Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009261.1 Hibiscus syriacus cultivar Beakdansim tig00112912_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: 923215
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:439 original size:21 final size:20
Alignment explanation
Indices: 355--516 Score: 79
Period size: 21 Copynumber: 7.8 Consensus size: 20
345 ATTAATATAT
355 ATACTATATATTTATATAC-TT-
1 ATACT-TATA-TTATAT-CTTTA
376 ATACTTATATTTATATACTTTA
1 ATACTTATA-TTATAT-CTTTA
398 ATACTTTAATAATTATA--TTTA
1 ATAC-TT-AT-ATTATATCTTTA
*
419 ATACTTATATTATATGGTTTA
1 ATACTTATATTATAT-CTTTA
*
440 ATA-TTTTATATATATGCTTT-
1 ATACTTATAT-TATAT-CTTTA
* *
460 A-ACTTATATACTTTATATTTA
1 ATACTTATAT--TATATCTTTA
*
481 ATACTTATA-TATATAGTTTA
1 ATACTTATATTATAT-CTTTA
*
501 ATACTTTATAGTATAT
1 ATAC-TTATATTATAT
517 ACTTATTACA
Statistics
Matches: 117, Mismatches: 8, Indels: 31
0.75 0.05 0.20
Matches are distributed among these distances:
18 6 0.05
19 7 0.06
20 37 0.32
21 41 0.35
22 16 0.14
23 2 0.02
24 7 0.06
25 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (20 bp):
ATACTTATATTATATCTTTA
Found at i:461 original size:42 final size:39
Alignment explanation
Indices: 376--517 Score: 110
Period size: 42 Copynumber: 3.4 Consensus size: 39
366 TTATATACTT
*
376 ATACTTATATTTATATACTTTAATACTTTA-ATAATTATATTTA
1 ATACTTATA-TTATATA-TTTAATA-TTTATAT-A-TATGTTTA
*
419 ATACTTATATTATATGGTTTAATATTTTATATATATGCTTT-
1 ATACTTATATTATAT-ATTTAATA-TTTATATATATG-TTTA
* *
460 A-ACTTATATACTTTATATTTAATACTTATATATATAGTTTA
1 ATACTTATAT--TATATATTTAATATTTATATATAT-GTTTA
*
501 ATACTTTATAGTATATA
1 ATAC-TTATATTATATA
518 CTTATTACAT
Statistics
Matches: 82, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
40 21 0.26
41 18 0.22
42 27 0.33
43 16 0.20
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (39 bp):
ATACTTATATTATATATTTAATATTTATATATATGTTTA
Found at i:505 original size:34 final size:35
Alignment explanation
Indices: 467--555 Score: 121
Period size: 34 Copynumber: 2.6 Consensus size: 35
457 TTTAACTTAT
*
467 ATACTTTATATTTA-ATACTTA-TATATATAGTTTA
1 ATACTTTATATTTATATACTTATTACATATA-TTTA
*
501 ATACTTTATA-GTATATACTTATTACATATATTTA
1 ATACTTTATATTTATATACTTATTACATATATTTA
*
535 ATACTTTATATTTATGTACTT
1 ATACTTTATATTTATATACTT
556 TTATACTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
33 2 0.04
34 31 0.65
35 15 0.31
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (35 bp):
ATACTTTATATTTATATACTTATTACATATATTTA
Found at i:560 original size:16 final size:14
Alignment explanation
Indices: 376--548 Score: 65
Period size: 14 Copynumber: 12.0 Consensus size: 14
366 TTATATACTT
376 ATAC-TTATATTTA
1 ATACTTTATATTTA
389 TATACTTTAATACTTTA
1 -ATACTTT-ATA-TTTA
*
406 ATA-ATTATATTTA
1 ATACTTTATATTTA
419 ATACTTATATTATATGGTTTA
1 ATAC---T-TTATA---TTTA
* *
440 ATATTTTATATAT-
1 ATACTTTATATTTA
* *
453 ATGCTTTA-ACTTA
1 ATACTTTATATTTA
466 TATACTTTATATTTA
1 -ATACTTTATATTTA
*
481 ATAC-TTATATAT-
1 ATACTTTATATTTA
*
493 ATAGTTTAATACTTT-
1 ATACTTT-ATA-TTTA
* * *
508 ATAGTATATACTTA
1 ATACTTTATATTTA
* *
522 TTAC-ATATATTTA
1 ATACTTTATATTTA
535 ATACTTTATATTTA
1 ATACTTTATATTTA
549 TGTACTTTTA
Statistics
Matches: 120, Mismatches: 20, Indels: 38
0.67 0.11 0.21
Matches are distributed among these distances:
12 5 0.04
13 35 0.29
14 36 0.30
15 16 0.13
16 6 0.05
17 9 0.08
18 6 0.05
21 7 0.06
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (14 bp):
ATACTTTATATTTA
Found at i:646 original size:19 final size:19
Alignment explanation
Indices: 603--639 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
593 TTTAATACTT
*
603 TATATACTTATAGTTTATA
1 TATATACTTATAGCTTATA
622 TATATACTTATA-CTTATA
1 TATATACTTATAGCTTATA
640 CTTTATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATACTTATAGCTTATA
Found at i:676 original size:34 final size:32
Alignment explanation
Indices: 605--694 Score: 94
Period size: 34 Copynumber: 2.8 Consensus size: 32
595 TAATACTTTA
*
605 TATACTTATAGTTTATAT-ATATACTTATACT
1 TATACTTATAGTTTATATAATATACTTAGACT
*
636 TATACTTTATAGTTTATATAATGGTA-TATAGACT
1 TATAC-TTATAGTTTATATAAT-ATACT-TAGACT
* *
670 TATACTTATATGTATATATACTATA
1 TATACTTATA-GTTTATATAATATA
695 TAGTTATATG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
31 5 0.10
32 13 0.27
33 10 0.20
34 21 0.43
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.49
Consensus pattern (32 bp):
TATACTTATAGTTTATATAATATACTTAGACT
Found at i:701 original size:23 final size:22
Alignment explanation
Indices: 620--706 Score: 69
Period size: 23 Copynumber: 4.1 Consensus size: 22
610 TTATAGTTTA
*
620 TATATATACTTATACTTATACT-
1 TATATAGACTTATACTTATA-TG
*
642 T-TATAG-TTTATA--TA-ATGG
1 TATATAGACTTATACTTATAT-G
660 TATATAGACTTATACTTATATG
1 TATATAGACTTATACTTATATG
* *
682 TATATATACTATATAGTTATATG
1 TATATAGACT-TATACTTATATG
705 TA
1 TA
707 CTATTTATAC
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
16 1 0.02
17 1 0.02
18 3 0.06
19 5 0.10
20 10 0.19
21 4 0.08
22 13 0.25
23 15 0.29
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (22 bp):
TATATAGACTTATACTTATATG
Found at i:702 original size:17 final size:17
Alignment explanation
Indices: 670--710 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
660 TATATAGACT
670 TATACT-TATATGTATA
1 TATACTATATATGTATA
686 TATACTATATA-GTTATA
1 TATACTATATATG-TATA
*
703 TGTACTAT
1 TATACTAT
711 TTATACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (17 bp):
TATACTATATATGTATA
Found at i:795 original size:23 final size:25
Alignment explanation
Indices: 726--814 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 25
716 CTAAACTTTA
* *
726 TATATA-TATATATATATATATACT
1 TATATACTTTATATATATATACACT
*
750 TATACTTTTAATTTATATATATATACAC-
1 TATA----TACTTTATATATATATACACT
* *
778 T-TATACTTTATATGTATATATACT
1 TATATACTTTATATATATATACACT
802 TATATACTTTATA
1 TATATACTTTATA
815 CTTTATATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
23 17 0.32
24 5 0.09
25 11 0.21
27 2 0.04
28 3 0.06
29 15 0.28
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (25 bp):
TATATACTTTATATATATATACACT
Found at i:841 original size:8 final size:8
Alignment explanation
Indices: 794--842 Score: 68
Period size: 8 Copynumber: 6.5 Consensus size: 8
784 TTTATATGTA
794 TATATACT
1 TATATACT
802 TATATACT
1 TATATACT
810 T-TATACT
1 TATATACT
817 T-TATA-T
1 TATATACT
*
823 TATATATT
1 TATATACT
831 TATATACT
1 TATATACT
839 TATA
1 TATA
843 ATGTATTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
6 2 0.05
7 15 0.39
8 21 0.55
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (8 bp):
TATATACT
Found at i:890 original size:25 final size:27
Alignment explanation
Indices: 840--893 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
830 TTATATACTT
*
840 ATAATGTATTAATGTATTAATCTATGC
1 ATAATGTATTAATGTATTAATATATGC
867 ATAA-GTA-TAATGTACTT-ATATATGC
1 ATAATGTATTAATGTA-TTAATATATGC
892 AT
1 AT
894 GTATCATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 16 0.64
26 5 0.20
27 4 0.16
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (27 bp):
ATAATGTATTAATGTATTAATATATGC
Found at i:1861 original size:21 final size:21
Alignment explanation
Indices: 1837--1894 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 21
1827 GGACGAGCAT
*
1837 ATCCGATTCTAAAGCTCGTGC
1 ATCCGATTCTAAAGCTCATGC
1858 ATCCGATTCTACTAAAGCTCATGC
1 ATCCGA-T-T-CTAAAGCTCATGC
1882 ATCCGATTCTAAA
1 ATCCGATTCTAAA
1895 CCCACTAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 11 0.33
22 2 0.06
23 2 0.06
24 18 0.55
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (21 bp):
ATCCGATTCTAAAGCTCATGC
Found at i:1877 original size:24 final size:24
Alignment explanation
Indices: 1845--1892 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1835 ATATCCGATT
*
1845 CTAAAGCTCGTGCATCCGATTCTA
1 CTAAAGCTCATGCATCCGATTCTA
1869 CTAAAGCTCATGCATCCGATTCTA
1 CTAAAGCTCATGCATCCGATTCTA
1893 AACCCACTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (24 bp):
CTAAAGCTCATGCATCCGATTCTA
Found at i:16102 original size:25 final size:27
Alignment explanation
Indices: 16059--16109 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
16049 GGAAGTGTAT
16059 AAATTCACTAAACTAGGGTCT-TATTA
1 AAATTCACTAAACTAGGGTCTATATTA
16085 AAATTCACTAAACT-GGGTCTATATT
1 AAATTCACTAAACTAGGGTCTATATT
16110 TTTGTTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (27 bp):
AAATTCACTAAACTAGGGTCTATATTA
Found at i:17961 original size:25 final size:24
Alignment explanation
Indices: 17933--17982 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
17923 TGTTGGGGCA
* *
17933 GTTTGACCCAATTTTGACTCGACCC
1 GTTTAACCCAA-TTTGACCCGACCC
*
17958 GTTTAACCCGATTTGACCCGACCC
1 GTTTAACCCAATTTGACCCGACCC
17982 G
1 G
17983 CTGACTGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.20, C:0.34, G:0.18, T:0.28
Consensus pattern (24 bp):
GTTTAACCCAATTTGACCCGACCC
Found at i:20170 original size:24 final size:24
Alignment explanation
Indices: 20107--20171 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
20097 TACCTGATTT
* *
20107 CTGACCTGAATTCTGATCTGATAC
1 CTGACCTGAATTCTGTTCTAATAC
*
20131 CTGACCTGGATTCTGTTCTAATAC
1 CTGACCTGAATTCTGTTCTAATAC
*
20155 TTGACCTGAATTCTGTT
1 CTGACCTGAATTCTGTT
20172 ATGATATATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (24 bp):
CTGACCTGAATTCTGTTCTAATAC
Found at i:30586 original size:30 final size:30
Alignment explanation
Indices: 30550--30612 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
30540 GATAATTTAG
30550 TTACTTGATTCGTACTTATCATCAATATAT
1 TTACTTGATTCGTACTTATCATCAATATAT
* *
30580 TTACTTGATTCGTACTTATTATCAGTATAT
1 TTACTTGATTCGTACTTATCATCAATATAT
30610 TTA
1 TTA
30613 TGTTATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (30 bp):
TTACTTGATTCGTACTTATCATCAATATAT
Found at i:43630 original size:38 final size:39
Alignment explanation
Indices: 43579--43654 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 39
43569 TAAAAAATTA
* *
43579 ATTTATTTAGAACTAGGT-AAAGTTTAGTTTTCTACTTC
1 ATTTATTTAGAACTAGGTAAAACTTTAATTTTCTACTTC
43617 ATTTATTTAGAACTAGGTAAAACTTTAATTTTCTACTT
1 ATTTATTTAGAACTAGGTAAAACTTTAATTTTCTACTT
43655 ATTAATATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 18 0.51
39 17 0.49
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (39 bp):
ATTTATTTAGAACTAGGTAAAACTTTAATTTTCTACTTC
Found at i:44071 original size:22 final size:23
Alignment explanation
Indices: 44034--44077 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
44024 TTCCTAGTTT
44034 AATTAAAATAAAGTATATAAATC
1 AATTAAAATAAAGTATATAAATC
44057 AATTAAAA-AAAGTATATAAAT
1 AATTAAAATAAAGTATATAAAT
44078 ATAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (23 bp):
AATTAAAATAAAGTATATAAATC
Found at i:44083 original size:23 final size:23
Alignment explanation
Indices: 44032--44083 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
44022 CTTTCCTAGT
44032 TTAATTAAAATAAAGTATATAAA
1 TTAATTAAAATAAAGTATATAAA
*
44055 TCAATTAAAA-AAAGTATATAAA
1 TTAATTAAAATAAAGTATATAAA
44077 TATAATT
1 T-TAATT
44084 CATATTAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (23 bp):
TTAATTAAAATAAAGTATATAAA
Found at i:55669 original size:32 final size:32
Alignment explanation
Indices: 55633--55719 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
55623 TCTCACTTGT
* * *
55633 ATTAAATGATTTCTTTCCTTTTGTTTGTGTAC
1 ATTAAATAATTTATTTCCTTTTGTTTATGTAC
*
55665 ATTAACTAATTTATTTCCTTTTGTTTATGTAC
1 ATTAAATAATTTATTTCCTTTTGTTTATGTAC
* * *
55697 ACTAACCT-ATTTATTTTCTTTTG
1 ATTAA-ATAATTTATTTCCTTTTG
55720 ATTGTGTCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
32 46 0.96
33 2 0.04
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.56
Consensus pattern (32 bp):
ATTAAATAATTTATTTCCTTTTGTTTATGTAC
Found at i:55849 original size:21 final size:20
Alignment explanation
Indices: 55807--55850 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
55797 GGATATTCAT
* *
55807 GAGAAAAATTTTTCAAAGAA
1 GAGAAAAAGTTTTCAAACAA
*
55827 GAGATAAAAGTTTTCAATCAA
1 GAGA-AAAAGTTTTCAAACAA
55848 GAG
1 GAG
55851 GTTGCGTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (20 bp):
GAGAAAAAGTTTTCAAACAA
Found at i:57503 original size:21 final size:20
Alignment explanation
Indices: 57465--57504 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
57455 GATCAATATT
*
57465 TTTGCATATGCATTTGCATA
1 TTTGCATATGCATCTGCATA
*
57485 TTTGCATTTTGCATCTGCAT
1 TTTGCA-TATGCATCTGCAT
57505 TTTATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (20 bp):
TTTGCATATGCATCTGCATA
Found at i:61434 original size:15 final size:15
Alignment explanation
Indices: 61401--61451 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
61391 TTACACTTGA
*
61401 AGAAGAAGAAG-AAAA
1 AGAA-AAGAAGCAAAG
61416 AGAAAAGAAGCAAAG
1 AGAAAAGAAGCAAAG
* *
61431 AGAAAATAAACAAAG
1 AGAAAAGAAGCAAAG
61446 A-AAAAG
1 AGAAAAG
61452 GGACAAGAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 10 0.32
15 21 0.68
ACGTcount: A:0.73, C:0.04, G:0.22, T:0.02
Consensus pattern (15 bp):
AGAAAAGAAGCAAAG
Found at i:62584 original size:32 final size:32
Alignment explanation
Indices: 62511--62572 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
62501 ATATTTAAAT
*
62511 ATTCAACATCAAATGTTGGGGCATCTTTGGAA
1 ATTCAACATCAAATATTGGGGCATCTTTGGAA
*
62543 ATTCAACATCGAATATTGGGGCATCTTTGG
1 ATTCAACATCAAATATTGGGGCATCTTTGG
62573 GGATTTAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (32 bp):
ATTCAACATCAAATATTGGGGCATCTTTGGAA
Found at i:62922 original size:33 final size:34
Alignment explanation
Indices: 62879--62968 Score: 105
Period size: 33 Copynumber: 2.7 Consensus size: 34
62869 CACCAAATTC
* * *
62879 TGAGAT-TGTTTCACTCGAAATAAAAATCATCTT
1 TGAGATCTGTTTCACTAGAAACAAAAACCATCTT
*
62912 TGAG-TCTGTTTCACTAGAAACAACAACCATCTT
1 TGAGATCTGTTTCACTAGAAACAAAAACCATCTT
* *
62945 TGAGATC-GTTTCTCTTGAAACAAA
1 TGAGATCTGTTTCACTAGAAACAAA
62969 TCTTATTTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
32 1 0.02
33 45 0.94
34 2 0.04
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Consensus pattern (34 bp):
TGAGATCTGTTTCACTAGAAACAAAAACCATCTT
Found at i:63104 original size:35 final size:33
Alignment explanation
Indices: 63066--63189 Score: 110
Period size: 35 Copynumber: 3.8 Consensus size: 33
63056 AGAAATGCCC
63066 ATCTTTAAGTCTGTTTCCCTTGAAACAAAACAAA
1 ATCTTTAAGTCTGTTTCCCTTGAAACAAAAC-AA
* * * **
63100 CATCTTTGAAAT-TATTTCCCTTGAAACGAATTAA
1 -ATCTTT-AAGTCTGTTTCCCTTGAAACAAAACAA
* **
63134 ATCTTTGAGTCTGTTTTTCTTGAAACAAAAC-A
1 ATCTTTAAGTCTGTTTCCCTTGAAACAAAACAA
* *
63166 ATCTTTGAGTC-GTTTCCTTTGAAA
1 ATCTTTAAGTCTGTTTCCCTTGAAA
63190 TGAATTTTAT
Statistics
Matches: 71, Mismatches: 16, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
31 10 0.14
32 14 0.20
33 20 0.28
34 2 0.03
35 22 0.31
36 3 0.04
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (33 bp):
ATCTTTAAGTCTGTTTCCCTTGAAACAAAACAA
Found at i:63564 original size:129 final size:128
Alignment explanation
Indices: 63293--63633 Score: 378
Period size: 129 Copynumber: 2.6 Consensus size: 128
63283 CCGTCAGAGT
* ** * * *
63293 GGAACCGTGTTATCACCTTTAGATGATCAGAACTCTTCATCGCGGATGAGCCGTGTCATCCCCGA
1 GGAACCGTGTTATCACTTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCTGA
* ** * **
63358 CCTGATCTCCTCATCACGTAGGTGCCGTGTCACCCCTAGATAACCAGTTGTCCTCATCACGTA
66 CCAGATCTCCTCATCACGTAGGAACCGTGTCAACCCTAGATAACCAGTACTCCTCATCACGTA
*
63421 GGAACCGTGTTATCACTTTTAGATGGCCAGAACGCTTCATCACGTATGAGCCGTGTCATCACCTG
1 GGAACCGTGTTATCACTTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATC-CCTG
* * * *
63486 ACCAGATCTCCTCATCACGTAGGAACCGTGTCAATCCTTGATAACCA-TAACTCTTCATCGCGTA
65 ACCAGATCTCCTCATCACGTAGGAACCGTGTCAACCCTAGATAACCAGT-ACTCCTCATCACGTA
* * * * * *
63550 TGATCCGTGCTATCACCCTTCCTAAAGATGGCGAAGAACTCTTCATCACGTATGAGCAGTGTCAT
1 GGAACCGTGTTATCA--CTT--T-TAGATGGC-CAGAACTCTTCATCACGTATGAGCCGTGTCAT
*
63615 CCCCTGACTAGATCTCCTC
60 -CCCTGACCAGATCTCCTC
63634 GTTATGTAGG
Statistics
Matches: 179, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
128 55 0.31
129 67 0.37
131 3 0.02
133 1 0.01
134 7 0.04
135 45 0.25
136 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (128 bp):
GGAACCGTGTTATCACTTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCTGA
CCAGATCTCCTCATCACGTAGGAACCGTGTCAACCCTAGATAACCAGTACTCCTCATCACGTA
Found at i:63850 original size:3 final size:3
Alignment explanation
Indices: 63842--63893 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
63832 GTCCGGATCG
* * * *
63842 ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ACT ACT ACT ATT ATT AATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
63891 ATT
1 ATT
63894 TATTTTAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:72972 original size:55 final size:56
Alignment explanation
Indices: 72913--73114 Score: 250
Period size: 55 Copynumber: 3.7 Consensus size: 56
72903 AATCAGACCC
*
72913 AGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTTTGAAAA-GAATACTT
1 AGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTTTGAAAATCAATACTT
* * * * * *
72968 AGTTTCTTTGAAAGCTCGTTTAATAATCATGAAGAAACTTCTGAAAATCAA-ACTT
1 AGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTTTGAAAATCAATACTT
* * * *
73023 AGTTTCTTTAAAAACTCATCTGAAAATAATCAAGAAACTTTCGAAAATCAAT-CTT
1 AGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTTTGAAAATCAATACTT
* * *
73078 AGCTTCTTTTAAAATTCATTTAAAAAT-ATCAAGAAAC
1 AGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAAC
73115 CCCTGAAAAT
Statistics
Matches: 123, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
54 10 0.08
55 111 0.90
56 2 0.02
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.34
Consensus pattern (56 bp):
AGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTTTGAAAATCAATACTT
Found at i:73100 original size:110 final size:109
Alignment explanation
Indices: 72913--73138 Score: 274
Period size: 110 Copynumber: 2.1 Consensus size: 109
72903 AATCAGACCC
* * * * *
72913 AGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTTTGAAAAGAATACTTAGTTTCTTTG
1 AGTTTCTTTAAAAACTCATCTAAAAATAATCAAGAAACTTTCGAAAACAATACTTAGCTTCTTTG
* * * * **
72978 AAAGCTCGTTTAATAATCATGAAGAAACTTCTGAAAATCAAACTT
66 AAAACTCATTTAAAAAT-ATCAAGAAACCCCTGAAAATCAAACTT
*
73023 AGTTTCTTTAAAAACTCATCTGAAAATAATCAAGAAACTTTCGAAAATCAAT-CTTAGCTTCTTT
1 AGTTTCTTTAAAAACTCATCTAAAAATAATCAAGAAACTTTCGAAAA-CAATACTTAGCTTCTTT
* * * **
73087 TAAAATTCATTTAAAAATATCAAGAAACCCCTGAAAATTAGGCTT
65 GAAAACTCATTTAAAAATATCAAGAAACCCCTGAAAATCAAACTT
73132 AGTTTCT
1 AGTTTCT
73139 AAAAAAATAG
Statistics
Matches: 98, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
109 28 0.29
110 67 0.68
111 3 0.03
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (109 bp):
AGTTTCTTTAAAAACTCATCTAAAAATAATCAAGAAACTTTCGAAAACAATACTTAGCTTCTTTG
AAAACTCATTTAAAAATATCAAGAAACCCCTGAAAATCAAACTT
Found at i:78763 original size:30 final size:31
Alignment explanation
Indices: 78707--78764 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
78697 GCACAAGACC
*
78707 AGACAAAAAGAAATCGAGTTAATTAAAAACA
1 AGACAAAAAGAAATCAAGTTAATTAAAAACA
* *
78738 AGACAAAAAG-AATTAAGTTAGTTAAAA
1 AGACAAAAAGAAATCAAGTTAATTAAAA
78765 TGATTATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.60, C:0.07, G:0.14, T:0.19
Consensus pattern (31 bp):
AGACAAAAAGAAATCAAGTTAATTAAAAACA
Found at i:92764 original size:5 final size:5
Alignment explanation
Indices: 92748--92783 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
92738 TTTCGCAAAG
* *
92748 ATAAA ATGAA ATAAA ATAAA ATAAA ACAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
92784 GTGAAAAGCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:92768 original size:15 final size:15
Alignment explanation
Indices: 92743--92789 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
92733 CAATTTTTCG
92743 CAAAGATAAAATGAAA
1 CAAA-ATAAAATGAAA
* *
92759 TAAAATAAAATAAAA
1 CAAAATAAAATGAAA
92774 CAAAATAAAAGTGAAA
1 CAAAATAAAA-TGAAA
92790 AGCGGTGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 19 0.73
16 7 0.27
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (15 bp):
CAAAATAAAATGAAA
Found at i:93035 original size:30 final size:30
Alignment explanation
Indices: 93001--93231 Score: 161
Period size: 30 Copynumber: 7.8 Consensus size: 30
92991 CATATTCGAT
93001 TTAAAGGAC-ATAAATAGCAAAAACATAAAC
1 TTAAAGGACTA-AAATAGCAAAAACATAAAC
* * *
93031 TTAAAGGGCTAAAATAG-TAAAACCTAAAAC
1 TTAAAGGACTAAAATAGCAAAAACAT-AAAC
* * * * ** *
93061 TTAAGGGTCTAAAATGGTATTAACAGAAAC
1 TTAAAGGACTAAAATAGCAAAAACATAAAC
* * *
93091 TTAAAGGACTAACAA-AAC-AAAACAAAAAT
1 TTAAAGGACTAA-AATAGCAAAAACATAAAC
*
93120 TTAAAGGAATAAAAT-GCCAAAAAC-TGAAAC
1 TTAAAGGACTAAAATAG-CAAAAACAT-AAAC
* * * * *
93150 TTAAAGGATTAAAATAACTAAAACAGAAAG
1 TTAAAGGACTAAAATAGCAAAAACATAAAC
* * *
93180 TTAAAGGACTAAAATAGAAAAAATATAAAG
1 TTAAAGGACTAAAATAGCAAAAACATAAAC
*
93210 TTAAAGGACTTAAATAG-AAAAA
1 TTAAAGGACTAAAATAGCAAAAA
93232 TAGAAATTTG
Statistics
Matches: 155, Mismatches: 36, Indels: 21
0.73 0.17 0.10
Matches are distributed among these distances:
28 2 0.01
29 30 0.19
30 117 0.75
31 6 0.04
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGCAAAAACATAAAC
Found at i:94897 original size:3 final size:3
Alignment explanation
Indices: 94889--94960 Score: 94
Period size: 3 Copynumber: 24.3 Consensus size: 3
94879 ATATATGATA
* *
94889 AAT AAT AAT AAT AA- ACAT AAT AAT AAT AAT AGT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
94934 AAT AAT AAT AAT AAT AA- ATT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
94961 TTTTTGGTAG
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
2 2 0.03
3 59 0.95
4 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:95606 original size:265 final size:266
Alignment explanation
Indices: 95228--95732 Score: 597
Period size: 265 Copynumber: 1.9 Consensus size: 266
95218 GGGTTTTGGA
* * *
95228 CATCTTTAGGAAGGGAGATAACACGGTTCCTACGCGATAAGGACGACTGGTTATCTTGGGGCGAT
1 CATCTTTAGGAAGGGAGATAACACAGTTCCTACGCGATAAGGACGACTGGTTATCTAGGGGCGAC
* * * * *** *
95293 ACGACTCCTACTTAATGAGGAGGTCTGGTCGAGGGATGGCACAGTTCCTATGTGATGAGGACGGT
66 ACGAATCCTACGTAATGAGGAGGTCTGGTCGAGGGATGACAAAGTTCCTACACGATGAGGACGGC
* *
95358 AGGCCATCTTT-AG-GGATGATAACACGATTCCTACGTGATGAGGACGACAT-GTTATCTAGGGG
131 AGACCATCTTTAAGAGG-TGATAACACGATTCCTACGCGATGAGGACGAC-TGGTTATCTAGGGG
*
95420 TGACACAGCTCCTACACGATGAGGAGGTCTGGTCCGTGGATGACAAAGTTTATATGTAATGAGGA
194 TGACACAGCTCCTACACGATGAGGAGGTCTAGTCCGTGGATGACAAAGTTTATATGTAATGAGGA
95485 TGGCAGGC
259 TGGCAGGC
* * * * *
95493 CATCTTTAGGAATGGTGATAACACAGTTCCTACGTGATGAGGACTGA-TGGTTATCTAGGGGTGA
1 CATCTTTAGGAAGGGAGATAACACAGTTCCTACGCGATAAGGAC-GACTGGTTATCTAGGGGCGA
* * * * * *
95557 CATGAATCCTACGTGATGAGGAGTTCTGGTTG-GTGGATGACAAAGTTCCTACACGATTAGGACT
65 CACGAATCCTACGTAATGAGGAGGTCTGGTCGAG-GGATGACAAAGTTCCTACACGATGAGGACG
* * * * * *
95621 GCATATCATCTTTAAGAATGGTGATAACACGGTTCCTACGCGTTGATGACGTCTGGTTATCTAGG
129 GCAGACCATCTTTAAG-A-GGTGATAACACGATTCCTACGCGATGAGGACGACTGGTTATCTAGG
* * ** *
95686 GGTGACGCGGCTCCTACGTGATGAGGAGGTCTAGTCGGTGGATGACA
192 GGTGACACAGCTCCTACACGATGAGGAGGTCTAGTCCGTGGATGACA
95733 CGGTTCCTAC
Statistics
Matches: 197, Mismatches: 36, Indels: 11
0.81 0.15 0.05
Matches are distributed among these distances:
264 1 0.01
265 111 0.56
266 4 0.02
267 1 0.01
268 78 0.40
269 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (266 bp):
CATCTTTAGGAAGGGAGATAACACAGTTCCTACGCGATAAGGACGACTGGTTATCTAGGGGCGAC
ACGAATCCTACGTAATGAGGAGGTCTGGTCGAGGGATGACAAAGTTCCTACACGATGAGGACGGC
AGACCATCTTTAAGAGGTGATAACACGATTCCTACGCGATGAGGACGACTGGTTATCTAGGGGTG
ACACAGCTCCTACACGATGAGGAGGTCTAGTCCGTGGATGACAAAGTTTATATGTAATGAGGATG
GCAGGC
Found at i:95739 original size:134 final size:134
Alignment explanation
Indices: 95148--95770 Score: 547
Period size: 134 Copynumber: 4.7 Consensus size: 134
95138 GGTCTGTTCG
* * * * * *
95148 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAGT-GGTGGATGAC-ACGTCTCATACG
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACAAAGT-TCCTACA
* * *** * * * * *
95211 TTATGAAGG-GTTTTGGACATCTTTAGGAAGGGAGATAACACGGTTCCTACGCGATAAGGACGAC
65 TGATG-AGGACTGCAGGCCATCTTTAAGAATGGTGATAACACGGTTCCTACGCGATGAGGACGAC
95275 TGGTTA
129 TGGTTA
* * * * * * * **
95281 TCTTGGGGCGATACGACTCCTACTTAATGAGGAGGTCTGGTCGAG-GGATGGCACAGTTCCTATG
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCG-GTGGATGACAAAGTTCCTACA
* * * *
95345 TGATGAGGACGGTAGGCCATCTTT-AG---GGATGATAACACGATTCCTACGTGATGAGGACGAC
65 TGATGAGGACTGCAGGCCATCTTTAAGAATGG-TGATAACACGGTTCCTACGCGATGAGGACGAC
95406 AT-GTTA
129 -TGGTTA
** * *
95412 TCTAGGGGTGACAC-AGCTCCTACACGATGAGGAGGTCTGGTCCGTGGATGACAAAGTT--TATA
1 TCTAGGGGTGACACGA-CTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACAAAGTTCCTACA
* * *
95474 TGTAATGAGGA-TGGCAGGCCATCTTTAGGAATGGTGATAACACAGTTCCTACGTGATGAGGACT
65 TG--ATGAGGACT-GCAGGCCATCTTTAAGAATGGTGATAACACGGTTCCTACGCGATGAGGAC-
95538 GA-TGGTTA
126 GACTGGTTA
* * * * *
95546 TCTAGGGGTGACATGAATCCTACGTGATGAGGAGTTCTGGTTGGTGGATGACAAAGTTCCTACAC
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACAAAGTTCCTACAT
* *** * * *
95611 GATTAGGACTGCATATCATCTTTAAGAATGGTGATAACACGGTTCCTACGCGTTGATGACGTCTG
66 GATGAGGACTGCAGGCCATCTTTAAGAATGGTGATAACACGGTTCCTACGCGATGAGGACGACTG
95676 GTTA
131 GTTA
* * * ** *
95680 TCTAGGGGTGACGCGGCTCCTACGTGATGAGGAGGTCTAGTCGGTGGATGACACGGTTCCTACGT
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACAAAGTTCCTACAT
*
95745 GATGATGAC-GACAGGCCATCTTTAAG
66 GATGAGGACTG-CAGGCCATCTTTAAG
95771 GATGATGGTT
Statistics
Matches: 393, Mismatches: 74, Indels: 45
0.77 0.14 0.09
Matches are distributed among these distances:
129 5 0.01
130 4 0.01
131 96 0.24
132 2 0.01
133 40 0.10
134 233 0.59
135 9 0.02
136 4 0.01
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.26
Consensus pattern (134 bp):
TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACAAAGTTCCTACAT
GATGAGGACTGCAGGCCATCTTTAAGAATGGTGATAACACGGTTCCTACGCGATGAGGACGACTG
GTTA
Found at i:95876 original size:30 final size:30
Alignment explanation
Indices: 95842--95928 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
95832 ATACAAAATA
* * *
95842 TGTTTTAAGGGAAACGACCTCAAAGATGT-T
1 TGTTTCAAGAGAAACGA-CTCAAAGATCTAT
95872 TGTTTCAAGAGAAACAGACTCAAAG-TCTAT
1 TGTTTCAAGAGAAAC-GACTCAAAGATCTAT
*
95902 TGTTTCAAGAGAAACAAACTCAAAGAT
1 TGTTTCAAGAGAAAC-GACTCAAAGAT
95929 TTTTCTTCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
29 2 0.04
30 45 0.90
31 3 0.06
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.26
Consensus pattern (30 bp):
TGTTTCAAGAGAAACGACTCAAAGATCTAT
Found at i:95987 original size:34 final size:35
Alignment explanation
Indices: 95922--95987 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
95912 GAAACAAACT
*
95922 CAAAGATTTTTCTTCAAAAGAAACTATCTCAAGAA
1 CAAAGATTTTTCTTCAAAAGAAACTAACTCAAGAA
* *
95957 CAAA-ATTTTTTTTCCAAAGAAA-TAAACTCAA
1 CAAAGATTTTTCTTCAAAAGAAACT-AACTCAA
95988 AGATAGGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 1 0.04
34 22 0.81
35 4 0.15
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (35 bp):
CAAAGATTTTTCTTCAAAAGAAACTAACTCAAGAA
Found at i:98359 original size:104 final size:104
Alignment explanation
Indices: 98179--98390 Score: 415
Period size: 104 Copynumber: 2.0 Consensus size: 104
98169 CAATGCTCTC
*
98179 AATGCAAGTATAGAGGCAATGCCCCCATTATTCTTCGATTGTCCATGCCCCTGAATCCATCAGGT
1 AATGCAAGTATAGAGGCAATGCCCCCATCATTCTTCGATTGTCCATGCCCCTGAATCCATCAGGT
98244 TATAGATCTTGCACTTCAGTGCCTTACAGTTTTCAATGG
66 TATAGATCTTGCACTTCAGTGCCTTACAGTTTTCAATGG
98283 AATGCAAGTATAGAGGCAATGCCCCCATCATTCTTCGATTGTCCATGCCCCTGAATCCATCAGGT
1 AATGCAAGTATAGAGGCAATGCCCCCATCATTCTTCGATTGTCCATGCCCCTGAATCCATCAGGT
98348 TATAGATCTTGCACTTCAGTGCCTTACAGTTTTCAATGG
66 TATAGATCTTGCACTTCAGTGCCTTACAGTTTTCAATGG
98387 AATG
1 AATG
98391 TCTGGATCTT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 107 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (104 bp):
AATGCAAGTATAGAGGCAATGCCCCCATCATTCTTCGATTGTCCATGCCCCTGAATCCATCAGGT
TATAGATCTTGCACTTCAGTGCCTTACAGTTTTCAATGG
Found at i:99385 original size:20 final size:19
Alignment explanation
Indices: 99356--99395 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
99346 AAATCATTTC
*
99356 ATTAGTTCTTATGCATTCAT
1 ATTAGCTCTTATGC-TTCAT
99376 ATTAGCTCTTATGCTTCAT
1 ATTAGCTCTTATGCTTCAT
99395 A
1 A
99396 CATTATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (19 bp):
ATTAGCTCTTATGCTTCAT
Found at i:105580 original size:29 final size:28
Alignment explanation
Indices: 105543--105631 Score: 74
Period size: 28 Copynumber: 3.0 Consensus size: 28
105533 TTCACACTTT
105543 TGTTGTTTTTTTTCCATTTTTTTTCTTTCA
1 TGTT-TTTTTTTTCC-TTTTTTTTCTTTCA
***
105573 TG-TTTTTTTTTCTCTTTTTCTTTCGAACAA
1 TGTTTTTTTTTTC-CTTTTT-TTTCTTTC-A
*
105603 CT-TTTTTTTTTTCTTTTTTTTTCTTTCA
1 -TGTTTTTTTTTTCCTTTTTTTTCTTTCA
105631 T
1 T
105632 TCAACATTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
27 1 0.02
28 15 0.32
29 12 0.26
30 8 0.17
31 11 0.23
ACGTcount: A:0.08, C:0.15, G:0.04, T:0.73
Consensus pattern (28 bp):
TGTTTTTTTTTTCCTTTTTTTTCTTTCA
Found at i:105642 original size:33 final size:31
Alignment explanation
Indices: 105575--105644 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 31
105565 TTCTTTCATG
*
105575 TTTTTTTTTCTCTTTTTCTTTCGAACAACTT
1 TTTTTTTTTCTCTTTTTCTTTCGAACAACAT
* *
105606 TTTTTTTTTCTTTTTTTTTCTTTC-ATTCAACAT
1 TTTTTTTTTC--TCTTTTTCTTTCGA-ACAACAT
105639 TTTTTT
1 TTTTTT
105645 GATAGAGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 10 0.30
32 1 0.03
33 22 0.67
ACGTcount: A:0.11, C:0.16, G:0.01, T:0.71
Consensus pattern (31 bp):
TTTTTTTTTCTCTTTTTCTTTCGAACAACAT
Found at i:114523 original size:3 final size:3
Alignment explanation
Indices: 114515--114555 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
114505 TATTTTATTT
*
114515 ATA ATA ATA GTA ATAA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
114556 AGTCGGGACG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:117419 original size:12 final size:11
Alignment explanation
Indices: 117402--117454 Score: 61
Period size: 12 Copynumber: 4.6 Consensus size: 11
117392 TTCGAGCTTG
117402 AATCGAGCTCAC
1 AATCGAGCT-AC
*
117414 AATCGAGCTTC
1 AATCGAGCTAC
*
117425 AATCGAGCTCAA
1 AATCGAGCT-AC
*
117437 AATCGAGCTTC
1 AATCGAGCTAC
117448 AATCGAG
1 AATCGAG
117455 TCTCGAGCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
11 17 0.49
12 18 0.51
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (11 bp):
AATCGAGCTAC
Found at i:117422 original size:23 final size:23
Alignment explanation
Indices: 117393--117454 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
117383 CGAGCTTAAT
* *
117393 TCGAGCTTGAATCGAGCTCACAA
1 TCGAGCTTCAATCGAGCTCAAAA
117416 TCGAGCTTCAATCGAGCTCAAAA
1 TCGAGCTTCAATCGAGCTCAAAA
117439 TCGAGCTTCAATCGAG
1 TCGAGCTTCAATCGAG
117455 TCTCGAGCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
TCGAGCTTCAATCGAGCTCAAAA
Found at i:117471 original size:11 final size:11
Alignment explanation
Indices: 117382--117454 Score: 78
Period size: 11 Copynumber: 6.5 Consensus size: 11
117372 TAACCCATCC
117382 TCGAGCTT-AA
1 TCGAGCTTCAA
*
117392 TTCGAGCTTGAA
1 -TCGAGCTTCAA
*
117404 TCGAGCTCACAA
1 TCGAGCT-TCAA
117416 TCGAGCTTCAA
1 TCGAGCTTCAA
117427 TCGAGC-TCAAAA
1 TCGAGCTTC--AA
117439 TCGAGCTTCAA
1 TCGAGCTTCAA
117450 TCGAG
1 TCGAG
117455 TCTCGAGCTT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
10 2 0.04
11 31 0.57
12 19 0.35
13 2 0.04
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (11 bp):
TCGAGCTTCAA
Found at i:118160 original size:35 final size:36
Alignment explanation
Indices: 118114--118214 Score: 123
Period size: 35 Copynumber: 2.8 Consensus size: 36
118104 ACATCACCTA
**
118114 TAAATACAAATATATTATTACAAATTT-TATTTGAT
1 TAAATACAAATATATTATTACAAATTTATATTCAAT
***
118149 TAAATACAAATATATTATTTATGGATTTATATTCAAT
1 TAAATACAAATATATTA-TTACAAATTTATATTCAAT
*
118186 TAAAATACGAATATATTATTACAAATTTA
1 T-AAATACAAATATATTATTACAAATTTA
118215 AATTTAAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
35 17 0.31
36 7 0.13
37 15 0.28
38 15 0.28
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
TAAATACAAATATATTATTACAAATTTATATTCAAT
Found at i:118231 original size:37 final size:36
Alignment explanation
Indices: 118114--118230 Score: 128
Period size: 37 Copynumber: 3.2 Consensus size: 36
118104 ACATCACCTA
*
118114 TAAATACAAATATATTATTACAAATTT-TATTTGAT
1 TAAATACAAATATATTATTACAAATTTATATTTAAT
*** *
118149 TAAATACAAATATATTATTTATGGATTTATATTCAAT
1 TAAATACAAATATATTA-TTACAAATTTATATTTAAT
* * *
118186 TAAAATACGAATATATTATTACAAATTTAAATTTAAA
1 T-AAATACAAATATATTATTACAAATTTATATTTAAT
118223 TACAATAC
1 TA-AATAC
118231 GGTGATGTAG
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
35 17 0.26
36 8 0.12
37 26 0.39
38 15 0.23
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (36 bp):
TAAATACAAATATATTATTACAAATTTATATTTAAT
Found at i:122673 original size:36 final size:36
Alignment explanation
Indices: 122626--122695 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
122616 AAATTCTAAA
122626 GTGTACCGATACACCATGCAATGTATCCATACACTG
1 GTGTACCGATACACCATGCAATGTATCCATACACTG
* * *
122662 GTGTACCGATACACCCTGTAGTGTATCCATACAC
1 GTGTACCGATACACCATGCAATGTATCCATACAC
122696 CTTTGACCGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (36 bp):
GTGTACCGATACACCATGCAATGTATCCATACACTG
Found at i:122693 original size:20 final size:19
Alignment explanation
Indices: 122625--122696 Score: 55
Period size: 20 Copynumber: 3.8 Consensus size: 19
122615 AAAATTCTAA
*
122625 AGTGTACCGATACACCATG
1 AGTGTACCGATACACCCTG
*
122644 CAATGTATCC-ATACA--CTG
1 -AGTGTA-CCGATACACCCTG
122662 -GTGTACCGATACACCCTG
1 AGTGTACCGATACACCCTG
122680 TAGTGTATCC-ATACACC
1 -AGTGTA-CCGATACACC
122697 TTTGACCGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
15 2 0.05
16 9 0.21
18 5 0.12
20 22 0.52
21 4 0.10
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (19 bp):
AGTGTACCGATACACCCTG
Found at i:125856 original size:30 final size:28
Alignment explanation
Indices: 125822--125881 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
125812 AGGGGGAGCT
*
125822 TAACATTTTCATATATTTTCCAACAATTGG
1 TAACAATTT-ATATATTTT-CAACAATTGG
* * *
125852 TAACAATTTGTATCTTTTTAACAATTGG
1 TAACAATTTATATATTTTCAACAATTGG
125880 TA
1 TA
125882 TCTTTTTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 11 0.42
29 7 0.27
30 8 0.31
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.45
Consensus pattern (28 bp):
TAACAATTTATATATTTTCAACAATTGG
Found at i:125875 original size:18 final size:18
Alignment explanation
Indices: 125852--125927 Score: 100
Period size: 18 Copynumber: 4.1 Consensus size: 18
125842 CAACAATTGG
125852 TAACAATTTGTATCTTTT
1 TAACAATTTGTATCTTTT
*
125870 TAACAATTGGTATCTTTT
1 TAACAATTTGTATCTTTT
125888 TAACAA-TTGATATCCTTTTGT
1 TAACAATTTG-TAT-C-TTT-T
125909 TAACAATTTGTATCTTTT
1 TAACAATTTGTATCTTTT
125927 T
1 T
125928 CATTAAACAT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
17 2 0.04
18 28 0.55
19 4 0.08
20 4 0.08
21 10 0.20
22 3 0.06
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.53
Consensus pattern (18 bp):
TAACAATTTGTATCTTTT
Found at i:126185 original size:35 final size:36
Alignment explanation
Indices: 126139--126207 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
126129 AAATTCTAAA
* *
126139 GTGTACTGATACA-CCAGCAGTGTATCCATACACTG
1 GTGTACCGATACACCCAGCAGTATATCCATACACTG
* *
126174 GTGTACCGATACACCCTGCAGTATATCTATACAC
1 GTGTACCGATACACCCAGCAGTATATCCATACAC
126208 CTTTGATTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 12 0.41
36 17 0.59
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (36 bp):
GTGTACCGATACACCCAGCAGTATATCCATACACTG
Found at i:127046 original size:22 final size:22
Alignment explanation
Indices: 127018--127065 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
127008 CAGAGGTGGA
127018 AGTGGTCCCCTGAGTAGCTGGT
1 AGTGGTCCCCTGAGTAGCTGGT
127040 AGTGGTCCCCTGAGTAGCTGGT
1 AGTGGTCCCCTGAGTAGCTGGT
127062 AGTG
1 AGTG
127066 TTCCAACCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.15, C:0.21, G:0.38, T:0.27
Consensus pattern (22 bp):
AGTGGTCCCCTGAGTAGCTGGT
Found at i:136286 original size:42 final size:42
Alignment explanation
Indices: 136215--136305 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
136205 CCTTAAGGAA
* *
136215 CACATTATATATTCCAATGGATCAAATATATGTCCTGAAGAAC
1 CACA-TATATATTCCAAAGGATCAAATATATATCCTGAAGAAC
* * * * *
136258 CGCATATATGTTCCAAAGGATTACATATATATCCTGAAGGAC
1 CACATATATATTCCAAAGGATCAAATATATATCCTGAAGAAC
136300 CACATA
1 CACATA
136306 GAACCCTCGA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 37 0.93
43 3 0.08
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (42 bp):
CACATATATATTCCAAAGGATCAAATATATATCCTGAAGAAC
Found at i:136304 original size:21 final size:21
Alignment explanation
Indices: 136240--136305 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
136230 AATGGATCAA
* * *
136240 ATATATGTCCTGAAGAACCGC
1 ATATATATCCTGAAGGACCAC
* * **
136261 ATATATGTTCC-AAAGGATTAC
1 ATATAT-ATCCTGAAGGACCAC
136282 ATATATATCCTGAAGGACCAC
1 ATATATATCCTGAAGGACCAC
136303 ATA
1 ATA
136306 GAACCCTCGA
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
20 3 0.09
21 27 0.82
22 3 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (21 bp):
ATATATATCCTGAAGGACCAC
Found at i:143220 original size:21 final size:21
Alignment explanation
Indices: 143191--143246 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
143181 ATAGAATTTG
*
143191 TCCCGAAGGACCACATATATA
1 TCCCGAAGGACCACATAAATA
* * *
143212 TCCCAAAGGATCACATAAATG
1 TCCCGAAGGACCACATAAATA
143233 TCCCGAAGGACCAC
1 TCCCGAAGGACCAC
143247 TCCTTAAGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.30, G:0.16, T:0.16
Consensus pattern (21 bp):
TCCCGAAGGACCACATAAATA
Found at i:145236 original size:21 final size:21
Alignment explanation
Indices: 145212--145251 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
145202 CCGAAGGACG
* *
145212 ACATATATATCCCGAATGATC
1 ACATAAATATCACGAATGATC
*
145233 ACATAAATGTCACGAATGA
1 ACATAAATATCACGAATGA
145252 CCACTCTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (21 bp):
ACATAAATATCACGAATGATC
Found at i:150706 original size:38 final size:38
Alignment explanation
Indices: 150664--150748 Score: 116
Period size: 38 Copynumber: 2.2 Consensus size: 38
150654 TTATTAAAGG
** * *
150664 ATTTATATTCAATTGAAATTCGAATATGTTATTTACGA
1 ATTTATATTCAATTGAAATAAGAAAATGTTATTTACAA
* *
150702 ATTTATATTCTATTGAAATAAGAAAATGTTATTTATAA
1 ATTTATATTCAATTGAAATAAGAAAATGTTATTTACAA
150740 ATTTATATT
1 ATTTATATT
150749 TGATTAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (38 bp):
ATTTATATTCAATTGAAATAAGAAAATGTTATTTACAA
Found at i:151659 original size:2 final size:2
Alignment explanation
Indices: 151654--151689 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
151644 TAAGTGTGTG
151654 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
151690 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:151694 original size:2 final size:2
Alignment explanation
Indices: 151689--151716 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
151679 ATATATATAT
151689 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
151717 GATGGTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:162003 original size:34 final size:34
Alignment explanation
Indices: 161960--162030 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
161950 ACACAACCAA
*
161960 GAATGACAAAGACGATGAAGAGGAGGTCGAATAT
1 GAATGACAAAGACGATGAAGAGGAGGTCAAATAT
161994 GAATGACAAAGACGATGAAGAGGAGGTCAAATAT
1 GAATGACAAAGACGATGAAGAGGAGGTCAAATAT
162028 GAA
1 GAA
162031 AAGGTATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.46, C:0.08, G:0.31, T:0.14
Consensus pattern (34 bp):
GAATGACAAAGACGATGAAGAGGAGGTCAAATAT
Found at i:164145 original size:17 final size:17
Alignment explanation
Indices: 164123--164177 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
164113 TTTGATAATT
164123 AAAATTGTTGGATCTTG
1 AAAATTGTTGGATCTTG
* ** *
164140 AAAATT-ATAAATCAT-
1 AAAATTGTTGGATCTTG
164155 AAAATTGTTGGATCTTG
1 AAAATTGTTGGATCTTG
164172 AAAATT
1 AAAATT
164178 AAAAATCATA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
15 6 0.21
16 10 0.36
17 12 0.43
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (17 bp):
AAAATTGTTGGATCTTG
Found at i:164158 original size:32 final size:32
Alignment explanation
Indices: 164122--164189 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
164112 TTTTGATAAT
*
164122 TAAAATTGTTGGATCTTGAAAATTATAAATCA
1 TAAAATTGTTGGATCTTGAAAATTAAAAATCA
164154 TAAAATTGTTGGATCTTGAAAATTAAAAATCA
1 TAAAATTGTTGGATCTTGAAAATTAAAAATCA
164186 TAAA
1 TAAA
164190 TTTTAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (32 bp):
TAAAATTGTTGGATCTTGAAAATTAAAAATCA
Found at i:164309 original size:20 final size:19
Alignment explanation
Indices: 164255--164311 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
164245 TAACAAATTC
164255 ATAAAGTTATAATTTTAAAA
1 ATAAA-TTATAATTTTAAAA
**
164275 ATTATTTTATAATTTTAAAA
1 A-TAAATTATAATTTTAAAA
164295 ATAAATTATACATTTTA
1 ATAAATTATA-ATTTTA
164312 TACATTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 7 0.23
20 22 0.71
21 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
ATAAATTATAATTTTAAAA
Found at i:165640 original size:17 final size:16
Alignment explanation
Indices: 165618--165651 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
165608 ATTTGTCATC
165618 ACTTAAAAAATATATTA
1 ACTTAAAAAATAT-TTA
*
165635 ACTTAAAATATATTTA
1 ACTTAAAAAATATTTA
165651 A
1 A
165652 ATATTTTATT
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:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ACTTAAAAAATATTTA
Found at i:165705 original size:29 final size:29
Alignment explanation
Indices: 165673--165770 Score: 101
Period size: 29 Copynumber: 3.3 Consensus size: 29
165663 TTAATTTAAT
* *
165673 ATATATATTACTATTATCTTTACTTAAAA
1 ATATATATTATTATTATCTTAACTTAAAA
* * *
165702 ATATATTTTATTCTTAT-TTCAAATTAAAA
1 ATATATATTATTATTATCTT-AACTTAAAA
*
165731 ATATATTTTATTATTATCTTAACTTTTAAAA
1 ATATATATTATTATTATCTTAAC--TTAAAA
165762 A-ATATATTA
1 ATATATATTA
165771 AAATATATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.04
29 39 0.68
30 9 0.16
31 7 0.12
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (29 bp):
ATATATATTATTATTATCTTAACTTAAAA
Found at i:165804 original size:62 final size:61
Alignment explanation
Indices: 165731--165849 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 61
165721 CAAATTAAAA
* *
165731 ATATATTTTATTATTATCTTAACTT-TTAAAAAATATATTAAAATATATAATTTTAAGTTAAG
1 ATATATTTTATTATTATCTTAAATTATAAAAAAATATATTAAAA-ATAT-ATTTTAAGTTAAG
* *
165793 ATATATTTTATTCTTATTTTAAATTAAGATAAAAAAATATATTAAAAATATATTTTA
1 ATATATTTTATTATTATCTTAAATT---ATAAAAAAATATATTAAAAATATATTTTA
165850 TTATTATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
62 22 0.45
64 6 0.12
65 4 0.08
66 17 0.35
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (61 bp):
ATATATTTTATTATTATCTTAAATTATAAAAAAATATATTAAAAATATATTTTAAGTTAAG
Found at i:166158 original size:16 final size:16
Alignment explanation
Indices: 166137--166170 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
166127 ACCCTTTGAT
166137 ATGTTTTTGACAACAA
1 ATGTTTTTGACAACAA
* *
166153 ATGTTTTTTACAATAA
1 ATGTTTTTGACAACAA
166169 AT
1 AT
166171 TTAAAGAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (16 bp):
ATGTTTTTGACAACAA
Found at i:166383 original size:19 final size:20
Alignment explanation
Indices: 166341--166383 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
166331 AAAATCGGGT
*
166341 GTTTTTAATAAAATATTTTA
1 GTTTTTAATAAAATATTTGA
*
166361 -TTTTTATTAAAATA-TTGA
1 GTTTTTAATAAAATATTTGA
166379 GTTTT
1 GTTTT
166384 AGGGTCTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (20 bp):
GTTTTTAATAAAATATTTGA
Found at i:168950 original size:29 final size:24
Alignment explanation
Indices: 168883--168945 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
168873 TTGGGCCCCA
168883 GGTCGGGTCTTGGTTTTAGCCTCG
1 GGTCGGGTCTTGGTTTTAGCCTCG
168907 GGTCGGGTCTTGGTTTTAGCCTCG
1 GGTCGGGTCTTGGTTTTAGCCTCG
168931 GGTCGGGTC-TGGTTT
1 GGTCGGGTCTTGGTTT
168946 GGGTTCCGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
23 6 0.15
24 33 0.85
ACGTcount: A:0.03, C:0.19, G:0.40, T:0.38
Consensus pattern (24 bp):
GGTCGGGTCTTGGTTTTAGCCTCG
Found at i:169183 original size:43 final size:44
Alignment explanation
Indices: 169106--169191 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 44
169096 GTAATTACAC
* * *
169106 TATTAAAATATAAGAACTAAAATAATAGTAAATATATTTTAACA
1 TATTAAAATATAAGAACTAAAATAAGAGAAAATATATATTAACA
169150 TATT-AAATAATAAGAA-TAAAATAAGA-AACAATATATATTAAC
1 TATTAAAAT-ATAAGAACTAAAATAAGAGAA-AATATATATTAAC
169192 TTAAAAGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 1 0.03
43 25 0.68
44 11 0.30
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (44 bp):
TATTAAAATATAAGAACTAAAATAAGAGAAAATATATATTAACA
Found at i:169257 original size:28 final size:28
Alignment explanation
Indices: 169226--169343 Score: 87
Period size: 28 Copynumber: 4.1 Consensus size: 28
169216 TAATATATTG
169226 TATCTTAATTTAAAATAAGAATAAAATA
1 TATCTTAATTTAAAATAAGAATAAAATA
* * * * **
169254 TATCTTCACTTATAAAT-ATATTTTAATA
1 TATCTTAATTTA-AAATAAGAATAAAATA
* * *
169282 TATTTTTAAAATTTAAGATAATAATAAAATA
1 TA-TCTT--AATTTAAAATAAGAATAAAATA
*
169313 TATTTTAATTTGAAAA-AAGAATAAAATA
1 TATCTTAATTT-AAAATAAGAATAAAATA
169341 TAT
1 TAT
169344 TTTTAAGTAA
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
28 38 0.55
29 10 0.14
30 7 0.10
31 14 0.20
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (28 bp):
TATCTTAATTTAAAATAAGAATAAAATA
Found at i:169316 original size:31 final size:29
Alignment explanation
Indices: 169230--169498 Score: 115
Period size: 31 Copynumber: 9.0 Consensus size: 29
169220 ATATTGTATC
* * *
169230 TTAATTTAAAATAAGAATAAAATATATCT
1 TTAATTTAAGATAATAATAAAATATATTT
* * * **
169259 TCACTTATAA-AT-ATATTTTAATATATTT
1 TTAATT-TAAGATAATAATAAAATATATTT
169287 TTAAAATTTAAGATAATAATAAAATATA-TT
1 TT--AATTTAAGATAATAATAAAATATATTT
* *
169317 TTAATTTGAA-AAAAGAATAAAATATATTT
1 TTAATTT-AAGATAATAATAAAATATATTT
* * *
169346 TTAAGTAAAGATAATAGTAATATATATATTTT
1 TTAATTTAAGATAATAATAA-A-ATATA-TTT
* *
169378 TTAAATTAATAATAA-AATATTTAAATAT-TTT
1 TTAATTTAA-GATAATAATA---AAATATATTT
* * **
169409 TTAAGTTAAGATATTTTTAAAAATATATTT
1 TTAATTTAAGATAATAAT-AAAATATATTT
* * *
169439 TGTAAGTGATGATAA-AGATAAAATATATATTT
1 T-TAATTTAAGATAATA-AT-AAA-ATATATTT
*
169471 TTACA-TTAAAATAA-AATAAAATATATTT
1 TTA-ATTTAAGATAATAATAAAATATATTT
169499 AACAAGTTAA
Statistics
Matches: 182, Mismatches: 36, Indels: 45
0.69 0.14 0.17
Matches are distributed among these distances:
28 41 0.23
29 34 0.19
30 22 0.12
31 51 0.28
32 24 0.13
33 8 0.04
34 1 0.01
35 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.43
Consensus pattern (29 bp):
TTAATTTAAGATAATAATAAAATATATTT
Found at i:170449 original size:29 final size:29
Alignment explanation
Indices: 170365--170452 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
170355 CCAAAATTTT
* *
170365 ATTTGAAAATTATTAACCGAACCAAATTA
1 ATTTGAAAATTATTAACAGAACCGAATTA
**
170394 ATTTGAAAATTATTAATTGAACCGAATTA
1 ATTTGAAAATTATTAACAGAACCGAATTA
* *
170423 ATTTAAAAATTATTAACAGAACTGAATTA
1 ATTTGAAAATTATTAACAGAACCGAATTA
170452 A
1 A
170453 CCAATGGTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34
Consensus pattern (29 bp):
ATTTGAAAATTATTAACAGAACCGAATTA
Found at i:170851 original size:55 final size:58
Alignment explanation
Indices: 170770--170889 Score: 183
Period size: 55 Copynumber: 2.1 Consensus size: 58
170760 AATCGGACCA
*
170770 AAATTTATTTGAAAATTATTAACTGAACCGAATT-A-TTGAAAATTATTAAC-GAACC
1 AAATTAATTTGAAAATTATTAACTGAACCGAATTAATTTGAAAATTATTAACAGAACC
* * *
170825 AAATTAATTTGAAAATTATTAACTGAACCGGATTAATTTGAAAGTTATTAACAGAACT
1 AAATTAATTTGAAAATTATTAACTGAACCGAATTAATTTGAAAATTATTAACAGAACC
170883 AAATTAA
1 AAATTAA
170890 CAATTTTTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
55 32 0.55
56 1 0.02
57 14 0.24
58 11 0.19
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (58 bp):
AAATTAATTTGAAAATTATTAACTGAACCGAATTAATTTGAAAATTATTAACAGAACC
Found at i:170862 original size:29 final size:29
Alignment explanation
Indices: 170771--170881 Score: 156
Period size: 29 Copynumber: 3.9 Consensus size: 29
170761 ATCGGACCAA
*
170771 AATTTATTTGAAAATTATTAACTGAACCG
1 AATTAATTTGAAAATTATTAACTGAACCG
*
170800 AATT-A-TTGAAAATTATTAAC-GAACCA
1 AATTAATTTGAAAATTATTAACTGAACCG
170826 AATTAATTTGAAAATTATTAACTGAACCG
1 AATTAATTTGAAAATTATTAACTGAACCG
* * *
170855 GATTAATTTGAAAGTTATTAACAGAAC
1 AATTAATTTGAAAATTATTAACTGAAC
170882 TAAATTAACA
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
26 9 0.12
27 16 0.22
28 16 0.22
29 33 0.45
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACTGAACCG
Found at i:170990 original size:29 final size:29
Alignment explanation
Indices: 170953--171010 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
170943 TGGTTCGGTT
170953 ATTTAAAAATTATTAACCA-AACCGAATTA
1 ATTTAAAAATTATTAA-CATAACCGAATTA
*
170982 ATTTGAAAATTATTAACATAACCGAATTA
1 ATTTAAAAATTATTAACATAACCGAATTA
171011 GCCGATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (29 bp):
ATTTAAAAATTATTAACATAACCGAATTA
Found at i:171010 original size:122 final size:124
Alignment explanation
Indices: 170831--171055 Score: 292
Period size: 122 Copynumber: 1.8 Consensus size: 124
170821 AACCAAATTA
* ** * * *
170831 ATTTGAAAATTATTAACTGAACCGGATTAATTTGAAAGTTATTAACAGAACTAAATTA-ACAATT
1 ATTTAAAAATTATTAACCAAACCGAATTAATTTGAAAATTATTAACAGAACCAAATTAGACAATT
** *
170895 TTTT-TTAAATTATTAACCAAATTAATCGAAGCAAAATTTTGGTTAATTTGGTTCGGTT
66 TTTTAAAAAATTATTAACCAAATTAATCGAAGAAAAATTTTGGTTAATTTGGTTCGGTT
* * * *
170953 ATTTAAAAATTATTAACCAAACCGAATTAATTTGAAAATTATTAACATAACCGAATTAGCCGATT
1 ATTTAAAAATTATTAACCAAACCGAATTAATTTGAAAATTATTAACAGAACCAAATTAGACAATT
* *
171018 TTTTAAAAAAATTATTAATCGAATTAATCGAAGAAAAA
66 TTTT-AAAAAATTATTAACCAAATTAATCGAAGAAAAA
171056 AATCGGTTTG
Statistics
Matches: 85, Mismatches: 15, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
122 50 0.59
123 8 0.09
125 27 0.32
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (124 bp):
ATTTAAAAATTATTAACCAAACCGAATTAATTTGAAAATTATTAACAGAACCAAATTAGACAATT
TTTTAAAAAATTATTAACCAAATTAATCGAAGAAAAATTTTGGTTAATTTGGTTCGGTT
Found at i:171101 original size:29 final size:30
Alignment explanation
Indices: 171067--171142 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
171057 ATCGGTTTGG
*
171067 TTAATCGAACCGAAATTTATTT-AAAATCA
1 TTAATCGAACCGAAATTAATTTGAAAATCA
* *
171096 TTAATCGAATCG-AATTAATTTGAAAATTA
1 TTAATCGAACCGAAATTAATTTGAAAATCA
*
171125 TTAACCGAACCG-AATTAA
1 TTAATCGAACCGAAATTAA
171143 CCGATTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
28 8 0.20
29 33 0.80
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (30 bp):
TTAATCGAACCGAAATTAATTTGAAAATCA
Found at i:175414 original size:26 final size:27
Alignment explanation
Indices: 175385--175436 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
175375 GGATTTATAG
175385 AAATG-CCCTAAAGTGTAAAATGACTA
1 AAATGCCCCTAAAGTGTAAAATGACTA
175411 AAATGCCCCTAAAGTGTAAAATGACT
1 AAATGCCCCTAAAGTGTAAAATGACT
175437 TAAAGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.23
Consensus pattern (27 bp):
AAATGCCCCTAAAGTGTAAAATGACTA
Found at i:179419 original size:17 final size:17
Alignment explanation
Indices: 179399--179438 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
179389 ATTTCAAAGT
179399 TATAATTATATAAAAAA
1 TATAATTATATAAAAAA
* * *
179416 TATATTTATATATAACA
1 TATAATTATATAAAAAA
179433 TATAAT
1 TATAAT
179439 AAAATTTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAATTATATAAAAAA
Found at i:179581 original size:21 final size:21
Alignment explanation
Indices: 179557--179596 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
179547 TAATAGATTA
179557 ATATATAATTTTAAAAATAGG
1 ATATATAATTTTAAAAATAGG
* * *
179578 ATATTTATTTTTTAAAATA
1 ATATATAATTTTAAAAATA
179597 TCAGAAAATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
ATATATAATTTTAAAAATAGG
Found at i:179684 original size:2 final size:2
Alignment explanation
Indices: 179677--179707 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
179667 AAACATTAAA
179677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
179708 ATTTATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:180298 original size:2 final size:2
Alignment explanation
Indices: 180291--180355 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
180281 TTTATCATAA
180291 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
180333 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
180356 CATAGGTAGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:181526 original size:3 final size:3
Alignment explanation
Indices: 181518--181563 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
181508 ATTTTTTATT
* * *
181518 TAA TAA TAA CAT TATA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
181564 ATATGATGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
3 34 0.94
4 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:181537 original size:16 final size:15
Alignment explanation
Indices: 181517--181557 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
181507 TATTTTTTAT
181517 TTAATAATAACATTA
1 TTAATAATAACATTA
* *
181532 TATAATAATAATAATA
1 T-TAATAATAACATTA
181548 TTAATAATAA
1 TTAATAATAA
181558 TAATAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAATAATAACATTA
Found at i:182471 original size:3 final size:3
Alignment explanation
Indices: 182463--182539 Score: 147
Period size: 3 Copynumber: 26.0 Consensus size: 3
182453 GGTCTACAAA
182463 ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
182510 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
182540 TATTCTAATT
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 71 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:183169 original size:19 final size:19
Alignment explanation
Indices: 183145--183210 Score: 114
Period size: 19 Copynumber: 3.4 Consensus size: 19
183135 GAGATCATGG
183145 AGAGAGAATCGAATAAAAA
1 AGAGAGAATCGAATAAAAA
183164 AGAGAGAATCGAATAAAAAA
1 AGAGAGAATCGAAT-AAAAA
183184 AGAGAGAATCGAATAAAAA
1 AGAGAGAATCGAATAAAAA
*
183203 TGAGAGAA
1 AGAGAGAA
183211 CAAATCGAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 26 0.58
20 19 0.42
ACGTcount: A:0.62, C:0.05, G:0.23, T:0.11
Consensus pattern (19 bp):
AGAGAGAATCGAATAAAAA
Found at i:183184 original size:20 final size:20
Alignment explanation
Indices: 183145--183202 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
183135 GAGATCATGG
183145 AGAGAGAATCGAAT-AAAAA
1 AGAGAGAATCGAATAAAAAA
183164 AGAGAGAATCGAATAAAAAA
1 AGAGAGAATCGAATAAAAAA
183184 AGAGAGAATCGAATAAAAA
1 AGAGAGAATCGAATAAAAA
183203 TGAGAGAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 14 0.37
20 24 0.63
ACGTcount: A:0.64, C:0.05, G:0.21, T:0.10
Consensus pattern (20 bp):
AGAGAGAATCGAATAAAAAA
Found at i:184096 original size:30 final size:30
Alignment explanation
Indices: 184041--184184 Score: 178
Period size: 29 Copynumber: 5.0 Consensus size: 30
184031 GGTTTATTTG
184041 TTTTTTCTATTTTAGTCCTTT-AATTT-TA
1 TTTTTTCTATTTTAGTCCTTTAAATTTCTA
184069 TTTTTTTCTATTTTAGTCCTTTAAATTTCTA
1 -TTTTTTCTATTTTAGTCCTTTAAATTTCTA
* *
184100 -TTTTTCTATTTTAGCCCTATAAATTTCTA
1 TTTTTTCTATTTTAGTCCTTTAAATTTCTA
**
184129 TTTTAGCTATTTTAGTCCTTTAAATTTC--
1 TTTTTTCTATTTTAGTCCTTTAAATTTCTA
*
184157 -TTTTT-T-TTTTAGTCCTTTAAGTTTCTA
1 TTTTTTCTATTTTAGTCCTTTAAATTTCTA
184184 T
1 T
184185 AATTTTTATT
Statistics
Matches: 100, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
25 18 0.18
26 1 0.01
27 3 0.03
29 48 0.48
30 28 0.28
31 2 0.02
ACGTcount: A:0.19, C:0.13, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTTTTCTATTTTAGTCCTTTAAATTTCTA
Found at i:184190 original size:25 final size:25
Alignment explanation
Indices: 184138--184192 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
184128 ATTTTAGCTA
* **
184138 TTTTAGTCCTTTAAATTTCTTTTTT
1 TTTTAGTCCTTTAAATTTCTATAAT
*
184163 TTTTAGTCCTTTAAGTTTCTATAAT
1 TTTTAGTCCTTTAAATTTCTATAAT
184188 TTTTA
1 TTTTA
184193 TTTCGGTCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.05, T:0.64
Consensus pattern (25 bp):
TTTTAGTCCTTTAAATTTCTATAAT
Found at i:184192 original size:59 final size:60
Alignment explanation
Indices: 184042--184192 Score: 176
Period size: 59 Copynumber: 2.6 Consensus size: 60
184032 GTTTATTTGT
*
184042 TTTTTCTATTTTAGTCCTTTAATTT-TAT-TTTTT-TCTATTTTAGTCCTTTAAATTTCTA
1 TTTTTCTATTTTAGTCCTTTAATTTCTATATTTTTAGCTATTTTAGTCCTTTAAATTTC-A
* *
184100 TTTTTCTATTTTAGCCCTATAAATTTC--TA-TTTTAGCTATTTTAGTCCTTTAAATTTC-
1 TTTTTCTATTTTAGTCCT-TTAATTTCTATATTTTTAGCTATTTTAGTCCTTTAAATTTCA
184157 TTTTT-T-TTTTAGTCCTTTAAGTTTCTATAATTTTTA
1 TTTTTCTATTTTAGTCCTTTAA-TTTCTAT-ATTTTTA
184193 TTTCGGTCCC
Statistics
Matches: 79, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
54 3 0.04
55 13 0.16
56 1 0.01
57 6 0.08
58 23 0.29
59 33 0.42
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.62
Consensus pattern (60 bp):
TTTTTCTATTTTAGTCCTTTAATTTCTATATTTTTAGCTATTTTAGTCCTTTAAATTTCA
Found at i:184400 original size:15 final size:16
Alignment explanation
Indices: 184373--184404 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
184363 TTATTTCGTA
184373 TATTTCCATTTGTATT
1 TATTTCCATTTGTATT
184389 TATTTCCA-TTGTATT
1 TATTTCCATTTGTATT
184404 T
1 T
184405 CTTTATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.19, C:0.12, G:0.06, T:0.62
Consensus pattern (16 bp):
TATTTCCATTTGTATT
Found at i:188212 original size:24 final size:24
Alignment explanation
Indices: 188146--188223 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
188136 ATTTCCTATT
*
188146 TGAATTCT-ATTATGATACCTGACA
1 TGAATTCTGA-TATGATACTTGACA
* *
188170 TGAATTCTGATCTGATACTTGACT
1 TGAATTCTGATATGATACTTGACA
* * *
188194 TGGATTCTGATATGATACTTAACC
1 TGAATTCTGATATGATACTTGACA
188218 TGAATT
1 TGAATT
188224 ATGTTTTGAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
24 44 0.98
25 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (24 bp):
TGAATTCTGATATGATACTTGACA
Found at i:188353 original size:35 final size:36
Alignment explanation
Indices: 188305--188374 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 36
188295 ATACGTGGAG
*
188305 GCTCCTCGACTTTGTGCTCTGGGCCTTACT-TACTA
1 GCTCCTCGACTTTGTGCTCAGGGCCTTACTGTACTA
* *
188340 GCTCCTCGGCTTTGTGCTCAGTGCCTTACTGTACT
1 GCTCCTCGACTTTGTGCTCAGGGCCTTACTGTACT
188375 TGACGGTGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 27 0.87
36 4 0.13
ACGTcount: A:0.10, C:0.31, G:0.21, T:0.37
Consensus pattern (36 bp):
GCTCCTCGACTTTGTGCTCAGGGCCTTACTGTACTA
Found at i:189327 original size:43 final size:44
Alignment explanation
Indices: 189240--189327 Score: 142
Period size: 43 Copynumber: 2.0 Consensus size: 44
189230 TTATAAAGAA
* *
189240 ATACCAGTAACGTTTTAATAAAAAGTTTTACATGTTTATGATTT
1 ATACCAGTAACGTTTTAATAAAAAGTTTTACATGTATATAATTT
*
189284 ATACCAGTAACGTTTTAA-GAAAAGTTTTACATGTATATAATTT
1 ATACCAGTAACGTTTTAATAAAAAGTTTTACATGTATATAATTT
189327 A
1 A
189328 CTCGCATCGG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 23 0.56
44 18 0.44
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (44 bp):
ATACCAGTAACGTTTTAATAAAAAGTTTTACATGTATATAATTT
Found at i:190173 original size:24 final size:24
Alignment explanation
Indices: 190146--190216 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
190136 AAACCTAATT
*
190146 CAGGCCAAGTATCATATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
*
190170 CAGGTCAAGTATCAAATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
* * *
190194 CATGTCAGGTATCATAACAGAAT
1 CAGGTCAAGTATCATATCAGAAT
190217 TCAAATCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAGAATC
Found at i:191012 original size:98 final size:98
Alignment explanation
Indices: 190843--191038 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
190833 CTGAATTTCA
190843 TATACATATTGTACTTCTGTTCAATTCAGTTTGGGCTTCGTGGTTGATTTGTCGAACAAATATCA
1 TATACATATTGTACTTCTGTTCAATTCAGTTTGGGCTTCGTGGTTGATTTGTCGAACAAATATCA
190908 AATTCTTAGTACTGAATACGATCTAGAGTTGAG
66 AATTCTTAGTACTGAATACGATCTAGAGTTGAG
190941 TATACATATTGTACTTCTGTTCAATTCAGTTTGGGCTTCGTGGTTGATTTGTCGAACAAATATCA
1 TATACATATTGTACTTCTGTTCAATTCAGTTTGGGCTTCGTGGTTGATTTGTCGAACAAATATCA
191006 AATTCTTAGTACTGAATACGATCTAGAGTTGAG
66 AATTCTTAGTACTGAATACGATCTAGAGTTGAG
191039 CTGAACAGAA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (98 bp):
TATACATATTGTACTTCTGTTCAATTCAGTTTGGGCTTCGTGGTTGATTTGTCGAACAAATATCA
AATTCTTAGTACTGAATACGATCTAGAGTTGAG
Found at i:192059 original size:16 final size:18
Alignment explanation
Indices: 192028--192060 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
192018 GTCAACAATT
192028 AGTCAACAGCCGGTCAAC
1 AGTCAACAGCCGGTCAAC
192046 AGTCAAC-G-CGGTCAA
1 AGTCAACAGCCGGTCAA
192061 AATTCAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.33, C:0.30, G:0.24, T:0.12
Consensus pattern (18 bp):
AGTCAACAGCCGGTCAAC
Found at i:192923 original size:11 final size:11
Alignment explanation
Indices: 192907--192931 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
192897 ATGTATTGCT
192907 TTTCAAAAGTA
1 TTTCAAAAGTA
192918 TTTCAAAAGTA
1 TTTCAAAAGTA
192929 TTT
1 TTT
192932 TTAATTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTCAAAAGTA
Found at i:193546 original size:42 final size:42
Alignment explanation
Indices: 193394--193533 Score: 199
Period size: 42 Copynumber: 3.3 Consensus size: 42
193384 AAGCTATTGG
* * * *
193394 AGAAGCATCGAAGGGAGATCTTCATGCTGTTGGTGATATGGA
1 AGAAGCATCAAAGAGAGATCTCCATGTTGTTGGTGATATGGA
* * *
193436 AGAAGCGTCAAAGAGAGATCTCCATGTTTTTGGTGATATGAA
1 AGAAGCATCAAAGAGAGATCTCCATGTTGTTGGTGATATGGA
*
193478 AGAAGAATCAAAGAGAGATCTCCATGTTGTTGGTGATATGGA
1 AGAAGCATCAAAGAGAGATCTCCATGTTGTTGGTGATATGGA
*
193520 AGAAGCTTCAAAGA
1 AGAAGCATCAAAGA
193534 AAAATCTTCA
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (42 bp):
AGAAGCATCAAAGAGAGATCTCCATGTTGTTGGTGATATGGA
Found at i:200934 original size:29 final size:30
Alignment explanation
Indices: 200901--200975 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
200891 TTATATCGAC
* * *
200901 ATGGATAATACATTATTATTTTT-GAATAG
1 ATGGATAATACATTATTATTTTTACAAAAA
*
200930 ATGGATAATCCATTATTATTTTTACAAAAA
1 ATGGATAATACATTATTATTTTTACAAAAA
*
200960 ATGAATAATACATTAT
1 ATGGATAATACATTAT
200976 AACCAACCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 22 0.56
30 17 0.44
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (30 bp):
ATGGATAATACATTATTATTTTTACAAAAA
Found at i:202394 original size:134 final size:134
Alignment explanation
Indices: 202230--202497 Score: 536
Period size: 134 Copynumber: 2.0 Consensus size: 134
202220 AACATATAAG
202230 CTAACGACAAAAGCATGAGATCCTTGATTAAGAGTTAACTTGACATTTCTTCTTACTCTCTTACA
1 CTAACGACAAAAGCATGAGATCCTTGATTAAGAGTTAACTTGACATTTCTTCTTACTCTCTTACA
202295 TTTTTTCACACCTCATCTTCAGTTATAAACATGTATAAACATAATTTATAATTTTTACATAAATA
66 TTTTTTCACACCTCATCTTCAGTTATAAACATGTATAAACATAATTTATAATTTTTACATAAATA
202360 AAAA
131 AAAA
202364 CTAACGACAAAAGCATGAGATCCTTGATTAAGAGTTAACTTGACATTTCTTCTTACTCTCTTACA
1 CTAACGACAAAAGCATGAGATCCTTGATTAAGAGTTAACTTGACATTTCTTCTTACTCTCTTACA
202429 TTTTTTCACACCTCATCTTCAGTTATAAACATGTATAAACATAATTTATAATTTTTACATAAATA
66 TTTTTTCACACCTCATCTTCAGTTATAAACATGTATAAACATAATTTATAATTTTTACATAAATA
202494 AAAA
131 AAAA
202498 TGTCAAAATT
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 134 1.00
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.37
Consensus pattern (134 bp):
CTAACGACAAAAGCATGAGATCCTTGATTAAGAGTTAACTTGACATTTCTTCTTACTCTCTTACA
TTTTTTCACACCTCATCTTCAGTTATAAACATGTATAAACATAATTTATAATTTTTACATAAATA
AAAA
Found at i:204728 original size:20 final size:22
Alignment explanation
Indices: 204683--204736 Score: 76
Period size: 20 Copynumber: 2.5 Consensus size: 22
204673 AGCCTTCTAA
204683 AATTCCTAAAAACAAAGAAAAGAT
1 AATTCCTAAAAACAAAG--AAGAT
204707 AATTCCTAAAAAC-AAG-AGAT
1 AATTCCTAAAAACAAAGAAGAT
204727 AATTCCTAAA
1 AATTCCTAAA
204737 GATAATTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 14 0.47
23 3 0.10
24 13 0.43
ACGTcount: A:0.57, C:0.15, G:0.07, T:0.20
Consensus pattern (22 bp):
AATTCCTAAAAACAAAGAAGAT
Found at i:205669 original size:311 final size:312
Alignment explanation
Indices: 205106--205730 Score: 1243
Period size: 311 Copynumber: 2.0 Consensus size: 312
205096 GTATAATTTA
205106 AACACTAATCAAATTCCCCCTCACTTATATGATGTTTTTCCTCAAGCATTTCTTAATCAACATGC
1 AACACTAATCAAATTCCCCCTCACTTATATGATGTTTTTCCTCAAGCATTTCTTAATCAACATGC
205171 CAAAATCAATAGTTGTAATTCTATAACTCACATCATATTTTAATCATCCAATGAACCAAAATCAC
66 CAAAATCAATAGTTGTAATTCTATAACTCACATCATATTTTAATCATCCAATGAACCAAAATCAC
205236 GACAATGAATTGAAATTAGAAAACATTCAAGCATGTGGCAAAGCTAGGAAATAAGTTAAATCAAA
131 GACAATGAATTGAAATTAGAAAACATTCAAGCATGTGGCAAAGCTAGGAAATAAGTTAAATCAAA
205301 ACAAGACATTTTGATAGCTCACTAATCTCATGATACAAGACTCATTACCCTCACAAAGGATTCAC
196 ACAAGACATTTTGATAGCTCACTAATCTCATGATACAAGACTCATTACCCTCACAAAGGATTCAC
205366 TCATTCCGCTCAAGTGTTTAAGGAC-AAGAAAAGCTCAAGTCAGAACAAGTC
261 TCATTCCGCTCAAGTGTTTAAGGACAAAGAAAAGCTCAAGTCAGAACAAGTC
205417 AACACTAATCAAATTCCCCCTCACTTATATGATGTTTTTCCTCAAGCATTTCTTAATCAACATGC
1 AACACTAATCAAATTCCCCCTCACTTATATGATGTTTTTCCTCAAGCATTTCTTAATCAACATGC
205482 CAAAATCAATAGTTGTAATTCTATAACTCACATCATATTTTAATCATCCAATGAACCAAAATCAC
66 CAAAATCAATAGTTGTAATTCTATAACTCACATCATATTTTAATCATCCAATGAACCAAAATCAC
205547 GACAATGAATTGAAATTAGAAAACATTCAAGCATGTGGCAAAGCTAGGAAATAAGTTAAATCAAA
131 GACAATGAATTGAAATTAGAAAACATTCAAGCATGTGGCAAAGCTAGGAAATAAGTTAAATCAAA
205612 ACAAGACATTTTGATAGCTCACTAATCTCATGATACAAGACTCATTACCCTCACAAAGGATTCAC
196 ACAAGACATTTTGATAGCTCACTAATCTCATGATACAAGACTCATTACCCTCACAAAGGATTCAC
205677 TCATTCCGCTCAAGTGTTTAAGGACAAAGAAAAGCTCAAGTCAGAACAAGTC
261 TCATTCCGCTCAAGTGTTTAAGGACAAAGAAAAGCTCAAGTCAGAACAAGTC
205729 AA
1 AA
205731 AGCATTTTAA
Statistics
Matches: 313, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
311 285 0.91
312 28 0.09
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (312 bp):
AACACTAATCAAATTCCCCCTCACTTATATGATGTTTTTCCTCAAGCATTTCTTAATCAACATGC
CAAAATCAATAGTTGTAATTCTATAACTCACATCATATTTTAATCATCCAATGAACCAAAATCAC
GACAATGAATTGAAATTAGAAAACATTCAAGCATGTGGCAAAGCTAGGAAATAAGTTAAATCAAA
ACAAGACATTTTGATAGCTCACTAATCTCATGATACAAGACTCATTACCCTCACAAAGGATTCAC
TCATTCCGCTCAAGTGTTTAAGGACAAAGAAAAGCTCAAGTCAGAACAAGTC
Found at i:206965 original size:10 final size:10
Alignment explanation
Indices: 206950--206975 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
206940 AAGCTTTATC
206950 TTTTTTTTCT
1 TTTTTTTTCT
206960 TTTTTTTTCT
1 TTTTTTTTCT
206970 TTTTTT
1 TTTTTT
206976 CTCTCACTGT
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:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:207018 original size:33 final size:34
Alignment explanation
Indices: 206981--207053 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
206971 TTTTTCTCTC
* *
206981 ACTGTTCGAACCAAAATTGTATTG-T-TGTTTTTT
1 ACTGTTCGAACCAAAACTGTACTGCTAT-TTTTTT
* *
207014 ACTGTTCTAACCAACACTGTACTGCTATTTTTTT
1 ACTGTTCGAACCAAAACTGTACTGCTATTTTTTT
207048 ACTGTT
1 ACTGTT
207054 TGAATAGTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 20 0.59
34 13 0.38
35 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (34 bp):
ACTGTTCGAACCAAAACTGTACTGCTATTTTTTT
Found at i:208045 original size:12 final size:12
Alignment explanation
Indices: 208002--208045 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
207992 TTCAAAGATG
*
208002 ATTAAAAAGGAA
1 ATTAAAAAGAAA
208014 ATTAAAAAGAAA
1 ATTAAAAAGAAA
* *
208026 GTTTAAAAGAAA
1 ATTAAAAAGAAA
208038 ATTCAAAA
1 ATT-AAAA
208046 TGGTAAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 23 0.88
13 3 0.12
ACGTcount: A:0.66, C:0.02, G:0.11, T:0.20
Consensus pattern (12 bp):
ATTAAAAAGAAA
Found at i:208623 original size:20 final size:21
Alignment explanation
Indices: 208598--208644 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
208588 TTCTAAAAAC
208598 AAATAAAAGAT-AATTCCTAA
1 AAATAAAAGATAAATTCCTAA
*
208618 AAATAAGAGATAAATTCCTAA
1 AAATAAAAGATAAATTCCTAA
*
208639 AGATAA
1 AAATAA
208645 TTCTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.23
Consensus pattern (21 bp):
AAATAAAAGATAAATTCCTAA
Found at i:212203 original size:12 final size:12
Alignment explanation
Indices: 212186--212244 Score: 77
Period size: 12 Copynumber: 5.0 Consensus size: 12
212176 CATAAATCAA
212186 AACAGAATTCAG
1 AACAGAATTCAG
212198 AACAG-ATATCAG
1 AACAGAAT-TCAG
*
212210 AACAGAATCCAG
1 AACAGAATTCAG
*
212222 ATCAGAA-TCAG
1 AACAGAATTCAG
212233 AACAGAATTCAG
1 AACAGAATTCAG
212245 GTCATTTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 11 0.28
12 27 0.68
13 2 0.05
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.15
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:212208 original size:24 final size:24
Alignment explanation
Indices: 212181--212267 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
212171 GATATCATAA
* *
212181 ATCAAAACAGAATTCAGAACAGAT
1 ATCAGAACAGAATTCAGATCAGAT
*
212205 ATCAGAACAGAATCCAGATCAGA-
1 ATCAGAACAGAATTCAGATCAGAT
* **
212228 ATCAGAACAGAATTCAGGTCATTT
1 ATCAGAACAGAATTCAGATCAGAT
212252 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
212268 AGTCGGAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
23 19 0.35
24 36 0.65
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATCAGAT
Found at i:212279 original size:24 final size:25
Alignment explanation
Indices: 212174--212281 Score: 91
Period size: 24 Copynumber: 4.5 Consensus size: 25
212164 AAACGAAGAT
* *
212174 ATCATAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
212198 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
212222 ATCAG-AATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
212245 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
212270 -TCGGAAATCAGA
1 ATCAGAAATCAGA
212282 TAAAATATTT
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
23 19 0.28
24 46 0.69
25 2 0.03
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:230044 original size:91 final size:91
Alignment explanation
Indices: 229941--230106 Score: 262
Period size: 91 Copynumber: 1.8 Consensus size: 91
229931 TGTTGGATTG
* * *
229941 AACAAGTTCTTCTCATTATGAACTTCTTC-TCTCTTGTTGGATGATTTCTTCTTATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCGTTGGATGAGTTCTTCTCATTATGAACTC
*
230005 TTCACTGGAAACACTGATGCAAGGTTA
65 TCCACTGGAAACACTGATGCAAGGTTA
*
230032 AACAAGTTCTTCTCATTATGAAGTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
*
230097 CCATTGGAAA
66 CCACTGGAAA
230107 TGTTGATTCA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
91 66 0.97
92 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.40
Consensus pattern (91 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
CCACTGGAAACACTGATGCAAGGTTA
Found at i:230235 original size:105 final size:106
Alignment explanation
Indices: 230032--230306 Score: 410
Period size: 105 Copynumber: 2.6 Consensus size: 106
230022 TGCAAGGTTA
* *
230032 AACAAGTTCTTCTCATTATGAAGTTCTTCTTCCTCGTT-GGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAA-CT-TTC-TCCT--TTAGGATGAGTTCTTCTCATTATGAACTA
*
230096 TCCATTGGAAATGTTGATTCACATCTTTCTGTGGTGAATTTGAAAGG
61 TCCA-TGGAAATGTTGATTCACATCCTTCTGTGGTGAATTTGAAAGG
*
230143 AACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTATTC-T
1 AACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTATCCAT
* *
230207 GGAAATGTTGGTTCACCTCCTTCTGTGGTGAATTTGAAAGG
66 GGAAATGTTGATTCACATCCTTCTGTGGTGAATTTGAAAGG
* *
230248 AACAAGTTCTTCTCATTATGAACTTTCTCTTTTACGATGAGTTCTTCTCATTATGAACT
1 AACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACT
230307 CTTCATTAAA
Statistics
Matches: 155, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
105 96 0.62
106 2 0.01
107 27 0.17
108 4 0.03
109 3 0.02
110 1 0.01
111 22 0.14
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (106 bp):
AACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTATCCAT
GGAAATGTTGATTCACATCCTTCTGTGGTGAATTTGAAAGG
Found at i:230492 original size:136 final size:136
Alignment explanation
Indices: 230247--230727 Score: 670
Period size: 136 Copynumber: 3.6 Consensus size: 136
230237 AATTTGAAAG
*
230247 GAACAAGTTCTTCTCATTATGAAC-T-TTCT-CTT-T-TAC-GATGAGTTCTTCTCATTATGAAC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCTTCTGT-CGGATGAGTTCTTCTCATTATGAAC
* * * * * *
230306 TCTTCATTAAAAATGTT-AATCCCTCAAACGAGGCGTCACTAATTCAAAATATCGTGAATCAAGT
65 TCTCCATTAGAAAT-TTCGATCCCTCAAGCGAGGCGTCACTAATTCGAAATATCGTGAATCGAGT
230370 GATAGGTC
129 GATAGGTC
230378 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCTTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCTTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * * *
230443 CTCCATTAGAAATTTCGATCCATCAAGCGAGGCGTCACTGATTCGAAATACCGTGAATCGAGTAA
66 CTCCATTAGAAATTTCGATCCCTCAAGCGAGGCGTCACTAATTCGAAATATCGTGAATCGAGTGA
230508 TAGGTC
131 TAGGTC
* *
230514 GAGCAAGCTCTTCTCATTATGAACTTCTTCTCCTTCTGTCGGATGAGTTCTTCTCATTATGTACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCTTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * *
230579 CTCCATTGGAAATTTCGATCCCTCAAGCTAGACGTCACTAATTCGAAATATCGTGAATCGAGTGA
66 CTCCATTAGAAATTTCGATCCCTCAAGCGAGGCGTCACTAATTCGAAATATCGTGAATCGAGTGA
* *
230644 TAGTTG
131 TAGGTC
* * * ** *
230650 GAACAAGATATTCTCATTATGAACTTCTTCTCCCTCTGTTAGATGAGTTCTTCTCATTATGGACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCTTCTGTCGGATGAGTTCTTCTCATTATGAACT
*
230715 CTCCATTGGAAAT
66 CTCCATTAGAAAT
230728 GTAGAAAACA
Statistics
Matches: 314, Mismatches: 29, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
131 23 0.07
132 1 0.00
133 4 0.01
134 3 0.01
135 4 0.01
136 279 0.89
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCTTCTGTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTAGAAATTTCGATCCCTCAAGCGAGGCGTCACTAATTCGAAATATCGTGAATCGAGTGA
TAGGTC
Found at i:230845 original size:42 final size:42
Alignment explanation
Indices: 230764--230858 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 42
230754 TATGAATGGT
* * * * *
230764 CCGAAGGACTT-ATCATCTTGCTCAAAAGTCTTACAGATGAG
1 CCGAAGGATTTAAGCATCATGCTCAAAAGACTTACAGATGAC
* **
230805 CCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGAC
1 CCGAAGGATTTAAGCATCATGCTCAAAAGACTTACAGATGAC
*
230847 CCGAAAGATTTA
1 CCGAAGGATTTA
230859 CAAATCAAGA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 10 0.23
42 34 0.77
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (42 bp):
CCGAAGGATTTAAGCATCATGCTCAAAAGACTTACAGATGAC
Found at i:235704 original size:20 final size:20
Alignment explanation
Indices: 235679--235717 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
235669 TTAAAAGAAG
* *
235679 TCTTCAATTAATTTTAAATT
1 TCTTCAATCAATTTCAAATT
235699 TCTTCAATCAATTTCAAAT
1 TCTTCAATCAATTTCAAAT
235718 ATATTGTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (20 bp):
TCTTCAATCAATTTCAAATT
Done.