Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009469.1 Kokia drynarioides strain JFW-HI SEQ_124177, 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: 332091
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 151 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1410 original size:40 final size:40
Alignment explanation
Indices: 1345--1464 Score: 159
Period size: 40 Copynumber: 3.0 Consensus size: 40
1335 TACATTTAAA
* * * *
1345 TATTCGGGCTTTGTGCCTAGTAGGCTTTTTGTCGGTGTATT
1 TATT-GGGCTTAGTGCCTAGCAGGCTTTGTGCCGGTGTATT
*
1386 TATTGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGTGTATT
1 TATTGGGCTTAGTGCCTAGCAGGCTTTGTGCCGGTGTATT
* * *
1426 TATCGGGCTTAGTGCATAGCAGGCTTTGTACCGGTGTAT
1 TATTGGGCTTAGTGCCTAGCAGGCTTTGTGCCGGTGTAT
1465 ACTATCAAGC
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 66 0.94
41 4 0.06
ACGTcount: A:0.13, C:0.17, G:0.31, T:0.38
Consensus pattern (40 bp):
TATTGGGCTTAGTGCCTAGCAGGCTTTGTGCCGGTGTATT
Found at i:12714 original size:31 final size:30
Alignment explanation
Indices: 12679--12775 Score: 81
Period size: 31 Copynumber: 3.2 Consensus size: 30
12669 CACATTGATA
12679 GAATTTATAAATGTAAAGGGTTAGATTTATT
1 GAATTTATAAATGTAAA-GGTTAGATTTATT
* * * * * * *
12710 GAATTATTTAGACT-T-AAGATCAAATTGATA
1 GAATT-TATA-AATGTAAAGGTTAGATTTATT
12740 GAATTTATAAATGTAAAAGGTTAGATTTATT
1 GAATTTATAAATGT-AAAGGTTAGATTTATT
12771 GAATT
1 GAATT
12776 ATTTAGACTT
Statistics
Matches: 47, Mismatches: 14, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
28 2 0.04
29 4 0.09
30 13 0.28
31 22 0.47
32 4 0.09
33 2 0.04
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.40
Consensus pattern (30 bp):
GAATTTATAAATGTAAAGGTTAGATTTATT
Found at i:12744 original size:30 final size:30
Alignment explanation
Indices: 12710--12804 Score: 86
Period size: 30 Copynumber: 3.1 Consensus size: 30
12700 TAGATTTATT
12710 GAATTATTTAGACTTAAGATCAAATTGATA
1 GAATTATTTAGACTTAAGATCAAATTGATA
* * * * * * *
12740 GAATT-TATA-AATGTAAAAGGTTAGATTTATT
1 GAATTATTTAGACT-T--AAGATCAAATTGATA
12771 GAATTATTTAGACTTAAGATCAAATTGATA
1 GAATTATTTAGACTTAAGATCAAATTGATA
12801 GAAT
1 GAAT
12805 ATGTAAATAT
Statistics
Matches: 46, Mismatches: 14, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
28 2 0.04
29 4 0.09
30 19 0.41
31 15 0.33
32 4 0.09
33 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (30 bp):
GAATTATTTAGACTTAAGATCAAATTGATA
Found at i:12812 original size:61 final size:61
Alignment explanation
Indices: 12664--12804 Score: 264
Period size: 61 Copynumber: 2.3 Consensus size: 61
12654 AGAATGTTTG
* *
12664 AAGATCACATTGATAGAATTTATAAATGTAAAGGGTTAGATTTATTGAATTATTTAGACTT
1 AAGATCAAATTGATAGAATTTATAAATGTAAAAGGTTAGATTTATTGAATTATTTAGACTT
12725 AAGATCAAATTGATAGAATTTATAAATGTAAAAGGTTAGATTTATTGAATTATTTAGACTT
1 AAGATCAAATTGATAGAATTTATAAATGTAAAAGGTTAGATTTATTGAATTATTTAGACTT
12786 AAGATCAAATTGATAGAAT
1 AAGATCAAATTGATAGAAT
12805 ATGTAAATAT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
61 78 1.00
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.38
Consensus pattern (61 bp):
AAGATCAAATTGATAGAATTTATAAATGTAAAAGGTTAGATTTATTGAATTATTTAGACTT
Found at i:13305 original size:20 final size:20
Alignment explanation
Indices: 13282--13319 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13272 TGAAGCTTTT
13282 AAATATTAATTAAAAATATA
1 AAATATTAATTAAAAATATA
*
13302 AAATATTTATTAAAAATA
1 AAATATTAATTAAAAATA
13320 AAAGCTCGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATATTAATTAAAAATATA
Found at i:13756 original size:80 final size:76
Alignment explanation
Indices: 13611--13767 Score: 226
Period size: 80 Copynumber: 2.0 Consensus size: 76
13601 GCAGATTGGT
* *
13611 GAGTGTGTTGGGCAATGTAGAGGCAACAAGGGGGGCCCTCCAACAAGGTGATACAACGTTTGAGG
1 GAGTGTGTTGGGCAAAGTAGAGGCAACAAGGGGGGCCCTCCAACAAGGTGATACAACATTTGAGG
13676 AAGTGATTGAC
66 AAGTGATTGAC
* *
13687 GAGTGTGTTGGGCAAAGTATG-GGCAACAAGGGGGGGGGGGCCTCCTACAAGGTGATACAACATT
1 GAGTGTGTTGGGCAAAGTA-GAGGCAACAA----GGGGGGCCCTCCAACAAGGTGATACAACATT
13751 TGAGGAAGTGATTGAC
61 TGAGGAAGTGATTGAC
13767 G
1 G
13768 TAATAATTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
76 26 0.36
77 1 0.01
80 45 0.62
ACGTcount: A:0.28, C:0.15, G:0.38, T:0.20
Consensus pattern (76 bp):
GAGTGTGTTGGGCAAAGTAGAGGCAACAAGGGGGGCCCTCCAACAAGGTGATACAACATTTGAGG
AAGTGATTGAC
Found at i:14727 original size:2 final size:2
Alignment explanation
Indices: 14720--14748 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14710 AACATCATTC
14720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14749 ACTTTTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16362 original size:6 final size:6
Alignment explanation
Indices: 16351--16416 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
16341 GGCCTAACAG
* * * *
16351 AATTTA AATTT- ATTTTA AGTTTA AATTT- ACTTAA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
16396 -ATTATA AATTTA AGTTTA AAT
1 AATT-TA AATTTA AATTTA AAT
16417 CTATTTAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
4 3 0.07
5 8 0.17
6 32 0.70
7 3 0.07
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:16375 original size:17 final size:17
Alignment explanation
Indices: 16351--16413 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
16341 GGCCTAACAG
16351 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* * *
16368 AGTTTAAATTTACTTAA
1 AATTTAAATTTATTTTA
*
16385 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
*
16402 AATTTAAGTTTA
1 AATTTAAATTTA
16414 AATCTATTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:16432 original size:22 final size:23
Alignment explanation
Indices: 16387--16433 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
16377 TTACTTAAAA
* **
16387 TTTAAATTTATTATAAATTTAAG
1 TTTAAATCTATTATAAATCAAAG
16410 TTTAAATCTATT-TAAATCAAAG
1 TTTAAATCTATTATAAATCAAAG
16432 TT
1 TT
16434 CAATTACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (23 bp):
TTTAAATCTATTATAAATCAAAG
Found at i:18301 original size:29 final size:29
Alignment explanation
Indices: 18269--18448 Score: 208
Period size: 28 Copynumber: 6.3 Consensus size: 29
18259 CCTAAACTAT
**
18269 CAAAAAATTACATTTTACCCCTGAACTTC
1 CAAAAAATTACATTTTACCCCCAAACTTC
18298 C-AAAAATTACATTTTACCCCCAAACTTC
1 CAAAAAATTACATTTTACCCCCAAACTTC
* * *
18326 TAAAAAATTCCATTTTGACCCCGAAACTT-
1 CAAAAAATTACATTTT-ACCCCCAAACTTC
18355 CAAAAAATTACATTTTTACCCCCAAACTT-
1 CAAAAAATTACA-TTTTACCCCCAAACTTC
* * * *
18384 CTAAAAATTCCATTTTACCCCGAAATTTC
1 CAAAAAATTACATTTTACCCCCAAACTTC
18413 C--AAAATTACATTTTTACCCCCAAACTTC
1 CAAAAAATTACA-TTTTACCCCCAAACTTC
*
18441 AAAAAAAT
1 CAAAAAAT
18449 CCATTTTTGA
Statistics
Matches: 128, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
27 8 0.06
28 54 0.42
29 46 0.36
30 20 0.16
ACGTcount: A:0.40, C:0.27, G:0.02, T:0.31
Consensus pattern (29 bp):
CAAAAAATTACATTTTACCCCCAAACTTC
Found at i:18453 original size:29 final size:29
Alignment explanation
Indices: 18262--18486 Score: 235
Period size: 29 Copynumber: 7.8 Consensus size: 29
18252 GAAGGTCCCT
*
18262 AAACTATCAAAAAATTACA-TTTTACCCCT
1 AAACT-TCAAAAAATTACATTTTTACCCCC
* *
18291 GAACTTCCAAAAATTACA-TTTTACCCCC
1 AAACTTCAAAAAATTACATTTTTACCCCC
* * *
18319 AAACTTCTAAAAAATTCCATTTTGACCCCG
1 AAACTTC-AAAAAATTACATTTTTACCCCC
18349 AAACTTCAAAAAATTACATTTTTACCCCC
1 AAACTTCAAAAAATTACATTTTTACCCCC
* * *
18378 AAACTTCTAAAAATTCCA-TTTTACCCCG
1 AAACTTCAAAAAATTACATTTTTACCCCC
* *
18406 AAATTTC-CAAAATTACATTTTTACCCCC
1 AAACTTCAAAAAATTACATTTTTACCCCC
* * * *
18434 AAACTTCAAAAAAATCCATTTTTGATCCCG
1 AAACTTCAAAAAATTACATTTTT-ACCCCC
18464 AAACTTGC-AAAAATTACTATTTT
1 AAACTT-CAAAAAATTAC-ATTTT
18487 GCGCCCGAGT
Statistics
Matches: 163, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
27 8 0.05
28 57 0.35
29 60 0.37
30 32 0.20
31 6 0.04
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCAAAAAATTACATTTTTACCCCC
Found at i:18476 original size:115 final size:117
Alignment explanation
Indices: 18262--18486 Score: 327
Period size: 115 Copynumber: 1.9 Consensus size: 117
18252 GAAGGTCCCT
18262 AAACTATCAAAAAATTACATTTTACCCCTGAACTTCCAAAAATTACATTTTACCCCCAAACTTCT
1 AAACTATCAAAAAATTACATTTTACCCCTGAACTTCCAAAAATTACATTTTACCCCCAAACTTCT
*
18327 AAAAAATTCCATTTTGACCCCGAAACTTCAAAAAATTAC-ATTTTTACCCCC
66 AAAAAAATCCATTTTGACCCCGAAACTTCAAAAAATTACTATTTTTACCCCC
* * *
18378 AAACT-TCTAAAAATTCCATTTTACCCC-GAAATTTCC-AAAATTACATTTTTACCCCCAAACTT
1 AAACTATCAAAAAATTACATTTTACCCCTG-AACTTCCAAAAATTACA-TTTTACCCCCAAACTT
*
18440 C-AAAAAAATCCATTTTTGATCCCGAAACTTGC-AAAAATTACTATTTT
64 CTAAAAAAATCCA-TTTTGACCCCGAAACTT-CAAAAAATTACTATTTT
18487 GCGCCCGAGT
Statistics
Matches: 99, Mismatches: 5, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
114 20 0.20
115 68 0.69
116 11 0.11
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (117 bp):
AAACTATCAAAAAATTACATTTTACCCCTGAACTTCCAAAAATTACATTTTACCCCCAAACTTCT
AAAAAAATCCATTTTGACCCCGAAACTTCAAAAAATTACTATTTTTACCCCC
Found at i:25472 original size:18 final size:18
Alignment explanation
Indices: 25449--25486 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
25439 TTTTAATTTT
25449 CAATTTCATCTTCTTCCC
1 CAATTTCATCTTCTTCCC
*
25467 CAATTTCATTTTCTTCCC
1 CAATTTCATCTTCTTCCC
25485 CA
1 CA
25487 TTTTTCCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.37, G:0.00, T:0.45
Consensus pattern (18 bp):
CAATTTCATCTTCTTCCC
Found at i:26131 original size:19 final size:21
Alignment explanation
Indices: 26107--26145 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
26097 CAATTTATTT
26107 TTATTT-TGGAAAA-CTATAC
1 TTATTTATGGAAAATCTATAC
*
26126 TTATTTATGTAAAATCTATA
1 TTATTTATGGAAAATCTATA
26146 AAATTATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (21 bp):
TTATTTATGGAAAATCTATAC
Found at i:26712 original size:17 final size:17
Alignment explanation
Indices: 26690--26725 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
26680 TATGCTATTT
26690 TTTTTTATAATTTTGAA
1 TTTTTTATAATTTTGAA
*
26707 TTTTTTATAATTTTTAA
1 TTTTTTATAATTTTGAA
26724 TT
1 TT
26726 ATTGTTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTTTATAATTTTGAA
Found at i:30466 original size:59 final size:60
Alignment explanation
Indices: 30374--30495 Score: 167
Period size: 59 Copynumber: 2.0 Consensus size: 60
30364 AATTTTAAGG
* *
30374 ATTTATTTTTTAAACTTCCTAATTTTGTACTACTAACAAATCATTTTG-TGTATTAA-AAA
1 ATTTACTTTGTAAACTTCCTAATTTTGTACTACTAACAAAT-ATTTTGTTGTATTAAGAAA
* * *
30433 ATTTACTTTGTAAATTTTCTAATTTTGTACTACTAACAAATTTTTTGTTTGTATTAAGAAA
1 ATTTACTTTGTAAACTTCCTAATTTTGTACTACTAACAAATATTTTG-TTGTATTAAGAAA
30494 AT
1 AT
30496 CTTTAAGGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
58 5 0.09
59 37 0.67
60 8 0.15
61 5 0.09
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (60 bp):
ATTTACTTTGTAAACTTCCTAATTTTGTACTACTAACAAATATTTTGTTGTATTAAGAAA
Found at i:30982 original size:28 final size:27
Alignment explanation
Indices: 30925--30998 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 27
30915 TTGAACCTCA
* * *
30925 AACCCAAAACTCTAAATCTAGAATCCTG
1 AACCCTAAACTC-AAACCTAGAACCCTG
*
30953 AACCCTAAACTCAAACCTCGAACCCTTG
1 AACCCTAAACTCAAACCTAGAACCC-TG
**
30981 AACTTTAAACTCAAACCT
1 AACCCTAAACTCAAACCT
30999 TGAATCCTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 10 0.26
28 29 0.74
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22
Consensus pattern (27 bp):
AACCCTAAACTCAAACCTAGAACCCTG
Found at i:40101 original size:2 final size:2
Alignment explanation
Indices: 40094--40132 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
40084 GCTCTTTGTT
40094 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40133 TGAGTTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52731 original size:18 final size:18
Alignment explanation
Indices: 52708--52745 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
52698 AGTATGAAGT
52708 AGAATAGTGAAAGAGTGA
1 AGAATAGTGAAAGAGTGA
52726 AGAATAGTGAAAGAGTGA
1 AGAATAGTGAAAGAGTGA
52744 AG
1 AG
52746 CAGAGAGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.34, T:0.16
Consensus pattern (18 bp):
AGAATAGTGAAAGAGTGA
Found at i:52901 original size:21 final size:20
Alignment explanation
Indices: 52877--52918 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
52867 TTTACCACTG
52877 TTTTAAGTTAAAAAGTATTTT
1 TTTTAAG-TAAAAAGTATTTT
* *
52898 TTTTGAGTGAAAAGTATTTT
1 TTTTAAGTAAAAAGTATTTT
52918 T
1 T
52919 AAAAGCACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (20 bp):
TTTTAAGTAAAAAGTATTTT
Found at i:55960 original size:34 final size:34
Alignment explanation
Indices: 55913--55983 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
55903 AAATAATTCT
*
55913 ATTGCAGACCTTTGATGCAAAAATTTTATATACA
1 ATTGCAGAACTTTGATGCAAAAATTTTATATACA
55947 ATTGCAGAACTTTGATGCAAAAATTTTATATACA
1 ATTGCAGAACTTTGATGCAAAAATTTTATATACA
55981 ATT
1 ATT
55984 TATCATGGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (34 bp):
ATTGCAGAACTTTGATGCAAAAATTTTATATACA
Found at i:56521 original size:19 final size:19
Alignment explanation
Indices: 56484--56522 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
56474 CTTCTTGAAA
* * *
56484 CTTTTTTTTTTGAATTTTT
1 CTTTTATTTTTAAAATTTT
56503 CTTTTATTTTTAAAATTTT
1 CTTTTATTTTTAAAATTTT
56522 C
1 C
56523 ATGTCATCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.72
Consensus pattern (19 bp):
CTTTTATTTTTAAAATTTT
Found at i:57539 original size:15 final size:16
Alignment explanation
Indices: 57521--57553 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57511 TTTAGTAATT
57521 ATATATT-TTTAAAAA
1 ATATATTATTTAAAAA
*
57536 ATATATTATTTAATAA
1 ATATATTATTTAAAAA
57552 AT
1 AT
57554 TGAAGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATATTATTTAAAAA
Found at i:58033 original size:105 final size:104
Alignment explanation
Indices: 57755--58068 Score: 540
Period size: 104 Copynumber: 3.0 Consensus size: 104
57745 TCATACTTAT
*
57755 AAATAAAAATTTTCATTTTATTAAAAGACTATAATATTGGTTTTGCATGATGTAATGTTATATTA
1 AAATAAAAATTTTCATTTTATTAATAGACTATAATATTGGTTTTGCATGATGTAATGTTATATTA
*
57820 GTAGAATCATGTAAACTGTTTTTATCTTATCAAAAAAAA
66 GTAGAATCATGTAAGCTGTTTTTATCTTATCAAAAAAAA
57859 AAA-AAAGAATTTTCATTTTATTAATAGACTATAATATTGGTTTTGCATGATGTAATGTTATATT
1 AAATAAA-AATTTTCATTTTATTAATAGACTATAATATTGGTTTTGCATGATGTAATGTTATATT
*
57923 AGTAGAATCATGTAAGTTGTTTTTATCTTATCAAAAAATAA
65 AGTAGAATCATGTAAGCTGTTTTTATCTTATCAAAAAA-AA
* *
57964 TAATAATAATTTTCATTTTATTAATAGACTATAATATTGGTTTTGCATGATGTAATGTTATATTA
1 AAATAAAAATTTTCATTTTATTAATAGACTATAATATTGGTTTTGCATGATGTAATGTTATATTA
* *
58029 GTAGAATCATGAAAGCTGTTTTTATCTTACCAAAAAAAA
66 GTAGAATCATGTAAGCTGTTTTTATCTTATCAAAAAAAA
58068 A
1 A
58069 TTTCATTTTA
Statistics
Matches: 198, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
103 3 0.02
104 97 0.49
105 96 0.48
106 2 0.01
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (104 bp):
AAATAAAAATTTTCATTTTATTAATAGACTATAATATTGGTTTTGCATGATGTAATGTTATATTA
GTAGAATCATGTAAGCTGTTTTTATCTTATCAAAAAAAA
Found at i:58147 original size:14 final size:15
Alignment explanation
Indices: 58128--58158 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
58118 AAAATCAAAT
58128 TTTATA-TTAAATTA
1 TTTATATTTAAATTA
58142 TTTATATTTAAATTA
1 TTTATATTTAAATTA
58157 TT
1 TT
58159 ATGTTTCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTATATTTAAATTA
Found at i:61933 original size:11 final size:11
Alignment explanation
Indices: 61917--61944 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
61907 CAGCATATTT
61917 ATATTCATGTA
1 ATATTCATGTA
61928 ATATTCATGTA
1 ATATTCATGTA
61939 ATATTC
1 ATATTC
61945 GTCTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (11 bp):
ATATTCATGTA
Found at i:65022 original size:61 final size:61
Alignment explanation
Indices: 64951--65077 Score: 159
Period size: 61 Copynumber: 2.1 Consensus size: 61
64941 TTTTTAAAAC
* * **
64951 TTTTAGAATTAGAA-TTAAATTGA-AAATTTTTGTAAATGTTAAGAGCTAAATTTATTGAATT
1 TTTTACAATTAGAACTAAAATT-ATAAA-TTTTGTAAACATTAAGAGCTAAATTTATTGAATT
* * *
65012 TTTTACAATTAGAACTAAAATTATAAATTTTGTAAACATTGAGAGTTAAATTTGTTGAATT
1 TTTTACAATTAGAACTAAAATTATAAATTTTGTAAACATTAAGAGCTAAATTTATTGAATT
65073 TTTTA
1 TTTTA
65078 GATTTAAGAT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
61 48 0.84
62 9 0.16
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (61 bp):
TTTTACAATTAGAACTAAAATTATAAATTTTGTAAACATTAAGAGCTAAATTTATTGAATT
Found at i:65093 original size:61 final size:63
Alignment explanation
Indices: 64978--65130 Score: 161
Period size: 61 Copynumber: 2.5 Consensus size: 63
64968 AATTGAAAAT
* * * *
64978 TTTTGTAAATGTTAAGAGCTAAATTTATTGAATTTTTTACAATTAGAACTAAAA-TTATA-AA
1 TTTTGTAAATATTGAGAGTTAAATTTGTTGAATTTTTTACAATTAGAACTAAAATTTATAGAA
* * * *
65039 TTTTGTAAACATTGAGAGTTAAATTTGTTGAATTTTTTAGATTTAAGATC-AAAATTTATAGAA
1 TTTTGTAAATATTGAGAGTTAAATTTGTTGAATTTTTTACAATT-AGAACTAAAATTTATAGAA
* * *
65102 -TGTATAAATAATGTAGAGTTAAATTTGTT
1 TTTTGTAAATATTG-AGAGTTAAATTTGTT
65131 ATTAAACCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
61 41 0.54
62 18 0.24
63 17 0.22
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.44
Consensus pattern (63 bp):
TTTTGTAAATATTGAGAGTTAAATTTGTTGAATTTTTTACAATTAGAACTAAAATTTATAGAA
Found at i:76775 original size:18 final size:16
Alignment explanation
Indices: 76742--76775 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
76732 TAAAAAAACT
76742 AATATTTAAATGTTTA
1 AATATTTAAATGTTTA
76758 AATATATTAAATGATTTA
1 AATAT-TTAAATG-TTTA
76776 GATTAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 7 0.44
18 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
AATATTTAAATGTTTA
Found at i:76782 original size:14 final size:13
Alignment explanation
Indices: 76763--76801 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
76753 GTTTAAATAT
76763 ATTAAATGATTTAG
1 ATTAAAT-ATTTAG
* *
76777 ATTAAACATTTAT
1 ATTAAATATTTAG
76790 ATTAAATATTTA
1 ATTAAATATTTA
76802 TCAATAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (13 bp):
ATTAAATATTTAG
Found at i:79951 original size:4 final size:4
Alignment explanation
Indices: 79942--79992 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
79932 ATTCTGTTTG
79942 TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT
1 TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT
79990 TGA
1 TGA
79993 GAAATGTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
TGAT
Found at i:90741 original size:18 final size:18
Alignment explanation
Indices: 90712--90755 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
90702 CGTTTTTTAG
*
90712 TATTGATTATGCATGTAA
1 TATTGCTTATGCATGTAA
*
90730 TTTTGCTTATGCATGTAA
1 TATTGCTTATGCATGTAA
90748 TATTGCTT
1 TATTGCTT
90756 TCACAAGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.50
Consensus pattern (18 bp):
TATTGCTTATGCATGTAA
Found at i:93770 original size:8 final size:9
Alignment explanation
Indices: 93738--93776 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
93728 TTTTAATCTT
93738 AATTATAAA
1 AATTATAAA
93747 AATTATAAA
1 AATTATAAA
*
93756 AATATTTAAA
1 AAT-TATAAA
*
93766 AATTTTAAA
1 AATTATAAA
93775 AA
1 AA
93777 GTAAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AATTATAAA
Found at i:98982 original size:24 final size:24
Alignment explanation
Indices: 98955--99034 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
98945 AAATAACTCA
98955 ATTTTCACTTCAATCATGTATCTG
1 ATTTTCACTTCAATCATGTATCTG
** * * * * * *
98979 ATTTTTTCATAAATGATAAATAACTCA
1 ATTTTCACTTCAATCAT--GTATCT-G
99006 ATTTTCACTTCAATCATGTATCTG
1 ATTTTCACTTCAATCATGTATCTG
99030 ATTTT
1 ATTTT
99035 TTCATACTCA
Statistics
Matches: 37, Mismatches: 16, Indels: 6
0.63 0.27 0.10
Matches are distributed among these distances:
24 17 0.46
25 4 0.11
26 4 0.11
27 12 0.32
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.46
Consensus pattern (24 bp):
ATTTTCACTTCAATCATGTATCTG
Found at i:99003 original size:51 final size:51
Alignment explanation
Indices: 98937--99040 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
98927 TGGATTTGCT
98937 TAAATGATAAATAACTCAATTTTCACTTCAATCATGTATCTGATTTTTTCA
1 TAAATGATAAATAACTCAATTTTCACTTCAATCATGTATCTGATTTTTTCA
98988 TAAATGATAAATAACTCAATTTTCACTTCAATCATGTATCTGATTTTTTCA
1 TAAATGATAAATAACTCAATTTTCACTTCAATCATGTATCTGATTTTTTCA
99039 TA
1 TA
99041 CTCATATCAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (51 bp):
TAAATGATAAATAACTCAATTTTCACTTCAATCATGTATCTGATTTTTTCA
Found at i:99035 original size:25 final size:25
Alignment explanation
Indices: 98956--99035 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
98946 AATAACTCAA
98956 TTTTCACTTCAATCATGTATCTGATT
1 TTTTCACTTCAATCATGTATCTGA-T
* * * * * *
98982 TTTTCA--TAAATGATAAATAACTCAA
1 TTTTCACTTCAATCAT--GTATCTGAT
99007 TTTTCACTTCAATCATGTATCTGAT
1 TTTTCACTTCAATCATGTATCTGAT
99032 TTTT
1 TTTT
99036 TCATACTCAT
Statistics
Matches: 38, Mismatches: 12, Indels: 9
0.64 0.20 0.15
Matches are distributed among these distances:
24 6 0.16
25 15 0.39
26 11 0.29
27 6 0.16
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.47
Consensus pattern (25 bp):
TTTTCACTTCAATCATGTATCTGAT
Found at i:100912 original size:71 final size:67
Alignment explanation
Indices: 100788--100921 Score: 178
Period size: 71 Copynumber: 1.9 Consensus size: 67
100778 ATCAACAATA
* ** *
100788 TAATGGTTTTGTCTTTTAACTTAATGAATAAACATTTATCACAACAACGTAGTTTTACCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAAAATAAACATTTATCAAAACAACGTAGTTTTACCTTTTAA
100853 GT
66 GT
* *
100855 TAATGGTTTTGACTTTTAACTTTAGAAAAAGGTAAACATTTATCAAAACGACGTAGTTTTGCCTT
1 TAATGGTTTTGACTTTTAAC-TTA-AAAAA--TAAACATTTATCAAAACAACGTAGTTTTACCTT
100920 TT
62 TT
100922 CTTATTCGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
67 19 0.33
68 3 0.05
69 3 0.05
71 32 0.56
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAAAATAAACATTTATCAAAACAACGTAGTTTTACCTTTTAA
GT
Found at i:103881 original size:33 final size:33
Alignment explanation
Indices: 103847--103910 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
103837 AATAAATAAT
* *
103847 TTTAATC-AAAATAAAATTAAGAAAATAACAAA
1 TTTAATCAAAAACAAAATTAAAAAAATAACAAA
*
103879 TTTAGTCAAAAACAAAATTAAAAAAATAACAA
1 TTTAATCAAAAACAAAATTAAAAAAATAACAA
103911 CTTTGAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.66, C:0.08, G:0.03, T:0.23
Consensus pattern (33 bp):
TTTAATCAAAAACAAAATTAAAAAAATAACAAA
Found at i:103909 original size:17 final size:17
Alignment explanation
Indices: 103859--103910 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
103849 TAATCAAAAT
*
103859 AAAATTAAGAAAATAAC
1 AAAATTAAAAAAATAAC
* ***
103876 AAATTTAGTCAAA-AAC
1 AAAATTAAAAAAATAAC
103892 AAAATTAAAAAAATAAC
1 AAAATTAAAAAAATAAC
103909 AA
1 AA
103911 CTTTGAATAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.69, C:0.08, G:0.04, T:0.19
Consensus pattern (17 bp):
AAAATTAAAAAAATAAC
Found at i:108997 original size:30 final size:30
Alignment explanation
Indices: 108961--109019 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
108951 ATTAATAAAA
*
108961 ATAAAATTACACTTTAATCTTTTTAAAATG
1 ATAAAATTACAATTTAATCTTTTTAAAATG
** *
108991 ATAAAATTTTAATTTAATTTTTTTAAAAT
1 ATAAAATTACAATTTAATCTTTTTAAAAT
109020 TATATTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (30 bp):
ATAAAATTACAATTTAATCTTTTTAAAATG
Found at i:109865 original size:52 final size:52
Alignment explanation
Indices: 109793--109893 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
109783 TTGAGTCCAA
* * * * *
109793 TTTTTAATTTTAATTTACTTTAAGTTTGAATTTGTTCTAAATTTAAATTCAT
1 TTTTTAATTTAAATTTACTTTAAATTTAAATTTATTCTAAATTAAAATTCAT
* *
109845 TTTTTAGTTTAAATTTACTTTAAATTTAAATTTATTGTAAATTAAAATT
1 TTTTTAATTTAAATTTACTTTAAATTTAAATTTATTCTAAATTAAAATT
109894 AATTAAAAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (52 bp):
TTTTTAATTTAAATTTACTTTAAATTTAAATTTATTCTAAATTAAAATTCAT
Found at i:109874 original size:17 final size:17
Alignment explanation
Indices: 109798--109893 Score: 70
Period size: 17 Copynumber: 5.6 Consensus size: 17
109788 TCCAATTTTT
*
109798 AATTTTAATTTACTTTA
1 AATTTAAATTTACTTTA
* * *
109815 AGTTTGAATTT-GTTCTA
1 AATTTAAATTTACTT-TA
* * *
109832 AATTTAAATTCATTTTTT
1 AATTTAAATTTA-CTTTA
*
109850 AGTTTAAATTTACTTTA
1 AATTTAAATTTACTTTA
109867 AATTTAAATTTA-TTGTA
1 AATTTAAATTTACTT-TA
*
109884 AATTAAAATT
1 AATTTAAATT
109894 AATTAAAAAG
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
16 4 0.07
17 44 0.72
18 11 0.18
19 2 0.03
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTACTTTA
Found at i:111739 original size:30 final size:30
Alignment explanation
Indices: 111703--111913 Score: 133
Period size: 30 Copynumber: 7.2 Consensus size: 30
111693 TATTGTCCAT
*
111703 AAATTATATTTTGACCCTCAAACTTTTTCA
1 AAATTATATTTTGACCCTCAAACTTTTACA
* *
111733 AAATTATATTTTGACACTTAAA-TTTTACAA
1 AAATTATATTTTGACCCTCAAACTTTTAC-A
* * *
111763 AAATTACATTTTTACCC-CTAAAC-TTTCCA
1 AAATTATATTTTGACCCTC-AAACTTTTACA
*
111792 AAATT-TCATTTTTGACCCTTAAA-TTTTACA
1 AAATTAT-A-TTTTGACCCTCAAACTTTTACA
* * * *
111822 AAATTACATTTTTA-CCTCTGAAC-TTTCCA
1 AAATTATATTTTGACCCTC-AAACTTTTACA
111851 AAATTCCAT-TTTTGACCCT-AAA-TTTTACAA
1 AAATT--ATATTTTGACCCTCAAACTTTTAC-A
* *
111881 AAATTACATTTT-ACCC-CTAAAC-TTTCCA
1 AAATTATATTTTGACCCTC-AAACTTTTACA
111909 AAATT
1 AAATT
111914 CCATTTTTAC
Statistics
Matches: 139, Mismatches: 23, Indels: 40
0.69 0.11 0.20
Matches are distributed among these distances:
28 14 0.10
29 46 0.33
30 75 0.54
31 4 0.03
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.41
Consensus pattern (30 bp):
AAATTATATTTTGACCCTCAAACTTTTACA
Found at i:111801 original size:29 final size:29
Alignment explanation
Indices: 111698--112187 Score: 337
Period size: 29 Copynumber: 16.7 Consensus size: 29
111688 CCGTATATTG
* *
111698 TCCATAAATTATATTTTGA-CCCTCAAACTTT
1 TCCA-AAATTACATTTTTACCCCT-AAAC-TT
* * * * * *
111729 TTCAAAATTATATTTTGACACTTAAATTT
1 TCCAAAATTACATTTTTACCCCTAAACTT
*
111758 TACAAAAATTACATTTTTACCCCTAAACTT
1 T-CCAAAATTACATTTTTACCCCTAAACTT
* * *
111788 TCCAAAATTTCATTTTTGACCCTTAAATTT
1 TCCAAAATTACATTTTT-ACCCCTAAACTT
* * *
111818 TACAAAATTACATTTTTACCTCTGAACTT
1 TCCAAAATTACATTTTTACCCCTAAACTT
* *
111847 TCCAAAATTCCATTTTTGA-CCCTAAATTT
1 TCCAAAATTACATTTTT-ACCCCTAAACTT
*
111876 TACAAAAATTACA-TTTTACCCCTAAACTT
1 T-CCAAAATTACATTTTTACCCCTAAACTT
*
111905 TCCAAAATTCCATTTTTA-CCCT-AA-TT
1 TCCAAAATTACATTTTTACCCCTAAACTT
*
111931 TCCCAAAAATTACATTTTCACCCCTAAACTT
1 T-CC-AAAATTACATTTTTACCCCTAAACTT
* * *
111962 TCCAAAATTCCATTTTTGA--CCTCAATTT
1 TCCAAAATTACATTTTT-ACCCCTAAACTT
*
111990 CTCCAAAAATTACATTTTTACCACTAAACTT
1 -TCC-AAAATTACATTTTTACCCCTAAACTT
* ** **
112021 TCCAAAATTCCATTTTTGA--TATAGATTTT
1 TCCAAAATTACATTTTT-ACCCCTA-AACTT
*
112050 TCCAAAAATTACA-TTTTACCCCCAAACTT
1 TCC-AAAATTACATTTTTACCCCTAAACTT
* **
112079 TCCAAAATTCCATTTTTTGACCCC-AATTTT
1 TCCAAAATTACA-TTTTT-ACCCCTAAACTT
* *
112109 TCAAAAAATTACA-TTTTACCTCC-GAACTT
1 TC-CAAAATTACATTTTTACC-CCTAAACTT
* * *
112138 CCCAAAATTCCATTTTTACCCC-AAAATT
1 TCCAAAATTACATTTTTACCCCTAAACTT
112166 TCCAAAAATTACCA-TTTTACCC
1 TCC-AAAATTA-CATTTTTACCC
112188 TCGAATTTCT
Statistics
Matches: 362, Mismatches: 67, Indels: 62
0.74 0.14 0.13
Matches are distributed among these distances:
26 3 0.01
27 4 0.01
28 64 0.18
29 147 0.41
30 117 0.32
31 27 0.07
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.39
Consensus pattern (29 bp):
TCCAAAATTACATTTTTACCCCTAAACTT
Found at i:111827 original size:59 final size:59
Alignment explanation
Indices: 111703--112187 Score: 541
Period size: 59 Copynumber: 8.3 Consensus size: 59
111693 TATTGTCCAT
* * * *
111703 AAATTATATTTTGA-CCCTCAAACTTTTTCAAAATT--ATATTTTGACACTTAAATTTTACAA
1 AAATTACATTTTTACCCCT-AAAC-TTTCCAAAATTCCAT-TTTTGAC-CCTAAATTTTACAA
*
111763 AAATTACATTTTTACCCCTAAACTTTCCAAAATTTCATTTTTGACCCTTAAATTTTAC-A
1 AAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCC-TAAATTTTACAA
* *
111822 AAATTACATTTTTACCTCTGAACTTTCCAAAATTCCATTTTTGACCCTAAATTTTACAA
1 AAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTTACAA
**
111881 AAATTACA-TTTTACCCCTAAACTTTCCAAAATTCCATTTTT-ACCCT-AATTTCCCAA
1 AAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTTACAA
* * *
111937 AAATTACATTTTCACCCCTAAACTTTCCAAAATTCCATTTTTGA-CCTCAATTTCTCCAA
1 AAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCTAAATTT-TACAA
* ** * *
111996 AAATTACATTTTTACCACTAAACTTTCCAAAATTCCATTTTTGA-TATAGATTTTTCCAA
1 AAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCTA-AATTTTACAA
* * *
112055 AAATTACA-TTTTACCCCCAAACTTTCCAAAATTCCATTTTTTGACCC-CAATTTTTCAAA
1 AAATTACATTTTTACCCCTAAACTTTCCAAAATTCCA-TTTTTGACCCTAAATTTTAC-AA
* * * * *
112114 AAATTACA-TTTTACCTCC-GAACTTCCCAAAATTCCATTTTT-ACCCCAAAATTTCCAA
1 AAATTACATTTTTACC-CCTAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTTACAA
112171 AAATTACCA-TTTTACCC
1 AAATTA-CATTTTTACCC
112188 TCGAATTTCT
Statistics
Matches: 378, Mismatches: 31, Indels: 35
0.85 0.07 0.08
Matches are distributed among these distances:
56 16 0.04
57 53 0.14
58 99 0.26
59 165 0.44
60 39 0.10
61 6 0.02
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (59 bp):
AAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTTACAA
Found at i:112194 original size:29 final size:31
Alignment explanation
Indices: 111710--112248 Score: 285
Period size: 29 Copynumber: 18.4 Consensus size: 31
111700 CATAAATTAT
* * *
111710 ATTTTGACCCTCAAACTTTTTC-AAAATTA-T
1 ATTTTTACCCTCAAAC-TTTCCAAAAATTACC
* * * * *
111740 ATTTTGACACTTAAATTTTACAAAAATTA-C
1 ATTTTTACCCTCAAACTTTCCAAAAATTACC
*
111770 ATTTTTACCC-CTAAACTTTCC-AAAATT-TC
1 ATTTTTACCCTC-AAACTTTCCAAAAATTACC
* * *
111799 ATTTTTGACCCTTAAATTTTAC-AAAATTA-C
1 ATTTTT-ACCCTCAAACTTTCCAAAAATTACC
*
111829 ATTTTTA-CCTCTGAACTTTCC-AAAATT-CC
1 ATTTTTACCCTC-AAACTTTCCAAAAATTACC
* *
111858 ATTTTTGACCCT-AAATTTTACAAAAATTA-C
1 ATTTTT-ACCCTCAAACTTTCCAAAAATTACC
111888 A-TTTTACCC-CTAAACTTTCC-AAAATT-CC
1 ATTTTTACCCTC-AAACTTTCCAAAAATTACC
111916 ATTTTTACCCT--AA-TTTCCCAAAAATTA-C
1 ATTTTTACCCTCAAACTTT-CCAAAAATTACC
*
111944 ATTTTCACCC-CTAAACTTTCC-AAAATT-CC
1 ATTTTTACCCTC-AAACTTTCCAAAAATTACC
*
111973 ATTTTTGA-CCTC-AATTTCTCCAAAAATTA-C
1 ATTTTT-ACCCTCAAACTT-TCCAAAAATTACC
112003 ATTTTTACCACT-AAACTTTCC-AAAATT-CC
1 ATTTTTACC-CTCAAACTTTCCAAAAATTACC
** **
112032 ATTTTTGA-TAT-AGATTTTTCCAAAAATTA-C
1 ATTTTT-ACCCTCA-AACTTTCCAAAAATTACC
*
112062 A-TTTTACCCCCAAACTTTCC-AAAATT-CC
1 ATTTTTACCCTCAAACTTTCCAAAAATTACC
** *
112090 ATTTTTTGACCC-CAATTTTTCAAAAAATTA-C
1 A-TTTTT-ACCCTCAAACTTTCCAAAAATTACC
* *
112121 A-TTTTA-CCTCCGAAC-TTCCCAAAATT-CC
1 ATTTTTACCCT-CAAACTTTCCAAAAATTACC
*
112149 ATTTTTACCC-CAAAATTTCCAAAAATTACC
1 ATTTTTACCCTCAAACTTTCCAAAAATTACC
* * *
112179 A-TTTTACCCTCGAA-TTTCTAAAAATTTCGC
1 ATTTTTACCCTCAAACTTTCCAAAAATTAC-C
*
112209 --TTTTAACCTCAAACTTTCTC-AAAATTACC
1 ATTTTTACCCTCAAACTTTC-CAAAAATTACC
112238 A-TTTTACCCTC
1 ATTTTTACCCTC
112249 GGGTATCCAA
Statistics
Matches: 397, Mismatches: 54, Indels: 116
0.70 0.10 0.20
Matches are distributed among these distances:
26 3 0.01
27 6 0.02
28 61 0.15
29 162 0.41
30 141 0.36
31 24 0.06
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (31 bp):
ATTTTTACCCTCAAACTTTCCAAAAATTACC
Found at i:112203 original size:58 final size:58
Alignment explanation
Indices: 111698--112248 Score: 495
Period size: 59 Copynumber: 9.4 Consensus size: 58
111688 CCGTATATTG
* * * **
111698 TCCATAAATTATATTTTGACCCTCAAACTTTTTCAAAATT--ATATTTTGACACTTAAATTT
1 TCCAAAAATTACATTTT-ACCCTCAAAC-TTTCCAAAATTCCAT-TTTTGAC-CCCAAATTT
* * *
111758 TACAAAAATTACATTTTTACCC-CTAAACTTTCCAAAATTTCATTTTTGACCCTTAAATTT
1 TCCAAAAATTACA-TTTTACCCTC-AAACTTTCCAAAATTCCATTTTTGACCC-CAAATTT
* * *
111818 TAC-AAAATTACATTTTTA-CCTCTGAACTTTCCAAAATTCCATTTTTGACCCTAAATTT
1 TCCAAAAATTACA-TTTTACCCTC-AAACTTTCCAAAATTCCATTTTTGACCCCAAATTT
* *
111876 TACAAAAATTACATTTTACCC-CTAAACTTTCCAAAATTCCATTTTT-A-CCCTAATTT
1 TCCAAAAATTACATTTTACCCTC-AAACTTTCCAAAATTCCATTTTTGACCCCAAATTT
* *
111932 CCCAAAAATTACATTTTCACCC-CTAAACTTTCCAAAATTCCATTTTTGACCTC-AATTT
1 TCCAAAAATTACATTTT-ACCCTC-AAACTTTCCAAAATTCCATTTTTGACCCCAAATTT
*** *
111990 CTCCAAAAATTACATTTTTACCACT-AAACTTTCCAAAATTCCATTTTTGA-TATAGATTTT
1 -TCCAAAAATTACA-TTTTACC-CTCAAACTTTCCAAAATTCCATTTTTGACCCCA-AATTT
* *
112050 TCCAAAAATTACATTTTACCCCCAAACTTTCCAAAATTCCATTTTTTGACCCCAATTTT
1 TCCAAAAATTACATTTTACCCTCAAACTTTCCAAAATTCCA-TTTTTGACCCCAAATTT
* * * *
112109 TCAAAAAATTACATTTTA-CCTCCGAACTTCCCAAAATTCCATTTTT-ACCCCAAAATT
1 TCCAAAAATTACATTTTACCCT-CAAACTTTCCAAAATTCCATTTTTGACCCCAAATTT
* * * ** * * *
112166 TCCAAAAATTACCATTTTACCCTCGAA-TTTCTAAAAATTTCGCTTTTAACCTCAAACTT
1 TCCAAAAATTA-CATTTTACCCTCAAACTTTC-CAAAATTCCATTTTTGACCCCAAATTT
112225 TCTC-AAAATTACCATTTTACCCTC
1 TC-CAAAAATTA-CATTTTACCCTC
112249 GGGTATCCAA
Statistics
Matches: 429, Mismatches: 36, Indels: 53
0.83 0.07 0.10
Matches are distributed among these distances:
56 22 0.05
57 53 0.12
58 101 0.24
59 201 0.47
60 46 0.11
61 6 0.01
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (58 bp):
TCCAAAAATTACATTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCCCAAATTT
Found at i:112755 original size:2 final size:2
Alignment explanation
Indices: 112748--112780 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
112738 GTTTTCAAAT
112748 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
112781 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:116332 original size:32 final size:31
Alignment explanation
Indices: 116295--116413 Score: 141
Period size: 31 Copynumber: 3.8 Consensus size: 31
116285 TGATATATAA
* *
116295 AATATTTAAAAAACTTAAATATAATAATAAAT
1 AATATTTAAATAA-TTTAATATAATAATAAAT
* * *
116327 TATATTTAAGTAATTTAATACAATAATAAAT
1 AATATTTAAATAATTTAATATAATAATAAAT
* *
116358 GATATTTACATAATTTAATATAATAA-AAAT
1 AATATTTAAATAATTTAATATAATAATAAAT
116388 GAAATATTTAAATAATTTAATATAAT
1 --AATATTTAAATAATTTAATATAAT
116414 GTTACATAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
30 4 0.05
31 38 0.51
32 32 0.43
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (31 bp):
AATATTTAAATAATTTAATATAATAATAAAT
Found at i:116409 original size:16 final size:16
Alignment explanation
Indices: 116359--116410 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
116349 ATAATAAATG
*
116359 ATATTTACATAATTTA
1 ATATTTAAATAATTTA
* **
116375 ATATAATAAA-AATGAA
1 ATAT-TTAAATAATTTA
116391 ATATTTAAATAATTTA
1 ATATTTAAATAATTTA
116407 ATAT
1 ATAT
116411 AATGTTACAT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
15 4 0.15
16 20 0.74
17 3 0.11
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
ATATTTAAATAATTTA
Found at i:116431 original size:63 final size:63
Alignment explanation
Indices: 116312--116440 Score: 136
Period size: 63 Copynumber: 2.0 Consensus size: 63
116302 AAAAAACTTA
* * * * * *
116312 AATATAATAATAAATTATATTTAAGTAATTTAATACAATAATAAATGATATTTACA-TAATTT
1 AATATAATAATAAATAATATTTAAATAATTTAATACAATAATAAATAAAATATACATTAATCT
* ** *
116374 AATATAATAA-AAATGAAATATTTAAATAATTTAATATAATGTTACATAAAATATACATTAATCT
1 AATATAATAATAAAT--AATATTTAAATAATTTAATACAATAATAAATAAAATATACATTAATCT
116438 AAT
1 AAT
116441 TTTTTTATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
61 4 0.07
62 10 0.19
63 32 0.59
64 8 0.15
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (63 bp):
AATATAATAATAAATAATATTTAAATAATTTAATACAATAATAAATAAAATATACATTAATCT
Found at i:117305 original size:24 final size:23
Alignment explanation
Indices: 117264--117325 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 23
117254 ATATTTTTTT
117264 TATTTTTAAATAAAAATAAATTTATA
1 TATTTTTAAAT---AATAAATTTATA
*
117290 TTTTTTTGAAATAATAAATTTATA
1 TATTTTT-AAATAATAAATTTATA
117314 TATTTTTAAATA
1 TATTTTTAAATA
117326 GCCCCATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 5 0.15
24 18 0.55
26 6 0.18
27 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTTTTAAATAATAAATTTATA
Found at i:121446 original size:3 final size:3
Alignment explanation
Indices: 121438--121477 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
121428 AGAGTTTCTT
121438 TTA 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 TTA T
121478 AACATTATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:121537 original size:3 final size:3
Alignment explanation
Indices: 121529--121553 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
121519 TTTAATCATC
121529 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
121554 CAAATGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:122240 original size:6 final size:6
Alignment explanation
Indices: 122229--122253 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
122219 CTCTACTTCT
122229 CATACA CATACA CATACA CATACA C
1 CATACA CATACA CATACA CATACA C
122254 TACCACCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (6 bp):
CATACA
Found at i:124223 original size:82 final size:82
Alignment explanation
Indices: 124086--124253 Score: 327
Period size: 82 Copynumber: 2.0 Consensus size: 82
124076 ATGTGTTGTG
124086 TCATACATTGGAGATGGTGGCACCAGTGAAGTGAGTAGACAAATAATCTCATACTTTATTTGCTT
1 TCATACATTGGAGATGGTGGCACCAGTGAAGTGAGTAGACAAATAATCTCATACTTTATTTGCTT
124151 ATTTTAGACTAGTTAGC
66 ATTTTAGACTAGTTAGC
*
124168 TCATACATTGGAGATGGTGGCACCAGTGAAGTGAGTAGACAAATAGTCTCATACTTTATTTGCTT
1 TCATACATTGGAGATGGTGGCACCAGTGAAGTGAGTAGACAAATAATCTCATACTTTATTTGCTT
124233 ATTTTAGACTAGTTAGC
66 ATTTTAGACTAGTTAGC
124250 TCAT
1 TCAT
124254 GGTTTTCCAT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 85 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.35
Consensus pattern (82 bp):
TCATACATTGGAGATGGTGGCACCAGTGAAGTGAGTAGACAAATAATCTCATACTTTATTTGCTT
ATTTTAGACTAGTTAGC
Found at i:132906 original size:96 final size:96
Alignment explanation
Indices: 132729--132913 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 96
132719 GAAAAGAATG
* ** * *
132729 TTCGATTATCTCGATTTGATGAAAGGTTGTACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATATTCAGAATCGA
* *
132794 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AAATAAAGAAACATTGCCTCGATTAAGGGTA
*
132825 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATATTC-GAAACTC
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATATTCAG-AA-TC
*
132889 -AAAATAAA-AGAATATTGCCTCGATT
64 GAAAATAAAGA-AACATTGCCTCGATT
132914 TTAAAGTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
95 2 0.03
96 73 0.95
97 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATATTCAGAATCGA
AAATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:133407 original size:88 final size:87
Alignment explanation
Indices: 133297--133543 Score: 295
Period size: 88 Copynumber: 2.8 Consensus size: 87
133287 GTAAAATGGG
* * *
133297 ATTTTTGGAAGTTTCGGAGTAAAAAATGGCATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTT
1 ATTTTTGGAAGTTTCGGGGTAAAAAATGGAATTTTTGGAAGTTT-GGGGTCAAAATGGAATTTTT
133362 GGAAGTTCGAGGATAAAAATGAA
65 GGAAGTTCGAGGATAAAAATGAA
* * *
133385 ATTTTTGGGAGTTTCGGGGTAAAAAAT--ATATTTTTGAAAGTTTCGAGGTCAAAATGGAATTTT
1 ATTTTTGGAAGTTTCGGGGTAAAAAATGGA-ATTTTTGGAAGTTT-GGGGTCAAAATGGAATTTT
* * * **
133448 TGGAATTTTTGAGGTTAAAAATGGG
64 TGGAA-GTTCGAGGATAAAAATGAA
* *
133473 ATTTTTGGAAG-TTCGGGGGT-AAAAATGGAATTTTTGGAAGTTATAGGGTCAAAATAGAATTTT
1 ATTTTTGGAAGTTTC-GGGGTAAAAAATGGAATTTTTGGAAGTT-TGGGGTCAAAATGGAATTTT
133536 TGGAAGTT
64 TGGAAGTT
133544 TCGGGGTCCT
Statistics
Matches: 135, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
87 46 0.34
88 87 0.64
89 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (87 bp):
ATTTTTGGAAGTTTCGGGGTAAAAAATGGAATTTTTGGAAGTTTGGGGTCAAAATGGAATTTTTG
GAAGTTCGAGGATAAAAATGAA
Found at i:133551 original size:29 final size:29
Alignment explanation
Indices: 133203--133550 Score: 304
Period size: 29 Copynumber: 12.0 Consensus size: 29
133193 ATTTGGGGTT
*
133203 TAAAAATGGAATTTTTAGACA-TTT-GGGG
1 TAAAAATGGAATTTTTGGA-AGTTTCGGGG
* *
133231 TAAAAATGGAA-TTTT-GAGAGTTTCGAGT
1 TAAAAATGGAATTTTTGGA-AGTTTCGGGG
* * * **
133259 TGAAAATGGAGA-TTTTAGAGGTTTAAGGG
1 TAAAAATGGA-ATTTTTGGAAGTTTCGGGG
* *
133288 T-AAAATGGGATTTTTGGAAGTTTCGGAG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
* *
133316 TAAAAAATGGCATTTTTGGAAGTTTGGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTCGGGG
*
133346 TAAAAATGGAATTTTTGGAAG-TTCGAGGA
1 TAAAAATGGAATTTTTGGAAGTTTCG-GGG
* *
133375 TAAAAATGAAATTTTTGGGAGTTTCGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
* *
133404 TAAAAAAT--ATATTTTTGAAAGTTTCGAGG
1 T-AAAAATGGA-ATTTTTGGAAGTTTCGGGG
* * * *
133433 TCAAAATGGAATTTTTGGAATTTTTGAGGT
1 TAAAAATGGAATTTTTGGAAGTTTCG-GGG
*
133463 TAAAAATGGGATTTTTGGAAG-TTCGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTC-GGGG
*
133492 TAAAAATGGAATTTTTGGAAGTTAT-AGGG
1 TAAAAATGGAATTTTTGGAAGTT-TCGGGG
* *
133521 TCAAAATAGAATTTTTGGAAGTTTCGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
133550 T
1 T
133551 CCTCTAAGGC
Statistics
Matches: 259, Mismatches: 43, Indels: 35
0.77 0.13 0.10
Matches are distributed among these distances:
26 3 0.01
27 8 0.03
28 52 0.20
29 136 0.53
30 59 0.23
31 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTCGGGG
Found at i:135329 original size:6 final size:6
Alignment explanation
Indices: 135312--135377 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
135302 ATATAAATAG
* *
135312 ATTTAA ATTTTAA ATTTATA A--TAA ATTTAA ATTTTA A-GTAA ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
135359 ACTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
135378 CTTGTTGGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
4 2 0.04
5 9 0.19
6 28 0.60
7 8 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:135340 original size:17 final size:17
Alignment explanation
Indices: 135315--135377 Score: 83
Period size: 17 Copynumber: 3.6 Consensus size: 17
135305 TAAATAGATT
135315 TAAATTTTAAATTTATAA
1 TAAA-TTTAAATTTATAA
135333 TAAATTTAAATTT-TAA
1 TAAATTTAAATTTATAA
* *
135349 GTAAATTTAAACTTAAAA
1 -TAAATTTAAATTTATAA
135367 TAAATTTAAAT
1 TAAATTTAAAT
135378 CTTGTTGGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
16 3 0.08
17 31 0.77
18 6 0.15
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:136738 original size:3 final size:3
Alignment explanation
Indices: 136730--136754 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
136720 GACAGGATAT
136730 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
136755 TGTACAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:142806 original size:27 final size:26
Alignment explanation
Indices: 142761--142814 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
142751 AGTTAAAATT
*
142761 ATTATAAAAATATAAAAATCTAATAA
1 ATTATAAAAAAATAAAAATCTAATAA
* *
142787 ATTATAAAAAAAATATAAATTTAATAA
1 ATTAT-AAAAAAATAAAAATCTAATAA
142814 A
1 A
142815 ACTTTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
ATTATAAAAAAATAAAAATCTAATAA
Found at i:143492 original size:19 final size:19
Alignment explanation
Indices: 143451--143529 Score: 56
Period size: 20 Copynumber: 4.2 Consensus size: 19
143441 AATTGTTATT
* *
143451 AAAA-TATTAAATTTGATAT
1 AAAATTATTAAAATT-ATAA
143470 AAAATTATTAAAATTATAAA
1 AAAATTATTAAAATTAT-AA
* *
143490 AAAATTGTAAAAACTTAT-A
1 AAAATTATTAAAA-TTATAA
* *
143509 AATATTA-TAAAAATATAA
1 AAAATTATTAAAATTATAA
143527 AAA
1 AAA
143530 TTCTAATAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
17 3 0.06
18 7 0.15
19 12 0.26
20 21 0.45
21 4 0.09
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (19 bp):
AAAATTATTAAAATTATAA
Found at i:143530 original size:19 final size:19
Alignment explanation
Indices: 143473--143530 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
143463 TTGATATAAA
* *
143473 ATTATTAAAATTATAAAAAA
1 ATTA-TAAAAATATAAAAAT
* *
143493 ATTGTAAAAACT-TATAAAT
1 ATTATAAAAA-TATAAAAAT
143512 ATTATAAAAATATAAAAAT
1 ATTATAAAAATATAAAAAT
143531 TCTAATAACG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 1 0.03
19 25 0.83
20 4 0.13
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
ATTATAAAAATATAAAAAT
Found at i:143558 original size:38 final size:36
Alignment explanation
Indices: 143468--143569 Score: 107
Period size: 38 Copynumber: 2.7 Consensus size: 36
143458 TAAATTTGAT
* * *
143468 ATAAAATTATTAAAATTATAAAAAAATTGTAAAAACTT
1 ATAAAATTATTAAAA--ATATAAAAATTCTAAAAACTA
*
143506 ATAAATATTA-TAAAAATATAAAAATTCTAATAACGTA
1 ATAAA-ATTATTAAAAATATAAAAATTCTAAAAAC-TA
*
143543 ATAAAACTTATTAAAAATATTAAAATT
1 ATAAAA-TTATTAAAAATATAAAAATT
143570 GATATAAACT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
36 17 0.31
37 9 0.16
38 25 0.45
39 4 0.07
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (36 bp):
ATAAAATTATTAAAAATATAAAAATTCTAAAAACTA
Found at i:143727 original size:31 final size:31
Alignment explanation
Indices: 143662--143728 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
143652 TTGTAATTCA
**
143662 AAAAAAAATTGTTTAAAATATTTAAAATTTT
1 AAAAAAAATTGTTTAAAATATTTAAAATAAT
*
143693 AAAAAAAA-TGTATTAGAAT-TCTTAAAATAAT
1 AAAAAAAATTGT-TTAAAATAT-TTAAAATAAT
143724 AAAAA
1 AAAAA
143729 TTACAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (31 bp):
AAAAAAAATTGTTTAAAATATTTAAAATAAT
Found at i:144369 original size:41 final size:38
Alignment explanation
Indices: 144306--144384 Score: 122
Period size: 41 Copynumber: 2.0 Consensus size: 38
144296 TTAAATATGT
144306 CTTATTAATTTTTTTAATATTTTTACAATTTGTTATAA
1 CTTATTAATTTTTTTAATATTTTTACAATTTGTTATAA
*
144344 CTTATTAGATTTTTTTTTATAATTTTTACAATTTGTTATAA
1 CTTATTA-A-TTTTTTTAAT-ATTTTTACAATTTGTTATAA
144385 TCATATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
38 7 0.19
39 1 0.03
40 9 0.24
41 20 0.54
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (38 bp):
CTTATTAATTTTTTTAATATTTTTACAATTTGTTATAA
Found at i:144521 original size:18 final size:17
Alignment explanation
Indices: 144497--144608 Score: 116
Period size: 17 Copynumber: 6.4 Consensus size: 17
144487 TAAAACTCCC
144497 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* * *
144515 ATTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
*
144532 GTTTAATTTTATTTTAAA
1 -TTTAAATTTATTTTAAA
* *
144550 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
144567 TTTAAATTTATTTTCAAT
1 TTTAAATTTATTTT-AAA
* *
144585 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
144602 TTTAAAT
1 TTTAAAT
144609 AAAGCTAAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
17 38 0.50
18 38 0.50
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:144530 original size:17 final size:18
Alignment explanation
Indices: 144498--144565 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
144488 AAAACTCCCT
*
144498 TTAAATTTATTTTAAAAA
1 TTAAATTTAGTTTAAAAA
*
144516 TTAAATTT-GTTTAAAAGT
1 TTAAATTTAGTTTAAAA-A
* * *
144534 TTAATTTTA-TTTTAAAT
1 TTAAATTTAGTTTAAAAA
*
144551 TTAAATTTAATTTAA
1 TTAAATTTAGTTTAA
144566 GTTTAAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
17 16 0.39
18 25 0.61
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTAAATTTAGTTTAAAAA
Found at i:144553 original size:6 final size:6
Alignment explanation
Indices: 144544--144576 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
144534 TTAATTTTAT
*
144544 TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
144577 TTTTCAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:144553 original size:11 final size:12
Alignment explanation
Indices: 144536--144586 Score: 52
Period size: 11 Copynumber: 4.4 Consensus size: 12
144526 TTAAAAGTTT
*
144536 AATTTTATTTTA
1 AATTTAATTTTA
*
144548 AATTTAAATTT-
1 AATTTAATTTTA
*
144559 AATTTAAGTTTA
1 AATTTAATTTTA
*
144571 AATTT-ATTTTC
1 AATTTAATTTTA
144582 AATTT
1 AATTT
144587 TAAAATTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
11 19 0.58
12 14 0.42
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (12 bp):
AATTTAATTTTA
Found at i:144589 original size:35 final size:33
Alignment explanation
Indices: 144497--144608 Score: 116
Period size: 35 Copynumber: 3.2 Consensus size: 33
144487 TAAAACTCCC
* *
144497 TTTAAATTTATTTTAAAAATTAAATTTGTTTAAAAG
1 TTTAAATTTATTTT-AAATTTAAATTTATTT--AAG
*
144533 TTTAATTTTATTTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAATTTAAATTT-ATTTAAG
* * *
144567 TTTAAATTTATTTTCAATTTTAAAATTATTATAAA
1 TTTAAATTTATTTT-AAATTTAAATTTATT-TAAG
144602 TTTAAAT
1 TTTAAAT
144609 AAAGCTAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
34 19 0.29
35 31 0.47
36 16 0.24
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (33 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTAAG
Found at i:145391 original size:20 final size:21
Alignment explanation
Indices: 145350--145387 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
145340 TAATAGCATT
145350 ATTATTAATATATTAATAATA
1 ATTATTAATATATTAATAATA
145371 ATTA-TAATAT-TTAATAA
1 ATTATTAATATATTAATAA
145388 ATAACTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 6 0.35
21 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTATTAATATATTAATAATA
Found at i:145398 original size:19 final size:20
Alignment explanation
Indices: 145355--145398 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
145345 GCATTATTAT
*
145355 TAATATATTAATAATAATTA
1 TAATATATTAATAATAACTA
145375 TAATAT-TTAATAAATAACTA
1 TAATATATTAAT-AATAACTA
145395 -AATA
1 TAATA
145399 AAAAAAGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATATATTAATAATAACTA
Found at i:146345 original size:30 final size:30
Alignment explanation
Indices: 146309--146646 Score: 346
Period size: 30 Copynumber: 11.4 Consensus size: 30
146299 GGAGGTCCCT
146309 AACTTCCAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATCCCATTTTTAACCCCAA
* * **
146339 AACTTCCAAAAATTCTATTTTT--CCCCCG
1 AACTTCCAAAAATCCCATTTTTAACCCCAA
* * * * *
146367 AACTTCAAAAAATTCCATTTTTGACCTCGA
1 AACTTCCAAAAATCCCATTTTTAACCCCAA
* * * **
146397 AACTTTCAAAAATTCTA-TTTT-ACCCCCG
1 AACTTCCAAAAATCCCATTTTTAACCCCAA
*
146425 AACTTCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATCCCATTTTTAACCCCAA
* * * *
146455 AACTTCAAAAAATTCCATTTTTACCCCCCA
1 AACTTCCAAAAATCCCATTTTTAACCCCAA
**
146485 AACTTCCAAAAATCCCATTTTTAACCTTAA
1 AACTTCCAAAAATCCCATTTTTAACCCCAA
* * *
146515 AACTTCCAAAAAATTCCATTTTTAAACCTAA
1 AACTTCC-AAAAATCCCATTTTTAACCCCAA
*
146546 AACTTCCAAAAATCTCA-TTTTAACCCCAA
1 AACTTCCAAAAATCCCATTTTTAACCCCAA
* *
146575 AACTTCCAAAAATCTCATTTTT-ACCCCCA
1 AACTTCCAAAAATCCCATTTTTAACCCCAA
* *
146604 AACTTCCAAAAATCCCATTTTTGACCTCAA
1 AACTTCCAAAAATCCCATTTTTAACCCCAA
* *
146634 AATTTCCCAAAAT
1 AACTTCCAAAAAT
146647 TACCCTTTTA
Statistics
Matches: 257, Mismatches: 44, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
28 42 0.16
29 62 0.24
30 126 0.49
31 27 0.11
ACGTcount: A:0.38, C:0.30, G:0.02, T:0.31
Consensus pattern (30 bp):
AACTTCCAAAAATCCCATTTTTAACCCCAA
Found at i:146400 original size:58 final size:59
Alignment explanation
Indices: 146309--146647 Score: 416
Period size: 58 Copynumber: 5.7 Consensus size: 59
146299 GGAGGTCCCT
*
146309 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCTATTTTT-CCCCCG
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCTATTTTTACCCCCA
* * * * * * *
146367 AACTTCAAAAAATTCCATTTTTGACCTCGAAACTTTCAAAAATTCTA-TTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCTATTTTTACCCCCA
* * *
146425 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCAAAAAATTCCATTTTTACCCCCCA
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCTATTTTTA-CCCCCA
** * * **
146485 AACTTCCAAAAATCCCATTTTTAACCTTAAAACTTCCAAAAAATTCCATTTTTAAACCTAA
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCC-AAAAATTCTATTTTT-ACCCCCA
*
146546 AACTTCCAAAAATCTCA-TTTTAACCCCAAAACTTCCAAAAA-TCTCATTTTTACCCCCA
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCT-ATTTTTACCCCCA
* * * *
146604 AACTTCCAAAAATCCCATTTTTGACCTCAAAATTTCCCAAAATT
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATT
146648 ACCCTTTTAC
Statistics
Matches: 240, Mismatches: 33, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
57 4 0.02
58 109 0.45
59 36 0.15
60 56 0.23
61 34 0.14
62 1 0.00
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.31
Consensus pattern (59 bp):
AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCTATTTTTACCCCCA
Found at i:149189 original size:17 final size:18
Alignment explanation
Indices: 149155--149207 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
149145 TAACTTCAAA
*
149155 AATAAATTATA-TATTTTT
1 AATAATTTATATTA-TTTT
*
149173 ACTAATTT-TATTATTTT
1 AATAATTTATATTATTTT
149190 AATAATTTATATTATTTT
1 AATAATTTATATTATTTT
149208 TATTTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
AATAATTTATATTATTTT
Found at i:149189 original size:18 final size:18
Alignment explanation
Indices: 149161--149209 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
149151 CAAAAATAAA
*
149161 TTATATATTTTTACTAATT
1 TTAT-TATTTTTAATAATT
149180 TTATTA-TTTTAATAATT
1 TTATTATTTTTAATAATT
149197 TATATTATTTTTA
1 T-TATTATTTTTA
149210 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 11 0.41
18 7 0.26
19 9 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTATTTTTAATAATT
Found at i:155084 original size:2 final size:2
Alignment explanation
Indices: 155077--155101 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
155067 GGCCAAAGAA
155077 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
155102 AAAGACGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:156665 original size:2 final size:2
Alignment explanation
Indices: 156660--156732 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
156650 TTTTTTCCTT
156660 TA TA TA 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 TA TA TA
156702 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
156733 GCATCTTTAA
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:159591 original size:20 final size:20
Alignment explanation
Indices: 159528--159615 Score: 72
Period size: 20 Copynumber: 4.4 Consensus size: 20
159518 GCCAGGAGCT
* *
159528 ATTTTAACTTGTTTGAAAAAC
1 ATTTTAACTTGGTT-AAAATC
* *
159549 ATTTTGAA-GT-GTTAAAATG
1 ATTTT-AACTTGGTTAAAATC
* *
159568 ATTTTAACTTGGTTGAAATT
1 ATTTTAACTTGGTTAAAATC
* *
159588 ATTTTGACTTGTTTAAAATC
1 ATTTTAACTTGGTTAAAATC
159608 ATTTTAAC
1 ATTTTAAC
159616 ATGATTTTAA
Statistics
Matches: 52, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
18 2 0.04
19 10 0.19
20 32 0.62
21 6 0.12
22 2 0.04
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (20 bp):
ATTTTAACTTGGTTAAAATC
Found at i:159604 original size:40 final size:40
Alignment explanation
Indices: 159528--159615 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
159518 GCCAGGAGCT
* *
159528 ATTTTAACTTGTTTGAAAAACATTTTGAAGTGTTAAAATG
1 ATTTTAACTTGGTTGAAAAACATTTTGAAGTGTTAAAATC
** **
159568 ATTTTAACTTGGTTG-AAATTATTTTGACTTGTTTAAAATC
1 ATTTTAACTTGGTTGAAAAACATTTTGAAGTG-TTAAAATC
159608 ATTTTAAC
1 ATTTTAAC
159616 ATGATTTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 12 0.29
40 29 0.71
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (40 bp):
ATTTTAACTTGGTTGAAAAACATTTTGAAGTGTTAAAATC
Found at i:160418 original size:18 final size:17
Alignment explanation
Indices: 160391--160454 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
160381 ATTGCTTTTC
*
160391 AAAATCATTTTTTAGATAA
1 AAAAT-ATTTTTGAGAT-A
160410 AAAATATTTTTGAGATA
1 AAAATATTTTTGAGATA
* *
160427 AAAATATTATT-AAAT-
1 AAAATATTTTTGAGATA
160442 AAAATATTTTTGA
1 AAAATATTTTTGA
160455 ATTTTTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
15 10 0.25
16 4 0.10
17 11 0.28
18 10 0.25
19 5 0.12
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (17 bp):
AAAATATTTTTGAGATA
Found at i:160781 original size:22 final size:22
Alignment explanation
Indices: 160756--160815 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
160746 GGGCCGAAAT
160756 TAAATTATAATTTTTACAAT-AG
1 TAAATTATAATTTTTA-AATGAG
* *
160778 TAAAAATATAATTTTTTAAATGAT
1 T-AAATTATAA-TTTTTAAATGAG
*
160802 TAAATTAAAATTTT
1 TAAATTATAATTTT
160816 ATTATTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
22 5 0.16
23 18 0.58
24 8 0.26
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (22 bp):
TAAATTATAATTTTTAAATGAG
Found at i:165703 original size:29 final size:30
Alignment explanation
Indices: 165639--165706 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
165629 AATCTCAAAA
165639 TTATACATGAACTTTAGTTTAATGTGCAATT
1 TTATACATGAACTTTAGTTT-ATGTGCAATT
* * *
165670 CTATACATGCACTTT-GATTT-TGTGTAATT
1 TTATACATGAACTTTAG-TTTATGTGCAATT
165699 TTATACAT
1 TTATACAT
165707 AATTTGATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 15 0.47
30 1 0.03
31 16 0.50
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (30 bp):
TTATACATGAACTTTAGTTTATGTGCAATT
Found at i:184873 original size:2 final size:2
Alignment explanation
Indices: 184866--184904 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
184856 TTCTTAAAGA
184866 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
184905 CTTAACATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:187077 original size:17 final size:16
Alignment explanation
Indices: 187041--187073 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
187031 AATAATATAG
187041 CAAATAAAAAGAAAAC
1 CAAATAAAAAGAAAAC
187057 CAAATGAAAAA-AAAAC
1 CAAAT-AAAAAGAAAAC
187073 C
1 C
187074 CAAAAAACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.73, C:0.15, G:0.06, T:0.06
Consensus pattern (16 bp):
CAAATAAAAAGAAAAC
Found at i:192326 original size:21 final size:21
Alignment explanation
Indices: 192289--192364 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
192279 AAAATGCATA
*
192289 AAAAATAACATCC-AAACAAC
1 AAAAATAACAACCAAAACAAC
*
192309 AAAAATAACAACCAAAACAGC
1 AAAAATAACAACCAAAACAAC
* * *
192330 AAAAAAAAAAACAACAAACAAC
1 AAAAATAACAACCA-AAACAAC
192352 ATTAAAATAACAA
1 A--AAAATAACAA
192365 AAATAACAGC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 12 0.27
21 17 0.39
22 7 0.16
24 8 0.18
ACGTcount: A:0.71, C:0.20, G:0.01, T:0.08
Consensus pattern (21 bp):
AAAAATAACAACCAAAACAAC
Found at i:192387 original size:23 final size:23
Alignment explanation
Indices: 192361--192404 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
192351 CATTAAAATA
*
192361 ACAAAAATAACAGCAAAAACAAC
1 ACAAAAATAACAACAAAAACAAC
*
192384 ACAAAAATAACAACCAAAACA
1 ACAAAAATAACAACAAAAACA
192405 GAAAAAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.70, C:0.23, G:0.02, T:0.05
Consensus pattern (23 bp):
ACAAAAATAACAACAAAAACAAC
Found at i:192405 original size:32 final size:32
Alignment explanation
Indices: 192345--192411 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
192335 AAAAAACAAC
** *
192345 AAACAACATTAAAATAACAAAAATAACAGCAA
1 AAACAACACAAAAATAACAAAAATAACAGAAA
*
192377 AAACAACACAAAAATAACAACCAA-AACAGAAA
1 AAACAACACAAAAATAACAA-AAATAACAGAAA
192409 AAA
1 AAA
192412 AAGCAATCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 28 0.93
33 2 0.07
ACGTcount: A:0.72, C:0.18, G:0.03, T:0.07
Consensus pattern (32 bp):
AAACAACACAAAAATAACAAAAATAACAGAAA
Found at i:192412 original size:23 final size:23
Alignment explanation
Indices: 192363--192413 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
192353 TTAAAATAAC
* *
192363 AAAAATAACAGCAAAAACAACAC
1 AAAAATAACAACAAAAACAACAA
*
192386 AAAAATAACAACCAAAACAGA-AA
1 AAAAATAACAACAAAAACA-ACAA
192409 AAAAA
1 AAAAA
192414 GCAATCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.75, C:0.18, G:0.04, T:0.04
Consensus pattern (23 bp):
AAAAATAACAACAAAAACAACAA
Found at i:192422 original size:21 final size:21
Alignment explanation
Indices: 192381--192447 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 21
192371 CAGCAAAAAC
* *
192381 AACACAAAAATAA-CAACCAA
1 AACAGAAAAAAAAGCAACCAA
*
192401 AACAGAAAAAAAAGCAATCAA
1 AACAGAAAAAAAAGCAACCAA
*
192422 AAAAGTAAAAAAACAGC-ACCAA
1 AACAG-AAAAAAA-AGCAACCAA
192444 AACA
1 AACA
192448 ATAATATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 11 0.29
21 10 0.26
22 14 0.37
23 3 0.08
ACGTcount: A:0.70, C:0.19, G:0.06, T:0.04
Consensus pattern (21 bp):
AACAGAAAAAAAAGCAACCAA
Found at i:199471 original size:20 final size:18
Alignment explanation
Indices: 199446--199510 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 18
199436 CTTCTTTAGA
199446 TTTTGTATCTCCTCATAACT
1 TTTTGTATCT-CTCATAA-T
199466 TTTTGTAT-TC-CATAAT
1 TTTTGTATCTCTCATAAT
*
199482 TATTTGTAATCTTTCATAATT
1 T-TTTGT-ATCTCTCATAA-T
199503 TTTTGTAT
1 TTTTGTAT
199511 GCGTTTGGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
16 2 0.05
17 10 0.26
18 3 0.08
19 4 0.10
20 18 0.46
21 2 0.05
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTTGTATCTCTCATAAT
Found at i:199626 original size:22 final size:22
Alignment explanation
Indices: 199583--199626 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
199573 TTATTTTTGC
**
199583 ATACTAATAAAATTTATTATAT
1 ATACTAATAAAATTTAAAATAT
*
199605 ATACTAATAAACTTTAAAATAT
1 ATACTAATAAAATTTAAAATAT
199627 TGAAAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (22 bp):
ATACTAATAAAATTTAAAATAT
Found at i:202240 original size:30 final size:31
Alignment explanation
Indices: 202206--202296 Score: 73
Period size: 30 Copynumber: 3.0 Consensus size: 31
202196 CCAAATAAGT
202206 AAAGGATCAAATTAAAAATAAAACAG-AATA
1 AAAGGATCAAATTAAAAATAAAACAGAAATA
** * *
202236 AAAGG-GGAATTTTAAAAAGAAAA-AGAATAATA
1 AAAGGATCAA-ATTAAAAATAAAACAG-A-AATA
* *
202268 AAAGGATTAAATTAAAACTAAAACA-AAAT
1 AAAGGATCAAATTAAAAATAAAACAGAAAT
202297 TTTAAGCTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
29 4 0.09
30 19 0.41
31 1 0.02
32 19 0.41
33 3 0.07
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.19
Consensus pattern (31 bp):
AAAGGATCAAATTAAAAATAAAACAGAAATA
Found at i:202283 original size:32 final size:32
Alignment explanation
Indices: 202206--202284 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 32
202196 CCAAATAAGT
* *
202206 AAAGGATCAAATTAAAAATAAAACAGAATAAA
1 AAAGGATTAAATTAAAAAGAAAACAGAATAAA
**
202238 AGGGGAATT---TTAAAAAGAAAA-AGAATAATA
1 AAAGG-ATTAAATTAAAAAGAAAACAGAATAA-A
202268 AAAGGATTAAATTAAAA
1 AAAGGATTAAATTAAAA
202285 CTAAAACAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
29 10 0.28
30 15 0.42
32 9 0.25
33 2 0.06
ACGTcount: A:0.65, C:0.03, G:0.14, T:0.19
Consensus pattern (32 bp):
AAAGGATTAAATTAAAAAGAAAACAGAATAAA
Found at i:203208 original size:13 final size:13
Alignment explanation
Indices: 203192--203216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
203182 TCTTGTTTTT
203192 ATTTCAAAGTGTA
1 ATTTCAAAGTGTA
203205 ATTTCAAAGTGT
1 ATTTCAAAGTGT
203217 TCGTAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
ATTTCAAAGTGTA
Found at i:206204 original size:22 final size:24
Alignment explanation
Indices: 206179--206224 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
206169 GAAAGTACCA
206179 AAGTAC-T-TAACAGAGGGCACAT
1 AAGTACTTGTAACAGAGGGCACAT
*
206201 AAGTGCTTGGTAACAGAGGGCACA
1 AAGTACTT-GTAACAGAGGGCACA
206225 CAAAGTGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 1 0.05
25 14 0.70
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (24 bp):
AAGTACTTGTAACAGAGGGCACAT
Found at i:206242 original size:48 final size:48
Alignment explanation
Indices: 206190--206317 Score: 149
Period size: 48 Copynumber: 2.7 Consensus size: 48
206180 AGTACTTAAC
* ** *
206190 AGAGGGCACATAAGTGCTTGGTAACAGAGGGCACACAAAGTGCTAATT
1 AGAGGGCACAAAAGTGCTTAATAACAGAGGGCACACAAAGTGCTAAAT
*
206238 AGAGGGCACACGAAA-TGC-TAATAACAGAGGGCACACACAGTGCTAAAT
1 AGAGGGCACA--AAAGTGCTTAATAACAGAGGGCACACAAAGTGCTAAAT
206286 AGAGGGCACAAAACGTGC-T-A-AACAGAGGGCAC
1 AGAGGGCACAAAA-GTGCTTAATAACAGAGGGCAC
206318 GCTAGTGTTC
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
46 15 0.21
47 1 0.01
48 50 0.70
49 3 0.04
50 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.28, T:0.13
Consensus pattern (48 bp):
AGAGGGCACAAAAGTGCTTAATAACAGAGGGCACACAAAGTGCTAAAT
Found at i:206245 original size:23 final size:23
Alignment explanation
Indices: 206177--206317 Score: 126
Period size: 23 Copynumber: 6.0 Consensus size: 23
206167 CAGAAAGTAC
* *
206177 CAAAGTACTTAACAGAGGGCACA
1 CAAAGTGCTAAACAGAGGGCACA
* *
206200 -TAAGTGCTTGGTAACAGAGGGCACA
1 CAAAGTGC-T--AAACAGAGGGCACA
**
206225 CAAAGTGCTAATTAGAGGGCACA
1 CAAAGTGCTAAACAGAGGGCACA
206248 CGAAA-TGCTAATAACAGAGGGCACA
1 C-AAAGTGCT-A-AACAGAGGGCACA
* *
206273 CACAGTGCTAAATAGAGGGCACA
1 CAAAGTGCTAAACAGAGGGCACA
206296 -AAACGTGCTAAACAGAGGGCAC
1 CAAA-GTGCTAAACAGAGGGCAC
206318 GCTAGTGTTC
Statistics
Matches: 97, Mismatches: 12, Indels: 18
0.76 0.09 0.14
Matches are distributed among these distances:
22 7 0.07
23 46 0.47
24 7 0.07
25 31 0.32
26 6 0.06
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (23 bp):
CAAAGTGCTAAACAGAGGGCACA
Found at i:207923 original size:30 final size:30
Alignment explanation
Indices: 207881--208051 Score: 152
Period size: 30 Copynumber: 5.8 Consensus size: 30
207871 AAAGGACCCT
* *
207881 AAACTATCCAAAAATTCCATTTTTGACATTA
1 AAACT-TCCAAAAATTCTATTTTTGACACTA
* * * *
207912 AAATTTCCAAAAATTATATTTTT-ACCCTC
1 AAACTTCCAAAAATTCTATTTTTGACACTA
* **
207941 AAACTTCCAAAAATTCTATTTTTGACCCCG
1 AAACTTCCAAAAATTCTATTTTTGACACTA
* * *
207971 AAACTCCCAAAAATTATA-TTTT-ACCCCT-
1 AAACTTCCAAAAATTCTATTTTTGA-CACTA
* * *
207999 AAACTTCCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCTATTTTTGACACTA
*
208029 AAACTTCCAAAAATTATATTTTT
1 AAACTTCCAAAAATTCTATTTTT
208052 TTTTATCCCC
Statistics
Matches: 116, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
28 16 0.14
29 38 0.33
30 58 0.50
31 4 0.03
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (30 bp):
AAACTTCCAAAAATTCTATTTTTGACACTA
Found at i:207948 original size:29 final size:28
Alignment explanation
Indices: 207916--208112 Score: 207
Period size: 29 Copynumber: 6.6 Consensus size: 28
207906 ACATTAAAAT
207916 TTCCAAAAATTATATTTTTACCCTCAAAC
1 TTCCAAAAATTATATTTTTACCC-CAAAC
*
207945 TTCCAAAAATTCTATTTTTGACCCCGAAAC
1 TTCCAAAAATTATATTTTT-ACCCC-AAAC
*
207975 TCCCAAAAATTATA-TTTTACCCCTAAAC
1 TTCCAAAAATTATATTTTTACCCC-AAAC
**
208003 TTCCAAAAATTCCATTTTTGACCCCAAAAC
1 TTCCAAAAATTATATTTTT-ACCCC-AAAC
208033 TTCCAAAAATTATATTTTTTTTTATCCCCAAAC
1 TTCCAAAAATTATA----TTTTTA-CCCCAAAC
** *
208066 TTCCAAAAATTCCATTTTGACCCCGAAAC
1 TTCCAAAAATTATATTTTTACCCC-AAAC
*
208095 TTCCAAAAATTACATTTT
1 TTCCAAAAATTATATTTT
208113 GCCCTCGAAT
Statistics
Matches: 144, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
28 24 0.17
29 53 0.37
30 41 0.28
33 17 0.12
34 9 0.06
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (28 bp):
TTCCAAAAATTATATTTTTACCCCAAAC
Found at i:208020 original size:58 final size:59
Alignment explanation
Indices: 207877--208112 Score: 300
Period size: 58 Copynumber: 3.9 Consensus size: 59
207867 CTCTAAAGGA
*** *
207877 CCCTAAACTATCCAAAAATTCCATTTTTGACATTAAAATTTCCAAAAATTATATTTTTA-
1 CCCTAAACT-TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTATATTTTTAC
* * *
207936 CCCTCAAACTTCCAAAAATTCTATTTTTGACCCCGAAACTCCCAAAAATTATA-TTTTAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTATATTTTTAC
207995 CCCTAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTATATTTTTTTTTATC
1 CCCTAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTATA----TTTTTA-C
* *
208059 CCC-AAACTTCCAAAAATTCCA-TTTTGACCCCGAAACTTCCAAAAATTACATTTT
1 CCCTAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTATATTTT
208113 GCCCTCGAAT
Statistics
Matches: 157, Mismatches: 12, Indels: 17
0.84 0.06 0.09
Matches are distributed among these distances:
58 54 0.34
59 44 0.28
60 5 0.03
62 27 0.17
63 23 0.15
64 4 0.03
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (59 bp):
CCCTAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTATATTTTTAC
Found at i:208141 original size:29 final size:29
Alignment explanation
Indices: 207916--208140 Score: 203
Period size: 29 Copynumber: 7.6 Consensus size: 29
207906 ACATTAAAAT
* *
207916 TTCCAAAAATTATATTTTTACCCTC-AAAC
1 TTCCAAAAATTACATTTTGACCC-CGAAAC
207945 TTCCAAAAATT-CTATTTTTGACCCCGAAAC
1 TTCCAAAAATTAC-A-TTTTGACCCCGAAAC
* * *
207975 TCCCAAAAATTATATTTT-ACCCCTAAAC
1 TTCCAAAAATTACATTTTGACCCCGAAAC
* *
208003 TTCCAAAAATTCCATTTTTGACCCCAAAAC
1 TTCCAAAAATTACA-TTTTGACCCCGAAAC
* *
208033 TTCCAAAAATTATATTTTTTTTTATCCCC-AAAC
1 TTCCAAAAATTACA----TTTTGA-CCCCGAAAC
*
208066 TTCCAAAAATTCCATTTTGACCCCGAAAC
1 TTCCAAAAATTACATTTTGACCCCGAAAC
208095 TTCCAAAAATTACATTTTG-CCCTCG-AA-
1 TTCCAAAAATTACATTTTGACCC-CGAAAC
*
208122 TGTCCAAAAATTTCATTTT
1 T-TCCAAAAATTACATTTT
208141 TTATCCCGAT
Statistics
Matches: 166, Mismatches: 17, Indels: 27
0.79 0.08 0.13
Matches are distributed among these distances:
27 1 0.01
28 45 0.27
29 50 0.30
30 44 0.27
33 22 0.13
34 4 0.02
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTGACCCCGAAAC
Found at i:208190 original size:29 final size:28
Alignment explanation
Indices: 207917--208192 Score: 102
Period size: 29 Copynumber: 9.4 Consensus size: 28
207907 CATTAAAATT
** *
207917 TCCAAAAATTATATTTTTACCCTCAAACT-
1 TCCAAAAATTCCA-TTTTACCC-CGAACTG
*
207946 TCCAAAAATTCTATTTTTGACCCCGAAACT-
1 TCCAAAAATTCCA-TTTT-ACCCCG-AACTG
* ** *
207976 CCCAAAAATTATATTTTACCCCTAAACT-
1 TCCAAAAATTCCATTTTACCCC-GAACTG
*
208004 TCCAAAAATTCCATTTTTGACCCCAAAACT-
1 TCCAAAAATTCCA-TTTT-ACCCC-GAACTG
** *
208034 TCCAAAAATTATATTTTTTTTTATCCCCAAACT-
1 TCCAAAAATTCCA-----TTTTA-CCCCGAACTG
208067 TCCAAAAATTCCATTTTGACCCCGAAACT-
1 TCCAAAAATTCCATTTT-ACCCCG-AACTG
* *
208096 TCCAAAAATTACATTTTGCCCTCGAA-TG
1 TCCAAAAATTCCATTTTACCC-CGAACTG
* * * *
208124 TCCAAAAATTTCATTTTTTATCCCG-ATTT
1 TCCAAAAATTCCA--TTTTACCCCGAACTG
* *
208153 TCCTTAAAATTACCATTTTACCCTCGGA-TG
1 TCC-AAAAATT-CCATTTTACCC-CGAACTG
208183 TCCAAAAATT
1 TCCAAAAATT
208193 TTGTTTTTGA
Statistics
Matches: 201, Mismatches: 25, Indels: 42
0.75 0.09 0.16
Matches are distributed among these distances:
27 1 0.00
28 45 0.22
29 68 0.34
30 58 0.29
31 3 0.01
33 17 0.08
34 9 0.04
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (28 bp):
TCCAAAAATTCCATTTTACCCCGAACTG
Found at i:208229 original size:59 final size:57
Alignment explanation
Indices: 208100--208258 Score: 151
Period size: 59 Copynumber: 2.7 Consensus size: 57
208090 GAAACTTCCA
* * * * *
208100 AAAATTACATTTTGCCCTCGAATGTCCAAAAATTTCATTTTTTATCCCGATTTTCCTT
1 AAAATTACATTTTACCCTCGGATGTCCAAAAATTTCATTTTTGATCCCAATTTT-CTC
** *
208158 AAAATTACCATTTTACCCTCGGATGTCCAAAAATTTTGTTTTTGATCCTAATCTTT-TC
1 AAAATTA-CATTTTACCCTCGGATGTCCAAAAATTTCATTTTTGATCCCAAT-TTTCTC
* * *
208216 AAAAGTTATCATTTTACCCCCAGG-TGTCTAAAAATTCCATTTT
1 AAAA-TTA-CATTTTACCCTC-GGATGTCCAAAAATTTCATTTT
208259 AACCCCGAAC
Statistics
Matches: 83, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
58 12 0.14
59 66 0.80
60 5 0.06
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (57 bp):
AAAATTACATTTTACCCTCGGATGTCCAAAAATTTCATTTTTGATCCCAATTTTCTC
Found at i:209227 original size:596 final size:596
Alignment explanation
Indices: 208095--209288 Score: 2248
Period size: 596 Copynumber: 2.0 Consensus size: 596
208085 ACCCCGAAAC
*
208095 TTCCAAAAATTACATTTTGCCCTCGAATGTCCAAAAATTTCATTTTTTATCCCGATTTTCCTTAA
1 TTCCAAAAATTACATTTTGCCCCCGAATGTCCAAAAATTTCATTTTTTATCCCGATTTTCCTTAA
208160 AATTACCATTTTACCCTCGGATGTCCAAAAATTTTGTTTTTGATCCTAATCTTTTCAAAAGTTAT
66 AATTACCATTTTACCCTCGGATGTCCAAAAATTTTGTTTTTGATCCTAATCTTTTCAAAAGTTAT
*
208225 CATTTTACCCCCAGGTGTCTAAAAATTCCATTTTAACCCCGAACTTCCCAAAATTACCGTTTTTC
131 CATTTTACCCCCAGGTGTCTAAAAATTCCATTTTAACCCCGAACTTCCCAAAATTACCGTTTTGC
208290 CCTCAAGAGTTCAAAATTACCATTTTGTCCCCGGGTATCCAAAGTCTCATTTTTCAACTCCGATT
196 CCTCAAGAGTTCAAAATTACCATTTTGTCCCCGGGTATCCAAAGTCTCATTTTTCAACTCCGATT
208355 GCTTTATTTTTCTTCCTCATCAATATTTGCATTTGAATTTAACTATTATGCACTCGTATTTTGCA
261 GCTTTATTTTTCTTCCTCATCAATATTTGCATTTGAATTTAACTATTATGCACTCGTATTTTGCA
208420 TTTTTTTTTATTTTTTTACCATTTATCTTCTTATTTATCTTACTTCGTGTTATTTAATATCCATT
326 TTTTTTTTTATTTTTTTACCATTTATCTTCTTATTTATCTTACTTCGTGTTATTTAATATCCATT
*
208485 ATTAACTGCTTTTTCAAATTAAACTCGCATGTTTGTTTTCAAAATTGTTTTCATAAAAACTTTAA
391 ATTAACTGCTTTTTCAAATTAAACTAGCATGTTTGTTTTCAAAATTGTTTTCATAAAAACTTTAA
* *
208550 AATCGAGGCAATATTTTTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGTAATT
456 AATCGAGGCAATATTTTTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAAGTGCAATT
* *
208615 TTTCTTCAAATCGAAATAATCGAATACCCTTAATTGAGGCAATGTTTCTTTATCTTCGATTCTGA
521 TTTCTTCAAATCGAAATAATCGAATACCCTTAATTGAGACAATGTTTCCTTATCTTCGATTCTGA
208680 AAATTTGTGCT
586 AAATTTGTGCT
208691 TTCCAAAAATTACATTTTGCCCCCGAATGTCCAAAAATTTCATTTTTTATCCCGATTTTCCTTAA
1 TTCCAAAAATTACATTTTGCCCCCGAATGTCCAAAAATTTCATTTTTTATCCCGATTTTCCTTAA
208756 AATTACCATTTTACCCTCGGATGTCCAAAAATTTTGTTTTTGATCCTAATCTTTTCAAAAGTTAT
66 AATTACCATTTTACCCTCGGATGTCCAAAAATTTTGTTTTTGATCCTAATCTTTTCAAAAGTTAT
* *
208821 CTTTTTACCCTC-GAGTGTCTAAAAATTCCATTTTTAACCCCGAACTTCCCAAAATTACCGTTTT
131 CATTTTACCCCCAG-GTGTCTAAAAATTCCA-TTTTAACCCCGAACTTCCCAAAATTACCGTTTT
*
208885 GCCCTCAAGAGTTCAACATTACCATTTTGTCCCCGGGTATCCAAAGTCTCATTTTTCAACTCCGA
194 GCCCTCAAGAGTTCAAAATTACCATTTTGTCCCCGGGTATCCAAAGTCTCATTTTTCAACTCCGA
*
208950 TTGCTTTATTTTTCTTCCTCATCAATATTTGCATTTGAATTTAACTATTATGCACTTGTATTTTG
259 TTGCTTTATTTTTCTTCCTCATCAATATTTGCATTTGAATTTAACTATTATGCACTCGTATTTTG
*
209015 CA-TTTTTTTTATTTTTTTACCATTTATCTTCTTATTTATCTTACTTCTTGTTATTTAATATCCA
324 CATTTTTTTTTATTTTTTTACCATTTATCTTCTTATTTATCTTACTTCGTGTTATTTAATATCCA
209079 TTATTAACTGCTTTTTCAAATTAAACTAGCATGTTTGTTTTCAAAATTGTTTTCATAAAAACTTT
389 TTATTAACTGCTTTTTCAAATTAAACTAGCATGTTTGTTTTCAAAATTGTTTTCATAAAAACTTT
209144 AAAATCGAGGCAATATTTTTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAAGTGCAA
454 AAAATCGAGGCAATATTTTTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAAGTGCAA
209209 TTTTTCTTCAAATCGAAATAATCGAATACCCTTAATTGAGACAATGTTTCCTTATCTTCGATTCT
519 TTTTTCTTCAAATCGAAATAATCGAATACCCTTAATTGAGACAATGTTTCCTTATCTTCGATTCT
209274 GAAAATTTGTGCT
584 GAAAATTTGTGCT
209287 TT
1 TT
209289 AACTTACTAG
Statistics
Matches: 584, Mismatches: 12, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
595 1 0.00
596 421 0.72
597 162 0.28
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (596 bp):
TTCCAAAAATTACATTTTGCCCCCGAATGTCCAAAAATTTCATTTTTTATCCCGATTTTCCTTAA
AATTACCATTTTACCCTCGGATGTCCAAAAATTTTGTTTTTGATCCTAATCTTTTCAAAAGTTAT
CATTTTACCCCCAGGTGTCTAAAAATTCCATTTTAACCCCGAACTTCCCAAAATTACCGTTTTGC
CCTCAAGAGTTCAAAATTACCATTTTGTCCCCGGGTATCCAAAGTCTCATTTTTCAACTCCGATT
GCTTTATTTTTCTTCCTCATCAATATTTGCATTTGAATTTAACTATTATGCACTCGTATTTTGCA
TTTTTTTTTATTTTTTTACCATTTATCTTCTTATTTATCTTACTTCGTGTTATTTAATATCCATT
ATTAACTGCTTTTTCAAATTAAACTAGCATGTTTGTTTTCAAAATTGTTTTCATAAAAACTTTAA
AATCGAGGCAATATTTTTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAAGTGCAATT
TTTCTTCAAATCGAAATAATCGAATACCCTTAATTGAGACAATGTTTCCTTATCTTCGATTCTGA
AAATTTGTGCT
Found at i:212478 original size:3 final size:3
Alignment explanation
Indices: 212470--212498 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
212460 ATCTACTTTC
212470 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
212499 AAGCCAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:215557 original size:12 final size:13
Alignment explanation
Indices: 215540--215568 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
215530 AGATTTCCTC
215540 TTTTTTTTTTCT-
1 TTTTTTTTTTCTA
215552 TTTTTTTTTTCTA
1 TTTTTTTTTTCTA
215565 TTTT
1 TTTT
215569 ATCTCTTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTTCTA
Found at i:217351 original size:20 final size:20
Alignment explanation
Indices: 217304--217352 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
217294 TGCATGGATT
*
217304 CTACCGATACAACACTGAAA
1 CTACCGATACAACACTAAAA
* *
217324 GTATCGATACAACA-TAACAA
1 CTACCGATACAACACTAA-AA
217344 CTACCGATA
1 CTACCGATA
217353 TTACAGGTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.45, C:0.27, G:0.10, T:0.18
Consensus pattern (20 bp):
CTACCGATACAACACTAAAA
Found at i:229434 original size:18 final size:17
Alignment explanation
Indices: 229411--229449 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
229401 TTACACCTTC
*
229411 CTCCCCGCTCCCTCTCGT
1 CTCCCCCCTCCCTCTC-T
229429 CTCCCCCCTCCCTCTCT
1 CTCCCCCCTCCCTCTCT
229446 CTCC
1 CTCC
229450 ATCTTCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.00, C:0.67, G:0.05, T:0.28
Consensus pattern (17 bp):
CTCCCCCCTCCCTCTCT
Found at i:230128 original size:96 final size:96
Alignment explanation
Indices: 229964--230145 Score: 226
Period size: 96 Copynumber: 1.9 Consensus size: 96
229954 AAGGATGTTT
** * * *
229964 GATTATCTCGATTTGAAGAAAGGTTGCACCTAATAAGTTAAGGCGCAATATTTCGGAATCGAAGA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAATATTTCGAAACCGAAGA
*
230029 T-AAAGAAACATTGCTTCGATTAAGGGTATTC
66 TAAAAG-AACATTGCCTCGATTAAGGGTATTC
* * *
230060 GATTATTTCGATTTGAAGAAAAATTGCACCTANTGAGTTAAGGCACAA-ATTTTCGAAACCCGAA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAATA-TTTCGAAA-CCGAA
*
230124 -ATAAAAGAATATTGCCTCGATT
64 GATAAAAGAACATTGCCTCGATT
230146 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
95 1 0.01
96 64 0.88
97 8 0.11
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAATATTTCGAAACCGAAGA
TAAAAGAACATTGCCTCGATTAAGGGTATTC
Found at i:230738 original size:59 final size:59
Alignment explanation
Indices: 230369--230739 Score: 566
Period size: 59 Copynumber: 6.3 Consensus size: 59
230359 AAATAGGTAG
* * * *
230369 TTTTGGAAGGTTCGGAGTCAAAAAT-GGATTTTTGGAAGTTCGGGGGTAAAATGGTTAT
1 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
* * *
230427 TTTTAGAAGGTTCGGGGTAAAAAAAAT-GGATTTTTGGGAGTTCGAGGGTAAAATGATAAT
1 TTTTAGAAGGTTCGGGGT--CAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
* * * * *
230487 TTTCAAAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAAT
1 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
*
230546 TTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
1 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
* * *
230605 TTTTAGAAGGTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGGGGGTAAAATGGTAAT
1 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
230664 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
1 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
230723 TTTTAGAAGGTTCGGGG
1 TTTTAGAAGGTTCGGGG
230740 ACCTTCGGGG
Statistics
Matches: 284, Mismatches: 26, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
58 22 0.08
59 212 0.75
60 50 0.18
ACGTcount: A:0.31, C:0.05, G:0.32, T:0.33
Consensus pattern (59 bp):
TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
Found at i:232451 original size:17 final size:17
Alignment explanation
Indices: 232416--232472 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
232406 TGGACTTTTC
** *
232416 TAAATTTAGTTTTATAA
1 TAAATTTAAATTTAAAA
*
232433 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
*
232450 TAAACTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
232467 TAAATT
1 TAAATT
232473 CAATTTCCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:233024 original size:96 final size:96
Alignment explanation
Indices: 232860--233041 Score: 226
Period size: 96 Copynumber: 1.9 Consensus size: 96
232850 AAGGATGTTT
** * * *
232860 GATTATCTCGATTTGAAGAAATGTTGCACCTAGTAAGTTAAGGCGCAATATTTCGGAATCGAAGA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCGAAACCGAAGA
*
232925 T-AAAGAAACATTGCTTCGATTAAGGGTATTC
66 TAAAAG-AACATTGCCTCGATTAAGGGTATTC
* * *
232956 GATTATTTCGATTTGAAGAAAAATTGCACCTATTGAGTTAAGGCACAA-ATTTTCGAAACCCGAA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTCGAAA-CCGAA
*
233020 -ATAAAAGAATATTGCCTCGATT
64 GATAAAAGAACATTGCCTCGATT
233042 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
95 1 0.01
96 64 0.88
97 8 0.11
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCGAAACCGAAGA
TAAAAGAACATTGCCTCGATTAAGGGTATTC
Found at i:238252 original size:6 final size:6
Alignment explanation
Indices: 238241--238275 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
238231 CTGTAGCGAT
* *
238241 GAGGAA GAGGAA GAGGAA GAGGAT GAGGGA GAGGA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGA
238276 CGGTAATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.54, T:0.03
Consensus pattern (6 bp):
GAGGAA
Found at i:238773 original size:2 final size:2
Alignment explanation
Indices: 238761--238790 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
238751 GTAGAACCTG
*
238761 CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
238791 ACTTCTCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:262185 original size:19 final size:19
Alignment explanation
Indices: 262154--262190 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
262144 CTTAGTTTGT
262154 TAAAACTTTAAAATCACGAG
1 TAAAACTTTAAAAT-ACGAG
262174 TAAAAC-TTAAAATACGA
1 TAAAACTTTAAAATACGA
262191 TCTTTGTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 7 0.41
20 6 0.35
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (19 bp):
TAAAACTTTAAAATACGAG
Done.