Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_pilon, 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: 5469637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 25
Found at i:2798404 original size:14 final size:14
Alignment explanation
Indices: 2798385--2798421 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2798375 CATCAATTAA
2798385 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2798399 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2798413 ACAAATCAA
1 ACAAATCAA
2798422 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2799840 original size:42 final size:42
Alignment explanation
Indices: 2799794--2799875 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
2799784 ATGACAGTGA
* *
2799794 CCTCTTGAACGATGGGAGGGGAATCTCGAGGAATGATAGGGG
1 CCTCTTCAACGATAGGAGGGGAATCTCGAGGAATGATAGGGG
* * * *
2799836 CCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CCTCTTCAACGATAGGAGGGGAATCTCGAGGAATGATAGG
2799876 CGAGTCAGGC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.26, C:0.16, G:0.37, T:0.22
Consensus pattern (42 bp):
CCTCTTCAACGATAGGAGGGGAATCTCGAGGAATGATAGGGG
Found at i:2800356 original size:33 final size:31
Alignment explanation
Indices: 2800296--2800357 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
2800286 AAAAATGACT
*
2800296 ATCGCAACGCAAAATGAATCGCTACGAGAGA
1 ATCGCAACGCAAAATGAATCGCAACGAGAGA
*
2800327 ATCGCAACGCGAAATGAAAATCGCAACGAGA
1 ATCGCAACGCAAAATG--AATCGCAACGAGA
2800358 CAAAACAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 15 0.56
33 12 0.44
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (31 bp):
ATCGCAACGCAAAATGAATCGCAACGAGAGA
Found at i:2800637 original size:94 final size:94
Alignment explanation
Indices: 2800491--2800870 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
2800481 ATGGATTGCA
* * *
2800491 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACACT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
2800555 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
2800584 TTACTTTCAACCAAAAGACAAAACAAAGACAAATATTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
2800649 TTAGCAGAATTGGCAGCAACCGAACAAAG
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
2800678 TTACTTTTAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
2800743 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
2800772 TTAC-TTCAACCAAACGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
2800836 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
2800866 TTACT
1 TTACT
2800871 AAGCAATCTA
Statistics
Matches: 271, Mismatches: 13, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
93 21 0.08
94 250 0.92
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2802486 original size:26 final size:25
Alignment explanation
Indices: 2802435--2802488 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
2802425 ATACCAAGTT
* *
2802435 AGATATACCAAAAACTACACTGTAA
1 AGATATACCAAAAACTAAACTATAA
2802460 AGATATACCAAAAACAATAAAC-ATAA
1 AGATATACCAAAAAC--TAAACTATAA
2802486 AGA
1 AGA
2802489 GTAGTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 15 0.60
26 6 0.24
27 4 0.16
ACGTcount: A:0.59, C:0.17, G:0.07, T:0.17
Consensus pattern (25 bp):
AGATATACCAAAAACTAAACTATAA
Found at i:2802631 original size:33 final size:33
Alignment explanation
Indices: 2802575--2802663 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 33
2802565 ATGACTATCA
**
2802575 CAACGCGGAAATGACTATCGCAACGAGAGAATCG
1 CAACGC-GAAATGAAAATCGCAACGAGAGAATCG
* * *
2802609 CAATGCGAAATTAAAATTGCAACGAGAGAATCG
1 CAACGCGAAATGAAAATCGCAACGAGAGAATCG
*
2802642 CAACGGGAAATGAAAATCGCAA
1 CAACGCGAAATGAAAATCGCAA
2802664 TGCGATTTTG
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 41 0.89
34 5 0.11
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
CAACGCGAAATGAAAATCGCAACGAGAGAATCG
Found at i:2802700 original size:14 final size:14
Alignment explanation
Indices: 2802680--2802717 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2802670 TTTGGTTTCG
2802680 CGTTGCGATTATCT
1 CGTTGCGATTATCT
* *
2802694 TGTTGCGATTCTCT
1 CGTTGCGATTATCT
2802708 CGTTGCGATT
1 CGTTGCGATT
2802718 TTTATTTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:2802745 original size:21 final size:21
Alignment explanation
Indices: 2802702--2802745 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2802692 CTTGTTGCGA
** *
2802702 TTCTCTCGTTGCGATTTTTAT
1 TTCTCTCGTTGCGATAGTCAT
2802723 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATAGTCAT
2802744 TT
1 TT
2802746 TCGTGTTACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.11, C:0.20, G:0.16, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATAGTCAT
Found at i:2802763 original size:20 final size:20
Alignment explanation
Indices: 2802740--2802780 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2802730 GTTGCGATAG
*
2802740 TCATTTTCGTGTTACGATTT
1 TCATTTTCATGTTACGATTT
*
2802760 TCATTTTCATGTTTCGATTT
1 TCATTTTCATGTTACGATTT
2802780 T
1 T
2802781 AAGTTTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.59
Consensus pattern (20 bp):
TCATTTTCATGTTACGATTT
Found at i:2803364 original size:20 final size:20
Alignment explanation
Indices: 2803339--2803552 Score: 207
Period size: 20 Copynumber: 10.6 Consensus size: 20
2803329 CTTTAAAAAT
2803339 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2803359 CGCGTTGCGATTTTATGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2803379 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * * *
2803400 CGCATTGCGATTTATGTATT
1 CGCGTTGCGATTTACGGATA
* *
2803420 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* * *
2803440 CGCGTTACGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
2803460 CTCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2803480 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
2803500 TGTCATTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
2803521 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
2803542 CTCGTTGCGAT
1 CGCGTTGCGAT
2803553 AGTCAGAATC
Statistics
Matches: 154, Mismatches: 33, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
20 103 0.67
21 51 0.33
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2803398 original size:41 final size:41
Alignment explanation
Indices: 2803341--2803552 Score: 311
Period size: 41 Copynumber: 5.2 Consensus size: 41
2803331 TTAAAAATCG
* *
2803341 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
2803382 CGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
2803422 CGTTGCGATTTACAGATACGCGTTACGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
2803462 CGTTACGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
2803503 CATTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
2803544 CGTTGCGAT
1 CGTTGCGAT
2803553 AGTCAGAATC
Statistics
Matches: 154, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 72 0.47
41 82 0.53
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:2803584 original size:20 final size:20
Alignment explanation
Indices: 2803561--2803613 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
2803551 ATAGTCAGAA
*
2803561 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
2803581 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
2803601 TCACGTTGCGATT
1 TCGCGTTGCGATT
2803614 CTGGAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:2803712 original size:20 final size:19
Alignment explanation
Indices: 2803663--2803716 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2803653 ATTCTTCATA
2803663 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
2803682 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
2803703 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
2803717 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:2804500 original size:12 final size:12
Alignment explanation
Indices: 2804483--2804511 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2804473 ATATTAATTT
2804483 ATAAATATTTGA
1 ATAAATATTTGA
2804495 ATAAATATTTGA
1 ATAAATATTTGA
2804507 ATAAA
1 ATAAA
2804512 AATTCATAAA
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:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (12 bp):
ATAAATATTTGA
Found at i:2804673 original size:22 final size:20
Alignment explanation
Indices: 2804632--2804679 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
2804622 CATAAGTATC
* *
2804632 ATATTTATATATATATAATA
1 ATATTAATATATATAAAATA
2804652 ATATTAATATAATATAAAAATA
1 ATATTAATAT-ATAT-AAAATA
2804674 ATATTA
1 ATATTA
2804680 TGGTAGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
21 4 0.17
22 11 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTAATATATATAAAATA
Found at i:2804771 original size:24 final size:24
Alignment explanation
Indices: 2804740--2804791 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2804730 TTTTATCCCA
*
2804740 TAAA-ATTATAAATAGTAAA-ATAT
1 TAAATATTAAAAATA-TAAATATAT
*
2804763 TAAATATTAAAAATATAAATATTT
1 TAAATATTAAAAATATAAATATAT
2804787 TAAAT
1 TAAAT
2804792 TCTCAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAATATTAAAAATATAAATATAT
Found at i:2804784 original size:15 final size:15
Alignment explanation
Indices: 2804740--2804785 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2804730 TTTTATCCCA
* *
2804740 TAAAATTATAAATAG
1 TAAAAATATAAATAT
2804755 T-AAAATATTAAATAT
1 TAAAAATA-TAAATAT
2804770 TAAAAATATAAATAT
1 TAAAAATATAAATAT
2804785 T
1 T
2804786 TTAAATTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 5 0.19
15 16 0.59
16 6 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
TAAAAATATAAATAT
Found at i:2808387 original size:28 final size:28
Alignment explanation
Indices: 2808355--2808418 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
2808345 CAATAATCAT
*
2808355 ATATTTAACTAAACTCAAATTCATACAC
1 ATATTTAACTAAACCCAAATTCATACAC
* *
2808383 ATATTTAACTAAACCCAAATTTATACAT
1 ATATTTAACTAAACCCAAATTCATACAC
2808411 ATATTTAA
1 ATATTTAA
2808419 AACATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (28 bp):
ATATTTAACTAAACCCAAATTCATACAC
Found at i:2810592 original size:18 final size:19
Alignment explanation
Indices: 2810546--2810592 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2810536 GAACCCTTAG
*
2810546 TGCATCGATGCACTAAGAG
1 TGCATCGATGCACTAAGAA
2810565 TGCATCGATGCA-TAA-AA
1 TGCATCGATGCACTAAGAA
2810582 TGCATTCGATG
1 TGCA-TCGATG
2810593 TTTCAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 9 0.35
19 12 0.46
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCACTAAGAA
Found at i:2810617 original size:64 final size:62
Alignment explanation
Indices: 2810544--2810721 Score: 234
Period size: 64 Copynumber: 2.8 Consensus size: 62
2810534 TTGAACCCTT
* *
2810544 AGTGCATCGATGCACTAAG-AGTGCATCGATGCATAAAATGCATTCGATGTTTCA-AACAAGCTT
1 AGTGCATCGATGCA-T-GGCAGTGCATCGATGCATAAAATGCATTCGATGTTTCATAA-AA-CCT
2810607 G
62 G
*
2810608 AGTGCATCGATGCATGGTCTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTG
1 AGTGCATCGATGCATGG-CAGTGCATCGATGCATAAAATGCATTCGATG-TTTCATAAAACCTG
* * *
2810672 AGTGCATCGATGCATGGCAATGCATCGATGCATAATATACATTCGATGTT
1 AGTGCATCGATGCATGGCAGTGCATCGATGCATAAAATGCATTCGATGTT
2810722 CAATTTATTC
Statistics
Matches: 103, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
62 3 0.03
63 28 0.27
64 63 0.61
65 7 0.07
66 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (62 bp):
AGTGCATCGATGCATGGCAGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAAACCTG
Found at i:2813444 original size:23 final size:23
Alignment explanation
Indices: 2813414--2813495 Score: 64
Period size: 23 Copynumber: 3.6 Consensus size: 23
2813404 GCATGGCCTT
2813414 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
2813437 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
* *
2813459 -TGTATCAATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
*
2813481 GATGCATTGATGCAC
1 G-TGCATCGATGCAC
2813496 TTTTATAATG
Statistics
Matches: 44, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
20 1 0.02
21 12 0.27
22 3 0.07
23 17 0.39
24 11 0.25
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:2817350 original size:21 final size:21
Alignment explanation
Indices: 2817326--2817365 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2817316 AAGATTATTT
2817326 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTGAAACA
**
2817347 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
2817366 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAACA
Found at i:2819358 original size:64 final size:62
Alignment explanation
Indices: 2819308--2819466 Score: 248
Period size: 64 Copynumber: 2.5 Consensus size: 62
2819298 GTGCACTAAG
2819308 AGTGCATCGATGCATAAAATGCATTCGATGTTTCA-AACAATCCTGAGTGCATCGATGCATGGTC
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTCATAA-AA-CCTGAGTGCATCGATGCATGG-C
* *
2819372 TGTGCATCGATGCATAAAATGCATTTGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGC
1 AGTGCATCGATGCATAAAATGCATTCGATG-TTTCATAAAACCTGAGTGCATCGATGCATGGC
*
2819435 AGTGCATCGATGCATAATATGCATTCGATGTT
1 AGTGCATCGATGCATAAAATGCATTCGATGTT
2819467 CAATTTATTC
Statistics
Matches: 88, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
62 2 0.02
63 28 0.32
64 49 0.56
65 7 0.08
66 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (62 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAAACCTGAGTGCATCGATGCATGGC
Found at i:2820621 original size:18 final size:19
Alignment explanation
Indices: 2820583--2820621 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2820573 TAAAATTTTT
*
2820583 AAAAATAAAAAATATTATA
1 AAAAATAAAAAATAATATA
2820602 AAAAATAAAAAATAAT-TA
1 AAAAATAAAAAATAATATA
2820620 AA
1 AA
2820622 TTTATGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAATAAAAAATAATATA
Found at i:2821609 original size:28 final size:28
Alignment explanation
Indices: 2821569--2821638 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
2821559 GGGAAAAATA
*
2821569 CCCATGTAGTCGTTAGACATGATCGTTG
1 CCCATATAGTCGTTAGACATGATCGTTG
* *
2821597 CCCATATAGTCGTTAGCCATGATTGTTG
1 CCCATATAGTCGTTAGACATGATCGTTG
*
2821625 CCAATATAGTCGTT
1 CCCATATAGTCGTT
2821639 GACCAACGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (28 bp):
CCCATATAGTCGTTAGACATGATCGTTG
Found at i:2824116 original size:19 final size:16
Alignment explanation
Indices: 2824082--2824113 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2824072 AAGAATTTAA
2824082 TTAAAAAAATAATATT
1 TTAAAAAAATAATATT
*
2824098 TTAAAAAAATTATATT
1 TTAAAAAAATAATATT
2824114 ATTATTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAAAAATAATATT
Found at i:2825326 original size:17 final size:16
Alignment explanation
Indices: 2825274--2825328 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 16
2825264 AGACTTAATT
2825274 TTAATTTTAAACTC-A
1 TTAATTTTAAACTCAA
2825289 TTAATATTTTAAAACTCAA
1 TT-A-ATTTT-AAACTCAA
2825308 TTAATTTTAAACTCAAA
1 TTAATTTTAAACTC-AA
2825325 TTAA
1 TTAA
2825329 AACACGCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.06
16 7 0.20
17 16 0.46
18 7 0.20
19 3 0.09
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAATTTTAAACTCAA
Found at i:2830519 original size:16 final size:16
Alignment explanation
Indices: 2830480--2830513 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2830470 AATATTTTGA
2830480 TAAATTT-ATTTTAAT
1 TAAATTTAATTTTAAT
*
2830495 TAAATTTAATTTTTAT
1 TAAATTTAATTTTAAT
2830511 TAA
1 TAA
2830514 TATTAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAAATTTAATTTTAAT
Found at i:2832686 original size:18 final size:19
Alignment explanation
Indices: 2832665--2832710 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
2832655 ATATAAAAAT
2832665 AAATATTTAAA-TTTTAAA
1 AAATATTTAAATTTTTAAA
* **
2832683 AAATA-TAAAATTTTTATT
1 AAATATTTAAATTTTTAAA
2832701 AAATATTTAA
1 AAATATTTAA
2832711 TAAAGTAGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 4 0.18
18 15 0.68
19 3 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATATTTAAATTTTTAAA
Found at i:2834263 original size:20 final size:20
Alignment explanation
Indices: 2834238--2834285 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2834228 GCTTCGTATT
2834238 CGTCGTCGCGCAGATTTTAC
1 CGTCGTCGCGCAGATTTTAC
*
2834258 CGTCGTCACGCAGATTTTAC
1 CGTCGTCGCGCAGATTTTAC
*
2834278 CATCGTCG
1 CGTCGTCG
2834286 ATGGAGAGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.31, G:0.23, T:0.29
Consensus pattern (20 bp):
CGTCGTCGCGCAGATTTTAC
Found at i:2837070 original size:18 final size:18
Alignment explanation
Indices: 2837047--2837092 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
2837037 AGGCATTTGA
* *
2837047 TCCTCTGGTTGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
2837065 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
2837083 TCCTCGTGCT
1 TCCTC-TGCT
2837093 GTTCTGGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.00, C:0.30, G:0.24, T:0.46
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:2837102 original size:18 final size:19
Alignment explanation
Indices: 2837057--2837107 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
2837047 TCCTCTGGTT
*
2837057 GTGCTTGTTCCTC-TGCTC
1 GTGCTGGTTCCTCGTGCTC
*
2837075 GTGCTTGTTCCTCGTGCT-
1 GTGCTGGTTCCTCGTGCTC
* *
2837093 GTTCTGGTTCATCGT
1 GTGCTGGTTCCTCGT
2837108 CGGAGTCGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.02, C:0.27, G:0.25, T:0.45
Consensus pattern (19 bp):
GTGCTGGTTCCTCGTGCTC
Found at i:2847047 original size:17 final size:18
Alignment explanation
Indices: 2847027--2847060 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2847017 AATTATTTTA
2847027 TAAT-ATTTTGAAAATTT
1 TAATAATTTTGAAAATTT
*
2847044 TAATAATTTTTAAAATT
1 TAATAATTTTGAAAATT
2847061 CAATAGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TAATAATTTTGAAAATTT
Found at i:2847058 original size:18 final size:19
Alignment explanation
Indices: 2847021--2847060 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2847011 ATCAATAATT
2847021 ATTTTATAATATTTTGAAA
1 ATTTTATAATATTTTGAAA
2847040 ATTTTAATAAT-TTTT-AAA
1 ATTTT-ATAATATTTTGAAA
2847058 ATT
1 ATT
2847061 CAATAGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 9 0.45
20 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTTTATAATATTTTGAAA
Found at i:2847065 original size:17 final size:20
Alignment explanation
Indices: 2847026--2847065 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 20
2847016 TAATTATTTT
*
2847026 ATAATATTTTGAAAATTTTA
1 ATAATATTTTGAAAATTTCA
2847046 ATAAT-TTTT-AAAA-TTCA
1 ATAATATTTTGAAAATTTCA
2847063 ATA
1 ATA
2847066 GTTAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 4 0.21
20 5 0.26
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
ATAATATTTTGAAAATTTCA
Found at i:2847746 original size:23 final size:23
Alignment explanation
Indices: 2847719--2847773 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
2847709 ACGAACAGAT
*
2847719 GTAAACGAACACAATAAATGAAC
1 GTAAACGAACACAATAAATAAAC
2847742 GTAAACGAACACAATAAATAAAC
1 GTAAACGAACACAATAAATAAAC
*
2847765 ATAAACGAA
1 GTAAACGAA
2847774 TATAAATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.60, C:0.16, G:0.11, T:0.13
Consensus pattern (23 bp):
GTAAACGAACACAATAAATAAAC
Found at i:2847998 original size:10 final size:10
Alignment explanation
Indices: 2847979--2848013 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
2847969 ATAAACGAAC
2847979 GAACATAAAT
1 GAACATAAAT
*
2847989 GAACAGAAAT
1 GAACATAAAT
2847999 GAACATAAAT
1 GAACATAAAT
2848009 GAACA
1 GAACA
2848014 AACATAAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.60, C:0.11, G:0.14, T:0.14
Consensus pattern (10 bp):
GAACATAAAT
Found at i:2848017 original size:24 final size:24
Alignment explanation
Indices: 2847952--2848036 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
2847942 GATTGAGCTA
* *
2847952 AACATAAATGAACACACATAAACG
1 AACATAAATGAACAAACAGAAACG
* * ** *
2847976 AACGA-ACATAAATGAACAGAAATG
1 AAC-ATAAATGAACAAACAGAAACG
*
2848000 AACATAAATGAACAAACATAAACG
1 AACATAAATGAACAAACAGAAACG
*
2848024 GACATAAATGAAC
1 AACATAAATGAAC
2848037 GAATATATTA
Statistics
Matches: 45, Mismatches: 14, Indels: 4
0.71 0.22 0.06
Matches are distributed among these distances:
23 1 0.02
24 43 0.96
25 1 0.02
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.13
Consensus pattern (24 bp):
AACATAAATGAACAAACAGAAACG
Found at i:2848018 original size:34 final size:34
Alignment explanation
Indices: 2847967--2848036 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
2847957 AAATGAACAC
* *
2847967 ACATAAACGAACGAACATAAATGAACAGAAATGA
1 ACATAAACGAACAAACATAAACGAACAGAAATGA
* * *
2848001 ACATAAATGAACAAACATAAACGGACATAAATGA
1 ACATAAACGAACAAACATAAACGAACAGAAATGA
2848035 AC
1 AC
2848037 GAATATATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.59, C:0.16, G:0.13, T:0.13
Consensus pattern (34 bp):
ACATAAACGAACAAACATAAACGAACAGAAATGA
Found at i:2848037 original size:14 final size:14
Alignment explanation
Indices: 2847952--2848039 Score: 65
Period size: 14 Copynumber: 6.1 Consensus size: 14
2847942 GATTGAGCTA
2847952 AACATAAATGAAC-
1 AACATAAATGAACG
*
2847965 ACACATAAACGAACG
1 A-ACATAAATGAACG
2847980 AACATAAATGAACAG
1 AACATAAATGAAC-G
* *
2847995 AA-ATGAACATAAATG
1 AACAT-AA-ATGAACG
*
2848010 AACA-AACATAAACG
1 AACATAA-ATGAACG
*
2848024 GACATAAATGAACG
1 AACATAAATGAACG
2848038 AA
1 AA
2848040 TATATTACTG
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
13 1 0.02
14 43 0.72
15 11 0.18
16 5 0.08
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.12
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:2857802 original size:17 final size:16
Alignment explanation
Indices: 2857780--2857813 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2857770 TTAAAGGCTA
*
2857780 TTTGTACTATTTCTCTC
1 TTTGTAATATTTC-CTC
2857797 TTTGTAATATTTCCTC
1 TTTGTAATATTTCCTC
2857813 T
1 T
2857814 ATTAGTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTGTAATATTTCCTC
Found at i:2869917 original size:22 final size:22
Alignment explanation
Indices: 2869889--2869971 Score: 132
Period size: 22 Copynumber: 3.8 Consensus size: 22
2869879 CACAAAGTCA
*
2869889 GATAAAAAATCGATCCGGATCG
1 GATAAAAAACCGATCCGGATCG
2869911 GATAAAAAACCGATCCGGATCG
1 GATAAAAAACCGATCCGGATCG
*
2869933 GATAAAAAACCGATTCGGATCG
1 GATAAAAAACCGATCCGGATCG
*
2869955 GAT-AAAAATCGATCCGG
1 GATAAAAAACCGATCCGG
2869972 TTTTTTTTAC
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 12 0.21
22 45 0.79
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (22 bp):
GATAAAAAACCGATCCGGATCG
Found at i:2870086 original size:15 final size:15
Alignment explanation
Indices: 2870066--2870099 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2870056 TTTCGGTTTG
2870066 AAAAAAACCAGATAT
1 AAAAAAACCAGATAT
*
2870081 AAAAAAACCGGATAT
1 AAAAAAACCAGATAT
2870096 AAAA
1 AAAA
2870100 TAATCGGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.68, C:0.12, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAAAACCAGATAT
Found at i:2870207 original size:14 final size:15
Alignment explanation
Indices: 2870172--2870209 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2870162 CATCAACGAT
2870172 AAATTACAATACTTA
1 AAATTACAATACTTA
*
2870187 AATATTACAAT-GTTA
1 AA-ATTACAATACTTA
2870202 AAATTACA
1 AAATTACA
2870210 TTGTCATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 7 0.33
16 8 0.38
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (15 bp):
AAATTACAATACTTA
Found at i:2870323 original size:21 final size:21
Alignment explanation
Indices: 2870299--2870340 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2870289 CTTCCAAGTT
2870299 CGATAATTGAAACAAAATTTA
1 CGATAATTGAAACAAAATTTA
*
2870320 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAATTTA
2870341 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (21 bp):
CGATAATTGAAACAAAATTTA
Found at i:2877589 original size:20 final size:20
Alignment explanation
Indices: 2877542--2877581 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2877532 ACTTTTTTCC
2877542 AAATTATTTGGCATAACAGG
1 AAATTATTTGGCATAACAGG
2877562 AAATTATTTGGCATAACAGG
1 AAATTATTTGGCATAACAGG
2877582 GTATTATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (20 bp):
AAATTATTTGGCATAACAGG
Found at i:2892239 original size:24 final size:24
Alignment explanation
Indices: 2892203--2892259 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
2892193 CATGACCGAG
* *
2892203 TTTGGTTTTTAGTTCACTCACTGA
1 TTTGATTTCTAGTTCACTCACTGA
2892227 TTTGATTTCTAGTTCACTCACTGA
1 TTTGATTTCTAGTTCACTCACTGA
2892251 TTTGATTTC
1 TTTGATTTC
2892260 CAGCCGTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.51
Consensus pattern (24 bp):
TTTGATTTCTAGTTCACTCACTGA
Found at i:2894529 original size:19 final size:21
Alignment explanation
Indices: 2894505--2894543 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2894495 TAGGGAAAGC
*
2894505 ATAATA-AAA-GTGAAATAAA
1 ATAATACAAATGTAAAATAAA
2894524 ATAATACAAATGTAAAATAA
1 ATAATACAAATGTAAAATAA
2894544 TGAGAGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 3 0.18
21 8 0.47
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.23
Consensus pattern (21 bp):
ATAATACAAATGTAAAATAAA
Found at i:2894734 original size:132 final size:134
Alignment explanation
Indices: 2894573--2894840 Score: 377
Period size: 133 Copynumber: 2.0 Consensus size: 134
2894563 ACATATGTAC
* *
2894573 ATATATAAAAAAATGTAAAATAATAGCGTATAAAGTAGAATAAATAAA-TTAATAAGAA-ATATA
1 ATATATAAAAAAATGTAAAATAATAGCGTATAAAGTAAAATAAATAAAGTTAATAAAAACATATA
*
2894636 AGAATATCAATACCATA-TATATAATAGCTAAATATGAGAGGGAGG-AAAAATATATATAATAAT
66 AGAATAT-AACACCATACTATATAATAGCT-AATATGAGAGGGAGGAAAAAATATATAT-ATAAT
*
2894699 CATAAAAA
128 -AGAAAAA
*
2894707 ATATA-AAAAAAATGTAAAAT-ATAGCGTATAAAGTAAAATAAATAAAGTTAGTAAAAACATATA
1 ATATATAAAAAAATGTAAAATAATAGCGTATAAAGTAAAATAAATAAAGTTAATAAAAACATATA
* * *
2894770 ATAATATTACACCATATCTATATAATAGCTAATATGAGAGGGAGGAAAAAATATGTATATAATAG
66 AGAATATAACACCATA-CTATATAATAGCTAATATGAGAGGGAGGAAAAAATATATATATAATAG
2894835 AAAAA
130 AAAAA
2894840 A
1 A
2894841 CTAATAATGA
Statistics
Matches: 121, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
132 25 0.21
133 37 0.31
134 36 0.30
135 23 0.19
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.26
Consensus pattern (134 bp):
ATATATAAAAAAATGTAAAATAATAGCGTATAAAGTAAAATAAATAAAGTTAATAAAAACATATA
AGAATATAACACCATACTATATAATAGCTAATATGAGAGGGAGGAAAAAATATATATATAATAGA
AAAA
Found at i:2895001 original size:8 final size:9
Alignment explanation
Indices: 2894986--2895028 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
2894976 AAAAACTAAT
2894986 AATAATATA
1 AATAATATA
2894995 AAT-ATATA
1 AATAATATA
2895003 AATAATATA
1 AATAATATA
*
2895012 ATGTAATATA
1 A-ATAATATA
*
2895022 AAAAATA
1 AATAATA
2895029 ATTAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 8 0.28
9 13 0.45
10 8 0.28
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
AATAATATA
Found at i:2895441 original size:215 final size:216
Alignment explanation
Indices: 2895062--2895488 Score: 781
Period size: 215 Copynumber: 2.0 Consensus size: 216
2895052 GATTAAATTG
2895062 AAAGAATTATAAGCTAGAGGTCAAAATTCAAAGCAATATTAAGGGTTAATTTCGATTTGGGGGGG
1 AAAGAATTATAAGCTAGAGGTCAAAATTCAAAGCAATATTAAGGGTTAATTTCGATTTGGGGGGG
2895127 GAAACGACTCTTTTAAGGTAACGAGGGATCAAAAGGGTAGTTTACCCTATTTTGACAGGAACACG
66 GAAACGACTCTTTTAAGGTAACGAGGGATCAAAAGGGTAGTTTACCCTATTTTGACAGGAACACG
2895192 CGGATGTTTTAAGTATAAAACTCAAAATTTTCTTCAAAATACTCATTTCTCTCTTCTCCAAGCC-
131 CGGATGTTTTAAGTATAAAACTCAAAATTTTCTTCAAAATACTCATTTCTCTCTTCTCCAAGCCA
*
2895256 GGGACACCCCCTCTCTAAACA
196 GGGACACCCCCCCTCTAAACA
2895277 AAAGAA-TATAAGCTAGAGGTCAAAATTCCAAAGC-A-ATTAAGGGTTAATTTCGATTTGGGGGG
1 AAAGAATTATAAGCTAGAGGTCAAAATT-CAAAGCAATATTAAGGGTTAATTTCGATTTGGGGGG
2895339 GGAAACGACTCTTTTAAAGGTAACGAGGGATCAAAAGGGTAGTTTACCCTATTTTAGACAGGAAC
65 GGAAACGACTCTTTT-AAGGTAACGAGGGATCAAAAGGGTAGTTTACCCTATTTT-GACAGGAAC
2895404 ACGCGGATGTTTTAAGTATAAAACTCAAAATTTTCTTCAAAATACTCATTTCTCTCTTCTCCAAG
128 ACGCGGATGTTTTAAGTATAAAACTCAAAATTTTCTTCAAAATACTCATTTCTCTCTTCTCCAAG
2895469 CCGAGGGACACCCCCCCTCT
193 CC-AGGGACACCCCCCCTCT
2895489 CTAACATTTC
Statistics
Matches: 206, Mismatches: 1, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
213 42 0.20
214 61 0.30
215 88 0.43
217 15 0.07
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (216 bp):
AAAGAATTATAAGCTAGAGGTCAAAATTCAAAGCAATATTAAGGGTTAATTTCGATTTGGGGGGG
GAAACGACTCTTTTAAGGTAACGAGGGATCAAAAGGGTAGTTTACCCTATTTTGACAGGAACACG
CGGATGTTTTAAGTATAAAACTCAAAATTTTCTTCAAAATACTCATTTCTCTCTTCTCCAAGCCA
GGGACACCCCCCCTCTAAACA
Found at i:2896629 original size:105 final size:105
Alignment explanation
Indices: 2896433--2897309 Score: 1499
Period size: 105 Copynumber: 8.3 Consensus size: 105
2896423 TGTTTCGAGG
* * * * *
2896433 CCAATATCTTTCGTTATGAAGTTGAAATTGGCTCCGAAAT-TGGGAAATTGTTTGTTGACAACCA
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG-AATCTGAGAAA-TGTTTGTTGACAACCA
* *
2896497 GCGGTCCCTTCGTTGTGAAGTTCAACTTGCGTTGTCTGGAGT
64 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * * *
2896539 CCAATATCTTTCGTTATGAAGTTGAAATTGACTCTGAATCTGAGAAATATTTATTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
2896604 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
2896644 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATATTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
*
2896709 GGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
2896749 CCAATATCCGTCGTTGTGAAGTTGAAATTGGCTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
2896814 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
2896854 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
*
2896919 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
2896959 CCAATATCTTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
2897024 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
2897064 CCAATATCTTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
*
2897129 GGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
2897169 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATTTG-GAAA-GTTGTTGTTGACAACCA
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATG-T-TTGTTGACAACCA
2897232 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
64 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
2897274 CCAATATCCTTCGTTGCGAAGTTGAAATTGACTCTG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG
2897310 GGTAAAACTT
Statistics
Matches: 743, Mismatches: 25, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
103 1 0.00
104 5 0.01
105 697 0.94
106 40 0.05
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:2898066 original size:5 final size:5
Alignment explanation
Indices: 2898058--2898097 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
2898048 TCTTTTTCTT
*
2898058 TTTTC TTTTC TTTTC TTTTC TTTT- TTCTTC TTTTT TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC
2898098 AACTTAGGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 2 0.06
5 27 0.87
6 2 0.06
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:2898076 original size:15 final size:16
Alignment explanation
Indices: 2898053--2898097 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
2898043 TTTCCTCTTT
2898053 TTCTT-TTTTCTTTTC
1 TTCTTCTTTTCTTTTC
2898068 TT-TTCTTTTCTTTT-
1 TTCTTCTTTTCTTTTC
*
2898082 TTCTTCTTTTTTTTTC
1 TTCTTCTTTTCTTTTC
2898098 AACTTAGGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.15
15 22 0.85
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTCTTCTTTTCTTTTC
Found at i:2908896 original size:140 final size:142
Alignment explanation
Indices: 2908740--2909020 Score: 467
Period size: 140 Copynumber: 2.0 Consensus size: 142
2908730 CATATGTACA
* *
2908740 TATATAAAAAAATGTAAAATAATAGCGTATAAAGTAGAATAAATAAAATTAATAAGAACATATAA
1 TATATAAAAAAATGTAAAATAATAGCGTATAAAGTAAAATAAATAAAATTAATAAAAACATATAA
* *
2908805 GAATATCAATACCATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAATATATATA-ATAA
66 GAATATCAACACCATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAAAATATATATATAA
2908869 TAATAGAAAAAT
131 TAATAGAAAAAT
* *
2908881 TATA-AAAAAAATGTAAAATAATAGCGTATAAAGTAAAATAAATAAAGTTAGTAAAAACATATAA
1 TATATAAAAAAATGTAAAATAATAGCGTATAAAGTAAAATAAATAAAATTAATAAAAACATATAA
* * *
2908945 TAATATTAACACCATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAAAATATGTATATAA
66 GAATATCAACACCATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAAAATATATATATAA
2909010 TAATAGAAAAA
131 TAATAGAAAAA
2909021 AACTAAATAA
Statistics
Matches: 130, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
140 111 0.85
141 19 0.15
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.26
Consensus pattern (142 bp):
TATATAAAAAAATGTAAAATAATAGCGTATAAAGTAAAATAAATAAAATTAATAAAAACATATAA
GAATATCAACACCATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAAAATATATATATAA
TAATAGAAAAAT
Found at i:2909031 original size:18 final size:17
Alignment explanation
Indices: 2909008--2909062 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
2908998 ATATGTATAT
2909008 AATAATAGAAAAAAACTA
1 AATAATAGAAAAAAA-TA
*
2909026 AATAAT-GAAGATAAATA
1 AATAATAGAA-AAAAATA
2909043 TAATAATA-AAAAAAAGTA
1 -AATAATAGAAAAAAA-TA
2909061 AA
1 AA
2909063 GAAATAATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
17 11 0.35
18 20 0.65
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (17 bp):
AATAATAGAAAAAAATA
Found at i:2909101 original size:140 final size:137
Alignment explanation
Indices: 2908739--2909108 Score: 320
Period size: 140 Copynumber: 2.6 Consensus size: 137
2908729 ACATATGTAC
* * * * * * *
2908739 ATATATAAAAAAATGTAAAATAATAGCGTATAAAGTAGAATAAATAAAATTAATAAGAACATATA
1 ATATA-AAAAAAATGTAAAATAATA--GTATAAAATAAAAAAAATAAAGTAAATAAAAACATAAA
* * * * * *
2908804 AGAATATCAATACCATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAATATATATAATAA
63 ATAAGATTAACAACATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAAAATATATAATAA
2908869 TAATAGAAAA
128 TAATAGAAAA
* * * * *
2908879 ATTATAAAAAAAATGTAAAATAATAGCGTATAAAGTAAAATAAATAAAGTTAGTAAAAACATATA
1 A-TATAAAAAAAATGTAAAATAATA--GTATAAAATAAAAAAAATAAAGTAAATAAAAACATAAA
* * *
2908944 ATAATATTAACACCATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAAAATATGTATATA
63 ATAAGATTAACAACATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAAAATATATA-ATA
2909009 ATAATAGAAAA
127 ATAATAGAAAA
* * * * **
2909020 A-A-ACTAAATAATG-AAGATAA-A-TATAATAATAAAAAAAAGTAAAG-AAATAATAGGATAAA
1 ATATA-AAAAAAATGTAAAATAATAGTATAA-AATAAAAAAAA-TAAAGTAAATAAAAACATAAA
2909079 ATGCAAGATGTATACATACATATATATATA
63 AT--AAGAT-TA-ACA-ACATATATATATA
2909109 TATATATATA
Statistics
Matches: 198, Mismatches: 22, Indels: 20
0.82 0.09 0.08
Matches are distributed among these distances:
134 5 0.03
135 20 0.10
136 5 0.03
137 5 0.03
138 9 0.05
139 11 0.06
140 124 0.63
141 19 0.10
ACGTcount: A:0.59, C:0.04, G:0.11, T:0.26
Consensus pattern (137 bp):
ATATAAAAAAAATGTAAAATAATAGTATAAAATAAAAAAAATAAAGTAAATAAAAACATAAAATA
AGATTAACAACATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAAAATATATAATAATAA
TAGAAAA
Found at i:2909105 original size:2 final size:2
Alignment explanation
Indices: 2909098--2909129 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2909088 GTATACATAC
2909098 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2909130 ACATATGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2909216 original size:13 final size:13
Alignment explanation
Indices: 2909191--2909245 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
2909181 ATAAAAAACT
2909191 AATAATAATATAA
1 AATAATAATATAA
2909204 AATATATAA-ATAA
1 AATA-ATAATATAA
*
2909217 TATAATGTAATATAA
1 AATAA--TAATATAA
2909232 AA-AATAAT-TAA
1 AATAATAATATAA
2909243 AAT
1 AAT
2909246 TAAAATCCCG
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
11 5 0.14
12 5 0.14
13 11 0.31
14 9 0.26
15 5 0.14
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
AATAATAATATAA
Found at i:2914949 original size:13 final size:13
Alignment explanation
Indices: 2914931--2914957 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2914921 TTACATACGC
2914931 GCATATGAAGACT
1 GCATATGAAGACT
2914944 GCATATGAAGACT
1 GCATATGAAGACT
2914957 G
1 G
2914958 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:2914979 original size:2 final size:2
Alignment explanation
Indices: 2914972--2915019 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
2914962 ACTATGTATT
*
2914972 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2915014 TT TA TA
1 TA TA TA
2915020 CATACATTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2916246 original size:3 final size:3
Alignment explanation
Indices: 2916234--2916276 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2916224 AAGATACTAA
2916234 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2916277 AATATATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2916761 original size:15 final size:16
Alignment explanation
Indices: 2916733--2916762 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2916723 ACAGAACCGG
2916733 AGAGAAAGGAAAAAAC
1 AGAGAAAGGAAAAAAC
2916749 AGAGAAA-GAAAAAA
1 AGAGAAAGGAAAAAA
2916763 AAACAACAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.73, C:0.03, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAGAAAGGAAAAAAC
Found at i:2916763 original size:16 final size:16
Alignment explanation
Indices: 2916733--2916763 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2916723 ACAGAACCGG
*
2916733 AGAGAAAGGAAAAAAC
1 AGAGAAAGAAAAAAAC
2916749 AGAGAAAGAAAAAAA
1 AGAGAAAGAAAAAAA
2916764 AACAACAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAGAAAGAAAAAAAC
Found at i:2917688 original size:20 final size:21
Alignment explanation
Indices: 2917651--2917691 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2917641 GATATTTTTA
**
2917651 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
2917672 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
2917692 ACATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:2929038 original size:1 final size:1
Alignment explanation
Indices: 2929032--2929079 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
2929022 ATGCTTGAAG
* * * * *
2929032 AAAAAAAAAGAAAGAAAAAAAAAGAAAAAAAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2929080 GGGGGGTCAA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:2929051 original size:11 final size:11
Alignment explanation
Indices: 2929029--2929076 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
2929019 ATTATGCTTG
2929029 AAGAAA-AAAA
1 AAGAAAGAAAA
2929039 AAGAAAGAAAA
1 AAGAAAGAAAA
2929050 AA-AAAGAAAA
1 AAGAAAGAAAA
*
2929060 AAAAAAGAAAA
1 AAGAAAGAAAA
2929071 AAGAAA
1 AAGAAA
2929077 AAAGGGGGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
10 16 0.46
11 19 0.54
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAAA
Found at i:2929066 original size:25 final size:25
Alignment explanation
Indices: 2929032--2929080 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2929022 ATGCTTGAAG
2929032 AAAAAAAAAGAAAGAAA-AAAAAAGA
1 AAAAAAAAAGAAA-AAAGAAAAAAGA
2929057 AAAAAAAAAGAAAAAAGAAAAAAG
1 AAAAAAAAAGAAAAAAGAAAAAAG
2929081 GGGGGTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAGAAAAAAGAAAAAAGA
Found at i:2929080 original size:14 final size:14
Alignment explanation
Indices: 2929029--2929079 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
2929019 ATTATGCTTG
2929029 AAGAAAAAAAAAGA
1 AAGAAAAAAAAAGA
2929043 AAGAAAAAAAAAGA
1 AAGAAAAAAAAAGA
*
2929057 AA-AAAAAAAGAAAA
1 AAGAAAAAAA-AAGA
2929071 AAGAAAAAA
1 AAGAAAAAA
2929080 GGGGGGTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 7 0.21
14 21 0.62
15 6 0.18
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAAGA
Found at i:2929448 original size:19 final size:18
Alignment explanation
Indices: 2929409--2929454 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
2929399 CTATTTCAAG
2929409 TTCAATTTA--TTTGAAA
1 TTCAATTTATTTTTGAAA
*
2929425 GTCAATTTATTTTTGGAAA
1 TTCAATTTATTTTT-GAAA
2929444 TTCAATTTATT
1 TTCAATTTATT
2929455 CTTTTCTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.52
Consensus pattern (18 bp):
TTCAATTTATTTTTGAAA
Found at i:2930543 original size:84 final size:84
Alignment explanation
Indices: 2930105--2930511 Score: 769
Period size: 84 Copynumber: 4.8 Consensus size: 84
2930095 TCTTAGACCA
2930105 ATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATG
1 ATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATG
2930170 ATCTGGTTGGACAGAACCC
66 ATCTGGTTGGACAGAACCC
2930189 ATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATG
1 ATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATG
2930254 ATCTGGTTGGACAGAACCC
66 ATCTGGTTGGACAGAACCC
2930273 ATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATG
1 ATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATG
2930338 ATCTGGTTGGACAGAACCC
66 ATCTGGTTGGACAGAACCC
*
2930357 ATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATG
**
2930422 ATCTGGTTGGACAGAACTA
66 ATCTGGTTGGACAGAACCC
* *
2930441 ATCATTGAAATTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATG
2930506 ATCTGG
66 ATCTGG
2930512 AAGTACAGAA
Statistics
Matches: 319, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 319 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.35
Consensus pattern (84 bp):
ATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATG
ATCTGGTTGGACAGAACCC
Found at i:2931620 original size:116 final size:112
Alignment explanation
Indices: 2931273--2931900 Score: 818
Period size: 113 Copynumber: 5.5 Consensus size: 112
2931263 TTTCAGAGAA
2931273 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
*
2931338 AACCTTTTGCTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAG
66 AACCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAGG-AG
*
2931386 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-G--GTAG-AGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
* * * ***
2931447 TTCAACCTTTTTGTTTGAATTCATCACTTGATGGATTATTGTTGCCA-GAGG
63 TTCAACC-TTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAGGA-G
*
2931498 AGGTTCATAATGAGAAGAACTTATCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTT
1 A-GTTCATAATGAGAAGAAC---TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
*
2931563 GTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAG
62 GTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAGG-AG
2931615 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
* * * * * * *
2931680 TTCAACCTTTTACCTGAATCCATCATTTGATGGATCAGCCTTTCCAGAGAA
63 TTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAG-GAG
2931731 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * * * * *
2931796 AACCTTTTACCTGAAGTCATCAATTGATGGATTATCTTTTCCA-GAG
66 AACCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAGGAG
** *
2931842 AAGTTCATAATGAGAAGAACTCATCTGAAGAATAAAGAAAAAGTTCATAATGAGAAGAA
1 -AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
2931901 CTCATCTGAA
Statistics
Matches: 459, Mismatches: 38, Indels: 37
0.86 0.07 0.07
Matches are distributed among these distances:
111 4 0.01
112 87 0.19
113 165 0.36
114 2 0.00
115 2 0.00
116 165 0.36
117 32 0.07
118 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (112 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAGGAG
Found at i:2931641 original size:229 final size:228
Alignment explanation
Indices: 2931238--2931900 Score: 946
Period size: 229 Copynumber: 2.9 Consensus size: 228
2931228 CAAAGATTCA
* * *
2931238 AATCTATCACTTGATGGATTATTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCACTTGATGGATTATTCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
2931303 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGG
*
2931368 ATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-G-GTAG-AGTTC
131 ATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAGAAGAAGTTC
***
2931430 ATAATGAGAAGAATTTGTTCAACCTTTTTGTTTG
196 ATAATGAGAAGAATTTGTTCAACC-TTTTACCTG
* * * * *
2931464 AATTCATCACTTGATGGATTATTGTTGCCAGAGGAGGTTCATAATGAGAAGAACTTATCATCTGA
1 AATCCATCACTTGATGGATTATTCTTTCCAGAGAAAGTTCATAATGAGAAGAAC---TCATCTGA
*
2931529 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGA
63 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGA
2931594 TGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAA
128 TGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGG-AGAAGAA
2931659 GTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
192 GTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * **
2931696 AATCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCACTTGATGGATTATTCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * * *
2931761 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAGTCATCAATTGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGG
* * * * ** *
2931826 ATTATCTTTTCCA-G-AGAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAATAAAGAAAAAGT
131 ATCAACATTGCCAGGTAG-AGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GGAGAAGAAGT
2931886 TCATAATGAGAAGAA
194 TCATAATGAGAAGAA
2931901 CTCATCTGAA
Statistics
Matches: 394, Mismatches: 34, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
225 35 0.09
226 48 0.12
227 2 0.01
228 19 0.05
229 206 0.52
230 1 0.00
232 54 0.14
233 29 0.07
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (228 bp):
AATCCATCACTTGATGGATTATTCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGG
ATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAGAAGAAGTTC
ATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:2931897 original size:40 final size:39
Alignment explanation
Indices: 2931840--2931979 Score: 214
Period size: 40 Copynumber: 3.6 Consensus size: 39
2931830 TCTTTTCCAG
2931840 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAATAAAGA
1 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAA-AAAGA
*
2931880 AAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAATG-
1 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAA-AAA-GA
2931920 AGAAGTTCATAATGAGAAGAACTCATCTGAAG--AAAGA
1 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGA
*
2931957 AGAAGTTCATAATAAGAAGAACT
1 AGAAGTTCATAATGAGAAGAACT
2931980 TGTTCAACTT
Statistics
Matches: 94, Mismatches: 4, Indels: 7
0.90 0.04 0.07
Matches are distributed among these distances:
36 1 0.01
37 25 0.27
40 67 0.71
41 1 0.01
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.20
Consensus pattern (39 bp):
AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGA
Found at i:2932312 original size:3 final size:3
Alignment explanation
Indices: 2932300--2932345 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
2932290 AAGATACTAA
2932300 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2932346 AATATATTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2932830 original size:15 final size:16
Alignment explanation
Indices: 2932802--2932831 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2932792 ACAGAACCGG
2932802 AGAGAAAGGAAAAAAC
1 AGAGAAAGGAAAAAAC
2932818 AGAGAAA-GAAAAAA
1 AGAGAAAGGAAAAAA
2932832 AAAACAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.73, C:0.03, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAGAAAGGAAAAAAC
Found at i:2932832 original size:16 final size:16
Alignment explanation
Indices: 2932802--2932832 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2932792 ACAGAACCGG
*
2932802 AGAGAAAGGAAAAAAC
1 AGAGAAAGAAAAAAAC
2932818 AGAGAAAGAAAAAAA
1 AGAGAAAGAAAAAAA
2932833 AAACAACAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAGAAAGAAAAAAAC
Found at i:2933766 original size:20 final size:21
Alignment explanation
Indices: 2933729--2933769 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2933719 GATATTTTTA
**
2933729 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
2933750 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
2933770 ACATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:2934577 original size:17 final size:18
Alignment explanation
Indices: 2934544--2934577 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2934534 CCGTTACTAG
2934544 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
2934562 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
2934578 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:2951215 original size:18 final size:18
Alignment explanation
Indices: 2951192--2951227 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2951182 TTCTTCAGGA
2951192 TGATGGCAACGACGATGT
1 TGATGGCAACGACGATGT
*
2951210 TGATGGCGACGACGATGT
1 TGATGGCAACGACGATGT
2951228 ACAAGAGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.22
Consensus pattern (18 bp):
TGATGGCAACGACGATGT
Found at i:2951762 original size:23 final size:23
Alignment explanation
Indices: 2951732--2951777 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2951722 TACAGGTTAG
**
2951732 GTACCGATTTAGCCACATTGAGT
1 GTACCGATACAGCCACATTGAGT
*
2951755 GTACCGATACATCCACATTGAGT
1 GTACCGATACAGCCACATTGAGT
2951778 ATACAGGTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (23 bp):
GTACCGATACAGCCACATTGAGT
Found at i:2951788 original size:23 final size:23
Alignment explanation
Indices: 2951744--2951793 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
2951734 ACCGATTTAG
* *
2951744 CCACATTGAGTGTACCGATACAT
1 CCACATTGAGTATACAGATACAT
*
2951767 CCACATTGAGTATACAGGTACAT
1 CCACATTGAGTATACAGATACAT
2951790 CCAC
1 CCAC
2951794 GTTAATGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (23 bp):
CCACATTGAGTATACAGATACAT
Found at i:2961831 original size:31 final size:31
Alignment explanation
Indices: 2961793--2961863 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
2961783 CTTTTAAAAC
2961793 TTGCAATATAATC-CCCAAACATTTAGTCCGT
1 TTGCAATATAATCTCCC-AACATTTAGTCCGT
* *
2961824 TTGCAATATAGTCTCTCAACATTTAGTCCGT
1 TTGCAATATAATCTCCCAACATTTAGTCCGT
*
2961855 TTGAAATAT
1 TTGCAATAT
2961864 GGTCCCCGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (31 bp):
TTGCAATATAATCTCCCAACATTTAGTCCGT
Found at i:2967455 original size:33 final size:33
Alignment explanation
Indices: 2967413--2967479 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
2967403 TTAAGAGAGT
2967413 CCGGCATATTCAGCTCCGTTATTGCAAATGCCC
1 CCGGCATATTCAGCTCCGTTATTGCAAATGCCC
2967446 CCGGCATATTCAGCTCCGTTATTGCAAATGCCC
1 CCGGCATATTCAGCTCCGTTATTGCAAATGCCC
2967479 C
1 C
2967480 TAGTACTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.34, G:0.18, T:0.27
Consensus pattern (33 bp):
CCGGCATATTCAGCTCCGTTATTGCAAATGCCC
Found at i:2972247 original size:75 final size:75
Alignment explanation
Indices: 2972163--2972314 Score: 295
Period size: 75 Copynumber: 2.0 Consensus size: 75
2972153 AGTAAAGAAC
*
2972163 AATAATAAACAAGATGAACTGGCATCTGACTAGATTTTAATGCTGACAATGAATTCTACTACTAA
1 AATAATAAACAAGATGAACTGGCATCTGACTAGATTTTAATGCTGACAATGAATCCTACTACTAA
2972228 TGATAAGTGG
66 TGATAAGTGG
2972238 AATAATAAACAAGATGAACTGGCATCTGACTAGATTTTAATGCTGACAATGAATCCTACTACTAA
1 AATAATAAACAAGATGAACTGGCATCTGACTAGATTTTAATGCTGACAATGAATCCTACTACTAA
2972303 TGATAAGTGG
66 TGATAAGTGG
2972313 AA
1 AA
2972315 ATACACTAAG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (75 bp):
AATAATAAACAAGATGAACTGGCATCTGACTAGATTTTAATGCTGACAATGAATCCTACTACTAA
TGATAAGTGG
Found at i:2974937 original size:35 final size:35
Alignment explanation
Indices: 2974896--2974963 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
2974886 TTCATGTTCA
2974896 AAATTCCAAAACACTTTAATTACACTCTAAACCCC
1 AAATTCCAAAACACTTTAATTACACTCTAAACCCC
* *
2974931 AAATTCCAAAATACTTTAATTACATTCTAAACC
1 AAATTCCAAAACACTTTAATTACACTCTAAACC
2974964 TTAATTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.29
Consensus pattern (35 bp):
AAATTCCAAAACACTTTAATTACACTCTAAACCCC
Found at i:2975014 original size:35 final size:35
Alignment explanation
Indices: 2974975--2975042 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
2974965 TAATTTAAAG
* *
2974975 TATTTTAGAATTTAGG-GTTTAAAATGTAATTGAAT
1 TATTTTAGAATCT-GGAGTTTAAAATGAAATTGAAT
*
2975010 TATTTTAGAATCTGGAGTTTAGAATGAAATTGA
1 TATTTTAGAATCTGGAGTTTAAAATGAAATTGA
2975043 GGATTATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 2 0.07
35 27 0.93
ACGTcount: A:0.37, C:0.01, G:0.19, T:0.43
Consensus pattern (35 bp):
TATTTTAGAATCTGGAGTTTAAAATGAAATTGAAT
Found at i:2978975 original size:9 final size:9
Alignment explanation
Indices: 2978961--2979008 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
2978951 ATGGTCTAAA
2978961 TGACCGGTT
1 TGACCGGTT
2978970 TGACCGGTTT
1 TGACCGG-TT
* *
2978980 TGGAGCAGATT
1 T-GA-CCGGTT
2978991 TGACCGGTT
1 TGACCGGTT
2979000 TGACCGGTT
1 TGACCGGTT
2979009 ACAATCGTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 20 0.62
10 5 0.16
11 5 0.16
12 2 0.06
ACGTcount: A:0.15, C:0.19, G:0.33, T:0.33
Consensus pattern (9 bp):
TGACCGGTT
Found at i:2981554 original size:24 final size:24
Alignment explanation
Indices: 2981527--2981617 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
2981517 TCGATTTGAT
2981527 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
* *
2981551 TTCTGGTTTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
* * *
2981575 TTATAATCTGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
2981599 TTTTGATATGATACTTGAC
1 TTCTGATCTGATACTTGAC
2981618 GTGAATTATG
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 1 0.02
24 53 0.96
25 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:2981626 original size:48 final size:48
Alignment explanation
Indices: 2981532--2981626 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
2981522 TTGATTTCTG
* * *
2981532 ATCTGATACTTGACATGGATTCTGGTTTGATATCTGACATGGATTATA
1 ATCTGATACTTGACATGGATTCTGATATGATATCTGACATGAATTATA
* * *
2981580 ATCTGATACTTGACCTGGATTTTGATATGATA-CTTGACGTGAATTAT
1 ATCTGATACTTGACATGGATTCTGATATGATATC-TGACATGAATTAT
2981627 GGTTTGATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
47 1 0.03
48 39 0.98
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (48 bp):
ATCTGATACTTGACATGGATTCTGATATGATATCTGACATGAATTATA
Found at i:2981634 original size:24 final size:24
Alignment explanation
Indices: 2981530--2981634 Score: 95
Period size: 24 Copynumber: 4.4 Consensus size: 24
2981520 ATTTGATTTC
* *
2981530 TGATCTGATACTTGACATGGATTC
1 TGATTTGATACTTGACATGGATTA
*
2981554 TGGTTTGATA-TCTGACATGGATTA
1 TGATTTGATACT-TGACATGGATTA
* * * *
2981578 TAATCTGATACTTGACCTGGATTT
1 TGATTTGATACTTGACATGGATTA
* * *
2981602 TGATATGATACTTGACGTGAATTA
1 TGATTTGATACTTGACATGGATTA
*
2981626 TGGTTTGAT
1 TGATTTGAT
2981635 TTTTTGATAT
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
23 1 0.02
24 62 0.97
25 1 0.02
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (24 bp):
TGATTTGATACTTGACATGGATTA
Found at i:2986284 original size:24 final size:24
Alignment explanation
Indices: 2986257--2986348 Score: 82
Period size: 24 Copynumber: 3.8 Consensus size: 24
2986247 TTCGATTTGA
2986257 TTTCTGATCTGATACTTGACATGG
1 TTTCTGATCTGATACTTGACATGG
2986281 TTTCTGA-CTTGATA-TCTGACATGG
1 TTTCTGATC-TGATACT-TGACATGG
* * * *
2986305 ATTATAATCTGATACTTGACCTGG
1 TTTCTGATCTGATACTTGACATGG
* *
2986329 AGTT-TGATATGATACTTGAC
1 -TTTCTGATCTGATACTTGAC
2986349 GTGAATTATG
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
23 2 0.04
24 50 0.89
25 4 0.07
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (24 bp):
TTTCTGATCTGATACTTGACATGG
Found at i:2986357 original size:48 final size:48
Alignment explanation
Indices: 2986263--2986357 Score: 106
Period size: 48 Copynumber: 2.0 Consensus size: 48
2986253 TTGATTTCTG
* *
2986263 ATCTGATACTTGACATGGTTTCTGACTTGATATCTGACATGGATTATA
1 ATCTGATACTTGACATGGGTTCTGACTTGATATCTGACATGAATTATA
* *
2986311 ATCTGATACTTGACCTGGAGTT-TGA-TATGATA-CTTGACGTGAATTAT
1 ATCTGATACTTGACATGG-GTTCTGACT-TGATATC-TGACATGAATTAT
2986358 GATTTGATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
47 2 0.05
48 36 0.90
49 2 0.05
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (48 bp):
ATCTGATACTTGACATGGGTTCTGACTTGATATCTGACATGAATTATA
Found at i:2986360 original size:24 final size:25
Alignment explanation
Indices: 2986297--2986365 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 25
2986287 ACTTGATATC
* * *
2986297 TGACATGG-ATTATAATCTGATACT
1 TGACCTGGAATTATGATATGATACT
*
2986321 TGACCTGGAGTT-TGATATGATACT
1 TGACCTGGAATTATGATATGATACT
* *
2986345 TGACGT-GAATTATGATTTGAT
1 TGACCTGGAATTATGATATGAT
2986366 TTTTTGATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
23 4 0.11
24 30 0.83
25 2 0.06
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (25 bp):
TGACCTGGAATTATGATATGATACT
Found at i:2990933 original size:24 final size:24
Alignment explanation
Indices: 2990906--2990996 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
2990896 TCGATTTGAT
2990906 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
* *
2990930 TTCTTATTTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
2990954 TTCTAATCTGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
2990978 TTTTGATATGATACTTGAC
1 TTCTGATCTGATACTTGAC
2990997 GTGAATTATG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
23 1 0.02
24 55 0.96
25 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:2991008 original size:24 final size:24
Alignment explanation
Indices: 2990962--2991013 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2990952 GATTCTAATC
* *
2990962 TGATACTTGACCTGGATTTTGATA
1 TGATACTTGACCTGAATTATGATA
* *
2990986 TGATACTTGACGTGAATTATGATT
1 TGATACTTGACCTGAATTATGATA
2991010 TGAT
1 TGAT
2991014 TTTTTGATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (24 bp):
TGATACTTGACCTGAATTATGATA
Found at i:2992909 original size:30 final size:30
Alignment explanation
Indices: 2992864--2992920 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
2992854 ACACGGTACC
*
2992864 TGATTTTCTGAATATTATTTATATGATATA
1 TGATTTACTGAATATTATTTATATGATATA
* *
2992894 TGATTTACTGTATATTTTTTATATGAT
1 TGATTTACTGAATATTATTTATATGAT
2992921 CTCTGGTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.56
Consensus pattern (30 bp):
TGATTTACTGAATATTATTTATATGATATA
Found at i:2992980 original size:19 final size:19
Alignment explanation
Indices: 2992956--2992994 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2992946 GATTTCTGAG
2992956 TATGAAATATTTTCATGTT
1 TATGAAATATTTTCATGTT
2992975 TATGAAATATTTTCATGTT
1 TATGAAATATTTTCATGTT
2992994 T
1 T
2992995 TAATGGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (19 bp):
TATGAAATATTTTCATGTT
Found at i:2994883 original size:22 final size:23
Alignment explanation
Indices: 2994857--2994913 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
2994847 TATTAAGATT
2994857 TTATTTTTAAAAAAAAT-AATTA
1 TTATTTTTAAAAAAAATAAATTA
* *
2994879 TTATTTTTTGGATAAATAATAAATTA
1 TTA-TTTTT--AAAAAAAATAAATTA
2994905 TTATTTTTA
1 TTATTTTTA
2994914 TGTATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
22 3 0.10
23 6 0.21
25 12 0.41
26 8 0.28
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
TTATTTTTAAAAAAAATAAATTA
Found at i:2996241 original size:2 final size:2
Alignment explanation
Indices: 2996236--2996304 Score: 104
Period size: 2 Copynumber: 34.5 Consensus size: 2
2996226 AAAACAACTA
2996236 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2996278 AT AT AT AT -T AT GT AT AA ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT A
2996305 CCATGTATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.02
2 59 0.97
3 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2996310 original size:20 final size:20
Alignment explanation
Indices: 2996277--2996316 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2996267 TATATATATA
**
2996277 TATATATATTATGTATAAAC
1 TATATATACCATGTATAAAC
2996297 TATATATACCATGTATAAAC
1 TATATATACCATGTATAAAC
2996317 AATAATACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (20 bp):
TATATATACCATGTATAAAC
Found at i:2996407 original size:39 final size:38
Alignment explanation
Indices: 2996323--2996402 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 38
2996313 AAACAATAAT
*
2996323 ACTATATAGTTTATATATGAAGTAATGAACTATATAGAA
1 ACTACATAGTTTATATA-GAAGTAATGAACTATATAGAA
* *
2996362 ACTACATAGTTTATATA-AA-TATATGAATTATATATAA
1 ACTACATAGTTTATATAGAAGTA-ATGAACTATATAGAA
2996399 ACTA
1 ACTA
2996403 TACATTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 2 0.05
37 19 0.51
39 16 0.43
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (38 bp):
ACTACATAGTTTATATAGAAGTAATGAACTATATAGAA
Found at i:2996498 original size:20 final size:22
Alignment explanation
Indices: 2996446--2996507 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
2996436 ATATATATTG
*
2996446 TATAAATTATATAGTTTATTAA
1 TATAAACTATATAGTTTATTAA
2996468 TATAAACTATATAGTTT-TTATA
1 TATAAACTATATAGTTTATTA-A
*
2996490 TATAGTA-TATATAGTTTA
1 TATA-AACTATATAGTTTA
2996508 GGGTTTAGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 3 0.09
22 31 0.89
23 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (22 bp):
TATAAACTATATAGTTTATTAA
Found at i:2996513 original size:7 final size:7
Alignment explanation
Indices: 2996503--2996591 Score: 97
Period size: 7 Copynumber: 12.7 Consensus size: 7
2996493 AGTATATATA
2996503 GTTTAGG
1 GTTTAGG
2996510 GTTTAGG
1 GTTTAGG
2996517 GTTTAGG
1 GTTTAGG
*
2996524 GTTTATG
1 GTTTAGG
*
2996531 GATTAGG
1 GTTTAGG
*
2996538 ATTTAGG
1 GTTTAGG
*
2996545 GGTTAGG
1 GTTTAGG
*
2996552 GGTTAGG
1 GTTTAGG
*
2996559 GGTTAGG
1 GTTTAGG
2996566 GTTTAGG
1 GTTTAGG
* *
2996573 ATCTAGG
1 GTTTAGG
*
2996580 GTTTAAG
1 GTTTAGG
2996587 GTTTA
1 GTTTA
2996592 TATTTATATT
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 69 1.00
ACGTcount: A:0.19, C:0.01, G:0.40, T:0.39
Consensus pattern (7 bp):
GTTTAGG
Found at i:2996599 original size:6 final size:6
Alignment explanation
Indices: 2996588--2996612 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2996578 GGGTTTAAGG
2996588 TTTATA TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA T
2996613 AAACTACATA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:2996645 original size:20 final size:19
Alignment explanation
Indices: 2996588--2996693 Score: 79
Period size: 23 Copynumber: 5.1 Consensus size: 19
2996578 GGGTTTAAGG
*
2996588 TTTATATTTATAT-TTATA
1 TTTATATTTATATACTATA
* *
2996606 TTTATATAAACTACATACTATGA
1 TTTATAT---TTATATACTAT-A
2996629 TTTATATTTATATACTATA
1 TTTATATTTATATACTATA
2996648 TTTTATACTATTTATATAAACTATAA
1 --TT-TA-TATTTATAT--ACTAT-A
2996674 TTTATATTTATATACTATA
1 TTTATATTTATATACTATA
2996693 T
1 T
2996694 ATATGAACTA
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
18 7 0.10
19 3 0.04
20 14 0.20
21 6 0.08
22 14 0.20
23 19 0.27
24 2 0.03
25 5 0.07
26 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.54
Consensus pattern (19 bp):
TTTATATTTATATACTATA
Found at i:2996656 original size:12 final size:13
Alignment explanation
Indices: 2996631--2996680 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
2996621 TACTATGATT
2996631 TATATTTATATAC
1 TATATTTATATAC
2996644 TATATTT-TATAC
1 TATATTTATATAC
*
2996656 TAT-TTATATAAAC
1 TATATT-TATATAC
2996669 TATAATTTATAT
1 TAT-ATTTATAT
2996681 TTATATACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 14 0.45
14 4 0.13
15 2 0.06
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATTTATATAC
Found at i:2996691 original size:33 final size:32
Alignment explanation
Indices: 2996644--2996710 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
2996634 ATTTATATAC
*
2996644 TATATTTTATACTATTTATATAAACTATAATT
1 TATATTTTATACTATATATATAAACTATAATT
* *
2996676 TATATTTATATACTATATATATGAACTATAGTT
1 TATATTT-TATACTATATATATAAACTATAATT
2996709 TA
1 TA
2996711 CGTATGAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (32 bp):
TATATTTTATACTATATATATAAACTATAATT
Found at i:2996786 original size:40 final size:40
Alignment explanation
Indices: 2996689--2996805 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 40
2996679 ATTTATATAC
* *
2996689 TATATATA-TGAACTATAGTTTACGTATGAACTATATGTAAA
1 TATATATACT-AACTATAGTTTACATAAGAACTATA-GTAAA
*
2996730 TATAGTAAACT-A-TATAGTTTACATAAGAACTATA-TAAA
1 TATA-TATACTAACTATAGTTTACATAAGAACTATAGTAAA
* *
2996768 TTTTATATACTAACTATAGTTTATATATA-AACTATAGT
1 -TATATATACTAACTATAGTTTACATA-AGAACTATAGT
2996806 TGATATTTAC
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
38 9 0.14
39 4 0.06
40 39 0.62
41 7 0.11
42 3 0.05
43 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.40
Consensus pattern (40 bp):
TATATATACTAACTATAGTTTACATAAGAACTATAGTAAA
Found at i:2996790 original size:18 final size:18
Alignment explanation
Indices: 2996769--2996998 Score: 66
Period size: 18 Copynumber: 12.4 Consensus size: 18
2996759 CTATATAAAT
2996769 TTTATATACT-AACTATAG
1 TTTATATA-TAAACTATAG
2996787 TTTATATATAAACTATAG
1 TTTATATATAAACTATAG
* *
2996805 TTGATAT-T-TAC-ATA-
1 TTTATATATAAACTATAG
** *
2996819 TGAACTATATAGACTAT-G
1 TTTA-TATATAAACTATAG
*
2996837 TAAATTTTATATACTAACTATAG
1 T---TTATATATA--AACTATAG
**
2996860 TTTATACGTAAACTATAG
1 TTTATATATAAACTATAG
*
2996878 -TTAGTATATAAAATTTACATAG
1 TTTA-TATAT-AAA-CT--ATAG
* *
2996900 TTCATATGTAAACTATATAG
1 TTTATATATAAAC--TATAG
**
2996920 TTTACTATATTTACATATAG
1 TTTA-TATATAAAC-TATAG
* **
2996940 TTCATACGTAAACTATAG
1 TTTATATATAAACTATAG
* * *
2996958 TTCATATATATAGTATA-
1 TTTATATATAAACTATAG
*
2996975 --TAAATATAAACTATAG
1 TTTATATATAAACTATAG
2996991 TTTATATA
1 TTTATATA
2996999 AATAGTATAA
Statistics
Matches: 152, Mismatches: 36, Indels: 48
0.64 0.15 0.20
Matches are distributed among these distances:
14 2 0.01
15 17 0.11
16 3 0.02
17 7 0.05
18 59 0.39
19 8 0.05
20 29 0.19
21 9 0.06
22 14 0.09
23 4 0.03
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (18 bp):
TTTATATATAAACTATAG
Found at i:2996900 original size:40 final size:41
Alignment explanation
Indices: 2996856--2996967 Score: 126
Period size: 40 Copynumber: 2.8 Consensus size: 41
2996846 TATACTAACT
*
2996856 ATAGTTTATACGTAAACTATAGTTAGTATATAAAATTTAC-
1 ATAGTTCATACGTAAACTATAGTTAGTATATAAAATTTACA
* * *
2996896 ATAGTTCATATGTAAACTATA--TAGTTTACT-ATATTTACA
1 ATAGTTCATACGTAAACTATAGTTAGTATA-TAAAATTTACA
2996935 TATAGTTCATACGTAAACTATAGTTCA-TATATA
1 -ATAGTTCATACGTAAACTATAGTT-AGTATATA
2996968 TAGTATATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
38 13 0.22
39 1 0.02
40 39 0.66
41 1 0.02
42 4 0.07
43 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (41 bp):
ATAGTTCATACGTAAACTATAGTTAGTATATAAAATTTACA
Found at i:2996919 original size:20 final size:19
Alignment explanation
Indices: 2996896--2996964 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 19
2996886 TAAAATTTAC
2996896 ATAGTTCATATGTAAACTAT
1 ATAGTTCATATGTAAAC-AT
* * **
2996916 ATAGTTTACTATATTTACAT
1 ATAGTTCA-TATGTAAACAT
*
2996936 ATAGTTCATACGTAAAC-T
1 ATAGTTCATATGTAAACAT
2996954 ATAGTTCATAT
1 ATAGTTCATAT
2996965 ATATAGTATA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
18 11 0.29
19 5 0.13
20 16 0.42
21 6 0.16
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.42
Consensus pattern (19 bp):
ATAGTTCATATGTAAACAT
Found at i:2996987 original size:33 final size:32
Alignment explanation
Indices: 2996948--2997014 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 32
2996938 AGTTCATACG
*
2996948 TAAACTATAGTTCATATATATAGTATATAAATA
1 TAAACTATAGTTCATATAAATAGTATA-AAATA
*
2996981 TAAACTATAGTTTATATAAATAGTATAAAATA
1 TAAACTATAGTTCATATAAATAGTATAAAATA
2997013 TA
1 TA
2997015 GTATATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 7 0.22
33 25 0.78
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (32 bp):
TAAACTATAGTTCATATAAATAGTATAAAATA
Found at i:2996989 original size:20 final size:19
Alignment explanation
Indices: 2996965--2997074 Score: 87
Period size: 23 Copynumber: 5.3 Consensus size: 19
2996955 TAGTTCATAT
2996965 ATATAGTATATAAATATAA
1 ATATAGTATATAAATATAA
2996984 ACTATAGTTTATATAAATAGTATAAA
1 A-TATAG--TATAT-AA-A-TAT-AA
2997010 ATATAGTATATAAATATAA
1 ATATAGTATATAAATATAA
**
2997029 ATCATAGTATGTAGTTTATATAA
1 AT-ATAGTA--TA-TAAATATAA
*
2997052 ATATA-AATATAAATATAA
1 ATATAGTATATAAATATAA
2997070 ATATA
1 ATATA
2997075 AATATAAACC
Statistics
Matches: 75, Mismatches: 5, Indels: 23
0.73 0.05 0.22
Matches are distributed among these distances:
18 12 0.16
19 7 0.09
20 14 0.19
21 2 0.03
22 12 0.16
23 16 0.21
24 1 0.01
25 8 0.11
26 3 0.04
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (19 bp):
ATATAGTATATAAATATAA
Found at i:2997017 original size:12 final size:13
Alignment explanation
Indices: 2996978--2997080 Score: 63
Period size: 12 Copynumber: 7.8 Consensus size: 13
2996968 TAGTATATAA
2996978 ATATAAACTATAGT
1 ATATAAA-TATAGT
*
2996992 TTATATAA-ATAGT
1 ATATA-AATATAGT
2997005 ATA-AAATATAGT
1 ATATAAATATAGT
*
2997017 ATATAAATATA-A
1 ATATAAATATAGT
* *
2997029 ATCATAGTATGTAGTTT
1 AT-ATA-AATATAG--T
*
2997046 ATATAAATATA-A
1 ATATAAATATAGT
*
2997058 ATATAAATATA-A
1 ATATAAATATAGT
2997070 ATATAAATATA
1 ATATAAATATA
2997081 AACCCTAAAC
Statistics
Matches: 72, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.03
12 34 0.47
13 17 0.24
14 8 0.11
15 6 0.08
16 3 0.04
17 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:2997057 original size:6 final size:6
Alignment explanation
Indices: 2997046--2997082 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
2997036 TATGTAGTTT
2997046 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA A
2997083 CCCTAAACCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:2997091 original size:7 final size:7
Alignment explanation
Indices: 2997079--2997173 Score: 111
Period size: 7 Copynumber: 13.7 Consensus size: 7
2997069 AATATAAATA
2997079 TAAACCC
1 TAAACCC
*
2997086 TAAACCT
1 TAAACCC
* *
2997093 TAGATCC
1 TAAACCC
*
2997100 TAAACCT
1 TAAACCC
2997107 TAAACCC
1 TAAACCC
2997114 T-AACCC
1 TAAACCC
2997120 TAAACCC
1 TAAACCC
2997127 TAAACCC
1 TAAACCC
* *
2997134 TAATCCA
1 TAAACCC
*
2997141 TAAACTC
1 TAAACCC
2997148 TAAACCC
1 TAAACCC
2997155 TAAACCC
1 TAAACCC
*
2997162 TAAATCC
1 TAAACCC
2997169 TAAAC
1 TAAAC
2997174 TATATATACT
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
6 6 0.08
7 65 0.92
ACGTcount: A:0.42, C:0.36, G:0.01, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:2997208 original size:22 final size:22
Alignment explanation
Indices: 2997169--2997232 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
2997159 CCCTAAATCC
*
2997169 TAAACTATATATACTATATATAA
1 TAAACTATATAT-TTATATATAA
2997192 -AAACTATATAGTTTATAT-TAA
1 TAAACTATATA-TTTATATATAA
*
2997213 TTAACTATATAATTTATATA
1 TAAACTATAT-ATTTATATA
2997233 GTATATATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
21 3 0.09
22 30 0.86
23 2 0.06
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (22 bp):
TAAACTATATATTTATATATAA
Found at i:2997312 original size:13 final size:11
Alignment explanation
Indices: 2997196--2997314 Score: 75
Period size: 11 Copynumber: 10.6 Consensus size: 11
2997186 ATATAAAAAC
*
2997196 TATATAGTTTA
1 TATATAATTTA
*
2997207 TAT-TAATTAA
1 TATATAATTTA
2997217 CTATATAATTTA
1 -TATATAATTTA
2997229 TATAGTATATATTA
1 TATA-TA-AT-TTA
*
2997243 TTTATAA-TTA
1 TATATAATTTA
*
2997253 TACATAATATATA
1 TATATAAT-T-TA
* *
2997266 AATATAA-AT-
1 TATATAATTTA
* *
2997275 TGTATAGTTTA
1 TATATAATTTA
*
2997286 TATATAATTCA
1 TATATAATTTA
2997297 TATATAATTTA
1 TATATAATTTA
2997308 TATATAA
1 TATATAA
2997315 ACTATGTATT
Statistics
Matches: 81, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
9 4 0.05
10 15 0.19
11 35 0.43
12 10 0.12
13 11 0.14
14 6 0.07
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (11 bp):
TATATAATTTA
Found at i:2997387 original size:2 final size:2
Alignment explanation
Indices: 2997380--2997485 Score: 58
Period size: 2 Copynumber: 52.5 Consensus size: 2
2997370 TTATACATGG
* * * * *
2997380 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA TA TA AA CTA TA CA GTT
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * * *
2997424 TA TA TA TA TA -A TA CA TA TA CTT TA TA TA TA AA CTA TA T- TA TT
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA
2997466 TA TA T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
2997486 TAGTTGTTTT
Statistics
Matches: 77, Mismatches: 18, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
1 4 0.05
2 69 0.90
3 4 0.05
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Done.