Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015333.1 Kokia drynarioides strain JFW-HI SEQ_130380, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 503969
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 387 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1787 original size:14 final size:13
Alignment explanation
Indices: 1770--1822 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
1760 CATCTTGACT
1770 TTTTTCTTCTTTTC
1 TTTTTCTT-TTTTC
*
1784 -TTTTATTTTTTC
1 TTTTTCTTTTTTC
*
1796 TTTTTCATTTTTC
1 TTTTTCTTTTTTC
1809 ATTTTTCATTTTTT
1 -TTTTTC-TTTTTT
1823 TTCTTGGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
12 5 0.16
13 16 0.50
14 6 0.19
15 5 0.16
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:1799 original size:6 final size:7
Alignment explanation
Indices: 1790--1821 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
1780 TTTCTTTTAT
1790 TTTTTC-
1 TTTTTCA
1796 TTTTTCA
1 TTTTTCA
1803 TTTTTCA
1 TTTTTCA
1810 TTTTTCA
1 TTTTTCA
1817 TTTTT
1 TTTTT
1822 TTTCTTGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCA
Found at i:5619 original size:109 final size:109
Alignment explanation
Indices: 5431--5632 Score: 298
Period size: 109 Copynumber: 1.9 Consensus size: 109
5421 ACATTTAACA
* ** *
5431 ATTTTAAATAGGATATTCAATTATTTAGGTTCAAGGAAAAATCATACCCAACATGTTTTGGCATA
1 ATTTTAAATAGGATATTCAATTATTTAGGTTCAAAGAAAAATCATACCCAACATGTTAGGGCACA
* * *
5496 ATTTCTCGAGTTCCCTAAAATAATAGAACATTGAGTATTTATCG
66 ATTTCTCGAATTCCCAAAAATAAAAGAACATTGAGTATTTATCG
* * *
5540 ATTTTGAATAGGATATTCAATTATTTAGGTTCAAAGAAAAATCGTACCCAATACT-TTAGGGCAC
1 ATTTTAAATAGGATATTCAATTATTTAGGTTCAAAGAAAAATCATACCCAACA-TGTTAGGGCAC
5604 AATTTCTCGAATTCCCAAAAATAAAAGAA
65 AATTTCTCGAATTCCCAAAAATAAAAGAA
5633 TATTACCTCG
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
109 81 0.99
110 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (109 bp):
ATTTTAAATAGGATATTCAATTATTTAGGTTCAAAGAAAAATCATACCCAACATGTTAGGGCACA
ATTTCTCGAATTCCCAAAAATAAAAGAACATTGAGTATTTATCG
Found at i:5911 original size:21 final size:21
Alignment explanation
Indices: 5878--5920 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5868 GCACATAGAT
5878 AATGCAATAAC-AAATACACAA
1 AATGCAATAACAAAATA-ACAA
* *
5899 AATGCATTCACAAAATAACAA
1 AATGCAATAACAAAATAACAA
5920 A
1 A
5921 TCAAATAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.60, C:0.19, G:0.05, T:0.16
Consensus pattern (21 bp):
AATGCAATAACAAAATAACAA
Found at i:8504 original size:39 final size:39
Alignment explanation
Indices: 8396--8561 Score: 190
Period size: 40 Copynumber: 4.2 Consensus size: 39
8386 ATAGCTTTAG
* * * *
8396 GGGTAAAAGATTGGATTGTTTCAATTTGCTCCATGGTCA
1 GGGTAAAAGATCGGATTGCTTCAATCTGCCCCATGGTCA
* * *
8435 GGGTAAGAGATCGGATGTTCTTCAATCTGCCCTC-TGGTTA
1 GGGTAAAAGATCGGAT-TGCTTCAATCTGCCC-CATGGTCA
* *
8475 GGGTAAAAGATTGGATTGCTTCAAGCTGCCCCATGGTCA
1 GGGTAAAAGATCGGATTGCTTCAATCTGCCCCATGGTCA
* *
8514 GGGTAAAAGATCGGATGGTCTTCAATCTGCCTCATGGTCA
1 GGGTAAAAGATCGGATTG-CTTCAATCTGCCCCATGGTCA
*
8554 AGGTAAAA
1 GGGTAAAA
8562 TATTAGATGT
Statistics
Matches: 106, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.01
39 48 0.45
40 56 0.53
41 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (39 bp):
GGGTAAAAGATCGGATTGCTTCAATCTGCCCCATGGTCA
Found at i:8527 original size:79 final size:79
Alignment explanation
Indices: 8396--8561 Score: 244
Period size: 79 Copynumber: 2.1 Consensus size: 79
8386 ATAGCTTTAG
* ** * * *
8396 GGGTAAAAGATTGGATTGTTTCAATTTGCTCCATGGTCAGGGTAAGAGATCGGATGTTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAAGCTGCCCCATGGTCAGGGTAAAAGATCGGATGGTCTTCAAT
*
8461 CTGCCCTC-TGGTTA
66 CTG-CCTCATGGTCA
8475 GGGTAAAAGATTGGATTGCTTCAAGCTGCCCCATGGTCAGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAAGCTGCCCCATGGTCAGGGTAAAAGATCGGATGGTCTTCAAT
8540 CTGCCTCATGGTCA
66 CTGCCTCATGGTCA
*
8554 AGGTAAAA
1 GGGTAAAA
8562 TATTAGATGT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
78 4 0.05
79 74 0.95
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (79 bp):
GGGTAAAAGATTGGATTGCTTCAAGCTGCCCCATGGTCAGGGTAAAAGATCGGATGGTCTTCAAT
CTGCCTCATGGTCA
Found at i:16128 original size:12 final size:12
Alignment explanation
Indices: 16111--16136 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16101 TTGATACTCG
16111 ATCTGGTTGCCT
1 ATCTGGTTGCCT
16123 ATCTGGTTGCCT
1 ATCTGGTTGCCT
16135 AT
1 AT
16137 GTAACTGGTC
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:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (12 bp):
ATCTGGTTGCCT
Found at i:22200 original size:30 final size:30
Alignment explanation
Indices: 22118--22210 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
22108 AAATTGGGGC
* ** *
22118 AAATTCAAATTTTTGAAAAGTTCGAGGGTC
1 AAATTCGAATTTTTGAAAAGTTTAAGGGTT
*
22148 AAATTGGAATTTTTGAAAAGTTTAAGGGTT
1 AAATTCGAATTTTTGAAAAGTTTAAGGGTT
* *
22178 AAATTCGAATTTTTTG-ATAGTTTAGGGGTT
1 AAATTCGAA-TTTTTGAAAAGTTTAAGGGTT
22208 AAA
1 AAA
22211 ACATAATTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
30 48 0.89
31 6 0.11
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (30 bp):
AAATTCGAATTTTTGAAAAGTTTAAGGGTT
Found at i:24801 original size:7 final size:7
Alignment explanation
Indices: 24789--24819 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
24779 AATGTAGTAA
24789 TTAGGGT
1 TTAGGGT
24796 TTAGGGT
1 TTAGGGT
24803 TTAGGGT
1 TTAGGGT
*
24810 TTAAGGT
1 TTAGGGT
24817 TTA
1 TTA
24820 TATAATTTAT
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:0.19, C:0.00, G:0.35, T:0.45
Consensus pattern (7 bp):
TTAGGGT
Found at i:26019 original size:31 final size:31
Alignment explanation
Indices: 25984--26070 Score: 81
Period size: 31 Copynumber: 2.8 Consensus size: 31
25974 ATGATTAAAT
25984 CAAAATTAAAGTTTCAAGTATATATTTGA-AC
1 CAAAATTAAAGTTTCAAGTATATATTT-ACAC
* * * * *
26015 CAAAATTAGATTTTCACGTGTATAATTACAC
1 CAAAATTAAAGTTTCAAGTATATATTTACAC
*
26046 C-AAATTAAAG-TTCATGTATACTATT
1 CAAAATTAAAGTTTCAAGTATA-TATT
26071 GCATATTAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
29 8 0.18
30 11 0.25
31 25 0.57
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (31 bp):
CAAAATTAAAGTTTCAAGTATATATTTACAC
Found at i:26418 original size:22 final size:21
Alignment explanation
Indices: 26393--26473 Score: 96
Period size: 22 Copynumber: 3.9 Consensus size: 21
26383 TTTGATGCTG
26393 TTTTTTACTGTTTTGGTTGCTA
1 TTTTTTACTGTTTTGGTTG-TA
*
26415 TTTTTTGCTGTTTTGGTGTTGTA
1 TTTTTTACTGTTTT-G-GTTGTA
*
26438 -TTTTTACTGTTTTAGTT-T-
1 TTTTTTACTGTTTTGGTTGTA
26456 TTTTTTACTGTTTTGGTT
1 TTTTTTACTGTTTTGGTT
26474 ACTGTTTTGG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
19 17 0.33
20 3 0.06
22 25 0.48
23 3 0.06
24 4 0.08
ACGTcount: A:0.07, C:0.06, G:0.19, T:0.68
Consensus pattern (21 bp):
TTTTTTACTGTTTTGGTTGTA
Found at i:26439 original size:23 final size:22
Alignment explanation
Indices: 26380--26473 Score: 92
Period size: 22 Copynumber: 4.5 Consensus size: 22
26370 ATTATATTGT
* *
26380 TGTTTT-GATGCTGTTTTTTAC
1 TGTTTTGGTTGCTATTTTTTAC
*
26401 TGTTTTGGTTGCTATTTTTTGC
1 TGTTTTGGTTGCTATTTTTTAC
26423 TGTTTTGGTGTTG-TA-TTTTTAC
1 TGTTTT-G-GTTGCTATTTTTTAC
*
26445 TGTTTTAGTT--T-TTTTTTAC
1 TGTTTTGGTTGCTATTTTTTAC
26464 TGTTTTGGTT
1 TGTTTTGGTT
26474 ACTGTTTTGG
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
19 17 0.27
20 3 0.05
21 6 0.10
22 30 0.48
23 3 0.05
24 4 0.06
ACGTcount: A:0.07, C:0.06, G:0.20, T:0.66
Consensus pattern (22 bp):
TGTTTTGGTTGCTATTTTTTAC
Found at i:26444 original size:44 final size:40
Alignment explanation
Indices: 26380--26481 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 40
26370 ATTATATTGT
* * *
26380 TGTTTTGATGCTGTTTTTTACTGTTTTGGTTGCTATTTTTTGC
1 TGTTTTGGTGCTGTTTTTTACTGTTTTAGTT--T-TTTTTTAC
*
26423 TGTTTTGGTGTTGTATTTTTACTGTTTTAGTTTTTTTTTAC
1 TGTTTTGGTGCTGT-TTTTTACTGTTTTAGTTTTTTTTTAC
*
26464 TGTTTTGGTTACTGTTTT
1 TGTTTTGG-TGCTGTTTT
26482 GGTGCTATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
41 18 0.35
42 5 0.10
43 12 0.24
44 16 0.31
ACGTcount: A:0.08, C:0.07, G:0.20, T:0.66
Consensus pattern (40 bp):
TGTTTTGGTGCTGTTTTTTACTGTTTTAGTTTTTTTTTAC
Found at i:26475 original size:12 final size:12
Alignment explanation
Indices: 26460--26504 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
26450 TAGTTTTTTT
26460 TTACTGTTTTGG
1 TTACTGTTTTGG
26472 TTACTGTTTTGG
1 TTACTGTTTTGG
26484 TGCTA-T-TTTTGG
1 T--TACTGTTTTGG
26496 TTACTGTTT
1 TTACTGTTT
26505 GTTGCTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.07
11 1 0.03
12 23 0.79
13 1 0.03
14 2 0.07
ACGTcount: A:0.09, C:0.09, G:0.22, T:0.60
Consensus pattern (12 bp):
TTACTGTTTTGG
Found at i:26517 original size:24 final size:24
Alignment explanation
Indices: 26466--26516 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
26456 TTTTTTACTG
26466 TTTTGGTTACTGTTTTGGTGCTAT
1 TTTTGGTTACTGTTTTGGTGCTAT
*
26490 TTTTGGTTACTG-TTTGTTGCTAT
1 TTTTGGTTACTGTTTTGGTGCTAT
26513 TTTT
1 TTTT
26517 TCTATTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.08, C:0.08, G:0.22, T:0.63
Consensus pattern (24 bp):
TTTTGGTTACTGTTTTGGTGCTAT
Found at i:27380 original size:16 final size:16
Alignment explanation
Indices: 27359--27408 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
27349 CTGGGATGAG
27359 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
*
27375 AATAAA-ATTTAATTA
1 AATAAATTTTTAATTA
*
27390 ATTGAAATTTTTATATTA
1 AAT-AAATTTTTA-ATTA
27408 A
1 A
27409 TTACAACTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 10 0.36
16 9 0.32
17 4 0.14
18 5 0.18
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:28689 original size:16 final size:16
Alignment explanation
Indices: 28661--28693 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
28651 AGATGACTAT
28661 ATAAAAAATTTTAATAA
1 ATAAAAAATTTT-ATAA
28678 ATAAAAAA-TTTATAA
1 ATAAAAAATTTTATAA
28693 A
1 A
28694 ATTATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 3 0.19
17 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAAAAATTTTATAA
Found at i:29419 original size:3 final size:3
Alignment explanation
Indices: 29411--29447 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
29401 ATATTCTGAT
29411 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
29448 ATTTTTTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:32282 original size:17 final size:17
Alignment explanation
Indices: 32260--32293 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
32250 ATCTGAGTCT
32260 ATGAACACAAGTATATC
1 ATGAACACAAGTATATC
*
32277 ATGAACACAAGTCTATC
1 ATGAACACAAGTATATC
32294 TCGACCTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.24
Consensus pattern (17 bp):
ATGAACACAAGTATATC
Found at i:34833 original size:20 final size:21
Alignment explanation
Indices: 34808--34847 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
34798 TTTTCAATGA
34808 ATTTTTATTTATA-AAATTAT
1 ATTTTTATTTATATAAATTAT
*
34828 ATTTTTATTTTTATAAATTA
1 ATTTTTATTTATATAAATTA
34848 AATAAAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTATTTATATAAATTAT
Found at i:37471 original size:59 final size:60
Alignment explanation
Indices: 37367--37534 Score: 177
Period size: 59 Copynumber: 2.8 Consensus size: 60
37357 TAAATTTAAT
* * *
37367 ATATATTTTT-TAATTTGGTATTTAAA--ATTTTTGAC-CTAATTTGGTATTTGAATTTGAC
1 ATAT-TTTTTCTAATTTGGTATCTAAACTTTTTTTGACTC-AATTTGGTACTTGAATTTGAC
* *
37425 A-ATTTTTTCTTATTT-GTTTCCTAAACTTTTTTTGACTCAATTTGGTACTTGAATTTGAC
1 ATATTTTTTCTAATTTGGTAT-CTAAACTTTTTTTGACTCAATTTGGTACTTGAATTTGAC
* * *
37484 ATTTTTTTTTCTAATTTGGTATCTAAGCTTTTTTTAGATTCAATTTGGTAC
1 A-TATTTTTTCTAATTTGGTATCTAAACTTTTTTT-GACTCAATTTGGTAC
37535 CTAAATTTAT
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
56 8 0.09
57 11 0.12
58 1 0.01
59 29 0.32
60 1 0.01
61 24 0.26
62 17 0.19
ACGTcount: A:0.24, C:0.10, G:0.11, T:0.55
Consensus pattern (60 bp):
ATATTTTTTCTAATTTGGTATCTAAACTTTTTTTGACTCAATTTGGTACTTGAATTTGAC
Found at i:37853 original size:19 final size:17
Alignment explanation
Indices: 37814--37848 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
37804 ATAAATTGAA
37814 AAAAAAAAGATATCAAAT
1 AAAAAAAA-ATATCAAAT
37832 AAAAAAAAATATCAAAT
1 AAAAAAAAATATCAAAT
37849 CTAAATAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAAAAAAATATCAAAT
Found at i:37937 original size:3 final size:3
Alignment explanation
Indices: 37929--37961 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
37919 ACGTAAGGAC
*
37929 TTA TTA TTA TTA TTA TTA TTA TT- TTA TTC TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
37962 AACATGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:41148 original size:14 final size:16
Alignment explanation
Indices: 41117--41150 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
41107 ATAATTTTTT
41117 TTATAAAGATTATATA
1 TTATAAAGATTATATA
41133 TTATAAA-ATT-TATA
1 TTATAAAGATTATATA
41147 TTAT
1 TTAT
41151 TTTAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 3 0.17
16 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTATAAAGATTATATA
Found at i:41855 original size:19 final size:19
Alignment explanation
Indices: 41822--41861 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
41812 ATTTAATTTT
41822 TATTTATATTAAATTTAAAA
1 TATTTATATTAAA-TTAAAA
*
41842 TATTT-TATTTAATTAAAA
1 TATTTATATTAAATTAAAA
41860 TA
1 TA
41862 CCATGTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTATATTAAATTAAAA
Found at i:42549 original size:21 final size:23
Alignment explanation
Indices: 42525--42571 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
42515 AAATGGTGAG
*
42525 ATTAAATTAAAT-TAAT-TTTAT
1 ATTAAAATAAATATAATGTTTAT
*
42546 ATTAAAATAAATATAATGTTTGT
1 ATTAAAATAAATATAATGTTTAT
42569 ATT
1 ATT
42572 GTTAATGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 4 0.18
23 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
ATTAAAATAAATATAATGTTTAT
Found at i:44657 original size:21 final size:21
Alignment explanation
Indices: 44628--44667 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
44618 ATTAAATTTT
*
44628 TTTCTTTTATGTTCTTTTAAC
1 TTTCCTTTATGTTCTTTTAAC
* *
44649 TTTCCTTTATTTTTTTTTA
1 TTTCCTTTATGTTCTTTTA
44668 TTTTTCATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTCCTTTATGTTCTTTTAAC
Found at i:44673 original size:21 final size:21
Alignment explanation
Indices: 44626--44673 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
44616 AAATTAAATT
*
44626 TTTTTCTTTTATGTTCTTTTA
1 TTTTTCCTTTATGTTCTTTTA
** * *
44647 ACTTTCCTTTATTTTTTTTTA
1 TTTTTCCTTTATGTTCTTTTA
44668 TTTTTC
1 TTTTTC
44674 ATTATCTTCT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTTCCTTTATGTTCTTTTA
Found at i:47418 original size:29 final size:30
Alignment explanation
Indices: 47384--47440 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
47374 AATGATTTCA
47384 TTAG-TTTTTTTTTGTTTAGAACTAAAAAG
1 TTAGTTTTTTTTTTGTTTAGAACTAAAAAG
47413 TTAGTTTTTTTTTTGTTTAGAACTAAAA
1 TTAGTTTTTTTTTTGTTTAGAACTAAAA
47441 CAAAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.30, C:0.04, G:0.12, T:0.54
Consensus pattern (30 bp):
TTAGTTTTTTTTTTGTTTAGAACTAAAAAG
Found at i:47881 original size:18 final size:18
Alignment explanation
Indices: 47860--47898 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
47850 ATTTTGGTTT
47860 TATATATTATA-TCATTTA
1 TATATATTA-AGTCATTTA
*
47878 TATATCTTAAGTCATTTA
1 TATATATTAAGTCATTTA
47896 TAT
1 TAT
47899 CACATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (18 bp):
TATATATTAAGTCATTTA
Found at i:51282 original size:29 final size:30
Alignment explanation
Indices: 51250--51320 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
51240 ATAAGGAAAA
*
51250 TGGGGTCAAAAATGAAA-TTTTGGAAAATT
1 TGGGGTCAAAAATCAAATTTTTGGAAAATT
* * *
51279 TGGGG-GATAAATTCAAATTTTTGGAAAGTT
1 TGGGGTCA-AAAATCAAATTTTTGGAAAATT
51309 TAGGGGTCAAAA
1 T-GGGGTCAAAA
51321 TCTATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
28 1 0.03
29 12 0.36
30 12 0.36
31 7 0.21
32 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (30 bp):
TGGGGTCAAAAATCAAATTTTTGGAAAATT
Found at i:51381 original size:30 final size:30
Alignment explanation
Indices: 51294--51429 Score: 114
Period size: 30 Copynumber: 4.5 Consensus size: 30
51284 GATAAATTCA
* *
51294 AATTTTTGGAAAGTTTAGGGGTCAAAATC-T
1 AATTTTTAGAAAGTTTAAGGGTCAAAA-CAT
* * * * *
51324 ATTTTTTTA-AAAATATAAAGGTAAAAACAT
1 A-ATTTTTAGAAAGTTTAAGGGTCAAAACAT
*
51354 AATTTTTAGAAAGTTTAAGGGTCAAAACAC
1 AATTTTTAGAAAGTTTAAGGGTCAAAACAT
* * ** *
51384 AGTTTTTAGAAAGCTCGAGGGTCAAAATAT
1 AATTTTTAGAAAGTTTAAGGGTCAAAACAT
*
51414 AATTTTTTGAAAGTTT
1 AATTTTTAGAAAGTTT
51430 GGGGGTTAAA
Statistics
Matches: 80, Mismatches: 23, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
29 7 0.09
30 68 0.85
31 5 0.06
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (30 bp):
AATTTTTAGAAAGTTTAAGGGTCAAAACAT
Found at i:52393 original size:124 final size:124
Alignment explanation
Indices: 52125--52710 Score: 782
Period size: 124 Copynumber: 4.7 Consensus size: 124
52115 ATCGGAGCCA
* * * * *
52125 TCTCTGTATCTCGTAAGGAAGATAATCGCTTCATCGTTTTGATCCACTTCTCTATATCTCATCAG
1 TCTCTGTATCTCATCAGGAAGATGACCGCTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAG
* * *
52190 GAAGAT-GAGGTTTGAAGTTTCACTCATATTGAGCTT-AGTTCCATTGTTTTGGTCCACT
66 GAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTT-CATTGTTTTGGTCCACT
* * *
52248 TCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTTTTGGTCCACTTCTCTGTATCTAATCAG
1 TCTCTGTATCTCATCAGGAAGATGACCGCTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAG
* * * ** *
52313 GAAGATGGGGGTTTGAAGTTTCACAT-ACATTAAACTTCGCTAAATTATTTTGGTCCACT
66 GAAGATGGGGGTTTGAAGTTTCAC-TCACATTGAGCTTCACTTCATTGTTTTGGTCCACT
*
52372 TCTCTGTATCTCATCAGGAAGATGACCGCTTCATCGTTTTGATCCACTTCTCTGGATCTCATCAG
1 TCTCTGTATCTCATCAGGAAGATGACCGCTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAG
** * *
52437 GAAGATGGGATTTTGAAGTTTCACTCACATTGAGCTTTACTTCATTGTTTTGGTCTACT
66 GAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGTTTTGGTCCACT
* * * * * *
52496 TCTTTGTATCTCATCAGGAAGAAGATCGCTTCATCATTTTAATCCACTTCTTTGTATCTCATCAG
1 TCTCTGTATCTCATCAGGAAGATGACCGCTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAG
* *
52561 GAAGATGGGGGTTTGAAGTTTCACTTACATTGAGCTTCACTTCATTGTTTTGGTCTACT
66 GAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGTTTTGGTCCACT
* * * ** * * *
52620 TCTTTGTATCTCATCAGGAATATGACCGCTTTATTATTTTGATCCACTTCTTTGTATCTTATCAA
1 TCTCTGTATCTCATCAGGAAGATGACCGCTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAG
*
52685 GAAGATGGTGGTTTGAAGTTTCACTC
66 GAAGATGGGGGTTTGAAGTTTCACTC
52711 TACTTCAACT
Statistics
Matches: 407, Mismatches: 52, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
123 64 0.16
124 341 0.84
125 2 0.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (124 bp):
TCTCTGTATCTCATCAGGAAGATGACCGCTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAG
GAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGTTTTGGTCCACT
Found at i:53093 original size:220 final size:225
Alignment explanation
Indices: 52550--53160 Score: 760
Period size: 220 Copynumber: 2.7 Consensus size: 225
52540 CACTTCTTTG
* * * *
52550 TATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTTACATTGAGCTTCA-CTTCATTGTTTTGG
1 TATCTCATCAGGAAGAT-AGGGTTTGAAGTTTCACTCACATTGAGCTT-AGCTTTATTATTTTGG
* * * * *
52614 TCTACTTCTTTGTATCTCATCAGGAATATGACCGCTTTATTATTTTGATCCACTTCTTTGTATCT
64 TCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTTTTGATCCACTTCTTTGTATCT
* *
52679 TATCAAGAAGAT-GGTGGTTTGAAGTTTCACTCTACTTCAACTCTACTCCACTATAACCTCAGGG
129 CATC-AGAAGATGGGT-GTTTGAAGTTTCACTCTACTT--ACTCTACT---CTATAACCTCAGAG
*
52743 ATGTTGAGCTTTGCTTCATTGTTTTGATCCCTTTCTCTA
187 ATGTTGAGCCTTGCTTCATTGTTTTGATCCCTTTCTCTA
* * * *
52782 TTTTTCATCAGGAAGATA-GGTTTGAAGTTTCACTCACATTGAGCTTTG-TTTCATTATTTTCGT
1 TATCTCATCAGGAAGATAGGGTTTGAAGTTTCACTCACATTGAGCTTAGCTTT-ATTATTTTGGT
* * * * *
52845 TCACTTCTCTGTATCTCTTCAAGAAGATGATCGCTTCATTGTTTTGATTCACTTCTTTGTATCTC
65 CCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTTTTGATCCACTTCTTTGTATCTC
* *
52910 ATCAGCAAGATGGGTGTTTGAAGTTTCACTCTAC-T-C-C-A-T-TGTAACCTGAGAGATGTTGA
130 ATCAG-AAGATGGGTGTTTGAAGTTTCACTCTACTTACTCTACTCTATAACCTCAGAGATGTTGA
* *
52969 GCACTT-CTTTATTGTTTTTATCCCTTTCTCTA
194 GC-CTTGCTTCATTGTTTTGATCCCTTTCTCTA
53001 TATCTCATCAGGAAGATAGGGTTTGAAGTTTCACTCACATTGAGCTTAGCTTTATTATTTTGGTC
1 TATCTCATCAGGAAGATAGGGTTTGAAGTTTCACTCACATTGAGCTTAGCTTTATTATTTTGGTC
* *
53066 CACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTTTTGATCCACTTCTCTATATCTCA
66 CACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTTTTGATCCACTTCTTTGTATCTCA
*
53131 TTAGAAAGATGGGCT-TTTGAAGTTTCACTC
131 TCAG-AAGATGGG-TGTTTGAAGTTTCACTC
53161 ACGTTGAACT
Statistics
Matches: 333, Mismatches: 38, Indels: 28
0.83 0.10 0.07
Matches are distributed among these distances:
219 59 0.18
220 126 0.38
221 4 0.01
223 1 0.00
224 1 0.00
225 1 0.00
226 1 0.00
229 5 0.02
230 117 0.35
231 3 0.01
232 15 0.05
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.42
Consensus pattern (225 bp):
TATCTCATCAGGAAGATAGGGTTTGAAGTTTCACTCACATTGAGCTTAGCTTTATTATTTTGGTC
CACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTTTTGATCCACTTCTTTGTATCTCA
TCAGAAGATGGGTGTTTGAAGTTTCACTCTACTTACTCTACTCTATAACCTCAGAGATGTTGAGC
CTTGCTTCATTGTTTTGATCCCTTTCTCTA
Found at i:53129 original size:48 final size:48
Alignment explanation
Indices: 53049--53141 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
53039 ATTGAGCTTA
* * * *
53049 GCTTTATTATTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACC
1 GCTTCATTATTTTGATCCACTTCTCTATATCTCATCAGAAAGATGACC
* *
53097 GCTTCATTGTTTTGATCCACTTCTCTATATCTCATTAGAAAGATG
1 GCTTCATTATTTTGATCCACTTCTCTATATCTCATCAGAAAGATG
53142 GGCTTTTGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.41
Consensus pattern (48 bp):
GCTTCATTATTTTGATCCACTTCTCTATATCTCATCAGAAAGATGACC
Found at i:53198 original size:124 final size:123
Alignment explanation
Indices: 52979--53213 Score: 307
Period size: 124 Copynumber: 1.9 Consensus size: 123
52969 GCACTTCTTT
* *
52979 ATTGTTTTTATCCCTTTCTCTATATCTCATCAGGAAGATAGGGTTTGAAGTTTCACTCACATTGA
1 ATTGTTTTGATCCCTTTCTCTATATCTCATCAGAAAGATAGGGTTTGAAGTTTCACTCACATTGA
* * * **
53044 GCTTAGCTTTATTATTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTC
66 ACTCAGCTTTATTATTTTGGACCACTTCTCTACATCTCATCAGGAAGATGACCGCTTC
* *
53102 ATTGTTTTGATCCAC-TTCTCTATATCTCATTAGAAAGAT-GGGCTTTTGAAGTTTCACTCACGT
1 ATTGTTTTGATCC-CTTTCTCTATATCTCATCAGAAAGATAGGG--TTTGAAGTTTCACTCACAT
*
53165 TGAACTCCA-CTTTATTGTTTT-GACCTACTTCTCTACATCTCATCAGGAA
63 TGAACT-CAGCTTTATTATTTTGGACC-ACTTCTCTACATCTCATCAGGAA
53214 AATGGGGTTT
Statistics
Matches: 97, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
122 3 0.03
123 37 0.38
124 56 0.58
125 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (123 bp):
ATTGTTTTGATCCCTTTCTCTATATCTCATCAGAAAGATAGGGTTTGAAGTTTCACTCACATTGA
ACTCAGCTTTATTATTTTGGACCACTTCTCTACATCTCATCAGGAAGATGACCGCTTC
Found at i:53387 original size:46 final size:46
Alignment explanation
Indices: 53289--53390 Score: 159
Period size: 46 Copynumber: 2.2 Consensus size: 46
53279 TGAGATAATA
*
53289 GTTTCAATCTACCTCTCTTGACTTAGGGGTAAAAGATTGGATGATG
1 GTTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGATG
** * *
53335 ACTTCAATTTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGATG
1 GTTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGATG
53381 GTTTCAATCT
1 GTTTCAATCT
53391 GTCCCGTGGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (46 bp):
GTTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGATG
Found at i:53429 original size:42 final size:40
Alignment explanation
Indices: 53366--53507 Score: 151
Period size: 42 Copynumber: 3.4 Consensus size: 40
53356 CTTAGGGGTA
** *
53366 AAAGATTGGATGATGGTTTCAATCTGTCCCGTGGTCG-GGAT
1 AAAGATTGGATGATGACTTCAATCTG-CCCATGGTCGAGG-T
* * *
53407 AAGAGATTGGATGATAACTTCAATATGCCCAATAGTCGAGGT
1 AA-AGATTGGATGATGACTTCAATCTGCCC-ATGGTCGAGGT
*
53449 AAAAGATTGGATGATGTCTTCAATCTGCCCCATGGTCGAGGT
1 -AAAGATTGGATGATGACTTCAATCTG-CCCATGGTCGAGGT
53491 AAATGATTGGATGATGA
1 AAA-GATTGGATGATGA
53508 TGTAACTTCA
Statistics
Matches: 84, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
41 8 0.10
42 69 0.82
43 7 0.08
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (40 bp):
AAAGATTGGATGATGACTTCAATCTGCCCATGGTCGAGGT
Found at i:53807 original size:49 final size:49
Alignment explanation
Indices: 53754--54043 Score: 146
Period size: 49 Copynumber: 5.9 Consensus size: 49
53744 CTACTTCTCT
* * *
53754 ACATCTTCAGGGTATAAGATTCACCGTTACAGCTTCAATATTTCCCTTC
1 ACATCTTCAGGGTATAAGATTCGCCGTTGCAGCTTCAATCTTTCCCTTC
* * * * *
53803 ACATC-TCTAAGGTATAAGGTTCGCCGTTGTAGCTTCCATCTTTCTCTATTC
1 ACATCTTC-AGGGTATAAGATTCGCCGTTGCAGCTTCAATCTTTC-C-CTTC
* * * *
53854 AC-T-TT-AGGATGTAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTC
1 ACATCTTCAGGGTATAAGATTCGCCGTTGCAGCTTCAATCTTTCCCTTC
* * * * * * * * * **
53900 ACATC-ACTAAGGTATAAGGTTTGTCATTACGGCTTCAACCTTTCCAATC
1 ACATCTTC-AGGGTATAAGATTCGCCGTTGCAGCTTCAATCTTTCCCTTC
* * * * * *
53949 ACATCTCCAAGGTATAAGATTCACCATTACTA-CTTTAATCTCTT-CCTTC
1 ACATCTTCAGGGTATAAGATTCGCCGTTGC-AGCTTCAATCT-TTCCCTTC
* * * * **
53998 ACAT-TCCTATGGTACAAGATTCGCTGTTGTGGCTTCAATCTTTCCC
1 ACATCTTC-AGGGTATAAGATTCGCCGTTGCAGCTTCAATCTTTCCC
54044 ATCTCGTCTT
Statistics
Matches: 180, Mismatches: 47, Indels: 28
0.71 0.18 0.11
Matches are distributed among these distances:
46 5 0.03
47 2 0.01
48 35 0.19
49 127 0.71
50 6 0.03
51 5 0.03
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (49 bp):
ACATCTTCAGGGTATAAGATTCGCCGTTGCAGCTTCAATCTTTCCCTTC
Found at i:54933 original size:7 final size:6
Alignment explanation
Indices: 54910--54952 Score: 54
Period size: 7 Copynumber: 7.2 Consensus size: 6
54900 TTGCTTTTTC
54910 TTCTTT TT-TTT TTCTTT ATTCTTT TTCCTTT TTC-TT TTCTTT T
1 TTCTTT TTCTTT TTCTTT -TTCTTT TT-CTTT TTCTTT TTCTTT T
54953 CTCTCTCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 10 0.30
6 11 0.33
7 12 0.36
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (6 bp):
TTCTTT
Found at i:54949 original size:18 final size:17
Alignment explanation
Indices: 54897--54971 Score: 57
Period size: 18 Copynumber: 4.4 Consensus size: 17
54887 TTGACCTCCC
*
54897 CTTTTGCTTTTTC--TT
1 CTTTTTCTTTTTCTTTT
54912 CTTTTT-TTTTTCTTTATT
1 CTTTTTCTTTTTC-TT-TT
54930 CTTTTTCCTTTTTCTTTT
1 CTTTTT-CTTTTTCTTTT
* * *
54948 CTTTTCTCTCTCTCTTCT
1 CTTTT-TCTTTTTCTTTT
54966 CTTTTT
1 CTTTTT
54972 TTGGATAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
14 6 0.12
15 5 0.10
17 1 0.02
18 28 0.57
19 3 0.06
20 6 0.12
ACGTcount: A:0.01, C:0.23, G:0.01, T:0.75
Consensus pattern (17 bp):
CTTTTTCTTTTTCTTTT
Found at i:55845 original size:23 final size:24
Alignment explanation
Indices: 55794--55838 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
55784 TTCATCTTGA
55794 CTTTTTCTTCTTTTCTTTTCTTTG
1 CTTTTTCTTCTTTTCTTTTCTTTG
55818 CTTTTTCTT-TTTTCTTTTCTT
1 CTTTTTCTTCTTTTCTTTTCTT
55839 GTGTTTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (24 bp):
CTTTTTCTTCTTTTCTTTTCTTTG
Found at i:55919 original size:17 final size:16
Alignment explanation
Indices: 55890--55932 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
55880 CCCTTTTCTT
55890 TTTCTTTTTTCTTTTA
1 TTTCTTTTTTCTTTTA
55906 TTTCTTTCTTTCTTTTA
1 TTTCTTT-TTTCTTTTA
**
55923 CCTCTTTTTT
1 TTTCTTTTTT
55933 GATAACAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTTTTCTTTTA
Found at i:60309 original size:59 final size:56
Alignment explanation
Indices: 60246--60415 Score: 137
Period size: 59 Copynumber: 2.9 Consensus size: 56
60236 GTCAAAATGA
* ** * * *
60246 AATTTTAGAAAATTTGAGGGCTAAATTTAAATTTTTGGAAAGTTTGGGGGTGAACTTAT
1 AATTTTAGAAAATTTGAGGGCAAAACAT-AATTTTTAGAAAGTTTAGGGGTCAAC--AT
* * * *
60305 AATTTTTGGAAATTTAAAGGTCAAAACATAATTTTTAGAAAGTTTAGGGGTCAACAT
1 AATTTTAGAAAATTT-GAGGGCAAAACATAATTTTTAGAAAGTTTAGGGGTCAACAT
* * * *
60362 AATTTTTAGAAAGTTTGAGAGTCAAAATATAATTTTGA-AAAGTTT-GTGGGTCAA
1 AA-TTTTAGAAAATTTGAG-GGCAAAACATAATTTTTAGAAAGTTTAG-GGGTCAA
60416 AACACCATTT
Statistics
Matches: 91, Mismatches: 16, Indels: 10
0.78 0.14 0.09
Matches are distributed among these distances:
56 1 0.01
57 20 0.22
58 26 0.29
59 36 0.40
60 8 0.09
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.37
Consensus pattern (56 bp):
AATTTTAGAAAATTTGAGGGCAAAACATAATTTTTAGAAAGTTTAGGGGTCAACAT
Found at i:60336 original size:29 final size:30
Alignment explanation
Indices: 60303--60428 Score: 120
Period size: 29 Copynumber: 4.3 Consensus size: 30
60293 GGGTGAACTT
* *
60303 ATAATTTTTGGAAA-TTTAAAGGTCAAAAC
1 ATAATTTTTAGAAAGTTTAGAGGTCAAAAC
*
60332 ATAATTTTTAGAAAGTTTAGGGGTC--AAC
1 ATAATTTTTAGAAAGTTTAGAGGTCAAAAC
*
60360 ATAATTTTTAGAAAGTTT-GAGAGTCAAAAT
1 ATAATTTTTAGAAAGTTTAGAG-GTCAAAAC
* *
60390 ATAATTTTGA-AAAGTTT-GTGGGTCAAAAC
1 ATAATTTTTAGAAAGTTTAG-AGGTCAAAAC
**
60419 ACCATTTTTA
1 ATAATTTTTA
60429 AATAACATAG
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
27 2 0.02
28 24 0.30
29 35 0.43
30 20 0.25
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (30 bp):
ATAATTTTTAGAAAGTTTAGAGGTCAAAAC
Found at i:60361 original size:28 final size:28
Alignment explanation
Indices: 60275--60377 Score: 109
Period size: 28 Copynumber: 3.6 Consensus size: 28
60265 GCTAAATTTA
* * *
60275 AATTTTTGGAAAGTTTGGGGGTGAACTTAT
1 AATTTTTAGAAAGTTTAGGGGTCAAC--AT
* **
60305 AATTTTTGGAAA-TTTAAAGGTCAAAACAT
1 AATTTTTAGAAAGTTTAGGGGTC--AACAT
60334 AATTTTTAGAAAGTTTAGGGGTCAACAT
1 AATTTTTAGAAAGTTTAGGGGTCAACAT
60362 AATTTTTAGAAAGTTT
1 AATTTTTAGAAAGTTT
60378 GAGAGTCAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
28 21 0.33
29 19 0.30
30 20 0.32
31 3 0.05
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (28 bp):
AATTTTTAGAAAGTTTAGGGGTCAACAT
Found at i:60385 original size:28 final size:28
Alignment explanation
Indices: 60329--60386 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
60319 TAAAGGTCAA
*
60329 AACATAATTTTTAGAAAGTTTAGGGGTC
1 AACATAATTTTTAGAAAGTTTAGGAGTC
60357 AACATAATTTTTAGAAAGTTT-GAGAGTC
1 AACATAATTTTTAGAAAGTTTAG-GAGTC
60385 AA
1 AA
60387 AATATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (28 bp):
AACATAATTTTTAGAAAGTTTAGGAGTC
Found at i:60396 original size:30 final size:30
Alignment explanation
Indices: 60234--60417 Score: 141
Period size: 30 Copynumber: 6.3 Consensus size: 30
60224 AGGAAAAACG
*
60234 GGGTCAAAATGA-AA-TTTTAGAAAATTTGA
1 GGGTCAAAAT-ATAATTTTTAGAAAGTTTGA
* * * *
60263 GGG-CTAAATTTAAATTTTTGGAAAGTTTGG
1 GGGTCAAAATAT-AATTTTTAGAAAGTTTGA
* ** * *
60293 GGGTGAACTTATAATTTTTGGAAA-TTTAA
1 GGGTCAAAATATAATTTTTAGAAAGTTTGA
* *
60322 AGGTCAAAACATAATTTTTAGAAAGTTT-A
1 GGGTCAAAATATAATTTTTAGAAAGTTTGA
*
60351 GGGGTC--AACATAATTTTTAGAAAGTTTGA
1 -GGGTCAAAATATAATTTTTAGAAAGTTTGA
* * *
60380 GAGTCAAAATATAATTTTGA-AAAGTTTGT
1 GGGTCAAAATATAATTTTTAGAAAGTTTGA
60409 GGGTCAAAA
1 GGGTCAAAA
60418 CACCATTTTT
Statistics
Matches: 122, Mismatches: 24, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
28 30 0.25
29 44 0.36
30 45 0.37
31 3 0.02
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (30 bp):
GGGTCAAAATATAATTTTTAGAAAGTTTGA
Found at i:60401 original size:28 final size:29
Alignment explanation
Indices: 60234--60417 Score: 119
Period size: 29 Copynumber: 6.3 Consensus size: 29
60224 AGGAAAAACG
*
60234 GGGTCAAAATGA-AATTTTAGAAAATTTGA
1 GGGTCAAAAT-ATAATTTTAGAAAGTTTGA
* * * *
60263 GGG-CTAAATTTAAATTTTTGGAAAGTTTGG
1 GGGTCAAAATAT-AA-TTTTAGAAAGTTTGA
* ** * *
60293 GGGTGAACTTATAATTTTTGGAAA-TTTAA
1 GGGTCAAAATATAA-TTTTAGAAAGTTTGA
* *
60322 AGGTCAAAACATAATTTTTAGAAAGTTT-A
1 GGGTCAAAATATAA-TTTTAGAAAGTTTGA
* *
60351 GGGGTCAACATA-ATTTTTAGAAAGTTTGA
1 -GGGTCAAAATATAATTTTAGAAAGTTTGA
* *
60380 GAGTCAAAATATAATTTT-GAAAAGTTTGT
1 GGGTCAAAATATAATTTTAG-AAAGTTTGA
60409 GGGTCAAAA
1 GGGTCAAAA
60418 CACCATTTTT
Statistics
Matches: 119, Mismatches: 27, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
28 28 0.24
29 50 0.42
30 38 0.32
31 3 0.03
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (29 bp):
GGGTCAAAATATAATTTTAGAAAGTTTGA
Found at i:62216 original size:124 final size:123
Alignment explanation
Indices: 61989--62230 Score: 333
Period size: 124 Copynumber: 2.0 Consensus size: 123
61979 GCTGTCGTTC
* ** * * *
61989 GGCTGAGGATCCACAATTGCTCGTAGAAAAAAGCTGTCAGAGGGATCGTGGACAGCCAGTAAATA
1 GGCTGAAGATCCACAACCGATCGTAGAAAAAAGCTGTCAAAGGGATCGTGGACAGCCAATAAATA
*
62054 AAGTTGCAGTTGGAATCTGCTAAGGCTGTGAATACACAACGAACATTCATTTACATTT
66 AAGTCGCAGTTGGAATCTGCTAAGGCTGTGAATACACAACGAACATTCATTTACATTT
* * *
62112 GGCTGAAGATCCACAACCGATCGTAGATAAAAGCTGTCAAAGGGATCGTTTGA-TGCCCAATAAA
1 GGCTGAAGATCCACAACCGATCGTAGAAAAAAGCTGTCAAAGGGATCG-TGGACAG-CCAATAAA
* * * *
62176 TAAAGTCGCAGTTGGAATCTGTTAAGGCTGTGAGTACACAATGAACATTCGTTTA
64 TAAAGTCGCAGTTGGAATCTGCTAAGGCTGTGAATACACAACGAACATTCATTTA
62231 TGCAGTATGA
Statistics
Matches: 103, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
123 43 0.42
124 60 0.58
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (123 bp):
GGCTGAAGATCCACAACCGATCGTAGAAAAAAGCTGTCAAAGGGATCGTGGACAGCCAATAAATA
AAGTCGCAGTTGGAATCTGCTAAGGCTGTGAATACACAACGAACATTCATTTACATTT
Found at i:65705 original size:29 final size:27
Alignment explanation
Indices: 65672--65781 Score: 125
Period size: 29 Copynumber: 4.0 Consensus size: 27
65662 CTGAAGAATG
65672 GTGGCAAAATTGTAAAATTTAGAAAATCA
1 GTGGCAAAATTGTAAAATTT-GAAAA-CA
65701 GTGGCAAAATTGTAAAATTTG-AAA-A
1 GTGGCAAAATTGTAAAATTTGAAAACA
65726 GTGGCAAAATTGTAAAATCTTGAAAAACA
1 GTGGCAAAATTGTAAAAT-TTG-AAAACA
* * * *
65755 ATGGCAGAACTATAAAATTTGTAAAAC
1 GTGGCAAAATTGTAAAATTTG-AAAAC
65782 GATGGTACAC
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
25 19 0.26
26 3 0.04
27 3 0.04
28 12 0.17
29 35 0.49
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.26
Consensus pattern (27 bp):
GTGGCAAAATTGTAAAATTTGAAAACA
Found at i:65735 original size:54 final size:55
Alignment explanation
Indices: 65672--65780 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 55
65662 CTGAAGAATG
* * * *
65672 GTGGCAAAATTGTAAAAT-TTAGAAAATCAGTGGCAAAATTGTAAAATTTG-AAAA
1 GTGGCAAAATTGTAAAATCTT-GAAAAACAATGGCAAAACTATAAAATTTGTAAAA
*
65726 GTGGCAAAATTGTAAAATCTTGAAAAACAATGGCAGAACTATAAAATTTGTAAAA
1 GTGGCAAAATTGTAAAATCTTGAAAAACAATGGCAAAACTATAAAATTTGTAAAA
65781 CGATGGTACA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
54 42 0.88
55 6 0.12
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (55 bp):
GTGGCAAAATTGTAAAATCTTGAAAAACAATGGCAAAACTATAAAATTTGTAAAA
Found at i:66905 original size:25 final size:26
Alignment explanation
Indices: 66873--66932 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
66863 TTGATCGTTA
66873 ACCATTGACCATTGACTTTCGA-TTG
1 ACCATTGACCATTGACTTTCGAGTTG
*** **
66898 ACCATTGAATGTTGACTTTTTAGTTG
1 ACCATTGACCATTGACTTTCGAGTTG
66924 ACCATTGAC
1 ACCATTGAC
66933 TTTTTTTGGG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 17 0.61
26 11 0.39
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (26 bp):
ACCATTGACCATTGACTTTCGAGTTG
Found at i:80402 original size:5 final size:5
Alignment explanation
Indices: 80392--80486 Score: 106
Period size: 5 Copynumber: 19.0 Consensus size: 5
80382 GGGGTAGGAC
*
80392 ATGAT ATGAT ATGCT ATGAT -TCGAT ATGAT ATGAT ATGAT ATGAT -TCGAT
1 ATGAT ATGAT ATGAT ATGAT AT-GAT ATGAT ATGAT ATGAT ATGAT AT-GAT
* * *
80442 ATGAT ATAAT ATGAT ACGAT ATGTT ATGAT ATGAT CA-GAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT -ATGAT ATGAT
80487 TTGCTATGAA
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
4 3 0.04
5 70 0.92
6 3 0.04
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (5 bp):
ATGAT
Found at i:80495 original size:25 final size:25
Alignment explanation
Indices: 80392--80487 Score: 124
Period size: 25 Copynumber: 3.8 Consensus size: 25
80382 GGGGTAGGAC
*
80392 ATGATATGATATGCTATGATTCGAT
1 ATGATATGATATGATATGATTCGAT
80417 ATGATATGATATGATATGATTCGAT
1 ATGATATGATATGATATGATTCGAT
* * *
80442 ATGATATAATATGATACGATAT-GTT
1 ATGATATGATATGATATGAT-TCGAT
80467 ATGATATGATCA-GATATGATT
1 ATGATATGAT-ATGATATGATT
80488 TGCTATGAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
24 1 0.02
25 60 0.95
26 2 0.03
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (25 bp):
ATGATATGATATGATATGATTCGAT
Found at i:81538 original size:8 final size:8
Alignment explanation
Indices: 81525--81555 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
81515 TAGTTATTTC
81525 TAAAAAAA
1 TAAAAAAA
81533 T-AAAAAA
1 TAAAAAAA
81540 TAAAAAAA
1 TAAAAAAA
81548 TAAAAAAA
1 TAAAAAAA
81556 ATATTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
TAAAAAAA
Found at i:81545 original size:15 final size:15
Alignment explanation
Indices: 81525--81554 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
81515 TAGTTATTTC
81525 TAAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
81540 TAAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
81555 AATATTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
TAAAAAAATAAAAAA
Found at i:85400 original size:21 final size:21
Alignment explanation
Indices: 85370--85426 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
85360 CGCGATACCT
*
85370 AGGTC-CGTGTCGTGACACTC
1 AGGTCTCGTGTCGTGACACCC
**
85390 AGGTCTCGTGTCGCAACACCC
1 AGGTCTCGTGTCGTGACACCC
*
85411 AGGTCTCGTGTTGTGA
1 AGGTCTCGTGTCGTGA
85427 TATAGCAGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (21 bp):
AGGTCTCGTGTCGTGACACCC
Found at i:87616 original size:12 final size:12
Alignment explanation
Indices: 87599--87626 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
87589 TAATATAAAG
87599 AAAATAAGAAGA
1 AAAATAAGAAGA
87611 AAAATAAGAAGA
1 AAAATAAGAAGA
87623 AAAA
1 AAAA
87627 GATGAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAATAAGAAGA
Found at i:96200 original size:23 final size:23
Alignment explanation
Indices: 96153--96197 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
96143 CATTATTTGA
96153 ATGCCCCTTAAAGTTTTGCATTT
1 ATGCCCCTTAAAGTTTTGCATTT
96176 ATGCCCC-TAAAGTTTTGCATTT
1 ATGCCCCTTAAAGTTTTGCATTT
96198 TATTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.42
Consensus pattern (23 bp):
ATGCCCCTTAAAGTTTTGCATTT
Found at i:100058 original size:43 final size:43
Alignment explanation
Indices: 99929--100085 Score: 145
Period size: 43 Copynumber: 3.7 Consensus size: 43
99919 TTGGAGGAAA
* * *
99929 TATATTGGTACACATAGTGCAT-TTCGGACAAGCCGAAGCAAT
1 TATACTGGCACACATAGTGCATCATCGGACAAGCCGAAGCAAT
* * * * **
99971 TATACTGGCACACATAATACATCATCGAATAAATCGAAGCAAT
1 TATACTGGCACACATAGTGCATCATCGGACAAGCCGAAGCAAT
* * * * *
100014 TATGCTGGCTCACACAGTGCATCATCGGACAAGCCAAAGTAAT
1 TATACTGGCACACATAGTGCATCATCGGACAAGCCGAAGCAAT
* * * *
100057 TATATTAGCACACAAAGTGTATCATCGGA
1 TATACTGGCACACATAGTGCATCATCGGA
100086 TAAACTAAAG
Statistics
Matches: 88, Mismatches: 26, Indels: 1
0.77 0.23 0.01
Matches are distributed among these distances:
42 18 0.20
43 70 0.80
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (43 bp):
TATACTGGCACACATAGTGCATCATCGGACAAGCCGAAGCAAT
Found at i:100833 original size:22 final size:24
Alignment explanation
Indices: 100790--100833 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
100780 TGATAAAGTA
100790 TTTTGATATAACAAATTAAAATGT
1 TTTTGATATAACAAATTAAAATGT
*
100814 TTTTGA-ATAA-AAGTTAAAAT
1 TTTTGATATAACAAATTAAAAT
100834 TGACAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAATGT
Found at i:102016 original size:27 final size:27
Alignment explanation
Indices: 101969--102026 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
101959 CATTAGAGCT
* * *
101969 AGAGCTCTAGAGATGGTCTTACAACCA
1 AGAGCTCTAAAGACGGCCTTACAACCA
101996 AGAGCTCTAAAGACGGCCTTACAACCA
1 AGAGCTCTAAAGACGGCCTTACAACCA
102023 AGAG
1 AGAG
102027 AAAAGATCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.17
Consensus pattern (27 bp):
AGAGCTCTAAAGACGGCCTTACAACCA
Found at i:102350 original size:23 final size:23
Alignment explanation
Indices: 102320--102365 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
102310 GGTTATGCAA
102320 ACTTTATTTTTGTGCTCTTGGTG
1 ACTTTATTTTTGTGCTCTTGGTG
102343 ACTTTATTTTTGTGCTCTTGGTG
1 ACTTTATTTTTGTGCTCTTGGTG
102366 CAAATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.13, G:0.22, T:0.57
Consensus pattern (23 bp):
ACTTTATTTTTGTGCTCTTGGTG
Found at i:103465 original size:15 final size:15
Alignment explanation
Indices: 103432--103476 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
103422 CGCGACAAAG
* *
103432 TCTTCCTCTTTCTCG
1 TCTTCTTCTTTCTCT
103447 TCTTC--CTTTCT-T
1 TCTTCTTCTTTCTCT
103459 TCTTCTTCTTTCTCT
1 TCTTCTTCTTTCTCT
103474 TCT
1 TCT
103477 ACCTTCTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.19
13 6 0.23
14 6 0.23
15 9 0.35
ACGTcount: A:0.00, C:0.36, G:0.02, T:0.62
Consensus pattern (15 bp):
TCTTCTTCTTTCTCT
Found at i:106117 original size:14 final size:14
Alignment explanation
Indices: 106098--106124 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
106088 GAATGGACAA
106098 GCATTTAGTGAGAC
1 GCATTTAGTGAGAC
106112 GCATTTAGTGAGA
1 GCATTTAGTGAGA
106125 AGAAACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (14 bp):
GCATTTAGTGAGAC
Found at i:109002 original size:16 final size:16
Alignment explanation
Indices: 108981--109011 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
108971 ACAATTATGT
*
108981 AAATATTATTAAAACC
1 AAATATTAGTAAAACC
108997 AAATATTAGTAAAAC
1 AAATATTAGTAAAAC
109012 AATCTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (16 bp):
AAATATTAGTAAAACC
Found at i:123177 original size:21 final size:21
Alignment explanation
Indices: 123139--123178 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
123129 ACCTACTATT
**
123139 AAGGAGGAAGTTGATGTTGGA
1 AAGGAGGAAGTCCATGTTGGA
*
123160 AAGGAGGAAGTCCTTGTTG
1 AAGGAGGAAGTCCATGTTG
123179 AATATGTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.05, G:0.40, T:0.25
Consensus pattern (21 bp):
AAGGAGGAAGTCCATGTTGGA
Found at i:127733 original size:24 final size:24
Alignment explanation
Indices: 127705--127779 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
127695 CCAAACAATC
127705 AAAATAACAATCAAAACAG-AAGCA
1 AAAATAACAATCAAAACAGCAA-CA
* * *
127729 AAAATAAAAATAAAAATAGCAACA
1 AAAATAACAATCAAAACAGCAACA
* *
127753 AAAATAACAACCAAAACAGCACCA
1 AAAATAACAATCAAAACAGCAACA
127777 AAA
1 AAA
127780 CAGTAAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 40 0.95
25 2 0.05
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.08
Consensus pattern (24 bp):
AAAATAACAATCAAAACAGCAACA
Found at i:127850 original size:21 final size:21
Alignment explanation
Indices: 127826--127866 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
127816 CAAAATAGTA
127826 AAAAATAGCA-ACAAAAACAGG
1 AAAAATA-CACACAAAAACAGG
127847 AAAAATACAGCACAAAAACA
1 AAAAATACA-CACAAAAACA
127867 ACAATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 7 0.39
22 9 0.50
ACGTcount: A:0.68, C:0.17, G:0.10, T:0.05
Consensus pattern (21 bp):
AAAAATACACACAAAAACAGG
Found at i:128534 original size:19 final size:20
Alignment explanation
Indices: 128498--128535 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
128488 ATTAGAAAGG
128498 AATAAAAACTCTTGTAAAAA
1 AATAAAAACTCTTGTAAAAA
*
128518 AATAAAACCTCTT-TAAAA
1 AATAAAAACTCTTGTAAAA
128536 TAAACGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (20 bp):
AATAAAAACTCTTGTAAAAA
Found at i:129989 original size:32 final size:32
Alignment explanation
Indices: 129903--129972 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
129893 CCCCAAAAAA
*
129903 TTTAAATACCAAATTAAG--AAAAATGTCAAG
1 TTTAAGTACCAAATTAAGAAAAAAATGTCAAG
129933 TTTAAGTACCAAATTAAGAAAAAAATGTCAAG
1 TTTAAGTACCAAATTAAGAAAAAAATGTCAAG
*
129965 TTTGAGTA
1 TTTAAGTA
129973 TTAAATTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 17 0.47
32 19 0.53
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.29
Consensus pattern (32 bp):
TTTAAGTACCAAATTAAGAAAAAAATGTCAAG
Found at i:130411 original size:11 final size:10
Alignment explanation
Indices: 130392--130443 Score: 52
Period size: 11 Copynumber: 5.0 Consensus size: 10
130382 ATATAAATTG
130392 TAAAATAATA
1 TAAAATAATA
130402 TAAGAATAATA
1 TAA-AATAATA
*
130413 -AATAATAAAA
1 TAA-AATAATA
*
130423 TAAAATAAAAA
1 TAAAAT-AATA
130434 TAAAATAATA
1 TAAAATAATA
130444 ATTGAATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 17 0.47
11 19 0.53
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (10 bp):
TAAAATAATA
Found at i:130415 original size:26 final size:26
Alignment explanation
Indices: 130392--130444 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
130382 ATATAAATTG
*
130392 TAAAATAATATAAGAATAATAAATAA
1 TAAAATAAAATAAGAATAATAAATAA
*
130418 TAAAATAAAATAAAAAT-A-AAATAA
1 TAAAATAAAATAAGAATAATAAATAA
130442 TAA
1 TAA
130445 TTGAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.36
25 1 0.04
26 15 0.60
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (26 bp):
TAAAATAAAATAAGAATAATAAATAA
Found at i:130435 original size:16 final size:17
Alignment explanation
Indices: 130394--130441 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
130384 ATAAATTGTA
* *
130394 AAATAATATAAGAATAAT
1 AAATAATAAAATAA-AAT
130412 AAATAATAAAATAAAAT
1 AAATAATAAAATAAAAT
130429 AAA-AATAAAATAA
1 AAATAATAAAATAA
130442 TAATTGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.36
17 6 0.21
18 12 0.43
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (17 bp):
AAATAATAAAATAAAAT
Found at i:133243 original size:21 final size:19
Alignment explanation
Indices: 133217--133270 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
133207 AAAATAAATG
133217 GTATCGATACTTGTCACAAAA
1 GTATCGATACTT-TCAC-AAA
* *
133238 GTATCGGTACCTTTCTCAAA
1 GTATCGATA-CTTTCACAAA
*
133258 GTATCAATACTTT
1 GTATCGATACTTT
133271 ACTTTAGTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.14
20 10 0.36
21 11 0.39
22 3 0.11
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (19 bp):
GTATCGATACTTTCACAAA
Found at i:135330 original size:17 final size:19
Alignment explanation
Indices: 135303--135341 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
135293 ATATGGAAAA
*
135303 AAAAATGAGAA-TGATGTG
1 AAAAATGAGAATTGAAGTG
135321 AAAAAT-AGAATTGAAGTG
1 AAAAATGAGAATTGAAGTG
135339 AAA
1 AAA
135342 TTTGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (19 bp):
AAAAATGAGAATTGAAGTG
Found at i:142992 original size:43 final size:43
Alignment explanation
Indices: 142927--143103 Score: 162
Period size: 43 Copynumber: 4.1 Consensus size: 43
142917 TACATCATTG
* * ** **
142927 GATAAATCAAA-AAAATATACTAGCACATATGGTGCATTATCA
1 GATAAATCAAAGGAAATATACTAGCACACACAGTGCACCATCA
*
142969 GATAAATCAAAGGAAATATACTAGCAGACACAGTGCACCATCA
1 GATAAATCAAAGGAAATATACTAGCACACACAGTGCACCATCA
** **
143012 GATAAATTGAAGGAAATATACTAGCACACGTAGTGCACCATCA
1 GATAAATCAAAGGAAATATACTAGCACACACAGTGCACCATCA
* * * * * *
143055 AATAAA-CTGAAGTAATTATACTAGCAC-CTACAGTGCATCATTA
1 GATAAATC-AAAGGAAATATACTAGCACAC-ACAGTGCACCATCA
143098 GATAAA
1 GATAAA
143104 CTAAAGTATA
Statistics
Matches: 111, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
42 12 0.11
43 99 0.89
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.23
Consensus pattern (43 bp):
GATAAATCAAAGGAAATATACTAGCACACACAGTGCACCATCA
Found at i:143111 original size:43 final size:42
Alignment explanation
Indices: 142904--143109 Score: 152
Period size: 43 Copynumber: 4.8 Consensus size: 42
142894 TTTATCCCAA
* ** *
142904 ACTAGCACCT-CAGTACATCATTGGATAAATCAAA-AAAATAT
1 ACTAGCACCTACAGTGCATCATCAGATAAAT-AAAGGAAATAT
* ** *
142945 ACTAGCACATATGGTGCATTATCAGATAAATCAAAGGAAATAT
1 ACTAGCACCTACAGTGCATCATCAGATAAAT-AAAGGAAATAT
* * *
142988 ACTAGCAGAC-ACAGTGCACCATCAGATAAATTGAAGGAAATAT
1 ACTAGCA-CCTACAGTGCATCATCAGATAAA-TAAAGGAAATAT
* * * * *
143031 ACTAGCA-C-ACGTAGTGCACCATCAAATAAACTGAAGTAATTAT
1 ACTAGCACCTAC--AGTGCATCATCAGATAAA-TAAAGGAAATAT
*
143074 ACTAGCACCTACAGTGCATCATTAGATAAACTAAAG
1 ACTAGCACCTACAGTGCATCATCAGATAAA-TAAAG
143110 TATAGCCTGT
Statistics
Matches: 134, Mismatches: 23, Indels: 14
0.78 0.13 0.08
Matches are distributed among these distances:
41 12 0.09
42 18 0.13
43 100 0.75
44 2 0.01
45 2 0.01
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.23
Consensus pattern (42 bp):
ACTAGCACCTACAGTGCATCATCAGATAAATAAAGGAAATAT
Found at i:154848 original size:23 final size:23
Alignment explanation
Indices: 154803--154848 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
154793 ATTCCATACA
*
154803 CATTTTGGTAGTTTTTGATATGTT
1 CATTTTGG-AGTTTTTGACATGTT
154827 CATTTTGG-GTTATTTGACATGT
1 CATTTTGGAGTT-TTTGACATGT
154849 AATATAGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 9 0.45
24 8 0.40
ACGTcount: A:0.17, C:0.07, G:0.22, T:0.54
Consensus pattern (23 bp):
CATTTTGGAGTTTTTGACATGTT
Found at i:171833 original size:21 final size:21
Alignment explanation
Indices: 171805--171850 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
171795 TCCATTTTCG
171805 ATTA-ATTTGCACTGACAGAT
1 ATTACATTTGCACTGACAGAT
171825 ATTACATTTGCACTGACAGAT
1 ATTACATTTGCACTGACAGAT
*
171846 TTTAC
1 ATTAC
171851 TCTTAATCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (21 bp):
ATTACATTTGCACTGACAGAT
Found at i:177239 original size:21 final size:21
Alignment explanation
Indices: 177213--177258 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
177203 GTATTGAGGC
177213 AGAAGAAGGAGAAAGA-AAAGA
1 AGAAGAA-GAGAAAGAGAAAGA
* *
177234 AGAAGAAGAGGAAGAGAAGGA
1 AGAAGAAGAGAAAGAGAAAGA
177255 AGAA
1 AGAA
177259 ATAGAAGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (21 bp):
AGAAGAAGAGAAAGAGAAAGA
Found at i:177687 original size:17 final size:18
Alignment explanation
Indices: 177661--177699 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
177651 GCATGCATTT
177661 TTTTTAATTGTCAT-TGCA
1 TTTTTAATTGTC-TCTGCA
177679 TTTTT-ATTGTCTCTGCA
1 TTTTTAATTGTCTCTGCA
177696 TTTT
1 TTTT
177700 ATTTGTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.15, C:0.13, G:0.10, T:0.62
Consensus pattern (18 bp):
TTTTTAATTGTCTCTGCA
Found at i:177705 original size:17 final size:17
Alignment explanation
Indices: 177662--177715 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
177652 CATGCATTTT
*
177662 TTTTAATTGTCAT-TGCA
1 TTTTATTTGTC-TCTGCA
177679 TTTT-TATTGTCTCTGCA
1 TTTTAT-TTGTCTCTGCA
177696 TTTTATTTGT-TCTAGCA
1 TTTTATTTGTCTCT-GCA
177713 TTT
1 TTT
177716 GCATTGTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 4 0.12
17 27 0.84
18 1 0.03
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (17 bp):
TTTTATTTGTCTCTGCA
Found at i:179909 original size:24 final size:23
Alignment explanation
Indices: 179862--179909 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
179852 CAATCAATCT
* *
179862 ATTTTCTATTAATTTGCTCCGAC
1 ATTTTATATTAATTTGCACCGAC
*
179885 ATTTTATATTACATTTGCACTGAC
1 ATTTTATATTA-ATTTGCACCGAC
179909 A
1 A
179910 AATTTTACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (23 bp):
ATTTTATATTAATTTGCACCGAC
Found at i:189634 original size:18 final size:18
Alignment explanation
Indices: 189591--189634 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
189581 CTCAAGCTCC
* *
189591 TTTGTATGCTTTTCTTGT
1 TTTGTTTGCTTTTCTTGG
*
189609 TTTATTTGCTTTTCTTGG
1 TTTGTTTGCTTTTCTTGG
189627 TTTGTTTG
1 TTTGTTTG
189635 ATTGAGGTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.05, C:0.09, G:0.18, T:0.68
Consensus pattern (18 bp):
TTTGTTTGCTTTTCTTGG
Found at i:192354 original size:20 final size:20
Alignment explanation
Indices: 192316--192354 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
192306 GCATTTTCGT
*
192316 AATTAAAAAAAGAATAAACA
1 AATTAAAAAAAGAAGAAACA
* *
192336 AATTAAAAAGATAAGAAAC
1 AATTAAAAAAAGAAGAAAC
192355 TTATCATCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.15
Consensus pattern (20 bp):
AATTAAAAAAAGAAGAAACA
Found at i:195039 original size:16 final size:16
Alignment explanation
Indices: 195018--195051 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
195008 CTTTCGAGAG
195018 TAAGAGCAACTAACTC
1 TAAGAGCAACTAACTC
*
195034 TAAGAGCAACTAGCTC
1 TAAGAGCAACTAACTC
195050 TA
1 TA
195052 GGTTAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.21
Consensus pattern (16 bp):
TAAGAGCAACTAACTC
Found at i:197402 original size:8 final size:8
Alignment explanation
Indices: 197380--197431 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
197370 CAAGAATACT
197380 AATAAAAA
1 AATAAAAA
* *
197388 TAGAAAAA
1 AATAAAAA
197396 AATAAAATA
1 AATAAAA-A
*
197405 AGATAAAGA
1 A-ATAAAAA
*
197414 AATAACAA
1 AATAAAAA
197422 AATAAAAA
1 AATAAAAA
197430 AA
1 AA
197432 ACAACCGACA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
8 25 0.74
9 4 0.12
10 5 0.15
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (8 bp):
AATAAAAA
Found at i:197473 original size:5 final size:5
Alignment explanation
Indices: 197463--197517 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
197453 TAAAATGCAT
* *
197463 AATAA AATAA AATAA AATAA AA-CA ACTAA CAATAAA AATAA AA-ATA
1 AATAA AATAA AATAA AATAA AATAA AATAA -AAT-AA AATAA AATA-A
197509 AATAA AATA
1 AATAA AATA
197518 TAAAACTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 3 0.07
5 30 0.73
6 6 0.15
7 2 0.05
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:200881 original size:22 final size:21
Alignment explanation
Indices: 200836--200881 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
200826 TTACAATGTA
* * *
200836 AAAATTAAATTAAAAAATATT
1 AAAATAAAAATAAAAAATACT
200857 AAAATAAAAATAAAAAATTACT
1 AAAATAAAAATAAAAAA-TACT
200879 AAA
1 AAA
200882 TTAATAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATAAAAATAAAAAATACT
Found at i:218331 original size:27 final size:26
Alignment explanation
Indices: 218299--218350 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
218289 AAATTAAATT
218299 ATAATTATTT-TTAAACATATAATTATC
1 ATAATT-TTTATTAAA-ATATAATTATC
*
218326 ATAATTTTTATTAAATTATAATTAT
1 ATAATTTTTATTAAAATATAATTAT
218351 TTTTAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (26 bp):
ATAATTTTTATTAAAATATAATTATC
Found at i:218348 original size:17 final size:17
Alignment explanation
Indices: 218326--218358 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
218316 TATAATTATC
218326 ATAATT-TTTATTAAATT
1 ATAATTATTT-TTAAATT
218343 ATAATTATTTTTAAAT
1 ATAATTATTTTTAAAT
218359 GTACAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATAATTATTTTTAAATT
Found at i:221161 original size:29 final size:30
Alignment explanation
Indices: 221108--221166 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
221098 GAATTAGATT
*
221108 AAATCAAAATTTCATATATAAAATTGCACA
1 AAATCAAAATTTCATATATAAAATTACACA
*
221138 AAATCAAAA-TTCATATATATAATTACACA
1 AAATCAAAATTTCATATATAAAATTACACA
221167 TTAAACTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTACACA
Found at i:221838 original size:18 final size:18
Alignment explanation
Indices: 221806--221857 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
221796 ACTTGACCAG
221806 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
221822 AATAAATTTAATTAATTA
1 AATAAATTTAATTAATTA
*
221840 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
221858 CAGCTTGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 9 0.28
17 5 0.16
18 18 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:222066 original size:15 final size:15
Alignment explanation
Indices: 222046--222096 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
222036 ACAAAATAAT
222046 AATATAAATTATTAA
1 AATATAAATTATTAA
*
222061 AATATAATATT-TT-T
1 AATATAA-ATTATTAA
* *
222075 AATATGAATGATTAA
1 AATATAAATTATTAA
222090 AATATAA
1 AATATAA
222097 TCTAATGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.29
15 15 0.54
16 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (15 bp):
AATATAAATTATTAA
Found at i:232719 original size:24 final size:24
Alignment explanation
Indices: 232672--232719 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
232662 TATTGATTAC
* *
232672 TAATATTTTTTTGTTAATTCTTTT
1 TAATATTTATTTGTTAAGTCTTTT
*
232696 TAATATTTATTTGTTAAGTGTTTT
1 TAATATTTATTTGTTAAGTCTTTT
232720 ATGTCCACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.08, T:0.67
Consensus pattern (24 bp):
TAATATTTATTTGTTAAGTCTTTT
Found at i:239116 original size:13 final size:13
Alignment explanation
Indices: 239098--239127 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
239088 CCACAAGAAA
*
239098 GAAAAGGGAAAAG
1 GAAAAGGAAAAAG
239111 GAAAAGGAAAAAG
1 GAAAAGGAAAAAG
239124 GAAA
1 GAAA
239128 GTCGCTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (13 bp):
GAAAAGGAAAAAG
Found at i:239656 original size:18 final size:17
Alignment explanation
Indices: 239619--239664 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
239609 GTATTGACGT
239619 AGAAGAAAGAAAAGAAGA
1 AGAA-AAAGAAAAGAAGA
*
239637 AGAAAAAGAATAGAATGA
1 AGAAAAAGAAAAGAA-GA
*
239655 AGATAAAGAA
1 AGAAAAAGAA
239665 GATCTTGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.07
Consensus pattern (17 bp):
AGAAAAAGAAAAGAAGA
Found at i:256480 original size:52 final size:51
Alignment explanation
Indices: 256424--256631 Score: 126
Period size: 52 Copynumber: 4.1 Consensus size: 51
256414 GAAATAGTTA
*
256424 AAAAAAATAAAAACTTTGTTTAAAAATTTAAAATTTTTTCTTTAAAATAACT
1 AAAAAAATAAAAACTTTATTTAAAAATTT-AAATTTTTTCTTTAAAATAACT
* ** * * ** *
256476 AAAAAAA-CAAATTTTTATTTTTAAAAATATAAACTTCCTCTTT---TTAA--
1 AAAAAAATAAAAACTTTA--TTTAAAAATTTAAATTTTTTCTTTAAAATAACT
* * ** * * * * **
256523 AAGAAAATCACTATTTTACTTAAAAATCTAAATTTTTAT-TTCGAAAA-AGTT
1 AAAAAAATAAAAACTTTATTTAAAAATTTAAATTTTT-TCTT-TAAAATAACT
*
256574 AAAAAAATCAAAACTTTATTTAAAAATTTAAAATTTTTTCTTTAAAATAACT
1 AAAAAAATAAAAACTTTATTTAAAAATTT-AAATTTTTTCTTTAAAATAACT
256626 AAAAAA
1 AAAAAA
256632 CAAATTTTTA
Statistics
Matches: 113, Mismatches: 30, Indels: 26
0.67 0.18 0.15
Matches are distributed among these distances:
46 16 0.14
47 7 0.06
48 7 0.06
49 4 0.04
51 34 0.30
52 35 0.31
53 10 0.09
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.39
Consensus pattern (51 bp):
AAAAAAATAAAAACTTTATTTAAAAATTTAAATTTTTTCTTTAAAATAACT
Found at i:256629 original size:150 final size:149
Alignment explanation
Indices: 256070--256741 Score: 885
Period size: 151 Copynumber: 4.5 Consensus size: 149
256060 AGTTTTTTTA
* * * * *
256070 TTAAAACAAAATCACTATTTTATTTCAAAATCAAAACTTTTATTTCG-AATAACTTAAAAAAATC
1 TTAAAAGAAAATCACTATTTTACTTAAAAATCAAAATTTTTATTTCGAAAT-AGTTAAAAAAATC
* * *
256134 AAAACTTTATTTAAAAA-TTAAAATTTTTTCTTTAAAATCATTAAAAAACATATTTTTATTTTT-
65 AAAACTTTATTTAAAAATTTAAAATTTTTTCTTTAAAATAACTAAAAAACAAATTTTTATTTTTA
256197 -AAATATAAACTTTCTCTTTT
130 AAAATATAAACTTTCTC-TTT
* * *
256217 TTTAAAGAAAATCACTATTTTACTTAAAAATCCAAACTTTTAATTT-GAAATAGTTAAAAAAAAA
1 TTAAAAGAAAATCACTATTTTACTTAAAAAT-CAAAATTTTTATTTCGAAATAGTT----AAAAA
* * *
256281 AATCAAAACTTTATTTAAAAATTT-AAAGTTTTTGTTTAAAATAACT-AAAAACATATTTTTATT
61 AATCAAAACTTTATTTAAAAATTTAAAATTTTTTCTTTAAAATAACTAAAAAACAAATTTTTATT
* *
256344 TTTAAAAATATAAACATTCTATTT
126 TTTAAAAATATAAACTTTCTCTTT
** *
256368 TTTTAAGAAAATCACTATTTTACTTAAAAATTC-AAATTTTTATTCCGAAATAGTTAAAAAAAAT
1 TTAAAAGAAAATCACTATTTTACTTAAAAA-TCAAAATTTTTATTTCGAAATAGTT-AAAAAAAT
* *
256432 AAAAACTTTGTTTAAAAATTTAAAATTTTTTCTTTAAAATAACTAAAAAAACAAATTTTTATTTT
64 CAAAACTTTATTTAAAAATTTAAAATTTTTTCTTTAAAATAACT-AAAAAACAAATTTTTATTTT
*
256497 TAAAAATATAAACTTCCTCTTT
128 TAAAAATATAAACTTTCTCTTT
* *
256519 TTAAAAGAAAATCACTATTTTACTTAAAAATCTAAATTTTTATTTCGAAAAAGTTAAAAAAATCA
1 TTAAAAGAAAATCACTATTTTACTTAAAAATCAAAATTTTTATTTCGAAATAGTTAAAAAAATCA
*
256584 AAACTTTATTTAAAAATTTAAAATTTTTTCTTTAAAATAACTAAAAAACAAATTTTTATTTCTAA
66 AAACTTTATTTAAAAATTTAAAATTTTTTCTTTAAAATAACTAAAAAACAAATTTTTATTTTTAA
*
256649 AAATATGAACTTTCTCTTT
131 AAATATAAACTTTCTCTTT
* * * *
256668 AT-AAATAAAAGCACTATTTTACTTAAAAATCAAAAATTTTTATTTCGAAATTATTTAAAAAGAA
1 TTAAAAGAAAATCACTATTTTACTTAAAAATC-AAAATTTTTATTTCGAAA-TAGTTAAAAA-AA
*
256732 CCAAAACTTT
63 TCAAAACTTT
256742 TCCCAAAATC
Statistics
Matches: 465, Mismatches: 42, Indels: 32
0.86 0.08 0.06
Matches are distributed among these distances:
147 31 0.07
148 69 0.15
149 77 0.17
150 89 0.19
151 182 0.39
152 17 0.04
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.41
Consensus pattern (149 bp):
TTAAAAGAAAATCACTATTTTACTTAAAAATCAAAATTTTTATTTCGAAATAGTTAAAAAAATCA
AAACTTTATTTAAAAATTTAAAATTTTTTCTTTAAAATAACTAAAAAACAAATTTTTATTTTTAA
AAATATAAACTTTCTCTTT
Found at i:257192 original size:3 final size:3
Alignment explanation
Indices: 257186--257211 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
257176 ACTAATAATA
257186 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
257212 AATTTAGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:257611 original size:42 final size:42
Alignment explanation
Indices: 257555--257867 Score: 430
Period size: 42 Copynumber: 7.5 Consensus size: 42
257545 TTAATGCTTA
* *
257555 GGCCTCTAATTGCAATGAAAAGTAAATGGACCTTCACACCTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
* ** *
257597 GGTCTCCGAATGCAATGAAAAGTAAATGGACCTCCACACTTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
* ** *
257639 GGCCTCTAAATACAATGAAAAGTAAATGGGTCTCCACACTTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
* * *
257681 GGCCTCTAAATGTAATGAAAAGTAAATGTACCTCCACACTTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
*
257723 GGCCTCTAAATGAAATGAAAAGTAAATGGACCTCCACACCTAG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCT-G
* *
257766 GG-CTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACATG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
* * *
257807 GGCCTCTGAATGCGATGAAAAGTAAATGGACCTCCACACCTA
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
*
257849 GGCCTGTAAATGCAATGAA
1 GGCCTCTAAATGCAATGAA
257868 TGCTTTCCTT
Statistics
Matches: 238, Mismatches: 31, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
41 3 0.01
42 232 0.97
43 3 0.01
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (42 bp):
GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
Found at i:275593 original size:20 final size:20
Alignment explanation
Indices: 275570--275609 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
275560 TTCATTATCC
275570 TTCTC-TTCTCTTCCTTTTTT
1 TTCTCTTTCTCTT-CTTTTTT
275590 TTCTCTTTTCTCTTCTTTTT
1 TTCTC-TTTCTCTTCTTTTT
275610 CAACACCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TTCTCTTTCTCTTCTTTTTT
Found at i:277384 original size:13 final size:14
Alignment explanation
Indices: 277368--277396 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
277358 GAATTAAATT
277368 AAAATAAA-AGAAA
1 AAAATAAACAGAAA
277381 AAAATAAACAGAAA
1 AAAATAAACAGAAA
277395 AA
1 AA
277397 TTGTAATGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.83, C:0.03, G:0.07, T:0.07
Consensus pattern (14 bp):
AAAATAAACAGAAA
Found at i:294077 original size:24 final size:24
Alignment explanation
Indices: 294049--294101 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
294039 GTGAGTACAT
294049 AGCTGAGAAATAACCAACTTGTAC
1 AGCTGAGAAATAACCAACTTGTAC
294073 AGCTGAGAAATAACCAACTTGTAC
1 AGCTGAGAAATAACCAACTTGTAC
294097 AGCTG
1 AGCTG
294102 CAAAAAGGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
AGCTGAGAAATAACCAACTTGTAC
Found at i:303076 original size:13 final size:14
Alignment explanation
Indices: 303058--303087 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
303048 TTCAATGCAA
303058 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
303071 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
303085 TCA
1 TCA
303088 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:305274 original size:17 final size:18
Alignment explanation
Indices: 305236--305276 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
305226 AACAAAAAGG
*
305236 AATGCAGTGACAAAATAA
1 AATGCAATGACAAAATAA
*
305254 AATGCAATGACAATA-AA
1 AATGCAATGACAAAATAA
305271 AATGCA
1 AATGCA
305277 TGAAAACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.17
Consensus pattern (18 bp):
AATGCAATGACAAAATAA
Found at i:307555 original size:20 final size:21
Alignment explanation
Indices: 307530--307569 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
307520 GCCAAAGAAT
*
307530 TTAAAACAAC-ACAAGTAAAA
1 TTAAAACAACTAAAAGTAAAA
*
307550 TTAAAATAACTAAAAGTAAA
1 TTAAAACAACTAAAAGTAAA
307570 TAGAAATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.65, C:0.10, G:0.05, T:0.20
Consensus pattern (21 bp):
TTAAAACAACTAAAAGTAAAA
Found at i:321842 original size:21 final size:21
Alignment explanation
Indices: 321805--321844 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
321795 TTCAACAAGG
**
321805 ACTTCCTCCTCTCCAACAGTA
1 ACTTCCTCCTCAACAACAGTA
321826 ACTTCCTCCTCAACAACAG
1 ACTTCCTCCTCAACAACAG
321845 GTTCCTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.42, G:0.05, T:0.25
Consensus pattern (21 bp):
ACTTCCTCCTCAACAACAGTA
Found at i:330596 original size:21 final size:19
Alignment explanation
Indices: 330572--330613 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
330562 ACAAGTATAA
*
330572 CTTCTATCGATACTCAACATG
1 CTTCTACCGATACT-AA-ATG
330593 CTTCTACCGATACTAAATG
1 CTTCTACCGATACTAAATG
330612 CT
1 CT
330614 CTAGAGAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.33
Consensus pattern (19 bp):
CTTCTACCGATACTAAATG
Found at i:331265 original size:18 final size:18
Alignment explanation
Indices: 331250--331372 Score: 156
Period size: 18 Copynumber: 6.8 Consensus size: 18
331240 AAATGCTCTT
*
331250 ACGAGCCAGTATGCTCCA
1 ACGAGCCAGTATGCTCAA
* *
331268 ATGAGTCAGTATGCTCAA
1 ACGAGCCAGTATGCTCAA
*
331286 ACGAGCCAATATGCTCAA
1 ACGAGCCAGTATGCTCAA
* *
331304 ACAAGCAAGTATGCTCAA
1 ACGAGCCAGTATGCTCAA
* *
331322 ACAAGTCAGTATGCTCAA
1 ACGAGCCAGTATGCTCAA
*
331340 ACGAGCCAGTATGCTCCA
1 ACGAGCCAGTATGCTCAA
*
331358 ACGAGCCAATATGCT
1 ACGAGCCAGTATGCT
331373 ATTCCTTTTG
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 90 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (18 bp):
ACGAGCCAGTATGCTCAA
Found at i:335216 original size:23 final size:23
Alignment explanation
Indices: 335156--335210 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
335146 TAAAGATTAT
335156 AATAATAAAGAGAAAGGAACTAA
1 AATAATAAAGAGAAAGGAACTAA
335179 AATAATAAAGAGAAAGGAACTAA
1 AATAATAAAGAGAAAGGAACTAA
335202 AATAATAAA
1 AATAATAAA
335211 AGGAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.67, C:0.04, G:0.15, T:0.15
Consensus pattern (23 bp):
AATAATAAAGAGAAAGGAACTAA
Found at i:335785 original size:33 final size:33
Alignment explanation
Indices: 335743--335809 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
335733 AATCGATCAA
335743 TTAAGTCAGCTAGAAATACTTCAACTTGTAAGT
1 TTAAGTCAGCTAGAAATACTTCAACTTGTAAGT
335776 TTAAGTCAGCTAGAAATACTTCAACTTGTAAGT
1 TTAAGTCAGCTAGAAATACTTCAACTTGTAAGT
335809 T
1 T
335810 ATATTTACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (33 bp):
TTAAGTCAGCTAGAAATACTTCAACTTGTAAGT
Found at i:335967 original size:48 final size:48
Alignment explanation
Indices: 335902--336196 Score: 335
Period size: 48 Copynumber: 6.4 Consensus size: 48
335892 AAATGTATAT
* *
335902 AAGCTGACGAGCATAAACGTATATAAGCTGACGAGCGTAAACATGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* *
335950 AAGCTGACAAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGCGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * * *
335998 AAGCTGACGAGCGTAAACATATATAAGCTGATGAGCGTAAACATGAGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
336046 AAGCTGACGA--G----CG----T--GCTGACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * * *
336082 AAGTTGACAAGCGTAAACATATATAAGCTGATGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * * * * *
336130 AAGCTAATGAGCGTAACCGTATATAAGCTGACAAGCATAAACGTGTGA
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
*
336178 AAGCTGGCGAGCGTAAACG
1 AAGCTGACGAGCGTAAACG
336197 CCTATGAATA
Statistics
Matches: 204, Mismatches: 31, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
36 27 0.13
38 2 0.01
42 2 0.01
46 2 0.01
48 171 0.84
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (48 bp):
AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
Found at i:336040 original size:24 final size:24
Alignment explanation
Indices: 335887--336196 Score: 194
Period size: 24 Copynumber: 12.4 Consensus size: 24
335877 AAACAATATA
*
335887 AGCGTAAATGTATATAAGCTGACG
1 AGCGTAAACGTATATAAGCTGACG
*
335911 AGCATAAACGTATATAAGCTGACG
1 AGCGTAAACGTATATAAGCTGACG
* * ** *
335935 AGCGTAAACATGTGCAAGCTGACA
1 AGCGTAAACGTATATAAGCTGACG
335959 AGCGTAAACGTATATAAGCTGACG
1 AGCGTAAACGTATATAAGCTGACG
****
335983 AGCGTAAACGTGCGCAAGCTGACG
1 AGCGTAAACGTATATAAGCTGACG
* *
336007 AGCGTAAACATATATAAGCTGATG
1 AGCGTAAACGTATATAAGCTGACG
*
336031 AGCGTAAAC--ATGAGCAAGCTGACG
1 AGCGTAAACGTAT-A-TAAGCTGACG
* * * *
336055 AGCGTGCTGACGAGCGTAAACGTGTGCAAGTTGACA
1 AGC--G-T-A--AACGT--A--TAT--AAGCTGACG
* *
336091 AGCGTAAACATATATAAGCTGATG
1 AGCGTAAACGTATATAAGCTGACG
* ** * *
336115 AGCGTAAACGTGTGCAAGCTAATG
1 AGCGTAAACGTATATAAGCTGACG
* *
336139 AGCGTAACCGTATATAAGCTGACA
1 AGCGTAAACGTATATAAGCTGACG
* * *
336163 AGCATAAACGTGTGA-AAGCTGGCG
1 AGCGTAAACGTAT-ATAAGCTGACG
336187 AGCGTAAACG
1 AGCGTAAACG
336197 CCTATGAATA
Statistics
Matches: 215, Mismatches: 54, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
22 2 0.01
23 1 0.00
24 185 0.86
25 1 0.00
26 3 0.01
27 1 0.00
28 2 0.01
30 5 0.02
32 1 0.00
33 1 0.00
34 2 0.01
36 11 0.05
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (24 bp):
AGCGTAAACGTATATAAGCTGACG
Found at i:336071 original size:36 final size:36
Alignment explanation
Indices: 336024--336095 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
336014 ACATATATAA
* *
336024 GCTGATGAGCGTAAACATGAGCAAGCTGACGAGCGT
1 GCTGACGAGCGTAAACATGAGCAAGCTGACAAGCGT
* * *
336060 GCTGACGAGCGTAAACGTGTGCAAGTTGACAAGCGT
1 GCTGACGAGCGTAAACATGAGCAAGCTGACAAGCGT
336096 AAACATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.33, T:0.18
Consensus pattern (36 bp):
GCTGACGAGCGTAAACATGAGCAAGCTGACAAGCGT
Found at i:336117 original size:84 final size:84
Alignment explanation
Indices: 335976--336143 Score: 273
Period size: 84 Copynumber: 2.0 Consensus size: 84
335966 ACGTATATAA
*
335976 GCTGACGAGCGTAAACGTGCGCAAGCTGACGAGCGTAAACATATATAAGCTGATGAGCGTAAACA
1 GCTGACGAGCGTAAACGTGCGCAAGCTGACAAGCGTAAACATATATAAGCTGATGAGCGTAAACA
*
336041 TGAGCAAGCTGACGAGCGT
66 TGAGCAAGCTAACGAGCGT
* * *
336060 GCTGACGAGCGTAAACGTGTGCAAGTTGACAAGCGTAAACATATATAAGCTGATGAGCGTAAACG
1 GCTGACGAGCGTAAACGTGCGCAAGCTGACAAGCGTAAACATATATAAGCTGATGAGCGTAAACA
* *
336125 TGTGCAAGCTAATGAGCGT
66 TGAGCAAGCTAACGAGCGT
336144 AACCGTATAT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.19
Consensus pattern (84 bp):
GCTGACGAGCGTAAACGTGCGCAAGCTGACAAGCGTAAACATATATAAGCTGATGAGCGTAAACA
TGAGCAAGCTAACGAGCGT
Found at i:336171 original size:132 final size:132
Alignment explanation
Indices: 335928--336191 Score: 384
Period size: 132 Copynumber: 2.0 Consensus size: 132
335918 ACGTATATAA
*
335928 GCTGACGAGCGTAAACATGTGCAAGCTGACAAGCGTAAACGTATATAAGCTGACGAGCGTAAACG
1 GCTGACGAGCGTAAACATGTGCAAGCTGACAAGCGTAAACATATATAAGCTGACGAGCGTAAACG
* ** * *
335993 TGCGCAAGCTGACGAGCGTAAACATATATAAGCTGATGAGCGTAAACATGAGCAAGCTGACGAGC
66 TGCGCAAGCTAACGAGCGTAAACATATATAAGCTGACAAGCATAAACATGAGAAAGCTGACGAGC
336058 GT
131 GT
* * *
336060 GCTGACGAGCGTAAACGTGTGCAAGTTGACAAGCGTAAACATATATAAGCTGATGAGCGTAAACG
1 GCTGACGAGCGTAAACATGTGCAAGCTGACAAGCGTAAACATATATAAGCTGACGAGCGTAAACG
* * * * * * *
336125 TGTGCAAGCTAATGAGCGTAACCGTATATAAGCTGACAAGCATAAACGTGTGAAAGCTGGCGAGC
66 TGCGCAAGCTAACGAGCGTAAACATATATAAGCTGACAAGCATAAACATGAGAAAGCTGACGAGC
336190 GT
131 GT
336192 AAACGCCTAT
Statistics
Matches: 116, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
132 116 1.00
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (132 bp):
GCTGACGAGCGTAAACATGTGCAAGCTGACAAGCGTAAACATATATAAGCTGACGAGCGTAAACG
TGCGCAAGCTAACGAGCGTAAACATATATAAGCTGACAAGCATAAACATGAGAAAGCTGACGAGC
GT
Found at i:342193 original size:22 final size:22
Alignment explanation
Indices: 342152--342198 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
342142 AAAAAGGGTT
*
342152 AAGGATTATAATAATAAAAAGA
1 AAGGATTAAAATAATAAAAAGA
*
342174 AAGGAATTAAAATAATAAAAGGA
1 AAGG-ATTAAAATAATAAAAAGA
342197 AA
1 AA
342199 ATTAGGGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (22 bp):
AAGGATTAAAATAATAAAAAGA
Done.