Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002995.1 Hibiscus syriacus cultivar Beakdansim tig00006195_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: 88627
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:393 original size:19 final size:19
Alignment explanation
Indices: 371--641 Score: 343
Period size: 19 Copynumber: 15.4 Consensus size: 19
361 CGGAAATTAC
*
371 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
390 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
404 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
423 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
437 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
456 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
475 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
489 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
507 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
525 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
544 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
563 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
582 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
596 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
615 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
634 AATCGCAA
1 AATCGCAA
642 CGAGAGATCG
Statistics
Matches: 223, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 40 0.18
15 2 0.01
16 10 0.04
17 10 0.04
18 37 0.17
19 124 0.56
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:455 original size:52 final size:52
Alignment explanation
Indices: 399--662 Score: 444
Period size: 52 Copynumber: 5.0 Consensus size: 52
389 AAATCCCAAC
399 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
451 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
503 ATG-AAATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
558 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
610 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG-ATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
661 AT
1 AT
663 TATAAACGCA
Statistics
Matches: 201, Mismatches: 4, Indels: 15
0.91 0.02 0.07
Matches are distributed among these distances:
50 9 0.04
51 33 0.16
52 109 0.54
53 1 0.00
54 1 0.00
55 21 0.10
56 18 0.09
57 9 0.04
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:709 original size:18 final size:19
Alignment explanation
Indices: 669--717 Score: 82
Period size: 18 Copynumber: 2.6 Consensus size: 19
659 AAATTATAAA
669 CGCATTGCGATTTTCATTTT
1 CGCATTGCGA-TTTCATTTT
689 CGCATTGCGATTTCA-TTT
1 CGCATTGCGATTTCATTTT
707 CGCATTGCGAT
1 CGCATTGCGAT
718 AGTCATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 14 0.48
19 5 0.17
20 10 0.34
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTCATTTT
Found at i:842 original size:14 final size:14
Alignment explanation
Indices: 823--858 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
813 CATCAATTAC
823 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
837 ACAAATCATCTTTT
1 ACAAATCAACTTTT
851 AC-AATCAA
1 ACAAATCAA
859 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2852 original size:14 final size:14
Alignment explanation
Indices: 2833--2889 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2823 GCGAAATGAA
*
2833 AATCGCAACGACAG
1 AATCGCAACGAAAG
2847 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2864 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2880 AATCGCAACG
1 AATCGCAACG
2890 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:2860 original size:33 final size:33
Alignment explanation
Indices: 2814--2906 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2804 GCGAAACCAA
*
2814 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2847 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2880 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2907 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:2871 original size:19 final size:19
Alignment explanation
Indices: 2777--2911 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2767 TAGTTTACTT
* *
2777 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2797 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2816 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2835 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2849 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2868 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2882 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2901 TCGCAATGCGA
1 TCGCAACGCGA
2912 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:2929 original size:19 final size:19
Alignment explanation
Indices: 2907--3035 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2897 AAAATCGCAA
2907 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2926 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2940 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2959 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2973 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2992 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3011 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3031 TGCGA
1 TGCGA
3036 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2949 original size:33 final size:33
Alignment explanation
Indices: 2907--2998 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2897 AAAATCGCAA
2907 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2940 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2973 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2999 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3199 original size:93 final size:93
Alignment explanation
Indices: 3083--3458 Score: 727
Period size: 93 Copynumber: 4.1 Consensus size: 93
3073 ATGGATTGCA
*
3083 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAAAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3147 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3175 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3240 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3268 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3333 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3361 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
3426 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3454 TTACT
1 TTACT
3459 AAGCAATCTA
Statistics
Matches: 281, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 277 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:5178 original size:14 final size:14
Alignment explanation
Indices: 5159--5248 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
5149 GTTGAAATGA
5159 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5173 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
5192 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5206 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5225 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5239 AATCGCAACG
1 AATCGCAACG
5249 CGAAATAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5197 original size:19 final size:19
Alignment explanation
Indices: 5173--5270 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
5163 GCAACGAGAG
*
5173 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
5192 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
5206 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
5225 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
5239 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
*
5258 AATCGCAATGCGA
1 AATCGCAACGCGA
5271 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:5198 original size:33 final size:33
Alignment explanation
Indices: 5152--5265 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
5142 TCTTTTGGTT
5152 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
5184 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5217 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
5250 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
5266 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 6 0.08
33 72 0.92
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:5301 original size:14 final size:14
Alignment explanation
Indices: 5282--5339 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 14
5272 TTTGGTTTCG
5282 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5296 CGTTGCGATTTTTCATTTCG
1 CGTTGCGA---TTC---TCT
5316 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5330 CGTTGCGATT
1 CGTTGCGATT
5340 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
14 20 0.56
17 6 0.17
20 10 0.28
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5374 original size:20 final size:20
Alignment explanation
Indices: 5323--5376 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
5313 TCGCGTTGCG
***
5323 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
*
5343 ATT-TCGCGTTGCGACAGTC
1 ATTCTCTCGTTGCGACAGTC
5362 ATTCTCTCGTTGCGA
1 ATTCTCTCGTTGCGA
5377 TTTTCATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.13, C:0.26, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:5377 original size:39 final size:33
Alignment explanation
Indices: 5266--5385 Score: 159
Period size: 34 Copynumber: 3.4 Consensus size: 33
5256 AAAATCGCAA
**
5266 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5299 TGCGATTTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGA-TTTTCATTTCGCGTTGCGATTCTCTCGT
5333 TGCGATTTTCATTTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCGT
5372 TGCGATTTTCATTT
1 TGCGATTTTCATTT
5386 ATCTCGTTGC
Statistics
Matches: 78, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
33 20 0.26
34 31 0.40
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:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:5383 original size:20 final size:20
Alignment explanation
Indices: 5289--5397 Score: 90
Period size: 20 Copynumber: 5.8 Consensus size: 20
5279 TCGCGTTGCG
5289 ATTCTCTCGTTGCGATTTTTC
1 ATTCTCTCGTTGCGA-TTTTC
*
5310 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
5323 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* ***
5343 ATT-TCGCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
5362 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
5382 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
5398 CTCTTCTGCA
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
13 3 0.04
14 9 0.13
19 15 0.22
20 25 0.37
21 16 0.24
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:5523 original size:33 final size:33
Alignment explanation
Indices: 5477--5547 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5467 AATACTAACT
5477 TGAAAATCACAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCACAACGAGAGAATAGCAACGCGAAA
* * *
5510 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCACAACGAGAGAATAGCAACGCGAAA
5543 TGAAA
1 TGAAA
5548 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:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCACAACGAGAGAATAGCAACGCGAAA
Found at i:5781 original size:22 final size:22
Alignment explanation
Indices: 5729--5783 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5719 TGGTTGTGAG
**
5729 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
5751 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
5773 GGATTTCTTCG
1 GGATTTCTTCG
5784 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:5955 original size:20 final size:20
Alignment explanation
Indices: 5930--6123 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
5920 CTTTAAATAT
5930 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5950 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
5972 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
5991 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
6011 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
6031 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
6051 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
6071 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
6091 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
6111 CGCGTTGCGATTT
1 CGCGTTGCGATTT
6124 TGGAAAATCG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:6095 original size:60 final size:60
Alignment explanation
Indices: 5932--6103 Score: 236
Period size: 60 Copynumber: 2.9 Consensus size: 60
5922 TTAAATATCG
* ** *
5932 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATACG
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACCGATACA
* *** * *
5993 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
*
6053 CGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTT
6104 TCATATTCGC
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.73
61 26 0.27
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
Found at i:6117 original size:60 final size:60
Alignment explanation
Indices: 5929--6244 Score: 232
Period size: 60 Copynumber: 5.2 Consensus size: 60
5919 GCTTTAAATA
* ** * *
5929 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTTCAGAT
* * *** * * *
5990 ACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * *
6050 ACACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * * * *
6110 TCGCGTTGCGATTT-TGGAAAATCGCAATGCGAATT-TG-ACTATCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTACGG-ATA-CGCATTGCGATTTATGTA-T-TCGCGTTGCGATTTTC-AGAT
* * ** * * *
6172 TCGCGTTGCGATTT-TGGACACTG-ATTTGCGATTCTGGGGA-TCGCGTTGCGATTTTTA-TT
1 TCGCGTTGCGATTTACGGATAC-GCA-TTGCGATT-TATGTATTCGCGTTGCGATTTTCAGAT
6231 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
6245 TGTTGGTCAT
Statistics
Matches: 207, Mismatches: 38, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
59 16 0.08
60 92 0.44
61 77 0.37
62 20 0.10
63 1 0.00
64 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
Found at i:6140 original size:21 final size:20
Alignment explanation
Indices: 6090--6187 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
6080 ATTTATGTGT
* * * *
6090 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
6110 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
6131 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
6151 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
6172 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
6188 GACACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:6182 original size:41 final size:41
Alignment explanation
Indices: 6090--6246 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
6080 ATTTATGTGT
* * *
6090 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
6131 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
6172 TCGCGTTGCGATTTTGGACACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
6212 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
6247 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:6420 original size:37 final size:36
Alignment explanation
Indices: 6377--6478 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
6367 ATAGTAGAAC
6377 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
6414 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
6448 TCTATCATATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
6479 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 32 0.53
37 28 0.47
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:6575 original size:21 final size:21
Alignment explanation
Indices: 6538--6577 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6528 ATGGGCATGG
*
6538 GACCCGAGTCCGACGGGTTCC
1 GACCCGAGCCCGACGGGTTCC
6559 GACCCGA-CCCGATCGGGTT
1 GACCCGAGCCCGA-CGGGTT
6578 GGGTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.15, C:0.38, G:0.33, T:0.15
Consensus pattern (21 bp):
GACCCGAGCCCGACGGGTTCC
Found at i:7477 original size:32 final size:32
Alignment explanation
Indices: 7412--7482 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
7402 ATAGTCAATG
* * ** * *
7412 AACTTTTAGGACATTTTTACTTTAGTCATTAA
1 AACTTTTAGAACATTTTCACTACAGTAACTAA
7444 AACTTTTAGAACATTTTCACTACAGTAACTAA
1 AACTTTTAGAACATTTTCACTACAGTAACTAA
7476 AA-TTTTA
1 AACTTTTA
7483 ATTCGTTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 5 0.15
32 28 0.85
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (32 bp):
AACTTTTAGAACATTTTCACTACAGTAACTAA
Found at i:12509 original size:31 final size:31
Alignment explanation
Indices: 12466--12526 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
12456 TGTGTGACCT
* *
12466 ATTTGTAATCTTATTAATAACTGGATGACTC
1 ATTTATAATCTTACTAATAACTGGATGACTC
* *
12497 ATTTATAATCTTACTAGTAATTGGATGACT
1 ATTTATAATCTTACTAATAACTGGATGACT
12527 TATGGTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (31 bp):
ATTTATAATCTTACTAATAACTGGATGACTC
Found at i:13787 original size:14 final size:14
Alignment explanation
Indices: 13768--13811 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
13758 TATAATTGGA
13768 TTTAGGGTTTAAGG
1 TTTAGGGTTTAAGG
*
13782 TTTAGGGTTTAAGA
1 TTTAGGGTTTAAGG
*
13796 TTTATGGTTT-AGG
1 TTTAGGGTTTAAGG
13809 TTT
1 TTT
13812 TAAGGCTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 5 0.19
14 22 0.81
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (14 bp):
TTTAGGGTTTAAGG
Found at i:13799 original size:21 final size:21
Alignment explanation
Indices: 13775--13815 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13765 GGATTTAGGG
13775 TTTAAGGTTTAGGGTTTAAGA
1 TTTAAGGTTTAGGGTTTAAGA
* *
13796 TTTATGGTTTAGGTTTTAAG
1 TTTAAGGTTTAGGGTTTAAG
13816 GCTTAGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (21 bp):
TTTAAGGTTTAGGGTTTAAGA
Found at i:13825 original size:21 final size:21
Alignment explanation
Indices: 13780--13825 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
13770 TAGGGTTTAA
* *
13780 GGTTTAGGGTTTAAGATTTAT
1 GGTTTAGGGTTTAAGACTTAG
* *
13801 GGTTTAGGTTTTAAGGCTTAG
1 GGTTTAGGGTTTAAGACTTAG
13822 GGTT
1 GGTT
13826 AATTACAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.33, T:0.46
Consensus pattern (21 bp):
GGTTTAGGGTTTAAGACTTAG
Found at i:13948 original size:11 final size:11
Alignment explanation
Indices: 13932--13993 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
13922 GTATTATAGA
13932 ATTTTTAATAT
1 ATTTTTAATAT
13943 ATTTTTAA-A-
1 ATTTTTAATAT
13952 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
13963 ATCAATAATGT
1 ATTTTTAATAT
13974 A-TTTTAATAT
1 ATTTTTAATAT
13984 ATTTTTAATA
1 ATTTTTAATA
13994 ATGTAATGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
9 5 0.13
10 14 0.36
11 20 0.51
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:15637 original size:16 final size:16
Alignment explanation
Indices: 15616--15648 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
15606 TAATAAATAA
15616 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
*
15632 ACGAACATAAACGAAC
1 ACGAACATAAACAAAC
15648 A
1 A
15649 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.24, G:0.09, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:15739 original size:20 final size:20
Alignment explanation
Indices: 15714--15753 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
15704 ATTTAAAGGA
* *
15714 TAAATGAATATAAACGAACG
1 TAAATGAACACAAACGAACG
15734 TAAATGAACACAAACGAACG
1 TAAATGAACACAAACGAACG
15754 AACATAATAA
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:0.55, C:0.15, G:0.15, T:0.15
Consensus pattern (20 bp):
TAAATGAACACAAACGAACG
Found at i:15779 original size:23 final size:23
Alignment explanation
Indices: 15750--15803 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
15740 AACACAAACG
* *
15750 AACGAACATAATAAATGAACATA
1 AACGAACACAATAAACGAACATA
*
15773 AACGAACACAATAAACGGACATA
1 AACGAACACAATAAACGAACATA
*
15796 AACAAACA
1 AACGAACA
15804 ACACAAACAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.61, C:0.19, G:0.09, T:0.11
Consensus pattern (23 bp):
AACGAACACAATAAACGAACATA
Found at i:15811 original size:23 final size:21
Alignment explanation
Indices: 15768--15823 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 21
15758 TAATAAATGA
* *
15768 ACATAAACGAACACAATAAAC
1 ACATAAACAAACACAACAAAC
15789 GGACATAAACAAACA-ACACAAAC
1 --ACATAAACAAACACA-ACAAAC
*
15812 ACAAAAACAAAC
1 ACATAAACAAAC
15824 TTATTCGAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 11 0.38
22 1 0.03
23 17 0.59
ACGTcount: A:0.64, C:0.25, G:0.05, T:0.05
Consensus pattern (21 bp):
ACATAAACAAACACAACAAAC
Found at i:38341 original size:37 final size:37
Alignment explanation
Indices: 38281--38385 Score: 93
Period size: 37 Copynumber: 2.8 Consensus size: 37
38271 CCTTTTCGTC
* * **
38281 CTACTAGGATTCAAATTTTTAAAAATAGGATAAAATT
1 CTACTAGGATTTAAAATCCTAAAAATAGGATAAAATT
* * * * * *
38318 TTGCTAGGATTTAAAATCCTAAAAGTATGATAGAGTT
1 CTACTAGGATTTAAAATCCTAAAAATAGGATAAAATT
* * *
38355 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAAATCCTAAAAATAGGAT
38386 CCACAAGCAC
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (37 bp):
CTACTAGGATTTAAAATCCTAAAAATAGGATAAAATT
Found at i:38955 original size:24 final size:24
Alignment explanation
Indices: 38928--39042 Score: 79
Period size: 23 Copynumber: 5.1 Consensus size: 24
38918 CTTTGCATTT
38928 TTATTATTACTATTATATTTATTA
1 TTATTATTACTATTATATTTATTA
* **
38952 TTATTTTTACTATTATATTT-TCC
1 TTATTATTACTATTATATTTATTA
*
38975 TT-TTATT-CTACT-TATTTA-TA
1 TTATTATTACTATTATATTTATTA
*
38995 TTATATATGTA-TATT-TTTTTA-TA
1 TTAT-TAT-TACTATTATATTTATTA
*
39018 TT-TTATTATTATTATATATT-TTA
1 TTATTATTACTATTATAT-TTATTA
39041 TT
1 TT
39043 TTCTCTTTCT
Statistics
Matches: 72, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
20 9 0.12
21 12 0.17
22 10 0.14
23 22 0.31
24 19 0.26
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (24 bp):
TTATTATTACTATTATATTTATTA
Found at i:39024 original size:28 final size:27
Alignment explanation
Indices: 38987--39039 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 27
38977 TTATTCTACT
*
38987 TATTTATATTATATATGTATATTTTTTTA
1 TATTTATATTAT-TAT-TATATATTTTTA
39016 TATTT-TATTATTATTATATATTTT
1 TATTTATATTATTATTATATATTTT
39040 ATTTTCTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.39
27 3 0.13
28 6 0.26
29 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (27 bp):
TATTTATATTATTATTATATATTTTTA
Found at i:39027 original size:18 final size:18
Alignment explanation
Indices: 38926--39042 Score: 62
Period size: 18 Copynumber: 6.4 Consensus size: 18
38916 TTCTTTGCAT
* *
38926 TTTTATTATTACTATTATA
1 TTTTATTATT-TTTTTATA
38945 -TTTATTATTATTTTTACTA
1 TTTTATTATT-TTTTTA-TA
* **
38964 TTATATT-TTCCTTT-TA
1 TTTTATTATTTTTTTATA
* *
38980 TTCTACTTATTTATATTATA
1 TTTTA-TTATTT-TTTTATA
*
39000 TATGTA-TATTTTTTTATA
1 T-TTTATTATTTTTTTATA
* *
39018 TTTTATTATTATTATATA
1 TTTTATTATTTTTTTATA
39036 TTTTATT
1 TTTTATT
39043 TTCTCTTTCT
Statistics
Matches: 76, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
16 6 0.08
17 5 0.07
18 43 0.57
19 11 0.14
20 8 0.11
21 3 0.04
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.67
Consensus pattern (18 bp):
TTTTATTATTTTTTTATA
Found at i:39070 original size:11 final size:11
Alignment explanation
Indices: 39056--39096 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
39046 TCTTTCTTTT
39056 TATTATTCTTG
1 TATTATTCTTG
39067 TATTATTACTTG
1 TATTATT-CTTG
* *
39079 TATTATTTTTA
1 TATTATTCTTG
39090 TATTATT
1 TATTATT
39097 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:39309 original size:2 final size:2
Alignment explanation
Indices: 39304--39334 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39294 TATATTTTAC
39304 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39335 TCTACACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39497 original size:2 final size:2
Alignment explanation
Indices: 39490--39516 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39480 GTATTGTTAT
39490 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
39517 TGTAATTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39613 original size:2 final size:2
Alignment explanation
Indices: 39608--39646 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
39598 TTTTTTATTT
39608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39647 TATTCGTACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44388 original size:15 final size:16
Alignment explanation
Indices: 44359--44392 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
44349 AAAAGAAGCT
44359 AAAAAGAAGAAAACAA
1 AAAAAGAAGAAAACAA
*
44375 AAAAAGAA-AGAACAA
1 AAAAAGAAGAAAACAA
44390 AAA
1 AAA
44393 TCAAAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAGAAGAAAACAA
Found at i:45043 original size:22 final size:22
Alignment explanation
Indices: 45010--45086 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
45000 GCTACCCCAT
45010 CAAACCGT-TGAGCATCAAATGC
1 CAAACC-TATGAGCATCAAATGC
45032 CAAACCTATGAGCATCAAATGC
1 CAAACCTATGAGCATCAAATGC
* *
45054 CAAGCCTTTGAGCATCAAATGC
1 CAAACCTATGAGCATCAAATGC
45076 CAAACCTATGA
1 CAAACCTATGA
45087 CCAAACATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 1 0.02
22 49 0.98
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (22 bp):
CAAACCTATGAGCATCAAATGC
Found at i:46400 original size:28 final size:26
Alignment explanation
Indices: 46349--46413 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 26
46339 CGTCATTTAA
*
46349 TTTATTAATT-TATATATATTTACTT
1 TTTATTTATTATATATATATTTACTT
46374 TTTATTTATTATATATATATTCATACTT
1 TTTATTTATTATATATATATT--TACTT
46402 TGTTA-TTATTAT
1 T-TTATTTATTAT
46414 TTTGTTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 9 0.26
26 10 0.29
28 13 0.37
29 3 0.09
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTATTTATTATATATATATTTACTT
Found at i:51103 original size:15 final size:14
Alignment explanation
Indices: 51086--51146 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 14
51076 ACAAAAAGGG
51086 CAAAAAAAAAAGAA
1 CAAAAAAAAAAGAA
51100 GCAAAAAAGAAGAA-AA
1 -CAAAAAA-AA-AAGAA
51116 CAAAAAAAGAAAGAA
1 CAAAAAAA-AAAGAA
51131 CAAAAATCAAAAAGAA
1 CAAAAA--AAAAAGAA
51147 AAGGGGACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.08
15 23 0.57
16 10 0.25
17 4 0.10
ACGTcount: A:0.79, C:0.08, G:0.11, T:0.02
Consensus pattern (14 bp):
CAAAAAAAAAAGAA
Found at i:51790 original size:22 final size:22
Alignment explanation
Indices: 51753--51832 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
51743 GCTACCCCAT
* *
51753 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGACCATCAAATGC
*
51775 CAAACCTATGACCATCAAATGC
1 CAAACCTTTGACCATCAAATGC
* *
51797 CAAACCTTTTAGCATCAAATGC
1 CAAACCTTTGACCATCAAATGC
*
51819 CAAATCTTTGACCA
1 CAAACCTTTGACCA
51833 AACATAATAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGACCATCAAATGC
Found at i:52267 original size:18 final size:19
Alignment explanation
Indices: 52244--52280 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
52234 TCAACATCAA
*
52244 ATATTGGGGCATT-TTTGG
1 ATATTGGAGCATTATTTGG
52262 ATATTGGAGCATTATTTGG
1 ATATTGGAGCATTATTTGG
52281 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.22, C:0.05, G:0.30, T:0.43
Consensus pattern (19 bp):
ATATTGGAGCATTATTTGG
Found at i:52758 original size:106 final size:106
Alignment explanation
Indices: 52573--53553 Score: 1426
Period size: 106 Copynumber: 9.3 Consensus size: 106
52563 CTCGAGAGTA
* * *
52573 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGTCAACGCAAGTTCAACTTCACAACAAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
52638 GACCGTTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
*
52679 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
52744 GACCGCTGGTTGTCAACAAACAACTTCTCAATTTCATATCC
66 GACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
* * *
52785 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGTCGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
52850 GACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
*
52891 AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
52956 GACCGCTGGTTGTCCATAAACAACTTC-CTAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCTC-AATTTCAGAGCC
*
52997 AATTTCAACTTAACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
53062 GACCGCTGGTTGTCAACAAACTACTTCTCAATTTTAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
*
53103 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * * *
53168 GACCGCTGGTTTTCAATAAACAATTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
* *
53209 AATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
53274 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
* * * *
53315 AATTTCAACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCTCAACTTCACGACGAAA
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACG-AA
* * *
53379 GGG-CGGCTGATTGTCAAC-AA-AA-TT-TC-A-TTCAGAGTC
64 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
* * * *
53415 AATTTTAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * * * ** *
53480 GACGGTTGGTTGTCAACAAATAATTTC-CTGGTTCCAGAGCC
66 GACCGCTGGTTGTCAACAAACAACTTCTC-AATTTCAGAGCC
*
53521 AATTTCAACTTCAC-GACGAAGGATATTAGACTC
1 AATTTCAACTTCACAG-CGAAGGATATTGGACTC
53554 GGAACAATGC
Statistics
Matches: 798, Mismatches: 63, Indels: 28
0.90 0.07 0.03
Matches are distributed among these distances:
99 5 0.01
100 74 0.09
101 4 0.01
102 3 0.00
103 5 0.01
104 2 0.00
105 5 0.01
106 694 0.87
107 6 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
Found at i:54339 original size:37 final size:37
Alignment explanation
Indices: 54282--54386 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
54272 CCTTTTCATC
*
54282 CTACTAGGATTCAAATTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
54319 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
54356 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
54387 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:54915 original size:2 final size:2
Alignment explanation
Indices: 54910--54939 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54900 GTTATTACCC
54910 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
54940 TTCTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54972 original size:21 final size:21
Alignment explanation
Indices: 54948--55056 Score: 68
Period size: 21 Copynumber: 5.2 Consensus size: 21
54938 ATTTCTTTTT
*
54948 TTATTATTAGTATTATATTTA
1 TTATTATTACTATTATATTTA
*
54969 TTATTTTTACTATTATATTT-
1 TTATTATTACTATTATATTTA
* *
54989 TCCTTTTATT-CTACT-TATTTA
1 T--TATTATTACTATTATATTTA
55010 TTATATATGTA-TATT-T-TTTA
1 TTAT-TAT-TACTATTATATTTA
* * *
55030 TATTTTATTATTATTATATTTT
1 T-TATTATTACTATTATATTTA
55052 TTATT
1 TTATT
55057 TTCTCTTTCT
Statistics
Matches: 68, Mismatches: 10, Indels: 20
0.69 0.10 0.20
Matches are distributed among these distances:
19 4 0.06
20 21 0.31
21 34 0.50
22 9 0.13
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATTATTACTATTATATTTA
Found at i:55053 original size:25 final size:27
Alignment explanation
Indices: 55006--55055 Score: 86
Period size: 25 Copynumber: 1.9 Consensus size: 27
54996 ATTCTACTTA
55006 TTTATTATATATGTATATTTTTTATAT
1 TTTATTATATATGTATATTTTTTATAT
55033 TTTATTAT-TAT-TATATTTTTTAT
1 TTTATTATATATGTATATTTTTTAT
55056 TTTCTCTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 12 0.52
26 3 0.13
27 8 0.35
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (27 bp):
TTTATTATATATGTATATTTTTTATAT
Found at i:55084 original size:11 final size:11
Alignment explanation
Indices: 55070--55110 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
55060 TCTTTCTTTT
55070 TATTATTCTTG
1 TATTATTCTTG
55081 TATTATTACTTG
1 TATTATT-CTTG
* *
55093 TATTATTTTTA
1 TATTATTCTTG
55104 TATTATT
1 TATTATT
55111 TATTTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:55224 original size:22 final size:21
Alignment explanation
Indices: 55199--55259 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 21
55189 TTTTTAGTGC
55199 TATTTTTATAATATTATACATA
1 TATTTTTATAATATTATAC-TA
55221 TATTTTCTATTAAT-TT-T-CTA
1 TATTTT-TA-TAATATTATACTA
*
55241 TATTTTTATTATCATTATA
1 TATTTTTATAAT-ATTATA
55260 TTATTTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 10 0.31
21 2 0.06
22 7 0.22
23 4 0.12
24 4 0.12
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTTATAATATTATACTA
Found at i:55268 original size:24 final size:24
Alignment explanation
Indices: 55241--55288 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
55231 TAATTTTCTA
55241 TATTTTTATTATCATT-ATATTATT
1 TATTTTT-TTATCATTGATATTATT
* *
55265 TATTTTTTTTTTATTGATATTATT
1 TATTTTTTTATCATTGATATTATT
55289 GTTGTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (24 bp):
TATTTTTTTATCATTGATATTATT
Found at i:55581 original size:23 final size:23
Alignment explanation
Indices: 55555--55602 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
55545 TCTTTTCGTC
55555 ATTTAATTTATTAATT-TATATAT
1 ATTTAATTT-TTAATTATATATAT
* *
55578 ATTTACTTTTTTATTATATATAT
1 ATTTAATTTTTAATTATATATAT
55601 AT
1 AT
55603 ATATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTAATTTTTAATTATATATAT
Found at i:55597 original size:2 final size:2
Alignment explanation
Indices: 55592--55618 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55582 ACTTTTTTAT
55592 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
55619 TATTCGTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55701 original size:23 final size:21
Alignment explanation
Indices: 55628--55705 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 21
55618 TTATTCGTAC
*
55628 TTTGTTATTA-TTATTTTGTTTA
1 TTTGTT-TTATTTATTTT-ATTA
*
55650 TTTGTTTTATTTATTTTCTT-
1 TTTGTTTTATTTATTTTATTA
*
55670 TTTCTTTTTATATATATTTTATTA
1 TTT-GTTTTAT-T-TATTTTATTA
55694 TTTGTTTT-TTTA
1 TTTGTTTTATTTA
55706 CTTACTATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
20 5 0.11
21 12 0.26
22 15 0.32
23 12 0.26
24 3 0.06
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTGTTTTATTTATTTTATTA
Found at i:58625 original size:141 final size:141
Alignment explanation
Indices: 58362--58642 Score: 395
Period size: 141 Copynumber: 2.0 Consensus size: 141
58352 TTATAATTTG
* * * * *
58362 ATAAGCTTAGTTTAAAGATCACAAGATATATGGAGTTCAATTTGAATATCTAAATTGAAATGTTC
1 ATAAACTTAGTCTAAAGAGCACAAGATATATGGAGTTCAATGTGAAGATCTAAATTGAAATGTTC
* *
58427 ATTAAGAAAACAAGCGGGGATAGCTCAGTTGGGAGAGCATCAAACTTAATATTTGAAGGTCACAT
66 ATTAAGAAAACAAGCGGGGATAGCTCAGTTGGGAGAGCATCAAACTTAAGATCTGAAGGTCACAT
*
58492 GTTTGATCCAC
131 GTTCGATCCAC
* * *
58503 ATAAACTTAGTCTGAAGAGCACAAGATCTATGGAGTTCAGA-GTGAAGGTCTAAATTGAAATGTT
1 ATAAACTTAGTCTAAAGAGCACAAGATATATGGAGTTCA-ATGTGAAGATCTAAATTGAAATGTT
* * *
58567 CATTAAGAAAACTAGCGGGGATAGCTCAGTTGGGAGAGCGTCAGA-TTGAAGATCTGAAGGTCAC
65 CATTAAGAAAACAAGCGGGGATAGCTCAGTTGGGAGAGCATCAAACTT-AAGATCTGAAGGTCAC
*
58631 GTGTTCGATCCA
129 ATGTTCGATCCA
58643 TGTTCACCGC
Statistics
Matches: 123, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
140 2 0.02
141 120 0.98
142 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (141 bp):
ATAAACTTAGTCTAAAGAGCACAAGATATATGGAGTTCAATGTGAAGATCTAAATTGAAATGTTC
ATTAAGAAAACAAGCGGGGATAGCTCAGTTGGGAGAGCATCAAACTTAAGATCTGAAGGTCACAT
GTTCGATCCAC
Found at i:59649 original size:13 final size:13
Alignment explanation
Indices: 59631--59656 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59621 CTGCATTTAA
59631 TTAAAATTGAATT
1 TTAAAATTGAATT
59644 TTAAAATTGAATT
1 TTAAAATTGAATT
59657 GGAGTATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TTAAAATTGAATT
Found at i:59933 original size:141 final size:141
Alignment explanation
Indices: 59676--59942 Score: 408
Period size: 141 Copynumber: 1.9 Consensus size: 141
59666 TTATAATTCG
* * * *
59676 ATAAGCTTAGTTTAAAGATCACAAAATATATGGAGTTCAGTCTGAATATCTAAATGGAAATGTTC
1 ATAAGCTTAGTCTAAAGAGCACAAAATATATGGAGTTCAGACTGAAGATCTAAATGGAAATGTTC
* *
59741 ATTAAGAAAACAAGCGGGGATAGCTCAGTTGGGAGAGCATCAGACTTAAGATTTGAAGGTCCCAT
66 ATTAAGAAAACAAGCGGGGATAGCTCAGTTGGGAGAGCATCAGACTGAAGATCTGAAGGTCCCAT
59806 GTTTGATCCAC
131 GTTTGATCCAC
* * * * * *
59817 ATAAGCTTAGTCTGAAGAGCACAAGATCTATGGAGTTCAGAGTGAAGGTCTAAATTGAAATGTTC
1 ATAAGCTTAGTCTAAAGAGCACAAAATATATGGAGTTCAGACTGAAGATCTAAATGGAAATGTTC
* *
59882 ATTAAGAAAACTAGCGGGGATAGCTCAGTTGGGAGAGCGTCAGACTGAAGATCTGAAGGTC
66 ATTAAGAAAACAAGCGGGGATAGCTCAGTTGGGAGAGCATCAGACTGAAGATCTGAAGGTC
59943 ACGTGTTCAA
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
141 112 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (141 bp):
ATAAGCTTAGTCTAAAGAGCACAAAATATATGGAGTTCAGACTGAAGATCTAAATGGAAATGTTC
ATTAAGAAAACAAGCGGGGATAGCTCAGTTGGGAGAGCATCAGACTGAAGATCTGAAGGTCCCAT
GTTTGATCCAC
Found at i:60376 original size:226 final size:226
Alignment explanation
Indices: 59975--60614 Score: 831
Period size: 226 Copynumber: 2.8 Consensus size: 226
59965 GTATCTAATT
* *
59975 TTATTATGATTT-AAGTCATTAGTTATTTTAAATATAATTACTATATTGTCGATAAGCTTACTGT
1 TTATTATGATTTGAA-TCATTAGTTATTTTAAATATAATTACTATATTATCGATAAGCTTAGT-T
* * * *
60039 GAAA-AGCACAAGATCTATGGAGTTTAGACTAAAGGTCTAAATTGAAATGTTCATTAAGAAAACT
64 CAAAGAGCACAAGATCTATGGAGTTCAGACTGAAGGTCTAAATTGAAATGTTCATTAAGAAAACA
* * * * *
60103 AGTGGGGATAGCTCAATTGGGAGAGCATCAGACTGAAG-ATCTGAAGGTTACGTGTTCGAA-CCA
129 AGTGGGAATAACTCAATTGGGAGAGCGTCAGATTGAAGAAT-TGAAGGTCACGTGTTC-AATCCA
* *
60166 CGTTC-ACAACATCTAGTTTTAATTGAATTGGAGTA
192 CGTTCGAC-ACATCTAATTTTAATTGAATTGCAGTA
* *
60201 TTATTATGGTTTGAATCATTAGTTATTTTAAATATTATTACTATATTATCGATAAGCTTAGTTCA
1 TTATTATGATTTGAATCATTAGTTATTTTAAATATAATTACTATATTATCGATAAGCTTAGTTCA
* *
60266 AAGAGCACAAGATCTATAGAGTTCAGACTGAAGGTCTAAATTAAAATGTTCATTAAGAAAACAAG
66 AAGAGCACAAGATCTATGGAGTTCAGACTGAAGGTCTAAATTGAAATGTTCATTAAGAAAACAAG
* * *
60331 CGAGAATAACTCAATTGGGAGAGCGTCAGATTGAAGAATTGAAGGTCACGTGTTCAATTCACGTT
131 TGGGAATAACTCAATTGGGAGAGCGTCAGATTGAAGAATTGAAGGTCACGTGTTCAATCCACGTT
* * *
60396 CGTCGCATCTAATTTTAATTGAATTGCATTA
196 CGACACATCTAATTTTAATTGAATTGCAGTA
* * * *
60427 TTATTATAATTTGATTCATTAGTTATTTTAAATGTAAAAAACAATTACTATATTATTGATAAGCT
1 TTATTATGATTTGAATCATTAGTTATTTTAAA--T-----ATAATTACTATATTATCGATAAGCT
** * * *
60492 TAGTTTGAAGAGCATAAGATCTATGGAGTTCAGATTGAAGATCTAAATTGAAATGTTCATTAAGA
59 TAGTTCAAAGAGCACAAGATCTATGGAGTTCAGACTGAAGGTCTAAATTGAAATGTTCATTAAGA
* *
60557 AAACAAGTGGGAATAACTCAATTGGGAGAGTGTCAGATTGAAGATTTGAAGGTCACGT
124 AAACAAGTGGGAATAACTCAATTGGGAGAGCGTCAGATTGAAGAATTGAAGGTCACGT
60615 TCATAGCATC
Statistics
Matches: 362, Mismatches: 40, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
225 6 0.02
226 216 0.60
227 5 0.01
228 1 0.00
233 134 0.37
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (226 bp):
TTATTATGATTTGAATCATTAGTTATTTTAAATATAATTACTATATTATCGATAAGCTTAGTTCA
AAGAGCACAAGATCTATGGAGTTCAGACTGAAGGTCTAAATTGAAATGTTCATTAAGAAAACAAG
TGGGAATAACTCAATTGGGAGAGCGTCAGATTGAAGAATTGAAGGTCACGTGTTCAATCCACGTT
CGACACATCTAATTTTAATTGAATTGCAGTA
Found at i:64062 original size:3 final size:3
Alignment explanation
Indices: 64054--64088 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
64044 AGTGATTCAT
64054 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
64089 TCCTTTTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:67252 original size:140 final size:140
Alignment explanation
Indices: 67100--67378 Score: 549
Period size: 140 Copynumber: 2.0 Consensus size: 140
67090 AAAATAAAAT
67100 TAGTATGCTCAAATTCAAAAATATAAAAATAAAGGATATCAGTGACCAAACTAAAAAAATGCCTA
1 TAGTATGCTCAAATTCAAAAATATAAAAATAAAGGATATCAGTGACCAAACTAAAAAAATGCCTA
*
67165 AACTAGGAGGATTTATAGATGATTAACCCATGAAATAGTGATTTAAATTTAAAAAACTCTCAAAG
66 AACTAGGAGGATTTATAGATGATTAACCCATGAAATAGTGATTTAAATTTAAAAAACTCTAAAAG
67230 TCTAGTGACA
131 TCTAGTGACA
67240 TAGTATGCTCAAATTCAAAAATATAAAAATAAAGGATATCAGTGACCAAACTAAAAAAATGCCTA
1 TAGTATGCTCAAATTCAAAAATATAAAAATAAAGGATATCAGTGACCAAACTAAAAAAATGCCTA
67305 AACTAGGAGGATTTATAGATGATTAACCCATGAAATAGTGATTTAAATTTAAAAAACTCTAAAAG
66 AACTAGGAGGATTTATAGATGATTAACCCATGAAATAGTGATTTAAATTTAAAAAACTCTAAAAG
67370 TCTAGTGAC
131 TCTAGTGAC
67379 CTGAGTGTGA
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 138 1.00
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.27
Consensus pattern (140 bp):
TAGTATGCTCAAATTCAAAAATATAAAAATAAAGGATATCAGTGACCAAACTAAAAAAATGCCTA
AACTAGGAGGATTTATAGATGATTAACCCATGAAATAGTGATTTAAATTTAAAAAACTCTAAAAG
TCTAGTGACA
Found at i:67971 original size:26 final size:27
Alignment explanation
Indices: 67928--67978 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
67918 TTATTTCGAA
* *
67928 AAAAAGATAATAATAAAATGTAAAGCT
1 AAAAAGATAAAAACAAAATGTAAAGCT
67955 AAAAA-ATAAAAACAAAATGTAAAG
1 AAAAAGATAAAAACAAAATGTAAAG
67979 AACCTTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.69, C:0.04, G:0.10, T:0.18
Consensus pattern (27 bp):
AAAAAGATAAAAACAAAATGTAAAGCT
Found at i:68826 original size:23 final size:22
Alignment explanation
Indices: 68792--68836 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
68782 TGAACAAGTT
68792 CTTCTCATTATGAACTTCTTCTC
1 CTTCTCATTATG-ACTTCTTCTC
*
68815 CTTCTTCA-TATGAGTTCTTCTC
1 CTTC-TCATTATGACTTCTTCTC
68837 ATTATGAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 8 0.40
24 3 0.15
ACGTcount: A:0.16, C:0.29, G:0.07, T:0.49
Consensus pattern (22 bp):
CTTCTCATTATGACTTCTTCTC
Found at i:69564 original size:22 final size:22
Alignment explanation
Indices: 69536--69609 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 22
69526 AATAAAGCTT
*
69536 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTAAAAAGAAAATCTA
** *
69558 TCATCTTTGGAGAGAAAATCTA
1 TCATCTTTAAAAAGAAAATCTA
** * *
69580 TCATCTTTGGAGAGAAAATATA
1 TCATCTTTAAAAAGAAAATCTA
69602 TCATCTTT
1 TCATCTTT
69610 GGAGAGTGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAAAATCTA
Found at i:69573 original size:20 final size:21
Alignment explanation
Indices: 69548--69615 Score: 102
Period size: 22 Copynumber: 3.2 Consensus size: 21
69538 ATCTTTAAAA
69548 AGAG-AATCTATCATCTTTGG
1 AGAGAAATCTATCATCTTTGG
69568 AGAGAAAATCTATCATCTTTGG
1 AGAG-AAATCTATCATCTTTGG
*
69590 AGAGAAAATATATCATCTTTGG
1 AGAG-AAATCTATCATCTTTGG
69612 AGAG
1 AGAG
69616 TGTAGATGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 4 0.09
22 41 0.91
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (21 bp):
AGAGAAATCTATCATCTTTGG
Found at i:69610 original size:22 final size:22
Alignment explanation
Indices: 69556--69615 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
69546 AAAGAGAATC
*
69556 TATCATCTTTGGAGAGAAAATC
1 TATCATCTTTGGAGAGAAAATA
69578 TATCATCTTTGGAGAGAAAATA
1 TATCATCTTTGGAGAGAAAATA
69600 TATCATCTTTGGAGAG
1 TATCATCTTTGGAGAG
69616 TGTAGATGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (22 bp):
TATCATCTTTGGAGAGAAAATA
Found at i:70076 original size:46 final size:46
Alignment explanation
Indices: 69989--70077 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 46
69979 TTCGTAAAAC
* * * *
69989 ATTTGACAACATATTCATCATTTCCTGTGGCTTCTGTACAGATGCT
1 ATTTGACAACACATTCATCATTTCATGTGACTTCTGCACAGATGCT
70035 ATTTGACAACACATTCATCATTTCATGTGAC-TCATGCACAGAT
1 ATTTGACAACACATTCATCATTTCATGTGACTTC-TGCACAGAT
70078 TTCTGGTTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 2 0.05
46 36 0.95
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.36
Consensus pattern (46 bp):
ATTTGACAACACATTCATCATTTCATGTGACTTCTGCACAGATGCT
Found at i:71801 original size:30 final size:24
Alignment explanation
Indices: 71733--71789 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
71723 TTGATAATTC
*
71733 TTCTGATACCGAGAAAATCCTGAA
1 TTCTGATTCCGAGAAAATCCTGAA
71757 TTCTGATTCCGAGAAAATCCTGAA
1 TTCTGATTCCGAGAAAATCCTGAA
71781 TTCTGATTC
1 TTCTGATTC
71790 TGACAAGGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (24 bp):
TTCTGATTCCGAGAAAATCCTGAA
Found at i:74464 original size:8 final size:8
Alignment explanation
Indices: 74451--74493 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
74441 CTTGATTCAA
74451 TTTTTCTT
1 TTTTTCTT
74459 TTTTTC-T
1 TTTTTCTT
*
74466 TTTTTC-C
1 TTTTTCTT
74473 TTTTTCTT
1 TTTTTCTT
*
74481 TTTTCCTT
1 TTTTTCTT
74489 TTTTT
1 TTTTT
74494 ATGAGTATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 13 0.43
8 17 0.57
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:74468 original size:7 final size:7
Alignment explanation
Indices: 74451--74492 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
74441 CTTGATTCAA
74451 TTTTTCTT
1 TTTTTC-T
74459 TTTTTCT
1 TTTTTCT
*
74466 TTTTTCC
1 TTTTTCT
74473 TTTTTCT
1 TTTTTCT
74480 TTTTTCCT
1 TTTTT-CT
74488 TTTTT
1 TTTTT
74493 TATGAGTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 18 0.58
8 13 0.42
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:74476 original size:14 final size:14
Alignment explanation
Indices: 74459--74491 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
74449 AATTTTTCTT
74459 TTTTTCTTTTTTCC
1 TTTTTCTTTTTTCC
74473 TTTTTCTTTTTTCC
1 TTTTTCTTTTTTCC
74487 TTTTT
1 TTTTT
74492 TTATGAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTCTTTTTTCC
Found at i:79343 original size:28 final size:26
Alignment explanation
Indices: 79288--79345 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
79278 AAACATTAAT
*
79288 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
79314 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
79342 AAAA
1 AAAA
79346 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:81791 original size:3 final size:3
Alignment explanation
Indices: 81783--81831 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
81773 ATTTGTAAAT
* **
81783 TAA TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA CGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
81830 TA
1 TA
81832 TATATTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:82186 original size:43 final size:43
Alignment explanation
Indices: 82139--82326 Score: 127
Period size: 43 Copynumber: 4.3 Consensus size: 43
82129 TTCCTACGCA
* *
82139 ATGAGGACG-GCTGGTTATCTAGGGGTGACACGGCTCTTACGCG
1 ATGAGGA-GAGCTGGTTATCTAGGGGTGACACGGCTCATACGTG
*
82182 ATGAGGAGATCTGG---TCT-GGGGAATGACACGGCTCATACGTG
1 ATGAGGAGAGCTGGTTATCTAGGGG--TGACACGGCTCATACGTG
* ** ** * * * *
82223 ATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
1 ATGAGGAGAGCTGGTTATCT--AGG-GGTGACACGGCTCATACGTG
* *
82269 ATGAGGACG-GCTGGTTATCTATGGTTGACACGGCTCATACGTG
1 ATGAGGA-GAGCTGGTTATCTAGGGGTGACACGGCTCATACGTG
* *
82312 ATGAAGAGATCTGGT
1 ATGAGGAGAGCTGGT
82327 CTGGGGATGA
Statistics
Matches: 113, Mismatches: 20, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
39 4 0.04
40 3 0.03
41 28 0.25
42 2 0.02
43 38 0.34
44 5 0.04
46 29 0.26
47 3 0.03
48 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (43 bp):
ATGAGGAGAGCTGGTTATCTAGGGGTGACACGGCTCATACGTG
Found at i:82240 original size:135 final size:134
Alignment explanation
Indices: 81998--82376 Score: 452
Period size: 130 Copynumber: 2.9 Consensus size: 134
81988 ACACTGCTCA
* ** * * *
81998 TACGCAATGAAGA-GGTCTGGTCGTCTAAGGGTGACACGGCTCCTACGTGATGAGGAAATATGGT
1 TACGCAATGAGGACGG-CTGGTTATCTAAGGGTGACACGGCTCATACGTGATGAGGAGATCTGGT
** *
82062 C-GAGGGATGACACTTCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAAGGTGATAACT
65 CTG-GGGATGACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTTTAGGAAAGGTGATAACA
82126 CGGTTCC
128 CGGTTCC
* * *
82133 TACGCAATGAGGACGGCTGGTTATCTAGGGGTGACACGGCTCTTACGCGATGAGGAGATCTGGTC
1 TACGCAATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCATACGTGATGAGGAGATCTGGTC
82198 TGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATC--T---AAAGGTGATAACACG
66 TGGGG-ATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAAGGTGATAACACG
82258 GTTCC
130 GTTCC
** * * *
82263 TACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTC
1 TACGCAATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCATACGTGATGAGGAGATCTGGTC
* * * * *
82328 TGGGGATGACACGGTTCCTACATGAT-AGGACG-GCTGGCCATCTTTAGGA
66 TGGGGATGACACGGCTCATACGTGATGAAGA-GTTCTGGCCATCTTTAGGA
82377 GTTATGGTTT
Statistics
Matches: 212, Mismatches: 23, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
128 12 0.06
129 19 0.09
130 83 0.39
133 2 0.01
135 65 0.31
136 31 0.15
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (134 bp):
TACGCAATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCATACGTGATGAGGAGATCTGGTC
TGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAAGGTGATAACACGG
TTCC
Found at i:82312 original size:89 final size:82
Alignment explanation
Indices: 82205--82364 Score: 221
Period size: 89 Copynumber: 1.9 Consensus size: 82
82195 GTCTGGGGAA
* * *
82205 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG---TCT---GGGGATAACACGGTTCCTACATGA
82270 TGAGGACGGCTGGTTATCTATGGT
60 T-AGGACGGCTGGTTATCTATGGT
*
82294 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATAGGAC
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATGATAGGAC
82359 GGCTGG
66 GGCTGG
82365 CCATCTTTAG
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
82 11 0.16
83 22 0.33
86 3 0.04
89 31 0.46
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.25
Consensus pattern (82 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATGATAGGAC
GGCTGGTTATCTATGGT
Found at i:82423 original size:28 final size:28
Alignment explanation
Indices: 82403--82464 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
82393 AAACCAAATT
82403 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
82431 AAAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
82459 AAAGAT
1 AAAGAT
82465 GATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:83480 original size:65 final size:64
Alignment explanation
Indices: 83374--83602 Score: 237
Period size: 67 Copynumber: 3.5 Consensus size: 64
83364 TTTCAAAATG
* ** * * * * *
83374 AACATATTCAAAGATTTACTTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT-AAGAG
1 AACAAATTCAAAGATTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATT-ATGTTTCAA-AG
83437 A
64 A
* *
83438 AACAGATTCAAAGATTTTTTTCCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAG
1 AACAAATTCAAAGATTTTTTT-CAAAAGAAATTATCTTAAGAGAGACAAAATTATGTTT-CAAAG
83503 A
64 A
* *
83504 AACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAA
1 AACAAATTCAAAGA-TTTT-TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTATGTTT-CAAA
83569 GA
63 GA
* *
83571 AACCAACTCAAAGATTTTTGTTACAAAAGAAA
1 AACAAATTCAAAGATTTTT-TT-CAAAAGAAA
83603 CAATCTCAAA
Statistics
Matches: 145, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
64 19 0.13
65 30 0.21
66 21 0.14
67 72 0.50
68 3 0.02
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (64 bp):
AACAAATTCAAAGATTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTATGTTTCAAAGA
Found at i:83492 original size:37 final size:38
Alignment explanation
Indices: 83446--83572 Score: 125
Period size: 37 Copynumber: 3.6 Consensus size: 38
83436 GAAACAGATT
83446 CAAAGATTTT-TTTCCAAAAGAAATTATCTTAAGAGAGA
1 CAAAGATTTTGTTTCC-AAAGAAATTATCTTAAGAGAGA
**
83484 CAAA-ATTTTGTTTCCAAAG-AA--A-C---A-A-ACT
1 CAAAGATTTTGTTTCCAAAGAAATTATCTTAAGAGAGA
*
83512 CAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAAGA-TTTTGTTTCCAAAGAAATTATCTTAAGAGAGA
83551 CAAA-ATTTTGTTTCCAAAGAAA
1 CAAAGATTTTGTTTCCAAAGAAA
83573 CCAACTCAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 25
0.70 0.06 0.25
Matches are distributed among these distances:
28 5 0.07
29 2 0.03
30 14 0.20
31 2 0.03
33 2 0.03
34 2 0.03
36 2 0.03
37 26 0.37
38 11 0.15
39 5 0.07
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (38 bp):
CAAAGATTTTGTTTCCAAAGAAATTATCTTAAGAGAGA
Found at i:83523 original size:30 final size:30
Alignment explanation
Indices: 83489--83619 Score: 109
Period size: 30 Copynumber: 4.1 Consensus size: 30
83479 AGAGACAAAA
*
83489 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
** * * *
83519 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AG----AT
* *
83556 TTTTGTTTCCAAAGAAACCAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
* *
83586 TTTTGTTACAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
83616 TTTT
1 TTTT
83620 TTTTTTTACA
Statistics
Matches: 78, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
30 49 0.63
31 2 0.03
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 2 0.03
37 19 0.24
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.33
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:83540 original size:67 final size:67
Alignment explanation
Indices: 83435--83602 Score: 284
Period size: 67 Copynumber: 2.5 Consensus size: 67
83425 TCATTTTAAG
* * *
83435 AGAAACAGATTCAAAGATTTTT-TTCCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTACAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
83499 AA
66 AA
*
83501 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTACAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
83566 AA
66 AA
*
83568 AGAAACCAACTCAAAGATTTTTGTTACAAAAGAAA
1 AGAAACAAACTCAAAGATTTTTGTTACAAAAGAAA
83603 CAATCTCAAA
Statistics
Matches: 96, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
66 20 0.21
67 76 0.79
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTACAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:83765 original size:29 final size:30
Alignment explanation
Indices: 83706--83893 Score: 99
Period size: 29 Copynumber: 6.5 Consensus size: 30
83696 GAGACAAAAC
* * *
83706 TTTGTTTCAAAATAAATAGACTCAAAGATT
1 TTTGTTTCAAAAGAAACAGACTCAAAAATT
*
83736 TTTGTTTCAAACGAAACA-ACTCAAAAA-T
1 TTTGTTTCAAAAGAAACAGACTCAAAAATT
* * * * *
83764 TTT-ATTCAAAAGGAACAAACTCCAAGATT
1 TTTGTTTCAAAAGAAACAGACTCAAAAATT
* * * *
83793 TTT-ATTCAAAAGGAACAAACTCAAAGA-T
1 TTTGTTTCAAAAGAAACAGACTCAAAAATT
* * * *
83821 TTT-TTTCAAGAGGAACAAACTCAAAGA--
1 TTTGTTTCAAAAGAAACAGACTCAAAAATT
* * * *
83848 TTT-TTTCAAGAGGAACAAACTCAAAGATT
1 TTTGTTTCAAAAGAAACAGACTCAAAAATT
83877 TTT-TTCCTCAAAAGAAA
1 TTTGTT--TCAAAAGAAA
83894 TTGTCTTTAA
Statistics
Matches: 138, Mismatches: 14, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
27 38 0.28
28 37 0.27
29 40 0.29
30 15 0.11
31 8 0.06
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.30
Consensus pattern (30 bp):
TTTGTTTCAAAAGAAACAGACTCAAAAATT
Found at i:83791 original size:57 final size:57
Alignment explanation
Indices: 83725--83878 Score: 188
Period size: 57 Copynumber: 2.7 Consensus size: 57
83715 AAATAAATAG
* *
83725 ACTCAAAGATTTTTGTTTCAAACGAAAC-AACTCAAAAATTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTT-ATTCAAAAGAAACAAACTCAAAAATTTTATTCAAAAGGAACAA
* * * * *
83782 ACTCCAAGATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGAAACAAACTCAAAAATTTTATTCAAAAGGAACAA
* * *
83839 ACTCAAAGA-TTTT-TTCAAGAGGAACAAACTCAAAGATTTT
1 ACTCAAAGATTTTTATTCAAAAGAAACAAACTCAAAAATTTT
83879 TTTCCTCAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
55 26 0.30
56 14 0.16
57 47 0.54
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.29
Consensus pattern (57 bp):
ACTCAAAGATTTTTATTCAAAAGAAACAAACTCAAAAATTTTATTCAAAAGGAACAA
Found at i:83879 original size:27 final size:27
Alignment explanation
Indices: 83725--83880 Score: 188
Period size: 27 Copynumber: 5.6 Consensus size: 27
83715 AAATAAATAG
* *
83725 ACTCAAAGATTTTTGTTTCAAACGAAAC-A
1 ACTCAAAGA--TTT-TTTCAAAAGGAACAA
*
83754 ACTCAAAAATTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTT-TTCAAAAGGAACAA
*
83782 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTT-TTCAAAAGGAACAA
*
83811 ACTCAAAGATTTTTTTCAAGAGGAACAA
1 ACTCAAAGA-TTTTTTCAAAAGGAACAA
*
83839 ACTCAAAGATTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTCAAAAGGAACAA
83866 ACTCAAAGATTTTTT
1 ACTCAAAGATTTTTT
83881 TCCTCAAAAG
Statistics
Matches: 117, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
26 1 0.01
27 46 0.39
28 30 0.26
29 40 0.34
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.29
Consensus pattern (27 bp):
ACTCAAAGATTTTTTCAAAAGGAACAA
Found at i:83879 original size:28 final size:28
Alignment explanation
Indices: 83725--83882 Score: 212
Period size: 28 Copynumber: 5.6 Consensus size: 28
83715 AAATAAATAG
* *
83725 ACTCAAAGATTTTTGTTTCAAACGAAAC-A
1 ACTCAAAGA-TTTT-TTTCAAAAGGAACAA
* *
83754 ACTCAAAAATTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTTTCAAAAGGAACAA
*
83782 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTT-TTCAAAAGGAACAA
*
83811 ACTCAAAGATTTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTTCAAAAGGAACAA
*
83839 ACTCAAAGA-TTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTTCAAAAGGAACAA
83866 ACTCAAAGATTTTTTTC
1 ACTCAAAGATTTTTTTC
83883 CTCAAAAGAA
Statistics
Matches: 117, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
27 37 0.32
28 45 0.38
29 35 0.30
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.30
Consensus pattern (28 bp):
ACTCAAAGATTTTTTTCAAAAGGAACAA
Found at i:84216 original size:36 final size:36
Alignment explanation
Indices: 84132--84235 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
84122 GAGAAAATGA
* * *
84132 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
84166 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
84202 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
84236 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:84263 original size:36 final size:36
Alignment explanation
Indices: 84133--84251 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
84123 AGAAAATGAT
* * * *
84133 GTCTCAAGCGAGACGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
84167 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
84203 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
84238 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
84252 TCAACTTTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 19 0.28
35 12 0.17
36 38 0.55
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:84320 original size:102 final size:104
Alignment explanation
Indices: 84203--84435 Score: 287
Period size: 105 Copynumber: 2.2 Consensus size: 104
84193 TAGAGAAATT
* *
84203 GTCTCAAGCGAGACAAAGTTTGTTTTTG-AG-AA-AACGATCTCAA-GTGAGATCAACTTTGTTT
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAAGAAACAACAATCT-AAGGTGAGATCAACTTTGTTT
* *
84264 A-ATGTGAAACAAATTCTAAATTTGGATCTCAAAGGGAAAAG
64 ATA-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* * *
84305 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTAATTTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTG-AAGAAACAACAATCTAAGGTGAGATCAACTTTGTTTA
* * *
84370 TAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
65 TAGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
**
84410 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
84436 AAAATCCTCA
Statistics
Matches: 113, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
101 5 0.04
102 21 0.19
103 2 0.02
104 4 0.04
105 80 0.71
106 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (104 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAAGAAACAACAATCTAAGGTGAGATCAACTTTGTTTAT
AGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:84939 original size:18 final size:18
Alignment explanation
Indices: 84906--84941 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
84896 ATGTATCATG
*
84906 TATGTATGTGTATGTATA
1 TATGTATGTATATGTATA
*
84924 TATGTATGTATGTGTATA
1 TATGTATGTATATGTATA
84942 CTTTTCTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (18 bp):
TATGTATGTATATGTATA
Found at i:86138 original size:12 final size:11
Alignment explanation
Indices: 86110--86147 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
86100 TCCTCTTTTG
*
86110 TTCTTTGCTTT
1 TTCTTTGATTT
86121 TTCTTTGATTT
1 TTCTTTGATTT
86132 TTGCTTTGATTT
1 TT-CTTTGATTT
86144 TTCT
1 TTCT
86148 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:86845 original size:46 final size:45
Alignment explanation
Indices: 86753--86846 Score: 152
Period size: 46 Copynumber: 2.1 Consensus size: 45
86743 ATAAATACAG
* *
86753 TGTTTCAAGGTGGAAAGAATGTTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
*
86798 TGTTTCAAGGTGGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGTGG-AAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
86844 TGT
1 TGT
86847 CAAAAATTGG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 13 0.29
46 32 0.71
ACGTcount: A:0.37, C:0.09, G:0.28, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Done.