Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008123.1 Hibiscus syriacus cultivar Beakdansim tig00110677_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: 770294
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:422832 original size:34 final size:33
Alignment explanation
Indices: 422786--422890 Score: 156
Period size: 34 Copynumber: 3.1 Consensus size: 33
422776 TTTATGTTTC
*
422786 GTAGCACTAGAGTGTATGCCCAAGACACTTAGT
1 GTAGCACTAGAGTGTATACCCAAGACACTTAGT
*
422819 GTAGGCACTAGAGTGTATACCCAAGGCACTTAGT
1 GTA-GCACTAGAGTGTATACCCAAGACACTTAGT
*
422853 GCATAACACTAGAGTGTATACCCAAGACACTTAGT
1 G--TAGCACTAGAGTGTATACCCAAGACACTTAGT
422888 GTA
1 GTA
422891 TTGGTGGGCA
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
33 5 0.08
34 29 0.45
35 29 0.45
36 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (33 bp):
GTAGCACTAGAGTGTATACCCAAGACACTTAGT
Found at i:422870 original size:35 final size:34
Alignment explanation
Indices: 422786--422890 Score: 151
Period size: 35 Copynumber: 3.1 Consensus size: 34
422776 TTTATGTTTC
*
422786 GTAG-CACTAGAGTGTATGCCCAAGACACTTAGT
1 GTAGACACTAGAGTGTATACCCAAGACACTTAGT
* *
422819 GTAGGCACTAGAGTGTATACCCAAGGCACTTAGT
1 GTAGACACTAGAGTGTATACCCAAGACACTTAGT
422853 GCATA-ACACTAGAGTGTATACCCAAGACACTTAGT
1 G--TAGACACTAGAGTGTATACCCAAGACACTTAGT
422888 GTA
1 GTA
422891 TTGGTGGGCA
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
33 6 0.09
34 28 0.43
35 29 0.45
36 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (34 bp):
GTAGACACTAGAGTGTATACCCAAGACACTTAGT
Found at i:426565 original size:31 final size:30
Alignment explanation
Indices: 426530--426596 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
426520 TATAAAGCAT
*
426530 AAAGTTTAGGGACCAAAA-TGGTAATTGTCTA
1 AAAGTTTAAGGACCAAAAGT-GTAATT-TCTA
*
426561 AAAGTTTAAGGATCAAAAGTGTAATTTCTA
1 AAAGTTTAAGGACCAAAAGTGTAATTTCTA
*
426591 AGAGTT
1 AAAGTT
426597 ATGTATTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 9 0.28
31 22 0.69
32 1 0.03
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.31
Consensus pattern (30 bp):
AAAGTTTAAGGACCAAAAGTGTAATTTCTA
Found at i:430982 original size:19 final size:19
Alignment explanation
Indices: 430960--431005 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
430950 ACTACTATAT
430960 TACTTGCATCTATTGTGTA
1 TACTTGCATCTATTGTGTA
430979 TACTTGCATCTATTGTGTA
1 TACTTGCATCTATTGTGTA
430998 TACTTGCA
1 TACTTGCA
431006 CAGATTTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (19 bp):
TACTTGCATCTATTGTGTA
Found at i:431852 original size:20 final size:20
Alignment explanation
Indices: 431829--431886 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
431819 ATTGTTTATT
431829 ATATATGATGTTTATCATGA
1 ATATATGATGTTTATCATGA
431849 ATATAT-A----TAT-AT--
1 ATATATGATGTTTATCATGA
431861 ATATATGATGTTTATCATGA
1 ATATATGATGTTTATCATGA
431881 ATATAT
1 ATATAT
431887 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 16
0.65 0.00 0.35
Matches are distributed among these distances:
12 6 0.20
13 1 0.03
14 2 0.07
15 3 0.10
17 3 0.10
18 2 0.07
19 1 0.03
20 12 0.40
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (20 bp):
ATATATGATGTTTATCATGA
Found at i:431856 original size:2 final size:2
Alignment explanation
Indices: 431849--431912 Score: 76
Period size: 2 Copynumber: 31.0 Consensus size: 2
431839 TTTATCATGA
* *
431849 AT AT AT AT AT AT AT AT AT GAT GT TT AT CAT GA- 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
431891 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
431913 GATGTTTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
1 1 0.02
2 49 0.89
3 5 0.09
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:431866 original size:32 final size:32
Alignment explanation
Indices: 431828--431898 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
431818 CATTGTTTAT
431828 TATATATGATGTTTATCATGAATATATATATA
1 TATATATGATGTTTATCATGAATATATATATA
431860 TATATATGATGTTTATCATGAATATATATATA
1 TATATATGATGTTTATCATGAATATATATATA
431892 TATATAT
1 TATATAT
431899 ATATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (32 bp):
TATATATGATGTTTATCATGAATATATATATA
Found at i:432227 original size:35 final size:34
Alignment explanation
Indices: 432148--432243 Score: 140
Period size: 34 Copynumber: 2.8 Consensus size: 34
432138 GTCATAGCAT
*
432148 TAGAGTGTATACCCAAGACACTTAGTGCAGTCGC
1 TAGAGTGTATACCCAAGACACTTAGTGCAGTCAC
* *
432182 TAGATTGTATACCCAAGACACTTGGTGCA-TAACAC
1 TAGAGTGTATACCCAAGACACTTAGTGCAGT--CAC
432217 TAGAGTGTATACCCAAGACACTTAGTG
1 TAGAGTGTATACCCAAGACACTTAGTG
432244 TATATGATGG
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
33 1 0.02
34 27 0.49
35 27 0.49
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (34 bp):
TAGAGTGTATACCCAAGACACTTAGTGCAGTCAC
Found at i:436510 original size:91 final size:91
Alignment explanation
Indices: 436355--436535 Score: 353
Period size: 91 Copynumber: 2.0 Consensus size: 91
436345 TTGCTTTGTT
*
436355 AAGTCTCAACTATTAAAAGTTATAAAATAGTCCCTTAACCATAGGTCATTGTTTTATTGAGTCCC
1 AAGTCTCAACTATTAAAAGTTATAAAATAGTCCCTTAACCATAGGTCATTATTTTATTGAGTCCC
436420 TAGACTATTAAAGTTATAAAATGGTC
66 TAGACTATTAAAGTTATAAAATGGTC
436446 AAGTCTCAACTATTAAAAGTTATAAAATAGTCCCTTAACCATAGGTCATTATTTTATTGAGTCCC
1 AAGTCTCAACTATTAAAAGTTATAAAATAGTCCCTTAACCATAGGTCATTATTTTATTGAGTCCC
436511 TAGACTATTAAAGTTATAAAATGGT
66 TAGACTATTAAAGTTATAAAATGGT
436536 TATTCATTTT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (91 bp):
AAGTCTCAACTATTAAAAGTTATAAAATAGTCCCTTAACCATAGGTCATTATTTTATTGAGTCCC
TAGACTATTAAAGTTATAAAATGGTC
Found at i:436824 original size:17 final size:18
Alignment explanation
Indices: 436802--436835 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
436792 TTTATCTTAT
436802 TTCATTATCTT-ATTTTC
1 TTCATTATCTTCATTTTC
*
436819 TTCATTTTCTTCATTTT
1 TTCATTATCTTCATTTT
436836 TCCTACTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68
Consensus pattern (18 bp):
TTCATTATCTTCATTTTC
Found at i:436827 original size:9 final size:9
Alignment explanation
Indices: 436802--436835 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
436792 TTTATCTTAT
*
436802 TTCATTATC
1 TTCATTTTC
436811 TT-ATTTTC
1 TTCATTTTC
436819 TTCATTTTC
1 TTCATTTTC
436828 TTCATTTT
1 TTCATTTT
436836 TCCTACTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68
Consensus pattern (9 bp):
TTCATTTTC
Found at i:440314 original size:20 final size:20
Alignment explanation
Indices: 440289--440338 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
440279 CACGTGAGGA
440289 TTATCTTCTT-TTTATT-TTAT
1 TTATCTT-TTATTTATTATT-T
440309 TTATCTTTTATTTATTATTT
1 TTATCTTTTATTTATTATTT
440329 TTATCATTTT
1 TTATC-TTTT
440339 TCATTGCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 2 0.07
20 19 0.70
21 6 0.22
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATCTTTTATTTATTATTT
Found at i:443056 original size:15 final size:14
Alignment explanation
Indices: 443032--443074 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
443022 TGAGTGTTTG
443032 TTTGTTTATTTTTA
1 TTTGTTTATTTTTA
443046 TTTGTTTTATTTTT-
1 TTTG-TTTATTTTTA
*
443060 TTATCTTTATTTTTA
1 TT-TGTTTATTTTTA
443075 ATATTAGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (14 bp):
TTTGTTTATTTTTA
Found at i:443079 original size:23 final size:23
Alignment explanation
Indices: 443036--443079 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
443026 TGTTTGTTTG
* *
443036 TTTATTTTTATTTGTTTTATTTT
1 TTTATCTTTATTTGTTATATTTT
443059 TTTATCTTTATTT-TTAATATT
1 TTTATCTTTATTTGTT-ATATT
443080 AGTTCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTATCTTTATTTGTTATATTTT
Found at i:445920 original size:20 final size:20
Alignment explanation
Indices: 445895--445944 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
445885 CACGTGAGGA
445895 TTATCTTCTT-TTTATT-TTAT
1 TTATCTT-TTATTTATTATT-T
445915 TTATCTTTTATTTATTATTT
1 TTATCTTTTATTTATTATTT
445935 TTATCATTTT
1 TTATC-TTTT
445945 TCATTGCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 2 0.07
20 19 0.70
21 6 0.22
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATCTTTTATTTATTATTT
Found at i:448813 original size:20 final size:20
Alignment explanation
Indices: 448768--448813 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
448758 GACCAACAAA
* *
448768 ATCGCAATGCGATCTCTAAT
1 ATCGCAACGCGATCTCCAAT
*
448788 -TCGCAACGCGATCTCCATT
1 ATCGCAACGCGATCTCCAAT
448807 ATCGCAA
1 ATCGCAA
448814 ATCAGTTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCTCCAAT
Found at i:448870 original size:20 final size:21
Alignment explanation
Indices: 448847--448899 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
448837 GATTATGACT
*
448847 ATCGCAATGCGAA-TAAGTAA
1 ATCGCAATGCGAATTAAGAAA
**
448867 ATCGCAATGCGAATTTGGAAA
1 ATCGCAATGCGAATTAAGAAA
448888 ATCGCAATGCGA
1 ATCGCAATGCGA
448900 TACTGACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
ATCGCAATGCGAATTAAGAAA
Found at i:448974 original size:21 final size:21
Alignment explanation
Indices: 448909--448981 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
448899 ATACTGACTA
* * *
448909 TCGCAATGCAATTTTCCTAAT
1 TCGCATTGCGATTTTCATAAT
* * *
448930 TAGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCATAAT
*
448950 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
*
448971 TCGCAATGCGA
1 TCGCATTGCGA
448982 ATACGTAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:448996 original size:20 final size:20
Alignment explanation
Indices: 448971--449082 Score: 136
Period size: 20 Copynumber: 5.5 Consensus size: 20
448961 TTTTCATAAT
448971 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
448991 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
449011 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
449032 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
449052 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
449072 TCGCAATGCGA
1 TCGCAATGCGA
449083 TTTACATAGC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.04
20 58 0.73
21 18 0.23
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:449002 original size:41 final size:41
Alignment explanation
Indices: 448847--449090 Score: 153
Period size: 41 Copynumber: 6.0 Consensus size: 41
448837 GATTATGACT
* **
448847 ATCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGA-AA
1 ATCGCAATGCGAATACGTAAATCGCAATGCG-ATTTTCATAA
* * *
448888 ATCGCAATGCG-ATAC-TGACTATCGCAATGCAATTTTCCTAA
1 ATCGCAATGCGAATACGT-A-AATCGCAATGCGATTTTCATAA
* * * * * **
448929 TTAGCATTGCGATTTACGT-ATTCGCGTTGCGATTTTCATAA
1 ATCGCAATGCGA-ATACGTAAATCGCAATGCGATTTTCATAA
* * *
448970 TTCGCAATGCGAATACGTAAATCGCAACGCGA--TTAAGTAA
1 ATCGCAATGCGAATACGTAAATCGCAATGCGATTTTCA-TAA
* * * * *
449010 ATCGCAATGCGAATTAGGAAAATCGCAATGCGA-ATACGTAA
1 ATCGCAATGCGAA-TACGTAAATCGCAATGCGATTTTCATAA
* * *
449051 ATCGCAATGCGAAT-CTTACTATCGCAATGCGATTTACATA
1 ATCGCAATGCGAATACGTA-AATCGCAATGCGATTTTCATA
449091 GCGCCATTCG
Statistics
Matches: 154, Mismatches: 37, Indels: 24
0.72 0.17 0.11
Matches are distributed among these distances:
39 5 0.03
40 41 0.27
41 103 0.67
42 1 0.01
43 3 0.02
44 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (41 bp):
ATCGCAATGCGAATACGTAAATCGCAATGCGATTTTCATAA
Found at i:450180 original size:42 final size:42
Alignment explanation
Indices: 450134--450224 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
450124 CCTCTTCAAC
* * * *
450134 GATGACAGTGGCCTCTTGAACGGTGGGGGGGGACTTTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
* *
450176 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
450218 GATGACA
1 GATGACA
450225 CAGGTGAGTC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.21, C:0.14, G:0.42, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:450186 original size:21 final size:21
Alignment explanation
Indices: 450162--450222 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
450152 AACGGTGGGG
* *
450162 GGGGACTTTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
450183 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
450204 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
450223 CACAGGTGAG
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.21, C:0.11, G:0.43, T:0.25
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:450604 original size:20 final size:20
Alignment explanation
Indices: 450566--450646 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
450556 GAATAATAGT
* *
450566 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACGCGAAAA
*
450586 TTACTTTCGCAACGTGAAAA
1 TTACTTTCGCAACGCGAAAA
* *
450606 TGACTATCGCAACGCGAAAA
1 TTACTTTCGCAACGCGAAAA
** * *
450626 TCGCTATCGCAACGCGGAAA
1 TTACTTTCGCAACGCGAAAA
450646 T
1 T
450647 GGCTATCTCA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
TTACTTTCGCAACGCGAAAA
Found at i:450651 original size:20 final size:20
Alignment explanation
Indices: 450592--450664 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
450582 AAACTTACTT
* *
450592 TCGCAACGTGAAAATGACTA
1 TCGCAACGCGAAAATGGCTA
*
450612 TCGCAACGCGAAAATCGCTA
1 TCGCAACGCGAAAATGGCTA
*
450632 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
* *
450652 TCTCAATGCGAAA
1 TCGCAACGCGAAA
450665 TGAAAATCGC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGGCTA
Found at i:450731 original size:19 final size:19
Alignment explanation
Indices: 450704--450839 Score: 76
Period size: 19 Copynumber: 7.6 Consensus size: 19
450694 GAAACACAAA
*
450704 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
450723 TCGCGTTGC-AATTT--TG
1 TCGCGTTGCGATTTTCATT
450739 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
450756 TCGCATTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
450772 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
450789 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
450808 TCCGCGTTGCGATAGTCATTT
1 T-CGCGTTGCGATTTTCA-TT
*
450829 TCGTGTTGCGA
1 TCGCGTTGCGA
450840 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 16, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
14 13 0.15
15 7 0.08
16 4 0.04
17 4 0.04
18 7 0.08
19 28 0.31
20 23 0.26
21 3 0.03
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:450780 original size:14 final size:14
Alignment explanation
Indices: 450726--450784 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
450716 TTTCATTTCG
*
450726 CGTTGCAATTTTGT
1 CGTTGCGATTTTGT
*
450740 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
450757 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
450773 CGTTGCGATTTT
1 CGTTGCGATTTT
450785 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 17 0.46
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:450798 original size:33 final size:33
Alignment explanation
Indices: 450709--450800 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
450699 ACAAATCGCA
* *
450709 TTGCGATTTTCATTTCGCGTTGCAATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
450742 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
450775 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
450801 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:450819 original size:20 final size:19
Alignment explanation
Indices: 450785--450839 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
450775 TTGCGATTTT
*
450785 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
450804 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
450824 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
450840 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:451416 original size:17 final size:18
Alignment explanation
Indices: 451380--451426 Score: 78
Period size: 17 Copynumber: 2.7 Consensus size: 18
451370 CTGGTCGATC
451380 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
451398 AGGTGATAGCTCT-GGTG
1 AGGTGATGGCTCTGGGTG
451415 AGGTGATGGCTC
1 AGGTGATGGCTC
451427 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.15, C:0.13, G:0.45, T:0.28
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:452794 original size:20 final size:20
Alignment explanation
Indices: 452746--452804 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
452736 AATAGTTTCT
* *
452746 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
452766 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
452786 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
452805 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:453080 original size:22 final size:22
Alignment explanation
Indices: 453053--453096 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
453043 GATGGAGATA
*
453053 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
453075 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
453097 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:453313 original size:20 final size:20
Alignment explanation
Indices: 453283--453355 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
453273 GATTATGTAT
*
453283 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
453303 TATTGCGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
453323 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
453343 TATCGCGTTGCGA
1 TATCGCGTTGCGA
453356 TTTTGTATTA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:455117 original size:38 final size:38
Alignment explanation
Indices: 455001--455121 Score: 135
Period size: 38 Copynumber: 3.3 Consensus size: 38
454991 AGTTGGAAAA
*
455001 TTCATCTTTGGTATGTGGCCAACTTTGCACATGAGAAT
1 TTCATCTTTGGTATGTGGCCAACTTTGCACATGGGAAT
* ** * * *
455039 TTCAT-TTTGGTTTGTGGTTAAC-TT--A-TTGGAAAA
1 TTCATCTTTGGTATGTGGCCAACTTTGCACATGGGAAT
*
455072 TTCATCTTTGGTAGGTGGCCAACTTTGCACATGGGAAT
1 TTCATCTTTGGTATGTGGCCAACTTTGCACATGGGAAT
455110 TTCATCTTTGGT
1 TTCATCTTTGGT
455122 CCCTAAAATA
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
33 9 0.14
34 14 0.22
35 2 0.03
36 2 0.03
37 15 0.23
38 22 0.34
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.41
Consensus pattern (38 bp):
TTCATCTTTGGTATGTGGCCAACTTTGCACATGGGAAT
Found at i:459823 original size:23 final size:23
Alignment explanation
Indices: 459797--459880 Score: 150
Period size: 23 Copynumber: 3.7 Consensus size: 23
459787 CTCATATAGA
459797 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
459820 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
459843 TGCACCGAAGTGCCGCATAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
459866 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
459881 TATAAAATGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.17
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:463228 original size:112 final size:112
Alignment explanation
Indices: 463025--463250 Score: 389
Period size: 112 Copynumber: 2.0 Consensus size: 112
463015 CACATCCCAC
*
463025 ACCGCTCGGTTTCACCCTTCAATTATTATATCATCTTGTTAGAAACAAAGGGAAGAAAGAATCAT
1 ACCGCTCGGTTTCACCCTTCAATTATTATATCATCTTGCTAGAAACAAAGGGAAGAAAGAATCAT
*
463090 CTCTCAGTCGATGCCCTGCATGTTCCTAAACATCAAAACGAACTCAT
66 CTCTCAGTCGATGCCCTGCATCTTCCTAAACATCAAAACGAACTCAT
* * *
463137 ACCGCTCGGTTTCACCCTTCAATTATTATATCATCTTGCTGGAAACGAAGGGCAGAAAGAATCAT
1 ACCGCTCGGTTTCACCCTTCAATTATTATATCATCTTGCTAGAAACAAAGGGAAGAAAGAATCAT
* *
463202 CTCTCAGTCGATGCCCTGTATCTTCCTAAACATCAAAACTAACTCAT
66 CTCTCAGTCGATGCCCTGCATCTTCCTAAACATCAAAACGAACTCAT
463249 AC
1 AC
463251 ACTTTTTCAG
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 107 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (112 bp):
ACCGCTCGGTTTCACCCTTCAATTATTATATCATCTTGCTAGAAACAAAGGGAAGAAAGAATCAT
CTCTCAGTCGATGCCCTGCATCTTCCTAAACATCAAAACGAACTCAT
Found at i:470030 original size:143 final size:141
Alignment explanation
Indices: 469752--470032 Score: 467
Period size: 143 Copynumber: 2.0 Consensus size: 141
469742 CACGAGAAAA
469752 AATTTAACGAAAAAAATCTACGAGGATAAGAGTAAAATTTTCATTAATATAAAAAAATATAATTG
1 AATTTAACGAAAAAAATCTACGAGGATAAGAGTAAAATTTTCATTAATATAAAAAAATATAATTG
469817 GATTTGCGGAATTGACTAACTTGTTGAATTTCATGTAAAAATTAATTATTTTTACTAGGGATCGG
66 GATTTGCGGAATTGACTAACTTGTTGAATTTCATGTAAAAATTAATTATTTTTACTAGGGATCGG
*
469882 TTGGGTCGAGT
131 ATGGGTCGAGT
*
469893 AATTTAACGAAAAAAA-CTATGAGGATAAGAGTAAAATTTTCATTAATATAAAAAAATAATATAA
1 AATTTAACGAAAAAAATCTACGAGGATAAGAGTAAAATTTTCATTAATAT--AAAAA-AATATAA
* *
469957 TTGGATTTGCGGAATTGATTAACTTGTTGAATTTCATGT-AAAATTAATTATTTTTATTAGGGAT
63 TTGGATTTGCGGAATTGACTAACTTGTTGAATTTCATGTAAAAATTAATTATTTTTACTAGGGAT
*
470021 GGGCATGGGTCG
128 CGG-ATGGGTCG
470033 GATTTTGGGT
Statistics
Matches: 131, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
140 32 0.24
141 16 0.12
142 31 0.24
143 52 0.40
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (141 bp):
AATTTAACGAAAAAAATCTACGAGGATAAGAGTAAAATTTTCATTAATATAAAAAAATATAATTG
GATTTGCGGAATTGACTAACTTGTTGAATTTCATGTAAAAATTAATTATTTTTACTAGGGATCGG
ATGGGTCGAGT
Found at i:477151 original size:20 final size:20
Alignment explanation
Indices: 477102--477158 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
477092 AGGGTGTCAA
**
477102 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CTATGC
* *
477123 AGTGTATCCATGCACTATGT
1 AGTGCATCCATGCACTATGC
477143 AGTGCATCCATGCACT
1 AGTGCATCCATGCACT
477159 CTATTTCGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (20 bp):
AGTGCATCCATGCACTATGC
Found at i:478550 original size:20 final size:19
Alignment explanation
Indices: 478516--478563 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
478506 AACGATTTTC
* *
478516 TTTTGAAAACAAAATTATA
1 TTTTGAAAACAAAATGAAA
*
478535 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAA-ACAAAATGAAA
478555 TTTTGAAAA
1 TTTTGAAAA
478564 ATGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.33
Consensus pattern (19 bp):
TTTTGAAAACAAAATGAAA
Found at i:479517 original size:20 final size:19
Alignment explanation
Indices: 479494--479692 Score: 141
Period size: 20 Copynumber: 10.0 Consensus size: 19
479484 AATATGTAAA
479494 TCGCAACACAGATGTCAAAT
1 TCGCAACAC-GATGTCAAAT
* *
479514 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACG-ATGTCAAAT
* *
479534 TCGTAACGCGATAGTCAAAT
1 TCGCAACACGAT-GTCAAAT
* *
479554 TCGCAACACAAAGTCAAAT
1 TCGCAACACGATGTCAAAT
* *
479573 TCACAACGCGATAGTCAAAT
1 TCGCAACACGAT-GTCAAAT
*
479593 TTGCAACACGATAGTCAAAT
1 TCGCAACACGAT-GTCAAAT
* * *
479613 TCGTAACACAAAAGTCAAAT
1 TCGCAACAC-GATGTCAAAT
** *
479633 TTACAACGCGAATTTGT-AAA-
1 TCGCAACACG-A--TGTCAAAT
*
479653 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GATGTCAAAT
479673 TCGCAACACGAATGTCAAAT
1 TCGCAACACG-ATGTCAAAT
479693 GTTTTTACGC
Statistics
Matches: 138, Mismatches: 30, Indels: 22
0.73 0.16 0.12
Matches are distributed among these distances:
18 2 0.01
19 21 0.15
20 108 0.78
21 5 0.04
22 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.21
Consensus pattern (19 bp):
TCGCAACACGATGTCAAAT
Found at i:479517 original size:40 final size:41
Alignment explanation
Indices: 479473--479692 Score: 192
Period size: 40 Copynumber: 5.5 Consensus size: 41
479463 AGTTTCCACT
*
479473 TTCGCAACGCGAATATGT-AAA-TCGCAACACAGATGTCAAA
1 TTCGCAACACGAATA-GTCAAATTCGCAACACAGATGTCAAA
* * *
479513 TTCGCAACGCGAA-AGTCAAATTCGTAACGC-GATAGTCAAA
1 TTCGCAACACGAATAGTCAAATTCGCAACACAGAT-GTCAAA
* *
479553 TTCGCAACAC-AA-AGTCAAATTCACAACGC-GATAGTCAAA
1 TTCGCAACACGAATAGTCAAATTCGCAACACAGAT-GTCAAA
* * * *
479592 TTTGCAACACG-ATAGTCAAATTCGTAACACAAAAGTCAAA
1 TTCGCAACACGAATAGTCAAATTCGCAACACAGATGTCAAA
** * * *
479632 TTTACAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACACGAA-TAGTCAAATTCGCAACACAGATGTCAAA
479672 TTCGCAACACGAAT-GTCAAAT
1 TTCGCAACACGAATAGTCAAAT
479693 GTTTTTACGC
Statistics
Matches: 151, Mismatches: 19, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
38 4 0.03
39 48 0.32
40 91 0.60
41 5 0.03
42 3 0.02
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.21
Consensus pattern (41 bp):
TTCGCAACACGAATAGTCAAATTCGCAACACAGATGTCAAA
Found at i:479659 original size:60 final size:59
Alignment explanation
Indices: 479473--479692 Score: 234
Period size: 60 Copynumber: 3.7 Consensus size: 59
479463 AGTTTCCACT
* * * *
479473 TTCGCAACGCGAATATGT-AAA-TCGCAACACAGATGTCAAATTCGCAACGCGAAAGTCAAA
1 TTCGCAACACG-ATA-GTCAAATTCGCAACACA-AAGTCAAATTCACAACGCGATAGTCAAA
* *
479533 TTCGTAACGCGATAGTCAAATTCGCAACACAAAGTCAAATTCACAACGCGATAGTCAAA
1 TTCGCAACACGATAGTCAAATTCGCAACACAAAGTCAAATTCACAACGCGATAGTCAAA
* * * *
479592 TTTGCAACACGATAGTCAAATTCGTAACACAAAAGTCAAATTTACAACGCGAATTTGT-AAA
1 TTCGCAACACGATAGTCAAATTCGCAACAC-AAAGTCAAATTCACAACGCG-A-TAGTCAAA
*
479653 -TCGCAACACAGA-AGTCAAATTCGCAACACGAATGTCAAAT
1 TTCGCAACAC-GATAGTCAAATTCGCAACAC-AAAGTCAAAT
479693 GTTTTTACGC
Statistics
Matches: 140, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
58 2 0.01
59 57 0.41
60 72 0.51
61 6 0.04
62 3 0.02
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.21
Consensus pattern (59 bp):
TTCGCAACACGATAGTCAAATTCGCAACACAAAGTCAAATTCACAACGCGATAGTCAAA
Found at i:481948 original size:21 final size:21
Alignment explanation
Indices: 481924--481973 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
481914 GTTAGGGGAA
*
481924 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGGTCGGTACT
* * *
481945 TTACGTCATGCGGTTGGTACT
1 TTACGTGATGAGGTCGGTACT
481966 TTACGTGA
1 TTACGTGA
481974 AGATAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCGGTACT
Found at i:482205 original size:4 final size:4
Alignment explanation
Indices: 482196--482241 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
482186 TTTTTCGGCA
* * * *
482196 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
482242 TCAGCGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:483925 original size:14 final size:14
Alignment explanation
Indices: 483903--483939 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
483893 TTTTGATTAA
483903 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
483917 TTTATTTGTAAAAG
1 TTGATTTGTAAAAG
483931 TTGATTTGT
1 TTGATTTGT
483940 TTAATTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:484181 original size:20 final size:20
Alignment explanation
Indices: 484156--484201 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
484146 GCAACGCTTA
484156 TTTCGCATTACGAATTTGAC
1 TTTCGCATTACGAATTTGAC
* **
484176 TTTCGCGTTGTGAATTTGAC
1 TTTCGCATTACGAATTTGAC
*
484196 ATTCGC
1 TTTCGC
484202 GTTGATCGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (20 bp):
TTTCGCATTACGAATTTGAC
Found at i:484202 original size:20 final size:20
Alignment explanation
Indices: 484167--484205 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
484157 TTCGCATTAC
*
484167 GAATTTGACTTTCGCGTTGT
1 GAATTTGACATTCGCGTTGT
484187 GAATTTGACATTCGCGTTG
1 GAATTTGACATTCGCGTTG
484206 ATCGCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41
Consensus pattern (20 bp):
GAATTTGACATTCGCGTTGT
Found at i:484514 original size:18 final size:18
Alignment explanation
Indices: 484491--484526 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
484481 AAGCCGGTTG
*
484491 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
484509 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
484527 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:486645 original size:28 final size:28
Alignment explanation
Indices: 486571--486637 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
486561 AAATTAGAAA
486571 TTACTCCCCCTTACTTTAACACTTATTC
1 TTACTCCCCCTTACTTTAACACTTATTC
486599 TTACTCCCCCTTACTTTAACACTTATTC
1 TTACTCCCCCTTACTTTAACACTTATTC
486627 TT-CTCCCCCTT
1 TTACTCCCCCTT
486638 TTTGTTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
27 9 0.23
28 30 0.77
ACGTcount: A:0.18, C:0.39, G:0.00, T:0.43
Consensus pattern (28 bp):
TTACTCCCCCTTACTTTAACACTTATTC
Found at i:488304 original size:204 final size:202
Alignment explanation
Indices: 487956--488362 Score: 796
Period size: 204 Copynumber: 2.0 Consensus size: 202
487946 AAAATGGGAA
487956 GATATTTAAAATCGATAGCTAACATAGCTTGACGAGAAGGAATACGTTTTCCCGGATTTGTAAGA
1 GATATTTAAAATCGATAGCTAACATAGCTTGACGAGAAGGAATACGTTTTCCCGGATTTGTAAGA
488021 ATCGAAATATTGATAATACCAATATCGGTGATTTCTAGACCCAGGATGATTGAAACACGAATTTT
66 ATCGAAATATTGATAATACCAATATCGGTGATTTCTAGACCCAGGATGATTGAAACACGAATTTT
488086 GGATAGTCAAGTTAGGATCAGTGGGATTGGGATTAGAAATTGGAATAGAAGGAGGATTTTGAGGT
131 GGATAGTCAAGTTAGGATCAGTGGGATTGGGATTAGAAATTGGAATAGAAGGAGGATTTTGAGGT
488151 GGATTTG
196 GGATTTG
488158 GATATTTAAAATCGATAGCTAACATAGCTTGACGAGAAGGAATACGTTCTTCCCGGATTTTGTAA
1 GATATTTAAAATCGATAGCTAACATAGCTTGACGAGAAGGAATACGTT-TTCCCGGA-TTTGTAA
488223 GAATCGAAATATTGATAATACCAATATCGGTGATTTCTAGACCCAGGATGATTGAAACACGAATT
64 GAATCGAAATATTGATAATACCAATATCGGTGATTTCTAGACCCAGGATGATTGAAACACGAATT
488288 TTGGATAGTCAAGTTAGGATCAGTGGGATTGGGATTAGAAATTGGAATAGAAGGAGGATTTTGAG
129 TTGGATAGTCAAGTTAGGATCAGTGGGATTGGGATTAGAAATTGGAATAGAAGGAGGATTTTGAG
488353 GTGGATTTG
194 GTGGATTTG
488362 G
1 G
488363 TTGACGACTA
Statistics
Matches: 203, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
202 48 0.24
203 8 0.04
204 147 0.72
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.30
Consensus pattern (202 bp):
GATATTTAAAATCGATAGCTAACATAGCTTGACGAGAAGGAATACGTTTTCCCGGATTTGTAAGA
ATCGAAATATTGATAATACCAATATCGGTGATTTCTAGACCCAGGATGATTGAAACACGAATTTT
GGATAGTCAAGTTAGGATCAGTGGGATTGGGATTAGAAATTGGAATAGAAGGAGGATTTTGAGGT
GGATTTG
Found at i:489082 original size:21 final size:21
Alignment explanation
Indices: 489058--489097 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
489048 CAGAACCCCA
*
489058 GGGGCGTATCGATTCCCCTGT
1 GGGGCGAATCGATTCCCCTGT
* *
489079 GGGGGGAATCGGTTCCCCT
1 GGGGCGAATCGATTCCCCT
489098 TCAAAGGGGG
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:0.10, C:0.28, G:0.38, T:0.25
Consensus pattern (21 bp):
GGGGCGAATCGATTCCCCTGT
Found at i:489106 original size:23 final size:21
Alignment explanation
Indices: 489080--489139 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 21
489070 TTCCCCTGTG
489080 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
489103 GGGGGAATCGGTT-CCCTCAA
1 GGGGGAATCGGTTCCCCTCAA
*
489123 GGGAGGAATCGATTCCC
1 GGG-GGAATCGGTTCCC
489140 TCTGCACCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 5 0.15
21 11 0.32
22 5 0.15
23 13 0.38
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:489130 original size:21 final size:21
Alignment explanation
Indices: 489080--489141 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
489070 TTCCCCTGTG
489080 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
489103 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
*
489123 GGGAGGAATCGATTCCCTC
1 GGG-GGAATCGGTTCCCTC
489142 TGCACCAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 5 0.14
21 16 0.43
22 3 0.08
23 13 0.35
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:496420 original size:24 final size:24
Alignment explanation
Indices: 496386--496439 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
496376 CCATCACATC
496386 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
496410 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
496434 ATCAAA
1 ATCAAA
496440 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:497170 original size:14 final size:14
Alignment explanation
Indices: 497151--497184 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
497141 GAAATCATTG
497151 AAAAATTATATAAA
1 AAAAATTATATAAA
*
497165 AAAAATTATGTAAA
1 AAAAATTATATAAA
497179 AAAAAT
1 AAAAAT
497185 AGAGATGGGG
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:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAAATTATATAAA
Found at i:497360 original size:20 final size:20
Alignment explanation
Indices: 497322--497528 Score: 155
Period size: 20 Copynumber: 10.5 Consensus size: 20
497312 CAAAATATTT
**
497322 GTGTTGCGAAACT-AAATTC
1 GTGTTGCGAATTTGAAATTC
497341 GTGTTGCGAATTTGAAATTC
1 GTGTTGCGAATTTGAAATTC
*
497361 -AGTTGCGAATTTGAAATTC
1 GTGTTGCGAATTTGAAATTC
*
497380 -AGTTGCGAATTTGAAATTC
1 GTGTTGCGAATTTGAAATTC
*
497399 -AGTTGCGAATTTGAAATTCC
1 GTGTTGCGAATTTGAAATT-C
* *
497419 GCGTTGCGAATTTG-ACTATC
1 GTGTTGCGAATTTGAAAT-TC
* *
497439 TTGTTGCGAATTTG-ACTATC
1 GTGTTGCGAATTTGAAAT-TC
* *
497459 GCGTTGCGAATTTG-ACTTC
1 GTGTTGCGAATTTGAAATTC
* *
497478 TGTGTTGCGATTTTG-ACTTC
1 -GTGTTGCGAATTTGAAATTC
497498 TGTGTTGCG-ATTT-ACAGATTC
1 -GTGTTGCGAATTTGA-A-ATTC
*
497519 GCGTTGCGAA
1 GTGTTGCGAA
497529 AATGGAAACT
Statistics
Matches: 165, Mismatches: 14, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
19 71 0.43
20 77 0.47
21 17 0.10
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.38
Consensus pattern (20 bp):
GTGTTGCGAATTTGAAATTC
Found at i:497365 original size:19 final size:19
Alignment explanation
Indices: 497343--497433 Score: 155
Period size: 19 Copynumber: 4.7 Consensus size: 19
497333 CTAAATTCGT
497343 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
497362 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
497381 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
497400 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-C-A
497421 GTTGCGAATTTGA
1 GTTGCGAATTTGA
497434 CTATCTTGTT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
19 55 0.80
20 1 0.01
21 13 0.19
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:498391 original size:21 final size:21
Alignment explanation
Indices: 498367--498415 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
498357 GGTATCAATA
498367 CACCATGATAGTGCACCGATG
1 CACCATGATAGTGCACCGATG
*
498388 CACCGTGATAGTGCACCGATG
1 CACCATGATAGTGCACCGATG
498409 CACCATG
1 CACCATG
498416 TTATGTGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (21 bp):
CACCATGATAGTGCACCGATG
Found at i:499853 original size:23 final size:23
Alignment explanation
Indices: 499823--499881 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
499813 CTTATAAATG
499823 CACCGAAGTGCCACGTAGAATTA
1 CACCGAAGTGCCACGTAGAATTA
* *
499846 CACCGAAGTGCCGCGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTA
*
499869 CACCGTAGTGCCA
1 CACCGAAGTGCCA
499882 TATAAGCCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.17
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTA
Found at i:500148 original size:31 final size:30
Alignment explanation
Indices: 500104--500163 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
500094 TATTGTATAG
*
500104 ACATATAATTTCCATACCTT-TATCACATAA
1 ACATATAATTTCCAT-CATTGTATCACATAA
*
500134 ACATATCATGTTCCATCATTGTATCACATA
1 ACATATAAT-TTCCATCATTGTATCACATA
500164 GCTTATATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCATTGTATCACATAA
Found at i:500234 original size:25 final size:25
Alignment explanation
Indices: 500206--500267 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
500196 CTTAATGCAT
500206 ATAATATGAATTCATG-TCATGTATC
1 ATAATATGAATT-ATGATCATGTATC
* *
500231 ATAATATGAAATGTGATCATGTATC
1 ATAATATGAATTATGATCATGTATC
*
500256 AAAATATTGAAT
1 ATAATA-TGAAT
500268 CTAGACTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.06
25 25 0.81
26 4 0.13
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (25 bp):
ATAATATGAATTATGATCATGTATC
Found at i:506595 original size:18 final size:20
Alignment explanation
Indices: 506572--506610 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
506562 AAATGTAATG
506572 GAAATGACAT-AAAT-AAAT
1 GAAATGACATGAAATCAAAT
*
506590 GAAATGAGATGAAATCAAAT
1 GAAATGACATGAAATCAAAT
506610 G
1 G
506611 CTTAACCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 4 0.22
20 5 0.28
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAATGACATGAAATCAAAT
Found at i:506796 original size:23 final size:23
Alignment explanation
Indices: 506770--506831 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
506760 CTCTTATAAA
506770 TGCACCGAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
**
506793 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
*
506816 TGCACCGTAGTGCCAT
1 TGCACCGAAGTGCCAT
506832 ATAAGCTTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCATGTAGAAT
Found at i:507544 original size:63 final size:64
Alignment explanation
Indices: 507450--507605 Score: 163
Period size: 64 Copynumber: 2.4 Consensus size: 64
507440 AATGAATGTA
* ** ** *
507450 TGCATCGATGCAC-CACACCATGCATCGATGCATAAATCTTATTCGATGTTTATA-TTTAAGGGG
1 TGCATCGATGCACTC-CA-TATGCATCGATGCATAAATCGCATTCGATGTTTATATTTTAAAAGA
507513 G
64 G
* ** * *
507514 TGCATCGATGCACTCCTTATGCATCGATGCATTGATGGCATTCGATGTTTGTATTTTAAAAGAG
1 TGCATCGATGCACTCCATATGCATCGATGCATAAATCGCATTCGATGTTTATATTTTAAAAGAG
* *
507578 TGCATCGATGCACTTCATGTGCATCGAT
1 TGCATCGATGCACTCCATATGCATCGAT
507606 ACACCTTGAA
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
63 29 0.38
64 46 0.61
65 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (64 bp):
TGCATCGATGCACTCCATATGCATCGATGCATAAATCGCATTCGATGTTTATATTTTAAAAGAG
Found at i:509686 original size:16 final size:17
Alignment explanation
Indices: 509652--509684 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
509642 TTTCGGTTTG
509652 AAAAAAACCGGTTTTTT
1 AAAAAAACCGGTTTTTT
*
509669 AAAAAAATCGGTTTTT
1 AAAAAAACCGGTTTTT
509685 AATCTGGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (17 bp):
AAAAAAACCGGTTTTTT
Found at i:513047 original size:22 final size:21
Alignment explanation
Indices: 513021--513075 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
513011 TAATTTTATA
513021 TTTTTAATAAT-TAAATAATAT
1 TTTTTAATAATATAAA-AATAT
*
513042 GTTTTTTATAATATAAAAATAT
1 -TTTTTAATAATATAAAAATAT
513064 TTTTTAA-AATAT
1 TTTTTAATAATAT
513076 TAACTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 5 0.17
21 6 0.20
22 15 0.50
23 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTTAATAATATAAAAATAT
Found at i:513068 original size:20 final size:21
Alignment explanation
Indices: 513018--513075 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
513008 TGATAATTTT
*
513018 ATATTTTTAATAAT-TAAATA
1 ATATTTTTTATAATATAAATA
513038 ATATGTTTTTTATAATATAAA-A
1 ATA--TTTTTTATAATATAAATA
*
513060 ATATTTTTTAAAATAT
1 ATATTTTTTATAATAT
513076 TAACTATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 15 0.45
22 14 0.42
23 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATATTTTTTATAATATAAATA
Found at i:514156 original size:58 final size:56
Alignment explanation
Indices: 514076--514230 Score: 161
Period size: 57 Copynumber: 2.7 Consensus size: 56
514066 AATTTAAAAT
* * *
514076 AAGGGTCATAATTTAAGGATGAAATTAAATTGTTCAAAAGTTTAAGGATCAATTTAG
1 AAGGGTCATAATTTAAGGATGAAATTAAAATATTC-AAAGTTTAAGGACCAATTTAG
*
514133 AAGGAGTCAT-ATTTTAGGAATGAAATTAAAATATTCAAAGTTTAAGGACCAATTTAAAAG
1 AAGG-GTCATAATTTAAGG-ATGAAATTAAAATATTCAAAGTTTAAGGACCAATTT---AG
** * *
514193 AAAAGTCATAATTT-AGAGATGAAACTAAAATATCCAAA
1 AAGGGTCATAATTTAAG-GATGAAATTAAAATATTCAAA
514231 AATTGAAGGA
Statistics
Matches: 83, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
57 29 0.35
58 20 0.24
59 25 0.30
60 9 0.11
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (56 bp):
AAGGGTCATAATTTAAGGATGAAATTAAAATATTCAAAGTTTAAGGACCAATTTAG
Found at i:514222 original size:59 final size:59
Alignment explanation
Indices: 514065--514230 Score: 187
Period size: 59 Copynumber: 2.8 Consensus size: 59
514055 TTTTGTGAAT
* * * * *
514065 CAATTTAAAATAAGGGTCATAATTTA-AGGATGAAATTAAATTGTTCAAAAGTTTAAGGAT
1 CAATTTAAAAGAAGAGTCATAATTTAGA-GATGAAATTAAAATATTC-AAAGTTTAAGGAC
* *
514125 CAATTTAGAAG--GAGTCATATTTTAG-GAATGAAATTAAAATATTCAAAGTTTAAGGAC
1 CAATTTAAAAGAAGAGTCATAATTTAGAG-ATGAAATTAAAATATTCAAAGTTTAAGGAC
* * *
514182 CAATTTAAAAGAAAAGTCATAATTTAGAGATGAAACTAAAATATCCAAA
1 CAATTTAAAAGAAGAGTCATAATTTAGAGATGAAATTAAAATATTCAAA
514231 AATTGAAGGA
Statistics
Matches: 89, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
57 23 0.26
58 26 0.29
59 30 0.34
60 10 0.11
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (59 bp):
CAATTTAAAAGAAGAGTCATAATTTAGAGATGAAATTAAAATATTCAAAGTTTAAGGAC
Found at i:514429 original size:57 final size:57
Alignment explanation
Indices: 514355--514503 Score: 194
Period size: 57 Copynumber: 2.6 Consensus size: 57
514345 CGATACTTTA
* * * **
514355 TTGAGTCTCCTGATTATTAAAAGTTATAAAATAGTCTCTAAATAAGGTAATATTTTG
1 TTGAGTCCCCTGATTATTAAAAGTTATAAAATAGTCCCCAAATAAGACAATATTTTG
* *
514412 TTGAGTCCCCTAATTATTAAAAGTTATAAAAT-GATCCCCAAATAAGACAATGTTTTG
1 TTGAGTCCCCTGATTATTAAAAGTTATAAAATAG-TCCCCAAATAAGACAATATTTTG
* *
514469 TTGAGTCCCC-GACTATTAAAAATTATAAAATAGTC
1 TTGAGTCCCCTGATTATTAAAAGTTATAAAATAGTC
514504 ACCTGACTAT
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
56 21 0.26
57 59 0.74
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (57 bp):
TTGAGTCCCCTGATTATTAAAAGTTATAAAATAGTCCCCAAATAAGACAATATTTTG
Found at i:515800 original size:69 final size:71
Alignment explanation
Indices: 515664--515802 Score: 237
Period size: 70 Copynumber: 2.0 Consensus size: 71
515654 TTAACTTTTG
* *
515664 TCATAATTGTATATATATTTTTTAATTTAATGCGATGATTATTTATTTTGTCATAAAAAAATTAC
1 TCATAATTGTATATATATTTTTTAATTTAATGCGATAATGATTTATTTTGTCATAAAAAAATTAC
515729 TAATAT
66 TAATAT
*
515735 TCATAATTGTATATCT-TTTTTTAATTTAATGCGATAATGATTTATTTTGTCAT-AAAAAATTAC
1 TCATAATTGTATATATATTTTTTAATTTAATGCGATAATGATTTATTTTGTCATAAAAAAATTAC
515798 TAATA
66 TAATA
515803 ATGACAAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 15 0.23
70 35 0.54
71 15 0.23
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.49
Consensus pattern (71 bp):
TCATAATTGTATATATATTTTTTAATTTAATGCGATAATGATTTATTTTGTCATAAAAAAATTAC
TAATAT
Found at i:521516 original size:19 final size:20
Alignment explanation
Indices: 521481--521518 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
521471 GAATATTAAA
*
521481 TGAGGTGAAATATGAAGTGT
1 TGAGCTGAAATATGAAGTGT
521501 TGAGCTGAAA-ATGAAGTG
1 TGAGCTGAAATATGAAGTG
521519 ATTTTCAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.37, C:0.03, G:0.34, T:0.26
Consensus pattern (20 bp):
TGAGCTGAAATATGAAGTGT
Found at i:522035 original size:2 final size:2
Alignment explanation
Indices: 522028--522079 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
522018 ATGTACATGC
**
522028 AT AT AT AT AT AT AT GC 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
522070 AT AT AT AT AT
1 AT AT AT AT AT
522080 GGTTATAGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:529434 original size:8 final size:8
Alignment explanation
Indices: 529423--529448 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
529413 ACCTCAAATC
529423 CTCCTCCG
1 CTCCTCCG
529431 CTCCTCCG
1 CTCCTCCG
529439 CTCCTCCG
1 CTCCTCCG
529447 CT
1 CT
529449 TTCCCCTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.62, G:0.12, T:0.27
Consensus pattern (8 bp):
CTCCTCCG
Found at i:531472 original size:20 final size:23
Alignment explanation
Indices: 531447--531490 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
531437 ATTAAGGTCA
531447 ATTTT-AA-TTCAGAT-TAATTT
1 ATTTTAAATTTCAGATATAATTT
531467 ATTTTAAATTTCAGATATAATTT
1 ATTTTAAATTTCAGATATAATTT
531490 A
1 A
531491 AATCGGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 2 0.10
22 7 0.33
23 7 0.33
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (23 bp):
ATTTTAAATTTCAGATATAATTT
Found at i:531690 original size:31 final size:31
Alignment explanation
Indices: 531652--531721 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
531642 CTTTTAAAAC
* *
531652 TTGCAATACAATCATCCAACATTTAGTTTGT
1 TTGCAATACAATCACCCAACATTTAGTTCGT
* *
531683 TTGCAATACAGTCCCCCAACATTTAGTTCGT
1 TTGCAATACAATCACCCAACATTTAGTTCGT
*
531714 TTGTAATA
1 TTGCAATA
531722 TGATCCCTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.37
Consensus pattern (31 bp):
TTGCAATACAATCACCCAACATTTAGTTCGT
Found at i:535745 original size:16 final size:16
Alignment explanation
Indices: 535724--535784 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
535714 TAATAAATAA
*
535724 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
*
535740 ACGAACATTAACGAAC
1 ACGAACATAAACGAAC
*
535756 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
535772 ACGAACATAAACG
1 ACGAACATAAACG
535785 TTAGAGACTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.56, C:0.23, G:0.11, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:536726 original size:14 final size:14
Alignment explanation
Indices: 536709--536768 Score: 93
Period size: 14 Copynumber: 4.3 Consensus size: 14
536699 AATGAACATA
536709 AACGAACATAACCG
1 AACGAACATAACCG
*
536723 AACGAATATAACCG
1 AACGAACATAACCG
*
536737 AACGAACATAGCCG
1 AACGAACATAACCG
*
536751 AACGAATATAACCG
1 AACGAACATAACCG
536765 AACG
1 AACG
536769 TTCACGAACG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.48, C:0.25, G:0.17, T:0.10
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:536741 original size:28 final size:28
Alignment explanation
Indices: 536709--536768 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
536699 AATGAACATA
536709 AACGAACATAACCGAACGAATATAACCG
1 AACGAACATAACCGAACGAATATAACCG
*
536737 AACGAACATAGCCGAACGAATATAACCG
1 AACGAACATAACCGAACGAATATAACCG
536765 AACG
1 AACG
536769 TTCACGAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.48, C:0.25, G:0.17, T:0.10
Consensus pattern (28 bp):
AACGAACATAACCGAACGAATATAACCG
Found at i:536845 original size:40 final size:40
Alignment explanation
Indices: 536800--536909 Score: 168
Period size: 40 Copynumber: 2.8 Consensus size: 40
536790 ATGAGACCTA
*
536800 TGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCT
1 TGTTCATGTTCGTTCATTTAATTAAACAAACACAAAATCT
* *
536840 TGTTCATGTTCGTTCATTTAATTAAACAAATATAAAATCT
1 TGTTCATGTTCGTTCATTTAATTAAACAAACACAAAATCT
* *
536880 TGTTCATGTTCGTTCAATTAA-TAAATAAAC
1 TGTTCATGTTCGTTCATTTAATTAAACAAAC
536910 GCACATAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
39 7 0.11
40 57 0.89
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (40 bp):
TGTTCATGTTCGTTCATTTAATTAAACAAACACAAAATCT
Found at i:543788 original size:21 final size:21
Alignment explanation
Indices: 543753--543807 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
543743 AGATATGAAT
* *
543753 TGAAAGGGAGAGAGGTGGCGCG
1 TGAAACGG-GAGAGGAGGCGCG
* *
543775 TGTAATGGGAGAGGAGGCGCG
1 TGAAACGGGAGAGGAGGCGCG
543796 TGAAACGGGAGA
1 TGAAACGGGAGA
543808 AGCCTTGGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.29, C:0.09, G:0.51, T:0.11
Consensus pattern (21 bp):
TGAAACGGGAGAGGAGGCGCG
Found at i:550906 original size:2 final size:2
Alignment explanation
Indices: 550894--550923 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
550884 TTATAATGTT
550894 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
550924 TAATTTCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:563356 original size:13 final size:13
Alignment explanation
Indices: 563338--563362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
563328 GGAGCATCTC
563338 AAAAAAAAAAACA
1 AAAAAAAAAAACA
563351 AAAAAAAAAAAC
1 AAAAAAAAAAAC
563363 CAGAATGTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACA
Found at i:563743 original size:105 final size:105
Alignment explanation
Indices: 563561--564231 Score: 1126
Period size: 105 Copynumber: 6.4 Consensus size: 105
563551 AGGTTTTACC
*
563561 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
563626 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
563666 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
563731 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
563771 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
563836 ACGAAGGGACCGCTGGTTGTCAACAAACGTTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
563876 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
563941 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
563981 CAGAGCCAGTTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
564046 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * ****
564086 CAGAGCCAGTTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTATAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* ** ** * * *
564151 ACGAAGGGGCCGCTGACTGTCAACCGACGATTTCCCAGTTC
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * *
564192 CAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
564232 GGAACAATAT
Statistics
Matches: 541, Mismatches: 24, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 496 0.92
106 45 0.08
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:577219 original size:26 final size:26
Alignment explanation
Indices: 577183--577249 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
577173 TTCGTGTTCT
577183 ATTTCGCGTTGCGATCGCGATTTTCC
1 ATTTCGCGTTGCGATCGCGATTTTCC
577209 ATTTCGCGTTGCGATCGCGATTTTCC
1 ATTTCGCGTTGCGATCGCGATTTTCC
577235 ATTTCGCGTTGCGAT
1 ATTTCGCGTTGCGAT
577250 AGTTGAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (26 bp):
ATTTCGCGTTGCGATCGCGATTTTCC
Found at i:577296 original size:20 final size:20
Alignment explanation
Indices: 577235--577296 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
577225 GCGATTTTCC
577235 ATTTCGCGTTGCGATAGT-T
1 ATTTCGCGTTGCGATAGTCT
** * **
577254 GAAAATCGCGTTGCAATTTTCT
1 --ATTTCGCGTTGCGATAGTCT
577276 ATTTCGCGTTGCGATAGTCT
1 ATTTCGCGTTGCGATAGTCT
577296 A
1 A
577297 CAGTTGTCGT
Statistics
Matches: 30, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
20 16 0.53
21 13 0.43
22 1 0.03
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.39
Consensus pattern (20 bp):
ATTTCGCGTTGCGATAGTCT
Found at i:578008 original size:6 final size:6
Alignment explanation
Indices: 577982--578059 Score: 135
Period size: 6 Copynumber: 13.5 Consensus size: 6
577972 TCTCGTCTCG
577982 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
578027 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
578060 AATACGTGTC
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.21
6 57 0.79
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:578186 original size:22 final size:22
Alignment explanation
Indices: 578158--578229 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
578148 AATTTGAAAA
578158 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
578180 ATCGCAAC-A-AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
578199 ATCACAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
578221 ATCGCAACG
1 ATCGCAACG
578230 CGAAATGCAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 11 0.30
20 3 0.08
21 3 0.08
22 20 0.54
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:578193 original size:41 final size:41
Alignment explanation
Indices: 578136--578228 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
578126 TTTTTTTTAA
* *
578136 ACTATCGCAACGAATTTGAAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACAAATTTGAAAAATCACAACGACAACTGTAG
*
578177 ACTATCGCAACAAATTTGGAAAATCACAACGACAACTGTAG
1 ACTATCGCAACAAATTTGAAAAATCACAACGACAACTGTAG
578218 ACTATCGCAAC
1 ACTATCGCAAC
578229 GCGAAATGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACAAATTTGAAAAATCACAACGACAACTGTAG
Found at i:581897 original size:31 final size:30
Alignment explanation
Indices: 581862--581921 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
581852 AAATTATATG
581862 TTTAGTACATAAACTATCAATTTTTGTTCAT
1 TTTAGTACATAAACTATC-ATTTTTGTTCAT
** * *
581893 TTTAGTATTTAAACTTTCATTTTTTTTCA
1 TTTAGTACATAAACTATCATTTTTGTTCA
581922 AAATTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (30 bp):
TTTAGTACATAAACTATCATTTTTGTTCAT
Found at i:582882 original size:2 final size:2
Alignment explanation
Indices: 582875--582912 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
582865 TCTAACCATA
582875 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
582913 TCTTTTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:583437 original size:20 final size:18
Alignment explanation
Indices: 583371--583437 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 18
583361 AAACATACTT
*
583371 AAAATAAATGATGAATTGA
1 AAAATAAAGGAT-AATTGA
*
583390 AGAAATAAAGAAATAA-TGA
1 A-AAATAAAG-GATAATTGA
583409 AAAATTAAAGGACTAAATTGA
1 AAAA-TAAAGGA-T-AATTGA
583430 AAAATAAA
1 AAAATAAA
583438 AAAATTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
18 4 0.10
19 11 0.28
20 15 0.38
21 9 0.23
ACGTcount: A:0.64, C:0.01, G:0.13, T:0.21
Consensus pattern (18 bp):
AAAATAAAGGATAATTGA
Found at i:589855 original size:122 final size:122
Alignment explanation
Indices: 589719--589940 Score: 435
Period size: 122 Copynumber: 1.8 Consensus size: 122
589709 GTGAAAACCT
589719 ACAAAATTAACATATATTGACCACATTTCACTTATCACCTTTCTAGTTCTAGATGCAATGATTAG
1 ACAAAATTAACATATATTGACCACATTTCACTTATCACCTTTCTAGTTCTAGATGCAATGATTAG
589784 TAATTTTTGGTTAAAAAACACAAATTTATAACATACGCGTGTGTGTGTGTGGGTTAA
66 TAATTTTTGGTTAAAAAACACAAATTTATAACATACGCGTGTGTGTGTGTGGGTTAA
589841 ACAAAATTAACATATATTGACCACATTTCACTTATCACCTTTCTAGTTCTAGATGCAATGATTAG
1 ACAAAATTAACATATATTGACCACATTTCACTTATCACCTTTCTAGTTCTAGATGCAATGATTAG
*
589906 TAATTTTTGGTTAAAAAATACAAATTTATAACATA
66 TAATTTTTGGTTAAAAAACACAAATTTATAACATA
589941 TGTGTATGTG
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 99 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (122 bp):
ACAAAATTAACATATATTGACCACATTTCACTTATCACCTTTCTAGTTCTAGATGCAATGATTAG
TAATTTTTGGTTAAAAAACACAAATTTATAACATACGCGTGTGTGTGTGTGGGTTAA
Found at i:589948 original size:6 final size:6
Alignment explanation
Indices: 589939--589964 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
589929 ATTTATAACA
589939 TATGTG TATGTG TATGTG TATGTG TA
1 TATGTG TATGTG TATGTG TATGTG TA
589965 AACCCATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (6 bp):
TATGTG
Found at i:593627 original size:23 final size:23
Alignment explanation
Indices: 593597--593656 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
593587 ATTGCAGCCT
593597 TTCAACGCTCAATAGTTAAACGA
1 TTCAACGCTCAATAGTTAAACGA
*
593620 TTCAACGCTCAATAGTTACACGA
1 TTCAACGCTCAATAGTTAAACGA
593643 TTCAACGCTCAATA
1 TTCAACGCTCAATA
593657 TTATTTGCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.27
Consensus pattern (23 bp):
TTCAACGCTCAATAGTTAAACGA
Found at i:593928 original size:21 final size:21
Alignment explanation
Indices: 593903--593946 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
593893 AATTTAGTTA
593903 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
593924 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
593945 AT
1 AT
593947 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:593947 original size:28 final size:28
Alignment explanation
Indices: 593916--593981 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
593906 AGTTTGTTAG
593916 TATAAATTATTAGTTTGTTAGTTTAAGT
1 TATAAATTATTAGTTTGTTAGTTTAAGT
*
593944 TAT-ATTATATTAGTTTGTTAGTTTAAGT
1 TATAAAT-TATTAGTTTGTTAGTTTAAGT
*
593972 TATATATTAT
1 TATAAATTAT
593982 ATTATATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.91
29 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (28 bp):
TATAAATTATTAGTTTGTTAGTTTAAGT
Found at i:594476 original size:17 final size:16
Alignment explanation
Indices: 594442--594500 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
594432 GATAATTTTC
594442 GTTTAAAAAATATTGT
1 GTTTAAAAAATATTGT
*
594458 GTTTAAAAATATTTAGTGTT
1 GTTTAAAAA-A--TATTG-T
*
594478 GTTTTAAAAAATATTTT
1 G-TTTAAAAAATATTGT
594495 GTTTAA
1 GTTTAA
594501 TTTATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
16 14 0.40
17 3 0.09
18 3 0.09
19 4 0.11
20 3 0.09
21 8 0.23
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (16 bp):
GTTTAAAAAATATTGT
Found at i:594504 original size:21 final size:22
Alignment explanation
Indices: 594462--594504 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
594452 TATTGTGTTT
**
594462 AAAAATATTTAGTGTTGTTTTA
1 AAAAATATTTAGTGTTAATTTA
*
594484 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTGTTAATTTA
594505 TATTATATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
AAAAATATTTAGTGTTAATTTA
Found at i:594786 original size:26 final size:25
Alignment explanation
Indices: 594735--594794 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
594725 TATAATAAAT
594735 AATTATTAGTAATCATTACTAAATCA
1 AATTATTAGTAATCATTAC-AAATCA
* *
594761 TATTATTATTAAATCATTA-AATATCA
1 AATTATTAGT-AATCATTACAA-ATCA
594787 AATTATTA
1 AATTATTA
594795 AATTAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 2 0.07
26 19 0.66
27 8 0.28
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (25 bp):
AATTATTAGTAATCATTACAAATCA
Found at i:597812 original size:23 final size:23
Alignment explanation
Indices: 597786--597849 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
597776 CAACTCATAT
597786 AATTACACCGAAGTGCCACGTAG
1 AATTACACCGAAGTGCCACGTAG
* *
597809 AATTACACCGGAGTGCCGCGTAG
1 AATTACACCGAAGTGCCACGTAG
* *
597832 AATTGCACCGTAGTGCCA
1 AATTACACCGAAGTGCCA
597850 TATAATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTACACCGAAGTGCCACGTAG
Found at i:598044 original size:103 final size:103
Alignment explanation
Indices: 597865--598180 Score: 569
Period size: 103 Copynumber: 3.1 Consensus size: 103
597855 TAATGTCCAT
* * * *
597865 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
597930 GACTTCACACATGTTCCAAAGAATACATATATGTTCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
597968 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
598033 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
598071 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
598136 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
598174 AAGGACC
1 AAGGACC
598181 GCGTAGACCC
Statistics
Matches: 205, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 205 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:599892 original size:21 final size:21
Alignment explanation
Indices: 599868--599912 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
599858 TCTGGTTTGT
* *
599868 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
599889 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
599910 TTG
1 TTG
599913 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.22, G:0.31, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:601214 original size:22 final size:22
Alignment explanation
Indices: 601188--601234 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
601178 CTCATCATTA
601188 GTAATCATATATGTATTTCTAT
1 GTAATCATATATGTATTTCTAT
601210 GTAATCATATATGTATTTCTAT
1 GTAATCATATATGTATTTCTAT
601232 GTA
1 GTA
601235 TTTATCCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.49
Consensus pattern (22 bp):
GTAATCATATATGTATTTCTAT
Found at i:601449 original size:49 final size:48
Alignment explanation
Indices: 601389--601599 Score: 341
Period size: 49 Copynumber: 4.3 Consensus size: 48
601379 TTTGATTTAT
*
601389 TAATTATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGTTAG
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTG-TAG
601438 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGGTAG
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTT-GTAG
* *
601487 TAATGATTAATAATAATTAAATTATTATTAATATTTAATGATTTAGTAG
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTT-GTAG
*
601536 TAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAG
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTG-TAG
601585 TAATGATTTAGTAAT
1 TAATGA-TTAGTAAT
601600 TATTAGTAAT
Statistics
Matches: 153, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
48 1 0.01
49 144 0.94
50 8 0.05
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (48 bp):
TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGTAG
Found at i:601840 original size:8 final size:8
Alignment explanation
Indices: 601816--601979 Score: 79
Period size: 8 Copynumber: 21.2 Consensus size: 8
601806 AATGATTTAA
601816 TAATGATTT
1 TAATGA-TT
601825 TAAT-ATT
1 TAATGATT
*
601832 TAATAATT
1 TAATGATT
*
601840 TGATGATT
1 TAATGATT
601848 TAGTCATGATTT
1 TA---ATGA-TT
601860 TAAT-ATT
1 TAATGATT
601867 TAATGATT
1 TAATGATT
*
601875 TGATGATT
1 TAATGATT
*
601883 TAAT-A-A
1 TAATGATT
601889 TAAT--TT
1 TAATGATT
601895 TAAT-ATT
1 TAATGATT
601902 T--TGATT
1 TAATGATT
*
601908 TAAT-A-A
1 TAATGATT
601914 TAAT--TT
1 TAATGATT
601920 TAAT-ATT
1 TAATGATT
601927 TAATGATT
1 TAATGATT
*
601935 TGATGATT
1 TAATGATT
601943 TAGTCATGATTT
1 TA---ATGA-TT
601955 TAAT-ATT
1 TAATGATT
601962 TAATGATT
1 TAATGATT
*
601970 TGATGATT
1 TAATGATT
601978 TA
1 TA
601980 GTCATGATTT
Statistics
Matches: 123, Mismatches: 13, Indels: 39
0.70 0.07 0.22
Matches are distributed among these distances:
5 1 0.01
6 20 0.16
7 29 0.24
8 49 0.40
9 8 0.07
11 8 0.07
12 8 0.07
ACGTcount: A:0.36, C:0.01, G:0.10, T:0.52
Consensus pattern (8 bp):
TAATGATT
Found at i:601857 original size:35 final size:35
Alignment explanation
Indices: 601807--601989 Score: 233
Period size: 35 Copynumber: 5.5 Consensus size: 35
601797 AACTATAAAA
* * *
601807 ATGATTTAATAATGATTTTAATATTTAATAATTTG
1 ATGATTTAGTCATGATTTTAATATTTAATGATTTG
601842 ATGATTTAGTCATGATTTTAATATTTAATGATTTG
1 ATGATTTAGTCATGATTTTAATATTTAATGATTTG
*
601877 ATGATTTA---AT-A--ATAAT-TTTAAT-ATTT-
1 ATGATTTAGTCATGATTTTAATATTTAATGATTTG
* * *
601903 -TGATTTAATAATAATTTTAATATTTAATGATTTG
1 ATGATTTAGTCATGATTTTAATATTTAATGATTTG
601937 ATGATTTAGTCATGATTTTAATATTTAATGATTTG
1 ATGATTTAGTCATGATTTTAATATTTAATGATTTG
601972 ATGATTTAGTCATGATTT
1 ATGATTTAGTCATGATTT
601990 GATAATAATC
Statistics
Matches: 130, Mismatches: 8, Indels: 20
0.82 0.05 0.13
Matches are distributed among these distances:
25 7 0.05
27 4 0.03
28 8 0.06
29 5 0.04
31 5 0.04
32 8 0.06
33 4 0.03
35 89 0.68
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.52
Consensus pattern (35 bp):
ATGATTTAGTCATGATTTTAATATTTAATGATTTG
Found at i:601912 original size:25 final size:26
Alignment explanation
Indices: 601860--601935 Score: 109
Period size: 25 Copynumber: 2.8 Consensus size: 26
601850 GTCATGATTT
601860 TAATATTTAATGATTTGATGATTTAATAA
1 TAAT-TTTAAT-ATTT-ATGATTTAATAA
601889 TAATTTTAATATTT-TGATTTAATAA
1 TAATTTTAATATTTATGATTTAATAA
601914 TAATTTTAATATTTAATGATTT
1 TAATTTTAATATTT-ATGATTT
601936 GATGATTTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
25 25 0.56
27 10 0.22
28 6 0.13
29 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (26 bp):
TAATTTTAATATTTATGATTTAATAA
Found at i:601920 original size:95 final size:94
Alignment explanation
Indices: 601800--602113 Score: 366
Period size: 95 Copynumber: 3.3 Consensus size: 94
601790 TTCAATTAAC
*
601800 TATAAAAATGATTTAATAATGATTTTAATATTTAATAATTTGATGATTTAGTCATGATTTTAATA
1 TATAATAATGATTTAATAATGATTTTAATATTTAATAATTTGATGATTTAGTCATGATTTTAATA
*
601865 TTTAATGATTTGATGATTTAATAATAATT
66 TTTAATGATTTGATGATTTAATAATGATT
* * *
601894 T-TAATATTTTGATTTAATAATAATTTTAATATTTAATGATTTGATGATTTAGTCATGATTTTAA
1 TATAATA--ATGATTTAATAATGATTTTAATATTTAATAATTTGATGATTTAGTCATGATTTTAA
* *
601958 TATTTAATGATTTGATGATTTAGTCATGATT
64 TATTTAATGATTTGATGATTTAATAATGATT
* * * *
601989 TGATAATAATCATTATAATAATGATTTAGTAATAATCATT-ATAA--TAATGATTTAATAATGAT
1 T-ATAATAATGATT-TAATAATGATTT--TAAT-AT--TTAATAATTTGATGATTTAGTCATGAT
* *
602051 TTTAATATTTAATGATGTGATAATTTAATAATGATT
59 TTTAATATTTAATGATTTGATGATTTAATAATGATT
* *
602087 TGATATTAATCATTATAATAATGATTT
1 T-ATAATAATGATT-TAATAATGATTT
602114 AGTAATAATC
Statistics
Matches: 191, Mismatches: 19, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
93 4 0.02
94 1 0.01
95 86 0.45
96 11 0.06
97 5 0.03
98 77 0.40
99 2 0.01
100 3 0.02
101 2 0.01
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (94 bp):
TATAATAATGATTTAATAATGATTTTAATATTTAATAATTTGATGATTTAGTCATGATTTTAATA
TTTAATGATTTGATGATTTAATAATGATT
Found at i:601953 original size:19 final size:19
Alignment explanation
Indices: 601929--601992 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
601919 TTAATATTTA
601929 ATGATTTGATGATTTAGTC
1 ATGATTTGATGATTTAGTC
*
601948 ATGATTTTAAT-ATTTA---
1 ATGA-TTTGATGATTTAGTC
601964 ATGATTTGATGATTTAGTC
1 ATGATTTGATGATTTAGTC
601983 ATGATTTGAT
1 ATGATTTGAT
601993 AATAATCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 5 0.13
16 9 0.24
19 19 0.50
20 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (19 bp):
ATGATTTGATGATTTAGTC
Found at i:602012 original size:26 final size:25
Alignment explanation
Indices: 601983--602248 Score: 233
Period size: 26 Copynumber: 10.6 Consensus size: 25
601973 TGATTTAGTC
601983 ATGATTTGATAATAATCATTATAATA
1 ATGATTT-ATAATAATCATTATAATA
602009 ATGATTTAGTAATAATCATTATAATA
1 ATGATTTA-TAATAATCATTATAATA
* *
602035 ATGA-TT-TAATAATGATTTTAATA
1 ATGATTTATAATAATCATTATAATA
* * * * * * *
602058 TTTAATGAT-GTGATAATT-TAATA
1 ATGATTTATAATAATCATTATAATA
*
602081 ATGATTTGATATTAATCATTATAATA
1 ATGATTT-ATAATAATCATTATAATA
602107 ATGATTTAGTAATAATCATTATAATA
1 ATGATTTA-TAATAATCATTATAATA
602133 ATGATTTAATAATAATCATTATAATA
1 ATGATTT-ATAATAATCATTATAATA
* *
602159 ATGATTTAATAGTAATGATT-TAATA
1 ATGATTT-ATAATAATCATTATAATA
* *
602184 ATGATTTAGTAATGAT-TTTATAATA
1 ATGATTTA-TAATAATCATTATAATA
* * *
602209 ATGATTCAATACTAATGATT-TAATA
1 ATGATT-TATAATAATCATTATAATA
*
602234 ATTA-TTACTAATAAT
1 ATGATTTA-TAATAAT
602249 TATGGAATAA
Statistics
Matches: 199, Mismatches: 28, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
23 26 0.13
24 19 0.10
25 52 0.26
26 101 0.51
27 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (25 bp):
ATGATTTATAATAATCATTATAATA
Found at i:602013 original size:37 final size:36
Alignment explanation
Indices: 601972--602248 Score: 151
Period size: 37 Copynumber: 7.4 Consensus size: 36
601962 TAATGATTTG
* *
601972 ATGATTTAGTCATGAT-TTGATAATAATCATTATAATA
1 ATGATTTAGTAATAATATT-ATAATAATCATT-TAATA
*
602009 ATGATTTAGTAATAATCATTATAATAATGATTTAATA
1 ATGATTTAGTAATAAT-ATTATAATAATCATTTAATA
* * *
602046 ATGATTT--TAAT-AT-TTAATGATGTGATAATTTAATA
1 ATGATTTAGTAATAATATT-AT-A-ATAATCATTTAATA
* * *
602081 ATGATTT-GATATTAATCATTATAATAATGATTTAGTA
1 ATGATTTAG-TAATAAT-ATTATAATAATCATTTAATA
*
602118 ATAATCATTA-TAATAATGATTTAATAATAATCATTATAATA
1 ATGAT--TTAGTAATAAT-A-TT-ATAATAATCATT-TAATA
* * * *
602159 ATGATTTAATAGTAATGATT-TAATAATGATTTAGTA
1 ATGATTTAGTAATAAT-ATTATAATAATCATTTAATA
* *
602195 ATGATTTTA-TAATAATGATTCAATACTAATGATTTAATA
1 ATGA-TTTAGTAATAAT-ATT--ATAATAATCATTTAATA
* *
602234 ATTA-TTACTAATAAT
1 ATGATTTAGTAATAAT
602249 TATGGAATAA
Statistics
Matches: 194, Mismatches: 24, Indels: 43
0.74 0.09 0.16
Matches are distributed among these distances:
32 2 0.01
33 2 0.01
34 3 0.02
35 22 0.11
36 18 0.09
37 60 0.31
38 28 0.14
39 30 0.15
40 21 0.11
41 8 0.04
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (36 bp):
ATGATTTAGTAATAATATTATAATAATCATTTAATA
Found at i:602077 original size:98 final size:98
Alignment explanation
Indices: 601842--602145 Score: 359
Period size: 98 Copynumber: 3.1 Consensus size: 98
601832 TAATAATTTG
* * * * * * *
601842 ATGATTTAGTCATGATTTTAATATTTAATGATTTGATGATTTAATAATAATTT--TAATATTTTG
1 ATGATTTAATAATGATTTTAATATTTAATGATGTGATAATTTAATAATGATTTGATAATA--ATC
* * * * * *
601905 ATT-TAATAATAATTT--TAATATTTAATGAT-TTG
64 ATTATAATAATGATTTAGTAATA-ATCATTATAATA
* * * * * *
601937 ATGATTTAGTCATGATTTTAATATTTAATGATTTGATGATTTAGTCATGATTTGATAATAATCAT
1 ATGATTTAATAATGATTTTAATATTTAATGATGTGATAATTTAATAATGATTTGATAATAATCAT
602002 TATAATAATGATTTAGTAATAATCATTATAATA
66 TATAATAATGATTTAGTAATAATCATTATAATA
*
602035 ATGATTTAATAATGATTTTAATATTTAATGATGTGATAATTTAATAATGATTTGATATTAATCAT
1 ATGATTTAATAATGATTTTAATATTTAATGATGTGATAATTTAATAATGATTTGATAATAATCAT
602100 TATAATAATGATTTAGTAATAATCATTATAATA
66 TATAATAATGATTTAGTAATAATCATTATAATA
602133 ATGATTTAATAAT
1 ATGATTTAATAAT
602146 AATCATTATA
Statistics
Matches: 185, Mismatches: 18, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
95 54 0.29
96 11 0.06
97 10 0.05
98 110 0.59
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (98 bp):
ATGATTTAATAATGATTTTAATATTTAATGATGTGATAATTTAATAATGATTTGATAATAATCAT
TATAATAATGATTTAGTAATAATCATTATAATA
Found at i:602400 original size:24 final size:24
Alignment explanation
Indices: 602352--602396 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
602342 GATTTGATAC
*
602352 TAATGATTTAGTAATTATTATTAA
1 TAATGATTTAGTAATTAATATTAA
*
602376 TAATGATTTA-TTATTAATATT
1 TAATGATTTAGTAATTAATATT
602397 TAATTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (24 bp):
TAATGATTTAGTAATTAATATTAA
Found at i:602403 original size:17 final size:17
Alignment explanation
Indices: 602363--602404 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
602353 AATGATTTAG
602363 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
602380 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
602397 TAATTATT
1 TAATTATT
602405 TAATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:602414 original size:21 final size:22
Alignment explanation
Indices: 602376--602419 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
602366 TTATTATTAA
* *
602376 TAATGATTTATTATTAAT-ATT
1 TAATGATTTAATACTAATGATT
*
602397 TAATTATTTAATACTAATGATT
1 TAATGATTTAATACTAATGATT
602419 T
1 T
602420 TCTAATGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
TAATGATTTAATACTAATGATT
Found at i:605201 original size:13 final size:13
Alignment explanation
Indices: 605162--605208 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
605152 CTCACAATAG
605162 CCTTATCTCCCTTT
1 CCTT-TCTCCCTTT
* *
605176 CTTCTTCTTCCTTT
1 CCT-TTCTCCCTTT
605190 CCTTTCTCCCTTT
1 CCTTTCTCCCTTT
605203 -CTTTCT
1 CCTTTCT
605209 TTCTTTCTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.21
13 9 0.32
14 12 0.43
15 1 0.04
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (13 bp):
CCTTTCTCCCTTT
Found at i:605443 original size:27 final size:27
Alignment explanation
Indices: 605414--605509 Score: 174
Period size: 27 Copynumber: 3.6 Consensus size: 27
605404 ACTGCAGCGG
* *
605414 CATGCAGCGGGGAACAGGAGGGGACGG
1 CATGCAGCGGGGAGCAGGAGGGGACGA
605441 CATGCAGCGGGGAGCAGGAGGGGACGA
1 CATGCAGCGGGGAGCAGGAGGGGACGA
605468 CATGCAGCGGGGAGCAGGAGGGGACGA
1 CATGCAGCGGGGAGCAGGAGGGGACGA
605495 CATGCAGCGGGGAGC
1 CATGCAGCGGGGAGC
605510 GGGACGTGCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.25, C:0.20, G:0.51, T:0.04
Consensus pattern (27 bp):
CATGCAGCGGGGAGCAGGAGGGGACGA
Found at i:606837 original size:27 final size:27
Alignment explanation
Indices: 606796--606858 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
606786 TGCTCGTTCG
*
606796 AAATT-GATAGCCAGGGTAGAATGGTT
1 AAATTGGATAGACAGGGTAGAATGGTT
606822 AAATTGGATAGACAGGGTAGAATGGTT
1 AAATTGGATAGACAGGGTAGAATGGTT
*
606849 AAAGTGGATA
1 AAATTGGATA
606859 CTCCCATGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 5 0.15
27 29 0.85
ACGTcount: A:0.38, C:0.05, G:0.32, T:0.25
Consensus pattern (27 bp):
AAATTGGATAGACAGGGTAGAATGGTT
Found at i:610971 original size:17 final size:17
Alignment explanation
Indices: 610949--610982 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
610939 TTATTTTATT
* *
610949 AATAATATATAATTAAA
1 AATAATAAATAAATAAA
610966 AATAATAAATAAATAAA
1 AATAATAAATAAATAAA
610983 TTTGAACGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAATAAATAAATAAA
Found at i:611557 original size:80 final size:82
Alignment explanation
Indices: 611411--611577 Score: 293
Period size: 80 Copynumber: 2.1 Consensus size: 82
611401 TATATATTCA
* * *
611411 AAATTATTACCTAGTTTTGTTATTTCTTTCTTTTTCTACATTTTTTTAAATATTGAGAATTATCA
1 AAATTATTACCTAGTTTTATTATTTCTTTCTTTTTCTACATTTTTTAAAATATTAAGAATTATCA
611476 TCATTTAAATATTGATC
66 TCATTTAAATATTGATC
611493 AAATTATTA-CTAGTTTTATTATTTCTTTCTTTTTCTACA-TTTTTAAAATATTAAGAATTATCA
1 AAATTATTACCTAGTTTTATTATTTCTTTCTTTTTCTACATTTTTTAAAATATTAAGAATTATCA
611556 TCATTTAAATATTGATC
66 TCATTTAAATATTGATC
611573 AAATT
1 AAATT
611578 GGCCTCTCGT
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
80 44 0.54
81 29 0.35
82 9 0.11
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.53
Consensus pattern (82 bp):
AAATTATTACCTAGTTTTATTATTTCTTTCTTTTTCTACATTTTTTAAAATATTAAGAATTATCA
TCATTTAAATATTGATC
Done.