Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 10 of 135
Found at i:2747653 original size:27 final size:27
Alignment explanation
Indices: 2747623--2747692 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
2747613 CAAAGTCCAC
*
2747623 TTACAAAGGTCCAAATTAAAGGCCCAA
1 TTACAAAGGCCCAAATTAAAGGCCCAA
*
2747650 TTACAAAGGCCCAAATTGAAGGCCCAA
1 TTACAAAGGCCCAAATTAAAGGCCCAA
*
2747677 TTACAATGGCCCAAAT
1 TTACAAAGGCCCAAAT
2747693 AGGCCCAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (27 bp):
TTACAAAGGCCCAAATTAAAGGCCCAA
Found at i:2747659 original size:14 final size:14
Alignment explanation
Indices: 2747623--2747690 Score: 63
Period size: 14 Copynumber: 5.0 Consensus size: 14
2747613 CAAAGTCCAC
*
2747623 TTACAAAGGTCCAAA
1 TTACAAAGG-CCCAA
2747638 TT--AAAGGCCCAA
1 TTACAAAGGCCCAA
2747650 TTACAAAGGCCCAAA
1 TTACAAAGGCCC-AA
*
2747665 TT--GAAGGCCCAA
1 TTACAAAGGCCCAA
*
2747677 TTACAATGGCCCAA
1 TTACAAAGGCCCAA
2747691 ATAGGCCCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
12 10 0.23
13 12 0.27
14 16 0.36
15 6 0.14
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (14 bp):
TTACAAAGGCCCAA
Found at i:2748944 original size:2 final size:2
Alignment explanation
Indices: 2748937--2748976 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2748927 ATGAGAGGGT
2748937 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2748977 TTTTTTAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2749515 original size:30 final size:29
Alignment explanation
Indices: 2749481--2749662 Score: 129
Period size: 30 Copynumber: 6.1 Consensus size: 29
2749471 TGTATTTTGA
2749481 CCCTATAACTTTCAAAAATTACATTTTTAC
1 CCCTA-AACTTTCAAAAATTACATTTTTAC
2749511 CCCTAAACTTTTCAAAAAATTACATTTTTAC
1 CCCTAAAC-TTTC-AAAAATTACATTTTTAC
* * * **
2749542 CCTTGAACTTTCCAAAATCCCATTTTTGAC
1 CCCTAAACTTTCAAAAATTACATTTTT-AC
* * *
2749572 TCC--GACTTCACCAAAAATTAC-TATTTTA-
1 CCCTAAACTT--TCAAAAATTACAT-TTTTAC
* * *
2749600 CCCTCAAACTTTCTAAAATTCCATTTTTAA
1 CCCT-AAACTTTCAAAAATTACATTTTTAC
* * *
2749630 CCCTAAATTTTCCCAAAATTACATTTTTGC
1 CCCTAAACTTT-CAAAAATTACATTTTTAC
2749660 CCC
1 CCC
2749663 CGAAAGTCAA
Statistics
Matches: 118, Mismatches: 22, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
28 6 0.05
29 36 0.31
30 49 0.42
31 27 0.23
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTCAAAAATTACATTTTTAC
Found at i:2749648 original size:59 final size:57
Alignment explanation
Indices: 2749474--2749656 Score: 170
Period size: 59 Copynumber: 3.1 Consensus size: 57
2749464 CAGAAATTGT
* * *
2749474 ATTTTGACCCTATAACTTTCAAAAATTACATTTTTACCCCTAAACTTTTCAAAAAATTAC
1 ATTTT-ACCCTA-AACTTTCAAAAATTCCATTTTTAACCCTAAA-TTTTCCAAAAATTAC
* * * * * * **
2749534 ATTTTTACCCTTGAACTTTCCAAAATCCCATTTTTGACTCC-GACTTCACCAAAAATTAC
1 A-TTTTACCC-TAAACTTTCAAAAATTCCATTTTTAAC-CCTAAATTTTCCAAAAATTAC
* *
2749593 TATTTTACCCTCAAACTTTCTAAAATTCCATTTTTAACCCTAAATTTTCCCAAAATTAC
1 -ATTTTACCCT-AAACTTTCAAAAATTCCATTTTTAACCCTAAATTTTCCAAAAATTAC
2749652 ATTTT
1 ATTTT
2749657 TGCCCCCGAA
Statistics
Matches: 97, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
58 8 0.08
59 55 0.57
60 27 0.28
61 7 0.07
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (57 bp):
ATTTTACCCTAAACTTTCAAAAATTCCATTTTTAACCCTAAATTTTCCAAAAATTAC
Found at i:2752477 original size:16 final size:16
Alignment explanation
Indices: 2752456--2752486 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2752446 ACACATGTTT
2752456 AATAATCCAAAAGAAA
1 AATAATCCAAAAGAAA
*
2752472 AATAATCCAATAGAA
1 AATAATCCAAAAGAA
2752487 TTTTTTTTAT
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:0.65, C:0.13, G:0.06, T:0.16
Consensus pattern (16 bp):
AATAATCCAAAAGAAA
Found at i:2752656 original size:19 final size:21
Alignment explanation
Indices: 2752634--2752675 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2752624 CTTGATTGTG
*
2752634 GTTTAGAA-TAAAG-TAAAAT
1 GTTTAAAATTAAAGATAAAAT
2752653 GTTTAAAATTAAAGATAAAAT
1 GTTTAAAATTAAAGATAAAAT
2752674 GT
1 GT
2752676 AAAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 5 0.25
21 8 0.40
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.33
Consensus pattern (21 bp):
GTTTAAAATTAAAGATAAAAT
Found at i:2757471 original size:2 final size:2
Alignment explanation
Indices: 2757459--2757507 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
2757449 TATAGTTAAA
2757459 AT AT CAT 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
2757502 AT AT AT
1 AT AT AT
2757508 TTGTTTTACA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2758105 original size:12 final size:12
Alignment explanation
Indices: 2758088--2758112 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2758078 ATTTTGTCTT
2758088 ATATGCCACGTC
1 ATATGCCACGTC
2758100 ATATGCCACGTC
1 ATATGCCACGTC
2758112 A
1 A
2758113 GCATATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (12 bp):
ATATGCCACGTC
Found at i:2759352 original size:30 final size:30
Alignment explanation
Indices: 2759316--2759383 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
2759306 AAAAGTACAA
* *
2759316 TTTTTAA-AGGATTAAATTAAAATTTTATCT
1 TTTTTAAGAGGACTAAAGTAAAATTTTA-CT
* *
2759346 TTTTTAAGAGGGCTAAAGTATAATTTTACT
1 TTTTTAAGAGGACTAAAGTAAAATTTTACT
2759376 TTTATTAA
1 TTT-TTAA
2759384 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (30 bp):
TTTTTAAGAGGACTAAAGTAAAATTTTACT
Found at i:2762864 original size:20 final size:19
Alignment explanation
Indices: 2762816--2762864 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2762806 AATGGTTTTC
2762816 CTTTTTTTTATTTCTTCTT
1 CTTTTTTTTATTTCTTCTT
* * *
2762835 CTTTAATTTTATTTTTTTTT
1 CTTT-TTTTTATTTCTTCTT
2762855 CTTATTTTTT
1 CTT-TTTTTT
2762865 TCATCTTCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.17
20 19 0.79
21 1 0.04
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (19 bp):
CTTTTTTTTATTTCTTCTT
Found at i:2767554 original size:15 final size:14
Alignment explanation
Indices: 2767527--2767565 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2767517 AAAATATCTC
2767527 TTTTAATTTTATATA
1 TTTT-ATTTTATATA
*
2767542 TTTTATTTCTATATT
1 TTTTATTT-TATATA
2767557 TTTTATTTT
1 TTTTATTTT
2767566 TAATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTATTTTATATA
Found at i:2767781 original size:19 final size:20
Alignment explanation
Indices: 2767753--2767793 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
2767743 TTGAACCTCA
*
2767753 AACCCGAACTCT-AATCTTG
1 AACCCAAACTCTGAATCTTG
*
2767772 AACCCAAACTTTGAATCTTG
1 AACCCAAACTCTGAATCTTG
2767792 AA
1 AA
2767794 TCTTTGAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.27
Consensus pattern (20 bp):
AACCCAAACTCTGAATCTTG
Found at i:2767800 original size:15 final size:15
Alignment explanation
Indices: 2767780--2767809 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2767770 TGAACCCAAA
*
2767780 CTTTGAATCTTGAAT
1 CTTTGAACCTTGAAT
2767795 CTTTGAACCTTGAAT
1 CTTTGAACCTTGAAT
2767810 TCCAAACCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (15 bp):
CTTTGAACCTTGAAT
Found at i:2771641 original size:31 final size:31
Alignment explanation
Indices: 2771600--2771671 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
2771590 ATTTAGGTTA
* *
2771600 GGACTGAAATTT-CAAAATTCATAAAGTATAT
1 GGACTAAAATTTAC-AAATTCAAAAAGTATAT
*
2771631 GGACTAAAATTTACCAATTCAAAAAGTATAT
1 GGACTAAAATTTACAAATTCAAAAAGTATAT
*
2771662 AGACTAAAAT
1 GGACTAAAAT
2771672 CAATCAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (31 bp):
GGACTAAAATTTACAAATTCAAAAAGTATAT
Found at i:2775570 original size:13 final size:13
Alignment explanation
Indices: 2775552--2775577 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2775542 AGCAGACAGT
2775552 GCTGACGTGGCAC
1 GCTGACGTGGCAC
2775565 GCTGACGTGGCAC
1 GCTGACGTGGCAC
2775578 TGACGACTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.38, T:0.15
Consensus pattern (13 bp):
GCTGACGTGGCAC
Found at i:2775766 original size:6 final size:6
Alignment explanation
Indices: 2775755--2775824 Score: 63
Period size: 6 Copynumber: 12.0 Consensus size: 6
2775745 TTAAAATAAT
** * * *
2775755 TTTAAA TTTAAA CATAAA TTTAAA TTTAAA TTTTAA --CAAA TTCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
2775801 TTTAAA AATAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
2775825 ATAAATCCAA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
4 2 0.04
6 48 0.96
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:2776406 original size:48 final size:49
Alignment explanation
Indices: 2776347--2776462 Score: 144
Period size: 48 Copynumber: 2.4 Consensus size: 49
2776337 GCCATTGCTA
* * * * *
2776347 CTTAAACCTTTCCTTTCATATCTTCGCGGTACTAGATTCGTCGT-TCGG
1 CTTAAATCTTTCCCTTCATATCTTCGCGGCACTAGATTCGCCGTCGCGG
** * *
2776395 CTTAAATCTTTCCCACCATATCTTCGTGGCACTGGATTCGCCGTCGCGG
1 CTTAAATCTTTCCCTTCATATCTTCGCGGCACTAGATTCGCCGTCGCGG
2776444 CTTAAATCTTTCCCTTCAT
1 CTTAAATCTTTCCCTTCAT
2776463 GTTTTTGAGG
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
48 36 0.64
49 20 0.36
ACGTcount: A:0.17, C:0.30, G:0.16, T:0.37
Consensus pattern (49 bp):
CTTAAATCTTTCCCTTCATATCTTCGCGGCACTAGATTCGCCGTCGCGG
Found at i:2776573 original size:100 final size:100
Alignment explanation
Indices: 2776413--2776956 Score: 847
Period size: 100 Copynumber: 5.5 Consensus size: 100
2776403 TTTCCCACCA
* * * * * * *
2776413 TATCTTCGTGGCACTGGATTCGCCGTCGCGG-CTTAAATCTTTCCCTTCATGTTTTTGAGGTACA
1 TATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGTTTCTGAGGTACA
* *
2776477 CGGTCCGTCGTTGCGACTTAGACCCTTCCCTTTAG
66 CGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTAG
* *
2776512 TATCTTTGTGGTACTTGATCCGCCATTGCGGTCTTAGATATTTCCCTTCATGTTTCTGAGGTACA
1 TATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGTTTCTGAGGTACA
* *
2776577 CGGTCCGCCGTTGCGACTTACACATTTCCCTTTAG
66 CGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTAG
* *
2776612 TATCTTTGTGGTACTGGATCCACCATTACGGTCTTAGATCTTTCCCTTCATGTTTCTGAGGTACA
1 TATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGTTTCTGAGGTACA
* *
2776677 CGGTCCGCCATTGCGACTTAAACCTTTCCCTTTAG
66 CGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTAG
2776712 TATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGTTTCTGAGGTACA
1 TATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGTTTCTGAGGTACA
*
2776777 CGGTCCGCCATTGCGACTTAGACCTTTCCCTTTAG
66 CGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTAG
* *
2776812 TATCTTTGTGGTACTAGATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGTTTTTGAGGTACA
1 TATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGTTTCTGAGGTACA
* * *
2776877 CGGTCTGCCGTTACGACTTGGACCTTTCCCTTTAG
66 CGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTAG
* * *
2776912 TATCTTTGCGGTACTGGATCCACCATTGCGGTCTTAGATTTTTCC
1 TATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCC
2776957 TTTTTGTATC
Statistics
Matches: 411, Mismatches: 33, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
99 25 0.06
100 386 0.94
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (100 bp):
TATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGTTTCTGAGGTACA
CGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTAG
Found at i:2777010 original size:51 final size:52
Alignment explanation
Indices: 2776601--2777010 Score: 168
Period size: 50 Copynumber: 8.2 Consensus size: 52
2776591 GACTTACACA
* * * *
2776601 TTTCCC-TTTAGTATCTTTGTGGTACTGGATCCACCATTACGGTCTTAGATC
1 TTTCCCTTTTAGTATCTTTGCGGTACTGGATCCACCATTGCGGTATTAAATC
* * * * * *
2776652 TTTCCC-TTCATGT-T-TCTGAGGTACACGG-TCCGCCATTGC-G-ACTTAAACC
1 TTTCCCTTTTA-GTATCTTTGCGGTAC-TGGATCCACCATTGCGGTA-TTAAATC
* * * *
2776701 TTTCCC-TTTAGTATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATC
1 TTTCCCTTTTAGTATCTTTGCGGTACTGGATCCACCATTGCGGTATTAAATC
* * * * * * *
2776752 TTTCCC-TTCATGT-T-TCTGAGGTACACGG-TCCGCCATTGC-G-ACTTAGACC
1 TTTCCCTTTTA-GTATCTTTGCGGTAC-TGGATCCACCATTGCGGTA-TTAAATC
* * * * *
2776801 TTTCCC-TTTAGTATCTTTGTGGTACTAGATCCGCCATTGCGGTCTTAGATC
1 TTTCCCTTTTAGTATCTTTGCGGTACTGGATCCACCATTGCGGTATTAAATC
* * * ** * * ** *
2776852 TTTCCC-TTCATGT-T-TTTGAGGTACACGG-TCTGCCGTTAC-G-ACTTGGACC
1 TTTCCCTTTTA-GTATCTTTGCGGTAC-TGGATCCACCATTGCGGTA-TTAAATC
* *
2776901 TTTCCC-TTTAGTATCTTTGCGGTACTGGATCCACCATTGCGGTCTTAGAT-
1 TTTCCCTTTTAGTATCTTTGCGGTACTGGATCCACCATTGCGGTATTAAATC
* * * * *
2776951 TTTTCCTTTTTGTATCTTTGTGGTACTGGATTCC-CCGTTTCGG-ATTAAATC
1 TTTCCCTTTTAGTATCTTTGCGGTACTGGA-TCCACCATTGCGGTATTAAATC
2777002 TTTCCCTTT
1 TTTCCCTTT
2777011 ATGCTTCTAA
Statistics
Matches: 275, Mismatches: 57, Indels: 54
0.71 0.15 0.14
Matches are distributed among these distances:
48 6 0.02
49 54 0.20
50 117 0.43
51 89 0.32
52 9 0.03
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.40
Consensus pattern (52 bp):
TTTCCCTTTTAGTATCTTTGCGGTACTGGATCCACCATTGCGGTATTAAATC
Found at i:2779081 original size:15 final size:15
Alignment explanation
Indices: 2779058--2779094 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
2779048 ATTTTTTTTA
2779058 TTCTCTTTTTCTGATT
1 TTCT-TTTTTCTGATT
*
2779074 TTCTTTTTTTTGATT
1 TTCTTTTTTCTGATT
2779089 TTCTTT
1 TTCTTT
2779095 ATTATAACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.05, C:0.14, G:0.05, T:0.76
Consensus pattern (15 bp):
TTCTTTTTTCTGATT
Found at i:2789421 original size:39 final size:40
Alignment explanation
Indices: 2789357--2789433 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 40
2789347 AAGAGGTATG
*
2789357 TCCAATATGAAAAGGGTTGTAACTCTTCAAAAGGTGTCTA
1 TCCAATATGAAAAGGGTTGTAACTCTTCAAAAGATGTCTA
* *
2789397 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGATGTC
1 TCCAATATGAAAAGGGTTGTAACTCTTCAAAAGATGTC
2789434 CATAAATAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 26 0.76
40 8 0.24
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGGTTGTAACTCTTCAAAAGATGTCTA
Found at i:2790838 original size:6 final size:6
Alignment explanation
Indices: 2790827--2790896 Score: 72
Period size: 6 Copynumber: 12.0 Consensus size: 6
2790817 TTAGAATAAT
** * * *
2790827 TTTAAA TTTAAA CATAAA TTTAAA TTTAAA TTTTAA --CAAA TTCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
2790873 TTTAAA ATTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
2790897 ATAAATCCAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
4 2 0.04
6 50 0.96
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:2790843 original size:18 final size:18
Alignment explanation
Indices: 2790822--2790902 Score: 67
Period size: 18 Copynumber: 4.3 Consensus size: 18
2790812 ATTATTTAGA
*
2790822 ATAATTTTAAATTTAAAC
1 ATAAATTTAAATTTAAAC
*
2790840 ATAAATTTAAATTTAAATTTTA
1 ATAAATTTAAATTTAAA----C
* *
2790862 ACAAATTCAAATTTAAA-
1 ATAAATTTAAATTTAAAC
2790879 ATTAAATTTAAATTTAAA-
1 A-TAAATTTAAATTTAAAC
2790897 ATAAAT
1 ATAAAT
2790903 CCAAAATGGG
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
17 6 0.12
18 31 0.60
22 15 0.29
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAATTTAAATTTAAAC
Found at i:2794077 original size:21 final size:20
Alignment explanation
Indices: 2794028--2794080 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
2794018 ATCGTTGTTT
*
2794028 TTAATTTCATTGTTATAATA
1 TTAATTTTATTGTTATAATA
2794048 TCTAATTTTATT-TCTATAATAA
1 T-TAATTTTATTGT-TATAAT-A
2794070 TTAATTTTATT
1 TTAATTTTATT
2794081 ATTAGTGCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (20 bp):
TTAATTTTATTGTTATAATA
Found at i:2796639 original size:95 final size:95
Alignment explanation
Indices: 2796534--2796722 Score: 378
Period size: 95 Copynumber: 2.0 Consensus size: 95
2796524 ATCCTTGTTG
2796534 CTGTTCTATAAAGTCCTGTCCAACCTTCTGCTTTGTGTAGCTGGTTGAAATTATTATGGACTGCT
1 CTGTTCTATAAAGTCCTGTCCAACCTTCTGCTTTGTGTAGCTGGTTGAAATTATTATGGACTGCT
2796599 CAAATAATACTGTAGCAACATTTTTGTTTT
66 CAAATAATACTGTAGCAACATTTTTGTTTT
2796629 CTGTTCTATAAAGTCCTGTCCAACCTTCTGCTTTGTGTAGCTGGTTGAAATTATTATGGACTGCT
1 CTGTTCTATAAAGTCCTGTCCAACCTTCTGCTTTGTGTAGCTGGTTGAAATTATTATGGACTGCT
2796694 CAAATAATACTGTAGCAACATTTTTGTTT
66 CAAATAATACTGTAGCAACATTTTTGTTT
2796723 ATTGATCCTG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (95 bp):
CTGTTCTATAAAGTCCTGTCCAACCTTCTGCTTTGTGTAGCTGGTTGAAATTATTATGGACTGCT
CAAATAATACTGTAGCAACATTTTTGTTTT
Found at i:2805589 original size:1 final size:1
Alignment explanation
Indices: 2805583--2805607 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2805573 AGCTACACAT
2805583 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
2805608 CCTTGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2805852 original size:16 final size:18
Alignment explanation
Indices: 2805813--2805846 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2805803 TAAGTTTATA
2805813 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
2805830 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
2805847 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:2806579 original size:31 final size:31
Alignment explanation
Indices: 2806541--2806696 Score: 79
Period size: 31 Copynumber: 5.3 Consensus size: 31
2806531 TTAATATAAT
2806541 ATTTGGTACTTGAACTTGACACTTTTTTCTA
1 ATTTGGTACTTGAACTTGACACTTTTTTCTA
* *
2806572 ATTTGGTA--T---C-T-AAACTTTTTTGACCCA
1 ATTTGGTACTTGAACTTGACACTTTTTT---CTA
* *
2806599 ATTTTGTACTTGAACTTGACATTTTTTTCTA
1 ATTTGGTACTTGAACTTGACACTTTTTTCTA
* * *
2806630 ATTTGATACCT-AAATT-----TTTTTTACTCA
1 ATTTGGTACTTGAACTTGACACTTTTTT-CT-A
* *
2806657 ATTTGGTA-TCTGAACTTGATATTTTTTTCTA
1 ATTTGGTACT-TGAACTTGACACTTTTTTCTA
2806688 ATTTGGTAC
1 ATTTGGTAC
2806697 CTAAACTTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 39
0.64 0.09 0.27
Matches are distributed among these distances:
24 9 0.10
25 7 0.08
26 3 0.03
27 18 0.20
28 4 0.04
29 2 0.02
30 4 0.04
31 27 0.29
32 3 0.03
33 7 0.08
34 8 0.09
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (31 bp):
ATTTGGTACTTGAACTTGACACTTTTTTCTA
Found at i:2806704 original size:31 final size:31
Alignment explanation
Indices: 2806611--2806704 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 31
2806601 TTTGTACTTG
* *
2806611 AACTTGACATTTTTTTCTAATTTGATACCTA
1 AACTTGATATTTTTTTCTAATTTGGTACCTA
* * *
2806642 AA--T--T-TTTTTTACTCAATTTGGTATCTG
1 AACTTGATATTTTTTTCT-AATTTGGTACCTA
2806669 AACTTGATATTTTTTTCTAATTTGGTACCTA
1 AACTTGATATTTTTTTCTAATTTGGTACCTA
2806700 AACTT
1 AACTT
2806705 TTTTAAATTC
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
26 8 0.16
27 12 0.24
29 2 0.04
31 19 0.39
32 8 0.16
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.51
Consensus pattern (31 bp):
AACTTGATATTTTTTTCTAATTTGGTACCTA
Found at i:2806719 original size:59 final size:58
Alignment explanation
Indices: 2806541--2806728 Score: 261
Period size: 58 Copynumber: 3.2 Consensus size: 58
2806531 TTAATATAAT
* * * *
2806541 ATTTGGTACTTGAACTTGACACTTTTTTCTAATTTGGTATCTAAACTTTTTTGACCCA
1 ATTTGGTACTTGAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTTTTTAACTCA
* * * *
2806599 ATTTTGTACTTGAACTTGACATTTTTTTCTAATTTGATACCTAAATTTTTTTTACTCA
1 ATTTGGTACTTGAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTTTTTAACTCA
* *
2806657 ATTTGGTA-TCTGAACTTGATATTTTTTTCTAATTTGGTACCTAAACTTTTTTAAATTCA
1 ATTTGGTACT-TGAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTTTTT-AACTCA
2806716 ATTTGGTACTTGA
1 ATTTGGTACTTGA
2806729 TTTTATTAAA
Statistics
Matches: 114, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
57 1 0.01
58 97 0.85
59 15 0.13
60 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.50
Consensus pattern (58 bp):
ATTTGGTACTTGAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTTTTTAACTCA
Found at i:2808001 original size:30 final size:30
Alignment explanation
Indices: 2807958--2808018 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
2807948 TTACAAGGGC
* *
2807958 ATTGGTGGGCTAGG-GGGTTTAGGCGGTGGA
1 ATTGGAGGCCTAGGTGGG-TTAGGCGGTGGA
*
2807988 ATTGGAGGCCTAGGTGGGTTAGGGGGTGGA
1 ATTGGAGGCCTAGGTGGGTTAGGCGGTGGA
2808018 A
1 A
2808019 CTGCTGGCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.16, C:0.07, G:0.52, T:0.25
Consensus pattern (30 bp):
ATTGGAGGCCTAGGTGGGTTAGGCGGTGGA
Found at i:2808044 original size:42 final size:42
Alignment explanation
Indices: 2807990--2808085 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 42
2807980 GCGGTGGAAT
* *
2807990 TGGAGGCCTAGGTGGGTTAGGGGGTGGAACTGCTGGCGGAGG
1 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGCTGGCGGAGG
* * * *
2808032 TGGAGGTCTAGGTGGTTTAGGGGGTGGAACCGGTGGTGGAGT
1 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGCTGGCGGAGG
2808074 TGGAGGTCTAGG
1 TGGAGGTCTAGG
2808086 CAGTGGGACC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.15, C:0.09, G:0.53, T:0.23
Consensus pattern (42 bp):
TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGCTGGCGGAGG
Found at i:2808097 original size:33 final size:33
Alignment explanation
Indices: 2808055--2808118 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
2808045 GGTTTAGGGG
*
2808055 GTGGAACCGGTGGTGGAGTTGGAGGTCTAGGCA
1 GTGGAACCGGCGGTGGAGTTGGAGGTCTAGGCA
*
2808088 GTGGGACCGGCGGTGGAGTTGGAGGTCTAGG
1 GTGGAACCGGCGGTGGAGTTGGAGGTCTAGG
2808119 TGGGGGTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.16, C:0.12, G:0.52, T:0.20
Consensus pattern (33 bp):
GTGGAACCGGCGGTGGAGTTGGAGGTCTAGGCA
Found at i:2808198 original size:57 final size:56
Alignment explanation
Indices: 2808100--2808237 Score: 192
Period size: 57 Copynumber: 2.5 Consensus size: 56
2808090 GGGACCGGCG
* *
2808100 GTGGAGTTGGAGGTCTAGGTGG-GG-GTGGTTGTCCAGGTACAGGTGGTGTAGGCA
1 GTGGAGCTGGAGGTCTAGGTGGTGGTGTGGTTGTCCAGATACAGGTGGTGTAGGCA
* *
2808154 GTGGAGGTGGAGGTCTAGGTGGTGGTAGTGGTTGTCCAGATACAGGTGGTGTAGGCG
1 GTGGAGCTGGAGGTCTAGGTGGTGGT-GTGGTTGTCCAGATACAGGTGGTGTAGGCA
*
2808211 GTGGAGCTGG-GGCTCCAGGTGGTGGTG
1 GTGGAGCTGGAGG-TCTAGGTGGTGGTG
2808238 GAAGCGGCGG
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
54 21 0.28
55 2 0.03
56 3 0.04
57 49 0.65
ACGTcount: A:0.14, C:0.10, G:0.51, T:0.25
Consensus pattern (56 bp):
GTGGAGCTGGAGGTCTAGGTGGTGGTGTGGTTGTCCAGATACAGGTGGTGTAGGCA
Found at i:2815697 original size:3 final size:3
Alignment explanation
Indices: 2815689--2815728 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2815679 AATTTCTATC
2815689 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2815729 ATATATTACG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2816386 original size:17 final size:18
Alignment explanation
Indices: 2816349--2816392 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 18
2816339 AATTTTAATT
2816349 TAATTTATAATATTATATA
1 TAATTT-TAATATTATATA
2816368 TAAATTTTAAT-TT-TATA
1 T-AATTTTAATATTATATA
2816385 TAATTTTA
1 TAATTTTA
2816393 TACTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.29
17 5 0.21
18 2 0.08
19 5 0.21
20 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTTTAATATTATATA
Found at i:2816400 original size:29 final size:30
Alignment explanation
Indices: 2816335--2816400 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
2816325 TAAAATTACT
*
2816335 CTTAAATTTTAATTTAATTTATAATATTATA
1 CTTAAATTTTAATTT-ATATATAATATTATA
*
2816366 -TATAAATTTTAATTT-TATATAATTTTATA
1 CT-TAAATTTTAATTTATATATAATATTATA
2816395 CTTAAA
1 CTTAAA
2816401 ATATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
29 16 0.52
30 2 0.06
31 13 0.42
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (30 bp):
CTTAAATTTTAATTTATATATAATATTATA
Found at i:2816484 original size:17 final size:19
Alignment explanation
Indices: 2816462--2816500 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
2816452 AAAAATAATA
*
2816462 TTATAAATTAT-TA-TATT
1 TTATAAATAATATATTATT
2816479 TTATAAATAATATATTATT
1 TTATAAATAATATATTATT
2816498 TTA
1 TTA
2816501 AAAAAATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 2 0.11
19 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATAAATAATATATTATT
Found at i:2816494 original size:16 final size:17
Alignment explanation
Indices: 2816462--2816494 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2816452 AAAAATAATA
*
2816462 TTATAAATTATTATATT
1 TTATAAATTAATATATT
2816479 TTATAAA-TAATATATT
1 TTATAAATTAATATATT
2816495 ATTTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATAAATTAATATATT
Found at i:2816653 original size:29 final size:30
Alignment explanation
Indices: 2816599--2816660 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
2816589 ATAAAGAGCA
* **
2816599 AATTATGTTCATACATAAATTTTTA-TTTG
1 AATTATGTTCATAAATAAATAATTATTTTG
*
2816628 AATTATTTTCATAAATAAATAATTATTTTG
1 AATTATGTTCATAAATAAATAATTATTTTG
2816658 AAT
1 AAT
2816661 CAATTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (30 bp):
AATTATGTTCATAAATAAATAATTATTTTG
Found at i:2818276 original size:23 final size:23
Alignment explanation
Indices: 2818227--2818277 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
2818217 ATTTTAAGAT
*
2818227 ATTT-GGATTCAAATAATTTTGG
1 ATTTAGGATTCAAATAATTTTCG
* * *
2818249 GTTTAGGATTGAATTAATTTTCG
1 ATTTAGGATTCAAATAATTTTCG
2818272 ATTTAG
1 ATTTAG
2818278 ATCTTTTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (23 bp):
ATTTAGGATTCAAATAATTTTCG
Found at i:2819219 original size:11 final size:11
Alignment explanation
Indices: 2819203--2819227 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2819193 TTTTATTTGT
2819203 TACAATTCATA
1 TACAATTCATA
2819214 TACAATTCATA
1 TACAATTCATA
2819225 TAC
1 TAC
2819228 CACTAATAGT
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:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (11 bp):
TACAATTCATA
Found at i:2823315 original size:25 final size:23
Alignment explanation
Indices: 2823278--2823381 Score: 84
Period size: 23 Copynumber: 4.4 Consensus size: 23
2823268 ACACTAGCGC
2823278 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTCT-GT
*
2823301 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTCTGT
* * * * *
2823326 GCTCTCTGATTAGTACTTTGTAT
1 GCTCTCTGTTTAGCACTGTCTGT
* * **
2823349 ACTCTCTGTTTAGCATTGAGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
2823372 GCTCTCTGTT
1 GCTCTCTGTT
2823382 GCCCACCACT
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
23 44 0.68
24 1 0.02
25 17 0.26
26 3 0.05
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTCTGT
Found at i:2826189 original size:19 final size:19
Alignment explanation
Indices: 2826137--2826190 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
2826127 TTATATCAGA
*
2826137 ATAAATTTTAAAATT-ATAT
1 ATAAATTTT-AATTTAATAT
*
2826156 ATAAATTTTAGTTTAATAT
1 ATAAATTTTAATTTAATAT
2826175 AT-AATTTTATATTTAA
1 ATAAATTTTA-ATTTAA
2826191 ATTTTGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 10 0.33
19 20 0.67
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATAAATTTTAATTTAATAT
Found at i:2826237 original size:30 final size:30
Alignment explanation
Indices: 2826177--2826250 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
2826167 TTTAATATAT
2826177 AATTTTATAT-TTAAATTTTGATTTTGTTC
1 AATTTTATATATTAAATTTTGATTTTGTTC
*
2826206 AATTTTATATATTAATTTTTG-TTTTGATTC
1 AATTTTATATATTAAATTTTGATTTTG-TTC
*
2826236 AATTCTTATAAATTA
1 AATT-TTATATATTA
2826251 TTAATAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 15 0.38
30 16 0.40
31 9 0.22
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.59
Consensus pattern (30 bp):
AATTTTATATATTAAATTTTGATTTTGTTC
Found at i:2827990 original size:23 final size:23
Alignment explanation
Indices: 2827954--2828014 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
2827944 TTATTTGCCG
* * *
2827954 TTGTGGCATGTTTTTCCTTTGTA
1 TTGTGGCACGTTTTTCCTCTGCA
* * *
2827977 TTGTGGCACATTTTTTCTCTGCC
1 TTGTGGCACGTTTTTCCTCTGCA
2828000 TTGTGGCACGTTTTT
1 TTGTGGCACGTTTTT
2828015 GTTTTATGGC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.08, C:0.18, G:0.21, T:0.52
Consensus pattern (23 bp):
TTGTGGCACGTTTTTCCTCTGCA
Found at i:2828368 original size:18 final size:19
Alignment explanation
Indices: 2828337--2828380 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2828327 TGATATTTCA
*
2828337 TTTTCTATT-TTTTTTTAGT
1 TTTTCTATTGTTTTGTTA-T
2828356 TTTTCT-TTGTTTTGTTAT
1 TTTTCTATTGTTTTGTTAT
2828374 TTTTCTA
1 TTTTCTA
2828381 CTACATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.77
Consensus pattern (19 bp):
TTTTCTATTGTTTTGTTAT
Found at i:2829357 original size:75 final size:76
Alignment explanation
Indices: 2829277--2829425 Score: 228
Period size: 76 Copynumber: 2.0 Consensus size: 76
2829267 CTAAATTCAC
*
2829277 GCTTTCTACATTATTTCTCAATAAATATATT-TTTTTCACGTAAATCACATTCCTTCATTTAATT
1 GCTTTCTACATTATTTCTCAACAAATATATTCTTTTTCACGTAAATCACATTCCTTCATTTAATT
2829341 ATTGAATTTAT
66 ATTGAATTTAT
* ** * * *
2829352 GCTTTCTACATTATTTCTCAACAAATATTTTCTTTTTCATTTATATCGCATTCCTTCATTTAGTT
1 GCTTTCTACATTATTTCTCAACAAATATATTCTTTTTCACGTAAATCACATTCCTTCATTTAATT
2829417 ATTGAATTT
66 ATTGAATTT
2829426 GTTAAAATAC
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
75 29 0.44
76 37 0.56
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.51
Consensus pattern (76 bp):
GCTTTCTACATTATTTCTCAACAAATATATTCTTTTTCACGTAAATCACATTCCTTCATTTAATT
ATTGAATTTAT
Found at i:2838075 original size:20 final size:21
Alignment explanation
Indices: 2838052--2838094 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2838042 AGTCCTTCTT
* *
2838052 TTATATAATTAAATTA-ATAA
1 TTATATAATAAAAATATATAA
2838072 TTATATAATAAAAATATATAA
1 TTATATAATAAAAATATATAA
2838093 TT
1 TT
2838095 TTTGTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTATATAATAAAAATATATAA
Found at i:2838648 original size:2 final size:2
Alignment explanation
Indices: 2838641--2838670 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2838631 TAATATCAAA
2838641 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
2838671 CTTTGTAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2840049 original size:17 final size:18
Alignment explanation
Indices: 2840015--2840049 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2840005 AATCCCACTT
*
2840015 TTCCCTTTCTCTTTTTCC
1 TTCCCTTTCTCTTCTTCC
2840033 TTCCCTTT-TCTTCTTCC
1 TTCCCTTTCTCTTCTTCC
2840050 CCTGTTTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (18 bp):
TTCCCTTTCTCTTCTTCC
Found at i:2840168 original size:14 final size:14
Alignment explanation
Indices: 2840145--2840178 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2840135 AGATATTAGT
2840145 TAATAATAATAAAA
1 TAATAATAATAAAA
* *
2840159 TAATACTAATTAAA
1 TAATAATAATAAAA
2840173 TAATAA
1 TAATAA
2840179 GTTATATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:2840202 original size:13 final size:12
Alignment explanation
Indices: 2840158--2840213 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 12
2840148 TAATAATAAA
*
2840158 ATAATACTAATT
1 ATAATATTAATT
*
2840170 A-AATAATAAGTT
1 ATAATATTAA-TT
*
2840182 ATATTATTATATT
1 ATAATATTA-ATT
2840195 ATAATATTAATT
1 ATAATATTAATT
2840207 AATAATA
1 -ATAATA
2840214 AATTAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
11 7 0.19
12 7 0.19
13 21 0.58
14 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (12 bp):
ATAATATTAATT
Found at i:2840712 original size:21 final size:21
Alignment explanation
Indices: 2840630--2840752 Score: 63
Period size: 21 Copynumber: 5.6 Consensus size: 21
2840620 ATCATCATTT
2840630 TAATTATATTATATTTTTTAA
1 TAATTATATTATATTTTTTAA
* * *
2840651 -AAATATCAACTA-ATTTCTTTTA
1 TAATTAT--ATTATATTT-TTTAA
* *
2840673 TATATTATTTTCA-AGTTTTTAA
1 TA-ATTATATT-ATATTTTTTAA
2840695 TAATTATATTATATTTTTTAA
1 TAATTATATTATATTTTTTAA
* * *
2840716 AAATATCATCATTTTTTTATTTTAA
1 TAAT-T-AT-ATTATATT-TTTTAA
*
2840741 TAATTATTTTAT
1 TAATTATATTAT
2840753 TTATAAAATT
Statistics
Matches: 75, Mismatches: 16, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
20 6 0.08
21 22 0.29
22 18 0.24
23 9 0.12
24 11 0.15
25 9 0.12
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.58
Consensus pattern (21 bp):
TAATTATATTATATTTTTTAA
Found at i:2840752 original size:17 final size:17
Alignment explanation
Indices: 2840730--2840763 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2840720 ATCATCATTT
2840730 TTTTATTT-TAATAATTA
1 TTTTATTTATAA-AATTA
2840747 TTTTATTTATAAAATTA
1 TTTTATTTATAAAATTA
2840764 AATTATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTATTTATAAAATTA
Found at i:2841067 original size:20 final size:21
Alignment explanation
Indices: 2841042--2841084 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2841032 ATTCCTTCTT
* *
2841042 TTATATAATTAAATTAT-TAA
1 TTATATAATAAAAATATATAA
2841062 TTATATAATAAAAATATATAA
1 TTATATAATAAAAATATATAA
2841083 TT
1 TT
2841085 TTTGTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTATATAATAAAAATATATAA
Found at i:2841147 original size:212 final size:215
Alignment explanation
Indices: 2840735--2841149 Score: 633
Period size: 211 Copynumber: 1.9 Consensus size: 215
2840725 CATTTTTTTA
2840735 TTTTAATAATTATTTTATTTATAAAATTAAATTATAAATATGTAATTGTATATATCTCAATATCT
1 TTTTAATAATTATTTTATTTATAAAATTAAA-TAT-AATATGTAATTGTATATATCTCAATATCT
* *
2840800 TAAAAATATTTAAAATTAAGAATTCTTTGTTTTATATAATTAAATTAATAATCATATAATAAAAT
64 TAAAAATATTTAAAATTAAGAATTCCTTCTTTTATATAATTAAATTAATAATCATATAATAAAAT
* *
2840865 ATATAATTTTTGTATTTATCATCATGTTAAACATATTTTATTTTTTAACAATATCAACTAATTTC
129 ATATAATTTTTGTATTTATCATCATGTTAAACATATTTTATTTTTTAAAAAAATCAACTAATTTC
2840930 TTTTATATATTATTTTGAAGTT
194 TTTTATATATTATTTTGAAGTT
*
2840952 TTTTAATAATTATTTTATTTATAAAA-TACAA-AT-AT-T-TAATTGTATATATCTCATTATCTT
1 TTTTAATAATTATTTTATTTATAAAATTA-AATATAATATGTAATTGTATATATCTCAATATCTT
* * * * *
2841012 AAAAATATTTAATATTTATAATTCCTTCTTTTATATAATTAAATTATTAATTATATAATAAAAAT
65 AAAAATATTTAAAATTAAGAATTCCTTCTTTTATATAATTAAATTAATAATCATATAAT-AAAAT
* * * *
2841077 ATATAATTTTTGTATTTATTATTATGTTAAATATGTTTTATTTTTTAAAAAAATCAACTAATTTC
129 ATATAATTTTTGTATTTATCATCATGTTAAACATATTTTATTTTTTAAAAAAATCAACTAATTTC
2841142 TTTTATAT
194 TTTTATAT
2841150 GTTTTTCTTT
Statistics
Matches: 182, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
211 75 0.41
212 73 0.40
213 2 0.01
215 2 0.01
216 2 0.01
217 28 0.15
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (215 bp):
TTTTAATAATTATTTTATTTATAAAATTAAATATAATATGTAATTGTATATATCTCAATATCTTA
AAAATATTTAAAATTAAGAATTCCTTCTTTTATATAATTAAATTAATAATCATATAATAAAATAT
ATAATTTTTGTATTTATCATCATGTTAAACATATTTTATTTTTTAAAAAAATCAACTAATTTCTT
TTATATATTATTTTGAAGTT
Found at i:2848339 original size:12 final size:12
Alignment explanation
Indices: 2848322--2848358 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2848312 TCCCTTTTCC
*
2848322 CTTTTTCTTTTT
1 CTTTTTCTTCTT
2848334 CTTTTTCTTCTT
1 CTTTTTCTTCTT
*
2848346 CCTTTTCTTCTT
1 CTTTTTCTTCTT
2848358 C
1 C
2848359 CCCTGTTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2848480 original size:14 final size:14
Alignment explanation
Indices: 2848457--2848490 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2848447 AGATATTAGT
2848457 TAATAATAATAAAA
1 TAATAATAATAAAA
* *
2848471 TAATACTAATTAAA
1 TAATAATAATAAAA
2848485 TAATAA
1 TAATAA
2848491 GTTATATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:2848514 original size:13 final size:12
Alignment explanation
Indices: 2848470--2848525 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 12
2848460 TAATAATAAA
*
2848470 ATAATACTAATT
1 ATAATATTAATT
*
2848482 A-AATAATAAGTT
1 ATAATATTAA-TT
*
2848494 ATATTATTATATT
1 ATAATATTA-ATT
2848507 ATAATATTAATT
1 ATAATATTAATT
2848519 AATAATA
1 -ATAATA
2848526 AATTAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
11 7 0.19
12 7 0.19
13 21 0.58
14 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (12 bp):
ATAATATTAATT
Found at i:2849025 original size:21 final size:21
Alignment explanation
Indices: 2848943--2849065 Score: 63
Period size: 21 Copynumber: 5.6 Consensus size: 21
2848933 ATCATCATTT
2848943 TAATTATATTATATTTTTTAA
1 TAATTATATTATATTTTTTAA
* * *
2848964 -AAATATCAACTA-ATTTCTTTTA
1 TAATTAT--ATTATATTT-TTTAA
* *
2848986 TATATTATTTTCA-AGTTTTTAA
1 TA-ATTATATT-ATATTTTTTAA
2849008 TAATTATATTATATTTTTTAA
1 TAATTATATTATATTTTTTAA
* * *
2849029 AAATATCATCATTTTTTTATTTTAA
1 TAAT-T-AT-ATTATATT-TTTTAA
*
2849054 TAATTATTTTAT
1 TAATTATATTAT
2849066 TTATAAAATT
Statistics
Matches: 75, Mismatches: 16, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
20 6 0.08
21 22 0.29
22 18 0.24
23 9 0.12
24 11 0.15
25 9 0.12
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.58
Consensus pattern (21 bp):
TAATTATATTATATTTTTTAA
Found at i:2849065 original size:17 final size:17
Alignment explanation
Indices: 2849043--2849076 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2849033 ATCATCATTT
2849043 TTTTATTT-TAATAATTA
1 TTTTATTTATAA-AATTA
2849060 TTTTATTTATAAAATTA
1 TTTTATTTATAAAATTA
2849077 AATTATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTATTTATAAAATTA
Found at i:2849378 original size:20 final size:21
Alignment explanation
Indices: 2849353--2849395 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2849343 ATTCCTTCTT
* *
2849353 TTATATAATTAAATTAT-TAA
1 TTATATAATAAAAATATATAA
2849373 TTATATAATAAAAATATATAA
1 TTATATAATAAAAATATATAA
2849394 TT
1 TT
2849396 TTTGTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTATATAATAAAAATATATAA
Found at i:2858252 original size:38 final size:38
Alignment explanation
Indices: 2858201--2858285 Score: 161
Period size: 38 Copynumber: 2.2 Consensus size: 38
2858191 ATAAAATAAA
2858201 ATTTTTATTATAATGATAGACATGTACAAAAGCTTAAG
1 ATTTTTATTATAATGATAGACATGTACAAAAGCTTAAG
*
2858239 ATTTTTATTATAATGATAGACATTTACAAAAGCTTAAG
1 ATTTTTATTATAATGATAGACATGTACAAAAGCTTAAG
2858277 ATTTTTATT
1 ATTTTTATT
2858286 TTCGGATTAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (38 bp):
ATTTTTATTATAATGATAGACATGTACAAAAGCTTAAG
Found at i:2862851 original size:18 final size:18
Alignment explanation
Indices: 2862830--2862864 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2862820 GATCAAAACT
*
2862830 ATGGTGGTGATCATCATC
1 ATGGTGATGATCATCATC
2862848 ATGGTGATGATCATCAT
1 ATGGTGATGATCATCAT
2862865 GGAACAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (18 bp):
ATGGTGATGATCATCATC
Found at i:2862854 original size:15 final size:15
Alignment explanation
Indices: 2862834--2862866 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2862824 AAAACTATGG
2862834 TGGTGATCATCATCA
1 TGGTGATCATCATCA
*
2862849 TGGTGATGATCATCA
1 TGGTGATCATCATCA
2862864 TGG
1 TGG
2862867 AACAGAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.33
Consensus pattern (15 bp):
TGGTGATCATCATCA
Found at i:2874712 original size:21 final size:19
Alignment explanation
Indices: 2874676--2874720 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
2874666 AAAAATCAAA
2874676 ATATATTTTCTTATTTTTT
1 ATATATTTTCTTATTTTTT
*
2874695 ATATATTCTTTTTAATTTTTT
1 ATATATT-TTCTT-ATTTTTT
*
2874716 TTATA
1 ATATA
2874721 AAACTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
21 11 0.50
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (19 bp):
ATATATTTTCTTATTTTTT
Found at i:2874841 original size:3 final size:3
Alignment explanation
Indices: 2874827--2874869 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2874817 TTGTGAAATT
2874827 TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2874870 TGGTAGAGGC
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2877152 original size:11 final size:11
Alignment explanation
Indices: 2877120--2877162 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
2877110 GCCCAACTTG
2877120 AATTTTAAATT
1 AATTTTAAATT
* *
2877131 AAGTTTGAATT
1 AATTTTAAATT
2877142 AATTTTAAATT
1 AATTTTAAATT
*
2877153 TA-TTTAAATT
1 AATTTTAAATT
2877163 TAAATACATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (11 bp):
AATTTTAAATT
Found at i:2877165 original size:22 final size:22
Alignment explanation
Indices: 2877120--2877162 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2877110 GCCCAACTTG
*
2877120 AATTTTAAATTAAGTTTGAATT
1 AATTTTAAATTAAGTTTAAATT
*
2877142 AATTTTAAATTTA-TTTAAATT
1 AATTTTAAATTAAGTTTAAATT
2877163 TAAATACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
AATTTTAAATTAAGTTTAAATT
Found at i:2879262 original size:29 final size:29
Alignment explanation
Indices: 2879216--2879357 Score: 111
Period size: 29 Copynumber: 4.9 Consensus size: 29
2879206 TTATAGGTCT
2879216 CTAAACTATCCAAAAATTA-CATTTTGA-CC
1 CTAAACT-TCCAAAAATTACCATTTT-ACCC
2879245 CTGAAACTTCCAAAAATTACCATTTTACCC
1 CT-AAACTTCCAAAAATTACCATTTTACCC
*
2879275 CTAAACTTTCC-AAGATT-CCATTTTTAACCC
1 CTAAAC-TTCCAAAAATTACCA-TTTT-ACCC
*
2879305 C--AATTTCACAAAAAATTACCATTTTACCC
1 CTAAACTTC-C-AAAAATTACCATTTTACCC
* *
2879334 CCAAACCTTTC-AAAATT-CCATTTT
1 CTAAA-CTTCCAAAAATTACCATTTT
2879358 TGACCCCGAT
Statistics
Matches: 95, Mismatches: 5, Indels: 27
0.75 0.04 0.21
Matches are distributed among these distances:
27 3 0.03
28 13 0.14
29 38 0.40
30 33 0.35
31 6 0.06
32 2 0.02
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (29 bp):
CTAAACTTCCAAAAATTACCATTTTACCC
Found at i:2879386 original size:60 final size:59
Alignment explanation
Indices: 2879254--2879598 Score: 426
Period size: 59 Copynumber: 5.9 Consensus size: 59
2879244 CCTGAAACTT
* * *
2879254 CCAAAAATTACCATTTTACCCCTAAA-CTTTCCAAGATTCCATTTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACCTTT-CAAAATTCCATTTTTAACCCCGATTTCA
* *
2879313 CAAAAAATTACCATTTTACCCCCAAACCTTTCAAAATTCCATTTTTGACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACCTTTCAAAATTCCATTTTTAACCCCGATTTCA
* * *
2879372 CCAAAAAATTACCATTTTATCCCCAAACCTTTCAAAATTTCATTTTTAACCTCGATTTCA
1 CC-AAAAATTACCATTTTACCCCCAAACCTTTCAAAATTCCATTTTTAACCCCGATTTCA
** * * *
2879432 CCAAAAATTACCATTTTACCCCCAAATATTTCAAAGTTCCATTTTTTACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACCTTTCAAAATTCCATTTTTAACCCCGATTTCA
* ** * * * *
2879491 CC-AAAATTACCAATTTACCCCTGAACCTTTTAAAATTCTATTTTTGA-CCCAATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACCTTTCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
2879548 CCAAAAACTACCATTTTACCCCCGAACATTCCAAAATCCCATTTTTAACCC
1 CCAAAAATTACCATTTTACCCCCAAACCTTTCAAAATTCCATTTTTAACCC
2879599 TAAATTTTTT
Statistics
Matches: 244, Mismatches: 38, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
57 10 0.04
58 72 0.30
59 103 0.42
60 59 0.24
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.34
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACCTTTCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:2879421 original size:119 final size:118
Alignment explanation
Indices: 2879254--2879598 Score: 448
Period size: 119 Copynumber: 2.9 Consensus size: 118
2879244 CCTGAAACTT
* * *
2879254 CCAAAAATTACCATTTTACCCCTAAA-CTTTCCAAGATTCCATTTTTAACCCCAATTTCACAAAA
1 CCAAAAATTACCATTTTACCCCTAAACCTTT-CAAAATTTCATTTTTAACCCCAATTTCACCAAA
* *
2879318 AATTACCATTTTACCCCCAAACCTTTCAAAATTCCATTTTTGACCCCGATTTCA
65 AATTACCATTTTACCCCCAAACATTTCAAAATTCCATTTTTAACCCCGATTTCA
* *
2879372 CCAAAAAATTACCATTTTATCCCC-AAACCTTTCAAAATTTCATTTTTAACCTCGATTTCACCAA
1 CC-AAAAATTACCATTTTA-CCCCTAAACCTTTCAAAATTTCATTTTTAACCCCAATTTCACCAA
* * * *
2879436 AAATTACCATTTTACCCCCAAATATTTCAAAGTTCCATTTTTTACCCTGATTTCA
64 AAATTACCATTTTACCCCCAAACATTTCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
2879491 CC-AAAATTACCAATTTACCCCTGAACCTTTTAAAA-TTCTATTTTTGA-CCCAATTTCACCAAA
1 CCAAAAATTACCATTTTACCCCTAAACCTTTCAAAATTTC-ATTTTTAACCCCAATTTCACCAAA
* * * *
2879553 AACTACCATTTTACCCCCGAACATTCCAAAATCCCATTTTTAACCC
65 AATTACCATTTTACCCCCAAACATTTCAAAATTCCATTTTTAACCC
2879599 TAAATTTTTT
Statistics
Matches: 199, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
116 59 0.30
117 32 0.16
118 2 0.01
119 98 0.49
120 8 0.04
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.34
Consensus pattern (118 bp):
CCAAAAATTACCATTTTACCCCTAAACCTTTCAAAATTTCATTTTTAACCCCAATTTCACCAAAA
ATTACCATTTTACCCCCAAACATTTCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:2884417 original size:28 final size:28
Alignment explanation
Indices: 2884363--2884421 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
2884353 TCATTTTTCT
*
2884363 TTTGGAATTAATTAAGTTTATGATTGAA
1 TTTGGAATTAATTAAGTTTATAATTGAA
**
2884391 TTTGGAATTAATTCTGTTTA-AATTTGAA
1 TTTGGAATTAATTAAGTTTATAA-TTGAA
2884419 TTT
1 TTT
2884422 ATTTAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.51
Consensus pattern (28 bp):
TTTGGAATTAATTAAGTTTATAATTGAA
Found at i:2887375 original size:2 final size:2
Alignment explanation
Indices: 2887368--2887420 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2887358 AAATAATACA
2887368 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
2887410 AT AT AT AT AT A
1 AT AT AT AT AT A
2887421 CCAAAATGGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2887769 original size:17 final size:17
Alignment explanation
Indices: 2887747--2887780 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2887737 TTTATAATAA
*
2887747 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
2887764 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
2887781 GAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:2896097 original size:282 final size:284
Alignment explanation
Indices: 2895700--2896260 Score: 937
Period size: 285 Copynumber: 2.0 Consensus size: 284
2895690 GTCTATATAA
*
2895700 GTCTTCCCTTCTAACATCACCATGATAACATATAGGGAAGGAATTTGTGTGGTAAAGGGATTGTA
1 GTCTTCCCTTCTAACATCACCATGATAACATATAGGGAAGGAATTTGTGTGGTAAAGAGATTGTA
* **
2895765 ACAGTCATTGACTTTTTCGAGTCTTGATTAATCATTTGGTTAACA-CCCCCCTTTTTTTTTGAGA
66 ACAGTCATTGACTTTTTCGAGTCTTGATTAATCATATGGTTAACACCCCCCCCCTTTTTTTGAGA
* * *
2895829 GCAAGTGCTTGTCAAGCTTAGCTGTGTGAGTAAAGATAGTAGGCTATTTTTGACTTGCTGCATTT
131 GCAAGTGCTTGTCAAGCTTAGCTGCGTGAGTAAAGATAGTAGGCAATTGTTGACTTGCTGCATTT
* * **
2895894 TTTATTCTAGTGTGTGCATAAGCTATGTTGATTAGGTCTATATTATCGTTTATGACATCTTTAGA
196 TGTATTCTAGTGTGTGCATAAGCTATGGTGATTAGGTCTATATTATAATTTATGACATCTTTAGA
2895959 CTCTTAATCTTCTTAAAACATATG
261 CTCTTAATCTTCTTAAAACATATG
2895983 GTCTTCCCTTCTAACATCACCATGATAACATATAGGGAAGGAATTTGTGTGGT-AAGAGATTGTA
1 GTCTTCCCTTCTAACATCACCATGATAACATATAGGGAAGGAATTTGTGTGGTAAAGAGATTGTA
*
2896047 ACAGTCATTGGCTTTTTCGAGTCTTGATTAATCATATGGTTAACACCCCCCCCCCCTTTTTTTGA
66 ACAGTCATTGACTTTTTCGAGTCTTGATTAATCATATGGTTAACA--CCCCCCCCCTTTTTTTGA
* * ** *
2896112 GAGCAATTGCTTGTCAAGCTTAGCTGCGTGAGTAATGATAGTATTCAATTGTTGACTTGTTGCAT
129 GAGCAAGTGCTTGTCAAGCTTAGCTGCGTGAGTAAAGATAGTAGGCAATTGTTGACTTGCTGCAT
2896177 TTTGTATTCTAGTGTGTGCATAAGCTATGGTGATTAGGTCTATATTATAATTTATGACATCTTTA
194 TTTGTATTCTAGTGTGTGCATAAGCTATGGTGATTAGGTCTATATTATAATTTATGACATCTTTA
2896242 GACTCTTAATCTTCTTAAA
259 GACTCTTAATCTTCTTAAA
2896261 CGTGATTTTG
Statistics
Matches: 258, Mismatches: 17, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
282 53 0.21
283 53 0.21
285 152 0.59
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (284 bp):
GTCTTCCCTTCTAACATCACCATGATAACATATAGGGAAGGAATTTGTGTGGTAAAGAGATTGTA
ACAGTCATTGACTTTTTCGAGTCTTGATTAATCATATGGTTAACACCCCCCCCCTTTTTTTGAGA
GCAAGTGCTTGTCAAGCTTAGCTGCGTGAGTAAAGATAGTAGGCAATTGTTGACTTGCTGCATTT
TGTATTCTAGTGTGTGCATAAGCTATGGTGATTAGGTCTATATTATAATTTATGACATCTTTAGA
CTCTTAATCTTCTTAAAACATATG
Found at i:2899374 original size:30 final size:30
Alignment explanation
Indices: 2899277--2899374 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 30
2899267 TGAATCATGG
* * *
2899277 AAAATTTTCTATTTAATCCTTTTATAATTTAT
1 AAAAATTTC-ATTTAAT-CTTTTAAAAATTAT
* *
2899309 AAAAA-TTCACTTTGATCTTTTTGAAAAA-GAT
1 AAAAATTTCA-TTTAATC-TTTT-AAAAATTAT
*
2899340 -AAAATTTGATTTAATCTTTTAAAAATTAT
1 AAAAATTTCATTTAATCTTTTAAAAATTAT
2899369 AAAAAT
1 AAAAAT
2899375 ATAGATAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
28 5 0.10
29 6 0.12
30 17 0.33
31 17 0.33
32 7 0.13
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (30 bp):
AAAAATTTCATTTAATCTTTTAAAAATTAT
Found at i:2921490 original size:11 final size:11
Alignment explanation
Indices: 2921450--2921500 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
2921440 AAGAGTTATA
*
2921450 CAAAAAAACAA
1 CAAAAAAACAG
*
2921461 CAAAAAAATAG
1 CAAAAAAACAG
**
2921472 CAGCAAAACAG
1 CAAAAAAACAG
2921483 CAAAAAAA-AG
1 CAAAAAAACAG
*
2921493 TAAAAAAA
1 CAAAAAAA
2921501 AAAGCAACTT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.75, C:0.14, G:0.08, T:0.04
Consensus pattern (11 bp):
CAAAAAAACAG
Found at i:2927384 original size:16 final size:17
Alignment explanation
Indices: 2927355--2927387 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2927345 GTTGAAGAGG
2927355 AATAAAAGAAAATAATA
1 AATAAAAGAAAATAATA
2927372 AATAAAA-AAAATAATA
1 AATAAAAGAAAATAATA
2927388 TGTTTCAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
AATAAAAGAAAATAATA
Found at i:2927760 original size:5 final size:5
Alignment explanation
Indices: 2927750--2927798 Score: 98
Period size: 5 Copynumber: 9.8 Consensus size: 5
2927740 CACACACCCA
2927750 CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCT
1 CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCT
2927799 ATATATAGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (5 bp):
CCCTT
Found at i:2928964 original size:202 final size:201
Alignment explanation
Indices: 2928598--2928975 Score: 544
Period size: 202 Copynumber: 1.9 Consensus size: 201
2928588 CAAAATAATA
* *
2928598 CAAATTATTAAATAAAAAATAATTAAAAAAAAGCAATTACGATAAATCAATCATATCACATCGAA
1 CAAATTATTAAATAAAAAATAATTAAAAAAAAGCAATTACAATAAATCAATAATATCACATCGAA
* * * * * * *
2928663 ATTTTGAAAAAAACTTTAATACTTTCATCATTTCAATCGGTTACCATTTAAAAGAAAAAGACGAA
66 ATTTTGAAAAAAAATATAATAATGTCATCATTTCAATCAGATACCATCTAAAAGAAAAAGACGAA
* * *
2928728 CCCCCGAACTCAGCCTACTTTACTTCTTTACAAACAATTTCCCTTTTTTCTAGTTGGTTGTTTGG
131 CACCCGAACTCAGCATACTTTACCTCTTTACAAACAATTTCCCTTTTTTCTAGTTGGTTGTTTGG
2928793 ATGAGT
196 ATGAGT
* * *
2928799 CAAATTGTTAAATGAAAAATAATTAAGAAAAA-CAATTACAATAAATCAATAATATCACATCGAA
1 CAAATTATTAAATAAAAAATAATTAAAAAAAAGCAATTACAATAAATCAATAATATCACATCGAA
* *
2928863 ATTTTGAAAAAAAATATAATAATCGTCGATCATTTCAATCAGATACCATCTAAAATG-AAGAGAG
66 ATTTTGAAAAAAAATATAATAAT-GTC-ATCATTTCAATCAGATACCATCTAAAA-GAAAAAGAC
* *
2928927 GAAGACCCGAACTCAGCATACTTTACCTCTTTACAAACATTTTCCCTTT
128 GAACACCCGAACTCAGCATACTTTACCTCTTTACAAACAATTTCCCTTT
2928976 CTTGGGGGGT
Statistics
Matches: 155, Mismatches: 19, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
200 50 0.32
201 31 0.20
202 73 0.47
203 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (201 bp):
CAAATTATTAAATAAAAAATAATTAAAAAAAAGCAATTACAATAAATCAATAATATCACATCGAA
ATTTTGAAAAAAAATATAATAATGTCATCATTTCAATCAGATACCATCTAAAAGAAAAAGACGAA
CACCCGAACTCAGCATACTTTACCTCTTTACAAACAATTTCCCTTTTTTCTAGTTGGTTGTTTGG
ATGAGT
Found at i:2930505 original size:14 final size:15
Alignment explanation
Indices: 2930486--2930518 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2930476 CCCATCAATG
2930486 TTTTCTTTTTTT-CT
1 TTTTCTTTTTTTCCT
2930500 TTTTCTTTTTTTCCT
1 TTTTCTTTTTTTCCT
2930515 TTTT
1 TTTT
2930519 GAATAATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTCTTTTTTTCCT
Found at i:2931785 original size:15 final size:16
Alignment explanation
Indices: 2931761--2931802 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
2931751 AGTTCAGGTT
* *
2931761 GTTTCTAGTTTGGA-C
1 GTTTCAAGTTTCGATC
2931776 GTTTCAAGTTTCGATC
1 GTTTCAAGTTTCGATC
*
2931792 TTTTCAAGTTT
1 GTTTCAAGTTT
2931803 AGGTAGTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (16 bp):
GTTTCAAGTTTCGATC
Found at i:2934105 original size:63 final size:63
Alignment explanation
Indices: 2934027--2934153 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
2934017 TTCATTGCTG
*
2934027 TTCTCATCGGCAGCTATTATTGCTATAATTATAATTTTTTACTGTTAAAACCTTTCCATTCAA
1 TTCTCATCGGCAGCTATTATTGCTATAATTATAAATTTTTACTGTTAAAACCTTTCCATTCAA
*
2934090 TTCTCATCGGCAGCTATTATTGCTATAATTATAAATTTTTACTGTTTAAACCTTTCCATTCAA
1 TTCTCATCGGCAGCTATTATTGCTATAATTATAAATTTTTACTGTTAAAACCTTTCCATTCAA
2934153 T
1 T
2934154 CACGTCTTTG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (63 bp):
TTCTCATCGGCAGCTATTATTGCTATAATTATAAATTTTTACTGTTAAAACCTTTCCATTCAA
Found at i:2934507 original size:3 final size:3
Alignment explanation
Indices: 2934499--2934524 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2934489 CAGCTAAAAA
2934499 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
2934525 ACAACAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:2941834 original size:31 final size:31
Alignment explanation
Indices: 2941796--2941858 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
2941786 ATTTCACTAT
2941796 TATGGAGCTCATGGTCTTGGCATGCCCCGAG
1 TATGGAGCTCATGGTCTTGGCATGCCCCGAG
2941827 TATGGAGCTCATGGTCTTGGCATGCCCCGAG
1 TATGGAGCTCATGGTCTTGGCATGCCCCGAG
2941858 T
1 T
2941859 GCTTCCCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.16, C:0.25, G:0.32, T:0.27
Consensus pattern (31 bp):
TATGGAGCTCATGGTCTTGGCATGCCCCGAG
Found at i:2943794 original size:16 final size:15
Alignment explanation
Indices: 2943769--2943804 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2943759 TGATTGGATC
2943769 ATTTTGATTCAAACA
1 ATTTTGATTCAAACA
*
2943784 ATTTGTGATTCAACCA
1 ATTT-TGATTCAAACA
2943800 ATTTT
1 ATTTT
2943805 AGGGTTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.44
Consensus pattern (15 bp):
ATTTTGATTCAAACA
Found at i:2944855 original size:32 final size:29
Alignment explanation
Indices: 2944787--2944857 Score: 72
Period size: 32 Copynumber: 2.3 Consensus size: 29
2944777 ATTATTTATT
2944787 GTATTTTTTAATTATTTAATGATATTTTA
1 GTATTTTTTAATTATTTAATGATATTTTA
* *
2944816 ATAATTTTTTCATGTCATTTATAT-ATAATTTTA
1 GT-ATTTTTTAAT-T-ATTTA-ATGAT-ATTTTA
2944849 GTATTTTTT
1 GTATTTTTT
2944858 TACCCTGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
29 1 0.03
30 9 0.26
31 1 0.03
32 14 0.41
33 9 0.26
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.62
Consensus pattern (29 bp):
GTATTTTTTAATTATTTAATGATATTTTA
Found at i:2946066 original size:21 final size:22
Alignment explanation
Indices: 2946042--2946082 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2946032 TACACTATTT
2946042 AAAATATAAT-ATATATTTAAA
1 AAAATATAATAATATATTTAAA
*
2946063 AAAATATAATAATTTATTTA
1 AAAATATAATAATATATTTA
2946083 GCTCTCCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATATAATAATATATTTAAA
Found at i:2947045 original size:99 final size:102
Alignment explanation
Indices: 2946849--2947047 Score: 289
Period size: 99 Copynumber: 2.0 Consensus size: 102
2946839 TTTAAAAAAT
2946849 TAAAAATTATAAATCAAATTATTAAATTTAATTGTGAAATTAAGAAATCACTCTTCCTCATAGGA
1 TAAAAATTATAAATCAAATTATTAAATTTAATTGTGAAATTAAGAAATCACTCTTCCTCATAGGA
*
2946914 TACTAATCCAAACTTTACTCCCATCAAGATCATATAA
66 TACTAATCCAAACATTACTCCCATCAAGATCATATAA
* * * **
2946951 TAAAAATTATGAATCAAATTATTAATTTTGATTGTGAAATTAA-ACCTC-C-CTTCCAT-ATAGG
1 TAAAAATTATAAATCAAATTATTAAATTTAATTGTGAAATTAAGAAATCACTCTTCC-TCATAGG
* *
2947012 ATACTAATCCAAACATTATTCCCATCAATATCATAT
65 ATACTAATCCAAACATTACTCCCATCAAGATCATAT
2947048 CTTGTCCTCC
Statistics
Matches: 88, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
99 43 0.49
100 2 0.02
101 3 0.03
102 40 0.45
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (102 bp):
TAAAAATTATAAATCAAATTATTAAATTTAATTGTGAAATTAAGAAATCACTCTTCCTCATAGGA
TACTAATCCAAACATTACTCCCATCAAGATCATATAA
Found at i:2954104 original size:21 final size:20
Alignment explanation
Indices: 2954072--2954134 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
2954062 TTTGTTGAGT
*
2954072 AATATAATAAAA-ATTATTAA
1 AATATAATAAAATA-TATAAA
2954092 AATATACATAAAATATATAAA
1 AATATA-ATAAAATATATAAA
* *
2954113 AATATAA-AAAACATAAAAA
1 AATATAATAAAATATATAAA
2954132 AAT
1 AAT
2954135 TTAAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 13 0.34
20 7 0.18
21 17 0.45
22 1 0.03
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (20 bp):
AATATAATAAAATATATAAA
Found at i:2954116 original size:10 final size:10
Alignment explanation
Indices: 2954072--2954134 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
2954062 TTTGTTGAGT
2954072 AATATAATAAA
1 AATAT-ATAAA
*
2954083 AAT-TATTAA
1 AATATATAAA
*
2954092 AATATACATAA
1 AATATATA-AA
2954103 AATATATAAA
1 AATATATAAA
2954113 AATATA-AAA
1 AATATATAAA
* *
2954122 AACATAAAAA
1 AATATATAAA
2954132 AAT
1 AAT
2954135 TTAAATTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
9 15 0.35
10 16 0.37
11 12 0.28
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (10 bp):
AATATATAAA
Found at i:2954132 original size:19 final size:19
Alignment explanation
Indices: 2954090--2954139 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
2954080 AAAAATTATT
* *
2954090 AAAATATACATAAAATATATA
1 AAAATATA-A-AAAACATAAA
2954111 AAAATATAAAAAACATAAA
1 AAAATATAAAAAACATAAA
*
2954130 AAAATTTAAA
1 AAAATATAAA
2954140 TTAAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 17 0.65
20 1 0.04
21 8 0.31
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATATAAAAAACATAAA
Found at i:2954157 original size:17 final size:17
Alignment explanation
Indices: 2954087--2954167 Score: 58
Period size: 17 Copynumber: 4.6 Consensus size: 17
2954077 AATAAAAATT
*
2954087 ATTAAAATATACATAAA
1 ATTAAAAAATACATAAA
* *
2954104 ATATATAAAAATATAAAAA
1 AT-TA-AAAAATACATAAA
* * *
2954123 ACATAAAAAA-A-TTTAA
1 A-TTAAAAAATACATAAA
2954139 ATTAAAAAATACATAAA
1 ATTAAAAAATACATAAA
2954156 ATTAAAAGAATA
1 ATTAAAA-AATA
2954168 TGAAATACAC
Statistics
Matches: 48, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
15 7 0.15
16 4 0.08
17 13 0.27
18 11 0.23
19 13 0.27
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.26
Consensus pattern (17 bp):
ATTAAAAAATACATAAA
Found at i:2961603 original size:14 final size:14
Alignment explanation
Indices: 2961580--2961613 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2961570 AATTATTTCG
*
2961580 TTATTATATTGTTA
1 TTATTTTATTGTTA
2961594 TTATTTTATTGTTA
1 TTATTTTATTGTTA
2961608 TTATTT
1 TTATTT
2961614 GAATATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (14 bp):
TTATTTTATTGTTA
Found at i:2968186 original size:11 final size:11
Alignment explanation
Indices: 2968170--2968196 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2968160 ATGATTCTCT
2968170 GAAAAAGAAAA
1 GAAAAAGAAAA
2968181 GAAAAAGAAAA
1 GAAAAAGAAAA
2968192 GAAAA
1 GAAAA
2968197 CTGATAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:2968780 original size:3 final size:3
Alignment explanation
Indices: 2968772--2968797 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2968762 ACTAGATGGG
2968772 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
2968798 AAGTGAGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:2974734 original size:18 final size:17
Alignment explanation
Indices: 2974711--2974768 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
2974701 ACAACGTCTT
2974711 TCAGACAAAGCTTCCATC
1 TCAGACAAA-CTTCCATC
*
2974729 TCAGACAAACTCTCC-TT
1 TCAGACAAACT-TCCATC
2974746 TCAGACAAAAACTTCCCATC
1 TCAGAC--AAACTT-CCATC
2974766 TCA
1 TCA
2974769 AATATCTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
17 9 0.27
18 13 0.39
19 7 0.21
20 4 0.12
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.24
Consensus pattern (17 bp):
TCAGACAAACTTCCATC
Found at i:2974751 original size:17 final size:17
Alignment explanation
Indices: 2974708--2974754 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
2974698 CATACAACGT
2974708 CTTTCAGACAAAGCTTC
1 CTTTCAGACAAAGCTTC
*
2974725 CATCTCAGACAAA-CTCTC
1 C-TTTCAGACAAAGCT-TC
2974743 CTTTCAGACAAA
1 CTTTCAGACAAA
2974755 AACTTCCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.34, C:0.32, G:0.09, T:0.26
Consensus pattern (17 bp):
CTTTCAGACAAAGCTTC
Found at i:2974791 original size:9 final size:9
Alignment explanation
Indices: 2974779--2974804 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2974769 AATATCTCAT
2974779 CATCATCAC
1 CATCATCAC
2974788 CATCATCAC
1 CATCATCAC
2974797 CATCATCA
1 CATCATCA
2974805 TCAAGCAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.23
Consensus pattern (9 bp):
CATCATCAC
Found at i:2977724 original size:28 final size:28
Alignment explanation
Indices: 2977687--2977744 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
2977677 GTACTCAACT
*
2977687 ACTCCTTTTTTAGAAAAAAAGAAGAGAGC
1 ACTCCTTTTTTAG-AAAAAAGAAGAAAGC
2977716 ACTCCTTTTTTAGAAAAAAGAAGAAAGC
1 ACTCCTTTTTTAGAAAAAAGAAGAAAGC
2977744 A
1 A
2977745 TTGCAATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.24
Consensus pattern (28 bp):
ACTCCTTTTTTAGAAAAAAGAAGAAAGC
Found at i:2982299 original size:20 final size:19
Alignment explanation
Indices: 2982225--2982298 Score: 53
Period size: 22 Copynumber: 3.8 Consensus size: 19
2982215 ATATTTTAAG
*
2982225 TAATTAATATAAAGTATTTA
1 TAATTAATATGAA-TATTTA
* *
2982245 TAAATTTAATTTGAATATATA
1 T-AA-TTAATATGAATATTTA
**
2982266 -AATT-ATATTTATAATTTA
1 TAATTAATATGAAT-ATTTA
2982284 TAATTAATATGAATA
1 TAATTAATATGAATA
2982299 AATGATAATT
Statistics
Matches: 40, Mismatches: 9, Indels: 11
0.67 0.15 0.18
Matches are distributed among these distances:
17 5 0.12
18 6 0.15
19 7 0.17
20 7 0.17
21 7 0.17
22 8 0.20
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
TAATTAATATGAATATTTA
Found at i:3003609 original size:3 final size:3
Alignment explanation
Indices: 3003603--3003639 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3003593 TTCAAAGCAA
3003603 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3003640 CGATCCTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3005328 original size:67 final size:67
Alignment explanation
Indices: 3005195--3005330 Score: 204
Period size: 67 Copynumber: 2.0 Consensus size: 67
3005185 CTATGTTCCC
* * *
3005195 ACTTTTAATGGTCCATGATTATTTTTTTTATGTTTGCATTCACTTTTGGGAATGCAACAAATTTA
1 ACTTTTAATGGTCCATGATTATTTTTTTTATGTTTGCATTCAATTCTGAGAATGCAACAAATTTA
3005260 GT
66 GT
*
3005262 ACTTTTAGTGGTCCATGATTATTTTCTTTATATGTTTGCATTCAATTCTGAGAATGCAAC-AA-T
1 ACTTTTAATGGTCCATGATTATTTT-TTT-TATGTTTGCATTCAATTCTGAGAATGCAACAAATT
3005325 TAGT
64 TAGT
3005329 AC
1 AC
3005331 GACGAACTTA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
67 31 0.49
68 5 0.08
69 27 0.43
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (67 bp):
ACTTTTAATGGTCCATGATTATTTTTTTTATGTTTGCATTCAATTCTGAGAATGCAACAAATTTA
GT
Found at i:3005660 original size:45 final size:46
Alignment explanation
Indices: 3005595--3005688 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 46
3005585 GACGACTGAA
*
3005595 AAAAAAATAATTAAATGAGAATCGTGCTGATAACGTGTTATAAAAT
1 AAAAAAATAATTAAATGAGAATCATGCTGATAACGTGTTATAAAAT
3005641 AAAAAAA-AATTAAATGAGAATCATGCTGATAACGTGTTATAAAAT
1 AAAAAAATAATTAAATGAGAATCATGCTGATAACGTGTTATAAAAT
3005686 AAA
1 AAA
3005689 GAGACAATAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 40 0.85
46 7 0.15
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.27
Consensus pattern (46 bp):
AAAAAAATAATTAAATGAGAATCATGCTGATAACGTGTTATAAAAT
Found at i:3012159 original size:54 final size:52
Alignment explanation
Indices: 3012100--3012206 Score: 187
Period size: 54 Copynumber: 2.0 Consensus size: 52
3012090 AGTTGCATTG
3012100 TAGTTGCCTTTTCTTCTAATGTAACTTTTGACTCTGCTTTGGTGGGTTATTGAA
1 TAGTTGCCTTTTCTTCTAATGTAACTTTTGA--CTGCTTTGGTGGGTTATTGAA
*
3012154 TAGTTGCCTTTTTTTCTAATGTAACTTTTGACTGCTTTGGTGGGTTATTGAA
1 TAGTTGCCTTTTCTTCTAATGTAACTTTTGACTGCTTTGGTGGGTTATTGAA
3012206 T
1 T
3012207 TTTCTCCATG
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
52 22 0.42
54 30 0.58
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.50
Consensus pattern (52 bp):
TAGTTGCCTTTTCTTCTAATGTAACTTTTGACTGCTTTGGTGGGTTATTGAA
Found at i:3016414 original size:31 final size:29
Alignment explanation
Indices: 3016374--3016463 Score: 87
Period size: 31 Copynumber: 3.1 Consensus size: 29
3016364 AAAAGAAAGG
*
3016374 TTTTGAATAGTTAAGTGATTTAAATAAAAA
1 TTTTTAATAGTTAAGTGA-TTAAATAAAAA
** *
3016404 TTTTTAAATAGTTAAACGATTAAATTATAAA
1 TTTTT-AATAGTTAAGTGATTAAA-TAAAAA
*
3016435 TTTTT-TTAGTTAAGTGA-T-AATAAAAA
1 TTTTTAATAGTTAAGTGATTAAATAAAAA
3016461 TTT
1 TTT
3016464 AGTGATTAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
26 8 0.16
27 2 0.04
28 1 0.02
29 9 0.18
30 9 0.18
31 21 0.42
ACGTcount: A:0.44, C:0.01, G:0.10, T:0.44
Consensus pattern (29 bp):
TTTTTAATAGTTAAGTGATTAAATAAAAA
Found at i:3016575 original size:26 final size:22
Alignment explanation
Indices: 3016544--3016609 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
3016534 TATAAGGAGA
*
3016544 AATTATTTTATGGATCTTTCTTATC
1 AATTATTTCAT-GATCTTT-TTA-C
3016569 ATATTA-TTCATGATCTTTTTAC
1 A-ATTATTTCATGATCTTTTTAC
* *
3016591 AATTATTTAATGATATTTT
1 AATTATTTCATGATCTTTT
3016610 AGTAATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 4 0.11
22 13 0.36
23 3 0.08
24 7 0.19
25 5 0.14
26 4 0.11
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (22 bp):
AATTATTTCATGATCTTTTTAC
Found at i:3020054 original size:22 final size:22
Alignment explanation
Indices: 3020029--3020071 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3020019 TAATTCCAAG
3020029 TTTAAATT-TGTACTAACTATTC
1 TTTAAATTATGT-CTAACTATTC
**
3020051 TTTATTTTATGTCTAACTATT
1 TTTAAATTATGTCTAACTATT
3020072 GTAATACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTAAATTATGTCTAACTATTC
Found at i:3023451 original size:24 final size:24
Alignment explanation
Indices: 3023392--3023456 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 24
3023382 GTTTAGAGTT
3023392 TTAATATTTATTTATAATTAATTA
1 TTAATATTTATTTATAATTAATTA
3023416 TT--TGATTATATTTA-AATTACATTA
1 TTAAT-ATT-TATTTATAATTA-ATTA
3023440 TTAATATTTATTTATAA
1 TTAATATTTATTTATAA
3023457 GTTTATTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
22 1 0.03
23 8 0.23
24 20 0.57
25 5 0.14
26 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
TTAATATTTATTTATAATTAATTA
Found at i:3024892 original size:21 final size:21
Alignment explanation
Indices: 3024868--3024914 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
3024858 GTGTCGAGCC
3024868 AATTTGGGTTAAA-TCA-ATTT
1 AATTTGGG-TAAATTCATATTT
3024888 GAATTTGGGTAAATTCATATTT
1 -AATTTGGGTAAATTCATATTT
3024910 AATTT
1 AATTT
3024915 ATTTGAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.17
21 16 0.67
22 4 0.17
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (21 bp):
AATTTGGGTAAATTCATATTT
Found at i:3028727 original size:2 final size:2
Alignment explanation
Indices: 3028722--3028750 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3028712 TATATATATA
3028722 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3028751 CGATTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3029865 original size:14 final size:16
Alignment explanation
Indices: 3029815--3029870 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
3029805 GTTTATTTTG
*
3029815 ATTTTATAT-ATTCAT
1 ATTTTATATAATTAAT
3029830 AATTTTTATATAATTAAT
1 -A-TTTTATATAATTAAT
3029848 ATTTTA-ATAATT-AT
1 ATTTTATATAATTAAT
3029862 ATTTTATAT
1 ATTTTATAT
3029871 TTCATTTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 8 0.22
15 8 0.22
16 6 0.17
17 9 0.25
18 5 0.14
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTATATAATTAAT
Found at i:3034745 original size:28 final size:27
Alignment explanation
Indices: 3034702--3034755 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
3034692 TATATTAATG
* * *
3034702 ATAAAAAAAGTAAAATTTTCTTTATCA
1 ATAAAAAAAATAAAATTGTCATTATCA
3034729 ATAAAATAAAATAAAATTGTCATTATC
1 ATAAAA-AAAATAAAATTGTCATTATC
3034756 CCATGAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (27 bp):
ATAAAAAAAATAAAATTGTCATTATCA
Found at i:3038701 original size:24 final size:24
Alignment explanation
Indices: 3038673--3038731 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
3038663 CCTGATTTAT
3038673 CTACAGATGTTGCTGATGAGGTT-C
1 CTACAGATGTTGCTGATG-GGTTGC
* *
3038697 CTACAGATGTTGCTGATGGTTTGG
1 CTACAGATGTTGCTGATGGGTTGC
3038721 CTACAGATGTT
1 CTACAGATGTT
3038732 ACTACTGAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 3 0.09
24 29 0.91
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.36
Consensus pattern (24 bp):
CTACAGATGTTGCTGATGGGTTGC
Found at i:3042493 original size:6 final size:6
Alignment explanation
Indices: 3042459--3042520 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
3042449 TAATAGGGAT
* * * *
3042459 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
*
3042506 TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTT
3042521 TGATCACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 40 0.85
7 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:3059119 original size:20 final size:20
Alignment explanation
Indices: 3059080--3059124 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
3059070 TAGGGTTCAT
3059080 GATTCAAGTTTGGAGATT-G
1 GATTCAAGTTTGGAGATTGG
3059099 GATTCAAAGTTTGGA-ATTTGG
1 GATTC-AAGTTTGGAGA-TTGG
3059120 GATTC
1 GATTC
3059125 GAGGTCGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.26
20 11 0.48
21 6 0.26
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.38
Consensus pattern (20 bp):
GATTCAAGTTTGGAGATTGG
Found at i:3059547 original size:42 final size:42
Alignment explanation
Indices: 3059489--3059576 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
3059479 AAAATGATGA
* *
3059489 AAAATTGTCATAGTAATTGA-CTAAG-TTTTAATTATTGGAAGG
1 AAAATTATCATAGTAATT-ATCTAAGCTTCT-ATTATTGGAAGG
3059531 AAAATTATCATAGTAATTATCTAAGCTTCTATTATTGGAAGG
1 AAAATTATCATAGTAATTATCTAAGCTTCTATTATTGGAAGG
3059573 AAAA
1 AAAA
3059577 CAACAACCGA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 1 0.02
42 38 0.90
43 3 0.07
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (42 bp):
AAAATTATCATAGTAATTATCTAAGCTTCTATTATTGGAAGG
Done.