Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009384.1 Hibiscus syriacus cultivar Beakdansim tig00113272_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: 65481
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:5520 original size:17 final size:19
Alignment explanation
Indices: 5487--5522 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
5477 TACTAATGAA
5487 TAATTTTCTACATTAATCT
1 TAATTTTCTACATTAATCT
5506 TAATTTT-TA-ATTAATCT
1 TAATTTTCTACATTAATCT
5523 ATGGTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 2 0.12
19 7 0.41
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATTTTCTACATTAATCT
Found at i:6153 original size:14 final size:13
Alignment explanation
Indices: 6134--6163 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
6124 AACTTTAATT
6134 TAATAAATTAAATA
1 TAATAAATTAAA-A
6148 TAATAAATTAAAA
1 TAATAAATTAAAA
6161 TAA
1 TAA
6164 GTTTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAATAAATTAAAA
Found at i:9290 original size:20 final size:20
Alignment explanation
Indices: 9196--9564 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
9186 GATTTTCCAT
* ** *
9196 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
9216 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
9236 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
9256 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
9276 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
9296 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
9316 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
9336 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
9356 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
9376 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
9396 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
9416 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
9436 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
9456 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
9476 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
9496 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
* *
9516 AATCGCAACG-ATAATCCGAA
1 AATCGCAACGCGT-ATCCGTA
* * *
9536 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
9556 AATCACAAC
1 AATCGCAAC
9565 ACTGAAATTT
Statistics
Matches: 303, Mismatches: 38, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
19 3 0.01
20 297 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:10274 original size:24 final size:24
Alignment explanation
Indices: 10235--10281 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
10225 AAATTTGGTC
10235 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
10259 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
10282 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:10473 original size:12 final size:12
Alignment explanation
Indices: 10456--10480 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10446 ATATAATCCT
10456 GAAGAAGAAAAA
1 GAAGAAGAAAAA
10468 GAAGAAGAAAAA
1 GAAGAAGAAAAA
10480 G
1 G
10481 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:12865 original size:33 final size:34
Alignment explanation
Indices: 12778--13146 Score: 317
Period size: 33 Copynumber: 10.5 Consensus size: 34
12768 CGGAAAATAC
* *
12778 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
12811 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
12845 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
* * * * * *
12883 AATCGCAACGAGAGAATCG-CAATGCGAAATGA-AAA
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACGATGAA
* *
12918 AATCGCAATGCGAAATGAAAATCGCAACG-CGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
12951 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
12989 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
13027 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
13060 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
* *
13098 AATCGCAACGCGAGAATCG-CAAT-GCGAA--ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCGC-AACGATGAA
13131 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
13147 TATAAACGCA
Statistics
Matches: 283, Mismatches: 28, Indels: 51
0.78 0.08 0.14
Matches are distributed among these distances:
32 3 0.01
33 106 0.37
34 36 0.13
35 20 0.07
36 3 0.01
37 2 0.01
38 93 0.33
39 14 0.05
40 6 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:12893 original size:52 final size:52
Alignment explanation
Indices: 12806--13146 Score: 574
Period size: 52 Copynumber: 6.4 Consensus size: 52
12796 AAATCCCAAC
12806 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
12859 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
12911 ATGAAAAAATCGCAATGCGAAATGAAAATCGCAACGCGAGAATCGCAATGCGAA
1 ATG--AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
12965 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
13022 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
13074 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGCGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
13126 ATGAAAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAAT
13147 TATAAACGCA
Statistics
Matches: 274, Mismatches: 7, Indels: 15
0.93 0.02 0.05
Matches are distributed among these distances:
52 153 0.56
53 18 0.07
54 54 0.20
55 3 0.01
56 1 0.00
57 45 0.16
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:13162 original size:19 final size:19
Alignment explanation
Indices: 12778--13146 Score: 420
Period size: 19 Copynumber: 20.8 Consensus size: 19
12768 CGGAAAATAC
*
12778 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
12797 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
12811 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
12831 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
12845 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
12864 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
12883 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
12897 AATCGCAATGCGAAATGAAAA
1 AATCGCAATGCGAAATG--AA
12918 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
12937 AATCGCAACGCG--A-G--
1 AATCGCAATGCGAAATGAA
12951 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
12970 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
12989 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
13008 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
13027 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
13046 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
13060 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
13079 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
13098 AATCGCAACGCG--A-G--
1 AATCGCAATGCGAAATGAA
13112 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
13131 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
13147 TATAAACGCA
Statistics
Matches: 301, Mismatches: 16, Indels: 66
0.79 0.04 0.17
Matches are distributed among these distances:
14 64 0.21
15 3 0.01
16 11 0.04
17 10 0.03
18 4 0.01
19 178 0.59
20 13 0.04
21 18 0.06
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:13262 original size:19 final size:19
Alignment explanation
Indices: 13153--13254 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
13143 AAATTATAAA
13153 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
13172 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
13192 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
13208 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
13225 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
13244 CGCATTGCGAT
1 CGCATTGCGAT
13255 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:13381 original size:14 final size:14
Alignment explanation
Indices: 13362--13398 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
13352 CATCAATTAC
13362 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
13376 ACAAATCATCTTTT
1 ACAAATCAACTTTT
13390 ACAAATCAA
1 ACAAATCAA
13399 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:15300 original size:19 final size:19
Alignment explanation
Indices: 15260--15394 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
15250 TAGTTTACTT
* *
15260 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
15280 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
15299 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
15318 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
15332 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
15351 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
15365 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
15384 TCGCAATGCGA
1 TCGCAACGCGA
15395 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:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:15335 original size:14 final size:14
Alignment explanation
Indices: 15316--15372 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
15306 GCGAAATGAA
*
15316 AATCGCAACGACAG
1 AATCGCAACGAAAG
15330 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
15347 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
15363 AATCGCAACG
1 AATCGCAACG
15373 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:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:15339 original size:33 final size:33
Alignment explanation
Indices: 15297--15389 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
15287 GCGAAACCAA
*
15297 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
15330 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
15363 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
15390 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:15386 original size:52 final size:54
Alignment explanation
Indices: 15260--15394 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
15250 TAGTTTACTT
*
15260 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
15318 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
15365 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
15395 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:15412 original size:19 final size:19
Alignment explanation
Indices: 15390--15518 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
15380 AAAATCGCAA
15390 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
15409 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
15423 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
15442 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
15456 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
15475 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
15494 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
15514 TGCGA
1 TGCGA
15519 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:15432 original size:33 final size:33
Alignment explanation
Indices: 15390--15481 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
15380 AAAATCGCAA
15390 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
15423 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
15456 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
15482 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:15721 original size:93 final size:93
Alignment explanation
Indices: 15562--15939 Score: 726
Period size: 93 Copynumber: 4.1 Consensus size: 93
15552 TTGAATGGAT
15562 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
15627 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
15655 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
15720 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
15748 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA-A-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
15810 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
15838 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
15903 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
15931 AAATTTACT
1 AAATTTACT
15940 AAGCAATCTA
Statistics
Matches: 281, Mismatches: 1, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
90 87 0.31
91 3 0.01
92 3 0.01
93 188 0.67
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:15873 original size:183 final size:186
Alignment explanation
Indices: 15562--15939 Score: 726
Period size: 183 Copynumber: 2.0 Consensus size: 186
15552 TTGAATGGAT
15562 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
15627 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
15692 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
15748 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA-A-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
15810 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
15875 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
15931 AAATTTACT
1 AAATTTACT
15940 AAGCAATCTA
Statistics
Matches: 191, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
183 154 0.81
184 1 0.01
185 2 0.01
186 34 0.18
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:17659 original size:14 final size:14
Alignment explanation
Indices: 17640--17729 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
17630 TTGAAATGAA
17640 AATCGCAACGAGAG
1 AATCGCAACGAGAG
17654 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
17671 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
17687 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
17706 AATCGCAACGAGAG
1 AATCGCAACGAGAG
17720 AATCGCAACG
1 AATCGCAACG
17730 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:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:17677 original size:33 final size:33
Alignment explanation
Indices: 17632--17746 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
17622 TCTTTTGGTT
17632 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
17665 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
17698 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
17731 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
17747 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:17678 original size:19 final size:18
Alignment explanation
Indices: 17639--17751 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
17629 GTTGAAATGA
17639 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
17654 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
17671 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
17687 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
17704 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
17720 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
17737 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
17752 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:17782 original size:14 final size:14
Alignment explanation
Indices: 17763--17817 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
17753 TTTGGTTTCG
17763 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
17777 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
17796 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
17810 CGTTGCGA
1 CGTTGCGA
17818 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:17795 original size:33 final size:33
Alignment explanation
Indices: 17747--17817 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
17737 AAAATCGCAA
**
17747 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
17780 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
17813 TGCGA
1 TGCGA
17818 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:17825 original size:33 final size:33
Alignment explanation
Indices: 17758--17839 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
17748 GCGATTTTGG
***
17758 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
17791 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
17824 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
17840 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:17844 original size:20 final size:20
Alignment explanation
Indices: 17770--17858 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
17760 TCGCGTTGCG
17770 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
17790 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
17803 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
17823 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
17843 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
17859 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:17980 original size:33 final size:33
Alignment explanation
Indices: 17938--18008 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
17928 AATACTAACT
*
17938 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
17971 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
18004 TGAAA
1 TGAAA
18009 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:18242 original size:22 final size:22
Alignment explanation
Indices: 18190--18244 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
18180 TGGTTGTGAG
**
18190 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
18212 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
18234 GGATTTCTTCG
1 GGATTTCTTCG
18245 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:18415 original size:20 final size:20
Alignment explanation
Indices: 18390--18584 Score: 214
Period size: 20 Copynumber: 9.7 Consensus size: 20
18380 CTTTAAATAT
18390 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
18410 CGCGTTGCGATTTTATGTATTTA
1 CGCGTTGCGA-TTTACGGA--TA
*
18433 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
18452 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
18472 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
18492 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
18512 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
18532 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
18552 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
18572 CGCGTTGCGATTT
1 CGCGTTGCGATTT
18585 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.01
20 122 0.83
21 13 0.09
22 8 0.05
23 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:18578 original size:60 final size:60
Alignment explanation
Indices: 18390--18584 Score: 246
Period size: 60 Copynumber: 3.2 Consensus size: 60
18380 CTTTAAATAT
**
18390 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTA-TTCGCGTTGCGATTTACGGATA
* * *** *
18452 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
18512 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
18572 CGCGTTGCGATTT
1 CGCGTTGCGATTT
18585 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
60 79 0.71
61 5 0.04
62 28 0.25
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:18601 original size:21 final size:20
Alignment explanation
Indices: 18577--18653 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
18567 ATATTCGCGT
18577 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
18598 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
18618 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
18640 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
18654 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:18664 original size:20 final size:20
Alignment explanation
Indices: 18639--18690 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
18629 AAGAATCGCG
*
18639 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
18659 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
18679 TTGCGATTCTGG
1 TTGCGATTCTGG
18691 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:19614 original size:14 final size:14
Alignment explanation
Indices: 19581--19623 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
19571 GATTATAAAA
19581 TAATATTTATTTAA-
1 TAATATTT-TTTAAG
19595 -AATATTTTTTAAG
1 TAATATTTTTTAAG
19608 TAATATTTTTTAAG
1 TAATATTTTTTAAG
19622 TA
1 TA
19624 TTAATCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.19
13 7 0.26
14 15 0.56
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (14 bp):
TAATATTTTTTAAG
Found at i:21369 original size:16 final size:17
Alignment explanation
Indices: 21350--21383 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
21340 GATTCAATTT
*
21350 AATTTTATA-AAAAATA
1 AATTTAATATAAAAATA
21366 AATTTAATATAAAAATA
1 AATTTAATATAAAAATA
21383 A
1 A
21384 GTATTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTTAATATAAAAATA
Found at i:22124 original size:19 final size:20
Alignment explanation
Indices: 22075--22124 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
22065 TTTATAATTC
*
22075 CATTAAAAGTTTGTGTTTTTT
1 CATTAAAA-ATTGTGTTTTTT
*
22096 -ATAAATAAATTGT-TTTTTT
1 CATTAA-AAATTGTGTTTTTT
22115 CATTAAAAAT
1 CATTAAAAAT
22125 AATATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (20 bp):
CATTAAAAATTGTGTTTTTT
Found at i:22132 original size:20 final size:20
Alignment explanation
Indices: 22108--22147 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
22098 AAATAAATTG
*
22108 TTTTTTTCATTAAAAATAATA
1 TTTTTATCATT-AAAATAATA
*
22129 TTTTTATTATTAAAATAAT
1 TTTTTATCATTAAAATAAT
22148 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTTATCATTAAAATAATA
Found at i:23780 original size:45 final size:44
Alignment explanation
Indices: 23731--23825 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 44
23721 AGTGAAAATA
* *
23731 TGAAAACATATAAA-AAATGTTTCAGTATTTTTATTATAATTGTTT
1 TGAAAA-ATA-AAACAAATGTTTCAATATTTTTATTAAAATTGTTT
*
23776 TGAAAATTAAAACAAATGTTTCAATATTTTTATTAAAATTGTTT
1 TGAAAAATAAAACAAATGTTTCAATATTTTTATTAAAATTGTTT
23820 TGAAAA
1 TGAAAA
23826 TTTAAAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 3 0.07
44 37 0.80
45 6 0.13
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (44 bp):
TGAAAAATAAAACAAATGTTTCAATATTTTTATTAAAATTGTTT
Found at i:23795 original size:44 final size:45
Alignment explanation
Indices: 23745--23832 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 45
23735 AACATATAAA
* *
23745 AAATGTTTCAGTATTTTTATTATAATTGTTTTGAAAA-TTAAAAC
1 AAATGTTTCAATATTTTTATTAAAATTGTTTTGAAAATTTAAAAC
23789 AAATGTTTCAATATTTTTATTAAAATTGTTTTGAAAATTTAAAA
1 AAATGTTTCAATATTTTTATTAAAATTGTTTTGAAAATTTAAAA
23833 AATAAAGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 35 0.85
45 6 0.15
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (45 bp):
AAATGTTTCAATATTTTTATTAAAATTGTTTTGAAAATTTAAAAC
Found at i:26303 original size:8 final size:8
Alignment explanation
Indices: 26253--26349 Score: 51
Period size: 8 Copynumber: 12.2 Consensus size: 8
26243 TTTTAATCTA
26253 AATATTA-
1 AATATTAT
* *
26260 ATTATTAA
1 AATATTAT
26268 AATATTTATT
1 AATA-TTA-T
*
26278 AATATTTTT
1 AATA-TTAT
*
26287 AATAATAT
1 AATATTAT
26295 AATATTAT
1 AATATTAT
*
26303 -AT-TTTT
1 AATATTAT
26309 AATATTAT
1 AATATTAT
**
26317 AATAAAAT
1 AATATTAT
26325 AATCATT-T
1 AAT-ATTAT
26333 -ATATTAT
1 AATATTAT
*
26340 AATAATAT
1 AATATTAT
26348 AA
1 AA
26350 GATATTGTAT
Statistics
Matches: 68, Mismatches: 14, Indels: 15
0.70 0.14 0.15
Matches are distributed among these distances:
6 6 0.09
7 13 0.19
8 33 0.49
9 9 0.13
10 7 0.10
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (8 bp):
AATATTAT
Found at i:26304 original size:22 final size:22
Alignment explanation
Indices: 26253--26320 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
26243 TTTTAATCTA
*
26253 AATATTA-ATTATTAA-AATAT
1 AATATTATATTTTTAATAATAT
*
26273 -TTATTAATATTTTTAATAATAT
1 AATATT-ATATTTTTAATAATAT
*
26295 AATATTATATTTTTAATATTAT
1 AATATTATATTTTTAATAATAT
26317 AATA
1 AATA
26321 AAATAATCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 4 0.10
20 1 0.03
21 7 0.17
22 24 0.60
23 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATTATATTTTTAATAATAT
Found at i:26327 original size:30 final size:34
Alignment explanation
Indices: 26269--26347 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 34
26259 AATTATTAAA
* *
26269 ATATTTATTAATATTTTTAATAATATAAT-A-TT
1 ATATTTATTAATATTTATAATAAAATAATCATTT
26301 ATATTT-TTAATA-TTATAATAAAATAATCATTT
1 ATATTTATTAATATTTATAATAAAATAATCATTT
*
26333 ATATTATAATAATAT
1 ATATT-TATTAATAT
26348 AAGATATTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.33
31 7 0.18
32 13 0.33
33 1 0.03
34 5 0.13
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (34 bp):
ATATTTATTAATATTTATAATAAAATAATCATTT
Found at i:26486 original size:8 final size:8
Alignment explanation
Indices: 26423--26503 Score: 51
Period size: 8 Copynumber: 9.8 Consensus size: 8
26413 TTTCATACAA
26423 ATAATATT
1 ATAATATT
*
26431 ATTATATT
1 ATAATATT
*
26439 ATTAATAATGA
1 A-TAAT-AT-T
26450 ATAATATT
1 ATAATATT
26458 ATTTATATATT
1 A--TA-ATATT
26469 -TAATA-T
1 ATAATATT
26475 -TAATATT
1 ATAATATT
*
26482 ATAATATA
1 ATAATATT
26490 ATAATATT
1 ATAATATT
*
26498 TTAATA
1 ATAATA
26504 AAAATATTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
6 6 0.10
7 4 0.07
8 29 0.50
9 5 0.09
10 8 0.14
11 6 0.10
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (8 bp):
ATAATATT
Found at i:26522 original size:31 final size:31
Alignment explanation
Indices: 26462--26525 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
26452 AATATTATTT
** *
26462 ATATATTTAATATTAATATTATAATATAATA
1 ATATATTTAATAAAAATATTAAAATATAATA
26493 ATAT-TTTAATAAAAATATTTAAAATATAATA
1 ATATATTTAATAAAAATA-TTAAAATATAATA
26524 AT
1 AT
26526 TAATATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
ATATATTTAATAAAAATATTAAAATATAATA
Found at i:26525 original size:23 final size:23
Alignment explanation
Indices: 26499--26546 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
26489 AATAATATTT
26499 TAATAAAAATATTTAAAATATAA
1 TAATAAAAATATTTAAAATATAA
* * *
26522 TAATTAATATTTTTAAAATATAA
1 TAATAAAAATATTTAAAATATAA
26545 TA
1 TA
26547 TAACACTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATAAAAATATTTAAAATATAA
Found at i:32379 original size:21 final size:21
Alignment explanation
Indices: 32353--32397 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
32343 GATTTCTGGG
* *
32353 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
32374 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
32395 CAA
1 CAA
32398 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:34149 original size:23 final size:22
Alignment explanation
Indices: 34090--34156 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
34080 TATGGACATC
*
34090 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
34112 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
34134 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
34157 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:37317 original size:21 final size:21
Alignment explanation
Indices: 37291--37335 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
37281 GATTTCTGGG
* *
37291 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
37312 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
37333 CAA
1 CAA
37336 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:39089 original size:23 final size:22
Alignment explanation
Indices: 39030--39096 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
39020 TATGGACATC
*
39030 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
39052 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
39074 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
39097 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:42323 original size:17 final size:17
Alignment explanation
Indices: 42290--42324 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42280 TATTTTGACA
* *
42290 AAAAAAATTATACGCTT
1 AAAAAAATTAAAAGCTT
42307 AAAAAAATTAAAAGCTT
1 AAAAAAATTAAAAGCTT
42324 A
1 A
42325 TCTTTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAAAAATTAAAAGCTT
Found at i:42560 original size:60 final size:60
Alignment explanation
Indices: 42421--42563 Score: 155
Period size: 60 Copynumber: 2.4 Consensus size: 60
42411 CTTTAAAATG
* * **
42421 TTCCAAGTTCATCCCTAAACTATGACTATAATTCTAAATTAATCCTTAAACTTTTGAACA
1 TTCCAATTTCATCCCCAAACTATGACTATAATTCTAAATTAATCCCCAAACTTTTGAACA
* * * * * **
42481 -GCTCAATGTCATCCTCAAACTATGACTTTCATTCTAAATTGGTCCCCAAACTTTTTGAACA
1 TTC-CAATTTCATCCCCAAACTATGACTATAATTCTAAATTAATCCCCAAAC-TTTTGAACA
42542 TTCCAATTTCA-CCCCAAACTAT
1 TTCCAATTTCATCCCCAAACTAT
42564 ATCTATATAC
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
59 1 0.02
60 48 0.73
61 16 0.24
62 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (60 bp):
TTCCAATTTCATCCCCAAACTATGACTATAATTCTAAATTAATCCCCAAACTTTTGAACA
Found at i:47226 original size:23 final size:23
Alignment explanation
Indices: 47191--47235 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
47181 CTACTTGATA
* *
47191 ATTTTTTTAAATATATATTTTAT
1 ATTTTTTTAAATAAAGATTTTAT
47214 ATTTTTATT-AATAAAGATTTTA
1 ATTTTT-TTAAATAAAGATTTTA
47236 AATAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTTTTTTAAATAAAGATTTTAT
Found at i:64451 original size:20 final size:21
Alignment explanation
Indices: 64423--64464 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
64413 CAACCAGCTG
64423 GCACATCAATTTCATCA-CCT
1 GCACATCAATTTCATCAGCCT
* *
64443 GCACCTCAATTTTATCAGCCT
1 GCACATCAATTTCATCAGCCT
64464 G
1 G
64465 TGCAGTCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.26, C:0.33, G:0.10, T:0.31
Consensus pattern (21 bp):
GCACATCAATTTCATCAGCCT
Done.