Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_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: 8859806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 41
Found at i:931653 original size:62 final size:62
Alignment explanation
Indices: 931582--931705 Score: 146
Period size: 62 Copynumber: 2.0 Consensus size: 62
931572 ATTTTCCATT
*
931582 TCGCATTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-ATTTCGCATTGCGATAGTTGAAAA
1 TCGCATTGCGATAGTCT-AAAATCGTCGTTGCGATTTTCCAAATT--CATTGCGATAGTTGAAAA
* * * * *
931644 TCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCATTGCGATAGTTTAAAA
1 TCGCATTGCGATAGTCTAAAATCGTCGTTGCGATTTTCCAAATTCATTGCGATAGTTGAAAA
931706 AAAAGATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
62 35 0.66
63 15 0.28
64 3 0.06
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (62 bp):
TCGCATTGCGATAGTCTAAAATCGTCGTTGCGATTTTCCAAATTCATTGCGATAGTTGAAAA
Found at i:931788 original size:6 final size:6
Alignment explanation
Indices: 931777--931836 Score: 120
Period size: 6 Copynumber: 10.0 Consensus size: 6
931767 GACACGTATT
931777 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
931825 ACCACG ACCACG
1 ACCACG ACCACG
931837 GACGGCGGCG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:933503 original size:17 final size:18
Alignment explanation
Indices: 933478--933512 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
933468 GTTTAGTTTG
933478 TCTTAA-TTTTTTTCCTT
1 TCTTAATTTTTTTTCCTT
*
933495 TCTTCATTTTTTTTCCTT
1 TCTTAATTTTTTTTCCTT
933513 ATATATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (18 bp):
TCTTAATTTTTTTTCCTT
Found at i:933865 original size:2 final size:2
Alignment explanation
Indices: 933858--933893 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
933848 AATATCTTTA
933858 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
933894 TGCAACTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:934702 original size:21 final size:20
Alignment explanation
Indices: 934616--934773 Score: 95
Period size: 21 Copynumber: 7.8 Consensus size: 20
934606 AAATGACCAA
**
934616 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
934635 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* **
934655 CAGAATCGCAAATC-AGTTTT
1 CAAAATCGCAACGCGA-TTTT
934675 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
934696 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
934717 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
934737 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
934758 AAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
934774 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 40 0.38
21 48 0.46
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:934764 original size:20 final size:20
Alignment explanation
Indices: 934739--934792 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
934729 GCGATTTTCC
* *
934739 AAAATCGCAACGCGAATATA
1 AAAATCGCAACGCGAACACA
934759 AAAATCGCAACGCGAACACA
1 AAAATCGCAACGCGAACACA
*
934779 TAAATCGCAACGCG
1 AAAATCGCAACGCG
934793 TATCCGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAACACA
Found at i:934802 original size:20 final size:20
Alignment explanation
Indices: 934760--934950 Score: 217
Period size: 20 Copynumber: 9.6 Consensus size: 20
934750 GCGAATATAA
* *
934760 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
934780 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
934800 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
934820 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
* *
934840 AAATTGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
934860 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
934880 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
934900 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
934920 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
934940 AAATCGCAACG
1 AAATCGCAACG
934951 ATAATCTGTA
Statistics
Matches: 146, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
19 1 0.01
20 143 0.98
21 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:935691 original size:24 final size:24
Alignment explanation
Indices: 935652--935698 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
935642 AAATTTGGTC
935652 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
935676 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
935699 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:935890 original size:12 final size:12
Alignment explanation
Indices: 935873--935897 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
935863 ATATAATCCT
935873 GAAGAAGAAAAA
1 GAAGAAGAAAAA
935885 GAAGAAGAAAAA
1 GAAGAAGAAAAA
935897 G
1 G
935898 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:938230 original size:33 final size:34
Alignment explanation
Indices: 938179--938410 Score: 219
Period size: 33 Copynumber: 6.7 Consensus size: 34
938169 CGGAAATTAC
*
938179 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
* *
938212 AATCCCAAC-ATGAAAATCGCAACGCGGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGC-GAAATGAA
*
938246 AATCGCAACGA-GATAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
* *
938279 AATCGCAATGCGGAAATGAAAATCGCAATGAGATAATCG-C
1 AATCGCAA--C-G--ATGAAAATCGCAATGCGA-AAT-GAA
*
938319 AAT-GCGAA--ATCAAAATCGCAATGCGAAATGAA
1 AATCGC-AACGATGAAAATCGCAATGCGAAATGAA
*
938351 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
938384 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--CG--ATGAAAATCGCAA
938411 CGAGAGAATC
Statistics
Matches: 163, Mismatches: 15, Indels: 37
0.76 0.07 0.17
Matches are distributed among these distances:
31 1 0.01
32 9 0.06
33 82 0.50
34 29 0.18
35 4 0.02
36 1 0.01
37 1 0.01
38 11 0.07
39 16 0.10
40 8 0.05
41 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACGATGAAAATCGCAATGCGAAATGAA
Found at i:938268 original size:67 final size:65
Alignment explanation
Indices: 938160--938391 Score: 216
Period size: 67 Copynumber: 3.4 Consensus size: 65
938150 GCATTTGACT
* * * * *
938160 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGA
1 ATCGCAACGC-GAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATGAAAATCGCAACA-GA
938225 AA
64 AA
938227 ATCGCAACGCGGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATGAAAATCGCAATGC-G
1 ATCGCAACGC-GAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATGAAAATCGCAA--CAG
*
938291 GAA
63 AAA
* ** * *
938294 AT-GAAAATCGCAATGAGATAATCGCAATGCGAAATCAAAATCGCAATGCGAAATGAAAATCGCA
1 ATCGCAACGCGAAATGA-A-AATCGCAA--CGAGAT---AATCGCAATGCGAAATGAAAATCGCA
*
938358 ACGAGAGA
59 AC-AGAAA
*
938366 ATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
938392 TGCGAAATGA
Statistics
Matches: 136, Mismatches: 17, Indels: 20
0.79 0.10 0.12
Matches are distributed among these distances:
65 6 0.04
66 5 0.04
67 68 0.50
69 6 0.04
70 1 0.01
71 8 0.06
72 32 0.24
73 10 0.07
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (65 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATGAAAATCGCAACAGAAA
Found at i:938284 original size:19 final size:19
Alignment explanation
Indices: 938193--938410 Score: 224
Period size: 19 Copynumber: 12.4 Consensus size: 19
938183 GCAACGAGAG
938193 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
938212 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
938226 AATCGCAACGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
938246 AATCGCAA--CG--A-GAT
1 AATCGCAATGCGAAATGAA
938260 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
938279 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
938299 AATCGCAAT--G--A-GAT
1 AATCGCAATGCGAAATGAA
*
938313 AATCGCAATGCGAAATCAA
1 AATCGCAATGCGAAATGAA
938332 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
938351 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
938365 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
938384 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
938403 AATCGCAA
1 AATCGCAA
938411 CGAGAGAATC
Statistics
Matches: 167, Mismatches: 10, Indels: 44
0.76 0.05 0.20
Matches are distributed among these distances:
14 43 0.26
15 3 0.02
16 6 0.04
17 5 0.03
18 4 0.02
19 76 0.46
20 30 0.18
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:938369 original size:52 final size:53
Alignment explanation
Indices: 938221--938432 Score: 365
Period size: 52 Copynumber: 4.0 Consensus size: 53
938211 AAATCCCAAC
* *
938221 ATGAAAATCGCAACGCGGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
938274 ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
938327 ATCAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
938379 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
938431 AT
1 AT
938433 TATAAACGCA
Statistics
Matches: 153, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
52 87 0.57
53 66 0.43
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:938421 original size:33 final size:32
Alignment explanation
Indices: 938278--938432 Score: 125
Period size: 33 Copynumber: 4.5 Consensus size: 32
938268 TGCGAAATGA
*
938278 AAATCGCAATGCGGAAATGAAAATCGCAATGAG
1 AAATCGCAATGC-GAAATGAAAATCGCAACGAG
* * *
938311 ATAATCGCAATGCGAAATCAAAATCGCAATGCG
1 A-AATCGCAATGCGAAATGAAAATCGCAACGAG
* * *
938344 AAAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATG
1 AAATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-G
938382 AAAATCGCAATGCGAAATGAAAATCGCAACGAG
1 -AAATCGCAATGCGAAATGAAAATCGCAACGAG
938415 AGAATCGCAATGCGAAAT
1 A-AATCGCAATGCGAAAT
938433 TATAAACGCA
Statistics
Matches: 98, Mismatches: 11, Indels: 26
0.73 0.08 0.19
Matches are distributed among these distances:
31 6 0.06
32 8 0.08
33 45 0.46
34 12 0.12
35 1 0.01
36 2 0.02
38 9 0.09
39 8 0.08
40 7 0.07
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (32 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAG
Found at i:938551 original size:52 final size:53
Alignment explanation
Indices: 938439--938554 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
938429 AAATTATAAA
938439 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
938492 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
938544 CGCATTGCGAT
1 CGCATTGCGAT
938555 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
Found at i:938562 original size:19 final size:19
Alignment explanation
Indices: 938457--938554 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
938447 GATTCTCTCG
938457 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
938477 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
938496 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
938510 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
938529 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
938548 TTGCGAT
1 TTGCGAT
938555 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:938680 original size:14 final size:13
Alignment explanation
Indices: 938652--938709 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 13
938642 TTATGTTCGC
*
938652 ATCAATTACACAA
1 ATCAATTATACAA
938665 ATCAACTTATACAA
1 ATCAA-TTATACAA
* *
938679 ATCATCTTTTACAA
1 ATCA-ATTATACAA
*
938693 ATCAATTAAAC-A
1 ATCAATTATACAA
938705 ATCAA
1 ATCAA
938710 AAAATAAGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
12 6 0.16
13 9 0.24
14 22 0.59
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (13 bp):
ATCAATTATACAA
Found at i:940665 original size:19 final size:19
Alignment explanation
Indices: 940620--940734 Score: 106
Period size: 19 Copynumber: 6.6 Consensus size: 19
940610 TAGTTTACTT
* **
940620 TCGCAACACGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
940639 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
940658 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
940672 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
940691 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
940705 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
940724 TCGCAATGCGA
1 TCGCAACGCGA
940735 TTTTGGTTTC
Statistics
Matches: 80, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
14 16 0.20
16 11 0.14
17 11 0.14
19 42 0.52
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:940675 original size:14 final size:14
Alignment explanation
Indices: 940656--940712 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
940646 GCGAAATGAA
*
940656 AATCGCAACGACAG
1 AATCGCAACGAAAG
940670 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
940687 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
940703 AATCGCAACG
1 AATCGCAACG
940713 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:940683 original size:33 final size:33
Alignment explanation
Indices: 940637--940729 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
940627 ACGAAACCAA
*
940637 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
940670 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
940703 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
940730 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:940752 original size:19 final size:18
Alignment explanation
Indices: 940730--940839 Score: 74
Period size: 19 Copynumber: 6.3 Consensus size: 18
940720 AAAATCGCAA
940730 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
940749 TGCGATCTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
940763 TGCGATTTTGGTTTTGCGT
1 TGCGATTTT-GTTTCGCGT
*
940782 TGCGATTATG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
940796 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
940815 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
940835 TGCGA
1 TGCGA
940840 AAGTAAACTA
Statistics
Matches: 72, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
14 22 0.31
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 31 0.43
20 12 0.17
ACGTcount: A:0.10, C:0.15, G:0.28, T:0.46
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:940772 original size:33 final size:33
Alignment explanation
Indices: 940730--940821 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
940720 AAAATCGCAA
940730 TGCGATTTTGGTTTCGCGTTGCGATCT-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGAT-TATGTCGT
*
940763 TGCGATTTTGGTTTTGCGTTGCGATTATGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTATGTCGT
**
940796 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
940822 TTAAGTTTCG
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 1 0.02
33 53 0.98
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTATGTCGT
Found at i:941140 original size:93 final size:93
Alignment explanation
Indices: 940887--941359 Score: 885
Period size: 93 Copynumber: 5.1 Consensus size: 93
940877 ATGGATTGCA
940887 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
940951 TAGCAGAATTAGCAGCAACCGAACAAATTTAT
66 TAGCAGAATTGGCAGCAACCGAAC-AA---AT
940983 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
941048 TAGCATAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
941076 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
941141 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
941169 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
941234 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
941262 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
941327 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
941355 TTACT
1 TTACT
941360 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 3, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
93 285 0.76
96 6 0.02
97 82 0.22
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:943084 original size:14 final size:14
Alignment explanation
Indices: 943065--943121 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
943055 TTGAAATGAA
943065 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
943079 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
943098 AATCGCAACGAGAG
1 AATCGCAACGAGAG
943112 AATCGCAACG
1 AATCGCAACG
943122 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:943097 original size:33 final size:33
Alignment explanation
Indices: 943057--943138 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
943047 TCTTTTGGTT
943057 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
943090 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
943123 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
943139 TGCGATTTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:943103 original size:19 final size:19
Alignment explanation
Indices: 943079--943143 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
943069 GCAACGAGAG
943079 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
943098 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
943112 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
943131 AATCGCAATGCGA
1 AATCGCAACGCGA
943144 TTTTCATTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:943189 original size:21 final size:21
Alignment explanation
Indices: 943163--943281 Score: 161
Period size: 21 Copynumber: 5.8 Consensus size: 21
943153 CGCGTTGCGA
943163 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
943184 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
943204 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
943225 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
943245 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
943266 TTATCTCGTTGCGATT
1 TTCTCTCGTTGCGATT
943282 CTTCTGCAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
20 34 0.41
21 49 0.59
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:943219 original size:41 final size:41
Alignment explanation
Indices: 943162--943279 Score: 227
Period size: 41 Copynumber: 2.9 Consensus size: 41
943152 TCGCGTTGCG
943162 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
943203 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
*
943244 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGA
1 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGA
943280 TTCTTCTGCA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 76 1.00
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
Found at i:943401 original size:33 final size:33
Alignment explanation
Indices: 943359--943429 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
943349 AATACTAACT
*
943359 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
943392 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
943425 TGAAA
1 TGAAA
943430 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:943663 original size:22 final size:22
Alignment explanation
Indices: 943611--943665 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
943601 TGGTTGTGAG
**
943611 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
943633 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
943655 GGATTTCTTCG
1 GGATTTCTTCG
943666 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:943842 original size:20 final size:20
Alignment explanation
Indices: 943812--944004 Score: 210
Period size: 20 Copynumber: 9.7 Consensus size: 20
943802 CTTTAAATAT
* *
943812 CGCGTTACGATTTACGGATT
1 CGCGTTGCGATTTACGGATA
*
943832 CTCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
*
943853 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
943872 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* * **
943892 CACATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
943912 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
943932 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
943952 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
943972 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
943992 CGCGTTGCGATTT
1 CGCGTTGCGATTT
944005 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 143 0.97
21 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:944021 original size:21 final size:21
Alignment explanation
Indices: 943991--944073 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
943981 ATTTTCATAT
*
943991 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
944012 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
944033 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
944054 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
944074 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:944064 original size:42 final size:43
Alignment explanation
Indices: 943971--944069 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
943961 ATTTATGTGT
* *
943971 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
944012 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
944054 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
944070 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:944539 original size:20 final size:20
Alignment explanation
Indices: 944514--944552 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
944504 TGACATACGA
944514 ATACGAGCCATACAAGCCAT
1 ATACGAGCCATACAAGCCAT
*
944534 ATACGAGCCATACGAGCCA
1 ATACGAGCCATACAAGCCA
944553 ATGGAGAGGT
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:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (20 bp):
ATACGAGCCATACAAGCCAT
Found at i:944546 original size:9 final size:9
Alignment explanation
Indices: 944514--944552 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
944504 TGACATACGA
944514 ATACGAGCC
1 ATACGAGCC
*
944523 ATACAAGCC
1 ATACGAGCC
944532 ATATACGAGCC
1 --ATACGAGCC
944543 ATACGAGCC
1 ATACGAGCC
944552 A
1 A
944553 ATGGAGAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 18 0.69
11 8 0.31
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (9 bp):
ATACGAGCC
Found at i:944603 original size:29 final size:29
Alignment explanation
Indices: 944559--944662 Score: 163
Period size: 29 Copynumber: 3.6 Consensus size: 29
944549 GCCAATGGAG
* **
944559 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
944588 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
**
944617 AGGTCGCCATGTAGTCCCGGCGACCAAGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
944646 AGGTCGCCATGTAGTCC
1 AGGTCGCCATGTAGTCC
944663 TAGCTCACGA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.16, C:0.30, G:0.32, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:945237 original size:47 final size:49
Alignment explanation
Indices: 945197--945289 Score: 129
Period size: 47 Copynumber: 1.9 Consensus size: 49
945187 TTATATAGTT
*
945197 AAAAAA-TAATTAAATAGTTTGT-TTTGTT-AATAGTTAGTTATATAAA
1 AAAAAATTAATTAAATAGTTTGTGTTAGTTAAATAGTTAGTTATATAAA
* *
945243 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAATTAATTAAATAGTTTGTGTTAGTTAAATAGTT-AGTTATAT
945290 TTGTTTGTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 6 0.15
47 14 0.35
48 5 0.12
49 7 0.17
50 8 0.20
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (49 bp):
AAAAAATTAATTAAATAGTTTGTGTTAGTTAAATAGTTAGTTATATAAA
Found at i:945366 original size:32 final size:33
Alignment explanation
Indices: 945330--945406 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
945320 TTAGTTAGTA
945330 AGTTTATTAGTAG-TATA-TTATAATGAAAA-AAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAGAAT
*
945362 AGTTTATTAGTTAGTTTTAGTTATATAAAAGAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAGAAT
*
945396 ATTTTATTAGT
1 AGTTTATTAGT
945407 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 10 0.26
33 8 0.21
34 17 0.44
35 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAGAAT
Found at i:947669 original size:17 final size:17
Alignment explanation
Indices: 947647--947679 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
947637 CAATGATTTT
*
947647 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
947664 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
947680 AATATTTAGT
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:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:947696 original size:24 final size:22
Alignment explanation
Indices: 947664--947732 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
947654 AAATCATTAC
947664 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
947686 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
947711 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
947733 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:947952 original size:35 final size:37
Alignment explanation
Indices: 947871--947957 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 37
947861 TTAGTATTCT
* * *
947871 ATAATTATTAGT-AATAATTATTAAATCATTAGTATTAA
1 ATAATTATTA-TAAATAATTACTAAATCAATAG-ACTAA
*
947909 ATCATTATTATAAATAATTACTAAAT-AATA-ACTAA
1 ATAATTATTATAAATAATTACTAAATCAATAGACTAA
947944 ATAATTATTATAAA
1 ATAATTATTATAAA
947958 ATCATTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 17 0.40
37 4 0.09
38 22 0.51
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (37 bp):
ATAATTATTATAAATAATTACTAAATCAATAGACTAA
Found at i:947964 original size:14 final size:13
Alignment explanation
Indices: 947941--948238 Score: 140
Period size: 12 Copynumber: 22.8 Consensus size: 13
947931 AAATAATAAC
*
947941 TAAATAATTATTA
1 TAAATCATTATTA
947954 TAAAATCATTATTA
1 T-AAATCATTATTA
*
947968 T-AATGATTATTA
1 TAAATCATTATTA
947980 TCAAATCATTACTAAATCA
1 T-AAATCATTA-T---T-A
*
947999 TCAAATCATTAAATATT
1 T-AAATCATT--AT-TA
948016 TAAATCATTA-T-
1 TAAATCATTATTA
* *
948027 TAAATCTTTTTTA
1 TAAATCATTATTA
*
948040 T-AATGATTATTA
1 TAAATCATTATTA
*
948052 CTAAATCATTACTA
1 -TAAATCATTATTA
*
948066 T-AATGATTATTA
1 TAAATCATTATTA
*
948078 TCAAATCATTACTA
1 T-AAATCATTATTA
*
948092 T-AATGATTATTA
1 TAAATCATTATTA
*
948104 TCAAATCATTA--C
1 T-AAATCATTATTA
* *
948116 TAAATCATCA-AA
1 TAAATCATTATTA
* * *
948128 TCAATAAATATT-
1 TAAATCATTATTA
948140 TAAATCATTA-T-
1 TAAATCATTATTA
* *
948151 TAAATTATTTTTA
1 TAAATCATTATTA
*
948164 T-AATGATTATTA
1 TAAATCATTATTA
948176 CTAAATCATTATTA
1 -TAAATCATTATTA
*
948190 T-AATGATTATTA
1 TAAATCATTATTA
*
948202 TCAAATCATTACTA
1 T-AAATCATTATTA
*
948216 T-AATGATTATTA
1 TAAATCATTATTA
948228 TCAAATCATTA
1 T-AAATCATTA
948239 CTAAATCATC
Statistics
Matches: 217, Mismatches: 40, Indels: 55
0.70 0.13 0.18
Matches are distributed among these distances:
11 25 0.12
12 86 0.40
13 7 0.03
14 73 0.34
15 1 0.00
16 8 0.04
17 1 0.00
18 3 0.01
19 11 0.05
20 1 0.00
21 1 0.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (13 bp):
TAAATCATTATTA
Found at i:947978 original size:12 final size:13
Alignment explanation
Indices: 947887--948238 Score: 152
Period size: 14 Copynumber: 27.1 Consensus size: 13
947877 ATTAGTAATA
947887 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
947901 AGTATTAAATCATT
1 ATTA-TAAATCATT
947915 ATTATAAAT-A--
1 ATTATAAATCATT
947925 ATTACTAAAT-A--
1 ATTA-TAAATCATT
* *
947936 ATAACTAAATAATT
1 ATTA-TAAATCATT
947950 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
947964 ATTAT-AATGATT
1 ATTATAAATCATT
947976 ATTATCAAATCATT
1 ATTAT-AAATCATT
947990 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
948009 AAATATTTAAATCATT
1 --AT-TATAAATCATT
*
948025 A-T-TAAATCTTT
1 ATTATAAATCATT
* *
948036 TTTAT-AATGATT
1 ATTATAAATCATT
948048 ATTACTAAATCATT
1 ATTA-TAAATCATT
* *
948062 ACTAT-AATGATT
1 ATTATAAATCATT
948074 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
948088 ACTAT-AATGATT
1 ATTATAAATCATT
948100 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
948114 A--CTAAATCATC
1 ATTATAAATCATT
* * * *
948125 A-AATCAATAAAT
1 ATTATAAATCATT
948137 ATT-TAAATCATT
1 ATTATAAATCATT
*
948149 A-T-TAAATTATT
1 ATTATAAATCATT
* *
948160 TTTAT-AATGATT
1 ATTATAAATCATT
948172 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
948186 ATTAT-AATGATT
1 ATTATAAATCATT
948198 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
948212 ACTAT-AATGATT
1 ATTATAAATCATT
948224 ATTATCAAATCATT
1 ATTAT-AAATCATT
948238 A
1 A
948239 CTAAATCATC
Statistics
Matches: 262, Mismatches: 44, Indels: 64
0.71 0.12 0.17
Matches are distributed among these distances:
10 4 0.02
11 40 0.15
12 88 0.34
13 12 0.05
14 92 0.35
15 1 0.00
16 8 0.03
17 1 0.00
18 3 0.01
19 11 0.04
20 1 0.00
21 1 0.00
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:947985 original size:26 final size:26
Alignment explanation
Indices: 947887--948238 Score: 247
Period size: 26 Copynumber: 14.2 Consensus size: 26
947877 ATTAGTAATA
* * *
947887 ATTATTA-AATCATTAGTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
947912 ATTATTATAA--ATAATTA-CTAAATA
1 ATTATTATAATGATTATTATC-AAATC
* * * *
947936 ATAACTA-AATAATTATTATAAAATC
1 ATTATTATAATGATTATTATCAAATC
947961 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
947987 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
948010 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
948033 TTTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
*
948059 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
948085 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * *
948111 ATTACTA-AATCATCA-AATC-AATA
1 ATTATTATAATGATTATTATCAAATC
* * * *
948134 AATATT-TAA--ATCATTATTAAATT
1 ATTATTATAATGATTATTATCAAATC
*
948157 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
948183 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
948209 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
948235 ATTA
1 ATTA
948239 CTAAATCATC
Statistics
Matches: 256, Mismatches: 49, Indels: 43
0.74 0.14 0.12
Matches are distributed among these distances:
21 8 0.03
22 4 0.02
23 31 0.12
24 26 0.10
25 34 0.13
26 151 0.59
27 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTATTATAATGATTATTATCAAATC
Found at i:948111 original size:124 final size:124
Alignment explanation
Indices: 947903--948296 Score: 659
Period size: 124 Copynumber: 3.2 Consensus size: 124
947893 AAATCATTAG
* * * * * *
947903 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACTA-AATAATTATTATAAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTA
*
947965 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
*
948024 TATTAAATCTTTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTA
*
948089 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCAATAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
* *
948148 TATTAAATTATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTA
948213 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
*
948272 TATTAAATAATTTTTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
948297 ATAAATACAT
Statistics
Matches: 256, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
121 17 0.07
123 18 0.07
124 221 0.86
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (124 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTA
CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:951060 original size:26 final size:24
Alignment explanation
Indices: 951002--951060 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
950992 AAAATAAACC
*
951002 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
951026 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
951054 TAATAAT
1 TAATAAT
951061 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:951855 original size:42 final size:47
Alignment explanation
Indices: 951799--951911 Score: 128
Period size: 50 Copynumber: 2.4 Consensus size: 47
951789 GTTTAAAGAC
*
951799 ACTAACAAATTAATTAATATTTTTT-TAT-AT-T-TA-ATAACTTAA
1 ACTAACAAACTAATTAATATTTTTTATATAATATATATATAACTTAA
*
951841 ACTAAGAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAA-T-ATTTTTTATATAATAT-ATATATAACTTAA
*
951891 ACTAATAAACTAATATAATAT
1 ACTAACAAACTAAT-TAATAT
951912 AACTTAAACT
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
42 15 0.25
43 1 0.02
44 7 0.12
45 3 0.05
46 2 0.03
47 1 0.02
49 4 0.07
50 23 0.39
51 3 0.05
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.42
Consensus pattern (47 bp):
ACTAACAAACTAATTAATATTTTTTATATAATATATATATAACTTAA
Found at i:951911 original size:28 final size:30
Alignment explanation
Indices: 951871--951933 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
951861 ATTTTTTATA
*
951871 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
951901 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
951929 TAATA
1 TAATA
951934 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:951940 original size:28 final size:28
Alignment explanation
Indices: 951875--951940 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
951865 TTTATATAAT
*
951875 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
951903 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
951931 ATAATTTATA
1 ATAATATATA
951941 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:951943 original size:21 final size:21
Alignment explanation
Indices: 951910--951958 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
951900 CTAATATAAT
951910 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
951931 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
951952 ATTAACT
1 A-TAACT
951959 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:952352 original size:21 final size:21
Alignment explanation
Indices: 952327--952398 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
952317 ACGCAACTAT
952327 GGATGCAACACATGCAGCTAC
1 GGATGCAACACATGCAGCTAC
* *
952348 GGATGCATGA-ATC-TCCCAGCTAT
1 GGATGCA--ACA-CAT-GCAGCTAC
*
952371 GGATGCAACGCATGCAGCTAC
1 GGATGCAACACATGCAGCTAC
952392 GGATGCA
1 GGATGCA
952399 GGAATCTCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
21 22 0.55
22 3 0.08
23 15 0.38
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.18
Consensus pattern (21 bp):
GGATGCAACACATGCAGCTAC
Found at i:952373 original size:44 final size:44
Alignment explanation
Indices: 952323--952413 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
952313 AATAACGCAA
*
952323 CTATGGATGCAACACATGCAGCTACGGATGCATGAATCTCCCAG
1 CTATGGATGCAACACATGCAGCTACGGATGCAGGAATCTCCCAG
*
952367 CTATGGATGCAACGCATGCAGCTACGGATGCAGGAATCTCCCAG
1 CTATGGATGCAACACATGCAGCTACGGATGCAGGAATCTCCCAG
952411 CTA
1 CTA
952414 GAATCTAGCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (44 bp):
CTATGGATGCAACACATGCAGCTACGGATGCAGGAATCTCCCAG
Found at i:952536 original size:20 final size:20
Alignment explanation
Indices: 952511--952548 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
952501 ACGTGCATGG
*
952511 CCCATGCACAGTTCCCACGT
1 CCCATGCACAGCTCCCACGT
952531 CCCATGCACAGCTCCCAC
1 CCCATGCACAGCTCCCAC
952549 ATGCATCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.50, G:0.13, T:0.16
Consensus pattern (20 bp):
CCCATGCACAGCTCCCACGT
Found at i:952667 original size:29 final size:29
Alignment explanation
Indices: 952634--952733 Score: 136
Period size: 29 Copynumber: 3.6 Consensus size: 29
952624 AACACCACAC
*
952634 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
*
952663 AGGTCGCCCGGATGCCATGGTGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
*
952692 AGGTCGCTC----GCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
*
952717 AGCTCGCCCGGATGCCA
1 AGGTCGCCCGGATGCCA
952734 CTGTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
25 22 0.36
29 39 0.64
ACGTcount: A:0.17, C:0.37, G:0.30, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:952922 original size:20 final size:20
Alignment explanation
Indices: 952897--952938 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
952887 AAAATATTTT
*
952897 TTTTTCTACCAGTTTTGTTA
1 TTTTTCTAACAGTTTTGTTA
952917 TTTTTCTAACAGTTTTGTTA
1 TTTTTCTAACAGTTTTGTTA
952937 TT
1 TT
952939 GTTGGACACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.62
Consensus pattern (20 bp):
TTTTTCTAACAGTTTTGTTA
Found at i:953361 original size:30 final size:31
Alignment explanation
Indices: 953327--953391 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
953317 AAATATTAGC
953327 CTAACA-TTTTACTGTTACACTTTTAAGTGT
1 CTAACATTTTTACTGTTACACTTTTAAGTGT
* * *
953357 CTAACATTTTTTTCTGTTATACTTTTAGGTGT
1 CTAACA-TTTTTACTGTTACACTTTTAAGTGT
953389 CTA
1 CTA
953392 CGCAGTAGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 6 0.20
32 24 0.80
ACGTcount: A:0.23, C:0.15, G:0.11, T:0.51
Consensus pattern (31 bp):
CTAACATTTTTACTGTTACACTTTTAAGTGT
Found at i:954078 original size:25 final size:25
Alignment explanation
Indices: 954032--954080 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
954022 TTTTTCTTAA
* *
954032 TTTTTTAAAAAATAATGTTTTAAAT
1 TTTTTTAAAAAATAAAGATTTAAAT
* *
954057 TTTTTTAGAAAGTAAAGATTTAAA
1 TTTTTTAAAAAATAAAGATTTAAA
954081 AAATATATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (25 bp):
TTTTTTAAAAAATAAAGATTTAAAT
Found at i:966636 original size:12 final size:12
Alignment explanation
Indices: 966619--966643 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
966609 CTAAACCATC
966619 AGCCTCAATATT
1 AGCCTCAATATT
966631 AGCCTCAATATT
1 AGCCTCAATATT
966643 A
1 A
966644 TCAACCTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (12 bp):
AGCCTCAATATT
Found at i:967172 original size:63 final size:64
Alignment explanation
Indices: 967073--967200 Score: 195
Period size: 63 Copynumber: 2.0 Consensus size: 64
967063 CATAGATGAA
* * *
967073 ATATCTAACAGTATAATCAGTTGTTTAATTGAGAAGTCTTACATAAATG-AAACAAACCTCAAT
1 ATATCTAACAATATAATCAGTTGTTTAACTGAGAAGTCCTACATAAATGAAAACAAACCTCAAT
* * *
967136 ATATCTAACAATATAATTAGTTGTTTTACTGAGAAGTCCTACATAAGTGAAAACAAACCTCAAT
1 ATATCTAACAATATAATCAGTTGTTTAACTGAGAAGTCCTACATAAATGAAAACAAACCTCAAT
967200 A
1 A
967201 CCTCTATTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
63 43 0.74
64 15 0.26
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (64 bp):
ATATCTAACAATATAATCAGTTGTTTAACTGAGAAGTCCTACATAAATGAAAACAAACCTCAAT
Found at i:969135 original size:111 final size:112
Alignment explanation
Indices: 968926--969136 Score: 316
Period size: 111 Copynumber: 1.9 Consensus size: 112
968916 GAAGCTAAAA
*
968926 AGCTTCGTAAACAAATTCTTTTAAGACTTAAGAATTAATCCCATTCCTTGTTTGAAATTTGAGAA
1 AGCTTCGTAAACAAATTCTTTTAAGACTTAAGAATAAATCCCATTCCTTGTTTGAAATTTGAGAA
* * ** * *
968991 TGATATGTAAATGCAAAGTTAAGTCTCCTTACCTCAGCTATGAAGTT
66 TGACATGTAAAAGCAAAAATAAGTCTACATACCTCAGCTATGAAGTT
* *
969038 AGCTTCTTAAA-AATTTCTTTTAAGACTTAAGAATAAATCCCATTCCTTGTTTGAAATTTGAGAA
1 AGCTTCGTAAACAAATTCTTTTAAGACTTAAGAATAAATCCCATTCCTTGTTTGAAATTTGAGAA
* *
969102 TGGCATGTAAAAGCAAAAATGAGTCTACATACCTC
66 TGACATGTAAAAGCAAAAATAAGTCTACATACCTC
969137 TTCATTCATA
Statistics
Matches: 88, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
111 78 0.89
112 10 0.11
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Consensus pattern (112 bp):
AGCTTCGTAAACAAATTCTTTTAAGACTTAAGAATAAATCCCATTCCTTGTTTGAAATTTGAGAA
TGACATGTAAAAGCAAAAATAAGTCTACATACCTCAGCTATGAAGTT
Found at i:973844 original size:19 final size:19
Alignment explanation
Indices: 973822--973867 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
973812 TTTTTGAAAA
*
973822 AAAATAAAGTTTAAGTACC
1 AAAACAAAGTTTAAGTACC
* *
973841 AAAACAGAGTTTAGGTACC
1 AAAACAAAGTTTAAGTACC
973860 AAAACAAA
1 AAAACAAA
973868 ACAAAAGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.20
Consensus pattern (19 bp):
AAAACAAAGTTTAAGTACC
Found at i:974594 original size:20 final size:21
Alignment explanation
Indices: 974566--974605 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
974556 AAAATGAAAT
*
974566 TTAACAAT-ACATAAATAATC
1 TTAAAAATAACATAAATAATC
*
974586 TTAAAAATAAGATAAATAAT
1 TTAAAAATAACATAAATAAT
974606 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (21 bp):
TTAAAAATAACATAAATAATC
Found at i:982178 original size:2 final size:2
Alignment explanation
Indices: 982171--982223 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
982161 ATTGTTATTA
982171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
982213 AT AT AT AT AT A
1 AT AT AT AT AT A
982224 GTTACAATAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:983606 original size:14 final size:16
Alignment explanation
Indices: 983587--983618 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
983577 AAAAAAAATC
983587 TTTTGT-TTTTTA-TT
1 TTTTGTCTTTTTACTT
983601 TTTTGTCTTTTTACTT
1 TTTTGTCTTTTTACTT
983617 TT
1 TT
983619 AACTAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.81
Consensus pattern (16 bp):
TTTTGTCTTTTTACTT
Found at i:983875 original size:39 final size:38
Alignment explanation
Indices: 983821--983896 Score: 116
Period size: 39 Copynumber: 2.0 Consensus size: 38
983811 ATTAGGTAAC
*
983821 ATTTTAAGTTAAATCGAAAATGTCACATTCTCTATAAT
1 ATTTTAAGTTAAATCGAAAATGTCACATTCTCCATAAT
* *
983859 ATTTTTAGTTACAATCGAAAATGTTACATTCTCCATAA
1 ATTTTAAGTTA-AATCGAAAATGTCACATTCTCCATAA
983897 CATATTCGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 10 0.29
39 24 0.71
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.39
Consensus pattern (38 bp):
ATTTTAAGTTAAATCGAAAATGTCACATTCTCCATAAT
Found at i:984176 original size:28 final size:24
Alignment explanation
Indices: 984115--984176 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 24
984105 TTTAGGTTAA
984115 AACTACCTTAAATTAACCTTATAT
1 AACTACCTTAAATTAACCTTATAT
*
984139 AGCTACCCTTAATATCTATACCTTATAT
1 AACTA-CCTTAA-AT-TA-ACCTTATAT
984167 AACTTACCTT
1 AAC-TACCTT
984177 CAGCATTCGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 4 0.13
25 6 0.19
26 2 0.06
27 2 0.06
28 15 0.48
29 2 0.06
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (24 bp):
AACTACCTTAAATTAACCTTATAT
Found at i:987600 original size:30 final size:30
Alignment explanation
Indices: 987566--987623 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
987556 CGTCTTCGTG
*
987566 AATTCCTCCTTCTAGATCCGTCATCCCTGT
1 AATTCCTCCTTCTAGATCCATCATCCCTGT
*
987596 AATTCCTTCTTCTAGATCCATCATCCCT
1 AATTCCTCCTTCTAGATCCATCATCCCT
987624 ATATGAGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.36, G:0.07, T:0.38
Consensus pattern (30 bp):
AATTCCTCCTTCTAGATCCATCATCCCTGT
Found at i:989337 original size:16 final size:16
Alignment explanation
Indices: 989318--989355 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
989308 ATCTTTAAAC
989318 TTTTCTA-CTCTTTCAG
1 TTTTCTATCT-TTTCAG
*
989334 TTTTCCATCTTTTCAG
1 TTTTCTATCTTTTCAG
989350 TTTTCT
1 TTTTCT
989356 TTTCACCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 17 0.89
17 2 0.11
ACGTcount: A:0.11, C:0.24, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTTCTATCTTTTCAG
Found at i:999398 original size:20 final size:20
Alignment explanation
Indices: 999304--999672 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
999294 GATTTTCCAT
* ** *
999304 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
999324 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
999344 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
999364 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
999384 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
999404 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
999424 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
999444 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
999464 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
999484 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
999504 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
999524 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
999544 AATCGCAACG-ATAATCTGTA
1 AATCGCAACGCGT-ATCCGTA
999564 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
999584 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
999604 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
999624 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
999644 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
999664 AATCACAAC
1 AATCGCAAC
999673 ACTTAAATTT
Statistics
Matches: 303, Mismatches: 36, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.01
20 295 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1000393 original size:24 final size:24
Alignment explanation
Indices: 1000354--1000400 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1000344 AAATTTGGTC
1000354 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1000378 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1000401 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1000592 original size:12 final size:12
Alignment explanation
Indices: 1000575--1000599 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1000565 ATATAATCCT
1000575 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1000587 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1000599 G
1 G
1000600 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1002904 original size:19 final size:19
Alignment explanation
Indices: 1002882--1003155 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
1002872 CGGAAAATAC
*
1002882 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1002901 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1002915 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1002935 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1002949 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1002968 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1002987 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
1003001 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
1003020 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1003039 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1003058 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1003077 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1003096 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1003110 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1003129 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1003148 AATCGCAA
1 AATCGCAA
1003156 CGAGATAATC
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 38 0.17
15 1 0.00
16 14 0.06
17 12 0.05
18 2 0.01
19 146 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1003033 original size:71 final size:74
Alignment explanation
Indices: 1002882--1003177 Score: 314
Period size: 71 Copynumber: 4.2 Consensus size: 74
1002872 CGGAAAATAC
* *
1002882 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-AAATCGCA
*
1002942 A--CG--A-GAG
63 ATGCGAAATGAA
*
1002949 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G-AATCGCAATG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATG
*
1003011 CGAAATTAA
66 CGAAATGAA
1003020 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAA
1003085 TGCGAAATGAA
64 TGCGAAATGAA
1003096 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAA
*
1003156 --CG--A-GAT
64 TGCGAAATGAA
1003162 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1003178 TATAAACGCA
Statistics
Matches: 203, Mismatches: 8, Indels: 34
0.83 0.03 0.14
Matches are distributed among these distances:
66 18 0.09
67 26 0.13
68 8 0.04
69 6 0.03
70 2 0.01
71 93 0.46
72 13 0.06
73 5 0.02
74 6 0.03
76 26 0.13
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (74 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATG
CGAAATGAA
Found at i:1003081 original size:109 final size:104
Alignment explanation
Indices: 1002910--1003177 Score: 446
Period size: 109 Copynumber: 2.5 Consensus size: 104
1002900 AAATCCCAAC
*
1002910 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
1002975 ATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
65 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
1003015 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAAAT
1003080 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
61 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
1003124 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAAT
1003178 TATAAACGCA
Statistics
Matches: 153, Mismatches: 5, Indels: 11
0.91 0.03 0.07
Matches are distributed among these distances:
104 34 0.22
105 16 0.10
106 2 0.01
107 2 0.01
108 1 0.01
109 98 0.64
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (104 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:1003143 original size:161 final size:157
Alignment explanation
Indices: 1002882--1003193 Score: 502
Period size: 161 Copynumber: 2.0 Consensus size: 157
1002872 CGGAAAATAC
*
1002882 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
1002947 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
1003012 GAAATTA-AAATCGCAATGCGAAATGAA
131 GAAATTATAAA-CGCAATGCGAAATGAA
* *
1003039 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
* *
1003103 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
61 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGC
*
1003168 AATGCGAAATTATAAACGCATTGCGA
126 AATGCGAAATTATAAACGCAATGCGA
1003194 TTTTCATTTC
Statistics
Matches: 143, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
157 25 0.17
159 1 0.01
161 98 0.69
162 19 0.13
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (157 bp):
AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
GAAATTATAAACGCAATGCGAAATGAA
Found at i:1003193 original size:52 final size:52
Alignment explanation
Indices: 1002910--1003177 Score: 437
Period size: 52 Copynumber: 5.0 Consensus size: 52
1002900 AAATCCCAAC
1002910 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1002963 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
1003015 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
1003072 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1003124 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1003176 AT
1 AT
1003178 TATAAACGCA
Statistics
Matches: 201, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
52 133 0.66
53 17 0.08
54 2 0.01
55 2 0.01
56 1 0.00
57 46 0.23
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1003293 original size:19 final size:19
Alignment explanation
Indices: 1003184--1003285 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1003174 AAATTATAAA
1003184 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1003203 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1003223 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1003239 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1003256 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1003275 CGCATTGCGAT
1 CGCATTGCGAT
1003286 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1003411 original size:14 final size:14
Alignment explanation
Indices: 1003392--1003428 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1003382 CATCAATTAC
1003392 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1003406 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1003420 ACAAATCAA
1 ACAAATCAA
1003429 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1005407 original size:14 final size:14
Alignment explanation
Indices: 1005388--1005444 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1005378 GCGAAATGAA
*
1005388 AATCGCAACGACAG
1 AATCGCAACGAAAG
1005402 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1005419 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1005435 AATCGCAACG
1 AATCGCAACG
1005445 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1005415 original size:33 final size:33
Alignment explanation
Indices: 1005369--1005461 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1005359 GCGAAACCAA
*
1005369 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1005402 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1005435 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1005462 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1005426 original size:19 final size:19
Alignment explanation
Indices: 1005332--1005466 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1005322 TAGTTTACTT
* *
1005332 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1005352 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1005371 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1005390 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1005404 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1005423 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1005437 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1005456 TCGCAATGCGA
1 TCGCAACGCGA
1005467 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1005484 original size:19 final size:19
Alignment explanation
Indices: 1005462--1005538 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
1005452 AAAATCGCAA
1005462 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1005481 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1005495 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1005514 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1005534 TGCGA
1 TGCGA
1005539 AAGTAAACTA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
14 11 0.23
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 20 0.42
20 13 0.27
ACGTcount: A:0.09, C:0.16, G:0.30, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1005873 original size:93 final size:93
Alignment explanation
Indices: 1005582--1006051 Score: 885
Period size: 93 Copynumber: 5.1 Consensus size: 93
1005572 TTGAATGGAT
*
1005582 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACATTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1005647 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1005675 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1005739 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1005767 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1005832 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1005860 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA-A-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1005922 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1005950 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1006015 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1006043 AAATTTACT
1 AAATTTACT
1006052 AAGCAATCTA
Statistics
Matches: 369, Mismatches: 4, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
90 86 0.23
91 3 0.01
92 94 0.25
93 186 0.50
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1006000 original size:183 final size:185
Alignment explanation
Indices: 1005582--1006051 Score: 899
Period size: 183 Copynumber: 2.6 Consensus size: 185
1005572 TTGAATGGAT
*
1005582 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACATTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1005647 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1005712 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1005767 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1005832 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
1005896 -ATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1005950 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1006015 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1006052 AAGCAATCTA
Statistics
Matches: 282, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
183 154 0.55
184 2 0.01
185 126 0.45
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1007776 original size:14 final size:14
Alignment explanation
Indices: 1007757--1007846 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
1007747 TTGAAATGAA
1007757 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1007771 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1007788 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1007804 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1007823 AATCGCAACGAGAT
1 AATCGCAACGAGAG
1007837 AATCGCAACG
1 AATCGCAACG
1007847 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1007794 original size:33 final size:33
Alignment explanation
Indices: 1007749--1007863 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
1007739 TCTTTTGGTT
1007749 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1007782 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1007815 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1007848 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1007864 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1007795 original size:19 final size:18
Alignment explanation
Indices: 1007756--1007868 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1007746 GTTGAAATGA
1007756 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1007771 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1007788 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1007804 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1007821 AAAATCGCAA--CGAGAT-
1 -AAATCGCAACGCGAGATG
*
1007837 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1007854 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1007869 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1007899 original size:14 final size:14
Alignment explanation
Indices: 1007880--1007936 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1007870 TTTGGTTTCG
1007880 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1007894 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1007913 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1007927 CGTTGCGATT
1 CGTTGCGATT
1007937 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1007918 original size:19 final size:19
Alignment explanation
Indices: 1007894--1007982 Score: 89
Period size: 19 Copynumber: 4.9 Consensus size: 19
1007884 GCGATTCTCT
1007894 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1007913 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
1007927 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
1007946 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
1007966 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
1007983 ATCTCGTTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.18
16 3 0.05
17 3 0.05
19 24 0.44
20 15 0.27
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1007974 original size:39 final size:33
Alignment explanation
Indices: 1007864--1007982 Score: 166
Period size: 33 Copynumber: 3.4 Consensus size: 33
1007854 AAAATCGCAA
**
1007864 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1007897 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1007930 TGCGATTTTCATTTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCGT
1007969 TGCGATTTTCATTT
1 TGCGATTTTCATTT
1007983 ATCTCGTTGC
Statistics
Matches: 78, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
33 51 0.65
35 1 0.01
36 1 0.01
37 1 0.01
39 24 0.31
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1008116 original size:33 final size:33
Alignment explanation
Indices: 1008074--1008144 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1008064 AATACTAACT
*
1008074 TGAAAATCGCAACGAGAGAATAGCAACACGAAA
1 TGAAAATCGCAACGACAGAATAGCAACACGAAA
* * *
1008107 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACACGAAA
1008140 TGAAA
1 TGAAA
1008145 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACACGAAA
Found at i:1008377 original size:22 final size:22
Alignment explanation
Indices: 1008325--1008379 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1008315 TGGTTGTGAG
**
1008325 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1008347 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1008369 GGATTTCTTCG
1 GGATTTCTTCG
1008380 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1008550 original size:20 final size:20
Alignment explanation
Indices: 1008525--1008717 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1008515 CTTTAAATAT
1008525 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1008545 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1008567 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1008586 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1008606 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1008626 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1008646 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1008666 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1008686 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1008706 CGCGTTGCGATT
1 CGCGTTGCGATT
1008718 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1008712 original size:60 final size:60
Alignment explanation
Indices: 1008525--1008717 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1008515 CTTTAAATAT
**
1008525 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1008586 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1008646 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1008706 CGCGTTGCGATT
1 CGCGTTGCGATT
1008718 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1008798 original size:20 final size:20
Alignment explanation
Indices: 1008773--1008824 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1008763 AAGAATCGCG
*
1008773 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1008793 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1008813 TTGCGATTCTGG
1 TTGCGATTCTGG
1008825 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1009379 original size:23 final size:23
Alignment explanation
Indices: 1009353--1009409 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
1009343 AAAGAAAAGG
* *
1009353 TGTCATAAAGGTATAGAAAAACA
1 TGTCATAAAAGTAGAGAAAAACA
1009376 TGTCATAAAAGTAGAGAAAAACA
1 TGTCATAAAAGTAGAGAAAAACA
1009399 TGTCATAAAAG
1 TGTCATAAAAG
1009410 CATAGTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.53, C:0.09, G:0.18, T:0.21
Consensus pattern (23 bp):
TGTCATAAAAGTAGAGAAAAACA
Found at i:1018264 original size:34 final size:34
Alignment explanation
Indices: 1018189--1018262 Score: 141
Period size: 33 Copynumber: 2.2 Consensus size: 34
1018179 AAGATTATGC
1018189 TTTTTTTAAATAAAAAAAAAATCATTTTTCCTCA
1 TTTTTTTAAATAAAAAAAAAATCATTTTTCCTCA
1018223 TTTTTTTAAAT-AAAAAAAAATCATTTTTCCTCA
1 TTTTTTTAAATAAAAAAAAAATCATTTTTCCTCA
1018256 TTTTTTT
1 TTTTTTT
1018263 TATCCCTACA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 29 0.73
34 11 0.28
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (34 bp):
TTTTTTTAAATAAAAAAAAAATCATTTTTCCTCA
Found at i:1019092 original size:52 final size:52
Alignment explanation
Indices: 1019030--1019132 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
1019020 AAATTGGACA
1019030 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
* *
1019082 CATAGAAATAGGAGATTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1019133 AATATTATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (52 bp):
CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
Found at i:1023672 original size:52 final size:52
Alignment explanation
Indices: 1023610--1023712 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
1023600 AAATTGGACA
1023610 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
* *
1023662 CATAGAAATAGGAGATTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1023713 AATATTATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (52 bp):
CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
Found at i:1025978 original size:3 final size:3
Alignment explanation
Indices: 1025970--1026051 Score: 130
Period size: 3 Copynumber: 27.7 Consensus size: 3
1025960 TTTTTATCCA
* *
1025970 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAC TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1026017 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1026052 AATATATATT
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
2 2 0.03
3 72 0.97
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1026063 original size:11 final size:11
Alignment explanation
Indices: 1026047--1026076 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1026037 TTATTATTAT
1026047 TATTAAATATA
1 TATTAAATATA
1026058 TATTAAATATA
1 TATTAAATATA
1026069 TA-TAAATA
1 TATTAAATA
1026077 ATTAATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAAATATA
Found at i:1027517 original size:13 final size:13
Alignment explanation
Indices: 1027501--1027547 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1027491 ATATAATAAA
1027501 TAAATATTTATTT
1 TAAATATTTATTT
*
1027514 TAAATAAATTATTT
1 TAAAT-ATTTATTT
1027528 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
1027541 TCAATAT
1 TAAATAT
1027548 CAAAGAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:1029924 original size:21 final size:21
Alignment explanation
Indices: 1029898--1029940 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1029888 ATTTTCGGCT
*
1029898 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGGTACCCATTCA
*
1029919 AGGGGAACCGGTACCCCTTCA
1 AGGGGAACCGGTACCCATTCA
1029940 A
1 A
1029941 CGAATATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGGTACCCATTCA
Found at i:1030015 original size:67 final size:67
Alignment explanation
Indices: 1029920--1030070 Score: 173
Period size: 67 Copynumber: 2.3 Consensus size: 67
1029910 ACCCATTCAA
* * * *
1029920 GGGGAACCGGTACCCCTTCAACGAATATG-ATTTCCAG-TATGCTAGAGGGGAATCGGTA-CCCC
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAT-TGCTAGAGGGGAATCGATACCCCC
1029982 AGGGG
65 A--GG
* * *
1029987 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGATTGCTAGAGGGGAATCGATACCCCCA
1030052 GG
66 GG
* *
1030054 GAGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1030071 ATGAGAAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
67 42 0.58
68 24 0.33
69 6 0.08
ACGTcount: A:0.26, C:0.27, G:0.28, T:0.19
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGATTGCTAGAGGGGAATCGATACCCCCA
GG
Found at i:1030498 original size:30 final size:31
Alignment explanation
Indices: 1030456--1030515 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1030446 AGAAAAAGTT
*
1030456 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
1030487 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
1030516 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:1030763 original size:22 final size:22
Alignment explanation
Indices: 1030736--1030777 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1030726 ATGGACATAA
1030736 TCTACGGGCACTTCGGTGCAAT
1 TCTACGGGCACTTCGGTGCAAT
1030758 TCTACGGGCACTTCGGTGCA
1 TCTACGGGCACTTCGGTGCA
1030778 TTTATACGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.26
Consensus pattern (22 bp):
TCTACGGGCACTTCGGTGCAAT
Found at i:1030785 original size:22 final size:22
Alignment explanation
Indices: 1030738--1030785 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1030728 GGACATAATC
*
1030738 TACGGGCACTTCGGTGCAATTC
1 TACGGGCACTTCGGTGCAATTA
*
1030760 TACGGGCACTTCGGTGCATTTA
1 TACGGGCACTTCGGTGCAATTA
1030782 TACG
1 TACG
1030786 AGCTGTGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (22 bp):
TACGGGCACTTCGGTGCAATTA
Found at i:1033295 original size:27 final size:27
Alignment explanation
Indices: 1033224--1033303 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
1033214 GATTACATTC
1033224 CATATTATG-A-TACATGACATGAATT
1 CATATTATGTATTACATGACATGAATT
** *
1033249 TGTCTTAAATGTATTACATGACATGAATT
1 CATATT--ATGTATTACATGACATGAATT
1033278 CATATTATGTATTACATGACATGAAT
1 CATATTATGTATTACATGACATGAAT
1033304 ATGCAGAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
25 3 0.07
27 23 0.51
28 1 0.02
29 18 0.40
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (27 bp):
CATATTATGTATTACATGACATGAATT
Found at i:1033380 original size:29 final size:30
Alignment explanation
Indices: 1033317--1033374 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1033307 CAGAAAAGTT
*
1033317 ATATGCACTATGTGATAAAGGTATGTAATG
1 ATATGCACTATGTGATAAAGGTATGAAATG
*
1033347 ATATGC-CTATGTG-TTAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTAT-GAAAT
1033375 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.32
29 11 0.44
30 6 0.24
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (30 bp):
ATATGCACTATGTGATAAAGGTATGAAATG
Found at i:1033622 original size:22 final size:22
Alignment explanation
Indices: 1033587--1033642 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
1033577 TTATGGACAT
1033587 AATTCTAACGGGCACTTCGGTGC
1 AATTCT-ACGGGCACTTCGGTGC
1033610 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1033632 AATTCTACGGG
1 AATTCTACGGG
1033643 AACAATCGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 27 0.82
23 6 0.18
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:1033663 original size:23 final size:22
Alignment explanation
Indices: 1033587--1033655 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
1033577 TTATGGACAT
* *
1033587 AATTCTAACGGGCACTTCGGTGC
1 AATTCT-ACGGGAACATCGGTGC
* *
1033610 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGAACATCGGTGC
1033632 AATTCTACGGGAACAATCGGTGC
1 AATTCTACGGGAAC-ATCGGTGC
1033655 A
1 A
1033656 TTTATACGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
22 29 0.67
23 14 0.33
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (22 bp):
AATTCTACGGGAACATCGGTGC
Found at i:1039607 original size:20 final size:20
Alignment explanation
Indices: 1039578--1039617 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1039568 TTCGGGCTAG
*
1039578 GGGAATCGGTACCCATTCAA
1 GGGAACCGGTACCCATTCAA
*
1039598 GGGAACCGGTACCCCTTCAA
1 GGGAACCGGTACCCATTCAA
1039618 CGAATATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (20 bp):
GGGAACCGGTACCCATTCAA
Found at i:1039691 original size:66 final size:67
Alignment explanation
Indices: 1039598--1039745 Score: 185
Period size: 67 Copynumber: 2.2 Consensus size: 67
1039588 ACCCATTCAA
* * *
1039598 GGGAACCGGTACCCCTTCAACGAATATG-ATTTCCAG-TATGCTAGAGGGGAATCGGTACCCCCA
1 GGGAACCGATACCCCTTCAACGAATATGAAATTCCAGAT-TGCTAGAGGGGAATCGATA-CCCCA
1039661 GGGG
64 GGGG
* * *
1039665 GGGAACCGATACCCC-TCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCAGG
1 GGGAACCGATACCCCTTCAACGAATATGAAATTCCAGATTGCTAGAGGGGAATCGATACCCCAGG
1039729 GG
66 GG
* *
1039731 AGGAACCGATTCCCC
1 GGGAACCGATACCCC
1039746 CATGAGAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
66 32 0.45
67 38 0.54
68 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (67 bp):
GGGAACCGATACCCCTTCAACGAATATGAAATTCCAGATTGCTAGAGGGGAATCGATACCCCAGG
GG
Found at i:1040077 original size:29 final size:29
Alignment explanation
Indices: 1040045--1040115 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
1040035 CCATATTTGA
** *
1040045 TACATGACATGAATTTGTCTTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
1040074 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
1040103 TACATGAC-TGAAT
1 TACATGACATGAAT
1040116 ATGCAGAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
28 5 0.13
29 33 0.87
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:1040172 original size:30 final size:31
Alignment explanation
Indices: 1040130--1040189 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1040120 AGAAAAAGTT
*
1040130 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
1040161 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
1040190 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:1040447 original size:22 final size:22
Alignment explanation
Indices: 1040419--1040463 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1040409 TTATGGACAT
1040419 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1040441 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1040463 A
1 A
1040464 TTTATACGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:1040471 original size:22 final size:22
Alignment explanation
Indices: 1040419--1040471 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1040409 TTATGGACAT
*
1040419 AATTCTACGGGCACTTCGGTGC
1 AATTATACGGGCACTTCGGTGC
*
1040441 AATTCTACGGGCACTTCGGTGC
1 AATTATACGGGCACTTCGGTGC
*
1040463 ATTTATACG
1 AATTATACG
1040472 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (22 bp):
AATTATACGGGCACTTCGGTGC
Found at i:1052793 original size:84 final size:84
Alignment explanation
Indices: 1052551--1053017 Score: 863
Period size: 84 Copynumber: 5.6 Consensus size: 84
1052541 TGGAACAAAT
1052551 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1052616 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
*
1052635 ATAATGTGCTCAATAG-ATCTTCTGGAA--GTTCTTTGAGTTATCTGATCTGATTGGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1052697 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
1052716 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1052781 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
1052800 ATAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1052864 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
1052883 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1052948 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
* *
1052967 ATAAGGATGCTCAATAGCATCTTCTGGAAGTG-TCTTTGAGTTATTTGATCT
1 ATAATG-TGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1053018 AGTTTGGTAA
Statistics
Matches: 374, Mismatches: 4, Indels: 10
0.96 0.01 0.03
Matches are distributed among these distances:
81 69 0.18
82 11 0.03
83 94 0.25
84 175 0.47
85 25 0.07
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.35
Consensus pattern (84 bp):
ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
AATCATTGAATTTGGAAGA
Found at i:1052938 original size:167 final size:168
Alignment explanation
Indices: 1052551--1053017 Score: 863
Period size: 167 Copynumber: 2.8 Consensus size: 168
1052541 TGGAACAAAT
1052551 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1052616 AATCATTGAATTTGGAAGAATAATGTGCTCAATAG-ATCTTCTGGAA--GTTCTTTGAGTTATCT
66 AATCATTGAATTTGGAAGAATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
1052678 GATCTGATTGGACAGAACCAATCATTGAATTTGGAAGA
131 GATCTGATTGGACAGAACCAATCATTGAATTTGGAAGA
1052716 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1052781 AATCATTGAATTTGGAAGAATAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
66 AATCATTGAATTTGGAAGAATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
*
1052845 GATCTGGTTGGACAGAACCAATCATTGAATTTGGAAGA
131 GATCTGATTGGACAGAACCAATCATTGAATTTGGAAGA
1052883 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
* *
1052948 AATCATTGAATTTGGAAGAATAAGGATGCTCAATAGCATCTTCTGGAAGTG-TCTTTGAGTTATT
66 AATCATTGAATTTGGAAGAATAATG-TGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1053012 TGATCT
130 TGATCT
1053018 AGTTTGGTAA
Statistics
Matches: 294, Mismatches: 3, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
164 4 0.01
165 106 0.36
167 142 0.48
168 23 0.08
169 19 0.06
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.35
Consensus pattern (168 bp):
ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
AATCATTGAATTTGGAAGAATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
GATCTGATTGGACAGAACCAATCATTGAATTTGGAAGA
Found at i:1054116 original size:113 final size:113
Alignment explanation
Indices: 1053755--1054181 Score: 711
Period size: 112 Copynumber: 3.8 Consensus size: 113
1053745 TCGAATCCAC
*
1053755 TTGATGGATCAGT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 TTGATGGATCA-TCTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1053819 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
64 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
* *
1053869 TTGATGGATTATCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
1053934 AGTT-ATAATGAGAAGAATTTGTTCAACCTTTTACCTTAATCCATCAT
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
1053981 TTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
1054046 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
* *
1054094 TTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATC-G-AGAAGAAAGAAGA
1 TTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
1054156 AGTTCATAATAAGAAGAATTTGTTCA
66 AGTTCATAATGAGAAGAATTTGTTCA
1054182 CTTTTTGCAT
Statistics
Matches: 298, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
110 37 0.12
111 1 0.00
112 134 0.45
113 113 0.38
114 13 0.04
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (113 bp):
TTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
Done.