Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 53 of 207
Found at i:15542179 original size:25 final size:22
Alignment explanation
Indices: 15542125--15542181 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 22
15542115 CACGATTTCA
*
15542125 TTTCCCCAATTTCCCAACTTCT
1 TTTCCCCAATTTCCCAACTTAT
*
15542147 TTTCCCCCAATTTCCCCCAAGTTAT
1 TTT-CCCCAATTT--CCCAACTTAT
15542172 TCTTCCCCAA
1 T-TTCCCCAA
15542182 AGTATTTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 3 0.10
23 9 0.31
25 15 0.52
26 2 0.07
ACGTcount: A:0.19, C:0.42, G:0.02, T:0.37
Consensus pattern (22 bp):
TTTCCCCAATTTCCCAACTTAT
Found at i:15542193 original size:14 final size:15
Alignment explanation
Indices: 15542157--15542195 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
15542147 TTTCCCCCAA
*
15542157 TTTCCCCCAAGTTAT
1 TTTCCCCAAAGTTAT
15542172 TCTTCCCCAAAG-TAT
1 T-TTCCCCAAAGTTAT
15542187 TTTCCCCAA
1 TTTCCCCAA
15542196 TTTCCCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 5 0.23
16 9 0.41
ACGTcount: A:0.23, C:0.36, G:0.05, T:0.36
Consensus pattern (15 bp):
TTTCCCCAAAGTTAT
Found at i:15542458 original size:33 final size:33
Alignment explanation
Indices: 15542416--15542483 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
15542406 CATCTATGTT
*
15542416 ATTCGAGTTAAATGAGATGAGTGTTGGGTATGA
1 ATTCGAGTTAAATGAGATGAGTGTTAGGTATGA
*
15542449 ATTCGAGTTAAATGAGATTAGTGTTAGGTATGA
1 ATTCGAGTTAAATGAGATGAGTGTTAGGTATGA
15542482 AT
1 AT
15542484 ATATGTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.35
Consensus pattern (33 bp):
ATTCGAGTTAAATGAGATGAGTGTTAGGTATGA
Found at i:15542746 original size:17 final size:17
Alignment explanation
Indices: 15542724--15542761 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
15542714 ATCCCAGGAA
15542724 CTTGCAGCCTCTACTTC
1 CTTGCAGCCTCTACTTC
*
15542741 CTTGCAGCCTTTACTTC
1 CTTGCAGCCTCTACTTC
15542758 CTTG
1 CTTG
15542762 TGAACTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.37, G:0.13, T:0.39
Consensus pattern (17 bp):
CTTGCAGCCTCTACTTC
Found at i:15544259 original size:24 final size:24
Alignment explanation
Indices: 15544232--15544284 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
15544222 TATTTGTATA
15544232 ATATTTGTAACTAAAATTAATATT
1 ATATTTGTAACTAAAATTAATATT
*
15544256 ATATTTGTATCTAAAATTAATATT
1 ATATTTGTAACTAAAATTAATATT
15544280 ATATT
1 ATATT
15544285 ATAAAATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
ATATTTGTAACTAAAATTAATATT
Found at i:15544436 original size:22 final size:22
Alignment explanation
Indices: 15544391--15544436 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
15544381 AACTTAATTA
*
15544391 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAACTGAC
15544413 ATTAATATTATACATAGA-TGAC
1 ATTAATATTATACATA-ACTGAC
15544435 AT
1 AT
15544437 AACTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (22 bp):
ATTAATATTATACATAACTGAC
Found at i:15544439 original size:56 final size:56
Alignment explanation
Indices: 15544376--15544526 Score: 293
Period size: 56 Copynumber: 2.7 Consensus size: 56
15544366 TATTGTAAGG
*
15544376 GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAGAT
1 GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
15544432 GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
1 GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
15544488 GACATAACTTAATTAATTAATATTATACATAACTTACAT
1 GACATAACTTAATTAATTAATATTATACATAACTTACAT
15544527 AAATTAATTA
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 94 1.00
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (56 bp):
GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
Found at i:15544492 original size:22 final size:22
Alignment explanation
Indices: 15544447--15544492 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
15544437 AACTTAATTA
* *
15544447 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATGAC
15544469 ATTAATATTATACATAAATGAC
1 ATTAATATTATACATAAATGAC
15544491 AT
1 AT
15544493 AACTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTAATATTATACATAAATGAC
Found at i:15544512 original size:34 final size:34
Alignment explanation
Indices: 15544469--15544615 Score: 180
Period size: 34 Copynumber: 4.5 Consensus size: 34
15544459 CATAACTTAC
15544469 ATTAATATTATACATAAATGACATAACTTAATTA
1 ATTAATATTATACATAAATGACATAACTTAATTA
* * *
15544503 ATTAATATTATACATAACTTACATAAATTAATTA
1 ATTAATATTATACATAAATGACATAACTTAATTA
* * *
15544537 GTT-A-A-TATACATAAATTACATAACTT-A--C
1 ATTAATATTATACATAAATGACATAACTTAATTA
* *
15544565 ATTAATATGATACATAAATGACATAACTTAGTTA
1 ATTAATATTATACATAAATGACATAACTTAATTA
15544599 ATTAATATTATACATAA
1 ATTAATATTATACATAA
15544616 CTTACAACTT
Statistics
Matches: 94, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.02
29 1 0.01
30 2 0.02
31 38 0.40
32 1 0.01
33 1 0.01
34 49 0.52
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (34 bp):
ATTAATATTATACATAAATGACATAACTTAATTA
Found at i:15544527 original size:9 final size:9
Alignment explanation
Indices: 15544513--15544741 Score: 60
Period size: 9 Copynumber: 26.7 Consensus size: 9
15544503 ATTAATATTA
15544513 TACATAACT
1 TACATAACT
*
15544522 TACATAAAT
1 TACATAACT
* *
15544531 TA-ATTAGT
1 TACATAACT
15544539 TA-AT-A-T
1 TACATAACT
*
15544545 -ACATAAAT
1 TACATAACT
15544553 TACATAACT
1 TACATAACT
*
15544562 TACATTAATAT
1 TACA-TAA-CT
*
15544573 GATACATAAAT
1 --TACATAACT
*
15544584 GACATAACT
1 TACATAACT
**
15544593 TAGTTAA-T
1 TACATAACT
*
15544601 TA-AT-ATT
1 TACATAACT
15544608 ATACATAACT
1 -TACATAACT
15544618 TAC--AACT
1 TACATAACT
15544625 TACATAACT
1 TACATAACT
**
15544634 TACATATTTT
1 TACATA-ACT
*
15544644 TA-ATTA-T
1 TACATAACT
* *
15544651 T-CGTAAAT
1 TACATAACT
15544659 TACATAACT
1 TACATAACT
* *
15544668 TACTTAATT
1 TACATAACT
*
15544677 TTCATAA--
1 TACATAACT
*
15544684 TAAATAACT
1 TACATAACT
*
15544693 TACATAAAT
1 TACATAACT
* *
15544702 AAC-T-TCT
1 TACATAACT
15544709 TACATAACT
1 TACATAACT
** *
15544718 TATGTGACT
1 TACATAACT
15544727 TACATAACT
1 TACATAACT
15544736 TACATA
1 TACATA
15544742 GCATAATTTT
Statistics
Matches: 159, Mismatches: 39, Indels: 44
0.66 0.16 0.18
Matches are distributed among these distances:
5 1 0.01
6 4 0.03
7 23 0.14
8 18 0.11
9 95 0.60
10 8 0.05
11 3 0.02
12 3 0.02
13 4 0.03
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (9 bp):
TACATAACT
Found at i:15544549 original size:56 final size:54
Alignment explanation
Indices: 15544376--15544550 Score: 230
Period size: 56 Copynumber: 3.1 Consensus size: 54
15544366 TATTGTAAGG
*
15544376 GACATAACTTAATTAATTAATATTATACATAACTTACATTAA-TATTATACATAGAT
1 GACATAACTTAATTAATTAATATTATACATAACTTACATAAATTATTATA-AT--AT
*
15544432 GACATAACTTAATTAATTAATATTATACATAACTTACATTAA-TATTATACATAAAT
1 GACATAACTTAATTAATTAATATTATACATAACTTACATAAATTATTATA-AT--AT
15544488 GACATAACTTAATTAATTAATATTATACATAACTTACATAAATTAATTAGTTAATAT
1 GACATAACTTAATTAATTAATATTATACATAACTTACATAAATT-ATTA--TAATAT
15544545 -ACATAA
1 GACATAA
15544551 ATTACATAAC
Statistics
Matches: 113, Mismatches: 2, Indels: 8
0.92 0.02 0.07
Matches are distributed among these distances:
56 102 0.90
57 3 0.03
58 4 0.04
59 2 0.02
60 2 0.02
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (54 bp):
GACATAACTTAATTAATTAATATTATACATAACTTACATAAATTATTATAATAT
Found at i:15544589 original size:96 final size:90
Alignment explanation
Indices: 15544413--15544621 Score: 303
Period size: 96 Copynumber: 2.3 Consensus size: 90
15544403 CATAACTTAC
* *
15544413 ATTAATATTATACATAGA-TGACATAACTTAATTAATTAATATTATACATAACTTACATTAATAT
1 ATTAATATTATACATA-ACTTACATAAATTAATTAATTAATATTATACATAACTTACATTAATAT
*
15544477 TATACATAAATGACATAACTTAATTA
65 GATACATAAATGACATAACTTAATTA
*
15544503 ATTAATATTATACATAACTTACATAAATTAATTAGTTAATATACATAAATTACATAACTTACATT
1 ATTAATATTATACATAACTTACATAAATTAATTAATTAATAT---T--A-TACATAACTTACATT
*
15544568 AATATGATACATAAATGACATAACTTAGTTA
60 AATATGATACATAAATGACATAACTTAATTA
15544599 ATTAATATTATACATAACTTACA
1 ATTAATATTATACATAACTTACA
15544622 ACTTACATAA
Statistics
Matches: 107, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
89 1 0.01
90 37 0.35
93 1 0.01
95 1 0.01
96 67 0.63
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (90 bp):
ATTAATATTATACATAACTTACATAAATTAATTAATTAATATTATACATAACTTACATTAATATG
ATACATAAATGACATAACTTAATTA
Found at i:15544696 original size:34 final size:34
Alignment explanation
Indices: 15544621--15544699 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
15544611 CATAACTTAC
* * ***
15544621 AACTTACATAACTTACATATTTTTAATTATTCGT
1 AACTTACATAACTTACATAATTTTAATAATAAAT
* * *
15544655 AAATTACATAACTTACTTAATTTTCATAATAAAT
1 AACTTACATAACTTACATAATTTTAATAATAAAT
15544689 AACTTACATAA
1 AACTTACATAA
15544700 ATAACTTCTT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.42
Consensus pattern (34 bp):
AACTTACATAACTTACATAATTTTAATAATAAAT
Found at i:15544772 original size:25 final size:25
Alignment explanation
Indices: 15544743--15544798 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
15544733 ACTTACATAG
* *
15544743 CATAATTTTCATAATACACAACTTA
1 CATAATTTGCATAATAAACAACTTA
** *
15544768 CATAATTTGGGTAATAAATAACTTA
1 CATAATTTGCATAATAAACAACTTA
15544793 CATAAT
1 CATAAT
15544799 ACATAACTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (25 bp):
CATAATTTGCATAATAAACAACTTA
Found at i:15550241 original size:66 final size:65
Alignment explanation
Indices: 15550143--15550313 Score: 191
Period size: 66 Copynumber: 2.6 Consensus size: 65
15550133 GAGCAAATTA
* * * * * * *
15550143 CACAATTTAAAGCGGAGGCAACATCGAGAGAAGCTGATGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTAAGGTTCAACAAAAG-TATGAAGAACTCCA
15550207 G
65 G
*
15550208 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTAAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTAAGGTTCAACAAAAGTATGAAGAACTCCA
15550273 G
65 G
* * * * *
15550274 CAGCAGCTTAGAGCAGATGCGGCAGCAAGAGAAGCAAAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTAAGG
15550314 CGGCAGCGAG
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 2 0.02
66 84 0.93
67 4 0.04
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.14
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTAAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:15550356 original size:21 final size:21
Alignment explanation
Indices: 15550285--15550396 Score: 107
Period size: 21 Copynumber: 5.3 Consensus size: 21
15550275 AGCAGCTTAG
* * * *
15550285 AGCAGATGCGGCAGCAAGAGA
1 AGCAGAGGCTGCAGCGAGGGA
* * *
15550306 AGCAAAGGCGGCAGCGAGAGA
1 AGCAGAGGCTGCAGCGAGGGA
* * *
15550327 AGAACAGGCTGCAGCAAGGGA
1 AGCAGAGGCTGCAGCGAGGGA
* **
15550348 AGTAGAGGCTAAAGCGAGGGA
1 AGCAGAGGCTGCAGCGAGGGA
15550369 AGCAGAGGCTGCAGCGAGGGA
1 AGCAGAGGCTGCAGCGAGGGA
15550390 AGCAGAG
1 AGCAGAG
15550397 CAGCGTCAAA
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 75 1.00
ACGTcount: A:0.37, C:0.17, G:0.42, T:0.04
Consensus pattern (21 bp):
AGCAGAGGCTGCAGCGAGGGA
Found at i:15550749 original size:43 final size:42
Alignment explanation
Indices: 15550701--15550899 Score: 179
Period size: 43 Copynumber: 4.5 Consensus size: 42
15550691 ATCTGCCAAA
* *
15550701 TTTAGCGGTGTTTTTGGTAAAAGCGCCGCTATAGATTAGGGTC
1 TTTAGCGGCGTTTTTGG-AAAAGCGCCGCTATAGATCAGGGTC
* ** *
15550744 TTTAGCGGCGTTTTTACGCGAAGCGCCGCTATATAGA-CAAAGGGTA
1 TTTAGCGGCGTTTTT-GGAAAAGCGCCGC--TATAGATC--AGGGTC
*
15550790 TTTAGCGGCGTTTTCTGGATAAGCGCCGGCTATAGATCAGGGTC
1 TTTAGCGGCGTTTT-TGGAAAAGCGCC-GCTATAGATCAGGGTC
* **
15550834 TATT-GCGGCGTTTGTGGGAAAAATGCCGCTATAGATCAGGGTC
1 T-TTAGCGGCGTTT-TTGGAAAAGCGCCGCTATAGATCAGGGTC
15550877 TATT-GCGGCGTTTTTGGGAAAAG
1 T-TTAGCGGCGTTTTT-GGAAAAG
15550900 TGCTGCTAAA
Statistics
Matches: 129, Mismatches: 16, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
42 1 0.01
43 58 0.45
44 24 0.19
45 15 0.12
46 28 0.22
47 3 0.02
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTATAGATCAGGGTC
Found at i:15550814 original size:46 final size:44
Alignment explanation
Indices: 15550700--15550823 Score: 117
Period size: 46 Copynumber: 2.8 Consensus size: 44
15550690 AATCTGCCAA
* **
15550700 ATTTAGCGGTGTTTTTGGTAAAAGCGCCGC--TATAGATTAGGGT
1 ATTTAGCGGCGTTTTTGG-AAAAGCGCCGCTATATAGAAAAGGGT
* * **
15550743 CTTTAGCGGCGTTTTTACGCGAAGCGCCGCTATATAGACAAAGGGT
1 ATTTAGCGGCGTTTTT-GGAAAAGCGCCGCTATATAGA-AAAGGGT
*
15550789 ATTTAGCGGCGTTTTCTGGATAAGCGCCGGCTATA
1 ATTTAGCGGCGTTTT-TGGAAAAGCGCC-GCTATA
15550824 GATCAGGGTC
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
43 23 0.36
44 1 0.02
45 6 0.09
46 27 0.42
47 7 0.11
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.31
Consensus pattern (44 bp):
ATTTAGCGGCGTTTTTGGAAAAGCGCCGCTATATAGAAAAGGGT
Found at i:15550862 original size:90 final size:89
Alignment explanation
Indices: 15550700--15550866 Score: 203
Period size: 90 Copynumber: 1.9 Consensus size: 89
15550690 AATCTGCCAA
* * * **
15550700 ATTTAGCGGTGTTTTTGGTAAAAGCGCCGCTATAGATTAGGGTCTTTAGCGGCGTTTTTACGCGA
1 ATTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATCAGGGTCTTTAGCGGCGTTTGTACGAAA
*
15550765 AGCGCCGCTATATAGACAAAGGGT
66 AACGCCGCTATATAGACAAAGGGT
* **
15550789 ATTTAGCGGCGTTTTCTGG-ATAAGCGCCGGCTATAGATCAGGGTCTATT-GCGGCGTTTGTGGG
1 ATTTAGCGGCGTTTT-TGGTAAAAGCGCC-GCTATAGATCAGGGTCT-TTAGCGGCGTTTGTACG
*
15550852 AAAAATGCCGCTATA
63 AAAAACGCCGCTATA
15550867 GATCAGGGTC
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
89 22 0.34
90 41 0.63
91 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (89 bp):
ATTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATCAGGGTCTTTAGCGGCGTTTGTACGAAA
AACGCCGCTATATAGACAAAGGGT
Found at i:15550922 original size:43 final size:43
Alignment explanation
Indices: 15550818--15550928 Score: 114
Period size: 43 Copynumber: 2.6 Consensus size: 43
15550808 ATAAGCGCCG
* * *
15550818 GCTATAGATCAGGGTCTATTGCGGCGTTTGTGGGAAAAATGCC
1 GCTAAAGACCAGGATCTATTGCGGCGTTTGTGGGAAAAATGCC
* * * * * *
15550861 GCTATAGATCAGGGTCTATTGCGGCGTTTTTGGGAAAAGTGCT
1 GCTAAAGACCAGGATCTATTGCGGCGTTTGTGGGAAAAATGCC
* * *
15550904 GCTAAAGGCCATGATCTATAGCGGC
1 GCTAAAGACCAGGATCTATTGCGGC
15550929 ACTTATATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (43 bp):
GCTAAAGACCAGGATCTATTGCGGCGTTTGTGGGAAAAATGCC
Found at i:15550962 original size:43 final size:44
Alignment explanation
Indices: 15550915--15551039 Score: 159
Period size: 43 Copynumber: 2.9 Consensus size: 44
15550905 CTAAAGGCCA
* *
15550915 TGATCTATAGCGGCACTTATATAAAAAACGCCGCTACAGAC-CC
1 TGATCTATAGCGGCGCTTATATAAAAAACGCCGCTAAAGACACC
15550958 TGATCTATAGCGGCGCTT-TCA-ACAAAAACGCCGCTAAAGACACC
1 TGATCTATAGCGGCGCTTAT-ATA-AAAAACGCCGCTAAAGACACC
* * *
15551002 -AATCTATAGCGGCGGTTATATTAAAAACGCCGCTAAAG
1 TGATCTATAGCGGCGCTTATATAAAAAACGCCGCTAAAG
15551040 CTCTTAGTCT
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
42 2 0.03
43 67 0.93
44 3 0.04
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (44 bp):
TGATCTATAGCGGCGCTTATATAAAAAACGCCGCTAAAGACACC
Found at i:15551132 original size:22 final size:22
Alignment explanation
Indices: 15551104--15551146 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
15551094 TAGCGGCGCT
* *
15551104 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCACTAAAAGCCTA
15551126 AAAAAGCGCCACTAAAAGCCT
1 AAAAAGCGCCACTAAAAGCCT
15551147 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCACTAAAAGCCTA
Found at i:15552737 original size:22 final size:21
Alignment explanation
Indices: 15552708--15552756 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
15552698 TTTTTTTATA
15552708 TTTTTTT-ATTAACTTTTGTCT
1 TTTTTTTAATT-ACTTTTGTCT
* *
15552729 TTTTCTTTAATTATTTTTTTCT
1 TTTT-TTTAATTACTTTTGTCT
15552751 TTTTTT
1 TTTTTT
15552757 AAGTTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.25
22 15 0.62
23 3 0.12
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTTTTAATTACTTTTGTCT
Found at i:15552796 original size:18 final size:16
Alignment explanation
Indices: 15552760--15552806 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
15552750 TTTTTTTAAG
*
15552760 TTTTATATTTTTCTTA
1 TTTTATTTTTTTCTTA
15552776 TTTTATTTTGTTTCTTTA
1 TTTTATTTT-TTTC-TTA
15552794 TTTTATTTATTTT
1 TTTTATTT-TTTT
15552807 TTGTTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 8 0.30
17 4 0.15
18 14 0.52
19 1 0.04
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTATTTTTTTCTTA
Found at i:15552958 original size:14 final size:14
Alignment explanation
Indices: 15552941--15553016 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
15552931 GTCTTATAAA
15552941 TTTTAAAAATATAT
1 TTTTAAAAATATAT
* *
15552955 TTTTGAAATTA-ATT
1 TTTTAAAAATATA-T
* * * *
15552969 TTTTTAAATTTTAAA
1 TTTTAAAAATAT-AT
15552984 TTTT--AAATATAT
1 TTTTAAAAATATAT
15552996 TTTTAAAAATATA-
1 TTTTAAAAATATAT
15553009 TTTTAAAA
1 TTTTAAAA
15553017 CAAAATAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
12 5 0.10
13 13 0.27
14 26 0.53
15 4 0.08
16 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (14 bp):
TTTTAAAAATATAT
Found at i:15552964 original size:36 final size:34
Alignment explanation
Indices: 15552863--15553141 Score: 180
Period size: 36 Copynumber: 8.0 Consensus size: 34
15552853 ATAATATATA
* *
15552863 ATTTT-TAAAATTT-AAAATATTATTTTT-AGATT
1 ATTTTATAAATTTTAAAAATA-TATTTTTGAAATT
* * *
15552895 ATTTTTTAAATTTTAAATAT-TATTTTTTTAAATT
1 ATTTTATAAATTTTAAAAATATA-TTTTTGAAATT
15552929 ATGTCTTATAAATTTTAAAAATATATTTTTGAAATT
1 AT-T-TTATAAATTTTAAAAATATATTTTTGAAATT
* *
15552965 AATTTTTTTAAATTTTAAATTTTAAATATATTTTTAAAAATAT
1 -A-TTTTATAAATTTT-AA----AAATATATTTTT-GAAAT-T
**** ***
15553008 ATTTTA-AAACAAAATAAAATA-ATTTAAAAAATAT
1 ATTTTATAAATTTTA-AAAATATATTTTTGAAAT-T
*
15553042 ATTTT-TAAATTTTAAATATATATTTTTGAAATT
1 ATTTTATAAATTTTAAAAATATATTTTTGAAATT
15553075 ATTTCTTATAAATTTTAAAAATATATTTTTGAAATT
1 A-TT-TTATAAATTTTAAAAATATATTTTTGAAATT
* * *
15553111 ATTTTTTTAATTTTAAATAT-TATTTTT-AAAT
1 ATTTTATAAATTTTAAAAATATATTTTTGAAAT
15553142 ATTAAATATA
Statistics
Matches: 198, Mismatches: 27, Indels: 44
0.74 0.10 0.16
Matches are distributed among these distances:
32 11 0.06
33 26 0.13
34 50 0.25
35 9 0.05
36 68 0.34
37 6 0.03
38 1 0.01
39 1 0.01
40 4 0.02
41 16 0.08
42 5 0.03
43 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (34 bp):
ATTTTATAAATTTTAAAAATATATTTTTGAAATT
Found at i:15553014 original size:13 final size:13
Alignment explanation
Indices: 15552983--15553016 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
15552973 TAAATTTTAA
*
15552983 ATTTTAAATATAT
1 ATTTTAAAAATAT
15552996 -TTTTAAAAATAT
1 ATTTTAAAAATAT
15553008 ATTTTAAAA
1 ATTTTAAAA
15553017 CAAAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTTAAAAATAT
Found at i:15553055 original size:22 final size:22
Alignment explanation
Indices: 15553028--15553074 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
15553018 AAAATAAAAT
*
15553028 AATTTAAAAAATATATTTTT-A
1 AATTTTAAAAATATATTTTTGA
*
15553049 AATTTTAAATATATATTTTTGA
1 AATTTTAAAAATATATTTTTGA
15553071 AATT
1 AATT
15553075 ATTTCTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
AATTTTAAAAATATATTTTTGA
Found at i:15553136 original size:20 final size:20
Alignment explanation
Indices: 15553108--15553158 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
15553098 TATTTTTGAA
* *
15553108 ATTATTTTTTTAATTTTAAAT
1 ATTA-TTTTTAAATATTAAAT
15553129 ATTATTTTTAAATATTAAAT
1 ATTATTTTTAAATATTAAAT
15553149 A-TATTTTTAA
1 ATTATTTTTAA
15553159 TAATATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 9 0.32
20 15 0.54
21 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTATTTTTAAATATTAAAT
Found at i:15553139 original size:13 final size:13
Alignment explanation
Indices: 15553121--15553145 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15553111 ATTTTTTTAA
15553121 TTTTAAATATTAT
1 TTTTAAATATTAT
15553134 TTTTAAATATTA
1 TTTTAAATATTA
15553146 AATATATTTT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAATATTAT
Found at i:15553165 original size:21 final size:20
Alignment explanation
Indices: 15553106--15553165 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
15553096 TATATTTTTG
* *
15553106 AAAT-TATTTTTTTAATTTT
1 AAATATATTTTTATAATATT
15553125 AAATATTATTTTTA-AATATT
1 AAATA-TATTTTTATAATATT
15553145 AAATATATTTTTAATAATATT
1 AAATATATTTTT-ATAATATT
15553166 TAAACATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 11 0.31
20 11 0.31
21 13 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AAATATATTTTTATAATATT
Found at i:15553243 original size:11 final size:11
Alignment explanation
Indices: 15553221--15553250 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
15553211 AAAAAGGTTT
15553221 AAATATATTTAA
1 AAATA-ATTTAA
15553233 AAATAATTTAA
1 AAATAATTTAA
15553244 AAATAAT
1 AAATAAT
15553251 AATTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATAATTTAA
Found at i:15553253 original size:14 final size:14
Alignment explanation
Indices: 15553234--15553260 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
15553224 TATATTTAAA
15553234 AATAATTTAAAAAT
1 AATAATTTAAAAAT
15553248 AATAATTTAAAAA
1 AATAATTTAAAAA
15553261 ATTCTGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATTTAAAAAT
Found at i:15553530 original size:20 final size:20
Alignment explanation
Indices: 15553505--15553575 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
15553495 GTTTTATAAT
15553505 ATATATATTTTAAATTTTAA
1 ATATATATTTTAAATTTTAA
15553525 ATATATA---T--ATTTTAA
1 ATATATATTTTAAATTTTAA
*
15553540 AT-TATTTTTCTAAATTTTAA
1 ATATATATTT-TAAATTTTAA
15553560 ATAT-TATTTTTAAATT
1 ATATATA-TTTTAAATT
15553576 ATTGTTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 16
0.69 0.03 0.27
Matches are distributed among these distances:
14 3 0.07
15 9 0.22
17 1 0.02
18 1 0.02
20 23 0.56
21 4 0.10
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATATATTTTAAATTTTAA
Found at i:15553530 original size:22 final size:23
Alignment explanation
Indices: 15553496--15553542 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
15553486 ATTTGAAATG
15553496 TTTTATAATATATATATTTTAAA
1 TTTTATAATATATATATTTTAAA
15553519 TTTTA-AATATATATATTTTAAA
1 TTTTATAATATATATATTTTAAA
15553541 TT
1 TT
15553543 ATTTTTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTATAATATATATATTTTAAA
Found at i:15553576 original size:33 final size:33
Alignment explanation
Indices: 15553512--15553608 Score: 124
Period size: 33 Copynumber: 2.8 Consensus size: 33
15553502 AATATATATA
15553512 TTTTAAATTTTAAATATATATATTTTAAATTATT-
1 TTTTAAATTTTAAATAT-TAT-TTTTAAATTATTG
15553546 TTTCTAAATTTTAAATATTATTTTTAAATTATTG
1 TTT-TAAATTTTAAATATTATTTTTAAATTATTG
* * *
15553580 TTTAAAAATTGAAATATTATTTTTTAAAT
1 TTTTAAATTTTAAATATTA-TTTTTAAAT
15553609 ATTAAATATA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
33 25 0.44
34 18 0.32
35 14 0.25
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (33 bp):
TTTTAAATTTTAAATATTATTTTTAAATTATTG
Found at i:15553617 original size:21 final size:21
Alignment explanation
Indices: 15553573--15553639 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
15553563 TTATTTTTAA
* *
15553573 ATTATTGTTTAAAAATTGAAAT
1 ATTATTTTTTAAATATT-AAAT
15553595 ATTATTTTTTAAATATTAAAT
1 ATTATTTTTTAAATATTAAAT
* *
15553616 A-TATTTTTAATAATATAAAAT
1 ATTATTTTTTA-AATATTAAAT
15553637 ATT
1 ATT
15553640 TAAATATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.21
21 15 0.38
22 16 0.41
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
ATTATTTTTTAAATATTAAAT
Found at i:15553624 original size:19 final size:19
Alignment explanation
Indices: 15553569--15553640 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 19
15553559 AATATTATTT
15553569 TTAAAT-TATTGTTTAAAAA
1 TTAAATATATT-TTTAAAAA
*
15553588 TTGAAATATTATTTTTTAAATA
1 TT-AAATA-TA-TTTTTAAAAA
*
15553610 TTAAATATATTTTTAATAA
1 TTAAATATATTTTTAAAAA
15553629 TATAAA-ATATTT
1 T-TAAATATATTT
15553641 AAATATTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 17 0.38
20 10 0.22
21 5 0.11
22 11 0.24
23 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TTAAATATATTTTTAAAAA
Found at i:15553645 original size:18 final size:19
Alignment explanation
Indices: 15553601--15553645 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
15553591 AAATATTATT
15553601 TTTTAAAT-ATTAAATATA
1 TTTTAAATAATTAAATATA
*
15553619 TTTTTAATAATATAAA-ATA
1 TTTTAAATAAT-TAAATATA
15553638 -TTTAAATA
1 TTTTAAATA
15553646 TTTTAAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 14 0.61
19 5 0.22
20 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTAAATAATTAAATATA
Found at i:15553741 original size:34 final size:33
Alignment explanation
Indices: 15553679--15553755 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
15553669 TTTATTATTA
* *
15553679 GTTTTATAATATTTTAAATGTATATTTTAATTT
1 GTTTTATAATTTTTTAAATGTATATTTTAAATT
*
15553712 GTTTTATAATTTTTTTAAT-TATAATTTTTAAATT
1 GTTTTATAATTTTTTAAATGTAT-A-TTTTAAATT
*
15553746 ATTTTA-AATT
1 GTTTTATAATT
15553756 ATGATTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 3 0.08
33 22 0.58
34 13 0.34
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
GTTTTATAATTTTTTAAATGTATATTTTAAATT
Found at i:15553745 original size:14 final size:14
Alignment explanation
Indices: 15553715--15553771 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
15553705 TTAATTTGTT
*
15553715 TTATAATTTTTTTAA
1 TTATAA-TTTTTAAA
15553730 TTATAATTTTTAAA
1 TTATAATTTTTAAA
15553744 -T-T-A-TTTTAAA
1 TTATAATTTTTAAA
*
15553754 TTATGATTTTTAAA
1 TTATAATTTTTAAA
15553768 TTAT
1 TTAT
15553772 TTAAAATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
10 7 0.19
11 2 0.05
12 2 0.05
13 2 0.05
14 18 0.49
15 6 0.16
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
TTATAATTTTTAAA
Found at i:15553755 original size:24 final size:24
Alignment explanation
Indices: 15553713--15553792 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 24
15553703 TTTTAATTTG
*
15553713 TTTTATAATT-TTTTTAATTATAAT
1 TTTTA-AATTATTTTAAATTATAAT
*
15553737 TTTTAAATTATTTTAAATTATGAT
1 TTTTAAATTATTTTAAATTATAAT
* *
15553761 TTTTAAATTATTTAAAATATATTAT
1 TTTTAAATTATTTTAAAT-TATAAT
15553786 TTTTAAA
1 TTTTAAA
15553793 AATATGGCCT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
23 4 0.08
24 34 0.68
25 12 0.24
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (24 bp):
TTTTAAATTATTTTAAATTATAAT
Found at i:15553876 original size:29 final size:31
Alignment explanation
Indices: 15553822--15553881 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
15553812 ATTATTTTTT
*
15553822 TATAATATTTTAAATATTTTTAAATTTTAAA
1 TATAATATTTTAAATATTATTAAATTTTAAA
15553853 TATAAT-TTTTATAA-ATTATT-AATTTTAAA
1 TATAATATTTTA-AATATTATTAAATTTTAAA
15553882 GATATTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 9 0.33
30 10 0.37
31 8 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
TATAATATTTTAAATATTATTAAATTTTAAA
Found at i:15553876 original size:139 final size:135
Alignment explanation
Indices: 15553594--15553887 Score: 314
Period size: 139 Copynumber: 2.1 Consensus size: 135
15553584 AAAATTGAAA
* *
15553594 TATTATTTTTTAAATATTAAATATATTTTTAATAATATAAAATATTTAAATATTTTAAAGATATG
1 TATTAATTTTTAAATATTAAATATATTTTTAATAATATAAAATATTT-AATATTTTAAAAATATG
* * **
15553659 ATCTTTCAAATTTATTATTAGTTTTATAATATTTTAAATGTATATTTTAATTTGTTTTATAATTT
65 ACCTTTCAAATGTATTATTAGTTTTATAATATTTTAAA-GTATATTTTAATTTGTAATATAATTT
*
15553724 TTTTAAT
129 TTTAAAT
* *
15553731 TA-TAATTTTTAAATTATTTTAAATTATGATTTTTAAATTATTTAAAATATATT-AT-TTTTAAA
1 TATTAATTTTTAAA-TA--TTAAA-TAT-ATTTTT-AATAATATAAAATAT-TTAATATTTTAAA
* *
15553793 AATATGGCCTTTCAAATGTATTATT-TTTTTATAATATTTTAAA-TAT-TTTTAAATTT-TAAAT
59 AATATGACCTTTCAAATGTATTATTAGTTTTATAATATTTTAAAGTATATTTT-AATTTGT-AAT
15553854 ATAATTTTTATAAAT
122 ATAATTTTT-TAAAT
*
15553869 TATTAATTTTAAAGATATT
1 TATTAATTTTTAA-ATATT
15553888 CAAAAAAATT
Statistics
Matches: 133, Mismatches: 12, Indels: 24
0.79 0.07 0.14
Matches are distributed among these distances:
136 15 0.11
137 24 0.18
138 6 0.05
139 33 0.25
140 32 0.24
141 8 0.06
142 13 0.10
143 2 0.02
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.55
Consensus pattern (135 bp):
TATTAATTTTTAAATATTAAATATATTTTTAATAATATAAAATATTTAATATTTTAAAAATATGA
CCTTTCAAATGTATTATTAGTTTTATAATATTTTAAAGTATATTTTAATTTGTAATATAATTTTT
TAAAT
Found at i:15554014 original size:7 final size:7
Alignment explanation
Indices: 15553997--15554026 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
15553987 TTTTTTAATA
15553997 TAATAATT
1 TAAT-ATT
15554005 TAATATT
1 TAATATT
15554012 TAATATT
1 TAATATT
15554019 TAATATT
1 TAATATT
15554026 T
1 T
15554027 TATTTTGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TAATATT
Found at i:15557314 original size:30 final size:30
Alignment explanation
Indices: 15557274--15557346 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
15557264 GGTTGCTCTA
* *
15557274 GGTGAAATGAACTCAAACTGCCTATGTTTG
1 GGTGATATGAACTCAAACCGCCTATGTTTG
** *
15557304 GGTGATATGAACTTGAACCGCTTATGTTTG
1 GGTGATATGAACTCAAACCGCCTATGTTTG
15557334 GGTGATATGAACT
1 GGTGATATGAACT
15557347 TGAACTGGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (30 bp):
GGTGATATGAACTCAAACCGCCTATGTTTG
Found at i:15559667 original size:71 final size:72
Alignment explanation
Indices: 15559575--15559725 Score: 241
Period size: 71 Copynumber: 2.1 Consensus size: 72
15559565 TTAAAATATA
* * * * *
15559575 TTTTTAAAAATATATTGAATATATTATAATTTTAATATTGGTTATACTTAACA-TTTTTTAATAT
1 TTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGCTATACATAACATTTTTTTAATAT
15559639 ATTTAAT
66 ATTTAAT
15559646 TTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGCTATACATAACATTTTTTTAATAT
1 TTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGCTATACATAACATTTTTTTAATAT
15559711 ATTTAAT
66 ATTTAAT
15559718 TTCTTTAA
1 TT-TTTAA
15559726 GTTTTTAAAC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 48 0.66
72 20 0.27
73 5 0.07
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (72 bp):
TTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGCTATACATAACATTTTTTTAATAT
ATTTAAT
Found at i:15559672 original size:20 final size:20
Alignment explanation
Indices: 15559634--15559674 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
15559624 AACATTTTTT
* * *
15559634 AATATATTTAATTTTTTAAA
1 AATATATTAAATATATTAAA
15559654 AATATATTAAATATATTAAA
1 AATATATTAAATATATTAAA
15559674 A
1 A
15559675 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATATTAAATATATTAAA
Found at i:15559841 original size:40 final size:41
Alignment explanation
Indices: 15559788--15559872 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 41
15559778 AAAAATATAT
* *
15559788 ATTAAGTACATAAATTTATGAATGTGTACTAAAATTAAAAA
1 ATTAAGTACATAAATTTATAAATATGTACTAAAATTAAAAA
* *
15559829 ATTAA-TATATAAATTTATAAATATGTATTAAAATTAAAAA
1 ATTAAGTACATAAATTTATAAATATGTACTAAAATTAAAAA
15559869 ATTA
1 ATTA
15559873 TAACCAACAC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 35 0.88
41 5 0.12
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (41 bp):
ATTAAGTACATAAATTTATAAATATGTACTAAAATTAAAAA
Found at i:15559842 original size:20 final size:18
Alignment explanation
Indices: 15559817--15559872 Score: 51
Period size: 22 Copynumber: 2.9 Consensus size: 18
15559807 GAATGTGTAC
15559817 TAAAATTAAAAAATTAAT
1 TAAAATTAAAAAATTAAT
*
15559835 ATATAAATTTATAAATATGT-AT
1 -TA-AAA-TTA-AAAAAT-TAAT
15559857 TAAAATTAAAAAATTA
1 TAAAATTAAAAAATTA
15559873 TAACCAACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
17 1 0.03
18 5 0.17
19 5 0.17
20 6 0.20
21 5 0.17
22 7 0.23
23 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TAAAATTAAAAAATTAAT
Found at i:15560381 original size:16 final size:17
Alignment explanation
Indices: 15560342--15560384 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
15560332 AATTTTAATT
*
15560342 TTTACTTTTTAATATATA
1 TTTA-TTTTTAATATAAA
*
15560360 TATATTTTTAA-ATAAA
1 TTTATTTTTAATATAAA
15560376 TTTATTTTT
1 TTTATTTTT
15560385 TAACAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 12 0.55
17 7 0.32
18 3 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTATTTTTAATATAAA
Found at i:15560404 original size:19 final size:20
Alignment explanation
Indices: 15560369--15560412 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
15560359 ATATATTTTT
*
15560369 AAATAAATTTATTTTTTAAC
1 AAATAAATCTATTTTTTAAC
15560389 AAATAAATCT-TTTTTTAAC
1 AAATAAATCTATTTTTTAAC
15560408 AAATA
1 AAATA
15560413 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATAAATCTATTTTTTAAC
Found at i:15560970 original size:15 final size:16
Alignment explanation
Indices: 15560945--15560974 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15560935 TTGACATGTG
15560945 TATATTTTATTTTTAA
1 TATATTTTATTTTTAA
15560961 TATA-TTTATTTTTA
1 TATATTTTATTTTTA
15560975 TTTCCATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATATTTTATTTTTAA
Found at i:15562673 original size:18 final size:18
Alignment explanation
Indices: 15562634--15562673 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
15562624 GTCAGACATG
* *
15562634 GAGGAAAGGGATATAATT
1 GAGGAAAAGGATATAATC
*
15562652 GAGGAAAAGGATATTATC
1 GAGGAAAAGGATATAATC
15562670 GAGG
1 GAGG
15562674 GTGATACTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.35, T:0.20
Consensus pattern (18 bp):
GAGGAAAAGGATATAATC
Found at i:15571289 original size:16 final size:16
Alignment explanation
Indices: 15571258--15571294 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
15571248 TATTTTTCAA
15571258 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
15571274 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
15571290 TATTA
1 TATTA
15571295 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:15571312 original size:19 final size:18
Alignment explanation
Indices: 15571280--15571315 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
15571270 TTATTATTTT
*
15571280 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
15571298 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
15571316 CAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:15574983 original size:41 final size:39
Alignment explanation
Indices: 15574936--15575025 Score: 108
Period size: 41 Copynumber: 2.3 Consensus size: 39
15574926 CATTTTGTTA
* * * *
15574936 TATATATATATGCATACGTACATATTTTTTTAATTTATTT
1 TATATATATATACATACGTACATATTATTTT-ATATACTT
* *
15574976 GTATATATATATACATACTTATATATTATTTTATATACTT
1 -TATATATATATACATACGTACATATTATTTTATATACTT
15575016 TATATATATA
1 TATATATATA
15575026 CATATATGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 10 0.23
40 6 0.14
41 27 0.63
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (39 bp):
TATATATATATACATACGTACATATTATTTTATATACTT
Found at i:15575031 original size:12 final size:12
Alignment explanation
Indices: 15574978--15575052 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 12
15574968 ATTTATTTGT
15574978 ATATATATATAC
1 ATATATATATAC
15574990 ATACT-TATATA-
1 ATA-TATATATAC
* *
15575001 TTATTTTATATAC
1 ATA-TATATATAC
*
15575014 TTTATATATATAC
1 -ATATATATATAC
* *
15575027 ATATATGTGTAC
1 ATATATATATAC
15575039 AT-T-TATATAC
1 ATATATATATAC
15575049 ATAT
1 ATAT
15575053 GTTTTTATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
10 7 0.14
11 5 0.10
12 26 0.52
13 9 0.18
14 3 0.06
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (12 bp):
ATATATATATAC
Found at i:15603895 original size:17 final size:17
Alignment explanation
Indices: 15603868--15603900 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
15603858 AAAAGAATTG
15603868 ATTATTAATTAGATTGAA
1 ATTATTAATTA-ATTGAA
15603886 ATTA-TAATTAATTGA
1 ATTATTAATTAATTGA
15603901 CATAGTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (17 bp):
ATTATTAATTAATTGAA
Found at i:15614800 original size:18 final size:18
Alignment explanation
Indices: 15614755--15614789 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
15614745 ATGAGTTTAC
*
15614755 AAATATTTTAAATTATTG
1 AAATCTTTTAAATTATTG
15614773 AAATCTTTTAAATTATT
1 AAATCTTTTAAATTATT
15614790 TATGATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (18 bp):
AAATCTTTTAAATTATTG
Found at i:15617921 original size:13 final size:13
Alignment explanation
Indices: 15617903--15617936 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
15617893 ATTCATTTAA
15617903 CATTTCATA-TTTT
1 CATTTCA-AGTTTT
15617916 CATTTCAAGTTTT
1 CATTTCAAGTTTT
15617929 CATTTCAA
1 CATTTCAA
15617937 ATGTCCCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 1 0.05
13 19 0.95
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.53
Consensus pattern (13 bp):
CATTTCAAGTTTT
Found at i:15617983 original size:13 final size:13
Alignment explanation
Indices: 15617964--15617995 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
15617954 ATCTATATCT
15617964 ATATAAACATTTC
1 ATATAAACATTTC
*
15617977 GTATAAACATTTC
1 ATATAAACATTTC
15617990 ATATAA
1 ATATAA
15617996 TTATTTTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (13 bp):
ATATAAACATTTC
Found at i:15618047 original size:27 final size:27
Alignment explanation
Indices: 15618017--15618070 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
15618007 TAGCTGATTC
15618017 ATATAAACA-TTCAATATATCT-ATTTTT
1 ATATAAACATTTC-ATATAT-TGATTTTT
*
15618044 ATATAACCATTTCATATATTGATTTTT
1 ATATAAACATTTCATATATTGATTTTT
15618071 CCACTTGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 1 0.04
27 20 0.83
28 3 0.12
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (27 bp):
ATATAAACATTTCATATATTGATTTTT
Found at i:15618058 original size:40 final size:40
Alignment explanation
Indices: 15617952--15618061 Score: 100
Period size: 40 Copynumber: 2.8 Consensus size: 40
15617942 CCCTTTTTAC
* * * *
15617952 ATATCTATATCTATATAAACATTTCGTATAAACATTTCAT
1 ATATCTATTTTTATATAACCATTTCATATAAACATTTCAT
** * *
15617992 ATAAT-TATTTTCGTATAGCTGA-TTCATATAAACA-TTCAAT
1 AT-ATCTATTTTTATATAAC-CATTTCATATAAACATTTC-AT
15618032 ATATCTATTTTTATATAACCATTTCATATA
1 ATATCTATTTTTATATAACCATTTCATATA
15618062 TTGATTTTTC
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
39 6 0.11
40 44 0.83
41 3 0.06
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.45
Consensus pattern (40 bp):
ATATCTATTTTTATATAACCATTTCATATAAACATTTCAT
Found at i:15618146 original size:25 final size:25
Alignment explanation
Indices: 15618113--15618174 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
15618103 ATACACGGGA
* *
15618113 ATAA-TGCTCACTCAAGCTGTAACT
1 ATAATTGCTCACACAAGCTGCAACT
* *
15618137 ATAATTGCTCACACGAGTTGCAACT
1 ATAATTGCTCACACAAGCTGCAACT
*
15618162 GTAATTGCTCACA
1 ATAATTGCTCACA
15618175 TAGGCTGTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 4 0.12
25 28 0.88
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (25 bp):
ATAATTGCTCACACAAGCTGCAACT
Found at i:15624365 original size:50 final size:50
Alignment explanation
Indices: 15624244--15624365 Score: 138
Period size: 50 Copynumber: 2.4 Consensus size: 50
15624234 GCCGAGAGAA
* * *
15624244 AAGATTCACCGATGTGGCTTTAATCTTTTTAACTGCAATGCCAGGGAAAT
1 AAGATTCACCGATGTGACTTTAAGCTTTTTAACTGCAATGCCAGGGAAAC
* * * * * *
15624294 AAGATTCGCTGTTGT-AGCTTTAAGCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCACCGATGTGA-CTTTAAGCTTTTTAACTGCAATGCCAGGGAAAC
*
15624344 AATATTCACCGATGTGACTTTA
1 AAGATTCACCGATGTGACTTTA
15624366 GCTGCTCCGC
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
50 56 0.98
51 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (50 bp):
AAGATTCACCGATGTGACTTTAAGCTTTTTAACTGCAATGCCAGGGAAAC
Found at i:15625744 original size:14 final size:13
Alignment explanation
Indices: 15625725--15625793 Score: 59
Period size: 13 Copynumber: 5.0 Consensus size: 13
15625715 TTAGCCTCTC
15625725 CATTTTTACTTTTT
1 CATTTTT-CTTTTT
15625739 CATTTTTTTCATTTTT
1 CA--TTTTTC-TTTTT
*
15625755 CATTTTTCATTTT
1 CATTTTTCTTTTT
* *
15625768 CATTTTTCATCTCT
1 CATTTTTC-TTTTT
15625782 C-TTTTTCTTTTT
1 CATTTTTCTTTTT
15625794 TTTTTGAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
12 3 0.07
13 18 0.40
14 11 0.24
15 1 0.02
16 12 0.27
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (13 bp):
CATTTTTCTTTTT
Found at i:15625788 original size:13 final size:13
Alignment explanation
Indices: 15625743--15625777 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
15625733 CTTTTTCATT
15625743 TTTTTCATTTTTCA
1 TTTTTCA-TTTTCA
15625757 TTTTTCATTTTCA
1 TTTTTCATTTTCA
15625770 TTTTTCAT
1 TTTTTCAT
15625778 CTCTCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTCATTTTCA
Found at i:15625794 original size:7 final size:7
Alignment explanation
Indices: 15625725--15625777 Score: 65
Period size: 7 Copynumber: 7.4 Consensus size: 7
15625715 TTAGCCTCTC
15625725 CATTTTT
1 CATTTTT
15625732 -ACTTTTT
1 CA-TTTTT
15625739 CATTTTTTT
1 CA--TTTTT
15625748 CATTTTT
1 CATTTTT
15625755 CATTTTT
1 CATTTTT
15625762 CA-TTTT
1 CATTTTT
15625768 CATTTTT
1 CATTTTT
15625775 CAT
1 CAT
15625778 CTCTCTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
6 7 0.17
7 26 0.63
8 1 0.02
9 7 0.17
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:15625794 original size:20 final size:20
Alignment explanation
Indices: 15625743--15625793 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
15625733 CTTTTTCATT
* *
15625743 TTTTTCATTTTTCATTTTTC
1 TTTTTCATTTTTCATCTCTC
*
15625763 ATTTTCATTTTTCATCTCTC
1 TTTTTCATTTTTCATCTCTC
15625783 TTTTTC-TTTTT
1 TTTTTCATTTTT
15625794 TTTTTGAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTCATTTTTCATCTCTC
Found at i:15627331 original size:35 final size:35
Alignment explanation
Indices: 15627289--15627373 Score: 161
Period size: 35 Copynumber: 2.4 Consensus size: 35
15627279 GTATAAATTC
*
15627289 ATGAATAATTATTTGTACCATATGATTATGAATGA
1 ATGAATAATAATTTGTACCATATGATTATGAATGA
15627324 ATGAATAATAATTTGTACCATATGATTATGAATGA
1 ATGAATAATAATTTGTACCATATGATTATGAATGA
15627359 ATGAATAATAATTTG
1 ATGAATAATAATTTG
15627374 GAAGAAAATC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (35 bp):
ATGAATAATAATTTGTACCATATGATTATGAATGA
Found at i:15631858 original size:3 final size:3
Alignment explanation
Indices: 15631850--15631896 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
15631840 AAGCAAAAAC
* *
15631850 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TGA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
15631897 GTGGAAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:15637509 original size:22 final size:20
Alignment explanation
Indices: 15637481--15637531 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
15637471 GAGTTTTAGT
15637481 TTTTATTTTTATTT-TTTTAA
1 TTTTATTTTT-TTTATTTTAA
15637501 TTAATTATTTTTTTTATTTTAA
1 TT--TTATTTTTTTTATTTTAA
15637523 TTTTATTTT
1 TTTTATTTT
15637532 CCAAAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
22 16 0.57
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTATTTTTTTTATTTTAA
Found at i:15639889 original size:11 final size:11
Alignment explanation
Indices: 15639875--15639921 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
15639865 AAAAAAAAGG
15639875 TATTTTAAAAA
1 TATTTTAAAAA
15639886 TATTTTAAAAA
1 TATTTTAAAAA
**
15639897 TA-TAAAAAAA
1 TATTTTAAAAA
15639907 GTATTTTAAAAA
1 -TATTTTAAAAA
15639919 TAT
1 TAT
15639922 AAAAAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 6 0.20
11 18 0.60
12 6 0.20
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:15639896 original size:33 final size:32
Alignment explanation
Indices: 15639847--15639934 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 32
15639837 ATAAACACCA
*
15639847 AAAAAAATTTTAAAAAATAAAAAAAAGGTATTTT
1 AAAAATATTTT-AAAAATAAAAAAAA-GTATTTT
15639881 AAAAATATTTTAAAAATATAAAAAAAGTATTTT
1 AAAAATATTTTAAAAATA-AAAAAAAGTATTTT
*
15639914 AAAAATA--TAAAAAATAAAAAA
1 AAAAATATTTTAAAAATAAAAAA
15639935 TAAAAATATT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
30 5 0.10
31 8 0.16
33 21 0.41
34 17 0.33
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (32 bp):
AAAAATATTTTAAAAATAAAAAAAAGTATTTT
Found at i:15639906 original size:22 final size:22
Alignment explanation
Indices: 15639881--15639927 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
15639871 AAGGTATTTT
15639881 AAAAATATTTTAAAAATATAAA
1 AAAAATATTTTAAAAATATAAA
*
15639903 AAAAGTATTTTAAAAATATAAA
1 AAAAATATTTTAAAAATATAAA
15639925 AAA
1 AAA
15639928 TAAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAAATATTTTAAAAATATAAA
Found at i:15642852 original size:27 final size:26
Alignment explanation
Indices: 15642822--15642892 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
15642812 ATAAAAATAC
* *
15642822 TAAAATTTTGTTAAAAATTATAAATTT
1 TAAAATTTTATTAAAAATGA-AAATTT
* **
15642849 TAAAACTTTATTATTAATGAAAATTT
1 TAAAATTTTATTAAAAATGAAAATTT
15642875 TAAAATTTTATTATAAAA
1 TAAAATTTTATTA-AAAA
15642893 AAATTAAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 18 0.51
27 17 0.49
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (26 bp):
TAAAATTTTATTAAAAATGAAAATTT
Found at i:15648673 original size:10 final size:9
Alignment explanation
Indices: 15648658--15648696 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
15648648 ATCGATTCAC
15648658 TTCTTTCTTT
1 TTCTTT-TTT
15648668 TTCTTTTCTT
1 TTCTTTT-TT
15648678 TTCTTTTTT
1 TTCTTTTTT
15648687 TT-TTTTTT
1 TTCTTTTTT
15648695 TT
1 TT
15648697 ACTGAAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.29
9 5 0.18
10 15 0.54
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:15648695 original size:16 final size:16
Alignment explanation
Indices: 15648661--15648693 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
15648651 GATTCACTTC
15648661 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTTTCT
15648677 TTTCTTTTT-TTTT-T
1 TTTCTTTTTCTTTTCT
15648691 TTT
1 TTT
15648694 TTTACTGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 4 0.24
16 9 0.53
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTCTTTTTCTTTTCT
Found at i:15649722 original size:24 final size:25
Alignment explanation
Indices: 15649695--15649753 Score: 93
Period size: 24 Copynumber: 2.4 Consensus size: 25
15649685 ATAAAAAATA
*
15649695 ACCAAAATATTATAACTTTTT-TTT
1 ACCAAAATATTATAAATTTTTATTT
15649719 ACCAAAATATTATAAATTTTTATTT
1 ACCAAAATATTATAAATTTTTATTT
*
15649744 ACTAAAATAT
1 ACCAAAATAT
15649754 AAAAAAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 20 0.62
25 12 0.38
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (25 bp):
ACCAAAATATTATAAATTTTTATTT
Found at i:15649920 original size:19 final size:19
Alignment explanation
Indices: 15649893--15649962 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
15649883 TCAACTCATT
*
15649893 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
15649912 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
15649930 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
15649949 TTTTAATTTAATAA
1 TTTTAATTTAATAA
15649963 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:15649941 original size:37 final size:37
Alignment explanation
Indices: 15649898--15649968 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
15649888 TCATTTTTTT
15649898 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
15649935 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
15649969 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:15650236 original size:30 final size:31
Alignment explanation
Indices: 15650177--15650238 Score: 99
Period size: 33 Copynumber: 2.0 Consensus size: 31
15650167 ATTATTTTCT
15650177 TTTTATTCCCCTTCAACTCATTTTTTTAGTAAA
1 TTTTATTCCCCTTCAACTCA--TTTTTAGTAAA
15650210 TTTTATTCCCCTTCAACTCA-TTTTAGTAA
1 TTTTATTCCCCTTCAACTCATTTTTAGTAA
15650239 TAATAAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 9 0.31
33 20 0.69
ACGTcount: A:0.24, C:0.23, G:0.03, T:0.50
Consensus pattern (31 bp):
TTTTATTCCCCTTCAACTCATTTTTAGTAAA
Found at i:15650330 original size:30 final size:31
Alignment explanation
Indices: 15650294--15650354 Score: 106
Period size: 32 Copynumber: 2.0 Consensus size: 31
15650284 AGTTTTATTA
15650294 TTACT-AAAATGAGTTGAAGGGGAATAAAAT
1 TTACTAAAAATGAGTTGAAGGGGAATAAAAT
15650324 TTACTAAAAAATGAGTTGAAGGGGAATAAAA
1 TTACT-AAAAATGAGTTGAAGGGGAATAAAA
15650355 AGAAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 5 0.17
32 24 0.83
ACGTcount: A:0.49, C:0.03, G:0.23, T:0.25
Consensus pattern (31 bp):
TTACTAAAAATGAGTTGAAGGGGAATAAAAT
Found at i:15650615 original size:19 final size:18
Alignment explanation
Indices: 15650559--15650615 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
15650549 AGTATTACTT
* *
15650559 AATAGTTTATTAAATGAG
1 AATAGTTTATTAAATAAA
*
15650577 AATAGTTTATTAAATTAA
1 AATAGTTTATTAAATAAA
15650595 AATAGATTTATTAAATAAA
1 AATAG-TTTATTAAATAAA
15650614 AA
1 AA
15650616 AATGAGTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
18 21 0.60
19 14 0.40
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.39
Consensus pattern (18 bp):
AATAGTTTATTAAATAAA
Found at i:15652346 original size:16 final size:17
Alignment explanation
Indices: 15652326--15652370 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
15652316 GAAATAGTTA
15652326 TATTTAGAACAATCATG
1 TATTTAGAACAATCATG
* *
15652343 -ATTTGGAACAA-CTTG
1 TATTTAGAACAATCATG
15652358 TATTTAGAACAAT
1 TATTTAGAACAAT
15652371 TGTGTTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 3 0.13
16 20 0.87
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (17 bp):
TATTTAGAACAATCATG
Found at i:15653223 original size:15 final size:15
Alignment explanation
Indices: 15653203--15653235 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
15653193 AATCACATTC
15653203 ATATTATATATACTA
1 ATATTATATATACTA
15653218 ATATTATATATACTA
1 ATATTATATATACTA
15653233 ATA
1 ATA
15653236 GGATTATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATTATATATACTA
Found at i:15656348 original size:40 final size:40
Alignment explanation
Indices: 15656198--15656387 Score: 169
Period size: 40 Copynumber: 4.8 Consensus size: 40
15656188 TTGAATGATG
* * * * *
15656198 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTTACTAAA
* * *
15656238 TCCGGACTAAGAT-CCGAAGGCATTTATGCGAGTTACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTACGAGTTACTAAA
* * *
15656277 TTCGTGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
*
15656316 TCCGGGTTAAGTCCCG-AGGCTATTTGTACGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGC-ATTTGTACGAGTTACTA-AA
* *
15656357 --CGGGCTATGTCCCGAAGGCATTTGAACGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGT
15656388 AGCTATATCC
Statistics
Matches: 125, Mismatches: 17, Indels: 17
0.79 0.11 0.11
Matches are distributed among these distances:
38 23 0.18
39 46 0.37
40 47 0.38
41 9 0.07
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
Found at i:15656380 original size:39 final size:38
Alignment explanation
Indices: 15656251--15656387 Score: 143
Period size: 39 Copynumber: 3.5 Consensus size: 38
15656241 GGACTAAGAT
* * * *
15656251 CCGAAGGCATTTATGCGAGTTACTAATTCGTGCTAAG-C
1 CCGAAGGCATTTGTACGAGTTACTAA-ACGGGCTAAGTC
* *
15656289 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTACGAGTTACTAAA--CGGGCTAAGTC
*
15656329 CCG-AGGCTATTTGTACGAGTTACTATAACGGGCTATGTC
1 CCGAAGGC-ATTTGTACGAGTTACTA-AACGGGCTAAGTC
*
15656368 CCGAAGGCATTTGAACGAGT
1 CCGAAGGCATTTGTACGAGT
15656388 AGCTATATCC
Statistics
Matches: 85, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
38 25 0.29
39 34 0.40
40 24 0.28
41 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (38 bp):
CCGAAGGCATTTGTACGAGTTACTAAACGGGCTAAGTC
Found at i:15664271 original size:39 final size:40
Alignment explanation
Indices: 15664168--15664352 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
15664158 TTGAATGATG
* * * *
15664168 TCCGGGCTAAGTCCCGCAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
15664207 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
15664248 TCCGGGCTAAG-CCTGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
15664287 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
15664326 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
15664353 AACGAGTAGT
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
39 36 0.29
40 79 0.63
41 10 0.08
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:15664374 original size:79 final size:79
Alignment explanation
Indices: 15664221--15664385 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
15664211 GGACTAAGAT
* * **
15664221 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCTGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
15664286 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
15664300 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGT
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
15664363 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
15664379 CCGAAGG
1 CCGAAGG
15664386 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.66
80 23 0.31
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:15666949 original size:16 final size:15
Alignment explanation
Indices: 15666928--15666961 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
15666918 TGCATAATCC
15666928 TATTAGTATATATATA
1 TATTAGTATATATA-A
15666944 TATTAGTATATATAA
1 TATTAGTATATATAA
15666959 TAT
1 TAT
15666962 GAATGTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TATTAGTATATATAA
Found at i:15672775 original size:40 final size:40
Alignment explanation
Indices: 15672738--15672867 Score: 196
Period size: 40 Copynumber: 3.3 Consensus size: 40
15672728 GCTACTCGTT
*
15672738 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
15672778 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
15672818 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
15672856 -AAATGCCTTCGG
1 CAAATGCCTTCGG
15672868 ATCTTTCGGA
Statistics
Matches: 85, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
37 12 0.14
38 7 0.08
39 15 0.18
40 49 0.58
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:15675757 original size:22 final size:22
Alignment explanation
Indices: 15675729--15675782 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
15675719 ATTTATGTTT
15675729 TTAACTTTTATTTATTTAATTA
1 TTAACTTTTATTTATTTAATTA
*
15675751 TTAACTTTTATTTATTTAATTT
1 TTAACTTTTATTTATTTAATTA
15675773 TTAACATTTT
1 TTAAC-TTTT
15675783 TGACATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.65
Consensus pattern (22 bp):
TTAACTTTTATTTATTTAATTA
Found at i:15676459 original size:19 final size:15
Alignment explanation
Indices: 15676422--15676463 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
15676412 TGCTTAAGGC
15676422 TTAATTAATTAATGG
1 TTAATTAATTAATGG
*
15676437 TTAATTAAGTTAATTG
1 TTAATTAA-TTAATGG
*
15676453 -TGATTAATTAA
1 TTAATTAATTAA
15676464 AATTTAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.17
15 14 0.58
16 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (15 bp):
TTAATTAATTAATGG
Found at i:15695183 original size:16 final size:16
Alignment explanation
Indices: 15695162--15695193 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
15695152 AATATGTACA
15695162 TGTCTAGGGTTGGATC
1 TGTCTAGGGTTGGATC
15695178 TGTCTAGGGTTGGATC
1 TGTCTAGGGTTGGATC
15695194 CTAATTGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTCTAGGGTTGGATC
Found at i:15700735 original size:43 final size:43
Alignment explanation
Indices: 15700696--15700789 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 43
15700686 ATTATTATGG
* * *
15700696 GATATTATCTTTTAGCAATTTGATTCTTAATGAG-ATATTATAA
1 GATATTATCTCTTAGCAATATGATTCCTAATG-GCATATTATAA
15700739 GATATTATCTCTTAGCAATATGATTCCTAATGGCATATTATAA
1 GATATTATCTCTTAGCAATATGATTCCTAATGGCATATTATAA
15700782 GATATTAT
1 GATATTAT
15700790 TATGGGCTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 1 0.02
43 46 0.98
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.44
Consensus pattern (43 bp):
GATATTATCTCTTAGCAATATGATTCCTAATGGCATATTATAA
Found at i:15701504 original size:181 final size:181
Alignment explanation
Indices: 15701200--15701564 Score: 649
Period size: 181 Copynumber: 2.0 Consensus size: 181
15701190 AACTTTCCAC
* *
15701200 TGTTAGTGCACATGGTTCCTGAAATCCACATGCCGGTGTGAAAGTCTATTGCATGTGTACAACTT
1 TGTTAGTGCACATGGTTCCTAAAATCCACATGCCGGTGTGAAAGCCTATTGCATGTGTACAACTT
15701265 CCAAAATGCTCTAATGTTCTAATTTCCACCCATTTTTCACTCCTATTGCTCCCAAGTGCCCTATT
66 CCAAAATGCTCTAATGTTCTAATTTCCACCCATTTTTCACTCCTATTGCTCCCAAGTGCCCTATT
15701330 AAGCATCAAAACACGAATATAAAGAATTAAGAGTGTACAATTTACCATTAA
131 AAGCATCAAAACACGAATATAAAGAATTAAGAGTGTACAATTTACCATTAA
*
15701381 TGTTAGTGCACATGGTTCCTAAAATCCACATGCCGGTGTGAAAGCCTATTGCATGTGTACAGCTT
1 TGTTAGTGCACATGGTTCCTAAAATCCACATGCCGGTGTGAAAGCCTATTGCATGTGTACAACTT
**
15701446 CTGAAATGCTCTAATGTTCTAATTTCCACCCATTTTTCACTCCTATTGCTCCCAAGTGCCCTATT
66 CCAAAATGCTCTAATGTTCTAATTTCCACCCATTTTTCACTCCTATTGCTCCCAAGTGCCCTATT
* * * *
15701511 AAGCATCAAAACATGAATATAAAGAATTAGGAGTGTATATTTTACCATTAA
131 AAGCATCAAAACACGAATATAAAGAATTAAGAGTGTACAATTTACCATTAA
15701562 TGT
1 TGT
15701565 CACATAATCA
Statistics
Matches: 175, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
181 175 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (181 bp):
TGTTAGTGCACATGGTTCCTAAAATCCACATGCCGGTGTGAAAGCCTATTGCATGTGTACAACTT
CCAAAATGCTCTAATGTTCTAATTTCCACCCATTTTTCACTCCTATTGCTCCCAAGTGCCCTATT
AAGCATCAAAACACGAATATAAAGAATTAAGAGTGTACAATTTACCATTAA
Found at i:15703454 original size:19 final size:18
Alignment explanation
Indices: 15703399--15703455 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
15703389 AATATACCGG
15703399 ATATTAATAAAAAATATT
1 ATATTAATAAAAAATATT
* **
15703417 A-ATAAATATTTAAAT-TT
1 ATATTAATA-AAAAATATT
15703434 ATATTTAATAAAAAATATT
1 ATA-TTAATAAAAAATATT
15703453 ATA
1 ATA
15703456 AAAATAGAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 7
0.69 0.14 0.17
Matches are distributed among these distances:
17 9 0.31
18 10 0.34
19 10 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATTAATAAAAAATATT
Found at i:15705375 original size:18 final size:18
Alignment explanation
Indices: 15705325--15705377 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
15705315 TTACTTTTAG
*
15705325 TTTA-TTTTTCATTTTAA
1 TTTATTTTTTCATTTCAA
* *
15705342 GTTATTGATTT-ATTTCAA
1 TTTATT-TTTTCATTTCAA
15705360 TTTATTTTTTCATTTCAA
1 TTTATTTTTTCATTTCAA
15705378 CGTGTTTCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 6 0.21
18 19 0.68
19 3 0.11
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTATTTTTTCATTTCAA
Found at i:15705418 original size:5 final size:5
Alignment explanation
Indices: 15705408--15705443 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
15705398 TTTTTAAAAT
*
15705408 AATTA AATTAA AATTA AATTA AATTA AATCA AATTA
1 AATTA AATT-A AATTA AATTA AATTA AATTA AATTA
15705444 GAGAAGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (5 bp):
AATTA
Found at i:15706100 original size:30 final size:33
Alignment explanation
Indices: 15706041--15706100 Score: 81
Period size: 30 Copynumber: 1.9 Consensus size: 33
15706031 TTTTTAACTT
15706041 TTTAAAAATATTTATACTAATTTTAATTTAATA
1 TTTAAAAATATTTATACTAATTTTAATTTAATA
* *
15706074 TTTAATAAT-TTTATA-T-ATTTTCATTTA
1 TTTAAAAATATTTATACTAATTTTAATTTA
15706101 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.40
31 1 0.04
32 6 0.24
33 8 0.32
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (33 bp):
TTTAAAAATATTTATACTAATTTTAATTTAATA
Found at i:15716499 original size:20 final size:21
Alignment explanation
Indices: 15716470--15716522 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
15716460 TTCAGGTTTA
15716470 TGGCTCAACATA-GGTTGATC
1 TGGCTCAACATAGGGTTGATC
* * *
15716490 TGGCTTAACATAGGGTTGCTG
1 TGGCTCAACATAGGGTTGATC
15716511 TGGCTCAACATA
1 TGGCTCAACATA
15716523 AGGATGCGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (21 bp):
TGGCTCAACATAGGGTTGATC
Found at i:15717891 original size:16 final size:17
Alignment explanation
Indices: 15717872--15717904 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
15717862 TTTTAGATGT
15717872 TAATTAATT-TAATTTA
1 TAATTAATTCTAATTTA
*
15717888 TAATTATTTCTAATTTA
1 TAATTAATTCTAATTTA
15717905 GGCTTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATTAATTCTAATTTA
Found at i:15727424 original size:20 final size:20
Alignment explanation
Indices: 15727380--15727520 Score: 104
Period size: 20 Copynumber: 7.0 Consensus size: 20
15727370 ACACCACACT
* *
15727380 AGAGGCATCATAGATGCATAAC
1 AGAGGCACCAAAG-TGCA-AAC
15727402 AGAGGCACCAAAGTGCAAAC
1 AGAGGCACCAAAGTGCAAAC
* * *
15727422 AGAGACA-CAAATGTGTAAGC
1 AGAGGCACCAAA-GTGCAAAC
** * *
15727442 AGAGGCACCGTAGTGCGAAT
1 AGAGGCACCAAAGTGCAAAC
* * *
15727462 AGAGACACCGAAGTGCGAAC
1 AGAGGCACCAAAGTGCAAAC
* * *
15727482 AAAGGCACCAAAGTGAAAAA
1 AGAGGCACCAAAGTGCAAAC
*
15727502 AGAGGCACCGAAGTGCAAA
1 AGAGGCACCAAAGTGCAAA
15727521 TCACGTACAA
Statistics
Matches: 93, Mismatches: 24, Indels: 6
0.76 0.20 0.05
Matches are distributed among these distances:
19 4 0.04
20 72 0.77
21 6 0.06
22 11 0.12
ACGTcount: A:0.43, C:0.20, G:0.27, T:0.10
Consensus pattern (20 bp):
AGAGGCACCAAAGTGCAAAC
Found at i:15735233 original size:29 final size:29
Alignment explanation
Indices: 15735112--15735263 Score: 142
Period size: 29 Copynumber: 5.2 Consensus size: 29
15735102 GTATCGACGC
***
15735112 CCATCGAATATGAAAAGGGATGGTGACGA
1 CCATCGAATATGAAAAGGGATGGTTTTGA
* * **
15735141 GCATCGAATATGAAAAGGGATAGTGATGA
1 CCATCGAATATGAAAAGGGATGGTTTTGA
* * *
15735170 TCATCGAATATGAAAAGGGATGGCTTTAA
1 CCATCGAATATGAAAAGGGATGGTTTTGA
**
15735199 TTATCGAATATGAAAAGGGATGGTTTTGA
1 CCATCGAATATGAAAAGGGATGGTTTTGA
* * * * *
15735228 CCATCGATTAAAGAAAATGAATTGTTTTGA
1 CCATCGAAT-ATGAAAAGGGATGGTTTTGA
15735258 CCATCG
1 CCATCG
15735264 TTTAGCACAC
Statistics
Matches: 103, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
29 81 0.79
30 22 0.21
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.26
Consensus pattern (29 bp):
CCATCGAATATGAAAAGGGATGGTTTTGA
Found at i:15756759 original size:12 final size:12
Alignment explanation
Indices: 15756738--15756767 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
15756728 AACCGAGGAA
15756738 GAAGAAGAAGAG
1 GAAGAAGAAGAG
*
15756750 GAAGAGGAAGAG
1 GAAGAAGAAGAG
15756762 GAAGAA
1 GAAGAA
15756768 AGAGGCGAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAGAG
Found at i:15777198 original size:25 final size:25
Alignment explanation
Indices: 15777152--15777207 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
15777142 TGATTTCCAA
*
15777152 AGAATTTGCCACAAATGCTTTCTAG
1 AGAATTTGCCACAAAGGCTTTCTAG
* * *
15777177 AGAATTTTCCATAAAGGTTTTCTAG
1 AGAATTTGCCACAAAGGCTTTCTAG
15777202 AGAATT
1 AGAATT
15777208 CTCGAGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (25 bp):
AGAATTTGCCACAAAGGCTTTCTAG
Found at i:15778112 original size:86 final size:85
Alignment explanation
Indices: 15777963--15778129 Score: 271
Period size: 86 Copynumber: 2.0 Consensus size: 85
15777953 GTATCAAGTT
* * *
15777963 CTTAAAAGATCATAAGATTTCCATTAAAATCCCTATTATAGACATTTTACTAAAATTTAAACTAC
1 CTTAAAAGATCATAACATTTCCATTAAAATCCCCATTACAGACATTTTACTAAAATTTAAACTAC
15778028 ATGCGACCCCCCATGCAACTA
66 ATGCGA-CCCCCATGCAACTA
* * *
15778049 CTTAAAATATCATAACATTTCCATTAGAATCCCCATTACAGACATTTTACTAAAATTTCAACTAC
1 CTTAAAAGATCATAACATTTCCATTAAAATCCCCATTACAGACATTTTACTAAAATTTAAACTAC
15778114 ATGCGACCCCCATGCA
66 ATGCGACCCCCATGCA
15778130 GGGCCTTCCT
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
85 10 0.13
86 65 0.87
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (85 bp):
CTTAAAAGATCATAACATTTCCATTAAAATCCCCATTACAGACATTTTACTAAAATTTAAACTAC
ATGCGACCCCCATGCAACTA
Found at i:15792994 original size:10 final size:10
Alignment explanation
Indices: 15792979--15793004 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
15792969 GTTGTATTTC
15792979 TTTTTTTCTT
1 TTTTTTTCTT
15792989 TTTTTTTCTT
1 TTTTTTTCTT
15792999 TTTTTT
1 TTTTTT
15793005 GATGTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:15797879 original size:17 final size:17
Alignment explanation
Indices: 15797844--15797877 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
15797834 AAGTGGTTAC
15797844 AAGGAGATGAAAGGTTT
1 AAGGAGATGAAAGGTTT
*
15797861 AAGGAAGATGGAAGGTT
1 AAGG-AGATGAAAGGTT
15797878 AAAGATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (17 bp):
AAGGAGATGAAAGGTTT
Found at i:15798022 original size:24 final size:24
Alignment explanation
Indices: 15797995--15798057 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
15797985 CATCTTTCAT
* *
15797995 CTTTCATCTCCCTTGACCTTCCAC
1 CTTTCATCTCCCTTAACCTTCAAC
* * *
15798019 CTTTCATCTTCTTTAACCTTTAAC
1 CTTTCATCTCCCTTAACCTTCAAC
15798043 CTTTCATCTCCCTTA
1 CTTTCATCTCCCTTA
15798058 TGTTGGGAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.16, C:0.38, G:0.02, T:0.44
Consensus pattern (24 bp):
CTTTCATCTCCCTTAACCTTCAAC
Found at i:15798178 original size:16 final size:16
Alignment explanation
Indices: 15798157--15798187 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15798147 TTCACTATTA
*
15798157 TGTCTTTTTTATTTTC
1 TGTCTTTTATATTTTC
15798173 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
15798188 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:15799822 original size:37 final size:35
Alignment explanation
Indices: 15799759--15799827 Score: 86
Period size: 37 Copynumber: 1.9 Consensus size: 35
15799749 GTTCCAAAAA
*
15799759 TAATATTATTTTAATAGTTTAATATTAAATTTAATT
1 TAATATTATCTTAATAGTTTAATATT-AATTTAATT
*
15799795 TAATACTTATCTTAATAGTATT-TTATTAATTTA
1 TAATA-TTATCTTAATAGT-TTAATATTAATTTA
15799828 GTATTAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 11 0.38
37 16 0.55
38 2 0.07
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (35 bp):
TAATATTATCTTAATAGTTTAATATTAATTTAATT
Found at i:15800791 original size:71 final size:71
Alignment explanation
Indices: 15800671--15800815 Score: 236
Period size: 71 Copynumber: 2.0 Consensus size: 71
15800661 GAAAAATGAT
* * * *
15800671 TAATTTGTGGTGTATTCAAACACCATATAAACTTATTTATTTACGTCTAGTGAATTTGTATTCGG
1 TAATTTGTGGTGTATTCAAACACCAAATAAACTTATTTATTTACATCTAGTGAATTTGCATTCGA
15800736 CTAGTA
66 CTAGTA
* *
15800742 TAATTTGTGGTGTATTCAAACACTAAATAAATTTATTTATTTACATCTAGTGAATTTGCATTCGA
1 TAATTTGTGGTGTATTCAAACACCAAATAAACTTATTTATTTACATCTAGTGAATTTGCATTCGA
15800807 CTAGTA
66 CTAGTA
15800813 TAA
1 TAA
15800816 ATTATTTCAT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (71 bp):
TAATTTGTGGTGTATTCAAACACCAAATAAACTTATTTATTTACATCTAGTGAATTTGCATTCGA
CTAGTA
Found at i:15801706 original size:7 final size:7
Alignment explanation
Indices: 15801694--15801739 Score: 56
Period size: 7 Copynumber: 6.1 Consensus size: 7
15801684 ATCTTCTCCA
15801694 ACCTTTC
1 ACCTTTC
15801701 ACCTTTC
1 ACCTTTC
*
15801708 ATCTTCCTC
1 ACCTT--TC
15801717 AACCTTTC
1 -ACCTTTC
15801725 ACCTTTC
1 ACCTTTC
15801732 ACCTTTC
1 ACCTTTC
15801739 A
1 A
15801740 TCTTCCTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 26 0.76
8 2 0.06
9 2 0.06
10 4 0.12
ACGTcount: A:0.17, C:0.41, G:0.00, T:0.41
Consensus pattern (7 bp):
ACCTTTC
Found at i:15801706 original size:24 final size:24
Alignment explanation
Indices: 15801677--15801732 Score: 96
Period size: 24 Copynumber: 2.3 Consensus size: 24
15801667 TGGATGTTCA
15801677 ACCTTTCATCTT-CTCCAACCTTTC
1 ACCTTTCATCTTCCT-CAACCTTTC
15801701 ACCTTTCATCTTCCTCAACCTTTC
1 ACCTTTCATCTTCCTCAACCTTTC
15801725 ACCTTTCA
1 ACCTTTCA
15801733 CCTTTCATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 29 0.94
25 2 0.06
ACGTcount: A:0.18, C:0.41, G:0.00, T:0.41
Consensus pattern (24 bp):
ACCTTTCATCTTCCTCAACCTTTC
Found at i:15801723 original size:17 final size:16
Alignment explanation
Indices: 15801699--15801746 Score: 64
Period size: 14 Copynumber: 3.1 Consensus size: 16
15801689 CTCCAACCTT
15801699 TCACCTTTCATCTTCC
1 TCACCTTTCATCTTCC
*
15801715 TCAACCTTTCACCTT--
1 TC-ACCTTTCATCTTCC
15801730 TCACCTTTCATCTTCC
1 TCACCTTTCATCTTCC
15801746 T
1 T
15801747 TAACTCTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 11 0.41
15 2 0.07
16 3 0.11
17 11 0.41
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.44
Consensus pattern (16 bp):
TCACCTTTCATCTTCC
Found at i:15801732 original size:31 final size:31
Alignment explanation
Indices: 15801694--15801763 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
15801684 ATCTTCTCCA
15801694 ACCTTTCACCTTTCATCTTCCTCAAC-CTTTC
1 ACCTTTCACCTTTCATCTTCCTCAACTC-TTC
*
15801725 ACCTTTCACCTTTCATCTTCCTTAACTCTTC
1 ACCTTTCACCTTTCATCTTCCTCAACTCTTC
15801756 ACCTTTCA
1 ACCTTTCA
15801764 TCTTATTGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.17, C:0.40, G:0.00, T:0.43
Consensus pattern (31 bp):
ACCTTTCACCTTTCATCTTCCTCAACTCTTC
Found at i:15802956 original size:6 final size:6
Alignment explanation
Indices: 15802945--15802990 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
15802935 GTTAATGAAC
15802945 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATT
15802991 GTAGCAATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Done.