Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015201.1 Kokia drynarioides strain JFW-HI SEQ_130245, 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: 585754
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 263 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:425455 original size:7 final size:7
Alignment explanation
Indices: 425440--425525 Score: 50
Period size: 7 Copynumber: 12.0 Consensus size: 7
425430 GCCTAACGGG
*
425440 AGAACAA
1 AGAAAAA
425447 AGAAAAA
1 AGAAAAA
* *
425454 AGAGAGA
1 AGAAAAA
425461 AGAAAAA
1 AGAAAAA
*
425468 A-AAAGA
1 AGAAAAA
425474 A-AAAAA
1 AGAAAAA
425480 AGAAAGAA
1 AGAAA-AA
*
425488 GGAAAAA
1 AGAAAAA
* *
425495 GGAAGAAGG
1 AGAA-AA-A
425504 AGAAAAA
1 AGAAAAA
*
425511 AGAGAAAG
1 AGA-AAAA
425519 AGAAAAA
1 AGAAAAA
425526 GTTTATTTTT
Statistics
Matches: 61, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
6 10 0.16
7 32 0.52
8 16 0.26
9 3 0.05
ACGTcount: A:0.74, C:0.01, G:0.24, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:425465 original size:14 final size:14
Alignment explanation
Indices: 425446--425526 Score: 69
Period size: 14 Copynumber: 5.7 Consensus size: 14
425436 CGGGAGAACA
425446 AAGAAAAAAGAGAG
1 AAGAAAAAAGAGAG
*
425460 AAGAAAAAA-AAAG
1 AAGAAAAAAGAGAG
*
425473 AA-AAAAAAGAAAG
1 AAGAAAAAAGAGAG
*
425486 AAGGAAAAAGGAAGAAG
1 AA-GAAAAAAG-AG-AG
*
425503 GAGAAAAAAGAGA-
1 AAGAAAAAAGAGAG
425516 AAGAGAAAAAG
1 AAGA-AAAAAG
425527 TTTATTTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
12 6 0.11
13 14 0.25
14 16 0.29
15 8 0.15
16 8 0.15
17 3 0.05
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAGAGAG
Found at i:425469 original size:15 final size:14
Alignment explanation
Indices: 425449--425526 Score: 56
Period size: 15 Copynumber: 5.5 Consensus size: 14
425439 GAGAACAAAG
425449 AAAAAAGAGAGAAGA
1 AAAAAAGA-AGAAGA
425464 AAAAAA-AAG-A-A
1 AAAAAAGAAGAAGA
*
425475 AAAAAAGAAAGAAGG
1 AAAAAAG-AAGAAGA
*
425490 AAAAAGGAAGAAGGA
1 AAAAAAGAAGAA-GA
425505 GAAAAAAG-AGAAAGA
1 -AAAAAAGAAG-AAGA
*
425520 GAAAAAG
1 AAAAAAG
425527 TTTATTTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
11 7 0.14
12 1 0.02
13 5 0.10
14 13 0.25
15 17 0.33
16 8 0.16
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAGAAGA
Found at i:425472 original size:24 final size:24
Alignment explanation
Indices: 425445--425526 Score: 71
Period size: 23 Copynumber: 3.5 Consensus size: 24
425435 ACGGGAGAAC
425445 AAAGAAAAAAGAGAGAAGAAAAAA
1 AAAGAAAAAAGAGAGAAGAAAAAA
* **
425469 AAAGAAAAAAAAGA-AAGAAGGAA
1 AAAGAAAAAAGAGAGAAGAAAAAA
* * *
425492 AAAGGAAGAAG-GAGAA-AAAAGAG
1 AAAGAAAAAAGAGAGAAGAAAA-AA
425515 AAAGAGAAAAAG
1 AAAGA-AAAAAG
425527 TTTATTTTTA
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
22 4 0.09
23 22 0.50
24 18 0.41
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (24 bp):
AAAGAAAAAAGAGAGAAGAAAAAA
Found at i:425544 original size:12 final size:12
Alignment explanation
Indices: 425527--425557 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
425517 AGAGAAAAAG
425527 TTTATTTTTAAA
1 TTTATTTTTAAA
425539 TTTATTTTTAAA
1 TTTATTTTTAAA
*
425551 ATTATTT
1 TTTATTT
425558 AATTTGTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTTTAAA
Found at i:429933 original size:17 final size:16
Alignment explanation
Indices: 429911--429952 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
429901 TTATTATTAT
429911 TTTTATTTTCTATCTTA
1 TTTTATTTTCTAT-TTA
429928 TTTTATTTATCTATTTA
1 TTTTATTT-TCTATTTA
429945 -TTTATTTT
1 TTTTATTTT
429953 TGTCCAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.04
16 7 0.29
17 11 0.46
18 5 0.21
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTATTTTCTATTTA
Found at i:431541 original size:43 final size:42
Alignment explanation
Indices: 431459--431551 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 42
431449 ATTAACATGT
* *
431459 TAAATTATATTATTTGACTCGTGTTAATATGGTTGCATGTTA
1 TAAATTATATTATTTGACTCGTATTAATATGCTTGCATGTTA
*
431501 CTAAATTATATTACTTT-ACTCTTATTAATAT-CTTGACATGTTA
1 -TAAATTATATTA-TTTGACTCGTATTAATATGCTTG-CATGTTA
*
431544 TTAATTAT
1 TAAATTAT
431552 GCAGTTCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
42 10 0.23
43 31 0.70
44 3 0.07
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (42 bp):
TAAATTATATTATTTGACTCGTATTAATATGCTTGCATGTTA
Found at i:432014 original size:6 final size:6
Alignment explanation
Indices: 432003--432051 Score: 89
Period size: 6 Copynumber: 8.2 Consensus size: 6
431993 CTCCAACCCT
*
432003 AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC AGAGCT AGAGCC
1 AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC
432051 A
1 A
432052 AAGCAAGAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.35, C:0.31, G:0.33, T:0.02
Consensus pattern (6 bp):
AGAGCC
Found at i:435327 original size:26 final size:27
Alignment explanation
Indices: 435272--435327 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
435262 TTTCAATAAA
* *
435272 TAAAATACGAATTTAAAATATATCATAC
1 TAAAATAC-AATTTAAAATATAACACAC
435300 TAAAATA-AATTTAAAA-ATAAACACAC
1 TAAAATACAATTTAAAATAT-AACACAC
435326 TA
1 TA
435328 CCTTTCTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 2 0.08
26 16 0.64
28 7 0.28
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.29
Consensus pattern (27 bp):
TAAAATACAATTTAAAATATAACACAC
Found at i:435370 original size:4 final size:4
Alignment explanation
Indices: 435363--435408 Score: 67
Period size: 4 Copynumber: 11.2 Consensus size: 4
435353 TCAATCTTCC
435363 TTCT TTCT TTC- TTCT TTCT TTCTT TTCT TTCTT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTC-T TTCT TTC-T TTCT TTCT TTCT T
435409 CTTCTGCCCG
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
3 3 0.08
4 28 0.72
5 8 0.21
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:435376 original size:11 final size:11
Alignment explanation
Indices: 435357--435411 Score: 69
Period size: 11 Copynumber: 5.0 Consensus size: 11
435347 TTCCTCTCAA
*
435357 TCTTCCTTCTT
1 TCTTTCTTCTT
435368 TCTTTCTTCTT
1 TCTTTCTTCTT
435379 TCTTTC-T-TT
1 TCTTTCTTCTT
435388 TCTTTCTTTTCTT
1 TCTTTC--TTCTT
435401 TCTTTCTTCTT
1 TCTTTCTTCTT
435412 CTGCCCGTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
9 8 0.21
10 1 0.03
11 21 0.54
12 1 0.03
13 8 0.21
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TCTTTCTTCTT
Found at i:435391 original size:9 final size:9
Alignment explanation
Indices: 435363--435405 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
435353 TCAATCTTCC
435363 TTCTTTC-T
1 TTCTTTCTT
435371 TTC-TTC-T
1 TTCTTTCTT
435378 TTCTTTCTT
1 TTCTTTCTT
435387 TTCTTTCTT
1 TTCTTTCTT
435396 TTCTTTCTT
1 TTCTTTCTT
435405 T
1 T
435406 CTTCTTCTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.21
8 6 0.18
9 20 0.61
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTCTTTCTT
Found at i:436154 original size:5 final size:6
Alignment explanation
Indices: 436136--436162 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
436126 ATCTATATAT
436136 AAGAAA AAGAAA AAGAAA AAGAAA AAG
1 AAGAAA AAGAAA AAGAAA AAGAAA AAG
436163 CAAAGTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:436786 original size:30 final size:28
Alignment explanation
Indices: 436736--436847 Score: 91
Period size: 30 Copynumber: 3.8 Consensus size: 28
436726 TAAAGATCAA
* *
436736 AAATTTTTTTATCAATTTTTAAGGGTTTT
1 AAATTTTTTT-TCAACTTTTAAGGATTTT
*
436765 AACAATTTTTTTTTAACTTTTAAGGATTTT
1 -A-AATTTTTTTTCAACTTTTAAGGATTTT
* *
436795 AAATTTTTTTTATCAATTTTTAAAG-TATTT
1 AAA-TTTTTTT-TCAACTTTTAAGGAT-TTT
* *
436825 AATTTTTTTTTCCAATTTTTAAG
1 AAATTTTTTTT-CAACTTTTAAG
436848 AAACCTAATA
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
28 3 0.04
29 26 0.38
30 31 0.45
31 9 0.13
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.59
Consensus pattern (28 bp):
AAATTTTTTTTCAACTTTTAAGGATTTT
Found at i:436828 original size:29 final size:29
Alignment explanation
Indices: 436736--436846 Score: 104
Period size: 29 Copynumber: 3.8 Consensus size: 29
436726 TAAAGATCAA
* *
436736 AAATTTTTTTATCAATTTTTAAGGGT-TTT
1 AAATTTTTTTTTCAATTTTTAA-AGTATTT
* *
436765 AACAATTTTTTTTT-AACTTTT-AAGGATTTT
1 -A-AATTTTTTTTTCAATTTTTAAAGTA-TTT
436795 AAATTTTTTTTATCAATTTTTAAAGTATTT
1 AAATTTTTTTT-TCAATTTTTAAAGTATTT
436825 -AATTTTTTTTTCCAATTTTTAA
1 AAATTTTTTTTT-CAATTTTTAA
436847 GAAACCTAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
28 12 0.18
29 23 0.34
30 19 0.28
31 14 0.21
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (29 bp):
AAATTTTTTTTTCAATTTTTAAAGTATTT
Found at i:438747 original size:56 final size:54
Alignment explanation
Indices: 438644--438748 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
438634 TTAATATTAT
* *
438644 ATTTGGTAAATTAATTTGACATTTTTTTAATTTGGTGTTAAGTTTTTTATTCCA
1 ATTTGGTAAATGAACTTGACATTTTTTTAATTTGGTGTTAAGTTTTTTATTCCA
* *
438698 ATTTGGTATATGAACTTGACACTTTTTTTTAATTTGGTATTTAAGTTTTTT
1 ATTTGGTAAATGAACTTGACA--TTTTTTTAATTTGGT-GTTAAGTTTTTT
438749 TTACAAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
54 18 0.41
56 15 0.34
57 11 0.25
ACGTcount: A:0.25, C:0.06, G:0.13, T:0.56
Consensus pattern (54 bp):
ATTTGGTAAATGAACTTGACATTTTTTTAATTTGGTGTTAAGTTTTTTATTCCA
Found at i:439572 original size:22 final size:22
Alignment explanation
Indices: 439529--439573 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
439519 TTTTAACTAG
* *
439529 AGTTTTTAATTCTAGTTTAATA
1 AGTTTTTAATTCTAATTGAATA
439551 AGTTTTTCAATTC-AATTGAATA
1 AGTTTTT-AATTCTAATTGAATA
439573 A
1 A
439574 CCACATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.49
Consensus pattern (22 bp):
AGTTTTTAATTCTAATTGAATA
Found at i:440577 original size:14 final size:14
Alignment explanation
Indices: 440558--440585 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
440548 AATATATTTG
440558 ATGCCCTAGTCAAC
1 ATGCCCTAGTCAAC
440572 ATGCCCTAGTCAAC
1 ATGCCCTAGTCAAC
440586 CTAATAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.14, T:0.21
Consensus pattern (14 bp):
ATGCCCTAGTCAAC
Found at i:441082 original size:21 final size:21
Alignment explanation
Indices: 441053--441095 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
441043 GACAAAAATT
441053 TTAAGTTATAT-TCTACTAATA
1 TTAAGTTAT-TCTCTACTAATA
* *
441074 TTAATTTATTCTTTACTAATA
1 TTAAGTTATTCTCTACTAATA
441095 T
1 T
441096 GAGATCAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (21 bp):
TTAAGTTATTCTCTACTAATA
Found at i:441116 original size:5 final size:5
Alignment explanation
Indices: 441106--441161 Score: 58
Period size: 5 Copynumber: 10.6 Consensus size: 5
441096 GAGATCAGGT
* * *
441106 TTTTA TTTTA TTTTA TTTTA TTATA TCTTTG TTTTA GTTTTTA TTTTG
1 TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA --TTTTA TTTTA
441154 TTTTA TTT
1 TTTTA TTT
441162 GTTTTTCAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 34 0.81
6 3 0.07
7 5 0.12
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:443879 original size:30 final size:30
Alignment explanation
Indices: 443845--443942 Score: 85
Period size: 30 Copynumber: 3.3 Consensus size: 30
443835 AAAAGGACAC
* *
443845 GCCTTTGTGGCAAATCTCTGTTAAAGGTAA
1 GCCTTTGTGGAAAATCTCTATTAAAGGTAA
* ** * *
443875 GCCTTTGCGGTGAA-C-CTCTTAAAGGTTTA
1 GCCTTTGTGGAAAATCTCTATTAAAGG-TAA
*
443904 -CCTTTGTGAAAAATCTCTATTAAAGGTAA
1 GCCTTTGTGGAAAATCTCTATTAAAGGTAA
*
443933 GCTTTTGTGG
1 GCCTTTGTGG
443943 TGAACCTCTT
Statistics
Matches: 51, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
28 18 0.35
29 6 0.12
30 27 0.53
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (30 bp):
GCCTTTGTGGAAAATCTCTATTAAAGGTAA
Found at i:443899 original size:28 final size:28
Alignment explanation
Indices: 443865--444014 Score: 88
Period size: 28 Copynumber: 5.2 Consensus size: 28
443855 CAAATCTCTG
*
443865 TTAAAGGTAAGCCTTTGCGGTGAACCTC
1 TTAAAGGTAAGCCTTTGTGGTGAACCTC
* *** *
443893 TTAAAGGTTTA-CCTTTGTGAAAAATCTCTA
1 TTAAAGG-TAAGCCTTTGTGGTGAA-C-CTC
*
443923 TTAAAGGTAAGCTTTTGTGGTGAACCTC
1 TTAAAGGTAAGCCTTTGTGGTGAACCTC
* ** * ** *
443951 TTAAAAG-ATTTCCTTTATGGCAAAACTC
1 TTAAAGGTA-AGCCTTTGTGGTGAACCTC
* * *
443979 TGAAAAGGTAAGCATTTGTGGTGAATCTC
1 T-TAAAGGTAAGCCTTTGTGGTGAACCTC
444008 TTAAAGG
1 TTAAAGG
444015 ATGACTTTTT
Statistics
Matches: 85, Mismatches: 30, Indels: 14
0.66 0.23 0.11
Matches are distributed among these distances:
27 1 0.01
28 42 0.49
29 23 0.27
30 19 0.22
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (28 bp):
TTAAAGGTAAGCCTTTGTGGTGAACCTC
Found at i:443911 original size:58 final size:58
Alignment explanation
Indices: 443846--444033 Score: 220
Period size: 58 Copynumber: 3.3 Consensus size: 58
443836 AAAGGACACG
* *
443846 CCTTTGTGGCAAATCTCTGTTAAAGGTAAGCCTTTGCGGTGAACCTCTTAAAGGTTTA
1 CCTTTGTGGCAAATCTCTGTTAAAGGTAAGCATTTGTGGTGAACCTCTTAAAGGTTTA
** * * *
443904 CCTTTGTGAAAAATCTCTATTAAAGGTAAGCTTTTGTGGTGAACCTCTTAAAAGATTT-
1 CCTTTGTGGCAAATCTCTGTTAAAGGTAAGCATTTGTGGTGAACCTCTT-AAAGGTTTA
* * * * * *
443962 CCTTTATGGCAAAACTCTG-AAAAGGTAAGCATTTGTGGTGAATCTCTTAAAGGATGA
1 CCTTTGTGGCAAATCTCTGTTAAAGGTAAGCATTTGTGGTGAACCTCTTAAAGGTTTA
*
444019 -CTTTTTGGCAAATCT
1 CCTTTGTGGCAAATCT
444034 TTGAAAGGAA
Statistics
Matches: 109, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
56 18 0.17
57 26 0.24
58 58 0.53
59 7 0.06
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (58 bp):
CCTTTGTGGCAAATCTCTGTTAAAGGTAAGCATTTGTGGTGAACCTCTTAAAGGTTTA
Found at i:447027 original size:30 final size:30
Alignment explanation
Indices: 446993--447055 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
446983 TACATGTACC
446993 AGATTCCTACCACTAAGGC-TCACATATAAT
1 AGATTCCTACCACTAAGGCGT-ACATATAAT
* * *
447023 AGATTCTTTCCACTAGGGCGTACATATAAT
1 AGATTCCTACCACTAAGGCGTACATATAAT
447053 AGA
1 AGA
447056 GAAAACCACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (30 bp):
AGATTCCTACCACTAAGGCGTACATATAAT
Found at i:450272 original size:12 final size:12
Alignment explanation
Indices: 450255--450299 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
450245 TAAATCAAGC
450255 AAAGAAAGGGAA
1 AAAGAAAGGGAA
*
450267 AAAGAAAGGAAA
1 AAAGAAAGGGAA
*
450279 AAAGAGAGGGAA
1 AAAGAAAGGGAA
*
450291 AAAGGAAGG
1 AAAGAAAGG
450300 AAATATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (12 bp):
AAAGAAAGGGAA
Found at i:450282 original size:24 final size:24
Alignment explanation
Indices: 450255--450302 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
450245 TAAATCAAGC
450255 AAAGAAAGGGAAAAAGAAAGGAAA
1 AAAGAAAGGGAAAAAGAAAGGAAA
* *
450279 AAAGAGAGGGAAAAAGGAAGGAAA
1 AAAGAAAGGGAAAAAGAAAGGAAA
450303 TATTTTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (24 bp):
AAAGAAAGGGAAAAAGAAAGGAAA
Found at i:453817 original size:32 final size:32
Alignment explanation
Indices: 453776--453838 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
453766 TTATTCAAGG
*
453776 TTGTTATTTTATTAATTTTGTTTTGACTAAAT
1 TTGTTATTTTATTAATTTTATTTTGACTAAAT
*
453808 TTGTTATTTTCTTAATTTTATTTTGACTAAA
1 TTGTTATTTTATTAATTTTATTTTGACTAAA
453839 ATGATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.05, G:0.08, T:0.62
Consensus pattern (32 bp):
TTGTTATTTTATTAATTTTATTTTGACTAAAT
Found at i:460101 original size:26 final size:26
Alignment explanation
Indices: 460065--460131 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
460055 TCAATCTTTG
*
460065 ACTGGTGAA-CCTCAGTTCGCAACTCA
1 ACTGGCGAACCCT-AGTTCGCAACTCA
* *
460091 ACTGGCGAACCCTAGTTCGTAACT-T
1 ACTGGCGAACCCTAGTTCGCAACTCA
*
460116 ACTTGGCAAACCCTAG
1 AC-TGGCGAACCCTAG
460132 CTCACCAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 2 0.06
26 30 0.86
27 3 0.09
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (26 bp):
ACTGGCGAACCCTAGTTCGCAACTCA
Found at i:476438 original size:44 final size:45
Alignment explanation
Indices: 476374--476464 Score: 166
Period size: 44 Copynumber: 2.0 Consensus size: 45
476364 TAGTCGCATA
*
476374 TGCAATGGTAGCTATAGATGTTATTAAACTACTATTGATTCCCTT
1 TGCAATGCTAGCTATAGATGTTATTAAACTACTATTGATTCCCTT
476419 TGCAATGCT-GCTATAGATGTTATTAAACTACTATTGATTCCCTT
1 TGCAATGCTAGCTATAGATGTTATTAAACTACTATTGATTCCCTT
476463 TG
1 TG
476465 ATCTAGATGG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 37 0.82
45 8 0.18
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.41
Consensus pattern (45 bp):
TGCAATGCTAGCTATAGATGTTATTAAACTACTATTGATTCCCTT
Found at i:477997 original size:48 final size:48
Alignment explanation
Indices: 477926--478022 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
477916 GCGGTGCATT
477926 AATTATTTTTGAGTAACTCAAATATCCACTTTTCATGTTCCCATGATA
1 AATTATTTTTGAGTAACTCAAATATCCACTTTTCATGTTCCCATGATA
477974 AATTATTTTTGAGTAACTCAAATATCCACTTTTCATGTTCCCATGATA
1 AATTATTTTTGAGTAACTCAAATATCCACTTTTCATGTTCCCATGATA
478022 A
1 A
478023 GCCTTTGAGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (48 bp):
AATTATTTTTGAGTAACTCAAATATCCACTTTTCATGTTCCCATGATA
Found at i:478651 original size:15 final size:15
Alignment explanation
Indices: 478613--478667 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
478603 TCACAATGTA
*
478613 AGTGCTCGCAGCATT
1 AGTGCTCGCAGCATC
* * *
478628 TGTGTTCGCAGCATG
1 AGTGCTCGCAGCATC
* *
478643 AGTGCTCGCAACACC
1 AGTGCTCGCAGCATC
478658 AGTGCTCGCA
1 AGTGCTCGCA
478668 TCTTTCAAGC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.24
Consensus pattern (15 bp):
AGTGCTCGCAGCATC
Found at i:491177 original size:30 final size:29
Alignment explanation
Indices: 491143--491354 Score: 160
Period size: 30 Copynumber: 7.1 Consensus size: 29
491133 TTGGCACTAT
*
491143 GGCTCACATATAATAAAGAACAGCCACAAA
1 GGCTCACATATAAT-AGGAACAGCCACAAA
* *
491173 GGCTCACATATAGTAGGAAACAGCCACGAA
1 GGCTCACATATAATAGG-AACAGCCACAAA
* * *
491203 GTCTCACATATAGTAGGAAACAGCCACGAA
1 GGCTCACATATAATAGG-AACAGCCACAAA
* * *
491233 GTCTCACATATAGTAGGAAACAGCCACGAA
1 GGCTCACATATAATAGG-AACAGCCACAAA
* *
491263 GTCTCACATATAATAGGAA-ATGGACACAAA
1 GGCTCACATATAATAGGAACA--GCCACAAA
* ** * **
491293 GGCTCTCATATACCA-AAACAATCACAAA
1 GGCTCACATATAATAGGAACAGCCACAAA
* *
491321 GGCTTACAAATATAATA-GAATAGCCACAAA
1 GGC-T-CACATATAATAGGAACAGCCACAAA
491351 GGCT
1 GGCT
491355 TTGACATATA
Statistics
Matches: 154, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
28 10 0.06
29 8 0.05
30 136 0.88
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (29 bp):
GGCTCACATATAATAGGAACAGCCACAAA
Found at i:491225 original size:60 final size:60
Alignment explanation
Indices: 491145--491304 Score: 232
Period size: 60 Copynumber: 2.7 Consensus size: 60
491135 GGCACTATGG
*
491145 CTCACATATAATA-AAGAACAGCCACAAAGGCTCACATATAGTAGGAAACAGCCACGAAGT
1 CTCACATATAATAGGA-AACAGCCACAAAGGCTCACATATAGTAGGAAACAGCCACGAAGT
* * *
491205 CTCACATATAGTAGGAAACAGCCACGAAGTCTCACATATAGTAGGAAACAGCCACGAAGT
1 CTCACATATAATAGGAAACAGCCACAAAGGCTCACATATAGTAGGAAACAGCCACGAAGT
** * *
491265 CTCACATATAATAGGAAATGGACACAAAGGCTCTCATATA
1 CTCACATATAATAGGAAACAGCCACAAAGGCTCACATATA
491305 CCAAAACAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 87 0.99
61 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (60 bp):
CTCACATATAATAGGAAACAGCCACAAAGGCTCACATATAGTAGGAAACAGCCACGAAGT
Found at i:491334 original size:60 final size:59
Alignment explanation
Indices: 491270--491385 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 59
491260 GAAGTCTCAC
* * * *
491270 ATATAATAGGAAATGGACACAAAGGCTCT-CATATACCAAAACAATCACAAAGGCTTACAA
1 ATATAATA-G-AATAGACACAAAGGCTCTACATATAACAAAACAACCACAAAAGCTTACAA
* *
491330 ATATAATAGAATAGCCACAAAGGCTTTGACATATAACAAAACAACCACAAAAGCTT
1 ATATAATAGAATAGACACAAAGGCTCT-ACATATAACAAAACAACCACAAAAGCTT
491386 CCATGTATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 15 0.31
59 1 0.02
60 32 0.67
ACGTcount: A:0.49, C:0.20, G:0.12, T:0.19
Consensus pattern (59 bp):
ATATAATAGAATAGACACAAAGGCTCTACATATAACAAAACAACCACAAAAGCTTACAA
Found at i:491378 original size:30 final size:29
Alignment explanation
Indices: 491287--491411 Score: 85
Period size: 30 Copynumber: 4.2 Consensus size: 29
491277 AGGAAATGGA
* * *
491287 CACAAAGGCTCT-CATATACCAAAACAAT
1 CACAAAGGCTTTACATATAACAAAACAAC
* * * *
491315 CACAAAGGC-TTACAAATATAATAGAATAGC
1 CACAAAGGCTTTAC--ATATAACAAAACAAC
491345 CACAAAGGCTTTGACATATAACAAAACAAC
1 CACAAAGGCTTT-ACATATAACAAAACAAC
* * *
491375 CACAAAAGC-TTCCATGTATAACAGAACAAC
1 CACAAAGGCTTTACA--TATAACAAAACAAC
*
491405 CATAAAG
1 CACAAAG
491412 ACTTCCACGT
Statistics
Matches: 74, Mismatches: 16, Indels: 12
0.73 0.16 0.12
Matches are distributed among these distances:
27 1 0.01
28 12 0.16
29 2 0.03
30 55 0.74
31 2 0.03
32 2 0.03
ACGTcount: A:0.49, C:0.23, G:0.10, T:0.18
Consensus pattern (29 bp):
CACAAAGGCTTTACATATAACAAAACAAC
Found at i:491395 original size:60 final size:58
Alignment explanation
Indices: 491287--491400 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 58
491277 AGGAAATGGA
* * * *
491287 CACAAAGGCTCTCATATACCAAAACAATCACAAAGGCTTACAAATATAATAGAATAGC
1 CACAAAGGCTCTCATATAACAAAACAACCACAAAAGCTTACAAATATAACAGAATAGC
* * **
491345 CACAAAGGCTTTGACATATAACAAAACAACCACAAAAGCTTCCATGTATAACAGAA
1 CACAAAGGCTCT--CATATAACAAAACAACCACAAAAGCTTACAAATATAACAGAA
491401 CAACCATAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
58 11 0.24
60 35 0.76
ACGTcount: A:0.48, C:0.23, G:0.11, T:0.18
Consensus pattern (58 bp):
CACAAAGGCTCTCATATAACAAAACAACCACAAAAGCTTACAAATATAACAGAATAGC
Found at i:495310 original size:20 final size:20
Alignment explanation
Indices: 495287--495324 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
495277 AGTCAAGTTT
* *
495287 CCAGTATTGTGGACAAGCCA
1 CCAGAATTGTAGACAAGCCA
495307 CCAGAATTGTAGACAAGC
1 CCAGAATTGTAGACAAGC
495325 TCCTAATACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (20 bp):
CCAGAATTGTAGACAAGCCA
Found at i:497044 original size:50 final size:50
Alignment explanation
Indices: 496990--497114 Score: 124
Period size: 50 Copynumber: 2.5 Consensus size: 50
496980 ATTTGATGTC
* **
496990 ATAGCTTCATTTTGCTCCATTGTAACTTTAGGGAGATAAGATTTGCTTTT
1 ATAGCTTCATTTTGCTCCACTACAACTTTAGGGAGATAAGATTTGCTTTT
* * * * ** * *
497040 ATAGCTTTAATTTGATCTACTACAACTTTAGGGTTATAGGATTTGGTTTT
1 ATAGCTTCATTTTGCTCCACTACAACTTTAGGGAGATAAGATTTGCTTTT
* * *
497090 GTAGCTTCATCTTGCTCTACTACAA
1 ATAGCTTCATTTTGCTCCACTACAA
497115 TTTTTAAGAG
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (50 bp):
ATAGCTTCATTTTGCTCCACTACAACTTTAGGGAGATAAGATTTGCTTTT
Found at i:497653 original size:305 final size:301
Alignment explanation
Indices: 497143--497831 Score: 884
Period size: 305 Copynumber: 2.3 Consensus size: 301
497133 TTTGTTTTTG
* * *
497143 TAGTTTTAATTCGACCCACTTCAACTTCAGGGGTATAGGATTTGATGTTGTAACTTCACTCCATT
1 TAGTTTTAATTCGACCCACTACAACTTTAGGGATATAGGATTTGATGTTGTAACTTCACTCCATT
* * *
497208 CCACTGCAACTTCATGGAGATTGAGACCCACTTAGTTTTAATCTGATCCACTGCAACTTCAGGGA
66 CCACTGCAACTTCAAGGAGATTAAGACCCACTTAGTTTTAATCTGATCCACTGCAAATTCAGGGA
* * * ***
497273 TATAGGATTCGGTGTTGTAACTTCACTCCATTCTACTATAACTTTAGGGAGATTGAGATCTGTTA
131 TAAAGGATTCGGTGTTGTAACTTCACTCCATTCCACTATAACTTCAGGGAGATTGAGATCCACTA
* * * * *
497338 CTGTTAGTTTTAATTTGATCCACTATAACTTTAGGGATATAGGATTTATTGTTGTAACTTCACTC
196 CTATTAGTTTTAATCTGATCCACTATAACTTCAGGGATATAGGATTCAGTGTTGTAACTTCACTC
* *
497403 CATTCCACTACAACTTTAGGGAAATTGAGATCCT-CTATTGT
261 CATTCCACTACAACTTTAGGGAAACTGAGAT-CTGCTACTGT
* * * *
497444 TAGTTTTAATCCGACCCACTACAACTTTAAGGATATAGGATTTGAT-TTGTAACTTTATTCCATT
1 TAGTTTTAATTCGACCCACTACAACTTTAGGGATATAGGATTTGATGTTGTAACTTCACTCCATT
* * * * *
497508 CCATTGTAACTTCAAGGAGATTAAGATCTACTACTTTTAGTTTTATTCTGATCCATTGCAAA-TC
66 CCACTGCAACTTCAAGGAGATTAAGA-C--CCAC--TTAGTTTTAATCTGATCCACTGCAAATTC
*
497572 TAGGGATAAAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGA-AACTTCAGGGAGATTGAGA
126 -AGGGATAAAGGATTCGGTGTTGTAACTTCACTCCATTCCACT-ATAACTTCAGGGAGATTGAGA
* *
497636 TCCACTACTATTAGTTTTAATCTGATCCACTGTAACTTCAGGGATATAGGATTCGGTGTTGTAAC
189 TCCACTACTATTAGTTTTAATCTGATCCACTATAACTTCAGGGATATAGGATTCAGTGTTGTAAC
** * * *
497701 TTCACTCCATTCCACTGTAACTTTAGGGAGACTGAGATTTGTTACTGT
254 TTCACTCCATTCCACTACAACTTTAGGGAAACTGAGATCTGCTACTGT
* * * *
497749 TAGTTTTAATTTGATCCATTACAACTTTAGGGATATAGGGTTT-ATTGTTGTAACTTCACTCCAT
1 TAGTTTTAATTCGACCCACTACAACTTTAGGGATATAGGATTTGA-TGTTGTAACTTCACTCCAT
* *
497813 TCCACTACAACTTTAAGGA
65 TCCACTGCAACTTCAAGGA
497832 TATAGGATTT
Statistics
Matches: 330, Mismatches: 48, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
300 38 0.12
301 42 0.13
303 3 0.01
304 4 0.01
305 212 0.64
306 31 0.09
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37
Consensus pattern (301 bp):
TAGTTTTAATTCGACCCACTACAACTTTAGGGATATAGGATTTGATGTTGTAACTTCACTCCATT
CCACTGCAACTTCAAGGAGATTAAGACCCACTTAGTTTTAATCTGATCCACTGCAAATTCAGGGA
TAAAGGATTCGGTGTTGTAACTTCACTCCATTCCACTATAACTTCAGGGAGATTGAGATCCACTA
CTATTAGTTTTAATCTGATCCACTATAACTTCAGGGATATAGGATTCAGTGTTGTAACTTCACTC
CATTCCACTACAACTTTAGGGAAACTGAGATCTGCTACTGT
Found at i:497826 original size:102 final size:102
Alignment explanation
Indices: 497143--497827 Score: 717
Period size: 102 Copynumber: 6.8 Consensus size: 102
497133 TTTGTTTTTG
* * * * *
497143 TAGTTTTAATTCGACCCACTTCAACTTCAGGGGTATAGGATTT-GATGTTGTAACTTCACTCCAT
1 TAGTTTTAATTTGATCCACTACAACTTTAGGGATATAGGATTTAG-TGTTGTAACTTCACTCCAT
* * * *
497207 TCCACTGCAACTTCATGGAGATTGAGA-C--CCAC--T
65 TCCACTACAACTTTAGGGAGATTGAGATCTACTACTGT
* * * **
497240 TAGTTTTAATCTGATCCACTGCAACTTCAGGGATATAGGATTCGGTGTTGTAACTTCACTCCATT
1 TAGTTTTAATTTGATCCACTACAACTTTAGGGATATAGGATTTAGTGTTGTAACTTCACTCCATT
* * **
497305 CTACTATAACTTTAGGGAGATTGAGATCTGTTACTGT
66 CCACTACAACTTTAGGGAGATTGAGATCTACTACTGT
* *
497342 TAGTTTTAATTTGATCCACTATAACTTTAGGGATATAGGATTTATTGTTGTAACTTCACTCCATT
1 TAGTTTTAATTTGATCCACTACAACTTTAGGGATATAGGATTTAGTGTTGTAACTTCACTCCATT
* *
497407 CCACTACAACTTTAGGGAAATTGAGATCCT-CTATTGT
66 CCACTACAACTTTAGGGAGATTGAGAT-CTACTACTGT
** * * * *
497444 TAGTTTTAATCCGACCCACTACAACTTTAAGGATATAGGATTT-GAT-TTGTAACTTTATTCCAT
1 TAGTTTTAATTTGATCCACTACAACTTTAGGGATATAGGATTTAG-TGTTGTAACTTCACTCCAT
* ** * * * *
497507 TCCATTGTAACTTCAAGGAGATTAAGATCTACTACTTT
65 TCCACTACAACTTTAGGGAGATTGAGATCTACTACTGT
* * * * * *
497545 TAGTTTT-ATTCTGATCCATTGCAAATCTAGGGATAAAGGATTTGGTGTTGTAACTTCACTCCAT
1 TAGTTTTAATT-TGATCCACTACAACTTTAGGGATATAGGATTTAGTGTTGTAACTTCACTCCAT
* * *
497609 TCCACTGA-AACTTCAGGGAGATTGAGATCCACTACTAT
65 TCCACT-ACAACTTTAGGGAGATTGAGATCTACTACTGT
* ** * **
497647 TAGTTTTAATCTGATCCACTGTAACTTCAGGGATATAGGATTCGGTGTTGTAACTTCACTCCATT
1 TAGTTTTAATTTGATCCACTACAACTTTAGGGATATAGGATTTAGTGTTGTAACTTCACTCCATT
** * * **
497712 CCACTGTAACTTTAGGGAGACTGAGATTTGTTACTGT
66 CCACTACAACTTTAGGGAGATTGAGATCTACTACTGT
* * *
497749 TAGTTTTAATTTGATCCATTACAACTTTAGGGATATAGGGTTTATTGTTGTAACTTCACTCCATT
1 TAGTTTTAATTTGATCCACTACAACTTTAGGGATATAGGATTTAGTGTTGTAACTTCACTCCATT
497814 CCACTACAACTTTA
66 CCACTACAACTTTA
497828 AGGATATAGG
Statistics
Matches: 487, Mismatches: 86, Indels: 25
0.81 0.14 0.04
Matches are distributed among these distances:
97 78 0.16
98 2 0.00
100 6 0.01
101 73 0.15
102 324 0.67
103 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (102 bp):
TAGTTTTAATTTGATCCACTACAACTTTAGGGATATAGGATTTAGTGTTGTAACTTCACTCCATT
CCACTACAACTTTAGGGAGATTGAGATCTACTACTGT
Found at i:497862 original size:152 final size:152
Alignment explanation
Indices: 497677--497977 Score: 406
Period size: 152 Copynumber: 2.0 Consensus size: 152
497667 GTAACTTCAG
* * * **
497677 GGATATAGGATTCGGTGTTGTAACTTCACTCCATTCCACTGTAACTTTAGGGAGACTGAGATTTG
1 GGATATAGGATTCGATGTTGTAACTTCACTCCATTCCACTGTAACTTCAAGGAGACTGAGATCCG
* * * * ** * * *
497742 TTACTGTTAGTTTTAATT-TGATCCATTACAACTTTAGGGATATAGGGTTTATTGTTGTAACTTC
66 CTACTATTAGTTTT-ATTCTGATCCACTACAAATCGAGGGATAAAGGATTTAGTGTTGTAACTTC
497806 ACTCCATTCCACTACAACTTTAA
130 ACTCCATTCCACTACAACTTTAA
* * *
497829 GGATATAGGATTTGATGTTGTAACTTCATTCCATTCCACTGTAACTTCAAGGAGATTGAGATCCG
1 GGATATAGGATTCGATGTTGTAACTTCACTCCATTCCACTGTAACTTCAAGGAGACTGAGATCCG
* *
497894 CTACTATTAGTTTTATTCTGATCCACTGCAAATCGAGGGATAAAGGATTTGGTGTTGTAACTTCA
66 CTACTATTAGTTTTATTCTGATCCACTACAAATCGAGGGATAAAGGATTTAGTGTTGTAACTTCA
*
497959 CTCCATTCCACTGCAACTT
131 CTCCATTCCACTACAACTT
497978 CAGGGAGATT
Statistics
Matches: 128, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
151 3 0.02
152 125 0.98
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (152 bp):
GGATATAGGATTCGATGTTGTAACTTCACTCCATTCCACTGTAACTTCAAGGAGACTGAGATCCG
CTACTATTAGTTTTATTCTGATCCACTACAAATCGAGGGATAAAGGATTTAGTGTTGTAACTTCA
CTCCATTCCACTACAACTTTAA
Found at i:497875 original size:50 final size:51
Alignment explanation
Indices: 497254--497875 Score: 182
Period size: 50 Copynumber: 12.3 Consensus size: 51
497244 TTTAATCTGA
* * * *
497254 TCCACTGCAACTTCAGGGATATAGGATTCG-GTGTTGTAACTTCACTCCAT
1 TCCACTGTAACTTTAGGGATATAGGATTTGACTGTTGTAACTTCACTCCAT
* * * * * * * * **
497304 TCTACTATAACTTTAGGGAGATTGAGATCTGTTACTGTTAGT--TTTAATTTGA-
1 TCCACTGTAACTTTAGGGATATAG-GAT-T-TGACTGTT-GTAACTTCACTCCAT
* *
497356 TCCACTATAACTTTAGGGATATAGGATTT-ATTGTTGTAACTTCACTCCAT
1 TCCACTGTAACTTTAGGGATATAGGATTTGACTGTTGTAACTTCACTCCAT
** * * * * ** * *
497406 TCCACTACAACTTTAGGGAAATTGAGATCCT--CTATTGTTAGTTTTAATCCGA-
1 TCCACTGTAACTTTAGGGATATAG-GAT-TTGACTGTTG-TAACTTCACTCC-AT
* ** * * *
497458 CCCACTACAACTTTAAGGATATAGGATTTGA-T-TTGTAACTTTATTCCAT
1 TCCACTGTAACTTTAGGGATATAGGATTTGACTGTTGTAACTTCACTCCAT
* * * * * * ** * * *
497507 TCCATTGTAACTTCAAGGAGAT-TAAGATCT-ACTACTTTTAGTTTTATTCTGA-
1 TCCACTGTAACTT-TAGG-GATATAGGATTTGACT-GTTGTAACTTCACTC-CAT
* * * * * *
497559 TCCATTGCAAATCTAGGGATAAAGGATTTG-GTGTTGTAACTTCACTCCAT
1 TCCACTGTAACTTTAGGGATATAGGATTTGACTGTTGTAACTTCACTCCAT
* * * * ** * ** * * *
497609 TCCACTGAAACTTCAGGGAGATTGAGA-TCCACTACTAT-TAGTTTTAATCTGA-
1 TCCACTGTAACTTTAGGGATATAG-GATTTGACT-GT-TGTAACTTCACTC-CAT
* * *
497661 TCCACTGTAACTTCAGGGATATAGGATTCG-GTGTTGTAACTTCACTCCAT
1 TCCACTGTAACTTTAGGGATATAGGATTTGACTGTTGTAACTTCACTCCAT
* * *
497711 TCCACTGTAACTTTAGGGAGACT-GAGATTTGTTACTGTTAGTTTTAATTTGA-TCCAT
1 TCCACTGTAACTTTAGGGATA-TAG-GATTTG--ACTGTT-G---TAACTTCACTCCAT
* *
497768 T--AC---AACTTTAGGGATATAGGGTTT-ATTGTTGTAACTTCACTCCAT
1 TCCACTGTAACTTTAGGGATATAGGATTTGACTGTTGTAACTTCACTCCAT
** * *
497813 TCCACTACAACTTTAAGGATATAGGATTTGA-TGTTGTAACTTCATTCCAT
1 TCCACTGTAACTTTAGGGATATAGGATTTGACTGTTGTAACTTCACTCCAT
497863 TCCACTGTAACTT
1 TCCACTGTAACTT
497876 CAAGGAGATT
Statistics
Matches: 411, Mismatches: 112, Indels: 98
0.66 0.18 0.16
Matches are distributed among these distances:
44 6 0.01
45 6 0.01
47 5 0.01
48 11 0.03
49 28 0.07
50 158 0.38
51 47 0.11
52 116 0.28
53 9 0.02
54 8 0.02
55 5 0.01
57 6 0.01
58 6 0.01
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (51 bp):
TCCACTGTAACTTTAGGGATATAGGATTTGACTGTTGTAACTTCACTCCAT
Found at i:497919 original size:102 final size:102
Alignment explanation
Indices: 497813--498143 Score: 430
Period size: 102 Copynumber: 3.3 Consensus size: 102
497803 TTCACTCCAT
* * * *
497813 TCCACTACAACTTTAAGGATATAGGATTTGATGTTGTAACTTCATTCCATTCCACTGTAACTTCA
1 TCCACTGCAACTTTAAGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCA
* * *
497878 AGGAGATTGAGATCCGCTACTATTAGTTTTATTCTGA
66 AGGAGATTGAGATCCGCTACTGTTAGTTTTAATCTAA
* ** * *
497915 TCCACTGCAAATCGAGGGATAAAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCA
1 TCCACTGCAACTTTAAGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCA
* * *
497980 GGGAGATTGAGATCCACTACTGTTAGCTTTAATCTAA
66 AGGAGATTGAGATCCGCTACTGTTAGTTTTAATCTAA
* * *
498017 TCCACTGTAACTTCAAGGATATAGGATTTGGTGTTGTAACTTCACTCTATTCCACTGCAACTTCA
1 TCCACTGCAACTTTAAGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCA
* * * * *
498082 AGGAGATTGAGATCTGCTATTGTT-GTTTTACTCCAT
66 AGGAGATTGAGATCCGCTACTGTTAGTTTTAATCTAA
* *
498118 TCCACCGCAACTTTAGGGATATAGGA
1 TCCACTGCAACTTTAAGGATATAGGA
498144 GTTGTCTATC
Statistics
Matches: 195, Mismatches: 34, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
101 30 0.15
102 165 0.85
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (102 bp):
TCCACTGCAACTTTAAGGATATAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCA
AGGAGATTGAGATCCGCTACTGTTAGTTTTAATCTAA
Found at i:497926 original size:356 final size:354
Alignment explanation
Indices: 497459--498111 Score: 1090
Period size: 356 Copynumber: 1.8 Consensus size: 354
497449 TTAATCCGAC
* *
497459 CCACTACAACTTTAAGGATATAGGATTTGATTTGTAACTTTATTCCATTCCATTGTAACTTCAAG
1 CCACTACAACTTTAAGGATATAGGATTTGATTTGTAACTTCATTCCATTCCACTGTAACTTCAAG
* * * *
497524 GAGATTAAGATCTACTACTTTTAGTTTTATTCTGATCCATTGCAAATCTAGGGATAAAGGATTTG
66 GAGATTAAGATCCACTACTATTAGTTTTATTCTGATCCACTGCAAATCGAGGGATAAAGGATTTG
*
497589 GTGTTGTAACTTCACTCCATTCCACTGAAACTTCAGGGAGATTGAGATCCACTACTATTAGTTTT
131 GTGTTGTAACTTCACTCCATTCCACTGAAACTTCAGGGAGATTGAGATCCACTACTATTAGCTTT
* * *
497654 AATCTGATCCACTGTAACTTCAGGGATATAGGATTCGGTGTTGTAACTTCACTCCATTCCACTGT
196 AATCTAATCCACTGTAACTTCAAGGATATAGGATTCGGTGTTGTAACTTCACTCCATTCCACTGC
* * * *
497719 AACTTTAGGGAGACTGAGATTTGTTACTGTTAGTTTTAATTTGATCCATTACAACTTTAGGGATA
261 AACTTCAAGGAGACTGAGATCTGCTACTGTT-GTTTTAATTTGATCCATTACAACTTTAGGGATA
497784 TAGGGTTTATTGTTGTAACTTCACTCCATT
325 TAGGGTTTATTGTTGTAACTTCACTCCATT
497814 CCACTACAACTTTAAGGATATAGGATTTGATGTTGTAACTTCATTCCATTCCACTGTAACTTCAA
1 CCACTACAACTTTAAGGATATAGGATTTGAT-TTGTAACTTCATTCCATTCCACTGTAACTTCAA
* *
497879 GGAGATTGAGATCCGCTACTATTAGTTTTATTCTGATCCACTGCAAATCGAGGGATAAAGGATTT
65 GGAGATTAAGATCCACTACTATTAGTTTTATTCTGATCCACTGCAAATCGAGGGATAAAGGATTT
* *
497944 GGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCCACTACTGTTAGCTT
130 GGTGTTGTAACTTCACTCCATTCCACTGAAACTTCAGGGAGATTGAGATCCACTACTATTAGCTT
* *
498009 TAATCTAATCCACTGTAACTTCAAGGATATAGGATTTGGTGTTGTAACTTCACTCTATTCCACTG
195 TAATCTAATCCACTGTAACTTCAAGGATATAGGATTCGGTGTTGTAACTTCACTCCATTCCACTG
* *
498074 CAACTTCAAGGAGATTGAGATCTGCTATTGTTGTTTTA
260 CAACTTCAAGGAGACTGAGATCTGCTACTGTTGTTTTA
498112 CTCCATTCCA
Statistics
Matches: 275, Mismatches: 22, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
355 37 0.13
356 238 0.87
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (354 bp):
CCACTACAACTTTAAGGATATAGGATTTGATTTGTAACTTCATTCCATTCCACTGTAACTTCAAG
GAGATTAAGATCCACTACTATTAGTTTTATTCTGATCCACTGCAAATCGAGGGATAAAGGATTTG
GTGTTGTAACTTCACTCCATTCCACTGAAACTTCAGGGAGATTGAGATCCACTACTATTAGCTTT
AATCTAATCCACTGTAACTTCAAGGATATAGGATTCGGTGTTGTAACTTCACTCCATTCCACTGC
AACTTCAAGGAGACTGAGATCTGCTACTGTTGTTTTAATTTGATCCATTACAACTTTAGGGATAT
AGGGTTTATTGTTGTAACTTCACTCCATT
Found at i:498039 original size:254 final size:254
Alignment explanation
Indices: 497575--498085 Score: 718
Period size: 254 Copynumber: 2.0 Consensus size: 254
497565 GCAAATCTAG
* *
497575 GGATAAAGGATTTGGTGTTGTAACTTCACTCCATTCCACTGAAACTTCAGGGAGATTGAGATCCA
1 GGATAAAGGATTTGATGTTGTAACTTCACTCCATTCCACTGAAACTTCAAGGAGATTGAGATCCA
* * *
497640 CTACTATTAGTTTTAATCTGATCCACTGTAACTTCAGGGATATAGGATTCGGTGTTGTAACTTCA
66 CTACTATTAGTTTTAATCTGATCCACTGCAACATCAGGGATAAAGGATTCGGTGTTGTAACTTCA
* * **** * * * *
497705 CTCCATTCCACTGTAACTTTAGGGAGACTGAGATTTGTTACTGTTAGTTTTAATTTGATCCATTA
131 CTCCATTCCACTGCAACTTCAGGGAGACTGAGATCCACTACTGTTAGCTTTAATCTAATCCACTA
* * * * *
497770 CAACTTTAGGGATATAGGGTTTATTGTTGTAACTTCACTCCATTCCACTACAACTTTAA
196 CAACTTCAAGGATATAGGATTTAGTGTTGTAACTTCACTCCATTCCACTACAACTTCAA
* * * *
497829 GGATATAGGATTTGATGTTGTAACTTCATTCCATTCCACTGTAACTTCAAGGAGATTGAGATCCG
1 GGATAAAGGATTTGATGTTGTAACTTCACTCCATTCCACTGAAACTTCAAGGAGATTGAGATCCA
* *
497894 CTACTATTAGTTTTATTCTGATCCACTGCAA-ATCGAGGGATAAAGGATTTGGTGTTGTAACTTC
66 CTACTATTAGTTTTAATCTGATCCACTGCAACATC-AGGGATAAAGGATTCGGTGTTGTAACTTC
*
497958 ACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCCACTACTGTTAGCTTTAATCTAATCCACT
130 ACTCCATTCCACTGCAACTTCAGGGAGACTGAGATCCACTACTGTTAGCTTTAATCTAATCCACT
** * * *
498023 GTAACTTCAAGGATATAGGATTTGGTGTTGTAACTTCACTCTATTCCACTGCAACTTCAA
195 ACAACTTCAAGGATATAGGATTTAGTGTTGTAACTTCACTCCATTCCACTACAACTTCAA
498083 GGA
1 GGA
498086 GATTGAGATC
Statistics
Matches: 224, Mismatches: 32, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
253 2 0.01
254 222 0.99
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35
Consensus pattern (254 bp):
GGATAAAGGATTTGATGTTGTAACTTCACTCCATTCCACTGAAACTTCAAGGAGATTGAGATCCA
CTACTATTAGTTTTAATCTGATCCACTGCAACATCAGGGATAAAGGATTCGGTGTTGTAACTTCA
CTCCATTCCACTGCAACTTCAGGGAGACTGAGATCCACTACTGTTAGCTTTAATCTAATCCACTA
CAACTTCAAGGATATAGGATTTAGTGTTGTAACTTCACTCCATTCCACTACAACTTCAA
Found at i:498128 original size:51 final size:51
Alignment explanation
Indices: 497958--498130 Score: 159
Period size: 51 Copynumber: 3.4 Consensus size: 51
497948 TTGTAACTTC
* ** *
497958 ACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCCACTACTGTTAGCTTT
1 ACTCCATTCCACTGCAACTTCAAGGAGATTGAGATCTGCTATTGTT-GCTTT
* * * * * * * * * ** *
498010 AATCTAATCCACTGTAACTTCAAGGATATAG-GATTTGGTGTTGTAACTTC
1 ACTCCATTCCACTGCAACTTCAAGGAGATTGAGATCTGCTATTGTTGCTTT
* *
498060 ACTCTATTCCACTGCAACTTCAAGGAGATTGAGATCTGCTATTGTTGTTTT
1 ACTCCATTCCACTGCAACTTCAAGGAGATTGAGATCTGCTATTGTTGCTTT
*
498111 ACTCCATTCCACCGCAACTT
1 ACTCCATTCCACTGCAACTT
498131 TAGGGATATA
Statistics
Matches: 90, Mismatches: 30, Indels: 3
0.73 0.24 0.02
Matches are distributed among these distances:
50 29 0.32
51 37 0.41
52 24 0.27
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (51 bp):
ACTCCATTCCACTGCAACTTCAAGGAGATTGAGATCTGCTATTGTTGCTTT
Found at i:510487 original size:12 final size:12
Alignment explanation
Indices: 510465--510499 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
510455 TATCAAGACG
510465 AGAATGAGAAAGA
1 AGAA-GAGAAAGA
510478 AGAAGAGAAAGA
1 AGAAGAGAAAGA
510490 AGAAGCAGAA
1 AGAAG-AGAA
510500 TCTGCCGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.63, C:0.03, G:0.31, T:0.03
Consensus pattern (12 bp):
AGAAGAGAAAGA
Found at i:522496 original size:14 final size:15
Alignment explanation
Indices: 522477--522506 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
522467 CTAGTGTTTT
522477 ACTATTCAT-TTATC
1 ACTATTCATCTTATC
522491 ACTATTCATCTTATC
1 ACTATTCATCTTATC
522506 A
1 A
522507 ATATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (15 bp):
ACTATTCATCTTATC
Found at i:522810 original size:21 final size:23
Alignment explanation
Indices: 522786--522840 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
522776 CCTATAACTT
*
522786 CTACCAATACAAGTAT-GCA-AA
1 CTACCAATACAAGTATAACATAA
* *
522807 CTACCGATACATGTATACACATAA
1 CTACCAATACAAGTATA-ACATAA
522831 CTACCAATAC
1 CTACCAATAC
522841 CCACAATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 14 0.52
23 2 0.07
24 11 0.41
ACGTcount: A:0.44, C:0.27, G:0.07, T:0.22
Consensus pattern (23 bp):
CTACCAATACAAGTATAACATAA
Found at i:523330 original size:31 final size:31
Alignment explanation
Indices: 523295--523425 Score: 95
Period size: 31 Copynumber: 3.9 Consensus size: 31
523285 TGTAATGGAC
*
523295 AAAAAAATTAAAGGAAAGGAAAAGAATGGGA
1 AAAAAAAGTAAAGGAAAGGAAAAGAATGGGA
* * *
523326 AAAAAAAGTAAAGGAAAAGTAAATAATTGTAAAGGAA
1 AAAAAAAGTAAAGG-AAAG-GAA-AA--G-AATGGGA
*
523363 AAAAACGTAAGGAAAGGAAAGGAAAAGAAT-GGA
1 AAAAA---AAGTAAAGGAAAGGAAAAGAATGGGA
*
523396 AAAAAAA-TAAAAAGTAAAGGAAAAGAATGG
1 AAAAAAAGT--AAAGGAAAGGAAAAGAATGG
523426 ACAGTTAAAG
Statistics
Matches: 78, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
30 2 0.03
31 30 0.38
32 5 0.06
33 9 0.12
34 4 0.05
35 1 0.01
36 1 0.01
37 12 0.15
38 2 0.03
39 4 0.05
40 8 0.10
ACGTcount: A:0.65, C:0.01, G:0.24, T:0.11
Consensus pattern (31 bp):
AAAAAAAGTAAAGGAAAGGAAAAGAATGGGA
Found at i:523386 original size:10 final size:10
Alignment explanation
Indices: 523371--523422 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
523361 AAAAAAACGT
*
523371 AAGGAAAGGA
1 AAGGAAAAGA
523381 AAGGAAAAGA
1 AAGGAAAAGA
* *
523391 ATGGAAAAAA
1 AAGGAAAAGA
**
523401 AATAAAAAGTA
1 AAGGAAAAG-A
523412 AAGGAAAAGA
1 AAGGAAAAGA
523422 A
1 A
523423 TGGACAGTTA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
10 24 0.75
11 8 0.25
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (10 bp):
AAGGAAAAGA
Found at i:528010 original size:26 final size:26
Alignment explanation
Indices: 527981--528043 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
527971 GACTCTAAAG
*
527981 ATACTGTATTGGCTCGTAAGAGCGAT
1 ATACTGTACTGGCTCGTAAGAGCGAT
528007 ATACTGTACTGGCTCGTAAGAGCGAT
1 ATACTGTACTGGCTCGTAAGAGCGAT
*
528033 TTACTG-ACTGG
1 ATACTGTACTGG
528044 ACTCATATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 5 0.14
26 30 0.86
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (26 bp):
ATACTGTACTGGCTCGTAAGAGCGAT
Found at i:528055 original size:26 final size:26
Alignment explanation
Indices: 527981--528055 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
527971 GACTCTAAAG
* *
527981 ATACTGTATTGGCTCGTAAGAGCGAT
1 ATACTGTACTGGCTCATAAGAGCGAT
*
528007 ATACTGTACTGGCTCGTAAGAGCGAT
1 ATACTGTACTGGCTCATAAGAGCGAT
* *
528033 TTACTG-ACTGGACTCATATGAGC
1 ATACTGTACTGG-CTCATAAGAGC
528056 AAAATTTACT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.11
26 39 0.89
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (26 bp):
ATACTGTACTGGCTCATAAGAGCGAT
Found at i:528151 original size:98 final size:98
Alignment explanation
Indices: 527978--528202 Score: 315
Period size: 98 Copynumber: 2.3 Consensus size: 98
527968 GAAGACTCTA
* * * *
527978 AAGATACTGTATTGGCTCGTAAGAGCGATATACTGTACTGGCTCGTAAGAGCGATTTACTGACTG
1 AAGATACTGTACTGGCTCGTAAGAGCGATATAATGTACTGGCTCGTAAGAGCGATTTACTAACTA
*
528043 GACTCATATGAGCAAAATTTACTGGGAGACTTG
66 GACTCATATGAGCAAAATTTACTGAGAGACTTG
* * * *
528076 AAGATATTGTACTGGCTCGTAAGAGTGATATAATGTATTGGCTCGTAAGTGCGATTTACTAACTA
1 AAGATACTGTACTGGCTCGTAAGAGCGATATAATGTACTGGCTCGTAAGAGCGATTTACTAACTA
* * *
528141 GACTCGTATGAGTAAAATTTATTGAGAGACTTG
66 GACTCATATGAGCAAAATTTACTGAGAGACTTG
* **
528174 AAGATACTATACTGGCTTATAAGAGCGAT
1 AAGATACTGTACTGGCTCGTAAGAGCGAT
528203 TTACTAATAG
Statistics
Matches: 110, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
98 110 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (98 bp):
AAGATACTGTACTGGCTCGTAAGAGCGATATAATGTACTGGCTCGTAAGAGCGATTTACTAACTA
GACTCATATGAGCAAAATTTACTGAGAGACTTG
Found at i:528231 original size:72 final size:72
Alignment explanation
Indices: 528121--528262 Score: 214
Period size: 72 Copynumber: 2.0 Consensus size: 72
528111 TATTGGCTCG
* * *
528121 TAAGTGCGATTTACTAACTAGACTCGTATGAGTAAAATTTATTGAGAGACTTGAAGATACTATAC
1 TAAGAGCGATTTACTAACTAGACTCGTATGAGCAAAATTTACTGAGAGACTTGAAGATACTATAC
528186 TGGCTTA
66 TGGCTTA
* * *
528193 TAAGAGCGATTTACTAA-TAGGGCTCGTATGAGCAAAATTTACTGGGAGACTTGAATATACTATA
1 TAAGAGCGATTTACTAACTA-GACTCGTATGAGCAAAATTTACTGAGAGACTTGAAGATACTATA
528257 CTGGCT
65 CTGGCT
528263 CGGAAGTGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 2 0.03
72 61 0.97
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (72 bp):
TAAGAGCGATTTACTAACTAGACTCGTATGAGCAAAATTTACTGAGAGACTTGAAGATACTATAC
TGGCTTA
Found at i:529365 original size:26 final size:26
Alignment explanation
Indices: 529336--529414 Score: 104
Period size: 26 Copynumber: 3.0 Consensus size: 26
529326 GACTCTAAAG
*
529336 ATACTGTATTGGCTCGTAAGAGCGAT
1 ATACTGTACTGGCTCGTAAGAGCGAT
* *
529362 ATACTGTACTGGCTCATAAAAGCGAT
1 ATACTGTACTGGCTCGTAAGAGCGAT
* * *
529388 ATACTATACTGGTTCGTAAGAGTGAT
1 ATACTGTACTGGCTCGTAAGAGCGAT
529414 A
1 A
529415 AATTGACTAG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (26 bp):
ATACTGTACTGGCTCGTAAGAGCGAT
Found at i:529505 original size:72 final size:72
Alignment explanation
Indices: 529388--529562 Score: 233
Period size: 72 Copynumber: 2.4 Consensus size: 72
529378 TAAAAGCGAT
* * * * * * * *
529388 ATACTATACTGGTTCGTAAGAGTGATAAATTGACTAGACTCGTATGAGCAAAATTTACTAGGAGA
1 ATACTGTACTGGCTCATAAGAGCGATATACTGACTGGGCTCGTATGAGCAAAATTTACTAGGAGA
*
529453 CTTGATG
66 CTTGAAG
*
529460 ATACTGTACTGGCTCATAAGAGCGATTTACTGACTGGGCTCGTATGAGCAAAATTTACTAGGAGA
1 ATACTGTACTGGCTCATAAGAGCGATATACTGACTGGGCTCGTATGAGCAAAATTTACTAGGAGA
529525 CTTGAAG
66 CTTGAAG
* * *
529532 ATATTGTACTGGCTCGTAAGATCGATATACT
1 ATACTGTACTGGCTCATAAGAGCGATATACT
529563 AAATTGGTTC
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 89 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (72 bp):
ATACTGTACTGGCTCATAAGAGCGATATACTGACTGGGCTCGTATGAGCAAAATTTACTAGGAGA
CTTGAAG
Found at i:529603 original size:26 final size:26
Alignment explanation
Indices: 529539--529612 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
529529 AAGATATTGT
529539 ACTGGCTCGTAAGA-TCGATATACTAA
1 ACTGGCTCGTAAGAGT-GATATACTAA
* * * ** *
529565 ATTGGTTCATAAGAGTGATATGTTGA
1 ACTGGCTCGTAAGAGTGATATACTAA
*
529591 ACTGGCTCGTAAGAGCGATATA
1 ACTGGCTCGTAAGAGTGATATA
529613 TTAATTATTT
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
26 35 0.97
27 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (26 bp):
ACTGGCTCGTAAGAGTGATATACTAA
Found at i:530634 original size:26 final size:26
Alignment explanation
Indices: 530605--530705 Score: 105
Period size: 26 Copynumber: 3.9 Consensus size: 26
530595 GACTCTAAAG
*
530605 ATACTGTATTGGCTCGTAAGAGCGAT
1 ATACTGTACTGGCTCGTAAGAGCGAT
* *
530631 ATACTGTACTGGCTCATAAAAGCGAT
1 ATACTGTACTGGCTCGTAAGAGCGAT
* * *
530657 ATACTATACTGGTTCGTAAGAGTGAT
1 ATACTGTACTGGCTCGTAAGAGCGAT
* * *
530683 AAACTG-ACTAGACTCGTATGAGC
1 ATACTGTACT-GGCTCGTAAGAGC
530706 AAAATTTACT
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
25 3 0.05
26 57 0.95
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.29
Consensus pattern (26 bp):
ATACTGTACTGGCTCGTAAGAGCGAT
Found at i:530774 original size:72 final size:72
Alignment explanation
Indices: 530657--530831 Score: 269
Period size: 72 Copynumber: 2.4 Consensus size: 72
530647 TAAAAGCGAT
* * * *
530657 ATACTATACTGGTTCGTAAGAGTGATAAACTGACTAGACTCGTATGAGCAAAATTTACTAGGAGA
1 ATACTGTACTGGCTCGTAAGAGCGATATACTGACTAGACTCGTATGAGCAAAATTTACTAGGAGA
530722 CTTGAAG
66 CTTGAAG
* * * *
530729 ATACTGTACTGGCTCATAAGAGCGATTTACTGACTGGGCTCGTATGAGCAAAATTTACTAGGAGA
1 ATACTGTACTGGCTCGTAAGAGCGATATACTGACTAGACTCGTATGAGCAAAATTTACTAGGAGA
530794 CTTGAAG
66 CTTGAAG
*
530801 ATACTGTACTGGCTCGTAAGATCGATATACT
1 ATACTGTACTGGCTCGTAAGAGCGATATACT
530832 AAATTGGTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 92 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (72 bp):
ATACTGTACTGGCTCGTAAGAGCGATATACTGACTAGACTCGTATGAGCAAAATTTACTAGGAGA
CTTGAAG
Found at i:530853 original size:26 final size:26
Alignment explanation
Indices: 530808--530881 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
530798 AAGATACTGT
* * *
530808 ACTGGCTCGTAAGATCGATATACTAA
1 ACTGACTCATAAGAGCGATATACTAA
* ** * * *
530834 ATTGGTTCATAAGAGTGATATGCTGA
1 ACTGACTCATAAGAGCGATATACTAA
530860 ACTGACTCATAAGAGCGATATA
1 ACTGACTCATAAGAGCGATATA
530882 TTAATTATTT
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (26 bp):
ACTGACTCATAAGAGCGATATACTAA
Found at i:531916 original size:26 final size:26
Alignment explanation
Indices: 531887--531944 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
531877 GACTCTAAAG
*
531887 ATACTGTATTGGCTCGTAAGAGCGAT
1 ATACTGTACTGGCTCGTAAGAGCGAT
* *
531913 ATACTGTACTGGCTTGTAAGAGTGAT
1 ATACTGTACTGGCTCGTAAGAGCGAT
*
531939 TTACTG
1 ATACTG
531945 ATTTGACTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (26 bp):
ATACTGTACTGGCTCGTAAGAGCGAT
Found at i:532118 original size:72 final size:73
Alignment explanation
Indices: 532029--532184 Score: 185
Period size: 72 Copynumber: 2.2 Consensus size: 73
532019 ACTGGCTCGT
* *
532029 AGCAATTTACT-GACTAGACTCATATGAGCAAATTTTACTA-GGAGACTTGAAGATTCTGTACGG
1 AGCAATTTACTAGACTAGACTCATATGAGCAAAATTTA-TAGGGAGACTTGAAGATACTGTACGG
532092 GC-TCGTAAG
65 GCAT-GTAAG
** * * *
532101 AGCAATTTACTAG-CTAGACTTGTATGAGCAAAATTTATAGGGAGACTTGGATATACTGTACTGG
1 AGCAATTTACTAGACTAGACTCATATGAGCAAAATTTATAGGGAGACTTGAAGATACTGTACGGG
532165 CATGTAAG
66 CATGTAAG
* *
532173 AGCGATATACTA
1 AGCAATTTACTA
532185 TACTGGCTCG
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
71 2 0.03
72 68 0.94
73 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (73 bp):
AGCAATTTACTAGACTAGACTCATATGAGCAAAATTTATAGGGAGACTTGAAGATACTGTACGGG
CATGTAAG
Found at i:532188 original size:26 final size:26
Alignment explanation
Indices: 532150--532210 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
532140 GGGAGACTTG
*
532150 GATATACTGTACTGGCAT-GTAAGAGC
1 GATATACTATACTGGC-TCGTAAGAGC
*
532176 GATATACTATACTGGCTCGTTAGAGC
1 GATATACTATACTGGCTCGTAAGAGC
*
532202 GATTTACTA
1 GATATACTA
532211 ACTCGTATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 1 0.03
26 30 0.97
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (26 bp):
GATATACTATACTGGCTCGTAAGAGC
Found at i:532293 original size:165 final size:166
Alignment explanation
Indices: 531949--532313 Score: 375
Period size: 165 Copynumber: 2.2 Consensus size: 166
531939 TTACTGATTT
* * * * ** * *
531949 GACTTGTATGAGCAAAATTTACTGGGAGACTCTGAAGATACTATTTTGG-TTCGAAAGAGCGATA
1 GACTCGTATGAGCAAAATTTACTGGGAGACT-TGGATATACTGTACTGGCAT-GTAAGAGCGATA
* * *
532013 TACTTTACTGGCTCGTAGCAATTTACTGACTAGACTCATATGAGCAAATTTTACTAGGAGACTTG
64 TACTATACTGGCTCGTAGCAATTTA-TGACTAGACTCATATGAGCAAAATTTACTAAGAGACTTG
* * ** * *
532078 AAGATTCTGTACGGGCTCGTAAGAGCAATTTACTAGCTA
128 AAGATACTGTACGAGCTCAAAAGAGCAATATACTAACTA
*
532117 GACTTGTATGAGCAAAATTTA-TAGGGAGACTTGGATATACTGTACTGGCATGTAAGAGCGATAT
1 GACTCGTATGAGCAAAATTTACT-GGGAGACTTGGATATACTGTACTGGCATGTAAGAGCGATAT
* *
532181 ACTATACTGGCTCGTTAGAGCGA-TT-T-ACTA-ACTCGTATGAGCAAAATTTACTAAGAGACTT
65 ACTATACTGGCTCG-T--AGCAATTTATGACTAGACTCATATGAGCAAAATTTACTAAGAGACTT
* * * *
532242 TAAGATACTGTA-GTAGCTCAAAAGTGCGATATACTAACTG
127 GAAGATACTGTACG-AGCTCAAAAGAGCAATATACTAACTA
* *
532282 GGCTCGTATGAGCTAAATTTACTGGGAGACTT
1 GACTCGTATGAGCAAAATTTACTGGGAGACTT
532314 AAAGAGATTG
Statistics
Matches: 165, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
164 1 0.01
165 83 0.50
166 5 0.03
167 39 0.24
168 31 0.19
169 2 0.01
170 4 0.02
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.30
Consensus pattern (166 bp):
GACTCGTATGAGCAAAATTTACTGGGAGACTTGGATATACTGTACTGGCATGTAAGAGCGATATA
CTATACTGGCTCGTAGCAATTTATGACTAGACTCATATGAGCAAAATTTACTAAGAGACTTGAAG
ATACTGTACGAGCTCAAAAGAGCAATATACTAACTA
Found at i:536238 original size:32 final size:32
Alignment explanation
Indices: 536197--536278 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
536187 AGTTAGTATT
*
536197 TGTTATCATTTCACAAAATTAAA-ATTG-TAATA
1 TGTTATCATTTCACAAAATGAAAGA-TGAT-ATA
* *
536229 TGTTATCA-TTCAATAAAATGAAAGATGATATT
1 TGTTATCATTTC-ACAAAATGAAAGATGATATA
536261 TGTTATCATTTCACAAAA
1 TGTTATCATTTCACAAAA
536279 CCATGTGTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
31 3 0.07
32 34 0.81
33 5 0.12
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.39
Consensus pattern (32 bp):
TGTTATCATTTCACAAAATGAAAGATGATATA
Found at i:536848 original size:145 final size:145
Alignment explanation
Indices: 536695--536985 Score: 555
Period size: 145 Copynumber: 2.0 Consensus size: 145
536685 CGAATCTTCG
536695 AAAATAAAGAACACTTATCGATTTTAAAATATGATGTTCAATTACTTAGGTTCAAAGAAAAATCA
1 AAAATAAAGAACACTTATCGATTTTAAAATATGATGTTCAATTACTTAGGTTCAAAGAAAAATCA
* *
536760 TACCCAATACGTTAGAGCACAATTTCTCGAGTACCCTAAAATAAAATAACATTAAATATTCATCG
66 CACCCAATACGTTAGAGCACAATTTCTCGAGTACCCTAAAATAAAAGAACATTAAATATTCATCG
536825 ATTTTTAAATAGTAT
131 ATTTTTAAATAGTAT
536840 AAAATAAAGAACACTTATCGATTTTAAAATATGATGTTCAATTACTTAGGTTCAAAGAAAAATCA
1 AAAATAAAGAACACTTATCGATTTTAAAATATGATGTTCAATTACTTAGGTTCAAAGAAAAATCA
*
536905 CACCCAATACGTTAGAGCACAATTTCTCGAGTTCCCTAAAATAAAAGAACATTAAATATTCATCG
66 CACCCAATACGTTAGAGCACAATTTCTCGAGTACCCTAAAATAAAAGAACATTAAATATTCATCG
536970 ATTTTTAAATAGTAT
131 ATTTTTAAATAGTAT
536985 A
1 A
536986 CTCAATTATT
Statistics
Matches: 143, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
145 143 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (145 bp):
AAAATAAAGAACACTTATCGATTTTAAAATATGATGTTCAATTACTTAGGTTCAAAGAAAAATCA
CACCCAATACGTTAGAGCACAATTTCTCGAGTACCCTAAAATAAAAGAACATTAAATATTCATCG
ATTTTTAAATAGTAT
Found at i:537698 original size:10 final size:10
Alignment explanation
Indices: 537678--537706 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
537668 TTGGTTAAGG
537678 AAAAATT-AA
1 AAAAATTAAA
537687 AAAAATTAAA
1 AAAAATTAAA
537697 AAAAATTAAA
1 AAAAATTAAA
537707 GAGCAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:539421 original size:23 final size:23
Alignment explanation
Indices: 539378--539423 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
539368 ATATTAAACT
*
539378 AACCCTAATACAAGACACTTTAA
1 AACCCTAATACAAAACACTTTAA
*
539401 AACCCTAATCCCAAAAC-CTTTAA
1 AACCCTAAT-ACAAAACACTTTAA
539424 CATTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.46, C:0.30, G:0.02, T:0.22
Consensus pattern (23 bp):
AACCCTAATACAAAACACTTTAA
Found at i:541084 original size:14 final size:14
Alignment explanation
Indices: 541051--541077 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
541041 TCTAAGCGGC
541051 CAAGATAAAGAAAA
1 CAAGATAAAGAAAA
541065 CAAGATAAAGAAA
1 CAAGATAAAGAAA
541078 GAAAGATTGG
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:0.70, C:0.07, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAGATAAAGAAAA
Found at i:541141 original size:18 final size:18
Alignment explanation
Indices: 541093--541141 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
541083 ATTGGGACAT
* *
541093 AGAAAAGCAAACAAGATAA
1 AGAAAAACAAA-AAGAAAA
*
541112 AGAAAAAAAAAAAGAAAA
1 AGAAAAACAAAAAGAAAA
*
541130 AGAAAATCAAAA
1 AGAAAAACAAAA
541142 TGTGACAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.78, C:0.06, G:0.12, T:0.04
Consensus pattern (18 bp):
AGAAAAACAAAAAGAAAA
Found at i:543191 original size:13 final size:12
Alignment explanation
Indices: 543159--543187 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
543149 TTAATCAATG
543159 AGTTTATAAAAT
1 AGTTTATAAAAT
543171 AGTTTATAAAAT
1 AGTTTATAAAAT
543183 AGTTT
1 AGTTT
543188 TATATTTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (12 bp):
AGTTTATAAAAT
Found at i:543269 original size:11 final size:12
Alignment explanation
Indices: 543246--543279 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
543236 TTACATTATT
543246 AAATA-AAATAA
1 AAATATAAATAA
543257 AAATATAAA-AA
1 AAATATAAATAA
543268 AAATATAAATAA
1 AAATATAAATAA
543280 GTATCAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAATATAAATAA
Found at i:543270 original size:17 final size:17
Alignment explanation
Indices: 543245--543278 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
543235 ATTACATTAT
*
543245 TAAATAAAATAAAAATA
1 TAAAAAAAATAAAAATA
*
543262 TAAAAAAAATATAAATA
1 TAAAAAAAATAAAAATA
543279 AGTATCAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAAAAAATAAAAATA
Found at i:543344 original size:26 final size:26
Alignment explanation
Indices: 543297--543359 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
543287 TAATTTTATC
*
543297 TAAATATAATTAAATAATAATTAATTA
1 TAAATA-AATGAAATAATAATTAATTA
543324 TAAATAAATGAAATAATAATTAATTA
1 TAAATAAATGAAATAATAATTAATTA
543350 TAAATAAATG
1 TAAATAAATG
543360 TTAAAAGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 29 0.83
27 6 0.17
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (26 bp):
TAAATAAATGAAATAATAATTAATTA
Found at i:545061 original size:11 final size:10
Alignment explanation
Indices: 545029--545053 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
545019 TGATGCTAGA
545029 AAAAAAAAAG
1 AAAAAAAAAG
545039 AAAAAAAAAG
1 AAAAAAAAAG
545049 AAAAA
1 AAAAA
545054 GAATAGAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:546360 original size:10 final size:10
Alignment explanation
Indices: 546345--546370 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
546335 TTCCATTTTC
546345 TTTCCTCTCT
1 TTTCCTCTCT
546355 TTTCCTCTCT
1 TTTCCTCTCT
546365 TTTCCT
1 TTTCCT
546371 TTGTCGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTCCTCTCT
Found at i:555971 original size:22 final size:21
Alignment explanation
Indices: 555937--555980 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
555927 AAATTTAAAC
555937 AAATAAAGAAAAGATAAAAAAT
1 AAATAAAGAAAAG-TAAAAAAT
*
555959 AAATAAA-ATAAAGTAAGAAAT
1 AAATAAAGA-AAAGTAAAAAAT
555980 A
1 A
555981 TCATATCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (21 bp):
AAATAAAGAAAAGTAAAAAAT
Found at i:559840 original size:29 final size:29
Alignment explanation
Indices: 559798--559858 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
559788 ATATTTGAGA
559798 TTCTTGTGATCGGTGTAAATAAGATACTT
1 TTCTTGTGATCGGTGTAAATAAGATACTT
* *
559827 TTCTTGTGATCGGTTTAAATAATATACTT
1 TTCTTGTGATCGGTGTAAATAAGATACTT
559856 TTC
1 TTC
559859 ACCATACAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.46
Consensus pattern (29 bp):
TTCTTGTGATCGGTGTAAATAAGATACTT
Found at i:573179 original size:18 final size:18
Alignment explanation
Indices: 573158--573214 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
573148 TGCAGTCTGC
*
573158 TGTGGCTGCATACT-AGCA
1 TGTGACTGCAT-CTGAGCA
*
573176 TGTGATTGCATCTGAGCA
1 TGTGACTGCATCTGAGCA
*
573194 TGTGACTGCATCTGATCA
1 TGTGACTGCATCTGAGCA
573212 TGT
1 TGT
573215 TGTGCCTCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 2 0.06
18 32 0.94
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (18 bp):
TGTGACTGCATCTGAGCA
Found at i:579461 original size:13 final size:13
Alignment explanation
Indices: 579443--579467 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
579433 ATTTATTTAG
579443 TTTAGATTAATAC
1 TTTAGATTAATAC
579456 TTTAGATTAATA
1 TTTAGATTAATA
579468 TCTCTCACAA
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:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTAGATTAATAC
Done.