Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold400
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: 2847997
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 17
Found at i:291376 original size:25 final size:26
Alignment explanation
Indices: 291342--291417 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 26
291332 AATTAGCATA
*
291342 ATATT-ATTAATAAATTTTTTAATAT
1 ATATTAATTAATAAATTTTTAAATAT
**
291367 -TATTAATTAA-AAAAATTTAAATAT
1 ATATTAATTAATAAATTTTTAAATAT
* *
291391 ATAATTATTTAATAAATTAATTAAATA
1 AT-ATTAATTAATAAATT-TTTAAATA
291418 AAATTAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
24 15 0.38
25 6 0.15
26 8 0.21
27 3 0.08
28 7 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATATTAATTAATAAATTTTTAAATAT
Found at i:293407 original size:23 final size:23
Alignment explanation
Indices: 293381--293424 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
293371 TAAAAATAAT
293381 AAAAATTT-TATTTTAATTTTTA
1 AAAAATTTATATTTTAATTTTTA
293403 AAAAATTTATATTTTAATTTTT
1 AAAAATTTATATTTTAATTTTT
293425 TTATCCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AAAAATTTATATTTTAATTTTTA
Found at i:293754 original size:28 final size:29
Alignment explanation
Indices: 293699--293755 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
293689 AATTATTATA
* * **
293699 TAATTAATAAAAATATTTTTATTTAAATT
1 TAATTAATAAAAATATATTAATAAAAATT
293728 TAATT-ATAAAAATATATTAATAAAAATT
1 TAATTAATAAAAATATATTAATAAAAATT
293756 AACTTTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TAATTAATAAAAATATATTAATAAAAATT
Found at i:294375 original size:6 final size:6
Alignment explanation
Indices: 294359--294423 Score: 60
Period size: 6 Copynumber: 10.7 Consensus size: 6
294349 TATTTAAAAA
** * * *
294359 TTAAA- TTAAAT TTAAAT TCGATT TTAAAC ATAAATTT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA--T TTAAAT TTAAAT
294408 TTAAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAA
294424 TATATTATTA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
5 5 0.11
6 38 0.81
8 4 0.09
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:294872 original size:23 final size:24
Alignment explanation
Indices: 294846--294903 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
294836 AATAATAATA
294846 AATAAAAAATATTAATA-CTT-TAT
1 AATAAAAAATA-TAATAGCTTATAT
** *
294869 AATATTAAATATAATATGGTTATAT
1 AATAAAAAATATAATA-GCTTATAT
294894 AATAAAAAAT
1 AATAAAAAAT
294904 TAAAACATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
22 5 0.19
23 9 0.33
24 2 0.07
25 11 0.41
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (24 bp):
AATAAAAAATATAATAGCTTATAT
Found at i:294913 original size:18 final size:18
Alignment explanation
Indices: 294892--294940 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
294882 ATATGGTTAT
294892 ATAATAAAAAATTAA-AA
1 ATAATAAAAAATTAATAA
* *
294909 CATAATATAATATTAATAA
1 -ATAATAAAAAATTAATAA
294928 ATAATAAATAAAT
1 ATAATAAA-AAAT
294941 ACACGAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAATAAAAAATTAATAA
Found at i:297151 original size:19 final size:20
Alignment explanation
Indices: 297117--297169 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
297107 GAGTTTCAGC
*
297117 TTTTTATATAAAATTTAAAT-
1 TTTTTAT-TAATATTTAAATA
297137 TTTTTATTAATATTTAAATA
1 TTTTTATTAATATTTAAATA
*
297157 ATTTT-TTAATATT
1 TTTTTATTAATATT
297170 ATTAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTATTAATATTTAAATA
Found at i:297161 original size:20 final size:20
Alignment explanation
Indices: 297118--297181 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
297108 AGTTTCAGCT
* *
297118 TTTTATATAAAATTTAAAT-T
1 TTTTAT-TAATATTTAAATAA
297138 TTTTATTAATATTTAAATAA
1 TTTTATTAATATTTAAATAA
*
297158 TTTT-TTAATATTATTAATAA
1 TTTTATTAATATT-TAAATAA
297178 TTTT
1 TTTT
297182 GTATTTATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
19 19 0.49
20 20 0.51
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTATTAATATTTAAATAA
Found at i:297162 original size:22 final size:20
Alignment explanation
Indices: 297134--297198 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 20
297124 ATAAAATTTA
297134 AATTTTTTATTAATATTTAAAT
1 AATTTTTTATTAATA-TT-AAT
* *
297156 AATTTTTTAATATTATTAAT
1 AATTTTTTATTAATATTAAT
*
297176 AATTTTGTATT--TATT-AT
1 AATTTTTTATTAATATTAAT
297193 AATTTT
1 AATTTT
297199 AAAATATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
17 8 0.21
18 4 0.10
20 12 0.31
21 2 0.05
22 13 0.33
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
AATTTTTTATTAATATTAAT
Found at i:297195 original size:20 final size:20
Alignment explanation
Indices: 297144--297198 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
297134 AATTTTTTAT
* *
297144 TAATATT-TAAATAATTTTT
1 TAATATTATTAATAATTTTG
297163 TAATATTATTAATAATTTTG
1 TAATATTATTAATAATTTTG
297183 T-AT-TTATT-ATAATTTT
1 TAATATTATTAATAATTTT
297199 AAAATATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 9 0.27
20 11 0.33
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TAATATTATTAATAATTTTG
Found at i:297223 original size:28 final size:28
Alignment explanation
Indices: 297188--297243 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 28
297178 TTTTGTATTT
297188 ATTATAATTTTAA-AATATAAAAATTAA
1 ATTATAATTTTAATAATATAAAAATTAA
297215 ATTATTAATTTTAATAATATAAAAATTAA
1 ATTA-TAATTTTAATAATATAAAAATTAA
297244 TTTTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 4 0.15
28 9 0.33
29 14 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTATAATTTTAATAATATAAAAATTAA
Found at i:297258 original size:29 final size:29
Alignment explanation
Indices: 297188--297259 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
297178 TTTTGTATTT
*
297188 ATTA-TAATTTTAA-AATATAAAAATTAA
1 ATTATTAATTATAATAATATAAAAATTAA
*
297215 ATTATTAATTTTAATAATATAAAAATTAA
1 ATTATTAATTATAATAATATAAAAATTAA
* * *
297244 TTTTTTTATTATAATA
1 ATTATTAATTATAATA
297260 TAGAGACGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 4 0.10
28 9 0.23
29 26 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTATTAATTATAATAATATAAAAATTAA
Found at i:297467 original size:19 final size:19
Alignment explanation
Indices: 297445--297485 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
297435 AATAAGAATG
297445 TTAAATGATAATATTTTTT
1 TTAAATGATAATATTTTTT
297464 TTAAATGATAATATTTTTT
1 TTAAATGATAATATTTTTT
297483 TTA
1 TTA
297486 TTTTTTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTAAATGATAATATTTTTT
Found at i:298375 original size:32 final size:31
Alignment explanation
Indices: 298313--298395 Score: 80
Period size: 32 Copynumber: 2.6 Consensus size: 31
298303 AATGTAAACA
* *
298313 TAATATAAATATATGAATATTTTAATTTTATC
1 TAATATAAAT-TATAAATATTTTAAATTTATC
*
298345 TAATATAAATTATAAAT-TTATTAAAATTTATG
1 TAATATAAATTATAAATATT-TT-AAATTTATC
*
298377 TAAAATATAATT-TAAATAT
1 TAATATA-AATTATAAATAT
298396 GATTATAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
30 2 0.05
31 8 0.19
32 28 0.65
33 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (31 bp):
TAATATAAATTATAAATATTTTAAATTTATC
Found at i:298424 original size:28 final size:29
Alignment explanation
Indices: 298374--298435 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
298364 ATTAAAATTT
* * * *
298374 ATGTAAAATATAATTTAAATATGATTATA
1 ATGTAAAAAATAATATAAATATGATAAAA
298403 ATGTAAAAAAT-ATATAAATATGATAAAA
1 ATGTAAAAAATAATATAAATATGATAAAA
298431 ATGTA
1 ATGTA
298436 CGAATTGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (29 bp):
ATGTAAAAAATAATATAAATATGATAAAA
Found at i:299163 original size:18 final size:19
Alignment explanation
Indices: 299128--299165 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
299118 GATATAGCAA
299128 TTTATATATTCGTATTATG
1 TTTATATATTCGTATTATG
*
299147 TTTATATATT-TTATTATG
1 TTTATATATTCGTATTATG
299165 T
1 T
299166 CATAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (19 bp):
TTTATATATTCGTATTATG
Found at i:299573 original size:10 final size:10
Alignment explanation
Indices: 299540--299573 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
299530 TGTAAATTAT
299540 TATTTATATA
1 TATTTATATA
*
299550 TATATATATA
1 TATTTATATA
299560 TATTTATATA
1 TATTTATATA
299570 TATT
1 TATT
299574 CCTAATTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TATTTATATA
Found at i:299911 original size:21 final size:22
Alignment explanation
Indices: 299876--299916 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
299866 AAAATTTAAT
299876 TATAAAAATATTTTAATATTGA
1 TATAAAAATATTTTAATATTGA
299898 TATAAAAATA-TTTAATATT
1 TATAAAAATATTTTAATATT
299917 TTTAAATAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TATAAAAATATTTTAATATTGA
Found at i:302005 original size:99 final size:99
Alignment explanation
Indices: 301886--302079 Score: 318
Period size: 99 Copynumber: 2.0 Consensus size: 99
301876 CACAATGTTG
* *
301886 AATTATGTATAACCTACAAAATTATTATGTAGAA-CTCATAATTTTAAGCGGTGGACCTCTATAT
1 AATTATGTATAACCTACAAAATTATTATGTAGAACCT-ATAATTTTAAGCGGTGGACCACTAAAT
*
301950 AATTTTGTGTTGTAATTGGATAGTTATAGGGATTA
65 AAGTTTGTGTTGTAATTGGATAGTTATAGGGATTA
* *
301985 AATTATGTATAACCTTCAAAATTATTATGTAGAACCTATAATTTTAAGTGGTGGACCACTAAATA
1 AATTATGTATAACCTACAAAATTATTATGTAGAACCTATAATTTTAAGCGGTGGACCACTAAATA
*
302050 AGTTTGTGTTGTAGTTGGATAGTTATAGGG
66 AGTTTGTGTTGTAATTGGATAGTTATAGGG
302080 TTGTAGAAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
99 86 0.98
100 2 0.02
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.39
Consensus pattern (99 bp):
AATTATGTATAACCTACAAAATTATTATGTAGAACCTATAATTTTAAGCGGTGGACCACTAAATA
AGTTTGTGTTGTAATTGGATAGTTATAGGGATTA
Found at i:305999 original size:3 final size:3
Alignment explanation
Indices: 305993--306027 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
305983 ATTATTATTA
305993 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
306028 CTCATCCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:309529 original size:78 final size:79
Alignment explanation
Indices: 309423--309624 Score: 228
Period size: 78 Copynumber: 2.6 Consensus size: 79
309413 TAATAACAGG
* * * * * * *
309423 GTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGAGGA-TTA
1 GTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATC-AAGATTTA
* *
309487 GAAAAAAAATCGGGA
65 GAAAAAAAAGCCGGA
* * *
309502 -TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTG
1 GTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAGATTTAG
** *
309566 GGAATAAAGCCGGA
66 AAAAAAAAGCCGGA
* *
309580 GTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 GTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
309625 GAAATAACGA
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
77 2 0.02
78 60 0.58
79 41 0.40
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (79 bp):
GTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAGATTTAG
AAAAAAAAGCCGGA
Found at i:309620 original size:28 final size:28
Alignment explanation
Indices: 309580--309647 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
309570 TAAAGCCGGA
** * *
309580 GTTGGAGTATCCCCTCGGAAGTAACGGG
1 GTTGGAGTATCCCCGAGGAAATAACGAG
*
309608 GTTGGAGTATCCCCGATGAAATAACGAG
1 GTTGGAGTATCCCCGAGGAAATAACGAG
309636 GTTGGAGTATCC
1 GTTGGAGTATCC
309648 TCGATTATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (28 bp):
GTTGGAGTATCCCCGAGGAAATAACGAG
Found at i:309699 original size:52 final size:52
Alignment explanation
Indices: 309636--309969 Score: 188
Period size: 52 Copynumber: 6.3 Consensus size: 52
309626 AAATAACGAG
*
309636 GTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* * ** * *
309688 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * * *
309741 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* **** * * *
309792 GTTGGAGTATCCCC--TCA-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTATGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
* *
309847 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * *
309901 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
* *
309952 GTTGGAATATCCTCGATT
1 GTTGGAGTATCCCCGATT
309970 GTGGAGAATT
Statistics
Matches: 213, Mismatches: 43, Indels: 53
0.69 0.14 0.17
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 1 0.00
51 36 0.17
52 79 0.37
53 34 0.16
54 28 0.13
55 18 0.08
56 2 0.01
57 3 0.01
58 5 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:309832 original size:28 final size:27
Alignment explanation
Indices: 309792--309860 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 27
309782 TAAAACCGGA
309792 GTTGGAGTATCCCCTCA-GAAATAACGGG
1 GTTGGAGTATCCCC-CATG-AATAACGGG
* *
309820 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCCATGAATAACGGG
309847 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
309861 GATTGTGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (27 bp):
GTTGGAGTATCCCCCATGAATAACGGG
Found at i:309875 original size:107 final size:105
Alignment explanation
Indices: 309522--309914 Score: 332
Period size: 107 Copynumber: 3.7 Consensus size: 105
309512 CCCTCGAAAA
* * * * * *
309522 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGAGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTTGGAATAAAACCGGAGTTGGAG
* *
309587 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAA
66 TATCCCCTC-GAAATAACGGGGTTGGAGTATCCCCGATG-AT
* * * *
309629 TAACGAGGTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
1 TAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTTGG-AATAAAACCGGAGTTGGA
* * ** * ** **
309694 GTAT-CCC-CG-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
65 GTATCCCCTCGAAATAACGG--GGTTGGAGTATCCCCGATGAT
* * * * * *
309731 AAAACCAGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG-ATAAAACCGGAGTT
1 -TAA-CGGGGTTGGAGTATCCCCGATTAT-GAAAAATTAGTATTTTTG-GAATAAAACCGGAGTT
309795 GGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAT
62 GGAGTATCCCCTC-GAAATAACGGGGTTGGAGTATCCCCGATGAT
* * * * *
309840 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 TAACGGGGTTGGAGTATCCCCGATTATGAA-AAATTAGT-ATTTTTGG-AATAAAACCGGAGTTG
309905 GAGTATCCCC
63 GAGTATCCCC
309915 GATTATAGAA
Statistics
Matches: 221, Mismatches: 47, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
102 1 0.00
103 4 0.02
104 45 0.20
105 20 0.09
106 18 0.08
107 73 0.33
108 33 0.15
109 27 0.12
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (105 bp):
TAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTTGGAATAAAACCGGAGTTGGAG
TATCCCCTCGAAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:309928 original size:212 final size:212
Alignment explanation
Indices: 309569--309974 Score: 629
Period size: 212 Copynumber: 1.9 Consensus size: 212
309559 TATTTTGGGA
* * *
309569 ATAAAGCCGGAGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
309634 AGGTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
66 AGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
* *
309699 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGA
131 CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTGGA
309763 AAAATTAGTGTTTTAGCG
195 AAAATTAGTGTTTTAGCG
*
309781 ATAAAACCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* * *
309845 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
66 AGGTTGGAGTATCCCCGATTATGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTAGAGTA
* * * *
309910 TCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATTGTGG
129 TCCCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGG
309974 A
194 A
309975 GAATTGATAA
Statistics
Matches: 176, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 31 0.18
212 106 0.60
213 39 0.22
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
AGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCG
Found at i:309947 original size:51 final size:53
Alignment explanation
Indices: 309851--309969 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 53
309841 AACGGGGTTG
* * *
309851 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
309905 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
* *
309956 GAATATCCTCGATT
1 GAGTATCCCCGATT
309970 GTGGAGAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 33 0.57
52 2 0.03
53 8 0.14
54 15 0.26
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:312355 original size:13 final size:13
Alignment explanation
Indices: 312337--312362 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
312327 ACAAAGATCC
312337 ATGTATCGATACA
1 ATGTATCGATACA
312350 ATGTATCGATACA
1 ATGTATCGATACA
312363 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:312358 original size:33 final size:33
Alignment explanation
Indices: 312316--312382 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
312306 AAAATTTCCA
***
312316 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
312349 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
312382 A
1 A
312383 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:312517 original size:21 final size:21
Alignment explanation
Indices: 312493--312549 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
312483 CATTTGTAGG
312493 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
312514 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
312535 ATGTATCGATACATT
1 ATGTATCGATACATT
312550 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:313248 original size:55 final size:54
Alignment explanation
Indices: 313164--314336 Score: 1720
Period size: 55 Copynumber: 21.3 Consensus size: 54
313154 ATAAATTGTA
* * * * *
313164 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
313219 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
313274 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * *
313329 TCCTGCTCTTTGAGGACTGGAAAATGTCACCAACTTGTGTGGGCTGTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
313384 TCCTGTTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
313439 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
313494 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
313549 TCCTGCTCTTTGAGGACTGGACAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
313604 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
313659 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
313714 TCCTGCTCGTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
313769 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
313824 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
313879 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
313934 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
313989 TCCTGCTCTTTGAGGACTGGACAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
314044 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
314099 TCCTGCTCGTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
314154 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
314209 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
314264 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
314319 TCCTGCTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
314337 AAAAAGCGGA
Statistics
Matches: 1050, Mismatches: 42, Indels: 52
0.92 0.04 0.05
Matches are distributed among these distances:
53 4 0.00
54 31 0.03
55 985 0.94
56 26 0.02
57 4 0.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:313406 original size:27 final size:27
Alignment explanation
Indices: 313324--313406 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
313314 GGGCTTTAAG
*
313324 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGATCTTTGAGGACTGGAA
* * * * *
313351 A-ATGTCAC-CAACTTGTGTGGGCTGTGAA
1 AGGTGTC-CTGATCTT-TGAGGACTG-GAA
*
313379 AGGTGTCCTGTTCTTTGAGGACTGGAA
1 AGGTGTCCTGATCTTTGAGGACTGGAA
313406 A
1 A
313407 ATGCCACCAA
Statistics
Matches: 39, Mismatches: 12, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
26 7 0.18
27 13 0.33
28 12 0.31
29 7 0.18
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (27 bp):
AGGTGTCCTGATCTTTGAGGACTGGAA
Found at i:313988 original size:29 final size:29
Alignment explanation
Indices: 313900--313988 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
313890 GAGGACTGAA
313900 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
** * *
313929 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA-
1 AGGTG-CCACCAACTTGTGTGGG-CTTTAAG
313955 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
313984 AGGTG
1 AGGTG
313989 TCCTGCTCTT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 9 0.20
28 9 0.20
29 13 0.29
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (29 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAG
Found at i:315349 original size:11 final size:11
Alignment explanation
Indices: 315318--315360 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
315308 CTTTTCTCTC
*
315318 TTTTTCTTTGT
1 TTTTTTTTTGT
315329 TTTGTTTTTTGT
1 TTT-TTTTTTGT
*
315341 TTTTTTTTTCT
1 TTTTTTTTTGT
315352 TTTTTTTTT
1 TTTTTTTTT
315361 TGAAGAGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:315354 original size:23 final size:23
Alignment explanation
Indices: 315318--315362 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
315308 CTTTTCTCTC
*
315318 TTTTTCTTTGTTTTGTTTTTTGT
1 TTTTTCTTTCTTTTGTTTTTTGT
* *
315341 TTTTTTTTTCTTTTTTTTTTTG
1 TTTTTCTTTCTTTTGTTTTTTG
315363 AAGAGAAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (23 bp):
TTTTTCTTTCTTTTGTTTTTTGT
Found at i:327893 original size:78 final size:79
Alignment explanation
Indices: 327781--327982 Score: 219
Period size: 78 Copynumber: 2.6 Consensus size: 79
327771 TAATAACAGG
* * * * * * *
327781 GTTGGAGTGTTCCCTTGAAAATAACAGGGCTGGAGTATCCCCGGTTGTGAGAAATCGAGGA-TTA
1 GTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATC-AAGATTTA
* *
327845 GAAAAAAAATCGGGA
65 GAAAAAAAAGCCGGA
* * * *
327860 -TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTG
1 GTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAGATTTAG
** *
327924 GGAATAAAGCCGGA
66 AAAAAAAAGCCGGA
* *
327938 GTTGGAGTATCCCCTTGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 GTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGAT
327983 GAAATAACGA
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
77 2 0.02
78 59 0.58
79 40 0.40
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (79 bp):
GTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAGATTTAG
AAAAAAAAGCCGGA
Found at i:327978 original size:28 final size:28
Alignment explanation
Indices: 327938--328010 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
327928 TAAAGCCGGA
* * *
327938 GTTGGAGTATCCCC-TTGGAAGTAACGGG
1 GTTGGAGTATCCCCGAT-GAAATAACGAG
327966 GTTGGAGTATCCCCGATGAAATAACGAG
1 GTTGGAGTATCCCCGATGAAATAACGAG
*
327994 GTTGGAGTATCCTCGAT
1 GTTGGAGTATCCCCGAT
328011 TATGAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 39 0.98
29 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.26
Consensus pattern (28 bp):
GTTGGAGTATCCCCGATGAAATAACGAG
Found at i:328057 original size:52 final size:52
Alignment explanation
Indices: 327994--328327 Score: 188
Period size: 52 Copynumber: 6.3 Consensus size: 52
327984 AAATAACGAG
*
327994 GTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* * ** * *
328046 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * * *
328099 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* **** * * *
328150 GTTGGAGTATCCCC--TCA-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTATGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
* *
328205 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * *
328259 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
* *
328310 GTTGGAATATCCTCGATT
1 GTTGGAGTATCCCCGATT
328328 GTGGAGAATT
Statistics
Matches: 213, Mismatches: 43, Indels: 53
0.69 0.14 0.17
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 1 0.00
51 36 0.17
52 79 0.37
53 34 0.16
54 28 0.13
55 18 0.08
56 2 0.01
57 3 0.01
58 5 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:328190 original size:28 final size:27
Alignment explanation
Indices: 328150--328218 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 27
328140 TAAAACCGGA
328150 GTTGGAGTATCCCCTCA-GAAATAACGGG
1 GTTGGAGTATCCCC-CATG-AATAACGGG
* *
328178 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCCATGAATAACGGG
328205 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
328219 GATTGTGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (27 bp):
GTTGGAGTATCCCCCATGAATAACGGG
Found at i:328233 original size:107 final size:105
Alignment explanation
Indices: 327880--328272 Score: 323
Period size: 107 Copynumber: 3.7 Consensus size: 105
327870 CCCTCGAAAA
* * * * * *
327880 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGAGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTTGGAATAAAACCGGAGTTGGAG
* * *
327945 TATCCCCTTGGAAGTAACGGGGTTGGAGTATCCCCGATGAAA
66 TATCCCC-TCGAAATAACGGGGTTGGAGTATCCCCGATG-AT
* * * *
327987 TAACGAGGTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
1 TAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTTGG-AATAAAACCGGAGTTGGA
* * ** * ** **
328052 GTAT-CCC-CG-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
65 GTATCCCCTCGAAATAACGG--GGTTGGAGTATCCCCGATGAT
* * * * * *
328089 AAAACCAGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG-ATAAAACCGGAGTT
1 -TAA-CGGGGTTGGAGTATCCCCGATTAT-GAAAAATTAGTATTTTTG-GAATAAAACCGGAGTT
328153 GGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAT
62 GGAGTATCCCCTC-GAAATAACGGGGTTGGAGTATCCCCGATGAT
* * * * *
328198 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 TAACGGGGTTGGAGTATCCCCGATTATGAA-AAATTAGT-ATTTTTGG-AATAAAACCGGAGTTG
328263 GAGTATCCCC
63 GAGTATCCCC
328273 GATTATAGAA
Statistics
Matches: 220, Mismatches: 48, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
102 1 0.00
103 4 0.02
104 45 0.20
105 20 0.09
106 17 0.08
107 73 0.33
108 33 0.15
109 27 0.12
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (105 bp):
TAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTTGGAATAAAACCGGAGTTGGAG
TATCCCCTCGAAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:328286 original size:212 final size:212
Alignment explanation
Indices: 327927--328332 Score: 620
Period size: 212 Copynumber: 1.9 Consensus size: 212
327917 TATTTTGGGA
* ** *
327927 ATAAAGCCGGAGTTGGAGTATCCCCTTGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
327992 AGGTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
66 AGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
* *
328057 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGA
131 CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTGGA
328121 AAAATTAGTGTTTTAGCG
195 AAAATTAGTGTTTTAGCG
*
328139 ATAAAACCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* * *
328203 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
66 AGGTTGGAGTATCCCCGATTATGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTAGAGTA
* * * *
328268 TCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATTGTGG
129 TCCCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGG
328332 A
194 A
328333 GAATTGATAA
Statistics
Matches: 175, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 31 0.18
212 105 0.60
213 39 0.22
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
AGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCG
Found at i:328305 original size:51 final size:53
Alignment explanation
Indices: 328209--328327 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 53
328199 AACGGGGTTG
* * *
328209 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
328263 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
* *
328314 GAATATCCTCGATT
1 GAGTATCCCCGATT
328328 GTGGAGAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 33 0.57
52 2 0.03
53 8 0.14
54 15 0.26
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:330708 original size:13 final size:13
Alignment explanation
Indices: 330690--330715 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
330680 ACAAAGATCC
330690 ATGTATCGATACA
1 ATGTATCGATACA
330703 ATGTATCGATACA
1 ATGTATCGATACA
330716 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:330711 original size:33 final size:33
Alignment explanation
Indices: 330669--330735 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
330659 AAAATTTCCA
***
330669 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
330702 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
330735 A
1 A
330736 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:330795 original size:13 final size:13
Alignment explanation
Indices: 330777--330814 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
330767 ACAATACTTA
330777 TGTATCGATACAT
1 TGTATCGATACAT
330790 TGTATCGATACAT
1 TGTATCGATACAT
330803 TGTATCGATACA
1 TGTATCGATACA
330815 AATTGTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:330896 original size:21 final size:21
Alignment explanation
Indices: 330872--330928 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
330862 CATTTGTAGG
330872 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
330893 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
330914 ATGTATCGATACATT
1 ATGTATCGATACATT
330929 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:330957 original size:14 final size:14
Alignment explanation
Indices: 330940--330967 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
330930 AAATTTTTTT
330940 TTTTTTTTTTTCAA
1 TTTTTTTTTTTCAA
330954 TTTTTTTTTTTCAA
1 TTTTTTTTTTTCAA
330968 ACACTTTATC
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:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTTTCAA
Found at i:334345 original size:90 final size:88
Alignment explanation
Indices: 334194--334368 Score: 226
Period size: 90 Copynumber: 2.0 Consensus size: 88
334184 CCTGGATCTA
* * *
334194 GTTCTCCTTCATTATTTTGTTTATTATTATCTATCACAAGTTTAATCATCATTTGTGTGTATGAT
1 GTTCTCCTTCATTATTTTGTTTATTATTATCTATCACAACTTTAATCATCATTTATATGTATGAT
334259 TTTCACAATTGCAAATTGATTCG
66 TTTCACAATTGCAAATTGATTCG
* * * * *
334282 GTTCTCTTTCATTATTTTTTGTTTGTTATTTTTTAAT-ACAACTTTAGTCATCATTTATATGTAT
1 GTTCTCCTTCATTA--TTTTGTTTATTATTATCT-ATCACAACTTTAATCATCATTTATATGTAT
* *
334346 GATTTTCACAATTTCGAATTGAT
63 GATTTTCACAATTGCAAATTGAT
334369 CCTACACAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
88 13 0.18
90 59 0.80
91 2 0.03
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (88 bp):
GTTCTCCTTCATTATTTTGTTTATTATTATCTATCACAACTTTAATCATCATTTATATGTATGAT
TTTCACAATTGCAAATTGATTCG
Found at i:336164 original size:12 final size:12
Alignment explanation
Indices: 336147--336171 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
336137 CAGCTTCTTT
336147 TAAGCTTTTACG
1 TAAGCTTTTACG
336159 TAAGCTTTTACG
1 TAAGCTTTTACG
336171 T
1 T
336172 GGTATCAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (12 bp):
TAAGCTTTTACG
Found at i:344561 original size:28 final size:27
Alignment explanation
Indices: 344495--344573 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
344485 AAAAGCCACC
344495 CTTTGTGTTTGTCAAAAATGGTGGTTA
1 CTTTGTGTTTGTCAAAAATGGTGGTTA
* *
344522 CTTTGTATTTGTCAAAAATGGTGGTTC
1 CTTTGTGTTTGTCAAAAATGGTGGTTA
* *
344549 CTTTTTTGTTTGTCAAAAATTGTGG
1 C-TTTGTGTTTGTCAAAAATGGTGG
344574 CTTATTGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 26 0.57
28 20 0.43
ACGTcount: A:0.22, C:0.09, G:0.23, T:0.47
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATGGTGGTTA
Found at i:344584 original size:28 final size:26
Alignment explanation
Indices: 344500--344585 Score: 91
Period size: 28 Copynumber: 3.1 Consensus size: 26
344490 CCACCCTTTG
*
344500 TGTTTGTCAAAAATGGTGGTTACTTTG
1 TGTTTGTCAAAAATGGTGGTTA-TTTT
* *
344527 TATTTGTCAAAAATGGTGGTTCCTTTTT
1 TGTTTGTCAAAAATGGTGGTT--ATTTT
*
344555 TGTTTGTCAAAAATTGTGGCTTATTGTT
1 TGTTTGTCAAAAATGGTGG-TTATT-TT
344583 TGT
1 TGT
344586 CAAATTTAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
27 22 0.45
28 25 0.51
29 2 0.04
ACGTcount: A:0.21, C:0.08, G:0.22, T:0.49
Consensus pattern (26 bp):
TGTTTGTCAAAAATGGTGGTTATTTT
Found at i:345257 original size:2 final size:2
Alignment explanation
Indices: 345252--345281 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
345242 TAATTTAGTG
345252 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
345282 GTATGTATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:345583 original size:3 final size:3
Alignment explanation
Indices: 345575--345615 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
345565 TATACACATC
345575 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
345616 GCACTTTCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:345777 original size:4 final size:4
Alignment explanation
Indices: 345768--345792 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
345758 AATCTTTAAT
345768 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
345793 ATGTTCTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:347010 original size:2 final size:2
Alignment explanation
Indices: 347003--347038 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
346993 CCTTCTGTAC
347003 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
347039 AGTTATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:348008 original size:22 final size:23
Alignment explanation
Indices: 347966--348008 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
347956 TTGACAATTC
**
347966 ATTTATTAGTATCATGTTCATGT
1 ATTTATTAGTATCATAATCATGT
347989 ATTTATT-GTATCATAATCAT
1 ATTTATTAGTATCATAATCAT
348009 ATTTAAAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (23 bp):
ATTTATTAGTATCATAATCATGT
Found at i:348277 original size:2 final size:2
Alignment explanation
Indices: 348270--348300 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
348260 AATACTTTTC
*
348270 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
348301 CTATCTGTCA
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:348619 original size:17 final size:17
Alignment explanation
Indices: 348593--348634 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
348583 ACGGAGTATC
*
348593 TTTTATTTTTTTA-AAA
1 TTTTAATTTTTTATAAA
348609 TATTTAA-TTTTTATAAA
1 T-TTTAATTTTTTATAAA
348626 TTTTAATTT
1 TTTTAATTT
348635 GGAGTATACT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTAATTTTTTATAAA
Found at i:348621 original size:16 final size:16
Alignment explanation
Indices: 348600--348634 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
348590 ATCTTTTATT
348600 TTTTTA-AAATATTTAA
1 TTTTTATAAAT-TTTAA
348616 TTTTTATAAATTTTAA
1 TTTTTATAAATTTTAA
348632 TTT
1 TTT
348635 GGAGTATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTTATAAATTTTAA
Found at i:349605 original size:8 final size:7
Alignment explanation
Indices: 349588--349617 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
349578 AATATATATT
349588 AAAAATA
1 AAAAATA
349595 AAAAATA
1 AAAAATA
349602 AAAAATA
1 AAAAATA
349609 AATAAATA
1 AA-AAATA
349617 A
1 A
349618 GACATGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 16 0.73
8 6 0.27
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAAAATA
Found at i:352348 original size:23 final size:23
Alignment explanation
Indices: 352322--352450 Score: 60
Period size: 23 Copynumber: 5.8 Consensus size: 23
352312 TTAAACTTAA
*
352322 TAATTTATATATCT-TATTATATT
1 TAATATATATAT-TATATTATATT
* *
352345 TAATATATTTATTATATTATATCG
1 TAATATATATATTATATTATAT-T
* * *
352369 T-AT-T-TAAAATATTTTATATT
1 TAATATATATATTATATTATATT
*
352389 T-ATATA-A-ATTATAATAT-TT
1 TAATATATATATTATATTATATT
* * *
352408 TAATAATTTATATGATA-TAAATT
1 TAAT-ATATATATTATATTATATT
*
352431 TAAAATATATATTCATATTA
1 TAATATATATATT-ATATTA
352451 AATTATATTT
Statistics
Matches: 78, Mismatches: 17, Indels: 21
0.67 0.15 0.18
Matches are distributed among these distances:
19 3 0.04
20 12 0.15
21 15 0.19
22 12 0.15
23 33 0.42
24 3 0.04
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TAATATATATATTATATTATATT
Found at i:352351 original size:9 final size:9
Alignment explanation
Indices: 352318--352417 Score: 61
Period size: 9 Copynumber: 11.3 Consensus size: 9
352308 TTGCTTAAAC
352318 TTAATA-AT
1 TTAATATAT
352326 TT-ATATAT
1 TTAATATAT
*
352334 CTTATTATAT
1 -TTAATATAT
352344 TTAATATAT
1 TTAATATAT
*
352353 TTATTATA-
1 TTAATATAT
*
352361 TTATATCGTAT
1 TTA-AT-ATAT
*
352372 TTAAAATAT
1 TTAATATAT
352381 TT--TATAT
1 TTAATATAT
*
352388 TTATATAAAT
1 TTA-ATATAT
352398 TATAATAT-T
1 T-TAATATAT
352407 TTAATA-AT
1 TTAATATAT
352415 TTA
1 TTA
352418 TATGATATAA
Statistics
Matches: 71, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
7 9 0.13
8 16 0.23
9 25 0.35
10 16 0.23
11 5 0.07
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (9 bp):
TTAATATAT
Found at i:352438 original size:33 final size:33
Alignment explanation
Indices: 352376--352438 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
352366 TCGTATTTAA
* * *
352376 AATATTTTATATTTATATAAATTATAATATTTT
1 AATAATTTATATTGATATAAATTAAAATATTTT
352409 AATAATTTATA-TGATATAAATTTAAAATAT
1 AATAATTTATATTGATATAAA-TTAAAATAT
352439 ATATTCATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (33 bp):
AATAATTTATATTGATATAAATTAAAATATTTT
Found at i:353325 original size:22 final size:23
Alignment explanation
Indices: 353280--353324 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
353270 TGAAACTGTA
353280 AGTCTCCTTTTTTATTTTTTTTT
1 AGTCTCCTTTTTTATTTTTTTTT
353303 AGTCTCCTTTTTTATTTTTTTT
1 AGTCTCCTTTTTTATTTTTTTT
353325 ATTGTTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.73
Consensus pattern (23 bp):
AGTCTCCTTTTTTATTTTTTTTT
Found at i:353339 original size:22 final size:23
Alignment explanation
Indices: 353280--353337 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
353270 TGAAACTGTA
*
353280 AGTCTCCTTTTTTATTTTTTTTT
1 AGTCTACTTTTTTATTTTTTTTT
*
353303 AGTCTCCTTTTTTATTTTTTTTAT
1 AGTCTACTTTTTTATTTTTTTT-T
*
353327 TGT-TACTTTTT
1 AGTCTACTTTTT
353338 ATCATTGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 29 0.91
24 3 0.09
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.72
Consensus pattern (23 bp):
AGTCTACTTTTTTATTTTTTTTT
Found at i:360364 original size:22 final size:22
Alignment explanation
Indices: 360336--360385 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
360326 TAAAAATAGA
360336 GAAGGTTTAGATAGATTTGTCC
1 GAAGGTTTAGATAGATTTGTCC
360358 GAAGGTTTAGATAGATTTGTCC
1 GAAGGTTTAGATAGATTTGTCC
*
360380 AAAGGT
1 GAAGGT
360386 CCAGAGGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (22 bp):
GAAGGTTTAGATAGATTTGTCC
Found at i:360425 original size:25 final size:25
Alignment explanation
Indices: 360374--360426 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
360364 TTAGATAGAT
* * *
360374 TTGTCCAAAGGTCCAGAGGGTAGGC
1 TTGTCCAAAGGTCCAGAAGGCAAGC
*
360399 TTGTCCAAAGGTCGAGAAGGCAAGC
1 TTGTCCAAAGGTCCAGAAGGCAAGC
360424 TTG
1 TTG
360427 ACTTATATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (25 bp):
TTGTCCAAAGGTCCAGAAGGCAAGC
Found at i:360474 original size:5 final size:5
Alignment explanation
Indices: 360460--360498 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
360450 TAAATATTTT
* *
360460 TTTAA TTTAA ATTAA TTTAA TTTAA TTTAA ATT-A TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
360499 AAATACTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 3 0.10
5 26 0.90
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TTTAA
Found at i:360476 original size:10 final size:10
Alignment explanation
Indices: 360461--360499 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
360451 AAATATTTTT
360461 TTAATTTAAA
1 TTAATTTAAA
*
360471 TTAATTTAAT
1 TTAATTTAAA
360481 TTAATTTAAA
1 TTAATTTAAA
360491 TT-ATTTAAA
1 TTAATTTAAA
360500 AATACTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTAATTTAAA
Found at i:360485 original size:20 final size:19
Alignment explanation
Indices: 360460--360498 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
360450 TAAATATTTT
360460 TTTAATTTAAATTAATTTAA
1 TTTAATTTAAATT-ATTTAA
360480 TTTAATTTAAATTATTTAA
1 TTTAATTTAAATTATTTAA
360499 AAATACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAATTTAAATTATTTAA
Found at i:360715 original size:16 final size:15
Alignment explanation
Indices: 360693--360728 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
360683 AATATTAAAA
*
360693 TTAAAATTTTATATT
1 TTAAAATATTATATT
360708 TATAAAATATTATATT
1 T-TAAAATATTATATT
360724 TTAAA
1 TTAAA
360729 TGTAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAAAATATTATATT
Found at i:361061 original size:3 final size:3
Alignment explanation
Indices: 361053--361103 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
361043 TCAAAAGTTG
361053 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
361101 AAT
1 AAT
361104 GAGGCCTTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:361177 original size:13 final size:13
Alignment explanation
Indices: 361161--361187 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
361151 AAATTAAAGT
361161 AAAAAAATTAATA
1 AAAAAAATTAATA
361174 AAAAAAATTAATA
1 AAAAAAATTAATA
361187 A
1 A
361188 GTAGAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAAAAATTAATA
Found at i:361904 original size:29 final size:29
Alignment explanation
Indices: 361858--361914 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
361848 TGATGTCATT
*
361858 TTAAATATGATGT-TTTTTTTAAAATTAAA
1 TTAAATATGATGTATTTTATT-AAATTAAA
361887 TTAAAT-TGATGTCATTTTATTAAATTAA
1 TTAAATATGATGT-ATTTTATTAAATTAA
361915 TATGATGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 6 0.24
29 13 0.52
30 6 0.24
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (29 bp):
TTAAATATGATGTATTTTATTAAATTAAA
Found at i:361908 original size:24 final size:22
Alignment explanation
Indices: 361881--361929 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 22
361871 TTTTTTTAAA
361881 ATTAAATTAA-ATTGATGTCATTTT
1 ATTAAATTAATA-TGATGT--TTTT
361905 ATTAAATTAATATGATGTTTTT
1 ATTAAATTAATATGATGTTTTT
361927 ATT
1 ATT
361930 TTTTAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.29
24 16 0.67
25 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (22 bp):
ATTAAATTAATATGATGTTTTT
Found at i:362254 original size:2 final size:2
Alignment explanation
Indices: 362247--362280 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
362237 TGTAAAACTC
362247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
362281 GATACCGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:363046 original size:20 final size:20
Alignment explanation
Indices: 363021--363071 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
363011 ACCCTTAAAT
363021 GTATCGATACACAATT-CAAA
1 GTATCGATACA-AATTGCAAA
**
363041 GTATCGATACATGTTGCAAA
1 GTATCGATACAAATTGCAAA
363061 GTATCGATACA
1 GTATCGATACA
363072 TGAAAAAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (20 bp):
GTATCGATACAAATTGCAAA
Found at i:363161 original size:13 final size:13
Alignment explanation
Indices: 363143--363168 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
363133 TACACCAAGT
363143 ATGTATCGATACA
1 ATGTATCGATACA
363156 ATGTATCGATACA
1 ATGTATCGATACA
363169 CAAAAACATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:363166 original size:32 final size:33
Alignment explanation
Indices: 363125--363188 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
363115 TAGCCAAACT
* **
363125 TGTATCGATACAC-CAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAACATGTATCGATACAA
363157 TGTATCGATACACAAAAACATGTATCGATACA
1 TGTATCGATACACAAAAACATGTATCGATACA
363189 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACAAAAACATGTATCGATACAA
Found at i:363246 original size:19 final size:20
Alignment explanation
Indices: 363222--363261 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
363212 GCTATATTTT
363222 TCAAATA-TGTATCGATACA
1 TCAAATATTGTATCGATACA
363241 TCAAATATTGTATCGATACA
1 TCAAATATTGTATCGATACA
363261 T
1 T
363262 TCACACGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (20 bp):
TCAAATATTGTATCGATACA
Found at i:369363 original size:13 final size:13
Alignment explanation
Indices: 369345--369383 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
369335 ACATTTTTCT
369345 TTGTATCGATACA
1 TTGTATCGATACA
369358 TTGTATCGATACA
1 TTGTATCGATACA
*
369371 CTGTATCGATACA
1 TTGTATCGATACA
369384 ATGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:371210 original size:37 final size:37
Alignment explanation
Indices: 371169--371284 Score: 96
Period size: 37 Copynumber: 3.1 Consensus size: 37
371159 GCAAATAAAT
371169 TTTATAATTAAGGAGGAGAATGCGCGAATTTGATAGA
1 TTTATAATTAAGGAGGAGAATGCGCGAATTTGATAGA
* * ** ** * *
371206 TTTATTCGA-TAATGA--ACGAAAACGTTAAATT-ATAAA
1 TTTA-T-AATTAAGGAGGA-GAATGCGCGAATTTGATAGA
371242 TTTTATAATTAAGGAGGAGAATGCGCGAATTTGATAGA
1 -TTTATAATTAAGGAGGAGAATGCGCGAATTTGATAGA
371280 TTTAT
1 TTTAT
371285 TCGATAATGA
Statistics
Matches: 55, Mismatches: 16, Indels: 16
0.63 0.18 0.18
Matches are distributed among these distances:
35 1 0.02
36 11 0.20
37 31 0.56
38 11 0.20
39 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.34
Consensus pattern (37 bp):
TTTATAATTAAGGAGGAGAATGCGCGAATTTGATAGA
Found at i:371284 original size:74 final size:74
Alignment explanation
Indices: 371163--371311 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
371153 ATCTTTGCAA
371163 ATAAATTTTATAATTAAGGAGGAGAATGCGCGAATTTGATAGATTTATTCGATAATGAACGAAAA
1 ATAAATTTTATAATTAAGGAGGAGAATGCGCGAATTTGATAGATTTATTCGATAATGAACGAAAA
371228 CGTTAAATT
66 CGTTAAATT
371237 ATAAATTTTATAATTAAGGAGGAGAATGCGCGAATTTGATAGATTTATTCGATAATGAACGAAAA
1 ATAAATTTTATAATTAAGGAGGAGAATGCGCGAATTTGATAGATTTATTCGATAATGAACGAAAA
371302 CGTTAAATT
66 CGTTAAATT
371311 A
1 A
371312 CCTTATTAAG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (74 bp):
ATAAATTTTATAATTAAGGAGGAGAATGCGCGAATTTGATAGATTTATTCGATAATGAACGAAAA
CGTTAAATT
Found at i:371880 original size:20 final size:20
Alignment explanation
Indices: 371855--371905 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
371845 ACCCTTAAAT
371855 GTATCGATACACAATT-CAAA
1 GTATCGATACA-AATTGCAAA
**
371875 GTATCGATACATGTTGCAAA
1 GTATCGATACAAATTGCAAA
371895 GTATCGATACA
1 GTATCGATACA
371906 TGAAAAAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (20 bp):
GTATCGATACAAATTGCAAA
Found at i:371995 original size:13 final size:13
Alignment explanation
Indices: 371977--372002 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
371967 TACACCAAGT
371977 ATGTATCGATACA
1 ATGTATCGATACA
371990 ATGTATCGATACA
1 ATGTATCGATACA
372003 CAAAAACATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:372000 original size:32 final size:33
Alignment explanation
Indices: 371959--372022 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
371949 TAGCCAAACT
* **
371959 TGTATCGATACAC-CAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAACATGTATCGATACAA
371991 TGTATCGATACACAAAAACATGTATCGATACA
1 TGTATCGATACACAAAAACATGTATCGATACA
372023 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACAAAAACATGTATCGATACAA
Found at i:372080 original size:19 final size:20
Alignment explanation
Indices: 372056--372095 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
372046 GCTATATTTT
372056 TCAAATA-TGTATCGATACA
1 TCAAATATTGTATCGATACA
372075 TCAAATATTGTATCGATACA
1 TCAAATATTGTATCGATACA
372095 T
1 T
372096 TCACACGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (20 bp):
TCAAATATTGTATCGATACA
Found at i:373107 original size:29 final size:30
Alignment explanation
Indices: 373075--373132 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
373065 TATCTGTGAT
* *
373075 TTGA-TATAAAA-ATTATTTATTTTTTAAAG
1 TTGAGTATAAAATA-TATTAATATTTTAAAG
373104 TTGAGTATAAAATATATTAATATTTTAAA
1 TTGAGTATAAAATATATTAATATTTTAAA
373133 ATATTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.16
30 20 0.80
31 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (30 bp):
TTGAGTATAAAATATATTAATATTTTAAAG
Found at i:373196 original size:19 final size:19
Alignment explanation
Indices: 373174--373217 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
373164 ATAATTATAC
*
373174 TTTTTATTAATTATTAATT
1 TTTTTATTAATTACTAATT
**
373193 TTTTTATTTTTTACTAATT
1 TTTTTATTAATTACTAATT
373212 TTTTTA
1 TTTTTA
373218 AATTATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTATTAATTACTAATT
Found at i:374705 original size:17 final size:16
Alignment explanation
Indices: 374662--374707 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
374652 GCGTTAGGTA
374662 AAAAAGAAAGAAAGAAG
1 AAAAAGAAA-AAAGAAG
**
374679 ATGAAGAAAAAAGAAAG
1 AAAAAGAAAAAAG-AAG
374696 AAAAAGAAAAAA
1 AAAAAGAAAAAA
374708 AATATGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAG
Found at i:374708 original size:20 final size:20
Alignment explanation
Indices: 374661--374709 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
374651 AGCGTTAGGT
* *
374661 AAAAAAGAAAGAAAGAAGATG
1 AAAAAA-AAAGAAAGAAAAAG
*
374682 AAGAAAAAAGAAAGAAAAAG
1 AAAAAAAAAGAAAGAAAAAG
374702 AAAAAAAA
1 AAAAAAAA
374710 TATGAAATGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAGAAAGAAAAAG
Found at i:374775 original size:48 final size:48
Alignment explanation
Indices: 374704--374801 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
374694 AGAAAAAGAA
*
374704 AAAAAATATGAAATGGAGTGGCTTGGGATTTGAACCCAGGCCACCCAT
1 AAAAAATATGAAATGGAGCGGCTTGGGATTTGAACCCAGGCCACCCAT
374752 AAAAAATATGAAATGGAGCGGCTTGGGATTTGAACCCAGGCCACCCAT
1 AAAAAATATGAAATGGAGCGGCTTGGGATTTGAACCCAGGCCACCCAT
374800 AA
1 AA
374802 TGAAAAATAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.19
Consensus pattern (48 bp):
AAAAAATATGAAATGGAGCGGCTTGGGATTTGAACCCAGGCCACCCAT
Found at i:375137 original size:21 final size:21
Alignment explanation
Indices: 375096--375134 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
375086 GTGATGTTTG
*
375096 CATTTGTTTTTTTTTTATTAT
1 CATTTGTTTTTGTTTTATTAT
375117 CATTT-TTTTTGTTTTATT
1 CATTTGTTTTTGTTTTATT
375135 TATATGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (21 bp):
CATTTGTTTTTGTTTTATTAT
Found at i:380630 original size:20 final size:20
Alignment explanation
Indices: 380586--380631 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
380576 AGATAAATTT
* *
380586 AAATATGATAAAAAATATTA
1 AAATATAATAAAAAATAATA
380606 AAATATAATAAAAAATAATA
1 AAATATAATAAAAAATAATA
*
380626 TAATAT
1 AAATAT
380632 TCTTATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
AAATATAATAAAAAATAATA
Found at i:380667 original size:24 final size:24
Alignment explanation
Indices: 380610--380667 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
380600 ATATTAAAAT
* * *
380610 ATAATAAAAAATAATATAATATTC
1 ATAATAAAAAATAAAAAAATATAC
*
380634 -TTATATAAAAATAAAAAAATATAC
1 ATAATA-AAAAATAAAAAAATATAC
380658 ATAATAAAAA
1 ATAATAAAAA
380668 CTATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
23 4 0.15
24 19 0.70
25 4 0.15
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
ATAATAAAAAATAAAAAAATATAC
Found at i:381007 original size:3 final size:3
Alignment explanation
Indices: 380999--381055 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
380989 TCAGGGAATC
* *
380999 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
381047 GAT AAT AAT
1 AAT AAT AAT
381056 TCTAATGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:389349 original size:46 final size:46
Alignment explanation
Indices: 389281--389396 Score: 144
Period size: 46 Copynumber: 2.5 Consensus size: 46
389271 AGAAGAATAA
*
389281 TTTGTAGCTTTCTCTATGCAAAAGTAAAGAG-TAGTTTGTTAGAGAG
1 TTTGTAGCTTTCTCTATACAAAAGTAAAGAGTTA-TTTGTTAGAGAG
* * * ** *
389327 TTTGTAGTTTTCTTTATACAAAAGTTACTAGTTATTTGTTGGAGAG
1 TTTGTAGCTTTCTCTATACAAAAGTAAAGAGTTATTTGTTAGAGAG
*
389373 TTTATAGCTTTCTCTATACAAAAG
1 TTTGTAGCTTTCTCTATACAAAAG
389397 CTACTAGTTG
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 57 0.97
47 2 0.03
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.42
Consensus pattern (46 bp):
TTTGTAGCTTTCTCTATACAAAAGTAAAGAGTTATTTGTTAGAGAG
Found at i:395650 original size:13 final size:13
Alignment explanation
Indices: 395629--395659 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
395619 AGAATGAATT
*
395629 GGAGAGGGAAGAG
1 GGAGCGGGAAGAG
395642 GGAGCGGGAAGAG
1 GGAGCGGGAAGAG
395655 GGAGC
1 GGAGC
395660 CTCCTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.06, G:0.61, T:0.00
Consensus pattern (13 bp):
GGAGCGGGAAGAG
Found at i:400262 original size:24 final size:24
Alignment explanation
Indices: 400233--400309 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
400223 AATAAAAATT
*
400233 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAAAA
* *
400257 AGCCACCATTTTTTACAAACAAAA
1 AGCCACCAATTTTGACAAACAAAA
*
400281 AGAAACCACC-ATTTCTGACAAACATAA
1 AG---CCACCAATTT-TGACAAACAAAA
400308 AG
1 AG
400310 GGTGGCTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
24 23 0.53
26 3 0.07
27 17 0.40
ACGTcount: A:0.47, C:0.26, G:0.08, T:0.19
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAAAA
Found at i:401641 original size:19 final size:20
Alignment explanation
Indices: 401596--401659 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 20
401586 CCTTCACCAT
* *
401596 TTATTAAATTAATCATCTTA
1 TTATTAAATTAATAATTTTA
401616 TCT-TT-AATTAATAATTTTA
1 T-TATTAAATTAATAATTTTA
401635 TTATTAAATTAA-AATATTTA
1 TTATTAAATTAATAAT-TTTA
*
401655 ATATT
1 TTATT
401660 TTTCCTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 1 0.03
19 18 0.49
20 17 0.46
21 1 0.03
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATTAAATTAATAATTTTA
Found at i:404819 original size:12 final size:12
Alignment explanation
Indices: 404802--404828 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
404792 TAAAAATTAA
404802 AAATTCAAATTC
1 AAATTCAAATTC
404814 AAATTCAAATTC
1 AAATTCAAATTC
404826 AAA
1 AAA
404829 AAATAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTCAAATTC
Found at i:405099 original size:50 final size:50
Alignment explanation
Indices: 404955--405117 Score: 256
Period size: 50 Copynumber: 3.3 Consensus size: 50
404945 AATAGAAAAT
*
404955 GCATGCATGGGAAAGCATAAAGATTGCAATTGGAGACAAAACATGCAGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
* * * *
405005 GCATGCATGGGAAAACA-CAAAATTGCAATTGGAGACAAAGCATGCGGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
*
405054 GCATGCATGGGAAAGCATAAAAATTGCAATTGAAGACAAAACATGCAGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
*
405104 ACATGCATGGGAAA
1 GCATGCATGGGAAA
405118 TGAAAAAAGC
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
49 44 0.44
50 57 0.56
ACGTcount: A:0.43, C:0.15, G:0.27, T:0.15
Consensus pattern (50 bp):
GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
Found at i:405602 original size:32 final size:31
Alignment explanation
Indices: 405566--405625 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
405556 AGCAAGCATT
405566 AAAGGGGGAAGA-AAGCAACTAAAAAAAAAAAA
1 AAAGGGGGAAGATAAGCAA--AAAAAAAAAAAA
*
405598 AAAGGGGGAGGATAAGCAAAAAAAAAAA
1 AAAGGGGGAAGATAAGCAAAAAAAAAAA
405626 GAATGAGCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 9 0.35
32 11 0.42
33 6 0.23
ACGTcount: A:0.67, C:0.05, G:0.25, T:0.03
Consensus pattern (31 bp):
AAAGGGGGAAGATAAGCAAAAAAAAAAAAAA
Found at i:405684 original size:47 final size:43
Alignment explanation
Indices: 405633--405727 Score: 109
Period size: 47 Copynumber: 2.1 Consensus size: 43
405623 AAAGAATGAG
*
405633 CAGCAAAAAACAACAGCAACAGCTCCAGTAGCCAACGACTGCAACTC
1 CAGCAAAAAACAACAGCAACAACTCC---AG-CAACGACTGCAACTC
*** *
405680 CAGCACGCAACAACAGCAGCAACTCCAGCAACGACTGCAACTC
1 CAGCAAAAAACAACAGCAACAACTCCAGCAACGACTGCAACTC
405723 CAGCA
1 CAGCA
405728 CGCAACAGCA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
43 20 0.47
44 2 0.05
47 21 0.49
ACGTcount: A:0.40, C:0.37, G:0.16, T:0.07
Consensus pattern (43 bp):
CAGCAAAAAACAACAGCAACAACTCCAGCAACGACTGCAACTC
Found at i:405743 original size:37 final size:39
Alignment explanation
Indices: 405665--405764 Score: 116
Period size: 43 Copynumber: 2.5 Consensus size: 39
405655 CTCCAGTAGC
405665 CAACGACTGCAACTCCAGCACGCAACAACAGCAGCAACTCCAG
1 CAACGACTGCAACTCCAGCACG--ACAACAGCAG--ACTCCAG
405708 CAACGACTGCAACTCCAGCACG-CAACAGCAG-CTCCAG
1 CAACGACTGCAACTCCAGCACGACAACAGCAGACTCCAG
* *
405745 CGA-GAGCAGCAACTCCAGCA
1 CAACGA-CTGCAACTCCAGCA
405765 GGTAGCAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
36 2 0.04
37 21 0.39
40 9 0.17
43 22 0.41
ACGTcount: A:0.35, C:0.39, G:0.19, T:0.07
Consensus pattern (39 bp):
CAACGACTGCAACTCCAGCACGACAACAGCAGACTCCAG
Found at i:405760 original size:18 final size:18
Alignment explanation
Indices: 405694--405764 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
405684 ACGCAACAAC
405694 AGCAGCAACTCCAGCAACG
1 AGCAGCAACTCCAGC-ACG
*
405713 A-CTGCAACTCCAGCACG
1 AGCAGCAACTCCAGCACG
* *
405730 CAACAGCAGCTCCAGCGA-G
1 -AGCAGCAACTCCAGC-ACG
405749 AGCAGCAACTCCAGCA
1 AGCAGCAACTCCAGCA
405765 GGTAGCAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.09
18 26 0.59
19 13 0.30
20 1 0.02
ACGTcount: A:0.34, C:0.38, G:0.21, T:0.07
Consensus pattern (18 bp):
AGCAGCAACTCCAGCACG
Found at i:406801 original size:53 final size:50
Alignment explanation
Indices: 406693--406813 Score: 147
Period size: 53 Copynumber: 2.3 Consensus size: 50
406683 CAATTGCTCG
406693 TAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCCTT
1 TAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTT-CTT
* **
406744 TAATCGAGGGGATACTCCAACCCCGGTTTTA-TTTCTAAAATATTAATTT-TT
1 TAATC--GGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTCTT
406795 CATAATCGGGGATACTCCA
1 --TAATCGGGGATACTCCA
406814 GTCCCGTTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
51 19 0.31
52 4 0.06
53 39 0.63
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (50 bp):
TAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTT
Found at i:406886 original size:79 final size:79
Alignment explanation
Indices: 406750--407135 Score: 628
Period size: 79 Copynumber: 4.9 Consensus size: 79
406740 CCTTTAATCG
*
406750 AGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCATAATCGGGGATACTCCAG
1 AGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCATAATCGGGGATACTCCAA
* *
406815 TCCCGTTATTTTCA
66 CCCCGTTATTTCCA
* *
406829 AGGGAATACTCCAACCCTGGTTTTATTTCTAAAATATTAATTTTTCATAATCGGGGATACTCCAA
1 AGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCATAATCGGGGATACTCCAA
* *
406894 TCCCGTTATTTTCA
66 CCCCGTTATTTCCA
* *
406908 AGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAG
1 AGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCATAATCGGGGATACTCCAA
*
406973 CCCCGTTATTTCCG
66 CCCCGTTATTTCCA
* * *
406987 AGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAA
1 AGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCATAATCGGGGATACTCCAA
407052 CCCCGTTATTTCCA
66 CCCCGTTATTTCCA
* * *
407066 AGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCTAA
1 AGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCATAATCGGGGATACTCCAA
407131 CCCCG
66 CCCCG
407136 ATTTTATTTT
Statistics
Matches: 289, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 289 1.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (79 bp):
AGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCATAATCGGGGATACTCCAA
CCCCGTTATTTCCA
Found at i:407215 original size:53 final size:50
Alignment explanation
Indices: 407067--407214 Score: 172
Period size: 53 Copynumber: 2.9 Consensus size: 50
407057 TTATTTCCAA
* *
407067 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATC
1 GGGGATACTCTAACCCC-GTTTTATTTCTAAAACACCAATTTTTCATAATC
* *
407118 GGGGATACTCTAACCCCGATTTTATTTTTTTAGAACACC-ATTTTTCCATAATC
1 GGGGATACTCTAACCCCG-TTTTA--TTTCTAAAACACCAATTTTT-CATAATC
* * *
407171 GGGGATACTCTAGCCCCGTTGTTATCTCTAAAATACCAATTTTT
1 GGGGATACTCTAACCCCGTT-TTATTTCTAAAACACCAATTTTT
407215 TTCTCGTCAG
Statistics
Matches: 82, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
50 1 0.01
51 30 0.37
52 14 0.17
53 37 0.45
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (50 bp):
GGGGATACTCTAACCCCGTTTTATTTCTAAAACACCAATTTTTCATAATC
Found at i:413379 original size:60 final size:60
Alignment explanation
Indices: 413286--413557 Score: 449
Period size: 60 Copynumber: 4.5 Consensus size: 60
413276 TAGCCCTTCA
* *
413286 AGTCCTCAAAGAGCAGGACACCTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACACCTCTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTT
413346 AGTCCTCAAAGAGCAGGACACCTCTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACACCTCTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTT
* *
413406 AGTCCTCAAAGAGCAGGACAACTTCTTCCTTTTAAAGCTCACACGAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGAC-ACCTCTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTT
* *
413467 AGTCCTCAAAGAGCAGGACACCTCTT-CTTTTAAAGCCCACACAAGTTGGTGGCACTTCTT
1 AGTCCTCAAAGAGCAGGACACCTCTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCT-TT
413527 AGTCCTCAAAGAGCAGGACA-CTCTCTCCTTT
1 AGTCCTCAAAGAGCAGGACACCTCT-TCCTTT
413558 CACCCTTTAG
Statistics
Matches: 200, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
59 32 0.16
60 106 0.53
61 62 0.31
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (60 bp):
AGTCCTCAAAGAGCAGGACACCTCTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTT
Found at i:413529 original size:121 final size:120
Alignment explanation
Indices: 413286--413546 Score: 452
Period size: 121 Copynumber: 2.2 Consensus size: 120
413276 TAGCCCTTCA
* *
413286 AGTCCTCAAAGAGCAGGACACCTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTAGTCC
1 AGTCCTCAAAGAGCAGGACAACTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTAGTCC
*
413351 TCAAAGAGCAGGACACCTCTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTT
66 TCAAAGAGCAGGACACCTCTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
*
413406 AGTCCTCAAAGAGCAGGACAACTTCTTCCTTTTAAAGCTCACACGAGTTGGTGGCACCTTTAGTC
1 AGTCCTCAAAGAGCAGGACAACTT-TTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTAGTC
*
413471 CTCAAAGAGCAGGACACCTCTT-CTTTTAAAGCCCACACAAGTTGGTGGCACTTCTT
65 CTCAAAGAGCAGGACACCTCTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT-TT
413527 AGTCCTCAAAGAGCAGGACA
1 AGTCCTCAAAGAGCAGGACA
413547 CTCTCTCCTT
Statistics
Matches: 134, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
120 52 0.39
121 82 0.61
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (120 bp):
AGTCCTCAAAGAGCAGGACAACTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTAGTCC
TCAAAGAGCAGGACACCTCTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:413642 original size:62 final size:61
Alignment explanation
Indices: 413566--414014 Score: 570
Period size: 62 Copynumber: 7.3 Consensus size: 61
413556 TTCACCCTTT
* *
413566 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-C
* *
413628 GGTCCTCAAAGAGCAGGACGCCTTTTCC-TTTCAAAGCCCACACAAGCTGGTGGCACCTTTTC
1 AGTCCTCAAAGAGCAGGACG-CTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTTC
* * ** * *
413690 AGTCCTCAAAAAGCAGGACACCTTCGCCTTTT-AAAGCCCACACAAGCTGGTGGCACCTTT-
1 AGTCCTCAAAGAGCAGGAC-GCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
413750 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGCTGGTGGCACCTTT-
1 AGTCCTCAAAGAGCAGGACG-CTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
413810 AGTCTTCAAAGAGCAGGACGC-TTTCGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTC
1 AGTCCTCAAAGAGCAGGACGCTTTTC-CTTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTTC
* *
413872 AGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACGCAAGTTGGTGGCACTTTTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-C
* * *
413934 AGTCCTCAAAGAGCAGGACGCCTTTT-CTTTTCAAAAAGCCCACACGAGTTGGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGACG-CTTTTCCTTTTC--AAAGCCCACACAAGTTGGTGGCACTTTTC
*
413997 AGCCCTCAAAGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
414015 TACAATTTAT
Statistics
Matches: 346, Mismatches: 27, Indels: 27
0.87 0.07 0.07
Matches are distributed among these distances:
58 4 0.01
59 5 0.01
60 97 0.28
61 11 0.03
62 165 0.48
63 40 0.12
64 24 0.07
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (61 bp):
AGTCCTCAAAGAGCAGGACGCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
Found at i:413786 original size:122 final size:124
Alignment explanation
Indices: 413558--414014 Score: 583
Period size: 122 Copynumber: 3.7 Consensus size: 124
413548 TCTCTCCTTT
* * *** *
413558 CACCCTTT-AGTCCTCAAAGAGCAGGATG-CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 CACCTTTTCAGTCCTCAAAGAGCAGGACGCCTTCGCCTTTTAAAAGCCCACACAAGTTGGTGGCA
* * *
413621 CTTTTCCGGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGCTGGTGG
66 CCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGCTGGTGG
* * *
413681 CACCTTTTCAGTCCTCAAAAAGCAGGACACCTTCGCCTTTT-AAAGCCCACACAAGCTGGTGGCA
1 CACCTTTTCAGTCCTCAAAGAGCAGGACGCCTTCGCCTTTTAAAAGCCCACACAAGTTGGTGGCA
413745 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGCTGGTGG
66 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGCTGGTGG
* * *
413803 CACC-TTT-AGTCTTCAAAGAGCAGGACGCTTTCGCC-TTTCAAAGCCCACACAAGTTGGTGGCA
1 CACCTTTTCAGTCCTCAAAGAGCAGGACGCCTTCGCCTTTTAAAAGCCCACACAAGTTGGTGGCA
* * *
413865 CTTTTTCAGTCCTCAAAGAGCAGGACGCC-TTTCCTTTTCAAAGCCCACGCAAGTTGGTGG
66 C-CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGCTGGTGG
** *
413925 CA-CTTTTCCAGTCCTCAAAGAGCAGGACGCCTT-TTCTTTTCAAAAAGCCCACACGAGTTGGTG
1 CACCTTTT-CAGTCCTCAAAGAGCAGGACGCCTTCGCCTTTT--AAAAGCCCACACAAGTTGGTG
* *
413988 GCACCTTCCAGCCCTCAAAGAGCAGGA
63 GCACCTTTCAGTCCTCAAAGAGCAGGA
414015 TACAATTTAT
Statistics
Matches: 294, Mismatches: 28, Indels: 22
0.85 0.08 0.06
Matches are distributed among these distances:
119 3 0.01
120 47 0.16
121 16 0.05
122 101 0.34
123 8 0.03
124 68 0.23
125 28 0.10
126 23 0.08
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (124 bp):
CACCTTTTCAGTCCTCAAAGAGCAGGACGCCTTCGCCTTTTAAAAGCCCACACAAGTTGGTGGCA
CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGCTGGTGG
Found at i:414725 original size:12 final size:12
Alignment explanation
Indices: 414708--414734 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
414698 TAAAAATTAA
414708 AAATTCAAATTC
1 AAATTCAAATTC
414720 AAATTCAAATTC
1 AAATTCAAATTC
414732 AAA
1 AAA
414735 AAATAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTCAAATTC
Found at i:415004 original size:50 final size:50
Alignment explanation
Indices: 414860--415022 Score: 256
Period size: 50 Copynumber: 3.3 Consensus size: 50
414850 AATAGAAAAT
*
414860 GCATGCATGGGAAAGCATAAAGATTGCAATTGGAGACAAAACATGCAGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
* * * *
414910 GCATGCATGGGAAAACA-CAAAATTGCAATTGGAGACAAAGCATGCGGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
*
414959 GCATGCATGGGAAAGCATAAAAATTGCAATTGAAGACAAAACATGCAGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
*
415009 ACATGCATGGGAAA
1 GCATGCATGGGAAA
415023 TGAAAAAAGC
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
49 44 0.44
50 57 0.56
ACGTcount: A:0.43, C:0.15, G:0.27, T:0.15
Consensus pattern (50 bp):
GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
Found at i:415274 original size:6 final size:6
Alignment explanation
Indices: 415263--415294 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
415253 AGCAAGGTGA
415263 AGCAAC AGCAAC AGCAAC AGCAACC AGCAAC A
1 AGCAAC AGCAAC AGCAAC AGCAA-C AGCAAC A
415295 TCAAACACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.50, C:0.34, G:0.16, T:0.00
Consensus pattern (6 bp):
AGCAAC
Found at i:415592 original size:47 final size:43
Alignment explanation
Indices: 415541--415635 Score: 109
Period size: 47 Copynumber: 2.1 Consensus size: 43
415531 AAAGAATGAG
*
415541 CAGCAAAAAACAACAGCAACAGCTCCAGTAGCCAACGACTGCAACTC
1 CAGCAAAAAACAACAGCAACAACTCC---AG-CAACGACTGCAACTC
*** *
415588 CAGCACGCAACAACAGCAGCAACTCCAGCAACGACTGCAACTC
1 CAGCAAAAAACAACAGCAACAACTCCAGCAACGACTGCAACTC
415631 CAGCA
1 CAGCA
415636 CGCAACAGCA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
43 20 0.47
44 2 0.05
47 21 0.49
ACGTcount: A:0.40, C:0.37, G:0.16, T:0.07
Consensus pattern (43 bp):
CAGCAAAAAACAACAGCAACAACTCCAGCAACGACTGCAACTC
Found at i:415651 original size:37 final size:39
Alignment explanation
Indices: 415573--415672 Score: 116
Period size: 43 Copynumber: 2.5 Consensus size: 39
415563 CTCCAGTAGC
415573 CAACGACTGCAACTCCAGCACGCAACAACAGCAGCAACTCCAG
1 CAACGACTGCAACTCCAGCACG--ACAACAGCAG--ACTCCAG
415616 CAACGACTGCAACTCCAGCACG-CAACAGCAG-CTCCAG
1 CAACGACTGCAACTCCAGCACGACAACAGCAGACTCCAG
* *
415653 CGA-GAGCAGCAACTCCAGCA
1 CAACGA-CTGCAACTCCAGCA
415673 GGTAGCAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
36 2 0.04
37 21 0.39
40 9 0.17
43 22 0.41
ACGTcount: A:0.35, C:0.39, G:0.19, T:0.07
Consensus pattern (39 bp):
CAACGACTGCAACTCCAGCACGACAACAGCAGACTCCAG
Found at i:415668 original size:18 final size:18
Alignment explanation
Indices: 415602--415672 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
415592 ACGCAACAAC
415602 AGCAGCAACTCCAGCAACG
1 AGCAGCAACTCCAGC-ACG
*
415621 A-CTGCAACTCCAGCACG
1 AGCAGCAACTCCAGCACG
* *
415638 CAACAGCAGCTCCAGCGA-G
1 -AGCAGCAACTCCAGC-ACG
415657 AGCAGCAACTCCAGCA
1 AGCAGCAACTCCAGCA
415673 GGTAGCAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.09
18 26 0.59
19 13 0.30
20 1 0.02
ACGTcount: A:0.34, C:0.38, G:0.21, T:0.07
Consensus pattern (18 bp):
AGCAGCAACTCCAGCACG
Found at i:416708 original size:53 final size:50
Alignment explanation
Indices: 416600--416720 Score: 147
Period size: 53 Copynumber: 2.3 Consensus size: 50
416590 CAATTGCTCG
416600 TAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCCTT
1 TAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTT-CTT
* **
416651 TAATCGAGGGGATACTCCAACCCCGGTTTTA-TTTCTAAAATATTAATTT-TT
1 TAATC--GGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTCTT
416702 CATAATCGGGGATACTCCA
1 --TAATCGGGGATACTCCA
416721 GTCCCGTTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
51 19 0.31
52 4 0.06
53 39 0.63
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (50 bp):
TAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTT
Done.