Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008932.1 Kokia drynarioides strain JFW-HI SEQ_123623, 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: 411669
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 79 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:5214 original size:59 final size:59
Alignment explanation
Indices: 5145--5300 Score: 215
Period size: 60 Copynumber: 2.6 Consensus size: 59
5135 AATGGAATTT
* *
5145 GGGGGTAAAAATGTAATTTTTGGAAAAATCGAGGTCAAAAATTCAATTTTGGAGAGTTC
1 GGGGGTAAAAATGTAATTTTTGGAAAAATCAAGGTCAAAAATGCAATTTTGGAGAGTTC
* * * * * *
5204 GGGGGTAAAAATATAATTTTTGAAAAAATTAGGGTAAAAAAATGCAATTTTGGAGAGTTT
1 GGGGGTAAAAATGTAATTTTTGGAAAAATCAAGGT-CAAAAATGCAATTTTGGAGAGTTC
*
5264 AGGGGTAAAAATGTAATTTTTGG-AAAATCAAGGTCAA
1 GGGGGTAAAAATGTAATTTTTGGAAAAATCAAGGTCAA
5301 TACAATTTTA
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
58 2 0.02
59 39 0.48
60 41 0.50
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.30
Consensus pattern (59 bp):
GGGGGTAAAAATGTAATTTTTGGAAAAATCAAGGTCAAAAATGCAATTTTGGAGAGTTC
Found at i:5285 original size:30 final size:30
Alignment explanation
Indices: 5146--5291 Score: 99
Period size: 29 Copynumber: 4.9 Consensus size: 30
5136 ATGGAATTTG
* *
5146 GGGGTAAAAATGTAATTTTTGGA-AAAATC
1 GGGGTAAAAATGTAATTTTTGGAGAAATTA
* * *
5175 GAGGTCAAAAAT-TCAA-TTTTGGAG-AGTTCG
1 GGGGT-AAAAATGT-AATTTTTGGAGAAATT-A
* * *
5205 GGGGTAAAAATATAATTTTTGAAAAAATTA
1 GGGGTAAAAATGTAATTTTTGGAGAAATTA
* **
5235 -GGGTAAAAAAATGCAA-TTTTGGAGAGTTTA
1 GGGGT--AAAAATGTAATTTTTGGAGAAATTA
5265 GGGGTAAAAATGTAATTTTTGGA-AAAT
1 GGGGTAAAAATGTAATTTTTGGAGAAAT
5292 CAAGGTCAAT
Statistics
Matches: 88, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
29 37 0.42
30 36 0.41
31 15 0.17
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (30 bp):
GGGGTAAAAATGTAATTTTTGGAGAAATTA
Found at i:5801 original size:36 final size:36
Alignment explanation
Indices: 5752--5841 Score: 171
Period size: 36 Copynumber: 2.5 Consensus size: 36
5742 GGTCAAAGCT
*
5752 CAAAACGATGCCGTTTTGAGGCTGAAACTCAGGCCC
1 CAAAACGACGCCGTTTTGAGGCTGAAACTCAGGCCC
5788 CAAAACGACGCCGTTTTGAGGCTGAAACTCAGGCCC
1 CAAAACGACGCCGTTTTGAGGCTGAAACTCAGGCCC
5824 CAAAACGACGCCGTTTTG
1 CAAAACGACGCCGTTTTG
5842 GAAGCTTATA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (36 bp):
CAAAACGACGCCGTTTTGAGGCTGAAACTCAGGCCC
Found at i:9790 original size:15 final size:15
Alignment explanation
Indices: 9772--9828 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
9762 CTTTCTTGCT
9772 CTTCTTTTTCTTATC
1 CTTCTTTTTCTTATC
*
9787 CTTCTTATCCTTCTTCTC
1 CTTCTT-T--TTCTTATC
* *
9805 CTTCTTATTCTTTTC
1 CTTCTTTTTCTTATC
*
9820 TTTCTTTTT
1 CTTCTTTTT
9829 TTTACTCTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 20 0.59
16 1 0.03
18 13 0.38
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTCTTTTTCTTATC
Found at i:9791 original size:9 final size:9
Alignment explanation
Indices: 9779--9812 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
9769 GCTCTTCTTT
9779 TTCTTATCC
1 TTCTTATCC
9788 TTCTTATCC
1 TTCTTATCC
*
9797 TTCTTCTCC
1 TTCTTATCC
9806 TTCTTAT
1 TTCTTAT
9813 TCTTTTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.09, C:0.32, G:0.00, T:0.59
Consensus pattern (9 bp):
TTCTTATCC
Found at i:11660 original size:16 final size:16
Alignment explanation
Indices: 11635--11682 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
11625 GCATGATTAC
* *
11635 AGTTTGGATTATTTTC
1 AGTTTAGATTATTTTA
* * *
11651 TGTTTCGATTACTTTA
1 AGTTTAGATTATTTTA
11667 AGTTTAGATTATTTTA
1 AGTTTAGATTATTTTA
11683 GATTATTTGT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.23, C:0.06, G:0.15, T:0.56
Consensus pattern (16 bp):
AGTTTAGATTATTTTA
Found at i:12387 original size:27 final size:29
Alignment explanation
Indices: 12349--12417 Score: 72
Period size: 31 Copynumber: 2.4 Consensus size: 29
12339 TGTTAGCTAC
12349 ACTTAAGA-AAAAC-TT-AACAGTGCAGTG
1 ACTTAA-ATAAAACTTTGAACAGTGCAGTG
* *
12376 ACTTAAATAAAAACTTTTGAATAGTTCAGTG
1 ACTTAAAT-AAAAC-TTTGAACAGTGCAGTG
12407 ACTTAAATAAA
1 ACTTAAATAAA
12418 TTTTTTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 1 0.03
27 6 0.17
28 5 0.14
30 5 0.14
31 18 0.51
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (29 bp):
ACTTAAATAAAACTTTGAACAGTGCAGTG
Found at i:12533 original size:1 final size:1
Alignment explanation
Indices: 12517--12559 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
12507 AATTTACCTT
* * * *
12517 AAAACAAAACAAAAAAAAAAAGATAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12560 GACAAGGCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.91, C:0.05, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:13217 original size:64 final size:62
Alignment explanation
Indices: 13138--13261 Score: 151
Period size: 62 Copynumber: 2.0 Consensus size: 62
13128 CCACAAGTGG
* * * * *
13138 GTTTCAAATCCATTTCTAAATTGCTTTTTTTAATGTATTGTACTATCTCCATGTTGAGTGTTTGC
1 GTTTCAAAGCCATTTCTAAATTG--GTTTTGAATGTATTGTAATAT-GCCATGTTGAGTGTTTGC
* *
13203 GTTTC-AAGCCATTTCTGAATTGGTTTTGAATGTATTGTAATATGGCATGTTGAGTGTTT
1 GTTTCAAAGCCATTTCTAAATTGGTTTTGAATGTATTGTAATATGCCATGTTGAGTGTTT
13262 TAGAACTTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
61 14 0.27
62 18 0.35
64 15 0.29
65 5 0.10
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.48
Consensus pattern (62 bp):
GTTTCAAAGCCATTTCTAAATTGGTTTTGAATGTATTGTAATATGCCATGTTGAGTGTTTGC
Found at i:13731 original size:205 final size:206
Alignment explanation
Indices: 13302--13769 Score: 586
Period size: 205 Copynumber: 2.3 Consensus size: 206
13292 GATTAGTTTT
*
13302 CATCTTTGATTGTCATCTATGTATTGGAATATGGTGTCTTGAATGTTTAAGAACTT-CTTGTTTT
1 CATCTTTGATTGTCATCTATGTATTGGAATATGGTGTCTTGAATGTTTAAGAACTTGTTTGTTTT
* *
13366 TGAATTTGGGTCTATATTCATCTTTGTTTGTCGACTTATTAAATTATGTATTCTAAATTTTGCAT
66 TGAATTTGGATCTATATTCATCTTTGTTTGTCGACTTATTAAATTATGTATTATAAATTTTGCAT
* * * ** *
13431 ACTAGATCTATGTATCGAAATATGGTGTGTTGAATGTTTAAAATCACATTTTTGCTCTTGGATTT
131 ACTAGATCAATGCATCGAAATATGGTGTGTTGAATGCTTAAAATCACACCTTCGCTCTTGGATTT
* *
13496 TGTTCTGCATT
196 TGTTCTACATC
** * * ** *
13507 TTTCTTGGTTTGTCATCTATGTATT-GAACTATACTATCTTGAATGTTTAAGAACTTGTTTG-TT
1 CATCTTTGATTGTCATCTATGTATTGGAA-TATGGTGTCTTGAATGTTTAAGAACTTGTTTGTTT
* * * * *
13570 TTGAATTTGGATCTATGTTCATTTTTGTTCT-TCGACTTATTAAATTATTTGTTATAATTTTTGC
65 TTGAATTTGGATCTATATTCATCTTTGTT-TGTCGACTTATTAAATTATGTATTATAAATTTTGC
* ***
13634 ATACTAGATCAATGCATTGAAATATGGTGTGTTGAATGCTTAAAATCTTGCCTTCGCTCTTGGAT
129 ATACTAGATCAATGCATCGAAATATGGTGTGTTGAATGCTTAAAATCACACCTTCGCTCTTGGAT
*
13699 TTT-TATCTATATC
194 TTTGT-TCTACATC
* * * *
13712 CATCTTTGATTGGCATCTATGCATTGGAATATGGTGTGTTGAATGTTTAAAAACTTGT
1 CATCTTTGATTGTCATCTATGTATTGGAATATGGTGTCTTGAATGTTTAAGAACTTGT
13770 CGCTGTTCTT
Statistics
Matches: 219, Mismatches: 39, Indels: 10
0.82 0.15 0.04
Matches are distributed among these distances:
204 4 0.02
205 208 0.95
206 7 0.03
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (206 bp):
CATCTTTGATTGTCATCTATGTATTGGAATATGGTGTCTTGAATGTTTAAGAACTTGTTTGTTTT
TGAATTTGGATCTATATTCATCTTTGTTTGTCGACTTATTAAATTATGTATTATAAATTTTGCAT
ACTAGATCAATGCATCGAAATATGGTGTGTTGAATGCTTAAAATCACACCTTCGCTCTTGGATTT
TGTTCTACATC
Found at i:17522 original size:16 final size:16
Alignment explanation
Indices: 17497--17528 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17487 TATTTTTTAA
17497 ATTTAATTTATTATTT
1 ATTTAATTTATTATTT
*
17513 ATTTATTTTATTATTT
1 ATTTAATTTATTATTT
17529 TCACATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTAATTTATTATTT
Found at i:25655 original size:23 final size:21
Alignment explanation
Indices: 25620--25675 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 21
25610 AAGGGCCCAT
*
25620 AAACCAAGCAAAATAGAAACATC
1 AAACAAAG-AAAATAGAAACA-C
*
25643 AAACAAAAGAAAATAGAAACAG
1 AAAC-AAAGAAAATAGAAACAC
25665 AAACAAAGAAA
1 AAACAAAGAAA
25676 GCCCAGAAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 7 0.23
22 4 0.13
23 16 0.53
24 3 0.10
ACGTcount: A:0.70, C:0.14, G:0.11, T:0.05
Consensus pattern (21 bp):
AAACAAAGAAAATAGAAACAC
Found at i:27541 original size:104 final size:104
Alignment explanation
Indices: 27382--27576 Score: 329
Period size: 104 Copynumber: 1.9 Consensus size: 104
27372 TGAAAAAAAA
*
27382 TTTCCTTGAAAAAATGGTTCCTAAACAATATTAGGAATCAAATAATAGATTGAGGATGAACTTTG
1 TTTCCATGAAAAAATGGTTCCTAAACAATATTAGGAATCAAATAATAGATTGAGGATGAACTTTG
* *
27447 CAATGACATTATATCGAATTTCAAATATGCGAAAGACAT
66 CAATGACATTATATCAAATTACAAATATGCGAAAGACAT
* *
27486 TTTCCATGAAACAATGGTTCCTAAACAATATTCA-GAATCAAATAATAGGTTGAGGATGAACTTT
1 TTTCCATGAAAAAATGGTTCCTAAACAATATT-AGGAATCAAATAATAGATTGAGGATGAACTTT
27550 GCAATGACATTATATCAAATTACAAAT
65 GCAATGACATTATATCAAATTACAAAT
27577 GAGAAACTAC
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
104 84 0.99
105 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (104 bp):
TTTCCATGAAAAAATGGTTCCTAAACAATATTAGGAATCAAATAATAGATTGAGGATGAACTTTG
CAATGACATTATATCAAATTACAAATATGCGAAAGACAT
Found at i:33062 original size:14 final size:14
Alignment explanation
Indices: 33045--33075 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
33035 TTTAGTTCTT
*
33045 TTTTTTTTCCTGCG
1 TTTTATTTCCTGCG
33059 TTTTATTTCCTGCG
1 TTTTATTTCCTGCG
33073 TTT
1 TTT
33076 CTGTAAGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.19, G:0.13, T:0.65
Consensus pattern (14 bp):
TTTTATTTCCTGCG
Found at i:33580 original size:26 final size:27
Alignment explanation
Indices: 33541--33591 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
33531 ATTTCTCTTT
* *
33541 TTTTTCTAATTTTATTTACAATATATA
1 TTTTTCTAAGTTTATTTAAAATATATA
33568 TTTTT-TAAGTTTATTTAAAATATA
1 TTTTTCTAAGTTTATTTAAAATATA
33592 CAACATTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTTTCTAAGTTTATTTAAAATATATA
Found at i:40588 original size:12 final size:12
Alignment explanation
Indices: 40571--40602 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
40561 GCTTATTATT
40571 ATCATCATCATG
1 ATCATCATCATG
40583 ATCATCATCATG
1 ATCATCATCATG
40595 ATCATCAT
1 ATCATCAT
40603 GATTCGTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (12 bp):
ATCATCATCATG
Found at i:41977 original size:17 final size:17
Alignment explanation
Indices: 41937--41978 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
41927 GACTATAAAA
*
41937 TAAATAATTTTAATTTT
1 TAAATAATTCTAATTTT
*
41954 TATATAATTCT-ATTTT
1 TAAATAATTCTAATTTT
41970 TCAAATAAT
1 T-AAATAAT
41979 AATTTATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (17 bp):
TAAATAATTCTAATTTT
Found at i:47999 original size:24 final size:24
Alignment explanation
Indices: 47972--48023 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
47962 TGGTCCCATT
47972 TTTCATTGCTCGAGCCGGAAAGGG
1 TTTCATTGCTCGAGCCGGAAAGGG
* *
47996 TTTCATTGCTTGAGCTGGAAAGGG
1 TTTCATTGCTCGAGCCGGAAAGGG
48020 TTTC
1 TTTC
48024 GTTTCCTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (24 bp):
TTTCATTGCTCGAGCCGGAAAGGG
Found at i:52390 original size:18 final size:17
Alignment explanation
Indices: 52349--52393 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
52339 GTTTCTTATG
52349 ATTATAAT-TATAAAAA
1 ATTATAATATATAAAAA
*
52365 A-AATAATATATAAAAA
1 ATTATAATATATAAAAA
52381 ATTATAA-ATATAA
1 ATTATAATATATAA
52394 TTACCCTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 5 0.20
16 16 0.64
17 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTATAATATATAAAAA
Found at i:54511 original size:21 final size:21
Alignment explanation
Indices: 54485--54525 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54475 AAAATCCAAT
* *
54485 ATAAATTTTAAATTCTAAACC
1 ATAAATTATAAATTCAAAACC
54506 ATAAATTATAAATTCAAAAC
1 ATAAATTATAAATTCAAAAC
54526 TTGAGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAAATTATAAATTCAAAACC
Found at i:54832 original size:59 final size:60
Alignment explanation
Indices: 54767--54880 Score: 171
Period size: 59 Copynumber: 1.9 Consensus size: 60
54757 TTGGTACCTA
*
54767 AACTTGACACTTTTT-TCTAATTTAGTACGTAAA-TATTTTTT-GACCCAATTTGGTGCTTG
1 AACTTGACACTTTTTCT-TAATTTAGTACCTAAACT-TTTTTTGGACCCAATTTGGTGCTTG
*
54826 AACTTGACACTTTTTCTTAATTTGGTACCTAAACTTTTTTTGGACCCAATTTGGT
1 AACTTGACACTTTTTCTTAATTTAGTACCTAAACTTTTTTTGGACCCAATTTGGT
54881 ACCCAAACTT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
59 35 0.70
60 15 0.30
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.46
Consensus pattern (60 bp):
AACTTGACACTTTTTCTTAATTTAGTACCTAAACTTTTTTTGGACCCAATTTGGTGCTTG
Found at i:54861 original size:31 final size:31
Alignment explanation
Indices: 54755--54861 Score: 73
Period size: 31 Copynumber: 3.5 Consensus size: 31
54745 TTAATATAAC
54755 ATTTGGTACCTAAACTTGACACTTTTT-TCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCT-TA
* * * **
54786 ATTTAGTACGTAAA--T---ATTTTTTGACCCA
1 ATTTGGTACCTAAACTTGACACTTTTT--CTTA
* * *
54814 ATTTGGTGCTTGAACTTGACACTTTTTCTTA
1 ATTTGGTACCTAAACTTGACACTTTTTCTTA
54845 ATTTGGTACCTAAACTT
1 ATTTGGTACCTAAACTT
54862 TTTTTGGACC
Statistics
Matches: 53, Mismatches: 15, Indels: 16
0.63 0.18 0.19
Matches are distributed among these distances:
26 6 0.11
28 11 0.21
29 1 0.02
30 1 0.02
31 28 0.53
33 6 0.11
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCTTA
Found at i:54900 original size:60 final size:58
Alignment explanation
Indices: 54755--54924 Score: 189
Period size: 60 Copynumber: 2.8 Consensus size: 58
54745 TTAATATAAC
* *
54755 ATTTGGTACCTAAACTTGACACTTTTTTCTAATTTAGTACGTAAATATTTTTTGACCCA
1 ATTTGGTACCTAAACTTGACA-TTTTTTCTAATTTGGTACCTAAATATTTTTTGACCCA
* * * *
54814 ATTTGGTGCTTGAACTTGACACTTTTTCTTAATTTGGTACCTAAACT-TTTTTTGGACCCA
1 ATTTGGTACCTAAACTTGACATTTTTTC-TAATTTGGTACCTAAA-TATTTTTT-GACCCA
* * * *
54874 ATTTGGTACCCAAACTTGGCATTTTTTCCTAATTTGATGCCTAAATTATTT
1 ATTTGGTACCTAAACTTGACATTTTTT-CTAATTTGGTACCTAAA-TATTT
54925 AAATATTATA
Statistics
Matches: 91, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
58 6 0.07
59 38 0.42
60 43 0.47
61 4 0.04
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (58 bp):
ATTTGGTACCTAAACTTGACATTTTTTCTAATTTGGTACCTAAATATTTTTTGACCCA
Found at i:55154 original size:30 final size:31
Alignment explanation
Indices: 55118--55241 Score: 107
Period size: 30 Copynumber: 4.2 Consensus size: 31
55108 GGACCCCAAA
*
55118 AAGTTTAAGTACCAACTTA-AAAAAAATGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAATGTC
* * *
55148 AAGTTTAGGTA-CAAATTAGAAAACAGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAATGTC
* * * *
55178 AAGTTTGAGTGCCAAAGTGGACAAAAAA----
1 AAGTTTAAGTACCAAATTAGA-AAAAAATGTC
* *
55206 AAGTTTAAGTACCAAATTAGGAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAATGTC
55237 AAGTT
1 AAGTT
55242 CAAATATCAA
Statistics
Matches: 70, Mismatches: 17, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
27 5 0.07
28 16 0.23
29 6 0.09
30 27 0.39
31 12 0.17
32 4 0.06
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAATGTC
Found at i:56471 original size:23 final size:23
Alignment explanation
Indices: 56428--56471 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
56418 AATATATATA
*
56428 TATATTTTTTAATTTGATTAAAT
1 TATATTTTTTAATTAGATTAAAT
56451 TATATTTTTTGAATTAG-TTAA
1 TATATTTTTT-AATTAGATTAA
56472 TTTTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (23 bp):
TATATTTTTTAATTAGATTAAAT
Found at i:62922 original size:12 final size:13
Alignment explanation
Indices: 62900--62930 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
62890 TTAAACCTAA
62900 ATTTAATTTTAAT
1 ATTTAATTTTAAT
62913 ATTTAA-TTTAAT
1 ATTTAATTTTAAT
62925 ATTTAA
1 ATTTAA
62931 ATGAAATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTTAATTTTAAT
Found at i:63064 original size:21 final size:22
Alignment explanation
Indices: 63038--63082 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
63028 AATTTAGATA
63038 AAAAAAATTAAAAATT-AAATT
1 AAAAAAATTAAAAATTAAAATT
* *
63059 AAAAAAATTCAATATTAAAATT
1 AAAAAAATTAAAAATTAAAATT
63081 AA
1 AA
63083 CATTAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAAAATTAAAAATTAAAATT
Found at i:63066 original size:14 final size:16
Alignment explanation
Indices: 63047--63078 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
63037 AAAAAAAATT
63047 AAAAATT-AA-ATTAA
1 AAAAATTCAATATTAA
63061 AAAAATTCAATATTAA
1 AAAAATTCAATATTAA
63077 AA
1 AA
63079 TTAACATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAATTCAATATTAA
Found at i:68252 original size:3 final size:3
Alignment explanation
Indices: 68237--68286 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
68227 TGATCCTCCC
* * *
68237 GAA GAA GAT GAA GAA GAA GAG GAA GAA -AA GAA TGAG GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA
68282 GAA GA
1 GAA GA
68287 TCCAGAAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.36, T:0.04
Consensus pattern (3 bp):
GAA
Found at i:69944 original size:31 final size:31
Alignment explanation
Indices: 69909--69969 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
69899 TATAAAATGA
*
69909 TTATTAAATTATTCAAAAATTTTCATTTAAG
1 TTATTAAACTATTCAAAAATTTTCATTTAAG
* * *
69940 TTATTGAACTATTCGAAAATTTTTATTTAA
1 TTATTAAACTATTCAAAAATTTTCATTTAA
69970 ATCACTTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (31 bp):
TTATTAAACTATTCAAAAATTTTCATTTAAG
Found at i:72847 original size:24 final size:24
Alignment explanation
Indices: 72819--72867 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
72809 AAAAAAAAGA
*
72819 CTGAATTGTAAAAGCAGAGGCGGG
1 CTGAATCGTAAAAGCAGAGGCGGG
*
72843 CTGAATCGTAAGAGCAGAGGCGGG
1 CTGAATCGTAAAAGCAGAGGCGGG
72867 C
1 C
72868 CATTATGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.16, G:0.39, T:0.14
Consensus pattern (24 bp):
CTGAATCGTAAAAGCAGAGGCGGG
Found at i:74610 original size:23 final size:22
Alignment explanation
Indices: 74577--74621 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
74567 CCAAATTAAA
*
74577 TAAAAAAAAATTAAGTATCAAAT
1 TAAAAAAAAATAAAGT-TCAAAT
*
74600 TAAAAATAAATAAAGTTCAAAT
1 TAAAAAAAAATAAAGTTCAAAT
74622 ACCAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (22 bp):
TAAAAAAAAATAAAGTTCAAAT
Found at i:74610 original size:33 final size:34
Alignment explanation
Indices: 74542--74613 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 34
74532 GGTACCAAAT
*
74542 TAAAAAAAAATATCAAGTTCAAATACCAAATTAAA
1 TAAAAAAAAATATCAAGTTCAAATA-CAAAATAAA
74577 TAAAAAAAAAT-T-AAGTATCAAATTA-AAAATAAA
1 TAAAAAAAAATATCAAGT-TCAAA-TACAAAATAAA
74610 TAAA
1 TAAA
74614 GTTCAAATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
33 15 0.44
34 6 0.18
35 13 0.38
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.24
Consensus pattern (34 bp):
TAAAAAAAAATATCAAGTTCAAATACAAAATAAA
Found at i:74618 original size:56 final size:59
Alignment explanation
Indices: 74503--74627 Score: 166
Period size: 58 Copynumber: 2.1 Consensus size: 59
74493 TAAATTTAGG
* *
74503 TACCAAATTAAATCTTAAAAAAAAGTTTAGGTACCAAATTAAAAAAAAATATCAAGTTCAAA
1 TACCAAATTAAA--TTAAAAAAAAGATTAAGTACCAAATTAAAAAAAAATA-CAAGTTCAAA
* *
74565 TACCAAATTAAA-TAAAAAAAA-ATTAAGTATCAAATTAAAAATAAATA-AAGTTCAAA
1 TACCAAATTAAATTAAAAAAAAGATTAAGTACCAAATTAAAAAAAAATACAAGTTCAAA
74621 TACCAAA
1 TACCAAA
74628 AATTATATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
56 16 0.27
58 22 0.37
59 9 0.15
62 12 0.20
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.25
Consensus pattern (59 bp):
TACCAAATTAAATTAAAAAAAAGATTAAGTACCAAATTAAAAAAAAATACAAGTTCAAA
Found at i:81490 original size:21 final size:19
Alignment explanation
Indices: 81466--81504 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
81456 ATAGCTTTAA
81466 TTTTTTCATTTAATTCTTCAC
1 TTTTTT-ATTTAATT-TTCAC
*
81487 TTTTTTATTTTATTTTCA
1 TTTTTTATTTAATTTTCA
81505 ATTACCGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTATTTAATTTTCAC
Found at i:81584 original size:2 final size:2
Alignment explanation
Indices: 81577--81605 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
81567 ATAAAAAGCT
81577 TA TA 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 T
81606 CATCCTATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:82581 original size:6 final size:6
Alignment explanation
Indices: 82570--82605 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
82560 GATCAGCTAA
* *
82570 TAGAGG TAGAGG TAGAGG GAGAGG TAGGGG TAGAGG
1 TAGAGG TAGAGG TAGAGG TAGAGG TAGAGG TAGAGG
82606 GCGTGGAGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.56, T:0.14
Consensus pattern (6 bp):
TAGAGG
Found at i:82594 original size:18 final size:18
Alignment explanation
Indices: 82571--82606 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
82561 ATCAGCTAAT
82571 AGAGGTAGAGGTAGAGGG
1 AGAGGTAGAGGTAGAGGG
*
82589 AGAGGTAGGGGTAGAGGG
1 AGAGGTAGAGGTAGAGGG
82607 CGTGGAGGAA
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:0.31, C:0.00, G:0.58, T:0.11
Consensus pattern (18 bp):
AGAGGTAGAGGTAGAGGG
Found at i:87629 original size:116 final size:116
Alignment explanation
Indices: 87374--87720 Score: 444
Period size: 116 Copynumber: 3.0 Consensus size: 116
87364 CCGATTGATT
* * * * * * * *
87374 ATAAAAAATTAATAACCCGAACTTGAAAATAATCCAAACTAAAAATGATTTGAACCTGGATTGAC
1 ATAAAAAGTCAATAACCCGAACCTGAAAATGATTCAAACCAGAAATGATTTGAACTTGGATTGAC
** * * ** * *
87439 CGAAATGACCTGAACCCAAGAATCCAATCCAATTGGCCTGAACTCAAACTCG
66 CGAAATGACCT-AAGTCAAGAATTCAATCCGATTAACCCGAACTCAAACCCG
* *
87491 ATAAAAAGTCAATAACCCGAACCAGAAAATGATTCAAACCAGAAGTGATTTGAACTTGGATTGAC
1 ATAAAAAGTCAATAACCCGAACCTGAAAATGATTCAAACCAGAAATGATTTGAACTTGGATTGAC
* *
87556 CGAAATGACCTTAGTCAAGAATTAAATCCGATTAACCCGAACTCAAACCCG
66 CGAAATGACCTAAGTCAAGAATTCAATCCGATTAACCCGAACTCAAACCCG
* * *
87607 ATGAAAAGTCAATAACCCGAACCTGAAAATGA-TCCAACCAGAAATTATTTGAACTTGGATTGAC
1 ATAAAAAGTCAATAACCCGAACCTGAAAATGATTCAAACCAGAAATGATTTGAACTTGGATTGAC
* *
87671 CGAACTGACCTGAGCTCAAGAATTCAATCCGATTAACCCGAACTCAAACC
66 CGAAATGACCTAAG-TCAAGAATTCAATCCGATTAACCCGAACTCAAACC
87721 TGATTGATCA
Statistics
Matches: 201, Mismatches: 28, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
115 41 0.20
116 94 0.47
117 66 0.33
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (116 bp):
ATAAAAAGTCAATAACCCGAACCTGAAAATGATTCAAACCAGAAATGATTTGAACTTGGATTGAC
CGAAATGACCTAAGTCAAGAATTCAATCCGATTAACCCGAACTCAAACCCG
Found at i:87778 original size:108 final size:107
Alignment explanation
Indices: 87632--87843 Score: 370
Period size: 108 Copynumber: 2.0 Consensus size: 107
87622 CCCGAACCTG
* * *
87632 AAAATGATCCAACCAGAAATTATTTGAACTTGGATTGACCGAACTGACCTGAGCTCAAGAATTCA
1 AAAATGATCCAACCAGAAATGATTTGAACTTGGATTGACCAAACTGACCTGAGCTCAAGAATCCA
87697 ATCCGATTAACCCGAACTCAAACCTGATTGATCATAAAAGAT
66 ATCCGATTAACCCGAACTCAAACCTGATTGATCATAAAAGAT
* *
87739 AAAATTATCCAAACCAGAAATGATTTGAACTTGGATTGACCAAACTGACCTGAGCTCTAGAATCC
1 AAAATGATCC-AACCAGAAATGATTTGAACTTGGATTGACCAAACTGACCTGAGCTCAAGAATCC
87804 AATCCGATTAACCCGAACTCAAACCTGATTGATCATAAAA
65 AATCCGATTAACCCGAACTCAAACCTGATTGATCATAAAA
87844 AGCCAATAAC
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
107 9 0.09
108 90 0.91
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (107 bp):
AAAATGATCCAACCAGAAATGATTTGAACTTGGATTGACCAAACTGACCTGAGCTCAAGAATCCA
ATCCGATTAACCCGAACTCAAACCTGATTGATCATAAAAGAT
Found at i:87868 original size:108 final size:108
Alignment explanation
Indices: 87642--87870 Score: 352
Period size: 108 Copynumber: 2.1 Consensus size: 108
87632 AAAATGATCC
* * *
87642 AACCAGAAATTATTTGAACTTGGATTGACCGAACTGACCTGAGCTCAAGAATTCAATCCGATTAA
1 AACCAGAAATGATTTGAACTTGGATTGACCAAACTGACCTGAGCTCAAGAATCCAATCCGATTAA
* * *
87707 CCCGAACTCAAACCTGATTGATCATAAAAGATAAAATTATCCA
66 CCCGAACTCAAACCTGATTGATCATAAAAGAGAAAATAACCCA
*
87750 AACCAGAAATGATTTGAACTTGGATTGACCAAACTGACCTGAGCTCTAGAATCCAATCCGATTAA
1 AACCAGAAATGATTTGAACTTGGATTGACCAAACTGACCTGAGCTCAAGAATCCAATCCGATTAA
**
87815 CCCGAACTCAAACCTGATTGATCATAAAA-AGCCAATAACCCA
66 CCCGAACTCAAACCTGATTGATCATAAAAGAGAAAATAACCCA
*
87857 AACCTGAAAATGAT
1 AACCAG-AAATGAT
87871 CCAAATCAGA
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
107 13 0.12
108 97 0.88
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (108 bp):
AACCAGAAATGATTTGAACTTGGATTGACCAAACTGACCTGAGCTCAAGAATCCAATCCGATTAA
CCCGAACTCAAACCTGATTGATCATAAAAGAGAAAATAACCCA
Found at i:98153 original size:4 final size:4
Alignment explanation
Indices: 98146--98170 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
98136 CATATATATG
98146 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
98171 TAAGTCATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:102165 original size:30 final size:30
Alignment explanation
Indices: 102078--102165 Score: 77
Period size: 31 Copynumber: 2.9 Consensus size: 30
102068 AATTAAGGAG
* * *
102078 AATTCTCAAAAAATTTTCAAGGTTTAGTTAT
1 AATTCTCAAAAAA-TTTAAAGGCTTAATTAT
* ** *
102109 AATTGTCAAAACTTTTATAGGGCTTAATTAT
1 AATTCTCAAAAAATTTA-AAGGCTTAATTAT
**
102140 AATTCTCAAAAAATTTGGAGGCTTAA
1 AATTCTCAAAAAATTTAAAGGCTTAA
102166 ATAATATTTT
Statistics
Matches: 43, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
30 10 0.23
31 33 0.77
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (30 bp):
AATTCTCAAAAAATTTAAAGGCTTAATTAT
Found at i:108534 original size:18 final size:19
Alignment explanation
Indices: 108491--108532 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
108481 GAATTGGTAA
*
108491 AAAAATAGAAATTCGAGAT
1 AAAAATAGAAAATCGAGAT
108510 AAAAATAGAAAATCGAGAT
1 AAAAATAGAAAATCGAGAT
108529 AAAA
1 AAAA
108533 TACTGGTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.64, C:0.05, G:0.14, T:0.17
Consensus pattern (19 bp):
AAAAATAGAAAATCGAGAT
Found at i:115952 original size:20 final size:20
Alignment explanation
Indices: 115927--115965 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
115917 ATATATATAT
115927 ATATATTATTT-ATTTATTTC
1 ATATA-TATTTGATTTATTTC
115947 ATATATATTTGATTTATTT
1 ATATATATTTGATTTATTT
115966 TTTTGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
ATATATATTTGATTTATTTC
Found at i:117022 original size:2 final size:2
Alignment explanation
Indices: 117015--117043 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
117005 ATTATGTATG
117015 TA TA 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 T
117044 TTATCATTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123954 original size:30 final size:31
Alignment explanation
Indices: 123880--123961 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 31
123870 AACTGTGTAC
* * * *
123880 AATTAAATCCAAATCAAAATTTTATGTATAT
1 AATTGAATCAAAATCAAAATTTAATATATAT
**
123911 GTTTGAATCAAAATCAAAATTTAATATATAT
1 AATTGAATCAAAATCAAAATTTAATATATAT
*
123942 AATT-ACTCAAAATCAAAATT
1 AATTGAATCAAAATCAAAATT
123962 CATGTATCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 15 0.36
31 27 0.64
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (31 bp):
AATTGAATCAAAATCAAAATTTAATATATAT
Found at i:124398 original size:13 final size:14
Alignment explanation
Indices: 124378--124410 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
124368 CGTATAATTT
124378 ATAAATATTCAAAA
1 ATAAATATTCAAAA
*
124392 A-AAATATTTAAAA
1 ATAAATATTCAAAA
124405 ATAAAT
1 ATAAAT
124411 TTTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAATATTCAAAA
Found at i:125830 original size:29 final size:29
Alignment explanation
Indices: 125734--125833 Score: 101
Period size: 30 Copynumber: 3.4 Consensus size: 29
125724 ACTGAGAACT
**
125734 TTTTAAAAATTTAAAGGATTTAATTAAAAA
1 TTTTAAAAATTTTGAGG-TTTAATTAAAAA
* ** * *
125764 TTTTAAAACTTTTGTAGGTTTGTTTAGAAT
1 TTTTAAAAATTTTG-AGGTTTAATTAAAAA
*
125794 TTTTAAAAATTTTGAGGTTTAAGTAAAAA
1 TTTTAAAAATTTTGAGGTTTAATTAAAAA
*
125823 TTTCAAAAATT
1 TTTTAAAAATT
125834 GAAGGGTACA
Statistics
Matches: 55, Mismatches: 14, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
29 20 0.36
30 32 0.58
31 3 0.05
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (29 bp):
TTTTAAAAATTTTGAGGTTTAATTAAAAA
Found at i:127411 original size:22 final size:22
Alignment explanation
Indices: 127383--127425 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
127373 CAAATAAATT
*
127383 ATATATATACATACGTATATAC
1 ATATATAAACATACGTATATAC
*
127405 ATATATAAACATACGTGTATA
1 ATATATAAACATACGTATATA
127426 TGTATGTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35
Consensus pattern (22 bp):
ATATATAAACATACGTATATAC
Found at i:128895 original size:17 final size:18
Alignment explanation
Indices: 128862--128898 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
128852 ATTTTAAAAA
128862 ATTATAACAAAAAAATTT
1 ATTATAACAAAAAAATTT
*
128880 ATTATAA-AAAATAATTT
1 ATTATAACAAAAAAATTT
128897 AT
1 AT
128899 ATGTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTATAACAAAAAAATTT
Found at i:144090 original size:6 final size:6
Alignment explanation
Indices: 144079--144106 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
144069 AAAACTATAC
144079 GAAAAA GAAAAA GAAAAA GAAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAA
144107 GATCAATGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:148985 original size:170 final size:166
Alignment explanation
Indices: 148711--149063 Score: 496
Period size: 170 Copynumber: 2.1 Consensus size: 166
148701 AATCTGAATG
* *
148711 ACATACATAAACACATATATACATACATGCATGCATGCATGCTTTTGGAGGGTTCTTGGAGGACC
1 ACATACATAAACACATATATACATACA--CATGCATGCATGCATTTGGAGGGTTCTTGGAGAACC
*
148776 ATATCCCAGGAACCATACGAAATCCATAAAAAACAAATGACATGCATACATACATACATTGACAA
64 ATATCCCAGGAACCATACAAAATCCATAAAAAACAAATGACATG----CATACATACATTGACAA
*
148841 AAGATGAACACATCAACACACGGGAACCATACAAGATCCAAATA
125 AAGATAAACACATCAACA-A-GGGAACCATACAAGATCCAAATA
*
148885 ACATACATAAACACATATATACAT-C-CATGCATGCATGCATTTGGAGGGTTCTTGGAGAATCAT
1 ACATACATAAACACATATATACATACACATGCATGCATGCATTTGGAGGGTTCTTGGAGAACCAT
* * * * *
148948 ATTCCGGGAACCATACAAAATCCA-AGAAAACCAAATGACATGCATGCATGCATTGACAAAAGAT
66 ATCCCAGGAACCATACAAAATCCATA-AAAAACAAATGACATGCATACATACATTGACAAAAGAT
* *
149012 AAACACATTAACAAGGGAACCATACAAGATCCAAATG
130 AAACACATCAACAAGGGAACCATACAAGATCCAAATA
149049 ACATACATAAACACA
1 ACATACATAAACACA
149064 CACGCGCACA
Statistics
Matches: 166, Mismatches: 12, Indels: 12
0.87 0.06 0.06
Matches are distributed among these distances:
164 37 0.22
165 1 0.01
166 31 0.19
169 1 0.01
170 71 0.43
173 1 0.01
174 24 0.14
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.20
Consensus pattern (166 bp):
ACATACATAAACACATATATACATACACATGCATGCATGCATTTGGAGGGTTCTTGGAGAACCAT
ATCCCAGGAACCATACAAAATCCATAAAAAACAAATGACATGCATACATACATTGACAAAAGATA
AACACATCAACAAGGGAACCATACAAGATCCAAATA
Found at i:151925 original size:71 final size:71
Alignment explanation
Indices: 151791--151932 Score: 182
Period size: 71 Copynumber: 2.0 Consensus size: 71
151781 ATTCAACAAA
* **
151791 CTAGCTCAAATAGTACCATAGTTCACTGGAGAACCTCTAATACTAGAGGTCTTGAGCTTAAGCCT
1 CTAGCTCAAATAGTACCATAGTTCACTGGAGAACCTCTAATACTAGAGATCTCCAGCTTAAGCCT
151856 TAACAT
66 TAACAT
* * *
151862 CTAGCTCAAGTAGTACCATAGTTCACTCGG-GATCTTCTATATACTA-AGATCTCCAG-TTCAAG
1 CTAGCTCAAATAGTACCATAGTTCACT-GGAGAACCTCTA-ATACTAGAGATCTCCAGCTT-AAG
151924 CCTTAACAT
63 CCTTAACAT
151933 ACATGCTAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
70 2 0.03
71 52 0.84
72 8 0.13
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (71 bp):
CTAGCTCAAATAGTACCATAGTTCACTGGAGAACCTCTAATACTAGAGATCTCCAGCTTAAGCCT
TAACAT
Found at i:153134 original size:21 final size:21
Alignment explanation
Indices: 153101--153140 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
153091 TTATGTTTAT
*
153101 ATCATAAAAAAATTAAAATTG
1 ATCATAAAAAAATAAAAATTG
**
153122 ATCATAATTAAATAAAAAT
1 ATCATAAAAAAATAAAAAT
153141 AAATTCATTT
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:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (21 bp):
ATCATAAAAAAATAAAAATTG
Found at i:154464 original size:57 final size:60
Alignment explanation
Indices: 154401--154513 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
154391 AATATATAAC
*
154401 ATTTAGTACGTGAA-TTTG-ACATTTTTTT-TAATTTGGTATCTAAATTTATTTTACTTA
1 ATTTAGTACGTGAACTTGGTACATTTTTTTCTAATTTGGTATCTAAATTTATTTTACTTA
* ** * * *
154458 ATTTAGTACTTGAACTTGGTATTTTTTTTTCTAATTTGGTATTTAAGTTTTTTTTA
1 ATTTAGTACGTGAACTTGGTACATTTTTTTCTAATTTGGTATCTAAATTTATTTTA
154514 GATTCAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
57 13 0.28
58 3 0.07
59 8 0.17
60 22 0.48
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.58
Consensus pattern (60 bp):
ATTTAGTACGTGAACTTGGTACATTTTTTTCTAATTTGGTATCTAAATTTATTTTACTTA
Found at i:156889 original size:21 final size:21
Alignment explanation
Indices: 156863--156903 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
156853 TGTGTATGTG
*
156863 AAATATT-ATGTGTTTAATTAT
1 AAATATTGAT-TGTGTAATTAT
156884 AAATATTGATTGTGTAATTA
1 AAATATTGATTGTGTAATTA
156904 ATTGGTGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (21 bp):
AAATATTGATTGTGTAATTAT
Found at i:157142 original size:24 final size:25
Alignment explanation
Indices: 157114--157192 Score: 124
Period size: 25 Copynumber: 3.2 Consensus size: 25
157104 TGTGTGCCTA
157114 CTGTTT-CCCAGCGCTTATGTGCTT
1 CTGTTTCCCCAGCGCTTATGTGCTT
157138 CTGTTTCCCCAGCGCTTATGTGCTT
1 CTGTTTCCCCAGCGCTTATGTGCTT
* * *
157163 CTGTTTCCCCAGCACTTATGCGTTT
1 CTGTTTCCCCAGCGCTTATGTGCTT
157188 CTGTT
1 CTGTT
157193 AAGTACTTCG
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 6 0.12
25 45 0.88
ACGTcount: A:0.09, C:0.30, G:0.19, T:0.42
Consensus pattern (25 bp):
CTGTTTCCCCAGCGCTTATGTGCTT
Found at i:169826 original size:31 final size:31
Alignment explanation
Indices: 169763--169826 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
169753 TCAACAGTCT
* *
169763 AATGACTTAAATAAAAACTTTCGAATAGTTC
1 AATGACTTAAATAAAAACTTTCAAATAATTC
* *
169794 AATGACTTAAATGAAAACTTTTAAATAATTC
1 AATGACTTAAATAAAAACTTTCAAATAATTC
169825 AA
1 AA
169827 CGTTGAATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (31 bp):
AATGACTTAAATAAAAACTTTCAAATAATTC
Found at i:174254 original size:2 final size:2
Alignment explanation
Indices: 174247--174273 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
174237 TTAAAATGCA
174247 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
174274 AAAGCTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:174812 original size:3 final size:3
Alignment explanation
Indices: 174804--174845 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
174794 AACAATTGGT
174804 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
174846 AATAAATCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:179660 original size:93 final size:91
Alignment explanation
Indices: 179444--179800 Score: 263
Period size: 96 Copynumber: 3.7 Consensus size: 91
179434 AATTCGTTTG
* * *
179444 ATCACTTTTAACTCGTTTTTCTTATTATACATCCAAAATTTGAGCATGGTAGAGGGATCAAAA-C
1 ATCACTTTTAACTCGTTTTTCTTATTATACA---ATAA---GAGCATAGTAGAGGGACCAAAATC
* *
179508 TATAATTTAACACAAAAAAAAATTTGTTT-AGTTC
60 -ATAATTTAAC-C-AAAAAAAACTTGTTTAATTTC
* ** * * *
179542 ATCACTTGTAAGGCGTATTTCTTATTATACAATGAAGAGCATAGTTGAGGGGCCAAAATCATAAT
1 ATCACTTTTAACTCGTTTTTCTTATTATACAAT-AAGAGCATAGTAGAGGGACCAAAATCATAAT
179607 TTAACCAAAAAAAACTTGTTTAATTTC
65 TTAACCAAAAAAAACTTGTTTAATTTC
* * * * *
179634 ATCACTTTTAACTCGTTTTTCTTTATTTTACATCCAAATTAGAGCATAATAGACGGACTAAAATC
1 ATCACTTTTAACTCGTTTTTC-TTA--TT--ATAC-AATAAGAGCATAGTAGAGGGACCAAAATC
*
179699 ATAATTTAACC-AAAAAACCTTGTTTAATTTC
60 ATAATTTAACCAAAAAAAACTTGTTTAATTTC
* * * * * * * *
179730 TTTAGTATTAAGTCGCTTTTCTTATTATATATCCAA-AATTGAGCATAGTAAAAGGACCAAAATC
1 ATCACTTTTAACTCGTTTTTCTTA-T-TATA--CAATAA--GAGCATAGTAGAGGGACCAAAATC
179794 ATAATTT
60 ATAATTT
179801 GACCCAACAA
Statistics
Matches: 210, Mismatches: 35, Indels: 31
0.76 0.13 0.11
Matches are distributed among these distances:
91 14 0.07
92 22 0.10
93 34 0.16
94 5 0.02
95 35 0.17
96 36 0.17
97 34 0.16
98 30 0.14
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (91 bp):
ATCACTTTTAACTCGTTTTTCTTATTATACAATAAGAGCATAGTAGAGGGACCAAAATCATAATT
TAACCAAAAAAAACTTGTTTAATTTC
Found at i:179709 original size:97 final size:97
Alignment explanation
Indices: 179444--179800 Score: 365
Period size: 95 Copynumber: 3.7 Consensus size: 97
179434 AATTCGTTTG
* * *
179444 ATCACTTTTAACTCGTTTTTCTTATTATACATCCAAAATTTGAGCATGGTAGAGGGATCAAAA-C
1 ATCACTTTTAACTCGTTTTTCTTATTATACATCCAAAATTAGAGCATAGTAGAGGGACCAAAATC
* *
179508 TATAATTTAACACAAAAAAAAATTTGTTT-AGTTC
66 -ATAATTTAAC-C-AAAAAAAACTTGTTTAATTTC
* ** * ** * *
179542 ATCACTTGTAAGGCGTATTTCTTATTATACA---ATGA--AGAGCATAGTTGAGGGGCCAAAATC
1 ATCACTTTTAACTCGTTTTTCTTATTATACATCCAAAATTAGAGCATAGTAGAGGGACCAAAATC
179602 ATAATTTAACCAAAAAAAACTTGTTTAATTTC
66 ATAATTTAACCAAAAAAAACTTGTTTAATTTC
* * * *
179634 ATCACTTTTAACTCGTTTTTCTTTATTTTACATCC-AAATTAGAGCATAATAGACGGACTAAAAT
1 ATCACTTTTAACTCGTTTTTC-TTATTATACATCCAAAATTAGAGCATAGTAGAGGGACCAAAAT
*
179698 CATAATTTAACC-AAAAAACCTTGTTTAATTTC
65 CATAATTTAACCAAAAAAAACTTGTTTAATTTC
* * * * * * * * *
179730 TTTAGTATTAAGTCGCTTTTCTTATTATATATCCAAAATT-GAGCATAGTAAAAGGACCAAAATC
1 ATCACTTTTAACTCGTTTTTCTTATTATACATCCAAAATTAGAGCATAGTAGAGGGACCAAAATC
179794 ATAATTT
66 ATAATTT
179801 GACCCAACAA
Statistics
Matches: 212, Mismatches: 38, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
91 14 0.07
92 22 0.10
93 37 0.17
94 1 0.00
95 41 0.19
96 39 0.18
97 31 0.15
98 27 0.13
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (97 bp):
ATCACTTTTAACTCGTTTTTCTTATTATACATCCAAAATTAGAGCATAGTAGAGGGACCAAAATC
ATAATTTAACCAAAAAAAACTTGTTTAATTTC
Found at i:179792 original size:95 final size:96
Alignment explanation
Indices: 179594--179815 Score: 268
Period size: 96 Copynumber: 2.3 Consensus size: 96
179584 AGTTGAGGGG
* * *
179594 CCAAAATCATAATTTAACCAAAAAAAACTTGTTTAATTTCATCACTTTTAACTCGTTTTTCTTTA
1 CCAAAATCATAATTTAACC-AAAAAACCTTGTTTAATTTCATCACTATTAACTCGCTTTTCTTTA
* * *
179659 TTTTACATCCAAATTAGAGCATAATAGACGGA
65 TTATACATCCAAATTAGAGCATAATAAAAGGA
* * * * *
179691 CTAAAATCATAATTTAACCAAAAAACCTTGTTTAATTTCTTTAGTATTAAGTCGCTTTTC-TTAT
1 CCAAAATCATAATTTAACCAAAAAACCTTGTTTAATTTCATCACTATTAACTCGCTTTTCTTTAT
* *
179755 TATATATCCAAAATT-GAGCATAGTAAAAGGA
66 TATACATCC-AAATTAGAGCATAATAAAAGGA
*
179786 CCAAAATCATAATTTGACCCAACAAAACCT
1 CCAAAATCATAATTT-AACCAA-AAAACCT
179816 CATCAACTTT
Statistics
Matches: 107, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
95 38 0.36
96 44 0.41
97 25 0.23
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.35
Consensus pattern (96 bp):
CCAAAATCATAATTTAACCAAAAAACCTTGTTTAATTTCATCACTATTAACTCGCTTTTCTTTAT
TATACATCCAAATTAGAGCATAATAAAAGGA
Found at i:184758 original size:6 final size:6
Alignment explanation
Indices: 184749--184778 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
184739 TTTATATATA
184749 CATCCC CATCCC CATCCC CATCCC CATCCC
1 CATCCC CATCCC CATCCC CATCCC CATCCC
184779 ACCATCTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.67, G:0.00, T:0.17
Consensus pattern (6 bp):
CATCCC
Found at i:191176 original size:32 final size:32
Alignment explanation
Indices: 191134--191195 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
191124 TAAAAACCTT
* **
191134 CATGATACTTTTACACAAATTCAGCCCATATC
1 CATGACACTTTTACACAAACCCAGCCCATATC
*
191166 CATGACACTTTTACCCAAACCCAGCCCATA
1 CATGACACTTTTACACAAACCCAGCCCATA
191196 AACACGGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.06, T:0.26
Consensus pattern (32 bp):
CATGACACTTTTACACAAACCCAGCCCATATC
Found at i:196964 original size:44 final size:44
Alignment explanation
Indices: 196896--196987 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
196886 CAAATCCTCT
* * * *
196896 TTTATTGCTAAAAATGGTCTAATTCTGCTATTAGTCCTTGTGGA
1 TTTAATGCTAAAAATGCTCAAATTCTGCTATTAATCCTTGTGGA
196940 TTTAATGCTAAAAATGCTCAAATTCTGCTATTAATCCTTGTGGA
1 TTTAATGCTAAAAATGCTCAAATTCTGCTATTAATCCTTGTGGA
196984 TTTA
1 TTTA
196988 GTTTTCTGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (44 bp):
TTTAATGCTAAAAATGCTCAAATTCTGCTATTAATCCTTGTGGA
Found at i:197169 original size:44 final size:45
Alignment explanation
Indices: 197098--197190 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 45
197088 GCAAATCCTC
* * *
197098 TTTATATGCTTAAAATGGTCAAGTTCTGCTATTAGTCCCTGTGGA
1 TTTATATGCTAAAAATGGTCAAATTCTGCTATTAATCCCTGTGGA
* * *
197143 TTTA-ATGCTAAAAATGGTCAAATTCTGTTATTAATCCTTGTGGG
1 TTTATATGCTAAAAATGGTCAAATTCTGCTATTAATCCCTGTGGA
197187 TTTA
1 TTTA
197191 GTTTTCTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 38 0.90
45 4 0.10
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (45 bp):
TTTATATGCTAAAAATGGTCAAATTCTGCTATTAATCCCTGTGGA
Found at i:197210 original size:203 final size:194
Alignment explanation
Indices: 196846--197342 Score: 658
Period size: 203 Copynumber: 2.5 Consensus size: 194
196836 CTAATGAATT
* * * * *
196846 ATGCAAAAAGAGTGTTTACCCTCGTCTTGATCCTGTAAGGCAAATCCTCTTT-TATTGCTAAAAA
1 ATGCAAAAGGATTGTTTACCCTTGTCTTGATCCAGTAAGGCAAATCCTCTTTATA-TGCTTAAAA
196910 TGGTCTAATTCTGCTATTAGTCCTTGTGGATTTAATGCTAAAAATGCTCAAATTCTGCTATTAAT
65 TGGTC-AATTCTGCTATTAGTCCTTGTGGATTTAATGCTAAAAATGCTCAAATTCTGCTATTAAT
* * * *
196975 CCTTGTGGATTTAGTTTTCTGTATTCTAATTTGCTCAGTTTTAGTTCTTATGCTTTTTGAAAGCT
129 CCTTGTGGATTTAGTTTTCTATACTCTAATTTG----G--TCAG--CTTATACTTTTTG-AAGCT
*
197040 CCAATGATCC
185 CCAATGAACC
*
197050 ATGCAAAAGGGTTG-TTACCCTTGTCTTGATCCAGTAAGGCAAATCCTCTTTATATGCTTAAAAT
1 ATGCAAAAGGATTGTTTACCCTTGTCTTGATCCAGTAAGGCAAATCCTCTTTATATGCTTAAAAT
* * *
197114 GGTCAAGTTCTGCTATTAGTCCCTGTGGATTTAATGCTAAAAATGGTCAAATTCTGTTATTAATC
66 GGTCAA-TTCTGCTATTAGTCCTTGTGGATTTAATGCTAAAAATGCTCAAATTCTGCTATTAATC
* *
197179 CTTGTGGGTTTAGTTTTCTATACTCTAATTTGGTCAGCTTATACTTTTTGAAGCTTCAATGAACC
130 CTTGTGGATTTAGTTTTCTATACTCTAATTTGGTCAGCTTATACTTTTTGAAGCTCCAATGAACC
* **
197244 ATGCAAAAGGATTGTTTACCCTTCATCTTGATCCAGTAAGGCAAATCCTGATTATATGC-TAAAA
1 ATGCAAAAGGATTGTTTACCCTT-GTCTTGATCCAGTAAGGCAAATCCTCTTTATATGCTTAAAA
*
197308 GTGGTCAAATTTTGCTATTAGTCCTTGTGGATTTA
65 -TGGTC-AATTCTGCTATTAGTCCTTGTGGATTTA
197343 GTTTTTTATA
Statistics
Matches: 265, Mismatches: 22, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
194 26 0.10
195 25 0.09
196 61 0.23
197 5 0.02
199 1 0.00
202 2 0.01
203 132 0.50
204 13 0.05
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (194 bp):
ATGCAAAAGGATTGTTTACCCTTGTCTTGATCCAGTAAGGCAAATCCTCTTTATATGCTTAAAAT
GGTCAATTCTGCTATTAGTCCTTGTGGATTTAATGCTAAAAATGCTCAAATTCTGCTATTAATCC
TTGTGGATTTAGTTTTCTATACTCTAATTTGGTCAGCTTATACTTTTTGAAGCTCCAATGAACC
Found at i:206736 original size:17 final size:17
Alignment explanation
Indices: 206714--206771 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
206704 CCAATAGAAT
206714 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
**
206731 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
*
206748 TTAAATTTA-CTTAAAA
1 TTAAATTTATTTTAAAA
206764 TTTAAATT
1 -TTAAATT
206772 AACGTCCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
16 4 0.11
17 31 0.89
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:207474 original size:3 final size:3
Alignment explanation
Indices: 207461--207538 Score: 50
Period size: 3 Copynumber: 25.7 Consensus size: 3
207451 TAAATAGCCT
* * * ** *
207461 TAA TGA TAA TAA TAA TAT TAA TAA TAA GT-A TAA TAC TAA TGG TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
* * *
207506 TAA TTAA TAA TAA TGA TAT TAA TAA TAT TAA TA
1 TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
207539 TTAAATATTA
Statistics
Matches: 55, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
2 1 0.02
3 50 0.91
4 4 0.07
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:207482 original size:9 final size:9
Alignment explanation
Indices: 207460--207538 Score: 61
Period size: 9 Copynumber: 8.7 Consensus size: 9
207450 ATAAATAGCC
*
207460 TTAATGATA
1 TTAATAATA
*
207469 ATAATAATA
1 TTAATAATA
207478 TTAATAATAA
1 TTAATAAT-A
*
207488 GT-ATAATA
1 TTAATAATA
* **
207496 CTAATGGTA
1 TTAATAATA
207505 TTAATTAATA
1 TTAA-TAATA
* *
207515 ATAATGATA
1 TTAATAATA
207524 TTAATAATA
1 TTAATAATA
207533 TTAATA
1 TTAATA
207539 TTAAATATTA
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
8 2 0.04
9 43 0.81
10 8 0.15
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (9 bp):
TTAATAATA
Found at i:208585 original size:29 final size:29
Alignment explanation
Indices: 208533--208643 Score: 102
Period size: 29 Copynumber: 3.8 Consensus size: 29
208523 AAAGGTCCCC
* *
208533 AAACTTCTCCAAAATTATATTTTTGACCTT
1 AAACTTC-CAAAAATTACATTTTTGACCTT
* *
208563 AAAACTTCCAAAAATTACA-TTTTCACCCCT
1 -AAACTTCCAAAAATTACATTTTTGA-CCTT
* *
208593 AAACTTCCAAAAATTCCATTTTTGA-CTCC
1 AAACTTCCAAAAATTACATTTTTGACCT-T
208622 AAACTTCC-AAAATTATCATTTT
1 AAACTTCCAAAAATTA-CATTTT
208644 AGCCCCGAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
28 7 0.10
29 36 0.54
30 17 0.25
31 7 0.10
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTGACCTT
Found at i:208629 original size:58 final size:58
Alignment explanation
Indices: 208529--208672 Score: 161
Period size: 57 Copynumber: 2.5 Consensus size: 58
208519 TCCTAAAGGT
* ** *
208529 CCCCAAACTTCTCCAAAATTATATTTTTGACCTTAAAACTTCCAAAAATTA-CATTTTCA-
1 CCCCAAACTTC-CAAAAATTCCATTTTTGACCTCAAAACTTCC-AAAATTATCATTTT-AG
*
208588 CCCCTAAACTTCCAAAAATTCCATTTTTGA-CTCCAAACTTCCAAAATTATCATTTTAG
1 CCCC-AAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAATTATCATTTTAG
*
208646 CCCCGAA-TGTCCAAAAATTCCATTTTT
1 CCCCAAACT-TCCAAAAATTCCATTTTT
208673 TATCCCGATT
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
56 1 0.01
57 28 0.37
58 20 0.27
59 19 0.25
60 7 0.09
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (58 bp):
CCCCAAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAATTATCATTTTAG
Found at i:208669 original size:28 final size:29
Alignment explanation
Indices: 208564--208671 Score: 107
Period size: 29 Copynumber: 3.8 Consensus size: 29
208554 TTTGACCTTA
* *
208564 AAACTTCCAAAAATTACATTTT-CACCCC
1 AAACTTCCAAAAATTCCATTTTAGACCCC
* *
208592 TAAACTTCCAAAAATTCCATTTTTGACTCC
1 -AAACTTCCAAAAATTCCATTTTAGACCCC
*
208622 AAACTTCC-AAAATTATCATTTTAG-CCCC
1 AAACTTCCAAAAATT-CCATTTTAGACCCC
*
208650 GAA-TGTCCAAAAATTCCATTTT
1 AAACT-TCCAAAAATTCCATTTT
208672 TTATCCCGAT
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
27 1 0.01
28 20 0.30
29 42 0.63
30 4 0.06
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTAGACCCC
Found at i:208672 original size:29 final size:28
Alignment explanation
Indices: 208569--208732 Score: 86
Period size: 29 Copynumber: 5.6 Consensus size: 28
208559 CCTTAAAACT
* * *
208569 TCCAAAAATTACATTTTCACCCCTAAACT-
1 TCCAAAAATTCCATTTTTACCCC-GAA-TG
* *
208598 TCCAAAAATTCCATTTTTGACTCCAAACT-
1 TCCAAAAATTCCATTTTT-ACCCCGAA-TG
*
208627 TCC-AAAATTATCA-TTTTAGCCCCGAATG
1 TCCAAAAATT-CCATTTTTA-CCCCGAATG
* * *
208655 TCCAAAAATTCCATTTTTTATCCCGATTT
1 TCCAAAAATTCCA-TTTTTACCCCGAATG
* *
208684 TCCTAAAAAATACCA-TTTTACCCTTGAATG
1 TCC--AAAAATTCCATTTTTACCC-CGAATG
*
208714 TCCAAAAAATTCCGTTTTT
1 TCC-AAAAATTCCATTTTT
208733 TATTCCAATT
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
27 2 0.02
28 20 0.19
29 57 0.53
30 19 0.18
31 9 0.08
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.36
Consensus pattern (28 bp):
TCCAAAAATTCCATTTTTACCCCGAATG
Found at i:208719 original size:59 final size:59
Alignment explanation
Indices: 208598--208847 Score: 192
Period size: 60 Copynumber: 4.3 Consensus size: 59
208588 CCCCTAAACT
* ** * * *
208598 TCCAAAAATTCCATTTTTGA-CTCCAAACTTCC--AAAATTATCATTTTAGCCCCGAATG
1 TCCAAAAATTCCATTTTTTATC-CCAATTTTCCTAAAAAATACCATTTTACCCCCGAATG
* **
208655 TCCAAAAATTCCATTTTTTATCCCGATTTTCCTAAAAAATACCATTTTACCCTTGAATG
1 TCCAAAAATTCCATTTTTTATCCCAATTTTCCTAAAAAATACCATTTTACCCCCGAATG
* * ** ** * *
208714 TCCAAAAAATTCCGTTTTTTATTCCAATTTTTTTAAAAGTTACCGTTTTACCCCCGAGTG
1 TCC-AAAAATTCCATTTTTTATCCCAATTTTCCTAAAAAATACCATTTTACCCCCGAATG
* * * * * *
208774 TCTAAAAATTCCA--TTTTAACCTCAAACTTTCAT-AAAATTACCATTTTACCCCC-AAGG
1 TCCAAAAATTCCATTTTTTATCC-C-AATTTTCCTAAAAAATACCATTTTACCCCCGAATG
208831 TCC-AAAATTACCATTTT
1 TCCAAAAATT-CCATTTT
208848 GCCCCCCCAG
Statistics
Matches: 152, Mismatches: 32, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
56 6 0.04
57 39 0.26
58 20 0.13
59 40 0.26
60 47 0.31
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.37
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTTATCCCAATTTTCCTAAAAAATACCATTTTACCCCCGAATG
Found at i:209190 original size:96 final size:96
Alignment explanation
Indices: 209077--209257 Score: 242
Period size: 96 Copynumber: 1.9 Consensus size: 96
209067 TTTTCTTTAA
*
209077 AATCGAGACAATATTTTTTTGT-TTCGAGTT-TCAAAAATTTGTC-CCTTAACTTACTAGGTGCA
1 AATCGAGACAATATTTTTTTATCTTCGA-TTCT-AAAAATTTG-CGCCTTAACTTACTAGGTGCA
**
209139 ATTTTTCTTCAAATCAAAATAATTGAATACCCTT
63 ACATTTCTTCAAATCAAAATAATTGAATACCCTT
* * * *
209173 AATCGAGGCAATGTTTTTTTATCTTCGATTCTGAAAATTTGCGCCTTAATTTACTAGGTGCAACA
1 AATCGAGACAATATTTTTTTATCTTCGATTCTAAAAATTTGCGCCTTAACTTACTAGGTGCAACA
*
209238 TTTCTTCAAATCGAAATAAT
66 TTTCTTCAAATCAAAATAAT
209258 CGAACATCTT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 1 0.01
96 67 0.91
97 6 0.08
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (96 bp):
AATCGAGACAATATTTTTTTATCTTCGATTCTAAAAATTTGCGCCTTAACTTACTAGGTGCAACA
TTTCTTCAAATCAAAATAATTGAATACCCTT
Found at i:211030 original size:102 final size:102
Alignment explanation
Indices: 210712--211068 Score: 377
Period size: 102 Copynumber: 3.5 Consensus size: 102
210702 GGCATACGAG
* * *
210712 GAAATGAAAATCAAATGCTACGATAAGGTTAAC-AGAGATTTCGAAATTCGAAATGGA-AAAAAA
1 GAAATGAAAATCAAATGCTACGATAAGCTTAACTA-AGAGTTCGAAA-T-GAAAT-AATAAAAAA
* * * ** *
210775 TAACAGCAGAGAAAT-AAAAATTTGAAGATGTGCCATGTAAA
62 AAAAAG-AGAGAAATAAAAAAATTGAAGATCCGCCATATAAA
* * * *
210816 GAAATG-AAATCAACTGCTACGATAAGCTTTAACTGAGAGTTCAAAATGAAA-AATGAAAAAAAA
1 GAAATGAAAATCAAATGCTACGATAAGC-TTAACTAAGAGTTCGAAATGAAATAATAAAAAAAAA
* *
210879 AACAGAG-AA-AAAAAAATGTGAAGATCCGCCATATTAA
65 AAGAGAGAAATAAAAAAAT-TGAAGATCCGCCATATAAA
* * * ** * *
210916 GAAATGAAAATCAAATGCTACGATAAGCTTAAGTAAGTGTTCGAAGTGAAATTTTCAAAAAGAAA
1 GAAATGAAAATCAAATGCTACGATAAGCTTAACTAAGAGTTCGAAATGAAATAATAAAAAAAAAA
*
210981 AGAGAGAAATAAAAAAATTGAAGATCCGGCATATAAA
66 AGAGAGAAATAAAAAAATTGAAGATCCGCCATATAAA
* *
211018 GAAATGAAAATCAAAAGCGACGATAAGCTTAACTAAGAGTTCGAAATGAAA
1 GAAATGAAAATCAAATGCTACGATAAGCTTAACTAAGAGTTCGAAATGAAA
211069 ATTAGAAATA
Statistics
Matches: 211, Mismatches: 33, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
99 8 0.04
100 44 0.21
101 42 0.20
102 69 0.33
103 28 0.13
104 20 0.09
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.20
Consensus pattern (102 bp):
GAAATGAAAATCAAATGCTACGATAAGCTTAACTAAGAGTTCGAAATGAAATAATAAAAAAAAAA
AGAGAGAAATAAAAAAATTGAAGATCCGCCATATAAA
Found at i:211067 original size:202 final size:205
Alignment explanation
Indices: 210670--211083 Score: 473
Period size: 204 Copynumber: 2.0 Consensus size: 205
210660 TTTTAGCTTT
** * * *
210670 AAAAAAACAAAGAAATGAAAATTTGAAGAGCCGGCATACGAGGAAATGAAAATCAAATGCTACGA
1 AAAAAAACAAAGAAAAAAAAATGTGAAGAGCCGCCATACGAAGAAATGAAAATCAAATGCTACGA
* * * * *
210735 TAAGGTTAACAGAGATTTCGAAATTCGAAATGGAAAAAAATAACAGCAGAGAAATAAAAATTTGA
66 TAAGCTTAACAGAGATTTCGAAAGTCGAAATGGAAAAAAAGAAAAGCAGAGAAATAAAAAATTGA
** * ** * *
210800 AGATGTGCCATGTAAAGAAATGAAATCAACTGCTACGATAAGCTTTAACTGAGAGTTCAAAATGA
131 AGATCCGCCATATAAAGAAATGAAATCAAAAGCGACGATAAGCTTTAACTAAGAGTTCAAAATGA
210865 AAAAT-GAAA
196 AAAATAGAAA
* * **
210874 AAAAAAACAGAGAAAAAAAAATGTGAAGATCCGCCATATTAAGAAATGAAAATCAAATGCTACGA
1 AAAAAAACAAAGAAAAAAAAATGTGAAGAGCCGCCATACGAAGAAATGAAAATCAAATGCTACGA
* ****
210939 TAAGCTTAAGTA-AG-TGTTCG-AAGT-GAAATTTTCAAAAAGAAAAG-AGAGAAATAAAAAAAT
66 TAAGCTTAA-CAGAGAT-TTCGAAAGTCGAAATGGAAAAAAAGAAAAGCAGAGAAAT-AAAAAAT
* *
210999 TGAAGATCCGGCATATAAAGAAATGAAAATCAAAAGCGACGATAAGC-TTAACTAAGAGTTCGAA
128 TGAAGATCCGCCATATAAAGAAATG-AAATCAAAAGCGACGATAAGCTTTAACTAAGAGTTCAAA
*
211063 ATGAAAATTAGAAA
192 ATGAAAAATAGAAA
*
211077 TAAAAAA
1 AAAAAAA
211084 TTGATGATCC
Statistics
Matches: 175, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
201 8 0.05
202 64 0.37
203 32 0.18
204 70 0.40
205 1 0.01
ACGTcount: A:0.52, C:0.10, G:0.18, T:0.19
Consensus pattern (205 bp):
AAAAAAACAAAGAAAAAAAAATGTGAAGAGCCGCCATACGAAGAAATGAAAATCAAATGCTACGA
TAAGCTTAACAGAGATTTCGAAAGTCGAAATGGAAAAAAAGAAAAGCAGAGAAATAAAAAATTGA
AGATCCGCCATATAAAGAAATGAAATCAAAAGCGACGATAAGCTTTAACTAAGAGTTCAAAATGA
AAAATAGAAA
Found at i:211093 original size:86 final size:88
Alignment explanation
Indices: 210985--211154 Score: 265
Period size: 87 Copynumber: 2.0 Consensus size: 88
210975 AAGAAAAGAG
* * *
210985 AGAAATAAAAAAATTGAAGATCCGGCATAT-AAAGAAATGAAAATCAAAA-GCGACGATAAGCTT
1 AGAAATAAAAAAATTGAAGATCCGCCATATAAAAAAAATGAAAAT-AAAATGAGACGATAAGCTT
211048 AACTAAGAGTTCGAAATGAAAATT
65 AACTAAGAGTTCGAAATGAAAATT
* *
211072 AGAAAT-AAAAAATTGATGATCCGCCATATAAAAAAAATGAAAATAAAATGATACGATAAGCTTA
1 AGAAATAAAAAAATTGAAGATCCGCCATATAAAAAAAATGAAAATAAAATGAGACGATAAGCTTA
211136 ACTAAGAGTTCGAAATGAA
66 ACTAAGAGTTCGAAATGAA
211155 TTTTTTTTAA
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
86 25 0.33
87 51 0.67
ACGTcount: A:0.54, C:0.10, G:0.16, T:0.21
Consensus pattern (88 bp):
AGAAATAAAAAAATTGAAGATCCGCCATATAAAAAAAATGAAAATAAAATGAGACGATAAGCTTA
ACTAAGAGTTCGAAATGAAAATT
Found at i:211241 original size:193 final size:190
Alignment explanation
Indices: 210884--211370 Score: 590
Period size: 193 Copynumber: 2.5 Consensus size: 190
210874 AAAAAAACAG
*
210884 AGAAA-AAAAAATGTGAAGATCCGCCATATTAAGAAATGAAAATCAAATGCTACGATAAGCTTAA
1 AGAAATAAAAAAT-TGAAGATCCGCCATATAAAGAAATGAAAATCAAATGCTACGATAAGCTTAA
* * * * * *
210948 GTAAGTGTTCGAAGTGAAATTTTCAAAAAGAAAAGAGAGAAATAAAAAAATTGAAGATCCGGCAT
65 CTAAGAGTTCGAAATGAAATTTTAAAAAAGAAAAGAAAGAAATAAAAAAATTGAAGATCCGCCAT
*
211013 ATAAAGAAATGAAAATCAAAAGCGACGATAAGCTTAACTAAGAGTTCGAAATGAAAA-TT-
130 ATAAAGAAAAGAAAATCAAAAGCGACGATAAGCTTAACTAAGAGTTCGAAATGAAAATTTC
* * * *
211072 AGAAATAAAAAATTGATGATCCGCCATATAAAAAAAATGAAAATAAAATGATACGATAAGCTTAA
1 AGAAATAAAAAATTGAAGATCCGCCATAT-AAAGAAATGAAAATCAAATGCTACGATAAGCTTAA
*
211137 CTAAGAGTTCGAAATGAATTTTTTTTAAAAAAG-AAAGCAAAGAAATAAAAAAAATTGAAGATCC
65 CTAAGAGTTCGAAATGAA---ATTTTAAAAAAGAAAAG-AAAGAAAT-AAAAAAATTGAAGATCC
* * * * * * *
211201 GCCATGTAAAGAAAAGAAAGTCAAATGCTACGATAAGCTTAACTAAGTGTTCTAAGTGAAAATTT
125 GCCATATAAAGAAAAGAAAATCAAAAGCGACGATAAGCTTAACTAAGAGTTCGAAATGAAAATTT
211266 C
190 C
* *
211267 AAAAATAAACAAATAATTGAAGATCCGGCC-TATAAAGAAATGAAAATCAATTGCTACGATAAGC
1 AGAAAT--A-AAA-AATTGAAGATCC-GCCATATAAAGAAATGAAAATCAAATGCTACGATAAGC
* * *
211331 TTAACTAAGA-TATCGAAATGAAAATTAAAAAAAAAAAAGA
61 TTAACTAAGAGT-TCGAAATGAAATTTTAAAAAAGAAAAGA
211371 GGAGAAAAGA
Statistics
Matches: 253, Mismatches: 30, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
188 20 0.08
189 53 0.21
191 4 0.02
192 17 0.07
193 70 0.28
194 2 0.01
195 14 0.06
196 4 0.02
197 2 0.01
198 50 0.20
199 14 0.06
200 3 0.01
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (190 bp):
AGAAATAAAAAATTGAAGATCCGCCATATAAAGAAATGAAAATCAAATGCTACGATAAGCTTAAC
TAAGAGTTCGAAATGAAATTTTAAAAAAGAAAAGAAAGAAATAAAAAAATTGAAGATCCGCCATA
TAAAGAAAAGAAAATCAAAAGCGACGATAAGCTTAACTAAGAGTTCGAAATGAAAATTTC
Found at i:211353 original size:92 final size:90
Alignment explanation
Indices: 211179--211368 Score: 246
Period size: 92 Copynumber: 2.1 Consensus size: 90
211169 GAAAGCAAAG
* *
211179 AAATAAAAAAAATTGAAGATCCGCCATGTAAAGAAAAGAAAGTCAAATGCTACGATAAGCTTAAC
1 AAATAAAAAAAATTGAAGATCCGCCATATAAAGAAAAGAAAATCAAATGCTACGATAAGCTTAAC
* * *
211244 TAAGTGTTCTAAGTGAAAATTTCAA
66 TAAGTGATCGAAATGAAAATTTCAA
* *
211269 AAATAAACAAATAATTGAAGATCCGGCC-TATAAAGAAATGAAAATCAATTGCTACGATAAGCTT
1 AAATAAA-AAA-AATTGAAGATCC-GCCATATAAAGAAAAGAAAATCAAATGCTACGATAAGCTT
211333 AACTAAGAT-ATCGAAATGAAAA-TT-AA
63 AACTAAG-TGATCGAAATGAAAATTTCAA
211359 AAA-AAAAAAA
1 AAATAAAAAAA
211369 GAGGAGAAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
87 1 0.01
88 3 0.03
89 3 0.03
90 12 0.13
91 5 0.06
92 61 0.69
93 4 0.04
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.22
Consensus pattern (90 bp):
AAATAAAAAAAATTGAAGATCCGCCATATAAAGAAAAGAAAATCAAATGCTACGATAAGCTTAAC
TAAGTGATCGAAATGAAAATTTCAA
Found at i:212429 original size:2 final size:2
Alignment explanation
Indices: 212422--212447 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
212412 GTAGCAGAGC
212422 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
212448 TTAACAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:213899 original size:12 final size:12
Alignment explanation
Indices: 213863--213905 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
213853 CACCCGCGGT
*
213863 CGAGGCCGAGGC
1 CGAGGACGAGGC
*
213875 CGAGGCCGAGGC
1 CGAGGACGAGGC
*
213887 CGAGGACGTGGC
1 CGAGGACGAGGC
*
213899 CGTGGAC
1 CGAGGAC
213906 CATGGTTCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.16, C:0.30, G:0.49, T:0.05
Consensus pattern (12 bp):
CGAGGACGAGGC
Found at i:213899 original size:18 final size:18
Alignment explanation
Indices: 213863--213900 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
213853 CACCCGCGGT
*
213863 CGAGGCCGAGGCCGAGGC
1 CGAGGCCGAGGACGAGGC
*
213881 CGAGGCCGAGGACGTGGC
1 CGAGGCCGAGGACGAGGC
213899 CG
1 CG
213901 TGGACCATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.32, G:0.50, T:0.03
Consensus pattern (18 bp):
CGAGGCCGAGGACGAGGC
Found at i:213903 original size:6 final size:6
Alignment explanation
Indices: 213863--213891 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
213853 CACCCGCGGT
213863 CGAGGC CGAGGC CGAGGC CGAGGC CGAGG
1 CGAGGC CGAGGC CGAGGC CGAGGC CGAGG
213892 ACGTGGCCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.52, T:0.00
Consensus pattern (6 bp):
CGAGGC
Found at i:227324 original size:20 final size:20
Alignment explanation
Indices: 227260--227325 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
227250 CATCTTAAAT
*
227260 TTTAGAATTATTAATATTTA
1 TTTAAAATTATTAATATTTA
* * *
227280 TTTATAATAATT-ATGTTTA
1 TTTAAAATTATTAATATTTA
** *
227299 AATAAAATTGTTAATATTTA
1 TTTAAAATTATTAATATTTA
227319 TTTAAAA
1 TTTAAAA
227326 ATTTATTTTT
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
19 13 0.38
20 21 0.62
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (20 bp):
TTTAAAATTATTAATATTTA
Found at i:235099 original size:67 final size:67
Alignment explanation
Indices: 235018--235153 Score: 193
Period size: 67 Copynumber: 2.0 Consensus size: 67
235008 GCATATGTTC
* * * *
235018 AGAATAGGTGATTTCATGAAATCCCGGAATCGAACATTTCGTT-TTTGCTGGTATCTCCCAGCTT
1 AGAATAGGTGATTTCATGAAATCCCGGAATCAAACATTTCATTCTTT-CCGGAATCTCCCAGCTT
235082 TTT
65 TTT
* * *
235085 AGAATAGGTGATTTCGTGAAATCCCGGAATCAAACGTTTCATTCTTTCCGGAATCTCCCGGCTTT
1 AGAATAGGTGATTTCATGAAATCCCGGAATCAAACATTTCATTCTTTCCGGAATCTCCCAGCTTT
235150 TT
66 TT
235152 AG
1 AG
235154 CTAAGATGGT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
67 58 0.95
68 3 0.05
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (67 bp):
AGAATAGGTGATTTCATGAAATCCCGGAATCAAACATTTCATTCTTTCCGGAATCTCCCAGCTTT
TT
Found at i:235282 original size:76 final size:76
Alignment explanation
Indices: 235156--235296 Score: 237
Period size: 76 Copynumber: 1.9 Consensus size: 76
235146 CTTTTTAGCT
* * *
235156 AAGATGGTAGTTGCTTCCCATTGCATATGTTTAGAATAGGTGATTTCATGAAATCCTGGAGTCGA
1 AAGATGATAGTTGCTTCCCACTGCATATGTTTAGAATAGGTGATTTCATGAAATCCCGGAGTCGA
235221 ACATTTCAGCC
66 ACATTTCAGCC
* *
235232 AAGATGATAGTTGTTTCCCACTGCATATGTTTTGAATAGGTGATTTCATGAAATCCCGGAGTCGA
1 AAGATGATAGTTGCTTCCCACTGCATATGTTTAGAATAGGTGATTTCATGAAATCCCGGAGTCGA
235297 TCATCTCATT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 60 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (76 bp):
AAGATGATAGTTGCTTCCCACTGCATATGTTTAGAATAGGTGATTTCATGAAATCCCGGAGTCGA
ACATTTCAGCC
Found at i:238034 original size:26 final size:26
Alignment explanation
Indices: 238000--238056 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
237990 TTCAATTTAC
*
238000 TTTAATTTAAGTTAT-TCAAAT-TAAAT
1 TTTATTTTAA-TTATAT-AAATATAAAT
238026 TTTATTTTAATTATATAAATATAAAT
1 TTTATTTTAATTATATAAATATAAAT
*
238052 ATTAT
1 TTTAT
238057 ATTTCTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (26 bp):
TTTATTTTAATTATATAAATATAAAT
Found at i:239720 original size:15 final size:16
Alignment explanation
Indices: 239684--239722 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
239674 TCCAAACTCA
239684 AAATAACCTAAACCCG
1 AAATAACCTAAACCCG
* *
239700 AAATAATCTACACCC-
1 AAATAACCTAAACCCG
239715 AAATAACC
1 AAATAACC
239723 AAAAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.51, C:0.31, G:0.03, T:0.15
Consensus pattern (16 bp):
AAATAACCTAAACCCG
Found at i:260239 original size:63 final size:63
Alignment explanation
Indices: 260160--260290 Score: 226
Period size: 63 Copynumber: 2.1 Consensus size: 63
260150 ATGTTGTCCC
*
260160 ATATTGCTTCCTACACCTCATGCATTGGTAAGAATTATTCTTCCCTTTGTGGTTTAGTAATTG
1 ATATTGCTTCCTACACCTCATGCATTGGTAACAATTATTCTTCCCTTTGTGGTTTAGTAATTG
** *
260223 ATATTGCTTCCTACACCTCATGTGTTGGTAACAATTATTCTTCTCTTTGTGGTTTAGTAATTG
1 ATATTGCTTCCTACACCTCATGCATTGGTAACAATTATTCTTCCCTTTGTGGTTTAGTAATTG
260286 ATATT
1 ATATT
260291 ACTAGGTACC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45
Consensus pattern (63 bp):
ATATTGCTTCCTACACCTCATGCATTGGTAACAATTATTCTTCCCTTTGTGGTTTAGTAATTG
Found at i:263363 original size:31 final size:30
Alignment explanation
Indices: 263290--263369 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
263280 TTATGATATT
*
263290 ATATATTAATATACATAAATATAATATGAAAA
1 ATATATTAA-A-ACATAAAAATAATATGAAAA
*
263322 AAAT-TATAAAACAATAAAAATAATATGAAAA
1 ATATAT-TAAAAC-ATAAAAATAATATGAAAA
*
263353 TTATATTAAAACATAAA
1 ATATATTAAAACATAAA
263370 TATTTAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
30 7 0.17
31 27 0.66
32 7 0.17
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.30
Consensus pattern (30 bp):
ATATATTAAAACATAAAAATAATATGAAAA
Found at i:264826 original size:22 final size:23
Alignment explanation
Indices: 264801--264855 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
264791 AATAAATTCA
* *
264801 AATAAATTAAAATACTT-ATCTT
1 AATAAATTAAAATAATTAATCAT
264823 AATATTAATTAAAATAATTAATCAT
1 AATA--AATTAAAATAATTAATCAT
264848 -ATAAATTA
1 AATAAATTA
264856 TTTAAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 9 0.32
24 15 0.54
25 4 0.14
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (23 bp):
AATAAATTAAAATAATTAATCAT
Found at i:267281 original size:21 final size:20
Alignment explanation
Indices: 267230--267292 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 20
267220 TTTAACCATA
267230 TAAAT-ATAAATAATTT-TT
1 TAAATAATAAATAATTTATT
267248 TAAATAA-AAATAATTTAATT
1 TAAATAATAAATAATTT-ATT
267268 T-AATAACTAAATAATTTATT
1 TAAATAA-TAAATAATTTATT
*
267288 AAAAT
1 TAAAT
267293 TTTTATAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
18 14 0.37
19 6 0.16
20 6 0.16
21 12 0.32
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATAATAAATAATTTATT
Found at i:269592 original size:20 final size:19
Alignment explanation
Indices: 269567--269614 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
269557 CAGATTTTGT
*
269567 AATTTTCGAATATTTAATTG
1 AATTTT-GAATAATTAATTG
* *
269587 AATTTTTAATAATTAATTT
1 AATTTTGAATAATTAATTG
269606 AA-TTTGAAT
1 AATTTTGAAT
269615 CAATAAACCG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 6 0.25
19 12 0.50
20 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (19 bp):
AATTTTGAATAATTAATTG
Found at i:292477 original size:17 final size:17
Alignment explanation
Indices: 292455--292497 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
292445 AGACATAGTA
292455 AAATATTAAAAATAAAT
1 AAATATTAAAAATAAAT
* *
292472 AAATATTTAAAATATAT
1 AAATATTAAAAATAAAT
*
292489 ATATATTAA
1 AAATATTAA
292498 TTTTTTAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATATTAAAAATAAAT
Found at i:296940 original size:21 final size:21
Alignment explanation
Indices: 296915--296978 Score: 119
Period size: 21 Copynumber: 3.0 Consensus size: 21
296905 TGTTACTGGA
*
296915 GGGACAGTCACTGGTGGGACT
1 GGGACGGTCACTGGTGGGACT
296936 GGGACGGTCACTGGTGGGACT
1 GGGACGGTCACTGGTGGGACT
296957 GGGACGGTCACTGGTGGGACT
1 GGGACGGTCACTGGTGGGACT
296978 G
1 G
296979 TGATGGGTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.16, C:0.19, G:0.47, T:0.19
Consensus pattern (21 bp):
GGGACGGTCACTGGTGGGACT
Found at i:297015 original size:87 final size:85
Alignment explanation
Indices: 296956--297135 Score: 261
Period size: 87 Copynumber: 2.1 Consensus size: 85
296946 CTGGTGGGAC
* *
296956 TGGGACGGTCACTGGTGGGACTGTGATGGGTGGTTTTGCAATTGGAGGGAGGTCAACTGGTGGCT
1 TGGGACGGTAACTGGAGGGACTGTGATGGGTGGTTTTGCAATTGGAGGGAGGTCAACTGGTGG--
*
297021 TTACAGGAGGAACAGTCACTGG
64 TGACAGGAGGAACAGTCACTGG
* *
297043 TGGGACGGTAATTGGAGGGACTGTGATGGGTGGTTTTGCAGTTGGAGGGAGGTCAACTGGTGGCT
1 TGGGACGGTAACTGGAGGGACTGTGATGGGTGGTTTTGCAATTGGAGGGAGGTCAACTGGTGG--
*
297108 TTACAGGAGGAACAGTCACTGG
64 TGACAGGAGGAACAGTCACTGG
*
297130 AGGGAC
1 TGGGAC
297136 TGTGATGGGT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.21, C:0.13, G:0.42, T:0.24
Consensus pattern (85 bp):
TGGGACGGTAACTGGAGGGACTGTGATGGGTGGTTTTGCAATTGGAGGGAGGTCAACTGGTGGTG
ACAGGAGGAACAGTCACTGG
Found at i:297172 original size:72 final size:72
Alignment explanation
Indices: 297059--297666 Score: 822
Period size: 72 Copynumber: 8.4 Consensus size: 72
297049 GGTAATTGGA
* * *
297059 GGGACTGTGATGGGTGGTTTTGCAGTTGGAGGGAGGTCAACTGGTGGCTTTACAGGAGGAACAGT
1 GGGACTGTAATGGGTGGTTTTGCAATTGGAGGGAGGTCAACTGGTGGCTTCACAGGAGGAACAGT
*
297124 CACTGGA
66 CACTGGT
* *
297131 GGGACTGTGATGGGTGGTTTTGCAATTGGGGGGAGGTCAACTGGTGGCTTCACAGGAGGAACAGT
1 GGGACTGTAATGGGTGGTTTTGCAATTGGAGGGAGGTCAACTGGTGGCTTCACAGGAGGAACAGT
*
297196 CACTGAT
66 CACTGGT
* * * * *
297203 GGGACTGTGATGGGTGGCTTTGAAATCGGAGGGAGCTCAACTGGTGGCTTCACAGGAGGAACAGT
1 GGGACTGTAATGGGTGGTTTTGCAATTGGAGGGAGGTCAACTGGTGGCTTCACAGGAGGAACAGT
297268 CACTGGT
66 CACTGGT
* * * * * *
297275 GGAACTGTAATAGGTGGCTTTGCAATTGGAGGGAGATCAACAGGTGGCTTTACAGGAGGAACAGT
1 GGGACTGTAATGGGTGGTTTTGCAATTGGAGGGAGGTCAACTGGTGGCTTCACAGGAGGAACAGT
* *
297340 AACTGGA
66 CACTGGT
* * *
297347 GGGACTGTGATGGGTGGTTCTGCAATTGGGGGGAGGTCAACTGGTGGCTTCACAGGAGGAACAGT
1 GGGACTGTAATGGGTGGTTTTGCAATTGGAGGGAGGTCAACTGGTGGCTTCACAGGAGGAACAGT
297412 CACTGGT
66 CACTGGT
** * *
297419 GGGACTGTAATGGGTGGCATTGCAATCGGAGGGAGCTCAACTGGTGGCTTCACAGGAGGAACAGT
1 GGGACTGTAATGGGTGGTTTTGCAATTGGAGGGAGGTCAACTGGTGGCTTCACAGGAGGAACAGT
297484 CACTGGT
66 CACTGGT
* * * * * * *
297491 GGAACTGTAATAGGTGGCTTTGCTATTGGAGGGAGATCAACAGGTGGCTTTACAGGAGGAACAGT
1 GGGACTGTAATGGGTGGTTTTGCAATTGGAGGGAGGTCAACTGGTGGCTTCACAGGAGGAACAGT
297556 CACTGGT
66 CACTGGT
* * * * *
297563 GGGTCTGTAATAGGCGGTTTTGCAATCGGAGGGAGTTCAACTGGTGGCTTCACAGGAGGAACAGT
1 GGGACTGTAATGGGTGGTTTTGCAATTGGAGGGAGGTCAACTGGTGGCTTCACAGGAGGAACAGT
*
297628 CACCGGT
66 CACTGGT
* *
297635 GGGACTGTAACT-GGTGGTTTTACTATTGGAGG
1 GGGACTGTAA-TGGGTGGTTTTGCAATTGGAGG
297667 AACAGTCACT
Statistics
Matches: 473, Mismatches: 62, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
72 472 1.00
73 1 0.00
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.24
Consensus pattern (72 bp):
GGGACTGTAATGGGTGGTTTTGCAATTGGAGGGAGGTCAACTGGTGGCTTCACAGGAGGAACAGT
CACTGGT
Found at i:297347 original size:216 final size:216
Alignment explanation
Indices: 297062--297644 Score: 968
Period size: 216 Copynumber: 2.7 Consensus size: 216
297052 AATTGGAGGG
* * * * * *
297062 ACTGTGATGGGTGGTTTTGCAGTTGGAGGGAGGTCAACTGGTGGCTTTACAGGAGGAACAGTCAC
1 ACTGTAATAGGTGGCTTTGCAATTGGAGGGAGATCAACAGGTGGCTTTACAGGAGGAACAGTCAC
297127 TGGAGGGACTGTGATGGGTGGTTTTGCAATTGGGGGGAGGTCAACTGGTGGCTTCACAGGAGGAA
66 TGGAGGGACTGTGATGGGTGGTTTTGCAATTGGGGGGAGGTCAACTGGTGGCTTCACAGGAGGAA
* * *
297192 CAGTCACTGATGGGACTGTGATGGGTGGCTTTGAAATCGGAGGGAGCTCAACTGGTGGCTTCACA
131 CAGTCACTGGTGGGACTGTAATGGGTGGCATTGAAATCGGAGGGAGCTCAACTGGTGGCTTCACA
297257 GGAGGAACAGTCACTGGTGGA
196 GGAGGAACAGTCACTGGTGGA
*
297278 ACTGTAATAGGTGGCTTTGCAATTGGAGGGAGATCAACAGGTGGCTTTACAGGAGGAACAGTAAC
1 ACTGTAATAGGTGGCTTTGCAATTGGAGGGAGATCAACAGGTGGCTTTACAGGAGGAACAGTCAC
*
297343 TGGAGGGACTGTGATGGGTGGTTCTGCAATTGGGGGGAGGTCAACTGGTGGCTTCACAGGAGGAA
66 TGGAGGGACTGTGATGGGTGGTTTTGCAATTGGGGGGAGGTCAACTGGTGGCTTCACAGGAGGAA
*
297408 CAGTCACTGGTGGGACTGTAATGGGTGGCATTGCAATCGGAGGGAGCTCAACTGGTGGCTTCACA
131 CAGTCACTGGTGGGACTGTAATGGGTGGCATTGAAATCGGAGGGAGCTCAACTGGTGGCTTCACA
297473 GGAGGAACAGTCACTGGTGGA
196 GGAGGAACAGTCACTGGTGGA
*
297494 ACTGTAATAGGTGGCTTTGCTATTGGAGGGAGATCAACAGGTGGCTTTACAGGAGGAACAGTCAC
1 ACTGTAATAGGTGGCTTTGCAATTGGAGGGAGATCAACAGGTGGCTTTACAGGAGGAACAGTCAC
* * * * * * * *
297559 TGGTGGGTCTGTAATAGGCGGTTTTGCAATCGGAGGGAGTTCAACTGGTGGCTTCACAGGAGGAA
66 TGGAGGGACTGTGATGGGTGGTTTTGCAATTGGGGGGAGGTCAACTGGTGGCTTCACAGGAGGAA
*
297624 CAGTCACCGGTGGGACTGTAA
131 CAGTCACTGGTGGGACTGTAA
297645 CTGGTGGTTT
Statistics
Matches: 343, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
216 343 1.00
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.23
Consensus pattern (216 bp):
ACTGTAATAGGTGGCTTTGCAATTGGAGGGAGATCAACAGGTGGCTTTACAGGAGGAACAGTCAC
TGGAGGGACTGTGATGGGTGGTTTTGCAATTGGGGGGAGGTCAACTGGTGGCTTCACAGGAGGAA
CAGTCACTGGTGGGACTGTAATGGGTGGCATTGAAATCGGAGGGAGCTCAACTGGTGGCTTCACA
GGAGGAACAGTCACTGGTGGA
Found at i:297711 original size:45 final size:45
Alignment explanation
Indices: 297617--297711 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
297607 TGGCTTCACA
* * *
297617 GGAGGAACAGTCACCGGTGGGACTGTAACTGGTGGTTTTACTATT
1 GGAGGAACAGTCACCGGTGGGACTGTAACTGGCGGTTTTACAATC
* *
297662 GGAGGAACAGTCACTGGTGGGACTGTAA-TAGGCGGTTTTGCAATC
1 GGAGGAACAGTCACCGGTGGGACTGTAACT-GGCGGTTTTACAATC
297707 GGAGG
1 GGAGG
297712 GAGTTCAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 1 0.02
45 43 0.98
ACGTcount: A:0.23, C:0.15, G:0.37, T:0.25
Consensus pattern (45 bp):
GGAGGAACAGTCACCGGTGGGACTGTAACTGGCGGTTTTACAATC
Found at i:297792 original size:45 final size:45
Alignment explanation
Indices: 297734--297819 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
297724 TGGCTTCACA
* *
297734 GGAGGAACAGTCACCGGTGGGACTGTAACTGGTGGTTTTACTATT
1 GGAGGAACAGTCACCGGTGGGACAGTAACCGGTGGTTTTACTATT
* * *
297779 GGAGGAACGGTCACTGGTGGGACAGTGACCGGTGGTTTTAC
1 GGAGGAACAGTCACCGGTGGGACAGTAACCGGTGGTTTTAC
297820 ATGGACTGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.21, C:0.16, G:0.37, T:0.26
Consensus pattern (45 bp):
GGAGGAACAGTCACCGGTGGGACAGTAACCGGTGGTTTTACTATT
Found at i:297795 original size:72 final size:72
Alignment explanation
Indices: 297662--297798 Score: 179
Period size: 72 Copynumber: 1.9 Consensus size: 72
297652 TTTTACTATT
* * * *
297662 GGAGGAACAGTCACTGGTGGGACTGTAATAGGCGGTTTTGCAATCGGAGGGAGTTCAACTGGTGG
1 GGAGGAACAGTCACCGGTGGGACTGTAATAGGCGGTTTTACAATCGGAGGAAGGTCAACTGGTGG
297727 CTTCACA
66 CTTCACA
* * *
297734 GGAGGAACAGTCACCGGTGGGACTGTAACT-GGTGGTTTTACTATTGGAGGAACGGTC-ACTGGT
1 GGAGGAACAGTCACCGGTGGGACTGTAA-TAGGCGGTTTTACAATCGGAGGAA-GGTCAACTGGT
297797 GG
64 GG
297799 GACAGTGACC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
72 52 0.93
73 4 0.07
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.24
Consensus pattern (72 bp):
GGAGGAACAGTCACCGGTGGGACTGTAATAGGCGGTTTTACAATCGGAGGAAGGTCAACTGGTGG
CTTCACA
Found at i:297817 original size:117 final size:117
Alignment explanation
Indices: 297545--297801 Score: 496
Period size: 117 Copynumber: 2.2 Consensus size: 117
297535 TGGCTTTACA
*
297545 GGAGGAACAGTCACTGGTGGGTCTGTAATAGGCGGTTTTGCAATCGGAGGGAGTTCAACTGGTGG
1 GGAGGAACAGTCACTGGTGGGACTGTAATAGGCGGTTTTGCAATCGGAGGGAGTTCAACTGGTGG
297610 CTTCACAGGAGGAACAGTCACCGGTGGGACTGTAACTGGTGGTTTTACTATT
66 CTTCACAGGAGGAACAGTCACCGGTGGGACTGTAACTGGTGGTTTTACTATT
297662 GGAGGAACAGTCACTGGTGGGACTGTAATAGGCGGTTTTGCAATCGGAGGGAGTTCAACTGGTGG
1 GGAGGAACAGTCACTGGTGGGACTGTAATAGGCGGTTTTGCAATCGGAGGGAGTTCAACTGGTGG
297727 CTTCACAGGAGGAACAGTCACCGGTGGGACTGTAACTGGTGGTTTTACTATT
66 CTTCACAGGAGGAACAGTCACCGGTGGGACTGTAACTGGTGGTTTTACTATT
*
297779 GGAGGAACGGTCACTGGTGGGAC
1 GGAGGAACAGTCACTGGTGGGAC
297802 AGTGACCGGT
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 138 1.00
ACGTcount: A:0.23, C:0.16, G:0.36, T:0.25
Consensus pattern (117 bp):
GGAGGAACAGTCACTGGTGGGACTGTAATAGGCGGTTTTGCAATCGGAGGGAGTTCAACTGGTGG
CTTCACAGGAGGAACAGTCACCGGTGGGACTGTAACTGGTGGTTTTACTATT
Found at i:301237 original size:24 final size:25
Alignment explanation
Indices: 301198--301245 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
301188 TGTTGCATAT
*
301198 GAAAATATGCCTAAATGAAGTGTTG
1 GAAAATATGCCAAAATGAAGTGTTG
301223 GAAAA-ATGCCAAAATGAAGTGTT
1 GAAAATATGCCAAAATGAAGTGTT
301246 TTTTCAGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.25
Consensus pattern (25 bp):
GAAAATATGCCAAAATGAAGTGTTG
Found at i:316955 original size:3 final size:3
Alignment explanation
Indices: 316947--316977 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
316937 ATTAATTACA
316947 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
316978 TTTCCCTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:324787 original size:23 final size:24
Alignment explanation
Indices: 324761--324808 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
324751 GAATATACTT
324761 AAATTACT-ATTTTACCTCAAAAC
1 AAATTACTCATTTTACCTCAAAAC
324784 AAATTACTCATTTTACCTCAAAAC
1 AAATTACTCATTTTACCTCAAAAC
324808 A
1 A
324809 TGATACTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATTACTCATTTTACCTCAAAAC
Found at i:328142 original size:3 final size:3
Alignment explanation
Indices: 328134--328169 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
328124 GGCCATTACA
* *
328134 ACC ACC ACC ATC ACC ACC ACC AAC ACC ACC ACC ACC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC
328170 GCCAAGTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.36, C:0.61, G:0.00, T:0.03
Consensus pattern (3 bp):
ACC
Found at i:328884 original size:22 final size:22
Alignment explanation
Indices: 328851--328902 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
328841 TTAAAATTTA
*
328851 AAATTATTTAAA-ATAATAAAAT
1 AAATAATTTAAATATAA-AAAAT
* *
328873 ATATAATTTAAATTTAAAAAAT
1 AAATAATTTAAATATAAAAAAT
328895 AAATAATT
1 AAATAATT
328903 GATTATGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATAATTTAAATATAAAAAAT
Found at i:330106 original size:24 final size:23
Alignment explanation
Indices: 330079--330124 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
330069 GGTTTAATTA
* *
330079 ATATGTTATTTATATTTTTTTATG
1 ATATGTTAATTAT-TTATTTTATG
*
330103 ATATTTTAATTATTTATTTTAT
1 ATATGTTAATTATTTATTTTAT
330125 TATTGTTGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
ATATGTTAATTATTTATTTTATG
Found at i:341689 original size:19 final size:19
Alignment explanation
Indices: 341667--341703 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
341657 TTTGGTTGCC
*
341667 TTTTTTGCTGTTTTGATAT
1 TTTTTTACTGTTTTGATAT
341686 TTTTTTACTGTTTTGATA
1 TTTTTTACTGTTTTGATA
341704 CTGTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.05, G:0.14, T:0.68
Consensus pattern (19 bp):
TTTTTTACTGTTTTGATAT
Found at i:341725 original size:12 final size:12
Alignment explanation
Indices: 341708--341750 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
341698 TTGATACTGT
341708 TATTTTTGTTAC
1 TATTTTTGTTAC
**
341720 TATTTTTGTTGT
1 TATTTTTGTTAC
341732 TATTTTTGTTAC
1 TATTTTTGTTAC
341744 TATTTTT
1 TATTTTT
341751 ATTGTTTTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.14, C:0.05, G:0.09, T:0.72
Consensus pattern (12 bp):
TATTTTTGTTAC
Found at i:341732 original size:24 final size:24
Alignment explanation
Indices: 341683--341756 Score: 96
Period size: 24 Copynumber: 3.0 Consensus size: 24
341673 GCTGTTTTGA
* *
341683 TATTTTT-TTACTGTTTTGATACTGT
1 TATTTTTGTTACTATTTT--TATTGT
*
341708 TATTTTTGTTACTATTTTTGTTGT
1 TATTTTTGTTACTATTTTTATTGT
341732 TATTTTTGTTACTATTTTTATTGT
1 TATTTTTGTTACTATTTTTATTGT
341756 T
1 T
341757 TTACCGCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
24 28 0.64
25 7 0.16
26 9 0.20
ACGTcount: A:0.15, C:0.05, G:0.11, T:0.69
Consensus pattern (24 bp):
TATTTTTGTTACTATTTTTATTGT
Found at i:341937 original size:27 final size:26
Alignment explanation
Indices: 341907--341957 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
341897 ATATAAAGAA
341907 TTTTTAATGTATTTTAAATTTATTTAT
1 TTTTTAATGT-TTTTAAATTTATTTAT
*
341934 TTTTTAATGTTTTTAAGTTTATTT
1 TTTTTAATGTTTTTAAATTTATTT
341958 GATATATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (26 bp):
TTTTTAATGTTTTTAAATTTATTTAT
Found at i:344509 original size:227 final size:226
Alignment explanation
Indices: 344100--344561 Score: 644
Period size: 227 Copynumber: 2.0 Consensus size: 226
344090 TGTTAAGAAA
* * ** *
344100 TGTAATGACTAGATGTTATCTTCGAATCAAATGATATGTTTGTGATTTGACACTAATCTACCATA
1 TGTAATGACTAGATGTTATATTCGAATCAAATGATATGTTTATGATTCAACACGAATCTACCATA
* * *
344165 CACCACCATGTTTGAGTTTTGACTAGAAGTGAGCATAACTCGAGAAAACTCAGGGGCAGGGGGAG
66 CACCACCATGTCTGAGTTTTGACCAGAAGTGAGCATAACTCGAGAAAACTC--GGG-AGGGGCAG
** *
344230 GCCCTGATTTAATGAGTTACATAATGTCTAAACTAAGGGTTCGTAGCTTTATGGTTGGCTTAAAT
128 GCCCCAATTTAACGAGTTACATAATGTCTAAACTAAGGGTTCGTAGCTTTATGGTTGGCTTAAAT
* ** *
344295 AAGACTGAGCTTAGTTTTATCTGTATGTTTGACC
193 AAGACCGAGCTTAGTTACATCTCTATGTTTGACC
* * * *
344329 TGTAATGACTAGATG-TATATTCGAGTCTAGTGATATGTTTTATGATTCAACACGGATCTACCAT
1 TGTAATGACTAGATGTTATATTCGAATCAAATGATATG-TTTATGATTCAACACGAATCTACCAT
344393 ACACCACTGCCATGTCTGAGTTTTGACCAGAAGTGAGCATAACTCGAGAAAACTC-GG-GGGGCA
65 ACACCA---CCATGTCTGAGTTTTGACCAGAAGTGAGCATAACTCGAGAAAACTCGGGAGGGGCA
* *
344456 GGCCCCAATTTAACGAGTTACATAATGTTTAAACTAAGGGTTTGTAGCTTTATGGTTGGCTTAAA
127 GGCCCCAATTTAACGAGTTACATAATGTCTAAACTAAGGGTTCGTAGCTTTATGGTTGGCTTAAA
344521 TAAGACCGAGCTTAGTTACATCTCTATGTTTGACC
192 TAAGACCGAGCTTAGTTACATCTCTATGTTTGACC
344556 TG-AATG
1 TGTAATG
344562 TAACATACTC
Statistics
Matches: 208, Mismatches: 21, Indels: 11
0.87 0.09 0.05
Matches are distributed among these distances:
226 4 0.02
227 98 0.47
228 18 0.09
229 44 0.21
232 44 0.21
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (226 bp):
TGTAATGACTAGATGTTATATTCGAATCAAATGATATGTTTATGATTCAACACGAATCTACCATA
CACCACCATGTCTGAGTTTTGACCAGAAGTGAGCATAACTCGAGAAAACTCGGGAGGGGCAGGCC
CCAATTTAACGAGTTACATAATGTCTAAACTAAGGGTTCGTAGCTTTATGGTTGGCTTAAATAAG
ACCGAGCTTAGTTACATCTCTATGTTTGACC
Found at i:345927 original size:22 final size:22
Alignment explanation
Indices: 345902--345944 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
345892 TAACAAATAA
*
345902 TTTTAAAATTATTAAAATTATTT
1 TTTTAAAA-TAATAAAATTATTT
*
345925 TTTTGAAATAATAAAATTAT
1 TTTTAAAATAATAAAATTAT
345945 GAAATCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTAAAATAATAAAATTATTT
Found at i:346974 original size:27 final size:27
Alignment explanation
Indices: 346944--347028 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 27
346934 AGTAATTTTA
346944 TTATTTTAAAAAAATAAATTTAATAAT
1 TTATTTTAAAAAAATAAATTTAATAAT
* *
346971 TTATATTT--CAAAAT-AATTTAAAAAAATT
1 TTAT-TTTAAAAAAATAAATTT--AATAA-T
*
346999 TATATTTTAAAAAAATAATTTTAATAAT
1 T-TATTTTAAAAAAATAAATTTAATAAT
347027 TT
1 TT
347029 TAAAGTCATT
Statistics
Matches: 45, Mismatches: 5, Indels: 16
0.68 0.08 0.24
Matches are distributed among these distances:
25 5 0.11
26 5 0.11
27 9 0.20
28 10 0.22
29 7 0.16
30 5 0.11
31 4 0.09
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
TTATTTTAAAAAAATAAATTTAATAAT
Found at i:354829 original size:2 final size:2
Alignment explanation
Indices: 354822--354864 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
354812 TTGACCATTC
354822 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
354865 CATAAAAGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.