Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, whole genome shotgun sequence
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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 3 of 109
Found at i:310707 original size:15 final size:15
Alignment explanation
Indices: 310626--310716 Score: 51
Period size: 17 Copynumber: 5.5 Consensus size: 15
310616 ATTATTAAAG
*
310626 TATATTGAAATTATT-
1 TATATT-AAAATATTA
310641 TATTATTAAAATTATTA
1 TA-TATTAAAA-TATTA
310658 -ATATTTAAGAATAATTA
1 TATA-TTAA-AAT-ATTA
* *
310675 TATTTTAATAATAATATT
1 TATATTAA-AAT-AT-TA
310693 TAATATTAAAATATTA
1 T-ATATTAAAATATTA
310709 TATATTAA
1 TATATTAA
310717 TATAAAAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
15 14 0.23
16 16 0.26
17 18 0.30
18 7 0.11
19 6 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TATATTAAAATATTA
Found at i:310732 original size:37 final size:37
Alignment explanation
Indices: 310647--310732 Score: 90
Period size: 36 Copynumber: 2.4 Consensus size: 37
310637 TATTTATTAT
* *
310647 TAAAATTA-TTAATATTTAAGAATAATTATATTTTAA
1 TAAAAATATTTAATATTTAAGAATAATTATATTTAAA
*
310683 TAATAATATTTAATA-TTAA-AAT-ATTATATATTAATA
1 TAAAAATATTTAATATTTAAGAATAATTATAT-TTAA-A
310719 TAAAAATACTTTAA
1 TAAAAATA-TTTAA
310733 ATAAAACTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
34 7 0.17
35 6 0.14
36 18 0.43
37 11 0.26
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (37 bp):
TAAAAATATTTAATATTTAAGAATAATTATATTTAAA
Found at i:310744 original size:51 final size:52
Alignment explanation
Indices: 310637--310750 Score: 128
Period size: 51 Copynumber: 2.2 Consensus size: 52
310627 ATATTGAAAT
** *
310637 TATTTATTATTAAAATTATTAATATTTAAGAATAATTATATTTTAATAATAA
1 TATTTATTATTAAAATTATTAATATTTAAGAATAAAAATATTTAAATAATAA
* *
310689 TATTTAATATTAAAA-TATT-ATATATTAA-TATAAAAATACTTTAAATAA-AA
1 TATTTATTATTAAAATTATTAATAT-TTAAGAATAAAAATA-TTTAAATAATAA
310739 CTATTTATTATT
1 -TATTTATTATT
310751 CTTTATATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
50 13 0.25
51 26 0.49
52 14 0.26
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (52 bp):
TATTTATTATTAAAATTATTAATATTTAAGAATAAAAATATTTAAATAATAA
Found at i:310857 original size:17 final size:17
Alignment explanation
Indices: 310832--310868 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
310822 AATAGTAATA
*
310832 TATATTATTAAAATATT
1 TATACTATTAAAATATT
310849 TATACTATTAAAATATT
1 TATACTATTAAAATATT
310866 TAT
1 TAT
310869 GTTTTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TATACTATTAAAATATT
Found at i:311129 original size:28 final size:27
Alignment explanation
Indices: 311097--311150 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
311087 TATATGTTAT
311097 TATTTATTATTAAAATAATAAATAATAC
1 TATTTATTATTAAAATAATAAA-AATAC
* *
311125 TATTTATTATTGAAATACTAAAAATA
1 TATTTATTATTAAAATAATAAAAATA
311151 TTTACGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (27 bp):
TATTTATTATTAAAATAATAAAAATAC
Found at i:311680 original size:14 final size:14
Alignment explanation
Indices: 311663--311689 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
311653 TGTAAAAATG
311663 CAAAAATTATTTTA
1 CAAAAATTATTTTA
311677 CAAAAATTATTTT
1 CAAAAATTATTTT
311690 CAATGAAACA
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:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
CAAAAATTATTTTA
Found at i:316943 original size:12 final size:11
Alignment explanation
Indices: 316894--316944 Score: 57
Period size: 12 Copynumber: 4.3 Consensus size: 11
316884 ATATATAATT
316894 TTTAATTATTTA
1 TTTAATT-TTTA
316906 TTTAATTTTATA
1 TTTAATTTT-TA
*
316918 TTTATATATTTA
1 TTTA-ATTTTTA
316930 TTTAATTTTATA
1 TTTAATTTT-TA
316942 TTT
1 TTT
316945 TTATTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 6 0.18
12 24 0.71
13 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTAATTTTTA
Found at i:316951 original size:17 final size:18
Alignment explanation
Indices: 316899--316949 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
316889 TAATTTTTAA
* *
316899 TTATTTATTTAATTTTATAT
1 TTATATATTT-ATTTAAT-T
316919 TTATATATTTATTTAATT
1 TTATATATTTATTTAATT
*
316937 TTATATTTTTATT
1 TTATATATTTATT
316950 AAAAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 13 0.46
19 6 0.21
20 9 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATATATTTATTTAATT
Found at i:317043 original size:32 final size:31
Alignment explanation
Indices: 316976--317056 Score: 110
Period size: 32 Copynumber: 2.6 Consensus size: 31
316966 ATTTAAAGTT
* * *
316976 AAATCAAATTAAGTGTAAAATATATAATATC
1 AAATCAAATTAAATTTAAAATATATAATATA
317007 AAATCAAATTAAATTT-AAATATTATAAATATA
1 AAATCAAATTAAATTTAAAATA-TAT-AATATA
317039 AAATCAAATTAAATTTAA
1 AAATCAAATTAAATTTAA
317057 TACAAAGACT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.11
31 17 0.39
32 21 0.48
33 1 0.02
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (31 bp):
AAATCAAATTAAATTTAAAATATATAATATA
Found at i:318687 original size:18 final size:17
Alignment explanation
Indices: 318666--318701 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
318656 GAATCGATCT
318666 TGGATTTTTTCTCGCCCC
1 TGGATTTTTTCTC-CCCC
318684 TGGATTTTTTCTCCCCC
1 TGGATTTTTTCTCCCCC
318701 T
1 T
318702 AATTGAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.06, C:0.33, G:0.14, T:0.47
Consensus pattern (17 bp):
TGGATTTTTTCTCCCCC
Found at i:318810 original size:40 final size:40
Alignment explanation
Indices: 318765--318844 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
318755 AGCGAACAAC
318765 GAGTTTTTCTTCTGGTGAAGGCTATGCATTGGTTATCTGT
1 GAGTTTTTCTTCTGGTGAAGGCTATGCATTGGTTATCTGT
*
318805 GAGTTTTTTTTCTGGTGAAGGCTATGCATTGGTTATCTGT
1 GAGTTTTTCTTCTGGTGAAGGCTATGCATTGGTTATCTGT
318845 AAAGCAGCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.15, C:0.11, G:0.28, T:0.46
Consensus pattern (40 bp):
GAGTTTTTCTTCTGGTGAAGGCTATGCATTGGTTATCTGT
Found at i:325701 original size:16 final size:15
Alignment explanation
Indices: 325656--325702 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
325646 AATCTTGAAA
325656 CTTTAAACCTTAAAAC
1 CTTTAAACCTT-AAAC
*
325672 CTTAAAATCC-TAAAC
1 CTTTAAA-CCTTAAAC
325687 CTTTGAAACCTTAAAC
1 CTTT-AAACCTTAAAC
325703 TGTGAAATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 9 0.35
16 15 0.58
17 2 0.08
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.30
Consensus pattern (15 bp):
CTTTAAACCTTAAAC
Found at i:325718 original size:16 final size:16
Alignment explanation
Indices: 325676--325718 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
325666 TAAAACCTTA
* *
325676 AAATCCTAAACCTTTG
1 AAATCCTAAAACTGTG
*
325692 AAA-CCTTAAACTGTG
1 AAATCCTAAAACTGTG
325707 AAATCCTAAAAC
1 AAATCCTAAAAC
325719 AAAACGCTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (16 bp):
AAATCCTAAAACTGTG
Found at i:330077 original size:15 final size:15
Alignment explanation
Indices: 330055--330096 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
330045 AACAAGAAAT
*
330055 AAAAAATAATAATAA
1 AAAAAATAATAAGAA
*
330070 AGAAAATAA-AAGAA
1 AAAAAATAATAAGAA
330084 AAACAAATAATAA
1 AAA-AAATAATAA
330097 AAGTTCAGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 6 0.27
15 14 0.64
16 2 0.09
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (15 bp):
AAAAAATAATAAGAA
Found at i:334785 original size:17 final size:17
Alignment explanation
Indices: 334755--334804 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
334745 TAAATTATCC
*
334755 ATAAAATATTAAATATA
1 ATAAAATATAAAATATA
*
334772 ATAAAGTATAAAATATA
1 ATAAAATATAAAATATA
*
334789 ATAAAATATTAAATAT
1 ATAAAATATAAAATAT
334805 TAGATTATCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
ATAAAATATAAAATATA
Found at i:348138 original size:16 final size:16
Alignment explanation
Indices: 348095--348139 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
348085 AAAAAAAAAT
348095 ATTTTTAT-TAATATA
1 ATTTTTATATAATATA
* *
348110 AATTATA-AT-ATATA
1 ATTTTTATATAATATA
348124 ATTTTTATATAATATA
1 ATTTTTATATAATATA
348140 TAACAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.43
15 8 0.35
16 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTTATATAATATA
Found at i:348139 original size:30 final size:29
Alignment explanation
Indices: 348095--348176 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 29
348085 AAAAAAAAAT
348095 ATTTTTAT-TAATATAAATTATAA-TATATA
1 ATTTTTATATAATATAAA-TATAATTAT-TA
*
348124 ATTTTTATATAATATATAACA-AATTATTA
1 ATTTTTATATAATATA-AATATAATTATTA
348153 ATATTTTATATAATATAAATATAA
1 AT-TTTTATATAATATAAATATAA
348177 AAATTATCAC
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
29 17 0.37
30 27 0.59
31 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTTTATATAATATAAATATAATTATTA
Found at i:353966 original size:34 final size:35
Alignment explanation
Indices: 353923--353992 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
353913 ATCAAATGTC
*
353923 TTAGTCCTACT-TGCTTGTCCATGGTAAAATTAAA
1 TTAGTCCTACTATGCATGTCCATGGTAAAATTAAA
*
353957 TTAGTCCTACTATGCATGTCCATGGTAAGATTAAA
1 TTAGTCCTACTATGCATGTCCATGGTAAAATTAAA
353992 T
1 T
353993 CCATATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 11 0.33
35 22 0.67
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (35 bp):
TTAGTCCTACTATGCATGTCCATGGTAAAATTAAA
Found at i:354844 original size:2 final size:2
Alignment explanation
Indices: 354837--354869 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
354827 TCTTTTTATT
354837 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
354870 CACTCAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:360522 original size:19 final size:19
Alignment explanation
Indices: 360482--360523 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
360472 ATATATTTTT
*
360482 AATTTTATATTTAAATTTA
1 AATTTTATATTTAAATTCA
*
360501 AATTTTATGTTTTAAA-TCA
1 AATTTTAT-ATTTAAATTCA
360520 AATT
1 AATT
360524 AATCAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
AATTTTATATTTAAATTCA
Found at i:370583 original size:14 final size:14
Alignment explanation
Indices: 370564--370591 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
370554 TAGCTCAAGG
370564 GTTAGAATAAACAT
1 GTTAGAATAAACAT
370578 GTTAGAATAAACAT
1 GTTAGAATAAACAT
370592 AATCATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
GTTAGAATAAACAT
Found at i:374385 original size:21 final size:20
Alignment explanation
Indices: 374344--374386 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
374334 ATACAAAAAA
*
374344 TTTTGTTTTGGATTTTGGAT
1 TTTTGTTTTGGAATTTGGAT
374364 TTTTAGTTTTGGGAATTT-GAT
1 TTTT-GTTTT-GGAATTTGGAT
374385 TT
1 TT
374387 AATTTTTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 10 0.50
22 6 0.30
ACGTcount: A:0.14, C:0.00, G:0.23, T:0.63
Consensus pattern (20 bp):
TTTTGTTTTGGAATTTGGAT
Found at i:374453 original size:28 final size:29
Alignment explanation
Indices: 374422--374477 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
374412 TTGGATCCTT
* *
374422 GGATTTTTTA-GTTTCTTGGTTTGATTTA
1 GGATATTTTAGGTTTCTAGGTTTGATTTA
374450 GGATATTTTAGGTTTCTAGGTTTGATTT
1 GGATATTTTAGGTTTCTAGGTTTGATTT
374478 CTAAGGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.16, C:0.04, G:0.23, T:0.57
Consensus pattern (29 bp):
GGATATTTTAGGTTTCTAGGTTTGATTTA
Found at i:375421 original size:15 final size:15
Alignment explanation
Indices: 375373--375418 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
375363 ATATTATTGC
375373 ATAATATTTTG-AT-
1 ATAATATTTTGTATA
* *
375386 ATTATTTTTTGTATA
1 ATAATATTTTGTATA
375401 ATAATATTTTGTA-A
1 ATAATATTTTGTATA
375415 ATAA
1 ATAA
375419 ATAAAAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 9 0.33
14 7 0.26
15 11 0.41
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (15 bp):
ATAATATTTTGTATA
Found at i:376456 original size:108 final size:108
Alignment explanation
Indices: 376272--376484 Score: 320
Period size: 108 Copynumber: 2.0 Consensus size: 108
376262 TAACTCATTT
* * * *
376272 ATTAATAACGAAATAATGTATATTATATGAAAATAAATAACTAATAAGTGTTCCTATAACCAATT
1 ATTAATAACAAAATAATGTATATTATATGAAAACAAATAACTAATAAGTGTTCCTACAACCAATC
*
376337 TTGTTTAGCTTGAAAGGCTTAAAATAACAACACATTCTCATAC
66 TCGTTTAGCTTGAAAGGCTTAAAATAACAACACATTCTCATAC
* * *
376380 ATTAATAACAAAATAATGTATATTATATGAAAACAAATTACTAATAAGTGCTT-TTACAACTAAT
1 ATTAATAACAAAATAATGTATATTATATGAAAACAAATAACTAATAAGTG-TTCCTACAACCAAT
* *
376444 CTCGTTTGGCTTGAAAGGCTTATAATAACAACACATTCTCA
65 CTCGTTTAGCTTGAAAGGCTTAAAATAACAACACATTCTCA
376485 CAAGATGCAT
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 92 0.98
109 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (108 bp):
ATTAATAACAAAATAATGTATATTATATGAAAACAAATAACTAATAAGTGTTCCTACAACCAATC
TCGTTTAGCTTGAAAGGCTTAAAATAACAACACATTCTCATAC
Found at i:385731 original size:3 final size:3
Alignment explanation
Indices: 385723--385761 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
385713 AAGTAAGGTG
385723 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
385762 ATATCACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:387195 original size:31 final size:31
Alignment explanation
Indices: 387136--387196 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
387126 ACAAAATAAT
* * *
387136 TATTCAAGGAATAACTCTTTTACGGAACAAC
1 TATTCAAAGAATAACTCTTTCACAGAACAAC
* *
387167 TATTCAAAGAATAATTCTTTCATAGAACAA
1 TATTCAAAGAATAACTCTTTCACAGAACAA
387197 TATATACCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (31 bp):
TATTCAAAGAATAACTCTTTCACAGAACAAC
Found at i:393384 original size:11 final size:11
Alignment explanation
Indices: 393368--393412 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
393358 TTACACGGGC
*
393368 AAAAAAGAAAA
1 AAAAAACAAAA
393379 AAAAAACAAAA
1 AAAAAACAAAA
**
393390 AAAAAGGAAAA
1 AAAAAACAAAA
393401 AAGAAAACAAAA
1 AA-AAAACAAAA
393413 GCAAGTCTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 21 0.75
12 7 0.25
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:393400 original size:18 final size:18
Alignment explanation
Indices: 393379--393413 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
393369 AAAAAGAAAA
393379 AAAAAACAAAAAAAAAGG
1 AAAAAACAAAAAAAAAGG
* *
393397 AAAAAAGAAAACAAAAG
1 AAAAAACAAAAAAAAAG
393414 CAAGTCTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAACAAAAAAAAAGG
Found at i:395210 original size:21 final size:21
Alignment explanation
Indices: 395163--395203 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
395153 AACATATTAC
395163 AATTTAAATATCACATTAAAA
1 AATTTAAATATCACATTAAAA
395184 AATTTAAATATCACATTAAA
1 AATTTAAATATCACATTAAA
395204 TATTTTACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (21 bp):
AATTTAAATATCACATTAAAA
Found at i:397866 original size:19 final size:19
Alignment explanation
Indices: 397844--397899 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 19
397834 ATTTTTGGAT
397844 AATTGTAATACTTTTCGAA
1 AATTGTAATACTTTTCGAA
397863 AA-T-T--TA-TTTTCGAA
1 AATTGTAATACTTTTCGAA
*
397877 TAATTGTAATACTTTTTGAA
1 -AATTGTAATACTTTTCGAA
397897 AAT
1 AAT
397900 GAATTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
14 8 0.27
15 4 0.13
16 1 0.03
17 2 0.07
18 1 0.03
19 7 0.23
20 7 0.23
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (19 bp):
AATTGTAATACTTTTCGAA
Found at i:397871 original size:34 final size:34
Alignment explanation
Indices: 397822--397899 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
397812 AAAAAATTAC
* * *
397822 TTTCAAAAATATATTTTTGGATAATTGTAATACT
1 TTTCGAAAATATATTTTCGAATAATTGTAATACT
*
397856 TTTCGAAAATTTATTTTCGAATAATTGTAATACT
1 TTTCGAAAATATATTTTCGAATAATTGTAATACT
*
397890 TTTTGAAAAT
1 TTTCGAAAAT
397900 GAATTTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.47
Consensus pattern (34 bp):
TTTCGAAAATATATTTTCGAATAATTGTAATACT
Found at i:397906 original size:34 final size:34
Alignment explanation
Indices: 397842--397906 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
397832 ATATTTTTGG
**
397842 ATAATTGTAATACTTTTCGAAAATTTATTTTCGA
1 ATAATTGTAATACTTTTCGAAAATGAATTTTCGA
*
397876 ATAATTGTAATACTTTTTGAAAATGAATTTT
1 ATAATTGTAATACTTTTCGAAAATGAATTTT
397907 TAATATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (34 bp):
ATAATTGTAATACTTTTCGAAAATGAATTTTCGA
Found at i:398499 original size:21 final size:21
Alignment explanation
Indices: 398475--398515 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
398465 AAATCATACA
398475 ATTATAATTCAAATTTTTTAG
1 ATTATAATTCAAATTTTTTAG
* *
398496 ATTATAATTTAATTTTTTTA
1 ATTATAATTCAAATTTTTTA
398516 TTGATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTATAATTCAAATTTTTTAG
Found at i:402925 original size:12 final size:12
Alignment explanation
Indices: 402886--402917 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
402876 AAAGAGCATG
402886 GCAAGTGCTAGT
1 GCAAGTGCTAGT
*
402898 GCTAGTGCTAGT
1 GCAAGTGCTAGT
402910 GCAAGTGC
1 GCAAGTGC
402918 AAATGCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.25
Consensus pattern (12 bp):
GCAAGTGCTAGT
Found at i:405687 original size:25 final size:23
Alignment explanation
Indices: 405653--405713 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 23
405643 CCATTAATTA
*
405653 TTTAAGTTTCTGCTTTTTTGTATTT
1 TTTAA-TTTCTGCTTTTTTCTA-TT
**
405678 TTTATATTTCATTTTTTTTTCTATT
1 TTTA-ATTTC-TGCTTTTTTCTATT
405703 TTTAATTTCTG
1 TTTAATTTCTG
405714 TATGTTTGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
23 1 0.03
24 5 0.17
25 14 0.47
26 10 0.33
ACGTcount: A:0.15, C:0.08, G:0.07, T:0.70
Consensus pattern (23 bp):
TTTAATTTCTGCTTTTTTCTATT
Found at i:413037 original size:19 final size:19
Alignment explanation
Indices: 412997--413036 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
412987 TTTTCCCATA
412997 TTCTTTTTTTTCCTTTCTT
1 TTCTTTTTTTTCCTTTCTT
*
413016 TTCTTTATTTTTTCTTTCTT
1 TTCTTT-TTTTTCCTTTCTT
413036 T
1 T
413037 CCTCGCTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (19 bp):
TTCTTTTTTTTCCTTTCTT
Found at i:414785 original size:18 final size:18
Alignment explanation
Indices: 414762--414800 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
414752 CAAATGAAGA
*
414762 AAACAAAATTAAAAAATT
1 AAACAAAATTAAAAAAAT
414780 AAACAAAATTAAAAAAAT
1 AAACAAAATTAAAAAAAT
414798 AAA
1 AAA
414801 ATAAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (18 bp):
AAACAAAATTAAAAAAAT
Found at i:414789 original size:10 final size:9
Alignment explanation
Indices: 414766--414815 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
414756 TGAAGAAAAC
414766 AAAATT-AA
1 AAAATTAAA
414774 AAAATTAAA
1 AAAATTAAA
414783 CAAAATTAAA
1 -AAAATTAAA
414793 AAAA-TAAA
1 AAAATTAAA
414801 ATAAA-TAATA
1 A-AAATTAA-A
414811 AAAAT
1 AAAAT
414816 AGAAATAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
8 11 0.30
9 15 0.41
10 11 0.30
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAATTAAA
Found at i:414806 original size:18 final size:18
Alignment explanation
Indices: 414767--414824 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
414757 GAAGAAAACA
*
414767 AAATTAAAAAATTAAACA-
1 AAATTAAAAAAATAAA-AT
414785 AAATTAAAAAAATAAAAT
1 AAATTAAAAAAATAAAAT
414803 AAA-TAATAAAAATAGAAAT
1 AAATTAA-AAAAATA-AAAT
414822 AAA
1 AAA
414825 CAATTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
17 4 0.11
18 25 0.69
19 7 0.19
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.21
Consensus pattern (18 bp):
AAATTAAAAAAATAAAAT
Found at i:416106 original size:8 final size:8
Alignment explanation
Indices: 416095--416272 Score: 62
Period size: 8 Copynumber: 21.6 Consensus size: 8
416085 ATCTTTTTGG
416095 TATTTTTT
1 TATTTTTT
416103 TA--TTTT
1 TATTTTTT
*
416109 CATTTTTT
1 TATTTTTT
*
416117 ATCTTTTTT
1 -TATTTTTT
*
416126 TA-TTTGT
1 TATTTTTT
416133 T-TTTTTT
1 TATTTTTT
*
416140 CATTTATTT
1 TATTT-TTT
416149 GTATTTTTCT
1 -TATTTTT-T
* * *
416159 CAATCTATT
1 -TATTTTTT
*
416168 TATTTATT
1 TATTTTTT
416176 TATTTATCTT
1 TATTT-T-TT
416186 TATTTTATT
1 TATTTT-TT
*
416195 TATTTATT
1 TATTTTTT
*
416203 TATTTGTT
1 TATTTTTT
*
416211 TA-TTTGT
1 TATTTTTT
416218 TATTTGTTAT
1 TATTT-TT-T
*
416228 T-TTATTT
1 TATTTTTT
416235 TATTTTCTT
1 TATTTT-TT
**
416244 TATTTGAT
1 TATTTTTT
* *
416252 TATTTATG
1 TATTTTTT
*
416260 TATTTATT
1 TATTTTTT
416268 TATTT
1 TATTT
416273 GTAAATATTT
Statistics
Matches: 126, Mismatches: 29, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
6 5 0.04
7 16 0.13
8 57 0.45
9 30 0.24
10 18 0.14
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (8 bp):
TATTTTTT
Found at i:416140 original size:31 final size:32
Alignment explanation
Indices: 416084--416144 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
416074 AAGCCAAGCC
416084 TATCTTTTTGGTATTTTTTTATTTTCATTTTT
1 TATCTTTTTGGTATTTTTTTATTTTCATTTTT
*
416116 TATCTTTTT-TTATTTGTTTT-TTTTCATTT
1 TATCTTTTTGGTATTT-TTTTATTTTCATTT
416145 ATTTGTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.11, C:0.07, G:0.05, T:0.77
Consensus pattern (32 bp):
TATCTTTTTGGTATTTTTTTATTTTCATTTTT
Found at i:416167 original size:20 final size:18
Alignment explanation
Indices: 416126--416168 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
416116 TATCTTTTTT
* *
416126 TATTTGTTTTTTTTCATT
1 TATTTGTTTTTTCTCATC
416144 TATTTGTATTTTTCTCAATC
1 TATTTGT-TTTTTCTC-ATC
416164 TATTT
1 TATTT
416169 ATTTATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 7 0.33
20 7 0.33
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (18 bp):
TATTTGTTTTTTCTCATC
Found at i:416173 original size:4 final size:4
Alignment explanation
Indices: 416164--416272 Score: 89
Period size: 4 Copynumber: 26.2 Consensus size: 4
416154 TTTCTCAATC
*
416164 TATT TATT TATT TATT TATCTT TATTT TATT TATT TATT TATT TGTT TATT
1 TATT TATT TATT TATT TA--TT TA-TT TATT TATT TATT TATT TATT TATT
* * * *
416215 T-GT TATT T-GT TATTT TATTT TATTT TCTT TATT TGA-T TATT TATG
1 TATT TATT TATT TA-TT TA-TT TA-TT TATT TATT T-ATT TATT TATT
416260 TATT TATT TATT T
1 TATT TATT TATT T
416273 GTAAATATTT
Statistics
Matches: 87, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
3 5 0.06
4 61 0.70
5 17 0.20
6 4 0.05
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:416198 original size:27 final size:26
Alignment explanation
Indices: 416164--416272 Score: 89
Period size: 27 Copynumber: 4.0 Consensus size: 26
416154 TTTCTCAATC
416164 TATTTATTTATTTATTTATCTTTATTT
1 TATTTATTTATTTATTT-TCTTTATTT
*
416191 TATTTATTTATTTA-TTTGTTTATTTGT
1 TATTTATTTATTTATTTTCTTTA-TT-T
416218 TATTTGTTATTTTATTTTATTTTCTTTATTT
1 TA--T-TTA-TTTA-TTTATTTTCTTTATTT
* * *
416249 GA-TTATTTATGTA-TTTATTTATTT
1 TATTTATTTATTTATTTTCTTTATTT
416273 GTAAATATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 19
0.74 0.05 0.20
Matches are distributed among these distances:
24 10 0.14
25 8 0.12
26 8 0.12
27 20 0.29
29 1 0.01
30 3 0.04
31 6 0.09
32 6 0.09
33 7 0.10
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (26 bp):
TATTTATTTATTTATTTTCTTTATTT
Found at i:416237 original size:49 final size:51
Alignment explanation
Indices: 416178--416274 Score: 128
Period size: 49 Copynumber: 1.9 Consensus size: 51
416168 TATTTATTTA
* *
416178 TTTATCTTTATTTTATTTATTT-ATTTATTTGTTTATTT-GTTATTTGTTAT
1 TTTATCTTTATTTTATTTATTTGA-TTATTTATGTATTTAGTTATTTGTTAT
* *
416228 TTTAT-TTTATTTTCTTTATTTGATTATTTATGTATTTATTTATTTGT
1 TTTATCTTTATTTTATTTATTTGATTATTTATGTATTTAGTTATTTGT
416275 AAATATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 27 0.66
50 14 0.34
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (51 bp):
TTTATCTTTATTTTATTTATTTGATTATTTATGTATTTAGTTATTTGTTAT
Found at i:416285 original size:49 final size:49
Alignment explanation
Indices: 416184--416286 Score: 111
Period size: 49 Copynumber: 2.1 Consensus size: 49
416174 TTTATTTATC
* * * * *
416184 TTTATTTTATTTATTTATTTATTTGTTTATTTGTTATTTGTTATTTTAT
1 TTTATTTTATTTATTTATTTATTTATGTATTTGTTATTTGTAAATATAT
* *
416233 TTTATTTTCTTTATTTGA-TTATTTATGTATTTATTTATTTGTAAATAT-T
1 TTTATTTTATTTATTT-ATTTATTTATGTATTT-GTTATTTGTAAATATAT
416282 TTTAT
1 TTTAT
416287 AAAAAGCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
49 33 0.73
50 12 0.27
ACGTcount: A:0.21, C:0.01, G:0.06, T:0.72
Consensus pattern (49 bp):
TTTATTTTATTTATTTATTTATTTATGTATTTGTTATTTGTAAATATAT
Found at i:416367 original size:13 final size:13
Alignment explanation
Indices: 416349--416374 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
416339 GGGTTCAAAT
416349 TTTTAAAAATAAA
1 TTTTAAAAATAAA
416362 TTTTAAAAATAAA
1 TTTTAAAAATAAA
416375 AATAAACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTTAAAAATAAA
Found at i:416386 original size:60 final size:60
Alignment explanation
Indices: 416308--416425 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 60
416298 AATATCTTTC
* *
416308 AAATAAAAATGAACTTTACCAACATATTAG-AGGGTTCAAATTTTTAAAAATAAATTTTAA
1 AAATAAAAATAAACTTTACCAACATA-TAGAAGGGTTCAAATTTCTAAAAATAAATTTTAA
* *
416368 AAATAAAAATAAACTTTACCAACATATCGAAGGGTTTAAATTTCTAAAAATAAATTTT
1 AAATAAAAATAAACTTTACCAACATATAGAAGGGTTCAAATTTCTAAAAATAAATTTT
416426 GAGTAAAGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 2 0.04
60 51 0.96
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.33
Consensus pattern (60 bp):
AAATAAAAATAAACTTTACCAACATATAGAAGGGTTCAAATTTCTAAAAATAAATTTTAA
Found at i:421816 original size:7 final size:7
Alignment explanation
Indices: 421798--421831 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
421788 AAATAGAATG
421798 AAAAAATT
1 AAAAAA-T
*
421806 AAAAAAC
1 AAAAAAT
421813 AAAAAAT
1 AAAAAAT
421820 AAAAAAT
1 AAAAAAT
421827 AAAAA
1 AAAAA
421832 TAAGGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:426766 original size:16 final size:16
Alignment explanation
Indices: 426747--426887 Score: 65
Period size: 16 Copynumber: 9.1 Consensus size: 16
426737 TCTTTTGTAT
426747 TTTATGTATT-TTATTA
1 TTTAT-TATTATTATTA
426763 TTTATTATTATTATTA
1 TTTATTATTATTATTA
* *
426779 TATATTAATA-TATGTA
1 TTTATTATTATTAT-TA
426795 --TATCT-TTATTTATTTA
1 TTTAT-TATTA-TTA-TTA
* *
426811 TTTATTTTTTATTAATA
1 TTTA-TTATTATTATTA
*
426828 TTTA-TATGTATT-GTA
1 TTTATTAT-TATTATTA
426843 TTTA-TA-TAGTTA-TA
1 TTTATTATTA-TTATTA
*
426857 TATATTATTATT-TTA
1 TTTATTATTATTATTA
426872 -TTATTATT-TTATTA
1 TTTATTATTATTATTA
426886 TT
1 TT
426888 AATTTTTTTT
Statistics
Matches: 99, Mismatches: 8, Indels: 37
0.69 0.06 0.26
Matches are distributed among these distances:
13 4 0.04
14 22 0.22
15 25 0.25
16 31 0.31
17 7 0.07
18 6 0.06
19 4 0.04
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:426817 original size:52 final size:51
Alignment explanation
Indices: 426747--426890 Score: 141
Period size: 52 Copynumber: 2.8 Consensus size: 51
426737 TCTTTTGTAT
* *
426747 TTTATGTATTTTATTATTTATTATTATTATTATATATTAATATATGTATATC
1 TTTATATA-TTTATTATTTATTATTATTATTATATATTAATATATGTATATA
* * * * * *
426799 TTTATTTATTTATTTATTTTTTATTAATATT-TATATGTATTGTATTTATATA
1 TTTATATATTTA-TTATTTATTATTATTATTATATAT-TAATATATGTATATA
*
426851 GTTATATATATTATTATTTTATTATTATT-TTAT-TATTAAT
1 TTTATATAT-TTATTA-TTTATTATTATTATTATATATTAAT
426891 TTTTTTTTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
51 12 0.16
52 49 0.65
53 14 0.19
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (51 bp):
TTTATATATTTATTATTTATTATTATTATTATATATTAATATATGTATATA
Found at i:427907 original size:37 final size:35
Alignment explanation
Indices: 427831--427910 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 35
427821 GAGCCGCTCC
*
427831 AGGTTT-TTTTTTTTTTTTTTTGAATTTTTTTATT
1 AGGTTTATTTTTTTTTTTTTTTGAATTTTTATATT
* **
427865 -TGTTTATTTTTTTTTTATTTTTTTATTTATTATATT
1 AGGTTTATTTTTTTTTT-TTTTTGAATTT-TTATATT
427901 AGGTTTATTT
1 AGGTTTATTT
427911 AATATTCTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
33 4 0.11
34 10 0.27
35 9 0.24
36 6 0.16
37 8 0.22
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (35 bp):
AGGTTTATTTTTTTTTTTTTTTGAATTTTTATATT
Found at i:427940 original size:6 final size:6
Alignment explanation
Indices: 427929--427986 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
427919 TTTTATCTTA
*
427929 TTTTAT TTTTAT TTTT-T TTTT-T TACTTT-T CTTTAT TTTTAT TATTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT T--TTTAT TTTTAT TTTTAT T-TTTAT
*
427977 TTATAT TTTT
1 TTTTAT TTTT
427987 TATTATCTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 10 0.23
6 24 0.55
7 10 0.23
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:427940 original size:11 final size:11
Alignment explanation
Indices: 427867--427985 Score: 52
Period size: 11 Copynumber: 10.7 Consensus size: 11
427857 TTTTTATTTG
*
427867 TTTATTTTTTT
1 TTTATTTTATT
*
427878 TTTATTTTTTT
1 TTTATTTTATT
*
427889 ATTTATTATATT
1 -TTTATTTTATT
*
427901 AGGTTTATTTAATAT
1 ---TTTATTTTAT-T
*
427916 TCT-TTTTA-T
1 TTTATTTTATT
*
427925 CTTATTTTATT
1 TTTATTTTATT
427936 TTTA-TTT-TT
1 TTTATTTTATT
*
427945 TTT-TTTTACT
1 TTTATTTTATT
*
427955 TTT-CTTTATT
1 TTTATTTTATT
427965 TTTATTATTTATT
1 TTTA-T-TTTATT
*
427978 TATATTTT
1 TTTATTTT
427986 TTATTATCTT
Statistics
Matches: 82, Mismatches: 15, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
9 10 0.12
10 20 0.24
11 22 0.27
12 12 0.15
13 9 0.11
14 8 0.10
15 1 0.01
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:427992 original size:29 final size:29
Alignment explanation
Indices: 427930--427986 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
427920 TTTATCTTAT
* * *
427930 TTTATTTTTATTTTTTTTTTTTACTTTTC
1 TTTATTTTTATTATTTATTTATACTTTTC
*
427959 TTTATTTTTATTATTTATTTATATTTTT
1 TTTATTTTTATTATTTATTTATACTTTT
427987 TATTATCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.81
Consensus pattern (29 bp):
TTTATTTTTATTATTTATTTATACTTTTC
Found at i:427998 original size:12 final size:13
Alignment explanation
Indices: 427869--427990 Score: 63
Period size: 13 Copynumber: 8.8 Consensus size: 13
427859 TTTATTTGTT
*
427869 TATTTTTTTTTTA
1 TATTTTTTATTTA
427882 T-TTTTTTATTTA
1 TATTTTTTATTTA
427894 TTATATTAGGTTTATTTAA
1 -TAT-TT---TTTATTT-A
427913 TATTCTTTTTATCTTA
1 TA-T-TTTTTAT-TTA
*
427929 T-TTTATT-TTTA
1 TATTTTTTATTTA
* *
427940 TTTTTTTTTTTTA
1 TATTTTTTATTTA
*
427953 CT-TTTCTTTATTTT
1 -TATTT-TTTATTTA
*
427967 TATTATTTATTTA
1 TATTTTTTATTTA
427980 TATTTTTTATT
1 TATTTTTTATT
427991 ATCTTTTTCT
Statistics
Matches: 86, Mismatches: 9, Indels: 28
0.70 0.07 0.23
Matches are distributed among these distances:
11 4 0.05
12 16 0.19
13 31 0.36
14 11 0.13
15 2 0.02
16 7 0.08
17 2 0.02
18 9 0.10
19 4 0.05
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (13 bp):
TATTTTTTATTTA
Found at i:427998 original size:13 final size:12
Alignment explanation
Indices: 427834--427998 Score: 51
Period size: 12 Copynumber: 13.5 Consensus size: 12
427824 CCGCTCCAGG
427834 TTTTTTT-TT-T
1 TTTTTTTATTAT
* *
427844 TTTTTTT-TGAA
1 TTTTTTTATTAT
427855 TTTTTTTATT-T
1 TTTTTTTATTAT
427866 GTTTATTTT-TT-T
1 -TTT-TTTTATTAT
*
427878 TTTATTTTTTTAT
1 TTT-TTTTATTAT
* * *
427891 TTATTATATTAGG
1 TTTTTTTATTA-T
* *
427904 TTTATTTAATAT
1 TTTTTTTATTAT
*
427916 TCTTTTTATCTTATT
1 T-TTTTT-TATTA-T
427931 TTATTTTTATT-T
1 TT-TTTTTATTAT
427943 TTTTTTT-TTACT
1 TTTTTTTATTA-T
*
427955 TTTCTTTATT-T
1 TTTTTTTATTAT
427966 TTATTATTTATTTAT
1 TT-TT-TTTA-TTAT
*
427981 ATTTTTTATTAT
1 TTTTTTTATTAT
*
427993 CTTTTT
1 TTTTTT
427999 CTTAAATAAA
Statistics
Matches: 116, Mismatches: 21, Indels: 34
0.68 0.12 0.20
Matches are distributed among these distances:
10 10 0.09
11 23 0.20
12 36 0.31
13 28 0.24
14 11 0.09
15 8 0.07
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTTTATTAT
Found at i:428151 original size:119 final size:120
Alignment explanation
Indices: 428007--428361 Score: 451
Period size: 119 Copynumber: 3.0 Consensus size: 120
427997 TTCTTAAATA
*
428007 AAAATC-AAATTTC-CAAAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA
1 AAAATCAAAATTTCAAAAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAGA
*
428069 AATACATTTTCAAAAAAGAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-
65 AATACATTTTCAAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
* ** *
428125 AAGAAT-AAAGTTT-TGAAAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTT-GA
1 AA-AATCAAAATTTCAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGA
** *
428187 AA-ACCAAAATTTTTGAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATTAATTTTCCTTG
65 AATA-C---ATTTTCAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTG
*
428246 AAAATCAAAATTTCAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAA
1 AAAATCAAAATTTCAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAA
* * *
428311 ATA-AATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
66 ATACATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
428362 CTACACAAGA
Statistics
Matches: 205, Mismatches: 17, Indels: 29
0.82 0.07 0.12
Matches are distributed among these distances:
117 1 0.00
118 7 0.03
119 93 0.45
120 38 0.19
121 18 0.09
122 44 0.21
123 3 0.01
124 1 0.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (120 bp):
AAAATCAAAATTTCAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAA
ATACATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
Found at i:428173 original size:60 final size:58
Alignment explanation
Indices: 428007--428361 Score: 407
Period size: 60 Copynumber: 6.0 Consensus size: 58
427997 TTCTTAAATA
**
428007 AAAATCAAATTTCCAAAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAT-AAATTTTGAAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTT
* * * *
428066 AGAAATACATTTTCAAAAAAGAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
1 A-AAATAAATTTTGAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
*
428125 AAGAATAAAGTTTTGAAAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTT
1 AA-AATAAA-TTTTGAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
* *
428185 GAAAACCAAAATTTTTG--AAAAAATATTTTT-AGGGAAAAGTTGAAAGTATTAATTTTCCTT
1 -AAAA--TAAA-TTTTGAAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTT
**
428245 GAAAATCAAAATTTCAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
1 -AAAAT--AAATTT-TGAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
** *
428307 AAAAATAAA-TTT-CCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 -AAAATAAATTTTGAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
428362 CTACACAAGA
Statistics
Matches: 260, Mismatches: 22, Indels: 30
0.83 0.07 0.10
Matches are distributed among these distances:
57 40 0.15
58 1 0.00
59 60 0.23
60 103 0.40
61 2 0.01
62 53 0.20
63 1 0.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (58 bp):
AAAATAAATTTTGAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
Found at i:428327 original size:179 final size:178
Alignment explanation
Indices: 428023--428361 Score: 522
Period size: 179 Copynumber: 1.9 Consensus size: 178
428013 AAATTTCCAA
* * *
428023 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATACATTTTCAAAAAAGA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAATTTCAAAAAAAA
*
428088 GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAAGTTTTGAAAAAAAATATTT
66 GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAG-TTTGAAAAAAAATATTT
428153 TTGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAACCAAAATTTTTG
130 TTGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAACCAAAATTTTTG
*
428202 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATTAATTTTCCTT-GAAAATCAAAATTTCAAAAAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT-AAAATTTC--AAAA
* **
428266 AAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTT-CCAAAAAATA
62 AAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTGAAAAAAAATA
* *
428329 TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
127 TTTTTGAGGAAAAGTTAAAAGTATCAATTTTCC
428362 CTACACAAGA
Statistics
Matches: 146, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
178 1 0.01
179 85 0.58
180 9 0.06
182 51 0.35
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (178 bp):
AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAATTTCAAAAAAAA
GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTGAAAAAAAATATTTT
TGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAACCAAAATTTTTG
Found at i:432273 original size:19 final size:19
Alignment explanation
Indices: 432251--432291 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
432241 AAAAAAAAAC
432251 AAAAAAACAAAAAAAGGAA
1 AAAAAAACAAAAAAAGGAA
* * *
432270 AAAAAAATAAGAAAATGAA
1 AAAAAAACAAAAAAAGGAA
432289 AAA
1 AAA
432292 GGGAGATTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.05
Consensus pattern (19 bp):
AAAAAAACAAAAAAAGGAA
Found at i:433630 original size:80 final size:80
Alignment explanation
Indices: 433535--433964 Score: 649
Period size: 80 Copynumber: 5.3 Consensus size: 80
433525 CCAAGTTCGT
*
433535 TGCCTCTATTTAGAGGAGCAATTTACTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTAC
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTAC
*
433600 TTTCCAAAGTCGTGG
66 TTTTCAAAGTCGTGG
* *
433615 TGCCTTTGTTTAGAGGAGCAATTTACTTTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAAT
1 TGCCTCTGTTTAGAGGAGCAATTTAC--TTTCCAAGTTCGT--TGCCTCTGTTTAGAGGAGCAAT
433679 TTACTTTTC-AAGTTCGT--
62 TTACTTTTCAAAG-TCGTGG
433696 TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATT
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTCC-AAGTTCGT--TGCCTCTGTTTAGAGGAGCAATT
433760 TACTTTTCAAAGTTCCGT--
63 TACTTTTCAAAG-T-CGTGG
433778 TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTAC
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTAC
*
433843 TTTCCAAAGTCGTGG
66 TTTTCAAAGTCGTGG
433858 TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTT
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTCC-AAGTT-CGTTGCCTCTGTTTAGAGGAGCAATTT
*
433923 ATTTTTCAAAGTCGTGG
64 ACTTTTCAAAGTCGTGG
433940 TGCCTCTGTTTAGAGGAGCAATTTA
1 TGCCTCTGTTTAGAGGAGCAATTTA
433965 TGTTTCTCAA
Statistics
Matches: 328, Mismatches: 9, Indels: 24
0.91 0.02 0.07
Matches are distributed among these distances:
78 3 0.01
79 5 0.02
80 129 0.39
81 42 0.13
82 115 0.35
83 34 0.10
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (80 bp):
TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTAC
TTTTCAAAGTCGTGG
Found at i:433631 original size:41 final size:40
Alignment explanation
Indices: 433515--434001 Score: 652
Period size: 41 Copynumber: 12.0 Consensus size: 40
433505 GTCTAGGAGT
*
433515 ATTTACCTTTCC-AAGTTCGT-TGCCTCTATTTAGAGGAGCA
1 ATTTA-CTTTCCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
433555 ATTTACTTTCC-AAGTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
*
433594 ATTTACTTTCCAAAGTCGTGGTGCCTTTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
*
433635 ATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTAC-TTTCCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
*
433677 ATTTACTTTTC-AAGTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
433716 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
*
433757 ATTTACTTTTCAAAGTTCCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAG-T-CGTGTGCCTCTGTTTAGAGGAGCA
433798 ATTTACTTTCC-AAGTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
433837 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
433878 ATTTACTTTCCAAAGTTCCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAG-T-CGTGTGCCTCTGTTTAGAGGAGCA
* *
433919 ATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
* * *
433960 ATTTATGTTTCTCAAAGTCGCTGAGCCTCTGTTTAGAAGAGC
1 ATTTA-CTTTC-CAAAGTCG-TGTGCCTCTGTTTAGAGGAGC
434002 TTTGGTCAAA
Statistics
Matches: 414, Mismatches: 13, Indels: 37
0.89 0.03 0.08
Matches are distributed among these distances:
39 123 0.30
40 23 0.06
41 191 0.46
42 44 0.11
43 32 0.08
44 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (40 bp):
ATTTACTTTCCAAAGTCGTGTGCCTCTGTTTAGAGGAGCA
Found at i:433847 original size:121 final size:120
Alignment explanation
Indices: 433515--434001 Score: 755
Period size: 121 Copynumber: 4.0 Consensus size: 120
433505 GTCTAGGAGT
* * *
433515 ATTTACCTTTCCAAGTTCGTTGCCTCTATTTAGAGGAGCAATTTACTTTCCAAGTTCGTTGCCTC
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAGTTCGTTGCCTC
*
433580 TGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTTTGTTTAGAGGAGCA
66 TGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
433635 ATTTACTTTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAGTTCGTTGC
1 ATTTAC-TTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAGTTCGTTGC
433699 CTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
63 CTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
433757 ATTTACTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAGTTCGTTGCCT
1 ATTTACTTTTCAAAGTT-CGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAGTTCGTTGCCT
433822 CTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
65 CTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* * *
433878 ATTTACTTTCCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAG-TCGTGGTG
1 ATTTACTTTTCAAAGTT-CGTTGCCTCTGTTTAGAGGAGCAATTTA-CTTTCCAAGTTCGT--TG
* * *
433942 CCTCTGTTTAGAGGAGCAATTTATGTTTCTCAAAGTCGCT-GAGCCTCTGTTTAGAAGAGC
62 CCTCTGTTTAGAGGAGCAATTTA-CTTTC-CAAAGTCG-TGGTGCCTCTGTTTAGAGGAGC
434002 TTTGGTCAAA
Statistics
Matches: 344, Mismatches: 12, Indels: 17
0.92 0.03 0.05
Matches are distributed among these distances:
120 10 0.03
121 164 0.48
122 111 0.32
123 28 0.08
124 4 0.01
125 26 0.08
126 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (120 bp):
ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAGTTCGTTGCCTC
TGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:434019 original size:1 final size:1
Alignment explanation
Indices: 434009--434075 Score: 62
Period size: 1 Copynumber: 67.0 Consensus size: 1
433999 AGCTTTGGTC
* * * * * * * *
434009 AAAAACAAAAAAACAAAAAAAACAAAAAAACAAAAAAAAACAAAAAAACAAAACAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
434074 AA
1 AA
434076 GTGACAACGT
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:434022 original size:8 final size:8
Alignment explanation
Indices: 434009--434075 Score: 93
Period size: 8 Copynumber: 8.4 Consensus size: 8
433999 AGCTTTGGTC
434009 AAAAACAA
1 AAAAACAA
434017 AAAAACAAA
1 AAAAAC-AA
434026 AAAAACAA
1 AAAAACAA
434034 AAAAACAA
1 AAAAACAA
434042 AAAAA-AA
1 AAAAACAA
434049 CAAAAA-AA
1 -AAAAACAA
*
434057 CAAAACAA
1 AAAAACAA
434065 AAAAACAA
1 AAAAACAA
434073 AAA
1 AAA
434076 GTGACAACGT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
7 6 0.11
8 40 0.74
9 8 0.15
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAACAA
Found at i:434062 original size:31 final size:31
Alignment explanation
Indices: 434008--434075 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
433998 GAGCTTTGGT
434008 CAAAAACAAAAAAACAAAAAAAACAAAAAAA
1 CAAAAACAAAAAAACAAAAAAAACAAAAAAA
434039 CAAAAA-AAAACAAA-AAAACAAAACAAAAAAA
1 CAAAAACAAAA-AAACAAAA-AAAACAAAAAAA
434070 CAAAAA
1 CAAAAA
434076 GTGACAACGT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
30 8 0.23
31 27 0.77
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (31 bp):
CAAAAACAAAAAAACAAAAAAAACAAAAAAA
Found at i:434082 original size:18 final size:17
Alignment explanation
Indices: 434009--434066 Score: 98
Period size: 18 Copynumber: 3.3 Consensus size: 17
433999 AGCTTTGGTC
434009 AAAAACAAAAAAACAAA
1 AAAAACAAAAAAACAAA
434026 AAAAACAAAAAAACAAAA
1 AAAAACAAAAAAAC-AAA
434044 AAAAACAAAAAAACAAA
1 AAAAACAAAAAAACAAA
434061 ACAAAA
1 A-AAAA
434067 AAACAAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
17 18 0.46
18 21 0.54
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAACAAAAAAACAAA
Found at i:434394 original size:11 final size:11
Alignment explanation
Indices: 434371--434407 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
434361 ATTTATATAG
434371 TTATATATATTA
1 TTATAT-TATTA
434383 TTATATTATTA
1 TTATATTATTA
*
434394 TTATTTTATTA
1 TTATATTATTA
434405 TTA
1 TTA
434408 ATTTTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATATTATTA
Found at i:434414 original size:14 final size:14
Alignment explanation
Indices: 434378--434407 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
434368 TAGTTATATA
*
434378 TATTATTATATTAT
1 TATTATTTTATTAT
434392 TATTATTTTATTAT
1 TATTATTTTATTAT
434406 TA
1 TA
434408 ATTTTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:434869 original size:25 final size:25
Alignment explanation
Indices: 434816--434869 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
434806 CTGAGAGTGA
*
434816 GAAAAATTTTTTAAAAATTTTTGGC
1 GAAAAATTTTTTAAAAATTTCTGGC
**
434841 GAAAAATTTTTCTGGAAATTTCTGG-
1 GAAAAATTTTT-TAAAAATTTCTGGC
434866 GAAA
1 GAAA
434870 TTTCCAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (25 bp):
GAAAAATTTTTTAAAAATTTCTGGC
Found at i:435397 original size:18 final size:18
Alignment explanation
Indices: 435374--435420 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
435364 CGCTCCAGGT
435374 TTTTTTTTTTTCTTTGA-A
1 TTTTTTTTTTTCTTT-ATA
* *
435392 TTTTTTTATTTGTTTATA
1 TTTTTTTTTTTCTTTATA
435410 TGTTTTTTTTT
1 T-TTTTTTTTT
435421 ATTTTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 15 0.62
19 8 0.33
ACGTcount: A:0.11, C:0.02, G:0.06, T:0.81
Consensus pattern (18 bp):
TTTTTTTTTTTCTTTATA
Found at i:435481 original size:17 final size:18
Alignment explanation
Indices: 435458--435497 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
435448 ATTTAATATT
435458 CTTTTTATCTTAGTTTTA
1 CTTTTTATCTTAGTTTTA
* *
435476 -TTTTTATTTTTGTTTTA
1 CTTTTTATCTTAGTTTTA
435493 CTTTT
1 CTTTT
435498 CTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (18 bp):
CTTTTTATCTTAGTTTTA
Found at i:435529 original size:27 final size:26
Alignment explanation
Indices: 435415--435531 Score: 64
Period size: 27 Copynumber: 4.3 Consensus size: 26
435405 TTATATGTTT
435415 TTTTTTATTTTTT-TTATTTA-TTATA
1 TTTTTTATTTTTTATT-TTTATTTATA
* ** * *
435440 TTAGGTTTATTTAATATTCTT-TTTATC
1 TT--TTTTATTTTTTATTTTTATTTATA
*
435467 TTAGTTTTA-TTTTTATTTTTGTTT-TA
1 TT--TTTTATTTTTTATTTTTATTTATA
435493 CTTTTCTTTATTTTTTATTATTTATTTATA
1 --TTT-TTTATTTTTTATT-TTTATTTATA
435523 TTTTTTATT
1 TTTTTTATT
435532 ATTCTGTTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
25 2 0.03
26 10 0.14
27 35 0.50
28 15 0.21
29 6 0.09
30 2 0.03
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.74
Consensus pattern (26 bp):
TTTTTTATTTTTTATTTTTATTTATA
Found at i:437918 original size:65 final size:62
Alignment explanation
Indices: 437775--437979 Score: 161
Period size: 65 Copynumber: 3.3 Consensus size: 62
437765 TTAACCTAAA
* * *
437775 GCATTTTTGGCCAAAAACGCCTTAATAATCCATACAAAAAATTTCAGAATGGATTATTTAAG
1 GCATTTTTTGCCAAAAACGCCTTAATAATCCATACAAAAAATTTCAGAATGAATTATTGAAG
* * *
437837 GCA-TTTTTGTCTAAAAATGCCTTCAATAATCCATACAAAAAAAAATTT-TGAGA-GAATTATTG
1 GCATTTTTTG-CCAAAAACGCCTT-AATAATCCATAC---AAAAAATTTCAGA-ATGAATTATTG
*
437899 GAG
60 AAG
* * * * * *
437902 GCATTTTTTGCCAAAAACACATTTAATAATCCTCTAAAAAAAATTT-A-AATGGATTATTGAAA
1 GCATTTTTTGCCAAAAACGC-CTTAATAATCC-ATACAAAAAATTTCAGAATGAATTATTGAAG
* *
437964 GTA-TTTTTGACAAAAA
1 GCATTTTTTGCCAAAAA
437980 AAATACCTTA
Statistics
Matches: 114, Mismatches: 19, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
61 18 0.16
62 26 0.23
63 21 0.18
65 29 0.25
66 20 0.18
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (62 bp):
GCATTTTTTGCCAAAAACGCCTTAATAATCCATACAAAAAATTTCAGAATGAATTATTGAAG
Found at i:437997 original size:64 final size:63
Alignment explanation
Indices: 437906--438566 Score: 345
Period size: 63 Copynumber: 10.5 Consensus size: 63
437896 TTGGAGGCAT
* * * * *
437906 TTTTTG-CCAAAAACACATTTAATAATCCTCTAAAAAAAATTT-AAATGGATTATTGAAAGTA
1 TTTTTGACAAAAAATACCTTTAATAATCCTCTCAAAAAAATTTGAAAGGGATTATTGAAAGTA
* * * *
437967 TTTTTGACAAAAAAAATACCTTAAATAATCC-CCCATAAAAATTT-ATTGAGGGGATTATT-AAA
1 TTTTTGAC--AAAAAATACCTTTAATAATCCTCTCAAAAAAATTTGA---AAGGGATTATTGAAA
*
438029 GGCA
61 -GTA
* * * * * * * **
438033 TTTTTGGCCAAAAATATCTTCAATAAT-TTCTCATAAAAATTTATTAAAAAGATTATTGAAAGTA
1 TTTTTGACAAAAAATACCTTTAATAATCCTCTCA-AAAAAATT-TGAAAGGGATTATTGAAAGTA
* * * ** * * * *
438097 TTTTTAGTC-AAAAACACCTTTAATAAT-CTTTTGAAAAATTTTAAAAAGGATTATTGAAGGTA
1 TTTTT-GACAAAAAATACCTTTAATAATCCTCTCAAAAAAATTTGAAAGGGATTATTGAAAGTA
* * * * ** * *
438159 TTTTTTG-CTAAAGATGCCTTTAATAATCCCCTTGAAAAAATTTGAAAGGAATTATTGAAGGTA
1 -TTTTTGACAAAAAATACCTTTAATAATCCTCTCAAAAAAATTTGAAAGGGATTATTGAAAGTA
* * * * *
438222 TTTTTTACCAAAAACACCTTTAATAATCC-CTTCAACAAAATTTGGAAGGGATTATTGAAAGTA
1 TTTTTGACAAAAAATACCTTTAATAATCCTC-TCAAAAAAATTTGAAAGGGATTATTGAAAGTA
* * * * *
438285 TTTTTTACCAAAAATACCTTTAATAAT-CTCTCATAAAAATTT-ATTGAGGAGATTATTGAAGGT
1 TTTTTGACAAAAAATACCTTTAATAATCCTCTCAAAAAAATTTGA--AAGG-GATTATTGAAAGT
438348 A
63 A
** * ** * ** *
438349 TTTTTGGTAAAAAATACTTTTAATAATCC-CTTGAAAAATTTTGAAAATGATTATTGAAAGCA
1 TTTTTGACAAAAAATACCTTTAATAATCCTCTCAAAAAAATTTGAAAGGGATTATTGAAAGTA
* * * * * *
438411 TTTTTTG-CCAAAAATA--TTTCAATAAT-CTTTCATAAAAATTTATGAAATGGATTATTTAAGG
1 -TTTTTGACAAAAAATACCTTT-AATAATCCTCTCA-AAAAAATT-TGAAAGGGATTATTGAAAG
*
438472 TT
62 TA
* * * *
438474 TTTTTGATC-AAAAATACCTTCAATAATCC-CTCATAAAAATTT-ATTAATGGGATTATTCAATG
1 TTTTTGA-CAAAAAATACCTTTAATAATCCTCTCAAAAAAATTTGA--AA-GGGATTATTGAAAG
*
438536 CA
62 TA
* * * *
438538 TGTTTGGCCAAAAATACCTTAAATAATCC
1 TTTTTGACAAAAAATACCTTTAATAATCC
438567 CATTGAATTT
Statistics
Matches: 466, Mismatches: 96, Indels: 73
0.73 0.15 0.11
Matches are distributed among these distances:
60 4 0.01
61 15 0.03
62 86 0.18
63 165 0.35
64 157 0.34
65 19 0.04
66 19 0.04
67 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.37
Consensus pattern (63 bp):
TTTTTGACAAAAAATACCTTTAATAATCCTCTCAAAAAAATTTGAAAGGGATTATTGAAAGTA
Found at i:438007 original size:63 final size:62
Alignment explanation
Indices: 437772--438567 Score: 403
Period size: 64 Copynumber: 12.6 Consensus size: 62
437762 GATTTAACCT
* * ** * * *
437772 AAAGCATTTTTGGCCAAAAACGCC-TTAATAATCCATACA-AAAAATTTCAGAATGGATTATTT
1 AAAGTATTTTTGACCAAAAATACCTTTAATAATCCCT-CATAAAAATTTGA-AATGGATTATTG
* * * * * * * * * *
437834 AAGGCATTTTTGTCTAAAAATGCCTTCAATAATCCATACAAAAAAAAATTTTGAGA-GAATTATT
1 AAAGTATTTTTGACCAAAAATACCTTTAATAATCCCT-C--ATAAAAA-TTTGAAATGGATTATT
437898 G
62 G
* * * * * * *
437899 GAGGCATTTTTTG-CCAAAAACACATTTAATAATCCTCTAAAAAAAATTT-AAATGGATTATTG
1 AAAGTA-TTTTTGACCAAAAATACCTTTAATAATCC-CTCATAAAAATTTGAAATGGATTATTG
* * * **
437961 AAAGTATTTTTGACAAAAAAAATACCTTAAATAATCCCCCATAAAAATTT-ATTGAGGGGATTAT
1 AAAGTATTTTTGAC--CAAAAATACCTTTAATAATCCCTCATAAAAATTTGA---AATGGATTAT
438025 T-
61 TG
* * * * ** * **
438026 AAAGGCATTTTTGGCCAAAAATATCTTCAATAATTTCTCATAAAAATTTATTAAAAAGATTATTG
1 AAA-GTATTTTTGACCAAAAATACCTTTAATAATCCCTCATAAAAA-TT-TGAAATGGATTATTG
* * ** * *
438091 AAAGTATTTTT-AGTCAAAAACACCTTTAATAAT--CTTTTGAAAAATTTTAAAAAGGATTATTG
1 AAAGTATTTTTGA-CCAAAAATACCTTTAATAATCCCTCAT-AAAAA-TTTGAAATGGATTATTG
* * * * *
438153 AAGGTATTTTTTG-CTAAAGATGCCTTTAATAATCCC-CTTGAAAAAATTTGAAA-GGAATTATT
1 AAAGTA-TTTTTGACCAAAAATACCTTTAATAATCCCTCAT--AAAAATTTGAAATGG-ATTATT
438215 G
62 G
* * * * *
438216 AAGGTATTTTTTACCAAAAACACCTTTAATAATCCCTTCA-ACAAAATTTGGAAGGGATTATTG
1 AAAGTATTTTTGACCAAAAATACCTTTAATAATCCC-TCATA-AAAATTTGAAATGGATTATTG
* * * *
438279 AAAGTATTTTTTACCAAAAATACCTTTAATAATCTCTCATAAAAATTT-ATTGAGGAGATTATTG
1 AAAGTATTTTTGACCAAAAATACCTTTAATAATCCCTCATAAAAATTTGA--AATG-GATTATTG
* *** *
438343 AAGGTATTTTTGGTAAAAAATACTTTTAATAATCCCT--TGAAAAATTTTGAAAAT-GATTATTG
1 AAAGTATTTTTGACCAAAAATACCTTTAATAATCCCTCAT-AAAAA-TTTG-AAATGGATTATTG
* **
438405 AAAGCATTTTTTG-CCAAAAATA--TTTCAATAATCTTTCATAAAAATTTATGAAATGGATTATT
1 AAAGTA-TTTTTGACCAAAAATACCTTT-AATAATCCCTCATAAAAA-TT-TGAAATGGATTATT
*
438467 T
62 G
* * * * *
438468 AAGGTTTTTTTGATCAAAAATACCTTCAATAATCCCTCATAAAAATTT-ATTAATGGGATTATTC
1 AAAGTATTTTTGACCAAAAATACCTTTAATAATCCCTCATAAAAATTTGA--AAT-GGATTATTG
* * * * *
438532 AATGCATGTTTGGCCAAAAATACCTTAAATAATCCC
1 AAAGTATTTTTGACCAAAAATACCTTTAATAATCCC
438568 ATTGAATTTT
Statistics
Matches: 578, Mismatches: 104, Indels: 102
0.74 0.13 0.13
Matches are distributed among these distances:
60 3 0.01
61 17 0.03
62 128 0.22
63 175 0.30
64 176 0.30
65 41 0.07
66 33 0.06
67 5 0.01
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (62 bp):
AAAGTATTTTTGACCAAAAATACCTTTAATAATCCCTCATAAAAATTTGAAATGGATTATTG
Found at i:438227 original size:126 final size:125
Alignment explanation
Indices: 437877--438567 Score: 487
Period size: 126 Copynumber: 5.5 Consensus size: 125
437867 CCATACAAAA
* * * * * * * * *
437877 AAAAATTTTG-AGAGAATTATTGGAGGCATTTTTTGCCAAAAACACATTTAATAATCCTCTAAAA
1 AAAAATTTTGAAAAGGATTATTGAAAGTATTTTTTGCCAAAAATACCTTTAATAATCC-CTCATA
* * * * * *
437941 AAAATTTA-AATG-GATTATTGAAAGTATTTTT-GACAAAAAAAATACCTTAAATAATCCCCCAT
65 AAAATTTATAAGGAGATTATTGAAGGTATTTTTAGTC---AAAAACACCTTTAATAAT--CCCTT
438003 -
125 G
** * * * * **
438003 AAAAATTTATTG-AGGGGATTATT-AAAGGCATTTTTGGCCAAAAATATCTTCAATAATTTCTCA
1 AAAAA-TT-TTGAAAAGGATTATTGAAA-GTATTTTTTGCCAAAAATACCTTTAATAATCCCTCA
** * **
438066 TAAAAATTTATTAAAAAGATTATTGAAAGTATTTTTAGTCAAAAACACCTTTAATAATCTTTTG
63 TAAAAATTTA-TAAGGAGATTATTGAAGGTATTTTTAGTCAAAAACACCTTTAATAATCCCTTG
* * * * * *
438130 AAAAATTTTAAAAAGGATTATTGAAGGTATTTTTTGCTAAAGATGCCTTTAATAATCCC-CTTGA
1 AAAAATTTTGAAAAGGATTATTGAAAGTATTTTTTGCCAAAAATACCTTTAATAATCCCTCAT--
* *
438194 AAAAATTTGA-AAGGA-ATTATTGAAGGTATTTTTTA-CCAAAAACACCTTTAATAATCCCTTC
64 AAAAATTT-ATAAGGAGATTATTGAAGGTA-TTTTTAGTCAAAAACACCTTTAATAATCCCTTG
* * * * *
438255 AACAAAATTTGGAAGGGATTATTGAAAGTATTTTTTACCAAAAATACCTTTAATAATCTCTCATA
1 AA-AAATTTTGAAAAGGATTATTGAAAGTATTTTTTGCCAAAAATACCTTTAATAATCCCTCATA
* * * * *
438320 AAAATTTATTGAGGAGATTATTGAAGGTATTTTTGGTAAAAAATACTTTTAATAATCCCTTG
65 AAAATTTA-TAAGGAGATTATTGAAGGTATTTTTAGTCAAAAACACCTTTAATAATCCCTTG
* * **
438382 AAAAATTTTGAAAATGATTATTGAAAGCATTTTTTGCCAAAAATA--TTTCAATAATCTTTCATA
1 AAAAATTTTGAAAAGGATTATTGAAAGTATTTTTTGCCAAAAATACCTTT-AATAATCCCTCATA
* * * * *
438445 AAAATTTATGAAATG-GATTATTTAAGGT-TTTTTTGATCAAAAATACCTTCAATAATCCCTCAT
65 AAAATTTAT--AAGGAGATTATTGAAGGTATTTTTAG-TCAAAAACACCTTTAATAATCCCT--T
438508 -
125 G
* ** * * * * * *
438508 AAAAATTTATTAATGGGATTATTCAATGCATGTTTGGCCAAAAATACCTTAAATAATCCC
1 AAAAATTT-TGAAAAGGATTATTGAAAGTATTTTTTGCCAAAAATACCTTTAATAATCCC
438568 ATTGAATTTT
Statistics
Matches: 451, Mismatches: 85, Indels: 56
0.76 0.14 0.09
Matches are distributed among these distances:
124 11 0.02
125 102 0.23
126 154 0.34
127 98 0.22
128 61 0.14
129 4 0.01
130 19 0.04
131 2 0.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (125 bp):
AAAAATTTTGAAAAGGATTATTGAAAGTATTTTTTGCCAAAAATACCTTTAATAATCCCTCATAA
AAATTTATAAGGAGATTATTGAAGGTATTTTTAGTCAAAAACACCTTTAATAATCCCTTG
Found at i:438344 original size:252 final size:253
Alignment explanation
Indices: 437923--438565 Score: 644
Period size: 252 Copynumber: 2.5 Consensus size: 253
437913 CAAAAACACA
* *
437923 TTTAATAATCCTCTAAAAAAAATTTAAATGGATTATTGAAAGTATTTTTGACAAAAAAAATACCT
1 TTTAATAATCCCCTAAAAAAAATTTAAATGGATTATTGAAAGTATTTTTGAC-AAAAAAACACCT
* * * *
437988 TAAATAATCCCCCATAAAAATTTATTGAGGGGATTATTAAAGGCATTTTTGGCCAAAAATATCTT
65 TAAATAATCCCCCATAAAAATTTATGGAAGGGATTATTAAAGGCATTTTTGACCAAAAATACCTT
* *
438053 CAATAATTTCTCATAAAAATTTATTAAAAAGATTATTGAAAGTATTTTTAGTCAAAAACACCTTT
130 CAATAATCTCTCATAAAAATTTATTAAAAAGATTATTGAAAGTATTTTTAGTAAAAAACACCTTT
** * *
438118 AATAATCTTTTGAAAAATTTTAAAAAGGATTATTGAAGGTATTTTTTGCTAAAGATGCC
195 AATAATCCCTTGAAAAATTTTAAAAAGGATTATTGAAAGCATTTTTTGCTAAAGATGCC
** * * *
438177 TTTAATAATCCCCTTGAAAAAATTTGAAA-GGAATTATTGAAGGTATTTTTTAC-CAAAAACACC
1 TTTAATAATCCCCTAAAAAAAATTT-AAATGG-ATTATTGAAAGTATTTTTGACAAAAAAACACC
* * * *
438240 TTTAATAATCCCTTCA-ACAAAA-TT-TGGAAGGGATTATTGAAA-GTATTTTTTACCAAAAATA
64 TTAAATAATCCC-CCATA-AAAATTTATGGAAGGGATTATT-AAAGGCATTTTTGACCAAAAATA
* * ** * * *
438301 CCTTTAATAATCTCTCATAAAAATTTATTGAGGAGATTATTGAAGGTATTTTTGGTAAAAAATAC
126 CCTTCAATAATCTCTCATAAAAATTTATTAAAAAGATTATTGAAAGTATTTTTAGTAAAAAACAC
* * * * * *
438366 TTTTAATAATCCCTTGAAAAATTTTGAAAATGATTATTGAAAGCATTTTTTGCCAAAAAT--A
191 CTTTAATAATCCCTTGAAAAATTTTAAAAAGGATTATTGAAAGCATTTTTTGCTAAAGATGCC
** * * * * * *
438427 TTTCAATAAT-CTTTCATAAAAATTTATGAAATGGATTATTTAAGGTTTTTTTGATC--AAAAAT
1 TTT-AATAATCCCCT-AAAAAAAATT-T-AAATGGATTATTGAAAGTATTTTTGA-CAAAAAAAC
* * * * * * *
438489 ACCTTCAATAATCCCTCATAAAAATTTAT-TAATGGGATTATTCAATGCATGTTTGGCCAAAAAT
61 ACCTTAAATAATCCCCCATAAAAATTTATGGAA-GGGATTATTAAAGGCATTTTTGACCAAAAAT
*
438553 ACCTTAAATAATC
125 ACCTTCAATAATC
438566 CCATTGAATT
Statistics
Matches: 323, Mismatches: 51, Indels: 31
0.80 0.13 0.08
Matches are distributed among these distances:
250 5 0.02
251 20 0.06
252 182 0.56
253 64 0.20
254 30 0.09
255 22 0.07
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (253 bp):
TTTAATAATCCCCTAAAAAAAATTTAAATGGATTATTGAAAGTATTTTTGACAAAAAAACACCTT
AAATAATCCCCCATAAAAATTTATGGAAGGGATTATTAAAGGCATTTTTGACCAAAAATACCTTC
AATAATCTCTCATAAAAATTTATTAAAAAGATTATTGAAAGTATTTTTAGTAAAAAACACCTTTA
ATAATCCCTTGAAAAATTTTAAAAAGGATTATTGAAAGCATTTTTTGCTAAAGATGCC
Found at i:438567 original size:64 final size:64
Alignment explanation
Indices: 437892--438567 Score: 486
Period size: 64 Copynumber: 10.7 Consensus size: 64
437882 TTTTGAGAGA
* * * * * ** *
437892 ATTATTGGAGGCATTTTTTGCCAAAAACACATTTAATAAT-CCTC-TAAAAA-AAATTTAAATGG
1 ATTATTGAAGGTATTTTTGGCCAAAAATACCTTTAATAATCCCTCATAAAAATTTA-TTAAAGGG
* * * * * * *
437954 ATTATTGAAAGTATTTTTGACAAAAAAAATACCTTAAATAATCCCCCATAAAAATTTATTGAGGG
1 ATTATTGAAGGTATTTTTGGC--CAAAAATACCTTTAATAATCCCTCATAAAAATTTATTAAAGG
438019 G
64 G
* * * * ** **
438020 ATTATTAAAGGCATTTTTGGCCAAAAATATCTTCAATAATTTCTCATAAAAATTTATTAAAAAG
1 ATTATTGAAGGTATTTTTGGCCAAAAATACCTTTAATAATCCCTCATAAAAATTTATTAAAGGG
* * * * ** * *
438084 ATTATTGAAAGTATTTTTAGTCAAAAACACCTTTAATAAT--CTTTTGAAAAATTT-TAAAAAGG
1 ATTATTGAAGGTATTTTTGGCCAAAAATACCTTTAATAATCCCTCAT-AAAAATTTATTAAAGGG
* * * * * * * *
438146 ATTATTGAAGGTATTTTTTGCTAAAGATGCCTTTAATAATCCC-CTTGAAAAAATT-TGAAAGGA
1 ATTATTGAAGGTATTTTTGGCCAAAAATACCTTTAATAATCCCTCAT-AAAAATTTATTAAAGGG
** * **
438209 ATTATTGAAGGTATTTTTTACCAAAAACACCTTTAATAATCCCTTCA-ACAAAA-TT-TGGAAGG
1 ATTATTGAAGGTATTTTTGGCCAAAAATACCTTTAATAATCCC-TCATA-AAAATTTATTAAAGG
438271 G
64 G
* ** * *
438272 ATTATTGAAAGTATTTTTTACCAAAAATACCTTTAATAATCTCTCATAAAAATTTATT-GAGGAG
1 ATTATTGAAGGTATTTTTGGCCAAAAATACCTTTAATAATCCCTCATAAAAATTTATTAAAGG-G
** * * **
438336 ATTATTGAAGGTATTTTTGGTAAAAAATACTTTTAATAATCCCT--TGAAAAATTT-TGAAAATG
1 ATTATTGAAGGTATTTTTGGCCAAAAATACCTTTAATAATCCCTCAT-AAAAATTTATTAAAGGG
* * * ** * *
438398 ATTATTGAAAGCATTTTTTGCCAAAAATA--TTTCAATAATCTTTCATAAAAATTTATGAAATGG
1 ATTATTGAAGGTATTTTTGGCCAAAAATACCTTT-AATAATCCCTCATAAAAATTTATTAAAGGG
* * ** * *
438461 ATTATTTAAGGTTTTTTTGATCAAAAATACCTTCAATAATCCCTCATAAAAATTTATTAATGGG
1 ATTATTGAAGGTATTTTTGGCCAAAAATACCTTTAATAATCCCTCATAAAAATTTATTAAAGGG
* * * * *
438525 ATTATTCAATGCATGTTTGGCCAAAAATACCTTAAATAATCCC
1 ATTATTGAAGGTATTTTTGGCCAAAAATACCTTTAATAATCCC
438568 ATTGAATTTT
Statistics
Matches: 484, Mismatches: 107, Indels: 44
0.76 0.17 0.07
Matches are distributed among these distances:
60 3 0.01
61 8 0.02
62 100 0.21
63 154 0.32
64 184 0.38
65 6 0.01
66 28 0.06
67 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.37
Consensus pattern (64 bp):
ATTATTGAAGGTATTTTTGGCCAAAAATACCTTTAATAATCCCTCATAAAAATTTATTAAAGGG
Found at i:438592 original size:189 final size:185
Alignment explanation
Indices: 437913--438592 Score: 551
Period size: 189 Copynumber: 3.6 Consensus size: 185
437903 CATTTTTTGC
* * * * * *
437913 CAAAAACACATTTAATAATCCTCTAAAAAAAATTTA--AATGGATTATTGAAAGTATTTTTGACA
1 CAAAAATACCTTTAATAATCCTC--ATAAAAATTTATTAAGGGATTATTGAAGGTATTTTTGGC-
* * * * * *
437976 AAAAAAATACCTTAAATAATCCCCCATAAAAATTTATTG-AGGGGATTATT-AAAGGCATTTTTG
63 -AAAAAATACCTTTAATAAT--CCCTTGAAAA-TT-TTGAAAGAGATTATTGAAA-GCATTTTTT
* * *
438039 GCCAAAAATATCTTCAATAAT-TTCTCATAAAAATTTATTAAAAAGATTATTGAAAGTATTTTTA
122 GCCAAAAATAT-TTCAATAATCTT-TCATAAAAATTTATGAAAAGGATTATTGAAAGTTTTTTTA
438103 GT
185 -T
* ** * * * *
438105 CAAAAACACCTTTAATAAT-CTTTTGAAAAATTT-TAAAAAGGATTATTGAAGGTATTTTTTGCT
1 CAAAAATACCTTTAATAATCCTCAT-AAAAATTTAT-TAAGGGATTATTGAAGGTATTTTTGGCA
* * * * * *
438168 AAAGATGCCTTTAATAATCCCCTTGAAAAAATTTGAAAG-GAATTATTGAAGGTATTTTTTACCA
64 AAAAATACCTTTAATAAT-CCCTTG-AAAATTTTGAAAGAG-ATTATTGAAAGCATTTTTTGCCA
* * * * *
438232 AAAACACCTTT-AATAATCCCTTCA-ACAAAA-TT-TGGAAGGGATTATTGAAAGTATTTTTTAC
126 AAAATA--TTTCAATAAT-CTTTCATA-AAAATTTATGAAAAGGATTATTGAAAGT-TTTTTTAT
* *
438293 CAAAAATACCTTTAATAATCTCTCATAAAAATTTATTGAGGAGATTATTGAAGGTATTTTTGGTA
1 CAAAAATACCTTTAATAATC-CTCATAAAAATTTATTAAGG-GATTATTGAAGGTATTTTTGGCA
*
438358 AAAAATACTTTTAATAATCCCTTGAAAAATTTTGAAA-ATGATTATTGAAAGCATTTTTTGCCAA
64 AAAAATACCTTTAATAATCCCTTG-AAAATTTTGAAAGA-GATTATTGAAAGCATTTTTTGCCAA
* * *
438422 AAATATTTCAATAATCTTTCATAAAAATTTATGAAATGGATTATTTAAGGTTTTTTTGAT
127 AAATATTTCAATAATCTTTCATAAAAATTTATGAAAAGGATTATTGAAAGTTTTTTT-AT
* * * * * *
438482 CAAAAATACCTTCAATAATCCCTCATAAAAATTTATTAATGGGATTATTCAATGCATGTTTGGCC
1 CAAAAATACCTTTAATAAT-CCTCATAAAAATTTATTAA-GGGATTATTGAAGGTATTTTTGGCA
* * *
438547 AAAAATACCTTAAATAATCCCATTG-AATTTTTTATAAGAGATTATT
64 AAAAATACCTTTAATAATCCC-TTGAAAATTTTGA-AAGAGATTATT
438593 CAAGGTATTT
Statistics
Matches: 395, Mismatches: 63, Indels: 63
0.76 0.12 0.12
Matches are distributed among these distances:
187 12 0.03
188 60 0.15
189 194 0.49
190 85 0.22
191 4 0.01
192 40 0.10
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (185 bp):
CAAAAATACCTTTAATAATCCTCATAAAAATTTATTAAGGGATTATTGAAGGTATTTTTGGCAAA
AAATACCTTTAATAATCCCTTGAAAATTTTGAAAGAGATTATTGAAAGCATTTTTTGCCAAAAAT
ATTTCAATAATCTTTCATAAAAATTTATGAAAAGGATTATTGAAAGTTTTTTTAT
Found at i:444291 original size:42 final size:43
Alignment explanation
Indices: 444244--444334 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
444234 AAAAAATCAT
*
444244 ATCATGCTTAAATTTGTGT-AAAAAATGTAACACACTTAATTA
1 ATCATGCTTAAATTTGTGTCAAAAAATGTAACACAATTAATTA
* * * * *
444286 ATCATGCTTAATTTTGTTTCAAAAATTTTAACTCAATTAATTA
1 ATCATGCTTAAATTTGTGTCAAAAAATGTAACACAATTAATTA
444329 ATCATG
1 ATCATG
444335 TTGATCCATT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 17 0.40
43 25 0.60
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.41
Consensus pattern (43 bp):
ATCATGCTTAAATTTGTGTCAAAAAATGTAACACAATTAATTA
Found at i:444900 original size:27 final size:26
Alignment explanation
Indices: 444862--444922 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
444852 TATTTTGTAT
444862 TTTAATTAAATTAATCGATTGAATTAA
1 TTTAATTAAATTAATCGATT-AATTAA
*
444889 TTTAA-TATAATTAATTGATTAATT-A
1 TTTAATTA-AATTAATCGATTAATTAA
*
444914 TTAAATTAA
1 TTTAATTAA
444923 TTTTAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 6 0.20
26 8 0.27
27 16 0.53
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (26 bp):
TTTAATTAAATTAATCGATTAATTAA
Found at i:444975 original size:17 final size:17
Alignment explanation
Indices: 444896--444981 Score: 68
Period size: 17 Copynumber: 4.9 Consensus size: 17
444886 TAATTTAATA
444896 TAATTAATTGATTAATTATT
1 TAATTAATT--TTAATT-TT
*
444916 AAATTAATTTTAATTTAT
1 TAATTAATTTTAATTT-T
***
444934 TAA-TAAAAATAATTTT
1 TAATTAATTTTAATTTT
**
444950 TAAAAAATTTTAATTTT
1 TAATTAATTTTAATTTT
444967 TAATTAA-TTTAATTT
1 TAATTAATTTTAATTT
444982 GAAAATCAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
16 12 0.23
17 24 0.45
18 9 0.17
20 8 0.15
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (17 bp):
TAATTAATTTTAATTTT
Found at i:445755 original size:22 final size:20
Alignment explanation
Indices: 445730--445776 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
445720 TTATATCATT
445730 TTTTTAATATTTAAAACTATTA
1 TTTTTAATATTTAAAA-T-TTA
* *
445752 TTTTTTATATTTTAAATTTA
1 TTTTTAATATTTAAAATTTA
445772 TTTTT
1 TTTTT
445777 TACGATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 1 0.04
22 14 0.61
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTAATATTTAAAATTTA
Found at i:445757 original size:23 final size:21
Alignment explanation
Indices: 445729--445778 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 21
445719 ATTATATCAT
445729 TTTTTTAATATTTAAAACTATTA
1 TTTTTTAATATTTAAAA-T-TTA
*
445752 TTTTTT-ATATTTTAAATTTA
1 TTTTTTAATATTTAAAATTTA
445772 TTTTTTA
1 TTTTTTA
445779 CGATTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 9 0.36
21 1 0.04
22 9 0.36
23 6 0.24
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTTAATATTTAAAATTTA
Found at i:446796 original size:16 final size:17
Alignment explanation
Indices: 446769--446807 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
446759 AATTAAAAGG
*
446769 ATTTTATAATTTTTATA
1 ATTTTATAATTTTAATA
446786 ATTTT-TAATTTTAATA
1 ATTTTATAATTTTAATA
*
446802 AATTTA
1 ATTTTA
446808 AAAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTATAATTTTAATA
Found at i:446921 original size:2 final size:2
Alignment explanation
Indices: 446916--446943 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
446906 AATTATAATG
446916 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
446944 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:447884 original size:167 final size:166
Alignment explanation
Indices: 447668--448019 Score: 385
Period size: 167 Copynumber: 2.1 Consensus size: 166
447658 AATTATGTCA
* * * *
447668 ATAATTTAAATTGTATCAACTTTGAAAAAGGATAATTTTGATCAATAAATAAATTATCATA-TCT
1 ATAACTTAAATTATATAAACTTTAAAAAAGGATAATTTTGATCAATAAATAAATTATCATATTC-
* * ** * *
447732 TAA-TCATTGTACAT-ATCAAATATAAAGTAGGATGACATCATTTAATCTAATTTTATTCATAAT
65 TAATTC--T-TACATAATCAAATACAAAATAAAATGACATCATTTAATCTAATTCTATTAATAAT
*
447795 ATTATCTTATAC-TATCTTATCATAATCTTATATACCAAAC
127 ATTATCTTAT-CTTATCCTATCATAATCTTATATACCAAAC
*
447835 ATAACTTAAATTATATAAACTTTAAAAAATGG-TAATTTTGA-CAAATAAATAAATTATCTTATT
1 ATAACTTAAATTATATAAACTTTAAAAAA-GGATAATTTTGATC-AATAAATAAATTATCATATT
* * * *
447898 CTAATTCTTACATACATCAAATACAAAATAAAATTATATTATTTAATTTAATTCTATTAATAATA
64 CTAATTCTTACATA-ATCAAATACAAAATAAAATGACATCATTTAATCTAATTCTATTAATAATA
* * * * *
447963 TTATCTTATCTTATCCTATTATAGTCTTGTGTACCAAAT
128 TTATCTTATCTTATCCTATCATAATCTTATATACCAAAC
*
448002 ATTACTTAAATTA-ATAAA
1 ATAACTTAAATTATATAAA
448020 ATTATTTTAT
Statistics
Matches: 156, Mismatches: 22, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
165 5 0.03
166 8 0.05
167 137 0.88
168 6 0.04
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (166 bp):
ATAACTTAAATTATATAAACTTTAAAAAAGGATAATTTTGATCAATAAATAAATTATCATATTCT
AATTCTTACATAATCAAATACAAAATAAAATGACATCATTTAATCTAATTCTATTAATAATATTA
TCTTATCTTATCCTATCATAATCTTATATACCAAAC
Found at i:451223 original size:26 final size:25
Alignment explanation
Indices: 451194--451261 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
451184 TATTATAGTA
*
451194 ATTTTATCAATTTTGGTAAAAAAAAT
1 ATTTTATCAATTTTGAT-AAAAAAAT
* *
451220 ATTTTCAT-AATTATGATAAGAAAAT
1 ATTTT-ATCAATTTTGATAAAAAAAT
* *
451245 ATTATAGCAATTTTGAT
1 ATTTTATCAATTTTGAT
451262 CAATCATGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 1 0.03
25 19 0.56
26 12 0.35
27 2 0.06
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (25 bp):
ATTTTATCAATTTTGATAAAAAAAT
Found at i:451292 original size:61 final size:59
Alignment explanation
Indices: 451163--451294 Score: 174
Period size: 61 Copynumber: 2.2 Consensus size: 59
451153 CGTAAGGACA
* **
451163 TTTTATAATTATGATAAGAAATATTATAGTAATTTTATCAATTTTGGTAAAAAAAATAT
1 TTTTATAATTATGATAAGAAATATTATAGCAATTTTATCAATCATGGTAAAAAAAATAT
* ** *
451222 TTTCATAATTATGATAAGAAAATATTATAGCAATTTTGATCAATCATGGTAGTAGAAATAT
1 TTTTATAATTATGATAAG-AAATATTATAGCAATTTT-ATCAATCATGGTAAAAAAAATAT
*
451283 TTTTGTAATTAT
1 TTTTATAATTAT
451295 AGTAAGTGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 17 0.27
60 17 0.27
61 28 0.45
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (59 bp):
TTTTATAATTATGATAAGAAATATTATAGCAATTTTATCAATCATGGTAAAAAAAATAT
Found at i:451756 original size:18 final size:18
Alignment explanation
Indices: 451733--451770 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
451723 CTAGGTATGC
*
451733 ATTTTAAAAACTTTTAGA
1 ATTTTAAAAACATTTAGA
451751 ATTTTAAAAACATTTAGA
1 ATTTTAAAAACATTTAGA
451769 AT
1 AT
451771 CTATTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (18 bp):
ATTTTAAAAACATTTAGA
Found at i:452438 original size:26 final size:27
Alignment explanation
Indices: 452392--452454 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
452382 TTTTGTTTTT
*
452392 TAAAAAATGTATTTAGTAAATG-AAAA
1 TAAAAAATGTATTTAGAAAATGAAAAA
*
452418 TAAAAAATGTTTTCTA-AAAATGCAAAAA
1 TAAAAAATGTATT-TAGAAAATG-AAAAA
452446 TAAGAAAAT
1 TAA-AAAAT
452455 AAATGAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 17 0.55
27 2 0.06
28 7 0.23
29 5 0.16
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.29
Consensus pattern (27 bp):
TAAAAAATGTATTTAGAAAATGAAAAA
Found at i:454610 original size:13 final size:13
Alignment explanation
Indices: 454592--454616 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
454582 TATAGATAAA
454592 ATGTGATAAGTTT
1 ATGTGATAAGTTT
454605 ATGTGATAAGTT
1 ATGTGATAAGTT
454617 AGTGACGTGG
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:0.00, G:0.24, T:0.44
Consensus pattern (13 bp):
ATGTGATAAGTTT
Found at i:458081 original size:6 final size:6
Alignment explanation
Indices: 458070--458104 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
458060 GAATTTGCTT
*
458070 TTTTGC TTTTGC TTTTGC TTTTGT TTTTGTC TTTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTG-C TTTT
458105 TTTATTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 22 0.85
7 4 0.15
ACGTcount: A:0.00, C:0.11, G:0.14, T:0.74
Consensus pattern (6 bp):
TTTTGC
Found at i:462262 original size:13 final size:13
Alignment explanation
Indices: 462231--462255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
462221 AAAATTTAAT
462231 AAAATAAATTTTC
1 AAAATAAATTTTC
462244 AAAATAAATTTT
1 AAAATAAATTTT
462256 ATTAATACGG
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:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATTTTC
Found at i:465325 original size:2 final size:2
Alignment explanation
Indices: 465318--465342 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
465308 GTAGGAATAT
465318 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
465343 GAAAATTGAA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:465786 original size:126 final size:126
Alignment explanation
Indices: 465561--465815 Score: 510
Period size: 126 Copynumber: 2.0 Consensus size: 126
465551 AAAAGTTATG
465561 AGCTCAATGTTGGTTTTTGGTCAAGATAGGTTTTTACTTTTCTTATTTTGGGCCCTTGTAAACAC
1 AGCTCAATGTTGGTTTTTGGTCAAGATAGGTTTTTACTTTTCTTATTTTGGGCCCTTGTAAACAC
465626 TTCAACAGCTTTGTTGGAGTCAAAAATTATTCATCAACTTTTTTGAAATTTTCTAACTTTC
66 TTCAACAGCTTTGTTGGAGTCAAAAATTATTCATCAACTTTTTTGAAATTTTCTAACTTTC
465687 AGCTCAATGTTGGTTTTTGGTCAAGATAGGTTTTTACTTTTCTTATTTTGGGCCCTTGTAAACAC
1 AGCTCAATGTTGGTTTTTGGTCAAGATAGGTTTTTACTTTTCTTATTTTGGGCCCTTGTAAACAC
465752 TTCAACAGCTTTGTTGGAGTCAAAAATTATTCATCAACTTTTTTGAAATTTTCTAACTTTC
66 TTCAACAGCTTTGTTGGAGTCAAAAATTATTCATCAACTTTTTTGAAATTTTCTAACTTTC
465813 AGC
1 AGC
465816 AGTAGTATTA
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 129 1.00
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (126 bp):
AGCTCAATGTTGGTTTTTGGTCAAGATAGGTTTTTACTTTTCTTATTTTGGGCCCTTGTAAACAC
TTCAACAGCTTTGTTGGAGTCAAAAATTATTCATCAACTTTTTTGAAATTTTCTAACTTTC
Found at i:467216 original size:3 final size:3
Alignment explanation
Indices: 467208--467233 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
467198 AGGAGTGGCC
467208 GTG GTG GTG GTG GTG GTG GTG GTG GT
1 GTG GTG GTG GTG GTG GTG GTG GTG GT
467234 AGAGGCCGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
GTG
Found at i:468053 original size:4 final size:4
Alignment explanation
Indices: 468044--468078 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
468034 GCAAACCAAT
*
468044 ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
468079 TAAATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:468089 original size:2 final size:2
Alignment explanation
Indices: 468076--468106 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
468066 GCATACATAC
*
468076 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
468107 AGTAGTAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:468916 original size:40 final size:39
Alignment explanation
Indices: 468854--468936 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 39
468844 AAAATGTGAG
*** *
468854 TTCACAAAAGTTTTGTTGAGTGGCCTTTACAAGATTTGAA
1 TTCACAAAAGTTTTGCAAAGTGGCCTTTACAAGATCT-AA
* *
468894 TTCACATAAGTTTTGCAAAGTGGCCTTTATAAGATCTAA
1 TTCACAAAAGTTTTGCAAAGTGGCCTTTACAAGATCTAA
468933 TTCA
1 TTCA
468937 AGACCTTTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 6 0.16
40 31 0.84
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (39 bp):
TTCACAAAAGTTTTGCAAAGTGGCCTTTACAAGATCTAA
Found at i:483839 original size:16 final size:16
Alignment explanation
Indices: 483818--483848 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
483808 ACTCACAAAC
483818 ATATAAACATACACAT
1 ATATAAACATACACAT
483834 ATATAAACATACACA
1 ATATAAACATACACA
483849 CGCATAAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (16 bp):
ATATAAACATACACAT
Found at i:493253 original size:20 final size:18
Alignment explanation
Indices: 493215--493257 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
493205 TATTAATATA
*
493215 TATTTAACAAATTAATTTT
1 TATTTAACAAA-TAAATTT
*
493234 TATTTAATAATATAAATTT
1 TATTTAACAA-ATAAATTT
493253 TATTT
1 TATTT
493258 TAGATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTAACAAATAAATTT
Found at i:494326 original size:37 final size:36
Alignment explanation
Indices: 494285--494359 Score: 87
Period size: 37 Copynumber: 2.1 Consensus size: 36
494275 ATTATAAAGT
**
494285 AAAATGAATTTTGTCCCATCAAAAAGAAATAAAAAAA
1 AAAATGAACGTTGTCCCATCAAAAA-AAATAAAAAAA
* * * *
494322 AAAATGAGCGTTGTCCCATTATAAAAAATAAAACAA
1 AAAATGAACGTTGTCCCATCAAAAAAAATAAAAAAA
494358 AA
1 AA
494360 TGTGTCTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 12 0.38
37 20 0.62
ACGTcount: A:0.57, C:0.12, G:0.09, T:0.21
Consensus pattern (36 bp):
AAAATGAACGTTGTCCCATCAAAAAAAATAAAAAAA
Found at i:494936 original size:13 final size:13
Alignment explanation
Indices: 494918--494949 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
494908 TACTTTTTTT
494918 TTATATAATAAAA
1 TTATATAATAAAA
494931 TTATAT-ATAAAA
1 TTATATAATAAAA
494943 -TATATAA
1 TTATATAA
494950 CTAATAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 7 0.39
13 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTATATAATAAAA
Found at i:497542 original size:14 final size:16
Alignment explanation
Indices: 497525--497561 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
497515 AATGAAATTA
497525 TTTATTTAC-TATA-T
1 TTTATTTACTTATACT
*
497539 TTTATTTTCTTATACT
1 TTTATTTACTTATACT
497555 TTTATTT
1 TTTATTT
497562 TGAATTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 4 0.20
16 8 0.40
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATTTACTTATACT
Found at i:499526 original size:59 final size:58
Alignment explanation
Indices: 499440--499573 Score: 157
Period size: 58 Copynumber: 2.3 Consensus size: 58
499430 TTTTAAAGCA
* ** * *
499440 TTTGAGAATTTTTA-TTTTAAGAGAAATTGATACTTTTAA-CTTTCCTTAAAATGTTTT
1 TTTGATAATTTTTATTTTTAAGAGAAATTGATACTTCCAATCTTTCCTCAAAAT-ATTT
* *
499497 TCTTGATAATTTTTATTTTTAAG-GAAAATTGGTACTTCCAATTTTTCCTCAAAATATTT
1 T-TTGATAATTTTTATTTTTAAGAG-AAATTGATACTTCCAATCTTTCCTCAAAATATTT
499556 TTTGATAATTTTTATTTT
1 TTTGATAATTTTTATTTT
499574 AGAAATTTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
57 1 0.02
58 30 0.45
59 24 0.36
60 11 0.17
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (58 bp):
TTTGATAATTTTTATTTTTAAGAGAAATTGATACTTCCAATCTTTCCTCAAAATATTT
Found at i:499691 original size:13 final size:14
Alignment explanation
Indices: 499675--499707 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
499665 AAATTTTCCC
499675 TAAAAATATT-TTT
1 TAAAAATATTATTT
*
499688 TAAAAATTTTATTT
1 TAAAAATATTATTT
499702 TAAAAA
1 TAAAAA
499708 AAATTGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAAAATATTATTT
Found at i:499722 original size:57 final size:57
Alignment explanation
Indices: 499570--499825 Score: 266
Period size: 58 Copynumber: 4.4 Consensus size: 57
499560 ATAATTTTTA
* * * * * **
499570 TTTTAGAAATTTTACTTTAAGAAAAATTGATACTCTCAACTTTT-CCTTAAAGCATT
1 TTTTAAAAATTTTATTTTAAGAAAAATTGATACTTTCAAATTTTCCCTAAAAATATT
* *
499626 TTTTAGAAAAATTTATTTTTAAGGAAAATTGATACTTTCAAATTTTCCCTAAAAATATT
1 TTTTA-AAAATTTTA-TTTTAAGAAAAATTGATACTTTCAAATTTTCCCTAAAAATATT
* * * *
499685 TTTTAAAAATTTTATTTTAAAAAAAATTGATATTTTCAACTTCTCCCTAAAAATATTT
1 TTTTAAAAATTTTATTTTAAGAAAAATTGATACTTTCAAATTTTCCCTAAAAATA-TT
* * *
499743 TTTTAAAATCTTTTTATTTTCAAGAAAAATTGATACTTTC-AACTTTCCCATAAAAATACT
1 TTTTAAAA--ATTTTATTTT-AAGAAAAATTGATACTTTCAAATTTTCCC-TAAAAATATT
* *
499803 TTTGAAAATTTTTATTTT-AGAAA
1 TTTTAAAAATTTTATTTTAAGAAA
499826 TTTTATTTTT
Statistics
Matches: 169, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
56 10 0.06
57 43 0.25
58 54 0.32
59 14 0.08
60 23 0.14
61 25 0.15
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (57 bp):
TTTTAAAAATTTTATTTTAAGAAAAATTGATACTTTCAAATTTTCCCTAAAAATATT
Found at i:499900 original size:13 final size:15
Alignment explanation
Indices: 499872--499910 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
499862 CCTTAAAAAT
*
499872 ACTTTTTTTTTGAAA
1 ACTTTTATTTTGAAA
499887 A-TTTTATTTT-AAA
1 ACTTTTATTTTGAAA
499900 ACTTTTATTTT
1 ACTTTTATTTT
499911 TAAGGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 17 0.77
15 1 0.05
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (15 bp):
ACTTTTATTTTGAAA
Found at i:499906 original size:76 final size:76
Alignment explanation
Indices: 499734--499955 Score: 314
Period size: 76 Copynumber: 2.9 Consensus size: 76
499724 CTTCTCCCTA
* * *
499734 AAAATATTT-TTTTAAAATCTTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTCCCATAAAA
1 AAAAT-TTTATTTTAAAA-C-TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTTAAAA
499798 ATAC-----TTTTG
63 ATACTTTTTTTTTG
499807 AAAATTTTTATTTTAGAAA-TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAA
1 AAAA-TTTTATTTTA-AAACTTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAA
499871 TACTTTTTTTTTG
64 TACTTTTTTTTTG
*
499884 AAAATTTTATTTTAAAACTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATA
1 AAAATTTTATTTTAAAACTTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATA
499949 CTTTTTT
66 CTTTTTT
499956 CTAAAAAATA
Statistics
Matches: 136, Mismatches: 4, Indels: 15
0.88 0.03 0.10
Matches are distributed among these distances:
72 45 0.33
73 7 0.05
74 6 0.04
75 6 0.04
76 63 0.46
77 9 0.07
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (76 bp):
AAAATTTTATTTTAAAACTTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATA
CTTTTTTTTTG
Found at i:500046 original size:14 final size:11
Alignment explanation
Indices: 500009--500038 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
499999 AAAATCATTA
500009 AAAAATAAAAT
1 AAAAATAAAAT
500020 AAAAATAAAAT
1 AAAAATAAAAT
500031 AAGAAATA
1 AA-AAATA
500039 CCAAATAATT
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:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:500072 original size:3 final size:3
Alignment explanation
Indices: 500059--500100 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
500049 CTAATCTAAT
500059 TAA TAAA TAA TAA TAA TAA TAA -AGA -AA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
500101 ATATATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:500086 original size:20 final size:20
Alignment explanation
Indices: 500063--500101 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
500053 TCTAATTAAT
500063 AAATAATAATAATAATAAAG
1 AAATAATAATAATAATAAAG
500083 AAATAATAATAATAATAAA
1 AAATAATAATAATAATAAA
500102 TATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
AAATAATAATAATAATAAAG
Found at i:500863 original size:17 final size:17
Alignment explanation
Indices: 500843--500882 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
500833 TGATCAAGAG
*
500843 AAAAAAATATAAAAATA
1 AAAAAAATAGAAAAATA
* *
500860 AAAATAATAGATAAATA
1 AAAAAAATAGAAAAATA
500877 AAAAAA
1 AAAAAA
500883 TATTAATAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAAAAATAGAAAAATA
Found at i:500868 original size:3 final size:3
Alignment explanation
Indices: 500851--500934 Score: 62
Period size: 3 Copynumber: 26.7 Consensus size: 3
500841 AGAAAAAAAT
* * * *
500851 ATA AAA ATA AAA ATA ATA GATAA ATA A-A AAA ATA TTA ATA GATTA ATA
1 ATA ATA ATA ATA ATA ATA -AT-A ATA ATA ATA ATA ATA ATA -A-TA ATA
* *
500899 ATA ATA ATA ATA ATA GTA ATA ATA ATGA AAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA AT
500935 TAAATTAAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
2 2 0.03
3 51 0.80
4 8 0.12
5 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:500889 original size:22 final size:23
Alignment explanation
Indices: 500862--500934 Score: 78
Period size: 22 Copynumber: 3.1 Consensus size: 23
500852 TAAAAATAAA
500862 AATAATAGATAAATAA-AAAAAT
1 AATAATAGATAAATAATAAAAAT
* * *
500884 ATTAATAGATTAATAATAATAAT
1 AATAATAGATAAATAATAAAAAT
500907 AATAATAG-TAATAATAATGAAAAAT
1 AATAATAGAT-A-AATAAT-AAAAAT
500932 AAT
1 AAT
500935 TAAATTAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
22 15 0.37
23 12 0.29
24 6 0.15
25 8 0.20
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (23 bp):
AATAATAGATAAATAATAAAAAT
Found at i:501082 original size:15 final size:14
Alignment explanation
Indices: 501043--501075 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
501033 TTTTTGTGCT
*
501043 TTTTTTAA-AATAA
1 TTTTTTAATAAAAA
501056 TTTTTTAATAAAAA
1 TTTTTTAATAAAAA
501070 TTTTTT
1 TTTTTT
501076 CATTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTTTAATAAAAA
Done.