGAC
1 GATTTGTTCACATATTATTCTGGC
40795130 GATTTGTTCACATATTATTCTGGC
1 GATTTGTTCACATATTATTCTGGC
*
40795154 GGTTTGT
1 GATTTGT
40795161 CTGTAACACT
Statistics
Matches: 77, Mismatches: 26, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 77 1.00
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.46
Consensus pattern (24 bp):
GATTTGTTCACATATTATTCTGGC
Found at i:40796546 original size:21 final size:21
Alignment explanation
Indices: 40796512--40796555 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40796502 CATTAACGTG
*
40796512 TCAATATTGTGACAC-CAACAT
1 TCAATATTGCGACACTCAA-AT
*
40796533 TCAATGTTGCGACACTCAAAT
1 TCAATATTGCGACACTCAAAT
40796554 TC
1 TC
40796556 GAGGCCAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (21 bp):
TCAATATTGCGACACTCAAAT
Found at i:40797310 original size:42 final size:42
Alignment explanation
Indices: 40797263--40797347 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
40797253 AATTCATTAG
40797263 AACCCTAAATATAAAATTAATTATGAAAACTTAAGTGAGATA
1 AACCCTAAATATAAAATTAATTATGAAAACTTAAGTGAGATA
* *
40797305 AACCCTAAATATGAAATTAATTATGAACACTTAAGTGAGATA
1 AACCCTAAATATAAAATTAATTATGAAAACTTAAGTGAGATA
40797347 A
1 A
40797348 TCTTCTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28
Consensus pattern (42 bp):
AACCCTAAATATAAAATTAATTATGAAAACTTAAGTGAGATA
Found at i:40798774 original size:21 final size:22
Alignment explanation
Indices: 40798740--40798781 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
40798730 ATTTAGGCTT
40798740 TATATATCATCCATCACACATA
1 TATATATCATCCATCACACATA
*
40798762 TATATAT-ATCCATTACACAT
1 TATATATCATCCATCACACAT
40798782 TCTTCTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (22 bp):
TATATATCATCCATCACACATA
Found at i:40802888 original size:88 final size:88
Alignment explanation
Indices: 40802725--40802904 Score: 270
Period size: 88 Copynumber: 2.0 Consensus size: 88
40802715 TTCACCGTTA
* *
40802725 AAAATTAGTGGTGGAGGAGGTGTAAAGCTGACTGAAGACATTTTTACAAAAAACAACAAGGAAAC
1 AAAATTAGTGGTGGAAGAGGTGTAAAGCTGACTAAAGACATTTTTACAAAAAACAACAAGGAAAC
**
40802790 ATATGTTTTTTCTTTTAGGAAAC
66 ATATGTTTTTTCTTTTAAAAAAC
* * * * *
40802813 AAAATTGGTGGTGGAAGAGGTGTAAAGCTGGCTAAAGACGTTTTTACAAAAAAACTATAAGGAAA
1 AAAATTAGTGGTGGAAGAGGTGTAAAGCTGACTAAAGACATTTTTAC-AAAAAACAACAAGGAAA
40802878 CATATGTTTTTTCTTTTAAAAAAC
65 CATATGTTTTTTCTTTTAAAAAAC
40802902 AAA
1 AAA
40802905 GGCCCTCAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
88 42 0.51
89 40 0.49
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (88 bp):
AAAATTAGTGGTGGAAGAGGTGTAAAGCTGACTAAAGACATTTTTACAAAAAACAACAAGGAAAC
ATATGTTTTTTCTTTTAAAAAAC
Found at i:40803435 original size:29 final size:29
Alignment explanation
Indices: 40803385--40803452 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
40803375 CACCTTTTTG
40803385 GCTTGCA-TTTGAACTGTCCGTCACTTTA
1 GCTTGCACTTTGAACTGTCCGTCACTTTA
* * *
40803413 GCTTGCACTTTGGACTGTTCGTCACTTTG
1 GCTTGCACTTTGAACTGTCCGTCACTTTA
*
40803442 GCTTGTACTTT
1 GCTTGCACTTT
40803453 AGACAACTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
28 7 0.20
29 28 0.80
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.43
Consensus pattern (29 bp):
GCTTGCACTTTGAACTGTCCGTCACTTTA
Found at i:40807254 original size:7 final size:7
Alignment explanation
Indices: 40807242--40807267 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40807232 TAGTCTCATC
40807242 TTTATAT
1 TTTATAT
40807249 TTTATAT
1 TTTATAT
40807256 TTTATAT
1 TTTATAT
40807263 TTTAT
1 TTTAT
40807268 GCTGCCTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTATAT
Found at i:40808172 original size:2 final size:2
Alignment explanation
Indices: 40808165--40808189 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40808155 TAACCCAATT
40808165 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
40808190 TAACATGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40809606 original size:11 final size:11
Alignment explanation
Indices: 40809590--40809614 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40809580 AAATTTTAAG
40809590 AAATTTAAACA
1 AAATTTAAACA
40809601 AAATTTAAACA
1 AAATTTAAACA
40809612 AAA
1 AAA
40809615 AAAAGTCATT
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATTTAAACA
Found at i:40810593 original size:35 final size:35
Alignment explanation
Indices: 40810553--40810619 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
40810543 GCTGGTTTCA
**
40810553 GTTGGATTAGCTCTTTTGAGCATTGGCGTGTTGTG
1 GTTGGATTAAATCTTTTGAGCATTGGCGTGTTGTG
*
40810588 GTTGGATTAAATCTTTTGAGTATTGGCGTGTT
1 GTTGGATTAAATCTTTTGAGCATTGGCGTGTT
40810620 TAGGGTGGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.15, C:0.09, G:0.31, T:0.45
Consensus pattern (35 bp):
GTTGGATTAAATCTTTTGAGCATTGGCGTGTTGTG
Found at i:40810643 original size:35 final size:34
Alignment explanation
Indices: 40810563--40810656 Score: 107
Period size: 35 Copynumber: 2.7 Consensus size: 34
40810553 GTTGGATTAG
* * *
40810563 CTCTTTTGAGCATTGGCGTGTTGTGGTTGGATTAA
1 CTCTTTTGAGTATTGGCGTGTT-TGGGTGGACTAA
*
40810598 ATCTTTTGAGTATTGGCGTGTTTAGGGTGGACTAA
1 CTCTTTTGAGTATTGGCGTGTTT-GGGTGGACTAA
* *
40810633 CTCTTGTGAGTACTTGGTGTGTTT
1 CTCTTTTGAGTA-TTGGCGTGTTT
40810657 TGGAGGGATT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
34 1 0.02
35 39 0.78
36 10 0.20
ACGTcount: A:0.15, C:0.11, G:0.31, T:0.44
Consensus pattern (34 bp):
CTCTTTTGAGTATTGGCGTGTTTGGGTGGACTAA
Found at i:40820438 original size:13 final size:13
Alignment explanation
Indices: 40820420--40820444 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40820410 TATAGATACT
40820420 AAACATTAAATTC
1 AAACATTAAATTC
40820433 AAACATTAAATT
1 AAACATTAAATT
40820445 ATTGTTTTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
AAACATTAAATTC
Found at i:40820565 original size:27 final size:29
Alignment explanation
Indices: 40820500--40820565 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
40820490 AACTATTTGG
40820500 AAGTTTTCATTTAAGTCACTGAACTATTCA
1 AAGTTTTCATTTAAGTCACTGAACTATT-A
* * *
40820530 ATAGTTTTTATTTAAGTCATTGGACTATT-
1 A-AGTTTTCATTTAAGTCACTGAACTATTA
40820559 AAGTTTT
1 AAGTTTT
40820566 TTTTTAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 6 0.19
29 1 0.03
30 1 0.03
31 24 0.75
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (29 bp):
AAGTTTTCATTTAAGTCACTGAACTATTA
Found at i:40829635 original size:17 final size:17
Alignment explanation
Indices: 40829613--40829645 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
40829603 ATTTAACAAT
40829613 CAAACAAGCTTACATAG
1 CAAACAAGCTTACATAG
40829630 CAAACAAGCTTACATA
1 CAAACAAGCTTACATA
40829646 CCTTATGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.24, G:0.09, T:0.18
Consensus pattern (17 bp):
CAAACAAGCTTACATAG
Found at i:40843157 original size:20 final size:20
Alignment explanation
Indices: 40843118--40843157 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
40843108 TTATAATACA
***
40843118 AATATATATACATTTTTTAT
1 AATATATATACATACATTAT
40843138 AATATATATACATACATTAT
1 AATATATATACATACATTAT
40843158 TCAAAACTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (20 bp):
AATATATATACATACATTAT
Found at i:40852572 original size:40 final size:40
Alignment explanation
Indices: 40852501--40852595 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
40852491 GTTTGCAATT
* *
40852501 CTGGTGGCTTGTCCATAATTCTGGCAGTTTATCTACATTA
1 CTGGTGGCTTGTCCACAATTCTAGCAGTTTATCTACATTA
* * **
40852541 CTGGTGGCTTGTCCAC-ATATCTAGTATTTTATCTGTATTA
1 CTGGTGGCTTGTCCACAAT-TCTAGCAGTTTATCTACATTA
40852581 CTGGTGGCTTGTCCA
1 CTGGTGGCTTGTCCA
40852596 TAAATTGGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
39 2 0.04
40 46 0.96
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (40 bp):
CTGGTGGCTTGTCCACAATTCTAGCAGTTTATCTACATTA
Found at i:40864649 original size:23 final size:21
Alignment explanation
Indices: 40864619--40864661 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40864609 GAACAAATGA
40864619 TTTTAAAACCATTAAAATTATTT
1 TTTTAAAA-CA-TAAAATTATTT
*
40864642 TTTTAAAATATAAAATTATT
1 TTTTAAAACATAAAATTATT
40864662 AAATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 1 0.05
23 8 0.42
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTAAAACATAAAATTATTT
Found at i:40865587 original size:14 final size:15
Alignment explanation
Indices: 40865561--40865591 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
40865551 ATAAACATTA
40865561 AAAATATATTTTAAT
1 AAAATATATTTTAAT
40865576 AAAATA-ATTTTAAT
1 AAAATATATTTTAAT
40865590 AA
1 AA
40865592 TTTTATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAATATATTTTAAT
Found at i:40866649 original size:20 final size:21
Alignment explanation
Indices: 40866611--40866649 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
40866601 TATTGGCATT
*
40866611 TAGTTGAGTAGTTGGATTGTA
1 TAGTTGAGTAGTTGAATTGTA
*
40866632 TAGTTGA-TAGTTTAATTG
1 TAGTTGAGTAGTTGAATTG
40866650 GTAGCTAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (21 bp):
TAGTTGAGTAGTTGAATTGTA
Found at i:40868213 original size:14 final size:17
Alignment explanation
Indices: 40868178--40868213 Score: 51
Period size: 14 Copynumber: 2.3 Consensus size: 17
40868168 GGAATGGTGA
40868178 ATTGATGAGAAATTGAG
1 ATTGATGAGAAATTGAG
40868195 ATTGAT-AG-AATTG-G
1 ATTGATGAGAAATTGAG
40868209 ATTGA
1 ATTGA
40868214 ATTTATAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.32
15 5 0.26
16 2 0.11
17 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (17 bp):
ATTGATGAGAAATTGAG
Found at i:40868326 original size:43 final size:43
Alignment explanation
Indices: 40868264--40868520 Score: 264
Period size: 43 Copynumber: 6.0 Consensus size: 43
40868254 TAGGTGACTT
* *
40868264 TTCGGTTTATTCCAATGATGCACTGTGTGTGCTAGTAGATTTAC
1 TTCGGTTTA-TCCAATGATGCACTGTGTGTGCTAGTATAGTTAC
* * *
40868308 TTCGGTTTATCCAATGATGCGCTGTGTGTGATAGTATAGTTGC
1 TTCGGTTTATCCAATGATGCACTGTGTGTGCTAGTATAGTTAC
* * * *
40868351 TTCAGCTTATCCAATGATGCACTGTGTGTG-TCGATATACTTAC
1 TTCGGTTTATCCAATGATGCACTGTGTGTGCTAG-TATAGTTAC
* * * * * * *
40868394 TTCGGTTTATACGATGATGCATTGTGGGTGTTAGAATAGTTGC
1 TTCGGTTTATCCAATGATGCACTGTGTGTGCTAGTATAGTTAC
* * * * *
40868437 TTCGGTATATTCGATGATGCACCGTGTGTGCCAGTATAGTTAC
1 TTCGGTTTATCCAATGATGCACTGTGTGTGCTAGTATAGTTAC
* * * *
40868480 TTCTGTATATCCAATGATGCATTGTGGGTGCTAGTATAGTT
1 TTCGGTTTATCCAATGATGCACTGTGTGTGCTAGTATAGTT
40868521 GCTTTGGTAT
Statistics
Matches: 174, Mismatches: 37, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
42 2 0.01
43 161 0.93
44 11 0.06
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.39
Consensus pattern (43 bp):
TTCGGTTTATCCAATGATGCACTGTGTGTGCTAGTATAGTTAC
Found at i:40868380 original size:86 final size:86
Alignment explanation
Indices: 40868274--40868524 Score: 299
Period size: 86 Copynumber: 2.9 Consensus size: 86
40868264 TTCGGTTTAT
* * ** *
40868274 TCCAATGATGCACTGTGTGTGCTAGTAGATTTACTTCGGTTTATCCAATGATGCGCTGTGTGTGA
1 TCCAATGATGCACTGTGTGTGCTAGTATACTTACTTCGGTTTATCCAATGATGCATTGTGGGTGA
40868339 TAGTATAGTTGCTTCAGCT-TA
66 TAGTATAGTTGCTTC-GCTATA
* * *
40868360 TCCAATGATGCACTGTGTGTG-TCGATATACTTACTTCGGTTTATACGATGATGCATTGTGGGTG
1 TCCAATGATGCACTGTGTGTGCTAG-TATACTTACTTCGGTTTATCCAATGATGCATTGTGGGTG
* * *
40868424 TTAGAATAGTTGCTTCGGTATA
65 ATAGTATAGTTGCTTCGCTATA
* * * * * * * *
40868446 TTCGATGATGCACCGTGTGTGCCAGTATAGTTACTTCTGTATATCCAATGATGCATTGTGGGTGC
1 TCCAATGATGCACTGTGTGTGCTAGTATACTTACTTCGGTTTATCCAATGATGCATTGTGGGTGA
40868511 TAGTATAGTTGCTT
66 TAGTATAGTTGCTT
40868525 TGGTATACCT
Statistics
Matches: 139, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
85 4 0.03
86 134 0.96
87 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (86 bp):
TCCAATGATGCACTGTGTGTGCTAGTATACTTACTTCGGTTTATCCAATGATGCATTGTGGGTGA
TAGTATAGTTGCTTCGCTATA
Found at i:40869263 original size:29 final size:29
Alignment explanation
Indices: 40869230--40869293 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
40869220 TTTTTGACTC
40869230 TAGATTGTAGGCCTTATAAATGAATGTGG
1 TAGATTGTAGGCCTTATAAATGAATGTGG
*
40869259 TAGATTGTAGGCTTTATAAATGAATGTGG
1 TAGATTGTAGGCCTTATAAATGAATGTGG
40869288 TAGATT
1 TAGATT
40869294 TATGCCACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.38
Consensus pattern (29 bp):
TAGATTGTAGGCCTTATAAATGAATGTGG
Found at i:40869351 original size:22 final size:22
Alignment explanation
Indices: 40869321--40869376 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 22
40869311 CTGTGGTGTA
*
40869321 GTGGTAAGGTGGCGACACAGGT
1 GTGGCAAGGTGGCGACACAGGT
*
40869343 GTGGCAAGGAGGTGGTGACACAGGT
1 GTGGC-A--AGGTGGCGACACAGGT
40869368 GTGGCAAGG
1 GTGGCAAGG
40869377 AGGTTAGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 7 0.24
23 1 0.03
24 1 0.03
25 20 0.69
ACGTcount: A:0.23, C:0.12, G:0.48, T:0.16
Consensus pattern (22 bp):
GTGGCAAGGTGGCGACACAGGT
Found at i:40869355 original size:25 final size:25
Alignment explanation
Indices: 40869327--40869380 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
40869317 TGTAGTGGTA
40869327 AGGTGGCGACACAGGTGTGGCAAGG
1 AGGTGGCGACACAGGTGTGGCAAGG
*
40869352 AGGTGGTGACACAGGTGTGGCAAGG
1 AGGTGGCGACACAGGTGTGGCAAGG
40869377 AGGT
1 AGGT
40869381 TAGAGGTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.24, C:0.13, G:0.48, T:0.15
Consensus pattern (25 bp):
AGGTGGCGACACAGGTGTGGCAAGG
Found at i:40870911 original size:27 final size:26
Alignment explanation
Indices: 40870875--40871090 Score: 216
Period size: 27 Copynumber: 8.0 Consensus size: 26
40870865 AAAGGTTGTT
* *
40870875 AAATGACCAAAATACCCCCATAGGGTA
1 AAATTACCAAAATACCCCGAT-GGGTA
* *
40870902 AAATAACCAAAATACCCTCGATGGTTA
1 AAATTACCAAAATACCC-CGATGGGTA
* * *
40870929 AAATTATCGAAATACCCCTTATGGGTA
1 AAATTACCAAAATACCCC-GATGGGTA
* * **
40870956 AAATTATCGAAATACTCTTGATGGGTA
1 AAATTACCAAAATAC-CCCGATGGGTA
*
40870983 AAATTACCGAAATACCCTCGATGGGTA
1 AAATTACCAAAATACCC-CGATGGGTA
*
40871010 AAATTACCAAAATACCCCCAATGGGTA
1 AAATTACCAAAATA-CCCCGATGGGTA
**
40871037 AAATTACTGAAATACCCTCGATGGGTA
1 AAATTACCAAAATACCC-CGATGGGTA
*
40871064 AAATTACCAAAATACCCCAATAGGGTA
1 AAATTACCAAAATACCCCGAT-GGGTA
40871091 GAATGACCGT
Statistics
Matches: 160, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
26 8 0.05
27 145 0.91
28 7 0.04
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (26 bp):
AAATTACCAAAATACCCCGATGGGTA
Found at i:40870955 original size:54 final size:53
Alignment explanation
Indices: 40870884--40871080 Score: 245
Period size: 54 Copynumber: 3.7 Consensus size: 53
40870874 TAAATGACCA
* * *
40870884 AAATACCC-CCATAGGGTAAAATAACCAAAATACCCTCGATGGTTAAAATTATCG
1 AAATACCCTCGAT-GGGTAAAATTACCAAAATACCCTCGATGGGTAAAATTA-CG
* * * * *
40870938 AAATACCC-CTTATGGGTAAAATTATCGAAATACTCTTGATGGGTAAAATTACCG
1 AAATACCCTC-GATGGGTAAAATTACCAAAATACCCTCGATGGGTAAAATTA-CG
* *
40870992 AAATACCCTCGATGGGTAAAATTACCAAAATACCCCCAATGGGTAAAATTACTG
1 AAATACCCTCGATGGGTAAAATTACCAAAATACCCTCGATGGGTAAAATTAC-G
40871046 AAATACCCTCGATGGGTAAAATTACCAAAATACCC
1 AAATACCCTCGATGGGTAAAATTACCAAAATACCC
40871081 CAATAGGGTA
Statistics
Matches: 125, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
53 1 0.01
54 121 0.97
55 3 0.02
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (53 bp):
AAATACCCTCGATGGGTAAAATTACCAAAATACCCTCGATGGGTAAAATTACG
Found at i:40871090 original size:81 final size:81
Alignment explanation
Indices: 40870884--40871080 Score: 272
Period size: 81 Copynumber: 2.4 Consensus size: 81
40870874 TAAATGACCA
* * * * * *
40870884 AAATACCC-CCATAGGGTAAAATAACCAAAATACCCTCGATGGTTAAAATTATCGAAATACCCCT
1 AAATACCCTCGAT-GGGTAAAATTACCAAAATACCCTCGATGGGTAAAATTACCAAAATACCCCC
*
40870948 TATGGGTAAAATTATCG
65 AATGGGTAAAATTATCG
* * *
40870965 AAATACTCTTGATGGGTAAAATTACCGAAATACCCTCGATGGGTAAAATTACCAAAATACCCCCA
1 AAATACCCTCGATGGGTAAAATTACCAAAATACCCTCGATGGGTAAAATTACCAAAATACCCCCA
40871030 ATGGGTAAAATTA-CTG
66 ATGGGTAAAATTATC-G
40871046 AAATACCCTCGATGGGTAAAATTACCAAAATACCC
1 AAATACCCTCGATGGGTAAAATTACCAAAATACCC
40871081 CAATAGGGTA
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
80 1 0.01
81 98 0.97
82 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (81 bp):
AAATACCCTCGATGGGTAAAATTACCAAAATACCCTCGATGGGTAAAATTACCAAAATACCCCCA
ATGGGTAAAATTATCG
Found at i:40877671 original size:7 final size:7
Alignment explanation
Indices: 40877659--40877690 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
40877649 TTATTATCAT
40877659 AACCCTA
1 AACCCTA
40877666 AACCCTA
1 AACCCTA
40877673 AACCCTA
1 AACCCTA
40877680 AACCCTA
1 AACCCTA
40877687 AACC
1 AACC
40877691 ACTCATTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.44, G:0.00, T:0.12
Consensus pattern (7 bp):
AACCCTA
Found at i:40886642 original size:20 final size:19
Alignment explanation
Indices: 40886605--40886641 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
40886595 CTTTTGTTTC
40886605 TCTTTATTCTCTTCTTTTA
1 TCTTTATTCTCTTCTTTTA
40886624 TCTTT-TTCTCTCTCTTTT
1 TCTTTATTCTCT-TCTTTT
40886642 TGGAAATCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTATTCTCTTCTTTTA
Found at i:40887843 original size:21 final size:21
Alignment explanation
Indices: 40887819--40887888 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
40887809 GGGCACACAC
40887819 CCATGTGACTGAGGGACACGA
1 CCATGTGACTGAGGGACACGA
* * * *
40887840 CCATATGGCTGAGAGACATG-
1 CCATGTGACTGAGGGACACGA
*
40887860 CCTGTGTGACTG-GGGTACACGA
1 CC-ATGTGACTGAGGG-ACACGA
*
40887882 CCGTGTG
1 CCATGTG
40887889 GGCAGACCGT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
20 4 0.11
21 31 0.84
22 2 0.05
ACGTcount: A:0.23, C:0.23, G:0.34, T:0.20
Consensus pattern (21 bp):
CCATGTGACTGAGGGACACGA
Found at i:40888514 original size:3 final size:3
Alignment explanation
Indices: 40888508--40888539 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
40888498 TTTTTTGTTG
40888508 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40888540 AAACAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:40893980 original size:17 final size:18
Alignment explanation
Indices: 40893954--40893989 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40893944 CACTATCCTA
*
40893954 TATTAGTTTATT-TAATT
1 TATTAATTTATTATAATT
40893971 TATTAATTTATTATAATT
1 TATTAATTTATTATAATT
40893989 T
1 T
40893990 TCTAACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TATTAATTTATTATAATT
Found at i:40902421 original size:2 final size:2
Alignment explanation
Indices: 40902414--40902447 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40902404 NNNNNNNNNT
40902414 TA 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 TA
40902448 AACACATTCT
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):
TA
Found at i:40903469 original size:24 final size:25
Alignment explanation
Indices: 40903417--40903469 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
40903407 ACCATATGTC
*
40903417 AACCACATCCAAACATACCACAATG
1 AACCACATCCAAACATACCACAAAG
* *
40903442 -ACCACATTCAAACATATCA-AAAG
1 AACCACATCCAAACATACCACAAAG
40903465 AACCA
1 AACCA
40903470 TTCATAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.51, C:0.32, G:0.04, T:0.13
Consensus pattern (25 bp):
AACCACATCCAAACATACCACAAAG
Found at i:40917560 original size:24 final size:24
Alignment explanation
Indices: 40917508--40917560 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
40917498 ACCATATGTC
*
40917508 AACCACATCCAAACATACCACAAT
1 AACCACATCCAAACATACCAAAAT
* * *
40917532 GACCACATTCAAACATATCAAAAT
1 AACCACATCCAAACATACCAAAAT
40917556 AACCA
1 AACCA
40917561 TTCATAGCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.32, G:0.02, T:0.15
Consensus pattern (24 bp):
AACCACATCCAAACATACCAAAAT
Found at i:40922270 original size:27 final size:27
Alignment explanation
Indices: 40921500--40922260 Score: 859
Period size: 27 Copynumber: 28.2 Consensus size: 27
40921490 AGAGGTCAAT
*
40921500 AAATGACCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
40921527 AAATGATCGAAATACCCTCATATGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * * *
40921554 AAATAACCCAAATACCCTCAAACGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * * *
40921581 AAATAACCAAAACACCCCTATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
40921608 GAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
40921635 AAATGATCGAAATA-CCCCATCA-GGTA
1 AAATGACCGAAATACCCCCAT-AGGGTA
*
40921661 AAATGACCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
***
40921688 AAATGACCGAAATACCCTTGTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
40921715 AAATAACCAAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
40921742 AATTGACC-AACATACCCCTATAGGGTA
1 AAATGACCGAA-ATACCCCCATAGGGTA
* *
40921769 GAATGACCGAAATACCTCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
40921796 AAATGACTGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
40921823 AAATGACCGAAATCCCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
40921850 ATATGACCGAAATACCCCCATTA-GGTA
1 AAATGACCGAAATACCCCCA-TAGGGTA
* *
40921877 AAATAATCGAAATACCCCCATAGGGGTA
1 AAATGACCGAAATACCCCCATA-GGGTA
* *
40921905 AAATGACCAAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* ** *
40921932 AACTGACTAAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
40921959 AAATGAACGAAAT-CCCCTGATAGGGTA
1 AAATGACCGAAATACCCC-CATAGGGTA
*
40921986 AAATGACTGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
40922013 AAATGATCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * **
40922040 AAATGATCAAAATACCCTGATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
40922067 AAATGACCAAAATAACCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
** *
40922094 AAATGATTGAAATACCCCGATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
40922121 AAATGACCGATATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * **
40922148 AAATAACCGAAATGCCCTTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
40922175 AAATGATCGAAATAACCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
40922202 AAATGACCG-AATATCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
** *
40922228 AAATGAATGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
40922255 AAATGA
1 AAATGA
40922261 TTGGCATACC
Statistics
Matches: 621, Mismatches: 102, Indels: 22
0.83 0.14 0.03
Matches are distributed among these distances:
26 54 0.09
27 537 0.86
28 30 0.05
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:40922534 original size:26 final size:26
Alignment explanation
Indices: 40922501--40922573 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
40922491 ACATAAACTG
*
40922501 TTACTGGCAGCTTTGCTGTTATACT-
1 TTACTGGCAGCTTTGCTGTGATACTA
* * *
40922526 TATACTGGCAGCTCTGCTGCGATGCTA
1 T-TACTGGCAGCTTTGCTGTGATACTA
40922553 TTACTGGCAGCTTTGCTGTGA
1 TTACTGGCAGCTTTGCTGTGA
40922574 CATTGGTGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.03
26 38 0.95
27 1 0.03
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGTGATACTA
Found at i:40922717 original size:28 final size:28
Alignment explanation
Indices: 40922676--40922832 Score: 194
Period size: 28 Copynumber: 5.6 Consensus size: 28
40922666 TTAATGCACT
*
40922676 ACACTATTACTGTATTGGGCTAAGGCCC
1 ACACTGTTACTGTATTGGGCTAAGGCCC
*
40922704 ACACTGATT-TTGTATTGGGCTAAGGCCC
1 ACACTG-TTACTGTATTGGGCTAAGGCCC
* *
40922732 ATACTGATT-CTGTATTGGCCTAAGGCCC
1 ACACTG-TTACTGTATTGGGCTAAGGCCC
* **
40922760 ACACTGTTACTGTATTAGGCTAAGGCTT
1 ACACTGTTACTGTATTGGGCTAAGGCCC
*
40922788 TCACTGTTACTGTATTGGGCTAAGGCCC
1 ACACTGTTACTGTATTGGGCTAAGGCCC
40922816 ACACTG-TACTGTCATTG
1 ACACTGTTACTGT-ATTG
40922833 AATAGGGCTC
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
27 8 0.07
28 101 0.91
29 2 0.02
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.32
Consensus pattern (28 bp):
ACACTGTTACTGTATTGGGCTAAGGCCC
Found at i:40931878 original size:15 final size:16
Alignment explanation
Indices: 40931858--40931887 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40931848 TAACAACTAA
40931858 TATATAAT-TATATTT
1 TATATAATATATATTT
40931873 TATATAATATATATT
1 TATATAATATATATT
40931888 AATTGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:40932700 original size:25 final size:25
Alignment explanation
Indices: 40932643--40932700 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
40932633 AAATTTCTCC
*
40932643 TAAATTTTAATTTCATTTAATTATT
1 TAAATTTTAATTTCATTGAATTATT
*
40932668 TAACTTTTCAATTT-ATTGAATT-TT
1 TAAATTTT-AATTTCATTGAATTATT
40932692 TAATATTTT
1 TAA-ATTTT
40932701 GTGCTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.18
25 18 0.64
26 5 0.18
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (25 bp):
TAAATTTTAATTTCATTGAATTATT
Found at i:40950552 original size:17 final size:19
Alignment explanation
Indices: 40950530--40950576 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 19
40950520 TTATCAAAAT
*
40950530 AAATCAAAA-AAA-ATTAA
1 AAATCAAAATAAATATGAA
40950547 AAATCAAAATAAATATGAA
1 AAATCAAAATAAATATGAA
40950566 AAATCGAAAAT
1 AAATC-AAAAT
40950577 TGAAACAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 3 0.12
19 9 0.35
20 5 0.19
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.19
Consensus pattern (19 bp):
AAATCAAAATAAATATGAA
Found at i:40950983 original size:27 final size:26
Alignment explanation
Indices: 40950918--40951005 Score: 86
Period size: 27 Copynumber: 3.3 Consensus size: 26
40950908 GAAGTGGTGT
* *
40950918 CTATCTGGTAGGTGCTATTAGTGACTC
1 CTATCTGATAGGTGC-ACTAGTGACTC
* * *
40950945 ATATTTGGTAGGTGTCACTAGTGACTC
1 CTATCTGATAGGTG-CACTAGTGACTC
* * *
40950972 CTATCTGATAGGCGCTCTAGTGACCC
1 CTATCTGATAGGTGCACTAGTGACTC
40950998 CTATCTGA
1 CTATCTGA
40951006 CAAGCGGCAC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
26 18 0.35
27 32 0.63
28 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (26 bp):
CTATCTGATAGGTGCACTAGTGACTC
Found at i:40953549 original size:89 final size:89
Alignment explanation
Indices: 40953438--40953620 Score: 330
Period size: 89 Copynumber: 2.1 Consensus size: 89
40953428 AAATTCATAC
* *
40953438 CCAATTAAGCCCCTGTTGTTAATTAAAATAATCGATTAAGCCCTTCCGTTAATAGTTTCTGTCAT
1 CCAATTAAACCCCTGTTATTAATTAAAATAATCGATTAAGCCCTTCCGTTAATAGTTTCTGTCAT
40953503 TGACTGTTAAAATAAATTGACAGA
66 TGACTGTTAAAATAAATTGACAGA
* *
40953527 CCAATTAAACCCCTGTTATTAATTAAAATAATCGGTTAAGCCCTTCCGTTAATAGTTTTTGTCAT
1 CCAATTAAACCCCTGTTATTAATTAAAATAATCGATTAAGCCCTTCCGTTAATAGTTTCTGTCAT
40953592 TGACTGTTAAAATAAATTGACAGA
66 TGACTGTTAAAATAAATTGACAGA
40953616 CCAAT
1 CCAAT
40953621 CAAATGATGA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (89 bp):
CCAATTAAACCCCTGTTATTAATTAAAATAATCGATTAAGCCCTTCCGTTAATAGTTTCTGTCAT
TGACTGTTAAAATAAATTGACAGA
Found at i:40953735 original size:10 final size:10
Alignment explanation
Indices: 40953722--40953799 Score: 63
Period size: 10 Copynumber: 8.1 Consensus size: 10
40953712 GATATAAACT
40953722 TATAAAAAAA
1 TATAAAAAAA
*
40953732 TATAAAAACA
1 TATAAAAAAA
* *
40953742 TAT-AAATAT
1 TATAAAAAAA
* *
40953751 TATCAAAAAG
1 TATAAAAAAA
40953761 TAT--AAAAA
1 TATAAAAAAA
* *
40953769 TATAATAAAG
1 TATAAAAAAA
*
40953779 TATAAAAAAT
1 TATAAAAAAA
40953789 TATAAAAAAA
1 TATAAAAAAA
40953799 T
1 T
40953800 TAATAAAACT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
8 7 0.13
9 6 0.11
10 40 0.75
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (10 bp):
TATAAAAAAA
Found at i:40953792 original size:20 final size:19
Alignment explanation
Indices: 40953722--40953796 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
40953712 GATATAAACT
*
40953722 TATAAAAAAATATAAAAA-
1 TATAAAAAATTATAAAAAG
* *
40953740 CATATAAATATTATCAAAAAG
1 TATA-AAAAATTAT-AAAAAG
40953761 TAT-AAAAA-TATAATAAAG
1 TATAAAAAATTATAA-AAAG
40953779 TATAAAAAATTATAAAAA
1 TATAAAAAATTATAAAAA
40953797 AATTAATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
17 2 0.04
18 13 0.28
19 19 0.41
20 10 0.22
21 2 0.04
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (19 bp):
TATAAAAAATTATAAAAAG
Found at i:40953797 original size:29 final size:29
Alignment explanation
Indices: 40953722--40953806 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
40953712 GATATAAACT
* *
40953722 TATAAAAAAATATAAAAACATATAA-ATAT
1 TATAAAAAAATATAAAAA-ATATAATAAAG
* *
40953751 TATCAAAAAGTAT-AAAAATATAATAAAG
1 TATAAAAAAATATAAAAAATATAATAAAG
*
40953779 TATAAAAAATTATAAAAAA-ATTAATAAA
1 TATAAAAAAATATAAAAAATA-TAATAAA
40953807 ACTTAATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
27 6 0.13
28 18 0.38
29 23 0.49
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (29 bp):
TATAAAAAAATATAAAAAATATAATAAAG
Found at i:40954437 original size:21 final size:21
Alignment explanation
Indices: 40954401--40954445 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
40954391 TTTTAAAGAA
*
40954401 TTAAATACATTTTTATAAAATT
1 TTAAATACAGTTTTAT-AAATT
*
40954423 TTAAATA-AGTTTTATTAATT
1 TTAAATACAGTTTTATAAATT
40954443 TTA
1 TTA
40954446 CAATTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 7 0.33
22 7 0.33
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
TTAAATACAGTTTTATAAATT
Found at i:40957335 original size:25 final size:25
Alignment explanation
Indices: 40957306--40957419 Score: 98
Period size: 25 Copynumber: 4.7 Consensus size: 25
40957296 TTTAAATTTA
40957306 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
**
40957331 TTATTTGATGTAATACGCATAGAAAGT
1 TTATTTGATGTAATA-AAATAG-AAGT
* ** *
40957358 TT-TTCGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
40957376 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
40957402 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
40957420 ACCCTAACCT
Statistics
Matches: 68, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
18 1 0.01
19 3 0.04
20 4 0.06
21 4 0.06
23 2 0.03
24 3 0.04
25 36 0.53
26 9 0.13
27 6 0.09
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.43
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:40957454 original size:24 final size:24
Alignment explanation
Indices: 40957415--40957508 Score: 109
Period size: 24 Copynumber: 3.8 Consensus size: 24
40957405 TTTGATGTAA
*
40957415 TAAAAACCCTAA-CCTAAGTTAAT
1 TAAAAACCCTAACCCTAAATTAAT
**
40957438 TAAAAACCCTAACCCTAACCTAAT
1 TAAAAACCCTAACCCTAAATTAAT
40957462 TAAAAACCCTAACCCTAACATAACCTAAT
1 TAAAAACCCTAACCCTAA-AT----TAAT
40957491 TAAAAACCCTAACCCTAA
1 TAAAAACCCTAACCCTAA
40957509 CCTAACCTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
23 12 0.20
24 27 0.44
29 22 0.36
ACGTcount: A:0.48, C:0.30, G:0.01, T:0.21
Consensus pattern (24 bp):
TAAAAACCCTAACCCTAAATTAAT
Found at i:40957691 original size:149 final size:139
Alignment explanation
Indices: 40957434--40957801 Score: 538
Period size: 149 Copynumber: 2.6 Consensus size: 139
40957424 TAACCTAAGT
* *
40957434 TAATTAAAAACCCTAACCCTAACCTAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACC
1 TAATTAAAAACCCTAA-CATAACATAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACC
*
40957499 CTAACCCTAACCTAACCTAATTAAAAACCCAAACCCTAACCTAACCTAATTAAAAACCCAAACCC
65 CTAACCCTAACATAACCTAATTAAAAACCCAAACCCTAACCTAACCTAATTAAAAACCCAAACCC
*
40957564 AAACCTAACC
130 AAACATAACC
*
40957574 TAATTAAAAACCCTAACCCTAACATAACCTAATTAATTAAAAACCCCAACCCTAACATAACCTAA
1 TAATT--AAA----AACCCTAACATAA-C--A-TAATTAAAAACCCTAACCCTAACATAACCTAA
* * *
40957639 TTAAAAACCCTAACCCTAGCATAACCTAATTAAAAACCCTAACCCTAGCCTAACCTAATTAAAAA
56 TTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCCAAACCCTAACCTAACCTAATTAAAAA
* * *
40957704 GCCTAACCCTAACATAACC
121 CCCAAACCCAAACATAACC
40957723 TAATTAAAAACCCTAACATAACATAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCC
1 TAATTAAAAACCCTAACATAACATAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCC
40957788 TAACCCTAACATAA
66 TAACCCTAACATAA
40957802 TAATTTTACA
Statistics
Matches: 205, Mismatches: 13, Indels: 21
0.86 0.05 0.09
Matches are distributed among these distances:
139 54 0.26
140 6 0.03
142 4 0.02
143 13 0.06
145 4 0.02
146 9 0.04
147 3 0.01
149 112 0.55
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.20
Consensus pattern (139 bp):
TAATTAAAAACCCTAACATAACATAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCC
TAACCCTAACATAACCTAATTAAAAACCCAAACCCTAACCTAACCTAATTAAAAACCCAAACCCA
AACATAACC
Found at i:40957798 original size:29 final size:29
Alignment explanation
Indices: 40957419--40957801 Score: 518
Period size: 29 Copynumber: 13.4 Consensus size: 29
40957409 ATGTAATAAA
* **
40957419 AACCCTAACCTAAGTTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
40957448 AA-CC---C-TAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
40957472 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
40957501 AACCCTAACCTAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
40957530 AACCCTAACCTAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
40957559 AACCCAAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
40957588 AACCCTAACATAACCTAATTAATTAAAAACCCC
1 AACCCTAACATAACC----TAATTAAAAACCCT
40957621 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
40957650 AACCCTAGCATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* * *
40957679 AACCCTAGCCTAACCTAATTAAAAAGCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
40957708 AACCCTAACATAACCTAATT--AAA----
1 AACCCTAACATAACCTAATTAAAAACCCT
*
40957731 AACCCTAACATAACATAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
40957760 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
40957789 AACCCTAACATAA
1 AACCCTAACATAA
40957802 TAATTTTACA
Statistics
Matches: 322, Mismatches: 17, Indels: 30
0.87 0.05 0.08
Matches are distributed among these distances:
23 19 0.06
24 19 0.06
25 6 0.02
27 3 0.01
28 3 0.01
29 244 0.76
33 28 0.09
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.20
Consensus pattern (29 bp):
AACCCTAACATAACCTAATTAAAAACCCT
Found at i:40961148 original size:124 final size:124
Alignment explanation
Indices: 40960928--40961276 Score: 565
Period size: 124 Copynumber: 2.8 Consensus size: 124
40960918 CCAAACTTGA
* * *
40960928 TACTGTAGCAAAATCGCATCCACGAGGGCGCGATTTCACAATTTTTTCTCAAATAGCATCTTGGT
1 TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGT
*
40960993 AGAAGCGATTTTATACTTTTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACC
66 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACC
* * *
40961052 TACTGTAGCAAAATAGCGTCCACGATGGCGCGATTTCACAATTTCTTCTCAAATAACATCCTGGT
1 TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGT
40961117 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACC
66 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACC
* * * * *
40961176 TATTGCAGCAAAATCGCGTCCACGAGGGCGAGATTTCATAATTTCTTCTCAAATAGCATCCTCGT
1 TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGT
*
40961241 AGAAGCGATTTTATACTATTGGAC-CAGAAACGTCAA
66 AGAAGCGATTTTATACTATTTG-CTCAGAAACGTCAA
40961277 CTCGAAATAA
Statistics
Matches: 208, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
124 207 1.00
125 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (124 bp):
TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGT
AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACC
Found at i:40964511 original size:12 final size:13
Alignment explanation
Indices: 40964494--40964522 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40964484 TTTAGATAAA
40964494 TTAATTCAT-ATT
1 TTAATTCATCATT
40964506 TTAATTCATCATT
1 TTAATTCATCATT
40964519 TTAA
1 TTAA
40964523 ACCTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAATTCATCATT
Found at i:40968304 original size:19 final size:18
Alignment explanation
Indices: 40968280--40968325 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
40968270 CGCTCCTTTT
* *
40968280 TGCATTCATTTCATGCATC
1 TGCATTCATGTCAT-CATA
40968299 TGCATTGCATGTCATCATA
1 TGCATT-CATGTCATCATA
40968318 TGCATTCA
1 TGCATTCA
40968326 AGATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 15 0.62
20 7 0.29
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (18 bp):
TGCATTCATGTCATCATA
Found at i:40977514 original size:175 final size:174
Alignment explanation
Indices: 40977319--40977801 Score: 810
Period size: 175 Copynumber: 2.8 Consensus size: 174
40977309 GAAGAAGCAA
*
40977319 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAAT-CTCATCTCCCTGAGATTA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT-ATCTCCCTGAGATTA
40977383 CAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
65 CAGTGGAGC-GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
* *
40977448 GTCTTATCTTCCTGAGATTACAGTGGAATAGACCAAAGAATTTCAG
129 GTCTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATCTCAG
40977494 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
40977559 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
66 AGTGGAGC-GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
* *
40977624 TCTTATCTCCCTGAGGTTACAGTGGAATAGACCGAAGAATCTCAG
130 TCTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATCTCAG
*
40977669 ATCTTATCCCCCTGAGATTA-AGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
* * * *
40977733 AGTGGAGCGAATTAAAATAATA-GATCTTACCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAA
66 AGTGGAGCG-ATTAAAATAA-AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
40977797 GTCTT
129 GTCTT
40977802 GCCGACTAGA
Statistics
Matches: 294, Mismatches: 11, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
173 1 0.00
174 105 0.36
175 186 0.63
176 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (174 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
AGTGGAGCGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGT
CTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATCTCAG
Found at i:40977554 original size:44 final size:43
Alignment explanation
Indices: 40977232--40977740 Score: 247
Period size: 44 Copynumber: 11.7 Consensus size: 43
40977222 TCGCATCGGG
* * * ** *
40977232 TCTTATCTCCCTGA-AGTTGCAGTGGAGCAGACTGAGGAAACGAG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCTA-GAA
* * * *
40977276 TCTTAT-TCCCCTGA-AGTCACAGTGGGGCAGACTGAAG-AAGCAAA
1 TCTTATCT-CCCTGAGA-TTACAGTGGAGCAGATTGAAGCTAG--AA
* *
40977320 TCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAG-AA
* ** *
40977364 TCTCATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCT--AGAA
* * * * * * *
40977408 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATC-AG-G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCTAGAA
* ** ** **
40977449 TCTTATCTTCCTGAGATTACAGTGGAATAGACCAAAGAATTTCAG-A
1 TCTTATCTCCCTGAGATTACAGTGGAGCAG---ATTGAAGCT-AGAA
*
40977495 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAG-AA
* * ** *
40977539 TCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATAAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCT--AGAA
* * * * * * *
40977583 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATC-AG-G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCTAGAA
* ** **
40977624 TCTTATCTCCCTGAGGTTACAGTGGAATAGACCGAAGAATCTCAG-A
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG---CT-AGAA
* *
40977670 TCTTATCCCCCTGAGATTA-AGCGGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAG-AA
*
40977713 TCCTATCTCCCTGAGATTACAGTGGAGC
1 TCTTATCTCCCTGAGATTACAGTGGAGC
40977741 GAATTAAAAT
Statistics
Matches: 356, Mismatches: 78, Indels: 62
0.72 0.16 0.12
Matches are distributed among these distances:
41 55 0.15
42 10 0.03
43 34 0.10
44 188 0.53
45 22 0.06
46 47 0.13
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAA
Found at i:40979650 original size:12 final size:13
Alignment explanation
Indices: 40979635--40979663 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40979625 TTTACATAAA
40979635 TTAATTCAT-ATT
1 TTAATTCATCATT
40979647 TTAATTCATCATT
1 TTAATTCATCATT
40979660 TTAA
1 TTAA
40979664 ACCTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAATTCATCATT
Found at i:40985050 original size:37 final size:37
Alignment explanation
Indices: 40984896--40985055 Score: 180
Period size: 37 Copynumber: 4.3 Consensus size: 37
40984886 ATAGTCCCTG
*
40984896 ATTTAGCGTGTTATAGGGTGGATTAGCTCTTATGAGC
1 ATTTGGCGTGTTATAGGGTGGATTAGCTCTTATGAGC
* *
40984933 ATTTAGCGTGTTATATGGTGGATTAGCTCTTATGAGC
1 ATTTGGCGTGTTATAGGGTGGATTAGCTCTTATGAGC
* ** * * **
40984970 ATTTGACACGTTATCGAGAAGATTAGCTCTTATGAGC
1 ATTTGGCGTGTTATAGGGTGGATTAGCTCTTATGAGC
* *
40985007 ATTTGGCGTGTTATCA-GGTGGATTATCTCTTACGAGC
1 ATTTGGCGTGTTAT-AGGGTGGATTAGCTCTTATGAGC
40985044 GA-TTGGCGTGTT
1 -ATTTGGCGTGTT
40985056 TCGATTGGAA
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
37 101 0.99
38 1 0.01
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.38
Consensus pattern (37 bp):
ATTTGGCGTGTTATAGGGTGGATTAGCTCTTATGAGC
Found at i:40986156 original size:49 final size:48
Alignment explanation
Indices: 40986046--40986159 Score: 147
Period size: 48 Copynumber: 2.4 Consensus size: 48
40986036 ATGGGCAGGG
* *
40986046 ACACGGCTGTGTGTCCCTATTTCAAAAGTTACACAACTTTGGCATTCC
1 ACACGGCCGTGTGTCCCTATTTCAAAAGTTACACAACTTGGGCATTCC
* * ** * *
40986094 ACGCGGCCATGTGTCCCTATTTTGAAAGTTGCACGACTTGGGGCATTCC
1 ACACGGCCGTGTGTCCCTATTTCAAAAGTTACACAACTT-GGGCATTCC
40986143 ACACGGCCGTGTGTCCC
1 ACACGGCCGTGTGTCCC
40986160 CTGTTTTTTG
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 32 0.58
49 23 0.42
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.28
Consensus pattern (48 bp):
ACACGGCCGTGTGTCCCTATTTCAAAAGTTACACAACTTGGGCATTCC
Found at i:40994405 original size:40 final size:40
Alignment explanation
Indices: 40994350--40994430 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
40994340 TTTTATGGTA
40994350 GAAAGGTATTTTAGTCTAGTTTCTAAGACATCAAGAGGAT
1 GAAAGGTATTTTAGTCTAGTTTCTAAGACATCAAGAGGAT
40994390 GAAAGGTATTTTAGTCTAGTTTCTAAGACATCAAGAGGAT
1 GAAAGGTATTTTAGTCTAGTTTCTAAGACATCAAGAGGAT
40994430 G
1 G
40994431 CTGATTTGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (40 bp):
GAAAGGTATTTTAGTCTAGTTTCTAAGACATCAAGAGGAT
Found at i:40999722 original size:27 final size:27
Alignment explanation
Indices: 40999688--40999757 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
40999678 AAAGAAAATA
*
40999688 AAAG-AAGAAACTGGAAA-GAAAAAAAG
1 AAAGAAAGAAA-TGAAAAGGAAAAAAAG
*
40999714 AAAGAAAGAAATGAAAAGGAATAAAAG
1 AAAGAAAGAAATGAAAAGGAAAAAAAG
*
40999741 AATA-AAAGAAATCAAAA
1 AA-AGAAAGAAATGAAAA
40999758 TTGAAAAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
26 9 0.24
27 28 0.74
28 1 0.03
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.07
Consensus pattern (27 bp):
AAAGAAAGAAATGAAAAGGAAAAAAAG
Found at i:41002546 original size:29 final size:29
Alignment explanation
Indices: 41002504--41002599 Score: 111
Period size: 29 Copynumber: 3.3 Consensus size: 29
41002494 CCATCAATGG
41002504 TACATAGTACCTGATAAATATAACACCGA
1 TACATAGTACCTGATAAATATAACACCGA
* * *
41002533 TACAGAGTGCCTGATAACTATAACACCGA
1 TACATAGTACCTGATAAATATAACACCGA
* * * *
41002562 TAGAAAGTACCTAATAAATGTAATCACCGA
1 TACATAGTACCTGATAAATATAA-CACCGA
*
41002592 CACATAGT
1 TACATAGT
41002600 GCTTGATGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
29 43 0.80
30 11 0.20
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.23
Consensus pattern (29 bp):
TACATAGTACCTGATAAATATAACACCGA
Found at i:41007709 original size:13 final size:14
Alignment explanation
Indices: 41007694--41007753 Score: 70
Period size: 13 Copynumber: 4.3 Consensus size: 14
41007684 ATTTCAATTT
41007694 TTTAATAATAAAT-
1 TTTAATAATAAATC
*
41007707 TTTAAAAATAATAATC
1 TTTAATAAT-A-AATC
41007723 TTTAATAAT-AATC
1 TTTAATAATAAATC
*
41007736 TTTAATAATAAATA
1 TTTAATAATAAATC
41007750 TTTA
1 TTTA
41007754 TTATAATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
13 21 0.52
14 8 0.20
15 3 0.08
16 8 0.20
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAATAATAAATC
Found at i:41007716 original size:16 final size:16
Alignment explanation
Indices: 41007697--41007746 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
41007687 TCAATTTTTT
41007697 AATAATAAAT-TTTAAA
1 AATAAT-AATCTTTAAA
41007713 AATAATAATCTTT---
1 AATAATAATCTTTAAA
*
41007726 AATAATAATCTTTAAT
1 AATAATAATCTTTAAA
41007742 AATAA
1 AATAA
41007747 ATATTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 13 0.43
15 3 0.10
16 14 0.47
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATAATCTTTAAA
Found at i:41021924 original size:50 final size:50
Alignment explanation
Indices: 41021858--41022145 Score: 292
Period size: 50 Copynumber: 5.7 Consensus size: 50
41021848 TCATTCGATA
* * * *
41021858 CACGTAGTAGCATTCACATAGTACTACACACGTGATCAAGTTTTACAGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACTTTTACGGTT
* *
41021908 CACGTAGTAGCCTTCACATAGTACTACACACATGATCAACTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACTTTTACGGTT
* * * * *
41021958 CACGTAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACTTTTA-CGGTT
* * * *
41022009 CACGTAGTAGCCTTCACACAGTAATACACACGTGACCAAAGCTTCT-CGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AA-CTTTTACGGTT
* * * * * * * *
41022060 CACATTGTAGCCTTCACTTAGTACTACACATGTAACC-ATTATTTATGGGATA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACT-TTTA-CGG-TT
*
41022112 CACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CACGTAGTAGCCTTCACATAGTACTACACACGTG
41022146 TTCATCGATA
Statistics
Matches: 195, Mismatches: 36, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
48 1 0.01
49 3 0.02
50 85 0.44
51 72 0.37
52 31 0.16
53 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACTTTTACGGTT
Found at i:41022092 original size:102 final size:102
Alignment explanation
Indices: 41021906--41022145 Score: 340
Period size: 102 Copynumber: 2.4 Consensus size: 102
41021896 AGTTTTACAG
* * * * * *
41021906 TTCACGTAGTAGCCTTCACATAGTACTACACACATGATCAACTTTTACGGTTCACGTAGTAGCCT
1 TTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAACTTCTACGGTACACATAGTAGCCT
*
41021971 TCACTTAGTACTACACATGTGACCATCATTTAT-CGA
66 TCACTTAGTACTACACATGTAACCATCATTTATGCGA
* *
41022007 TTCACGTAGTAGCCTTCACACAGTAATACACACGTGACCAAAGCTTCT-CGGTACACATTGTAGC
1 TTCACGTAGTAGCCTTCACACAGTACTACACACGTGACC-AA-CTTCTACGGTACACATAGTAGC
* *
41022071 CTTCACTTAGTACTACACATGTAACCATTATTTATGGGA
64 CTTCACTTAGTACTACACATGTAACCATCATTTATGCGA
*
41022110 TACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 TTCACGTAGTAGCCTTCACACAGTACTACACACGTG
41022146 TTCATCGATA
Statistics
Matches: 123, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
101 35 0.28
102 48 0.39
103 40 0.33
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (102 bp):
TTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAACTTCTACGGTACACATAGTAGCCT
TCACTTAGTACTACACATGTAACCATCATTTATGCGA
Found at i:41024896 original size:43 final size:43
Alignment explanation
Indices: 41024840--41025024 Score: 273
Period size: 43 Copynumber: 4.3 Consensus size: 43
41024830 TTTAGAAAAA
*
41024840 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTTCCAC
* * * * *
41024883 AAATGCCGCTAAAGACCGGGACATTTAGTGACG-TTTTTCCCAC
1 AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTT-CCAC
41024926 AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTTCCAC
** *
41024969 AAACGCCGCTAAAGATTAGGACCTTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTTCCAC
41025012 AAACGCCGCTAAA
1 AAACGCCGCTAAA
41025025 AACATGACTT
Statistics
Matches: 126, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
42 5 0.04
43 116 0.92
44 5 0.04
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTTCCAC
Found at i:41025245 original size:18 final size:18
Alignment explanation
Indices: 41025222--41025281 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
41025212 TTAAAACAAG
41025222 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
*** * *
41025240 TTACATAAGAAAATT-G-T
1 TTACAT-TCTATATTAGAA
41025257 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
41025275 TTACATT
1 TTACATT
41025282 AGAATTACAT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 14 0.48
19 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (18 bp):
TTACATTCTATATTAGAA
Found at i:41030301 original size:13 final size:13
Alignment explanation
Indices: 41030283--41030307 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41030273 TGTCAATCTA
41030283 TTACATTAATTTG
1 TTACATTAATTTG
41030296 TTACATTAATTT
1 TTACATTAATTT
41030308 ATTTATTTAT
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:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
TTACATTAATTTG
Found at i:41030892 original size:19 final size:19
Alignment explanation
Indices: 41030868--41030905 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
41030858 TCTAGACTCT
41030868 AAATCCTAAACC-CTAACCC
1 AAATCCT-AACCTCTAACCC
41030887 AAATCCTAACCTCTAACCC
1 AAATCCTAACCTCTAACCC
41030906 CTACACCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.18
Consensus pattern (19 bp):
AAATCCTAACCTCTAACCC
Found at i:41031161 original size:14 final size:14
Alignment explanation
Indices: 41031126--41031162 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
41031116 ATCCTAAATT
41031126 AACCATATACCCTA
1 AACCATATACCCTA
**
41031140 AATTATATACCCTA
1 AACCATATACCCTA
41031154 AACCATATA
1 AACCATATA
41031163 TATTAAACCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (14 bp):
AACCATATACCCTA
Found at i:41031687 original size:83 final size:82
Alignment explanation
Indices: 41031534--41031693 Score: 266
Period size: 83 Copynumber: 1.9 Consensus size: 82
41031524 TCAAAAACGG
*
41031534 GCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAA
1 GCATTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAA
*
41031599 TGCCGCTAAAGGGCCGA
66 CGCCGCTAAAGGGCCGA
* * *
41031616 GCATTAGCGTCGCTTCTTCAAAAACGCCGCTAAAGGCCCCGAGCATTAGCGTCGCTTCTTCAAAA
1 GCATTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGG-CCCGAGCATTAGCGGCGCTTCTTCAAAA
41031681 ACGCCGCTAAAGG
65 ACGCCGCTAAAGG
41031694 CCCCAAAAAC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
82 33 0.46
83 39 0.54
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.20
Consensus pattern (82 bp):
GCATTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAA
CGCCGCTAAAGGGCCGA
Found at i:41031697 original size:42 final size:41
Alignment explanation
Indices: 41031534--41031696 Score: 263
Period size: 41 Copynumber: 4.0 Consensus size: 41
41031524 TCAAAAACGG
* *
41031534 GCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
* *
41031575 GCATTAGCGGCGCTTCTTCAAAAATGCCGCTAAAGGGCCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
*
41031616 GCATTAGCGTCGCTTCTTCAAAAACGCCGCTAAAGGCCCCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGG-CCCGA
*
41031658 GCATTAGCGTCGCTTCTTCAAAAACGCCGCTAAAGGCCC
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCC
41031697 CAAAAACTCA
Statistics
Matches: 114, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
41 74 0.65
42 40 0.35
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (41 bp):
GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
Found at i:41031780 original size:39 final size:40
Alignment explanation
Indices: 41031737--41031824 Score: 135
Period size: 39 Copynumber: 2.2 Consensus size: 40
41031727 TAGGCTTTTT
41031737 CGGCGCTTTT-CAAAAAACGCCGCTAATGCTT-ATTTTTAG
1 CGGCG-TTTTCCAAAAAACGCCGCTAATGCTTGATTTTTAG
*
41031776 CGGCGTTTTCCAAAAAGCGCCGCTAATGCTTGATTTTTAG
1 CGGCGTTTTCCAAAAAACGCCGCTAATGCTTGATTTTTAG
*
41031816 TGGCGTTTT
1 CGGCGTTTT
41031825 TTGTCTAAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
38 4 0.09
39 25 0.56
40 16 0.36
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (40 bp):
CGGCGTTTTCCAAAAAACGCCGCTAATGCTTGATTTTTAG
Found at i:41031848 original size:12 final size:12
Alignment explanation
Indices: 41031831--41031856 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41031821 TTTTTTGTCT
41031831 AAACGCCGCTAA
1 AAACGCCGCTAA
41031843 AAACGCCGCTAA
1 AAACGCCGCTAA
41031855 AA
1 AA
41031857 GCCTGTTTTT
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:41032223 original size:23 final size:23
Alignment explanation
Indices: 41032150--41032224 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
41032140 ATAAGTGCCA
* *
41032150 CACTGATATGTAGTCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
41032173 CACT-AATATGTAGCCGTAGCTAC
1 CACTGAA-ATGTAGCCGAAGCTAC
41032196 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
41032219 CACTGA
1 CACTGA
41032225 TCAATAACAC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.02
23 43 0.93
24 2 0.04
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:41036311 original size:15 final size:16
Alignment explanation
Indices: 41036286--41036315 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41036276 TTTTTGAGAG
41036286 TTTTATATTTAATTTT
1 TTTTATATTTAATTTT
41036302 TTTTAT-TTTAATTT
1 TTTTATATTTAATTT
41036316 GCATTTCTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATATTTAATTTT
Found at i:41038143 original size:23 final size:23
Alignment explanation
Indices: 41038099--41038151 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
41038089 TTTTTTTAAT
* *
41038099 TATTTTATATTCTTTTTCTTTTAC
1 TATTTTTTACTCTTTTTCTTTT-C
41038123 -ATTTTTTACTCTTTATT-TTTTC
1 TATTTTTTACTCTTT-TTCTTTTC
41038145 TATTTTT
1 TATTTTT
41038152 CTTCATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 1 0.04
23 22 0.88
24 2 0.08
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (23 bp):
TATTTTTTACTCTTTTTCTTTTC
Found at i:41038616 original size:3 final size:3
Alignment explanation
Indices: 41038610--41038659 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
41038600 AAAGAAGAGA
41038610 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41038658 AA
1 AA
41038660 AAGTAAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:41051951 original size:12 final size:12
Alignment explanation
Indices: 41051936--41051966 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
41051926 TAATTAATAT
41051936 TATTATTATTAC
1 TATTATTATTAC
*
41051948 TATTATTATTGC
1 TATTATTATTAC
41051960 TATTATT
1 TATTATT
41051967 TATATATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:41057439 original size:19 final size:20
Alignment explanation
Indices: 41057405--41057444 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
41057395 AATATATTTC
41057405 AAAAAAATAGAAAAAA-GAG
1 AAAAAAATAGAAAAAATGAG
41057424 AAAAAAATA-AAGAAAATGAG
1 AAAAAAATAGAA-AAAATGAG
41057444 A
1 A
41057445 GGCCAAGGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 13 0.68
20 4 0.21
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (20 bp):
AAAAAAATAGAAAAAATGAG
Found at i:41058789 original size:45 final size:45
Alignment explanation
Indices: 41058728--41059543 Score: 1175
Period size: 45 Copynumber: 18.1 Consensus size: 45
41058718 GGAGTAGGTT
* *
41058728 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAACGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
41058773 GAAGATAGCAGGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
41058818 AAAGATAGCAGGTCTTGTCTTCCTGTATTGGCAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
41058863 GAAGATAGCAGGTTTTGTCTTCCTGTATTAGCAACGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
41058908 GAAGATAGCAGATATTGTCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
41058953 AAAGATAGCA-AGTCTTGTCTTCCTGTATTGGTAGCGAAGTAGATT
1 GAAGATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
41058998 GAAGATAGCAGGTCTTATCTTCCTGTATTGGCAGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
41059043 GAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
41059088 AAAGATAGCAAATCTTATCTTCCTGTATTGGCAGCGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
41059133 GAAGATAGTAGGTTTTTATCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCA-GATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
41059179 GAAGATAGTAGGTCTTATCTTCCTGTATTGACAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
41059224 GAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
41059269 GAAGATAGCAGGTCTTGTCTTTCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
41059314 GAATATAGCAGATCTTGTCTTCCTGTATTAGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
41059359 GAAGATAGCAGCTCTTGTCTTCCCGTATTGGCAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
41059404 GAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
41059449 GAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
41059494 GAAGATAGCAGATCTTGTCTTCTTGTACTGGCAGTGAAGCAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
41059539 GAAGA
1 GAAGA
41059544 CATCAGCCTT
Statistics
Matches: 698, Mismatches: 70, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
44 1 0.00
45 656 0.94
46 41 0.06
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
Found at i:41062506 original size:51 final size:50
Alignment explanation
Indices: 41062410--41062569 Score: 284
Period size: 50 Copynumber: 3.2 Consensus size: 50
41062400 TAAGTACTTC
* * *
41062410 TGATTAGTGACAAGTGATAAGTGCTAGTTTAGCTACATTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGTTTAGCTACACTTATCTGATCAG
41062460 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAG-TTTAGCTACACTTATCTGATCAG
41062511 TGATAAGTGACAAGTGATAAGTGGTAGTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGTTTAGCTACACTTATCTGATCAG
41062561 TGATAAGTG
1 TGATAAGTG
41062570 GTAGCTTTAG
Statistics
Matches: 106, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
50 57 0.54
51 49 0.46
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (50 bp):
TGATAAGTGACAAGTGATAAGTGGTAGTTTAGCTACACTTATCTGATCAG
Found at i:41062575 original size:87 final size:87
Alignment explanation
Indices: 41062472--41062744 Score: 292
Period size: 87 Copynumber: 3.1 Consensus size: 87
41062462 ATAAGTGACA
41062472 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGACAAGTGATAAGTGGTA
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGACAAGTGATAAGTGGTA
41062537 GTTTAGCTACACTTATCTGATC
66 GTTTAGCTACACTTATCTGATC
* *
41062559 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGA-TAGCT--TTAGCT-G
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGACAAG-TGATAAG-TGG
* * * * **
41062620 CA-CTTATCTGATCAATAATAAGTGA-C
64 TAGTTTAGCT-A-CACT--TATCTGATC
* * *
41062646 AAGTGATAAGTGGTAGC-GTAGCTACACTTATTTGATC-GATGACAAGTGACAAGTGATAAGTGG
1 -AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG-TGATAAGTGACAAGTGATAAGTGG
*
41062709 TAGCTTTAGCTACACTTATCTAATC
64 TAG-TTTAGCTACACTTATCTGATC
*
41062734 AGTGACAAGTG
1 AGTGATAAGTG
41062745 ACAAGTGATA
Statistics
Matches: 150, Mismatches: 21, Indels: 30
0.75 0.10 0.15
Matches are distributed among these distances:
84 5 0.03
85 6 0.04
86 7 0.05
87 93 0.62
88 25 0.17
89 8 0.05
90 1 0.01
91 5 0.03
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (87 bp):
AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGACAAGTGATAAGTGGTA
GTTTAGCTACACTTATCTGATC
Found at i:41062588 original size:37 final size:37
Alignment explanation
Indices: 41062523--41062643 Score: 199
Period size: 37 Copynumber: 3.3 Consensus size: 37
41062513 ATAAGTGACA
41062523 AGTGATAAGTGGTAG-TTTAGCTACACTTATCTGATC
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
41062559 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
* *
41062596 AGTGATAAGTGATAGCTTTAGCTGCACTTATCTGATC
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
* *
41062633 AATAATAAGTG
1 AGTGATAAGTG
41062644 ACAAGTGATA
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 15 0.19
37 65 0.81
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (37 bp):
AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
Found at i:41062740 original size:51 final size:51
Alignment explanation
Indices: 41062596--41062755 Score: 225
Period size: 51 Copynumber: 3.2 Consensus size: 51
41062586 TTATCTGATC
* * * * *
41062596 AGTGATAAGTGATAGCTTTAGCTGCACTTATCTGATCAATAATAAGTGACA
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACA
* *
41062647 AGTGATAAGTGGTAGC-GTAGCTACACTTATTTGATC-GATGACAAGTGACA
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG-TGACAAGTGACA
*
41062697 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGTGACAAGTGACA
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACA
41062748 AGTGATAA
1 AGTGATAA
41062756 ATGTGATCCG
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
50 43 0.45
51 52 0.54
52 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (51 bp):
AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACA
Found at i:41063252 original size:13 final size:14
Alignment explanation
Indices: 41063217--41063254 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
41063207 AGGTCCTATT
*
41063217 TATTATGAATATAA
1 TATTATGAAGATAA
*
41063231 TATTTTGAAGAT-A
1 TATTATGAAGATAA
41063244 TATTATGAAGA
1 TATTATGAAGA
41063255 ATTTTAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (14 bp):
TATTATGAAGATAA
Found at i:41063485 original size:44 final size:44
Alignment explanation
Indices: 41063418--41064162 Score: 396
Period size: 44 Copynumber: 16.7 Consensus size: 44
41063408 GATAGCAAAC
* *
41063418 CTTATCTCCCTGAAGTTGTAGTGGAGCAGTTTGAAGATACTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAAT
*
41063462 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCA-ATTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-ATACTAAT
* * * * *
41063506 CCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAACGATA--AAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-GAA-GATACTAAT
** * * * **
41063550 AC-TATAC-CTTTGAAATTGCAGTAGG-TCAGATTAAATCTACCATAACAAGT
1 -CTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTGAAGATA-C-T---AA-T
* * **
41063600 CTTATCTCTCTGAAGTTGCAGTGGAGCATATTGAAGCCACTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAAT
* * * ** * *
41063644 CTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGCCACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAAT
*** * * * * * *
41063688 CTTATCTATATGAAGTTGCAGTAGAGTAGGTTAAAG-TAACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-ACTAAT
* * * * * * *
41063732 CTTATCCCCCTAAAGTTGCAGTGGGGCAGGTTGAAGATGCGAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAAT
* * * * * *
41063776 TTTATCTCCCTGAAGTTGTAGAGGAGCAGACTAAAGATAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CTAAT
* * *
41063821 CTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--AT--ACT--A-AT
* * * * * * *
41063872 CTTATCTCTCTGAAGTTGTAGTAGAGCAGA-T-CATAT-CAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAAT
* *
41063913 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTT--A-A-ACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAAT
* *
41063953 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAAT
* * *
41063997 CCTATCTCTCTGAAGTTACAGTGGAGCAGATT-AA-A-ACGATGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAC--T-AAT
* * * * * * *
41064041 CCTATAC-CTCTAAAGTTGCAGTAGG-TCAGATTAAACCATAACCAAT
1 CTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTGAA-GAT-ACTAAT
* *
41064087 CTTATCTCTCTGAAGTTGCAGCGGAGCAGATTGAA-ACTACTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TACTAAT
* * *
41064131 CCTATCTCCCTAAAGTTGCAGTGGAGCGGATT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
41064163 AAAACGATGA
Statistics
Matches: 544, Mismatches: 110, Indels: 94
0.73 0.15 0.13
Matches are distributed among these distances:
40 34 0.06
41 30 0.06
42 5 0.01
43 6 0.01
44 314 0.58
45 53 0.10
46 30 0.06
47 5 0.01
48 1 0.00
49 11 0.02
50 28 0.05
51 27 0.05
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAAT
Found at i:41063929 original size:41 final size:40
Alignment explanation
Indices: 41063872--41064027 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
41063862 AATTACAGAT
* * * *
41063872 CTTATCTCTCTGAAGTTGTAGTAGAGCAGATCATATCAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCA-AACAAAC
* * * *
41063913 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAACAAAC
* * *
41063953 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACTAATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TCAA---AC-AAAC
* *
41063998 C-TATCTCTCTGAAGTTACAGTGGAGCAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
41064028 TAAAACGATG
Statistics
Matches: 93, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
40 32 0.34
41 31 0.33
43 1 0.01
44 27 0.29
45 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (40 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAACAAAC
Found at i:41064113 original size:134 final size:134
Alignment explanation
Indices: 41063946--41064229 Score: 473
Period size: 134 Copynumber: 2.1 Consensus size: 134
41063936 GAGCAGGTTA
* * * *
41063946 AACCAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACTAATCCTATCTCTCTGAA
1 AACCAATCTTATCTTCCTGAAGTTGCAGCGGAGCAGATTGAAACTACTAATCCTATCTCCCTAAA
41064011 GTTACAGTGGAGCAGATTAAAACGATGAATCCTATACCTCTAAAGTTGCAGTAGGTCAGATTAAA
66 GTTACAGTGGAGCAGATTAAAACGATGAATCCTATACCTCTAAAGTTGCAGTAGGTCAGATTAAA
41064076 CCAT
131 CCAT
41064080 AACCAATCTTATC-TCTCTGAAGTTGCAGCGGAGCAGATTGAAACTACTAATCCTATCTCCCTAA
1 AACCAATCTTATCTTC-CTGAAGTTGCAGCGGAGCAGATTGAAACTACTAATCCTATCTCCCTAA
* * *
41064144 AGTTGCAGTGGAGCGGATTAAAACGATGAATCCTATACCTCTGAAGTTGCAGTAGGTCAGATTAA
65 AGTTACAGTGGAGCAGATTAAAACGATGAATCCTATACCTCTAAAGTTGCAGTAGGTCAGATTAA
41064209 ACCAT
130 ACCAT
*
41064214 AACAAATCTTAT-TTCC
1 AACCAATCTTATCTTCC
41064230 CTAGCGTTAA
Statistics
Matches: 140, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
133 3 0.02
134 137 0.98
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (134 bp):
AACCAATCTTATCTTCCTGAAGTTGCAGCGGAGCAGATTGAAACTACTAATCCTATCTCCCTAAA
GTTACAGTGGAGCAGATTAAAACGATGAATCCTATACCTCTAAAGTTGCAGTAGGTCAGATTAAA
CCAT
Found at i:41064163 original size:90 final size:86
Alignment explanation
Indices: 41063913--41064210 Score: 268
Period size: 90 Copynumber: 3.4 Consensus size: 86
41063903 CATATCAAAC
* * * * *
41063913 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAC-C-AATCTTATCTTCCTGAAGTTGCAGTG
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAACACTAATCCTATCTCCCTAAAGTTGCAGTG
* * *
41063976 GAGCAGATTGAAGCTACTAAT
66 GAGCAGATTAAACCTACCAAT
* * *
41063997 CCTATCTCTCTGAAGTTACAGTGGAGCAGATTAAA-ACGATGAATCCTATAC-CTCTAAAGTTGC
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAACAC--T-AATCCTAT-CTCCCTAAAGTTGC
*
41064060 AGTAGG-TCAGATTAAACCATAACCAAT
62 AGT-GGAGCAGATTAAACC-T-ACCAAT
*
41064087 CTTATCTCTCTGAAGTTGCAGCGGAGCAGATTGAAACTACTAATCCTATCTCCCTAAAGTTGCAG
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAGATT-AAAC-ACTAATCCTATCTCCCTAAAGTTGCAG
* * * **
41064152 TGGAGCGGATTAAAACGATGAAT
64 TGGAGCAGATTAAACCTACCAAT
* *
41064175 CCTATAC-CTCTGAAGTTGCAGTAGG-TCAGATTAAAC
1 CTTAT-CTCTCTGAAGTTGCAGT-GGAGCAGATTAAAC
41064211 CATAACAAAT
Statistics
Matches: 173, Mismatches: 25, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
84 32 0.18
87 4 0.02
88 56 0.32
89 10 0.06
90 65 0.38
91 4 0.02
93 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (86 bp):
CTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAACACTAATCCTATCTCCCTAAAGTTGCAGTG
GAGCAGATTAAACCTACCAAT
Found at i:41064176 original size:44 final size:42
Alignment explanation
Indices: 41063874--41064215 Score: 245
Period size: 44 Copynumber: 7.9 Consensus size: 42
41063864 TTACAGATCT
* * * *
41063874 TATCTCTCTGAAGTTGTAGTAGAGCAGATCATATC-A-AA-CC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTA-AACGATAATCC
* * * *
41063914 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAC--CAATCT
1 -TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAACGATAATCC
* *
41063955 TATCT-TCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACTAATCC
1 TATCTCT-CTGAAGTTGCAGTGGAGCAGATT-AAACGA-TAATCC
*
41063999 TATCTCTCTGAAGTTACAGTGGAGCAGATTAAAACGATGAATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATT-AAACGAT-AATCC
* * * *
41064043 TATAC-CTCTAAAGTTGCAGTAGG-TCAGATTAAACCATAACCAATCT
1 TAT-CTCTCTGAAGTTGCAGT-GGAGCAGATTAAACGAT----AATCC
* *
41064089 TATCTCTCTGAAGTTGCAGCGGAGCAGATTGAAACTACTAATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATT-AAACGA-TAATCC
* * *
41064133 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACGATGAATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATT-AAACGAT-AATCC
* *
41064177 TATAC-CTCTGAAGTTGCAGTAGG-TCAGATTAAACCATAA
1 TAT-CTCTCTGAAGTTGCAGT-GGAGCAGATTAAACGATAA
41064216 CAAATCTTAT
Statistics
Matches: 242, Mismatches: 38, Indels: 41
0.75 0.12 0.13
Matches are distributed among these distances:
40 31 0.13
41 30 0.12
42 2 0.01
43 14 0.06
44 123 0.51
45 10 0.04
46 26 0.11
47 5 0.02
48 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (42 bp):
TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAACGATAATCC
Done.