Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002377.1 Hibiscus syriacus cultivar Beakdansim tig00004858_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: 64668
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:519 original size:20 final size:20
Alignment explanation
Indices: 496--586 Score: 71
Period size: 20 Copynumber: 4.5 Consensus size: 20
486 GATTTTCCAT
* *
496 ATCGCAACGCGAATATGA-AA
1 ATCGCAACGCGAACA-CATAA
516 ATCGCAACGCGAACACATAA
1 ATCGCAACGCGAACACATAA
* *
536 ATCGCAACGCGTATC-CGTAA
1 ATCGCAACGCG-AACACATAA
* * *
556 ATCGCAACGTGTATC-CGTAA
1 ATCGCAACGCG-AACACATAA
576 ATCGCAACGCG
1 ATCGCAACGCG
587 TATGGGTAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
19 1 0.02
20 60 0.95
21 2 0.03
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAACACATAA
Found at i:589 original size:20 final size:20
Alignment explanation
Indices: 514--857 Score: 402
Period size: 20 Copynumber: 17.5 Consensus size: 20
504 GCGAATATGA
* *
514 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
534 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
554 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
574 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
594 -AATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
613 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
633 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
653 AAA-CTGCAA--CGTAT-CGT
1 AAATC-GCAACGCGTATCCGT
670 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
690 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
710 -AATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
729 AAATCGCAACG-ATAATCTGT
1 AAATCGCAACGCGT-ATCCGT
749 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
769 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
789 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
* *
809 AAATCGCAACG-ATAACCGT
1 AAATCGCAACGCGTATCCGT
* * *
828 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
848 AAATCACAAC
1 AAATCGCAAC
858 ACTTAAATTT
Statistics
Matches: 280, Mismatches: 31, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
17 10 0.04
18 6 0.02
19 57 0.20
20 204 0.73
21 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:705 original size:116 final size:117
Alignment explanation
Indices: 514--857 Score: 410
Period size: 116 Copynumber: 2.9 Consensus size: 117
504 GCGAATATGA
* * *
514 AAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAAT
1 AAATCGCAACGCGTATC-CGTAAATCGCAA--CGTATCCGTAAATCGCAACGAGTATCCGTAAAT
** * * *
578 CGCAACGCGTATGGGTAATCGCAATGCGTATCCGTATATCGCAACGCGT-ATCCGT
63 CGCAACGCGTATCCGTAATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCCGT
*
633 AAATCGCAACGCGTATCCGTAAA-CTGCAACGTAT-CGTAAATCGCAACGCGTATCCGTAAATCG
1 AAATCGCAACGCGTATCCGTAAATC-GCAACGTATCCGTAAATCGCAACGAGTATCCGTAAATCG
* *
696 CAATGCGTATCCGTAATCGCAACGCGTATCCGTAAATCGCAACGATAATCTGT
65 CAACGCGTATCCGTAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
* *
749 AAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATC
1 AAATCGCAACGCGTATCCGTAAATCGCAACG-T-ATCCGTAAATCGCAACGAGTATCCGTAAATC
* * * * * *
814 GCAACG-ATAACCGTAAATCGCAACGAGAATCTGTAAATCACAAC
64 GCAACGCGTATCCGT-AATCGCAACGCGTATCCGTAAATCGCAAC
858 ACTTAAATTT
Statistics
Matches: 197, Mismatches: 20, Indels: 16
0.85 0.09 0.07
Matches are distributed among these distances:
115 1 0.01
116 101 0.51
117 7 0.04
118 9 0.05
119 77 0.39
120 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (117 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGTATCCGTAAATCGCAACGAGTATCCGTAAATCGC
AACGCGTATCCGTAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
Found at i:1573 original size:24 final size:24
Alignment explanation
Indices: 1534--1580 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1524 AAATTTGGTC
1534 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1558 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1581 GATTTCAGAA
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:4048 original size:19 final size:19
Alignment explanation
Indices: 4026--4298 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
4016 CGGAAAATAC
*
4026 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4045 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
4059 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
4079 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
4093 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4112 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4131 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
4145 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
4164 AATCGCAATGCG-AATGAA
1 AATCGCAATGCGAAATGAA
4182 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4201 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4220 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4239 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
4253 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4272 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4291 AATCGCAA
1 AATCGCAA
4299 CGAGATAATC
Statistics
Matches: 224, Mismatches: 8, Indels: 44
0.81 0.03 0.16
Matches are distributed among these distances:
14 38 0.17
15 1 0.00
16 14 0.06
17 12 0.05
18 19 0.08
19 127 0.57
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:4113 original size:33 final size:36
Alignment explanation
Indices: 4026--4320 Score: 297
Period size: 33 Copynumber: 8.4 Consensus size: 36
4016 CGGAAAATAC
* *
4026 AATCGCAACGCGAAATGAAAATCCCAA-C--ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAATGAA
*
4059 AATCGCAATGCGGAAATGAAAATCGCAA-CG-A-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAAGCGAATGAA
4093 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAA
* *
4131 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAA
4164 AATCGCAATGCG-AATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAA
4201 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAA
4239 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAA
*
4272 AATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAT
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAATGAA
4305 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
4321 TATAAACGCA
Statistics
Matches: 235, Mismatches: 9, Indels: 36
0.84 0.03 0.13
Matches are distributed among these distances:
33 97 0.41
34 31 0.13
35 13 0.06
36 12 0.05
37 31 0.13
38 51 0.22
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (36 bp):
AATCGCAATGCGAAATGAAAATCGCAAGCGAATGAA
Found at i:4286 original size:160 final size:156
Alignment explanation
Indices: 4026--4336 Score: 500
Period size: 160 Copynumber: 2.0 Consensus size: 156
4016 CGGAAAATAC
*
4026 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
4091 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
4156 GAAATTA-AAATCGCAATGCGAATGAA
131 GAAATTATAAA-CGCAATGCGAATGAA
* *
4182 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
* *
4246 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
61 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGC
*
4311 AATGCGAAATTATAAACGCATTGCGA
126 AATGCGAAATTATAAACGCAATGCGA
4337 TTTTCATTTC
Statistics
Matches: 143, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
156 25 0.17
158 1 0.01
160 98 0.69
161 19 0.13
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (156 bp):
AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
GAAATTATAAACGCAATGCGAATGAA
Found at i:4336 original size:52 final size:52
Alignment explanation
Indices: 4054--4320 Score: 428
Period size: 52 Copynumber: 5.0 Consensus size: 52
4044 AAATCCCAAC
4054 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
4107 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
4159 ATTAAAATCGCAATGCG-AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
4215 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
4267 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
4319 AT
1 AT
4321 TATAAACGCA
Statistics
Matches: 199, Mismatches: 9, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
51 14 0.07
52 118 0.59
53 19 0.10
55 3 0.02
56 31 0.16
57 14 0.07
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:4436 original size:19 final size:19
Alignment explanation
Indices: 4327--4428 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
4317 AAATTATAAA
4327 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
4346 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
4366 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
4382 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
4399 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
4418 CGCATTGCGAT
1 CGCATTGCGAT
4429 AGTCATTTTG
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:4553 original size:14 final size:14
Alignment explanation
Indices: 4534--4570 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4524 CATCAATTAC
4534 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4548 ACAAATCATCTTTT
1 ACAAATCAACTTTT
4562 ACAAATCAA
1 ACAAATCAA
4571 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:6524 original size:14 final size:14
Alignment explanation
Indices: 6505--6561 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
6495 GCGAAATGAA
*
6505 AATCGCAACGACAG
1 AATCGCAACGAAAG
6519 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
6536 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
6552 AATCGCAACG
1 AATCGCAACG
6562 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:6532 original size:33 final size:33
Alignment explanation
Indices: 6486--6577 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
6476 GCGAAACCAA
*
6486 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
6519 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
6552 AATCGCAACGCGAAATG-AAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
6578 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 9 0.16
33 47 0.84
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:6543 original size:19 final size:19
Alignment explanation
Indices: 6449--6582 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
6439 TAGTTTACTT
* *
6449 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
6469 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
6488 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
6507 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
6521 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
6540 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
6554 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
6572 TCGCAATGCGA
1 TCGCAACGCGA
6583 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
18 12 0.12
19 35 0.36
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:6600 original size:19 final size:19
Alignment explanation
Indices: 6578--6654 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
6568 GAAATCGCAA
6578 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
6597 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
6611 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
6630 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
6650 TGCGA
1 TGCGA
6655 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:6985 original size:93 final size:93
Alignment explanation
Indices: 6697--7164 Score: 867
Period size: 93 Copynumber: 5.1 Consensus size: 93
6687 TTGAATGGAT
*
6697 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACATTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
6762 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
6790 AAATTTACTTTCAACCAAAAGACAAAAC-AAGAC-AA-A-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
6851 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
6879 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
6944 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
6972 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA-A-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
7035 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
7063 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
7128 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
7156 AAATTTACT
1 AAATTTACT
7165 AAGCAATCTA
Statistics
Matches: 365, Mismatches: 4, Indels: 12
0.96 0.01 0.03
Matches are distributed among these distances:
89 80 0.22
90 6 0.02
91 93 0.25
92 8 0.02
93 178 0.49
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:7109 original size:184 final size:182
Alignment explanation
Indices: 6697--7164 Score: 891
Period size: 184 Copynumber: 2.6 Consensus size: 182
6687 TTGAATGGAT
*
6697 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACATTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
6762 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAGACAAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAGACAAAT
6827 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
6879 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
6944 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAGAC-AA
*
7009 ATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
129 ATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
7063 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
7128 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
7165 AAGCAATCTA
Statistics
Matches: 281, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
182 120 0.43
183 5 0.02
184 156 0.56
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (182 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAGACAAAT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:8880 original size:14 final size:14
Alignment explanation
Indices: 8861--8950 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
8851 TTGAAATGAA
8861 AATCGCAACGAGAG
1 AATCGCAACGAGAG
8875 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
8892 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
8908 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
8927 AATCGCAACGAGAT
1 AATCGCAACGAGAG
8941 AATCGCAACG
1 AATCGCAACG
8951 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:8898 original size:33 final size:33
Alignment explanation
Indices: 8853--8967 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
8843 TCTTTTGGTT
8853 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
8886 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
8919 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
8952 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
8968 TGCGATTTGG
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:8899 original size:19 final size:18
Alignment explanation
Indices: 8860--8972 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
8850 GTTGAAATGA
8860 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
8875 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
8892 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
8908 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
8925 AAAATCGCAA--CGAGAT-
1 -AAATCGCAACGCGAGATG
*
8941 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
8958 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
8973 TTTGGTTTCG
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:9002 original size:14 final size:14
Alignment explanation
Indices: 8983--9039 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
8973 TTTGGTTTCG
8983 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
8997 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
9016 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
9030 CGTTGCGATT
1 CGTTGCGATT
9040 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:9021 original size:19 final size:19
Alignment explanation
Indices: 8997--9085 Score: 89
Period size: 19 Copynumber: 4.9 Consensus size: 19
8987 GCGATTCTCT
8997 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
9016 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
9030 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
9049 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
9069 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
9086 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:9077 original size:39 final size:33
Alignment explanation
Indices: 8978--9085 Score: 162
Period size: 33 Copynumber: 3.1 Consensus size: 33
8968 TGCGATTTGG
8978 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
9011 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
9044 TTTCGCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTT--G-C-G--ATTCTCTCGTTGCGATTTTCA
9083 TTT
1 TTT
9086 ATCTCGTTGC
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
33 42 0.61
35 1 0.01
36 1 0.01
37 1 0.01
39 24 0.35
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.45
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:9219 original size:33 final size:33
Alignment explanation
Indices: 9177--9247 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
9167 AATACTAACT
*
9177 TGAAAATCGCAACGAGAGAATAGCAACACGAAA
1 TGAAAATCGCAACGACAGAATAGCAACACGAAA
* * *
9210 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACACGAAA
9243 TGAAA
1 TGAAA
9248 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:9481 original size:22 final size:22
Alignment explanation
Indices: 9429--9483 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
9419 TGGTTGTGAG
**
9429 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
9451 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
9473 GGATTTCTTCG
1 GGATTTCTTCG
9484 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:9653 original size:20 final size:20
Alignment explanation
Indices: 9628--9820 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
9618 CTTTAAATAT
9628 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
9648 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
9670 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
9689 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
9709 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
9729 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
9749 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
9769 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
9789 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
9809 CGCGTTGCGATT
1 CGCGTTGCGATT
9821 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:9815 original size:60 final size:60
Alignment explanation
Indices: 9628--9820 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
9618 CTTTAAATAT
**
9628 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
9689 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
9749 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
9809 CGCGTTGCGATT
1 CGCGTTGCGATT
9821 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:9901 original size:20 final size:20
Alignment explanation
Indices: 9876--9927 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
9866 AAGAATCGCG
*
9876 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
9896 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
9916 TTGCGATTCTGG
1 TTGCGATTCTGG
9928 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:10478 original size:21 final size:22
Alignment explanation
Indices: 10454--10508 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
10444 AAAGAAAAGG
* *
10454 TGTCATAAAGGT-ATAAAAACA
1 TGTCATAAAAGTAAGAAAAACA
10475 TGTCATAAAAGTAGAGAAAAACA
1 TGTCATAAAAGTA-AGAAAAACA
10498 TGTCATAAAAG
1 TGTCATAAAAG
10509 CATAGTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 11 0.37
23 19 0.63
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.22
Consensus pattern (22 bp):
TGTCATAAAAGTAAGAAAAACA
Found at i:10532 original size:37 final size:36
Alignment explanation
Indices: 10466--10535 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
10456 TCATAAAGGT
*
10466 ATAAAAACATGTCATAAAAGTAGAGAAAAACATGTC
1 ATAAAAACATGTCATAAAAGTAGAAAAAAACATGTC
*
10502 ATAAAAGCATAGTCATTAAAAGTA-AAAAAAACAT
1 ATAAAAACAT-GTCA-TAAAAGTAGAAAAAAACAT
10536 TATAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 9 0.30
37 13 0.43
38 8 0.27
ACGTcount: A:0.59, C:0.10, G:0.11, T:0.20
Consensus pattern (36 bp):
ATAAAAACATGTCATAAAAGTAGAAAAAAACATGTC
Found at i:10544 original size:38 final size:36
Alignment explanation
Indices: 10466--10545 Score: 90
Period size: 38 Copynumber: 2.2 Consensus size: 36
10456 TCATAAAGGT
* * *
10466 ATAAAAACATGTCATAAAAGTAGAGAAAAACATGTC
1 ATAAAAACATGTCATAAAAGTAGAAAAAAACATATA
*
10502 ATAAAAGCATAGTCATTAAAAGTA-AAAAAAACATTATA
1 ATAAAAACAT-GTCA-TAAAAGTAGAAAAAAACA-TATA
10540 ATAAAA
1 ATAAAA
10546 TACTAATGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 9 0.24
37 12 0.32
38 16 0.43
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
ATAAAAACATGTCATAAAAGTAGAAAAAAACATATA
Found at i:19293 original size:34 final size:34
Alignment explanation
Indices: 19218--19291 Score: 141
Period size: 33 Copynumber: 2.2 Consensus size: 34
19208 AAGATTATGC
19218 TTTTTTTAAATAAAAAAAAAATCATTTTTCCTCA
1 TTTTTTTAAATAAAAAAAAAATCATTTTTCCTCA
19252 TTTTTTTAAAT-AAAAAAAAATCATTTTTCCTCA
1 TTTTTTTAAATAAAAAAAAAATCATTTTTCCTCA
19285 TTTTTTT
1 TTTTTTT
19292 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:20124 original size:52 final size:52
Alignment explanation
Indices: 20062--20164 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
20052 AAATTGGACA
20062 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
* *
20114 CATAGAAATAGGAGATTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
20165 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:24709 original size:52 final size:52
Alignment explanation
Indices: 24647--24749 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
24637 AAATTGGACA
24647 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
* *
24699 CATAGAAATAGGAGATTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
24750 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:27025 original size:3 final size:3
Alignment explanation
Indices: 27019--27110 Score: 157
Period size: 3 Copynumber: 30.7 Consensus size: 3
27009 TTTTTATCCA
* *
27019 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
27067 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
27111 AATATATATT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:27122 original size:11 final size:11
Alignment explanation
Indices: 27106--27137 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
27096 TTATTATTAT
27106 TATTAAATATA
1 TATTAAATATA
27117 TATTAAATATA
1 TATTAAATATA
27128 TATATAAATA
1 TAT-TAAATA
27138 ATTAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:28600 original size:13 final size:13
Alignment explanation
Indices: 28584--28630 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
28574 ATATAATAAA
28584 TAAATATTTATTT
1 TAAATATTTATTT
*
28597 TAAATAAATTATTT
1 TAAAT-ATTTATTT
28611 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
28624 TCAATAT
1 TAAATAT
28631 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:31022 original size:20 final size:21
Alignment explanation
Indices: 30993--31032 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
30983 TTTCGGGCTA
*
30993 GGGAATCGGTA-CCCTTCAAG
1 GGGAACCGGTACCCCTTCAAG
31013 GGGAACCGGTACCCCTTCAA
1 GGGAACCGGTACCCCTTCAA
31033 CGAATATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (21 bp):
GGGAACCGGTACCCCTTCAAG
Found at i:31094 original size:68 final size:68
Alignment explanation
Indices: 31012--31164 Score: 193
Period size: 68 Copynumber: 2.2 Consensus size: 68
31002 TACCCTTCAA
* * * *
31012 GGGGAACCGGTACCCCTTCAACGAATATG-ATTTCCAG-TATGCTAGAGGGGAATCGGTACCCCC
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAT-TGCTAGAGGGGAATCGATACCCCC
31075 AGGGG
65 A-GGG
* * *
31080 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGATTGCTAGAGGGGAATCGATACCCCCA
31145 GGG
66 GGG
* *
31148 GAGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
31165 ATGAGAAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
68 43 0.58
69 30 0.41
70 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.28, T:0.19
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGATTGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:31501 original size:29 final size:29
Alignment explanation
Indices: 31467--31538 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
31457 CATATTATGA
** *
31467 TACATGACATGAATTTGTCTTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
31496 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
31525 TACATGACATGAAT
1 TACATGACATGAAT
31539 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:31594 original size:30 final size:31
Alignment explanation
Indices: 31552--31611 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
31542 CAGAAAAGTT
*
31552 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
31583 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
31612 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:31905 original size:22 final size:22
Alignment explanation
Indices: 31831--31897 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
31821 TTATGGACAT
31831 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
31853 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
31875 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
31897 A
1 A
31898 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:37966 original size:21 final size:21
Alignment explanation
Indices: 37940--37982 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
37930 TTTTCGGGCT
*
37940 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGGTACCCATTCA
*
37961 AGGGGAACCGGTACCCCTTCA
1 AGGGGAACCGGTACCCATTCA
37982 A
1 A
37983 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:38057 original size:67 final size:68
Alignment explanation
Indices: 37962--38113 Score: 200
Period size: 68 Copynumber: 2.2 Consensus size: 68
37952 ACCCATTCAA
* * * *
37962 GGGGAACCGGTACCCCTTCAACGAATATG-ATTTCCAG-TATGCTAGAGGGGAATCGGTACCCCC
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAT-TGCTAGAGGGGAATCGATACCCCC
38025 AGGG
65 AGGG
* * *
38029 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGATTGCTAGAGGGGAATCGATACCCCCA
38094 GGG
66 GGG
* *
38097 GAGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
38114 ATGAGAAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
67 25 0.34
68 48 0.65
69 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.19
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGATTGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:38450 original size:29 final size:29
Alignment explanation
Indices: 38416--38487 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
38406 CATATTATGA
** *
38416 TACATGACATGAATTTGTCTTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
38445 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
38474 TACATGACATGAAT
1 TACATGACATGAAT
38488 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:38544 original size:30 final size:31
Alignment explanation
Indices: 38502--38561 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
38492 AGAAAAAGTT
*
38502 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
38533 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
38562 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:38809 original size:22 final size:22
Alignment explanation
Indices: 38781--38825 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
38771 TTATGGACAT
38781 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
38803 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
38825 A
1 A
38826 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:38833 original size:22 final size:22
Alignment explanation
Indices: 38781--38833 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
38771 TTATGGACAT
*
38781 AATTCTACGGGCACTTCGGTGC
1 AATTATACGGGCACTTCGGTGC
*
38803 AATTCTACGGGCACTTCGGTGC
1 AATTATACGGGCACTTCGGTGC
*
38825 ATTTATACG
1 AATTATACG
38834 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:51175 original size:84 final size:84
Alignment explanation
Indices: 51034--51505 Score: 908
Period size: 84 Copynumber: 5.6 Consensus size: 84
51024 TGGAACAAAT
51034 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
51099 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
*
51118 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
51183 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
51202 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
51267 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
51286 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
51351 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
51370 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
51435 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
* *
51454 ATAAGGATGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCT
1 ATAATG-TGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
51506 AGTTTGGTAA
Statistics
Matches: 383, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
84 339 0.89
85 44 0.11
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.35
Consensus pattern (84 bp):
ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACC
AATCATTGAATTTGGAAGA
Found at i:52474 original size:113 final size:113
Alignment explanation
Indices: 52253--52689 Score: 743
Period size: 113 Copynumber: 3.9 Consensus size: 113
52243 TCGAATCCAC
* *
52253 TTGATGGATCAGT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 TTGATGGATTA-TCTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
52317 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
64 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
*
52367 TTGATGGATTATCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
52432 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTTAATCCATCAT
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
*
52480 TTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
52545 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
*
52593 TTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
52657 AGTTCATAATAAGAAGAATTTGTTCAACTTTTT
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTT
52690 GCATAATTCT
Statistics
Matches: 308, Mismatches: 14, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
112 71 0.23
113 224 0.73
114 13 0.04
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
Found at i:53014 original size:3 final size:3
Alignment explanation
Indices: 53008--53093 Score: 145
Period size: 3 Copynumber: 28.7 Consensus size: 3
52998 TTTTTATCCA
* *
53008 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAC TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
53056 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
53094 AATATATATT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:53105 original size:11 final size:11
Alignment explanation
Indices: 53089--53120 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
53079 TTATTATTAT
53089 TATTAAATATA
1 TATTAAATATA
53100 TATTAAATATA
1 TATTAAATATA
53111 TATATAAATA
1 TAT-TAAATA
53121 ATTAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:54576 original size:13 final size:13
Alignment explanation
Indices: 54560--54606 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
54550 ATATAATAAA
54560 TAAATATTTATTT
1 TAAATATTTATTT
*
54573 TAAATAAATTATTT
1 TAAAT-ATTTATTT
54587 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
54600 TCAATAT
1 TAAATAT
54607 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:55484 original size:21 final size:21
Alignment explanation
Indices: 55460--55499 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
55450 TTGGTTTTCC
55460 GGAAAATGAATTACTGGAACT
1 GGAAAATGAATTACTGGAACT
55481 GGAAAATGAATTACTGGAA
1 GGAAAATGAATTACTGGAA
55500 TTTAAATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.23
Consensus pattern (21 bp):
GGAAAATGAATTACTGGAACT
Found at i:55519 original size:14 final size:15
Alignment explanation
Indices: 55478--55523 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
55468 AATTACTGGA
*
55478 ACTGGAAAATGAATT
1 ACTGGAAAATAAATT
**
55493 ACTGGAATTTAAATT
1 ACTGGAAAATAAATT
55508 -CTGGAAAATAAATT
1 ACTGGAAAATAAATT
55522 AC
1 AC
55524 ATTTCTGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (15 bp):
ACTGGAAAATAAATT
Found at i:55778 original size:49 final size:50
Alignment explanation
Indices: 55681--55779 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
55671 TACAAATATT
*
55681 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
55731 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
55780 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 9 0.21
49 25 0.60
50 8 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:55911 original size:23 final size:20
Alignment explanation
Indices: 55864--55911 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 20
55854 AATAGTGTTA
55864 TATTATATTTTTAAAATATT
1 TATTATATTTTTAAAATATT
* *
55884 AATTAGTATATTTTAAATATCTT
1 TATTA-TAT-TTTTAAA-ATATT
55907 TATTA
1 TATTA
55912 AAATATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.18
21 3 0.14
22 7 0.32
23 8 0.36
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TATTATATTTTTAAAATATT
Found at i:56056 original size:22 final size:23
Alignment explanation
Indices: 56031--56074 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
56021 GATTATTTTA
56031 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
56053 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
56075 AATAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:56317 original size:42 final size:42
Alignment explanation
Indices: 56266--56380 Score: 153
Period size: 42 Copynumber: 2.8 Consensus size: 42
56256 ATCAATTACA
*
56266 TTCCGGAAAATCAATTACGTAAAACAAACACGGGAAAACATT
1 TTCCGGAAAATCAATTACGTGAAACAAACACGGGAAAACATT
* * *
56308 TTCCGGAAAA-CGAACTACATGAAACAAATACGGGAAAACATT
1 TTCCGGAAAATC-AATTACGTGAAACAAACACGGGAAAACATT
* *
56350 TTCC-AAAAATGAATTACGTGAAACAAACACG
1 TTCCGGAAAATCAATTACGTGAAACAAACACG
56381 AAAATTTGAG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
41 22 0.35
42 40 0.65
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAATCAATTACGTGAAACAAACACGGGAAAACATT
Done.