Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 8 of 222
Found at i:2641509 original size:11 final size:11
Alignment explanation
Indices: 2641444--2641478 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
2641434 GGTCTCTCCT
2641444 TTTTCTTTTTC
1 TTTTCTTTTTC
2641455 TTTTTCTTTTTC
1 -TTTTCTTTTTC
2641467 TTTTCTTTTTC
1 TTTTCTTTTTC
2641478 T
1 T
2641479 CCTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:2651791 original size:60 final size:61
Alignment explanation
Indices: 2651706--2651847 Score: 146
Period size: 60 Copynumber: 2.3 Consensus size: 61
2651696 CCTTTCCTTT
* * * * **
2651706 TTGAAATTTTTAGAATTAGAGCT-AAATTATCATATTATGTAAATGTTGAGAGCTAAATTTA
1 TTGAATTTTTTAGAATTAGAACTAAAATGA-CAAATTATGTAAACATTGAGAGCTAAATTTA
* * * *
2651767 TTG-ATTTTTTAGAATTCA-AACTAAAATGACAAATTTTGTAAACATTGAGGGTTAAATTTG
1 TTGAATTTTTTAGAATT-AGAACTAAAATGACAAATTATGTAAACATTGAGAGCTAAATTTA
*
2651827 TTGAATTTTTTAGATTTAGAA
1 TTGAATTTTTTAGAATTAGAA
2651848 TCAAAACGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
60 43 0.65
61 23 0.35
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (61 bp):
TTGAATTTTTTAGAATTAGAACTAAAATGACAAATTATGTAAACATTGAGAGCTAAATTTA
Found at i:2660720 original size:30 final size:30
Alignment explanation
Indices: 2660676--2660735 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2660666 TAAAATGTTA
*
2660676 TTATTCTTTGACGGATTAAATTATAAATTT
1 TTATTCTTTGACGGATCAAATTATAAATTT
*
2660706 TTATT-TTTGAACGGATCAAATTTTAAATTT
1 TTATTCTTTG-ACGGATCAAATTATAAATTT
2660736 AAATTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (30 bp):
TTATTCTTTGACGGATCAAATTATAAATTT
Found at i:2660742 original size:30 final size:29
Alignment explanation
Indices: 2660682--2660742 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
2660672 GTTATTATTC
* **
2660682 TTTGACGGATTAAATTATAAATTTTTATT
1 TTTGACGGATCAAATTATAAATTTAAATT
*
2660711 TTTGAACGGATCAAATTTTAAATTTAAATT
1 TTTG-ACGGATCAAATTATAAATTTAAATT
2660741 TT
1 TT
2660743 AAAGAGGTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (29 bp):
TTTGACGGATCAAATTATAAATTTAAATT
Found at i:2667442 original size:20 final size:20
Alignment explanation
Indices: 2667417--2667456 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2667407 GAATGAACTT
*
2667417 ATTATTTTGCTTTTTAACCA
1 ATTATTTTGCTTTTGAACCA
*
2667437 ATTATTTTGGTTTTGAACCA
1 ATTATTTTGCTTTTGAACCA
2667457 TCCCTATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (20 bp):
ATTATTTTGCTTTTGAACCA
Found at i:2668267 original size:43 final size:43
Alignment explanation
Indices: 2668206--2668292 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
2668196 TCCCTCAAGG
2668206 TGTTCCACCAGAGTGTAAACGCCCAAGGTTCTAAAATCAAACC
1 TGTTCCACCAGAGTGTAAACGCCCAAGGTTCTAAAATCAAACC
*
2668249 TGTTCCACCAGAGTGTAAACGCCCAGGGTTCTAAAATCAAACC
1 TGTTCCACCAGAGTGTAAACGCCCAAGGTTCTAAAATCAAACC
2668292 T
1 T
2668293 CTCCTCTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (43 bp):
TGTTCCACCAGAGTGTAAACGCCCAAGGTTCTAAAATCAAACC
Found at i:2670109 original size:26 final size:27
Alignment explanation
Indices: 2670060--2670110 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2670050 AATAACTAAA
* *
2670060 TAAATAATTAAAAATTCATAAAATTTT
1 TAAAGAATAAAAAATTCATAAAATTTT
*
2670087 TAAAGAATAAAAAATT-ATTAAATT
1 TAAAGAATAAAAAATTCATAAAATT
2670111 GGTTCAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (27 bp):
TAAAGAATAAAAAATTCATAAAATTTT
Found at i:2675897 original size:70 final size:67
Alignment explanation
Indices: 2675799--2675930 Score: 167
Period size: 70 Copynumber: 1.9 Consensus size: 67
2675789 CTGAATAAAT
* * * *
2675799 AAAGGCAAAACTACGTCATTTTGATAAATGTTTACCTATTCTAAAGTTAAAAGTCAAAATCATTA
1 AAAGGCAAAACTACATCATTTTGATAAATATTTA-CTAAT-T-AAGTTAAAAGGCAAAATCATTA
2675864 AGTTA
63 AGTTA
* *
2675869 AAAGGCAAAACTATAT-AGTTTTGATAAATATTTACTAATTAAGTTAAAAGGCAAAATTATTA
1 AAAGGCAAAACTACATCA-TTTTGATAAATATTTACTAATTAAGTTAAAAGGCAAAATCATTA
2675931 TATTTGTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
67 20 0.36
68 1 0.02
69 5 0.09
70 29 0.53
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.33
Consensus pattern (67 bp):
AAAGGCAAAACTACATCATTTTGATAAATATTTACTAATTAAGTTAAAAGGCAAAATCATTAAGT
TA
Found at i:2679182 original size:5 final size:6
Alignment explanation
Indices: 2679164--2679189 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2679154 AAAAAATATA
2679164 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
2679190 TGAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:2683205 original size:24 final size:23
Alignment explanation
Indices: 2683162--2683207 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2683152 AGTGTTGTTA
*
2683162 ATATATTTTGAAAACAAATTTAG
1 ATATATTCTGAAAACAAATTTAG
2683185 ATATATTACTGAAAATC-AATTTA
1 ATATATT-CTGAAAA-CAAATTTA
2683208 TTTTCCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 12 0.60
25 1 0.05
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (23 bp):
ATATATTCTGAAAACAAATTTAG
Found at i:2684882 original size:6 final size:6
Alignment explanation
Indices: 2684873--2684897 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2684863 TTATAATTAT
2684873 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
2684898 CAATTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:2684952 original size:20 final size:21
Alignment explanation
Indices: 2684914--2684954 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2684904 TATTATATAA
*
2684914 ATATTTTTTATTTAACACATTC
1 ATATTTTATATTT-ACACATTC
2684936 ATATTTTATATTT-CACATT
1 ATATTTTATATTTACACATT
2684955 TCGATAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATTTTATATTTACACATTC
Found at i:2688583 original size:31 final size:31
Alignment explanation
Indices: 2688545--2688603 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2688535 GTCACTGAAC
*
2688545 TATTCGAAAGTTT-TCATTTAAGTAACTAAAT
1 TATTCGAAA-TTTATAATTTAAGTAACTAAAT
*
2688576 TATTCGAAATTTATAATTTAAGTCACTA
1 TATTCGAAATTTATAATTTAAGTAACTA
2688604 GGCCGTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.42
Consensus pattern (31 bp):
TATTCGAAATTTATAATTTAAGTAACTAAAT
Found at i:2690271 original size:24 final size:23
Alignment explanation
Indices: 2690228--2690273 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2690218 AGTGTTGTTA
*
2690228 ATATATTTTGAAAACAAATTTAG
1 ATATATTCTGAAAACAAATTTAG
2690251 ATATATTACTGAAAATC-AATTTA
1 ATATATT-CTGAAAA-CAAATTTA
2690274 TTTTCCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 12 0.60
25 1 0.05
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (23 bp):
ATATATTCTGAAAACAAATTTAG
Found at i:2693145 original size:46 final size:46
Alignment explanation
Indices: 2693044--2693247 Score: 333
Period size: 46 Copynumber: 4.5 Consensus size: 46
2693034 CTTACGTATG
* *
2693044 ACCACTTATCAC-TTGTC-CTTGAACAGATAAGTGTACCT-AGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
2693087 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
* *
2693133 AGCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGTT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
*
2693179 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
*
2693225 ACCACTTATCACTTTATCACTTG
1 ACCACTTATCACTTTGTCACTTG
2693248 TCACTGATCA
Statistics
Matches: 150, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
43 12 0.08
44 5 0.03
45 19 0.13
46 114 0.76
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (46 bp):
ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
Found at i:2695501 original size:17 final size:17
Alignment explanation
Indices: 2695459--2695501 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
2695449 ATAGTTTATA
2695459 TATATTTTATATACATT
1 TATATTTTATATACATT
* * *
2695476 CATATTTTTTATGATATT
1 TATATTTTATAT-ACATT
2695494 TATATTTT
1 TATATTTT
2695502 CATGTTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (17 bp):
TATATTTTATATACATT
Found at i:2697780 original size:28 final size:28
Alignment explanation
Indices: 2697744--2697798 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2697734 TAAAACGATA
*
2697744 TTTATATTTTAAAAATTCAA-TTAAAATT
1 TTTAAATTTTAAAAATT-AATTTAAAATT
*
2697772 TTTAAATTTTAGAAATTAATTTAAAAT
1 TTTAAATTTTAAAAATTAATTTAAAAT
2697799 ATAAATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
TTTAAATTTTAAAAATTAATTTAAAATT
Found at i:2698525 original size:24 final size:24
Alignment explanation
Indices: 2698497--2698548 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2698487 TTCGTAGGTA
** *
2698497 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTACACTAATAAATACT
* *
2698521 AAATATATTACACTAATAAGTACT
1 AAATAAATTACACTAATAAATACT
2698545 AAAT
1 AAAT
2698549 CTTCTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33
Consensus pattern (24 bp):
AAATAAATTACACTAATAAATACT
Found at i:2700683 original size:16 final size:16
Alignment explanation
Indices: 2700650--2700683 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2700640 AATTTTTGTT
* *
2700650 AACATTAATGGGAGAC
1 AACATTAATGGAAAAC
2700666 AACATTAATGGAAAAC
1 AACATTAATGGAAAAC
2700682 AA
1 AA
2700684 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGAAAAC
Found at i:2703513 original size:21 final size:21
Alignment explanation
Indices: 2703487--2703527 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2703477 AGATGAGCAA
* *
2703487 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2703508 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2703528 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2712916 original size:31 final size:31
Alignment explanation
Indices: 2712881--2713039 Score: 164
Period size: 31 Copynumber: 5.3 Consensus size: 31
2712871 TTCATTTGAA
* *
2712881 TTGATTTGTTTATGGTTATACATTGCCGAAT
1 TTGATTTGTATATGGATATACATTGCCGAAT
*
2712912 TTGATTTGTATATGGATATACATTGCTGAA-
1 TTGATTTGTATATGGATATACATTGCCGAAT
* * * * *
2712942 TTAATTTATATATGGTTATACATTACCAAAT
1 TTGATTTGTATATGGATATACATTGCCGAAT
* *
2712973 TTGATTTGTATAT--ATATACATTGACAAAT
1 TTGATTTGTATATGGATATACATTGCCGAAT
* * **
2713002 TTGATTCGTATATGGATATATATCACCGAA-
1 TTGATTTGTATATGGATATACATTGCCGAAT
2713032 TTGATTTG
1 TTGATTTG
2713040 AGCTTTGGAT
Statistics
Matches: 104, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
29 25 0.24
30 31 0.30
31 48 0.46
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (31 bp):
TTGATTTGTATATGGATATACATTGCCGAAT
Found at i:2712956 original size:61 final size:59
Alignment explanation
Indices: 2712877--2712995 Score: 175
Period size: 61 Copynumber: 2.0 Consensus size: 59
2712867 TGTCTTCATT
* * * * *
2712877 TGAATTGATTTGTTTATGGTTATACATTGCCGAATTTGATTTGTATATGGATATACATTGC
1 TGAATTAATTTATATATGGTTATACATTACCAAATTTGATTTGTATAT--ATATACATTGC
2712938 TGAATTAATTTATATATGGTTATACATTACCAAATTTGATTTGTATATATATACATTG
1 TGAATTAATTTATATATGGTTATACATTACCAAATTTGATTTGTATATATATACATTG
2712996 ACAAATTTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 10 0.19
61 43 0.81
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (59 bp):
TGAATTAATTTATATATGGTTATACATTACCAAATTTGATTTGTATATATATACATTGC
Found at i:2728797 original size:18 final size:18
Alignment explanation
Indices: 2728748--2728797 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
2728738 GTAGTGATTC
*
2728748 AATTCGATTAATTCGGGT
1 AATTCGATTAATTTGGGT
**
2728766 AATTCGGGTAATTTGGGT
1 AATTCGATTAATTTGGGT
2728784 AATTCGATTAATTT
1 AATTCGATTAATTT
2728798 TTAACCAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (18 bp):
AATTCGATTAATTTGGGT
Found at i:2735688 original size:11 final size:13
Alignment explanation
Indices: 2735664--2735695 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2735654 TAGTTCATTA
2735664 ATATTTTAATATG
1 ATATTTTAATATG
2735677 AT-TTTTAA-ATG
1 ATATTTTAATATG
2735688 ATATTTTA
1 ATATTTTA
2735696 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:2745474 original size:12 final size:12
Alignment explanation
Indices: 2745457--2745482 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2745447 TAATCATTGT
2745457 AATCATAATGAC
1 AATCATAATGAC
2745469 AATCATAATGAC
1 AATCATAATGAC
2745481 AA
1 AA
2745483 AAGAAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (12 bp):
AATCATAATGAC
Found at i:2745976 original size:22 final size:22
Alignment explanation
Indices: 2745948--2745991 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2745938 TAACTTCGGT
2745948 CACAAACAAAATTTTTTACTTA
1 CACAAACAAAATTTTTTACTTA
2745970 CACAAACAAAATTTTTTACTTA
1 CACAAACAAAATTTTTTACTTA
2745992 GTTATTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (22 bp):
CACAAACAAAATTTTTTACTTA
Found at i:2752795 original size:20 final size:20
Alignment explanation
Indices: 2752766--2752808 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2752756 AAAATAAACA
* **
2752766 TATAATTATTCATTTAATAT
1 TATAAGTATTCAAATAATAT
2752786 TATAAGTATTCAAATAATAT
1 TATAAGTATTCAAATAATAT
2752806 TAT
1 TAT
2752809 TTAAATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (20 bp):
TATAAGTATTCAAATAATAT
Found at i:2755605 original size:18 final size:19
Alignment explanation
Indices: 2755572--2755609 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2755562 AGACTCCAGG
*
2755572 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
2755591 TCTGATT-TCTTCAATCAT
1 TCTGATTCTCTTCAATCAT
2755609 T
1 T
2755610 GCTTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:2760883 original size:110 final size:110
Alignment explanation
Indices: 2760629--2761028 Score: 628
Period size: 110 Copynumber: 3.7 Consensus size: 110
2760619 AATTCAAGAT
* * * *
2760629 GATATTTGGCAATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGCACG-TTCCTCGA
1 GATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
**
2760691 ATTTCCAAACGCAAAACATTACCTTATTTTGAAA-TTTTTGGAAG
66 ATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTTAAAAG
*
2760735 GATATTTAGCTATTTGGTTGAACAAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
1 GATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
* * *
2760800 ATTTCCAAACGTAAAACATTGCCTTATTTTGAAATTTTTTAAAAA
66 ATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTTAAAAG
*
2760845 AATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
1 GATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
* * *
2760910 ATTTCCAAACGCAAAATATTACCTTATTTTGAATTTTTTTTAAAG
66 ATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTTAAAAG
* *
2760955 GATATTTAGCTATTTGGTTGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTTGA
1 GATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
2761020 ATTTCCAAA
66 ATTTCCAAA
2761029 TGTAAAATAT
Statistics
Matches: 269, Mismatches: 21, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
106 22 0.08
108 28 0.10
109 39 0.14
110 180 0.67
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (110 bp):
GATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
ATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTTAAAAG
Found at i:2761177 original size:4 final size:4
Alignment explanation
Indices: 2761168--2761202 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
2761158 AACAAATATC
2761168 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2761203 CTAAGACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2762416 original size:14 final size:14
Alignment explanation
Indices: 2762397--2762424 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2762387 GCCAAAAGCT
2762397 CCGTAGCGCCTCCG
1 CCGTAGCGCCTCCG
2762411 CCGTAGCGCCTCCG
1 CCGTAGCGCCTCCG
2762425 TGGGTGGCGG
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:0.07, C:0.50, G:0.29, T:0.14
Consensus pattern (14 bp):
CCGTAGCGCCTCCG
Found at i:2764517 original size:19 final size:19
Alignment explanation
Indices: 2764480--2764517 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2764470 CTACCTTTCT
*
2764480 TCTTTCTCTTCTCATCCTC
1 TCTTTCTCATCTCATCCTC
2764499 TCTTTCTCAATCTCA-CCTC
1 TCTTTCTC-ATCTCATCCTC
2764518 CCCAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.11, C:0.42, G:0.00, T:0.47
Consensus pattern (19 bp):
TCTTTCTCATCTCATCCTC
Found at i:2765001 original size:154 final size:154
Alignment explanation
Indices: 2764771--2765054 Score: 541
Period size: 154 Copynumber: 1.8 Consensus size: 154
2764761 AATATTATAA
2764771 AACATAAAAATATTAAAATTAAATAATAATATAGAAATGGAATTTTTTTCTCCAAATTTCTCATC
1 AACATAAAAATATTAAAATTAAATAATAATATAGAAATGGAATTTTTTTCTCCAAATTTCTCATC
*
2764836 CAAATATAGTCTAAAAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAATT
66 CAAATACAGTCTAAAAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAATT
2764901 ATATATTGTATCATCAAAATTTTC
131 ATATATTGTATCATCAAAATTTTC
*
2764925 AACATGAAAATATTAAAATTAAATAATAATATAGAAATGGAATTTTTTTCTCCAAATTTCTCATC
1 AACATAAAAATATTAAAATTAAATAATAATATAGAAATGGAATTTTTTTCTCCAAATTTCTCATC
*
2764990 CAAATACAGTCTAAGAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAATT
66 CAAATACAGTCTAAAAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAATT
2765055 TCTCATCAAA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
154 127 1.00
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (154 bp):
AACATAAAAATATTAAAATTAAATAATAATATAGAAATGGAATTTTTTTCTCCAAATTTCTCATC
CAAATACAGTCTAAAAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAATT
ATATATTGTATCATCAAAATTTTC
Found at i:2767960 original size:31 final size:28
Alignment explanation
Indices: 2767913--2767970 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
2767903 TTATAAATGG
*
2767913 TATATATATGTGTATAAAGTGTTTGAATA
1 TATATATATGTATATAAA-TGTTTGAATA
*
2767942 TATATATATGCTTATATAAATTTTTGAAT
1 TATATATATG--TATATAAATGTTTGAAT
2767971 TAAGTTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.40
30 8 0.32
31 7 0.28
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (28 bp):
TATATATATGTATATAAATGTTTGAATA
Found at i:2768981 original size:41 final size:41
Alignment explanation
Indices: 2768921--2769265 Score: 528
Period size: 41 Copynumber: 8.4 Consensus size: 41
2768911 GGTTTTAAAA
* *
2768921 CCTAGCAGGCTAAGGGCCGGTGAACTGAATAAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
* *
2768962 CCTAGTAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
*
2769003 CCTAGCAGGCTAAGTGCCGGTGAACTGAATAAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
* * *
2769044 CCTAGCAGGCTAAGTGTCGGTGATCTGAATTAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
* *
2769085 CCTAGCAGGCTAAGTGCCGATGAACTGAATCGGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
* * *
2769126 CCTAGCAGGTTAAGTGCCGGTGATCTGAATTAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
2769167 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
* * * *
2769208 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTTTAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
*
2769249 CCTAACAGGCTAAGTGC
1 CCTAGCAGGCTAAGTGC
2769266 TAGTGAATCT
Statistics
Matches: 276, Mismatches: 28, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 276 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
Found at i:2769651 original size:35 final size:35
Alignment explanation
Indices: 2769588--2769657 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
2769578 TTCGATGAAG
* **
2769588 TGCAAGTGATAAGCACATATATGGATTTAGATATA
1 TGCAAGTGATAAACACATATATACATTTAGATATA
* * *
2769623 TGCAGGTGATAAATACATATATACATTTAGTTATA
1 TGCAAGTGATAAACACATATATACATTTAGATATA
2769658 ATAACTGTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (35 bp):
TGCAAGTGATAAACACATATATACATTTAGATATA
Found at i:2771362 original size:11 final size:11
Alignment explanation
Indices: 2771346--2771376 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
2771336 AAAAATATTT
2771346 AAATTAAATAA
1 AAATTAAATAA
2771357 AAATTAAATAA
1 AAATTAAATAA
2771368 AAATGTAAA
1 AAAT-TAAA
2771377 AATAAAAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AAATTAAATAA
Found at i:2775473 original size:21 final size:21
Alignment explanation
Indices: 2775447--2775487 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2775437 AGATGAGCAA
* *
2775447 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2775468 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2775488 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2782839 original size:15 final size:15
Alignment explanation
Indices: 2782821--2782859 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
2782811 AAAATTAAAA
2782821 AAATTAAAAAATTTT
1 AAATTAAAAAATTTT
2782836 AAATTAAAAAATTTT
1 AAATTAAAAAATTTT
2782851 AAATTAAAA
1 AAATTAAAA
2782860 CATTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATTAAAAAATTTT
Found at i:2785263 original size:17 final size:17
Alignment explanation
Indices: 2785213--2785270 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
2785203 GGGTGAGAAG
*
2785213 TAAAAGTTTTGAGGAAAAA
1 TAAAAG-TTTGAGG-GAAA
*
2785232 TAAAAAGTTT-TGGGAAA
1 T-AAAAGTTTGAGGGAAA
2785249 TAAAAGTTTGAGGGAAA
1 TAAAAGTTTGAGGGAAA
2785266 GTAAA
1 -TAAA
2785271 TGAGCTGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 8 0.24
17 10 0.30
18 6 0.18
19 4 0.12
20 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (17 bp):
TAAAAGTTTGAGGGAAA
Found at i:2794451 original size:19 final size:19
Alignment explanation
Indices: 2794414--2794451 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2794404 CTACCTTTCT
*
2794414 TCTTTCTCTTCTCATCCTC
1 TCTTTCTCATCTCATCCTC
2794433 TCTTTCTCAATCTCA-CCTC
1 TCTTTCTC-ATCTCATCCTC
2794452 CCCAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.11, C:0.42, G:0.00, T:0.47
Consensus pattern (19 bp):
TCTTTCTCATCTCATCCTC
Found at i:2794532 original size:19 final size:19
Alignment explanation
Indices: 2794502--2794538 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2794492 AAAAATATAA
2794502 ATTTTGGAATTTTTATGAAT
1 ATTTTGGAATTTTT-TGAAT
2794522 ATTTT-GAATTTTTTGAA
1 ATTTTGGAATTTTTTGAA
2794539 AAGTATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (19 bp):
ATTTTGGAATTTTTTGAAT
Found at i:2795115 original size:19 final size:18
Alignment explanation
Indices: 2795065--2795115 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
2795055 TAAAAATATT
*
2795065 TAATAATATAAAACATAAA
1 TAATAATATAAAA-TTAAA
2795084 -AA-AATATTAAAATTAAA
1 TAATAATA-TAAAATTAAA
2795101 TAATAATATAGAAAT
1 TAATAATATA-AAAT
2795116 GAAAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
17 8 0.30
18 11 0.41
19 8 0.30
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
TAATAATATAAAATTAAA
Found at i:2798743 original size:28 final size:29
Alignment explanation
Indices: 2798692--2798746 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
2798682 TGGAATGAGC
*
2798692 CACTTAAAAAATTATTTATAGAAATAGGT
1 CACTTAAAAAATTATTTACAGAAATAGGT
*
2798721 CACTTAAAAAA-TATTTACCGAAATAG
1 CACTTAAAAAATTATTTACAGAAATAG
2798747 TCCAAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (29 bp):
CACTTAAAAAATTATTTACAGAAATAGGT
Found at i:2800487 original size:47 final size:47
Alignment explanation
Indices: 2800418--2800515 Score: 196
Period size: 47 Copynumber: 2.1 Consensus size: 47
2800408 ATTATTCGAG
2800418 TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT
1 TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT
2800465 TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT
1 TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT
2800512 TTAT
1 TTAT
2800516 GTTTTATATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (47 bp):
TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT
Found at i:2800944 original size:20 final size:21
Alignment explanation
Indices: 2800907--2800948 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
2800897 TAAAAAAAAA
*
2800907 TTATACTATTTTTTATAATTT
1 TTATACTATTTTTAATAATTT
2800928 TTATACT-TTTTTAATAATTT
1 TTATACTATTTTTAATAATTT
2800948 T
1 T
2800949 AATTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATACTATTTTTAATAATTT
Found at i:2802397 original size:17 final size:17
Alignment explanation
Indices: 2802375--2802413 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2802365 GGCCCCAAAT
2802375 TATAAGATGTAATACAA
1 TATAAGATGTAATACAA
2802392 TATAAGATGTAATACAA
1 TATAAGATGTAATACAA
2802409 TATAA
1 TATAA
2802414 CAAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (17 bp):
TATAAGATGTAATACAA
Found at i:2804270 original size:44 final size:44
Alignment explanation
Indices: 2804204--2804291 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
2804194 TAAAAAAAAT
* * *
2804204 CAATTCTCTTATTGTAAAACATTTATAAGAATTTATTCAAGGGA
1 CAATTCTATCATTGTAAAACATTTAAAAGAATTTATTCAAGGGA
* *
2804248 CAATTCTATCATTGTAAGACATTTAAAAGAATTTATTTAAGGGA
1 CAATTCTATCATTGTAAAACATTTAAAAGAATTTATTCAAGGGA
2804292 AAGGATGGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (44 bp):
CAATTCTATCATTGTAAAACATTTAAAAGAATTTATTCAAGGGA
Found at i:2805646 original size:64 final size:64
Alignment explanation
Indices: 2805556--2805684 Score: 240
Period size: 64 Copynumber: 2.0 Consensus size: 64
2805546 AACAAAATGG
2805556 TAGCTTCTTTAGGAACAGAAAGGAACAAGATTTTGATACCCAATGAAGAGAAACAAAGATGAAA
1 TAGCTTCTTTAGGAACAGAAAGGAACAAGATTTTGATACCCAATGAAGAGAAACAAAGATGAAA
* *
2805620 TAGCTTCTTTAGGAACAGAAATGAACAAGCTTTTGATACCCAATGAAGAGAAACAAAGATGAAA
1 TAGCTTCTTTAGGAACAGAAAGGAACAAGATTTTGATACCCAATGAAGAGAAACAAAGATGAAA
2805684 T
1 T
2805685 CTTTCTAAGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.22
Consensus pattern (64 bp):
TAGCTTCTTTAGGAACAGAAAGGAACAAGATTTTGATACCCAATGAAGAGAAACAAAGATGAAA
Found at i:2807469 original size:27 final size:27
Alignment explanation
Indices: 2807439--2807495 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
2807429 TTTATATTTT
2807439 ATATTT-AA-TAATATAAAACATAAAAAA
1 ATATTTAAATTAA-ATAAAA-ATAAAAAA
*
2807466 ATATTTAAATTAAATAAAAATAAAATA
1 ATATTTAAATTAAATAAAAATAAAAAA
2807493 ATA
1 ATA
2807496 ATGTAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 16 0.59
28 8 0.30
29 3 0.11
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (27 bp):
ATATTTAAATTAAATAAAAATAAAAAA
Found at i:2813143 original size:123 final size:122
Alignment explanation
Indices: 2812919--2813143 Score: 328
Period size: 123 Copynumber: 1.8 Consensus size: 122
2812909 GGACAACAGG
*
2812919 CATTCCTGAAGAATTAGGAAGCTTGAAATTATTGATTTTTCTAGAGCTGACTCAATGGTTGTATT
1 CATTCCTGAAGAATTAGGAAGCTTGAAATTATTAATTTTTCTAGAGCTGACTCAATGGTTGTATT
* ****
2812984 CCTACTTCATTTGCTAATTTGAGCAATTTGGTCCTCAGGACAACAGGCTTTTTGGTCC
66 CCAACTTCATTTGCTAATTTGAGC-ATCCCATCCTCAGGACAACAGGCTTTTTGGTCC
* *
2813042 CATTCCTGAAGATTTAAGG-AGCTTGAAATTATTAATTTTTCTAGAGTTGACTCAATGGTTGTAT
1 CATTCCTGAAGAATT-AGGAAGCTTGAAATTATTAATTTTTCTAGAGCTGACTCAATGGTTGTAT
2813106 TCCAACTTCATTTGCTAATTTGAGTC-TCCCATACCTCA
65 TCCAACTTCATTTGCTAATTTGAG-CATCCCAT-CCTCA
2813144 AGAAATCTCT
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
122 2 0.02
123 85 0.93
124 4 0.04
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.38
Consensus pattern (122 bp):
CATTCCTGAAGAATTAGGAAGCTTGAAATTATTAATTTTTCTAGAGCTGACTCAATGGTTGTATT
CCAACTTCATTTGCTAATTTGAGCATCCCATCCTCAGGACAACAGGCTTTTTGGTCC
Found at i:2819426 original size:21 final size:21
Alignment explanation
Indices: 2819387--2819427 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2819377 ATCTGCTCAA
* *
2819387 ACTCCACCTGTTTTAGAGTAC
1 ACTCCACCTGCTGTAGAGTAC
*
2819408 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTAGAGTA
2819428 TTGCTCATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTAGAGTAC
Found at i:2824691 original size:16 final size:16
Alignment explanation
Indices: 2824657--2824704 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2824647 CTGCCCAAGC
* *
2824657 TTTCTTTTATATGCAA
1 TTTCTTTTATCTTCAA
2824673 TTTACTTTTA-CTTCAA
1 TTT-CTTTTATCTTCAA
*
2824689 TTTTTTTTATCTTCAA
1 TTTCTTTTATCTTCAA
2824705 AATATTTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 5 0.19
16 16 0.59
17 6 0.22
ACGTcount: A:0.23, C:0.15, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTCTTTTATCTTCAA
Found at i:2827979 original size:13 final size:13
Alignment explanation
Indices: 2827961--2827986 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2827951 CCCCTTCGAC
2827961 TCGTATTTGGATT
1 TCGTATTTGGATT
2827974 TCGTATTTGGATT
1 TCGTATTTGGATT
2827987 CTAATCCTGA
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:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (13 bp):
TCGTATTTGGATT
Found at i:2832660 original size:72 final size:71
Alignment explanation
Indices: 2832551--2832818 Score: 374
Period size: 72 Copynumber: 3.7 Consensus size: 71
2832541 CATTCGACGC
* * *
2832551 ATCTTCTAACAACTTGAGTGGCCCAATTCCAAATTGGTTATGCAATATGAGTCAACTTCACACTT
1 ATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTT-TGCAATATGAGTCAACTTCACACTT
2832616 TCGATGT
65 TCGATGT
* * *
2832623 ATCTTATAACAATTTGAGTGGCTCAATTCCAAATTGGTTATGCAATATGAGTCATCTTCACACTT
1 ATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTT-TGCAATATGAGTCAACTTCACACTT
*
2832688 TCGAAGT
65 TCGATGT
* * * * * *
2832695 ATCTCATAACAATTTGAGTGGCTCAATTCCAAATTGCTTGGACAATATGAGCCAACTTTACATTT
1 ATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTTG-CAATATGAGTCAACTTCACACTT
*
2832760 TCTATGT
65 TCGATGT
2832767 ATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTTGGCAATATGAGT
1 ATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTT-GCAATATGAGT
2832819 GCTCTGAGTT
Statistics
Matches: 176, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
71 1 0.01
72 174 0.99
73 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (71 bp):
ATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTTGCAATATGAGTCAACTTCACACTTT
CGATGT
Found at i:2838711 original size:17 final size:17
Alignment explanation
Indices: 2838689--2838727 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
2838679 GGCCCCAAAT
*
2838689 TATAAGATGTAATTCAA
1 TATAAGATGTAATACAA
2838706 TATAAGATGTAATACAA
1 TATAAGATGTAATACAA
2838723 TATAA
1 TATAA
2838728 CAAAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.33
Consensus pattern (17 bp):
TATAAGATGTAATACAA
Found at i:2839769 original size:29 final size:30
Alignment explanation
Indices: 2839712--2839771 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2839702 CATATTTCAG
*
2839712 GAGCCACATAGGTTGGACACACAGCCATGT
1 GAGCCACATAGGCTGGACACACAGCCATGT
2839742 GAGCCACATAGGCTGG-CACACAGCCATGT
1 GAGCCACATAGGCTGGACACACAGCCATGT
2839771 G
1 G
2839772 CCAGATCGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.15
Consensus pattern (30 bp):
GAGCCACATAGGCTGGACACACAGCCATGT
Found at i:2841341 original size:11 final size:11
Alignment explanation
Indices: 2841327--2841378 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
2841317 AAAATTTAAA
2841327 ATTTTAAAAAT
1 ATTTTAAAAAT
2841338 ATTTT-AAAA-
1 ATTTTAAAAAT
2841347 A---TAAAAAT
1 ATTTTAAAAAT
*
2841355 ATTTTTAAAAT
1 ATTTTAAAAAT
2841366 ATTTTTAAAAAT
1 A-TTTTAAAAAT
2841378 A
1 A
2841379 AAAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
6 1 0.03
7 4 0.12
8 1 0.03
9 1 0.03
10 4 0.12
11 12 0.36
12 10 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:2841363 original size:12 final size:12
Alignment explanation
Indices: 2841348--2841378 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
2841338 ATTTTAAAAA
2841348 TAAAAATATTTT
1 TAAAAATATTTT
2841360 T-AAAATATTTT
1 TAAAAATATTTT
2841371 TAAAAATA
1 TAAAAATA
2841379 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAAATATTTT
Found at i:2841377 original size:29 final size:28
Alignment explanation
Indices: 2841327--2841382 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
2841317 AAAATTTAAA
2841327 ATTTTAAAAATATTTTAAAAATAAAAAT
1 ATTTTAAAAATATTTTAAAAATAAAAAT
*
2841355 ATTTTTAAAATATTTTTAAAAATAAAAA
1 ATTTTAAAAATA-TTTTAAAAATAAAAA
2841383 AATAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATTTTAAAAATATTTTAAAAATAAAAAT
Found at i:2841382 original size:18 final size:17
Alignment explanation
Indices: 2841331--2841366 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2841321 TTTAAAATTT
2841331 TAAAAATATTTTAAAAA
1 TAAAAATATTTTAAAAA
*
2841348 TAAAAATATTTTTAAAA
1 TAAAAATATTTTAAAAA
2841365 TA
1 TA
2841367 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAAATATTTTAAAAA
Found at i:2853024 original size:18 final size:19
Alignment explanation
Indices: 2853001--2853039 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
2852991 AGGTTTATAT
2853001 AATTAGATAAGTT-AAAAA
1 AATTAGATAAGTTCAAAAA
2853019 AATTAGATAAGTTCAAAAA
1 AATTAGATAAGTTCAAAAA
2853038 AA
1 AA
2853040 ACACACACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.26
Consensus pattern (19 bp):
AATTAGATAAGTTCAAAAA
Found at i:2855602 original size:13 final size:14
Alignment explanation
Indices: 2855586--2855619 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
2855576 AATAAATATA
2855586 TATTTTTT-ATTTT
1 TATTTTTTAATTTT
2855599 TATTTTTTAATTTT
1 TATTTTTTAATTTT
2855613 TAATTTT
1 T-ATTTT
2855620 AAAATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 6 0.32
15 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:2855674 original size:25 final size:25
Alignment explanation
Indices: 2855627--2855676 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2855617 TTTAAAATAC
* *
2855627 TTTAAAATTTTTTTATTTTTTTATT
1 TTTAAAATTTTTTTATGTGTTTATT
2855652 TTTAAAATATTTTTT-TGTGTTTATT
1 TTTAAAAT-TTTTTTATGTGTTTATT
2855677 AAAAATCGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (25 bp):
TTTAAAATTTTTTTATGTGTTTATT
Found at i:2856883 original size:18 final size:18
Alignment explanation
Indices: 2856853--2856910 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
2856843 ATAAATGATT
2856853 TTTTATAAA-TATTTTTAA
1 TTTTA-AAATTATTTTTAA
*
2856871 TTTTAAAATTATTTTTTAT
1 TTTTAAAATTA-TTTTTAA
*
2856890 TTTTGAAAATTATTTTAAA
1 TTTT-AAAATTATTTTTAA
2856909 TT
1 TT
2856911 ATTTTGTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 3 0.09
18 7 0.21
19 17 0.50
20 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTAAAATTATTTTTAA
Found at i:2856887 original size:20 final size:20
Alignment explanation
Indices: 2856864--2856905 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2856854 TTTATAAATA
2856864 TTTTTAATTTT-AAAATTAT
1 TTTTTAATTTTGAAAATTAT
*
2856883 TTTTTATTTTTGAAAATTAT
1 TTTTTAATTTTGAAAATTAT
2856903 TTT
1 TTT
2856906 AAATTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTAATTTTGAAAATTAT
Found at i:2862861 original size:50 final size:50
Alignment explanation
Indices: 2862738--2862986 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
2862728 GATAATAACA
* * ** * *
2862738 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* * *
2862789 TGCCCATGCCATGTCCCAGACATAGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
2862839 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
2862889 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
2862944 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
2862987 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:2862917 original size:100 final size:104
Alignment explanation
Indices: 2862737--2862986 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
2862727 TGATAATAAC
**
2862737 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
2862802 TCCCAGACATAGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATAGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
2862839 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
*
2862902 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATAGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
2862944 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
2862987 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATAGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:2863102 original size:13 final size:13
Alignment explanation
Indices: 2863081--2863112 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2863071 GCTTGGATCA
*
2863081 TCATCAAATAAAT
1 TCATAAAATAAAT
2863094 TCATAAAATAAAT
1 TCATAAAATAAAT
2863107 TCATAA
1 TCATAA
2863113 TTTCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:2864626 original size:19 final size:18
Alignment explanation
Indices: 2864582--2864631 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
2864572 ATAAATGAAT
2864582 TTTTATAAA-TATTTTTAA
1 TTTTA-AAACTATTTTTAA
* *
2864600 TTTTAAAATTATTTTTAT
1 TTTTAAAACTATTTTTAA
2864618 TTTTGAAAACTATT
1 TTTT-AAAACTATT
2864632 ATGAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.11
18 17 0.61
19 8 0.29
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTAAAACTATTTTTAA
Found at i:2865458 original size:26 final size:26
Alignment explanation
Indices: 2865412--2865461 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2865402 TTAATTATAA
*
2865412 TAATTAAAAATATATTATATAAAAAC
1 TAATTAAAAATATAATATATAAAAAC
*
2865438 TAATTAAAAAT-TAAATGTATAAAA
1 TAATTAAAAATAT-AATATATAAAA
2865462 TCACATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
TAATTAAAAATATAATATATAAAAAC
Found at i:2872178 original size:29 final size:29
Alignment explanation
Indices: 2872144--2872201 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2872134 TTAAAATTTT
* * *
2872144 TTTAATAGTATAAGGATTAAATTGATCTA
1 TTTAATAATAAAAGGACTAAATTGATCTA
*
2872173 TTTAATAATAAAAGGACTAATTTGATCTA
1 TTTAATAATAAAAGGACTAAATTGATCTA
2872202 ATTCGTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (29 bp):
TTTAATAATAAAAGGACTAAATTGATCTA
Found at i:2880378 original size:15 final size:16
Alignment explanation
Indices: 2880360--2880401 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
2880350 TCGCCCACAT
2880360 AGTTCGCATCAT-ATG
1 AGTTCGCATCATGATG
*
2880375 AGTTCGCA-CGTGATG
1 AGTTCGCATCATGATG
*
2880390 GGTTCGCATCAT
1 AGTTCGCATCAT
2880402 CATGCAACCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (16 bp):
AGTTCGCATCATGATG
Found at i:2881841 original size:27 final size:27
Alignment explanation
Indices: 2881807--2881871 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
2881797 AATTTATAAA
2881807 ATGAATGTTTA-GATTTTAATAATTTTT
1 ATGAATGTTTATGATTTT-ATAATTTTT
** * *
2881834 ATTTATGTTTATTATTTTTTAATTTTT
1 ATGAATGTTTATGATTTTATAATTTTT
2881861 ATGAATGTTTA
1 ATGAATGTTTA
2881872 AAATTTTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (27 bp):
ATGAATGTTTATGATTTTATAATTTTT
Found at i:2881877 original size:27 final size:27
Alignment explanation
Indices: 2881807--2881879 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
2881797 AATTTATAAA
* *
2881807 ATGAATGTTT-AGATTTTAATAATTTTT
1 ATGAATGTTTAAAATTTT-TTAATTTTT
** **
2881834 ATTTATGTTTATTATTTTTTAATTTTT
1 ATGAATGTTTAAAATTTTTTAATTTTT
2881861 ATGAATGTTTAAAATTTTT
1 ATGAATGTTTAAAATTTTT
2881880 AATGAGTTCT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
27 31 0.86
28 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (27 bp):
ATGAATGTTTAAAATTTTTTAATTTTT
Found at i:2882070 original size:28 final size:30
Alignment explanation
Indices: 2882015--2882080 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
2882005 TTCATATTTT
2882015 AAATAATTTTAATGATTTTAAATTTTT-AA
1 AAATAATTTTAATGATTTTAAATTTTTAAA
* * *
2882044 AAATAATTTTTAT-TTTTTTAATTTTTAAA
1 AAATAATTTTAATGATTTTAAATTTTTAAA
2882073 AAATAATT
1 AAATAATT
2882081 AAATACTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 11 0.33
29 22 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
AAATAATTTTAATGATTTTAAATTTTTAAA
Found at i:2884393 original size:29 final size:30
Alignment explanation
Indices: 2884343--2884416 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 30
2884333 TAAACCTCTT
**
2884343 CACTTTCCTCCCAAAACTTTTACT-CCCTCC
1 CACTTTCC-CCCTTAACTTTTACTCCCCTCC
2884373 CACTTTCCCCCTTAACTTTTACTCCCCTCC
1 CACTTTCCCCCTTAACTTTTACTCCCCTCC
*
2884403 CATCTTACCCCCTT
1 CA-CTTTCCCCCTT
2884417 CTACCCCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 13 0.33
30 16 0.41
31 10 0.26
ACGTcount: A:0.16, C:0.49, G:0.00, T:0.35
Consensus pattern (30 bp):
CACTTTCCCCCTTAACTTTTACTCCCCTCC
Found at i:2915929 original size:12 final size:12
Alignment explanation
Indices: 2915912--2915960 Score: 98
Period size: 12 Copynumber: 4.1 Consensus size: 12
2915902 CGAACTAGAG
2915912 TACCCTTATGTT
1 TACCCTTATGTT
2915924 TACCCTTATGTT
1 TACCCTTATGTT
2915936 TACCCTTATGTT
1 TACCCTTATGTT
2915948 TACCCTTATGTT
1 TACCCTTATGTT
2915960 T
1 T
2915961 TACTTGAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.51
Consensus pattern (12 bp):
TACCCTTATGTT
Found at i:2919419 original size:16 final size:17
Alignment explanation
Indices: 2919388--2919420 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2919378 TTTTTGTGCA
*
2919388 TTTAGTGTACTATATTT
1 TTTAATGTACTATATTT
2919405 TTTAATGTA-TATATTT
1 TTTAATGTACTATATTT
2919421 AAATAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.27, C:0.03, G:0.09, T:0.61
Consensus pattern (17 bp):
TTTAATGTACTATATTT
Found at i:2922186 original size:6 final size:7
Alignment explanation
Indices: 2922167--2922198 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2922157 AATACTTTAG
2922167 AGAAAAA
1 AGAAAAA
2922174 AGAAAAA
1 AGAAAAA
2922181 AGAAAAA
1 AGAAAAA
2922188 AG-AAAA
1 AGAAAAA
2922194 AGAAA
1 AGAAA
2922199 GACAGCCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:2922186 original size:14 final size:13
Alignment explanation
Indices: 2922167--2922198 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
2922157 AATACTTTAG
2922167 AGAAAAAAGAAAAA
1 AGAAAAAAG-AAAA
2922181 AGAAAAAAGAAAA
1 AGAAAAAAGAAAA
2922194 AGAAA
1 AGAAA
2922199 GACAGCCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AGAAAAAAGAAAA
Found at i:2922260 original size:7 final size:7
Alignment explanation
Indices: 2922248--2922278 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2922238 TAAGGAACCC
*
2922248 AACATCG
1 AACATCA
2922255 AACATCA
1 AACATCA
2922262 AACATCA
1 AACATCA
2922269 AACATCA
1 AACATCA
2922276 AAC
1 AAC
2922279 TTTTTTGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.55, C:0.29, G:0.03, T:0.13
Consensus pattern (7 bp):
AACATCA
Found at i:2922838 original size:21 final size:20
Alignment explanation
Indices: 2922812--2922871 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 20
2922802 AGTAATCTAT
2922812 TAAATGAGTCTTGAATAAATA
1 TAAATGAGT-TTGAATAAATA
*
2922833 TAAATGAGTTTGTTTATAAATA
1 TAAATGAGTTTG--AATAAATA
2922855 TAAATG-GTTTGAATAAA
1 TAAATGAGTTTGAATAAA
2922872 ATTTGTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 5 0.14
20 3 0.09
21 14 0.40
22 13 0.37
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (20 bp):
TAAATGAGTTTGAATAAATA
Found at i:2928546 original size:20 final size:20
Alignment explanation
Indices: 2928521--2928561 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2928511 AATTTCGTTG
2928521 GGTTAAATTCGATTAATTGT
1 GGTTAAATTCGATTAATTGT
2928541 GGTTAAATTCGATTAATTGT
1 GGTTAAATTCGATTAATTGT
2928561 G
1 G
2928562 TTATACTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.44
Consensus pattern (20 bp):
GGTTAAATTCGATTAATTGT
Found at i:2936341 original size:5 final size:5
Alignment explanation
Indices: 2936326--2936366 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
2936316 CTTTCCCCTA
2936326 ATTTCT ATTTT ATTTT A-TTT ATTTT ATTTT ATTTT CATTTT
1 ATTT-T ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT -ATTTT
2936367 CCCCTTCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 20 0.61
6 9 0.27
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:2936350 original size:14 final size:14
Alignment explanation
Indices: 2936331--2936359 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2936321 CCCTAATTTC
2936331 TATTTTATTTTATT
1 TATTTTATTTTATT
2936345 TATTTTATTTTATT
1 TATTTTATTTTATT
2936359 T
1 T
2936360 TCATTTTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTATTTTATT
Found at i:2939408 original size:4 final size:4
Alignment explanation
Indices: 2939399--2939435 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
2939389 CTAATAATTT
*
2939399 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAG TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
2939436 AGACAACGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:2946531 original size:5 final size:6
Alignment explanation
Indices: 2946513--2946548 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
2946503 ACAGATAATA
2946513 TTATTT TTATTT TTATTT TTATGTT TTATGTT TTAT
1 TTATTT TTATTT TTATTT TTAT-TT TTAT-TT TTAT
2946549 CCTAACTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 16 0.55
7 13 0.45
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:2947395 original size:17 final size:17
Alignment explanation
Indices: 2947363--2947411 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
2947353 CTTAATACAT
2947363 ATTTTATATTT-A-TTAA
1 ATTTTA-ATTTAATTTAA
*
2947379 TATTTT-ATTTAGTTTAA
1 -ATTTTAATTTAATTTAA
2947396 ATTTTAATTTAATTTA
1 ATTTTAATTTAATTTA
2947412 GTTGATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 18 0.67
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTTTAATTTAATTTAA
Found at i:2947421 original size:22 final size:22
Alignment explanation
Indices: 2947380--2947421 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2947370 ATTTATTAAT
* *
2947380 ATTTTATTTAGTTTAAATTTTA
1 ATTTAATTTAGTTGAAATTTTA
*
2947402 ATTTAATTTAGTTGATATTT
1 ATTTAATTTAGTTGAAATTT
2947422 ATAAATAGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (22 bp):
ATTTAATTTAGTTGAAATTTTA
Found at i:2963757 original size:45 final size:45
Alignment explanation
Indices: 2963707--2963804 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
2963697 GCTTCCTCTG
* * *
2963707 TGATGCTTGCCATCAAAAGATCTTGACCTTGACCTCTTTCTATCC
1 TGATGCTTGCCATCAAAAGATCTTGACCTCGACCGCCTTCTATCC
**
2963752 TGATGCTTGCCATCAGCAGATCTTGACCTCGACCGCCTTCTATCC
1 TGATGCTTGCCATCAAAAGATCTTGACCTCGACCGCCTTCTATCC
*
2963797 CGATGCTT
1 TGATGCTT
2963805 AGATTTCTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.33
Consensus pattern (45 bp):
TGATGCTTGCCATCAAAAGATCTTGACCTCGACCGCCTTCTATCC
Found at i:2964647 original size:42 final size:42
Alignment explanation
Indices: 2964523--2964681 Score: 169
Period size: 42 Copynumber: 3.8 Consensus size: 42
2964513 AGACCTCCTC
* *
2964523 CTTCGCCTATAACTGATTGGTGATCTTGACTTTGACCTTGA-
1 CTTCGCCGATAACTAATTGGTGATCTTGACTTTGACCTTGAT
* * * * *
2964564 CTTTCGCCTATAAATGATCGGTGATCTTGACTTGGACCTTGAT
1 C-TTCGCCGATAACTAATTGGTGATCTTGACTTTGACCTTGAT
* * *
2964607 CTTCGCCGATAACTAATTGGTGATCTAGTCTTTGATCTTGAT
1 CTTCGCCGATAACTAATTGGTGATCTTGACTTTGACCTTGAT
* ** *
2964649 CTTCTCCGATAACTAAGGGGTGATTTTGA-TTTG
1 CTTCGCCGATAACTAATTGGTGATCTTGACTTTG
2964682 GATCTTGACC
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
41 5 0.05
42 93 0.94
43 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (42 bp):
CTTCGCCGATAACTAATTGGTGATCTTGACTTTGACCTTGAT
Found at i:2964671 original size:84 final size:84
Alignment explanation
Indices: 2964523--2964689 Score: 192
Period size: 84 Copynumber: 2.0 Consensus size: 84
2964513 AGACCTCCTC
* * * * * *
2964523 CTTCGCCTATAACTGATTGGTGATCTTGACTTTGACCTTGACTTTCGCCTATAAATGATCGGTGA
1 CTTCGCCGATAACTAATTGGTGATCTAGACTTTGACCTTGACTTTCGCCGATAAATAAGCGGTGA
2964588 TCTTGACTTGGACCTTGAT
66 TCTTGACTTGGACCTTGAT
* * * * *
2964607 CTTCGCCGATAACTAATTGGTGATCTAGTCTTTGATCTTGA-TCTTCTCCGATAACTAAGGGGTG
1 CTTCGCCGATAACTAATTGGTGATCTAGACTTTGACCTTGACT-TTCGCCGATAAATAAGCGGTG
* * *
2964671 ATTTTGATTTGGATCTTGA
65 ATCTTGACTTGGACCTTGA
2964690 CCTTGCACGA
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
83 1 0.01
84 67 0.99
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (84 bp):
CTTCGCCGATAACTAATTGGTGATCTAGACTTTGACCTTGACTTTCGCCGATAAATAAGCGGTGA
TCTTGACTTGGACCTTGAT
Found at i:2976064 original size:10 final size:10
Alignment explanation
Indices: 2976049--2976073 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2976039 CAAGAAAGAT
2976049 AAAAAAGAAA
1 AAAAAAGAAA
2976059 AAAAAAGAAA
1 AAAAAAGAAA
2976069 AAAAA
1 AAAAA
2976074 GAGAGAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:2983815 original size:98 final size:98
Alignment explanation
Indices: 2983646--2984304 Score: 1030
Period size: 98 Copynumber: 6.7 Consensus size: 98
2983636 AAACCATAGT
* * *
2983646 TTGCAATCTAAAATATCGAAGCCACATCGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
2983711 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * *
2983744 TTGCAATTTAAAGGATCGAAGCCACAACGGCAAATCTTACTTCTGGCAATGCAGCGGAGCAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
2983809 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* *
2983842 TTGCAATTTAAAAGATCTAAGCCACAAAGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
* * *
2983907 GAAGCTACAACAGCGAATTTCATTTCCCCAACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * * *
2983940 TTGCAAATTGAAGGATCGAAGCCACAACGGCGAATCTTACTCCTGGCGATGCAGCGGAGCAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
* * *
2984005 GAAGCTACAACAACGAATCTCATTTCCCCGATA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * *
2984038 TTGCAATTTAAAAGATCGAAGCCACAACGGTGAATCTTACTTCTGGCGATGCAGTGGAACAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
* *
2984103 GAAGCTACAACGGCGAATCTCATTTCCCCGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * * *
2984136 TTGCAATTTAAAAGATCGAAGCCACAATGGTGAATCTTACTTCTGGCGATGCAGTGGAACAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
*
2984201 GAAGCTACAACGGCGAATCTCACTTCCCCGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * *
2984234 ATGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAGCGGAACAGAT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTT-CTGGCGATGCAGCGGAGCAGAT
2984299 TGAAGC
65 TGAAGC
2984305 CGCAACGGCA
Statistics
Matches: 519, Mismatches: 41, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
98 493 0.95
99 26 0.05
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (98 bp):
TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
GAAGCTACAACAGCGAATCTCACTTCCCCGACA
Found at i:2990053 original size:72 final size:72
Alignment explanation
Indices: 2989953--2990153 Score: 271
Period size: 72 Copynumber: 2.8 Consensus size: 72
2989943 TTAGAATATC
* * * * *
2989953 TCGACGCATCTTCTAACAAGTTGAGTGGCCCAATTCCAAATTGGTTATGCAATATGAGTCAACTT
1 TCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTT
2990018 AGCCA-TT
66 -GCCAGTT
* *
2990025 TTGATGCATCTTATAACAATTTGAGTGGCTCAATTCCAAATTGCTT-GGACAATATGAGTCAACT
1 TCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGG-CAATATGAGTCAACT
*
2990089 TGGCAGTT
65 TGCCAGTT
* * *
2990097 TCGATGTATCTTATAACAATTTGAGTGGCCAAATTCCAAATTGCTTAGGCAAAATGA
1 TCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGA
2990154 ATGCTCTCTT
Statistics
Matches: 113, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
71 4 0.04
72 107 0.95
73 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (72 bp):
TCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTT
GCCAGTT
Found at i:2993649 original size:18 final size:20
Alignment explanation
Indices: 2993622--2993660 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
2993612 AATTTAAATT
*
2993622 TTTTATAAA-TATTTT-AAA
1 TTTTAAAAATTATTTTGAAA
2993640 TTTTAAAAATTATTTTGAAA
1 TTTTAAAAATTATTTTGAAA
2993660 T
1 T
2993661 ATTTTGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 6 0.33
20 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTTAAAAATTATTTTGAAA
Found at i:2995089 original size:29 final size:30
Alignment explanation
Indices: 2994986--2995155 Score: 121
Period size: 30 Copynumber: 5.7 Consensus size: 30
2994976 TTTTTTTTTG
* * * * * *
2994986 CATTTTAACTCCTGAACTTTTTTAAAATTT
1 CATTTTAACCCCTAAAATTTCTTGAAATTA
** * ** *
2995016 CATTTTAACCTTTAAACTTTCTCAAAAGTA
1 CATTTTAACCCCTAAAATTTCTTGAAATTA
*
2995046 CATTTCAACCCCTAAAATATT-TT-AAATTA
1 CATTTTAACCCCTAAAAT-TTCTTGAAATTA
* *
2995075 TATTTTGACCCCTAAAATTTCTTGAAATTA
1 CATTTTAACCCCTAAAATTTCTTGAAATTA
* * *
2995105 CATTTTAACCCTTACAATTTCTTAAAATTA
1 CATTTTAACCCCTAAAATTTCTTGAAATTA
* *
2995135 CACTTTT-GCCCCAAAAATTTC
1 CA-TTTTAACCCCTAAAATTTC
2995156 GCTGCGTTTA
Statistics
Matches: 110, Mismatches: 26, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
28 2 0.02
29 22 0.20
30 80 0.73
31 6 0.05
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.42
Consensus pattern (30 bp):
CATTTTAACCCCTAAAATTTCTTGAAATTA
Found at i:2995096 original size:59 final size:60
Alignment explanation
Indices: 2995028--2995155 Score: 136
Period size: 59 Copynumber: 2.1 Consensus size: 60
2995018 TTTTAACCTT
* *
2995028 TAAACTTTCTCAAAAGTACATTTCAACCCCTAAAATATT-TT-AAATTATA-TTTTGACCCC
1 TAAAATTTCTCAAAAGTACATTTCAACCCCTAAAAT-TTCTTAAAATTACACTTTTG-CCCC
** * * * *
2995087 TAAAATTTCTTGAAATTACATTTTAACCCTTACAATTTCTTAAAATTACACTTTTGCCCC
1 TAAAATTTCTCAAAAGTACATTTCAACCCCTAAAATTTCTTAAAATTACACTTTTGCCCC
*
2995147 AAAAATTTC
1 TAAAATTTC
2995156 GCTGCGTTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
58 2 0.04
59 31 0.54
60 19 0.33
61 5 0.09
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (60 bp):
TAAAATTTCTCAAAAGTACATTTCAACCCCTAAAATTTCTTAAAATTACACTTTTGCCCC
Found at i:2995473 original size:3 final size:3
Alignment explanation
Indices: 2995465--2995521 Score: 55
Period size: 3 Copynumber: 18.3 Consensus size: 3
2995455 GACCAAACGG
2995465 AGA AGA AGA AGA AGA AGAA AGA A-A AGAA AGAA AGAA AGA AGA A-A AGA
1 AGA AGA AGA AGA AGA AG-A AGA AGA AG-A AG-A AG-A AGA AGA AGA AGA
*
2995512 GGA AGA AGA A
1 AGA AGA AGA A
2995522 AGAAAAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 4 0.08
3 30 0.62
4 14 0.29
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2995488 original size:4 final size:4
Alignment explanation
Indices: 2995479--2995536 Score: 54
Period size: 4 Copynumber: 15.5 Consensus size: 4
2995469 GAAGAAGAAG
* *
2995479 AAGA AAGAA AAGA AAGA AAGA AAG- AAGA AA-A GAGG AAG- AAGA AAGA
1 AAGA AAG-A AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
2995525 AA-A AA-A AAGA AA
1 AAGA AAGA AAGA AA
2995537 AAATAAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
3 14 0.30
4 28 0.61
5 4 0.09
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:2995636 original size:12 final size:12
Alignment explanation
Indices: 2995615--2995692 Score: 61
Period size: 13 Copynumber: 6.0 Consensus size: 12
2995605 CGAACCCGAC
2995615 CCAAAAAAAAAA
1 CCAAAAAAAAAA
2995627 CCAAATAAAAAAGA
1 CCAAA-AAAAAA-A
2995641 CCCAAAACCAAAAAA
1 -CCAAAA--AAAAAA
2995656 TCCAAAAAAAAAA
1 -CCAAAAAAAAAA
*
2995669 --AAAAAAAAACC
1 CCAAAAAAAAA-A
2995680 CCAAAGAAAAAAA
1 CCAAA-AAAAAAA
2995693 AGAAGCCCAC
Statistics
Matches: 54, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
10 9 0.17
12 5 0.09
13 15 0.28
14 8 0.15
15 12 0.22
16 5 0.09
ACGTcount: A:0.76, C:0.19, G:0.03, T:0.03
Consensus pattern (12 bp):
CCAAAAAAAAAA
Found at i:2995638 original size:15 final size:14
Alignment explanation
Indices: 2995617--2995670 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
2995607 AACCCGACCC
2995617 AAAAAAAAAACCAA
1 AAAAAAAAAACCAA
* *
2995631 ATAAAAAAGACCCAA
1 A-AAAAAAAAACCAA
* *
2995646 AACCAAAAAATCCAA
1 AA-AAAAAAAACCAA
2995661 AAAAAAAAAA
1 AAAAAAAAAA
2995671 AAAAAAACCC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.78, C:0.17, G:0.02, T:0.04
Consensus pattern (14 bp):
AAAAAAAAAACCAA
Found at i:2995642 original size:27 final size:29
Alignment explanation
Indices: 2995612--2995668 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
2995602 ACCCGAACCC
*
2995612 GACCCAAAA-AAAAAA-CCAAATAAAAAA
1 GACCCAAAACAAAAAATCCAAAAAAAAAA
2995639 GACCCAAAACCAAAAAATCCAAAAAAAAAA
1 GACCCAAAA-CAAAAAATCCAAAAAAAAAA
2995669 AAAAAAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 9 0.35
29 6 0.23
30 11 0.42
ACGTcount: A:0.72, C:0.21, G:0.04, T:0.04
Consensus pattern (29 bp):
GACCCAAAACAAAAAATCCAAAAAAAAAA
Found at i:2995675 original size:22 final size:22
Alignment explanation
Indices: 2995650--2995693 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2995640 ACCCAAAACC
*
2995650 AAAAAATCCAAAAAAAAAAAAA
1 AAAAAACCCAAAAAAAAAAAAA
* *
2995672 AAAAAACCCCAAAGAAAAAAAA
1 AAAAAACCCAAAAAAAAAAAAA
2995694 GAAGCCCACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.82, C:0.14, G:0.02, T:0.02
Consensus pattern (22 bp):
AAAAAACCCAAAAAAAAAAAAA
Found at i:2995676 original size:23 final size:23
Alignment explanation
Indices: 2995650--2995693 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2995640 ACCCAAAACC
*
2995650 AAAAAATCCAAAAAAAAAAAAAA
1 AAAAAACCCAAAAAAAAAAAAAA
* *
2995673 AAAAACCCCAAAGAAAAAAAA
1 AAAAAACCCAAAAAAAAAAAA
2995694 GAAGCCCACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.82, C:0.14, G:0.02, T:0.02
Consensus pattern (23 bp):
AAAAAACCCAAAAAAAAAAAAAA
Found at i:2995852 original size:25 final size:25
Alignment explanation
Indices: 2995807--2995859 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
2995797 GAAGCAGGCC
*
2995807 AAAGGAAAAAGAAGGAAAAAAA-GA
1 AAAGGAAAAAAAAGGAAAAAAAGGA
**
2995831 AAAGAGAAAAAAAAGGGGAAAAAGGA
1 AAAG-GAAAAAAAAGGAAAAAAAGGA
2995857 AAA
1 AAA
2995860 AAGGAAGGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.17
25 15 0.62
26 5 0.21
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (25 bp):
AAAGGAAAAAAAAGGAAAAAAAGGA
Found at i:2995915 original size:22 final size:22
Alignment explanation
Indices: 2995887--2995930 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2995877 TGTAGCTCTC
2995887 TCGGTCAAGCTCGTATTTTTGA
1 TCGGTCAAGCTCGTATTTTTGA
*
2995909 TCGGTCAATCTCGTATTTTTGA
1 TCGGTCAAGCTCGTATTTTTGA
2995931 GCTTTTTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.43
Consensus pattern (22 bp):
TCGGTCAAGCTCGTATTTTTGA
Found at i:2996207 original size:17 final size:17
Alignment explanation
Indices: 2996187--2996249 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
2996177 ATTGTAAATA
2996187 TTCAAAAAATTCGTGTT
1 TTCAAAAAATTCGTGTT
*
2996204 TTCAAAACATTTC-TCGTGT
1 TTCAAAA-AATTCGT-GT-T
**
2996223 TTCAAAATTTTCGTGTT
1 TTCAAAAAATTCGTGTT
2996240 TT-AAAAAATT
1 TTCAAAAAATT
2996250 TTTCTCGTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
16 6 0.16
17 11 0.29
18 12 0.32
19 9 0.24
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (17 bp):
TTCAAAAAATTCGTGTT
Found at i:2996236 original size:36 final size:37
Alignment explanation
Indices: 2996187--2996285 Score: 112
Period size: 36 Copynumber: 2.7 Consensus size: 37
2996177 ATTGTAAATA
* *
2996187 TTCAAAAAATTCGTGTTTTCAAAACA-TTTCTCGTGT
1 TTCAAAATATTCGTGTTTTCAAAAAATTTTCTCGTGT
*
2996223 TTCAAAATTTTCGTGTTTT-AAAAAATTTTTCTCGTGT
1 TTCAAAATATTCGTGTTTTCAAAAAA-TTTTCTCGTGT
** *
2996260 TAAAAAAATATTCATGTTTTCAAAAA
1 T-TCAAAATATTCGTGTTTTCAAAAA
2996286 TAAGGCAACG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
35 5 0.10
36 17 0.33
37 11 0.21
38 14 0.27
39 5 0.10
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.43
Consensus pattern (37 bp):
TTCAAAATATTCGTGTTTTCAAAAAATTTTCTCGTGT
Found at i:2996247 original size:18 final size:18
Alignment explanation
Indices: 2996196--2996251 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
2996186 ATTCAAAAAA
*
2996196 TTCGTGTTTTCAAAACATT
1 TTCGTGTTTT-AAAAAATT
*
2996215 TCTCGTG-TTT-CAAAATT
1 T-TCGTGTTTTAAAAAATT
2996232 TTCGTGTTTTAAAAAATT
1 TTCGTGTTTTAAAAAATT
2996250 TT
1 TT
2996252 TCTCGTGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 5 0.16
17 9 0.29
18 8 0.26
19 4 0.13
20 5 0.16
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.50
Consensus pattern (18 bp):
TTCGTGTTTTAAAAAATT
Found at i:2996525 original size:18 final size:18
Alignment explanation
Indices: 2996502--2996882 Score: 225
Period size: 17 Copynumber: 21.2 Consensus size: 18
2996492 AAAATTCTAT
*
2996502 TTTTCAAAATTTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
2996520 TTTTCAAAAAAAATTCTCGTG
1 TTTTC---AAAAATTTTCGTG
2996541 -TTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
2996558 TTTTCAAAAATTCTCGTG
1 TTTTCAAAAATTTTCGTG
*
2996576 TTTTCAAAAATTTTGGTG
1 TTTTCAAAAATTTTCGTG
* * *
2996594 -TTTCAAAAATCTTAGTA
1 TTTTCAAAAATTTTCGTG
2996611 TTTTCAAAAA-TTTCG-G
1 TTTTCAAAAATTTTCGTG
*
2996627 TGTTTC-AAAATCTTCGTG
1 T-TTTCAAAAATTTTCGTG
2996645 TTTTCTAAAAA-TTTC-TG
1 TTTTC-AAAAATTTTCGTG
*
2996662 TGTTTCAAAAATTTTCGTT
1 T-TTTCAAAAATTTTCGTG
* *
2996681 TTTTCACAAATTTCCGTG
1 TTTTCAAAAATTTTCGTG
** * * *
2996699 TTTTCAATGACTCTAGTG
1 TTTTCAAAAATTTTCGTG
* * *
2996717 -TTTCACAAATTGTCATGTTT
1 TTTTCAAAAATTTTC--G-TG
* ***
2996737 TTTTTAAAAAAAAT-GTG
1 TTTTCAAAAATTTTCGTG
* *
2996754 TTTTGAAAAATTATCAGTG
1 TTTTCAAAAATTTTC-GTG
*
2996773 -TTTCAAAAA-TTGCTGTG
1 TTTTCAAAAATTTTC-GTG
*
2996790 TTTT-AAAAATTTTCGTATT
1 TTTTCAAAAATTTTCG--TG
*** *
2996809 TTTTTTTAAATTTTCATG
1 TTTTCAAAAATTTTCGTG
*
2996827 -TTTCAAAAATTTTTGTG
1 TTTTCAAAAATTTTCGTG
* *
2996844 TTTTTAAAAAATTCTCGTG
1 -TTTTCAAAAATTTTCGTG
2996863 -TTTCAAAAATTTTCGT-
1 TTTTCAAAAATTTTCGTG
2996879 TTTT
1 TTTT
2996883 TTTAAAAAAT
Statistics
Matches: 275, Mismatches: 61, Indels: 55
0.70 0.16 0.14
Matches are distributed among these distances:
16 5 0.02
17 109 0.40
18 100 0.36
19 29 0.11
20 13 0.05
21 19 0.07
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (18 bp):
TTTTCAAAAATTTTCGTG
Found at i:2996532 original size:38 final size:38
Alignment explanation
Indices: 2996490--2996602 Score: 137
Period size: 38 Copynumber: 3.1 Consensus size: 38
2996480 CACGTCGTCG
* *
2996490 AAAAAATTCT-ATTTTTCAAAATTTTTCGTGTTTTCAA
1 AAAAAATTCTCATGTTTCAAAAATTTTCGTGTTTTCAA
*
2996527 AAAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC--
1 AAAAAATTCTCATGTTTCAAAAATTTTCGTGTTTTCAA
* *
2996563 -AAAAATTCTCGTGTTTTCAAAAATTTTGGTG-TTTCAA
1 AAAAAATTCTCATG-TTTCAAAAATTTTCGTGTTTTCAA
2996600 AAA
1 AAA
2996603 TCTTAGTATT
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
35 17 0.25
36 16 0.24
37 10 0.15
38 24 0.36
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (38 bp):
AAAAAATTCTCATGTTTCAAAAATTTTCGTGTTTTCAA
Found at i:2996550 original size:17 final size:17
Alignment explanation
Indices: 2996528--2996701 Score: 135
Period size: 18 Copynumber: 9.9 Consensus size: 17
2996518 TGTTTTCAAA
2996528 AAAAATTCTCGTGTTTC
1 AAAAATTCTCGTGTTTC
*
2996545 AAAAATTTTCGTGTTTTC
1 AAAAATTCTCGTG-TTTC
2996563 AAAAATTCTCGTGTTTTC
1 AAAAATTCTCGTG-TTTC
* *
2996581 AAAAATTTTGGTGTTTC
1 AAAAATTCTCGTGTTTC
* *
2996598 AAAAA-TCTTAGTATTTTC
1 AAAAATTC-TCGT-GTTTC
2996616 AAAAATT-TCGGTGTTTC
1 AAAAATTCTC-GTGTTTC
2996633 -AAAA-TCTTCGTGTTTTC
1 AAAAATTC-TCGTG-TTTC
2996650 TAAAAATT-TCTGTGTTTC
1 -AAAAATTCTC-GTGTTTC
* *
2996668 AAAAATTTTCGTTTTTTC
1 AAAAATTCTCG-TGTTTC
*
2996686 ACAAATT-TCCGTGTTT
1 AAAAATTCT-CGTGTTT
2996702 TCAATGACTC
Statistics
Matches: 130, Mismatches: 12, Indels: 30
0.76 0.07 0.17
Matches are distributed among these distances:
15 1 0.01
16 8 0.06
17 48 0.37
18 64 0.49
19 8 0.06
20 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (17 bp):
AAAAATTCTCGTGTTTC
Found at i:2996694 original size:35 final size:35
Alignment explanation
Indices: 2996528--2996701 Score: 194
Period size: 35 Copynumber: 5.0 Consensus size: 35
2996518 TGTTTTCAAA
*
2996528 AAAAATTCTCGTG-TTTCAAAAATTT-TCGTGTTTTC
1 AAAAATTTTCGTGTTTTCAAAAATTTCT-GTG-TTTC
*
2996563 AAAAATTCTCGTGTTTTCAAAAATTT-TGGTGTTTC
1 AAAAATTTTCGTGTTTTCAAAAATTTCT-GTGTTTC
* * * *
2996598 AAAAATCTTAGTATTTTCAAAAATTTCGGTGTTTC
1 AAAAATTTTCGTGTTTTCAAAAATTTCTGTGTTTC
*
2996633 -AAAATCTTCGTGTTTTCTAAAAATTTCTGTGTTTC
1 AAAAATTTTCGTGTTTTC-AAAAATTTCTGTGTTTC
* * *
2996668 AAAAATTTTCGTTTTTTCACAAATTTCCGTGTTT
1 AAAAATTTTCGTGTTTTCAAAAATTTCTGTGTTT
2996702 TCAATGACTC
Statistics
Matches: 122, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
34 15 0.12
35 76 0.62
36 31 0.25
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (35 bp):
AAAAATTTTCGTGTTTTCAAAAATTTCTGTGTTTC
Found at i:2996855 original size:19 final size:19
Alignment explanation
Indices: 2996831--2996893 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 19
2996821 TTCATGTTTC
*
2996831 AAAAATTTTTGTGTTTTTA
1 AAAAATTTTCGTGTTTTTA
* *
2996850 AAAAATTCTCGTG--TTTC
1 AAAAATTTTCGTGTTTTTA
*
2996867 AAAAATTTTCGTTTTTTTTA
1 AAAAATTTTCG-TGTTTTTA
2996887 AAAAATT
1 AAAAATT
2996894 CGTGCTTCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
17 13 0.37
18 1 0.03
19 11 0.31
20 10 0.29
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (19 bp):
AAAAATTTTCGTGTTTTTA
Found at i:2996894 original size:37 final size:37
Alignment explanation
Indices: 2996777--2996915 Score: 137
Period size: 37 Copynumber: 3.9 Consensus size: 37
2996767 TCAGTGTTTC
*
2996777 AAAAATTGCT-GTGTTTTAAAAATTTTCGTATTTTTTT-
1 AAAAATT-CTCGTGTTTCAAAAATTTTCGT-TTTTTTTA
** * * * *
2996814 TTAAATTTTCATGTTTCAAAAATTTTTG-TGTTTTTA
1 AAAAATTCTCGTGTTTCAAAAATTTTCGTTTTTTTTA
2996850 AAAAATTCTCGTGTTTCAAAAATTTTCGTTTTTTTTA
1 AAAAATTCTCGTGTTTCAAAAATTTTCGTTTTTTTTA
* *
2996887 AAAAA-T-TCGTGCTTC-AAAATTCTCGTTTT
1 AAAAATTCTCGTGTTTCAAAAATTTTCGTTTT
2996916 AAAAAAAATT
Statistics
Matches: 84, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
34 13 0.15
35 14 0.17
36 25 0.30
37 32 0.38
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.52
Consensus pattern (37 bp):
AAAAATTCTCGTGTTTCAAAAATTTTCGTTTTTTTTA
Found at i:2998182 original size:19 final size:18
Alignment explanation
Indices: 2998153--2998195 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2998143 AATAATGTAT
*
2998153 TTTTAATTTTAATATTATAA
1 TTTT-ATTTTAATAATA-AA
*
2998173 TTTTATTTTATTAATAAA
1 TTTTATTTTAATAATAAA
2998191 TTTTA
1 TTTTA
2998196 ATAGTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 10 0.48
20 4 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTATTTTAATAATAAA
Found at i:2998197 original size:32 final size:29
Alignment explanation
Indices: 2998157--2998231 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 29
2998147 ATGTATTTTT
*
2998157 AATTTTAATATTATAATTTTATTTTATTAATA
1 AATTTTAATATT-TAATTTAATTTTA--AATA
2998189 AATTTTAATAGTTTAATTTAATTTTAAATA
1 AATTTTAATA-TTTAATTTAATTTTAAATA
2998219 ATATTCTTAATAT
1 A-ATT-TTAATAT
2998232 ATTATTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 5 0.13
31 4 0.10
32 28 0.72
33 2 0.05
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (29 bp):
AATTTTAATATTTAATTTAATTTTAAATA
Found at i:3002082 original size:16 final size:16
Alignment explanation
Indices: 3002049--3002082 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3002039 AACTCCTGTT
* *
3002049 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
3002065 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
3002081 AA
1 AA
3002083 TATAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Done.